Multiple sequence alignment - TraesCS2A01G441000

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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 TraesCS2A01G441000 chr2A 100.000 2339 0 0 1 2339 691214092 691216430 0.000000e+00 4320.0
1 TraesCS2A01G441000 chr2A 93.382 408 26 1 3 409 74855188 74854781 9.250000e-169 603.0
2 TraesCS2A01G441000 chr2A 89.954 438 28 8 1909 2339 691184879 691185307 3.400000e-153 551.0
3 TraesCS2A01G441000 chr2A 93.175 337 22 1 1383 1719 691184167 691184502 5.810000e-136 494.0
4 TraesCS2A01G441000 chr2A 96.739 92 3 0 397 488 455340400 455340491 1.120000e-33 154.0
5 TraesCS2A01G441000 chr1A 95.282 869 41 0 484 1352 260842048 260842916 0.000000e+00 1378.0
6 TraesCS2A01G441000 chr1A 93.069 404 27 1 1 403 260841648 260842051 7.200000e-165 590.0
7 TraesCS2A01G441000 chr1A 92.822 404 28 1 1 403 253313559 253313962 3.350000e-163 584.0
8 TraesCS2A01G441000 chr1A 92.439 410 30 1 1 409 277626877 277626468 3.350000e-163 584.0
9 TraesCS2A01G441000 chr1A 94.949 99 5 0 392 490 547849181 547849083 3.110000e-34 156.0
10 TraesCS2A01G441000 chr1D 95.167 869 42 0 484 1352 494486684 494487552 0.000000e+00 1373.0
11 TraesCS2A01G441000 chr4D 94.822 869 45 0 484 1352 126638493 126639361 0.000000e+00 1356.0
12 TraesCS2A01G441000 chr4D 93.564 404 25 1 1 403 463910411 463910814 3.330000e-168 601.0
13 TraesCS2A01G441000 chr4D 93.317 404 25 2 1 403 126638094 126638496 1.550000e-166 595.0
14 TraesCS2A01G441000 chr5A 94.361 869 49 0 484 1352 634633391 634632523 0.000000e+00 1334.0
15 TraesCS2A01G441000 chr5A 93.671 869 54 1 484 1352 343043545 343042678 0.000000e+00 1299.0
16 TraesCS2A01G441000 chr5A 93.902 410 24 1 1 409 634633791 634633382 3.300000e-173 617.0
17 TraesCS2A01G441000 chr5A 92.439 410 30 1 1 409 343043945 343043536 3.350000e-163 584.0
18 TraesCS2A01G441000 chr3B 94.131 869 51 0 484 1352 541062498 541061630 0.000000e+00 1323.0
19 TraesCS2A01G441000 chr3B 93.023 43 3 0 1734 1776 822727868 822727910 1.940000e-06 63.9
20 TraesCS2A01G441000 chr4A 94.023 870 51 1 484 1352 438390793 438391662 0.000000e+00 1317.0
21 TraesCS2A01G441000 chr4A 93.069 404 27 1 1 403 438390393 438390796 7.200000e-165 590.0
22 TraesCS2A01G441000 chr5D 93.807 872 51 1 484 1352 63607102 63607973 0.000000e+00 1308.0
23 TraesCS2A01G441000 chr5D 97.778 45 1 0 1735 1779 13999856 13999812 6.930000e-11 78.7
24 TraesCS2A01G441000 chr6B 93.585 873 52 4 484 1352 28113668 28112796 0.000000e+00 1299.0
25 TraesCS2A01G441000 chr2D 90.424 1013 55 15 1362 2339 547695963 547694958 0.000000e+00 1295.0
26 TraesCS2A01G441000 chr2D 92.623 366 21 1 1362 1721 547762128 547761763 2.660000e-144 521.0
27 TraesCS2A01G441000 chr2D 88.558 437 36 9 1903 2339 547761682 547761260 3.450000e-143 518.0
28 TraesCS2A01G441000 chr2B 94.460 361 20 0 1361 1721 654356525 654356165 7.300000e-155 556.0
29 TraesCS2A01G441000 chr2B 90.736 421 26 7 1923 2339 654324684 654324273 1.220000e-152 549.0
30 TraesCS2A01G441000 chr2B 93.496 369 22 1 1364 1732 654325258 654324892 4.390000e-152 547.0
31 TraesCS2A01G441000 chr2B 88.991 436 33 8 1909 2339 654356079 654355654 2.060000e-145 525.0
32 TraesCS2A01G441000 chr2B 94.949 99 3 2 392 488 647539347 647539445 1.120000e-33 154.0
33 TraesCS2A01G441000 chr2B 94.898 98 3 2 399 495 751263661 751263565 4.030000e-33 152.0
34 TraesCS2A01G441000 chr2B 93.204 103 6 1 392 493 13713010 13713112 1.450000e-32 150.0
35 TraesCS2A01G441000 chr3D 95.918 98 4 0 392 489 43315914 43315817 2.410000e-35 159.0
36 TraesCS2A01G441000 chr4B 98.864 88 1 0 400 487 429694756 429694669 8.650000e-35 158.0
37 TraesCS2A01G441000 chr7B 95.789 95 4 0 398 492 733608895 733608801 1.120000e-33 154.0
38 TraesCS2A01G441000 chr7B 89.362 47 5 0 1734 1780 641142796 641142750 2.510000e-05 60.2
39 TraesCS2A01G441000 chr1B 92.453 106 4 4 399 502 134494721 134494618 5.210000e-32 148.0
40 TraesCS2A01G441000 chr7D 86.111 72 6 4 1707 1776 593247896 593247827 8.960000e-10 75.0


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 TraesCS2A01G441000 chr2A 691214092 691216430 2338 False 4320.0 4320 100.0000 1 2339 1 chr2A.!!$F2 2338
1 TraesCS2A01G441000 chr2A 691184167 691185307 1140 False 522.5 551 91.5645 1383 2339 2 chr2A.!!$F3 956
2 TraesCS2A01G441000 chr1A 260841648 260842916 1268 False 984.0 1378 94.1755 1 1352 2 chr1A.!!$F2 1351
3 TraesCS2A01G441000 chr1D 494486684 494487552 868 False 1373.0 1373 95.1670 484 1352 1 chr1D.!!$F1 868
4 TraesCS2A01G441000 chr4D 126638094 126639361 1267 False 975.5 1356 94.0695 1 1352 2 chr4D.!!$F2 1351
5 TraesCS2A01G441000 chr5A 634632523 634633791 1268 True 975.5 1334 94.1315 1 1352 2 chr5A.!!$R2 1351
6 TraesCS2A01G441000 chr5A 343042678 343043945 1267 True 941.5 1299 93.0550 1 1352 2 chr5A.!!$R1 1351
7 TraesCS2A01G441000 chr3B 541061630 541062498 868 True 1323.0 1323 94.1310 484 1352 1 chr3B.!!$R1 868
8 TraesCS2A01G441000 chr4A 438390393 438391662 1269 False 953.5 1317 93.5460 1 1352 2 chr4A.!!$F1 1351
9 TraesCS2A01G441000 chr5D 63607102 63607973 871 False 1308.0 1308 93.8070 484 1352 1 chr5D.!!$F1 868
10 TraesCS2A01G441000 chr6B 28112796 28113668 872 True 1299.0 1299 93.5850 484 1352 1 chr6B.!!$R1 868
11 TraesCS2A01G441000 chr2D 547694958 547695963 1005 True 1295.0 1295 90.4240 1362 2339 1 chr2D.!!$R1 977
12 TraesCS2A01G441000 chr2D 547761260 547762128 868 True 519.5 521 90.5905 1362 2339 2 chr2D.!!$R2 977
13 TraesCS2A01G441000 chr2B 654324273 654325258 985 True 548.0 549 92.1160 1364 2339 2 chr2B.!!$R2 975
14 TraesCS2A01G441000 chr2B 654355654 654356525 871 True 540.5 556 91.7255 1361 2339 2 chr2B.!!$R3 978

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
403 406 0.175989 CTCGCCCCTTTGTCCTACTC 59.824 60.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2327 0.111061 TCCACCAGCTGATGCAGTTT 59.889 50.0 17.39 0.0 42.74 2.66 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
93 94 0.618458 ACTATGTGGCCCATTGACGT 59.382 50.000 17.69 6.42 34.86 4.34
121 122 3.895041 GGGTTCTTTCAATCCCACTTTCA 59.105 43.478 0.00 0.00 39.68 2.69
172 174 7.920682 GCTTGGAGTTATACAAAAATGGTATGG 59.079 37.037 0.00 0.00 33.68 2.74
245 247 3.881937 ACTATAACACTCCAACGGGAC 57.118 47.619 0.00 0.00 38.64 4.46
291 294 3.281727 TGGTGCCAGATATGGAAGTTC 57.718 47.619 11.49 0.00 0.00 3.01
350 353 2.102420 CGTTACATGGCACTCTCCCATA 59.898 50.000 0.00 0.00 41.02 2.74
382 385 6.701340 ACACTTGCTAATAGACACATGAAGA 58.299 36.000 0.00 0.00 0.00 2.87
383 386 6.591834 ACACTTGCTAATAGACACATGAAGAC 59.408 38.462 0.00 0.00 0.00 3.01
399 402 2.529389 ACCTCGCCCCTTTGTCCT 60.529 61.111 0.00 0.00 0.00 3.85
400 403 1.229400 ACCTCGCCCCTTTGTCCTA 60.229 57.895 0.00 0.00 0.00 2.94
401 404 1.221021 CCTCGCCCCTTTGTCCTAC 59.779 63.158 0.00 0.00 0.00 3.18
402 405 1.265454 CCTCGCCCCTTTGTCCTACT 61.265 60.000 0.00 0.00 0.00 2.57
403 406 0.175989 CTCGCCCCTTTGTCCTACTC 59.824 60.000 0.00 0.00 0.00 2.59
404 407 1.221021 CGCCCCTTTGTCCTACTCC 59.779 63.158 0.00 0.00 0.00 3.85
405 408 1.608154 GCCCCTTTGTCCTACTCCC 59.392 63.158 0.00 0.00 0.00 4.30
406 409 0.914902 GCCCCTTTGTCCTACTCCCT 60.915 60.000 0.00 0.00 0.00 4.20
407 410 1.205055 CCCCTTTGTCCTACTCCCTC 58.795 60.000 0.00 0.00 0.00 4.30
408 411 1.273896 CCCCTTTGTCCTACTCCCTCT 60.274 57.143 0.00 0.00 0.00 3.69
409 412 1.834263 CCCTTTGTCCTACTCCCTCTG 59.166 57.143 0.00 0.00 0.00 3.35
410 413 2.541466 CCTTTGTCCTACTCCCTCTGT 58.459 52.381 0.00 0.00 0.00 3.41
411 414 2.907042 CCTTTGTCCTACTCCCTCTGTT 59.093 50.000 0.00 0.00 0.00 3.16
412 415 3.055747 CCTTTGTCCTACTCCCTCTGTTC 60.056 52.174 0.00 0.00 0.00 3.18
413 416 2.233305 TGTCCTACTCCCTCTGTTCC 57.767 55.000 0.00 0.00 0.00 3.62
414 417 1.431633 TGTCCTACTCCCTCTGTTCCA 59.568 52.381 0.00 0.00 0.00 3.53
415 418 2.158219 TGTCCTACTCCCTCTGTTCCAA 60.158 50.000 0.00 0.00 0.00 3.53
416 419 2.904434 GTCCTACTCCCTCTGTTCCAAA 59.096 50.000 0.00 0.00 0.00 3.28
417 420 3.326880 GTCCTACTCCCTCTGTTCCAAAA 59.673 47.826 0.00 0.00 0.00 2.44
418 421 4.019231 GTCCTACTCCCTCTGTTCCAAAAT 60.019 45.833 0.00 0.00 0.00 1.82
419 422 5.189145 GTCCTACTCCCTCTGTTCCAAAATA 59.811 44.000 0.00 0.00 0.00 1.40
420 423 5.425539 TCCTACTCCCTCTGTTCCAAAATAG 59.574 44.000 0.00 0.00 0.00 1.73
421 424 5.425539 CCTACTCCCTCTGTTCCAAAATAGA 59.574 44.000 0.00 0.00 32.42 1.98
422 425 6.100424 CCTACTCCCTCTGTTCCAAAATAGAT 59.900 42.308 0.00 0.00 32.88 1.98
423 426 5.749462 ACTCCCTCTGTTCCAAAATAGATG 58.251 41.667 0.00 0.00 32.88 2.90
424 427 5.488919 ACTCCCTCTGTTCCAAAATAGATGA 59.511 40.000 0.00 0.00 32.88 2.92
425 428 5.745227 TCCCTCTGTTCCAAAATAGATGAC 58.255 41.667 0.00 0.00 32.88 3.06
426 429 4.884164 CCCTCTGTTCCAAAATAGATGACC 59.116 45.833 0.00 0.00 32.88 4.02
427 430 4.884164 CCTCTGTTCCAAAATAGATGACCC 59.116 45.833 0.00 0.00 32.88 4.46
428 431 5.500234 CTCTGTTCCAAAATAGATGACCCA 58.500 41.667 0.00 0.00 32.88 4.51
429 432 5.886609 TCTGTTCCAAAATAGATGACCCAA 58.113 37.500 0.00 0.00 28.72 4.12
430 433 5.710099 TCTGTTCCAAAATAGATGACCCAAC 59.290 40.000 0.00 0.00 28.72 3.77
431 434 5.640147 TGTTCCAAAATAGATGACCCAACT 58.360 37.500 0.00 0.00 0.00 3.16
432 435 6.074648 TGTTCCAAAATAGATGACCCAACTT 58.925 36.000 0.00 0.00 0.00 2.66
433 436 6.553100 TGTTCCAAAATAGATGACCCAACTTT 59.447 34.615 0.00 0.00 0.00 2.66
434 437 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
435 438 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
436 439 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
437 440 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
438 441 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
439 442 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
440 443 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
441 444 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
442 445 9.802039 AATAGATGACCCAACTTTGTACTAAAA 57.198 29.630 0.00 0.00 0.00 1.52
443 446 9.975218 ATAGATGACCCAACTTTGTACTAAAAT 57.025 29.630 0.00 0.00 0.00 1.82
444 447 8.706322 AGATGACCCAACTTTGTACTAAAATT 57.294 30.769 0.00 0.00 0.00 1.82
445 448 9.802039 AGATGACCCAACTTTGTACTAAAATTA 57.198 29.630 0.00 0.00 0.00 1.40
447 450 8.983702 TGACCCAACTTTGTACTAAAATTAGT 57.016 30.769 10.43 10.43 45.39 2.24
471 474 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
472 475 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
473 476 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
474 477 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
475 478 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
476 479 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
477 480 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
478 481 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
479 482 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
480 483 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
481 484 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
482 485 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
491 494 2.097825 GAACGGAGGGAGTACTTGCTA 58.902 52.381 0.00 0.00 0.00 3.49
520 527 2.533266 AGAAGACACGAAGCACATGT 57.467 45.000 0.00 0.00 0.00 3.21
564 571 1.210722 GAGGTTTGGAAGAGGCTAGGG 59.789 57.143 0.00 0.00 0.00 3.53
610 617 0.904649 TGAGGTTGATCGTGCTGGAT 59.095 50.000 0.00 0.00 0.00 3.41
718 725 3.653164 TCAGCTTGGTATCTATGGTGGA 58.347 45.455 0.00 0.00 0.00 4.02
749 756 6.420604 CGAAAATTAGTGCACAAGGAAACAAT 59.579 34.615 21.04 2.36 0.00 2.71
751 758 7.481275 AAATTAGTGCACAAGGAAACAATTG 57.519 32.000 21.04 3.24 0.00 2.32
770 777 7.704271 ACAATTGAGAATGCAACTCAGATATG 58.296 34.615 20.51 18.85 0.00 1.78
810 817 6.253298 CCCTCACATACAATTTTGTAAATGCG 59.747 38.462 7.20 4.48 45.74 4.73
813 820 6.521477 TCACATACAATTTTGTAAATGCGTCG 59.479 34.615 7.20 0.00 45.74 5.12
897 905 3.820467 TCAATGTTGACGCCTCTTTTGAT 59.180 39.130 0.00 0.00 31.01 2.57
1029 1037 2.833943 AGCTTTAGCCCTCAAATTTGGG 59.166 45.455 17.90 14.78 46.00 4.12
1040 1048 5.010282 CCTCAAATTTGGGCTAACACTAGT 58.990 41.667 17.90 0.00 0.00 2.57
1166 1177 2.299013 TCAATGACTGCTTCCACTACGT 59.701 45.455 0.00 0.00 0.00 3.57
1212 1223 8.270744 AGATTCAAACATTGTAATAGAGAGGCT 58.729 33.333 0.00 0.00 0.00 4.58
1401 1412 4.487282 AGGCTATGGGTAGAGTTGGATA 57.513 45.455 0.00 0.00 0.00 2.59
1423 1434 2.329267 TGGATCGCATTCCTAGGACAT 58.671 47.619 12.22 5.81 36.68 3.06
1455 1466 6.662414 TTGTAATGACTAAATCCTGCTTCG 57.338 37.500 0.00 0.00 0.00 3.79
1456 1467 5.116180 TGTAATGACTAAATCCTGCTTCGG 58.884 41.667 0.00 0.00 0.00 4.30
1500 1511 3.953712 TCCTCACGTTCTTTGCTCATA 57.046 42.857 0.00 0.00 0.00 2.15
1515 1526 5.684550 TGCTCATAAACAGCATCATCATC 57.315 39.130 0.00 0.00 42.09 2.92
1622 1639 1.581447 CTTTCGCTCCTTGGGCAAC 59.419 57.895 0.00 0.00 0.00 4.17
1715 1732 8.690884 TCAATCCAACAAGTCAAAAACTATCAA 58.309 29.630 0.00 0.00 37.17 2.57
1738 1755 9.368416 TCAATAAGATAGCACTACTCTAACCAT 57.632 33.333 0.00 0.00 0.00 3.55
1741 1758 6.398234 AGATAGCACTACTCTAACCATGTG 57.602 41.667 0.00 0.00 0.00 3.21
1743 1760 6.780031 AGATAGCACTACTCTAACCATGTGAT 59.220 38.462 0.00 0.00 0.00 3.06
1761 1778 5.744171 TGTGATACATGTGGTAAGCAATCT 58.256 37.500 9.11 0.00 35.14 2.40
1766 1783 8.046708 TGATACATGTGGTAAGCAATCTAAACT 58.953 33.333 9.11 0.00 35.14 2.66
1770 1787 8.893727 ACATGTGGTAAGCAATCTAAACTATTC 58.106 33.333 0.00 0.00 0.00 1.75
1772 1789 8.856153 TGTGGTAAGCAATCTAAACTATTCAA 57.144 30.769 0.00 0.00 0.00 2.69
1825 1853 5.130350 TCTTTTCTTTTTGTCGGATCCACT 58.870 37.500 13.41 0.00 0.00 4.00
1895 2179 3.250762 TGTCGTGCCTTTCATTCTTTGAG 59.749 43.478 0.00 0.00 35.27 3.02
1942 2258 2.295253 AATGCGAACGGGAAGTAGAG 57.705 50.000 0.00 0.00 0.00 2.43
2059 2382 2.555547 GCCGGCAGCAAACTCAACT 61.556 57.895 24.80 0.00 42.97 3.16
2068 2391 2.551459 AGCAAACTCAACTGACTCATGC 59.449 45.455 0.00 0.00 0.00 4.06
2110 2433 2.224159 ATGCGGGAGGTCCAACACT 61.224 57.895 0.00 0.00 37.91 3.55
2113 2436 1.293498 CGGGAGGTCCAACACTGAG 59.707 63.158 0.00 0.00 37.91 3.35
2242 2565 1.299468 GACGAGCTCCGCCATGTAG 60.299 63.158 8.47 0.00 43.32 2.74
2304 2627 2.045045 CATGTCATGGCCGGTGGT 60.045 61.111 1.90 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 7.543172 GCAATGAAATCTGACATGTTATGTTGT 59.457 33.333 0.00 0.00 45.03 3.32
172 174 1.089920 TAAGCAGACCGTACCGAGAC 58.910 55.000 0.00 0.00 0.00 3.36
229 231 1.667151 CCGTCCCGTTGGAGTGTTA 59.333 57.895 0.00 0.00 42.85 2.41
237 239 2.667199 GTTCACCCCGTCCCGTTG 60.667 66.667 0.00 0.00 0.00 4.10
250 253 4.507691 CCAAATAGGGTTAGGTGTGGTTCA 60.508 45.833 0.00 0.00 0.00 3.18
291 294 0.250295 TGACTTTTGCCGGACAGGAG 60.250 55.000 5.05 7.27 45.00 3.69
324 327 1.542915 AGAGTGCCATGTAACGTACGT 59.457 47.619 16.72 16.72 0.00 3.57
382 385 1.229400 TAGGACAAAGGGGCGAGGT 60.229 57.895 0.00 0.00 0.00 3.85
383 386 1.221021 GTAGGACAAAGGGGCGAGG 59.779 63.158 0.00 0.00 0.00 4.63
399 402 6.672218 TCATCTATTTTGGAACAGAGGGAGTA 59.328 38.462 0.00 0.00 42.39 2.59
400 403 5.488919 TCATCTATTTTGGAACAGAGGGAGT 59.511 40.000 0.00 0.00 42.39 3.85
401 404 5.819901 GTCATCTATTTTGGAACAGAGGGAG 59.180 44.000 0.00 0.00 42.39 4.30
402 405 5.339200 GGTCATCTATTTTGGAACAGAGGGA 60.339 44.000 0.00 0.00 42.39 4.20
403 406 4.884164 GGTCATCTATTTTGGAACAGAGGG 59.116 45.833 0.00 0.00 42.39 4.30
404 407 4.884164 GGGTCATCTATTTTGGAACAGAGG 59.116 45.833 0.00 0.00 42.39 3.69
405 408 5.500234 TGGGTCATCTATTTTGGAACAGAG 58.500 41.667 0.00 0.00 42.39 3.35
406 409 5.512942 TGGGTCATCTATTTTGGAACAGA 57.487 39.130 0.00 0.00 42.39 3.41
407 410 5.711976 AGTTGGGTCATCTATTTTGGAACAG 59.288 40.000 0.00 0.00 42.39 3.16
408 411 5.640147 AGTTGGGTCATCTATTTTGGAACA 58.360 37.500 0.00 0.00 0.00 3.18
409 412 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
410 413 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
411 414 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
412 415 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
413 416 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
414 417 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
415 418 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
416 419 9.802039 TTTTAGTACAAAGTTGGGTCATCTATT 57.198 29.630 0.00 0.00 0.00 1.73
417 420 9.975218 ATTTTAGTACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
418 421 9.802039 AATTTTAGTACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
419 422 8.706322 AATTTTAGTACAAAGTTGGGTCATCT 57.294 30.769 0.00 0.00 0.00 2.90
421 424 9.582648 ACTAATTTTAGTACAAAGTTGGGTCAT 57.417 29.630 1.15 0.00 41.92 3.06
422 425 8.983702 ACTAATTTTAGTACAAAGTTGGGTCA 57.016 30.769 1.15 0.00 41.92 4.02
445 448 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
446 449 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
447 450 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
448 451 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
449 452 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
450 453 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
451 454 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
452 455 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
453 456 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
454 457 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
455 458 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
456 459 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
457 460 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
458 461 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
459 462 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
460 463 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
461 464 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
462 465 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
463 466 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
464 467 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
465 468 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
466 469 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
467 470 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
468 471 1.621814 CAAGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
469 472 1.263356 CAAGTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
470 473 0.108281 GCAAGTACTCCCTCCGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
471 474 0.896226 AGCAAGTACTCCCTCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
472 475 2.226962 TAGCAAGTACTCCCTCCGTT 57.773 50.000 0.00 0.00 0.00 4.44
473 476 2.308690 GATAGCAAGTACTCCCTCCGT 58.691 52.381 0.00 0.00 0.00 4.69
474 477 2.294791 CTGATAGCAAGTACTCCCTCCG 59.705 54.545 0.00 0.00 0.00 4.63
475 478 2.630580 CCTGATAGCAAGTACTCCCTCC 59.369 54.545 0.00 0.00 0.00 4.30
476 479 2.630580 CCCTGATAGCAAGTACTCCCTC 59.369 54.545 0.00 0.00 0.00 4.30
477 480 2.022918 ACCCTGATAGCAAGTACTCCCT 60.023 50.000 0.00 0.00 0.00 4.20
478 481 2.103263 CACCCTGATAGCAAGTACTCCC 59.897 54.545 0.00 0.00 0.00 4.30
479 482 2.766828 ACACCCTGATAGCAAGTACTCC 59.233 50.000 0.00 0.00 0.00 3.85
480 483 4.888239 TCTACACCCTGATAGCAAGTACTC 59.112 45.833 0.00 0.00 0.00 2.59
481 484 4.868268 TCTACACCCTGATAGCAAGTACT 58.132 43.478 0.00 0.00 0.00 2.73
482 485 5.360144 TCTTCTACACCCTGATAGCAAGTAC 59.640 44.000 0.00 0.00 0.00 2.73
525 532 6.869206 ACCTCCTTTGCTTTAGTACATAGA 57.131 37.500 0.00 0.00 0.00 1.98
610 617 5.881923 AAAAGGTATTCCAGTATCGCCTA 57.118 39.130 0.00 0.00 35.89 3.93
718 725 5.049405 CCTTGTGCACTAATTTTCGTCTCTT 60.049 40.000 19.41 0.00 0.00 2.85
749 756 7.012989 CCATTCATATCTGAGTTGCATTCTCAA 59.987 37.037 18.28 12.03 40.68 3.02
751 758 6.072618 CCCATTCATATCTGAGTTGCATTCTC 60.073 42.308 11.08 11.08 31.68 2.87
770 777 1.988107 TGAGGGCTATGATCCCCATTC 59.012 52.381 7.44 0.00 45.03 2.67
810 817 0.599204 TGGACGCCTTTGAAGACGAC 60.599 55.000 6.46 0.32 35.38 4.34
813 820 1.808411 TCATGGACGCCTTTGAAGAC 58.192 50.000 0.00 0.00 0.00 3.01
897 905 1.555075 GTACCCTTCAGCATGTCCTGA 59.445 52.381 0.00 0.00 39.94 3.86
1029 1037 1.468914 GCCCTTTGCACTAGTGTTAGC 59.531 52.381 23.44 13.93 40.77 3.09
1040 1048 4.675161 TGCATCCCGCCCTTTGCA 62.675 61.111 0.00 0.00 42.41 4.08
1053 1061 4.202441 AGTTGAAGATTAGGCGATTGCAT 58.798 39.130 7.38 1.37 45.35 3.96
1069 1077 8.774546 ATCACCTCTAGATTATCTGAGTTGAA 57.225 34.615 17.82 8.46 32.11 2.69
1381 1392 5.491982 CATTATCCAACTCTACCCATAGCC 58.508 45.833 0.00 0.00 0.00 3.93
1401 1412 2.705658 TGTCCTAGGAATGCGATCCATT 59.294 45.455 14.65 8.59 46.57 3.16
1423 1434 9.461312 AGGATTTAGTCATTACAAAATACAGCA 57.539 29.630 0.00 0.00 0.00 4.41
1455 1466 5.183904 ACTCAACTGGCAAAAGATATTCACC 59.816 40.000 0.00 0.00 0.00 4.02
1456 1467 6.259550 ACTCAACTGGCAAAAGATATTCAC 57.740 37.500 0.00 0.00 0.00 3.18
1500 1511 5.183331 GGATATGCAGATGATGATGCTGTTT 59.817 40.000 0.00 0.00 42.98 2.83
1515 1526 4.213694 GCTCAAGTCTTGATGGATATGCAG 59.786 45.833 15.60 1.79 39.30 4.41
1622 1639 3.119849 CCTGACAAAATGTAAAGAGGCCG 60.120 47.826 0.00 0.00 0.00 6.13
1630 1647 6.770303 TGTGTGAAGATCCTGACAAAATGTAA 59.230 34.615 0.00 0.00 0.00 2.41
1632 1649 5.132502 TGTGTGAAGATCCTGACAAAATGT 58.867 37.500 0.00 0.00 0.00 2.71
1661 1678 1.014564 GCTACACAACTGGAGCGACC 61.015 60.000 0.00 0.00 44.74 4.79
1689 1706 8.231692 TGATAGTTTTTGACTTGTTGGATTGA 57.768 30.769 0.00 0.00 39.86 2.57
1715 1732 8.580720 CACATGGTTAGAGTAGTGCTATCTTAT 58.419 37.037 0.00 0.00 0.00 1.73
1738 1755 5.744171 AGATTGCTTACCACATGTATCACA 58.256 37.500 0.00 0.00 0.00 3.58
1741 1758 8.438676 AGTTTAGATTGCTTACCACATGTATC 57.561 34.615 0.00 0.00 0.00 2.24
1743 1760 9.899661 AATAGTTTAGATTGCTTACCACATGTA 57.100 29.630 0.00 0.00 0.00 2.29
1780 1798 0.763035 AAACGGGTGGAGTAGTGCTT 59.237 50.000 0.00 0.00 0.00 3.91
1825 1853 6.532302 TGAGCGCTTAACAAGAATATAAACGA 59.468 34.615 13.26 0.00 0.00 3.85
1985 2308 6.312180 GCAGTTTTGCTTAAGGTACTACGTAT 59.688 38.462 4.29 0.00 46.95 3.06
1986 2309 5.634859 GCAGTTTTGCTTAAGGTACTACGTA 59.365 40.000 4.29 0.00 46.95 3.57
1987 2310 4.450080 GCAGTTTTGCTTAAGGTACTACGT 59.550 41.667 4.29 0.00 46.95 3.57
1988 2311 4.954442 GCAGTTTTGCTTAAGGTACTACG 58.046 43.478 4.29 0.00 46.95 3.51
2004 2327 0.111061 TCCACCAGCTGATGCAGTTT 59.889 50.000 17.39 0.00 42.74 2.66
2079 2402 0.951558 CCCGCATGTTATACAAGGCC 59.048 55.000 0.00 0.00 31.42 5.19
2110 2433 2.046988 CCGCATGTCAGGTGCTCA 60.047 61.111 0.00 0.00 40.37 4.26
2113 2436 2.359850 TTCCCGCATGTCAGGTGC 60.360 61.111 0.00 0.00 39.18 5.01


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

AutoCloner maintained by Alex Coulton.