Origin IGS: aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga .........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 tccatctggcgttaattttaaagtgattttttctttttttatgctcatgttagaaccctttaaaggtattatatgttcaccttctgagccaaattcccagtcattagcaaaagtaaagatacttaaaatgcaaaataaaattgttagaaaaaattttttcattgttgtctcctccataaaatttttgttaacttatcatatcatttttttcaaaattatgctatacttaaaaaaataaaaattattgtaaataaaataaatttgaaaggagaagtatggaaaataatcaacaaataccgccttatgtaagaagaacagtttcacctgtt Mask Tandem Repeat Region ================================================ aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga Find is-nt database================================================ Query_seq: FN1985:FN1986|FN1985:FN1986:Inner membrane protein:hypothetical protein:<-->:488728..489056 329 aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1985:FN1986|FN1985:FN1986:Inner membrane protein:hypothetical protein:<-->:488728..489056 329 aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1985:FN1986|FN1985:FN1986:Inner membrane protein:hypothetical protein:<-->:488728..489056 329 aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 6 End: 131 ..... M K L F F L H K A V F V D Y F P Y F S F Q I Y F I Y N N F Y F F K Y S I I L K K M I ...................................................................................................................................................................................................... Protein_Len: 59 Strand: + Start: 153 End: 329 ........................................................................................................................................................ M E E T T M K K F F L T I L F C I L S I F T F A N D W E F G S E G E H I I P L K G S N M S I K K E K I T L K L T P D G Protein_Len: 60 Strand: - Start: 95 End: 307 .............................................................................................. I H Y T L L F K I S S V V I F F N K R V I K N Q M K L I K V K A L S Q S N P E S P S C I I G K F P E L M L M F F S F I M ...................... Protein_Len: 42 Strand: - Start: 24 End: 149 ....................... M L R Y K N I I K W V E G K L N I K N V I I K I K K L I A Y N Q F F H Y S L N V F M .................................................................................................................................................................................... aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga 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================================================ aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -3.5 Tail_Score: -5.86609 Start: 76 End: 88 Full_Region: CCTTTCAAATTTATT TTATT TAC AATAA TTTTTATTTTTTTAA ...........................................................................TTATTTACAATAA................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: FN1985:FN1986|FN1985:FN1986:Inner membrane protein:hypothetical protein:<-->:488728..489056 329 aacaggtgaaactgttcttcttacataaggcggtatttgttgattattttccatacttctcctttcaaatttattttatttacaataatttttatttttttaagtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaaattttttctaacaattttattttgcattttaagtatctttacttttgctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcataaaaaaagaaaaaatcactttaaaattaacgccagatgga Intra-Species Hit: Count: 1 Min: 1 Max: 289 Len: 289 Subject: NC_003454_FN1985_FN1986|Inner membrane protein:hypothetical protein|NEGATIVE:POSITIVE|[488728,489056]|329 HSP 1 e-value: 1.0E-30 bit: 135.0 Len: 68 Query Start:222 Query End:289 Subject Strand: POSITIVE Subject Start: 222 Subject End: 289 .............................................................................................................................................................................................................................gctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcat........................................ .............................................................................................................................................................................................................................gctaatgactgggaatttggctcagaaggtgaacatataatacctttaaagggttctaacatgagcat........................................ HSP 2 e-value: 4.0E-21 bit: 103.0 Len: 73 Query Start:103 Query End:175 Subject Strand: POSITIVE Subject Start: 103 Subject End: 175 ......................................................................................................agtatagcataattttgnnnnnnntgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaa.......................................................................................................................................................... ......................................................................................................agtatagcataattttgaaaaaaatgatatgataagttaacaaaaattttatggaggagacaacaatgaaaaa.......................................................................................................................................................... HSP 3 e-value: 8.0E-10 bit: 65.9 Len: 33 Query Start:1 Query End:33 Subject Strand: POSITIVE Subject Start: 1 Subject End: 33 aacaggtgaaactgttcttcttacataaggcgg........................................................................................................................................................................................................................................................................................................ aacaggtgaaactgttcttcttacataaggcgg........................................................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGGUGAAACUGUUCUUCUUACAUAAGGCGGUAUUUGUUGAUUAUUUUCCAUACUUCUCCUUUCAAAUUUAUUUUAUUUACAAUAAUUUUUAUUUUUUUAAGUAUAGCAUAAUUUUGAAAAAAAUGAUAUGAUAAGUUAACAAAAAUUUUAUGGAGGAGACAACAAUGAAAAAAUUUUUUCUAACAAUUUUAUUUUGCAUUUUAAGUAUCUUUACUUUUGCUAAUGACUGGGAAUUUGGCUCAGAAGGUGAACAUAUAAUACCUUUAAAGGGUUCUAACAUGAGCAU ...(((((....(((((.((((..((((((..((..((((((....(((((((((.......(((((((.((((..((((((.((.(((....))).)).))))))....)))).)))))))....((((.......))))..........)))))))))..)))))).(((((....)))))..))..))))))...(((....(((((....))))).)))......(((((.......))))))))).))))).....))))).......((((......)))).. (-46.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCUCAUGUUAGAACCCUUUAAAGGUAUUAUAUGUUCACCUUCUGAGCCAAAUUCCCAGUCAUUAGCAAAAGUAAAGAUACUUAAAAUGCAAAAUAAAAUUGUUAGAAAAAAUUUUUUCAUUGUUGUCUCCUCCAUAAAAUUUUUGUUAACUUAUCAUAUCAUUUUUUUCAAAAUUAUGCUAUACUUAAAAAAAUAAAAAUUAUUGUAAAUAAAAUAAAUUUGAAAGGAGAAGUAUGGAAAAUAAUCAACAAAUACCGCCUUAUGUAAGAAGAACAGUUUCACCUGUU .......................((((......(((((..((((((((.(................(((.(((((....)))))....))).........(((((.((......((((((((.....((((((.((......(((((((.((..........((((((((..................))))))))..........)).)))))))......))..))))))...))))))))...))))))).....).)))).).)))..))))).....))))... (-36.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 788 60 11 151 102 NC_003454:FN1985|5end_Inner_membrane_protein_488637..488867_NEGATIVE 306 160 113 228 179 NC_003454:FN1825|5end_hypothetical_protein_313994..314224_POSITIVE 270 79 32 118 69 NC_003454:FN1836|5end_Tetratricopeptide_repeat_family_protein_326714..326944_NEGATIVE 261 77 31 117 67 NC_003454:FN1868|5end_Hypothetical_cytosolic_protein_360433..360663_NEGATIVE 256 67 38 226 197 NC_003454:FN1818|5end_Hemolysin_activator_protein_precursor_306955..307185_NEGATIVE 250 77 40 136 95 NC_003454:FN0504|5end_Arginine_permease_1155009..1155239_NEGATIVE 250 279 232 115 70 NC_003454:FN1999|5end_HIPA_protein_500262..500492_POSITIVE 247 31 3 52 19 NC_003454:FN1172|5end_Phosphate_acetyltransferase_1834625..1834855_NEGATIVE 247 90 49 130 86 NC_003454:FN2046|5end_Acetyltransferase_551360..551590_NEGATIVE 238 60 15 120 72 NC_003454:FN0377|5end_Iron(III)-transport_system_permease_protein_sfuB_1007464..1007694_POSITIVE 236 64 35 102 73 NC_003454:FN0968|5end_hypothetical_protein_1621809..1622039_NEGATIVE 235 64 28 104 65 NC_003454:FN1035|5end_Iron-sulfur_flavoprotein_1688280..1688510_POSITIVE 233 45 1 204 155 NC_003454:FN1624|5end_preprotein_translocase_SecY_132360..132590_NEGATIVE 231 110 61 147 97 NC_003454:FN0947|5end_hypothetical_protein_1600457..1600687_POSITIVE 231 66 27 93 48 NC_003454:FN0623|5end_Malonate_transporter_1281952..1282182_POSITIVE 231 60 12 104 58 NC_003454:FN0298|5end_Histidyl-tRNA_synthetase_931133..931363_POSITIVE 228 225 182 197 143 NC_003454:FN1863|5end_L-beta-lysine_5,6-aminomutase_alpha_subunit_354678..354908_NEGATIVE 225 78 47 112 84 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 223 231 197 39 1 NC_003454:FN1328|5end_Exodeoxyribonuclease_VII_small_subunit_1983129..1983359_NEGATIVE 223 85 47 129 85 NC_003454:FN2078|5end_Transcriptional_regulator,_DeoR_family_590266..590496_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 79 32 107 58 NC_003454:FN1837|3end_putative_nucleotide-binding_protein_326725..326875_NEGATIVE 261 77 31 97 47 NC_003454:FN1869|3end_hypothetical_protein_360453..360603_NEGATIVE 250 77 40 101 60 NC_003454:FN0505|3end_Anthranilate_synthase_component_II_1155044..1155194_NEGATIVE 242 77 31 97 47 NC_003454:FN1935|3end_Adenine-specific_methyltransferase_436060..436210_NEGATIVE 238 60 15 136 88 NC_003454:FN0376|3end_Iron(III)-transport_ATP-binding_protein_sfuC_1007560..1007710_POSITIVE 236 64 35 105 76 NC_003454:FN0969|3end_hypothetical_protein_1621806..1621956_NEGATIVE 235 64 28 89 50 NC_003454:FN1034|3end_Transcriptional_regulator,_TetR_family_1688345..1688495_POSITIVE 232 69 24 88 38 NC_003454:FN1287|3end_Bacterial_Protein_Translation_Initiation_Factor_1_(IF-1)_1944415..1944565_NEGATIVE 231 66 27 72 27 NC_003454:FN0622|3end_N-glycosylase/DNA_lyase_1282011..1282161_POSITIVE 231 60 12 92 46 NC_003454:FN0297|3end_ATPase_associated_with_chromosome_architecture/replication_931201..931351_POSITIVE 226 245 201 43 2 NC_003454:FN0883|3end_hypothetical_protein_1544625..1544775_POSITIVE 223 62 26 147 112 NC_003454:FN0876|3end_Gamma-glutamyltranspeptidase_1535794..1535944_NEGATIVE 223 85 47 53 9 NC_003454:FN2079|3end_ABC_transporter_ATP-binding_protein_590342..590492_NEGATIVE 215 86 41 105 68 NC_003454:FN1519|3end_23S_rRNA_methyltransferase_24088..24238_NEGATIVE 212 90 41 98 40 NC_003454:FN1384|3end_IAA_acetyltransferase_2037888..2038038_NEGATIVE 212 50 4 122 63 NC_003454:FN0924|3end_hypothetical_protein_1579962..1580112_POSITIVE 212 76 31 96 52 NC_003454:FN0226|3end_4-hydroxythreonine-4-phosphate_dehydrogenase_853091..853241_NEGATIVE 211 65 36 92 59 NC_003454:FN1649|3end_Oligopeptide_transport_ATP-binding_protein_oppD_143327..143477_NEGATIVE 209 70 30 110 72 NC_003454:FN1541|3end_Heptaprenyl_diphosphate_synthase_component_II_56275..56425_POSITIVE 207 80 32 95 54 NC_003454:FN0203|3end_Glutaconate_CoA-transferase_subunit_B_829631..829781_POSITIVE