Origin IGS: aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag .........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 ctgacaattaacaattgaattacgtcaggctttcagccctcccaacggggatattgctttttccccaacgcttcgcattgggctgaattattacgccctttcagggcttttacagcattcagttctcagtaatcagccttgcattccccccctttgaagggggaaaaaggggagatgaagcattgggtttgtttattgaatggattgtaatacctttgccatcgagtataaatattaatgataggagatt Mask Tandem Repeat Region ================================================ aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag Find is-nt database================================================ Query_seq: TF0827:TF0828|TF0827:TF0828:conserved hypothetical protein:hypothetical protein:->->:886980..887229 250 aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0827:TF0828|TF0827:TF0828:conserved hypothetical protein:hypothetical protein:->->:886980..887229 250 aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0827:TF0828|TF0827:TF0828:conserved hypothetical protein:hypothetical protein:->->:886980..887229 250 aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 9 End: 122 ........ M I N I Y T R W Q R Y Y N P F N K Q T Q C F I S P F S P F K G G E C K A D Y ................................................................................................................................ Protein_Len: 38 Strand: + Start: 16 End: 129 ............... M F I L D G K G I T I H S I N K P N A S S P L F P P S K G G N A R L I T E N ......................................................................................................................... Protein_Len: 37 Strand: - Start: 122 End: 232 ......................................................................................................................... Q S S F A T F A R F P R L L E A W H S A N P F F C Y G R Q S P Q F G S T M .................. Protein_Len: 47 Strand: - Start: 97 End: 237 ................................................................................................ L P P I C P Q N S L V S H Q L L G S L A Y Y N L G I R L T P S F A I D G N P P S F A Q R L E M ............. Protein_Len: 54 Strand: - Start: 3 End: 164 .. R R D N I N I S S P L P I V I W E I F L G L A E D G R K G G E F P P F A L S I V S F Q I S Y F G Q F P T I M ...................................................................................... aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag 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================================================ aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -9.1 Tail_Score: -4.11484 Start: 144 End: 156 Full_Region: gggctgaattattac gccct ttc agggc ttttacagcattcag ...............................................................................................................................................gccctttcagggc.............................................................................................. Find igs database================================================ Query_seq: TF0827:TF0828|TF0827:TF0828:conserved hypothetical protein:hypothetical protein:->->:886980..887229 250 aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag Intra-Species Hit: Count: 10 Min: 1 Max: 250 Len: 250 Subject: tfor_TF0827_TF0828|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[886980,887229]|250 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 250 Query Start:1 Query End:250 Subject Strand: POSITIVE Subject Start: 1 Subject End: 250 aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaannnnnnnaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag aatctcctatcattaatatttatactcgatggcaaaggtattacaatccattcaataaacaaacccaatgcttcatctcccctttttcccccttcaaagggggggaatgcaaggctgattactgagaactgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattcaattgttaattgtcag Subject: tfor_TF1182_TF1184|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1268999,1269143]|145 HSP 1 e-value: 2.0E-16 bit: 87.7 Len: 60 Query Start:135 Query End:194 Subject Strand: POSITIVE Subject Start: 13 Subject End: 72 ......................................................................................................................................gctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcgttggggaaaaag........................................................ ......................................................................................................................................gctgtaacagccctgaaagggcgagataattcagcccaatgcgaagcgtttgggaaaaag........................................................ HSP 2 e-value: 4.0E-11 bit: 69.9 Len: 39 Query Start:211 Query End:249 Subject Strand: POSITIVE Subject Start: 90 Subject End: 128 ..................................................................................................................................................................................................................agggctgaaagcctgacgtaattcaattgttaattgtca. ..................................................................................................................................................................................................................agggctgtaagcctgacgtaattcaattgttaattgtca. Subject: tfor_TF2998_TF2999|surface antigen BspA:conserved hypothetical protein|POSITIVE:POSITIVE|[3215212,3215705]|494 HSP 1 e-value: 4.0E-14 bit: 79.8 Len: 48 Query Start:135 Query End:182 Subject Strand: NEGATIVE Subject Start: 264 Subject End: 311 ......................................................................................................................................gctgtaaaagccctgaaagggcgtaataattcagcccaatgcgaagcg.................................................................... ......................................................................................................................................gctgtaagagccctgaaagggcgtaataattcagcccaatgcgtagcg.................................................................... HSP 2 e-value: 6.0E-7 bit: 56.0 Len: 36 Query Start:209 Query End:244 Subject Strand: NEGATIVE Subject Start: 191 Subject End: 226 ................................................................................................................................................................................................................ggagggctgaaagcctgacgtaattcaattgttaat...... ................................................................................................................................................................................................................ggagggctgaaagcctgacataattcaatggttaat...... Subject: tfor_TF2823_TF2824|TPR-containing protein:nucleoside-transporting protein nupG|POSITIVE:POSITIVE|[3014398,3014840]|443 HSP 1 e-value: 2.0E-13 bit: 77.8 Len: 101 Query Start:135 Query End:235 Subject Strand: POSITIVE Subject Start: 337 Subject End: 436 ......................................................................................................................................gctgtaaaagccctgaaagggc-gtaataattcagcccaatgcgaagcgttggggaaaaagcaatatccccgttgggagggctgaaagcctgacgtaattca............... ......................................................................................................................................gctgtaacagccctgaaagggctgtgttaattcagcccaatgcgaagcgttggggaaagag--gtaacacccatgggagggctgaaagcctgaattaattca............... Subject: tfor_TF2438_TF2439|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2616218,2616519]|302 HSP 1 e-value: 1.0E-11 bit: 71.9 Len: 48 Query Start:128 Query End:175 Subject Strand: NEGATIVE Subject Start: 179 Subject End: 226 ...............................................................................................................................actgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatg........................................................................... ...............................................................................................................................actgactgctgtaaaagccctgaaagggcgcattaattcagcccaatg........................................................................... HSP 2 e-value: 1.0E-8 bit: 61.9 Len: 39 Query Start:209 Query End:247 Subject Strand: NEGATIVE Subject Start: 97 Subject End: 135 ................................................................................................................................................................................................................ggagggctgaaagcctgacgtaattcaattgttaattgt... ................................................................................................................................................................................................................ggagggctgaaagcctgacataatttaattgttaattgt... Subject: tfor_TF2500_TF2501|ABC transporter, ATP-binding protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[2675363,2676419]|1057 HSP 1 e-value: 6.0E-10 bit: 65.9 Len: 41 Query Start:209 Query End:249 Subject Strand: POSITIVE Subject Start: 287 Subject End: 327 ................................................................................................................................................................................................................ggagggctgaaagcctgacgtaattcaattgttaattgtca. ................................................................................................................................................................................................................ggagggatgaaagcctgacgtaattcagttgttaattgtca. HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 40 Query Start:137 Query End:176 Subject Strand: POSITIVE Subject Start: 206 Subject End: 245 ........................................................................................................................................tgtaaaagccctgaaagggcgtaataattcagcccaatgc.......................................................................... ........................................................................................................................................tgtaaaagccctgaaagggcgcattaattcagcccaatgc.......................................................................... Subject: tfor_TF0018_TF0019|hypothetical protein:heat shock protein ClpB|POSITIVE:POSITIVE|[12152,12589]|438 HSP 1 e-value: 6.0E-10 bit: 65.9 Len: 41 Query Start:209 Query End:249 Subject Strand: NEGATIVE Subject Start: 15 Subject End: 55 ................................................................................................................................................................................................................ggagggctgaaagcctgacgtaattcaattgttaattgtca. ................................................................................................................................................................................................................ggagggctgaaagcctgacgtaattcagttgttaatggtca. HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 39 Query Start:137 Query End:175 Subject Strand: NEGATIVE Subject Start: 101 Subject End: 139 ........................................................................................................................................tgtaaaagccctgaaagggcgtaataattcagcccaatg........................................................................... ........................................................................................................................................tgtaacagccctgaaagggcgcattaattcagcccaatg........................................................................... Subject: tfor_TF2815_TF2816|meso-diaminopimelate D-dehydrogenase:hypothetical protein|POSITIVE:POSITIVE|[3006481,3007064]|584 HSP 1 e-value: 2.0E-9 bit: 63.9 Len: 40 Query Start:210 Query End:249 Subject Strand: POSITIVE Subject Start: 464 Subject End: 503 .................................................................................................................................................................................................................gagggctgaaagcctgacgtaattcaattgttaattgtca. .................................................................................................................................................................................................................gagggctgaaagcctgacataattcaattgttaatggtca. HSP 2 e-value: 1.0E-8 bit: 61.9 Len: 47 Query Start:129 Query End:175 Subject Strand: NEGATIVE Subject Start: 258 Subject End: 304 ................................................................................................................................ctgaatgctgtaaaagccctgaaagggcgtaataattcagcccaatg........................................................................... ................................................................................................................................ctgactgctttaaaagccctgaaagggcgcattaattcagcccaatg........................................................................... Subject: tfor_TF0685_TF0686|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[731193,732338]|1146 HSP 1 e-value: 2.0E-9 bit: 63.9 Len: 36 Query Start:209 Query End:244 Subject Strand: NEGATIVE Subject Start: 752 Subject End: 787 ................................................................................................................................................................................................................ggagggctgaaagcctgacgtaattcaattgttaat...... ................................................................................................................................................................................................................ggagggctgtaagcctgacgtaattcaattgttaat...... HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 39 Query Start:137 Query End:175 Subject Strand: NEGATIVE Subject Start: 832 Subject End: 870 ........................................................................................................................................tgtaaaagccctgaaagggcgtaataattcagcccaatg........................................................................... ........................................................................................................................................tgtaacagccctgaaagggcgcattaattcagcccaatg........................................................................... Subject: tfor_TF1762_TF1763|hypothetical protein:K+-dependent Na+/Ca+ exchanger related-protein|POSITIVE:POSITIVE|[1899709,1900545]|837 HSP 1 e-value: 1.0E-7 bit: 58.0 Len: 41 Query Start:135 Query End:175 Subject Strand: NEGATIVE Subject Start: 76 Subject End: 116 ......................................................................................................................................gctgtaaaagccctgaaagggcgtaataattcagcccaatg........................................................................... ......................................................................................................................................gctgtaaaagccctgaaagggcgcgttaattcagcccaatg........................................................................... HSP 2 e-value: 6.0E-7 bit: 56.0 Len: 28 Query Start:209 Query End:236 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 28 ................................................................................................................................................................................................................ggagggctgaaagcctgacgtaattcaa.............. ................................................................................................................................................................................................................ggagggctgaaagcctgacgtaattcaa.............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUCCUAUCAUUAAUAUUUAUACUCGAUGGCAAAGGUAUUACAAUCCAUUCAAUAAACAAACCCAAUGCUUCAUCUCCCCUUUUUCCCCCUUCAAAGGGGGGGAAUGCAAGGCUGAUUACUGAGAACUGAAUGCUGUAAAAGCCCUGAAAGGGCGUAAUAAUUCAGCCCAAUGCGAAGCGUUGGGGAAAAAGCAAUAUCCCCGUUGGGAGGGCUGAAAGCCUGACGUAAUUCAAUUGUUAAUUGUCAG .............................((((((............................(((((((((((.........((..((((((....))))))..)).(((.((((((((((...............))))..((((.....))))........))))))...)))))))))))))).....((((((.((((....))))((((.....))))...........))))))..)))))). (-71.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGACAAUUAACAAUUGAAUUACGUCAGGCUUUCAGCCCUCCCAACGGGGAUAUUGCUUUUUCCCCAACGCUUCGCAUUGGGCUGAAUUAUUACGCCCUUUCAGGGCUUUUACAGCAUUCAGUUCUCAGUAAUCAGCCUUGCAUUCCCCCCCUUUGAAGGGGGAAAAAGGGGAGAUGAAGCAUUGGGUUUGUUUAUUGAAUGGAUUGUAAUACCUUUGCCAUCGAGUAUAAAUAUUAAUGAUAGGAGAUU (((((((((........))))..))))).((.(((((((((((....))))...((((((((((((........(((..(((((((.(((((..((((.....))))......(((.....)))...))))))))))))))).(((((((........)))))))...))))))..))))))..)))).(((((((....(.(((.((((.....)))).))).)..)))))))....))).))...... (-74.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 977 230 181 64 15 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 905 190 143 212 165 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 905 190 143 212 165 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 858 190 141 187 138 tfor:TF2641|5end_riboflavin_kinase/FAD_synthase_2809681..2809911_POSITIVE 844 188 143 121 76 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 817 187 141 231 185 tfor:TF2351|5end_acetate_kinase_2515480..2515710_POSITIVE 774 180 134 225 174 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 751 196 153 219 175 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 751 188 143 230 183 tfor:TF0468|5end_hypothetical_protein_486929..487159_POSITIVE 733 185 141 231 187 tfor:TF1175|5end_membrane-fusion_protein_1258140..1258370_POSITIVE 711 209 163 171 122 tfor:TF0499|5end_hypothetical_protein_526257..526487_POSITIVE 694 200 153 229 184 tfor:TF1516|5end_transposase_fragment_1626407..1626637_POSITIVE 652 188 143 226 171 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 652 188 143 220 165 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 624 106 70 37 1 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 611 190 143 158 101 tfor:TF2127|5end_hypothetical_protein_2304038..2304268_POSITIVE 603 199 153 230 175 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 574 188 143 220 165 tfor:TF0366|5end_hypothetical_protein_383564..383794_POSITIVE 574 188 143 220 165 tfor:TF0362|5end_hypothetical_protein_379952..380182_POSITIVE 574 188 143 153 98 tfor:TF0350|5end_hypothetical_protein_370794..371024_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 966 229 181 77 29 tfor:TF2350|3end_hypothetical_protein_2515364..2515514_POSITIVE 886 190 144 47 1 tfor:TF0344|3end_hypothetical_protein_366963..367113_POSITIVE 860 190 143 117 70 tfor:TF2025|3end_hypothetical_protein_2182180..2182330_POSITIVE 857 190 143 124 77 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 838 190 144 47 1 tfor:TF1585|3end_hypothetical_protein_1690610..1690760_POSITIVE 810 190 143 124 77 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 745 249 201 103 54 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 717 190 142 59 1 tfor:TF0958|3end_conserved_hypothetical_protein_1004909..1005059_POSITIVE 710 180 135 145 100 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 681 197 151 48 1 tfor:TF1584|3end_hypothetical_protein_1690603..1690753_POSITIVE 675 230 181 57 6 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE 653 226 181 71 25 tfor:TF2922|3end_surface_antigen_BspA_3121538..3121688_POSITIVE 652 188 143 116 61 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 571 226 181 48 2 tfor:TF2169|3end_hypothetical_protein_2345354..2345504_POSITIVE 570 120 74 60 9 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 570 226 184 41 1 tfor:TF0343|3end_hypothetical_protein_366923..367073_POSITIVE 506 190 143 73 24 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 483 125 90 65 25 tfor:TF1166|3end_ABC_transporter,_permease_component_1248603..1248753_POSITIVE 472 202 165 47 1 tfor:TF2126|3end_S-adenosylhomocysteine_hydrolase_2303996..2304146_POSITIVE 447 106 64 142 100 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE