Multiple sequence alignment - TraesCS1D01G384200

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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 TraesCS1D01G384200 chr1D 100.000 2243 0 0 1 2243 458229195 458231437 0.000000e+00 4143.0
1 TraesCS1D01G384200 chr1D 91.654 647 39 5 1530 2163 458257708 458258352 0.000000e+00 881.0
2 TraesCS1D01G384200 chr1D 82.972 969 109 29 601 1533 458256888 458257836 0.000000e+00 824.0
3 TraesCS1D01G384200 chr1D 85.734 729 80 12 1530 2241 458161427 458162148 0.000000e+00 749.0
4 TraesCS1D01G384200 chr1D 99.160 119 1 0 1415 1533 458230724 458230842 4.850000e-52 215.0
5 TraesCS1D01G384200 chr1B 90.653 888 59 2 596 1459 628994308 628995195 0.000000e+00 1158.0
6 TraesCS1D01G384200 chr1B 91.283 803 48 10 596 1379 628811169 628811968 0.000000e+00 1075.0
7 TraesCS1D01G384200 chr1B 94.524 694 33 3 596 1285 629053652 629054344 0.000000e+00 1066.0
8 TraesCS1D01G384200 chr1B 91.114 799 54 10 596 1385 629091916 629092706 0.000000e+00 1066.0
9 TraesCS1D01G384200 chr1B 89.950 806 62 13 596 1385 628975243 628976045 0.000000e+00 1022.0
10 TraesCS1D01G384200 chr1B 93.084 694 43 4 596 1285 628917964 628918656 0.000000e+00 1011.0
11 TraesCS1D01G384200 chr1B 92.785 693 43 5 596 1285 628899025 628899713 0.000000e+00 996.0
12 TraesCS1D01G384200 chr1B 88.561 813 62 17 596 1385 628856172 628856976 0.000000e+00 957.0
13 TraesCS1D01G384200 chr1B 86.298 832 87 16 712 1528 628827217 628828036 0.000000e+00 880.0
14 TraesCS1D01G384200 chr1B 86.022 837 89 17 712 1528 628874761 628875589 0.000000e+00 872.0
15 TraesCS1D01G384200 chr1B 94.737 513 27 0 75 587 506139106 506139618 0.000000e+00 798.0
16 TraesCS1D01G384200 chr1B 83.860 570 68 9 983 1528 628804554 628805123 2.550000e-144 521.0
17 TraesCS1D01G384200 chr1B 85.681 433 42 10 1097 1528 628951033 628951446 2.640000e-119 438.0
18 TraesCS1D01G384200 chr1B 80.989 526 89 9 1 522 336780699 336781217 7.460000e-110 407.0
19 TraesCS1D01G384200 chr1B 79.388 490 90 11 1 485 328919452 328919935 3.570000e-88 335.0
20 TraesCS1D01G384200 chr1B 91.414 198 17 0 1262 1459 628918663 628918860 2.840000e-69 272.0
21 TraesCS1D01G384200 chr2B 95.392 586 27 0 1 586 753634762 753634177 0.000000e+00 933.0
22 TraesCS1D01G384200 chr2B 93.478 46 3 0 1872 1917 13489607 13489562 4.000000e-08 69.4
23 TraesCS1D01G384200 chr4A 94.247 591 27 1 1 591 725785480 725786063 0.000000e+00 896.0
24 TraesCS1D01G384200 chr1A 87.699 691 60 8 1530 2205 550721309 550721989 0.000000e+00 782.0
25 TraesCS1D01G384200 chr1A 95.957 470 19 0 1530 1999 550793880 550794349 0.000000e+00 763.0
26 TraesCS1D01G384200 chr1A 86.126 728 68 19 1530 2241 550661711 550662421 0.000000e+00 754.0
27 TraesCS1D01G384200 chr1A 85.383 732 77 17 1530 2241 550647050 550647771 0.000000e+00 732.0
28 TraesCS1D01G384200 chr1A 85.498 662 78 13 1584 2241 550675535 550676182 0.000000e+00 675.0
29 TraesCS1D01G384200 chr1A 85.347 662 79 13 1584 2241 550685311 550685958 0.000000e+00 669.0
30 TraesCS1D01G384200 chr1A 97.426 272 7 0 1262 1533 550793727 550793998 4.360000e-127 464.0
31 TraesCS1D01G384200 chr1A 93.281 253 13 1 1995 2243 550806756 550807008 9.780000e-99 370.0
32 TraesCS1D01G384200 chr1A 87.108 287 29 6 1584 1869 550694923 550695202 3.590000e-83 318.0
33 TraesCS1D01G384200 chr1A 87.676 284 15 6 1262 1528 550721152 550721432 1.670000e-81 313.0
34 TraesCS1D01G384200 chr5B 83.146 534 79 10 1 528 647978526 647979054 5.600000e-131 477.0
35 TraesCS1D01G384200 chr5B 84.689 209 32 0 12 220 578820941 578820733 2.260000e-50 209.0
36 TraesCS1D01G384200 chr7B 80.718 529 93 8 4 528 511839049 511838526 9.650000e-109 403.0
37 TraesCS1D01G384200 chr7B 80.675 533 85 15 4 528 511807615 511807093 4.490000e-107 398.0
38 TraesCS1D01G384200 chr7B 90.909 66 6 0 521 586 458382837 458382902 3.070000e-14 89.8
39 TraesCS1D01G384200 chr5D 81.283 187 35 0 1924 2110 407925136 407924950 3.860000e-33 152.0
40 TraesCS1D01G384200 chr6D 95.588 68 3 0 522 589 162257846 162257913 2.360000e-20 110.0


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 TraesCS1D01G384200 chr1D 458229195 458231437 2242 False 2179.0 4143 99.5800 1 2243 2 chr1D.!!$F2 2242
1 TraesCS1D01G384200 chr1D 458256888 458258352 1464 False 852.5 881 87.3130 601 2163 2 chr1D.!!$F3 1562
2 TraesCS1D01G384200 chr1D 458161427 458162148 721 False 749.0 749 85.7340 1530 2241 1 chr1D.!!$F1 711
3 TraesCS1D01G384200 chr1B 628994308 628995195 887 False 1158.0 1158 90.6530 596 1459 1 chr1B.!!$F12 863
4 TraesCS1D01G384200 chr1B 628811169 628811968 799 False 1075.0 1075 91.2830 596 1379 1 chr1B.!!$F5 783
5 TraesCS1D01G384200 chr1B 629053652 629054344 692 False 1066.0 1066 94.5240 596 1285 1 chr1B.!!$F13 689
6 TraesCS1D01G384200 chr1B 629091916 629092706 790 False 1066.0 1066 91.1140 596 1385 1 chr1B.!!$F14 789
7 TraesCS1D01G384200 chr1B 628975243 628976045 802 False 1022.0 1022 89.9500 596 1385 1 chr1B.!!$F11 789
8 TraesCS1D01G384200 chr1B 628899025 628899713 688 False 996.0 996 92.7850 596 1285 1 chr1B.!!$F9 689
9 TraesCS1D01G384200 chr1B 628856172 628856976 804 False 957.0 957 88.5610 596 1385 1 chr1B.!!$F7 789
10 TraesCS1D01G384200 chr1B 628827217 628828036 819 False 880.0 880 86.2980 712 1528 1 chr1B.!!$F6 816
11 TraesCS1D01G384200 chr1B 628874761 628875589 828 False 872.0 872 86.0220 712 1528 1 chr1B.!!$F8 816
12 TraesCS1D01G384200 chr1B 506139106 506139618 512 False 798.0 798 94.7370 75 587 1 chr1B.!!$F3 512
13 TraesCS1D01G384200 chr1B 628917964 628918860 896 False 641.5 1011 92.2490 596 1459 2 chr1B.!!$F15 863
14 TraesCS1D01G384200 chr1B 628804554 628805123 569 False 521.0 521 83.8600 983 1528 1 chr1B.!!$F4 545
15 TraesCS1D01G384200 chr1B 336780699 336781217 518 False 407.0 407 80.9890 1 522 1 chr1B.!!$F2 521
16 TraesCS1D01G384200 chr2B 753634177 753634762 585 True 933.0 933 95.3920 1 586 1 chr2B.!!$R2 585
17 TraesCS1D01G384200 chr4A 725785480 725786063 583 False 896.0 896 94.2470 1 591 1 chr4A.!!$F1 590
18 TraesCS1D01G384200 chr1A 550661711 550662421 710 False 754.0 754 86.1260 1530 2241 1 chr1A.!!$F2 711
19 TraesCS1D01G384200 chr1A 550647050 550647771 721 False 732.0 732 85.3830 1530 2241 1 chr1A.!!$F1 711
20 TraesCS1D01G384200 chr1A 550675535 550676182 647 False 675.0 675 85.4980 1584 2241 1 chr1A.!!$F3 657
21 TraesCS1D01G384200 chr1A 550685311 550685958 647 False 669.0 669 85.3470 1584 2241 1 chr1A.!!$F4 657
22 TraesCS1D01G384200 chr1A 550793727 550794349 622 False 613.5 763 96.6915 1262 1999 2 chr1A.!!$F8 737
23 TraesCS1D01G384200 chr1A 550721152 550721989 837 False 547.5 782 87.6875 1262 2205 2 chr1A.!!$F7 943
24 TraesCS1D01G384200 chr5B 647978526 647979054 528 False 477.0 477 83.1460 1 528 1 chr5B.!!$F1 527
25 TraesCS1D01G384200 chr7B 511838526 511839049 523 True 403.0 403 80.7180 4 528 1 chr7B.!!$R2 524
26 TraesCS1D01G384200 chr7B 511807093 511807615 522 True 398.0 398 80.6750 4 528 1 chr7B.!!$R1 524

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
618 626 0.878523 GTACGCAACTGCCTGTGTCA 60.879 55.0 0.0 0.0 40.44 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2282 0.042581 TAGGTGGTGATCCTCTGCCA 59.957 55.0 0.0 0.0 36.6 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
38 39 1.777878 TCTTCCCTTTGTAAGCCCACA 59.222 47.619 0.00 0.00 0.00 4.17
70 71 3.077556 ACGCGCTCCCAATCTCCT 61.078 61.111 5.73 0.00 0.00 3.69
105 106 3.181445 TGCATTGTGTACAGGTTCTCCTT 60.181 43.478 0.00 0.00 43.07 3.36
136 137 7.119846 GGCTTGATCTTAACTTCTTTTGCTAGA 59.880 37.037 0.00 0.00 0.00 2.43
413 418 1.920835 GGTCCCAAGCTGTCCTCCT 60.921 63.158 0.00 0.00 0.00 3.69
443 448 2.755650 GTGAAAACAGCGGAGAGAGAA 58.244 47.619 0.00 0.00 0.00 2.87
591 599 3.248495 CCTAACGAGAGGGGAAAACTC 57.752 52.381 0.00 0.00 32.39 3.01
593 601 4.021916 CCTAACGAGAGGGGAAAACTCTA 58.978 47.826 0.00 0.00 44.89 2.43
594 602 3.957591 AACGAGAGGGGAAAACTCTAC 57.042 47.619 0.00 0.00 44.89 2.59
618 626 0.878523 GTACGCAACTGCCTGTGTCA 60.879 55.000 0.00 0.00 40.44 3.58
663 676 2.280628 CCCTCGCTCTTTGGATGTTAC 58.719 52.381 0.00 0.00 0.00 2.50
872 891 2.363795 TCGGAGCCTCCATTCGGT 60.364 61.111 12.13 0.00 35.91 4.69
932 951 4.322953 GCAAACCAAAACCATCCATCTCAT 60.323 41.667 0.00 0.00 0.00 2.90
1045 1095 0.363512 CGTGACGAGAAGCATTGACG 59.636 55.000 0.00 0.00 0.00 4.35
1046 1096 1.698165 GTGACGAGAAGCATTGACGA 58.302 50.000 0.00 0.00 0.00 4.20
1140 1193 1.682684 CTACTGGAGGGTGAGGCGT 60.683 63.158 0.00 0.00 0.00 5.68
1185 1238 1.942586 GCCGTGAGTTTTGGGTACGAT 60.943 52.381 0.00 0.00 36.94 3.73
1403 1499 7.388776 ACGAGTGTGTATTAGACAGTACTGTTA 59.611 37.037 28.49 18.64 45.05 2.41
1429 1525 6.509418 ACAGAAGTTGCTTACTGTTGAAAA 57.491 33.333 0.00 0.00 40.03 2.29
1466 1562 9.463443 CGAATGAAATGACAGTGTATCTATGTA 57.537 33.333 0.00 0.00 0.00 2.29
1469 1565 9.755804 ATGAAATGACAGTGTATCTATGTACAG 57.244 33.333 0.33 0.00 35.40 2.74
1470 1566 8.749354 TGAAATGACAGTGTATCTATGTACAGT 58.251 33.333 0.33 0.00 38.45 3.55
1471 1567 9.239002 GAAATGACAGTGTATCTATGTACAGTC 57.761 37.037 0.33 0.00 36.38 3.51
1472 1568 8.526667 AATGACAGTGTATCTATGTACAGTCT 57.473 34.615 0.33 0.00 36.38 3.24
1473 1569 7.321745 TGACAGTGTATCTATGTACAGTCTG 57.678 40.000 0.33 0.00 36.38 3.51
1474 1570 6.137794 ACAGTGTATCTATGTACAGTCTGC 57.862 41.667 0.33 0.00 36.38 4.26
1475 1571 5.652452 ACAGTGTATCTATGTACAGTCTGCA 59.348 40.000 0.33 0.00 36.38 4.41
1476 1572 6.152831 ACAGTGTATCTATGTACAGTCTGCAA 59.847 38.462 0.33 0.00 36.38 4.08
1477 1573 6.694844 CAGTGTATCTATGTACAGTCTGCAAG 59.305 42.308 0.33 0.00 36.38 4.01
1478 1574 5.460419 GTGTATCTATGTACAGTCTGCAAGC 59.540 44.000 0.33 0.00 35.40 4.01
1479 1575 3.526931 TCTATGTACAGTCTGCAAGCC 57.473 47.619 0.33 0.00 0.00 4.35
1480 1576 2.159240 TCTATGTACAGTCTGCAAGCCG 60.159 50.000 0.33 0.00 0.00 5.52
1481 1577 0.321671 ATGTACAGTCTGCAAGCCGT 59.678 50.000 0.33 0.00 0.00 5.68
1482 1578 0.599991 TGTACAGTCTGCAAGCCGTG 60.600 55.000 0.00 0.00 0.00 4.94
1483 1579 0.600255 GTACAGTCTGCAAGCCGTGT 60.600 55.000 0.00 0.00 0.00 4.49
1484 1580 0.319555 TACAGTCTGCAAGCCGTGTC 60.320 55.000 0.00 0.00 0.00 3.67
1485 1581 1.595109 CAGTCTGCAAGCCGTGTCA 60.595 57.895 0.00 0.00 0.00 3.58
1486 1582 1.595382 AGTCTGCAAGCCGTGTCAC 60.595 57.895 0.00 0.00 0.00 3.67
1487 1583 1.595382 GTCTGCAAGCCGTGTCACT 60.595 57.895 0.65 0.00 0.00 3.41
1488 1584 1.146041 TCTGCAAGCCGTGTCACTT 59.854 52.632 0.65 0.00 0.00 3.16
1489 1585 1.159713 TCTGCAAGCCGTGTCACTTG 61.160 55.000 0.65 0.43 44.88 3.16
1491 1587 3.736483 CAAGCCGTGTCACTTGCT 58.264 55.556 10.19 10.19 37.11 3.91
1492 1588 2.912986 CAAGCCGTGTCACTTGCTA 58.087 52.632 14.87 0.00 37.11 3.49
1493 1589 0.512952 CAAGCCGTGTCACTTGCTAC 59.487 55.000 14.87 0.00 37.11 3.58
1494 1590 0.105964 AAGCCGTGTCACTTGCTACA 59.894 50.000 14.87 0.00 32.82 2.74
1495 1591 0.600255 AGCCGTGTCACTTGCTACAC 60.600 55.000 13.40 0.00 42.04 2.90
1496 1592 0.600255 GCCGTGTCACTTGCTACACT 60.600 55.000 0.65 0.00 43.04 3.55
1497 1593 1.139989 CCGTGTCACTTGCTACACTG 58.860 55.000 0.65 0.00 43.04 3.66
1498 1594 1.139989 CGTGTCACTTGCTACACTGG 58.860 55.000 0.65 0.00 43.04 4.00
1499 1595 1.269569 CGTGTCACTTGCTACACTGGA 60.270 52.381 0.65 0.00 43.04 3.86
1500 1596 2.801699 CGTGTCACTTGCTACACTGGAA 60.802 50.000 0.65 0.00 43.04 3.53
1501 1597 3.403038 GTGTCACTTGCTACACTGGAAT 58.597 45.455 0.00 0.00 42.17 3.01
1502 1598 3.187227 GTGTCACTTGCTACACTGGAATG 59.813 47.826 0.00 0.00 42.17 2.67
1503 1599 2.744202 GTCACTTGCTACACTGGAATGG 59.256 50.000 0.00 0.00 0.00 3.16
1504 1600 2.086869 CACTTGCTACACTGGAATGGG 58.913 52.381 0.00 0.00 0.00 4.00
1505 1601 1.985159 ACTTGCTACACTGGAATGGGA 59.015 47.619 0.00 0.00 0.00 4.37
1506 1602 2.578021 ACTTGCTACACTGGAATGGGAT 59.422 45.455 0.00 0.00 0.00 3.85
1507 1603 3.010584 ACTTGCTACACTGGAATGGGATT 59.989 43.478 0.00 0.00 0.00 3.01
1508 1604 3.737559 TGCTACACTGGAATGGGATTT 57.262 42.857 0.00 0.00 0.00 2.17
1509 1605 4.853468 TGCTACACTGGAATGGGATTTA 57.147 40.909 0.00 0.00 0.00 1.40
1510 1606 5.186256 TGCTACACTGGAATGGGATTTAA 57.814 39.130 0.00 0.00 0.00 1.52
1511 1607 5.575157 TGCTACACTGGAATGGGATTTAAA 58.425 37.500 0.00 0.00 0.00 1.52
1512 1608 5.417580 TGCTACACTGGAATGGGATTTAAAC 59.582 40.000 0.00 0.00 0.00 2.01
1513 1609 5.652452 GCTACACTGGAATGGGATTTAAACT 59.348 40.000 0.00 0.00 0.00 2.66
1514 1610 6.826741 GCTACACTGGAATGGGATTTAAACTA 59.173 38.462 0.00 0.00 0.00 2.24
1515 1611 7.502561 GCTACACTGGAATGGGATTTAAACTAT 59.497 37.037 0.00 0.00 0.00 2.12
1516 1612 9.408648 CTACACTGGAATGGGATTTAAACTATT 57.591 33.333 0.00 0.00 0.00 1.73
1517 1613 8.664669 ACACTGGAATGGGATTTAAACTATTT 57.335 30.769 0.00 0.00 0.00 1.40
1518 1614 8.749354 ACACTGGAATGGGATTTAAACTATTTC 58.251 33.333 0.00 0.00 0.00 2.17
1519 1615 8.971073 CACTGGAATGGGATTTAAACTATTTCT 58.029 33.333 0.00 0.00 0.00 2.52
1520 1616 8.971073 ACTGGAATGGGATTTAAACTATTTCTG 58.029 33.333 0.00 0.00 0.00 3.02
1521 1617 8.893563 TGGAATGGGATTTAAACTATTTCTGT 57.106 30.769 0.00 0.00 0.00 3.41
1522 1618 9.320295 TGGAATGGGATTTAAACTATTTCTGTT 57.680 29.630 0.00 0.00 0.00 3.16
1523 1619 9.803315 GGAATGGGATTTAAACTATTTCTGTTC 57.197 33.333 0.00 0.00 0.00 3.18
1527 1623 9.308000 TGGGATTTAAACTATTTCTGTTCATGT 57.692 29.630 0.00 0.00 0.00 3.21
1528 1624 9.573133 GGGATTTAAACTATTTCTGTTCATGTG 57.427 33.333 0.00 0.00 0.00 3.21
1544 1640 5.826601 TCATGTGTGCTTACTGTTGAAAA 57.173 34.783 0.00 0.00 0.00 2.29
1610 1718 0.600255 AGCCGTGTCACTTGCTACAC 60.600 55.000 13.40 0.00 42.04 2.90
1828 1945 4.388499 CCAACCGAGGTCCCCGTG 62.388 72.222 0.00 0.00 0.00 4.94
2090 2216 3.777478 CCTGTCTATTTAAGCCGAACGA 58.223 45.455 0.00 0.00 0.00 3.85
2133 2259 0.537188 CGCCAGCTTCCCTCTTCTTA 59.463 55.000 0.00 0.00 0.00 2.10
2156 2282 2.590092 GCCTCGTAACCATGGCCT 59.410 61.111 13.04 1.18 39.49 5.19
2177 2303 1.346068 GGCAGAGGATCACCACCTATC 59.654 57.143 0.00 0.00 37.93 2.08
2178 2304 2.042464 GCAGAGGATCACCACCTATCA 58.958 52.381 0.00 0.00 37.93 2.15
2179 2305 2.435805 GCAGAGGATCACCACCTATCAA 59.564 50.000 0.00 0.00 37.93 2.57
2180 2306 3.072184 GCAGAGGATCACCACCTATCAAT 59.928 47.826 0.00 0.00 37.93 2.57
2199 2325 4.081365 TCAATGCAATGTTGATGCCTGAAT 60.081 37.500 0.85 0.00 43.16 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.826024 GCGTGATGGAGGATGGACT 59.174 57.895 0.00 0.00 0.00 3.85
70 71 0.740149 CAATGCAATTCGGCTGCCTA 59.260 50.000 17.92 2.11 39.13 3.93
105 106 3.055819 AGAAGTTAAGATCAAGCCGCTCA 60.056 43.478 0.00 0.00 0.00 4.26
136 137 2.692368 ATGAGGGTGGCGTGGGAT 60.692 61.111 0.00 0.00 0.00 3.85
170 171 3.055385 ACCGAGAAAAGCTACAGCCAATA 60.055 43.478 0.00 0.00 43.38 1.90
396 400 1.298014 CAGGAGGACAGCTTGGGAC 59.702 63.158 0.00 0.00 0.00 4.46
413 418 0.878523 CTGTTTTCACGGCGAGGACA 60.879 55.000 16.62 11.01 0.00 4.02
434 439 1.691163 CCCCTTCCCTCTTCTCTCTCC 60.691 61.905 0.00 0.00 0.00 3.71
443 448 2.041928 CAGCCTCCCCTTCCCTCT 59.958 66.667 0.00 0.00 0.00 3.69
591 599 1.993370 GGCAGTTGCGTACTCAAGTAG 59.007 52.381 5.63 2.94 43.26 2.57
592 600 1.616865 AGGCAGTTGCGTACTCAAGTA 59.383 47.619 5.63 0.00 43.26 2.24
593 601 0.393077 AGGCAGTTGCGTACTCAAGT 59.607 50.000 0.00 0.00 43.26 3.16
594 602 0.792640 CAGGCAGTTGCGTACTCAAG 59.207 55.000 0.00 0.00 43.26 3.02
602 610 1.009675 GTTGACACAGGCAGTTGCG 60.010 57.895 0.00 0.00 43.26 4.85
872 891 2.677836 CAGCAGCCGTTTTATAAGCTCA 59.322 45.455 0.00 0.00 31.93 4.26
1045 1095 0.179108 CCTTCCGTCATCTTCCGGTC 60.179 60.000 0.00 0.00 44.51 4.79
1046 1096 1.614241 CCCTTCCGTCATCTTCCGGT 61.614 60.000 0.00 0.00 44.51 5.28
1185 1238 3.093057 GTTCTGGGAGTAGCTCTTGAGA 58.907 50.000 1.30 0.00 0.00 3.27
1403 1499 7.801716 TTCAACAGTAAGCAACTTCTGTATT 57.198 32.000 10.63 0.00 39.72 1.89
1429 1525 5.181811 TGTCATTTCATTCGCAGTTTCAGAT 59.818 36.000 0.00 0.00 0.00 2.90
1466 1562 1.595382 GACACGGCTTGCAGACTGT 60.595 57.895 3.99 0.00 0.00 3.55
1467 1563 1.595109 TGACACGGCTTGCAGACTG 60.595 57.895 0.00 0.00 0.00 3.51
1468 1564 1.595382 GTGACACGGCTTGCAGACT 60.595 57.895 0.00 0.00 0.00 3.24
1469 1565 1.160329 AAGTGACACGGCTTGCAGAC 61.160 55.000 0.00 0.00 0.00 3.51
1470 1566 1.146041 AAGTGACACGGCTTGCAGA 59.854 52.632 0.00 0.00 0.00 4.26
1471 1567 1.280746 CAAGTGACACGGCTTGCAG 59.719 57.895 0.00 0.00 36.17 4.41
1472 1568 3.419828 CAAGTGACACGGCTTGCA 58.580 55.556 0.00 0.00 36.17 4.08
1474 1570 0.512952 GTAGCAAGTGACACGGCTTG 59.487 55.000 25.69 14.95 43.42 4.01
1475 1571 0.105964 TGTAGCAAGTGACACGGCTT 59.894 50.000 25.69 14.13 35.73 4.35
1476 1572 0.600255 GTGTAGCAAGTGACACGGCT 60.600 55.000 24.49 24.49 36.88 5.52
1477 1573 1.860078 GTGTAGCAAGTGACACGGC 59.140 57.895 14.94 14.94 36.88 5.68
1480 1576 2.526304 TCCAGTGTAGCAAGTGACAC 57.474 50.000 0.00 0.00 45.15 3.67
1481 1577 3.402110 CATTCCAGTGTAGCAAGTGACA 58.598 45.455 0.00 0.00 0.00 3.58
1482 1578 2.744202 CCATTCCAGTGTAGCAAGTGAC 59.256 50.000 0.00 0.00 0.00 3.67
1483 1579 2.290260 CCCATTCCAGTGTAGCAAGTGA 60.290 50.000 0.00 0.00 0.00 3.41
1484 1580 2.086869 CCCATTCCAGTGTAGCAAGTG 58.913 52.381 0.00 0.00 0.00 3.16
1485 1581 1.985159 TCCCATTCCAGTGTAGCAAGT 59.015 47.619 0.00 0.00 0.00 3.16
1486 1582 2.787473 TCCCATTCCAGTGTAGCAAG 57.213 50.000 0.00 0.00 0.00 4.01
1487 1583 3.737559 AATCCCATTCCAGTGTAGCAA 57.262 42.857 0.00 0.00 0.00 3.91
1488 1584 3.737559 AAATCCCATTCCAGTGTAGCA 57.262 42.857 0.00 0.00 0.00 3.49
1489 1585 5.652452 AGTTTAAATCCCATTCCAGTGTAGC 59.348 40.000 0.00 0.00 0.00 3.58
1490 1586 8.980481 ATAGTTTAAATCCCATTCCAGTGTAG 57.020 34.615 0.00 0.00 0.00 2.74
1491 1587 9.762381 AAATAGTTTAAATCCCATTCCAGTGTA 57.238 29.630 0.00 0.00 0.00 2.90
1492 1588 8.664669 AAATAGTTTAAATCCCATTCCAGTGT 57.335 30.769 0.00 0.00 0.00 3.55
1493 1589 8.971073 AGAAATAGTTTAAATCCCATTCCAGTG 58.029 33.333 0.00 0.00 0.00 3.66
1494 1590 8.971073 CAGAAATAGTTTAAATCCCATTCCAGT 58.029 33.333 0.00 0.00 0.00 4.00
1495 1591 8.971073 ACAGAAATAGTTTAAATCCCATTCCAG 58.029 33.333 0.00 0.00 0.00 3.86
1496 1592 8.893563 ACAGAAATAGTTTAAATCCCATTCCA 57.106 30.769 0.00 0.00 0.00 3.53
1497 1593 9.803315 GAACAGAAATAGTTTAAATCCCATTCC 57.197 33.333 0.00 0.00 0.00 3.01
1501 1597 9.308000 ACATGAACAGAAATAGTTTAAATCCCA 57.692 29.630 0.00 0.00 0.00 4.37
1502 1598 9.573133 CACATGAACAGAAATAGTTTAAATCCC 57.427 33.333 0.00 0.00 0.00 3.85
1505 1601 9.410556 GCACACATGAACAGAAATAGTTTAAAT 57.589 29.630 0.00 0.00 0.00 1.40
1506 1602 8.629158 AGCACACATGAACAGAAATAGTTTAAA 58.371 29.630 0.00 0.00 0.00 1.52
1507 1603 8.165239 AGCACACATGAACAGAAATAGTTTAA 57.835 30.769 0.00 0.00 0.00 1.52
1508 1604 7.744087 AGCACACATGAACAGAAATAGTTTA 57.256 32.000 0.00 0.00 0.00 2.01
1509 1605 6.639632 AGCACACATGAACAGAAATAGTTT 57.360 33.333 0.00 0.00 0.00 2.66
1510 1606 6.639632 AAGCACACATGAACAGAAATAGTT 57.360 33.333 0.00 0.00 0.00 2.24
1511 1607 6.936900 AGTAAGCACACATGAACAGAAATAGT 59.063 34.615 0.00 0.00 0.00 2.12
1512 1608 7.095060 ACAGTAAGCACACATGAACAGAAATAG 60.095 37.037 0.00 0.00 0.00 1.73
1513 1609 6.710295 ACAGTAAGCACACATGAACAGAAATA 59.290 34.615 0.00 0.00 0.00 1.40
1514 1610 5.532406 ACAGTAAGCACACATGAACAGAAAT 59.468 36.000 0.00 0.00 0.00 2.17
1515 1611 4.881273 ACAGTAAGCACACATGAACAGAAA 59.119 37.500 0.00 0.00 0.00 2.52
1516 1612 4.450976 ACAGTAAGCACACATGAACAGAA 58.549 39.130 0.00 0.00 0.00 3.02
1517 1613 4.071961 ACAGTAAGCACACATGAACAGA 57.928 40.909 0.00 0.00 0.00 3.41
1518 1614 4.273235 TCAACAGTAAGCACACATGAACAG 59.727 41.667 0.00 0.00 0.00 3.16
1519 1615 4.195416 TCAACAGTAAGCACACATGAACA 58.805 39.130 0.00 0.00 0.00 3.18
1520 1616 4.811555 TCAACAGTAAGCACACATGAAC 57.188 40.909 0.00 0.00 0.00 3.18
1521 1617 5.826601 TTTCAACAGTAAGCACACATGAA 57.173 34.783 0.00 0.00 0.00 2.57
1522 1618 5.826601 TTTTCAACAGTAAGCACACATGA 57.173 34.783 0.00 0.00 0.00 3.07
1523 1619 6.361481 CAGATTTTCAACAGTAAGCACACATG 59.639 38.462 0.00 0.00 0.00 3.21
1524 1620 6.262944 TCAGATTTTCAACAGTAAGCACACAT 59.737 34.615 0.00 0.00 0.00 3.21
1525 1621 5.588246 TCAGATTTTCAACAGTAAGCACACA 59.412 36.000 0.00 0.00 0.00 3.72
1526 1622 6.060028 TCAGATTTTCAACAGTAAGCACAC 57.940 37.500 0.00 0.00 0.00 3.82
1527 1623 6.691754 TTCAGATTTTCAACAGTAAGCACA 57.308 33.333 0.00 0.00 0.00 4.57
1528 1624 7.166473 CAGTTTCAGATTTTCAACAGTAAGCAC 59.834 37.037 0.00 0.00 0.00 4.40
1544 1640 5.181811 TGTCATTTCATTCGCAGTTTCAGAT 59.818 36.000 0.00 0.00 0.00 2.90
1610 1718 8.971073 ACAGAAATAGTTTAAATCCCATTCCAG 58.029 33.333 0.00 0.00 0.00 3.86
1710 1822 8.029642 ACGGTAAGATCTGAAAAACAATAGTG 57.970 34.615 0.00 0.00 0.00 2.74
1861 1978 2.640826 GGACCGGATATGGGGTTTATGA 59.359 50.000 9.46 0.00 36.46 2.15
2090 2216 0.608308 GGCTAGGGTTCTTTTGCCGT 60.608 55.000 0.00 0.00 0.00 5.68
2133 2259 2.288025 ATGGTTACGAGGCGGTGGT 61.288 57.895 0.00 0.00 0.00 4.16
2156 2282 0.042581 TAGGTGGTGATCCTCTGCCA 59.957 55.000 0.00 0.00 36.60 4.92
2177 2303 3.239587 TCAGGCATCAACATTGCATTG 57.760 42.857 7.04 7.04 41.95 2.82
2178 2304 3.965379 TTCAGGCATCAACATTGCATT 57.035 38.095 0.00 0.00 41.95 3.56
2179 2305 3.792401 CATTCAGGCATCAACATTGCAT 58.208 40.909 0.00 0.00 41.95 3.96
2180 2306 2.675603 GCATTCAGGCATCAACATTGCA 60.676 45.455 0.00 0.00 41.95 4.08


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

AutoCloner maintained by Alex Coulton.