Origin IGS: gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tggatggaagtcatttcttaggaagcggccctcggccgcttttttaagagttgagacaaagtcattttgtctcagtaaagcttgctactagataaactagcaagttttattgaaataaaataagactctgaaaggaagagcac Mask Tandem Repeat Region ================================================ gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca Find is-nt database================================================ Query_seq: SMT_1452:SMT_1453|SMT_1452:SMT_1453:ABC-type uncharacterized transport system, ATPase component:K07335 basic membrane protein A and related proteins:<-<-:1436302..1436444 143 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1452:SMT_1453|SMT_1452:SMT_1453:ABC-type uncharacterized transport system, ATPase component:K07335 basic membrane protein A and related proteins:<-<-:1436302..1436444 143 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1452:SMT_1453|SMT_1452:SMT_1453:ABC-type uncharacterized transport system, ATPase component:K07335 basic membrane protein A and related proteins:<-<-:1436302..1436444 143 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca Predict ORF larger than 30AA ================================================ gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca 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================================================ gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -4.3 Tail_Score: -2.73529 Start: 24 End: 79 Full_Region: CCTTTCAGAGTCTTA TTTTATTTCAATAAAACTTGCTAGT TTATCT AGTAGCAAGCTTTACTGAGACAAAA TGACTTTGTCTCAAC .......................TTTTATTTCAATAAAACTTGCTAGTTTATCTAGTAGCAAGCTTTACTGAGACAAAA................................................................ TransTerm Strand: + Conf: 42 HP_score: -2.3 Tail_Score: -3.01712 Start: 68 End: 94 Full_Region: CTAGTAGCAAGCTTT ACTGAGACAAA ATGAC TTTGTCTCAAC TCTTAAAAAAGCGGC ...................................................................ACTGAGACAAAATGACTTTGTCTCAAC................................................. TransTerm Strand: + Conf: 91 HP_score: -12.8 Tail_Score: -3.14931 Start: 105 End: 119 Full_Region: TCAACTCTTAAAAAA GCGGCC GAG GGCCGC TTCCTAAGAAATGAC ........................................................................................................GCGGCCGAGGGCCGC........................ Find igs database================================================ Query_seq: SMT_1452:SMT_1453|SMT_1452:SMT_1453:ABC-type uncharacterized transport system, ATPase component:K07335 basic membrane protein A and related proteins:<-<-:1436302..1436444 143 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca Intra-Species Hit: Count: 1 Min: 1 Max: 143 Len: 143 Subject: smit_SMT_1452_SMT_1453|ABC-type uncharacterized transport system, ATPase component:K07335 basic membrane protein A and related proteins|NEGATIVE:NEGATIVE|[1436302,1436444]|143 HSP 1 e-value: 8.0E-76 bit: 283.0 Len: 143 Query Start:1 Query End:143 Subject Strand: POSITIVE Subject Start: 1 Subject End: 143 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca Inter-species Hit: Count: 3 Min: 1 Max: 143 Len: 143 Subject: NC_008533_SPD_0739_SPD_0740|probable membrane lipoprotein TmpC precursor:sugar ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[751478,751620]|143 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 143 Query Start:1 Query End:143 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 143 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttgtctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggcccttggccgcttcctaagaaatgacttccatcca Subject: NC_003098_spr0747_spr0748|hypothetical protein:ABC transporter ATP-binding protein - ribose/galactose transport|POSITIVE:POSITIVE|[743947,744089]|143 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 143 Query Start:1 Query End:143 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 143 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttgtctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggcccttggccgcttcctaagaaatgacttccatcca Subject: NC_003028_SP_0845_SP_0846|lipoprotein:sugar ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[792473,792615]|143 HSP 1 e-value: 7.0E-64 bit: 244.0 Len: 143 Query Start:1 Query End:143 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 143 gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttatctagtagcaagctttactgagacaaaatgactttgtctcaactcttaaaaaagcggccgagggccgcttcctaagaaatgacttccatcca gtgctcttcctttcagagtcttattttatttcaataaaacttgctagtttgtctagtagcaagctttacttagacaaaatgactttgtctcaactcttaaaaaagcggcccttggccgcttcctaagaaatgacttccatcca Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCUCUUCCUUUCAGAGUCUUAUUUUAUUUCAAUAAAACUUGCUAGUUUAUCUAGUAGCAAGCUUUACUGAGACAAAAUGACUUUGUCUCAACUCUUAAAAAAGCGGCCGAGGGCCGCUUCCUAAGAAAUGACUUCCAUCCA .............(((((((..(((((.(((((.((((.(((((((.(......).))))))).)))).))))).))))))))))))..(((..(((((...((((((((...))))))))..)))))..))).......... (-42.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAUGGAAGUCAUUUCUUAGGAAGCGGCCCUCGGCCGCUUUUUUAAGAGUUGAGACAAAGUCAUUUUGUCUCAGUAAAGCUUGCUACUAGAUAAACUAGCAAGUUUUAUUGAAAUAAAAUAAGACUCUGAAAGGAAGAGCAC ..........(((.((((((((((((((((...)))))).)))))))))).)))..((.(((((((((((.((((((((((((((((..........)))))))))))))))).)))))))..)))).))............. (-50.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 964 140 91 231 182 smit:SMT_1452|5end_ABC-type_uncharacterized_transport_system,_ATPase_component_1436211..1436441_NEGATIVE 302 136 102 79 39 smit:SMT_274|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_215221..215451_POSITIVE 296 119 79 191 150 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 290 125 83 200 162 smit:SMT_1535|5end_exodeoxyribonuclease_V_alpha_chain_1518067..1518297_POSITIVE 286 125 93 66 29 smit:SMT_1213|5end_fatty_acid/phospholipid_synthesis_protein_PlsX_1172655..1172885_NEGATIVE 284 137 104 100 70 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 278 128 81 50 1 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 276 123 83 144 101 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 276 139 105 231 189 smit:SMT_555|5end_K09015_Fe-S_cluster_assembly_protein_SufD_472271..472501_POSITIVE 274 140 102 52 7 smit:SMT_1302|5end_hypothetical_protein_1263883..1264113_POSITIVE 268 136 104 226 186 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 267 119 80 150 103 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 265 125 83 182 144 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 265 125 83 182 144 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 265 125 83 182 144 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 264 140 105 91 41 smit:SMT_416|5end_ribonuclease_Z_359423..359653_POSITIVE 263 140 105 201 155 smit:SMT_1291|5end_hypothetical_protein_1253875..1254105_POSITIVE 263 139 104 50 10 smit:SMT_653|5end_positive_transcriptional_regulator_MutR_family_564155..564385_NEGATIVE 262 140 91 91 30 smit:SMT_1416|5end_hypothetical_protein_1400829..1401059_NEGATIVE 259 120 94 128 102 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 125 93 69 32 smit:SMT_1214|3end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1172652..1172802_NEGATIVE 284 137 104 67 37 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 276 123 83 142 99 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 269 139 104 143 112 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 265 125 83 67 29 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 265 125 103 132 113 smit:SMT_2092|3end_malolactic_enzyme_1987040..1987190_NEGATIVE 265 125 83 67 29 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 265 125 83 67 29 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 264 140 105 76 26 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE 263 139 104 48 8 smit:SMT_654|3end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_564157..564307_NEGATIVE 262 140 91 94 33 smit:SMT_1417|3end_spermidine_synthase_1400826..1400976_NEGATIVE 259 120 94 128 102 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 259 120 94 128 102 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 254 125 83 60 8 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE 251 125 81 64 1 smit:SMT_951|3end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_898995..899145_NEGATIVE 251 133 98 47 7 smit:SMT_411|3end_thymidylate_synthase_356415..356565_POSITIVE 250 125 104 64 42 smit:SMT_1075|3end_hypothetical_protein_1013870..1014020_POSITIVE 248 139 91 107 55 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 239 121 87 50 12 smit:SMT_1992|3end_carboxynorspermidine_decarboxylase_1918557..1918707_NEGATIVE 236 124 83 85 42 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE