Origin IGS: ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt .........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 aagtatcttaggttacttgtttggttattaagtaatttcggccaaaagtacggttttttcatcggattagcacttttcaatccggctgtatgtccggaaaaaccgtgagagtcccactttacaggaccggtctctatacttggttcgaaaaaacaaaatgacgcacacgcttttcgcagggaataacagagcaaaaaagaggcacgactctcccgagcggtgcctccttcaaaaacatgagatcagataattacttcgtttctatatgaatgtgatcc Mask Tandem Repeat Region ================================================ ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt Find is-nt database================================================ Query_seq: PG0195:PG0196|PG0195:PG0196:rubrerythrin:peptidase, M16 family:->->:232765..233042 278 ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0195:PG0196|PG0195:PG0196:rubrerythrin:peptidase, M16 family:->->:232765..233042 278 ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0195:PG0196|PG0195:PG0196:rubrerythrin:peptidase, M16 family:->->:232765..233042 278 ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 41 End: 142 ........................................ M F L K E A P L G R V V P L F C S V I P C E K R V R H F V F S N Q V ........................................................................................................................................ Protein_Len: 40 Strand: + Start: 90 End: 209 ......................................................................................... M L F P A K S V C V I L F F R T K Y R D R S C K V G L S R F F R T Y S R I E K C ..................................................................... Protein_Len: 60 Strand: + Start: 85 End: 276 .................................................................................... M L C Y S L R K A C A S F C F F E P S I E T G P V K W D S H G F S G H T A G L K S A N P M K K P Y F W P K L L N N Q T S .. Protein_Len: 31 Strand: - Start: 121 End: 213 ........................................................................................................................ K T K E F W T Y L G T R Y L P V R V T K G S M C G S Q F T S M ................................................................. Protein_Len: 56 Strand: - Start: 32 End: 199 ............................... R I E H K Q L L C R E P S D H R K K A R N N G A F L T H T M K N K R V L Y L S R D Q L T P S E R N K R V Y L R M ............................................................................... ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt 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================================================ ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.0 Tail_Score: -5.27399 Start: 53 End: 80 Full_Region: CTCATGTTTTTGAAG GAGGCACCGCTC GGGA GAGTCGTGCCTC TTTTTTGCTCTGTTA ....................................................GAGGCACCGCTCGGGAGAGTCGTGCCTC...................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG0195:PG0196|PG0195:PG0196:rubrerythrin:peptidase, M16 family:->->:232765..233042 278 ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt Intra-Species Hit: Count: 1 Min: 1 Max: 278 Len: 278 Subject: NC_002950_PG0195_PG0196|rubrerythrin:peptidase, M16 family|POSITIVE:POSITIVE|[232765,233042]|278 HSP 1 e-value: 1.0E-156 bit: 551.0 Len: 278 Query Start:1 Query End:278 Subject Strand: POSITIVE Subject Start: 1 Subject End: 278 ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt ggatcacattcatatagaaacgaagtaattatctgatctcatgtttttgaaggaggcaccgctcgggagagtcgtgcctcttttttgctctgttattccctgcgaaaagcgtgtgcgtcattttgttttttcgaaccaagtatagagaccggtcctgtaaagtgggactctcacggtttttccggacatacagccggattgaaaagtgctaatccgatgaaaaaaccgtacttttggccgaaattacttaataaccaaacaagtaacctaagatactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAUCACAUUCAUAUAGAAACGAAGUAAUUAUCUGAUCUCAUGUUUUUGAAGGAGGCACCGCUCGGGAGAGUCGUGCCUCUUUUUUGCUCUGUUAUUCCCUGCGAAAAGCGUGUGCGUCAUUUUGUUUUUUCGAACCAAGUAUAGAGACCGGUCCUGUAAAGUGGGACUCUCACGGUUUUUCCGGACAUACAGCCGGAUUGAAAAGUGCUAAUCCGAUGAAAAAACCGUACUUUUGGCCGAAAUUACUUAAUAACCAAACAAGUAACCUAAGAUACUU ((......(((.....)))...((((((((......((((........(((((((((((.((((....)))).))))))))))).((((..(((.......((((((.(((....)))..)))))).......)))..))))..)))).(((.((...((((((((....((.(((.....)))))....((..(((((((........))))))).))......)).)))))).))))).)))))))).....))....(((((........))))) (-72.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAUCUUAGGUUACUUGUUUGGUUAUUAAGUAAUUUCGGCCAAAAGUACGGUUUUUUCAUCGGAUUAGCACUUUUCAAUCCGGCUGUAUGUCCGGAAAAACCGUGAGAGUCCCACUUUACAGGACCGGUCUCUAUACUUGGUUCGAAAAAACAAAAUGACGCACACGCUUUUCGCAGGGAAUAACAGAGCAAAAAAGAGGCACGACUCUCCCGAGCGGUGCCUCCUUCAAAAACAUGAGAUCAGAUAAUUACUUCGUUUCUAUAUGAAUGUGAUCC ..(.((((((.(((..((((((.((((((..((..((((((((((....((((((((((...(((((((((.............))))...)))))))))))))))((((((((.........))))...)))).....)))).))))))..))..............((.....))....)))))).))))))....(((((((..(((....)))..))))))).......))).))))))).....((((((((((......))))).))))).. (-72.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 426 73 32 170 113 NC_002950:PG0323|5end_hypothetical_protein_357388..357618_NEGATIVE 402 119 73 81 21 NC_002950:PG1566|5end_glutamyl-tRNA_synthetase_1647401..1647631_NEGATIVE 387 98 51 165 116 NC_002950:PG1369|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1450407..1450637_NEGATIVE 379 88 53 42 6 NC_002950:PG0574|5end_hypothetical_protein_629018..629248_POSITIVE 374 100 56 191 135 NC_002950:PG1732|5end_integrase/recombinase_XerD_1820171..1820401_POSITIVE 365 106 61 206 154 NC_002950:PG1276|5end_DNA-binding_protein,_histone-like_family_1352945..1353175_POSITIVE 365 106 61 206 154 NC_002950:PG0566|5end_DNA-binding_protein,_histone-like_family_623441..623671_NEGATIVE 364 96 52 225 182 NC_002950:PG0349|5end_hydrolase,_haloacid_dehalogenase-like_family_384459..384689_POSITIVE 357 94 52 207 164 NC_002950:PG1951|5end_glutaminyl-tRNA_synthetase_2041142..2041372_POSITIVE 355 119 71 47 3 NC_002950:PG2188|5end_diaminopimelate_decarboxylase_2295781..2296011_NEGATIVE 355 105 61 112 55 NC_002950:PG1027|5end_hypothetical_protein_1089439..1089669_NEGATIVE 353 119 71 149 104 NC_002950:PG1172|5end_iron-sulfur_cluster_binding_protein,_putative_1251173..1251403_POSITIVE 344 77 33 49 6 NC_002950:PG0246|5end_hypothetical_protein_281241..281471_NEGATIVE 337 80 34 218 150 NC_002950:PG0647|5end_iron_compound_ABC_transporter,_permease_protein_700113..700343_NEGATIVE 334 79 34 128 85 NC_002950:PG1354|5end_hydrolase,_carbon-nitrogen_family_1434765..1434995_NEGATIVE 334 83 45 116 72 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 334 118 71 122 50 NC_002950:PG0488|5end_Holliday_junction_DNA_helicase_RuvB_528169..528399_POSITIVE 332 210 161 166 109 NC_002950:PG0724|5end_prolyl_oligopeptidase_family_protein_775229..775459_POSITIVE 329 92 55 221 175 NC_002950:PG1179|5end_hypothetical_protein_1261132..1261362_NEGATIVE 329 77 31 60 11 NC_002950:PG0446|5end_thiF_protein_486599..486829_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 187 141 91 45 NC_002950:PG1411|3end_potassium_uptake_protein_TrkA,_putative_1493481..1493631_NEGATIVE 387 98 51 79 30 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 379 88 53 42 6 NC_002950:PG0573|3end_S-adenosyl-methyltransferase_MraW_629098..629248_POSITIVE 361 100 57 52 8 NC_002950:PG0516|3end_hypothetical_protein_557937..558087_NEGATIVE 353 119 71 71 26 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 353 217 174 101 49 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 348 76 32 65 9 NC_002950:PG1142|3end_exopolysaccharide_synthesis-related_protein_1224571..1224721_NEGATIVE 337 110 61 62 5 NC_002950:PG0130|3end_phosphoglyceromutase_151922..152072_NEGATIVE 334 117 73 150 109 NC_002950:PG1655|3end_hypothetical_protein_1737384..1737534_POSITIVE 334 79 34 131 88 NC_002950:PG1355|3end_acyltransferase,_putative_1434762..1434912_NEGATIVE 331 78 32 141 84 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 329 92 55 143 97 NC_002950:PG1180|3end_hypothetical_protein_1261210..1261360_NEGATIVE 328 185 141 125 80 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 325 98 52 69 17 NC_002950:PG0736|3end_ribonuclease_HII_786293..786443_POSITIVE 323 88 48 66 10 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 322 87 42 137 82 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 321 99 51 60 2 NC_002950:PG1634|3end_hypothetical_protein_1714723..1714873_NEGATIVE 320 188 147 71 19 NC_002950:PG0790|3end_GTP-binding_protein_Obg_841399..841549_NEGATIVE 318 75 36 73 23 NC_002950:PG1561|3end_dTDP-4-dehydrorhamnose_reductase_1640138..1640288_NEGATIVE 318 78 32 55 10 NC_002950:PG0731|3end_hypothetical_protein_782020..782170_NEGATIVE