Multiple sequence alignment - TraesCS3D01G510900

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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 TraesCS3D01G510900 chr3D 100.000 4659 0 0 1 4659 595759730 595764388 0.000000e+00 8604.0
1 TraesCS3D01G510900 chr3D 85.102 1819 160 44 907 2648 595678849 595680633 0.000000e+00 1755.0
2 TraesCS3D01G510900 chr3D 87.488 1055 118 11 2672 3721 595680910 595681955 0.000000e+00 1205.0
3 TraesCS3D01G510900 chr3D 85.880 1034 127 17 2673 3700 595858786 595859806 0.000000e+00 1083.0
4 TraesCS3D01G510900 chr3D 84.404 1167 99 36 907 2012 595277025 595275881 0.000000e+00 1070.0
5 TraesCS3D01G510900 chr3D 85.189 1060 131 22 2672 3720 595711880 595712924 0.000000e+00 1064.0
6 TraesCS3D01G510900 chr3D 83.446 1184 149 30 2923 4083 595286611 595285452 0.000000e+00 1057.0
7 TraesCS3D01G510900 chr3D 82.374 834 92 26 907 1722 595710596 595711392 0.000000e+00 675.0
8 TraesCS3D01G510900 chr3D 83.812 661 71 21 907 1553 595855582 595856220 3.100000e-166 595.0
9 TraesCS3D01G510900 chr3D 86.596 470 47 6 2189 2648 595275883 595275420 5.380000e-139 505.0
10 TraesCS3D01G510900 chr3D 80.278 431 44 16 907 1299 596113173 596112746 2.120000e-73 287.0
11 TraesCS3D01G510900 chr3D 82.784 273 26 13 1716 1976 595711611 595711874 1.690000e-54 224.0
12 TraesCS3D01G510900 chr3D 76.827 479 51 23 297 743 595278155 595277705 1.020000e-51 215.0
13 TraesCS3D01G510900 chr3D 90.654 107 7 3 818 921 434025888 434025782 6.290000e-29 139.0
14 TraesCS3D01G510900 chr3D 88.350 103 11 1 806 908 22679043 22679144 6.330000e-24 122.0
15 TraesCS3D01G510900 chr3D 88.350 103 11 1 806 908 22767915 22767814 6.330000e-24 122.0
16 TraesCS3D01G510900 chr3D 92.453 53 4 0 297 349 595737388 595737440 5.000000e-10 76.8
17 TraesCS3D01G510900 chr3A 93.504 1832 72 23 936 2747 726536740 726538544 0.000000e+00 2680.0
18 TraesCS3D01G510900 chr3A 95.415 1047 41 1 2703 3749 726538611 726539650 0.000000e+00 1661.0
19 TraesCS3D01G510900 chr3A 93.642 928 22 6 3745 4659 726542375 726543278 0.000000e+00 1352.0
20 TraesCS3D01G510900 chr3A 85.756 1025 103 27 2711 3721 726381884 726380889 0.000000e+00 1044.0
21 TraesCS3D01G510900 chr3A 85.445 955 99 21 1716 2649 726440155 726441090 0.000000e+00 957.0
22 TraesCS3D01G510900 chr3A 86.744 860 101 9 2669 3524 726688589 726689439 0.000000e+00 944.0
23 TraesCS3D01G510900 chr3A 93.217 575 26 5 38 608 726535905 726536470 0.000000e+00 833.0
24 TraesCS3D01G510900 chr3A 87.445 677 62 9 1118 1784 726686868 726687531 0.000000e+00 758.0
25 TraesCS3D01G510900 chr3A 82.837 839 88 23 1365 2172 726389294 726388481 0.000000e+00 701.0
26 TraesCS3D01G510900 chr3A 85.057 609 70 11 2040 2636 726687683 726688282 6.670000e-168 601.0
27 TraesCS3D01G510900 chr3A 85.714 483 57 5 2178 2648 726382731 726382249 2.500000e-137 499.0
28 TraesCS3D01G510900 chr3A 85.185 486 34 13 907 1360 726390034 726389555 9.130000e-127 464.0
29 TraesCS3D01G510900 chr3A 96.281 242 9 0 609 850 726536502 726536743 9.390000e-107 398.0
30 TraesCS3D01G510900 chr3A 89.547 287 23 5 2672 2952 726441364 726441649 1.590000e-94 357.0
31 TraesCS3D01G510900 chr3A 88.732 213 22 1 907 1117 726686627 726686839 4.620000e-65 259.0
32 TraesCS3D01G510900 chr3A 81.702 235 30 7 3826 4060 726444626 726444847 2.860000e-42 183.0
33 TraesCS3D01G510900 chr3A 77.843 343 40 17 297 608 726513738 726514075 3.700000e-41 180.0
34 TraesCS3D01G510900 chr3A 80.296 203 10 11 617 811 726390612 726390432 4.890000e-25 126.0
35 TraesCS3D01G510900 chr3B 93.782 1367 53 11 609 1975 798951288 798952622 0.000000e+00 2025.0
36 TraesCS3D01G510900 chr3B 83.507 1534 165 52 2706 4217 798639536 798641003 0.000000e+00 1351.0
37 TraesCS3D01G510900 chr3B 97.230 722 20 0 2703 3424 798953526 798954247 0.000000e+00 1223.0
38 TraesCS3D01G510900 chr3B 95.142 741 33 3 2000 2739 798952730 798953468 0.000000e+00 1166.0
39 TraesCS3D01G510900 chr3B 83.986 1174 109 28 907 2018 798637450 798638606 0.000000e+00 1053.0
40 TraesCS3D01G510900 chr3B 91.667 552 44 2 3426 3976 798966452 798967002 0.000000e+00 763.0
41 TraesCS3D01G510900 chr3B 89.796 588 30 10 4082 4659 798967002 798967569 0.000000e+00 726.0
42 TraesCS3D01G510900 chr3B 84.101 673 72 22 1118 1784 798990501 798991144 6.620000e-173 617.0
43 TraesCS3D01G510900 chr3B 84.615 572 64 11 2087 2648 798638603 798639160 8.810000e-152 547.0
44 TraesCS3D01G510900 chr3B 87.041 463 19 18 38 470 798950450 798950901 7.010000e-133 484.0
45 TraesCS3D01G510900 chr3B 92.857 140 10 0 469 608 798951117 798951256 2.200000e-48 204.0
46 TraesCS3D01G510900 chr3B 94.318 88 5 0 825 912 809833124 809833037 8.130000e-28 135.0
47 TraesCS3D01G510900 chr3B 82.993 147 17 6 3905 4050 799515577 799515438 4.890000e-25 126.0
48 TraesCS3D01G510900 chr3B 91.071 56 0 1 299 349 798636224 798636279 2.330000e-08 71.3
49 TraesCS3D01G510900 chr3B 90.385 52 1 4 3801 3850 799304240 799304289 1.080000e-06 65.8
50 TraesCS3D01G510900 chr3B 100.000 32 0 0 4317 4348 799515167 799515136 5.030000e-05 60.2
51 TraesCS3D01G510900 chr5D 81.313 198 35 2 382 579 529785645 529785840 4.830000e-35 159.0
52 TraesCS3D01G510900 chr5D 86.822 129 8 5 618 743 529794473 529794595 8.130000e-28 135.0
53 TraesCS3D01G510900 chr5D 89.610 77 4 2 615 687 116712942 116712866 1.380000e-15 95.3
54 TraesCS3D01G510900 chr2D 91.667 96 8 0 825 920 117843123 117843028 2.920000e-27 134.0
55 TraesCS3D01G510900 chr2D 94.253 87 5 0 825 911 643235907 643235821 2.920000e-27 134.0
56 TraesCS3D01G510900 chr2D 90.588 85 2 4 615 697 395318598 395318678 1.770000e-19 108.0
57 TraesCS3D01G510900 chr2B 92.391 92 7 0 825 916 167084529 167084620 1.050000e-26 132.0
58 TraesCS3D01G510900 chr5A 88.571 105 11 1 808 912 399293679 399293782 4.890000e-25 126.0
59 TraesCS3D01G510900 chr1A 90.000 90 4 3 615 702 37142575 37142661 1.370000e-20 111.0
60 TraesCS3D01G510900 chr1A 88.889 90 5 3 615 702 289628591 289628677 6.380000e-19 106.0


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 TraesCS3D01G510900 chr3D 595759730 595764388 4658 False 8604.000000 8604 100.000000 1 4659 1 chr3D.!!$F3 4658
1 TraesCS3D01G510900 chr3D 595678849 595681955 3106 False 1480.000000 1755 86.295000 907 3721 2 chr3D.!!$F4 2814
2 TraesCS3D01G510900 chr3D 595285452 595286611 1159 True 1057.000000 1057 83.446000 2923 4083 1 chr3D.!!$R3 1160
3 TraesCS3D01G510900 chr3D 595855582 595859806 4224 False 839.000000 1083 84.846000 907 3700 2 chr3D.!!$F6 2793
4 TraesCS3D01G510900 chr3D 595710596 595712924 2328 False 654.333333 1064 83.449000 907 3720 3 chr3D.!!$F5 2813
5 TraesCS3D01G510900 chr3D 595275420 595278155 2735 True 596.666667 1070 82.609000 297 2648 3 chr3D.!!$R5 2351
6 TraesCS3D01G510900 chr3A 726535905 726543278 7373 False 1384.800000 2680 94.411800 38 4659 5 chr3A.!!$F3 4621
7 TraesCS3D01G510900 chr3A 726380889 726382731 1842 True 771.500000 1044 85.735000 2178 3721 2 chr3A.!!$R1 1543
8 TraesCS3D01G510900 chr3A 726686627 726689439 2812 False 640.500000 944 86.994500 907 3524 4 chr3A.!!$F4 2617
9 TraesCS3D01G510900 chr3A 726440155 726444847 4692 False 499.000000 957 85.564667 1716 4060 3 chr3A.!!$F2 2344
10 TraesCS3D01G510900 chr3A 726388481 726390612 2131 True 430.333333 701 82.772667 617 2172 3 chr3A.!!$R2 1555
11 TraesCS3D01G510900 chr3B 798950450 798954247 3797 False 1020.400000 2025 93.210400 38 3424 5 chr3B.!!$F4 3386
12 TraesCS3D01G510900 chr3B 798636224 798641003 4779 False 755.575000 1351 85.794750 299 4217 4 chr3B.!!$F3 3918
13 TraesCS3D01G510900 chr3B 798966452 798967569 1117 False 744.500000 763 90.731500 3426 4659 2 chr3B.!!$F5 1233
14 TraesCS3D01G510900 chr3B 798990501 798991144 643 False 617.000000 617 84.101000 1118 1784 1 chr3B.!!$F1 666

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
19 20 0.478507 CCCCACACACCTCTCCTTTT 59.521 55.000 0.00 0.0 0.00 2.27 F
733 1261 0.535335 GGTCCTCGCACCACAGAATA 59.465 55.000 0.00 0.0 36.32 1.75 F
996 2081 1.071987 CCTTGACAGACTGCCTGCA 59.928 57.895 1.25 0.0 46.81 4.41 F
2378 5493 0.252103 ATCGAGGTGTAGGGGTGTGT 60.252 55.000 0.00 0.0 0.00 3.72 F
