Origin IGS: ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctctccaactatcgcaggktacacagcagataaatcagaaatcccagctgtaagtggagttcaagcgaaagatcaagaccgcgttgaaacagtcacttatcgtaaggatgcccaaaaagctgttatccgttacgtaagcactaacggcaatcatgttctcaaaacagatgaa Mask Tandem Repeat Region ================================================ ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga Find is-nt database================================================ Query_seq: SMT_2121:SMT_2122|SMT_2121:SMT_2122:putative mucus binding protein:cell surface protein precursor:<-<-:2007236..2007408 173 ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2121:SMT_2122|SMT_2121:SMT_2122:putative mucus binding protein:cell surface protein precursor:<-<-:2007236..2007408 173 ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2121:SMT_2122|SMT_2121:SMT_2122:putative mucus binding protein:cell surface protein precursor:<-<-:2007236..2007408 173 ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 4 End: 135 ... M C F E N M I A V S A Y V T D N S F L G I L T I S D C F N A V L I F R L N S T Y S W D F ...................................... Protein_Len: 54 Strand: - Start: 1 End: 162 E D T K L V H N G N T S V Y R I V A K Q A D K R Y T V T E V R D Q D K A Q V G S V A P I E S K D A T Y G A M ........... ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga 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================================================ ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2121:SMT_2122|SMT_2121:SMT_2122:putative mucus binding protein:cell surface protein precursor:<-<-:2007236..2007408 173 ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga Intra-Species Hit: Count: 2 Min: 1 Max: 173 Len: 173 Subject: smit_SMT_2121_SMT_2122|putative mucus binding protein:cell surface protein precursor|NEGATIVE:NEGATIVE|[2007236,2007408]|173 HSP 1 e-value: 7.0E-93 bit: 340.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggagaga Subject: smit_SMT_2068_SMT_2069|hypothetical protein predicted by Glimmer/Critica:K02035 peptide/nickel transport system substrate-binding protein|NEGATIVE:POSITIVE|[1974573,1974795]|223 HSP 1 e-value: 5.0E-91 bit: 334.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtamcctgcgatagttggag... ttcatctgttttgagaacatgattgccgttagtgcttacgtaacggataacagctttttgggcatccttacgataagtgactgtttcaacgcggtcttgatctttcgcttgaactccacttacagctgggatttctgatttatctgctgtgtaacctgcgatagttggag... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAUCUGUUUUGAGAACAUGAUUGCCGUUAGUGCUUACGUAACGGAUAACAGCUUUUUGGGCAUCCUUACGAUAAGUGACUGUUUCAACGCGGUCUUGAUCUUUCGCUUGAACUCCACUUACAGCUGGGAUUUCUGAUUUAUCUGCUGUGUAMCCUGCGAUAGUUGGAGAGA .(((...((...((((.((.((((((.((((((((((((((((.((((....(((.....)))))))))))).))))).)))).....)))))))).)).))))..)).))).(((((((((((((..((((.........))))))))))...........)).)))))... (-42.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCUCCAACUAUCGCAGGKUACACAGCAGAUAAAUCAGAAAUCCCAGCUGUAAGUGGAGUUCAAGCGAAAGAUCAAGACCGCGUUGAAACAGUCACUUAUCGUAAGGAUGCCCAAAAAGCUGUUAUCCGUUACGUAAGCACUAACGGCAAUCAUGUUCUCAAAACAGAUGAA ..........((((.........(((((.((....))....((((..((.((((((((..((((((((............))).)))))....)))))))).))..)))).........)))))...((((((.((....))))))))...................)))).. (-35.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 978 130 81 221 172 smit:SMT_2121|5end_putative_mucus_binding_protein_2007145..2007375_NEGATIVE 978 130 81 221 172 smit:SMT_2068|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1974482..1974712_NEGATIVE 313 129 81 219 173 smit:SMT_1212|5end_acyl_carrier_protein,_putative_1171657..1171887_NEGATIVE 302 130 85 80 21 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 298 116 71 64 23 smit:SMT_1530|5end_K07456_DNA_mismatch_repair_protein_MutS2_1515346..1515576_NEGATIVE 294 169 123 56 13 smit:SMT_2117|5end_transcription-repair_coupling_factor_2004560..2004790_NEGATIVE 294 138 91 170 104 smit:SMT_303|5end_hypothetical_protein_245364..245594_POSITIVE 293 169 123 83 22 smit:SMT_753|5end_chorismate_synthase_657967..658197_NEGATIVE 290 148 102 62 15 smit:SMT_957|5end_UDP-glucose_4-epimerase_905003..905233_NEGATIVE 290 148 102 62 15 smit:SMT_950|5end_UDP-glucose_4-epimerase_898696..898926_NEGATIVE 286 153 113 211 163 smit:SMT_368|5end_hypothetical_protein_303662..303892_POSITIVE 282 140 91 219 147 smit:SMT_1397|5end_mutator_MutT_protein_1372727..1372957_POSITIVE 282 106 61 105 62 smit:SMT_1303|5end_tRNA-dihydrouridine_synthase_1265731..1265961_NEGATIVE 282 130 89 179 128 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 282 150 102 50 6 smit:SMT_911|5end_hypothetical_protein_862023..862253_POSITIVE 279 167 121 153 102 smit:SMT_1647|5end_3-isopropylmalate_dehydratase_small_subunit_1633403..1633633_POSITIVE 278 112 72 208 157 smit:SMT_166|5end_hypothetical_protein_112987..113217_POSITIVE 277 100 51 51 1 smit:SMT_1077|5end_GTP_cyclohydrolase_I_1015410..1015640_NEGATIVE 275 46 2 203 156 smit:SMT_1786|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763540..1763770_NEGATIVE 275 140 92 159 102 smit:SMT_721|5end_Tn5252,_relaxase_628754..628984_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 87 43 65 15 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 320 99 51 123 69 smit:SMT_357|3end_tRNA_(guanine-N7-)-methyltransferase_293900..294050_POSITIVE 293 158 114 151 102 smit:SMT_1124|3end_pyrrolidone-carboxylate_peptidase_1060225..1060375_NEGATIVE 293 130 81 73 10 smit:SMT_929|3end_hypothetical_protein_883202..883352_NEGATIVE 293 169 123 73 12 smit:SMT_754|3end_3-dehydroquinate_synthase_657977..658127_NEGATIVE 292 138 91 78 32 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 279 167 121 143 92 smit:SMT_1646|3end_3-isopropylmalate_dehydratase_large_subunit_1633473..1633623_POSITIVE 277 100 51 70 20 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 275 46 2 75 28 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 271 147 101 147 95 smit:SMT_1436|3end_conserved_hypothetical_protein_TIGR00147_1420374..1420524_NEGATIVE 270 126 89 144 103 smit:SMT_1202|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1163945..1164095_NEGATIVE 269 140 96 91 41 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 267 96 53 107 58 smit:SMT_1570|3end_hypothetical_protein_1563250..1563400_NEGATIVE 264 67 25 45 10 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 263 168 123 151 100 smit:SMT_1264|3end_oligoendopeptidase_F_1230734..1230884_POSITIVE 263 68 25 97 54 smit:SMT_603|3end_hypothetical_protein_518532..518682_POSITIVE 262 127 87 148 105 smit:SMT_1004|3end_thioredoxin_945824..945974_POSITIVE 262 68 26 131 96 smit:SMT_815|3end_hypothetical_protein_723677..723827_NEGATIVE 261 147 107 144 106 smit:SMT_1852|3end_1,4-alpha-glucan_branching_enzyme_1816467..1816617_NEGATIVE 261 46 1 151 100 smit:SMT_1222|3end_pneumococcal_surface_protein_A_1185683..1185833_NEGATIVE