Origin IGS: taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaatgaacgcgccctttcagggctttgtcagttgtcagttcagcagctcaacaaagctcttaaccgcaaggttcgcaaaggggggcggacgtcgggcccgcccctttccttcacagcctgtggtta Mask Tandem Repeat Region ================================================ taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca Find is-nt database================================================ Query_seq: TF0537:TF0539|TF0537:TF0539:conserved hypothetical protein:hypothetical protein:->->:566897..567023 127 taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0537:TF0539|TF0537:TF0539:conserved hypothetical protein:hypothetical protein:->->:566897..567023 127 taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0537:TF0539|TF0537:TF0539:conserved hypothetical protein:hypothetical protein:->->:566897..567023 127 taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 3 End: 95 .. G C A T F S L P P G S T R G G K R V K R N L A K N L Q Q V S M ................................ Protein_Len: 41 Strand: - Start: 2 End: 124 . V V P Q S P F P R A R R G G G K A F R A T L L K T S S S F Q C S V F G Q F P A N M ... taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca 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================================================ taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 85 HP_score: -11.9 Tail_Score: -3.90291 Start: 23 End: 45 Full_Region: caaggttcgcaaagg ggggcggac gtcgg gcccgcccc tttccttcacagcct ......................ggggcggacgtcgggcccgcccc.................................................................................. Find igs database================================================ Query_seq: TF0537:TF0539|TF0537:TF0539:conserved hypothetical protein:hypothetical protein:->->:566897..567023 127 taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: tfor_TF0537_TF0539|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[566897,567023]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca taaccacaggctgtgaaggaaaggggcgggcccgacgtccgcccccctttgcgaaccttgcggttaagagctttgttgagctgctgaactgacaactgacaaagccctgaaagggcgcgttcattca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCACAGGCUGUGAAGGAAAGGGGCGGGCCCGACGUCCGCCCCCCUUUGCGAACCUUGCGGUUAAGAGCUUUGUUGAGCUGCUGAACUGACAACUGACAAAGCCCUGAAAGGGCGCGUUCAUUCA (((((.((((.((..((((...(((((((((.....)))))))))))))..))...)))).))))).((((.(((((.((.(((......).)).))))))).((((.....))))..))))..... (-51.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUGAACGCGCCCUUUCAGGGCUUUGUCAGUUGUCAGUUCAGCAGCUCAACAAAGCUCUUAACCGCAAGGUUCGCAAAGGGGGGCGGACGUCGGGCCCGCCCCUUUCCUUCACAGCCUGUGGUUA ...................((((((((((.((((((.......))))))..))))))))))((((((((.((((.(..(((((((((((.(.....).)))))))...))))..))))))))))))) (-50.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 669 120 72 200 151 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 539 66 23 230 186 tfor:TF0542|5end_hypothetical_protein_571918..572148_POSITIVE 534 49 1 210 160 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 524 120 73 157 111 tfor:TF2641|5end_riboflavin_kinase/FAD_synthase_2809681..2809911_POSITIVE 513 116 71 89 36 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 511 120 72 206 143 tfor:TF1175|5end_membrane-fusion_protein_1258140..1258370_POSITIVE 478 120 78 182 131 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 478 120 78 182 131 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 473 89 41 77 19 tfor:TF1592|5end_hypothetical_protein_1708325..1708555_POSITIVE 473 89 41 77 19 tfor:TF1590|5end_hypothetical_protein_1705811..1706041_POSITIVE 467 120 78 188 137 tfor:TF2172|5end_hypothetical_protein_2345822..2346052_POSITIVE 467 120 78 182 131 tfor:TF2173|5end_hypothetical_protein_2345816..2346046_POSITIVE 431 50 8 227 173 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 416 63 26 209 171 tfor:TF2931|5end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3134275..3134505_POSITIVE 405 120 73 204 158 tfor:TF2351|5end_acetate_kinase_2515480..2515710_POSITIVE 403 47 4 106 52 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 391 90 47 224 160 tfor:TF0027|5end_conserved_hypothetical_protein_22866..23096_POSITIVE 388 68 21 172 122 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 386 49 6 183 133 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 386 66 24 194 148 tfor:TF1048|5end_permease_1109241..1109471_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 539 66 23 90 46 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 534 49 1 75 25 tfor:TF0537|3end_conserved_hypothetical_protein_566836..566986_POSITIVE 511 120 73 150 88 tfor:TF1170|3end_conserved_hypothetical_protein_1252799..1252949_POSITIVE 502 120 74 94 42 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 467 120 78 78 27 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 431 50 8 64 10 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 425 120 80 94 50 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 423 120 78 125 77 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 385 62 26 146 98 tfor:TF2548|3end_30S_ribosomal_protein_S12_2731704..2731854_POSITIVE 375 60 14 117 66 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 375 63 23 71 21 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 375 70 29 43 1 tfor:TF0020|3end_possible_glycoprotein_endopeptidase_16029..16179_POSITIVE 373 66 23 64 13 tfor:TF2883|3end_peptidyl-prolyl_cis-trans_isomerase_3075129..3075279_POSITIVE 371 65 21 133 93 tfor:TF1069|3end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1139794..1139944_POSITIVE 369 49 9 147 108 tfor:TF1325|3end_L-fucose_isomerase_1405870..1406020_POSITIVE 369 57 11 148 91 tfor:TF0405|3end_conserved_hypothetical_protein_424308..424458_POSITIVE 368 47 8 55 3 tfor:TF2217|3end_hypothetical_protein_2390165..2390315_POSITIVE 367 66 22 51 4 tfor:TF1900|3end_conserved_hypothetical_protein_2056532..2056682_POSITIVE 366 60 11 151 69 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 365 62 21 59 12 tfor:TF1734|3end_conserved_hypothetical_protein_1860118..1860268_POSITIVE