Origin IGS: ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tattttgaaaagccaccgaaaaaggaattactctttaaggtggcttttatagaagtaaagtttaggctagaaaaacaagaaataacgcaccatttttggtgcgttttgcttttttatgctataatggatttataaaaataaaggagtttgcc Mask Tandem Repeat Region ================================================ ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata Find is-nt database================================================ Query_seq: SMT_737:SMT_738|SMT_737:SMT_738:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-<-:642837..642988 152 ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_737:SMT_738|SMT_737:SMT_738:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-<-:642837..642988 152 ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_737:SMT_738|SMT_737:SMT_738:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-<-:642837..642988 152 ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 21 End: 113 .................... L D M I A Y F L L V C W F H H T I E Q K E L R F K V E I F A M ....................................... ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata 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================================================ ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -6.0 Tail_Score: -4.85599 Start: 41 End: 77 Full_Region: CCATTATAGCATAAA AAAGCAAAACGCACCA AAAA TGGTGCGTTATTTCTTG TTTTTCTAGCCTAAA ........................................AAAGCAAAACGCACCAAAAATGGTGCGTTATTTCTTG........................................................................... TransTerm Strand: - Conf: 95 HP_score: -7.7 Tail_Score: -5.34555 Start: 44 End: 74 Full_Region: aggctagaaaaacaa gaaataacgcacca tttt tggtgcgttttgc ttttttatgctataa ...........................................gaaataacgcaccatttttggtgcgttttgc.............................................................................. TransTerm Strand: + Conf: 100 HP_score: -9.6 Tail_Score: -4.80417 Start: 47 End: 70 Full_Region: TAGCATAAAAAAGCA AAACGCACCA AAAA TGGTGCGTTA TTTCTTGTTTTTCTA ..............................................AAACGCACCAAAAATGGTGCGTTA.................................................................................. TransTerm Strand: - Conf: 100 HP_score: -11.3 Tail_Score: -4.90477 Start: 50 End: 67 Full_Region: aaaaacaagaaataa cgcacca tttt tggtgcg ttttgcttttttatg .................................................cgcaccatttttggtgcg..................................................................................... Find igs database================================================ Query_seq: SMT_737:SMT_738|SMT_737:SMT_738:hypothetical protein:hypothetical protein predicted by Glimmer/Critica:<-<-:642837..642988 152 ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: smit_SMT_737_SMT_738|hypothetical protein:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:NEGATIVE|[642837,642988]|152 HSP 1 e-value: 3.0E-81 bit: 301.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata ggcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccaccttaaagagtaattcctttttcggtggcttttcaaaata Inter-species Hit: Count: 2 Min: 2 Max: 115 Len: 114 Subject: NC_003028_SP_1049_SP_1050|hypothetical protein:transcriptional regulator, putative|POSITIVE:POSITIVE|[987861,988051]|191 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 114 Query Start:2 Query End:115 Subject Strand: NEGATIVE Subject Start: 77 Subject End: 190 .gcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccacct..................................... .gcaaactcctttatttttataaatccattatagcataaaaaagcataacgcaccaaaaatggtgcgttatttcttgtttttctatcctaaactttacttctataaaagtcacct..................................... Subject: NC_008533_SPD_0929_SPD_0930|hypothetical protein:transcriptional regulator, putative|POSITIVE:POSITIVE|[941970,942413]|444 HSP 1 e-value: 6.0E-49 bit: 194.0 Len: 114 Query Start:2 Query End:115 Subject Strand: NEGATIVE Subject Start: 330 Subject End: 443 .gcaaactcctttatttttataaatccattatagcataaaaaagcaaaacgcaccaaaaatggtgcgttatttcttgtttttctagcctaaactttacttctataaaagccacct..................................... .gcaaactcctttatttttataaatccattatagcataaaaaagcataacgcaccaaaaatggtgcgttatttcttgtgtttctatcctaaactttacttctataaaagtcacct..................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAACUCCUUUAUUUUUAUAAAUCCAUUAUAGCAUAAAAAAGCAAAACGCACCAAAAAUGGUGCGUUAUUUCUUGUUUUUCUAGCCUAAACUUUACUUCUAUAAAAGCCACCU ((.......(((((....))))).........((.((.(((((((((((((((((....))))))))).....)))))))).)))).....................))..... (-20.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGGCUUUUAUAGAAGUAAAGUUUAGGCUAGAAAAACAAGAAAUAACGCACCAUUUUUGGUGCGUUUUGCUUUUUUAUGCUAUAAUGGAUUUAUAAAAAUAAAGGAGUUUGC ...((((((..((.........))..))))))..............(((((((((....)))))))))..((((((((((..(((((.....)))))...)))))))))).... (-26.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 822 90 41 182 133 smit:SMT_737|5end_hypothetical_protein_642746..642976_NEGATIVE 260 37 5 126 97 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 253 110 62 141 94 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 243 88 61 186 154 smit:SMT_2083|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1982411..1982641_POSITIVE 238 43 3 142 95 smit:SMT_1633|5end_formate--tetrahydrofolate_ligase_1619240..1619470_POSITIVE 238 88 48 227 182 smit:SMT_1117|5end_competence_protein_CglA_1054703..1054933_NEGATIVE 236 110 61 123 56 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 232 87 52 228 192 smit:SMT_395|5end_hypothetical_protein_324459..324689_POSITIVE 228 68 25 84 36 smit:SMT_1994|5end_phosphoglycerate_mutase_1920501..1920731_NEGATIVE 228 89 42 121 65 smit:SMT_1830|5end_galactose-6-phosphate_isomerase_1799338..1799568_POSITIVE 227 88 41 231 179 smit:SMT_358|5end_hypothetical_protein_293947..294177_POSITIVE 226 88 60 38 3 smit:SMT_394|5end_K07729_putative_transcriptional_regulator_324260..324490_POSITIVE 222 96 60 212 165 smit:SMT_1227|5end_site-specific_recombinase,_phage_integrase_family_1190465..1190695_NEGATIVE 219 97 51 45 4 smit:SMT_540|5end_DNA_gyrase,_B_subunit_456358..456588_POSITIVE 218 99 53 60 12 smit:SMT_994|5end_nicotinate-nucleotide_adenylyltransferase_936105..936335_NEGATIVE 218 56 27 148 120 smit:SMT_591|5end_K02029_polar_amino_acid_transport_system_permease_protein_508108..508338_POSITIVE 215 66 42 37 15 smit:SMT_897|5end_serine_O-acetyltransferase_844632..844862_NEGATIVE 213 99 51 56 1 smit:SMT_1496|5end_conserved_hypothetical_protein_TIGR00150_1480999..1481229_POSITIVE 210 100 53 216 163 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 210 88 43 53 10 smit:SMT_767|5end_hypothetical_protein_676454..676684_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 37 5 65 36 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 247 80 32 92 47 smit:SMT_142|3end_hypothetical_protein_93409..93559_NEGATIVE 238 88 48 151 106 smit:SMT_1118|3end_hypothetical_protein_1054779..1054929_NEGATIVE 228 68 25 50 2 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 227 88 41 104 52 smit:SMT_357|3end_tRNA_(guanine-N7-)-methyltransferase_293900..294050_POSITIVE 225 88 42 49 11 smit:SMT_120|3end_hypothetical_protein_72943..73093_POSITIVE 217 92 52 141 99 smit:SMT_1597|3end_K02032_peptide/nickel_transport_system_ATP-binding_protein_1587987..1588137_POSITIVE 217 63 39 29 2 smit:SMT_1449|3end_K08591_putative_membrane_protein_1432658..1432808_POSITIVE 217 106 61 102 54 smit:SMT_1052|3end_hypothetical_protein_predicted_by_Glimmer/Critica_992554..992704_POSITIVE 212 86 46 132 100 smit:SMT_1530|3end_K07456_DNA_mismatch_repair_protein_MutS2_1513010..1513160_NEGATIVE 210 99 51 96 40 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 210 88 43 56 13 smit:SMT_768|3end_hypothetical_protein_676451..676601_NEGATIVE 204 110 67 141 95 smit:SMT_830|3end_hypothetical_protein_765064..765214_NEGATIVE 203 88 51 55 21 smit:SMT_147|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_98016..98166_POSITIVE 198 88 50 52 6 smit:SMT_986|3end_threonyl-tRNA_synthetase_931684..931834_POSITIVE 197 77 34 79 46 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 197 88 59 110 82 smit:SMT_263|3end_hypothetical_protein_predicted_by_Glimmer/Critica_202379..202529_NEGATIVE 196 101 61 56 14 smit:SMT_1243|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1204469..1204619_POSITIVE 195 98 51 82 26 smit:SMT_159|3end_hypothetical_protein_104615..104765_POSITIVE 190 88 41 76 23 smit:SMT_589|3end_hypothetical_protein_506827..506977_POSITIVE