Origin IGS: cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgacaattaatttcgtccttgggcctcgggcggtgagccgacggagctgcgagcaggtcgaaagaaaatcaggctgtccgagccaagcgagtcacctgattttctgacctgcaagcctcgcgaag Mask Tandem Repeat Region ================================================ cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Find is-nt database================================================ Query_seq: TF2668:TF2670|TF2668:TF2670:hypothetical protein:hypothetical protein:->->:2842794..2842918 125 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2668:TF2670|TF2668:TF2670:hypothetical protein:hypothetical protein:->->:2842794..2842918 125 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2668:TF2670|TF2668:TF2670:hypothetical protein:hypothetical protein:->->:2842794..2842918 125 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 12 End: 116 ........... 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: 33 Strand: - Start: 22 End: 120 ..................... F I L H S A Q S P C G S K R E V Q E C S R R S V A R P G L V F N M ..... cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca 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================================================ cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -4.2 Tail_Score: -3.58343 Start: 22 End: 62 Full_Region: GAGGCTTGCAGGTCA GAAAATCAGGTGACTCG CTTGGCT CGGACAGCCTGATTTTC TTTCGACCTGCTCGC .....................GAAAATCAGGTGACTCGCTTGGCTCGGACAGCCTGATTTTC............................................................... Find igs database================================================ Query_seq: TF2668:TF2670|TF2668:TF2670:hypothetical protein:hypothetical protein:->->:2842794..2842918 125 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Intra-Species Hit: Count: 9 Min: 1 Max: 125 Len: 125 Subject: tfor_TF2668_TF2670|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2842794,2842918]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Subject: tfor_TF2664_TF2666|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2841791,2841957]|167 HSP 1 e-value: 9.0E-63 bit: 240.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 29 Subject End: 153 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca Subject: tfor_TF2665_TF2667|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2842296,2842534]|239 HSP 1 e-value: 8.0E-54 bit: 210.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 29 Subject End: 142 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaa........... cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggcttggacagcctgattttctttcgccctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaa........... Subject: tfor_TF1838_TF1839|tRNA/rRNA methyltransferase:conserved hypothetical protein|POSITIVE:POSITIVE|[1988806,1989486]|681 HSP 1 e-value: 4.0E-46 bit: 184.0 Len: 125 Query Start:1 Query End:125 Subject Strand: NEGATIVE Subject Start: 254 Subject End: 378 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca cttcgcgacgcttgcaggtcggaaaatcaggtaactcgcttggctcggacagcctgattttctttcgccctgctcgctgcttcgtcggctcaccgcccgaggcccatggacgaaataaattgtca Subject: tfor_TF2914_TF2915|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3109704,3110561]|858 HSP 1 e-value: 2.0E-39 bit: 163.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 78 Subject End: 203 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggct-cggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca cttcgcgaggcttgcaggtcggaaaatcaggtaactcgcttcgcttcggacagcctgattttctttcgccctgctcgctgctccgtcggctcaccacctgaggcccatggacaaaattaattgtca Subject: tfor_TF2922_TF2923|surface antigen BspA:hypothetical protein|POSITIVE:POSITIVE|[3121599,3122307]|709 HSP 1 e-value: 4.0E-37 bit: 155.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 216 Subject End: 329 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggctcggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaa........... cttcgcgacgctcgcaggtcggaaaatcaggtaactcgcttcgctcggacagcctgattttctttcgccctgctcgctgctccgtcggctcaccacccgaggcccatggacgaa........... Subject: tfor_TF2920_TF2921|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[3117231,3118637]|1407 HSP 1 e-value: 4.0E-37 bit: 155.