Origin IGS: agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaagatagaccagaaacgccagaatcttctttaaaaatcaagaggctggcgaaaatagaactagaaaaatcctgatgagagtatcagaaagtcattggggaagtaaaagtctagggaatagatggaaccaatcgcaatgggccttatcacaatcgggtatctagggagttcctaaaacattggagcttccaaatacttattataaagtaggaatcaaggagtattaatctgagtctatgttagatagaacctactgtcatttggactgtgcggaggataaagataggaaacttcatttaaaaaatattcaatcctctgaataggaaataaaagtatcgtcctaataaagtgcaaactaaacttctgaattgtgttataatagataaatattggatggctaggagagagtgtatctttctctaaatgaagaaatagaaagaacagagaggtaaagct Mask Tandem Repeat Region ================================================ agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Find is-nt database================================================ Query_seq: SSA_2174:SSA_2175|SSA_2174:SSA_2175:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:hypothetical protein:<-<-:2172780..2173235 456 agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2174:SSA_2175|SSA_2174:SSA_2175:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:hypothetical protein:<-<-:2172780..2173235 456 agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2174:SSA_2175|SSA_2174:SSA_2175:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:hypothetical protein:<-<-:2172780..2173235 456 agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 44 End: 157 ........................................... M H S L L A I Q Y L S I I T Q F R S L V C T L L G R Y F Y F L F R G L N I F ........................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 13 End: 219 ............ M F F L F L H L E K D T L S P S H P I F I Y Y N T I Q K F S L H F I R T I L L F P I Q R I E Y F L N E V S Y L Y P P H S ............................................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 304 End: 393 ............................................................................................................................................................................................................................................................................................................... M V I R P I A I G S I Y S L D F Y F P N D F L I L S S G F F ............................................................... Protein_Len: 46 Strand: - Start: 296 End: 433 ....................................................................................................................................................................................................................................................................................................... I G S Q S L A W Q S Q N W R N G L S K S G W H S E S V R M L I K R T R N E G A E Q N K F F M ....................... Protein_Len: 30 Strand: - Start: 250 End: 339 ......................................................................................................................................................................................................................................................... K I I L I Q F S W H K L F E R S V R N H Y P G N R N T G D M ..................................................................................................................... agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 229 End: 258 ....................................................................................................................................................................................................................................ATTAATACTCCTTGATTCCTACTTTATAAT...................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -3.5 Tail_Score: -5.09225 Start: 135 End: 152 Full_Region: GATACTTTTATTTCC TATTCAG AGGA TTGAATA TTTTTTAAATGAAGT ......................................................................................................................................TATTCAGAGGATTGAATA................................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_2174:SSA_2175|SSA_2174:SSA_2175:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:hypothetical protein:<-<-:2172780..2173235 456 agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Intra-Species Hit: Count: 1 Min: 1 Max: 456 Len: 456 Subject: NC_009009_SSA_2174_SSA_2175|2,3,4, 5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2172780,2173235]|456 HSP 1 e-value: 0.0 bit: 904.0 Len: 456 Query Start:1 Query End:456 Subject Strand: POSITIVE Subject Start: 1 Subject End: 456 agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc agctttacctctctgttctttctatttcttcatttagagaaagatacactctctcctagccatccaatatttatctattataacacaattcagaagtttagtttgcactttattaggacgatacttttatttcctattcagaggattgaatattttttaaatgaagtttcctatctttatcctccgcacagtccaaatgacagtaggttctatctaacatagactcagattaatactccttgattcctactttataataagtatttggaagctccaatgttttaggaactccctagatacccgattgtgataaggcccattgcgattggttccatctattccctagacttttacttccccaatgactttctgatactctcatcaggatttttctagttctattttcgccagcctcttgatttttaaagaagattctggcgtttctggtctatcttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUUACCUCUCUGUUCUUUCUAUUUCUUCAUUUAGAGAAAGAUACACUCUCUCCUAGCCAUCCAAUAUUUAUCUAUUAUAACACAAUUCAGAAGUUUAGUUUGCACUUUAUUAGGACGAUACUUUUAUUUCCUAUUCAGAGGAUUGAAUAUUUUUUAAAUGAAGUUUCCUAUCUUUAUCCUCCGCACAGUCCAAAUGACAGUAGGUUCUAUCUAACAUAGACUCAGAUUAAUACUCCUUGAUUCCUACUUUAUAAUAAGUAUUUGGAAGCUCCAAUGUUUUAGGAACUCCCUAGAUACCCGAUUGUGAUAAGGCCCAUUGCGAUUGGUUCCAUCUAUUCCCUAGACUUUUACUUCCCCAAUGACUUUCUGAUACUCUCAUCAGGAUUUUUCUAGUUCUAUUUUCGCCAGCCUCUUGAUUUUUAAAGAAGAUUCUGGCGUUUCUGGUCUAUCUUC ......((((..(((((.((((((...((((.....((((.((.....)).))))..........((((......)))).............))))..)))..(((.......(((((.((((....)))))))))....((((((.((..(((((......)))))......))...)))))).)))......))).))))).))))..........((((((.((((.......((.(((.....(((((......)))))...(((((.......((((..((((.....(((((..(((((((..((.......))..)))))))....)))))))))..)))).....))))).))).))..(((((((......)))))))..................((((((..((((...........))))..))))))..)))))))))).... (-85.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGAUAGACCAGAAACGCCAGAAUCUUCUUUAAAAAUCAAGAGGCUGGCGAAAAUAGAACUAGAAAAAUCCUGAUGAGAGUAUCAGAAAGUCAUUGGGGAAGUAAAAGUCUAGGGAAUAGAUGGAACCAAUCGCAAUGGGCCUUAUCACAAUCGGGUAUCUAGGGAGUUCCUAAAACAUUGGAGCUUCCAAAUACUUAUUAUAAAGUAGGAAUCAAGGAGUAUUAAUCUGAGUCUAUGUUAGAUAGAACCUACUGUCAUUUGGACUGUGCGGAGGAUAAAGAUAGGAAACUUCAUUUAAAAAAUAUUCAAUCCUCUGAAUAGGAAAUAAAAGUAUCGUCCUAAUAAAGUGCAAACUAAACUUCUGAAUUGUGUUAUAAUAGAUAAAUAUUGGAUGGCUAGGAGAGAGUGUAUCUUUCUCUAAAUGAAGAAAUAGAAAGAACAGAGAGGUAAAGCU .((.((((((((((..((((((..((((...........))))..))))))....(((.(((.......((((((((((.((.........((((((.((........(((((.....)))))........)).))))))))))))))......((((((...(((((((((.........)))))))))..))))))..........)))).......))).))).)))).)))))).)).......((((.(((((.((((.(((...(((((((((((...((....))...))))............)))))))..(((((.(((....)))..)))))....))).)))).....((((........(((((((((......))))..)))))..((((((((.....))))))))....)))).........).))))..))))...... (-108.93) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 830 60 11 151 102 NC_009009:SSA_2174|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2172689..2172919_NEGATIVE 330 448 408 70 18 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 321 418 375 86 33 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 315 358 316 139 87 NC_009009:SSA_2068|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_2071311..2071541_NEGATIVE 313 348 302 57 5 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 308 225 182 77 31 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 304 450 404 140 95 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 301 329 284 69 18 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 298 349 301 148 102 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 297 304 263 55 6 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 297 65 23 149 98 NC_009009:SSA_0540|5end_Glycerol_uptake_facilitator_protein,_putative_534955..535185_POSITIVE 297 360 314 100 50 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 296 50 2 175 124 NC_009009:SSA_0311|5end_hypothetical_protein_305877..306107_POSITIVE 293 59 11 149 103 NC_009009:SSA_1888|5end_hypothetical_protein_1886025..1886255_NEGATIVE 291 387 354 36 1 NC_009009:SSA_1176|5end_Acetoin_dehydrogenase,_E1_component,_beta_subunit,_putative_1205405..1205635_NEGATIVE 287 317 271 167 125 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 284 210 162 140 93 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 284 60 12 193 143 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 282 210 162 161 108 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 281 440 391 144 93 NC_009009:SSA_2014|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014807..2015037_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 450 407 148 104 NC_009009:SSA_0047|3end_NAD(P)H_dehydrogenase_(Quinone),_putative_52284..52434_NEGATIVE 330 448 408 85 33 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 304 450 404 139 94 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 297 360 314 113 63 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 284 412 380 77 38 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 284 210 162 147 100 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 284 60 12 117 67 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 282 326 282 47 5 NC_009009:SSA_0136|3end_ABC_transporter,_Zn_porter,_putative_131804..131954_POSITIVE 281 333 292 44 5 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 281 450 407 48 7 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 280 417 371 91 45 NC_009009:SSA_1900|3end_N_utilization_substance_protein_A,_putative_1894750..1894900_NEGATIVE 278 450 407 91 52 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 274 378 333 149 92 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 272 325 284 52 14 NC_009009:SSA_0715|3end_DNA_uptake_protein,_putative_701486..701636_POSITIVE 272 310 262 151 99 NC_009009:SSA_0296|3end_Transcriptional_regulator,_XRE_family,_putative_289013..289163_NEGATIVE 270 386 342 147 95 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 268 329 288 56 7 NC_009009:SSA_1493|3end_hypothetical_protein_1498929..1499079_NEGATIVE 266 329 291 43 4 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 265 319 290 149 122 NC_009009:SSA_1438|3end_Acetyltransferase,_putative_1443142..1443292_NEGATIVE 264 140 91 118 75 NC_009009:SSA_1235|3end_Dihydroorotase,_putative_1259959..1260109_NEGATIVE