Origin IGS: tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt .........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 aattgtacttttttattttatatttattttgtttattatcaatatcttagatcccctcactgcctatataataatgtataaaggactcataaaggtatttcgaggtgcaaaggtacaaactttctcgaaataatcactcatatatatagaagtaataaaccttaagatttttaatttaacaaaatataactaccataacactatattaacttaacgaagttctctacttcttcaaaaacaagacctaaggagataataaaacggacaatatataaaatatgcgatgcaccaaagaaattgatgcatcgcatatttttcagttataagcattgacta Mask Tandem Repeat Region ================================================ tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt Find is-nt database================================================ Query_seq: PI0455:PI0456|PI0455:PI0456:hypothetical protein:30S ribosomal protein S12:->->:428563..428898 336 tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0455:PI0456|PI0455:PI0456:hypothetical protein:30S ribosomal protein S12:->->:428563..428898 336 tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0455:PI0456|PI0455:PI0456:hypothetical protein:30S ribosomal protein S12:->->:428563..428898 336 tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 7 End: 102 ...... M L I T E K Y A M H Q F L W C I A Y F I Y C P F Y Y L L R S C F .......................................................................................................................................................................................................................................... Protein_Len: 39 Strand: + Start: 17 End: 133 ................ M K N M R C I N F F G A S H I L Y I V R F I I S L G L V F E E V E N F V K L I ........................................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 169 End: 270 ........................................................................................................................................................................ M L R F I T S I Y M S D Y F E K V C T F A P R N T F M S P L Y I I I .................................................................. Protein_Len: 43 Strand: - Start: 207 End: 335 .............................................................................................................................................................................................................. K S F T Q V K A G R F V K I L G K Y M I I Y A T L P D L I N I I F L I F I F Y F L V M . Protein_Len: 42 Strand: - Start: 7 End: 132 ...... H K Y S F F I R H M L K K P A D C I K Y I T R K I I E K P R T K S S T S F K T L N M ............................................................................................................................................................................................................ tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt 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================================================ tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -9.4 Tail_Score: -3.55907 Start: 16 End: 68 Full_Region: TAGTCAATGCTTATA ACTGAAAAATATGCGATGCATCAA TTTCT TTGGTGCATCGCATATTTTATATA TTGTCCGTTTTATTA ...............ACTGAAAAATATGCGATGCATCAATTTCTTTGGTGCATCGCATATTTTATATA............................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -16.4 Tail_Score: -3.33587 Start: 18 End: 66 Full_Region: GTCAATGCTTATAAC TGAAAAATATGCGATGCATCAA TTTCT TTGGTGCATCGCATATTTTATA TATTGTCCGTTTTAT .................TGAAAAATATGCGATGCATCAATTTCTTTGGTGCATCGCATATTTTATA.............................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -16.8 Tail_Score: -3.22076 Start: 20 End: 64 Full_Region: CAATGCTTATAACTG AAAAATATGCGATGCATCAA TTTCT TTGGTGCATCGCATATTTTA TATATTGTCCGTTTT ...................AAAAATATGCGATGCATCAATTTCTTTGGTGCATCGCATATTTTA................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -14.5 Tail_Score: -4.78149 Start: 25 End: 59 Full_Region: ggacaatatataaaa tatgcgatgcaccaa agaaa ttgatgcatcgcata tttttcagttataag ........................tatgcgatgcaccaaagaaattgatgcatcgcata..................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 39 HP_score: -2.2 Tail_Score: -2.59154 Start: 102 End: 126 Full_Region: CCTTAGGTCTTGTTT TTGAAGAAGT AGAGA ACTTCGTTAA GTTAATATAGTGTTA .....................................................................................................TTGAAGAAGTAGAGAACTTCGTTAA.................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PI0455:PI0456|PI0455:PI0456:hypothetical protein:30S ribosomal protein S12:->->:428563..428898 336 tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattgataataaacaaaataaatataaaataaaaaagtacaatt Intra-Species Hit: Count: 1 Min: 1 Max: 297 Len: 297 Subject: pint_PI0455_PI0456|hypothetical protein:30S ribosomal protein S12|POSITIVE:POSITIVE|[428563,428898]|336 HSP 1 e-value: 1.0E-167 bit: 589.0 Len: 297 Query Start:1 Query End:297 Subject Strand: POSITIVE Subject Start: 1 Subject End: 297 tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattg....................................... tagtcaatgcttataactgaaaaatatgcgatgcatcaatttctttggtgcatcgcatattttatatattgtccgttttattatctccttaggtcttgtttttgaagaagtagagaacttcgttaagttaatatagtgttatggtagttatattttgttaaattaaaaatcttaaggtttattacttctatatatatgagtgattatttcgagaaagtttgtacctttgcacctcgaaatacctttatgagtcctttatacattattatataggcagtgaggggatctaagatattg....................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUCAAUGCUUAUAACUGAAAAAUAUGCGAUGCAUCAAUUUCUUUGGUGCAUCGCAUAUUUUAUAUAUUGUCCGUUUUAUUAUCUCCUUAGGUCUUGUUUUUGAAGAAGUAGAGAACUUCGUUAAGUUAAUAUAGUGUUAUGGUAGUUAUAUUUUGUUAAAUUAAAAAUCUUAAGGUUUAUUACUUCUAUAUAUAUGAGUGAUUAUUUCGAGAAAGUUUGUACCUUUGCACCUCGAAAUACCUUUAUGAGUCCUUUAUACAUUAUUAUAUAGGCAGUGAGGGGAUCUAAGAUAUUG (((.(((....((((((((.(((((((((((((((((((.....))))))))))))))))))).........((((..((((((...(((((.((........)).(((((.....))))).))))).....))))))..))))))))))))..))))))........((((((.(((((.(((((((((((((....((((..(((((((((((((.......))))....)))))))))....((((((...))))))))))..)))))))).)))))..))))))))))).... (-72.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUAUCUUAGAUCCCCUCACUGCCUAUAUAAUAAUGUAUAAAGGACUCAUAAAGGUAUUUCGAGGUGCAAAGGUACAAACUUUCUCGAAAUAAUCACUCAUAUAUAUAGAAGUAAUAAACCUUAAGAUUUUUAAUUUAACAAAAUAUAACUACCAUAACACUAUAUUAACUUAACGAAGUUCUCUACUUCUUCAAAAACAAGACCUAAGGAGAUAAUAAAACGGACAAUAUAUAAAAUAUGCGAUGCACCAAAGAAAUUGAUGCAUCGCAUAUUUUUCAGUUAUAAGCAUUGACUA ((((.((((((........(((..(((((((...(((...........)))...(((((((((((((((....)))).......)))))))).))).......))))))).)))........)))))).................(((((((............((((..((((..(((((.....))))).((........))..))))..))))..................(((((((((((((((.(((.....))).)))))))))))))))..)))))))...)))).... (-55.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 118 71 198 151 pint:PI1340|5end_hypothetical_protein_1256568..1256798_POSITIVE 270 63 21 156 117 pint:PI0855|5end_hypothetical_protein_789094..789324_POSITIVE 259 56 12 156 109 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 249 234 210 35 4 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 247 79 31 74 27 pint:PI0470|5end_50S_ribosomal_protein_L14_437371..437601_POSITIVE 244 244 202 154 115 pint:PI0376|5end_conserved_hypothetical_protein_346417..346647_POSITIVE 243 81 46 169 130 pint:PI1765|5end_fructanase,_glycoside_hydrolase_family_1691281..1691511_POSITIVE 243 250 202 141 77 pint:PI0279|5end_hypothetical_protein_265600..265830_POSITIVE 242 127 88 220 175 pint:PI1958|5end_hypothetical_protein_1916582..1916812_POSITIVE 242 238 194 218 168 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 242 79 33 218 166 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 241 79 32 215 169 pint:PI1777|5end_conserved_hypothetical_protein_1709402..1709632_POSITIVE 239 245 209 56 12 pint:PI2123|5end_adenine_phosphoribosyltransferase_2071711..2071941_POSITIVE 239 128 84 225 190 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 239 128 84 167 132 pint:PI0565|5end_hypothetical_protein_511479..511709_POSITIVE 238 61 26 96 62 pint:PI0419|5end_conserved_hypothetical_protein_386701..386931_POSITIVE 238 61 26 61 27 pint:PI0418|5end_hypothetical_protein_386666..386896_POSITIVE 237 246 204 180 128 pint:PI0283|5end_Zn-dependent_peptidase_267554..267784_POSITIVE 236 236 207 140 112 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 235 120 72 174 111 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 63 21 70 28 pint:PI0455|3end_hypothetical_protein_428502..428652_POSITIVE 312 118 71 144 97 pint:PI1338|3end_phosphoserine_phosphatase_1256594..1256744_POSITIVE 249 234 210 141 110 pint:PI0169|3end_hypothetical_protein_164036..164186_POSITIVE 248 109 69 74 29 pint:PI0670|3end_hypothetical_protein_611280..611430_POSITIVE 247 79 31 68 21 pint:PI0469|3end_30S_ribosomal_protein_S17_437445..437595_POSITIVE 243 81 46 61 22 pint:PI1764|3end_conserved_hypothetical_protein_1691253..1691403_POSITIVE 243 250 202 86 22 pint:PI0278|3end_hypothetical_protein_265625..265775_POSITIVE 242 127 88 132 87 pint:PI1957|3end_calcium-transporting_ATPase_1916574..1916724_POSITIVE 238 61 26 143 109 pint:PI0420|3end_hypothetical_protein_386828..386978_POSITIVE 238 61 26 45 11 pint:PI0417|3end_hypothetical_protein_386730..386880_POSITIVE 236 236 207 140 112 pint:PI0090|3end_amidophosphoribosyltransferase_89160..89310_POSITIVE 230 115 74 53 5 pint:PI1944|3end_hypothetical_protein_1901990..1902140_POSITIVE 229 59 25 122 90 pint:PI1089|3end_conserved_hypothetical_protein_1014040..1014190_POSITIVE 229 62 33 72 42 pint:PI0915|3end_hypothetical_protein_845997..846147_POSITIVE 226 289 246 73 30 pint:PI0811|3end_protease/hemagglutinin_PrtT,_streptopain_family_749937..750087_POSITIVE 226 268 222 68 11 pint:PI0516|3end_ferredoxin,_4Fe-4S_476108..476258_POSITIVE 225 255 221 68 29 pint:PI2012|3end_hypothetical_protein_1971555..1971705_POSITIVE 224 254 212 144 80 pint:PI0196|3end_hypothetical_protein_188643..188793_POSITIVE 223 234 207 90 51 pint:PI0537|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_492412..492562_POSITIVE 222 145 103 72 29 pint:PI1676|3end_phosphatidate_cytidylyltransferase_1591773..1591923_POSITIVE