Origin IGS: aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaaatgcccatttcttctagtcaatgatttgatttaaaagattaaaaaaactctcaatttatttataactgttttaaataaaaatgtagtaggcctattggaatcttgattgaatccgatttttcctagctatgaaatataaaaataaaaaaagaaaggtagagcgcgtgttctaatttgaacacgaacggaaaacttttctaaaaattcagaagagaaggggagttctgctttgaattgaagccggtctaatcttctcaatatcatcaaaattaagaaagaaaggaattgaacccaccctaaaagcagtgggaaaaagatagttggtctagcgagcatcgctcactgcacccaactcctattttccctttgttttttgacgggtttggtatcttatatt Mask Tandem Repeat Region ================================================ aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc Find is-nt database================================================ Query_seq: SMT_1505:SMT_1506|SMT_1505:SMT_1506:purine-nucleoside phosphorylase:Cl-channel, voltage-gated family protein:<-<-:1488606..1489005 400 aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1505:SMT_1506|SMT_1505:SMT_1506:purine-nucleoside phosphorylase:Cl-channel, voltage-gated family protein:<-<-:1488606..1489005 400 aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1505:SMT_1506|SMT_1505:SMT_1506:purine-nucleoside phosphorylase:Cl-channel, voltage-gated family protein:<-<-:1488606..1489005 400 aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 9 End: 98 ........ M P N P S K N K G K I G V G C S E R C S L D Q L S F S H C F .............................................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 62 End: 268 ............................................................. M L A R P T I F F P L L L G W V Q F L S F L I L M I L R R L D R L Q F K A E L P F S S E F L E K F S V R V Q I R T R A L .................................................................................................................................... aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc 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================================================ aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -4.9 Tail_Score: -5.04249 Start: 33 End: 90 Full_Region: caccctaaaagcagt gggaaaaagatagttggtctagcgagc atc gctcactgcacccaactcctattttccc tttgttttttgacgg ................................gggaaaaagatagttggtctagcgagcatcgctcactgcacccaactcctattttccc...................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_1505:SMT_1506|SMT_1505:SMT_1506:purine-nucleoside phosphorylase:Cl-channel, voltage-gated family protein:<-<-:1488606..1489005 400 aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttctttttttatttttatatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc Intra-Species Hit: Count: 1 Min: 1 Max: 400 Len: 400 Subject: smit_SMT_1505_SMT_1506|purine-nucleoside phosphorylase:Cl-channel, voltage-gated family protein|NEGATIVE:NEGATIVE|[1488606,1489005]|400 HSP 1 e-value: 1.0E-137 bit: 490.0 Len: 247 Query Start:1 Query End:247 Subject Strand: POSITIVE Subject Start: 1 Subject End: 247 aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... aatataagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgatgatattgagaagattagaccggcttcaattcaaagcagaactccccttctcttctgaatttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... HSP 2 e-value: 5.0E-61 bit: 236.0 Len: 140 Query Start:261 Query End:400 Subject Strand: POSITIVE Subject Start: 261 Subject End: 400 ....................................................................................................................................................................................................................................................................atatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagnnnnnnnaatcttttaaatcaaatcattgactagaagaaatgggcatttc ....................................................................................................................................................................................................................................................................atatttcatagctaggaaaaatcggattcaatcaagattccaataggcctactacatttttatttaaaacagttataaataaattgagagtttttttaatcttttaaatcaaatcattgactagaagaaatgggcatttc Inter-species Hit: Count: 3 Min: 6 Max: 247 Len: 242 Subject: NC_008533_SPD_0729_SPD_0730|hemolysin-related protein:purine nucleoside phosphorylase|POSITIVE:POSITIVE|[743379,744035]|657 HSP 1 e-value: 1.0E-55 bit: 218.0 Len: 130 Query Start:6 Query End:135 Subject Strand: NEGATIVE Subject Start: 369 Subject End: 498 .....aagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgat......................................................................................................................................................................................................................................................................... .....aagataccaaacccatcaaaaagcgaagggaaaataggagttgggcgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtggggtcaattcctttctttcttaattttgat......................................................................................................................................................................................................................................................................... HSP 2 e-value: 1.0E-15 bit: 85.7 Len: 55 Query Start:193 Query End:247 Subject Strand: NEGATIVE Subject Start: 254 Subject End: 308 ................................................................................................................................................................................................atttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... ................................................................................................................................................................................................atttttagaaaagttttctactcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... HSP 3 e-value: 1.0E-6 bit: 56.0 Len: 44 Query Start:204 Query End:247 Subject Strand: NEGATIVE Subject Start: 523 Subject End: 566 ...........................................................................................................................................................................................................agttttccgttcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... ...........................................................................................................................................................................................................agttttccgctcgtgttcaaatcaaaacacacgctctacctttc......................................................................................................................................................... Subject: NC_003098_spr0737_spr0738|Conserved hypothetical protein, truncation:Purine nucleoside phosphorylase (inosine phosphorylase)|POSITIVE:POSITIVE|[735848,736504]|657 HSP 1 e-value: 1.0E-55 bit: 218.0 Len: 130 Query Start:6 Query End:135 Subject Strand: NEGATIVE Subject Start: 369 Subject End: 498 .....aagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctttcttaattttgat......................................................................................................................................................................................................................................................................... .....aagataccaaacccatcaaaaagcgaagggaaaataggagttgggcgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtggggtcaattcctttctttcttaattttgat......................................................................................................................................................................................................................................................................... HSP 2 e-value: 1.0E-15 bit: 85.7 Len: 55 Query Start:193 Query End:247 Subject Strand: NEGATIVE Subject Start: 254 Subject End: 308 ................................................................................................................................................................................................atttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... ................................................................................................................................................................................................atttttagaaaagttttctactcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... HSP 3 e-value: 1.0E-6 bit: 56.0 Len: 44 Query Start:204 Query End:247 Subject Strand: NEGATIVE Subject Start: 523 Subject End: 566 ...........................................................................................................................................................................................................agttttccgttcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... ...........................................................................................................................................................................................................agttttccgctcgtgttcaaatcaaaacacacgctctacctttc......................................................................................................................................................... Subject: NC_003028_SP_0834_SP_0835|hemolysin-related protein:purine nucleoside phosphorylase, family 1|POSITIVE:POSITIVE|[783000,783652]|653 HSP 1 e-value: 4.0E-43 bit: 176.0 Len: 117 Query Start:6 Query End:122 Subject Strand: NEGATIVE Subject Start: 378 Subject End: 494 .....aagataccaaacccgtcaaaaaacaaagggaaaataggagttgggtgcagtgagcgatgctcgctagaccaactatctttttcccactgcttttagggtgggttcaattcctttctt...................................................................................................................................................................................................................................................................................... .....aagataccaaacccatcaaaaagcgaagggaaaataggagttgggcgcagtgagcgatgctcgctagatcaactatctttttcccactacttttagggtggggtcaattcctttctt...................................................................................................................................................................................................................................................................................... HSP 2 e-value: 4.0E-15 bit: 83.8 Len: 54 Query Start:194 Query End:247 Subject Strand: NEGATIVE Subject Start: 254 Subject End: 307 .................................................................................................................................................................................................tttttagaaaagttttccgttcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... .................................................................................................................................................................................................tttttagaaaagttttctactcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... HSP 3 e-value: 1.0E-6 bit: 56.0 Len: 44 Query Start:204 Query End:247 Subject Strand: NEGATIVE Subject Start: 519 Subject End: 562 ...........................................................................................................................................................................................................agttttccgttcgtgttcaaattagaacacgcgctctacctttc......................................................................................................................................................... ...........................................................................................................................................................................................................agttttccgctcgtgttcaaatcaaaacacacgctctacctttc......................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUACCAAACCCGUCAAAAAACAAAGGGAAAAUAGGAGUUGGGUGCAGUGAGCGAUGCUCGCUAGACCAACUAUCUUUUUCCCACUGCUUUUAGGGUGGGUUCAAUUCCUUUCUUUCUUAAUUUUGAUGAUAUUGAGAAGAUUAGACCGGCUUCAAUUCAAAGCAGAACUCCCCUUCUCUUCUGAAUUUUUAGAAAAGUUUUCCGUUCGUGUUCAAAUUAGAACACGCGCUCUACCUUUC ...................(((((...(((((((.(((((((((...((((((((...))))))).).)))))).)))))))))).........((((.((((((.....((.((((.((((((.........))))))))))..))....((((.......)))).))))))))))....((((((....))))))..)))))..((.(((((((......))))))).)).......... (-66.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAGGUAGAGCGCGUGUUCUAAUUUGAACACGAACGGAAAACUUUUCUAAAAAUUCAGAAGAGAAGGGGAGUUCUGCUUUGAAUUGAAGCCGGUCUAAUCUUCUCAAUAUCAUCAAAAUUAAGAAAGAAAGGAAUUGAACCCACCCUAAAAGCAGUGGGAAAAAGAUAGUUGGUCUAGCGAGCAUCGCUCACUGCACCCAACUCCUAUUUUCCCUUUGUUUUUUGACGGGUUUGGUAUCUU (((((((...(..(((((((......)))))))..).....))))))).............(((((((..((..(.(((((.....))))).)..))..))))))).......................((((.((..(((((.....((((((((.(((((((....((((((..(((.((((...)))).)))...))))))....))))))).))))))))....)))))..)).)))) (-76.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1017 90 41 186 137 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 434 115 74 114 73 smit:SMT_545|5end_hypothetical_protein_predicted_by_Glimmer/Critica_461249..461479_POSITIVE 406 100 51 227 179 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 374 67 29 158 121 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 351 48 1 149 96 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 322 50 3 146 99 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 316 50 1 189 141 smit:SMT_898|5end_polyribonucleotide_nucleotidyltransferase_846861..847091_NEGATIVE 316 114 84 175 146 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 315 73 40 73 39 smit:SMT_247|5end_K02996_small_subunit_ribosomal_protein_S9_183062..183292_POSITIVE 302 65 25 222 185 smit:SMT_603|5end_hypothetical_protein_517961..518191_POSITIVE 301 100 51 225 173 smit:SMT_1828|5end_PTS_system,_galactose-specific_IIC_component_1797668..1797898_POSITIVE 301 100 51 125 73 smit:SMT_1827|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1797568..1797798_POSITIVE 301 74 36 231 194 smit:SMT_1477|5end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1460376..1460606_NEGATIVE 292 70 37 136 112 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 291 218 171 229 178 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 287 62 24 165 130 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 284 188 151 182 137 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 283 99 52 82 39 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 278 90 46 97 44 smit:SMT_2074|5end_dTDP-glucose_4,6-dehydratase_1977021..1977251_POSITIVE 277 240 202 227 180 smit:SMT_1304|5end_hypothetical_protein_1266630..1266860_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 65 25 145 108 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 301 100 51 99 47 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 297 106 74 62 30 smit:SMT_1261|3end_MutT/NUDIX_family_protein_1227094..1227244_POSITIVE 294 59 13 61 7 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 284 188 151 148 103 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE 284 217 172 55 12 smit:SMT_688|3end_carbamoyl-phosphate_synthase_small_chain_599576..599726_NEGATIVE 278 90 46 70 17 smit:SMT_2073|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1977074..1977224_POSITIVE 275 105 61 66 22 smit:SMT_762|3end_cation-transporting_ATPase,_E1-E2_family_protein_667368..667518_NEGATIVE 270 118 83 62 24 smit:SMT_1858|3end_K03497_chromosome_partitioning_protein,_ParB_family_1821687..1821837_NEGATIVE 268 61 24 38 2 smit:SMT_890|3end_K02029_polar_amino_acid_transport_system_permease_protein_837692..837842_POSITIVE 266 64 28 138 102 smit:SMT_1991|3end_K03706_transcriptional_pleiotropic_repressor_1917770..1917920_NEGATIVE 266 63 21 56 3 smit:SMT_1766|3end_sucrose-6-phosphate_hydrolase_1743101..1743251_POSITIVE 265 80 33 85 18 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE 263 69 25 79 30 smit:SMT_756|3end_3-dehydroquinate_dehydratase_659907..660057_NEGATIVE 262 175 140 62 20 smit:SMT_2020|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1937914..1938064_POSITIVE 262 80 37 150 99 smit:SMT_1414|3end_hypothetical_protein_1397361..1397511_NEGATIVE 259 136 95 101 54 smit:SMT_1067|3end_alanine_racemase_1006952..1007102_POSITIVE 257 100 56 145 95 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 257 75 31 69 35 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 257 103 63 133 76 smit:SMT_446|3end_ABC-type_cobalt_transport_system,_ATPase_component_386335..386485_POSITIVE