Multiple sequence alignment - TraesCS2A01G399000

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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 TraesCS2A01G399000 chr2A 100.000 6138 0 0 1 6138 652296148 652290011 0.000000e+00 11335.0
1 TraesCS2A01G399000 chr2A 81.149 557 73 22 1 534 595347682 595347135 9.520000e-113 418.0
2 TraesCS2A01G399000 chr2A 97.561 205 5 0 711 915 652297229 652297433 9.790000e-93 351.0
3 TraesCS2A01G399000 chr2D 94.545 3831 119 28 916 4693 507756186 507752393 0.000000e+00 5834.0
4 TraesCS2A01G399000 chr2D 96.445 1294 37 3 4846 6138 507752339 507751054 0.000000e+00 2126.0
5 TraesCS2A01G399000 chr2D 94.118 68 4 0 4318 4385 507752725 507752658 3.030000e-18 104.0
6 TraesCS2A01G399000 chr2B 94.388 2245 78 14 3931 6138 596414291 596412058 0.000000e+00 3404.0
7 TraesCS2A01G399000 chr2B 91.289 861 61 10 2300 3152 596416183 596415329 0.000000e+00 1162.0
8 TraesCS2A01G399000 chr2B 95.972 571 20 1 3156 3726 596415262 596414695 0.000000e+00 924.0
9 TraesCS2A01G399000 chr2B 92.419 620 37 5 916 1534 596417811 596417201 0.000000e+00 876.0
10 TraesCS2A01G399000 chr2B 83.270 263 29 6 1615 1877 596417011 596416764 1.720000e-55 228.0
11 TraesCS2A01G399000 chr2B 88.827 179 7 3 3720 3891 596414465 596414293 2.240000e-49 207.0
12 TraesCS2A01G399000 chr2B 92.647 68 5 0 4318 4385 596413827 596413760 1.410000e-16 99.0
13 TraesCS2A01G399000 chr6B 99.344 915 6 0 1 915 707282097 707283011 0.000000e+00 1657.0
14 TraesCS2A01G399000 chr6B 97.561 205 5 0 711 915 707277127 707276923 9.790000e-93 351.0
15 TraesCS2A01G399000 chr6B 83.898 118 15 4 6019 6134 219571081 219570966 6.500000e-20 110.0
16 TraesCS2A01G399000 chr1B 99.344 915 6 0 1 915 511440776 511441690 0.000000e+00 1657.0
17 TraesCS2A01G399000 chr1B 96.070 916 29 5 1 915 328267978 328268887 0.000000e+00 1485.0
18 TraesCS2A01G399000 chr1B 97.561 205 5 0 711 915 511435806 511435602 9.790000e-93 351.0
19 TraesCS2A01G399000 chr1B 96.447 197 7 0 722 918 328262678 328262482 5.930000e-85 326.0
20 TraesCS2A01G399000 chr1D 96.448 563 19 1 1 562 438035924 438036486 0.000000e+00 928.0
21 TraesCS2A01G399000 chr7D 95.915 563 22 1 1 562 17372338 17371776 0.000000e+00 911.0
22 TraesCS2A01G399000 chr7D 90.735 626 20 4 55 646 78266152 78265531 0.000000e+00 800.0
23 TraesCS2A01G399000 chr7D 84.478 670 50 25 188 848 87242075 87242699 4.070000e-171 612.0
24 TraesCS2A01G399000 chr7D 86.609 463 28 19 480 915 78265505 78265050 1.200000e-131 481.0
25 TraesCS2A01G399000 chr7D 81.967 122 20 2 6014 6134 489114706 489114586 1.090000e-17 102.0
26 TraesCS2A01G399000 chr7D 100.000 29 0 0 1 29 78266184 78266156 3.000000e-03 54.7
27 TraesCS2A01G399000 chr7A 98.165 436 7 1 1 436 701880255 701879821 0.000000e+00 760.0
28 TraesCS2A01G399000 chr7A 96.188 446 12 5 471 915 701879822 701879381 0.000000e+00 725.0
29 TraesCS2A01G399000 chr7A 95.694 209 7 1 709 915 701883962 701884170 9.860000e-88 335.0
30 TraesCS2A01G399000 chr7A 89.474 133 13 1 4907 5038 65461566 65461698 3.810000e-37 167.0
31 TraesCS2A01G399000 chr7A 81.967 122 20 2 6014 6134 556299832 556299712 1.090000e-17 102.0
32 TraesCS2A01G399000 chr1A 80.677 502 62 16 4912 5410 551490221 551490690 2.100000e-94 357.0
33 TraesCS2A01G399000 chr6D 78.431 255 45 9 5886 6135 427568677 427568926 2.290000e-34 158.0
34 TraesCS2A01G399000 chr6A 82.114 123 20 2 6013 6134 156751569 156751690 3.030000e-18 104.0
35 TraesCS2A01G399000 chr7B 81.967 122 20 2 6014 6134 517394351 517394231 1.090000e-17 102.0
36 TraesCS2A01G399000 chr4D 73.864 264 51 15 5886 6138 387756775 387756519 8.470000e-14 89.8


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 TraesCS2A01G399000 chr2A 652290011 652296148 6137 True 11335.000000 11335 100.000000 1 6138 1 chr2A.!!$R2 6137
1 TraesCS2A01G399000 chr2A 595347135 595347682 547 True 418.000000 418 81.149000 1 534 1 chr2A.!!$R1 533
2 TraesCS2A01G399000 chr2D 507751054 507756186 5132 True 2688.000000 5834 95.036000 916 6138 3 chr2D.!!$R1 5222
3 TraesCS2A01G399000 chr2B 596412058 596417811 5753 True 985.714286 3404 91.258857 916 6138 7 chr2B.!!$R1 5222
4 TraesCS2A01G399000 chr6B 707282097 707283011 914 False 1657.000000 1657 99.344000 1 915 1 chr6B.!!$F1 914
5 TraesCS2A01G399000 chr1B 511440776 511441690 914 False 1657.000000 1657 99.344000 1 915 1 chr1B.!!$F2 914
6 TraesCS2A01G399000 chr1B 328267978 328268887 909 False 1485.000000 1485 96.070000 1 915 1 chr1B.!!$F1 914
7 TraesCS2A01G399000 chr1D 438035924 438036486 562 False 928.000000 928 96.448000 1 562 1 chr1D.!!$F1 561
8 TraesCS2A01G399000 chr7D 17371776 17372338 562 True 911.000000 911 95.915000 1 562 1 chr7D.!!$R1 561
9 TraesCS2A01G399000 chr7D 87242075 87242699 624 False 612.000000 612 84.478000 188 848 1 chr7D.!!$F1 660
10 TraesCS2A01G399000 chr7D 78265050 78266184 1134 True 445.233333 800 92.448000 1 915 3 chr7D.!!$R3 914
11 TraesCS2A01G399000 chr7A 701879381 701880255 874 True 742.500000 760 97.176500 1 915 2 chr7A.!!$R2 914

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
117 121 1.093159 CCTCTTGCACCAGAAGATGC 58.907 55.0 0.00 0.0 42.40 3.91 F
1342 1641 0.106918 TTCCTCGTGTTTTGCAGGGT 60.107 50.0 0.00 0.0 34.05 4.34 F
1387 1686 0.322008 GCTTCCCAGACAACTCAGGG 60.322 60.0 0.00 0.0 43.44 4.45 F
2225 2898 0.995675 ATCCAGAACCCCATCCCCAG 60.996 60.0 0.00 0.0 0.00 4.45 F
3079 3835 3.003480 GTGGAGTGTAGAAATCAGTGCC 58.997 50.0 0.00 0.0 0.00 5.01 F
4731 5840 0.244721 GAATTTGAGCACTGGTGGGC 59.755 55.0 2.84 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2238 0.322975 CACAGCAGTTAGGGAGCAGT 59.677 55.000 0.0 0.0 0.00 4.40 R
2757 3513 1.206115 GAAAAGGCACGCACAAACGG 61.206 55.000 0.0 0.0 37.37 4.44 R
3253 4073 4.081406 ACTAAACATGCCAGCAATCAGAA 58.919 39.130 0.0 0.0 0.00 3.02 R
3576 4396 3.730715 GCATAATTTATCAACCGCTGCAC 59.269 43.478 0.0 0.0 0.00 4.57 R
4892 6001 0.178992 TCACCAAGGGGCTGTTTCAG 60.179 55.000 0.0 0.0 37.90 3.02 R
5988 7098 0.665369 GTCCACGACAACACCTACCG 60.665 60.000 0.0 0.0 32.09 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
117 121 1.093159 CCTCTTGCACCAGAAGATGC 58.907 55.000 0.00 0.00 42.40 3.91
761 1057 4.321675 GGAGGGTGTAATTGCAAAAATCGT 60.322 41.667 1.71 0.00 0.00 3.73
922 1218 4.214545 TGGGTGTATTTTACTCAACTTGCG 59.785 41.667 0.00 0.00 0.00 4.85
926 1222 6.913673 GGTGTATTTTACTCAACTTGCGAAAA 59.086 34.615 0.00 0.00 0.00 2.29
997 1293 1.142870 AGTACAAAAGGCAGAGGCACA 59.857 47.619 0.00 0.00 43.71 4.57
1081 1377 4.150454 CCGCCCTCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1082 1378 2.520741 CGCCCTCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1083 1379 2.123033 GCCCTCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1171 1470 2.124693 GCCTCCTCGTCCTCCTCTG 61.125 68.421 0.00 0.00 0.00 3.35
1269 1568 1.060465 GCCGCGTCCTTTTTCGATC 59.940 57.895 4.92 0.00 0.00 3.69
1273 1572 0.645868 GCGTCCTTTTTCGATCTCCG 59.354 55.000 0.00 0.00 40.25 4.63
1278 1577 3.245519 GTCCTTTTTCGATCTCCGTATGC 59.754 47.826 0.00 0.00 39.75 3.14
1342 1641 0.106918 TTCCTCGTGTTTTGCAGGGT 60.107 50.000 0.00 0.00 34.05 4.34
1376 1675 0.741221 GCTCACGGTAAGCTTCCCAG 60.741 60.000 8.97 3.86 36.80 4.45
1387 1686 0.322008 GCTTCCCAGACAACTCAGGG 60.322 60.000 0.00 0.00 43.44 4.45
1406 1705 4.453136 CAGGGCATCATTTTGTTTTCCTTG 59.547 41.667 0.00 0.00 0.00 3.61
1433 1732 3.052869 TCTGGCTGTGATTCTACTAGGGA 60.053 47.826 0.00 0.00 0.00 4.20
1448 1747 7.601942 TCTACTAGGGAAGGAAGATAATTGGA 58.398 38.462 0.00 0.00 0.00 3.53
1454 1753 3.214696 AGGAAGATAATTGGAAGGGCG 57.785 47.619 0.00 0.00 0.00 6.13
1457 1756 3.066760 GGAAGATAATTGGAAGGGCGTTG 59.933 47.826 0.00 0.00 0.00 4.10
1458 1757 3.366052 AGATAATTGGAAGGGCGTTGT 57.634 42.857 0.00 0.00 0.00 3.32
1474 1773 6.097839 AGGGCGTTGTTAGTTATTGAGAGATA 59.902 38.462 0.00 0.00 0.00 1.98
1476 1775 7.042658 GGGCGTTGTTAGTTATTGAGAGATAAG 60.043 40.741 0.00 0.00 0.00 1.73
1477 1776 7.705325 GGCGTTGTTAGTTATTGAGAGATAAGA 59.295 37.037 0.00 0.00 0.00 2.10
1478 1777 9.084164 GCGTTGTTAGTTATTGAGAGATAAGAA 57.916 33.333 0.00 0.00 0.00 2.52
1500 1805 5.733620 AACTGATTCAATTGGTGCTTGAT 57.266 34.783 5.42 0.00 32.94 2.57
1551 1863 8.739972 CATTGCTCTAGGTTTAAATTAGTTGGT 58.260 33.333 0.00 0.00 0.00 3.67
1553 1865 7.455058 TGCTCTAGGTTTAAATTAGTTGGTCA 58.545 34.615 0.00 0.00 0.00 4.02
1595 1907 2.495669 CGATGCCCAATTAGGTTTGGTT 59.504 45.455 2.81 0.00 43.92 3.67
1610 1922 1.236616 TGGTTCGATGGCTGCTGTTG 61.237 55.000 0.00 0.00 0.00 3.33
1611 1923 1.237285 GGTTCGATGGCTGCTGTTGT 61.237 55.000 0.00 0.00 0.00 3.32
1625 2039 5.193663 TGCTGTTGTTTAGCTTTATTGCA 57.806 34.783 0.00 0.00 41.66 4.08
1709 2123 4.919774 TGGCTAAATTGGGAGTTACAGA 57.080 40.909 0.00 0.00 0.00 3.41
1715 2129 6.481644 GCTAAATTGGGAGTTACAGAGATCAG 59.518 42.308 0.00 0.00 0.00 2.90
1744 2158 6.771076 TGATTTAGCTATTAGTGTGTTTGCG 58.229 36.000 0.00 0.00 0.00 4.85
1751 2165 5.856455 GCTATTAGTGTGTTTGCGTCAAAAT 59.144 36.000 6.59 0.00 35.03 1.82
1814 2228 3.560068 GCGGAGGTTTGATGTATTAGGTG 59.440 47.826 0.00 0.00 0.00 4.00
1824 2238 8.956426 GTTTGATGTATTAGGTGATCAAAAGGA 58.044 33.333 0.00 0.00 43.11 3.36
1825 2239 8.506168 TTGATGTATTAGGTGATCAAAAGGAC 57.494 34.615 0.00 0.00 33.05 3.85
1826 2240 7.861629 TGATGTATTAGGTGATCAAAAGGACT 58.138 34.615 0.00 0.00 0.00 3.85
1827 2241 7.770433 TGATGTATTAGGTGATCAAAAGGACTG 59.230 37.037 0.00 0.00 0.00 3.51
1828 2242 5.880332 TGTATTAGGTGATCAAAAGGACTGC 59.120 40.000 0.00 0.00 0.00 4.40
1829 2243 4.640771 TTAGGTGATCAAAAGGACTGCT 57.359 40.909 0.00 0.00 0.00 4.24
1830 2244 3.064900 AGGTGATCAAAAGGACTGCTC 57.935 47.619 0.00 0.00 0.00 4.26
1831 2245 2.087646 GGTGATCAAAAGGACTGCTCC 58.912 52.381 0.00 0.00 36.71 4.70
1832 2246 2.087646 GTGATCAAAAGGACTGCTCCC 58.912 52.381 0.00 0.00 37.25 4.30
1833 2247 1.988107 TGATCAAAAGGACTGCTCCCT 59.012 47.619 0.00 0.00 37.25 4.20
1834 2248 3.055094 GTGATCAAAAGGACTGCTCCCTA 60.055 47.826 0.00 0.00 37.25 3.53
1903 2317 8.474710 AATGATCTGCCAAAGCTTAGATAATT 57.525 30.769 11.53 11.53 40.80 1.40
1904 2318 9.578576 AATGATCTGCCAAAGCTTAGATAATTA 57.421 29.630 14.29 0.00 33.66 1.40
1905 2319 8.978874 TGATCTGCCAAAGCTTAGATAATTAA 57.021 30.769 9.02 0.00 40.80 1.40
1906 2320 9.578576 TGATCTGCCAAAGCTTAGATAATTAAT 57.421 29.630 9.02 0.00 40.80 1.40
1929 2343 6.852420 TTTATAGATATCGAAGGACCAGGG 57.148 41.667 0.00 0.00 0.00 4.45
1977 2391 9.456147 GAGCTATTCTCTCTCATACCAACTATA 57.544 37.037 0.00 0.00 38.78 1.31
2072 2486 5.820947 CAGTACAGAAAGTTGGGTAAAGTGT 59.179 40.000 0.00 0.00 0.00 3.55
2101 2515 9.150348 GGGCATTTTAAATGGATAAATATTCCG 57.850 33.333 17.89 0.00 0.00 4.30
2171 2844 5.466058 CCACTTAACAAAATGCAGCAAATGA 59.534 36.000 0.00 0.00 0.00 2.57
2225 2898 0.995675 ATCCAGAACCCCATCCCCAG 60.996 60.000 0.00 0.00 0.00 4.45
2251 2924 6.198403 GGTTTCCGTTTTGAATTTCTTGAGAC 59.802 38.462 0.00 0.00 0.00 3.36
2446 3195 7.601508 ACTTAGGAAATTAGTTGTACTGTTCGG 59.398 37.037 0.00 0.00 0.00 4.30
2457 3206 3.382227 TGTACTGTTCGGAAACTCACTCA 59.618 43.478 0.00 0.00 36.30 3.41
2598 3351 4.614284 GCACATTTCTTTGAGATGTCGTTG 59.386 41.667 1.50 0.00 35.63 4.10
3025 3781 7.721402 AGTCTTTCATATCAGCCTACTAACAG 58.279 38.462 0.00 0.00 0.00 3.16
3079 3835 3.003480 GTGGAGTGTAGAAATCAGTGCC 58.997 50.000 0.00 0.00 0.00 5.01
3091 3847 9.045223 GTAGAAATCAGTGCCTTTTGAATTTTT 57.955 29.630 0.00 0.00 0.00 1.94
3129 3885 3.259876 TCCTACGACTGTGTAGCCATTTT 59.740 43.478 10.16 0.00 40.40 1.82
3253 4073 8.087303 TGGCAAATGCTATCATAGATCTATCT 57.913 34.615 12.50 5.99 41.70 1.98
3576 4396 6.281405 AGGTAATATTCCAACGCTTAGTCAG 58.719 40.000 0.00 0.00 0.00 3.51
3598 4418 3.730715 GTGCAGCGGTTGATAAATTATGC 59.269 43.478 0.00 0.00 0.00 3.14
3807 4872 5.117745 CACATTACGTCTTCTCTGACAGTTG 59.882 44.000 1.59 0.00 36.82 3.16
3920 4985 4.261825 GCGCTGTCTATCTCTGTTTCCTAT 60.262 45.833 0.00 0.00 0.00 2.57
4307 5381 9.575783 TTTGAAACCTGTATCACTTTTGTTTAC 57.424 29.630 0.00 0.00 0.00 2.01
4313 5387 9.623000 ACCTGTATCACTTTTGTTTACTAAAGT 57.377 29.630 13.97 13.97 47.00 2.66
4382 5465 6.569179 TCTGTTATGTTTCCTTTTACAGGC 57.431 37.500 0.00 0.00 43.55 4.85
4412 5495 0.608035 TCCACGGCCAAAATCACCTC 60.608 55.000 2.24 0.00 0.00 3.85
4496 5603 6.573664 TGACCAGATTCACCAAACTAAATG 57.426 37.500 0.00 0.00 0.00 2.32
4577 5686 4.058124 TGTGCTGTCAGAACATAACAGAC 58.942 43.478 9.82 0.00 42.37 3.51
4624 5733 4.564769 CCTCACTTCTTTCGTTAGATCTGC 59.435 45.833 5.18 0.00 0.00 4.26
4689 5798 1.888512 GATTGCAAAGTGAAGGCCAGA 59.111 47.619 5.01 0.00 0.00 3.86
4731 5840 0.244721 GAATTTGAGCACTGGTGGGC 59.755 55.000 2.84 0.00 0.00 5.36
4753 5862 2.897326 AGTAACCATCCTGTTTTTGCCC 59.103 45.455 0.00 0.00 0.00 5.36
4754 5863 1.799933 AACCATCCTGTTTTTGCCCA 58.200 45.000 0.00 0.00 0.00 5.36
4755 5864 1.341080 ACCATCCTGTTTTTGCCCAG 58.659 50.000 0.00 0.00 0.00 4.45
4783 5892 9.151471 TGTTCGATCCTTTAAATTGTTCTCTAG 57.849 33.333 0.00 0.00 0.00 2.43
4808 5917 4.515361 TCGTTGGTAAAACTGAAAGACCA 58.485 39.130 0.00 0.00 35.56 4.02
4809 5918 4.333372 TCGTTGGTAAAACTGAAAGACCAC 59.667 41.667 0.00 0.00 36.91 4.16
4820 5929 5.123936 ACTGAAAGACCACCTTCACTTAAC 58.876 41.667 0.00 0.00 37.43 2.01
4886 5995 4.439700 GCAGCAAGTTAAGATGACATGCAT 60.440 41.667 0.00 0.00 42.39 3.96
4936 6045 2.167487 GGGAACACTAGAAGCTGGAGAG 59.833 54.545 0.00 0.00 0.00 3.20
4939 6048 4.161377 GGAACACTAGAAGCTGGAGAGAAT 59.839 45.833 0.00 0.00 0.00 2.40
5167 6276 4.966005 GGAGTTTTCCGCAAAGCC 57.034 55.556 0.00 0.00 32.79 4.35
5281 6391 7.491048 GTGGAATAAAAGCTTGTTTTGAGTTGA 59.509 33.333 0.00 0.00 0.00 3.18
5282 6392 8.037758 TGGAATAAAAGCTTGTTTTGAGTTGAA 58.962 29.630 0.00 0.00 0.00 2.69
5283 6393 8.542953 GGAATAAAAGCTTGTTTTGAGTTGAAG 58.457 33.333 0.00 0.00 0.00 3.02
5284 6394 9.301153 GAATAAAAGCTTGTTTTGAGTTGAAGA 57.699 29.630 0.00 0.00 0.00 2.87
5285 6395 9.822185 AATAAAAGCTTGTTTTGAGTTGAAGAT 57.178 25.926 0.00 0.00 0.00 2.40
5286 6396 9.822185 ATAAAAGCTTGTTTTGAGTTGAAGATT 57.178 25.926 0.00 0.00 0.00 2.40
5287 6397 7.529880 AAAGCTTGTTTTGAGTTGAAGATTG 57.470 32.000 0.00 0.00 0.00 2.67
5292 6402 4.037923 TGTTTTGAGTTGAAGATTGGAGCC 59.962 41.667 0.00 0.00 0.00 4.70
5336 6446 2.105466 GCTACTCCTGTGCTGCTGC 61.105 63.158 8.89 8.89 40.20 5.25
5351 6461 2.046023 TGCCTGCTGCTACGCAAT 60.046 55.556 0.00 0.00 39.80 3.56
5432 6542 3.325870 TCTGACTAATGCAGAACAACGG 58.674 45.455 0.00 0.00 39.29 4.44
5459 6569 6.039616 CAGTACTAGGAGAAAAGCTCACATC 58.960 44.000 0.00 0.00 45.81 3.06
5483 6593 1.985614 CAGCCATGTGAGGACCAGA 59.014 57.895 0.00 0.00 0.00 3.86
5750 6860 1.218316 GGTGAAGACGGCGGAGATT 59.782 57.895 13.24 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 121 2.946346 GCATGGCCAACAACCTGGG 61.946 63.158 10.96 0.00 36.92 4.45
689 966 0.751643 CGTTCCCCATTCCACATCCC 60.752 60.000 0.00 0.00 0.00 3.85
761 1057 1.670295 CGTATTTGCACAGCTGGCATA 59.330 47.619 24.38 20.84 41.58 3.14
922 1218 7.277174 TGGATTGAGAACCTTCTTTCTTTTC 57.723 36.000 0.00 0.00 37.73 2.29
926 1222 5.536538 GGTTTGGATTGAGAACCTTCTTTCT 59.463 40.000 0.00 0.00 39.71 2.52
997 1293 0.611896 CGGAGGAAGCCCACCATTTT 60.612 55.000 0.00 0.00 42.60 1.82
1130 1426 4.824515 ACGCGGAGAGGGAGGGAG 62.825 72.222 12.47 0.00 36.53 4.30
1131 1427 4.377760 AACGCGGAGAGGGAGGGA 62.378 66.667 12.47 0.00 36.53 4.20
1221 1520 4.292178 GGGGCAGAGAGATCGGCG 62.292 72.222 0.00 0.00 0.00 6.46
1262 1561 0.384309 AGCGCATACGGAGATCGAAA 59.616 50.000 11.47 0.00 42.43 3.46
1269 1568 2.202932 AGGCAAGCGCATACGGAG 60.203 61.111 11.47 0.00 41.24 4.63
1278 1577 4.899239 CCCTAGGCGAGGCAAGCG 62.899 72.222 8.32 0.00 45.17 4.68
1376 1675 3.256631 ACAAAATGATGCCCTGAGTTGTC 59.743 43.478 0.00 0.00 0.00 3.18
1387 1686 7.653311 AGACTAACAAGGAAAACAAAATGATGC 59.347 33.333 0.00 0.00 0.00 3.91
1406 1705 5.331876 AGTAGAATCACAGCCAGACTAAC 57.668 43.478 0.00 0.00 0.00 2.34
1433 1732 3.053619 ACGCCCTTCCAATTATCTTCCTT 60.054 43.478 0.00 0.00 0.00 3.36
1448 1747 4.901868 TCTCAATAACTAACAACGCCCTT 58.098 39.130 0.00 0.00 0.00 3.95
1474 1773 5.796424 AGCACCAATTGAATCAGTTTCTT 57.204 34.783 7.12 0.00 35.23 2.52
1476 1775 5.531634 TCAAGCACCAATTGAATCAGTTTC 58.468 37.500 7.12 0.00 33.85 2.78
1477 1776 5.534207 TCAAGCACCAATTGAATCAGTTT 57.466 34.783 7.12 0.00 33.85 2.66
1478 1777 5.733620 ATCAAGCACCAATTGAATCAGTT 57.266 34.783 7.12 0.00 39.92 3.16
1480 1779 6.695713 CACATATCAAGCACCAATTGAATCAG 59.304 38.462 7.12 0.00 39.92 2.90
1481 1780 6.406065 CCACATATCAAGCACCAATTGAATCA 60.406 38.462 7.12 0.00 39.92 2.57
1482 1781 5.981315 CCACATATCAAGCACCAATTGAATC 59.019 40.000 7.12 0.00 39.92 2.52
1483 1782 5.163385 CCCACATATCAAGCACCAATTGAAT 60.163 40.000 7.12 0.00 39.92 2.57
1484 1783 4.160065 CCCACATATCAAGCACCAATTGAA 59.840 41.667 7.12 0.00 39.92 2.69
1500 1805 7.014711 TGTTCTTTTAACTGAATTGCCCACATA 59.985 33.333 0.00 0.00 0.00 2.29
1553 1865 5.393902 CGTTAGAAACAACGTAACCAGTT 57.606 39.130 0.00 0.00 44.77 3.16
1563 1875 3.907894 TTGGGCATCGTTAGAAACAAC 57.092 42.857 0.00 0.00 0.00 3.32
1595 1907 2.076100 CTAAACAACAGCAGCCATCGA 58.924 47.619 0.00 0.00 0.00 3.59
1610 1922 7.962918 CGATATACCCATGCAATAAAGCTAAAC 59.037 37.037 0.00 0.00 34.99 2.01
1611 1923 7.663905 ACGATATACCCATGCAATAAAGCTAAA 59.336 33.333 0.00 0.00 34.99 1.85
1625 2039 6.486657 CCAATGACAGAAAACGATATACCCAT 59.513 38.462 0.00 0.00 0.00 4.00
1709 2123 8.381636 ACTAATAGCTAAATCAATGCCTGATCT 58.618 33.333 0.00 0.00 44.43 2.75
1715 2129 7.264373 ACACACTAATAGCTAAATCAATGCC 57.736 36.000 0.00 0.00 0.00 4.40
1755 2169 9.189156 ACCATTACATTCAACATGCTAATAAGT 57.811 29.630 0.00 0.00 0.00 2.24
1814 2228 2.797177 AGGGAGCAGTCCTTTTGATC 57.203 50.000 0.00 0.00 43.36 2.92
1824 2238 0.322975 CACAGCAGTTAGGGAGCAGT 59.677 55.000 0.00 0.00 0.00 4.40
1825 2239 0.322975 ACACAGCAGTTAGGGAGCAG 59.677 55.000 0.00 0.00 0.00 4.24
1826 2240 0.764890 AACACAGCAGTTAGGGAGCA 59.235 50.000 0.00 0.00 0.00 4.26
1827 2241 1.270839 TGAACACAGCAGTTAGGGAGC 60.271 52.381 0.00 0.00 0.00 4.70
1828 2242 2.037772 AGTGAACACAGCAGTTAGGGAG 59.962 50.000 7.68 0.00 0.00 4.30
1829 2243 2.047061 AGTGAACACAGCAGTTAGGGA 58.953 47.619 7.68 0.00 0.00 4.20
1830 2244 2.550830 AGTGAACACAGCAGTTAGGG 57.449 50.000 7.68 0.00 0.00 3.53
1831 2245 3.496130 CAGAAGTGAACACAGCAGTTAGG 59.504 47.826 7.68 0.00 0.00 2.69
1832 2246 4.122776 ACAGAAGTGAACACAGCAGTTAG 58.877 43.478 7.68 0.00 0.00 2.34
1833 2247 4.137116 ACAGAAGTGAACACAGCAGTTA 57.863 40.909 7.68 0.00 0.00 2.24
1834 2248 2.991250 ACAGAAGTGAACACAGCAGTT 58.009 42.857 7.68 0.00 0.00 3.16
1903 2317 8.978472 CCCTGGTCCTTCGATATCTATAAATTA 58.022 37.037 0.34 0.00 0.00 1.40
1904 2318 7.092846 CCCCTGGTCCTTCGATATCTATAAATT 60.093 40.741 0.34 0.00 0.00 1.82
1905 2319 6.384305 CCCCTGGTCCTTCGATATCTATAAAT 59.616 42.308 0.34 0.00 0.00 1.40
1906 2320 5.720041 CCCCTGGTCCTTCGATATCTATAAA 59.280 44.000 0.34 0.00 0.00 1.40
1907 2321 5.015924 TCCCCTGGTCCTTCGATATCTATAA 59.984 44.000 0.34 0.00 0.00 0.98
1908 2322 4.542931 TCCCCTGGTCCTTCGATATCTATA 59.457 45.833 0.34 0.00 0.00 1.31
1929 2343 0.904394 TTGGGCATTTGGGCTCTTCC 60.904 55.000 0.00 0.00 42.84 3.46
2038 2452 9.981114 CCCAACTTTCTGTACTGAAAATTTAAT 57.019 29.630 23.09 8.13 35.79 1.40
2039 2453 8.973182 ACCCAACTTTCTGTACTGAAAATTTAA 58.027 29.630 23.09 5.94 35.79 1.52
2040 2454 8.528044 ACCCAACTTTCTGTACTGAAAATTTA 57.472 30.769 23.09 6.53 35.79 1.40
2139 2812 5.582665 TGCATTTTGTTAAGTGGGTCAAAAC 59.417 36.000 0.00 0.00 40.72 2.43
2154 2827 7.269316 TCATATCATCATTTGCTGCATTTTGT 58.731 30.769 1.84 0.00 0.00 2.83
2225 2898 5.353111 TCAAGAAATTCAAAACGGAAACCC 58.647 37.500 0.00 0.00 0.00 4.11
2251 2924 2.287668 GGTGTAGCAGTATAGCACCTCG 60.288 54.545 0.00 0.00 44.35 4.63
2446 3195 9.477484 TCTGTAGTTTTATCTTGAGTGAGTTTC 57.523 33.333 0.00 0.00 0.00 2.78
2548 3299 6.020389 CCCTCCTTAATTTTCCCTTGGTAAA 58.980 40.000 0.00 0.00 0.00 2.01
2598 3351 8.538409 AAATAATTGTTTGCACTGAGAAATCC 57.462 30.769 0.00 0.00 0.00 3.01
2645 3401 1.665679 CCACCATGAATTCGGTCTTCG 59.334 52.381 2.32 0.00 40.90 3.79
2757 3513 1.206115 GAAAAGGCACGCACAAACGG 61.206 55.000 0.00 0.00 37.37 4.44
3034 3790 7.223582 CACGACAGAGCATTAGAGATTTTACAT 59.776 37.037 0.00 0.00 0.00 2.29
3091 3847 9.053840 CAGTCGTAGGAATGAAAGTCTAGTATA 57.946 37.037 7.05 0.00 40.59 1.47
3113 3869 5.629079 AAGCTAAAAATGGCTACACAGTC 57.371 39.130 0.00 0.00 37.87 3.51
3129 3885 7.402862 AGAAGCTATTTAAGGACCAAAGCTAA 58.597 34.615 0.00 0.00 0.00 3.09
3253 4073 4.081406 ACTAAACATGCCAGCAATCAGAA 58.919 39.130 0.00 0.00 0.00 3.02
3544 4364 6.929606 AGCGTTGGAATATTACCTTATCAGAC 59.070 38.462 0.00 0.00 0.00 3.51
3576 4396 3.730715 GCATAATTTATCAACCGCTGCAC 59.269 43.478 0.00 0.00 0.00 4.57
3598 4418 8.108999 TCCATTTATCCCATGTTATCATAGGTG 58.891 37.037 0.00 0.00 35.04 4.00
3807 4872 4.272018 GCGATTGCATGAGATATGGGATAC 59.728 45.833 0.00 0.00 42.15 2.24
3920 4985 4.785914 TGAAAATAGACACCAGGGACCATA 59.214 41.667 0.00 0.00 0.00 2.74
4311 5385 0.617413 CCAGAGCCCAAGTGATCACT 59.383 55.000 22.89 22.89 44.94 3.41
4312 5386 0.615331 TCCAGAGCCCAAGTGATCAC 59.385 55.000 18.47 18.47 0.00 3.06
4313 5387 0.907486 CTCCAGAGCCCAAGTGATCA 59.093 55.000 0.00 0.00 0.00 2.92
4398 5481 2.222227 AGGAAGAGGTGATTTTGGCC 57.778 50.000 0.00 0.00 0.00 5.36
4496 5603 3.504863 CAGTGTGTCAATATTTGCAGCC 58.495 45.455 0.00 0.00 0.00 4.85
4577 5686 4.756642 TGAGCTACAGTTGTTCAATTCTGG 59.243 41.667 0.00 0.00 32.92 3.86
4644 5753 6.748333 ACTGTCATTTTCACCAGATGTATG 57.252 37.500 0.00 0.00 0.00 2.39
4648 5757 5.694231 TCAACTGTCATTTTCACCAGATG 57.306 39.130 0.00 0.00 0.00 2.90
4689 5798 7.117285 TCATCAAATCTCAGCTACACATACT 57.883 36.000 0.00 0.00 0.00 2.12
4753 5862 6.254281 ACAATTTAAAGGATCGAACACCTG 57.746 37.500 9.35 0.94 36.56 4.00
4754 5863 6.715264 AGAACAATTTAAAGGATCGAACACCT 59.285 34.615 0.00 0.00 38.23 4.00
4755 5864 6.909909 AGAACAATTTAAAGGATCGAACACC 58.090 36.000 0.00 0.00 0.00 4.16
4783 5892 6.140786 GGTCTTTCAGTTTTACCAACGATTC 58.859 40.000 0.00 0.00 0.00 2.52
4808 5917 6.485313 TGTCGAAATCAATGTTAAGTGAAGGT 59.515 34.615 0.00 0.00 33.43 3.50
4809 5918 6.898041 TGTCGAAATCAATGTTAAGTGAAGG 58.102 36.000 0.00 0.00 33.43 3.46
4820 5929 6.228273 ACAACAGTACTGTCGAAATCAATG 57.772 37.500 28.04 20.09 44.13 2.82
4892 6001 0.178992 TCACCAAGGGGCTGTTTCAG 60.179 55.000 0.00 0.00 37.90 3.02
4936 6045 3.157087 TGAAAACTGGGCTTCTCCATTC 58.843 45.455 0.00 0.00 36.05 2.67
4939 6048 1.202927 CCTGAAAACTGGGCTTCTCCA 60.203 52.381 0.00 0.00 36.21 3.86
5172 6281 4.155280 GTGTGTGTACAACATATTGGGGTC 59.845 45.833 0.00 0.00 41.97 4.46
5281 6391 2.957402 TGTTGTGAGGCTCCAATCTT 57.043 45.000 12.86 0.00 0.00 2.40
5282 6392 2.575279 AGATGTTGTGAGGCTCCAATCT 59.425 45.455 12.86 12.49 0.00 2.40
5283 6393 2.996631 AGATGTTGTGAGGCTCCAATC 58.003 47.619 12.86 10.66 0.00 2.67
5284 6394 3.446442 AAGATGTTGTGAGGCTCCAAT 57.554 42.857 12.86 2.15 0.00 3.16
5285 6395 2.957402 AAGATGTTGTGAGGCTCCAA 57.043 45.000 12.86 12.64 0.00 3.53
5286 6396 2.373169 AGAAAGATGTTGTGAGGCTCCA 59.627 45.455 12.86 6.82 0.00 3.86
5287 6397 3.064900 AGAAAGATGTTGTGAGGCTCC 57.935 47.619 12.86 4.00 0.00 4.70
5292 6402 2.160417 GCCGGAAGAAAGATGTTGTGAG 59.840 50.000 5.05 0.00 0.00 3.51
5351 6461 3.938963 GGTAAGCGAGGTTGATGAATCAA 59.061 43.478 1.55 1.55 43.94 2.57
5432 6542 6.072064 TGTGAGCTTTTCTCCTAGTACTGTAC 60.072 42.308 9.93 9.93 41.18 2.90
5483 6593 2.754658 CACGTAGTCCGGAGCCCT 60.755 66.667 3.06 0.09 41.61 5.19
5750 6860 2.642254 CGACCTCAACTACCCGGCA 61.642 63.158 0.00 0.00 0.00 5.69
5836 6946 2.355837 GCACGCAGAACCTGACGA 60.356 61.111 14.20 0.00 35.69 4.20
5988 7098 0.665369 GTCCACGACAACACCTACCG 60.665 60.000 0.00 0.00 32.09 4.02


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

AutoCloner maintained by Alex Coulton.