Origin IGS: gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt .........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 aagaagtgagaaaaacgaagatgctgtttggtaaataaaagaatgtaatgcagcaggattgaaagaagggatagcagactatcagacgtatctctggataccagtggataaatagattagaaatcagctgtttatttttgagcggctggttttttatgcattgtggtataatgaagctattacagtttcagaaaggatttcgattttgtcatacaaatttctacttttcgaccttgaccatacgctgctggattttgatacggcagaagatattgccttgactcattttttggaggagcaaggcgtaacggagattcagacctacaaagactattatattccc Mask Tandem Repeat Region ================================================ gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt Find is-nt database================================================ Query_seq: SSA_1311:SSA_1312|SSA_1311:SSA_1312:Hydrolase, haloacid dehalogenase-like family, putative:RADC-like protein, putative:<-<-:1328484..1328826 343 gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1311:SSA_1312|SSA_1311:SSA_1312:Hydrolase, haloacid dehalogenase-like family, putative:RADC-like protein, putative:<-<-:1328484..1328826 343 gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1311:SSA_1312|SSA_1311:SSA_1312:Hydrolase, haloacid dehalogenase-like family, putative:RADC-like protein, putative:<-<-:1328484..1328826 343 gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 7 End: 120 ...... M I V F V G L N L R Y A L L L Q K M S Q G N I F C R I K I Q Q R M V K V E K ............................................................................................................................................................................................................................... Protein_Len: 39 Strand: + Start: 71 End: 187 ...................................................................... M S S A V S K S S S V W S R S K S R N L Y D K I E I L S E T V I A S L Y H N A ............................................................................................................................................................ Protein_Len: 37 Strand: + Start: 231 End: 341 ...................................................................................................................................................................................................................................... M Y P L V S R D T S D S L L S L L S I L L H Y I L L F T K Q H L R F S H F .. Protein_Len: 57 Strand: + Start: 172 End: 342 ........................................................................................................................................................................... M I P Q C I K N Q P L K N K Q L I S N L F I H W Y P E I R L I V C Y P F F Q S C C I T F F Y L P N S I F V F L T S . Protein_Len: 60 Strand: - Start: 66 End: 263 ................................................................. I L I W C R I T L T S F Y F N T H C F R F G K Q F Q L L K M I G C H M F F W G S L F L C S I E L R N I W Q Y G S I R R M ................................................................................ Protein_Len: 60 Strand: - Start: 1 End: 228 E L F H T L A I D E A T D F D L L T H D L D F L L F K Y S L I S I R E S V T I A E N Y W L A Y F V L R E F I F L Q N R M ................................................................................................................... gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt 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================================================ gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -4.7 Tail_Score: -5.3236 Start: 195 End: 220 Full_Region: taaatagattagaaa tcagctgttta tttt tgagcggctgg ttttttatgcattgt ..................................................................................................................................................................................................tcagctgtttatttttgagcggctgg........................................................................................................................... Find igs database================================================ Query_seq: SSA_1311:SSA_1312|SSA_1311:SSA_1312:Hydrolase, haloacid dehalogenase-like family, putative:RADC-like protein, putative:<-<-:1328484..1328826 343 gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt Intra-Species Hit: Count: 1 Min: 1 Max: 343 Len: 343 Subject: NC_009009_SSA_1311_SSA_1312|Hydrolase, haloacid dehalogenase-like family, putative:RADC-like protein, putative|NEGATIVE:NEGATIVE|[1328484,1328826]|343 HSP 1 e-value: 0.0 bit: 680.0 Len: 343 Query Start:1 Query End:343 Subject Strand: POSITIVE Subject Start: 1 Subject End: 343 gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt gggaatataatagtctttgtaggtctgaatctccgttacgccttgctcctccaaaaaatgagtcaaggcaatatcttctgccgtatcaaaatccagcagcgtatggtcaaggtcgaaaagtagaaatttgtatgacaaaatcgaaatcctttctgaaactgtaatagcttcattataccacaatgcataaaaaaccagccgctcaaaaataaacagctgatttctaatctatttatccactggtatccagagatacgtctgatagtctgctatcccttctttcaatcctgctgcattacattcttttatttaccaaacagcatcttcgtttttctcacttctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAUAUAAUAGUCUUUGUAGGUCUGAAUCUCCGUUACGCCUUGCUCCUCCAAAAAAUGAGUCAAGGCAAUAUCUUCUGCCGUAUCAAAAUCCAGCAGCGUAUGGUCAAGGUCGAAAAGUAGAAAUUUGUAUGACAAAAUCGAAAUCCUUUCUGAAACUGUAAUAGCUUCAUUAUACCACAAUGCAUAAAAAACCAGCCGCUCAAAAAUAAACAGCUGAUUUCUAAUCUAUUUAUCCACUGGUAUCCAGAGAUACGUCUGAUAGUCUGCUAUCCCUUCUUUCAAUCCUGCUGCAUUACAUUCUUUUAUUUACCAAACAGCAUCUUCGUUUUUCUCACUUCUU ((((((.((((.((....(((((..((((..........(((((((((...........))).))))))............((((((......((((((((..((((....((((..((((....))))...)))).................((((.(((...))).)))).....................))))..))))............))))....................((((...)))).))))))...(((((....)))))......))))..))))).)))))).))))))...................................... (-59.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAGUGAGAAAAACGAAGAUGCUGUUUGGUAAAUAAAAGAAUGUAAUGCAGCAGGAUUGAAAGAAGGGAUAGCAGACUAUCAGACGUAUCUCUGGAUACCAGUGGAUAAAUAGAUUAGAAAUCAGCUGUUUAUUUUUGAGCGGCUGGUUUUUUAUGCAUUGUGGUAUAAUGAAGCUAUUACAGUUUCAGAAAGGAUUUCGAUUUUGUCAUACAAAUUUCUACUUUUCGACCUUGACCAUACGCUGCUGGAUUUUGAUACGGCAGAAGAUAUUGCCUUGACUCAUUUUUUGGAGGAGCAAGGCGUAACGGAGAUUCAGACCUACAAAGACUAUUAUAUUCCC .....................((((....)))).......((((((((((..(.(((.(((((......(((((....)))))...((((((...((((.((((..(.......(...((((((((((((((((....))))))))))))))))....)..((((((....(((((((.....)))))))..((((...((((.((((.....))))..........)))))))).))))))..)..)))))))).))))))............((((((.(((........)))...))))))..........))))).))).)......)))))))))).. (-85.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 970 70 21 161 112 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 344 100 59 207 169 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 334 83 41 40 6 NC_009009:SSA_0581|5end_Conserved_uncharacterized_protein_573329..573559_POSITIVE 333 290 242 124 71 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 325 126 95 27 2 NC_009009:SSA_1064|5end_hypothetical_protein_1081065..1081295_NEGATIVE 324 295 257 51 5 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 321 296 262 163 128 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 316 276 231 175 124 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 312 109 61 222 177 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 306 294 251 55 8 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 306 290 242 183 134 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 304 87 41 225 166 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 299 294 260 60 31 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 299 52 11 65 22 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 299 52 19 43 4 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 299 53 12 196 142 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 298 297 258 145 98 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 298 115 74 220 161 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 297 52 13 96 48 NC_009009:SSA_1902|5end_tRNA_(guanine-N(7)-)-methyltransferase,_putative_1897391..1897621_NEGATIVE 296 89 41 60 3 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 269 230 131 92 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 333 290 242 137 84 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 324 295 257 50 4 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 321 296 262 119 84 NC_009009:SSA_0487|3end_Delta-aminolevulinic_acid_dehydratase,_putative_488400..488550_POSITIVE 309 67 25 139 100 NC_009009:SSA_0684|3end_Fibril-like_structure_subunit_FibA,_putative_668893..669043_POSITIVE 307 97 59 150 116 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 299 294 260 103 74 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 298 87 41 147 107 NC_009009:SSA_2067|3end_hypothetical_protein_2070876..2071026_POSITIVE 298 90 41 106 64 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 297 52 13 99 51 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 294 102 61 136 93 NC_009009:SSA_0637|3end_Tryptophan_synthase_beta_chain,_putative_627022..627172_POSITIVE 293 110 61 47 4 NC_009009:SSA_2114|3end_Transcriptional_repressor_of_purine_operon,_putative_2116714..2116864_NEGATIVE 290 289 241 119 67 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 289 230 184 112 72 NC_009009:SSA_1643|3end_hypothetical_protein_1644610..1644760_NEGATIVE 286 95 53 97 50 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 285 297 256 142 103 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 285 83 41 51 8 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 284 300 252 81 34 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 282 53 13 145 96 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 281 110 62 58 13 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE