Origin IGS: ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 catatactttctccaattcttttattaaattaccatttattatataattttaaatttattttatcaagaacttttatattcatattttttatatatatgaatataatatcataattctattaaaattctaaaaaatttttttaaataattgttgacaatctttttagattattatatacttgttccaatatcaaaaatagattacttaaaataaataaccatccagagaaacggagggactggcccaatgatgtttcagcaacctacttaaatgtgtggtgctaattccagagagatggagaggaaaattgaaacaagaactaatccatactctataaggtatggattttttaattaagtaagaatttattatagaaagtagggatataa Mask Tandem Repeat Region ================================================ ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg Find is-nt database================================================ Query_seq: FN0660:FN0661|FN0660:FN0661:ABC transporter ATP-binding protein:hypothetical protein:<-->:1317479..1317868 390 ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0660:FN0661|FN0660:FN0661:ABC transporter ATP-binding protein:hypothetical protein:<-->:1317479..1317868 390 ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0660:FN0661|FN0660:FN0661:ABC transporter ATP-binding protein:hypothetical protein:<-->:1317479..1317868 390 ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 182 .. M S L L S I I N S Y L I K K S I P Y R V W I S S C F N F P L H L S G I S T T H L S R L L K H H W A S P S V S L D G Y L F ................................................................................................................................................................................................................ Protein_Len: 35 Strand: + Start: 143 End: 247 .............................................................................................................................................. M G Q S L R F S G W L F I L S N L F L I L E Q V Y N N L K R L S T I I ............................................................................................................................................... Protein_Len: 36 Strand: - Start: 280 End: 387 ....................................................................................................................................................................................................................................................................................... S I I N M Y I F F I F I F T R S L I F K F N Y L L H Y N L L L I P S L M ... Protein_Len: 46 Strand: - Start: 109 End: 246 ............................................................................................................ C W V N L Y T A S V D N P W D R R K E P H N N I K L L R N K I N S C T Y L L R F L N D V I M ................................................................................................................................................ ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg 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: 89 Start: 211 End: 240 ..................................................................................................................................................................................................................GTTGACAATCTTTTTAGATTATTATATACT...................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 87 Start: 323 End: 352 ..................................................................................................................................................................................................................................................................................................................................CTTGATAAAATAAATTTAAAATTATATAAT...................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 284 End: 313 ...........................................................................................................................................................................................................................................................................................ATTCATATTTTTTATATATATGAATATAAT............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -6.7 Tail_Score: -5.28481 Start: 45 End: 66 Full_Region: tgaaacaagaactaa tccatactct ata aggtatgga ttttttaattaagta ............................................tccatactctataaggtatgga.................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 46 HP_score: -4.0 Tail_Score: -2.83371 Start: 283 End: 319 Full_Region: TTAATAGAATTATGA TATTATATTCATATAT ATAAA AAATATGAATATAAAA GTTCTTGATAAAATA ..........................................................................................................................................................................................................................................................................................TATTATATTCATATATATAAAAAATATGAATATAAAA....................................................................... TransTerm Strand: - Conf: 61 HP_score: -6.6 Tail_Score: -2.89079 Start: 285 End: 317 Full_Region: ttttatcaagaactt ttatattcatattt tttat atatatgaatataa tatcataattctatt ............................................................................................................................................................................................................................................................................................ttatattcatattttttatatatatgaatataa......................................................................... Find igs database================================================ Query_seq: FN0660:FN0661|FN0660:FN0661:ABC transporter ATP-binding protein:hypothetical protein:<-->:1317479..1317868 390 ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattatttaaaaaaattttttagaattttaatagaattatgatattatattcatatatataaaaaatatgaatataaaagttcttgataaaataaatttaaaattatataataaatggtaatttaataaaagaattggagaaagtatatg Intra-Species Hit: Count: 1 Min: 1 Max: 248 Len: 248 Subject: NC_003454_FN0660_FN0661|ABC transporter ATP-binding protein:hypothetical protein|NEGATIVE:POSITIVE|[1317479,1317868]|390 HSP 1 e-value: 1.0E-138 bit: 492.0 Len: 248 Query Start:1 Query End:248 Subject Strand: POSITIVE Subject Start: 1 Subject End: 248 ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattattt.............................................................................................................................................. ttatatccctactttctataataaattcttacttaattaaaaaatccataccttatagagtatggattagttcttgtttcaattttcctctccatctctctggaattagcaccacacatttaagtaggttgctgaaacatcattgggccagtccctccgtttctctggatggttatttattttaagtaatctatttttgatattggaacaagtatataataatctaaaaagattgtcaacaattattt.............................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAUCCCUACUUUCUAUAAUAAAUUCUUACUUAAUUAAAAAAUCCAUACCUUAUAGAGUAUGGAUUAGUUCUUGUUUCAAUUUUCCUCUCCAUCUCUCUGGAAUUAGCACCACACAUUUAAGUAGGUUGCUGAAACAUCAUUGGGCCAGUCCCUCCGUUUCUCUGGAUGGUUAUUUAUUUUAAGUAAUCUAUUUUUGAUAUUGGAACAAGUAUAUAAUAAUCUAAAAAGAUUGUCAACAAUUAUUU ..........................................((((((((((.....).)))))))))....(((((((((((.......((((......))))............((...((((((((((((............(((((.(((............))))))))..........)))))))))))).))..)))))))))))......(((((((....)))))))............ (-46.95) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAUUGUUGACAAUCUUUUUAGAUUAUUAUAUACUUGUUCCAAUAUCAAAAAUAGAUUACUUAAAAUAAAUAACCAUCCAGAGAAACGGAGGGACUGGCCCAAUGAUGUUUCAGCAACCUACUUAAAUGUGUGGUGCUAAUUCCAGAGAGAUGGAGAGGAAAAUUGAAACAAGAACUAAUCCAUACUCUAUAAGGUAUGGAUUUUUUAAUUAAGUAAGAAUUUAUUAUAGAAAGUAGGGAUAUAA ..........(((.(((((....))))).)))......((((((.((.((...((((((((.((((.............(((...((((((..(((.....))).....)))))).(((.(((((......))).)))))...(((((......))))).))).((((((((........((((((((((......))))))))))))))))))...))))))))))))...))..)).))))))... (-49.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 883 140 91 231 182 NC_003454:FN0660|5end_ABC_transporter_ATP-binding_protein_1317388..1317618_NEGATIVE 596 135 91 220 175 NC_003454:FN0355|5end_S-adenosylmethionine_synthetase_987227..987457_NEGATIVE 299 114 71 146 87 NC_003454:FN2108|5end_galactose-1-phosphate_uridylyltransferase_619319..619549_POSITIVE 287 89 44 41 5 NC_003454:FN1380|5end_Citrate_lyase_beta_chain_2027248..2027478_POSITIVE 285 127 81 151 110 NC_003454:FN2092|5end_Integral_membrane_protein_603111..603341_NEGATIVE 280 198 151 142 94 NC_003454:FN1246|5end_Lipooligosaccharide_cholinephosphotransferase_1903192..1903422_NEGATIVE 269 150 101 227 177 NC_003454:FN1540|5end_Iron-sulfur_cluster-binding_protein_53055..53285_POSITIVE 267 178 136 81 47 NC_003454:FN0226|5end_4-hydroxythreonine-4-phosphate_dehydrogenase_854089..854319_NEGATIVE 263 171 131 187 138 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 260 166 122 122 73 NC_003454:FN1713|5end_tRNA_(Uracil-5-)_-methyltransferase_207494..207724_POSITIVE 249 94 55 90 46 NC_003454:FN0263|5end_Peptidyl-prolyl_cis-trans_isomerase_890064..890294_POSITIVE 247 98 53 215 172 NC_003454:FN0909|5end_DNA_repair_protein_radC_1567654..1567884_NEGATIVE 246 127 86 162 116 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 244 158 124 67 35 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 241 185 154 158 126 NC_003454:FN0335|5end_Outer_membrane_porin_F_969675..969905_NEGATIVE 234 184 144 76 42 NC_003454:FN0032|5end_hypothetical_protein_669778..670008_NEGATIVE 233 134 98 120 78 NC_003454:FN0014|5end_Transporter_652565..652795_POSITIVE 231 169 126 190 141 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 231 169 126 86 37 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 231 170 123 54 8 NC_003454:FN1852|5end_hypothetical_protein_341616..341846_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 114 71 146 87 NC_003454:FN2107|3end_galactokinase_619399..619549_POSITIVE 287 89 44 38 2 NC_003454:FN1379|3end_Citrate_lyase_beta_chain_2027325..2027475_POSITIVE 280 198 151 129 81 NC_003454:FN1247|3end_LOS_biosynthesis_enzyme_LBGB_1903205..1903355_NEGATIVE 267 178 136 56 22 NC_003454:FN0227|3end_hypothetical_protein_854114..854264_NEGATIVE 246 127 86 143 97 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 243 99 53 123 83 NC_003454:FN1449|3end_Fusobacterium_outer_membrane_protein_family_2118612..2118762_NEGATIVE 241 185 154 85 53 NC_003454:FN0336|3end_hypothetical_protein_969748..969898_NEGATIVE 234 99 55 115 56 NC_003454:FN2076|3end_MunI_regulatory_protein_587536..587686_NEGATIVE 233 134 98 114 72 NC_003454:FN0013|3end_Transporter_652639..652789_POSITIVE 229 99 64 102 62 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 226 99 53 136 78 NC_003454:FN1893|3end_Fusobacterium_outer_membrane_protein_family_374412..374562_NEGATIVE 220 97 51 92 44 NC_003454:FN1928|3end_Transcriptional_regulator,_MerR_family_427964..428114_NEGATIVE 219 160 111 74 20 NC_003454:FN0752|3end_Proline_iminopeptidase_1410721..1410871_NEGATIVE 218 97 55 148 107 NC_003454:FN0132|3end_Hemolysin_769183..769333_POSITIVE 218 133 91 49 3 NC_003454:FN1658|3end_prolyl-tRNA_synthetase_153188..153338_NEGATIVE 217 115 71 54 1 NC_003454:FN0112|3end_hypothetical_protein_746600..746750_POSITIVE 216 162 123 89 51 NC_003454:FN0352|3end_NA+/H+_antiporter_NHAC_985000..985150_POSITIVE 214 174 139 102 64 NC_003454:FN0171|3end_Hypothetical_cytosolic_protein_796921..797071_POSITIVE 214 170 123 110 54 NC_003454:FN1734|3end_V-type_ATP_synthase_subunit_B_232882..233032_NEGATIVE 213 166 121 113 72 NC_003454:FN1521|3end_Dipeptide_transport_system_permease_protein_dppB_27406..27556_POSITIVE