Origin IGS: tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggtgtttcttcatggaatgcgtctttaccagccgatgagcctttcgcttgtcggctttttctaatgagtctcggcttgacaagaaggagctagctgggctatcatagggacggaggaaaaaca Mask Tandem Repeat Region ================================================ tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct Find is-nt database================================================ Query_seq: SSA_1712:SSA_1713|SSA_1712:SSA_1713:Arsenate reductase (ArsC), glutaredoxin family, putative:D-3-phosphoglycerate dehydrogenase, putative:<-<-:1700175..1700298 124 tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1712:SSA_1713|SSA_1712:SSA_1713:Arsenate reductase (ArsC), glutaredoxin family, putative:D-3-phosphoglycerate dehydrogenase, putative:<-<-:1700175..1700298 124 tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1712:SSA_1713|SSA_1712:SSA_1713:Arsenate reductase (ArsC), glutaredoxin family, putative:D-3-phosphoglycerate dehydrogenase, putative:<-<-:1700175..1700298 124 tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct Predict ORF larger than 30AA ================================================ tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct 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================================================ tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1712:SSA_1713|SSA_1712:SSA_1713:Arsenate reductase (ArsC), glutaredoxin family, putative:D-3-phosphoglycerate dehydrogenase, putative:<-<-:1700175..1700298 124 tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_009009_SSA_1712_SSA_1713|Arsenate reductase (ArsC), glutaredoxin family, putative:D-3-phosphoglycerate dehydrogenase, putative|NEGATIVE:NEGATIVE|[1700175,1700298]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct tgtttttcctccgtccctatgatagcccagctagctccttcttgtcaagccgagactcattagaaaaagccgacaagcgaaaggctcatcggctggtaaagacgcattccatgaagaaacacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUUCCUCCGUCCCUAUGAUAGCCCAGCUAGCUCCUUCUUGUCAAGCCGAGACUCAUUAGAAAAAGCCGACAAGCGAAAGGCUCAUCGGCUGGUAAAGACGCAUUCCAUGAAGAAACACCU .((((((((.......((((((((((...))))......(((((......))))).))).)))....((((((..(((.....)))..)))))))).))))))..................... (-24.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGUUUCUUCAUGGAAUGCGUCUUUACCAGCCGAUGAGCCUUUCGCUUGUCGGCUUUUUCUAAUGAGUCUCGGCUUGACAAGAAGGAGCUAGCUGGGCUAUCAUAGGGACGGAGGAAAAACA ..((.(((((((........(((((((((((((.((..(((.....)))..)).(((((((((..(((((....)))))...)))))))))..))))).......))))))))))))))).)). (-40.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1052 60 11 151 102 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 397 55 11 141 93 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 363 50 1 162 115 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 352 58 13 54 5 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 349 59 11 148 95 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 346 50 1 94 41 NC_009009:SSA_0706|5end_RNA_helicase,_putative_691363..691593_POSITIVE 345 50 12 174 129 NC_009009:SSA_1647|5end_hypothetical_protein_1647169..1647399_NEGATIVE 345 60 11 148 100 NC_009009:SSA_0066|5end_hypothetical_protein_67602..67832_POSITIVE 342 50 8 144 101 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 340 55 12 57 10 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 340 109 66 59 14 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 337 90 41 169 120 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 334 110 63 184 132 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 331 58 11 102 57 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 326 58 11 132 66 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 324 69 29 229 178 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 323 53 13 117 87 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 320 53 11 137 88 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 319 110 70 186 141 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 319 53 12 207 162 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 55 11 107 59 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 352 58 13 53 4 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 345 60 11 143 95 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 331 58 11 109 64 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 326 58 11 117 51 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 323 53 13 120 90 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 320 53 11 62 13 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 318 111 74 62 29 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 316 55 24 148 114 NC_009009:SSA_0684|3end_Fibril-like_structure_subunit_FibA,_putative_668893..669043_POSITIVE 314 58 11 52 2 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 314 58 14 149 105 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 314 42 2 52 15 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 310 50 8 44 5 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 308 46 10 101 61 NC_009009:SSA_0088|3end_V-type_sodium_ATPase,_subunit_C,_putative_90023..90173_POSITIVE 307 54 25 42 12 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 306 110 67 58 18 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 305 70 23 56 2 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 303 92 51 57 12 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 302 51 12 42 1 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 302 120 76 54 9 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE