Origin IGS: ctctactcctgactaagatacaaaggacgatagctgcccttgaaaaatagggaatgacgctgactttccatgaaaggcaagacaggcatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcacagagggttccaggcgtgttcaattatcaagatacaaagggccttagctgcccgtgaaaaataggggatggcgctgactttccacaaaaggcaagacagacatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaagccttcttaactagtctagaagtgctaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttagcacttctagactagttaagaaggcttgtatcttagaaattgaacacggactacctgcctcttgaaaaaagatgtctgtcttgccttttgtggaaagtcagcgccatcccctatttttcacgggcagctaaggccctttgtatcttgataattgaacacgcctggaaccctctgtgaaaaagataggtcttccaaggagtatttactccttgatcagaactcctattttcacgttgtgctcttacaggctttgtatcttagaaattgaacacggactacctgcctcttgaaaaaagatgcctgtcttgcctttcatggaaagtcagcgtcattccctatttttcaagggcagctatcgtcctttgtatcttagtcaggagtagag Mask Tandem Repeat Region ================================================ ctctactcctgactaagatacaaaggacgatagctgcccttgaaaaatagggaatgacgctgactttccatgaaaggcaagacaggcatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcacagagggttccaggcgtgttcaattatcaagatacaaagggccttagctgcccgtgaaaaataggggatggcgctgactttccacaaaaggcaagacagacatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaagccttcttaactagtctagaagtgctaa Find is-nt database================================================ Query_seq: SMT_841:SMT_842|SMT_841:SMT_842:dihydrodipicolinate reductase:hypothetical protein:<-<-:788116..788503 388 ctctactcctgactaagatacaaaggacgatagctgcccttgaaaaatagggaatgacgctgactttccatgaaaggcaagacaggcatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcacagagggttccaggcgtgttcaattatcaagatacaaagggccttagctgcccgtgaaaaataggggatggcgctgactttccacaaaaggcaagacagacatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaagccttcttaactagtctagaagtgctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_841:SMT_842|SMT_841:SMT_842:dihydrodipicolinate reductase:hypothetical protein:<-<-:788116..788503 388 ctctactcctgactaagatacaaaggacgatagctgcccttgaaaaatagggaatgacgctgactttccatgaaaggcaagacaggcatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcacagagggttccaggcgtgttcaattatcaagatacaaagggccttagctgcccgtgaaaaataggggatggcgctgactttccacaaaaggcaagacagacatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaagccttcttaactagtctagaagtgctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_841:SMT_842|SMT_841:SMT_842:dihydrodipicolinate reductase:hypothetical protein:<-<-:788116..788503 388 ctctactcctgactaagatacaaaggacgatagctgcccttgaaaaatagggaatgacgctgactttccatgaaaggcaagacaggcatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcacagagggttccaggcgtgttcaattatcaagatacaaagggccttagctgcccgtgaaaaataggggatggcgctgactttccacaaaaggcaagacagacatcttttttcaagaggcaggtagtccgtgttcaatttctaagatacaagccttcttaactagtctagaagtgctaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 11 Max: 346 Len: 336 Subject: UniRef90_Q97PP7 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 1.0E-17 bit: 90.9 Len: 135 Query Start:212 Query End:346 Subject Strand: null Subject Start: 1 Subject End: 45 ................................................................................................................................................................................................................... L N T D Y L P L E K R C L S C L L W K V S A I P Y F S R A A K A L C I L I I E H A W N P L .......................................... ................................................................................................................................................................................................................... M N T D Y L P L E K R C L S C L S W K V S A I P Y F S E A A K V L C I L I I E H A W N P V .......................................... HSP 2 e-value: 6.0E-12 bit: 72.0 Len: 111 Query Start:11 Query End:121 Subject Strand: null Subject Start: 1 Subject End: 37 .......... L N T D Y L P L E K R C L S C L S W K V S V I P Y F S R A A I V L C I L V ........................................................................................................................................................................................................................................................................... .......... M N T D Y L P L E K R C L S C L S W K V S A I P Y F S E A A K V L C I L I ........................................................................................................................................................................................................................................................................... ctctactcctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttctaagatacaagccttcttaactagtctagaagtgctaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 272 End: 367 ............................................................................................................................................................................................................................................................................... M G D G A D F P Q K A R Q T S F F K R Q V V R V Q F L R Y K P S ..................... Protein_Len: 45 Strand: - Start: 212 End: 346 ................................................................................................................................................................................................................... L P N W A H E I I L I C L A K A A R S F Y P I A S V K W L L C S L C R K E L P L Y D T N M .......................................... Protein_Len: 38 Strand: - Start: 121 End: 234 ........................................................................................................................ N R L Y L A Q L L V V H F Y S N Q D L L L Y E K S S R D K E C L T G P T N M .......................................................................................................................................................... Protein_Len: 42 Strand: - Start: 99 End: 224 .................................................................................................. S A P L G H E I E L I C L R Y S C L T F I P T R I L S Y I S R P L G I K K V S P E M .................................................................................................................................................................... Protein_Len: 40 Strand: - Start: 2 End: 121 . R S R V L I C L V I A A R S F Y P I V S V K W S L C S L C R K E L P L Y D T N M ........................................................................................................................................................................................................................................................................... ctctactcctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttctaagatacaagccttcttaactagtctagaagtgctaa 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================================================ ctctactcctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttctaagatacaagccttcttaactagtctagaagtgctaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_841:SMT_842|SMT_841:SMT_842:dihydrodipicolinate reductase:hypothetical protein:<-<-:788116..788503 388 ctctactcctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttctaagatacaagccttcttaactagtctagaagtgctaa Intra-Species Hit: Count: 1 Min: 122 Max: 388 Len: 267 Subject: smit_SMT_841_SMT_842|dihydrodipicolinate reductase:hypothetical protein|NEGATIVE:NEGATIVE|[788116,788503]|388 HSP 1 e-value: 9.0E-44 bit: 178.0 Len: 90 Query Start:122 Query End:211 Subject Strand: POSITIVE Subject Start: 122 Subject End: 211 .........................................................................................................................tttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttca................................................................................................................................................................................. .........................................................................................................................tttctaagatacaaagcctgtaagagcacaacgtgaaaataggagttctgatcaaggagtaaatactccttggaagacctatctttttca................................................................................................................................................................................. HSP 2 e-value: 4.0E-15 bit: 83.8 Len: 42 Query Start:347 Query End:388 Subject Strand: POSITIVE Subject Start: 347 Subject End: 388 ..........................................................................................................................................................................................................................................................................................................................................................tttctaagatacaagccttcttaactagtctagaagtgctaa ..........................................................................................................................................................................................................................................................................................................................................................tttctaagatacaagccttcttaactagtctagaagtgctaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUAAGAUACAAAGCCUGUAAGAGCACAACGUGAAAAUAGGAGUUCUGAUCAAGGAGUAAAUACUCCUUGGAAGACCUAUCUUUUUCACAGAGGGUUCCAGGCGUGUUCAAUUAUCAAGAUACAAAGGGCCUUAGCUGCCCGUGAAAAAUAGGGGAUGGCGCUGACUUUCCACAAAAGGCAAGACAGACAUCUUUUUUCAAGAGGCAGGUAGUCCGUGUUCAAUUUCUAAGAUACAAGCCUUCUUAACUAGUCUAGAAGUGCUAA ..(((.(((......(((((...((((.....(((((((.(((((.(((..(((((((((....))))))))).))).)).)))))))))).....)))))))))...............((.(((..((((..((.((((((.(((((((....(((((...(((.(((.((......)).))).))).)))))))))))).).))))).)))))).)))))....))).)))....((((((((..(....)..))))).))).. (-80.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGCACUUCUAGACUAGUUAAGAAGGCUUGUAUCUUAGAAAUUGAACACGGACUACCUGCCUCUUGAAAAAAGAUGUCUGUCUUGCCUUUUGUGGAAAGUCAGCGCCAUCCCCUAUUUUUCACGGGCAGCUAAGGCCCUUUGUAUCUUGAUAAUUGAACACGCCUGGAACCCUCUGUGAAAAAGAUAGGUCUUCCAAGGAGUAUUUACUCCUUGAUCAGAACUCCUAUUUUCACGUUGUGCUCUUACAGGCUUUGUAUCUUAGAAA ..(((.(((((.((....)).))))))))....(((.(((....(((((.((.((..((((((..(((((((.((((.(((.(((.((......)).))).)))...)))).....))))))).))))))...))..))..))).))...........(((.(((((((.(.(..((((((...((((((..(((((((((((....))))))))....)))..))))))))))))..).).))...)))))..))).))).))).. (-69.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 835 230 181 217 168 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 415 48 8 139 99 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 370 49 5 139 95 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 346 222 182 108 65 smit:SMT_226|5end_putative_L-glutamine-D-fructose-6-phosphate_amidotransferase_163630..163860_POSITIVE 326 106 68 73 30 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 325 166 121 143 96 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 320 47 5 138 96 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 319 161 127 77 38 smit:SMT_1008|5end_hypothetical_protein_948021..948251_NEGATIVE 317 168 122 57 12 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 312 194 154 58 10 smit:SMT_1606|5end_glutamate_racemase_1595857..1596087_POSITIVE 310 139 92 199 154 smit:SMT_110|5end_alpha-L-fucosidase_57445..57675_POSITIVE 309 217 180 44 4 smit:SMT_2171|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2042271..2042501_POSITIVE 309 195 158 174 138 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 308 44 8 167 132 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 308 44 8 39 4 smit:SMT_545|5end_hypothetical_protein_predicted_by_Glimmer/Critica_461249..461479_POSITIVE 304 200 151 222 173 smit:SMT_898|5end_polyribonucleotide_nucleotidyltransferase_846861..847091_NEGATIVE 303 170 128 96 44 smit:SMT_676|5end_DNA_helicase_II_585266..585496_NEGATIVE 302 74 32 229 181 smit:SMT_153|5end_sensor_histidine_kinase,_putative_101443..101673_POSITIVE 295 234 191 146 89 smit:SMT_2089|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_related_enzyme_1984987..1985217_POSITIVE 295 234 191 146 89 smit:SMT_291|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_234197..234427_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 106 68 76 33 smit:SMT_596|3end_K03976_putative_transcription_regulator_512590..512740_NEGATIVE 308 44 8 134 99 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 303 170 128 59 7 smit:SMT_677|3end_DNA_topoisomerase_I_585303..585453_NEGATIVE 295 234 191 145 88 smit:SMT_2088|3end_glucose-1-phosphate_thymidylyltransferase_1985066..1985216_POSITIVE 295 234 191 145 88 smit:SMT_290|3end_glucose-1-phosphate_thymidylyltransferase_234276..234426_POSITIVE 289 110 66 69 20 smit:SMT_665|3end_NAD+_kinase_575927..576077_NEGATIVE 282 230 187 91 36 smit:SMT_1349|3end_K03075_preprotein_translocase_SecG_subunit_1327604..1327754_NEGATIVE 281 216 172 96 45 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 276 224 181 45 5 smit:SMT_849|3end_hypothetical_protein_795150..795300_NEGATIVE 276 249 201 108 55 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 272 230 184 110 66 smit:SMT_1697|3end_hypothetical_protein_1680182..1680332_POSITIVE 270 119 75 73 29 smit:SMT_1821|3end_Mg2+_and_Co2+_transporter_1794515..1794665_POSITIVE 269 170 130 148 98 smit:SMT_833|3end_hypothetical_protein_predicted_by_Glimmer/Critica_775183..775333_NEGATIVE 268 140 91 135 69 smit:SMT_783|3end_K03710_GntR_family_transcriptional_regulator_695389..695539_POSITIVE 268 135 94 81 37 smit:SMT_327|3end_hypothetical_protein_264704..264854_POSITIVE 267 121 82 142 101 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 262 160 130 81 57 smit:SMT_1211|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1171470..1171620_POSITIVE 261 168 123 58 12 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 261 170 124 97 38 smit:SMT_1112|3end_K02248_competence_protein_ComGF_1051387..1051537_NEGATIVE 258 226 182 48 4 smit:SMT_1732|3end_transcriptional_repressor_protein,_putative_1716962..1717112_POSITIVE