Multiple sequence alignment - TraesCS2D01G326800

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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 TraesCS2D01G326800 chr2D 100.000 4328 0 0 1 4328 420173213 420168886 0.000000e+00 7993.0
1 TraesCS2D01G326800 chr2A 96.385 3485 106 11 852 4328 570007129 570010601 0.000000e+00 5720.0
2 TraesCS2D01G326800 chr2B 96.749 2953 85 6 821 3766 492622631 492619683 0.000000e+00 4911.0
3 TraesCS2D01G326800 chr2B 97.772 404 9 0 3760 4163 492619563 492619160 0.000000e+00 697.0
4 TraesCS2D01G326800 chr2B 83.651 630 77 6 91 697 492623373 492622747 1.750000e-158 569.0
5 TraesCS2D01G326800 chr2B 81.705 563 76 11 1 538 492705934 492705374 1.100000e-120 444.0
6 TraesCS2D01G326800 chr2B 79.541 479 55 23 613 1070 492705361 492704905 7.030000e-78 302.0
7 TraesCS2D01G326800 chr2B 90.991 222 20 0 1066 1287 492624122 492623901 2.530000e-77 300.0
8 TraesCS2D01G326800 chr2B 96.450 169 5 1 4161 4328 492619037 492618869 1.190000e-70 278.0
9 TraesCS2D01G326800 chr2B 89.720 107 11 0 3718 3824 74002823 74002929 2.100000e-28 137.0
10 TraesCS2D01G326800 chr3B 83.270 263 38 3 4 260 615389820 615390082 2.010000e-58 237.0
11 TraesCS2D01G326800 chr3D 80.312 320 56 3 20 332 476474646 476474327 7.240000e-58 235.0
12 TraesCS2D01G326800 chr5B 72.973 666 137 27 23 658 11468134 11467482 4.420000e-45 193.0
13 TraesCS2D01G326800 chr5B 93.878 98 6 0 3726 3823 383513030 383512933 9.700000e-32 148.0
14 TraesCS2D01G326800 chr5D 81.081 222 34 7 372 588 476188241 476188459 2.070000e-38 171.0
15 TraesCS2D01G326800 chr5D 93.878 98 6 0 3726 3823 330393613 330393516 9.700000e-32 148.0
16 TraesCS2D01G326800 chr5D 79.856 139 16 10 39 171 411898610 411898742 1.660000e-14 91.6
17 TraesCS2D01G326800 chr6D 94.118 102 6 0 3720 3821 437332593 437332694 5.800000e-34 156.0
18 TraesCS2D01G326800 chr4B 93.137 102 7 0 3720 3821 21371130 21371231 2.700000e-32 150.0
19 TraesCS2D01G326800 chr7A 87.500 120 13 2 3720 3838 573432806 573432688 2.100000e-28 137.0
20 TraesCS2D01G326800 chr7A 80.147 136 27 0 39 174 735361348 735361213 7.660000e-18 102.0
21 TraesCS2D01G326800 chr1A 89.189 111 9 3 3713 3822 181775696 181775588 7.550000e-28 135.0
22 TraesCS2D01G326800 chr6B 77.143 210 38 6 27 231 60601275 60601479 3.540000e-21 113.0
23 TraesCS2D01G326800 chr5A 76.027 146 19 12 41 178 523656240 523656377 1.300000e-05 62.1


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 TraesCS2D01G326800 chr2D 420168886 420173213 4327 True 7993 7993 100.0000 1 4328 1 chr2D.!!$R1 4327
1 TraesCS2D01G326800 chr2A 570007129 570010601 3472 False 5720 5720 96.3850 852 4328 1 chr2A.!!$F1 3476
2 TraesCS2D01G326800 chr2B 492618869 492624122 5253 True 1351 4911 93.1226 91 4328 5 chr2B.!!$R1 4237
3 TraesCS2D01G326800 chr2B 492704905 492705934 1029 True 373 444 80.6230 1 1070 2 chr2B.!!$R2 1069

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
775 1522 0.037697 AGGCGCGTCTATTTGTGTCA 60.038 50.0 13.78 0.0 0.00 3.58 F
797 1544 0.099082 GCGTTGGACCGTGTTTTTGA 59.901 50.0 0.00 0.0 0.00 2.69 F
2013 2767 0.328258 CAGGGTTAGGGAACAGTGGG 59.672 60.0 0.00 0.0 37.29 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2767 0.463833 CCTTCCCCCTACGCACATTC 60.464 60.000 0.0 0.0 0.0 2.67 R
2063 2817 3.383761 GCAACCAACAAATTGTCTCCAG 58.616 45.455 0.0 0.0 33.6 3.86 R
3906 4785 0.592637 TGCAGTGCGAACTTGAATGG 59.407 50.000 11.2 0.0 0.0 3.16 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
47 48 7.778083 TCGAAATAGTCATTTTAGAGTAGGCA 58.222 34.615 0.00 0.00 34.44 4.75
51 52 8.682936 AATAGTCATTTTAGAGTAGGCAATGG 57.317 34.615 0.00 0.00 0.00 3.16
81 82 0.975135 TGTTACGATTCAACCCCGGA 59.025 50.000 0.73 0.00 0.00 5.14
83 84 0.108041 TTACGATTCAACCCCGGAGC 60.108 55.000 0.73 0.00 0.00 4.70
84 85 0.974010 TACGATTCAACCCCGGAGCT 60.974 55.000 0.73 0.00 0.00 4.09
85 86 1.521681 CGATTCAACCCCGGAGCTC 60.522 63.158 0.73 4.71 0.00 4.09
86 87 1.602237 GATTCAACCCCGGAGCTCA 59.398 57.895 17.19 0.00 0.00 4.26
87 88 0.462759 GATTCAACCCCGGAGCTCAG 60.463 60.000 17.19 12.02 0.00 3.35
88 89 2.543067 ATTCAACCCCGGAGCTCAGC 62.543 60.000 17.19 0.00 0.00 4.26
89 90 3.710722 CAACCCCGGAGCTCAGCT 61.711 66.667 17.19 0.00 43.88 4.24
102 762 1.890573 GCTCAGCTCGGGATAGATCCT 60.891 57.143 8.45 0.00 46.35 3.24
113 773 5.839063 TCGGGATAGATCCTCTAAACAATGT 59.161 40.000 8.45 0.00 46.35 2.71
178 838 2.094234 ACAACATCATCATCGTCGGACA 60.094 45.455 9.10 0.00 0.00 4.02
185 845 4.112634 TCATCATCGTCGGACAATTCTTC 58.887 43.478 9.10 0.00 0.00 2.87
189 849 1.693083 CGTCGGACAATTCTTCGGGC 61.693 60.000 9.10 0.00 0.00 6.13
190 850 0.672401 GTCGGACAATTCTTCGGGCA 60.672 55.000 2.62 0.00 0.00 5.36
236 899 5.500645 AAAAACTAATCCGAGCTATTGGC 57.499 39.130 0.00 0.00 42.19 4.52
242 905 0.836606 TCCGAGCTATTGGCCATGAA 59.163 50.000 6.09 0.00 43.05 2.57
249 912 2.760092 GCTATTGGCCATGAACCTTCAA 59.240 45.455 6.09 0.00 36.41 2.69
261 924 7.260603 CCATGAACCTTCAAAGTAATGAATCC 58.739 38.462 0.00 0.00 41.13 3.01
396 1100 3.050275 GCAGTGCTGTCGAACCCC 61.050 66.667 8.18 0.00 0.00 4.95
407 1111 4.547367 GAACCCCGCATCCTCCGG 62.547 72.222 0.00 0.00 45.17 5.14
516 1221 2.338620 CAACGACGGCAGAGTGGA 59.661 61.111 0.00 0.00 0.00 4.02
525 1257 1.517257 GCAGAGTGGACGTCGATGG 60.517 63.158 9.92 0.00 0.00 3.51
526 1258 1.934220 GCAGAGTGGACGTCGATGGA 61.934 60.000 9.92 0.00 0.00 3.41
527 1259 0.741326 CAGAGTGGACGTCGATGGAT 59.259 55.000 9.92 0.00 0.00 3.41
528 1260 0.741326 AGAGTGGACGTCGATGGATG 59.259 55.000 9.92 0.00 35.23 3.51
529 1261 0.872021 GAGTGGACGTCGATGGATGC 60.872 60.000 9.92 0.00 32.12 3.91
530 1262 2.104132 TGGACGTCGATGGATGCG 59.896 61.111 9.92 0.00 32.12 4.73
531 1263 2.658593 GGACGTCGATGGATGCGG 60.659 66.667 9.92 0.00 32.12 5.69
532 1264 2.104331 GACGTCGATGGATGCGGT 59.896 61.111 9.90 0.00 32.12 5.68
533 1265 2.202743 ACGTCGATGGATGCGGTG 60.203 61.111 9.90 0.00 32.12 4.94
534 1266 2.202743 CGTCGATGGATGCGGTGT 60.203 61.111 0.00 0.00 0.00 4.16
535 1267 2.230940 CGTCGATGGATGCGGTGTC 61.231 63.158 0.00 0.00 0.00 3.67
536 1268 2.104132 TCGATGGATGCGGTGTCG 59.896 61.111 0.00 0.00 39.81 4.35
537 1269 2.961721 CGATGGATGCGGTGTCGG 60.962 66.667 0.00 0.00 36.79 4.79
538 1270 2.186903 GATGGATGCGGTGTCGGT 59.813 61.111 0.00 0.00 36.79 4.69
539 1271 2.125147 ATGGATGCGGTGTCGGTG 60.125 61.111 0.00 0.00 36.79 4.94
540 1272 3.680620 ATGGATGCGGTGTCGGTGG 62.681 63.158 0.00 0.00 36.79 4.61
689 1421 2.997897 GCCAGAGGAGGACACCGT 60.998 66.667 0.00 0.00 34.73 4.83
690 1422 2.973899 CCAGAGGAGGACACCGTG 59.026 66.667 0.00 0.00 34.73 4.94
722 1467 5.383476 TGATGCAAATCCAACCCAAATTTT 58.617 33.333 0.00 0.00 0.00 1.82
723 1468 6.537355 TGATGCAAATCCAACCCAAATTTTA 58.463 32.000 0.00 0.00 0.00 1.52
724 1469 7.000472 TGATGCAAATCCAACCCAAATTTTAA 59.000 30.769 0.00 0.00 0.00 1.52
727 1472 5.473162 GCAAATCCAACCCAAATTTTAAGCT 59.527 36.000 0.00 0.00 0.00 3.74
758 1503 1.535860 CCAAACGGACAGCAAAACAGG 60.536 52.381 0.00 0.00 0.00 4.00
762 1509 2.427410 GACAGCAAAACAGGCGCG 60.427 61.111 0.00 0.00 36.08 6.86
764 1511 2.427410 CAGCAAAACAGGCGCGTC 60.427 61.111 0.21 0.21 36.08 5.19
765 1512 2.591715 AGCAAAACAGGCGCGTCT 60.592 55.556 7.80 7.80 36.08 4.18
775 1522 0.037697 AGGCGCGTCTATTTGTGTCA 60.038 50.000 13.78 0.00 0.00 3.58
785 1532 1.163420 ATTTGTGTCAGCGCGTTGGA 61.163 50.000 22.99 7.29 0.00 3.53
797 1544 0.099082 GCGTTGGACCGTGTTTTTGA 59.901 50.000 0.00 0.00 0.00 2.69
802 1549 1.606668 TGGACCGTGTTTTTGATCAGC 59.393 47.619 0.00 0.00 0.00 4.26
803 1550 1.606668 GGACCGTGTTTTTGATCAGCA 59.393 47.619 0.00 0.00 0.00 4.41
815 1562 1.168714 GATCAGCACAGACCCAAACC 58.831 55.000 0.00 0.00 0.00 3.27
817 1564 1.227823 CAGCACAGACCCAAACCGA 60.228 57.895 0.00 0.00 0.00 4.69
818 1565 1.071471 AGCACAGACCCAAACCGAG 59.929 57.895 0.00 0.00 0.00 4.63
820 1567 1.752198 CACAGACCCAAACCGAGGA 59.248 57.895 0.00 0.00 0.00 3.71
858 1605 3.423154 CGCGTTGGAGTTGCCCTC 61.423 66.667 0.00 0.00 39.67 4.30
917 1665 0.721718 GAGCTCAATCCAACGGTTCG 59.278 55.000 9.40 0.00 0.00 3.95
926 1674 1.519751 CCAACGGTTCGGCCAAATCA 61.520 55.000 2.24 0.00 36.97 2.57
974 1728 5.163663 GCCCATATTTTCAACTGATCAACGA 60.164 40.000 0.00 0.00 0.00 3.85
1013 1767 2.185310 AAACCGATGCCGCCTTCTCT 62.185 55.000 0.00 0.00 0.00 3.10
1019 1773 2.762043 GCCGCCTTCTCTCCCTCT 60.762 66.667 0.00 0.00 0.00 3.69
1048 1802 2.043450 CGAGTCTGGGCCTCCTCT 60.043 66.667 4.53 0.00 0.00 3.69
1180 1934 1.451567 CTCGTCTCCGCCTACTCCA 60.452 63.158 0.00 0.00 0.00 3.86
1230 1984 4.332543 TTCTCCGCCTCCCCCTGT 62.333 66.667 0.00 0.00 0.00 4.00
1517 2271 1.154205 GGCTGCATTGACGACGCTAT 61.154 55.000 0.50 0.00 0.00 2.97
1869 2623 3.319122 AGTTGCCAGAAAAAGATGTGGTC 59.681 43.478 0.00 0.00 32.20 4.02
1891 2645 2.912956 ACCTGGACTAGCTTGATTGGAA 59.087 45.455 0.00 0.00 0.00 3.53
2013 2767 0.328258 CAGGGTTAGGGAACAGTGGG 59.672 60.000 0.00 0.00 37.29 4.61
2063 2817 9.265901 TCATGCAGCTATAATTAAGAGAAACTC 57.734 33.333 0.00 0.00 0.00 3.01
2253 3007 1.246649 TGTGCCGAGAAATGCATTGT 58.753 45.000 13.82 3.17 40.07 2.71
2539 3293 4.464008 TCTAGGACATTCAAATGATGCCC 58.536 43.478 9.62 5.31 39.67 5.36
2742 3496 0.034186 CTAAATGTGGGCAGCTGGGA 60.034 55.000 17.12 0.00 0.00 4.37
2873 3627 5.923733 TTTAGTGAGATGGAGAGAGGAAC 57.076 43.478 0.00 0.00 0.00 3.62
2889 3643 5.919755 AGAGGAACTATTAAGCCTAACAGC 58.080 41.667 0.00 0.00 41.55 4.40
3102 3856 1.699566 TGATGGTGGGGTATGGGGG 60.700 63.158 0.00 0.00 0.00 5.40
3254 4008 6.482973 GCTGAAAAATGGGAAGAGATAGAGAG 59.517 42.308 0.00 0.00 0.00 3.20
3261 4015 4.141274 TGGGAAGAGATAGAGAGACTGAGG 60.141 50.000 0.00 0.00 0.00 3.86
3361 4115 2.621998 GGCATAACTACAGCCGAGACTA 59.378 50.000 0.00 0.00 38.86 2.59
3408 4162 7.228507 TGACCGCATTAGCTCATTTACATAAAT 59.771 33.333 0.00 0.00 39.10 1.40
3427 4181 9.118300 ACATAAATTCTGGAATCAGCTTTAGAG 57.882 33.333 0.00 0.00 40.69 2.43
3428 4182 9.334947 CATAAATTCTGGAATCAGCTTTAGAGA 57.665 33.333 0.00 0.00 40.69 3.10
3493 4247 2.360165 CTGTTGCAAGAGCCAAGAAGTT 59.640 45.455 11.04 0.00 41.13 2.66
3537 4291 8.213518 TGTGCATTTATCTTCTTCAATAGTCC 57.786 34.615 0.00 0.00 0.00 3.85
3578 4332 4.211374 CGGCAAAAGTCCTCTTATTATCCG 59.789 45.833 0.00 0.00 33.09 4.18
3581 4335 5.467063 GCAAAAGTCCTCTTATTATCCGAGG 59.533 44.000 0.00 0.00 44.48 4.63
