Origin IGS: aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgacaattaaccattgacaattaatttcgtccttgggcctcgggcggtgagccgacggagctgcgagcagggcgaaagaaaatcaggctgtccgagccaagcgagtcacctgattttctgacctgcaagcctcgcgaaggtgtgtgaagcgcacgaagccttgactt Mask Tandem Repeat Region ================================================ aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca Find is-nt database================================================ Query_seq: TF2664:TF2666|TF2664:TF2666:hypothetical protein:hypothetical protein:->->:2841791..2841957 167 aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2664:TF2666|TF2664:TF2666:hypothetical protein:hypothetical protein:->->:2841791..2841957 167 aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2664:TF2666|TF2664:TF2666:hypothetical protein:hypothetical protein:->->:2841791..2841957 167 aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 40 End: 144 ....................................... M Q V R K S G D S L G S D S L I F F R P A R S S V G S P P E A Q G R N ....................... Protein_Len: 35 Strand: - Start: 50 End: 154 ................................................. F I L H S A Q S P C G S K R E G Q E C S R R S V A R P G L V F N I T M ............. aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca 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================================================ aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -4.2 Tail_Score: -3.58343 Start: 50 End: 90 Full_Region: GAGGCTTGCAGGTCA GAAAATCAGGTGACTCG CTTGGCT CGGACAGCCTGATTTTC TTTCGCCCTGCTCGC .................................................GAAAATCAGGTGACTCGCTTGGCTCGGACAGCCTGATTTTC............................................................................. Find igs database================================================ Query_seq: TF2664:TF2666|TF2664:TF2666:hypothetical protein:hypothetical protein:->->:2841791..2841957 167 aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca Intra-Species Hit: Count: 9 Min: 1 Max: 167 Len: 167 Subject: tfor_TF2664_TF2666|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2841791,2841957]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca Subject: tfor_TF2665_TF2667|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2842296,2842534]|239 HSP 1 e-value: 9.0E-73 bit: 274.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaa......................... aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggcttggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaa......................... Subject: tfor_TF2668_TF2670|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2842794,2842918]|125 HSP 1 e-value: 1.0E-62 bit: 240.0 Len: 125 Query Start:29 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 ............................cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca.............. ............................cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca.............. Subject: tfor_TF2500_TF2501|ABC transporter, ATP-binding protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[2675363,2676419]|1057 HSP 1 e-value: 7.0E-61 bit: 234.0 Len: 165 Query Start:3 Query End:167 Subject Strand: NEGATIVE Subject Start: 515 Subject End: 680 ..gtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggct-cggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggttaattgtca ..gtcaaggcttcgtgcgcttcacacgccttcgcgacgctcgcaggtcggaaaatcaggtaactcgcttcgcttcggacagcctgattttctttcgccctgctcgctgctccgtcagctcaccgcccgaggcccatcgacgaaattaattgtcaatggttaattgtca Subject: tfor_TF2914_TF2915|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3109704,3110561]|858 HSP 1 e-value: 7.0E-55 bit: 214.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 50 Subject End: 205 aagtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggct-cggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaat............ aagtcaaggcttcgtgctcttcacacgccttcgcgaggcttgcaggtcggaaaatcaggtaactcgcttcgcttcggacagcctgattttctttcgccctgctcgctgctccgtcggctcaccacctgaggcccatggacaaaattaattgtcaat............ Subject: tfor_TF1838_TF1839|tRNA/rRNA methyltransferase:conserved hypothetical protein|POSITIVE:POSITIVE|[1988806,1989486]|681 HSP 1 e-value: 3.0E-54 bit: 212.0 Len: 143 Query Start:18 Query End:160 Subject Strand: NEGATIVE Subject Start: 247 Subject End: 389 .................gcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaatggtta....... .................gcttcgcacgccttcgcgacgcttgcaggtcggaaaatcaggtaactcgcttggctcggacagcctgattttctttcgccctgctcgctgcttcgtcggctcaccgcccgaggcccatggacgaaataaattgtcaatggtta....... Subject: tfor_TF2920_TF2921|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3117231,3118637]|1407 HSP 1 e-value: 1.0E-53 bit: 210.0 Len: 153 Query Start:3 Query End:155 Subject Strand: POSITIVE Subject Start: 246 Subject End: 399 ..gtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggct-cggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtcaat............ ..gtcaaggcttcgtgcgcttcacacgccttcgcgacacttgcaggtcggaaaatcaggtaactcgcttcgcttcagacagcctgattttctttcgccctgctcgctgctccatcggctcaccgcccgaggcccatggacgaaattaattgtcaat............ Subject: tfor_TF2922_TF2923|surface antigen BspA:hypothetical protein|POSITIVE:POSITIVE|[3121599,3122307]|709 HSP 1 e-value: 2.0E-52 bit: 206.0 Len: 140 Query Start:3 Query End:142 Subject Strand: POSITIVE Subject Start: 190 Subject End: 329 ..gtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaa......................... ..gtcaaggcttcgtgcgcttcacacgccttcgcgacgctcgcaggtcggaaaatcaggtaactcgcttcgctcggacagcctgattttctttcgccctgctcgctgctccgtcggctcaccacccgaggcccatggacgaa......................... Subject: tfor_TF0685_TF0686|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[731193,732338]|1146 HSP 1 e-value: 7.0E-52 bit: 204.0 Len: 134 Query Start:3 Query End:136 Subject Strand: POSITIVE Subject Start: 247 Subject End: 381 ..gtcaaggcttcgtgcgcttcacacaccttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggct-cggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaag............................... ..gtcaaggcttcgtgcgcttcacacgccttcgcgacgcttgcaggtcggaaaatcaggtaactcgcttcgcttcggacagcctgattttctttcgccctgctcgctgctccgtcggctcaccgcccgaggcccaag............................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUCAAGGCUUCGUGCGCUUCACACACCUUCGCGAGGCUUGCAGGUCAGAAAAUCAGGUGACUCGCUUGGCUCGGACAGCCUGAUUUUCUUUCGCCCUGCUCGCAGCUCCGUCGGCUCACCGCCCGAGGCCCAAGGACGAAAUUAAUUGUCAAUGGUUAAUUGUCA ..(((..(((((((.(((.........((..((.(((((..(((((.(((((((((((((...(((.......)))...))))))))))))...).)))))..))..)))))..)).....))).)))))))....)))..((((((((......)))))))).... (-55.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAAUUAACCAUUGACAAUUAAUUUCGUCCUUGGGCCUCGGGCGGUGAGCCGACGGAGCUGCGAGCAGGGCGAAAGAAAAUCAGGCUGUCCGAGCCAAGCGAGUCACCUGAUUUUCUGACCUGCAAGCCUCGCGAAGGUGUGUGAAGCGCACGAAGCCUUGACUU ...((((.....))))............(((...((((.(((.(((.(..(((..(((((..((..(((((.....(((((((((((.((.(((.......)).).)))))))))))))..)))))..))))).))..)))......).))).))).)))).))).. (-57.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1132 140 91 70 21 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 1112 130 81 215 166 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 1112 130 81 215 166 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 1103 140 91 135 86 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 1037 130 81 67 18 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 999 140 91 227 178 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 880 140 97 44 1 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 846 60 11 69 20 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 818 48 1 218 171 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 732 60 11 127 78 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 713 142 104 39 1 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 712 48 1 210 162 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 693 41 3 231 193 tfor:TF1846|5end_hypothetical_protein_1996726..1996956_POSITIVE 684 40 3 231 194 tfor:TF1660|5end_hypothetical_protein_1775269..1775499_POSITIVE 554 142 116 27 1 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 507 140 117 25 1 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 485 140 94 50 1 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 465 140 94 80 23 tfor:TF1494|5end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_1594016..1594246_POSITIVE 464 135 93 220 163 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 457 140 95 50 4 tfor:TF0462|5end_possible_cobalamin_biosynthesis_precorrin-3_methylase_477600..477830_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1103 140 91 135 86 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 971 117 71 151 104 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 953 48 3 99 54 tfor:TF1187|3end_hypothetical_protein_1269872..1270022_POSITIVE 875 48 3 125 80 tfor:TF1844|3end_hypothetical_protein_1996693..1996843_POSITIVE 875 48 3 99 54 tfor:TF1659|3end_hypothetical_protein_1775209..1775359_POSITIVE 875 48 3 115 70 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 870 48 3 125 80 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 870 48 3 115 70 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 818 48 1 125 78 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 808 48 1 99 52 tfor:TF0598|3end_hypothetical_protein_629500..629650_POSITIVE 794 126 81 151 105 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 716 48 1 125 77 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 716 48 1 125 77 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 473 33 3 151 121 tfor:TF2817|3end_hypothetical_protein_3007626..3007776_POSITIVE 453 141 104 132 96 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 445 129 82 106 65 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 444 133 94 62 22 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 437 119 75 133 98 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 431 120 71 90 36 tfor:TF0337|3end_hypothetical_protein_360711..360861_POSITIVE 428 34 3 124 98 tfor:TF1842|3end_hypothetical_protein_1992800..1992950_POSITIVE