Multiple sequence alignment - TraesCS6D01G224500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G224500 chr6D 100.000 2772 0 0 1 2772 316413055 316410284 0.000000e+00 5120.0
1 TraesCS6D01G224500 chr6D 83.133 581 74 13 2213 2772 417460592 417460015 2.460000e-140 508.0
2 TraesCS6D01G224500 chr6D 83.397 524 54 20 2213 2716 67870882 67871392 3.250000e-124 455.0
3 TraesCS6D01G224500 chr6D 77.797 581 95 21 2213 2772 316410017 316410584 7.400000e-86 327.0
4 TraesCS6D01G224500 chr6D 89.412 85 8 1 2300 2384 172115694 172115611 3.780000e-19 106.0
5 TraesCS6D01G224500 chr6B 94.126 732 39 2 542 1270 508184385 508185115 0.000000e+00 1110.0
6 TraesCS6D01G224500 chr6B 90.724 539 29 7 1294 1832 508185205 508185722 0.000000e+00 699.0
7 TraesCS6D01G224500 chr6B 91.316 380 17 7 82 459 508184020 508184385 3.190000e-139 505.0
8 TraesCS6D01G224500 chr6B 78.938 546 87 17 2213 2736 628901893 628901354 2.040000e-91 346.0
9 TraesCS6D01G224500 chr6B 87.747 253 27 3 2515 2764 628901361 628901612 2.700000e-75 292.0
10 TraesCS6D01G224500 chr6B 85.714 196 19 4 1818 2007 508185746 508185938 6.060000e-47 198.0
11 TraesCS6D01G224500 chr6B 82.353 221 20 7 1992 2208 508185959 508186164 1.020000e-39 174.0
12 TraesCS6D01G224500 chr6A 92.543 751 31 8 545 1270 454350130 454349380 0.000000e+00 1053.0
13 TraesCS6D01G224500 chr6A 92.412 738 29 7 1308 2039 454349293 454348577 0.000000e+00 1027.0
14 TraesCS6D01G224500 chr6A 92.291 454 15 5 1 451 454350573 454350137 6.520000e-176 627.0
15 TraesCS6D01G224500 chr1B 81.724 580 85 12 2213 2772 464104839 464105417 5.410000e-127 464.0
16 TraesCS6D01G224500 chr1B 79.196 572 95 19 2214 2764 348496012 348495444 2.610000e-100 375.0
17 TraesCS6D01G224500 chr1B 83.003 353 53 7 2425 2772 348495388 348495738 2.070000e-81 313.0
18 TraesCS6D01G224500 chr1B 87.895 190 22 1 2214 2402 348493414 348493603 3.590000e-54 222.0
19 TraesCS6D01G224500 chr5B 81.851 562 72 18 2214 2754 486270992 486271544 1.960000e-121 446.0
20 TraesCS6D01G224500 chr5B 82.979 94 9 6 455 546 369953317 369953405 8.230000e-11 78.7
21 TraesCS6D01G224500 chr2B 81.204 548 82 13 2215 2742 442089226 442088680 3.300000e-114 422.0
22 TraesCS6D01G224500 chr5D 80.420 572 87 13 2213 2762 125961375 125961943 1.990000e-111 412.0
23 TraesCS6D01G224500 chr5A 80.115 523 69 15 2214 2721 540388319 540388821 9.440000e-95 357.0
24 TraesCS6D01G224500 chr2A 79.158 499 84 13 2250 2731 496462939 496462444 7.400000e-86 327.0
25 TraesCS6D01G224500 chr2A 83.704 135 22 0 2278 2412 21553352 21553218 8.060000e-26 128.0
26 TraesCS6D01G224500 chr4D 77.187 583 100 17 2214 2772 474985025 474984452 2.680000e-80 309.0
27 TraesCS6D01G224500 chr3D 77.799 536 95 17 2248 2764 134345587 134345057 2.680000e-80 309.0
28 TraesCS6D01G224500 chr3D 82.734 278 32 5 2213 2474 10380937 10381214 1.660000e-57 233.0
29 TraesCS6D01G224500 chr3D 85.393 178 18 3 2214 2391 5396849 5397018 7.890000e-41 178.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G224500 chr6D 316410284 316413055 2771 True 5120.000000 5120 100.000000 1 2772 1 chr6D.!!$R2 2771
1 TraesCS6D01G224500 chr6D 417460015 417460592 577 True 508.000000 508 83.133000 2213 2772 1 chr6D.!!$R3 559
2 TraesCS6D01G224500 chr6D 67870882 67871392 510 False 455.000000 455 83.397000 2213 2716 1 chr6D.!!$F1 503
3 TraesCS6D01G224500 chr6D 316410017 316410584 567 False 327.000000 327 77.797000 2213 2772 1 chr6D.!!$F2 559
4 TraesCS6D01G224500 chr6B 508184020 508186164 2144 False 537.200000 1110 88.846600 82 2208 5 chr6B.!!$F2 2126
5 TraesCS6D01G224500 chr6B 628901354 628901893 539 True 346.000000 346 78.938000 2213 2736 1 chr6B.!!$R1 523
6 TraesCS6D01G224500 chr6A 454348577 454350573 1996 True 902.333333 1053 92.415333 1 2039 3 chr6A.!!$R1 2038
7 TraesCS6D01G224500 chr1B 464104839 464105417 578 False 464.000000 464 81.724000 2213 2772 1 chr1B.!!$F1 559
8 TraesCS6D01G224500 chr1B 348495444 348496012 568 True 375.000000 375 79.196000 2214 2764 1 chr1B.!!$R1 550
9 TraesCS6D01G224500 chr1B 348493414 348495738 2324 False 267.500000 313 85.449000 2214 2772 2 chr1B.!!$F2 558
10 TraesCS6D01G224500 chr5B 486270992 486271544 552 False 446.000000 446 81.851000 2214 2754 1 chr5B.!!$F2 540
11 TraesCS6D01G224500 chr2B 442088680 442089226 546 True 422.000000 422 81.204000 2215 2742 1 chr2B.!!$R1 527
12 TraesCS6D01G224500 chr5D 125961375 125961943 568 False 412.000000 412 80.420000 2213 2762 1 chr5D.!!$F1 549
13 TraesCS6D01G224500 chr5A 540388319 540388821 502 False 357.000000 357 80.115000 2214 2721 1 chr5A.!!$F1 507
14 TraesCS6D01G224500 chr4D 474984452 474985025 573 True 309.000000 309 77.187000 2214 2772 1 chr4D.!!$R1 558
15 TraesCS6D01G224500 chr3D 134345057 134345587 530 True 309.000000 309 77.799000 2248 2764 1 chr3D.!!$R1 516

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
76 77 0.105224 CAGCAGAGCTCCTGATCCAG 59.895 60.0 10.93 0.0 45.78 3.86 F
472 476 0.108281 GGTACTGCCTCTTCGGTTCC 60.108 60.0 0.00 0.0 34.25 3.62 F
1248 1277 0.041238 TAGAGCACAGCCCTACCAGT 59.959 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1145 0.179015 TTTTGTCGCTTGCCCAGGTA 60.179 50.0 0.00 0.00 0.00 3.08 R
1714 1810 0.325933 CAACCAGAGAGCCCATCACA 59.674 55.0 0.00 0.00 0.00 3.58 R
2066 2244 0.817013 CCTTACAAGTACCGGCGGTA 59.183 55.0 33.42 33.42 37.09 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.342942 GTTGTACACAGTACTTTTAGTTCAGC 58.657 38.462 0.00 0.00 0.00 4.26
29 30 6.575267 TGTACACAGTACTTTTAGTTCAGCA 58.425 36.000 8.57 0.00 0.00 4.41
30 31 7.214381 TGTACACAGTACTTTTAGTTCAGCAT 58.786 34.615 8.57 0.00 0.00 3.79
38 39 9.297037 AGTACTTTTAGTTCAGCATGGTTATTT 57.703 29.630 0.00 0.00 36.16 1.40
50 51 6.808212 CAGCATGGTTATTTAAGACAAACTGG 59.192 38.462 0.00 0.00 0.00 4.00
58 59 4.715534 TTAAGACAAACTGGGTGATCCA 57.284 40.909 0.00 0.00 44.79 3.41
72 73 1.050204 GATCCAGCAGAGCTCCTGAT 58.950 55.000 18.41 9.30 45.78 2.90
73 74 1.001181 GATCCAGCAGAGCTCCTGATC 59.999 57.143 18.41 14.24 45.78 2.92
74 75 1.047596 TCCAGCAGAGCTCCTGATCC 61.048 60.000 18.41 2.56 45.78 3.36
75 76 1.335882 CCAGCAGAGCTCCTGATCCA 61.336 60.000 18.41 0.00 45.78 3.41
76 77 0.105224 CAGCAGAGCTCCTGATCCAG 59.895 60.000 10.93 0.00 45.78 3.86
77 78 1.227615 GCAGAGCTCCTGATCCAGC 60.228 63.158 10.93 0.00 45.78 4.85
78 79 1.446791 CAGAGCTCCTGATCCAGCC 59.553 63.158 10.93 0.00 45.78 4.85
79 80 1.765657 AGAGCTCCTGATCCAGCCC 60.766 63.158 10.93 0.00 36.17 5.19
80 81 2.041762 AGCTCCTGATCCAGCCCA 59.958 61.111 5.10 0.00 36.17 5.36
348 350 7.747357 GCTTTCTTTCCAAATTATGCACATTTG 59.253 33.333 19.71 19.71 40.11 2.32
399 402 4.576873 TGTTTTGCGTTCCTTGATGTTCTA 59.423 37.500 0.00 0.00 0.00 2.10
443 447 7.441836 TGCTTTTCAGTTCAGACAGTTCTATA 58.558 34.615 0.00 0.00 0.00 1.31
466 470 5.904362 AAAAATGATGGTACTGCCTCTTC 57.096 39.130 0.00 0.00 38.35 2.87
467 471 2.898729 ATGATGGTACTGCCTCTTCG 57.101 50.000 0.00 0.00 38.35 3.79
468 472 0.824109 TGATGGTACTGCCTCTTCGG 59.176 55.000 0.00 0.00 38.35 4.30
469 473 0.824759 GATGGTACTGCCTCTTCGGT 59.175 55.000 0.00 0.00 38.35 4.69
470 474 1.207329 GATGGTACTGCCTCTTCGGTT 59.793 52.381 0.00 0.00 38.35 4.44
471 475 0.606604 TGGTACTGCCTCTTCGGTTC 59.393 55.000 0.00 0.00 38.35 3.62
472 476 0.108281 GGTACTGCCTCTTCGGTTCC 60.108 60.000 0.00 0.00 34.25 3.62
473 477 0.606604 GTACTGCCTCTTCGGTTCCA 59.393 55.000 0.00 0.00 34.25 3.53
474 478 1.207329 GTACTGCCTCTTCGGTTCCAT 59.793 52.381 0.00 0.00 34.25 3.41
475 479 1.568504 ACTGCCTCTTCGGTTCCATA 58.431 50.000 0.00 0.00 34.25 2.74
476 480 1.906574 ACTGCCTCTTCGGTTCCATAA 59.093 47.619 0.00 0.00 34.25 1.90
477 481 2.505819 ACTGCCTCTTCGGTTCCATAAT 59.494 45.455 0.00 0.00 34.25 1.28
478 482 3.709653 ACTGCCTCTTCGGTTCCATAATA 59.290 43.478 0.00 0.00 34.25 0.98
479 483 4.348168 ACTGCCTCTTCGGTTCCATAATAT 59.652 41.667 0.00 0.00 34.25 1.28
480 484 5.542635 ACTGCCTCTTCGGTTCCATAATATA 59.457 40.000 0.00 0.00 34.25 0.86
481 485 6.042781 ACTGCCTCTTCGGTTCCATAATATAA 59.957 38.462 0.00 0.00 34.25 0.98
482 486 6.833041 TGCCTCTTCGGTTCCATAATATAAA 58.167 36.000 0.00 0.00 34.25 1.40
483 487 7.284074 TGCCTCTTCGGTTCCATAATATAAAA 58.716 34.615 0.00 0.00 34.25 1.52
484 488 7.444183 TGCCTCTTCGGTTCCATAATATAAAAG 59.556 37.037 0.00 0.00 34.25 2.27
485 489 7.573283 GCCTCTTCGGTTCCATAATATAAAAGC 60.573 40.741 0.00 0.00 34.25 3.51
486 490 7.444183 CCTCTTCGGTTCCATAATATAAAAGCA 59.556 37.037 0.00 0.00 0.00 3.91
487 491 8.918202 TCTTCGGTTCCATAATATAAAAGCAT 57.082 30.769 0.00 0.00 0.00 3.79
488 492 9.349713 TCTTCGGTTCCATAATATAAAAGCATT 57.650 29.630 0.00 0.00 0.00 3.56
489 493 9.965824 CTTCGGTTCCATAATATAAAAGCATTT 57.034 29.630 0.00 0.00 42.41 2.32
502 506 4.766404 AAAGCATTTTTAGCGCTAGTGT 57.234 36.364 17.98 2.64 31.62 3.55
503 507 5.873179 AAAGCATTTTTAGCGCTAGTGTA 57.127 34.783 17.98 0.00 31.62 2.90
504 508 5.470845 AAGCATTTTTAGCGCTAGTGTAG 57.529 39.130 17.98 10.15 34.11 2.74
505 509 4.504858 AGCATTTTTAGCGCTAGTGTAGT 58.495 39.130 17.98 0.46 37.01 2.73
506 510 4.330074 AGCATTTTTAGCGCTAGTGTAGTG 59.670 41.667 17.98 13.28 39.26 2.74
514 518 3.183237 CGCTAGTGTAGTGCCAAAAAC 57.817 47.619 0.00 0.00 0.00 2.43
515 519 2.546368 CGCTAGTGTAGTGCCAAAAACA 59.454 45.455 0.00 0.00 0.00 2.83
516 520 3.002862 CGCTAGTGTAGTGCCAAAAACAA 59.997 43.478 0.00 0.00 0.00 2.83
517 521 4.320202 CGCTAGTGTAGTGCCAAAAACAAT 60.320 41.667 0.00 0.00 0.00 2.71
518 522 5.154222 GCTAGTGTAGTGCCAAAAACAATC 58.846 41.667 0.00 0.00 0.00 2.67
519 523 5.048713 GCTAGTGTAGTGCCAAAAACAATCT 60.049 40.000 0.00 0.00 0.00 2.40
520 524 5.852282 AGTGTAGTGCCAAAAACAATCTT 57.148 34.783 0.00 0.00 0.00 2.40
521 525 6.952773 AGTGTAGTGCCAAAAACAATCTTA 57.047 33.333 0.00 0.00 0.00 2.10
522 526 7.524717 AGTGTAGTGCCAAAAACAATCTTAT 57.475 32.000 0.00 0.00 0.00 1.73
523 527 8.630054 AGTGTAGTGCCAAAAACAATCTTATA 57.370 30.769 0.00 0.00 0.00 0.98
524 528 9.243105 AGTGTAGTGCCAAAAACAATCTTATAT 57.757 29.630 0.00 0.00 0.00 0.86
525 529 9.855021 GTGTAGTGCCAAAAACAATCTTATATT 57.145 29.630 0.00 0.00 0.00 1.28
574 578 6.099341 AGAAAATTTACCCTGCTAATTTGCG 58.901 36.000 7.37 2.67 33.78 4.85
587 591 4.676924 GCTAATTTGCGGTTGCTGATATTC 59.323 41.667 0.00 0.00 43.34 1.75
644 651 6.624352 TGAAATTAGCTGGTCAATATGAGC 57.376 37.500 0.00 2.74 44.54 4.26
711 728 5.691508 TCTTTAGCGCTAACGTATTTGAC 57.308 39.130 28.76 0.00 42.83 3.18
948 965 1.331756 GCCATCCTTGTACTCGCATTG 59.668 52.381 0.00 0.00 0.00 2.82
995 1018 2.979678 AGCCTCCAAGACCTTAACTTGA 59.020 45.455 0.00 0.00 44.92 3.02
1119 1145 1.654954 CTAGCGGCGTGGACTACAGT 61.655 60.000 9.37 0.00 0.00 3.55
1179 1205 4.157817 GGTACGTGGTGCAGTACG 57.842 61.111 18.05 18.05 42.86 3.67
1196 1222 4.904724 CAGTACGACGATCATTGCTAGTAC 59.095 45.833 0.00 0.00 34.97 2.73
1204 1230 3.688694 TCATTGCTAGTACCAACGGTT 57.311 42.857 0.00 0.00 37.09 4.44
1211 1237 4.708421 TGCTAGTACCAACGGTTCTCTTAT 59.292 41.667 0.00 0.00 35.10 1.73
1217 1243 8.019656 AGTACCAACGGTTCTCTTATTGATAT 57.980 34.615 0.00 0.00 37.09 1.63
1239 1268 1.404851 GGACCTCAAGTAGAGCACAGC 60.405 57.143 0.00 0.00 43.31 4.40
1240 1269 0.610687 ACCTCAAGTAGAGCACAGCC 59.389 55.000 0.00 0.00 43.31 4.85
1248 1277 0.041238 TAGAGCACAGCCCTACCAGT 59.959 55.000 0.00 0.00 0.00 4.00
1252 1281 0.250727 GCACAGCCCTACCAGTTTGA 60.251 55.000 0.00 0.00 0.00 2.69
1270 1299 7.202526 CAGTTTGACAAAATGGTTCATGTACT 58.797 34.615 18.29 0.00 33.17 2.73
1271 1300 7.167968 CAGTTTGACAAAATGGTTCATGTACTG 59.832 37.037 18.29 6.88 33.17 2.74
1272 1301 6.707440 TTGACAAAATGGTTCATGTACTGT 57.293 33.333 2.29 0.00 0.00 3.55
1273 1302 7.809546 TTGACAAAATGGTTCATGTACTGTA 57.190 32.000 2.29 0.00 0.00 2.74
1274 1303 7.433708 TGACAAAATGGTTCATGTACTGTAG 57.566 36.000 2.29 0.00 0.00 2.74
1275 1304 6.995686 TGACAAAATGGTTCATGTACTGTAGT 59.004 34.615 2.29 0.00 0.00 2.73
1276 1305 7.172532 TGACAAAATGGTTCATGTACTGTAGTC 59.827 37.037 2.29 4.93 0.00 2.59
1278 1307 6.374417 AAATGGTTCATGTACTGTAGTCCT 57.626 37.500 2.29 0.00 0.00 3.85
1280 1309 3.767673 TGGTTCATGTACTGTAGTCCTCC 59.232 47.826 2.29 0.00 0.00 4.30
1281 1310 3.767673 GGTTCATGTACTGTAGTCCTCCA 59.232 47.826 2.29 0.00 0.00 3.86
1283 1312 4.317530 TCATGTACTGTAGTCCTCCAGT 57.682 45.455 0.00 0.00 43.90 4.00
1287 1316 2.875094 ACTGTAGTCCTCCAGTACGT 57.125 50.000 0.00 0.00 40.03 3.57
1288 1317 3.988976 ACTGTAGTCCTCCAGTACGTA 57.011 47.619 0.00 0.00 40.03 3.57
1289 1318 3.604582 ACTGTAGTCCTCCAGTACGTAC 58.395 50.000 18.10 18.10 40.03 3.67
1291 1320 4.260170 CTGTAGTCCTCCAGTACGTACTT 58.740 47.826 25.35 11.85 33.96 2.24
1292 1321 5.046304 ACTGTAGTCCTCCAGTACGTACTTA 60.046 44.000 25.35 15.22 40.03 2.24
1314 1410 7.499232 ACTTACTGATTAGTTTCTTTGTGTGCT 59.501 33.333 0.00 0.00 38.36 4.40
1427 1523 2.358737 GCGACCAGGACACCAAGG 60.359 66.667 0.00 0.00 0.00 3.61
1636 1732 4.648626 TCGACGTCCACGACCCCT 62.649 66.667 10.58 0.00 43.02 4.79
1779 1875 1.126488 CTGATGGGCTAGGCAAGAGA 58.874 55.000 19.14 0.00 0.00 3.10
1781 1877 1.127343 GATGGGCTAGGCAAGAGACT 58.873 55.000 19.14 0.00 36.68 3.24
1814 1910 2.622436 CCTTCTCCGAATTGTCCAGTC 58.378 52.381 0.00 0.00 0.00 3.51
1816 1912 0.530744 TCTCCGAATTGTCCAGTCCG 59.469 55.000 0.00 0.00 0.00 4.79
1822 1918 0.872388 AATTGTCCAGTCCGCGTTTC 59.128 50.000 4.92 0.00 0.00 2.78
1924 2061 2.030981 GTGGTAGATCCTCCGATTCGAC 60.031 54.545 7.83 0.00 37.07 4.20
1928 2065 1.797211 GATCCTCCGATTCGACCGCT 61.797 60.000 7.83 0.00 0.00 5.52
1971 2108 7.519649 GCACTTTGAAATATAGACTCTCCATGC 60.520 40.741 0.00 0.00 0.00 4.06
1972 2109 6.995091 ACTTTGAAATATAGACTCTCCATGCC 59.005 38.462 0.00 0.00 0.00 4.40
2016 2194 2.109609 TCGTGTTATCGGATGTACGC 57.890 50.000 14.47 11.29 0.00 4.42
2059 2237 3.741029 CGGTCCACGTGAAGATGAT 57.259 52.632 19.30 0.00 37.93 2.45
2060 2238 2.010145 CGGTCCACGTGAAGATGATT 57.990 50.000 19.30 0.00 37.93 2.57
2061 2239 2.346803 CGGTCCACGTGAAGATGATTT 58.653 47.619 19.30 0.00 37.93 2.17
2062 2240 2.094258 CGGTCCACGTGAAGATGATTTG 59.906 50.000 19.30 0.00 37.93 2.32
2063 2241 3.074412 GGTCCACGTGAAGATGATTTGT 58.926 45.455 19.30 0.00 0.00 2.83
2064 2242 4.250464 GGTCCACGTGAAGATGATTTGTA 58.750 43.478 19.30 0.00 0.00 2.41
2066 2244 5.354234 GGTCCACGTGAAGATGATTTGTATT 59.646 40.000 19.30 0.00 0.00 1.89
2067 2245 6.537301 GGTCCACGTGAAGATGATTTGTATTA 59.463 38.462 19.30 0.00 0.00 0.98
2068 2246 7.399523 GTCCACGTGAAGATGATTTGTATTAC 58.600 38.462 19.30 0.00 0.00 1.89
2069 2247 6.537301 TCCACGTGAAGATGATTTGTATTACC 59.463 38.462 19.30 0.00 0.00 2.85
2070 2248 6.410845 CACGTGAAGATGATTTGTATTACCG 58.589 40.000 10.90 0.00 0.00 4.02
2071 2249 5.006358 ACGTGAAGATGATTTGTATTACCGC 59.994 40.000 0.00 0.00 0.00 5.68
2072 2250 5.558273 CGTGAAGATGATTTGTATTACCGCC 60.558 44.000 0.00 0.00 0.00 6.13
2073 2251 4.509970 TGAAGATGATTTGTATTACCGCCG 59.490 41.667 0.00 0.00 0.00 6.46
2074 2252 3.399330 AGATGATTTGTATTACCGCCGG 58.601 45.455 0.00 0.00 0.00 6.13
2075 2253 2.695127 TGATTTGTATTACCGCCGGT 57.305 45.000 15.63 15.63 40.16 5.28
2076 2254 3.815856 TGATTTGTATTACCGCCGGTA 57.184 42.857 12.92 12.92 37.09 4.02
2077 2255 3.456280 TGATTTGTATTACCGCCGGTAC 58.544 45.455 17.03 8.23 37.97 3.34
2078 2256 3.132646 TGATTTGTATTACCGCCGGTACT 59.867 43.478 17.03 13.74 37.97 2.73
2079 2257 3.608316 TTTGTATTACCGCCGGTACTT 57.392 42.857 17.03 9.29 37.97 2.24
2084 2262 2.652941 TTACCGCCGGTACTTGTAAG 57.347 50.000 17.03 0.00 37.97 2.34
2093 2271 3.492313 CGGTACTTGTAAGGTACACGTC 58.508 50.000 1.31 0.00 39.90 4.34
2098 2276 6.749118 GGTACTTGTAAGGTACACGTCTATTG 59.251 42.308 1.31 0.00 39.90 1.90
2103 2281 6.151691 TGTAAGGTACACGTCTATTGAACAC 58.848 40.000 0.00 0.00 32.89 3.32
2104 2282 4.859304 AGGTACACGTCTATTGAACACA 57.141 40.909 0.00 0.00 0.00 3.72
2208 2387 7.613585 TGTAGATGTGGGTTTAATTCTCGTAA 58.386 34.615 0.00 0.00 0.00 3.18
2209 2388 6.980051 AGATGTGGGTTTAATTCTCGTAAC 57.020 37.500 0.00 0.00 0.00 2.50
2210 2389 6.469410 AGATGTGGGTTTAATTCTCGTAACA 58.531 36.000 0.00 0.00 0.00 2.41
2211 2390 7.110155 AGATGTGGGTTTAATTCTCGTAACAT 58.890 34.615 0.00 0.00 0.00 2.71
2256 2437 8.744568 TTGATTTGCCCTTAAATTCAAAAACT 57.255 26.923 0.00 0.00 32.97 2.66
2339 2522 6.087555 CCGACATTTTGAAAACTTCATAACGG 59.912 38.462 0.00 0.00 39.84 4.44
2457 4407 6.475596 TCTCAGTTTGAGCTCATATGATCA 57.524 37.500 19.04 5.38 43.95 2.92
2460 4410 6.589135 TCAGTTTGAGCTCATATGATCACAT 58.411 36.000 19.04 0.00 40.16 3.21
2704 4667 3.518634 AACTTTCCAAGCGCTCAAAAA 57.481 38.095 12.06 10.49 0.00 1.94
2725 4688 6.949578 AAAAATCGTCAATGTTTGCCATAG 57.050 33.333 0.00 0.00 31.97 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.040062 TCACCCAGTTTGTCTTAAATAACCATG 60.040 37.037 0.00 0.00 0.00 3.66
29 30 7.007723 TCACCCAGTTTGTCTTAAATAACCAT 58.992 34.615 0.00 0.00 0.00 3.55
30 31 6.366340 TCACCCAGTTTGTCTTAAATAACCA 58.634 36.000 0.00 0.00 0.00 3.67
50 51 1.145819 GGAGCTCTGCTGGATCACC 59.854 63.158 14.64 0.00 39.88 4.02
58 59 1.688269 GCTGGATCAGGAGCTCTGCT 61.688 60.000 14.64 0.00 43.06 4.24
234 236 4.035278 TGAACCGTTGAACAAACCAATC 57.965 40.909 0.00 0.00 35.13 2.67
348 350 8.020861 TGACATAACAAATAGACCGTTTGTAC 57.979 34.615 4.86 0.00 46.01 2.90
458 462 4.974645 ATATTATGGAACCGAAGAGGCA 57.025 40.909 0.00 0.00 46.52 4.75
459 463 7.573283 GCTTTTATATTATGGAACCGAAGAGGC 60.573 40.741 0.00 0.00 46.52 4.70
461 465 8.378172 TGCTTTTATATTATGGAACCGAAGAG 57.622 34.615 0.00 0.00 0.00 2.85
462 466 8.918202 ATGCTTTTATATTATGGAACCGAAGA 57.082 30.769 0.00 0.00 0.00 2.87
463 467 9.965824 AAATGCTTTTATATTATGGAACCGAAG 57.034 29.630 0.00 0.00 0.00 3.79
470 474 9.405587 GCGCTAAAAATGCTTTTATATTATGGA 57.594 29.630 0.00 0.00 36.61 3.41
471 475 9.410556 AGCGCTAAAAATGCTTTTATATTATGG 57.589 29.630 8.99 0.00 36.61 2.74
475 479 9.450807 CACTAGCGCTAAAAATGCTTTTATATT 57.549 29.630 19.37 0.00 40.06 1.28
476 480 8.621286 ACACTAGCGCTAAAAATGCTTTTATAT 58.379 29.630 19.37 0.00 40.06 0.86
477 481 7.981142 ACACTAGCGCTAAAAATGCTTTTATA 58.019 30.769 19.37 0.00 40.06 0.98
478 482 6.852664 ACACTAGCGCTAAAAATGCTTTTAT 58.147 32.000 19.37 0.00 40.06 1.40
479 483 6.249035 ACACTAGCGCTAAAAATGCTTTTA 57.751 33.333 19.37 0.00 40.06 1.52
480 484 5.121221 ACACTAGCGCTAAAAATGCTTTT 57.879 34.783 19.37 0.00 40.06 2.27
481 485 4.766404 ACACTAGCGCTAAAAATGCTTT 57.234 36.364 19.37 0.00 40.06 3.51
482 486 4.935808 ACTACACTAGCGCTAAAAATGCTT 59.064 37.500 19.37 2.95 40.06 3.91
483 487 4.330074 CACTACACTAGCGCTAAAAATGCT 59.670 41.667 19.37 7.88 42.58 3.79
484 488 4.578601 CACTACACTAGCGCTAAAAATGC 58.421 43.478 19.37 0.00 0.00 3.56
485 489 4.494199 GGCACTACACTAGCGCTAAAAATG 60.494 45.833 19.37 15.69 34.42 2.32
486 490 3.621715 GGCACTACACTAGCGCTAAAAAT 59.378 43.478 19.37 6.96 34.42 1.82
487 491 2.997986 GGCACTACACTAGCGCTAAAAA 59.002 45.455 19.37 0.00 34.42 1.94
488 492 2.028839 TGGCACTACACTAGCGCTAAAA 60.029 45.455 19.37 0.00 34.42 1.52
489 493 1.546923 TGGCACTACACTAGCGCTAAA 59.453 47.619 19.37 0.00 34.42 1.85
490 494 1.179152 TGGCACTACACTAGCGCTAA 58.821 50.000 19.37 2.13 34.42 3.09
491 495 1.179152 TTGGCACTACACTAGCGCTA 58.821 50.000 17.75 17.75 34.42 4.26
492 496 0.320374 TTTGGCACTACACTAGCGCT 59.680 50.000 17.26 17.26 34.42 5.92
493 497 1.153353 TTTTGGCACTACACTAGCGC 58.847 50.000 0.00 0.00 33.25 5.92
494 498 2.546368 TGTTTTTGGCACTACACTAGCG 59.454 45.455 0.00 0.00 0.00 4.26
495 499 4.561735 TTGTTTTTGGCACTACACTAGC 57.438 40.909 0.00 0.00 0.00 3.42
496 500 6.560253 AGATTGTTTTTGGCACTACACTAG 57.440 37.500 0.00 0.00 0.00 2.57
497 501 6.952773 AAGATTGTTTTTGGCACTACACTA 57.047 33.333 0.00 0.00 0.00 2.74
498 502 5.852282 AAGATTGTTTTTGGCACTACACT 57.148 34.783 0.00 0.00 0.00 3.55
499 503 9.855021 AATATAAGATTGTTTTTGGCACTACAC 57.145 29.630 0.00 0.00 0.00 2.90
522 526 9.565090 TGCTACTACTTCTTCCGTCTTATAATA 57.435 33.333 0.00 0.00 0.00 0.98
523 527 8.461249 TGCTACTACTTCTTCCGTCTTATAAT 57.539 34.615 0.00 0.00 0.00 1.28
524 528 7.870509 TGCTACTACTTCTTCCGTCTTATAA 57.129 36.000 0.00 0.00 0.00 0.98
525 529 7.870509 TTGCTACTACTTCTTCCGTCTTATA 57.129 36.000 0.00 0.00 0.00 0.98
526 530 6.770746 TTGCTACTACTTCTTCCGTCTTAT 57.229 37.500 0.00 0.00 0.00 1.73
527 531 6.432162 TCTTTGCTACTACTTCTTCCGTCTTA 59.568 38.462 0.00 0.00 0.00 2.10
528 532 5.243283 TCTTTGCTACTACTTCTTCCGTCTT 59.757 40.000 0.00 0.00 0.00 3.01
529 533 4.765856 TCTTTGCTACTACTTCTTCCGTCT 59.234 41.667 0.00 0.00 0.00 4.18
530 534 5.056894 TCTTTGCTACTACTTCTTCCGTC 57.943 43.478 0.00 0.00 0.00 4.79
531 535 5.464030 TTCTTTGCTACTACTTCTTCCGT 57.536 39.130 0.00 0.00 0.00 4.69
532 536 6.780706 TTTTCTTTGCTACTACTTCTTCCG 57.219 37.500 0.00 0.00 0.00 4.30
536 540 9.011095 GGGTAAATTTTCTTTGCTACTACTTCT 57.989 33.333 0.00 0.00 0.00 2.85
537 541 9.011095 AGGGTAAATTTTCTTTGCTACTACTTC 57.989 33.333 0.00 0.00 0.00 3.01
538 542 8.793592 CAGGGTAAATTTTCTTTGCTACTACTT 58.206 33.333 0.00 0.00 0.00 2.24
539 543 7.094334 GCAGGGTAAATTTTCTTTGCTACTACT 60.094 37.037 0.00 0.00 0.00 2.57
540 544 7.027760 GCAGGGTAAATTTTCTTTGCTACTAC 58.972 38.462 0.00 0.00 0.00 2.73
574 578 0.588252 ATGCGCGAATATCAGCAACC 59.412 50.000 12.10 0.00 43.19 3.77
587 591 5.325494 TGGTACAAGTTTAATTAATGCGCG 58.675 37.500 0.00 0.00 31.92 6.86
711 728 5.291128 GGGTTTAGTTGATCACACTATCACG 59.709 44.000 14.48 0.00 35.63 4.35
948 965 1.597742 TCTTGGAGACTTTGCTGTGC 58.402 50.000 0.00 0.00 0.00 4.57
995 1018 1.073722 CCACGCCCAGCCATGATAT 59.926 57.895 0.00 0.00 0.00 1.63
1119 1145 0.179015 TTTTGTCGCTTGCCCAGGTA 60.179 50.000 0.00 0.00 0.00 3.08
1179 1205 3.486108 CGTTGGTACTAGCAATGATCGTC 59.514 47.826 12.95 0.00 43.23 4.20
1196 1222 6.765989 TCCAATATCAATAAGAGAACCGTTGG 59.234 38.462 0.00 0.00 34.14 3.77
1204 1230 8.324191 ACTTGAGGTCCAATATCAATAAGAGA 57.676 34.615 0.00 0.00 32.82 3.10
1211 1237 5.425217 TGCTCTACTTGAGGTCCAATATCAA 59.575 40.000 0.00 0.00 42.87 2.57
1217 1243 2.300152 CTGTGCTCTACTTGAGGTCCAA 59.700 50.000 0.00 0.00 42.87 3.53
1239 1268 3.895041 ACCATTTTGTCAAACTGGTAGGG 59.105 43.478 29.27 14.88 34.56 3.53
1240 1269 5.068460 TGAACCATTTTGTCAAACTGGTAGG 59.932 40.000 30.07 12.44 34.92 3.18
1248 1277 7.106439 ACAGTACATGAACCATTTTGTCAAA 57.894 32.000 0.00 0.00 0.00 2.69
1252 1281 6.430000 GGACTACAGTACATGAACCATTTTGT 59.570 38.462 0.00 0.00 0.00 2.83
1270 1299 3.988976 AGTACGTACTGGAGGACTACA 57.011 47.619 26.87 0.00 34.72 2.74
1271 1300 5.293079 CAGTAAGTACGTACTGGAGGACTAC 59.707 48.000 30.20 21.91 44.85 2.73
1272 1301 5.423015 CAGTAAGTACGTACTGGAGGACTA 58.577 45.833 30.20 12.34 44.85 2.59
1273 1302 4.260170 CAGTAAGTACGTACTGGAGGACT 58.740 47.826 30.20 20.63 44.85 3.85
1274 1303 4.612932 CAGTAAGTACGTACTGGAGGAC 57.387 50.000 30.20 19.02 44.85 3.85
1285 1314 8.975439 ACACAAAGAAACTAATCAGTAAGTACG 58.025 33.333 0.00 0.00 33.48 3.67
1287 1316 8.770828 GCACACAAAGAAACTAATCAGTAAGTA 58.229 33.333 0.00 0.00 33.48 2.24
1288 1317 7.499232 AGCACACAAAGAAACTAATCAGTAAGT 59.501 33.333 0.00 0.00 33.48 2.24
1289 1318 7.865707 AGCACACAAAGAAACTAATCAGTAAG 58.134 34.615 0.00 0.00 33.48 2.34
1291 1320 7.639039 CAAGCACACAAAGAAACTAATCAGTA 58.361 34.615 0.00 0.00 33.48 2.74
1292 1321 6.498304 CAAGCACACAAAGAAACTAATCAGT 58.502 36.000 0.00 0.00 36.19 3.41
1299 1394 2.493278 ACTGCAAGCACACAAAGAAACT 59.507 40.909 0.00 0.00 37.60 2.66
1305 1401 1.135141 GGAACACTGCAAGCACACAAA 60.135 47.619 0.00 0.00 37.60 2.83
1306 1402 0.455410 GGAACACTGCAAGCACACAA 59.545 50.000 0.00 0.00 37.60 3.33
1314 1410 0.882927 GCCGTACTGGAACACTGCAA 60.883 55.000 7.77 0.00 42.00 4.08
1384 1480 1.746615 CTGGATGGAGTTGGTGGCG 60.747 63.158 0.00 0.00 0.00 5.69
1651 1747 2.463589 ATTTGGACGAGGAAGGCGCA 62.464 55.000 10.83 0.00 0.00 6.09
1714 1810 0.325933 CAACCAGAGAGCCCATCACA 59.674 55.000 0.00 0.00 0.00 3.58
1779 1875 2.952310 GAGAAGGGAAACAAAGCACAGT 59.048 45.455 0.00 0.00 0.00 3.55
1781 1877 2.306847 GGAGAAGGGAAACAAAGCACA 58.693 47.619 0.00 0.00 0.00 4.57
1814 1910 2.388232 CGGGAAGAAGGAAACGCGG 61.388 63.158 12.47 0.00 35.65 6.46
1816 1912 2.687805 GGCGGGAAGAAGGAAACGC 61.688 63.158 0.00 0.00 45.53 4.84
1822 1918 1.741770 CAACTCGGCGGGAAGAAGG 60.742 63.158 16.65 0.00 0.00 3.46
1924 2061 1.132199 CGTACAAGCACGAGTAGCGG 61.132 60.000 0.00 0.00 44.69 5.52
1945 2082 7.519649 GCATGGAGAGTCTATATTTCAAAGTGC 60.520 40.741 0.00 0.00 0.00 4.40
1971 2108 1.327460 CAAGACACGTCACAACACAGG 59.673 52.381 0.00 0.00 0.00 4.00
1972 2109 1.267532 GCAAGACACGTCACAACACAG 60.268 52.381 0.00 0.00 0.00 3.66
2042 2220 3.074412 ACAAATCATCTTCACGTGGACC 58.926 45.455 17.00 0.00 0.00 4.46
2043 2221 6.422776 AATACAAATCATCTTCACGTGGAC 57.577 37.500 17.00 0.00 0.00 4.02
2053 2231 3.181458 ACCGGCGGTAATACAAATCATCT 60.181 43.478 33.31 0.00 32.11 2.90
2054 2232 3.135994 ACCGGCGGTAATACAAATCATC 58.864 45.455 33.31 0.00 32.11 2.92
2056 2234 2.695127 ACCGGCGGTAATACAAATCA 57.305 45.000 33.31 0.00 32.11 2.57
2057 2235 3.721035 AGTACCGGCGGTAATACAAATC 58.279 45.455 37.72 22.97 40.12 2.17
2058 2236 3.825143 AGTACCGGCGGTAATACAAAT 57.175 42.857 37.72 16.00 40.12 2.32
2059 2237 3.260740 CAAGTACCGGCGGTAATACAAA 58.739 45.455 37.72 16.16 40.12 2.83
2060 2238 2.233431 ACAAGTACCGGCGGTAATACAA 59.767 45.455 37.72 16.97 40.12 2.41
2061 2239 1.824230 ACAAGTACCGGCGGTAATACA 59.176 47.619 37.72 17.79 40.12 2.29
2062 2240 2.584492 ACAAGTACCGGCGGTAATAC 57.416 50.000 37.72 28.53 40.12 1.89
2063 2241 3.068024 CCTTACAAGTACCGGCGGTAATA 59.932 47.826 37.72 23.89 40.12 0.98
2064 2242 2.159057 CCTTACAAGTACCGGCGGTAAT 60.159 50.000 37.72 34.34 40.12 1.89
2066 2244 0.817013 CCTTACAAGTACCGGCGGTA 59.183 55.000 33.42 33.42 37.09 4.02
2067 2245 1.187567 ACCTTACAAGTACCGGCGGT 61.188 55.000 35.91 35.91 40.16 5.68
2068 2246 0.817013 TACCTTACAAGTACCGGCGG 59.183 55.000 27.06 27.06 0.00 6.13
2069 2247 1.202114 TGTACCTTACAAGTACCGGCG 59.798 52.381 0.00 0.00 39.49 6.46
2070 2248 2.610433 GTGTACCTTACAAGTACCGGC 58.390 52.381 0.00 0.00 40.93 6.13
2071 2249 2.228822 ACGTGTACCTTACAAGTACCGG 59.771 50.000 0.00 0.00 46.77 5.28
2072 2250 3.559238 ACGTGTACCTTACAAGTACCG 57.441 47.619 3.48 0.00 46.77 4.02
2077 2255 6.864685 TGTTCAATAGACGTGTACCTTACAAG 59.135 38.462 0.00 0.00 40.93 3.16
2078 2256 6.642131 GTGTTCAATAGACGTGTACCTTACAA 59.358 38.462 0.00 0.00 40.93 2.41
2079 2257 6.151691 GTGTTCAATAGACGTGTACCTTACA 58.848 40.000 0.00 0.00 36.08 2.41
2084 2262 5.910637 TTTGTGTTCAATAGACGTGTACC 57.089 39.130 0.00 0.00 33.32 3.34
2208 2387 2.875933 CGGGTGTGACACAACTAAATGT 59.124 45.455 22.44 0.00 35.75 2.71
2209 2388 2.875933 ACGGGTGTGACACAACTAAATG 59.124 45.455 22.44 10.34 35.75 2.32
2210 2389 3.202829 ACGGGTGTGACACAACTAAAT 57.797 42.857 22.44 3.89 35.75 1.40
2211 2390 2.695127 ACGGGTGTGACACAACTAAA 57.305 45.000 22.44 0.00 35.75 1.85
2256 2437 1.864711 CGAGCTTGGACAAAAACGAGA 59.135 47.619 0.00 0.00 0.00 4.04
2281 2463 7.119407 GGTCAAAGGACAAAAGTATAAGAGGAC 59.881 40.741 0.00 0.00 46.17 3.85
2567 4521 4.875536 CCACGACTTCCATGAATGTCATTA 59.124 41.667 0.00 0.00 34.28 1.90
2704 4667 5.895636 TCTATGGCAAACATTGACGATTT 57.104 34.783 0.00 0.00 43.38 2.17
2706 4669 5.895636 TTTCTATGGCAAACATTGACGAT 57.104 34.783 0.00 0.00 43.38 3.73


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.