Multiple sequence alignment - TraesCS4D01G141100

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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 TraesCS4D01G141100 chr4D 100.000 1932 0 0 1 1932 125096754 125094823 0.000000e+00 3568.0
1 TraesCS4D01G141100 chr4D 100.000 286 0 0 2174 2459 125094581 125094296 1.670000e-146 529.0
2 TraesCS4D01G141100 chr4D 96.181 288 8 2 2174 2458 41197451 41197738 3.700000e-128 468.0
3 TraesCS4D01G141100 chr4D 92.281 285 16 5 1652 1932 28420239 28419957 1.370000e-107 399.0
4 TraesCS4D01G141100 chr4D 88.106 227 12 5 101 327 509807777 509807988 3.140000e-64 255.0
5 TraesCS4D01G141100 chr4D 87.912 182 20 2 110 290 125095528 125095348 1.920000e-51 213.0
6 TraesCS4D01G141100 chr4D 87.912 182 20 2 1227 1407 125096645 125096465 1.920000e-51 213.0
7 TraesCS4D01G141100 chr4B 95.592 794 33 1 794 1585 189082356 189081563 0.000000e+00 1271.0
8 TraesCS4D01G141100 chr4B 91.667 360 26 2 1 359 189085895 189085539 1.700000e-136 496.0
9 TraesCS4D01G141100 chr4B 87.113 194 23 2 98 290 189081935 189081743 4.120000e-53 219.0
10 TraesCS4D01G141100 chr4B 88.136 177 19 2 1227 1402 189085786 189085611 2.480000e-50 209.0
11 TraesCS4D01G141100 chr4B 93.443 61 1 2 358 415 189085500 189085440 1.210000e-13 87.9
12 TraesCS4D01G141100 chr4A 93.359 768 26 4 508 1250 445073779 445074546 0.000000e+00 1112.0
13 TraesCS4D01G141100 chr4A 95.349 344 16 0 1239 1582 445074710 445075053 4.620000e-152 547.0
14 TraesCS4D01G141100 chr4A 93.315 359 16 4 1 359 445073274 445073624 7.790000e-145 523.0
15 TraesCS4D01G141100 chr4A 92.226 283 17 4 1654 1932 471170331 471170050 1.770000e-106 396.0
16 TraesCS4D01G141100 chr4A 88.701 177 18 2 1224 1399 445073380 445073555 5.330000e-52 215.0
17 TraesCS4D01G141100 chr4A 90.722 97 2 2 358 449 445073660 445073754 3.320000e-24 122.0
18 TraesCS4D01G141100 chr6D 96.886 289 6 2 2174 2459 455521108 455520820 4.760000e-132 481.0
19 TraesCS4D01G141100 chr6D 96.503 286 10 0 2174 2459 420557130 420557415 7.960000e-130 473.0
20 TraesCS4D01G141100 chr6D 92.857 280 17 2 1656 1932 10676577 10676298 1.060000e-108 403.0
21 TraesCS4D01G141100 chr6D 91.459 281 18 5 1656 1932 455521436 455521158 4.960000e-102 381.0
22 TraesCS4D01G141100 chr6A 96.886 289 6 2 2174 2459 286335758 286336046 4.760000e-132 481.0
23 TraesCS4D01G141100 chr6A 93.190 279 14 4 1654 1928 286335426 286335703 2.940000e-109 405.0
24 TraesCS4D01G141100 chr7D 96.194 289 8 2 2174 2459 178946453 178946165 1.030000e-128 470.0
25 TraesCS4D01G141100 chr7D 92.933 283 15 4 1654 1932 16184357 16184638 8.190000e-110 407.0
26 TraesCS4D01G141100 chr7D 92.883 281 11 8 1656 1932 178946768 178946493 1.370000e-107 399.0
27 TraesCS4D01G141100 chr7D 93.040 273 16 2 1656 1925 78862186 78862458 1.770000e-106 396.0
28 TraesCS4D01G141100 chr5D 96.194 289 8 2 2174 2459 41226813 41227101 1.030000e-128 470.0
29 TraesCS4D01G141100 chr5D 96.181 288 8 2 2174 2458 489733224 489733511 3.700000e-128 468.0
30 TraesCS4D01G141100 chr5D 95.848 289 9 2 2174 2459 543593677 543593965 4.790000e-127 464.0
31 TraesCS4D01G141100 chr2D 96.181 288 8 2 2175 2459 134646628 134646341 3.700000e-128 468.0
32 TraesCS4D01G141100 chr1D 92.527 281 16 4 1656 1932 425566814 425566535 4.930000e-107 398.0
33 TraesCS4D01G141100 chr5A 84.810 158 9 1 101 258 698615843 698615985 7.090000e-31 145.0


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 TraesCS4D01G141100 chr4D 125094296 125096754 2458 True 1130.75 3568 93.9560 1 2459 4 chr4D.!!$R2 2458
1 TraesCS4D01G141100 chr4B 189081563 189085895 4332 True 456.58 1271 91.1902 1 1585 5 chr4B.!!$R1 1584
2 TraesCS4D01G141100 chr4A 445073274 445075053 1779 False 503.80 1112 92.2892 1 1582 5 chr4A.!!$F1 1581
3 TraesCS4D01G141100 chr6D 455520820 455521436 616 True 431.00 481 94.1725 1656 2459 2 chr6D.!!$R2 803
4 TraesCS4D01G141100 chr6A 286335426 286336046 620 False 443.00 481 95.0380 1654 2459 2 chr6A.!!$F1 805
5 TraesCS4D01G141100 chr7D 178946165 178946768 603 True 434.50 470 94.5385 1656 2459 2 chr7D.!!$R1 803

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
494 565 0.10212 CAGCGTCCCTCACTCATCTC 59.898 60.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 4644 0.252193 CCCTCCTTTCCCATTTGCCA 60.252 55.0 0.0 0.0 0.0 4.92 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
68 69 1.279840 GAACAACGCTGGTGCTGAC 59.720 57.895 0.00 0.00 36.97 3.51
92 93 2.368548 TGCTCAAGTGCTGAAGAAGGTA 59.631 45.455 0.00 0.00 32.17 3.08
101 102 0.739462 TGAAGAAGGTACATGCGGCG 60.739 55.000 0.51 0.51 0.00 6.46
313 314 1.517257 CATCCGGTGTCGTCTGAGC 60.517 63.158 0.00 0.00 33.95 4.26
323 324 2.429351 CGTCTGAGCGACACGAAGC 61.429 63.158 0.00 0.00 42.98 3.86
325 326 1.081175 TCTGAGCGACACGAAGCAG 60.081 57.895 0.00 0.00 35.48 4.24
327 328 1.069924 CTGAGCGACACGAAGCAGAG 61.070 60.000 0.00 0.00 35.48 3.35
404 446 1.525784 CGCGATTGCTGTCTTTTCTCG 60.526 52.381 0.00 0.00 39.65 4.04
464 535 6.942532 ATACACCACAACACCATGAATATC 57.057 37.500 0.00 0.00 0.00 1.63
465 536 4.922206 ACACCACAACACCATGAATATCT 58.078 39.130 0.00 0.00 0.00 1.98
466 537 4.701651 ACACCACAACACCATGAATATCTG 59.298 41.667 0.00 0.00 0.00 2.90
467 538 4.701651 CACCACAACACCATGAATATCTGT 59.298 41.667 0.00 0.00 0.00 3.41
468 539 5.879777 CACCACAACACCATGAATATCTGTA 59.120 40.000 0.00 0.00 0.00 2.74
469 540 5.880332 ACCACAACACCATGAATATCTGTAC 59.120 40.000 0.00 0.00 0.00 2.90
470 541 5.879777 CCACAACACCATGAATATCTGTACA 59.120 40.000 0.00 0.00 0.00 2.90
471 542 6.543465 CCACAACACCATGAATATCTGTACAT 59.457 38.462 0.00 0.00 0.00 2.29
472 543 7.254898 CCACAACACCATGAATATCTGTACATC 60.255 40.741 0.00 0.00 0.00 3.06
473 544 6.767902 ACAACACCATGAATATCTGTACATCC 59.232 38.462 0.00 0.00 0.00 3.51
474 545 6.499106 ACACCATGAATATCTGTACATCCA 57.501 37.500 0.00 0.00 0.00 3.41
475 546 6.291377 ACACCATGAATATCTGTACATCCAC 58.709 40.000 0.00 0.00 0.00 4.02
476 547 6.126796 ACACCATGAATATCTGTACATCCACA 60.127 38.462 0.00 0.00 0.00 4.17
477 548 6.426025 CACCATGAATATCTGTACATCCACAG 59.574 42.308 0.00 0.00 46.04 3.66
478 549 5.410746 CCATGAATATCTGTACATCCACAGC 59.589 44.000 0.00 0.00 44.62 4.40
479 550 4.620982 TGAATATCTGTACATCCACAGCG 58.379 43.478 0.00 0.00 44.62 5.18
480 551 4.099419 TGAATATCTGTACATCCACAGCGT 59.901 41.667 0.00 0.00 44.62 5.07
481 552 2.586258 ATCTGTACATCCACAGCGTC 57.414 50.000 0.00 0.00 44.62 5.19
482 553 0.530744 TCTGTACATCCACAGCGTCC 59.469 55.000 0.00 0.00 44.62 4.79
483 554 0.460284 CTGTACATCCACAGCGTCCC 60.460 60.000 0.00 0.00 39.54 4.46
484 555 0.902984 TGTACATCCACAGCGTCCCT 60.903 55.000 0.00 0.00 0.00 4.20
485 556 0.179108 GTACATCCACAGCGTCCCTC 60.179 60.000 0.00 0.00 0.00 4.30
486 557 0.613572 TACATCCACAGCGTCCCTCA 60.614 55.000 0.00 0.00 0.00 3.86
487 558 1.448540 CATCCACAGCGTCCCTCAC 60.449 63.158 0.00 0.00 0.00 3.51
488 559 1.610673 ATCCACAGCGTCCCTCACT 60.611 57.895 0.00 0.00 0.00 3.41
489 560 1.608717 ATCCACAGCGTCCCTCACTC 61.609 60.000 0.00 0.00 0.00 3.51
490 561 2.574018 CCACAGCGTCCCTCACTCA 61.574 63.158 0.00 0.00 0.00 3.41
491 562 1.593787 CACAGCGTCCCTCACTCAT 59.406 57.895 0.00 0.00 0.00 2.90
492 563 0.459237 CACAGCGTCCCTCACTCATC 60.459 60.000 0.00 0.00 0.00 2.92
493 564 0.613292 ACAGCGTCCCTCACTCATCT 60.613 55.000 0.00 0.00 0.00 2.90
494 565 0.102120 CAGCGTCCCTCACTCATCTC 59.898 60.000 0.00 0.00 0.00 2.75
495 566 0.323816 AGCGTCCCTCACTCATCTCA 60.324 55.000 0.00 0.00 0.00 3.27
496 567 0.179124 GCGTCCCTCACTCATCTCAC 60.179 60.000 0.00 0.00 0.00 3.51
497 568 1.468985 CGTCCCTCACTCATCTCACT 58.531 55.000 0.00 0.00 0.00 3.41
498 569 1.821753 CGTCCCTCACTCATCTCACTT 59.178 52.381 0.00 0.00 0.00 3.16
499 570 3.017442 CGTCCCTCACTCATCTCACTTA 58.983 50.000 0.00 0.00 0.00 2.24
500 571 3.634448 CGTCCCTCACTCATCTCACTTAT 59.366 47.826 0.00 0.00 0.00 1.73
501 572 4.261405 CGTCCCTCACTCATCTCACTTATC 60.261 50.000 0.00 0.00 0.00 1.75
502 573 4.892934 GTCCCTCACTCATCTCACTTATCT 59.107 45.833 0.00 0.00 0.00 1.98
503 574 4.892345 TCCCTCACTCATCTCACTTATCTG 59.108 45.833 0.00 0.00 0.00 2.90
504 575 4.039004 CCCTCACTCATCTCACTTATCTGG 59.961 50.000 0.00 0.00 0.00 3.86
505 576 4.892345 CCTCACTCATCTCACTTATCTGGA 59.108 45.833 0.00 0.00 0.00 3.86
506 577 5.009911 CCTCACTCATCTCACTTATCTGGAG 59.990 48.000 0.00 0.00 0.00 3.86
549 620 5.867716 GCCTCGAGTTCATTGTCTAGTTTAA 59.132 40.000 12.31 0.00 0.00 1.52
562 633 6.403878 TGTCTAGTTTAATAACTGGTGCCTC 58.596 40.000 0.00 0.00 44.22 4.70
635 884 2.287009 CCAAAGAACAAGGCGACTCAAC 60.287 50.000 0.00 0.00 42.68 3.18
675 924 3.483085 CGCGAGCTATATATGAACGTCGA 60.483 47.826 0.00 0.00 0.00 4.20
722 984 3.392616 ACACCAGACCAGAATATCCATCC 59.607 47.826 0.00 0.00 0.00 3.51
731 993 5.191323 ACCAGAATATCCATCCCATGAGATC 59.809 44.000 0.00 0.00 0.00 2.75
733 995 6.296836 CCAGAATATCCATCCCATGAGATCAA 60.297 42.308 0.00 0.00 0.00 2.57
734 996 7.347252 CAGAATATCCATCCCATGAGATCAAT 58.653 38.462 0.00 0.00 0.00 2.57
735 997 8.491958 CAGAATATCCATCCCATGAGATCAATA 58.508 37.037 0.00 0.00 0.00 1.90
736 998 9.238914 AGAATATCCATCCCATGAGATCAATAT 57.761 33.333 0.00 0.00 0.00 1.28
867 3717 3.192466 GGTGCCGATTATAACAAGTCGT 58.808 45.455 5.70 0.00 32.55 4.34
958 3817 5.276915 GCTTAGGCTATTTAGTCTCGCAAAC 60.277 44.000 0.00 0.00 39.36 2.93
996 3855 2.097918 CTTCTCGTCGGTCGTCGG 59.902 66.667 9.65 2.31 40.80 4.79
1344 4378 0.443869 CGTGCATGCACTACTTCCAC 59.556 55.000 39.46 17.38 44.16 4.02
1451 4485 2.971598 CGGTCAAGGCCACCTCCAT 61.972 63.158 5.01 0.00 30.89 3.41
1495 4529 1.795768 TTGCTTCGAGTGCAAGTAGG 58.204 50.000 19.33 0.00 44.24 3.18
1585 4621 3.748048 CCGAGTAATGCTACATTCATGGG 59.252 47.826 0.00 0.00 0.00 4.00
1586 4622 3.748048 CGAGTAATGCTACATTCATGGGG 59.252 47.826 0.00 0.00 0.00 4.96
1587 4623 4.718961 GAGTAATGCTACATTCATGGGGT 58.281 43.478 0.00 0.00 0.00 4.95
1588 4624 5.129368 AGTAATGCTACATTCATGGGGTT 57.871 39.130 0.00 0.00 0.00 4.11
1589 4625 5.518865 AGTAATGCTACATTCATGGGGTTT 58.481 37.500 0.00 0.00 0.00 3.27
1590 4626 5.594317 AGTAATGCTACATTCATGGGGTTTC 59.406 40.000 0.00 0.00 0.00 2.78
1591 4627 3.448093 TGCTACATTCATGGGGTTTCA 57.552 42.857 0.00 0.00 0.00 2.69
1592 4628 3.088532 TGCTACATTCATGGGGTTTCAC 58.911 45.455 0.00 0.00 0.00 3.18
1593 4629 3.245229 TGCTACATTCATGGGGTTTCACT 60.245 43.478 0.00 0.00 0.00 3.41
1594 4630 3.129287 GCTACATTCATGGGGTTTCACTG 59.871 47.826 0.00 0.00 0.00 3.66
1595 4631 3.243359 ACATTCATGGGGTTTCACTGT 57.757 42.857 0.00 0.00 0.00 3.55
1596 4632 2.892852 ACATTCATGGGGTTTCACTGTG 59.107 45.455 0.17 0.17 0.00 3.66
1597 4633 2.746279 TTCATGGGGTTTCACTGTGT 57.254 45.000 7.79 0.00 0.00 3.72
1598 4634 2.270352 TCATGGGGTTTCACTGTGTC 57.730 50.000 7.79 0.36 0.00 3.67
1599 4635 1.492599 TCATGGGGTTTCACTGTGTCA 59.507 47.619 7.79 0.00 0.00 3.58
1600 4636 2.108075 TCATGGGGTTTCACTGTGTCAT 59.892 45.455 7.79 1.72 0.00 3.06
1601 4637 2.746279 TGGGGTTTCACTGTGTCATT 57.254 45.000 7.79 0.00 0.00 2.57
1602 4638 3.866703 TGGGGTTTCACTGTGTCATTA 57.133 42.857 7.79 0.00 0.00 1.90
1603 4639 4.380843 TGGGGTTTCACTGTGTCATTAT 57.619 40.909 7.79 0.00 0.00 1.28
1604 4640 4.078537 TGGGGTTTCACTGTGTCATTATG 58.921 43.478 7.79 0.00 0.00 1.90
1605 4641 4.202514 TGGGGTTTCACTGTGTCATTATGA 60.203 41.667 7.79 0.00 0.00 2.15
1618 4654 4.685924 GTCATTATGACTTGGCAAATGGG 58.314 43.478 17.19 0.00 43.73 4.00
1619 4655 4.402155 GTCATTATGACTTGGCAAATGGGA 59.598 41.667 17.19 0.00 43.73 4.37
1620 4656 5.022122 TCATTATGACTTGGCAAATGGGAA 58.978 37.500 0.00 0.00 0.00 3.97
1621 4657 5.483231 TCATTATGACTTGGCAAATGGGAAA 59.517 36.000 0.00 0.00 0.00 3.13
1622 4658 3.967332 ATGACTTGGCAAATGGGAAAG 57.033 42.857 0.00 0.00 0.00 2.62
1623 4659 1.969923 TGACTTGGCAAATGGGAAAGG 59.030 47.619 0.00 0.00 0.00 3.11
1624 4660 2.247358 GACTTGGCAAATGGGAAAGGA 58.753 47.619 0.00 0.00 0.00 3.36
1625 4661 2.232208 GACTTGGCAAATGGGAAAGGAG 59.768 50.000 0.00 0.00 0.00 3.69
1626 4662 1.551883 CTTGGCAAATGGGAAAGGAGG 59.448 52.381 0.00 0.00 0.00 4.30
1627 4663 0.252193 TGGCAAATGGGAAAGGAGGG 60.252 55.000 0.00 0.00 0.00 4.30
1628 4664 0.977627 GGCAAATGGGAAAGGAGGGG 60.978 60.000 0.00 0.00 0.00 4.79
1629 4665 1.617018 GCAAATGGGAAAGGAGGGGC 61.617 60.000 0.00 0.00 0.00 5.80
1630 4666 0.977627 CAAATGGGAAAGGAGGGGCC 60.978 60.000 0.00 0.00 0.00 5.80
1631 4667 2.181523 AAATGGGAAAGGAGGGGCCC 62.182 60.000 17.12 17.12 41.08 5.80
1633 4669 4.062032 GGGAAAGGAGGGGCCCAC 62.062 72.222 27.72 19.96 40.39 4.61
1634 4670 4.062032 GGAAAGGAGGGGCCCACC 62.062 72.222 29.86 29.86 37.37 4.61
1644 4680 4.957057 GGCCCACCCACCTAAAAA 57.043 55.556 0.00 0.00 0.00 1.94
1645 4681 3.392066 GGCCCACCCACCTAAAAAT 57.608 52.632 0.00 0.00 0.00 1.82
1646 4682 2.535836 GGCCCACCCACCTAAAAATA 57.464 50.000 0.00 0.00 0.00 1.40
1647 4683 2.384828 GGCCCACCCACCTAAAAATAG 58.615 52.381 0.00 0.00 0.00 1.73
1648 4684 2.024751 GGCCCACCCACCTAAAAATAGA 60.025 50.000 0.00 0.00 0.00 1.98
1649 4685 3.288092 GCCCACCCACCTAAAAATAGAG 58.712 50.000 0.00 0.00 0.00 2.43
1650 4686 3.898482 CCCACCCACCTAAAAATAGAGG 58.102 50.000 0.00 0.00 38.92 3.69
1651 4687 3.526019 CCCACCCACCTAAAAATAGAGGA 59.474 47.826 0.00 0.00 36.61 3.71
1652 4688 4.385310 CCCACCCACCTAAAAATAGAGGAG 60.385 50.000 0.00 0.00 36.61 3.69
2349 5389 5.778862 TGAACATTGTAGATGAGTTCGTCA 58.221 37.500 4.32 0.00 40.95 4.35
2383 5426 5.661312 TCCGAAGAAGAATTTGATAGGGAGA 59.339 40.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.401699 CTTGAGCAGGGTCAGCACCA 62.402 60.000 1.16 0.00 45.94 4.17
68 69 0.035881 TCTTCAGCACTTGAGCAGGG 59.964 55.000 0.00 0.00 37.07 4.45
293 294 0.243907 CTCAGACGACACCGGATGTT 59.756 55.000 9.46 0.00 43.56 2.71
295 296 1.517257 GCTCAGACGACACCGGATG 60.517 63.158 9.46 5.32 40.78 3.51
313 314 1.914051 CATGTACTCTGCTTCGTGTCG 59.086 52.381 0.00 0.00 0.00 4.35
319 320 3.242673 GCTGCATTCATGTACTCTGCTTC 60.243 47.826 0.00 0.00 34.02 3.86
323 324 2.871022 GGAGCTGCATTCATGTACTCTG 59.129 50.000 0.00 0.00 0.00 3.35
325 326 3.129871 GAGGAGCTGCATTCATGTACTC 58.870 50.000 8.35 0.00 0.00 2.59
327 328 2.158842 AGGAGGAGCTGCATTCATGTAC 60.159 50.000 8.35 0.00 0.00 2.90
404 446 2.500098 GGAGGAACAAATTAAAGGGGGC 59.500 50.000 0.00 0.00 0.00 5.80
465 536 0.902984 AGGGACGCTGTGGATGTACA 60.903 55.000 0.00 0.00 0.00 2.90
466 537 0.179108 GAGGGACGCTGTGGATGTAC 60.179 60.000 0.00 0.00 0.00 2.90
467 538 0.613572 TGAGGGACGCTGTGGATGTA 60.614 55.000 0.00 0.00 0.00 2.29
468 539 1.913262 TGAGGGACGCTGTGGATGT 60.913 57.895 0.00 0.00 0.00 3.06
469 540 1.448540 GTGAGGGACGCTGTGGATG 60.449 63.158 0.00 0.00 0.00 3.51
470 541 1.608717 GAGTGAGGGACGCTGTGGAT 61.609 60.000 0.00 0.00 39.64 3.41
471 542 2.203640 AGTGAGGGACGCTGTGGA 60.204 61.111 0.00 0.00 37.99 4.02
472 543 1.892819 ATGAGTGAGGGACGCTGTGG 61.893 60.000 0.00 0.00 39.64 4.17
473 544 0.459237 GATGAGTGAGGGACGCTGTG 60.459 60.000 0.00 0.00 39.64 3.66
474 545 0.613292 AGATGAGTGAGGGACGCTGT 60.613 55.000 0.00 0.00 39.64 4.40
475 546 0.102120 GAGATGAGTGAGGGACGCTG 59.898 60.000 0.00 0.00 39.64 5.18
476 547 0.323816 TGAGATGAGTGAGGGACGCT 60.324 55.000 0.00 0.00 42.47 5.07
477 548 0.179124 GTGAGATGAGTGAGGGACGC 60.179 60.000 0.00 0.00 0.00 5.19
478 549 1.468985 AGTGAGATGAGTGAGGGACG 58.531 55.000 0.00 0.00 0.00 4.79
479 550 4.892934 AGATAAGTGAGATGAGTGAGGGAC 59.107 45.833 0.00 0.00 0.00 4.46
480 551 4.892345 CAGATAAGTGAGATGAGTGAGGGA 59.108 45.833 0.00 0.00 0.00 4.20
481 552 4.039004 CCAGATAAGTGAGATGAGTGAGGG 59.961 50.000 0.00 0.00 0.00 4.30
482 553 4.892345 TCCAGATAAGTGAGATGAGTGAGG 59.108 45.833 0.00 0.00 0.00 3.86
483 554 5.009911 CCTCCAGATAAGTGAGATGAGTGAG 59.990 48.000 0.00 0.00 0.00 3.51
484 555 4.892345 CCTCCAGATAAGTGAGATGAGTGA 59.108 45.833 0.00 0.00 0.00 3.41
485 556 4.648762 ACCTCCAGATAAGTGAGATGAGTG 59.351 45.833 0.00 0.00 0.00 3.51
486 557 4.648762 CACCTCCAGATAAGTGAGATGAGT 59.351 45.833 0.00 0.00 31.79 3.41
487 558 4.892345 TCACCTCCAGATAAGTGAGATGAG 59.108 45.833 0.00 0.00 34.44 2.90
488 559 4.646945 GTCACCTCCAGATAAGTGAGATGA 59.353 45.833 0.00 0.00 39.76 2.92
489 560 4.202202 GGTCACCTCCAGATAAGTGAGATG 60.202 50.000 0.00 0.00 39.76 2.90
490 561 3.964031 GGTCACCTCCAGATAAGTGAGAT 59.036 47.826 0.00 0.00 39.76 2.75
491 562 3.245622 TGGTCACCTCCAGATAAGTGAGA 60.246 47.826 0.00 0.00 39.76 3.27
492 563 3.099905 TGGTCACCTCCAGATAAGTGAG 58.900 50.000 0.00 0.00 39.76 3.51
493 564 3.184382 TGGTCACCTCCAGATAAGTGA 57.816 47.619 0.00 0.00 36.92 3.41
494 565 3.491619 CGATGGTCACCTCCAGATAAGTG 60.492 52.174 0.00 0.00 41.05 3.16
495 566 2.695666 CGATGGTCACCTCCAGATAAGT 59.304 50.000 0.00 0.00 41.05 2.24
496 567 2.695666 ACGATGGTCACCTCCAGATAAG 59.304 50.000 0.00 0.00 41.05 1.73
497 568 2.747177 ACGATGGTCACCTCCAGATAA 58.253 47.619 0.00 0.00 41.05 1.75
498 569 2.454336 ACGATGGTCACCTCCAGATA 57.546 50.000 0.00 0.00 41.05 1.98
499 570 2.431057 GTTACGATGGTCACCTCCAGAT 59.569 50.000 0.00 0.00 41.05 2.90
500 571 1.822990 GTTACGATGGTCACCTCCAGA 59.177 52.381 0.00 0.00 41.05 3.86
501 572 1.548719 TGTTACGATGGTCACCTCCAG 59.451 52.381 0.00 0.00 41.05 3.86
502 573 1.634960 TGTTACGATGGTCACCTCCA 58.365 50.000 0.00 0.00 42.01 3.86
503 574 2.093658 ACATGTTACGATGGTCACCTCC 60.094 50.000 0.00 0.00 0.00 4.30
504 575 2.930040 CACATGTTACGATGGTCACCTC 59.070 50.000 0.00 0.00 0.00 3.85
505 576 2.935238 GCACATGTTACGATGGTCACCT 60.935 50.000 0.00 0.00 0.00 4.00
506 577 1.396996 GCACATGTTACGATGGTCACC 59.603 52.381 0.00 0.00 0.00 4.02
549 620 2.038557 ACGTTTCTGAGGCACCAGTTAT 59.961 45.455 6.78 0.00 35.71 1.89
635 884 0.366871 CGTCGTCGGAATTGCTCTTG 59.633 55.000 0.00 0.00 0.00 3.02
736 998 9.537192 ACTAGTTACATACGCAAAGCATTTATA 57.463 29.630 0.00 0.00 35.03 0.98
867 3717 1.320344 AACGATGGCTACGAGGCTGA 61.320 55.000 10.29 0.00 41.96 4.26
958 3817 2.478831 GCTGCTAGCTGCCTTAGTTAG 58.521 52.381 30.25 10.67 41.59 2.34
976 3835 2.672307 ACGACCGACGAGAAGGCT 60.672 61.111 0.00 0.00 45.77 4.58
996 3855 1.810030 GGCGTTGGAGGACATCGAC 60.810 63.158 0.00 0.00 43.22 4.20
1495 4529 4.746611 CAGACAATTTTCAAGCTGGTTTCC 59.253 41.667 0.00 0.00 0.00 3.13
1597 4633 4.608269 TCCCATTTGCCAAGTCATAATGA 58.392 39.130 0.00 0.00 0.00 2.57
1598 4634 5.341872 TTCCCATTTGCCAAGTCATAATG 57.658 39.130 0.00 0.00 0.00 1.90
1599 4635 5.104817 CCTTTCCCATTTGCCAAGTCATAAT 60.105 40.000 0.00 0.00 0.00 1.28
1600 4636 4.222588 CCTTTCCCATTTGCCAAGTCATAA 59.777 41.667 0.00 0.00 0.00 1.90
1601 4637 3.768757 CCTTTCCCATTTGCCAAGTCATA 59.231 43.478 0.00 0.00 0.00 2.15
1602 4638 2.568509 CCTTTCCCATTTGCCAAGTCAT 59.431 45.455 0.00 0.00 0.00 3.06
1603 4639 1.969923 CCTTTCCCATTTGCCAAGTCA 59.030 47.619 0.00 0.00 0.00 3.41
1604 4640 2.232208 CTCCTTTCCCATTTGCCAAGTC 59.768 50.000 0.00 0.00 0.00 3.01
1605 4641 2.250924 CTCCTTTCCCATTTGCCAAGT 58.749 47.619 0.00 0.00 0.00 3.16
1606 4642 1.551883 CCTCCTTTCCCATTTGCCAAG 59.448 52.381 0.00 0.00 0.00 3.61
1607 4643 1.643310 CCTCCTTTCCCATTTGCCAA 58.357 50.000 0.00 0.00 0.00 4.52
1608 4644 0.252193 CCCTCCTTTCCCATTTGCCA 60.252 55.000 0.00 0.00 0.00 4.92
1609 4645 0.977627 CCCCTCCTTTCCCATTTGCC 60.978 60.000 0.00 0.00 0.00 4.52
1610 4646 1.617018 GCCCCTCCTTTCCCATTTGC 61.617 60.000 0.00 0.00 0.00 3.68
1611 4647 0.977627 GGCCCCTCCTTTCCCATTTG 60.978 60.000 0.00 0.00 0.00 2.32
1612 4648 1.392131 GGCCCCTCCTTTCCCATTT 59.608 57.895 0.00 0.00 0.00 2.32
1613 4649 2.636617 GGGCCCCTCCTTTCCCATT 61.637 63.158 12.23 0.00 38.62 3.16
1614 4650 3.029981 GGGCCCCTCCTTTCCCAT 61.030 66.667 12.23 0.00 38.62 4.00
1615 4651 4.626745 TGGGCCCCTCCTTTCCCA 62.627 66.667 22.27 0.00 45.87 4.37
1616 4652 4.062032 GTGGGCCCCTCCTTTCCC 62.062 72.222 22.27 0.00 39.22 3.97
1617 4653 4.062032 GGTGGGCCCCTCCTTTCC 62.062 72.222 22.27 6.49 34.62 3.13
1627 4663 2.024751 TCTATTTTTAGGTGGGTGGGCC 60.025 50.000 0.00 0.00 0.00 5.80
1628 4664 3.288092 CTCTATTTTTAGGTGGGTGGGC 58.712 50.000 0.00 0.00 0.00 5.36
1629 4665 3.526019 TCCTCTATTTTTAGGTGGGTGGG 59.474 47.826 0.00 0.00 34.30 4.61
1630 4666 4.227527 ACTCCTCTATTTTTAGGTGGGTGG 59.772 45.833 0.00 0.00 34.30 4.61
1631 4667 5.437191 ACTCCTCTATTTTTAGGTGGGTG 57.563 43.478 0.00 0.00 34.30 4.61
1632 4668 6.964086 TCTTACTCCTCTATTTTTAGGTGGGT 59.036 38.462 0.00 0.00 34.30 4.51
1633 4669 7.433537 TCTTACTCCTCTATTTTTAGGTGGG 57.566 40.000 0.00 0.00 34.30 4.61
1634 4670 6.987404 GCTCTTACTCCTCTATTTTTAGGTGG 59.013 42.308 0.00 0.00 34.30 4.61
1635 4671 7.556844 TGCTCTTACTCCTCTATTTTTAGGTG 58.443 38.462 0.00 0.00 34.30 4.00
1636 4672 7.735326 TGCTCTTACTCCTCTATTTTTAGGT 57.265 36.000 0.00 0.00 34.30 3.08
1637 4673 8.646900 AGATGCTCTTACTCCTCTATTTTTAGG 58.353 37.037 0.00 0.00 0.00 2.69
1640 4676 8.543774 TGAAGATGCTCTTACTCCTCTATTTTT 58.456 33.333 0.00 0.00 36.73 1.94
1641 4677 8.083828 TGAAGATGCTCTTACTCCTCTATTTT 57.916 34.615 0.00 0.00 36.73 1.82
1642 4678 7.667575 TGAAGATGCTCTTACTCCTCTATTT 57.332 36.000 0.00 0.00 36.73 1.40
1643 4679 7.124901 TGTTGAAGATGCTCTTACTCCTCTATT 59.875 37.037 0.00 0.00 36.73 1.73
1644 4680 6.609212 TGTTGAAGATGCTCTTACTCCTCTAT 59.391 38.462 0.00 0.00 36.73 1.98
1645 4681 5.952347 TGTTGAAGATGCTCTTACTCCTCTA 59.048 40.000 0.00 0.00 36.73 2.43
1646 4682 4.774726 TGTTGAAGATGCTCTTACTCCTCT 59.225 41.667 0.00 0.00 36.73 3.69
1647 4683 5.078411 TGTTGAAGATGCTCTTACTCCTC 57.922 43.478 0.00 0.00 36.73 3.71
1648 4684 4.622695 GCTGTTGAAGATGCTCTTACTCCT 60.623 45.833 0.00 0.00 36.73 3.69
1649 4685 3.620821 GCTGTTGAAGATGCTCTTACTCC 59.379 47.826 0.00 0.00 36.73 3.85
1650 4686 3.620821 GGCTGTTGAAGATGCTCTTACTC 59.379 47.826 0.00 0.00 36.73 2.59
1651 4687 3.604582 GGCTGTTGAAGATGCTCTTACT 58.395 45.455 0.00 0.00 36.73 2.24
1652 4688 2.349886 CGGCTGTTGAAGATGCTCTTAC 59.650 50.000 0.00 0.00 36.73 2.34
1664 4700 3.932580 CTAGTGGCGCGGCTGTTGA 62.933 63.158 33.23 10.23 0.00 3.18
1684 4722 2.202427 GCAATTTTAGCGCGCGGT 60.202 55.556 37.43 37.43 0.00 5.68
1692 4730 2.596862 GCGCTAAAACGGGCAATTTTAG 59.403 45.455 20.04 20.04 45.95 1.85
1693 4731 2.597520 GCGCTAAAACGGGCAATTTTA 58.402 42.857 0.00 5.41 41.86 1.52
1725 4763 1.873903 CGCCCGCTGAAGCAACTATAT 60.874 52.381 2.79 0.00 42.21 0.86
1762 4802 2.459934 CGCGCTGAACTACATATGACA 58.540 47.619 10.38 0.00 0.00 3.58
1764 4804 1.487482 GCGCGCTGAACTACATATGA 58.513 50.000 26.67 0.00 0.00 2.15
2378 5418 1.207791 TGCAAGATCCTCCTTCTCCC 58.792 55.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.