Origin IGS: aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccagttgtaaagctgannnnnttaattaattaannnnngcgattggccacggtgaaatttaaaggttctcctcgccaaagcactttttggtaaaccagatgtccttctt Mask Tandem Repeat Region ================================================ aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg Find is-nt database================================================ Query_seq: SMT_1920:SMT_1921|SMT_1920:SMT_1921:ABC transporter, ATP-binding protein:D-alanine-activating enzyme:<-->:1863216..1863324 109 aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1920:SMT_1921|SMT_1920:SMT_1921:ABC transporter, ATP-binding protein:D-alanine-activating enzyme:<-->:1863216..1863324 109 aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1920:SMT_1921|SMT_1920:SMT_1921:ABC transporter, ATP-binding protein:D-alanine-activating enzyme:<-->:1863216..1863324 109 aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg Predict ORF larger than 30AA ================================================ aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg 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================================================ aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1920:SMT_1921|SMT_1920:SMT_1921:ABC transporter, ATP-binding protein:D-alanine-activating enzyme:<-->:1863216..1863324 109 aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: smit_SMT_1920_SMT_1921|ABC transporter, ATP-binding protein:D-alanine-activating enzyme|NEGATIVE:POSITIVE|[1863216,1863324]|109 HSP 1 e-value: 9.0E-38 bit: 157.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg aagaaggacatctggtttaccaaaaagtgctttggcgaggagaacctttaaatttcaccgtggccaatcgcnnnnnttaattaattaannnnntcagctttacaactgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAGGACAUCUGGUUUACCAAAAAGUGCUUUGGCGAGGAGAACCUUUAAAUUUCACCGUGGCCAAUCGCNNNNNUUAAUUAAUUAANNNNNUCAGCUUUACAACUGG ..((((......(((....)))....(((..(((((.(((.(((.........))).)).).))))).)))..........................))))........ (-14.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAGUUGUAAAGCUGANNNNNUUAAUUAAUUAANNNNNGCGAUUGGCCACGGUGAAAUUUAAAGGUUCUCCUCGCCAAAGCACUUUUUGGUAAACCAGAUGUCCUUCUU .(((((....))))).......................((..(((((...((.(((.........))).))..))))).))....(((((....))))).......... (-19.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 924 70 21 161 112 smit:SMT_1920|5end_ABC_transporter,_ATP-binding_protein_1863125..1863355_NEGATIVE 331 46 1 116 69 smit:SMT_2064|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1972182..1972412_POSITIVE 297 48 7 183 149 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 294 60 13 53 6 smit:SMT_648|5end_L-lactate_dehydrogenase_554315..554545_POSITIVE 289 67 24 184 134 smit:SMT_1534|5end_signal_peptidase_I_1517218..1517448_POSITIVE 283 70 29 210 158 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 281 69 28 208 157 smit:SMT_269|5end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_207725..207955_POSITIVE 274 70 26 51 3 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 258 69 25 203 157 smit:SMT_1353|5end_GTP-binding_protein_1331589..1331819_NEGATIVE 256 48 5 209 159 smit:SMT_152|5end_sensor_histidine_kinase,_putative_100759..100989_POSITIVE 253 71 31 63 24 smit:SMT_465|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_protein_403244..403474_POSITIVE 253 71 31 63 24 smit:SMT_417|5end_short_chain_dehydrogenase_360373..360603_POSITIVE 249 66 34 226 183 smit:SMT_1189|5end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1147754..1147984_NEGATIVE 244 68 26 68 5 smit:SMT_1922|5end_exonuclease_RexA_1865998..1866228_NEGATIVE 244 68 26 68 5 smit:SMT_1484|5end_exonuclease_RexA_1464936..1465166_NEGATIVE 244 49 3 198 135 smit:SMT_922|5end_RNA-binding_protein_876566..876796_NEGATIVE 244 42 2 66 23 smit:SMT_204|5end_K02012_iron(III)_transport_system_substrate-binding_protein_135971..136201_NEGATIVE 242 46 2 58 6 smit:SMT_1380|5end_pyrroline-5-carboxylate_reductase_1358464..1358694_NEGATIVE 236 66 27 59 19 smit:SMT_940|5end_tRNA_pseudouridine_synthase_A_892764..892994_NEGATIVE 235 70 25 93 41 smit:SMT_1407|5end_ribonuclease_HII_1386309..1386539_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 70 26 67 19 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 253 71 31 42 3 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 253 71 31 42 3 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE 242 46 2 54 2 smit:SMT_1381|3end_gamma-glutamyl_phosphate_reductase_1358468..1358618_NEGATIVE 237 49 9 66 24 smit:SMT_110|3end_alpha-L-fucosidase_59207..59357_POSITIVE 235 70 25 106 54 smit:SMT_1408|3end_GTP-binding_protein_1386296..1386446_NEGATIVE 234 63 26 72 34 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE 234 70 27 64 10 smit:SMT_234|3end_aminopeptidase_PepS_174151..174301_POSITIVE 233 71 31 144 101 smit:SMT_1791|3end_hypothetical_protein_1766433..1766583_POSITIVE 232 63 26 74 47 smit:SMT_513|3end_16S_rRNA_processing_protein_RimM_441467..441617_POSITIVE 231 66 26 147 106 smit:SMT_176|3end_30S_ribosomal_protein_S3_118814..118964_POSITIVE 230 68 25 100 42 smit:SMT_1317|3end_glycosyltransferase_1283587..1283737_POSITIVE 223 46 10 44 3 smit:SMT_1583|3end_polysaccharide_transporter,_PST_family_1574609..1574759_POSITIVE 221 71 52 45 22 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 220 71 34 41 6 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE 217 68 32 38 1 smit:SMT_127|3end_transcriptional_regulator,_PadR_family_78237..78387_NEGATIVE 215 70 23 129 74 smit:SMT_1570|3end_hypothetical_protein_1563250..1563400_NEGATIVE 213 48 1 66 25 smit:SMT_1272|3end_K02006_cobalt_transport_system_ATP-binding_protein_1237004..1237154_POSITIVE 213 67 30 149 117 smit:SMT_1064|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1004419..1004569_POSITIVE 211 46 1 121 75 smit:SMT_1936|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1874189..1874339_POSITIVE