Origin IGS: aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt .........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 aacggtattgcaaaaataagcatttcgcttaacagttaatcttcccctcgtcggattatcctggcggggggattttttatgtgatgtggaaaaccgaggaaaatgccgaggtttttgatctttttacatagcttctaattagcctttgtactcttggcgtgccttgcggttaattttcgaggtatttaaccgctgaggccgctaaggaatttttggggaatctttgtatcttattt Mask Tandem Repeat Region ================================================ aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt Find is-nt database================================================ Query_seq: TDE2707:TDE2708|TDE2707:TDE2708:hypothetical protein:hypothetical protein:-><-:2754990..2755225 236 aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2707:TDE2708|TDE2707:TDE2708:hypothetical protein:hypothetical protein:-><-:2754990..2755225 236 aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2707:TDE2708|TDE2707:TDE2708:hypothetical protein:hypothetical protein:-><-:2754990..2755225 236 aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 109 End: 198 ............................................................................................................ T F L D F V E A N E E T K W M V Y F I G G G P Y D S S P F M ...................................... aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt 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================================================ aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 49 HP_score: -3.6 Tail_Score: -3.34984 Start: 29 End: 86 Full_Region: taattagcctttgta ctcttggcgtgccttgcggttaatt ttcgaggt atttaaccgctgaggccgctaagga atttttggggaatct ............................ctcttggcgtgccttgcggttaattttcgaggtatttaaccgctgaggccgctaagga...................................................................................................................................................... TransTerm Strand: - Conf: 58 HP_score: -7.1 Tail_Score: -2.60508 Start: 30 End: 85 Full_Region: aattagcctttgtac tcttggcgtgccttgcggttaatt ttcgaggt atttaaccgctgaggccgctaagg aatttttggggaatc .............................tcttggcgtgccttgcggttaattttcgaggtatttaaccgctgaggccgctaagg....................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -12.9 Tail_Score: -5.40625 Start: 165 End: 194 Full_Region: cttaacagttaatct tcccctcgtcgga tta tcctggcgggggga ttttttatgtgatgt ....................................................................................................................................................................tcccctcgtcggattatcctggcgggggga.......................................... TransTerm Strand: + Conf: 71 HP_score: -5.0 Tail_Score: -4.62336 Start: 206 End: 220 Full_Region: GGGAAGATTAACTGT TAAGCG AAA TGCTTA TTTTTGCAATACCGT .............................................................................................................................................................................................................TAAGCGAAATGCTTA................ Find igs database================================================ Query_seq: TDE2707:TDE2708|TDE2707:TDE2708:hypothetical protein:hypothetical protein:-><-:2754990..2755225 236 aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt Intra-Species Hit: Count: 1 Min: 1 Max: 236 Len: 236 Subject: NC_002967_TDE2707_TDE2708|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2754990,2755225]|236 HSP 1 e-value: 1.0E-131 bit: 468.0 Len: 236 Query Start:1 Query End:236 Subject Strand: POSITIVE Subject Start: 1 Subject End: 236 aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt aaataagatacaaagattccccaaaaattccttagcggcctcagcggttaaatacctcgaaaattaaccgcaaggcacgccaagagtacaaaggctaattagaagctatgtaaaaagatcaaaaacctcggcattttcctcggttttccacatcacataaaaaatccccccgccaggataatccgacgaggggaagattaactgttaagcgaaatgcttatttttgcaataccgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAGAUACAAAGAUUCCCCAAAAAUUCCUUAGCGGCCUCAGCGGUUAAAUACCUCGAAAAUUAACCGCAAGGCACGCCAAGAGUACAAAGGCUAAUUAGAAGCUAUGUAAAAAGAUCAAAAACCUCGGCAUUUUCCUCGGUUUUCCACAUCACAUAAAAAAUCCCCCCGCCAGGAUAAUCCGACGAGGGGAAGAUUAACUGUUAAGCGAAAUGCUUAUUUUUGCAAUACCGUU ................((((((........(((.(((((((..((((((((............)))))))).)))).))).)))..((((..((((.......)))).)))).............(.((((.(((.((((.(((...........................))))))).))))))).).))))))....(((.((...((((((.......))))))...)).))) (-55.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGGUAUUGCAAAAAUAAGCAUUUCGCUUAACAGUUAAUCUUCCCCUCGUCGGAUUAUCCUGGCGGGGGGAUUUUUUAUGUGAUGUGGAAAACCGAGGAAAAUGCCGAGGUUUUUGAUCUUUUUACAUAGCUUCUAAUUAGCCUUUGUACUCUUGGCGUGCCUUGCGGUUAAUUUUCGAGGUAUUUAACCGCUGAGGCCGCUAAGGAAUUUUUGGGGAAUCUUUGUAUCUUAUUU ...(((((((((((..(((((.....)))))...((((((..((((((((((((......))))))))))))....((((((((.((.(((((((..((......))..))))))).))....))))))))......)))))).)))))).((((((((.(((((((((((((............)))))))).)))))))))))))..................)))))...... (-81.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 87 44 76 27 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 373 94 54 135 96 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 365 79 31 142 87 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 362 47 3 192 148 NC_002967:TDE0866|5end_hypothetical_protein_887614..887844_POSITIVE 354 84 44 217 172 NC_002967:TDE0725|5end_exopolysaccharide_biosynthesis_protein_763465..763695_POSITIVE 352 84 44 202 157 NC_002967:TDE0724|5end_hypothetical_protein_761853..762083_POSITIVE 323 80 35 152 108 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 311 74 31 140 87 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 310 93 64 141 112 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 309 189 143 124 76 NC_002967:TDE1329|5end_ATPase,_AAA_family_1363503..1363733_POSITIVE 302 61 31 145 117 NC_002967:TDE0161|5end_hypothetical_protein_187829..188059_NEGATIVE 300 47 18 210 175 NC_002967:TDE2748|5end_acetyltransferase,_GNAT_family_2805108..2805338_POSITIVE 297 179 131 119 65 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 292 175 139 161 128 NC_002967:TDE1086|5end_conserved_hypothetical_protein_TIGR00255_1117786..1118016_POSITIVE 288 97 55 60 21 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 287 210 170 230 169 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 286 103 64 225 184 NC_002967:TDE1345|5end_DNA_primase_1383439..1383669_POSITIVE 283 195 151 141 89 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 283 90 43 159 114 NC_002967:TDE1876|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_1897679..1897909_NEGATIVE 283 203 170 62 31 NC_002967:TDE1856|5end_radical_SAM_domain_protein_1883133..1883363_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 80 31 56 7 NC_002967:TDE2707|3end_hypothetical_protein_2754929..2755079_POSITIVE 373 94 54 71 32 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 368 77 35 89 41 NC_002967:TDE0471|3end_BNR_domain_protein_526657..526807_NEGATIVE 365 79 31 80 25 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 362 47 3 97 53 NC_002967:TDE0865|3end_hypothetical_protein_887599..887749_POSITIVE 343 90 46 126 69 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 331 110 61 79 26 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 319 80 31 74 26 NC_002967:TDE1012|3end_tex_protein,_putative_1043926..1044076_POSITIVE 310 93 64 86 57 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 297 179 131 80 26 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 293 228 182 49 7 NC_002967:TDE1442|3end_histidyl-tRNA_synthetase_1488842..1488992_POSITIVE 292 175 139 145 112 NC_002967:TDE1085|3end_UDP-N-acetylmuramate--L-alanine_ligase_1117850..1118000_POSITIVE 288 79 37 53 2 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 286 103 64 56 15 NC_002967:TDE1344|3end_hypothetical_protein_1383350..1383500_POSITIVE 283 203 170 62 31 NC_002967:TDE1855|3end_hypothetical_protein_1883213..1883363_POSITIVE 281 219 171 71 25 NC_002967:TDE0562|3end_hypothetical_protein_595581..595731_POSITIVE 279 95 55 138 99 NC_002967:TDE0857|3end_lipoprotein,_putative_879598..879748_POSITIVE 278 96 64 136 91 NC_002967:TDE2733|3end_hypothetical_protein_2789126..2789276_POSITIVE 278 80 32 116 66 NC_002967:TDE1287|3end_transcription-repair_coupling_factor_1326285..1326435_POSITIVE 277 193 167 81 60 NC_002967:TDE2204|3end_Na+/H+_antiporter_family_protein_2242550..2242700_POSITIVE