Multiple sequence alignment - TraesCS2A01G486500

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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 TraesCS2A01G486500 chr2A 100.000 3810 0 0 1 3810 721651928 721655737 0.000000e+00 7036.0
1 TraesCS2A01G486500 chr2D 96.169 1514 42 6 773 2275 586902723 586904231 0.000000e+00 2460.0
2 TraesCS2A01G486500 chr2D 95.699 837 29 6 2340 3176 586904205 586905034 0.000000e+00 1339.0
3 TraesCS2A01G486500 chr2D 91.837 637 49 1 3177 3810 586904999 586905635 0.000000e+00 885.0
4 TraesCS2A01G486500 chr2D 88.268 537 41 10 248 777 349161301 349160780 1.160000e-174 623.0
5 TraesCS2A01G486500 chr2D 87.616 541 40 10 248 781 349158413 349157893 1.510000e-168 603.0
6 TraesCS2A01G486500 chr2D 82.031 128 17 5 3048 3174 344444333 344444211 1.870000e-18 104.0
7 TraesCS2A01G486500 chr2D 84.946 93 12 2 3042 3133 151431684 151431775 4.050000e-15 93.5
8 TraesCS2A01G486500 chr2B 95.756 1508 51 6 774 2275 708384767 708386267 0.000000e+00 2418.0
9 TraesCS2A01G486500 chr2B 91.616 1491 104 10 2335 3810 708386236 708387720 0.000000e+00 2041.0
10 TraesCS2A01G486500 chr2B 91.358 81 6 1 2267 2346 220825865 220825945 4.020000e-20 110.0
11 TraesCS2A01G486500 chr4D 87.132 816 47 17 1 779 210629007 210628213 0.000000e+00 872.0
12 TraesCS2A01G486500 chr4D 87.145 809 48 14 1 775 210631964 210631178 0.000000e+00 867.0
13 TraesCS2A01G486500 chr1D 85.172 816 56 22 1 777 141849963 141850752 0.000000e+00 776.0
14 TraesCS2A01G486500 chr1D 75.430 407 80 16 3228 3617 4003508 4003105 3.020000e-41 180.0
15 TraesCS2A01G486500 chr1D 95.775 71 3 0 2274 2344 30673403 30673473 8.650000e-22 115.0
16 TraesCS2A01G486500 chr1D 82.308 130 21 2 3048 3176 276504566 276504438 1.120000e-20 111.0
17 TraesCS2A01G486500 chr4A 89.482 637 29 10 1 601 76952367 76953001 0.000000e+00 771.0
18 TraesCS2A01G486500 chr4A 77.191 719 108 32 82 777 119295230 119295915 6.010000e-98 368.0
19 TraesCS2A01G486500 chr4A 75.875 514 101 17 3235 3728 598286947 598287457 1.370000e-59 241.0
20 TraesCS2A01G486500 chr4A 71.566 415 87 17 3338 3729 44977684 44978090 2.440000e-12 84.2
21 TraesCS2A01G486500 chr7B 87.112 644 60 16 145 777 304981333 304981964 0.000000e+00 708.0
22 TraesCS2A01G486500 chr1B 85.491 641 64 18 145 777 657971998 657972617 3.210000e-180 641.0
23 TraesCS2A01G486500 chr1B 84.891 642 69 14 145 778 657974862 657975483 1.160000e-174 623.0
24 TraesCS2A01G486500 chr1B 81.804 643 50 28 1 601 493855495 493854878 9.580000e-131 477.0
25 TraesCS2A01G486500 chr1A 83.807 704 73 21 87 777 61654114 61653439 6.950000e-177 630.0
26 TraesCS2A01G486500 chr1A 75.048 517 97 24 3228 3724 585344540 585345044 1.070000e-50 211.0
27 TraesCS2A01G486500 chr1A 95.775 71 3 0 2274 2344 58286504 58286574 8.650000e-22 115.0
28 TraesCS2A01G486500 chr4B 83.835 532 42 16 248 777 500075511 500076000 2.070000e-127 466.0
29 TraesCS2A01G486500 chr4B 95.833 72 2 1 2274 2344 535337144 535337215 8.650000e-22 115.0
30 TraesCS2A01G486500 chr3A 78.311 438 77 16 3176 3599 648851172 648851605 2.260000e-67 267.0
31 TraesCS2A01G486500 chr3A 97.222 36 1 0 3096 3131 745268664 745268629 1.140000e-05 62.1
32 TraesCS2A01G486500 chr6B 82.927 246 15 7 1 222 382765681 382765923 3.000000e-46 196.0
33 TraesCS2A01G486500 chr6B 88.889 81 3 2 703 777 382767238 382767318 1.130000e-15 95.3
34 TraesCS2A01G486500 chr3B 77.778 315 55 12 3338 3645 479550065 479550371 3.020000e-41 180.0
35 TraesCS2A01G486500 chr5D 77.011 261 44 13 3280 3530 84204051 84203797 6.640000e-28 135.0
36 TraesCS2A01G486500 chrUn 97.183 71 2 0 2274 2344 143844412 143844342 1.860000e-23 121.0
37 TraesCS2A01G486500 chr7D 97.183 71 2 0 2274 2344 114820221 114820151 1.860000e-23 121.0
38 TraesCS2A01G486500 chr7D 95.775 71 3 0 2274 2344 35304205 35304275 8.650000e-22 115.0
39 TraesCS2A01G486500 chr7D 95.775 71 3 0 2274 2344 131639143 131639213 8.650000e-22 115.0
40 TraesCS2A01G486500 chr5B 92.683 82 4 2 2261 2342 696221946 696221867 2.400000e-22 117.0
41 TraesCS2A01G486500 chr3D 72.235 425 96 17 3177 3594 500412521 500412930 1.120000e-20 111.0
42 TraesCS2A01G486500 chr3D 83.929 112 16 2 3048 3159 598343432 598343323 5.210000e-19 106.0
43 TraesCS2A01G486500 chr6A 79.167 120 9 12 3048 3165 352669798 352669693 6.830000e-08 69.4


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 TraesCS2A01G486500 chr2A 721651928 721655737 3809 False 7036.000000 7036 100.000000 1 3810 1 chr2A.!!$F1 3809
1 TraesCS2A01G486500 chr2D 586902723 586905635 2912 False 1561.333333 2460 94.568333 773 3810 3 chr2D.!!$F2 3037
2 TraesCS2A01G486500 chr2D 349157893 349161301 3408 True 613.000000 623 87.942000 248 781 2 chr2D.!!$R2 533
3 TraesCS2A01G486500 chr2B 708384767 708387720 2953 False 2229.500000 2418 93.686000 774 3810 2 chr2B.!!$F2 3036
4 TraesCS2A01G486500 chr4D 210628213 210631964 3751 True 869.500000 872 87.138500 1 779 2 chr4D.!!$R1 778
5 TraesCS2A01G486500 chr1D 141849963 141850752 789 False 776.000000 776 85.172000 1 777 1 chr1D.!!$F2 776
6 TraesCS2A01G486500 chr4A 76952367 76953001 634 False 771.000000 771 89.482000 1 601 1 chr4A.!!$F2 600
7 TraesCS2A01G486500 chr4A 119295230 119295915 685 False 368.000000 368 77.191000 82 777 1 chr4A.!!$F3 695
8 TraesCS2A01G486500 chr4A 598286947 598287457 510 False 241.000000 241 75.875000 3235 3728 1 chr4A.!!$F4 493
9 TraesCS2A01G486500 chr7B 304981333 304981964 631 False 708.000000 708 87.112000 145 777 1 chr7B.!!$F1 632
10 TraesCS2A01G486500 chr1B 657971998 657975483 3485 False 632.000000 641 85.191000 145 778 2 chr1B.!!$F1 633
11 TraesCS2A01G486500 chr1B 493854878 493855495 617 True 477.000000 477 81.804000 1 601 1 chr1B.!!$R1 600
12 TraesCS2A01G486500 chr1A 61653439 61654114 675 True 630.000000 630 83.807000 87 777 1 chr1A.!!$R1 690
13 TraesCS2A01G486500 chr1A 585344540 585345044 504 False 211.000000 211 75.048000 3228 3724 1 chr1A.!!$F2 496

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
641 3665 0.036022 TCCACAATCGCACATCCACA 59.964 50.0 0.0 0.0 0.0 4.17 F
1891 7885 0.529833 AGAGATCTGCACCGTCACTG 59.470 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 8294 0.033228 CTTCTAGATGCAGAGGCCGG 59.967 60.000 0.0 0.0 40.13 6.13 R
3639 9656 1.066422 GCTCGACGCATGAGGATGA 59.934 57.895 0.0 0.0 38.92 2.92 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
64 65 7.339177 TGAATCCCAGAATCAATCATCCTAT 57.661 36.000 0.00 0.00 0.00 2.57
107 132 7.079475 ACGTGTGTCCTTTTTATTTATTTCCG 58.921 34.615 0.00 0.00 0.00 4.30
189 224 6.601332 AGTCCTCATGTTTTTCTTAGTCCAA 58.399 36.000 0.00 0.00 0.00 3.53
378 419 3.850923 GGCGACGTCGATTGTCAA 58.149 55.556 39.74 0.00 43.02 3.18
379 420 1.702299 GGCGACGTCGATTGTCAAG 59.298 57.895 39.74 9.55 43.02 3.02
380 421 1.683790 GGCGACGTCGATTGTCAAGG 61.684 60.000 39.74 8.77 43.02 3.61
381 422 1.702299 CGACGTCGATTGTCAAGGC 59.298 57.895 33.35 0.00 43.02 4.35
382 423 1.702299 GACGTCGATTGTCAAGGCG 59.298 57.895 13.89 4.70 36.37 5.52
403 451 3.664025 CGCAAGTTTCGGTTTGATTCTTC 59.336 43.478 0.00 0.00 0.00 2.87
474 526 8.031864 CCACTAGTGCTTATTATCCATCTACTG 58.968 40.741 17.86 0.00 0.00 2.74
505 3502 3.192230 CGTTGCCGCCGCTAATCA 61.192 61.111 0.00 0.00 35.36 2.57
631 3655 2.601804 TCACGTACACATCCACAATCG 58.398 47.619 0.00 0.00 0.00 3.34
632 3656 1.060553 CACGTACACATCCACAATCGC 59.939 52.381 0.00 0.00 0.00 4.58
633 3657 1.337354 ACGTACACATCCACAATCGCA 60.337 47.619 0.00 0.00 0.00 5.10
634 3658 1.060553 CGTACACATCCACAATCGCAC 59.939 52.381 0.00 0.00 0.00 5.34
635 3659 2.073056 GTACACATCCACAATCGCACA 58.927 47.619 0.00 0.00 0.00 4.57
636 3660 1.825090 ACACATCCACAATCGCACAT 58.175 45.000 0.00 0.00 0.00 3.21
637 3661 1.739466 ACACATCCACAATCGCACATC 59.261 47.619 0.00 0.00 0.00 3.06
638 3662 1.064505 CACATCCACAATCGCACATCC 59.935 52.381 0.00 0.00 0.00 3.51
639 3663 1.339920 ACATCCACAATCGCACATCCA 60.340 47.619 0.00 0.00 0.00 3.41
640 3664 1.064505 CATCCACAATCGCACATCCAC 59.935 52.381 0.00 0.00 0.00 4.02
641 3665 0.036022 TCCACAATCGCACATCCACA 59.964 50.000 0.00 0.00 0.00 4.17
642 3666 0.880441 CCACAATCGCACATCCACAA 59.120 50.000 0.00 0.00 0.00 3.33
643 3667 1.473677 CCACAATCGCACATCCACAAT 59.526 47.619 0.00 0.00 0.00 2.71
644 3668 2.478370 CCACAATCGCACATCCACAATC 60.478 50.000 0.00 0.00 0.00 2.67
645 3669 1.398041 ACAATCGCACATCCACAATCG 59.602 47.619 0.00 0.00 0.00 3.34
650 3674 0.804364 GCACATCCACAATCGCTTCA 59.196 50.000 0.00 0.00 0.00 3.02
662 3686 4.278170 ACAATCGCTTCAGATTCCAACAAA 59.722 37.500 0.00 0.00 38.66 2.83
665 3689 5.452078 TCGCTTCAGATTCCAACAAATTT 57.548 34.783 0.00 0.00 0.00 1.82
666 3690 5.841810 TCGCTTCAGATTCCAACAAATTTT 58.158 33.333 0.00 0.00 0.00 1.82
677 3701 9.444534 GATTCCAACAAATTTTATTGCGTTTTT 57.555 25.926 6.46 0.00 33.52 1.94
895 6880 5.181056 TGCCATATAAATGTGGAATAGCACG 59.819 40.000 9.69 0.00 41.09 5.34
1039 7024 9.062524 ACTGTAAAGATTGTAACATTAGCACAA 57.937 29.630 0.00 0.00 36.66 3.33
1187 7172 9.944376 TGATAATTATGACCCTATTTCTACAGC 57.056 33.333 1.78 0.00 0.00 4.40
1278 7263 3.804036 TGATCACCACAACTCTTTTCGT 58.196 40.909 0.00 0.00 0.00 3.85
1280 7265 2.980568 TCACCACAACTCTTTTCGTGT 58.019 42.857 0.00 0.00 0.00 4.49
1353 7338 7.041508 GCAATTCACTATATAGCTGATATGGCC 60.042 40.741 9.78 0.00 33.34 5.36
1486 7475 8.948631 ATGAACTATTAGGTGTACATGTGAAG 57.051 34.615 9.11 0.00 0.00 3.02
1891 7885 0.529833 AGAGATCTGCACCGTCACTG 59.470 55.000 0.00 0.00 0.00 3.66
2001 7995 3.947612 AGTGTTCGTCCTAGGGATCTA 57.052 47.619 9.46 0.00 32.73 1.98
2298 8294 5.461516 TTTTATAAAAGGAGGAGGACCCC 57.538 43.478 6.54 0.00 36.73 4.95
2299 8295 1.908643 ATAAAAGGAGGAGGACCCCC 58.091 55.000 0.00 0.00 36.73 5.40
2300 8296 0.619543 TAAAAGGAGGAGGACCCCCG 60.620 60.000 0.00 0.00 37.58 5.73
2301 8297 3.945064 AAAGGAGGAGGACCCCCGG 62.945 68.421 0.00 0.00 37.58 5.73
2313 8309 2.844362 CCCCGGCCTCTGCATCTA 60.844 66.667 0.00 0.00 40.13 1.98
2314 8310 2.739784 CCCGGCCTCTGCATCTAG 59.260 66.667 0.00 0.00 40.13 2.43
2315 8311 1.834378 CCCGGCCTCTGCATCTAGA 60.834 63.158 0.00 0.00 40.13 2.43
2316 8312 1.402896 CCCGGCCTCTGCATCTAGAA 61.403 60.000 0.00 0.00 40.13 2.10
2317 8313 0.033228 CCGGCCTCTGCATCTAGAAG 59.967 60.000 0.00 0.00 40.13 2.85
2318 8314 1.035923 CGGCCTCTGCATCTAGAAGA 58.964 55.000 0.00 0.00 40.13 2.87
2319 8315 1.617850 CGGCCTCTGCATCTAGAAGAT 59.382 52.381 0.00 0.00 40.13 2.40
2329 8325 4.485024 CATCTAGAAGATGCATGCAACC 57.515 45.455 26.68 19.07 44.69 3.77
2330 8326 3.632643 TCTAGAAGATGCATGCAACCA 57.367 42.857 26.68 0.00 0.00 3.67
2331 8327 3.273434 TCTAGAAGATGCATGCAACCAC 58.727 45.455 26.68 17.68 0.00 4.16
2332 8328 2.211250 AGAAGATGCATGCAACCACT 57.789 45.000 26.68 19.57 0.00 4.00
2333 8329 2.522185 AGAAGATGCATGCAACCACTT 58.478 42.857 26.68 24.16 0.00 3.16
2334 8330 2.895404 AGAAGATGCATGCAACCACTTT 59.105 40.909 26.68 12.11 0.00 2.66
2335 8331 4.081406 AGAAGATGCATGCAACCACTTTA 58.919 39.130 26.68 0.00 0.00 1.85
2336 8332 4.708421 AGAAGATGCATGCAACCACTTTAT 59.292 37.500 26.68 15.59 0.00 1.40
2337 8333 5.186409 AGAAGATGCATGCAACCACTTTATT 59.814 36.000 26.68 9.75 0.00 1.40
2338 8334 6.377996 AGAAGATGCATGCAACCACTTTATTA 59.622 34.615 26.68 0.00 0.00 0.98
2339 8335 6.528537 AGATGCATGCAACCACTTTATTAA 57.471 33.333 26.68 0.00 0.00 1.40
2340 8336 7.116075 AGATGCATGCAACCACTTTATTAAT 57.884 32.000 26.68 1.78 0.00 1.40
2341 8337 7.558604 AGATGCATGCAACCACTTTATTAATT 58.441 30.769 26.68 1.01 0.00 1.40
2342 8338 8.694540 AGATGCATGCAACCACTTTATTAATTA 58.305 29.630 26.68 0.00 0.00 1.40
2343 8339 9.480053 GATGCATGCAACCACTTTATTAATTAT 57.520 29.630 26.68 0.14 0.00 1.28
2344 8340 8.870160 TGCATGCAACCACTTTATTAATTATC 57.130 30.769 20.30 0.00 0.00 1.75
2345 8341 8.473219 TGCATGCAACCACTTTATTAATTATCA 58.527 29.630 20.30 0.00 0.00 2.15
2346 8342 8.971321 GCATGCAACCACTTTATTAATTATCAG 58.029 33.333 14.21 0.00 0.00 2.90
2350 8346 9.185192 GCAACCACTTTATTAATTATCAGATGC 57.815 33.333 0.00 0.00 0.00 3.91
2444 8440 6.377146 AGGGTGTCAATTGTGGAATTACATAC 59.623 38.462 5.13 0.00 30.20 2.39
2665 8661 6.985117 TCTTTGCATGCTATGGATATTTTCC 58.015 36.000 20.33 0.00 45.69 3.13
2773 8769 4.823442 TGTAATTATGCTCCATGGCTCTTG 59.177 41.667 6.96 0.00 0.00 3.02
2949 8945 9.482627 TGTACATTGTTTATTGAAACCCAATTC 57.517 29.630 0.00 0.00 42.55 2.17
3033 9029 3.521727 ACCCAGTCTCACCACTAAAGAT 58.478 45.455 0.00 0.00 0.00 2.40
3043 9039 9.469807 GTCTCACCACTAAAGATTAGACATATG 57.530 37.037 0.00 0.00 33.86 1.78
3123 9131 3.243704 GCACACAACCAACACCAATACAT 60.244 43.478 0.00 0.00 0.00 2.29
3139 9147 6.651643 ACCAATACATACACACACAAATACGT 59.348 34.615 0.00 0.00 0.00 3.57
3160 9168 5.405571 ACGTCAACAACTAGCAAAGTCATAG 59.594 40.000 0.00 0.00 37.50 2.23
3165 9173 8.097038 TCAACAACTAGCAAAGTCATAGAAGAT 58.903 33.333 0.00 0.00 37.50 2.40
3273 9282 2.222213 TCCACGATTGCAAACTACAACG 59.778 45.455 1.71 3.94 0.00 4.10
3307 9316 3.558418 CGCATCAATCATCTCATGACACA 59.442 43.478 0.00 0.00 43.01 3.72
3390 9403 2.054021 TCACTGGATCCAACCACAAGA 58.946 47.619 17.00 3.37 35.91 3.02
3520 9536 1.011595 TCAGACCTAGGCTTCCTCCT 58.988 55.000 9.30 0.00 40.21 3.69
3556 9573 0.322816 ATCCATGACAGCACCACCAC 60.323 55.000 0.00 0.00 0.00 4.16
3599 9616 3.379372 CGCCATCACTTTTTCATGATCCT 59.621 43.478 0.00 0.00 33.18 3.24
3639 9656 1.303561 ACCATCGCCACTGCACAAT 60.304 52.632 0.00 0.00 37.32 2.71
3685 9711 4.984295 TCCATCTCACCATCAAAGTCAAA 58.016 39.130 0.00 0.00 0.00 2.69
3741 9767 4.429212 CGGTGATCACGGCCGTCA 62.429 66.667 31.80 19.53 40.53 4.35
3742 9768 2.813908 GGTGATCACGGCCGTCAC 60.814 66.667 30.38 30.38 41.07 3.67
3744 9770 1.666553 GTGATCACGGCCGTCACAA 60.667 57.895 32.13 19.17 41.35 3.33
3797 9823 1.072332 CACCACCATCCGGTTGACA 59.928 57.895 14.27 0.00 46.31 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.098914 ACTTGCATGGAAAGGTGTTCTA 57.901 40.909 0.00 0.00 0.00 2.10
17 18 3.377798 TCACGTACGTATACTTGCATGGA 59.622 43.478 22.34 6.58 32.04 3.41
64 65 1.202371 CGTATCCGGCTTGCACTCTTA 60.202 52.381 0.00 0.00 0.00 2.10
246 281 7.650504 GCCAAAACTAAAACCTAACCTTTACAG 59.349 37.037 0.00 0.00 0.00 2.74
279 318 5.411831 TCACTAGATGCATGTTCTGAGTT 57.588 39.130 2.46 0.00 0.00 3.01
343 382 3.119673 TCGCCGAAACACATGCAATTATT 60.120 39.130 0.00 0.00 0.00 1.40
376 417 0.248866 AAACCGAAACTTGCGCCTTG 60.249 50.000 4.18 0.00 0.00 3.61
377 418 0.248866 CAAACCGAAACTTGCGCCTT 60.249 50.000 4.18 0.00 0.00 4.35
378 419 1.098712 TCAAACCGAAACTTGCGCCT 61.099 50.000 4.18 0.00 0.00 5.52
379 420 0.039527 ATCAAACCGAAACTTGCGCC 60.040 50.000 4.18 0.00 0.00 6.53
380 421 1.713932 GAATCAAACCGAAACTTGCGC 59.286 47.619 0.00 0.00 0.00 6.09
381 422 3.268013 AGAATCAAACCGAAACTTGCG 57.732 42.857 0.00 0.00 0.00 4.85
382 423 4.606961 TGAAGAATCAAACCGAAACTTGC 58.393 39.130 0.00 0.00 30.99 4.01
403 451 5.895636 AGCTAGATCGATCCTTGTAGATG 57.104 43.478 21.66 3.41 0.00 2.90
474 526 0.582005 GCAACGGCGATGGAGTAATC 59.418 55.000 16.62 0.00 0.00 1.75
505 3502 2.513738 TGCAGGGGATTAAGCTAATGGT 59.486 45.455 0.00 0.00 0.00 3.55
631 3655 0.804364 TGAAGCGATTGTGGATGTGC 59.196 50.000 0.00 0.00 0.00 4.57
632 3656 2.349590 TCTGAAGCGATTGTGGATGTG 58.650 47.619 0.00 0.00 0.00 3.21
633 3657 2.768253 TCTGAAGCGATTGTGGATGT 57.232 45.000 0.00 0.00 0.00 3.06
634 3658 3.003068 GGAATCTGAAGCGATTGTGGATG 59.997 47.826 0.00 0.00 33.96 3.51
635 3659 3.209410 GGAATCTGAAGCGATTGTGGAT 58.791 45.455 0.00 0.00 33.96 3.41
636 3660 2.027285 TGGAATCTGAAGCGATTGTGGA 60.027 45.455 0.00 0.00 33.96 4.02
637 3661 2.358957 TGGAATCTGAAGCGATTGTGG 58.641 47.619 0.00 0.00 33.96 4.17
638 3662 3.189080 TGTTGGAATCTGAAGCGATTGTG 59.811 43.478 0.00 0.00 33.96 3.33
639 3663 3.411446 TGTTGGAATCTGAAGCGATTGT 58.589 40.909 0.00 0.00 33.96 2.71
640 3664 4.424061 TTGTTGGAATCTGAAGCGATTG 57.576 40.909 0.00 0.00 33.96 2.67
641 3665 5.649782 ATTTGTTGGAATCTGAAGCGATT 57.350 34.783 0.00 0.00 36.38 3.34
642 3666 5.649782 AATTTGTTGGAATCTGAAGCGAT 57.350 34.783 0.00 0.00 0.00 4.58
643 3667 5.452078 AAATTTGTTGGAATCTGAAGCGA 57.548 34.783 0.00 0.00 0.00 4.93
644 3668 7.816945 ATAAAATTTGTTGGAATCTGAAGCG 57.183 32.000 0.00 0.00 0.00 4.68
645 3669 7.959109 GCAATAAAATTTGTTGGAATCTGAAGC 59.041 33.333 15.20 0.00 33.05 3.86
650 3674 7.961325 AACGCAATAAAATTTGTTGGAATCT 57.039 28.000 15.20 0.00 33.05 2.40
690 3714 5.355350 ACAATTGTACTAGCAGAAGCAATCC 59.645 40.000 9.97 0.00 45.49 3.01
843 6828 4.754114 GCCAAAATGTTTTAAGCATGACCA 59.246 37.500 0.00 0.00 32.18 4.02
844 6829 4.996758 AGCCAAAATGTTTTAAGCATGACC 59.003 37.500 0.00 0.00 33.49 4.02
895 6880 4.747810 ACACTAATGCTTTAATGGCTTGC 58.252 39.130 5.89 0.00 0.00 4.01
1039 7024 3.487563 TGCGCGATCGAATACTATCAT 57.512 42.857 21.57 0.00 38.10 2.45
1187 7172 7.715657 TGATTTCAGATTATTTGGGGATTTCG 58.284 34.615 0.00 0.00 0.00 3.46
1224 7209 8.579850 TTTTATCAAATCTCATAGCAGGTGTT 57.420 30.769 0.00 0.00 0.00 3.32
1306 7291 0.322456 TTGTCGGCTTGATGGGAAGG 60.322 55.000 0.00 0.00 0.00 3.46
1353 7338 8.370493 ACATAAGAATATGAATTCACCTGTCG 57.630 34.615 11.07 0.00 43.44 4.35
1472 7461 8.773404 ACTATCTTAAACTTCACATGTACACC 57.227 34.615 0.00 0.00 0.00 4.16
1878 7872 0.738762 CTCCATCAGTGACGGTGCAG 60.739 60.000 4.93 0.00 0.00 4.41
2275 8271 5.834460 GGGGTCCTCCTCCTTTTATAAAAA 58.166 41.667 11.62 0.00 35.33 1.94
2276 8272 5.461516 GGGGTCCTCCTCCTTTTATAAAA 57.538 43.478 10.16 10.16 35.33 1.52
2296 8292 2.844362 TAGATGCAGAGGCCGGGG 60.844 66.667 2.18 0.00 40.13 5.73
2297 8293 1.402896 TTCTAGATGCAGAGGCCGGG 61.403 60.000 2.18 0.00 40.13 5.73
2298 8294 0.033228 CTTCTAGATGCAGAGGCCGG 59.967 60.000 0.00 0.00 40.13 6.13
2299 8295 1.035923 TCTTCTAGATGCAGAGGCCG 58.964 55.000 0.00 0.00 40.13 6.13
2300 8296 3.042871 CATCTTCTAGATGCAGAGGCC 57.957 52.381 0.00 0.00 44.69 5.19
2309 8305 3.881688 GTGGTTGCATGCATCTTCTAGAT 59.118 43.478 23.37 0.00 34.74 1.98
2310 8306 3.054875 AGTGGTTGCATGCATCTTCTAGA 60.055 43.478 23.37 0.00 0.00 2.43
2311 8307 3.276857 AGTGGTTGCATGCATCTTCTAG 58.723 45.455 23.37 0.00 0.00 2.43
2312 8308 3.354948 AGTGGTTGCATGCATCTTCTA 57.645 42.857 23.37 1.46 0.00 2.10
2313 8309 2.211250 AGTGGTTGCATGCATCTTCT 57.789 45.000 23.37 18.06 0.00 2.85
2314 8310 3.308438 AAAGTGGTTGCATGCATCTTC 57.692 42.857 23.37 16.28 0.00 2.87
2315 8311 5.410355 AATAAAGTGGTTGCATGCATCTT 57.590 34.783 23.37 18.95 0.00 2.40
2316 8312 6.528537 TTAATAAAGTGGTTGCATGCATCT 57.471 33.333 23.37 14.35 0.00 2.90
2317 8313 7.775397 AATTAATAAAGTGGTTGCATGCATC 57.225 32.000 23.37 20.66 0.00 3.91
2318 8314 9.480053 GATAATTAATAAAGTGGTTGCATGCAT 57.520 29.630 23.37 7.12 0.00 3.96
2319 8315 8.473219 TGATAATTAATAAAGTGGTTGCATGCA 58.527 29.630 18.46 18.46 0.00 3.96
2320 8316 8.870160 TGATAATTAATAAAGTGGTTGCATGC 57.130 30.769 11.82 11.82 0.00 4.06
2324 8320 9.185192 GCATCTGATAATTAATAAAGTGGTTGC 57.815 33.333 0.00 0.00 0.00 4.17
2773 8769 4.444056 GCATGTTGTGTTGTGTATGTTTCC 59.556 41.667 0.00 0.00 0.00 3.13
3043 9039 6.103997 TCGTGTTTGTATCCTCTTGATAACC 58.896 40.000 0.00 0.00 37.69 2.85
3123 9131 5.581479 AGTTGTTGACGTATTTGTGTGTGTA 59.419 36.000 0.00 0.00 0.00 2.90
3139 9147 7.441836 TCTTCTATGACTTTGCTAGTTGTTGA 58.558 34.615 0.00 0.00 37.17 3.18
3249 9257 3.006940 TGTAGTTTGCAATCGTGGATCC 58.993 45.455 4.20 4.20 0.00 3.36
3273 9282 6.706716 AGATGATTGATGCGGATATGATCATC 59.293 38.462 25.42 25.42 44.15 2.92
3307 9316 7.950512 TGTTCAATAATCTTGTTGTCCATGTT 58.049 30.769 0.00 0.00 32.07 2.71
3340 9352 3.714798 ACTTGAGTGTTGTTCCCTTCCTA 59.285 43.478 0.00 0.00 0.00 2.94
3390 9403 5.014123 TCAGGGTGAAAACCTAGATTCATGT 59.986 40.000 8.26 0.00 37.82 3.21
3475 9491 2.810870 TTGGTTATACCCGGCAATGT 57.189 45.000 0.00 0.00 37.50 2.71
3520 9536 3.402095 ATCCGGTCTCGAGCTCCGA 62.402 63.158 33.71 24.44 46.05 4.55
3599 9616 2.673893 CGCACATCACAGGTAGTTGCTA 60.674 50.000 0.00 0.00 0.00 3.49
3630 9647 2.022195 GCATGAGGATGATTGTGCAGT 58.978 47.619 0.00 0.00 33.09 4.40
3639 9656 1.066422 GCTCGACGCATGAGGATGA 59.934 57.895 0.00 0.00 38.92 2.92
3685 9711 4.828387 GGTTTATCTCTCTAGATCCGGTGT 59.172 45.833 0.00 0.00 41.71 4.16
3741 9767 1.276622 ATGACCTCCTACGGCTTTGT 58.723 50.000 0.00 0.00 0.00 2.83
3742 9768 2.403252 AATGACCTCCTACGGCTTTG 57.597 50.000 0.00 0.00 0.00 2.77
3744 9770 2.431057 CTGTAATGACCTCCTACGGCTT 59.569 50.000 0.00 0.00 0.00 4.35
3759 9785 4.760204 GGTGGCTTCAAACAGTACTGTAAT 59.240 41.667 28.13 17.37 44.13 1.89
3769 9795 1.327303 GATGGTGGTGGCTTCAAACA 58.673 50.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.