Origin IGS: tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagtattgtatgtataacagccccaaccatcccaaaaaaagccaaaacgacgtcgaatacgttaataaaaaacaaagcaaggaggatttgctcaaaaaataatttatgtttgcaaccgataattgttaggagaaa Mask Tandem Repeat Region ================================================ tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta Find is-nt database================================================ Query_seq: TF2543:TF2544|TF2543:TF2544:RNA polymerase sigma-70 factor, ECF subfamily:cytidine deaminase:->->:2728327..2728461 135 tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2543:TF2544|TF2543:TF2544:RNA polymerase sigma-70 factor, ECF subfamily:cytidine deaminase:->->:2728327..2728461 135 tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2543:TF2544|TF2543:TF2544:RNA polymerase sigma-70 factor, ECF subfamily:cytidine deaminase:->->:2728327..2728461 135 tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 29 End: 133 ............................ M N Y F L S K S S L L C F L L T Y S T S F W L F L G W L G L L Y I Q Y .. Protein_Len: 41 Strand: + Start: 13 End: 135 ............ M I G C K H K L F F E Q I L L A L F F I N V F D V V L A F F G M V G A V I H T I L Protein_Len: 30 Strand: - Start: 37 End: 126 .................................... K K L L D E K S Q K K N V Y E V D N Q S K K P H N P S N Y M ......... Protein_Len: 43 Strand: - Start: 3 End: 131 .. R R V I I P Q L C L N N K S C I R R A K N K I L T N S T T K A K K P I T P A T I C V M .... tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta 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================================================ tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2543:TF2544|TF2543:TF2544:RNA polymerase sigma-70 factor, ECF subfamily:cytidine deaminase:->->:2728327..2728461 135 tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: tfor_TF2543_TF2544|RNA polymerase sigma-70 factor, ECF subfamily:cytidine deaminase|POSITIVE:POSITIVE|[2728327,2728461]|135 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggcnnnnnnngggatggttggggctgttatacatacaatacta tttctcctaacaattatcggttgcaaacataaattattttttgagcaaatcctccttgctttgttttttattaacgtattcgacgtcgttttggctttttttgggatggttggggctgttatacatacaatacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUCCUAACAAUUAUCGGUUGCAAACAUAAAUUAUUUUUUGAGCAAAUCCUCCUUGCUUUGUUUUUUAUUAACGUAUUCGACGUCGUUUUGGCUUUUUUUGGGAUGGUUGGGGCUGUUAUACAUACAAUACUA ....(((((((.....(((..(((....(((((..((.....((((((.......)))))).))..)))))....)))..)))...(((((..(......)..)))))))))))).................... (-21.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAUUGUAUGUAUAACAGCCCCAACCAUCCCAAAAAAAGCCAAAACGACGUCGAAUACGUUAAUAAAAAACAAAGCAAGGAGGAUUUGCUCAAAAAAUAAUUUAUGUUUGCAACCGAUAAUUGUUAGGAGAAA ...(((((..((((.((((.............................(((((.....)))))............((((((.....))))))..............))))))))..))))).............. (-15.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 127 81 92 38 tfor:TF2343|5end_ribosome_recycling_factor_2506862..2507092_POSITIVE 370 118 73 231 179 tfor:TF0506|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_helicase_531031..531261_POSITIVE 360 119 74 229 196 tfor:TF3036|5end_glucose/galactose_transporter_3261667..3261897_POSITIVE 347 121 81 56 10 tfor:TF1499|5end_3-oxyacyl-[acyl-carrier_protein]_synthase_1598394..1598624_POSITIVE 344 116 75 89 46 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 343 116 85 177 146 tfor:TF1347|5end_conserved_hypothetical_protein_1426171..1426401_POSITIVE 343 118 75 200 144 tfor:TF0044|5end_conserved_hypothetical_protein_48334..48564_POSITIVE 342 113 71 221 180 tfor:TF2572|5end_50S_ribosomal_protein_L30_2743081..2743311_POSITIVE 337 118 77 148 112 tfor:TF2788|5end_hypothetical_protein_2972201..2972431_POSITIVE 336 87 43 106 65 tfor:TF2520|5end_conserved_hypothetical_protein_2698917..2699147_POSITIVE 334 117 72 214 168 tfor:TF2220|5end_CTn_integrase-recombinase_protein_2392424..2392654_POSITIVE 331 118 75 207 142 tfor:TF0541|5end_conserved_hypothetical_protein_568473..568703_POSITIVE 329 116 71 192 149 tfor:TF1804|5end_hypothetical_protein_1947101..1947331_POSITIVE 322 117 74 194 131 tfor:TF1406|5end_transposase_1481758..1481988_POSITIVE 321 116 75 192 152 tfor:TF2849|5end_histidinol-phosphate_transaminase_3037288..3037518_POSITIVE 318 116 73 217 166 tfor:TF1515|5end_hypothetical_protein_1625307..1625537_POSITIVE 312 129 84 62 7 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 312 115 75 183 129 tfor:TF2434|5end_conserved_hypothetical_protein_2613969..2614199_POSITIVE 312 123 81 193 140 tfor:TF2037|5end_conserved_hypothetical_protein;_possible_anaerobic_ribonucleoside-triphosphate_reductase_2196754..2196984_POSITIVE 312 119 71 57 12 tfor:TF1734|5end_conserved_hypothetical_protein_1856556..1856786_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 121 81 72 26 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 344 116 75 84 41 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 343 107 76 71 34 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 343 116 85 140 109 tfor:TF1346|3end_hypothetical_protein_1426214..1426364_POSITIVE 337 118 77 125 89 tfor:TF2787|3end_30S_ribosomal_protein_S1_2972258..2972408_POSITIVE 336 87 43 106 65 tfor:TF2519|3end_membrane_protein,_metallopeptidase_M23/M37_family_2698997..2699147_POSITIVE 331 118 75 150 85 tfor:TF0540|3end_conserved_hypothetical_protein;_possible_surface_protein_568496..568646_POSITIVE 329 116 71 131 88 tfor:TF1803|3end_conserved_hypothetical_protein_1947120..1947270_POSITIVE 318 112 75 151 105 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 303 120 75 76 28 tfor:TF1173|3end_ABC_transporter,_permease_component_1256651..1256801_POSITIVE 300 116 75 132 92 tfor:TF1608|3end_sulfate_transporter_1728463..1728613_POSITIVE 292 120 72 95 40 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 290 119 82 48 12 tfor:TF1465|3end_modulator_of_DNA_gyrase_1555544..1555694_POSITIVE 289 121 81 46 8 tfor:TF1758|3end_conserved_hypothetical_protein_1895544..1895694_POSITIVE 287 126 91 130 95 tfor:TF2297|3end_hypothetical_protein_2449673..2449823_POSITIVE 284 115 72 108 59 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 283 130 84 96 45 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 283 118 75 83 39 tfor:TF0952|3end_conserved_hypothetical_protein_998009..998159_POSITIVE 282 100 51 97 50 tfor:TF0624|3end_Xaa-Pro_dipeptidase_(aminopeptidase_P)_661015..661165_POSITIVE 282 118 79 138 103 tfor:TF0469|3end_hypothetical_protein_487228..487378_POSITIVE