Multiple sequence alignment - TraesCS2D01G527300

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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 TraesCS2D01G527300 chr2D 100.000 3736 0 0 1585 5320 615063362 615059627 0.000000e+00 6900
1 TraesCS2D01G527300 chr2D 100.000 1279 0 0 1 1279 615064946 615063668 0.000000e+00 2362
2 TraesCS2D01G527300 chr2D 84.038 2318 344 12 1585 3880 25354407 25352094 0.000000e+00 2207
3 TraesCS2D01G527300 chr2A 95.517 2409 94 12 1585 3986 745266890 745264489 0.000000e+00 3838
4 TraesCS2D01G527300 chr2A 96.438 1881 51 9 3444 5320 745265001 745263133 0.000000e+00 3088
5 TraesCS2D01G527300 chr2A 83.945 2317 346 12 1585 3879 27969765 27967453 0.000000e+00 2194
6 TraesCS2D01G527300 chr2A 95.865 532 16 2 754 1279 745267431 745266900 0.000000e+00 856
7 TraesCS2D01G527300 chr2A 91.745 424 28 3 333 750 745272773 745272351 2.760000e-162 582
8 TraesCS2D01G527300 chr2A 84.188 468 62 9 3504 3965 745265031 745264570 1.360000e-120 444
9 TraesCS2D01G527300 chr2A 82.239 518 82 8 3444 3956 745264971 745264459 6.330000e-119 438
10 TraesCS2D01G527300 chr2B 94.689 2410 115 9 1585 3986 749421335 749418931 0.000000e+00 3729
11 TraesCS2D01G527300 chr2B 94.380 1886 81 14 3444 5320 749419443 749417574 0.000000e+00 2872
12 TraesCS2D01G527300 chr2B 83.937 2540 372 20 1585 4097 41147294 41144764 0.000000e+00 2398
13 TraesCS2D01G527300 chr2B 91.589 642 52 2 100 741 749423299 749422660 0.000000e+00 885
14 TraesCS2D01G527300 chr2B 96.422 531 15 3 752 1279 749421874 749421345 0.000000e+00 872
15 TraesCS2D01G527300 chr2B 86.535 505 62 4 3444 3945 749419413 749418912 7.790000e-153 551
16 TraesCS2D01G527300 chr2B 84.569 499 69 5 3474 3968 749419473 749418979 6.190000e-134 488
17 TraesCS2D01G527300 chr2B 82.553 470 72 7 3444 3908 749419383 749418919 6.420000e-109 405


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 TraesCS2D01G527300 chr2D 615059627 615064946 5319 True 4631.000000 6900 100.000000 1 5320 2 chr2D.!!$R2 5319
1 TraesCS2D01G527300 chr2D 25352094 25354407 2313 True 2207.000000 2207 84.038000 1585 3880 1 chr2D.!!$R1 2295
2 TraesCS2D01G527300 chr2A 27967453 27969765 2312 True 2194.000000 2194 83.945000 1585 3879 1 chr2A.!!$R1 2294
3 TraesCS2D01G527300 chr2A 745263133 745267431 4298 True 1732.800000 3838 90.849400 754 5320 5 chr2A.!!$R3 4566
4 TraesCS2D01G527300 chr2B 41144764 41147294 2530 True 2398.000000 2398 83.937000 1585 4097 1 chr2B.!!$R1 2512
5 TraesCS2D01G527300 chr2B 749417574 749423299 5725 True 1400.285714 3729 90.105286 100 5320 7 chr2B.!!$R2 5220

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
188 189 0.464036 CTTCCCCATCCGTGAATCGA 59.536 55.0 0.00 0.0 42.86 3.59 F
901 1678 0.560688 AAAGGAGAGGGGCCAAAACA 59.439 50.0 4.39 0.0 0.00 2.83 F
2111 2895 1.049289 GGGAGAAGGCCACCGTCTAT 61.049 60.0 5.01 0.0 42.06 1.98 F
3718 4700 0.029300 TCTCAGCAAGCGCAACAAAC 59.971 50.0 11.47 0.0 42.27 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2829 4.671590 TCCCAGTCGTCGAGGGCA 62.672 66.667 12.79 2.19 42.52 5.36 R
2537 3321 2.289694 GGTGTACACATCTGGAAGCACT 60.290 50.000 26.51 0.00 0.00 4.40 R
3723 4705 0.036483 TGCGTTTGCTGAGAGCCATA 60.036 50.000 0.00 0.00 41.51 2.74 R
4991 6040 1.759445 CTATGTGAGGACCTGACCTGG 59.241 57.143 8.76 0.00 40.73 4.45 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
23 24 6.295719 GTCCATCCTAAAACTAGTTCCTGA 57.704 41.667 8.95 4.24 0.00 3.86
24 25 6.107343 GTCCATCCTAAAACTAGTTCCTGAC 58.893 44.000 8.95 4.34 0.00 3.51
25 26 5.189145 TCCATCCTAAAACTAGTTCCTGACC 59.811 44.000 8.95 0.00 0.00 4.02
26 27 5.045869 CCATCCTAAAACTAGTTCCTGACCA 60.046 44.000 8.95 0.00 0.00 4.02
27 28 5.740290 TCCTAAAACTAGTTCCTGACCAG 57.260 43.478 8.95 0.00 0.00 4.00
39 40 3.055209 CCTGACCAGGCAGATGATATG 57.945 52.381 0.86 0.00 42.44 1.78
40 41 2.424557 CTGACCAGGCAGATGATATGC 58.575 52.381 2.95 2.95 43.09 3.14
47 48 2.556144 GCAGATGATATGCCTCCACA 57.444 50.000 0.00 0.00 37.73 4.17
48 49 2.149578 GCAGATGATATGCCTCCACAC 58.850 52.381 0.00 0.00 37.73 3.82
49 50 2.775890 CAGATGATATGCCTCCACACC 58.224 52.381 0.00 0.00 0.00 4.16
50 51 1.701847 AGATGATATGCCTCCACACCC 59.298 52.381 0.00 0.00 0.00 4.61
51 52 1.701847 GATGATATGCCTCCACACCCT 59.298 52.381 0.00 0.00 0.00 4.34
52 53 1.595311 TGATATGCCTCCACACCCTT 58.405 50.000 0.00 0.00 0.00 3.95
53 54 2.770447 TGATATGCCTCCACACCCTTA 58.230 47.619 0.00 0.00 0.00 2.69
54 55 2.705658 TGATATGCCTCCACACCCTTAG 59.294 50.000 0.00 0.00 0.00 2.18
55 56 2.561209 TATGCCTCCACACCCTTAGA 57.439 50.000 0.00 0.00 0.00 2.10
56 57 1.668826 ATGCCTCCACACCCTTAGAA 58.331 50.000 0.00 0.00 0.00 2.10
57 58 0.690762 TGCCTCCACACCCTTAGAAC 59.309 55.000 0.00 0.00 0.00 3.01
58 59 0.984995 GCCTCCACACCCTTAGAACT 59.015 55.000 0.00 0.00 0.00 3.01
59 60 1.339151 GCCTCCACACCCTTAGAACTG 60.339 57.143 0.00 0.00 0.00 3.16
60 61 1.339151 CCTCCACACCCTTAGAACTGC 60.339 57.143 0.00 0.00 0.00 4.40
61 62 1.347707 CTCCACACCCTTAGAACTGCA 59.652 52.381 0.00 0.00 0.00 4.41
62 63 1.771854 TCCACACCCTTAGAACTGCAA 59.228 47.619 0.00 0.00 0.00 4.08
63 64 2.375174 TCCACACCCTTAGAACTGCAAT 59.625 45.455 0.00 0.00 0.00 3.56
64 65 3.157087 CCACACCCTTAGAACTGCAATT 58.843 45.455 0.00 0.00 0.00 2.32
65 66 3.573967 CCACACCCTTAGAACTGCAATTT 59.426 43.478 0.00 0.00 0.00 1.82
66 67 4.764823 CCACACCCTTAGAACTGCAATTTA 59.235 41.667 0.00 0.00 0.00 1.40
67 68 5.418840 CCACACCCTTAGAACTGCAATTTAT 59.581 40.000 0.00 0.00 0.00 1.40
68 69 6.071391 CCACACCCTTAGAACTGCAATTTATT 60.071 38.462 0.00 0.00 0.00 1.40
69 70 7.122055 CCACACCCTTAGAACTGCAATTTATTA 59.878 37.037 0.00 0.00 0.00 0.98
70 71 7.968405 CACACCCTTAGAACTGCAATTTATTAC 59.032 37.037 0.00 0.00 0.00 1.89
71 72 7.668052 ACACCCTTAGAACTGCAATTTATTACA 59.332 33.333 0.00 0.00 0.00 2.41
72 73 8.519526 CACCCTTAGAACTGCAATTTATTACAA 58.480 33.333 0.00 0.00 0.00 2.41
73 74 8.520351 ACCCTTAGAACTGCAATTTATTACAAC 58.480 33.333 0.00 0.00 0.00 3.32
74 75 8.519526 CCCTTAGAACTGCAATTTATTACAACA 58.480 33.333 0.00 0.00 0.00 3.33
80 81 9.289303 GAACTGCAATTTATTACAACATAGTGG 57.711 33.333 0.00 0.00 0.00 4.00
81 82 8.574251 ACTGCAATTTATTACAACATAGTGGA 57.426 30.769 0.00 0.00 0.00 4.02
82 83 9.019656 ACTGCAATTTATTACAACATAGTGGAA 57.980 29.630 0.00 0.00 0.00 3.53
83 84 9.289303 CTGCAATTTATTACAACATAGTGGAAC 57.711 33.333 0.00 0.00 0.00 3.62
84 85 8.247562 TGCAATTTATTACAACATAGTGGAACC 58.752 33.333 0.00 0.00 37.80 3.62
85 86 8.247562 GCAATTTATTACAACATAGTGGAACCA 58.752 33.333 0.00 0.00 37.80 3.67
86 87 9.567848 CAATTTATTACAACATAGTGGAACCAC 57.432 33.333 15.25 15.25 46.50 4.16
95 96 3.094386 GTGGAACCACTGCAGAACA 57.906 52.632 23.35 6.68 43.12 3.18
96 97 1.388547 GTGGAACCACTGCAGAACAA 58.611 50.000 23.35 0.00 43.12 2.83
97 98 1.065551 GTGGAACCACTGCAGAACAAC 59.934 52.381 23.35 8.46 43.12 3.32
98 99 1.064758 TGGAACCACTGCAGAACAACT 60.065 47.619 23.35 0.00 0.00 3.16
118 119 3.910627 ACTCAATCCCTAACTCAACCACT 59.089 43.478 0.00 0.00 0.00 4.00
125 126 3.610911 CCTAACTCAACCACTGGGAATC 58.389 50.000 0.00 0.00 38.05 2.52
162 163 4.776349 ACACAATTGTTGTACTCCAGTGA 58.224 39.130 8.77 0.00 43.23 3.41
174 175 2.039084 ACTCCAGTGACAATGACTTCCC 59.961 50.000 4.07 0.00 0.00 3.97
176 177 1.073763 CCAGTGACAATGACTTCCCCA 59.926 52.381 4.07 0.00 0.00 4.96
178 179 3.012518 CAGTGACAATGACTTCCCCATC 58.987 50.000 0.00 0.00 0.00 3.51
186 187 1.209504 TGACTTCCCCATCCGTGAATC 59.790 52.381 0.00 0.00 0.00 2.52
188 189 0.464036 CTTCCCCATCCGTGAATCGA 59.536 55.000 0.00 0.00 42.86 3.59
197 198 2.754472 TCCGTGAATCGATTGGCTATG 58.246 47.619 16.96 4.69 42.86 2.23
277 278 4.788925 TGCTTACTTGGGCTATAATGGT 57.211 40.909 0.00 0.00 0.00 3.55
291 292 6.001460 GCTATAATGGTAATGTTGTAGGCCA 58.999 40.000 5.01 0.00 0.00 5.36
307 308 8.512138 GTTGTAGGCCAATATAACATGGAATAC 58.488 37.037 5.01 7.99 39.12 1.89
322 323 8.908786 ACATGGAATACGATGAGTTTATCAAT 57.091 30.769 0.00 0.00 42.53 2.57
327 328 4.882671 ACGATGAGTTTATCAATGCACC 57.117 40.909 0.00 0.00 42.53 5.01
330 331 2.431454 TGAGTTTATCAATGCACCGCA 58.569 42.857 0.00 0.00 36.44 5.69
331 332 2.816672 TGAGTTTATCAATGCACCGCAA 59.183 40.909 0.00 0.00 35.86 4.85
345 346 3.052036 CACCGCAAAAATTCTTCCTGTG 58.948 45.455 0.00 0.00 0.00 3.66
372 373 6.911250 ATGTTGATGATATTGATGCATGGT 57.089 33.333 2.46 0.00 0.00 3.55
373 374 6.718522 TGTTGATGATATTGATGCATGGTT 57.281 33.333 2.46 0.00 0.00 3.67
424 425 8.696043 AGTGCTTCCATTTAAATGCTATATCA 57.304 30.769 20.67 10.88 35.08 2.15
463 464 3.117550 ACTGCCATTAGGTGCCATTATCA 60.118 43.478 0.00 0.00 37.19 2.15
514 515 9.797642 ATAATAAACATATCAACATGCTCAGGA 57.202 29.630 0.00 0.00 0.00 3.86
542 543 4.262851 GGGCCATGAAGTTTGTTTTGGTAT 60.263 41.667 4.39 0.00 0.00 2.73
567 568 8.903570 TGACAATACTAATTTTTATTGCACCG 57.096 30.769 14.34 0.00 38.67 4.94
582 583 2.685388 TGCACCGTGTTCTTCATTTTGA 59.315 40.909 0.00 0.00 0.00 2.69
613 614 6.952935 AGTGTTTCTATTCAGTAAGAAGCG 57.047 37.500 0.00 0.00 40.15 4.68
617 618 4.720649 TCTATTCAGTAAGAAGCGTGCT 57.279 40.909 0.00 0.00 40.15 4.40
619 620 6.392625 TCTATTCAGTAAGAAGCGTGCTAT 57.607 37.500 0.00 0.00 40.15 2.97
629 630 2.611974 AGCGTGCTATTTTTCAACCG 57.388 45.000 0.00 0.00 0.00 4.44
636 637 4.798387 GTGCTATTTTTCAACCGCTATTGG 59.202 41.667 0.00 0.00 0.00 3.16
658 659 7.936496 TGGTGAACAAGAGCAATATGAAATA 57.064 32.000 0.00 0.00 0.00 1.40
695 696 9.747898 TTTCACCTATTTAAAGCTTAATCCAGA 57.252 29.630 0.00 0.00 0.00 3.86
699 700 9.700831 ACCTATTTAAAGCTTAATCCAGATTGT 57.299 29.630 0.00 0.00 32.50 2.71
709 710 6.038714 GCTTAATCCAGATTGTTGAAGTAGGG 59.961 42.308 3.10 0.00 32.50 3.53
729 730 9.892130 AGTAGGGTTATATATTTTAGCTCATGC 57.108 33.333 0.00 0.00 40.05 4.06
730 731 9.110502 GTAGGGTTATATATTTTAGCTCATGCC 57.889 37.037 0.00 0.00 40.80 4.40
741 742 2.333069 AGCTCATGCCTCTATGCCTAA 58.667 47.619 0.00 0.00 40.80 2.69
742 743 2.707791 AGCTCATGCCTCTATGCCTAAA 59.292 45.455 0.00 0.00 40.80 1.85
743 744 3.137176 AGCTCATGCCTCTATGCCTAAAA 59.863 43.478 0.00 0.00 40.80 1.52
744 745 3.885297 GCTCATGCCTCTATGCCTAAAAA 59.115 43.478 0.00 0.00 0.00 1.94
775 1551 2.100252 CGTCGGGACCTCTTTAGCATTA 59.900 50.000 0.00 0.00 0.00 1.90
867 1644 4.972440 GCATTTGAGTTGAGAGTGAAACAC 59.028 41.667 0.00 0.00 41.43 3.32
879 1656 2.024414 GTGAAACACAAGCCCAAGAGT 58.976 47.619 0.00 0.00 36.32 3.24
901 1678 0.560688 AAAGGAGAGGGGCCAAAACA 59.439 50.000 4.39 0.00 0.00 2.83
1905 2689 2.184631 ACCTCCTTCTCCCCCTCCA 61.185 63.158 0.00 0.00 0.00 3.86
2111 2895 1.049289 GGGAGAAGGCCACCGTCTAT 61.049 60.000 5.01 0.00 42.06 1.98
2537 3321 2.106566 GAGGAGATGGAGAGCAAGTCA 58.893 52.381 0.00 0.00 0.00 3.41
3371 4173 2.084546 GTGCAGTCTGGATTTGGTACC 58.915 52.381 4.43 4.43 0.00 3.34
3642 4624 3.624861 GCAACAACCAGGATATGTCTCTG 59.375 47.826 0.00 2.35 0.00 3.35
3707 4689 1.419012 CCAGGATATGGCTCTCAGCAA 59.581 52.381 0.00 0.00 44.75 3.91
3708 4690 2.550423 CCAGGATATGGCTCTCAGCAAG 60.550 54.545 0.00 0.00 44.75 4.01
3709 4691 1.072015 AGGATATGGCTCTCAGCAAGC 59.928 52.381 0.00 0.00 44.75 4.01
3710 4692 1.146637 GATATGGCTCTCAGCAAGCG 58.853 55.000 0.00 0.00 44.75 4.68
3711 4693 0.883814 ATATGGCTCTCAGCAAGCGC 60.884 55.000 0.00 0.00 44.75 5.92
3712 4694 2.242797 TATGGCTCTCAGCAAGCGCA 62.243 55.000 11.47 0.00 44.75 6.09
3713 4695 3.052082 GGCTCTCAGCAAGCGCAA 61.052 61.111 11.47 0.00 44.75 4.85
3714 4696 2.175322 GCTCTCAGCAAGCGCAAC 59.825 61.111 11.47 0.00 41.89 4.17
3715 4697 2.610694 GCTCTCAGCAAGCGCAACA 61.611 57.895 11.47 0.00 41.89 3.33
3716 4698 1.944035 CTCTCAGCAAGCGCAACAA 59.056 52.632 11.47 0.00 42.27 2.83
3717 4699 0.308684 CTCTCAGCAAGCGCAACAAA 59.691 50.000 11.47 0.00 42.27 2.83
3718 4700 0.029300 TCTCAGCAAGCGCAACAAAC 59.971 50.000 11.47 0.00 42.27 2.93
3719 4701 0.248580 CTCAGCAAGCGCAACAAACA 60.249 50.000 11.47 0.00 42.27 2.83
3720 4702 0.248580 TCAGCAAGCGCAACAAACAG 60.249 50.000 11.47 0.00 42.27 3.16
3721 4703 1.066257 AGCAAGCGCAACAAACAGG 59.934 52.632 11.47 0.00 42.27 4.00
3722 4704 1.950630 GCAAGCGCAACAAACAGGG 60.951 57.895 11.47 0.00 38.36 4.45
3723 4705 1.437160 CAAGCGCAACAAACAGGGT 59.563 52.632 11.47 0.00 0.00 4.34
3724 4706 0.665835 CAAGCGCAACAAACAGGGTA 59.334 50.000 11.47 0.00 0.00 3.69
3725 4707 1.269448 CAAGCGCAACAAACAGGGTAT 59.731 47.619 11.47 0.00 0.00 2.73
3726 4708 0.881118 AGCGCAACAAACAGGGTATG 59.119 50.000 11.47 0.00 0.00 2.39
3727 4709 0.109319 GCGCAACAAACAGGGTATGG 60.109 55.000 0.30 0.00 0.00 2.74
3728 4710 0.109319 CGCAACAAACAGGGTATGGC 60.109 55.000 0.00 0.00 0.00 4.40
3729 4711 1.256812 GCAACAAACAGGGTATGGCT 58.743 50.000 0.00 0.00 0.00 4.75
3738 4720 1.065199 CAGGGTATGGCTCTCAGCAAA 60.065 52.381 0.00 0.00 44.75 3.68
3769 4781 1.211457 AGGTTATGGCTCTCAGCAAGG 59.789 52.381 0.00 0.00 44.75 3.61
3819 4831 1.312815 GCAACAGACTGGATATGGCC 58.687 55.000 7.51 0.00 0.00 5.36
3932 4977 3.431725 GCGCAACAGCCTGGGTAC 61.432 66.667 0.30 0.00 0.00 3.34
3975 5020 0.546507 TGGGTATGGTGCACCTCAGA 60.547 55.000 34.75 16.83 36.25 3.27
4023 5068 1.251251 AGCACCACAATCTGGCTTTC 58.749 50.000 0.00 0.00 45.32 2.62
4098 5143 1.074926 GGATCTCCTCCTCAGGGCA 60.075 63.158 0.00 0.00 41.29 5.36
4304 5349 3.681897 CAGATGAAGTGGCTGTCAAGTAC 59.318 47.826 0.00 0.00 0.00 2.73
4655 5703 7.100458 ACCATTATTTGCCTCAGTTACATTC 57.900 36.000 0.00 0.00 0.00 2.67
4702 5750 9.586732 AGGCTTGTAATAATTAGGCATGATAAA 57.413 29.630 0.00 0.00 35.81 1.40
4825 5873 9.813080 GAAATGTAATGAACAACTCAGTAAGAC 57.187 33.333 0.00 0.00 42.70 3.01
4959 6008 4.102524 AGTCTGTCCTGATTGGTACACAAA 59.897 41.667 0.00 0.00 43.46 2.83
5009 6058 1.557269 GCCAGGTCAGGTCCTCACAT 61.557 60.000 0.00 0.00 35.37 3.21
5043 6092 2.853077 CAACCCCTTTTCTCCTCCCTAT 59.147 50.000 0.00 0.00 0.00 2.57
5050 6099 4.843516 CCTTTTCTCCTCCCTATCTGCTAT 59.156 45.833 0.00 0.00 0.00 2.97
5062 6111 7.888105 TCCCTATCTGCTATACATATCCTTCT 58.112 38.462 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.107343 GTCAGGAACTAGTTTTAGGATGGAC 58.893 44.000 10.02 6.07 36.02 4.02
1 2 5.189145 GGTCAGGAACTAGTTTTAGGATGGA 59.811 44.000 10.02 0.00 36.02 3.41
2 3 5.045869 TGGTCAGGAACTAGTTTTAGGATGG 60.046 44.000 10.02 0.00 36.02 3.51
3 4 6.049955 TGGTCAGGAACTAGTTTTAGGATG 57.950 41.667 10.02 3.43 36.02 3.51
4 5 6.301169 CTGGTCAGGAACTAGTTTTAGGAT 57.699 41.667 10.02 0.00 36.02 3.24
5 6 5.740290 CTGGTCAGGAACTAGTTTTAGGA 57.260 43.478 10.02 3.11 36.02 2.94
20 21 2.424557 GCATATCATCTGCCTGGTCAG 58.575 52.381 10.65 10.65 33.44 3.51
21 22 2.556144 GCATATCATCTGCCTGGTCA 57.444 50.000 0.00 0.00 33.44 4.02
28 29 2.149578 GTGTGGAGGCATATCATCTGC 58.850 52.381 0.00 0.00 38.93 4.26
29 30 2.551721 GGGTGTGGAGGCATATCATCTG 60.552 54.545 0.00 0.00 0.00 2.90
30 31 1.701847 GGGTGTGGAGGCATATCATCT 59.298 52.381 0.00 0.00 0.00 2.90
31 32 1.701847 AGGGTGTGGAGGCATATCATC 59.298 52.381 0.00 0.00 0.00 2.92
32 33 1.825105 AGGGTGTGGAGGCATATCAT 58.175 50.000 0.00 0.00 0.00 2.45
33 34 1.595311 AAGGGTGTGGAGGCATATCA 58.405 50.000 0.00 0.00 0.00 2.15
34 35 2.972713 TCTAAGGGTGTGGAGGCATATC 59.027 50.000 0.00 0.00 0.00 1.63
35 36 3.060479 TCTAAGGGTGTGGAGGCATAT 57.940 47.619 0.00 0.00 0.00 1.78
36 37 2.504175 GTTCTAAGGGTGTGGAGGCATA 59.496 50.000 0.00 0.00 0.00 3.14
37 38 1.282157 GTTCTAAGGGTGTGGAGGCAT 59.718 52.381 0.00 0.00 0.00 4.40
38 39 0.690762 GTTCTAAGGGTGTGGAGGCA 59.309 55.000 0.00 0.00 0.00 4.75
39 40 0.984995 AGTTCTAAGGGTGTGGAGGC 59.015 55.000 0.00 0.00 0.00 4.70
40 41 1.339151 GCAGTTCTAAGGGTGTGGAGG 60.339 57.143 0.00 0.00 0.00 4.30
41 42 1.347707 TGCAGTTCTAAGGGTGTGGAG 59.652 52.381 0.00 0.00 0.00 3.86
42 43 1.429930 TGCAGTTCTAAGGGTGTGGA 58.570 50.000 0.00 0.00 0.00 4.02
43 44 2.270352 TTGCAGTTCTAAGGGTGTGG 57.730 50.000 0.00 0.00 0.00 4.17
44 45 4.853924 AAATTGCAGTTCTAAGGGTGTG 57.146 40.909 0.00 0.00 0.00 3.82
45 46 7.668052 TGTAATAAATTGCAGTTCTAAGGGTGT 59.332 33.333 0.00 0.00 0.00 4.16
46 47 8.050778 TGTAATAAATTGCAGTTCTAAGGGTG 57.949 34.615 0.00 0.00 0.00 4.61
47 48 8.520351 GTTGTAATAAATTGCAGTTCTAAGGGT 58.480 33.333 0.00 0.00 34.01 4.34
48 49 8.519526 TGTTGTAATAAATTGCAGTTCTAAGGG 58.480 33.333 0.00 0.00 34.01 3.95
54 55 9.289303 CCACTATGTTGTAATAAATTGCAGTTC 57.711 33.333 0.00 0.00 34.01 3.01
55 56 9.019656 TCCACTATGTTGTAATAAATTGCAGTT 57.980 29.630 0.00 0.00 34.01 3.16
56 57 8.574251 TCCACTATGTTGTAATAAATTGCAGT 57.426 30.769 0.00 0.00 34.01 4.40
57 58 9.289303 GTTCCACTATGTTGTAATAAATTGCAG 57.711 33.333 0.00 0.00 34.01 4.41
58 59 8.247562 GGTTCCACTATGTTGTAATAAATTGCA 58.752 33.333 0.00 0.00 0.00 4.08
59 60 8.247562 TGGTTCCACTATGTTGTAATAAATTGC 58.752 33.333 0.00 0.00 0.00 3.56
60 61 9.567848 GTGGTTCCACTATGTTGTAATAAATTG 57.432 33.333 13.97 0.00 34.42 2.32
61 62 9.528489 AGTGGTTCCACTATGTTGTAATAAATT 57.472 29.630 21.13 0.00 44.42 1.82
62 63 8.956426 CAGTGGTTCCACTATGTTGTAATAAAT 58.044 33.333 21.86 0.00 44.45 1.40
63 64 7.094549 GCAGTGGTTCCACTATGTTGTAATAAA 60.095 37.037 21.86 0.00 44.45 1.40
64 65 6.373216 GCAGTGGTTCCACTATGTTGTAATAA 59.627 38.462 21.86 0.00 44.45 1.40
65 66 5.878116 GCAGTGGTTCCACTATGTTGTAATA 59.122 40.000 21.86 0.00 44.45 0.98
66 67 4.700213 GCAGTGGTTCCACTATGTTGTAAT 59.300 41.667 21.86 0.00 44.45 1.89
67 68 4.069304 GCAGTGGTTCCACTATGTTGTAA 58.931 43.478 21.86 0.00 44.45 2.41
68 69 3.071747 TGCAGTGGTTCCACTATGTTGTA 59.928 43.478 21.86 9.00 44.45 2.41
69 70 2.158682 TGCAGTGGTTCCACTATGTTGT 60.159 45.455 21.86 0.00 44.45 3.32
70 71 2.485426 CTGCAGTGGTTCCACTATGTTG 59.515 50.000 21.86 12.56 44.45 3.33
71 72 2.371841 TCTGCAGTGGTTCCACTATGTT 59.628 45.455 21.86 0.00 44.45 2.71
72 73 1.977854 TCTGCAGTGGTTCCACTATGT 59.022 47.619 21.86 0.24 44.45 2.29
73 74 2.744202 GTTCTGCAGTGGTTCCACTATG 59.256 50.000 21.86 13.82 44.45 2.23
74 75 2.371841 TGTTCTGCAGTGGTTCCACTAT 59.628 45.455 21.86 1.30 44.45 2.12
75 76 1.765904 TGTTCTGCAGTGGTTCCACTA 59.234 47.619 21.86 8.86 44.45 2.74
76 77 0.546122 TGTTCTGCAGTGGTTCCACT 59.454 50.000 17.56 17.56 46.85 4.00
77 78 1.065551 GTTGTTCTGCAGTGGTTCCAC 59.934 52.381 14.67 13.45 37.23 4.02
78 79 1.064758 AGTTGTTCTGCAGTGGTTCCA 60.065 47.619 14.67 0.00 0.00 3.53
79 80 1.604278 GAGTTGTTCTGCAGTGGTTCC 59.396 52.381 14.67 0.00 0.00 3.62
80 81 2.288666 TGAGTTGTTCTGCAGTGGTTC 58.711 47.619 14.67 6.23 0.00 3.62
81 82 2.418368 TGAGTTGTTCTGCAGTGGTT 57.582 45.000 14.67 0.00 0.00 3.67
82 83 2.418368 TTGAGTTGTTCTGCAGTGGT 57.582 45.000 14.67 0.00 0.00 4.16
83 84 2.227388 GGATTGAGTTGTTCTGCAGTGG 59.773 50.000 14.67 0.00 0.00 4.00
84 85 2.227388 GGGATTGAGTTGTTCTGCAGTG 59.773 50.000 14.67 0.00 0.00 3.66
85 86 2.107204 AGGGATTGAGTTGTTCTGCAGT 59.893 45.455 14.67 0.00 0.00 4.40
86 87 2.787994 AGGGATTGAGTTGTTCTGCAG 58.212 47.619 7.63 7.63 0.00 4.41
87 88 2.957402 AGGGATTGAGTTGTTCTGCA 57.043 45.000 0.00 0.00 0.00 4.41
88 89 4.327680 AGTTAGGGATTGAGTTGTTCTGC 58.672 43.478 0.00 0.00 0.00 4.26
89 90 5.551233 TGAGTTAGGGATTGAGTTGTTCTG 58.449 41.667 0.00 0.00 0.00 3.02
90 91 5.825593 TGAGTTAGGGATTGAGTTGTTCT 57.174 39.130 0.00 0.00 0.00 3.01
91 92 5.181433 GGTTGAGTTAGGGATTGAGTTGTTC 59.819 44.000 0.00 0.00 0.00 3.18
92 93 5.070685 GGTTGAGTTAGGGATTGAGTTGTT 58.929 41.667 0.00 0.00 0.00 2.83
93 94 4.104102 TGGTTGAGTTAGGGATTGAGTTGT 59.896 41.667 0.00 0.00 0.00 3.32
94 95 4.455877 GTGGTTGAGTTAGGGATTGAGTTG 59.544 45.833 0.00 0.00 0.00 3.16
95 96 4.351111 AGTGGTTGAGTTAGGGATTGAGTT 59.649 41.667 0.00 0.00 0.00 3.01
96 97 3.910627 AGTGGTTGAGTTAGGGATTGAGT 59.089 43.478 0.00 0.00 0.00 3.41
97 98 4.256920 CAGTGGTTGAGTTAGGGATTGAG 58.743 47.826 0.00 0.00 0.00 3.02
98 99 3.009033 CCAGTGGTTGAGTTAGGGATTGA 59.991 47.826 0.00 0.00 0.00 2.57
118 119 2.668632 GCGTCCACAGGATTCCCA 59.331 61.111 0.00 0.00 32.73 4.37
153 154 2.039084 GGGAAGTCATTGTCACTGGAGT 59.961 50.000 0.00 0.00 0.00 3.85
162 163 0.991920 ACGGATGGGGAAGTCATTGT 59.008 50.000 0.00 0.00 0.00 2.71
174 175 0.588252 GCCAATCGATTCACGGATGG 59.412 55.000 15.28 10.68 44.54 3.51
176 177 3.006859 TCATAGCCAATCGATTCACGGAT 59.993 43.478 15.28 11.94 42.82 4.18
178 179 2.754472 TCATAGCCAATCGATTCACGG 58.246 47.619 7.92 8.15 42.82 4.94
186 187 2.668457 GCCGAGTTATCATAGCCAATCG 59.332 50.000 0.00 0.00 0.00 3.34
188 189 3.769739 TGCCGAGTTATCATAGCCAAT 57.230 42.857 0.00 0.00 0.00 3.16
197 198 3.601443 AGGAGCATATGCCGAGTTATC 57.399 47.619 23.96 12.59 43.38 1.75
252 253 2.550830 ATAGCCCAAGTAAGCATCCG 57.449 50.000 0.00 0.00 0.00 4.18
277 278 8.221251 TCCATGTTATATTGGCCTACAACATTA 58.779 33.333 15.95 8.64 42.94 1.90
307 308 3.846023 GCGGTGCATTGATAAACTCATCG 60.846 47.826 0.00 0.00 32.72 3.84
316 317 5.070770 AGAATTTTTGCGGTGCATTGATA 57.929 34.783 0.00 0.00 38.76 2.15
322 323 1.686052 AGGAAGAATTTTTGCGGTGCA 59.314 42.857 0.00 0.00 36.47 4.57
327 328 2.295909 TCCCACAGGAAGAATTTTTGCG 59.704 45.455 0.00 0.00 40.08 4.85
345 346 6.335471 TGCATCAATATCATCAACATTCCC 57.665 37.500 0.00 0.00 0.00 3.97
372 373 6.716628 ACTGGCATCTAAAGAAGTCATTCAAA 59.283 34.615 0.00 0.00 37.94 2.69
373 374 6.240894 ACTGGCATCTAAAGAAGTCATTCAA 58.759 36.000 0.00 0.00 37.94 2.69
484 485 7.530010 AGCATGTTGATATGTTTATTATCGCC 58.470 34.615 0.00 0.00 0.00 5.54
489 490 9.797642 ATCCTGAGCATGTTGATATGTTTATTA 57.202 29.630 0.00 0.00 0.00 0.98
501 502 2.295349 GCCCAATATCCTGAGCATGTTG 59.705 50.000 0.00 0.00 0.00 3.33
502 503 2.590821 GCCCAATATCCTGAGCATGTT 58.409 47.619 0.00 0.00 0.00 2.71
503 504 1.202976 GGCCCAATATCCTGAGCATGT 60.203 52.381 0.00 0.00 0.00 3.21
514 515 5.760484 AAACAAACTTCATGGCCCAATAT 57.240 34.783 0.00 0.00 0.00 1.28
542 543 8.516234 ACGGTGCAATAAAAATTAGTATTGTCA 58.484 29.630 16.54 13.37 39.09 3.58
565 566 9.329913 CTAACTAAATCAAAATGAAGAACACGG 57.670 33.333 0.00 0.00 0.00 4.94
599 600 6.743575 AAAATAGCACGCTTCTTACTGAAT 57.256 33.333 0.00 0.00 33.71 2.57
602 603 5.927030 TGAAAAATAGCACGCTTCTTACTG 58.073 37.500 0.00 0.00 0.00 2.74
608 609 2.908626 CGGTTGAAAAATAGCACGCTTC 59.091 45.455 0.00 0.00 0.00 3.86
613 614 4.798387 CCAATAGCGGTTGAAAAATAGCAC 59.202 41.667 0.00 0.00 0.00 4.40
617 618 6.016192 TGTTCACCAATAGCGGTTGAAAAATA 60.016 34.615 0.00 0.00 37.07 1.40
619 620 4.098044 TGTTCACCAATAGCGGTTGAAAAA 59.902 37.500 0.00 0.00 37.07 1.94
658 659 9.927668 CTTTAAATAGGTGAAACATGGTTGAAT 57.072 29.630 0.00 0.00 39.98 2.57
741 742 5.677567 AGGTCCCGACGTATGATAATTTTT 58.322 37.500 0.00 0.00 0.00 1.94
742 743 5.070047 AGAGGTCCCGACGTATGATAATTTT 59.930 40.000 0.00 0.00 0.00 1.82
743 744 4.587684 AGAGGTCCCGACGTATGATAATTT 59.412 41.667 0.00 0.00 0.00 1.82
744 745 4.150359 AGAGGTCCCGACGTATGATAATT 58.850 43.478 0.00 0.00 0.00 1.40
745 746 3.764218 AGAGGTCCCGACGTATGATAAT 58.236 45.455 0.00 0.00 0.00 1.28
746 747 3.219176 AGAGGTCCCGACGTATGATAA 57.781 47.619 0.00 0.00 0.00 1.75
747 748 2.945080 AGAGGTCCCGACGTATGATA 57.055 50.000 0.00 0.00 0.00 2.15
749 750 1.843368 AAAGAGGTCCCGACGTATGA 58.157 50.000 0.00 0.00 0.00 2.15
750 751 2.543238 GCTAAAGAGGTCCCGACGTATG 60.543 54.545 0.00 0.00 0.00 2.39
775 1551 8.010733 TCTGTTTTTCTTTCTTCATCACCATT 57.989 30.769 0.00 0.00 0.00 3.16
841 1618 4.613925 TCACTCTCAACTCAAATGCTCT 57.386 40.909 0.00 0.00 0.00 4.09
867 1644 2.555757 CTCCTTTTCACTCTTGGGCTTG 59.444 50.000 0.00 0.00 0.00 4.01
879 1656 0.856982 TTTGGCCCCTCTCCTTTTCA 59.143 50.000 0.00 0.00 0.00 2.69
901 1678 1.138859 GGGCTCAGTTTTGCTTGGTTT 59.861 47.619 0.00 0.00 0.00 3.27
2045 2829 4.671590 TCCCAGTCGTCGAGGGCA 62.672 66.667 12.79 2.19 42.52 5.36
2537 3321 2.289694 GGTGTACACATCTGGAAGCACT 60.290 50.000 26.51 0.00 0.00 4.40
3371 4173 0.958091 TTGATTGTTGCGGTTGAGGG 59.042 50.000 0.00 0.00 0.00 4.30
3520 4352 3.812019 GCTGCTGCGCTTGCTGAT 61.812 61.111 26.46 0.00 39.69 2.90
3642 4624 4.043200 GGGCTGCTGCGTTTGGTC 62.043 66.667 9.65 0.00 40.82 4.02
3701 4683 0.248580 CTGTTTGTTGCGCTTGCTGA 60.249 50.000 9.73 0.00 40.12 4.26
3704 4686 1.950630 CCCTGTTTGTTGCGCTTGC 60.951 57.895 9.73 0.00 39.78 4.01
3707 4689 0.881118 CATACCCTGTTTGTTGCGCT 59.119 50.000 9.73 0.00 0.00 5.92
3708 4690 0.109319 CCATACCCTGTTTGTTGCGC 60.109 55.000 0.00 0.00 0.00 6.09
3709 4691 0.109319 GCCATACCCTGTTTGTTGCG 60.109 55.000 0.00 0.00 0.00 4.85
3710 4692 1.202348 GAGCCATACCCTGTTTGTTGC 59.798 52.381 0.00 0.00 0.00 4.17
3711 4693 2.749621 GAGAGCCATACCCTGTTTGTTG 59.250 50.000 0.00 0.00 0.00 3.33
3712 4694 2.375174 TGAGAGCCATACCCTGTTTGTT 59.625 45.455 0.00 0.00 0.00 2.83
3713 4695 1.985159 TGAGAGCCATACCCTGTTTGT 59.015 47.619 0.00 0.00 0.00 2.83
3714 4696 2.636830 CTGAGAGCCATACCCTGTTTG 58.363 52.381 0.00 0.00 0.00 2.93
3715 4697 1.065126 GCTGAGAGCCATACCCTGTTT 60.065 52.381 0.00 0.00 34.48 2.83
3716 4698 0.543749 GCTGAGAGCCATACCCTGTT 59.456 55.000 0.00 0.00 34.48 3.16
3717 4699 0.618680 TGCTGAGAGCCATACCCTGT 60.619 55.000 0.00 0.00 41.51 4.00
3718 4700 0.543277 TTGCTGAGAGCCATACCCTG 59.457 55.000 0.00 0.00 41.51 4.45
3719 4701 1.065126 GTTTGCTGAGAGCCATACCCT 60.065 52.381 0.00 0.00 41.51 4.34
3720 4702 1.383523 GTTTGCTGAGAGCCATACCC 58.616 55.000 0.00 0.00 41.51 3.69
3721 4703 1.009829 CGTTTGCTGAGAGCCATACC 58.990 55.000 0.00 0.00 41.51 2.73
3722 4704 0.375106 GCGTTTGCTGAGAGCCATAC 59.625 55.000 0.00 0.00 41.51 2.39
3723 4705 0.036483 TGCGTTTGCTGAGAGCCATA 60.036 50.000 0.00 0.00 41.51 2.74
3724 4706 1.302752 TGCGTTTGCTGAGAGCCAT 60.303 52.632 0.00 0.00 41.51 4.40
3725 4707 1.962822 CTGCGTTTGCTGAGAGCCA 60.963 57.895 0.00 0.00 41.51 4.75
3726 4708 2.866028 CTGCGTTTGCTGAGAGCC 59.134 61.111 0.00 0.00 41.51 4.70
3727 4709 2.175322 GCTGCGTTTGCTGAGAGC 59.825 61.111 0.00 0.00 42.14 4.09
3728 4710 1.496393 CTGCTGCGTTTGCTGAGAG 59.504 57.895 0.00 0.00 42.14 3.20
3729 4711 2.610694 GCTGCTGCGTTTGCTGAGA 61.611 57.895 0.00 0.00 42.14 3.27
3738 4720 1.746615 CATAACCTGGCTGCTGCGT 60.747 57.895 9.65 0.00 40.82 5.24
3975 5020 1.331214 CCAAAAGGTGGCTGTGATGT 58.669 50.000 0.00 0.00 41.72 3.06
4023 5068 1.226435 GTAGAGTCCGAGCACTGCG 60.226 63.158 0.00 0.00 0.00 5.18
4098 5143 2.945668 GCTGAGTGTCAACCTTTTGTCT 59.054 45.455 0.00 0.00 34.02 3.41
4655 5703 5.770417 CCTATACTAGACCAAAGTTAGCCG 58.230 45.833 0.00 0.00 0.00 5.52
4702 5750 5.926663 AGATCAACTCATAGTGCATGTGAT 58.073 37.500 0.00 0.00 33.06 3.06
4825 5873 9.434420 TGCCTGATTAAGATAAACAAAATTTGG 57.566 29.630 10.71 0.00 34.12 3.28
4849 5897 8.763356 CAATCTCTTAGTTACTGATGAATCTGC 58.237 37.037 0.00 0.00 0.00 4.26
4991 6040 1.759445 CTATGTGAGGACCTGACCTGG 59.241 57.143 8.76 0.00 40.73 4.45
5009 6058 8.383374 AGAAAAGGGGTTGTACATACATACTA 57.617 34.615 0.00 0.00 35.89 1.82
5043 6092 8.363390 CAAAGTGAGAAGGATATGTATAGCAGA 58.637 37.037 0.00 0.00 0.00 4.26
5062 6111 6.563422 GCATTGCCAACTATTATCAAAGTGA 58.437 36.000 0.00 0.00 0.00 3.41
5212 6261 6.436843 TCATCATCATCATCTATGCATTGC 57.563 37.500 3.54 0.46 35.38 3.56
5213 6262 8.213518 TCATCATCATCATCATCTATGCATTG 57.786 34.615 3.54 2.26 35.38 2.82
5214 6263 8.844244 CATCATCATCATCATCATCTATGCATT 58.156 33.333 3.54 0.00 35.38 3.56
5216 6265 6.767902 CCATCATCATCATCATCATCTATGCA 59.232 38.462 0.00 0.00 35.38 3.96
5217 6266 6.768381 ACCATCATCATCATCATCATCTATGC 59.232 38.462 0.00 0.00 35.38 3.14
5218 6267 7.987458 TCACCATCATCATCATCATCATCTATG 59.013 37.037 0.00 0.00 36.88 2.23
5219 6268 8.090788 TCACCATCATCATCATCATCATCTAT 57.909 34.615 0.00 0.00 0.00 1.98
5220 6269 7.490657 TCACCATCATCATCATCATCATCTA 57.509 36.000 0.00 0.00 0.00 1.98
5222 6271 8.910351 ATATCACCATCATCATCATCATCATC 57.090 34.615 0.00 0.00 0.00 2.92
5224 6273 7.092623 TGGATATCACCATCATCATCATCATCA 60.093 37.037 4.83 0.00 34.77 3.07
5225 6274 7.280356 TGGATATCACCATCATCATCATCATC 58.720 38.462 4.83 0.00 34.77 2.92
5226 6275 7.208064 TGGATATCACCATCATCATCATCAT 57.792 36.000 4.83 0.00 34.77 2.45
5227 6276 6.630203 TGGATATCACCATCATCATCATCA 57.370 37.500 4.83 0.00 34.77 3.07


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

AutoCloner maintained by Alex Coulton.