Multiple sequence alignment - TraesCS7A01G492700

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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 TraesCS7A01G492700 chr7A 100.000 1931 0 0 667 2597 681614442 681612512 0.000000e+00 3567.0
1 TraesCS7A01G492700 chr7A 92.741 923 44 9 679 1595 681579502 681580407 0.000000e+00 1312.0
2 TraesCS7A01G492700 chr7A 85.699 944 82 29 672 1595 681387164 681388074 0.000000e+00 946.0
3 TraesCS7A01G492700 chr7A 100.000 431 0 0 1 431 681615108 681614678 0.000000e+00 797.0
4 TraesCS7A01G492700 chr7A 85.423 686 78 10 924 1593 681260662 681261341 0.000000e+00 693.0
5 TraesCS7A01G492700 chr7A 93.271 431 5 3 1 431 681578992 681579398 4.750000e-172 614.0
6 TraesCS7A01G492700 chr7A 80.328 244 14 21 673 904 681254271 681254492 1.240000e-33 154.0
7 TraesCS7A01G492700 chr7A 80.412 194 12 19 1 179 681386604 681386786 9.760000e-25 124.0
8 TraesCS7A01G492700 chr7A 89.552 67 6 1 184 250 681253944 681254009 1.660000e-12 84.2
9 TraesCS7A01G492700 chr7B 85.048 1993 139 82 668 2597 664936504 664938400 0.000000e+00 1882.0
10 TraesCS7A01G492700 chr7B 85.272 937 75 24 667 1595 664797134 664798015 0.000000e+00 907.0
11 TraesCS7A01G492700 chr7B 87.899 752 74 7 854 1598 664969516 664968775 0.000000e+00 869.0
12 TraesCS7A01G492700 chr7B 78.414 908 129 42 702 1593 665003783 665002927 1.770000e-146 529.0
13 TraesCS7A01G492700 chr7B 84.864 403 40 6 1193 1595 665284269 665283888 1.130000e-103 387.0
14 TraesCS7A01G492700 chr7B 84.305 223 15 13 64 275 664977250 664977037 1.580000e-47 200.0
15 TraesCS7A01G492700 chr7B 100.000 28 0 0 1 28 664796565 664796592 5.000000e-03 52.8
16 TraesCS7A01G492700 chr7D 83.856 1530 143 58 671 2135 589869475 589867985 0.000000e+00 1362.0
17 TraesCS7A01G492700 chr7D 88.034 936 79 16 667 1595 589857743 589858652 0.000000e+00 1077.0
18 TraesCS7A01G492700 chr7D 84.316 950 93 29 672 1598 590064277 590063361 0.000000e+00 878.0
19 TraesCS7A01G492700 chr7D 82.147 941 96 39 681 1595 590330256 590329362 0.000000e+00 741.0
20 TraesCS7A01G492700 chr7D 85.274 292 9 9 2311 2597 589867762 589867500 1.180000e-68 270.0
21 TraesCS7A01G492700 chr7D 80.899 267 25 14 1 266 589857266 589857507 1.230000e-43 187.0
22 TraesCS7A01G492700 chr7D 78.000 150 10 13 1 137 590064763 590064624 3.580000e-09 73.1
23 TraesCS7A01G492700 chr2A 85.561 187 12 4 2341 2517 756509023 756508842 5.710000e-42 182.0


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 TraesCS7A01G492700 chr7A 681612512 681615108 2596 True 2182.00 3567 100.0000 1 2597 2 chr7A.!!$R1 2596
1 TraesCS7A01G492700 chr7A 681578992 681580407 1415 False 963.00 1312 93.0060 1 1595 2 chr7A.!!$F4 1594
2 TraesCS7A01G492700 chr7A 681260662 681261341 679 False 693.00 693 85.4230 924 1593 1 chr7A.!!$F1 669
3 TraesCS7A01G492700 chr7A 681386604 681388074 1470 False 535.00 946 83.0555 1 1595 2 chr7A.!!$F3 1594
4 TraesCS7A01G492700 chr7B 664936504 664938400 1896 False 1882.00 1882 85.0480 668 2597 1 chr7B.!!$F1 1929
5 TraesCS7A01G492700 chr7B 664968775 664969516 741 True 869.00 869 87.8990 854 1598 1 chr7B.!!$R1 744
6 TraesCS7A01G492700 chr7B 665002927 665003783 856 True 529.00 529 78.4140 702 1593 1 chr7B.!!$R3 891
7 TraesCS7A01G492700 chr7B 664796565 664798015 1450 False 479.90 907 92.6360 1 1595 2 chr7B.!!$F2 1594
8 TraesCS7A01G492700 chr7D 589867500 589869475 1975 True 816.00 1362 84.5650 671 2597 2 chr7D.!!$R2 1926
9 TraesCS7A01G492700 chr7D 590329362 590330256 894 True 741.00 741 82.1470 681 1595 1 chr7D.!!$R1 914
10 TraesCS7A01G492700 chr7D 589857266 589858652 1386 False 632.00 1077 84.4665 1 1595 2 chr7D.!!$F1 1594
11 TraesCS7A01G492700 chr7D 590063361 590064763 1402 True 475.55 878 81.1580 1 1598 2 chr7D.!!$R3 1597

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
779 1173 0.329632 AGCTACTCCCCCTCCTCCTA 60.33 60.0 0.0 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 3154 0.106719 AATCATTGTAGCCGGGTGGG 60.107 55.0 18.4 0.78 39.58 4.61 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
37 39 6.208797 TCTGCACCACCTGTATATGTAGTATC 59.791 42.308 0.00 0.00 0.00 2.24
318 549 3.210227 GAAGATGGAAGCTTTAGGAGGC 58.790 50.000 0.00 0.00 41.66 4.70
321 552 1.820056 GGAAGCTTTAGGAGGCGGC 60.820 63.158 0.00 0.00 0.00 6.53
322 553 1.222113 GAAGCTTTAGGAGGCGGCT 59.778 57.895 13.09 13.09 34.52 5.52
325 556 2.268920 CTTTAGGAGGCGGCTGCA 59.731 61.111 31.16 15.07 45.35 4.41
388 636 2.014010 ACAATCATTTGTGCCACCCT 57.986 45.000 0.00 0.00 44.36 4.34
389 637 1.895131 ACAATCATTTGTGCCACCCTC 59.105 47.619 0.00 0.00 44.36 4.30
391 639 1.843368 ATCATTTGTGCCACCCTCTG 58.157 50.000 0.00 0.00 0.00 3.35
393 641 0.883833 CATTTGTGCCACCCTCTGTC 59.116 55.000 0.00 0.00 0.00 3.51
403 668 2.368439 CACCCTCTGTCTCTCTCTCTG 58.632 57.143 0.00 0.00 0.00 3.35
428 693 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
429 694 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
430 695 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
728 1117 6.135290 TGTTGCCTGCATATAATTCTGTTC 57.865 37.500 0.00 0.00 0.00 3.18
729 1118 5.067674 TGTTGCCTGCATATAATTCTGTTCC 59.932 40.000 0.00 0.00 0.00 3.62
730 1119 5.052693 TGCCTGCATATAATTCTGTTCCT 57.947 39.130 0.00 0.00 0.00 3.36
758 1152 6.430000 TCGCTTGCTTCTCCTTTACTTATTTT 59.570 34.615 0.00 0.00 0.00 1.82
759 1153 7.040686 TCGCTTGCTTCTCCTTTACTTATTTTT 60.041 33.333 0.00 0.00 0.00 1.94
779 1173 0.329632 AGCTACTCCCCCTCCTCCTA 60.330 60.000 0.00 0.00 0.00 2.94
880 1325 1.800805 CAGAGTCACATCACACCACC 58.199 55.000 0.00 0.00 0.00 4.61
917 1369 1.452108 CCTCACCTCGGGCAATTCC 60.452 63.158 0.00 0.00 0.00 3.01
