Origin IGS: taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagtcaagggacataaggttctgttgtacgaaaagccacctgttgttttgtgccacagaacttgtaactttcagaaatacaaagagccgattctcaataagagagtcggctctttgtgttttgttagctataatagcaacaaacacatttgaaggaaagtggaagaaagatta Mask Tandem Repeat Region ================================================ taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca Find is-nt database================================================ Query_seq: PI1177:PI1178|PI1177:PI1178:hypothtical protein:histidyl-tRNA synthetase:->->:1099215..1099388 174 taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1177:PI1178|PI1177:PI1178:hypothtical protein:histidyl-tRNA synthetase:->->:1099215..1099388 174 taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1177:PI1178|PI1177:PI1178:hypothtical protein:histidyl-tRNA synthetase:->->:1099215..1099388 174 taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 28 End: 174 ........................... M F V A I I A N K T Q R A D S L I E N R L F V F L K V T S S V A Q N N R W L F V Q Q N L M S L D S Protein_Len: 43 Strand: - Start: 25 End: 153 ........................ I H K N S N Y S V F C L S G V R K N L I P E K Y K Q F N C T R H C L V V P P K E Y L M ..................... Protein_Len: 53 Strand: - Start: 3 End: 161 .. D K K W K G E F T N T A I I A L L V C L A S E R I S F R S K T N R F T V L E T A C F L L H S K T C C F R M ............. taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca 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: 81 Start: 15 End: 44 ..............CTTTCCTTCAAATGTGTTTGTTGCTATTAT.................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 40 End: 69 .......................................GTCGGCTCTTTGTGTTTTGTTAGCTATAAT......................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.6 Tail_Score: -3.89614 Start: 56 End: 96 Full_Region: TTATAGCTAACAAAA CACAAAGAGCCGACTCTC TTATT GAGAATCGGCTCTTTGTA TTTCTGAAAGTTACA .......................................................CACAAAGAGCCGACTCTCTTATTGAGAATCGGCTCTTTGTA.............................................................................. TransTerm Strand: - Conf: 100 HP_score: -20.0 Tail_Score: -4.70169 Start: 56 End: 96 Full_Region: tgtaactttcagaaa tacaaagagccgattctc aataa gagagtcggctctttgtg ttttgttagctataa .......................................................tacaaagagccgattctcaataagagagtcggctctttgtg.............................................................................. TransTerm Strand: + Conf: 100 HP_score: -18.2 Tail_Score: -3.5362 Start: 58 End: 94 Full_Region: ATAGCTAACAAAACA CAAAGAGCCGACTCTC TTATT GAGAATCGGCTCTTTG TATTTCTGAAAGTTA .........................................................CAAAGAGCCGACTCTCTTATTGAGAATCGGCTCTTTG................................................................................ TransTerm Strand: - Conf: 100 HP_score: -20.4 Tail_Score: -3.96156 Start: 58 End: 94 Full_Region: taactttcagaaata caaagagccgattctc aataa gagagtcggctctttg tgttttgttagctat .........................................................caaagagccgattctcaataagagagtcggctctttg................................................................................ TransTerm Strand: + Conf: 100 HP_score: -13.2 Tail_Score: -4.40003 Start: 62 End: 90 Full_Region: CTAACAAAACACAAA GAGCCGACTCTC TTATT GAGAATCGGCTC TTTGTATTTCTGAAA .............................................................GAGCCGACTCTCTTATTGAGAATCGGCTC.................................................................................... Find igs database================================================ Query_seq: PI1177:PI1178|PI1177:PI1178:hypothtical protein:histidyl-tRNA synthetase:->->:1099215..1099388 174 taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: pint_PI1177_PI1178|hypothtical protein:histidyl-tRNA synthetase|POSITIVE:POSITIVE|[1099215,1099388]|174 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca taatctttcttccactttccttcaaatgtgtttgttgctattatagctaacaaaacacaaagagccgactctcttattgagaatcggctctttgtatttctgaaagttacaagttctgtggcacaaaacaacaggtggcttttcgtacaacagaaccttatgtcccttgactca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCUUUCUUCCACUUUCCUUCAAAUGUGUUUGUUGCUAUUAUAGCUAACAAAACACAAAGAGCCGACUCUCUUAUUGAGAAUCGGCUCUUUGUAUUUCUGAAAGUUACAAGUUCUGUGGCACAAAACAACAGGUGGCUUUUCGUACAACAGAACCUUAUGUCCCUUGACUCA .............((((((...........((((((((((...)))).))))))..((((((((((((.((((.....)))).))))))))))))......)))))).....((((((((((.((...(....).))))).........))))))).....(((....)))... (-47.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUCAAGGGACAUAAGGUUCUGUUGUACGAAAAGCCACCUGUUGUUUUGUGCCACAGAACUUGUAACUUUCAGAAAUACAAAGAGCCGAUUCUCAAUAAGAGAGUCGGCUCUUUGUGUUUUGUUAGCUAUAAUAGCAACAAACACAUUUGAAGGAAAGUGGAAGAAAGAUUA ...(((....)))...(((((((((.(((((((((((.....))).)))))))).)))))))))....(((((.((((((((((((((((((((((.....))))))))))))))))))))))(((.((((...))))))).....(((((......)))))...))))).... (-67.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 102 62 199 154 pint:PI0135|5end_internalin-related_protein_125849..126079_POSITIVE 304 93 56 208 167 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 296 92 60 161 123 pint:PI1405|5end_conserved_hypothetical_protein_1326035..1326265_POSITIVE 292 93 59 37 3 pint:PI1869|5end_hypothetical_protein_1815131..1815361_POSITIVE 286 160 112 229 174 pint:PI0739|5end_conserved_hypothetical_protein_671794..672024_POSITIVE 281 93 51 125 84 pint:PI1948|5end_hypothetical_protein_1903084..1903314_POSITIVE 270 150 115 231 194 pint:PI0110|5end_ABC_transport_system,_ATP-binding_protein_107136..107366_POSITIVE 269 125 85 165 126 pint:PI0049|5end_outer_membrane_receptor_protein_(iron_transport)_48605..48835_POSITIVE 267 160 111 228 173 pint:PI1224|5end_sensor_histidine_kinase_and_response_regulator_1144574..1144804_POSITIVE 264 158 112 65 12 pint:PI1385|5end_3-deoxy-d-manno-octulosonic_acid_8-phosphate_synthase_(DAHP_synthase,_Class_I)_1306224..1306454_POSITIVE 263 165 121 188 143 pint:PI1099|5end_low_molecular_weight_protein-tyrosine-phosphatase_1023059..1023289_POSITIVE 256 38 5 152 117 pint:PI0528|5end_hypothetical_protein_482791..483021_POSITIVE 255 103 61 63 3 pint:PI0223|5end_topoisomerase_IA_218377..218607_POSITIVE 249 168 121 107 66 pint:PI1760|5end_hypothetical_protein_1684413..1684643_POSITIVE 248 89 56 163 133 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 246 147 107 71 19 pint:PI0845|5end_peptidyl-dipeptidase_778272..778502_POSITIVE 245 157 117 92 46 pint:PI0707|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_643358..643588_POSITIVE 244 90 43 194 158 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 242 157 113 71 26 pint:PI1076|5end_hypothetical_protein_998893..999123_POSITIVE 241 89 50 226 190 pint:PI2025|5end_conserved_hypothetical_protein_1979028..1979258_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 109 62 47 1 pint:PI1177|3end_hypothtical_protein_1099154..1099304_POSITIVE 296 92 60 45 7 pint:PI1404|3end_hypothetical_protein_1325999..1326149_POSITIVE 259 96 62 137 110 pint:PI0083|3end_tyrosyl-tRNA_synthetase_84115..84265_POSITIVE 257 92 52 44 5 pint:PI0685|3end_elongation_factor_G_623048..623198_POSITIVE 257 146 109 128 83 pint:PI0641|3end_conserved_hypothetical_protein_584560..584710_POSITIVE 245 157 117 48 2 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 242 95 57 109 75 pint:PI2024|3end_hypothetical_protein_1978985..1979135_POSITIVE 242 95 57 83 49 pint:PI2022|3end_hypothetical_protein_1978959..1979109_POSITIVE 242 157 111 54 1 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 240 77 31 137 84 pint:PI1550|3end_conserved_hypothetical_protein_1467703..1467853_POSITIVE 236 168 133 109 77 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 235 98 59 142 102 pint:PI1761|3end_hypothetical_protein_1684543..1684693_POSITIVE 235 39 3 146 109 pint:PI0241|3end_possible_tetracycline_resistance_element_/mobilization_regulatory_protein_240036..240186_POSITIVE 232 159 117 88 54 pint:PI0432|3end_hypothetical_protein_405037..405187_POSITIVE 232 159 117 124 90 pint:PI0433|3end_hypothetical_protein_405073..405223_POSITIVE 231 95 63 147 117 pint:PI0352|3end_hypothetical_protein_325934..326084_POSITIVE 230 165 123 77 33 pint:PI2019|3end_elongation_factor_P_1976774..1976924_POSITIVE 229 99 62 61 14 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE 228 162 133 35 2 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE 226 47 4 113 72 pint:PI1513|3end_conserved_hypothetical_protein_1432502..1432652_POSITIVE