Origin IGS: cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacacctcttcccaaaatttccttgcgcccgcctgcgaggcgcgaggaaaatcttaaaatcgttaaagactgcatcaatacattgatcgcagatttgttgaaaacttttccggcatttttcgtaaagaagctattggcaatttcctacctttgtacacgtaaacggtttccgcg Mask Tandem Repeat Region ================================================ cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta Find is-nt database================================================ Query_seq: TF2038:TF2039|TF2038:TF2039:hypothetical protein:possible cell-cycle regulation histidine triad (HIT) protein:->->:2199283..2199457 175 cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2038:TF2039|TF2038:TF2039:hypothetical protein:possible cell-cycle regulation histidine triad (HIT) protein:->->:2199283..2199457 175 cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2038:TF2039|TF2038:TF2039:hypothetical protein:possible cell-cycle regulation histidine triad (HIT) protein:->->:2199283..2199457 175 cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 81 End: 173 ................................................................................ M C D Q C I D A V F N D F K I F L A P R R R A Q G N F G K R C .. Protein_Len: 47 Strand: + Start: 34 End: 174 ................................. M A N S F F T K N A G K V F N K S A I N V L M Q S L T I L R F S S R L A G G R K E I L G R G V . Protein_Len: 30 Strand: - Start: 16 End: 105 ............... T Y L P L F N G I A E K R F I G S F N E V F R R D I Y Q H M ...................................................................... Protein_Len: 52 Strand: - Start: 3 End: 158 .. P F R K R T C L Y S I A L L K K V F F A P F T K L L D A I L T N I C D K V I K L N E E R R A P P R L S M ................. cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta 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================================================ cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.8 Tail_Score: -4.07885 Start: 125 End: 157 Full_Region: TAACGATTTTAAGAT TTTCCTCGCGCCTCG CAGG CGGGCGCAAGGAAA TTTTGGGAAGAGGTG ............................................................................................................................TTTCCTCGCGCCTCGCAGGCGGGCGCAAGGAAA.................. Find igs database================================================ Query_seq: TF2038:TF2039|TF2038:TF2039:hypothetical protein:possible cell-cycle regulation histidine triad (HIT) protein:->->:2199283..2199457 175 cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: tfor_TF2038_TF2039|hypothetical protein:possible cell-cycle regulation histidine triad (HIT) protein|POSITIVE:POSITIVE|[2199283,2199457]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta cgcggaaaccgtttacgtgtacaaaggtaggaaattgccaatagcttctttacgaaaaatgccggaaaagttttcaacaaatctgcgatcaatgtattgatgcagtctttaacgattttaagattttcctcgcgcctcgcaggcgggcgcaaggaaattttgggaagaggtgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCGGAAACCGUUUACGUGUACAAAGGUAGGAAAUUGCCAAUAGCUUCUUUACGAAAAAUGCCGGAAAAGUUUUCAACAAAUCUGCGAUCAAUGUAUUGAUGCAGUCUUUAACGAUUUUAAGAUUUUCCUCGCGCCUCGCAGGCGGGCGCAAGGAAAUUUUGGGAAGAGGUGUUA ((((...........))))......(((((....)))))....(((((((..(((((.....((..((((............((((.(((((....))))))))).))))..))..........((((((.(((((.((....))))))).)))))))))))..))))))).... (-49.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACACCUCUUCCCAAAAUUUCCUUGCGCCCGCCUGCGAGGCGCGAGGAAAAUCUUAAAAUCGUUAAAGACUGCAUCAAUACAUUGAUCGCAGAUUUGUUGAAAACUUUUCCGGCAUUUUUCGUAAAGAAGCUAUUGGCAAUUUCCUACCUUUGUACACGUAAACGGUUUCCGCG ..................((((((((((((((....)).))))))))))))......((((((((.....(((((((((....))))).))))