Multiple sequence alignment - TraesCS2B01G112300

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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 TraesCS2B01G112300 chr2B 100.000 2597 0 0 1 2597 75687520 75684924 0.000000e+00 4796.0
1 TraesCS2B01G112300 chr2B 94.444 108 6 0 654 761 75617342 75617235 1.600000e-37 167.0
2 TraesCS2B01G112300 chr5D 93.655 788 39 2 1821 2597 450523548 450524335 0.000000e+00 1168.0
3 TraesCS2B01G112300 chr5D 93.401 788 36 6 1821 2597 445111954 445112736 0.000000e+00 1153.0
4 TraesCS2B01G112300 chr5D 87.697 634 53 10 1804 2413 521104232 521103600 0.000000e+00 715.0
5 TraesCS2B01G112300 chr5D 82.696 549 73 15 1 542 546925458 546925991 3.910000e-128 468.0
6 TraesCS2B01G112300 chr5D 92.632 95 5 2 678 772 112025250 112025158 4.510000e-28 135.0
7 TraesCS2B01G112300 chr1A 93.647 787 38 3 1822 2597 504105563 504104778 0.000000e+00 1166.0
8 TraesCS2B01G112300 chr1A 84.740 557 69 9 1 545 94111356 94110804 6.320000e-151 544.0
9 TraesCS2B01G112300 chr1A 96.429 84 2 1 678 761 492004797 492004715 1.250000e-28 137.0
10 TraesCS2B01G112300 chr1D 93.139 787 42 3 1822 2597 435762367 435761582 0.000000e+00 1144.0
11 TraesCS2B01G112300 chr1D 90.276 617 48 3 1808 2413 490442959 490442344 0.000000e+00 797.0
12 TraesCS2B01G112300 chr1D 86.982 169 17 5 1 166 22783729 22783563 4.410000e-43 185.0
13 TraesCS2B01G112300 chr1D 89.286 112 7 4 678 786 393766036 393766145 4.510000e-28 135.0
14 TraesCS2B01G112300 chr4D 93.130 786 42 3 1823 2597 1616627 1615843 0.000000e+00 1142.0
15 TraesCS2B01G112300 chr4D 85.895 553 67 10 1 546 4822044 4821496 1.730000e-161 579.0
16 TraesCS2B01G112300 chr6B 93.020 788 42 4 1822 2597 146837210 146836424 0.000000e+00 1138.0
17 TraesCS2B01G112300 chr6B 80.857 350 55 11 1 342 116112209 116112554 5.510000e-67 265.0
18 TraesCS2B01G112300 chr7D 93.011 787 42 4 1822 2597 634755014 634755798 0.000000e+00 1136.0
19 TraesCS2B01G112300 chr7D 82.843 204 18 12 633 825 40410431 40410628 1.600000e-37 167.0
20 TraesCS2B01G112300 chr7D 73.250 557 110 30 12 543 575529269 575528727 1.600000e-37 167.0
21 TraesCS2B01G112300 chr7A 93.112 784 41 4 1825 2597 276420 275639 0.000000e+00 1136.0
22 TraesCS2B01G112300 chr7A 83.057 543 70 15 6 541 674071480 674070953 8.410000e-130 473.0
23 TraesCS2B01G112300 chr7A 84.548 343 30 9 1822 2142 19375936 19375595 4.170000e-83 318.0
24 TraesCS2B01G112300 chr7A 75.551 544 95 31 13 541 37852930 37853450 1.550000e-57 233.0
25 TraesCS2B01G112300 chr6D 92.893 788 45 2 1821 2597 471620253 471619466 0.000000e+00 1134.0
26 TraesCS2B01G112300 chr6D 95.960 99 1 3 677 775 54019094 54019189 9.620000e-35 158.0
27 TraesCS2B01G112300 chr6D 75.069 361 59 18 1 354 46872678 46873014 3.480000e-29 139.0
28 TraesCS2B01G112300 chr2A 84.063 1142 106 38 602 1722 50965585 50964499 0.000000e+00 1031.0
29 TraesCS2B01G112300 chr2A 90.416 553 44 7 1 547 423188683 423188134 0.000000e+00 719.0
30 TraesCS2B01G112300 chr2A 89.865 148 14 1 614 761 50960863 50960717 3.410000e-44 189.0
31 TraesCS2B01G112300 chr2A 97.917 48 1 0 1717 1764 50964312 50964265 1.660000e-12 84.2
32 TraesCS2B01G112300 chr2D 87.183 788 60 12 582 1343 47428558 47427786 0.000000e+00 857.0
33 TraesCS2B01G112300 chr2D 90.762 617 46 2 1808 2413 43809631 43810247 0.000000e+00 813.0
34 TraesCS2B01G112300 chr2D 89.460 389 28 5 1409 1790 47427776 47427394 1.810000e-131 479.0
35 TraesCS2B01G112300 chr2D 74.478 431 81 26 114 533 247440142 247440554 2.670000e-35 159.0
36 TraesCS2B01G112300 chr2D 97.561 82 0 1 679 760 47423353 47423274 3.480000e-29 139.0
37 TraesCS2B01G112300 chr2D 91.753 97 7 1 678 773 358032033 358032129 1.620000e-27 134.0
38 TraesCS2B01G112300 chr2D 75.000 324 64 16 32 345 562343660 562343344 1.620000e-27 134.0
39 TraesCS2B01G112300 chr7B 86.743 611 60 9 1822 2413 742336797 742336189 0.000000e+00 660.0
40 TraesCS2B01G112300 chr7B 82.766 441 63 12 3 437 117792111 117792544 5.240000e-102 381.0
41 TraesCS2B01G112300 chr7B 74.719 356 66 18 114 462 221792940 221793278 1.250000e-28 137.0
42 TraesCS2B01G112300 chr3B 84.819 415 51 11 74 483 50152727 50153134 8.650000e-110 407.0
43 TraesCS2B01G112300 chr3B 96.591 88 1 2 664 750 598977531 598977617 7.490000e-31 145.0
44 TraesCS2B01G112300 chrUn 83.824 272 22 9 1821 2073 356521271 356521539 3.340000e-59 239.0
45 TraesCS2B01G112300 chrUn 82.979 282 23 11 1817 2079 33281469 33281194 5.590000e-57 231.0
46 TraesCS2B01G112300 chr4B 83.955 268 17 6 1814 2056 94788312 94788046 1.550000e-57 233.0
47 TraesCS2B01G112300 chr1B 83.410 217 20 10 1817 2031 438040616 438040818 1.230000e-43 187.0
48 TraesCS2B01G112300 chr4A 91.743 109 7 2 662 770 647034205 647034311 1.610000e-32 150.0
49 TraesCS2B01G112300 chr4A 85.714 147 9 7 678 814 646898317 646898461 7.490000e-31 145.0
50 TraesCS2B01G112300 chr4A 80.255 157 21 6 678 825 646986619 646986774 2.730000e-20 110.0
51 TraesCS2B01G112300 chr6A 98.810 84 0 1 677 760 61022630 61022548 5.790000e-32 148.0
52 TraesCS2B01G112300 chr3D 97.500 80 0 2 679 758 455600647 455600724 4.510000e-28 135.0
53 TraesCS2B01G112300 chr3D 94.318 88 5 0 663 750 455601146 455601233 4.510000e-28 135.0


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 TraesCS2B01G112300 chr2B 75684924 75687520 2596 True 4796.000000 4796 100.0000 1 2597 1 chr2B.!!$R2 2596
1 TraesCS2B01G112300 chr5D 450523548 450524335 787 False 1168.000000 1168 93.6550 1821 2597 1 chr5D.!!$F2 776
2 TraesCS2B01G112300 chr5D 445111954 445112736 782 False 1153.000000 1153 93.4010 1821 2597 1 chr5D.!!$F1 776
