Origin IGS: tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg .........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 cgtacagtacagtcagtgattattgagatctgttttgtttcttaacaccggcattaaaaattatccgaagcgttcttccgttgagtcattgcttttatgaagaggatgctaaagtacacattactttctggagctgtgcggagataacaagattgaaacagctaatcgcaaagaagcgga Mask Tandem Repeat Region ================================================ tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg Find is-nt database================================================ Query_seq: PG1584:PG1585|PG1584:PG1585:batC protein:batD protein:->->:1662215..1662394 180 tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1584:PG1585|PG1584:PG1585:batC protein:batD protein:->->:1662215..1662394 180 tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1584:PG1585|PG1584:PG1585:batC protein:batD protein:->->:1662215..1662394 180 tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 20 End: 124 ................... M F Q S C Y L R T A P E S N V Y F S I L F I K A M T Q R K N A S D N F ........................................................ Protein_Len: 50 Strand: - Start: 2 End: 151 . R K K A I L Q K L R T I E A C S W F T I H V K A D E E Y F C H S L P L V S R I I K L A P T L F C F M ............................. tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg 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================================================ tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1584:PG1585|PG1584:PG1585:batC protein:batD protein:->->:1662215..1662394 180 tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_002950_PG1584_PG1585|batC protein:batD protein|POSITIVE:POSITIVE|[1662215,1662394]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg tccgcttctttgcgattagctgtttcaatcttgttatctccgcacagctccagaaagtaatgtgtactttagcatcctcttcataaaagcaatgactcaacggaagaacgcttcggataatttttaatgccggtgttaagaaacaaaacagatctcaataatcactgactgtactgtacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGCUUCUUUGCGAUUAGCUGUUUCAAUCUUGUUAUCUCCGCACAGCUCCAGAAAGUAAUGUGUACUUUAGCAUCCUCUUCAUAAAAGCAAUGACUCAACGGAAGAACGCUUCGGAUAAUUUUUAAUGCCGGUGUUAAGAAACAAAACAGAUCUCAAUAAUCACUGACUGUACUGUACG ..(((......)))......((((((...............((((((((......)))..)))))...((((((((....((((.......)))).....(.((((....)))).)...............))))))))))))))..((((.((............))))))........ (-28.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUACAGUACAGUCAGUGAUUAUUGAGAUCUGUUUUGUUUCUUAACACCGGCAUUAAAAAUUAUCCGAAGCGUUCUUCCGUUGAGUCAUUGCUUUUAUGAAGAGGAUGCUAAAGUACACAUUACUUUCUGGAGCUGUGCGGAGAUAACAAGAUUGAAACAGCUAAUCGCAAAGAAGCGGA ((((((((.(((..((((((..((((((.(......)..))))))...(((.((........))))).(((((((((.(((.((((....))))..)))..))))))))).........))))))..)))..)))))))).........................((((......)))). (-40.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 50 1 218 175 NC_002950:PG2066|5end_lipoprotein,_putative_2162116..2162346_POSITIVE 329 76 33 79 30 NC_002950:PG1063|5end_transcriptional_regulator,_putative_1131056..1131286_POSITIVE 307 78 32 170 125 NC_002950:PG2074|5end_hypothetical_protein_2174661..2174891_NEGATIVE 307 78 32 170 125 NC_002950:PG1670|5end_hypothetical_protein_1755853..1756083_NEGATIVE 307 78 32 170 125 NC_002950:PG1265|5end_hypothetical_protein_1345182..1345412_NEGATIVE 307 78 32 170 125 NC_002950:PG0102|5end_hypothetical_protein_121003..121233_POSITIVE 299 50 2 180 122 NC_002950:PG0522|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_566901..567131_NEGATIVE 298 79 38 220 181 NC_002950:PG0303|5end_ferredoxin_338651..338881_POSITIVE 292 50 1 159 114 NC_002950:PG1185|5end_hypothetical_protein_1267752..1267982_NEGATIVE 292 57 11 59 13 NC_002950:PG0883|5end_hypothetical_protein_945121..945351_POSITIVE 291 77 31 60 3 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 289 50 1 73 15 NC_002950:PG2139|5end_hypothetical_protein_2245648..2245878_POSITIVE 288 40 1 125 69 NC_002950:PG1012|5end_tRNA-i(6)A37_modification_enzyme_MiaB_1071480..1071710_NEGATIVE 282 41 3 228 190 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 280 115 72 83 37 NC_002950:PG1728|5end_cytidine/deoxycytidylate_deaminase_family_protein_1817644..1817874_POSITIVE 276 53 19 119 82 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 275 48 1 132 88 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 274 53 11 179 139 NC_002950:PG1697|5end_type_II_restriction_endonuclease,_putative_1781020..1781250_POSITIVE 274 50 4 218 142 NC_002950:PG1081|5end_acetate_kinase_1149627..1149857_NEGATIVE 274 70 22 137 82 NC_002950:PG0545|5end_hypothetical_protein_598043..598273_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 50 1 127 84 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 335 49 1 139 95 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 331 50 3 76 27 NC_002950:PG1858|3end_flavodoxin_1956538..1956688_NEGATIVE 319 56 12 149 103 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 318 50 1 149 94 NC_002950:PG0472|3end_iron-sulfur_cluster_binding_protein,_putative_514414..514564_POSITIVE 305 50 4 135 76 NC_002950:PG0021|3end_TIM-barrel_protein,_putative,_NifR3_family_24122..24272_NEGATIVE 292 57 11 62 16 NC_002950:PG0882|3end_hypothetical_protein_945204..945354_POSITIVE 286 50 3 64 1 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 283 73 40 36 8 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 282 41 3 139 101 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 276 53 19 111 74 NC_002950:PG1225|3end_ABC_transporter,_ATP-binding_protein_1303336..1303486_POSITIVE 276 80 38 73 21 NC_002950:PG0261|3end_ISPg3,_transposase_293862..294012_NEGATIVE 275 48 1 118 74 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 274 70 22 92 37 NC_002950:PG0544|3end_type_I_restriction-modification_system,_M_subunit,_putative_598078..598228_POSITIVE 268 133 96 84 38 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 268 50 5 151 102 NC_002950:PG2067|3end_pyridoxal_phosphate_biosynthetic_protein_PdxA_2164392..2164542_POSITIVE 267 82 44 88 40 NC_002950:PG0742|3end_antigen_PgaA_789300..789450_NEGATIVE 267 119 72 56 13 NC_002950:PG0661|3end_hypothetical_protein_709692..709842_NEGATIVE 266 50 2 112 56 NC_002950:PG1797|3end_DNA-binding_response_regulator/sensor_histidine_kinase_1892978..1893128_POSITIVE 265 135 94 136 89 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE