Origin IGS: tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taataattatcatttccctgcgaaaaggaaataataaaaatcaataacaatcggtctgattattcgtattggataatcagaccgattcttttttcaaccttattagggtaaatcgaggcttataaaagtgtaaacatttttcacaagtgtaactattgtataactatca Mask Tandem Repeat Region ================================================ tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta Find is-nt database================================================ Query_seq: PI1072:PI1073|PI1072:PI1073:hypothetical protein:hemogluttinin A-related protein (HagA):->->:990564..990732 169 tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1072:PI1073|PI1072:PI1073:hypothetical protein:hemogluttinin A-related protein (HagA):->->:990564..990732 169 tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1072:PI1073|PI1072:PI1073:hypothetical protein:hemogluttinin A-related protein (HagA):->->:990564..990732 169 tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta Predict ORF larger than 30AA ================================================ tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta 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================================================ tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -5.9 Tail_Score: -5.39905 Start: 75 End: 129 Full_Region: TACCCTAATAAGGTT GAAAAAAGAATCGGTCTGATTATCC AATAC GAATAATCAGACCGATTGTTATTGA TTTTTATTATTTCCT ..........................................................................GAAAAAAGAATCGGTCTGATTATCCAATACGAATAATCAGACCGATTGTTATTGA........................................ TransTerm Strand: - Conf: 100 HP_score: -15.7 Tail_Score: -5.06103 Start: 82 End: 122 Full_Region: aataaaaatcaataa caatcggtctgattattcg tat tggataatcagaccgattc ttttttcaaccttat .................................................................................caatcggtctgattattcgtattggataatcagaccgattc............................................... TransTerm Strand: - Conf: 100 HP_score: -17.4 Tail_Score: -4.62085 Start: 85 End: 119 Full_Region: aaaaatcaataacaa tcggtctgattattcg tat tggataatcagaccga ttcttttttcaacct ....................................................................................tcggtctgattattcgtattggataatcagaccga.................................................. Find igs database================================================ Query_seq: PI1072:PI1073|PI1072:PI1073:hypothetical protein:hemogluttinin A-related protein (HagA):->->:990564..990732 169 tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: pint_PI1072_PI1073|hypothetical protein:hemogluttinin A-related protein (HagA)|POSITIVE:POSITIVE|[990564,990732]|169 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta tgatagttatacaatagttacacttgtgaaaaatgtttacacttttataagcctcgatttaccctaataaggttgaaaaaagaatcggtctgattatccaatacgaataatcagaccgattgttattgatttttattatttccttttcgcagggaaatgataattatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAGUUAUACAAUAGUUACACUUGUGAAAAAUGUUUACACUUUUAUAAGCCUCGAUUUACCCUAAUAAGGUUGAAAAAAGAAUCGGUCUGAUUAUCCAAUACGAAUAAUCAGACCGAUUGUUAUUGAUUUUUAUUAUUUCCUUUUCGCAGGGAAAUGAUAAUUAUUA ......................(((((((((..((....)).)))))))))......((((.(((....))).))))..((.(((((((((((((((.(.....).))))))))))))))).))..((((..(((((((((((((.....)))))))))))))..)))) (-44.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAUUAUCAUUUCCCUGCGAAAAGGAAAUAAUAAAAAUCAAUAACAAUCGGUCUGAUUAUUCGUAUUGGAUAAUCAGACCGAUUCUUUUUUCAACCUUAUUAGGGUAAAUCGAGGCUUAUAAAAGUGUAAACAUUUUUCACAAGUGUAACUAUUGUAUAACUAUCA ......((((.((((((.(.....).)))))).))))....(((((..(((((((((((((((((.....))))))))))))))))).........((((.....))))......(.((((..(((((((....)))))))...)))).)...)))))........... (-39.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 464 48 2 136 90 pint:PI0004|5end_hypothetical_protein_6199..6429_POSITIVE 435 42 2 130 90 pint:PI0200|5end_hypothetical_protein_191545..191775_POSITIVE 395 46 2 123 79 pint:PI1057|5end_hypothetical_protein_977286..977516_POSITIVE 393 44 2 132 90 pint:PI0182|5end_hypothetical_protein_174093..174323_POSITIVE 384 42 5 158 121 pint:PI1601|5end_hypothetical_protein_1530282..1530512_POSITIVE 379 46 6 170 130 pint:PI1168|5end_hypothetical_protein_1089696..1089926_POSITIVE 379 46 6 162 122 pint:PI1167|5end_hypothetical_protein_1089688..1089918_POSITIVE 377 49 5 96 52 pint:PI0928|5end_hypothetical_protein_859851..860081_POSITIVE 374 45 2 134 90 pint:PI1733|5end_hypothetical_protein_1652160..1652390_POSITIVE 372 50 2 127 79 pint:PI1869|5end_hypothetical_protein_1815131..1815361_POSITIVE 368 42 1 185 142 pint:PI0841|5end_hypothetical_protein_775406..775636_POSITIVE 367 50 2 166 118 pint:PI1694|5end_hypothetical_protein_1609717..1609947_POSITIVE 366 54 11 152 110 pint:PI0755|5end_hypothetical_protein_686691..686921_POSITIVE 360 63 23 106 70 pint:PI1922|5end_hypothetical_protein_1865219..1865449_POSITIVE 347 42 2 130 90 pint:PI0061|5end_hypothetical_protein_60500..60730_POSITIVE 346 89 42 57 1 pint:PI2055|5end_hypothetical_protein_2012999..2013229_POSITIVE 343 41 1 44 3 pint:PI0759|5end_hypothetical_protein_693763..693993_POSITIVE 342 56 12 57 10 pint:PI1814|5end_hypothetical_protein_1752953..1753183_POSITIVE 341 49 4 173 128 pint:PI1679|5end_hypothetical_protein_1594744..1594974_POSITIVE 337 56 14 158 118 pint:PI1129|5end_hypothetical_protein_1055377..1055607_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 42 5 71 34 pint:PI1600|3end_conserved_hypothetical_protein_1530275..1530425_POSITIVE 342 56 12 110 63 pint:PI1813|3end_hypothetical_protein_1753086..1753236_POSITIVE 333 66 23 84 43 pint:PI0051|3end_hypothetical_protein_53388..53538_POSITIVE 324 49 2 49 1 pint:PI0098|3end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_95532..95682_POSITIVE 317 48 5 122 76 pint:PI0688|3end_hypothetical_protein_625750..625900_POSITIVE 313 43 2 84 43 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 299 89 45 54 1 pint:PI2054|3end_hypothetical_protein_2013076..2013226_POSITIVE 291 48 2 61 15 pint:PI2172|3end_hypothetical_protein_2113991..2114141_POSITIVE 288 54 12 72 31 pint:PI1117|3end_glycosyl_transferase,_family_2_1042279..1042429_POSITIVE 274 46 6 56 16 pint:PI1485|3end_hypothetical_protein_1405339..1405489_POSITIVE 269 66 23 49 7 pint:PI1165|3end_hypothetical_protein_1089636..1089786_POSITIVE 264 41 1 106 58 pint:PI0669|3end_hypothetical_protein_611147..611297_POSITIVE 256 63 23 64 24 pint:PI1424|3end_probable_peptidase_family_M48_1344044..1344194_POSITIVE 251 50 23 101 74 pint:PI1391|3end_hypothetical_protein_1311694..1311844_POSITIVE 237 55 12 46 4 pint:PI0103|3end_conserved_hypothetical_protein;_possible_permease_99100..99250_POSITIVE 229 46 1 67 14 pint:PI1946|3end_hypothetical_protein_1903020..1903170_POSITIVE 229 159 136 127 98 pint:PI1869|3end_hypothetical_protein_1815426..1815576_POSITIVE 228 48 5 119 76 pint:PI0186|3end_hypothetical_protein_178003..178153_POSITIVE 224 145 113 141 108 pint:PI2091|3end_DNA_processing_protein_2049226..2049376_POSITIVE 224 110 66 145 101 pint:PI0882|3end_conserved_hypothetical_protein;_possible_para-aminobenzoate_synthase_component_I_816203..816353_POSITIVE