Origin IGS: agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca .........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 tgattaggtattccctttttcacagcacaagcgtttatccatcgtctttttttcggctttttcccctcggaggcaaagccaagcctttgcaggataaagagcggatagaagctcctgagttttggtattgtcaaataatatgtctaagttaggggcagaataacaaactgattgttgaaccacaaaaaaagacgaaattattcccatgactaagacaatcacattcaatgaactgagaagaatcaaagacagcttgcccgatggcgct Mask Tandem Repeat Region ================================================ agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca Find is-nt database================================================ Query_seq: PG0246:PG0248|PG0246:PG0248:hypothetical protein:translation initation factor SUI1, putative:<-<-:281332..281599 268 agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0246:PG0248|PG0246:PG0248:hypothetical protein:translation initation factor SUI1, putative:<-<-:281332..281599 268 agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0246:PG0248|PG0246:PG0248:hypothetical protein:translation initation factor SUI1, putative:<-<-:281332..281599 268 agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 7 End: 117 ...... M G Q A V F D S S Q F I E C D C L S H G N N F V F F C G S T I S L L F C P ....................................................................................................................................................... Protein_Len: 60 Strand: + Start: 17 End: 262 ................ M S L I L L S S L N V I V L V M G I I S S F F V V Q Q S V C Y S A P N L D I L F D N T K T Q E L L S A L Y P A K A W L C ...... Protein_Len: 44 Strand: + Start: 135 End: 266 ...................................................................................................................................... M T I P K L R S F Y P L F I L Q R L G F A S E G K K P K K R R W I N A C A V K K G I P N .. Protein_Len: 32 Strand: - Start: 164 End: 259 ................................................................................................................................................................... G S K I R C L S P K A E S P F F G F F L R H I F A Q A T F F P M ......... Protein_Len: 49 Strand: - Start: 120 End: 266 ....................................................................................................................... S L C I I Q C Y W F E P A E I R E K D Q L P K A K G G L P F L R F F S S P Y V S T S H F L S Y R M .. agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca 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================================================ agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0246:PG0248|PG0246:PG0248:hypothetical protein:translation initation factor SUI1, putative:<-<-:281332..281599 268 agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca Intra-Species Hit: Count: 1 Min: 1 Max: 268 Len: 268 Subject: NC_002950_PG0246_PG0248|hypothetical protein:translation initation factor SUI1, putative|NEGATIVE:NEGATIVE|[281332,281599]|268 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 268 Query Start:1 Query End:268 Subject Strand: POSITIVE Subject Start: 1 Subject End: 268 agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtcnnnnnnngtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgnnnnnnngacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca agcgccatcgggcaagctgtctttgattcttctcagttcattgaatgtgattgtcttagtcatgggaataatttcgtctttttttgtggttcaacaatcagtttgttattctgcccctaacttagacatattatttgacaataccaaaactcaggagcttctatccgctctttatcctgcaaaggcttggctttgcctccgaggggaaaaagccgaaaaaaagacgatggataaacgcttgtgctgtgaaaaagggaatacctaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGCCAUCGGGCAAGCUGUCUUUGAUUCUUCUCAGUUCAUUGAAUGUGAUUGUCUUAGUCAUGGGAAUAAUUUCGUCUUUUUUUGUGGUUCAACAAUCAGUUUGUUAUUCUGCCCCUAACUUAGACAUAUUAUUUGACAAUACCAAAACUCAGGAGCUUCUAUCCGCUCUUUAUCCUGCAAAGGCUUGGCUUUGCCUCCGAGGGGAAAAAGCCGAAAAAAAGACGAUGGAUAAACGCUUGUGCUGUGAAAAAGGGAAUACCUAAUCA .....(((.(.((((((.......((..(((((.((((.((((...((((((((((.(((...(((...(((..((.......((((......))))......))..)))...)))...))).))))).)))))....)))).....)))).)))))..))((((((((((((..(((....))).((((((((..(((....)))..))))))))...))))).).))))))...)))))).).)))....(((.....)))..... (-64.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUAGGUAUUCCCUUUUUCACAGCACAAGCGUUUAUCCAUCGUCUUUUUUUCGGCUUUUUCCCCUCGGAGGCAAAGCCAAGCCUUUGCAGGAUAAAGAGCGGAUAGAAGCUCCUGAGUUUUGGUAUUGUCAAAUAAUAUGUCUAAGUUAGGGGCAGAAUAACAAACUGAUUGUUGAACCACAAAAAAAGACGAAAUUAUUCCCAUGACUAAGACAAUCACAUUCAAUGAACUGAGAAGAAUCAAAGACAGCUUGCCCGAUGGCGCU (((..(((.....)))...))).(((..((((((((.....(((((((((((((.(((((((..((((((((((........))))))).)))..))))))).)).....((((((((.((...(((((((...)))))))....)).))))))))....((((((.....)))))).......)))))))))))............................((((......)))).........)))).))))(((....)))))) (-65.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 953 50 1 141 92 NC_002950:PG0246|5end_hypothetical_protein_281241..281471_NEGATIVE 413 206 165 55 6 NC_002950:PG0128|5end_hypothetical_protein_149594..149824_POSITIVE 396 195 152 228 186 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 390 198 152 57 5 NC_002950:PG1255|5end_recombination_protein_RecR_1332751..1332981_NEGATIVE 379 214 175 76 36 NC_002950:PG1487|5end_hypothetical_protein_1561468..1561698_POSITIVE 377 216 177 96 48 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 368 206 161 230 179 NC_002950:PG2149|5end_hypothetical_protein_2257658..2257888_NEGATIVE 365 205 167 218 179 NC_002950:PG0092|5end_transporter,_putative_108598..108828_NEGATIVE 361 45 1 61 15 NC_002950:PG0685|5end_ABC_transporter,_ATP-binding_protein_740116..740346_POSITIVE 360 205 164 69 17 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 353 203 166 88 34 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 350 220 175 66 21 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 348 207 164 218 173 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 347 207 163 189 128 NC_002950:PG2080|5end_adenosylmethionine--8-amino-7-oxononanoate_transaminase_2180679..2180909_NEGATIVE 341 50 1 228 173 NC_002950:PG1121|5end_asparaginyl-tRNA_synthetase_1197555..1197785_NEGATIVE 339 190 151 173 119 NC_002950:PG0794|5end_penicillin-binding_protein_1A,_putative_846411..846641_POSITIVE 334 217 177 216 165 NC_002950:PG1604|5end_immunoreactive_84_kDa_antigen_PG93_1682737..1682967_POSITIVE 334 206 165 120 60 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 333 215 174 99 36 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 332 206 161 228 186 NC_002950:PG1682|5end_glycosyl_transferase,_group_1_family_protein_1768385..1768615_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 198 152 60 8 NC_002950:PG1256|3end_ribonuclease,_Rne/Rng_family_1332748..1332898_NEGATIVE 379 206 165 48 2 NC_002950:PG0127|3end_ferrochelatase_149667..149817_POSITIVE 356 213 173 79 37 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 350 206 161 128 91 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 348 207 166 78 30 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 336 198 151 139 83 NC_002950:PG1014|3end_TPR_domain_protein_1075855..1076005_POSITIVE 336 207 161 86 29 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 335 206 165 66 12 NC_002950:PG1237|3end_transcriptional_regulator,_LuxR_family_1312908..1313058_POSITIVE 332 216 173 50 2 NC_002950:PG1476|3end_conjugative_transposon_protein_TraM_1551858..1552008_NEGATIVE 332 214 179 151 119 NC_002950:PG0474|3end_low-specificity_L-threonine_aldolase_515011..515161_NEGATIVE 331 204 161 74 22 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 328 200 154 68 24 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 326 217 185 73 35 NC_002950:PG1849|3end_DNA_repair_protein_RecN_1947379..1947529_NEGATIVE 322 240 198 66 23 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 319 205 164 119 84 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 318 214 177 63 17 NC_002950:PG1371|3end_phosphorylase_family_protein_1452352..1452502_NEGATIVE 314 207 165 148 105 NC_002950:PG2001|3end_signal_peptidase_I_2089458..2089608_NEGATIVE 314 196 155 70 24 NC_002950:PG0810|3end_hypothetical_protein_871977..872127_NEGATIVE 312 188 143 47 6 NC_002950:PG1920|3end_ribosomal_protein_L30_2016307..2016457_NEGATIVE 311 199 153 84 36 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE