Origin IGS: attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatcggcgaaaggatgatgcgcgatatcgataagatgttcggaatctttttcagtcctttattcatcatttgtctatctaaggtgggcgtttggctctgcccgcattcgcatgcaaatttagataaaatctccgagattttatctaaatttgccgcttctaaaaaagcgattgaat Mask Tandem Repeat Region ================================================ attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc Find is-nt database================================================ Query_seq: TF0611:TF0610|TF0611:TF0610:lysine decarboxylase:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:->->:643424..643599 176 attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0611:TF0610|TF0611:TF0610:lysine decarboxylase:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:->->:643424..643599 176 attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0611:TF0610|TF0611:TF0610:lysine decarboxylase:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:->->:643424..643599 176 attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc Predict ORF larger than 30AA ================================================ Protein_Len: 57 Strand: + Start: 6 End: 176 ..... M A F L E A A N L D K I S E I L S K F A C E C G Q S Q T P T L D R Q M M N K G L K K I P N I L S I S R I I L S P I Protein_Len: 32 Strand: - Start: 58 End: 153 ......................................................... I Q M R I R A S G F A W R L Y V F S S Y L V S F S E S C R I S M ....................... Protein_Len: 58 Strand: - Start: 2 End: 175 . E I A K K S A A F K S L I E S I K D L N A H S H P C L W V G V K S L C I I F L P S F F I G F M K D I D R M M R E G M . attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc 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================================================ attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -16.8 Tail_Score: -3.28791 Start: 21 End: 68 Full_Region: gctctgcccgcattc gcatgcaaatttagataaaatct ccg agattttatctaaatttgccgc ttctaaaaaagcgat ....................gcatgcaaatttagataaaatctccgagattttatctaaatttgccgc............................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -14.4 Tail_Score: -3.62591 Start: 29 End: 59 Full_Region: gcattcgcatgcaaa tttagataaaatct ccg agattttatctaaa tttgccgcttctaaa ............................tttagataaaatctccgagattttatctaaa..................................................................................................................... Find igs database================================================ Query_seq: TF0611:TF0610|TF0611:TF0610:lysine decarboxylase:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase:->->:643424..643599 176 attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: tfor_TF0611_TF0610|lysine decarboxylase:conserved hypothetical protein; possible phosphatidylglycerophosphate synthase|POSITIVE:POSITIVE|[643424,643599]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc attcaatcgcttttttagaagcggcaaatttagataaaatctcggagattttatctaaatttgcatgcgaatgcgggcagagccaaacgcccaccttagatagacaaatgatgaataaaggactgaaaaagattccgaacatcttatcgatatcgcgcatcatcctttcgccgatc HSP 2 e-value: 2.0E-12 bit: 73.8 Len: 41 Query Start:24 Query End:64 Subject Strand: NEGATIVE Subject Start: 24 Subject End: 64 .......................gcaaatttagataaaatctcggagattttatctaaatttgc................................................................................................................ .......................gcaaatttagataaaatctccgagattttatctaaatttgc................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCAAUCGCUUUUUUAGAAGCGGCAAAUUUAGAUAAAAUCUCGGAGAUUUUAUCUAAAUUUGCAUGCGAAUGCGGGCAGAGCCAAACGCCCACCUUAGAUAGACAAAUGAUGAAUAAAGGACUGAAAAAGAUUCCGAACAUCUUAUCGAUAUCGCGCAUCAUCCUUUCGCCGAUC .......((((((....))))))((((((((((((((((((.....))))))))))))))))))..((((....((((..........)))).........................(((((.(((....(((..(((........)))..))).....))))))))))))..... (-49.