Origin IGS: catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agggtaaagggaagtcccttccccttttcgcctgactttcccttgcccattcgaaagagagaagaagagaatacttcattctcttcgggcataagaagagagggtgtgtgaagatcgtgatcgagcggttttgaagtgaaccctgaatgttttgtatcgaactttcagggttcactgcatttggcacactccttttccgtttttacagacacagctcttatggtataagtcggccttgcatacatgacggcaggtcaaacggcatggattcctataccgaaaggagctatacttcggctcattataactgaaagaggaaagagaaggggaacgatcgggctgtccggatagctttgattgggggagcaaagctatcggattatacaccggcgagcatg Mask Tandem Repeat Region ================================================ catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct Find is-nt database================================================ Query_seq: PG0672:PG0674|PG0672:PG0674:iron compound ABC transporter, ATP-binding protein:indolepyruvate ferredoxin oxidoreductase, beta subunit:-><-:723901..724298 398 catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0672:PG0674|PG0672:PG0674:iron compound ABC transporter, ATP-binding protein:indolepyruvate ferredoxin oxidoreductase, beta subunit:-><-:723901..724298 398 catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0672:PG0674|PG0672:PG0674:iron compound ABC transporter, ATP-binding protein:indolepyruvate ferredoxin oxidoreductase, beta subunit:-><-:723901..724298 398 catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 12 End: 224 ........... M Y N P I A L L P Q S K L S G Q P D R S P S L S S F S Y N E P K Y S S F R Y R N P C R L T C R H V C K A D L Y H K S C V .............................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 231 End: 320 ...................................................................................................................................................................................................................................... M K V R Y K T F R V H F K T A R S R S S H T L S S Y A R R E .............................................................................. Protein_Len: 30 Strand: + Start: 307 End: 396 .................................................................................................................................................................................................................................................................................................................. M P E E N E V F S S S L F R M G K G K S G E K G K G L P F T .. Protein_Len: 60 Strand: + Start: 212 End: 397 ................................................................................................................................................................................................................... M P N A V N P E S S I Q N I Q G S L Q N R S I T I F T H P L F L C P K R M K Y S L L L S F E W A R E S Q A K R G R D F P . Protein_Len: 30 Strand: - Start: 174 End: 263 ............................................................................................................................................................................. V M L A T D T F V S F S H A L H L S G Q F N S V F C E P N M ....................................................................................................................................... Protein_Len: 34 Strand: - Start: 155 End: 256 .......................................................................................................................................................... T H L A S K Y W L L Q T Q L F P F P T H W I C H V R F T R Y L V N M .............................................................................................................................................. Protein_Len: 54 Strand: - Start: 91 End: 252 .......................................................................................... N Y H A S T Y S R E T Y S D M G N S R G D H I C P R S I G Y S S H R Y F R F L L T G F A T F G S L E I C F M .................................................................................................................................................. Protein_Len: 35 Strand: - Start: 51 End: 155 .................................................. G S L G I T G R R K G R E T I I L R L I A G K P I P I W A T Q G A T M ................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 2 End: 91 . H E G T Y L G I A K S G W D F S D P C G S R E G E R E E K M ................................................................................................................................................................................................................................................................................................................... catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct 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================================================ catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.1 Tail_Score: -3.54919 Start: 220 End: 267 Full_Region: gtgatcgagcggttt tgaagtgaaccctgaatgttt tgtatc gaactttcagggttcactgca tttggcacactcctt ...........................................................................................................................................................................................................................tgaagtgaaccctgaatgttttgtatcgaactttcagggttcactgca................................................................................................................................... TransTerm Strand: + Conf: 57 HP_score: -6.5 Tail_Score: -3.17075 Start: 229 End: 258 Full_Region: GCCAAATGCAGTGAA CCCTGAAAGTT CGATACAA AACATTCAGGG TTCACTTCAAAACCG ....................................................................................................................................................................................................................................CCCTGAAAGTTCGATACAAAACATTCAGGG............................................................................................................................................ TransTerm Strand: + Conf: 79 HP_score: -10.0 Tail_Score: -3.76634 Start: 313 End: 335 Full_Region: TCTCTTCTTATGCCC GAAGAGAATG AAG TATTCTCTTC TTCTCTCTTTCGAAT ........................................................................................................................................................................................................................................................................................................................GAAGAGAATGAAGTATTCTCTTC............................................................... TransTerm Strand: - Conf: 40 HP_score: -2.4 Tail_Score: -2.79452 Start: 322 End: 335 Full_Region: attcgaaagagagaa gaag agaata cttc attctcttcgggcat .................................................................................................................................................................................................................................................................................................................................gaagagaatacttc............................................................... Find igs database================================================ Query_seq: PG0672:PG0674|PG0672:PG0674:iron compound ABC transporter, ATP-binding protein:indolepyruvate ferredoxin oxidoreductase, beta subunit:-><-:723901..724298 398 catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct Intra-Species Hit: Count: 1 Min: 1 Max: 398 Len: 398 Subject: NC_002950_PG0672_PG0674|iron compound ABC transporter, ATP-binding protein:indolepyruvate ferredoxin oxidoreductase, beta subunit|POSITIVE:NEGATIVE|[723901,724298]|398 HSP 1 e-value: 0.0 bit: 789.0 Len: 398 Query Start:1 Query End:398 Subject Strand: POSITIVE Subject Start: 1 Subject End: 398 catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct catgctcgccggtgtataatccgatagctttgctcccccaatcaaagctatccggacagcccgatcgttccccttctctttcctctttcagttataatgagccgaagtatagctcctttcggtataggaatccatgccgtttgacctgccgtcatgtatgcaaggccgacttataccataagagctgtgtctgtaaaaacggaaaaggagtgtgccaaatgcagtgaaccctgaaagttcgatacaaaacattcagggttcacttcaaaaccgctcgatcacgatcttcacacaccctctcttcttatgcccgaagagaatgaagtattctcttcttctctctttcgaatgggcaagggaaagtcaggcgaaaaggggaagggacttccctttaccct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUGCUCGCCGGUGUAUAAUCCGAUAGCUUUGCUCCCCCAAUCAAAGCUAUCCGGACAGCCCGAUCGUUCCCCUUCUCUUUCCUCUUUCAGUUAUAAUGAGCCGAAGUAUAGCUCCUUUCGGUAUAGGAAUCCAUGCCGUUUGACCUGCCGUCAUGUAUGCAAGGCCGACUUAUACCAUAAGAGCUGUGUCUGUAAAAACGGAAAAGGAGUGUGCCAAAUGCAGUGAACCCUGAAAGUUCGAUACAAAACAUUCAGGGUUCACUUCAAAACCGCUCGAUCACGAUCUUCACACACCCUCUCUUCUUAUGCCCGAAGAGAAUGAAGUAUUCUCUUCUUCUCUCUUUCGAAUGGGCAAGGGAAAGUCAGGCGAAAAGGGGAAGGGACUUCCCUUUACCCU .....((((((((((....(((((((((((((..........))))))))).))))......((((((....(((((.(((((...((((.......))))....((((((((((.((..((((((((...((.(((....((((.....)))).....))).))....))))))))..)))))))))).))........)))))))))).(.((....((.(((((((((((((.(((........))).))))))))))))).)).....)).)....)))))).....))))).....((((..((((((((((((..((((......))))...))))))).....)))))..)))).....)))))..((((((((((....)))))).)))) (-136.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGUAAAGGGAAGUCCCUUCCCCUUUUCGCCUGACUUUCCCUUGCCCAUUCGAAAGAGAGAAGAAGAGAAUACUUCAUUCUCUUCGGGCAUAAGAAGAGAGGGUGUGUGAAGAUCGUGAUCGAGCGGUUUUGAAGUGAACCCUGAAUGUUUUGUAUCGAACUUUCAGGGUUCACUGCAUUUGGCACACUCCUUUUCCGUUUUUACAGACACAGCUCUUAUGGUAUAAGUCGGCCUUGCAUACAUGACGGCAGGUCAAACGGCAUGGAUUCCUAUACCGAAAGGAGCUAUACUUCGGCUCAUUAUAACUGAAAGAGGAAAGAGAAGGGGAACGAUCGGGCUGUCCGGAUAGCUUUGAUUGGGGGAGCAAAGCUAUCGGAUUAUACACCGGCGAGCAUG ((((..(((((....))))).)))).((((((...(((((...(((((.(((....)))....(((((((((.....))))))))))))))......)))))((((((((..((((((......((.(...((.(((((((((((((.((((......)))).))))))))))))).))..).))...((((((((((.(((((.(((....(((((((.(((((((.(....((.(((.....((((.....))))....))).))...).)))))))..)))))))...(....)..........)))))))).)...))))))))).)))))).....(((((.(((((((((.((....)).)))))))))))))))))))))))))))).... (-149.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 168 121 142 99 NC_002950:PG1977|5end_hypothetical_protein_2066693..2066923_NEGATIVE 397 170 135 76 40 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 392 76 35 201 152 NC_002950:PG2028|5end_ebsC_protein_2126027..2126257_POSITIVE 392 67 22 122 67 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 387 379 338 180 132 NC_002950:PG1024|5end_hypothetical_protein_1086698..1086928_POSITIVE 381 49 8 220 185 NC_002950:PG1619|5end_biotin_synthesis_protein_BioC,_putative_1698568..1698798_POSITIVE 377 105 62 230 177 NC_002950:PG1003|5end_hypothetical_protein_1059232..1059462_POSITIVE 377 70 21 168 110 NC_002950:PG0882|5end_hypothetical_protein_944195..944425_POSITIVE 376 178 131 53 2 NC_002950:PG1251|5end_hypothetical_protein_1327779..1328009_POSITIVE 374 139 100 140 93 NC_002950:PG1087|5end_radical_SAM_protein,_TIGR01212_family_1153805..1154035_POSITIVE 372 178 131 53 2 NC_002950:PG1363|5end_hypothetical_protein_1443804..1444034_POSITIVE 368 89 47 118 70 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 363 108 63 164 115 NC_002950:PG0534|5end_hypothetical_protein_583242..583472_POSITIVE 361 260 211 102 53 NC_002950:PG0554|5end_hypothetical_protein_611465..611695_POSITIVE 359 190 148 189 136 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 354 177 132 64 15 NC_002950:PG1576|5end_L-aspartate_oxidase_1653016..1653246_POSITIVE 351 178 131 178 125 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 349 70 22 195 140 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 348 168 131 64 19 NC_002950:PG1486|5end_conjugative_transposon_protein_TraA_1561166..1561396_NEGATIVE 348 149 101 109 38 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 475 267 223 52 8 NC_002950:PG2192|3end_peptidase,_M23/M37_family_2299334..2299484_POSITIVE 399 168 121 112 69 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 393 79 31 66 5 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 390 84 41 107 52 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 378 262 223 50 11 NC_002950:PG0343|3end_methionine_gamma-lyase_377181..377331_NEGATIVE 368 146 101 150 103 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 368 90 42 137 85 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 368 89 47 110 62 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 357 90 41 82 16 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 357 160 112 89 37 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 350 360 311 60 13 NC_002950:PG1285|3end_glucosamine-6-phosphate_deaminase_1364941..1365091_POSITIVE 348 63 21 149 104 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 348 149 101 146 75 NC_002950:PG1310|3end_exsB_protein_1389826..1389976_POSITIVE 342 67 21 151 110 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 341 61 21 83 39 NC_002950:PG2068|3end_glycerol-3-phosphate_cytidylyltransferase_2164872..2165022_POSITIVE 338 378 331 90 39 NC_002950:PG0130|3end_phosphoglyceromutase_151922..152072_NEGATIVE 337 320 273 85 31 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 333 50 8 124 83 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 333 386 342 58 12 NC_002950:PG0025|3end_fumarylacetoacetate_hydrolase_family_protein_29196..29346_POSITIVE 332 86 47 77 36 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE