Origin IGS: taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt .........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 acgatataaatagagcaaatgagtttcggtattccggaaagtcgatcatcctgtgatgaacaagataccctccataccttctttgcttttgttaataatcagtcaaaatttatgtagtccggattgtttgtcttttccccgagagagagattattcgtttttaccctactaacggttgaagacgctgcaaatatagcgtttttttttatgaacgacaaatttttta Mask Tandem Repeat Region ================================================ taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt Find is-nt database================================================ Query_seq: TF0381:TF0382|TF0381:TF0382:cell cycle protein:transcription termination factor:->->:403089..403314 226 taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0381:TF0382|TF0381:TF0382:cell cycle protein:transcription termination factor:->->:403089..403314 226 taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0381:TF0382|TF0381:TF0382:cell cycle protein:transcription termination factor:->->:403089..403314 226 taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 9 End: 125 ........ M S F I K K N A I F A A S S T V S R V K T N N L S L G E K T N N P D Y I N F D ..................................................................................................... Protein_Len: 35 Strand: - Start: 113 End: 217 ................................................................................................................ M F K S Q N N V F A F F T H L T D Q E D C S S R S E P I G F S M Q E M ......... Protein_Len: 39 Strand: - Start: 58 End: 174 ......................................................... Y P L F S Y D R E R P F S L C D P S C L N Q S I I L L L L S P I S P I K N M M .................................................... Protein_Len: 34 Strand: - Start: 2 End: 103 . F F K D N M F F F A I N A A D E V T L L T F V F L R E R P S F V F M ........................................................................................................................... taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt 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: 81 Start: 8 End: 37 .......TTTGTCGTTCATAAAAAAAAACGCTATATT............................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -2.5 Tail_Score: -6.22802 Start: 29 End: 44 Full_Region: actaacggttgaaga cgctg caaata tagcg tttttttttatgaac ............................cgctgcaaatatagcg...................................................................................................................................................................................... Find igs database================================================ Query_seq: TF0381:TF0382|TF0381:TF0382:cell cycle protein:transcription termination factor:->->:403089..403314 226 taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: tfor_TF0381_TF0382|cell cycle protein:transcription termination factor|POSITIVE:POSITIVE|[403089,403314]|226 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 taaaaaatttgtcgttcatnnnnnnnnncgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt taaaaaatttgtcgttcataaaaaaaaacgctatatttgcagcgtcttcaaccgttagtagggtaaaaacgaataatctctctctcggggaaaagacaaacaatccggactacataaattttgactgattattaacaaaagcaaagaaggtatggagggtatcttgttcatcacaggatgatcgactttccggaataccgaaactcatttgctctatttatatcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAUUUGUCGUUCAUAAAAAAAAACGCUAUAUUUGCAGCGUCUUCAACCGUUAGUAGGGUAAAAACGAAUAAUCUCUCUCUCGGGGAAAAGACAAACAAUCCGGACUACAUAAAUUUUGACUGAUUAUUAACAAAAGCAAAGAAGGUAUGGAGGGUAUCUUGUUCAUCACAGGAUGAUCGACUUUCCGGAAUACCGAAACUCAUUUGCUCUAUUUAUAUCGU ...(((((((((.((((............((.......))...(((((...(((..((.((((..............))))))..)))....))))).........))))...)))))))))....(((...(((....((((((((.(((((((((((((((((((.....))))))).....)))))))...))))).....)).))))))....))).))).. (-45.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAUAUAAAUAGAGCAAAUGAGUUUCGGUAUUCCGGAAAGUCGAUCAUCCUGUGAUGAACAAGAUACCCUCCAUACCUUCUUUGCUUUUGUUAAUAAUCAGUCAAAAUUUAUGUAGUCCGGAUUGUUUGUCUUUUCCCCGAGAGAGAGAUUAUUCGUUUUUACCCUACUAACGGUUGAAGACGCUGCAAAUAUAGCGUUUUUUUUUAUGAACGACAAAUUUUUUA ..(((((.(((((((((((.(((.(((((....)))))..(((..(((((....)))))....)))...........))).))))).)))))).)).))).(((.........((((..(((((.((((.((((((....)))))).)))).)))))...)))).........((..((((((((((......))))))))))..))......))).......... (-47.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 202 167 228 195 tfor:TF1459|5end_possible_protease_1548434..1548664_POSITIVE 359 192 153 212 165 tfor:TF2205|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2379055..2379285_POSITIVE 335 90 41 114 64 tfor:TF0679|5end_hypothetical_protein_721155..721385_POSITIVE 335 90 41 62 12 tfor:TF0678|5end_hypothetical_protein_721103..721333_POSITIVE 334 187 144 165 111 tfor:TF0044|5end_conserved_hypothetical_protein_48334..48564_POSITIVE 326 199 156 192 141 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 326 200 159 179 131 tfor:TF1550|5end_excinuclease_ABC,_subunit_B_1654841..1655071_POSITIVE 313 207 164 210 165 tfor:TF2581|5end_50S_ribosomal_protein_L17_2748814..2749044_POSITIVE 296 216 179 128 85 tfor:TF0194|5end_hypothetical_protein_215193..215423_POSITIVE 291 187 141 213 163 tfor:TF0518|5end_glutaminyl-tRNA_synthetase_541770..542000_POSITIVE 288 198 153 195 144 tfor:TF2577|5end_30S_ribosomal_protein_S13_2746308..2746538_POSITIVE 287 185 149 37 1 tfor:TF1916|5end_conserved_hypothetical_protein;_possible_ATPase_2068530..2068760_POSITIVE 284 87 41 222 174 tfor:TF2215|5end_conserved_hypothetical_protein_2387501..2387731_POSITIVE 283 200 152 60 12 tfor:TF3114|5end_hypothetical_protein_3349134..3349364_POSITIVE 282 185 141 57 2 tfor:TF2365|5end_conserved_hypothetical_protein_2530658..2530888_POSITIVE 282 198 152 222 178 tfor:TF2183|5end_hypothetical_protein_2355362..2355592_POSITIVE 282 193 152 156 121 tfor:TF1161|5end_large_conductance_mechanosensitive_channel_protein_1240931..1241161_POSITIVE 282 74 36 172 139 tfor:TF0037|5end_sialic_acid-specific_9-O-acetylesterase_37836..38066_POSITIVE 280 198 155 125 69 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 280 206 161 219 179 tfor:TF1890|5end_hypothetical_protein_2042045..2042275_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 213 171 111 63 tfor:TF3080|3end_conserved_hypothetical_protein_3314423..3314573_POSITIVE 421 213 171 111 63 tfor:TF1458|3end_conserved_hypothetical_protein_1548381..1548531_POSITIVE 359 192 153 81 34 tfor:TF2202|3end_hypothetical_protein_2379004..2379154_POSITIVE 343 200 153 75 23 tfor:TF1286|3end_hypothetical_protein_1369689..1369839_POSITIVE 334 187 144 148 94 tfor:TF0043|3end_conserved_hypothetical_protein_48397..48547_POSITIVE 296 216 179 95 52 tfor:TF0193|3end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_215240..215390_POSITIVE 290 200 154 103 50 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 282 185 141 66 11 tfor:TF2364|3end_conserved_hypothetical_protein;_possible_DNA_binding_protein,_excisionase_family_2530747..2530897_POSITIVE 282 74 36 151 118 tfor:TF0036|3end_beta-hexosaminidase_precursor_37895..38045_POSITIVE 281 200 153 96 38 tfor:TF0629|3end_hypothetical_protein_666710..666860_POSITIVE 277 197 152 151 103 tfor:TF1641|3end_hypothetical_protein_1749186..1749336_POSITIVE 277 199 154 118 68 tfor:TF0299|3end_hypothetical_protein_325365..325515_POSITIVE 270 202 162 57 22 tfor:TF0968|3end_hypothetical_protein_1019608..1019758_POSITIVE 270 199 156 61 13 tfor:TF0505|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_531103..531253_POSITIVE 269 200 159 121 84 tfor:TF0115|3end_sulfatase_126771..126921_POSITIVE 268 215 175 137 97 tfor:TF0217|3end_50S_ribosomal_protein_L35_243194..243344_POSITIVE 267 90 50 134 81 tfor:TF1483|3end_glycosyltransferase_family_protein_1578825..1578975_POSITIVE 265 218 176 100 61 tfor:TF1994|3end_acyl-CoA_synthetase_2147228..2147378_POSITIVE 265 90 41 64 24 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 263 184 141 142 97 tfor:TF1027|3end_hypothetical_protein_1085897..1086047_POSITIVE