Origin IGS: tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg .........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 cactgccttgaggtctttttcgcttggattttcaaggtagtagtcagtgattgcgtcctcaatatagtcttgaatagtacgacgaagtgggcgtgctnnnnnttaattaattaannnnnaagctcgtacagtttactacgatcacatcacaacccaaagcaattgcagcagatgcaacagctgctcaaaaatcaatcgttacatttggaccatggactccagtaggtggaacatctaacgatgcgattacattatctgatgcagaaaaagctaaagatgataaattcaaccttgttaactctccagaagtaactggttatgttccagataacgctaccgtagaagcgactgcagcaatcgatgcagaagcggatgactacaagattacagttctttatactcca Mask Tandem Repeat Region ================================================ tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg Find is-nt database================================================ Query_seq: SMT_1807:SMT_1808|SMT_1807:SMT_1808:putative mucus binding protein:hypothetical protein predicted by Glimmer/Critica:<-->:1784134..1784537 404 tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1807:SMT_1808|SMT_1807:SMT_1808:putative mucus binding protein:hypothetical protein predicted by Glimmer/Critica:<-->:1784134..1784537 404 tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1807:SMT_1808|SMT_1807:SMT_1808:putative mucus binding protein:hypothetical protein predicted by Glimmer/Critica:<-->:1784134..1784537 404 tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 7 End: 150 ...... M K N C N L V V I R F C I D C C S R F Y G S V I W N I T S Y F W R V N K V E F I I F S F F C I R .............................................................................................................................................................................................................................................................. Protein_Len: 34 Strand: + Start: 116 End: 217 ................................................................................................................... M N L S S L A F S A S D N V I A S L D V P P T G V H G P N V T I D F ........................................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 298 End: 402 ......................................................................................................................................................................................................................................................................................................... M X X X H A H F V V L F K T I L R T Q S L T T T L K I Q A K K T S R Q .. Protein_Len: 42 Strand: - Start: 170 End: 295 ......................................................................................................................................................................... I N W R S S D M T W I Y R N I K S C S N C R S C N S Q T T I H D Y Y V T R A X X X M ............................................................................................................. Protein_Len: 60 Strand: - Start: 1 End: 264 Y G T V E P S N V L N F K D D K A K E A D S L T I A D N S T G G V P T W P G F T V I S K Q A A T A D A A I A K P Q S T M ............................................................................................................................................ tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg 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================================================ tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -4.1 Tail_Score: -3.82484 Start: 224 End: 246 Full_Region: ATTGATTTTTGAGCA GCTGTTGCA TCTGC TGCAATTGC TTTGGGTTGTGATGT ...............................................................................................................................................................................................................................GCTGTTGCATCTGCTGCAATTGC.............................................................................................................................................................. Find igs database================================================ Query_seq: SMT_1807:SMT_1808|SMT_1807:SMT_1808:putative mucus binding protein:hypothetical protein predicted by Glimmer/Critica:<-->:1784134..1784537 404 tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg Intra-Species Hit: Count: 1 Min: 1 Max: 404 Len: 404 Subject: smit_SMT_1807_SMT_1808|putative mucus binding protein:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[1784134,1784537]|404 HSP 1 e-value: 0.0 bit: 741.0 Len: 404 Query Start:1 Query End:404 Subject Strand: POSITIVE Subject Start: 1 Subject End: 404 tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg tggagtataaagaactgtaatcttgtagtcatccgcttctgcatcgattgctgcagtcgcttctacggtagcgttatctggaacataaccagttacttctggagagttaacaaggttgaatttatcatctttagctttttctgcatcagataatgtaatcgcatcgttagatgttccacctactggagtccatggtccaaatgtaacgattgatttttgagcagctgttgcatctgctgcaattgctttgggttgtgatgtgatcgtagtaaactgtacgagcttnnnnnttaattaattaannnnnagcacgcccacttcgtcgtactattcaagactatattgaggacgcaatcactgactactaccttgaaaatccaagcgaaaaagacctcaaggcagtg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAGUAUAAAGAACUGUAAUCUUGUAGUCAUCCGCUUCUGCAUCGAUUGCUGCAGUCGCUUCUACGGUAGCGUUAUCUGGAACAUAACCAGUUACUUCUGGAGAGUUAACAAGGUUGAAUUUAUCAUCUUUAGCUUUUUCUGCAUCAGAUAAUGUAAUCGCAUCGUUAGAUGUUCCACCUACUGGAGUCCAUGGUCCAAAUGUAACGAUUGAUUUUUGAGCAGCUGUUGCAUCUGCUGCAAUUGCUUUGGGUUGUGAUGUGAUCGUAGUAAACUGUACGAGCUUNNNNNUUAAUUAAUUAANNNNNAGCACGCCCACUUCGUCGUACUAUUCAAGACUAUAUUGAGGACGCAAUCACUGACUACUACCUUGAAAAUCCAAGCGAAAAAGACCUCAAGGCAGUG .............(((((...((((..(((....((....(((.....))).))..((((((...((((.(((((((((((.......((((......))))...((....(((((((((.........)))))))))....)).))))))))))).)))).(((((((.((.....(((...(((...))).)))....)).))))))).((((((..((.(((.((((((.....)))))).)))...((((((((((((.((.(((((...((..((.(((......((((....)))).....))).))..))....(((...........)))..))))).)).))).))))).)))).....))..)))))).))))))....)))..))))))))). (-97.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACUGCCUUGAGGUCUUUUUCGCUUGGAUUUUCAAGGUAGUAGUCAGUGAUUGCGUCCUCAAUAUAGUCUUGAAUAGUACGACGAAGUGGGCGUGCUNNNNNUUAAUUAAUUAANNNNNAAGCUCGUACAGUUUACUACGAUCACAUCACAACCCAAAGCAAUUGCAGCAGAUGCAACAGCUGCUCAAAAAUCAAUCGUUACAUUUGGACCAUGGACUCCAGUAGGUGGAACAUCUAACGAUGCGAUUACAUUAUCUGAUGCAGAAAAAGCUAAAGAUGAUAAAUUCAACCUUGUUAACUCUCCAGAAGUAACUGGUUAUGUUCCAGAUAACGCUACCGUAGAAGCGACUGCAGCAAUCGAUGCAGAAGCGGAUGACUACAAGAUUACAGUUCUUUAUACUCCA .(((((((((((((((.........))).)))))))))))).....((((((.(((((.(......((((.(((((....((((.(((((((((((.............................)))).))))))).)).)).......((((...(((..(((((.....)))))..)))...............(((((.((((((.....(((......((((.(((((((....)))).......(((((((...((.......))...)))))))...))).)))).))).....)))))).))))).)))).))))).))))..((((........)))).(((((........)))))..).))))).......))))))................ (-96.55) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1029 80 31 171 122 smit:SMT_1807|5end_putative_mucus_binding_protein_1784043..1784273_NEGATIVE 378 247 207 200 151 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 355 69 35 101 63 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 352 253 221 130 93 smit:SMT_1223|5end_pneumococcal_surface_protein_A_1187780..1188010_NEGATIVE 349 74 31 187 141 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 340 86 42 93 43 smit:SMT_2111|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999303..1999533_POSITIVE 340 50 1 60 2 smit:SMT_1071|5end_hypothetical_protein_1010058..1010288_POSITIVE 339 82 41 80 39 smit:SMT_1939|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1876278..1876508_POSITIVE 337 80 37 226 174 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 337 72 33 163 121 smit:SMT_489|5end_K01999_branched-chain_amino_acid_transport_system_substrate-binding_protein_423669..423899_POSITIVE 334 80 32 172 128 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 333 78 34 80 41 smit:SMT_2059|5end_hypothetical_protein_1967881..1968111_POSITIVE 333 78 34 80 41 smit:SMT_2056|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1966323..1966553_POSITIVE 333 78 34 80 41 smit:SMT_1892|5end_hypothetical_protein_1845595..1845825_POSITIVE 333 69 22 118 70 smit:SMT_521|5end_K02005_HlyD_family_secretion_protein_445566..445796_POSITIVE 331 60 15 177 138 smit:SMT_314|5end_biotin_carboxylase_254277..254507_POSITIVE 330 247 202 55 5 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 327 78 32 119 70 smit:SMT_1709|5end_aminopeptidase_P_1695450..1695680_NEGATIVE 325 75 32 205 163 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 325 213 176 36 1 smit:SMT_789|5end_hypothetical_protein_701072..701302_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 80 35 55 1 smit:SMT_2123|3end_hypothetical_protein_2008541..2008691_POSITIVE 349 75 31 148 93 smit:SMT_1443|3end_23S_rRNA_m(5)U_1939_methyltransferase_1426503..1426653_NEGATIVE 340 86 42 54 4 smit:SMT_2110|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999344..1999494_POSITIVE 330 247 202 97 47 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 330 78 33 58 1 smit:SMT_780|3end_peptidase_family_U32_688752..688902_NEGATIVE 322 53 11 65 19 smit:SMT_1979|3end_possible_cell_surface_protein_1910282..1910432_NEGATIVE 317 69 24 74 29 smit:SMT_1751|3end_indole-3-glycerol_phosphate_synthase_1729865..1730015_POSITIVE 317 69 21 144 89 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 316 82 42 142 100 smit:SMT_1892|3end_hypothetical_protein_1846193..1846343_POSITIVE 314 147 101 108 57 smit:SMT_828|3end_surface_protein_Rib_751186..751336_NEGATIVE 303 73 34 150 101 smit:SMT_988|3end_N-acetylneuraminate_lyase_932242..932392_NEGATIVE 301 76 50 151 125 smit:SMT_2099|3end_putative_zinc-binding_dehydrogenase_1992263..1992413_POSITIVE 299 248 202 60 11 smit:SMT_1939|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1876453..1876603_POSITIVE 299 262 223 146 115 smit:SMT_787|3end_K02440_glycerol_uptake_facilitator_protein_698088..698238_NEGATIVE 297 246 207 82 38 smit:SMT_2055|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1966017..1966167_POSITIVE 297 60 11 139 77 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 293 200 154 72 16 smit:SMT_157|3end_hypothetical_protein_103871..104021_POSITIVE 292 368 322 151 107 smit:SMT_2083|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1983006..1983156_POSITIVE 290 72 31 146 105 smit:SMT_1554|3end_isoleucyl-tRNA_synthetase_1539912..1540062_POSITIVE 290 71 37 151 103 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE