Origin IGS: ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt .........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 aatgttgtaaattaaaaagtaataatgtataaagcgataatctatttcattttttcgttttatttcaggcctcaaatatagtttgaaaatttgactatcaacaataataagccatttttttttcaaaaaagtacaattttccccatacggtcctaaatatttccgtaaaaagagaaaaaaagacaggcttgtagaaggggcaacgcctttaataaatcctcgcatatttacctaaaatgattttttatgcaaaaaaaataaggcaatgacactggatatccttgcaccgtaaaaattattttttcattgccttgcggttaccttatcgccaagtttgcaaagaacaatgcaaaggcacgaaatgaaaagagagtcgtaaaccatagaaagttcgg Mask Tandem Repeat Region ================================================ ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt Find is-nt database================================================ Query_seq: TF0181:TF0182|TF0181:TF0182:ATP-dependent DNA helicase:DNA-binding protein, HU-related:->->:194924..195318 395 ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0181:TF0182|TF0181:TF0182:ATP-dependent DNA helicase:DNA-binding protein, HU-related:->->:194924..195318 395 ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0181:TF0182|TF0181:TF0182:ATP-dependent DNA helicase:DNA-binding protein, HU-related:->->:194924..195318 395 ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 171 End: 395 .......................................................................................................................................................................... M R G F I K G V A P S T S L S F F L F L R K Y L G P Y G E N C T F L K K K W L I I V D S Q I F K L Y L R P E I K R K N E Protein_Len: 43 Strand: - Start: 164 End: 292 ................................................................................................................................................................... T F I R P N I L P T A G E V L R D K K R K K R F Y K P G Y P S F Q V K K F F F H S I M ....................................................................................................... Protein_Len: 33 Strand: - Start: 3 End: 101 .. F K R H N V V R K E N R A K A N N K A F K A I L Y G C P L S F I M ...................................................................................................................................................................................................................................................................................................... ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt 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================================================ ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0181:TF0182|TF0181:TF0182:ATP-dependent DNA helicase:DNA-binding protein, HU-related:->->:194924..195318 395 ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt Intra-Species Hit: Count: 1 Min: 1 Max: 395 Len: 395 Subject: tfor_TF0181_TF0182|ATP-dependent DNA helicase:DNA-binding protein, HU-related|POSITIVE:POSITIVE|[194924,195318]|395 HSP 1 e-value: 0.0 bit: 640.0 Len: 395 Query Start:1 Query End:395 Subject Strand: POSITIVE Subject Start: 1 Subject End: 395 ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttannnnnnnngcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtcnnnnnnnctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgnnnnnnnnntggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt ccgaactttctatggtttacgactctcttttcatttcgtgcctttgcattgttctttgcaaacttggcgataaggtaaccgcaaggcaatgaaaaaataatttttacggtgcaaggatatccagtgtcattgccttattttttttgcataaaaaatcattttaggtaaatatgcgaggatttattaaaggcgttgccccttctacaagcctgtctttttttctctttttacggaaatatttaggaccgtatggggaaaattgtacttttttgaaaaaaaaatggcttattattgttgatagtcaaattttcaaactatatttgaggcctgaaataaaacgaaaaaatgaaatagattatcgctttatacattattactttttaatttacaacatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGAACUUUCUAUGGUUUACGACUCUCUUUUCAUUUCGUGCCUUUGCAUUGUUCUUUGCAAACUUGGCGAUAAGGUAACCGCAAGGCAAUGAAAAAAUAAUUUUUACGGUGCAAGGAUAUCCAGUGUCAUUGCCUUAUUUUUUUUGCAUAAAAAAUCAUUUUAGGUAAAUAUGCGAGGAUUUAUUAAAGGCGUUGCCCCUUCUACAAGCCUGUCUUUUUUUCUCUUUUUACGGAAAUAUUUAGGACCGUAUGGGGAAAAUUGUACUUUUUUGAAAAAAAAAUGGCUUAUUAUUGUUGAUAGUCAAAUUUUCAAACUAUAUUUGAGGCCUGAAAUAAAACGAAAAAAUGAAAUAGAUUAUCGCUUUAUACAUUAUUACUUUUUAAUUUACAACAUU ..(((((......))))).(((...(((((((((((((((((((((((........))))))...))).....((((((.((.(((((((((.((((....)))).........((....))....))))))))).....((((((((((....(((......)))...))))))))))..........)))))))).......((.((((......((((((((...(((((............))))).)))))))).........((((((((.....(((((.((((....)))))))))..)))))))).........)))).)).......))))...))))))).)))...))).................................. (-80.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUUGUAAAUUAAAAAGUAAUAAUGUAUAAAGCGAUAAUCUAUUUCAUUUUUUCGUUUUAUUUCAGGCCUCAAAUAUAGUUUGAAAAUUUGACUAUCAACAAUAAUAAGCCAUUUUUUUUUCAAAAAAGUACAAUUUUCCCCAUACGGUCCUAAAUAUUUCCGUAAAAAGAGAAAAAAAGACAGGCUUGUAGAAGGGGCAACGCCUUUAAUAAAUCCUCGCAUAUUUACCUAAAAUGAUUUUUUAUGCAAAAAAAAUAAGGCAAUGACACUGGAUAUCCUUGCACCGUAAAAAUUAUUUUUUCAUUGCCUUGCGGUUACCUUAUCGCCAAGUUUGCAAAGAACAAUGCAAAGGCACGAAAUGAAAAGAGAGUCGUAAACCAUAGAAAGUUCGG ....(((((.((((........)))).)))))..(((...(((((......(((((.(((((((((..(((((....((((((.........))))))........(((((((.((((((((((..((((......)))).....(((((............)))))......))))))))))..)))))))....)))))...((((((..............(((((.....)))))...((((.((((((......((((((((((....(((((...((((...))))....)))))..))))))))))(((((......)))))....)))))).))))......))))))..))))))))).))))).........)))))....))). (-80.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 562 170 122 131 83 tfor:TF1095|5end_transposase_1164343..1164573_POSITIVE 434 170 122 132 83 tfor:TF0670|5end_possible_transposase_714069..714299_POSITIVE 406 170 122 93 44 tfor:TF2479|5end_conserved_hypothetical_protein_2655992..2656222_POSITIVE 406 170 122 93 44 tfor:TF1264|5end_possible_transposase_1351290..1351520_POSITIVE 360 148 107 90 41 tfor:TF1865|5end_conserved_hypothetical_protein;_possible_transposase_2021532..2021762_POSITIVE 355 88 41 205 155 tfor:TF0480|5end_ornithine_carbamoyltransferase_498550..498780_POSITIVE 351 67 39 231 203 tfor:TF0373|5end_conserved_hypothetical_protein,_yngK-related_391038..391268_POSITIVE 318 86 51 218 177 tfor:TF2777|5end_hypothetical_protein_2961595..2961825_POSITIVE 318 86 51 93 52 tfor:TF2776|5end_hypothetical_protein_2961470..2961700_POSITIVE 309 229 186 231 188 tfor:TF0830|5end_hypothetical_protein_887610..887840_POSITIVE 308 46 1 230 189 tfor:TF2684|5end_conserved_hypothetical_protein;_possible_CvpA_family_protein_2860692..2860922_POSITIVE 307 84 41 57 7 tfor:TF2214|5end_peptidyl-prolyl_cis-trans_isomerase_2386897..2387127_POSITIVE 305 225 186 228 173 tfor:TF2531|5end_possible_dipeptidyl-peptidase_III_2713045..2713275_POSITIVE 304 70 23 227 163 tfor:TF3072|5end_conserved_hypothetical_protein_3295302..3295532_POSITIVE 303 69 26 144 101 tfor:TF2618|5end_integral_membrane_protein,_possible_zinc_transporter_2795215..2795445_POSITIVE 301 86 42 50 8 tfor:TF2974|5end_conserved_hypothetical_protein;_possible_hydrolase_3181418..3181648_POSITIVE 299 228 187 127 86 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 298 70 22 60 10 tfor:TF2524|5end_conserved_hypothetical_protein;_possible_endonuclease/exonuclease/phosphatase_family_protein_2702910..2703140_POSITIVE 298 80 33 229 176 tfor:TF2498|5end_electron_transfer_flavoprotein,_alpha_subunit_2672801..2673031_POSITIVE 297 76 36 72 31 tfor:TF1888|5end_RNA_polymerase_ECF-type_sigma_factor_2040940..2041170_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 562 170 122 54 6 tfor:TF1094|3end_conserved_hypothetical_protein_1164346..1164496_POSITIVE 406 170 122 58 9 tfor:TF1263|3end_DNA-mismatch_repair_protein_1351335..1351485_POSITIVE 312 228 186 50 6 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 297 188 141 54 8 tfor:TF2142|3end_hypothetical_protein_2319212..2319362_POSITIVE 297 87 48 136 91 tfor:TF1865|3end_conserved_hypothetical_protein;_possible_transposase_2022406..2022556_POSITIVE 297 235 192 150 103 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 294 129 87 146 107 tfor:TF0940|3end_transposase_982040..982190_POSITIVE 292 211 174 86 49 tfor:TF2119|3end_conserved_hypothetical_protein_2292188..2292338_POSITIVE 292 210 171 150 110 tfor:TF0494|3end_conserved_hypothetical_protein_520906..521056_POSITIVE 290 239 191 104 43 tfor:TF2312|3end_conserved_hypothetical_protein;_possible_glycosyl_transferase_2472522..2472672_POSITIVE 287 79 31 130 88 tfor:TF0538|3end_hypothetical_protein_567135..567285_POSITIVE 284 88 46 148 103 tfor:TF2835|3end_stationary-phase_survival_protein_SurE_3025960..3026110_POSITIVE 284 220 172 74 21 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 281 94 51 145 102 tfor:TF3131|3end_uracil-DNA_glycosylase_3365248..3365398_POSITIVE 281 209 161 113 64 tfor:TF0459|3end_sulfatase_476836..476986_POSITIVE 279 81 41 37 5 tfor:TF2833|3end_lipid_A_disaccharide_synthase_3025183..3025333_POSITIVE 278 79 31 140 98 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 278 79 31 130 88 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 276 41 1 94 56 tfor:TF1034|3end_conserved_hypothetical_protein_1095901..1096051_POSITIVE 275 145 106 78 37 tfor:TF0954|3end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_999272..999422_POSITIVE