Origin IGS: aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatattccaaaatataaaaatatgaactgcacccaaaatcttggacacaagattggaggtgcagttttttgtgtctaaattaacaagagaagataaattgacaaaagtaacttaattgtttataattttagtaaataaatttaaggaggtattttt Mask Tandem Repeat Region ================================================ aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt Find is-nt database================================================ Query_seq: FN1972:FN1973|FN1972:FN1973:hypothetical protein:Translation initiation inhibitor:<-<-:472162..472319 158 aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1972:FN1973|FN1972:FN1973:hypothetical protein:Translation initiation inhibitor:<-<-:472162..472319 158 aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1972:FN1973|FN1972:FN1973:hypothetical protein:Translation initiation inhibitor:<-<-:472162..472319 158 aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt Predict ORF larger than 30AA ================================================ aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt 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: 92 Start: 31 End: 60 ..............................ATTGACAAAAGTAACTTAATTGTTTATAAT.................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -4.3 Tail_Score: -5.28983 Start: 87 End: 136 Full_Region: TGTTAATTTAGACAC AAAAAACTGCACCTCCAATCTTG TGTC CAAGATTTTGGGTGCAGTTCATA TTTTTATATTTTGGA ......................................................................................AAAAAACTGCACCTCCAATCTTGTGTCCAAGATTTTGGGTGCAGTTCATA...................... TransTerm Strand: + Conf: 72 HP_score: -6.9 Tail_Score: -4.25747 Start: 89 End: 134 Full_Region: TTAATTTAGACACAA AAAACTGCACCTCCAATCTTG TGTC CAAGATTTTGGGTGCAGTTCA TATTTTTATATTTTG ........................................................................................AAAACTGCACCTCCAATCTTGTGTCCAAGATTTTGGGTGCAGTTCA........................ TransTerm Strand: + Conf: 95 HP_score: -12.1 Tail_Score: -3.65109 Start: 93 End: 130 Full_Region: TTTAGACACAAAAAA CTGCACCTCCAATCTTG TGTC CAAGATTTTGGGTGCAG TTCATATTTTTATAT ............................................................................................CTGCACCTCCAATCTTGTGTCCAAGATTTTGGGTGCAG............................ TransTerm Strand: - Conf: 100 HP_score: -9.9 Tail_Score: -5.4251 Start: 93 End: 130 Full_Region: atataaaaatatgaa ctgcacccaaaatcttg gaca caagattggaggtgcag ttttttgtgtctaaa ............................................................................................ctgcacccaaaatcttggacacaagattggaggtgcag............................ Find igs database================================================ Query_seq: FN1972:FN1973|FN1972:FN1973:hypothetical protein:Translation initiation inhibitor:<-<-:472162..472319 158 aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_003454_FN1972_FN1973|hypothetical protein:Translation initiation inhibitor|NEGATIVE:NEGATIVE|[472162,472319]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt aaaaatacctccttaaatttatttactaaaattataaacaattaagttacttttgtcaatttatcttctcttgttaatttagacacaaaaaactgcacctccaatcttgtgtccaagattttgggtgcagttcatatttttatattttggaatatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUACCUCCUUAAAUUUAUUUACUAAAAUUAUAAACAAUUAAGUUACUUUUGUCAAUUUAUCUUCUCUUGUUAAUUUAGACACAAAAAACUGCACCUCCAAUCUUGUGUCCAAGAUUUUGGGUGCAGUUCAUAUUUUUAUAUUUUGGAAUAUUUU .((((((..(((..((.........(((((...((((.....((((((((....)).)))))).......))))...)))))........((((((((((..(((((((....)))))))..))))))))))............))..))).)))))) (-30.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUUCCAAAAUAUAAAAAUAUGAACUGCACCCAAAAUCUUGGACACAAGAUUGGAGGUGCAGUUUUUUGUGUCUAAAUUAACAAGAGAAGAUAAAUUGACAAAAGUAACUUAAUUGUUUAUAAUUUUAGUAAAUAAAUUUAAGGAGGUAUUUUU ((((((((((...............((((((((((...(((((((....)))))))...))))))))))(((((..(((((..(((((...(((.((..((....))..)).)))..)))))......)))))...))))).....))).))))))). (-36.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 909 130 81 221 172 NC_003454:FN1972|5end_hypothetical_protein_472071..472301_NEGATIVE 857 138 91 142 95 NC_003454:FN0840|5end_Transposase_1501361..1501591_POSITIVE 848 130 84 123 77 NC_003454:FN1446|5end_Transposase_2116033..2116263_POSITIVE 848 130 84 135 89 NC_003454:FN1887|5end_Transposase_371671..371901_POSITIVE 813 140 91 145 95 NC_003454:FN0485|5end_Transposase_1130267..1130497_POSITIVE 787 136 91 142 97 NC_003454:FN0135|5end_Transposase_770238..770468_POSITIVE 776 135 91 141 97 NC_003454:FN0786|5end_Transposase_1442465..1442695_POSITIVE 763 134 91 140 97 NC_003454:FN1443|5end_Transposase_2111518..2111748_NEGATIVE 603 135 92 216 170 NC_003454:FN0210|5end_Transcriptional_regulator,_COPG_family_836998..837228_POSITIVE 389 135 91 209 161 NC_003454:FN1444|5end_GMP_synthase_[glutamine-hydrolyzing]_2111585..2111815_POSITIVE 386 132 91 72 31 NC_003454:FN0839|5end_hypothetical_protein_1501426..1501656_NEGATIVE 383 113 79 231 200 NC_003454:FN0234|5end_hypothetical_protein_859499..859729_NEGATIVE 242 82 50 211 179 NC_003454:FN0341|5end_transport_protein_975381..975611_NEGATIVE 235 135 93 106 65 NC_003454:FN0130|5end_ABC_transporter_ATP-binding_protein_758586..758816_POSITIVE 224 133 94 130 96 NC_003454:FN0219|5end_Autolysin_response_regulator_843316..843546_NEGATIVE 221 130 87 201 160 NC_003454:FN0288|5end_Hypoxanthine-guanine_phosphoribosyltransferase_915765..915995_NEGATIVE 217 121 94 181 152 NC_003454:FN0045|5end_Shikimate_5-dehydrogenase_683012..683242_POSITIVE 216 140 92 204 151 NC_003454:FN2019|5end_Ribosome-binding_factor_A_522292..522522_NEGATIVE 215 136 104 154 125 NC_003454:FN1423|5end_Flavoprotein_2090070..2090300_NEGATIVE 214 140 93 112 58 NC_003454:FN1236|5end_Choline_transport_protein_1893480..1893710_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 848 130 84 138 92 NC_003454:FN1886|3end_hypothetical_protein_371754..371904_POSITIVE 813 140 91 70 20 NC_003454:FN0484|3end_Lipase_1130272..1130422_POSITIVE 810 134 91 77 34 NC_003454:FN0235|3end_ABC_transporter_ATP-binding_protein_859674..859824_NEGATIVE 788 140 91 90 43 NC_003454:FN1905|3end_168_kDa_surface-layer_protein_precursor_393653..393803_NEGATIVE 752 130 87 74 31 NC_003454:FN1547|3end_PTS_permease_for_N-acetylglucosamine_and_glucose_61801..61951_NEGATIVE 750 140 91 89 40 NC_003454:FN1464|3end_1-deoxy-D-xylulose-5-phosphate_synthase_2145954..2146104_NEGATIVE 621 134 92 83 41 NC_003454:FN1221|3end_hypothetical_protein_1881290..1881440_POSITIVE 604 139 91 92 45 NC_003454:FN1500|3end_Nickel_transport_ATP-binding_protein_nikE_5193..5343_NEGATIVE 458 133 91 83 41 NC_003454:FN1463|3end_pyridoxine_biosynthesis_protein_2145924..2146074_POSITIVE 456 140 91 92 43 NC_003454:FN1545|3end_Ferredoxin_like_protein_59497..59647_POSITIVE 415 137 91 49 3 NC_003454:FN1019|3end_3-hydroxybutyryl-CoA_dehydrogenase_1672945..1673095_NEGATIVE 395 140 92 97 49 NC_003454:FN1904|3end_Transcriptional_regulator,_MarR_family_393633..393783_POSITIVE 383 130 87 68 26 NC_003454:FN0178|3end_UNC-44_ankyrins_802390..802540_NEGATIVE 381 135 91 81 37 NC_003454:FN1498|3end_Integral_membrane_protein_3542..3692_POSITIVE 368 140 91 83 36 NC_003454:FN1546|3end_translation_elongation_factor_EF-G_59529..59679_NEGATIVE 367 135 92 77 38 NC_003454:FN0435|3end_Purine_nucleoside_phosphorylase_1077821..1077971_POSITIVE 355 140 91 77 30 NC_003454:FN1144|3end_hypothetical_protein_1793403..1793553_NEGATIVE 317 140 91 88 39 NC_003454:FN1499|3end_Cell_surface_protein_5166..5316_POSITIVE 308 132 91 84 43 NC_003454:FN1143|3end_glucosamine-6-phosphate_deaminase_1793365..1793515_POSITIVE 301 130 87 79 44 NC_003454:FN0980|3end_hypothetical_protein_1632815..1632965_POSITIVE