Multiple sequence alignment - TraesCS3B01G595000

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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 TraesCS3B01G595000 chr3B 100.000 3353 0 0 1 3353 818159703 818156351 0.000000e+00 6192.0
1 TraesCS3B01G595000 chr3B 84.236 1827 207 34 984 2764 818319431 818321222 0.000000e+00 1703.0
2 TraesCS3B01G595000 chr3A 85.195 1844 221 27 984 2787 740928058 740929889 0.000000e+00 1845.0
3 TraesCS3B01G595000 chr3A 95.422 415 19 0 2133 2547 740404118 740403704 0.000000e+00 662.0
4 TraesCS3B01G595000 chr3A 92.806 417 27 3 2938 3353 740397854 740397440 4.790000e-168 601.0
5 TraesCS3B01G595000 chr3A 94.056 286 14 2 2535 2818 740402244 740401960 6.650000e-117 431.0
6 TraesCS3B01G595000 chr3A 96.350 137 4 1 2811 2946 740400829 740400693 1.210000e-54 224.0
7 TraesCS3B01G595000 chr3D 84.875 1838 212 33 984 2785 608333833 608332026 0.000000e+00 1794.0
8 TraesCS3B01G595000 chr3D 93.341 886 38 8 2471 3353 608209947 608209080 0.000000e+00 1290.0
9 TraesCS3B01G595000 chr3D 83.122 1185 141 30 1635 2785 608350950 608349791 0.000000e+00 1026.0
10 TraesCS3B01G595000 chr3D 86.320 519 65 6 984 1500 608422903 608423417 8.120000e-156 560.0
11 TraesCS3B01G595000 chr3D 86.321 424 52 4 1897 2314 608423780 608424203 1.100000e-124 457.0
12 TraesCS3B01G595000 chr3D 82.258 372 44 6 1540 1911 608423415 608423764 5.440000e-78 302.0
13 TraesCS3B01G595000 chr3D 95.082 61 3 0 2988 3048 608425633 608425693 2.750000e-16 97.1
14 TraesCS3B01G595000 chr6B 90.900 978 88 1 1 978 246666317 246667293 0.000000e+00 1312.0
15 TraesCS3B01G595000 chrUn 90.798 978 89 1 1 978 190881136 190882112 0.000000e+00 1306.0
16 TraesCS3B01G595000 chrUn 89.831 708 72 0 1 708 155412905 155413612 0.000000e+00 909.0
17 TraesCS3B01G595000 chrUn 89.831 708 72 0 1 708 424608891 424608184 0.000000e+00 909.0
18 TraesCS3B01G595000 chr4B 89.195 981 101 4 1 980 585733624 585732648 0.000000e+00 1219.0
19 TraesCS3B01G595000 chr7D 87.984 982 115 3 1 981 25381179 25382158 0.000000e+00 1157.0
20 TraesCS3B01G595000 chr2B 87.678 982 116 3 1 978 741520376 741521356 0.000000e+00 1138.0
21 TraesCS3B01G595000 chr2D 87.360 981 119 5 3 981 209116177 209117154 0.000000e+00 1120.0
22 TraesCS3B01G595000 chr7A 80.041 982 186 9 1 978 33490196 33491171 0.000000e+00 719.0


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 TraesCS3B01G595000 chr3B 818156351 818159703 3352 True 6192.000 6192 100.00000 1 3353 1 chr3B.!!$R1 3352
1 TraesCS3B01G595000 chr3B 818319431 818321222 1791 False 1703.000 1703 84.23600 984 2764 1 chr3B.!!$F1 1780
2 TraesCS3B01G595000 chr3A 740928058 740929889 1831 False 1845.000 1845 85.19500 984 2787 1 chr3A.!!$F1 1803
3 TraesCS3B01G595000 chr3A 740397440 740404118 6678 True 479.500 662 94.65850 2133 3353 4 chr3A.!!$R1 1220
4 TraesCS3B01G595000 chr3D 608332026 608333833 1807 True 1794.000 1794 84.87500 984 2785 1 chr3D.!!$R2 1801
5 TraesCS3B01G595000 chr3D 608209080 608209947 867 True 1290.000 1290 93.34100 2471 3353 1 chr3D.!!$R1 882
6 TraesCS3B01G595000 chr3D 608349791 608350950 1159 True 1026.000 1026 83.12200 1635 2785 1 chr3D.!!$R3 1150
7 TraesCS3B01G595000 chr3D 608422903 608425693 2790 False 354.025 560 87.49525 984 3048 4 chr3D.!!$F1 2064
8 TraesCS3B01G595000 chr6B 246666317 246667293 976 False 1312.000 1312 90.90000 1 978 1 chr6B.!!$F1 977
9 TraesCS3B01G595000 chrUn 190881136 190882112 976 False 1306.000 1306 90.79800 1 978 1 chrUn.!!$F2 977
10 TraesCS3B01G595000 chrUn 155412905 155413612 707 False 909.000 909 89.83100 1 708 1 chrUn.!!$F1 707
11 TraesCS3B01G595000 chrUn 424608184 424608891 707 True 909.000 909 89.83100 1 708 1 chrUn.!!$R1 707
12 TraesCS3B01G595000 chr4B 585732648 585733624 976 True 1219.000 1219 89.19500 1 980 1 chr4B.!!$R1 979
13 TraesCS3B01G595000 chr7D 25381179 25382158 979 False 1157.000 1157 87.98400 1 981 1 chr7D.!!$F1 980
14 TraesCS3B01G595000 chr2B 741520376 741521356 980 False 1138.000 1138 87.67800 1 978 1 chr2B.!!$F1 977
15 TraesCS3B01G595000 chr2D 209116177 209117154 977 False 1120.000 1120 87.36000 3 981 1 chr2D.!!$F1 978
16 TraesCS3B01G595000 chr7A 33490196 33491171 975 False 719.000 719 80.04100 1 978 1 chr7A.!!$F1 977

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
756 760 0.033796 ATCTGTGCTGGGTCCAATGG 60.034 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 2486 0.250234 CCATGCTCACCTCGAGGAAA 59.75 55.0 37.69 22.25 46.21 3.13 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
27 28 2.333688 GGTTCATACCTGGAGGCTTC 57.666 55.000 0.00 0.00 41.53 3.86
77 78 6.418226 CGGAACTACATCGAAGAAGGATTAAG 59.582 42.308 0.00 0.00 43.58 1.85
89 90 4.104897 AGAAGGATTAAGCCAGGGGTATTC 59.895 45.833 13.21 5.10 0.00 1.75
149 150 3.359950 GTTTTGGAGATGCCCTCATTCT 58.640 45.455 5.71 0.00 43.76 2.40
188 189 0.541063 TGCACTCGGAACTGGGAGTA 60.541 55.000 0.00 0.00 41.37 2.59
238 239 2.098934 ACTCTCAGAGTGCATTAGCTCG 59.901 50.000 6.50 0.00 41.76 5.03
263 264 3.347077 CTCCTGAGCTGGTTTGAAGAT 57.653 47.619 0.00 0.00 0.00 2.40
278 279 3.673902 TGAAGATGCAACGGAAGATGAA 58.326 40.909 0.00 0.00 35.71 2.57
285 286 1.394917 CAACGGAAGATGAAAGAGCGG 59.605 52.381 0.00 0.00 35.71 5.52
302 303 1.451028 GGTCATGGTGCAGAGCCTC 60.451 63.158 0.00 0.00 0.00 4.70
305 306 1.415659 GTCATGGTGCAGAGCCTCTAT 59.584 52.381 0.00 0.00 0.00 1.98
315 316 2.636893 CAGAGCCTCTATGCCTTATGGT 59.363 50.000 0.00 0.00 35.27 3.55
332 333 0.167251 GGTTGGCACGGAATAACACG 59.833 55.000 0.00 0.00 0.00 4.49
356 357 4.202172 CGGGAGGGAAAGAAGATAGAAGAC 60.202 50.000 0.00 0.00 0.00 3.01
362 363 1.394618 AGAAGATAGAAGACGCGGCT 58.605 50.000 9.84 9.84 0.00 5.52
365 366 0.665835 AGATAGAAGACGCGGCTGAG 59.334 55.000 19.28 0.00 0.00 3.35
398 399 1.064946 GCGACGACTCATGGAGGAG 59.935 63.158 0.00 0.00 40.79 3.69
405 406 0.546267 ACTCATGGAGGAGTGGCAGT 60.546 55.000 0.00 0.00 46.02 4.40
407 408 0.252421 TCATGGAGGAGTGGCAGTCT 60.252 55.000 20.97 7.99 0.00 3.24
410 411 3.117131 TCATGGAGGAGTGGCAGTCTATA 60.117 47.826 20.97 6.88 0.00 1.31
433 434 1.466851 GGCAAGGCAAGCAAAGTCCT 61.467 55.000 3.65 0.00 0.00 3.85
437 438 2.653115 GCAAGCAAAGTCCTGGCC 59.347 61.111 0.00 0.00 0.00 5.36
444 445 1.841556 AAAGTCCTGGCCGAGGTCA 60.842 57.895 17.55 0.00 43.37 4.02
476 477 0.533085 GGAGCACTCCGGATTTAGGC 60.533 60.000 3.57 4.64 40.36 3.93
491 492 2.180159 TAGGCTGGGTCAAGGCGAAC 62.180 60.000 0.00 0.00 46.86 3.95
557 558 1.067776 GTGGTCTTCAGGAACGACGAT 60.068 52.381 0.00 0.00 33.55 3.73
566 567 1.066143 AGGAACGACGATGGAGCATTT 60.066 47.619 0.00 0.00 0.00 2.32
569 570 2.386661 ACGACGATGGAGCATTTCTT 57.613 45.000 0.00 0.00 0.00 2.52
588 589 2.133281 TGGAGCTGCATGCAATTACT 57.867 45.000 22.88 16.01 45.94 2.24
626 630 1.891150 CCACAGAAAATGGAGCTGCTT 59.109 47.619 6.82 0.00 39.87 3.91
657 661 2.185350 CGGCAGAACTCGCAGGAT 59.815 61.111 0.00 0.00 0.00 3.24
683 687 8.654485 TTTTTCATATATCCAGCCTGCATATT 57.346 30.769 0.00 0.00 0.00 1.28
756 760 0.033796 ATCTGTGCTGGGTCCAATGG 60.034 55.000 0.00 0.00 0.00 3.16
762 766 1.598701 GCTGGGTCCAATGGTCAAGC 61.599 60.000 0.00 4.16 0.00 4.01
787 791 1.672881 GAAGGCTATGCTCGCAAACAT 59.327 47.619 0.00 0.00 0.00 2.71
791 795 3.070018 GGCTATGCTCGCAAACATAGAT 58.930 45.455 16.80 0.00 45.65 1.98
879 883 6.405842 GGGGGTAACAAATAATCTGAGCAAAG 60.406 42.308 0.00 0.00 39.74 2.77
881 885 7.029563 GGGTAACAAATAATCTGAGCAAAGTG 58.970 38.462 0.00 0.00 39.74 3.16
952 956 9.921637 AGAAATTCCTGCGTTTTATGAATAAAA 57.078 25.926 4.48 4.48 39.24 1.52
1111 1115 1.376683 GCCGTGTGTAAGCCATGGA 60.377 57.895 18.40 0.00 40.75 3.41
1134 1138 1.176619 ACTCACACGGACCATCGACA 61.177 55.000 0.00 0.00 0.00 4.35
1264 1271 1.276138 CGCCCATATCTGATGGCAGTA 59.724 52.381 15.30 0.00 44.22 2.74
1275 1282 0.762842 ATGGCAGTAGCACCGGGATA 60.763 55.000 6.32 0.00 44.61 2.59
1278 1285 1.202770 GGCAGTAGCACCGGGATAAAT 60.203 52.381 6.32 0.00 44.61 1.40
1344 1351 4.589675 GAACCCCACGGCCCAACA 62.590 66.667 0.00 0.00 0.00 3.33
1345 1352 3.879180 GAACCCCACGGCCCAACAT 62.879 63.158 0.00 0.00 0.00 2.71
1348 1355 2.035626 CCCACGGCCCAACATTCT 59.964 61.111 0.00 0.00 0.00 2.40
1387 1394 4.366684 CCCCCACCCACCTGCTTC 62.367 72.222 0.00 0.00 0.00 3.86
1388 1395 4.366684 CCCCACCCACCTGCTTCC 62.367 72.222 0.00 0.00 0.00 3.46
1389 1396 3.260100 CCCACCCACCTGCTTCCT 61.260 66.667 0.00 0.00 0.00 3.36
1391 1398 2.034687 CACCCACCTGCTTCCTGG 59.965 66.667 0.00 0.00 36.24 4.45
1392 1399 2.450502 ACCCACCTGCTTCCTGGT 60.451 61.111 0.00 0.00 43.26 4.00
1394 1401 0.550147 ACCCACCTGCTTCCTGGTAT 60.550 55.000 0.00 0.00 40.86 2.73
1396 1403 1.207791 CCACCTGCTTCCTGGTATCT 58.792 55.000 0.00 0.00 40.86 1.98
1397 1404 1.139853 CCACCTGCTTCCTGGTATCTC 59.860 57.143 0.00 0.00 40.86 2.75
1398 1405 1.833630 CACCTGCTTCCTGGTATCTCA 59.166 52.381 0.00 0.00 40.86 3.27
1450 1457 2.997075 ATCTACAACGACGGCGCCA 61.997 57.895 28.98 1.99 42.48 5.69
1460 1467 2.125310 CGGCGCCATCCTTGTGTA 60.125 61.111 28.98 0.00 0.00 2.90
1469 1476 3.149196 CCATCCTTGTGTACAGCAAACT 58.851 45.455 0.00 0.00 0.00 2.66
1487 1494 1.002430 ACTGGACAGCATCGACACATT 59.998 47.619 0.00 0.00 0.00 2.71
1573 1580 2.443390 TCGAATCCCCCTCCGACC 60.443 66.667 0.00 0.00 0.00 4.79
1574 1581 2.762459 CGAATCCCCCTCCGACCA 60.762 66.667 0.00 0.00 0.00 4.02
1599 1606 2.647529 TCTGTGTCGCGTATCACAAT 57.352 45.000 24.40 0.00 42.67 2.71
1624 1631 2.179427 AGATCCATGTGACCGTTGAGA 58.821 47.619 0.00 0.00 0.00 3.27
1655 1662 2.354188 CGTTGTGAGCGTGACCGA 60.354 61.111 0.00 0.00 35.63 4.69
1657 1664 2.355837 TTGTGAGCGTGACCGAGC 60.356 61.111 0.00 0.00 35.63 5.03
1660 1667 4.724602 TGAGCGTGACCGAGCAGC 62.725 66.667 0.00 0.00 35.63 5.25
1697 1704 1.738099 GCGACGATGTGCTGGTTCT 60.738 57.895 0.00 0.00 0.00 3.01
1703 1710 1.406069 CGATGTGCTGGTTCTTAGGCT 60.406 52.381 0.00 0.00 0.00 4.58
1705 1712 3.493350 CGATGTGCTGGTTCTTAGGCTAT 60.493 47.826 0.00 0.00 0.00 2.97
1706 1713 3.543680 TGTGCTGGTTCTTAGGCTATC 57.456 47.619 0.00 0.00 0.00 2.08
1707 1714 3.107601 TGTGCTGGTTCTTAGGCTATCT 58.892 45.455 0.00 0.00 0.00 1.98
1767 1774 2.005960 GCTATGTGCTCGAGTCCCGT 62.006 60.000 15.13 6.22 39.75 5.28
1801 1808 0.383949 GGTGTCGGTGCACATTTTGT 59.616 50.000 20.43 0.00 40.89 2.83
1803 1810 2.116366 GTGTCGGTGCACATTTTGTTC 58.884 47.619 20.43 0.00 39.07 3.18
1804 1811 1.268285 TGTCGGTGCACATTTTGTTCG 60.268 47.619 20.43 10.30 0.00 3.95
1815 1823 3.437741 ACATTTTGTTCGATTACCCCGAC 59.562 43.478 0.00 0.00 35.61 4.79
1820 1828 2.299582 TGTTCGATTACCCCGACAAAGA 59.700 45.455 0.00 0.00 35.61 2.52
1834 1842 3.301835 CGACAAAGATAAGAATGGCGTCG 60.302 47.826 0.00 0.00 39.40 5.12
1836 1844 3.617263 ACAAAGATAAGAATGGCGTCGAC 59.383 43.478 5.18 5.18 0.00 4.20
1866 1874 0.101399 ACGCACTCTCGATGTCCATC 59.899 55.000 0.00 0.00 34.56 3.51
1879 1887 2.046292 TGTCCATCCACACACTTGAGA 58.954 47.619 0.00 0.00 0.00 3.27
1893 1901 2.777692 ACTTGAGAAGGTCACCAAGGAA 59.222 45.455 0.00 0.00 40.02 3.36
1913 1951 4.099419 GGAACCAGAAAAGTTGTTGTGGAT 59.901 41.667 15.83 8.02 43.08 3.41
2004 2042 1.227263 GTCGCGTATGGGCATGAGT 60.227 57.895 5.77 0.00 0.00 3.41
2010 2048 0.546122 GTATGGGCATGAGTGGTGGA 59.454 55.000 0.00 0.00 0.00 4.02
2167 2205 1.930656 ATGTGGTTCCTCCCCCAGG 60.931 63.158 0.00 0.00 45.15 4.45
2197 2241 1.204786 TCCAATCCACCACGGTCCAT 61.205 55.000 0.00 0.00 35.57 3.41
2258 2303 3.392616 CTGATGCCCAACCTACCTCTTAT 59.607 47.826 0.00 0.00 0.00 1.73
2321 2408 4.422840 CAACACTTGTTCAGCATGTTCAA 58.577 39.130 0.00 0.00 35.83 2.69
2362 2449 5.386924 AGGTGACATACTAGATGTAGACCC 58.613 45.833 19.42 12.61 36.22 4.46
2498 2598 3.182967 GAGTGCTCGACTAATTGTCCAG 58.817 50.000 0.00 0.00 42.49 3.86
2536 2636 8.930760 GTCATAGTTATCATGCTCCAGTTATTC 58.069 37.037 0.00 0.00 0.00 1.75
2597 4177 7.892609 TGTAGTGAATTTGTCTGTTAGCTCTA 58.107 34.615 0.00 0.00 0.00 2.43
2607 4187 5.697178 TGTCTGTTAGCTCTACTCGCTATAG 59.303 44.000 0.00 0.00 39.50 1.31
2689 4401 0.962356 AGGCATGTTCCCGCAGAAAG 60.962 55.000 0.00 0.00 35.85 2.62
2740 4455 7.012989 ACACTGTATCATGTGATCAATCATTGG 59.987 37.037 0.00 0.00 39.30 3.16
3075 9364 3.075283 TCACAAGCAAGGGGGAAAGATAA 59.925 43.478 0.00 0.00 0.00 1.75
3086 9375 3.365472 GGGAAAGATAATGTGCAAGGGT 58.635 45.455 0.00 0.00 0.00 4.34
3091 9380 3.009723 AGATAATGTGCAAGGGTGTTCG 58.990 45.455 0.00 0.00 0.00 3.95
3157 9446 3.161817 CGTTTTCGCCTGTACCCG 58.838 61.111 0.00 0.00 36.22 5.28
3166 9455 2.264794 CTGTACCCGCCACTGGTC 59.735 66.667 0.00 0.00 37.31 4.02
3167 9456 3.310860 CTGTACCCGCCACTGGTCC 62.311 68.421 0.00 0.00 37.31 4.46
3168 9457 3.001406 GTACCCGCCACTGGTCCT 61.001 66.667 0.00 0.00 37.31 3.85
3169 9458 1.683365 GTACCCGCCACTGGTCCTA 60.683 63.158 0.00 0.00 37.31 2.94
3170 9459 1.047034 GTACCCGCCACTGGTCCTAT 61.047 60.000 0.00 0.00 37.31 2.57
3171 9460 1.046472 TACCCGCCACTGGTCCTATG 61.046 60.000 0.00 0.00 37.31 2.23
3172 9461 2.063979 CCCGCCACTGGTCCTATGA 61.064 63.158 0.00 0.00 0.00 2.15
3173 9462 1.410850 CCCGCCACTGGTCCTATGAT 61.411 60.000 0.00 0.00 0.00 2.45
3174 9463 0.034059 CCGCCACTGGTCCTATGATC 59.966 60.000 0.00 0.00 0.00 2.92
3175 9464 0.034059 CGCCACTGGTCCTATGATCC 59.966 60.000 0.00 0.00 0.00 3.36
3176 9465 0.034059 GCCACTGGTCCTATGATCCG 59.966 60.000 0.00 0.00 0.00 4.18
3177 9466 1.414158 CCACTGGTCCTATGATCCGT 58.586 55.000 0.00 0.00 0.00 4.69
3178 9467 1.762957 CCACTGGTCCTATGATCCGTT 59.237 52.381 0.00 0.00 0.00 4.44
3179 9468 2.963101 CCACTGGTCCTATGATCCGTTA 59.037 50.000 0.00 0.00 0.00 3.18
3180 9469 3.243771 CCACTGGTCCTATGATCCGTTAC 60.244 52.174 0.00 0.00 0.00 2.50
3181 9470 3.383505 CACTGGTCCTATGATCCGTTACA 59.616 47.826 0.00 0.00 0.00 2.41
3182 9471 4.028131 ACTGGTCCTATGATCCGTTACAA 58.972 43.478 0.00 0.00 0.00 2.41
3197 9503 0.251653 TACAACGCTCTCCCCTGTCT 60.252 55.000 0.00 0.00 0.00 3.41
3208 9514 4.425772 TCTCCCCTGTCTACAAATCTGAA 58.574 43.478 0.00 0.00 0.00 3.02
3226 9532 3.567397 TGAAGCCTAGAGGAGTGGATAC 58.433 50.000 0.00 0.00 37.39 2.24
3262 9568 4.521146 CTCAGGAGTTTTATGACATGCCT 58.479 43.478 0.00 0.00 0.00 4.75
3300 9606 0.099791 ACGCGACCCAAACAAAACTG 59.900 50.000 15.93 0.00 0.00 3.16
3304 9610 2.857748 GCGACCCAAACAAAACTGAAAG 59.142 45.455 0.00 0.00 42.29 2.62
3321 9628 0.942252 AAGAGGCCGACGAAACAAAC 59.058 50.000 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.392998 ACAGCAAGCCCATTCCGTAG 60.393 55.000 0.00 0.00 0.00 3.51
77 78 1.819632 CGCACAGAATACCCCTGGC 60.820 63.158 0.00 0.00 36.03 4.85
89 90 1.572085 CTCTTCCACAAGCCGCACAG 61.572 60.000 0.00 0.00 0.00 3.66
149 150 6.485984 AGTGCATAATTTTCCAAAACATTGCA 59.514 30.769 10.80 10.80 37.07 4.08
211 212 4.935352 AATGCACTCTGAGAGTAGATCC 57.065 45.455 15.73 2.56 41.37 3.36
259 260 4.326826 TCTTTCATCTTCCGTTGCATCTT 58.673 39.130 0.00 0.00 0.00 2.40
263 264 1.806542 GCTCTTTCATCTTCCGTTGCA 59.193 47.619 0.00 0.00 0.00 4.08
278 279 1.376424 CTGCACCATGACCGCTCTT 60.376 57.895 0.00 0.00 0.00 2.85
285 286 0.826715 TAGAGGCTCTGCACCATGAC 59.173 55.000 26.95 0.00 0.00 3.06
315 316 1.870383 GCGTGTTATTCCGTGCCAA 59.130 52.632 0.00 0.00 0.00 4.52
332 333 2.040178 TCTATCTTCTTTCCCTCCCGC 58.960 52.381 0.00 0.00 0.00 6.13
362 363 2.306341 GCACTCTTGCTGCTATCTCA 57.694 50.000 0.00 0.00 46.17 3.27
377 378 1.508545 CTCCATGAGTCGTCGCACT 59.491 57.895 0.00 0.00 0.00 4.40
398 399 2.620251 TGCCATGTATAGACTGCCAC 57.380 50.000 0.00 0.00 0.00 5.01
405 406 2.092484 TGCTTGCCTTGCCATGTATAGA 60.092 45.455 0.00 0.00 0.00 1.98
407 408 2.433662 TGCTTGCCTTGCCATGTATA 57.566 45.000 0.00 0.00 0.00 1.47
410 411 0.034337 CTTTGCTTGCCTTGCCATGT 59.966 50.000 0.00 0.00 0.00 3.21
433 434 2.281484 GCTGTTTGACCTCGGCCA 60.281 61.111 2.24 0.00 0.00 5.36
437 438 1.016130 ATCGCTGCTGTTTGACCTCG 61.016 55.000 0.00 0.00 0.00 4.63
444 445 1.302752 TGCTCCATCGCTGCTGTTT 60.303 52.632 0.00 0.00 0.00 2.83
471 472 1.485294 TTCGCCTTGACCCAGCCTAA 61.485 55.000 0.00 0.00 0.00 2.69
472 473 1.916273 TTCGCCTTGACCCAGCCTA 60.916 57.895 0.00 0.00 0.00 3.93
476 477 1.597027 AACGTTCGCCTTGACCCAG 60.597 57.895 0.00 0.00 0.00 4.45
491 492 2.491152 GTGCATGCCCCATCAACG 59.509 61.111 16.68 0.00 0.00 4.10
527 528 3.537206 GAAGACCACGCCCACTGCT 62.537 63.158 0.00 0.00 38.05 4.24
557 558 1.830279 CAGCTCCAAGAAATGCTCCA 58.170 50.000 0.00 0.00 33.03 3.86
566 567 1.552578 AATTGCATGCAGCTCCAAGA 58.447 45.000 21.50 3.38 45.94 3.02
569 570 2.133281 AGTAATTGCATGCAGCTCCA 57.867 45.000 21.50 5.91 45.94 3.86
626 630 4.376176 GCCGCCCTTTTGCATGCA 62.376 61.111 18.46 18.46 0.00 3.96
663 667 5.763698 CCTCAATATGCAGGCTGGATATATG 59.236 44.000 32.93 29.01 39.91 1.78
665 669 4.784838 ACCTCAATATGCAGGCTGGATATA 59.215 41.667 32.93 21.38 39.91 0.86
671 675 1.134007 TCCACCTCAATATGCAGGCTG 60.134 52.381 10.94 10.94 32.32 4.85
683 687 1.279496 CCTCCTGACAATCCACCTCA 58.721 55.000 0.00 0.00 0.00 3.86
716 720 2.465813 AGATCCTCTTCCACACTCTGG 58.534 52.381 0.00 0.00 42.29 3.86
756 760 2.012673 CATAGCCTTCACCTGCTTGAC 58.987 52.381 0.00 0.00 39.00 3.18
762 766 1.156645 GCGAGCATAGCCTTCACCTG 61.157 60.000 0.00 0.00 0.00 4.00
787 791 3.889538 CCACGTCACCTTCCATCTATCTA 59.110 47.826 0.00 0.00 0.00 1.98
791 795 1.191535 CCCACGTCACCTTCCATCTA 58.808 55.000 0.00 0.00 0.00 1.98
879 883 2.832661 TGGTGCTTGCACCCACAC 60.833 61.111 33.41 14.97 44.38 3.82
881 885 3.605664 GGTGGTGCTTGCACCCAC 61.606 66.667 33.41 28.66 44.38 4.61
952 956 5.828299 TTTTGAATTCAACCACGTCTCTT 57.172 34.783 20.35 0.00 35.28 2.85
980 984 1.748493 TCGCAGCAAGTTGGTTCTTTT 59.252 42.857 4.45 0.00 0.00 2.27
981 985 1.388547 TCGCAGCAAGTTGGTTCTTT 58.611 45.000 4.45 0.00 0.00 2.52
982 986 1.267806 CATCGCAGCAAGTTGGTTCTT 59.732 47.619 4.45 0.00 0.00 2.52
996 1000 2.738139 CACGTCTGGTGCATCGCA 60.738 61.111 0.00 0.00 40.33 5.10
1111 1115 2.214181 GATGGTCCGTGTGAGTCGCT 62.214 60.000 5.11 0.00 0.00 4.93
1134 1138 1.366366 CTGACCAGTTCCCGTCGTT 59.634 57.895 0.00 0.00 0.00 3.85
1202 1206 1.205655 TGGAGAAGACGCATCTGAAGG 59.794 52.381 0.00 0.00 34.48 3.46
1264 1271 0.629058 ACCCAATTTATCCCGGTGCT 59.371 50.000 0.00 0.00 0.00 4.40
1275 1282 2.275380 GGCGCTGGTCACCCAATTT 61.275 57.895 7.64 0.00 41.27 1.82
1400 1407 0.684153 ATTCTTCCCCAACCCATGCG 60.684 55.000 0.00 0.00 0.00 4.73
1401 1408 1.114627 GATTCTTCCCCAACCCATGC 58.885 55.000 0.00 0.00 0.00 4.06
1412 1419 1.064463 TGATGCCACTGGGATTCTTCC 60.064 52.381 3.19 0.00 41.77 3.46
1414 1421 2.512896 AGATGATGCCACTGGGATTCTT 59.487 45.455 3.19 0.00 32.75 2.52
1424 1431 1.588404 CGTCGTTGTAGATGATGCCAC 59.412 52.381 0.00 0.00 0.00 5.01
1425 1432 1.470805 CCGTCGTTGTAGATGATGCCA 60.471 52.381 0.00 0.00 0.00 4.92
1450 1457 3.149196 CCAGTTTGCTGTACACAAGGAT 58.851 45.455 9.69 1.15 41.02 3.24
1456 1463 1.264288 GCTGTCCAGTTTGCTGTACAC 59.736 52.381 0.00 0.00 36.78 2.90
1460 1467 1.242076 GATGCTGTCCAGTTTGCTGT 58.758 50.000 0.00 0.00 41.02 4.40
1469 1476 2.183478 AAATGTGTCGATGCTGTCCA 57.817 45.000 0.00 0.00 0.00 4.02
1470 1477 2.351726 GGTAAATGTGTCGATGCTGTCC 59.648 50.000 0.00 0.00 0.00 4.02
1487 1494 2.975536 CCCTGAACTCGGCGGTAA 59.024 61.111 7.21 0.00 0.00 2.85
1550 1557 0.105913 GGAGGGGGATTCGAGAGTCT 60.106 60.000 0.00 0.00 0.00 3.24
1573 1580 2.046283 TACGCGACACAGAACTCTTG 57.954 50.000 15.93 0.00 0.00 3.02
1574 1581 2.228103 TGATACGCGACACAGAACTCTT 59.772 45.455 15.93 0.00 0.00 2.85
1599 1606 0.392863 CGGTCACATGGATCTTGCCA 60.393 55.000 0.00 0.00 43.23 4.92
1641 1648 3.558099 CTGCTCGGTCACGCTCACA 62.558 63.158 0.00 0.00 40.69 3.58
1660 1667 3.977244 GTTGGTTGCGGCTGTGGG 61.977 66.667 0.00 0.00 0.00 4.61
1697 1704 1.336887 GCGGCATCGAAGATAGCCTAA 60.337 52.381 15.80 0.00 45.12 2.69
1703 1710 2.355837 GGCGCGGCATCGAAGATA 60.356 61.111 29.32 0.00 45.12 1.98
1732 1739 3.254060 CATAGCTGTGCTCGTACAAGTT 58.746 45.455 0.00 0.00 40.44 2.66
1767 1774 2.776526 ACCCACAACAGCTCCCCA 60.777 61.111 0.00 0.00 0.00 4.96
1801 1808 3.899052 ATCTTTGTCGGGGTAATCGAA 57.101 42.857 0.00 0.00 38.42 3.71
1803 1810 4.940463 TCTTATCTTTGTCGGGGTAATCG 58.060 43.478 0.00 0.00 0.00 3.34
1804 1811 6.204882 CCATTCTTATCTTTGTCGGGGTAATC 59.795 42.308 0.00 0.00 0.00 1.75
1815 1823 3.301835 CGTCGACGCCATTCTTATCTTTG 60.302 47.826 26.59 0.00 0.00 2.77
1820 1828 1.535437 GGTCGTCGACGCCATTCTTAT 60.535 52.381 32.27 0.00 39.60 1.73
1866 1874 2.213499 GTGACCTTCTCAAGTGTGTGG 58.787 52.381 0.00 0.00 0.00 4.17
1879 1887 1.518367 TCTGGTTCCTTGGTGACCTT 58.482 50.000 2.11 0.00 34.52 3.50
1893 1901 4.277476 TCATCCACAACAACTTTTCTGGT 58.723 39.130 0.00 0.00 0.00 4.00
1913 1951 2.040442 TCCGGCCATCCTTCCTCA 59.960 61.111 2.24 0.00 0.00 3.86
1935 1973 1.300697 GAACAACACGCGGTCCTCT 60.301 57.895 12.47 0.00 0.00 3.69
1993 2031 0.632835 AATCCACCACTCATGCCCAT 59.367 50.000 0.00 0.00 0.00 4.00
2004 2042 1.568504 AGAAGTAGGCGAATCCACCA 58.431 50.000 0.00 0.00 37.29 4.17
2010 2048 4.637534 TCGTAGTACAAGAAGTAGGCGAAT 59.362 41.667 0.38 0.00 32.35 3.34
2127 2165 0.324614 ACATGTCGCTGTCCAATCCA 59.675 50.000 0.00 0.00 0.00 3.41
2155 2193 1.619363 CCATGACCTGGGGGAGGAA 60.619 63.158 0.00 0.00 46.33 3.36
2197 2241 6.036735 GTGTTATTGCTTCTTGGCGTATTAGA 59.963 38.462 0.00 0.00 34.52 2.10
2258 2303 3.972227 GCCAAGAGCTCTTCGCAA 58.028 55.556 32.85 0.00 39.40 4.85
2321 2408 2.108250 ACCTTGCCACCAAACAGTCTAT 59.892 45.455 0.00 0.00 0.00 1.98
2362 2449 1.212688 TCCAATACCATGTGAGGCCTG 59.787 52.381 12.00 0.00 0.00 4.85
2399 2486 0.250234 CCATGCTCACCTCGAGGAAA 59.750 55.000 37.69 22.25 46.21 3.13
2689 4401 5.065218 AGTGATGTGCAAATCTCGTTTATCC 59.935 40.000 17.76 0.00 0.00 2.59
2740 4455 0.465287 AATCCGGGGCAATTTCATGC 59.535 50.000 0.00 0.00 45.67 4.06
2920 6332 6.757237 TGTCCATGTTCAGCAAAATTTGTAT 58.243 32.000 7.60 0.00 0.00 2.29
2963 9222 7.068103 TGTGTGAATGTTTCTTTGTGGTAATCT 59.932 33.333 0.00 0.00 0.00 2.40
3075 9364 2.268076 GGCGAACACCCTTGCACAT 61.268 57.895 0.00 0.00 0.00 3.21
3157 9446 0.034059 CGGATCATAGGACCAGTGGC 59.966 60.000 9.78 1.63 0.00 5.01
3162 9451 4.395959 GTTGTAACGGATCATAGGACCA 57.604 45.455 0.00 0.00 0.00 4.02
3176 9465 0.320697 ACAGGGGAGAGCGTTGTAAC 59.679 55.000 0.00 0.00 0.00 2.50
3177 9466 0.606604 GACAGGGGAGAGCGTTGTAA 59.393 55.000 0.00 0.00 0.00 2.41
3178 9467 0.251653 AGACAGGGGAGAGCGTTGTA 60.252 55.000 0.00 0.00 0.00 2.41
3179 9468 0.251653 TAGACAGGGGAGAGCGTTGT 60.252 55.000 0.00 0.00 0.00 3.32
3180 9469 0.173708 GTAGACAGGGGAGAGCGTTG 59.826 60.000 0.00 0.00 0.00 4.10
3181 9470 0.251653 TGTAGACAGGGGAGAGCGTT 60.252 55.000 0.00 0.00 0.00 4.84
3182 9471 0.251653 TTGTAGACAGGGGAGAGCGT 60.252 55.000 0.00 0.00 0.00 5.07
3197 9503 5.127845 CACTCCTCTAGGCTTCAGATTTGTA 59.872 44.000 0.00 0.00 34.44 2.41
3208 9514 1.202952 CCGTATCCACTCCTCTAGGCT 60.203 57.143 0.00 0.00 34.44 4.58
3248 9554 2.161410 GTCACGCAGGCATGTCATAAAA 59.839 45.455 0.00 0.00 0.00 1.52
3300 9606 1.223187 TTGTTTCGTCGGCCTCTTTC 58.777 50.000 0.00 0.00 0.00 2.62
3304 9610 1.203313 CGTTTGTTTCGTCGGCCTC 59.797 57.895 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.