Origin IGS: cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt .........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 acagttatcatttaaaatagaggggcaaagataggggttttgctctgcttgtgcaatagatggcccggaggttgcctgacgaagagcgtgggcctatttcgaaaaaaaatgagatgtagatgtcgtaagagaacatctccggacttaaaagaccactatagtaagtgtcgtcatgcattaaaatttcaatacgttaaccataggagggcagcctcgtttgggagcatatgatttttcacgtacctttgtgcgctttttataaaag Mask Tandem Repeat Region ================================================ cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt Find is-nt database================================================ Query_seq: TF1688:TF1689|TF1688:TF1689:conserved hypothetical protein; possible periplasmic protein:conserved hypothetical protein:->->:1804943..1805207 265 cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1688:TF1689|TF1688:TF1689:conserved hypothetical protein; possible periplasmic protein:conserved hypothetical protein:->->:1804943..1805207 265 cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1688:TF1689|TF1688:TF1689:conserved hypothetical protein; possible periplasmic protein:conserved hypothetical protein:->->:1804943..1805207 265 cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 156 End: 251 ........................................................................................................................................................... M F F R N R P T L F V R Q P P G H L L H K Q S K T P I F A P L F .............. Protein_Len: 60 Strand: + Start: 76 End: 255 ........................................................................... M E I L M H D D T Y Y S G L L S P E M F S Y D I Y I S F F F E I G P R S S S G N L R A I Y C T S R A K P L S L P L Y F K .......... Protein_Len: 60 Strand: - Start: 38 End: 235 ..................................... A R R H N V Y Q F K L A H R C K S Y H D K L D P S T R K R C R C R M K K R F L G V S K T L C G G P W R N C L C L L V G M .............................. cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt 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================================================ PromScan Matrix: RpoN Strand: - Score: 87 Start: 190 End: 206 .............................................................................................................................................................................................ATGGCCCGGAGGTTGCC........................................................... cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1688:TF1689|TF1688:TF1689:conserved hypothetical protein; possible periplasmic protein:conserved hypothetical protein:->->:1804943..1805207 265 cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt Intra-Species Hit: Count: 1 Min: 1 Max: 265 Len: 265 Subject: tfor_TF1688_TF1689|conserved hypothetical protein; possible periplasmic protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1804943,1805207]|265 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 265 Query Start:1 Query End:265 Subject Strand: POSITIVE Subject Start: 1 Subject End: 265 cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcannnnnnnncgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt cttttataaaaagcgcacaaaggtacgtgaaaaatcatatgctcccaaacgaggctgccctcctatggttaacgtattgaaattttaatgcatgacgacacttactatagtggtcttttaagtccggagatgttctcttacgacatctacatctcattttttttcgaaataggcccacgctcttcgtcaggcaacctccgggccatctattgcacaagcagagcaaaacccctatctttgcccctctattttaaatgataactgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUAUAAAAAGCGCACAAAGGUACGUGAAAAAUCAUAUGCUCCCAAACGAGGCUGCCCUCCUAUGGUUAACGUAUUGAAAUUUUAAUGCAUGACGACACUUACUAUAGUGGUCUUUUAAGUCCGGAGAUGUUCUCUUACGACAUCUACAUCUCAUUUUUUUUCGAAAUAGGCCCACGCUCUUCGUCAGGCAACCUCCGGGCCAUCUAUUGCACAAGCAGAGCAAAACCCCUAUCUUUGCCCCUCUAUUUUAAAUGAUAACUGU ......(((((((.(..((((((((.((((....)))).(((((......((((.((((..............(((((((....)))))))..(((((......((((...((.((....)).)).(((((((...............))))))).............))))((....))...))))).)))).))))............(((....)))))))).......))))))))...).)).)))))............ (-50.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGUUAUCAUUUAAAAUAGAGGGGCAAAGAUAGGGGUUUUGCUCUGCUUGUGCAAUAGAUGGCCCGGAGGUUGCCUGACGAAGAGCGUGGGCCUAUUUCGAAAAAAAAUGAGAUGUAGAUGUCGUAAGAGAACAUCUCCGGACUUAAAAGACCACUAUAGUAAGUGUCGUCAUGCAUUAAAAUUUCAAUACGUUAACCAUAGGAGGGCAGCCUCGUUUGGGAGCAUAUGAUUUUUCACGUACCUUUGUGCGCUUUUUAUAAAAG ................(((((((((((....(((((((..((((((((....)).............((((((((((..(....((((((.....((((..(........(((((((...(.((....)).))))))))...........(((((((......))))..))).....)..)))).....)))))).......)..)))))))))).....))))))..(((....)))...)))))))))).))))))))..... (-66.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 443 205 166 214 168 tfor:TF2160|5end_magnesium_chelatase,_subunit_I_2335974..2336204_POSITIVE 404 207 173 73 32 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 383 219 171 185 130 tfor:TF0431|5end_hypothetical_protein_452178..452408_POSITIVE 383 219 171 170 115 tfor:TF0430|5end_hypothetical_protein_452163..452393_POSITIVE 381 204 173 62 25 tfor:TF2817|5end_hypothetical_protein_3007358..3007588_POSITIVE 381 204 173 217 180 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 381 204 173 217 180 tfor:TF1185|5end_hypothetical_protein_1269238..1269468_POSITIVE 373 209 165 77 33 tfor:TF0218|5end_translation_initiation_factor_3_(IF-3)_243182..243412_POSITIVE 369 219 175 205 155 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 368 220 171 223 158 tfor:TF0462|5end_possible_cobalamin_biosynthesis_precorrin-3_methylase_477600..477830_POSITIVE 366 224 190 225 173 tfor:TF1037|5end_iron_(III)_ABC_transporter,_ATP-binding_protein_1098194..1098424_POSITIVE 363 220 181 47 3 tfor:TF2893|5end_conserved_hypothetical_protein;_possible_phosphoesterase_3080766..3080996_POSITIVE 363 207 174 67 30 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 360 204 168 58 9 tfor:TF2801|5end_outer_membrane_protein,_TonB_dependent_receptor_2986285..2986515_POSITIVE 354 220 172 54 8 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 352 219 175 226 176 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 349 79 40 190 158 tfor:TF0142|5end_subtilisin-like_serine_proteinase_149740..149970_POSITIVE 347 204 173 219 182 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 345 208 162 65 4 tfor:TF1465|5end_modulator_of_DNA_gyrase_1554148..1554378_POSITIVE 344 97 53 202 157 tfor:TF1467|5end_conserved_hypothetical_protein_1557011..1557241_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 213 171 144 99 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 343 204 168 39 1 tfor:TF2800|3end_anti-sigma_factor_2986346..2986496_POSITIVE 338 218 172 103 60 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 332 214 171 44 5 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 332 224 181 70 22 tfor:TF1156|3end_oxidoreductase,_FAD-binding_1238092..1238242_POSITIVE 330 214 173 54 2 tfor:TF2428|3end_conserved_hypothetical_protein_2610525..2610675_POSITIVE 327 190 144 49 5 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 326 204 174 127 92 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 325 214 171 45 1 tfor:TF0433|3end_60_kDa_inner_membrane_protein_455386..455536_POSITIVE 324 65 21 64 28 tfor:TF2657|3end_conserved_hypothetical_protein_2830873..2831023_POSITIVE 323 214 171 75 27 tfor:TF1655|3end_long-chain-fatty-acid-CoA_ligase_1771068..1771218_POSITIVE 323 238 196 71 25 tfor:TF1367|3end_hypothetical_protein_1447272..1447422_POSITIVE 323 238 196 67 21 tfor:TF1368|3end_hypothetical_protein_1447268..1447418_POSITIVE 321 220 171 73 19 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 315 207 168 148 101 tfor:TF1145|3end_anaerobic_C4-dicarboxylate_membrane_transporter_1227180..1227330_POSITIVE 313 238 196 71 25 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 313 238 196 67 21 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 313 202 161 71 16 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 313 206 161 151 103 tfor:TF0461|3end_ATP:cob(I)alamin_adenosyltransferase_477642..477792_POSITIVE 313 201 161 55 6 tfor:TF0167|3end_conserved_hypothetical_protein_178234..178384_POSITIVE