Origin IGS: taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgattttgtgtgaatttttgtgagatagatgaatgataatggaactttgtatattgccgactgtactgatatgccggagaaagatcgatgccctccgtgtccgtgccgagaggggtattccatccggcagacacagagagcatccataagggtta Mask Tandem Repeat Region ================================================ taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc Find is-nt database================================================ Query_seq: TF0959:TF0960|TF0959:TF0960:periplasmic protease:beta-galactosidase:->->:1008601..1008757 157 taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0959:TF0960|TF0959:TF0960:periplasmic protease:beta-galactosidase:->->:1008601..1008757 157 taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0959:TF0960|TF0959:TF0960:periplasmic protease:beta-galactosidase:->->:1008601..1008757 157 taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 9 End: 155 ........ M D A L C V C R M E Y P S R H G H G G H R S F S G I S V Q S A I Y K V P L S F I Y L T K I H T K S .. Protein_Len: 48 Strand: + Start: 13 End: 156 ............ M L S V S A G W N T P L G T D T E G I D L S P A Y Q Y S R Q Y T K F H Y H S S I S Q K F T Q N H . Protein_Len: 46 Strand: + Start: 20 End: 157 ................... M C L P D G I P L S A R T R R A S I F L R H I S T V G N I Q S S I I I H L S H K N S H K I I Protein_Len: 38 Strand: - Start: 10 End: 123 ......... P H E R H R G S P I G R E A R V R L A D I K R R C I L V T P L I C L E M I M .................................. Protein_Len: 42 Strand: - Start: 2 End: 127 . V R I S A R Q T Q R I S Y G E R C P C P P C R D K E P M D T C D A I Y L T G N D N M .............................. taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc 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================================================ taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0959:TF0960|TF0959:TF0960:periplasmic protease:beta-galactosidase:->->:1008601..1008757 157 taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: tfor_TF0959_TF0960|periplasmic protease:beta-galactosidase|POSITIVE:POSITIVE|[1008601, 1008757]|157 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc taacccttatggatgctctctgtgtctgccggatggaatacccctctcggcacggacacggagggcatcgatctttctccggcatatcagtacagtcggcaatatacaaagttccattatcattcatctatctcacaaaaattcacacaaaatcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCCUUAUGGAUGCUCUCUGUGUCUGCCGGAUGGAAUACCCCUCUCGGCACGGACACGGAGGGCAUCGAUCUUUCUCCGGCAUAUCAGUACAGUCGGCAAUAUACAAAGUUCCAUUAUCAUUCAUCUAUCUCACAAAAAUUCACACAAAAUCAUC ........((.((((((((((((((((((((((.((.....)).)).))))..)))))))))))))))).))......(((((...........))))).......................................................... (-44.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAUUUUGUGUGAAUUUUUGUGAGAUAGAUGAAUGAUAAUGGAACUUUGUAUAUUGCCGACUGUACUGAUAUGCCGGAGAAAGAUCGAUGCCCUCCGUGUCCGUGCCGAGAGGGGUAUUCCAUCCGGCAGACACAGAGAGCAUCCAUAAGGGUUA ..............((((((((((......................(((((((((((............)))))).))))).......(((((.(((.(((((..(((((.((..((....)).)))))))))))).))).))))))))))))))). (-41.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 465 90 41 203 152 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 436 70 21 213 155 tfor:TF0839|5end_aminopeptidasem_M28_family_890442..890672_POSITIVE 428 60 14 68 18 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 421 53 16 230 191 tfor:TF2729|5end_possible_outer_membrane_protein_2908216..2908446_POSITIVE 417 85 41 230 172 tfor:TF2843|5end_conserved_hypothetical_protein;_possible_lipoprotein_3032814..3033044_POSITIVE 415 90 43 178 118 tfor:TF2847|5end_hypothetical_protein_3034744..3034974_POSITIVE 403 70 24 173 121 tfor:TF2022|5end_conserved_hypothetical_protein_2178524..2178754_POSITIVE 403 70 25 226 181 tfor:TF0541|5end_conserved_hypothetical_protein_568473..568703_POSITIVE 401 90 41 206 149 tfor:TF2473|5end_poly(A)_polymerase/tRNA_nucleotidyltransferase_2650470..2650700_POSITIVE 398 70 23 50 1 tfor:TF2809|5end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_2999832..3000062_POSITIVE 398 100 54 43 1 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 397 60 12 92 41 tfor:TF2296|5end_hypothetical_protein_2448892..2449122_POSITIVE 394 60 11 211 161 tfor:TF0413|5end_succinyl-diaminopimelate_desuccinylase_430434..430664_POSITIVE 390 70 21 215 164 tfor:TF2196|5end_hypothetical_protein_2371678..2371908_POSITIVE 387 65 26 158 115 tfor:TF3108|5end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3338732..3338962_POSITIVE 385 70 21 141 71 tfor:TF0775|5end_ABC_transporter,_permease_component_823664..823894_POSITIVE 384 70 22 197 138 tfor:TF0947|5end_extracellular_protease_990627..990857_POSITIVE 383 90 42 80 27 tfor:TF2038|5end_hypothetical_protein_2198978..2199208_POSITIVE 381 59 11 174 116 tfor:TF0142|5end_subtilisin-like_serine_proteinase_149740..149970_POSITIVE 379 58 16 80 43 tfor:TF1559|5end_glycosyltransferase_1665879..1666109_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 500 59 12 69 22 tfor:TF0959|3end_periplasmic_protease_1008540..1008690_POSITIVE 427 68 21 55 7 tfor:TF0699|3end_pyridoxal_phosphate_biosynthetic_protein_742745..742895_POSITIVE 415 90 43 111 51 tfor:TF2845|3end_hypothetical_protein_3034757..3034907_POSITIVE 401 90 41 124 67 tfor:TF2472|3end_GAF_domain-containing_protein_2650468..2650618_POSITIVE 394 60 11 60 10 tfor:TF0412|3end_conserved_hypothetical_protein_430363..430513_POSITIVE 387 65 26 82 39 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 385 70 21 127 57 tfor:TF0774|3end_membrane-fusion_protein;_36_kDa_antigen_823730..823880_POSITIVE 379 58 16 80 43 tfor:TF1558|3end_possible_heme_biosynthesis_protein_1665959..1666109_POSITIVE 377 88 43 149 99 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 376 55 11 121 77 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 375 70 23 51 4 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 372 68 22 138 64 tfor:TF3086|3end_conserved_hypothetical_protein_3319949..3320099_POSITIVE 372 98 52 71 17 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 368 50 4 125 84 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 366 66 24 150 105 tfor:TF2021|3end_hypothetical_protein_2178588..2178738_POSITIVE 366 75 36 85 33 tfor:TF1163|3end_two-component_system_response_regulator_1243771..1243921_POSITIVE 364 65 21 49 6 tfor:TF0543|3end_glycine_cleavage_system_p-protein_575180..575330_POSITIVE 363 56 13 69 13 tfor:TF1771|3end_prolipoprotein_diacylglyceryl_transferase_1910607..1910757_POSITIVE 362 80 31 143 93 tfor:TF2893|3end_conserved_hypothetical_protein;_possible_phosphoesterase_3082039..3082189_POSITIVE 362 90 41 98 50 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE