Origin IGS: tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatttacgctctggaattttctcgtttactgtcccacaaaacgtggtgtgagaacttttctcttttggtctgggaagcaaaaaattctcgcgccacaacgaaaaagttctcgcgccacttttttcagagatattgctgtccggtaaaatttcttcag .........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 ctgaagaaattttaccggacagcaatatctctgaaaaaagtggcgcgagaactttttcgttgtggcgcgagaattttttgcttcccagaccaaaagagaaaagttctcacaccacgttttgtgggacagtaaacgagaaaattccagagcgtaaatcagccgaatgcgagatgagggggggacacggcgagacaataaaaaaggactgcacccaaaacttattggatgcagcccccatatactaagaagatggagctcgagagtctccga Mask Tandem Repeat Region ================================================ tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatttacgctctggaattttctcgtttactgtcccacaaaacgtggtgtgagaacttttctcttttggtctgggaagcaaaaaattctcgcgccacaacgaaaaagttctcgcgccacttttttcagagatattgctgtccggtaaaatttcttcag Find is-nt database================================================ Query_seq: PG0541:PG0542|PG0541:PG0542:hypothetical protein:hypothetical protein:-><-:595197..595466 270 tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatttacgctctggaattttctcgtttactgtcccacaaaacgtggtgtgagaacttttctcttttggtctgggaagcaaaaaattctcgcgccacaacgaaaaagttctcgcgccacttttttcagagatattgctgtccggtaaaatttcttcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0541:PG0542|PG0541:PG0542:hypothetical protein:hypothetical protein:-><-:595197..595466 270 tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatttacgctctggaattttctcgtttactgtcccacaaaacgtggtgtgagaacttttctcttttggtctgggaagcaaaaaattctcgcgccacaacgaaaaagttctcgcgccacttttttcagagatattgctgtccggtaaaatttcttcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0541:PG0542|PG0541:PG0542:hypothetical protein:hypothetical protein:-><-:595197..595466 270 tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatttacgctctggaattttctcgtttactgtcccacaaaacgtggtgtgagaacttttctcttttggtctgggaagcaaaaaattctcgcgccacaacgaaaaagttctcgcgccacttttttcagagatattgctgtccggtaaaatttcttcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 117 Max: 245 Len: 129 Subject: UniRef90_Q7MUH1 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 8.0E-9 bit: 61.6 Len: 129 Query Start:117 Query End:245 Subject Strand: null Subject Start: 9 Subject End: 51 .................................................................................................................... L R S G I F S F T V P Q N V V * E L F S F G L G S K K F S R H N E K V L A P L F S E I ......................... .................................................................................................................... L G S K I F P F A T P Q N A V R K L F Y F G V G S K K F S R H N E K I L A P L F Q G I ......................... tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttgctgtccggtaaaatttcttcag Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 33 End: 161 ................................ M G A A S N K F W V Q S F F I V S P C P P L I S H S A D L R S G I F S F T V P Q N V V ............................................................................................................. Protein_Len: 32 Strand: + Start: 161 End: 256 ................................................................................................................................................................ M R T F L F W S G K Q K I L A P Q R K S S R A T F F R D I A V R .............. Protein_Len: 60 Strand: + Start: 31 End: 270 .............................. M W G L H P I S F G C S P F L L S R R V P P S S R I R L I Y A L E F S R L L S H K T W C E N F S L L V W E A K N S R A T Protein_Len: 43 Strand: - Start: 142 End: 270 ............................................................................................................................................. Q G V F R P T L V K R K Q D P F C F I R A G C R F L E R A V K K L S I A T R Y F K K M Protein_Len: 30 Strand: - Start: 120 End: 209 ....................................................................................................................... A R S N E R K S D W L V H H S F K E R K T Q S A F F E R A M ............................................................. Protein_Len: 60 Strand: - Start: 29 End: 262 ............................ G H G G R M E C E A S K R E P I K E N V T G C F T T H S S K E K P R P L L F N E R W L S F T R A G S K E S I N S D P L M ........ Protein_Len: 38 Strand: - Start: 3 End: 116 .. S V R S S W R R L I H P S C G I L K P H L G K K N D R R T G G E D R M R S M .......................................................................................................................................................... tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttgctgtccggtaaaatttcttcag 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: 82 Start: 233 End: 262 ........................................................................................................................................................................................................................................TTTTTCAGAGATATTGCTGTCCGGTAAAAT........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttgctgtccggtaaaatttcttcag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.1 Tail_Score: -5.60689 Start: 37 End: 68 Full_Region: CTTCTTAGTATATGG GGGCTGCATCCAA TAAGTT TTGGGTGCAGTCC TTTTTTATTGTCTCG ....................................GGGCTGCATCCAATAAGTTTTGGGTGCAGTCC.......................................................................................................................................................................................................... TransTerm Strand: - Conf: 60 HP_score: -2.7 Tail_Score: -4.3739 Start: 155 End: 210 Full_Region: cgagaactttttcgt tgtggcgcgagaattttttgctt cccagaccaa aagagaaaagttctcacaccacg ttttgtgggacagta ..........................................................................................................................................................tgtggcgcgagaattttttgcttcccagaccaaaagagaaaagttctcacaccacg............................................................ TransTerm Strand: + Conf: 72 HP_score: -6.3 Tail_Score: -4.34402 Start: 163 End: 175 Full_Region: CACAAAACGTGGTGT GAGAA CTT TTCTC TTTTGGTCTGGGAAG ..................................................................................................................................................................GAGAACTTTTCTC............................................................................................... Find igs database================================================ Query_seq: PG0541:PG0542|PG0541:PG0542:hypothetical protein:hypothetical protein:-><-:595197..595466 270 tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttgctgtccggtaaaatttcttcag Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_002950_PG0541_PG0542|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[595197,595466]|270 HSP 1 e-value: 2.0E-59 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgat.......................................................................................................................................................... tcggagactctcgagctccatcttcttagtatatgggggctgcatccaataagttttgggtgcagtccttttttattgtctcgccgtgtccccccctcatctcgcattcggctgat.......................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGAGACUCUCGAGCUCCAUCUUCUUAGUAUAUGGGGGCUGCAUCCAAUAAGUUUUGGGUGCAGUCCUUUUUUAUUGUCUCGCCGUGUCCCCCCCUCAUCUCGCAUUCGGCUGAU ..((((.((....)))))).......(((((...(((((((((((((((......)))))))))))))))...)))))....(((((((..............)))..)))).... (-39.34) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAGCCGAAUGCGAGAUGAGGGGGGGACACGGCGAGACAAUAAAAAAGGACUGCACCCAAAACUUAUUGGAUGCAGCCCCCAUAUACUAAGAAGAUGGAGCUCGAGAGUCUCCGA .(((.(((....)).).)))...((((((.(..((((.(.........((.(((((.((((......)))).))))))).((((...........)))).))))).).)))))).. (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 502 48 1 228 181 NC_002950:PG0356|5end_hypothetical_protein_390611..390841_POSITIVE 402 110 61 187 125 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 376 80 33 183 128 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 358 100 51 114 58 NC_002950:PG0920|5end_glycosyl_transferase,_group_2_family_protein_981025..981255_NEGATIVE 349 47 8 199 155 NC_002950:PG1522|5end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1600170..1600400_NEGATIVE 342 48 2 90 45 NC_002950:PG0295|5end_DNA_processing_protein_DprA,_putative_331300..331530_NEGATIVE 333 99 54 231 184 NC_002950:PG0687|5end_succinate-semialdehyde_dehydrogenase_744523..744753_NEGATIVE 332 50 9 198 163 NC_002950:PG0417|5end_ATP-dependent_protease_ATP-binding_subunit_458624..458854_NEGATIVE 325 90 42 231 164 NC_002950:PG1282|5end_hypothetical_protein_1360035..1360265_POSITIVE 325 48 1 138 69 NC_002950:PG1211|5end_hexapeptide_transferase_family_protein_1290801..1291031_POSITIVE 317 110 66 62 8 NC_002950:PG1728|5end_cytidine/deoxycytidylate_deaminase_family_protein_1817644..1817874_POSITIVE 311 47 3 64 22 NC_002950:PG1324|5end_Holliday_junction_resolvase_1403431..1403661_NEGATIVE 308 48 1 217 171 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 305 67 26 190 138 NC_002950:PG0868|5end_mobilization_protein_931853..932083_NEGATIVE 303 47 3 173 124 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 301 79 32 163 111 NC_002950:PG2142|5end_GTP-binding_protein_Era_2247585..2247815_POSITIVE 301 60 12 73 22 NC_002950:PG1583|5end_batB_protein_1660315..1660545_POSITIVE 301 47 1 220 175 NC_002950:PG0831|5end_hypothetical_protein_887403..887633_POSITIVE 300 59 11 177 115 NC_002950:PG2048|5end_hypothetical_protein_2148514..2148744_NEGATIVE 300 86 42 44 2 NC_002950:PG0573|5end_S-adenosyl-methyltransferase_MraW_628083..628313_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 68 21 61 2 NC_002950:PG0186|3end_lipoprotein_RagB_222997..223147_POSITIVE 376 80 33 70 15 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 371 68 31 54 15 NC_002950:PG0541|3end_hypothetical_protein_595136..595286_POSITIVE 346 77 35 95 49 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 342 48 2 97 52 NC_002950:PG0296|3end_phosphoribosylformylglycinamidine_synthase_331293..331443_NEGATIVE 338 110 62 74 29 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 329 47 2 96 52 NC_002950:PG1244|3end_ISPg1,_transposase_1320699..1320849_POSITIVE 329 47 2 96 52 NC_002950:PG0549|3end_ISPg1,_transposase_605987..606137_NEGATIVE 329 47 2 96 52 NC_002950:PG0460|3end_ISPg1,_transposase_503102..503252_POSITIVE 327 44 1 122 74 NC_002950:PG0635|3end_ribosomal_protein_L11_methyltransferase_686838..686988_NEGATIVE 319 68 28 47 6 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 317 80 34 62 23 NC_002950:PG0435|3end_capsular_polysaccharide_biosythesis_protein,_putative_472708..472858_NEGATIVE 309 100 55 76 13 NC_002950:PG2125|3end_transcriptional_regulator,_AraC_family_2231376..2231526_NEGATIVE 309 97 51 120 70 NC_002950:PG1205|3end_DNA-binding_protein,_histone-like_family_1284503..1284653_POSITIVE 308 79 33 69 26 NC_002950:PG1321|3end_formate--tetrahydrofolate_ligase_1399656..1399806_NEGATIVE 308 48 1 137 91 NC_002950:PG0283|3end_efflux_transporter,_MFP_component,_RND_family_316995..317145_NEGATIVE 306 98 51 74 18 NC_002950:PG0626|3end_hypothetical_protein_680346..680496_POSITIVE 303 110 65 56 6 NC_002950:PG0731|3end_hypothetical_protein_782020..782170_NEGATIVE 302 110 62 70 23 NC_002950:PG0062|3end_TPR_domain_protein_75810..75960_POSITIVE 301 79 32 84 32 NC_002950:PG2141|3end_3-oxoacyl-(acyl_carrier_protein)_synthase_2247586..2247736_POSITIVE