Multiple sequence alignment - TraesCS2D01G430300

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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 TraesCS2D01G430300 chr2D 100.000 2198 0 0 1 2198 542709581 542711778 0.000000e+00 4060.0
1 TraesCS2D01G430300 chr2D 86.672 1148 84 32 937 2031 542328748 542329879 0.000000e+00 1208.0
2 TraesCS2D01G430300 chr2D 96.920 552 17 0 48 599 365796181 365796732 0.000000e+00 926.0
3 TraesCS2D01G430300 chr2D 95.856 555 23 0 48 602 118536926 118537480 0.000000e+00 898.0
4 TraesCS2D01G430300 chr2D 89.286 672 43 13 697 1356 542777730 542778384 0.000000e+00 815.0
5 TraesCS2D01G430300 chr2D 83.887 813 62 37 753 1542 542543754 542544520 0.000000e+00 712.0
6 TraesCS2D01G430300 chr2D 91.611 298 14 5 1527 1816 542544477 542544771 3.400000e-108 401.0
7 TraesCS2D01G430300 chr2D 88.966 145 6 1 1848 1982 542544768 542544912 1.040000e-38 171.0
8 TraesCS2D01G430300 chr2D 93.590 78 5 0 2121 2198 542329921 542329998 1.380000e-22 117.0
9 TraesCS2D01G430300 chr2D 86.585 82 9 2 619 699 110981272 110981192 3.010000e-14 89.8
10 TraesCS2D01G430300 chr2D 96.296 54 1 1 1 53 514573108 514573161 1.080000e-13 87.9
11 TraesCS2D01G430300 chr2D 86.076 79 11 0 621 699 621137132 621137054 3.890000e-13 86.1
12 TraesCS2D01G430300 chr2D 90.476 63 5 1 1 63 267106079 267106140 5.030000e-12 82.4
13 TraesCS2D01G430300 chr5D 97.468 553 11 2 48 599 537321177 537320627 0.000000e+00 941.0
14 TraesCS2D01G430300 chr5D 92.188 64 4 1 636 699 48357212 48357274 3.010000e-14 89.8
15 TraesCS2D01G430300 chr3A 96.751 554 15 3 48 601 664700799 664701349 0.000000e+00 920.0
16 TraesCS2D01G430300 chr4D 96.739 552 16 1 48 599 437945200 437945749 0.000000e+00 918.0
17 TraesCS2D01G430300 chr2B 90.935 695 28 12 1272 1938 647539444 647540131 0.000000e+00 902.0
18 TraesCS2D01G430300 chr2B 82.979 799 56 31 806 1571 647450897 647451648 0.000000e+00 649.0
19 TraesCS2D01G430300 chr2B 86.063 574 44 18 697 1256 647603588 647604139 3.140000e-163 584.0
20 TraesCS2D01G430300 chr2B 88.787 437 24 11 842 1277 647538946 647539358 1.510000e-141 512.0
21 TraesCS2D01G430300 chr2B 84.815 540 37 19 1498 2016 647451607 647452122 3.260000e-138 501.0
22 TraesCS2D01G430300 chr2B 87.000 100 8 5 602 699 693857139 693857235 8.300000e-20 108.0
23 TraesCS2D01G430300 chr2B 86.316 95 13 0 2104 2198 647452249 647452343 1.070000e-18 104.0
24 TraesCS2D01G430300 chr3D 96.036 555 15 2 48 602 566433041 566433588 0.000000e+00 896.0
25 TraesCS2D01G430300 chr7D 95.668 554 24 0 48 601 147817560 147818113 0.000000e+00 891.0
26 TraesCS2D01G430300 chr7D 96.154 546 15 2 48 593 565436297 565436836 0.000000e+00 887.0
27 TraesCS2D01G430300 chr7D 96.296 54 1 1 1 53 48134708 48134761 1.080000e-13 87.9
28 TraesCS2D01G430300 chr6D 95.683 556 18 1 48 603 357779977 357780526 0.000000e+00 889.0
29 TraesCS2D01G430300 chr6D 100.000 48 0 0 1 48 244343428 244343475 3.010000e-14 89.8
30 TraesCS2D01G430300 chr2A 82.458 781 62 37 725 1477 685410410 685411143 4.010000e-172 614.0
31 TraesCS2D01G430300 chr2A 83.570 633 48 26 833 1418 685491402 685492025 1.920000e-150 542.0
32 TraesCS2D01G430300 chr2A 80.132 755 60 40 754 1477 685373446 685374141 4.240000e-132 481.0
33 TraesCS2D01G430300 chr2A 83.734 541 46 32 833 1357 685626706 685627220 7.100000e-130 473.0
34 TraesCS2D01G430300 chr2A 80.088 683 49 44 765 1435 685380421 685381028 5.610000e-116 427.0
35 TraesCS2D01G430300 chr2A 86.737 377 18 13 1494 1851 685381048 685381411 7.360000e-105 390.0
36 TraesCS2D01G430300 chr2A 85.567 291 24 10 1572 1851 685374179 685374462 2.760000e-74 289.0
37 TraesCS2D01G430300 chr2A 79.944 359 20 23 1867 2198 685381470 685381803 1.320000e-52 217.0
38 TraesCS2D01G430300 chr2A 94.595 37 0 1 797 833 685491355 685491389 3.050000e-04 56.5
39 TraesCS2D01G430300 chr6B 91.667 108 9 0 594 701 25605854 25605961 1.360000e-32 150.0
40 TraesCS2D01G430300 chr4B 92.000 100 8 0 600 699 524703277 524703178 8.180000e-30 141.0
41 TraesCS2D01G430300 chr1B 88.889 99 11 0 604 702 685492997 685493095 2.960000e-24 122.0
42 TraesCS2D01G430300 chr1B 84.466 103 15 1 597 699 377927313 377927414 1.390000e-17 100.0
43 TraesCS2D01G430300 chr4A 91.860 86 7 0 617 702 112574372 112574287 1.070000e-23 121.0
44 TraesCS2D01G430300 chrUn 87.879 99 12 0 604 702 252268922 252268824 1.380000e-22 117.0
45 TraesCS2D01G430300 chrUn 86.869 99 13 0 604 702 252268543 252268445 6.410000e-21 111.0
46 TraesCS2D01G430300 chr7B 86.538 104 12 2 597 699 659240103 659240205 1.780000e-21 113.0
47 TraesCS2D01G430300 chr1D 93.651 63 2 2 1 62 289494851 289494790 2.320000e-15 93.5
48 TraesCS2D01G430300 chr1D 98.039 51 0 1 1 51 368307534 368307485 1.080000e-13 87.9
49 TraesCS2D01G430300 chr1D 94.545 55 2 1 1 55 223305025 223305078 1.400000e-12 84.2
50 TraesCS2D01G430300 chr1D 91.525 59 5 0 1 59 27638563 27638505 5.030000e-12 82.4
51 TraesCS2D01G430300 chr5B 90.625 64 6 0 636 699 358308121 358308184 3.890000e-13 86.1
52 TraesCS2D01G430300 chr5B 87.879 66 6 2 639 703 670696276 670696212 2.340000e-10 76.8
53 TraesCS2D01G430300 chr5A 90.164 61 6 0 1 61 463519665 463519605 1.810000e-11 80.5
54 TraesCS2D01G430300 chr6A 92.500 40 3 0 663 702 207177821 207177782 8.480000e-05 58.4


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 TraesCS2D01G430300 chr2D 542709581 542711778 2197 False 4060.000000 4060 100.000000 1 2198 1 chr2D.!!$F5 2197
1 TraesCS2D01G430300 chr2D 365796181 365796732 551 False 926.000000 926 96.920000 48 599 1 chr2D.!!$F3 551
2 TraesCS2D01G430300 chr2D 118536926 118537480 554 False 898.000000 898 95.856000 48 602 1 chr2D.!!$F1 554
3 TraesCS2D01G430300 chr2D 542777730 542778384 654 False 815.000000 815 89.286000 697 1356 1 chr2D.!!$F6 659
