Origin IGS: gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagatatataatagcatataaattttaatctgtaaagggtaagcttcataaatttcaataatttataaaatgtcaattatttttaataaattcgaatattttcaacatctaaatatgc Mask Tandem Repeat Region ================================================ gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Find is-nt database================================================ Query_seq: TDE1288:TDE1289|TDE1288:TDE1289:CAAX amino terminal protease family protein:hypothetical protein:->->:1327336..1327453 118 gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1288:TDE1289|TDE1288:TDE1289:CAAX amino terminal protease family protein:hypothetical protein:->->:1327336..1327453 118 gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1288:TDE1289|TDE1288:TDE1289:CAAX amino terminal protease family protein:hypothetical protein:->->:1327336..1327453 118 gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Predict ORF larger than 30AA ================================================ gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 82 End: 111 .................................................................................CTTTACAGATTAAAATTTATATGCTATTAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1288:TDE1289|TDE1288:TDE1289:CAAX amino terminal protease family protein:hypothetical protein:->->:1327336..1327453 118 gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_002967_TDE1288_TDE1289|CAAX amino terminal protease family protein:hypothetical protein|POSITIVE:POSITIVE|[1327336,1327453]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt gcatatttagatgttgaaaatattcgaatttattaaaaataattgacattttataaattattgaaatttatgaagcttaccctttacagattaaaatttatatgctattatatatctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUAUUUAGAUGUUGAAAAUAUUCGAAUUUAUUAAAAAUAAUUGACAUUUUAUAAAUUAUUGAAAUUUAUGAAGCUUACCCUUUACAGAUUAAAAUUUAUAUGCUAUUAUAUAUCUU ((((((.(((((.(((((....))))))))))................(((((((((((.....)))))))))))........................))))))............. (-12.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUAUAUAAUAGCAUAUAAAUUUUAAUCUGUAAAGGGUAAGCUUCAUAAAUUUCAAUAAUUUAUAAAAUGUCAAUUAUUUUUAAUAAAUUCGAAUAUUUUCAACAUCUAAAUAUGC ..(((((.....(((.(((...(((((.....))))).))).)))..(((((((.....)))))))...)))))...................(((....)))............... ( -9.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 202 90 42 104 71 NC_002967:TDE1468|5end_glycoprotease_family_protein_1517336..1517566_NEGATIVE 193 89 42 141 90 NC_002967:TDE1875|5end_hypothetical_protein_1896906..1897136_NEGATIVE 171 39 1 49 12 NC_002967:TDE2776|5end_proline_iminopeptidase_2827364..2827594_POSITIVE 167 92 71 24 6 NC_002967:TDE1277|5end_Fe-hydrogenase_large_subunit_family_protein_1310681..1310911_POSITIVE 165 109 66 128 86 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 164 90 43 211 170 NC_002967:TDE1452|5end_hypothetical_protein_1498891..1499121_POSITIVE 162 110 61 221 168 NC_002967:TDE0252|5end_hypothetical_protein_286263..286493_POSITIVE 162 87 41 64 14 NC_002967:TDE0152|5end_amino_acid_permease_family_protein_174477..174707_NEGATIVE 160 110 61 93 42 NC_002967:TDE1624|5end_glycine_dehydrogenase_subunit_2_1673519..1673749_NEGATIVE 156 98 51 217 168 NC_002967:TDE2673|5end_hypothetical_protein_2712377..2712607_NEGATIVE 155 106 69 231 184 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 151 89 55 168 124 NC_002967:TDE0778|5end_ribosomal_protein_L24_811487..811717_POSITIVE 149 106 73 105 71 NC_002967:TDE0342|5end_integral_membrane_protein_MviN_383741..383971_NEGATIVE 148 97 53 111 58 NC_002967:TDE1880|5end_hypothetical_protein_1902535..1902765_POSITIVE 148 110 75 48 1 NC_002967:TDE1715|5end_phosphoglycerate_kinase_1770762..1770992_NEGATIVE 146 99 55 213 171 NC_002967:TDE0961|5end_DnaJ_domain_protein_983519..983749_POSITIVE 146 106 69 54 12 NC_002967:TDE0622|5end_radical_SAM_domain_protein_655718..655948_NEGATIVE 145 86 74 104 92 NC_002967:TDE1681|5end_V-type_ATP_synthase_subunit_D_1733537..1733767_NEGATIVE 145 85 62 105 82 NC_002967:TDE0682|5end_preprotein_translocase,_YajC_subunit_721078..721308_NEGATIVE 144 89 59 214 180 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 202 90 42 107 74 NC_002967:TDE1469|3end_conserved_hypothetical_protein_TIGR00150_1517333..1517483_NEGATIVE 193 89 42 108 57 NC_002967:TDE1876|3end_glycosyl_transferase,_WecB/TagA/CpsF_family_1896939..1897089_NEGATIVE 169 85 48 116 77 NC_002967:TDE0452|3end_hypothetical_protein_509949..510099_NEGATIVE 167 104 66 107 63 NC_002967:TDE2565|3end_hypothetical_protein_2590392..2590542_NEGATIVE 165 109 66 95 53 NC_002967:TDE1484|3end_hypothetical_protein_1529744..1529894_POSITIVE 162 87 41 53 3 NC_002967:TDE0153|3end_coenzyme_A_disulfide_reductase,_putative_174488..174638_NEGATIVE 160 110 61 93 42 NC_002967:TDE1625|3end_glycine_cleavage_system_P_protein,_subunit_1_1673519..1673669_NEGATIVE 159 105 69 56 17 NC_002967:TDE2162|3end_NOL1/NOP2/sun_family_protein_2195560..2195710_POSITIVE 156 98 51 129 80 NC_002967:TDE2674|3end_hypothetical_protein_2712465..2712615_NEGATIVE 145 86 74 93 81 NC_002967:TDE1682|3end_V-type_ATP_synthase_subunit_B_1733548..1733698_NEGATIVE 145 105 61 102 49 NC_002967:TDE1499|3end_adenylosuccinate_lyase,_putative_1546788..1546938_POSITIVE 144 97 65 64 35 NC_002967:TDE2647|3end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_2686002..2686152_NEGATIVE 144 35 10 125 100 NC_002967:TDE0940|3end_hypothetical_protein_963635..963785_POSITIVE 141 89 73 47 30 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 141 110 61 88 37 NC_002967:TDE1697|3end_phosphoglycerate_mutase_1755516..1755666_NEGATIVE 140 25 1 120 96 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 139 78 34 98 53 NC_002967:TDE2297|3end_TPR_domain_protein_2336339..2336489_NEGATIVE 137 84 45 138 95 NC_002967:TDE2271|3end_HAM1_protein_2308481..2308631_NEGATIVE 137 105 71 79 48 NC_002967:TDE0905|3end_hypothetical_protein_923228..923378_POSITIVE 133 82 42 46 9 NC_002967:TDE2713|3end_RNA_methyltransferase,_TrmH_family_2769557..2769707_NEGATIVE