Origin IGS: tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcgagcaaaattagcgaaaaagccggagattctgtggagagtacgtctcgaaattttgcatggaaagaacgctgctataatatgacagaaggtaattcggttgttttca Mask Tandem Repeat Region ================================================ tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc Find is-nt database================================================ Query_seq: TF1667:TF1668|TF1667:TF1668:biotin acetyl-CoA carboxylase ligase/biotin operon repressor bifunctional protein:possible glycosylhydrolase:->->:1780372..1780480 109 tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1667:TF1668|TF1667:TF1668:biotin acetyl-CoA carboxylase ligase/biotin operon repressor bifunctional protein:possible glycosylhydrolase:->->:1780372..1780480 109 tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1667:TF1668|TF1667:TF1668:biotin acetyl-CoA carboxylase ligase/biotin operon repressor bifunctional protein:possible glycosylhydrolase:->->:1780372..1780480 109 tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 14 End: 109 ............. M T F C H I I A A F F P C K I S R R T L H R I S G F F A N F A R Protein_Len: 33 Strand: - Start: 2 End: 100 . F V V S N G E T M N Y C R E K W A F N R S T S E V S D G A K E S M ......... tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc 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================================================ tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1667:TF1668|TF1667:TF1668:biotin acetyl-CoA carboxylase ligase/biotin operon repressor bifunctional protein:possible glycosylhydrolase:->->:1780372..1780480 109 tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: tfor_TF1667_TF1668|biotin acetyl-CoA carboxylase ligase/biotin operon repressor bifunctional protein:possible glycosylhydrolase|POSITIVE:POSITIVE|[1780372, 1780480]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc tgaaaacaaccgaattaccttctgtcatattatagcagcgttctttccatgcaaaatttcgagacgtactctccacagaatctccggctttttcgctaattttgctcgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAACAACCGAAUUACCUUCUGUCAUAUUAUAGCAGCGUUCUUUCCAUGCAAAAUUUCGAGACGUACUCUCCACAGAAUCUCCGGCUUUUUCGCUAAUUUUGCUCGC .(((((...(((.......((((((............((((.......))))........((((.....)))).))))))....)))..)))))............... (-14.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGAGCAAAAUUAGCGAAAAAGCCGGAGAUUCUGUGGAGAGUACGUCUCGAAAUUUUGCAUGGAAAGAACGCUGCUAUAAUAUGACAGAAGGUAAUUCGGUUGUUUUCA ...............((((((((((((..((((((.((((.....))))........(((((.......)).))).........)))))).....))))))).))))). (-24.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 100 51 60 10 tfor:TF1543|5end_conserved_hypothetical_protein_1649429..1649659_POSITIVE 316 69 32 227 193 tfor:TF2187|5end_conserved_hypothetical_protein_2361693..2361923_POSITIVE 312 95 56 73 36 tfor:TF1661|5end_conserved_hypothetical_protein_1776065..1776295_POSITIVE 301 100 56 135 92 tfor:TF1873|5end_possible_hemolysin_secretion_protein_2026745..2026975_POSITIVE 301 100 56 135 92 tfor:TF1131|5end_membrane-fusion_protein;_possible_hemolysin_secretion_protein_1207611..1207841_POSITIVE 292 96 56 198 150 tfor:TF0782|5end_ThiJ/PfpI_family_protein_835976..836206_POSITIVE 290 89 43 78 16 tfor:TF0780|5end_alpha-L-arabinofuranosidase,_precursor_A_831944..832174_POSITIVE 289 95 58 194 166 tfor:TF2086|5end_transglutaminase-related_protein_2253931..2254161_POSITIVE 287 90 48 230 201 tfor:TF1545|5end_conserved_hypothetical_protein_1651134..1651364_POSITIVE 282 97 57 36 1 tfor:TF2898|5end_conserved_hypothetical_protein_3087061..3087291_POSITIVE 282 90 43 111 58 tfor:TF1963|5end_hypothetical_protein_2113359..2113589_POSITIVE 281 100 51 68 15 tfor:TF1145|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1225799..1226029_POSITIVE 273 88 41 194 137 tfor:TF2044|5end_excinuclease_ABC,_subunit_A_2203228..2203458_POSITIVE 272 88 41 137 87 tfor:TF2985|5end_glycosyltransferase_protein_3200307..3200537_POSITIVE 272 88 48 43 2 tfor:TF2031|5end_conserved_hypothetical_protein_2186605..2186835_POSITIVE 272 88 47 44 4 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 272 95 56 196 158 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 270 63 22 196 159 tfor:TF3074|5end_tonB-dependent_receptor_HmuR_3300421..3300651_POSITIVE 270 68 23 67 25 tfor:TF2583|5end_possible_ABC_transporter,__permease_component_2750206..2750436_POSITIVE 269 98 51 175 133 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 100 51 53 3 tfor:TF1542|3end_transcriptional_regulator_1649502..1649652_POSITIVE 301 100 56 121 78 tfor:TF1872|3end_ABC_transporter,_ATP-binding/permease_component_2026811..2026961_POSITIVE 301 100 56 121 78 tfor:TF1130|3end_ABC_transporter_ATP-binding_protein/permease_component_1207677..1207827_POSITIVE 292 96 56 146 98 tfor:TF0781|3end_serine_protease_inhibitor_836004..836154_POSITIVE 279 48 11 40 1 tfor:TF1698|3end_mobilization_protein_1819782..1819932_POSITIVE 275 77 35 69 21 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 272 88 41 137 87 tfor:TF2984|3end_glycosyltransferase_3200387..3200537_POSITIVE 272 88 47 44 4 tfor:TF0762|3end_chromate_transport_protein_809755..809905_POSITIVE 270 68 23 64 22 tfor:TF2582|3end_ABC_transporter,_ATP-binding_protein_2750283..2750433_POSITIVE 269 98 51 68 26 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 268 98 56 117 71 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 267 96 60 56 15 tfor:TF2992|3end_hexapeptide_transferase_family_protein_3209691..3209841_POSITIVE 266 96 57 96 50 tfor:TF2730|3end_thiol:disulfide_interchange_protein_2910946..2911096_POSITIVE 266 48 10 65 23 tfor:TF1110|3end_conserved_hypothetical_protein_1180837..1180987_POSITIVE 259 74 34 75 35 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 258 77 37 149 95 tfor:TF2043|3end_fructokinase_2203270..2203420_POSITIVE 257 87 42 63 25 tfor:TF1440|3end_hypothetical_protein_1525659..1525809_POSITIVE 256 76 34 81 42 tfor:TF2805|3end_zinc_protease_2996665..2996815_POSITIVE 254 88 51 110 79 tfor:TF2588|3end_coproporphryninogen_III_oxidase_2753432..2753582_POSITIVE 253 95 56 109 58 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE