Origin IGS: tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcttcctcaacgatgaacgagccaataaagcccgaagctcctgttattaatattctttttttcattaaaataatgtgaaacgcttgcaaagatacgaacttttttgttactttgtaaatataattaaagcgcaattgacaatgggaaaggaaaaaaagagtaaaagacga Mask Tandem Repeat Region ================================================ tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca Find is-nt database================================================ Query_seq: PI0008:PI0009|PI0008:PI0009:exoribonuclease II (ribonuclease II):NAD-dependent epimerase/dehydratase family protein:->->:9622..9792 171 tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0008:PI0009|PI0008:PI0009:exoribonuclease II (ribonuclease II):NAD-dependent epimerase/dehydratase family protein:->->:9622..9792 171 tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0008:PI0009|PI0008:PI0009:exoribonuclease II (ribonuclease II):NAD-dependent epimerase/dehydratase family protein:->->:9622..9792 171 tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 37 End: 171 .................................... M R F N Y I Y K V T K K F V S L Q A F H I I L M K K R I L I T G A S G F I G S F I V E E A Protein_Len: 32 Strand: - Start: 1 End: 96 R R K S K K E K G M T L Q A K I I N V F Y C F L E Y R Q L R K M ........................................................................... tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca 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================================================ tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0008:PI0009|PI0008:PI0009:exoribonuclease II (ribonuclease II):NAD-dependent epimerase/dehydratase family protein:->->:9622..9792 171 tcgtcttttactctttttttcctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca Intra-Species Hit: Count: 1 Min: 21 Max: 171 Len: 151 Subject: pint_PI0008_PI0009|exoribonuclease II (ribonuclease II):NAD-dependent epimerase/dehydratase family protein|POSITIVE:POSITIVE|[9622,9792]|171 HSP 1 e-value: 5.0E-68 bit: 258.0 Len: 151 Query Start:21 Query End:171 Subject Strand: POSITIVE Subject Start: 21 Subject End: 171 ....................cctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgnnnnnnngaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca ....................cctttcccattgtcaattgcgctttaattatatttacaaagtaacaaaaaagttcgtatctttgcaagcgtttcacattattttaatgaaaaaaagaatattaataacaggagcttcgggctttattggctcgttcatcgttgaggaagca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUCCCAUUGUCAAUUGCGCUUUAAUUAUAUUUACAAAGUAACAAAAAAGUUCGUAUCUUUGCAAGCGUUUCACAUUAUUUUAAUGAAAAAAAGAAUAUUAAUAACAGGAGCUUCGGGCUUUAUUGGCUCGUUCAUCGUUGAGGAAGCA ....(((..((((.(((.(((((((((..((((..((..............))..))))..))).))))))....(((((...)))))...........))).))))..)))((((((((((.....)))))..(((....))).))))). (-23.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUUCCUCAACGAUGAACGAGCCAAUAAAGCCCGAAGCUCCUGUUAUUAAUAUUCUUUUUUUCAUUAAAAUAAUGUGAAACGCUUGCAAAGAUACGAACUUUUUUGUUACUUUGUAAAUAUAAUUAAAGCGCAAUUGACAAUGGGAAAGG .((((..(((....)))..))))................(((((((.(((((........((((((.........))))))(((((((((((..(((((....)))))..)))))))...........))))..))))).))))))).... (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 148 101 143 91 pint:PI0656|5end_peptidase_T_(tripeptide_aminopeptidase)_599833..600063_POSITIVE 303 149 110 53 10 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 298 150 108 173 128 pint:PI1649|5end_hypothetical_protein_1563080..1563310_POSITIVE 294 150 113 55 10 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 288 141 108 161 128 pint:PI0354|5end_hypothetical_protein_325886..326116_POSITIVE 286 148 109 58 4 pint:PI0376|5end_conserved_hypothetical_protein_346417..346647_POSITIVE 278 145 108 190 150 pint:PI0974|5end_hypothetical_protein_899371..899601_POSITIVE 277 148 106 55 5 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 276 150 108 208 155 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 276 147 104 82 47 pint:PI0107|5end_2-methylthioadenine_synthetase_103280..103510_POSITIVE 272 150 110 108 56 pint:PI1854|5end_possible_glycosyl_transferase_1800925..1801155_POSITIVE 271 149 108 206 167 pint:PI0304|5end_hypothetical_protein_288582..288812_POSITIVE 269 150 105 77 21 pint:PI1501|5end_GTP-binding_elongation_factor_family_protein_TypA/BipA_1421424..1421654_POSITIVE 267 146 108 225 183 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 266 150 107 109 51 pint:PI0661|5end_hypothetical_protein_603956..604186_POSITIVE 264 150 103 179 121 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 264 150 109 89 42 pint:PI0954|5end_hypothetical_protein_885567..885797_POSITIVE 263 149 106 33 1 pint:PI1800|5end_hypothetical_protein_1733723..1733953_POSITIVE 263 150 103 87 34 pint:PI1420|5end_probable_membrane_protein_1340123..1340353_POSITIVE 263 149 104 65 11 pint:PI0590|5end_ribosomal_large_subunit_pseudouridine_synthase_B_536963..537193_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 150 109 146 98 pint:PI0581|3end_conserved_hypothetical_protein_532589..532739_POSITIVE 327 143 110 135 103 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE 307 149 108 85 50 pint:PI0925|3end_ribosomal_protein_L11_methyltransferase_856638..856788_POSITIVE 298 150 108 141 96 pint:PI1646|3end_hypothetical_protein_1563128..1563278_POSITIVE 288 141 108 129 96 pint:PI0352|3end_hypothetical_protein_325934..326084_POSITIVE 284 141 110 111 76 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE 283 150 101 86 37 pint:PI0779|3end_predicted_TPR-repeat-containing_protein_715800..715950_POSITIVE 278 145 108 138 98 pint:PI0972|3end_glycine_cleavage_system_H_protein_2_899399..899549_POSITIVE 276 147 104 39 4 pint:PI0106|3end_ABC_transport_system,_ATP-binding/permease_103317..103467_POSITIVE 274 149 105 131 98 pint:PI1800|3end_hypothetical_protein_1733901..1734051_POSITIVE 274 149 105 49 16 pint:PI1799|3end_30S_ribosomal_protein_S2_1733819..1733969_POSITIVE 274 150 106 119 75 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 273 142 110 114 78 pint:PI1890|3end_cell_division_protein_FtsW_1834072..1834222_POSITIVE 272 146 117 136 106 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 268 146 111 142 106 pint:PI0195|3end_epimerase/reductase_188202..188352_POSITIVE 266 150 107 70 12 pint:PI0660|3end_conserved_hypothetical_protein_603997..604147_POSITIVE 262 146 108 123 73 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 260 140 107 53 21 pint:PI1418|3end_UDP-N-acetylglucosamine_2-epimerase_1339201..1339351_POSITIVE 258 150 110 122 93 pint:PI1529|3end_cytosine/adenosine_deaminase_1450377..1450527_POSITIVE 257 149 108 124 88 pint:PI1607|3end_ABC-related_lipoprotein_releasing_system,_ATP-binding_protein_1535834..1535984_POSITIVE