Origin IGS: taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgtcgccctcttatttggtcgagtgcgtagggcaaatccaccttcggaaagcgttttcctaagagtgcgagtgttttaacgtcgtcgttggcgtgctgtcggataaattctgaagtttccaagtgccgtttataataatgcagaaaaagtta Mask Tandem Repeat Region ================================================ taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa Find is-nt database================================================ Query_seq: PI2099:PI2100|PI2099:PI2100:D-alanyl-D-alanine dipeptidase:conserved hypothetical protein:->->:2053338..2053490 153 taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2099:PI2100|PI2099:PI2100:D-alanyl-D-alanine dipeptidase:conserved hypothetical protein:->->:2053338..2053490 153 taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2099:PI2100|PI2099:PI2100:D-alanyl-D-alanine dipeptidase:conserved hypothetical protein:->->:2053338..2053490 153 taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 10 End: 153 ......... M H Y Y K R H L E T S E F I R Q H A N D D V K T L A L L G K R F P K V D L P Y A L D Q I R G R Q taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa 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: 17 End: 46 ................ATTCTGAAGTTTCCAAGTGCCGTTTATAAT........................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2099:PI2100|PI2099:PI2100:D-alanyl-D-alanine dipeptidase:conserved hypothetical protein:->->:2053338..2053490 153 taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: pint_PI2099_PI2100|D-alanyl-D-alanine dipeptidase:conserved hypothetical protein|POSITIVE:POSITIVE|[2053338,2053490]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa taactttttctgcattattataaacggcacttggaaacttcagaatttatccgacagcacgccaacgacgacgttaaaacactcgcactcttaggaaaacgctttccgaaggtggatttgccctacgcactcgaccaaataagagggcgacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUUUUCUGCAUUAUUAUAAACGGCACUUGGAAACUUCAGAAUUUAUCCGACAGCACGCCAACGACGACGUUAAAACACUCGCACUCUUAGGAAAACGCUUUCCGAAGGUGGAUUUGCCCUACGCACUCGACCAAAUAAGAGGGCGACAA ........................((((..(((((..............)))))..)).))..((((....)))).......((((.(((((((((((....)))))...(((.((..(((.....))).)).)))...)))))).))))... (-31.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCGCCCUCUUAUUUGGUCGAGUGCGUAGGGCAAAUCCACCUUCGGAAAGCGUUUUCCUAAGAGUGCGAGUGUUUUAACGUCGUCGUUGGCGUGCUGUCGGAUAAAUUCUGAAGUUUCCAAGUGCCGUUUAUAAUAAUGCAGAAAAAGUUA ((((.((((((.(((((....))))).).)))))...((((((((.(((((....))))).))).))).)).((((..((((.((.(.((((...(((.(((((.....))))))))..))))))).))))...))))..))))......... (-35.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 73 42 79 52 pint:PI1429|5end_L-aspartate_oxidase_1347650..1347880_POSITIVE 329 150 106 175 130 pint:PI2036|5end_hypothetical_protein_1989239..1989469_POSITIVE 328 133 94 121 74 pint:PI0938|5end_hypothetical_protein_869345..869575_POSITIVE 324 148 102 55 7 pint:PI1362|5end_60Kd_inner_membrane_protein_1279820..1280050_POSITIVE 309 148 102 182 125 pint:PI1628|5end_hypothetical_protein_1551082..1551312_POSITIVE 304 106 61 195 133 pint:PI1620|5end__two-component_system_sensor_protein_1543956..1544186_POSITIVE 303 94 52 94 41 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 303 70 25 194 153 pint:PI0431|5end_Xaa-Pro_aminopeptidase_403064..403294_POSITIVE 303 149 117 33 1 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 300 149 107 221 178 pint:PI0167|5end_hypothetical_protein_163164..163394_POSITIVE 299 85 41 61 9 pint:PI1758|5end_hypothetical_protein_1683207..1683437_POSITIVE 298 125 81 220 171 pint:PI2078|5end_hypothetical_protein_2036053..2036283_POSITIVE 298 125 81 59 10 pint:PI2077|5end_hypothetical_protein_2035892..2036122_POSITIVE 295 132 100 63 29 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 295 59 12 189 133 pint:PI0766|5end_conserved_hypothetical_protein_700781..701011_POSITIVE 293 130 83 231 180 pint:PI1707|5end_GTP-binding_protein_1623795..1624025_POSITIVE 292 137 98 90 56 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 290 150 105 78 5 pint:PI1313|5end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1229710..1229940_POSITIVE 287 150 106 193 151 pint:PI0178|5end_2-oxoglutarate_synthase,_subunit_korA_169524..169754_POSITIVE 286 127 82 185 139 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 73 42 44 17 pint:PI1428|3end_quinolinate_synthetase_A_1347695..1347845_POSITIVE 335 148 101 112 56 pint:PI2113|3end_hypothetical_protein_2064278..2064428_POSITIVE 320 148 105 48 5 pint:PI1361|3end_CTP_synthase_(UTP-ammonia_lyase)_1279893..1280043_POSITIVE 304 150 101 121 78 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 303 94 52 104 51 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 303 70 25 151 110 pint:PI0430|3end_periplasmic_protease;_MdsD_protein_403101..403251_POSITIVE 295 150 101 136 78 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 295 59 12 150 94 pint:PI0765|3end_conserved_hypothetical_protein;_possible_surface_protein_700822..700972_POSITIVE 289 116 72 140 97 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 286 127 82 62 16 pint:PI1783|3end_possible_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_1716158..1716308_POSITIVE 285 67 29 136 94 pint:PI1131|3end_folylpolyglutamate_synthase_1058484..1058634_POSITIVE 277 149 106 71 18 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 276 139 99 151 90 pint:PI1922|3end_hypothetical_protein_1865454..1865604_POSITIVE 276 148 101 126 68 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 276 115 72 139 93 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 276 139 99 147 86 pint:PI0061|3end_hypothetical_protein_60690..60840_POSITIVE 276 150 102 75 35 pint:PI0005|3end_hypothetical_protein_7450..7600_POSITIVE 275 128 83 79 22 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 275 135 93 61 15 pint:PI1017|3end_ISPg3-related_transposase,_C-terminal_region_937661..937811_POSITIVE 268 134 94 73 29 pint:PI1102|3end_conserved_hypothetical_protein_1026247..1026397_POSITIVE