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCGGCGAAAGGAUGAUGCGCGAUAUCGAUAAGAUGUUCGGAAUCUUUUUCAGUCCUUUAUUCAUCAUUUGUCUAUCUAAGGUGGGCGUUUGGCUCUGCCCGCAUUCGCAUGCAAAUUUAGAUAAAAUCUCCGAGAUUUUAUCUAAAUUUGCCGCUUCUAAAAAAGCGAUUGAAU .....(((((.((((((((...((((((.....)))))).((((....))))...........))))))))...........(((((((........))))))).)))))..((((((((((((((((((.....))))))))))))))))))(((((......)))))....... (-55.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 96 53 56 11 tfor:TF2097|5end_glucose_inhibited_division_protein_A_2269137..2269367_POSITIVE 360 96 61 41 5 tfor:TF0684|5end_conserved_hypothetical_protein_728853..729083_POSITIVE 354 99 61 231 181 tfor:TF1064|5end_ampG_permease_1134004..1134234_POSITIVE 352 107 63 98 50 tfor:TF2879|5end_tRNA_(guanine-N-1)-methyltransferase_3068254..3068484_POSITIVE 351 103 63 79 42 tfor:TF1055|5end_hypothetical_protein_1119646..1119876_POSITIVE 347 107 62 216 160 tfor:TF0444|5end_Na+-translocating_NADH-quinone_oxidoreductase,_subunit_5_465869..466099_POSITIVE 339 170 133 182 145 tfor:TF1489|5end_argininosuccinate_lyase_1588904..1589134_POSITIVE 338 110 63 58 7 tfor:TF0941|5end_transposase_fragment_981973..982203_POSITIVE 334 122 82 197 152 tfor:TF2058|5end_possible_ATP-dependent_DNA_helicase_2222372..2222602_POSITIVE 332 50 5 198 156 tfor:TF0943|5end_transposase_984419..984649_POSITIVE 331 91 63 47 21 tfor:TF2266|5end_transfer_region-related_protein,_TraQ_2434369..2434599_POSITIVE 327 90 43 114 72 tfor:TF2271|5end_conserved_hypothetical_protein_2435802..2436032_POSITIVE 327 90 41 205 148 tfor:TF0542|5end_hypothetical_protein_571918..572148_POSITIVE 325 83 43 94 56 tfor:TF1181|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_1267522..1267752_POSITIVE 322 66 35 204 173 tfor:TF2382|5end_transposase_2546867..2547097_POSITIVE 319 92 61 105 61 tfor:TF0746|5end_possible_DNA_polymerase_III_792261..792491_POSITIVE 316 90 44 163 107 tfor:TF1434|5end_transketolase_1517485..1517715_POSITIVE 315 89 45 35 2 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 313 84 41 156 113 tfor:TF0983|5end_nitroreductase_family_protein,__possible_NADH_dehydrogenase/NAD(P)H_nitroreductase_1039394..1039624_POSITIVE 310 91 60 61 27 tfor:TF0594|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_626971..627201_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 509 68 22 70 22 tfor:TF0611|3end_lysine_decarboxylase_643363..643513_POSITIVE 337 107 64 47 2 tfor:TF2878|3end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3068283..3068433_POSITIVE 332 50 5 147 105 tfor:TF0942|3end_transposase_984448..984598_POSITIVE 327 90 41 65 8 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 323 110 69 45 1 tfor:TF0940|3end_transposase_982040..982190_POSITIVE 322 66 35 68 37 tfor:TF2381|3end_muramidase/hemagglutinin_2546811..2546961_POSITIVE 319 92 61 72 28 tfor:TF0744|3end_DNA_polymerase_III_subunit,_gamma/tau_792308..792458_POSITIVE 318 71 35 150 113 tfor:TF1933|3end_methionyl-tRNA_synthetase_2081884..2082034_POSITIVE 316 90 44 149 93 tfor:TF1433|3end_ribose_5-phosphate_isomerase_1517551..1517701_POSITIVE 315 89 45 56 23 tfor:TF2848|3end_cobalamin_biosynthesis_protein_3037389..3037539_POSITIVE 310 91 60 61 27 tfor:TF0593|3end_membrane-associated_phospholipid_phosphatase_627051..627201_POSITIVE 302 110 62 88 28 tfor:TF2173|3end_hypothetical_protein_2346063..2346213_POSITIVE 301 108 61 102 48 tfor:TF2900|3end_conserved_hypothetical_protein_3090029..3090179_POSITIVE 298 97 58 147 104 tfor:TF1782|3end_conserved_hypothetical_protein_1923333..1923483_POSITIVE 295 89 43 58 18 tfor:TF2762|3end_conserved_hypothetical_protein_2946134..2946284_POSITIVE 295 89 63 64 38 tfor:TF2148|3end_conserved_hypothetical_protein_2322189..2322339_POSITIVE 294 169 135 115 80 tfor:TF2656|3end_valyl-tRNA_synthetase_2829822..2829972_POSITIVE 289 90 41 55 11 tfor:TF3104|3end_outer_membrane_protein,_TonB_dependent_receptor_3337450..3337600_POSITIVE 286 90 43 148 105 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 285 170 130 130 92 tfor:TF2180|3end_phosphoribosylamine--glycine_ligase_2353931..2354081_POSITIVE