3 TraesCS2B01G112300 chr5D 521103600 521104232 632 True 715.000000 715 87.6970 1804 2413 1 chr5D.!!$R2 609
4 TraesCS2B01G112300 chr5D 546925458 546925991 533 False 468.000000 468 82.6960 1 542 1 chr5D.!!$F3 541
5 TraesCS2B01G112300 chr1A 504104778 504105563 785 True 1166.000000 1166 93.6470 1822 2597 1 chr1A.!!$R3 775
6 TraesCS2B01G112300 chr1A 94110804 94111356 552 True 544.000000 544 84.7400 1 545 1 chr1A.!!$R1 544
7 TraesCS2B01G112300 chr1D 435761582 435762367 785 True 1144.000000 1144 93.1390 1822 2597 1 chr1D.!!$R2 775
8 TraesCS2B01G112300 chr1D 490442344 490442959 615 True 797.000000 797 90.2760 1808 2413 1 chr1D.!!$R3 605
9 TraesCS2B01G112300 chr4D 1615843 1616627 784 True 1142.000000 1142 93.1300 1823 2597 1 chr4D.!!$R1 774
10 TraesCS2B01G112300 chr4D 4821496 4822044 548 True 579.000000 579 85.8950 1 546 1 chr4D.!!$R2 545
11 TraesCS2B01G112300 chr6B 146836424 146837210 786 True 1138.000000 1138 93.0200 1822 2597 1 chr6B.!!$R1 775
12 TraesCS2B01G112300 chr7D 634755014 634755798 784 False 1136.000000 1136 93.0110 1822 2597 1 chr7D.!!$F2 775
13 TraesCS2B01G112300 chr7A 275639 276420 781 True 1136.000000 1136 93.1120 1825 2597 1 chr7A.!!$R1 772
14 TraesCS2B01G112300 chr7A 674070953 674071480 527 True 473.000000 473 83.0570 6 541 1 chr7A.!!$R3 535
15 TraesCS2B01G112300 chr7A 37852930 37853450 520 False 233.000000 233 75.5510 13 541 1 chr7A.!!$F1 528
16 TraesCS2B01G112300 chr6D 471619466 471620253 787 True 1134.000000 1134 92.8930 1821 2597 1 chr6D.!!$R1 776
17 TraesCS2B01G112300 chr2A 423188134 423188683 549 True 719.000000 719 90.4160 1 547 1 chr2A.!!$R1 546
18 TraesCS2B01G112300 chr2A 50960717 50965585 4868 True 434.733333 1031 90.6150 602 1764 3 chr2A.!!$R2 1162
19 TraesCS2B01G112300 chr2D 43809631 43810247 616 False 813.000000 813 90.7620 1808 2413 1 chr2D.!!$F1 605
20 TraesCS2B01G112300 chr2D 47427394 47428558 1164 True 668.000000 857 88.3215 582 1790 2 chr2D.!!$R3 1208
21 TraesCS2B01G112300 chr7B 742336189 742336797 608 True 660.000000 660 86.7430 1822 2413 1 chr7B.!!$R1 591

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
560 591 0.036388 ACATACAGTGGGCGTTGGAG 60.036 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1772 0.39113 ACCAAGTGCATACGCGATGT 60.391 50.0 15.93 0.0 42.97 3.06 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
71 73 4.083590 GCTCCTCTTGCTCACTTAGTTTTG 60.084 45.833 0.00 0.00 0.00 2.44
100 105 5.050490 TCGCCTAATGCTAGCTAAGAAAAG 58.950 41.667 17.23 3.87 38.05 2.27
105 110 8.244113 GCCTAATGCTAGCTAAGAAAAGAAAAA 58.756 33.333 17.23 0.00 36.87 1.94
454 476 9.816354 AAGAACAAATAAAACTAAACAGCACAT 57.184 25.926 0.00 0.00 0.00 3.21
493 524 0.979187 TCACCGACCCATAACCCCTC 60.979 60.000 0.00 0.00 0.00 4.30
505 536 0.540365 AACCCCTCATGCACCACAAG 60.540 55.000 0.00 0.00 0.00 3.16
523 554 3.094572 CAAGGCTTCAAATCATGGGAGT 58.905 45.455 0.00 0.00 0.00 3.85
533 564 8.737168 TTCAAATCATGGGAGTTTAGTATCTG 57.263 34.615 0.00 0.00 0.00 2.90
554 585 5.638596 TGTATAGATACATACAGTGGGCG 57.361 43.478 0.00 0.00 38.28 6.13
555 586 5.074804 TGTATAGATACATACAGTGGGCGT 58.925 41.667 0.00 0.00 38.28 5.68
556 587 5.537295 TGTATAGATACATACAGTGGGCGTT 59.463 40.000 0.00 0.00 38.28 4.84
557 588 3.179443 AGATACATACAGTGGGCGTTG 57.821 47.619 0.00 0.00 0.00 4.10
558 589 2.158957 AGATACATACAGTGGGCGTTGG 60.159 50.000 0.00 0.00 0.00 3.77
559 590 1.268066 TACATACAGTGGGCGTTGGA 58.732 50.000 0.00 0.00 0.00 3.53
560 591 0.036388 ACATACAGTGGGCGTTGGAG 60.036 55.000 0.00 0.00 0.00 3.86
561 592 0.249120 CATACAGTGGGCGTTGGAGA 59.751 55.000 0.00 0.00 0.00 3.71
562 593 1.134401 CATACAGTGGGCGTTGGAGAT 60.134 52.381 0.00 0.00 0.00 2.75
563 594 0.249120 TACAGTGGGCGTTGGAGATG 59.751 55.000 0.00 0.00 0.00 2.90
564 595 2.045926 AGTGGGCGTTGGAGATGC 60.046 61.111 0.00 0.00 39.65 3.91
569 600 3.499737 GCGTTGGAGATGCCCGTG 61.500 66.667 0.00 0.00 34.03 4.94
570 601 2.264480 CGTTGGAGATGCCCGTGA 59.736 61.111 0.00 0.00 34.97 4.35
571 602 2.100631 CGTTGGAGATGCCCGTGAC 61.101 63.158 0.00 0.00 34.97 3.67
572 603 2.100631 GTTGGAGATGCCCGTGACG 61.101 63.158 0.00 0.00 34.97 4.35
574 605 3.771160 GGAGATGCCCGTGACGGT 61.771 66.667 23.73 3.92 46.80 4.83
575 606 2.264794 GAGATGCCCGTGACGGTT 59.735 61.111 23.73 7.19 46.80 4.44
576 607 1.514087 GAGATGCCCGTGACGGTTA 59.486 57.895 23.73 11.61 46.80 2.85
577 608 0.804933 GAGATGCCCGTGACGGTTAC 60.805 60.000 23.73 12.37 46.80 2.50
578 609 1.079681 GATGCCCGTGACGGTTACA 60.080 57.895 23.73 17.69 46.80 2.41
579 610 0.671163 GATGCCCGTGACGGTTACAA 60.671 55.000 23.73 3.55 46.80 2.41
580 611 0.952010 ATGCCCGTGACGGTTACAAC 60.952 55.000 23.73 5.45 46.80 3.32
594 625 1.794512 TACAACGGGTTTAACGCTCC 58.205 50.000 10.30 0.00 34.00 4.70
600 631 2.036571 GGTTTAACGCTCCCGGTGG 61.037 63.158 0.00 0.00 39.22 4.61
610 641 4.278513 CCCGGTGGAAAGGGCACA 62.279 66.667 0.00 0.00 41.34 4.57
612 643 2.561037 CCGGTGGAAAGGGCACAAC 61.561 63.158 0.00 0.00 0.00 3.32
637 668 1.006571 ATCGTTCACGTGCGTCCTT 60.007 52.632 11.67 0.00 40.80 3.36
649 680 3.305094 CGTGCGTCCTTATTGTACGAATT 59.695 43.478 0.00 0.00 42.99 2.17
650 681 4.574759 GTGCGTCCTTATTGTACGAATTG 58.425 43.478 0.00 0.00 38.89 2.32
652 683 5.289193 GTGCGTCCTTATTGTACGAATTGTA 59.711 40.000 0.00 0.00 38.89 2.41
750 781 4.803426 GACTCCCGGCAGACGCAG 62.803 72.222 0.00 0.00 42.52 5.18
757 788 2.320587 CGGCAGACGCAGCTCTTTT 61.321 57.895 0.00 0.00 41.24 2.27
899 950 3.108289 CAGCGCTCACACGTGGAG 61.108 66.667 21.57 22.03 34.88 3.86
948 999 3.244105 GCTTCTCGCGCTGTTCAA 58.756 55.556 5.56 0.00 0.00 2.69
951 1002 0.861837 CTTCTCGCGCTGTTCAACTT 59.138 50.000 5.56 0.00 0.00 2.66
986 1037 1.348938 CGCACCAAACGTTCAACGA 59.651 52.632 18.84 0.00 46.05 3.85
988 1039 0.375803 GCACCAAACGTTCAACGAGT 59.624 50.000 18.84 5.41 46.05 4.18
1041 1103 4.445162 GGGAGAGGAGAGATCTCTACGAAA 60.445 50.000 26.07 0.00 45.23 3.46
1051 1116 1.544691 TCTCTACGAAACCCAGCTGAC 59.455 52.381 17.39 0.14 0.00 3.51
1099 1165 5.989168 CACTGACACAATCTACAACTACCAA 59.011 40.000 0.00 0.00 0.00 3.67
1344 1410 1.313772 ACTCGAGAGTCCATCCATCG 58.686 55.000 21.68 0.00 36.92 3.84
1345 1411 0.595588 CTCGAGAGTCCATCCATCGG 59.404 60.000 6.58 0.00 34.29 4.18
1350 1416 0.668706 GAGTCCATCCATCGGCATCG 60.669 60.000 0.00 0.00 37.82 3.84
1353 1419 2.281002 CATCCATCGGCATCGGCA 60.281 61.111 0.00 0.00 43.71 5.69
1355 1421 1.152984 ATCCATCGGCATCGGCAAA 60.153 52.632 0.00 0.00 43.71 3.68
1385 1451 2.894731 ACATGTCTTCTCTCCTGTCCA 58.105 47.619 0.00 0.00 0.00 4.02
1386 1452 3.448934 ACATGTCTTCTCTCCTGTCCAT 58.551 45.455 0.00 0.00 0.00 3.41
1387 1453 3.450457 ACATGTCTTCTCTCCTGTCCATC 59.550 47.826 0.00 0.00 0.00 3.51
1397 1463 4.099633 TCTCCTGTCCATCTTCTCAATGT 58.900 43.478 0.00 0.00 0.00 2.71
1405 1471 2.762535 TCTTCTCAATGTTCCCCGTC 57.237 50.000 0.00 0.00 0.00 4.79
1407 1473 2.028112 TCTTCTCAATGTTCCCCGTCTG 60.028 50.000 0.00 0.00 0.00 3.51
1418 1484 2.359169 CCCGTCTGGCTCCAGCTTA 61.359 63.158 10.99 0.00 43.31 3.09
1536 1605 1.135859 CGCCTCATGTTTCTGAACTGC 60.136 52.381 0.00 0.00 36.70 4.40
1540 1609 3.058432 CCTCATGTTTCTGAACTGCAGTG 60.058 47.826 22.49 8.37 45.14 3.66
1549 1618 2.998670 CTGAACTGCAGTGTGATACAGG 59.001 50.000 22.49 0.00 39.85 4.00
1552 1621 2.179427 ACTGCAGTGTGATACAGGCTA 58.821 47.619 20.97 0.00 34.40 3.93
1596 1665 4.891277 CAAATGAATTCGTTTGTCAGGC 57.109 40.909 31.75 0.00 43.95 4.85
1624 1694 6.258727 AGTTCAAGACAACAGTAGTGACAATG 59.741 38.462 4.09 0.76 0.00 2.82
1629 1699 7.658179 AGACAACAGTAGTGACAATGTATTG 57.342 36.000 4.09 3.17 43.26 1.90
1680 1754 4.410492 ACAGCTGAATTTGATGTTCGAC 57.590 40.909 23.35 0.00 29.04 4.20
1705 1779 1.347097 CCCGCATCTCATACATCGCG 61.347 60.000 0.00 0.00 42.21 5.87
1764 2030 3.479269 CGACCGCGCCTTCTTCAC 61.479 66.667 0.00 0.00 0.00 3.18
1792 2058 5.621228 CGATTCCGTTTTTCTTTCAAGACAG 59.379 40.000 0.00 0.00 34.13 3.51
1793 2059 6.511121 CGATTCCGTTTTTCTTTCAAGACAGA 60.511 38.462 0.00 0.00 34.13 3.41
1794 2060 5.734855 TCCGTTTTTCTTTCAAGACAGAG 57.265 39.130 0.00 0.00 34.13 3.35
1795 2061 4.574828 TCCGTTTTTCTTTCAAGACAGAGG 59.425 41.667 0.00 0.00 34.13 3.69
1796 2062 4.282873 CGTTTTTCTTTCAAGACAGAGGC 58.717 43.478 0.00 0.00 34.13 4.70
1797 2063 4.201910 CGTTTTTCTTTCAAGACAGAGGCA 60.202 41.667 0.00 0.00 34.13 4.75
1798 2064 5.650543 GTTTTTCTTTCAAGACAGAGGCAA 58.349 37.500 0.00 0.00 34.13 4.52
1799 2065 5.913137 TTTTCTTTCAAGACAGAGGCAAA 57.087 34.783 0.00 0.00 34.13 3.68
1800 2066 5.913137 TTTCTTTCAAGACAGAGGCAAAA 57.087 34.783 0.00 0.00 34.13 2.44
1801 2067 5.505173 TTCTTTCAAGACAGAGGCAAAAG 57.495 39.130 0.00 0.00 34.13 2.27
1802 2068 4.780815 TCTTTCAAGACAGAGGCAAAAGA 58.219 39.130 0.00 0.00 0.00 2.52
1803 2069 5.380043 TCTTTCAAGACAGAGGCAAAAGAT 58.620 37.500 0.00 0.00 0.00 2.40
1804 2070 5.829924 TCTTTCAAGACAGAGGCAAAAGATT 59.170 36.000 0.00 0.00 0.00 2.40
1805 2071 6.322201 TCTTTCAAGACAGAGGCAAAAGATTT 59.678 34.615 0.00 0.00 0.00 2.17
2008 2874 0.593128 AAACAGACATCGCAGCCAAC 59.407 50.000 0.00 0.00 0.00 3.77
2014 2880 0.037590 ACATCGCAGCCAACCCTAAA 59.962 50.000 0.00 0.00 0.00 1.85
2182 3055 2.358125 CACCATGGCGTCCAACGA 60.358 61.111 13.04 0.00 46.05 3.85
2217 3133 0.235665 CGCAAACATCTGAGCACGTT 59.764 50.000 0.00 0.00 0.00 3.99
2246 3162 1.665916 CTGACACACCTCAGCACCG 60.666 63.158 0.00 0.00 31.57 4.94
2283 3199 2.479837 CAGCCGACACAACTTGAAGTA 58.520 47.619 0.00 0.00 0.00 2.24
2296 3226 9.219603 CACAACTTGAAGTATTTGGAAGATCTA 57.780 33.333 0.00 0.00 0.00 1.98
2375 4209 2.367241 TGACTTGACATCTCCACCGAAA 59.633 45.455 0.00 0.00 0.00 3.46
2560 5769 4.326766 GCCAAGAACGCGCTGCAA 62.327 61.111 5.73 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
443 465 7.120579 CCCACTTGTAAGATTATGTGCTGTTTA 59.879 37.037 0.00 0.00 0.00 2.01
454 476 2.508300 GAGGGCCCCACTTGTAAGATTA 59.492 50.000 21.43 0.00 0.00 1.75
493 524 0.675083 TTGAAGCCTTGTGGTGCATG 59.325 50.000 0.00 0.00 35.27 4.06
505 536 4.706962 ACTAAACTCCCATGATTTGAAGCC 59.293 41.667 0.00 0.00 0.00 4.35
533 564 5.640189 ACGCCCACTGTATGTATCTATAC 57.360 43.478 0.00 0.00 34.78 1.47
542 573 0.249120 TCTCCAACGCCCACTGTATG 59.751 55.000 0.00 0.00 0.00 2.39
547 578 2.045926 GCATCTCCAACGCCCACT 60.046 61.111 0.00 0.00 0.00 4.00
548 579 3.134127 GGCATCTCCAACGCCCAC 61.134 66.667 0.00 0.00 40.07 4.61
551 582 4.778143 ACGGGCATCTCCAACGCC 62.778 66.667 0.00 0.00 45.47 5.68
552 583 3.499737 CACGGGCATCTCCAACGC 61.500 66.667 0.00 0.00 36.21 4.84
553 584 2.100631 GTCACGGGCATCTCCAACG 61.101 63.158 0.00 0.00 36.21 4.10
554 585 2.100631 CGTCACGGGCATCTCCAAC 61.101 63.158 0.00 0.00 36.21 3.77
555 586 2.264480 CGTCACGGGCATCTCCAA 59.736 61.111 0.00 0.00 36.21 3.53
556 587 3.770040 CCGTCACGGGCATCTCCA 61.770 66.667 8.94 0.00 44.15 3.86
566 597 0.875474 AACCCGTTGTAACCGTCACG 60.875 55.000 0.00 0.00 0.00 4.35
567 598 1.298602 AAACCCGTTGTAACCGTCAC 58.701 50.000 0.00 0.00 0.00 3.67
568 599 2.869192 GTTAAACCCGTTGTAACCGTCA 59.131 45.455 0.00 0.00 0.00 4.35
569 600 2.096958 CGTTAAACCCGTTGTAACCGTC 60.097 50.000 0.00 0.00 0.00 4.79
570 601 1.864082 CGTTAAACCCGTTGTAACCGT 59.136 47.619 0.00 0.00 0.00 4.83
571 602 1.398324 GCGTTAAACCCGTTGTAACCG 60.398 52.381 0.00 0.00 0.00 4.44
572 603 1.872952 AGCGTTAAACCCGTTGTAACC 59.127 47.619 0.00 0.00 0.00 2.85
573 604 2.096268 GGAGCGTTAAACCCGTTGTAAC 60.096 50.000 0.00 0.00 0.00 2.50
574 605 2.142319 GGAGCGTTAAACCCGTTGTAA 58.858 47.619 0.00 0.00 0.00 2.41
575 606 1.607767 GGGAGCGTTAAACCCGTTGTA 60.608 52.381 0.00 0.00 34.03 2.41
576 607 0.886043 GGGAGCGTTAAACCCGTTGT 60.886 55.000 0.00 0.00 34.03 3.32
577 608 1.871077 GGGAGCGTTAAACCCGTTG 59.129 57.895 0.00 0.00 34.03 4.10
578 609 4.384599 GGGAGCGTTAAACCCGTT 57.615 55.556 0.00 0.00 34.03 4.44
594 625 2.203422 TTGTGCCCTTTCCACCGG 60.203 61.111 0.00 0.00 32.30 5.28
600 631 1.234821 TCATCACGTTGTGCCCTTTC 58.765 50.000 0.00 0.00 32.98 2.62
628 659 4.092383 ACAATTCGTACAATAAGGACGCAC 59.908 41.667 0.00 0.00 36.54 5.34
650 681 9.968743 GGCTATGCTAAATTTTACGATACATAC 57.031 33.333 0.00 0.00 0.00 2.39
652 683 8.615878 TGGCTATGCTAAATTTTACGATACAT 57.384 30.769 0.00 0.00 0.00 2.29
665 696 1.207089 ACAGACGCTGGCTATGCTAAA 59.793 47.619 10.80 0.00 35.51 1.85
672 703 0.323087 TGGACTACAGACGCTGGCTA 60.323 55.000 10.80 0.00 35.51 3.93
828 868 2.979676 CGTCTGGCTTTGGCTGCA 60.980 61.111 0.50 0.00 38.73 4.41
829 869 2.669569 TCGTCTGGCTTTGGCTGC 60.670 61.111 0.00 0.00 38.73 5.25
830 870 2.684843 GCTCGTCTGGCTTTGGCTG 61.685 63.158 0.00 0.00 38.73 4.85
831 871 2.359230 GCTCGTCTGGCTTTGGCT 60.359 61.111 0.00 0.00 38.73 4.75
832 872 2.669569 TGCTCGTCTGGCTTTGGC 60.670 61.111 0.00 0.00 37.82 4.52
834 874 2.856032 CGTGCTCGTCTGGCTTTG 59.144 61.111 0.00 0.00 0.00 2.77
883 934 3.295273 TCTCCACGTGTGAGCGCT 61.295 61.111 11.27 11.27 34.88 5.92
899 950 2.656007 TGACGCGACGTGGTTGTC 60.656 61.111 15.93 14.75 41.37 3.18
922 973 2.883253 GCGAGAAGCGTCTGGAGC 60.883 66.667 15.37 10.13 43.41 4.70
948 999 2.659610 GTGGAGCGAGGCTGAAGT 59.340 61.111 0.00 0.00 39.88 3.01
995 1046 3.545124 TATATGCTTGGCCGGGCGG 62.545 63.158 24.45 19.07 38.57 6.13
1041 1103 0.178932 TACTGGTCTGTCAGCTGGGT 60.179 55.000 15.13 3.32 38.26 4.51
1051 1116 2.093764 AGCAAGCTTAGCTACTGGTCTG 60.094 50.000 18.04 0.86 41.32 3.51
1276 1342 1.372087 GAAGAAGGCGCAGACCATGG 61.372 60.000 11.19 11.19 31.70 3.66
1311 1377 2.488545 TCTCGAGTCTTCACTACAAGGC 59.511 50.000 13.13 0.00 30.63 4.35
1336 1402 1.446516 TTTGCCGATGCCGATGGATG 61.447 55.000 0.00 0.00 38.22 3.51
1353 1419 0.623723 AGACATGTATGGGCCGGTTT 59.376 50.000 1.90 0.00 0.00 3.27
1355 1421 0.180406 GAAGACATGTATGGGCCGGT 59.820 55.000 1.90 0.00 0.00 5.28
1385 1451 2.840651 AGACGGGGAACATTGAGAAGAT 59.159 45.455 0.00 0.00 0.00 2.40
1386 1452 2.028112 CAGACGGGGAACATTGAGAAGA 60.028 50.000 0.00 0.00 0.00 2.87
1387 1453 2.350522 CAGACGGGGAACATTGAGAAG 58.649 52.381 0.00 0.00 0.00 2.85
1397 1463 3.003173 CTGGAGCCAGACGGGGAA 61.003 66.667 11.08 0.00 46.30 3.97
1405 1471 3.756739 CAGACTAAGCTGGAGCCAG 57.243 57.895 12.17 12.17 46.15 4.85
1418 1484 2.338809 TGAACATGAACCCTCCAGACT 58.661 47.619 0.00 0.00 0.00 3.24
1426 1492 2.159057 GGCATTCCATGAACATGAACCC 60.159 50.000 15.21 8.56 41.20 4.11
1428 1494 3.444742 TGAGGCATTCCATGAACATGAAC 59.555 43.478 15.21 0.00 41.20 3.18
1536 1605 3.179830 GTTCGTAGCCTGTATCACACTG 58.820 50.000 0.00 0.00 0.00 3.66
1540 1609 3.846360 ACTTGTTCGTAGCCTGTATCAC 58.154 45.455 0.00 0.00 0.00 3.06
1549 1618 2.336554 TGACGGTACTTGTTCGTAGC 57.663 50.000 0.00 0.00 37.25 3.58
1552 1621 2.806608 ACATGACGGTACTTGTTCGT 57.193 45.000 0.00 0.00 39.99 3.85
1594 1663 2.565841 ACTGTTGTCTTGAACTGAGCC 58.434 47.619 0.00 0.00 0.00 4.70
1596 1665 5.460419 GTCACTACTGTTGTCTTGAACTGAG 59.540 44.000 0.00 0.00 0.00 3.35
1659 1733 3.189287 GGTCGAACATCAAATTCAGCTGT 59.811 43.478 14.67 0.00 0.00 4.40
1696 1770 2.135139 CCAAGTGCATACGCGATGTAT 58.865 47.619 15.93 0.00 44.73 2.29
1698 1772 0.391130 ACCAAGTGCATACGCGATGT 60.391 50.000 15.93 0.00 42.97 3.06
1705 1779 1.134946 GCCATTGGACCAAGTGCATAC 59.865 52.381 20.34 1.47 33.22 2.39
1764 2030 6.995180 TCTTGAAAGAAAAACGGAATCGTTCG 60.995 38.462 4.64 0.00 44.25 3.95
1778 2044 5.652014 TCTTTTGCCTCTGTCTTGAAAGAAA 59.348 36.000 0.00 0.00 36.68 2.52
1779 2045 5.192927 TCTTTTGCCTCTGTCTTGAAAGAA 58.807 37.500 0.00 0.00 36.68 2.52
1781 2047 5.702349 ATCTTTTGCCTCTGTCTTGAAAG 57.298 39.130 0.00 0.00 0.00 2.62
1782 2048 6.275335 CAAATCTTTTGCCTCTGTCTTGAAA 58.725 36.000 0.00 0.00 0.00 2.69
1783 2049 5.737063 GCAAATCTTTTGCCTCTGTCTTGAA 60.737 40.000 12.74 0.00 39.38 2.69
1784 2050 4.261741 GCAAATCTTTTGCCTCTGTCTTGA 60.262 41.667 12.74 0.00 39.38 3.02
1785 2051 3.985925 GCAAATCTTTTGCCTCTGTCTTG 59.014 43.478 12.74 0.00 39.38 3.02
1786 2052 3.893813 AGCAAATCTTTTGCCTCTGTCTT 59.106 39.130 18.48 0.00 45.98 3.01
1787 2053 3.494332 AGCAAATCTTTTGCCTCTGTCT 58.506 40.909 18.48 0.00 45.98 3.41
1788 2054 3.505293 AGAGCAAATCTTTTGCCTCTGTC 59.495 43.478 18.48 10.82 45.98 3.51
1789 2055 3.494332 AGAGCAAATCTTTTGCCTCTGT 58.506 40.909 18.48 2.95 45.98 3.41
1790 2056 4.516365 AAGAGCAAATCTTTTGCCTCTG 57.484 40.909 18.48 0.00 46.49 3.35
1828 2176 3.135530 CAGGGGTCATCCTCCTTTTCTAG 59.864 52.174 0.00 0.00 33.94 2.43
1829 2177 3.115390 CAGGGGTCATCCTCCTTTTCTA 58.885 50.000 0.00 0.00 33.94 2.10
1911 2763 3.674138 CGGCGGCTTTAGTCTTACTGTTA 60.674 47.826 7.61 0.00 0.00 2.41
2008 2874 5.959583 ACCTCAGGTCTTAGATTTTAGGG 57.040 43.478 0.00 0.00 0.00 3.53
2102 2975 3.003480 ACAGTTTTGAAGATAGAGCGGC 58.997 45.455 0.00 0.00 0.00 6.53
2217 3133 4.961511 GTGTCAGTGGCGACCGCA 62.962 66.667 16.47 0.00 44.11 5.69
2246 3162 1.228124 TGGTGGTACTTGGCAGCAC 60.228 57.895 0.00 0.00 42.32 4.40
2283 3199 4.060038 ACGCACGATAGATCTTCCAAAT 57.940 40.909 0.00 0.00 41.38 2.32


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

AutoCloner maintained by Alex Coulton.