Origin IGS: gaaataatctgagaacaatatcttatccttatatttccagcgagcaggagatggtgtgagtcctgcattccctaatgataagattatcctctcaaacaatcaagtctgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc .........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 ggtatctcctttataaataataacaaattaaaaaccacgacttccaaaaaggacgaaaatcgtggtaccacctttattcgaaaaaagactcagcttttttcctcttatcccgtaacgtggggaacgtcaaatcttacttcattcagacttgattgtttgagaggataatcttatcattagggaatgcaggactcacaccatctcctgctcgctggaaatataaggataagatattgttctcagattatttc Mask Tandem Repeat Region ================================================ gaaataatctgagaacaatatcttatccttatatttccagcgagcaggagatggtgtgagtcctgcattccctaatgataagattatcctctcaaacaatcaagtctgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Find is-nt database================================================ Query_seq: SMT_1553:SMT_1554|SMT_1553:SMT_1554:K04074 cell division initiation protein:isoleucyl-tRNA synthetase:->->:1536929..1537179 251 gaaataatctgagaacaatatcttatccttatatttccagcgagcaggagatggtgtgagtcctgcattccctaatgataagattatcctctcaaacaatcaagtctgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1553:SMT_1554|SMT_1553:SMT_1554:K04074 cell division initiation protein:isoleucyl-tRNA synthetase:->->:1536929..1537179 251 gaaataatctgagaacaatatcttatccttatatttccagcgagcaggagatggtgtgagtcctgcattccctaatgataagattatcctctcaaacaatcaagtctgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1553:SMT_1554|SMT_1553:SMT_1554:K04074 cell division initiation protein:isoleucyl-tRNA synthetase:->->:1536929..1537179 251 gaaataatctgagaacaatatcttatccttatatttccagcgagcaggagatggtgtgagtcctgcattccctaatgataagattatcctctcaaacaatcaagtctgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 2 Min: 2 Max: 106 Len: 105 Subject: UniRef90_Q8CYG3 Cluster: Hypothetical protein spr1503; n=1; Streptococcus pneumoniae R6|Rep: Hypothetical protein spr1503 - Streptococcus pneumoniae (strain ATCC BAA-255 / R6) HSP 1 e-value: 2.0E-8 bit: 60.1 Len: 105 Query Start:2 Query End:106 Subject Strand: null Subject Start: 19 Subject End: 53 . K * S E N N I L S L Y F Q R A G D G V S P A F P N D K I I L S N N Q V ................................................................................................................................................. . K Y S E N N I L S L Y S Q R A G D G V S P A F P I D K I I L S N Y Q V ................................................................................................................................................. Subject: UniRef90_Q97PG1 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 1.0E-7 bit: 57.8 Len: 105 Query Start:2 Query End:106 Subject Strand: null Subject Start: 19 Subject End: 53 . K * S E N N I L S L Y F Q R A G D G V S P A F P N D K I I L S N N Q V ................................................................................................................................................. . K Y S E N N I L S L Y F Q R A G D G V S P V I P I D K I I L S K T Q V ................................................................................................................................................. gnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 103 End: 225 ...................................................................................................... T Q I F Y S K V N G V N R S L L F F A S D K K S Y L H Y W S K R G K Q F D H N K M .......................... Protein_Len: 54 Strand: - Start: 87 End: 248 ...................................................................................... G R L C D L R F S T L N S T G W T V P Y S S F L Q T K K R I F T T G R N E D K K S T T T K L K N N N I F S M ... Protein_Len: 33 Strand: - Start: 1 End: 99 F Y D S F L I K D K Y K W R A P S P T L G A N G L S L I I R E F M ........................................................................................................................................................ gnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc 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: 84 Start: 75 End: 104 ..........................................................................CTTGATTGTTTGAGAGGATAATCTTATCAT................