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 272 Subject End: 397 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggct-cggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca cttcgcgacacttgcaggtcggaaaatcaggtaactcgcttcgcttcagacagcctgattttctttcgccctgctcgctgctccatcggctcaccgcccgaggcccatggacgaaattaattgtca Subject: tfor_TF2500_TF2501|ABC transporter, ATP-binding protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[2675363,2676419]|1057 HSP 1 e-value: 4.0E-37 bit: 155.0 Len: 125 Query Start:1 Query End:125 Subject Strand: NEGATIVE Subject Start: 529 Subject End: 654 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggct-cggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaaggacgaaattaattgtca cttcgcgacgctcgcaggtcggaaaatcaggtaactcgcttcgcttcggacagcctgattttctttcgccctgctcgctgctccgtcagctcaccgcccgaggcccatcgacgaaattaattgtca Subject: tfor_TF0685_TF0686|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[731193,732338]|1146 HSP 1 e-value: 2.0E-36 bit: 153.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 273 Subject End: 381 cttcgcgaggcttgcaggtcagaaaatcaggtgactcgcttggct-cggacagcctgattttctttcgacctgctcgcagctccgtcggctcaccgcccgaggcccaag................. cttcgcgacgcttgcaggtcggaaaatcaggtaactcgcttcgcttcggacagcctgattttctttcgccctgctcgctgctccgtcggctcaccgcccgaggcccaag................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCGCGAGGCUUGCAGGUCAGAAAAUCAGGUGACUCGCUUGGCUCGGACAGCCUGAUUUUCUUUCGACCUGCUCGCAGCUCCGUCGGCUCACCGCCCGAGGCCCAAGGACGAAAUUAAUUGUCA ....((((.....(((((((((((((((((((...(((.......)))...))))))))))))...))))))))))).((..((..(((.....)))))..)).....(((((......))))). (-46.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAAUUAAUUUCGUCCUUGGGCCUCGGGCGGUGAGCCGACGGAGCUGCGAGCAGGUCGAAAGAAAAUCAGGCUGUCCGAGCCAAGCGAGUCACCUGAUUUUCUGACCUGCAAGCCUCGCGAAG ...........(((((.....(((..((..(((....))).))..)))((..(((((((...(((((((((((.((.(((.......)).).))))))))))))))))))))..))...))))). (-47.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1037 110 61 68 19 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 1023 100 51 213 164 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 1023 100 51 213 164 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 998 110 61 133 84 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 948 100 51 65 16 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 904 110 61 225 176 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 843 114 71 46 3 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 724 47 1 85 38 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 714 114 72 39 1 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 644 46 5 141 100 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 576 41 1 231 191 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 554 114 88 27 1 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 507 112 89 25 1 tfor:TF3105|5end_hypothetical_protein_3338068..3338298_POSITIVE 472 113 75 51 1 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 457 105 65 68 15 tfor:TF0722|5end_pyruvate_dehydrogenase_E3_component(dihydrolipoamide_dehydrogenase)_772873..773103_POSITIVE 455 104 61 190 146 tfor:TF2810|5end_conserved_hypothetical_protein_3000583..3000813_POSITIVE 453 113 76 50 14 tfor:TF2337|5end_conserved_hypothetical_protein_2497997..2498227_POSITIVE 452 113 72 51 4 tfor:TF0462|5end_possible_cobalamin_biosynthesis_precorrin-3_methylase_477600..477830_POSITIVE 426 100 52 63 3 tfor:TF1602|5end_L-aspartate_oxidase_1715579..1715809_POSITIVE 425 107 68 220 165 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 998 110 61 133 84 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 891 89 43 151 104 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 877 50 1 130 80 tfor:TF1187|3end_hypothetical_protein_1269872..1270022_POSITIVE 816 98 51 151 103 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 815 60 11 140 90 tfor:TF1659|3end_hypothetical_protein_1775209..1775359_POSITIVE 799 50 1 146 96 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 794 50 1 146 96 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 739 60 11 140 90 tfor:TF0598|3end_hypothetical_protein_629500..629650_POSITIVE 701 45 1 150 106 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 668 45 3 150 108 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 668 45 3 150 108 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 630 45 1 150 106 tfor:TF1844|3end_hypothetical_protein_1996693..1996843_POSITIVE 554 45 1 150 106 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 453 113 76 132 96 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 425 89 43 88 36 tfor:TF0337|3end_hypothetical_protein_360711..360861_POSITIVE 422 105 68 62 23 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 412 100 52 61 1 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 411 90 47 132 98 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 406 104 71 38 5 tfor:TF2809|3end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_3000511..3000661_POSITIVE 406 89 46 126 84 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE