Origin IGS: ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt .........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 aagtataatgtattgaatatgtactgacagtgtttgccactgtttattttaatcgcacaaaggtaaagatattttttttcaaacgaagggcttggcaatatatttgatcataattaaagataaaagccatgcaggcagtacgatggtacatggtgccatcggtgctccggcatggggttaaagagtgtaattcaatagatataaactaaatatagtagag Mask Tandem Repeat Region ================================================ ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt Find is-nt database================================================ Query_seq: TF1261:TF1262|TF1261:TF1262:GrpE-related chaperonin; HSP-70 cofactor:PDZ domain protein:->->:1347253..1347472 220 ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1261:TF1262|TF1261:TF1262:GrpE-related chaperonin; HSP-70 cofactor:PDZ domain protein:->->:1347253..1347472 220 ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1261:TF1262|TF1261:TF1262:GrpE-related chaperonin; HSP-70 cofactor:PDZ domain protein:->->:1347253..1347472 220 ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 19 End: 174 .................. M S I E L H S L T P C R S T D G T M Y H R T A C M A F I F N Y D Q I Y C Q A L R L K K N I F T F V R L K .............................................. Protein_Len: 33 Strand: + Start: 120 End: 218 ....................................................................................................................... M L P S P S F E K K Y L Y L C A I K I N S G K H C Q Y I F N T L Y .. Protein_Len: 31 Strand: - Start: 117 End: 209 .................................................................................................................... I Y Q W A R R K F F F I K V K T R N F Y V T A F V T L V Y E M ........... Protein_Len: 36 Strand: - Start: 43 End: 150 .......................................... G W A P A G I A G H V M T S G A H S K D K I I I L Y I A L G K T Q F F M ...................................................................... ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt 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================================================ ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -6.9 Tail_Score: -4.84539 Start: 45 End: 95 Full_Region: ATTACACTCTTTAAC CCCATGCCGGAGCACCGATGGCAC CAT GTACCATCGTACTGCCTGCATGGC TTTTATCTTTAATTA ............................................CCCATGCCGGAGCACCGATGGCACCATGTACCATCGTACTGCCTGCATGGC............................................................................................................................. TransTerm Strand: + Conf: 82 HP_score: -10.4 Tail_Score: -3.49096 Start: 46 End: 94 Full_Region: TTACACTCTTTAACC CCATGCCGGAGCACCGATGGCAC CAT GTACCATCGTACTGCCTGCATGG CTTTTATCTTTAATT .............................................CCATGCCGGAGCACCGATGGCACCATGTACCATCGTACTGCCTGCATGG.............................................................................................................................. Find igs database================================================ Query_seq: TF1261:TF1262|TF1261:TF1262:GrpE-related chaperonin; HSP-70 cofactor:PDZ domain protein:->->:1347253..1347472 220 ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt Intra-Species Hit: Count: 1 Min: 1 Max: 220 Len: 220 Subject: tfor_TF1261_TF1262|GrpE-related chaperonin; HSP-70 cofactor:PDZ domain protein|POSITIVE:POSITIVE|[1347253,1347472]|220 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 220 Query Start:1 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 220 ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgnnnnnnnntatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt ctctactatatttagtttatatctattgaattacactctttaaccccatgccggagcaccgatggcaccatgtaccatcgtactgcctgcatggcttttatctttaattatgatcaaatatattgccaagcccttcgtttgaaaaaaaatatctttacctttgtgcgattaaaataaacagtggcaaacactgtcagtacatattcaatacattatactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUACUAUAUUUAGUUUAUAUCUAUUGAAUUACACUCUUUAACCCCAUGCCGGAGCACCGAUGGCACCAUGUACCAUCGUACUGCCUGCAUGGCUUUUAUCUUUAAUUAUGAUCAAAUAUAUUGCCAAGCCCUUCGUUUGAAAAAAAAUAUCUUUACCUUUGUGCGAUUAAAAUAAACAGUGGCAAACACUGUCAGUACAUAUUCAAUACAUUAUACUU ....((((....)))).((((..(((((((((((...........((((((.((.....((((((.((...)).)))))).....)).))))))............(((.(((((...........(((((.....)))))..............(((....))).))))).)))..((((((.....))))))..)))...))))))))...))))... (-41.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAUAAUGUAUUGAAUAUGUACUGACAGUGUUUGCCACUGUUUAUUUUAAUCGCACAAAGGUAAAGAUAUUUUUUUUCAAACGAAGGGCUUGGCAAUAUAUUUGAUCAUAAUUAAAGAUAAAAGCCAUGCAGGCAGUACGAUGGUACAUGGUGCCAUCGGUGCUCCGGCAUGGGGUUAAAGAGUGUAAUUCAAUAGAUAUAAACUAAAUAUAGUAGAG .(((.((((.((((((((.(((((.(((((((.....)))))))..((((((((.......(((..((((((...((.((((.(....)..)))).)).)))))).))).................((((((.((.(((((((((((((...)))))))).))))))).)))))))))))))).))))))))))))).)).)).)))............. (-55.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 89 44 61 10 tfor:TF0777|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_826098..826328_POSITIVE 381 90 45 209 158 tfor:TF2466|5end_pyruvate_kinase_2644385..2644615_POSITIVE 373 90 45 81 30 tfor:TF2161|5end_conserved_hypothetical_protein_2336972..2337202_POSITIVE 369 95 51 54 12 tfor:TF3014|5end_oxidoreductase,_short-chain_dehydrogenase/reductase_family_3237623..3237853_POSITIVE 364 90 44 63 16 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 363 87 44 36 7 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 363 87 44 36 7 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 360 90 48 103 56 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 359 86 41 64 15 tfor:TF0421|5end_alpha-L-fucosidase_436021..436251_POSITIVE 357 97 51 228 161 tfor:TF0859|5end_conserved_hypothetical_protein_911753..911983_POSITIVE 355 98 51 56 12 tfor:TF2014|5end_dipeptidyl_aminopeptidase_IV_2169398..2169628_POSITIVE 352 96 53 147 102 tfor:TF2587|5end_hypothetical_protein_2751956..2752186_POSITIVE 350 87 41 64 17 tfor:TF1797|5end_SNF_family_transporter_1937136..1937366_POSITIVE 349 96 51 68 24 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 347 90 49 76 29 tfor:TF1885|5end_conserved_hypothetical_protein_2037307..2037537_POSITIVE 347 98 51 72 6 tfor:TF1537|5end_hypothetical_protein_1642906..1643136_POSITIVE 345 100 51 99 52 tfor:TF0682|5end_outer_membrane_protein,_TonB_dependent_receptor_724450..724680_POSITIVE 343 82 44 184 145 tfor:TF2941|5end_50S_ribosomal_protein_L1_3141828..3142058_POSITIVE 343 90 46 119 64 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 342 87 45 228 185 tfor:TF2398|5end_magnesium_chelatase,_D/I_family_2569549..2569779_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 89 44 56 5 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 373 90 45 78 27 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 364 90 44 58 11 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 350 87 41 64 17 tfor:TF1796|3end_ABC_transporter,_ATP-binding_protein_1937216..1937366_POSITIVE 343 99 51 68 17 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 343 99 51 64 13 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 334 90 44 128 77 tfor:TF1775|3end_oxidoreductase,_Gfo/Idh/MocA_family_1914618..1914768_POSITIVE 332 100 51 51 13 tfor:TF0323|3end_NAD-dependent_epimerase/dehydratase_family_protein_351053..351203_POSITIVE 330 95 51 140 91 tfor:TF0405|3end_conserved_hypothetical_protein_424308..424458_POSITIVE 329 98 52 140 94 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 327 89 48 144 106 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE 326 94 52 45 2 tfor:TF1261|3end_GrpE-related_chaperonin;_HSP-70_cofactor_1347192..1347342_POSITIVE 325 90 46 74 28 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 319 90 44 149 85 tfor:TF1782|3end_conserved_hypothetical_protein_1923333..1923483_POSITIVE 317 90 48 81 48 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 316 95 51 140 85 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 316 94 60 134 98 tfor:TF2319|3end_acyl_carrier_protein_2476588..2476738_POSITIVE 316 85 46 141 93 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 316 87 44 102 54 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 315 95 60 37 9 tfor:TF0326|3end_hypothetical_protein_354317..354467_POSITIVE