Origin IGS: actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt .........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 aatttttttgacttccatagtaattttgataaaacgtttatgttagtgtctttgtttttaaattctaccgcaaatgtattcattttatattagaatgccaaataaaactatgtctttttatttacttactaacaaattttaaagtctcaaagtttttatttcccccaaacacgttgcaaaatagcccattaatgcttgctttttgctactttaagagtagtaagacatatatattataatacttttgtcatttttcgggttttatacttatacatttgcttatttgcccaatattaatctttttaacttataaatccaattcaaagatgaatttattgcggttaagattattttgtctatctttgcaacatgaatgaaaacttgaacaaattatataaggagcaaattgcggcattggcgcaaagcattggcagt Mask Tandem Repeat Region ================================================ actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt Find is-nt database================================================ Query_seq: PI0592:PI0593|PI0592:PI0593:DNA mismatch repair protein:NAD-specific glutamate dehydrogenase:->->:542672..543106 435 actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0592:PI0593|PI0592:PI0593:DNA mismatch repair protein:NAD-specific glutamate dehydrogenase:->->:542672..543106 435 actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0592:PI0593|PI0592:PI0593:DNA mismatch repair protein:NAD-specific glutamate dehydrogenase:->->:542672..543106 435 actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 21 End: 125 .................... M P Q F A P Y I I C S S F H S C C K D R Q N N L N R N K F I F E L D L ...................................................................................................................................................................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 61 End: 153 ............................................................ M H V A K I D K I I L T A I N S S L N W I Y K L K R L I L G K .......................................................................................................................................................................................................................................................................................... Protein_Len: 53 Strand: - Start: 200 End: 358 ....................................................................................................................................................................................................... L I Y T K S S K F Y C F A L M L P S N Q L T N P P F L F K S V K F N T L L Y I F L C L K I Q C E L I F H M ............................................................................. Protein_Len: 33 Strand: - Start: 142 End: 240 ............................................................................................................................................. Y Q A F L C I Y L Y L V R F I V F T N Y Y I H R V V R L T A F L M ................................................................................................................................................................................................... Protein_Len: 37 Strand: - Start: 62 End: 172 ............................................................. E H Q L S L C F L R L R L L N M K S N S K Y T L F I L I P C I L L H I L M ....................................................................................................................................................................................................................................................................... actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt 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: 83 Start: 88 End: 117 .......................................................................................ATTCAAAGATGAATTTATTGCGGTTAAGAT.............................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0592:PI0593|PI0592:PI0593:DNA mismatch repair protein:NAD-specific glutamate dehydrogenase:->->:542672..543106 435 actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtcaaaaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 426 Len: 426 Subject: pint_PI0592_PI0593|DNA mismatch repair protein:NAD-specific glutamate dehydrogenase|POSITIVE:POSITIVE|[542672,543106]|435 HSP 1 e-value: 0.0 bit: 844.0 Len: 426 Query Start:1 Query End:426 Subject Strand: POSITIVE Subject Start: 1 Subject End: 426 actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtc......... actgccaatgctttgcgccaatgccgcaatttgctccttatataatttgttcaagttttcattcatgttgcaaagatagacaaaataatcttaaccgcaataaattcatctttgaattggatttataagttaaaaagattaatattgggcaaataagcaaatgtataagtataaaacccgaaaaatgacaaaagtattataatatatatgtcttactactcttaaagtagcaaaaagcaagcattaatgggctattttgcaacgtgtttgggggaaataaaaactttgagactttaaaatttgttagtaagtaaataaaaagacatagttttatttggcattctaatataaaatgaatacatttgcggtagaatttaaaaacaaagacactaacataaacgttttatcaaaattactatggaagtc......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGCCAAUGCUUUGCGCCAAUGCCGCAAUUUGCUCCUUAUAUAAUUUGUUCAAGUUUUCAUUCAUGUUGCAAAGAUAGACAAAAUAAUCUUAACCGCAAUAAAUUCAUCUUUGAAUUGGAUUUAUAAGUUAAAAAGAUUAAUAUUGGGCAAAUAAGCAAAUGUAUAAGUAUAAAACCCGAAAAAUGACAAAAGUAUUAUAAUAUAUAUGUCUUACUACUCUUAAAGUAGCAAAAAGCAAGCAUUAAUGGGCUAUUUUGCAACGUGUUUGGGGGAAAUAAAAACUUUGAGACUUUAAAAUUUGUUAGUAAGUAAAUAAAAAGACAUAGUUUUAUUUGGCAUUCUAAUAUAAAAUGAAUACAUUUGCGGUAGAAUUUAAAAACAAAGACACUAACAUAAACGUUUUAUCAAAAUUACUAUGGAAGUC (((.(((..((.(((((.......)))))...))...........((((((....((..((..((((((((((.(((((......(((((((....((.(((((((((.........)))))))))..))....)))))))(((((..((......)).)))))............((((......((((.(.((((....)))).).))))...(((((.....))))).................)))))))))))))))))))..))..)).))))))...(((((............(((((((...(((((((((........)))))))))..((((((.....(((((....)))))....))))))..............)))))))...........))))).......))).))). (-75.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUUCCAUAGUAAUUUUGAUAAAACGUUUAUGUUAGUGUCUUUGUUUUUAAAUUCUACCGCAAAUGUAUUCAUUUUAUAUUAGAAUGCCAAAUAAAACUAUGUCUUUUUAUUUACUUACUAACAAAUUUUAAAGUCUCAAAGUUUUUAUUUCCCCCAAACACGUUGCAAAAUAGCCCAUUAAUGCUUGCUUUUUGCUACUUUAAGAGUAGUAAGACAUAUAUAUUAUAAUACUUUUGUCAUUUUUCGGGUUUUAUACUUAUACAUUUGCUUAUUUGCCCAAUAUUAAUCUUUUUAACUUAUAAAUCCAAUUCAAAGAUGAAUUUAUUGCGGUUAAGAUUAUUUUGUCUAUCUUUGCAACAUGAAUGAAAACUUGAACAAAUUAUAUAAGGAGCAAAUUGCGGCAUUGGCGCAAAGCAUUGGCAGU .(((.(((..((.((((((....(((((...((((((((.............((((((....(((((....))))).....))))))...((((((((........))))))))...)))))))).....(((((.(.....).)))))............))))).)))))).(((((...(((((.((..((((((.(((((...(((((..((((.(..(((....)))..).))))....(((((((((.....((((.(((((((..(..((..(((...((((((...(((((....(((..((((((....)))))).)))..)))))))))))..)))..))..)..)))).))).)))))))))))))...))))).)))))))))))..)))))))))).))...))..))).))) (-76.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 277 231 194 135 pint:PI0845|5end_peptidyl-dipeptidase_778272..778502_POSITIVE 331 46 3 92 44 pint:PI1425|5end_conserved_hypothetical_protein_1344488..1344718_POSITIVE 328 68 22 80 32 pint:PI0837|5end_conserved_hypothetical_protein_772308..772538_POSITIVE 303 48 3 184 144 pint:PI1480|5end_xanthine/uracil_permease_family_protein_1402675..1402905_POSITIVE 301 42 2 75 27 pint:PI1364|5end_dipeptidyl_peptidase_IV_1281862..1282092_POSITIVE 301 50 1 58 9 pint:PI0580|5end_Holliday_junction_DNA_helicase_524178..524408_POSITIVE 294 38 3 134 101 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 292 35 4 90 60 pint:PI0768|5end_conserved_hypothetical_protein;_possible_acetyltransferase_704072..704302_POSITIVE 287 36 1 216 177 pint:PI2073|5end_mobilization_protein_2031995..2032225_POSITIVE 286 267 221 96 48 pint:PI1820|5end_hypothetical_protein_1759962..1760192_POSITIVE 286 41 8 223 185 pint:PI0922|5end_conserved_hypothetical_protein_852844..853074_POSITIVE 285 38 1 71 36 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 282 35 2 228 193 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 280 28 2 38 13 pint:PI1551|5end_HesA/MoeB/ThiF_family_protein_1467787..1468017_POSITIVE 274 268 225 228 178 pint:PI1675|5end_TonB-dependent_outer_membrane_receptor_1588107..1588337_POSITIVE 271 50 2 84 32 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 269 59 15 170 123 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 267 280 237 125 69 pint:PI0270|5end_conserved_hypothetical_protein_261388..261618_POSITIVE 265 37 1 229 193 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 263 51 15 55 5 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 50 1 70 30 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 328 68 22 65 17 pint:PI0836|3end_conserved_hypothetical_protein_772373..772523_POSITIVE 314 272 231 151 99 pint:PI0844|3end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_778316..778466_POSITIVE 301 42 2 55 7 pint:PI1363|3end_hypothetical_protein_1281922..1282072_POSITIVE 298 274 237 71 35 pint:PI1726|3end_ATP-dependent_DNA_helicase_1645542..1645692_POSITIVE 293 50 2 100 28 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 282 35 2 48 13 pint:PI2093|3end_hypothetical_protein_2049440..2049590_POSITIVE 269 59 15 89 42 pint:PI1670|3end_hypothetical_protein_1587026..1587176_POSITIVE 267 280 237 137 81 pint:PI0269|3end_conserved_hypothetical_protein_261480..261630_POSITIVE 267 250 207 70 29 pint:PI0138|3end_hypothetical_protein_131365..131515_POSITIVE 265 273 235 126 94 pint:PI2087|3end_dihydropicolinate_reductase_2044255..2044405_POSITIVE 258 36 1 41 8 pint:PI2036|3end_hypothetical_protein_1989516..1989666_POSITIVE 258 270 226 53 3 pint:PI0447|3end_DNA-directed_RNA_polymerase,_beta'_subunit_421755..421905_POSITIVE 258 37 1 86 45 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 257 49 1 105 46 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 253 37 1 69 31 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 251 100 57 54 6 pint:PI0328|3end_conserved_hypothetical_protein_309993..310143_POSITIVE 251 37 4 80 49 pint:PI0033|3end_peptidylprolyl_isomerase_37101..37251_POSITIVE 250 40 1 66 34 pint:PI0728|3end_integrase_661508..661658_POSITIVE 249 52 18 96 64 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE