Origin IGS: taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgtatttgtttttaatgaataaatcttttttaccattttacaaggttatattgtttcacgttttttttctccttcggatgtgcataggtacggagacctacggtacgcggagagcctgtctgcttcttcgcgtacatatgtaatatacgtcaattggattttatatctgccgtacttcgtttccattttgcttatcaccagttaagcgaatcatactaaacaacgtggcaaagataaaaggattctttttacaatgcaaatcttttttggtgttttttataaaaaacacacaactcctctccccaagggggctctttgtaataaccta Mask Tandem Repeat Region ================================================ taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt Find is-nt database================================================ Query_seq: TF2338:TF2339|TF2338:TF2339:conserved hypothetical protein:hypothetical protein:->->:2500067..2500395 329 taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2338:TF2339|TF2338:TF2339:conserved hypothetical protein:hypothetical protein:->->:2500067..2500395 329 taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2338:TF2339|TF2338:TF2339:conserved hypothetical protein:hypothetical protein:->->:2500067..2500395 329 taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 7 End: 165 ...... M T K S P L G E R S C V F F I K N T K K D L H C K K N P F I F A T L F S M I R L T G D K Q N G N E V R Q I .................................................................................................................................................................... Protein_Len: 51 Strand: + Start: 128 End: 280 ............................................................................................................................... M V I S K M E T K Y G R Y K I Q L T Y I T Y V R E E A D R L S A Y R R S P Y L C T S E G E K K R E T I ................................................. Protein_Len: 38 Strand: + Start: 183 End: 296 ...................................................................................................................................................................................... M L H M Y A K K Q T G S P R T V G L R T Y A H P K E K K N V K Q Y N L V K W ................................. Protein_Len: 45 Strand: - Start: 189 End: 323 ............................................................................................................................................................................................ M H V R L L L C A R R T G Y T E T G I C M R L L F F V H F L I V K Y F P L F S K N M L F M ...... Protein_Len: 60 Strand: - Start: 127 End: 306 .............................................................................................................................. S T I L L I S V F Y P L Y L I W N V Y I V Y T R S S A S L S E A Y R L D G Y R H V D S P S F F R S V I Y G Q L I T F F M ....................... Protein_Len: 58 Strand: - Start: 3 End: 176 .. T I V F L G R P S L L Q T N K I F F V L F S K C Q L F F G K I K A V N N L I I R K V P S L C F P F S T R C I Y F G M ......................................................................................................................................................... taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt 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================================================ taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 61 HP_score: -7.2 Tail_Score: -2.98223 Start: 193 End: 227 Full_Region: ggtacggagacctac ggtacgcggagagc ctgtct gcttcttcgcgtaca tatgtaatatacgtc ................................................................................................................................................................................................ggtacgcggagagcctgtctgcttcttcgcgtaca...................................................................................................... Find igs database================================================ Query_seq: TF2338:TF2339|TF2338:TF2339:conserved hypothetical protein:hypothetical protein:->->:2500067..2500395 329 taggttattacaaagagcccccttggggagaggagttgtgtgttttttataaaaaacaccaaaaaagatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggagaaaaaaaacgtgaaacaatataaccttgtaaaatggtaaaaaagatttattcattaaaaacaaatacgt Intra-Species Hit: Count: 1 Min: 1 Max: 260 Len: 260 Subject: tfor_TF2338_TF2339|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2500067,2500395]|329 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:67 Query End:260 Subject Strand: POSITIVE Subject Start: 67 Subject End: 260 ..................................................................gatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggag..................................................................... ..................................................................gatttgcattgtaaaaagaatccttttatctttgccacgttgtttagtatgattcgcttaactggtgataagcaaaatggaaacgaagtacggcagatataaaatccaattgacgtatattacatatgtacgcgaagaagcagacaggctctccgcgtaccgtaggtctccgtacctatgcacatccgaaggag..................................................................... HSP 2 e-value: 6.0E-20 bit: 99.6 Len: 50 Query Start:1 Query End:50 Subject Strand: POSITIVE Subject Start: 1 Subject End: 50 taggttattacaaagagcccccttggggagaggagttgtgtgttttttat....................................................................................................................................................................................................................................................................................... taggttattacaaagagcccccttggggagaggagttgtgtgttttttat....................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUUAUUACAAAGAGCCCCCUUGGGGAGAGGAGUUGUGUGUUUUUUAUAAAAAACACCAAAAAAGAUUUGCAUUGUAAAAAGAAUCCUUUUAUCUUUGCCACGUUGUUUAGUAUGAUUCGCUUAACUGGUGAUAAGCAAAAUGGAAACGAAGUACGGCAGAUAUAAAAUCCAAUUGACGUAUAUUACAUAUGUACGCGAAGAAGCAGACAGGCUCUCCGCGUACCGUAGGUCUCCGUACCUAUGCACAUCCGAAGGAG ..((((.........)))).((((((((((((...(((.((((((((....)))))))))))......(((((................((((((.((((((...(((((((.......(((((.....))))))))))))..((....))......)))))).)))))).....(((.(((((((.....))))))))))....)))))....))))))..((..(((((((......))))))).))..)).)))).. (-65.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUUCGGAUGUGCAUAGGUACGGAGACCUACGGUACGCGGAGAGCCUGUCUGCUUCUUCGCGUACAUAUGUAAUAUACGUCAAUUGGAUUUUAUAUCUGCCGUACUUCGUUUCCAUUUUGCUUAUCACCAGUUAAGCGAAUCAUACUAAACAACGUGGCAAAGAUAAAAGGAUUCUUUUUACAAUGCAAAUCUUUUUUGGUGUUUUUUAUAAAAAACACACAACUCCUCUCCCCAAGGGGGCUCUUUGUAAUAACCUA .(((....((((((((((.(((.(....).))).(((((((((((((......)).))))))))))).))))).....)))))....))).....(((((((((..............((((((((........))))))))...............))))..)))))..(((.......((((((.((.........(((((((((((....)))))))).))).......(((....)))))...))))))...))). (-67.45) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 238 196 126 83 tfor:TF1742|5end_TPR_repeat-containing_protein_1873129..1873359_POSITIVE 409 254 213 131 72 tfor:TF2187|5end_conserved_hypothetical_protein_2361693..2361923_POSITIVE 394 238 197 193 139 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 389 238 197 81 38 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 386 238 193 85 36 tfor:TF1003|5end_conserved_hypothetical_protein;_possible_secreted_glycosylhydrolase_1058177..1058407_POSITIVE 373 259 218 81 45 tfor:TF1137|5end_asparaginyl-tRNA_synthetase_(asparagine--tRNA_ligase)_1212443..1212673_POSITIVE 371 239 197 62 15 tfor:TF3055|5end_hypothetical_protein_3278775..3279005_POSITIVE 368 257 211 211 143 tfor:TF1350|5end_possible_transcriptional_regulator_1429639..1429869_POSITIVE 367 255 211 208 140 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 366 240 192 169 105 tfor:TF0819|5end_phosphoglycerate_mutase_878447..878677_POSITIVE 364 238 193 221 165 tfor:TF2345|5end_dGTP_triphosphohydrolase_2508372..2508602_POSITIVE 362 250 205 185 143 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 360 228 194 179 140 tfor:TF1466|5end_DNA_gyrase_modulator_1555469..1555699_POSITIVE 358 257 220 152 116 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 358 254 217 187 138 tfor:TF0160|5end_conserved_hypothetical_protein;_possible_Fic_family_protein_170327..170557_POSITIVE 356 237 193 227 180 tfor:TF2364|5end_conserved_hypothetical_protein;_possible_DNA_binding_protein,_excisionase_family_2530362..2530592_POSITIVE 354 256 212 217 175 tfor:TF2044|5end_excinuclease_ABC,_subunit_A_2203228..2203458_POSITIVE 354 229 189 125 89 tfor:TF0463|5end_precorrin-6Y_C5,15-methyltransferase_479015..479245_POSITIVE 353 255 212 196 142 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 351 240 196 170 122 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 238 193 60 11 tfor:TF1002|3end_replicative_DNA_helicase_1058232..1058382_POSITIVE 371 239 197 96 49 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 356 237 193 65 18 tfor:TF2363|3end_conserved_hypothetical_protein_2530280..2530430_POSITIVE 354 229 189 125 89 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 353 255 212 132 78 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 343 236 194 102 60 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 340 260 211 116 60 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 335 238 197 151 114 tfor:TF2046|3end_polyribonucleotide_nucleotidyltransferase_2210152..2210302_POSITIVE 334 239 197 77 28 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 324 249 203 129 67 tfor:TF1048|3end_permease_1110217..1110367_POSITIVE 324 238 192 151 95 tfor:TF0818|3end_bifunctional_protein:__aspartokinase_I;_homoserine_dehydrogenase_878517..878667_POSITIVE 322 259 221 137 92 tfor:TF1487|3end_orotate_phosphoribosyltransferase_1588522..1588672_POSITIVE 321 259 211 61 12 tfor:TF1928|3end_conserved_hypothetical_protein_2076124..2076274_POSITIVE 321 249 202 55 12 tfor:TF0664|3end_small_protein_B_(SMPB)_709570..709720_POSITIVE 319 244 201 132 82 tfor:TF2182|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_2355400..2355550_POSITIVE 317 250 205 72 13 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 317 258 213 145 110 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 313 238 197 60 2 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 312 240 191 150 98 tfor:TF0487|3end_xylulose_kinase_510174..510324_POSITIVE 311 258 214 86 25 tfor:TF0959|3end_periplasmic_protease_1008540..1008690_POSITIVE