Origin IGS: tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttaagctcctcttttccaaaaccatactaaaattttaagaattatgcaataatacgaatttcttgcggttaaattaatcatcgatcaaataaaccgcagcgagcgccaagggaaaagattattaagaaaaaccgtaggtttgtcttaatgataatccacaccttaacttaggggagatttttaagagggggagctaaaaaatgtttcccctcttaaatggcgttttgaaaagatgaggggttataggggagaagaaaaacttttgctcca Mask Tandem Repeat Region ================================================ tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag Find is-nt database================================================ Query_seq: TDE0723:TDE0724|TDE0723:TDE0724:hypothetical protein:hypothetical protein:->->:761722..761992 271 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0723:TDE0724|TDE0723:TDE0724:hypothetical protein:hypothetical protein:->->:761722..761992 271 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0723:TDE0724|TDE0723:TDE0724:hypothetical protein:hypothetical protein:->->:761722..761992 271 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 103 End: 198 ...................................................................................................... T L T H I I M L V F R R N K K I I K E R P A R Q P K N S R H N M ......................................................................... tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag 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================================================ tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 62 HP_score: -7.0 Tail_Score: -3.09681 Start: 59 End: 86 Full_Region: aggggagatttttaa gagggggagc taaaaaat gtttcccctc ttaaatggcgttttg ..........................................................gagggggagctaaaaaatgtttcccctc......................................................................................................................................................................................... TransTerm Strand: + Conf: 72 HP_score: -7.9 Tail_Score: -3.7398 Start: 120 End: 152 Full_Region: TTAAGGTGTGGATTA TCATTAAGACAAACC TAC GGTTTTTCTTAATAA TCTTTTCCCTTGGCG .......................................................................................................................TCATTAAGACAAACCTACGGTTTTTCTTAATAA....................................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -9.6 Tail_Score: -2.96152 Start: 123 End: 149 Full_Region: AGGTGTGGATTATCA TTAAGACAAACC TAC GGTTTTTCTTAA TAATCTTTTCCCTTG ..........................................................................................................................TTAAGACAAACCTACGGTTTTTCTTAA.......................................................................................................................... Find igs database================================================ Query_seq: TDE0723:TDE0724|TDE0723:TDE0724:hypothetical protein:hypothetical protein:->->:761722..761992 271 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag Intra-Species Hit: Count: 5 Min: 1 Max: 271 Len: 271 Subject: NC_002967_TDE0723_TDE0724|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[761722,761992]|271 HSP 1 e-value: 1.0E-152 bit: 537.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagttaaggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtatggttttggaaaagaggagcttaag Subject: NC_002967_TDE0724_TDE0725|hypothetical protein:exopolysaccharide biosynthesis protein|POSITIVE:POSITIVE|[763298,763604]|307 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 247 Query Start:1 Query End:247 Subject Strand: POSITIVE Subject Start: 21 Subject End: 268 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagtta-aggtgtggattatcattaagacaaacctacggtttttcttaataatcttttcccttggcgctcgctgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtattattgcataattcttaaaattttagtat........................ tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggggaacattttttagccccccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctgcggtttttcttaataatcttttcgcttggcgtttactgcggtttatttgatcgatgattaatttaaccgcaagaaattcgtcttattgcataattcttaaaattttagtat........................ Subject: NC_002967_TDE0722_TDE0723|lipoprotein, putative:hypothetical protein|POSITIVE:POSITIVE|[759925,760443]|519 HSP 1 e-value: 6.0E-69 bit: 262.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 21 Subject End: 182 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagtta-aggtgtggattatcattaagacaaacctacggtttttcttaataatcttttccctt............................................................................................................ tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg-aacattttttagct-cccctcttaaaaatctcccctaagttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctt............................................................................................................ Subject: NC_002967_TDE0715_TDE0716|hypothetical protein:CAAX amino terminal protease family protein|POSITIVE:POSITIVE|[750611,750967]|357 HSP 1 e-value: 3.0E-64 bit: 246.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 21 Subject End: 182 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagaggggaaacattttttagctccccctcttaaaaatctcccctaagtta-aggtgtggattatcattaagacaaacctacggtttttcttaataatcttttccctt............................................................................................................ tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg-aacattttttagct-cccctcttaaaaatctcccctgatttagaggtatggattgtcattaagacaaacctacggtttttcttaataatcttttccctt............................................................................................................ Subject: NC_002967_TDE0969_TDE0970|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[994636,994908]|273 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 97 Query Start:67 Query End:163 Subject Strand: POSITIVE Subject Start: 170 Subject End: 266 ..................................................................acattttttagctccccctcttaaaaatctcccctaagtta-aggtgtggattatcattaagacaaacctacggtttttcttaataatcttttccctt............................................................................................................ ..................................................................acattttttagctcccc-tcttaaaaatctcccctaagttagaggcatggattgtcattaagacaaacctgcggtttttcttaataatcttttccctt............................................................................................................ HSP 2 e-value: 2.0E-28 bit: 127.0 Len: 64 Query Start:1 Query End:64 Subject Strand: POSITIVE Subject Start: 21 Subject End: 84 tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg............................................................................................................................................................................................................... tggagcaaaagtttttcttctcccctataacccctcatcttttcaaaacgccatttaagagggg............................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAGCAAAAGUUUUUCUUCUCCCCUAUAACCCCUCAUCUUUUCAAAACGCCAUUUAAGAGGGGAAACAUUUUUUAGCUCCCCCUCUUAAAAAUCUCCCCUAAGUUAAGGUGUGGAUUAUCAUUAAGACAAACCUACGGUUUUUCUUAAUAAUCUUUUCCCUUGGCGCUCGCUGCGGUUUAUUUGAUCGAUGAUUAAUUUAACCGCAAGAAAUUCGUAUUAUUGCAUAAUUCUUAAAAUUUUAGUAUGGUUUUGGAAAAGAGGAGCUUAAG ........(((((((((((.(((.....((((........((((.....((..(((((((((((................)))))))))))............(((((((.(.(((((((...(((((.(((((...))))).))))))))))))...))))))))....)).((((((...((((((...))))))...))))))..))))...(((....)))......................))))..))).)))))))))))... (-70.99) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAAGCUCCUCUUUUCCAAAACCAUACUAAAAUUUUAAGAAUUAUGCAAUAAUACGAAUUUCUUGCGGUUAAAUUAAUCAUCGAUCAAAUAAACCGCAGCGAGCGCCAAGGGAAAAGAUUAUUAAGAAAAACCGUAGGUUUGUCUUAAUGAUAAUCCACACCUUAACUUAGGGGAGAUUUUUAAGAGGGGGAGCUAAAAAAUGUUUCCCCUCUUAAAUGGCGUUUUGAAAAGAUGAGGGGUUAUAGGGGAGAAGAAAAACUUUUGCUCCA ....(((((((((((((...............................................(((((((......(((...)))......)))))))..((((((((..(((....((((((((((.(((((...))))).))))))))))..)))...(((((...)))))......(((((((((((((((........))))))))))))))))))))))).)))))...))))))))...(((((((((.....))))).)))). (-81.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 51 14 213 170 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 393 59 14 226 179 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 381 63 21 200 160 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 369 208 161 135 94 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 367 53 11 180 137 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 359 65 21 118 76 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 359 65 21 97 55 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 359 65 21 219 177 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 358 64 21 208 169 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 337 64 21 102 62 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 334 43 2 220 182 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 326 200 153 197 149 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 318 64 21 200 161 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 317 179 161 25 7 NC_002967:TDE2314|5end_hypothetical_protein_2352054..2352284_POSITIVE 317 179 161 112 94 NC_002967:TDE1981|5end_hypothetical_protein_1992016..1992246_POSITIVE 312 206 162 185 147 NC_002967:TDE0545|5end_hypothetical_protein_584774..585004_POSITIVE 310 180 136 57 6 NC_002967:TDE2504|5end_O-sialoglycoprotein_endopeptidase_2529001..2529231_POSITIVE 309 190 148 165 114 NC_002967:TDE0883|5end_16S_rRNA_processing_protein_RimM_901685..901915_POSITIVE 301 182 141 180 133 NC_002967:TDE0857|5end_lipoprotein,_putative_878313..878543_POSITIVE 300 192 157 44 10 NC_002967:TDE1593|5end_Fe-hydrogenase_1642999..1643229_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 383 202 161 104 66 NC_002967:TDE2099|3end_hypothetical_protein_2125229..2125379_POSITIVE 369 208 161 73 32 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 369 187 143 59 12 NC_002967:TDE2159|3end_hypothetical_protein_2193874..2194024_POSITIVE 352 206 161 47 7 NC_002967:TDE2707|3end_hypothetical_protein_2754929..2755079_POSITIVE 334 43 2 133 95 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 326 180 131 115 76 NC_002967:TDE2261|3end_hypothetical_protein_2297915..2298065_NEGATIVE 321 49 6 131 72 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 321 50 7 69 30 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 318 64 21 68 29 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 317 179 161 60 42 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 315 44 4 108 69 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 310 180 136 55 4 NC_002967:TDE2503|3end_hypothetical_protein_2529079..2529229_POSITIVE 309 178 132 138 93 NC_002967:TDE2742|3end_site-specific_recombinase,_phage_integrase_family_2796850..2797000_NEGATIVE 301 179 133 70 14 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 300 192 157 50 16 NC_002967:TDE1594|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_1642993..1643143_NEGATIVE 298 41 7 150 120 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 297 63 23 112 72 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 285 101 76 151 123 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 284 195 153 68 9 NC_002967:TDE2731|3end_TIM-barrel_protein,_putative,_NifR3_family_2788453..2788603_POSITIVE 283 50 2 151 97 NC_002967:TDE1542|3end_hypothetical_protein_1586128..1586278_POSITIVE