Origin IGS: taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttccggatgcacatcgccctgccactttacgtcattaacgatcgttttacggcggggcagtccttgagttggttagttgtttaaatgtttttgtttagcaatctcggtaaacaaaaaaaacaacatatcaatcatcgcagctcaagtctttta Mask Tandem Repeat Region ================================================ taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta Find is-nt database================================================ Query_seq: TF3099:TF3100|TF3099:TF3100:conserved hypothetical protein:conserved hypothetical protein:->->:3331168..3331324 157 taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3099:TF3100|TF3099:TF3100:conserved hypothetical protein:conserved hypothetical protein:->->:3331168..3331324 157 taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3099:TF3100|TF3099:TF3100:conserved hypothetical protein:conserved hypothetical protein:->->:3331168..3331324 157 taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta Predict ORF larger than 30AA ================================================ taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta 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================================================ taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF3099:TF3100|TF3099:TF3100:conserved hypothetical protein:conserved hypothetical protein:->->:3331168..3331324 157 taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: tfor_TF3099_TF3100|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3331168,3331324]|157 HSP 1 e-value: 8.0E-70 bit: 264.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 taaaagacttgagctgcgatgattgatatgttgnnnnnnnngtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta taaaagacttgagctgcgatgattgatatgttgttttttttgtttaccgagattgctaaacaaaaacatttaaacaactaaccaactcaaggactgccccgccgtaaaacgatcgttaatgacgtaaagtggcagggcgatgtgcatccggaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGACUUGAGCUGCGAUGAUUGAUAUGUUGUUUUUUUUGUUUACCGAGAUUGCUAAACAAAAACAUUUAAACAACUAACCAACUCAAGGACUGCCCCGCCGUAAAACGAUCGUUAAUGACGUAAAGUGGCAGGGCGAUGUGCAUCCGGAAAUUA .............(((.((((.(((....(((((((((((((((((.((....)).)))))))))).....)))))))....))).........(((((.((((....(((.(((....))))))....)))).))))).....)))))))...... (-35.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUCCGGAUGCACAUCGCCCUGCCACUUUACGUCAUUAACGAUCGUUUUACGGCGGGGCAGUCCUUGAGUUGGUUAGUUGUUUAAAUGUUUUUGUUUAGCAAUCUCGGUAAACAAAAAAAACAACAUAUCAAUCAUCGCAGCUCAAGUCUUUUA ........((.(((.....((((((((.....(((((......)).))).....))))))))......(((.(((((..(((((((.....((((((((((.(......).)))))))))))))))))..))))))))..)))..)).......... (-43.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 148 101 177 120 tfor:TF1181|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_1267522..1267752_POSITIVE 342 140 91 163 107 tfor:TF2231|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_2400307..2400537_POSITIVE 342 145 101 45 1 tfor:TF1340|5end_pantoate--beta-alanine_ligase_1421280..1421510_POSITIVE 339 104 66 89 42 tfor:TF2438|5end_hypothetical_protein_2615781..2616011_POSITIVE 332 138 94 228 187 tfor:TF1315|5end_purine_nucleoside_phosphorylase_1390236..1390466_POSITIVE 329 140 91 87 46 tfor:TF2206|5end_conserved_hypothetical_protein;_possible_sugar_phosphate_isomerase/epimerase_2379969..2380199_POSITIVE 326 150 109 186 138 tfor:TF2395|5end_conserved_hypothetical_protein_2566532..2566762_POSITIVE 322 140 91 74 26 tfor:TF1896|5end_conserved_hypothetical_protein;_possible_phage-related_protein_2047858..2048088_POSITIVE 321 140 94 63 9 tfor:TF2327|5end_conserved_hypothetical_protein;_possible_lipoprotein_2485709..2485939_POSITIVE 320 150 101 216 185 tfor:TF0617|5end_alpha-1,2-mannosidase_650862..651092_POSITIVE 316 148 101 178 133 tfor:TF1252|5end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1334361..1334591_POSITIVE 314 150 101 186 140 tfor:TF2129|5end_possible_3-oxoacyl-(acyl-carrier-protein)_synthase_2305464..2305694_POSITIVE 314 150 101 78 8 tfor:TF0813|5end_glycosyl_hydrolase,_secreted_870677..870907_POSITIVE 313 139 91 171 113 tfor:TF0464|5end_precorrin_methylase_480211..480441_POSITIVE 309 112 82 228 193 tfor:TF2949|5end_dihydroxynaphthoate_synthase_(naphthoate_synthase)_3156578..3156808_POSITIVE 309 140 94 223 176 tfor:TF2904|5end_ATP-dependent__helicase,_possible_UvrD/REP_helicase_domain_protein_3098903..3099133_POSITIVE 309 149 102 160 97 tfor:TF2829|5end_conserved_hypothetical_protein_3019562..3019792_POSITIVE 309 139 92 168 127 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 308 118 86 60 21 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 306 139 91 139 73 tfor:TF3088|5end_conserved_hypothetical_protein_3322512..3322742_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 139 95 56 18 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 354 140 95 40 2 tfor:TF2912|3end_hypothetical_protein_3108000..3108150_POSITIVE 336 96 55 75 29 tfor:TF1174|3end_ABC_transporter,_permease_component_1257896..1258046_POSITIVE 329 140 91 48 7 tfor:TF2205|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2380010..2380160_POSITIVE 328 150 101 112 60 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 322 140 91 61 13 tfor:TF1895|3end_hypothetical_protein_2047925..2048075_POSITIVE 318 145 109 151 116 tfor:TF2394|3end_integrase/recombinase_XerD_2566590..2566740_POSITIVE 317 144 101 47 2 tfor:TF0064|3end_conserved_hypothetical_protein_70412..70562_POSITIVE 316 150 101 94 38 tfor:TF2392|3end_alpha-galactosidase_2565506..2565656_POSITIVE 311 150 103 140 90 tfor:TF2895|3end_hypothetical_protein_3084192..3084342_POSITIVE 306 139 91 129 63 tfor:TF3087|3end_conserved_hypothetical_protein_3322582..3322732_POSITIVE 306 139 91 85 30 tfor:TF2113|3end_phosphoribosylaminoimidazole_carboxylase_2283086..2283236_POSITIVE 304 138 92 143 94 tfor:TF2627|3end_SAM-dependent_methyltransferase_2800754..2800904_POSITIVE 302 99 55 65 16 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE 302 150 102 75 16 tfor:TF1379|3end_conserved_hypothetical_protein_1456670..1456820_POSITIVE 302 150 101 68 9 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 300 140 99 73 37 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 296 130 90 144 94 tfor:TF2368|3end_uridine_phosphorylase_2534618..2534768_POSITIVE 295 140 91 119 55 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 293 150 101 53 6 tfor:TF2455|3end_conserved_hypothetical_protein;_possible_membrane_protein_2632437..2632587_POSITIVE