Multiple sequence alignment - TraesCS5D01G065000

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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 TraesCS5D01G065000 chr5D 100.000 3643 0 0 1 3643 60466142 60469784 0.000000e+00 6728
1 TraesCS5D01G065000 chr5D 91.889 937 71 5 2 936 60255752 60254819 0.000000e+00 1304
2 TraesCS5D01G065000 chr5D 93.612 814 52 0 2830 3643 41696389 41695576 0.000000e+00 1216
3 TraesCS5D01G065000 chr5D 86.752 234 16 8 1434 1666 3967382 3967601 2.810000e-61 246
4 TraesCS5D01G065000 chr5A 93.774 1044 47 8 932 1964 48881008 48882044 0.000000e+00 1552
5 TraesCS5D01G065000 chr5A 92.766 788 46 5 2028 2807 48882417 48883201 0.000000e+00 1129
6 TraesCS5D01G065000 chr5A 80.137 146 24 4 1019 1162 572500591 572500449 1.790000e-18 104
7 TraesCS5D01G065000 chr2D 93.355 933 56 6 2 931 276936604 276935675 0.000000e+00 1375
8 TraesCS5D01G065000 chr2D 93.041 934 62 3 2 935 285349158 285350088 0.000000e+00 1362
9 TraesCS5D01G065000 chr2D 93.742 815 49 2 2829 3643 30355182 30355994 0.000000e+00 1221
10 TraesCS5D01G065000 chr7D 93.333 930 57 3 2 928 145919904 145918977 0.000000e+00 1369
11 TraesCS5D01G065000 chr7D 92.696 931 61 7 2 928 616465764 616464837 0.000000e+00 1336
12 TraesCS5D01G065000 chr7D 92.680 929 61 6 2 927 164762035 164761111 0.000000e+00 1332
13 TraesCS5D01G065000 chr7D 92.672 928 61 5 2 928 576644888 576643967 0.000000e+00 1330
14 TraesCS5D01G065000 chr1D 92.565 928 65 4 2 928 481641433 481642357 0.000000e+00 1328
15 TraesCS5D01G065000 chr6B 92.275 932 63 8 4 934 626810098 626809175 0.000000e+00 1314
16 TraesCS5D01G065000 chr3D 94.002 817 47 1 2827 3643 11422411 11421597 0.000000e+00 1236
17 TraesCS5D01G065000 chr3D 93.627 816 49 1 2828 3643 581791739 581792551 0.000000e+00 1216
18 TraesCS5D01G065000 chr5B 92.875 814 58 0 2830 3643 161154909 161155722 0.000000e+00 1182
19 TraesCS5D01G065000 chr5B 93.569 622 36 3 2195 2814 70277460 70276841 0.000000e+00 924
20 TraesCS5D01G065000 chr5B 80.741 135 24 2 1033 1167 553947841 553947973 1.790000e-18 104
21 TraesCS5D01G065000 chr6D 92.883 815 54 2 2829 3643 445039460 445040270 0.000000e+00 1181
22 TraesCS5D01G065000 chr6D 83.709 577 85 7 2056 2630 14187282 14187851 1.490000e-148 536
23 TraesCS5D01G065000 chr6D 80.769 572 96 9 2061 2630 14204881 14205440 5.590000e-118 435
24 TraesCS5D01G065000 chr6D 81.944 216 30 6 1019 1226 281845056 281845270 1.340000e-39 174
25 TraesCS5D01G065000 chrUn 92.289 830 62 2 2814 3643 29278717 29279544 0.000000e+00 1177
26 TraesCS5D01G065000 chr7B 92.326 821 57 5 2828 3643 725969220 725970039 0.000000e+00 1162
27 TraesCS5D01G065000 chr4B 92.270 815 63 0 2829 3643 103018606 103017792 0.000000e+00 1157
28 TraesCS5D01G065000 chr6A 86.667 555 52 7 1019 1551 15452686 15453240 2.420000e-166 595
29 TraesCS5D01G065000 chr6A 83.226 620 88 12 2013 2630 15454611 15455216 4.110000e-154 555


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 TraesCS5D01G065000 chr5D 60466142 60469784 3642 False 6728.0 6728 100.0000 1 3643 1 chr5D.!!$F2 3642
1 TraesCS5D01G065000 chr5D 60254819 60255752 933 True 1304.0 1304 91.8890 2 936 1 chr5D.!!$R2 934
2 TraesCS5D01G065000 chr5D 41695576 41696389 813 True 1216.0 1216 93.6120 2830 3643 1 chr5D.!!$R1 813
3 TraesCS5D01G065000 chr5A 48881008 48883201 2193 False 1340.5 1552 93.2700 932 2807 2 chr5A.!!$F1 1875
4 TraesCS5D01G065000 chr2D 276935675 276936604 929 True 1375.0 1375 93.3550 2 931 1 chr2D.!!$R1 929
5 TraesCS5D01G065000 chr2D 285349158 285350088 930 False 1362.0 1362 93.0410 2 935 1 chr2D.!!$F2 933
6 TraesCS5D01G065000 chr2D 30355182 30355994 812 False 1221.0 1221 93.7420 2829 3643 1 chr2D.!!$F1 814
7 TraesCS5D01G065000 chr7D 145918977 145919904 927 True 1369.0 1369 93.3330 2 928 1 chr7D.!!$R1 926
8 TraesCS5D01G065000 chr7D 616464837 616465764 927 True 1336.0 1336 92.6960 2 928 1 chr7D.!!$R4 926
9 TraesCS5D01G065000 chr7D 164761111 164762035 924 True 1332.0 1332 92.6800 2 927 1 chr7D.!!$R2 925
10 TraesCS5D01G065000 chr7D 576643967 576644888 921 True 1330.0 1330 92.6720 2 928 1 chr7D.!!$R3 926
11 TraesCS5D01G065000 chr1D 481641433 481642357 924 False 1328.0 1328 92.5650 2 928 1 chr1D.!!$F1 926
12 TraesCS5D01G065000 chr6B 626809175 626810098 923 True 1314.0 1314 92.2750 4 934 1 chr6B.!!$R1 930
13 TraesCS5D01G065000 chr3D 11421597 11422411 814 True 1236.0 1236 94.0020 2827 3643 1 chr3D.!!$R1 816
14 TraesCS5D01G065000 chr3D 581791739 581792551 812 False 1216.0 1216 93.6270 2828 3643 1 chr3D.!!$F1 815
15 TraesCS5D01G065000 chr5B 161154909 161155722 813 False 1182.0 1182 92.8750 2830 3643 1 chr5B.!!$F1 813
16 TraesCS5D01G065000 chr5B 70276841 70277460 619 True 924.0 924 93.5690 2195 2814 1 chr5B.!!$R1 619
17 TraesCS5D01G065000 chr6D 445039460 445040270 810 False 1181.0 1181 92.8830 2829 3643 1 chr6D.!!$F4 814
18 TraesCS5D01G065000 chr6D 14187282 14187851 569 False 536.0 536 83.7090 2056 2630 1 chr6D.!!$F1 574
19 TraesCS5D01G065000 chr6D 14204881 14205440 559 False 435.0 435 80.7690 2061 2630 1 chr6D.!!$F2 569
20 TraesCS5D01G065000 chrUn 29278717 29279544 827 False 1177.0 1177 92.2890 2814 3643 1 chrUn.!!$F1 829
21 TraesCS5D01G065000 chr7B 725969220 725970039 819 False 1162.0 1162 92.3260 2828 3643 1 chr7B.!!$F1 815
22 TraesCS5D01G065000 chr4B 103017792 103018606 814 True 1157.0 1157 92.2700 2829 3643 1 chr4B.!!$R1 814
23 TraesCS5D01G065000 chr6A 15452686 15455216 2530 False 575.0 595 84.9465 1019 2630 2 chr6A.!!$F1 1611

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
886 899 0.179121 GACGCGGATCCATGTGTGTA 60.179 55.0 12.47 0.0 0.00 2.90 F
994 1007 0.885196 GGCGAGTGAGAGAGTCAACT 59.115 55.0 0.00 0.0 36.74 3.16 F
2235 3614 1.192146 TGACCGAGGAAGAACTGGGG 61.192 60.0 0.00 0.0 40.29 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 3482 0.167470 TCTTTAGGACAGTCGCGACG 59.833 55.0 31.56 26.74 36.20 5.12 R
2457 3839 0.666577 CCAAAGGACTCGACACCGAC 60.667 60.0 0.00 0.00 40.30 4.79 R
3176 4571 0.731417 GCAAGGTAGATGCAGCAGTG 59.269 55.0 4.07 0.00 43.29 3.66 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
41 42 3.563508 CAAAATGCATAACGCTCACACA 58.436 40.909 0.00 0.00 43.06 3.72
163 164 0.819259 AACTGCAGTTGCCATGTCGT 60.819 50.000 30.66 2.58 41.18 4.34
318 320 9.777297 ATAGTTGCCATGATTTAAAAACTTTGT 57.223 25.926 0.00 0.00 0.00 2.83
410 412 1.123928 CCTTAGGAGTGGCCACCTAG 58.876 60.000 32.29 19.97 39.48 3.02
476 480 5.063564 GCAAAACAACATGTTCGGGTAAAAA 59.936 36.000 8.48 0.00 40.14 1.94
479 483 5.838531 ACAACATGTTCGGGTAAAAAGAA 57.161 34.783 8.48 0.00 0.00 2.52
547 552 2.035704 CCTGCAAAACACATGGCAACTA 59.964 45.455 0.00 0.00 35.59 2.24
627 636 2.627221 TGCCATGTACACTGCAAAACAT 59.373 40.909 16.42 0.00 32.91 2.71
654 663 2.203480 GGCAGCTTGGGTGTGGAA 60.203 61.111 0.00 0.00 33.19 3.53
730 741 2.222213 CGTGAATGAAAACTGGCGTGTA 59.778 45.455 0.00 0.00 0.00 2.90
747 758 1.000060 TGTAGGCGAACTGCTAAACGT 60.000 47.619 0.00 0.00 45.43 3.99
753 764 1.455786 CGAACTGCTAAACGTCCACAG 59.544 52.381 0.00 0.00 0.00 3.66
760 771 1.746322 TAAACGTCCACAGACCGGCA 61.746 55.000 0.00 0.00 40.12 5.69
788 801 0.389757 TGATGAAACGGACGTGTGGA 59.610 50.000 0.00 0.00 0.00 4.02
816 829 1.604593 GAATGCCCACACACCAGCT 60.605 57.895 0.00 0.00 0.00 4.24
835 848 1.480954 CTTAGTCCTACGTGGCACCAT 59.519 52.381 12.86 2.92 35.26 3.55
879 892 1.813753 CAAACGGACGCGGATCCAT 60.814 57.895 12.47 0.00 38.87 3.41
881 894 2.515996 AAACGGACGCGGATCCATGT 62.516 55.000 12.47 9.21 38.87 3.21
886 899 0.179121 GACGCGGATCCATGTGTGTA 60.179 55.000 12.47 0.00 0.00 2.90
909 922 1.228245 AGATGCAAACGCCCACACT 60.228 52.632 0.00 0.00 0.00 3.55
928 941 2.940410 ACTTGTGGGTGTTAGTGTTTCG 59.060 45.455 0.00 0.00 0.00 3.46
987 1000 3.134792 GGCGAGGCGAGTGAGAGA 61.135 66.667 0.00 0.00 0.00 3.10
988 1001 2.407210 GCGAGGCGAGTGAGAGAG 59.593 66.667 0.00 0.00 0.00 3.20
994 1007 0.885196 GGCGAGTGAGAGAGTCAACT 59.115 55.000 0.00 0.00 36.74 3.16
1310 1323 2.584608 CCTCCCCAAGGTGCGTAG 59.415 66.667 0.00 0.00 40.67 3.51
1339 1373 3.605749 CTTCTTCCTTGGCCGCCGA 62.606 63.158 4.58 1.12 0.00 5.54
1385 1420 3.498071 CAGGTGGTGGTGGTGGGT 61.498 66.667 0.00 0.00 0.00 4.51
1397 1432 3.239253 GTGGGTCACGACTGGGGT 61.239 66.667 0.00 0.00 0.00 4.95
1558 1593 1.901591 CAGTTCCAGGTGCTGTGATT 58.098 50.000 5.27 0.00 0.00 2.57
1562 1597 2.189594 TCCAGGTGCTGTGATTCTTG 57.810 50.000 0.00 0.00 0.00 3.02
1584 1619 4.003648 GGTTCCAGGTGTATTCTGACTTG 58.996 47.826 0.00 0.00 34.36 3.16
1590 1625 5.063944 CCAGGTGTATTCTGACTTGATTTCG 59.936 44.000 0.00 0.00 34.36 3.46
1611 1646 3.128242 CGGCATTCATTCTTCTTCTTGCT 59.872 43.478 0.00 0.00 0.00 3.91
1710 1756 6.878389 ACTGAAGCAAATGTTCAAAGGAAAAA 59.122 30.769 0.00 0.00 33.56 1.94
1733 1779 6.618287 AAATAAAGCGGATGATGATTCGAA 57.382 33.333 0.00 0.00 31.45 3.71
1745 1791 3.924114 TGATTCGAAGGGGCTAATTGA 57.076 42.857 3.35 0.00 0.00 2.57
1748 1794 4.580167 TGATTCGAAGGGGCTAATTGATTG 59.420 41.667 3.35 0.00 0.00 2.67
1749 1795 3.924114 TCGAAGGGGCTAATTGATTGA 57.076 42.857 0.00 0.00 0.00 2.57
1796 1842 7.906160 TGAAGAAGCGTAGATTTATTAACTGC 58.094 34.615 0.00 0.00 34.67 4.40
1799 1845 8.804688 AGAAGCGTAGATTTATTAACTGCTAG 57.195 34.615 0.00 0.00 34.67 3.42
1845 2163 7.940850 TCCAAACTGTTTCCTGAAAATTAGAG 58.059 34.615 2.13 0.00 31.33 2.43
1881 2230 6.984740 TTGCTAACATTTCGCAAAAGTAAG 57.015 33.333 0.00 0.00 40.33 2.34
1934 2328 8.929487 AGATTATTTTTGTGGGTCCAAAACTAA 58.071 29.630 9.88 9.88 42.34 2.24
1942 2336 6.424883 TGTGGGTCCAAAACTAAAGTCTAAA 58.575 36.000 0.00 0.00 0.00 1.85
1999 3378 6.155827 GCCTTGTAGATGTAGTCATGATCTC 58.844 44.000 0.00 0.00 34.06 2.75
2235 3614 1.192146 TGACCGAGGAAGAACTGGGG 61.192 60.000 0.00 0.00 40.29 4.96
2361 3743 8.800370 TTCCATTTTATGTAGCTCATACACAA 57.200 30.769 0.00 0.00 47.00 3.33
2377 3759 7.939782 TCATACACAACAATTCATGTCAAACT 58.060 30.769 0.00 0.00 42.99 2.66
2457 3839 2.058595 ATCGGGGGTGAGAAGGACG 61.059 63.158 0.00 0.00 0.00 4.79
2647 4029 5.504173 GCGAGGAAGCACATAATTAAGAACC 60.504 44.000 0.00 0.00 37.05 3.62
2653 4035 7.121315 GGAAGCACATAATTAAGAACCAAGTCT 59.879 37.037 0.00 0.00 0.00 3.24
2663 4045 2.125350 CCAAGTCTGCGAGGAGGC 60.125 66.667 0.00 0.00 0.00 4.70
2687 4076 6.693342 CGCATAACTAAGAACCGAGTAAAAG 58.307 40.000 0.00 0.00 0.00 2.27
2689 4078 6.036844 GCATAACTAAGAACCGAGTAAAAGGG 59.963 42.308 0.00 0.00 0.00 3.95
2799 4189 6.018343 GTCAGAGATAGGCTTCAATAAAGTGC 60.018 42.308 0.00 0.00 37.31 4.40
2814 4204 1.755179 AGTGCACTGCTGTTGTCTTT 58.245 45.000 20.97 0.00 0.00 2.52
2815 4205 1.672881 AGTGCACTGCTGTTGTCTTTC 59.327 47.619 20.97 0.00 0.00 2.62
2816 4206 1.672881 GTGCACTGCTGTTGTCTTTCT 59.327 47.619 10.32 0.00 0.00 2.52
2817 4207 2.872245 GTGCACTGCTGTTGTCTTTCTA 59.128 45.455 10.32 0.00 0.00 2.10
2818 4208 3.312421 GTGCACTGCTGTTGTCTTTCTAA 59.688 43.478 10.32 0.00 0.00 2.10
2819 4209 4.023707 GTGCACTGCTGTTGTCTTTCTAAT 60.024 41.667 10.32 0.00 0.00 1.73
2820 4210 4.023792 TGCACTGCTGTTGTCTTTCTAATG 60.024 41.667 1.98 0.00 0.00 1.90
2821 4211 4.023707 GCACTGCTGTTGTCTTTCTAATGT 60.024 41.667 0.00 0.00 0.00 2.71
2822 4212 5.446709 CACTGCTGTTGTCTTTCTAATGTG 58.553 41.667 0.00 0.00 0.00 3.21
2823 4213 4.516698 ACTGCTGTTGTCTTTCTAATGTGG 59.483 41.667 0.00 0.00 0.00 4.17
2824 4214 4.460263 TGCTGTTGTCTTTCTAATGTGGT 58.540 39.130 0.00 0.00 0.00 4.16
2970 4361 4.772624 TCTAGGCAACATCTGTCACTACTT 59.227 41.667 0.00 0.00 41.41 2.24
3025 4420 3.308904 GGGCCTAATACCAAACAGACCTT 60.309 47.826 0.84 0.00 0.00 3.50
3043 4438 2.299867 CCTTGCAGCCAAACCTAACATT 59.700 45.455 0.00 0.00 0.00 2.71
3051 4446 4.770531 AGCCAAACCTAACATTTAAGACCC 59.229 41.667 0.00 0.00 0.00 4.46
3176 4571 3.128242 CACCAATCCATCTTCAGAGTTGC 59.872 47.826 0.00 0.00 0.00 4.17
3208 4603 2.187946 CTTGCCCGGTCTAGCTGG 59.812 66.667 0.00 0.00 43.41 4.85
3256 4651 4.379243 CACCCTCCTGCGCGAGTT 62.379 66.667 12.10 0.00 0.00 3.01
3262 4657 0.459237 CTCCTGCGCGAGTTCATCTT 60.459 55.000 12.10 0.00 0.00 2.40
3275 4670 2.279517 ATCTTCGCGCATCGGACC 60.280 61.111 8.75 0.00 39.05 4.46
3611 5008 1.616725 GGAATCCAACTCCCATGCACA 60.617 52.381 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.681733 GGCTGAGAGAGGTTGTGTGA 59.318 55.000 0.00 0.00 0.00 3.58
41 42 1.562783 GTAGGTGGCTGAGAGAGGTT 58.437 55.000 0.00 0.00 0.00 3.50
163 164 2.805671 CGACATGGCAACTGTAGTTCAA 59.194 45.455 0.00 0.00 35.83 2.69
222 223 1.277273 CTGGCACTTGACCTGAGATGA 59.723 52.381 0.00 0.00 0.00 2.92
431 433 3.119291 CCATGTCTCTTTGTAGCGCTAG 58.881 50.000 19.48 8.15 0.00 3.42
627 636 0.966875 CCAAGCTGCCAGTTGCCATA 60.967 55.000 0.00 0.00 40.16 2.74
654 663 2.600769 ACACGCCCGTCTCCTCTT 60.601 61.111 0.00 0.00 0.00 2.85
730 741 0.669625 GGACGTTTAGCAGTTCGCCT 60.670 55.000 0.00 0.00 44.04 5.52
747 758 2.847234 AAGGTGCCGGTCTGTGGA 60.847 61.111 1.90 0.00 0.00 4.02
760 771 1.069513 TCCGTTTCATCACACGAAGGT 59.930 47.619 0.00 0.00 38.76 3.50
788 801 4.404098 GGGCATTCACCCGGTCGT 62.404 66.667 0.00 0.00 40.98 4.34
816 829 1.563924 ATGGTGCCACGTAGGACTAA 58.436 50.000 5.55 0.00 41.22 2.24
835 848 4.083537 GGTGCACGAATCTTGACATGTTTA 60.084 41.667 11.45 0.00 0.00 2.01
879 892 0.320050 TTGCATCTCGCCTACACACA 59.680 50.000 0.00 0.00 41.33 3.72
881 894 1.438651 GTTTGCATCTCGCCTACACA 58.561 50.000 0.00 0.00 41.33 3.72
909 922 2.093075 TCCGAAACACTAACACCCACAA 60.093 45.455 0.00 0.00 0.00 3.33
943 956 1.300697 GTGCTTTGTCGGACTCGGT 60.301 57.895 9.88 0.00 36.95 4.69
994 1007 3.458163 GCCGGACTCCATGGTCGA 61.458 66.667 12.58 0.00 37.12 4.20
996 1009 4.530857 CCGCCGGACTCCATGGTC 62.531 72.222 12.58 2.28 35.66 4.02
1310 1323 3.254411 CCAAGGAAGAAGAAACCAAGAGC 59.746 47.826 0.00 0.00 0.00 4.09
1339 1373 2.049985 GCGTCAGTGCGTCACTCT 60.050 61.111 9.15 0.00 43.43 3.24
1523 1558 0.108804 ACTGCGTGATGTAGAACCCG 60.109 55.000 0.00 0.00 33.97 5.28
1558 1593 3.907474 TCAGAATACACCTGGAACCAAGA 59.093 43.478 0.00 0.00 32.73 3.02
1562 1597 3.983044 AGTCAGAATACACCTGGAACC 57.017 47.619 0.00 0.00 32.73 3.62
1584 1619 6.129053 AGAAGAAGAATGAATGCCGAAATC 57.871 37.500 0.00 0.00 0.00 2.17
1590 1625 4.715527 AGCAAGAAGAAGAATGAATGCC 57.284 40.909 0.00 0.00 33.19 4.40
1611 1646 0.625980 TCAGGTCCCCCATGGCATTA 60.626 55.000 6.09 0.00 0.00 1.90
1682 1727 6.405538 TCCTTTGAACATTTGCTTCAGTTTT 58.594 32.000 0.00 0.00 0.00 2.43
1710 1756 6.293626 CCTTCGAATCATCATCCGCTTTATTT 60.294 38.462 0.00 0.00 0.00 1.40
1714 1760 2.874701 CCTTCGAATCATCATCCGCTTT 59.125 45.455 0.00 0.00 0.00 3.51
1719 1765 1.072965 AGCCCCTTCGAATCATCATCC 59.927 52.381 0.00 0.00 0.00 3.51
1724 1770 4.437682 TCAATTAGCCCCTTCGAATCAT 57.562 40.909 0.00 0.00 0.00 2.45
1729 1775 3.924114 TCAATCAATTAGCCCCTTCGA 57.076 42.857 0.00 0.00 0.00 3.71
1733 1779 5.961897 AGATTCATCAATCAATTAGCCCCT 58.038 37.500 0.00 0.00 41.03 4.79
1745 1791 9.186837 AGCATAGAAGTTCAAAGATTCATCAAT 57.813 29.630 5.50 0.00 0.00 2.57
1748 1794 8.206325 TCAGCATAGAAGTTCAAAGATTCATC 57.794 34.615 5.50 0.00 0.00 2.92
1749 1795 8.571461 TTCAGCATAGAAGTTCAAAGATTCAT 57.429 30.769 5.50 0.00 0.00 2.57
1813 2131 7.630242 TTCAGGAAACAGTTTGGATCATATC 57.370 36.000 2.34 0.00 0.00 1.63
1814 2132 8.421249 TTTTCAGGAAACAGTTTGGATCATAT 57.579 30.769 2.34 0.00 0.00 1.78
1826 2144 9.346725 GTATTTGCTCTAATTTTCAGGAAACAG 57.653 33.333 0.00 0.00 31.27 3.16
1881 2230 8.723942 AGTGTTTGTGTCCTGATTATAGAATC 57.276 34.615 3.04 3.04 41.72 2.52
2003 3382 7.986085 AGTTTTGCAACATCTACAGAGTTAT 57.014 32.000 0.00 0.00 35.05 1.89
2006 3385 5.701290 GGTAGTTTTGCAACATCTACAGAGT 59.299 40.000 23.70 0.00 35.05 3.24
2008 3387 5.616270 TGGTAGTTTTGCAACATCTACAGA 58.384 37.500 23.70 13.97 35.05 3.41
2010 3389 5.825679 AGTTGGTAGTTTTGCAACATCTACA 59.174 36.000 23.70 10.07 35.05 2.74
2011 3390 6.313744 AGTTGGTAGTTTTGCAACATCTAC 57.686 37.500 18.56 18.56 35.05 2.59
2015 3394 4.097286 ACGAAGTTGGTAGTTTTGCAACAT 59.903 37.500 0.00 0.00 37.78 2.71
2047 3426 2.715046 CTCCTGCAGGCATGAACTTTA 58.285 47.619 28.91 5.53 34.44 1.85
2048 3427 1.542492 CTCCTGCAGGCATGAACTTT 58.458 50.000 28.91 0.00 34.44 2.66
2103 3482 0.167470 TCTTTAGGACAGTCGCGACG 59.833 55.000 31.56 26.74 36.20 5.12
2109 3488 6.350361 GGGAGTAGAACTTCTTTAGGACAGTC 60.350 46.154 0.00 0.00 0.00 3.51
2187 3566 2.029666 GGGGATGATGACGCCTCG 59.970 66.667 0.00 0.00 37.38 4.63
2193 3572 2.648059 CAAGGAAGTGGGGATGATGAC 58.352 52.381 0.00 0.00 0.00 3.06
2235 3614 2.346803 TGAAACTTCTCGGCATACTGC 58.653 47.619 0.00 0.00 44.08 4.40
2358 3740 5.593909 TCCTGAGTTTGACATGAATTGTTGT 59.406 36.000 0.00 0.00 39.18 3.32
2361 3743 5.829924 AGTTCCTGAGTTTGACATGAATTGT 59.170 36.000 0.00 0.00 42.79 2.71
2377 3759 1.902508 CAGTAAGCCTCCAGTTCCTGA 59.097 52.381 0.00 0.00 32.44 3.86
2457 3839 0.666577 CCAAAGGACTCGACACCGAC 60.667 60.000 0.00 0.00 40.30 4.79
2647 4029 2.507992 CGCCTCCTCGCAGACTTG 60.508 66.667 0.00 0.00 0.00 3.16
2663 4045 6.237755 CCTTTTACTCGGTTCTTAGTTATGCG 60.238 42.308 0.00 0.00 0.00 4.73
2665 4047 7.101700 ACCCTTTTACTCGGTTCTTAGTTATG 58.898 38.462 0.00 0.00 0.00 1.90
2666 4048 7.250032 ACCCTTTTACTCGGTTCTTAGTTAT 57.750 36.000 0.00 0.00 0.00 1.89
2687 4076 3.629142 AAACCAGCTCATACACTACCC 57.371 47.619 0.00 0.00 0.00 3.69
2689 4078 7.010552 CACATCTAAAACCAGCTCATACACTAC 59.989 40.741 0.00 0.00 0.00 2.73
2799 4189 5.446709 CACATTAGAAAGACAACAGCAGTG 58.553 41.667 0.00 0.00 0.00 3.66
2970 4361 6.489022 CAGCATCCCTTCATCAATTGAATAGA 59.511 38.462 13.09 8.26 43.30 1.98
3025 4420 4.830046 TCTTAAATGTTAGGTTTGGCTGCA 59.170 37.500 0.50 0.00 0.00 4.41
3126 4521 1.452953 CTGCGACGGCCTCATACCTA 61.453 60.000 0.00 0.00 38.85 3.08
3153 4548 4.582869 CAACTCTGAAGATGGATTGGTGA 58.417 43.478 0.00 0.00 0.00 4.02
3176 4571 0.731417 GCAAGGTAGATGCAGCAGTG 59.269 55.000 4.07 0.00 43.29 3.66
3256 4651 1.588932 GTCCGATGCGCGAAGATGA 60.589 57.895 12.10 0.00 44.57 2.92
3275 4670 3.414700 GCGCTGTGTTGACTCGGG 61.415 66.667 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.