Origin IGS: aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac .........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 gtttctaagttttaattcgtttgttcaatctatctataatataatttgtttttgccttcgcatttgattcgttacgaatatcatgccaaagattttcggcacccccgaatctgacatttctgcagatgacatgtcagcacatgtaagtatttagtgacaaaatgtcgggtatcatccggtt Mask Tandem Repeat Region ================================================ aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac Find is-nt database================================================ Query_seq: TF2440:TF2441|TF2440:TF2441:conserved hypothetical protein; possible DNA mismatch repair protein:10 kDa chaperonin:->->:2618198..2618378 181 aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2440:TF2441|TF2440:TF2441:conserved hypothetical protein; possible DNA mismatch repair protein:10 kDa chaperonin:->->:2618198..2618378 181 aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2440:TF2441|TF2440:TF2441:conserved hypothetical protein; possible DNA mismatch repair protein:10 kDa chaperonin:->->:2618198..2618378 181 aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 32 End: 145 ............................... M L T C A D M S S A E M S D S G V P K I F G M I F V T N Q M R R Q K Q I I L .................................... Protein_Len: 40 Strand: + Start: 55 End: 174 ...................................................... M C R N V R F G G A E N L W H D I R N E S N A K A K T N Y I I D R L N K R I K T ....... aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac 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: 142 End: 171 .............................................................................................................................................TTTAATTCGTTTGTTCAATCTATCTATAAT.......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2440:TF2441|TF2440:TF2441:conserved hypothetical protein; possible DNA mismatch repair protein:10 kDa chaperonin:->->:2618198..2618378 181 aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: tfor_TF2440_TF2441|conserved hypothetical protein; possible DNA mismatch repair protein:10 kDa chaperonin|POSITIVE:POSITIVE|[2618198,2618378]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac aaccggatgatacccgacattttgtcactaaatacttacatgtgctgacatgtcatctgcagaaatgtcagattcgggggtgccgaaaatctttggcatgatattcgtaacgaatcaaatgcgaaggcaaaaacaaattatattatagatagattgaacaaacgaattaaaacttagaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCGGAUGAUACCCGACAUUUUGUCACUAAAUACUUACAUGUGCUGACAUGUCAUCUGCAGAAAUGUCAGAUUCGGGGGUGCCGAAAAUCUUUGGCAUGAUAUUCGUAACGAAUCAAAUGCGAAGGCAAAAACAAAUUAUAUUAUAGAUAGAUUGAACAAACGAAUUAAAACUUAGAAAC ...((((((...(((((....................((((((....)))))).(((((((....)).)))))))))).((((((((....))))))))..))))))...((.......(((....)))....(((.((((.......)))).)))......))................. (-39.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUCUAAGUUUUAAUUCGUUUGUUCAAUCUAUCUAUAAUAUAAUUUGUUUUUGCCUUCGCAUUUGAUUCGUUACGAAUAUCAUGCCAAAGAUUUUCGGCACCCCCGAAUCUGACAUUUCUGCAGAUGACAUGUCAGCACAUGUAAGUAUUUAGUGACAAAAUGUCGGGUAUCAUCCGGUU ................(((..((............((((......))))...(((((..((((((.....(((((((((((((((.........(((((.....))))).(((((((.((.......)).)))))))..))))...)))))).))))).)))))).))))).))..))).. (-32.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 96 51 197 138 tfor:TF0729|5end_DNA_primase_780107..780337_POSITIVE 347 83 41 75 32 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 338 88 43 54 14 tfor:TF0299|5end_hypothetical_protein_324821..325051_POSITIVE 333 109 65 65 7 tfor:TF1682|5end_hydrolase_1796409..1796639_POSITIVE 329 86 43 173 140 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 323 100 57 178 124 tfor:TF1468|5end_beta-galactosidase_1557785..1558015_POSITIVE 318 88 41 191 150 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 318 88 41 151 110 tfor:TF1917|5end_hypothetical_protein_2069997..2070227_POSITIVE 314 77 35 50 4 tfor:TF2907|5end_CDP-diacylglycerol-serine-O-phosphatidyltransfera_se_3102861..3103091_POSITIVE 314 85 41 65 10 tfor:TF2522|5end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_(dUTPase)_2701558..2701788_POSITIVE 313 80 31 224 163 tfor:TF1744|5end_phenylacetate-CoA_ligase_1877822..1878052_POSITIVE 308 100 57 92 47 tfor:TF2700|5end_possible_nifS-like_aminotransferase_2872855..2873085_POSITIVE 307 85 41 79 36 tfor:TF1995|5end_exonuclease_2147148..2147378_POSITIVE 306 100 54 51 1 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 306 85 42 176 121 tfor:TF1551|5end_hypothetical_protein_1656864..1657094_POSITIVE 305 85 42 149 102 tfor:TF0995|5end_conserved_hypothetical_protein_1049695..1049925_POSITIVE 305 80 40 144 106 tfor:TF0617|5end_alpha-1,2-mannosidase_650862..651092_POSITIVE 304 97 52 178 131 tfor:TF1932|5end_pigmentation_and_extracellular_proteinase_regulator_2078542..2078772_POSITIVE 303 87 42 150 95 tfor:TF0398|5end_Fe-S_oxidoreductase_418984..419214_POSITIVE 303 86 41 63 16 tfor:TF0141|5end_exodeoxyribonuclease_VII,_large_subunit_148422..148652_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 107 65 133 79 tfor:TF2792|3end_30S_ribosomal_protein_S15_2977599..2977749_POSITIVE 333 109 65 87 29 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE 329 86 45 97 55 tfor:TF0629|3end_hypothetical_protein_666710..666860_POSITIVE 323 100 57 150 96 tfor:TF1467|3end_conserved_hypothetical_protein_1557837..1557987_POSITIVE 313 96 54 61 6 tfor:TF1327|3end_L-fucose_permease_1407195..1407345_POSITIVE 307 85 41 79 36 tfor:TF1994|3end_acyl-CoA_synthetase_2147228..2147378_POSITIVE 305 80 36 48 8 tfor:TF1755|3end_periplasmic_protease_1892867..1893017_POSITIVE 303 87 42 150 95 tfor:TF0397|3end_ferredoxin-like_protein_419064..419214_POSITIVE 302 100 51 139 81 tfor:TF0251|3end_conserved_hypothetical_protein;_possible_exporter_283529..283679_POSITIVE 301 77 42 42 2 tfor:TF2906|3end_phosphatidylserine_decarboxylase_3102933..3103083_POSITIVE 300 87 42 106 47 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 298 88 42 46 2 tfor:TF2353|3end_conserved_hypothetical_protein_2518608..2518758_POSITIVE 294 86 42 143 84 tfor:TF0994|3end_maltose_O-acetyltransferase_1049782..1049932_POSITIVE 294 86 44 44 1 tfor:TF0140|3end_exodeoxyribonuclease_VII,_small_subunit_148483..148633_POSITIVE 291 98 56 123 86 tfor:TF2914|3end_hypothetical_protein_3109643..3109793_POSITIVE 290 85 45 140 98 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 289 89 44 67 6 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 287 100 51 144 83 tfor:TF0803|3end_hypothetical_protein_861979..862129_POSITIVE 286 100 51 101 46 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 283 88 44 63 11 tfor:TF1047|3end_tRNA_pseudouridylate_synthetase_A_(pseudouridylate_synthase_I)_1109318..1109468_POSITIVE