Multiple sequence alignment - TraesCS3D01G199400

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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 TraesCS3D01G199400 chr3D 100.000 5511 0 0 1 5511 225522929 225528439 0.000000e+00 10178.0
1 TraesCS3D01G199400 chr3D 89.437 142 13 2 5372 5511 611659464 611659605 1.580000e-40 178.0
2 TraesCS3D01G199400 chr3B 96.700 4818 125 12 311 5121 354947682 354942892 0.000000e+00 7986.0
3 TraesCS3D01G199400 chr3B 95.374 281 11 2 1 281 354947961 354947683 3.920000e-121 446.0
4 TraesCS3D01G199400 chr3B 90.845 142 10 2 5372 5510 604696184 604696325 2.620000e-43 187.0
5 TraesCS3D01G199400 chr3A 97.284 4345 86 12 700 5030 323103774 323099448 0.000000e+00 7341.0
6 TraesCS3D01G199400 chr3A 96.724 641 15 3 69 708 323104595 323103960 0.000000e+00 1062.0
7 TraesCS3D01G199400 chr3A 92.683 369 19 7 5016 5381 323097717 323097354 4.890000e-145 525.0
8 TraesCS3D01G199400 chr3A 97.826 46 1 0 1 46 323104634 323104589 4.580000e-11 80.5
9 TraesCS3D01G199400 chr7D 93.200 250 15 2 1887 2135 486463533 486463781 3.140000e-97 366.0
10 TraesCS3D01G199400 chr6B 88.259 247 26 2 1886 2132 656031912 656031669 5.400000e-75 292.0
11 TraesCS3D01G199400 chr6B 87.500 232 28 1 1900 2131 455134362 455134592 3.270000e-67 267.0
12 TraesCS3D01G199400 chr6A 87.854 247 30 0 1886 2132 579954027 579953781 1.940000e-74 291.0
13 TraesCS3D01G199400 chr2A 87.747 253 24 2 1887 2136 73540767 73541015 6.980000e-74 289.0
14 TraesCS3D01G199400 chr6D 87.449 247 30 1 1886 2132 433766929 433766684 3.250000e-72 283.0
15 TraesCS3D01G199400 chr2D 87.607 234 29 0 1898 2131 27826577 27826810 7.030000e-69 272.0
16 TraesCS3D01G199400 chr1D 92.908 141 8 1 5373 5511 364113838 364113698 2.600000e-48 204.0
17 TraesCS3D01G199400 chr4D 90.909 143 9 3 5372 5511 329142551 329142410 7.290000e-44 189.0
18 TraesCS3D01G199400 chr5B 89.333 150 13 2 5365 5511 643423188 643423337 9.430000e-43 185.0
19 TraesCS3D01G199400 chr2B 89.189 148 14 2 5366 5511 593629748 593629895 3.390000e-42 183.0
20 TraesCS3D01G199400 chr2B 90.000 140 12 1 5374 5511 801189321 801189182 4.390000e-41 180.0
21 TraesCS3D01G199400 chr1B 88.435 147 14 3 5368 5511 489267553 489267699 2.040000e-39 174.0
22 TraesCS3D01G199400 chr4B 88.732 142 14 1 5372 5511 384406005 384406146 7.340000e-39 172.0


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 TraesCS3D01G199400 chr3D 225522929 225528439 5510 False 10178.000 10178 100.00000 1 5511 1 chr3D.!!$F1 5510
1 TraesCS3D01G199400 chr3B 354942892 354947961 5069 True 4216.000 7986 96.03700 1 5121 2 chr3B.!!$R1 5120
2 TraesCS3D01G199400 chr3A 323097354 323104634 7280 True 2252.125 7341 96.12925 1 5381 4 chr3A.!!$R1 5380

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
84 85 4.058817 GAGATCTGTTGGTGAAGTTTCGT 58.941 43.478 0.00 0.0 0.00 3.85 F
964 1163 4.703575 AGCCAAGTCACTACAGTATAACGA 59.296 41.667 0.00 0.0 0.00 3.85 F
1841 2040 0.955428 GGCGCACATGTTCTTCTGGA 60.955 55.000 10.83 0.0 0.00 3.86 F
2329 2530 0.894141 TGAATGGGCAATTGTTCCCG 59.106 50.000 14.35 0.0 45.60 5.14 F
3474 3691 1.191535 CCGAGATGGTTGGTCCTGTA 58.808 55.000 0.00 0.0 37.07 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1657 1.003580 ACTTGGCATGTAGGGTCAGTG 59.996 52.381 3.94 0.00 0.00 3.66 R
2258 2459 4.047822 CAAAAGCTTCAACGGCATTACAA 58.952 39.130 0.00 0.00 0.00 2.41 R
3701 3918 1.860950 CGTGAAGACACTTCACCACAG 59.139 52.381 27.42 16.03 44.29 3.66 R
4122 4339 2.899256 CCATTTTCTTTCCCAGCCTCAA 59.101 45.455 0.00 0.00 0.00 3.02 R
5392 7369 0.250124 TTTAGCTCCCACCACACGTG 60.250 55.000 15.48 15.48 42.62 4.49 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
36 37 6.117488 GGATCGGTTTTGGATCTAGGTTTTA 58.883 40.000 0.00 0.00 40.11 1.52
42 43 7.255346 CGGTTTTGGATCTAGGTTTTACTTGTT 60.255 37.037 0.00 0.00 0.00 2.83
46 47 7.319052 TGGATCTAGGTTTTACTTGTTGGTA 57.681 36.000 0.00 0.00 0.00 3.25
84 85 4.058817 GAGATCTGTTGGTGAAGTTTCGT 58.941 43.478 0.00 0.00 0.00 3.85
108 109 9.160576 CGTGTTTGTTATTTTTGTTATCGAAGA 57.839 29.630 0.00 0.00 45.75 2.87
171 172 6.229936 TGTTGCTTCGATTTACTATAGGGT 57.770 37.500 4.43 0.00 0.00 4.34
193 194 5.346551 GGTTGTAATTGGTAATTTTGGCGAC 59.653 40.000 0.00 0.00 32.38 5.19
333 335 5.163992 ACAACAAAGTCTACATCGTTATGCG 60.164 40.000 0.00 0.00 43.01 4.73
393 395 6.071221 TGAGCTGATCAAAATTAGGCATGTTT 60.071 34.615 0.00 0.00 34.02 2.83
504 506 5.817816 CAGGAAGATGGGTAACTACATGTTC 59.182 44.000 2.30 0.00 42.98 3.18
628 630 6.927294 ACCTGTTAGCTATGCTCAATAAAC 57.073 37.500 0.00 0.00 40.44 2.01
668 670 9.143155 TCTGCACATAAATATGTTACTCCTAGA 57.857 33.333 3.35 0.00 43.99 2.43
858 1057 5.356470 GGAGTTCATCTTGCTATGCTCTTTT 59.644 40.000 0.00 0.00 0.00 2.27
859 1058 6.192234 AGTTCATCTTGCTATGCTCTTTTG 57.808 37.500 0.00 0.00 0.00 2.44
860 1059 5.709164 AGTTCATCTTGCTATGCTCTTTTGT 59.291 36.000 0.00 0.00 0.00 2.83
964 1163 4.703575 AGCCAAGTCACTACAGTATAACGA 59.296 41.667 0.00 0.00 0.00 3.85
967 1166 5.125097 CCAAGTCACTACAGTATAACGAGGT 59.875 44.000 0.00 0.00 0.00 3.85
1298 1497 8.347035 CCTGTTCTTTTTACCTTCGAACATTTA 58.653 33.333 0.00 0.00 41.87 1.40
1458 1657 2.945668 GCCACAAGAATATGTCCCTGAC 59.054 50.000 0.00 0.00 0.00 3.51
1524 1723 4.574013 CCATCTGTTCTTCCTTATGCAGTC 59.426 45.833 0.00 0.00 0.00 3.51
1841 2040 0.955428 GGCGCACATGTTCTTCTGGA 60.955 55.000 10.83 0.00 0.00 3.86
1950 2150 6.468956 CGTTAAGACATGCATTTGACCAATAC 59.531 38.462 0.00 0.00 0.00 1.89
2052 2252 7.866898 TGGTGATTTTGTGTCACATAAATCAAG 59.133 33.333 31.23 0.00 45.99 3.02
2258 2459 7.442666 CCTAAGAAAAACTCAGAACAGTAAGCT 59.557 37.037 0.00 0.00 0.00 3.74
2329 2530 0.894141 TGAATGGGCAATTGTTCCCG 59.106 50.000 14.35 0.00 45.60 5.14
2594 2811 9.851686 ATGGAAGATTGCTAGTTATTGATGTTA 57.148 29.630 0.00 0.00 0.00 2.41
2595 2812 9.851686 TGGAAGATTGCTAGTTATTGATGTTAT 57.148 29.630 0.00 0.00 0.00 1.89
2602 2819 8.437360 TGCTAGTTATTGATGTTATCTGTTGG 57.563 34.615 0.00 0.00 0.00 3.77
2603 2820 7.498900 TGCTAGTTATTGATGTTATCTGTTGGG 59.501 37.037 0.00 0.00 0.00 4.12
2604 2821 7.499232 GCTAGTTATTGATGTTATCTGTTGGGT 59.501 37.037 0.00 0.00 0.00 4.51
2605 2822 7.865706 AGTTATTGATGTTATCTGTTGGGTC 57.134 36.000 0.00 0.00 0.00 4.46
2606 2823 7.402054 AGTTATTGATGTTATCTGTTGGGTCA 58.598 34.615 0.00 0.00 0.00 4.02
2607 2824 7.888021 AGTTATTGATGTTATCTGTTGGGTCAA 59.112 33.333 0.00 0.00 0.00 3.18
2608 2825 5.957842 TTGATGTTATCTGTTGGGTCAAC 57.042 39.130 4.04 4.04 43.78 3.18
2609 2826 5.241403 TGATGTTATCTGTTGGGTCAACT 57.759 39.130 11.36 0.00 43.85 3.16
2760 2977 7.715249 ACTTTCTGCTTCTTACTGTTGATACAA 59.285 33.333 0.00 0.00 32.92 2.41
2765 2982 8.220755 TGCTTCTTACTGTTGATACAAAAGTT 57.779 30.769 11.68 0.00 32.83 2.66
3170 3387 5.185828 GGACAATCCCTATGCAAAGTTCTTT 59.814 40.000 0.00 0.00 0.00 2.52
3416 3633 8.755696 TTCAATTATTAAATGTGACTTGTGGC 57.244 30.769 0.00 0.00 0.00 5.01
3474 3691 1.191535 CCGAGATGGTTGGTCCTGTA 58.808 55.000 0.00 0.00 37.07 2.74
3701 3918 9.274206 GGAATATCAAGTGAATACTAGTTTCCC 57.726 37.037 0.00 0.00 35.69 3.97
3781 3998 2.262423 AGTGTCTGCTTTCAACCTCC 57.738 50.000 0.00 0.00 0.00 4.30
3925 4142 2.813754 TGAAGCAAGAATTAAGCAGCGT 59.186 40.909 0.00 0.00 0.00 5.07
4092 4309 5.230516 CACATGATTGTAATGGCATCAAACG 59.769 40.000 0.00 0.00 33.76 3.60
4122 4339 5.971763 TGCTGTTGAAAAACAAGTTGGTAT 58.028 33.333 7.96 0.00 39.30 2.73
4322 4539 4.331108 TGGACATGGATCGTCAAAATTGA 58.669 39.130 0.00 0.00 34.97 2.57
4323 4540 4.764308 TGGACATGGATCGTCAAAATTGAA 59.236 37.500 0.00 0.00 39.21 2.69
4420 4637 6.591935 AGTTGGTTCTCTTACAATCAGTTCA 58.408 36.000 0.00 0.00 0.00 3.18
4676 4896 3.007940 TGGAACATGGAAGGACAGTACAG 59.992 47.826 0.00 0.00 0.00 2.74
4751 4971 7.322664 GGGAATCTGCATTCACTTTTTATTCA 58.677 34.615 2.65 0.00 39.14 2.57
4776 4996 3.044986 CCGCTTGACTGAATTGTTGTTG 58.955 45.455 0.00 0.00 0.00 3.33
4778 4998 4.104776 CGCTTGACTGAATTGTTGTTGTT 58.895 39.130 0.00 0.00 0.00 2.83
4838 5067 0.685458 ACCCCTTCCATAGCGTACGT 60.685 55.000 17.90 6.37 0.00 3.57
4980 5209 3.596214 AGTTTCACTCGTCACTGTTTGT 58.404 40.909 0.00 0.00 0.00 2.83
5129 7104 4.884247 AGGACGCTTCTTAATAGGCATAC 58.116 43.478 0.00 0.00 0.00 2.39
5175 7150 1.108727 TTGCCCCAAGACAACTGCTG 61.109 55.000 0.00 0.00 0.00 4.41
5233 7209 4.567318 CCCCCTAATCACTGCTGC 57.433 61.111 0.00 0.00 0.00 5.25
5234 7210 1.918253 CCCCCTAATCACTGCTGCT 59.082 57.895 0.00 0.00 0.00 4.24
5235 7211 0.257039 CCCCCTAATCACTGCTGCTT 59.743 55.000 0.00 0.00 0.00 3.91
5247 7223 0.469494 TGCTGCTTGGTCTTGTCAGA 59.531 50.000 0.00 0.00 0.00 3.27
5308 7285 3.084786 GGAAAAATCTGAGACCAGTGGG 58.915 50.000 15.21 0.00 41.16 4.61
5312 7289 0.617413 ATCTGAGACCAGTGGGCAAG 59.383 55.000 19.84 14.67 41.16 4.01
5353 7330 7.981225 ACAATAGCAATCATCGCCTTTTAAAAT 59.019 29.630 0.09 0.00 0.00 1.82
5383 7360 8.814038 AGAGAACAATAAATTAGGACAATGCT 57.186 30.769 0.00 0.00 0.00 3.79
5384 7361 9.905713 AGAGAACAATAAATTAGGACAATGCTA 57.094 29.630 0.00 0.00 0.00 3.49
5387 7364 9.221775 GAACAATAAATTAGGACAATGCTAACG 57.778 33.333 0.00 0.00 33.14 3.18
5388 7365 7.193595 ACAATAAATTAGGACAATGCTAACGC 58.806 34.615 0.00 0.00 33.14 4.84
5389 7366 7.067008 ACAATAAATTAGGACAATGCTAACGCT 59.933 33.333 0.00 0.00 33.14 5.07
5390 7367 5.485662 AAATTAGGACAATGCTAACGCTC 57.514 39.130 0.00 0.00 33.14 5.03
5391 7368 3.603158 TTAGGACAATGCTAACGCTCA 57.397 42.857 0.00 0.00 36.97 4.26
5392 7369 1.726853 AGGACAATGCTAACGCTCAC 58.273 50.000 0.00 0.00 36.97 3.51
5393 7370 1.001974 AGGACAATGCTAACGCTCACA 59.998 47.619 0.00 0.00 36.97 3.58
5394 7371 1.128692 GGACAATGCTAACGCTCACAC 59.871 52.381 0.00 0.00 36.97 3.82
5395 7372 0.790207 ACAATGCTAACGCTCACACG 59.210 50.000 0.00 0.00 36.97 4.49
5409 7386 3.056458 CACGTGTGGTGGGAGCTA 58.944 61.111 7.58 0.00 43.16 3.32
5410 7387 1.369692 CACGTGTGGTGGGAGCTAA 59.630 57.895 7.58 0.00 43.16 3.09
5411 7388 0.250124 CACGTGTGGTGGGAGCTAAA 60.250 55.000 7.58 0.00 43.16 1.85
5412 7389 0.250166 ACGTGTGGTGGGAGCTAAAC 60.250 55.000 0.00 0.00 0.00 2.01
5413 7390 0.953960 CGTGTGGTGGGAGCTAAACC 60.954 60.000 5.23 5.23 34.38 3.27
5414 7391 0.608308 GTGTGGTGGGAGCTAAACCC 60.608 60.000 1.85 1.85 46.87 4.11
5419 7396 3.723922 GGGAGCTAAACCCGCCCA 61.724 66.667 0.00 0.00 41.43 5.36
5420 7397 2.437895 GGAGCTAAACCCGCCCAC 60.438 66.667 0.00 0.00 0.00 4.61
5421 7398 2.349755 GAGCTAAACCCGCCCACA 59.650 61.111 0.00 0.00 0.00 4.17
5422 7399 2.033602 AGCTAAACCCGCCCACAC 59.966 61.111 0.00 0.00 0.00 3.82
5423 7400 3.428282 GCTAAACCCGCCCACACG 61.428 66.667 0.00 0.00 0.00 4.49
5424 7401 3.428282 CTAAACCCGCCCACACGC 61.428 66.667 0.00 0.00 0.00 5.34
5431 7408 4.690719 CGCCCACACGCCCTAACA 62.691 66.667 0.00 0.00 0.00 2.41
5432 7409 2.045340 GCCCACACGCCCTAACAT 60.045 61.111 0.00 0.00 0.00 2.71
5433 7410 1.222387 GCCCACACGCCCTAACATA 59.778 57.895 0.00 0.00 0.00 2.29
5434 7411 1.093496 GCCCACACGCCCTAACATAC 61.093 60.000 0.00 0.00 0.00 2.39
5435 7412 0.250793 CCCACACGCCCTAACATACA 59.749 55.000 0.00 0.00 0.00 2.29
5436 7413 1.651987 CCACACGCCCTAACATACAG 58.348 55.000 0.00 0.00 0.00 2.74
5437 7414 1.206132 CCACACGCCCTAACATACAGA 59.794 52.381 0.00 0.00 0.00 3.41
5438 7415 2.354303 CCACACGCCCTAACATACAGAA 60.354 50.000 0.00 0.00 0.00 3.02
5439 7416 3.531538 CACACGCCCTAACATACAGAAT 58.468 45.455 0.00 0.00 0.00 2.40
5440 7417 4.442332 CCACACGCCCTAACATACAGAATA 60.442 45.833 0.00 0.00 0.00 1.75
5441 7418 4.506654 CACACGCCCTAACATACAGAATAC 59.493 45.833 0.00 0.00 0.00 1.89
5442 7419 3.734231 CACGCCCTAACATACAGAATACG 59.266 47.826 0.00 0.00 0.00 3.06
5443 7420 2.729882 CGCCCTAACATACAGAATACGC 59.270 50.000 0.00 0.00 0.00 4.42
5444 7421 3.064931 GCCCTAACATACAGAATACGCC 58.935 50.000 0.00 0.00 0.00 5.68
5445 7422 3.493699 GCCCTAACATACAGAATACGCCA 60.494 47.826 0.00 0.00 0.00 5.69
5446 7423 4.802918 GCCCTAACATACAGAATACGCCAT 60.803 45.833 0.00 0.00 0.00 4.40
5447 7424 4.690748 CCCTAACATACAGAATACGCCATG 59.309 45.833 0.00 0.00 0.00 3.66
5448 7425 5.297547 CCTAACATACAGAATACGCCATGT 58.702 41.667 0.00 0.00 0.00 3.21
5449 7426 5.405571 CCTAACATACAGAATACGCCATGTC 59.594 44.000 0.00 0.00 0.00 3.06
5450 7427 4.400529 ACATACAGAATACGCCATGTCA 57.599 40.909 0.00 0.00 0.00 3.58
5451 7428 4.960938 ACATACAGAATACGCCATGTCAT 58.039 39.130 0.00 0.00 0.00 3.06
5452 7429 4.991056 ACATACAGAATACGCCATGTCATC 59.009 41.667 0.00 0.00 0.00 2.92
5453 7430 2.473816 ACAGAATACGCCATGTCATCG 58.526 47.619 0.00 0.00 0.00 3.84
5454 7431 1.193203 CAGAATACGCCATGTCATCGC 59.807 52.381 0.00 0.00 0.00 4.58
5455 7432 1.202521 AGAATACGCCATGTCATCGCA 60.203 47.619 3.26 0.00 0.00 5.10
5456 7433 1.800586 GAATACGCCATGTCATCGCAT 59.199 47.619 3.26 0.00 0.00 4.73
5457 7434 1.150827 ATACGCCATGTCATCGCATG 58.849 50.000 3.26 0.00 44.18 4.06
5458 7435 1.498043 TACGCCATGTCATCGCATGC 61.498 55.000 7.91 7.91 43.46 4.06
5459 7436 2.825975 CGCCATGTCATCGCATGCA 61.826 57.895 19.57 5.34 43.46 3.96
5460 7437 1.658114 GCCATGTCATCGCATGCAT 59.342 52.632 19.57 7.64 43.46 3.96
5461 7438 0.663269 GCCATGTCATCGCATGCATG 60.663 55.000 22.70 22.70 43.46 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.179468 ACACGCCACTACCAACAAGT 59.821 50.000 0.00 0.00 0.00 3.16
42 43 2.445119 AACCCACACGCCACTACCA 61.445 57.895 0.00 0.00 0.00 3.25
46 47 3.476031 CTCCAACCCACACGCCACT 62.476 63.158 0.00 0.00 0.00 4.00
108 109 6.265876 TGCAATACCATGATCAAACATGCTAT 59.734 34.615 16.92 0.00 44.11 2.97
111 112 4.684877 TGCAATACCATGATCAAACATGC 58.315 39.130 0.00 7.03 44.11 4.06
171 172 6.334102 AGTCGCCAAAATTACCAATTACAA 57.666 33.333 0.00 0.00 0.00 2.41
284 285 8.564574 GTGTACAGATGAAAAGGTACAATTGAA 58.435 33.333 13.59 0.00 45.21 2.69
292 294 7.554835 ACTTTGTTGTGTACAGATGAAAAGGTA 59.445 33.333 18.51 0.00 38.19 3.08
333 335 4.661125 TCATTCTGTACAATTTGATGCGC 58.339 39.130 0.00 0.00 0.00 6.09
393 395 8.839343 CACCTACAATCATCAAAATACTATGCA 58.161 33.333 0.00 0.00 0.00 3.96
532 534 6.216662 TGGAGGGTCAAATCTAATAAAGTCCA 59.783 38.462 0.00 0.00 0.00 4.02
628 630 1.875009 TGCAGAAACTCTCAGCACAG 58.125 50.000 0.00 0.00 41.26 3.66
787 983 8.710749 TTCTGGATAGCTGGCATAAAAATAAT 57.289 30.769 0.00 0.00 0.00 1.28
964 1163 0.668535 GCTTTGAAGGAAACGCACCT 59.331 50.000 0.00 0.00 39.69 4.00
967 1166 1.333619 GACAGCTTTGAAGGAAACGCA 59.666 47.619 0.00 0.00 0.00 5.24
1160 1359 7.557719 CCATAGGTGATCCAACTTCTGTATTTT 59.442 37.037 0.00 0.00 31.86 1.82
1298 1497 3.012518 GCCTGTGAGAGCAACATGTTAT 58.987 45.455 11.53 2.69 0.00 1.89
1458 1657 1.003580 ACTTGGCATGTAGGGTCAGTG 59.996 52.381 3.94 0.00 0.00 3.66
1524 1723 4.557695 GCAGTGATTCCTAGGACACTATCG 60.558 50.000 26.45 18.47 40.84 2.92
1841 2040 6.096001 ACAAAAGAGAACAATGAGAGCAAGTT 59.904 34.615 0.00 0.00 0.00 2.66
2258 2459 4.047822 CAAAAGCTTCAACGGCATTACAA 58.952 39.130 0.00 0.00 0.00 2.41
2603 2820 6.331061 CCAACAGTACTCTATGGTAGTTGAC 58.669 44.000 15.99 0.00 33.52 3.18
2604 2821 5.421056 CCCAACAGTACTCTATGGTAGTTGA 59.579 44.000 15.99 0.00 33.52 3.18
2605 2822 5.187186 ACCCAACAGTACTCTATGGTAGTTG 59.813 44.000 14.08 12.11 32.50 3.16
2606 2823 5.339477 ACCCAACAGTACTCTATGGTAGTT 58.661 41.667 14.08 2.28 31.75 2.24
2607 2824 4.944177 ACCCAACAGTACTCTATGGTAGT 58.056 43.478 14.08 6.03 31.75 2.73
2608 2825 4.954202 TGACCCAACAGTACTCTATGGTAG 59.046 45.833 14.08 5.56 31.75 3.18
2609 2826 4.938028 TGACCCAACAGTACTCTATGGTA 58.062 43.478 14.08 2.09 31.75 3.25
2662 2879 8.737168 AGCTATTATGCTGAAAGATGTTGTAA 57.263 30.769 0.00 0.00 42.33 2.41
2787 3004 7.450074 TCAGCTCAAGATAGGAACAAACTTAA 58.550 34.615 0.00 0.00 0.00 1.85
3114 3331 5.172934 GTCATTACCGTTGTATTGGTCAGA 58.827 41.667 0.00 0.00 39.70 3.27
3170 3387 4.458989 GCCTCACCAATTGACTTGATAACA 59.541 41.667 7.12 0.00 36.97 2.41
3416 3633 2.477825 CGCTACCATTCACCTGATGAG 58.522 52.381 0.00 0.00 38.99 2.90
3474 3691 7.555554 CAGAAGTCCATGTCCTTATGAAAATCT 59.444 37.037 9.45 0.00 32.94 2.40
3701 3918 1.860950 CGTGAAGACACTTCACCACAG 59.139 52.381 27.42 16.03 44.29 3.66
3721 3938 3.049912 GACCACGGAAAAAGAATGCAAC 58.950 45.455 0.00 0.00 0.00 4.17
3781 3998 5.830000 TTTGAAGCTTGGATCATGATCAG 57.170 39.130 31.49 23.20 39.54 2.90
3925 4142 3.901222 TGTGACTCAACTTGGACCATCTA 59.099 43.478 0.00 0.00 0.00 1.98
4122 4339 2.899256 CCATTTTCTTTCCCAGCCTCAA 59.101 45.455 0.00 0.00 0.00 3.02
4322 4539 7.595502 CGAGCTAATATTAACTCCGTTCTCATT 59.404 37.037 16.62 0.00 0.00 2.57
4323 4540 7.085116 CGAGCTAATATTAACTCCGTTCTCAT 58.915 38.462 16.62 0.00 0.00 2.90
4420 4637 3.864789 TCTTCAGCCTTCCTTGTCTTT 57.135 42.857 0.00 0.00 0.00 2.52
4751 4971 0.962356 CAATTCAGTCAAGCGGGCCT 60.962 55.000 0.84 0.00 0.00 5.19
4776 4996 1.135689 CAGGCGACACCAAAGCATAAC 60.136 52.381 0.00 0.00 43.14 1.89
4778 4998 1.305219 GCAGGCGACACCAAAGCATA 61.305 55.000 0.00 0.00 43.14 3.14
4819 5048 0.685458 ACGTACGCTATGGAAGGGGT 60.685 55.000 16.72 0.00 42.36 4.95
5003 5232 9.665719 TTACATCTCTGTTTACTATTTGCATCA 57.334 29.630 0.00 0.00 36.79 3.07
5129 7104 3.197790 CGGTTGCGCCCATCTCTG 61.198 66.667 4.18 0.00 0.00 3.35
5175 7150 6.490566 AATGTGTTATTTGTAGGAACCGTC 57.509 37.500 0.00 0.00 0.00 4.79
5232 7208 3.118905 AGTCTTCTGACAAGACCAAGC 57.881 47.619 10.25 0.00 45.82 4.01
5233 7209 4.697514 TGAAGTCTTCTGACAAGACCAAG 58.302 43.478 13.67 0.00 45.82 3.61
5234 7210 4.753516 TGAAGTCTTCTGACAAGACCAA 57.246 40.909 13.67 0.00 45.82 3.67
5235 7211 4.590647 AGATGAAGTCTTCTGACAAGACCA 59.409 41.667 13.67 4.02 45.82 4.02
5266 7242 7.581424 TTCCCATGGGATTTTTAAAGGAATT 57.419 32.000 34.21 0.00 44.74 2.17
5283 7259 4.157289 CACTGGTCTCAGATTTTTCCCATG 59.843 45.833 0.00 0.00 43.49 3.66
5284 7260 4.338879 CACTGGTCTCAGATTTTTCCCAT 58.661 43.478 0.00 0.00 43.49 4.00
5295 7271 0.976641 TACTTGCCCACTGGTCTCAG 59.023 55.000 0.00 0.00 46.10 3.35
5381 7358 3.932289 ACACGTGTGAGCGTTAGC 58.068 55.556 22.71 0.00 43.83 3.09
5390 7367 2.094757 TAGCTCCCACCACACGTGTG 62.095 60.000 36.13 36.13 45.23 3.82
5391 7368 1.404479 TTAGCTCCCACCACACGTGT 61.404 55.000 17.22 17.22 41.26 4.49
5392 7369 0.250124 TTTAGCTCCCACCACACGTG 60.250 55.000 15.48 15.48 42.62 4.49
5393 7370 0.250166 GTTTAGCTCCCACCACACGT 60.250 55.000 0.00 0.00 0.00 4.49
5394 7371 0.953960 GGTTTAGCTCCCACCACACG 60.954 60.000 0.00 0.00 0.00 4.49
5395 7372 0.608308 GGGTTTAGCTCCCACCACAC 60.608 60.000 4.06 0.00 44.05 3.82
5396 7373 1.765074 GGGTTTAGCTCCCACCACA 59.235 57.895 4.06 0.00 44.05 4.17
5397 7374 1.376812 CGGGTTTAGCTCCCACCAC 60.377 63.158 9.52 0.14 44.81 4.16
5398 7375 3.074281 CGGGTTTAGCTCCCACCA 58.926 61.111 9.52 0.00 44.81 4.17
5399 7376 2.437895 GCGGGTTTAGCTCCCACC 60.438 66.667 9.52 5.20 44.81 4.61
5400 7377 2.437895 GGCGGGTTTAGCTCCCAC 60.438 66.667 9.52 0.00 44.81 4.61
5401 7378 3.723922 GGGCGGGTTTAGCTCCCA 61.724 66.667 9.52 0.00 44.81 4.37
5402 7379 3.723922 TGGGCGGGTTTAGCTCCC 61.724 66.667 0.00 0.00 41.41 4.30
5403 7380 2.437895 GTGGGCGGGTTTAGCTCC 60.438 66.667 0.00 0.00 33.29 4.70
5404 7381 2.038837 GTGTGGGCGGGTTTAGCTC 61.039 63.158 0.00 0.00 35.22 4.09
5405 7382 2.033602 GTGTGGGCGGGTTTAGCT 59.966 61.111 0.00 0.00 34.52 3.32
5406 7383 3.428282 CGTGTGGGCGGGTTTAGC 61.428 66.667 0.00 0.00 0.00 3.09
5407 7384 3.428282 GCGTGTGGGCGGGTTTAG 61.428 66.667 0.00 0.00 0.00 1.85
5414 7391 2.581208 TATGTTAGGGCGTGTGGGCG 62.581 60.000 0.00 0.00 43.46 6.13
5415 7392 1.093496 GTATGTTAGGGCGTGTGGGC 61.093 60.000 0.00 0.00 41.35 5.36
5416 7393 0.250793 TGTATGTTAGGGCGTGTGGG 59.749 55.000 0.00 0.00 0.00 4.61
5417 7394 1.206132 TCTGTATGTTAGGGCGTGTGG 59.794 52.381 0.00 0.00 0.00 4.17
5418 7395 2.665649 TCTGTATGTTAGGGCGTGTG 57.334 50.000 0.00 0.00 0.00 3.82
5419 7396 3.906720 ATTCTGTATGTTAGGGCGTGT 57.093 42.857 0.00 0.00 0.00 4.49
5420 7397 3.734231 CGTATTCTGTATGTTAGGGCGTG 59.266 47.826 0.00 0.00 0.00 5.34
5421 7398 3.797865 GCGTATTCTGTATGTTAGGGCGT 60.798 47.826 0.00 0.00 0.00 5.68
5422 7399 2.729882 GCGTATTCTGTATGTTAGGGCG 59.270 50.000 0.00 0.00 0.00 6.13
5423 7400 3.064931 GGCGTATTCTGTATGTTAGGGC 58.935 50.000 0.00 0.00 0.00 5.19
5424 7401 4.330944 TGGCGTATTCTGTATGTTAGGG 57.669 45.455 0.00 0.00 0.00 3.53
5425 7402 5.297547 ACATGGCGTATTCTGTATGTTAGG 58.702 41.667 0.00 0.00 0.00 2.69
5426 7403 5.983118 TGACATGGCGTATTCTGTATGTTAG 59.017 40.000 0.00 0.00 0.00 2.34
5427 7404 5.908341 TGACATGGCGTATTCTGTATGTTA 58.092 37.500 0.00 0.00 0.00 2.41
5428 7405 4.765273 TGACATGGCGTATTCTGTATGTT 58.235 39.130 0.00 0.00 0.00 2.71
5429 7406 4.400529 TGACATGGCGTATTCTGTATGT 57.599 40.909 0.00 0.00 0.00 2.29
5430 7407 4.090498 CGATGACATGGCGTATTCTGTATG 59.910 45.833 0.00 0.00 0.00 2.39
5431 7408 4.237724 CGATGACATGGCGTATTCTGTAT 58.762 43.478 0.00 0.00 0.00 2.29
5432 7409 3.638484 CGATGACATGGCGTATTCTGTA 58.362 45.455 0.00 0.00 0.00 2.74
5433 7410 2.473816 CGATGACATGGCGTATTCTGT 58.526 47.619 0.00 0.00 0.00 3.41
5434 7411 1.193203 GCGATGACATGGCGTATTCTG 59.807 52.381 6.68 0.00 0.00 3.02
5435 7412 1.202521 TGCGATGACATGGCGTATTCT 60.203 47.619 16.36 0.00 36.74 2.40
5436 7413 1.217001 TGCGATGACATGGCGTATTC 58.783 50.000 16.36 0.00 36.74 1.75
5437 7414 1.532437 CATGCGATGACATGGCGTATT 59.468 47.619 15.71 0.00 43.05 1.89
5438 7415 1.150827 CATGCGATGACATGGCGTAT 58.849 50.000 15.71 5.69 43.05 3.06
5439 7416 1.498043 GCATGCGATGACATGGCGTA 61.498 55.000 15.71 3.54 46.14 4.42
5440 7417 2.827051 GCATGCGATGACATGGCGT 61.827 57.895 16.36 13.79 46.14 5.68
5441 7418 2.051614 GCATGCGATGACATGGCG 60.052 61.111 16.36 5.19 46.14 5.69
5442 7419 0.663269 CATGCATGCGATGACATGGC 60.663 55.000 14.93 14.87 46.14 4.40
5443 7420 0.663269 GCATGCATGCGATGACATGG 60.663 55.000 33.99 1.70 46.14 3.66


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

AutoCloner maintained by Alex Coulton.