Origin IGS: aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc .........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 gaaagcaaaaggctccttgaaaataggacaaaagcagggcagtgctaatccgatagcagcttgccctgctttttataaatctccgatagaatgggtactttacctcatggtcagtgagtcttttgaactacaacgaagtaatgatttagggctgactccggagttggaatcagcccttatccccgacccaaagaaatcggatgaaaaccaaacattcagaacacccctcgaaactttatatcctaaacgtatcaaacctttgcacttcagggcggaatgtacgatacagccatttttagcacgcgccaatacggcttaaaagtattgtagtatctttatggtctgtt Mask Tandem Repeat Region ================================================ aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc Find is-nt database================================================ Query_seq: PG0912:PG0914|PG0912:PG0914:polysaccharide transport protein, putative:hypothetical protein:<-<-:975447..975793 347 aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0912:PG0914|PG0912:PG0914:polysaccharide transport protein, putative:hypothetical protein:<-<-:975447..975793 347 aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0912:PG0914|PG0912:PG0914:polysaccharide transport protein, putative:hypothetical protein:<-<-:975447..975793 347 aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 39 End: 245 ...................................... M A R A K N G C I V H S A L K C K G L I R L G Y K V S R G V L N V W F S S D F F G S G I R A D S N S G V S P K S L L R C ...................................................................................................... Protein_Len: 32 Strand: - Start: 52 End: 147 ................................................... F H S Y R V N R G S T C L N S V N L I Y L K S P H E S H K T K M ........................................................................................................................................................................................................ Protein_Len: 60 Strand: - Start: 32 End: 331 ............................... K K P D P I L A S E L E P T L G L D N S R Q L E F S E S V M L Y L V W E I P S K Y F A P C A A I P N A S G Q K Q G I K M ................ aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc 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================================================ aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 52 HP_score: -4.2 Tail_Score: -3.5002 Start: 161 End: 210 Full_Region: ATCCGATTTCTTTGG GTCGGGGATAAGGGCTGATTCC AACTCC GGAGTCAGCCCTAAATCATTAC TTCGTTGTAGTTCAA ................................................................................................................................................................GTCGGGGATAAGGGCTGATTCCAACTCCGGAGTCAGCCCTAAATCATTAC......................................................................................................................................... TransTerm Strand: + Conf: 57 HP_score: -5.8 Tail_Score: -3.48466 Start: 165 End: 206 Full_Region: GATTTCTTTGGGTCG GGGATAAGGGCTGATTCC AACTCC GGAGTCAGCCCTAAATCA TTACTTCGTTGTAGT ....................................................................................................................................................................GGGATAAGGGCTGATTCCAACTCCGGAGTCAGCCCTAAATCA............................................................................................................................................. TransTerm Strand: + Conf: 66 HP_score: -9.3 Tail_Score: -2.68356 Start: 166 End: 205 Full_Region: ATTTCTTTGGGTCGG GGATAAGGGCTGATTCC AACTCC GGAGTCAGCCCTAAATC ATTACTTCGTTGTAG .....................................................................................................................................................................GGATAAGGGCTGATTCCAACTCCGGAGTCAGCCCTAAATC.............................................................................................................................................. TransTerm Strand: + Conf: 65 HP_score: -8.3 Tail_Score: -2.87756 Start: 168 End: 203 Full_Region: TTCTTTGGGTCGGGG ATAAGGGCTGATTCC AACTCC GGAGTCAGCCCTAAA TCATTACTTCGTTGT .......................................................................................................................................................................ATAAGGGCTGATTCCAACTCCGGAGTCAGCCCTAAA................................................................................................................................................ TransTerm Strand: - Conf: 85 HP_score: -12.0 Tail_Score: -3.28712 Start: 172 End: 199 Full_Region: cgaagtaatgattta gggctgactccg gagt tggaatcagccc ttatccccgacccaa ...........................................................................................................................................................................gggctgactccggagttggaatcagccc.................................................................................................................................................... TransTerm Strand: + Conf: 67 HP_score: -9.3 Tail_Score: -2.93623 Start: 274 End: 319 Full_Region: CTATCGGAGATTTAT AAAAAGCAGGGCAAGCTGCTA TCGGAT TAGCACTGCCCTGCTTTTG TCCTATTTTCAAGGA .................................................................................................................................................................................................................................................................................AAAAAGCAGGGCAAGCTGCTATCGGATTAGCACTGCCCTGCTTTTG............................ TransTerm Strand: - Conf: 93 HP_score: -9.2 Tail_Score: -4.89852 Start: 279 End: 314 Full_Region: gaaaataggacaaaa gcagggcagtgcta atccga tagcagcttgccctgc tttttataaatctcc ......................................................................................................................................................................................................................................................................................gcagggcagtgctaatccgatagcagcttgccctgc................................. Find igs database================================================ Query_seq: PG0912:PG0914|PG0912:PG0914:polysaccharide transport protein, putative:hypothetical protein:<-<-:975447..975793 347 aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc Intra-Species Hit: Count: 1 Min: 1 Max: 347 Len: 347 Subject: NC_002950_PG0912_PG0914|polysaccharide transport protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[975447,975793]|347 HSP 1 e-value: 0.0 bit: 688.0 Len: 347 Query Start:1 Query End:347 Subject Strand: POSITIVE Subject Start: 1 Subject End: 347 aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc aacagaccataaagatactacaatacttttaagccgtattggcgcgtgctaaaaatggctgtatcgtacattccgccctgaagtgcaaaggtttgatacgtttaggatataaagtttcgaggggtgttctgaatgtttggttttcatccgatttctttgggtcggggataagggctgattccaactccggagtcagccctaaatcattacttcgttgtagttcaaaagactcactgaccatgaggtaaagtacccattctatcggagatttataaaaagcagggcaagctgctatcggattagcactgccctgcttttgtcctattttcaaggagccttttgctttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGACCAUAAAGAUACUACAAUACUUUUAAGCCGUAUUGGCGCGUGCUAAAAAUGGCUGUAUCGUACAUUCCGCCCUGAAGUGCAAAGGUUUGAUACGUUUAGGAUAUAAAGUUUCGAGGGGUGUUCUGAAUGUUUGGUUUUCAUCCGAUUUCUUUGGGUCGGGGAUAAGGGCUGAUUCCAACUCCGGAGUCAGCCCUAAAUCAUUACUUCGUUGUAGUUCAAAAGACUCACUGACCAUGAGGUAAAGUACCCAUUCUAUCGGAGAUUUAUAAAAAGCAGGGCAAGCUGCUAUCGGAUUAGCACUGCCCUGCUUUUGUCCUAUUUUCAAGGAGCCUUUUGCUUUC ..((((((.....(((((.............((((((.(((((....)))))..)))))))))))((((.(((......)))))))...))))))..(((((((((((((.............)))))))))))))..((((((..((((((.....((((((...(((.((((((((((((......))))))))))))..))).(((((((((.(((((((....))...))).)).))))))))).).)))))....))))))........((((((((((((.(.(((((......)))))))))))))))))).............)))))).......... (-115.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAGCAAAAGGCUCCUUGAAAAUAGGACAAAAGCAGGGCAGUGCUAAUCCGAUAGCAGCUUGCCCUGCUUUUUAUAAAUCUCCGAUAGAAUGGGUACUUUACCUCAUGGUCAGUGAGUCUUUUGAACUACAACGAAGUAAUGAUUUAGGGCUGACUCCGGAGUUGGAAUCAGCCCUUAUCCCCGACCCAAAGAAAUCGGAUGAAAACCAAACAUUCAGAACACCCCUCGAAACUUUAUAUCCUAAACGUAUCAAACCUUUGCACUUCAGGGCGGAAUGUACGAUACAGCCAUUUUUAGCACGCGCCAAUACGGCUUAAAAGUAUUGUAGUAUCUUUAUGGUCUGUU .....((((((((((.((((..(((((..((((((((((((((((((......)))))..)))))))))))))........((((......)))).......))).))..)))).)))))))))).................(((..((((((((.((((....)))).)))))))).)))...((((.(((((....(((((.........)))))....(..((((.(((..((((.....)))).(((.........)))..)))))))..)....((((((((.((........))....(((.....)))......))))))))...)))))..)))).... (-97.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1019 80 31 171 122 NC_002950:PG0912|5end_polysaccharide_transport_protein,_putative_975356..975586_NEGATIVE 392 80 33 227 174 NC_002950:PG2029|5end_hypothetical_protein_2126543..2126773_POSITIVE 392 215 172 57 8 NC_002950:PG0429|5end_pyruvate_synthase_466100..466330_POSITIVE 388 156 111 150 106 NC_002950:PG1354|5end_hydrolase,_carbon-nitrogen_family_1434765..1434995_NEGATIVE 383 168 121 208 157 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 377 314 276 211 157 NC_002950:PG1487|5end_hypothetical_protein_1561468..1561698_POSITIVE 359 197 151 228 187 NC_002950:PG0433|5end_tetrapyrrole_methylase_family_protein_471396..471626_NEGATIVE 358 167 121 73 17 NC_002950:PG1353|5end_orotate_phosphoribosyltransferase_1433833..1434063_NEGATIVE 358 80 33 96 46 NC_002950:PG0094|5end_outer_membrane_efflux_protein,_putative_111193..111423_NEGATIVE 356 76 31 51 6 NC_002950:PG0026|5end_hypothetical_protein_29234..29464_POSITIVE 355 314 279 226 182 NC_002950:PG2222|5end_acyltransferase,_HtrB/MsbB_family_2336757..2336987_POSITIVE 354 190 141 163 119 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 353 80 33 216 179 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 353 189 146 202 158 NC_002950:PG0883|5end_hypothetical_protein_945121..945351_POSITIVE 348 176 131 181 130 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 348 297 254 155 110 NC_002950:PG1172|5end_iron-sulfur_cluster_binding_protein,_putative_1251173..1251403_POSITIVE 343 200 157 208 163 NC_002950:PG2100|5end_immunoreactive_63_kDa_antigen_PG102_2210191..2210421_NEGATIVE 343 208 161 168 116 NC_002950:PG0446|5end_thiF_protein_486599..486829_POSITIVE 342 200 152 115 62 NC_002950:PG1639|5end_hypothetical_protein_1719919..1720149_NEGATIVE 342 76 32 48 4 NC_002950:PG0603|5end_cytidylate_kinase_659570..659800_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 435 200 170 36 5 NC_002950:PG1121|3end_asparaginyl-tRNA_synthetase_1196146..1196296_NEGATIVE 422 200 171 55 25 NC_002950:PG0435|3end_capsular_polysaccharide_biosythesis_protein,_putative_472708..472858_NEGATIVE 399 320 274 63 4 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 396 78 33 63 7 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 373 337 291 141 97 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 370 330 281 71 21 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 366 90 41 76 22 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 356 168 121 53 2 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 354 190 141 83 39 NC_002950:PG0283|3end_efflux_transporter,_MFP_component,_RND_family_316995..317145_NEGATIVE 349 315 278 109 69 NC_002950:PG1232|3end_glutamate_dehydrogenase_1308274..1308424_NEGATIVE 348 176 131 92 41 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 348 297 254 77 32 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 343 200 157 121 76 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 343 154 111 151 109 NC_002950:PG1355|3end_acyltransferase,_putative_1434762..1434912_NEGATIVE 342 200 152 99 46 NC_002950:PG1640|3end_DNA-damage-inducible_protein_F_1719935..1720085_NEGATIVE 340 198 155 96 32 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 340 339 292 101 40 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 338 200 155 56 8 NC_002950:PG2177|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_2285266..2285416_NEGATIVE 335 198 157 112 64 NC_002950:PG0021|3end_TIM-barrel_protein,_putative,_NifR3_family_24122..24272_NEGATIVE 333 169 122 128 68 NC_002950:PG0430|3end_ferrodoxin_oxidoreductase_beta_subunit_469073..469223_POSITIVE