Origin IGS: tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat .........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 ataggcactgaacacataaattgagacgcaaaaataacactcctgtttagatctagtgaaactatgaacaggagtgttttattatgaccgaaaaaggttattccgtagaaactaagttacccttcatcaaaataaaaaatgatagaaattaaataaggtaatcacgcctagccttgcaatcaaaatttagaaaaggttatcacaaagctaatcgagctaaaaaatcgacaaaaaagcactttgcaaaatctttgcaaagtgctttgaaacgttgatataatcgtattgattaacgttttgagaattgtgaagctttacgagctttcttaagacctggtttggaaagtatgagtttcagttggactaaaaatagtgtaaaatcaatattctatagttttcaactgcctttttatttcaaaaaatttgtataagttttattgaatgagggaaatttcaagtaaacaacttagctgttattactcccgaatagagtttcccactgagttattgataatgggannnnnttaattaattaannnnnaaaggtttcagattttcttaggcgatagaaaatctgaaacctatgctcttca Mask Tandem Repeat Region ================================================ tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat Find is-nt database================================================ Query_seq: SMT_250:SMT_251|SMT_250:SMT_251:site-specific recombinase, phage integrase family:hypothetical protein:<-<-:185347..185939 593 tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_250:SMT_251|SMT_250:SMT_251:site-specific recombinase, phage integrase family:hypothetical protein:<-<-:185347..185939 593 tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_250:SMT_251|SMT_250:SMT_251:site-specific recombinase, phage integrase family:hypothetical protein:<-<-:185347..185939 593 tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 209 End: 301 ................................................................................................................................................................................................................ M D F T L F L V Q L K L I L S K P G L K K A R K A S Q F S K R .................................................................................................................................................................................................................................................................................................... Protein_Len: 41 Strand: + Start: 289 End: 411 ................................................................................................................................................................................................................................................................................................ M L K T L I N T I I S T F Q S T L Q R F C K V L F C R F F S S I S F V I T F S K F ...................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 493 End: 591 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ M T F F G H N K T L L F I V S L D L N R S V I F A S Q F M C S V P .. Protein_Len: 33 Strand: - Start: 322 End: 420 ................................................................................................................................................................................................................................................................................................................................. R K L A S Q L S K A F H K K T S K K A R N A K H Y G K R F K S Q M ............................................................................................................................................................................. Protein_Len: 30 Strand: - Start: 166 End: 255 ..................................................................................................................................................................... V F K K F Y F P L Q F S Y F I S K V S N K T W S F S M S E M .................................................................................................................................................................................................................................................................................................................................................. tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat 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================================================ tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.8 Tail_Score: -5.35222 Start: 332 End: 358 Full_Region: TATCAACGTTTCAAA GCACTTTGCAAA GAT TTTGCAAAGTGC TTTTTTGTCGATTTT ...........................................................................................................................................................................................................................................................................................................................................GCACTTTGCAAAGATTTTGCAAAGTGC........................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -16.8 Tail_Score: -3.58037 Start: 332 End: 358 Full_Region: aaaatcgacaaaaaa gcactttgcaaa atc tttgcaaagtgc tttgaaacgttgata ...........................................................................................................................................................................................................................................................................................................................................gcactttgcaaaatctttgcaaagtgc........................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 59 HP_score: -2.2 Tail_Score: -4.71061 Start: 515 End: 559 Full_Region: TTTTCGGTCATAATA AAACACTCCTGTTCATAGTT TCACT AGATCTAAACAGGAGTGTTA TTTTTGCGTCTCAAT ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAACACTCCTGTTCATAGTTTCACTAGATCTAAACAGGAGTGTTA.................................. TransTerm Strand: - Conf: 68 HP_score: -4.0 Tail_Score: -4.77165 Start: 518 End: 556 Full_Region: gagacgcaaaaataa cactcctgtttaga tctagtgaaac tatgaacaggagtg ttttattatgaccga .....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................cactcctgtttagatctagtgaaactatgaacaggagtg..................................... Find igs database================================================ Query_seq: SMT_250:SMT_251|SMT_250:SMT_251:site-specific recombinase, phage integrase family:hypothetical protein:<-<-:185347..185939 593 tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat Intra-Species Hit: Count: 1 Min: 1 Max: 593 Len: 593 Subject: smit_SMT_250_SMT_251|site-specific recombinase, phage integrase family:hypothetical protein|NEGATIVE:NEGATIVE|[185347,185939]|593 HSP 1 e-value: 0.0 bit: 1116.0 Len: 593 Query Start:1 Query End:593 Subject Strand: POSITIVE Subject Start: 1 Subject End: 593 tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat tgaagagcataggtttcagattttctatcgcctaagaaaatctgaaacctttnnnnnttaattaattaannnnntcccattatcaataactcagtgggaaactctattcgggagtaataacagctaagttgtttacttgaaatttccctcattcaataaaacttatacaaattttttgaaataaaaaggcagttgaaaactatagaatattgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaacgtttcaaagcactttgcaaagattttgcaaagtgcttttttgtcgattttttagctcgattagctttgtgataaccttttctaaattttgattgcaaggctaggcgtgattaccttatttaatttctatcattttttattttgatgaagggtaacttagtttctacggaataacctttttcggtcataataaaacactcctgttcatagtttcactagatctaaacaggagtgttatttttgcgtctcaatttatgtgttcagtgcctat Inter-species Hit: Count: 1 Min: 210 Max: 322 Len: 113 Subject: NC_009009_SSA_2025_SSA_2388|Conserved hypothetical GTPase protein:hypothetical protein|POSITIVE:NEGATIVE|[2031073,2031756]|684 HSP 1 e-value: 1.0E-40 bit: 168.0 Len: 113 Query Start:210 Query End:322 Subject Strand: NEGATIVE Subject Start: 97 Subject End: 209 .................................................................................................................................................................................................................ttgattttacactatttttagtccaactgaaactcatactttccaaaccaggtcttaagaaagctcgtaaagcttcacaattctcaaaacgttaatcaatacgattatatcaa............................................................................................................................................................................................................................................................................... .................................................................................................................................................................................................................ttgatattacgctgtttttagtccaactgaaatccatactttccaaaccaggtcttaagaaagctcgtaaagcatcacaattctcaaaacgttaatcaacacgattatatcaa............................................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUUUUACACUAUUUUUAGUCCAACUGAAACUCAUACUUUCCAAACCAGGUCUUAAGAAAGCUCGUAAAGCUUCACAAUUCUCAAAACGUUAAUCAAUACGAUUAUAUCAA ((((((..((.....((((((.....))))))......(((.((......))....))).(((((.....)))))...............)).)))))).............. (-10.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUAUAAUCGUAUUGAUUAACGUUUUGAGAAUUGUGAAGCUUUACGAGCUUUCUUAAGACCUGGUUUGGAAAGUAUGAGUUUCAGUUGGACUAAAAAUAGUGUAAAAUCAA .((((....(((((((....(((((((((((((((((((....))))))...))))))))))...))).....))))))).......(((.((((....)))).))).)))). (-21.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 67 21 54 11 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 262 66 21 123 75 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 258 79 31 62 12 smit:SMT_376|5end_DNA_(cytosine-5-)-methyltransferase_312900..313130_POSITIVE 257 86 43 189 129 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 255 56 12 55 12 smit:SMT_1398|5end_dihydroorotase_1373204..1373434_POSITIVE 255 86 42 197 157 smit:SMT_109|5end_beta-galactosidase_53925..54155_POSITIVE 253 67 28 77 35 smit:SMT_1639|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1625819..1626049_NEGATIVE 249 95 57 191 150 smit:SMT_845|5end_hypothetical_protein_791868..792098_NEGATIVE 240 58 11 122 77 smit:SMT_2160|5end_cell_division_protein_FtsA_2033524..2033754_POSITIVE 236 70 21 101 51 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 231 84 42 104 66 smit:SMT_1920|5end_ABC_transporter,_ATP-binding_protein_1863125..1863355_NEGATIVE 230 90 43 215 168 smit:SMT_1645|5end_hypothetical_protein_1631738..1631968_POSITIVE 230 75 43 217 188 smit:SMT_853|5end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_799285..799515_NEGATIVE 224 78 34 93 48 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 221 98 55 215 156 smit:SMT_1960|5end_UDP-galactopyranose_mutase_1892899..1893129_POSITIVE 221 79 39 192 139 smit:SMT_1377|5end_hypothetical_protein_1355873..1356103_NEGATIVE 221 80 31 120 65 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 221 98 55 215 156 smit:SMT_287|5end_UDP-galactopyranose_mutase_230082..230312_POSITIVE 220 67 24 134 79 smit:SMT_1643|5end_2-isopropylmalate_synthase_1629130..1629360_POSITIVE 219 107 64 78 40 smit:SMT_252|5end_K07720_two-component_system,_response_regulator_YesN_188992..189222_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 86 42 65 25 smit:SMT_108|3end_hypothetical_protein_53873..54023_POSITIVE 237 75 32 91 45 smit:SMT_1115|3end_K02245_competence_protein_ComGC_1052473..1052623_NEGATIVE 226 64 21 151 105 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 221 56 14 42 1 smit:SMT_1397|3end_mutator_MutT_protein_1373271..1373421_POSITIVE 219 107 64 97 59 smit:SMT_253|3end_sensor_histidine_kinase_188973..189123_NEGATIVE 215 105 61 62 9 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 214 89 51 150 115 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 213 98 53 135 89 smit:SMT_1099|3end_protein_tyrosine_phosphatase_1042044..1042194_NEGATIVE 213 65 22 40 1 smit:SMT_490|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_425493..425643_POSITIVE 211 65 23 49 4 smit:SMT_948|3end_hypothetical_protein_predicted_by_Glimmer/Critica_896655..896805_NEGATIVE 208 55 12 92 51 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 207 74 39 140 111 smit:SMT_1376|3end_tetrapyrrole_(corrin/porphyrin)_methylase_family_protein_1354675..1354825_NEGATIVE 207 77 40 132 87 smit:SMT_856|3end_peroxide_resistance_protein,non-heme_iron-containing_ferritin_800130..800280_NEGATIVE 205 68 24 55 8 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 205 100 60 111 75 smit:SMT_1530|3end_K07456_DNA_mismatch_repair_protein_MutS2_1513010..1513160_NEGATIVE 204 78 39 151 99 smit:SMT_1378|3end_DNA_polymerase_III,_delta'_subunit_1355913..1356063_NEGATIVE 203 49 3 105 62 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 202 63 32 138 104 smit:SMT_426|3end_hypothetical_protein_368804..368954_POSITIVE 201 67 23 132 84 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 201 65 22 122 88 smit:SMT_1372|3end_hypothetical_protein_1350803..1350953_NEGATIVE