Origin IGS: tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga .........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.........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 tcattatcgtttgtatataaagcaaacgtttaggcataaaccctaaataaaatcaaaaaaaagtcgattcatctcttctcaacaatatacatctgcgcttcggataagaaaaaaaacgttgattcagaatggaaagcttgattttttttattgctgtccgataaaactataaaagcaataaatattgtcccctcagtccctataaatagtaccttcatatttccttcttaaaaagtaagcccctcttatggctgatatagctttttttagtgaacagccgttgcagagaacgaatataagctctataaatgtgcagaatctcttcttctgtggggttcccaagccttagaaatgaaactataggtgcgcgtatatgcttaattcggctatttttagcggatagcaatgaaagctggaatatcctcaaataggatgtgcaaaagaacggtgagtgagaacttaagggactttcggaaaagcgaggggcagagagggaaaaaagaaaggtgcggtcaattttaatcaaccacaccttccattatca Mask Tandem Repeat Region ================================================ tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Find is-nt database================================================ Query_seq: TF0489:TF0490|TF0489:TF0490:D-xylose-proton symporter:conserved hypothetical protein:->->:513130..513673 544 tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0489:TF0490|TF0489:TF0490:D-xylose-proton symporter:conserved hypothetical protein:->->:513130..513673 544 tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0489:TF0490|TF0489:TF0490:D-xylose-proton symporter:conserved hypothetical protein:->->:513130..513673 544 tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 13 End: 327 ............ M W L I K I D R T F L F S L S A P R F S E S P L S S H S P F F C T S Y L R I F Q L S L L S A K N S R I K H I R A P I V S ......................................................................................................................................................................................................................... Protein_Len: 49 Strand: + Start: 203 End: 349 .......................................................................................................................................................................................................... M G T P Q K K R F C T F I E L I F V L C N G C S L K K A I S A I R G A Y F L R R K Y E G T I Y R D ................................................................................................................................................................................................... Protein_Len: 49 Strand: + Start: 327 End: 473 ...................................................................................................................................................................................................................................................................................................................................... M K V L F I G T E G T I F I A F I V L S D S N K K N Q A F H S E S T F F F L S E A Q M Y I V E K R ....................................................................... Protein_Len: 32 Strand: + Start: 394 End: 489 ......................................................................................................................................................................................................................................................................................................................................................................................................... M K K I K L S I L N Q R F F S Y P K R R C I L L R R D E S T F F ....................................................... Protein_Len: 41 Strand: - Start: 376 End: 498 ....................................................................................................................................................................................................................................................................................................................................................................................... L K I P C C Y F F D L K G N Q I L T K K R I R L A S T Y Q Q S S I F R S K K S K M .............................................. Protein_Len: 33 Strand: - Start: 199 End: 297 ...................................................................................................................................................................................................... P K P V G C F F L N Q V N I S S I N T R Q L P Q E S F F A I D A M ....................................................................................................................................................................................................................................................... Protein_Len: 40 Strand: - Start: 117 End: 236 .................................................................................................................... K L I N W S E N S D A L F L R I L C I R A G I T E N R L S P F G V S S S I R C M .................................................................................................................................................................................................................................................................................................................... Protein_Len: 40 Strand: - Start: 26 End: 145 ......................... F Q G C R E K K G R Q G E S K R F D R L N E S V T R K C M R N S S I G A K M A M ............................................................................................................................................................................................................................................................................................................................................................................................................... tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga 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================================================ tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -3.2 Tail_Score: -5.52384 Start: 284 End: 294 Full_Region: taagcccctcttatg gctg ata tagc tttttttagtgaaca ...........................................................................................................................................................................................................................................................................................gctgatatagc.......................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF0489:TF0490|TF0489:TF0490:D-xylose-proton symporter:conserved hypothetical protein:->->:513130..513673 544 tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Intra-Species Hit: Count: 2 Min: 1 Max: 544 Len: 544 Subject: tfor_TF0489_TF0490|D-xylose-proton symporter:conserved hypothetical protein|POSITIVE:POSITIVE|[513130,513673]|544 HSP 1 e-value: 0.0 bit: 894.0 Len: 544 Query Start:1 Query End:544 Subject Strand: POSITIVE Subject Start: 1 Subject End: 544 tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactnnnnnnngctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaatnnnnnnnntcaagctttccattctgaatcaacgnnnnnnnncttatccgaagcgcagatgtatattgttgagaagagatgaatcgacnnnnnnnngattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga tgataatggaaggtgtggttgattaaaattgaccgcacctttcttttttccctctctgcccctcgcttttccgaaagtcccttaagttctcactcaccgttcttttgcacatcctatttgaggatattccagctttcattgctatccgctaaaaatagccgaattaagcatatacgcgcacctatagtttcatttctaaggcttgggaaccccacagaagaagagattctgcacatttatagagcttatattcgttctctgcaacggctgttcactaaaaaaagctatatcagccataagaggggcttactttttaagaaggaaatatgaaggtactatttatagggactgaggggacaatatttattgcttttatagttttatcggacagcaataaaaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Subject: tfor_TF0480_TF0481|ornithine carbamoyltransferase:possible anti-sigma factor|POSITIVE:POSITIVE|[499650,499873]|224 HSP 1 e-value: 5.0E-37 bit: 157.0 Len: 141 Query Start:404 Query End:544 Subject Strand: POSITIVE Subject Start: 86 Subject End: 224 ...................................................................................................................................................................................................................................................................................................................................................................................................................tcaagctttccattctgaatcaacgnnnnnnnncttatccgaagcgcagatgtatattgttgagaagagatgaatcgacnnnnnnnngattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga ...................................................................................................................................................................................................................................................................................................................................................................................................................tcaagctttccattctgaatcaacgtttcttt-cttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttt-gattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAAUGGAAGGUGUGGUUGAUUAAAAUUGACCGCACCUUUCUUUUUUCCCUCUCUGCCCCUCGCUUUUCCGAAAGUCCCUUAAGUUCUCACUCACCGUUCUUUUGCACAUCCUAUUUGAGGAUAUUCCAGCUUUCAUUGCUAUCCGCUAAAAAUAGCCGAAUUAAGCAUAUACGCGCACCUAUAGUUUCAUUUCUAAGGCUUGGGAACCCCACAGAAGAAGAGAUUCUGCACAUUUAUAGAGCUUAUAUUCGUUCUCUGCAACGGCUGUUCACUAAAAAAAGCUAUAUCAGCCAUAAGAGGGGCUUACUUUUUAAGAAGGAAAUAUGAAGGUACUAUUUAUAGGGACUGAGGGGACAAUAUUUAUUGCUUUUAUAGUUUUAUCGGACAGCAAUAAAAAAAAUCAAGCUUUCCAUUCUGAAUCAACGUUUUUUUUCUUAUCCGAAGCGCAGAUGUAUAUUGUUGAGAAGAGAUGAAUCGACUUUUUUUUGAUUUUAUUUAGGGUUUAUGCCUAAACGUUUGCUUUAUAUACAAACGAUAAUGA .......((((((((((((..((....))..))))))))))))......((((...((((((((...........((((((((((((...(..(((...(((((((((..(((((.....))))).....((((((....((.....))....((((((((......((......))(((....(((..((.(((((....((((((...)))).)).))))).))..))).........(((((........))))).)))..))))))))........))))))......))..(((((((......))))))).)))))))...)))..)....))))).))))))))))))).))...(((((((((.((...(......).)).))))))))).(((((((((..(((......)))....(((((((((((.....(((.(..(....)..).)))..)))))))))))............)))))))))....))))............((((((.........))))))....... (-125.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUUAUCGUUUGUAUAUAAAGCAAACGUUUAGGCAUAAACCCUAAAUAAAAUCAAAAAAAAGUCGAUUCAUCUCUUCUCAACAAUAUACAUCUGCGCUUCGGAUAAGAAAAAAAACGUUGAUUCAGAAUGGAAAGCUUGAUUUUUUUUAUUGCUGUCCGAUAAAACUAUAAAAGCAAUAAAUAUUGUCCCCUCAGUCCCUAUAAAUAGUACCUUCAUAUUUCCUUCUUAAAAAGUAAGCCCCUCUUAUGGCUGAUAUAGCUUUUUUUAGUGAACAGCCGUUGCAGAGAACGAAUAUAAGCUCUAUAAAUGUGCAGAAUCUCUUCUUCUGUGGGGUUCCCAAGCCUUAGAAAUGAAACUAUAGGUGCGCGUAUAUGCUUAAUUCGGCUAUUUUUAGCGGAUAGCAAUGAAAGCUGGAAUAUCCUCAAAUAGGAUGUGCAAAAGAACGGUGAGUGAGAACUUAAGGGACUUUCGGAAAAGCGAGGGGCAGAGAGGGAAAAAAGAAAGGUGCGGUCAAUUUUAAUCAACCACACCUUCCAUUAUCA .......(((((((.......)))))))............((((.............(((((((((((((((.(((..(((((........(((...(....)...)))........)))))...))))))))....))))))))))((((((((.....(((....)))...))))))))...(((.(((((((((((((......(((...(((((....(((((((.(((((((.(((.((((.(((((((.....(((......)))...)))))))...))))...((((.(((((...(((.((((((.(((((((.........)))))))....(((((((........))).)))))))))).)))))))))))))))))))))).((...((((.......))))..(((((((.....)))))))))..))))).))...))))).)))..)))))))...........)))))))))..))))......(.((((((.(((..((....))..))).)))))).)....... (-133.69) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 100 51 199 141 tfor:TF2810|5end_conserved_hypothetical_protein_3000583..3000813_POSITIVE 367 73 32 199 140 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 357 67 28 69 32 tfor:TF0093|5end_outer_membrane_protein,_TonB_dependent_receptor_100497..100727_POSITIVE 350 52 12 205 162 tfor:TF2900|5end_conserved_hypothetical_protein_3088252..3088482_POSITIVE 336 60 11 158 112 tfor:TF0352|5end_transposase_element_371223..371453_POSITIVE 334 110 61 154 108 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 331 74 32 45 6 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 331 98 51 225 170 tfor:TF1684|5end_zinc_protease_1797396..1797626_POSITIVE 326 96 57 231 190 tfor:TF0984|5end_possible_mucin-desulfating_sulfatase_(MdsC_protein)_1040259..1040489_POSITIVE 320 79 33 220 161 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 316 100 55 176 118 tfor:TF2295|5end_hypothetical_protein_2448164..2448394_POSITIVE 313 99 53 65 22 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 312 99 53 55 9 tfor:TF2511|5end_RNA_binding_protein_2689910..2690140_POSITIVE 309 94 51 231 190 tfor:TF2729|5end_possible_outer_membrane_protein_2908216..2908446_POSITIVE 307 91 55 80 36 tfor:TF0644|5end_pyruvate_phosphate_dikinase_685784..686014_POSITIVE 307 100 53 129 75 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 305 80 32 97 53 tfor:TF3135|5end_hypothetical_protein_3369821..3370051_POSITIVE 304 180 132 100 46 tfor:TF2048|5end_conserved_hypothetical_protein_2210643..2210873_POSITIVE 301 79 31 207 148 tfor:TF1296|5end_possible_DNA-binding_protein,_histone-like_family_1378432..1378662_POSITIVE 301 83 42 188 152 tfor:TF0540|5end_conserved_hypothetical_protein;_possible_surface_protein_567286..567516_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 43 8 83 48 tfor:TF0489|3end_D-xylose-proton_symporter_513069..513219_POSITIVE 357 67 28 41 4 tfor:TF0092|3end_outer_membrane_protein_100549..100699_POSITIVE 336 60 11 81 35 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 332 107 61 55 8 tfor:TF2809|3end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_3000511..3000661_POSITIVE 331 74 32 45 6 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 331 98 51 92 37 tfor:TF1682|3end_hydrolase_1797343..1797493_POSITIVE 319 250 203 82 29 tfor:TF1540|3end_possible_ATPase_1645987..1646137_POSITIVE 312 390 344 62 7 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 307 100 53 96 42 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 305 80 32 109 65 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 301 83 42 145 109 tfor:TF0539|3end_hypothetical_protein_567323..567473_POSITIVE 297 86 49 54 17 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 296 218 176 68 32 tfor:TF1156|3end_oxidoreductase,_FAD-binding_1238092..1238242_POSITIVE 294 80 34 128 69 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 294 75 33 149 100 tfor:TF1008|3end_rod_shape-determining_protein_MreC_1064374..1064524_POSITIVE 294 77 33 60 20 tfor:TF0167|3end_conserved_hypothetical_protein_178234..178384_POSITIVE 292 83 49 150 124 tfor:TF1660|3end_hypothetical_protein_1775600..1775750_POSITIVE 291 94 52 145 96 tfor:TF0117|3end_2-dehydro-3-deoxygluconokinase_129808..129958_POSITIVE 290 79 35 80 34 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 289 90 50 63 24 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE