Origin IGS: tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta .........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 taaggaattgtattcttaaatatctgtgctcttaatctttggttgcatataaaccacactccaaaagttagattttaattgtctgacttttggagtttttttgttgaattaagtcggaagcaaaagtggcggttgtgaacagattttaaagtttaaaaaggcgaaaagaaatttttgagtacaaaaaaagcaccgattggtgcttatga Mask Tandem Repeat Region ================================================ tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta Find is-nt database================================================ Query_seq: SSA_1272:SSA_1274|SSA_1272:SSA_1274:50S ribosomal protein L31 type B, putative:hypothetical protein:-><-:1295398..1295606 209 tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1272:SSA_1274|SSA_1272:SSA_1274:50S ribosomal protein L31 type B, putative:hypothetical protein:-><-:1295398..1295606 209 tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1272:SSA_1274|SSA_1272:SSA_1274:50S ribosomal protein L31 type B, putative:hypothetical protein:-><-:1295398..1295606 209 tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 3 End: 98 .. M S T N R C F F C T Q K F L F A F L N F K I C S Q P P L L L P T ............................................................................................................... tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta 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================================================ tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.1 Tail_Score: -5.83226 Start: 115 End: 151 Full_Region: tgcatataaaccaca ctccaaaagttagat tttaatt gtctgacttttggag tttttttgttgaatt ..................................................................................................................ctccaaaagttagattttaattgtctgacttttggag.......................................................... Find igs database================================================ Query_seq: SSA_1272:SSA_1274|SSA_1272:SSA_1274:50S ribosomal protein L31 type B, putative:hypothetical protein:-><-:1295398..1295606 209 tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_009009_SSA_1272_SSA_1274|50S ribosomal protein L31 type B, putative:hypothetical protein|POSITIVE:NEGATIVE|[1295398,1295606]|209 HSP 1 e-value: 5.0E-90 bit: 331.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 tcataagcaccaatcggtgcnnnnnnngtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacnnnnnnnctccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta tcataagcaccaatcggtgctttttttgtactcaaaaatttcttttcgcctttttaaactttaaaatctgttcacaaccgccacttttgcttccgacttaattcaacaaaaaaactccaaaagtcagacaattaaaatctaacttttggagtgtggtttatatgcaaccaaagattaagagcacagatatttaagaatacaattcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUAAGCACCAAUCGGUGCUUUUUUUGUACUCAAAAAUUUCUUUUCGCCUUUUUAAACUUUAAAAUCUGUUCACAACCGCCACUUUUGCUUCCGACUUAAUUCAACAAAAAAACUCCAAAAGUCAGACAAUUAAAAUCUAACUUUUGGAGUGUGGUUUAUAUGCAACCAAAGAUUAAGAGCACAGAUAUUUAAGAAUACAAUUCCUUA ....(((((((....)))))))((((((....)))))).....................((((((((((((.(......((.......))......(((((((..........(((((((((((.(((.........))).))))))))))).(((((.......)))))..))))))).).)))))).)))))).............. (-42.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAAUUGUAUUCUUAAAUAUCUGUGCUCUUAAUCUUUGGUUGCAUAUAAACCACACUCCAAAAGUUAGAUUUUAAUUGUCUGACUUUUGGAGUUUUUUUGUUGAAUUAAGUCGGAAGCAAAAGUGGCGGUUGUGAACAGAUUUUAAAGUUUAAAAAGGCGAAAAGAAAUUUUUGAGUACAAAAAAAGCACCGAUUGGUGCUUAUGA .......((((((((..((((.(((.((((.((((.((((((((.((((....((((.(((((((((((((((.......)))))))))))))))...(((((((.............)))))))))))....))))....)))..))))).))))...))))...))).))))..))))))))...(((((((....))))))).... (-61.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 160 114 146 100 NC_009009:SSA_1361|5end_ORFA,_transposon_ISSsa2_1377168..1377398_POSITIVE 378 160 114 146 100 NC_009009:SSA_0573|5end_hypothetical_protein_568732..568962_NEGATIVE 378 160 114 146 100 NC_009009:SSA_0265|5end_ORFA,_transposon_ISSsa1_259391..259621_POSITIVE 340 153 111 191 152 NC_009009:SSA_1218|5end_DNA_repair_protein_radC,_putative_1240459..1240689_NEGATIVE 276 97 59 230 184 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 269 157 115 84 43 NC_009009:SSA_1248|5end_hypothetical_protein_1273263..1273493_NEGATIVE 269 50 7 209 160 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 261 96 66 72 39 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 251 49 7 50 12 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 250 105 63 54 3 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 248 89 41 146 91 NC_009009:SSA_2284|5end_Histidyl-tRNA_synthetase,_putative_2287272..2287502_NEGATIVE 244 97 67 82 54 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 243 120 78 205 170 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 242 85 41 206 166 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 241 81 42 137 95 NC_009009:SSA_2078|5end_hypothetical_protein_2083837..2084067_NEGATIVE 241 44 4 192 136 NC_009009:SSA_1409|5end_DTDP-glucose-4,6-dehydratase,_putative_1422255..1422485_NEGATIVE 240 97 66 226 192 NC_009009:SSA_1337|5end_hypothetical_protein_1351091..1351321_NEGATIVE 238 98 63 230 192 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 231 30 2 74 40 NC_009009:SSA_0809|5end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791146..791376_POSITIVE 231 98 65 221 185 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 160 114 68 22 NC_009009:SSA_1360|3end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1377170..1377320_POSITIVE 378 160 114 77 31 NC_009009:SSA_0574|3end_YdjX_protein,_putative_568801..568951_NEGATIVE 378 160 114 51 5 NC_009009:SSA_0264|3end_PEP_phosphonomutase-like_protein,_putative_259376..259526_POSITIVE 340 153 111 68 29 NC_009009:SSA_1219|3end_Sortase,_putative_1240582..1240732_NEGATIVE 323 156 114 67 27 NC_009009:SSA_0617|3end_Membrane_protease_subunits,_stomatin/prohibitin-like_protein_(SPFH_domain/band_7_family),_putative_611438..611588_POSITIVE 323 160 115 46 2 NC_009009:SSA_0323|3end_Flavoprotein,_putative_315624..315774_NEGATIVE 269 157 115 72 31 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE 261 96 66 85 52 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 251 49 7 46 8 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 250 109 70 42 1 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 246 22 3 64 43 NC_009009:SSA_0701|3end_Cation_transporter_CorA_family,_putative_685356..685506_POSITIVE 240 97 66 117 83 NC_009009:SSA_1338|3end_hypothetical_protein_1351200..1351350_NEGATIVE 238 108 66 130 93 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 235 50 5 147 107 NC_009009:SSA_1793|3end_Histidine_kinase_(sensor_protein),_putative_1775126..1775276_NEGATIVE 234 50 6 147 100 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 227 108 71 51 9 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 224 90 41 117 74 NC_009009:SSA_2299|3end_hypothetical_protein_2300655..2300805_NEGATIVE 224 98 58 131 93 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE 221 109 77 41 13 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 220 83 45 127 95 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE