Origin IGS: ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacgttcccctttctagatacagtctaacaaatcaagaacttaattgggaccatttcgcctattctgtctcctttaccgtctcaactgcacaaaaaagagaggtcacgcctctctcaggg Mask Tandem Repeat Region ================================================ ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt Find is-nt database================================================ Query_seq: SMT_101:SMT_102|SMT_101:SMT_102:cell division protein:competence-specific global transcription modulator:->->:34128..34247 120 ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_101:SMT_102|SMT_101:SMT_102:cell division protein:competence-specific global transcription modulator:->->:34128..34247 120 ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_101:SMT_102|SMT_101:SMT_102:cell division protein:competence-specific global transcription modulator:->->:34128..34247 120 ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt Predict ORF larger than 30AA ================================================ ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt 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================================================ ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_101:SMT_102|SMT_101:SMT_102:cell division protein:competence-specific global transcription modulator:->->:34128..34247 120 ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt Intra-Species Hit: Count: 2 Min: 1 Max: 120 Len: 120 Subject: smit_SMT_101_SMT_102|cell division protein:competence-specific global transcription modulator|POSITIVE:POSITIVE|[34128,34247]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt Subject: smit_SMT_1091_SMT_1092|competence-specific global transcription modulator:transcription antitermination factor|NEGATIVE:NEGATIVE|[1033131,1033249]|119 HSP 1 e-value: 1.0E-9 bit: 63.9 Len: 120 Query Start:1 Query End:120 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 119 ccctgagagaggcgtgacctctcttttttgtgcagttgagacggtaaaggagacagaataggcgaaatggtcccaattaagttcttgatttgttagactgtatctagaaaggggaacgtt ccctgagagaggcaagacctctcttttttatgcagtttagacggtgtagggaacagaat-ggagaaaagaaccgaattggcttcattatttgttaaactgtatctagaaagggggacgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCUGAGAGAGGCGUGACCUCUCUUUUUUGUGCAGUUGAGACGGUAAAGGAGACAGAAUAGGCGAAAUGGUCCCAAUUAAGUUCUUGAUUUGUUAGACUGUAUCUAGAAAGGGGAACGUU ((((((((((((.....))))))))....((((((((..(((((...(((((....(((.((.((.....)))).)))...)))))...))))).))))))))......))))....... (-34.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGUUCCCCUUUCUAGAUACAGUCUAACAAAUCAAGAACUUAAUUGGGACCAUUUCGCCUAUUCUGUCUCCUUUACCGUCUCAACUGCACAAAAAAGAGAGGUCACGCCUCUCUCAGGG .......((((...(((((...)))))........(((...(((..(((((...............)))))..)))...)))..............(((((((.....))))))).)))) (-21.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 50 1 218 178 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 311 44 1 62 24 smit:SMT_111|5end_alpha-1,2-mannosidase,_putative_61304..61534_NEGATIVE 298 88 41 144 92 smit:SMT_1799|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1773416..1773646_POSITIVE 291 45 3 73 16 smit:SMT_2023|5end_tryptophan_synthase,_alpha_subunit_1939315..1939545_POSITIVE 291 45 3 73 16 smit:SMT_1818|5end_tryptophan_synthase,_alpha_subunit_1792190..1792420_POSITIVE 290 69 24 61 16 smit:SMT_1139|5end_rRNA_(guanine-N1-)-methyltransferase_1079755..1079985_POSITIVE 287 49 1 93 36 smit:SMT_1255|5end_cell_division_protein_FtsH_1221811..1222041_NEGATIVE 282 43 2 52 3 smit:SMT_672|5end_hypothetical_protein_580604..580834_POSITIVE 278 57 11 71 14 smit:SMT_903|5end_hypothetical_protein_852310..852540_NEGATIVE 275 52 13 131 89 smit:SMT_1891|5end_putative_dihydrolipoamide_S-acetyltransferase_1844373..1844603_POSITIVE 275 52 13 131 89 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 270 75 33 90 46 smit:SMT_927|5end_KH_domain_protein_882677..882907_NEGATIVE 268 88 42 144 93 smit:SMT_2018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1936760..1936990_POSITIVE 267 53 13 47 1 smit:SMT_778|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_686870..687100_POSITIVE 266 45 4 57 16 smit:SMT_1646|5end_3-isopropylmalate_dehydratase_large_subunit_1632011..1632241_POSITIVE 265 56 15 134 94 smit:SMT_601|5end_hypothetical_protein_516864..517094_POSITIVE 264 55 11 201 162 smit:SMT_1105|5end_K03217_preprotein_translocase_YidC_subunit_1047632..1047862_NEGATIVE 263 53 14 142 94 smit:SMT_993|5end_hypothetical_protein_935476..935706_NEGATIVE 262 43 1 191 146 smit:SMT_495|5end_bacterial_peptide_chain_release_factor_2_(RF-2)_429038..429268_POSITIVE 261 75 33 52 5 smit:SMT_1845|5end_K01191_alpha-mannosidase_1809663..1809893_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 48 4 147 98 smit:SMT_1156|3end_K07485_transposase_1100158..1100308_POSITIVE 291 45 3 137 80 smit:SMT_1753|3end_tryptophan_synthase_beta_chain_1731652..1731802_POSITIVE 290 57 11 75 26 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 285 47 3 81 36 smit:SMT_2075|3end_phosphoribosylamine--glycine_ligase_1977769..1977919_NEGATIVE 278 57 11 87 30 smit:SMT_904|3end_hypothetical_protein_852294..852444_NEGATIVE 277 45 5 71 31 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE 266 45 4 53 12 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 265 50 2 63 17 smit:SMT_1113|3end_hypothetical_protein_1051811..1051961_NEGATIVE 265 56 15 122 82 smit:SMT_600|3end_ADP-ribose_pyrophosphatase_516932..517082_POSITIVE 263 53 14 142 94 smit:SMT_994|3end_nicotinate-nucleotide_adenylyltransferase_935476..935626_NEGATIVE 260 46 2 151 98 smit:SMT_760|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_665693..665843_NEGATIVE 259 87 42 85 39 smit:SMT_918|3end_hypothetical_protein_871290..871440_NEGATIVE 257 45 2 143 94 smit:SMT_1529|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1512776..1512926_NEGATIVE 254 49 2 112 62 smit:SMT_473|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_409634..409784_NEGATIVE 246 48 1 112 29 smit:SMT_1062|3end_hypothetical_protein_1000648..1000798_POSITIVE 243 48 3 147 98 smit:SMT_864|3end_K07485_transposase_814971..815121_POSITIVE 243 65 31 40 1 smit:SMT_203|3end_putative_ABC_transporter_BitD_133821..133971_NEGATIVE 242 75 33 58 11 smit:SMT_1774|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1750151..1750301_NEGATIVE 242 50 1 72 8 smit:SMT_1198|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1158837..1158987_NEGATIVE 242 48 4 119 80 smit:SMT_1005|3end_possible_aluminum_resistance_protein_946679..946829_POSITIVE