Origin IGS: tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt .........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 aattagtcaaatcttaagggaaccatatcccaaattttcgcatttctcagaaagagcgatctttctttatttctaacctgtatatacactccttccaaagcttaaaaccacacaattgtacaaaaaaacgcttgaatatccaaaatatatatctttgcggaccctaattccttctaatacccccgatttacccacattgtgaaggaggggtgtaacggctatactctcaaggagcttcaatgtgatatgatttaattatttgggatatgcttagaagattaggccggagcattcatagccccccttagcccctctgacctcaaaggctaacgcgataataggcagatagaactgcgtaaatacaagcaaagagagatttattcacaaaaaatatactaaacttatatctttggacgctataagttcattgatacggtaaacttgtaattagttaggagctacatagacaaaaca Mask Tandem Repeat Region ================================================ tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Find is-nt database================================================ Query_seq: TF0892:TF0893|TF0892:TF0893:conserved hypothetical protein:conserved hypothetical protein:->->:941420..941893 474 tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0892:TF0893|TF0892:TF0893:conserved hypothetical protein:conserved hypothetical protein:->->:941420..941893 474 tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0892:TF0893|TF0892:TF0893:conserved hypothetical protein:conserved hypothetical protein:->->:941420..941893 474 tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 94 End: 201 ............................................................................................. M N L S L L V F T Q F Y L P I I A L A F E V R G A K G G Y E C S G L I F ................................................................................................................................................................................................................................................................................. Protein_Len: 57 Strand: + Start: 229 End: 399 .................................................................................................................................................................................................................................... M T L K L L E S I A V T P L L H N V G K S G V L E G I R V R K D I Y F G Y S S V F L Y N C V V L S F G R S V Y T G ........................................................................... Protein_Len: 33 Strand: + Start: 327 End: 425 ...................................................................................................................................................................................................................................................................................................................................... M F W I F K R F F V Q L C G F K L W K E C I Y R L E I K K D R S F ................................................. Protein_Len: 32 Strand: + Start: 377 End: 469 ........................................................................................................................................................................................................................................................................................................................................................................................ M E G V Y I Q V R N K E R S L F L R N A K I W D M V P L R F D * ..... Protein_Len: 46 Strand: - Start: 311 End: 448 ...................................................................................................................................................................................................................................................................................................................... P G C L Y I N Q I N L R K K T C N H P K L S Q F S H I Y L N S I F F S R E K Q S I R F N P M .......................... tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 331 End: 360 ..........................................................................................................................................................................................................................................................................................................................................TTTGGATATTCAAGCGTTTTTTTGTACAAT.................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 250 End: 279 .........................................................................................................................................................................................................................................................ATTGTGAAGGAGGGGTGTAACGGCTATACT................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -2.1 Tail_Score: -3.36671 Start: 117 End: 136 Full_Region: CTCTTTGCTTGTATT TACGCAG TTCTAT CTGCCTA TTATCGCGTTAGCCT ....................................................................................................................TACGCAGTTCTATCTGCCTA.................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 76 HP_score: -6.2 Tail_Score: -4.56367 Start: 410 End: 425 Full_Region: ttttcgcatttctca gaaaga gcga tctttc tttatttctaacctg .........................................................................................................................................................................................................................................................................................................................................................................................................................gaaagagcgatctttc................................................. Find igs database================================================ Query_seq: TF0892:TF0893|TF0892:TF0893:conserved hypothetical protein:conserved hypothetical protein:->->:941420..941893 474 tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Intra-Species Hit: Count: 1 Min: 1 Max: 474 Len: 474 Subject: tfor_TF0892_TF0893|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[941420,941893]|474 HSP 1 e-value: 0.0 bit: 898.0 Len: 474 Query Start:1 Query End:474 Subject Strand: POSITIVE Subject Start: 1 Subject End: 474 tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgnnnnnnngtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt tgttttgtctatgtagctcctaactaattacaagtttaccgtatcaatgaacttatagcgtccaaagatataagtttagtatattttttgtgaataaatctctctttgcttgtatttacgcagttctatctgcctattatcgcgttagcctttgaggtcagaggggctaaggggggctatgaatgctccggcctaatcttctaagcatatcccaaataattaaatcatatcacattgaagctccttgagagtatagccgttacacccctccttcacaatgtgggtaaatcgggggtattagaaggaattagggtccgcaaagatatatattttggatattcaagcgtttttttgtacaattgtgtggttttaagctttggaaggagtgtatatacaggttagaaataaagaaagatcgctctttctgagaaatgcgaaaatttgggatatggttcccttaagatttgactaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUGUCUAUGUAGCUCCUAACUAAUUACAAGUUUACCGUAUCAAUGAACUUAUAGCGUCCAAAGAUAUAAGUUUAGUAUAUUUUUUGUGAAUAAAUCUCUCUUUGCUUGUAUUUACGCAGUUCUAUCUGCCUAUUAUCGCGUUAGCCUUUGAGGUCAGAGGGGCUAAGGGGGGCUAUGAAUGCUCCGGCCUAAUCUUCUAAGCAUAUCCCAAAUAAUUAAAUCAUAUCACAUUGAAGCUCCUUGAGAGUAUAGCCGUUACACCCCUCCUUCACAAUGUGGGUAAAUCGGGGGUAUUAGAAGGAAUUAGGGUCCGCAAAGAUAUAUAUUUUGGAUAUUCAAGCGUUUUUUUGUACAAUUGUGUGGUUUUAAGCUUUGGAAGGAGUGUAUAUACAGGUUAGAAAUAAAGAAAGAUCGCUCUUUCUGAGAAAUGCGAAAAUUUGGGAUAUGGUUCCCUUAAGAUUUGACUAAUU .(((..((((...(((((((............................(((((....((((....((((((((((..((.....(((........))).....))..)))))))))))))))))))..(((((((......((....)).....))).)))))))))))((((((((((((.(((((..((........))..))))).((((((((....(((((((((.(((..((((((((((...(((((..(((....(((((...........).))))....)))..)))))..)))))......(((((.(((........))))))))........)))))..)))......)))))))))...((((..(((((((((.((.......(((....)))......)))))))))))..))....))....)))))))))))))))))))).))))..)))..... (-114.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAGUCAAAUCUUAAGGGAACCAUAUCCCAAAUUUUCGCAUUUCUCAGAAAGAGCGAUCUUUCUUUAUUUCUAACCUGUAUAUACACUCCUUCCAAAGCUUAAAACCACACAAUUGUACAAAAAAACGCUUGAAUAUCCAAAAUAUAUAUCUUUGCGGACCCUAAUUCCUUCUAAUACCCCCGAUUUACCCACAUUGUGAAGGAGGGGUGUAACGGCUAUACUCUCAAGGAGCUUCAAUGUGAUAUGAUUUAAUUAUUUGGGAUAUGCUUAGAAGAUUAGGCCGGAGCAUUCAUAGCCCCCCUUAGCCCCUCUGACCUCAAAGGCUAACGCGAUAAUAGGCAGAUAGAACUGCGUAAAUACAAGCAAAGAGAGAUUUAUUCACAAAAAAUAUACUAAACUUAUAUCUUUGGACGCUAUAAGUUCAUUGAUACGGUAAACUUGUAAUUAGUUAGGAGCUACAUAGACAAAACA .....(((.........((((......)))).....((((((......(((((((....)))))))............(((((((............((((..........((....))..........))))...........)))))))....))))))......(((((.(((((.....(((((((((....(((((((((((((((.....((((((.(((.....)))....(((((....((..((((((.((((((.....)))))).))))))..))..))))).)))))).......))))))))...(((....((....)).....((.((((......)))).))............))).......))))))).................((((..(((((.......)))))..)))).)))))).)))..)))))..))))).......)))...... (-99.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 188 141 87 40 tfor:TF2189|5end_conserved_hypothetical_protein_2363455..2363685_POSITIVE 427 190 141 54 8 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 422 190 141 209 164 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 419 190 142 85 25 tfor:TF0829|5end_conserved_hypothetical_protein_887760..887990_POSITIVE 406 198 157 145 102 tfor:TF1423|5end_cell_division_protein_(ftsW)_1505942..1506172_POSITIVE 400 201 163 99 63 tfor:TF1598|5end_conserved_hypothetical_protein_1713358..1713588_POSITIVE 386 190 147 179 138 tfor:TF0261|5end_conserved_hypothetical_protein_291784..292014_POSITIVE 377 188 141 213 169 tfor:TF2215|5end_conserved_hypothetical_protein_2387501..2387731_POSITIVE 366 190 141 186 121 tfor:TF2129|5end_possible_3-oxoacyl-(acyl-carrier-protein)_synthase_2305464..2305694_POSITIVE 361 190 149 160 123 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 361 190 149 56 19 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 360 198 151 96 53 tfor:TF2723|5end_30S_ribosomal_protein_S20_2897689..2897919_POSITIVE 359 176 132 206 164 tfor:TF0536|5end_conserved_hypothetical_protein_561917..562147_POSITIVE 358 294 256 42 8 tfor:TF0243|5end_conserved_hypothetical_protein_273728..273958_POSITIVE 356 190 142 84 36 tfor:TF0680|5end_tail-specific_protease_721393..721623_POSITIVE 353 190 142 110 54 tfor:TF0022|5end_two-component_system_sensor_histidine_kinase_17295..17525_POSITIVE 348 190 142 219 185 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 348 190 143 68 27 tfor:TF1417|5end_conserved_hypothetical_protein_1499544..1499774_POSITIVE 346 189 149 49 21 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 346 188 143 73 33 tfor:TF1268|5end_conserved_hypothetical_protein_1354085..1354315_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 200 151 48 7 tfor:TF1350|3end_possible_transcriptional_regulator_1430636..1430786_POSITIVE 428 188 141 87 40 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 419 190 142 90 30 tfor:TF0830|3end_hypothetical_protein_887845..887995_POSITIVE 400 201 163 79 43 tfor:TF1597|3end_TatD_family_protein_1713418..1713568_POSITIVE 361 190 149 103 69 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 356 190 142 100 52 tfor:TF0679|3end_hypothetical_protein_721489..721639_POSITIVE 356 190 149 124 88 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 348 190 142 142 108 tfor:TF2245|3end_conserved_hypothetical_protein_2421291..2421441_POSITIVE 346 188 143 73 33 tfor:TF1266|3end_conserved_hypothetical_protein_1354165..1354315_POSITIVE 344 206 162 81 32 tfor:TF0537|3end_conserved_hypothetical_protein_566836..566986_POSITIVE 343 195 156 140 100 tfor:TF2272|3end_conserved_hypothetical_protein_2436514..2436664_POSITIVE 341 297 251 139 91 tfor:TF0271|3end_oxidase/dehydrogenase_298530..298680_POSITIVE 339 188 148 57 8 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 335 175 140 38 1 tfor:TF2039|3end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199835..2199985_POSITIVE 334 189 148 101 56 tfor:TF3121|3end_nicotinate_phosphoribosyltransferase_3356124..3356274_POSITIVE 333 190 145 110 73 tfor:TF1002|3end_replicative_DNA_helicase_1058232..1058382_POSITIVE 329 192 158 101 61 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 329 210 161 83 30 tfor:TF0239|3end_conserved_hypothetical_protein_270323..270473_POSITIVE 328 181 149 72 46 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 327 192 152 49 11 tfor:TF1725|3end_hypothetical_protein_1852094..1852244_POSITIVE