Origin IGS: gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagatagtctatcatatttctaggatttatgctatactagttgggttgccaaatctgtgggggaatcaactaatgatgctcctctcatgtgatgcaacccttggcgcttagcttctttcgccaagcatattacacgcggtaaagccgctaaaggagaaaac Mask Tandem Repeat Region ================================================ gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt Find is-nt database================================================ Query_seq: SSA_1485:SSA_1486|SSA_1485:SSA_1486:Citrulline cluster-linked gene, putative:hypothetical protein:<-->:1492900..1493061 162 gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1485:SSA_1486|SSA_1485:SSA_1486:Citrulline cluster-linked gene, putative:hypothetical protein:<-->:1492900..1493061 162 gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1485:SSA_1486|SSA_1485:SSA_1486:Citrulline cluster-linked gene, putative:hypothetical protein:<-->:1492900..1493061 162 gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 32 End: 127 ............................... M C L A K E A K R Q G L H H M R G A S L V D S P T D L A T Q L V ................................... Protein_Len: 35 Strand: - Start: 54 End: 158 ..................................................... A G L T A D C S L L M M L Q N G W L N P L G V L I A Y I R S I H Y V M .... gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt 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================================================ gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -4.1 Tail_Score: -2.87468 Start: 80 End: 102 Full_Region: gttgccaaatctgtg ggggaatca actaa tgatgctcc tctcatgtgatgcaa ...............................................................................ggggaatcaactaatgatgctcc............................................................ Find igs database================================================ Query_seq: SSA_1485:SSA_1486|SSA_1485:SSA_1486:Citrulline cluster-linked gene, putative:hypothetical protein:<-->:1492900..1493061 162 gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_009009_SSA_1485_SSA_1486|Citrulline cluster-linked gene, putative:hypothetical protein|NEGATIVE:POSITIVE|[1492900,1493061]|162 HSP 1 e-value: 4.0E-87 bit: 321.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt gttttctcctttagcggctttaccgcgtgtaatatgcttggcgaaagaagctaagcgccaagggttgcatcacatgagaggagcatcattagttgattcccccacagatttggcaacccaactagtatagcataaatcctagaaatatgatagactatcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUCUCCUUUAGCGGCUUUACCGCGUGUAAUAUGCUUGGCGAAAGAAGCUAAGCGCCAAGGGUUGCAUCACAUGAGAGGAGCAUCAUUAGUUGAUUCCCCCACAGAUUUGGCAACCCAACUAGUAUAGCAUAAAUCCUAGAAAUAUGAUAGACUAUCUUU ..(((((......((((.....)))).(((.(((((((((((.......))))))).....(((((((......((.(.((.(.((((.....)))).).))).))......))))))).....)))).)))........)))))................. (-41.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGAUAGUCUAUCAUAUUUCUAGGAUUUAUGCUAUACUAGUUGGGUUGCCAAAUCUGUGGGGGAAUCAACUAAUGAUGCUCCUCUCAUGUGAUGCAACCCUUGGCGCUUAGCUUCUUUCGCCAAGCAUAUUACACGCGGUAAAGCCGCUAAAGGAGAAAAC ...((((...))))...(((((......((((((.........(((((((...((.((.(((((.((((.....))))..))))).)).))...)))))))..((((...((...))..)))).))))))......((((.....))))....))))).... (-44.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1005 60 11 151 102 NC_009009:SSA_1485|5end_Citrulline_cluster-linked_gene,_putative_1492809..1493039_NEGATIVE 345 94 53 176 123 NC_009009:SSA_0532|5end_Propanediol_utilization_protein_PduB,_putative_528244..528474_POSITIVE 331 60 17 53 6 NC_009009:SSA_0686|5end_Fe2+/Zn2+_uptake_regulation_protein,_putative_669556..669786_POSITIVE 317 60 15 51 4 NC_009009:SSA_1792|5end_Preprotein_translocase_subunit_YidC,_putative_1774036..1774266_POSITIVE 315 120 75 48 8 NC_009009:SSA_0652|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_635036..635266_POSITIVE 313 68 25 217 169 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 305 76 35 51 3 NC_009009:SSA_0726|5end_FmtA-like_protein,_putative_710905..711135_POSITIVE 305 68 25 70 9 NC_009009:SSA_0304|5end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301143..301373_POSITIVE 304 87 44 40 1 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 302 79 33 231 180 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 302 79 33 221 166 NC_009009:SSA_1256|5end_NAD-dependent_deacetylase,_putative_1283094..1283324_NEGATIVE 297 86 41 207 154 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 297 80 31 215 158 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 294 84 42 180 132 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 294 142 101 207 163 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 293 58 12 142 86 NC_009009:SSA_0606|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_594532..594762_NEGATIVE 293 59 13 196 121 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 293 67 21 157 116 NC_009009:SSA_0111|5end_30S_ribosomal_protein_S19,_putative_110672..110902_POSITIVE 292 58 14 69 4 NC_009009:SSA_0324|5end_Conserved_uncharacterized_protein_317019..317249_POSITIVE 290 60 12 59 1 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 57 14 148 98 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 351 44 13 58 24 NC_009009:SSA_1397|3end_hypothetical_protein_1410995..1411145_POSITIVE 317 56 11 147 110 NC_009009:SSA_1418|3end_Conserved_uncharacterized_protein_1428139..1428289_NEGATIVE 304 84 41 60 11 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE 293 58 12 84 28 NC_009009:SSA_0607|3end_ABC_transporter,_permease_component,_putative_594590..594740_NEGATIVE 293 67 21 71 30 NC_009009:SSA_0110|3end_50S_ribosomal_protein_L2,_putative_110666..110816_POSITIVE 288 90 41 111 65 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 288 60 15 122 67 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 282 50 6 137 87 NC_009009:SSA_1257|3end_hypothetical_protein_1283106..1283256_NEGATIVE 277 55 11 65 24 NC_009009:SSA_1201|3end_hypothetical_protein_1226518..1226668_POSITIVE 276 90 42 127 79 NC_009009:SSA_1748|3end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1733543..1733693_NEGATIVE 276 83 46 40 12 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 275 87 41 89 43 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 273 78 36 70 27 NC_009009:SSA_2255|3end_Transcriptional_regulator,_XRE_family,_putative_2250730..2250880_POSITIVE 271 58 11 122 62 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 269 60 15 151 104 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 268 70 27 91 45 NC_009009:SSA_1470|3end_3-dehydroquinate_dehydratase,_putative_1476307..1476457_NEGATIVE 268 69 40 142 111 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 267 110 73 67 37 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 267 60 16 118 68 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE