Origin IGS: tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta .........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 taatttaccgccttatcttcacaaagcgcttgcaaagtgcggtgggtttcagtagaatttgcgggctttaattatagaagccgtttagtgtaatcatttattaaacgggtattacgataggtaatactaacaatgtctccgatttggggactatataacaggtagctttcacctccttttcttgttgttttgatgtaagaattgtgatggtgttagttttttattagctaaatttattggagctctggtcta Mask Tandem Repeat Region ================================================ tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta Find is-nt database================================================ Query_seq: AA00370:AA00371|AA00370:AA00371:30S ribosomal protein S10:transcriptional regulator:->->:249069..249320 252 tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00370:AA00371|AA00370:AA00371:30S ribosomal protein S10:transcriptional regulator:->->:249069..249320 252 tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00370:AA00371|AA00370:AA00371:30S ribosomal protein S10:transcriptional regulator:->->:249069..249320 252 tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 45 End: 149 ............................................ M T I L T S K Q Q E K E V K A T C Y I V P K S E T L L V L P I V I P V ....................................................................................................... Protein_Len: 40 Strand: + Start: 59 End: 178 .......................................................... M K T T R K G G E S Y L L Y S P Q I G D I V S I T Y R N T R L I N D Y T K R L L .......................................................................... tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta 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: 84 Start: 195 End: 224 ..................................................................................................................................................................................................CTTGCAAAGTGCGGTGGGTTTCAGTAGAAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00370:AA00371|AA00370:AA00371:30S ribosomal protein S10:transcriptional regulator:->->:249069..249320 252 tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 252 Len: 252 Subject: aact_AA00370_AA00371|30S ribosomal protein S10:transcriptional regulator|POSITIVE:POSITIVE|[249069,249320]|252 HSP 1 e-value: 1.0E-140 bit: 500.0 Len: 252 Query Start:1 Query End:252 Subject Strand: POSITIVE Subject Start: 1 Subject End: 252 tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta tagaccagagctccaataaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggcttctataattaaagcccgcaaattctactgaaacccaccgcactttgcaagcgctttgtgaagataaggcggtaaatta Inter-species Hit: Count: 3 Min: 1 Max: 174 Len: 174 Subject: NC_007146_NTHI0936_NTHI0937|putative HTH-type transcriptional regulator:30S ribosomal protein S10|POSITIVE:POSITIVE|[902842,903077]|236 HSP 1 e-value: 1.0E-32 bit: 141.0 Len: 174 Query Start:1 Query End:174 Subject Strand: NEGATIVE Subject Start: 63 Subject End: 236 tagaccagagctccaataaa-tttagctaataaaaaa-ctaacacca-tcacaattcttacatcaaaacaacaagaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggct.............................................................................. tagaccagagctccaataaaatttagctaataaaaaaactaacaccaatcacaattctaacttcaaatata---gaaaaggaggtgcaagttacctgttatatagtctccaaatcggaaacattgttagcctgacatatcgtcatgcccgttcaataaatgattacattaaacggct.............................................................................. Subject: NC_000907_HI0775_HI0776|transcriptional regulator:30S ribosomal protein S10|POSITIVE:POSITIVE|[838515,838704]|190 HSP 1 e-value: 1.0E-23 bit: 111.0 Len: 104 Query Start:71 Query End:174 Subject Strand: NEGATIVE Subject Start: 63 Subject End: 166 ......................................................................agaaaaggaggtgaaagctacctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggct.............................................................................. ......................................................................agaaaaggaggtgcaagttacctgttatatagtctccaaatcggaaacattgttagcctgacatatcgtcatgcccgttcaataaatgattacattaaacggct.............................................................................. Subject: NC_002663_PM1416_PM1417|30S ribosomal protein S10:hypothetical protein|NEGATIVE:POSITIVE|[1598573,1598906]|334 HSP 1 e-value: 5.0E-23 bit: 109.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 tagaccagagctccaat--aaatttagctaataaaaaactaacaccatcacaattcttacatcaaaacaacaagaaaaggaggtgaaagct-acctgttatatagtccccaaatcggagacattgttagtattacctatcgtaatacccgtttaataaatgattacactaaacggct.............................................................................. tagaccagagctccaatcaaaatttagctaataaaaaactaacaccaacacttttcttacttctaaa-aac--gaaaagg-ggtgcaagttgacctgtt-tatagtttcccaatcggaaacattttacgtattacctattgtaatactcgtttaataaatgattacattaaacggct.............................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACCAGAGCUCCAAUAAAUUUAGCUAAUAAAAAACUAACACCAUCACAAUUCUUACAUCAAAACAACAAGAAAAGGAGGUGAAAGCUACCUGUUAUAUAGUCCCCAAAUCGGAGACAUUGUUAGUAUUACCUAUCGUAAUACCCGUUUAAUAAAUGAUUACACUAAACGGCU .....(((((((........((((.....)))).......((((.((....(((((.............)))))...))))))..))))..))).......(((.((.....)).))).......(((((((.....)))))))(((((((..............))))))).. (-26.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCGUUUAGUGUAAUCAUUUAUUAAACGGGUAUUACGAUAGGUAAUACUAACAAUGUCUCCGAUUUGGGGACUAUAUAACAGGUAGCUUUCACCUCCUUUUCUUGUUGUUUUGAUGUAAGAAUUGUGAUGGUGUUAGUUUUUUAUUAGCUAAAUUUAUUGGAGCUCUGGUCUA ..((((((((((........))))))))))(((((((.....))))))).......((((((.....)))))).......(((..(((((((((((((..((((((...........))))))..).)).))))((((((.......)))))).......)))))))))..... (-42.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 150 102 69 17 aact:AA02044|5end_phosphotransferase_system_enzyme_II,_galactitol_specific,_protein_A_1391488..1391718_POSITIVE 284 124 88 43 6 aact:AA02084|5end_conserved_hypothetical_protein_1417843..1418073_POSITIVE 262 150 103 52 15 aact:AA02342|5end_ISRSO11/IS150_related_transposase,_orfB_1599565..1599795_POSITIVE 262 150 103 52 15 aact:AA02117|5end_probable_transposase_1445207..1445437_POSITIVE 262 150 103 52 15 aact:AA01077|5end_transposase_746284..746514_POSITIVE 262 150 103 52 15 aact:AA00010|5end_transposase_orfB_fragment_5711..5941_POSITIVE 234 91 51 57 10 aact:AA00047|5end_formate_dependent_nitrite_reductase,_cytochrome_c552_36753..36983_POSITIVE 232 129 86 160 103 aact:AA01460|5end_hypothetical_protein_981412..981642_POSITIVE 228 150 102 58 4 aact:AA01757|5end_cobalt_transport_ATP-binding_protein_1187137..1187367_POSITIVE 228 117 77 108 63 aact:AA00936|5end_ribose_ABC_transporter,_permease_protein,_C-terminal_646289..646519_POSITIVE 228 119 80 63 26 aact:AA00858|5end_arginine_ABC_transporter,_ATP-binding_protein_590991..591221_POSITIVE 227 119 84 217 183 aact:AA01592|5end_hypothetical_protein_1070950..1071180_POSITIVE 225 146 107 161 125 aact:AA00820|5end_succinyl-diaminopimelate_desuccinylase_563326..563556_POSITIVE 224 146 104 104 54 aact:AA02933|5end_conserved_hypothetical_protein_(HesA/MoeB/ThiF_family_protein)_2053467..2053697_POSITIVE 224 106 69 112 74 aact:AA01715|5end_conserved_hypothetical_protein_1160480..1160710_POSITIVE 222 138 91 142 100 aact:AA01727|5end_conserved_hypothetical_protein_(possible_HipA_protein)_1168227..1168457_POSITIVE 222 115 74 188 142 aact:AA01296|5end_shikimate_kinase_(shikimic_acid_kinase_I)_878384..878614_POSITIVE 221 108 67 125 78 aact:AA02398|5end_DNA_primase_1649021..1649251_POSITIVE 221 117 73 122 68 aact:AA01615|5end_lipoprotein_releasing_system_transmembrane_1091186..1091416_POSITIVE 221 138 91 51 6 aact:AA00171|5end_DNA-binding_protein_121485..121715_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 150 102 88 36 aact:AA02043|3end_tagatose_6-phosphate_kinase_1391587..1391737_POSITIVE 262 150 103 55 18 aact:AA02341|3end_hypothetical_protein_1599648..1599798_POSITIVE 262 150 103 55 18 aact:AA02116|3end_hypothetical_protein_1445290..1445440_POSITIVE 262 150 103 55 18 aact:AA01076|3end_hypothetical_protein_746367..746517_POSITIVE 262 150 103 55 18 aact:AA00009|3end_hypothetical_protein_(possible_transposase_fragment)_5794..5944_POSITIVE 237 150 101 147 101 aact:AA01220|3end_competence_protein_F;_amidophosphoribosyltransferase_833538..833688_POSITIVE 235 106 75 66 32 aact:AA00957|3end_porphobilinogen_deaminase_(hydroxymethylbilane_synthase)_661943..662093_POSITIVE 233 123 86 129 90 aact:AA01894|3end_conserved_hypothetical_protein_(possible_transthyretin-like_periplasmic_protein)_1279457..1279607_POSITIVE 228 150 102 58 4 aact:AA01756|3end_cobalt_membrane_transport_protein_1187217..1187367_POSITIVE 228 117 77 67 22 aact:AA00935|3end_ribose_ABC_transporter,_permease_protein,_N-terminal_646328..646478_POSITIVE 228 119 80 39 2 aact:AA00856|3end_arginine_ABC_transporter,_periplasmic-binding_protein_591047..591197_POSITIVE 227 119 84 58 24 aact:AA01589|3end_conserved_hypothetical_protein_1070871..1071021_POSITIVE 224 146 104 101 51 aact:AA02932|3end_lytic_murein_transglycosylase_A_2053544..2053694_POSITIVE 224 106 69 54 16 aact:AA01711|3end_conserved_hypothetical_protein_1160502..1160652_POSITIVE 222 138 91 139 97 aact:AA01726|3end_conserved_hypothetical_protein_(possible_HipA-like_protein_1168304..1168454_POSITIVE 219 117 76 149 103 aact:AA02477|3end_PTS_system,_N-acetylglucosamine-permease_IIABC_component_1713371..1713521_POSITIVE 217 130 86 102 60 aact:AA01764|3end_hypothetical_protein_1191698..1191848_POSITIVE 215 167 132 90 58 aact:AA02969|3end_beta_tyrosinase_(tyrosine_phenol-lyase)_2076417..2076567_POSITIVE 215 115 74 150 115 aact:AA01295|3end_3-dehydroquinate_synthase_878437..878587_POSITIVE 211 149 102 89 54 aact:AA01018|3end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_712300..712450_POSITIVE