Origin IGS: gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt .........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 aaaaaaactccttttttaaagaaaagtggggtattcaatgtgagctacctaaatgctttgtatcatcttcatccagtttcgtaaaagaaaaaactctaattacagataggaattagagttcagcttacaagattagatggttagtttctataaatacaaaaccatttcacatttcccttcgccagtcttaactgtatcaggttcaatgggtatcatctcagcctaaagcaccccaaatgtctttattatttaattatataaatattataacaaacgattttttccagttcaagaaattgaactggaaatacagcagatctttctttggttagatcgatac Mask Tandem Repeat Region ================================================ gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt Find is-nt database================================================ Query_seq: SMT_444:SMT_445|SMT_444:SMT_445:thiamine-phosphate pyrophosphorylase:hypothetical protein:->->:384109..384448 340 gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_444:SMT_445|SMT_444:SMT_445:thiamine-phosphate pyrophosphorylase:hypothetical protein:->->:384109..384448 340 gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_444:SMT_445|SMT_444:SMT_445:thiamine-phosphate pyrophosphorylase:hypothetical protein:->->:384109..384448 340 gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M D L T K E R S A V F P V Q F L E L E K I V C Y N I Y I I K ........................................................................................................................................................................................................................................................ Protein_Len: 35 Strand: - Start: 83 End: 187 .................................................................................. I I L Y Y L C K P H K L S L H Y G N F R I C N L S A F P F T F H N Q M ......................................................................................................................................................... Protein_Len: 46 Strand: - Start: 12 End: 149 ........... G F F S R S Y K W N L K K F Q F F D N T I I N I Y N F L L S M Q P A K P Q S S V W Q V Q Y M ............................................................................................................................................................................................... gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt 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: 48 End: 77 ...............................................CTTGAACTGGAAAAAATCGTTTGTTATAAT....................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 125 End: 154 ............................................................................................................................CTTAACTGTATCAGGTTCAATGGGTATCAT.......................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 67 End: 96 ..................................................................TTTGTTATAATATTTATATAATTAAATAAT.................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -8.3 Tail_Score: -3.16079 Start: 30 End: 63 Full_Region: AAAGAAAGATCTGCT GTATTTCCAGTTCAA TTTC TTGAACTGGAAAAAA TCGTTTGTTATAATA .............................GTATTTCCAGTTCAATTTCTTGAACTGGAAAAAA..................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 95 HP_score: -5.8 Tail_Score: -5.79595 Start: 223 End: 247 Full_Region: ATCTTGTAAGCTGAA CTCTAATTCC TATCT GTAATTAGAG TTTTTTCTTTTACGA ..............................................................................................................................................................................................................................CTCTAATTCCTATCTGTAATTAGAG............................................................................................. Find igs database================================================ Query_seq: SMT_444:SMT_445|SMT_444:SMT_445:thiamine-phosphate pyrophosphorylase:hypothetical protein:->->:384109..384448 340 gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggagttttttt Intra-Species Hit: Count: 2 Min: 1 Max: 333 Len: 333 Subject: smit_SMT_444_SMT_445|thiamine-phosphate pyrophosphorylase:hypothetical protein|POSITIVE:POSITIVE|[384109,384448]|340 HSP 1 e-value: 0.0 bit: 660.0 Len: 333 Query Start:1 Query End:333 Subject Strand: POSITIVE Subject Start: 1 Subject End: 333 gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggag....... gtatcgatctaaccaaagaaagatctgctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgatacaaagcatttaggtagctcacattgaataccccacttttctttaaaaaaggag....... Subject: smit_SMT_441_SMT_442|L-lactate oxidase:transcriptional regulator, putative|POSITIVE:POSITIVE|[381340,381791]|452 HSP 1 e-value: 1.0E-54 bit: 214.0 Len: 215 Query Start:85 Query End:299 Subject Strand: POSITIVE Subject Start: 138 Subject End: 353 ....................................................................................taattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgtatttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttctttta-cgaaactggatgaagatgatacaaagcatttaggtagctc......................................... ....................................................................................taattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaacgttttttcgtatggcgaaatgaacaatctaatcttgtaagctaaactctaattcttgattgtaattggagtttttttgtttatataagctgaatgaaggtgatacaaagcatttaggtagctc......................................... Inter-species Hit: Count: 3 Min: 27 Max: 280 Len: 254 Subject: NC_008533_SPD_0624_SPD_0625|thiamine-phosphate pyrophosphorylase:hypothetical protein|POSITIVE:POSITIVE|[646558,647114]|557 HSP 1 e-value: 9.0E-90 bit: 331.0 Len: 254 Query Start:27 Query End:280 Subject Strand: POSITIVE Subject Start: 140 Subject End: 394 ..........................gctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgt-atttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgata............................................................ ..........................gctgtatttccagttcaatttcttgaactagtataaaatgtgtgttataataatcacataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatgtttttttcgtatgtcgaaaagaactgtctaatcttgtaagctgaactctaattcgtatctgtaattagagttttttcttttacgaaactggatgaagatgata............................................................ Subject: NC_003098_spr0630_spr0631|Thiamin-phosphate pyrophosphorylase:hypothetical protein|POSITIVE:POSITIVE|[639027,639550]|524 HSP 1 e-value: 9.0E-90 bit: 331.0 Len: 254 Query Start:27 Query End:280 Subject Strand: POSITIVE Subject Start: 140 Subject End: 394 ..........................gctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgt-atttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgata............................................................ ..........................gctgtatttccagttcaatttcttgaactagtataaaatgtgtgttataataatcacataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatgtttttttcgtatgtcgaaaagaactgtctaatcttgtaagctgaactctaattcgtatctgtaattagagttttttcttttacgaaactggatgaagatgata............................................................ Subject: NC_003028_SP_0718_SP_0719|thiamine-phosphate pyrophosphorylase:hypothetical protein|POSITIVE:POSITIVE|[684442,684999]|558 HSP 1 e-value: 2.0E-87 bit: 323.0 Len: 254 Query Start:27 Query End:280 Subject Strand: POSITIVE Subject Start: 140 Subject End: 394 ..........................gctgtatttccagttcaatttcttgaactggaaaaaatcgtttgttataatatttatataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatggttttgt-atttatagaaactaaccatctaatcttgtaagctgaactctaattcctatctgtaattagagttttttcttttacgaaactggatgaagatgata............................................................ ..........................gctgtatttccagttcaatttcttgaactagtataaaatgtgtgttataataatcacataattaaataataaagacatttggggtgctttaggctgagatgatacccattgaacctgatacagttaagactggcgaagggaaatgtgaaatgtttttttcgtatgtcgaaaagaactgtctaatcttgtaagctgaactctaatttgtatctgtaattagagttttttcttttacgaaactggatgaagatgata............................................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGUAUUUCCAGUUCAAUUUCUUGAACUGGAAAAAAUCGUUUGUUAUAAUAUUUAUAUAAUUAAAUAAUAAAGACAUUUGGGGUGCUUUAGGCUGAGAUGAUACCCAUUGAACCUGAUACAGUUAAGACUGGCGAAGGGAAAUGUGAAAUGGUUUUGUAUUUAUAGAAACUAACCAUCUAAUCUUGUAAGCUGAACUCUAAUUCCUAUCUGUAAUUAGAGUUUUUUCUUUUACGAAACUGGAUGAAGAUGAUA ......((((((((((((....))))))))))))..(((((((.......((((((......)))))).......((((..(...((((((((...(((((...(.((((...(((....((((....))))....)))..)))).)...(((((((.........)))))))..)))))...)))).)))).(((((((((((.(.....).)))))))))))..............)..)))).))))))). (-63.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCAUCUUCAUCCAGUUUCGUAAAAGAAAAAACUCUAAUUACAGAUAGGAAUUAGAGUUCAGCUUACAAGAUUAGAUGGUUAGUUUCUAUAAAUACAAAACCAUUUCACAUUUCCCUUCGCCAGUCUUAACUGUAUCAGGUUCAAUGGGUAUCAUCUCAGCCUAAAGCACCCCAAAUGUCUUUAUUAUUUAAUUAUAUAAAUAUUAUAACAAACGAUUUUUUCCAGUUCAAGAAAUUGAACUGGAAAUACAGC ..................((((.(((((...((((((((((.(.....).))))))))))..((((..((((((((((((((.................))))))))................)))))).........((((....((((......)))))))).))))..........)))))..((((((......)))))).........))))...((((((((((((....))))))))))))...... (-48.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 140 93 72 3 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 285 138 91 196 148 smit:SMT_125|5end_hypothetical_protein_77664..77894_NEGATIVE 278 119 78 210 162 smit:SMT_2064|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1972182..1972412_POSITIVE 271 140 91 101 54 smit:SMT_1994|5end_phosphoglycerate_mutase_1920501..1920731_NEGATIVE 270 147 108 63 21 smit:SMT_1999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1922792..1923022_NEGATIVE 270 147 108 63 21 smit:SMT_1665|5end_cell_wall_surface_anchor_family_protein_1656335..1656565_NEGATIVE 269 140 93 192 134 smit:SMT_923|5end_methionyl-tRNA_formyltransferase_877494..877724_NEGATIVE 269 129 81 84 22 smit:SMT_472|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_409494..409724_NEGATIVE 269 129 81 84 22 smit:SMT_469|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_405812..406042_NEGATIVE 264 148 105 50 9 smit:SMT_2082|5end_ATP-dependent_nuclease_subunit_B_1982286..1982516_NEGATIVE 262 136 91 91 48 smit:SMT_1828|5end_PTS_system,_galactose-specific_IIC_component_1797668..1797898_POSITIVE 262 157 120 119 84 smit:SMT_535|5end_hypothetical_protein_454215..454445_POSITIVE 260 140 91 216 150 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 260 156 111 205 164 smit:SMT_961|5end_K02016_iron_complex_transport_system_substrate-binding_protein_907809..908039_NEGATIVE 259 129 85 129 94 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 259 180 131 93 37 smit:SMT_1343|5end_O-methyltransferase_1320994..1321224_NEGATIVE 257 138 91 193 147 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 255 214 172 165 127 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 253 139 91 169 114 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 252 118 81 229 184 smit:SMT_890|5end_K02029_polar_amino_acid_transport_system_permease_protein_836953..837183_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 126 82 58 18 smit:SMT_2004|3end_K00783_hypothetical_protein_1925489..1925639_POSITIVE 290 140 93 114 45 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 290 126 82 58 18 smit:SMT_86|3end_K00783_hypothetical_protein_17035..17185_NEGATIVE 271 140 91 67 20 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 264 34 7 58 31 smit:SMT_444|3end_thiamine-phosphate_pyrophosphorylase_384048..384198_POSITIVE 262 136 91 65 22 smit:SMT_1827|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1797722..1797872_POSITIVE 260 137 92 141 103 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE 259 180 131 91 35 smit:SMT_1344|3end_oligoendopeptidase_F_1320996..1321146_NEGATIVE 247 118 72 67 2 smit:SMT_1662|3end_histidine_protein_kinase_1651305..1651455_NEGATIVE 245 160 121 149 109 smit:SMT_702|3end_hypothetical_protein_611946..612096_NEGATIVE 243 117 73 58 26 smit:SMT_609|3end_laminin-binding_surface_protein_521731..521881_POSITIVE 242 134 92 62 23 smit:SMT_1929|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1869690..1869840_NEGATIVE 239 39 1 77 30 smit:SMT_2091|3end_hypothetical_protein_1987037..1987187_POSITIVE 239 116 71 89 37 smit:SMT_889|3end_K02029_polar_amino_acid_transport_system_permease_protein_837023..837173_POSITIVE 239 116 78 137 90 smit:SMT_872|3end_hypothetical_protein_820331..820481_NEGATIVE 239 116 78 137 90 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 238 118 73 61 19 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE 234 140 91 67 18 smit:SMT_2008|3end_K07485_transposase_1928165..1928315_NEGATIVE 234 127 81 146 107 smit:SMT_1067|3end_alanine_racemase_1006952..1007102_POSITIVE 234 221 182 67 35 smit:SMT_1027|3end_K02026_multiple_sugar_transport_system_permease_protein_962641..962791_NEGATIVE