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.5 Tail_Score: -3.23393 Start: 150 End: 173 Full_Region: ggtaccacctttatt cgaaaaaag actcag cttttttcc tcttatcccgtaacg .....................................................................................................................................................cgaaaaaagactcagcttttttcc.............................................................................. TransTerm Strand: - Conf: 53 HP_score: -6.0 Tail_Score: -2.53822 Start: 151 End: 172 Full_Region: gtaccacctttattc gaaaaaag actcag cttttttc ctcttatcccgtaac ......................................................................................................................................................gaaaaaagactcagcttttttc............................................................................... TransTerm Strand: + Conf: 80 HP_score: -6.2 Tail_Score: -5.10877 Start: 187 End: 217 Full_Region: CGAATAAAGGTGGTA CCACGATTTTCG TCCTTTT TGGAAGTCGTGG TTTTTAATTTGTTAT ..........................................................................................................................................................................................CCACGATTTTCGTCCTTTTTGGAAGTCGTGG.................................. Find igs database================================================ Query_seq: SMT_1553:SMT_1554|SMT_1553:SMT_1554:K04074 cell division initiation protein:isoleucyl-tRNA synthetase:->->:1536929..1537179 251 gnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Intra-Species Hit: Count: 1 Min: 107 Max: 251 Len: 145 Subject: smit_SMT_1553_SMT_1554|K04074 cell division initiation protein:isoleucyl-tRNA synthetase|POSITIVE:POSITIVE|[1536929,1537179]|251 HSP 1 e-value: 9.0E-77 bit: 287.0 Len: 145 Query Start:107 Query End:251 Subject Strand: POSITIVE Subject Start: 107 Subject End: 251 ..........................................................................................................tgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc ..........................................................................................................tgaatgaagtaagatttgacgttccccacgttacgggataagaggaaaaaagctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Inter-species Hit: Count: 3 Min: 114 Max: 251 Len: 138 Subject: NC_008533_SPD_1472_SPD_1473|isoleucyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[1490789,1491040]|252 HSP 1 e-value: 4.0E-54 bit: 212.0 Len: 138 Query Start:114 Query End:251 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 139 .................................................................................................................agtaagatttgacgttccccacgttacgggataagaggaaaaaag-ctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc .................................................................................................................agtaagatttgacgttccccacgttacgggataagagggagaaagactaaaactttttccgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Subject: NC_003098_spr1502_spr1503|isoleucyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[1483258,1483400]|143 HSP 1 e-value: 4.0E-54 bit: 212.0 Len: 138 Query Start:114 Query End:251 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 139 .................................................................................................................agtaagatttgacgttccccacgttacgggataagaggaaaaaag-ctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc .................................................................................................................agtaagatttgacgttccccacgttacgggataagagggagaaagactaaaactttttccgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Subject: NC_003028_SP_1659_SP_1660|isoleucyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[1562038,1562180]|143 HSP 1 e-value: 4.0E-54 bit: 212.0 Len: 138 Query Start:114 Query End:251 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 139 .................................................................................................................agtaagatttgacgttccccacgttacgggataagaggaaaaaag-ctgagtcttttttcgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc .................................................................................................................agtaagatttgacgtttcccacgttacgggataagagggagaaagactaaatctttttccgaataaaggtggtaccacgattttcgtcctttttggaagtcgtggtttttaatttgttattatttataaaggagatacc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAGAUUUGACGUUCCCCACGUUACGGGAUAAGAGGAAAAAAGCUGAGUCUUUUUUCGAAUAAAGGUGGUACCACGAUUUUCGUCCUUUUUGGAAGUCGUGGUUUUUAAUUUGUUAUUAUUUAUAAAGGAGAUACC .(((.....((((((.....))))))..((((((...((((((((......)))))))).((((((......(((((((((((((.......)))))))))))))......)))))).))))))..........))). (-31.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAUCUCCUUUAUAAAUAAUAACAAAUUAAAAACCACGACUUCCAAAAAGGACGAAAAUCGUGGUACCACCUUUAUUCGAAAAAAGACUCAGCUUUUUUCCUCUUAUCCCGUAACGUGGGGAACGUCAAAUCUUACU .((.(((((.((((...................((((((((.(((.....))).)....))))))).............((((((((......))))))))..........))))...)))))))............. (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 50 10 126 79 smit:SMT_146|5end_sugar_transport_system_permease_protein_96664..96894_POSITIVE 291 59 11 103 41 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 284 107 69 223 179 smit:SMT_1921|5end_D-alanine-activating_enzyme_1863185..1863415_POSITIVE 281 59 16 137 85 smit:SMT_796|5end_K03734_thiamine_biosynthesis_lipoprotein_704211..704441_POSITIVE 277 110 66 51 5 smit:SMT_1127|5end_transcriptional_regulator,_MarR_family_1061556..1061786_NEGATIVE 275 100 51 153 97 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 273 104 67 215 172 smit:SMT_1230|5end_hypothetical_protein_1191423..1191653_POSITIVE 272 108 66 51 5 smit:SMT_1648|5end_hypothetical_protein_1634024..1634254_POSITIVE 272 108 67 194 141 smit:SMT_1190|5end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1148232..1148462_NEGATIVE 268 102 67 204 172 smit:SMT_2042|5end_K04077_chaperonin_GroEL_(Hsp60)_1953889..1954119_NEGATIVE 268 56 11 56 7 smit:SMT_1426|5end_K03095_SprT-like_protein_1411313..1411543_NEGATIVE 267 60 16 83 37 smit:SMT_2014|5end_tryptophan_synthase_beta_chain_1932471..1932701_POSITIVE 265 52 13 198 148 smit:SMT_1263|5end_hypothetical_protein_1228104..1228334_POSITIVE 265 97 58 78 31 smit:SMT_838|5end_cation_efflux_family_protein_782924..783154_POSITIVE 264 89 47 67 21 smit:SMT_1434|5end_neopullulanase_1419645..1419875_NEGATIVE 260 100 52 205 160 smit:SMT_1084|5end_hypothetical_protein_1021925..1022155_NEGATIVE 254 99 51 140 97 smit:SMT_933|5end_ATP-dependent_RNA_helicase_885631..885861_NEGATIVE 252 106 67 230 184 smit:SMT_1053|5end_ABC_transporter_permease_protein_993671..993901_NEGATIVE 251 110 68 159 121 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 251 109 74 43 4 smit:SMT_1538|5end_two-component_response_regulator_YvqC_1523301..1523531_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 110 66 146 104 smit:SMT_1171|3end_hypothetical_protein_1118222..1118372_NEGATIVE 268 102 67 80 48 smit:SMT_2043|3end_putative_mucus_binding_protein_1954013..1954163_NEGATIVE 268 56 11 69 20 smit:SMT_1427|3end_S1_RNA_binding_domain_protein_1411300..1411450_NEGATIVE 267 60 16 53 7 smit:SMT_2013|3end_alpha-glycerophosphate_oxidase_1932521..1932671_POSITIVE 257 107 64 88 46 smit:SMT_631|3end_glycerate_kinase_537307..537457_POSITIVE 248 96 55 146 104 smit:SMT_234|3end_aminopeptidase_PepS_174151..174301_POSITIVE 245 116 73 69 10 smit:SMT_1024|3end_transcriptional_regulator,_MarR_family_958961..959111_NEGATIVE 240 100 52 105 45 smit:SMT_630|3end_phosphoserine_phosphatase_536183..536333_POSITIVE 239 90 50 80 38 smit:SMT_2053|3end_hypothetical_membrane_associated_protein_1963754..1963904_NEGATIVE 239 60 15 63 17 smit:SMT_865|3end_50S_ribosomal_protein_L1_815022..815172_NEGATIVE 237 104 66 68 10 smit:SMT_866|3end_50S_ribosomal_protein_L11_815809..815959_NEGATIVE 235 89 47 74 33 smit:SMT_1523|3end_ferrochelatase_1503390..1503540_NEGATIVE 235 49 20 68 38 smit:SMT_148|3end_glycoprotein_endopeptidase_98601..98751_POSITIVE 232 104 66 111 72 smit:SMT_75|3end_hypothetical_protein_2754..2904_POSITIVE 230 48 2 69 18 smit:SMT_329|3end_hypothetical_protein_265883..266033_POSITIVE 229 102 62 58 6 smit:SMT_2052|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1960662..1960812_NEGATIVE 229 105 64 44 5 smit:SMT_1989|3end_multimodular_transpeptidase-transglycosylase_1917119..1917269_NEGATIVE 227 110 66 148 110 smit:SMT_1244|3end_putative_repressor_protein_1205149..1205299_POSITIVE 226 105 66 71 21 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 226 80 46 120 77 smit:SMT_473|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_409634..409784_NEGATIVE