Multiple sequence alignment - TraesCS2A01G017300

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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 TraesCS2A01G017300 chr2A 100.000 3995 0 0 1 3995 8144112 8140118 0.000000e+00 7378.0
1 TraesCS2A01G017300 chr2A 86.675 758 88 8 857 1601 23296699 23295942 0.000000e+00 828.0
2 TraesCS2A01G017300 chr2A 97.059 374 10 1 1 373 758748817 758749190 2.620000e-176 628.0
3 TraesCS2A01G017300 chr2A 92.494 413 13 7 321 733 758749218 758749612 3.460000e-160 575.0
4 TraesCS2A01G017300 chr2A 87.238 478 57 2 2525 3002 23294098 23293625 3.510000e-150 542.0
5 TraesCS2A01G017300 chr2A 86.820 478 59 2 2525 3002 22833414 22833887 7.600000e-147 531.0
6 TraesCS2A01G017300 chr2A 86.813 364 45 2 3632 3995 726770898 726770538 1.730000e-108 403.0
7 TraesCS2A01G017300 chr2A 82.335 334 52 7 3635 3968 694975982 694975656 2.350000e-72 283.0
8 TraesCS2A01G017300 chr2A 94.118 68 4 0 1594 1661 22832127 22832194 1.960000e-18 104.0
9 TraesCS2A01G017300 chr2A 92.647 68 5 0 1594 1661 23295385 23295318 9.140000e-17 99.0
10 TraesCS2A01G017300 chr2D 93.895 1851 85 12 2145 3989 8978988 8980816 0.000000e+00 2767.0
11 TraesCS2A01G017300 chr2D 95.757 872 33 2 734 1601 8976984 8977855 0.000000e+00 1402.0
12 TraesCS2A01G017300 chr2D 87.442 860 94 8 746 1601 21112334 21111485 0.000000e+00 977.0
13 TraesCS2A01G017300 chr2D 97.178 567 12 1 1594 2160 8978392 8978954 0.000000e+00 955.0
14 TraesCS2A01G017300 chr2D 81.530 758 97 24 2526 3240 21108147 21107390 5.750000e-163 584.0
15 TraesCS2A01G017300 chr6B 95.510 735 33 0 1 735 166025963 166025229 0.000000e+00 1175.0
16 TraesCS2A01G017300 chr1D 94.823 734 21 8 1 733 420084991 420085708 0.000000e+00 1129.0
17 TraesCS2A01G017300 chr1D 81.163 361 59 9 3631 3989 64137348 64136995 8.450000e-72 281.0
18 TraesCS2A01G017300 chr7B 96.447 591 20 1 1 590 22546661 22547251 0.000000e+00 974.0
19 TraesCS2A01G017300 chr7B 85.638 752 96 7 857 1601 657050979 657051725 0.000000e+00 780.0
20 TraesCS2A01G017300 chr7B 86.157 484 63 4 2522 3002 656955884 656956366 1.650000e-143 520.0
21 TraesCS2A01G017300 chrUn 87.054 757 86 8 857 1601 146958119 146957363 0.000000e+00 845.0
22 TraesCS2A01G017300 chrUn 87.054 757 86 8 857 1601 348794450 348793694 0.000000e+00 845.0
23 TraesCS2A01G017300 chrUn 86.394 757 91 8 857 1601 154137432 154138188 0.000000e+00 817.0
24 TraesCS2A01G017300 chrUn 86.129 757 93 8 857 1601 247073377 247072621 0.000000e+00 806.0
25 TraesCS2A01G017300 chrUn 86.379 602 70 8 1012 1601 154162289 154162890 0.000000e+00 647.0
26 TraesCS2A01G017300 chrUn 86.402 478 61 2 2525 3002 154140033 154140506 1.650000e-143 520.0
27 TraesCS2A01G017300 chrUn 92.647 68 5 0 1594 1661 146956806 146956739 9.140000e-17 99.0
28 TraesCS2A01G017300 chrUn 92.647 68 5 0 1594 1661 154138746 154138813 9.140000e-17 99.0
29 TraesCS2A01G017300 chrUn 92.647 68 5 0 1594 1661 154163447 154163514 9.140000e-17 99.0
30 TraesCS2A01G017300 chrUn 92.647 68 5 0 1594 1661 233291852 233291785 9.140000e-17 99.0
31 TraesCS2A01G017300 chrUn 92.647 68 5 0 1594 1661 247072064 247071997 9.140000e-17 99.0
32 TraesCS2A01G017300 chrUn 92.647 68 5 0 1594 1661 351637293 351637226 9.140000e-17 99.0
33 TraesCS2A01G017300 chr2B 82.042 813 83 30 2511 3283 34547801 34547012 5.630000e-178 634.0
34 TraesCS2A01G017300 chr2B 85.593 354 36 10 3636 3989 485752196 485752534 1.370000e-94 357.0
35 TraesCS2A01G017300 chr2B 85.714 77 10 1 3557 3632 34458326 34458250 3.310000e-11 80.5
36 TraesCS2A01G017300 chr5D 97.059 374 10 1 1 373 524493347 524493720 2.620000e-176 628.0
37 TraesCS2A01G017300 chr5D 93.548 372 9 6 321 692 524493748 524494104 1.260000e-149 540.0
38 TraesCS2A01G017300 chr5D 87.978 366 35 8 3632 3995 46726557 46726915 1.330000e-114 424.0
39 TraesCS2A01G017300 chr3D 97.059 374 10 1 1 373 572164167 572164540 2.620000e-176 628.0
40 TraesCS2A01G017300 chr3D 96.296 378 9 1 1 373 585103336 585103713 2.040000e-172 616.0
41 TraesCS2A01G017300 chr3D 93.462 413 12 6 321 733 572164568 572164965 2.050000e-167 599.0
42 TraesCS2A01G017300 chr4B 96.257 374 13 1 1 373 527645720 527645347 2.640000e-171 612.0
43 TraesCS2A01G017300 chr4B 92.476 412 13 7 321 732 527645319 527644926 1.250000e-159 573.0
44 TraesCS2A01G017300 chr3B 96.257 374 13 1 1 373 71296373 71296746 2.640000e-171 612.0
45 TraesCS2A01G017300 chr3B 96.078 357 11 1 377 733 71296815 71297168 2.680000e-161 579.0
46 TraesCS2A01G017300 chr3A 95.733 375 14 1 1 373 30762673 30762299 1.590000e-168 603.0
47 TraesCS2A01G017300 chr3A 90.824 425 17 5 321 738 30762271 30761862 2.100000e-152 549.0
48 TraesCS2A01G017300 chr3A 84.286 210 20 4 526 733 11532621 11532423 4.070000e-45 193.0
49 TraesCS2A01G017300 chr5B 79.436 851 150 22 740 1579 652097917 652098753 2.680000e-161 579.0
50 TraesCS2A01G017300 chr7D 87.195 492 59 2 2511 3002 121904852 121904365 1.250000e-154 556.0
51 TraesCS2A01G017300 chr7D 89.109 101 11 0 3530 3630 121904167 121904067 4.190000e-25 126.0
52 TraesCS2A01G017300 chr6D 87.393 349 32 6 3631 3979 65757097 65757433 1.350000e-104 390.0
53 TraesCS2A01G017300 chr6A 86.179 369 37 8 3631 3989 82105190 82104826 1.740000e-103 387.0
54 TraesCS2A01G017300 chr4A 84.273 337 47 5 3632 3968 636665468 636665138 1.380000e-84 324.0


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 TraesCS2A01G017300 chr2A 8140118 8144112 3994 True 7378.000000 7378 100.000000 1 3995 1 chr2A.!!$R1 3994
1 TraesCS2A01G017300 chr2A 758748817 758749612 795 False 601.500000 628 94.776500 1 733 2 chr2A.!!$F2 732
2 TraesCS2A01G017300 chr2A 23293625 23296699 3074 True 489.666667 828 88.853333 857 3002 3 chr2A.!!$R4 2145
3 TraesCS2A01G017300 chr2A 22832127 22833887 1760 False 317.500000 531 90.469000 1594 3002 2 chr2A.!!$F1 1408
4 TraesCS2A01G017300 chr2D 8976984 8980816 3832 False 1708.000000 2767 95.610000 734 3989 3 chr2D.!!$F1 3255
5 TraesCS2A01G017300 chr2D 21107390 21112334 4944 True 780.500000 977 84.486000 746 3240 2 chr2D.!!$R1 2494
6 TraesCS2A01G017300 chr6B 166025229 166025963 734 True 1175.000000 1175 95.510000 1 735 1 chr6B.!!$R1 734
7 TraesCS2A01G017300 chr1D 420084991 420085708 717 False 1129.000000 1129 94.823000 1 733 1 chr1D.!!$F1 732
8 TraesCS2A01G017300 chr7B 22546661 22547251 590 False 974.000000 974 96.447000 1 590 1 chr7B.!!$F1 589
9 TraesCS2A01G017300 chr7B 657050979 657051725 746 False 780.000000 780 85.638000 857 1601 1 chr7B.!!$F3 744
10 TraesCS2A01G017300 chrUn 348793694 348794450 756 True 845.000000 845 87.054000 857 1601 1 chrUn.!!$R2 744
11 TraesCS2A01G017300 chrUn 154137432 154140506 3074 False 478.666667 817 88.481000 857 3002 3 chrUn.!!$F1 2145
12 TraesCS2A01G017300 chrUn 146956739 146958119 1380 True 472.000000 845 89.850500 857 1661 2 chrUn.!!$R4 804
13 TraesCS2A01G017300 chrUn 247071997 247073377 1380 True 452.500000 806 89.388000 857 1661 2 chrUn.!!$R5 804
14 TraesCS2A01G017300 chrUn 154162289 154163514 1225 False 373.000000 647 89.513000 1012 1661 2 chrUn.!!$F2 649
15 TraesCS2A01G017300 chr2B 34547012 34547801 789 True 634.000000 634 82.042000 2511 3283 1 chr2B.!!$R2 772
16 TraesCS2A01G017300 chr5D 524493347 524494104 757 False 584.000000 628 95.303500 1 692 2 chr5D.!!$F2 691
17 TraesCS2A01G017300 chr3D 572164167 572164965 798 False 613.500000 628 95.260500 1 733 2 chr3D.!!$F2 732
18 TraesCS2A01G017300 chr4B 527644926 527645720 794 True 592.500000 612 94.366500 1 732 2 chr4B.!!$R1 731
19 TraesCS2A01G017300 chr3B 71296373 71297168 795 False 595.500000 612 96.167500 1 733 2 chr3B.!!$F1 732
20 TraesCS2A01G017300 chr3A 30761862 30762673 811 True 576.000000 603 93.278500 1 738 2 chr3A.!!$R2 737
21 TraesCS2A01G017300 chr5B 652097917 652098753 836 False 579.000000 579 79.436000 740 1579 1 chr5B.!!$F1 839
22 TraesCS2A01G017300 chr7D 121904067 121904852 785 True 341.000000 556 88.152000 2511 3630 2 chr7D.!!$R1 1119

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
32 34 0.782384 GATCACGACGACGCAAAGTT 59.218 50.000 7.30 0.0 43.96 2.66 F
432 582 1.746470 TCTCCACGACGAGCTTGATA 58.254 50.000 8.31 0.0 0.00 2.15 F
1290 1449 2.072487 GGAGCCAGGGAGCACCATA 61.072 63.158 1.58 0.0 42.46 2.74 F
2842 5776 0.517316 GGCAACTCGTAAAGCACAGG 59.483 55.000 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1214 1373 0.394192 CCTGACTCTGGTGCACAAGA 59.606 55.000 22.67 22.67 0.00 3.02 R
1468 1651 0.908198 AGACTCAGGACCTTGATGCC 59.092 55.000 0.00 0.00 0.00 4.40 R
2955 5889 1.371183 CACCGCTGAGAAAGGGTCA 59.629 57.895 0.00 0.00 37.13 4.02 R
3903 6899 0.749649 AGGTGCGTGCCAAATTTCAA 59.250 45.000 0.00 0.00 0.00 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
32 34 0.782384 GATCACGACGACGCAAAGTT 59.218 50.000 7.30 0.00 43.96 2.66
396 546 4.888239 AGTATGTGCTGAGAGTAACGGTAT 59.112 41.667 0.00 0.00 0.00 2.73
432 582 1.746470 TCTCCACGACGAGCTTGATA 58.254 50.000 8.31 0.00 0.00 2.15
950 1107 4.388499 CGTGGCCAGGTTACCGCT 62.388 66.667 17.47 0.00 34.18 5.52
1113 1272 4.828925 GTCAGCCAGAGCCTCCGC 62.829 72.222 0.00 0.00 41.25 5.54
1140 1299 3.254166 TCCAAATTTGCAGCTCTGTTCTC 59.746 43.478 12.92 0.00 0.00 2.87
1211 1370 3.041940 CTTTCGGAGCAACGCCGT 61.042 61.111 9.54 0.00 46.34 5.68
1214 1373 4.595538 TCGGAGCAACGCCGTTGT 62.596 61.111 28.40 16.58 46.34 3.32
1254 1413 4.143333 GGCGACGCTCCCAAGCTA 62.143 66.667 20.77 0.00 46.91 3.32
1260 1419 3.188786 GCTCCCAAGCTACACGCG 61.189 66.667 3.53 3.53 45.55 6.01
1290 1449 2.072487 GGAGCCAGGGAGCACCATA 61.072 63.158 1.58 0.00 42.46 2.74
1355 1523 5.122519 TGTCTGCAGTCTAACATTGTTCAA 58.877 37.500 14.67 0.00 0.00 2.69
1356 1524 5.007626 TGTCTGCAGTCTAACATTGTTCAAC 59.992 40.000 14.67 5.79 0.00 3.18
1432 1615 5.054390 TGTTTAATCGGGTTCATTTCAGC 57.946 39.130 0.00 0.00 0.00 4.26
1468 1651 3.751246 CAAGCACCATGGCCACCG 61.751 66.667 8.16 2.70 0.00 4.94
1680 2570 1.786937 AACAAACATGGGGAACTGCA 58.213 45.000 0.00 0.00 0.00 4.41
1681 2571 2.014010 ACAAACATGGGGAACTGCAT 57.986 45.000 0.00 0.00 0.00 3.96
1682 2572 3.168035 ACAAACATGGGGAACTGCATA 57.832 42.857 0.00 0.00 0.00 3.14
1683 2573 3.711863 ACAAACATGGGGAACTGCATAT 58.288 40.909 0.00 0.00 0.00 1.78
2078 3157 3.207265 TGCACAGTTCTTTTCAGGCTA 57.793 42.857 0.00 0.00 0.00 3.93
2079 3158 3.550820 TGCACAGTTCTTTTCAGGCTAA 58.449 40.909 0.00 0.00 0.00 3.09
2506 5418 4.321601 GCTGTGTGGTATTAATTTGCACCA 60.322 41.667 4.05 4.05 38.72 4.17
2633 5547 2.401766 GCAGTGCCAGGATGAACCG 61.402 63.158 2.85 0.00 44.74 4.44
2636 5550 2.046023 TGCCAGGATGAACCGCAG 60.046 61.111 0.00 0.00 44.74 5.18
2748 5662 4.170468 TGCCTTCCTCAAGTTCTTCTTT 57.830 40.909 0.00 0.00 33.63 2.52
2842 5776 0.517316 GGCAACTCGTAAAGCACAGG 59.483 55.000 0.00 0.00 0.00 4.00
2856 5790 3.142174 AGCACAGGAAGCTTCTAACAAC 58.858 45.455 25.05 8.14 39.87 3.32
2865 5799 1.135286 GCTTCTAACAACATGGCCAGC 60.135 52.381 13.05 0.00 0.00 4.85
2955 5889 3.385115 AGGGACGGATTACTCCTTTGAT 58.615 45.455 0.00 0.00 39.65 2.57
2979 5913 1.005340 CTTTCTCAGCGGTGCAGATC 58.995 55.000 10.38 0.00 0.00 2.75
3065 6029 5.885881 TGCAGACTTTGTGTTAAATTCGTT 58.114 33.333 0.00 0.00 0.00 3.85
3069 6033 7.186804 CAGACTTTGTGTTAAATTCGTTGTCT 58.813 34.615 0.00 0.00 0.00 3.41
3073 6037 7.855904 ACTTTGTGTTAAATTCGTTGTCTGATC 59.144 33.333 0.00 0.00 0.00 2.92
3121 6093 2.092538 ACTGATGATAGCTTGCTTGCCT 60.093 45.455 0.00 0.00 0.00 4.75
3129 6118 0.243095 GCTTGCTTGCCTCTTTCCTG 59.757 55.000 0.00 0.00 0.00 3.86
3183 6175 5.572896 GTGGCAGCATGTTTTAACTGTATTC 59.427 40.000 0.00 0.00 39.31 1.75
3252 6244 5.426833 AGAACTCTATGGTCTTTAGGCATGT 59.573 40.000 0.00 0.00 40.40 3.21
3290 6282 1.760613 TGTCGTTGAACTTCAGGAGGT 59.239 47.619 0.00 0.00 0.00 3.85
3308 6300 2.946990 AGGTACCATTTTATTTCGGGCG 59.053 45.455 15.94 0.00 0.00 6.13
3313 6305 3.129113 ACCATTTTATTTCGGGCGTTACC 59.871 43.478 0.00 0.00 37.93 2.85
3319 6311 1.022451 TTTCGGGCGTTACCTGCATC 61.022 55.000 0.00 0.00 45.54 3.91
3325 6317 1.202580 GGCGTTACCTGCATCTCTGAT 60.203 52.381 0.00 0.00 34.51 2.90
3393 6385 2.038426 TCTCGACATGCCAAAGAGGAAA 59.962 45.455 0.00 0.00 41.22 3.13
3399 6391 2.922740 TGCCAAAGAGGAAACGTACT 57.077 45.000 0.00 0.00 41.22 2.73
3405 6397 4.152402 CCAAAGAGGAAACGTACTGATGTG 59.848 45.833 0.00 0.00 41.22 3.21
3415 6407 4.566004 ACGTACTGATGTGCTGTGTAAAT 58.434 39.130 0.00 0.00 0.00 1.40
3505 6497 3.063997 CGACCTGCATGATTCTGTAAACC 59.936 47.826 0.00 0.00 0.00 3.27
3507 6499 4.012374 ACCTGCATGATTCTGTAAACCAG 58.988 43.478 0.00 0.00 42.97 4.00
3533 6525 9.173939 GCATGTGCTAATTTGTTATCTTCATAC 57.826 33.333 0.00 0.00 38.21 2.39
3553 6545 0.103208 ATGCTCTGCTAGGTACACGC 59.897 55.000 0.00 0.00 0.00 5.34
3607 6599 3.521531 TGGATCCCACAACAGTGCTATAA 59.478 43.478 9.90 0.00 31.87 0.98
3608 6600 4.130118 GGATCCCACAACAGTGCTATAAG 58.870 47.826 0.00 0.00 31.87 1.73
3618 6610 6.595716 ACAACAGTGCTATAAGGAATGAGTTC 59.404 38.462 2.91 0.00 33.39 3.01
3639 6631 8.624701 AGTTCATCTCATTTTTGCGATAATTG 57.375 30.769 0.00 0.00 0.00 2.32
3651 6643 3.123050 GCGATAATTGAAAATGGTGCCC 58.877 45.455 0.00 0.00 0.00 5.36
3653 6645 4.362279 CGATAATTGAAAATGGTGCCCAG 58.638 43.478 0.41 0.00 36.75 4.45
3658 6650 0.899717 GAAAATGGTGCCCAGGCTCA 60.900 55.000 10.58 8.81 42.51 4.26
3665 6657 1.228956 TGCCCAGGCTCATTTGCTT 60.229 52.632 10.58 0.00 42.51 3.91
3667 6659 1.953231 GCCCAGGCTCATTTGCTTCC 61.953 60.000 0.08 0.00 38.26 3.46
3684 6676 3.500680 GCTTCCGGTGAACAGTAAATTCA 59.499 43.478 0.00 0.00 33.68 2.57
3712 6704 8.969121 AAAAAGAGCAAACAAATTCAAAAAGG 57.031 26.923 0.00 0.00 0.00 3.11
3713 6705 7.686438 AAAGAGCAAACAAATTCAAAAAGGT 57.314 28.000 0.00 0.00 0.00 3.50
3714 6706 6.908870 AGAGCAAACAAATTCAAAAAGGTC 57.091 33.333 0.00 0.00 0.00 3.85
3715 6707 6.643388 AGAGCAAACAAATTCAAAAAGGTCT 58.357 32.000 0.00 0.00 0.00 3.85
3716 6708 6.536224 AGAGCAAACAAATTCAAAAAGGTCTG 59.464 34.615 0.00 0.00 31.07 3.51
3717 6709 5.585844 AGCAAACAAATTCAAAAAGGTCTGG 59.414 36.000 0.00 0.00 0.00 3.86
3737 6729 5.820947 TCTGGACCTTTTACACAAGAAAGAC 59.179 40.000 0.00 0.00 35.41 3.01
3757 6749 4.220821 AGACGAGAGAATTTTCTAGGTGCA 59.779 41.667 10.22 0.00 37.73 4.57
3798 6790 2.028203 TGGACATTTCACGAGCTCATGA 60.028 45.455 8.72 8.72 0.00 3.07
3856 6851 9.558648 GCAATTTTTGAAAGTTTCTTTGACAAT 57.441 25.926 16.33 4.32 0.00 2.71
3876 6871 8.348507 TGACAATCCAAATTTGTTATTTTTGCC 58.651 29.630 16.73 4.93 37.43 4.52
3903 6899 3.181476 GCTTGTCAAATGTCCAAACACCT 60.181 43.478 0.00 0.00 38.48 4.00
3912 6908 6.923928 AATGTCCAAACACCTTGAAATTTG 57.076 33.333 0.00 0.00 38.48 2.32
3933 6929 2.197577 GCACGCACCTAGAAGATTCTC 58.802 52.381 0.00 0.00 38.70 2.87
3946 6942 6.371595 AGAAGATTCTCTCAACTTCCATGT 57.628 37.500 0.00 0.00 39.33 3.21
3952 6948 8.105829 AGATTCTCTCAACTTCCATGTGTAAAT 58.894 33.333 0.00 0.00 0.00 1.40
3953 6949 9.383519 GATTCTCTCAACTTCCATGTGTAAATA 57.616 33.333 0.00 0.00 0.00 1.40
3954 6950 8.547967 TTCTCTCAACTTCCATGTGTAAATAC 57.452 34.615 0.00 0.00 0.00 1.89
3961 6957 8.950210 CAACTTCCATGTGTAAATACTTCAGAT 58.050 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 189 2.602933 CGTTCTCCGACGTGTTTGTCTA 60.603 50.000 0.00 0.00 39.56 2.59
385 535 0.317352 GCCCGTCGATACCGTTACTC 60.317 60.000 0.00 0.00 37.05 2.59
386 536 1.729881 GCCCGTCGATACCGTTACT 59.270 57.895 0.00 0.00 37.05 2.24
419 569 1.524355 CTGCCAATATCAAGCTCGTCG 59.476 52.381 0.00 0.00 0.00 5.12
636 793 4.323477 CCGGACCGAAGTGCCCAA 62.323 66.667 17.49 0.00 0.00 4.12
891 1048 0.323999 TGTAGAGGCAAGCGAGGGTA 60.324 55.000 0.00 0.00 0.00 3.69
1140 1299 2.047274 ACCACGGCAATGTCCTCG 60.047 61.111 0.00 0.00 0.00 4.63
1211 1370 1.209261 TGACTCTGGTGCACAAGACAA 59.791 47.619 20.42 5.79 0.00 3.18
1214 1373 0.394192 CCTGACTCTGGTGCACAAGA 59.606 55.000 22.67 22.67 0.00 3.02
1254 1413 1.274167 TCCAAGATTCCTAACGCGTGT 59.726 47.619 14.98 5.77 0.00 4.49
1260 1419 2.422093 CCCTGGCTCCAAGATTCCTAAC 60.422 54.545 0.00 0.00 0.00 2.34
1290 1449 3.482436 GATGGTGTCTCGGATCTCTAGT 58.518 50.000 0.00 0.00 0.00 2.57
1355 1523 5.633830 CATCAACTGGACATTTTGCTAGT 57.366 39.130 0.00 0.00 0.00 2.57
1414 1594 2.650322 GGGCTGAAATGAACCCGATTA 58.350 47.619 0.00 0.00 31.32 1.75
1428 1608 2.915869 GCCTTTATCCCGGGCTGA 59.084 61.111 18.49 0.00 42.31 4.26
1432 1615 2.280865 GCTCGCCTTTATCCCGGG 60.281 66.667 16.85 16.85 0.00 5.73
1468 1651 0.908198 AGACTCAGGACCTTGATGCC 59.092 55.000 0.00 0.00 0.00 4.40
1471 1654 3.843027 ACATTCAGACTCAGGACCTTGAT 59.157 43.478 0.00 0.00 0.00 2.57
1682 2572 9.151471 GAAATTGATACCGTGTATGCACTATAT 57.849 33.333 12.30 9.03 43.16 0.86
1683 2573 8.364894 AGAAATTGATACCGTGTATGCACTATA 58.635 33.333 12.30 4.64 43.16 1.31
1777 2690 4.393990 CAGACAGAGCTATGCAAATCAACA 59.606 41.667 8.60 0.00 0.00 3.33
2078 3157 5.580022 ACCTGGTGGCTAAGAATAAATGTT 58.420 37.500 0.00 0.00 36.63 2.71
2079 3158 5.044846 AGACCTGGTGGCTAAGAATAAATGT 60.045 40.000 2.82 0.00 36.63 2.71
2506 5418 7.880160 ATATAATGCTGGTACACACAAACAT 57.120 32.000 0.00 0.00 0.00 2.71
2650 5564 3.116091 CACTTTCAGTGGGCTTGGT 57.884 52.632 0.00 0.00 42.35 3.67
2667 5581 3.069016 ACACCTTGATACACGACTTGACA 59.931 43.478 0.00 0.00 0.00 3.58
2795 5709 2.270275 CGAGAATGTCGTGAAGCTCT 57.730 50.000 0.00 0.00 44.20 4.09
2842 5776 2.819608 TGGCCATGTTGTTAGAAGCTTC 59.180 45.455 19.11 19.11 0.00 3.86
2856 5790 2.439701 CAGGACCTGCTGGCCATG 60.440 66.667 5.51 10.39 36.63 3.66
2865 5799 1.926511 GCACCATTTCGCAGGACCTG 61.927 60.000 17.83 17.83 34.12 4.00
2955 5889 1.371183 CACCGCTGAGAAAGGGTCA 59.629 57.895 0.00 0.00 37.13 4.02
2979 5913 9.935241 AGATACAGATATTAAGCTATGTTGTGG 57.065 33.333 0.00 0.00 0.00 4.17
3065 6029 7.179076 TCTGATTCTCATCAAAGATCAGACA 57.821 36.000 9.56 0.00 39.04 3.41
3094 6066 4.892433 AGCAAGCTATCATCAGTCCATAC 58.108 43.478 0.00 0.00 0.00 2.39
3121 6093 6.463049 GCAAGGAGCATATACTACAGGAAAGA 60.463 42.308 0.00 0.00 44.79 2.52
3183 6175 1.478105 TCAGGACGACATGATCCACAG 59.522 52.381 14.88 7.00 37.47 3.66
3273 6265 2.036733 TGGTACCTCCTGAAGTTCAACG 59.963 50.000 14.36 0.23 37.07 4.10
3274 6266 3.764237 TGGTACCTCCTGAAGTTCAAC 57.236 47.619 14.36 0.87 37.07 3.18
3283 6275 4.578928 CCCGAAATAAAATGGTACCTCCTG 59.421 45.833 14.36 0.00 37.07 3.86
3284 6276 4.788679 CCCGAAATAAAATGGTACCTCCT 58.211 43.478 14.36 0.00 37.07 3.69
3290 6282 4.335037 GGTAACGCCCGAAATAAAATGGTA 59.665 41.667 0.00 0.00 0.00 3.25
3308 6300 6.144556 AAGCTCAATCAGAGATGCAGGTAAC 61.145 44.000 0.00 0.00 43.49 2.50
3313 6305 3.271729 ACAAGCTCAATCAGAGATGCAG 58.728 45.455 0.00 0.00 43.49 4.41
3393 6385 3.653539 TTACACAGCACATCAGTACGT 57.346 42.857 0.00 0.00 0.00 3.57
3455 6447 9.475620 TCATATGTACCTAGAAGAAGTCAAAGA 57.524 33.333 1.90 0.00 0.00 2.52
3507 6499 9.173939 GTATGAAGATAACAAATTAGCACATGC 57.826 33.333 0.00 0.00 42.49 4.06
3516 6508 8.133627 GCAGAGCATGTATGAAGATAACAAATT 58.866 33.333 0.00 0.00 0.00 1.82
3521 6513 6.589523 CCTAGCAGAGCATGTATGAAGATAAC 59.410 42.308 0.00 0.00 0.00 1.89
3523 6515 5.777223 ACCTAGCAGAGCATGTATGAAGATA 59.223 40.000 0.00 0.00 0.00 1.98
3524 6516 4.592351 ACCTAGCAGAGCATGTATGAAGAT 59.408 41.667 0.00 0.00 0.00 2.40
3525 6517 3.963374 ACCTAGCAGAGCATGTATGAAGA 59.037 43.478 0.00 0.00 0.00 2.87
3526 6518 4.333913 ACCTAGCAGAGCATGTATGAAG 57.666 45.455 0.00 0.00 0.00 3.02
3527 6519 4.649218 TGTACCTAGCAGAGCATGTATGAA 59.351 41.667 0.00 0.00 0.00 2.57
3528 6520 4.038042 GTGTACCTAGCAGAGCATGTATGA 59.962 45.833 0.00 0.00 0.00 2.15
3533 6525 1.845266 CGTGTACCTAGCAGAGCATG 58.155 55.000 0.00 0.00 0.00 4.06
3553 6545 4.082571 AGGCCTGAATTTGTGATTTTCTCG 60.083 41.667 3.11 0.00 0.00 4.04
3651 6643 0.962356 ACCGGAAGCAAATGAGCCTG 60.962 55.000 9.46 0.00 34.23 4.85
3653 6645 0.960364 TCACCGGAAGCAAATGAGCC 60.960 55.000 9.46 0.00 34.23 4.70
3658 6650 1.981256 ACTGTTCACCGGAAGCAAAT 58.019 45.000 9.46 0.00 32.62 2.32
3665 6657 6.452494 TTTTTGAATTTACTGTTCACCGGA 57.548 33.333 9.46 0.00 35.47 5.14
3712 6704 5.820947 TCTTTCTTGTGTAAAAGGTCCAGAC 59.179 40.000 0.00 0.00 34.08 3.51
3713 6705 5.820947 GTCTTTCTTGTGTAAAAGGTCCAGA 59.179 40.000 0.00 0.00 34.08 3.86
3714 6706 5.277345 CGTCTTTCTTGTGTAAAAGGTCCAG 60.277 44.000 0.00 0.00 34.08 3.86
3715 6707 4.573201 CGTCTTTCTTGTGTAAAAGGTCCA 59.427 41.667 0.00 0.00 34.08 4.02
3716 6708 4.812626 TCGTCTTTCTTGTGTAAAAGGTCC 59.187 41.667 0.00 0.00 34.08 4.46
3717 6709 5.751990 TCTCGTCTTTCTTGTGTAAAAGGTC 59.248 40.000 0.00 0.00 34.08 3.85
3720 6712 7.464830 TTCTCTCGTCTTTCTTGTGTAAAAG 57.535 36.000 0.00 0.00 34.49 2.27
3730 6722 7.093992 CACCTAGAAAATTCTCTCGTCTTTCT 58.906 38.462 0.00 0.00 39.18 2.52
3737 6729 4.260538 GCATGCACCTAGAAAATTCTCTCG 60.261 45.833 14.21 0.00 38.70 4.04
3757 6749 5.296531 GTCCAAACACCTTGAAATTTTGCAT 59.703 36.000 0.00 0.00 37.17 3.96
3833 6828 9.447157 TGGATTGTCAAAGAAACTTTCAAAAAT 57.553 25.926 4.34 0.00 0.00 1.82
3856 6851 6.049149 TCGTGGCAAAAATAACAAATTTGGA 58.951 32.000 21.74 10.00 35.21 3.53
3876 6871 1.872952 TGGACATTTGACAAGCTCGTG 59.127 47.619 0.00 0.00 0.00 4.35
3903 6899 0.749649 AGGTGCGTGCCAAATTTCAA 59.250 45.000 0.00 0.00 0.00 2.69
3912 6908 1.134670 AGAATCTTCTAGGTGCGTGCC 60.135 52.381 0.00 0.00 35.34 5.01
3933 6929 8.322906 TGAAGTATTTACACATGGAAGTTGAG 57.677 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.