Origin IGS: ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg .........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 cctgatctatgccggacgtaggctataacctacgccggccaaagtacataacctgcggcagacgtagagcataattcgacagtgcgtcaaaacagtattcgagactatctcgaagctcgattaaaaaatatacctccttgtatattttttaatcacgagttttaggccttttacccgccatggacggttgtgatataagtggtagagttttacttacagaaccaccacacttcctgtgaagaatgggtagttgctaagtttagatgccgaacaacttacag Mask Tandem Repeat Region ================================================ ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg Find is-nt database================================================ Query_seq: TDE2541:TDE2542|TDE2541:TDE2542:hypothetical protein:antigen, putative:-><-:2569250..2569530 281 ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2541:TDE2542|TDE2541:TDE2542:hypothetical protein:antigen, putative:-><-:2569250..2569530 281 ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2541:TDE2542|TDE2541:TDE2542:hypothetical protein:antigen, putative:-><-:2569250..2569530 281 ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 38 End: 130 ..................................... M L H R K C G G S V S K T L P L I S Q P S M A G K R P K T R D ....................................................................................................................................................... Protein_Len: 40 Strand: + Start: 137 End: 256 ........................................................................................................................................ M Y K E V Y F L I E L R D S L E Y C F D A L S N Y A L R L P Q V M Y F G R R R L ......................... Protein_Len: 33 Strand: + Start: 174 End: 272 ............................................................................................................................................................................. M V S N T V L T H C R I M L Y V C R R L C T L A G V G Y S L R P A ......... ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg 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================================================ ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 68 HP_score: -5.8 Tail_Score: -4.19276 Start: 123 End: 166 Full_Region: gagactatctcgaag ctcgattaaaaaatatac ctcctt gtatattttttaatcacgag ttttaggccttttac ..........................................................................................................................ctcgattaaaaaatatacctccttgtatattttttaatcacgag................................................................................................................... TransTerm Strand: - Conf: 49 HP_score: -4.1 Tail_Score: -3.10843 Start: 124 End: 167 Full_Region: cgagactatctcgaa gctcgattaaaaaatatac ctcctt gtatattttttaatcacga gttttaggcctttta ...........................................................................................................................gctcgattaaaaaatatacctccttgtatattttttaatcacga.................................................................................................................. TransTerm Strand: + Conf: 71 HP_score: -9.5 Tail_Score: -2.93623 Start: 168 End: 184 Full_Region: ATTTTTTAATCGAGC TTCGAGA TAG TCTCGAA TACTGTTTTGACGCA .......................................................................................................................................................................TTCGAGATAGTCTCGAA................................................................................................. TransTerm Strand: + Conf: 51 HP_score: -4.3 Tail_Score: -3.33492 Start: 214 End: 253 Full_Region: ACTGTCGAATTATGC TCTACGTCTGCCGCAGGT TATGT ACTTTGGCCGGCGTAGG TTATAGCCTACGTCC .....................................................................................................................................................................................................................TCTACGTCTGCCGCAGGTTATGTACTTTGGCCGGCGTAGG............................ TransTerm Strand: + Conf: 52 HP_score: -5.6 Tail_Score: -2.59881 Start: 215 End: 252 Full_Region: CTGTCGAATTATGCT CTACGTCTGCCGCAGGT TATGT ACTTTGGCCGGCGTAG GTTATAGCCTACGTC ......................................................................................................................................................................................................................CTACGTCTGCCGCAGGTTATGTACTTTGGCCGGCGTAG............................. Find igs database================================================ Query_seq: TDE2541:TDE2542|TDE2541:TDE2542:hypothetical protein:antigen, putative:-><-:2569250..2569530 281 ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg Intra-Species Hit: Count: 1 Min: 1 Max: 281 Len: 281 Subject: NC_002967_TDE2541_TDE2542|hypothetical protein:antigen, putative|POSITIVE:NEGATIVE|[2569250,2569530]|281 HSP 1 e-value: 1.0E-158 bit: 557.0 Len: 281 Query Start:1 Query End:281 Subject Strand: POSITIVE Subject Start: 1 Subject End: 281 ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg ctgtaagttgttcggcatctaaacttagcaactacccattcttcacaggaagtgtggtggttctgtaagtaaaactctaccacttatatcacaaccgtccatggcgggtaaaaggcctaaaactcgtgattaaaaaatatacaaggaggtatattttttaatcgagcttcgagatagtctcgaatactgttttgacgcactgtcgaattatgctctacgtctgccgcaggttatgtactttggccggcgtaggttatagcctacgtccggcatagatcagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUAAGUUGUUCGGCAUCUAAACUUAGCAACUACCCAUUCUUCACAGGAAGUGUGGUGGUUCUGUAAGUAAAACUCUACCACUUAUAUCACAACCGUCCAUGGCGGGUAAAAGGCCUAAAACUCGUGAUUAAAAAAUAUACAAGGAGGUAUAUUUUUUAAUCGAGCUUCGAGAUAGUCUCGAAUACUGUUUUGACGCACUGUCGAAUUAUGCUCUACGUCUGCCGCAGGUUAUGUACUUUGGCCGGCGUAGGUUAUAGCCUACGUCCGGCAUAGAUCAGG ..((((((.((((((((..........((...(((((...((((....)))).(((((((((.(((((((...........)))))))....))))).))))...)))))....))...........(((((((((((((((......)))))))))))))))..((.((((((((((.......)))))))))).))..))))))))...))).)))..(((..(((.....))).((...((((((((((((....))))))).)))))..))..))). (-87.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUGAUCUAUGCCGGACGUAGGCUAUAACCUACGCCGGCCAAAGUACAUAACCUGCGGCAGACGUAGAGCAUAAUUCGACAGUGCGUCAAAACAGUAUUCGAGACUAUCUCGAAGCUCGAUUAAAAAAUAUACCUCCUUGUAUAUUUUUUAAUCACGAGUUUUAGGCCUUUUACCCGCCAUGGACGGUUGUGAUAUAAGUGGUAGAGUUUUACUUACAGAACCACCACACUUCCUGUGAAGAAUGGGUAGUUGCUAAGUUUAGAUGCCGAACAACUUACAG .(((......(((((.((((((......)))))))))))..((((.......(((((.....))))).......((((.....(((((.((((....((((((.....))))))(((((((((((((((((((......)))))))))))))))..))))....(((...(((((((...(((..((((.((...(((((((.......))))))))).)))).)))..((((....))))..)))))))..)))..)))).)))))))))..)))).))) (-87.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 253 212 55 14 NC_002967:TDE1247|5end_hypothetical_protein_1281623..1281853_POSITIVE 363 169 121 118 68 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 357 270 221 202 154 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 351 117 88 39 5 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 349 270 221 61 7 NC_002967:TDE2746|5end_type_I_restriction-modification_system,_M_subunit_2802135..2802365_NEGATIVE 341 126 88 170 135 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 341 253 212 180 123 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 340 270 223 70 24 NC_002967:TDE2180|5end_tRNA_modification_GTPase_2212008..2212238_NEGATIVE 335 255 221 56 19 NC_002967:TDE0836|5end_Na(+)-translocating_NADH-quinone_reductase,_C_subunit_856096..856326_NEGATIVE 332 270 223 143 85 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 332 107 67 221 179 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 329 268 221 63 7 NC_002967:TDE1541|5end_metallo-beta-lactamase_family_protein_1584898..1585128_POSITIVE 328 115 75 115 71 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 328 270 221 144 83 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 328 180 131 196 150 NC_002967:TDE2489|5end_peptide_chain_release_factor_1_2512476..2512706_NEGATIVE 328 268 221 68 25 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 321 260 212 168 117 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 321 263 221 53 9 NC_002967:TDE2217|5end_galactose/glucose-binding_lipoprotein_2257975..2258205_NEGATIVE 320 270 221 186 132 NC_002967:TDE1354|5end_hypothetical_protein_1394886..1395116_POSITIVE 319 250 201 178 137 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 169 121 136 86 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 358 279 234 60 2 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 356 251 212 145 95 NC_002967:TDE2423|3end_ribosomal_protein_L10_2453417..2453567_NEGATIVE 349 270 221 58 4 NC_002967:TDE2747|3end_type_I_restriction-modification_system,_R_subunit_2802138..2802288_NEGATIVE 340 270 223 83 37 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 335 255 221 59 22 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 334 259 222 76 34 NC_002967:TDE2143|3end_penicillin-binding_protein_2180484..2180634_POSITIVE 334 276 242 140 94 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 334 248 201 101 55 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 326 257 213 75 34 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE 325 232 196 135 92 NC_002967:TDE1844|3end_DNA_integrase_1873197..1873347_NEGATIVE 320 270 221 151 97 NC_002967:TDE1353|3end_rod_shape-determining_protein_RodA_1394931..1395081_POSITIVE 319 270 221 94 54 NC_002967:TDE0131|3end_hypothetical_protein_152101..152251_POSITIVE 318 248 204 135 87 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 317 247 204 78 41 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 315 260 211 110 61 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 315 113 95 44 26 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 311 280 240 56 1 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 308 270 222 128 69 NC_002967:TDE2734|3end_hypothetical_protein_2789861..2790011_POSITIVE 306 248 201 73 29 NC_002967:TDE1652|3end_ABC_transporter,_ATP-binding/permease_protein_1698857..1699007_NEGATIVE