Origin IGS: caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag .........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 ctcatcatattcgagatactccagcggtgccttacatactatacattcatctttcatatttattattttagttgttttttataaattgtctagtatcgtaggagtgggtgattcaaaatgaggagattaaagaaaaaatatatagaacgatatgtgattctatgctataattacaaacatgaaacaaaacaacattccgcagcagacacattttataggtgtcttg Mask Tandem Repeat Region ================================================ caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag Find is-nt database================================================ Query_seq: TDE2637:TDE2638|TDE2637:TDE2638:hypothetical protein:hypothetical protein:<-->:2677407..2677632 226 caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2637:TDE2638|TDE2637:TDE2638:hypothetical protein:hypothetical protein:<-->:2677407..2677632 226 caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2637:TDE2638|TDE2637:TDE2638:hypothetical protein:hypothetical protein:<-->:2677407..2677632 226 caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 16 End: 111 ............... M C L L R N V V L F H V C N Y S I E S H I V L Y I F S L I S S F ................................................................................................................... Protein_Len: 36 Strand: - Start: 2 End: 109 . L C R Y F T D A A S H Q K T E H K Y N Y C L I V Y R E I Y K K K L R R M ..................................................................................................................... caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag 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: 83 Start: 56 End: 85 .......................................................ATAGAACGATATGTGATTCTATGCTATAAT............................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2637:TDE2638|TDE2637:TDE2638:hypothetical protein:hypothetical protein:<-->:2677407..2677632 226 caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: NC_002967_TDE2637_TDE2638|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2677407,2677632]|226 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag caagacacctataaaatgtgtctgctgcggaatgttgttttgtttcatgtttgtaattatagcatagaatcacatatcgttctatatattttttctttaatctcctcattttgaatcacccactcctacgatactagacaatttataaaaaacaactaaaataataaatatgaaagatgaatgtatagtatgtaaggcaccgctggagtatctcgaatatgatgag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGACACCUAUAAAAUGUGUCUGCUGCGGAAUGUUGUUUUGUUUCAUGUUUGUAAUUAUAGCAUAGAAUCACAUAUCGUUCUAUAUAUUUUUUCUUUAAUCUCCUCAUUUUGAAUCACCCACUCCUACGAUACUAGACAAUUUAUAAAAAACAACUAAAAUAAUAAAUAUGAAAGAUGAAUGUAUAGUAUGUAAGGCACCGCUGGAGUAUCUCGAAUAUGAUGAG ..((((((.........)))))).....((((((.(((...(((..(((((.........)))))..))).)))...))))))..................(((.(((((((((...((((((.(((((.((((((.(((.(((((..............................)))))))).)))))))).)))....).))).))...))))).)))).))) (-35.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAUCAUAUUCGAGAUACUCCAGCGGUGCCUUACAUACUAUACAUUCAUCUUUCAUAUUUAUUAUUUUAGUUGUUUUUUAUAAAUUGUCUAGUAUCGUAGGAGUGGGUGAUUCAAAAUGAGGAGAUUAAAGAAAAAAUAUAUAGAACGAUAUGUGAUUCUAUGCUAUAAUUACAAACAUGAAACAAAACAACAUUCCGCAGCAGACACAUUUUAUAGGUGUCUUG (((((.....(((...((((((.(((((((...(((...((((....((.((...(((.....)))...)).)).....))))...)))...))))))).))))))..)))......)))))........((((...((((((......))))))..))))..........................................((((((.........)))))).. (-37.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 844 50 1 141 92 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 301 47 2 187 138 NC_002967:TDE1021|5end_lipoprotein,_putative_1053564..1053794_NEGATIVE 279 50 8 222 176 NC_002967:TDE1123|5end_sigma_factor_regulatory_protein,_putative_1155422..1155652_NEGATIVE 277 68 22 111 72 NC_002967:TDE1881|5end_methyltransferase,_putative_1903000..1903230_POSITIVE 269 68 24 48 6 NC_002967:TDE1446|5end_hypothetical_protein_1491970..1492200_POSITIVE 268 63 22 175 129 NC_002967:TDE2745|5end_fic_family_protein_2800696..2800926_NEGATIVE 262 55 22 46 12 NC_002967:TDE0569|5end_hypothetical_protein_599636..599866_POSITIVE 249 50 2 136 81 NC_002967:TDE0827|5end_hypothetical_protein_848053..848283_NEGATIVE 249 65 24 42 4 NC_002967:TDE0592|5end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631938..632168_NEGATIVE 246 133 99 139 96 NC_002967:TDE1723|5end_hypothetical_protein_1776635..1776865_POSITIVE 245 137 92 118 77 NC_002967:TDE1527|5end_hypothetical_protein_1570804..1571034_POSITIVE 244 66 21 53 10 NC_002967:TDE1927|5end_phenylalanyl-tRNA_synthetase_beta_subunit_1943984..1944214_POSITIVE 243 130 90 174 133 NC_002967:TDE0857|5end_lipoprotein,_putative_878313..878543_POSITIVE 242 126 84 217 172 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 241 60 19 111 56 NC_002967:TDE1166|5end_hypothetical_protein_1198717..1198947_NEGATIVE 239 56 19 205 169 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 238 48 1 76 22 NC_002967:TDE0076|5end_aldolase,_DeoC/FbaB_family_87386..87616_NEGATIVE 235 206 167 223 185 NC_002967:TDE2299|5end_apolipoprotein_N-acyltransferase_2338280..2338510_POSITIVE 232 220 171 109 53 NC_002967:TDE1617|5end_hypothetical_protein_1664859..1665089_NEGATIVE 232 214 175 231 194 NC_002967:TDE1141|5end_tail_fiber_domain_protein_1171443..1171673_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 50 8 148 102 NC_002967:TDE1124|3end_hypothetical_protein_1155496..1155646_NEGATIVE 277 68 22 89 50 NC_002967:TDE1880|3end_hypothetical_protein_1903058..1903208_POSITIVE 260 53 16 139 99 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 253 219 191 41 9 NC_002967:TDE0794|3end_hypothetical_protein_819224..819374_NEGATIVE 252 58 17 72 36 NC_002967:TDE2159|3end_hypothetical_protein_2193874..2194024_POSITIVE 251 207 169 68 23 NC_002967:TDE2276|3end_hypothetical_protein_2311945..2312095_NEGATIVE 245 137 92 121 80 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 241 60 19 114 59 NC_002967:TDE1167|3end_hypothetical_protein_1198714..1198864_NEGATIVE 231 130 87 125 83 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 229 50 16 134 93 NC_002967:TDE2495|3end_hypothetical_protein_2518735..2518885_NEGATIVE 229 44 3 75 28 NC_002967:TDE0692|3end_hypothetical_protein_729920..730070_POSITIVE 227 63 22 134 96 NC_002967:TDE0967|3end_hypothetical_protein_992529..992679_POSITIVE 226 63 25 43 5 NC_002967:TDE1549|3end_recombination_protein_RecR_1592807..1592957_POSITIVE 226 130 89 148 110 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 225 55 16 104 64 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 223 32 3 50 19 NC_002967:TDE0128|3end_HAMP_domain/GGDEF_domain/EAL_domain_protein_148725..148875_POSITIVE 222 42 17 51 25 NC_002967:TDE2542|3end_antigen,_putative_2569441..2569591_NEGATIVE 220 218 189 58 25 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 218 217 181 60 23 NC_002967:TDE0236|3end_PIN_domain_protein_269647..269797_POSITIVE 217 60 19 62 22 NC_002967:TDE0905|3end_hypothetical_protein_923228..923378_POSITIVE