Origin IGS: ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgacaagtaattgaaaaactcctcaattggtgttgaaaaattgagtttctttcttggccttgaatagattttcgctgttatttcatctatatctccgtcctttagttgtttca .........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 tgaaacaactaaaggacggagatatagatgaaataacagcgaaaatctattcaaggccaagaaagaaactcaatttttcaacaccaattgaggagtttttcaattacttgtcgtaaatttgcacttgcttgttgaattcgcattactttcaatgaaagttaaatacgttaaatattcgccaatttaactccaatcagattcaatgatttcacttttctaccgtttaatatgtaatccattgaaataaaataacttacaaatactgtcactaatctattttcctcaaaattgattggtaatgacaaatgcgaatacaatgtattctctcattaaagacgagcctgatatagattggggggatgatttggattgggttaaatttacactattgtgcgaggaatcagacgaaggcaaggattacttgaaacttgcaaagaaaggagttttatgtcatgggtatgctgtgcgaggtaacttatactatgctaa Mask Tandem Repeat Region ================================================ ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgacaagtaattgaaaaactcctcaattggtgttgaaaaattgagtttctttcttggccttgaatagattttcgctgttatttcatctatatctccgtcctttagttgtttca Find is-nt database================================================ Query_seq: TF3055:TF3056|TF3055:TF3056:hypothetical protein:conserved hypothetical protein:->->:3279095..3279583 489 ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgacaagtaattgaaaaactcctcaattggtgttgaaaaattgagtttctttcttggccttgaatagattttcgctgttatttcatctatatctccgtcctttagttgtttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3055:TF3056|TF3055:TF3056:hypothetical protein:conserved hypothetical protein:->->:3279095..3279583 489 ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgacaagtaattgaaaaactcctcaattggtgttgaaaaattgagtttctttcttggccttgaatagattttcgctgttatttcatctatatctccgtcctttagttgtttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 2 Min: 380 Max: 487 Len: 108 Subject: gi|60681629|ref|YP_211773.1| putative IS element [Bacteroides fragilis NCTC 9343] HSP 1 e-value: 8.0E-6 bit: 46.6 Len: 108 Query Start:380 Query End:487 Subject Strand: null Subject Start: 279 Subject End: 314 ........................................................................................................................................................................................................................................................................................................................................................................................... K Q L K D G D I D E I T A K I Y S R P R K K L N F S T P I E E F F N Y L .. ........................................................................................................................................................................................................................................................................................................................................................................................... K K I N D T D I D A I M N K I N N R P R K K L D F S T P F E M F S S Y L .. Subject: UniRef90_Q5LDG6 Cluster: Putative IS element; n=2; Bacteroides fragilis NCTC 9343|Rep: Putative IS element - Bacteroides fragilis (strain ATCC 25285 / NCTC 9343) HSP 1 e-value: 8.0E-6 bit: 46.6 Len: 108 Query Start:380 Query End:487 Subject Strand: null Subject Start: 279 Subject End: 314 ........................................................................................................................................................................................................................................................................................................................................................................................... K Q L K D G D I D E I T A K I Y S R P R K K L N F S T P I E E F F N Y L .. ........................................................................................................................................................................................................................................................................................................................................................................................... K K I N D T D I D A I M N K I N N R P R K K L D F S T P F E M F S S Y L .. Find nr database================================================ Query_seq: TF3055:TF3056|TF3055:TF3056:hypothetical protein:conserved hypothetical protein:->->:3279095..3279583 489 ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 11 End: 106 .......... M S Y L A Q H T H D I K L L S L Q V S S N P C L R L I P R T I V ............................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 43 Strand: + Start: 76 End: 204 ........................................................................... M P S S D S S H N S V N L T Q S K S S P Q S I S G S S L M R E Y I V F A F V I T N Q F ............................................................................................................................................................................................................................................................................................. Protein_Len: 33 Strand: + Start: 120 End: 218 ....................................................................................................................... M Q I I P P I Y I R L V F N E R I H C I R I C H Y Q S I L R K I D ............................................................................................................................................................................................................................................................................... Protein_Len: 49 Strand: + Start: 173 End: 319 ............................................................................................................................................................................ M Y S H L S L P I N F E E N R L V T V F V S Y F I S M D Y I L N G R K V K S L N L I G V K L A N I .......................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 377 End: 466 ........................................................................................................................................................................................................................................................................................................................................................................................ S L Y N F F E E I P T S F N L K K R P R S Y I K A T I E D M ....................... Protein_Len: 31 Strand: - Start: 19 End: 111 .................. R A C C V W S M F S R E K C T E L L G Q R R R I G R V I T Y M .......................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 3 End: 197 .. G R V A Y G H C L V G K K A L K L Y D K G E D S E E C L L T F K V W D L D D G W D I D P E D K I L S Y M T N A N T M V M .................................................................................................................................................................................................................................................................................................... ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnca 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================================================ ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3055:TF3056|TF3055:TF3056:hypothetical protein:conserved hypothetical protein:->->:3279095..3279583 489 ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnca Intra-Species Hit: Count: 1 Min: 1 Max: 379 Len: 379 Subject: tfor_TF3055_TF3056|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3279095,3279583]|489 HSP 1 e-value: 0.0 bit: 751.0 Len: 379 Query Start:1 Query End:379 Subject Strand: POSITIVE Subject Start: 1 Subject End: 379 ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacga.............................................................................................................. ttagcatagtataagttacctcgcacagcatacccatgacataaaactcctttctttgcaagtttcaagtaatccttgccttcgtctgattcctcgcacaatagtgtaaatttaacccaatccaaatcatccccccaatctatatcaggctcgtctttaatgagagaatacattgtattcgcatttgtcattaccaatcaattttgaggaaaatagattagtgacagtatttgtaagttattttatttcaatggattacatattaaacggtagaaaagtgaaatcattgaatctgattggagttaaattggcgaatatttaacgtatttaactttcattgaaagtaatgcgaattcaacaagcaagtgcaaatttacga.............................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGCAUAGUAUAAGUUACCUCGCACAGCAUACCCAUGACAUAAAACUCCUUUCUUUGCAAGUUUCAAGUAAUCCUUGCCUUCGUCUGAUUCCUCGCACAAUAGUGUAAAUUUAACCCAAUCCAAAUCAUCCCCCCAAUCUAUAUCAGGCUCGUCUUUAAUGAGAGAAUACAUUGUAUUCGCAUUUGUCAUUACCAAUCAAUUUUGAGGAAAAUAGAUUAGUGACAGUAUUUGUAAGUUAUUUUAUUUCAAUGGAUUACAUAUUAAACGGUAGAAAAGUGAAAUCAUUGAAUCUGAUUGGAGUUAAAUUGGCGAAUAUUUAACGUAUUUAACUUUCAUUGAAAGUAAUGCGAAUUCAACAAGCAAGUGCAAAUUUACGA ...((((.(((.....))).(((((..((........(((.................(((((..(......)..)))))....(((((((.....((((....))))..(((......)))......................)))))))..))).(((((((((((((((...((((((((..(((((((((...(((.(((((....))))).))))))))))))............((((.(((((((((((((.((.(((..((.........))..)))...))))))).)))))))).))))..)))))))).....)))))...))))))))))..))..))))).............)))).......... (-68.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUAAAUUUGCACUUGCUUGUUGAAUUCGCAUUACUUUCAAUGAAAGUUAAAUACGUUAAAUAUUCGCCAAUUUAACUCCAAUCAGAUUCAAUGAUUUCACUUUUCUACCGUUUAAUAUGUAAUCCAUUGAAAUAAAAUAACUUACAAAUACUGUCACUAAUCUAUUUUCCUCAAAAUUGAUUGGUAAUGACAAAUGCGAAUACAAUGUAUUCUCUCAUUAAAGACGAGCCUGAUAUAGAUUGGGGGGAUGAUUUGGAUUGGGUUAAAUUUACACUAUUGUGCGAGGAAUCAGACGAAGGCAAGGAUUACUUGAAACUUGCAAAGAAAGGAGUUUUAUGUCAUGGGUAUGCUGUGCGAGGUAACUUAUACUAUGCUAA ..((...(((((((.((((..(.((..........(((((..((.(((((.....((((.....((((((((((((((.((((((...((((((((((.((..((..........))..)).))).))))))).............(((((...(((.(((((((((.....(((...(((.((..((((((.....(.((((((...)))))).)))))))..)))))...))).)))))))))...))).)))))))))))))))).........)))).)))))......))))....((((.....)))).))))).))..)))))..........)))..))))....)))))))...)).............. (-77.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 96 51 211 165 tfor:TF2383|5end_hypothetical_protein_2548300..2548530_POSITIVE 299 98 57 143 87 tfor:TF2487|5end_transposase_2663010..2663240_POSITIVE 287 90 51 92 52 tfor:TF3160|5end_conserved_hypothetical_protein_3395531..3395761_POSITIVE 278 162 122 50 15 tfor:TF1824|5end_ABC_transporter,_ATP-binding_protein_1972537..1972767_POSITIVE 275 156 116 147 87 tfor:TF2892|5end_seryl-tRNA_synthetase_3079309..3079539_POSITIVE 275 120 71 199 147 tfor:TF2567|5end_30S_ribosomal_protein_S14_2740867..2741097_POSITIVE 269 96 58 194 149 tfor:TF1315|5end_purine_nucleoside_phosphorylase_1390236..1390466_POSITIVE 268 99 55 230 189 tfor:TF2996|5end_hypothetical_protein_3210802..3211032_POSITIVE 268 95 54 224 168 tfor:TF0830|5end_hypothetical_protein_887610..887840_POSITIVE 265 178 136 99 50 tfor:TF0874|5end_transposase_925685..925915_POSITIVE 265 98 58 60 10 tfor:TF0584|5end_phosphopantetheinyl_transferase_613755..613985_POSITIVE 264 55 15 115 62 tfor:TF2986|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_3201818..3202048_POSITIVE 264 97 73 76 49 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 264 97 73 69 42 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 264 99 54 206 162 tfor:TF0117|5end_2-dehydro-3-deoxygluconokinase_128682..128912_POSITIVE 261 120 74 194 151 tfor:TF2758|5end_hypothetical_protein_2942392..2942622_POSITIVE 261 60 14 79 27 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 259 120 76 189 155 tfor:TF0933|5end_conserved_hypothetical_protein;_possible_DNA_repair_protein_972397..972627_POSITIVE 259 195 151 147 103 tfor:TF0299|5end_hypothetical_protein_324821..325051_POSITIVE 258 89 44 202 141 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 90 51 92 52 tfor:TF3159|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_3395611..3395761_POSITIVE 275 156 116 139 79 tfor:TF2891|3end_lipoprotein_3079381..3079531_POSITIVE 269 108 74 63 15 tfor:TF3118|3end_conserved_hypothetical_protein_3352824..3352974_POSITIVE 267 99 51 129 70 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 265 98 58 54 4 tfor:TF0583|3end_possible_gliding_motility-related_protein_613829..613979_POSITIVE 264 59 22 105 59 tfor:TF2613|3end_conserved_hypothetical_protein_2789798..2789948_POSITIVE 261 120 74 57 14 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE 259 195 151 114 70 tfor:TF0298|3end_dipeptidase_324868..325018_POSITIVE 257 90 47 75 21 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 256 136 94 144 99 tfor:TF0155|3end_conserved_hypothetical_protein_165057..165207_POSITIVE 253 143 109 41 9 tfor:TF2744|3end_methionyl-tRNA_formyltransferase_2927378..2927528_POSITIVE 253 180 133 69 27 tfor:TF1792|3end_acid_phosphatase_1933319..1933469_POSITIVE 250 56 18 104 60 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE 247 98 51 68 16 tfor:TF3091|3end_50S_ribosomal_protein_L13_3324787..3324937_POSITIVE 247 319 277 111 65 tfor:TF3057|3end_conserved_hypothetical_protein_3281238..3281388_POSITIVE 245 98 51 67 15 tfor:TF1665|3end_conserved_hypothetical_protein_1779578..1779728_POSITIVE 245 182 143 56 13 tfor:TF1032|3end_possible_internalin-related_protein_1092842..1092992_POSITIVE 245 317 277 123 78 tfor:TF0464|3end_precorrin_methylase_482108..482258_POSITIVE 244 199 153 117 68 tfor:TF0556|3end_Bacteroides_aerotolerance_protein,_BatA_589149..589299_POSITIVE 243 98 56 67 29 tfor:TF1109|3end_lipoprotein_1179997..1180147_POSITIVE