Origin IGS: tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtttctccgtccataataagaaagtcaacaaggaaatatctctttcctcactgactttctattgtcttaaatcaacaagcctccgcacgaataaaactttcggctggca Mask Tandem Repeat Region ================================================ tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact Find is-nt database================================================ Query_seq: TDE1310:TDE1311|TDE1310:TDE1311:modulator of DNA gyrase family protein:ABC transporter, ATP-binding/permease protein:->->:1347401..1347510 110 tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1310:TDE1311|TDE1310:TDE1311:modulator of DNA gyrase family protein:ABC transporter, ATP-binding/permease protein:->->:1347401..1347510 110 tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1310:TDE1311|TDE1310:TDE1311:modulator of DNA gyrase family protein:ABC transporter, ATP-binding/permease protein:->->:1347401..1347510 110 tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact Predict ORF larger than 30AA ================================================ tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact 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================================================ tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -11.7 Tail_Score: -3.78934 Start: 51 End: 90 Full_Region: TGATTTAAGACAATA GAAAGTCAGTGAGGAAA GAGATA TTTCCTTGTTGACTTTC TTATTATGGACGGAG ..................................................GAAAGTCAGTGAGGAAAGAGATATTTCCTTGTTGACTTTC.................... TransTerm Strand: + Conf: 79 HP_score: -6.7 Tail_Score: -4.51812 Start: 55 End: 86 Full_Region: TTAAGACAATAGAAA GTCAGTGAGGAAA GAGATA TTTCCTTGTTGAC TTTCTTATTATGGAC ......................................................GTCAGTGAGGAAAGAGATATTTCCTTGTTGAC........................ Find igs database================================================ Query_seq: TDE1310:TDE1311|TDE1310:TDE1311:modulator of DNA gyrase family protein:ABC transporter, ATP-binding/permease protein:->->:1347401..1347510 110 tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE1310_TDE1311|modulator of DNA gyrase family protein:ABC transporter, ATP-binding/permease protein|POSITIVE:POSITIVE|[1347401,1347510]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact tgccagccgaaagttttattcgtgcggaggcttgttgatttaagacaatagaaagtcagtgaggaaagagatatttccttgttgactttcttattatggacggagaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCCAGCCGAAAGUUUUAUUCGUGCGGAGGCUUGUUGAUUUAAGACAAUAGAAAGUCAGUGAGGAAAGAGAUAUUUCCUUGUUGACUUUCUUAUUAUGGACGGAGAAACU ...........((((((.(((((.((.....(((((.......))))).((((((((((..((((((......))))))..)))))))))).....)).))))))))))) (-34.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUCUCCGUCCAUAAUAAGAAAGUCAACAAGGAAAUAUCUCUUUCCUCACUGACUUUCUAUUGUCUUAAAUCAACAAGCCUCCGCACGAAUAAAACUUUCGGCUGGCA .(((.........((((((.((((((((...((((((......))))))...))))))))))))))........)))..(((...((.((((.......)))))).))). (-28.53) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 33 3 127 97 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 333 33 5 219 191 NC_002967:TDE0712|5end_hypothetical_protein_746963..747193_NEGATIVE 331 41 14 205 178 NC_002967:TDE2146|5end_hydrolase,_alpha/beta_fold_family_2183060..2183290_POSITIVE 328 65 21 210 169 NC_002967:TDE0738|5end_hypothetical_protein_775934..776164_NEGATIVE 311 46 2 108 60 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 288 38 2 218 174 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 283 38 1 225 181 NC_002967:TDE0921|5end_ABC_transporter,_ATP-binding/permease_protein_941857..942087_NEGATIVE 282 30 11 213 194 NC_002967:TDE1691|5end_hypothetical_protein_1748273..1748503_NEGATIVE 281 35 5 208 181 NC_002967:TDE1830|5end_hypothetical_protein_1863583..1863813_POSITIVE 269 36 6 129 108 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 263 64 24 114 55 NC_002967:TDE1662|5end_replicative_DNA_helicase_1715898..1716128_POSITIVE 263 50 2 77 30 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 263 36 3 124 95 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 262 37 1 221 189 NC_002967:TDE1188|5end_NAD(P)_transhydrogenase,_beta_subunit_1216622..1216852_NEGATIVE 262 38 3 140 112 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 261 90 42 173 112 NC_002967:TDE1343|5end_trypsin_domain/PDZ_domain_protein_1380546..1380776_POSITIVE 260 36 2 200 165 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 259 61 21 59 19 NC_002967:TDE2369|5end_hypothetical_protein_2402292..2402522_POSITIVE 257 50 2 181 122 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 250 65 25 182 145 NC_002967:TDE0667|5end_FeS_assembly_protein_SufB_704290..704520_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 33 3 34 4 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 335 91 51 41 1 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE 332 38 1 140 95 NC_002967:TDE2504|3end_O-sialoglycoprotein_endopeptidase_2530097..2530247_POSITIVE 331 36 1 108 77 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 325 36 2 47 16 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 282 30 11 48 29 NC_002967:TDE1693|3end_hypothetical_protein_1748438..1748588_NEGATIVE 278 30 1 137 106 NC_002967:TDE2690|3end_hypothetical_protein_2728743..2728893_NEGATIVE 272 41 11 151 121 NC_002967:TDE1368|3end_hypothetical_protein_1409427..1409577_NEGATIVE 263 45 5 101 67 NC_002967:TDE1088|3end_hypothetical_protein_1119275..1119425_NEGATIVE 263 36 3 56 27 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 262 38 3 143 115 NC_002967:TDE0273|3end_ABC_transporter,_ATP-binding/permease_protein_302867..303017_NEGATIVE 261 90 42 108 47 NC_002967:TDE1342|3end_hypothetical_protein_1380561..1380711_POSITIVE 257 50 2 76 17 NC_002967:TDE2235|3end_methylaspartate_ammonia-lyase_2273350..2273500_NEGATIVE 249 36 1 142 113 NC_002967:TDE0930|3end_hypothetical_protein_952843..952993_NEGATIVE 246 45 2 87 33 NC_002967:TDE2152|3end_hypothetical_protein_2188804..2188954_NEGATIVE 245 44 2 74 37 NC_002967:TDE2446|3end_malate_dehydrogenase_2474774..2474924_NEGATIVE 245 36 10 35 9 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 244 47 2 58 7 NC_002967:TDE1884|3end_hypothetical_protein_1905874..1906024_NEGATIVE 242 34 2 64 41 NC_002967:TDE2766|3end_motility_protein_A_2820095..2820245_NEGATIVE 242 35 1 140 98 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE