Origin IGS: agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag .........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 ctttgactcctaattcaaaattattcttatattcacattataacattttataattaaaaaaattaataaaatagaattttaaaattaaaaaatttaataaaaaattaatttagtcaaaaataacagtataaattgttttatattcaaacaaataaaattaaaaaattataaaatttttataaaaacattgacattatatgaactgtatgttaatataggtcgaatgtattgaaatcaagtgttttgaaaaaaatgatttcagaaaactagatattaaaggaaatagaggaggcagttatgaaaaaggttttatctttgattttcttatcacttcttact Mask Tandem Repeat Region ================================================ agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag Find is-nt database================================================ Query_seq: FN1258:FN1259|FN1258:FN1259:C4-dicarboxylate-binding protein:Uracil-DNA glycosylase:<-->:1914884..1915222 339 agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1258:FN1259|FN1258:FN1259:C4-dicarboxylate-binding protein:Uracil-DNA glycosylase:<-->:1914884..1915222 339 agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1258:FN1259|FN1258:FN1259:C4-dicarboxylate-binding protein:Uracil-DNA glycosylase:<-->:1914884..1915222 339 agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 45 End: 143 ............................................ M P P L F P L I S S F L K S F F S K H L I S I H S T Y I N I Q F I .................................................................................................................................................................................................... Protein_Len: 42 Strand: - Start: 111 End: 236 .............................................................................................................. Y M R G I N V Y L E Y L T L T K I F I K Y N K L K I Q K F I F C N I S N N K V L N M ....................................................................................................... Protein_Len: 37 Strand: - Start: 2 End: 112 . Y S T I L F D F I F G K E Y S G G R N G K I D L K R F D N K E F C K I E M ................................................................................................................................................................................................................................... agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag 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: 90 Start: 124 End: 153 ...........................................................................................................................ATTGACATTATATGAACTGTATGTTAATAT.......................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -5.3 Tail_Score: -5.52347 Start: 158 End: 174 Full_Region: ATAATGTCAATGTTT TTATAAA AAT TTTATAA TTTTTTAATTTTATT .............................................................................................................................................................TTATAAAAATTTTATAA..................................................................................................................................................................... Find igs database================================================ Query_seq: FN1258:FN1259|FN1258:FN1259:C4-dicarboxylate-binding protein:Uracil-DNA glycosylase:<-->:1914884..1915222 339 agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatgtttttataaaaattttataattttttaattttatttgtttgaatataaaacaatttatactgttatttttgactaaattaattttttattaaattttttaattttaaaattctattttattaatttttttaattataaaatgttataatgtgaatataagaataattttgaattaggagtcaaag Intra-Species Hit: Count: 1 Min: 1 Max: 339 Len: 339 Subject: NC_003454_FN1258_FN1259|C4-dicarboxylate-binding protein:Uracil-DNA glycosylase|NEGATIVE:POSITIVE|[1914884,1915222]|339 HSP 1 e-value: 2.0E-69 bit: 264.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcannnnnnncaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatg......................................................................................................................................................................................... agtaagaagtgataagaaaatcaaagataaaacctttttcataactgcctcctctatttcctttaatatctagttttctgaaatcatttttttcaaaacacttgatttcaatacattcgacctatattaacatacagttcatataatgtcaatg......................................................................................................................................................................................... HSP 2 e-value: 6.0E-20 bit: 99.6 Len: 50 Query Start:290 Query End:339 Subject Strand: POSITIVE Subject Start: 290 Subject End: 339 .................................................................................................................................................................................................................................................................................................taaaatgttataatgtgaatataagaataattttgaattaggagtcaaag .................................................................................................................................................................................................................................................................................................taaaatgttataatgtgaatataagaataattttgaattaggagtcaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAGAAGUGAUAAGAAAAUCAAAGAUAAAACCUUUUUCAUAACUGCCUCCUCUAUUUCCUUUAAUAUCUAGUUUUCUGAAAUCAUUUUUUUCAAAACACUUGAUUUCAAUACAUUCGACCUAUAUUAACAUACAGUUCAUAUAAUGUCAAUGUUUUUAUAAAAAUUUUAUAAUUUUUUAAUUUUAUUUGUUUGAAUAUAAAACAAUUUAUACUGUUAUUUUUGACUAAAUUAAUUUUUUAUUAAAUUUUUUAAUUUUAAAAUUCUAUUUUAUUAAUUUUUUUAAUUAUAAAAUGUUAUAAUGUGAAUAUAAGAAUAAUUUUGAAUUAGGAGUCAAAG .(.((((((((((.(((((((...(((((.....................................))))).)))))))...)))))))))).).......((((((((.........(((.(((((.(((.....))).)))))..)))..((((((((((...((.(((((((.(((((.......((((((.......))))))...............((((..((((((((.....((..((((((........))))))..))...))))))))..))))...))))).))))))).))...))))))))))...........)))))))).. (-47.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUGACUCCUAAUUCAAAAUUAUUCUUAUAUUCACAUUAUAACAUUUUAUAAUUAAAAAAAUUAAUAAAAUAGAAUUUUAAAAUUAAAAAAUUUAAUAAAAAAUUAAUUUAGUCAAAAAUAACAGUAUAAAUUGUUUUAUAUUCAAACAAAUAAAAUUAAAAAAUUAUAAAAUUUUUAUAAAAACAUUGACAUUAUAUGAACUGUAUGUUAAUAUAGGUCGAAUGUAUUGAAAUCAAGUGUUUUGAAAAAAAUGAUUUCAGAAAACUAGAUAUUAAAGGAAAUAGAGGAGGCAGUUAUGAAAAAGGUUUUAUCUUUGAUUUUCUUAUCACUUCUUACU ...(((..(((..((((.((((.(((((.((((..(.((((((.(((((((((((....((((((((......(((((((........)))))))........)))))))).............((((((((....))))))))...................)))))))))))..))))))..((((((((.((((((.(((.....))).))))))))).))))).((((.(((.(((.((((((((.......)))))))).))).))).)))).)..)))).)))))..)))).))))..)))..)))....((((......))))......... (-50.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 783 80 31 171 122 NC_003454:FN1258|5end_C4-dicarboxylate-binding_protein_1914793..1915023_NEGATIVE 303 57 13 121 80 NC_003454:FN0018|5end_hypothetical_protein_656448..656678_NEGATIVE 282 90 46 151 99 NC_003454:FN0928|5end_O-sialoglycoprotein_endopeptidase_1583026..1583256_NEGATIVE 273 78 35 143 84 NC_003454:FN1584|5end_Beta-lactamase_96158..96388_NEGATIVE 266 86 47 142 98 NC_003454:FN0700|5end_Protein_translocase_subunit_secF_1358286..1358516_POSITIVE 260 66 21 137 88 NC_003454:FN0821|5end_hypothetical_protein_1480859..1481089_POSITIVE 259 79 35 138 84 NC_003454:FN1914|5end_Anti-sigma_F_factor_antagonist_411990..412220_NEGATIVE 248 99 56 134 97 NC_003454:FN1327|5end_Dimethylallyltransferase_1982915..1983145_NEGATIVE 247 55 13 104 62 NC_003454:FN0458|5end_hypothetical_protein_1103738..1103968_POSITIVE 246 81 52 67 40 NC_003454:FN0381|5end_hypothetical_protein_1012348..1012578_POSITIVE 245 87 49 130 97 NC_003454:FN1754|5end_thiazole_synthase_251117..251347_NEGATIVE 241 80 32 223 171 NC_003454:FN1073|5end_hypothetical_protein_1720403..1720633_POSITIVE 241 64 25 113 70 NC_003454:FN0149|5end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_777486..777716_POSITIVE 240 77 31 115 80 NC_003454:FN0311|5end_anaerobic_ribonucleoside_triphosphate_reductase_947125..947355_POSITIVE 240 86 44 135 95 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 238 95 51 147 88 NC_003454:FN1756|5end_ThiS_protein_251935..252165_NEGATIVE 237 87 45 51 6 NC_003454:FN1371|5end_Ribonuclease_HII_2020002..2020232_NEGATIVE 234 53 19 125 86 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 233 53 20 139 107 NC_003454:FN0049|5end_hypothetical_protein_686351..686581_POSITIVE 232 75 36 124 85 NC_003454:FN0772|5end_Flavodoxin_1428694..1428924_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 78 35 88 29 NC_003454:FN1585|3end_hypothetical_protein_96213..96363_NEGATIVE 266 53 11 82 40 NC_003454:FN0807|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1467157..1467307_NEGATIVE 266 86 47 142 98 NC_003454:FN0699|3end_Protein_translocase_subunit_secD_1358366..1358516_POSITIVE 259 79 35 137 83 NC_003454:FN1915|3end_Anti-sigma_B_factor_411991..412141_NEGATIVE 248 99 56 132 95 NC_003454:FN1328|3end_Exodeoxyribonuclease_VII_small_subunit_1982917..1983067_NEGATIVE 247 55 13 89 47 NC_003454:FN0457|3end_hypothetical_protein_1103803..1103953_POSITIVE 241 64 25 73 30 NC_003454:FN0148|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_777526..777676_POSITIVE 240 86 44 133 93 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 239 55 22 37 1 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 239 74 46 150 118 NC_003454:FN0929|3end_ATP/GTP_hydrolase_1583007..1583157_NEGATIVE 238 95 51 134 75 NC_003454:FN1757|3end_thiamine_biosynthesis_protein_ThiC_251948..252098_NEGATIVE 232 75 36 127 88 NC_003454:FN0771|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1428777..1428927_POSITIVE 232 100 52 133 81 NC_003454:FN0502|3end_Phosphoheptose_isomerase_1152063..1152213_NEGATIVE 231 56 31 88 61 NC_003454:FN1868|3end_Hypothetical_cytosolic_protein_359615..359765_NEGATIVE 225 79 32 118 51 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 225 72 35 72 30 NC_003454:FN2113|3end_hypothetical_protein_623738..623888_NEGATIVE 224 77 34 77 28 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 222 79 33 123 75 NC_003454:FN1627|3end_SSU_ribosomal_protein_S5P_133062..133212_NEGATIVE 218 79 35 47 5 NC_003454:FN1920|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_415879..416029_NEGATIVE 218 120 71 140 99 NC_003454:FN1625|3end_LSU_ribosomal_protein_L15P_132385..132535_NEGATIVE