Origin IGS: tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat .........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 atagatgatctcatctgatccttggtagctttccctacatgaagtctttgtaaatcaaaaagaactagaaacatcactcatttgtgagaactctagttcttttttcgtatttcaagaagtagtcattcaattgttgataaattgactagttttttgatatataggactaaaagtctgtttaaaaataacgattagtgatga Mask Tandem Repeat Region ================================================ tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat Find is-nt database================================================ Query_seq: SMT_827:SMT_828|SMT_827:SMT_828:hypothetical protein:surface protein Rib:-><-:751075..751275 201 tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_827:SMT_828|SMT_827:SMT_828:hypothetical protein:surface protein Rib:-><-:751075..751275 201 tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_827:SMT_828|SMT_827:SMT_828:hypothetical protein:surface protein Rib:-><-:751075..751275 201 tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat Predict ORF larger than 30AA ================================================ tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat 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================================================ tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -4.2 Tail_Score: -4.98531 Start: 103 End: 140 Full_Region: TGAAATACGAAAAAA GAACTAGAGTTCTCAC AAATGA GTGATGTTTCTAGTTC TTTTTGATTTACAAA ......................................................................................................GAACTAGAGTTCTCACAAATGAGTGATGTTTCTAGTTC............................................................. TransTerm Strand: - Conf: 76 HP_score: -4.4 Tail_Score: -5.32699 Start: 103 End: 114 Full_Region: atcactcatttgtga gaac tcta gttc ttttttcgtatttca ......................................................................................................gaactctagttc....................................................................................... Find igs database================================================ Query_seq: SMT_827:SMT_828|SMT_827:SMT_828:hypothetical protein:surface protein Rib:-><-:751075..751275 201 tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: smit_SMT_827_SMT_828|hypothetical protein:surface protein Rib|POSITIVE:NEGATIVE|[751075,751275]|201 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat tcatcactaatcgttatttttaaacagacttttagtcctatatatcaaaaaactagtcaatttatcaacaattgaatgactacttcttgaaatacgaaaaaagaactagagttctcacaaatgagtgatgtttctagttctttttgatttacaaagacttcatgtagggaaagctaccaaggatcagatgagatcatctat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUCACUAAUCGUUAUUUUUAAACAGACUUUUAGUCCUAUAUAUCAAAAAACUAGUCAAUUUAUCAACAAUUGAAUGACUACUUCUUGAAAUACGAAAAAAGAACUAGAGUUCUCACAAAUGAGUGAUGUUUCUAGUUCUUUUUGAUUUACAAAGACUUCAUGUAGGGAAAGCUACCAAGGAUCAGAUGAGAUCAUCUAU (((((.......(((.......))).(((((((((((((((((..........((((((.((((........))))))))))..((((.((((....((((((((((((((...((((......))))...)))))))))))))).))))...))))....)))))))....))))..)))).)).))))).......... (-45.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGAUGAUCUCAUCUGAUCCUUGGUAGCUUUCCCUACAUGAAGUCUUUGUAAAUCAAAAAGAACUAGAAACAUCACUCAUUUGUGAGAACUCUAGUUCUUUUUUCGUAUUUCAAGAAGUAGUCAUUCAAUUGUUGAUAAAUUGACUAGUUUUUUGAUAUAUAGGACUAAAAGUCUGUUUAAAAAUAACGAUUAGUGAUGA ........(((((.((((((....((((......))))....(((((.........(((((((((((((....((((......))))....)))))))))))))..((((.((((((((((((((.(((.....))).....)))))).)))))))).)))).))))).....................))))))))).)) (-48.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 200 152 206 159 smit:SMT_1088|5end_hypothetical_protein_1024346..1024576_NEGATIVE 269 198 155 100 52 smit:SMT_1797|5end_threonine_dehydratase_1772684..1772914_NEGATIVE 261 197 160 224 186 smit:SMT_848|5end_hypothetical_protein_795153..795383_NEGATIVE 259 199 151 160 104 smit:SMT_564|5end_23S_rRNA_Gm2251_methyltransferase_482717..482947_NEGATIVE 255 199 170 59 26 smit:SMT_587|5end_ATP_synthase_epsilon_chain_503950..504180_POSITIVE 250 199 154 86 29 smit:SMT_243|5end_PTS_system,_mannose-specific_IIC_component_180901..181131_NEGATIVE 243 138 102 213 172 smit:SMT_1800|5end_exonuclease_RexA_1773788..1774018_NEGATIVE 243 148 101 106 52 smit:SMT_1639|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1625819..1626049_NEGATIVE 241 197 154 91 32 smit:SMT_1554|5end_isoleucyl-tRNA_synthetase_1537040..1537270_POSITIVE 241 48 5 69 28 smit:SMT_824|5end_asparaginyl-tRNA_synthetase_748393..748623_NEGATIVE 238 178 133 159 99 smit:SMT_1318|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1283511..1283741_POSITIVE 232 199 158 127 86 smit:SMT_1905|5end_peptidyl-tRNA_hydrolase_1853769..1853999_NEGATIVE 228 88 52 185 151 smit:SMT_674|5end_K07010_putative_glutamine_amidotransferase_581561..581791_POSITIVE 224 146 107 112 76 smit:SMT_138|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_89262..89492_POSITIVE 223 157 115 62 24 smit:SMT_937|5end_dipeptidase_889579..889809_POSITIVE 221 116 72 158 107 smit:SMT_1128|5end_surface_antigen_1063140..1063370_NEGATIVE 221 170 122 213 163 smit:SMT_968|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_914015..914245_NEGATIVE 220 195 164 223 183 smit:SMT_324|5end_K02029_polar_amino_acid_transport_system_permease_protein_262070..262300_NEGATIVE 216 169 122 147 93 smit:SMT_857|5end_endo-beta-N-acetylglucosaminidase_802491..802721_NEGATIVE 216 176 132 66 16 smit:SMT_156|5end_hypothetical_protein_102869..103099_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 199 151 115 59 smit:SMT_565|3end_polypeptide_deformylase_482762..482912_NEGATIVE 257 175 131 91 38 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 255 199 170 48 15 smit:SMT_586|3end_ATP_synthase_F1,_beta_subunit_504019..504169_POSITIVE 241 48 5 46 5 smit:SMT_825|3end_aspartate_aminotransferase_748416..748566_NEGATIVE 238 180 131 76 21 smit:SMT_916|3end_3-hydroxy-3-methylglutaryl-CoA_reductase_868730..868880_NEGATIVE 231 179 131 66 2 smit:SMT_1598|3end_malolactic_regulator,_LysR_family_1588361..1588511_NEGATIVE 230 129 82 117 78 smit:SMT_1949|3end_IS1381_transposase_protein_B_1883987..1884137_POSITIVE 223 199 151 71 38 smit:SMT_823|3end_putative_mucus_binding_protein_740995..741145_NEGATIVE 220 195 164 46 6 smit:SMT_325|3end_K02029_polar_amino_acid_transport_system_permease_protein_262247..262397_NEGATIVE 219 140 91 112 45 smit:SMT_1656|3end_glutamine_ABC_transporter_ATP-binding_protein_1645172..1645322_NEGATIVE 219 195 153 69 17 smit:SMT_1074|3end_catabolite_control_protein_A_1012275..1012425_NEGATIVE 217 192 153 99 54 smit:SMT_1754|3end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1732363..1732513_NEGATIVE 216 169 122 113 59 smit:SMT_858|3end_triosephosphate_isomerase_802525..802675_NEGATIVE 213 178 134 118 73 smit:SMT_1458|3end_K02040_phosphate_transport_system_substrate-binding_protein_1440602..1440752_POSITIVE 213 198 160 55 13 smit:SMT_896|3end_hypothetical_protein_843119..843269_NEGATIVE 212 178 131 84 25 smit:SMT_1217|3end_hypothetical_protein_1176166..1176316_NEGATIVE 210 198 154 50 4 smit:SMT_581|3end_ATP_synthase_A_chain_499069..499219_POSITIVE 210 150 107 126 77 smit:SMT_548|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_467039..467189_POSITIVE 210 197 164 73 48 smit:SMT_540|3end_DNA_gyrase,_B_subunit_457157..457307_POSITIVE 208 150 106 87 29 smit:SMT_1728|3end_exodeoxyribonuclease_VII_large_subunit_1714668..1714818_POSITIVE