Origin IGS: atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat .........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 atttttcctacttaaaactcatcacgaacataggtaaatgtcaattctaccatatgactttgccctctttctaaacaaatggttgacatatctgtaacatataagactgggccagtgtctttctcaagcnnnnnttaattaattaannnnnggatttccttttctaactggattttatcccaaagat Mask Tandem Repeat Region ================================================ atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat Find is-nt database================================================ Query_seq: SMT_1902:SMT_1903|SMT_1902:SMT_1903:proton-translocating NADH-quinone oxidoreductase, chain L:hypothetical protein:<-->:1852364..1852550 187 atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1902:SMT_1903|SMT_1902:SMT_1903:proton-translocating NADH-quinone oxidoreductase, chain L:hypothetical protein:<-->:1852364..1852550 187 atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1902:SMT_1903|SMT_1902:SMT_1903:proton-translocating NADH-quinone oxidoreductase, chain L:hypothetical protein:<-->:1852364..1852550 187 atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat Predict ORF larger than 30AA ================================================ atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat 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================================================ atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1902:SMT_1903|SMT_1902:SMT_1903:proton-translocating NADH-quinone oxidoreductase, chain L:hypothetical protein:<-->:1852364..1852550 187 atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: smit_SMT_1902_SMT_1903|proton-translocating NADH-quinone oxidoreductase, chain L:hypothetical protein|NEGATIVE:POSITIVE|[1852364,1852550]|187 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat atctttgggataaaatccagttagaaaaggaaatccnnnnnttaattaattaannnnngcttgagaaagacactggcccagtcttatatgttacagatatgtcaaccatttgtttagaaagagggcaaagtcatatggtagaattgacatttacctatgttcgtgatgagttttaagtaggaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUUGGGAUAAAAUCCAGUUAGAAAAGGAAAUCCNNNNNUUAAUUAAUUAANNNNNGCUUGAGAAAGACACUGGCCCAGUCUUAUAUGUUACAGAUAUGUCAACCAUUUGUUUAGAAAGAGGGCAAAGUCAUAUGGUAGAAUUGACAUUUACCUAUGUUCGUGAUGAGUUUUAAGUAGGAAAAAU .(((...((((...))))....))).................................((((((((....(((..((((..((((...((..((((((.........)))))).))..)))))))).....((((.((((((.......))))))))))...))).....))))))))......... (-30.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUCCUACUUAAAACUCAUCACGAACAUAGGUAAAUGUCAAUUCUACCAUAUGACUUUGCCCUCUUUCUAAACAAAUGGUUGACAUAUCUGUAACAUAUAAGACUGGGCCAGUGUCUUUCUCAAGCNNNNNUUAAUUAAUUAANNNNNGGAUUUCCUUUUCUAACUGGAUUUUAUCCCAAAGAU ..........(((.........(((...(((((((((((....))).)))).)))).....((((((((.....(((.(((.....)))...))).......))))..))))..)))..................................((((.(((..........)))....))))..))).. (-23.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 110 61 201 152 smit:SMT_1902|5end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852273..1852503_NEGATIVE 612 150 101 231 182 smit:SMT_1951|5end_ABC_transporter,_ATP-binding_protein_1886061..1886291_NEGATIVE 273 82 59 94 69 smit:SMT_777|5end_hypothetical_protein_686770..687000_NEGATIVE 271 138 96 65 17 smit:SMT_816|5end_SWF/SNF_family_helicase_727440..727670_NEGATIVE 255 122 81 45 3 smit:SMT_393|5end_hypothetical_protein_predicted_by_Glimmer/Critica_323973..324203_POSITIVE 251 131 92 58 11 smit:SMT_165|5end_anaerobic_ribonucleoside-triphosphate_reductase_110762..110992_POSITIVE 250 119 73 140 84 smit:SMT_2031|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1945761..1945991_NEGATIVE 250 170 121 95 46 smit:SMT_952|5end_hypothetical_protein_900912..901142_NEGATIVE 241 149 106 74 29 smit:SMT_1303|5end_tRNA-dihydrouridine_synthase_1265731..1265961_NEGATIVE 239 174 136 162 111 smit:SMT_865|5end_50S_ribosomal_protein_L1_815711..815941_NEGATIVE 237 118 74 134 91 smit:SMT_217|5end_hypothetical_protein_149236..149466_POSITIVE 234 112 71 48 1 smit:SMT_1750|5end_anthranilate_phosphoribosyltransferase_1728011..1728241_POSITIVE 233 115 72 105 53 smit:SMT_917|5end_hydroxymethylglutaryl-CoA_synthase_871176..871406_NEGATIVE 232 138 94 128 85 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 229 169 123 72 34 smit:SMT_397|5end_NAD(+)_synthetase_326519..326749_POSITIVE 228 129 82 152 111 smit:SMT_1433|5end_hypothetical_protein_1417783..1418013_NEGATIVE 228 118 73 217 176 smit:SMT_1331|5end_hypothetical_protein_1306236..1306466_NEGATIVE 219 115 73 42 4 smit:SMT_1793|5end_inosine-5'-monophosphate_dehydrogenase_1767985..1768215_POSITIVE 218 170 123 108 55 smit:SMT_1500|5end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483384..1483614_POSITIVE 217 139 96 188 148 smit:SMT_2037|5end_lysine_decarboxylase_1948260..1948490_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 93 61 93 55 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 252 148 109 150 109 smit:SMT_128|3end_K03449_MFS_transporter,_CP_family,_cyanate_transporter_78702..78852_NEGATIVE 250 119 73 76 20 smit:SMT_2032|3end_hydrolase,_alpha/beta_fold_family_1945825..1945975_NEGATIVE 250 170 121 108 59 smit:SMT_953|3end_hypothetical_protein_900899..901049_NEGATIVE 239 174 136 64 13 smit:SMT_866|3end_50S_ribosomal_protein_L11_815809..815959_NEGATIVE 237 140 92 151 101 smit:SMT_937|3end_dipeptidase_890741..890891_POSITIVE 232 138 94 139 92 smit:SMT_1628|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1616610..1616760_NEGATIVE 229 169 123 75 37 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 225 125 88 148 106 smit:SMT_1187|3end_adenylosuccinate_lyase_1145067..1145217_NEGATIVE 222 139 95 129 72 smit:SMT_1467|3end_hydroxyacylglutathione_hydrolase_1448004..1448154_NEGATIVE 218 170 123 69 16 smit:SMT_1499|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1483425..1483575_POSITIVE 213 117 73 105 54 smit:SMT_1334|3end_hypothetical_protein_1308748..1308898_NEGATIVE 212 119 73 76 19 smit:SMT_1768|3end_hydrolase,_alpha/beta_fold_family_1744123..1744273_NEGATIVE 212 132 97 37 6 smit:SMT_1434|3end_neopullulanase_1417903..1418053_NEGATIVE 212 143 114 40 12 smit:SMT_979|3end_K03709_Mn-dependent_transcriptional_regulator_927399..927549_POSITIVE 210 132 93 134 98 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 210 93 59 37 2 smit:SMT_755|3end_shikimate_5-dehydrogenase_659063..659213_NEGATIVE 209 110 62 125 57 smit:SMT_1435|3end_phosphoribosylanthranilate_isomerase_1419807..1419957_NEGATIVE 209 166 122 143 98 smit:SMT_634|3end_ribonucleoside-diphosphate_reductase_alpha_chain_540618..540768_POSITIVE 208 139 100 77 39 smit:SMT_2165|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2039630..2039780_POSITIVE