2439 5554 1.068472 GTCCCGACATGATAGGTAGCG 60.068 57.143 0.00 0.0 0.00 4.26 F
2506 5622 1.398390 CCACTGCCGCAAGAATAGAAC 59.602 52.381 0.00 0.0 43.02 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 2822 1.211212 TGCACTGATCCTAGCAGCAAT 59.789 47.619 0.00 0.00 36.86 3.56 R
2361 5476 1.183030 TCACACACCCCTACACCTCG 61.183 60.000 0.00 0.00 0.00 4.63 R
2506 5622 2.158841 GTGTAGTAACAATGGTGCACCG 59.841 50.000 30.07 18.69 37.36 4.94 R
3227 9056 0.171455 GTGTCTAGGCTGTCGACCTG 59.829 60.000 14.12 7.20 38.26 4.00 R
3286 9115 0.178990 ACTGCTGGACCTTGGGAAAC 60.179 55.000 0.00 0.00 0.00 2.78 R
4287 12995 0.899019 GTCTCCTTGTCCTCCTCCAC 59.101 60.000 0.00 0.00 0.00 4.02 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
17 18 3.906980 CCCCACACACCTCTCCTT 58.093 61.111 0.00 0.00 0.00 3.36
18 19 2.155065 CCCCACACACCTCTCCTTT 58.845 57.895 0.00 0.00 0.00 3.11
19 20 0.478507 CCCCACACACCTCTCCTTTT 59.521 55.000 0.00 0.00 0.00 2.27
20 21 1.133482 CCCCACACACCTCTCCTTTTT 60.133 52.381 0.00 0.00 0.00 1.94
141 146 1.294780 CTTGCACCGCTCTCCTTCT 59.705 57.895 0.00 0.00 0.00 2.85
286 296 3.950794 TTCTCCGTGTGCATCCGCC 62.951 63.158 0.00 0.00 37.32 6.13
495 911 7.206789 TGAATGTAACTGATTTCCATCCCTA 57.793 36.000 0.00 0.00 0.00 3.53
501 917 3.913163 ACTGATTTCCATCCCTAGGATCC 59.087 47.826 11.48 2.48 40.98 3.36
586 1002 4.142026 CCGTGTCAGGTAGGATTACATTGA 60.142 45.833 0.00 0.00 0.00 2.57
733 1261 0.535335 GGTCCTCGCACCACAGAATA 59.465 55.000 0.00 0.00 36.32 1.75
996 2081 1.071987 CCTTGACAGACTGCCTGCA 59.928 57.895 1.25 0.00 46.81 4.41
1373 2794 5.918011 CAGTTAATACTAGCTGCTAGAGTGC 59.082 44.000 36.09 21.45 37.49 4.40
1374 2795 5.830991 AGTTAATACTAGCTGCTAGAGTGCT 59.169 40.000 36.09 22.87 37.49 4.40
1375 2796 6.999272 AGTTAATACTAGCTGCTAGAGTGCTA 59.001 38.462 36.09 20.98 37.49 3.49
1395 2822 1.377202 GTGCAAATCAGCCCCTCGA 60.377 57.895 0.00 0.00 0.00 4.04
1402 2829 3.207669 CAGCCCCTCGATTGCTGC 61.208 66.667 15.21 0.00 45.09 5.25
1577 4042 4.322801 CCAGTGTTAAAGTACTCCTCAGGG 60.323 50.000 0.00 0.00 0.00 4.45
1584 4049 3.423058 AGTACTCCTCAGGGGCTAATT 57.577 47.619 0.00 0.00 34.39 1.40
1795 4702 6.208402 TCAATGCAAGTTGTAATCAAGCCTTA 59.792 34.615 4.48 0.00 33.97 2.69
1889 4830 7.815840 TTTTTCTGGACAGAACATTACATCA 57.184 32.000 13.89 0.00 46.13 3.07
1890 4831 8.408043 TTTTTCTGGACAGAACATTACATCAT 57.592 30.769 13.89 0.00 46.13 2.45
1891 4832 8.408043 TTTTCTGGACAGAACATTACATCATT 57.592 30.769 13.89 0.00 46.13 2.57
1892 4833 9.513906 TTTTCTGGACAGAACATTACATCATTA 57.486 29.630 13.89 0.00 46.13 1.90
1893 4834 9.685276 TTTCTGGACAGAACATTACATCATTAT 57.315 29.630 13.89 0.00 46.13 1.28
1895 4836 9.764363 TCTGGACAGAACATTACATCATTATAC 57.236 33.333 0.00 0.00 33.91 1.47
1896 4837 9.770097 CTGGACAGAACATTACATCATTATACT 57.230 33.333 0.00 0.00 0.00 2.12
1897 4838 9.546428 TGGACAGAACATTACATCATTATACTG 57.454 33.333 0.00 0.00 0.00 2.74
1898 4839 9.764363 GGACAGAACATTACATCATTATACTGA 57.236 33.333 0.00 0.00 0.00 3.41
1931 4872 7.277539 TCTGTTCACAATGAAAAACATTTGTCC 59.722 33.333 0.00 0.00 45.60 4.02
2275 5379 9.967346 GAGGATAATAAACAAAATAGCCTTTCC 57.033 33.333 0.00 0.00 34.48 3.13
2361 5476 7.307632 CGAATACAATTGTGATGAGAGGGAATC 60.308 40.741 21.42 0.00 0.00 2.52
2378 5493 0.252103 ATCGAGGTGTAGGGGTGTGT 60.252 55.000 0.00 0.00 0.00 3.72
2412 5527 4.556697 AGGAGGAAAGTGGGTGAAATTTT 58.443 39.130 0.00 0.00 0.00 1.82
2439 5554 1.068472 GTCCCGACATGATAGGTAGCG 60.068 57.143 0.00 0.00 0.00 4.26
2506 5622 1.398390 CCACTGCCGCAAGAATAGAAC 59.602 52.381 0.00 0.00 43.02 3.01
2515 5631 2.422597 CAAGAATAGAACGGTGCACCA 58.577 47.619 34.16 16.07 35.14 4.17
2569 5685 4.817318 TGCCGCATGTCCTATATGATTA 57.183 40.909 0.00 0.00 0.00 1.75
2639 5777 2.280389 ATATCTGCTGGGCACGCG 60.280 61.111 3.53 3.53 33.79 6.01
2771 6521 7.601886 CCATGTGTATTTTTATGGTTGCTCAAA 59.398 33.333 0.00 0.00 36.25 2.69
2905 6667 8.150945 TCCTTATAGTATCTGCTGGAATTGTTC 58.849 37.037 0.00 0.00 0.00 3.18
2917 6797 3.614616 TGGAATTGTTCACGTTTTTGTGC 59.385 39.130 0.00 0.00 39.73 4.57
2943 6825 4.640201 TGTTCTGCAGCCTAAATATTGTCC 59.360 41.667 9.47 0.00 0.00 4.02
3227 9056 3.990959 AAGGAAGGACCATCACTCTTC 57.009 47.619 0.00 0.00 42.04 2.87
3286 9115 4.118410 CCAAGATCGAAGACATTGAGAGG 58.882 47.826 0.00 0.00 42.51 3.69
3318 9147 1.531423 CAGCAGTGCCTCATCTTTGT 58.469 50.000 12.58 0.00 0.00 2.83
3498 9330 1.959985 CAGGAGCTCGGACACTATCAT 59.040 52.381 7.83 0.00 0.00 2.45
3564 9396 1.812922 AGCAGCGCATCCTCTTTCG 60.813 57.895 11.47 0.00 0.00 3.46
3613 9445 2.076100 CTGGCGCACTACAAGATTCAA 58.924 47.619 10.83 0.00 0.00 2.69
3626 9458 4.245660 CAAGATTCAAAGCGAGTCTACCA 58.754 43.478 0.00 0.00 39.64 3.25
3628 9460 4.688021 AGATTCAAAGCGAGTCTACCATC 58.312 43.478 0.00 0.00 38.83 3.51
3629 9461 3.953712 TTCAAAGCGAGTCTACCATCA 57.046 42.857 0.00 0.00 0.00 3.07
3630 9462 3.232213 TCAAAGCGAGTCTACCATCAC 57.768 47.619 0.00 0.00 0.00 3.06
3729 9575 0.533491 TCCAGTAGTGGCGCGTTATT 59.467 50.000 12.14 0.00 44.60 1.40
4035 12707 7.344093 TCTCCATTCATACCCATTGCAATTAAA 59.656 33.333 9.83 0.00 0.00 1.52
4174 12882 5.633830 ACCACATGAATGTCATTGACTTC 57.366 39.130 17.26 16.46 39.39 3.01
4226 12934 1.070786 GTTGTCCTCGTCCTTGCCA 59.929 57.895 0.00 0.00 0.00 4.92
4238 12946 1.710244 TCCTTGCCATTGGAGGAGAAA 59.290 47.619 6.95 0.00 34.74 2.52
4253 12961 0.178929 AGAAAGAGGAGGACGGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
4287 12995 4.814294 GGCGTGGTGTAGGAGCCG 62.814 72.222 0.00 0.00 38.28 5.52
4344 13054 0.184451 CCTTAGCCACCATGGAGCAT 59.816 55.000 26.13 16.49 40.96 3.79
4369 13083 3.073062 GTGGCATAGGACCTTATGTGGAT 59.927 47.826 0.00 0.00 34.29 3.41
4413 13127 0.971386 ATTTGGGCTGCAAGGTCTTG 59.029 50.000 0.50 6.36 43.14 3.02
4650 13371 2.185387 GTAGGGAAGGGCTACTTGACA 58.815 52.381 0.00 0.00 40.21 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.364972 AAAAAGGAGAGGTGTGTGGG 57.635 50.000 0.00 0.00 0.00 4.61
29 30 9.723601 GACGGGGGTTATACAATATTTACAATA 57.276 33.333 0.00 0.00 0.00 1.90
30 31 8.442374 AGACGGGGGTTATACAATATTTACAAT 58.558 33.333 0.00 0.00 0.00 2.71
31 32 7.804147 AGACGGGGGTTATACAATATTTACAA 58.196 34.615 0.00 0.00 0.00 2.41
32 33 7.377696 AGACGGGGGTTATACAATATTTACA 57.622 36.000 0.00 0.00 0.00 2.41
33 34 8.681486 AAAGACGGGGGTTATACAATATTTAC 57.319 34.615 0.00 0.00 0.00 2.01
34 35 7.938490 GGAAAGACGGGGGTTATACAATATTTA 59.062 37.037 0.00 0.00 0.00 1.40
35 36 6.774170 GGAAAGACGGGGGTTATACAATATTT 59.226 38.462 0.00 0.00 0.00 1.40
36 37 6.102174 AGGAAAGACGGGGGTTATACAATATT 59.898 38.462 0.00 0.00 0.00 1.28
48 49 1.306226 AGGAGAGGAAAGACGGGGG 60.306 63.158 0.00 0.00 0.00 5.40
49 50 0.324830 AGAGGAGAGGAAAGACGGGG 60.325 60.000 0.00 0.00 0.00 5.73
180 188 3.207354 GGAAGATCTCCGTCCGCA 58.793 61.111 0.00 0.00 33.86 5.69
286 296 2.095008 TCTCAAGAACACTAGAGCAGCG 60.095 50.000 0.00 0.00 0.00 5.18
428 487 2.752354 GTGCACCAACTACAATGGCATA 59.248 45.455 5.22 0.00 41.89 3.14
586 1002 0.038744 CATGAGACCAGGCAACCCTT 59.961 55.000 0.00 0.00 40.33 3.95
635 1161 2.341414 TTCGCGAGAAGCAATGATGGG 61.341 52.381 9.59 0.00 46.92 4.00
777 1305 8.243426 TGGACAATCTTTTTATCTTGTGCATAC 58.757 33.333 4.66 0.00 42.49 2.39
996 2081 1.168714 GCTTCTTCGGTGGCATTCTT 58.831 50.000 0.00 0.00 0.00 2.52
1372 2793 2.110296 GGGCTGATTTGCACCTAGC 58.890 57.895 0.00 0.00 45.96 3.42
1395 2822 1.211212 TGCACTGATCCTAGCAGCAAT 59.789 47.619 0.00 0.00 36.86 3.56
1402 2829 5.480642 ACAGGATATTGCACTGATCCTAG 57.519 43.478 18.41 15.39 46.30 3.02
1869 4810 9.764363 GTATAATGATGTAATGTTCTGTCCAGA 57.236 33.333 0.00 0.00 35.27 3.86
1870 4811 9.770097 AGTATAATGATGTAATGTTCTGTCCAG 57.230 33.333 0.00 0.00 0.00 3.86
1871 4812 9.546428 CAGTATAATGATGTAATGTTCTGTCCA 57.454 33.333 0.00 0.00 0.00 4.02
1872 4813 9.764363 TCAGTATAATGATGTAATGTTCTGTCC 57.236 33.333 0.00 0.00 0.00 4.02
1892 4833 9.288576 TCATTGTGAACAGAAAAGATTCAGTAT 57.711 29.630 0.00 0.00 34.57 2.12
1893 4834 8.675705 TCATTGTGAACAGAAAAGATTCAGTA 57.324 30.769 0.00 0.00 34.57 2.74
1894 4835 7.572523 TCATTGTGAACAGAAAAGATTCAGT 57.427 32.000 0.00 0.00 36.92 3.41
1895 4836 8.861033 TTTCATTGTGAACAGAAAAGATTCAG 57.139 30.769 0.00 0.00 35.89 3.02
1896 4837 9.650539 TTTTTCATTGTGAACAGAAAAGATTCA 57.349 25.926 9.28 0.00 40.00 2.57
1897 4838 9.906111 GTTTTTCATTGTGAACAGAAAAGATTC 57.094 29.630 9.28 0.00 40.00 2.52
1898 4839 9.434420 TGTTTTTCATTGTGAACAGAAAAGATT 57.566 25.926 9.28 0.00 40.00 2.40
1931 4872 4.223320 ACCAACTATTGCTTGTTGTTCG 57.777 40.909 0.00 0.00 41.16 3.95
2275 5379 2.817258 TGCGACTAACCAAATCAAAGGG 59.183 45.455 0.00 0.00 0.00 3.95
2361 5476 1.183030 TCACACACCCCTACACCTCG 61.183 60.000 0.00 0.00 0.00 4.63
2378 5493 5.221521 CCACTTTCCTCCTTATCGATCATCA 60.222 44.000 0.00 0.00 0.00 3.07
2412 5527 4.407621 ACCTATCATGTCGGGACAAACATA 59.592 41.667 5.50 2.46 45.41 2.29
2455 5570 4.707448 ACTCTTCTCCACGTATGATGACTT 59.293 41.667 0.00 0.00 0.00 3.01
2506 5622 2.158841 GTGTAGTAACAATGGTGCACCG 59.841 50.000 30.07 18.69 37.36 4.94
2515 5631 8.534333 CACATGTCTTACTGTGTAGTAACAAT 57.466 34.615 0.00 0.00 42.81 2.71
2639 5777 2.910482 CGTGTAGCAACAAATGTCATGC 59.090 45.455 2.70 2.70 37.36 4.06
2771 6521 4.461781 AGCTTAGCATGCAAAGTTCAAGAT 59.538 37.500 21.98 6.85 0.00 2.40
2905 6667 3.541903 GCAGAACAATGCACAAAAACGTG 60.542 43.478 0.00 0.00 45.77 4.49
2917 6797 6.567050 ACAATATTTAGGCTGCAGAACAATG 58.433 36.000 20.43 6.32 0.00 2.82
3227 9056 0.171455 GTGTCTAGGCTGTCGACCTG 59.829 60.000 14.12 7.20 38.26 4.00
3286 9115 0.178990 ACTGCTGGACCTTGGGAAAC 60.179 55.000 0.00 0.00 0.00 2.78
3318 9147 2.626266 TCGTCCTCTAGCTGTTTGTTGA 59.374 45.455 0.00 0.00 0.00 3.18
3498 9330 7.615757 TCTCATAGATCTTCACCTTAACACTGA 59.384 37.037 0.00 0.00 0.00 3.41
3505 9337 8.830915 ACTCTTTCTCATAGATCTTCACCTTA 57.169 34.615 0.00 0.00 0.00 2.69
3599 9431 4.926238 AGACTCGCTTTGAATCTTGTAGTG 59.074 41.667 0.00 0.00 25.66 2.74
3613 9445 2.425312 CAGAGTGATGGTAGACTCGCTT 59.575 50.000 0.00 0.00 42.93 4.68
3674 9519 7.307337 CCAGCAAAATAAAACTGGTTGATGAAC 60.307 37.037 1.82 0.00 43.86 3.18
4012 12684 8.680039 AATTTAATTGCAATGGGTATGAATGG 57.320 30.769 13.82 0.00 0.00 3.16
4076 12748 5.982356 TGTTATGATCCTCCTCACTTCAAG 58.018 41.667 0.00 0.00 0.00 3.02
4226 12934 3.111484 GTCCTCCTCTTTCTCCTCCAAT 58.889 50.000 0.00 0.00 0.00 3.16
4238 12946 1.908793 CACACCACCGTCCTCCTCT 60.909 63.158 0.00 0.00 0.00 3.69
4253 12961 1.676968 CCCCATCGTTGTCCTCACA 59.323 57.895 0.00 0.00 0.00 3.58
4287 12995 0.899019 GTCTCCTTGTCCTCCTCCAC 59.101 60.000 0.00 0.00 0.00 4.02
4326 13034 1.679680 CAATGCTCCATGGTGGCTAAG 59.320 52.381 24.47 11.50 37.47 2.18
4344 13054 2.849943 ACATAAGGTCCTATGCCACCAA 59.150 45.455 0.00 0.00 34.80 3.67
4369 13083 2.747022 CCACGTCACCCACCATGA 59.253 61.111 0.00 0.00 0.00 3.07
4413 13127 2.266689 CTTGCAGCCCAAATGCCC 59.733 61.111 0.00 0.00 43.18 5.36
4480 13194 4.165760 CCGTAACCTCCCCTCCTATAAAT 58.834 47.826 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.