Multiple sequence alignment - TraesCS2A01G501800

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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 TraesCS2A01G501800 chr2A 100.000 4004 0 0 1 4004 729837231 729833228 0.000000e+00 7395.0
1 TraesCS2A01G501800 chr2D 91.817 2432 108 41 703 3114 596196913 596194553 0.000000e+00 3304.0
2 TraesCS2A01G501800 chr2D 90.818 501 32 4 3517 4004 596193828 596193329 0.000000e+00 658.0
3 TraesCS2A01G501800 chr2D 82.178 202 33 3 428 628 596197136 596196937 1.910000e-38 171.0
4 TraesCS2A01G501800 chr2B 94.062 1701 79 12 667 2359 724750156 724748470 0.000000e+00 2562.0
5 TraesCS2A01G501800 chr2B 93.037 876 48 8 2344 3215 724748456 724747590 0.000000e+00 1267.0
6 TraesCS2A01G501800 chr2B 92.808 584 37 4 3419 4002 724741862 724741284 0.000000e+00 841.0
7 TraesCS2A01G501800 chr2B 93.833 454 21 5 227 679 724750562 724750115 0.000000e+00 676.0
8 TraesCS2A01G501800 chr2B 89.583 192 16 3 3204 3393 724742352 724742163 1.440000e-59 241.0
9 TraesCS2A01G501800 chr2B 84.959 246 24 3 1 233 724752727 724752482 1.860000e-58 237.0
10 TraesCS2A01G501800 chr1D 84.783 92 4 4 2050 2131 376984773 376984864 2.560000e-12 84.2
11 TraesCS2A01G501800 chr3B 84.043 94 5 5 2048 2131 766325329 766325422 9.220000e-12 82.4


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 TraesCS2A01G501800 chr2A 729833228 729837231 4003 True 7395.000000 7395 100.00000 1 4004 1 chr2A.!!$R1 4003
1 TraesCS2A01G501800 chr2D 596193329 596197136 3807 True 1377.666667 3304 88.27100 428 4004 3 chr2D.!!$R1 3576
2 TraesCS2A01G501800 chr2B 724747590 724752727 5137 True 1185.500000 2562 91.47275 1 3215 4 chr2B.!!$R2 3214
3 TraesCS2A01G501800 chr2B 724741284 724742352 1068 True 541.000000 841 91.19550 3204 4002 2 chr2B.!!$R1 798


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
951 2900 0.108804 AACATACACGACCCGCTCTG 60.109 55.0 0.00 0.0 0.0 3.35 F
1975 3928 0.309922 CGTACTACACCATCCGCGAT 59.690 55.0 8.23 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 4277 0.522180 TCGAGAAGAGAAGCGTGGAC 59.478 55.0 0.0 0.0 0.00 4.02 R
3801 6531 0.104304 ACGGAGAGAAGTTGTGCGTT 59.896 50.0 0.0 0.0 44.52 4.84 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
20 21 1.616865 TCATCGTCTTCTTTCCCACGT 59.383 47.619 0.00 0.00 33.89 4.49
29 30 3.053831 TCTTTCCCACGTTCTTGATCC 57.946 47.619 0.00 0.00 0.00 3.36
47 48 3.292159 GAACCACCCACAACCGCC 61.292 66.667 0.00 0.00 0.00 6.13
57 58 2.433491 CAACCGCCGACCGAATCA 60.433 61.111 0.00 0.00 40.02 2.57
66 67 1.901085 GACCGAATCACCTGCCTCT 59.099 57.895 0.00 0.00 0.00 3.69
68 69 1.194781 ACCGAATCACCTGCCTCTGT 61.195 55.000 0.00 0.00 0.00 3.41
120 132 3.120385 CGCTGCCATGCTTGTCGA 61.120 61.111 0.00 0.00 0.00 4.20
123 135 1.855213 GCTGCCATGCTTGTCGACAA 61.855 55.000 28.07 28.07 0.00 3.18
126 138 1.237285 GCCATGCTTGTCGACAACCT 61.237 55.000 26.53 13.38 0.00 3.50
128 140 1.511850 CATGCTTGTCGACAACCTCA 58.488 50.000 26.53 22.09 0.00 3.86
131 143 1.295792 GCTTGTCGACAACCTCAACA 58.704 50.000 26.53 4.45 0.00 3.33
132 144 1.873591 GCTTGTCGACAACCTCAACAT 59.126 47.619 26.53 0.00 0.00 2.71
133 145 2.096218 GCTTGTCGACAACCTCAACATC 60.096 50.000 26.53 0.00 0.00 3.06
134 146 1.778334 TGTCGACAACCTCAACATCG 58.222 50.000 17.62 0.00 0.00 3.84
135 147 1.067974 TGTCGACAACCTCAACATCGT 59.932 47.619 17.62 0.00 34.47 3.73
136 148 1.455786 GTCGACAACCTCAACATCGTG 59.544 52.381 11.55 0.00 34.47 4.35
184 197 1.515521 GAAGAACCTGCAACCCCACG 61.516 60.000 0.00 0.00 0.00 4.94
236 2176 1.059913 CCCCCTGCACCCTAAGATAG 58.940 60.000 0.00 0.00 0.00 2.08
246 2186 5.604231 TGCACCCTAAGATAGATGAAGTGAT 59.396 40.000 0.00 0.00 0.00 3.06
249 2189 6.426328 CACCCTAAGATAGATGAAGTGATTGC 59.574 42.308 0.00 0.00 0.00 3.56
259 2200 2.627699 TGAAGTGATTGCTTTTCCACCC 59.372 45.455 0.00 0.00 0.00 4.61
311 2252 0.888285 AGTGCACTGCTGCTTCCTTC 60.888 55.000 20.97 0.00 44.57 3.46
312 2253 0.888285 GTGCACTGCTGCTTCCTTCT 60.888 55.000 10.32 0.00 44.57 2.85
313 2254 0.604780 TGCACTGCTGCTTCCTTCTC 60.605 55.000 1.98 0.00 44.57 2.87
324 2265 2.093973 GCTTCCTTCTCCACTGAATCGA 60.094 50.000 0.00 0.00 0.00 3.59
337 2278 7.974675 TCCACTGAATCGACTAATTCAAATTC 58.025 34.615 1.24 0.00 43.22 2.17
379 2320 5.560183 CGTCCAGTAAAACTGTTGATCAACC 60.560 44.000 30.66 16.16 44.50 3.77
383 2324 4.755123 AGTAAAACTGTTGATCAACCGAGG 59.245 41.667 30.66 20.73 40.46 4.63
485 2426 5.182950 TCAATTCAGGCTTTCGCTATTTCAA 59.817 36.000 0.00 0.00 36.09 2.69
528 2470 7.174080 TCCAAATACACGATTCAAGAATGACAA 59.826 33.333 0.00 0.00 34.61 3.18
559 2501 4.276678 TCTGCTCTGAAAACCACATGAAAG 59.723 41.667 0.00 0.00 0.00 2.62
682 2624 5.977489 AAGAAAAACATGTAGGCTTACCC 57.023 39.130 0.00 0.00 36.11 3.69
684 2626 5.254115 AGAAAAACATGTAGGCTTACCCTC 58.746 41.667 0.00 0.00 44.96 4.30
685 2627 4.650972 AAAACATGTAGGCTTACCCTCA 57.349 40.909 0.00 0.00 44.96 3.86
686 2628 4.650972 AAACATGTAGGCTTACCCTCAA 57.349 40.909 0.00 0.00 44.96 3.02
687 2629 4.650972 AACATGTAGGCTTACCCTCAAA 57.349 40.909 0.00 0.00 44.96 2.69
688 2630 4.650972 ACATGTAGGCTTACCCTCAAAA 57.349 40.909 0.00 0.00 44.96 2.44
689 2631 4.993028 ACATGTAGGCTTACCCTCAAAAA 58.007 39.130 0.00 0.00 44.96 1.94
733 2675 4.256920 GCAGCCACACCCAGAATATATAG 58.743 47.826 0.00 0.00 0.00 1.31
740 2682 7.453393 CCACACCCAGAATATATAGTTCACAT 58.547 38.462 4.15 0.00 0.00 3.21
760 2702 1.838112 TATCTTTGCCACAAGCCAGG 58.162 50.000 0.00 0.00 42.71 4.45
818 2760 2.959516 TCCTCAGCAGACATACAAACG 58.040 47.619 0.00 0.00 0.00 3.60
845 2787 2.238942 TCAGAAGACGCAGCAAAAGA 57.761 45.000 0.00 0.00 0.00 2.52
910 2854 2.287547 CGCCTTTGCAACTAAGCTTTCA 60.288 45.455 3.20 0.00 37.32 2.69
916 2860 5.418310 TTGCAACTAAGCTTTCACTGTAC 57.582 39.130 3.20 0.00 34.99 2.90
951 2900 0.108804 AACATACACGACCCGCTCTG 60.109 55.000 0.00 0.00 0.00 3.35
957 2906 2.028190 CGACCCGCTCTGCATAGG 59.972 66.667 0.83 0.00 0.00 2.57
959 2908 4.227134 ACCCGCTCTGCATAGGCG 62.227 66.667 17.18 17.18 45.35 5.52
965 2914 1.144716 CTCTGCATAGGCGGCAAGA 59.855 57.895 13.08 5.03 46.35 3.02
967 2916 2.124736 TGCATAGGCGGCAAGACC 60.125 61.111 13.08 0.00 45.35 3.85
985 2934 1.610522 ACCTGCAGCAAACAGTTGATC 59.389 47.619 8.66 0.00 36.83 2.92
1261 3210 3.684990 AGCTCGCGCTCAACCTCA 61.685 61.111 5.56 0.00 45.15 3.86
1291 3240 1.812922 CTCCACGGTCAGCTCATGC 60.813 63.158 0.00 0.00 40.05 4.06
1292 3241 2.046988 CCACGGTCAGCTCATGCA 60.047 61.111 0.00 0.00 42.74 3.96
1293 3242 1.450848 CCACGGTCAGCTCATGCAT 60.451 57.895 0.00 0.00 42.74 3.96
1294 3243 1.712018 CCACGGTCAGCTCATGCATG 61.712 60.000 21.07 21.07 42.74 4.06
1353 3306 1.203065 GCTGCACTGCAAACTGAAAC 58.797 50.000 4.99 0.00 38.41 2.78
1363 3316 4.439057 TGCAAACTGAAACGAACTCTACT 58.561 39.130 0.00 0.00 0.00 2.57
1366 3319 5.220605 GCAAACTGAAACGAACTCTACTGTT 60.221 40.000 0.00 0.00 0.00 3.16
1370 3323 5.519206 ACTGAAACGAACTCTACTGTTGTTC 59.481 40.000 0.00 9.44 37.36 3.18
1475 3428 1.039068 CGATCTGGACAGGAGCATCT 58.961 55.000 0.00 0.00 33.73 2.90
1622 3575 3.134574 ACTGCTGGAACGGTAATCAAA 57.865 42.857 0.00 0.00 36.83 2.69
1627 3580 4.580995 TGCTGGAACGGTAATCAAAAGAAA 59.419 37.500 0.00 0.00 36.83 2.52
1653 3606 1.376037 TGTGCACAACGGACACACA 60.376 52.632 19.28 0.00 41.63 3.72
1975 3928 0.309922 CGTACTACACCATCCGCGAT 59.690 55.000 8.23 0.00 0.00 4.58
2329 4282 3.442996 CCTCAAGGTGATCGTCCAC 57.557 57.895 9.00 2.20 36.37 4.02
2366 4348 0.806102 TAACCGCGCTCATGCTCTTC 60.806 55.000 5.56 0.00 36.97 2.87
2370 4352 1.790387 GCGCTCATGCTCTTCGTTT 59.210 52.632 0.00 0.00 36.97 3.60
2374 4356 2.923655 CGCTCATGCTCTTCGTTTAAGA 59.076 45.455 0.00 0.00 42.07 2.10
2377 4359 4.784710 GCTCATGCTCTTCGTTTAAGATGC 60.785 45.833 0.00 0.00 43.32 3.91
2378 4360 4.252878 TCATGCTCTTCGTTTAAGATGCA 58.747 39.130 11.50 11.50 44.73 3.96
2383 4365 7.139896 TGCTCTTCGTTTAAGATGCATTTTA 57.860 32.000 0.00 2.52 43.32 1.52
2384 4366 7.243487 TGCTCTTCGTTTAAGATGCATTTTAG 58.757 34.615 9.39 0.25 43.32 1.85
2385 4367 7.119116 TGCTCTTCGTTTAAGATGCATTTTAGA 59.881 33.333 9.39 3.29 43.32 2.10
2387 4369 9.994432 CTCTTCGTTTAAGATGCATTTTAGAAT 57.006 29.630 9.39 0.00 43.32 2.40
2412 4401 1.115467 TTTGGTGGAACAATTGGCGT 58.885 45.000 10.83 0.00 44.16 5.68
2423 4412 0.958382 AATTGGCGTGCGTACACCAT 60.958 50.000 14.29 0.00 44.40 3.55
2430 4419 3.550992 GCGTACACCATGTCGCCG 61.551 66.667 11.96 3.89 39.31 6.46
2464 4453 2.273538 ATCCAGAATGAGCATCCAGC 57.726 50.000 0.00 0.00 39.69 4.85
2595 4584 5.319139 TCGTAAACTGACGAGATAAACGAG 58.681 41.667 0.00 0.00 46.43 4.18
2664 4653 1.378646 TGTTCGTGGCCACCAAACA 60.379 52.632 32.36 32.36 34.18 2.83
2665 4654 0.753479 TGTTCGTGGCCACCAAACAT 60.753 50.000 32.36 0.00 34.18 2.71
2910 4906 4.731503 CTGCTGCTGTTGCGCGTC 62.732 66.667 8.43 0.00 43.34 5.19
3037 5033 0.466922 AGCCATGGCCTTGACTATGC 60.467 55.000 33.14 13.41 43.17 3.14
3246 5245 1.775039 GCGCTGAGCTGTGTGAACAA 61.775 55.000 1.78 0.00 44.04 2.83
3247 5247 0.041839 CGCTGAGCTGTGTGAACAAC 60.042 55.000 1.78 0.00 0.00 3.32
3263 5263 4.082300 TGAACAACTGTTGTGCTTGTGATT 60.082 37.500 27.19 10.20 44.59 2.57
3270 5270 4.814147 TGTTGTGCTTGTGATTTGTGAAA 58.186 34.783 0.00 0.00 0.00 2.69
3312 5312 3.631686 AGTATGCGCAGATTATTTGGCAA 59.368 39.130 18.32 0.00 33.72 4.52
3330 5330 1.070843 CAACTTCTTGTGTGCCGTACG 60.071 52.381 8.69 8.69 0.00 3.67
3335 5335 1.358725 CTTGTGTGCCGTACGATGGG 61.359 60.000 18.76 0.06 0.00 4.00
3372 5372 0.859232 AGCAACTTCGTGTAGCGTTG 59.141 50.000 0.00 0.00 42.13 4.10
3384 5384 0.742990 TAGCGTTGCATACACCAGCC 60.743 55.000 0.00 0.00 0.00 4.85
3393 5393 1.003580 CATACACCAGCCAGTTCACCT 59.996 52.381 0.00 0.00 0.00 4.00
3425 5700 2.961062 AGTTGATTTGCAAAGGTGAGCT 59.039 40.909 18.19 7.79 38.44 4.09
3436 5711 4.171005 CAAAGGTGAGCTATGCATTTGTG 58.829 43.478 3.54 0.00 0.00 3.33
3448 5723 3.446799 TGCATTTGTGCTTCAACACTTC 58.553 40.909 1.86 0.00 41.30 3.01
3496 5772 3.932710 TCTGAATAATTGTGTGAGCGACC 59.067 43.478 0.00 0.00 0.00 4.79
3520 6237 6.293081 CCGAGGAACTGATGCACAAATAATAG 60.293 42.308 0.00 0.00 41.55 1.73
3573 6290 2.347490 GAAAGCTGGCCTCGGTGA 59.653 61.111 3.32 0.00 0.00 4.02
3590 6315 4.227527 TCGGTGATGGATAGATAGAGGCTA 59.772 45.833 0.00 0.00 0.00 3.93
3591 6316 4.336993 CGGTGATGGATAGATAGAGGCTAC 59.663 50.000 0.00 0.00 0.00 3.58
3652 6382 0.891373 CTTCACTTCAGCCTCTCGGA 59.109 55.000 0.00 0.00 0.00 4.55
3658 6388 4.200283 CAGCCTCTCGGAGTCGGC 62.200 72.222 23.85 23.85 42.79 5.54
3662 6392 4.180946 CTCTCGGAGTCGGCGGTG 62.181 72.222 7.21 0.00 36.95 4.94
3696 6426 2.760159 CGCCGGGCAATTCGTCATT 61.760 57.895 20.71 0.00 0.00 2.57
3789 6519 2.626785 TGCCCGATATCCCTTATTCCA 58.373 47.619 0.00 0.00 0.00 3.53
3801 6531 3.495983 CCCTTATTCCACCGTGCATATGA 60.496 47.826 6.97 0.00 0.00 2.15
3956 6686 2.589014 CAAGCCAAGAAGCGAAATGAC 58.411 47.619 0.00 0.00 38.01 3.06
3961 6691 3.070018 CCAAGAAGCGAAATGACTGACT 58.930 45.455 0.00 0.00 0.00 3.41
3971 6701 4.327357 CGAAATGACTGACTGATACACCAC 59.673 45.833 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.970640 TTCGGATCAAGAACGTGGGA 59.029 50.000 0.00 0.00 0.00 4.37
20 21 1.060729 TGGGTGGTTCGGATCAAGAA 58.939 50.000 0.00 0.00 0.00 2.52
29 30 3.656045 GCGGTTGTGGGTGGTTCG 61.656 66.667 0.00 0.00 0.00 3.95
47 48 1.519455 GAGGCAGGTGATTCGGTCG 60.519 63.158 0.00 0.00 0.00 4.79
52 53 1.086634 GCGACAGAGGCAGGTGATTC 61.087 60.000 0.00 0.00 0.00 2.52
117 129 1.778334 CACGATGTTGAGGTTGTCGA 58.222 50.000 0.00 0.00 36.28 4.20
120 132 2.831685 TAGCACGATGTTGAGGTTGT 57.168 45.000 0.00 0.00 0.00 3.32
123 135 2.423577 GGTTTAGCACGATGTTGAGGT 58.576 47.619 0.00 0.00 0.00 3.85
126 138 1.270412 ACCGGTTTAGCACGATGTTGA 60.270 47.619 0.00 0.00 0.00 3.18
128 140 1.153353 CACCGGTTTAGCACGATGTT 58.847 50.000 2.97 0.00 0.00 2.71
131 143 1.435577 GTTCACCGGTTTAGCACGAT 58.564 50.000 2.97 0.00 0.00 3.73
132 144 0.600782 GGTTCACCGGTTTAGCACGA 60.601 55.000 2.97 0.00 0.00 4.35
133 145 0.881159 TGGTTCACCGGTTTAGCACG 60.881 55.000 2.97 0.00 39.43 5.34
134 146 0.589708 GTGGTTCACCGGTTTAGCAC 59.410 55.000 24.09 24.09 39.43 4.40
135 147 0.535553 GGTGGTTCACCGGTTTAGCA 60.536 55.000 2.97 9.14 44.95 3.49
136 148 2.250646 GGTGGTTCACCGGTTTAGC 58.749 57.895 2.97 6.11 44.95 3.09
175 188 3.198953 TTAGGGGTGCGTGGGGTTG 62.199 63.158 0.00 0.00 0.00 3.77
184 197 2.772515 ACCTTGTCTATCTTAGGGGTGC 59.227 50.000 0.00 0.00 31.91 5.01
187 200 2.104963 GCCACCTTGTCTATCTTAGGGG 59.895 54.545 0.00 0.00 31.91 4.79
236 2176 4.488879 GGTGGAAAAGCAATCACTTCATC 58.511 43.478 0.00 0.00 0.00 2.92
246 2186 2.494530 GGTGCGGGTGGAAAAGCAA 61.495 57.895 0.00 0.00 41.56 3.91
249 2189 2.989253 GGGGTGCGGGTGGAAAAG 60.989 66.667 0.00 0.00 0.00 2.27
311 2252 6.968131 TTTGAATTAGTCGATTCAGTGGAG 57.032 37.500 0.00 0.00 44.33 3.86
312 2253 7.824289 AGAATTTGAATTAGTCGATTCAGTGGA 59.176 33.333 9.81 0.00 44.33 4.02
313 2254 7.978982 AGAATTTGAATTAGTCGATTCAGTGG 58.021 34.615 9.81 0.00 44.33 4.00
379 2320 6.040878 AGTAAACGGAATCTAATGTTCCTCG 58.959 40.000 3.69 0.00 42.36 4.63
383 2324 7.955864 GTGACAAGTAAACGGAATCTAATGTTC 59.044 37.037 0.00 0.00 0.00 3.18
416 2357 6.142818 ACGATTGAGAGAACTAGAGATTGG 57.857 41.667 0.00 0.00 0.00 3.16
426 2367 1.921230 GGCTTCGACGATTGAGAGAAC 59.079 52.381 0.00 0.00 0.00 3.01
485 2426 5.782893 TTTGGATTCGTCTTTCATTGGTT 57.217 34.783 0.00 0.00 0.00 3.67
498 2439 6.344572 TCTTGAATCGTGTATTTGGATTCG 57.655 37.500 8.06 0.00 45.61 3.34
528 2470 1.661463 TTTCAGAGCAGATGGGTCCT 58.339 50.000 0.00 0.00 45.21 3.85
593 2535 6.858993 GCGGCGTCAAAATTATATGGATTTTA 59.141 34.615 9.37 1.05 35.54 1.52
613 2555 2.664851 TTGTCACAAGAGGCGGCG 60.665 61.111 0.51 0.51 0.00 6.46
686 2628 5.184711 TCAAGCCTGCATGTTTTTCTTTTT 58.815 33.333 0.00 0.00 0.00 1.94
687 2629 4.768583 TCAAGCCTGCATGTTTTTCTTTT 58.231 34.783 0.00 0.00 0.00 2.27
688 2630 4.374399 CTCAAGCCTGCATGTTTTTCTTT 58.626 39.130 0.00 0.00 0.00 2.52
689 2631 3.243975 CCTCAAGCCTGCATGTTTTTCTT 60.244 43.478 0.00 0.00 0.00 2.52
690 2632 2.298163 CCTCAAGCCTGCATGTTTTTCT 59.702 45.455 0.00 0.00 0.00 2.52
691 2633 2.680577 CCTCAAGCCTGCATGTTTTTC 58.319 47.619 0.00 0.00 0.00 2.29
692 2634 1.270465 GCCTCAAGCCTGCATGTTTTT 60.270 47.619 0.00 0.00 34.35 1.94
693 2635 0.319405 GCCTCAAGCCTGCATGTTTT 59.681 50.000 0.00 0.00 34.35 2.43
694 2636 0.828762 TGCCTCAAGCCTGCATGTTT 60.829 50.000 0.00 0.00 42.71 2.83
695 2637 1.228644 TGCCTCAAGCCTGCATGTT 60.229 52.632 0.00 0.00 42.71 2.71
696 2638 1.677966 CTGCCTCAAGCCTGCATGT 60.678 57.895 0.00 0.00 42.71 3.21
697 2639 3.064987 GCTGCCTCAAGCCTGCATG 62.065 63.158 0.00 0.00 42.71 4.06
698 2640 2.754658 GCTGCCTCAAGCCTGCAT 60.755 61.111 0.00 0.00 42.71 3.96
733 2675 4.622740 GCTTGTGGCAAAGATAATGTGAAC 59.377 41.667 11.81 0.00 41.35 3.18
760 2702 8.655651 TGTGGTTAACTTTGGATTGAAATTTC 57.344 30.769 11.41 11.41 0.00 2.17
818 2760 2.602660 GCTGCGTCTTCTGATTTCTCTC 59.397 50.000 0.00 0.00 0.00 3.20
845 2787 1.228154 GCCCCCGTTTTCTCACTGT 60.228 57.895 0.00 0.00 0.00 3.55
904 2848 0.887387 TTGGGCGGTACAGTGAAAGC 60.887 55.000 0.00 0.00 0.00 3.51
910 2854 1.349688 TGATTCTTTGGGCGGTACAGT 59.650 47.619 0.00 0.00 0.00 3.55
916 2860 4.578516 TGTATGTTATGATTCTTTGGGCGG 59.421 41.667 0.00 0.00 0.00 6.13
951 2900 2.182842 CAGGTCTTGCCGCCTATGC 61.183 63.158 0.00 0.00 43.70 3.14
965 2914 1.610522 GATCAACTGTTTGCTGCAGGT 59.389 47.619 17.12 0.00 38.22 4.00
967 2916 1.400629 CCGATCAACTGTTTGCTGCAG 60.401 52.381 10.11 10.11 39.67 4.41
974 2923 2.641197 GGGCACCGATCAACTGTTT 58.359 52.632 0.00 0.00 40.86 2.83
1261 3210 1.211969 CGTGGAGGACGTTGTCGAT 59.788 57.895 0.00 0.00 43.50 3.59
1317 3270 3.061848 CCAAGACGGGCGCCAAAT 61.062 61.111 30.85 13.09 0.00 2.32
1340 3293 3.951979 AGAGTTCGTTTCAGTTTGCAG 57.048 42.857 0.00 0.00 0.00 4.41
1353 3306 4.750098 ACCAATGAACAACAGTAGAGTTCG 59.250 41.667 0.00 0.00 43.36 3.95
1363 3316 2.234661 TGCAACCAACCAATGAACAACA 59.765 40.909 0.00 0.00 0.00 3.33
1366 3319 1.411977 CCTGCAACCAACCAATGAACA 59.588 47.619 0.00 0.00 0.00 3.18
1370 3323 1.001181 CTTCCCTGCAACCAACCAATG 59.999 52.381 0.00 0.00 0.00 2.82
1622 3575 4.496341 CGTTGTGCACACAGAAGATTTCTT 60.496 41.667 21.56 0.00 42.94 2.52
1627 3580 1.202639 TCCGTTGTGCACACAGAAGAT 60.203 47.619 21.56 0.00 42.94 2.40
1653 3606 2.995939 CAGTTCAGATACACACACGCAT 59.004 45.455 0.00 0.00 0.00 4.73
2258 4211 2.361104 GTGCAGGAAATGGGCGGA 60.361 61.111 0.00 0.00 0.00 5.54
2324 4277 0.522180 TCGAGAAGAGAAGCGTGGAC 59.478 55.000 0.00 0.00 0.00 4.02
2326 4279 2.065993 TTTCGAGAAGAGAAGCGTGG 57.934 50.000 0.00 0.00 0.00 4.94
2327 4280 5.444745 GGTTAATTTCGAGAAGAGAAGCGTG 60.445 44.000 0.00 0.00 0.00 5.34
2329 4282 4.259451 CGGTTAATTTCGAGAAGAGAAGCG 60.259 45.833 10.44 10.44 0.00 4.68
2374 4356 8.732531 CCACCAAAAATGAATTCTAAAATGCAT 58.267 29.630 7.05 0.00 42.09 3.96
2378 4360 9.844257 TGTTCCACCAAAAATGAATTCTAAAAT 57.156 25.926 7.05 0.00 0.00 1.82
2383 4365 7.229106 CCAATTGTTCCACCAAAAATGAATTCT 59.771 33.333 7.05 0.00 0.00 2.40
2384 4366 7.361894 CCAATTGTTCCACCAAAAATGAATTC 58.638 34.615 4.43 0.00 0.00 2.17
2385 4367 6.238981 GCCAATTGTTCCACCAAAAATGAATT 60.239 34.615 4.43 0.00 0.00 2.17
2387 4369 4.578105 GCCAATTGTTCCACCAAAAATGAA 59.422 37.500 4.43 0.00 0.00 2.57
2396 4385 1.372872 GCACGCCAATTGTTCCACC 60.373 57.895 4.43 0.00 0.00 4.61
2412 4401 2.433491 GGCGACATGGTGTACGCA 60.433 61.111 19.95 0.00 43.42 5.24
2430 4419 2.231964 TCTGGATTGTTCAAGCAATGGC 59.768 45.455 3.35 0.00 38.98 4.40
2485 4474 3.800628 GCAGGTTTTGGCATGAGAC 57.199 52.632 0.00 0.00 0.00 3.36
2595 4584 2.100631 CGGTTGTCTCGGCCACATC 61.101 63.158 2.24 0.00 0.00 3.06
2641 4630 1.525077 GGTGGCCACGAACAGTTCA 60.525 57.895 29.08 0.00 0.00 3.18
2664 4653 1.938585 TTCCAGGTCGAAGAGGACAT 58.061 50.000 0.86 0.00 36.95 3.06
2665 4654 1.712056 TTTCCAGGTCGAAGAGGACA 58.288 50.000 0.86 0.00 36.95 4.02
2736 4732 4.438346 GTGAACACCTGCACGAGT 57.562 55.556 0.00 0.00 0.00 4.18
2982 4978 1.815421 CTCGTCCTTGGGAATGCGG 60.815 63.158 0.00 0.00 31.38 5.69
3037 5033 8.815141 AGTAGTAGTAGTAGTACATCACATCG 57.185 38.462 20.04 0.00 37.48 3.84
3081 5079 0.526211 AACATCTCTGCACGCTACGA 59.474 50.000 0.00 0.00 0.00 3.43
3133 5132 2.930019 CCACTGCAGGGACCTCCA 60.930 66.667 20.22 0.00 38.24 3.86
3134 5133 4.416738 GCCACTGCAGGGACCTCC 62.417 72.222 20.22 0.00 37.47 4.30
3135 5134 3.640407 TGCCACTGCAGGGACCTC 61.640 66.667 20.22 3.98 44.23 3.85
3246 5245 3.443329 TCACAAATCACAAGCACAACAGT 59.557 39.130 0.00 0.00 0.00 3.55
3247 5247 4.031418 TCACAAATCACAAGCACAACAG 57.969 40.909 0.00 0.00 0.00 3.16
3296 5296 4.361451 AGAAGTTGCCAAATAATCTGCG 57.639 40.909 0.00 0.00 0.00 5.18
3312 5312 0.386476 TCGTACGGCACACAAGAAGT 59.614 50.000 16.52 0.00 0.00 3.01
3330 5330 5.643379 TTCTAGAACAAACAATGCCCATC 57.357 39.130 0.00 0.00 0.00 3.51
3335 5335 5.979517 AGTTGCTTTCTAGAACAAACAATGC 59.020 36.000 18.96 7.64 0.00 3.56
3372 5372 0.804989 GTGAACTGGCTGGTGTATGC 59.195 55.000 0.00 0.00 0.00 3.14
3401 5662 4.685924 CTCACCTTTGCAAATCAACTTGT 58.314 39.130 13.23 0.00 33.73 3.16
3403 5664 3.385755 AGCTCACCTTTGCAAATCAACTT 59.614 39.130 13.23 0.00 33.73 2.66
3436 5711 0.110464 GAGCTGCGAAGTGTTGAAGC 60.110 55.000 0.00 0.00 0.00 3.86
3448 5723 1.706301 CACACATCTTCGAGCTGCG 59.294 57.895 0.00 0.00 42.69 5.18
3496 5772 4.944962 TTATTTGTGCATCAGTTCCTCG 57.055 40.909 0.00 0.00 0.00 4.63
3520 6237 0.404426 ACACCCCCACTTAAAGGAGC 59.596 55.000 0.00 0.00 0.00 4.70
3573 6290 3.951037 CGCAGTAGCCTCTATCTATCCAT 59.049 47.826 0.00 0.00 37.52 3.41
3590 6315 1.968017 CACAGCCAACCATCGCAGT 60.968 57.895 0.00 0.00 0.00 4.40
3591 6316 1.642037 CTCACAGCCAACCATCGCAG 61.642 60.000 0.00 0.00 0.00 5.18
3662 6392 2.125269 CGTCCATGTCCGGTTCCC 60.125 66.667 0.00 0.00 0.00 3.97
3789 6519 4.608032 TGCGTTCATATGCACGGT 57.392 50.000 25.40 0.00 41.26 4.83
3801 6531 0.104304 ACGGAGAGAAGTTGTGCGTT 59.896 50.000 0.00 0.00 44.52 4.84
3956 6686 1.406069 GGCTGGTGGTGTATCAGTCAG 60.406 57.143 0.00 0.00 41.88 3.51
3961 6691 0.904649 CTCAGGCTGGTGGTGTATCA 59.095 55.000 15.73 0.00 0.00 2.15
3971 6701 2.834549 TCCTCTTTACTTCTCAGGCTGG 59.165 50.000 15.73 5.63 0.00 4.85



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

AutoCloner maintained by Alex Coulton.