Multiple sequence alignment - TraesCS4D01G281100

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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 TraesCS4D01G281100 chr4D 100.000 3289 0 0 1 3289 452311626 452314914 0.000000e+00 6074
1 TraesCS4D01G281100 chr4D 84.801 2316 264 43 986 3269 452383850 452386109 0.000000e+00 2246
2 TraesCS4D01G281100 chr4D 78.587 1387 193 53 933 2273 452548133 452549461 0.000000e+00 821
3 TraesCS4D01G281100 chr4D 79.915 936 127 32 2399 3286 452549955 452550877 5.990000e-177 630
4 TraesCS4D01G281100 chr4B 94.978 2549 95 18 762 3286 565526800 565529339 0.000000e+00 3967
5 TraesCS4D01G281100 chr4B 84.925 1393 171 19 986 2357 565602556 565603930 0.000000e+00 1373
6 TraesCS4D01G281100 chr4B 78.489 1390 202 50 923 2273 565733659 565734990 0.000000e+00 821
7 TraesCS4D01G281100 chr4B 90.302 629 41 9 759 1368 565525152 565525779 0.000000e+00 806
8 TraesCS4D01G281100 chr4B 86.233 523 60 5 2517 3030 565604046 565604565 1.030000e-154 556
9 TraesCS4D01G281100 chr4B 78.533 927 129 36 2399 3286 565735481 565736376 2.230000e-151 545
10 TraesCS4D01G281100 chr4A 83.768 1226 112 37 2067 3269 14738769 14737608 0.000000e+00 1081
11 TraesCS4D01G281100 chr4A 83.776 1017 127 20 995 1987 14744618 14743616 0.000000e+00 929
12 TraesCS4D01G281100 chr4A 78.923 1281 183 44 922 2165 14358984 14357754 0.000000e+00 789
13 TraesCS4D01G281100 chr4A 79.721 932 127 29 2409 3289 14357138 14356218 4.660000e-173 617
14 TraesCS4D01G281100 chr3A 78.449 877 167 17 926 1786 23670969 23670099 1.330000e-153 553
15 TraesCS4D01G281100 chr3A 76.844 881 177 21 931 1790 23691656 23690782 3.840000e-129 472
16 TraesCS4D01G281100 chr3A 76.760 895 177 23 916 1789 23700630 23699746 3.840000e-129 472
17 TraesCS4D01G281100 chr3D 78.723 799 157 9 1004 1792 13334650 13335445 3.760000e-144 521
18 TraesCS4D01G281100 chr7D 93.930 313 19 0 20 332 407271470 407271782 1.070000e-129 473
19 TraesCS4D01G281100 chr7D 93.038 316 22 0 20 335 407270012 407269697 2.310000e-126 462
20 TraesCS4D01G281100 chr7D 93.625 251 14 2 520 768 407272620 407272870 1.110000e-99 374
21 TraesCS4D01G281100 chr7D 96.512 86 3 0 360 445 4511732 4511647 3.420000e-30 143
22 TraesCS4D01G281100 chr7D 94.667 75 4 0 442 516 407272124 407272198 2.070000e-22 117
23 TraesCS4D01G281100 chr7D 93.333 75 5 0 442 516 407269358 407269284 9.650000e-21 111
24 TraesCS4D01G281100 chr1D 92.971 313 22 0 20 332 14665926 14666238 1.080000e-124 457
25 TraesCS4D01G281100 chr1D 94.239 243 11 3 518 758 14667076 14667317 5.180000e-98 368
26 TraesCS4D01G281100 chr1D 93.243 74 5 0 442 515 14666581 14666654 3.470000e-20 110
27 TraesCS4D01G281100 chr5D 88.718 195 20 2 474 666 520288098 520288292 1.530000e-58 237
28 TraesCS4D01G281100 chr5D 90.909 99 7 2 347 444 37920405 37920308 7.410000e-27 132
29 TraesCS4D01G281100 chr3B 95.455 88 4 0 358 445 75584740 75584827 1.230000e-29 141
30 TraesCS4D01G281100 chr3B 93.103 87 6 0 358 444 65214142 65214056 9.580000e-26 128
31 TraesCS4D01G281100 chr2B 92.857 98 5 2 349 444 166044471 166044568 1.230000e-29 141
32 TraesCS4D01G281100 chr7A 91.089 101 9 0 344 444 612375592 612375692 1.590000e-28 137
33 TraesCS4D01G281100 chrUn 92.553 94 7 0 351 444 348315101 348315194 5.720000e-28 135
34 TraesCS4D01G281100 chrUn 93.407 91 6 0 354 444 427230703 427230613 5.720000e-28 135
35 TraesCS4D01G281100 chr7B 86.957 115 8 4 336 445 701408154 701408266 4.460000e-24 122


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 TraesCS4D01G281100 chr4D 452311626 452314914 3288 False 6074.000000 6074 100.000000 1 3289 1 chr4D.!!$F1 3288
1 TraesCS4D01G281100 chr4D 452383850 452386109 2259 False 2246.000000 2246 84.801000 986 3269 1 chr4D.!!$F2 2283
2 TraesCS4D01G281100 chr4D 452548133 452550877 2744 False 725.500000 821 79.251000 933 3286 2 chr4D.!!$F3 2353
3 TraesCS4D01G281100 chr4B 565525152 565529339 4187 False 2386.500000 3967 92.640000 759 3286 2 chr4B.!!$F1 2527
4 TraesCS4D01G281100 chr4B 565602556 565604565 2009 False 964.500000 1373 85.579000 986 3030 2 chr4B.!!$F2 2044
5 TraesCS4D01G281100 chr4B 565733659 565736376 2717 False 683.000000 821 78.511000 923 3286 2 chr4B.!!$F3 2363
6 TraesCS4D01G281100 chr4A 14737608 14738769 1161 True 1081.000000 1081 83.768000 2067 3269 1 chr4A.!!$R1 1202
7 TraesCS4D01G281100 chr4A 14743616 14744618 1002 True 929.000000 929 83.776000 995 1987 1 chr4A.!!$R2 992
8 TraesCS4D01G281100 chr4A 14356218 14358984 2766 True 703.000000 789 79.322000 922 3289 2 chr4A.!!$R3 2367
9 TraesCS4D01G281100 chr3A 23670099 23670969 870 True 553.000000 553 78.449000 926 1786 1 chr3A.!!$R1 860
10 TraesCS4D01G281100 chr3A 23690782 23691656 874 True 472.000000 472 76.844000 931 1790 1 chr3A.!!$R2 859
11 TraesCS4D01G281100 chr3A 23699746 23700630 884 True 472.000000 472 76.760000 916 1789 1 chr3A.!!$R3 873
12 TraesCS4D01G281100 chr3D 13334650 13335445 795 False 521.000000 521 78.723000 1004 1792 1 chr3D.!!$F1 788
13 TraesCS4D01G281100 chr7D 407271470 407272870 1400 False 321.333333 473 94.074000 20 768 3 chr7D.!!$F1 748
14 TraesCS4D01G281100 chr7D 407269284 407270012 728 True 286.500000 462 93.185500 20 516 2 chr7D.!!$R2 496
15 TraesCS4D01G281100 chr1D 14665926 14667317 1391 False 311.666667 457 93.484333 20 758 3 chr1D.!!$F1 738

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
789 1531 0.673644 CGCCTCACTCCGTTCCAAAT 60.674 55.0 0.00 0.00 0.0 2.32 F
1074 3466 0.802494 GCGAGATTTTGCTCCGGAAA 59.198 50.0 5.23 0.00 0.0 3.13 F
1796 4234 1.619807 ATCAATTTGCAGGGCCAGGC 61.620 55.0 6.18 10.12 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 4389 0.259065 ATGAGAGGGCACGAGGAGTA 59.741 55.000 0.0 0.0 0.00 2.59 R
2022 4473 0.677731 AGATGACACCGGCACCATTG 60.678 55.000 0.0 0.0 0.00 2.82 R
2602 5503 2.695359 TGACCATCGGTACTTTTCAGC 58.305 47.619 0.0 0.0 35.25 4.26 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
59 60 1.506262 CGGTTTGTAGCATGCCACC 59.494 57.895 15.66 11.81 0.00 4.61
85 86 1.803334 GACGGCACTCCACATAACAA 58.197 50.000 0.00 0.00 0.00 2.83
87 88 1.071699 ACGGCACTCCACATAACAAGT 59.928 47.619 0.00 0.00 0.00 3.16
96 97 4.331968 TCCACATAACAAGTTGATGACCC 58.668 43.478 10.54 0.00 0.00 4.46
99 100 5.003160 CACATAACAAGTTGATGACCCTCA 58.997 41.667 10.54 0.00 0.00 3.86
122 123 5.062183 CACAACATCAACTACACTCATACGG 59.938 44.000 0.00 0.00 0.00 4.02
131 132 1.146930 ACTCATACGGCATGGCAGG 59.853 57.895 20.37 6.34 35.16 4.85
176 177 2.426023 GGCGGCGATTCCCATAGT 59.574 61.111 12.98 0.00 0.00 2.12
210 211 1.226802 CGATGACACTCCTCCAGCG 60.227 63.158 0.00 0.00 33.50 5.18
260 261 0.949105 GCACAATGACGACGACCCTT 60.949 55.000 0.00 0.00 0.00 3.95
306 307 0.812811 CACTCATGCGGCATGCTAGT 60.813 55.000 32.60 27.84 46.63 2.57
308 309 1.345741 ACTCATGCGGCATGCTAGTAT 59.654 47.619 32.60 13.81 46.63 2.12
318 319 2.557056 GCATGCTAGTATCCCACGTAGA 59.443 50.000 11.37 0.00 0.00 2.59
332 333 3.120546 CCACGTAGAATCAACTTGCAGTG 60.121 47.826 0.00 0.00 0.00 3.66
335 336 1.597742 AGAATCAACTTGCAGTGCGT 58.402 45.000 11.20 0.00 0.00 5.24
336 337 1.265095 AGAATCAACTTGCAGTGCGTG 59.735 47.619 11.20 8.11 0.00 5.34
367 684 9.886132 TTCTTTTTCAATATACTGTACTCCCTC 57.114 33.333 0.00 0.00 0.00 4.30
368 685 9.268282 TCTTTTTCAATATACTGTACTCCCTCT 57.732 33.333 0.00 0.00 0.00 3.69
369 686 9.319143 CTTTTTCAATATACTGTACTCCCTCTG 57.681 37.037 0.00 0.00 0.00 3.35
370 687 7.973048 TTTCAATATACTGTACTCCCTCTGT 57.027 36.000 0.00 0.00 0.00 3.41
371 688 9.483489 TTTTCAATATACTGTACTCCCTCTGTA 57.517 33.333 0.00 0.00 0.00 2.74
372 689 9.483489 TTTCAATATACTGTACTCCCTCTGTAA 57.517 33.333 0.00 0.00 0.00 2.41
373 690 9.483489 TTCAATATACTGTACTCCCTCTGTAAA 57.517 33.333 0.00 0.00 0.00 2.01
374 691 8.910944 TCAATATACTGTACTCCCTCTGTAAAC 58.089 37.037 0.00 0.00 0.00 2.01
375 692 8.692710 CAATATACTGTACTCCCTCTGTAAACA 58.307 37.037 0.00 0.00 0.00 2.83
376 693 8.834004 ATATACTGTACTCCCTCTGTAAACAA 57.166 34.615 0.00 0.00 0.00 2.83
377 694 5.881923 ACTGTACTCCCTCTGTAAACAAA 57.118 39.130 0.00 0.00 0.00 2.83
378 695 6.435292 ACTGTACTCCCTCTGTAAACAAAT 57.565 37.500 0.00 0.00 0.00 2.32
379 696 7.549147 ACTGTACTCCCTCTGTAAACAAATA 57.451 36.000 0.00 0.00 0.00 1.40
380 697 8.147244 ACTGTACTCCCTCTGTAAACAAATAT 57.853 34.615 0.00 0.00 0.00 1.28
381 698 9.263446 ACTGTACTCCCTCTGTAAACAAATATA 57.737 33.333 0.00 0.00 0.00 0.86
386 703 7.988028 ACTCCCTCTGTAAACAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
387 704 6.984474 TCCCTCTGTAAACAAATATAAGAGCG 59.016 38.462 0.00 0.00 0.00 5.03
388 705 6.761714 CCCTCTGTAAACAAATATAAGAGCGT 59.238 38.462 0.00 0.00 0.00 5.07
389 706 7.280205 CCCTCTGTAAACAAATATAAGAGCGTT 59.720 37.037 0.00 0.00 0.00 4.84
390 707 8.665685 CCTCTGTAAACAAATATAAGAGCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
398 715 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
407 724 9.654663 AAGAGCGTTTAGATCACTAAAATAGTT 57.345 29.630 0.00 0.00 45.97 2.24
440 757 8.319057 TGCTCTTATATTTCTTTACAGAGGGA 57.681 34.615 0.00 0.00 0.00 4.20
441 758 8.424918 TGCTCTTATATTTCTTTACAGAGGGAG 58.575 37.037 0.00 0.00 0.00 4.30
442 759 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
450 767 5.895807 TCTTTACAGAGGGAGTACCAGTTA 58.104 41.667 0.00 0.00 43.89 2.24
467 784 5.163437 ACCAGTTAGCTAGCTACATTGTACC 60.163 44.000 24.09 5.14 0.00 3.34
469 786 4.885907 AGTTAGCTAGCTACATTGTACCGA 59.114 41.667 24.09 2.60 0.00 4.69
486 803 2.223595 ACCGAGAGTGCGATGAAGTATG 60.224 50.000 0.00 0.00 0.00 2.39
516 833 3.795150 GCGCTGAAGATTCAAAACAACCA 60.795 43.478 0.00 0.00 36.64 3.67
517 834 4.549458 CGCTGAAGATTCAAAACAACCAT 58.451 39.130 0.00 0.00 36.64 3.55
518 835 4.383649 CGCTGAAGATTCAAAACAACCATG 59.616 41.667 0.00 0.00 36.64 3.66
528 1264 4.336993 TCAAAACAACCATGTACTGTCACC 59.663 41.667 0.00 0.00 39.40 4.02
590 1331 2.448926 TGTACCGGTGTGAATGACAG 57.551 50.000 19.93 0.00 34.28 3.51
603 1344 3.050275 GACAGGCGCAAGGACCAC 61.050 66.667 10.83 0.00 38.28 4.16
626 1367 3.434319 GGCATGCACTCCCGTGTG 61.434 66.667 21.36 0.00 43.16 3.82
654 1395 1.176619 ACACACGTCCGTCATCTCCA 61.177 55.000 0.00 0.00 0.00 3.86
701 1442 2.105528 GGCGCCTTAATCGGACGA 59.894 61.111 22.15 0.00 0.00 4.20
759 1501 6.661805 AGTGGTTGTTTTCAAGTCTTTTCCTA 59.338 34.615 0.00 0.00 40.74 2.94
760 1502 6.972901 GTGGTTGTTTTCAAGTCTTTTCCTAG 59.027 38.462 0.00 0.00 40.74 3.02
784 1526 2.240162 AATCCCGCCTCACTCCGTTC 62.240 60.000 0.00 0.00 0.00 3.95
789 1531 0.673644 CGCCTCACTCCGTTCCAAAT 60.674 55.000 0.00 0.00 0.00 2.32
807 1549 4.459089 GAGGTGCTGACGGCCCTC 62.459 72.222 21.06 21.06 44.66 4.30
835 1577 1.006832 CGTAAGAACAAGCCCCATCG 58.993 55.000 0.00 0.00 43.02 3.84
846 1588 2.280389 CCCATCGCCATCGGACAG 60.280 66.667 0.00 0.00 36.13 3.51
888 1630 3.332034 GAAACCCTAGAAGTAAGCGCAA 58.668 45.455 11.47 0.00 0.00 4.85
894 1636 2.770164 AGAAGTAAGCGCAATCCACT 57.230 45.000 11.47 1.50 0.00 4.00
972 1714 1.002792 CCCGCCGCTAAAGCTAATTTC 60.003 52.381 0.00 0.00 39.32 2.17
1074 3466 0.802494 GCGAGATTTTGCTCCGGAAA 59.198 50.000 5.23 0.00 0.00 3.13
1419 3821 2.480419 CGCCGATCCCAAGATATTTGAC 59.520 50.000 0.00 0.00 30.90 3.18
1518 3932 2.883621 GACGGTCCCTTCCTCGTC 59.116 66.667 0.00 0.00 43.62 4.20
1585 4002 3.698040 TGTTTACTCATCCGAGACTACCC 59.302 47.826 0.00 0.00 42.34 3.69
1745 4177 4.853924 ACTGGACCATGAAAATTGTGAC 57.146 40.909 0.00 0.00 0.00 3.67
1795 4233 1.779221 TATCAATTTGCAGGGCCAGG 58.221 50.000 6.18 0.00 0.00 4.45
1796 4234 1.619807 ATCAATTTGCAGGGCCAGGC 61.620 55.000 6.18 10.12 0.00 4.85
1797 4235 2.203818 AATTTGCAGGGCCAGGCA 60.204 55.556 17.56 17.56 38.46 4.75
1798 4236 2.586293 AATTTGCAGGGCCAGGCAC 61.586 57.895 20.61 10.64 40.23 5.01
1950 4389 6.151817 GGGACATCAAGCTTGAAACTATTCTT 59.848 38.462 31.55 10.30 41.13 2.52
2022 4473 1.358759 CACACTGGTTGGTTTCGCC 59.641 57.895 0.00 0.00 37.90 5.54
2054 4505 4.508124 CGGTGTCATCTTCCTAAATACAGC 59.492 45.833 0.00 0.00 0.00 4.40
2307 4795 2.048690 GCGGCCGCCATTTTGAAA 60.049 55.556 39.89 0.00 34.56 2.69
2389 5269 5.508153 CCACTGGTCTCTAATCCACTAATCG 60.508 48.000 0.00 0.00 0.00 3.34
2391 5271 3.958147 TGGTCTCTAATCCACTAATCGCA 59.042 43.478 0.00 0.00 0.00 5.10
2393 5273 3.984633 GTCTCTAATCCACTAATCGCAGC 59.015 47.826 0.00 0.00 0.00 5.25
2438 5318 9.482627 GTTAATCTCTGACATGGGTTAGATAAG 57.517 37.037 0.00 0.00 38.75 1.73
2526 5420 6.479006 TGTCCATTTCAGTCTGATCAGAAAT 58.521 36.000 26.70 18.71 40.29 2.17
2536 5431 7.922278 TCAGTCTGATCAGAAATTTTTGTTTGG 59.078 33.333 26.70 4.44 39.48 3.28
2553 5448 5.537188 TGTTTGGTAAACATCATTCTTGGC 58.463 37.500 3.20 0.00 45.79 4.52
2633 5534 1.450312 GATGGTCAAGCCCTGGACG 60.450 63.158 0.00 0.00 34.87 4.79
2647 5548 3.007614 CCCTGGACGAAAGGAGTTTTCTA 59.992 47.826 0.00 0.00 42.47 2.10
2783 5695 1.471287 TGCTGTCGTCGTTGCTATAGT 59.529 47.619 0.84 0.00 0.00 2.12
2800 5712 8.534333 TGCTATAGTACATTAGCAGCAATAAC 57.466 34.615 19.88 0.00 44.32 1.89
2892 5816 3.865745 CGACATAGCAACTAAGGAGGTTG 59.134 47.826 0.00 0.00 44.60 3.77
3000 5929 5.165911 CAAGACGAATTGCTGCTATGATT 57.834 39.130 0.00 0.00 0.00 2.57
3007 5936 4.843220 ATTGCTGCTATGATTACTTGCC 57.157 40.909 0.00 0.00 0.00 4.52
3018 5947 7.254932 GCTATGATTACTTGCCAGAAAAGGTAG 60.255 40.741 0.00 0.00 0.00 3.18
3028 5957 4.760204 GCCAGAAAAGGTAGCAAGTTCTTA 59.240 41.667 0.00 0.00 0.00 2.10
3117 6066 7.389053 GCAATCCTCCACATAAGTCCTATTTAG 59.611 40.741 0.00 0.00 0.00 1.85
3286 6246 6.149129 ACCAAAGTGGAGTTCAATCTTTTC 57.851 37.500 0.18 0.00 40.96 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.824166 GTTGCGAGCCATGCTGCG 62.824 66.667 0.00 0.00 39.88 5.18
3 4 4.487412 GGTTGCGAGCCATGCTGC 62.487 66.667 0.00 0.00 39.88 5.25
4 5 3.818787 GGGTTGCGAGCCATGCTG 61.819 66.667 17.67 0.00 43.10 4.41
10 11 2.268076 ATGTTGTGGGTTGCGAGCC 61.268 57.895 15.74 15.74 43.89 4.70
11 12 1.081242 CATGTTGTGGGTTGCGAGC 60.081 57.895 0.00 0.00 0.00 5.03
12 13 1.580942 CCATGTTGTGGGTTGCGAG 59.419 57.895 0.00 0.00 44.79 5.03
13 14 3.756802 CCATGTTGTGGGTTGCGA 58.243 55.556 0.00 0.00 44.79 5.10
59 60 3.414700 GGAGTGCCGTCGTGCTTG 61.415 66.667 7.14 0.00 0.00 4.01
70 71 4.455533 TCATCAACTTGTTATGTGGAGTGC 59.544 41.667 0.00 0.00 0.00 4.40
85 86 3.072915 TGATGTTGTGAGGGTCATCAACT 59.927 43.478 16.31 7.94 42.01 3.16
87 88 3.786368 TGATGTTGTGAGGGTCATCAA 57.214 42.857 0.00 0.00 42.01 2.57
96 97 6.033937 CGTATGAGTGTAGTTGATGTTGTGAG 59.966 42.308 0.00 0.00 0.00 3.51
99 100 5.168569 CCGTATGAGTGTAGTTGATGTTGT 58.831 41.667 0.00 0.00 0.00 3.32
122 123 2.283143 TACATGGGGTCCTGCCATGC 62.283 60.000 21.17 0.00 43.33 4.06
131 132 1.598130 GCCGATGCTACATGGGGTC 60.598 63.158 10.15 0.00 33.53 4.46
171 172 1.728971 GCGCTGCTAGCCAATACTATG 59.271 52.381 13.29 0.00 38.18 2.23
172 173 2.086054 GCGCTGCTAGCCAATACTAT 57.914 50.000 13.29 0.00 38.18 2.12
260 261 2.683859 GCTGCGAGCTGTTGATGCA 61.684 57.895 0.00 0.00 38.45 3.96
306 307 4.081365 TGCAAGTTGATTCTACGTGGGATA 60.081 41.667 7.16 0.00 0.00 2.59
308 309 2.037902 TGCAAGTTGATTCTACGTGGGA 59.962 45.455 7.16 0.00 0.00 4.37
332 333 6.751888 AGTATATTGAAAAAGAAATGGCACGC 59.248 34.615 0.00 0.00 0.00 5.34
362 679 6.984474 CGCTCTTATATTTGTTTACAGAGGGA 59.016 38.462 4.76 0.00 36.40 4.20
363 680 6.761714 ACGCTCTTATATTTGTTTACAGAGGG 59.238 38.462 8.36 8.36 38.95 4.30
364 681 7.772332 ACGCTCTTATATTTGTTTACAGAGG 57.228 36.000 0.00 0.00 0.00 3.69
372 689 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
381 698 9.654663 AACTATTTTAGTGATCTAAACGCTCTT 57.345 29.630 0.00 0.00 43.20 2.85
414 731 8.938883 TCCCTCTGTAAAGAAATATAAGAGCAT 58.061 33.333 0.00 0.00 0.00 3.79
415 732 8.319057 TCCCTCTGTAAAGAAATATAAGAGCA 57.681 34.615 0.00 0.00 0.00 4.26
416 733 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
419 736 9.984190 GGTACTCCCTCTGTAAAGAAATATAAG 57.016 37.037 0.00 0.00 0.00 1.73
420 737 9.496710 TGGTACTCCCTCTGTAAAGAAATATAA 57.503 33.333 0.00 0.00 0.00 0.98
421 738 9.144298 CTGGTACTCCCTCTGTAAAGAAATATA 57.856 37.037 0.00 0.00 0.00 0.86
422 739 7.624077 ACTGGTACTCCCTCTGTAAAGAAATAT 59.376 37.037 0.00 0.00 0.00 1.28
423 740 6.958192 ACTGGTACTCCCTCTGTAAAGAAATA 59.042 38.462 0.00 0.00 0.00 1.40
424 741 5.785940 ACTGGTACTCCCTCTGTAAAGAAAT 59.214 40.000 0.00 0.00 0.00 2.17
425 742 5.152934 ACTGGTACTCCCTCTGTAAAGAAA 58.847 41.667 0.00 0.00 0.00 2.52
426 743 4.748701 ACTGGTACTCCCTCTGTAAAGAA 58.251 43.478 0.00 0.00 0.00 2.52
427 744 4.399483 ACTGGTACTCCCTCTGTAAAGA 57.601 45.455 0.00 0.00 0.00 2.52
428 745 5.394333 GCTAACTGGTACTCCCTCTGTAAAG 60.394 48.000 0.00 0.00 0.00 1.85
429 746 4.465305 GCTAACTGGTACTCCCTCTGTAAA 59.535 45.833 0.00 0.00 0.00 2.01
430 747 4.021916 GCTAACTGGTACTCCCTCTGTAA 58.978 47.826 0.00 0.00 0.00 2.41
431 748 3.268856 AGCTAACTGGTACTCCCTCTGTA 59.731 47.826 0.00 0.00 0.00 2.74
432 749 2.043252 AGCTAACTGGTACTCCCTCTGT 59.957 50.000 0.00 0.00 0.00 3.41
433 750 2.741145 AGCTAACTGGTACTCCCTCTG 58.259 52.381 0.00 0.00 0.00 3.35
434 751 3.688991 GCTAGCTAACTGGTACTCCCTCT 60.689 52.174 7.70 0.00 0.00 3.69
435 752 2.624364 GCTAGCTAACTGGTACTCCCTC 59.376 54.545 7.70 0.00 0.00 4.30
436 753 2.245287 AGCTAGCTAACTGGTACTCCCT 59.755 50.000 17.69 0.00 0.00 4.20
437 754 2.668625 AGCTAGCTAACTGGTACTCCC 58.331 52.381 17.69 0.00 0.00 4.30
438 755 4.205587 TGTAGCTAGCTAACTGGTACTCC 58.794 47.826 25.74 9.98 36.16 3.85
439 756 6.183360 ACAATGTAGCTAGCTAACTGGTACTC 60.183 42.308 25.74 10.69 36.16 2.59
440 757 5.657302 ACAATGTAGCTAGCTAACTGGTACT 59.343 40.000 25.74 5.29 36.16 2.73
441 758 5.903810 ACAATGTAGCTAGCTAACTGGTAC 58.096 41.667 25.74 14.64 35.86 3.34
442 759 6.040166 GGTACAATGTAGCTAGCTAACTGGTA 59.960 42.308 25.74 20.42 0.00 3.25
443 760 5.163437 GGTACAATGTAGCTAGCTAACTGGT 60.163 44.000 25.74 21.32 0.00 4.00
444 761 5.290386 GGTACAATGTAGCTAGCTAACTGG 58.710 45.833 25.74 17.22 0.00 4.00
450 767 3.552875 TCTCGGTACAATGTAGCTAGCT 58.447 45.455 23.12 23.12 0.00 3.32
467 784 2.223595 ACCATACTTCATCGCACTCTCG 60.224 50.000 0.00 0.00 0.00 4.04
469 786 3.027412 AGACCATACTTCATCGCACTCT 58.973 45.455 0.00 0.00 0.00 3.24
486 803 1.663135 GAATCTTCAGCGCTTCAGACC 59.337 52.381 7.50 4.23 0.00 3.85
516 833 1.080093 CGCACCGGTGACAGTACAT 60.080 57.895 38.30 0.00 0.00 2.29
517 834 2.337170 CGCACCGGTGACAGTACA 59.663 61.111 38.30 0.00 0.00 2.90
518 835 2.431942 CCGCACCGGTGACAGTAC 60.432 66.667 38.30 17.72 42.73 2.73
558 1299 4.456566 ACACCGGTACATGGTTATTTTGAC 59.543 41.667 6.87 0.00 37.72 3.18
590 1331 4.980805 TCACGTGGTCCTTGCGCC 62.981 66.667 17.00 0.00 0.00 6.53
603 1344 2.401766 GGGAGTGCATGCCTTCACG 61.402 63.158 16.68 0.00 38.19 4.35
626 1367 2.245532 GACGTGTGTGCTGCGTTC 59.754 61.111 0.00 0.00 39.06 3.95
674 1415 2.676632 TTAAGGCGCCGTCTGATTAA 57.323 45.000 20.96 14.99 0.00 1.40
720 1461 1.904287 ACCACTGATTTTAAGGCGCA 58.096 45.000 10.83 0.00 0.00 6.09
784 1526 1.926511 GCCGTCAGCACCTCATTTGG 61.927 60.000 0.00 0.00 42.97 3.28
807 1549 2.153247 GCTTGTTCTTACGACAGTCACG 59.847 50.000 0.41 0.00 0.00 4.35
813 1555 0.759959 TGGGGCTTGTTCTTACGACA 59.240 50.000 0.00 0.00 0.00 4.35
835 1577 2.962253 GCGCTACTGTCCGATGGC 60.962 66.667 0.00 0.00 0.00 4.40
843 1585 0.804989 GAAATTGGCTGCGCTACTGT 59.195 50.000 9.73 0.00 0.00 3.55
846 1588 0.179163 GTGGAAATTGGCTGCGCTAC 60.179 55.000 9.73 0.00 0.00 3.58
888 1630 1.078848 GAACAGGCAGCGAGTGGAT 60.079 57.895 0.00 0.00 0.00 3.41
894 1636 4.717629 CGGACGAACAGGCAGCGA 62.718 66.667 0.00 0.00 0.00 4.93
963 1705 1.797025 GCCCTATCGCGAAATTAGCT 58.203 50.000 15.24 0.00 0.00 3.32
990 1732 2.275418 GAATCCATGGTGGCCGGT 59.725 61.111 12.58 0.00 37.47 5.28
993 3385 3.219198 GGCGAATCCATGGTGGCC 61.219 66.667 12.58 12.14 37.47 5.36
1419 3821 3.197766 TCCCCTCTGCAGTACAAAGTATG 59.802 47.826 14.67 0.00 0.00 2.39
1585 4002 2.897436 TGAGATCATTTCGCTCCACTG 58.103 47.619 0.00 0.00 0.00 3.66
1622 4039 4.134563 GTTGGTGGCAAACGGATAGATAT 58.865 43.478 0.00 0.00 0.00 1.63
1745 4177 1.695893 CTGCTCGCCCACATTGTACG 61.696 60.000 0.00 0.00 0.00 3.67
1800 4238 2.428569 ATGAGTATACCGCGCGCG 60.429 61.111 43.73 43.73 39.44 6.86
1950 4389 0.259065 ATGAGAGGGCACGAGGAGTA 59.741 55.000 0.00 0.00 0.00 2.59
2022 4473 0.677731 AGATGACACCGGCACCATTG 60.678 55.000 0.00 0.00 0.00 2.82
2054 4505 3.937706 CTCAACTGTAAAGAGCCCATCTG 59.062 47.826 0.00 0.00 38.67 2.90
2273 4747 2.349886 GCCGCTTCACTTCTTGTATGAG 59.650 50.000 0.00 0.00 0.00 2.90
2393 5273 8.598041 AGATTAACCAAATATAGAGCCTAGTGG 58.402 37.037 0.00 0.00 0.00 4.00
2438 5318 1.896220 TTGGAACTGTGTCTGCCATC 58.104 50.000 0.00 0.00 0.00 3.51
2536 5431 6.985188 TCTGTAGCCAAGAATGATGTTTAC 57.015 37.500 0.00 0.00 0.00 2.01
2602 5503 2.695359 TGACCATCGGTACTTTTCAGC 58.305 47.619 0.00 0.00 35.25 4.26
2684 5586 8.833734 ACACTATCATCCATATCTTCCATGAAT 58.166 33.333 0.00 0.00 0.00 2.57
2691 5593 9.988815 AGTAAACACACTATCATCCATATCTTC 57.011 33.333 0.00 0.00 0.00 2.87
2718 5630 4.394300 GTCAGCTAATCTTGTTGATGCTGT 59.606 41.667 11.04 0.00 45.14 4.40
2783 5695 6.825944 TGTTTGGTTATTGCTGCTAATGTA 57.174 33.333 0.00 0.00 0.00 2.29
2800 5712 7.608308 TTTTCTGAATTTTCCAGTTGTTTGG 57.392 32.000 0.00 0.00 39.70 3.28
2987 5916 3.619419 TGGCAAGTAATCATAGCAGCAA 58.381 40.909 0.00 0.00 0.00 3.91
3000 5929 3.780804 TGCTACCTTTTCTGGCAAGTA 57.219 42.857 0.00 0.00 0.00 2.24
3074 6003 6.398918 AGGATTGCACGTGGAATAGATATAC 58.601 40.000 31.50 18.35 36.19 1.47
3117 6066 2.766239 GCTCTCTGCTTTCAGGCTC 58.234 57.895 0.00 0.00 40.69 4.70


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

AutoCloner maintained by Alex Coulton.