Origin IGS: atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa .........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 ttgtgttctcctaattttttcacatttcccctcccattatatttatagggattatttgaaaaaaagcgtaaatttagaaaaaattctttgcggcctttgcgccccctgcggttaaattcatcccctaaaaaaaatcctcccttttcaaagccttaaaaaaggtgtataattaaagatatggctaatgat Mask Tandem Repeat Region ================================================ atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Find is-nt database================================================ Query_seq: TDE2435:TDE2436|TDE2435:TDE2436:hypothetical protein:hypothetical protein:<-->:2466553..2466741 189 atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2435:TDE2436|TDE2435:TDE2436:hypothetical protein:hypothetical protein:<-->:2466553..2466741 189 atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2435:TDE2436|TDE2435:TDE2436:hypothetical protein:hypothetical protein:<-->:2466553..2466741 189 atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 78 End: 176 ............................................................................. G C P A C L G C L I K E L N V S K K L Y D R Y I Y H S P F H S F M ............. atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 20 End: 49 ...................CTTTTCAAAGCCTTAAAAAAGGTGTATAAT............................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 106 End: 135 .........................................................................................................TTTGAAAAAAAGCGTAAATTTAGAAAAAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2435:TDE2436|TDE2435:TDE2436:hypothetical protein:hypothetical protein:<-->:2466553..2466741 189 atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: NC_002967_TDE2435_TDE2436|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2466553,2466741]|189 HSP 1 e-value: 3.0E-76 bit: 285.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 189 atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggannnnnnnnaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgcnnnnnnncaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa atcattagccatatctttaattatacaccttttttaaggctttgaaaagggaggattttttttaggggatgaatttaaccgcagggggcgcaaaggccgcaaagaattttttctaaatttacgctttttttcaaataatccctataaatataatgggaggggaaatgtgaaaaaattaggagaacacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUUAGCCAUAUCUUUAAUUAUACACCUUUUUUAAGGCUUUGAAAAGGGAGGAUUUUUUUUAGGGGAUGAAUUUAACCGCAGGGGGCGCAAAGGCCGCAAAGAAUUUUUUCUAAAUUUACGCUUUUUUUCAAAUAAUCCCUAUAAAUAUAAUGGGAGGGGAAAUGUGAAAAAAUUAGGAGAACACAA .((((...((...(((...((((((..((((((((((....)))))))))).............(((((((((...((..((..(.(((......))).)..((((....))))........))..)).)))).....))))).....)))))).)))..))....))))................... (-34.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUGUUCUCCUAAUUUUUUCACAUUUCCCCUCCCAUUAUAUUUAUAGGGAUUAUUUGAAAAAAAGCGUAAAUUUAGAAAAAAUUCUUUGCGGCCUUUGCGCCCCCUGCGGUUAAAUUCAUCCCCUAAAAAAAAUCCUCCCUUUUCAAAGCCUUAAAAAAGGUGUAUAAUUAAAGAUAUGGCUAAUGAU ......................((((..((...........(((.(((((......((((...((.((((.....((((....))))....(((......)))...)))).))...))))..))))).))).........((((.....(((((....)))))........))))....))..)))).. (-24.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 998 100 51 191 142 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 667 110 65 227 181 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 561 105 64 230 189 NC_002967:TDE1061|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1086646..1086876_POSITIVE 561 105 64 103 62 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 545 180 131 138 88 NC_002967:TDE1905|5end_hypothetical_protein_1923877..1924107_NEGATIVE 535 110 63 220 172 NC_002967:TDE1345|5end_DNA_primase_1383439..1383669_POSITIVE 478 105 64 194 151 NC_002967:TDE0162|5end_hypothetical_protein_187898..188128_POSITIVE 475 107 72 155 120 NC_002967:TDE0597|5end_hypothetical_protein_637212..637442_NEGATIVE 436 100 53 107 51 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 436 100 53 183 127 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 393 100 52 180 129 NC_002967:TDE2264|5end_ABC_transporter,_ATP-binding/permease_protein_2302033..2302263_NEGATIVE 392 110 70 41 1 NC_002967:TDE2160|5end_hypothetical_protein_2193968..2194198_NEGATIVE 381 109 72 147 109 NC_002967:TDE0944|5end_hypothetical_protein_966247..966477_POSITIVE 366 104 77 134 108 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 353 97 55 52 9 NC_002967:TDE1223|5end_zinc_ABC_transporter,_permease_protein_1257835..1258065_NEGATIVE 348 110 70 160 121 NC_002967:TDE2242|5end_antigen,_putative_2282034..2282264_NEGATIVE 348 105 72 152 119 NC_002967:TDE0977|5end_hypothetical_protein_1000415..1000645_POSITIVE 343 180 133 197 149 NC_002967:TDE1992|5end_OmpA_family_protein_2009464..2009694_POSITIVE 342 90 41 169 109 NC_002967:TDE0008|5end_copper-translocating_P-type_ATPase_10891..11121_POSITIVE 336 100 51 115 50 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 535 110 63 51 3 NC_002967:TDE1344|3end_hypothetical_protein_1383350..1383500_POSITIVE 433 111 73 62 22 NC_002967:TDE2261|3end_hypothetical_protein_2297915..2298065_NEGATIVE 392 110 70 136 96 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 381 109 72 92 54 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 366 104 77 70 44 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 357 100 75 60 29 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 353 97 55 47 4 NC_002967:TDE1224|3end_zinc_ABC_transporter,_permease_protein_1257840..1257990_NEGATIVE 343 112 73 151 93 NC_002967:TDE2237|3end_hypothetical_protein_2276298..2276448_NEGATIVE 332 105 72 120 88 NC_002967:TDE2733|3end_hypothetical_protein_2789126..2789276_POSITIVE 329 89 41 147 99 NC_002967:TDE0024|3end_glycosyl_hydrolase,_family_3_29419..29569_NEGATIVE 328 100 55 149 100 NC_002967:TDE0451|3end_arginine_deiminase_509965..510115_POSITIVE 320 109 73 66 29 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 316 130 81 112 51 NC_002967:TDE1645|3end_polypeptide_deformylase_1695543..1695693_NEGATIVE 312 102 65 43 1 NC_002967:TDE1636|3end_surface_antigen,_putative_1683517..1683667_NEGATIVE 301 111 73 72 34 NC_002967:TDE2090|3end_NAD(P)H-dependent_glycerol-3-phosphate_dehydrogenase_2117563..2117713_NEGATIVE 299 107 73 121 93 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 298 99 51 57 17 NC_002967:TDE1399|3end_prolipoprotein_diacylglyceryl_transferase_1440489..1440639_POSITIVE 288 69 28 50 7 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 288 69 28 50 7 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 288 69 28 70 27 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE