Multiple sequence alignment - TraesCS2D01G278900

Loading Multiple Alignment...

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 TraesCS2D01G278900 chr2D 100.000 5792 0 0 1 5792 350066975 350061184 0.000000e+00 10696.0
1 TraesCS2D01G278900 chr2D 100.000 3300 0 0 6566 9865 350060410 350057111 0.000000e+00 6095.0
2 TraesCS2D01G278900 chr2D 91.409 1944 129 24 3230 5145 535953169 535951236 0.000000e+00 2630.0
3 TraesCS2D01G278900 chr2D 95.369 1058 45 3 6566 7619 454091666 454090609 0.000000e+00 1679.0
4 TraesCS2D01G278900 chr2D 94.105 967 52 5 1 965 498274283 498273320 0.000000e+00 1465.0
5 TraesCS2D01G278900 chr2D 91.955 808 21 14 7329 8127 350063747 350062975 0.000000e+00 1092.0
6 TraesCS2D01G278900 chr2D 95.195 666 28 3 5131 5792 454092992 454092327 0.000000e+00 1050.0
7 TraesCS2D01G278900 chr2D 89.574 681 57 9 6940 7613 61018810 61019483 0.000000e+00 852.0
8 TraesCS2D01G278900 chr2D 82.812 1024 97 47 7122 8127 318163446 318164408 0.000000e+00 843.0
9 TraesCS2D01G278900 chr2D 85.679 405 46 9 7729 8130 433987419 433987024 5.510000e-112 416.0
10 TraesCS2D01G278900 chr2D 96.970 33 1 0 8862 8894 90713774 90713742 1.000000e-03 56.5
11 TraesCS2D01G278900 chr2D 96.875 32 1 0 8863 8894 90505272 90505241 5.000000e-03 54.7
12 TraesCS2D01G278900 chr2D 100.000 28 0 0 1007 1034 35778515 35778542 1.800000e-02 52.8
13 TraesCS2D01G278900 chr6D 97.274 2568 60 4 3230 5792 377718672 377721234 0.000000e+00 4346.0
14 TraesCS2D01G278900 chr6D 96.883 1925 47 5 3231 5147 68150741 68148822 0.000000e+00 3210.0
15 TraesCS2D01G278900 chr6D 94.264 1569 46 11 6566 8127 377722068 377723599 0.000000e+00 2359.0
16 TraesCS2D01G278900 chr6D 94.065 1567 56 11 6566 8127 68145833 68144299 0.000000e+00 2344.0
17 TraesCS2D01G278900 chr6D 94.542 971 44 5 1 965 449137094 449138061 0.000000e+00 1491.0
18 TraesCS2D01G278900 chr6D 94.508 965 50 3 1 965 41923646 41924607 0.000000e+00 1485.0
19 TraesCS2D01G278900 chr6D 93.822 777 25 7 3229 4002 434943728 434944484 0.000000e+00 1147.0
20 TraesCS2D01G278900 chr6D 92.574 808 32 13 7329 8125 434924928 434925718 0.000000e+00 1134.0
21 TraesCS2D01G278900 chr6D 92.893 802 18 12 7330 8127 377718672 377719438 0.000000e+00 1129.0
22 TraesCS2D01G278900 chr6D 92.884 801 18 9 7331 8127 68150741 68149976 0.000000e+00 1127.0
23 TraesCS2D01G278900 chr6D 95.545 651 27 2 5143 5792 68147113 68146464 0.000000e+00 1040.0
24 TraesCS2D01G278900 chr6D 85.000 240 30 5 5074 5310 434941406 434941642 1.280000e-58 239.0
25 TraesCS2D01G278900 chr2A 96.709 2127 44 2 1131 3231 467233903 467231777 0.000000e+00 3517.0
26 TraesCS2D01G278900 chr2A 96.233 584 20 1 8369 8952 467231384 467230803 0.000000e+00 955.0
27 TraesCS2D01G278900 chr2A 83.607 732 88 15 8950 9655 753698732 753698007 0.000000e+00 658.0
28 TraesCS2D01G278900 chr2A 97.107 242 7 0 8130 8371 467231782 467231541 9.220000e-110 409.0
29 TraesCS2D01G278900 chr2A 100.000 29 0 0 1083 1111 467233973 467233945 5.000000e-03 54.7
30 TraesCS2D01G278900 chr2A 100.000 28 0 0 8860 8887 743987902 743987929 1.800000e-02 52.8
31 TraesCS2D01G278900 chr5D 96.514 1922 49 8 3231 5145 115061118 115063028 0.000000e+00 3162.0
32 TraesCS2D01G278900 chr5D 90.448 1340 100 14 3828 5145 410959792 410958459 0.000000e+00 1740.0
33 TraesCS2D01G278900 chr5D 94.429 1059 51 5 6566 7619 61577129 61578184 0.000000e+00 1622.0
34 TraesCS2D01G278900 chr5D 94.209 967 52 4 1 965 98664814 98665778 0.000000e+00 1472.0
35 TraesCS2D01G278900 chr5D 92.694 917 61 5 4882 5792 61575191 61576107 0.000000e+00 1317.0
36 TraesCS2D01G278900 chr5D 91.511 801 26 12 7331 8127 115061118 115061880 0.000000e+00 1064.0
37 TraesCS2D01G278900 chr5D 88.818 626 60 7 6945 7561 105062326 105061702 0.000000e+00 760.0
38 TraesCS2D01G278900 chr5D 82.763 789 96 26 7362 8127 136065075 136065846 0.000000e+00 667.0
39 TraesCS2D01G278900 chr5D 84.648 697 77 14 8950 9620 272361352 272362044 0.000000e+00 667.0
40 TraesCS2D01G278900 chr5D 94.079 152 8 1 8949 9099 402739223 402739374 7.710000e-56 230.0
41 TraesCS2D01G278900 chr5D 89.506 162 14 1 5142 5300 88958612 88958773 1.680000e-47 202.0
42 TraesCS2D01G278900 chr5D 88.060 67 7 1 5715 5781 156061386 156061321 2.950000e-10 78.7
43 TraesCS2D01G278900 chr5D 100.000 28 0 0 1007 1034 441566670 441566697 1.800000e-02 52.8
44 TraesCS2D01G278900 chr2B 95.766 1866 56 4 1069 2911 415354019 415355884 0.000000e+00 2987.0
45 TraesCS2D01G278900 chr2B 97.030 808 24 0 8130 8937 415358433 415359240 0.000000e+00 1360.0
46 TraesCS2D01G278900 chr2B 90.794 945 56 9 8948 9864 673628021 673627080 0.000000e+00 1234.0
47 TraesCS2D01G278900 chr2B 88.172 558 42 9 8950 9484 158046015 158046571 2.320000e-180 643.0
48 TraesCS2D01G278900 chr2B 96.667 330 10 1 2903 3231 415358109 415358438 1.870000e-151 547.0
49 TraesCS2D01G278900 chr1D 87.817 1970 166 43 3230 5145 420985520 420987469 0.000000e+00 2241.0
50 TraesCS2D01G278900 chr1D 92.352 1569 100 13 3231 4789 76299416 76300974 0.000000e+00 2215.0
51 TraesCS2D01G278900 chr1D 88.582 1813 144 47 3654 5425 315866720 315864930 0.000000e+00 2143.0
52 TraesCS2D01G278900 chr1D 87.346 1620 141 37 3702 5289 342748173 342746586 0.000000e+00 1797.0
53 TraesCS2D01G278900 chr1D 95.265 1056 48 2 6566 7619 315863926 315862871 0.000000e+00 1672.0
54 TraesCS2D01G278900 chr1D 92.244 1083 49 6 6566 7619 76302711 76303787 0.000000e+00 1502.0
55 TraesCS2D01G278900 chr1D 94.330 970 46 6 1 965 430109454 430108489 0.000000e+00 1478.0
56 TraesCS2D01G278900 chr1D 94.221 969 44 7 1 965 278101508 278102468 0.000000e+00 1469.0
57 TraesCS2D01G278900 chr1D 90.333 931 64 12 8952 9859 74530146 74531073 0.000000e+00 1197.0
58 TraesCS2D01G278900 chr1D 91.635 801 27 16 7331 8127 76299416 76300180 0.000000e+00 1072.0
59 TraesCS2D01G278900 chr1D 93.119 654 38 5 5144 5792 76301338 76301989 0.000000e+00 952.0
60 TraesCS2D01G278900 chr1D 96.364 275 10 0 5500 5774 315864937 315864663 4.200000e-123 453.0
61 TraesCS2D01G278900 chr3B 91.057 1353 108 9 3803 5145 494227145 494228494 0.000000e+00 1816.0
62 TraesCS2D01G278900 chr3B 89.715 1332 112 18 3830 5145 713230305 713231627 0.000000e+00 1677.0
63 TraesCS2D01G278900 chr3B 82.764 673 89 18 6957 7617 575794593 575793936 8.590000e-160 575.0
64 TraesCS2D01G278900 chr3B 88.581 289 26 3 7329 7617 575798618 575798337 2.640000e-90 344.0
65 TraesCS2D01G278900 chr3B 96.970 33 1 0 8860 8892 48671157 48671125 1.000000e-03 56.5
66 TraesCS2D01G278900 chr3B 92.105 38 2 1 1007 1044 751843966 751843930 1.800000e-02 52.8
67 TraesCS2D01G278900 chr5B 87.484 1574 150 34 3604 5145 461725127 461726685 0.000000e+00 1772.0
68 TraesCS2D01G278900 chr5B 89.005 955 67 16 8942 9864 339919911 339918963 0.000000e+00 1147.0
69 TraesCS2D01G278900 chr5B 84.097 698 81 13 8950 9621 544408064 544408757 0.000000e+00 647.0
70 TraesCS2D01G278900 chr5B 84.030 670 84 15 6572 7228 574540043 574539384 3.030000e-174 623.0
71 TraesCS2D01G278900 chr5B 96.667 60 1 1 5638 5696 112830848 112830907 2.270000e-16 99.0
72 TraesCS2D01G278900 chr5B 96.364 55 2 0 5638 5692 112830802 112830856 3.790000e-14 91.6
73 TraesCS2D01G278900 chr5B 100.000 28 0 0 1007 1034 294771667 294771694 1.800000e-02 52.8
74 TraesCS2D01G278900 chr5B 100.000 28 0 0 1007 1034 601344197 601344224 1.800000e-02 52.8
75 TraesCS2D01G278900 chr7D 94.207 1053 39 8 6566 7615 154707119 154706086 0.000000e+00 1587.0
76 TraesCS2D01G278900 chr7D 94.099 966 50 2 1 966 126989401 126988443 0.000000e+00 1461.0
77 TraesCS2D01G278900 chr7D 94.676 432 19 3 5350 5778 154707956 154707526 0.000000e+00 667.0
78 TraesCS2D01G278900 chr7D 83.520 358 38 14 4964 5300 213280354 213280711 2.070000e-81 315.0
79 TraesCS2D01G278900 chr7D 86.567 67 8 1 5715 5781 164015408 164015473 1.370000e-08 73.1
80 TraesCS2D01G278900 chr4D 94.542 971 45 3 1 964 481887995 481887026 0.000000e+00 1493.0
81 TraesCS2D01G278900 chr4D 89.468 940 72 11 8949 9864 309961938 309962874 0.000000e+00 1162.0
82 TraesCS2D01G278900 chr4D 82.903 813 94 36 7331 8127 333390673 333391456 0.000000e+00 689.0
83 TraesCS2D01G278900 chr4D 85.608 403 48 8 7729 8127 90385378 90385774 1.980000e-111 414.0
84 TraesCS2D01G278900 chr4D 90.196 51 5 0 5641 5691 432098763 432098813 6.390000e-07 67.6
85 TraesCS2D01G278900 chr3D 94.404 965 51 1 1 965 580657320 580656359 0.000000e+00 1480.0
86 TraesCS2D01G278900 chr3D 85.024 414 51 9 7718 8127 133199705 133200111 2.560000e-110 411.0
87 TraesCS2D01G278900 chr3D 96.154 52 2 0 5641 5692 73167692 73167641 1.770000e-12 86.1
88 TraesCS2D01G278900 chr7A 82.886 1601 184 60 6566 8133 580229746 580228203 0.000000e+00 1356.0
89 TraesCS2D01G278900 chrUn 92.021 940 50 6 8949 9865 315367084 315366147 0.000000e+00 1297.0
90 TraesCS2D01G278900 chrUn 87.617 428 28 9 8949 9353 357402398 357402823 3.220000e-129 473.0
91 TraesCS2D01G278900 chr7B 91.702 940 55 8 8949 9865 632977845 632976906 0.000000e+00 1282.0
92 TraesCS2D01G278900 chr7B 87.500 768 83 8 9108 9864 725976477 725977242 0.000000e+00 874.0
93 TraesCS2D01G278900 chr7B 81.652 823 99 38 7331 8129 360891753 360890959 3.890000e-178 636.0
94 TraesCS2D01G278900 chr6A 90.426 940 59 13 8948 9864 128442738 128441807 0.000000e+00 1208.0
95 TraesCS2D01G278900 chr5A 89.087 953 63 19 8944 9864 640352153 640353096 0.000000e+00 1146.0
96 TraesCS2D01G278900 chr5A 87.986 283 33 1 5019 5300 373669599 373669881 5.710000e-87 333.0
97 TraesCS2D01G278900 chr4B 87.908 918 78 17 8961 9864 594442297 594441399 0.000000e+00 1050.0
98 TraesCS2D01G278900 chr4B 84.561 421 45 17 7716 8127 151758467 151758876 5.550000e-107 399.0
99 TraesCS2D01G278900 chr4B 100.000 28 0 0 1007 1034 633294012 633293985 1.800000e-02 52.8
100 TraesCS2D01G278900 chr3A 82.493 1011 126 30 6566 7561 488867394 488868368 0.000000e+00 839.0
101 TraesCS2D01G278900 chr3A 87.007 431 33 8 8948 9355 646736588 646736158 1.940000e-126 464.0
102 TraesCS2D01G278900 chr3A 92.308 52 4 0 5534 5585 612072690 612072639 3.820000e-09 75.0
103 TraesCS2D01G278900 chr3A 94.444 36 0 2 1007 1040 576603367 576603402 5.000000e-03 54.7
104 TraesCS2D01G278900 chr1B 86.552 699 79 10 6569 7255 405104478 405103783 0.000000e+00 756.0
105 TraesCS2D01G278900 chr1B 86.375 411 40 12 7729 8127 435303543 435303949 1.520000e-117 435.0
106 TraesCS2D01G278900 chr1B 89.057 265 27 2 5528 5792 405105224 405104962 2.660000e-85 327.0
107 TraesCS2D01G278900 chr1B 97.059 34 1 0 8860 8893 493871936 493871969 3.850000e-04 58.4
108 TraesCS2D01G278900 chr1B 100.000 28 0 0 1007 1034 377075338 377075311 1.800000e-02 52.8
109 TraesCS2D01G278900 chr6B 84.736 701 73 16 8949 9621 462140772 462141466 0.000000e+00 671.0
110 TraesCS2D01G278900 chr6B 84.692 699 77 15 8949 9621 669336045 669336739 0.000000e+00 671.0
111 TraesCS2D01G278900 chr6B 88.462 78 8 1 5615 5692 69158659 69158735 1.050000e-14 93.5
112 TraesCS2D01G278900 chr6B 96.970 33 1 0 8862 8894 177274398 177274366 1.000000e-03 56.5
113 TraesCS2D01G278900 chr6B 100.000 28 0 0 1007 1034 107879816 107879843 1.800000e-02 52.8
114 TraesCS2D01G278900 chr4A 87.611 565 45 13 8950 9491 570909632 570909070 5.030000e-177 632.0
115 TraesCS2D01G278900 chr1A 82.969 458 64 10 7680 8129 393211434 393210983 1.540000e-107 401.0
116 TraesCS2D01G278900 chr1A 96.970 33 1 0 8861 8893 573813626 573813594 1.000000e-03 56.5


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 TraesCS2D01G278900 chr2D 350057111 350066975 9864 True 8395.500000 10696 100.000000 1 9865 2 chr2D.!!$R7 9864
1 TraesCS2D01G278900 chr2D 535951236 535953169 1933 True 2630.000000 2630 91.409000 3230 5145 1 chr2D.!!$R6 1915
2 TraesCS2D01G278900 chr2D 498273320 498274283 963 True 1465.000000 1465 94.105000 1 965 1 chr2D.!!$R5 964
3 TraesCS2D01G278900 chr2D 454090609 454092992 2383 True 1364.500000 1679 95.282000 5131 7619 2 chr2D.!!$R8 2488
4 TraesCS2D01G278900 chr2D 350062975 350063747 772 True 1092.000000 1092 91.955000 7329 8127 1 chr2D.!!$R3 798
5 TraesCS2D01G278900 chr2D 61018810 61019483 673 False 852.000000 852 89.574000 6940 7613 1 chr2D.!!$F2 673
6 TraesCS2D01G278900 chr2D 318163446 318164408 962 False 843.000000 843 82.812000 7122 8127 1 chr2D.!!$F3 1005
7 TraesCS2D01G278900 chr6D 377718672 377723599 4927 False 2611.333333 4346 94.810333 3230 8127 3 chr6D.!!$F4 4897
8 TraesCS2D01G278900 chr6D 68144299 68150741 6442 True 1930.250000 3210 94.844250 3231 8127 4 chr6D.!!$R1 4896
9 TraesCS2D01G278900 chr6D 449137094 449138061 967 False 1491.000000 1491 94.542000 1 965 1 chr6D.!!$F3 964
10 TraesCS2D01G278900 chr6D 41923646 41924607 961 False 1485.000000 1485 94.508000 1 965 1 chr6D.!!$F1 964
11 TraesCS2D01G278900 chr6D 434924928 434925718 790 False 1134.000000 1134 92.574000 7329 8125 1 chr6D.!!$F2 796
12 TraesCS2D01G278900 chr6D 434941406 434944484 3078 False 693.000000 1147 89.411000 3229 5310 2 chr6D.!!$F5 2081
13 TraesCS2D01G278900 chr2A 467230803 467233973 3170 True 1233.925000 3517 97.512250 1083 8952 4 chr2A.!!$R2 7869
14 TraesCS2D01G278900 chr2A 753698007 753698732 725 True 658.000000 658 83.607000 8950 9655 1 chr2A.!!$R1 705
15 TraesCS2D01G278900 chr5D 115061118 115063028 1910 False 2113.000000 3162 94.012500 3231 8127 2 chr5D.!!$F8 4896
16 TraesCS2D01G278900 chr5D 410958459 410959792 1333 True 1740.000000 1740 90.448000 3828 5145 1 chr5D.!!$R3 1317
17 TraesCS2D01G278900 chr5D 98664814 98665778 964 False 1472.000000 1472 94.209000 1 965 1 chr5D.!!$F2 964
18 TraesCS2D01G278900 chr5D 61575191 61578184 2993 False 1469.500000 1622 93.561500 4882 7619 2 chr5D.!!$F7 2737
19 TraesCS2D01G278900 chr5D 105061702 105062326 624 True 760.000000 760 88.818000 6945 7561 1 chr5D.!!$R1 616
20 TraesCS2D01G278900 chr5D 136065075 136065846 771 False 667.000000 667 82.763000 7362 8127 1 chr5D.!!$F3 765
21 TraesCS2D01G278900 chr5D 272361352 272362044 692 False 667.000000 667 84.648000 8950 9620 1 chr5D.!!$F4 670
22 TraesCS2D01G278900 chr2B 415354019 415359240 5221 False 1631.333333 2987 96.487667 1069 8937 3 chr2B.!!$F2 7868
23 TraesCS2D01G278900 chr2B 673627080 673628021 941 True 1234.000000 1234 90.794000 8948 9864 1 chr2B.!!$R1 916
24 TraesCS2D01G278900 chr2B 158046015 158046571 556 False 643.000000 643 88.172000 8950 9484 1 chr2B.!!$F1 534
25 TraesCS2D01G278900 chr1D 420985520 420987469 1949 False 2241.000000 2241 87.817000 3230 5145 1 chr1D.!!$F3 1915
26 TraesCS2D01G278900 chr1D 342746586 342748173 1587 True 1797.000000 1797 87.346000 3702 5289 1 chr1D.!!$R1 1587
27 TraesCS2D01G278900 chr1D 430108489 430109454 965 True 1478.000000 1478 94.330000 1 965 1 chr1D.!!$R2 964
28 TraesCS2D01G278900 chr1D 278101508 278102468 960 False 1469.000000 1469 94.221000 1 965 1 chr1D.!!$F2 964
29 TraesCS2D01G278900 chr1D 76299416 76303787 4371 False 1435.250000 2215 92.337500 3231 8127 4 chr1D.!!$F4 4896
30 TraesCS2D01G278900 chr1D 315862871 315866720 3849 True 1422.666667 2143 93.403667 3654 7619 3 chr1D.!!$R3 3965
31 TraesCS2D01G278900 chr1D 74530146 74531073 927 False 1197.000000 1197 90.333000 8952 9859 1 chr1D.!!$F1 907
32 TraesCS2D01G278900 chr3B 494227145 494228494 1349 False 1816.000000 1816 91.057000 3803 5145 1 chr3B.!!$F1 1342
33 TraesCS2D01G278900 chr3B 713230305 713231627 1322 False 1677.000000 1677 89.715000 3830 5145 1 chr3B.!!$F2 1315
34 TraesCS2D01G278900 chr3B 575793936 575798618 4682 True 459.500000 575 85.672500 6957 7617 2 chr3B.!!$R3 660
35 TraesCS2D01G278900 chr5B 461725127 461726685 1558 False 1772.000000 1772 87.484000 3604 5145 1 chr5B.!!$F2 1541
36 TraesCS2D01G278900 chr5B 339918963 339919911 948 True 1147.000000 1147 89.005000 8942 9864 1 chr5B.!!$R1 922
37 TraesCS2D01G278900 chr5B 544408064 544408757 693 False 647.000000 647 84.097000 8950 9621 1 chr5B.!!$F3 671
38 TraesCS2D01G278900 chr5B 574539384 574540043 659 True 623.000000 623 84.030000 6572 7228 1 chr5B.!!$R2 656
39 TraesCS2D01G278900 chr7D 126988443 126989401 958 True 1461.000000 1461 94.099000 1 966 1 chr7D.!!$R1 965
40 TraesCS2D01G278900 chr7D 154706086 154707956 1870 True 1127.000000 1587 94.441500 5350 7615 2 chr7D.!!$R2 2265
41 TraesCS2D01G278900 chr4D 481887026 481887995 969 True 1493.000000 1493 94.542000 1 964 1 chr4D.!!$R1 963
42 TraesCS2D01G278900 chr4D 309961938 309962874 936 False 1162.000000 1162 89.468000 8949 9864 1 chr4D.!!$F2 915
43 TraesCS2D01G278900 chr4D 333390673 333391456 783 False 689.000000 689 82.903000 7331 8127 1 chr4D.!!$F3 796
44 TraesCS2D01G278900 chr3D 580656359 580657320 961 True 1480.000000 1480 94.404000 1 965 1 chr3D.!!$R2 964
45 TraesCS2D01G278900 chr7A 580228203 580229746 1543 True 1356.000000 1356 82.886000 6566 8133 1 chr7A.!!$R1 1567
46 TraesCS2D01G278900 chrUn 315366147 315367084 937 True 1297.000000 1297 92.021000 8949 9865 1 chrUn.!!$R1 916
47 TraesCS2D01G278900 chr7B 632976906 632977845 939 True 1282.000000 1282 91.702000 8949 9865 1 chr7B.!!$R2 916
48 TraesCS2D01G278900 chr7B 725976477 725977242 765 False 874.000000 874 87.500000 9108 9864 1 chr7B.!!$F1 756
49 TraesCS2D01G278900 chr7B 360890959 360891753 794 True 636.000000 636 81.652000 7331 8129 1 chr7B.!!$R1 798
50 TraesCS2D01G278900 chr6A 128441807 128442738 931 True 1208.000000 1208 90.426000 8948 9864 1 chr6A.!!$R1 916
51 TraesCS2D01G278900 chr5A 640352153 640353096 943 False 1146.000000 1146 89.087000 8944 9864 1 chr5A.!!$F2 920
52 TraesCS2D01G278900 chr4B 594441399 594442297 898 True 1050.000000 1050 87.908000 8961 9864 1 chr4B.!!$R1 903
53 TraesCS2D01G278900 chr3A 488867394 488868368 974 False 839.000000 839 82.493000 6566 7561 1 chr3A.!!$F1 995
54 TraesCS2D01G278900 chr1B 405103783 405105224 1441 True 541.500000 756 87.804500 5528 7255 2 chr1B.!!$R2 1727
55 TraesCS2D01G278900 chr6B 462140772 462141466 694 False 671.000000 671 84.736000 8949 9621 1 chr6B.!!$F3 672
56 TraesCS2D01G278900 chr6B 669336045 669336739 694 False 671.000000 671 84.692000 8949 9621 1 chr6B.!!$F4 672
57 TraesCS2D01G278900 chr4A 570909070 570909632 562 True 632.000000 632 87.611000 8950 9491 1 chr4A.!!$R1 541

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
875 901 0.095935 CTTTGAGAAGCGTGCGATGG 59.904 55.000 0.00 0.00 0.00 3.51 F
1060 1086 0.037139 CCACCCGGTGTAATCGAACA 60.037 55.000 16.55 0.00 0.00 3.18 F
1159 1212 0.729140 CAATCGAAACAACCCGCTGC 60.729 55.000 0.00 0.00 0.00 5.25 F
1443 1496 1.107945 AGAAGCCTCTAGAAGCGTCC 58.892 55.000 21.14 9.30 38.11 4.79 F
2086 2177 3.729526 CACATTTAGTGCAGAACTCGG 57.270 47.619 0.00 0.00 42.15 4.63 F
3400 5731 1.770658 CCCCTATTCCTGCATGTCTGA 59.229 52.381 0.00 0.00 0.00 3.27 F
3940 6299 0.393132 GGACTGAGGGGCTTTGCTAC 60.393 60.000 0.00 0.00 0.00 3.58 F
4681 7052 0.884704 GCGGAGTTTGAAGGCAGTCA 60.885 55.000 0.00 0.00 0.00 3.41 F
5207 9350 1.144716 CGCTCTTGCTGGCCAGATA 59.855 57.895 37.21 21.08 36.97 1.98 F
5222 9365 2.422519 CCAGATATTGAAGCAGGCAGGT 60.423 50.000 0.00 0.00 0.00 4.00 F
5774 9967 2.710902 CGGCAGTGAGGTCGGATGA 61.711 63.158 0.00 0.00 30.96 2.92 F
7528 14028 2.037144 GGGGTGTACATCGGACAGTAT 58.963 52.381 0.00 0.00 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2124 0.958876 CACTGGATGAGCTGCTTGCA 60.959 55.000 2.53 0.00 45.94 4.08 R
2038 2129 1.367599 GAGTGCACTGGATGAGCTGC 61.368 60.000 27.27 0.95 33.37 5.25 R
2632 2727 1.381872 AGGGATCCACGAGTGAGGG 60.382 63.158 15.23 0.00 0.00 4.30 R
2713 2810 3.129871 GACATCAGGCTCTGCTTCATAC 58.870 50.000 0.00 0.00 0.00 2.39 R
3600 5931 0.106469 TCCAGGAGGATGGACTCTCG 60.106 60.000 0.00 0.00 44.56 4.04 R
5363 9551 1.000731 TCGGCTGCCCAAAGAAAATTG 59.999 47.619 14.12 0.00 0.00 2.32 R
5712 9905 4.077184 CCCTACCGCCTCACGCAA 62.077 66.667 0.00 0.00 41.76 4.85 R
6978 13319 4.949856 TCGCTACTCCATATATCATCTGCA 59.050 41.667 0.00 0.00 0.00 4.41 R
7272 13756 1.723608 CCACGCTGTTGCTGGTTTCA 61.724 55.000 0.00 0.00 34.79 2.69 R
7448 13939 2.683933 GAGAGCCCCGAACCTGGA 60.684 66.667 0.00 0.00 0.00 3.86 R
7623 14167 0.389296 TACTCGTTCGGCCACACATG 60.389 55.000 2.24 0.00 0.00 3.21 R
9138 16246 0.729690 GGGAGATTTGCAGCTTCGAC 59.270 55.000 0.00 0.00 0.00 4.20 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
51 52 0.251916 TGAACCTCTGGTTATGGCCG 59.748 55.000 0.00 0.00 46.95 6.13
88 89 0.674895 GGCCACTTGCTCTTCGACAT 60.675 55.000 0.00 0.00 40.92 3.06
186 187 1.483827 CTAAGCATCCACAGAGCCTCA 59.516 52.381 0.00 0.00 0.00 3.86
223 224 7.607991 AGTTGTAGATGTAGTTCAGATTTTGGG 59.392 37.037 0.00 0.00 0.00 4.12
278 279 0.905357 CGGATCAAAGGTCTCCCAGT 59.095 55.000 0.00 0.00 0.00 4.00
875 901 0.095935 CTTTGAGAAGCGTGCGATGG 59.904 55.000 0.00 0.00 0.00 3.51
920 946 1.074566 CCAAACAGGCCTCTCCTTTCT 59.925 52.381 0.00 0.00 44.75 2.52
922 948 1.734655 AACAGGCCTCTCCTTTCTCA 58.265 50.000 0.00 0.00 44.75 3.27
926 952 1.293498 GCCTCTCCTTTCTCACGCA 59.707 57.895 0.00 0.00 0.00 5.24
929 955 0.605589 CTCTCCTTTCTCACGCAGGT 59.394 55.000 0.00 0.00 0.00 4.00
930 956 1.001406 CTCTCCTTTCTCACGCAGGTT 59.999 52.381 0.00 0.00 0.00 3.50
936 962 2.623878 TTCTCACGCAGGTTTGGTTA 57.376 45.000 0.00 0.00 0.00 2.85
941 967 0.179001 ACGCAGGTTTGGTTAGGCTT 60.179 50.000 0.00 0.00 0.00 4.35
969 995 1.527380 AACCAAACACGCCCGACAT 60.527 52.632 0.00 0.00 0.00 3.06
971 997 1.081509 CCAAACACGCCCGACATTG 60.082 57.895 0.00 0.00 0.00 2.82
972 998 1.652012 CAAACACGCCCGACATTGT 59.348 52.632 0.00 0.00 0.00 2.71
973 999 0.660005 CAAACACGCCCGACATTGTG 60.660 55.000 0.00 0.00 38.28 3.33
975 1001 4.101790 CACGCCCGACATTGTGCC 62.102 66.667 0.00 0.00 0.00 5.01
1054 1080 4.789123 GCGCCCACCCGGTGTAAT 62.789 66.667 16.55 0.00 44.74 1.89
1055 1081 2.512974 CGCCCACCCGGTGTAATC 60.513 66.667 16.55 1.79 37.36 1.75
1056 1082 2.512974 GCCCACCCGGTGTAATCG 60.513 66.667 16.55 0.42 0.00 3.34
1057 1083 3.021473 GCCCACCCGGTGTAATCGA 62.021 63.158 16.55 0.00 0.00 3.59
1058 1084 1.597989 CCCACCCGGTGTAATCGAA 59.402 57.895 16.55 0.00 0.00 3.71
1059 1085 0.741927 CCCACCCGGTGTAATCGAAC 60.742 60.000 16.55 0.00 0.00 3.95
1060 1086 0.037139 CCACCCGGTGTAATCGAACA 60.037 55.000 16.55 0.00 0.00 3.18
1067 1093 0.733566 GTGTAATCGAACACGCGGGA 60.734 55.000 19.19 1.29 40.31 5.14
1159 1212 0.729140 CAATCGAAACAACCCGCTGC 60.729 55.000 0.00 0.00 0.00 5.25
1318 1371 3.549423 CGTATATCGACGACACCACCAAT 60.549 47.826 0.00 0.00 45.82 3.16
1401 1454 3.136260 GCTTCTTCTCCATCTCCCTCAAT 59.864 47.826 0.00 0.00 0.00 2.57
1443 1496 1.107945 AGAAGCCTCTAGAAGCGTCC 58.892 55.000 21.14 9.30 38.11 4.79
2033 2124 4.347000 TGGGTTAGTGCAGAACTAGAAAGT 59.653 41.667 10.42 0.00 42.38 2.66
2038 2129 3.812053 AGTGCAGAACTAGAAAGTGCAAG 59.188 43.478 12.93 0.00 37.36 4.01
2086 2177 3.729526 CACATTTAGTGCAGAACTCGG 57.270 47.619 0.00 0.00 42.15 4.63
2090 2181 3.887621 TTTAGTGCAGAACTCGGCTAT 57.112 42.857 3.55 0.00 40.56 2.97
2166 2261 5.699839 CATAAAACCTTTTTCTCTGGTCCG 58.300 41.667 0.00 0.00 32.98 4.79
2632 2727 4.515567 CCTTTTTCTGTGTAGTCAGTTCCC 59.484 45.833 0.00 0.00 36.85 3.97
2713 2810 7.414098 GCTTATTGCCTTACCGATAATATGTGG 60.414 40.741 0.00 0.00 35.15 4.17
2758 2855 2.523245 TGGATTGGTACTGCAATGCAA 58.477 42.857 9.92 0.00 38.41 4.08
2792 2889 5.655488 AGTCAGATTACAGAAATGGTCGAG 58.345 41.667 0.00 0.00 0.00 4.04
2933 5263 1.818674 CAGGCCTTGTTTGTATGGGAC 59.181 52.381 0.00 0.00 0.00 4.46
3092 5423 9.088987 AGAAACCAAACACCTATGATTTATTGT 57.911 29.630 0.00 0.00 0.00 2.71
3200 5531 4.940046 ACTAACACTCATGCAGGATTCTTG 59.060 41.667 0.00 0.00 0.00 3.02
3223 5554 5.831997 GTTGCAAACTGGAGTTTTATGAGT 58.168 37.500 0.00 0.00 45.07 3.41
3225 5556 5.129634 TGCAAACTGGAGTTTTATGAGTCA 58.870 37.500 1.90 0.00 45.07 3.41
3226 5557 5.239306 TGCAAACTGGAGTTTTATGAGTCAG 59.761 40.000 1.90 0.00 45.07 3.51
3227 5558 5.239525 GCAAACTGGAGTTTTATGAGTCAGT 59.760 40.000 1.90 0.00 45.07 3.41
3228 5559 6.426937 GCAAACTGGAGTTTTATGAGTCAGTA 59.573 38.462 1.90 0.00 45.07 2.74
3386 5717 4.794616 TCTCCGGAGAGATAATACCCCTAT 59.205 45.833 30.49 0.00 44.42 2.57
3400 5731 1.770658 CCCCTATTCCTGCATGTCTGA 59.229 52.381 0.00 0.00 0.00 3.27
3401 5732 2.224475 CCCCTATTCCTGCATGTCTGAG 60.224 54.545 0.00 0.00 0.00 3.35
3402 5733 2.437281 CCCTATTCCTGCATGTCTGAGT 59.563 50.000 0.00 0.00 0.00 3.41
3403 5734 3.643320 CCCTATTCCTGCATGTCTGAGTA 59.357 47.826 0.00 0.00 0.00 2.59
3404 5735 4.285517 CCCTATTCCTGCATGTCTGAGTAT 59.714 45.833 0.00 0.00 0.00 2.12
3600 5931 1.383456 TTGCTTGAGTGTGGGTGCAC 61.383 55.000 8.80 8.80 39.51 4.57
3764 6100 3.067106 GGACAAGTGTCACTGTACATGG 58.933 50.000 6.18 0.00 46.47 3.66
3801 6160 3.614150 CGTGTACAGTGCTCAGGTACATT 60.614 47.826 19.48 0.00 46.17 2.71
3940 6299 0.393132 GGACTGAGGGGCTTTGCTAC 60.393 60.000 0.00 0.00 0.00 3.58
4002 6361 1.087771 CGTGGCCAATTACTCCGACC 61.088 60.000 7.24 0.00 0.00 4.79
4046 6406 2.282180 GGCAAAGTTGGGCGGAGA 60.282 61.111 0.00 0.00 0.00 3.71
4574 6942 5.437060 ACTGTAATAAAATGCGGAGATGGT 58.563 37.500 0.00 0.00 0.00 3.55
4675 7046 3.876300 CGAGGCGGAGTTTGAAGG 58.124 61.111 0.00 0.00 0.00 3.46
4681 7052 0.884704 GCGGAGTTTGAAGGCAGTCA 60.885 55.000 0.00 0.00 0.00 3.41
4986 7415 1.201880 GGCGACTACCTCGTCTTCTTT 59.798 52.381 0.00 0.00 44.08 2.52
5207 9350 1.144716 CGCTCTTGCTGGCCAGATA 59.855 57.895 37.21 21.08 36.97 1.98
5222 9365 2.422519 CCAGATATTGAAGCAGGCAGGT 60.423 50.000 0.00 0.00 0.00 4.00
5363 9551 4.722700 TCTTGGGCAGCCGGCTTC 62.723 66.667 30.60 24.27 44.01 3.86
5774 9967 2.710902 CGGCAGTGAGGTCGGATGA 61.711 63.158 0.00 0.00 30.96 2.92
5786 9979 4.814294 GGATGAAGGCGGACGCGT 62.814 66.667 13.85 13.85 43.06 6.01
7030 13373 3.064324 GGCCGGAGCAAAGCACAT 61.064 61.111 5.05 0.00 42.56 3.21
7496 13987 2.263895 TACCCCTACTCCTGCATGTT 57.736 50.000 0.00 0.00 0.00 2.71
7528 14028 2.037144 GGGGTGTACATCGGACAGTAT 58.963 52.381 0.00 0.00 0.00 2.12
7619 14163 2.668212 CCATGTGTGGCCGAACGT 60.668 61.111 0.00 0.00 39.01 3.99
7620 14164 2.555782 CATGTGTGGCCGAACGTG 59.444 61.111 13.64 13.64 0.00 4.49
7621 14165 2.668212 ATGTGTGGCCGAACGTGG 60.668 61.111 0.00 0.00 0.00 4.94
7629 14173 2.668212 CCGAACGTGGCCATGTGT 60.668 61.111 30.95 19.92 0.00 3.72
7630 14174 2.555782 CGAACGTGGCCATGTGTG 59.444 61.111 30.95 21.39 0.00 3.82
7820 14414 1.304381 GCATGGTGGGGTGTCACAT 60.304 57.895 5.12 0.00 39.27 3.21
7851 14447 5.431765 CTGGGTCACTTCATAAATAGTGCT 58.568 41.667 0.00 0.00 41.16 4.40
7867 14463 1.059098 TGCTCAGGGACAAGTGTCAT 58.941 50.000 13.21 0.00 46.47 3.06
7914 14510 3.056821 GTGTACAGTGCTCAGGTACATCA 60.057 47.826 19.48 2.73 46.17 3.07
7929 14556 1.686587 ACATCAGTCTTGTCGGTGTCA 59.313 47.619 0.00 0.00 0.00 3.58
8077 14733 1.718757 GCTTTGCTAGCCCCGATGTG 61.719 60.000 13.29 0.00 44.48 3.21
8138 14795 7.876582 GGCCAATTACTCCGATAAGTACTATTT 59.123 37.037 0.00 0.00 31.57 1.40
8249 14909 6.016777 CCATTGGGTCAGTGCTATAAATCTTC 60.017 42.308 0.00 0.00 0.00 2.87
8424 15243 6.264518 GGAAACTGAATAGGAAAAGACCAACA 59.735 38.462 0.00 0.00 0.00 3.33
8692 15511 7.663630 ATCGCATATGTTAATTGTGAAAACG 57.336 32.000 4.29 0.00 33.97 3.60
8695 15514 8.604890 TCGCATATGTTAATTGTGAAAACGATA 58.395 29.630 4.29 0.00 0.00 2.92
8729 15548 6.887626 TTATTCAGTGTTTACCCTGGAAAC 57.112 37.500 0.00 0.00 37.32 2.78
8827 15647 5.422331 CACTGAACCTAATAAGAGTCCCTCA 59.578 44.000 0.00 0.00 32.06 3.86
8919 15785 1.613317 AACATGCGGTGGATCGGAGA 61.613 55.000 0.00 0.00 45.75 3.71
8942 15808 8.540507 AGAGAGTATTATAGTTGTGACCATGT 57.459 34.615 0.00 0.00 0.00 3.21
8943 15809 8.417106 AGAGAGTATTATAGTTGTGACCATGTG 58.583 37.037 0.00 0.00 0.00 3.21
9041 16011 0.599060 GGAAAATCGGGCGAAAACCA 59.401 50.000 0.00 0.00 0.00 3.67
9104 16199 1.266867 GGCAAAGCCCACCCATGAAT 61.267 55.000 0.00 0.00 44.06 2.57
9162 16270 1.078143 GCTGCAAATCTCCCGAGGT 60.078 57.895 0.00 0.00 0.00 3.85
9220 16328 0.180406 ACTCAACTGACACCGCCTTT 59.820 50.000 0.00 0.00 0.00 3.11
9363 16691 2.512286 CGACATGCCACCGCTCAT 60.512 61.111 0.00 0.00 35.36 2.90
9453 16781 3.047280 GAACGCCGCACCACATCA 61.047 61.111 0.00 0.00 0.00 3.07
9461 16789 4.033776 CACCACATCAGGGGCCGT 62.034 66.667 0.00 0.00 0.00 5.68
9825 17235 5.569630 GCACATGAAAGGAGAGGAAGAACTA 60.570 44.000 0.00 0.00 0.00 2.24
9839 17249 2.826428 AGAACTATACGACGACGCCTA 58.174 47.619 7.30 0.00 43.96 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.474077 GCCATGTTCCTCCATGTTGTC 59.526 52.381 0.00 0.00 40.50 3.18
88 89 4.635765 GCTACAAGATAGCATCAACACCAA 59.364 41.667 1.06 0.00 40.14 3.67
186 187 6.881065 ACTACATCTACAACTGCAATGACATT 59.119 34.615 6.19 0.00 0.00 2.71
223 224 2.359967 CCCGGGAACAGGAGAGGAC 61.360 68.421 18.48 0.00 0.00 3.85
278 279 2.096013 CACGAGAGAGCTGTTCATCGTA 59.904 50.000 18.77 0.00 43.94 3.43
633 649 1.613630 CCCTACTGCCTCACCACCT 60.614 63.158 0.00 0.00 0.00 4.00
722 741 0.181350 GGGAGATGGAAATCTGGCGT 59.819 55.000 0.00 0.00 0.00 5.68
752 773 4.200283 GAGCGAGGTGAGGGCGAG 62.200 72.222 0.00 0.00 0.00 5.03
855 881 0.792640 CATCGCACGCTTCTCAAAGT 59.207 50.000 0.00 0.00 34.79 2.66
875 901 1.341209 CTGGTTTTTCTGTTGGGCCTC 59.659 52.381 4.53 0.00 0.00 4.70
887 913 2.355615 CCTGTTTGGTTGCCTGGTTTTT 60.356 45.455 0.00 0.00 0.00 1.94
916 942 1.757682 AACCAAACCTGCGTGAGAAA 58.242 45.000 0.00 0.00 0.00 2.52
920 946 0.887387 GCCTAACCAAACCTGCGTGA 60.887 55.000 0.00 0.00 0.00 4.35
922 948 0.179001 AAGCCTAACCAAACCTGCGT 60.179 50.000 0.00 0.00 0.00 5.24
926 952 2.171003 GCATCAAGCCTAACCAAACCT 58.829 47.619 0.00 0.00 37.23 3.50
929 955 2.170166 CCTGCATCAAGCCTAACCAAA 58.830 47.619 0.00 0.00 44.83 3.28
930 956 1.838112 CCTGCATCAAGCCTAACCAA 58.162 50.000 0.00 0.00 44.83 3.67
936 962 1.980772 GGTTGCCTGCATCAAGCCT 60.981 57.895 15.84 0.00 44.83 4.58
941 967 0.388659 GTGTTTGGTTGCCTGCATCA 59.611 50.000 0.00 0.00 0.00 3.07
987 1013 4.544047 TGTCGTGCCTGCACAGCA 62.544 61.111 21.01 15.30 46.47 4.41
989 1015 3.720193 GCTGTCGTGCCTGCACAG 61.720 66.667 21.01 12.37 46.47 3.66
1040 1066 0.741927 GTTCGATTACACCGGGTGGG 60.742 60.000 29.44 13.63 40.75 4.61
1041 1067 0.037139 TGTTCGATTACACCGGGTGG 60.037 55.000 29.44 12.53 37.94 4.61
1042 1068 1.073177 GTGTTCGATTACACCGGGTG 58.927 55.000 25.21 25.21 41.99 4.61
1043 1069 0.388907 CGTGTTCGATTACACCGGGT 60.389 55.000 13.38 3.22 44.32 5.28
1044 1070 1.689352 GCGTGTTCGATTACACCGGG 61.689 60.000 13.38 0.00 44.32 5.73
1046 1072 1.339134 CGCGTGTTCGATTACACCG 59.661 57.895 13.38 13.26 44.32 4.94
1047 1073 1.689352 CCCGCGTGTTCGATTACACC 61.689 60.000 13.38 6.75 44.32 4.16
1048 1074 0.733566 TCCCGCGTGTTCGATTACAC 60.734 55.000 4.92 9.84 43.86 2.90
1049 1075 0.733566 GTCCCGCGTGTTCGATTACA 60.734 55.000 4.92 0.00 39.71 2.41
1050 1076 0.733566 TGTCCCGCGTGTTCGATTAC 60.734 55.000 4.92 0.00 39.71 1.89
1051 1077 0.173935 ATGTCCCGCGTGTTCGATTA 59.826 50.000 4.92 0.00 39.71 1.75
1052 1078 1.079405 ATGTCCCGCGTGTTCGATT 60.079 52.632 4.92 0.00 39.71 3.34
1054 1080 2.431771 CATGTCCCGCGTGTTCGA 60.432 61.111 4.92 0.00 39.71 3.71
1055 1081 2.726691 GACATGTCCCGCGTGTTCG 61.727 63.158 15.31 0.00 46.49 3.95
1056 1082 2.388232 GGACATGTCCCGCGTGTTC 61.388 63.158 31.37 5.45 46.49 3.18
1057 1083 2.358247 GGACATGTCCCGCGTGTT 60.358 61.111 31.37 0.00 46.49 3.32
1067 1093 0.392998 GAATGGACAGCCGGACATGT 60.393 55.000 5.05 6.33 36.79 3.21
1159 1212 3.121030 CGGTCTGCTTCGGCCAAG 61.121 66.667 2.24 7.07 40.91 3.61
1318 1371 3.766691 GGCGGCGACAAGTAGGGA 61.767 66.667 12.98 0.00 0.00 4.20
1401 1454 2.184322 GGCTGAGGAACGCGATGA 59.816 61.111 15.93 0.00 0.00 2.92
2033 2124 0.958876 CACTGGATGAGCTGCTTGCA 60.959 55.000 2.53 0.00 45.94 4.08
2038 2129 1.367599 GAGTGCACTGGATGAGCTGC 61.368 60.000 27.27 0.95 33.37 5.25
2085 2176 9.549078 AGCTAAATCTAGTAAAAACTCATAGCC 57.451 33.333 0.00 0.00 0.00 3.93
2632 2727 1.381872 AGGGATCCACGAGTGAGGG 60.382 63.158 15.23 0.00 0.00 4.30
2713 2810 3.129871 GACATCAGGCTCTGCTTCATAC 58.870 50.000 0.00 0.00 0.00 2.39
2792 2889 4.759183 AGCAAGACCAAAATCAGAGTTCTC 59.241 41.667 0.00 0.00 0.00 2.87
2844 2941 4.104579 TGCTATATTTGCCAGGAAGGATCA 59.895 41.667 0.00 0.00 41.22 2.92
3015 5346 3.384146 CCATGTGCAAGGCCAATGTATAA 59.616 43.478 5.01 0.00 0.00 0.98
3092 5423 5.827267 TGTTTTTCTCATCATGACAAGTGGA 59.173 36.000 0.00 0.00 0.00 4.02
3200 5531 5.831997 ACTCATAAAACTCCAGTTTGCAAC 58.168 37.500 0.00 0.00 46.47 4.17
3223 5554 4.155462 GTGAGAATACCACGACAGTACTGA 59.845 45.833 29.30 5.21 0.00 3.41
3225 5556 4.698583 GTGAGAATACCACGACAGTACT 57.301 45.455 0.00 0.00 0.00 2.73
3386 5717 8.885693 ATATACTATACTCAGACATGCAGGAA 57.114 34.615 4.84 0.00 0.00 3.36
3400 5731 7.774157 CGATGTACACCCCAGATATACTATACT 59.226 40.741 0.00 0.00 0.00 2.12
3401 5732 7.013083 CCGATGTACACCCCAGATATACTATAC 59.987 44.444 0.00 0.00 0.00 1.47
3402 5733 7.058525 CCGATGTACACCCCAGATATACTATA 58.941 42.308 0.00 0.00 0.00 1.31
3403 5734 5.892119 CCGATGTACACCCCAGATATACTAT 59.108 44.000 0.00 0.00 0.00 2.12
3404 5735 5.014438 TCCGATGTACACCCCAGATATACTA 59.986 44.000 0.00 0.00 0.00 1.82
3600 5931 0.106469 TCCAGGAGGATGGACTCTCG 60.106 60.000 0.00 0.00 44.56 4.04
3801 6160 2.640989 CCGACACCGACAAGACGA 59.359 61.111 0.00 0.00 38.22 4.20
3940 6299 4.207165 ACAATAATTCAAGACATCGGGGG 58.793 43.478 0.00 0.00 0.00 5.40
4423 6789 1.332195 CCCACTCTCAGTCACAGACA 58.668 55.000 0.00 0.00 34.60 3.41
4675 7046 3.046087 TTGAGCTGCGCTGACTGC 61.046 61.111 19.32 9.84 39.88 4.40
5207 9350 1.065126 GGTCTACCTGCCTGCTTCAAT 60.065 52.381 0.00 0.00 0.00 2.57
5222 9365 1.522355 CTAGACGCGACCCGGTCTA 60.522 63.158 15.93 7.46 42.52 2.59
5363 9551 1.000731 TCGGCTGCCCAAAGAAAATTG 59.999 47.619 14.12 0.00 0.00 2.32
5712 9905 4.077184 CCCTACCGCCTCACGCAA 62.077 66.667 0.00 0.00 41.76 4.85
6974 13315 7.415653 CGCTACTCCATATATCATCTGCACTAA 60.416 40.741 0.00 0.00 0.00 2.24
6978 13319 4.949856 TCGCTACTCCATATATCATCTGCA 59.050 41.667 0.00 0.00 0.00 4.41
7030 13373 3.473647 CATCCGCTCCCCTCTGCA 61.474 66.667 0.00 0.00 0.00 4.41
7102 13468 4.761845 TGCGACGCCGGCCATTTA 62.762 61.111 23.46 1.37 36.06 1.40
7272 13756 1.723608 CCACGCTGTTGCTGGTTTCA 61.724 55.000 0.00 0.00 34.79 2.69
7448 13939 2.683933 GAGAGCCCCGAACCTGGA 60.684 66.667 0.00 0.00 0.00 3.86
7496 13987 5.243060 CGATGTACACCCCAGATATACTCAA 59.757 44.000 0.00 0.00 0.00 3.02
7623 14167 0.389296 TACTCGTTCGGCCACACATG 60.389 55.000 2.24 0.00 0.00 3.21
7624 14168 0.535335 ATACTCGTTCGGCCACACAT 59.465 50.000 2.24 0.00 0.00 3.21
7625 14169 0.389296 CATACTCGTTCGGCCACACA 60.389 55.000 2.24 0.00 0.00 3.72
7626 14170 0.389426 ACATACTCGTTCGGCCACAC 60.389 55.000 2.24 0.00 0.00 3.82
7627 14171 0.389296 CACATACTCGTTCGGCCACA 60.389 55.000 2.24 0.00 0.00 4.17
7628 14172 0.389426 ACACATACTCGTTCGGCCAC 60.389 55.000 2.24 0.00 0.00 5.01
7629 14173 1.135315 GTACACATACTCGTTCGGCCA 60.135 52.381 2.24 0.00 0.00 5.36
7630 14174 1.133790 AGTACACATACTCGTTCGGCC 59.866 52.381 0.00 0.00 36.97 6.13
7631 14175 2.448219 GAGTACACATACTCGTTCGGC 58.552 52.381 0.00 0.00 46.03 5.54
7820 14414 0.476771 GAAGTGACCCAGGGGACAAA 59.523 55.000 11.37 0.00 41.12 2.83
7851 14447 3.389656 TGTACAATGACACTTGTCCCTGA 59.610 43.478 6.91 0.00 44.15 3.86
7867 14463 0.998928 ACCCCAGCCATCATGTACAA 59.001 50.000 0.00 0.00 0.00 2.41
7914 14510 1.120530 AACCTGACACCGACAAGACT 58.879 50.000 0.00 0.00 0.00 3.24
7929 14556 2.671070 CCGACTGCATCCCAACCT 59.329 61.111 0.00 0.00 0.00 3.50
8039 14695 2.997315 CCTCAGTCCGACTGCCCA 60.997 66.667 21.75 6.02 45.54 5.36
8077 14733 3.617263 AGACGGCGAGACAATAATTCAAC 59.383 43.478 16.62 0.00 0.00 3.18
8249 14909 5.186996 ACTGTTAATGGACAAAGTTGCAG 57.813 39.130 0.00 0.00 0.00 4.41
8383 15202 6.240894 TCAGTTTCCTATGCAAGACTTTGAT 58.759 36.000 0.00 0.00 36.36 2.57
8398 15217 6.200878 TGGTCTTTTCCTATTCAGTTTCCT 57.799 37.500 0.00 0.00 0.00 3.36
8424 15243 7.092079 CACACAACATCCATTCACAAATGTAT 58.908 34.615 0.00 0.00 40.63 2.29
8695 15514 8.241367 GGTAAACACTGAATAATCCGAAAACAT 58.759 33.333 0.00 0.00 0.00 2.71
8729 15548 5.591472 AGGTCAACATCATACATCACCATTG 59.409 40.000 0.00 0.00 0.00 2.82
8827 15647 5.840149 ACATATGCATAATGTTCCCACCATT 59.160 36.000 11.13 0.00 36.53 3.16
8919 15785 7.500992 CCACATGGTCACAACTATAATACTCT 58.499 38.462 0.00 0.00 0.00 3.24
9041 16011 1.115326 GGCTTGGCCCTTGTTGTTCT 61.115 55.000 0.00 0.00 44.06 3.01
9062 16034 1.342174 GTGTGTGTTAGTCTTCGGGGA 59.658 52.381 0.00 0.00 0.00 4.81
9067 16039 3.138304 TGCCATGTGTGTGTTAGTCTTC 58.862 45.455 0.00 0.00 0.00 2.87
9104 16199 2.354891 CGTGTGGGCGACGTGTTA 60.355 61.111 0.00 0.00 32.06 2.41
9138 16246 0.729690 GGGAGATTTGCAGCTTCGAC 59.270 55.000 0.00 0.00 0.00 4.20
9162 16270 1.960040 AATGGATGTCGAGGCAGCGA 61.960 55.000 0.00 0.00 38.07 4.93
9342 16670 4.856801 GCGGTGGCATGTCGGGAT 62.857 66.667 0.00 0.00 39.62 3.85
9363 16691 4.742201 GGCGTTGCTGCTCGAGGA 62.742 66.667 15.58 11.15 34.52 3.71
9825 17235 1.372582 TCTTGTAGGCGTCGTCGTAT 58.627 50.000 3.66 0.00 39.49 3.06
9839 17249 0.106149 GGGTGTCGTGACCTTCTTGT 59.894 55.000 5.73 0.00 36.14 3.16


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

AutoCloner maintained by Alex Coulton.