Origin IGS: gcctgaatctttcgggaaactaccgccggaaagtctgtccccgttgtgggagaggctttctgtgcggtcatgatcttcccgatatgcgatgcgactgtaggacggtacaactgcaatcgcatcacttcgaattccttcgacgacattatcatgactgtctctgtctgccttgtctcagggaaatagcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact .........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 agtaattgtaactattgttattaaagtgataatcggttcttttttcggtctcccatcgaggacatttccttatcgatgcatttggagtatttcctctgcggaggcatttgctatttccctgagacaaggcagacagagacagtcatgataatgtcgtcgaaggaattcgaagtgatgcgattgcagttgtaccgtcctacagtcgcatcgcatatcgggaagatcatgaccgcacagaaagcctctcccacaacggggacagactttccggcggtagtttcccgaaagattcaggc Mask Tandem Repeat Region ================================================ gcctgaatctttcgggaaactaccgccggaaagtctgtccccgttgtgggagaggctttctgtgcggtcatgatcttcccgatatgcgatgcgactgtaggacggtacaactgcaatcgcatcacttcgaattccttcgacgacattatcatgactgtctctgtctgccttgtctcagggaaatagcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact Find is-nt database================================================ Query_seq: PG1416:PG1417|PG1416:PG1417:enoyl-(acyl-carrier-protein) reductase II:fumarate hydratase class I, anaerobic:->->:1501139..1501434 296 gcctgaatctttcgggaaactaccgccggaaagtctgtccccgttgtgggagaggctttctgtgcggtcatgatcttcccgatatgcgatgcgactgtaggacggtacaactgcaatcgcatcacttcgaattccttcgacgacattatcatgactgtctctgtctgccttgtctcagggaaatagcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1416:PG1417|PG1416:PG1417:enoyl-(acyl-carrier-protein) reductase II:fumarate hydratase class I, anaerobic:->->:1501139..1501434 296 gcctgaatctttcgggaaactaccgccggaaagtctgtccccgttgtgggagaggctttctgtgcggtcatgatcttcccgatatgcgatgcgactgtaggacggtacaactgcaatcgcatcacttcgaattccttcgacgacattatcatgactgtctctgtctgccttgtctcagggaaatagcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1416:PG1417|PG1416:PG1417:enoyl-(acyl-carrier-protein) reductase II:fumarate hydratase class I, anaerobic:->->:1501139..1501434 296 gcctgaatctttcgggaaactaccgccggaaagtctgtccccgttgtgggagaggctttctgtgcggtcatgatcttcccgatatgcgatgcgactgtaggacggtacaactgcaatcgcatcacttcgaattccttcgacgacattatcatgactgtctctgtctgccttgtctcagggaaatagcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 2 Min: 21 Max: 185 Len: 165 Subject: UniRef90_A1ZTG9 Cluster: Putative orphan protein; n=1; Microscilla marina ATCC 23134|Rep: Putative orphan protein - Microscilla marina ATCC 23134 HSP 1 e-value: 8.0E-7 bit: 55.1 Len: 165 Query Start:21 Query End:185 Subject Strand: null Subject Start: 11 Subject End: 64 .................... Y R R K V C P R C G R G F L C G H D L P D M - R C D C R T V Q L Q S H H F E F L R R H Y H D C L C L P C L R E I ............................................................................................................... .................... H E Q K Q C P R C G A G F E C - - K V G D V V N C Q C Y E V Q V Q A R T N E F L A N A Y Y D C L C K N C L A E I ............................................................................................................... Subject: UniRef90_Q64TC2 Cluster: Hypothetical protein; n=1; Bacteroides fragilis|Rep: Hypothetical protein - Bacteroides fragilis HSP 1 e-value: 1.0E-6 bit: 54.7 Len: 159 Query Start:27 Query End:185 Subject Strand: null Subject Start: 4 Subject End: 55 .......................... R K V C P R C G R G F L C G H D L P D M R C D C R T V Q L Q S H H F E F L R R H Y H D C L C L P C L R E I ............................................................................................................... .......................... K K V C P C C G A V F Q C R H D - N I L L C H C A T V K L D S L Q R A Y I K E H F P D C L C H D C L K K I ............................................................................................................... gcctgaatctttcgggaaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact Predict ORF larger than 30AA ================================================ Protein_Len: 59 Strand: + Start: 7 End: 183 ...... M F R E T T A G K S V P V V G E A F C A V M I F P I C D A T V G R Y N C N R I T S N S F D D I I M T V S V C L V S G K ................................................................................................................. Protein_Len: 60 Strand: + Start: 3 End: 224 .. M N L S G N Y R R K V C P R C G R G F L C G H D L P D M R C D C R T V Q L Q S H H F E F L R R H Y H D C L C L P C L R E ........................................................................ Protein_Len: 47 Strand: + Start: 155 End: 295 .......................................................................................................................................................... M S L S A L S Q G N S K C L R R G N T P N A S I R K C P R W E T E K R T D Y H F N N N S Y N Y . Protein_Len: 47 Strand: - Start: 152 End: 292 ....................................................................................................................................................... S Q R Q R G Q R L S I A F A E A S S I S W I C R Y P F T R S P L G F F S G I I V K I V I T V M .... Protein_Len: 60 Strand: - Start: 3 End: 242 .. A T M I K G I H S A V T P R Y L Q L R M V E F E K S S M I M V T E T Q R T E P F Y C I G G C L F Y E L H M S L S I D E M ...................................................... Protein_Len: 44 Strand: - Start: 1 End: 132 G S D K P F S G G S L R D G N H S L S E T R D H D E R Y A I R S Y S P V V A I A D S R M .................................................................................................................................................................... gcctgaatctttcgggaaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact 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================================================ gcctgaatctttcgggaaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -2.3 Tail_Score: -3.05343 Start: 19 End: 73 Full_Region: TGAATCTTTCGGGAA ACTACCGCCGGAAAGTCTGTCCC CGTTGT GGGAGAGGCTTTCTGTGCGGTCATGA TCTTCCCGATATGCG ..................ACTACCGCCGGAAAGTCTGTCCCCGTTGTGGGAGAGGCTTTCTGTGCGGTCATGA............................................................................................................................................................................................................................... TransTerm Strand: - Conf: 56 HP_score: -5.4 Tail_Score: -3.53761 Start: 20 End: 70 Full_Region: atatcgggaagatca tgaccgcacagaaagcctctccc acaacg gggacagactttccggcggtag tttcccgaaagattc ...................tgaccgcacagaaagcctctcccacaacggggacagactttccggcggtag.................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 65 HP_score: -9.5 Tail_Score: -2.74701 Start: 21 End: 70 Full_Region: AATCTTTCGGGAAAC TACCGCCGGAAAGTCTGTCCC CGTTGT GGGAGAGGCTTTCTGTGCGGTCA TGATCTTCCCGATAT ....................TACCGCCGGAAAGTCTGTCCCCGTTGTGGGAGAGGCTTTCTGTGCGGTCA.................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 63 HP_score: -9.3 Tail_Score: -2.90496 Start: 23 End: 67 Full_Region: tcgggaagatcatga ccgcacagaaagcctctccc acaacg gggacagactttccggcgg tagtttcccgaaaga ......................ccgcacagaaagcctctcccacaacggggacagactttccggcgg..................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 38 HP_score: -2.3 Tail_Score: -2.55253 Start: 90 End: 121 Full_Region: CTTCCCGATATGCGA TGCGACTGTAG GACGGTACAA CTGCAATCGCA TCACTTCGAATTCCT .........................................................................................TGCGACTGTAGGACGGTACAACTGCAATCGCA............................................................................................................................................................................... Find igs database================================================ Query_seq: PG1416:PG1417|PG1416:PG1417:enoyl-(acyl-carrier-protein) reductase II:fumarate hydratase class I, anaerobic:->->:1501139..1501434 296 gcctgaatctttcgggaaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcaaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact Intra-Species Hit: Count: 1 Min: 187 Max: 296 Len: 110 Subject: NC_002950_PG1416_PG1417|enoyl-(acyl-carrier-protein) reductase II:fumarate hydratase class I, anaerobic|POSITIVE:POSITIVE|[1501139,1501434]|296 HSP 1 e-value: 8.0E-56 bit: 218.0 Len: 110 Query Start:187 Query End:296 Subject Strand: POSITIVE Subject Start: 187 Subject End: 296 ..........................................................................................................................................................................................caaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact ..........................................................................................................................................................................................caaatgcctccgcagaggaaatactccaaatgcatcgataaggaaatgtcctcgatgggagaccgaaaaaagaaccgattatcactttaataacaatagttacaattact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUGCCUCCGCAGAGGAAAUACUCCAAAUGCAUCGAUAAGGAAAUGUCCUCGAUGGGAGACCGAAAAAAGAACCGAUUAUCACUUUAAUAACAAUAGUUACAAUUACU ......((((....)))).....((((.....((((((...(((....))))))))))))).............................((((....))))........ (-17.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAUUGUAACUAUUGUUAUUAAAGUGAUAAUCGGUUCUUUUUUCGGUCUCCCAUCGAGGACAUUUCCUUAUCGAUGCAUUUGGAGUAUUUCCUCUGCGGAGGCAUUUG .........((((((((((((....)))))))).)))).........((((((((..(((((.((((((..((......))..)))).)).))))))).))))))..... (-26.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 50 5 212 157 NC_002950:PG1497|5end_DNA-binding_protein,_histone-like_family_1574085..1574315_POSITIVE 329 59 12 94 48 NC_002950:PG0494|5end_hypothetical_protein_535366..535596_NEGATIVE 322 54 12 85 44 NC_002950:PG0083|5end_hypothetical_protein_96952..97182_POSITIVE 321 67 21 86 43 NC_002950:PG0026|5end_hypothetical_protein_29234..29464_POSITIVE 311 57 11 200 139 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 304 40 5 56 19 NC_002950:PG0742|5end_antigen_PgaA_790637..790867_NEGATIVE 293 59 11 53 10 NC_002950:PG1572|5end_hypothetical_protein_1651252..1651482_NEGATIVE 289 50 5 200 145 NC_002950:PG1382|5end_hypothetical_protein_1461331..1461561_POSITIVE 289 78 31 206 149 NC_002950:PG0996|5end_conserved_hypothetical_protein_TIGR01777_1055592..1055822_POSITIVE 284 80 32 93 45 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 284 80 32 93 45 NC_002950:PG1059|5end_hypothetical_protein_1126495..1126725_NEGATIVE 279 66 25 171 119 NC_002950:PG0071|5end_UDP-3-O-acyl-GlcNAc_deacetylase/beta-hydroxyacyl-[acyl_carrier_protein]_dehydratase_FabZ_86119..86349_NEGATIVE 278 77 31 72 26 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 276 59 12 181 117 NC_002950:PG1834|5end_glycogen_synthase-related_protein_1926155..1926385_POSITIVE 275 50 3 206 162 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 274 38 4 69 30 NC_002950:PG0141|5end_spoOJ_protein_164747..164977_NEGATIVE 273 63 23 147 105 NC_002950:PG1751|5end_aminotransferase,_class_V_1837280..1837510_POSITIVE 270 59 12 63 15 NC_002950:PG1935|5end_50S_ribosomal_protein_L2_2023192..2023422_NEGATIVE 269 66 25 175 140 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 269 50 6 58 20 NC_002950:PG0020|5end_transcriptional_regulator,_MarR_family_23382..23612_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 54 12 79 38 NC_002950:PG0082|3end_hypothetical_protein_97026..97176_POSITIVE 317 53 14 47 9 NC_002950:PG1633|3end_galactokinase_1714619..1714769_POSITIVE 314 60 11 121 73 NC_002950:PG0571|3end_aspartate-semialdehyde_dehydrogenase_627492..627642_POSITIVE 305 59 12 63 19 NC_002950:PG1608|3end_methylmalonyl-CoA_decarboxylase,_beta_subunit_1688685..1688835_NEGATIVE 303 66 33 125 89 NC_002950:PG0655|3end_hypothetical_protein_706887..707037_POSITIVE 276 59 13 64 8 NC_002950:PG1512|3end_hypothetical_protein_1587813..1587963_NEGATIVE 275 66 29 147 109 NC_002950:PG1677|3end_phosphoglycerate_kinase_1763678..1763828_POSITIVE 274 38 4 61 22 NC_002950:PG0142|3end_SpoOJ_regulator_protein_164755..164905_NEGATIVE 270 59 12 56 8 NC_002950:PG1936|3end_ribosomal_protein_L23_2023199..2023349_NEGATIVE 265 83 41 70 24 NC_002950:PG1835|3end_lipoprotein,_putative_1928520..1928670_POSITIVE 262 77 32 69 31 NC_002950:PG1856|3end_cytidine/deoxycytidylate_deaminase_family_protein_1955484..1955634_NEGATIVE 260 88 41 97 49 NC_002950:PG2227|3end_hypothetical_protein_2342744..2342894_POSITIVE 260 88 42 148 108 NC_002950:PG0791|3end_adenylate_kinase_842593..842743_NEGATIVE 260 64 21 59 14 NC_002950:PG0054|3end_single-stranded-DNA-specific_exonuclease_RecJ_66899..67049_POSITIVE 259 52 12 151 105 NC_002950:PG0453|3end_hypothetical_protein_496670..496820_POSITIVE 257 64 24 55 4 NC_002950:PG0621|3end_hypothetical_protein_676020..676170_POSITIVE 255 79 35 74 28 NC_002950:PG0352|3end_sialidase,_putative_388847..388997_POSITIVE 254 37 3 145 102 NC_002950:PG0902|3end_alpha-1,2-mannosidase_family_protein_966746..966896_NEGATIVE 254 64 31 36 4 NC_002950:PG0637|3end_thiamine_monophosphate_kinase_689064..689214_NEGATIVE 253 60 13 150 92 NC_002950:PG1242|3end_replicative_DNA_helicase_1319101..1319251_POSITIVE