1005 1470 1.345741 CGCTCACCAGATATCATGGGT 59.654 52.381 19.24 14.07 42.48 4.51
1008 1473 3.834813 GCTCACCAGATATCATGGGTCTA 59.165 47.826 19.24 8.42 42.48 2.59
1017 1482 3.537874 ATGGGTCTAGACGCCGCC 61.538 66.667 30.50 19.79 42.77 6.13
1246 1720 2.441532 GCTCCATGGCCATGCTGT 60.442 61.111 36.08 4.84 37.49 4.40
1323 1797 3.948735 CACGGGTGGAGTAATTGGT 57.051 52.632 0.00 0.00 0.00 3.67
1618 2123 1.267982 CGAGTCATCTGCGTCTCTCTG 60.268 57.143 0.00 0.00 0.00 3.35
1623 2128 2.016318 CATCTGCGTCTCTCTGTCTCT 58.984 52.381 0.00 0.00 0.00 3.10
1625 2130 0.373370 CTGCGTCTCTCTGTCTCTCG 59.627 60.000 0.00 0.00 0.00 4.04
1626 2131 0.320858 TGCGTCTCTCTGTCTCTCGT 60.321 55.000 0.00 0.00 0.00 4.18
1733 2259 1.694696 AGCGAAGTGGACCTCTCTTTT 59.305 47.619 0.00 0.00 0.00 2.27
1776 2305 2.373938 GGTCGAGCCTGAACAATCG 58.626 57.895 2.39 0.00 36.54 3.34
1777 2306 0.108804 GGTCGAGCCTGAACAATCGA 60.109 55.000 2.39 0.00 41.51 3.59
1778 2307 1.671850 GGTCGAGCCTGAACAATCGAA 60.672 52.381 2.39 0.00 44.84 3.71
1779 2308 1.656095 GTCGAGCCTGAACAATCGAAG 59.344 52.381 0.00 0.00 44.84 3.79
1801 2330 1.149361 ATTGTACATACACCGCCGCG 61.149 55.000 5.59 5.59 35.64 6.46
1840 2377 1.265095 CGCTCTATCATGGCGCAAATT 59.735 47.619 10.83 0.00 42.28 1.82
1858 2395 2.988010 TTAAGCAGCTGATCGTGGAT 57.012 45.000 20.43 0.00 0.00 3.41
1859 2396 2.229675 TAAGCAGCTGATCGTGGATG 57.770 50.000 20.43 0.00 0.00 3.51
1860 2397 0.463295 AAGCAGCTGATCGTGGATGG 60.463 55.000 20.43 0.00 0.00 3.51
1862 2399 0.462581 GCAGCTGATCGTGGATGGAA 60.463 55.000 20.43 0.00 0.00 3.53
1864 2401 2.569059 CAGCTGATCGTGGATGGAAAT 58.431 47.619 8.42 0.00 0.00 2.17
1866 2403 1.605710 GCTGATCGTGGATGGAAATGG 59.394 52.381 0.00 0.00 0.00 3.16
1867 2404 2.746142 GCTGATCGTGGATGGAAATGGA 60.746 50.000 0.00 0.00 0.00 3.41
1869 2406 4.139786 CTGATCGTGGATGGAAATGGAAT 58.860 43.478 0.00 0.00 0.00 3.01
1871 2408 3.643199 TCGTGGATGGAAATGGAATCA 57.357 42.857 0.00 0.00 0.00 2.57
1872 2409 4.169059 TCGTGGATGGAAATGGAATCAT 57.831 40.909 0.00 0.00 34.56 2.45
1873 2410 5.303259 TCGTGGATGGAAATGGAATCATA 57.697 39.130 0.00 0.00 32.44 2.15
1875 2412 6.125719 TCGTGGATGGAAATGGAATCATAAA 58.874 36.000 0.00 0.00 32.44 1.40
1877 2414 6.039717 CGTGGATGGAAATGGAATCATAAAGT 59.960 38.462 0.00 0.00 32.44 2.66
1879 2416 7.707893 GTGGATGGAAATGGAATCATAAAGTTG 59.292 37.037 0.00 0.00 32.44 3.16
1880 2417 7.147689 TGGATGGAAATGGAATCATAAAGTTGG 60.148 37.037 0.00 0.00 32.44 3.77
1979 2522 1.807742 CTCGCGGGGAATTGTGTAAAA 59.192 47.619 6.13 0.00 0.00 1.52
2016 2562 9.660180 ATCTCTTGTAAACTCTACTTCCATTTC 57.340 33.333 0.00 0.00 0.00 2.17
2022 2568 7.929785 TGTAAACTCTACTTCCATTTCGTCTTT 59.070 33.333 0.00 0.00 0.00 2.52
2028 2574 7.211573 TCTACTTCCATTTCGTCTTTTGTACA 58.788 34.615 0.00 0.00 0.00 2.90
2029 2575 6.687081 ACTTCCATTTCGTCTTTTGTACAA 57.313 33.333 3.59 3.59 0.00 2.41
2032 2578 7.496591 ACTTCCATTTCGTCTTTTGTACAAGTA 59.503 33.333 8.56 0.58 0.00 2.24
2033 2579 7.181143 TCCATTTCGTCTTTTGTACAAGTAC 57.819 36.000 8.56 7.54 36.63 2.73
2034 2580 6.987992 TCCATTTCGTCTTTTGTACAAGTACT 59.012 34.615 8.56 0.00 37.00 2.73
2035 2581 7.170320 TCCATTTCGTCTTTTGTACAAGTACTC 59.830 37.037 8.56 0.01 37.00 2.59
2036 2582 7.170998 CCATTTCGTCTTTTGTACAAGTACTCT 59.829 37.037 8.56 0.00 37.00 3.24
2037 2583 9.188588 CATTTCGTCTTTTGTACAAGTACTCTA 57.811 33.333 8.56 0.00 37.00 2.43
2038 2584 8.566008 TTTCGTCTTTTGTACAAGTACTCTAC 57.434 34.615 8.56 0.00 37.00 2.59
2062 2608 1.820010 TTCGCTCTTGCTCTGCCTCA 61.820 55.000 0.00 0.00 36.97 3.86
2135 2683 6.331369 TCAATTCAACTTCCAGAATTCACC 57.669 37.500 8.44 0.00 41.20 4.02
2136 2684 5.048782 TCAATTCAACTTCCAGAATTCACCG 60.049 40.000 8.44 0.00 41.20 4.94
2138 2686 1.200020 CAACTTCCAGAATTCACCGCC 59.800 52.381 8.44 0.00 0.00 6.13
2139 2687 0.693049 ACTTCCAGAATTCACCGCCT 59.307 50.000 8.44 0.00 0.00 5.52
2141 2689 2.162681 CTTCCAGAATTCACCGCCTTT 58.837 47.619 8.44 0.00 0.00 3.11
2143 2691 1.351017 TCCAGAATTCACCGCCTTTCT 59.649 47.619 8.44 0.00 0.00 2.52
2144 2692 1.740025 CCAGAATTCACCGCCTTTCTC 59.260 52.381 8.44 0.00 0.00 2.87
2145 2693 2.616510 CCAGAATTCACCGCCTTTCTCT 60.617 50.000 8.44 0.00 0.00 3.10
2146 2694 2.675348 CAGAATTCACCGCCTTTCTCTC 59.325 50.000 8.44 0.00 0.00 3.20
2150 2740 0.891373 TCACCGCCTTTCTCTCTCTG 59.109 55.000 0.00 0.00 0.00 3.35
2165 2755 3.829601 TCTCTCTGTCTGTTTTCCCTCTC 59.170 47.826 0.00 0.00 0.00 3.20
2166 2756 3.831911 CTCTCTGTCTGTTTTCCCTCTCT 59.168 47.826 0.00 0.00 0.00 3.10
2169 2759 4.999310 TCTGTCTGTTTTCCCTCTCTCTA 58.001 43.478 0.00 0.00 0.00 2.43
2170 2760 5.013547 TCTGTCTGTTTTCCCTCTCTCTAG 58.986 45.833 0.00 0.00 0.00 2.43
2171 2761 4.999310 TGTCTGTTTTCCCTCTCTCTAGA 58.001 43.478 0.00 0.00 0.00 2.43
2173 2763 6.019748 TGTCTGTTTTCCCTCTCTCTAGAAT 58.980 40.000 0.00 0.00 0.00 2.40
2175 2765 7.039270 GTCTGTTTTCCCTCTCTCTAGAATTC 58.961 42.308 0.00 0.00 0.00 2.17
2176 2766 6.726299 TCTGTTTTCCCTCTCTCTAGAATTCA 59.274 38.462 8.44 0.00 0.00 2.57
2178 2768 6.498651 TGTTTTCCCTCTCTCTAGAATTCACT 59.501 38.462 8.44 0.00 0.00 3.41
2180 2770 5.458451 TCCCTCTCTCTAGAATTCACTGA 57.542 43.478 8.44 1.87 0.00 3.41
2181 2771 5.832221 TCCCTCTCTCTAGAATTCACTGAA 58.168 41.667 8.44 0.00 0.00 3.02
2182 2772 6.439487 TCCCTCTCTCTAGAATTCACTGAAT 58.561 40.000 8.44 0.00 33.25 2.57
2183 2773 6.900186 TCCCTCTCTCTAGAATTCACTGAATT 59.100 38.462 15.55 15.55 43.77 2.17
2184 2774 7.401493 TCCCTCTCTCTAGAATTCACTGAATTT 59.599 37.037 16.48 10.07 41.56 1.82
2185 2775 8.046107 CCCTCTCTCTAGAATTCACTGAATTTT 58.954 37.037 16.48 13.73 41.56 1.82
2196 2786 4.323417 TCACTGAATTTTATGACAGCGGT 58.677 39.130 0.00 0.00 34.25 5.68
2197 2787 4.759693 TCACTGAATTTTATGACAGCGGTT 59.240 37.500 0.00 0.00 34.25 4.44
2198 2788 5.935206 TCACTGAATTTTATGACAGCGGTTA 59.065 36.000 0.00 0.00 34.25 2.85
2202 2792 5.935206 TGAATTTTATGACAGCGGTTAGACA 59.065 36.000 0.00 0.00 0.00 3.41
2258 2858 4.202295 GCATGAGAGAGAGAGAGAGAGAGA 60.202 50.000 0.00 0.00 0.00 3.10
2260 2860 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
2262 2862 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2263 2863 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2293 2908 1.750778 GAGAGAGAGAGAGTTGGGCAG 59.249 57.143 0.00 0.00 0.00 4.85
2297 2912 3.672295 GAGAGAGTTGGGCAGGCGG 62.672 68.421 0.00 0.00 0.00 6.13
2326 2941 2.309504 GGGGAGGGAGGAAAGTGGG 61.310 68.421 0.00 0.00 0.00 4.61
2365 2980 1.340889 TCCAAAGCATGTCTTGTTGCC 59.659 47.619 0.00 0.00 39.72 4.52
2517 3144 0.754957 CAGATCTGGGCGAGTCTCCT 60.755 60.000 15.38 0.00 0.00 3.69
2518 3145 0.467290 AGATCTGGGCGAGTCTCCTC 60.467 60.000 0.00 0.00 0.00 3.71
2519 3146 0.467290 GATCTGGGCGAGTCTCCTCT 60.467 60.000 0.00 0.00 35.43 3.69
2520 3147 0.467290 ATCTGGGCGAGTCTCCTCTC 60.467 60.000 0.00 0.00 35.43 3.20
2521 3148 2.043852 TGGGCGAGTCTCCTCTCC 60.044 66.667 0.00 0.00 41.12 3.71
2522 3149 2.043852 GGGCGAGTCTCCTCTCCA 60.044 66.667 0.00 0.00 43.22 3.86
2523 3150 2.124693 GGGCGAGTCTCCTCTCCAG 61.125 68.421 0.00 0.00 43.22 3.86
2524 3151 1.379309 GGCGAGTCTCCTCTCCAGT 60.379 63.158 0.00 0.00 41.42 4.00
2525 3152 1.381165 GGCGAGTCTCCTCTCCAGTC 61.381 65.000 0.00 0.00 41.42 3.51
2526 3153 0.678366 GCGAGTCTCCTCTCCAGTCA 60.678 60.000 0.00 0.00 35.43 3.41
2527 3154 1.091537 CGAGTCTCCTCTCCAGTCAC 58.908 60.000 0.00 0.00 35.43 3.67
2528 3155 1.470051 GAGTCTCCTCTCCAGTCACC 58.530 60.000 0.00 0.00 34.69 4.02
2538 3168 3.000819 CAGTCACCCACCCGGCTA 61.001 66.667 0.00 0.00 33.26 3.93
2572 3202 0.918983 TGGATTCCCCAACTGCTAGG 59.081 55.000 0.00 0.00 43.29 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 1.178276 CCTACTCCGCCTATAGCTGG 58.822 60.000 0.00 0.00 40.39 4.85
318 549 0.877649 AAGTAGATCGCATGCAGCCG 60.878 55.000 19.57 0.57 41.38 5.52
321 552 4.225984 GAGAGTAAGTAGATCGCATGCAG 58.774 47.826 19.57 10.78 0.00 4.41
322 553 3.632145 TGAGAGTAAGTAGATCGCATGCA 59.368 43.478 19.57 5.34 0.00 3.96
325 556 6.398234 AACATGAGAGTAAGTAGATCGCAT 57.602 37.500 0.00 0.00 34.38 4.73
388 636 4.096681 AGAGAGACAGAGAGAGAGACAGA 58.903 47.826 0.00 0.00 0.00 3.41
389 637 4.161189 AGAGAGAGACAGAGAGAGAGACAG 59.839 50.000 0.00 0.00 0.00 3.51
391 639 4.404073 AGAGAGAGAGACAGAGAGAGAGAC 59.596 50.000 0.00 0.00 0.00 3.36
393 641 4.648762 AGAGAGAGAGAGACAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
403 668 4.892934 AGAGAGAGAGAGAGAGAGAGAGAC 59.107 50.000 0.00 0.00 0.00 3.36
728 1117 1.153469 GGAGAAGCAAGCGAGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
729 1118 0.248843 AAGGAGAAGCAAGCGAGGAG 59.751 55.000 0.00 0.00 0.00 3.69
730 1119 0.687354 AAAGGAGAAGCAAGCGAGGA 59.313 50.000 0.00 0.00 0.00 3.71
758 1152 0.561680 GGAGGAGGGGGAGTAGCTAA 59.438 60.000 0.00 0.00 0.00 3.09
759 1153 0.329632 AGGAGGAGGGGGAGTAGCTA 60.330 60.000 0.00 0.00 0.00 3.32
779 1173 2.676748 GAGGTGATGATGGAGAGGAGT 58.323 52.381 0.00 0.00 0.00 3.85
917 1369 6.049149 TCCAAGAAATAGTTTATGCGAGAGG 58.951 40.000 0.00 0.00 0.00 3.69
988 1453 5.080337 GTCTAGACCCATGATATCTGGTGA 58.920 45.833 12.13 5.81 31.44 4.02
989 1454 4.082517 CGTCTAGACCCATGATATCTGGTG 60.083 50.000 17.23 10.46 31.44 4.17
1005 1470 1.065273 GATTTCGGCGGCGTCTAGA 59.935 57.895 31.06 8.65 0.00 2.43
1008 1473 2.202756 GAGATTTCGGCGGCGTCT 60.203 61.111 31.06 25.32 0.00 4.18
1017 1482 1.268234 GCCGCCAATTCAGAGATTTCG 60.268 52.381 0.00 0.00 0.00 3.46
1505 2010 4.953868 CGGCCACGAACACGGTGA 62.954 66.667 16.29 0.00 44.60 4.02
1542 2047 3.521796 GCCCGCATCTTCTTGGCC 61.522 66.667 0.00 0.00 36.07 5.36
1618 2123 2.670414 CTGAATTGCTGGAACGAGAGAC 59.330 50.000 0.00 0.00 0.00 3.36
1623 2128 0.874390 GTGCTGAATTGCTGGAACGA 59.126 50.000 0.00 0.00 0.00 3.85
1625 2130 0.244721 GGGTGCTGAATTGCTGGAAC 59.755 55.000 0.00 0.00 0.00 3.62
1626 2131 0.899717 GGGGTGCTGAATTGCTGGAA 60.900 55.000 0.00 0.00 0.00 3.53
1669 2174 2.431260 CCAAGGCAATGCACGCAC 60.431 61.111 7.79 2.10 0.00 5.34
1673 2178 2.824071 CTTCGGCCAAGGCAATGCAC 62.824 60.000 13.87 0.00 44.11 4.57
1674 2179 2.599875 TTCGGCCAAGGCAATGCA 60.600 55.556 13.87 0.00 44.11 3.96
1675 2180 2.182537 CTTCGGCCAAGGCAATGC 59.817 61.111 13.87 0.00 44.11 3.56
1696 2222 0.179113 GCTTCCGCTTCTCTGGAGAG 60.179 60.000 0.00 0.00 43.36 3.20
1724 2250 1.136110 GCGGAGGAGAGAAAAGAGAGG 59.864 57.143 0.00 0.00 0.00 3.69
1733 2259 0.972471 TTCTGCATGCGGAGGAGAGA 60.972 55.000 27.25 12.97 34.87 3.10
1759 2288 1.656095 CTTCGATTGTTCAGGCTCGAC 59.344 52.381 0.00 0.00 39.60 4.20
1776 2305 3.311596 GGCGGTGTATGTACAATTCCTTC 59.688 47.826 0.00 0.00 38.04 3.46
1777 2306 3.275999 GGCGGTGTATGTACAATTCCTT 58.724 45.455 0.00 0.00 38.04 3.36
1778 2307 2.740580 CGGCGGTGTATGTACAATTCCT 60.741 50.000 0.00 0.00 38.04 3.36
1779 2308 1.595794 CGGCGGTGTATGTACAATTCC 59.404 52.381 0.00 0.00 38.04 3.01
1817 2346 3.771491 CGCCATGATAGAGCGCGC 61.771 66.667 26.66 26.66 43.72 6.86
1822 2351 4.023792 TGCTTAATTTGCGCCATGATAGAG 60.024 41.667 4.18 0.00 0.00 2.43
1823 2352 3.882288 TGCTTAATTTGCGCCATGATAGA 59.118 39.130 4.18 0.00 0.00 1.98
1824 2353 4.224433 CTGCTTAATTTGCGCCATGATAG 58.776 43.478 4.18 0.00 0.00 2.08
1826 2355 2.800629 GCTGCTTAATTTGCGCCATGAT 60.801 45.455 4.18 0.00 0.00 2.45
1840 2377 1.202568 CCATCCACGATCAGCTGCTTA 60.203 52.381 9.47 0.00 0.00 3.09
1858 2395 6.259893 TCCCAACTTTATGATTCCATTTCCA 58.740 36.000 0.00 0.00 34.31 3.53
1859 2396 6.790232 TCCCAACTTTATGATTCCATTTCC 57.210 37.500 0.00 0.00 34.31 3.13
1869 2406 9.342308 CAGAGCTAATTATTCCCAACTTTATGA 57.658 33.333 0.00 0.00 0.00 2.15
1871 2408 7.779798 TGCAGAGCTAATTATTCCCAACTTTAT 59.220 33.333 0.00 0.00 0.00 1.40
1872 2409 7.116075 TGCAGAGCTAATTATTCCCAACTTTA 58.884 34.615 0.00 0.00 0.00 1.85
1873 2410 5.951747 TGCAGAGCTAATTATTCCCAACTTT 59.048 36.000 0.00 0.00 0.00 2.66
1875 2412 5.116084 TGCAGAGCTAATTATTCCCAACT 57.884 39.130 0.00 0.00 0.00 3.16
1877 2414 4.279169 GCATGCAGAGCTAATTATTCCCAA 59.721 41.667 14.21 0.00 0.00 4.12
1879 2416 3.192212 GGCATGCAGAGCTAATTATTCCC 59.808 47.826 21.36 0.00 0.00 3.97
1880 2417 3.822735 TGGCATGCAGAGCTAATTATTCC 59.177 43.478 21.36 0.00 0.00 3.01
1888 2431 2.723322 AATTCTGGCATGCAGAGCTA 57.277 45.000 21.36 6.82 0.00 3.32
1932 2475 1.666189 GAGGCGGAAATACAGAGCAAC 59.334 52.381 0.00 0.00 0.00 4.17
1979 2522 9.523168 AGAGTTTACAAGAGATTACAGTAGAGT 57.477 33.333 0.00 0.00 0.00 3.24
2029 2575 5.462405 CAAGAGCGAAACAAGTAGAGTACT 58.538 41.667 0.00 0.00 41.73 2.73
2032 2578 3.060602 GCAAGAGCGAAACAAGTAGAGT 58.939 45.455 0.00 0.00 0.00 3.24
2033 2579 3.713889 GCAAGAGCGAAACAAGTAGAG 57.286 47.619 0.00 0.00 0.00 2.43
2046 2592 2.107903 GCTGAGGCAGAGCAAGAGC 61.108 63.158 0.00 0.00 38.69 4.09
2047 2593 1.295746 TGCTGAGGCAGAGCAAGAG 59.704 57.895 7.89 0.00 43.47 2.85
2048 2594 3.475192 TGCTGAGGCAGAGCAAGA 58.525 55.556 7.89 0.00 43.47 3.02
2062 2608 6.499699 TGATCTGTCTATAATTCCAGGATGCT 59.500 38.462 0.00 0.00 31.97 3.79
2135 2683 1.543802 ACAGACAGAGAGAGAAAGGCG 59.456 52.381 0.00 0.00 0.00 5.52
2136 2684 3.676291 AACAGACAGAGAGAGAAAGGC 57.324 47.619 0.00 0.00 0.00 4.35
2138 2686 4.994217 GGGAAAACAGACAGAGAGAGAAAG 59.006 45.833 0.00 0.00 0.00 2.62
2139 2687 4.656112 AGGGAAAACAGACAGAGAGAGAAA 59.344 41.667 0.00 0.00 0.00 2.52
2141 2689 3.829601 GAGGGAAAACAGACAGAGAGAGA 59.170 47.826 0.00 0.00 0.00 3.10
2143 2691 3.829601 GAGAGGGAAAACAGACAGAGAGA 59.170 47.826 0.00 0.00 0.00 3.10
2144 2692 3.831911 AGAGAGGGAAAACAGACAGAGAG 59.168 47.826 0.00 0.00 0.00 3.20
2145 2693 3.829601 GAGAGAGGGAAAACAGACAGAGA 59.170 47.826 0.00 0.00 0.00 3.10
2146 2694 3.831911 AGAGAGAGGGAAAACAGACAGAG 59.168 47.826 0.00 0.00 0.00 3.35
2150 2740 5.986501 TTCTAGAGAGAGGGAAAACAGAC 57.013 43.478 0.00 0.00 31.77 3.51
2169 2759 7.246311 CGCTGTCATAAAATTCAGTGAATTCT 58.754 34.615 27.07 18.55 40.77 2.40
2170 2760 6.470235 CCGCTGTCATAAAATTCAGTGAATTC 59.530 38.462 27.07 15.89 40.77 2.17
2171 2761 6.071952 ACCGCTGTCATAAAATTCAGTGAATT 60.072 34.615 22.70 22.70 43.07 2.17
2173 2763 4.759693 ACCGCTGTCATAAAATTCAGTGAA 59.240 37.500 8.27 8.27 39.73 3.18
2175 2765 4.685169 ACCGCTGTCATAAAATTCAGTG 57.315 40.909 0.00 0.00 37.91 3.66
2176 2766 6.092259 GTCTAACCGCTGTCATAAAATTCAGT 59.908 38.462 0.00 0.00 0.00 3.41
2178 2768 5.935206 TGTCTAACCGCTGTCATAAAATTCA 59.065 36.000 0.00 0.00 0.00 2.57
2180 2770 5.123344 GGTGTCTAACCGCTGTCATAAAATT 59.877 40.000 0.00 0.00 39.81 1.82
2181 2771 4.634443 GGTGTCTAACCGCTGTCATAAAAT 59.366 41.667 0.00 0.00 39.81 1.82
2182 2772 3.998341 GGTGTCTAACCGCTGTCATAAAA 59.002 43.478 0.00 0.00 39.81 1.52
2183 2773 3.592059 GGTGTCTAACCGCTGTCATAAA 58.408 45.455 0.00 0.00 39.81 1.40
2184 2774 3.241067 GGTGTCTAACCGCTGTCATAA 57.759 47.619 0.00 0.00 39.81 1.90
2185 2775 2.953466 GGTGTCTAACCGCTGTCATA 57.047 50.000 0.00 0.00 39.81 2.15
2186 2776 3.834732 GGTGTCTAACCGCTGTCAT 57.165 52.632 0.00 0.00 39.81 3.06
2234 2824 3.455543 TCTCTCTCTCTCTCTCTCATGCA 59.544 47.826 0.00 0.00 0.00 3.96
2235 2825 4.063689 CTCTCTCTCTCTCTCTCTCATGC 58.936 52.174 0.00 0.00 0.00 4.06
2258 2858 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2260 2860 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2262 2862 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2263 2863 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
2299 2914 3.742248 CTCCCTCCCCGTCCTCCTC 62.742 73.684 0.00 0.00 0.00 3.71
2300 2915 3.756783 CTCCCTCCCCGTCCTCCT 61.757 72.222 0.00 0.00 0.00 3.69
2301 2916 4.862823 CCTCCCTCCCCGTCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
2302 2917 2.817420 TTTCCTCCCTCCCCGTCCTC 62.817 65.000 0.00 0.00 0.00 3.71
2303 2918 2.824388 CTTTCCTCCCTCCCCGTCCT 62.824 65.000 0.00 0.00 0.00 3.85
2304 2919 2.285144 TTTCCTCCCTCCCCGTCC 60.285 66.667 0.00 0.00 0.00 4.79
2305 2920 1.612739 ACTTTCCTCCCTCCCCGTC 60.613 63.158 0.00 0.00 0.00 4.79
2306 2921 1.918800 CACTTTCCTCCCTCCCCGT 60.919 63.158 0.00 0.00 0.00 5.28
2307 2922 2.670148 CCACTTTCCTCCCTCCCCG 61.670 68.421 0.00 0.00 0.00 5.73
2308 2923 2.309504 CCCACTTTCCTCCCTCCCC 61.310 68.421 0.00 0.00 0.00 4.81
2309 2924 2.985116 GCCCACTTTCCTCCCTCCC 61.985 68.421 0.00 0.00 0.00 4.30
2326 2941 2.433318 GCTCACGTCAGGGTCAGC 60.433 66.667 0.00 0.00 0.00 4.26
2459 3085 1.039785 TCCCGTCTCCAGATCTGCTG 61.040 60.000 17.76 11.49 44.49 4.41
2512 3139 0.251832 GTGGGTGACTGGAGAGGAGA 60.252 60.000 0.00 0.00 0.00 3.71
2517 3144 2.603473 CGGGTGGGTGACTGGAGA 60.603 66.667 0.00 0.00 0.00 3.71
2518 3145 3.706373 CCGGGTGGGTGACTGGAG 61.706 72.222 0.00 0.00 0.00 3.86
2527 3154 0.106719 AATCATTGTAGCCGGGTGGG 60.107 55.000 18.40 0.78 39.58 4.61
2528 3155 1.405105 CAAATCATTGTAGCCGGGTGG 59.595 52.381 18.40 0.40 38.77 4.61
2538 3168 3.135167 GGAATCCATGGGCAAATCATTGT 59.865 43.478 13.02 0.00 38.85 2.71
2569 3199 5.456497 CGCGAGAAAATTTATACGTGACCTA 59.544 40.000 0.00 0.00 34.05 3.08
2570 3200 4.266976 CGCGAGAAAATTTATACGTGACCT 59.733 41.667 0.00 0.00 34.05 3.85
2571 3201 4.502558 CGCGAGAAAATTTATACGTGACC 58.497 43.478 0.00 0.32 34.05 4.02
2572 3202 4.502558 CCGCGAGAAAATTTATACGTGAC 58.497 43.478 8.23 3.20 34.05 3.67


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

AutoCloner maintained by Alex Coulton.