Origin IGS: acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa .........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 tttctaaaaatagtacgatttacaaaagctgccagctcgaaataaaacaacctaaaaagcttgtttttgcatctacctagctggtcgattcttctaagcaggagcttctgtatcagtccgttttagtatatcacaattcccagcatttttgaacagaaaaaaaggactcttccagccagctaaagccagaaaaatcctttatgt Mask Tandem Repeat Region ================================================ acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa Find is-nt database================================================ Query_seq: SSA_0690:SSA_0691|SSA_0690:SSA_0691:Recombinational DNA repair protein (RecF pathway), putative:D-ala,D-ala ligase, putative:->->:675169..675372 204 acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0690:SSA_0691|SSA_0690:SSA_0691:Recombinational DNA repair protein (RecF pathway), putative:D-ala,D-ala ligase, putative:->->:675169..675372 204 acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0690:SSA_0691|SSA_0690:SSA_0691:Recombinational DNA repair protein (RecF pathway), putative:D-ala,D-ala ligase, putative:->->:675169..675372 204 acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 10 End: 108 ......... M F L A L A G W K S P F F L F K N A G N C D I L K R T D T E A P A ................................................................................................ Protein_Len: 38 Strand: + Start: 89 End: 202 ........................................................................................ M I Q K L L L R R I D Q L G R C K N K L F R L F Y F E L A A F V N R T I F R .. acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa 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: 82 Start: 51 End: 80 ..................................................GTTCAAAAATGCTGGGAATTGTGATATACT............................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0690:SSA_0691|SSA_0690:SSA_0691:Recombinational DNA repair protein (RecF pathway), putative:D-ala,D-ala ligase, putative:->->:675169..675372 204 acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 204 Len: 204 Subject: NC_009009_SSA_0690_SSA_0691|Recombinational DNA repair protein (RecF pathway), putative:D-ala,D-ala ligase, putative|POSITIVE:POSITIVE|[675169,675372]|204 HSP 1 e-value: 2.0E-99 bit: 363.0 Len: 204 Query Start:1 Query End:204 Subject Strand: POSITIVE Subject Start: 1 Subject End: 204 acataaaggatttttctggctttagctggctggaagagtccnnnnnnnctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa acataaaggatttttctggctttagctggctggaagagtcctttttttctgttcaaaaatgctgggaattgtgatatactaaaacggactgatacagaagctcctgcttagaagaatcgaccagctaggtagatgcaaaaacaagctttttaggttgttttatttcgagctggcagcttttgtaaatcgtactatttttagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUAAAGGAUUUUUCUGGCUUUAGCUGGCUGGAAGAGUCCUUUUUUUCUGUUCAAAAAUGCUGGGAAUUGUGAUAUACUAAAACGGACUGAUACAGAAGCUCCUGCUUAGAAGAAUCGACCAGCUAGGUAGAUGCAAAAACAAGCUUUUUAGGUUGUUUUAUUUCGAGCUGGCAGCUUUUGUAAAUCGUACUAUUUUUAGAAA ....((((((((((((..(((......)))..)))))))))))).......((((((((((.((.((.((((...........)))).....((((((((((((.(((..(((..(((.(((.....))).)))...(((((((.((....)).))))))).)))..))).)).))))))))))..)).)).))))))).))). (-60.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUAAAAAUAGUACGAUUUACAAAAGCUGCCAGCUCGAAAUAAAACAACCUAAAAAGCUUGUUUUUGCAUCUACCUAGCUGGUCGAUUCUUCUAAGCAGGAGCUUCUGUAUCAGUCCGUUUUAGUAUAUCACAAUUCCCAGCAUUUUUGAACAGAAAAAAAGGACUCUUCCAGCCAGCUAAAGCCAGAAAAAUCCUUUAUGU (((((...........((((((((.(((((.((.(((.(((..(((((((.((....)).)))))))...(((.(((.....))).)))..)))..))).))))))).))))..)))).((((((((.........(((....((....))....))).....(((....))).....)))))))).)))))............ (-36.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 42 16 47 19 NC_009009:SSA_0400|5end_hypothetical_protein_398251..398481_NEGATIVE 331 188 144 83 41 NC_009009:SSA_1202|5end_Dfp-like_protein,_putative_1226450..1226680_POSITIVE 325 56 14 56 10 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 320 54 17 175 138 NC_009009:SSA_0226|5end_60_kDa_chaperonin_218947..219177_POSITIVE 306 49 1 206 155 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 305 55 16 190 137 NC_009009:SSA_0390|5end_hypothetical_protein_385002..385232_POSITIVE 304 58 16 198 153 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 299 42 18 47 23 NC_009009:SSA_1371|5end_FmtA-like_protein,_putative_1388832..1389062_NEGATIVE 297 67 22 48 7 NC_009009:SSA_1292|5end_hypothetical_protein_1311578..1311808_NEGATIVE 296 53 11 153 112 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 294 134 98 61 20 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 292 150 101 212 166 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 291 137 94 71 23 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 291 138 99 226 178 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 286 130 89 202 166 NC_009009:SSA_2170|5end_hypothetical_protein_2170240..2170470_NEGATIVE 284 145 104 64 27 NC_009009:SSA_2196|5end_Conserved_uncharacterized_protein_2197330..2197560_NEGATIVE 283 170 121 202 167 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 283 177 132 158 114 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 282 69 24 54 9 NC_009009:SSA_0868|5end_hypothetical_protein_861535..861765_NEGATIVE 281 126 85 215 173 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 67 24 66 15 NC_009009:SSA_2323|3end_Transporter,_putative_2328850..2329000_POSITIVE 346 44 5 86 47 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 331 188 144 71 29 NC_009009:SSA_1201|3end_hypothetical_protein_1226518..1226668_POSITIVE 320 54 17 151 114 NC_009009:SSA_0225|3end_10_kDa_chaperonin_219003..219153_POSITIVE 313 65 22 131 91 NC_009009:SSA_1746|3end_hypothetical_protein_1732292..1732442_NEGATIVE 304 58 16 142 97 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 297 67 22 72 31 NC_009009:SSA_1293|3end_hypothetical_protein_1311554..1311704_NEGATIVE 294 134 98 68 27 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 294 46 8 137 95 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 284 145 104 80 43 NC_009009:SSA_2197|3end_hypothetical_protein_2197314..2197464_NEGATIVE 279 46 2 54 5 NC_009009:SSA_0862|3end_MurM,_putative_852992..853142_NEGATIVE 277 170 123 86 28 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 276 133 96 66 28 NC_009009:SSA_1400|3end_Pyridoxal_kinase,_putative_1412206..1412356_NEGATIVE 276 41 3 52 3 NC_009009:SSA_0425|3end_Glycosyltransferase,_putative_422230..422380_NEGATIVE 273 50 1 90 44 NC_009009:SSA_1511|3end_Glycosyltransferase,_putative_1515450..1515600_NEGATIVE 272 47 3 99 57 NC_009009:SSA_1538|3end_hypothetical_protein_1544918..1545068_POSITIVE 269 69 27 137 96 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 267 54 13 137 96 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 266 54 19 150 120 NC_009009:SSA_2124|3end_Dehydrogenase,_eukaryotic-like,_putative_2128557..2128707_NEGATIVE 266 49 18 44 2 NC_009009:SSA_1591|3end_Dipeptidase,_putative_1593403..1593553_NEGATIVE