Origin IGS: accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga .........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 tcctttctcttttgaaattttatggacgaaaaaagttgccttcgggtgacttttttgttacaatagctagaaaaattattcactgtaatactcaatgaaaatcaaagagcagacaaggaagctagccataggttgctcannnnnttaattaattaannnnngctgctgcatctatcgtcgttgtagacgctcgtggt Mask Tandem Repeat Region ================================================ accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Find is-nt database================================================ Query_seq: SMT_740:SMT_741|SMT_740:SMT_741:50S ribosomal protein L10:K06147 ATP-binding cassette, subfamily B, bacterial:<-<-:644207..644403 197 accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_740:SMT_741|SMT_740:SMT_741:50S ribosomal protein L10:K06147 ATP-binding cassette, subfamily B, bacterial:<-<-:644207..644403 197 accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_740:SMT_741|SMT_740:SMT_741:50S ribosomal protein L10:K06147 ATP-binding cassette, subfamily B, bacterial:<-<-:644207..644403 197 accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 103 End: 195 ...................................................................................................... M S I T V N N F S S Y C N K K V T R R Q L F S S I K F Q K R K .. accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 134 End: 163 .....................................................................................................................................GTTGCCTTCGGGTGACTTTTTTGTTACAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_740:SMT_741|SMT_740:SMT_741:50S ribosomal protein L10:K06147 ATP-binding cassette, subfamily B, bacterial:<-<-:644207..644403 197 accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Intra-Species Hit: Count: 1 Min: 1 Max: 197 Len: 197 Subject: smit_SMT_740_SMT_741|50S ribosomal protein L10:K06147 ATP-binding cassette, subfamily B, bacterial|NEGATIVE:NEGATIVE|[644207,644403]|197 HSP 1 e-value: 5.0E-90 bit: 331.0 Len: 197 Query Start:1 Query End:197 Subject Strand: POSITIVE Subject Start: 1 Subject End: 197 accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga accacgagcgtctacaacgacgatagatgcagcagcnnnnnttaattaattaannnnntgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaaagga Inter-species Hit: Count: 2 Min: 59 Max: 193 Len: 135 Subject: NC_008533_SPD_1190_SPD_1191|Atz/Trz family protein:ABC transporter, ATP-binding/permease protein|NEGATIVE:NEGATIVE|[1217306,1217606]|301 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 135 Query Start:59 Query End:193 Subject Strand: POSITIVE Subject Start: 163 Subject End: 297 ..........................................................tgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaa.... ..........................................................tgagcaacctacggctagcttcctagtttgctctttgattttcattgagtattacagtgaacaatttttctagctattgtaacaaaaaagtcactcgaaggcaacttttttcgtccataaactttcaaaagagaa.... Subject: NC_003028_SP_1356_SP_1357|chlorohydrolase:ABC transporter, ATP-binding/permease protein|NEGATIVE:NEGATIVE|[1277067,1277457]|391 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 135 Query Start:59 Query End:193 Subject Strand: POSITIVE Subject Start: 253 Subject End: 387 ..........................................................tgagcaacctatggctagcttccttgtctgctctttgattttcattgagtattacagtgaataatttttctagctattgtaacaaaaaagtcacccgaaggcaacttttttcgtccataaaatttcaaaagagaa.... ..........................................................tgagcaacctacggctagcttcctagtttgctctttgattttcattgagtattacagtgaacaatttttctagctattgtaacaaaaaagtcactcgaaggcaacttttttcgtccataaactttcaaaagagaa.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGCAACCUAUGGCUAGCUUCCUUGUCUGCUCUUUGAUUUUCAUUGAGUAUUACAGUGAAUAAUUUUUCUAGCUAUUGUAACAAAAAAGUCACCCGAAGGCAACUUUUUUCGUCCAUAAAAUUUCAAAAGAGAA ((..(.((..((((((((.(((.((((.(((((..((.....))..)))))..)))).)))........)))))))).))...((((((((..((....))..)))))))).)..)).....((((....)))). (-25.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUCUUUUGAAAUUUUAUGGACGAAAAAAGUUGCCUUCGGGUGACUUUUUUGUUACAAUAGCUAGAAAAAUUAUUCACUGUAAUACUCAAUGAAAAUCAAAGAGCAGACAAGGAAGCUAGCCAUAGGUUGCUCA ......(((((....((((.(((.((((((((..((....))..)))))))))))...))))............((((.((.......)).))))..)))))((((((....((.......)).....)))))). (-30.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 911 50 1 199 150 smit:SMT_740|5end_50S_ribosomal_protein_L10_644116..644346_NEGATIVE 706 50 1 96 47 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 662 50 1 96 47 smit:SMT_123|5end_hypothetical_protein_75391..75621_POSITIVE 627 50 1 96 47 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 585 50 1 96 47 smit:SMT_1911|5end_hypothetical_protein_1857614..1857844_POSITIVE 565 50 8 225 183 smit:SMT_1535|5end_exodeoxyribonuclease_V_alpha_chain_1518067..1518297_POSITIVE 520 48 8 205 165 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 520 48 8 205 165 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 520 48 8 205 165 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 506 50 1 96 47 smit:SMT_867|5end_hypothetical_protein_816316..816546_POSITIVE 377 45 8 198 158 smit:SMT_1335|5end_RNA_polymerase_sigma_factor_RpoD_1310201..1310431_NEGATIVE 306 39 8 231 200 smit:SMT_662|5end_A/G-specific_adenine_glycosylase_573827..574057_NEGATIVE 296 39 3 86 48 smit:SMT_2034|5end_hydrolase,_haloacid_dehalogenase-like_family_1946671..1946901_POSITIVE 294 69 21 177 134 smit:SMT_1248|5end_Na+/H+_antiporter_1210529..1210759_NEGATIVE 291 60 12 209 156 smit:SMT_1158|5end_DNA_gyrase_subunit_B_1103957..1104187_NEGATIVE 288 113 72 153 115 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 288 113 72 153 115 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 286 49 2 106 62 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 285 48 2 142 96 smit:SMT_884|5end_hypothetical_protein_predicted_by_Glimmer/Critica_832306..832536_NEGATIVE 277 49 2 221 175 smit:SMT_2078|5end_acetyl_xylan_esterase,_putative_1979571..1979801_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 681 50 1 85 36 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE 662 50 1 89 40 smit:SMT_1075|3end_hypothetical_protein_1013870..1014020_POSITIVE 634 50 1 55 6 smit:SMT_1217|3end_hypothetical_protein_1176166..1176316_NEGATIVE 595 54 12 48 6 smit:SMT_1535|3end_exodeoxyribonuclease_V_alpha_chain_1520513..1520663_POSITIVE 585 50 1 56 7 smit:SMT_1910|3end_pyruvate-formate_lyase_activating_enzyme_1857654..1857804_POSITIVE 583 50 1 75 26 smit:SMT_235|3end_hypothetical_protein_174391..174541_POSITIVE 571 49 1 88 40 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 547 54 12 93 49 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 541 50 3 68 24 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 522 50 3 51 7 smit:SMT_916|3end_3-hydroxy-3-methylglutaryl-CoA_reductase_868730..868880_NEGATIVE 520 48 8 90 50 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 520 48 8 90 50 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 520 48 8 90 50 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 511 50 9 39 1 smit:SMT_1356|3end_fibronectin-binding_protein-like_protein_A_1334269..1334419_POSITIVE 490 54 15 93 54 smit:SMT_1689|3end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1673139..1673289_POSITIVE 486 50 8 53 11 smit:SMT_663|3end_phosphate_acetyltransferase_574016..574166_NEGATIVE 466 50 1 89 40 smit:SMT_951|3end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_898995..899145_NEGATIVE 339 59 19 47 1 smit:SMT_1598|3end_malolactic_regulator,_LysR_family_1588361..1588511_NEGATIVE 315 70 29 42 7 smit:SMT_1767|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1743243..1743393_NEGATIVE 310 54 20 35 1 smit:SMT_1570|3end_hypothetical_protein_1563250..1563400_NEGATIVE