Multiple sequence alignment - TraesCS2A01G387900

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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 TraesCS2A01G387900 chr2A 100.000 3538 0 0 1 3538 634106459 634109996 0.000000e+00 6534.0
1 TraesCS2A01G387900 chr2A 86.022 930 89 12 1 923 634606308 634607203 0.000000e+00 959.0
2 TraesCS2A01G387900 chr2A 81.879 894 91 39 1486 2326 634607641 634608516 0.000000e+00 688.0
3 TraesCS2A01G387900 chr2A 85.890 489 47 13 2711 3181 634609099 634609583 5.270000e-138 501.0
4 TraesCS2A01G387900 chr2A 82.633 357 35 12 2329 2684 634608577 634608907 1.240000e-74 291.0
5 TraesCS2A01G387900 chr2A 90.805 87 8 0 3321 3407 634609709 634609795 2.230000e-22 117.0
6 TraesCS2A01G387900 chr2D 97.315 1676 39 5 1492 3165 490578307 490579978 0.000000e+00 2841.0
7 TraesCS2A01G387900 chr2D 97.147 1437 29 4 1 1428 490576884 490578317 0.000000e+00 2416.0
8 TraesCS2A01G387900 chr2D 84.936 936 90 17 3 923 490657892 490658791 0.000000e+00 900.0
9 TraesCS2A01G387900 chr2D 81.971 893 92 37 1486 2326 490659239 490660114 0.000000e+00 693.0
10 TraesCS2A01G387900 chr2D 88.660 485 38 6 958 1425 490658768 490659252 3.060000e-160 575.0
11 TraesCS2A01G387900 chr2D 85.802 486 50 11 2710 3181 490660607 490661087 6.820000e-137 497.0
12 TraesCS2A01G387900 chr2D 95.593 295 10 2 3247 3538 490580014 490580308 1.490000e-128 470.0
13 TraesCS2A01G387900 chr2D 82.922 486 38 26 1881 2326 490126217 490125737 2.560000e-106 396.0
14 TraesCS2A01G387900 chr2D 80.913 482 76 11 958 1431 490127686 490127213 2.010000e-97 366.0
15 TraesCS2A01G387900 chr2D 81.724 290 28 10 2395 2684 490660265 490660529 5.950000e-53 219.0
16 TraesCS2A01G387900 chr2D 90.476 84 8 0 3319 3402 490124743 490124660 1.040000e-20 111.0
17 TraesCS2A01G387900 chr2D 92.424 66 5 0 3319 3384 490661208 490661273 1.050000e-15 95.3
18 TraesCS2A01G387900 chr2D 88.732 71 6 1 3169 3239 490661093 490661161 6.290000e-13 86.1
19 TraesCS2A01G387900 chr2B 94.902 1530 48 15 2009 3517 574717805 574719325 0.000000e+00 2366.0
20 TraesCS2A01G387900 chr2B 95.035 1430 64 5 1 1426 574715886 574717312 0.000000e+00 2241.0
21 TraesCS2A01G387900 chr2B 93.824 1101 38 6 1492 2565 574676793 574677890 0.000000e+00 1629.0
22 TraesCS2A01G387900 chr2B 93.865 815 27 9 2747 3538 574690049 574690863 0.000000e+00 1206.0
23 TraesCS2A01G387900 chr2B 96.098 615 20 3 192 806 574675676 574676286 0.000000e+00 1000.0
24 TraesCS2A01G387900 chr2B 94.231 520 28 1 911 1428 574676284 574676803 0.000000e+00 793.0
25 TraesCS2A01G387900 chr2B 91.304 506 18 2 1492 1972 574717304 574717808 0.000000e+00 667.0
26 TraesCS2A01G387900 chr2B 88.958 480 44 5 958 1428 575137646 575138125 5.090000e-163 584.0
27 TraesCS2A01G387900 chr2B 86.570 484 44 10 2714 3181 575141805 575142283 6.770000e-142 514.0
28 TraesCS2A01G387900 chr2B 84.158 505 61 14 1801 2297 575138471 575138964 4.130000e-129 472.0
29 TraesCS2A01G387900 chr2B 91.343 335 28 1 3 337 575136700 575137033 1.160000e-124 457.0
30 TraesCS2A01G387900 chr2B 85.714 322 44 1 958 1277 574039951 574039630 4.370000e-89 339.0
31 TraesCS2A01G387900 chr2B 83.438 320 34 14 1486 1791 575138109 575138423 2.690000e-71 279.0
32 TraesCS2A01G387900 chr2B 76.892 489 81 22 441 921 574040394 574039930 7.580000e-62 248.0
33 TraesCS2A01G387900 chr2B 94.937 158 6 1 2602 2759 574677887 574678042 2.730000e-61 246.0
34 TraesCS2A01G387900 chr2B 89.444 180 13 4 2152 2326 573941947 573941769 4.600000e-54 222.0
35 TraesCS2A01G387900 chr2B 79.612 309 36 12 1499 1785 574038200 574037897 2.790000e-46 196.0
36 TraesCS2A01G387900 chr2B 100.000 93 0 0 64 156 574675584 574675676 4.700000e-39 172.0
37 TraesCS2A01G387900 chr2B 79.111 225 28 11 3319 3531 575142407 575142624 1.710000e-28 137.0
38 TraesCS2A01G387900 chr2B 100.000 71 0 0 1427 1497 67298229 67298299 7.970000e-27 132.0
39 TraesCS2A01G387900 chr2B 100.000 71 0 0 1427 1497 354662904 354662974 7.970000e-27 132.0
40 TraesCS2A01G387900 chr2B 93.976 83 4 1 1427 1508 19162089 19162007 1.330000e-24 124.0
41 TraesCS2A01G387900 chr2B 92.857 84 4 1 1427 1508 571204017 571204100 1.730000e-23 121.0
42 TraesCS2A01G387900 chr2B 91.667 84 7 0 3319 3402 573940775 573940692 2.230000e-22 117.0
43 TraesCS2A01G387900 chr2B 91.667 84 7 0 3319 3402 574035622 574035539 2.230000e-22 117.0
44 TraesCS2A01G387900 chr2B 87.805 82 10 0 2506 2587 573941524 573941443 2.910000e-16 97.1
45 TraesCS2A01G387900 chr2B 87.805 82 10 0 2506 2587 574036371 574036290 2.910000e-16 97.1
46 TraesCS2A01G387900 chrUn 82.911 474 70 8 962 1431 259671365 259670899 1.960000e-112 416.0
47 TraesCS2A01G387900 chrUn 82.365 482 40 25 1881 2326 259669930 259669458 9.270000e-101 377.0
48 TraesCS2A01G387900 chr6B 100.000 71 0 0 1427 1497 630553916 630553986 7.970000e-27 132.0
49 TraesCS2A01G387900 chr6B 100.000 70 0 0 1427 1496 455079827 455079896 2.870000e-26 130.0
50 TraesCS2A01G387900 chr6B 98.611 72 1 0 1427 1498 28503711 28503640 1.030000e-25 128.0
51 TraesCS2A01G387900 chr6B 91.304 92 4 4 1427 1517 695772231 695772143 4.800000e-24 122.0
52 TraesCS2A01G387900 chr1A 100.000 70 0 0 1427 1496 30192199 30192130 2.870000e-26 130.0
53 TraesCS2A01G387900 chr1A 93.333 45 2 1 921 965 412460385 412460428 8.200000e-07 65.8
54 TraesCS2A01G387900 chr5D 92.000 50 3 1 920 969 269578722 269578674 6.340000e-08 69.4
55 TraesCS2A01G387900 chr3D 95.238 42 2 0 925 966 127334673 127334714 2.280000e-07 67.6
56 TraesCS2A01G387900 chr3D 93.023 43 1 2 925 965 506698394 506698352 1.060000e-05 62.1
57 TraesCS2A01G387900 chr4B 95.238 42 1 1 925 966 95188074 95188114 8.200000e-07 65.8
58 TraesCS2A01G387900 chr1D 95.122 41 2 0 925 965 326287728 326287768 8.200000e-07 65.8


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 TraesCS2A01G387900 chr2A 634106459 634109996 3537 False 6534.000000 6534 100.000000 1 3538 1 chr2A.!!$F1 3537
1 TraesCS2A01G387900 chr2A 634606308 634609795 3487 False 511.200000 959 85.445800 1 3407 5 chr2A.!!$F2 3406
2 TraesCS2A01G387900 chr2D 490576884 490580308 3424 False 1909.000000 2841 96.685000 1 3538 3 chr2D.!!$F1 3537
3 TraesCS2A01G387900 chr2D 490657892 490661273 3381 False 437.914286 900 86.321286 3 3384 7 chr2D.!!$F2 3381
4 TraesCS2A01G387900 chr2D 490124660 490127686 3026 True 291.000000 396 84.770333 958 3402 3 chr2D.!!$R1 2444
5 TraesCS2A01G387900 chr2B 574715886 574719325 3439 False 1758.000000 2366 93.747000 1 3517 3 chr2B.!!$F6 3516
6 TraesCS2A01G387900 chr2B 574690049 574690863 814 False 1206.000000 1206 93.865000 2747 3538 1 chr2B.!!$F4 791
7 TraesCS2A01G387900 chr2B 574675584 574678042 2458 False 768.000000 1629 95.818000 64 2759 5 chr2B.!!$F5 2695
8 TraesCS2A01G387900 chr2B 575136700 575142624 5924 False 407.166667 584 85.596333 3 3531 6 chr2B.!!$F7 3528
9 TraesCS2A01G387900 chrUn 259669458 259671365 1907 True 396.500000 416 82.638000 962 2326 2 chrUn.!!$R1 1364

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
389 481 1.821216 ATTTAAGGCCACGACACCAG 58.179 50.0 5.01 0.0 0.00 4.00 F
1433 1566 0.235926 GTCTTTGCTCGCAAGTGGTC 59.764 55.0 4.39 0.0 37.24 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1597 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.0 44.29 3.32 R
3240 6975 1.004745 TCCCATCCAAAGGCTTCTGTC 59.995 52.381 0.00 0.0 0.00 3.51 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
269 287 5.143369 AGATTAGCTTTTGATCCATTCCCC 58.857 41.667 0.00 0.00 0.00 4.81
389 481 1.821216 ATTTAAGGCCACGACACCAG 58.179 50.000 5.01 0.00 0.00 4.00
422 516 6.293790 GGGTGTGACAACAAATAGGTAGTTTC 60.294 42.308 1.89 0.00 38.27 2.78
428 523 7.094805 TGACAACAAATAGGTAGTTTCTGATGC 60.095 37.037 0.00 0.00 0.00 3.91
447 542 4.305989 TGCAATTGAGACAACTTTGGAC 57.694 40.909 10.34 0.00 0.00 4.02
668 767 6.405278 AACAAGTTTCTCCAATGGTAAAGG 57.595 37.500 0.00 0.00 0.00 3.11
1418 1551 9.665719 ATTTAAGAAACAATTTGTGGTTGTCTT 57.334 25.926 2.13 9.46 37.24 3.01
1419 1552 9.495572 TTTAAGAAACAATTTGTGGTTGTCTTT 57.504 25.926 2.13 0.00 37.24 2.52
1420 1553 6.966435 AGAAACAATTTGTGGTTGTCTTTG 57.034 33.333 2.13 0.00 37.24 2.77
1421 1554 5.351189 AGAAACAATTTGTGGTTGTCTTTGC 59.649 36.000 2.13 0.00 37.24 3.68
1422 1555 4.470334 ACAATTTGTGGTTGTCTTTGCT 57.530 36.364 0.15 0.00 34.93 3.91
1423 1556 4.432712 ACAATTTGTGGTTGTCTTTGCTC 58.567 39.130 0.15 0.00 34.93 4.26
1424 1557 2.842208 TTTGTGGTTGTCTTTGCTCG 57.158 45.000 0.00 0.00 0.00 5.03
1425 1558 0.380378 TTGTGGTTGTCTTTGCTCGC 59.620 50.000 0.00 0.00 0.00 5.03
1426 1559 0.746204 TGTGGTTGTCTTTGCTCGCA 60.746 50.000 0.00 0.00 0.00 5.10
1427 1560 0.380378 GTGGTTGTCTTTGCTCGCAA 59.620 50.000 0.00 0.00 0.00 4.85
1428 1561 0.662619 TGGTTGTCTTTGCTCGCAAG 59.337 50.000 4.39 0.48 37.24 4.01
1429 1562 0.663153 GGTTGTCTTTGCTCGCAAGT 59.337 50.000 4.39 0.00 37.24 3.16
1430 1563 1.597937 GGTTGTCTTTGCTCGCAAGTG 60.598 52.381 4.39 2.98 37.24 3.16
1431 1564 0.662619 TTGTCTTTGCTCGCAAGTGG 59.337 50.000 4.39 0.74 37.24 4.00
1432 1565 0.463654 TGTCTTTGCTCGCAAGTGGT 60.464 50.000 4.39 0.00 37.24 4.16
1433 1566 0.235926 GTCTTTGCTCGCAAGTGGTC 59.764 55.000 4.39 0.00 37.24 4.02
1434 1567 1.205064 CTTTGCTCGCAAGTGGTCG 59.795 57.895 4.39 0.00 37.24 4.79
1435 1568 2.175184 CTTTGCTCGCAAGTGGTCGG 62.175 60.000 4.39 0.00 37.24 4.79
1436 1569 2.652382 TTTGCTCGCAAGTGGTCGGA 62.652 55.000 4.39 0.00 37.24 4.55
1437 1570 3.112709 GCTCGCAAGTGGTCGGAC 61.113 66.667 0.00 0.00 39.48 4.79
1438 1571 2.432628 CTCGCAAGTGGTCGGACC 60.433 66.667 20.36 20.36 39.22 4.46
1439 1572 3.934391 CTCGCAAGTGGTCGGACCC 62.934 68.421 23.81 14.91 37.50 4.46
1440 1573 4.003788 CGCAAGTGGTCGGACCCT 62.004 66.667 23.81 16.82 37.50 4.34
1441 1574 2.430367 GCAAGTGGTCGGACCCTT 59.570 61.111 23.81 21.08 37.50 3.95
1442 1575 1.671379 GCAAGTGGTCGGACCCTTC 60.671 63.158 23.81 13.97 37.50 3.46
1443 1576 1.003718 CAAGTGGTCGGACCCTTCC 60.004 63.158 23.81 9.51 37.50 3.46
1444 1577 2.222013 AAGTGGTCGGACCCTTCCC 61.222 63.158 23.81 7.17 38.99 3.97
1445 1578 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
1446 1579 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
1447 1580 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
1448 1581 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
1449 1582 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
1450 1583 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
1451 1584 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
1452 1585 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
1453 1586 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
1454 1587 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
1455 1588 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
1456 1589 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
1481 1614 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
1482 1615 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
1483 1616 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
1484 1617 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
1485 1618 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
1486 1619 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
1487 1620 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
1488 1621 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
1489 1622 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
1490 1623 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
1536 1670 4.799564 TTGAACCTTGAAACTTGCAAGT 57.200 36.364 26.36 26.36 40.79 3.16
1644 1803 2.373540 TGGTGAACATACGCTGTACC 57.626 50.000 4.48 4.48 36.98 3.34
1700 1862 5.348451 AGCATTGTGGAATTTTCGTAATTGC 59.652 36.000 9.18 9.18 0.00 3.56
2084 2901 9.720769 ATCTTTCCAAATAAGACGAGAAAGTAA 57.279 29.630 9.40 0.00 40.51 2.24
2122 2943 5.880332 TGGTATCTGGTTTGAAGTAATCTGC 59.120 40.000 0.00 0.00 0.00 4.26
2363 5714 6.204108 ACCTGTTGTTAAAGAACGGAGTAATG 59.796 38.462 8.42 0.00 45.00 1.90
2591 6009 6.969993 TGGCATAAACCTAGTTCACTTTTT 57.030 33.333 0.00 0.00 0.00 1.94
2826 6520 5.045797 GTGTCCCTAACAATCTACTCCCTTT 60.046 44.000 0.00 0.00 40.31 3.11
2952 6647 5.751243 TTACAGAAGAGTTTGTGCTTTCC 57.249 39.130 0.00 0.00 31.07 3.13
3239 6974 2.041485 TCCCTGGTTCATGCATCTTTCA 59.959 45.455 0.00 0.00 0.00 2.69
3240 6975 2.426024 CCCTGGTTCATGCATCTTTCAG 59.574 50.000 0.00 3.02 0.00 3.02
3242 6977 3.128242 CCTGGTTCATGCATCTTTCAGAC 59.872 47.826 14.53 0.65 0.00 3.51
3243 6978 3.753815 TGGTTCATGCATCTTTCAGACA 58.246 40.909 0.00 0.00 0.00 3.41
3291 7058 6.535865 ACTCTCTAGCGGAGTTATATACATCG 59.464 42.308 10.91 0.00 40.65 3.84
3409 7176 8.855110 TCTAGATCTCATGATGTACCTTTTCTC 58.145 37.037 0.00 0.00 32.19 2.87
3417 7184 6.877611 TGATGTACCTTTTCTCTTTTGACC 57.122 37.500 0.00 0.00 0.00 4.02
3442 7220 1.448540 CGCCGTGCTCCTGAAGAAT 60.449 57.895 0.00 0.00 0.00 2.40
3531 7314 0.250424 GGCCAAGCATGCAAAAACCT 60.250 50.000 21.98 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 287 4.510167 AGGAACCCTATGAGACCAAATG 57.490 45.455 0.00 0.00 28.47 2.32
389 481 2.028130 TGTTGTCACACCCCAAATGAC 58.972 47.619 0.00 0.00 42.54 3.06
422 516 4.921515 CCAAAGTTGTCTCAATTGCATCAG 59.078 41.667 0.00 0.00 0.00 2.90
428 523 7.775397 AATTTGTCCAAAGTTGTCTCAATTG 57.225 32.000 0.00 0.00 33.32 2.32
447 542 8.914654 ACATCGTCAAACATTTGTCATAATTTG 58.085 29.630 4.36 0.00 39.18 2.32
668 767 5.022021 GTCAATGTTAATGTTAGTGCTCGC 58.978 41.667 0.00 0.00 0.00 5.03
1364 1493 2.703416 CAGAGTGTTCATTAGGCAGCA 58.297 47.619 0.00 0.00 0.00 4.41
1365 1494 1.399791 GCAGAGTGTTCATTAGGCAGC 59.600 52.381 0.00 0.00 0.00 5.25
1366 1495 2.012673 GGCAGAGTGTTCATTAGGCAG 58.987 52.381 0.00 0.00 0.00 4.85
1417 1550 2.250939 CCGACCACTTGCGAGCAAA 61.251 57.895 11.83 0.00 35.33 3.68
1418 1551 2.664851 CCGACCACTTGCGAGCAA 60.665 61.111 10.28 10.28 0.00 3.91
1419 1552 3.611674 TCCGACCACTTGCGAGCA 61.612 61.111 0.00 0.00 0.00 4.26
1420 1553 3.112709 GTCCGACCACTTGCGAGC 61.113 66.667 0.00 0.00 0.00 5.03
1421 1554 2.432628 GGTCCGACCACTTGCGAG 60.433 66.667 13.05 0.00 38.42 5.03
1422 1555 3.998672 GGGTCCGACCACTTGCGA 61.999 66.667 19.43 0.00 41.02 5.10
1423 1556 3.530910 AAGGGTCCGACCACTTGCG 62.531 63.158 19.43 0.00 41.02 4.85
1424 1557 1.671379 GAAGGGTCCGACCACTTGC 60.671 63.158 19.43 9.88 41.02 4.01
1425 1558 1.003718 GGAAGGGTCCGACCACTTG 60.004 63.158 19.43 0.00 41.02 3.16
1426 1559 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
1427 1560 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
1428 1561 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
1429 1562 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
1430 1563 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
1431 1564 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
1432 1565 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
1433 1566 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
1434 1567 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
1435 1568 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
1436 1569 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
1437 1570 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
1438 1571 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
1439 1572 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
1451 1584 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
1454 1587 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
1455 1588 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
1456 1589 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
1457 1590 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
1463 1596 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
1464 1597 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
1465 1598 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
1466 1599 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
1467 1600 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
1489 1622 4.210955 GGAAATGACAATTGCGAGCAAAAA 59.789 37.500 14.76 0.00 39.55 1.94
1490 1623 3.740321 GGAAATGACAATTGCGAGCAAAA 59.260 39.130 14.76 0.00 39.55 2.44
1644 1803 5.290386 CGAAGTCCTGCTAATTACCTAAGG 58.710 45.833 0.00 0.00 0.00 2.69
1686 1848 3.944775 CGCAACGCAATTACGAAAATT 57.055 38.095 4.79 0.00 36.70 1.82
1700 1862 4.621526 TTACATGAAAATTTGCGCAACG 57.378 36.364 24.99 6.40 0.00 4.10
2084 2901 6.367983 ACCAGATACCAATATGATTTGCTGT 58.632 36.000 0.00 0.00 0.00 4.40
2122 2943 4.481930 TGTTTCTTGAACAACCGCATAG 57.518 40.909 0.00 0.00 44.95 2.23
2333 5684 4.124238 CGTTCTTTAACAACAGGTGGAGA 58.876 43.478 0.00 0.00 35.16 3.71
2438 5819 7.065803 CGTGATCTTTAACAGGTCAATATTGGT 59.934 37.037 15.36 2.63 44.78 3.67
2591 6009 7.642194 CGTTGTGAACTAGTTTTATCTTTTGCA 59.358 33.333 10.02 0.00 0.00 4.08
2709 6234 6.642733 TTTGTTAGGGAAATCCATCTCTCT 57.357 37.500 1.22 0.00 38.24 3.10
2710 6235 6.264067 CCATTTGTTAGGGAAATCCATCTCTC 59.736 42.308 1.22 0.00 38.24 3.20
2826 6520 5.276820 CGTGATGCGCAATATTCTACAAAGA 60.277 40.000 17.11 0.00 0.00 2.52
2952 6647 1.508088 GCTTTGCCACCTCAATCGG 59.492 57.895 0.00 0.00 0.00 4.18
3220 6953 3.349927 TCTGAAAGATGCATGAACCAGG 58.650 45.455 2.46 0.00 38.67 4.45
3239 6974 1.005215 CCCATCCAAAGGCTTCTGTCT 59.995 52.381 0.00 0.00 0.00 3.41
3240 6975 1.004745 TCCCATCCAAAGGCTTCTGTC 59.995 52.381 0.00 0.00 0.00 3.51
3242 6977 2.220653 TTCCCATCCAAAGGCTTCTG 57.779 50.000 0.00 1.30 0.00 3.02
3243 6978 2.899900 GTTTTCCCATCCAAAGGCTTCT 59.100 45.455 0.00 0.00 0.00 2.85
3291 7058 9.530129 CAGACGTATATTTCACTCAAAGAAAAC 57.470 33.333 0.00 0.00 38.36 2.43
3409 7176 1.866925 GGCGAGGTTCGGTCAAAAG 59.133 57.895 0.34 0.00 40.84 2.27


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

AutoCloner maintained by Alex Coulton.