Origin IGS: ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga .........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 tcttgctccttacgctttaatttggtttgcaaaaatagtaaatatccttagtaatcggaaaaatacaatcgctcctctctcgatctttcctcgcgggatgagaggaaggtagagagaagagcgactgcagcgggaataatctctgtcgggtgcgcgcggcctataatcgagatcttgtatccccggtcc Mask Tandem Repeat Region ================================================ ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga Find is-nt database================================================ Query_seq: PG0593:PG0594|PG0593:PG0594:htrA protein:RNA polymerase sigma-70 factor:->->:651999..652187 189 ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0593:PG0594|PG0593:PG0594:htrA protein:RNA polymerase sigma-70 factor:->->:651999..652187 189 ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0593:PG0594|PG0593:PG0594:htrA protein:RNA polymerase sigma-70 factor:->->:651999..652187 189 ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 17 End: 139 ................ M S I I G R A H P T E I I P A A V A L L S T F L S S R E E R S R E E R L Y F S D Y .................................................. Protein_Len: 37 Strand: + Start: 60 End: 170 ........................................................... M Q S L F S L P S S H P A R K D R E R S D C I F P I T K D I Y Y F C K P N ................... Protein_Len: 56 Strand: + Start: 10 End: 177 ......... M Q D L D Y R P R A P D R D Y S R C S R S S L Y L P L I P R G K I E R G A I V F F R L L R I F T I F A N Q I K A ............ Protein_Len: 30 Strand: - Start: 81 End: 170 ................................................................................ R G R M G R P F I S L P A I T N K R N S L I N V I K A F W M ................... ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga 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================================================ ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.9 Tail_Score: -4.08349 Start: 66 End: 121 Full_Region: TTATTCCCGCTGCAG TCGCTCTTCTCTCTACCTTCCTCTC ATCCC GCGAGGAAAGATCGAGAGAGGAGCGA TTGTATTTTTCCGAT .................................................................TCGCTCTTCTCTCTACCTTCCTCTCATCCCGCGAGGAAAGATCGAGAGAGGAGCGA.................................................................... Find igs database================================================ Query_seq: PG0593:PG0594|PG0593:PG0594:htrA protein:RNA polymerase sigma-70 factor:->->:651999..652187 189 ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: NC_002950_PG0593_PG0594|htrA protein:RNA polymerase sigma-70 factor|POSITIVE:POSITIVE|[651999,652187]|189 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 189 ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga ggaccggggatacaagatctcgattataggccgcgcgcacccgacagagattattcccgctgcagtcgctcttctctctaccttcctctcatcccgcgaggaaagatcgagagaggagcgattgtatttttccgattactaaggatatttactatttttgcaaaccaaattaaagcgtaaggagcaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGACCGGGGAUACAAGAUCUCGAUUAUAGGCCGCGCGCACCCGACAGAGAUUAUUCCCGCUGCAGUCGCUCUUCUCUCUACCUUCCUCUCAUCCCGCGAGGAAAGAUCGAGAGAGGAGCGAUUGUAUUUUUCCGAUUACUAAGGAUAUUUACUAUUUUUGCAAACCAAAUUAAAGCGUAAGGAGCAAGA (((.((((((((....(((((........((.....))........))))))))))))).((((((((((((((((((..(.((((((.(.....).)))))).)...))))))))))))))))))....)))......................((((((...((..............)).)))))) (-60.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUGCUCCUUACGCUUUAAUUUGGUUUGCAAAAAUAGUAAAUAUCCUUAGUAAUCGGAAAAAUACAAUCGCUCCUCUCUCGAUCUUUCCUCGCGGGAUGAGAGGAAGGUAGAGAGAAGAGCGACUGCAGCGGGAAUAAUCUCUGUCGGGUGCGCGCGGCCUAUAAUCGAGAUCUUGUAUCCCCGGUCC ...((((((....(((........((((((.......))))))......)))....))).........((((((.((((((...((((((((.........))))))))..)))))).))))))..))).((((.(((((((((((.((.((....)).)).)))...)))))....))).)))).... (-55.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 70 28 71 34 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 421 120 71 162 106 NC_002950:PG0124|5end_hypothetical_protein_146234..146464_NEGATIVE 420 70 21 214 164 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 394 73 31 62 16 NC_002950:PG0291|5end_hypothetical_protein_325457..325687_POSITIVE 377 78 35 49 2 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 373 68 27 230 185 NC_002950:PG0632|5end_biopolymer_transport_protein_ExbD,_putative_684877..685107_POSITIVE 369 80 31 215 161 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 368 70 28 226 163 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 367 44 1 172 125 NC_002950:PG0671|5end_iron_compound_ABC_transporter,_permease_protein_721888..722118_POSITIVE 365 39 1 103 62 NC_002950:PG2145|5end_polysaccharide_deacetylase_2253253..2253483_POSITIVE 365 69 21 192 138 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 364 100 51 222 165 NC_002950:PG1003|5end_hypothetical_protein_1059232..1059462_POSITIVE 362 49 3 209 161 NC_002950:PG1488|5end_hypothetical_protein_1561747..1561977_POSITIVE 357 69 28 192 125 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 355 74 31 70 29 NC_002950:PG2065|5end_conserved_hypothetical_protein_TIGR00048_2161000..2161230_POSITIVE 353 109 61 228 184 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 353 79 31 216 162 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 349 70 21 139 89 NC_002950:PG0854|5end_hypothetical_protein_914870..915100_POSITIVE 346 99 57 221 154 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 345 69 29 187 155 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 70 28 74 37 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 420 70 21 135 85 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 416 120 75 47 3 NC_002950:PG2072|3end_UvrD/REP_helicase_domain_protein_2170757..2170907_POSITIVE 416 79 33 59 17 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 394 73 31 59 13 NC_002950:PG0290|3end_hypothetical_protein_325534..325684_POSITIVE 377 69 22 131 89 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 375 100 51 75 9 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 373 86 41 139 83 NC_002950:PG0021|3end_TIM-barrel_protein,_putative,_NifR3_family_24122..24272_NEGATIVE 365 39 1 60 19 NC_002950:PG2144|3end_hypothetical_protein_2253290..2253440_POSITIVE 364 100 51 147 90 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 357 89 41 118 62 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 356 123 81 77 33 NC_002950:PG0915|3end_hypothetical_protein_977057..977207_POSITIVE 354 70 29 57 6 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 353 120 82 88 56 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 349 70 21 138 88 NC_002950:PG0853|3end_DNA-binding_protein,_histone-like_family_914949..915099_POSITIVE 346 145 103 131 93 NC_002950:PG1836|3end_nucleoside_permease_NupG_1929858..1930008_POSITIVE 345 68 30 85 39 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 343 63 31 117 75 NC_002950:PG0799|3end_hypothetical_protein_854599..854749_POSITIVE 342 120 82 83 46 NC_002950:PG0324|3end_histidine_ammonia-lyase_357589..357739_NEGATIVE 340 45 1 61 21 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE