Origin IGS: tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca .........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 tgagggaataaccgcttaaacagacctttaaatggtcgggtaatattcgggcaaaagtacaaaagtttcctttaaatccaagcacttgagataaaaaacacagaaaggactttgcgctcttcatcgctctaccacaccctttttctaccctttccggaatgctaacctatgaccatcttttctatggattttctttgcagatatggctcaaagaattcgtcaaaagaacactga Mask Tandem Repeat Region ================================================ tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca Find is-nt database================================================ Query_seq: TF2980:TF2981|TF2980:TF2981:possible alpha-amylase:conserved hypothetical protein:->->:3195875..3196108 234 tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2980:TF2981|TF2980:TF2981:possible alpha-amylase:conserved hypothetical protein:->->:3195875..3196108 234 tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2980:TF2981|TF2980:TF2981:possible alpha-amylase:conserved hypothetical protein:->->:3195875..3196108 234 tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 75 End: 233 .......................................................................... M P E R V E K G C G R A M K S A K S F L C F L S Q V L G F K G N F C T F A R I L P D H L K V C L S G Y S L . Protein_Len: 37 Strand: - Start: 2 End: 112 . L T R K V F E K L W I Q L S F G Y F L H D Y T L M G S L T S F P H P L A M .......................................................................................................................... tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca 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================================================ tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2980:TF2981|TF2980:TF2981:possible alpha-amylase:conserved hypothetical protein:->->:3195875..3196108 234 tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: tfor_TF2980_TF2981|possible alpha-amylase:conserved hypothetical protein|POSITIVE:POSITIVE|[3195875,3196108]|234 HSP 1 e-value: 1.0E-130 bit: 464.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca tcagtgttcttttgacgaattctttgagccatatctgcaaagaaaatccatagaaaagatggtcataggttagcattccggaaagggtagaaaaagggtgtggtagagcgatgaagagcgcaaagtcctttctgtgttttttatctcaagtgcttggatttaaaggaaacttttgtacttttgcccgaatattacccgaccatttaaaggtctgtttaagcggttattccctca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGUGUUCUUUUGACGAAUUCUUUGAGCCAUAUCUGCAAAGAAAAUCCAUAGAAAAGAUGGUCAUAGGUUAGCAUUCCGGAAAGGGUAGAAAAAGGGUGUGGUAGAGCGAUGAAGAGCGCAAAGUCCUUUCUGUGUUUUUUAUCUCAAGUGCUUGGAUUUAAAGGAAACUUUUGUACUUUUGCCCGAAUAUUACCCGACCAUUUAAAGGUCUGUUUAAGCGGUUAUUCCCUCA ............((((...(((((((((......)).))))))).....(((((..((((((((...((........)).....((((((.....((((..........(((((((((((((.((....)).)))))))))))))..((((((........((((....)))).))))))..)))).....)))))))))))))).....))))).......))))........ (-56.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGGAAUAACCGCUUAAACAGACCUUUAAAUGGUCGGGUAAUAUUCGGGCAAAAGUACAAAAGUUUCCUUUAAAUCCAAGCACUUGAGAUAAAAAACACAGAAAGGACUUUGCGCUCUUCAUCGCUCUACCACACCCUUUUUCUACCCUUUCCGGAAUGCUAACCUAUGACCAUCUUUUCUAUGGAUUUUCUUUGCAGAUAUGGCUCAAAGAAUUCGUCAAAAGAACACUGA ((((((.....)).))))..(((.........(((((((((..(((((.((.((..(((.(((((..((((((..((((((....))).)))...........))))))....(((........)))...........)))))..)))..)).)).)))))...))))..)))))((((((..((((((..((((((.((......)))))))))))))).))))))...))). (-44.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 128 86 84 31 tfor:TF2798|5end_conserved_hypothetical_protein_2984023..2984253_POSITIVE 335 119 77 145 101 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 331 110 64 62 12 tfor:TF2434|5end_conserved_hypothetical_protein_2613969..2614199_POSITIVE 331 135 98 202 161 tfor:TF1959|5end_conserved_hypothetical_protein_2109377..2109607_POSITIVE 330 137 95 161 119 tfor:TF1284|5end_glyceraldehyde_3-phosphate_dehydrogenase_1367939..1368169_POSITIVE 329 125 81 152 110 tfor:TF0620|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_654711..654941_POSITIVE 319 110 61 71 32 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 314 138 93 146 95 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 314 120 80 219 182 tfor:TF0520|5end_tetraacyldisaccharide_4'-kinase_544752..544982_POSITIVE 313 138 94 187 131 tfor:TF1850|5end_Na+/H+-exchanging_protein_1998542..1998772_POSITIVE 309 119 73 219 179 tfor:TF1653|5end_hypothetical_protein_1766201..1766431_POSITIVE 309 130 82 69 26 tfor:TF1336|5end_hypothetical_protein_1418626..1418856_POSITIVE 309 119 73 219 179 tfor:TF0979|5end_hypothetical_protein_1032838..1033068_POSITIVE 309 120 76 165 119 tfor:TF0730|5end_conserved_hypothetical_protein_782249..782479_POSITIVE 309 110 69 214 163 tfor:TF0729|5end_DNA_primase_780107..780337_POSITIVE 307 134 95 213 171 tfor:TF1212|5end_conserved_hypothetical_protein_1299792..1300022_POSITIVE 306 120 78 62 19 tfor:TF2392|5end_alpha-galactosidase_2563384..2563614_POSITIVE 305 119 74 99 47 tfor:TF0995|5end_conserved_hypothetical_protein_1049695..1049925_POSITIVE 305 110 65 144 108 tfor:TF0748|5end_ATP-dependent_protease_La_792890..793120_POSITIVE 304 108 61 127 83 tfor:TF0039|5end_conserved_hypothetical_protein_41407..41637_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 120 71 59 14 tfor:TF0333|3end_hypothetical_protein_359444..359594_POSITIVE 362 225 187 126 84 tfor:TF3045|3end_two-component_system_response_regulator_3274633..3274783_POSITIVE 359 127 84 136 98 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 347 128 86 58 5 tfor:TF2797|3end_cytochrome_d_oxidase,_subunit_I_2984077..2984227_POSITIVE 335 119 77 145 101 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 331 110 64 56 6 tfor:TF2433|3end_possible_UDP-2,3-diacylglucosamine_hydrolase_2614043..2614193_POSITIVE 329 125 81 142 100 tfor:TF0619|3end_ubiquinone_biosynthesis_methyltransferase_654781..654931_POSITIVE 309 120 76 116 70 tfor:TF0729|3end_DNA_primase_782280..782430_POSITIVE 306 120 78 62 19 tfor:TF2391|3end_conserved_hypothetical_protein_2563464..2563614_POSITIVE 306 119 80 73 24 tfor:TF2109|3end_possible_metallo-beta-lactamase_family_protein_2278960..2279110_POSITIVE 305 119 74 106 54 tfor:TF0994|3end_maltose_O-acetyltransferase_1049782..1049932_POSITIVE 305 110 65 84 48 tfor:TF0746|3end_possible_DNA_polymerase_III_792910..793060_POSITIVE 303 118 73 74 29 tfor:TF0280|3end_hypothetical_protein_309036..309186_POSITIVE 303 120 78 65 16 tfor:TF0063|3end_conserved_hypothetical_protein_68490..68640_POSITIVE 298 110 64 151 102 tfor:TF0777|3end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_827053..827203_POSITIVE 297 118 78 51 7 tfor:TF2526|3end_outer_membrane_protein,_TonB_dependent_receptor_2709007..2709157_POSITIVE 296 120 72 51 2 tfor:TF0958|3end_conserved_hypothetical_protein_1004909..1005059_POSITIVE 293 136 97 50 3 tfor:TF2019|3end_dipeptidyl_peptidase_VI_2176401..2176551_POSITIVE 291 118 73 56 11 tfor:TF3057|3end_conserved_hypothetical_protein_3281238..3281388_POSITIVE 291 129 83 138 82 tfor:TF1635|3end_conserved_hypothetical_protein;_possible_helicase_1746831..1746981_POSITIVE