Origin IGS: gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc .........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 ggttttgtgcgggtttcaacctttcttttaaaaatatacgggcatcttctgcgttgcttcaaaaaaaacaatcttcgacgtatcagtaccgccaggatggcggtggctccaagcaaaatcgagttcgcactgcgaactcgcagctaaagaatgaacacggacgttcattctttagcgtgcctgcgggtgtttttttcttgcgccttgaatctgctccggctgattc Mask Tandem Repeat Region ================================================ gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc Find is-nt database================================================ Query_seq: TDE0975:TDE0976|TDE0975:TDE0976:hypothetical protein:hypothetical protein:->->:999940..1000165 226 gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0975:TDE0976|TDE0975:TDE0976:hypothetical protein:hypothetical protein:->->:999940..1000165 226 gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0975:TDE0976|TDE0975:TDE0976:hypothetical protein:hypothetical protein:->->:999940..1000165 226 gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 59 End: 196 .......................................................... M N V R V H S L A A S S Q C E L D F A W S H R H P G G T D T S K I V F F E A T Q K M P V Y F .............................. Protein_Len: 47 Strand: + Start: 84 End: 224 ................................................................................... M R V R S A N S I L L G A T A I L A V L I R R R L F F L K Q R R R C P Y I F K R K V E T R T K .. Protein_Len: 46 Strand: - Start: 83 End: 220 .................................................................................. S R T R L A F E I K S P A V A M R A T S I R R L N N K K F C R L L H G Y I K L L F T S V R M ...... Protein_Len: 36 Strand: - Start: 76 End: 183 ........................................................................... E K A A L E C H S S S K A Q L W R W G P P V S V D F I T K K S A V C F M ........................................... Protein_Len: 60 Strand: - Start: 3 End: 191 .. A S E L R L F F V G A P V S F F S R G H E N K L Q S N A T R V R N Q K S G G G D Q R Y Q Y T S S Q K K Q L L A S S A R M ................................... gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc 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================================================ gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 65 HP_score: -3.1 Tail_Score: -4.54306 Start: 40 End: 96 Full_Region: aaatcgagttcgcac tgcgaactcgcagctaaagaatgaac acggac gttcattctttagcgtgcctgcggg tgtttttttcttgcg .......................................tgcgaactcgcagctaaagaatgaacacggacgttcattctttagcgtgcctgcggg.................................................................................................................................. TransTerm Strand: - Conf: 64 HP_score: -7.4 Tail_Score: -3.61178 Start: 57 End: 78 Full_Region: gaactcgcagctaaa gaatgaac acggac gttcattc tttagcgtgcctgcg ........................................................gaatgaacacggacgttcattc.................................................................................................................................................... TransTerm Strand: - Conf: 55 HP_score: -3.3 Tail_Score: -3.94188 Start: 60 End: 75 Full_Region: ctcgcagctaaagaa tgaac acggac gttca ttctttagcgtgcct ...........................................................tgaacacggacgttca....................................................................................................................................................... TransTerm Strand: + Conf: 95 HP_score: -12.0 Tail_Score: -4.4078 Start: 86 End: 108 Full_Region: GTTCATTCTTTAGCT GCGAGTTCGC AGT GCGAACTCGA TTTTGCTTGGAGCCA .....................................................................................GCGAGTTCGCAGTGCGAACTCGA...................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -15.5 Tail_Score: -3.24146 Start: 87 End: 107 Full_Region: TTCATTCTTTAGCTG CGAGTTCGC AGT GCGAACTCG ATTTTGCTTGGAGCC ......................................................................................CGAGTTCGCAGTGCGAACTCG....................................................................................................................... Find igs database================================================ Query_seq: TDE0975:TDE0976|TDE0975:TDE0976:hypothetical protein:hypothetical protein:->->:999940..1000165 226 gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc Intra-Species Hit: Count: 2 Min: 1 Max: 226 Len: 226 Subject: NC_002967_TDE0975_TDE0976|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[999940,1000165]|226 HSP 1 e-value: 3.0E-98 bit: 359.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 gaatcagccggagcagattcaaggcgcaagnnnnnnncacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgnnnnnnnngaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc gaatcagccggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattgttttttttgaagcaacgcagaagatgcccgtatatttttaaaagaaaggttgaaacccgcacaaaacc Subject: NC_002967_TDE0568_TDE0569|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[599289,599775]|487 HSP 1 e-value: 2.0E-62 bit: 240.0 Len: 150 Query Start:9 Query End:158 Subject Strand: POSITIVE Subject Start: 236 Subject End: 385 ........cggagcagattcaaggcgcaagnnnnnnncacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattttgcttggagccaccgccatcctggcggtactgatacgtcgaagattg.................................................................... ........cggagcagattcaaggcgcaagaaaaaaacacccgcaggcacgctaaagaatgaacgtccgtgttcattctttagctgcgagttcgcagtgcgaactcgattctgcttggagccaccgccatcctggcggtactgatacgtcgaggattg.................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUCAGCCGGAGCAGAUUCAAGGCGCAAGAAAAAAACACCCGCAGGCACGCUAAAGAAUGAACGUCCGUGUUCAUUCUUUAGCUGCGAGUUCGCAGUGCGAACUCGAUUUUGCUUGGAGCCACCGCCAUCCUGGCGGUACUGAUACGUCGAAGAUUGUUUUUUUUGAAGCAACGCAGAAGAUGCCCGUAUAUUUUUAAAAGAAAGGUUGAAACCCGCACAAAACC ...((((((((.(((..(((..(..((..((((((((((..(.((((((.(((((((((((((((....)))))))))))))))..(((((((((...)))))))))....)))))).....((((((.....))))))..............)..))))))))))...))..)...)))..))))).....((((....)))).))))))............... (-77.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUUUGUGCGGGUUUCAACCUUUCUUUUAAAAAUAUACGGGCAUCUUCUGCGUUGCUUCAAAAAAAACAAUCUUCGACGUAUCAGUACCGCCAGGAUGGCGGUGGCUCCAAGCAAAAUCGAGUUCGCACUGCGAACUCGCAGCUAAAGAAUGAACACGGACGUUCAUUCUUUAGCGUGCCUGCGGGUGUUUUUUUCUUGCGCCUUGAAUCUGCUCCGGCUGAUUC ........((((((.........................((((......(((((((...................)))))))....(((((((.....))))))))).)).........(((((((((...)))))))))..((((((((((((((......))))))))))))))..)))))).(((((.........)))))..(((((.((....)).))))) (-75.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 527 48 1 95 34 NC_002967:TDE0827|5end_hypothetical_protein_848053..848283_NEGATIVE 490 190 142 227 180 NC_002967:TDE2010|5end_hypothetical_protein_2031318..2031548_POSITIVE 482 139 94 222 175 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 465 153 116 42 1 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 445 106 63 213 166 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 441 108 63 205 158 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 415 140 98 156 108 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 403 90 50 228 188 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 401 138 93 192 142 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 384 138 97 204 146 NC_002967:TDE2601|5end_surface_antigen,_putative_2638490..2638720_POSITIVE 384 128 83 216 167 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 384 126 83 74 27 NC_002967:TDE0353|5end_lipase/acylhydrolase,_GDSL_family_398338..398568_NEGATIVE 374 145 104 73 18 NC_002967:TDE1999|5end_DNA_polymerase_III_domain_protein_2017063..2017293_POSITIVE 374 139 93 108 42 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 365 132 91 125 71 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 361 90 45 223 178 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 356 130 82 208 137 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 353 48 6 110 65 NC_002967:TDE2604|5end_hypothetical_protein_2645774..2646004_NEGATIVE 345 48 7 217 156 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 344 129 82 231 180 NC_002967:TDE2489|5end_peptide_chain_release_factor_1_2512476..2512706_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 490 190 142 76 29 NC_002967:TDE2009|3end_hypothetical_protein_2031247..2031397_POSITIVE 458 150 104 52 5 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 438 88 42 49 3 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 435 137 98 151 106 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 414 209 161 92 45 NC_002967:TDE2011|3end_hypothetical_protein_2033482..2033632_POSITIVE 402 121 83 68 29 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 401 138 93 60 10 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 385 130 82 143 96 NC_002967:TDE0341|3end_ribonucleotide-diphosphate_reductase_alpha_subunit_379589..379739_NEGATIVE 380 139 98 72 25 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 377 120 71 134 84 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 374 145 104 73 18 NC_002967:TDE1998|3end_phosphohexose_mutase_family_protein_2017143..2017293_POSITIVE 354 136 94 50 5 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 353 138 94 48 1 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE 352 168 124 103 62 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 348 120 78 133 89 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 340 138 94 77 28 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 332 128 81 72 7 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 332 139 91 86 41 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 326 90 41 128 79 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 326 76 38 140 107 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE