Origin IGS: ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattccttaaaaaacaagtttgaaatcttagttaaaaggcttttgtttcattatctttcatattttcttgaaaagttgattaatttcctgctttaaatttatgataaacgtttaacagttttttctcttttttaacataaaaggcttgcattttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga .........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 tcattcattcctccaaaaatcttatcacatttaatagtaaccgttttcgataaaaaatgcaagccttttatgttaaaaaagagaaaaaactgttaaacgtttatcataaatttaaagcaggaaattaatcaacttttcaagaaaatatgaaagataatgaaacaaaagccttttaactaagatttcaaacttgttttttaaggaattcctgctaaaacagtcaaaatcaatcaatctaaagcgagcttactaagtggatagaatattttttctgcaaaacgcttgacatatttctaaaacatgataaaataatagtcgtaagggcggataaaatcgctttcaaacaagaacaaaattttatataaggagatttttgcaa Mask Tandem Repeat Region ================================================ ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattccttaaaaaacaagtttgaaatcttagttaaaaggcttttgtttcattatctttcatattttcttgaaaagttgattaatttcctgctttaaatttatgataaacgtttaacagttttttctcttttttaacataaaaggcttgcattttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga Find is-nt database================================================ Query_seq: SMT_913:SMT_914|SMT_913:SMT_914:putative sucrose-specific PTS permease, enzyme II:sucrose-6-phosphate hydrolase:<-->:865900..866278 379 ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattccttaaaaaacaagtttgaaatcttagttaaaaggcttttgtttcattatctttcatattttcttgaaaagttgattaatttcctgctttaaatttatgataaacgtttaacagttttttctcttttttaacataaaaggcttgcattttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_913:SMT_914|SMT_913:SMT_914:putative sucrose-specific PTS permease, enzyme II:sucrose-6-phosphate hydrolase:<-->:865900..866278 379 ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattccttaaaaaacaagtttgaaatcttagttaaaaggcttttgtttcattatctttcatattttcttgaaaagttgattaatttcctgctttaaatttatgataaacgtttaacagttttttctcttttttaacataaaaggcttgcattttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_913:SMT_914|SMT_913:SMT_914:putative sucrose-specific PTS permease, enzyme II:sucrose-6-phosphate hydrolase:<-->:865900..866278 379 ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattccttaaaaaacaagtttgaaatcttagttaaaaggcttttgtttcattatctttcatattttcttgaaaagttgattaatttcctgctttaaatttatgataaacgtttaacagttttttctcttttttaacataaaaggcttgcattttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 177 Max: 323 Len: 147 Subject: UniRef90_Q97PB7 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 4.0E-7 bit: 55.8 Len: 147 Query Start:177 Query End:323 Subject Strand: null Subject Start: 1 Subject End: 49 ................................................................................................................................................................................ M Q A F Y V K K E K K L L N V Y H K F K A G N * S T F Q E N M K D N E T K A F * L R F Q T C F L R ........................................................ ................................................................................................................................................................................ M Q A F Y V K K E E K L S K D Y H K I N T G N Q S N F Y E N V K D N E I K Y F L T K V S N L F F K ........................................................ ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 1 End: 141 M Q K S P Y I K F C S C L K A I L S A L T T I I L S C F R N M S S V L Q K K Y S I H L V S S L .............................................................................................................................................................................................................................................. Protein_Len: 40 Strand: + Start: 146 End: 265 ................................................................................................................................................. M I D F D C F S R N S L K N K F E I L V K R L L F H Y L S Y F L E K L I N F L L .................................................................................................................. Protein_Len: 35 Strand: - Start: 18 End: 122 ................. I F N Q E Q K F A I K D A R V V I I K D H K L F I D L T K C F F Y E M ................................................................................................................................................................................................................................................................. ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga 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================================================ ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_913:SMT_914|SMT_913:SMT_914:putative sucrose-specific PTS permease, enzyme II:sucrose-6-phosphate hydrolase:<-->:865900..866278 379 ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga Intra-Species Hit: Count: 2 Min: 1 Max: 379 Len: 379 Subject: smit_SMT_913_SMT_914|putative sucrose-specific PTS permease, enzyme II:sucrose-6-phosphate hydrolase|NEGATIVE:POSITIVE|[865900,866278]|379 HSP 1 e-value: 4.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaatt........................................................................................................................................................................................................... ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaatt........................................................................................................................................................................................................... HSP 2 e-value: 2.0E-23 bit: 111.0 Len: 56 Query Start:324 Query End:379 Subject Strand: POSITIVE Subject Start: 324 Subject End: 379 ...................................................................................................................................................................................................................................................................................................................................tttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga ...................................................................................................................................................................................................................................................................................................................................tttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga Subject: smit_SMT_1945_SMT_1946|putative dihydrolipoamide S-acetyltransferase:sucrose-6-phosphate hydrolase|POSITIVE:POSITIVE|[1880707,1880941]|235 HSP 1 e-value: 2.0E-23 bit: 111.0 Len: 56 Query Start:324 Query End:379 Subject Strand: POSITIVE Subject Start: 180 Subject End: 235 ...................................................................................................................................................................................................................................................................................................................................tttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga ...................................................................................................................................................................................................................................................................................................................................tttttatcgaaaacggttactattaaatgtgataagatttttggaggaatgaatga HSP 2 e-value: 4.0E-9 bit: 63.9 Len: 32 Query Start:145 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 32 ................................................................................................................................................attgattgattttgactgttttagcaggaatt........................................................................................................................................................................................................... ................................................................................................................................................attgattgattttgactgttttagcaggaatt........................................................................................................................................................................................................... Inter-species Hit: Count: 3 Min: 1 Max: 375 Len: 375 Subject: NC_003098_spr1566_spr1568|Phosphotransferase system enzyme II:Sucrose-6-phosphate hydrolase|NEGATIVE:POSITIVE|[1548388,1548763]|376 HSP 1 e-value: 8.0E-69 bit: 262.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtaagctcgctttagattgattgattttgactgttttagcaggaatt........................................................................................................................................................................................................... ttgcaaaaatctccttatataacattttgttcttgtttgaaagcgattttattcgcccttacgactattattttatcatgttttaaaaatatgtcaagcgttttgcagaaaaaatattctatccacttagtgggcaagttttagattgattgtttttgactgtttcatcaggaatt........................................................................................................................................................................................................... HSP 2 e-value: 3.0E-16 bit: 87.7 Len: 52 Query Start:324 Query End:375 Subject Strand: POSITIVE Subject Start: 325 Subject End: 376 ...................................................................................................................................................................................................................................................................................................................................tttttatcgaaaacggttactattaaatgtgataagatttttggaggaatga.... ...................................................................................................................................................................................................................................................................................................................................tttttatcgaaaacagttactattaaaagtgataagatttttggaggaatga.... Subject: NC_008533_SPD_1532_SPD_1533|PTS system IIABC components:hypothetical protein|NEGATIVE:NEGATIVE|[1555919,1556044]|126 HSP 1 e-value: 4.0E-58 bit: 226.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccac............................................................................................................................................................................................................................................................. ttgcaaaaatctccttatataacattttgttcttgtttgaaagcgattttattcgcccttacgactattattttatcatgttttaaaaatatgtcaagcgttttgcagaaaaaatattctatccac............................................................................................................................................................................................................................................................. Subject: NC_003028_SP_1722_SP_1723|PTS system IIABC components:hypothetical protein|NEGATIVE:NEGATIVE|[1626987,1627111]|125 HSP 1 e-value: 3.0E-53 bit: 210.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 ttgcaaaaatctccttatataaaattttgttcttgtttgaaagcgattttatccgcccttacgactattattttatcatgttttagaaatatgtcaagcgttttgcagaaaaaatattctatccac............................................................................................................................................................................................................................................................. ttgcaaaaatctccttatataacattttgttcttgtttgaaagcgattttattcgcccttacgactattattttatcatgttttaaaaatatgtcaagcgttttgcagaaaaaa-attctatccac............................................................................................................................................................................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCAAAAAUCUCCUUAUAUAAAAUUUUGUUCUUGUUUGAAAGCGAUUUUAUCCGCCCUUACGACUAUUAUUUUAUCAUGUUUUAGAAAUAUGUCAAGCGUUUUGCAGAAAAAAUAUUCUAUCCACUUAGUAAGCUCGCUUUAGAUUGAUUGAUUUUGACUGUUUUAGCAGGAAUUCCUUAAAAAACAAGUUUGAAAUCUUAGUUAAAAGGCUUUUGUUUCAUUAUCUUUCAUAUUUUCUUGAAAAGUUGAUUAAUUUCCUGCUUUAAAUUUAUGAUAAACGUUUAACAGUUUUUUCUCUUUUUUAACAUAAAAGGCUUGCAUUUUUUAUCGAAAACGGUUACUAUUAAAUGUGAUAAGAUUUUUGGAGGAAUGA .........(((((....((((((((...(((......)))...)))))))).................((((((((((((((....((((.((.((.((((((..((((......)))).........((((((.(..((((..((((..((....(((((((..((((((((....((((..(((.....((((((...((((....))))...)))))).....(((((........))))).)))..)))).)))))))).....................))))))).....))....))))..)))).)))))))...........)))))).))))))))))))))))))))))....)))))..... (-66.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUUCCUCCAAAAAUCUUAUCACAUUUAAUAGUAACCGUUUUCGAUAAAAAAUGCAAGCCUUUUAUGUUAAAAAAGAGAAAAAACUGUUAAACGUUUAUCAUAAAUUUAAAGCAGGAAAUUAAUCAACUUUUCAAGAAAAUAUGAAAGAUAAUGAAACAAAAGCCUUUUAACUAAGAUUUCAAACUUGUUUUUUAAGGAAUUCCUGCUAAAACAGUCAAAAUCAAUCAAUCUAAAGCGAGCUUACUAAGUGGAUAGAAUAUUUUUUCUGCAAAACGCUUGACAUAUUUCUAAAACAUGAUAAAAUAAUAGUCGUAAGGGCGGAUAAAAUCGCUUUCAAACAAGAACAAAAUUUUAUAUAAGGAGAUUUUUGCAA .........((((((((((...........(((((((((((((.(((.............(((((.......))))).......((((((....(((((...)))))....((((((((.....(((..((((((........))))))....)))........((((..(((.(((........))))))....))))..))))))))..))))))............))).)))))).).))))))....((.((...(((((.(((((...(((((.........((........)).........)).)))....))))).)))))..)).)).........................))))))))))... (-59.17) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 840 140 91 231 182 smit:SMT_913|5end_putative_sucrose-specific_PTS_permease,_enzyme_II_865809..866039_NEGATIVE 281 70 25 71 25 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 275 139 100 39 1 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 268 88 41 108 61 smit:SMT_2121|5end_putative_mucus_binding_protein_2007145..2007375_NEGATIVE 268 88 41 108 61 smit:SMT_2068|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1974482..1974712_NEGATIVE 265 170 125 90 40 smit:SMT_1824|5end_hypothetical_protein_1796126..1796356_POSITIVE 264 137 94 211 157 smit:SMT_268|5end_penicillin-binding_protein_2X_205471..205701_POSITIVE 258 84 41 51 10 smit:SMT_1648|5end_hypothetical_protein_1634024..1634254_POSITIVE 258 99 52 152 96 smit:SMT_1428|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1414622..1414852_NEGATIVE 256 83 42 223 173 smit:SMT_178|5end_50S_ribosomal_protein_L29_119161..119391_POSITIVE 255 180 134 209 155 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 249 177 133 186 142 smit:SMT_168|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_113670..113900_POSITIVE 248 182 158 104 77 smit:SMT_761|5end_prephenate_dehydrogenase_667150..667380_NEGATIVE 248 182 158 104 77 smit:SMT_752|5end_prephenate_dehydrogenase_656791..657021_NEGATIVE 246 66 26 106 69 smit:SMT_1850|5end_K01421_putative_membrane_protein_1815062..1815292_POSITIVE 244 264 226 223 184 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 243 179 131 152 101 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 242 164 121 136 97 smit:SMT_1295|5end_transcriptional_regulator_CtsR_1256830..1257060_POSITIVE 240 179 134 196 132 smit:SMT_1651|5end_chromosome_segregation_SMC_protein_1636998..1637228_POSITIVE 240 64 41 229 203 smit:SMT_1011|5end_xanthine_phosphoribosyltransferase_948831..949061_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 139 100 42 4 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 248 182 158 94 67 smit:SMT_753|3end_chorismate_synthase_656801..656951_NEGATIVE 243 66 41 82 53 smit:SMT_1010|3end_hypothetical_protein_948761..948911_POSITIVE 243 179 131 143 92 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 237 67 25 74 19 smit:SMT_1417|3end_spermidine_synthase_1400826..1400976_NEGATIVE 235 100 51 59 12 smit:SMT_328|3end_23S_rRNA_methyltransferase_264863..265013_POSITIVE 234 140 98 76 31 smit:SMT_2052|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1960662..1960812_NEGATIVE 233 159 112 119 69 smit:SMT_178|3end_50S_ribosomal_protein_L29_119447..119597_POSITIVE 229 179 134 48 7 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 228 260 211 67 6 smit:SMT_1498|3end_transcriptional_regulator,_LytR_family_1483093..1483243_POSITIVE 220 320 273 126 78 smit:SMT_840|3end_tRNA_nucleotidyltransferase_(CCA-adding_enzyme)_786062..786212_NEGATIVE 219 240 195 91 43 smit:SMT_1473|3end_hypothetical_protein_1455119..1455269_POSITIVE 215 139 92 88 31 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 215 88 43 81 43 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 215 139 94 130 84 smit:SMT_484|3end_hypothetical_protein_419659..419809_NEGATIVE 213 84 44 85 40 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 213 57 11 136 87 smit:SMT_1372|3end_hypothetical_protein_1350803..1350953_NEGATIVE 213 237 191 115 75 smit:SMT_793|3end_K02029_polar_amino_acid_transport_system_permease_protein_702571..702721_NEGATIVE 211 67 32 63 27 smit:SMT_1691|3end_putative_deoxyribonuclease_1675249..1675399_POSITIVE 211 85 44 134 92 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE