Origin IGS: ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggagataaacgaaaagcgtattttcttaagtagtcaaagcagttaatgtagacgggcgaccctcagtgttcgcccgtcataacgccgattatgaacatccccccttcaaagggggaatgcaaaagcgaagcgcacgaagccttgaccttttggttacttttgggtcaagccaaaagtgacagaaaaattatatcaggctttcagccctgccggtaggagattcttcgctcacgctctgaatgacaaaaaacggtgtcccgaacgcagaggtacatcccccagcccccccccttcaaagggggaatgcagagcagaccgctgactactgatcgctaacaaataaaagaaacagaa Mask Tandem Repeat Region ================================================ ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta Find is-nt database================================================ Query_seq: TF1169:TF1171|TF1169:TF1171:lipoprotein ABC transporter, permease component:ABC transporter, ATP-binding protein:->->:1251634..1251989 356 ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1169:TF1171|TF1169:TF1171:lipoprotein ABC transporter, permease component:ABC transporter, ATP-binding protein:->->:1251634..1251989 356 ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1169:TF1171|TF1169:TF1171:lipoprotein ABC transporter, permease component:ABC transporter, ATP-binding protein:->->:1251634..1251989 356 ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 16 End: 123 ............... M L A I S S Q R S A L H S P F E G G G L G D V P L R S G H R F L S F R A ......................................................................................................................................................................................................................................... Protein_Len: 37 Strand: + Start: 41 End: 151 ........................................ M L C I P P L K G G G W G M Y L C V R D T V F C H S E R E R R I S Y R Q G ............................................................................................................................................................................................................. Protein_Len: 37 Strand: - Start: 179 End: 289 .................................................................................................................................................................................. K Q S S G F T V L L D L S R A S R K Q M G G K F P P H E Y D A N H R A F M ................................................................... Protein_Len: 45 Strand: - Start: 142 End: 276 ............................................................................................................................................. R C P Q F G S I I K R D S K A Q G L L L W F T L A E H A E S K C E G K S P P I N M I P T M ................................................................................ Protein_Len: 48 Strand: - Start: 36 End: 179 ................................... R D A R C E G K S P P P S P S T G R R E P C R K K D N L A H A F F R R G A P S F A Q Y L K E T M ................................................................................................................................................................................. ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -13.2 Tail_Score: -3.21595 Start: 236 End: 259 Full_Region: TGCGCTTCGCTTTTG CATTCCCCCT TTGA AGGGGGGATG TTCATAATCGGCGTT ...........................................................................................................................................................................................................................................CATTCCCCCTTTGAAGGGGGGATG................................................................................................. TransTerm Strand: + Conf: 51 HP_score: -5.0 Tail_Score: -3.16608 Start: 274 End: 308 Full_Region: GTTCATAATCGGCGT TATGACGGGCGAAC ACTGAG GGTCGCCCGTCTACA TTAACTGCTTTGACT .................................................................................................................................................................................................................................................................................TATGACGGGCGAACACTGAGGGTCGCCCGTCTACA................................................ TransTerm Strand: + Conf: 76 HP_score: -12.7 Tail_Score: -2.56288 Start: 277 End: 304 Full_Region: CATAATCGGCGTTAT GACGGGCGAAC ACTGAG GGTCGCCCGTC TACATTAACTGCTTT ....................................................................................................................................................................................................................................................................................GACGGGCGAACACTGAGGGTCGCCCGTC.................................................... Find igs database================================================ Query_seq: TF1169:TF1171|TF1169:TF1171:lipoprotein ABC transporter, permease component:ABC transporter, ATP-binding protein:->->:1251634..1251989 356 ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaagggggggggctgggggatgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta Intra-Species Hit: Count: 6 Min: 1 Max: 356 Len: 356 Subject: tfor_TF1169_TF1171|lipoprotein ABC transporter, permease component:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[1251634,1251989]|356 HSP 1 e-value: 1.0E-155 bit: 549.0 Len: 277 Query Start:80 Query End:356 Subject Strand: POSITIVE Subject Start: 80 Subject End: 356 ...............................................................................atgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta ...............................................................................atgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctcctaccggcagggctgaaagcctgatataatttttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttcgcttttgcattccccctttgaaggggggatgttcataatcggcgttatgacgggcgaacactgagggtcgcccgtctacattaactgctttgactacttaagaaaatacgcttttcgtttatctccta HSP 2 e-value: 1.0E-27 bit: 125.0 Len: 63 Query Start:1 Query End:63 Subject Strand: POSITIVE Subject Start: 1 Subject End: 63 ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaa..................................................................................................................................................................................................................................................................................................... ttctgtttcttttatttgttagcgatcagtagtcagcggtctgctctgcattccccctttgaa..................................................................................................................................................................................................................................................................................................... Subject: tfor_TF2500_TF2501|ABC transporter, ATP-binding protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[2675363,2676419]|1057 HSP 1 e-value: 1.0E-24 bit: 115.0 Len: 58 Query Start:171 Query End:228 Subject Strand: NEGATIVE Subject Start: 661 Subject End: 718 ..........................................................................................................................................................................ttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttc................................................................................................................................ ..........................................................................................................................................................................ttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttc................................................................................................................................ HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 31 Query Start:110 Query End:140 Subject Strand: NEGATIVE Subject Start: 718 Subject End: 748 .............................................................................................................tgtcattcagagcgtgagcgaagaatctcct........................................................................................................................................................................................................................ .............................................................................................................tgtcattcagagcgtaagcgaagaatctcct........................................................................................................................................................................................................................ Subject: tfor_TF2922_TF2923|surface antigen BspA:hypothetical protein|POSITIVE:POSITIVE|[3121599,3122307]|709 HSP 1 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:178 Query End:228 Subject Strand: POSITIVE Subject Start: 159 Subject End: 209 .................................................................................................................................................................................acttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttc................................................................................................................................ .................................................................................................................................................................................acttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttc................................................................................................................................ HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 31 Query Start:108 Query End:138 Subject Strand: POSITIVE Subject Start: 420 Subject End: 450 ...........................................................................................................tttgtcattcagagcgtgagcgaagaatctc.......................................................................................................................................................................................................................... ...........................................................................................................tttgtcattcagagcgtaagcgaagaatctc.......................................................................................................................................................................................................................... Subject: tfor_TF2920_TF2921|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3117231,3118637]|1407 HSP 1 e-value: 2.0E-20 bit: 101.0 Len: 59 Query Start:170 Query End:228 Subject Strand: POSITIVE Subject Start: 207 Subject End: 265 .........................................................................................................................................................................tttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttc................................................................................................................................ .........................................................................................................................................................................tttctgttacttttggcttgacccaaaagtaacccaaaggtcaaggcttcgtgcgcttc................................................................................................................................ HSP 2 e-value: 1.0E-15 bit: 85.7 Len: 59 Query Start:80 Query End:138 Subject Strand: POSITIVE Subject Start: 701 Subject End: 759 ...............................................................................atgtacctctgcgttcgggacaccgttttttgtcattcagagcgtgagcgaagaatctc.......................................................................................................................................................................................................................... ...............................................................................atgttcctctgcgttcgggacatcgtcttttgtcattcagagcgtaagcgaagaatctc.......................................................................................................................................................................................................................... HSP 3 e-value: 3.0E-6 bit: 54.0 Len: 31 Query Start:108 Query End:138 Subject Strand: POSITIVE Subject Start: 410 Subject End: 440 ...........................................................................................................tttgtcattcagagcgtgagcgaagaatctc.......................................................................................................................................................................................................................... ...........................................................................................................tttgtcattcagagcgtaagcgaagaatctc.......................................................................................................................................................................................................................... Subject: tfor_TF0538_TF0540|hypothetical protein:conserved hypothetical protein; possible surface protein|POSITIVE:POSITIVE|[567196,567425]|230 HSP 1 e-value: 4.0E-18 bit: 93.7 Len: 59 Query Start:170 Query End:228 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 60 .........................................................................................................................................................................tttctgtcacttttggcttgacccaaaagtaaccaaaaggtcaaggcttcgtgcgcttc................................................................................................................................ .........................................................................................................................................................................tttctctcacttttggcttgactcaaaagtaacccaaaggtcaaggcttcgtgcgcttc................................................................................................................................ HSP 2 e-value: 6.0E-8 bit: 60.0 Len: 34 Query Start:107 Query End:140 Subject Strand: NEGATIVE Subject Start: 60 Subject End: 93 ..........................................................................................................ttttgtcattcagagcgtgagcgaagaatctcct........................................................................................................................................................................................................................ ..........................................................................................................ttttgtcattcagagcgtaagcgaagaatctcct........................................................................................................................................................................................................................ Subject: tfor_TF1838_TF1839|tRNA/rRNA methyltransferase:conserved hypothetical protein|POSITIVE:POSITIVE|[1988806,1989486]|681 HSP 1 e-value: 2.0E-10 bit: 67.9 Len: 53 Query Start:168 Query End:220 Subject Strand: NEGATIVE Subject Start: 384 Subject End: 437 .......................................................................................................................................................................tttttctgtcacttttggcttgacccaaaa-gtaaccaaaaggtcaaggcttcg........................................................................................................................................ .......................................................................................................................................................................tttttccgttacttttggcttgacccaaaaagtaacccaaaggtcaaggcttcg........................................................................................................................................ HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 31 Query Start:108 Query End:138 Subject Strand: NEGATIVE Subject Start: 151 Subject End: 181 ...........................................................................................................tttgtcattcagagcgtgagcgaagaatctc.......................................................................................................................................................................................................................... ...........................................................................................................tttgtcattcagagcgtaagcgaagaatctc.......................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGUUUCUUUUAUUUGUUAGCGAUCAGUAGUCAGCGGUCUGCUCUGCAUUCCCCCUUUGAAGGGGGGGGGCUGGGGGAUGUACCUCUGCGUUCGGGACACCGUUUUUUGUCAUUCAGAGCGUGAGCGAAGAAUCUCCUACCGGCAGGGCUGAAAGCCUGAUAUAAUUUUUCUGUCACUUUUGGCUUGACCCAAAAGUAACCAAAAGGUCAAGGCUUCGUGCGCUUCGCUUUUGCAUUCCCCCUUUGAAGGGGGGAUGUUCAUAAUCGGCGUUAUGACGGGCGAACACUGAGGGUCGCCCGUCUACAUUAACUGCUUUGACUACUUAAGAAAAUACGCUUUUCGUUUAUCUCCUA ....................(((((..(((.((((((..((.(((((((..(((((((....))))))).((.((((((((...((((.((((((..((((........)))).....))))))))).)....)))))))))).))))))).))..).))))).....((((((((.((((((((......)))))))).)).....(((((((((.....(((((........(((((((((((....)))))))))))........)))))...(((((((((...(....).)))))))))..........))))))))).....))))))...)))..)))))......... (-134.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAGAUAAACGAAAAGCGUAUUUUCUUAAGUAGUCAAAGCAGUUAAUGUAGACGGGCGACCCUCAGUGUUCGCCCGUCAUAACGCCGAUUAUGAACAUCCCCCCUUCAAAGGGGGAAUGCAAAAGCGAAGCGCACGAAGCCUUGACCUUUUGGUUACUUUUGGGUCAAGCCAAAAGUGACAGAAAAAUUAUAUCAGGCUUUCAGCCCUGCCGGUAGGAGAUUCUUCGCUCACGCUCUGAAUGACAAAAAACGGUGUCCCGAACGCAGAGGUACAUCCCCCAGCCCCCCCCCUUCAAAGGGGGAAUGCAGAGCAGACCGCUGACUACUGAUCGCUAACAAAUAAAAGAAACAGAA .((((((((..(.....)..))))))))..((((((((..((.(((..(((.(((((((((.(......).))))))))).................(((.(((((((..(((((((...((...(((((((.((..((((((((((..((((.(((((((((((......))))))))))).))))..)))....)))))))..))((((....)))).....))))))).((.(((((...((((........)))).......)))))))..........))...)))))))..))))))).)))....)))))).))))))))))........................... (-115.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 990 97 51 165 118 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 990 97 51 61 14 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 953 230 181 186 137 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 947 230 181 214 165 tfor:TF1846|5end_hypothetical_protein_1996726..1996956_POSITIVE 947 230 181 108 59 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 905 230 181 91 41 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 895 230 181 215 166 tfor:TF1660|5end_hypothetical_protein_1775269..1775499_POSITIVE 876 97 51 59 12 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 853 97 51 68 21 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 853 97 51 226 181 tfor:TF0540|5end_conserved_hypothetical_protein;_possible_surface_protein_567286..567516_POSITIVE 807 228 181 231 184 tfor:TF1843|5end_surface_antigen_BspA_1992834..1993064_POSITIVE 802 230 181 108 59 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 793 97 51 61 16 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 779 66 21 131 83 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 759 100 51 216 169 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 652 80 31 207 159 tfor:TF0536|5end_conserved_hypothetical_protein_561917..562147_POSITIVE 631 236 198 43 1 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 600 143 103 131 92 tfor:TF2777|5end_hypothetical_protein_2961595..2961825_POSITIVE 596 69 22 229 182 tfor:TF0959|5end_periplasmic_protease_1005218..1005448_POSITIVE 538 150 101 82 27 tfor:TF2816|5end_hypothetical_protein_3006925..3007155_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 976 230 181 142 93 tfor:TF2817|3end_hypothetical_protein_3007626..3007776_POSITIVE 953 230 181 57 8 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 947 230 181 101 52 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 947 230 181 91 42 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 947 230 181 101 52 tfor:TF1844|3end_hypothetical_protein_1996693..1996843_POSITIVE 947 230 181 75 26 tfor:TF1187|3end_hypothetical_protein_1269872..1270022_POSITIVE 918 230 181 101 52 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 918 230 181 75 26 tfor:TF0598|3end_hypothetical_protein_629500..629650_POSITIVE 895 230 181 75 26 tfor:TF1659|3end_hypothetical_protein_1775209..1775359_POSITIVE 883 97 51 129 83 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 878 230 181 101 52 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 875 230 181 119 70 tfor:TF1842|3end_hypothetical_protein_1992800..1992950_POSITIVE 836 97 51 108 64 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 816 230 181 91 42 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 802 230 181 101 52 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 757 230 184 47 1 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 742 290 241 115 60 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 732 97 51 87 37 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 703 105 61 48 4 tfor:TF1483|3end_glycosyltransferase_family_protein_1578825..1578975_POSITIVE 669 137 91 150 104 tfor:TF0534|3end_hypothetical_protein_559768..559918_POSITIVE