Multiple sequence alignment - TraesCS5D01G439500

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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 TraesCS5D01G439500 chr5D 100.000 5234 0 0 1 5234 493128639 493123406 0.000000e+00 9666.0
1 TraesCS5D01G439500 chr5D 81.679 131 17 5 5089 5219 338659591 338659714 9.270000e-18 102.0
2 TraesCS5D01G439500 chr5D 81.111 90 16 1 4831 4919 310495780 310495691 2.610000e-08 71.3
3 TraesCS5D01G439500 chr5B 91.944 2768 146 34 2196 4932 608208239 608205518 0.000000e+00 3805.0
4 TraesCS5D01G439500 chr5B 94.495 2180 71 21 2196 4352 608352298 608350145 0.000000e+00 3315.0
5 TraesCS5D01G439500 chr5B 93.444 1388 77 6 817 2198 608209711 608208332 0.000000e+00 2047.0
6 TraesCS5D01G439500 chr5B 93.276 1279 74 4 932 2198 608353669 608352391 0.000000e+00 1875.0
7 TraesCS5D01G439500 chr5B 96.493 827 25 4 1 826 608211028 608210205 0.000000e+00 1363.0
8 TraesCS5D01G439500 chr5B 94.425 574 27 5 376 947 608354257 608353687 0.000000e+00 878.0
9 TraesCS5D01G439500 chr5B 91.061 537 26 9 4555 5090 608348649 608348134 0.000000e+00 706.0
10 TraesCS5D01G439500 chr5B 97.187 391 10 1 1 390 608356307 608355917 0.000000e+00 660.0
11 TraesCS5D01G439500 chr5B 93.981 216 8 2 4348 4562 608349874 608349663 6.540000e-84 322.0
12 TraesCS5D01G439500 chr5B 89.313 131 13 1 5092 5221 608348100 608347970 4.190000e-36 163.0
13 TraesCS5D01G439500 chr5B 91.837 49 4 0 4853 4901 144801973 144801925 9.400000e-08 69.4
14 TraesCS5D01G439500 chr5A 92.140 2201 118 18 1 2191 616150327 616148172 0.000000e+00 3055.0
15 TraesCS5D01G439500 chr5A 93.542 1533 75 8 2192 3713 616148079 616146560 0.000000e+00 2261.0
16 TraesCS5D01G439500 chr5A 88.393 896 52 21 4359 5231 616145756 616144890 0.000000e+00 1031.0
17 TraesCS5D01G439500 chr5A 88.754 578 32 9 3714 4271 616146314 616145750 0.000000e+00 676.0
18 TraesCS5D01G439500 chr5A 81.061 132 18 5 5100 5230 616350306 616350431 1.200000e-16 99.0
19 TraesCS5D01G439500 chr5A 80.451 133 18 3 5101 5232 569527363 569527238 1.550000e-15 95.3
20 TraesCS5D01G439500 chr6A 88.202 178 12 4 1074 1242 595586520 595586343 2.470000e-48 204.0
21 TraesCS5D01G439500 chr6D 85.000 180 20 3 1074 1252 450088746 450088573 5.390000e-40 176.0
22 TraesCS5D01G439500 chr4B 74.850 334 45 25 4914 5230 31683996 31684307 1.190000e-21 115.0
23 TraesCS5D01G439500 chr3B 81.203 133 21 2 5098 5230 144483558 144483686 2.580000e-18 104.0
24 TraesCS5D01G439500 chr3A 74.030 335 43 20 4914 5228 49327068 49327378 4.310000e-16 97.1
25 TraesCS5D01G439500 chr3A 79.545 132 18 8 5102 5231 381912 382036 9.340000e-13 86.1
26 TraesCS5D01G439500 chr3A 83.333 84 14 0 4834 4917 502090221 502090304 1.560000e-10 78.7
27 TraesCS5D01G439500 chr2B 82.692 104 16 2 4788 4890 567985272 567985170 2.010000e-14 91.6
28 TraesCS5D01G439500 chr4D 97.826 46 0 1 689 733 54336228 54336273 1.560000e-10 78.7
29 TraesCS5D01G439500 chr4D 87.037 54 6 1 4841 4894 13238533 13238481 5.660000e-05 60.2
30 TraesCS5D01G439500 chr1A 81.250 96 16 2 4790 4884 570262348 570262442 5.620000e-10 76.8
31 TraesCS5D01G439500 chr3D 79.000 100 12 5 4951 5049 301888852 301888761 5.660000e-05 60.2


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 TraesCS5D01G439500 chr5D 493123406 493128639 5233 True 9666.000000 9666 100.000000 1 5234 1 chr5D.!!$R2 5233
1 TraesCS5D01G439500 chr5B 608205518 608211028 5510 True 2405.000000 3805 93.960333 1 4932 3 chr5B.!!$R2 4931
2 TraesCS5D01G439500 chr5B 608347970 608356307 8337 True 1131.285714 3315 93.391143 1 5221 7 chr5B.!!$R3 5220
3 TraesCS5D01G439500 chr5A 616144890 616150327 5437 True 1755.750000 3055 90.707250 1 5231 4 chr5A.!!$R2 5230

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
793 2477 0.931005 GGCTCCGCAATAGTTTCTCG 59.069 55.0 0.00 0.00 0.00 4.04 F
1589 3823 0.034670 GGACCAAGGAGCTGCTCAAT 60.035 55.0 28.95 15.45 31.08 2.57 F
1991 4225 0.257328 TGGACAACAAGCCCAAGACA 59.743 50.0 0.00 0.00 0.00 3.41 F
2004 4238 1.000233 CAAGACACTGCGCACAATGC 61.000 55.0 5.66 2.19 40.69 3.56 F
3573 5917 0.110295 TGCAACCCTGTGTATGCACT 59.890 50.0 15.25 0.00 43.32 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 3852 0.035630 GAGCAGCATCACCTTGTCCT 60.036 55.000 0.00 0.0 0.00 3.85 R
3186 5526 1.674962 CTTTCTCAGCCAATAGCCTGC 59.325 52.381 0.00 0.0 45.47 4.85 R
3396 5737 2.159014 GCATGATGAGTACCCACCGTAA 60.159 50.000 0.00 0.0 0.00 3.18 R
3898 6501 2.907910 ACTGGTAGTACAACGTAGCG 57.092 50.000 2.06 0.0 0.00 4.26 R
4688 8640 0.376152 CGCCATTCACTGATGTGCTC 59.624 55.000 0.00 0.0 43.49 4.26 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
442 2122 7.136289 AGAAGAACAAAAACGTGTAACTTCA 57.864 32.000 18.32 0.00 41.81 3.02
488 2168 2.158885 GGCACTCAGGATTTAGAGGACC 60.159 54.545 0.00 0.00 36.20 4.46
540 2221 4.688021 CAAGGTGGAGAGTCACTTATAGC 58.312 47.826 0.00 0.00 37.75 2.97
564 2245 2.496070 GGTGAGTGCTGAGTACATACCA 59.504 50.000 16.90 2.46 31.18 3.25
665 2349 3.125316 GGTGCACTGAAGGTCTAAAATCG 59.875 47.826 17.98 0.00 0.00 3.34
669 2353 3.125316 CACTGAAGGTCTAAAATCGCACC 59.875 47.826 0.00 0.00 0.00 5.01
696 2380 9.413048 ACAAGTGTTCGAAAGTTTTGAAAATAA 57.587 25.926 17.99 4.25 0.00 1.40
793 2477 0.931005 GGCTCCGCAATAGTTTCTCG 59.069 55.000 0.00 0.00 0.00 4.04
995 3214 1.153086 CGCCTCCTTCAATCCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
1295 3523 0.886490 CCGACTTGCAAGTTCAGCCT 60.886 55.000 31.58 8.42 39.88 4.58
1299 3527 0.595095 CTTGCAAGTTCAGCCTCACC 59.405 55.000 18.65 0.00 0.00 4.02
1352 3580 1.292223 CACCTTCTTCGCTTCCGGA 59.708 57.895 0.00 0.00 34.56 5.14
1409 3637 3.988678 AGGTCCCCGTCCCTCGAA 61.989 66.667 0.00 0.00 42.86 3.71
1447 3675 0.948141 GATGATAGGCTGCACGGAGC 60.948 60.000 0.50 1.35 45.96 4.70
1457 3691 2.357517 CACGGAGCCTGCGAGTTT 60.358 61.111 14.02 0.00 34.49 2.66
1460 3694 2.747855 GGAGCCTGCGAGTTTGGG 60.748 66.667 0.00 0.00 0.00 4.12
1512 3746 0.671472 CCTGATTGCGCTCTGTGACA 60.671 55.000 9.73 0.00 0.00 3.58
1538 3772 3.379372 CGACCTTGAAGGATTACCGACTA 59.621 47.826 19.83 0.00 37.67 2.59
1553 3787 3.196463 CCGACTACACATCTACTCGTCT 58.804 50.000 0.00 0.00 0.00 4.18
1589 3823 0.034670 GGACCAAGGAGCTGCTCAAT 60.035 55.000 28.95 15.45 31.08 2.57
1618 3852 2.498481 CTGGGGTCCTTACGATTACACA 59.502 50.000 0.00 0.00 0.00 3.72
1692 3926 2.557805 GCATGCTGGTGTGTGACG 59.442 61.111 11.37 0.00 0.00 4.35
1717 3951 2.043992 TCAAGAACGAGAACCCCTTCA 58.956 47.619 0.00 0.00 0.00 3.02
1719 3953 1.420430 AGAACGAGAACCCCTTCACA 58.580 50.000 0.00 0.00 0.00 3.58
1991 4225 0.257328 TGGACAACAAGCCCAAGACA 59.743 50.000 0.00 0.00 0.00 3.41
2004 4238 1.000233 CAAGACACTGCGCACAATGC 61.000 55.000 5.66 2.19 40.69 3.56
2077 4311 3.084039 TCAAGGGAGTCATTGTTGATGC 58.916 45.455 7.08 0.00 36.23 3.91
2113 4347 1.693083 GATGACTCGGCGTTTTCGGG 61.693 60.000 6.85 0.00 44.29 5.14
2120 4354 1.792301 GGCGTTTTCGGGCTTACTC 59.208 57.895 0.00 0.00 44.29 2.59
2191 4425 4.299796 GGCTTGCCCCACCCTGAA 62.300 66.667 0.00 0.00 0.00 3.02
2253 4583 7.698130 GGAAAATATTCTCCTTCGTGTCAAATG 59.302 37.037 0.13 0.00 35.79 2.32
2262 4592 2.139917 TCGTGTCAAATGTTCCTTCCG 58.860 47.619 0.00 0.00 0.00 4.30
2312 4642 5.013079 TGACTCCTGGTAATTGTTCATCTGT 59.987 40.000 0.00 0.00 0.00 3.41
2378 4709 7.009174 CACAATTTGGTTGGCGAATTATCTTAC 59.991 37.037 0.78 0.00 42.28 2.34
2657 4996 7.074502 GCAGATAGAAATTAATGCTGCACTAC 58.925 38.462 3.57 0.00 44.72 2.73
3110 5449 7.930217 TGATCTGTTCTAAACTTCAAAACCTG 58.070 34.615 0.00 0.00 0.00 4.00
3130 5469 5.948162 ACCTGTCAATGTTCTGAATGCTATT 59.052 36.000 0.00 0.00 0.00 1.73
3186 5526 6.072397 TCCATATAACTGGTTTTGTTGTTCCG 60.072 38.462 0.00 0.00 37.57 4.30
3232 5572 4.559153 ACCATGCACAAAATTTAGCTCAC 58.441 39.130 0.00 0.00 0.00 3.51
3467 5808 2.435372 TCATATGCCCTGTTTCCCAC 57.565 50.000 0.00 0.00 0.00 4.61
3573 5917 0.110295 TGCAACCCTGTGTATGCACT 59.890 50.000 15.25 0.00 43.32 4.40
3618 5962 5.611374 ACATAGCTACGGCAACTATCAATT 58.389 37.500 0.00 0.00 41.70 2.32
3719 6308 4.246458 GTGAAGCTTATGATACGATCCCC 58.754 47.826 0.00 0.00 0.00 4.81
3724 6313 3.258372 GCTTATGATACGATCCCCTGTCA 59.742 47.826 0.00 0.00 0.00 3.58
3742 6331 3.632643 TCATCATTTGACCTGCAGCTA 57.367 42.857 8.66 0.00 0.00 3.32
3747 6336 4.953667 TCATTTGACCTGCAGCTATAGAG 58.046 43.478 8.66 0.00 0.00 2.43
3817 6410 8.629158 GGCACCATGTTTGTAAATATGATAAGA 58.371 33.333 13.50 0.00 39.11 2.10
3910 6513 9.775060 GAATTATTTATCTTCGCTACGTTGTAC 57.225 33.333 0.00 0.00 0.00 2.90
3911 6514 9.525409 AATTATTTATCTTCGCTACGTTGTACT 57.475 29.630 0.00 0.00 0.00 2.73
4151 6760 1.993948 GACCCCCTCCGGTAAAGCT 60.994 63.158 0.00 0.00 35.79 3.74
4152 6761 1.540617 ACCCCCTCCGGTAAAGCTT 60.541 57.895 0.00 0.00 33.04 3.74
4165 6774 1.043022 AAAGCTTTCTGCCACCCTTG 58.957 50.000 5.69 0.00 44.23 3.61
4205 6819 7.832187 TCCGAGTTAATTTGAATTGGAGGTATT 59.168 33.333 0.00 0.00 0.00 1.89
4206 6820 9.116067 CCGAGTTAATTTGAATTGGAGGTATTA 57.884 33.333 0.00 0.00 0.00 0.98
4687 8639 4.218417 ACAGCAACTGTTTTTCTGAAGTGT 59.782 37.500 16.29 0.00 42.59 3.55
4688 8640 4.560035 CAGCAACTGTTTTTCTGAAGTGTG 59.440 41.667 7.90 0.00 0.00 3.82
4689 8641 4.458989 AGCAACTGTTTTTCTGAAGTGTGA 59.541 37.500 0.00 0.00 0.00 3.58
4690 8642 4.795278 GCAACTGTTTTTCTGAAGTGTGAG 59.205 41.667 0.00 0.00 0.00 3.51
4691 8643 4.622701 ACTGTTTTTCTGAAGTGTGAGC 57.377 40.909 0.00 0.00 0.00 4.26
4692 8644 4.009675 ACTGTTTTTCTGAAGTGTGAGCA 58.990 39.130 0.00 0.00 0.00 4.26
4693 8645 4.142600 ACTGTTTTTCTGAAGTGTGAGCAC 60.143 41.667 0.00 0.00 45.57 4.40
4697 8649 3.473923 TTCTGAAGTGTGAGCACATCA 57.526 42.857 6.59 6.66 46.80 3.07
4699 8651 2.916702 TGAAGTGTGAGCACATCAGT 57.083 45.000 6.59 0.00 44.97 3.41
4700 8652 2.486918 TGAAGTGTGAGCACATCAGTG 58.513 47.619 6.59 0.00 44.97 3.66
4803 8755 1.302511 GTGGCGGCTCCTTGAAGAA 60.303 57.895 11.43 0.00 35.26 2.52
4821 8773 3.178046 AGAAGGAAGAAGGTTCTCCCTC 58.822 50.000 0.00 0.00 45.47 4.30
4833 8785 3.028098 TCCCTCCCTAGCCCTCGT 61.028 66.667 0.00 0.00 0.00 4.18
4941 8894 6.476380 TCGTTCGTCTAAGTTTGTGTGTTTAT 59.524 34.615 0.00 0.00 0.00 1.40
4982 8935 6.137794 TCTAATCTTCTCTTCATCGGTGAC 57.862 41.667 0.00 0.00 33.11 3.67
4995 8948 2.241171 GGTGACGGTTACTGTTGGC 58.759 57.895 0.00 0.00 0.00 4.52
4999 8952 2.166584 GACGGTTACTGTTGGCGTGC 62.167 60.000 0.00 0.00 0.00 5.34
5000 8953 1.959226 CGGTTACTGTTGGCGTGCT 60.959 57.895 0.00 0.00 0.00 4.40
5001 8954 1.574428 GGTTACTGTTGGCGTGCTG 59.426 57.895 0.00 0.00 0.00 4.41
5002 8955 1.574428 GTTACTGTTGGCGTGCTGG 59.426 57.895 0.00 0.00 0.00 4.85
5003 8956 1.147376 TTACTGTTGGCGTGCTGGT 59.853 52.632 0.00 0.00 0.00 4.00
5004 8957 0.882927 TTACTGTTGGCGTGCTGGTC 60.883 55.000 0.00 0.00 0.00 4.02
5005 8958 2.034048 TACTGTTGGCGTGCTGGTCA 62.034 55.000 0.00 0.00 0.00 4.02
5139 9124 4.189639 AGTCGTTGTTGGATAGAAGGTC 57.810 45.455 0.00 0.00 0.00 3.85
5143 9128 4.768448 TCGTTGTTGGATAGAAGGTCTACA 59.232 41.667 0.00 0.00 30.79 2.74
5145 9130 5.105877 CGTTGTTGGATAGAAGGTCTACAGA 60.106 44.000 0.00 0.00 30.79 3.41
5151 9136 4.957327 GGATAGAAGGTCTACAGACTTGGT 59.043 45.833 9.15 0.00 44.20 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 113 6.682113 GCTGAGTGTTTTGGCATGATTCATAT 60.682 38.462 0.00 0.00 0.00 1.78
430 2110 7.810759 AGTGAAAACAAATTTGAAGTTACACGT 59.189 29.630 24.64 11.89 37.54 4.49
442 2122 6.218746 GGCTGAGATGAGTGAAAACAAATTT 58.781 36.000 0.00 0.00 0.00 1.82
488 2168 0.246635 ATCACCACCGAGAACCTTCG 59.753 55.000 0.00 0.00 40.18 3.79
540 2221 2.820059 TGTACTCAGCACTCACCAAG 57.180 50.000 0.00 0.00 0.00 3.61
564 2245 6.149474 CCTCACTTCATTAACCGAAGAACAAT 59.851 38.462 18.68 0.00 42.05 2.71
669 2353 6.683090 TTTCAAAACTTTCGAACACTTGTG 57.317 33.333 0.00 0.00 0.00 3.33
793 2477 4.757594 TGCCAAAAACCATCATAATCTGC 58.242 39.130 0.00 0.00 0.00 4.26
1126 3348 1.898574 GTGGTGTGGTTCCTGCTGG 60.899 63.158 2.58 2.58 0.00 4.85
1326 3554 1.696832 GCGAAGAAGGTGCGGATGAC 61.697 60.000 0.00 0.00 0.00 3.06
1352 3580 3.251571 GAAGTATTCAAAGTCGCCGTCT 58.748 45.455 0.00 0.00 46.62 4.18
1424 3652 1.270465 CCGTGCAGCCTATCATCATCA 60.270 52.381 0.00 0.00 0.00 3.07
1447 3675 1.079127 ACGATCCCAAACTCGCAGG 60.079 57.895 0.00 0.00 38.42 4.85
1449 3677 2.032634 GCACGATCCCAAACTCGCA 61.033 57.895 0.00 0.00 38.42 5.10
1475 3709 0.319641 GGAGATAATGGTCGCCGTCC 60.320 60.000 0.00 0.00 0.00 4.79
1512 3746 0.899720 TAATCCTTCAAGGTCGCCGT 59.100 50.000 2.50 0.00 36.53 5.68
1538 3772 3.011119 GTCCTCAGACGAGTAGATGTGT 58.989 50.000 0.00 0.00 37.59 3.72
1553 3787 0.041684 TCCTCCATGCTCTGTCCTCA 59.958 55.000 0.00 0.00 0.00 3.86
1618 3852 0.035630 GAGCAGCATCACCTTGTCCT 60.036 55.000 0.00 0.00 0.00 3.85
1692 3926 3.006644 AGGGGTTCTCGTTCTTGAAGTAC 59.993 47.826 0.00 0.00 0.00 2.73
1717 3951 1.089481 CAATGGGATGTAGCGCGTGT 61.089 55.000 8.43 0.00 0.00 4.49
1719 3953 2.180204 GCAATGGGATGTAGCGCGT 61.180 57.895 8.43 0.00 0.00 6.01
1963 4197 2.159114 GGCTTGTTGTCCACATGTTTGT 60.159 45.455 0.00 0.00 34.43 2.83
2077 4311 4.633126 AGTCATCGACCAAAATGTCATCAG 59.367 41.667 0.00 0.00 34.88 2.90
2113 4347 1.279271 TCCTTTGGCCAGAGAGTAAGC 59.721 52.381 24.46 0.00 0.00 3.09
2120 4354 2.692041 GGATTCATTCCTTTGGCCAGAG 59.308 50.000 16.42 16.42 41.78 3.35
2144 4378 1.878775 CTTGAAAGCCAAGCTCCCG 59.121 57.895 0.00 0.00 44.90 5.14
2154 4388 2.578495 CGAGTGCATGTTCTTGAAAGC 58.422 47.619 0.00 0.00 0.00 3.51
2156 4390 1.266718 GCCGAGTGCATGTTCTTGAAA 59.733 47.619 0.00 0.00 40.77 2.69
2191 4425 1.212935 AGGTGCTTCCACTTTCAGTGT 59.787 47.619 3.30 0.00 44.50 3.55
2253 4583 0.240945 CCAATGCACACGGAAGGAAC 59.759 55.000 0.00 0.00 0.00 3.62
2312 4642 6.437928 GTCACAAGCATGTTGATAACAAGAA 58.562 36.000 12.90 0.00 45.86 2.52
2378 4709 3.019564 AGCATAAAAGGGTAGCAGCAAG 58.980 45.455 0.00 0.00 0.00 4.01
3186 5526 1.674962 CTTTCTCAGCCAATAGCCTGC 59.325 52.381 0.00 0.00 45.47 4.85
3232 5572 5.459107 GCTATGAACATTCCGTACAGTACTG 59.541 44.000 21.44 21.44 0.00 2.74
3396 5737 2.159014 GCATGATGAGTACCCACCGTAA 60.159 50.000 0.00 0.00 0.00 3.18
3467 5808 7.376866 GCTGTATGATGATTAAAAATGGACACG 59.623 37.037 0.00 0.00 0.00 4.49
3522 5863 6.151985 AGTGAACTTGTTGAAACATTGTGGTA 59.848 34.615 0.00 0.00 38.95 3.25
3523 5864 5.047377 AGTGAACTTGTTGAAACATTGTGGT 60.047 36.000 0.00 0.00 38.95 4.16
3724 6313 5.306419 TCTCTATAGCTGCAGGTCAAATGAT 59.694 40.000 23.94 11.69 0.00 2.45
3875 6468 8.956426 AGCGAAGATAAATAATTCCAACTTTGA 58.044 29.630 0.00 0.00 0.00 2.69
3895 6498 3.120060 ACTGGTAGTACAACGTAGCGAAG 60.120 47.826 2.06 0.00 0.00 3.79
3898 6501 2.907910 ACTGGTAGTACAACGTAGCG 57.092 50.000 2.06 0.00 0.00 4.26
3910 6513 4.969484 AGGTAACAGGACAAAACTGGTAG 58.031 43.478 0.00 0.00 38.69 3.18
3911 6514 5.366186 TGTAGGTAACAGGACAAAACTGGTA 59.634 40.000 0.00 0.00 40.23 3.25
3912 6515 3.945640 AGGTAACAGGACAAAACTGGT 57.054 42.857 0.00 0.00 40.23 4.00
4151 6760 0.823356 GACAGCAAGGGTGGCAGAAA 60.823 55.000 0.00 0.00 39.11 2.52
4152 6761 1.228245 GACAGCAAGGGTGGCAGAA 60.228 57.895 0.00 0.00 39.11 3.02
4165 6774 4.489679 AACTCGGAATTTTTCAGACAGC 57.510 40.909 0.00 0.00 30.75 4.40
4422 7325 3.771479 AGGGGGAAGCTGAAATTTGAATC 59.229 43.478 0.00 0.00 0.00 2.52
4606 8532 2.036733 ACAGCTTTACTTGTACGCTCCA 59.963 45.455 0.00 0.00 0.00 3.86
4610 8536 2.412089 CAGGACAGCTTTACTTGTACGC 59.588 50.000 0.00 0.00 0.00 4.42
4687 8639 1.456296 GCCATTCACTGATGTGCTCA 58.544 50.000 0.00 0.00 43.49 4.26
4688 8640 0.376152 CGCCATTCACTGATGTGCTC 59.624 55.000 0.00 0.00 43.49 4.26
4689 8641 1.651240 GCGCCATTCACTGATGTGCT 61.651 55.000 0.00 0.00 43.49 4.40
4690 8642 1.226491 GCGCCATTCACTGATGTGC 60.226 57.895 0.00 0.00 43.49 4.57
4691 8643 0.806868 AAGCGCCATTCACTGATGTG 59.193 50.000 2.29 0.00 45.07 3.21
4692 8644 2.401583 TAAGCGCCATTCACTGATGT 57.598 45.000 2.29 0.00 0.00 3.06
4693 8645 2.223340 GGTTAAGCGCCATTCACTGATG 60.223 50.000 2.29 0.00 0.00 3.07
4694 8646 2.017049 GGTTAAGCGCCATTCACTGAT 58.983 47.619 2.29 0.00 0.00 2.90
4695 8647 1.003118 AGGTTAAGCGCCATTCACTGA 59.997 47.619 2.29 0.00 0.00 3.41
4696 8648 1.398390 GAGGTTAAGCGCCATTCACTG 59.602 52.381 2.29 0.00 0.00 3.66
4697 8649 1.279271 AGAGGTTAAGCGCCATTCACT 59.721 47.619 2.29 0.00 0.00 3.41
4698 8650 1.739067 AGAGGTTAAGCGCCATTCAC 58.261 50.000 2.29 0.00 0.00 3.18
4699 8651 2.489938 AAGAGGTTAAGCGCCATTCA 57.510 45.000 2.29 0.00 0.00 2.57
4700 8652 4.634443 TCTTTAAGAGGTTAAGCGCCATTC 59.366 41.667 2.29 0.00 29.71 2.67
4833 8785 2.267642 GCTACATGCACCACGGGA 59.732 61.111 0.00 0.00 42.31 5.14
4982 8935 1.959226 AGCACGCCAACAGTAACCG 60.959 57.895 0.00 0.00 0.00 4.44
4993 8946 2.562912 CAACATGACCAGCACGCC 59.437 61.111 0.00 0.00 0.00 5.68
4994 8947 2.187599 GACCAACATGACCAGCACGC 62.188 60.000 0.00 0.00 0.00 5.34
4995 8948 0.884259 TGACCAACATGACCAGCACG 60.884 55.000 0.00 0.00 0.00 5.34
5005 8958 1.305213 GGCCCCACATGACCAACAT 60.305 57.895 0.00 0.00 40.17 2.71
5090 9043 2.049063 GAGCGAGCTGACGGTGTT 60.049 61.111 0.84 0.00 43.81 3.32
5170 9155 5.301551 TGTCATGGCAGTACAAAGAACATTT 59.698 36.000 0.00 0.00 0.00 2.32
5171 9156 4.826733 TGTCATGGCAGTACAAAGAACATT 59.173 37.500 0.00 0.00 0.00 2.71
5172 9157 4.397420 TGTCATGGCAGTACAAAGAACAT 58.603 39.130 0.00 0.00 0.00 2.71
5186 9171 6.261603 TCAATCTATTCATCAACTGTCATGGC 59.738 38.462 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.