Origin IGS: atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat .........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 atatactccttaaaatcttccaatggttcgtcaaaagccggcgacatatagaaatttggttgctttaaaatgtctggccgacgattaggaaatctttttacagattcttcatgttgctttttatagagtattttgtattgtaaaagttctaaataattatacacttcaaccatgtattcatccggaattgattccaatttttcctgaacagtagttaacagcatacatagcctccttaacatttttagtatatcacaaattgtcaagtttttctataattgattgagtatacttaaaatccgctcat Mask Tandem Repeat Region ================================================ atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat Find is-nt database================================================ Query_seq: TDE0670:TDE0671|TDE0670:TDE0671:ATP-dependent protease La:PIN domain protein:->->:710454..710760 307 atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0670:TDE0671|TDE0670:TDE0671:ATP-dependent protease La:PIN domain protein:->->:710454..710760 307 atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0670:TDE0671|TDE0670:TDE0671:ATP-dependent protease La:PIN domain protein:->->:710454..710760 307 atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 42 End: 305 ......................................... M T I C D I L K M L R R L C M L L T T V Q E K L E S I P D E Y M V E V Y N Y L E L L Q Y K I L Y K K Q H E E S V K R F P .. Protein_Len: 40 Strand: - Start: 97 End: 216 ................................................................................................ Q E P F I P I L E P H I C P Q L T Y N N L V K V I C F V R Y F A V H L I Q L F M ........................................................................................... atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat 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: 82 Start: 32 End: 61 ...............................ATAGAAAAACTTGACAATTTGTGATATACT...................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0670:TDE0671|TDE0670:TDE0671:ATP-dependent protease La:PIN domain protein:->->:710454..710760 307 atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat Intra-Species Hit: Count: 1 Min: 1 Max: 307 Len: 307 Subject: NC_002967_TDE0670_TDE0671|ATP-dependent protease La:PIN domain protein|POSITIVE:POSITIVE|[710454,710760]|307 HSP 1 e-value: 1.0E-173 bit: 609.0 Len: 307 Query Start:1 Query End:307 Subject Strand: POSITIVE Subject Start: 1 Subject End: 307 atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat atgagcggattttaagtatactcaatcaattatagaaaaacttgacaatttgtgatatactaaaaatgttaaggaggctatgtatgctgttaactactgttcaggaaaaattggaatcaattccggatgaatacatggttgaagtgtataattatttagaacttttacaatacaaaatactctataaaaagcaacatgaagaatctgtaaaaagatttcctaatcgtcggccagacattttaaagcaaccaaatttctatatgtcgccggcttttgacgaaccattggaagattttaaggagtatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAGCGGAUUUUAAGUAUACUCAAUCAAUUAUAGAAAAACUUGACAAUUUGUGAUAUACUAAAAAUGUUAAGGAGGCUAUGUAUGCUGUUAACUACUGUUCAGGAAAAAUUGGAAUCAAUUCCGGAUGAAUACAUGGUUGAAGUGUAUAAUUAUUUAGAACUUUUACAAUACAAAAUACUCUAUAAAAAGCAACAUGAAGAAUCUGUAAAAAGAUUUCCUAAUCGUCGGCCAGACAUUUUAAAGCAACCAAAUUUCUAUAUGUCGCCGGCUUUUGACGAACCAUUGGAAGAUUUUAAGGAGUAUAU .(((((((......(((((((..........((((.....(((((((.(((...........))).)))))))....)))))))))))........)))))))......((((.......(((..(((((((((((.......))))))..)))))..)))......)))).....(((((((.(((((.....((((..((((((......)))))).....(((((((((.(((((......................)))))...))))...)))))..)).)).....))))).))))))).. (-59.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUACUCCUUAAAAUCUUCCAAUGGUUCGUCAAAAGCCGGCGACAUAUAGAAAUUUGGUUGCUUUAAAAUGUCUGGCCGACGAUUAGGAAAUCUUUUUACAGAUUCUUCAUGUUGCUUUUUAUAGAGUAUUUUGUAUUGUAAAAGUUCUAAAUAAUUAUACACUUCAACCAUGUAUUCAUCCGGAAUUGAUUCCAAUUUUUCCUGAACAGUAGUUAACAGCAUACAUAGCCUCCUUAACAUUUUUAGUAUAUCACAAAUUGUCAAGUUUUUCUAUAAUUGAUUGAGUAUACUUAAAAUCCGCUCAU .(((((((.....((((..........(((((.......)))))..((((((((..((((((((..(((((((..(((....(.((((((((..(((((((((......((...((((((....))))))...))..))))))))).....................................((((....))))....)))))))).).(((((.....)).)))...)))......))))))).)))).))))..((((....))))))))))))...)))))))))))................ (-49.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 269 222 74 19 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 255 280 246 109 71 NC_002967:TDE2662|5end_lipoprotein,_putative_2698650..2698880_NEGATIVE 254 276 237 128 81 NC_002967:TDE0182|5end_ABC_transporter,_ATP-binding_protein_216783..217013_NEGATIVE 253 269 226 58 11 NC_002967:TDE1515|5end_permease_domain_protein_1561978..1562208_POSITIVE 251 258 214 109 60 NC_002967:TDE1541|5end_metallo-beta-lactamase_family_protein_1584898..1585128_POSITIVE 250 270 223 56 11 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 249 289 251 205 162 NC_002967:TDE0382|5end_hypothetical_protein_434393..434623_POSITIVE 248 234 200 70 38 NC_002967:TDE1441|5end_dTDP-glucose_4,6-dehydratase_1486247..1486477_POSITIVE 248 269 224 197 164 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 247 155 111 91 40 NC_002967:TDE2246|5end_hypothetical_protein_2286132..2286362_POSITIVE 246 268 224 202 161 NC_002967:TDE1300|5end_hypothetical_protein_1337419..1337649_NEGATIVE 245 258 216 129 94 NC_002967:TDE1948|5end_ABC_transporter,_permease_protein_1964551..1964781_NEGATIVE 242 287 249 63 7 NC_002967:TDE1682|5end_V-type_ATP_synthase_subunit_B_1734843..1735073_NEGATIVE 242 100 51 137 96 NC_002967:TDE1645|5end_polypeptide_deformylase_1696052..1696282_NEGATIVE 242 295 261 53 11 NC_002967:TDE1308|5end_transketolase_1342463..1342693_POSITIVE 240 293 261 58 15 NC_002967:TDE2007|5end_ABC_transporter,_ATP-binding/permease_protein_2026819..2027049_POSITIVE 239 247 203 65 11 NC_002967:TDE2589|5end_putative_aminopeptidase_1_2626406..2626636_NEGATIVE 239 277 232 52 10 NC_002967:TDE0349|5end_phosphoenolpyruvate_synthase,_putative_391093..391323_POSITIVE 238 300 262 220 178 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 237 288 242 222 173 NC_002967:TDE2528|5end_hypothetical_protein_2556912..2557142_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 280 246 143 105 NC_002967:TDE2663|3end_isoleucyl-tRNA_synthetase_2698616..2698766_NEGATIVE 254 276 237 128 81 NC_002967:TDE0183|3end_ABC_transporter,_permease_protein_216783..216933_NEGATIVE 251 258 214 79 30 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE 249 231 191 138 101 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 248 234 200 51 19 NC_002967:TDE1440|3end_glucose-1-phosphate_thymidylyltransferase_1486308..1486458_POSITIVE 248 269 224 133 100 NC_002967:TDE0690|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_728078..728228_POSITIVE 245 258 216 136 101 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 242 287 249 61 5 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 242 100 51 140 99 NC_002967:TDE1646|3end_hypothetical_protein_1696049..1696199_NEGATIVE 235 290 252 127 77 NC_002967:TDE2236|3end_methylaspartate_mutase,_E_subunit_2274660..2274810_NEGATIVE 233 299 260 95 51 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 231 151 111 58 17 NC_002967:TDE2164|3end_hypothetical_protein_2196248..2196398_NEGATIVE 228 257 217 110 64 NC_002967:TDE1598|3end_ABC_transporter,_ATP-binding_protein_1647402..1647552_NEGATIVE 228 87 41 42 2 NC_002967:TDE0378|3end_hypothetical_protein_432516..432666_POSITIVE 227 269 224 106 69 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 225 96 69 47 15 NC_002967:TDE2618|3end_PHP_domain_protein_2660347..2660497_POSITIVE 225 107 76 99 61 NC_002967:TDE1637|3end_DNA_polymerase_I_1688962..1689112_POSITIVE 224 293 259 58 18 NC_002967:TDE0940|3end_hypothetical_protein_963635..963785_POSITIVE 223 283 245 58 33 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 223 295 269 31 1 NC_002967:TDE1307|3end_hypothetical_protein_1342521..1342671_POSITIVE