Origin IGS: taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca .........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 tgattacaatccaggaagtattgcaatttattaactttttatcacacaacacaatcatgatgaaaaagacactgttgattacatttttttctttgattcgtatgttcatgctttttgaccgcacaggacagttggatgtctgatttccgagaaggtcgcatccggagtacgtgcaaatctgtcgggaagtacaaagtaattccgattta Mask Tandem Repeat Region ================================================ taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca Find is-nt database================================================ Query_seq: TF3033:TF3034|TF3033:TF3034:S1 RNA binding domain protein, S1 ribosomal protein:conserved hypothetical protein:->->:3259044..3259252 209 taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF3033:TF3034|TF3033:TF3034:S1 RNA binding domain protein, S1 ribosomal protein:conserved hypothetical protein:->->:3259044..3259252 209 taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF3033:TF3034|TF3033:TF3034:S1 RNA binding domain protein, S1 ribosomal protein:conserved hypothetical protein:->->:3259044..3259252 209 taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 4 End: 165 ... M G I T L Y F P T D L H V L R M R P S R K S D I Q L S C A V K K H E H T N Q R K K C N Q Q C L F H H D C V V ............................................ Protein_Len: 59 Strand: + Start: 32 End: 208 ............................... M C T Y S G C D L L G N Q T S N C P V R S K S M N I R I K E K N V I N S V F F I M I V L C D K K L I N C N T S W I V I . Protein_Len: 46 Strand: - Start: 70 End: 207 ..................................................................... V D L Q G T R D F L M F M R I L S F F T I L L T K K M M I T N H S L F N I F Q L V E Q I T M .. Protein_Len: 31 Strand: - Start: 3 End: 95 .. I P I V K Y K G V S K C T S R I R G E R F D S M W S D Q A T M .................................................................................................................. taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca 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================================================ taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 41 HP_score: -2.4 Tail_Score: -2.90496 Start: 70 End: 83 Full_Region: tttttgaccgcacag gaca gttgga tgtc tgatttccgagaagg .....................................................................gacagttggatgtc.............................................................................................................................. Find igs database================================================ Query_seq: TF3033:TF3034|TF3033:TF3034:S1 RNA binding domain protein, S1 ribosomal protein:conserved hypothetical protein:->->:3259044..3259252 209 taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: tfor_TF3033_TF3034|S1 RNA binding domain protein, S1 ribosomal protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3259044,3259252]|209 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagnnnnnnntgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca taaatcggaattactttgtacttcccgacagatttgcacgtactccggatgcgaccttctcggaaatcagacatccaactgtcctgtgcggtcaaaaagcatgaacatacgaatcaaagaaaaaaatgtaatcaacagtgtctttttcatcatgattgtgttgtgtgataaaaagttaataaattgcaatacttcctggattgtaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCGGAAUUACUUUGUACUUCCCGACAGAUUUGCACGUACUCCGGAUGCGACCUUCUCGGAAAUCAGACAUCCAACUGUCCUGUGCGGUCAAAAAGCAUGAACAUACGAAUCAAAGAAAAAAAUGUAAUCAACAGUGUCUUUUUCAUCAUGAUUGUGUUGUGUGAUAAAAAGUUAAUAAAUUGCAAUACUUCCUGGAUUGUAAUCA ......((((.(((...))).)))).(((......((((....((((((........)).)))).....((((......))))..)))).((((...((((..(.(((..(((..(((((......(((.....)))...))))))))...))).)..))))...)))).....))).....((((((((.((....)))))))))).. (-38.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUACAAUCCAGGAAGUAUUGCAAUUUAUUAACUUUUUAUCACACAACACAAUCAUGAUGAAAAAGACACUGUUGAUUACAUUUUUUUCUUUGAUUCGUAUGUUCAUGCUUUUUGACCGCACAGGACAGUUGGAUGUCUGAUUUCCGAGAAGGUCGCAUCCGGAGUACGUGCAAAUCUGUCGGGAAGUACAAAGUAAUUCCGAUUUA .((((......((((((((((.(((......(((....))).........(((((((....((((((((...(((.....)))))))))))..))))).)).)))..))))))))))...((((.(((((......)))))...(((((.((........)))))))...)))).)))).(((((((..(((...))).)))))))... (-41.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 90 45 205 165 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 366 90 44 226 172 tfor:TF0786|5end_pyridoxal_phosphate_biosynthetic_protein_838563..838793_POSITIVE 353 58 14 98 38 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 339 60 18 60 25 tfor:TF2337|5end_conserved_hypothetical_protein_2497997..2498227_POSITIVE 338 68 21 74 20 tfor:TF1174|5end_ABC_transporter,_permease_component_1256584..1256814_POSITIVE 337 90 46 221 166 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 329 62 23 88 43 tfor:TF0761|5end_conserved_hypothetical_protein_806412..806642_POSITIVE 328 70 21 125 76 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 324 89 44 216 175 tfor:TF1804|5end_hypothetical_protein_1947101..1947331_POSITIVE 323 69 26 51 3 tfor:TF1508|5end_anti-sigma_factor_1616345..1616575_POSITIVE 323 119 73 60 9 tfor:TF0832|5end_conserved_hypothetical_protein_888466..888696_POSITIVE 322 90 44 61 8 tfor:TF2501|5end_DNA_mismatch_repair_protein_2676280..2676510_POSITIVE 322 59 17 207 165 tfor:TF2490|5end_4-hydroxyphenylacetate-3-hydroxylase/4-hydroxybut_yryl_dehydratase_2665218..2665448_POSITIVE 321 90 43 86 34 tfor:TF1475|5end_glucose-6-phosphate_1-dehydrogenase_1568034..1568264_POSITIVE 321 86 45 206 154 tfor:TF0587|5end_outer_membrane_protein_618319..618549_POSITIVE 320 88 42 196 145 tfor:TF2239|5end_hypothetical_protein_2414537..2414767_POSITIVE 319 110 61 203 151 tfor:TF2444|5end_regulatory_protein_RecX_2620957..2621187_POSITIVE 319 50 14 229 194 tfor:TF0410|5end_8-amino-7-oxononanoate_synthase_427605..427835_POSITIVE 318 89 50 227 188 tfor:TF2602|5end_tRNA-(5-methylaminomethyl-2-thiouridylate)_methyltransferase_2775086..2775316_POSITIVE 312 64 26 66 24 tfor:TF1149|5end_conserved_hypothetical_protein;_possible_branched-chain_amino_acid_aminotransferase_1229218..1229448_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 60 18 142 107 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 338 68 21 61 7 tfor:TF1173|3end_ABC_transporter,_permease_component_1256651..1256801_POSITIVE 325 61 26 103 60 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 321 90 43 95 43 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 311 53 16 74 41 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 310 70 21 76 36 tfor:TF1197|3end_transcriptional_regulator_1281414..1281564_POSITIVE 309 90 46 127 84 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 308 89 45 65 21 tfor:TF0300|3end_hypothetical_protein_325541..325691_POSITIVE 306 87 43 61 4 tfor:TF2575|3end_methionine_aminopeptidase_2745985..2746135_POSITIVE 306 86 44 60 23 tfor:TF0382|3end_transcription_termination_factor_405228..405378_POSITIVE 304 70 21 135 87 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 304 70 21 135 87 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 303 90 43 151 106 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 302 64 22 70 27 tfor:TF0774|3end_membrane-fusion_protein;_36_kDa_antigen_823730..823880_POSITIVE 302 64 21 47 13 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 300 90 43 71 16 tfor:TF2805|3end_zinc_protease_2996665..2996815_POSITIVE 299 89 44 146 106 tfor:TF1524|3end_tryptophanyl-tRNA_synthetase_1632027..1632177_POSITIVE 298 52 25 65 24 tfor:TF0478|3end_conserved_hypothetical_protein_498627..498777_POSITIVE 297 90 43 60 4 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE 296 62 28 142 108 tfor:TF0637|3end_TPR-repeat-containing_protein_675410..675560_POSITIVE