Origin IGS: tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca .........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 tgaaaagtgaaaagtagtcaacagtaattaatgttgtcaatgtaggggcgaaccttgtgttcgccctttttttgtgtgatgtccgaacgcgtaaatcaatgacgaattacgaattacgaacgccatcctttgtcattccgaacgtagtgaggaatcccgtggggaaaagaatgagattcttcgcttcgctctgaatgacaaattaatggttaattgttaattgtca Mask Tandem Repeat Region ================================================ tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca Find is-nt database================================================ Query_seq: TF2997:TF2998|TF2997:TF2998:hypothetical protein:surface antigen BspA:->->:3211725..3211950 226 tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2997:TF2998|TF2997:TF2998:hypothetical protein:surface antigen BspA:->->:3211725..3211950 226 tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2997:TF2998|TF2997:TF2998:hypothetical protein:surface antigen BspA:->->:3211725..3211950 226 tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 127 End: 225 .............................................................................................................................. M D L R V R T S H K K R A N T R F A P T L T T L I T V D Y F S L F . Protein_Len: 55 Strand: - Start: 36 End: 200 ................................... L S A F F R M R K G V P N R V V N P I V F S P T R L E Y N T M S K R T R V D C L F L A F V L N A G V N V V N M .......................... Protein_Len: 41 Strand: - Start: 10 End: 132 ......... C N V M L K D N L A F R L I E N K E G R S E E S R E S H C L I A N T I R L E D N M .............................................................................................. tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca 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================================================ tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 67 HP_score: -9.1 Tail_Score: -2.52795 Start: 160 End: 182 Full_Region: ACATCACACAAAAAA AGGGCGAAC ACAAG GTTCGCCCC TACATTGACAACATT ...............................................................................................................................................................AGGGCGAACACAAGGTTCGCCCC............................................ TransTerm Strand: - Conf: 100 HP_score: -12.6 Tail_Score: -5.74122 Start: 161 End: 181 Full_Region: atgttgtcaatgtag gggcgaac cttgt gttcgccc tttttttgtgtgatg ................................................................................................................................................................gggcgaaccttgtgttcgccc............................................. Find igs database================================================ Query_seq: TF2997:TF2998|TF2997:TF2998:hypothetical protein:surface antigen BspA:->->:3211725..3211950 226 tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca Intra-Species Hit: Count: 8 Min: 1 Max: 226 Len: 226 Subject: tfor_TF2997_TF2998|hypothetical protein:surface antigen BspA|POSITIVE:POSITIVE|[3211725,3211950]|226 HSP 1 e-value: 1.0E-112 bit: 406.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacnnnnnnngggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaattcgtaattcgtcattgatttacgcgttcggacatcacacaaaaaaagggcgaacacaaggttcgcccctacattgacaacattaattactgttgactacttttcacttttca Subject: tfor_TF2921_TF2922|hypothetical protein:surface antigen BspA|POSITIVE:POSITIVE|[3118851,3119261]|411 HSP 1 e-value: 5.0E-38 bit: 159.0 Len: 103 Query Start:8 Query End:110 Subject Strand: POSITIVE Subject Start: 81 Subject End: 184 .......taacaattaaccattaatttgtcattcagagcg-aagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcg.................................................................................................................... .......taacaattaaccattaatttgtcattcagagcgtaagcgaagaatctttttcctttccccacgggattcctcactacgttcggaatgacaaagggtggcgttcg.................................................................................................................... HSP 2 e-value: 3.0E-24 bit: 113.0 Len: 103 Query Start:8 Query End:110 Subject Strand: POSITIVE Subject Start: 253 Subject End: 357 .......taacaattaaccattaatttgtcattcagagcg-aagcgaagaatctcat-tcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcg.................................................................................................................... .......taacaattaaccattaatttgtcattcagagcgtaagcgaagaatctcttccctcttccccgtgagattcctcactacgttcggaatgacaaagggcggcgttcg.................................................................................................................... Subject: tfor_TF2823_TF2824|TPR-containing protein:nucleoside-transporting protein nupG|POSITIVE:POSITIVE|[3014398,3014840]|443 HSP 1 e-value: 2.0E-34 bit: 147.0 Len: 105 Query Start:10 Query End:114 Subject Strand: NEGATIVE Subject Start: 88 Subject End: 193 .........acaattaaccattaatttgtcattcagagcgaagcgaagaatctcat-tcttttccccacgggattcctcactacgttcggaatgacaaaggatggcgttcgtaat................................................................................................................ .........acaattaaccattaatttgtcattcagagcgaagcgaagaatctcttcccttttccccgcgagattcctcactgcgttcggaatgacaaagggtggcgttcgtaat................................................................................................................ Subject: tfor_TF2816_TF2817|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3007245,3007497]|253 HSP 1 e-value: 4.0E-23 bit: 109.0 Len: 100 Query Start:1 Query End:100 Subject Strand: NEGATIVE Subject Start: 105 Subject End: 206 tgacaattaacaattaaccattaatttgtcattcagagcgaagcgaagaatctcatt--cttttccccacgggattcctcactacgttcggaatgacaaagg.............................................................................................................................. tgaccattgacaattaacaattaatttgtcattcagagcaaagcgaagaatctcctttccttttcctcgcgggattcctcactgtgttcggaatgacaaagg.............................................................................................................................. Subject: tfor_TF1588_TF1589|hypothetical protein:surface antigen BspA|POSITIVE:POSITIVE|[1702621,1703328]|708 HSP 1 e-value: 9.0E-15 bit: 81.8 Len: 75 Query Start:25 Query End:99 Subject Strand: POSITIVE Subject Start: 482 Subject End: 558 ........................tttgtcattcagagcg-aagcgaagaatctcattc-ttttccccacgggattcctcactacgttcggaatgacaaag............................................................................................................................... ........................tttgtcattcagagcgtaagcgaagaatctttttccttttcctcacgagattcctcactgcgttcggaatgacaaag............................................................................................................................... HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 75 Query Start:26 Query End:100 Subject Strand: POSITIVE Subject Start: 199 Subject End: 273 .........................ttgtcattcagagcgaagcgaagaatctcattcttttccccacgggattcctcactacgttcggaatgacaaagg.............................................................................................................................. .........................ttgtcattcagagcgaagcgatgaatcttttccttttcggggcgggattcctcactgcgttcggaatgacaaagg.............................................................................................................................. HSP 3 e-value: 8.0E-6 bit: 52.0 Len: 45 Query Start:85 Query End:129 Subject Strand: POSITIVE Subject Start: 590 Subject End: 635 ....................................................................................ttcggaatgacaaag-gatggcgttcgtaattcgtaattcgtcatt................................................................................................. ....................................................................................ttcggaatgacaaagaggaggcgttcgtaattcgtaatttgtcatt................................................................................................. Subject: tfor_TF1590_TF1591|hypothetical protein:surface antigen BspA|POSITIVE:POSITIVE|[1706104,1706526]|423 HSP 1 e-value: 4.0E-14 bit: 79.8 Len: 74 Query Start:26 Query End:99 Subject Strand: POSITIVE Subject Start: 249 Subject End: 324 .........................ttgtcattcagagcg-aagcgaagaatctcattc-ttttccccacgggattcctcactacgttcggaatgacaaag............................................................................................................................... .........................ttgtcattcagagcgtaagcgaagaatctttttccttttcctcacgagattcctcactgcgttcggaatgacaaag............................................................................................................................... HSP 2 e-value: 8.0E-6 bit: 52.0 Len: 45 Query Start:85 Query End:129 Subject Strand: POSITIVE Subject Start: 333 Subject End: 378 ....................................................................................ttcggaatgacaaag-gatggcgttcgtaattcgtaattcgtcatt................................................................................................. ....................................................................................ttcggaatgacaaagaggaggcgttcgtaattcgtaatttgtcatt................................................................................................. Subject: tfor_TF1846_TF1847|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1997076,1997528]|453 HSP 1 e-value: 3.0E-8 bit: 60.0 Len: 30 Query Start:10 Query End:39 Subject Strand: NEGATIVE Subject Start: 56 Subject End: 85 .........acaattaaccattaatttgtcattcagagc........................................................................................................................................................................................... .........acaattaaccattaatttgtcattcagagc........................................................................................................................................................................................... HSP 2 e-value: 8.0E-6 bit: 52.0 Len: 26 Query Start:161 Query End:186 Subject Strand: NEGATIVE Subject Start: 163 Subject End: 188 ................................................................................................................................................................gggcgaacacaaggttcgcccctaca........................................ ................................................................................................................................................................gggcgaacacaaggttcgcccctaca........................................ Subject: tfor_TF2996_TF2997|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3211182,3211547]|366 HSP 1 e-value: 8.0E-6 bit: 52.0 Len: 26 Query Start:161 Query End:186 Subject Strand: POSITIVE Subject Start: 88 Subject End: 113 ................................................................................................................................................................gggcgaacacaaggttcgcccctaca........................................ ................................................................................................................................................................gggcgaacacaaggttcgcccctaca........................................ HSP 2 e-value: 8.0E-6 bit: 52.0 Len: 30 Query Start:10 Query End:39 Subject Strand: POSITIVE Subject Start: 257 Subject End: 286 .........acaattaaccattaatttgtcattcagagc........................................................................................................................................................................................... .........acaattaacaattaatttgtcattcagagc........................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAAUUAACAAUUAACCAUUAAUUUGUCAUUCAGAGCGAAGCGAAGAAUCUCAUUCUUUUCCCCACGGGAUUCCUCACUACGUUCGGAAUGACAAAGGAUGGCGUUCGUAAUUCGUAAUUCGUCAUUGAUUUACGCGUUCGGACAUCACACAAAAAAAGGGCGAACACAAGGUUCGCCCCUACAUUGACAACAUUAAUUACUGUUGACUACUUUUCACUUUUCA (((.......((((...(((((..((((((((((.(((((.((.((.(((((((..............))))))).)).)).))))).)))))))))).))))).(((((.(((.(((((.(((....))).))))).))))))))..............((((((((.....))))))))....)))).(((((........)))))........)))....... (-68.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAGUGAAAAGUAGUCAACAGUAAUUAAUGUUGUCAAUGUAGGGGCGAACCUUGUGUUCGCCCUUUUUUUGUGUGAUGUCCGAACGCGUAAAUCAAUGACGAAUUACGAAUUACGAACGCCAUCCUUUGUCAUUCCGAACGUAGUGAGGAAUCCCGUGGGGAAAAGAAUGAGAUUCUUCGCUUCGCUCUGAAUGACAAAUUAAUGGUUAAUUGUUAAUUGUCA .............(((((.((((((((((....((((((.((.((((((((((.....)))))))))).....((((.........))))......)).))))))......))))))....(((((..((((((((((.((.((.(((((((((((.(((..........))).))))))))))).)).)).))))))))))...)))))....)))).)))).). (-69.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 763 80 31 153 103 tfor:TF2777|5end_hypothetical_protein_2961595..2961825_POSITIVE 761 110 61 72 23 tfor:TF0542|5end_hypothetical_protein_571918..572148_POSITIVE 745 60 11 70 21 tfor:TF2816|5end_hypothetical_protein_3006925..3007155_POSITIVE 729 80 31 220 169 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 692 80 31 175 124 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 683 60 11 139 89 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 665 59 11 130 82 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 659 110 68 73 31 tfor:TF1846|5end_hypothetical_protein_1996726..1996956_POSITIVE 659 54 11 46 3 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 649 60 11 139 89 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 629 109 68 204 156 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 619 104 68 52 16 tfor:TF1844|5end_hypothetical_protein_1996389..1996619_POSITIVE 604 59 11 52 3 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 604 54 13 153 112 tfor:TF1660|5end_hypothetical_protein_1775269..1775499_POSITIVE 588 54 11 132 89 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 586 110 68 98 46 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 586 110 68 64 12 tfor:TF1184|5end_hypothetical_protein_1269004..1269234_POSITIVE 583 100 56 52 4 tfor:TF2776|5end_hypothetical_protein_2961470..2961700_POSITIVE 579 108 68 92 46 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 569 210 161 80 19 tfor:TF2438|5end_hypothetical_protein_2615781..2616011_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 810 100 51 77 28 tfor:TF0369|3end_hypothetical_protein_386186..386336_POSITIVE 742 60 11 125 76 tfor:TF1483|3end_glycosyltransferase_family_protein_1578825..1578975_POSITIVE 722 58 11 85 38 tfor:TF2817|3end_hypothetical_protein_3007626..3007776_POSITIVE 693 106 61 51 5 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 692 80 31 64 13 tfor:TF1841|3end_hypothetical_protein_1992267..1992417_POSITIVE 601 190 141 69 19 tfor:TF1838|3end_tRNA/rRNA_methyltransferase_1988745..1988895_POSITIVE 590 54 16 39 1 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 590 54 16 39 1 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 561 64 25 151 112 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 559 54 20 39 5 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 535 59 16 45 1 tfor:TF1844|3end_hypothetical_protein_1996693..1996843_POSITIVE 498 70 24 137 90 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 498 70 27 46 1 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 428 186 161 54 28 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 410 39 10 35 6 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 380 54 11 121 78 tfor:TF0016|3end_hypothetical_protein_10581..10731_POSITIVE 371 54 11 113 70 tfor:TF0017|3end_hypothetical_protein_11231..11381_POSITIVE 366 53 25 150 121 tfor:TF0534|3end_hypothetical_protein_559768..559918_POSITIVE 352 110 69 51 11 tfor:TF1760|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1899413..1899563_POSITIVE 345 110 67 140 98 tfor:TF1890|3end_hypothetical_protein_2043093..2043243_POSITIVE