Origin IGS: taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcaagagtgaccggcgcttaagcaaagagaggctttgcacataagggaaagcaccctctacaggtaagggaaaggcgagggtgctttccgagacaataagataagtgaatta Mask Tandem Repeat Region ================================================ taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Find is-nt database================================================ Query_seq: TF1980:TF1981|TF1980:TF1981:conserved hypothetical protein:mannose-6-phosphate isomerase:->->:2130921..2131035 115 taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1980:TF1981|TF1980:TF1981:conserved hypothetical protein:mannose-6-phosphate isomerase:->->:2130921..2131035 115 taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1980:TF1981|TF1980:TF1981:conserved hypothetical protein:mannose-6-phosphate isomerase:->->:2130921..2131035 115 taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M H L S Y C L G K H P R L S L T C R G C F P L C A K P L F A ....................... Protein_Len: 33 Strand: + Start: 16 End: 114 ............... M V S E S T L A F P L P V E G A F P Y V Q S L S L L K R R S L L L . taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 56 HP_score: -4.7 Tail_Score: -3.48395 Start: 23 End: 68 Full_Region: CTTATCTTATTGTCT CGGAAAGCACCCTCGCC TTTCCCTTACCT GTAGAGGGTGCTTTCCC TTATGTGCAAAGCCT ......................CGGAAAGCACCCTCGCCTTTCCCTTACCTGTAGAGGGTGCTTTCCC............................................... TransTerm Strand: + Conf: 61 HP_score: -8.2 Tail_Score: -2.68823 Start: 24 End: 67 Full_Region: TTATCTTATTGTCTC GGAAAGCACCCTCGCC TTTCCCTTACCT GTAGAGGGTGCTTTCC CTTATGTGCAAAGCC .......................GGAAAGCACCCTCGCCTTTCCCTTACCTGTAGAGGGTGCTTTCC................................................ Find igs database================================================ Query_seq: TF1980:TF1981|TF1980:TF1981:conserved hypothetical protein:mannose-6-phosphate isomerase:->->:2130921..2131035 115 taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Intra-Species Hit: Count: 2 Min: 1 Max: 115 Len: 115 Subject: tfor_TF1980_TF1981|conserved hypothetical protein:mannose-6-phosphate isomerase|POSITIVE:POSITIVE|[2130921,2131035]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta taattcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta Subject: tfor_TF1824_TF1825|ABC transporter, ATP-binding protein:mannose-6-phosphate isomerase|POSITIVE:POSITIVE|[1973571,1973717]|147 HSP 1 e-value: 3.0E-50 bit: 198.0 Len: 112 Query Start:4 Query End:115 Subject Strand: POSITIVE Subject Start: 37 Subject End: 147 ...ttcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgctttcccttatgtgcaaagcctctctttgcttaagcgccggtcactcttgctta ...ttcacttatcttattgtctcggaaagcaccctcgcctttcccttacctgtagagggtgcttt-ccttatgtacaaagcctctctttgcttaagcgccggtcactcttgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUCACUUAUCUUAUUGUCUCGGAAAGCACCCUCGCCUUUCCCUUACCUGUAGAGGGUGCUUUCCCUUAUGUGCAAAGCCUCUCUUUGCUUAAGCGCCGGUCACUCUUGCUUA .......................(((((((((((((..(............)..))))))))))))).......((((((.....)))))).((((((..((.....)))))))) (-32.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAAGAGUGACCGGCGCUUAAGCAAAGAGAGGCUUUGCACAUAAGGGAAAGCACCCUCUACAGGUAAGGGAAAGGCGAGGGUGCUUUCCGAGACAAUAAGAUAAGUGAAUUA .................((((((.((((((.....)))))).......(((((((((((((..(............)..)))))))))))))............))))))..... (-36.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 104 66 48 3 tfor:TF2598|5end_conserved_hypothetical_protein_2771032..2771262_POSITIVE 386 62 23 188 141 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 368 90 44 160 116 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 365 100 51 206 151 tfor:TF0180|5end_carboxynorspermidine_decarboxylase_191267..191497_POSITIVE 359 70 23 225 161 tfor:TF2270|5end_conserved_hypothetical_protein_2435463..2435693_POSITIVE 354 90 45 205 152 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 349 68 21 207 161 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 348 78 32 153 98 tfor:TF2582|5end_ABC_transporter,_ATP-binding_protein_2749433..2749663_POSITIVE 345 98 55 229 184 tfor:TF2647|5end_transcriptional_regulator,_possible_arylsulfatase_regulator_2816796..2817026_POSITIVE 343 100 54 175 124 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 340 70 21 172 122 tfor:TF2281|5end_hypothetical_protein_2439574..2439804_POSITIVE 339 66 21 70 17 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 337 58 17 112 65 tfor:TF1049|5end_cobyrinic_acid_a,c-diamide_synthase_1110140..1110370_POSITIVE 335 67 24 182 139 tfor:TF1825|5end_mannose-6-phosphate_isomerase_1973578..1973808_POSITIVE 334 68 22 197 145 tfor:TF1296|5end_possible_DNA-binding_protein,_histone-like_family_1378432..1378662_POSITIVE 334 60 13 99 55 tfor:TF0300|5end_hypothetical_protein_325309..325539_POSITIVE 330 106 61 91 43 tfor:TF2487|5end_transposase_2663010..2663240_POSITIVE 326 68 29 223 177 tfor:TF0497|5end_conserved_hypothetical_protein_524058..524288_POSITIVE 325 62 21 217 168 tfor:TF0669|5end_hypothetical_protein_713384..713614_POSITIVE 321 90 44 195 143 tfor:TF0127|5end_conserved_hypothetical_protein_138026..138256_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 441 67 24 68 26 tfor:TF0939|3end_ISPg1_transposase,_IS1106-related_transposase_981115..981265_POSITIVE 396 110 61 64 11 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 349 90 43 44 2 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 339 66 21 65 12 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 339 67 27 75 34 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 338 83 54 51 16 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE 337 58 17 109 62 tfor:TF1048|3end_permease_1110217..1110367_POSITIVE 335 67 24 67 24 tfor:TF1980|3end_conserved_hypothetical_protein_2130860..2131010_POSITIVE 334 60 13 75 31 tfor:TF0299|3end_hypothetical_protein_325365..325515_POSITIVE 326 86 43 124 70 tfor:TF3115|3end_possible_sugar_kinase_3352025..3352175_POSITIVE 322 91 54 51 8 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 320 100 51 99 47 tfor:TF0223|3end_conserved_hypothetical_protein_250310..250460_POSITIVE 308 70 23 130 78 tfor:TF1182|3end_hypothetical_protein_1268938..1269088_POSITIVE 308 103 74 147 119 tfor:TF1059|3end_possible_xanthan_lyase_1130317..1130467_POSITIVE 308 70 22 98 42 tfor:TF0351|3end_hypothetical_protein_371226..371376_POSITIVE 307 62 23 43 1 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 306 101 61 64 17 tfor:TF1156|3end_oxidoreductase,_FAD-binding_1238092..1238242_POSITIVE 302 70 22 61 6 tfor:TF0337|3end_hypothetical_protein_360711..360861_POSITIVE 299 67 23 141 102 tfor:TF2245|3end_conserved_hypothetical_protein_2421291..2421441_POSITIVE 297 59 11 88 45 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE