Multiple sequence alignment - TraesCS2B01G221500

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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 TraesCS2B01G221500 chr2B 100.000 4256 0 0 1 4256 211376146 211380401 0.000000e+00 7860.0
1 TraesCS2B01G221500 chr2D 92.970 2219 104 13 1889 4090 153806472 153808655 0.000000e+00 3186.0
2 TraesCS2B01G221500 chr2D 90.904 1693 94 25 237 1902 153804785 153806444 0.000000e+00 2218.0
3 TraesCS2B01G221500 chr2D 91.071 168 13 2 4086 4253 153810400 153810565 4.280000e-55 226.0
4 TraesCS2B01G221500 chr2A 94.767 1758 74 7 1888 3630 147462314 147460560 0.000000e+00 2721.0
5 TraesCS2B01G221500 chr2A 91.951 1702 79 25 238 1903 147464019 147462340 0.000000e+00 2331.0
6 TraesCS2B01G221500 chr2A 92.326 430 32 1 3686 4114 147460425 147459996 1.010000e-170 610.0
7 TraesCS2B01G221500 chr2A 86.207 232 19 11 16 240 147464425 147464200 5.500000e-59 239.0
8 TraesCS2B01G221500 chr2A 89.655 87 9 0 3634 3720 147460518 147460432 1.250000e-20 111.0
9 TraesCS2B01G221500 chr2A 81.429 140 19 6 3495 3630 279056120 279056256 1.620000e-19 108.0
10 TraesCS2B01G221500 chr7A 81.429 140 19 6 3495 3630 243645596 243645732 1.620000e-19 108.0
11 TraesCS2B01G221500 chr7A 87.500 48 6 0 4015 4062 240527612 240527565 5.940000e-04 56.5
12 TraesCS2B01G221500 chr3A 81.429 140 19 5 3495 3630 102531187 102531051 1.620000e-19 108.0
13 TraesCS2B01G221500 chr3A 98.039 51 1 0 4064 4114 640948227 640948277 5.860000e-14 89.8
14 TraesCS2B01G221500 chr3A 97.959 49 1 0 4066 4114 641008526 641008574 7.580000e-13 86.1
15 TraesCS2B01G221500 chr5A 80.851 141 17 9 3496 3630 647108594 647108458 7.530000e-18 102.0
16 TraesCS2B01G221500 chr4A 84.466 103 12 3 3495 3594 539749848 539749747 9.740000e-17 99.0
17 TraesCS2B01G221500 chr4A 78.571 140 24 5 3495 3630 176859818 176859955 2.110000e-13 87.9
18 TraesCS2B01G221500 chr4A 94.545 55 2 1 4060 4114 67142905 67142852 2.730000e-12 84.2
19 TraesCS2B01G221500 chr4D 81.818 121 17 4 3496 3613 57080429 57080547 3.500000e-16 97.1
20 TraesCS2B01G221500 chr7D 91.803 61 5 0 3700 3760 162835494 162835434 7.580000e-13 86.1
21 TraesCS2B01G221500 chr5D 80.952 105 19 1 3637 3740 485938038 485937934 9.810000e-12 82.4
22 TraesCS2B01G221500 chr3B 80.189 106 16 4 3638 3741 526121062 526120960 1.640000e-09 75.0
23 TraesCS2B01G221500 chr3B 93.878 49 3 0 4064 4112 663083266 663083314 1.640000e-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 TraesCS2B01G221500 chr2B 211376146 211380401 4255 False 7860.000000 7860 100.000000 1 4256 1 chr2B.!!$F1 4255
1 TraesCS2B01G221500 chr2D 153804785 153810565 5780 False 1876.666667 3186 91.648333 237 4253 3 chr2D.!!$F1 4016
2 TraesCS2B01G221500 chr2A 147459996 147464425 4429 True 1202.400000 2721 90.981200 16 4114 5 chr2A.!!$R1 4098

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
895 1126 0.036022 AGAGCCACTTGGAGTCTTGC 59.964 55.0 0.0 0.0 37.39 4.01 F
2173 2461 0.108138 CATCAACGACCTCACCTCCC 60.108 60.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 2463 0.178301 GGTAGAAGCCTTCCGGGAAG 59.822 60.0 26.57 26.57 39.17 3.46 R
4172 6296 0.321653 CACTTCCCACCACAGCTACC 60.322 60.0 0.00 0.00 0.00 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
123 126 6.750148 TGTTCTAATGCGGGTTAATGTTTTT 58.250 32.000 0.00 0.00 0.00 1.94
126 129 6.982852 TCTAATGCGGGTTAATGTTTTTCAA 58.017 32.000 0.00 0.00 0.00 2.69
127 130 7.434492 TCTAATGCGGGTTAATGTTTTTCAAA 58.566 30.769 0.00 0.00 0.00 2.69
128 131 8.091449 TCTAATGCGGGTTAATGTTTTTCAAAT 58.909 29.630 0.00 0.00 0.00 2.32
129 132 7.503521 AATGCGGGTTAATGTTTTTCAAATT 57.496 28.000 0.00 0.00 0.00 1.82
132 135 7.189512 TGCGGGTTAATGTTTTTCAAATTTTG 58.810 30.769 2.59 2.59 0.00 2.44
133 136 6.141527 GCGGGTTAATGTTTTTCAAATTTTGC 59.858 34.615 4.19 0.00 0.00 3.68
259 447 3.121030 CCTGAAGGCTTGTCCGCG 61.121 66.667 3.46 0.00 40.77 6.46
292 480 4.742201 GGGCGTCTGCTGAAGCGA 62.742 66.667 21.31 0.00 46.18 4.93
296 484 1.803519 CGTCTGCTGAAGCGAGACC 60.804 63.158 19.82 9.58 45.83 3.85
327 516 2.028190 CGCAGGCGAGACATAGGG 59.972 66.667 8.15 0.00 42.83 3.53
347 536 2.681591 GCCCCTCTTTACCACCCC 59.318 66.667 0.00 0.00 0.00 4.95
356 545 1.735571 CTTTACCACCCCAAATCGACG 59.264 52.381 0.00 0.00 0.00 5.12
357 546 0.686224 TTACCACCCCAAATCGACGT 59.314 50.000 0.00 0.00 0.00 4.34
358 547 0.037139 TACCACCCCAAATCGACGTG 60.037 55.000 0.00 0.00 0.00 4.49
359 548 1.302192 CCACCCCAAATCGACGTGT 60.302 57.895 0.00 0.00 0.00 4.49
363 560 1.345415 ACCCCAAATCGACGTGTAACT 59.655 47.619 0.00 0.00 31.75 2.24
372 569 7.799447 CCAAATCGACGTGTAACTATTTTTCAA 59.201 33.333 0.00 0.00 31.75 2.69
377 574 6.476243 ACGTGTAACTATTTTTCAATCGCT 57.524 33.333 0.00 0.00 31.75 4.93
383 580 8.346300 TGTAACTATTTTTCAATCGCTTGTGAA 58.654 29.630 0.00 0.00 33.87 3.18
384 581 9.176181 GTAACTATTTTTCAATCGCTTGTGAAA 57.824 29.630 0.00 2.66 40.93 2.69
400 597 2.023673 TGAAATAGCAAATCCGGGCAG 58.976 47.619 0.00 0.00 0.00 4.85
401 598 0.746659 AAATAGCAAATCCGGGCAGC 59.253 50.000 0.00 0.67 0.00 5.25
402 599 0.395586 AATAGCAAATCCGGGCAGCA 60.396 50.000 0.00 0.00 0.00 4.41
403 600 0.820891 ATAGCAAATCCGGGCAGCAG 60.821 55.000 0.00 0.00 0.00 4.24
405 602 2.123428 GCAAATCCGGGCAGCAGAT 61.123 57.895 0.00 0.00 0.00 2.90
406 603 2.028130 CAAATCCGGGCAGCAGATC 58.972 57.895 0.00 0.00 0.00 2.75
407 604 0.749091 CAAATCCGGGCAGCAGATCA 60.749 55.000 0.00 0.00 0.00 2.92
409 606 0.536687 AATCCGGGCAGCAGATCATG 60.537 55.000 0.00 0.00 0.00 3.07
430 629 2.146342 AGAATCAAACACAGCCGTGAG 58.854 47.619 7.16 0.00 46.80 3.51
437 636 1.329256 ACACAGCCGTGAGAGTAGTT 58.671 50.000 7.16 0.00 46.80 2.24
445 644 4.156373 AGCCGTGAGAGTAGTTAAAGACTC 59.844 45.833 9.14 9.14 42.06 3.36
454 653 3.305398 AGTTAAAGACTCTGGTGCTCG 57.695 47.619 0.00 0.00 31.20 5.03
455 654 2.628657 AGTTAAAGACTCTGGTGCTCGT 59.371 45.455 0.00 0.00 31.20 4.18
462 661 1.299541 CTCTGGTGCTCGTTTTGTGT 58.700 50.000 0.00 0.00 0.00 3.72
482 696 4.035208 GTGTCTGTTTCGTTCTGAACCAAT 59.965 41.667 14.48 0.00 35.97 3.16
491 705 4.222145 TCGTTCTGAACCAATAAGGCTAGT 59.778 41.667 14.48 0.00 43.14 2.57
510 724 6.350194 GGCTAGTTGCTAAAATAAAGCCAAGT 60.350 38.462 5.20 0.00 42.39 3.16
548 762 0.253894 TATGGCTCATGCACACTGCT 59.746 50.000 0.00 0.00 45.31 4.24
549 763 1.030488 ATGGCTCATGCACACTGCTC 61.030 55.000 0.00 0.00 45.31 4.26
550 764 2.747822 GGCTCATGCACACTGCTCG 61.748 63.158 0.00 0.00 45.31 5.03
551 765 1.739196 GCTCATGCACACTGCTCGA 60.739 57.895 0.00 0.00 45.31 4.04
552 766 1.694018 GCTCATGCACACTGCTCGAG 61.694 60.000 8.45 8.45 45.31 4.04
553 767 1.694018 CTCATGCACACTGCTCGAGC 61.694 60.000 30.42 30.42 45.31 5.03
554 768 2.435586 ATGCACACTGCTCGAGCC 60.436 61.111 33.23 17.63 45.31 4.70
569 783 2.045926 GCCCTACTGCACCTGTGG 60.046 66.667 0.00 0.00 0.00 4.17
583 797 3.093057 ACCTGTGGCGGCATTAAAATAA 58.907 40.909 17.19 0.00 0.00 1.40
603 817 3.921119 ACCGACGTGTTATAGTGTTCA 57.079 42.857 0.00 0.00 0.00 3.18
665 884 2.367567 TGCCTGATTAGGGATTACGTCC 59.632 50.000 5.56 0.00 44.75 4.79
680 899 1.340889 ACGTCCGCCTAAACTTGTACA 59.659 47.619 0.00 0.00 0.00 2.90
682 901 1.730612 GTCCGCCTAAACTTGTACAGC 59.269 52.381 0.00 0.00 0.00 4.40
735 954 3.536956 TCCACTACATCTTTTAGGCCG 57.463 47.619 0.00 0.00 0.00 6.13
817 1048 4.430007 GCCGGCATCGTATATGAGATAAA 58.570 43.478 24.80 0.00 33.95 1.40
890 1121 1.072965 CCTGAAAGAGCCACTTGGAGT 59.927 52.381 0.00 0.00 38.98 3.85
895 1126 0.036022 AGAGCCACTTGGAGTCTTGC 59.964 55.000 0.00 0.00 37.39 4.01
933 1164 3.236618 GACAACAACACGCCGAGCC 62.237 63.158 0.00 0.00 0.00 4.70
962 1193 3.902150 TGATCACATAGCTAAGCTACGC 58.098 45.455 0.00 0.00 44.24 4.42
999 1234 2.497107 GCACATTGATGCATACACCC 57.503 50.000 0.00 0.00 45.39 4.61
1000 1235 1.750206 GCACATTGATGCATACACCCA 59.250 47.619 0.00 0.00 45.39 4.51
1001 1236 2.166050 GCACATTGATGCATACACCCAA 59.834 45.455 0.00 0.00 45.39 4.12
1002 1237 3.368220 GCACATTGATGCATACACCCAAA 60.368 43.478 0.00 0.00 45.39 3.28
1037 1272 1.089481 CAATCATACGGTGCAGCGGT 61.089 55.000 37.73 25.83 34.85 5.68
1603 1838 2.332654 GCCTTTGTACCAGCACCGG 61.333 63.158 0.00 0.00 0.00 5.28
1618 1853 3.933722 CGGGGCCTGATGCTCGAT 61.934 66.667 6.48 0.00 43.53 3.59
1645 1880 1.509923 GACCTACTTCCCCGTCGTG 59.490 63.158 0.00 0.00 0.00 4.35
1861 2096 4.246206 CGCGTCGTGCCGGAGATA 62.246 66.667 5.05 0.00 42.08 1.98
1867 2102 2.353607 GTGCCGGAGATAGACGCG 60.354 66.667 5.05 3.53 0.00 6.01
1876 2111 1.177256 AGATAGACGCGCCGGGTAAT 61.177 55.000 6.84 3.95 0.00 1.89
1877 2112 0.319297 GATAGACGCGCCGGGTAATT 60.319 55.000 6.84 0.00 0.00 1.40
1878 2113 0.961019 ATAGACGCGCCGGGTAATTA 59.039 50.000 6.84 1.00 0.00 1.40
1879 2114 0.743688 TAGACGCGCCGGGTAATTAA 59.256 50.000 6.84 0.00 0.00 1.40
1883 2118 1.354155 GCGCCGGGTAATTAAGCAC 59.646 57.895 2.18 0.00 0.00 4.40
1916 2194 2.031870 GCTATTTTTCCCATTCGGCCT 58.968 47.619 0.00 0.00 0.00 5.19
1947 2225 2.193536 GCTGACACGGCCCAGTTTT 61.194 57.895 8.32 0.00 33.19 2.43
1956 2234 2.886523 ACGGCCCAGTTTTTAAGGTAAC 59.113 45.455 0.00 0.00 0.00 2.50
2143 2431 1.870055 GCCCAAGACGTACGAGGTGA 61.870 60.000 24.41 0.00 0.00 4.02
2146 2434 1.471287 CCAAGACGTACGAGGTGATGA 59.529 52.381 24.41 0.00 0.00 2.92
2164 2452 2.422597 TGACCAACATCATCAACGACC 58.577 47.619 0.00 0.00 0.00 4.79
2173 2461 0.108138 CATCAACGACCTCACCTCCC 60.108 60.000 0.00 0.00 0.00 4.30
2175 2463 0.898789 TCAACGACCTCACCTCCCTC 60.899 60.000 0.00 0.00 0.00 4.30
2184 2472 1.612442 CACCTCCCTCTTCCCGGAA 60.612 63.158 0.73 0.00 0.00 4.30
2337 2625 2.019951 CGTCGTGTCCAAGAACCGG 61.020 63.158 0.00 0.00 0.00 5.28
2371 2659 3.941657 GAGGACGTGCTGCTGGACC 62.942 68.421 16.62 0.00 0.00 4.46
2493 2781 4.933064 CGCGCCATCGTCTCCTCC 62.933 72.222 0.00 0.00 38.14 4.30
2496 2784 4.933064 GCCATCGTCTCCTCCGCG 62.933 72.222 0.00 0.00 0.00 6.46
2647 2935 0.025384 CGACTACGACATCGCGTACA 59.975 55.000 5.77 0.00 43.61 2.90
2648 2936 1.527591 CGACTACGACATCGCGTACAA 60.528 52.381 5.77 0.00 43.61 2.41
2649 2937 2.713011 GACTACGACATCGCGTACAAT 58.287 47.619 5.77 0.00 43.61 2.71
2661 2949 0.457166 CGTACAATCTCACCGCGGAA 60.457 55.000 35.90 18.67 0.00 4.30
2938 3226 1.078426 GACATGGTTCGGTGAGGGG 60.078 63.158 0.00 0.00 0.00 4.79
2986 3274 2.331451 GTTGCGTGTGCCAACTCC 59.669 61.111 0.00 0.00 41.78 3.85
2999 3290 2.280628 CCAACTCCGAGCATTACCTTC 58.719 52.381 0.00 0.00 0.00 3.46
3075 3366 3.682377 GGTGTTTCCTTTTTGTTGTGTGG 59.318 43.478 0.00 0.00 0.00 4.17
3192 3483 3.744660 CAGTTGTACCTTCCTCAAAGCT 58.255 45.455 0.00 0.00 33.29 3.74
3343 3636 8.506437 TCGCTTATAATTGCTTATTTGGAGATG 58.494 33.333 0.00 0.00 0.00 2.90
3361 3654 3.460648 GTCACATGGACAGTAGGGC 57.539 57.895 0.00 0.00 46.19 5.19
3366 3659 3.157087 CACATGGACAGTAGGGCTTTTT 58.843 45.455 0.00 0.00 0.00 1.94
3431 3724 1.022982 CACTGCAGCATGACATCGGT 61.023 55.000 15.27 0.00 39.69 4.69
3436 3729 1.466360 GCAGCATGACATCGGTTGAAC 60.466 52.381 0.00 0.00 39.69 3.18
3475 3769 0.168128 GGTGAAATGAACGCCGGAAG 59.832 55.000 5.05 0.00 0.00 3.46
3678 4010 6.085573 GCAATTAAACAACCCAAAATCATGC 58.914 36.000 0.00 0.00 0.00 4.06
3707 4039 9.171877 GATTGAGATGTTTTGACCTTCTAATCT 57.828 33.333 0.00 0.00 0.00 2.40
3748 4121 5.339990 CATGTTTTTAGAATCCCGCGAATT 58.660 37.500 8.23 7.09 0.00 2.17
3757 4130 0.539986 TCCCGCGAATTAAAGAGGCT 59.460 50.000 8.23 0.00 0.00 4.58
3832 4205 6.548321 ACTTCTTAAATGTGTGTGGGGATAA 58.452 36.000 0.00 0.00 0.00 1.75
3884 4257 7.383361 CGAATGTCCGCTTTCAATTTATTTTC 58.617 34.615 0.00 0.00 0.00 2.29
3917 4290 8.853345 CCGAACTATTCAAAACAATCAAAGATG 58.147 33.333 0.00 0.00 0.00 2.90
4044 4419 8.462589 AAATTTAGGGACAATTGCATTTTTGT 57.537 26.923 5.05 9.23 38.71 2.83
4118 6242 9.143631 CATCTAACAAATTCAGAAAATCAACCC 57.856 33.333 0.00 0.00 0.00 4.11
4121 6245 6.101650 ACAAATTCAGAAAATCAACCCCTC 57.898 37.500 0.00 0.00 0.00 4.30
4126 6250 5.789643 TCAGAAAATCAACCCCTCAAAAG 57.210 39.130 0.00 0.00 0.00 2.27
4128 6252 5.896678 TCAGAAAATCAACCCCTCAAAAGAA 59.103 36.000 0.00 0.00 0.00 2.52
4129 6253 6.382570 TCAGAAAATCAACCCCTCAAAAGAAA 59.617 34.615 0.00 0.00 0.00 2.52
4130 6254 6.479990 CAGAAAATCAACCCCTCAAAAGAAAC 59.520 38.462 0.00 0.00 0.00 2.78
4154 6278 6.042437 ACAAATTCAGAAAATCTCCAAAGGCT 59.958 34.615 0.00 0.00 0.00 4.58
4162 6286 2.806945 TCTCCAAAGGCTAATGTGGG 57.193 50.000 6.61 0.00 0.00 4.61
4171 6295 4.034285 AGGCTAATGTGGGTTATATGGC 57.966 45.455 0.00 0.00 0.00 4.40
4172 6296 2.747446 GGCTAATGTGGGTTATATGGCG 59.253 50.000 0.00 0.00 0.00 5.69
4177 6301 1.071071 TGTGGGTTATATGGCGGTAGC 59.929 52.381 0.00 0.00 44.18 3.58
4191 6315 0.321653 GGTAGCTGTGGTGGGAAGTG 60.322 60.000 0.00 0.00 0.00 3.16
4225 6349 3.195825 CGGTAGTTGGAGAGGAGTTTGAT 59.804 47.826 0.00 0.00 0.00 2.57
4241 6365 7.846823 AGGAGTTTGATCTAAGGGATTCTCTTA 59.153 37.037 5.88 5.88 34.33 2.10
4243 6367 7.493367 AGTTTGATCTAAGGGATTCTCTTACG 58.507 38.462 1.69 0.29 34.33 3.18
4253 6377 4.153117 GGGATTCTCTTACGCATGCTATTG 59.847 45.833 17.13 2.03 0.00 1.90
4254 6378 4.153117 GGATTCTCTTACGCATGCTATTGG 59.847 45.833 17.13 1.61 0.00 3.16
4255 6379 4.400529 TTCTCTTACGCATGCTATTGGA 57.599 40.909 17.13 6.60 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 8.590339 TGTTAAACGCGTATGAAAAATGTATC 57.410 30.769 14.46 0.00 0.00 2.24
88 90 4.262045 CCGCATTAGAACAATGTTAAACGC 59.738 41.667 0.00 0.26 0.00 4.84
242 430 3.121030 CGCGGACAAGCCTTCAGG 61.121 66.667 0.00 0.00 38.53 3.86
245 433 3.793144 CAGCGCGGACAAGCCTTC 61.793 66.667 8.83 0.00 0.00 3.46
279 467 0.457681 GAGGTCTCGCTTCAGCAGAC 60.458 60.000 16.71 16.71 42.70 3.51
281 469 1.153667 GGAGGTCTCGCTTCAGCAG 60.154 63.158 0.00 0.00 42.21 4.24
282 470 1.188219 AAGGAGGTCTCGCTTCAGCA 61.188 55.000 0.00 0.00 42.21 4.41
283 471 0.459411 GAAGGAGGTCTCGCTTCAGC 60.459 60.000 16.82 0.00 37.12 4.26
292 480 1.309499 CGCGAGACAGAAGGAGGTCT 61.309 60.000 0.00 0.00 46.51 3.85
296 484 1.515952 CTGCGCGAGACAGAAGGAG 60.516 63.158 12.10 0.00 37.41 3.69
327 516 2.437895 GTGGTAAAGAGGGGCGCC 60.438 66.667 21.18 21.18 0.00 6.53
347 536 8.702408 TTGAAAAATAGTTACACGTCGATTTG 57.298 30.769 0.00 0.00 0.00 2.32
356 545 7.801315 TCACAAGCGATTGAAAAATAGTTACAC 59.199 33.333 21.96 0.00 0.00 2.90
357 546 7.866729 TCACAAGCGATTGAAAAATAGTTACA 58.133 30.769 21.96 0.00 0.00 2.41
358 547 8.722342 TTCACAAGCGATTGAAAAATAGTTAC 57.278 30.769 21.96 0.00 0.00 2.50
359 548 9.906660 ATTTCACAAGCGATTGAAAAATAGTTA 57.093 25.926 21.96 0.00 43.20 2.24
363 560 8.026026 TGCTATTTCACAAGCGATTGAAAAATA 58.974 29.630 21.96 22.81 43.20 1.40
372 569 4.496341 CGGATTTGCTATTTCACAAGCGAT 60.496 41.667 0.00 0.00 41.77 4.58
377 574 2.165437 GCCCGGATTTGCTATTTCACAA 59.835 45.455 0.73 0.00 0.00 3.33
383 580 0.395586 TGCTGCCCGGATTTGCTATT 60.396 50.000 0.73 0.00 0.00 1.73
384 581 0.820891 CTGCTGCCCGGATTTGCTAT 60.821 55.000 0.73 0.00 0.00 2.97
400 597 5.556355 TGTGTTTGATTCTCATGATCTGC 57.444 39.130 0.00 0.00 0.00 4.26
401 598 5.448768 GGCTGTGTTTGATTCTCATGATCTG 60.449 44.000 0.00 0.00 0.00 2.90
402 599 4.639310 GGCTGTGTTTGATTCTCATGATCT 59.361 41.667 0.00 0.00 0.00 2.75
403 600 4.495349 CGGCTGTGTTTGATTCTCATGATC 60.495 45.833 0.00 0.00 0.00 2.92
405 602 2.743664 CGGCTGTGTTTGATTCTCATGA 59.256 45.455 0.00 0.00 0.00 3.07
406 603 2.485426 ACGGCTGTGTTTGATTCTCATG 59.515 45.455 0.00 0.00 0.00 3.07
407 604 2.485426 CACGGCTGTGTTTGATTCTCAT 59.515 45.455 17.96 0.00 41.34 2.90
409 606 2.143122 TCACGGCTGTGTTTGATTCTC 58.857 47.619 24.61 0.00 46.49 2.87
418 617 1.329256 AACTACTCTCACGGCTGTGT 58.671 50.000 24.61 8.61 46.49 3.72
430 629 5.394224 AGCACCAGAGTCTTTAACTACTC 57.606 43.478 7.90 7.90 42.02 2.59
437 636 3.746045 AAACGAGCACCAGAGTCTTTA 57.254 42.857 0.00 0.00 0.00 1.85
445 644 1.003545 CAGACACAAAACGAGCACCAG 60.004 52.381 0.00 0.00 0.00 4.00
446 645 1.013596 CAGACACAAAACGAGCACCA 58.986 50.000 0.00 0.00 0.00 4.17
447 646 1.014352 ACAGACACAAAACGAGCACC 58.986 50.000 0.00 0.00 0.00 5.01
448 647 2.825086 AACAGACACAAAACGAGCAC 57.175 45.000 0.00 0.00 0.00 4.40
449 648 2.222931 CGAAACAGACACAAAACGAGCA 60.223 45.455 0.00 0.00 0.00 4.26
454 653 4.965062 TCAGAACGAAACAGACACAAAAC 58.035 39.130 0.00 0.00 0.00 2.43
455 654 5.387279 GTTCAGAACGAAACAGACACAAAA 58.613 37.500 0.00 0.00 34.69 2.44
491 705 6.024552 CCAGACTTGGCTTTATTTTAGCAA 57.975 37.500 0.00 0.00 40.42 3.91
548 762 2.037367 AGGTGCAGTAGGGCTCGA 59.963 61.111 0.00 0.00 34.04 4.04
549 763 2.185350 CAGGTGCAGTAGGGCTCG 59.815 66.667 0.00 0.00 34.04 5.03
550 764 1.078848 CACAGGTGCAGTAGGGCTC 60.079 63.158 0.00 0.00 34.04 4.70
551 765 2.596851 CCACAGGTGCAGTAGGGCT 61.597 63.158 0.00 0.00 34.04 5.19
552 766 2.045926 CCACAGGTGCAGTAGGGC 60.046 66.667 0.00 0.00 0.00 5.19
553 767 2.045926 GCCACAGGTGCAGTAGGG 60.046 66.667 0.00 0.00 0.00 3.53
554 768 2.434884 CGCCACAGGTGCAGTAGG 60.435 66.667 0.00 0.00 0.00 3.18
569 783 2.223089 ACGTCGGTTATTTTAATGCCGC 60.223 45.455 12.38 8.65 37.81 6.53
583 797 3.568538 GTGAACACTATAACACGTCGGT 58.431 45.455 0.00 0.00 0.00 4.69
646 865 2.609737 GCGGACGTAATCCCTAATCAGG 60.610 54.545 0.00 0.00 46.04 3.86
665 884 6.040878 ACTAATAGCTGTACAAGTTTAGGCG 58.959 40.000 0.00 0.00 0.00 5.52
680 899 6.545298 ACGGCAGTAGTAGTTTACTAATAGCT 59.455 38.462 0.00 0.00 42.45 3.32
682 901 7.167136 GCAACGGCAGTAGTAGTTTACTAATAG 59.833 40.741 0.00 0.00 40.36 1.73
735 954 5.684550 ACACGTTTTCTATTGGGTTTCTC 57.315 39.130 0.00 0.00 0.00 2.87
817 1048 2.663852 CTCCGGTTTCGTGGCGTT 60.664 61.111 0.00 0.00 33.95 4.84
933 1164 2.216046 AGCTATGTGATCAACGGCATG 58.784 47.619 0.00 0.00 0.00 4.06
962 1193 8.729756 TCAATGTGCCATTCGATTTATATAAGG 58.270 33.333 0.00 0.00 0.00 2.69
1037 1272 1.250840 TTGGCTCGAGCTGCTCTGTA 61.251 55.000 34.46 11.25 41.70 2.74
1603 1838 1.004440 GGTATCGAGCATCAGGCCC 60.004 63.158 0.00 0.00 46.50 5.80
1618 1853 0.259938 GGAAGTAGGTCCTCCCGGTA 59.740 60.000 0.00 0.00 38.74 4.02
1861 2096 0.529119 CTTAATTACCCGGCGCGTCT 60.529 55.000 9.90 0.00 0.00 4.18
1867 2102 1.093496 AGCGTGCTTAATTACCCGGC 61.093 55.000 0.00 0.00 0.00 6.13
1876 2111 2.314647 GCCGTGTCAGCGTGCTTAA 61.315 57.895 0.00 0.00 0.00 1.85
1877 2112 2.736995 GCCGTGTCAGCGTGCTTA 60.737 61.111 0.00 0.00 0.00 3.09
1878 2113 4.609018 AGCCGTGTCAGCGTGCTT 62.609 61.111 0.00 0.00 35.85 3.91
1883 2118 1.361668 AAATAGCAGCCGTGTCAGCG 61.362 55.000 0.00 0.00 34.64 5.18
1947 2225 1.058284 ACTGGGCCGTGTTACCTTAA 58.942 50.000 0.00 0.00 0.00 1.85
1956 2234 1.875963 GTTCATCAACTGGGCCGTG 59.124 57.895 0.00 0.00 0.00 4.94
2143 2431 3.009723 GGTCGTTGATGATGTTGGTCAT 58.990 45.455 0.00 0.00 41.36 3.06
2146 2434 2.038426 TGAGGTCGTTGATGATGTTGGT 59.962 45.455 0.00 0.00 0.00 3.67
2164 2452 2.060980 CCGGGAAGAGGGAGGTGAG 61.061 68.421 0.00 0.00 0.00 3.51
2173 2461 1.137282 GTAGAAGCCTTCCGGGAAGAG 59.863 57.143 33.18 23.97 41.71 2.85
2175 2463 0.178301 GGTAGAAGCCTTCCGGGAAG 59.822 60.000 26.57 26.57 39.17 3.46
2184 2472 3.771160 CCGGCGTGGTAGAAGCCT 61.771 66.667 6.01 0.00 46.43 4.58
2217 2505 3.866582 GTCTCCCAGCATCCCGGG 61.867 72.222 16.85 16.85 44.60 5.73
2337 2625 1.004918 CTCCCAGAACACCACCGTC 60.005 63.158 0.00 0.00 0.00 4.79
2371 2659 1.784525 GAACTCACGTTCACCTCCAG 58.215 55.000 0.00 0.00 46.88 3.86
2493 2781 0.304098 CGAGGTAGTAGAAGGACGCG 59.696 60.000 3.53 3.53 0.00 6.01
2496 2784 2.355444 GCAGTCGAGGTAGTAGAAGGAC 59.645 54.545 0.00 0.00 0.00 3.85
2619 2907 0.602638 TGTCGTAGTCGTACACCCGT 60.603 55.000 0.00 0.00 38.33 5.28
2647 2935 1.517832 CCTCTTCCGCGGTGAGATT 59.482 57.895 34.67 0.00 0.00 2.40
2648 2936 3.082579 GCCTCTTCCGCGGTGAGAT 62.083 63.158 34.67 0.00 0.00 2.75
2649 2937 3.760035 GCCTCTTCCGCGGTGAGA 61.760 66.667 34.67 30.02 0.00 3.27
2661 2949 1.606531 GATGACCAGCTTGGCCTCT 59.393 57.895 3.32 0.00 42.67 3.69
2923 3211 3.728373 GGCCCCTCACCGAACCAT 61.728 66.667 0.00 0.00 0.00 3.55
2986 3274 5.934043 TGATATGAATGGAAGGTAATGCTCG 59.066 40.000 0.00 0.00 0.00 5.03
2999 3290 6.611381 AGTTTGACACGTTTGATATGAATGG 58.389 36.000 0.00 0.00 0.00 3.16
3049 3340 6.255453 CACACAACAAAAAGGAAACACCATAG 59.745 38.462 0.00 0.00 42.04 2.23
3075 3366 3.187700 CTGGTAGTATTCTCCGCACAAC 58.812 50.000 0.00 0.00 0.00 3.32
3192 3483 0.407918 GGGTCCCATGAAAAGGTCCA 59.592 55.000 1.78 0.00 0.00 4.02
3325 3618 6.839124 TGTGACATCTCCAAATAAGCAATT 57.161 33.333 0.00 0.00 0.00 2.32
3343 3636 0.905357 AGCCCTACTGTCCATGTGAC 59.095 55.000 7.22 7.22 44.72 3.67
3366 3659 1.530323 GAAGCTCCGTTGGGCTAAAA 58.470 50.000 0.00 0.00 37.87 1.52
3377 3670 1.593196 TCACAACAAAGGAAGCTCCG 58.407 50.000 0.00 0.00 42.75 4.63
3378 3671 3.569701 TCATTCACAACAAAGGAAGCTCC 59.430 43.478 0.00 0.00 36.58 4.70
3448 3741 2.095466 GCGTTCATTTCACCCGATTTCA 60.095 45.455 0.00 0.00 0.00 2.69
3451 3745 0.808755 GGCGTTCATTTCACCCGATT 59.191 50.000 0.00 0.00 0.00 3.34
3454 3748 2.478746 CGGCGTTCATTTCACCCG 59.521 61.111 0.00 0.00 0.00 5.28
3462 3756 3.322254 AGATATTCTCTTCCGGCGTTCAT 59.678 43.478 6.01 0.00 0.00 2.57
3623 3917 7.225011 AGGAAAAACAAAGGACTCTAAGTAGG 58.775 38.462 0.00 0.00 0.00 3.18
3678 4010 5.709164 AGAAGGTCAAAACATCTCAATCCTG 59.291 40.000 0.00 0.00 0.00 3.86
3748 4121 2.009774 GCGATTGCAAGAGCCTCTTTA 58.990 47.619 15.55 0.00 42.15 1.85
3784 4157 4.764308 TCCATTTTGATGATCCACGTTTCA 59.236 37.500 0.00 0.00 0.00 2.69
3789 4162 4.970662 AGTTCCATTTTGATGATCCACG 57.029 40.909 0.00 0.00 0.00 4.94
3851 4224 2.171725 GCGGACATTCGGTACCTGC 61.172 63.158 10.90 0.00 0.00 4.85
3884 4257 9.931210 GATTGTTTTGAATAGTTCGGGTATAAG 57.069 33.333 0.00 0.00 0.00 1.73
4044 4419 5.716228 TCAACACGTAGGTTCTAAATAGGGA 59.284 40.000 0.00 0.00 0.00 4.20
4050 4425 9.146984 CTCATATTTCAACACGTAGGTTCTAAA 57.853 33.333 0.00 0.00 0.00 1.85
4126 6250 8.768019 CCTTTGGAGATTTTCTGAATTTGTTTC 58.232 33.333 0.00 0.00 34.72 2.78
4128 6252 6.707608 GCCTTTGGAGATTTTCTGAATTTGTT 59.292 34.615 0.00 0.00 0.00 2.83
4129 6253 6.042437 AGCCTTTGGAGATTTTCTGAATTTGT 59.958 34.615 0.00 0.00 0.00 2.83
4130 6254 6.461640 AGCCTTTGGAGATTTTCTGAATTTG 58.538 36.000 0.00 0.00 0.00 2.32
4147 6271 5.278957 GCCATATAACCCACATTAGCCTTTG 60.279 44.000 0.00 0.00 0.00 2.77
4154 6278 4.563993 GCTACCGCCATATAACCCACATTA 60.564 45.833 0.00 0.00 0.00 1.90
4162 6286 2.224209 ACCACAGCTACCGCCATATAAC 60.224 50.000 0.00 0.00 36.60 1.89
4171 6295 1.079127 CTTCCCACCACAGCTACCG 60.079 63.158 0.00 0.00 0.00 4.02
4172 6296 0.321653 CACTTCCCACCACAGCTACC 60.322 60.000 0.00 0.00 0.00 3.18
4177 6301 1.002087 GGACTACACTTCCCACCACAG 59.998 57.143 0.00 0.00 0.00 3.66
4191 6315 2.363359 CCAACTACCGGTATGGGACTAC 59.637 54.545 21.96 0.00 44.64 2.73
4203 6327 2.561419 TCAAACTCCTCTCCAACTACCG 59.439 50.000 0.00 0.00 0.00 4.02
4225 6349 4.501571 GCATGCGTAAGAGAATCCCTTAGA 60.502 45.833 0.00 0.00 43.02 2.10


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

AutoCloner maintained by Alex Coulton.