Origin IGS: gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt .........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 aaactcatagtttttgagaagatgattcgtcatcttctttttttactctttgtccactgtagtaggtttaagaaaagcggctccataatatctatagaggatgtacccgcgacaaatagtacatctcagaaatagtatatattcatttttgagatgatagtttgttgtcttctatgttgtattttttatgaaatatatatccaagtatgtttaggaagagtttgataatattatttttttgtacctagggcacaaaaataatataaataaatcgagcataaataagatgtatttattgacgagttaattttatttatgataaactggtatggttgtttttggaaccaaaaatttaatatataaatatatatgtgtttctaagaactgtaaaaatttaagttgagagaaaaaggagaaaac Mask Tandem Repeat Region ================================================ gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt Find is-nt database================================================ Query_seq: SMT_822:SMT_823|SMT_822:SMT_823:putative mucus binding protein:putative mucus binding protein:<-<-:740665..741084 420 gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_822:SMT_823|SMT_822:SMT_823:putative mucus binding protein:putative mucus binding protein:<-<-:740665..741084 420 gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_822:SMT_823|SMT_822:SMT_823:putative mucus binding protein:putative mucus binding protein:<-<-:740665..741084 420 gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 50 End: 187 ................................................. M Y I Y I L N F W F Q K Q P Y Q F I I N K I N S S I N T S Y L C S I Y L Y Y F C A L G T K K ......................................................................................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 283 End: 375 .......................................................................................................................................................................................................................................................................................... M L F L R C T I C R G Y I L Y R Y Y G A A F L K P T T V D K E ............................................. Protein_Len: 42 Strand: - Start: 289 End: 414 ................................................................................................................................................................................................................................................................................................ K Q S T S N T A P V D E I S I I S G S K K F R S C H V F L L F L L H R I M K E F V M ...... gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt 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: 29 End: 58 ............................TTTTACAGTTCTTAGAAACACATATATATT.......................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 76 End: 105 ...........................................................................GTTCCAAAAACAACCATACCAGTTTATCAT........................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 101 End: 130 ....................................................................................................ATTTATTGACGAGTTAATTTTATTTATGAT.................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_822:SMT_823|SMT_822:SMT_823:putative mucus binding protein:putative mucus binding protein:<-<-:740665..741084 420 gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt Intra-Species Hit: Count: 1 Min: 1 Max: 420 Len: 420 Subject: smit_SMT_822_SMT_823|putative mucus binding protein:putative mucus binding protein|NEGATIVE:NEGATIVE|[740665,741084]|420 HSP 1 e-value: 0.0 bit: 749.0 Len: 420 Query Start:1 Query End:420 Subject Strand: POSITIVE Subject Start: 1 Subject End: 420 gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacnnnnnnntaatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtnnnnnnngaagatgacgaatcatcttctcaaaaactatgagttt gttttctcctttttctctcaacttaaatttttacagttcttagaaacacatatatatttatatattaaatttttggttccaaaaacaaccataccagtttatcataaataaaattaactcgtcaataaatacatcttatttatgctcgatttatttatattatttttgtgccctaggtacaaaaaaataatattatcaaactcttcctaaacatacttggatatatatttcataaaaaatacaacatagaagacaacaaactatcatctcaaaaatgaatatatactatttctgagatgtactatttgtcgcgggtacatcctctatagatattatggagccgcttttcttaaacctactacagtggacaaagagtaaaaaaagaagatgacgaatcatcttctcaaaaactatgagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUCUCCUUUUUCUCUCAACUUAAAUUUUUACAGUUCUUAGAAACACAUAUAUAUUUAUAUAUUAAAUUUUUGGUUCCAAAAACAACCAUACCAGUUUAUCAUAAAUAAAAUUAACUCGUCAAUAAAUACAUCUUAUUUAUGCUCGAUUUAUUUAUAUUAUUUUUGUGCCCUAGGUACAAAAAAAUAAUAUUAUCAAACUCUUCCUAAACAUACUUGGAUAUAUAUUUCAUAAAAAAUACAACAUAGAAGACAACAAACUAUCAUCUCAAAAAUGAAUAUAUACUAUUUCUGAGAUGUACUAUUUGUCGCGGGUACAUCCUCUAUAGAUAUUAUGGAGCCGCUUUUCUUAAACCUACUACAGUGGACAAAGAGUAAAAAAAGAAGAUGACGAAUCAUCUUCUCAAAAACUAUGAGUUU (((((((....(((((...(((((((....))).))))...)))))...(((((((((((.........((((((....))))))...........(((((..(((((((((......(((...(((((((.....)))))))...))))))))))))....((((((((((...))))))))))......................))))).....)))))))))))...................)))))))...(((((..(((((((.(((((.........))))).)))))))((((.(((((.((((.......((((((((...))))))))))))...........((((....))))))))).)))).....(((((((((....)))))))))...........))))) (-77.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUCAUAGUUUUUGAGAAGAUGAUUCGUCAUCUUCUUUUUUUACUCUUUGUCCACUGUAGUAGGUUUAAGAAAAGCGGCUCCAUAAUAUCUAUAGAGGAUGUACCCGCGACAAAUAGUACAUCUCAGAAAUAGUAUAUAUUCAUUUUUGAGAUGAUAGUUUGUUGUCUUCUAUGUUGUAUUUUUUAUGAAAUAUAUAUCCAAGUAUGUUUAGGAAGAGUUUGAUAAUAUUAUUUUUUUGUACCUAGGGCACAAAAAUAAUAUAAAUAAAUCGAGCAUAAAUAAGAUGUAUUUAUUGACGAGUUAAUUUUAUUUAUGAUAAACUGGUAUGGUUGUUUUUGGAACCAAAAAUUUAAUAUAUAAAUAUAUAUGUGUUUCUAAGAACUGUAAAAAUUUAAGUUGAGAGAAAAAGGAGAAAAC ...(((.........((((((((((....))))))))))(((((.(((((.((((.((((((...(((...((........))...)))..)))))).)))).(((..(((((((((.((.(((((((((((((((....))).)))))))))))))).)))))))))..............((((((.(((((((((......(((((((((.....((((((...(((((((((((.(((.(....)))).)))))))))))............((((((((((((..((((......))))..)))))))))))).)))))).((((....(((((((....)))))))...)))).))))))))))))))))))))))))..)))............)))))))))).)))..... (-94.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 716 50 1 141 92 smit:SMT_822|5end_putative_mucus_binding_protein_740574..740804_NEGATIVE 362 348 303 220 176 smit:SMT_863|5end_K07485_transposase_813585..813815_POSITIVE 352 343 303 216 176 smit:SMT_1090|5end_K07485_transposase_1025089..1025319_POSITIVE 341 348 303 222 176 smit:SMT_1812|5end_K07485_transposase_1786418..1786648_POSITIVE 319 342 303 178 139 smit:SMT_1033|5end_K07485_transposase_969792..970022_POSITIVE 283 344 303 201 148 smit:SMT_878|5end_excinuclease_ABC,_subunit_C_826249..826479_NEGATIVE 279 345 301 222 171 smit:SMT_152|5end_sensor_histidine_kinase,_putative_100759..100989_POSITIVE 274 349 312 37 1 smit:SMT_1119|5end_alcohol_dehydrogenase,_zinc-containing_1056292..1056522_NEGATIVE 273 344 301 74 15 smit:SMT_2171|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2042271..2042501_POSITIVE 270 340 293 163 117 smit:SMT_2114|5end_x-prolyl-dipeptidyl_aminopeptidase_2001484..2001714_POSITIVE 266 345 301 184 140 smit:SMT_1652|5end_Cof_family_protein_1640534..1640764_POSITIVE 264 339 292 175 127 smit:SMT_489|5end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_423669..423899_POSITIVE 258 340 291 176 124 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 254 367 321 155 101 smit:SMT_1586|5end_K07177_PDZ_domain-containing_protein_1575714..1575944_POSITIVE 254 388 341 138 94 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 252 379 335 149 108 smit:SMT_1544|5end_mevalonate_kinase_1528884..1529114_NEGATIVE 252 345 309 61 24 smit:SMT_246|5end_alcohol_dehydrogenase_183004..183234_NEGATIVE 251 338 292 124 65 smit:SMT_126|5end_hypothetical_membrane_associated_protein_78250..78480_NEGATIVE 243 345 310 172 129 smit:SMT_1698|5end_CMP-binding_factor_1680092..1680322_POSITIVE 242 339 291 116 69 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 524 375 336 84 40 smit:SMT_1157|3end_septation_ring_formation_regulator_EzrA_1100202..1100352_NEGATIVE 365 390 343 53 10 smit:SMT_865|3end_50S_ribosomal_protein_L1_815022..815172_NEGATIVE 341 348 303 90 44 smit:SMT_1811|3end_hypothetical_protein_1786366..1786516_POSITIVE 319 342 303 65 26 smit:SMT_1032|3end_putative_biotin_operon_repressor_969759..969909_POSITIVE 287 187 145 43 1 smit:SMT_824|3end_asparaginyl-tRNA_synthetase_747050..747200_NEGATIVE 263 350 303 92 30 smit:SMT_1858|3end_K03497_chromosome_partitioning_protein,_ParB_family_1821687..1821837_NEGATIVE 251 338 292 137 78 smit:SMT_127|3end_transcriptional_regulator,_PadR_family_78237..78387_NEGATIVE 241 347 301 137 98 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 240 97 69 41 6 smit:SMT_1680|3end_hypothetical_protein_1664173..1664323_POSITIVE 236 45 1 128 81 smit:SMT_277|3end_capsular_polysaccharide_biosynthesis_homolog_YwqC_220333..220483_POSITIVE 232 300 252 129 84 smit:SMT_446|3end_ABC-type_cobalt_transport_system,_ATPase_component_386335..386485_POSITIVE 231 350 310 75 33 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE 231 369 323 87 39 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 230 330 288 97 54 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 229 333 291 149 106 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 228 349 308 85 47 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 226 348 301 50 5 smit:SMT_1154|3end_tryptophanyl-tRNA_synthetase_1098154..1098304_NEGATIVE 224 374 339 131 82 smit:SMT_1049|3end_hypothetical_protein_989213..989363_POSITIVE 221 405 362 80 27 smit:SMT_687|3end_carbamoyl-phosphate_synthase,_large_subunit_596088..596238_NEGATIVE 219 414 373 94 48 smit:SMT_162|3end_hypothetical_protein_107134..107284_POSITIVE