3628 4382 3.411517 CCCTCCCTTGGATGCCGT 61.412 66.667 0.00 0.00 0.00 5.68
3843 4722 7.602644 GGTATTAGCTAATTGCATAGTGCTGTA 59.397 37.037 23.47 0.00 45.31 2.74
3906 4785 5.276963 CCATGTTTGTCTGTTTTGTGAATGC 60.277 40.000 0.00 0.00 0.00 3.56
4048 4927 8.679288 AAGAAAATTGTCTAGCGAATTTCATG 57.321 30.769 0.00 0.00 31.93 3.07
4158 5037 4.333372 ACTTTTGGAGTTTGCTTGCAAATG 59.667 37.500 21.25 5.07 36.09 2.32
4163 5042 4.039004 TGGAGTTTGCTTGCAAATGTGTAT 59.961 37.500 21.25 6.38 0.00 2.29
4250 5254 6.496218 AGCTGAAAATCCTGGATCTTTTCTTT 59.504 34.615 24.86 15.48 38.86 2.52
4286 5291 3.838244 TTCTGAACACCACTTGCTACT 57.162 42.857 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 2.351350 CGTAACAAAGAAAGCGGCCATT 60.351 45.455 2.24 0.00 0.00 3.16
51 52 2.894307 ATCGTAACAAAGAAAGCGGC 57.106 45.000 0.00 0.00 0.00 6.53
54 55 4.915667 GGGTTGAATCGTAACAAAGAAAGC 59.084 41.667 0.00 0.00 0.00 3.51
81 82 1.544724 GATCTATCCCGAGCTGAGCT 58.455 55.000 6.69 6.69 43.88 4.09
102 762 2.742053 GAGGCAGCGAACATTGTTTAGA 59.258 45.455 3.08 0.00 0.00 2.10
113 773 1.153765 CACATCTCGAGGCAGCGAA 60.154 57.895 13.56 0.00 40.13 4.70
178 838 3.763360 TGTTCATCATTGCCCGAAGAATT 59.237 39.130 0.00 0.00 0.00 2.17
185 845 4.216902 ACATCATATGTTCATCATTGCCCG 59.783 41.667 1.90 0.00 41.63 6.13
221 884 1.421268 TCATGGCCAATAGCTCGGATT 59.579 47.619 10.96 0.00 43.05 3.01
234 897 4.462483 TCATTACTTTGAAGGTTCATGGCC 59.538 41.667 0.00 0.00 37.00 5.36
236 899 7.093814 TGGATTCATTACTTTGAAGGTTCATGG 60.094 37.037 0.00 0.00 38.90 3.66
242 905 7.643123 AGGTATGGATTCATTACTTTGAAGGT 58.357 34.615 0.00 0.00 38.90 3.50
261 924 2.604855 CGCCGCTGTCTAGTAAGGTATG 60.605 54.545 0.00 0.00 0.00 2.39
383 1087 3.950794 GATGCGGGGTTCGACAGCA 62.951 63.158 2.13 2.13 42.43 4.41
385 1089 2.511600 GGATGCGGGGTTCGACAG 60.512 66.667 0.00 0.00 42.43 3.51
417 1122 2.571216 CGGCATACCCCTACCTCCG 61.571 68.421 0.00 0.00 0.00 4.63
460 1165 0.529378 ACGAAGTAGTACAAGGCCCG 59.471 55.000 0.00 0.00 41.94 6.13
516 1221 2.202743 CACCGCATCCATCGACGT 60.203 61.111 0.00 0.00 0.00 4.34
537 1269 4.360405 ATCCACCAACGGCCCCAC 62.360 66.667 0.00 0.00 0.00 4.61
538 1270 4.358841 CATCCACCAACGGCCCCA 62.359 66.667 0.00 0.00 0.00 4.96
600 1332 1.071019 CTTCACCATCGTCACCGTCG 61.071 60.000 0.00 0.00 35.01 5.12
601 1333 0.242825 TCTTCACCATCGTCACCGTC 59.757 55.000 0.00 0.00 35.01 4.79
603 1335 0.458543 CCTCTTCACCATCGTCACCG 60.459 60.000 0.00 0.00 0.00 4.94
606 1338 1.596934 GGCCTCTTCACCATCGTCA 59.403 57.895 0.00 0.00 0.00 4.35
611 1343 2.370445 CCCTCGGCCTCTTCACCAT 61.370 63.158 0.00 0.00 0.00 3.55
615 1347 3.003173 CCACCCTCGGCCTCTTCA 61.003 66.667 0.00 0.00 0.00 3.02
635 1367 0.324645 ACATGCCATTCTTCCCCACC 60.325 55.000 0.00 0.00 0.00 4.61
636 1368 0.819582 CACATGCCATTCTTCCCCAC 59.180 55.000 0.00 0.00 0.00 4.61
676 1408 4.083862 GCCCACGGTGTCCTCCTC 62.084 72.222 7.45 0.00 0.00 3.71
690 1422 0.031178 GATTTGCATCATGGACGCCC 59.969 55.000 0.00 0.00 0.00 6.13
697 1429 3.613494 TTGGGTTGGATTTGCATCATG 57.387 42.857 0.00 0.00 0.00 3.07
698 1430 4.847990 ATTTGGGTTGGATTTGCATCAT 57.152 36.364 0.00 0.00 0.00 2.45
722 1467 3.254657 CGTTTGGACCCATTTTCAGCTTA 59.745 43.478 0.00 0.00 0.00 3.09
723 1468 2.035832 CGTTTGGACCCATTTTCAGCTT 59.964 45.455 0.00 0.00 0.00 3.74
724 1469 1.613437 CGTTTGGACCCATTTTCAGCT 59.387 47.619 0.00 0.00 0.00 4.24
727 1472 2.366640 TCCGTTTGGACCCATTTTCA 57.633 45.000 0.00 0.00 40.17 2.69
749 1494 0.168128 AATAGACGCGCCTGTTTTGC 59.832 50.000 5.73 0.00 0.00 3.68
758 1503 0.247301 GCTGACACAAATAGACGCGC 60.247 55.000 5.73 0.00 0.00 6.86
762 1509 1.068474 ACGCGCTGACACAAATAGAC 58.932 50.000 5.73 0.00 0.00 2.59
764 1511 1.464023 CCAACGCGCTGACACAAATAG 60.464 52.381 11.83 0.00 0.00 1.73
765 1512 0.515127 CCAACGCGCTGACACAAATA 59.485 50.000 11.83 0.00 0.00 1.40
775 1522 4.903010 AACACGGTCCAACGCGCT 62.903 61.111 5.73 0.00 37.37 5.92
785 1532 2.020720 TGTGCTGATCAAAAACACGGT 58.979 42.857 0.00 0.00 33.96 4.83
797 1544 0.606401 CGGTTTGGGTCTGTGCTGAT 60.606 55.000 0.00 0.00 0.00 2.90
802 1549 0.320771 CTCCTCGGTTTGGGTCTGTG 60.321 60.000 0.00 0.00 0.00 3.66
803 1550 1.481056 CCTCCTCGGTTTGGGTCTGT 61.481 60.000 0.00 0.00 0.00 3.41
817 1564 4.316823 TGTCTGGTCCGCCCTCCT 62.317 66.667 0.00 0.00 0.00 3.69
818 1565 4.083862 GTGTCTGGTCCGCCCTCC 62.084 72.222 0.00 0.00 0.00 4.30
858 1605 2.945447 CTCACCAGAGCTCTCTTCTG 57.055 55.000 14.96 6.69 37.98 3.02
878 1626 3.575630 TCATCTGTTTCTTCGACCTTCG 58.424 45.455 0.00 0.00 42.10 3.79
880 1628 3.007398 AGCTCATCTGTTTCTTCGACCTT 59.993 43.478 0.00 0.00 0.00 3.50
885 1633 4.033817 GGATTGAGCTCATCTGTTTCTTCG 59.966 45.833 19.04 0.00 0.00 3.79
917 1665 3.848272 TCGAACTCAATTGATTTGGCC 57.152 42.857 15.03 0.00 35.92 5.36
926 1674 1.531149 CGCCTGTGTTCGAACTCAATT 59.469 47.619 27.30 0.00 32.72 2.32
1013 1767 1.305046 GTCGGGGTGAGAAGAGGGA 60.305 63.158 0.00 0.00 0.00 4.20
1019 1773 1.074423 AGACTCGTCGGGGTGAGAA 59.926 57.895 0.00 0.00 36.11 2.87
1146 1900 3.941657 GAGCTTGGCGGCGAAGTCT 62.942 63.158 22.81 19.50 37.29 3.24
1230 1984 1.609501 CCAGAGGAAGGTGTCGGGA 60.610 63.158 0.00 0.00 30.16 5.14
1401 2155 1.220749 GTAGGCATGCACGGAGGAA 59.779 57.895 21.36 0.00 0.00 3.36
1501 2255 1.926510 CTTCATAGCGTCGTCAATGCA 59.073 47.619 0.00 0.00 42.76 3.96
1517 2271 1.798223 CCATTTCGTCGAACAGCTTCA 59.202 47.619 7.29 0.00 0.00 3.02
1869 2623 2.237143 TCCAATCAAGCTAGTCCAGGTG 59.763 50.000 0.00 0.00 34.44 4.00
1891 2645 5.208294 TCAAGTCCTCTCCTACAATAGGT 57.792 43.478 1.88 0.00 46.32 3.08
2013 2767 0.463833 CCTTCCCCCTACGCACATTC 60.464 60.000 0.00 0.00 0.00 2.67
2063 2817 3.383761 GCAACCAACAAATTGTCTCCAG 58.616 45.455 0.00 0.00 33.60 3.86
2253 3007 9.452287 TCACACAAAAATTCATCATGATCTCTA 57.548 29.630 4.86 0.00 0.00 2.43
2274 3028 5.376854 AAACCAAGCTGTTGATATCACAC 57.623 39.130 4.48 7.84 35.46 3.82
2539 3293 6.807720 GTGAGCATCTGATCATATAGTGACAG 59.192 42.308 1.01 0.00 42.80 3.51
2873 3627 4.683832 AGTGACGCTGTTAGGCTTAATAG 58.316 43.478 7.83 7.83 32.80 1.73
2889 3643 3.003689 ACAGAATGGCAAGAAAAGTGACG 59.996 43.478 0.00 0.00 43.62 4.35
3102 3856 1.608590 TTGCAGGCACTAAGCAAAGTC 59.391 47.619 0.00 0.00 42.92 3.01
3254 4008 1.819288 TCTTCATCGTGTCCCTCAGTC 59.181 52.381 0.00 0.00 0.00 3.51
3261 4015 3.797039 TCCATGATTCTTCATCGTGTCC 58.203 45.455 0.00 0.00 44.69 4.02
3361 4115 9.774413 CGGTCAATTAGTTATTTACCCTTCTAT 57.226 33.333 0.76 0.00 37.25 1.98
3423 4177 6.010850 AGTCAGCCGGTCATTATATTCTCTA 58.989 40.000 1.90 0.00 0.00 2.43
3424 4178 4.835615 AGTCAGCCGGTCATTATATTCTCT 59.164 41.667 1.90 0.00 0.00 3.10
3425 4179 4.926238 CAGTCAGCCGGTCATTATATTCTC 59.074 45.833 1.90 0.00 0.00 2.87
3426 4180 4.800914 GCAGTCAGCCGGTCATTATATTCT 60.801 45.833 1.90 0.00 37.23 2.40
3427 4181 3.433615 GCAGTCAGCCGGTCATTATATTC 59.566 47.826 1.90 0.00 37.23 1.75
3428 4182 3.403038 GCAGTCAGCCGGTCATTATATT 58.597 45.455 1.90 0.00 37.23 1.28
3493 4247 5.110598 GCACAATGGATGCATAATTCACAA 58.889 37.500 0.00 0.00 42.88 3.33
3537 4291 1.202973 CGCCACGCTCTAATGAGACG 61.203 60.000 0.00 3.40 42.73 4.18
3578 4332 4.580167 TGCCAATATTAGCAACATCACCTC 59.420 41.667 6.06 0.00 35.69 3.85
3628 4382 9.959721 GGAACTAAATGGATTAGGAGCATAATA 57.040 33.333 0.84 0.00 44.49 0.98
3906 4785 0.592637 TGCAGTGCGAACTTGAATGG 59.407 50.000 11.20 0.00 0.00 3.16
4048 4927 2.057137 TGCTCATCCAAATGGCCTAC 57.943 50.000 3.32 0.00 33.42 3.18
4158 5037 6.851330 GCGCAAAAATAGTTCCAGATATACAC 59.149 38.462 0.30 0.00 0.00 2.90
4163 5042 6.292649 CGTATGCGCAAAAATAGTTCCAGATA 60.293 38.462 17.11 0.00 0.00 1.98
4265 5269 4.067896 CAGTAGCAAGTGGTGTTCAGAAT 58.932 43.478 0.00 0.00 0.00 2.40
4286 5291 1.962807 CAAATGAAGTCTTGGGGCACA 59.037 47.619 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.