Multiple sequence alignment - TraesCS2A01G082700

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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 TraesCS2A01G082700 chr2A 100.000 3201 0 0 1 3201 37861326 37864526 0.000000e+00 5912.0
1 TraesCS2A01G082700 chr2A 93.404 2274 113 19 960 3201 37969730 37971998 0.000000e+00 3334.0
2 TraesCS2A01G082700 chr2A 92.250 1600 77 15 1628 3201 37384230 37385808 0.000000e+00 2224.0
3 TraesCS2A01G082700 chr2A 86.480 1753 176 24 960 2661 37952900 37954642 0.000000e+00 1868.0
4 TraesCS2A01G082700 chr2A 88.561 813 37 10 1 757 37968919 37969731 0.000000e+00 935.0
5 TraesCS2A01G082700 chr2A 86.216 798 53 27 1 757 37948856 37949637 0.000000e+00 811.0
6 TraesCS2A01G082700 chr2A 94.393 428 20 2 1 424 37383773 37384200 0.000000e+00 654.0
7 TraesCS2A01G082700 chr2A 97.749 311 7 0 2509 2819 38018849 38019159 1.310000e-148 536.0
8 TraesCS2A01G082700 chr2A 85.503 338 37 6 422 757 37952574 37952901 3.060000e-90 342.0
9 TraesCS2A01G082700 chr2A 91.057 123 11 0 960 1082 37949636 37949758 1.980000e-37 167.0
10 TraesCS2A01G082700 chr2B 93.097 2260 124 22 960 3201 57040535 57042780 0.000000e+00 3280.0
11 TraesCS2A01G082700 chr2B 93.303 2180 121 15 960 3124 57116272 57118441 0.000000e+00 3193.0
12 TraesCS2A01G082700 chr2B 81.244 981 148 25 1013 1969 57111002 57111970 0.000000e+00 760.0
13 TraesCS2A01G082700 chr2B 79.961 1028 169 27 964 1969 57035398 57036410 0.000000e+00 723.0
14 TraesCS2A01G082700 chr2B 90.597 553 33 11 1983 2520 57036508 57037056 0.000000e+00 715.0
15 TraesCS2A01G082700 chr2B 87.340 624 35 8 171 757 57115657 57116273 0.000000e+00 675.0
16 TraesCS2A01G082700 chr2B 87.092 612 35 8 183 757 57039932 57040536 0.000000e+00 652.0
17 TraesCS2A01G082700 chr2B 87.154 397 40 8 2095 2480 57112155 57112551 1.050000e-119 440.0
18 TraesCS2A01G082700 chr2B 95.960 198 8 0 763 960 678564996 678564799 3.980000e-84 322.0
19 TraesCS2A01G082700 chr2B 94.949 198 10 0 763 960 675513330 675513133 8.620000e-81 311.0
20 TraesCS2A01G082700 chr2B 96.067 178 7 0 3 180 57115462 57115639 1.120000e-74 291.0
21 TraesCS2A01G082700 chr2D 91.672 1489 94 18 960 2432 34582025 34583499 0.000000e+00 2036.0
22 TraesCS2A01G082700 chr2D 89.479 979 70 15 983 1934 34560144 34561116 0.000000e+00 1206.0
23 TraesCS2A01G082700 chr2D 89.246 623 31 12 171 757 34581404 34582026 0.000000e+00 747.0
24 TraesCS2A01G082700 chr2D 89.015 619 33 10 171 757 34547604 34548219 0.000000e+00 734.0
25 TraesCS2A01G082700 chr2D 91.519 507 40 1 2538 3044 34584994 34585497 0.000000e+00 695.0
26 TraesCS2A01G082700 chr2D 85.983 585 48 16 1954 2520 34541305 34541873 2.130000e-166 595.0
27 TraesCS2A01G082700 chr2D 93.820 178 11 0 3 180 34547403 34547580 5.260000e-68 268.0
28 TraesCS2A01G082700 chr2D 92.697 178 12 1 3 180 34581202 34581378 4.100000e-64 255.0
29 TraesCS2A01G082700 chr2D 84.579 214 28 4 1925 2137 34561198 34561407 1.160000e-49 207.0
30 TraesCS2A01G082700 chr2D 91.045 67 4 2 2691 2756 562214711 562214776 4.400000e-14 89.8
31 TraesCS2A01G082700 chr4A 95.455 198 9 0 763 960 707871003 707871200 1.850000e-82 316.0
32 TraesCS2A01G082700 chr7D 95.431 197 8 1 763 959 66087076 66086881 2.400000e-81 313.0
33 TraesCS2A01G082700 chr7D 86.709 158 20 1 3044 3200 88846849 88846692 1.180000e-39 174.0
34 TraesCS2A01G082700 chr7D 80.952 105 16 2 2683 2786 450085500 450085399 2.650000e-11 80.5
35 TraesCS2A01G082700 chr1B 94.949 198 10 0 763 960 685905483 685905680 8.620000e-81 311.0
36 TraesCS2A01G082700 chr1B 86.207 87 12 0 2688 2774 110124435 110124521 9.450000e-16 95.3
37 TraesCS2A01G082700 chr5B 94.444 198 10 1 763 960 531603648 531603452 1.440000e-78 303.0
38 TraesCS2A01G082700 chr5B 91.367 139 12 0 3062 3200 141462306 141462168 1.170000e-44 191.0
39 TraesCS2A01G082700 chr3B 92.929 198 14 0 763 960 15545945 15546142 4.040000e-74 289.0
40 TraesCS2A01G082700 chr6A 87.374 198 25 0 763 960 540517496 540517299 8.930000e-56 228.0
41 TraesCS2A01G082700 chr1D 94.928 138 6 1 763 900 361119931 361120067 6.950000e-52 215.0
42 TraesCS2A01G082700 chr1D 100.000 54 0 0 903 956 361124855 361124908 2.030000e-17 100.0
43 TraesCS2A01G082700 chr6D 87.421 159 19 1 3044 3201 265994567 265994409 7.050000e-42 182.0
44 TraesCS2A01G082700 chr7A 87.261 157 19 1 3044 3199 90171522 90171366 9.120000e-41 178.0
45 TraesCS2A01G082700 chr1A 89.051 137 15 0 3064 3200 65910043 65909907 1.530000e-38 171.0


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 TraesCS2A01G082700 chr2A 37861326 37864526 3200 False 5912.00 5912 100.00000 1 3201 1 chr2A.!!$F1 3200
1 TraesCS2A01G082700 chr2A 37968919 37971998 3079 False 2134.50 3334 90.98250 1 3201 2 chr2A.!!$F5 3200
2 TraesCS2A01G082700 chr2A 37383773 37385808 2035 False 1439.00 2224 93.32150 1 3201 2 chr2A.!!$F3 3200
3 TraesCS2A01G082700 chr2A 37948856 37954642 5786 False 797.00 1868 87.31400 1 2661 4 chr2A.!!$F4 2660
4 TraesCS2A01G082700 chr2B 57035398 57042780 7382 False 1342.50 3280 87.68675 183 3201 4 chr2B.!!$F1 3018
5 TraesCS2A01G082700 chr2B 57111002 57118441 7439 False 1071.80 3193 89.02160 3 3124 5 chr2B.!!$F2 3121
6 TraesCS2A01G082700 chr2D 34581202 34585497 4295 False 933.25 2036 91.28350 3 3044 4 chr2D.!!$F5 3041
7 TraesCS2A01G082700 chr2D 34560144 34561407 1263 False 706.50 1206 87.02900 983 2137 2 chr2D.!!$F4 1154
8 TraesCS2A01G082700 chr2D 34541305 34541873 568 False 595.00 595 85.98300 1954 2520 1 chr2D.!!$F1 566
9 TraesCS2A01G082700 chr2D 34547403 34548219 816 False 501.00 734 91.41750 3 757 2 chr2D.!!$F3 754

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
395 4904 0.043940 ATCTCCTGGTGCTCCTTCCT 59.956 55.0 6.34 0.0 34.23 3.36 F
919 5501 0.099436 GGTCGCTGCAATTTAGCTGG 59.901 55.0 0.00 0.0 39.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 9441 0.179084 ACGTATGATTCGTGGGCCAG 60.179 55.0 6.4 0.73 40.07 4.85 R
2903 12312 1.094785 AATGGCGGAAGGTTGATTCG 58.905 50.0 0.0 0.00 0.00 3.34 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
90 4550 5.854481 AGATATTAGGAAGGAGGGATTTGCT 59.146 40.000 0.00 0.00 0.00 3.91
194 4689 6.087291 CGAACATCTTCTGCTGATTTGTTTTC 59.913 38.462 13.60 5.25 0.00 2.29
382 4891 1.415273 GCTTCCTCCCCCTAATCTCCT 60.415 57.143 0.00 0.00 0.00 3.69
392 4901 2.122768 CCTAATCTCCTGGTGCTCCTT 58.877 52.381 6.34 0.00 34.23 3.36
395 4904 0.043940 ATCTCCTGGTGCTCCTTCCT 59.956 55.000 6.34 0.00 34.23 3.36
404 4913 1.764454 GCTCCTTCCTCCTCTCCCC 60.764 68.421 0.00 0.00 0.00 4.81
410 4940 2.364317 CCTCCTCTCCCCGCTCAA 60.364 66.667 0.00 0.00 0.00 3.02
411 4941 2.430610 CCTCCTCTCCCCGCTCAAG 61.431 68.421 0.00 0.00 0.00 3.02
470 5023 0.923358 TGACACAGAACCCAAACCCT 59.077 50.000 0.00 0.00 0.00 4.34
528 5087 2.503061 CCAGATACTGCTGCGGCT 59.497 61.111 20.27 1.00 39.59 5.52
650 5232 2.053244 GGAGGAGGTCACCATCATCAT 58.947 52.381 0.00 0.00 0.00 2.45
692 5274 2.202919 CACCATCATCTCCGCGCA 60.203 61.111 8.75 0.00 0.00 6.09
757 5339 4.681978 AACACCTCTGGCGCGACC 62.682 66.667 10.82 11.50 39.84 4.79
769 5351 3.474693 GGCGCGACCAATTAGTTTTAA 57.525 42.857 12.10 0.00 38.86 1.52
770 5352 3.824151 GGCGCGACCAATTAGTTTTAAA 58.176 40.909 12.10 0.00 38.86 1.52
771 5353 4.417506 GGCGCGACCAATTAGTTTTAAAT 58.582 39.130 12.10 0.00 38.86 1.40
772 5354 4.497966 GGCGCGACCAATTAGTTTTAAATC 59.502 41.667 12.10 0.00 38.86 2.17
773 5355 4.201558 GCGCGACCAATTAGTTTTAAATCG 59.798 41.667 12.10 0.00 0.00 3.34
774 5356 4.201558 CGCGACCAATTAGTTTTAAATCGC 59.798 41.667 0.00 14.00 38.18 4.58
775 5357 4.201558 GCGACCAATTAGTTTTAAATCGCG 59.798 41.667 0.00 0.00 32.37 5.87
776 5358 4.726704 CGACCAATTAGTTTTAAATCGCGG 59.273 41.667 6.13 0.00 0.00 6.46
777 5359 4.989044 ACCAATTAGTTTTAAATCGCGGG 58.011 39.130 6.13 0.00 0.00 6.13
778 5360 3.794564 CCAATTAGTTTTAAATCGCGGGC 59.205 43.478 6.13 0.00 0.00 6.13
779 5361 2.810028 TTAGTTTTAAATCGCGGGCG 57.190 45.000 6.13 6.74 41.35 6.13
788 5370 4.771356 TCGCGGGCGAAACTCGAG 62.771 66.667 14.01 11.84 46.01 4.04
791 5373 4.771356 CGGGCGAAACTCGAGCGA 62.771 66.667 13.61 0.00 43.74 4.93
792 5374 2.202756 GGGCGAAACTCGAGCGAT 60.203 61.111 13.61 0.00 43.74 4.58
793 5375 2.231618 GGGCGAAACTCGAGCGATC 61.232 63.158 13.61 7.47 43.74 3.69
794 5376 2.231618 GGCGAAACTCGAGCGATCC 61.232 63.158 13.61 3.94 43.74 3.36
795 5377 1.226717 GCGAAACTCGAGCGATCCT 60.227 57.895 13.61 0.00 43.74 3.24
796 5378 1.475441 GCGAAACTCGAGCGATCCTG 61.475 60.000 13.61 0.00 43.74 3.86
797 5379 0.867753 CGAAACTCGAGCGATCCTGG 60.868 60.000 13.61 0.00 43.74 4.45
798 5380 1.148759 GAAACTCGAGCGATCCTGGC 61.149 60.000 13.61 0.00 0.00 4.85
799 5381 2.890847 AAACTCGAGCGATCCTGGCG 62.891 60.000 13.61 0.00 35.00 5.69
816 5398 3.207669 GCAATCGCTGGCTGGGAG 61.208 66.667 15.76 5.51 41.00 4.30
817 5399 3.207669 CAATCGCTGGCTGGGAGC 61.208 66.667 15.76 0.92 41.00 4.70
834 5416 4.344474 CCTCCCCGCGACGCTATC 62.344 72.222 19.02 0.00 0.00 2.08
864 5446 1.846648 GCGATCTGCGGTAATCACG 59.153 57.895 0.00 0.00 41.29 4.35
871 5453 2.837280 CGGTAATCACGCGATCGC 59.163 61.111 29.80 29.80 39.84 4.58
872 5454 1.657487 CGGTAATCACGCGATCGCT 60.657 57.895 34.69 19.98 39.84 4.93
873 5455 1.846648 GGTAATCACGCGATCGCTG 59.153 57.895 34.69 28.87 39.84 5.18
874 5456 1.199370 GTAATCACGCGATCGCTGC 59.801 57.895 34.69 17.45 39.84 5.25
895 5477 1.636988 CGAAACGACGCTAAATCCCT 58.363 50.000 0.00 0.00 0.00 4.20
896 5478 1.997606 CGAAACGACGCTAAATCCCTT 59.002 47.619 0.00 0.00 0.00 3.95
897 5479 2.028883 CGAAACGACGCTAAATCCCTTC 59.971 50.000 0.00 0.00 0.00 3.46
898 5480 1.636988 AACGACGCTAAATCCCTTCG 58.363 50.000 0.00 0.00 0.00 3.79
899 5481 0.804933 ACGACGCTAAATCCCTTCGC 60.805 55.000 0.00 0.00 0.00 4.70
901 5483 3.319904 CGCTAAATCCCTTCGCGG 58.680 61.111 6.13 0.00 40.11 6.46
902 5484 1.520787 CGCTAAATCCCTTCGCGGT 60.521 57.895 6.13 0.00 40.11 5.68
903 5485 1.488261 CGCTAAATCCCTTCGCGGTC 61.488 60.000 6.13 0.00 40.11 4.79
904 5486 1.488261 GCTAAATCCCTTCGCGGTCG 61.488 60.000 6.13 0.00 0.00 4.79
905 5487 1.488261 CTAAATCCCTTCGCGGTCGC 61.488 60.000 6.13 5.16 35.26 5.19
906 5488 1.952102 TAAATCCCTTCGCGGTCGCT 61.952 55.000 6.13 0.00 39.32 4.93
907 5489 4.514577 ATCCCTTCGCGGTCGCTG 62.515 66.667 6.13 7.23 39.32 5.18
911 5493 3.490759 CTTCGCGGTCGCTGCAAT 61.491 61.111 6.13 0.00 39.32 3.56
912 5494 3.027170 CTTCGCGGTCGCTGCAATT 62.027 57.895 6.13 0.00 39.32 2.32
913 5495 2.513065 CTTCGCGGTCGCTGCAATTT 62.513 55.000 6.13 0.00 39.32 1.82
914 5496 1.292571 TTCGCGGTCGCTGCAATTTA 61.293 50.000 6.13 0.00 39.32 1.40
915 5497 1.296867 CGCGGTCGCTGCAATTTAG 60.297 57.895 13.51 0.00 39.32 1.85
916 5498 1.583709 GCGGTCGCTGCAATTTAGC 60.584 57.895 8.20 2.10 35.55 3.09
917 5499 1.982073 GCGGTCGCTGCAATTTAGCT 61.982 55.000 8.20 0.00 39.00 3.32
918 5500 0.247814 CGGTCGCTGCAATTTAGCTG 60.248 55.000 0.00 1.12 39.00 4.24
919 5501 0.099436 GGTCGCTGCAATTTAGCTGG 59.901 55.000 0.00 0.00 39.00 4.85
920 5502 0.099436 GTCGCTGCAATTTAGCTGGG 59.901 55.000 0.00 7.39 44.13 4.45
921 5503 2.481212 CGCTGCAATTTAGCTGGGA 58.519 52.632 0.00 0.00 45.07 4.37
922 5504 0.099436 CGCTGCAATTTAGCTGGGAC 59.901 55.000 0.00 0.00 45.07 4.46
923 5505 1.176527 GCTGCAATTTAGCTGGGACA 58.823 50.000 0.00 0.00 38.14 4.02
934 5516 3.068881 TGGGACAGGCCGAAAGAG 58.931 61.111 0.00 0.00 37.63 2.85
935 5517 1.535444 TGGGACAGGCCGAAAGAGA 60.535 57.895 0.00 0.00 37.63 3.10
936 5518 1.219393 GGGACAGGCCGAAAGAGAG 59.781 63.158 0.00 0.00 37.63 3.20
937 5519 1.219393 GGACAGGCCGAAAGAGAGG 59.781 63.158 0.00 0.00 0.00 3.69
944 5526 3.339547 CCGAAAGAGAGGCCCAAAA 57.660 52.632 0.00 0.00 0.00 2.44
945 5527 1.616159 CCGAAAGAGAGGCCCAAAAA 58.384 50.000 0.00 0.00 0.00 1.94
946 5528 1.541588 CCGAAAGAGAGGCCCAAAAAG 59.458 52.381 0.00 0.00 0.00 2.27
947 5529 1.541588 CGAAAGAGAGGCCCAAAAAGG 59.458 52.381 0.00 0.00 37.03 3.11
972 5554 0.669625 GCCGAAACTACACTCCGCTT 60.670 55.000 0.00 0.00 0.00 4.68
1049 8895 3.886505 GACCTTATCTCAGACATCCTCGT 59.113 47.826 0.00 0.00 0.00 4.18
1152 8998 2.582498 GACCGCTGGTTCCGATCG 60.582 66.667 8.51 8.51 35.25 3.69
1352 9207 0.248417 CCACATCTCGTCGAGCTCAG 60.248 60.000 17.61 6.88 0.00 3.35
1546 9401 5.041191 AGAACTCCTCATTGTCAACACTT 57.959 39.130 0.00 0.00 0.00 3.16
1586 9441 2.026262 TGCTCTGGGACCAAGGTTATTC 60.026 50.000 0.00 0.00 0.00 1.75
1590 9445 1.005450 TGGGACCAAGGTTATTCTGGC 59.995 52.381 0.00 0.00 0.00 4.85
1823 9721 1.270465 TGACAGCAGTCCAGTGTCATG 60.270 52.381 6.80 0.00 44.35 3.07
1824 9729 0.604780 ACAGCAGTCCAGTGTCATGC 60.605 55.000 3.24 3.24 37.15 4.06
1869 9774 2.427453 GCTCGTTCTCCATGGTCTTAGA 59.573 50.000 12.58 3.99 0.00 2.10
2169 10175 7.231317 AGTGAGAAATTATTCAGGCAAGAAACA 59.769 33.333 0.00 0.00 38.06 2.83
2238 10245 0.256752 CCATGAAGCTCCATGTCCCA 59.743 55.000 12.34 0.00 41.65 4.37
2271 10278 0.101399 ACGAATGGCGCTCTAGACAG 59.899 55.000 7.64 0.00 46.04 3.51
2358 10365 1.361668 GAGCACATGATCAACCGCGT 61.362 55.000 4.92 0.00 0.00 6.01
2407 10421 6.156519 CCTTTGGCACCTAAGTTATGTTTTC 58.843 40.000 9.51 0.00 0.00 2.29
2411 10425 6.977213 TGGCACCTAAGTTATGTTTTCTTTC 58.023 36.000 0.00 0.00 0.00 2.62
2443 10462 0.820074 TTGCCGGTTGTCGTTCCATT 60.820 50.000 1.90 0.00 37.11 3.16
2606 12014 0.034574 TCCACCGAAATGATGTGGGG 60.035 55.000 7.95 0.00 0.00 4.96
2615 12023 4.261322 CGAAATGATGTGGGGATGATGAAC 60.261 45.833 0.00 0.00 0.00 3.18
2635 12043 9.178758 GATGAACTACCTTGACTTTATGGAAAT 57.821 33.333 0.00 0.00 0.00 2.17
2761 12169 4.351938 CGGACGTGGTCTGCGGAA 62.352 66.667 0.00 0.00 31.96 4.30
2769 12177 0.036732 TGGTCTGCGGAAAAGATGCT 59.963 50.000 0.00 0.00 0.00 3.79
2888 12297 4.080243 TCCACCTTCCGCCAAATAGAAATA 60.080 41.667 0.00 0.00 0.00 1.40
2939 12348 6.012333 TCCGCCATTTGGGGTATAATTATAGT 60.012 38.462 12.12 0.00 46.91 2.12
3005 12414 8.246871 GTGGATTTCTTTCCTCTTTTAATCCAG 58.753 37.037 12.48 0.00 45.90 3.86
3017 12426 7.389053 CCTCTTTTAATCCAGCGAGCTAATTAT 59.611 37.037 0.00 0.00 0.00 1.28
3021 12430 4.899352 ATCCAGCGAGCTAATTATTCCT 57.101 40.909 0.00 0.00 0.00 3.36
3096 12505 5.570320 ACTTGTTTAGTGGCCATCTACAAT 58.430 37.500 9.72 5.62 35.19 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 4550 0.386476 ACGACAAAGGTGAGTGCGTA 59.614 50.000 0.00 0.00 0.00 4.42
194 4689 3.922240 GCATTACACTTTTGTCAGCATGG 59.078 43.478 0.00 0.00 37.15 3.66
250 4758 0.034059 CCACTCCACACTCCTGACAC 59.966 60.000 0.00 0.00 0.00 3.67
382 4891 0.616111 GAGAGGAGGAAGGAGCACCA 60.616 60.000 2.07 0.00 38.94 4.17
392 4901 2.863019 CTTGAGCGGGGAGAGGAGGA 62.863 65.000 0.00 0.00 0.00 3.71
395 4904 1.229209 AACTTGAGCGGGGAGAGGA 60.229 57.895 0.00 0.00 0.00 3.71
404 4913 1.032114 GGGAATGGGGAACTTGAGCG 61.032 60.000 0.00 0.00 0.00 5.03
410 4940 2.677228 CGCTGGGAATGGGGAACT 59.323 61.111 0.00 0.00 0.00 3.01
411 4941 2.440247 CCGCTGGGAATGGGGAAC 60.440 66.667 0.00 0.00 39.53 3.62
470 5023 4.813235 GCCATGGGTTAGCCGGCA 62.813 66.667 31.54 12.31 38.28 5.69
528 5087 2.034066 CTTTGGGAGGCCGCAGAA 59.966 61.111 9.31 0.00 36.56 3.02
692 5274 2.046314 CGGCCTTGTCGATTGGGT 60.046 61.111 0.00 0.00 29.41 4.51
757 5339 3.480668 CGCCCGCGATTTAAAACTAATTG 59.519 43.478 8.23 0.00 42.83 2.32
758 5340 3.374678 TCGCCCGCGATTTAAAACTAATT 59.625 39.130 8.23 0.00 44.01 1.40
759 5341 2.937799 TCGCCCGCGATTTAAAACTAAT 59.062 40.909 8.23 0.00 44.01 1.73
760 5342 2.344950 TCGCCCGCGATTTAAAACTAA 58.655 42.857 8.23 0.00 44.01 2.24
761 5343 2.007360 TCGCCCGCGATTTAAAACTA 57.993 45.000 8.23 0.00 44.01 2.24
762 5344 2.843669 TCGCCCGCGATTTAAAACT 58.156 47.368 8.23 0.00 44.01 2.66
774 5356 4.771356 TCGCTCGAGTTTCGCCCG 62.771 66.667 15.13 7.15 40.21 6.13
775 5357 2.202756 ATCGCTCGAGTTTCGCCC 60.203 61.111 15.13 0.00 40.21 6.13
776 5358 2.231618 GGATCGCTCGAGTTTCGCC 61.232 63.158 15.13 6.04 40.21 5.54
777 5359 1.226717 AGGATCGCTCGAGTTTCGC 60.227 57.895 15.13 0.00 40.21 4.70
778 5360 0.867753 CCAGGATCGCTCGAGTTTCG 60.868 60.000 15.13 9.45 42.10 3.46
779 5361 1.148759 GCCAGGATCGCTCGAGTTTC 61.149 60.000 15.13 8.42 0.00 2.78
780 5362 1.153549 GCCAGGATCGCTCGAGTTT 60.154 57.895 15.13 0.00 0.00 2.66
781 5363 2.496817 GCCAGGATCGCTCGAGTT 59.503 61.111 15.13 0.00 0.00 3.01
782 5364 3.893763 CGCCAGGATCGCTCGAGT 61.894 66.667 15.13 0.00 0.00 4.18
799 5381 3.207669 CTCCCAGCCAGCGATTGC 61.208 66.667 0.00 0.00 43.24 3.56
800 5382 3.207669 GCTCCCAGCCAGCGATTG 61.208 66.667 0.00 0.00 34.48 2.67
817 5399 4.344474 GATAGCGTCGCGGGGAGG 62.344 72.222 12.30 10.03 0.00 4.30
818 5400 4.685026 CGATAGCGTCGCGGGGAG 62.685 72.222 12.30 0.00 44.33 4.30
846 5428 1.846648 CGTGATTACCGCAGATCGC 59.153 57.895 0.23 0.23 36.73 4.58
854 5436 2.837280 GCGATCGCGTGATTACCG 59.163 61.111 26.12 13.02 40.36 4.02
876 5458 1.636988 AGGGATTTAGCGTCGTTTCG 58.363 50.000 0.00 0.00 0.00 3.46
877 5459 2.028883 CGAAGGGATTTAGCGTCGTTTC 59.971 50.000 0.00 0.00 0.00 2.78
878 5460 1.997606 CGAAGGGATTTAGCGTCGTTT 59.002 47.619 0.00 0.00 0.00 3.60
879 5461 1.636988 CGAAGGGATTTAGCGTCGTT 58.363 50.000 0.00 0.00 0.00 3.85
880 5462 0.804933 GCGAAGGGATTTAGCGTCGT 60.805 55.000 0.00 0.00 0.00 4.34
881 5463 1.925052 GCGAAGGGATTTAGCGTCG 59.075 57.895 0.00 0.00 0.00 5.12
885 5467 1.488261 CGACCGCGAAGGGATTTAGC 61.488 60.000 8.23 0.00 46.37 3.09
886 5468 1.488261 GCGACCGCGAAGGGATTTAG 61.488 60.000 8.23 0.00 46.37 1.85
887 5469 1.519898 GCGACCGCGAAGGGATTTA 60.520 57.895 8.23 0.00 46.37 1.40
888 5470 2.818274 GCGACCGCGAAGGGATTT 60.818 61.111 8.23 0.00 46.37 2.17
889 5471 3.771160 AGCGACCGCGAAGGGATT 61.771 61.111 8.23 0.00 46.37 3.01
890 5472 4.514577 CAGCGACCGCGAAGGGAT 62.515 66.667 8.23 0.00 46.37 3.85
898 5480 1.583709 GCTAAATTGCAGCGACCGC 60.584 57.895 6.25 6.25 42.33 5.68
899 5481 0.247814 CAGCTAAATTGCAGCGACCG 60.248 55.000 6.65 0.00 43.97 4.79
900 5482 0.099436 CCAGCTAAATTGCAGCGACC 59.901 55.000 6.65 0.00 43.97 4.79
901 5483 0.099436 CCCAGCTAAATTGCAGCGAC 59.901 55.000 6.65 0.00 43.97 5.19
902 5484 0.035534 TCCCAGCTAAATTGCAGCGA 60.036 50.000 6.65 0.00 43.97 4.93
903 5485 0.099436 GTCCCAGCTAAATTGCAGCG 59.901 55.000 6.65 3.18 43.97 5.18
904 5486 1.133790 CTGTCCCAGCTAAATTGCAGC 59.866 52.381 4.50 4.50 39.41 5.25
905 5487 1.747355 CCTGTCCCAGCTAAATTGCAG 59.253 52.381 0.00 0.00 34.99 4.41
906 5488 1.838112 CCTGTCCCAGCTAAATTGCA 58.162 50.000 0.00 0.00 34.99 4.08
907 5489 0.457443 GCCTGTCCCAGCTAAATTGC 59.543 55.000 0.00 0.00 0.00 3.56
908 5490 1.106285 GGCCTGTCCCAGCTAAATTG 58.894 55.000 0.00 0.00 0.00 2.32
909 5491 0.394352 CGGCCTGTCCCAGCTAAATT 60.394 55.000 0.00 0.00 0.00 1.82
910 5492 1.224592 CGGCCTGTCCCAGCTAAAT 59.775 57.895 0.00 0.00 0.00 1.40
911 5493 1.485294 TTCGGCCTGTCCCAGCTAAA 61.485 55.000 0.00 0.00 0.00 1.85
912 5494 1.485294 TTTCGGCCTGTCCCAGCTAA 61.485 55.000 0.00 0.00 0.00 3.09
913 5495 1.899437 CTTTCGGCCTGTCCCAGCTA 61.899 60.000 0.00 0.00 0.00 3.32
914 5496 3.249189 TTTCGGCCTGTCCCAGCT 61.249 61.111 0.00 0.00 0.00 4.24
915 5497 2.747855 CTTTCGGCCTGTCCCAGC 60.748 66.667 0.00 0.00 0.00 4.85
916 5498 1.078848 CTCTTTCGGCCTGTCCCAG 60.079 63.158 0.00 0.00 0.00 4.45
917 5499 1.535444 TCTCTTTCGGCCTGTCCCA 60.535 57.895 0.00 0.00 0.00 4.37
918 5500 1.219393 CTCTCTTTCGGCCTGTCCC 59.781 63.158 0.00 0.00 0.00 4.46
919 5501 1.219393 CCTCTCTTTCGGCCTGTCC 59.781 63.158 0.00 0.00 0.00 4.02
920 5502 1.448717 GCCTCTCTTTCGGCCTGTC 60.449 63.158 0.00 0.00 40.43 3.51
921 5503 2.665603 GCCTCTCTTTCGGCCTGT 59.334 61.111 0.00 0.00 40.43 4.00
925 5507 0.893727 TTTTGGGCCTCTCTTTCGGC 60.894 55.000 4.53 0.00 45.55 5.54
926 5508 1.541588 CTTTTTGGGCCTCTCTTTCGG 59.458 52.381 4.53 0.00 0.00 4.30
927 5509 1.541588 CCTTTTTGGGCCTCTCTTTCG 59.458 52.381 4.53 0.00 0.00 3.46
947 5529 2.098831 GTGTAGTTTCGGCCGAGCC 61.099 63.158 29.20 21.77 46.75 4.70
948 5530 1.077089 GAGTGTAGTTTCGGCCGAGC 61.077 60.000 29.20 23.85 0.00 5.03
949 5531 0.458025 GGAGTGTAGTTTCGGCCGAG 60.458 60.000 29.20 0.00 0.00 4.63
950 5532 1.588082 GGAGTGTAGTTTCGGCCGA 59.412 57.895 27.28 27.28 0.00 5.54
951 5533 1.804326 CGGAGTGTAGTTTCGGCCG 60.804 63.158 22.12 22.12 0.00 6.13
952 5534 2.098831 GCGGAGTGTAGTTTCGGCC 61.099 63.158 0.00 0.00 34.66 6.13
953 5535 0.669625 AAGCGGAGTGTAGTTTCGGC 60.670 55.000 0.00 0.00 39.21 5.54
954 5536 2.642139 TAAGCGGAGTGTAGTTTCGG 57.358 50.000 0.00 0.00 0.00 4.30
955 5537 2.665052 GGTTAAGCGGAGTGTAGTTTCG 59.335 50.000 0.00 0.00 0.00 3.46
956 5538 3.922910 AGGTTAAGCGGAGTGTAGTTTC 58.077 45.455 0.00 0.00 0.00 2.78
957 5539 3.613432 CGAGGTTAAGCGGAGTGTAGTTT 60.613 47.826 0.00 0.00 0.00 2.66
958 5540 2.094854 CGAGGTTAAGCGGAGTGTAGTT 60.095 50.000 0.00 0.00 0.00 2.24
959 5541 1.471684 CGAGGTTAAGCGGAGTGTAGT 59.528 52.381 0.00 0.00 0.00 2.73
960 5542 1.741706 TCGAGGTTAAGCGGAGTGTAG 59.258 52.381 0.00 0.00 0.00 2.74
972 5554 2.741985 TCGCGGTCGTCGAGGTTA 60.742 61.111 6.13 0.00 42.43 2.85
1049 8895 3.755628 GTACCTCGCGTGGAGCCA 61.756 66.667 32.11 12.01 44.76 4.75
1152 8998 1.478510 TGGAGCTGATCGAGAACCTTC 59.521 52.381 0.00 0.00 0.00 3.46
1214 9060 1.004440 GTCTCGCCAGCCTGAAGTT 60.004 57.895 0.00 0.00 0.00 2.66
1326 9181 2.422479 CTCGACGAGATGTGGGAAAGTA 59.578 50.000 20.25 0.00 0.00 2.24
1352 9207 1.550976 AGTTTGTGATCCGGGAGAGAC 59.449 52.381 0.00 0.00 0.00 3.36
1466 9321 4.094442 GGAACCTTACAATAGTTTGCGAGG 59.906 45.833 0.00 6.48 40.99 4.63
1546 9401 2.169352 GCATCACTTCCTCTAGGCTTGA 59.831 50.000 0.00 0.00 34.44 3.02
1586 9441 0.179084 ACGTATGATTCGTGGGCCAG 60.179 55.000 6.40 0.73 40.07 4.85
1780 9678 3.554259 CATTGCCTGGATTGATCATCG 57.446 47.619 0.00 0.00 31.73 3.84
1823 9721 6.624352 TCAAGATCTTTACATTATGCAGGC 57.376 37.500 4.86 0.00 0.00 4.85
1824 9729 7.013083 AGCTTCAAGATCTTTACATTATGCAGG 59.987 37.037 4.86 0.00 0.00 4.85
1869 9774 6.260936 GGAGGACGTCAATGACATGATTTAAT 59.739 38.462 18.91 0.00 32.09 1.40
2238 10245 3.119495 GCCATTCGTTGTTCCAGCTAAAT 60.119 43.478 0.00 0.00 0.00 1.40
2271 10278 7.693952 TGTTCTTAAAATCCATCTTGATACGC 58.306 34.615 0.00 0.00 0.00 4.42
2358 10365 4.330944 ACACAATTTGACACCTCGTCTA 57.669 40.909 2.79 0.00 45.60 2.59
2606 12014 7.987458 TCCATAAAGTCAAGGTAGTTCATCATC 59.013 37.037 0.00 0.00 0.00 2.92
2761 12169 2.439156 GGCGGCTCCAGCATCTTT 60.439 61.111 0.00 0.00 44.36 2.52
2769 12177 4.424711 GTTGGATGGGCGGCTCCA 62.425 66.667 15.00 15.00 39.78 3.86
2835 12244 5.680594 TTGGCTGAAGATTAATTTGGCAT 57.319 34.783 0.00 0.00 0.00 4.40
2888 12297 5.105756 GGTTGATTCGAATGATGGAAGGTTT 60.106 40.000 16.96 0.00 0.00 3.27
2903 12312 1.094785 AATGGCGGAAGGTTGATTCG 58.905 50.000 0.00 0.00 0.00 3.34
3036 12445 7.722285 TGGCACTATTCACCCTTAATTATTACC 59.278 37.037 0.00 0.00 0.00 2.85
3096 12505 5.954757 TGTCCCAAAGTTTAGGTGGAATAA 58.045 37.500 0.00 0.00 34.05 1.40
3124 12533 2.979678 TCCTCCTTCTTTAGCACCAACT 59.020 45.455 0.00 0.00 0.00 3.16
3129 12538 1.279271 TGCCTCCTCCTTCTTTAGCAC 59.721 52.381 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.