Multiple sequence alignment - TraesCS2A01G337000

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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 TraesCS2A01G337000 chr2A 100.000 4099 0 0 1 4099 570605919 570610017 0.000000e+00 7570.0
1 TraesCS2A01G337000 chr2A 89.091 55 4 2 2701 2754 530381027 530381080 2.640000e-07 67.6
2 TraesCS2A01G337000 chr2B 91.808 4187 215 55 1 4099 491714747 491710601 0.000000e+00 5714.0
3 TraesCS2A01G337000 chr2B 98.182 55 1 0 3684 3738 491711046 491710992 3.370000e-16 97.1
4 TraesCS2A01G337000 chr2B 89.091 55 4 2 2701 2754 464466983 464467036 2.640000e-07 67.6
5 TraesCS2A01G337000 chr2D 92.637 3857 161 51 272 4099 419367248 419363486 0.000000e+00 5435.0
6 TraesCS2A01G337000 chr2D 93.728 287 18 0 3 289 419367581 419367295 8.140000e-117 431.0
7 TraesCS2A01G337000 chr2D 89.091 55 4 2 2701 2754 392526361 392526414 2.640000e-07 67.6
8 TraesCS2A01G337000 chr7D 77.075 506 80 26 2482 2964 176166385 176166877 4.060000e-65 259.0
9 TraesCS2A01G337000 chr7D 87.143 70 7 2 2703 2771 101095145 101095077 1.220000e-10 78.7
10 TraesCS2A01G337000 chr7A 88.889 63 6 1 2709 2771 103214920 103214859 4.390000e-10 76.8
11 TraesCS2A01G337000 chr1A 93.878 49 3 0 2708 2756 319320881 319320929 1.580000e-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 TraesCS2A01G337000 chr2A 570605919 570610017 4098 False 7570.00 7570 100.0000 1 4099 1 chr2A.!!$F2 4098
1 TraesCS2A01G337000 chr2B 491710601 491714747 4146 True 2905.55 5714 94.9950 1 4099 2 chr2B.!!$R1 4098
2 TraesCS2A01G337000 chr2D 419363486 419367581 4095 True 2933.00 5435 93.1825 3 4099 2 chr2D.!!$R1 4096

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
652 748 0.028902 AAACGAGCAACTGTTTCGCC 59.971 50.000 12.97 0.0 37.84 5.54 F
1533 1650 0.250901 TCTTCACCAAAGAGCTGCCC 60.251 55.000 0.00 0.0 39.12 5.36 F
2259 2376 1.216977 CCATCCTAACGTCGTGCCA 59.783 57.895 0.00 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2343 0.834612 GATGGTCCAACCCACCGATA 59.165 55.000 0.00 0.00 37.50 2.92 R
2420 2549 1.338105 CGGTTGCCTGAGATTCTCACA 60.338 52.381 12.38 7.49 35.39 3.58 R
3688 3848 0.040425 GCCAACACACGTCCATGTTC 60.040 55.000 6.43 0.00 36.92 3.18 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
50 51 1.597663 CGAATTGACTCCCGCCATAAC 59.402 52.381 0.00 0.00 0.00 1.89
249 261 4.176271 GCCAATTCAAATCTGCACTTACC 58.824 43.478 0.00 0.00 0.00 2.85
258 270 6.945435 TCAAATCTGCACTTACCAAGGAAATA 59.055 34.615 0.00 0.00 0.00 1.40
330 410 2.558359 ACTGACAGACGATCATCACACA 59.442 45.455 10.08 0.00 0.00 3.72
346 426 2.794350 CACACACGCTCAAATTTTTCCC 59.206 45.455 0.00 0.00 0.00 3.97
474 569 3.680786 TCCACGTCCACAGCTCCG 61.681 66.667 0.00 0.00 0.00 4.63
484 579 3.344215 CAGCTCCGCGCATCATCC 61.344 66.667 8.75 0.00 42.61 3.51
524 619 1.152963 AACTGCACCGGGGATATGC 60.153 57.895 8.67 7.64 39.88 3.14
550 645 1.217244 CAGCAGGAAAATGGCCAGC 59.783 57.895 13.05 7.25 38.11 4.85
564 659 0.247814 GCCAGCGATTCGTGTTCATG 60.248 55.000 8.03 0.00 0.00 3.07
565 660 1.078709 CCAGCGATTCGTGTTCATGT 58.921 50.000 8.03 0.00 0.00 3.21
566 661 1.464608 CCAGCGATTCGTGTTCATGTT 59.535 47.619 8.03 0.00 0.00 2.71
567 662 2.474526 CCAGCGATTCGTGTTCATGTTC 60.475 50.000 8.03 0.00 0.00 3.18
568 663 1.390123 AGCGATTCGTGTTCATGTTCG 59.610 47.619 8.03 12.10 0.00 3.95
569 664 1.388768 GCGATTCGTGTTCATGTTCGA 59.611 47.619 8.03 0.00 0.00 3.71
570 665 2.029244 GCGATTCGTGTTCATGTTCGAT 59.971 45.455 8.03 1.22 32.54 3.59
591 686 2.161855 CACATTGGCCTACAAAGCAGA 58.838 47.619 3.32 0.00 43.46 4.26
652 748 0.028902 AAACGAGCAACTGTTTCGCC 59.971 50.000 12.97 0.00 37.84 5.54
657 753 0.602638 AGCAACTGTTTCGCCGATCA 60.603 50.000 0.00 0.00 0.00 2.92
795 899 0.450583 TTTCATCGGACGGTCGAGAG 59.549 55.000 1.43 4.22 42.69 3.20
798 902 2.762234 ATCGGACGGTCGAGAGCAC 61.762 63.158 1.43 0.00 42.69 4.40
799 903 4.813526 CGGACGGTCGAGAGCACG 62.814 72.222 1.43 0.73 36.33 5.34
800 904 3.735029 GGACGGTCGAGAGCACGT 61.735 66.667 1.43 0.00 43.62 4.49
801 905 2.202324 GACGGTCGAGAGCACGTC 60.202 66.667 9.61 9.61 46.38 4.34
808 912 2.179517 GAGAGCACGTCCAGACCG 59.820 66.667 0.00 0.00 0.00 4.79
860 977 3.787001 CCCGCCCTCCTCAAGTCC 61.787 72.222 0.00 0.00 0.00 3.85
881 998 1.852067 CTTCCCCTTGTCGCCAAACG 61.852 60.000 0.00 0.00 45.62 3.60
953 1070 1.268283 CCCCACCTCTCCTCTTCCAC 61.268 65.000 0.00 0.00 0.00 4.02
981 1098 1.750399 ATGGTGTGATCGGCCAAGC 60.750 57.895 2.24 0.00 35.74 4.01
1281 1398 4.008933 ACCAGGCTCACCGTGCTC 62.009 66.667 0.00 0.00 42.76 4.26
1284 1401 3.753434 AGGCTCACCGTGCTCTCG 61.753 66.667 0.00 0.00 42.76 4.04
1533 1650 0.250901 TCTTCACCAAAGAGCTGCCC 60.251 55.000 0.00 0.00 39.12 5.36
1932 2049 3.429141 CTGCACAGCAAGGAGGCG 61.429 66.667 0.00 0.00 38.41 5.52
2259 2376 1.216977 CCATCCTAACGTCGTGCCA 59.783 57.895 0.00 0.00 0.00 4.92
2420 2549 8.006741 CGAATCGGAACAAAATTTCTGAATTT 57.993 30.769 0.00 0.00 45.06 1.82
2579 2708 0.102481 CGTCCAACATACTCCTCGGG 59.898 60.000 0.00 0.00 0.00 5.14
2741 2870 4.711949 AGCTTCGGGGTGCTGCTG 62.712 66.667 0.00 0.00 38.21 4.41
2975 3104 1.658717 GATGCCGGAGATCGTCGTG 60.659 63.158 5.05 3.57 37.11 4.35
2982 3111 2.630714 GAGATCGTCGTGCGCATCG 61.631 63.158 15.91 19.29 41.07 3.84
3159 3300 7.043325 CGGTAATTTACGGAAGATTCTGAAGAG 60.043 40.741 8.37 0.00 37.03 2.85
3230 3371 3.131396 CACCGTGTGCTTTCTACTTTCT 58.869 45.455 0.00 0.00 0.00 2.52
3272 3413 8.571336 TGAATTTCTTGATTCTTCTTCCTTGTC 58.429 33.333 0.00 0.00 37.04 3.18
3330 3471 1.365633 GGCGATAGGAGAGGCACTG 59.634 63.158 0.00 0.00 41.55 3.66
3338 3479 1.676384 GAGAGGCACTGCTGGTTCT 59.324 57.895 0.00 0.00 41.55 3.01
3339 3480 0.673022 GAGAGGCACTGCTGGTTCTG 60.673 60.000 0.00 0.00 41.55 3.02
3340 3481 1.123861 AGAGGCACTGCTGGTTCTGA 61.124 55.000 0.00 0.00 41.55 3.27
3464 3614 6.688813 GCTGCTTTTGTGCAACTATTATACTC 59.311 38.462 0.00 0.00 42.83 2.59
3528 3678 6.211587 TGCCATGAAATTAAGTGGAATCAG 57.788 37.500 0.00 0.00 33.53 2.90
3534 3684 5.415701 TGAAATTAAGTGGAATCAGGAGCAC 59.584 40.000 0.00 0.00 0.00 4.40
3535 3685 4.574674 ATTAAGTGGAATCAGGAGCACA 57.425 40.909 0.00 0.00 0.00 4.57
3542 3692 3.009363 TGGAATCAGGAGCACAATCTTCA 59.991 43.478 0.00 0.00 0.00 3.02
3544 3694 4.511527 GAATCAGGAGCACAATCTTCAGA 58.488 43.478 0.00 0.00 0.00 3.27
3570 3730 1.062002 GCCACCGTAAATGTCATGTCG 59.938 52.381 0.00 0.00 0.00 4.35
3590 3750 2.285026 CGAGTGTCACGTCAGTTTGTTG 60.285 50.000 0.00 0.00 0.00 3.33
3613 3773 1.538634 CCGTGGTACGACTTTTCCACA 60.539 52.381 6.45 0.00 46.05 4.17
3661 3821 1.148310 AAGCAACGAGAACATGGACG 58.852 50.000 0.00 0.00 0.00 4.79
3662 3822 0.033504 AGCAACGAGAACATGGACGT 59.966 50.000 0.00 0.00 40.64 4.34
3663 3823 0.163788 GCAACGAGAACATGGACGTG 59.836 55.000 0.00 0.00 38.92 4.49
3664 3824 1.497991 CAACGAGAACATGGACGTGT 58.502 50.000 0.00 0.00 38.92 4.49
3665 3825 1.864711 CAACGAGAACATGGACGTGTT 59.135 47.619 9.49 9.49 44.53 3.32
3695 3855 7.755582 AAGAAAAAGAAAAACGAGAACATGG 57.244 32.000 0.00 0.00 0.00 3.66
3696 3856 7.095695 AGAAAAAGAAAAACGAGAACATGGA 57.904 32.000 0.00 0.00 0.00 3.41
3697 3857 6.972901 AGAAAAAGAAAAACGAGAACATGGAC 59.027 34.615 0.00 0.00 0.00 4.02
3738 3898 4.191015 GTCCCCGGCCAAGATCCC 62.191 72.222 2.24 0.00 0.00 3.85
3739 3899 4.431524 TCCCCGGCCAAGATCCCT 62.432 66.667 2.24 0.00 0.00 4.20
3742 3943 4.113815 CCGGCCAAGATCCCTGCA 62.114 66.667 2.24 0.00 0.00 4.41
3780 3981 1.980951 AATGCGTGCGTGCCTGTATG 61.981 55.000 0.00 0.00 0.00 2.39
3847 4048 3.990318 AAAACAAAAGGGAGAAGAGCG 57.010 42.857 0.00 0.00 0.00 5.03
3860 4061 1.023513 AAGAGCGAGATGGTTGCAGC 61.024 55.000 0.00 0.00 38.16 5.25
3879 4080 2.740055 GGACACACAGCAGCGGAG 60.740 66.667 0.00 0.00 0.00 4.63
3893 4101 2.335323 CGGAGCAGATCGGAGATCA 58.665 57.895 11.94 0.00 45.12 2.92
3894 4102 0.887247 CGGAGCAGATCGGAGATCAT 59.113 55.000 11.94 0.00 45.12 2.45
3895 4103 1.402588 CGGAGCAGATCGGAGATCATG 60.403 57.143 11.94 8.34 45.12 3.07
3896 4104 1.672441 GGAGCAGATCGGAGATCATGC 60.672 57.143 18.05 18.05 45.12 4.06
3897 4105 1.000618 GAGCAGATCGGAGATCATGCA 59.999 52.381 23.03 0.00 45.12 3.96
3898 4106 1.146637 GCAGATCGGAGATCATGCAC 58.853 55.000 19.52 0.00 45.12 4.57
3933 4141 4.218200 CCATGTCTGTCATTAGTTGGCAAA 59.782 41.667 0.00 0.00 40.05 3.68
3946 4154 8.872845 CATTAGTTGGCAAAGCTTTTATAAAGG 58.127 33.333 9.53 3.05 0.00 3.11
3995 4203 1.809207 GGGGCGACAATCAATGTGG 59.191 57.895 0.00 0.00 44.12 4.17
4021 4230 4.027674 TCCAAGGAAATCGATCCACAAA 57.972 40.909 7.77 0.00 42.27 2.83
4031 4240 4.630894 TCGATCCACAAACAATAATGGC 57.369 40.909 0.00 0.00 31.87 4.40
4078 4287 0.808125 TGTGTTTGCAACAGCTCGTT 59.192 45.000 0.00 0.00 43.10 3.85
4087 4296 2.049433 CAGCTCGTTCGGTCCGTT 60.049 61.111 11.88 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.753107 CGTTAAAGCATGGTTATATCCCGT 59.247 41.667 11.15 0.00 0.00 5.28
10 11 6.870971 TTCGTTAAAGCATGGTTATATCCC 57.129 37.500 11.15 0.00 0.00 3.85
11 12 8.564574 TCAATTCGTTAAAGCATGGTTATATCC 58.435 33.333 11.15 0.00 0.00 2.59
50 51 4.925646 GCTCCTCTTTTAATTGGCAAAGTG 59.074 41.667 3.01 0.00 32.67 3.16
237 249 5.648092 GTGTATTTCCTTGGTAAGTGCAGAT 59.352 40.000 0.00 0.00 0.00 2.90
258 270 0.898320 ATGCTGAGCTAGGAACGTGT 59.102 50.000 5.83 0.00 0.00 4.49
330 410 2.223947 GGTGTGGGAAAAATTTGAGCGT 60.224 45.455 0.00 0.00 0.00 5.07
346 426 0.391528 TCATGATGGCGTCAGGTGTG 60.392 55.000 19.58 10.89 40.92 3.82
474 569 1.026182 TGGTTCACTGGATGATGCGC 61.026 55.000 0.00 0.00 37.11 6.09
484 579 1.502231 CTTCGTGGACTGGTTCACTG 58.498 55.000 10.02 4.66 0.00 3.66
550 645 3.303229 TGATCGAACATGAACACGAATCG 59.697 43.478 0.00 0.00 38.22 3.34
564 659 2.627945 TGTAGGCCAATGTGATCGAAC 58.372 47.619 5.01 0.00 0.00 3.95
565 660 3.342377 TTGTAGGCCAATGTGATCGAA 57.658 42.857 5.01 0.00 0.00 3.71
566 661 3.270027 CTTTGTAGGCCAATGTGATCGA 58.730 45.455 5.01 0.00 31.81 3.59
567 662 2.223340 GCTTTGTAGGCCAATGTGATCG 60.223 50.000 5.01 0.00 31.81 3.69
568 663 2.754552 TGCTTTGTAGGCCAATGTGATC 59.245 45.455 5.01 0.00 31.81 2.92
569 664 2.756760 CTGCTTTGTAGGCCAATGTGAT 59.243 45.455 5.01 0.00 31.81 3.06
570 665 2.161855 CTGCTTTGTAGGCCAATGTGA 58.838 47.619 5.01 0.00 31.81 3.58
591 686 0.178533 GCTGCTGCTCTTGAGATCCT 59.821 55.000 8.53 0.00 36.03 3.24
652 748 2.157474 TCAACAGTGCGTGAAATGATCG 59.843 45.455 0.00 0.00 0.00 3.69
657 753 2.942376 TCAACTCAACAGTGCGTGAAAT 59.058 40.909 0.00 0.00 31.06 2.17
772 876 1.400990 CGACCGTCCGATGAAACGTC 61.401 60.000 0.00 0.00 37.19 4.34
795 899 1.078759 CATTCTCGGTCTGGACGTGC 61.079 60.000 0.00 0.00 0.00 5.34
798 902 0.458543 CCACATTCTCGGTCTGGACG 60.459 60.000 0.00 0.00 0.00 4.79
799 903 0.608640 ACCACATTCTCGGTCTGGAC 59.391 55.000 0.00 0.00 0.00 4.02
800 904 1.001974 CAACCACATTCTCGGTCTGGA 59.998 52.381 0.00 0.00 33.17 3.86
801 905 1.442769 CAACCACATTCTCGGTCTGG 58.557 55.000 0.00 0.00 33.17 3.86
808 912 2.228822 ACAAATCCGCAACCACATTCTC 59.771 45.455 0.00 0.00 0.00 2.87
860 977 3.068881 TGGCGACAAGGGGAAGAG 58.931 61.111 0.00 0.00 37.44 2.85
881 998 3.080319 AGAAGCTTCACAAATGGCTCTC 58.920 45.455 27.57 0.00 33.63 3.20
882 999 3.151912 AGAAGCTTCACAAATGGCTCT 57.848 42.857 27.57 0.00 33.63 4.09
1533 1650 1.705337 GGGATGGCATGTCGACGTTG 61.705 60.000 7.76 10.65 0.00 4.10
1599 1716 3.443045 ATGCCGCCGAAGCCTTTG 61.443 61.111 0.00 0.00 34.57 2.77
1863 1980 2.347731 CGGTAGGTTCTTCTTGGCTTC 58.652 52.381 0.00 0.00 0.00 3.86
1932 2049 2.297597 AGTGTAGCTATTCGGGCTCATC 59.702 50.000 0.00 0.00 40.74 2.92
2166 2283 1.621992 TCTCCTTGAGACGCTTCACT 58.378 50.000 0.00 0.00 33.35 3.41
2226 2343 0.834612 GATGGTCCAACCCACCGATA 59.165 55.000 0.00 0.00 37.50 2.92
2236 2353 1.067425 CACGACGTTAGGATGGTCCAA 60.067 52.381 0.00 0.00 39.61 3.53
2259 2376 1.827969 CTGAAGTAGTAGGCCTGCAGT 59.172 52.381 23.78 5.81 0.00 4.40
2418 2547 3.149196 GGTTGCCTGAGATTCTCACAAA 58.851 45.455 16.82 8.37 35.39 2.83
2420 2549 1.338105 CGGTTGCCTGAGATTCTCACA 60.338 52.381 12.38 7.49 35.39 3.58
2741 2870 2.202987 CCCGTCAGCATCTCCAGC 60.203 66.667 0.00 0.00 0.00 4.85
3105 3234 2.034879 CATGCTGGGTGACACCGAC 61.035 63.158 18.40 10.45 39.83 4.79
3159 3300 4.688413 ACGCAAGAAGACAAGATTCTCTTC 59.312 41.667 3.24 3.24 41.88 2.87
3272 3413 4.346129 GCAGCTAATCCAAAGAATTCGTG 58.654 43.478 0.00 2.61 0.00 4.35
3330 3471 1.615883 TCTGTCTGTCTCAGAACCAGC 59.384 52.381 10.49 0.00 42.46 4.85
3338 3479 8.575649 TGTAATTACATACTCTGTCTGTCTCA 57.424 34.615 14.35 0.00 39.39 3.27
3339 3480 9.672086 GATGTAATTACATACTCTGTCTGTCTC 57.328 37.037 27.01 9.95 46.20 3.36
3340 3481 9.190317 TGATGTAATTACATACTCTGTCTGTCT 57.810 33.333 27.01 4.87 46.20 3.41
3371 3515 3.899734 TCGCAACAAAATCAACTCCATG 58.100 40.909 0.00 0.00 0.00 3.66
3372 3516 4.672542 CGATCGCAACAAAATCAACTCCAT 60.673 41.667 0.26 0.00 0.00 3.41
3373 3517 3.364864 CGATCGCAACAAAATCAACTCCA 60.365 43.478 0.26 0.00 0.00 3.86
3374 3518 3.163594 CGATCGCAACAAAATCAACTCC 58.836 45.455 0.26 0.00 0.00 3.85
3375 3519 3.599514 CACGATCGCAACAAAATCAACTC 59.400 43.478 16.60 0.00 0.00 3.01
3376 3520 3.554524 CACGATCGCAACAAAATCAACT 58.445 40.909 16.60 0.00 0.00 3.16
3410 3554 8.433421 TTTCTTCGGGTAGATGATTGTTAATC 57.567 34.615 0.00 0.00 38.40 1.75
3528 3678 3.128242 CCAATGTCTGAAGATTGTGCTCC 59.872 47.826 8.88 0.00 35.03 4.70
3534 3684 2.165030 GGTGGCCAATGTCTGAAGATTG 59.835 50.000 7.24 4.44 36.24 2.67
3535 3685 2.450476 GGTGGCCAATGTCTGAAGATT 58.550 47.619 7.24 0.00 0.00 2.40
3542 3692 2.091541 CATTTACGGTGGCCAATGTCT 58.908 47.619 7.24 0.00 0.00 3.41
3544 3694 1.816224 GACATTTACGGTGGCCAATGT 59.184 47.619 16.53 16.53 41.51 2.71
3570 3730 2.536928 GCAACAAACTGACGTGACACTC 60.537 50.000 3.68 1.43 0.00 3.51
3626 3786 4.034510 CGTTGCTTTCACAGAAAACTCTCT 59.965 41.667 0.00 0.00 0.00 3.10
3627 3787 4.034048 TCGTTGCTTTCACAGAAAACTCTC 59.966 41.667 0.00 0.00 0.00 3.20
3669 3829 8.655970 CCATGTTCTCGTTTTTCTTTTTCTTTT 58.344 29.630 0.00 0.00 0.00 2.27
3670 3830 8.032451 TCCATGTTCTCGTTTTTCTTTTTCTTT 58.968 29.630 0.00 0.00 0.00 2.52
3671 3831 7.488150 GTCCATGTTCTCGTTTTTCTTTTTCTT 59.512 33.333 0.00 0.00 0.00 2.52
3672 3832 6.972901 GTCCATGTTCTCGTTTTTCTTTTTCT 59.027 34.615 0.00 0.00 0.00 2.52
3673 3833 6.075572 CGTCCATGTTCTCGTTTTTCTTTTTC 60.076 38.462 0.00 0.00 0.00 2.29
3674 3834 5.741982 CGTCCATGTTCTCGTTTTTCTTTTT 59.258 36.000 0.00 0.00 0.00 1.94
3675 3835 5.163693 ACGTCCATGTTCTCGTTTTTCTTTT 60.164 36.000 0.00 0.00 32.62 2.27
3676 3836 4.334481 ACGTCCATGTTCTCGTTTTTCTTT 59.666 37.500 0.00 0.00 32.62 2.52
3677 3837 3.875134 ACGTCCATGTTCTCGTTTTTCTT 59.125 39.130 0.00 0.00 32.62 2.52
3678 3838 3.247648 CACGTCCATGTTCTCGTTTTTCT 59.752 43.478 0.00 0.00 34.30 2.52
3679 3839 3.001939 ACACGTCCATGTTCTCGTTTTTC 59.998 43.478 0.00 0.00 34.30 2.29
3680 3840 2.940410 ACACGTCCATGTTCTCGTTTTT 59.060 40.909 0.00 0.00 34.30 1.94
3681 3841 2.286833 CACACGTCCATGTTCTCGTTTT 59.713 45.455 0.00 0.00 34.30 2.43
3682 3842 1.864711 CACACGTCCATGTTCTCGTTT 59.135 47.619 0.00 0.00 34.30 3.60
3683 3843 1.202486 ACACACGTCCATGTTCTCGTT 60.202 47.619 0.00 0.00 34.30 3.85
3684 3844 0.387929 ACACACGTCCATGTTCTCGT 59.612 50.000 0.00 0.00 36.99 4.18
3685 3845 1.192312 CAACACACGTCCATGTTCTCG 59.808 52.381 6.43 0.00 36.92 4.04
3686 3846 1.531149 CCAACACACGTCCATGTTCTC 59.469 52.381 6.43 0.00 36.92 2.87
3687 3847 1.593196 CCAACACACGTCCATGTTCT 58.407 50.000 6.43 0.00 36.92 3.01
3688 3848 0.040425 GCCAACACACGTCCATGTTC 60.040 55.000 6.43 0.00 36.92 3.18
3689 3849 1.781025 CGCCAACACACGTCCATGTT 61.781 55.000 4.02 4.02 39.63 2.71
3690 3850 2.250939 CGCCAACACACGTCCATGT 61.251 57.895 0.00 0.00 0.00 3.21
3691 3851 2.555782 CGCCAACACACGTCCATG 59.444 61.111 0.00 0.00 0.00 3.66
3692 3852 2.668212 CCGCCAACACACGTCCAT 60.668 61.111 0.00 0.00 0.00 3.41
3695 3855 4.307908 GTGCCGCCAACACACGTC 62.308 66.667 0.00 0.00 37.96 4.34
3738 3898 0.526954 GCCGCCTTCATCATTTGCAG 60.527 55.000 0.00 0.00 0.00 4.41
3739 3899 1.512230 GCCGCCTTCATCATTTGCA 59.488 52.632 0.00 0.00 0.00 4.08
3742 3943 0.676466 TGACGCCGCCTTCATCATTT 60.676 50.000 0.00 0.00 0.00 2.32
3780 3981 1.706287 GCAAGTACGCCTGCCTAAGC 61.706 60.000 6.41 0.00 40.48 3.09
3812 4013 3.296322 TGTTTTTGTTCCATCATCGGC 57.704 42.857 0.00 0.00 0.00 5.54
3838 4039 1.285578 GCAACCATCTCGCTCTTCTC 58.714 55.000 0.00 0.00 0.00 2.87
3847 4048 0.321919 TGTCCAGCTGCAACCATCTC 60.322 55.000 8.66 0.00 0.00 2.75
3860 4061 3.046087 CCGCTGCTGTGTGTCCAG 61.046 66.667 3.35 0.00 35.49 3.86
3876 4077 1.672441 GCATGATCTCCGATCTGCTCC 60.672 57.143 0.00 0.00 0.00 4.70
3879 4080 1.146637 GTGCATGATCTCCGATCTGC 58.853 55.000 0.00 15.19 0.00 4.26
3882 4090 1.146637 GCAGTGCATGATCTCCGATC 58.853 55.000 11.09 0.00 0.00 3.69
3883 4091 0.466963 TGCAGTGCATGATCTCCGAT 59.533 50.000 15.37 0.00 31.71 4.18
3884 4092 0.460811 GTGCAGTGCATGATCTCCGA 60.461 55.000 22.87 0.00 41.91 4.55
3885 4093 0.461516 AGTGCAGTGCATGATCTCCG 60.462 55.000 22.87 0.00 41.91 4.63
3886 4094 1.015109 CAGTGCAGTGCATGATCTCC 58.985 55.000 22.87 6.29 41.91 3.71
3887 4095 0.377554 GCAGTGCAGTGCATGATCTC 59.622 55.000 35.84 7.09 41.91 2.75
3888 4096 2.478989 GCAGTGCAGTGCATGATCT 58.521 52.632 35.84 10.78 41.91 2.75
3896 4104 2.282674 ATGGGGTGCAGTGCAGTG 60.283 61.111 20.42 17.56 40.08 3.66
3897 4105 2.282674 CATGGGGTGCAGTGCAGT 60.283 61.111 20.42 0.00 40.08 4.40
3898 4106 2.282674 ACATGGGGTGCAGTGCAG 60.283 61.111 20.42 8.24 40.08 4.41
3912 4120 4.082571 GCTTTGCCAACTAATGACAGACAT 60.083 41.667 0.00 0.00 41.45 3.06
3933 4141 5.492887 ACCTCCTTCCTCCTTTATAAAAGCT 59.507 40.000 0.00 0.00 0.00 3.74
3946 4154 2.585153 GGCCGAACCTCCTTCCTC 59.415 66.667 0.00 0.00 34.51 3.71
3979 4187 4.792106 GCCACATTGATTGTCGCC 57.208 55.556 0.00 0.00 36.55 5.54
3982 4190 3.554934 TGGATAGGCCACATTGATTGTC 58.445 45.455 5.01 0.00 43.33 3.18
3995 4203 3.244561 TGGATCGATTTCCTTGGATAGGC 60.245 47.826 0.00 0.00 44.37 3.93
3997 4205 4.960938 TGTGGATCGATTTCCTTGGATAG 58.039 43.478 0.00 0.00 36.68 2.08
4021 4230 2.945008 CACTCACATCGGCCATTATTGT 59.055 45.455 2.24 0.00 0.00 2.71
4031 4240 4.952262 ATTGTTCATTCACTCACATCGG 57.048 40.909 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.