Multiple sequence alignment - TraesCS4A01G083200

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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 TraesCS4A01G083200 chr4A 100.000 3482 0 0 1 3482 86989133 86992614 0.000000e+00 6431.0
1 TraesCS4A01G083200 chr4D 91.552 3113 133 52 1 3046 378451695 378448646 0.000000e+00 4172.0
2 TraesCS4A01G083200 chr4D 95.692 441 15 3 3040 3480 378448622 378448186 0.000000e+00 706.0
3 TraesCS4A01G083200 chr4B 92.641 2514 91 39 998 3473 464955152 464952695 0.000000e+00 3531.0
4 TraesCS4A01G083200 chr4B 85.132 760 55 21 271 999 464955925 464955193 0.000000e+00 725.0
5 TraesCS4A01G083200 chr4B 87.701 187 10 5 1 186 464958016 464957842 4.560000e-49 206.0
6 TraesCS4A01G083200 chr3B 75.333 300 54 18 1663 1954 813200788 813200501 3.650000e-25 126.0
7 TraesCS4A01G083200 chr7B 86.207 116 12 4 1820 1933 17356909 17356796 4.720000e-24 122.0
8 TraesCS4A01G083200 chr5D 86.207 116 12 4 1820 1933 321998766 321998879 4.720000e-24 122.0
9 TraesCS4A01G083200 chr5D 80.000 125 23 2 2296 2419 487598567 487598444 1.330000e-14 91.6
10 TraesCS4A01G083200 chr2B 75.627 279 48 17 1663 1933 723045883 723046149 1.700000e-23 121.0
11 TraesCS4A01G083200 chr7A 85.841 113 12 4 1820 1930 17262676 17262786 2.200000e-22 117.0
12 TraesCS4A01G083200 chr5B 72.934 351 69 25 1070 1410 600338384 600338050 7.950000e-17 99.0
13 TraesCS4A01G083200 chr5B 81.034 116 20 2 2296 2410 600133843 600133729 1.330000e-14 91.6
14 TraesCS4A01G083200 chr5A 79.200 125 24 2 2296 2419 608360440 608360317 6.190000e-13 86.1


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 TraesCS4A01G083200 chr4A 86989133 86992614 3481 False 6431.000000 6431 100.000000 1 3482 1 chr4A.!!$F1 3481
1 TraesCS4A01G083200 chr4D 378448186 378451695 3509 True 2439.000000 4172 93.622000 1 3480 2 chr4D.!!$R1 3479
2 TraesCS4A01G083200 chr4B 464952695 464958016 5321 True 1487.333333 3531 88.491333 1 3473 3 chr4B.!!$R1 3472

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
702 2557 0.108804 TTCTCGCCTCCGTTAGCTTG 60.109 55.0 0.0 0.0 35.54 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 4593 0.378257 CGCGGATGTTCCTTCCAATG 59.622 55.0 0.0 0.0 33.3 2.82 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
117 118 3.143728 AGGGAAAAGAAATGCGTACGTT 58.856 40.909 17.90 2.87 0.00 3.99
121 122 5.077424 GGAAAAGAAATGCGTACGTTGTAG 58.923 41.667 17.90 0.00 0.00 2.74
122 123 5.107375 GGAAAAGAAATGCGTACGTTGTAGA 60.107 40.000 17.90 0.00 0.00 2.59
123 124 6.401796 GGAAAAGAAATGCGTACGTTGTAGAT 60.402 38.462 17.90 0.00 0.00 1.98
187 188 4.767255 CTGCGCCCCTGTCTGGTC 62.767 72.222 4.18 0.00 0.00 4.02
193 194 4.803426 CCCTGTCTGGTCGCGCTC 62.803 72.222 5.56 0.00 0.00 5.03
194 195 4.803426 CCTGTCTGGTCGCGCTCC 62.803 72.222 5.56 8.79 0.00 4.70
195 196 4.056125 CTGTCTGGTCGCGCTCCA 62.056 66.667 18.62 18.62 0.00 3.86
215 2035 2.359850 TCCACTCCCGTTGCATGC 60.360 61.111 11.82 11.82 0.00 4.06
240 2060 2.808206 GCCATGGACCGGGTCTAGG 61.808 68.421 25.39 21.18 32.47 3.02
241 2061 2.808206 CCATGGACCGGGTCTAGGC 61.808 68.421 25.39 10.34 32.47 3.93
242 2062 2.838225 ATGGACCGGGTCTAGGCG 60.838 66.667 25.39 0.00 32.47 5.52
243 2063 3.369410 ATGGACCGGGTCTAGGCGA 62.369 63.158 25.39 0.00 32.47 5.54
244 2064 3.525545 GGACCGGGTCTAGGCGAC 61.526 72.222 25.39 4.44 42.07 5.19
252 2072 2.045131 GTCTAGGCGACCACGTCCT 61.045 63.158 0.00 0.00 45.89 3.85
253 2073 2.044555 TCTAGGCGACCACGTCCTG 61.045 63.158 3.10 0.00 45.89 3.86
254 2074 2.034532 TAGGCGACCACGTCCTGA 59.965 61.111 3.10 0.00 45.89 3.86
287 2123 1.537202 GCCCCGCAATCATGATTAGTC 59.463 52.381 20.32 11.47 0.00 2.59
401 2255 8.361139 GCTGCTTAATTAATGAGTAGGACTAGA 58.639 37.037 14.65 0.00 0.00 2.43
422 2276 1.469308 AGCAGTAGCACGTCTGTACTC 59.531 52.381 4.18 0.00 45.49 2.59
538 2392 1.077212 AGCCAGCATCGCCAATCTT 60.077 52.632 0.00 0.00 0.00 2.40
560 2414 4.776322 TGGAATGGACGGCGCAGG 62.776 66.667 13.26 4.07 0.00 4.85
643 2498 2.125269 ATCGGTTACGGTGCAGCC 60.125 61.111 10.90 2.64 41.39 4.85
674 2529 0.168568 GAGACAAGACGACGACCTCC 59.831 60.000 0.00 0.00 0.00 4.30
702 2557 0.108804 TTCTCGCCTCCGTTAGCTTG 60.109 55.000 0.00 0.00 35.54 4.01
705 2560 1.810030 CGCCTCCGTTAGCTTGGTC 60.810 63.158 0.00 0.00 0.00 4.02
707 2562 0.460459 GCCTCCGTTAGCTTGGTCTC 60.460 60.000 0.00 0.00 0.00 3.36
708 2563 1.187087 CCTCCGTTAGCTTGGTCTCT 58.813 55.000 0.00 0.00 0.00 3.10
710 2565 2.096248 CTCCGTTAGCTTGGTCTCTCT 58.904 52.381 0.00 0.00 0.00 3.10
711 2566 2.093106 TCCGTTAGCTTGGTCTCTCTC 58.907 52.381 0.00 0.00 0.00 3.20
732 2587 1.874872 GGCTCTCTCTATAACTCGCGT 59.125 52.381 5.77 0.00 0.00 6.01
733 2588 2.350007 GGCTCTCTCTATAACTCGCGTG 60.350 54.545 5.77 6.24 0.00 5.34
800 2655 0.603065 AAGAATCAAAAGGCGCCACC 59.397 50.000 31.54 0.33 39.61 4.61
801 2656 0.539438 AGAATCAAAAGGCGCCACCA 60.539 50.000 31.54 7.71 43.14 4.17
852 2707 0.456995 GGCGACACCGAAAGAGAGAG 60.457 60.000 0.00 0.00 38.22 3.20
853 2708 0.522180 GCGACACCGAAAGAGAGAGA 59.478 55.000 0.00 0.00 38.22 3.10
854 2709 1.466697 GCGACACCGAAAGAGAGAGAG 60.467 57.143 0.00 0.00 38.22 3.20
855 2710 2.077627 CGACACCGAAAGAGAGAGAGA 58.922 52.381 0.00 0.00 38.22 3.10
856 2711 2.095213 CGACACCGAAAGAGAGAGAGAG 59.905 54.545 0.00 0.00 38.22 3.20
857 2712 3.340034 GACACCGAAAGAGAGAGAGAGA 58.660 50.000 0.00 0.00 0.00 3.10
858 2713 3.343617 ACACCGAAAGAGAGAGAGAGAG 58.656 50.000 0.00 0.00 0.00 3.20
859 2714 3.008594 ACACCGAAAGAGAGAGAGAGAGA 59.991 47.826 0.00 0.00 0.00 3.10
860 2715 3.623060 CACCGAAAGAGAGAGAGAGAGAG 59.377 52.174 0.00 0.00 0.00 3.20
861 2716 3.517901 ACCGAAAGAGAGAGAGAGAGAGA 59.482 47.826 0.00 0.00 0.00 3.10
862 2717 4.122776 CCGAAAGAGAGAGAGAGAGAGAG 58.877 52.174 0.00 0.00 0.00 3.20
863 2718 4.141937 CCGAAAGAGAGAGAGAGAGAGAGA 60.142 50.000 0.00 0.00 0.00 3.10
864 2719 5.046529 CGAAAGAGAGAGAGAGAGAGAGAG 58.953 50.000 0.00 0.00 0.00 3.20
865 2720 5.163509 CGAAAGAGAGAGAGAGAGAGAGAGA 60.164 48.000 0.00 0.00 0.00 3.10
866 2721 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
867 2722 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
868 2723 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
869 2724 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
891 2746 3.935828 AGCGAGAGACAAGAATTAAAGCC 59.064 43.478 0.00 0.00 0.00 4.35
1128 3041 0.896226 AGTTCCTCTTCGGCTACACC 59.104 55.000 0.00 0.00 0.00 4.16
1416 3329 2.964389 GCCGCGATGCTCTTCTCC 60.964 66.667 8.23 0.00 0.00 3.71
1419 3332 2.226896 CGCGATGCTCTTCTCCACG 61.227 63.158 0.00 0.00 0.00 4.94
1467 3380 4.021925 GAGGACACCTGGCGCCTT 62.022 66.667 29.70 9.20 31.76 4.35
1655 3568 3.229293 TCATCTCCTGCTATGACCTCAG 58.771 50.000 0.00 0.00 0.00 3.35
2133 4046 0.815734 GCATTCAGGTGAGCAAGCAT 59.184 50.000 0.00 0.00 0.00 3.79
2134 4047 2.019249 GCATTCAGGTGAGCAAGCATA 58.981 47.619 0.00 0.00 0.00 3.14
2464 4383 3.777925 CCGTCGCGTTCAAGCAGG 61.778 66.667 5.77 0.00 36.85 4.85
2559 4478 0.614979 TGTAGGCCTCTCCTCGCTTT 60.615 55.000 9.68 0.00 43.20 3.51
2570 4496 0.320421 CCTCGCTTTCTTTGGACGGA 60.320 55.000 0.00 0.00 0.00 4.69
2571 4497 1.508632 CTCGCTTTCTTTGGACGGAA 58.491 50.000 0.00 0.00 0.00 4.30
2601 4527 1.599419 GCACTTTTTACGTGGCAGTGG 60.599 52.381 16.16 0.00 36.22 4.00
2652 4578 3.181447 TGAAGCATTTGCCATTGGGAAAA 60.181 39.130 23.79 9.73 45.43 2.29
2658 4584 4.342862 TTTGCCATTGGGAAAATTCGAA 57.657 36.364 18.79 0.00 39.93 3.71
2662 4588 3.848726 CCATTGGGAAAATTCGAAGGTG 58.151 45.455 3.35 0.00 35.59 4.00
2666 4592 5.599999 TTGGGAAAATTCGAAGGTGAAAA 57.400 34.783 3.35 0.00 0.00 2.29
2667 4593 4.939271 TGGGAAAATTCGAAGGTGAAAAC 58.061 39.130 3.35 0.00 0.00 2.43
2718 4645 5.814705 CCAGATTCTTAGCTTCATTTCGACT 59.185 40.000 0.00 0.00 0.00 4.18
2719 4646 6.314896 CCAGATTCTTAGCTTCATTTCGACTT 59.685 38.462 0.00 0.00 0.00 3.01
2720 4647 7.492669 CCAGATTCTTAGCTTCATTTCGACTTA 59.507 37.037 0.00 0.00 0.00 2.24
2771 4699 0.550914 AGAATTATGCCCCGGCTGAA 59.449 50.000 7.35 1.43 42.51 3.02
2794 4722 1.268032 GGGCGTTTGAGTTGCGATATG 60.268 52.381 0.00 0.00 0.00 1.78
2830 4758 2.176273 GGATACAGCTGCTGCGGTG 61.176 63.158 28.39 15.71 46.39 4.94
2866 4794 5.181433 GGCCTCCTCCGAACATAAATAAATC 59.819 44.000 0.00 0.00 0.00 2.17
2878 4806 9.396022 GAACATAAATAAATCCTCCAGAGTTCA 57.604 33.333 0.00 0.00 34.02 3.18
2884 4812 9.844257 AAATAAATCCTCCAGAGTTCATCTAAG 57.156 33.333 0.00 0.00 36.10 2.18
2886 4814 3.034635 TCCTCCAGAGTTCATCTAAGCC 58.965 50.000 0.00 0.00 36.10 4.35
2904 4832 0.171903 CCAGCCCTGCGAATTTTCAG 59.828 55.000 0.00 2.05 0.00 3.02
2912 4847 4.226761 CCTGCGAATTTTCAGTACCAAAC 58.773 43.478 0.00 0.00 0.00 2.93
2936 4871 5.277202 CGATATTTGTCAGCTGGATGAAGTG 60.277 44.000 15.13 0.00 0.00 3.16
2947 4882 4.616835 GCTGGATGAAGTGTGTTCCATTTC 60.617 45.833 0.00 0.00 39.53 2.17
2961 4896 5.918011 TGTTCCATTTCAACGCTCATTTTAC 59.082 36.000 0.00 0.00 0.00 2.01
2962 4897 5.697473 TCCATTTCAACGCTCATTTTACA 57.303 34.783 0.00 0.00 0.00 2.41
2963 4898 6.078202 TCCATTTCAACGCTCATTTTACAA 57.922 33.333 0.00 0.00 0.00 2.41
2965 4900 6.806249 TCCATTTCAACGCTCATTTTACAATC 59.194 34.615 0.00 0.00 0.00 2.67
2966 4901 6.585702 CCATTTCAACGCTCATTTTACAATCA 59.414 34.615 0.00 0.00 0.00 2.57
2973 4926 7.858052 ACGCTCATTTTACAATCAGAAAAAG 57.142 32.000 0.00 0.00 0.00 2.27
2991 4944 7.550712 AGAAAAAGACTTCTGTTTTCTGCATT 58.449 30.769 18.34 5.10 45.35 3.56
2997 4950 2.151202 TCTGTTTTCTGCATTCCGTCC 58.849 47.619 0.00 0.00 0.00 4.79
3040 4993 1.076332 GTCCACGTCTTAAAGCGCAT 58.924 50.000 11.47 0.00 0.00 4.73
3042 4995 0.796312 CCACGTCTTAAAGCGCATGT 59.204 50.000 11.47 0.00 0.00 3.21
3060 5043 4.142816 GCATGTAGTGTAGTGGCTTTTCTG 60.143 45.833 0.00 0.00 0.00 3.02
3150 5133 5.107143 CCTTTCTTGAAGAAGCGAAAGAGAG 60.107 44.000 7.76 0.00 42.92 3.20
3164 5147 4.279671 CGAAAGAGAGCCCTGTAGATGTAT 59.720 45.833 0.00 0.00 0.00 2.29
3165 5148 5.537188 GAAAGAGAGCCCTGTAGATGTATG 58.463 45.833 0.00 0.00 0.00 2.39
3250 5233 4.003648 CCTCCAAGCGAACTAAATCAAGT 58.996 43.478 0.00 0.00 0.00 3.16
3336 5319 4.737649 GCTGCAAACAGTTCTAGCCTTTTT 60.738 41.667 0.00 0.00 46.30 1.94
3345 5328 0.748367 CTAGCCTTTTTCCTCCCGGC 60.748 60.000 0.00 0.00 40.99 6.13
3363 5346 3.250744 CGGCCACTGATAACCGTATATG 58.749 50.000 2.24 0.00 40.77 1.78
3369 5352 4.031765 CACTGATAACCGTATATGCGCATC 59.968 45.833 29.11 12.14 0.00 3.91
3373 5356 2.455674 ACCGTATATGCGCATCATGT 57.544 45.000 29.11 14.96 36.63 3.21
3416 5399 0.319555 GCTCCCCCGCAAAAGAAAAC 60.320 55.000 0.00 0.00 0.00 2.43
3417 5400 0.317160 CTCCCCCGCAAAAGAAAACC 59.683 55.000 0.00 0.00 0.00 3.27
3421 5404 1.118965 CCCGCAAAAGAAAACCCCCT 61.119 55.000 0.00 0.00 0.00 4.79
3422 5405 0.033366 CCGCAAAAGAAAACCCCCTG 59.967 55.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.427592 GCAGCAGCAGCAGTACTAGC 61.428 60.000 4.63 1.88 45.49 3.42
69 70 5.866092 CCCTTTTAATTTCTTTGCTGAGAGC 59.134 40.000 0.00 0.00 42.82 4.09
70 71 7.219484 TCCCTTTTAATTTCTTTGCTGAGAG 57.781 36.000 0.00 0.00 0.00 3.20
117 118 0.459899 CAGGCAGCGGTACATCTACA 59.540 55.000 0.00 0.00 0.00 2.74
187 188 4.803426 GAGTGGAGGTGGAGCGCG 62.803 72.222 0.00 0.00 0.00 6.86
188 189 4.459089 GGAGTGGAGGTGGAGCGC 62.459 72.222 0.00 0.00 0.00 5.92
189 190 3.775654 GGGAGTGGAGGTGGAGCG 61.776 72.222 0.00 0.00 0.00 5.03
190 191 3.775654 CGGGAGTGGAGGTGGAGC 61.776 72.222 0.00 0.00 0.00 4.70
191 192 1.913762 AACGGGAGTGGAGGTGGAG 60.914 63.158 0.00 0.00 46.69 3.86
192 193 2.203182 AACGGGAGTGGAGGTGGA 59.797 61.111 0.00 0.00 46.69 4.02
193 194 2.347490 CAACGGGAGTGGAGGTGG 59.653 66.667 0.00 0.00 46.69 4.61
194 195 2.358737 GCAACGGGAGTGGAGGTG 60.359 66.667 0.00 0.00 46.69 4.00
195 196 2.224159 ATGCAACGGGAGTGGAGGT 61.224 57.895 0.00 0.00 46.69 3.85
241 2061 4.778415 CGCCTCAGGACGTGGTCG 62.778 72.222 0.00 0.00 43.34 4.79
242 2062 1.870055 TAACGCCTCAGGACGTGGTC 61.870 60.000 13.03 0.00 42.68 4.02
243 2063 1.466025 TTAACGCCTCAGGACGTGGT 61.466 55.000 13.03 2.74 42.68 4.16
244 2064 1.012486 GTTAACGCCTCAGGACGTGG 61.012 60.000 13.03 0.00 42.68 4.94
245 2065 1.012486 GGTTAACGCCTCAGGACGTG 61.012 60.000 13.03 0.00 42.68 4.49
246 2066 1.291272 GGTTAACGCCTCAGGACGT 59.709 57.895 7.29 7.29 46.07 4.34
247 2067 1.447314 GGGTTAACGCCTCAGGACG 60.447 63.158 11.44 0.00 0.00 4.79
249 2069 1.980052 CTGGGTTAACGCCTCAGGA 59.020 57.895 18.87 0.00 0.00 3.86
250 2070 1.745489 GCTGGGTTAACGCCTCAGG 60.745 63.158 18.87 0.00 31.69 3.86
252 2072 2.349755 GGCTGGGTTAACGCCTCA 59.650 61.111 18.87 5.08 40.62 3.86
253 2073 2.437895 GGGCTGGGTTAACGCCTC 60.438 66.667 18.87 10.62 43.29 4.70
254 2074 4.043100 GGGGCTGGGTTAACGCCT 62.043 66.667 18.87 0.00 43.29 5.52
257 2077 4.708386 TGCGGGGCTGGGTTAACG 62.708 66.667 0.00 0.00 0.00 3.18
287 2123 3.774599 GAGGGCAGCGTAATGGGGG 62.775 68.421 0.00 0.00 0.00 5.40
334 2172 4.021016 AGCGAAGGAGGAAGCGATTATATT 60.021 41.667 0.00 0.00 34.34 1.28
336 2174 2.891580 AGCGAAGGAGGAAGCGATTATA 59.108 45.455 0.00 0.00 34.34 0.98
337 2175 1.689273 AGCGAAGGAGGAAGCGATTAT 59.311 47.619 0.00 0.00 34.34 1.28
343 2193 1.200252 GGAAAAAGCGAAGGAGGAAGC 59.800 52.381 0.00 0.00 0.00 3.86
344 2194 1.464997 CGGAAAAAGCGAAGGAGGAAG 59.535 52.381 0.00 0.00 0.00 3.46
401 2255 1.887198 AGTACAGACGTGCTACTGCTT 59.113 47.619 0.00 0.00 36.17 3.91
422 2276 6.074034 GGGTTGAATAAACAAACGGACAAATG 60.074 38.462 0.00 0.00 40.86 2.32
524 2378 0.254178 ACCTCAAGATTGGCGATGCT 59.746 50.000 0.00 0.00 0.00 3.79
526 2380 1.019673 CCACCTCAAGATTGGCGATG 58.980 55.000 0.00 0.00 0.00 3.84
538 2392 2.668632 GCCGTCCATTCCACCTCA 59.331 61.111 0.00 0.00 0.00 3.86
620 2474 1.356527 GCACCGTAACCGATGGACAC 61.357 60.000 0.00 0.00 37.69 3.67
643 2498 2.094957 GTCTTGTCTCTCTTCACCCTCG 60.095 54.545 0.00 0.00 0.00 4.63
674 2529 3.132481 GAGGCGAGAAGAGGAGGCG 62.132 68.421 0.00 0.00 0.00 5.52
702 2557 0.180406 AGAGAGAGCCGAGAGAGACC 59.820 60.000 0.00 0.00 0.00 3.85
705 2560 4.894784 AGTTATAGAGAGAGCCGAGAGAG 58.105 47.826 0.00 0.00 0.00 3.20
707 2562 3.678072 CGAGTTATAGAGAGAGCCGAGAG 59.322 52.174 0.00 0.00 0.00 3.20
708 2563 3.655486 CGAGTTATAGAGAGAGCCGAGA 58.345 50.000 0.00 0.00 0.00 4.04
710 2565 2.144730 GCGAGTTATAGAGAGAGCCGA 58.855 52.381 0.00 0.00 0.00 5.54
711 2566 1.136197 CGCGAGTTATAGAGAGAGCCG 60.136 57.143 0.00 0.00 0.00 5.52
733 2588 0.038890 AGGAGCCCAAAGAGAAAGGC 59.961 55.000 0.00 0.00 46.13 4.35
842 2697 6.097554 TCTCTCTCTCTCTCTCTCTCTCTTTC 59.902 46.154 0.00 0.00 0.00 2.62
852 2707 2.362397 TCGCTCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
853 2708 2.363680 CTCGCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
854 2709 2.362397 TCTCGCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
855 2710 2.363680 CTCTCGCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
856 2711 2.362397 TCTCTCGCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
857 2712 2.101582 GTCTCTCGCTCTCTCTCTCTCT 59.898 54.545 0.00 0.00 0.00 3.10
858 2713 2.159099 TGTCTCTCGCTCTCTCTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
859 2714 1.831106 TGTCTCTCGCTCTCTCTCTCT 59.169 52.381 0.00 0.00 0.00 3.10
860 2715 2.309528 TGTCTCTCGCTCTCTCTCTC 57.690 55.000 0.00 0.00 0.00 3.20
861 2716 2.236146 TCTTGTCTCTCGCTCTCTCTCT 59.764 50.000 0.00 0.00 0.00 3.10
862 2717 2.627945 TCTTGTCTCTCGCTCTCTCTC 58.372 52.381 0.00 0.00 0.00 3.20
863 2718 2.779755 TCTTGTCTCTCGCTCTCTCT 57.220 50.000 0.00 0.00 0.00 3.10
864 2719 4.370364 AATTCTTGTCTCTCGCTCTCTC 57.630 45.455 0.00 0.00 0.00 3.20
865 2720 5.906113 TTAATTCTTGTCTCTCGCTCTCT 57.094 39.130 0.00 0.00 0.00 3.10
866 2721 5.005299 GCTTTAATTCTTGTCTCTCGCTCTC 59.995 44.000 0.00 0.00 0.00 3.20
867 2722 4.867608 GCTTTAATTCTTGTCTCTCGCTCT 59.132 41.667 0.00 0.00 0.00 4.09
868 2723 4.033472 GGCTTTAATTCTTGTCTCTCGCTC 59.967 45.833 0.00 0.00 0.00 5.03
869 2724 3.935828 GGCTTTAATTCTTGTCTCTCGCT 59.064 43.478 0.00 0.00 0.00 4.93
983 2854 1.404047 CCATGCCGGTCAACAAATTCC 60.404 52.381 1.90 0.00 0.00 3.01
2133 4046 1.817941 GCGGGCCGAGAATTTGCTA 60.818 57.895 33.44 0.00 0.00 3.49
2134 4047 3.134127 GCGGGCCGAGAATTTGCT 61.134 61.111 33.44 0.00 0.00 3.91
2178 4097 7.962918 CAGAGTTAATTAACATCCAAGGAAACG 59.037 37.037 26.06 0.36 38.62 3.60
2308 4227 2.575262 GTTGCGCTGCTTCATCGC 60.575 61.111 9.73 7.92 46.88 4.58
2559 4478 3.253188 CAGCAGAATTTTCCGTCCAAAGA 59.747 43.478 0.00 0.00 0.00 2.52
2570 4496 5.231991 CACGTAAAAAGTGCAGCAGAATTTT 59.768 36.000 14.05 14.05 32.52 1.82
2571 4497 4.739716 CACGTAAAAAGTGCAGCAGAATTT 59.260 37.500 0.00 0.00 32.52 1.82
2601 4527 2.183300 CATGCCATGCCACACTGC 59.817 61.111 0.00 0.00 0.00 4.40
2612 4538 4.845447 GGGAGCCATGCCATGCCA 62.845 66.667 0.00 0.00 36.78 4.92
2613 4539 4.534824 AGGGAGCCATGCCATGCC 62.535 66.667 0.00 0.00 40.01 4.40
2614 4540 3.224324 CAGGGAGCCATGCCATGC 61.224 66.667 0.00 0.00 40.01 4.06
2615 4541 1.076559 TTCAGGGAGCCATGCCATG 60.077 57.895 0.00 0.00 40.01 3.66
2616 4542 1.229359 CTTCAGGGAGCCATGCCAT 59.771 57.895 0.00 0.00 40.01 4.40
2621 4547 1.481871 CAAATGCTTCAGGGAGCCAT 58.518 50.000 0.00 0.00 42.01 4.40
2652 4578 5.278957 CCTTCCAATGTTTTCACCTTCGAAT 60.279 40.000 0.00 0.00 0.00 3.34
2654 4580 3.568007 CCTTCCAATGTTTTCACCTTCGA 59.432 43.478 0.00 0.00 0.00 3.71
2655 4581 3.568007 TCCTTCCAATGTTTTCACCTTCG 59.432 43.478 0.00 0.00 0.00 3.79
2656 4582 5.163457 TGTTCCTTCCAATGTTTTCACCTTC 60.163 40.000 0.00 0.00 0.00 3.46
2658 4584 4.285863 TGTTCCTTCCAATGTTTTCACCT 58.714 39.130 0.00 0.00 0.00 4.00
2662 4588 4.485163 CGGATGTTCCTTCCAATGTTTTC 58.515 43.478 0.00 0.00 33.30 2.29
2666 4592 1.463674 GCGGATGTTCCTTCCAATGT 58.536 50.000 0.00 0.00 33.30 2.71
2667 4593 0.378257 CGCGGATGTTCCTTCCAATG 59.622 55.000 0.00 0.00 33.30 2.82
2718 4645 9.101325 GGGGCAGCTACATATATATCCTAATAA 57.899 37.037 0.00 0.00 0.00 1.40
2719 4646 7.678598 GGGGGCAGCTACATATATATCCTAATA 59.321 40.741 0.00 0.00 0.00 0.98
2720 4647 6.502158 GGGGGCAGCTACATATATATCCTAAT 59.498 42.308 0.00 0.00 0.00 1.73
2771 4699 2.542907 CGCAACTCAAACGCCCACT 61.543 57.895 0.00 0.00 0.00 4.00
2794 4722 0.379669 CCACTGCATTTCAGCGGATC 59.620 55.000 1.26 0.00 45.70 3.36
2866 4794 2.768527 TGGCTTAGATGAACTCTGGAGG 59.231 50.000 2.58 0.00 35.28 4.30
2878 4806 1.626356 TTCGCAGGGCTGGCTTAGAT 61.626 55.000 0.00 0.00 0.00 1.98
2884 4812 1.153765 GAAAATTCGCAGGGCTGGC 60.154 57.895 0.00 0.00 0.00 4.85
2886 4814 0.883833 ACTGAAAATTCGCAGGGCTG 59.116 50.000 10.98 0.00 36.47 4.85
2904 4832 5.447279 CCAGCTGACAAATATCGTTTGGTAC 60.447 44.000 17.39 0.00 33.92 3.34
2912 4847 4.813161 ACTTCATCCAGCTGACAAATATCG 59.187 41.667 17.39 0.00 0.00 2.92
2947 4882 7.621832 TTTTCTGATTGTAAAATGAGCGTTG 57.378 32.000 0.00 0.00 0.00 4.10
2966 4901 6.515272 TGCAGAAAACAGAAGTCTTTTTCT 57.485 33.333 16.79 16.79 45.94 2.52
2973 4926 3.251004 ACGGAATGCAGAAAACAGAAGTC 59.749 43.478 0.00 0.00 0.00 3.01
2979 4932 1.974265 TGGACGGAATGCAGAAAACA 58.026 45.000 0.00 0.00 0.00 2.83
2982 4935 2.083774 GACATGGACGGAATGCAGAAA 58.916 47.619 0.00 0.00 28.84 2.52
2991 4944 6.918067 ATGAGATTAATAGACATGGACGGA 57.082 37.500 0.00 0.00 0.00 4.69
3040 4993 3.399330 GCAGAAAAGCCACTACACTACA 58.601 45.455 0.00 0.00 0.00 2.74
3150 5133 4.528596 AGGACATACATACATCTACAGGGC 59.471 45.833 0.00 0.00 0.00 5.19
3164 5147 6.683861 GCATCAAGACAGTGATAGGACATACA 60.684 42.308 0.00 0.00 36.04 2.29
3165 5148 5.694006 GCATCAAGACAGTGATAGGACATAC 59.306 44.000 0.00 0.00 36.04 2.39
3250 5233 8.452868 ACTTAATTAAGAACCCATGCCCATATA 58.547 33.333 27.92 0.00 37.08 0.86
3345 5328 2.666508 GCGCATATACGGTTATCAGTGG 59.333 50.000 0.30 0.00 0.00 4.00
3363 5346 3.561310 TCAATCCTCTTAACATGATGCGC 59.439 43.478 0.00 0.00 0.00 6.09
3369 5352 7.412346 CGAACTCAGTTCAATCCTCTTAACATG 60.412 40.741 17.81 0.00 42.05 3.21
3373 5356 5.926542 CACGAACTCAGTTCAATCCTCTTAA 59.073 40.000 17.81 0.00 42.05 1.85
3416 5399 9.785982 TCAGTTTTTATTTTATTTTTCAGGGGG 57.214 29.630 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.