Multiple sequence alignment - TraesCS3B01G409300

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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 TraesCS3B01G409300 chr3B 100.000 2535 0 0 1 2535 644909390 644911924 0.000000e+00 4682.0
1 TraesCS3B01G409300 chr3B 90.244 82 7 1 1 82 642072954 642072874 3.450000e-19 106.0
2 TraesCS3B01G409300 chr3D 86.900 1832 137 60 666 2461 482595648 482597412 0.000000e+00 1958.0
3 TraesCS3B01G409300 chr3D 92.715 453 32 1 79 531 482594772 482595223 0.000000e+00 652.0
4 TraesCS3B01G409300 chr3D 94.915 118 5 1 522 639 482595452 482595568 1.550000e-42 183.0
5 TraesCS3B01G409300 chr3D 94.828 58 3 0 2478 2535 482597560 482597617 9.660000e-15 91.6
6 TraesCS3B01G409300 chr3A 91.158 1097 44 15 746 1806 625532855 625533934 0.000000e+00 1439.0
7 TraesCS3B01G409300 chr3A 87.674 576 21 13 1896 2469 625534004 625534531 2.140000e-175 625.0
8 TraesCS3B01G409300 chr3A 79.035 539 102 10 81 612 324524926 324524392 2.400000e-95 359.0
9 TraesCS3B01G409300 chr3A 92.308 52 2 2 1843 1892 625533928 625533979 3.500000e-09 73.1
10 TraesCS3B01G409300 chrUn 79.406 539 100 10 81 612 126584585 126585119 1.110000e-98 370.0
11 TraesCS3B01G409300 chrUn 79.221 539 101 10 81 612 126582466 126583000 5.150000e-97 364.0
12 TraesCS3B01G409300 chrUn 79.035 539 102 10 81 612 126590404 126590938 2.400000e-95 359.0
13 TraesCS3B01G409300 chr2A 79.035 539 102 10 81 612 328684820 328685354 2.400000e-95 359.0
14 TraesCS3B01G409300 chr6A 78.987 533 99 12 81 605 267869677 267869150 4.010000e-93 351.0
15 TraesCS3B01G409300 chr6A 88.060 134 13 2 1392 1522 16984402 16984269 3.380000e-34 156.0
16 TraesCS3B01G409300 chr4A 78.667 525 103 8 81 599 275386013 275386534 8.690000e-90 340.0
17 TraesCS3B01G409300 chr1D 78.895 507 94 12 81 579 56662001 56662502 5.230000e-87 331.0
18 TraesCS3B01G409300 chr7A 90.244 82 7 1 1 82 676711369 676711449 3.450000e-19 106.0
19 TraesCS3B01G409300 chr7A 90.123 81 6 2 1 80 374573947 374574026 1.240000e-18 104.0
20 TraesCS3B01G409300 chr7A 89.024 82 8 1 1 82 46521718 46521798 1.600000e-17 100.0
21 TraesCS3B01G409300 chr2D 91.139 79 6 1 1 79 102586511 102586434 3.450000e-19 106.0
22 TraesCS3B01G409300 chr2B 91.139 79 5 2 1 78 557762572 557762649 3.450000e-19 106.0
23 TraesCS3B01G409300 chr1A 91.139 79 6 1 1 79 534939692 534939769 3.450000e-19 106.0
24 TraesCS3B01G409300 chr1A 89.610 77 8 0 1 77 463193334 463193410 5.770000e-17 99.0
25 TraesCS3B01G409300 chr1A 88.095 84 8 2 1 83 549414384 549414466 5.770000e-17 99.0


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 TraesCS3B01G409300 chr3B 644909390 644911924 2534 False 4682.000000 4682 100.0000 1 2535 1 chr3B.!!$F1 2534
1 TraesCS3B01G409300 chr3D 482594772 482597617 2845 False 721.150000 1958 92.3395 79 2535 4 chr3D.!!$F1 2456
2 TraesCS3B01G409300 chr3A 625532855 625534531 1676 False 712.366667 1439 90.3800 746 2469 3 chr3A.!!$F1 1723
3 TraesCS3B01G409300 chr3A 324524392 324524926 534 True 359.000000 359 79.0350 81 612 1 chr3A.!!$R1 531
4 TraesCS3B01G409300 chrUn 126582466 126585119 2653 False 367.000000 370 79.3135 81 612 2 chrUn.!!$F2 531
5 TraesCS3B01G409300 chrUn 126590404 126590938 534 False 359.000000 359 79.0350 81 612 1 chrUn.!!$F1 531
6 TraesCS3B01G409300 chr2A 328684820 328685354 534 False 359.000000 359 79.0350 81 612 1 chr2A.!!$F1 531
7 TraesCS3B01G409300 chr6A 267869150 267869677 527 True 351.000000 351 78.9870 81 605 1 chr6A.!!$R2 524
8 TraesCS3B01G409300 chr4A 275386013 275386534 521 False 340.000000 340 78.6670 81 599 1 chr4A.!!$F1 518
9 TraesCS3B01G409300 chr1D 56662001 56662502 501 False 331.000000 331 78.8950 81 579 1 chr1D.!!$F1 498

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
810 3226 0.373716 GCAACGGATAAGAACGCCAG 59.626 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 4160 0.318441 AGACACATACACAGCGCAGT 59.682 50.0 11.47 4.25 0.0 4.4 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
22 23 5.640189 GGGCTTCCTTAGGAAAAAGTTAC 57.360 43.478 15.17 0.88 41.54 2.50
23 24 5.074804 GGGCTTCCTTAGGAAAAAGTTACA 58.925 41.667 15.17 0.00 41.54 2.41
24 25 5.537295 GGGCTTCCTTAGGAAAAAGTTACAA 59.463 40.000 15.17 0.00 41.54 2.41
25 26 6.210784 GGGCTTCCTTAGGAAAAAGTTACAAT 59.789 38.462 15.17 0.00 41.54 2.71
26 27 7.090808 GGCTTCCTTAGGAAAAAGTTACAATG 58.909 38.462 15.17 0.04 41.54 2.82
27 28 7.090808 GCTTCCTTAGGAAAAAGTTACAATGG 58.909 38.462 15.17 0.00 41.54 3.16
28 29 7.039993 GCTTCCTTAGGAAAAAGTTACAATGGA 60.040 37.037 15.17 0.00 41.54 3.41
29 30 8.950007 TTCCTTAGGAAAAAGTTACAATGGAT 57.050 30.769 11.81 0.00 38.93 3.41
30 31 8.950007 TCCTTAGGAAAAAGTTACAATGGATT 57.050 30.769 0.00 0.00 0.00 3.01
31 32 8.802267 TCCTTAGGAAAAAGTTACAATGGATTG 58.198 33.333 0.00 0.00 43.26 2.67
32 33 8.034804 CCTTAGGAAAAAGTTACAATGGATTGG 58.965 37.037 0.00 0.00 41.96 3.16
33 34 8.713708 TTAGGAAAAAGTTACAATGGATTGGA 57.286 30.769 4.45 0.00 41.96 3.53
34 35 7.610580 AGGAAAAAGTTACAATGGATTGGAA 57.389 32.000 4.45 0.00 41.96 3.53
35 36 8.206126 AGGAAAAAGTTACAATGGATTGGAAT 57.794 30.769 0.36 0.00 42.16 3.01
36 37 8.314021 AGGAAAAAGTTACAATGGATTGGAATC 58.686 33.333 0.36 0.00 42.16 2.52
56 57 8.940397 GGAATCCTCCAATATTCCTATGAAAA 57.060 34.615 6.80 0.00 45.16 2.29
57 58 9.539194 GGAATCCTCCAATATTCCTATGAAAAT 57.461 33.333 6.80 0.00 45.16 1.82
72 73 9.448438 TCCTATGAAAATCTTTCAATTCGAAGA 57.552 29.630 3.35 0.00 34.32 2.87
73 74 9.713740 CCTATGAAAATCTTTCAATTCGAAGAG 57.286 33.333 3.35 0.00 34.32 2.85
74 75 9.713740 CTATGAAAATCTTTCAATTCGAAGAGG 57.286 33.333 3.35 0.00 34.32 3.69
75 76 6.381801 TGAAAATCTTTCAATTCGAAGAGGC 58.618 36.000 3.35 0.00 38.43 4.70
76 77 4.972514 AATCTTTCAATTCGAAGAGGCC 57.027 40.909 3.35 0.00 38.43 5.19
77 78 3.703001 TCTTTCAATTCGAAGAGGCCT 57.297 42.857 3.86 3.86 38.43 5.19
78 79 4.021102 TCTTTCAATTCGAAGAGGCCTT 57.979 40.909 6.77 0.00 38.43 4.35
79 80 3.753272 TCTTTCAATTCGAAGAGGCCTTG 59.247 43.478 6.77 0.00 38.43 3.61
89 90 3.738282 CGAAGAGGCCTTGAATAGATTCG 59.262 47.826 6.77 9.44 39.62 3.34
94 95 4.698575 AGGCCTTGAATAGATTCGACTTC 58.301 43.478 0.00 0.00 39.62 3.01
110 111 3.062234 CGACTTCGGCTTTATCAACTTCC 59.938 47.826 0.00 0.00 35.37 3.46
123 124 4.594123 TCAACTTCCGTGTCATGTAGAA 57.406 40.909 0.00 0.00 0.00 2.10
163 164 6.891908 AGAAATGATACTTGGTAGGTGCAAAT 59.108 34.615 0.00 0.00 0.00 2.32
369 2490 3.612423 GCATTGGTTAATCGAAAAGGCAC 59.388 43.478 0.00 0.00 0.00 5.01
372 2493 5.461032 TTGGTTAATCGAAAAGGCACAAT 57.539 34.783 0.00 0.00 0.00 2.71
420 2541 9.761504 TTCAATTTTTGATGTTGCTTTCTATCA 57.238 25.926 0.00 0.00 39.84 2.15
421 2542 9.932207 TCAATTTTTGATGTTGCTTTCTATCAT 57.068 25.926 0.00 0.00 34.08 2.45
424 2545 9.932207 ATTTTTGATGTTGCTTTCTATCATTCA 57.068 25.926 0.00 0.00 30.45 2.57
441 2562 9.956720 CTATCATTCACCCAATTTCATAAGAAC 57.043 33.333 0.00 0.00 32.39 3.01
505 2626 7.217200 TGATAGAGCCGCTTAATTCATAAAGT 58.783 34.615 0.00 0.00 0.00 2.66
641 3000 8.934023 AAAACAATCCATGAACTAAAGGAGTA 57.066 30.769 0.00 0.00 37.44 2.59
642 3001 9.533831 AAAACAATCCATGAACTAAAGGAGTAT 57.466 29.630 0.00 0.00 37.44 2.12
645 3004 8.432805 ACAATCCATGAACTAAAGGAGTATAGG 58.567 37.037 0.00 0.00 37.44 2.57
647 3006 7.841282 TCCATGAACTAAAGGAGTATAGGAG 57.159 40.000 0.00 0.00 37.44 3.69
650 3009 8.527810 CCATGAACTAAAGGAGTATAGGAGATC 58.472 40.741 0.00 0.00 37.44 2.75
651 3010 7.747155 TGAACTAAAGGAGTATAGGAGATCG 57.253 40.000 0.00 0.00 37.44 3.69
652 3011 7.288560 TGAACTAAAGGAGTATAGGAGATCGT 58.711 38.462 0.00 0.00 37.44 3.73
653 3012 7.778853 TGAACTAAAGGAGTATAGGAGATCGTT 59.221 37.037 0.00 0.00 37.44 3.85
654 3013 8.536340 AACTAAAGGAGTATAGGAGATCGTTT 57.464 34.615 0.00 0.00 37.44 3.60
655 3014 9.638176 AACTAAAGGAGTATAGGAGATCGTTTA 57.362 33.333 0.00 0.00 37.44 2.01
656 3015 9.287373 ACTAAAGGAGTATAGGAGATCGTTTAG 57.713 37.037 17.76 17.76 45.97 1.85
657 3016 9.504708 CTAAAGGAGTATAGGAGATCGTTTAGA 57.495 37.037 15.74 0.00 44.73 2.10
658 3017 7.989416 AAGGAGTATAGGAGATCGTTTAGAG 57.011 40.000 0.00 0.00 0.00 2.43
660 3019 7.391620 AGGAGTATAGGAGATCGTTTAGAGAG 58.608 42.308 0.00 0.00 0.00 3.20
661 3020 7.236019 AGGAGTATAGGAGATCGTTTAGAGAGA 59.764 40.741 0.00 0.00 0.00 3.10
662 3021 7.879160 GGAGTATAGGAGATCGTTTAGAGAGAA 59.121 40.741 0.00 0.00 0.00 2.87
663 3022 8.611654 AGTATAGGAGATCGTTTAGAGAGAAC 57.388 38.462 0.00 0.00 0.00 3.01
664 3023 8.212312 AGTATAGGAGATCGTTTAGAGAGAACA 58.788 37.037 0.00 0.00 0.00 3.18
694 3106 5.722263 TGTTTCCTTCGAATTGATACGGTA 58.278 37.500 0.00 0.00 0.00 4.02
696 3108 6.477688 TGTTTCCTTCGAATTGATACGGTATC 59.522 38.462 18.97 18.97 35.74 2.24
718 3130 2.650765 GCGCACAGTAATAGTACGATCG 59.349 50.000 14.88 14.88 35.20 3.69
719 3131 3.223953 CGCACAGTAATAGTACGATCGG 58.776 50.000 20.98 1.23 35.20 4.18
785 3201 3.863424 CCCATCGCATACGTGGTAATATC 59.137 47.826 0.00 0.00 38.20 1.63
810 3226 0.373716 GCAACGGATAAGAACGCCAG 59.626 55.000 0.00 0.00 0.00 4.85
846 3263 2.097825 CCAGCCCAAAAGATCCAAGAG 58.902 52.381 0.00 0.00 0.00 2.85
857 3274 3.169099 AGATCCAAGAGGCGCACTATAT 58.831 45.455 10.83 2.79 33.74 0.86
858 3275 4.344978 AGATCCAAGAGGCGCACTATATA 58.655 43.478 10.83 0.00 33.74 0.86
861 3278 6.607600 AGATCCAAGAGGCGCACTATATAATA 59.392 38.462 10.83 0.00 33.74 0.98
862 3279 6.791867 TCCAAGAGGCGCACTATATAATAT 57.208 37.500 10.83 0.00 33.74 1.28
864 3281 7.041721 TCCAAGAGGCGCACTATATAATATTG 58.958 38.462 10.83 0.00 33.74 1.90
865 3282 7.041721 CCAAGAGGCGCACTATATAATATTGA 58.958 38.462 10.83 0.00 0.00 2.57
899 3316 1.473677 CGTACCTGTCACCGTCCATTA 59.526 52.381 0.00 0.00 0.00 1.90
908 3325 2.507886 TCACCGTCCATTACCATTCCAT 59.492 45.455 0.00 0.00 0.00 3.41
912 3329 2.504367 GTCCATTACCATTCCATCCCG 58.496 52.381 0.00 0.00 0.00 5.14
1332 3754 1.406180 GTTGTTAAACCTGCCACCGTT 59.594 47.619 0.00 0.00 0.00 4.44
1387 3809 2.815647 GCCGTCAAGAAGAGCGGG 60.816 66.667 0.00 0.00 39.63 6.13
1538 3960 3.474570 AGCAGCCTCGCTAAGGGG 61.475 66.667 4.38 0.00 46.32 4.79
1545 3967 2.836360 TCGCTAAGGGGCCTACCG 60.836 66.667 0.84 0.00 41.60 4.02
1593 4016 6.320926 TCCATCGATCTTGGCATAAATGAAAA 59.679 34.615 0.00 0.00 34.06 2.29
1711 4156 2.233922 TCAAGATCGAAGGGAGGTTCAC 59.766 50.000 0.00 0.00 0.00 3.18
1713 4158 2.104170 AGATCGAAGGGAGGTTCACTC 58.896 52.381 0.00 0.00 45.84 3.51
1772 4233 2.188062 TGCAGTGATGCAATGACTCA 57.812 45.000 0.00 0.00 35.15 3.41
1787 4252 2.070783 GACTCAATTCGGTGCGGTTTA 58.929 47.619 0.00 0.00 0.00 2.01
1804 4269 0.945813 TTACCGGTTTTCGTTGCCTG 59.054 50.000 15.04 0.00 37.11 4.85
1821 4286 1.159285 CTGATCTTTGGCGCTGTGAA 58.841 50.000 7.64 0.00 0.00 3.18
1822 4287 1.536766 CTGATCTTTGGCGCTGTGAAA 59.463 47.619 7.64 0.80 0.00 2.69
1826 4293 3.451141 TCTTTGGCGCTGTGAAATTTT 57.549 38.095 7.64 0.00 0.00 1.82
1830 4297 3.717400 TGGCGCTGTGAAATTTTAACA 57.283 38.095 7.64 0.00 0.00 2.41
1889 4357 0.760567 TCTGATGGATCCCACGGAGG 60.761 60.000 9.90 0.00 35.80 4.30
1935 4425 6.585695 ATCCAGAACGACTAAACTGAACTA 57.414 37.500 0.00 0.00 32.90 2.24
1936 4426 6.395426 TCCAGAACGACTAAACTGAACTAA 57.605 37.500 0.00 0.00 32.90 2.24
1971 4461 4.394439 AGGAACTAGCTAGCTAAACAGC 57.606 45.455 24.20 12.16 36.02 4.40
2047 4538 3.306989 CCTGCACACTTGGAAGATGAGTA 60.307 47.826 0.00 0.00 0.00 2.59
2048 4539 4.511527 CTGCACACTTGGAAGATGAGTAT 58.488 43.478 0.00 0.00 0.00 2.12
2052 4543 5.874810 GCACACTTGGAAGATGAGTATGTAA 59.125 40.000 0.00 0.00 0.00 2.41
2064 4555 4.436332 TGAGTATGTAACATGCTGCTCTG 58.564 43.478 0.00 1.05 0.00 3.35
2065 4556 3.801698 AGTATGTAACATGCTGCTCTGG 58.198 45.455 0.00 0.00 0.00 3.86
2084 4575 6.106648 TCTGGGCATCAATCTTCACTATAG 57.893 41.667 0.00 0.00 0.00 1.31
2100 4591 6.763355 TCACTATAGATTCCATTTCCTGCTC 58.237 40.000 6.78 0.00 0.00 4.26
2157 4648 3.646162 CAGAGCTGTTATATGTACCCCCA 59.354 47.826 0.00 0.00 0.00 4.96
2158 4649 3.646637 AGAGCTGTTATATGTACCCCCAC 59.353 47.826 0.00 0.00 0.00 4.61
2207 4699 1.600636 CCCTCGGCAGTTTTCAGCA 60.601 57.895 0.00 0.00 33.89 4.41
2315 4807 6.619446 GCATCATAAAACATCTATCGTGAGGC 60.619 42.308 0.00 0.00 35.49 4.70
2316 4808 5.912892 TCATAAAACATCTATCGTGAGGCA 58.087 37.500 0.00 0.00 0.00 4.75
2403 4896 1.627864 TTTAGTGCTTCCCAAAGGCC 58.372 50.000 0.00 0.00 32.79 5.19
2406 4899 0.829182 AGTGCTTCCCAAAGGCCAAG 60.829 55.000 5.01 0.00 32.79 3.61
2434 4927 2.141517 CTCAGGTGCAGTGCTATATGC 58.858 52.381 17.60 0.00 42.86 3.14
2476 5018 1.610886 GGGCGGTTAATCTGGCTATCC 60.611 57.143 9.24 0.00 45.74 2.59
2514 5138 1.269958 ACTCTGCCTATGCACAGTCA 58.730 50.000 0.00 0.00 42.20 3.41
2519 5143 2.751259 CTGCCTATGCACAGTCACAATT 59.249 45.455 0.00 0.00 44.23 2.32
2531 5155 2.236146 AGTCACAATTATGTCTCGGCCA 59.764 45.455 2.24 0.00 37.82 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.074804 TGTAACTTTTTCCTAAGGAAGCCC 58.925 41.667 0.00 0.00 43.06 5.19
2 3 7.039993 TCCATTGTAACTTTTTCCTAAGGAAGC 60.040 37.037 0.00 0.00 43.06 3.86
3 4 8.404107 TCCATTGTAACTTTTTCCTAAGGAAG 57.596 34.615 0.00 0.00 43.06 3.46
4 5 8.950007 ATCCATTGTAACTTTTTCCTAAGGAA 57.050 30.769 0.00 0.00 40.27 3.36
5 6 8.802267 CAATCCATTGTAACTTTTTCCTAAGGA 58.198 33.333 0.00 0.00 33.22 3.36
6 7 8.034804 CCAATCCATTGTAACTTTTTCCTAAGG 58.965 37.037 0.00 0.00 36.06 2.69
7 8 8.802267 TCCAATCCATTGTAACTTTTTCCTAAG 58.198 33.333 0.00 0.00 36.06 2.18
8 9 8.713708 TCCAATCCATTGTAACTTTTTCCTAA 57.286 30.769 0.00 0.00 36.06 2.69
9 10 8.713708 TTCCAATCCATTGTAACTTTTTCCTA 57.286 30.769 0.00 0.00 36.06 2.94
10 11 7.610580 TTCCAATCCATTGTAACTTTTTCCT 57.389 32.000 0.00 0.00 36.06 3.36
11 12 8.479313 GATTCCAATCCATTGTAACTTTTTCC 57.521 34.615 0.00 0.00 36.06 3.13
46 47 9.448438 TCTTCGAATTGAAAGATTTTCATAGGA 57.552 29.630 0.00 0.00 35.79 2.94
47 48 9.713740 CTCTTCGAATTGAAAGATTTTCATAGG 57.286 33.333 0.00 0.00 35.79 2.57
48 49 9.713740 CCTCTTCGAATTGAAAGATTTTCATAG 57.286 33.333 0.00 0.00 35.79 2.23
49 50 8.184192 GCCTCTTCGAATTGAAAGATTTTCATA 58.816 33.333 0.00 0.00 35.79 2.15
50 51 7.031975 GCCTCTTCGAATTGAAAGATTTTCAT 58.968 34.615 0.00 0.00 35.79 2.57
51 52 6.381801 GCCTCTTCGAATTGAAAGATTTTCA 58.618 36.000 0.00 0.36 35.79 2.69
52 53 5.802451 GGCCTCTTCGAATTGAAAGATTTTC 59.198 40.000 0.00 0.00 35.79 2.29
53 54 5.478332 AGGCCTCTTCGAATTGAAAGATTTT 59.522 36.000 0.00 0.00 35.79 1.82
54 55 5.012893 AGGCCTCTTCGAATTGAAAGATTT 58.987 37.500 0.00 0.00 35.79 2.17
55 56 4.593956 AGGCCTCTTCGAATTGAAAGATT 58.406 39.130 0.00 0.00 35.79 2.40
56 57 4.227864 AGGCCTCTTCGAATTGAAAGAT 57.772 40.909 0.00 0.00 35.79 2.40
57 58 3.703001 AGGCCTCTTCGAATTGAAAGA 57.297 42.857 0.00 0.00 35.79 2.52
58 59 3.753272 TCAAGGCCTCTTCGAATTGAAAG 59.247 43.478 5.23 0.00 35.79 2.62
59 60 3.750371 TCAAGGCCTCTTCGAATTGAAA 58.250 40.909 5.23 0.00 35.79 2.69
60 61 3.417069 TCAAGGCCTCTTCGAATTGAA 57.583 42.857 5.23 0.00 34.74 2.69
61 62 3.417069 TTCAAGGCCTCTTCGAATTGA 57.583 42.857 5.23 0.00 0.00 2.57
62 63 5.118990 TCTATTCAAGGCCTCTTCGAATTG 58.881 41.667 19.03 17.31 0.00 2.32
63 64 5.359194 TCTATTCAAGGCCTCTTCGAATT 57.641 39.130 19.03 8.54 0.00 2.17
64 65 5.559148 ATCTATTCAAGGCCTCTTCGAAT 57.441 39.130 5.23 14.49 0.00 3.34
65 66 5.359194 AATCTATTCAAGGCCTCTTCGAA 57.641 39.130 5.23 7.56 0.00 3.71
66 67 4.499865 CGAATCTATTCAAGGCCTCTTCGA 60.500 45.833 5.23 0.00 36.10 3.71
67 68 3.738282 CGAATCTATTCAAGGCCTCTTCG 59.262 47.826 5.23 7.42 36.61 3.79
68 69 4.747605 GTCGAATCTATTCAAGGCCTCTTC 59.252 45.833 5.23 0.00 36.61 2.87
69 70 4.407296 AGTCGAATCTATTCAAGGCCTCTT 59.593 41.667 5.23 0.00 36.61 2.85
70 71 3.964031 AGTCGAATCTATTCAAGGCCTCT 59.036 43.478 5.23 0.00 36.61 3.69
71 72 4.329462 AGTCGAATCTATTCAAGGCCTC 57.671 45.455 5.23 0.00 36.61 4.70
72 73 4.698575 GAAGTCGAATCTATTCAAGGCCT 58.301 43.478 0.00 0.00 36.61 5.19
73 74 3.491267 CGAAGTCGAATCTATTCAAGGCC 59.509 47.826 0.00 0.00 43.02 5.19
74 75 3.491267 CCGAAGTCGAATCTATTCAAGGC 59.509 47.826 1.43 0.00 43.02 4.35
75 76 3.491267 GCCGAAGTCGAATCTATTCAAGG 59.509 47.826 1.43 0.00 43.02 3.61
76 77 4.363999 AGCCGAAGTCGAATCTATTCAAG 58.636 43.478 1.43 0.00 43.02 3.02
77 78 4.386867 AGCCGAAGTCGAATCTATTCAA 57.613 40.909 1.43 0.00 43.02 2.69
78 79 4.386867 AAGCCGAAGTCGAATCTATTCA 57.613 40.909 1.43 0.00 43.02 2.57
79 80 6.641314 TGATAAAGCCGAAGTCGAATCTATTC 59.359 38.462 1.43 0.00 43.02 1.75
89 90 3.062234 CGGAAGTTGATAAAGCCGAAGTC 59.938 47.826 0.00 0.00 41.11 3.01
94 95 2.073816 ACACGGAAGTTGATAAAGCCG 58.926 47.619 0.00 0.00 46.40 5.52
110 111 8.217115 GCTTATATTGTGATTCTACATGACACG 58.783 37.037 0.00 0.00 34.72 4.49
269 2390 4.099881 AGTTGTGGAATTGCACTTTGATGT 59.900 37.500 27.36 5.90 0.00 3.06
280 2401 7.439157 TTTCACTAGATGAGTTGTGGAATTG 57.561 36.000 0.00 0.00 38.99 2.32
321 2442 7.330454 CACCTAGTACTGTCATGATATTGATGC 59.670 40.741 5.39 0.00 0.00 3.91
336 2457 5.234329 CGATTAACCAATGCACCTAGTACTG 59.766 44.000 5.39 0.00 0.00 2.74
403 2524 5.357878 GGGTGAATGATAGAAAGCAACATCA 59.642 40.000 0.00 0.00 32.32 3.07
424 2545 8.664669 ACCATTAAGTTCTTATGAAATTGGGT 57.335 30.769 12.67 13.16 40.17 4.51
505 2626 8.538701 CGGACTACTCCTAGGTTAGAGAATATA 58.461 40.741 20.60 0.00 33.79 0.86
639 2998 8.380743 TGTTCTCTCTAAACGATCTCCTATAC 57.619 38.462 0.00 0.00 0.00 1.47
641 3000 7.883391 TTGTTCTCTCTAAACGATCTCCTAT 57.117 36.000 0.00 0.00 0.00 2.57
642 3001 7.013464 GGATTGTTCTCTCTAAACGATCTCCTA 59.987 40.741 13.24 0.00 42.99 2.94
643 3002 6.183360 GGATTGTTCTCTCTAAACGATCTCCT 60.183 42.308 13.24 0.00 42.99 3.69
645 3004 6.565234 TGGATTGTTCTCTCTAAACGATCTC 58.435 40.000 13.24 6.84 42.99 2.75
647 3006 7.278868 ACATTGGATTGTTCTCTCTAAACGATC 59.721 37.037 7.42 7.42 42.82 3.69
650 3009 6.727824 ACATTGGATTGTTCTCTCTAAACG 57.272 37.500 0.00 0.00 0.00 3.60
651 3010 8.023706 GGAAACATTGGATTGTTCTCTCTAAAC 58.976 37.037 0.00 0.00 38.85 2.01
652 3011 7.944554 AGGAAACATTGGATTGTTCTCTCTAAA 59.055 33.333 0.00 0.00 38.85 1.85
653 3012 7.461749 AGGAAACATTGGATTGTTCTCTCTAA 58.538 34.615 0.00 0.00 38.85 2.10
654 3013 7.020827 AGGAAACATTGGATTGTTCTCTCTA 57.979 36.000 0.00 0.00 38.85 2.43
655 3014 5.885465 AGGAAACATTGGATTGTTCTCTCT 58.115 37.500 0.00 0.00 38.85 3.10
656 3015 6.581171 AAGGAAACATTGGATTGTTCTCTC 57.419 37.500 0.00 0.00 38.85 3.20
657 3016 5.182001 CGAAGGAAACATTGGATTGTTCTCT 59.818 40.000 0.00 0.00 38.85 3.10
658 3017 5.181245 TCGAAGGAAACATTGGATTGTTCTC 59.819 40.000 0.00 0.00 38.85 2.87
660 3019 5.371115 TCGAAGGAAACATTGGATTGTTC 57.629 39.130 0.00 0.00 38.85 3.18
661 3020 5.782893 TTCGAAGGAAACATTGGATTGTT 57.217 34.783 0.00 0.00 41.49 2.83
662 3021 5.982890 ATTCGAAGGAAACATTGGATTGT 57.017 34.783 3.35 0.00 35.40 2.71
663 3022 6.389091 TCAATTCGAAGGAAACATTGGATTG 58.611 36.000 3.35 0.00 35.40 2.67
664 3023 6.588719 TCAATTCGAAGGAAACATTGGATT 57.411 33.333 3.35 0.00 35.40 3.01
694 3106 2.288729 TCGTACTATTACTGTGCGCGAT 59.711 45.455 12.10 0.00 41.81 4.58
696 3108 2.095384 TCGTACTATTACTGTGCGCG 57.905 50.000 0.00 0.00 41.81 6.86
846 3263 7.169982 GGTGATCTCAATATTATATAGTGCGCC 59.830 40.741 4.18 0.00 0.00 6.53
857 3274 3.244422 GGCGTGGGGTGATCTCAATATTA 60.244 47.826 0.00 0.00 0.00 0.98
858 3275 2.487265 GGCGTGGGGTGATCTCAATATT 60.487 50.000 0.00 0.00 0.00 1.28
861 3278 1.224592 GGCGTGGGGTGATCTCAAT 59.775 57.895 0.00 0.00 0.00 2.57
862 3279 2.668632 GGCGTGGGGTGATCTCAA 59.331 61.111 0.00 0.00 0.00 3.02
864 3281 2.420568 TACGGCGTGGGGTGATCTC 61.421 63.158 24.86 0.00 0.00 2.75
865 3282 2.363276 TACGGCGTGGGGTGATCT 60.363 61.111 24.86 0.00 0.00 2.75
899 3316 2.000701 TGGAGCGGGATGGAATGGT 61.001 57.895 0.00 0.00 0.00 3.55
908 3325 4.631740 TGGACTGGTGGAGCGGGA 62.632 66.667 0.00 0.00 0.00 5.14
912 3329 2.032681 GGTGTGGACTGGTGGAGC 59.967 66.667 0.00 0.00 0.00 4.70
940 3357 3.892122 TCGGTCTCGAGCTCACTC 58.108 61.111 15.40 0.66 40.88 3.51
952 3371 0.753848 CCTCTCTTCCCCTCTCGGTC 60.754 65.000 0.00 0.00 0.00 4.79
965 3384 2.092103 ACTGTATCGCTTCCTCCTCTCT 60.092 50.000 0.00 0.00 0.00 3.10
966 3385 2.303175 ACTGTATCGCTTCCTCCTCTC 58.697 52.381 0.00 0.00 0.00 3.20
1224 3646 1.372997 GAAGAAGGCGTCGCTGTCA 60.373 57.895 18.11 0.00 0.00 3.58
1332 3754 1.612146 TCCCCATCTGCTCCGAACA 60.612 57.895 0.00 0.00 0.00 3.18
1541 3963 3.420214 GAACGCGATGAGGCCGGTA 62.420 63.158 15.93 0.00 0.00 4.02
1608 4034 5.591067 AGAAGAGCTCGCAAACTACTACTAT 59.409 40.000 8.37 0.00 0.00 2.12
1609 4035 4.942483 AGAAGAGCTCGCAAACTACTACTA 59.058 41.667 8.37 0.00 0.00 1.82
1610 4036 3.759618 AGAAGAGCTCGCAAACTACTACT 59.240 43.478 8.37 0.00 0.00 2.57
1611 4037 3.854809 CAGAAGAGCTCGCAAACTACTAC 59.145 47.826 8.37 0.00 0.00 2.73
1711 4156 0.390340 ACATACACAGCGCAGTGGAG 60.390 55.000 32.29 23.45 43.72 3.86
1713 4158 0.950555 ACACATACACAGCGCAGTGG 60.951 55.000 32.29 19.28 43.72 4.00
1715 4160 0.318441 AGACACATACACAGCGCAGT 59.682 50.000 11.47 4.25 0.00 4.40
1787 4252 0.536460 ATCAGGCAACGAAAACCGGT 60.536 50.000 0.00 0.00 43.93 5.28
1804 4269 2.927553 ATTTCACAGCGCCAAAGATC 57.072 45.000 2.29 0.00 0.00 2.75
1830 4297 9.476202 CATGTGATTCATGCATTATCTTTCAAT 57.524 29.630 15.84 4.42 45.69 2.57
1889 4357 1.396301 CGATGCTGAACCTCTGCTTTC 59.604 52.381 7.00 4.00 41.21 2.62
1942 4432 9.602568 GTTTAGCTAGCTAGTTCCTTTTATCTT 57.397 33.333 23.03 0.00 0.00 2.40
1962 4452 3.182744 GCCGAGAGCAAGCTGTTTAGC 62.183 57.143 0.00 0.00 45.76 3.09
2047 4538 2.020694 GCCCAGAGCAGCATGTTACAT 61.021 52.381 0.00 0.00 42.97 2.29
2048 4539 0.677731 GCCCAGAGCAGCATGTTACA 60.678 55.000 0.00 0.00 42.97 2.41
2064 4555 6.597280 GGAATCTATAGTGAAGATTGATGCCC 59.403 42.308 3.20 0.00 42.38 5.36
2065 4556 7.164122 TGGAATCTATAGTGAAGATTGATGCC 58.836 38.462 3.20 0.00 42.38 4.40
2084 4575 4.775236 AGTACAGAGCAGGAAATGGAATC 58.225 43.478 0.00 0.00 0.00 2.52
2100 4591 3.004629 TGTGGCTCAATGCAAAAGTACAG 59.995 43.478 0.00 0.00 45.15 2.74
2157 4648 4.790718 AGGTAAAAGACTGACCAAAGGT 57.209 40.909 4.70 0.00 39.44 3.50
2158 4649 6.371825 GTGATAGGTAAAAGACTGACCAAAGG 59.628 42.308 4.70 0.00 35.56 3.11
2272 4764 4.694037 TGATGCACTCTCATCTCAGTTTTG 59.306 41.667 0.00 0.00 42.44 2.44
2315 4807 5.070770 ACACAGAAGAGATGCTCTAGTTG 57.929 43.478 0.00 0.46 40.28 3.16
2316 4808 5.949354 AGTACACAGAAGAGATGCTCTAGTT 59.051 40.000 0.00 0.00 40.28 2.24
2323 4815 3.329386 TGCAAGTACACAGAAGAGATGC 58.671 45.455 0.00 0.00 0.00 3.91
2372 4864 6.071391 TGGGAAGCACTAAAAATCATTTCCTC 60.071 38.462 0.00 0.00 34.65 3.71
2403 4896 5.617751 GCACTGCACCTGAGTAAAATACTTG 60.618 44.000 0.00 0.00 39.59 3.16
2406 4899 4.003648 AGCACTGCACCTGAGTAAAATAC 58.996 43.478 3.30 0.00 0.00 1.89
2434 4927 6.529220 CCCTAGACTCTGGATTTATCTTTGG 58.471 44.000 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.