Origin IGS: aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta .........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 tacgctacctcactttctgatagatgattctctgcccaacctcaatttagatttactttgcttttgaatttcaaggtaataagcgaagaaggtcacacggaccttcttcacttacttgttttcatgctcggggtaagaacctccactggaggtttttctttctttttgatttcagggcaagaatctaaaaaggtccacaggaccttcctcgctttctcatttctaggctcagggtaaaaaggtccacaggaccttctctcactttcttatttcaagatgagaggctgaaaacctccactggaggttt Mask Tandem Repeat Region ================================================ aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta Find is-nt database================================================ Query_seq: SMT_397:SMT_398|SMT_397:SMT_398:NAD(+) synthetase:hypothetical protein:->->:327484..327790 307 aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_397:SMT_398|SMT_397:SMT_398:NAD(+) synthetase:hypothetical protein:->->:327484..327790 307 aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_397:SMT_398|SMT_397:SMT_398:NAD(+) synthetase:hypothetical protein:->->:327484..327790 307 aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 108 End: 197 ........................................................................................................... M W T F L D S C P E I K K K E K P P V E V L T P S M K T S K .............................................................................................................. Protein_Len: 33 Strand: + Start: 197 End: 295 .................................................................................................................................................................................................... M K K V R V T F F A Y Y L E I Q K Q S K S K L R L G R E S S I R K ............ Protein_Len: 45 Strand: - Start: 123 End: 257 .......................................................................................................................... I R A R F D F L F F F R W H L N K G R A H F C T L S S P G H S R R R K N G Q F E F A F Y M .................................................. Protein_Len: 59 Strand: - Start: 74 End: 250 ......................................................................... G S G L F S F A L F T R H V K K S E Q G S I L F F S F G G T S T R V G L M F V L L H L L D T H G E E S I V K F N L L M ......................................................... aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta 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================================================ aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.1 Tail_Score: -4.62069 Start: 55 End: 67 Full_Region: AAGAAAGTGAGAGAA GGTCC TGT GGACC TTTTTACCCTGAGCC ......................................................GGTCCTGTGGACC................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 75 HP_score: -9.1 Tail_Score: -3.59471 Start: 55 End: 67 Full_Region: ggctcagggtaaaaa ggtcc aca ggacc ttctctcactttctt ......................................................ggtccacaggacc................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -9.1 Tail_Score: -4.8143 Start: 104 End: 116 Full_Region: TGAGAAAGCGAGGAA GGTCC TGT GGACC TTTTTAGATTCTTGC .......................................................................................................GGTCCTGTGGACC............................................................................................................................................................................................... TransTerm Strand: - Conf: 71 HP_score: -9.1 Tail_Score: -3.26546 Start: 104 End: 116 Full_Region: gcaagaatctaaaaa ggtcc aca ggacc ttcctcgctttctca .......................................................................................................ggtccacaggacc............................................................................................................................................................................................... TransTerm Strand: + Conf: 75 HP_score: -9.1 Tail_Score: -3.61398 Start: 156 End: 168 Full_Region: AAAAAGAAAGAAAAA CCTCC AGT GGAGG TTCTTACCCCGAGCA ...........................................................................................................................................................CCTCCAGTGGAGG........................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -9.1 Tail_Score: -5.63012 Start: 156 End: 168 Full_Region: tgctcggggtaagaa cctcc act ggagg tttttctttcttttt ...........................................................................................................................................................cctccactggagg........................................................................................................................................... TransTerm Strand: - Conf: 86 HP_score: -9.0 Tail_Score: -4.30576 Start: 190 End: 231 Full_Region: ttttgaatttcaagg taataagcgaagaaggtc acacg gaccttcttcacttacttg ttttcatgctcgggg .............................................................................................................................................................................................taataagcgaagaaggtcacacggaccttcttcacttacttg............................................................................ TransTerm Strand: - Conf: 100 HP_score: -11.0 Tail_Score: -4.27443 Start: 193 End: 229 Full_Region: ttgaatttcaaggta ataagcgaagaaggtc acacg gaccttcttcacttac ttgttttcatgctcg ................................................................................................................................................................................................ataagcgaagaaggtcacacggaccttcttcacttac.............................................................................. TransTerm Strand: + Conf: 100 HP_score: -16.7 Tail_Score: -3.19246 Start: 194 End: 228 Full_Region: GAGCATGAAAACAAG TAAGTGAAGAAGGTC CGTGT GACCTTCTTCGCTTA TTACCTTGAAATTCA .................................................................................................................................................................................................TAAGTGAAGAAGGTCCGTGTGACCTTCTTCGCTTA............................................................................... TransTerm Strand: + Conf: 100 HP_score: -14.0 Tail_Score: -3.73336 Start: 197 End: 225 Full_Region: CATGAAAACAAGTAA GTGAAGAAGGTC CGTGT GACCTTCTTCGC TTATTACCTTGAAAT ....................................................................................................................................................................................................GTGAAGAAGGTCCGTGTGACCTTCTTCGC.................................................................................. TransTerm Strand: - Conf: 93 HP_score: -11.8 Tail_Score: -3.70405 Start: 197 End: 225 Full_Region: atttcaaggtaataa gcgaagaaggtc acacg gaccttcttcac ttacttgttttcatg ....................................................................................................................................................................................................gcgaagaaggtcacacggaccttcttcac.................................................................................. Find igs database================================================ Query_seq: SMT_397:SMT_398|SMT_397:SMT_398:NAD(+) synthetase:hypothetical protein:->->:327484..327790 307 aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta Intra-Species Hit: Count: 1 Min: 1 Max: 307 Len: 307 Subject: smit_SMT_397_SMT_398|NAD(+) synthetase:hypothetical protein|POSITIVE:POSITIVE|[327484,327790]|307 HSP 1 e-value: 1.0E-173 bit: 609.0 Len: 307 Query Start:1 Query End:307 Subject Strand: POSITIVE Subject Start: 1 Subject End: 307 aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtcctgtggacctttttaccctgagcctagaaatgagaaagcgaggaaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggttcttaccccgagcatgaaaacaagtaagtgaagaaggtccgtgtgaccttcttcgcttattaccttgaaattcaaaagcaaagtaaatctaaattgaggttgggcagagaatcatctatcagaaagtgaggtagcgta Inter-species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_003028_SP_1419_SP_1420|acetyltransferase, GNAT family:NAD(+) synthetase|NEGATIVE:NEGATIVE|[1340460,1340808]|349 HSP 1 e-value: 2.0E-22 bit: 107.0 Len: 58 Query Start:1 Query End:58 Subject Strand: NEGATIVE Subject Start: 240 Subject End: 297 aaacctccagtggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtc......................................................................................................................................................................................................................................................... aaacctccactggaggttttcagcctctcatcttgaaataagaaagtgagagaaggtc......................................................................................................................................................................................................................................................... HSP 2 e-value: 5.0E-17 bit: 89.7 Len: 69 Query Start:102 Query End:170 Subject Strand: NEGATIVE Subject Start: 280 Subject End: 348 .....................................................................................................aaggtcctgtggacctttttagattcttgccctgaaatcaaaaagaaagaaaaacctccagtggaggtt......................................................................................................................................... .....................................................................................................aaggtccgggggacctttttagcttcttgccctgaaattaaaaagcaagaaaaacctccactggaggtt......................