Origin IGS: tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt .........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 aattaaagatatttatgttaatactcgcaaagatagacttattaaatgacttagataaatttaatgagttaaaaaaacataaatatatagttaaaatatgtttctcttttattttattcaacactgtcgttggccgtttcctttacagatacagaggcgcacatggatcaagggtctcactctaccatcatatcatcgtgttacgatataagtagtcatgtataaatgcgaattagattttcgatttacgagaaatctctacta Mask Tandem Repeat Region ================================================ tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Find is-nt database================================================ Query_seq: TF1457:TF1458|TF1457:TF1458:conserved hypothetical protein; possible transporter:conserved hypothetical protein:->->:1544311..1544574 264 tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1457:TF1458|TF1457:TF1458:conserved hypothetical protein; possible transporter:conserved hypothetical protein:->->:1544311..1544574 264 tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1457:TF1458|TF1457:TF1458:conserved hypothetical protein; possible transporter:conserved hypothetical protein:->->:1544311..1544574 264 tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 141 End: 263 ............................................................................................................................................ M L N K I K E K H I L T I Y L C F F N S L N L S K S F N K S I F A S I N I N I F N . Protein_Len: 37 Strand: - Start: 57 End: 167 ........................................................ I T V R H Y S P L T L G K I W T R R Q I Q L P F P W R C H Q I F Y F L F M ................................................................................................. Protein_Len: 60 Strand: - Start: 53 End: 256 .................................................... H Y L S V R S G H A G R Y R Y L F R G V V T N F L I F S F C I K V I Y K H K K L E N F K D L D N L L D I K A L I L M F M ........ Protein_Len: 33 Strand: - Start: 43 End: 141 .......................................... V H S S I D Y C S S I I T S H S G Q D M H A E T D T F S V A L S M ........................................................................................................................... tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 168 End: 197 .......................................................................................................................................................................GTTAAAAAAACATAAATATATAGTTAAAAT................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1457:TF1458|TF1457:TF1458:conserved hypothetical protein; possible transporter:conserved hypothetical protein:->->:1544311..1544574 264 tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: tfor_TF1457_TF1458|conserved hypothetical protein; possible transporter:conserved hypothetical protein|POSITIVE:POSITIVE|[1544311,1544574]|264 HSP 1 e-value: 1.0E-135 bit: 482.0 Len: 264 Query Start:1 Query End:264 Subject Strand: POSITIVE Subject Start: 1 Subject End: 264 tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgnnnnnnnaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt tagtagagatttctcgtaaatcgaaaatctaattcgcatttatacatgactacttatatcgtaacacgatgatatgatggtagagtgagacccttgatccatgtgcgcctctgtatctgtaaaggaaacggccaacgacagtgttgaataaaataaaagagaaacatattttaactatatatttatgtttttttaactcattaaatttatctaagtcatttaataagtctatctttgcgagtattaacataaatatctttaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAGAGAUUUCUCGUAAAUCGAAAAUCUAAUUCGCAUUUAUACAUGACUACUUAUAUCGUAACACGAUGAUAUGAUGGUAGAGUGAGACCCUUGAUCCAUGUGCGCCUCUGUAUCUGUAAAGGAAACGGCCAACGACAGUGUUGAAUAAAAUAAAAGAGAAACAUAUUUUAACUAUAUAUUUAUGUUUUUUUAACUCAUUAAAUUUAUCUAAGUCAUUUAAUAAGUCUAUCUUUGCGAGUAUUAACAUAAAUAUCUUUAAUU ...(((((((..((((((((.((((.......)))).((((((..((((((..(((((((((......))))))))).(((((((((((..((((....((.(((((....))))).))..)))).......(((((....)))))...........(((((((((((...............)))))))))))..)))))....))))))..))))))...)))))).....)))))))).............)))))))... (-49.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAAGAUAUUUAUGUUAAUACUCGCAAAGAUAGACUUAUUAAAUGACUUAGAUAAAUUUAAUGAGUUAAAAAAACAUAAAUAUAUAGUUAAAAUAUGUUUCUCUUUUAUUUUAUUCAACACUGUCGUUGGCCGUUUCCUUUACAGAUACAGAGGCGCACAUGGAUCAAGGGUCUCACUCUACCAUCAUAUCAUCGUGUUACGAUAUAAGUAGUCAUGUAUAAAUGCGAAUUAGAUUUUCGAUUUACGAGAAAUCUCUACUA ..((((..(((((((((((.....((.....))..((((((((((((...........)))))))))))).....)))))))))))....)))).....(((((((............((((......))))..(((......(((((((((.(((((.(...........).)))))................((((.....))))....)).))).)))).....)))...................)))))))........ (-45.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 119 71 128 74 tfor:TF2444|5end_regulatory_protein_RecX_2620957..2621187_POSITIVE 332 138 93 86 41 tfor:TF0797|5end_conserved_hypothetical_protein_853296..853526_POSITIVE 324 113 73 138 98 tfor:TF3061|5end_conserved_hypothetical_protein_3285022..3285252_POSITIVE 322 137 91 210 163 tfor:TF2177|5end_hypothetical_protein_2349281..2349511_POSITIVE 321 138 92 131 81 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 321 138 92 80 30 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 312 119 77 191 147 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 310 146 106 231 191 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 307 120 75 48 1 tfor:TF2090|5end_phosphoribosylglycinamide_formyltransferase_2258692..2258922_POSITIVE 306 119 71 228 173 tfor:TF2911|5end_hypothetical_protein_3105871..3106101_POSITIVE 306 133 94 169 130 tfor:TF1929|5end_conserved_hypothetical_protein_2076049..2076279_POSITIVE 306 130 82 55 11 tfor:TF1553|5end_copper_homeostasis_protein_1658873..1659103_POSITIVE 302 120 75 189 143 tfor:TF0454|5end_xanthine/uracil_permease_family_protein_472087..472317_POSITIVE 301 138 93 60 10 tfor:TF1819|5end_cation_efflux_system_AcrB/AcrD/AcrF_family;_ABC_transporter,_ATP-binding/permease_component_1958681..1958911_POSITIVE 301 143 106 44 2 tfor:TF1152|5end_permease,_major_facilitator_superfamily_1233267..1233497_POSITIVE 301 139 97 70 29 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 300 130 83 66 7 tfor:TF1592|5end_hypothetical_protein_1708325..1708555_POSITIVE 300 130 83 66 7 tfor:TF1590|5end_hypothetical_protein_1705811..1706041_POSITIVE 299 146 103 82 22 tfor:TF2654|5end_arginyl-tRNA_synthetase_2822692..2822922_POSITIVE 299 109 61 229 176 tfor:TF2401|5end_conserved_hypothetical_protein_2573174..2573404_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 119 71 144 90 tfor:TF2443|3end_amidophosphoribosyl-transferase_2621053..2621203_POSITIVE 321 138 92 99 49 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 301 138 93 53 3 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 296 137 92 143 99 tfor:TF2184|3end_conserved_hypothetical_protein_2357043..2357193_POSITIVE 295 144 103 35 1 tfor:TF2176|3end_hypothetical_protein_2349185..2349335_POSITIVE 290 133 93 63 27 tfor:TF1002|3end_replicative_DNA_helicase_1058232..1058382_POSITIVE 287 137 92 128 87 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 287 128 81 62 12 tfor:TF0636|3end_beta-galactosidase_673284..673434_POSITIVE 286 118 85 91 60 tfor:TF2044|3end_excinuclease_ABC,_subunit_A_2206163..2206313_POSITIVE 286 140 91 142 99 tfor:TF1327|3end_L-fucose_permease_1407195..1407345_POSITIVE 282 132 92 59 14 tfor:TF1266|3end_conserved_hypothetical_protein_1354165..1354315_POSITIVE 282 110 61 99 45 tfor:TF0898|3end_hypothetical_protein_945730..945880_POSITIVE 281 131 91 116 72 tfor:TF1868|3end_conserved_hypothetical_protein;_possible_transposase_2023043..2023193_POSITIVE 279 144 103 35 1 tfor:TF2170|3end_hypothetical_protein_2345070..2345220_POSITIVE 278 144 104 36 4 tfor:TF0348|3end_hypothetical_protein_370447..370597_POSITIVE 276 137 95 150 108 tfor:TF1263|3end_DNA-mismatch_repair_protein_1351335..1351485_POSITIVE 275 110 66 83 42 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 274 114 74 149 109 tfor:TF3004|3end_phosphoribosylformylglycinamidine_(FGAM)_synthase_3224576..3224726_POSITIVE 274 132 91 151 111 tfor:TF1843|3end_surface_antigen_BspA_1996189..1996339_POSITIVE 274 143 104 72 33 tfor:TF1579|3end_hypothetical_protein_1687274..1687424_POSITIVE