4 TraesCS2D01G430300 chr2D 542328748 542329998 1250 False 662.500000 1208 90.131000 937 2198 2 chr2D.!!$F7 1261
5 TraesCS2D01G430300 chr2D 542543754 542544912 1158 False 428.000000 712 88.154667 753 1982 3 chr2D.!!$F8 1229
6 TraesCS2D01G430300 chr5D 537320627 537321177 550 True 941.000000 941 97.468000 48 599 1 chr5D.!!$R1 551
7 TraesCS2D01G430300 chr3A 664700799 664701349 550 False 920.000000 920 96.751000 48 601 1 chr3A.!!$F1 553
8 TraesCS2D01G430300 chr4D 437945200 437945749 549 False 918.000000 918 96.739000 48 599 1 chr4D.!!$F1 551
9 TraesCS2D01G430300 chr2B 647538946 647540131 1185 False 707.000000 902 89.861000 842 1938 2 chr2B.!!$F4 1096
10 TraesCS2D01G430300 chr2B 647603588 647604139 551 False 584.000000 584 86.063000 697 1256 1 chr2B.!!$F1 559
11 TraesCS2D01G430300 chr2B 647450897 647452343 1446 False 418.000000 649 84.703333 806 2198 3 chr2B.!!$F3 1392
12 TraesCS2D01G430300 chr3D 566433041 566433588 547 False 896.000000 896 96.036000 48 602 1 chr3D.!!$F1 554
13 TraesCS2D01G430300 chr7D 147817560 147818113 553 False 891.000000 891 95.668000 48 601 1 chr7D.!!$F2 553
14 TraesCS2D01G430300 chr7D 565436297 565436836 539 False 887.000000 887 96.154000 48 593 1 chr7D.!!$F3 545
15 TraesCS2D01G430300 chr6D 357779977 357780526 549 False 889.000000 889 95.683000 48 603 1 chr6D.!!$F2 555
16 TraesCS2D01G430300 chr2A 685410410 685411143 733 False 614.000000 614 82.458000 725 1477 1 chr2A.!!$F1 752
17 TraesCS2D01G430300 chr2A 685626706 685627220 514 False 473.000000 473 83.734000 833 1357 1 chr2A.!!$F2 524
18 TraesCS2D01G430300 chr2A 685373446 685374462 1016 False 385.000000 481 82.849500 754 1851 2 chr2A.!!$F3 1097
19 TraesCS2D01G430300 chr2A 685380421 685381803 1382 False 344.666667 427 82.256333 765 2198 3 chr2A.!!$F4 1433
20 TraesCS2D01G430300 chr2A 685491355 685492025 670 False 299.250000 542 89.082500 797 1418 2 chr2A.!!$F5 621

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
650 653 0.46729 AGCGCCTCAAAGGGACAAAA 60.467 50.0 2.29 0.0 35.37 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1924 0.03563 ACAGACGGGTACGCTAGTCT 60.036 55.0 12.64 12.64 46.04 3.24 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
23 24 4.418328 CCAATTCCGGCCGGGTCA 62.418 66.667 42.36 27.21 37.00 4.02
24 25 2.124320 CAATTCCGGCCGGGTCAT 60.124 61.111 42.36 28.15 37.00 3.06
25 26 1.147376 CAATTCCGGCCGGGTCATA 59.853 57.895 42.36 22.14 37.00 2.15
26 27 1.147600 AATTCCGGCCGGGTCATAC 59.852 57.895 42.36 0.00 37.00 2.39
27 28 2.333701 AATTCCGGCCGGGTCATACC 62.334 60.000 42.36 0.00 37.60 2.73
74 75 7.450124 TGGGAAGAAGAGTACATCGATATAC 57.550 40.000 5.69 5.69 0.00 1.47
177 178 6.603201 GCTAGATTAGAGGCTAGACATGAGAT 59.397 42.308 0.00 0.00 36.97 2.75
603 606 1.376812 GGTGGAGTTGGCCTAACGG 60.377 63.158 3.32 0.00 44.15 4.44
604 607 1.675219 GTGGAGTTGGCCTAACGGA 59.325 57.895 3.32 0.00 44.15 4.69
605 608 0.672711 GTGGAGTTGGCCTAACGGAC 60.673 60.000 3.32 3.38 44.15 4.79
611 614 4.611961 GGCCTAACGGACAAGACC 57.388 61.111 0.00 0.00 38.64 3.85
638 641 2.892425 CGAACCCATCAGCGCCTC 60.892 66.667 2.29 0.00 0.00 4.70
639 642 2.268920 GAACCCATCAGCGCCTCA 59.731 61.111 2.29 0.00 0.00 3.86
640 643 1.377202 GAACCCATCAGCGCCTCAA 60.377 57.895 2.29 0.00 0.00 3.02
641 644 0.960364 GAACCCATCAGCGCCTCAAA 60.960 55.000 2.29 0.00 0.00 2.69
642 645 0.962356 AACCCATCAGCGCCTCAAAG 60.962 55.000 2.29 0.00 0.00 2.77
643 646 2.117156 CCCATCAGCGCCTCAAAGG 61.117 63.158 2.29 0.00 38.80 3.11
644 647 2.117156 CCATCAGCGCCTCAAAGGG 61.117 63.158 2.29 0.00 35.37 3.95
645 648 1.078214 CATCAGCGCCTCAAAGGGA 60.078 57.895 2.29 0.00 35.37 4.20
646 649 1.078143 ATCAGCGCCTCAAAGGGAC 60.078 57.895 2.29 0.00 35.37 4.46
647 650 1.841302 ATCAGCGCCTCAAAGGGACA 61.841 55.000 2.29 0.00 35.37 4.02
648 651 1.600636 CAGCGCCTCAAAGGGACAA 60.601 57.895 2.29 0.00 35.37 3.18
649 652 1.150536 AGCGCCTCAAAGGGACAAA 59.849 52.632 2.29 0.00 35.37 2.83
650 653 0.467290 AGCGCCTCAAAGGGACAAAA 60.467 50.000 2.29 0.00 35.37 2.44
651 654 0.603065 GCGCCTCAAAGGGACAAAAT 59.397 50.000 0.00 0.00 35.37 1.82
652 655 1.402852 GCGCCTCAAAGGGACAAAATC 60.403 52.381 0.00 0.00 35.37 2.17
660 663 3.990466 GGACAAAATCCGGCCGAA 58.010 55.556 30.73 6.63 37.88 4.30
661 664 1.504900 GGACAAAATCCGGCCGAAC 59.495 57.895 30.73 7.93 37.88 3.95
662 665 1.504900 GACAAAATCCGGCCGAACC 59.495 57.895 30.73 2.48 0.00 3.62
674 677 4.272100 CGAACCGGACGTCCATTT 57.728 55.556 32.80 24.00 35.14 2.32
675 678 1.785321 CGAACCGGACGTCCATTTG 59.215 57.895 32.80 24.16 35.14 2.32
676 679 1.632046 CGAACCGGACGTCCATTTGG 61.632 60.000 32.80 26.39 35.14 3.28
677 680 1.302993 AACCGGACGTCCATTTGGG 60.303 57.895 32.80 26.04 35.14 4.12
678 681 2.437716 CCGGACGTCCATTTGGGG 60.438 66.667 32.80 20.82 37.22 4.96
679 682 2.349755 CGGACGTCCATTTGGGGT 59.650 61.111 32.80 0.00 37.22 4.95
680 683 1.743995 CGGACGTCCATTTGGGGTC 60.744 63.158 32.80 3.24 37.90 4.46
681 684 1.743995 GGACGTCCATTTGGGGTCG 60.744 63.158 29.75 10.13 38.82 4.79
682 685 1.004200 GACGTCCATTTGGGGTCGT 60.004 57.895 3.51 4.30 45.07 4.34
683 686 1.296056 GACGTCCATTTGGGGTCGTG 61.296 60.000 3.51 0.00 43.50 4.35
684 687 2.686816 CGTCCATTTGGGGTCGTGC 61.687 63.158 0.00 0.00 37.22 5.34
685 688 2.359354 TCCATTTGGGGTCGTGCG 60.359 61.111 0.00 0.00 37.22 5.34
686 689 3.439540 CCATTTGGGGTCGTGCGG 61.440 66.667 0.00 0.00 0.00 5.69
687 690 2.671619 CATTTGGGGTCGTGCGGT 60.672 61.111 0.00 0.00 0.00 5.68
688 691 2.671619 ATTTGGGGTCGTGCGGTG 60.672 61.111 0.00 0.00 0.00 4.94
689 692 4.939368 TTTGGGGTCGTGCGGTGG 62.939 66.667 0.00 0.00 0.00 4.61
693 696 4.309950 GGGTCGTGCGGTGGAGTT 62.310 66.667 0.00 0.00 0.00 3.01
694 697 3.041940 GGTCGTGCGGTGGAGTTG 61.042 66.667 0.00 0.00 0.00 3.16
695 698 2.028484 GTCGTGCGGTGGAGTTGA 59.972 61.111 0.00 0.00 0.00 3.18
722 725 1.127397 GTACGCGAGCAGGTAAAAACC 59.873 52.381 15.93 0.00 0.00 3.27
723 726 1.232621 ACGCGAGCAGGTAAAAACCC 61.233 55.000 15.93 0.00 0.00 4.11
724 727 1.231958 CGCGAGCAGGTAAAAACCCA 61.232 55.000 0.00 0.00 0.00 4.51
725 728 0.955905 GCGAGCAGGTAAAAACCCAA 59.044 50.000 0.00 0.00 0.00 4.12
726 729 1.068541 GCGAGCAGGTAAAAACCCAAG 60.069 52.381 0.00 0.00 0.00 3.61
887 932 3.321682 CAGACTTTCCAAGCCCAAAATCA 59.678 43.478 0.00 0.00 0.00 2.57
888 933 3.966665 AGACTTTCCAAGCCCAAAATCAA 59.033 39.130 0.00 0.00 0.00 2.57
889 934 4.408596 AGACTTTCCAAGCCCAAAATCAAA 59.591 37.500 0.00 0.00 0.00 2.69
890 935 5.104569 AGACTTTCCAAGCCCAAAATCAAAA 60.105 36.000 0.00 0.00 0.00 2.44
891 936 5.693961 ACTTTCCAAGCCCAAAATCAAAAT 58.306 33.333 0.00 0.00 0.00 1.82
892 937 5.764686 ACTTTCCAAGCCCAAAATCAAAATC 59.235 36.000 0.00 0.00 0.00 2.17
1154 1206 2.029380 TCAAGAGCAAGCGCAAGTACTA 60.029 45.455 11.47 0.00 42.27 1.82
1219 1280 0.829333 GCTCATCAAGCCTCTCCTCA 59.171 55.000 0.00 0.00 45.92 3.86
1385 1601 1.034838 TATTTGGTGGGCGTGCATCC 61.035 55.000 0.00 0.00 0.00 3.51
1477 1712 0.451783 CGCAGGCCAGTAATGGAAAC 59.548 55.000 14.70 1.96 0.00 2.78
1511 1746 3.454082 CAGCTCCTCCTTCCTGATTAAGT 59.546 47.826 0.00 0.00 0.00 2.24
1512 1747 4.080638 CAGCTCCTCCTTCCTGATTAAGTT 60.081 45.833 0.00 0.00 0.00 2.66
1711 1990 2.596631 TCGTCCCGATCGATCCCC 60.597 66.667 18.66 4.29 32.30 4.81
1787 2085 3.819337 CTGATAAACAGCATAGCAGCCAT 59.181 43.478 0.00 0.00 39.86 4.40
1819 2117 1.009829 GCTGCATGTACTACAGTGGC 58.990 55.000 10.61 0.13 33.87 5.01
1858 2162 1.826487 GACGCCCACAGGTTTTGGT 60.826 57.895 0.00 0.00 34.57 3.67
1958 2312 2.536761 AAAATCCCCGCGATTCGATA 57.463 45.000 8.23 0.00 40.47 2.92
1991 2353 4.215742 TAGCCGGCCGTCCAATCG 62.216 66.667 26.15 7.77 0.00 3.34
2049 2478 6.825610 TGTTCATTAGTTGCCAAAAAGGAAT 58.174 32.000 4.77 0.00 41.22 3.01
2054 2483 9.434420 TCATTAGTTGCCAAAAAGGAATATTTG 57.566 29.630 0.00 0.00 41.22 2.32
2055 2484 9.218440 CATTAGTTGCCAAAAAGGAATATTTGT 57.782 29.630 0.00 0.00 41.22 2.83
2057 2486 9.921637 TTAGTTGCCAAAAAGGAATATTTGTAG 57.078 29.630 0.00 0.00 41.22 2.74
2058 2487 7.962441 AGTTGCCAAAAAGGAATATTTGTAGT 58.038 30.769 0.00 0.00 41.22 2.73
2059 2488 9.084533 AGTTGCCAAAAAGGAATATTTGTAGTA 57.915 29.630 0.00 0.00 41.22 1.82
2060 2489 9.135843 GTTGCCAAAAAGGAATATTTGTAGTAC 57.864 33.333 0.00 0.00 41.22 2.73
2061 2490 8.644374 TGCCAAAAAGGAATATTTGTAGTACT 57.356 30.769 0.00 0.00 41.22 2.73
2062 2491 8.736244 TGCCAAAAAGGAATATTTGTAGTACTC 58.264 33.333 0.00 0.00 41.22 2.59
2075 2504 6.905544 TTGTAGTACTCGTAGTGATCTCTG 57.094 41.667 0.00 0.00 0.00 3.35
2144 2599 5.163248 CCAAAAGGGGAAGGTTAATTTGTGT 60.163 40.000 0.00 0.00 0.00 3.72
2150 2605 4.262420 GGGAAGGTTAATTTGTGTGTGCAT 60.262 41.667 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.332312 TATGACCCGGCCGGAATTGG 62.332 60.000 45.44 29.46 37.50 3.16
7 8 1.147376 TATGACCCGGCCGGAATTG 59.853 57.895 45.44 29.86 37.50 2.32
8 9 1.147600 GTATGACCCGGCCGGAATT 59.852 57.895 45.44 28.29 37.50 2.17
9 10 2.814835 GGTATGACCCGGCCGGAAT 61.815 63.158 45.44 33.01 37.50 3.01
10 11 3.472726 GGTATGACCCGGCCGGAA 61.473 66.667 45.44 29.29 37.50 4.30
18 19 2.839162 TACCCCGCGGTATGACCC 60.839 66.667 26.12 0.00 42.18 4.46
32 33 4.035112 TCCCAATATGTCGGGGATATACC 58.965 47.826 0.00 0.00 45.83 2.73
39 40 2.438021 TCTTCTTCCCAATATGTCGGGG 59.562 50.000 5.51 0.00 43.29 5.73
40 41 3.134804 ACTCTTCTTCCCAATATGTCGGG 59.865 47.826 0.00 0.00 44.60 5.14
41 42 4.408182 ACTCTTCTTCCCAATATGTCGG 57.592 45.455 0.00 0.00 0.00 4.79
42 43 5.902681 TGTACTCTTCTTCCCAATATGTCG 58.097 41.667 0.00 0.00 0.00 4.35
43 44 6.642950 CGATGTACTCTTCTTCCCAATATGTC 59.357 42.308 0.00 0.00 0.00 3.06
44 45 6.323996 TCGATGTACTCTTCTTCCCAATATGT 59.676 38.462 0.00 0.00 0.00 2.29
45 46 6.749139 TCGATGTACTCTTCTTCCCAATATG 58.251 40.000 0.00 0.00 0.00 1.78
46 47 6.978674 TCGATGTACTCTTCTTCCCAATAT 57.021 37.500 0.00 0.00 0.00 1.28
74 75 8.581057 ACATGTACTAAATTTCGCTCTATCAG 57.419 34.615 0.00 0.00 0.00 2.90
177 178 3.674997 GATGTTGCTTCCTCACACCTAA 58.325 45.455 0.00 0.00 0.00 2.69
525 528 1.986631 TCCGTTTGGGTAGGGATTTGA 59.013 47.619 0.00 0.00 37.00 2.69
562 565 1.865788 CGACCCCAAACGGACGTCTA 61.866 60.000 16.46 0.00 0.00 2.59
621 624 2.892425 GAGGCGCTGATGGGTTCG 60.892 66.667 7.64 0.00 0.00 3.95
622 625 0.960364 TTTGAGGCGCTGATGGGTTC 60.960 55.000 7.64 0.00 0.00 3.62
623 626 0.962356 CTTTGAGGCGCTGATGGGTT 60.962 55.000 7.64 0.00 0.00 4.11
624 627 1.377725 CTTTGAGGCGCTGATGGGT 60.378 57.895 7.64 0.00 0.00 4.51
625 628 2.117156 CCTTTGAGGCGCTGATGGG 61.117 63.158 7.64 0.00 0.00 4.00
626 629 2.117156 CCCTTTGAGGCGCTGATGG 61.117 63.158 7.64 2.49 32.73 3.51
627 630 1.078214 TCCCTTTGAGGCGCTGATG 60.078 57.895 7.64 0.00 32.73 3.07
628 631 1.078143 GTCCCTTTGAGGCGCTGAT 60.078 57.895 7.64 0.00 32.73 2.90
629 632 2.050836 TTGTCCCTTTGAGGCGCTGA 62.051 55.000 7.64 0.00 32.73 4.26
630 633 1.172180 TTTGTCCCTTTGAGGCGCTG 61.172 55.000 7.64 0.00 32.73 5.18
631 634 0.467290 TTTTGTCCCTTTGAGGCGCT 60.467 50.000 7.64 0.00 32.73 5.92
632 635 0.603065 ATTTTGTCCCTTTGAGGCGC 59.397 50.000 0.00 0.00 32.73 6.53
633 636 1.202348 GGATTTTGTCCCTTTGAGGCG 59.798 52.381 0.00 0.00 41.50 5.52
634 637 1.202348 CGGATTTTGTCCCTTTGAGGC 59.798 52.381 0.00 0.00 44.77 4.70
635 638 1.818674 CCGGATTTTGTCCCTTTGAGG 59.181 52.381 0.00 0.00 44.77 3.86
636 639 1.202348 GCCGGATTTTGTCCCTTTGAG 59.798 52.381 5.05 0.00 44.77 3.02
637 640 1.253100 GCCGGATTTTGTCCCTTTGA 58.747 50.000 5.05 0.00 44.77 2.69
638 641 0.246360 GGCCGGATTTTGTCCCTTTG 59.754 55.000 5.05 0.00 44.77 2.77
639 642 1.248101 CGGCCGGATTTTGTCCCTTT 61.248 55.000 20.10 0.00 44.77 3.11
640 643 1.677633 CGGCCGGATTTTGTCCCTT 60.678 57.895 20.10 0.00 44.77 3.95
641 644 2.045340 CGGCCGGATTTTGTCCCT 60.045 61.111 20.10 0.00 44.77 4.20
642 645 1.676303 TTCGGCCGGATTTTGTCCC 60.676 57.895 27.83 0.00 44.77 4.46
643 646 1.504900 GTTCGGCCGGATTTTGTCC 59.495 57.895 27.83 0.00 44.10 4.02
644 647 1.504900 GGTTCGGCCGGATTTTGTC 59.495 57.895 27.83 2.43 0.00 3.18
645 648 3.676216 GGTTCGGCCGGATTTTGT 58.324 55.556 27.83 0.00 0.00 2.83
657 660 1.632046 CCAAATGGACGTCCGGTTCG 61.632 60.000 28.70 15.54 39.43 3.95
658 661 1.303091 CCCAAATGGACGTCCGGTTC 61.303 60.000 28.70 5.95 39.43 3.62
659 662 1.302993 CCCAAATGGACGTCCGGTT 60.303 57.895 28.70 22.21 39.43 4.44
660 663 2.349755 CCCAAATGGACGTCCGGT 59.650 61.111 28.70 17.63 39.43 5.28
661 664 2.437716 CCCCAAATGGACGTCCGG 60.438 66.667 28.70 22.35 39.43 5.14
662 665 1.743995 GACCCCAAATGGACGTCCG 60.744 63.158 28.70 15.23 39.43 4.79
663 666 1.743995 CGACCCCAAATGGACGTCC 60.744 63.158 28.17 28.17 38.48 4.79
664 667 3.884900 CGACCCCAAATGGACGTC 58.115 61.111 7.13 7.13 38.48 4.34
666 669 2.686816 GCACGACCCCAAATGGACG 61.687 63.158 0.00 6.57 46.60 4.79
667 670 2.686816 CGCACGACCCCAAATGGAC 61.687 63.158 0.00 0.00 37.39 4.02
668 671 2.359354 CGCACGACCCCAAATGGA 60.359 61.111 0.00 0.00 37.39 3.41
669 672 3.439540 CCGCACGACCCCAAATGG 61.440 66.667 0.00 0.00 0.00 3.16
670 673 2.671619 ACCGCACGACCCCAAATG 60.672 61.111 0.00 0.00 0.00 2.32
671 674 2.671619 CACCGCACGACCCCAAAT 60.672 61.111 0.00 0.00 0.00 2.32
672 675 4.939368 CCACCGCACGACCCCAAA 62.939 66.667 0.00 0.00 0.00 3.28
676 679 4.309950 AACTCCACCGCACGACCC 62.310 66.667 0.00 0.00 0.00 4.46
677 680 3.041940 CAACTCCACCGCACGACC 61.042 66.667 0.00 0.00 0.00 4.79
678 681 2.028484 TCAACTCCACCGCACGAC 59.972 61.111 0.00 0.00 0.00 4.34
679 682 2.028484 GTCAACTCCACCGCACGA 59.972 61.111 0.00 0.00 0.00 4.35
680 683 3.041940 GGTCAACTCCACCGCACG 61.042 66.667 0.00 0.00 0.00 5.34
681 684 1.961277 CAGGTCAACTCCACCGCAC 60.961 63.158 0.00 0.00 39.13 5.34
682 685 2.137528 TCAGGTCAACTCCACCGCA 61.138 57.895 0.00 0.00 39.13 5.69
683 686 1.668151 GTCAGGTCAACTCCACCGC 60.668 63.158 0.00 0.00 39.13 5.68
684 687 1.372997 CGTCAGGTCAACTCCACCG 60.373 63.158 0.00 0.00 39.13 4.94
685 688 0.963962 TACGTCAGGTCAACTCCACC 59.036 55.000 0.00 0.00 0.00 4.61
686 689 1.665161 CGTACGTCAGGTCAACTCCAC 60.665 57.143 7.22 0.00 0.00 4.02
687 690 0.594602 CGTACGTCAGGTCAACTCCA 59.405 55.000 7.22 0.00 0.00 3.86
688 691 0.731855 GCGTACGTCAGGTCAACTCC 60.732 60.000 17.90 0.00 0.00 3.85
689 692 1.063951 CGCGTACGTCAGGTCAACTC 61.064 60.000 17.90 0.00 33.53 3.01
690 693 1.081641 CGCGTACGTCAGGTCAACT 60.082 57.895 17.90 0.00 33.53 3.16
691 694 1.063951 CTCGCGTACGTCAGGTCAAC 61.064 60.000 17.90 0.00 41.18 3.18
692 695 1.208358 CTCGCGTACGTCAGGTCAA 59.792 57.895 17.90 0.00 41.18 3.18
693 696 2.865308 CTCGCGTACGTCAGGTCA 59.135 61.111 17.90 0.00 41.18 4.02
694 697 2.576317 GCTCGCGTACGTCAGGTC 60.576 66.667 17.90 0.00 41.18 3.85
695 698 3.324099 CTGCTCGCGTACGTCAGGT 62.324 63.158 17.90 0.00 41.18 4.00
887 932 1.952621 TCGGAGAGAGGTGGGATTTT 58.047 50.000 0.00 0.00 0.00 1.82
888 933 2.043227 GATCGGAGAGAGGTGGGATTT 58.957 52.381 0.00 0.00 43.63 2.17
889 934 1.710816 GATCGGAGAGAGGTGGGATT 58.289 55.000 0.00 0.00 43.63 3.01
890 935 0.178947 GGATCGGAGAGAGGTGGGAT 60.179 60.000 0.00 0.00 43.63 3.85
891 936 1.230497 GGATCGGAGAGAGGTGGGA 59.770 63.158 0.00 0.00 43.63 4.37
892 937 1.834822 GGGATCGGAGAGAGGTGGG 60.835 68.421 0.00 0.00 43.63 4.61
1204 1256 0.473326 GGCATGAGGAGAGGCTTGAT 59.527 55.000 0.00 0.00 0.00 2.57
1219 1280 0.997363 ATGGATGGATGGATCGGCAT 59.003 50.000 0.00 0.00 0.00 4.40
1385 1601 1.007387 GTTTTGCAGCCCTTCACGG 60.007 57.895 0.00 0.00 0.00 4.94
1440 1667 2.395360 GCATTAACGCGGAGGTGCA 61.395 57.895 12.47 0.00 33.09 4.57
1616 1889 1.388547 GCCCGGACTGCATTTTATCA 58.611 50.000 0.73 0.00 0.00 2.15
1647 1924 0.035630 ACAGACGGGTACGCTAGTCT 60.036 55.000 12.64 12.64 46.04 3.24
1711 1990 1.455383 AAAACAGCGCAGGTCCTTGG 61.455 55.000 11.47 0.00 33.74 3.61
1787 2085 1.032794 ATGCAGCGACGGAGATTCTA 58.967 50.000 0.00 0.00 0.00 2.10
1819 2117 1.158484 CCATCGATCTGTGGCAGCTG 61.158 60.000 10.11 10.11 0.00 4.24
1905 2246 1.136446 CCGCGAAAGGAACAGTTAACG 60.136 52.381 8.23 0.00 0.00 3.18
1991 2353 4.736631 GGCTCGTTTGCGCGTTCC 62.737 66.667 8.43 0.00 38.14 3.62
2049 2478 9.043079 CAGAGATCACTACGAGTACTACAAATA 57.957 37.037 0.00 0.00 0.00 1.40
2053 2482 5.128335 TCCAGAGATCACTACGAGTACTACA 59.872 44.000 0.00 0.00 0.00 2.74
2054 2483 5.599732 TCCAGAGATCACTACGAGTACTAC 58.400 45.833 0.00 0.00 0.00 2.73
2055 2484 5.866159 TCCAGAGATCACTACGAGTACTA 57.134 43.478 0.00 0.00 0.00 1.82
2056 2485 4.757019 TCCAGAGATCACTACGAGTACT 57.243 45.455 0.00 0.00 0.00 2.73
2057 2486 5.297278 ACAATCCAGAGATCACTACGAGTAC 59.703 44.000 0.00 0.00 0.00 2.73
2058 2487 5.437946 ACAATCCAGAGATCACTACGAGTA 58.562 41.667 0.00 0.00 0.00 2.59
2059 2488 4.274147 ACAATCCAGAGATCACTACGAGT 58.726 43.478 0.00 0.00 0.00 4.18
2060 2489 4.909696 ACAATCCAGAGATCACTACGAG 57.090 45.455 0.00 0.00 0.00 4.18
2061 2490 5.651530 GAAACAATCCAGAGATCACTACGA 58.348 41.667 0.00 0.00 0.00 3.43
2062 2491 4.500837 CGAAACAATCCAGAGATCACTACG 59.499 45.833 0.00 0.00 0.00 3.51
2066 2495 4.499183 ACTCGAAACAATCCAGAGATCAC 58.501 43.478 0.00 0.00 33.53 3.06
2075 2504 1.366854 GCGGGGACTCGAAACAATCC 61.367 60.000 0.00 0.00 0.00 3.01
2101 2530 8.850156 CCTTTTGGAGTATAATCCTACAATTGG 58.150 37.037 19.38 9.03 44.07 3.16
2105 2552 6.679303 TCCCCTTTTGGAGTATAATCCTACAA 59.321 38.462 19.38 7.67 44.07 2.41
2163 2618 5.598005 CCCTGATTAGGCACCAAATAAATGA 59.402 40.000 0.00 0.00 43.16 2.57


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

AutoCloner maintained by Alex Coulton.