..((((..(...(((((...((.......))..)))))...)..)))).....................))))))))..... (-45.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 170 121 82 35 tfor:TF1931|5end_ATPase/GTPase_2078123..2078353_POSITIVE 421 154 122 132 93 tfor:TF2912|5end_hypothetical_protein_3106508..3106738_POSITIVE 420 170 129 58 3 tfor:TF0349|5end_hypothetical_protein_370367..370597_POSITIVE 414 165 128 79 26 tfor:TF2165|5end_hypothetical_protein_2341654..2341884_POSITIVE 409 165 132 228 180 tfor:TF2177|5end_hypothetical_protein_2349281..2349511_POSITIVE 389 168 126 216 156 tfor:TF0344|5end_hypothetical_protein_366722..366952_POSITIVE 387 163 132 230 184 tfor:TF0369|5end_hypothetical_protein_385933..386163_POSITIVE 379 168 125 147 79 tfor:TF1814|5end_conserved_hypothetical_protein;_possible_biotin_synthase_related_domain_containing_protein_1955325..1955555_POSITIVE 374 169 127 157 114 tfor:TF2664|5end_hypothetical_protein_2841399..2841629_POSITIVE 371 170 124 209 151 tfor:TF3087|5end_conserved_hypothetical_protein_3319878..3320108_POSITIVE 366 170 122 114 58 tfor:TF2108|5end_hypothetical_protein_2277385..2277615_POSITIVE 366 150 103 198 137 tfor:TF0449|5end_transposase_467891..468121_POSITIVE 364 170 132 206 156 tfor:TF1638|5end_conserved_hypothetical_protein_1747359..1747589_POSITIVE 363 150 101 161 112 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 361 170 131 101 57 tfor:TF2643|5end_possible_O-antigen_transporter_2811744..2811974_POSITIVE 361 154 112 224 180 tfor:TF1409|5end_outer_membrane_protein_TolC_1485479..1485709_POSITIVE 356 164 122 109 49 tfor:TF2996|5end_hypothetical_protein_3210802..3211032_POSITIVE 356 170 131 85 41 tfor:TF0433|5end_60_kDa_inner_membrane_protein_453357..453587_POSITIVE 355 151 112 73 21 tfor:TF1780|5end_formiminotransferase-cyclodeaminases_1921114..1921344_POSITIVE 354 170 123 190 134 tfor:TF2915|5end_hypothetical_protein_3110422..3110652_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 170 121 82 35 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 420 170 129 58 3 tfor:TF0348|3end_hypothetical_protein_370447..370597_POSITIVE 417 170 132 57 4 tfor:TF2170|3end_hypothetical_protein_2345070..2345220_POSITIVE 416 170 132 57 4 tfor:TF2176|3end_hypothetical_protein_2349185..2349335_POSITIVE 416 170 132 58 5 tfor:TF0368|3end_hypothetical_protein_385834..385984_POSITIVE 409 165 132 53 5 tfor:TF2164|3end_hypothetical_protein_2341708..2341858_POSITIVE 387 168 132 57 3 tfor:TF0342|3end_hypothetical_protein_366643..366793_POSITIVE 366 170 122 85 29 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 366 169 131 145 98 tfor:TF0998|3end_[acyl-carrier-protein]_S-malonyltransferase_1052977..1053127_POSITIVE 366 150 103 138 77 tfor:TF0448|3end_hypothetical_protein_467911..468061_POSITIVE 361 170 131 104 60 tfor:TF2642|3end_acetylornithine_deacetylase_2811827..2811977_POSITIVE 356 164 122 76 16 tfor:TF2994|3end_hypothetical_protein_3210849..3210999_POSITIVE 348 149 118 47 11 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 348 170 128 126 73 tfor:TF1730|3end_diaminopimelate_decarboxylase_1855907..1856057_POSITIVE 345 170 122 81 35 tfor:TF0583|3end_possible_gliding_motility-related_protein_613829..613979_POSITIVE 340 170 126 58 1 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 339 170 124 143 98 tfor:TF0710|3end_two_component_system_histidine_kinase_761385..761535_POSITIVE 335 170 131 136 101 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 335 170 131 126 91 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 333 170 124 84 43 tfor:TF1841|3end_hypothetical_protein_1992267..1992417_POSITIVE