Origin IGS: ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact .........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 agtccgatgaactttattcgcctgagccctgaattataaaagagaagaaaatttcagttgatgttattcacctgagcttggaaataggagactgaggcaaatcttggataaaccgattatcttgataatagccataattttctttattggtcttacaaatttggttttatacctattctatcgacgggagaagaatattcagaaaaaatgtacttctaaaattgaaggtcttgtggttgattatgacaaccgtaatgaaatggctatccctttgcctgttgtagaatatctcgtgaatgggacaatatacagaaaaaaattgaatatccttattatgtagaaactcctaggaagaaagagcaaaagggtgtctttgacaggaaatatattcttggtgctggaaataatttacagttaagagaaatatttccaaaaggctcggcc Mask Tandem Repeat Region ================================================ ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact Find is-nt database================================================ Query_seq: SSA_1317:SSA_1318|SSA_1317:SSA_1318:hypothetical protein:GTP-binding protein lepA, putative:<-<-:1333635..1334078 444 ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1317:SSA_1318|SSA_1317:SSA_1318:hypothetical protein:GTP-binding protein lepA, putative:<-<-:1333635..1334078 444 ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1317:SSA_1318|SSA_1317:SSA_1318:hypothetical protein:GTP-binding protein lepA, putative:<-<-:1333635..1334078 444 ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 20 End: 109 ................... M S L N C K L F P A P R I Y F L S K T P F C S F F L G V S T ............................................................................................................................................................................................................................................................................................................................................... Protein_Len: 55 Strand: + Start: 37 End: 201 .................................... M I S S T K N I F P V K D T L L L F L P R S F Y I I R I F N F F L Y I V P F T R Y S T T G K G I A I S L R L S ................................................................................................................................................................................................................................................... Protein_Len: 50 Strand: + Start: 120 End: 269 ....................................................................................................................... M Q F F S V Y C P I H E I F Y N R Q R D S H F I T V V I I N H K T F N F R S T F F L N I L L P S I E ............................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 285 End: 374 ............................................................................................................................................................................................................................................................................................ M C K T N K E N Y G Y Y Q D N R F I Q D L P Q S P I S K L R ...................................................................... Protein_Len: 45 Strand: - Start: 164 End: 298 ................................................................................................................................................................... L L C L S L W K M V T T M I L W L V K L K L L V N K R F I R R G D I S Y T Y F W I Q L V M .................................................................................................................................................. Protein_Len: 60 Strand: - Start: 108 End: 353 ........................................................................................................... P I A M E N R N D Y D V V L G E I K S T C K K Q I N K E R R Y F L Y L V L N T L G I F F I I A I I L I I P K D L I Q R M ........................................................................................... Protein_Len: 53 Strand: - Start: 1 End: 159 A S G K P F I E R L Q L N N G A G L I Y K R D F V G K Q E K K R P T E V Y Y P Y E I K K Q I N D W E R S M ............................................................................................................................................................................................................................................................................................. ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact 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================================================ ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.9 Tail_Score: -3.21416 Start: 324 End: 338 Full_Region: ctgaggcaaatcttg gataa accga ttatc ttgataatagccata ...................................................................................................................................................................................................................................................................................................................................gataaaccgattatc.......................................................................................................... TransTerm Strand: + Conf: 43 HP_score: -3.0 Tail_Score: -2.71706 Start: 370 End: 391 Full_Region: CTCCTATTTCCAAGC TCAGGTGA ATAACA TCAACTGA AATTTTCTTCTCTTT .................................................................................................................................................................................................................................................................................................................................................................................TCAGGTGAATAACATCAACTGA..................................................... Find igs database================================================ Query_seq: SSA_1317:SSA_1318|SSA_1317:SSA_1318:hypothetical protein:GTP-binding protein lepA, putative:<-<-:1333635..1334078 444 ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact Intra-Species Hit: Count: 1 Min: 1 Max: 444 Len: 444 Subject: NC_009009_SSA_1317_SSA_1318|hypothetical protein:GTP-binding protein lepA, putative|NEGATIVE:NEGATIVE|[1333635,1334078]|444 HSP 1 e-value: 0.0 bit: 839.0 Len: 444 Query Start:1 Query End:444 Subject Strand: POSITIVE Subject Start: 1 Subject End: 444 ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaannnnnnnctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact ggccgagccttttggaaatatttctcttaactgtaaattatttccagcaccaagaatatatttcctgtcaaagacacccttttgctctttcttcctaggagtttctacataataaggatattcaatttttttctgtatattgtcccattcacgagatattctacaacaggcaaagggatagccatttcattacggttgtcataatcaaccacaagaccttcaattttagaagtacattttttctgaatattcttctcccgtcgatagaataggtataaaaccaaatttgtaagaccaataaagaaaattatggctattatcaagataatcggtttatccaagatttgcctcagtctcctatttccaagctcaggtgaataacatcaactgaaattttcttctcttttataattcagggctcaggcgaataaagttcatcggact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCCGAGCCUUUUGGAAAUAUUUCUCUUAACUGUAAAUUAUUUCCAGCACCAAGAAUAUAUUUCCUGUCAAAGACACCCUUUUGCUCUUUCUUCCUAGGAGUUUCUACAUAAUAAGGAUAUUCAAUUUUUUUCUGUAUAUUGUCCCAUUCACGAGAUAUUCUACAACAGGCAAAGGGAUAGCCAUUUCAUUACGGUUGUCAUAAUCAACCACAAGACCUUCAAUUUUAGAAGUACAUUUUUUCUGAAUAUUCUUCUCCCGUCGAUAGAAUAGGUAUAAAACCAAAUUUGUAAGACCAAUAAAGAAAAUUAUGGCUAUUAUCAAGAUAAUCGGUUUAUCCAAGAUUUGCCUCAGUCUCCUAUUUCCAAGCUCAGGUGAAUAACAUCAACUGAAAUUUUCUUCUCUUUUAUAAUUCAGGGCUCAGGCGAAUAAAGUUCAUCGGACU .(((((((((((((((((((...........((((...((((((........((((.....((((((..(((((((......)).))))).....)))))).)))).........(((((....................))))).......))))))...))))..(((((((..(((((((((........(((((.......)))))..............((((((((.......))))))))..(((((.....(((....((((.(((.....)))..))))....))).....)))))....))))))))).....(((((.....))))).....)))))))........)))))))))..((((.(((......))).)))).......................))))))).)))......((((.....)))) (-89.65) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCCGAUGAACUUUAUUCGCCUGAGCCCUGAAUUAUAAAAGAGAAGAAAAUUUCAGUUGAUGUUAUUCACCUGAGCUUGGAAAUAGGAGACUGAGGCAAAUCUUGGAUAAACCGAUUAUCUUGAUAAUAGCCAUAAUUUUCUUUAUUGGUCUUACAAAUUUGGUUUUAUACCUAUUCUAUCGACGGGAGAAGAAUAUUCAGAAAAAAUGUACUUCUAAAAUUGAAGGUCUUGUGGUUGAUUAUGACAACCGUAAUGAAAUGGCUAUCCCUUUGCCUGUUGUAGAAUAUCUCGUGAAUGGGACAAUAUACAGAAAAAAAUUGAAUAUCCUUAUUAUGUAGAAACUCCUAGGAAGAAAGAGCAAAAGGGUGUCUUUGACAGGAAAUAUAUUCUUGGUGCUGGAAAUAAUUUACAGUUAAGAGAAAUAUUUCCAAAAGGCUCGGCC ...................(((.((((((((((...................)))))....(((((..(((((..((((.....((((((.....(((..(((..((((((.....)))))).)))....)))....((((((.(((..((((((.......(((.....)))(((((((.(((((((.((((.(((((.......))))).)))).......(((((....((.(((.((((((.....))))))..))).))....))))).)))))))))))))).........))))))...))).))))))...........................))))))........))))....)))))....)))))((((((((.(((((...((((...........))))...)))))))))))))....)))))))). (-107.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 873 110 61 201 152 NC_009009:SSA_1317|5end_hypothetical_protein_1333544..1333774_NEGATIVE 441 377 331 210 162 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 317 377 331 212 165 NC_009009:SSA_0067|5end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_68005..68235_POSITIVE 308 190 143 169 117 NC_009009:SSA_1871|5end_Penicillin-binding_protein_2X,_putative_1868873..1869103_NEGATIVE 300 370 329 115 76 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 295 235 196 231 196 NC_009009:SSA_0416|5end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_411890..412120_POSITIVE 289 298 253 231 192 NC_009009:SSA_0766|5end_hypothetical_protein_746242..746472_POSITIVE 286 376 331 58 6 NC_009009:SSA_0166|5end_hypothetical_protein_164641..164871_POSITIVE 285 366 324 197 151 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 284 370 328 181 131 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 284 359 314 126 84 NC_009009:SSA_1278|5end_Rhodanese-like_domain_protein,_putative_1299877..1300107_NEGATIVE 283 385 341 52 9 NC_009009:SSA_0030|5end_Phosphoribosylformylglycinamidine_synthase,_putative_32610..32840_POSITIVE 282 378 331 183 132 NC_009009:SSA_0366|5end_hypothetical_protein_357506..357736_POSITIVE 281 118 76 120 86 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 281 375 337 198 152 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 280 370 333 120 80 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 279 390 347 78 30 NC_009009:SSA_1306|5end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324910..1325140_NEGATIVE 276 258 212 223 172 NC_009009:SSA_1817|5end_Conserved_uncharacterized_protein_1805595..1805825_NEGATIVE 274 49 1 224 178 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 273 50 2 57 12 NC_009009:SSA_0463|5end_Cobyrinic_acid_A,C-diamide_synthase,_putative_466865..467095_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 370 329 125 86 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 290 105 62 75 30 NC_009009:SSA_0392|3end_hypothetical_protein_388303..388453_POSITIVE 287 226 181 128 84 NC_009009:SSA_1166|3end_hypothetical_protein_1192350..1192500_POSITIVE 284 359 314 133 91 NC_009009:SSA_1279|3end_Oxidoreductase,_putative_1299870..1300020_NEGATIVE 280 370 333 108 68 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 279 390 347 67 19 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE 275 373 331 50 10 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 272 404 364 51 11 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 268 364 321 92 53 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 266 97 61 93 57 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 262 375 332 139 96 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 262 390 345 134 94 NC_009009:SSA_2051|3end_Oligoendopeptidase,_putative_2056607..2056757_POSITIVE 261 99 51 107 66 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 261 240 193 142 96 NC_009009:SSA_1818|3end_Very_short_patch_repair_endonuclease,_putative_1805655..1805805_NEGATIVE 260 107 72 134 85 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 256 99 63 135 99 NC_009009:SSA_1732|3end_Uracil_phosphoribosyltransferase,_putative_1716916..1717066_NEGATIVE 256 211 171 134 94 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE 255 365 329 120 82 NC_009009:SSA_2279|3end_hypothetical_protein_2281671..2281821_NEGATIVE 255 375 331 111 54 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 255 185 141 135 97 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE