Origin IGS: gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgtttatcacttaaattcctttaattgctgtttcgctccccttgtcgctctttcaaaactaccttcaccgccccttgttcggattttattttcagacgaagctcttttcgtcaaaatcttatcggctgaaaatcggaaaaggcaaattctgctaaaagagctcgtcagaaaatagaaagttcgggatttgctctcagagcaatcgtcagaaaatctgacagagtcatttcgctccaaaatagcttttcagaaaatctgacggactgacttgtctttaaaagaacttagattgcttgaagaatagtttattttcctcgaaaaaatctcagaacatatgtaaaaattcgtctcttgttctcaggggaaaaaatctttcatgaagaatcttcctttttgccacaaaatcagaaattccacctgtaaaaattcgctttttgttcttttgggactgatttcacatgtgaaattaagtattttgagctctgggaagctcatttctcacagaaactaggcattcttacacaggttctttttccttc Mask Tandem Repeat Region ================================================ gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa Find is-nt database================================================ Query_seq: SSA_0796:SSA_0797|SSA_0796:SSA_0797:ABC-NBD transporters with duplicated ATPase domains, putative:Transcriptional regulator, putative:->->:779121..779660 540 gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0796:SSA_0797|SSA_0796:SSA_0797:ABC-NBD transporters with duplicated ATPase domains, putative:Transcriptional regulator, putative:->->:779121..779660 540 gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0796:SSA_0797|SSA_0796:SSA_0797:ABC-NBD transporters with duplicated ATPase domains, putative:Transcriptional regulator, putative:->->:779121..779660 540 gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 45 End: 179 ............................................ M S F P E L K I L N F T C E I S P K R T K S E F L Q V E F L I L W Q K G R F F M K D F F P ......................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 113 End: 211 ................................................................................................................ M F T G G I S D F V A K R K I L H E R F F P L R T R D E F L H M F ......................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 300 End: 530 ........................................................................................................................................................................................................................................................................................................... M L E R N D S V R F S D D C S E S K S R T F Y F L T S S F S R I C L F R F S A D K I L T K R A S S E N K I R T R G G E G .......... Protein_Len: 34 Strand: - Start: 414 End: 515 ............................................................................................................................................................................................................................................................................................................................................................................................................................. G I L N Q R F S S R R F I F D S C P A T F T T K F S R C P S R F L M ......................... Protein_Len: 46 Strand: - Start: 388 End: 525 ................................................................................................................................................................................................................................................................................................................................................................................................... C F K G K G I K L R Y S K S S F L K T Q F Y F G F L P R H L Y N Q F L S L P L S V A I L P M ............... Protein_Len: 30 Strand: - Start: 368 End: 457 ............................................................................................................................................................................................................................................................................................................................................................................... K R V L E K L L I Q R K R N E A S L I K V F L A E D S F L M ................................................................................... Protein_Len: 31 Strand: - Start: 276 End: 368 ................................................................................................................................................................................................................................................................................... D T L N E S F S N Q L S I V R D S K R V I A R L A F G S S E M ............................................................................................................................................................................ Protein_Len: 40 Strand: - Start: 120 End: 239 ....................................................................................................................... L H F K Q N Q P L F S S E E H F I K E G S F L L R I K V Y T R L N K R P F Y V M ............................................................................................................................................................................................................................................................................................................. Protein_Len: 44 Strand: - Start: 32 End: 163 ............................... N R H S I L K G S S L I S L K V H S I L G L L V F L S N K C T S N R I K H C F P L N K M ......................................................................................................................................................................................................................................................................................................................................................................................... gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa 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================================================ gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0796:SSA_0797|SSA_0796:SSA_0797:ABC-NBD transporters with duplicated ATPase domains, putative:Transcriptional regulator, putative:->->:779121..779660 540 gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa Intra-Species Hit: Count: 1 Min: 1 Max: 540 Len: 540 Subject: NC_009009_SSA_0796_SSA_0797|ABC-NBD transporters with duplicated ATPase domains, putative:Transcriptional regulator, putative|POSITIVE:POSITIVE|[779121,779660]|540 HSP 1 e-value: 0.0 bit: 1070.0 Len: 540 Query Start:1 Query End:540 Subject Strand: POSITIVE Subject Start: 1 Subject End: 540 gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa gaaggaaaaagaacctgtgtaagaatgcctagtttctgtgagaaatgagcttcccagagctcaaaatacttaatttcacatgtgaaatcagtcccaaaagaacaaaaagcgaatttttacaggtggaatttctgattttgtggcaaaaaggaagattcttcatgaaagattttttcccctgagaacaagagacgaatttttacatatgttctgagattttttcgaggaaaataaactattcttcaagcaatctaagttcttttaaagacaagtcagtccgtcagattttctgaaaagctattttggagcgaaatgactctgtcagattttctgacgattgctctgagagcaaatcccgaactttctattttctgacgagctcttttagcagaatttgccttttccgattttcagccgataagattttgacgaaaagagcttcgtctgaaaataaaatccgaacaaggggcggtgaaggtagttttgaaagagcgacaaggggagcgaaacagcaattaaaggaatttaagtgataaacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGGAAAAAGAACCUGUGUAAGAAUGCCUAGUUUCUGUGAGAAAUGAGCUUCCCAGAGCUCAAAAUACUUAAUUUCACAUGUGAAAUCAGUCCCAAAAGAACAAAAAGCGAAUUUUUACAGGUGGAAUUUCUGAUUUUGUGGCAAAAAGGAAGAUUCUUCAUGAAAGAUUUUUUCCCCUGAGAACAAGAGACGAAUUUUUACAUAUGUUCUGAGAUUUUUUCGAGGAAAAUAAACUAUUCUUCAAGCAAUCUAAGUUCUUUUAAAGACAAGUCAGUCCGUCAGAUUUUCUGAAAAGCUAUUUUGGAGCGAAAUGACUCUGUCAGAUUUUCUGACGAUUGCUCUGAGAGCAAAUCCCGAACUUUCUAUUUUCUGACGAGCUCUUUUAGCAGAAUUUGCCUUUUCCGAUUUUCAGCCGAUAAGAUUUUGACGAAAAGAGCUUCGUCUGAAAAUAAAAUCCGAACAAGGGGCGGUGAAGGUAGUUUUGAAAGAGCGACAAGGGGAGCGAAACAGCAAUUAAAGGAAUUUAAGUGAUAAACAA (((((((..(((((.(((((((((((.....((((((.(.(....).)..(((.(((.(((((((((....((((((((.(((((((...((................))....))))))).))))))))....)))))).))).....((((((.((((.....))))..)))))).))).)))..))))))..))))))))))).)))))....)))))))((((((.........))))))...((...(((((((((((((......(((((..(((((((...(((((..((.(((((((...))))))).))...)))))...))))))).((((((...))))))...................)))))..(((((((...(((((((.((((((.(((((((((((.(((..((.((((......)))).))))).))))))))....(((......))).))).))))))))))))))))))))..........((......))..)))))))))))))..))........ (-141.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUAUCACUUAAAUUCCUUUAAUUGCUGUUUCGCUCCCCUUGUCGCUCUUUCAAAACUACCUUCACCGCCCCUUGUUCGGAUUUUAUUUUCAGACGAAGCUCUUUUCGUCAAAAUCUUAUCGGCUGAAAAUCGGAAAAGGCAAAUUCUGCUAAAAGAGCUCGUCAGAAAAUAGAAAGUUCGGGAUUUGCUCUCAGAGCAAUCGUCAGAAAAUCUGACAGAGUCAUUUCGCUCCAAAAUAGCUUUUCAGAAAAUCUGACGGACUGACUUGUCUUUAAAAGAACUUAGAUUGCUUGAAGAAUAGUUUAUUUUCCUCGAAAAAAUCUCAGAACAUAUGUAAAAAUUCGUCUCUUGUUCUCAGGGGAAAAAAUCUUUCAUGAAGAAUCUUCCUUUUUGCCACAAAAUCAGAAAUUCCACCUGUAAAAAUUCGCUUUUUGUUCUUUUGGGACUGAUUUCACAUGUGAAAUUAAGUAUUUUGAGCUCUGGGAAGCUCAUUUCUCACAGAAACUAGGCAUUCUUACACAGGUUCUUUUUCCUUC ..........................(((((((((..((((...........................(((..(...)..))).((((((((((.(((((.((((((((.(.((.(((.((..(..(((.....)))....)..))))).))).))))))))))))).)))))))))).....))))...(((((((((((..((((((((...(((((.((((..((((.......))))..)))))))))...))))))))....(((((((((.((((((((..(((((..((((.(((.........))).))))...))))).((((((.(((........)))....))))))((((((((....(((((...)))))...(((..(((((...)))))...))).)))).))))................))))))))))))).(((((((....))))))))))).......)))))))).)))............)))))..)))).........(((........))).. (-122.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 59 14 220 169 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 354 389 341 219 164 NC_009009:SSA_2144|5end_Glutamyl-tRNA_synthetase,_putative_2145772..2146002_NEGATIVE 343 390 342 44 4 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 339 126 87 52 9 NC_009009:SSA_0695|5end_hypothetical_protein_678449..678679_POSITIVE 335 507 462 150 90 NC_009009:SSA_2162|5end_hypothetical_protein_2160592..2160822_POSITIVE 323 450 404 65 12 NC_009009:SSA_2299|5end_hypothetical_protein_2301545..2301775_NEGATIVE 322 418 371 192 151 NC_009009:SSA_0348|5end_CAAX_amino_terminal_protease_family,_putative_340288..340518_POSITIVE 322 61 25 202 166 NC_009009:SSA_0162|5end_hypothetical_protein_161391..161621_POSITIVE 317 505 462 76 25 NC_009009:SSA_1536|5end_Biotin_synthase,_putative_1543609..1543839_POSITIVE 315 510 464 77 38 NC_009009:SSA_1591|5end_Dipeptidase,_putative_1595451..1595681_NEGATIVE 313 507 464 158 108 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 311 505 463 50 10 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 309 430 387 215 169 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 308 539 494 83 34 NC_009009:SSA_1059|5end_hypothetical_protein_1076153..1076383_POSITIVE 308 309 271 61 11 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 308 420 376 165 109 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 305 315 274 177 136 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 304 517 471 200 157 NC_009009:SSA_0115|5end_50S_ribosomal_protein_L29,_putative_112402..112632_POSITIVE 303 408 361 157 101 NC_009009:SSA_1109|5end_ABC_transporter_ATP_binding/permease_protein,_putative_1133718..1133948_POSITIVE 300 507 465 173 136 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 507 465 89 47 NC_009009:SSA_0036|3end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_42050..42200_NEGATIVE 354 389 341 112 57 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE 322 418 371 146 105 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 314 507 464 75 33 NC_009009:SSA_1777|3end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1764427..1764577_NEGATIVE 311 505 463 48 8 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 308 539 494 61 12 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 308 309 271 71 21 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 303 408 361 143 87 NC_009009:SSA_1107|3end_Lipid/multidrug/protein-type_ABC_exporter,_ATP_binding/membrane-spanning_protein,_putative_1133784..1133934_POSITIVE 299 350 307 151 104 NC_009009:SSA_0999|3end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_998781..998931_NEGATIVE 298 413 372 48 2 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 293 380 338 48 2 NC_009009:SSA_0585|3end_hypothetical_protein_577286..577436_POSITIVE 292 80 31 148 97 NC_009009:SSA_2320|3end_hypothetical_protein_2322302..2322452_NEGATIVE 289 50 3 73 20 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 287 469 426 54 5 NC_009009:SSA_2204|3end_hypothetical_protein_2205507..2205657_POSITIVE 284 502 464 56 11 NC_009009:SSA_2255|3end_Transcriptional_regulator,_XRE_family,_putative_2250730..2250880_POSITIVE 284 475 435 116 62 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 284 360 311 135 70 NC_009009:SSA_1347|3end_PhnA_protein,_putative_1364791..1364941_NEGATIVE 284 420 372 142 104 NC_009009:SSA_0806|3end_hypothetical_protein_789478..789628_POSITIVE 283 506 470 48 15 NC_009009:SSA_0409|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_404697..404847_NEGATIVE 282 352 312 52 7 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE