Origin IGS: gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat .........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 attttagatatttttgaataaaaatacttgacatttttatccgttttaagtatactcaagccacacacaaacgatacacactgtttttcactagactcgctcattatcctccttttgggtgagtcttctttttttattccattttatttttttacataagtttatgttcgtacagtttaccc Mask Tandem Repeat Region ================================================ gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat Find is-nt database================================================ Query_seq: TDE0304:TDE0305|TDE0304:TDE0305:hypothetical protein:GTP-binding protein YchF:-><-:335553..335734 182 gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0304:TDE0305|TDE0304:TDE0305:hypothetical protein:GTP-binding protein YchF:-><-:335553..335734 182 gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0304:TDE0305|TDE0304:TDE0305:hypothetical protein:GTP-binding protein YchF:-><-:335553..335734 182 gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 46 End: 180 ............................................. M K K E D S P K R R I M S E S S E K Q C V S F V C G L S I L K T D K N V K Y F Y S K I S K .. Protein_Len: 34 Strand: - Start: 64 End: 165 ............................................................... G F P P Y H A L R T F F L T Y R K H T A Q T Y K F R I F I D L I K M ................. Protein_Len: 43 Strand: - Start: 27 End: 155 .......................... T F F Y F P I F F S S E G L L L I I L S D L S F C H T D N T H P K L I S L V S L F T M ........................... gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat 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: 90 Start: 127 End: 156 ..............................................................................................................................CTTGACATTTTTATCCGTTTTAAGTATACT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0304:TDE0305|TDE0304:TDE0305:hypothetical protein:GTP-binding protein YchF:-><-:335553..335734 182 gggtaaactgtacgaacataaacttatgtaaaaaaataaaatggaataaaaaaagaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_002967_TDE0304_TDE0305|hypothetical protein:GTP-binding protein YchF|POSITIVE:NEGATIVE|[335553,335734]|182 HSP 1 e-value: 9.0E-67 bit: 254.0 Len: 128 Query Start:55 Query End:182 Subject Strand: POSITIVE Subject Start: 55 Subject End: 182 ......................................................gaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat ......................................................gaagactcacccaaaaggaggataatgagcgagtctagtgaaaaacagtgtgtatcgtttgtgtgtggcttgagtatacttaaaacggataaaaatgtcaagtatttttattcaaaaatatctaaaat HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 29 Query Start:1 Query End:29 Subject Strand: POSITIVE Subject Start: 1 Subject End: 29 gggtaaactgtacgaacataaacttatgt......................................................................................................................................................... gggtaaactgtacgaacataaacttatgt......................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUAAACUGUACGAACAUAAACUUAUGUAAAAAAAUAAAAUGGAAUAAAAAAAGAAGACUCACCCAAAAGGAGGAUAAUGAGCGAGUCUAGUGAAAAACAGUGUGUAUCGUUUGUGUGUGGCUUGAGUAUACUUAAAACGGAUAAAAAUGUCAAGUAUUUUUAUUCAAAAAUAUCUAAAAU (((((.(((((....((((((((.((..((..........................((((((.(.((............)).).)))))).((.....))..))..))..))))))))...))...))).))))).....(((((((((((.....)))))))))))............... (-29.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUAGAUAUUUUUGAAUAAAAAUACUUGACAUUUUUAUCCGUUUUAAGUAUACUCAAGCCACACACAAACGAUACACACUGUUUUUCACUAGACUCGCUCAUUAUCCUCCUUUUGGGUGAGUCUUCUUUUUUUAUUCCAUUUUAUUUUUUUACAUAAGUUUAUGUUCGUACAGUUUACCC ..((((((....)))))).....((((((((.((........)).))))))))...............((((..(((...............(((((((((((............)))))))))))...........................(((((....)))))..)))..)))).... (-26.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 162 122 205 162 NC_002967:TDE1079|5end_DNA-binding_protein/PTS_system,_IIA_component_1111120..1111350_POSITIVE 262 109 73 190 159 NC_002967:TDE2214|5end_hypothetical_protein_2253050..2253280_POSITIVE 256 129 86 110 64 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 243 145 109 90 51 NC_002967:TDE1472|5end_flagellar_hook-associated_protein_1520715..1520945_NEGATIVE 242 142 102 33 3 NC_002967:TDE0353|5end_lipase/acylhydrolase,_GDSL_family_398338..398568_NEGATIVE 241 120 71 109 53 NC_002967:TDE2667|5end_hypothetical_protein_2704374..2704604_POSITIVE 241 84 49 70 30 NC_002967:TDE1376|5end_hypothetical_protein_1418586..1418816_POSITIVE 237 109 70 230 195 NC_002967:TDE1446|5end_hypothetical_protein_1491970..1492200_POSITIVE 236 155 111 130 86 NC_002967:TDE2110|5end_orotidine_5'-phosphate_decarboxylase_2135329..2135559_POSITIVE 236 121 83 187 161 NC_002967:TDE2008|5end_ABC_transporter,_ATP-binding/permease_protein_2028578..2028808_POSITIVE 235 129 88 208 169 NC_002967:TDE2180|5end_tRNA_modification_GTPase_2212008..2212238_NEGATIVE 234 124 81 66 24 NC_002967:TDE1674|5end_hypothetical_protein_1728591..1728821_NEGATIVE 231 128 83 46 3 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 229 124 99 133 109 NC_002967:TDE0220|5end_hypothetical_protein_254005..254235_NEGATIVE 228 127 81 146 84 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 228 128 81 65 14 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 228 109 67 201 157 NC_002967:TDE0941|5end_NLP/P60_family_protein_964102..964332_NEGATIVE 222 89 44 212 169 NC_002967:TDE1888|5end_hypothetical_protein_1909500..1909730_NEGATIVE 221 86 42 185 134 NC_002967:TDE2314|5end_hypothetical_protein_2352054..2352284_POSITIVE 221 95 54 227 179 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 137 101 51 15 NC_002967:TDE0462|3end_metallo-beta-lactamase_family_protein_516178..516328_NEGATIVE 272 162 122 50 7 NC_002967:TDE1078|3end_metallo-beta-lactamase_family_protein_1111045..1111195_POSITIVE 243 145 109 45 6 NC_002967:TDE1473|3end_flagellin_FlaG,_putative_1520760..1520910_NEGATIVE 241 84 49 47 7 NC_002967:TDE1375|3end_pantetheine-phosphate_adenylyltransferase_1418643..1418793_POSITIVE 238 108 65 66 29 NC_002967:TDE1937|3end_hypothetical_protein_1953448..1953598_POSITIVE 238 130 86 41 1 NC_002967:TDE0359|3end_ABC_transporter,_ATP-binding/permease_protein_402193..402343_NEGATIVE 229 124 99 92 68 NC_002967:TDE0221|3end_hypothetical_protein_254046..254196_NEGATIVE 221 95 54 141 93 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 220 123 82 40 8 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 218 125 99 48 14 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 217 131 101 122 88 NC_002967:TDE0064|3end_diphosphate--fructose-6-phosphate_1-phosphotransferase_71335..71485_NEGATIVE 213 130 83 55 8 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 213 130 83 65 18 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 212 112 71 107 59 NC_002967:TDE1121|3end_hypothetical_protein_1152814..1152964_NEGATIVE 210 157 118 53 11 NC_002967:TDE1445|3end_hypothetical_protein_1491079..1491229_NEGATIVE 209 98 55 67 16 NC_002967:TDE1198|3end_S-adenosyl-methyltransferase_MraW_1231419..1231569_POSITIVE 208 150 101 71 20 NC_002967:TDE0522|3end_hypothetical_protein_569244..569394_POSITIVE 207 124 82 148 115 NC_002967:TDE0610|3end_3-hydroxyacyl-CoA_dehydrogenase,_putative_646357..646507_NEGATIVE 206 130 100 150 115 NC_002967:TDE2742|3end_site-specific_recombinase,_phage_integrase_family_2796850..2797000_NEGATIVE 204 91 57 45 12 NC_002967:TDE0409|3end_hypothetical_protein_462133..462283_POSITIVE