Origin IGS: acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tggtttgttctataatgaatgggttattagttctgtaaaaaagttatgagccatgagtcataacccctgagtttggaacctgcatgctgaggccactcatggattataacccatagctcataattccatgtgtgctgt Mask Tandem Repeat Region ================================================ acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca Find is-nt database================================================ Query_seq: PG0377:PG0378|PG0377:PG0378:30S ribosomal protein S2:elongation factor Ts:->->:407906..408043 138 acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0377:PG0378|PG0377:PG0378:30S ribosomal protein S2:elongation factor Ts:->->:407906..408043 138 acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0377:PG0378|PG0377:PG0378:30S ribosomal protein S2:elongation factor Ts:->->:407906..408043 138 acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca Predict ORF larger than 30AA ================================================ acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca 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================================================ acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -3.1 Tail_Score: -5.0133 Start: 75 End: 96 Full_Region: GTTCCAAACTCAGGG GTTATGACT CAT GGCTCATAAC TTTTTTACAGAACTA ..........................................................................GTTATGACTCATGGCTCATAAC.......................................... Find igs database================================================ Query_seq: PG0377:PG0378|PG0377:PG0378:30S ribosomal protein S2:elongation factor Ts:->->:407906..408043 138 acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_002950_PG0377_PG0378|30S ribosomal protein S2:elongation factor Ts|POSITIVE:POSITIVE|[407906,408043]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca acagcacacatggaattatgagctatgggttataatccatgagtggcctcagcatgcaggttccaaactcaggggttatgactcatggctcataacttttttacagaactaataacccattcattatagaacaaacca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGCACACAUGGAAUUAUGAGCUAUGGGUUAUAAUCCAUGAGUGGCCUCAGCAUGCAGGUUCCAAACUCAGGGGUUAUGACUCAUGGCUCAUAACUUUUUUACAGAACUAAUAACCCAUUCAUUAUAGAACAAACCA ..........(((..(((((((((((((((((((((((.(((((((((((.....).)))))....))))).)))))))))))))))))))))))........................(((......)))....))) (-45.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGUUUGUUCUAUAAUGAAUGGGUUAUUAGUUCUGUAAAAAAGUUAUGAGCCAUGAGUCAUAACCCCUGAGUUUGGAACCUGCAUGCUGAGGCCACUCAUGGAUUAUAACCCAUAGCUCAUAAUUCCAUGUGUGCUGU (..((..(((......)))..))..)................(((((((.((((((((.......(((.(((.((.......)).))).)))..)))))))).)))))))..(((((.((((......)))).))))) (-35.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 50 1 216 163 NC_002950:PG1065|5end_dihydroorotate_dehydrogenase_1132327..1132557_POSITIVE 351 75 35 38 1 NC_002950:PG1770|5end_hypothetical_protein_1857284..1857514_POSITIVE 350 75 37 219 170 NC_002950:PG1641|5end_phosphotyrosine_protein_phosphatase_1721763..1721993_NEGATIVE 335 89 41 158 115 NC_002950:PG1542|5end_collagenase_1620788..1621018_POSITIVE 321 70 22 221 158 NC_002950:PG0006|5end_MATE_efflux_family_protein_6332..6562_NEGATIVE 316 66 24 79 30 NC_002950:PG0522|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_566901..567131_NEGATIVE 308 90 47 223 179 NC_002950:PG1934|5end_30S_ribosomal_protein_S19_2022345..2022575_NEGATIVE 307 70 28 197 161 NC_002950:PG0351|5end_hypothetical_protein_386774..387004_POSITIVE 303 89 41 216 164 NC_002950:PG1663|5end_ABC_transporter,_ATP-binding_protein_1745129..1745359_POSITIVE 302 90 45 69 27 NC_002950:PG1732|5end_integrase/recombinase_XerD_1820171..1820401_POSITIVE 302 100 54 170 115 NC_002950:PG1061|5end_ISPg6,_transposase_1129818..1130048_NEGATIVE 298 90 43 213 178 NC_002950:PG1395|5end_cell_shape-determining_protein_MreC,_putative_1477669..1477899_NEGATIVE 298 80 35 215 164 NC_002950:PG0728|5end_hypothetical_protein_779807..780037_NEGATIVE 295 78 35 48 8 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 295 61 27 152 101 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 291 65 23 212 171 NC_002950:PG1522|5end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1600170..1600400_NEGATIVE 290 74 35 209 173 NC_002950:PG0363|5end_hypothetical_protein_397470..397700_POSITIVE 289 64 21 159 116 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 289 88 41 61 14 NC_002950:PG1070|5end_L-lysine_2,3-aminomutase_1136629..1136859_POSITIVE 289 76 36 110 69 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 509 70 21 50 1 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 337 89 41 88 39 NC_002950:PG1808|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1902955..1903105_NEGATIVE 335 89 41 145 102 NC_002950:PG1541|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620855..1621005_POSITIVE 316 66 24 82 33 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE 289 64 21 144 101 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE 286 88 45 103 48 NC_002950:PG1581|3end_hypothetical_protein_1659404..1659554_POSITIVE 286 60 18 118 56 NC_002950:PG0499|3end_hypothetical_protein_539142..539292_POSITIVE 285 76 36 58 6 NC_002950:PG0776|3end_electron_transfer_flavoprotein,_alpha_subunit_829165..829315_NEGATIVE 276 80 34 88 40 NC_002950:PG1906|3end_ISPg1,_transposase_2006572..2006722_POSITIVE 276 80 34 88 40 NC_002950:PG1624|3end_ISPg1,_transposase_1706188..1706338_NEGATIVE 276 80 34 88 40 NC_002950:PG1448|3end_ISPg1,_transposase_1533449..1533599_POSITIVE 276 80 34 88 40 NC_002950:PG1320|3end_ISPg1,_transposase,_internal_deletion_1399467..1399617_POSITIVE 276 80 34 88 40 NC_002950:PG1197|3end_ISPg1,_transposase_1275475..1275625_NEGATIVE 276 80 34 88 40 NC_002950:PG1177|3end_ISPg1,_transposase_1257794..1257944_NEGATIVE 276 80 34 88 40 NC_002950:PG1031|3end_ISPg1,_transposase_1093081..1093231_NEGATIVE 276 80 34 88 40 NC_002950:PG0825|3end_ISPg1,_transposase_882063..882213_NEGATIVE 276 80 34 88 40 NC_002950:PG0184|3end_ISPg1,_transposase_217567..217717_POSITIVE 275 60 19 127 80 NC_002950:PG1692|3end_ABC_transporter,_ATP-binding_protein_1776514..1776664_NEGATIVE 274 89 41 54 6 NC_002950:PG2178|3end_NADH:ubiquinone_oxidoreductase,_Na_translocating,_E_subunit_2286523..2286673_NEGATIVE 274 63 21 102 62 NC_002950:PG0672|3end_iron_compound_ABC_transporter,_ATP-binding_protein_723840..723990_POSITIVE