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCUCCAGUGGAGGUUUUCAGCCUCUCAUCUUGAAAUAAGAAAGUGAGAGAAGGUCCUGUGGACCUUUUUACCCUGAGCCUAGAAAUGAGAAAGCGAGGAAGGUCCUGUGGACCUUUUUAGAUUCUUGCCCUGAAAUCAAAAAGAAAGAAAAACCUCCAGUGGAGGUU .((((((((.(((((((((((...((((((.(((.........))))))))).((((((...((((((((((.(.((...(.((....)).)..)).)))))))))))...)))))).......(((((....((....))..))))).).)))))))))).)))))))) (-66.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCUCCACUGGAGGUUUUUCUUUCUUUUUGAUUUCAGGGCAAGAAUCUAAAAAGGUCCACAGGACCUUCCUCGCUUUCUCAUUUCUAGGCUCAGGGUAAAAAGGUCCACAGGACCUUCUCUCACUUUCUUAUUUCAAGAUGAGAGGCUGAAAACCUCCACUGGAGGUUU ((((((((.((((((((((((((((.((((((..(.((((.(((........(((((((...((((((((((.((((..........))))..)))).....))))))...)))))))......))))))))..)))))).)))))...))))))))))).)))))))). (-64.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 99 51 155 106 smit:SMT_1788|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1765029..1765259_NEGATIVE 393 99 51 155 106 smit:SMT_1197|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1158751..1158981_NEGATIVE 360 110 63 165 122 smit:SMT_864|5end_K07485_transposase_814322..814552_POSITIVE 337 139 91 82 15 smit:SMT_807|5end_hypothetical_protein_predicted_by_Glimmer/Critica_716815..717045_NEGATIVE 320 136 94 213 175 smit:SMT_1994|5end_phosphoglycerate_mutase_1920501..1920731_NEGATIVE 288 137 95 216 167 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 288 137 95 216 167 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 286 110 63 66 7 smit:SMT_1216|5end_hypothetical_protein_1174879..1175109_POSITIVE 285 100 55 119 75 smit:SMT_167|5end_acetyltransferase,_GNAT_family_113171..113401_POSITIVE 281 105 61 229 181 smit:SMT_1184|5end_phosphotransferase_system,_mannose/fructose/N-acetylgalactosamine-specific_component_IIB_1142037..1142267_NEGATIVE 279 133 95 56 11 smit:SMT_415|5end_hypothetical_protein_358785..359015_POSITIVE 277 133 99 208 179 smit:SMT_1590|5end_DNA-entry_nuclease_1578565..1578795_POSITIVE 276 132 93 230 190 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 273 134 96 80 31 smit:SMT_1976|5end_immunoglobulin_A1_protease_1906950..1907180_POSITIVE 272 108 75 33 3 smit:SMT_1891|5end_putative_dihydrolipoamide_S-acetyltransferase_1844373..1844603_POSITIVE 272 108 75 33 3 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 267 86 46 66 19 smit:SMT_1531|5end_hypothetical_protein_1515997..1516227_NEGATIVE 267 97 52 197 137 smit:SMT_133|5end_L-serine_dehydratase_beta_subunit_85237..85467_NEGATIVE 266 119 74 53 5 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 266 66 22 68 23 smit:SMT_145|5end_hypothetical_protein_95873..96103_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 99 51 69 20 smit:SMT_1198|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1158837..1158987_NEGATIVE 360 49 1 119 72 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 322 131 91 94 59 smit:SMT_699|3end_K03106_signal_recognition_particle,_subunit_SRP54_609941..610091_NEGATIVE 310 168 124 78 36 smit:SMT_441|3end_L-lactate_oxidase_381279..381429_POSITIVE 300 110 61 71 7 smit:SMT_141|3end_K03495_glucose_inhibited_division_protein_A_93401..93551_POSITIVE 298 70 23 85 29 smit:SMT_1847|3end_hypothetical_protein_1812697..1812847_POSITIVE 298 70 22 91 39 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 295 83 42 64 15 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 285 100 55 75 31 smit:SMT_166|3end_hypothetical_protein_113207..113357_POSITIVE 279 133 95 63 18 smit:SMT_414|3end_K03665_GTP-binding_protein_HflX_358872..359022_POSITIVE 273 76 44 148 113 smit:SMT_1891|3end_putative_dihydrolipoamide_S-acetyltransferase_1845019..1845169_POSITIVE 267 86 46 69 22 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 264 59 14 52 3 smit:SMT_1486|3end_hypothetical_protein_1466444..1466594_POSITIVE 262 66 28 73 31 smit:SMT_839|3end_ABC_transporter,_ATP-binding_protein_784194..784344_NEGATIVE 261 134 91 71 36 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 259 134 94 84 21 smit:SMT_943|3end_hypothetical_protein_894136..894286_NEGATIVE 259 106 61 55 8 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 257 135 91 82 34 smit:SMT_1722|3end_x-prolyl-dipeptidyl_aminopeptidase_1709012..1709162_POSITIVE 253 34 5 83 42 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE 252 110 61 78 24 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE