Origin IGS: ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata .........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 tataaatgtatatttttaaatatgtaaatccatacatctgtatggattttttatatataaatatagcgaaaaactatagtttgaatgatcaaaaagtattgagattatttgtatagggggttttaaagtgttaaaatagaagtgtcgggttttcaggtttatcaattgttatggctataataatataataatctttgaaaatcatacaaaaaaataaagataaaggatgctaagg Mask Tandem Repeat Region ================================================ ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata Find is-nt database================================================ Query_seq: SMT_1172:SMT_1173|SMT_1172:SMT_1173:hypothetical protein:CMP-N-acetylneuraminate-beta-galactosamide-alpha -2,3-sialyltransferase:<-<-:1124597..1124831 235 ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1172:SMT_1173|SMT_1172:SMT_1173:hypothetical protein:CMP-N-acetylneuraminate-beta-galactosamide-alpha -2,3-sialyltransferase:<-<-:1124597..1124831 235 ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1172:SMT_1173|SMT_1172:SMT_1173:hypothetical protein:CMP-N-acetylneuraminate-beta-galactosamide-alpha -2,3-sialyltransferase:<-<-:1124597..1124831 235 ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 71 End: 217 ...................................................................... M I N L K T R H F Y F N T L K P P I Q I I S I L F D H S N Y S F S L Y L Y I K N P Y R C M D L H I .................. Protein_Len: 36 Strand: - Start: 123 End: 230 .......................................................................................................................... V F L R L V K Q D N L S Y N K A I N I Y L F D M C I Y P N V Y K F I Y M ..... ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata 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================================================ ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -8.5 Tail_Score: -3.81137 Start: 190 End: 207 Full_Region: TTTATATATAAAAAA TCCATAC AGAT GTATGGA TTTACATATTTAAAA .............................................................................................................................................................................................TCCATACAGATGTATGGA............................ Find igs database================================================ Query_seq: SMT_1172:SMT_1173|SMT_1172:SMT_1173:hypothetical protein:CMP-N-acetylneuraminate-beta-galactosamide-alpha -2,3-sialyltransferase:<-<-:1124597..1124831 235 ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata Intra-Species Hit: Count: 1 Min: 1 Max: 235 Len: 235 Subject: smit_SMT_1172_SMT_1173|hypothetical protein:CMP-N-acetylneuraminate-beta-galactosamide-alpha -2,3-sialyltransferase|NEGATIVE:NEGATIVE|[1124597, 1124831]|235 HSP 1 e-value: 1.0E-118 bit: 424.0 Len: 235 Query Start:1 Query End:235 Subject Strand: POSITIVE Subject Start: 1 Subject End: 235 ccttagcatcctttatctttannnnnnngtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata ccttagcatcctttatctttatttttttgtatgattttcaaagattattatattattatagccataacaattgataaacctgaaaacccgacacttctattttaacactttaaaaccccctatacaaataatctcaatactttttgatcattcaaactatagtttttcgctatatttatatataaaaaatccatacagatgtatggatttacatatttaaaaatatacatttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUAGCAUCCUUUAUCUUUAUUUUUUUGUAUGAUUUUCAAAGAUUAUUAUAUUAUUAUAGCCAUAACAAUUGAUAAACCUGAAAACCCGACACUUCUAUUUUAACACUUUAAAACCCCCUAUACAAAUAAUCUCAAUACUUUUUGAUCAUUCAAACUAUAGUUUUUCGCUAUAUUUAUAUAUAAAAAAUCCAUACAGAUGUAUGGAUUUACAUAUUUAAAAAUAUACAUUUAUA ...................(((((((..(((((...............(((((...((((((...(((.(((((...............((....))..((((((....))))))..................)))))....(((((....))))).....)))....))))))...)))))....((((((((((....)))))))))).)))))..))))))).......... (-32.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAUGUAUAUUUUUAAAUAUGUAAAUCCAUACAUCUGUAUGGAUUUUUUAUAUAUAAAUAUAGCGAAAAACUAUAGUUUGAAUGAUCAAAAAGUAUUGAGAUUAUUUGUAUAGGGGGUUUUAAAGUGUUAAAAUAGAAGUGUCGGGUUUUCAGGUUUAUCAAUUGUUAUGGCUAUAAUAAUAUAAUAAUCUUUGAAAAUCAUACAAAAAAAUAAAGAUAAAGGAUGCUAAGG ..........((((((((.((((((((((((((((....))))))))...)))))))).....(((((.((((((.((...(((((((((............)))))))))..))...))))))....)))))........((((..((((((((((.((((..((((((((....))))))))...))))..)))))))))))))).......))))))))............. (-41.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 807 120 71 211 162 smit:SMT_1172|5end_hypothetical_protein_1124506..1124736_NEGATIVE 254 95 55 52 17 smit:SMT_836|5end_cell_surface_protein_precursor_779832..780062_NEGATIVE 252 119 82 175 137 smit:SMT_354|5end_hypothetical_protein_291343..291573_POSITIVE 241 109 61 92 50 smit:SMT_1928|5end_O-methyltransferase_family_protein_1869652..1869882_NEGATIVE 229 179 132 119 65 smit:SMT_1292|5end_K02050_sulfonate/nitrate/taurine_transport_system_permease_protein_1254179..1254409_POSITIVE 221 170 132 144 98 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 221 170 132 144 98 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 221 170 132 144 98 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 218 119 82 101 58 smit:SMT_556|5end_putative_aminotransferase_473544..473774_POSITIVE 211 170 136 162 122 smit:SMT_1535|5end_exodeoxyribonuclease_V_alpha_chain_1518067..1518297_POSITIVE 208 90 55 199 166 smit:SMT_118|5end_K02026_multiple_sugar_transport_system_permease_protein_69430..69660_POSITIVE 206 99 60 48 1 smit:SMT_1202|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1164097..1164327_NEGATIVE 206 99 60 225 178 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 204 171 136 214 183 smit:SMT_289|5end_glycosyltransferase_232184..232414_POSITIVE 203 39 8 185 149 smit:SMT_1670|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1658613..1658843_POSITIVE 203 192 157 221 183 smit:SMT_208|5end_leucyl-tRNA_synthetase_139977..140207_POSITIVE 196 170 126 209 159 smit:SMT_1139|5end_rRNA_(guanine-N1-)-methyltransferase_1079755..1079985_POSITIVE 196 121 94 119 93 smit:SMT_564|5end_23S_rRNA_Gm2251_methyltransferase_482717..482947_NEGATIVE 194 172 139 59 21 smit:SMT_623|5end_50S_ribosomal_protein_L21_529412..529642_POSITIVE 193 170 132 207 161 smit:SMT_1592|5end_putative_hemolysin_1579655..1579885_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 119 82 116 78 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE 241 109 61 54 12 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 218 119 82 90 47 smit:SMT_555|3end_K09015_Fe-S_cluster_assembly_protein_SufD_473613..473763_POSITIVE 196 121 94 74 48 smit:SMT_565|3end_polypeptide_deformylase_482762..482912_NEGATIVE 191 206 162 71 26 smit:SMT_1662|3end_histidine_protein_kinase_1651305..1651455_NEGATIVE 190 126 93 78 51 smit:SMT_1692|3end_hypothetical_protein_1675815..1675965_POSITIVE 190 46 6 124 73 smit:SMT_1087|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_1023281..1023431_NEGATIVE 189 158 118 104 59 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 189 44 2 70 29 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 188 46 1 135 94 smit:SMT_1358|3end_dihydroorotate_dehydrogenase_B_1336254..1336404_NEGATIVE 186 147 113 151 109 smit:SMT_2027|3end_competence-specific_global_transcription_modulator_1943025..1943175_NEGATIVE 186 147 113 151 109 smit:SMT_1091|3end_competence-specific_global_transcription_modulator_1032561..1032711_NEGATIVE 186 122 88 65 31 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 186 147 113 151 109 smit:SMT_102|3end_competence-specific_global_transcription_modulator_34667..34817_POSITIVE 181 170 134 138 98 smit:SMT_123|3end_hypothetical_protein_75623..75773_POSITIVE 180 121 87 114 81 smit:SMT_902|3end_hypothetical_protein_851424..851574_NEGATIVE 179 119 71 60 21 smit:SMT_1693|3end_dimethyladenosine_transferase_1676752..1676902_POSITIVE 176 97 58 139 104 smit:SMT_1113|3end_hypothetical_protein_1051811..1051961_NEGATIVE 174 18 1 103 85 smit:SMT_1513|3end_hypothetical_protein_1494761..1494911_NEGATIVE 174 174 132 151 102 smit:SMT_1291|3end_hypothetical_protein_1254296..1254446_POSITIVE