Origin IGS: tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc .........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 gaaaataggagaaattttaagttctatttaaggttggatgtgtatactataatcattaaataaagacctcctaatattatttgaaacagataacactgatttagtttgaatttgattttcatctaatatctttatttaatagaactcctaaactttttcataataatctcctgcaaaagtcacctgtctgggtggcttttgttttatcatccatgatataatagaagcaaacggaggacggaaa Mask Tandem Repeat Region ================================================ tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Find is-nt database================================================ Query_seq: SMT_1995:SMT_1996|SMT_1995:SMT_1996:phosphoglycerate mutase:hypothetical protein predicted by Glimmer/Critica:<-<-:1920841..1921084 244 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1995:SMT_1996|SMT_1995:SMT_1996:phosphoglycerate mutase:hypothetical protein predicted by Glimmer/Critica:<-<-:1920841..1921084 244 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1995:SMT_1996|SMT_1995:SMT_1996:phosphoglycerate mutase:hypothetical protein predicted by Glimmer/Critica:<-<-:1920841..1921084 244 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 110 End: 214 ............................................................................................................. M K I L D E N Q I Q T K S V L S V S N N I R R S L F N D Y S I H I Q P .............................. Protein_Len: 32 Strand: + Start: 123 End: 218 .......................................................................................................................... M K I K F K L N Q C Y L F Q I I L G G L Y L M I I V Y T S N L K .......................... Protein_Len: 31 Strand: - Start: 27 End: 119 .......................... I M S S L V F A V W V P S K Q L L N N H F L K P T R N F L S M ............................................................................................................................. tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc 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================================================ tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.4 Tail_Score: -4.4767 Start: 44 End: 71 Full_Region: cataataatctcctg caaaagtcacct gtct gggtggcttttg ttttatcatccatga ...........................................caaaagtcacctgtctgggtggcttttg............................................................................................................................................................................. TransTerm Strand: - Conf: 81 HP_score: -5.5 Tail_Score: -5.20781 Start: 49 End: 66 Full_Region: taatctcctgcaaaa gtcacct gtct gggtggc ttttgttttatcatc ................................................gtcacctgtctgggtggc.................................................................................................................................................................................. Find igs database================================================ Query_seq: SMT_1995:SMT_1996|SMT_1995:SMT_1996:phosphoglycerate mutase:hypothetical protein predicted by Glimmer/Critica:<-<-:1920841..1921084 244 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Intra-Species Hit: Count: 3 Min: 1 Max: 244 Len: 244 Subject: smit_SMT_2062_SMT_2063|phosphoglycerate mutase:hypothetical protein|NEGATIVE:NEGATIVE|[1971516,1971759]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Subject: smit_SMT_1995_SMT_1996|phosphoglycerate mutase:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:NEGATIVE|[1920841,1921084]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Subject: smit_SMT_200_SMT_201|hypothetical protein:phosphoglycerate mutase|POSITIVE:POSITIVE|[131225,131468]|244 HSP 1 e-value: 1.0E-136 bit: 484.0 Len: 244 Query Start:1 Query End:244 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 244 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc Inter-species Hit: Count: 3 Min: 1 Max: 244 Len: 244 Subject: NC_008533_SPD_0220_SPD_0222|hypothetical protein:phosphoglycerate mutase family protein|POSITIVE:POSITIVE|[210876,212466]|1591 HSP 1 e-value: 1.0E-112 bit: 404.0 Len: 244 Query Start:1 Query End:244 Subject Strand: NEGATIVE Subject Start: 1349 Subject End: 1591 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc tttccgtcctccgtttgcttctattatatcatgaatgataaaataaaagccacccatacaggcgacttttgaaggagattattatgaaaaagtttaggagttc-attaaataaagatattagatgaaaatcaaattcaaactaattcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatctaatcttaaatagaacttaaaatttctcctattttc Subject: NC_003028_SP_0239_SP_0240|hypothetical protein:phosphoglycerate mutase family protein|POSITIVE:POSITIVE|[209714,209956]|243 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 244 Query Start:1 Query End:244 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 243 tttccgtcctccgtttgcttctattatatcatggatgataaaacaaaagccacccagacaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc tttccgtcctccgtttgcttctattatatcatgaatgataaaataaaagccacccatacaggcgacttttgaaggagattattatgaaaaagtttaggagttc-attaaataaagatattagatgaaaatcaaattcaaactaattcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacgtctaatcttaaatagaacttaaaatttctcctattttc Subject: NC_003098_spr0218_spr0219|hypothetical protein:Phosphoglycerate mutase 2 paralog|POSITIVE:POSITIVE|[212223,212408]|186 HSP 1 e-value: 4.0E-85 bit: 315.0 Len: 187 Query Start:58 Query End:244 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 186 .........................................................acaggtgacttttgcaggagattattatgaaaaagtttaggagttctattaaataaagatattagatgaaaatcaaattcaaactaaatcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatccaaccttaaatagaacttaaaatttctcctattttc .........................................................acaggcgacttttgaaggagattattatgaaaaagtttaggagttc-attaaataaagatattagatgaaaatcaaattcaaactaattcagtgttatctgtttcaaataatattaggaggtctttatttaatgattatagtatacacatctaatcttaaatagaacttaaaatttctcctattttc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCCGUCCUCCGUUUGCUUCUAUUAUAUCAUGGAUGAUAAAACAAAAGCCACCCAGACAGGUGACUUUUGCAGGAGAUUAUUAUGAAAAAGUUUAGGAGUUCUAUUAAAUAAAGAUAUUAGAUGAAAAUCAAAUUCAAACUAAAUCAGUGUUAUCUGUUUCAAAUAAUAUUAGGAGGUCUUUAUUUAAUGAUUAUAGUAUACACAUCCAACCUUAAAUAGAACUUAAAAUUUCUCCUAUUUUC .....(((.(((((................))))).)))....((((((.((((......)))).)))))).((((((.............(((((((.(((.((((((((((((((....(((....)))................((((((((.((...)).)))))))).....))))))))))))))......((....))....)))))))))).............))))))...... (-45.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAUAGGAGAAAUUUUAAGUUCUAUUUAAGGUUGGAUGUGUAUACUAUAAUCAUUAAAUAAAGACCUCCUAAUAUUAUUUGAAACAGAUAACACUGAUUUAGUUUGAAUUUGAUUUUCAUCUAAUAUCUUUAUUUAAUAGAACUCCUAAACUUUUUCAUAAUAAUCUCCUGCAAAAGUCACCUGUCUGGGUGGCUUUUGUUUUAUCAUCCAUGAUAUAAUAGAAGCAAACGGAGGACGGAAA (((((((((((.((((((((((...)))))))))).................((((((((((((((..........(((((((...))))))).......((((..((((.......)))).))))..)))))))))))).)).))))))....))))).......(((((.(((((((((((((....)))))))))))))..(((((....)))))..............)))))....... (-54.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 900 80 31 171 122 smit:SMT_2062|5end_phosphoglycerate_mutase_1971425..1971655_NEGATIVE 900 80 31 171 122 smit:SMT_1995|5end_phosphoglycerate_mutase_1920750..1920980_NEGATIVE 900 80 31 171 122 smit:SMT_201|5end_phosphoglycerate_mutase_131329..131559_POSITIVE 436 90 45 194 149 smit:SMT_1836|5end_cytidine/deoxycytidylate_deaminase_family_protein_1804498..1804728_NEGATIVE 436 90 45 194 149 smit:SMT_1674|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1660501..1660731_NEGATIVE 351 204 163 200 159 smit:SMT_211|5end_hypothetical_protein_predicted_by_Glimmer/Critica_144135..144365_POSITIVE 316 74 41 155 121 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 316 74 41 155 121 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 296 77 42 69 22 smit:SMT_297|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_238547..238777_POSITIVE 275 165 124 219 174 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 250 164 124 158 112 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 250 164 124 158 112 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 250 164 124 158 112 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 247 50 1 130 70 smit:SMT_835|5end_polypeptide_deformylase_777549..777779_NEGATIVE 245 50 4 137 94 smit:SMT_766|5end_hypothetical_protein_674530..674760_NEGATIVE 244 50 7 148 95 smit:SMT_692|5end_hypothetical_protein_603550..603780_NEGATIVE 242 81 46 116 78 smit:SMT_763|5end_alpha-amylase_667866..668096_POSITIVE 241 66 23 197 148 smit:SMT_486|5end_hypothetical_protein_422305..422535_NEGATIVE 240 35 4 36 1 smit:SMT_493|5end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427137..427367_POSITIVE 236 56 11 68 26 smit:SMT_176|5end_30S_ribosomal_protein_S3_118081..118311_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 726 220 171 66 17 smit:SMT_2063|3end_hypothetical_protein_1971670..1971820_NEGATIVE 726 220 171 66 17 smit:SMT_200|3end_hypothetical_protein_131164..131314_POSITIVE 435 218 171 65 18 smit:SMT_210|3end_acetyltransferase,_GNAT_family_143876..144026_POSITIVE 338 102 74 32 3 smit:SMT_217|3end_hypothetical_protein_149888..150038_POSITIVE 297 90 49 42 1 smit:SMT_1086|3end_K01992_ABC-2_type_transport_system_permease_protein_1022542..1022692_NEGATIVE 288 220 171 75 25 smit:SMT_1837|3end_adenylosuccinate_synthetase_1804698..1804848_NEGATIVE 288 220 171 75 25 smit:SMT_1675|3end_adenylosuccinate_synthetase_1660701..1660851_NEGATIVE 288 220 171 75 25 smit:SMT_103|3end_adenylosuccinate_synthetase_42174..42324_POSITIVE 282 76 31 143 93 smit:SMT_305|3end_seryl-tRNA_synthetase_247577..247727_NEGATIVE 245 50 4 144 101 smit:SMT_767|3end_hypothetical_protein_674523..674673_NEGATIVE 245 59 11 128 83 smit:SMT_137|3end_hypothetical_protein_88137..88287_NEGATIVE 241 164 127 43 1 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 241 164 127 43 1 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 241 164 127 43 1 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 240 35 4 36 1 smit:SMT_492|3end_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_427217..427367_POSITIVE 236 56 11 55 13 smit:SMT_175|3end_50S_ribosomal_protein_L22_118148..118298_POSITIVE 235 34 4 74 32 smit:SMT_1395|3end_K07025_putative_hydrolase_of_the_HAD_superfamily_1372082..1372232_POSITIVE 227 78 48 58 21 smit:SMT_1154|3end_tryptophanyl-tRNA_synthetase_1098154..1098304_NEGATIVE 227 75 49 36 10 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 225 55 11 61 24 smit:SMT_458|3end_hypothetical_protein_predicted_by_Glimmer/Critica_396729..396879_NEGATIVE