Origin IGS: tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt .........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 aaaattgatatttatatggtaatatctttaataaagataatgctaaaaatttacaaaataagacgggttcttagggcagagccctaagcggttcttttgaagataggaggggttataggggaggaaagaaatcttttatccgaaaaagtgtctttcctcccctaattaatcaggaggtgagagaagtgttagcagaaaattcagagata Mask Tandem Repeat Region ================================================ tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt Find is-nt database================================================ Query_seq: TDE2097:TDE2098|TDE2097:TDE2098:hypothetical protein:hypothetical protein:<-<-:2124832..2125040 209 tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2097:TDE2098|TDE2097:TDE2098:hypothetical protein:hypothetical protein:<-<-:2124832..2125040 209 tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2097:TDE2098|TDE2097:TDE2098:hypothetical protein:hypothetical protein:<-<-:2124832..2125040 209 tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt Predict ORF larger than 30AA ================================================ tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt 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================================================ tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -12.2 Tail_Score: -3.14564 Start: 45 End: 95 Full_Region: aagataggaggggtt ataggggaggaaagaaatctttt atccga aaaagtgtctttcctcccctaa ttaatcaggaggtga ............................................ataggggaggaaagaaatcttttatccgaaaaagtgtctttcctcccctaa.................................................................................................................. TransTerm Strand: - Conf: 93 HP_score: -13.9 Tail_Score: -2.77899 Start: 48 End: 92 Full_Region: ataggaggggttata ggggaggaaagaaatctttt atccga aaaagtgtctttcctcccc taattaatcaggagg ...............................................ggggaggaaagaaatcttttatccgaaaaagtgtctttcctcccc..................................................................................................................... TransTerm Strand: + Conf: 62 HP_score: -2.9 Tail_Score: -4.56887 Start: 137 End: 151 Full_Region: CTTAGGGCTCTGCCC TAAGA ACCCG TCTTA TTTTGTAAATTTTTA ........................................................................................................................................TAAGAACCCGTCTTA.......................................................... Find igs database================================================ Query_seq: TDE2097:TDE2098|TDE2097:TDE2098:hypothetical protein:hypothetical protein:<-<-:2124832..2125040 209 tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_002967_TDE2097_TDE2098|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2124832,2125040]|209 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt tatctctgaattttctgctaacacttctctcacctcctgattaattaggggaggaaagacactttttcggataaaagatttctttcctcccctataacccctcctatcttcaaaagaaccgcttagggctctgccctaagaacccgtcttattttgtaaatttttagcattatctttattaaagatattaccatataaatatcaatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUCUGAAUUUUCUGCUAACACUUCUCUCACCUCCUGAUUAAUUAGGGGAGGAAAGACACUUUUUCGGAUAAAAGAUUUCUUUCCUCCCCUAUAACCCCUCCUAUCUUCAAAAGAACCGCUUAGGGCUCUGCCCUAAGAACCCGUCUUAUUUUGUAAAUUUUUAGCAUUAUCUUUAUUAAAGAUAUUACCAUAUAAAUAUCAAUUUU ......((((..(..((((((........................((((((((((((((..(((((......)))))...))))))))))))))...................((((....((((((((...))))))))......)))).............))))))..)..)))).....((((((........))))))...... (-51.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUGAUAUUUAUAUGGUAAUAUCUUUAAUAAAGAUAAUGCUAAAAAUUUACAAAAUAAGACGGGUUCUUAGGGCAGAGCCCUAAGCGGUUCUUUUGAAGAUAGGAGGGGUUAUAGGGGAGGAAAGAAAUCUUUUAUCCGAAAAAGUGUCUUUCCUCCCCUAAUUAAUCAGGAGGUGAGAGAAGUGUUAGCAGAAAAUUCAGAGAUA ....(((((((((...(((((.((((((.....)))))).)))))....(((((....(((((.(..((((((((((...)))))))).))..))))))...........(((((((((((((((((((...(((((......)))))..))))))))))))))..))))).....)))))..)))))))))................. (-61.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 992 140 91 231 182 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 691 100 51 200 150 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 662 130 84 202 154 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 531 145 101 215 168 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 459 147 101 195 135 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 403 90 45 150 106 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 398 136 91 216 173 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 380 87 46 72 29 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 357 127 83 210 165 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 338 128 83 116 70 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 338 128 83 95 49 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 338 128 83 217 171 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 324 42 2 151 114 NC_002967:TDE1276|5end_hypothetical_protein_1310619..1310849_NEGATIVE 321 148 101 194 137 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 313 160 112 163 112 NC_002967:TDE1549|5end_recombination_protein_RecR_1592140..1592370_POSITIVE 311 148 107 114 57 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 310 130 81 202 157 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 307 70 27 172 120 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 301 154 115 77 44 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 299 147 106 141 98 NC_002967:TDE2712|5end_hypothetical_protein_2769008..2769238_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 691 100 51 146 96 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 550 130 83 79 36 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 500 89 47 47 5 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 436 90 46 115 71 NC_002967:TDE1008|3end_flagellar_protein,_putative_1032806..1032956_POSITIVE 380 87 46 85 42 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 380 90 47 83 42 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 344 150 101 110 63 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 341 90 45 80 36 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 313 160 112 145 94 NC_002967:TDE1548|3end_conserved_hypothetical_protein_TIGR00103_1592202..1592352_POSITIVE 311 148 107 108 51 NC_002967:TDE1197|3end_conserved_hypothetical_protein_TIGR00242_1230466..1230616_POSITIVE 310 130 81 70 25 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 308 149 101 133 91 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 307 159 114 62 24 NC_002967:TDE1062|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1090387..1090537_POSITIVE 307 70 27 85 33 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 301 154 115 77 44 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 299 147 106 44 1 NC_002967:TDE2711|3end_hypothetical_protein_2768991..2769141_POSITIVE 299 140 100 77 31 NC_002967:TDE1499|3end_adenylosuccinate_lyase,_putative_1546788..1546938_POSITIVE 293 69 23 137 85 NC_002967:TDE1865|3end_peptidase,_M16_family_1889141..1889291_NEGATIVE 292 100 51 125 59 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 287 70 39 64 32 NC_002967:TDE2337|3end_aminopeptidase_2374604..2374754_POSITIVE