Origin IGS: ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat .........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 atatatatgaggctattatttgaagtagcctcattttttaatattgacaaaatttataaaaaatgttaaaattatcttggaaataaaccatcaagagagattgagggacaggcccgttgagatctcagcaacctacgtaaaatgtgtggtgctaattcctgatagatggaaaagattataatacatctctctatctggaattggatagagtttttttattttaatattttgttaattttttaaggagggaaaa Mask Tandem Repeat Region ================================================ ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Find is-nt database================================================ Query_seq: FN0355:FN0356|FN0355:FN0356:S-adenosylmethionine synthetase:Lactoylglutathione lyase:<-<-:987318..987570 253 ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0355:FN0356|FN0355:FN0356:S-adenosylmethionine synthetase:Lactoylglutathione lyase:<-<-:987318..987570 253 ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0355:FN0356|FN0355:FN0356:S-adenosylmethionine synthetase:Lactoylglutathione lyase:<-<-:987318..987570 253 ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 29 End: 118 ............................ M K I K K L Y P I P D R E M Y Y N L F H L S G I S T T H F T ....................................................................................................................................... Protein_Len: 44 Strand: + Start: 48 End: 179 ............................................... M Q F Q I E R C I I I F S I Y Q E L A P H I L R R L L R S Q R A C P S I S L D G L F P R .......................................................................... Protein_Len: 46 Strand: - Start: 76 End: 213 ........................................................................... L R K W R D P I L V V C K V Y T A S I E V P R D R L R E Q H N I E L I I K V N K I F K T L M ........................................ ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 91 Start: 182 End: 211 .....................................................................................................................................................................................ATTGACAAAATTTATAAAAAATGTTAAAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -5.9 Tail_Score: -6.11229 Start: 44 End: 65 Full_Region: gattataatacatct ctctatctg gaat tggatagag tttttttattttaat ...........................................ctctatctggaattggatagag............................................................................................................................................................................................ TransTerm Strand: + Conf: 56 HP_score: -2.1 Tail_Score: -4.42062 Start: 147 End: 166 Full_Region: TCTCAACGGGCCTGT CCCTCAA TCTCTC TTGATGG TTTATTTCCAAGATA ..................................................................................................................................................CCCTCAATCTCTCTTGATGG....................................................................................... Find igs database================================================ Query_seq: FN0355:FN0356|FN0355:FN0356:S-adenosylmethionine synthetase:Lactoylglutathione lyase:<-<-:987318..987570 253 ttttccctccttaaaaaattaacaaaatattaaaataaaaaaactctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Intra-Species Hit: Count: 1 Min: 44 Max: 253 Len: 210 Subject: NC_003454_FN0355_FN0356|S-adenosylmethionine synthetase:Lactoylglutathione lyase|NEGATIVE:NEGATIVE|[987318,987570]|253 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:44 Query End:253 Subject Strand: POSITIVE Subject Start: 44 Subject End: 253 ...........................................ctctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat ...........................................ctctatccaattccagatagagagatgtattataatcttttccatctatcaggaattagcaccacacattttacgtaggttgctgagatctcaacgggcctgtccctcaatctctcttgatggtttatttccaagataattttaacattttttataaattttgtcaatattaaaaaatgaggctacttcaaataatagcctcatatatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUAUCCAAUUCCAGAUAGAGAGAUGUAUUAUAAUCUUUUCCAUCUAUCAGGAAUUAGCACCACACAUUUUACGUAGGUUGCUGAGAUCUCAACGGGCCUGUCCCUCAAUCUCUCUUGAUGGUUUAUUUCCAAGAUAAUUUUAACAUUUUUUAUAAAUUUUGUCAAUAUUAAAAAAUGAGGCUACUUCAAAUAAUAGCCUCAUAUAUAU (((((((........))))))).((((((..((.(((((......(((((((((.((((((((((.........)).)).)))))).........(((.....)))........))))))))).........))))).))..).)))))...........................(((((((((.(......).)))))))))...... (-44.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUAUGAGGCUAUUAUUUGAAGUAGCCUCAUUUUUUAAUAUUGACAAAAUUUAUAAAAAAUGUUAAAAUUAUCUUGGAAAUAAACCAUCAAGAGAGAUUGAGGGACAGGCCCGUUGAGAUCUCAGCAACCUACGUAAAAUGUGUGGUGCUAAUUCCUGAUAGAUGGAAAAGAUUAUAAUACAUCUCUCUAUCUGGAAUUGGAUAGAG ......(((((((((((......))))))))))).((((((((((................)))))))))).((((..((((............((((..(..((((.....))).)..)..)))).(((.(((((((...))))).)))))...)))).))))((((...............)))).((((((((......)))))))) (-53.85) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 903 90 41 224 175 NC_003454:FN0355|5end_S-adenosylmethionine_synthetase_987227..987457_NEGATIVE 615 88 41 228 182 NC_003454:FN0660|5end_ABC_transporter_ATP-binding_protein_1317388..1317618_NEGATIVE 288 64 33 93 50 NC_003454:FN1999|5end_HIPA_protein_500262..500492_POSITIVE 278 44 2 44 12 NC_003454:FN0299|5end_Aspartyl-tRNA_synthetase_932393..932623_POSITIVE 273 55 11 50 3 NC_003454:FN1467|5end_hypothetical_protein_2149207..2149437_POSITIVE 262 70 23 202 141 NC_003454:FN2019|5end_Ribosome-binding_factor_A_522292..522522_NEGATIVE 259 120 75 107 60 NC_003454:FN1532|5end_murein_hydrolase_exporter_45319..45549_NEGATIVE 254 44 1 231 182 NC_003454:FN0727|5end_hypothetical_protein_1385507..1385737_NEGATIVE 251 97 51 50 5 NC_003454:FN0856|5end_glycogen_branching_enzyme_1516524..1516754_NEGATIVE 247 140 98 128 87 NC_003454:FN1829|5end_hypothetical_protein_318556..318786_NEGATIVE 243 119 80 222 180 NC_003454:FN0182|5end_Sarcosine_oxidase_alpha_subunit_807066..807296_NEGATIVE 241 86 41 218 171 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 240 112 74 73 19 NC_003454:FN1863|5end_L-beta-lysine_5,6-aminomutase_alpha_subunit_354678..354908_NEGATIVE 233 128 98 129 99 NC_003454:FN1522|5end_Dipeptide_transport_system_permease_protein_dppC_27327..27557_POSITIVE 230 114 77 63 34 NC_003454:FN1723|5end_glucose-inhibited_division_protein_A_222645..222875_NEGATIVE 226 87 44 106 68 NC_003454:FN1410|5end_Transporter_2069934..2070164_POSITIVE 225 61 34 73 37 NC_003454:FN1525|5end_Dipeptide_transport_ATP-binding_protein_dppF_30523..30753_POSITIVE 223 118 75 84 35 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 223 106 64 71 36 NC_003454:FN0206|5end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_832758..832988_POSITIVE 223 113 79 68 33 NC_003454:FN0007|5end_glucose-inhibited_division_protein_A_645938..646168_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 64 33 142 99 NC_003454:FN1998|3end_HIPA_protein_500391..500541_POSITIVE 283 204 161 51 2 NC_003454:FN1984|3end_Glutaredoxin-like_protein_487204..487354_POSITIVE 259 120 75 76 29 NC_003454:FN1533|3end_Electron_transfer_flavoprotein_alpha-subunit_45350..45500_NEGATIVE 247 140 98 113 72 NC_003454:FN1830|3end_DNA_polymerase_III_subunits_gamma_and_tau_318571..318721_NEGATIVE 246 204 173 64 28 NC_003454:FN1985|3end_Inner_membrane_protein_487273..487423_NEGATIVE 244 44 8 66 32 NC_003454:FN0967|3end_CbiD_protein_1619923..1620073_NEGATIVE 240 112 74 73 19 NC_003454:FN1864|3end_DNA_mismatch_repair_protein_mutS_354678..354828_NEGATIVE 233 128 98 128 98 NC_003454:FN1521|3end_Dipeptide_transport_system_permease_protein_dppB_27406..27556_POSITIVE 230 136 91 150 102 NC_003454:FN0853|3end_Glycogen_synthase_1510922..1511072_NEGATIVE 230 114 77 54 25 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 225 61 34 134 98 NC_003454:FN1524|3end_Dipeptide_transport_ATP-binding_protein_dppD_30664..30814_POSITIVE 223 106 64 41 6 NC_003454:FN0205|3end_Sodium/glutamate_symport_carrier_protein_832808..832958_POSITIVE 218 63 33 132 100 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 213 138 105 29 1 NC_003454:FN1658|3end_prolyl-tRNA_synthetase_153188..153338_NEGATIVE 209 119 82 44 3 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 207 201 166 83 47 NC_003454:FN1149|3end_ATP-dependent_nuclease_subunit_A_1799277..1799427_NEGATIVE 205 135 98 133 99 NC_003454:FN0771|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1428777..1428927_POSITIVE 205 87 43 139 80 NC_003454:FN0067|3end_Isoleucyl-tRNA_synthetase_707418..707568_POSITIVE 204 168 124 117 65 NC_003454:FN1224|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1882540..1882690_NEGATIVE 203 201 166 77 40 NC_003454:FN1148|3end_Serine/threonine_sodium_symporter_1799264..1799414_POSITIVE