Origin IGS: cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcggtttttacgtttattttgtctgaacaaagataacgcaaattttgccggcaaaccgtaattttcatgtttaattttgttagcaggcttattatttgtctgttgtgaaaggattatgagcgttaaccgatggttgttcagcggtcagtatgccgtgtaggggcgaacctcg Mask Tandem Repeat Region ================================================ cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt Find is-nt database================================================ Query_seq: TF1716:TF1717|TF1716:TF1717:hypothetical protein:DNA mismatch repair protein:->->:1837771..1837944 174 cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1716:TF1717|TF1716:TF1717:hypothetical protein:DNA mismatch repair protein:->->:1837771..1837944 174 cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1716:TF1717|TF1716:TF1717:hypothetical protein:DNA mismatch repair protein:->->:1837771..1837944 174 cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 32 End: 172 ............................... M N N H R L T L I I L S Q Q T N N K P A N K I K H E N Y G L P A K F A L S L F R Q N K R K N R .. Protein_Len: 32 Strand: + Start: 78 End: 173 ............................................................................. M I S L L T K L N M K I T V C R Q N L R Y L C S D K I N V K T D . cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt 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================================================ cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1716:TF1717|TF1716:TF1717:hypothetical protein:DNA mismatch repair protein:->->:1837771..1837944 174 cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: tfor_TF1716_TF1717|hypothetical protein:DNA mismatch repair protein|POSITIVE:POSITIVE|[1837771,1837944]|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 cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt cgaggttcgcccctacacggcatactgaccgctgaacaaccatcggttaacgctcataatcctttcacaacagacaaataataagcctgctaacaaaattaaacatgaaaattacggtttgccggcaaaatttgcgttatctttgttcagacaaaataaacgtaaaaaccgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAGGUUCGCCCCUACACGGCAUACUGACCGCUGAACAACCAUCGGUUAACGCUCAUAAUCCUUUCACAACAGACAAAUAAUAAGCCUGCUAACAAAAUUAAACAUGAAAAUUACGGUUUGCCGGCAAAAUUUGCGUUAUCUUUGUUCAGACAAAAUAAACGUAAAAACCGAUU .(((....(((.......)))....((((((.((......)).))))))...)))..((((.......................(((.((.(((..((((.........))))...))).)).)))....((((((((...(((((....)))))...))))))))....)))) (-33.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGGUUUUUACGUUUAUUUUGUCUGAACAAAGAUAACGCAAAUUUUGCCGGCAAACCGUAAUUUUCAUGUUUAAUUUUGUUAGCAGGCUUAUUAUUUGUCUGUUGUGAAAGGAUUAUGAGCGUUAACCGAUGGUUGUUCAGCGGUCAGUAUGCCGUGUAGGGGCGAACCUCG .(((((((...((((((((...((((..((((((..((((..((..((((.((....))))))..))..))))...))))))((((((((.........)))))))).....)))).)))))))).)))))))((((((((.(((((......)))))....)))).))))... (-49.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 50 1 108 28 tfor:TF2438|5end_hypothetical_protein_2615781..2616011_POSITIVE 382 46 1 109 55 tfor:TF1577|5end_hypothetical_protein_1685960..1686190_POSITIVE 380 46 3 40 1 tfor:TF1955|5end_amino_acid_exporter,_possible_threonine_efflux_protein_2106952..2107182_POSITIVE 358 45 2 54 2 tfor:TF1332|5end_cytochrome_c-type_synthesis_protein_(cytochrome_c_biogenesis_protein);_ABC_transporter,_permease_1410957..1411187_POSITIVE 348 46 1 110 65 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 340 47 1 75 16 tfor:TF0799|5end_conserved_hypothetical_protein_855191..855421_POSITIVE 326 56 18 131 85 tfor:TF1231|5end_NAD-dependent_DNA_ligase_1315235..1315465_POSITIVE 326 33 4 65 35 tfor:TF0146|5end_glutamine-dependent_NAD(+)_synthetase_154855..155085_POSITIVE 324 48 1 86 26 tfor:TF1710|5end_possible_cell_filamentation_protein_1829679..1829909_POSITIVE 323 44 1 56 4 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 322 45 1 165 111 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 317 47 1 67 16 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 316 49 4 226 173 tfor:TF2904|5end_ATP-dependent__helicase,_possible_UvrD/REP_helicase_domain_protein_3098903..3099133_POSITIVE 315 53 14 226 190 tfor:TF0183|5end_conserved_hypothetical_protein_195954..196184_POSITIVE 314 41 1 231 185 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 308 55 11 48 10 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 307 56 19 230 198 tfor:TF2852|5end_conserved_hypothetical_protein_3038966..3039196_POSITIVE 307 57 11 204 152 tfor:TF2448|5end_conserved_hypothetical_protein_2624962..2625192_POSITIVE 306 50 2 75 27 tfor:TF1297|5end_hypothetical_protein_1379024..1379254_POSITIVE 304 49 1 69 14 tfor:TF0282|5end_probable_tonB-linked_outer_membrane_receptor_309101..309331_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 500 34 2 35 3 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 358 45 1 142 99 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 314 41 1 103 57 tfor:TF0537|3end_conserved_hypothetical_protein_566836..566986_POSITIVE 311 46 1 94 50 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 309 63 25 67 25 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 308 46 1 52 10 tfor:TF1934|3end_hypothetical_protein_2084079..2084229_POSITIVE 299 42 1 73 37 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 299 148 115 49 12 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 298 150 115 46 8 tfor:TF2979|3end_possible_outer_membrane__protein_3193164..3193314_POSITIVE 297 46 3 140 99 tfor:TF2814|3end_prolipoprotein_diacylglyceryl_transferase_3005424..3005574_POSITIVE 296 49 3 131 90 tfor:TF2884|3end_conserved_hypothetical_protein_3075748..3075898_POSITIVE 295 46 3 58 3 tfor:TF2248|3end_transfer_region-related_protein,_TraB_2423068..2423218_POSITIVE 294 56 11 151 100 tfor:TF2447|3end_lipoprotein_2624990..2625140_POSITIVE 292 45 3 107 62 tfor:TF1042|3end_possible_surface_antigen_with_leucine-rich_repeat_1105295..1105445_POSITIVE 290 46 2 115 56 tfor:TF1944|3end_conserved_hypothetical_protein_2093309..2093459_POSITIVE 289 49 6 116 69 tfor:TF3039|3end_ABC_transporter,_ATP-binding_protein_3267697..3267847_POSITIVE 288 48 7 143 98 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 286 48 1 101 41 tfor:TF1109|3end_lipoprotein_1179997..1180147_POSITIVE 283 48 1 77 6 tfor:TF2112|3end_glycine_cleavage_H_protein_2282573..2282723_POSITIVE 281 67 30 77 43 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE