Multiple sequence alignment - TraesCS2D01G413400

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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 TraesCS2D01G413400 chr2D 100.000 4356 0 0 1 4356 527903517 527907872 0.000000e+00 8045.0
1 TraesCS2D01G413400 chr2D 92.929 792 41 5 1896 2679 567941457 567942241 0.000000e+00 1138.0
2 TraesCS2D01G413400 chr2B 90.364 2335 107 32 2067 4356 625543152 625545413 0.000000e+00 2957.0
3 TraesCS2D01G413400 chr2B 92.913 1806 97 22 287 2079 625541348 625543135 0.000000e+00 2597.0
4 TraesCS2D01G413400 chr2B 88.732 284 26 5 1 282 625540760 625541039 4.170000e-90 342.0
5 TraesCS2D01G413400 chr2A 90.688 1772 99 36 160 1902 672770054 672771788 0.000000e+00 2298.0
6 TraesCS2D01G413400 chr2A 94.113 1342 56 10 2124 3457 672772132 672773458 0.000000e+00 2019.0
7 TraesCS2D01G413400 chr2A 93.571 420 13 4 3578 3983 672773459 672773878 8.010000e-172 614.0
8 TraesCS2D01G413400 chr2A 89.504 343 14 9 4012 4333 672773879 672774220 8.720000e-112 414.0
9 TraesCS2D01G413400 chr2A 90.206 194 11 4 1896 2081 30978476 30978669 3.360000e-61 246.0
10 TraesCS2D01G413400 chr2A 86.667 135 13 4 1 134 672767706 672767836 1.260000e-30 145.0
11 TraesCS2D01G413400 chr2A 95.714 70 3 0 131 200 672769987 672770056 3.560000e-21 113.0
12 TraesCS2D01G413400 chr2A 97.727 44 1 0 3608 3651 602765347 602765390 4.670000e-10 76.8
13 TraesCS2D01G413400 chr6B 90.709 1044 78 7 867 1909 70511700 70512725 0.000000e+00 1373.0
14 TraesCS2D01G413400 chr6B 85.714 315 43 2 1200 1513 506271041 506270728 9.030000e-87 331.0
15 TraesCS2D01G413400 chr5D 93.038 790 40 8 1896 2677 263473866 263474648 0.000000e+00 1140.0
16 TraesCS2D01G413400 chr5D 95.745 47 1 1 3605 3650 520064173 520064219 1.680000e-09 75.0
17 TraesCS2D01G413400 chr7D 92.803 792 42 8 1896 2679 114196772 114197556 0.000000e+00 1133.0
18 TraesCS2D01G413400 chr6D 92.803 792 42 8 1896 2679 427840187 427839403 0.000000e+00 1133.0
19 TraesCS2D01G413400 chr6D 92.551 792 44 8 1896 2679 10212598 10211814 0.000000e+00 1122.0
20 TraesCS2D01G413400 chr6D 80.409 342 50 11 1173 1513 294414693 294414368 1.210000e-60 244.0
21 TraesCS2D01G413400 chr6D 93.617 47 3 0 3608 3654 312732347 312732301 2.170000e-08 71.3
22 TraesCS2D01G413400 chr4D 92.757 497 24 7 1896 2384 505744179 505743687 0.000000e+00 708.0
23 TraesCS2D01G413400 chr4D 91.667 48 4 0 4142 4189 353546223 353546270 2.810000e-07 67.6
24 TraesCS2D01G413400 chr7A 90.656 503 33 4 1896 2390 190647993 190648489 0.000000e+00 656.0
25 TraesCS2D01G413400 chr7A 95.652 46 2 0 3605 3650 678173993 678174038 1.680000e-09 75.0
26 TraesCS2D01G413400 chr4A 90.946 497 31 8 1896 2384 309736801 309737291 0.000000e+00 656.0
27 TraesCS2D01G413400 chr5A 86.070 201 9 6 1896 2088 539439213 539439402 9.560000e-47 198.0
28 TraesCS2D01G413400 chr5B 100.000 44 0 0 3607 3650 492786618 492786575 1.000000e-11 82.4
29 TraesCS2D01G413400 chr7B 97.727 44 1 0 3607 3650 696616023 696616066 4.670000e-10 76.8
30 TraesCS2D01G413400 chr3D 97.727 44 1 0 3608 3651 531683835 531683792 4.670000e-10 76.8
31 TraesCS2D01G413400 chr1A 97.674 43 1 0 3609 3651 592078784 592078826 1.680000e-09 75.0


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 TraesCS2D01G413400 chr2D 527903517 527907872 4355 False 8045.000000 8045 100.000000 1 4356 1 chr2D.!!$F1 4355
1 TraesCS2D01G413400 chr2D 567941457 567942241 784 False 1138.000000 1138 92.929000 1896 2679 1 chr2D.!!$F2 783
2 TraesCS2D01G413400 chr2B 625540760 625545413 4653 False 1965.333333 2957 90.669667 1 4356 3 chr2B.!!$F1 4355
3 TraesCS2D01G413400 chr2A 672767706 672774220 6514 False 933.833333 2298 91.709500 1 4333 6 chr2A.!!$F3 4332
4 TraesCS2D01G413400 chr6B 70511700 70512725 1025 False 1373.000000 1373 90.709000 867 1909 1 chr6B.!!$F1 1042
5 TraesCS2D01G413400 chr5D 263473866 263474648 782 False 1140.000000 1140 93.038000 1896 2677 1 chr5D.!!$F1 781
6 TraesCS2D01G413400 chr7D 114196772 114197556 784 False 1133.000000 1133 92.803000 1896 2679 1 chr7D.!!$F1 783
7 TraesCS2D01G413400 chr6D 427839403 427840187 784 True 1133.000000 1133 92.803000 1896 2679 1 chr6D.!!$R4 783
8 TraesCS2D01G413400 chr6D 10211814 10212598 784 True 1122.000000 1122 92.551000 1896 2679 1 chr6D.!!$R1 783

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
778 3292 0.536724 AGCTGACACTGTCACACACA 59.463 50.000 7.84 0.0 37.67 3.72 F
779 3293 0.652592 GCTGACACTGTCACACACAC 59.347 55.000 7.84 0.0 37.67 3.82 F
782 3296 1.001406 TGACACTGTCACACACACACA 59.999 47.619 7.84 0.0 37.67 3.72 F
1560 4093 1.135689 CGTGCAATTACTTCCACTGCC 60.136 52.381 0.00 0.0 31.92 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 4636 1.812571 GTTGCTACAGGTGACCCAATG 59.187 52.381 0.00 0.00 0.0 2.82 R
2741 5453 2.457366 ACGGGAAATGTCAGACAGTC 57.543 50.000 9.64 8.73 0.0 3.51 R
2745 5457 7.940178 AAAATTTAAACGGGAAATGTCAGAC 57.060 32.000 0.00 0.00 0.0 3.51 R
3490 6209 1.019650 ACCCCCTATCACTCTCCAGT 58.980 55.000 0.00 0.00 0.0 4.00 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
39 41 2.111878 CGGCAGGATGATGACCCC 59.888 66.667 0.00 0.00 39.69 4.95
40 42 2.745308 CGGCAGGATGATGACCCCA 61.745 63.158 0.00 0.00 39.69 4.96
41 43 1.849116 GGCAGGATGATGACCCCAT 59.151 57.895 0.00 0.00 39.69 4.00
42 44 1.067295 GGCAGGATGATGACCCCATA 58.933 55.000 0.00 0.00 39.69 2.74
43 45 1.004044 GGCAGGATGATGACCCCATAG 59.996 57.143 0.00 0.00 39.69 2.23
44 46 1.701847 GCAGGATGATGACCCCATAGT 59.298 52.381 0.00 0.00 39.69 2.12
45 47 2.107204 GCAGGATGATGACCCCATAGTT 59.893 50.000 0.00 0.00 39.69 2.24
206 2400 2.993899 CGAGGGTATAATCATGGCGAAC 59.006 50.000 0.00 0.00 0.00 3.95
230 2432 5.724328 TGTTTGCACAATAAAACCTCAACA 58.276 33.333 0.00 0.00 35.80 3.33
269 2471 8.578593 TCTAAGTTTAGGATCTACTCCCTCTA 57.421 38.462 0.00 0.00 46.27 2.43
301 2807 3.175109 AGGACGTTTTTCGACACTCTT 57.825 42.857 0.00 0.00 42.86 2.85
304 2810 3.519497 GACGTTTTTCGACACTCTTTCG 58.481 45.455 0.00 0.00 42.86 3.46
309 2815 2.701073 TTCGACACTCTTTCGGACTC 57.299 50.000 0.00 0.00 37.09 3.36
311 2817 3.049708 TCGACACTCTTTCGGACTCTA 57.950 47.619 0.00 0.00 37.09 2.43
361 2870 9.374711 AGGGGAGTAAATACAAATTTTCTTTCA 57.625 29.630 0.00 0.00 34.10 2.69
374 2883 7.718334 AATTTTCTTTCAGGGATTAACCGAT 57.282 32.000 0.00 0.00 40.11 4.18
375 2884 7.718334 ATTTTCTTTCAGGGATTAACCGATT 57.282 32.000 0.00 0.00 40.11 3.34
376 2885 7.533289 TTTTCTTTCAGGGATTAACCGATTT 57.467 32.000 0.00 0.00 40.11 2.17
379 2888 7.153217 TCTTTCAGGGATTAACCGATTTTTC 57.847 36.000 0.00 0.00 40.11 2.29
399 2908 4.944962 TCTTTTTACATGCCATCACTCG 57.055 40.909 0.00 0.00 0.00 4.18
406 2915 0.897621 ATGCCATCACTCGTCAGACA 59.102 50.000 0.41 0.00 0.00 3.41
407 2916 0.678950 TGCCATCACTCGTCAGACAA 59.321 50.000 0.41 0.00 0.00 3.18
410 2919 1.273606 CCATCACTCGTCAGACAACCT 59.726 52.381 0.41 0.00 0.00 3.50
433 2942 7.147966 ACCTTTAGAATATTTTAAACCTGGCCG 60.148 37.037 7.00 0.00 0.00 6.13
487 2996 4.522722 GACATAGGGTCTATAGTGCCAC 57.477 50.000 14.71 0.00 43.46 5.01
489 2998 4.493618 ACATAGGGTCTATAGTGCCACAT 58.506 43.478 14.71 6.96 0.00 3.21
665 3179 2.867975 CCAAAGTCCAAGCAAGCAAAAG 59.132 45.455 0.00 0.00 0.00 2.27
666 3180 3.430651 CCAAAGTCCAAGCAAGCAAAAGA 60.431 43.478 0.00 0.00 0.00 2.52
667 3181 4.183101 CAAAGTCCAAGCAAGCAAAAGAA 58.817 39.130 0.00 0.00 0.00 2.52
668 3182 3.722728 AGTCCAAGCAAGCAAAAGAAG 57.277 42.857 0.00 0.00 0.00 2.85
669 3183 3.290710 AGTCCAAGCAAGCAAAAGAAGA 58.709 40.909 0.00 0.00 0.00 2.87
673 3187 4.586001 TCCAAGCAAGCAAAAGAAGAGAAT 59.414 37.500 0.00 0.00 0.00 2.40
695 3209 1.000731 GATCCATCGCTCTCCCTCAAG 59.999 57.143 0.00 0.00 0.00 3.02
708 3222 1.480137 CCCTCAAGACGAGAAGCATCT 59.520 52.381 0.00 0.00 45.45 2.90
728 3242 0.678048 CAAGCTAGCTTCCACCCCAC 60.678 60.000 27.08 0.00 33.42 4.61
778 3292 0.536724 AGCTGACACTGTCACACACA 59.463 50.000 7.84 0.00 37.67 3.72
779 3293 0.652592 GCTGACACTGTCACACACAC 59.347 55.000 7.84 0.00 37.67 3.82
780 3294 2.006552 GCTGACACTGTCACACACACA 61.007 52.381 7.84 0.00 37.67 3.72
781 3295 1.660607 CTGACACTGTCACACACACAC 59.339 52.381 7.84 0.00 37.67 3.82
782 3296 1.001406 TGACACTGTCACACACACACA 59.999 47.619 7.84 0.00 37.67 3.72
783 3297 1.393539 GACACTGTCACACACACACAC 59.606 52.381 4.17 0.00 32.09 3.82
784 3298 1.270571 ACACTGTCACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
785 3299 1.803555 CACTGTCACACACACACACAA 59.196 47.619 0.00 0.00 0.00 3.33
786 3300 2.225255 CACTGTCACACACACACACAAA 59.775 45.455 0.00 0.00 0.00 2.83
787 3301 2.225491 ACTGTCACACACACACACAAAC 59.775 45.455 0.00 0.00 0.00 2.93
788 3302 2.222027 TGTCACACACACACACAAACA 58.778 42.857 0.00 0.00 0.00 2.83
789 3303 2.031595 TGTCACACACACACACAAACAC 60.032 45.455 0.00 0.00 0.00 3.32
790 3304 2.031595 GTCACACACACACACAAACACA 60.032 45.455 0.00 0.00 0.00 3.72
791 3305 2.031595 TCACACACACACACAAACACAC 60.032 45.455 0.00 0.00 0.00 3.82
792 3306 1.950216 ACACACACACACAAACACACA 59.050 42.857 0.00 0.00 0.00 3.72
793 3307 2.359214 ACACACACACACAAACACACAA 59.641 40.909 0.00 0.00 0.00 3.33
794 3308 2.979151 CACACACACACAAACACACAAG 59.021 45.455 0.00 0.00 0.00 3.16
795 3309 1.984990 CACACACACAAACACACAAGC 59.015 47.619 0.00 0.00 0.00 4.01
796 3310 1.611006 ACACACACAAACACACAAGCA 59.389 42.857 0.00 0.00 0.00 3.91
797 3311 2.252747 CACACACAAACACACAAGCAG 58.747 47.619 0.00 0.00 0.00 4.24
957 3490 2.792222 TCCCCCGGGAATTCCTCT 59.208 61.111 26.32 0.00 42.05 3.69
1560 4093 1.135689 CGTGCAATTACTTCCACTGCC 60.136 52.381 0.00 0.00 31.92 4.85
1663 4202 8.601845 AATTTGATGATTTATGTGCCATCATG 57.398 30.769 0.00 0.00 43.10 3.07
1674 4213 2.812591 GTGCCATCATGATTAGCTCTGG 59.187 50.000 22.01 14.59 0.00 3.86
1675 4214 1.811359 GCCATCATGATTAGCTCTGGC 59.189 52.381 16.24 16.24 40.68 4.85
1709 4248 7.766738 TGGTTTCCCAGAAAATTAACTGAAAAC 59.233 33.333 19.49 19.49 35.17 2.43
1717 4256 9.617975 CAGAAAATTAACTGAAAACCATCTCTC 57.382 33.333 6.08 0.00 36.38 3.20
1833 4375 7.284489 TGCAGAGTGATTTTTGTTACCTTTAGT 59.716 33.333 0.00 0.00 0.00 2.24
1839 4381 9.394477 GTGATTTTTGTTACCTTTAGTCATGTC 57.606 33.333 0.00 0.00 0.00 3.06
1873 4415 5.464965 ACACTTTGTACTTTTGTCGTGAG 57.535 39.130 0.00 0.00 0.00 3.51
1905 4542 3.259876 ACAACGGGACAGCTCAATAGTTA 59.740 43.478 0.00 0.00 0.00 2.24
1934 4571 5.124936 AGGTGTTTGTGAACTTTTACTGGTC 59.875 40.000 0.00 0.00 36.70 4.02
1996 4636 7.615582 TCATGTTTCTGAAGGACATATGAAC 57.384 36.000 10.38 1.37 32.17 3.18
2031 4678 5.698832 TGTAGCAACCTCATTTGATTTTCG 58.301 37.500 0.00 0.00 0.00 3.46
2343 5047 9.676861 ATCAATTGATCACATTGAGAAAGACTA 57.323 29.630 24.44 9.97 37.67 2.59
2394 5098 7.240674 GAAAACAATTTCTGTGGTTTTTGACC 58.759 34.615 0.00 0.00 43.66 4.02
2475 5183 3.209410 GTCCAAATGGTCCTCTATGCTG 58.791 50.000 0.00 0.00 36.34 4.41
2741 5453 4.796038 AAAAACTCCATGCATTCTCTGG 57.204 40.909 0.00 0.00 0.00 3.86
2745 5457 2.093075 ACTCCATGCATTCTCTGGACTG 60.093 50.000 0.00 0.00 35.29 3.51
2974 5687 3.710722 CTCCTGCTGAACCCCGCT 61.711 66.667 0.00 0.00 0.00 5.52
3049 5762 2.224257 GCTGATCAAGATGAGGGAGGTC 60.224 54.545 0.00 0.00 0.00 3.85
3067 5780 3.432588 ACGAGGGAGAGCGACGTG 61.433 66.667 0.00 0.00 35.91 4.49
3100 5813 2.097825 GTGATCCTGCTGGAAATGCTT 58.902 47.619 17.04 0.00 46.80 3.91
3121 5834 2.187946 CAGAAGGAGGCGGCGAAT 59.812 61.111 12.98 0.00 0.00 3.34
3313 6026 2.572284 CCGTCCTTGAGACCGGAC 59.428 66.667 9.46 0.10 43.08 4.79
3489 6208 5.834460 TCATAGAGGGTTTGTACTACCAGA 58.166 41.667 16.31 4.95 37.40 3.86
3490 6209 6.258354 TCATAGAGGGTTTGTACTACCAGAA 58.742 40.000 16.31 3.29 37.40 3.02
3491 6210 4.886496 AGAGGGTTTGTACTACCAGAAC 57.114 45.455 16.31 7.08 37.40 3.01
3492 6211 4.490706 AGAGGGTTTGTACTACCAGAACT 58.509 43.478 16.31 6.89 37.40 3.01
3493 6212 4.283722 AGAGGGTTTGTACTACCAGAACTG 59.716 45.833 16.31 0.00 37.40 3.16
3533 6255 1.269102 CGGTCTGTATAGCTTCCGTGG 60.269 57.143 0.00 0.00 34.38 4.94
3664 6392 6.522625 AGATCACTATGTATGGATCCTTCG 57.477 41.667 14.23 0.00 37.46 3.79
3813 6563 1.084370 GCACTAAGCGGCGACATCTT 61.084 55.000 12.98 6.93 0.00 2.40
3814 6564 0.924090 CACTAAGCGGCGACATCTTC 59.076 55.000 12.98 0.00 0.00 2.87
3817 6567 1.590238 CTAAGCGGCGACATCTTCTTG 59.410 52.381 12.98 0.00 0.00 3.02
3818 6568 0.320771 AAGCGGCGACATCTTCTTGT 60.321 50.000 12.98 0.00 0.00 3.16
3819 6569 0.737715 AGCGGCGACATCTTCTTGTC 60.738 55.000 12.98 0.00 42.10 3.18
3828 6578 4.992688 GACATCTTCTTGTCGACATCTCT 58.007 43.478 20.80 0.00 36.93 3.10
3829 6579 5.398603 ACATCTTCTTGTCGACATCTCTT 57.601 39.130 20.80 0.23 0.00 2.85
3830 6580 5.788450 ACATCTTCTTGTCGACATCTCTTT 58.212 37.500 20.80 0.78 0.00 2.52
3831 6581 6.925211 ACATCTTCTTGTCGACATCTCTTTA 58.075 36.000 20.80 0.81 0.00 1.85
3832 6582 6.809196 ACATCTTCTTGTCGACATCTCTTTAC 59.191 38.462 20.80 0.00 0.00 2.01
3960 6710 2.022035 TGAATCTACCCTCCCATGTCCT 60.022 50.000 0.00 0.00 0.00 3.85
3961 6711 2.897823 ATCTACCCTCCCATGTCCTT 57.102 50.000 0.00 0.00 0.00 3.36
3986 6736 4.024387 CAGTGCTAAAACGTCTGGCTTTTA 60.024 41.667 7.34 0.00 0.00 1.52
4004 6756 1.823797 TAACCATTTACACCGGCACC 58.176 50.000 0.00 0.00 0.00 5.01
4006 6758 1.673009 CCATTTACACCGGCACCGT 60.673 57.895 0.00 0.00 37.81 4.83
4023 6775 2.132762 CCGTGGTCACAAGAACAGTAC 58.867 52.381 1.90 0.00 43.42 2.73
4029 6781 2.971915 GTCACAAGAACAGTACGACTCG 59.028 50.000 0.00 0.00 0.00 4.18
4032 6784 1.979469 CAAGAACAGTACGACTCGCTG 59.021 52.381 0.00 1.57 36.41 5.18
4093 6860 7.511714 AGGAGAGTAAAACCTAGAGTTGGTAAA 59.488 37.037 0.00 0.00 39.19 2.01
4295 7072 0.729478 CGCGTGATCCGTATAGCTGG 60.729 60.000 0.00 0.00 39.32 4.85
4296 7073 1.009389 GCGTGATCCGTATAGCTGGC 61.009 60.000 0.00 0.00 39.32 4.85
4297 7074 0.598562 CGTGATCCGTATAGCTGGCT 59.401 55.000 0.00 0.00 0.00 4.75
4298 7075 1.667177 CGTGATCCGTATAGCTGGCTG 60.667 57.143 5.25 0.00 0.00 4.85
4299 7076 0.969149 TGATCCGTATAGCTGGCTGG 59.031 55.000 5.25 0.00 0.00 4.85
4344 7121 2.247790 GCCACAGCGTTCACAGAAT 58.752 52.632 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 7.010460 TGTGATGAGCGTATCTTTGAAACTATG 59.990 37.037 5.13 0.00 0.00 2.23
40 42 7.041721 TGTGATGAGCGTATCTTTGAAACTAT 58.958 34.615 5.13 0.00 0.00 2.12
41 43 6.394809 TGTGATGAGCGTATCTTTGAAACTA 58.605 36.000 5.13 0.00 0.00 2.24
42 44 5.237815 TGTGATGAGCGTATCTTTGAAACT 58.762 37.500 5.13 0.00 0.00 2.66
43 45 5.530519 TGTGATGAGCGTATCTTTGAAAC 57.469 39.130 5.13 0.00 0.00 2.78
44 46 8.437360 AATATGTGATGAGCGTATCTTTGAAA 57.563 30.769 5.13 0.00 0.00 2.69
45 47 8.437360 AAATATGTGATGAGCGTATCTTTGAA 57.563 30.769 5.13 0.00 0.00 2.69
106 109 5.706916 CAAACCCTTCATATGCATGATAGC 58.293 41.667 10.16 0.00 40.85 2.97
110 113 3.634504 AGCAAACCCTTCATATGCATGA 58.365 40.909 10.16 0.00 39.47 3.07
125 128 2.552743 AGCTCGGAACCTTTTAGCAAAC 59.447 45.455 0.00 0.00 35.63 2.93
206 2400 5.809562 TGTTGAGGTTTTATTGTGCAAACAG 59.190 36.000 0.00 0.00 35.01 3.16
282 2484 3.600909 CGAAAGAGTGTCGAAAAACGTCC 60.601 47.826 0.00 0.00 41.02 4.79
301 2807 8.665643 TTTACAAGATGTTTTTAGAGTCCGAA 57.334 30.769 0.00 0.00 0.00 4.30
361 2870 8.862085 TGTAAAAAGAAAAATCGGTTAATCCCT 58.138 29.630 0.00 0.00 0.00 4.20
371 2880 7.329226 AGTGATGGCATGTAAAAAGAAAAATCG 59.671 33.333 3.81 0.00 0.00 3.34
374 2883 6.640499 CGAGTGATGGCATGTAAAAAGAAAAA 59.360 34.615 3.81 0.00 0.00 1.94
375 2884 6.148948 CGAGTGATGGCATGTAAAAAGAAAA 58.851 36.000 3.81 0.00 0.00 2.29
376 2885 5.240623 ACGAGTGATGGCATGTAAAAAGAAA 59.759 36.000 3.81 0.00 0.00 2.52
379 2888 4.154015 TGACGAGTGATGGCATGTAAAAAG 59.846 41.667 3.81 0.00 0.00 2.27
406 2915 8.537016 GGCCAGGTTTAAAATATTCTAAAGGTT 58.463 33.333 0.00 0.00 0.00 3.50
407 2916 7.147966 CGGCCAGGTTTAAAATATTCTAAAGGT 60.148 37.037 2.24 0.00 0.00 3.50
410 2919 6.097129 CCCGGCCAGGTTTAAAATATTCTAAA 59.903 38.462 2.24 0.00 38.74 1.85
433 2942 4.488790 CCATGTGATGGCTAGCCC 57.511 61.111 30.81 16.86 44.70 5.19
487 2996 5.370679 TGATTACCTCATGTCATGTGGATG 58.629 41.667 31.32 12.54 44.58 3.51
489 2998 5.045651 ACTTGATTACCTCATGTCATGTGGA 60.046 40.000 31.32 16.29 44.58 4.02
565 3076 3.576078 TGAATAGTGTGGGCAATAGGG 57.424 47.619 0.00 0.00 0.00 3.53
665 3179 3.006752 AGAGCGATGGATCCATTCTCTTC 59.993 47.826 33.12 23.90 40.39 2.87
666 3180 2.971330 AGAGCGATGGATCCATTCTCTT 59.029 45.455 33.12 24.16 40.39 2.85
667 3181 2.562298 GAGAGCGATGGATCCATTCTCT 59.438 50.000 35.95 35.95 43.01 3.10
668 3182 2.353605 GGAGAGCGATGGATCCATTCTC 60.354 54.545 30.74 30.74 37.22 2.87
669 3183 1.622811 GGAGAGCGATGGATCCATTCT 59.377 52.381 27.93 24.72 36.70 2.40
673 3187 0.829602 GAGGGAGAGCGATGGATCCA 60.830 60.000 18.88 18.88 33.24 3.41
708 3222 0.840288 TGGGGTGGAAGCTAGCTTGA 60.840 55.000 33.91 17.33 36.26 3.02
728 3242 6.008696 TGGTGGTATTCTTTGGGGTAATAG 57.991 41.667 0.00 0.00 0.00 1.73
778 3292 2.158559 TCTGCTTGTGTGTTTGTGTGT 58.841 42.857 0.00 0.00 0.00 3.72
779 3293 2.916716 GTTCTGCTTGTGTGTTTGTGTG 59.083 45.455 0.00 0.00 0.00 3.82
780 3294 2.556189 TGTTCTGCTTGTGTGTTTGTGT 59.444 40.909 0.00 0.00 0.00 3.72
781 3295 3.214697 TGTTCTGCTTGTGTGTTTGTG 57.785 42.857 0.00 0.00 0.00 3.33
782 3296 3.932545 TTGTTCTGCTTGTGTGTTTGT 57.067 38.095 0.00 0.00 0.00 2.83
783 3297 4.091800 CCTTTTGTTCTGCTTGTGTGTTTG 59.908 41.667 0.00 0.00 0.00 2.93
784 3298 4.244862 CCTTTTGTTCTGCTTGTGTGTTT 58.755 39.130 0.00 0.00 0.00 2.83
785 3299 3.368323 CCCTTTTGTTCTGCTTGTGTGTT 60.368 43.478 0.00 0.00 0.00 3.32
786 3300 2.166254 CCCTTTTGTTCTGCTTGTGTGT 59.834 45.455 0.00 0.00 0.00 3.72
787 3301 2.426738 TCCCTTTTGTTCTGCTTGTGTG 59.573 45.455 0.00 0.00 0.00 3.82
788 3302 2.689983 CTCCCTTTTGTTCTGCTTGTGT 59.310 45.455 0.00 0.00 0.00 3.72
789 3303 2.544486 GCTCCCTTTTGTTCTGCTTGTG 60.544 50.000 0.00 0.00 0.00 3.33
790 3304 1.683385 GCTCCCTTTTGTTCTGCTTGT 59.317 47.619 0.00 0.00 0.00 3.16
791 3305 1.682854 TGCTCCCTTTTGTTCTGCTTG 59.317 47.619 0.00 0.00 0.00 4.01
792 3306 1.959282 CTGCTCCCTTTTGTTCTGCTT 59.041 47.619 0.00 0.00 0.00 3.91
793 3307 1.613836 CTGCTCCCTTTTGTTCTGCT 58.386 50.000 0.00 0.00 0.00 4.24
794 3308 0.038801 GCTGCTCCCTTTTGTTCTGC 60.039 55.000 0.00 0.00 0.00 4.26
795 3309 0.600057 GGCTGCTCCCTTTTGTTCTG 59.400 55.000 0.00 0.00 0.00 3.02
796 3310 0.185901 TGGCTGCTCCCTTTTGTTCT 59.814 50.000 0.00 0.00 0.00 3.01
797 3311 0.600057 CTGGCTGCTCCCTTTTGTTC 59.400 55.000 0.00 0.00 0.00 3.18
818 3332 1.682854 GGTGGAGATCTCTCTCTGCTG 59.317 57.143 21.81 0.00 46.11 4.41
819 3333 1.750332 CGGTGGAGATCTCTCTCTGCT 60.750 57.143 21.81 0.00 46.11 4.24
820 3334 0.667993 CGGTGGAGATCTCTCTCTGC 59.332 60.000 21.81 5.15 46.11 4.26
957 3490 3.089874 CTCCGGGGAGCAATGGGA 61.090 66.667 0.00 0.00 35.31 4.37
1560 4093 5.682212 AAGGTAAACTTGGCTTGAAAGCAAG 60.682 40.000 16.39 17.27 44.97 4.01
1709 4248 7.493743 AATCGATCAAATCAAAGAGAGATGG 57.506 36.000 0.00 0.00 0.00 3.51
1717 4256 8.340443 TGAGCAGAATAATCGATCAAATCAAAG 58.660 33.333 0.00 0.00 0.00 2.77
1833 4375 3.829026 AGTGTAGCAGTGAAGAGACATGA 59.171 43.478 0.00 0.00 0.00 3.07
1839 4381 5.533482 AGTACAAAGTGTAGCAGTGAAGAG 58.467 41.667 0.00 0.00 32.84 2.85
1873 4415 3.582780 CTGTCCCGTTGTCTAGTAAACC 58.417 50.000 0.00 0.00 0.00 3.27
1905 4542 9.581099 CAGTAAAAGTTCACAAACACCTTTATT 57.419 29.630 0.00 0.00 37.88 1.40
1934 4571 1.966451 GTCCCAGCCAACAACTCCG 60.966 63.158 0.00 0.00 0.00 4.63
1996 4636 1.812571 GTTGCTACAGGTGACCCAATG 59.187 52.381 0.00 0.00 0.00 2.82
2031 4678 3.627577 ACTGAACAACACAGATCAACACC 59.372 43.478 0.00 0.00 38.55 4.16
2394 5098 8.594687 CACCTCAAAAGTTATTGACAACAAAAG 58.405 33.333 0.00 0.00 39.54 2.27
2433 5141 4.285863 ACATGTCCTTTTCAAACCCTCAA 58.714 39.130 0.00 0.00 0.00 3.02
2475 5183 5.216566 TGCAATCGTACAAGAAATGTAGC 57.783 39.130 0.00 0.00 45.00 3.58
2622 5333 5.749462 AGTGGGAAAATCTCATGGTAAGAG 58.251 41.667 0.00 0.00 34.42 2.85
2741 5453 2.457366 ACGGGAAATGTCAGACAGTC 57.543 50.000 9.64 8.73 0.00 3.51
2745 5457 7.940178 AAAATTTAAACGGGAAATGTCAGAC 57.060 32.000 0.00 0.00 0.00 3.51
3049 5762 3.432588 ACGTCGCTCTCCCTCGTG 61.433 66.667 0.00 0.00 33.55 4.35
3067 5780 1.527370 GATCACCCCCAGGCTGTAC 59.473 63.158 14.43 0.00 36.11 2.90
3100 5813 4.087892 GCCGCCTCCTTCTGAGCA 62.088 66.667 0.00 0.00 39.98 4.26
3235 5948 1.267574 TGAGCTTCGCCTCATTCCCT 61.268 55.000 0.00 0.00 36.96 4.20
3313 6026 2.480416 CCTCTTCAGGATCCGTTTCGAG 60.480 54.545 5.98 9.67 43.65 4.04
3416 6129 5.730296 ATACTAATACTACCCTGCTGCTG 57.270 43.478 0.00 0.00 0.00 4.41
3417 6130 6.749036 AAATACTAATACTACCCTGCTGCT 57.251 37.500 0.00 0.00 0.00 4.24
3489 6208 1.366435 ACCCCCTATCACTCTCCAGTT 59.634 52.381 0.00 0.00 0.00 3.16
3490 6209 1.019650 ACCCCCTATCACTCTCCAGT 58.980 55.000 0.00 0.00 0.00 4.00
3491 6210 2.182516 AACCCCCTATCACTCTCCAG 57.817 55.000 0.00 0.00 0.00 3.86
3492 6211 2.359994 GGTAACCCCCTATCACTCTCCA 60.360 54.545 0.00 0.00 0.00 3.86
3493 6212 2.327373 GGTAACCCCCTATCACTCTCC 58.673 57.143 0.00 0.00 0.00 3.71
3646 6374 6.732896 AAAGACGAAGGATCCATACATAGT 57.267 37.500 15.82 3.68 0.00 2.12
3664 6392 1.947456 ACCTCCGCAAGTTCAAAAGAC 59.053 47.619 0.00 0.00 0.00 3.01
3813 6563 5.707242 ACAGTAAAGAGATGTCGACAAGA 57.293 39.130 24.13 0.00 0.00 3.02
3814 6564 5.119279 CCAACAGTAAAGAGATGTCGACAAG 59.881 44.000 24.13 5.09 0.00 3.16
3817 6567 4.806330 TCCAACAGTAAAGAGATGTCGAC 58.194 43.478 9.11 9.11 0.00 4.20
3818 6568 5.661056 ATCCAACAGTAAAGAGATGTCGA 57.339 39.130 0.00 0.00 0.00 4.20
3819 6569 5.446473 GCAATCCAACAGTAAAGAGATGTCG 60.446 44.000 0.00 0.00 0.00 4.35
3821 6571 4.702131 GGCAATCCAACAGTAAAGAGATGT 59.298 41.667 0.00 0.00 0.00 3.06
3822 6572 4.201851 CGGCAATCCAACAGTAAAGAGATG 60.202 45.833 0.00 0.00 0.00 2.90
3823 6573 3.941483 CGGCAATCCAACAGTAAAGAGAT 59.059 43.478 0.00 0.00 0.00 2.75
3824 6574 3.334691 CGGCAATCCAACAGTAAAGAGA 58.665 45.455 0.00 0.00 0.00 3.10
3825 6575 2.420022 CCGGCAATCCAACAGTAAAGAG 59.580 50.000 0.00 0.00 0.00 2.85
3826 6576 2.432444 CCGGCAATCCAACAGTAAAGA 58.568 47.619 0.00 0.00 0.00 2.52
3827 6577 1.135402 GCCGGCAATCCAACAGTAAAG 60.135 52.381 24.80 0.00 0.00 1.85
3828 6578 0.885196 GCCGGCAATCCAACAGTAAA 59.115 50.000 24.80 0.00 0.00 2.01
3829 6579 0.963355 GGCCGGCAATCCAACAGTAA 60.963 55.000 30.85 0.00 0.00 2.24
3830 6580 1.377987 GGCCGGCAATCCAACAGTA 60.378 57.895 30.85 0.00 0.00 2.74
3831 6581 2.676471 GGCCGGCAATCCAACAGT 60.676 61.111 30.85 0.00 0.00 3.55
3832 6582 2.361610 AGGCCGGCAATCCAACAG 60.362 61.111 30.85 0.00 0.00 3.16
3868 6618 1.512230 CATGCATGTTTGGGTCCGG 59.488 57.895 18.91 0.00 0.00 5.14
3960 6710 2.289547 GCCAGACGTTTTAGCACTGAAA 59.710 45.455 0.00 0.00 0.00 2.69
3961 6711 1.871039 GCCAGACGTTTTAGCACTGAA 59.129 47.619 0.00 0.00 0.00 3.02
3986 6736 1.238625 CGGTGCCGGTGTAAATGGTT 61.239 55.000 1.90 0.00 35.56 3.67
4004 6756 1.784856 CGTACTGTTCTTGTGACCACG 59.215 52.381 0.00 0.00 0.00 4.94
4006 6758 2.691526 AGTCGTACTGTTCTTGTGACCA 59.308 45.455 0.00 0.00 0.00 4.02
4023 6775 0.319555 TTTTCAGACCCAGCGAGTCG 60.320 55.000 8.54 8.54 39.31 4.18
4029 6781 1.166531 ACTGCGTTTTCAGACCCAGC 61.167 55.000 0.00 0.00 37.51 4.85
4032 6784 2.459934 CAAAACTGCGTTTTCAGACCC 58.540 47.619 13.84 0.00 42.78 4.46
4093 6860 8.980610 GTAGCCGGTGTTAAAACAAATAAAAAT 58.019 29.630 1.90 0.00 41.21 1.82
4098 6865 5.996513 TCTGTAGCCGGTGTTAAAACAAATA 59.003 36.000 1.90 0.00 41.21 1.40
4137 6904 0.890683 CACTGAACCCAGATTTGGCC 59.109 55.000 0.00 0.00 43.58 5.36
4212 6979 2.171237 TCAGATGGTGATGGATGACCAC 59.829 50.000 0.00 0.00 46.64 4.16
4295 7072 1.668751 TCGCGGAATTGTTTATCCAGC 59.331 47.619 6.13 0.00 35.34 4.85
4296 7073 3.809832 AGATCGCGGAATTGTTTATCCAG 59.190 43.478 6.13 0.00 35.34 3.86
4297 7074 3.804036 AGATCGCGGAATTGTTTATCCA 58.196 40.909 6.13 0.00 35.34 3.41
4298 7075 4.272504 TCAAGATCGCGGAATTGTTTATCC 59.727 41.667 6.13 0.00 0.00 2.59
4299 7076 5.006746 AGTCAAGATCGCGGAATTGTTTATC 59.993 40.000 6.13 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.