Origin IGS: agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctatgaaaagaagatattttcaaattataaaacttatgcaaaaagataagaatatcccgcaacgagatattgcaaaaaagttaaaaatatccttggcctatgtaaataaaattttattcgatatggagcatgatgggtttttgtataccgaaggtgttcctccttttggtaaaaagcggcttagcaaaaaagctttaacagcttttgaagagtgcagg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctgcactcttcaaaagctgttaaagcttttttgctaagccgctttttaccaaaaggaggaacaccttcggtatacaaaaacccatcatgctccatatcgaataaaattttatttacataggccaaggatatttttaacttttttgcaatatctcgttgcgggatattcttatctttttgcataagttttataatttgaaaatatcttcttttcatagactgacattatacaaaaataacgttcaaagtcaagctgttttatataaaaaagtgaacatgctataataaaagtatcttatttttgtatatcaatatcttgacaagttgtaattttgattgtatagttaaaggcgcttgtttttaacaagtctatatcgctatatgcgtaaaaggagtttaatcgcact Mask Tandem Repeat Region ================================================ agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctatgaaaagaagatattttcaaattataaaacttatgcaaaaagataagaatatcccgcaacgagatattgcaaaaaagttaaaaatatccttggcctatgtaaataaaattttattcgatatggagcatgatgggtttttgtataccgaaggtgttcctccttttggtaaaaagcggcttagcaaaaaagctttaacagcttttgaagagtgcagg Find is-nt database================================================ Query_seq: TDE1259:TDE1260|TDE1259:TDE1260:amino acid carrier family protein:cholinephosphate cytidylyltransferase/choline kinase:<-->:1293761..1294167 407 agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctatgaaaagaagatattttcaaattataaaacttatgcaaaaagataagaatatcccgcaacgagatattgcaaaaaagttaaaaatatccttggcctatgtaaataaaattttattcgatatggagcatgatgggtttttgtataccgaaggtgttcctccttttggtaaaaagcggcttagcaaaaaagctttaacagcttttgaagagtgcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1259:TDE1260|TDE1259:TDE1260:amino acid carrier family protein:cholinephosphate cytidylyltransferase/choline kinase:<-->:1293761..1294167 407 agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctatgaaaagaagatattttcaaattataaaacttatgcaaaaagataagaatatcccgcaacgagatattgcaaaaaagttaaaaatatccttggcctatgtaaataaaattttattcgatatggagcatgatgggtttttgtataccgaaggtgttcctccttttggtaaaaagcggcttagcaaaaaagctttaacagcttttgaagagtgcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1259:TDE1260|TDE1259:TDE1260:amino acid carrier family protein:cholinephosphate cytidylyltransferase/choline kinase:<-->:1293761..1294167 407 agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctatgaaaagaagatattttcaaattataaaacttatgcaaaaagataagaatatcccgcaacgagatattgcaaaaaagttaaaaatatccttggcctatgtaaataaaattttattcgatatggagcatgatgggtttttgtataccgaaggtgttcctccttttggtaaaaagcggcttagcaaaaaagctttaacagcttttgaagagtgcagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 192 Max: 407 Len: 216 Subject: UniRef90_Q7WYX5 Cluster: CTP:phosphocholine cytidylyltransferase/choline kinase; n=2; Treponema denticola|Rep: CTP:phosphocholine cytidylyltransferase/choline kinase - Treponema denticola HSP 1 e-value: 9.0E-35 bit: 147.0 Len: 216 Query Start:192 Query End:407 Subject Strand: null Subject Start: 1 Subject End: 72 ............................................................................................................................................................................................... M K R R Y F Q I I K L M Q K D K N I P Q R D I A K K L K I S L A Y V N K I L F D M E H D G F L Y T E G V P P F G K K R L S K K A L T A F E E C R ............................................................................................................................................................................................... M K R R Y F Q I I K L M Q K D K N I P Q R D I A K K L K I S L A Y V N K I L F D M E H D G F L Y T E G V P P F G K K R L S K K A L T A F E E C R agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 2 End: 109 . M R L N S F Y A Y S D I D L L K T S A F N Y T I K I T T C Q D I D I Q K .......................................................................................................................................................................................................................................................................................................... Protein_Len: 38 Strand: + Start: 122 End: 235 ......................................................................................................................... M I A C S L F Y I K Q L D F E R Y F C I M S V Y E K K I F S N Y K T Y A K R ............................................................................................................................................................................ Protein_Len: 30 Strand: + Start: 295 End: 384 ...................................................................................................................................................................................................................................................................................................... M K F Y S I W S M M G F C I P K V F L L L V K S G L A K K L ....................... Protein_Len: 60 Strand: + Start: 192 End: 407 ............................................................................................................................................................................................... M K R R Y F Q I I K L M Q K D K N I P Q R D I A K K L K I S L A Y V N K I L F D M E H D G F L Y T E G V P P F G K K R L Protein_Len: 39 Strand: - Start: 290 End: 406 ................................................................................................................................................................................................................................................................................................. T F L I K N S I S C S P N K Y V S P T G G K P L F R S L L F A K V A K S S H M . Protein_Len: 44 Strand: - Start: 126 End: 257 ............................................................................................................................. L M N V K K Y L V A Q S Q V N N K Y L T L R H F S S I K L N Y F K H L F I L I D R L S M ...................................................................................................................................................... agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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: 88 Start: 63 End: 92 ..............................................................CTTGACAAGTTGTAATTTTGATTGTATAGT........................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 122 End: 151 .........................................................................................................................TTTTATATAAAAAAGTGAACATGCTATAAT................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 213 End: 242 ....................................................................................................................................................................................................................ATTCTTATCTTTTTGCATAAGTTTTATAAT..................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 43 End: 72 ..........................................GTTAAAAACAAGCGCCTTTAACTATACAAT............................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -7.3 Tail_Score: -4.14576 Start: 242 End: 258 Full_Region: ttaacttttttgcaa tatctcg ttg cgggata ttcttatctttttgc .................................................................................................................................................................................................................................................tatctcgttgcgggata..................................................................................................................................................... Find igs database================================================ Query_seq: TDE1259:TDE1260|TDE1259:TDE1260:amino acid carrier family protein:cholinephosphate cytidylyltransferase/choline kinase:<-->:1293761..1294167 407 agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: NC_002967_TDE1259_TDE1260|amino acid carrier family protein:cholinephosphate cytidylyltransferase/choline kinase|NEGATIVE:POSITIVE|[1293761,1294167]|407 HSP 1 e-value: 1.0E-104 bit: 379.0 Len: 191 Query Start:1 Query End:191 Subject Strand: POSITIVE Subject Start: 1 Subject End: 191 agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtct........................................................................................................................................................................................................................ agtgcgattaaactccttttacgcatatagcgatatagacttgttaaaaacaagcgcctttaactatacaatcaaaattacaacttgtcaagatattgatatacaaaaataagatacttttattatagcatgttcacttttttatataaaacagcttgactttgaacgttatttttgtataatgtcagtct........................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGCGAUUAAACUCCUUUUACGCAUAUAGCGAUAUAGACUUGUUAAAAACAAGCGCCUUUAACUAUACAAUCAAAAUUACAACUUGUCAAGAUAUUGAUAUACAAAAAUAAGAUACUUUUAUUAUAGCAUGUUCACUUUUUUAUAUAAAACAGCUUGACUUUGAACGUUAUUUUUGUAUAAUGUCAGUCU ((.(((...............(((.....))).......(((((.....))))))))))................................(((((...((((((((((((....((.((((....(((.((((...............)))))))......)))).)))))))))))))))))))..... (-25.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACUGACAUUAUACAAAAAUAACGUUCAAAGUCAAGCUGUUUUAUAUAAAAAAGUGAACAUGCUAUAAUAAAAGUAUCUUAUUUUUGUAUAUCAAUAUCUUGACAAGUUGUAAUUUUGAUUGUAUAGUUAAAGGCGCUUGUUUUUAACAAGUCUAUAUCGCUAUAUGCGUAAAAGGAGUUUAAUCGCACU ((((((((..(((((((...(((.((((((.((((((.((((..(((((.((((((((..(((((........))))).)))))))).))))).)))).))))))...))).))).))).)))))))(((((((((....)))))))))..))).....(((.....))).......)))))......... (-37.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 840 60 11 151 102 NC_002967:TDE1259|5end_amino_acid_carrier_family_protein_1293670..1293900_NEGATIVE 291 70 22 186 135 NC_002967:TDE1593|5end_Fe-hydrogenase_1642999..1643229_NEGATIVE 250 62 22 90 44 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 239 100 53 167 111 NC_002967:TDE0497|5end_hypothetical_protein_551880..552110_NEGATIVE 223 65 22 84 38 NC_002967:TDE0123|5end_hypothetical_protein_142223..142453_NEGATIVE 215 41 13 46 25 NC_002967:TDE2709|5end_BNR_domain_protein_2766358..2766588_NEGATIVE 208 46 3 71 33 NC_002967:TDE0728|5end_FAD-binding_protein,_putative_767206..767436_POSITIVE 207 58 13 154 106 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 201 60 16 118 79 NC_002967:TDE0229|5end_ATPase_family_protein_262746..262976_NEGATIVE 198 60 13 166 122 NC_002967:TDE1886|5end_MiaB-like_tRNA_modifying_enzyme_1908488..1908718_NEGATIVE 196 130 81 77 27 NC_002967:TDE1283|5end_extracellular_solute-binding_lipoprotein,_putative_1317403..1317633_POSITIVE 196 189 153 158 122 NC_002967:TDE1109|5end_decarboxylase,_pyridoxal-dependent_family_1143080..1143310_POSITIVE 195 25 3 136 105 NC_002967:TDE0183|5end_ABC_transporter,_permease_protein_218591..218821_NEGATIVE 194 60 11 183 127 NC_002967:TDE2297|5end_TPR_domain_protein_2337019..2337249_NEGATIVE 194 188 150 163 121 NC_002967:TDE1839|5end_hypothetical_protein_1871221..1871451_NEGATIVE 194 188 150 188 146 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 194 188 150 186 144 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 194 188 150 223 181 NC_002967:TDE1799|5end_hypothetical_protein_1837264..1837494_NEGATIVE 193 148 111 190 157 NC_002967:TDE2172|5end_hypothetical_protein_2202768..2202998_NEGATIVE 192 58 19 74 34 NC_002967:TDE1897|5end_phosphoribosylglycinamide_formyltransferase_1918109..1918339_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 60 15 108 60 NC_002967:TDE0461|3end_hypothetical_protein_516125..516275_POSITIVE 250 62 22 84 38 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 239 100 53 121 65 NC_002967:TDE0498|3end_hypothetical_protein_551926..552076_NEGATIVE 223 65 22 63 17 NC_002967:TDE0124|3end_rhomboid_family_protein_142244..142394_NEGATIVE 213 59 11 54 26 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 208 46 3 65 27 NC_002967:TDE0727|3end_iron-sulfur_cluster-binding_protein_767280..767430_POSITIVE 207 98 53 136 85 NC_002967:TDE2180|3end_tRNA_modification_GTPase_2210590..2210740_NEGATIVE 207 55 22 23 1 NC_002967:TDE0266|3end_hypothetical_protein_297767..297917_NEGATIVE 204 67 23 66 17 NC_002967:TDE1494|3end_chemotaxis_protein_CheY_1539596..1539746_POSITIVE 201 45 2 151 115 NC_002967:TDE2636|3end_hypothetical_protein_2676749..2676899_POSITIVE 201 60 16 65 26 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 200 59 11 69 5 NC_002967:TDE0236|3end_PIN_domain_protein_269647..269797_POSITIVE 197 57 22 34 2 NC_002967:TDE1808|3end_hypothetical_protein_1844084..1844234_NEGATIVE 196 130 81 65 15 NC_002967:TDE1282|3end_hypothetical_protein_1317471..1317621_POSITIVE 194 60 11 89 33 NC_002967:TDE2298|3end_galactokinase,_putative_2337113..2337263_NEGATIVE 194 188 150 60 18 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 194 188 150 67 25 NC_002967:TDE1836|3end_hypothetical_protein_1868514..1868664_NEGATIVE 194 188 150 63 21 NC_002967:TDE1821|3end_hypothetical_protein_1854815..1854965_NEGATIVE 194 188 150 63 21 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 194 188 150 60 18 NC_002967:TDE1800|3end_hypothetical_protein_1837427..1837577_NEGATIVE