Origin IGS: aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtgccctcctcttttttaatttaattctttactaattttgtcataattgattatagcatatatctaaaaaaaataatagattgctataaataaaaaatgaagtaaaaaacagtttattgctaagctattttttacttacatttcaataaataatattatatatt Mask Tandem Repeat Region ================================================ aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact Find is-nt database================================================ Query_seq: FN0453:FN0454|FN0453:FN0454:Xaa-Pro aminopeptidase:Aldehyde dehydrogenase B:->->:1099442..1099606 165 aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0453:FN0454|FN0453:FN0454:Xaa-Pro aminopeptidase:Aldehyde dehydrogenase B:->->:1099442..1099606 165 aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0453:FN0454|FN0453:FN0454:Xaa-Pro aminopeptidase:Aldehyde dehydrogenase B:->->:1099442..1099606 165 aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact Predict ORF larger than 30AA ================================================ aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact 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: 81 Start: 6 End: 35 .....TTTTACTTACATTTCAATAAATAATATTAT.................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -6.7 Tail_Score: -5.72622 Start: 25 End: 67 Full_Region: TATTATTTATTGAAA TGTAAGTAAAAAATAGCTTA GCAA TAAACTGTTTTTTACTTCA TTTTTTATTTATAGC ........................TGTAAGTAAAAAATAGCTTAGCAATAAACTGTTTTTTACTTCA.................................................................................................. Find igs database================================================ Query_seq: FN0453:FN0454|FN0453:FN0454:Xaa-Pro aminopeptidase:Aldehyde dehydrogenase B:->->:1099442..1099606 165 aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactgttttttacttcattttttatttatagcaatctattattttttttagatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: NC_003454_FN0453_FN0454|Xaa-Pro aminopeptidase:Aldehyde dehydrogenase B|POSITIVE:POSITIVE|[1099442,1099606]|165 HSP 1 e-value: 3.0E-29 bit: 129.0 Len: 65 Query Start:101 Query End:165 Subject Strand: POSITIVE Subject Start: 101 Subject End: 165 ....................................................................................................gatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact ....................................................................................................gatatatgctataatcaattatgacaaaattagtaaagaattaaattaaaaaagaggagggcact HSP 2 e-value: 3.0E-23 bit: 109.0 Len: 55 Query Start:1 Query End:55 Subject Strand: POSITIVE Subject Start: 1 Subject End: 55 aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactg.............................................................................................................. aatatataatattatttattgaaatgtaagtaaaaaatagcttagcaataaactg.............................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUAUAAUAUUAUUUAUUGAAAUGUAAGUAAAAAAUAGCUUAGCAAUAAACUGUUUUUUACUUCAUUUUUUAUUUAUAGCAAUCUAUUAUUUUUUUUAGAUAUAUGCUAUAAUCAAUUAUGACAAAAUUAGUAAAGAAUUAAAUUAAAAAAGAGGAGGGCACU ....((((((..........((((((.(((((((((((((.(((....))).)))))))))))))))))))....(((((((((((((..(....)..)))))...))))))))...)))))).......................................... (-30.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGCCCUCCUCUUUUUUAAUUUAAUUCUUUACUAAUUUUGUCAUAAUUGAUUAUAGCAUAUAUCUAAAAAAAAUAAUAGAUUGCUAUAAAUAAAAAAUGAAGUAAAAAACAGUUUAUUGCUAAGCUAUUUUUUACUUACAUUUCAAUAAAUAAUAUUAUAUAUU .................................((((.((((....((((.((((((((...(((((..........))))))))))))).....(((((((((((((((.((((((....)))))).)))))))))).)))))))))..)))).))))...... (-25.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 90 41 128 85 NC_003454:FN0797|5end_hypothetical_protein_1455799..1456029_NEGATIVE 228 89 53 57 25 NC_003454:FN0595|5end_UDP-N-acetylglucosamine_acyltransferase_1249228..1249458_POSITIVE 205 39 12 146 119 NC_003454:FN1217|5end_Holliday_junction_DNA_helicase_ruvB_1877597..1877827_NEGATIVE 203 100 63 56 19 NC_003454:FN1208|5end_1-deoxy-D-xylulose-5-phosphate_synthase_1868601..1868831_NEGATIVE 197 84 42 102 48 NC_003454:FN2058|5end_Fusobacterium_outer_membrane_protein_family_571095..571325_NEGATIVE 195 97 51 96 38 NC_003454:FN0946|5end_Zinc_metalloprotease_1599634..1599864_POSITIVE 192 72 31 170 126 NC_003454:FN0902|5end_5-formyltetrahydrofolate_cyclo-ligase_1560549..1560779_POSITIVE 190 85 56 37 3 NC_003454:FN2098|5end_MRP-family_nucleotide-binding_protein_608146..608376_NEGATIVE 190 108 64 92 44 NC_003454:FN2076|5end_MunI_regulatory_protein_587766..587996_NEGATIVE 187 113 75 38 2 NC_003454:FN0953|5end_hypothetical_protein_1610246..1610476_NEGATIVE 186 74 43 117 82 NC_003454:FN0838|5end_hypothetical_protein_1500747..1500977_POSITIVE 186 127 87 105 64 NC_003454:FN0074|5end_Ethanolamine_utilization_protein_eutS_713328..713558_POSITIVE 184 99 53 55 4 NC_003454:FN0286|5end_hypothetical_protein_914425..914655_NEGATIVE 182 97 56 134 92 NC_003454:FN1407|5end_Glutamate_formiminotransferase_2066430..2066660_POSITIVE 182 104 61 142 97 NC_003454:FN0444|5end_Phosphoadenosine_phosphosulfate_reductase_1083074..1083304_POSITIVE 181 100 54 147 98 NC_003454:FN0943|5end_Sensory_Transduction_Protein_Kinase_1596800..1597030_POSITIVE 180 130 91 72 33 NC_003454:FN1848|5end_Metal_dependent_hydrolase_337112..337342_POSITIVE 179 97 52 132 84 NC_003454:FN1212|5end_hypothetical_protein_1873168..1873398_NEGATIVE 179 100 53 143 94 NC_003454:FN0830|5end_hypothetical_protein_1490254..1490484_POSITIVE 179 77 35 230 189 NC_003454:FN1741|5end_ATP_synthase_subunit_I_240477..240707_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 68 25 62 21 NC_003454:FN0046|3end_3-dehydroquinate_dehydratase_684265..684415_POSITIVE 236 70 28 69 26 NC_003454:FN0453|3end_Xaa-Pro_aminopeptidase_1099381..1099531_POSITIVE 228 89 53 39 7 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE 224 76 38 97 59 NC_003454:FN1218|3end_hypothetical_protein_1877812..1877962_NEGATIVE 206 60 25 62 29 NC_003454:FN0129|3end_Urease_accessory_protein_ureG_758370..758520_POSITIVE 203 100 63 42 5 NC_003454:FN1209|3end_Hypothetical_RNA_binding_protein_1868615..1868765_NEGATIVE 193 60 19 48 3 NC_003454:FN0339|3end_hypothetical_protein_972588..972738_POSITIVE 186 127 87 130 89 NC_003454:FN0073|3end_Dihydropteroate_synthase_713433..713583_POSITIVE 186 87 41 98 57 NC_003454:FN1923|3end_Adenine-specific_methyltransferase_419607..419757_NEGATIVE 182 97 56 116 74 NC_003454:FN1406|3end_histidine_ammonia-lyase_2066492..2066642_POSITIVE 182 78 38 97 60 NC_003454:FN1811|3end_Manganese_transport_system_ATP-binding_protein_mntA_292161..292311_NEGATIVE 180 130 91 88 49 NC_003454:FN1847|3end_DTDP-4-dehydrorhamnose_3,5-epimerase_337208..337358_POSITIVE 179 97 52 121 73 NC_003454:FN1213|3end_hypothetical_protein_1873179..1873329_NEGATIVE 178 73 33 99 56 NC_003454:FN0054|3end_tyrosyl-tRNA_synthetase_692136..692286_POSITIVE 177 84 42 58 12 NC_003454:FN0986|3end_phosphoribosylaminoimidazole_synthetase_1637845..1637995_NEGATIVE 177 73 40 140 110 NC_003454:FN1614|3end_MG(2+)_chelatase_family_protein_123509..123659_NEGATIVE 176 60 15 78 36 NC_003454:FN0232|3end_hypothetical_protein_857821..857971_NEGATIVE 176 89 41 94 54 NC_003454:FN0078|3end_Ethanolamine_utilization_protein_eutA_717715..717865_POSITIVE 175 101 65 122 91 NC_003454:FN1017|3end_hypothetical_protein_1672164..1672314_POSITIVE 175 77 36 113 71 NC_003454:FN1797|3end_Spermidine/putrescine_transport_ATP-binding_protein_potA_280031..280181_POSITIVE