Multiple sequence alignment - TraesCS1D01G429000

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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 TraesCS1D01G429000 chr1D 100.000 2402 0 0 1 2402 480940195 480937794 0.000000e+00 4436
1 TraesCS1D01G429000 chr1D 85.828 1510 191 16 1 1504 452581292 452579800 0.000000e+00 1581
2 TraesCS1D01G429000 chr6D 97.543 1506 21 7 1 1504 153176517 153175026 0.000000e+00 2562
3 TraesCS1D01G429000 chr6D 97.236 1411 37 1 1 1411 69504179 69502771 0.000000e+00 2388
4 TraesCS1D01G429000 chr6D 90.164 610 41 8 1629 2229 65107743 65108342 0.000000e+00 776
5 TraesCS1D01G429000 chr6D 88.925 614 45 10 1630 2229 60125062 60124458 0.000000e+00 736
6 TraesCS1D01G429000 chr6D 96.610 177 6 0 2226 2402 65109026 65109202 6.490000e-76 294
7 TraesCS1D01G429000 chr6D 96.610 177 6 0 2226 2402 200489211 200489387 6.490000e-76 294
8 TraesCS1D01G429000 chr7D 96.815 1507 33 5 1 1504 274862408 274860914 0.000000e+00 2503
9 TraesCS1D01G429000 chr7D 96.045 177 7 0 2226 2402 461390738 461390562 3.020000e-74 289
10 TraesCS1D01G429000 chr7D 91.584 202 16 1 2201 2402 90045673 90045473 6.540000e-71 278
11 TraesCS1D01G429000 chr4D 96.959 1480 39 3 1 1480 270688062 270689535 0.000000e+00 2479
12 TraesCS1D01G429000 chr4D 90.939 607 39 7 1629 2229 473079759 473080355 0.000000e+00 802
13 TraesCS1D01G429000 chr4D 86.993 592 40 12 1645 2229 363693359 363692798 1.210000e-177 632
14 TraesCS1D01G429000 chr4D 95.480 177 8 0 2226 2402 363692123 363691947 1.410000e-72 283
15 TraesCS1D01G429000 chr4A 94.328 1481 79 4 1 1480 521299093 521300569 0.000000e+00 2265
16 TraesCS1D01G429000 chr4A 90.897 1505 127 3 1 1505 429502174 429503668 0.000000e+00 2012
17 TraesCS1D01G429000 chr2D 86.698 1496 180 12 17 1506 10068180 10069662 0.000000e+00 1642
18 TraesCS1D01G429000 chr2D 90.413 605 44 7 1629 2229 293685008 293685602 0.000000e+00 784
19 TraesCS1D01G429000 chr2D 92.308 533 35 4 1629 2155 548745694 548746226 0.000000e+00 752
20 TraesCS1D01G429000 chr2D 95.480 177 8 0 2226 2402 548746896 548747072 1.410000e-72 283
21 TraesCS1D01G429000 chr1A 86.288 1495 189 9 13 1504 544569061 544570542 0.000000e+00 1611
22 TraesCS1D01G429000 chr1A 86.579 611 51 19 1627 2229 344296265 344296852 0.000000e+00 645
23 TraesCS1D01G429000 chr5D 90.954 608 42 6 1627 2229 46715153 46715752 0.000000e+00 806
24 TraesCS1D01G429000 chr5D 90.413 605 44 5 1629 2229 477021492 477020898 0.000000e+00 784
25 TraesCS1D01G429000 chr5D 97.143 175 5 0 2228 2402 460192913 460192739 1.810000e-76 296
26 TraesCS1D01G429000 chr5D 95.480 177 8 0 2226 2402 462073185 462073361 1.410000e-72 283
27 TraesCS1D01G429000 chr7B 89.604 606 47 5 1629 2229 68531861 68532455 0.000000e+00 756
28 TraesCS1D01G429000 chr7B 82.473 639 59 30 1627 2229 126207582 126208203 5.920000e-141 510
29 TraesCS1D01G429000 chr3D 79.538 650 59 31 1629 2241 231731516 231732128 1.730000e-106 396
30 TraesCS1D01G429000 chr6B 96.045 177 7 0 2226 2402 82531130 82530954 3.020000e-74 289


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 TraesCS1D01G429000 chr1D 480937794 480940195 2401 True 4436.0 4436 100.0000 1 2402 1 chr1D.!!$R2 2401
1 TraesCS1D01G429000 chr1D 452579800 452581292 1492 True 1581.0 1581 85.8280 1 1504 1 chr1D.!!$R1 1503
2 TraesCS1D01G429000 chr6D 153175026 153176517 1491 True 2562.0 2562 97.5430 1 1504 1 chr6D.!!$R3 1503
3 TraesCS1D01G429000 chr6D 69502771 69504179 1408 True 2388.0 2388 97.2360 1 1411 1 chr6D.!!$R2 1410
4 TraesCS1D01G429000 chr6D 60124458 60125062 604 True 736.0 736 88.9250 1630 2229 1 chr6D.!!$R1 599
5 TraesCS1D01G429000 chr6D 65107743 65109202 1459 False 535.0 776 93.3870 1629 2402 2 chr6D.!!$F2 773
6 TraesCS1D01G429000 chr7D 274860914 274862408 1494 True 2503.0 2503 96.8150 1 1504 1 chr7D.!!$R2 1503
7 TraesCS1D01G429000 chr4D 270688062 270689535 1473 False 2479.0 2479 96.9590 1 1480 1 chr4D.!!$F1 1479
8 TraesCS1D01G429000 chr4D 473079759 473080355 596 False 802.0 802 90.9390 1629 2229 1 chr4D.!!$F2 600
9 TraesCS1D01G429000 chr4D 363691947 363693359 1412 True 457.5 632 91.2365 1645 2402 2 chr4D.!!$R1 757
10 TraesCS1D01G429000 chr4A 521299093 521300569 1476 False 2265.0 2265 94.3280 1 1480 1 chr4A.!!$F2 1479
11 TraesCS1D01G429000 chr4A 429502174 429503668 1494 False 2012.0 2012 90.8970 1 1505 1 chr4A.!!$F1 1504
12 TraesCS1D01G429000 chr2D 10068180 10069662 1482 False 1642.0 1642 86.6980 17 1506 1 chr2D.!!$F1 1489
13 TraesCS1D01G429000 chr2D 293685008 293685602 594 False 784.0 784 90.4130 1629 2229 1 chr2D.!!$F2 600
14 TraesCS1D01G429000 chr2D 548745694 548747072 1378 False 517.5 752 93.8940 1629 2402 2 chr2D.!!$F3 773
15 TraesCS1D01G429000 chr1A 544569061 544570542 1481 False 1611.0 1611 86.2880 13 1504 1 chr1A.!!$F2 1491
16 TraesCS1D01G429000 chr1A 344296265 344296852 587 False 645.0 645 86.5790 1627 2229 1 chr1A.!!$F1 602
17 TraesCS1D01G429000 chr5D 46715153 46715752 599 False 806.0 806 90.9540 1627 2229 1 chr5D.!!$F1 602
18 TraesCS1D01G429000 chr5D 477020898 477021492 594 True 784.0 784 90.4130 1629 2229 1 chr5D.!!$R2 600
19 TraesCS1D01G429000 chr7B 68531861 68532455 594 False 756.0 756 89.6040 1629 2229 1 chr7B.!!$F1 600
20 TraesCS1D01G429000 chr7B 126207582 126208203 621 False 510.0 510 82.4730 1627 2229 1 chr7B.!!$F2 602
21 TraesCS1D01G429000 chr3D 231731516 231732128 612 False 396.0 396 79.5380 1629 2241 1 chr3D.!!$F1 612

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
829 834 2.114625 TGGACCGACCAGACGAGT 59.885 61.111 0.0 0.0 44.64 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2250 0.395586 CCCGGAATGGAGCCATGAAA 60.396 55.0 0.73 0.0 42.0 2.69 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
102 104 2.703007 CCCTCTCTCCCCTATCAAACTG 59.297 54.545 0.00 0.00 0.00 3.16
111 113 2.544685 CCTATCAAACTGCCACTCTCG 58.455 52.381 0.00 0.00 0.00 4.04
141 143 5.064962 CGACCCTATACTAGATAGCTTTCGG 59.935 48.000 0.00 0.00 0.00 4.30
666 668 4.651962 CCTCTACAAAAAGTTTTCCCCCAA 59.348 41.667 0.32 0.00 0.00 4.12
707 709 4.965532 AGATGACAAGGTTCTAGTGGCTAT 59.034 41.667 0.00 0.00 0.00 2.97
741 743 3.381045 CAGCTTATTATCGAACCTGCGA 58.619 45.455 0.00 0.00 45.22 5.10
829 834 2.114625 TGGACCGACCAGACGAGT 59.885 61.111 0.00 0.00 44.64 4.18
1304 1311 7.042335 ACGCTAAGAAATATTGTAGCAGACTT 58.958 34.615 18.73 0.00 39.13 3.01
1305 1312 7.222999 ACGCTAAGAAATATTGTAGCAGACTTC 59.777 37.037 18.73 0.00 39.13 3.01
1323 1330 4.488770 ACTTCTCTCTCTCTGGGTTTTCT 58.511 43.478 0.00 0.00 0.00 2.52
1385 1392 5.013599 AGTGGCTAAATTTTCTCTCCTCTGT 59.986 40.000 0.00 0.00 0.00 3.41
1526 1535 9.691362 AAAACATACAGTTATTTGTGATCAACC 57.309 29.630 0.00 0.00 40.26 3.77
1527 1536 7.391148 ACATACAGTTATTTGTGATCAACCC 57.609 36.000 0.00 0.00 32.93 4.11
1528 1537 7.175104 ACATACAGTTATTTGTGATCAACCCT 58.825 34.615 0.00 0.00 32.93 4.34
1529 1538 7.669722 ACATACAGTTATTTGTGATCAACCCTT 59.330 33.333 0.00 0.00 32.93 3.95
1530 1539 6.331369 ACAGTTATTTGTGATCAACCCTTG 57.669 37.500 0.00 0.00 32.93 3.61
1531 1540 6.068010 ACAGTTATTTGTGATCAACCCTTGA 58.932 36.000 0.00 0.00 45.01 3.02
1532 1541 6.207417 ACAGTTATTTGTGATCAACCCTTGAG 59.793 38.462 0.00 0.00 43.98 3.02
1533 1542 5.183904 AGTTATTTGTGATCAACCCTTGAGC 59.816 40.000 0.00 0.00 45.81 4.26
1534 1543 1.909700 TTGTGATCAACCCTTGAGCC 58.090 50.000 0.00 0.00 45.05 4.70
1535 1544 1.067295 TGTGATCAACCCTTGAGCCT 58.933 50.000 0.00 0.00 45.05 4.58
1536 1545 1.003580 TGTGATCAACCCTTGAGCCTC 59.996 52.381 0.00 0.00 45.05 4.70
1537 1546 1.003580 GTGATCAACCCTTGAGCCTCA 59.996 52.381 0.00 0.00 45.05 3.86
1538 1547 1.280133 TGATCAACCCTTGAGCCTCAG 59.720 52.381 0.00 0.00 45.05 3.35
1539 1548 0.622665 ATCAACCCTTGAGCCTCAGG 59.377 55.000 0.00 0.00 43.98 3.86
1540 1549 0.473694 TCAACCCTTGAGCCTCAGGA 60.474 55.000 5.25 0.00 34.08 3.86
1541 1550 0.622665 CAACCCTTGAGCCTCAGGAT 59.377 55.000 5.25 0.00 0.00 3.24
1542 1551 0.915364 AACCCTTGAGCCTCAGGATC 59.085 55.000 0.43 0.43 38.78 3.36
1543 1552 0.252881 ACCCTTGAGCCTCAGGATCA 60.253 55.000 7.85 7.85 46.95 2.92
1548 1557 0.757512 TGAGCCTCAGGATCATCTGC 59.242 55.000 7.85 0.00 43.58 4.26
1549 1558 1.050204 GAGCCTCAGGATCATCTGCT 58.950 55.000 3.32 0.00 38.12 4.24
1550 1559 1.417145 GAGCCTCAGGATCATCTGCTT 59.583 52.381 3.32 0.00 38.12 3.91
1551 1560 1.417145 AGCCTCAGGATCATCTGCTTC 59.583 52.381 0.00 0.00 34.91 3.86
1552 1561 1.542987 GCCTCAGGATCATCTGCTTCC 60.543 57.143 0.00 0.00 34.91 3.46
1553 1562 1.270199 CCTCAGGATCATCTGCTTCCG 60.270 57.143 0.00 0.00 34.61 4.30
1554 1563 0.105593 TCAGGATCATCTGCTTCCGC 59.894 55.000 0.00 0.00 34.61 5.54
1555 1564 0.883814 CAGGATCATCTGCTTCCGCC 60.884 60.000 0.00 0.00 34.61 6.13
1556 1565 1.053264 AGGATCATCTGCTTCCGCCT 61.053 55.000 0.00 0.00 34.61 5.52
1557 1566 0.602372 GGATCATCTGCTTCCGCCTC 60.602 60.000 0.00 0.00 34.43 4.70
1558 1567 0.105593 GATCATCTGCTTCCGCCTCA 59.894 55.000 0.00 0.00 34.43 3.86
1559 1568 0.763652 ATCATCTGCTTCCGCCTCAT 59.236 50.000 0.00 0.00 34.43 2.90
1560 1569 0.105593 TCATCTGCTTCCGCCTCATC 59.894 55.000 0.00 0.00 34.43 2.92
1561 1570 0.106335 CATCTGCTTCCGCCTCATCT 59.894 55.000 0.00 0.00 34.43 2.90
1562 1571 0.106335 ATCTGCTTCCGCCTCATCTG 59.894 55.000 0.00 0.00 34.43 2.90
1563 1572 1.220206 CTGCTTCCGCCTCATCTGT 59.780 57.895 0.00 0.00 34.43 3.41
1564 1573 1.078918 TGCTTCCGCCTCATCTGTG 60.079 57.895 0.00 0.00 34.43 3.66
1565 1574 1.817099 GCTTCCGCCTCATCTGTGG 60.817 63.158 0.00 0.00 34.62 4.17
1566 1575 1.900351 CTTCCGCCTCATCTGTGGA 59.100 57.895 2.54 0.00 40.52 4.02
1567 1576 0.460987 CTTCCGCCTCATCTGTGGAC 60.461 60.000 2.54 0.00 41.88 4.02
1568 1577 1.899437 TTCCGCCTCATCTGTGGACC 61.899 60.000 2.54 0.00 41.88 4.46
1569 1578 2.659063 CCGCCTCATCTGTGGACCA 61.659 63.158 2.54 0.00 35.32 4.02
1570 1579 1.448540 CGCCTCATCTGTGGACCAC 60.449 63.158 18.28 18.28 34.56 4.16
1571 1580 1.892819 CGCCTCATCTGTGGACCACT 61.893 60.000 24.81 2.35 35.11 4.00
1572 1581 1.195115 GCCTCATCTGTGGACCACTA 58.805 55.000 24.81 13.70 35.11 2.74
1573 1582 1.555075 GCCTCATCTGTGGACCACTAA 59.445 52.381 24.81 13.34 35.11 2.24
1574 1583 2.171448 GCCTCATCTGTGGACCACTAAT 59.829 50.000 24.81 14.95 35.11 1.73
1575 1584 3.388024 GCCTCATCTGTGGACCACTAATA 59.612 47.826 24.81 8.47 35.11 0.98
1576 1585 4.141711 GCCTCATCTGTGGACCACTAATAA 60.142 45.833 24.81 3.79 35.11 1.40
1577 1586 5.360591 CCTCATCTGTGGACCACTAATAAC 58.639 45.833 24.81 0.00 35.11 1.89
1578 1587 5.129485 CCTCATCTGTGGACCACTAATAACT 59.871 44.000 24.81 0.99 35.11 2.24
1579 1588 6.352222 CCTCATCTGTGGACCACTAATAACTT 60.352 42.308 24.81 0.00 35.11 2.66
1580 1589 7.016153 TCATCTGTGGACCACTAATAACTTT 57.984 36.000 24.81 0.00 35.11 2.66
1581 1590 6.878923 TCATCTGTGGACCACTAATAACTTTG 59.121 38.462 24.81 9.70 35.11 2.77
1582 1591 6.428083 TCTGTGGACCACTAATAACTTTGA 57.572 37.500 24.81 0.00 35.11 2.69
1583 1592 6.228258 TCTGTGGACCACTAATAACTTTGAC 58.772 40.000 24.81 0.00 35.11 3.18
1584 1593 6.042781 TCTGTGGACCACTAATAACTTTGACT 59.957 38.462 24.81 0.00 35.11 3.41
1585 1594 5.995282 TGTGGACCACTAATAACTTTGACTG 59.005 40.000 24.81 0.00 35.11 3.51
1586 1595 5.411669 GTGGACCACTAATAACTTTGACTGG 59.588 44.000 17.84 0.00 0.00 4.00
1587 1596 4.395231 GGACCACTAATAACTTTGACTGGC 59.605 45.833 0.00 0.00 0.00 4.85
1588 1597 4.332828 ACCACTAATAACTTTGACTGGCC 58.667 43.478 0.00 0.00 0.00 5.36
1589 1598 4.202524 ACCACTAATAACTTTGACTGGCCA 60.203 41.667 4.71 4.71 0.00 5.36
1590 1599 4.156008 CCACTAATAACTTTGACTGGCCAC 59.844 45.833 0.00 0.00 0.00 5.01
1591 1600 5.003804 CACTAATAACTTTGACTGGCCACT 58.996 41.667 0.00 0.00 0.00 4.00
1592 1601 6.170506 CACTAATAACTTTGACTGGCCACTA 58.829 40.000 0.00 0.00 0.00 2.74
1593 1602 6.653320 CACTAATAACTTTGACTGGCCACTAA 59.347 38.462 0.00 0.00 0.00 2.24
1594 1603 7.336931 CACTAATAACTTTGACTGGCCACTAAT 59.663 37.037 0.00 0.00 0.00 1.73
1595 1604 8.545472 ACTAATAACTTTGACTGGCCACTAATA 58.455 33.333 0.00 0.00 0.00 0.98
1596 1605 9.391006 CTAATAACTTTGACTGGCCACTAATAA 57.609 33.333 0.00 0.00 0.00 1.40
1597 1606 5.959618 AACTTTGACTGGCCACTAATAAC 57.040 39.130 0.00 0.00 0.00 1.89
1598 1607 5.242795 ACTTTGACTGGCCACTAATAACT 57.757 39.130 0.00 0.00 0.00 2.24
1599 1608 5.631119 ACTTTGACTGGCCACTAATAACTT 58.369 37.500 0.00 0.00 0.00 2.66
1600 1609 6.068670 ACTTTGACTGGCCACTAATAACTTT 58.931 36.000 0.00 0.00 0.00 2.66
1601 1610 5.957842 TTGACTGGCCACTAATAACTTTG 57.042 39.130 0.00 0.00 0.00 2.77
1602 1611 5.235850 TGACTGGCCACTAATAACTTTGA 57.764 39.130 0.00 0.00 0.00 2.69
1603 1612 5.001232 TGACTGGCCACTAATAACTTTGAC 58.999 41.667 0.00 0.00 0.00 3.18
1604 1613 5.221843 TGACTGGCCACTAATAACTTTGACT 60.222 40.000 0.00 0.00 0.00 3.41
1605 1614 5.003804 ACTGGCCACTAATAACTTTGACTG 58.996 41.667 0.00 0.00 0.00 3.51
1606 1615 4.980573 TGGCCACTAATAACTTTGACTGT 58.019 39.130 0.00 0.00 0.00 3.55
1607 1616 6.116711 TGGCCACTAATAACTTTGACTGTA 57.883 37.500 0.00 0.00 0.00 2.74
1608 1617 6.535540 TGGCCACTAATAACTTTGACTGTAA 58.464 36.000 0.00 0.00 0.00 2.41
1609 1618 6.653320 TGGCCACTAATAACTTTGACTGTAAG 59.347 38.462 0.00 0.00 42.29 2.34
1610 1619 6.877322 GGCCACTAATAACTTTGACTGTAAGA 59.123 38.462 0.00 0.00 37.43 2.10
1611 1620 7.553044 GGCCACTAATAACTTTGACTGTAAGAT 59.447 37.037 0.00 0.00 37.43 2.40
1612 1621 9.595823 GCCACTAATAACTTTGACTGTAAGATA 57.404 33.333 0.00 0.00 37.43 1.98
2118 2211 1.599518 CTTGGCTGCCGTGTTGGTA 60.600 57.895 14.98 0.00 41.21 3.25
2157 2251 2.732094 CGCCCGTCGTTTCGTCTT 60.732 61.111 0.00 0.00 0.00 3.01
2271 3052 2.028567 CCAACCCTGTCAGAGAGAAGAC 60.029 54.545 0.00 0.00 35.37 3.01
2366 3147 0.963962 GGGCATCGTTCGGTATCCTA 59.036 55.000 0.00 0.00 0.00 2.94
2384 3165 4.275810 TCCTACTAATACTTGGAGCACGT 58.724 43.478 0.00 0.00 0.00 4.49
2391 3172 2.165319 ACTTGGAGCACGTAGAAACC 57.835 50.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 113 5.163632 GCTATCTAGTATAGGGTCGAAAGCC 60.164 48.000 0.00 0.00 43.79 4.35
141 143 2.304092 ACCCAACCGAAAAGGAGTTTC 58.696 47.619 0.00 0.00 45.00 2.78
515 517 2.041755 CAAAGGAAAGAAGGCCTAGGGT 59.958 50.000 5.16 0.00 33.20 4.34
666 668 6.183361 TGTCATCTATGGAGTGGGAGTATAGT 60.183 42.308 0.00 0.00 0.00 2.12
707 709 6.183360 CGATAATAAGCTGGTTTGCCAAACTA 60.183 38.462 18.97 12.83 45.51 2.24
741 743 3.684788 CAGCAGCATTAGTAAGACGGTTT 59.315 43.478 0.00 0.00 0.00 3.27
1182 1189 0.180171 CCACCGATGGCCAGATGTTA 59.820 55.000 13.05 0.00 39.82 2.41
1304 1311 3.169099 CCAGAAAACCCAGAGAGAGAGA 58.831 50.000 0.00 0.00 0.00 3.10
1305 1312 2.903135 ACCAGAAAACCCAGAGAGAGAG 59.097 50.000 0.00 0.00 0.00 3.20
1385 1392 3.330701 ACAAGTTCAGCTGGAGGGAATTA 59.669 43.478 15.13 0.00 0.00 1.40
1506 1515 7.227873 TCAAGGGTTGATCACAAATAACTGTA 58.772 34.615 0.00 0.00 37.77 2.74
1507 1516 6.068010 TCAAGGGTTGATCACAAATAACTGT 58.932 36.000 0.00 0.00 37.77 3.55
1508 1517 6.573664 TCAAGGGTTGATCACAAATAACTG 57.426 37.500 0.00 0.00 37.77 3.16
1509 1518 5.183904 GCTCAAGGGTTGATCACAAATAACT 59.816 40.000 0.00 0.00 39.30 2.24
1510 1519 5.402398 GCTCAAGGGTTGATCACAAATAAC 58.598 41.667 0.00 0.00 39.30 1.89
1511 1520 4.462483 GGCTCAAGGGTTGATCACAAATAA 59.538 41.667 0.00 0.00 39.30 1.40
1512 1521 4.016444 GGCTCAAGGGTTGATCACAAATA 58.984 43.478 0.00 0.00 39.30 1.40
1513 1522 2.827921 GGCTCAAGGGTTGATCACAAAT 59.172 45.455 0.00 0.00 39.30 2.32
1514 1523 2.158475 AGGCTCAAGGGTTGATCACAAA 60.158 45.455 0.00 0.00 39.30 2.83
1515 1524 1.425066 AGGCTCAAGGGTTGATCACAA 59.575 47.619 0.00 0.00 39.30 3.33
1516 1525 1.003580 GAGGCTCAAGGGTTGATCACA 59.996 52.381 10.25 0.00 39.30 3.58
1517 1526 1.003580 TGAGGCTCAAGGGTTGATCAC 59.996 52.381 16.28 0.00 39.30 3.06
1518 1527 1.280133 CTGAGGCTCAAGGGTTGATCA 59.720 52.381 19.29 0.00 39.30 2.92
1519 1528 1.407989 CCTGAGGCTCAAGGGTTGATC 60.408 57.143 19.29 0.00 39.30 2.92
1520 1529 0.622665 CCTGAGGCTCAAGGGTTGAT 59.377 55.000 19.29 0.00 39.30 2.57
1521 1530 0.473694 TCCTGAGGCTCAAGGGTTGA 60.474 55.000 19.29 5.65 38.17 3.18
1522 1531 0.622665 ATCCTGAGGCTCAAGGGTTG 59.377 55.000 19.29 5.42 0.00 3.77
1523 1532 0.915364 GATCCTGAGGCTCAAGGGTT 59.085 55.000 19.29 11.93 0.00 4.11
1524 1533 0.252881 TGATCCTGAGGCTCAAGGGT 60.253 55.000 19.29 17.24 0.00 4.34
1525 1534 1.072015 GATGATCCTGAGGCTCAAGGG 59.928 57.143 19.29 16.87 0.00 3.95
1526 1535 2.048601 AGATGATCCTGAGGCTCAAGG 58.951 52.381 19.29 19.99 0.00 3.61
1527 1536 2.807472 GCAGATGATCCTGAGGCTCAAG 60.807 54.545 19.29 13.03 36.29 3.02
1528 1537 1.140452 GCAGATGATCCTGAGGCTCAA 59.860 52.381 19.29 4.84 36.29 3.02
1529 1538 0.757512 GCAGATGATCCTGAGGCTCA 59.242 55.000 17.68 17.68 36.29 4.26
1530 1539 1.050204 AGCAGATGATCCTGAGGCTC 58.950 55.000 7.79 7.79 36.29 4.70
1531 1540 1.417145 GAAGCAGATGATCCTGAGGCT 59.583 52.381 0.00 0.00 36.29 4.58
1532 1541 1.542987 GGAAGCAGATGATCCTGAGGC 60.543 57.143 0.00 0.00 36.29 4.70
1533 1542 1.270199 CGGAAGCAGATGATCCTGAGG 60.270 57.143 0.00 0.00 36.29 3.86
1534 1543 2.151881 CGGAAGCAGATGATCCTGAG 57.848 55.000 3.41 0.00 36.29 3.35
1548 1557 0.460987 GTCCACAGATGAGGCGGAAG 60.461 60.000 0.00 0.00 0.00 3.46
1549 1558 1.596934 GTCCACAGATGAGGCGGAA 59.403 57.895 0.00 0.00 0.00 4.30
1550 1559 2.359169 GGTCCACAGATGAGGCGGA 61.359 63.158 0.00 0.00 0.00 5.54
1551 1560 2.187946 GGTCCACAGATGAGGCGG 59.812 66.667 0.00 0.00 0.00 6.13
1552 1561 1.448540 GTGGTCCACAGATGAGGCG 60.449 63.158 17.59 0.00 34.08 5.52
1553 1562 1.195115 TAGTGGTCCACAGATGAGGC 58.805 55.000 24.02 0.00 36.74 4.70
1554 1563 5.129485 AGTTATTAGTGGTCCACAGATGAGG 59.871 44.000 24.02 0.00 36.74 3.86
1555 1564 6.227298 AGTTATTAGTGGTCCACAGATGAG 57.773 41.667 24.02 0.00 36.74 2.90
1556 1565 6.620877 AAGTTATTAGTGGTCCACAGATGA 57.379 37.500 24.02 10.72 36.74 2.92
1557 1566 6.878923 TCAAAGTTATTAGTGGTCCACAGATG 59.121 38.462 24.02 9.12 36.74 2.90
1558 1567 6.879458 GTCAAAGTTATTAGTGGTCCACAGAT 59.121 38.462 24.02 17.69 36.74 2.90
1559 1568 6.042781 AGTCAAAGTTATTAGTGGTCCACAGA 59.957 38.462 24.02 11.90 36.74 3.41
1560 1569 6.147821 CAGTCAAAGTTATTAGTGGTCCACAG 59.852 42.308 24.02 1.19 36.74 3.66
1561 1570 5.995282 CAGTCAAAGTTATTAGTGGTCCACA 59.005 40.000 24.02 4.53 36.74 4.17
1562 1571 5.411669 CCAGTCAAAGTTATTAGTGGTCCAC 59.588 44.000 14.68 14.68 34.10 4.02
1563 1572 5.556915 CCAGTCAAAGTTATTAGTGGTCCA 58.443 41.667 0.00 0.00 0.00 4.02
1564 1573 4.395231 GCCAGTCAAAGTTATTAGTGGTCC 59.605 45.833 0.00 0.00 0.00 4.46
1565 1574 4.395231 GGCCAGTCAAAGTTATTAGTGGTC 59.605 45.833 0.00 0.00 0.00 4.02
1566 1575 4.202524 TGGCCAGTCAAAGTTATTAGTGGT 60.203 41.667 0.00 0.00 0.00 4.16
1567 1576 4.156008 GTGGCCAGTCAAAGTTATTAGTGG 59.844 45.833 5.11 0.00 0.00 4.00
1568 1577 5.003804 AGTGGCCAGTCAAAGTTATTAGTG 58.996 41.667 5.11 0.00 0.00 2.74
1569 1578 5.242795 AGTGGCCAGTCAAAGTTATTAGT 57.757 39.130 5.11 0.00 0.00 2.24
1570 1579 7.865706 ATTAGTGGCCAGTCAAAGTTATTAG 57.134 36.000 18.68 0.00 0.00 1.73
1571 1580 9.169592 GTTATTAGTGGCCAGTCAAAGTTATTA 57.830 33.333 18.68 0.00 0.00 0.98
1572 1581 7.888546 AGTTATTAGTGGCCAGTCAAAGTTATT 59.111 33.333 18.68 0.00 0.00 1.40
1573 1582 7.402862 AGTTATTAGTGGCCAGTCAAAGTTAT 58.597 34.615 18.68 3.38 0.00 1.89
1574 1583 6.775708 AGTTATTAGTGGCCAGTCAAAGTTA 58.224 36.000 18.68 0.00 0.00 2.24
1575 1584 5.631119 AGTTATTAGTGGCCAGTCAAAGTT 58.369 37.500 18.68 0.00 0.00 2.66
1576 1585 5.242795 AGTTATTAGTGGCCAGTCAAAGT 57.757 39.130 18.68 9.90 0.00 2.66
1577 1586 6.206634 TCAAAGTTATTAGTGGCCAGTCAAAG 59.793 38.462 18.68 0.00 0.00 2.77
1578 1587 6.016610 GTCAAAGTTATTAGTGGCCAGTCAAA 60.017 38.462 18.68 7.37 0.00 2.69
1579 1588 5.472137 GTCAAAGTTATTAGTGGCCAGTCAA 59.528 40.000 18.68 10.41 0.00 3.18
1580 1589 5.001232 GTCAAAGTTATTAGTGGCCAGTCA 58.999 41.667 18.68 6.64 0.00 3.41
1581 1590 5.122396 CAGTCAAAGTTATTAGTGGCCAGTC 59.878 44.000 18.68 0.00 0.00 3.51
1582 1591 5.003804 CAGTCAAAGTTATTAGTGGCCAGT 58.996 41.667 19.15 19.15 0.00 4.00
1583 1592 5.003804 ACAGTCAAAGTTATTAGTGGCCAG 58.996 41.667 5.11 0.00 0.00 4.85
1584 1593 4.980573 ACAGTCAAAGTTATTAGTGGCCA 58.019 39.130 0.00 0.00 0.00 5.36
1585 1594 6.877322 TCTTACAGTCAAAGTTATTAGTGGCC 59.123 38.462 0.00 0.00 0.00 5.36
1586 1595 7.900782 TCTTACAGTCAAAGTTATTAGTGGC 57.099 36.000 0.00 0.00 0.00 5.01
1604 1613 9.595823 GGCAGTCAAAGTTATTAGTATCTTACA 57.404 33.333 0.00 0.00 0.00 2.41
1605 1614 9.043079 GGGCAGTCAAAGTTATTAGTATCTTAC 57.957 37.037 0.00 0.00 0.00 2.34
1606 1615 7.924412 CGGGCAGTCAAAGTTATTAGTATCTTA 59.076 37.037 0.00 0.00 0.00 2.10
1607 1616 6.761714 CGGGCAGTCAAAGTTATTAGTATCTT 59.238 38.462 0.00 0.00 0.00 2.40
1608 1617 6.281405 CGGGCAGTCAAAGTTATTAGTATCT 58.719 40.000 0.00 0.00 0.00 1.98
1609 1618 5.050295 GCGGGCAGTCAAAGTTATTAGTATC 60.050 44.000 0.00 0.00 0.00 2.24
1610 1619 4.814771 GCGGGCAGTCAAAGTTATTAGTAT 59.185 41.667 0.00 0.00 0.00 2.12
1611 1620 4.081309 AGCGGGCAGTCAAAGTTATTAGTA 60.081 41.667 0.00 0.00 0.00 1.82
1612 1621 3.007635 GCGGGCAGTCAAAGTTATTAGT 58.992 45.455 0.00 0.00 0.00 2.24
1613 1622 3.063997 CAGCGGGCAGTCAAAGTTATTAG 59.936 47.826 0.00 0.00 0.00 1.73
1614 1623 3.006940 CAGCGGGCAGTCAAAGTTATTA 58.993 45.455 0.00 0.00 0.00 0.98
1615 1624 1.812571 CAGCGGGCAGTCAAAGTTATT 59.187 47.619 0.00 0.00 0.00 1.40
1616 1625 1.453155 CAGCGGGCAGTCAAAGTTAT 58.547 50.000 0.00 0.00 0.00 1.89
1617 1626 0.605319 CCAGCGGGCAGTCAAAGTTA 60.605 55.000 0.00 0.00 0.00 2.24
1618 1627 1.898574 CCAGCGGGCAGTCAAAGTT 60.899 57.895 0.00 0.00 0.00 2.66
1619 1628 2.281761 CCAGCGGGCAGTCAAAGT 60.282 61.111 0.00 0.00 0.00 2.66
1620 1629 1.898574 AACCAGCGGGCAGTCAAAG 60.899 57.895 1.46 0.00 37.90 2.77
1621 1630 2.192861 CAACCAGCGGGCAGTCAAA 61.193 57.895 1.46 0.00 37.90 2.69
1622 1631 2.594303 CAACCAGCGGGCAGTCAA 60.594 61.111 1.46 0.00 37.90 3.18
1623 1632 4.641645 CCAACCAGCGGGCAGTCA 62.642 66.667 1.46 0.00 37.90 3.41
1624 1633 4.643387 ACCAACCAGCGGGCAGTC 62.643 66.667 1.46 0.00 37.90 3.51
1625 1634 4.954970 CACCAACCAGCGGGCAGT 62.955 66.667 1.46 0.00 37.90 4.40
1925 2008 2.675423 TCGGACCAGCTAGCGTGT 60.675 61.111 9.55 10.56 0.00 4.49
1928 2011 3.905678 CCCTCGGACCAGCTAGCG 61.906 72.222 9.55 4.28 0.00 4.26
2092 2185 1.222936 CGGCAGCCAAGATCTCCTT 59.777 57.895 13.30 0.00 34.91 3.36
2118 2211 1.915489 TGGCTATTGAGGTGGTGATGT 59.085 47.619 0.00 0.00 0.00 3.06
2151 2245 2.632377 GAATGGAGCCATGAAAGACGA 58.368 47.619 2.18 0.00 36.68 4.20
2152 2246 1.672881 GGAATGGAGCCATGAAAGACG 59.327 52.381 2.18 0.00 36.68 4.18
2153 2247 1.672881 CGGAATGGAGCCATGAAAGAC 59.327 52.381 2.18 0.00 36.68 3.01
2154 2248 1.408683 CCGGAATGGAGCCATGAAAGA 60.409 52.381 0.00 0.00 42.00 2.52
2155 2249 1.027357 CCGGAATGGAGCCATGAAAG 58.973 55.000 0.00 0.00 42.00 2.62
2156 2250 0.395586 CCCGGAATGGAGCCATGAAA 60.396 55.000 0.73 0.00 42.00 2.69
2157 2251 1.227102 CCCGGAATGGAGCCATGAA 59.773 57.895 0.73 0.00 42.00 2.57
2271 3052 2.030007 TGCTCTTGGGCAAATCTTTTCG 60.030 45.455 0.00 0.00 39.43 3.46
2366 3147 5.909621 TTCTACGTGCTCCAAGTATTAGT 57.090 39.130 0.00 0.00 29.24 2.24


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

AutoCloner maintained by Alex Coulton.