Origin IGS: atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacattttttaatttcaagccgtaaaaatacaactattttacaaatcacaaaatcgcgtcggagaaaaagaattgtcccgaattttcacttgccggataaaccttcggcaaccgaacacgtcttaatatcgattttattcttttgacgat Mask Tandem Repeat Region ================================================ atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt Find is-nt database================================================ Query_seq: TF0412:TF0413|TF0412:TF0413:conserved hypothetical protein:succinyl-diaminopimelate desuccinylase:->->:430424..430573 150 atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0412:TF0413|TF0412:TF0413:conserved hypothetical protein:succinyl-diaminopimelate desuccinylase:->->:430424..430573 150 atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0412:TF0413|TF0412:TF0413:conserved hypothetical protein:succinyl-diaminopimelate desuccinylase:->->:430424..430573 150 atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 1 End: 102 M V K R I K S I L R R V R L P K V Y P A S E N S G Q F F F S D A I L ................................................ Protein_Len: 32 Strand: - Start: 28 End: 123 ........................... S T N P Q R L N I R C T F I R S L E K E G V R N Q S K Y F L Q M ........................... Protein_Len: 44 Strand: - Start: 8 End: 139 ....... F F L I S I L V H E T A S P K D P L H F N P V I R K R R R S K T I Q L I T T N K R S S M ........... atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt 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================================================ atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0412:TF0413|TF0412:TF0413:conserved hypothetical protein:succinyl-diaminopimelate desuccinylase:->->:430424..430573 150 atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: tfor_TF0412_TF0413|conserved hypothetical protein:succinyl-diaminopimelate desuccinylase|POSITIVE:POSITIVE|[430424,430573]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt atcgtcaaaagaataaaatcgatattaagacgtgttcggttgccgaaggtttatccggcaagtgaaaattcgggacaattctttttctccgacgcgattttgtgatttgtaaaatagttgtatttttacggcttgaaattaaaaaatgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGUCAAAAGAAUAAAAUCGAUAUUAAGACGUGUUCGGUUGCCGAAGGUUUAUCCGGCAAGUGAAAAUUCGGGACAAUUCUUUUUCUCCGACGCGAUUUUGUGAUUUGUAAAAUAGUUGUAUUUUUACGGCUUGAAAUUAAAAAAUGUU .((..((((...(((((((((.............((((.((((((..........)))))).))))...((((((.((....)).)).))))..)))))))))..))))......(((((((....))))))).)).............. (-32.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUUUUUUAAUUUCAAGCCGUAAAAAUACAACUAUUUUACAAAUCACAAAAUCGCGUCGGAGAAAAAGAAUUGUCCCGAAUUUUCACUUGCCGGAUAAACCUUCGGCAACCGAACACGUCUUAAUAUCGAUUUUAUUCUUUUGACGAU .....................((((((.........))))))..............(((((((..((.(((((((....((...(((..((((((((......))))))))..)))....)).......))))))).))..))))))).. (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 60 18 222 177 tfor:TF0960|5end_beta-galactosidase_1008618..1008848_POSITIVE 357 80 32 204 158 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 357 80 32 100 54 tfor:TF3106|5end_hypothetical_protein_3338355..3338585_POSITIVE 344 97 55 164 121 tfor:TF0259|5end_conserved_hypothetical_protein_289750..289980_POSITIVE 335 74 31 231 183 tfor:TF0219|5end_threonyl-tRNA_synthetase_243843..244073_POSITIVE 333 99 51 46 1 tfor:TF1860|5end_aspartate_carbamoyltransferase,_catalytic_subunit_2016191..2016421_POSITIVE 330 78 31 118 60 tfor:TF2654|5end_arginyl-tRNA_synthetase_2822692..2822922_POSITIVE 322 75 31 56 5 tfor:TF0597|5end_hypothetical_protein_628788..629018_POSITIVE 320 64 21 229 189 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 316 98 52 206 153 tfor:TF2794|5end_possible_transcriptional_regulator_2979938..2980168_POSITIVE 315 78 31 57 1 tfor:TF2244|5end_possible_mobilization_protein_2419425..2419655_POSITIVE 312 94 54 76 44 tfor:TF1912|5end_transcriptional_regulator,_TetR_family_2065970..2066200_POSITIVE 308 88 41 107 55 tfor:TF2435|5end_DNA_repair_protein_radC_2614352..2614582_POSITIVE 307 98 53 66 26 tfor:TF3020|5end_possible_sulfatase_3243559..3243789_POSITIVE 306 58 20 223 168 tfor:TF1207|5end_outer_membrane_receptor,_TonB-dependent_1290062..1290292_POSITIVE 304 94 54 138 93 tfor:TF2985|5end_glycosyltransferase_protein_3200307..3200537_POSITIVE 303 59 28 192 156 tfor:TF0944|5end_TonB-dependent_receptor_986340..986570_POSITIVE 302 75 37 47 12 tfor:TF2918|5end_hypothetical_protein_3114084..3114314_POSITIVE 302 97 56 195 161 tfor:TF2913|5end_conserved_hypothetical_protein_3107910..3108140_POSITIVE 302 77 33 130 84 tfor:TF1260|5end_chaperone_protein_DnaJ_1345325..1345555_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 424 74 31 87 31 tfor:TF0959|3end_periplasmic_protease_1008540..1008690_POSITIVE 322 75 31 143 97 tfor:TF0666|3end_conserved_hypothetical_protein_710945..711095_POSITIVE 318 58 16 151 98 tfor:TF3143|3end_conserved_hypothetical_protein;_possible_membrane_protein_3379227..3379377_POSITIVE 316 98 52 76 23 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE 315 74 31 58 26 tfor:TF1422|3end_GLCNAC_transferase_(UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)-pyr_ophosphoryl-undecaprenol_N-acetylglucosamine_transferase)_1505823..1505973_POSITIVE 313 75 31 145 90 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 313 76 35 76 23 tfor:TF0308|3end_hypothetical_protein_334082..334232_POSITIVE 312 77 31 151 100 tfor:TF1838|3end_tRNA/rRNA_methyltransferase_1988745..1988895_POSITIVE 305 75 37 147 111 tfor:TF1138|3end_ribosomal_large_subunit_pseudouridine_synthase_B_1215238..1215388_POSITIVE 304 94 54 138 93 tfor:TF2984|3end_glycosyltransferase_3200387..3200537_POSITIVE 302 75 37 44 9 tfor:TF2917|3end_conserved_hypothetical_protein_3114161..3114311_POSITIVE 300 63 27 51 15 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 299 60 17 133 76 tfor:TF2873|3end_conserved_hypothetical_protein_3064966..3065116_POSITIVE 299 76 31 63 19 tfor:TF2629|3end_conserved_hypothetical_protein;_possible_lactoylglutathione_lyase_2801768..2801918_POSITIVE 297 80 32 118 71 tfor:TF3003|3end_hypothetical_protein_3220629..3220779_POSITIVE 295 120 71 45 1 tfor:TF1859|3end_aspartate_carbamoyltransferase,_regulatory_subunit_2016255..2016405_POSITIVE 291 66 29 85 32 tfor:TF1932|3end_pigmentation_and_extracellular_proteinase_regulator_2079755..2079905_POSITIVE 290 74 31 73 22 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 288 127 81 72 18 tfor:TF0602|3end_aminotripeptidase;_peptidase_T_633472..633622_POSITIVE 286 76 34 128 91 tfor:TF1262|3end_PDZ_domain_protein_1348831..1348981_POSITIVE