Origin IGS: gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga .........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 tctgcttatacgattaatataataattcagatgtaaagttaagcataaaaattgaaatactaaaaacaaaccgtgttttatgtctaaataagggggtataaaagtgccttttggtaggttttttcgctaagattttagaaacataactacattctactaaaaaagtatataggtttcaattaaaaagtatatactttttatgcgaaaagtatataggtttttatttgatgggttttaggaaggtgtaggaacggtatttcaaaagctgtgaaagtaaaatgcttttgcaaatttgtagttgaaaatcaggtgtttatggttaatcttatagggcgaacataatataaaaaagctattcgggtgaataaaagtatattaaaaac Mask Tandem Repeat Region ================================================ gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaatannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga Find is-nt database================================================ Query_seq: PI1201:PI1202|PI1201:PI1202:peptidyl-arginine deiminase:UvrD/REP helicase:->->:1117896..1118278 383 gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1201:PI1202|PI1201:PI1202:peptidyl-arginine deiminase:UvrD/REP helicase:->->:1117896..1118278 383 gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1201:PI1202|PI1201:PI1202:peptidyl-arginine deiminase:UvrD/REP helicase:->->:1117896..1118278 383 gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 18 End: 122 ................. M H P N S F F I L C S P Y K I N H K H L I F N Y K F A K A F Y F H S F ..................................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 94 End: 183 ............................................................................................. M Q K H F T F T A F E I P F L H L P K T H Q I K T Y I L F A ........................................................................................................................................................................................................ Protein_Len: 39 Strand: + Start: 251 End: 367 .......................................................................................................................................................................................................................................................... M L A K K P T K R H F Y T P L F R H K T R F V F S I S I F M L N F T S E L L Y ................ Protein_Len: 33 Strand: + Start: 285 End: 383 ............................................................................................................................................................................................................................................................................................ M P P Y L D I K H G L F L V F Q F L C L T L H L N Y Y I N R I S R gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga 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: 87 Start: 204 End: 233 ...........................................................................................................................................................................................................ATTGAAACCTATATACTTTTTTAGTAGAAT...................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -3.8 Tail_Score: -4.8622 Start: 168 End: 197 Full_Region: CCATCAAATAAAAAC CTATATACTTTT CGCATA AAAAGTATATAC TTTTTAATTGAAACC .......................................................................................................................................................................CTATATACTTTTCGCATAAAAAGTATATAC.......................................................................................................................................................................................... TransTerm Strand: + Conf: 67 HP_score: -7.3 Tail_Score: -3.5125 Start: 169 End: 196 Full_Region: CATCAAATAAAAACC TATATACTTTT CGCATA AAAAGTATATA CTTTTTAATTGAAAC ........................................................................................................................................................................TATATACTTTTCGCATAAAAAGTATATA........................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1201:PI1202|PI1201:PI1202:peptidyl-arginine deiminase:UvrD/REP helicase:->->:1117896..1118278 383 gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga Intra-Species Hit: Count: 1 Min: 1 Max: 383 Len: 383 Subject: pint_PI1201_PI1202|peptidyl-arginine deiminase:UvrD/REP helicase|POSITIVE:POSITIVE|[1117896,1118278]|383 HSP 1 e-value: 0.0 bit: 759.0 Len: 383 Query Start:1 Query End:383 Subject Strand: POSITIVE Subject Start: 1 Subject End: 383 gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga gtttttaatatacttttattcacccgaatagcttttttatattatgttcgccctataagattaaccataaacacctgattttcaactacaaatttgcaaaagcattttactttcacagcttttgaaataccgttcctacaccttcctaaaacccatcaaataaaaacctatatacttttcgcataaaaagtatatactttttaattgaaacctatatacttttttagtagaatgtagttatgtttctaaaatcttagcgaaaaaacctaccaaaaggcacttttatacccccttatttagacataaaacacggtttgtttttagtatttcaatttttatgcttaactttacatctgaattattatattaatcgtataagcaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUAAUAUACUUUUAUUCACCCGAAUAGCUUUUUUAUAUUAUGUUCGCCCUAUAAGAUUAACCAUAAACACCUGAUUUUCAACUACAAAUUUGCAAAAGCAUUUUACUUUCACAGCUUUUGAAAUACCGUUCCUACACCUUCCUAAAACCCAUCAAAUAAAAACCUAUAUACUUUUCGCAUAAAAAGUAUAUACUUUUUAAUUGAAACCUAUAUACUUUUUUAGUAGAAUGUAGUUAUGUUUCUAAAAUCUUAGCGAAAAAACCUACCAAAAGGCACUUUUAUACCCCCUUAUUUAGACAUAAAACACGGUUUGUUUUUAGUAUUUCAAUUUUUAUGCUUAACUUUACAUCUGAAUUAUUAUAUUAAUCGUAUAAGCAGA ((((..((((......(((((....)))))(((((((.........(((((....(((((((.............................((((.(((((((..............)))))))))))..(((..(((((...............((((.((((((..(((((((((((......))))))))))).)))))).))))........((((.....))))...)))))..))).......))))))))))))..........)))))))...............)))).))))..........((((((..(((((((...(((((..(((..........)))..)))))...)))))))....))))))... (-57.45) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUGCUUAUACGAUUAAUAUAAUAAUUCAGAUGUAAAGUUAAGCAUAAAAAUUGAAAUACUAAAAACAAACCGUGUUUUAUGUCUAAAUAAGGGGGUAUAAAAGUGCCUUUUGGUAGGUUUUUUCGCUAAGAUUUUAGAAACAUAACUACAUUCUACUAAAAAAGUAUAUAGGUUUCAAUUAAAAAGUAUAUACUUUUUAUGCGAAAAGUAUAUAGGUUUUUAUUUGAUGGGUUUUAGGAAGGUGUAGGAACGGUAUUUCAAAAGCUGUGAAAGUAAAAUGCUUUUGCAAAUUUGUAGUUGAAAAUCAGGUGUUUAUGGUUAAUCUUAUAGGGCGAACAUAAUAUAAAAAAGCUAUUCGGGUGAAUAAAAGUAUAUUAAAAAC ....((((((.(((((((...((((..((..((.....((((..(((((..((((((((((...........(((((((...((((....(((((((((....)))))))))..)))).....((.....)).....)))))))..((((((..(.((((((.............((((.((((((.((((((((((((....))))))))))).).)))))).))))....)))))).)..))))))....))))))))))....((..(((((.....)))))..))..)))))..))))....))..)).)))).))))))).)))))).......(((((((.......(((((....)))))....)))))))..... (-78.83) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 148 101 199 145 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 255 120 71 53 9 pint:PI0126|5end_conserved_hypothetical_protein_117925..118155_POSITIVE 250 56 13 192 153 pint:PI0890|5end_ribose_5-phosphate_isomerase_B_820417..820647_POSITIVE 250 146 110 199 152 pint:PI0767|5end_possible_TonB-dependent_receptor_701915..702145_POSITIVE 250 136 92 200 159 pint:PI0480|5end_preprotein_translocase,_SecY_subunit_441576..441806_POSITIVE 239 349 308 213 170 pint:PI0426|5end_conserved_hypothetical_protein_389345..389575_POSITIVE 235 157 112 53 12 pint:PI0576|5end_helicase,_UvrD/Rep_520226..520456_POSITIVE 228 293 256 121 65 pint:PI1052|5end_fructose-1,6-bisphosphatase_970492..970722_POSITIVE 225 144 102 225 181 pint:PI1332|5end_aminotransferase,_possible_pyridoxal-phosphate-dependent_aminotransferase_1249374..1249604_POSITIVE 225 67 22 137 99 pint:PI0155|5end_conserved_hypothetical_protein_148290..148520_POSITIVE 224 162 129 111 80 pint:PI1115|5end_conserved_hypothetical_protein_1039244..1039474_POSITIVE 221 146 102 87 50 pint:PI0917|5end_phosphoglycolate_phosphatase_846371..846601_POSITIVE 221 62 25 179 136 pint:PI0762|5end_mannose-6-phosphate_isomerase,_class_I_696420..696650_POSITIVE 220 86 45 46 6 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 214 356 311 217 168 pint:PI0615|5end_hydrolase,_haloacid_dehalogenase-like_family_564551..564781_POSITIVE 213 63 24 63 14 pint:PI0100|5end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_95843..96073_POSITIVE 212 135 93 121 85 pint:PI1760|5end_hypothetical_protein_1684413..1684643_POSITIVE 212 356 312 154 111 pint:PI1096|5end_glycosyltransferase_1020217..1020447_POSITIVE 211 302 276 163 131 pint:PI1684|5end_dimethyladenosine_transferase_1601073..1601303_POSITIVE 210 150 101 166 119 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 54 21 102 59 pint:PI0292|3end_ISPg-3_transposase_fragment_275904..276054_POSITIVE 250 56 13 50 11 pint:PI0889|3end_pyruvate_kinase_820355..820505_POSITIVE 231 315 273 43 1 pint:PI2051|3end_hypothetical_protein_2007835..2007985_POSITIVE 227 145 101 112 62 pint:PI2005|3end_potassium_uptake_protein_1964367..1964517_POSITIVE 225 157 128 68 44 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 225 67 22 78 40 pint:PI0154|3end_possible_UDP-2,3-diacylglucosamine_hydrolase_148311..148461_POSITIVE 221 146 117 111 84 pint:PI0010|3end_conserved_hypothetical_protein_11679..11829_POSITIVE 219 180 131 106 54 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 215 147 101 135 81 pint:PI1441|3end_hypothetical_protein_1363673..1363823_POSITIVE 212 149 115 34 3 pint:PI0507|3end_transcriptional_regulator_466547..466697_POSITIVE 212 299 256 64 24 pint:PI0082|3end_conserved_hypothetical_protein_(possible_phosphoglycerol_transferase)_82711..82861_POSITIVE 210 150 101 102 55 pint:PI0603|3end_3-dehydroquinate_synthase_550841..550991_POSITIVE 206 149 101 84 46 pint:PI0659|3end_hypothetical_protein_603396..603546_POSITIVE 205 80 31 132 62 pint:PI0549|3end_hypothetical_protein_500691..500841_POSITIVE 205 147 101 136 75 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 204 158 115 39 3 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 202 318 281 73 42 pint:PI0983|3end_hypothetical_protein_909991..910141_POSITIVE 201 170 138 75 49 pint:PI0302|3end_hypothetical_protein_287019..287169_POSITIVE 200 148 101 67 25 pint:PI1549|3end_conserved_hypothetical_protein_1467382..1467532_POSITIVE 197 136 110 139 114 pint:PI1747|3end_membrane-bound_lytic_murein_transglycosylase_D_1668579..1668729_POSITIVE