Origin IGS: taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt .........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 actacgagggaataaaccgcatacgtcgaccctgacagaaagtcaggtcgacctaaccgagcgtttaggtcgaccttacggagcaaataggtcgtccttacagagcggttaggtcgacctaaaacggacggaaggtcgtcctaaccggagcggcacgtcgtctttgcaaaacgagagaaatgccgattgcgtttctctcgtttctcttta Mask Tandem Repeat Region ================================================ taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngactttctgtcagggtcgacgtatgcggtttattccctcgtagt Find is-nt database================================================ Query_seq: TF0883:TF0884|TF0883:TF0884:hypothetical protein:hypothetical protein:->->:937533..937742 210 taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0883:TF0884|TF0883:TF0884:hypothetical protein:hypothetical protein:->->:937533..937742 210 taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0883:TF0884|TF0883:TF0884:hypothetical protein:hypothetical protein:->->:937533..937742 210 taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt Predict ORF larger than 30AA ================================================ taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt 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================================================ taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 61 HP_score: -8.2 Tail_Score: -2.87132 Start: 63 End: 106 Full_Region: AGACGACGTGCCGCT CCGGTTAGGACGACCT TCCGTCCGTTTT AGGTCGACCTAACCGC TCTGTAAGGACGACC ..............................................................CCGGTTAGGACGACCTTCCGTCCGTTTTAGGTCGACCTAACCGC........................................................................................................ TransTerm Strand: + Conf: 76 HP_score: -9.6 Tail_Score: -3.76402 Start: 90 End: 123 Full_Region: ACCTTCCGTCCGTTT TAGGTCGACCTAAC CGCTCT GTAAGGACGACCTA TTTGCTCCGTAAGGT .........................................................................................TAGGTCGACCTAACCGCTCTGTAAGGACGACCTA....................................................................................... TransTerm Strand: + Conf: 100 HP_score: -15.7 Tail_Score: -4.04206 Start: 132 End: 169 Full_Region: CGACCTATTTGCTCC GTAAGGTCGACCTAAAC GCTC GGTTAGGTCGACCTGAC TTTCTGTCAGGGTCG ...................................................................................................................................GTAAGGTCGACCTAAACGCTCGGTTAGGTCGACCTGAC......................................... TransTerm Strand: + Conf: 67 HP_score: -5.3 Tail_Score: -4.21974 Start: 151 End: 194 Full_Region: GGTCGACCTAAACGC TCGGTTAGGTCGACCTGAC TTTCT GTCAGGGTCGACGTATGCGG TTTATTCCCTCGTAG ......................................................................................................................................................TCGGTTAGGTCGACCTGACTTTCTGTCAGGGTCGACGTATGCGG................ TransTerm Strand: + Conf: 56 HP_score: -6.6 Tail_Score: -3.12702 Start: 152 End: 193 Full_Region: GTCGACCTAAACGCT CGGTTAGGTCGACCTGAC TTTCT GTCAGGGTCGACGTATGCG GTTTATTCCCTCGTA .......................................................................................................................................................CGGTTAGGTCGACCTGACTTTCTGTCAGGGTCGACGTATGCG................. Find igs database================================================ Query_seq: TF0883:TF0884|TF0883:TF0884:hypothetical protein:hypothetical protein:->->:937533..937742 210 taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt Intra-Species Hit: Count: 2 Min: 1 Max: 210 Len: 210 Subject: tfor_TF0883_TF0884|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[937533,937742]|210 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1 Subject End: 210 taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt Subject: tfor_TF0862_TF0864|conserved hypothetical protein fragment:O-succinylbenzoate--CoA ligase|POSITIVE:POSITIVE|[914520,914709]|190 HSP 1 e-value: 2.0E-24 bit: 113.0 Len: 149 Query Start:62 Query End:210 Subject Strand: POSITIVE Subject Start: 32 Subject End: 180 .............................................................tccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt .............................................................tccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagt Inter-species Hit: Count: 3 Min: 1 Max: 210 Len: 210 Subject: NC_002950_PG0665_PG0668|beta-galactosidase:TonB-dependent receptor|POSITIVE:POSITIVE|[715306,717590]|2285 HSP 1 e-value: 2.0E-96 bit: 353.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1368 Subject End: 1577 taaagagaaacgagagaaacgcaatcggcatttctctcgttttgcaaagacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt taaagagaaacgagagaaatgcaatcggcatttctctcgttttgcaaagacgacgtactgctccggttaggacgaccttccgtccgttttaggtcgacctaatcgctctgtaaggacgacctatttgctccgcaaggtcgacctaaacgctcggttaggtcgacctgacttcttgtcagggtcgacgtatgcggtttattcccttgtagt Subject: NC_002950_PG1496_PG1497|hypothetical protein:DNA-binding protein, histone-like family|POSITIVE:POSITIVE|[1573758,1574224]|467 HSP 1 e-value: 4.0E-69 bit: 262.0 Len: 152 Query Start:59 Query End:210 Subject Strand: NEGATIVE Subject Start: 121 Subject End: 272 ..........................................................cgctccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt ..........................................................cgctccggttaggtcgaccttccgtccgttttaggtcgacctaaacgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacggccggttatgtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt Subject: NC_002950_PG1519_PG1521|hypothetical protein:O-succinylbenzoic acid--CoA ligase|POSITIVE:NEGATIVE|[1597486,1598143]|658 HSP 1 e-value: 1.0E-10 bit: 67.9 Len: 46 Query Start:155 Query End:200 Subject Strand: POSITIVE Subject Start: 585 Subject End: 630 ..........................................................................................................................................................ttaggtcgacctgactttctgtcagggtcgacgtatgcggtttatt.......... ..........................................................................................................................................................ttaggtcgacctgactttctgtcagggtcggcgtgtgtggtttatt.......... HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 52 Query Start:49 Query End:100 Subject Strand: POSITIVE Subject Start: 545 Subject End: 596 ................................................gacgacgtgccgctccggttaggacgaccttccgtccgttttaggtcgacct.............................................................................................................. ................................................gacgacgtatcgttccggttaggacgaccctccgtctgttttaggtcgacct.............................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGAGAAACGAGAGAAACGCAAUCGGCAUUUCUCUCGUUUUGCAAAGACGACGUGCCGCUCCGGUUAGGACGACCUUCCGUCCGUUUUAGGUCGACCUAACCGCUCUGUAAGGACGACCUAUUUGCUCCGUAAGGUCGACCUAAACGCUCGGUUAGGUCGACCUGACUUUCUGUCAGGGUCGACGUAUGCGGUUUAUUCCCUCGUAGU ....(..((((((((((((.((.....)).))))))))))))..)....((((.(.(((((.((((...(((((......)))))..(((((((((((((.((.((...(((.((....)))))..))...)).)))))))))))))...)))).((.(((((((((((.....)))).))))))).)).)))))......).))))... (-85.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUACGAGGGAAUAAACCGCAUACGUCGACCCUGACAGAAAGUCAGGUCGACCUAACCGAGCGUUUAGGUCGACCUUACGGAGCAAAUAGGUCGUCCUUACAGAGCGGUUAGGUCGACCUAAAACGGACGGAAGGUCGUCCUAACCGGAGCGGCACGUCGUCUUUGCAAAACGAGAGAAAUGCCGAUUGCGUUUCUCUCGUUUCUCUUUA .....((((((.......(((...((((....))))........(((((((((((((((..(....(((.((((((............)))))).)))....)..))))))))))))))).....((((((...(((((((.....))).))))...)))))).)))..((((((((((((((.....)))))))))))))))))))).. (-92.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 543 166 132 177 143 tfor:TF0864|5end_O-succinylbenzoate--CoA_ligase_914570..914800_POSITIVE 481 90 43 67 9 tfor:TF1664|5end_conserved_hypothetical_protein_1778761..1778991_POSITIVE 476 97 51 81 16 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 423 100 51 223 166 tfor:TF0152|5end_RNA_polymerase_ECF-type_sigma_factor_162021..162251_POSITIVE 412 100 55 223 170 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 410 79 35 70 33 tfor:TF1023|5end_ABC_transporter,_permease_component_1079197..1079427_POSITIVE 408 110 64 231 184 tfor:TF0457|5end_beta-glucanase_precursor_474099..474329_POSITIVE 405 195 151 180 132 tfor:TF0037|5end_sialic_acid-specific_9-O-acetylesterase_37836..38066_POSITIVE 395 98 54 227 176 tfor:TF1462|5end_erythronate-4-phosphate_dehydrogenase_1552184..1552414_POSITIVE 394 99 51 99 21 tfor:TF1945|5end_glycerate_dehydrogenase_2093229..2093459_POSITIVE 392 106 61 228 167 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 386 118 73 56 7 tfor:TF2165|5end_hypothetical_protein_2341654..2341884_POSITIVE 385 197 151 175 118 tfor:TF0975|5end_hypothetical_protein_1023994..1024224_POSITIVE 384 110 63 124 78 tfor:TF1250|5end_possible_cation_efflux_pump_1332324..1332554_POSITIVE 382 90 42 228 177 tfor:TF2684|5end_conserved_hypothetical_protein;_possible_CvpA_family_protein_2860692..2860922_POSITIVE 381 99 54 216 168 tfor:TF1835|5end_possible_dihydroxy-acid_dehydratase_1984201..1984431_POSITIVE 380 60 11 71 4 tfor:TF2898|5end_conserved_hypothetical_protein_3087061..3087291_POSITIVE 378 98 51 213 153 tfor:TF2992|5end_hexapeptide_transferase_family_protein_3209042..3209272_POSITIVE 377 97 53 186 136 tfor:TF2248|5end_transfer_region-related_protein,_TraB_2422551..2422781_POSITIVE 376 66 21 84 38 tfor:TF1474|5end_6-phosphogluconolactonase_1567342..1567572_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 105 64 57 16 tfor:TF0862|3end_conserved_hypothetical_protein_fragment_914459..914609_POSITIVE 411 96 55 151 100 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 410 79 35 52 15 tfor:TF1022|3end_chromosomal_replication_initiator_ATPase,_DnaA_1079259..1079409_POSITIVE 404 99 51 67 19 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 394 99 51 99 21 tfor:TF1944|3end_conserved_hypothetical_protein_2093309..2093459_POSITIVE 384 110 63 76 30 tfor:TF1249|3end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1332356..1332506_POSITIVE 377 100 51 58 5 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 375 167 121 147 96 tfor:TF2945|3end_DNA-directed_RNA_polymerase_beta'_subunit_3151802..3151952_POSITIVE 367 99 51 115 51 tfor:TF2827|3end_conserved_hypothetical_protein_3019642..3019792_POSITIVE 362 86 41 84 22 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 360 98 54 136 98 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 353 100 60 63 10 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 353 149 103 83 29 tfor:TF0178|3end_ferritin_188223..188373_POSITIVE 351 99 54 136 72 tfor:TF0808|3end_cation_efflux_system_protein_865421..865571_POSITIVE 351 67 24 128 80 tfor:TF0624|3end_Xaa-Pro_dipeptidase_(aminopeptidase_P)_661015..661165_POSITIVE 348 120 75 134 79 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 347 105 61 145 93 tfor:TF2024|3end_conserved_hypothetical_protein_2181979..2182129_POSITIVE 347 118 73 78 30 tfor:TF0252|3end_hypothetical_protein_283759..283909_POSITIVE 346 100 51 62 10 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 345 88 41 89 38 tfor:TF0185|3end_4-alpha-glucanotransferase_(amylomaltase)_199256..199406_POSITIVE