Origin IGS: aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggtttcagatggaacttcttggcgaccaaaggcgttgaggatatgcgatggatgtccggatatgtgctgatggcgatatggtcaggctatctctttgtggaaaagtacattcctataagatgatggctgggacaaatgggcagtggattgtttactatattgtcaaactgctcctctttgtcgtcataggagtcttcaccgcacctttcacctgcttgtgggcagtgttcagggtaataaaggcttttcggtaagaggcggcaagaataacatctataaagaagaaagaatatgagtacgcacaatataccactcacatcggcatcatcatttgcaaatccaaaagcaggacgatt Mask Tandem Repeat Region ================================================ aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta Find is-nt database================================================ Query_seq: PI0242:PI0243|PI0242:PI0243:hypothetical protein:hypothetical protein:->->:240288..240645 358 aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0242:PI0243|PI0242:PI0243:hypothetical protein:hypothetical protein:->->:240288..240645 358 aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0242:PI0243|PI0242:PI0243:hypothetical protein:hypothetical protein:->->:240288..240645 358 aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 44 End: 199 ........................................... M V Y C A Y S Y S F F F I D V I L A A S Y R K A F I T L N T A H K Q V K G A V K T P M T T K R S S L T I ............................................................................................................................................................... Protein_Len: 60 Strand: + Start: 40 End: 267 ....................................... M S G I L C V L I F F L L Y R C Y S C R L L P K S L Y Y P E H C P Q A G E R C G E D S Y D D K E E Q F D N I V N N P L P ........................................................................................... Protein_Len: 34 Strand: - Start: 237 End: 338 ............................................................................................................................................................................................................................................ R I P I Y K E V F L Y G S W I A M L V Y G S M W R M D E V G K T A M .................... Protein_Len: 60 Strand: - Start: 106 End: 309 ......................................................................................................... V A W L C T F P A T F V G I V V F L L L K V I Y Y V I W Q G N T G A M M K Y S H V K G C L S L R V M D G D A C I R V D M ................................................. Protein_Len: 50 Strand: - Start: 65 End: 214 ................................................................ I R E E K Y I N N K G G R V S F G K N G Q V S G V L L H F T R H L S R H R C L P A T Q C Y L L C D M ................................................................................................................................................ Protein_Len: 30 Strand: - Start: 1 End: 90 I T R S K S K C I I I G I H T T Y Q A Y E Y E K K K I S T M ............................................................................................................................................................................................................................................................................ aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta 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================================================ aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0242:PI0243|PI0242:PI0243:hypothetical protein:hypothetical protein:->->:240288..240645 358 aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta Intra-Species Hit: Count: 1 Min: 1 Max: 358 Len: 358 Subject: pint_PI0242_PI0243|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[240288,240645]|358 HSP 1 e-value: 0.0 bit: 710.0 Len: 358 Query Start:1 Query End:358 Subject Strand: POSITIVE Subject Start: 1 Subject End: 358 aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta aatcgtcctgcttttggatttgcaaatgatgatgccgatgtgagtggtatattgtgcgtactcatattctttcttctttatagatgttattcttgccgcctcttaccgaaaagcctttattaccctgaacactgcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttataggaatgtacttttccacaaagagatagcctgaccatatcgccatcagcacatatccggacatccatcgcatatcctcaacgcctttggtcgccaagaagttccatctgaaaccta Inter-species Hit: Count: 1 Min: 134 Max: 257 Len: 124 Subject: tfor_TF1303_TF1304|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1384759,1385147]|389 HSP 1 e-value: 4.0E-24 bit: 113.0 Len: 124 Query Start:134 Query End:257 Subject Strand: POSITIVE Subject Start: 113 Subject End: 237 .....................................................................................................................................gcccacaagcaggtgaaaggtgcggtgaagactcctatgacgacaaagaggagcagtttgacaatatagtaaacaatccactgcccatttgtcccagccatcatcttata-ggaatgtacttttc..................................................................................................... .....................................................................................................................................gcccacaagcaggtgaaaggagcggtgaagactcctatgatgacaaagaggaggagtttgaagatatagtaaaatacccactgccagtttgttcctgcaatcattttatagggaatgaacttttc..................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCCACAAGCAGGUGAAAGGUGCGGUGAAGACUCCUAUGACGACAAAGAGGAGCAGUUUGACAAUAUAGUAAACAAUCCACUGCCCAUUUGUCCCAGCCAUCAUCUUAUAGGAAUGUACUUUUC ((......))....((((((((((........((((((((.((((((..((.((((((((((......))...)))...))))))).))))))............)))))))).)))))))))) (-27.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAGUACAUUCCUAUAAGAUGAUGGCUGGGACAAAUGGGCAGUGGAUUGUUUACUAUAUUGUCAAACUGCUCCUCUUUGUCGUCAUAGGAGUCUUCACCGCACCUUUCACCUGCUUGUGGGC .........((((((((..(((((..(..((((((....(((((((....(....)..)))))))....)).))))..)..))))))))))))).....(((((.............))))).. (-31.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 54 11 47 3 pint:PI0407|5end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_372973..373203_POSITIVE 346 50 5 52 6 pint:PI0883|5end_para-aminobenzoate_synthase_component_I_816131..816361_POSITIVE 323 60 11 161 94 pint:PI1953|5end_possible_ABC-type_permease_1907135..1907365_POSITIVE 320 31 1 63 37 pint:PI1416|5end_cation-transporting_ATPase_1335901..1336131_POSITIVE 315 59 12 180 129 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 314 48 5 156 105 pint:PI0898|5end_conserved_hypothetical_protein_828474..828704_POSITIVE 308 61 21 48 14 pint:PI0949|5end_endonuclease_882264..882494_POSITIVE 307 42 1 61 14 pint:PI2176|5end_conserved_hypothetical_protein_2116484..2116714_POSITIVE 304 99 52 68 10 pint:PI0545|5end_sugar_kinase_496411..496641_POSITIVE 303 49 3 172 126 pint:PI0101|5end_lauroyl/myristoyl_acyltransferase_96729..96959_POSITIVE 302 54 12 59 11 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 300 46 9 215 173 pint:PI0047|5end_phosphomethylpyrimidine_kinase_45964..46194_POSITIVE 299 120 78 52 6 pint:PI0314|5end_conserved_hypothetical_protein_295552..295782_POSITIVE 291 46 1 172 118 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 291 45 9 41 8 pint:PI0780|5end_DNA_gyrase,_subunit_A_(DNA_topoisomerase_(ATP-hydrolyzing))_715902..716132_POSITIVE 289 46 1 52 1 pint:PI1727|5end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1645680..1645910_POSITIVE 289 47 4 99 49 pint:PI0267|5end_conjugative_transposon_protein,_TraQ_258786..259016_POSITIVE 288 60 11 58 4 pint:PI1187|5end_conserved_hypothetical_protein_1106692..1106922_POSITIVE 286 46 1 135 82 pint:PI0679|5end_hypothetical_protein_616804..617034_POSITIVE 285 49 1 67 25 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 54 11 47 3 pint:PI0406|3end_hypothetical_protein_373053..373203_POSITIVE 341 50 7 44 1 pint:PI0882|3end_conserved_hypothetical_protein;_possible_para-aminobenzoate_synthase_component_I_816203..816353_POSITIVE 335 120 75 145 100 pint:PI0799|3end_alpha-amylase_family_protein_738854..739004_POSITIVE 314 48 5 139 88 pint:PI0897|3end_ferredoxin,_4Fe-4S_828537..828687_POSITIVE 303 49 3 89 43 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 296 50 6 90 38 pint:PI0422|3end_conserved_hypothetical_protein_388025..388175_POSITIVE 292 60 11 119 60 pint:PI0879|3end_hypothetical_protein_814051..814201_POSITIVE 288 60 11 58 4 pint:PI1186|3end_conserved_hypothetical_protein_1106772..1106922_POSITIVE 283 48 8 75 36 pint:PI1892|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1835547..1835697_POSITIVE 283 54 13 66 23 pint:PI0960|3end_hypothetical_protein_891381..891531_POSITIVE 282 31 1 56 28 pint:PI0126|3end_conserved_hypothetical_protein_118589..118739_POSITIVE 279 58 12 62 18 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE 278 56 12 151 100 pint:PI0979|3end_transcriptional_regulator,_tetR_family_905678..905828_POSITIVE 278 46 5 66 13 pint:PI0830|3end_conserved_hypothetical_protein_768206..768356_POSITIVE 277 43 1 146 93 pint:PI0115|3end_hypothetical_protein_108669..108819_POSITIVE 267 38 5 74 41 pint:PI1770|3end_4-alpha-glucanotransferase_1699998..1700148_POSITIVE 265 49 1 149 94 pint:PI1736|3end_topoisomerase_IV,_subunit_A_1657090..1657240_POSITIVE 264 49 6 89 44 pint:PI0925|3end_ribosomal_protein_L11_methyltransferase_856638..856788_POSITIVE 262 55 11 106 68 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 262 100 71 46 19 pint:PI0156|3end_conserved_hypothetical_protein_150913..151063_POSITIVE