Origin IGS: cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta .........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 tagcatgtgtttgactttgttttgtattatccagcaatcctctattcacgctgtataataatttgtagcatgtgtttgactttgttttgtattatccccgtttccacgatgtcccatgctgtcgctgatgtatttgcaggaaactaaaaaggaacgttgttttgttctaatgcgttctctctatgggtagtgtaaaagtcgcattttttatgtaagtttgcaggcctattgaaggcgtccgacg Mask Tandem Repeat Region ================================================ cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta Find is-nt database================================================ Query_seq: TF1401:TF1403|TF1401:TF1403:Holliday junction DNA helicase:hypothetical protein:->->:1477671..1477914 244 cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1401:TF1403|TF1401:TF1403:Holliday junction DNA helicase:hypothetical protein:->->:1477671..1477914 244 cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1401:TF1403|TF1401:TF1403:Holliday junction DNA helicase:hypothetical protein:->->:1477671..1477914 244 cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 74 End: 196 ......................................................................... M R T K Q R S F L V S C K Y I S D S M G H R G N G D N T K Q S Q T H A T N Y Y T A ................................................ Protein_Len: 46 Strand: - Start: 101 End: 238 .................................................................................................... N G A F V D A V A H S M T S V P I I C F L T L C M S C I I I C R S Y L I A P Y Y L V F D F M ...... cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta 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================================================ cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1401:TF1403|TF1401:TF1403:Holliday junction DNA helicase:hypothetical protein:->->:1477671..1477914 244 cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: tfor_TF1401_TF1403|Holliday junction DNA helicase:hypothetical protein|POSITIVE:POSITIVE|[1477671,1477914]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta cgtcggacgccttcaataggcctgcaaacttacataaaaaatgcgacttttacactacccatagagagaacgcattagaacaaaacaacgttcctttttagtttcctgcaaatacatcagcgacagcatgggacatcgtggaaacggggataatacaaaacaaagtcaaacacatgctacaaattattatacagcgtgaatagaggattgctggataatacaaaacaaagtcaaacacatgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUCGGACGCCUUCAAUAGGCCUGCAAACUUACAUAAAAAAUGCGACUUUUACACUACCCAUAGAGAGAACGCAUUAGAACAAAACAACGUUCCUUUUUAGUUUCCUGCAAAUACAUCAGCGACAGCAUGGGACAUCGUGGAAACGGGGAUAAUACAAAACAAAGUCAAACACAUGCUACAAAUUAUUAUACAGCGUGAAUAGAGGAUUGCUGGAUAAUACAAAACAAAGUCAAACACAUGCUA .((((...((((.....)))).((((((((.........((((((.(((((............)))))..)))))).((((........))))......))))...))))..........)))).(((((.(((...((((.....(.(((.............)))...).....))))....((((((.(((((............))))).)))))).........))).....))))).. (-46.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAUGUGUUUGACUUUGUUUUGUAUUAUCCAGCAAUCCUCUAUUCACGCUGUAUAAUAAUUUGUAGCAUGUGUUUGACUUUGUUUUGUAUUAUCCCCGUUUCCACGAUGUCCCAUGCUGUCGCUGAUGUAUUUGCAGGAAACUAAAAAGGAACGUUGUUUUGUUCUAAUGCGUUCUCUCUAUGGGUAGUGUAAAAGUCGCAUUUUUUAUGUAAGUUUGCAGGCCUAUUGAAGGCGUCCGACG .((((((.(((.(((..((((...((((((.((((..............)))).))))))......))))...))).)))..................(((....)))......))))))((((..(((((....((((....)......((((((......))))))..)))......((.((((((..((((((....((((.....))))...)))))).)))))).))..))))))))). (-53.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 150 118 58 25 tfor:TF2911|5end_hypothetical_protein_3105871..3106101_POSITIVE 322 153 117 75 39 tfor:TF2038|5end_hypothetical_protein_2198978..2199208_POSITIVE 313 150 101 77 22 tfor:TF2033|5end_conserved_hypothetical_protein_2191529..2191759_POSITIVE 310 150 106 110 53 tfor:TF2187|5end_conserved_hypothetical_protein_2361693..2361923_POSITIVE 309 150 104 182 133 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 309 150 101 67 19 tfor:TF1332|5end_cytochrome_c-type_synthesis_protein_(cytochrome_c_biogenesis_protein);_ABC_transporter,_permease_1410957..1411187_POSITIVE 309 143 107 134 102 tfor:TF1229|5end_hypothetical_protein_1314619..1314849_POSITIVE 304 179 131 74 22 tfor:TF1261|5end_GrpE-related_chaperonin;_HSP-70_cofactor_1346504..1346734_POSITIVE 303 149 101 58 12 tfor:TF2331|5end_conserved_hypothetical_protein_2491073..2491303_POSITIVE 303 148 101 218 170 tfor:TF1448|5end_possible_competence_protein_1531711..1531941_POSITIVE 302 149 108 224 182 tfor:TF2020|5end_muconate_cycloisomerase_2176321..2176551_POSITIVE 302 149 116 214 181 tfor:TF0666|5end_conserved_hypothetical_protein_710461..710691_POSITIVE 301 152 120 168 141 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 299 149 106 173 119 tfor:TF0633|5end_hypothetical_protein_668922..669152_POSITIVE 297 147 105 74 26 tfor:TF1236|5end_L-rhamnose_isomerase_1320743..1320973_POSITIVE 296 150 106 103 60 tfor:TF0690|5end_preprotein_translocase_subunit_735243..735473_POSITIVE 295 150 105 59 8 tfor:TF0361|5end_hypothetical_protein_379458..379688_POSITIVE 292 148 107 189 124 tfor:TF2761|5end_thioredoxin_2945390..2945620_POSITIVE 292 151 121 67 34 tfor:TF2243|5end_possible_mobilization_protein_2417384..2417614_POSITIVE 291 230 190 59 16 tfor:TF1596|5end_hypothetical_protein_1711225..1711455_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 148 105 65 10 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 333 150 118 63 30 tfor:TF2909|3end_GTP-binding_protein,_possible_GTP1/OBG_family_3105956..3106106_POSITIVE 295 150 105 59 8 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 288 151 115 132 96 tfor:TF3120|3end_HD_superfamily_hydrolase_3354775..3354925_POSITIVE 286 128 89 53 12 tfor:TF2341|3end_hypothetical_protein_2506027..2506177_POSITIVE 285 150 105 58 8 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 285 149 101 112 58 tfor:TF0982|3end_conserved_hypothetical_protein_1039474..1039624_POSITIVE 281 147 118 137 107 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 281 150 101 81 29 tfor:TF1674|3end_ATP_synthase,_A_subunit_1788695..1788845_POSITIVE 281 177 131 122 84 tfor:TF0784|3end_possible_biopolymer_transport_protein_837881..838031_POSITIVE 280 150 106 80 22 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 280 150 101 70 9 tfor:TF0007|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_3599..3749_POSITIVE 279 221 192 84 53 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 279 147 101 46 5 tfor:TF0617|3end_alpha-1,2-mannosidase_653239..653389_POSITIVE 276 138 104 75 44 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 274 149 116 118 81 tfor:TF2273|3end_conserved_hypothetical_protein_2436708..2436858_POSITIVE 272 151 112 122 70 tfor:TF1774|3end_arylsulfatase_precursor_1912939..1913089_POSITIVE 272 150 108 67 21 tfor:TF0881|3end_conserved_hypothetical_protein_935993..936143_POSITIVE 271 168 130 42 4 tfor:TF1460|3end_6-phosphogluconate_dehydrogenase_1550790..1550940_POSITIVE 270 148 101 59 2 tfor:TF0358|3end_hypothetical_protein_376304..376454_POSITIVE