Origin IGS: atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc .........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 gaggtttgtttctcctatttatttttgatttctattctattataacatgattttaataaaaacggataggcaggacctacccgttctcaatgttttcatgctattgttggtttcaacttgtagatttacaagttgaattgaactcgggctaaagttaattagccgatttgagccggaacgggatgctgtgtgaaaaagataaacttccttgtattcgtcgaatactgcgtcagttttctattttcnnnnnttaattaattaannnnngtactggggagat Mask Tandem Repeat Region ================================================ atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc Find is-nt database================================================ Query_seq: SMT_230:SMT_231|SMT_230:SMT_231:hypothetical protein predicted by Glimmer/Critica:translation elongation factor G:<-->:165921..166200 280 atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_230:SMT_231|SMT_230:SMT_231:hypothetical protein predicted by Glimmer/Critica:translation elongation factor G:<-->:165921..166200 280 atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_230:SMT_231|SMT_230:SMT_231:hypothetical protein predicted by Glimmer/Critica:translation elongation factor G:<-->:165921..166200 280 atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 122 End: 238 ......................................................................................................................... M N F S P S S I Q L V N L Q V E T N N S M K T L R T G R S C L S V F I K I M L .......................................... atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc 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: 86 End: 115 .....................................................................................TTTCACACAGCATCCCGTTCCGGCTCAAAT..................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -2.8 Tail_Score: -3.53012 Start: 115 End: 137 Full_Region: caagttgaattgaac tcgggctaa agttaa ttagccga tttgagccggaacgg ..................................................................................................................tcgggctaaagttaattagccga............................................................................................................................................... TransTerm Strand: + Conf: 93 HP_score: -9.7 Tail_Score: -5.08601 Start: 198 End: 218 Full_Region: TGAAAACATTGAGAA CGGGTAGGT CCT GCCTATCCG TTTTTATTAAAATCA .....................................................................................................................................................................................................CGGGTAGGTCCTGCCTATCCG.............................................................. TransTerm Strand: - Conf: 63 HP_score: -6.8 Tail_Score: -3.47387 Start: 198 End: 218 Full_Region: tgattttaataaaaa cggatagg cagga cctacccg ttctcaatgttttca .....................................................................................................................................................................................................cggataggcaggacctacccg.............................................................. Find igs database================================================ Query_seq: SMT_230:SMT_231|SMT_230:SMT_231:hypothetical protein predicted by Glimmer/Critica:translation elongation factor G:<-->:165921..166200 280 atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: smit_SMT_230_SMT_231|hypothetical protein predicted by Glimmer/Critica:translation elongation factor G|NEGATIVE:POSITIVE|[165921,166200]|280 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 280 Query Start:1 Query End:280 Subject Strand: POSITIVE Subject Start: 1 Subject End: 280 atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc atctccccagtacnnnnnttaattaattaannnnngaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaattcaacttgtaaatctacaagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc Inter-species Hit: Count: 3 Min: 36 Max: 280 Len: 245 Subject: NC_008533_SPD_0252_SPD_0253|ribosomal protein S7:translation elongation factor G|POSITIVE:POSITIVE|[248466,248889]|424 HSP 1 e-value: 8.0E-59 bit: 228.0 Len: 119 Query Start:162 Query End:280 Subject Strand: POSITIVE Subject Start: 306 Subject End: 424 .................................................................................................................................................................aagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc .................................................................................................................................................................aagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcgtgttataatagaatagaaatcaaaaataaataggagaaacaaacctc HSP 2 e-value: 9.0E-31 bit: 135.0 Len: 108 Query Start:36 Query End:143 Subject Strand: POSITIVE Subject Start: 150 Subject End: 257 ...................................gaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaa......................................................................................................................................... ...................................gaaaataggaaactgacgcagtattcgatgaatacaaggagttttatctttttcgcgcagcatcccgttccagctcatatcggctaactaactttagcccgggttcaa......................................................................................................................................... Subject: NC_003098_spr0249_spr0250|30S ribosomal protein S7:elongation factor EF-2|POSITIVE:POSITIVE|[248465,248888]|424 HSP 1 e-value: 8.0E-59 bit: 228.0 Len: 119 Query Start:162 Query End:280 Subject Strand: POSITIVE Subject Start: 306 Subject End: 424 .................................................................................................................................................................aagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc .................................................................................................................................................................aagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcgtgttataatagaatagaaatcaaaaataaataggagaaacaaacctc HSP 2 e-value: 9.0E-31 bit: 135.0 Len: 108 Query Start:36 Query End:143 Subject Strand: POSITIVE Subject Start: 150 Subject End: 257 ...................................gaaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaa......................................................................................................................................... ...................................gaaaataggaaactgacgcagtattcgatgaatacaaggagttttatctttttcgcgcagcatcccgttccagctcatatcggctaactaactttagcccgggttcaa......................................................................................................................................... Subject: NC_003028_SP_0272_SP_0273|30S ribosomal protein S7:elongation factor EF-2|POSITIVE:POSITIVE|[248009,248432]|424 HSP 1 e-value: 8.0E-59 bit: 228.0 Len: 119 Query Start:162 Query End:280 Subject Strand: POSITIVE Subject Start: 306 Subject End: 424 .................................................................................................................................................................aagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcatgttataatagaatagaaatcaaaaataaataggagaaacaaacctc .................................................................................................................................................................aagttgaaaccaacaatagcatgaaaacattgagaacgggtaggtcctgcctatccgtttttattaaaatcgtgttataatagaatagaaatcaaaaataaataggagaaacaaacctc HSP 2 e-value: 6.0E-35 bit: 149.0 Len: 107 Query Start:37 Query End:143 Subject Strand: POSITIVE Subject Start: 151 Subject End: 257 ....................................aaaatagaaaactgacgcagtattcgacgaatacaaggaagtttatctttttcacacagcatcccgttccggctcaaatcggctaattaactttagcccgagttcaa......................................................................................................................................... ....................................aaaataggaaactgacgcagtattcgacgaatacaaggagttttatctttttcacgcagcatcccgttccagctcacatcggctaactaactttagcccgggttcaa......................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAUAGAAAACUGACGCAGUAUUCGACGAAUACAAGGAAGUUUAUCUUUUUCACACAGCAUCCCGUUCCGGCUCAAAUCGGCUAAUUAACUUUAGCCCGAGUUCAAUUCAACUUGUAAAUCUACAAGUUGAAACCAACAAUAGCAUGAAAACAUUGAGAACGGGUAGGUCCUGCCUAUCCGUUUUUAUUAAAAUCAUGUUAUAAUAGAAUAGAAAUCAAAAAUAAAUAGGAGAAACAAACCUC (((((.((((((((..(...((((((...))))))..)..))))).)))))))).............((((..........((((((......)))))).((.(((..(((((((((((....))))))))))).......(((((((((......((((((((((((((.....))))))))))))))......))))))))).........))).))...........))))........... (-70.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGUUUGUUUCUCCUAUUUAUUUUUGAUUUCUAUUCUAUUAUAACAUGAUUUUAAUAAAAACGGAUAGGCAGGACCUACCCGUUCUCAAUGUUUUCAUGCUAUUGUUGGUUUCAACUUGUAGAUUUACAAGUUGAAUUGAACUCGGGCUAAAGUUAAUUAGCCGAUUUGAGCCGGAACGGGAUGCUGUGUGAAAAAGAUAAACUUCCUUGUAUUCGUCGAAUACUGCGUCAGUUUUCUAUUUUC (((((((((((((((((((..((((((.((.....((...........))....))))))))..)))))).))......((((((((..(((....)))(((...(((.(.(((((((((((....))))))))))).).)))...((((((......))))))......))).))))))))..............)))))))))))............(((.((((...)))).)))....... (-59.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 963 100 51 226 177 smit:SMT_230|5end_hypothetical_protein_predicted_by_Glimmer/Critica_165830..166060_NEGATIVE 424 60 11 228 179 smit:SMT_898|5end_polyribonucleotide_nucleotidyltransferase_846861..847091_NEGATIVE 314 93 53 72 24 smit:SMT_652|5end_transporter,_putative_563215..563445_NEGATIVE 303 188 148 150 106 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 299 109 62 152 101 smit:SMT_817|5end_aminotransferase_728699..728929_NEGATIVE 298 200 152 86 44 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 298 109 67 208 168 smit:SMT_1129|5end_hypothetical_protein_1063926..1064156_NEGATIVE 289 84 41 203 149 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 289 196 151 80 34 smit:SMT_416|5end_ribonuclease_Z_359423..359653_POSITIVE 289 178 135 230 181 smit:SMT_235|5end_hypothetical_protein_174081..174311_POSITIVE 288 76 33 109 60 smit:SMT_545|5end_hypothetical_protein_predicted_by_Glimmer/Critica_461249..461479_POSITIVE 283 84 46 163 125 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 282 192 158 159 121 smit:SMT_1279|5end_translation_elongation_factor_Ts_1242331..1242561_POSITIVE 282 188 147 76 33 smit:SMT_1216|5end_hypothetical_protein_1174879..1175109_POSITIVE 281 178 137 228 194 smit:SMT_865|5end_50S_ribosomal_protein_L1_815711..815941_NEGATIVE 273 84 41 188 132 smit:SMT_2015|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1932655..1932885_POSITIVE 270 86 41 191 144 smit:SMT_976|5end_hypothetical_protein_925183..925413_NEGATIVE 269 99 57 217 175 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 269 197 164 80 43 smit:SMT_957|5end_UDP-glucose_4-epimerase_905003..905233_NEGATIVE 269 197 164 80 43 smit:SMT_950|5end_UDP-glucose_4-epimerase_898696..898926_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 188 148 79 35 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 299 109 62 144 93 smit:SMT_818|3end_cystathionine_gamma-synthase_728707..728857_NEGATIVE 289 196 151 65 19 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE 282 192 158 80 42 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 281 178 137 130 96 smit:SMT_866|3end_50S_ribosomal_protein_L11_815809..815959_NEGATIVE 270 86 41 122 75 smit:SMT_977|3end_conserved_hypothetical_protein,_Rrf2_family_protein_925252..925402_NEGATIVE 269 99 57 107 65 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 263 97 55 79 19 smit:SMT_381|3end_hypothetical_protein_317437..317587_POSITIVE 263 97 55 79 19 smit:SMT_371|3end_hypothetical_protein_305906..306056_POSITIVE 262 86 41 124 88 smit:SMT_2034|3end_hydrolase,_haloacid_dehalogenase-like_family_1947257..1947407_POSITIVE 262 118 72 139 86 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 258 106 63 64 21 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 258 106 64 116 66 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE 256 184 155 120 94 smit:SMT_1257|3end_acetolactate_synthase_small_subunit_1222697..1222847_NEGATIVE 254 177 136 53 18 smit:SMT_1006|3end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_947122..947272_POSITIVE 254 106 70 109 64 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 254 85 41 137 98 smit:SMT_261|3end_ImpB/MucB/SamB_family_protein_201655..201805_POSITIVE 251 76 48 87 50 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 251 76 48 87 50 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 251 76 48 87 50 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE