Origin IGS: caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat .........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 attattaggagagattaattcttttagagatacaaaggtactatatttttttaaacaacctttagaggaaatgctaaatgtagaatgtttttcgttttttatttattaattttgcggaatgattggaaaagacaaataaactgctgcttttgacgctgacgataccttgtgggactgtcagtcgcacttcgatgctgcagaaaaggaatatcaggatatattgagcgattacggaacacctgcagaagtttctgctgcgctgttcaaaaccgaaacagccaatatgcccttg Mask Tandem Repeat Region ================================================ caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat Find is-nt database================================================ Query_seq: PI1366:PI1367|PI1366:PI1367:conserved hypothetical protein; possible hydrolase, HAD superfamily:redox-sensitive transcriptional activator, OxyR:->->:1286708..1286999 292 caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1366:PI1367|PI1366:PI1367:conserved hypothetical protein; possible hydrolase, HAD superfamily:redox-sensitive transcriptional activator, OxyR:->->:1286708..1286999 292 caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1366:PI1367|PI1366:PI1367:conserved hypothetical protein; possible hydrolase, HAD superfamily:redox-sensitive transcriptional activator, OxyR:->->:1286708..1286999 292 caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 48 End: 191 ............................................... M Q V F R N R S I Y P D I P F L Q H R S A T D S P T R Y R Q R Q K Q Q F I C L F Q S F R K I N K ..................................................................................................... Protein_Len: 60 Strand: + Start: 10 End: 216 ......... M G C F G F E Q R S R N F C R C S V I A Q Y I L I F L F C S I E V R L T V P Q G I V S V K S S S L F V F S N H S A K L I ............................................................................ Protein_Len: 34 Strand: + Start: 191 End: 292 .............................................................................................................................................................................................. M K N E K H S T F S I S S K G C L K K Y S T F V S L K E L I S P N N Protein_Len: 31 Strand: - Start: 187 End: 279 .......................................................................................................................................................................................... Y I F F S F C E V N L M E E L P Q K F F Y L V K T D R F S N M ............. Protein_Len: 33 Strand: - Start: 72 End: 170 ....................................................................... Y I R I N R K Q L M S T R S V T G C P I T L T L L L L K N T K E M .......................................................................................................................... Protein_Len: 41 Strand: - Start: 2 End: 124 . L A Y Q S N R N Q V A C C F S R C T N R L R E I Y G S I G K R C C R L A V S L G M ........................................................................................................................................................................ Protein_Len: 42 Strand: - Start: 1 End: 126 L P M N A T E T K F L A A S V E A P T G Y D S L I D Q Y E K E A A D F H S Q C D W M ...................................................................................................................................................................... caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat 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================================================ caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1366:PI1367|PI1366:PI1367:conserved hypothetical protein; possible hydrolase, HAD superfamily:redox-sensitive transcriptional activator, OxyR:->->:1286708..1286999 292 caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgcaaaattaataaataaaaaacgaaaaacattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: pint_PI1366_PI1367|conserved hypothetical protein; possible hydrolase, HAD superfamily:redox-sensitive transcriptional activator, OxyR|POSITIVE:POSITIVE|[1286708,1286999]|292 HSP 1 e-value: 5.0E-97 bit: 355.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgc................................................................................................................. caagggcatattggctgtttcggttttgaacagcgcagcagaaacttctgcaggtgttccgtaatcgctcaatatatcctgatattccttttctgcagcatcgaagtgcgactgacagtcccacaaggtatcgtcagcgtcaaaagcagcagtttatttgtcttttccaatcattccgc................................................................................................................. HSP 2 e-value: 1.0E-29 bit: 131.0 Len: 87 Query Start:206 Query End:292 Subject Strand: POSITIVE Subject Start: 206 Subject End: 292 .............................................................................................................................................................................................................cattctacatttagcatttcctctaaaggttgtttnnnnnnntatagtacctttgtatctctaaaagaattaatctctcctaataat .............................................................................................................................................................................................................cattctacatttagcatttcctctaaaggttgtttaaaaaaatatagtacctttgtatctctaaaagaattaatctctcctaataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGGGCAUAUUGGCUGUUUCGGUUUUGAACAGCGCAGCAGAAACUUCUGCAGGUGUUCCGUAAUCGCUCAAUAUAUCCUGAUAUUCCUUUUCUGCAGCAUCGAAGUGCGACUGACAGUCCCACAAGGUAUCGUCAGCGUCAAAAGCAGCAGUUUAUUUGUCUUUUCCAAUCAUUCCGCAAAAUUAAUAAAUAAAAAACGAAAAACAUUCUACAUUUAGCAUUUCCUCUAAAGGUUGUUUAAAAAAAUAUAGUACCUUUGUAUCUCUAAAAGAAUUAAUCUCUCCUAAUAAU ..(((..((((((((.(((.(((........(((((.(((((....)))))..)))))))).))).)).))))))..))).......(((((..(.((...(((((.(((.(((((.((.((....)).)).))))))))...(((((((.((((.(((((.((((..........................)))).)))))))))........(((((........))))).)))))))...............)))))...))).))))).................... (-52.97) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUUAGGAGAGAUUAAUUCUUUUAGAGAUACAAAGGUACUAUAUUUUUUUAAACAACCUUUAGAGGAAAUGCUAAAUGUAGAAUGUUUUUCGUUUUUUAUUUAUUAAUUUUGCGGAAUGAUUGGAAAAGACAAAUAAACUGCUGCUUUUGACGCUGACGAUACCUUGUGGGACUGUCAGUCGCACUUCGAUGCUGCAGAAAAGGAAUAUCAGGAUAUAUUGAGCGAUUACGGAACACCUGCAGAAGUUUCUGCUGCGCUGUUCAAAACCGAAACAGCCAAUAUGCCCUUG ((((((....(((((((.(((((((((((..............................)))))))))))....((((((.((((((.....)))))).)))))).)))))))....)))))).................((((.((..((((((((((((...((....))...)))))).))....)))).)).))))............(((.(((((((.((..((.(((((((((.(((((....))))).).).)))).....))).))..))))))))).))).. (-61.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 53 13 231 195 pint:PI0970|5end_hypothetical_protein_897254..897484_POSITIVE 354 138 95 60 13 pint:PI0097|5end_aspartate_aminotransferase_93235..93465_POSITIVE 350 60 11 71 15 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 348 150 102 68 17 pint:PI0988|5end_hypothetical_protein_912347..912577_POSITIVE 345 140 91 222 182 pint:PI1872|5end_glycosyl_transferase,_group_2_family_protein_1817057..1817287_POSITIVE 345 46 4 199 157 pint:PI0520|5end_hypothetical_protein_478755..478985_POSITIVE 344 58 11 224 175 pint:PI1950|5end_iron-regulated_membrane_permease_1904468..1904698_POSITIVE 340 70 22 195 148 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 339 128 87 198 142 pint:PI2115|5end_hypothetical_protein_2064966..2065196_POSITIVE 337 50 1 214 159 pint:PI0706|5end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_642226..642456_POSITIVE 332 138 96 95 50 pint:PI2021|5end_DNA_repair_protein_1977925..1978155_POSITIVE 332 57 13 45 2 pint:PI1073|5end_hemogluttinin_A-related_protein_(HagA)_990593..990823_POSITIVE 329 150 108 61 12 pint:PI1068|5end_nucleolar_protein,_Sun_(Fmu)_family_protein;_tRNA/rRNA_cytosine-C5-methylase_984743..984973_POSITIVE 327 150 106 201 154 pint:PI2171|5end_conserved_hypothetical_protein_2112735..2112965_POSITIVE 326 50 2 195 139 pint:PI1421|5end_hypothetical_protein_1341801..1342031_POSITIVE 325 74 34 44 1 pint:PI2031|5end_hypothetical_protein_1986053..1986283_POSITIVE 324 149 103 133 73 pint:PI1542|5end_mobilization_protein_1461728..1461958_POSITIVE 324 149 102 55 10 pint:PI0864|5end_dihydrodipicolinate_synthase_800527..800757_POSITIVE 324 150 108 108 57 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 323 50 3 147 106 pint:PI1651|5end_hypothetical_protein_1563845..1564075_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 138 91 120 47 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 354 138 95 50 3 pint:PI0096|3end_glycerol-3-phosphate_cytidylyltransferase_93305..93455_POSITIVE 345 69 21 114 60 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 342 160 113 150 92 pint:PI1237|3end_ATP-dependent_DNA_helicase_1161480..1161630_POSITIVE 341 149 105 83 29 pint:PI0242|3end_hypothetical_protein_240227..240377_POSITIVE 333 120 78 130 83 pint:PI0147|3end_HIT_family_protein_141308..141458_POSITIVE 324 149 103 96 36 pint:PI1540|3end_hypothetical_protein_1461771..1461921_POSITIVE 323 50 3 123 82 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE 322 47 5 124 78 pint:PI1487|3end_hypothetical_protein_1407940..1408090_POSITIVE 321 70 26 126 76 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 309 58 14 149 99 pint:PI1712|3end_hypothetical_protein_1627774..1627924_POSITIVE 309 134 95 66 14 pint:PI0791|3end_conserved_hypothetical_protein_729109..729259_POSITIVE 308 70 21 74 16 pint:PI0634|3end_conserved_hypothetical_protein_581121..581271_POSITIVE 307 70 22 79 36 pint:PI0033|3end_peptidylprolyl_isomerase_37101..37251_POSITIVE 304 138 92 105 47 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 302 60 11 116 65 pint:PI0760|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_695989..696139_POSITIVE 302 132 93 150 96 pint:PI0475|3end_50S_ribosomal_protein_L6_440096..440246_POSITIVE 301 69 21 141 84 pint:PI0642|3end_thioredoxin_family_protein_585582..585732_POSITIVE 301 140 91 125 66 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE 301 51 11 51 2 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE