Multiple sequence alignment - TraesCS2A01G203200

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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 TraesCS2A01G203200 chr2A 100.000 4158 0 0 1 4158 178575285 178571128 0.000000e+00 7679
1 TraesCS2A01G203200 chr2D 95.250 3495 109 31 7 3490 170777878 170781326 0.000000e+00 5481
2 TraesCS2A01G203200 chr2D 82.709 347 32 13 3671 4013 170781499 170781821 2.450000e-72 283
3 TraesCS2A01G203200 chr2D 87.826 115 13 1 3999 4113 170781978 170782091 2.610000e-27 134
4 TraesCS2A01G203200 chr2B 93.270 3774 143 49 108 3831 225847320 225843608 0.000000e+00 5459
5 TraesCS2A01G203200 chr2B 90.323 155 14 1 3999 4153 225841882 225841729 7.050000e-48 202
6 TraesCS2A01G203200 chr2B 89.928 139 13 1 4015 4153 225841127 225840990 1.190000e-40 178
7 TraesCS2A01G203200 chr2B 86.139 101 14 0 3907 4007 225842163 225842063 4.390000e-20 110
8 TraesCS2A01G203200 chr5B 93.981 947 49 2 888 1826 678579935 678578989 0.000000e+00 1426
9 TraesCS2A01G203200 chr4B 91.587 939 77 1 888 1826 405288822 405287886 0.000000e+00 1295
10 TraesCS2A01G203200 chr7B 96.970 462 8 2 1477 1938 232271979 232272434 0.000000e+00 771
11 TraesCS2A01G203200 chr7B 94.737 152 5 2 1790 1941 232271117 232270969 2.500000e-57 233
12 TraesCS2A01G203200 chr7B 92.857 140 10 0 1124 1263 232271830 232271969 1.960000e-48 204


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 TraesCS2A01G203200 chr2A 178571128 178575285 4157 True 7679.00 7679 100.0000 1 4158 1 chr2A.!!$R1 4157
1 TraesCS2A01G203200 chr2D 170777878 170782091 4213 False 1966.00 5481 88.5950 7 4113 3 chr2D.!!$F1 4106
2 TraesCS2A01G203200 chr2B 225840990 225847320 6330 True 1487.25 5459 89.9150 108 4153 4 chr2B.!!$R1 4045
3 TraesCS2A01G203200 chr5B 678578989 678579935 946 True 1426.00 1426 93.9810 888 1826 1 chr5B.!!$R1 938
4 TraesCS2A01G203200 chr4B 405287886 405288822 936 True 1295.00 1295 91.5870 888 1826 1 chr4B.!!$R1 938
5 TraesCS2A01G203200 chr7B 232271830 232272434 604 False 487.50 771 94.9135 1124 1938 2 chr7B.!!$F1 814

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
642 653 0.036858 GCCTCGCTGTTTCTTCCTCT 60.037 55.000 0.00 0.0 0.00 3.69 F
1362 1389 1.228552 GGGCCTCAAGAACAAGCCA 60.229 57.895 0.84 0.0 45.72 4.75 F
2648 2676 0.508641 CTCCACGAAACACAGCGAAG 59.491 55.000 0.00 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2549 2577 0.882474 CGAGGGACTTGACGAACTCT 59.118 55.0 0.0 0.0 44.22 3.24 R
2992 3021 0.250295 CCTTGGCGTCCTTGTTCTCA 60.250 55.0 0.0 0.0 0.00 3.27 R
3525 3570 0.039798 GCACGGACGTAGAACAGTCA 60.040 55.0 0.0 0.0 39.01 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.202756 GACCCTGAAGCTACGCGG 60.203 66.667 12.47 0.00 0.00 6.46
53 54 1.667236 GGTCATGCAACCATCGATCA 58.333 50.000 2.53 0.00 39.27 2.92
56 57 3.304257 GGTCATGCAACCATCGATCAATC 60.304 47.826 2.53 0.00 39.27 2.67
281 288 8.718158 AGGAAGAAAAGGAAAGAAGAATTGAT 57.282 30.769 0.00 0.00 0.00 2.57
282 289 9.152327 AGGAAGAAAAGGAAAGAAGAATTGATT 57.848 29.630 0.00 0.00 0.00 2.57
316 323 2.650322 GATCCCCACGGCAGAATTAAA 58.350 47.619 0.00 0.00 0.00 1.52
317 324 1.828979 TCCCCACGGCAGAATTAAAC 58.171 50.000 0.00 0.00 0.00 2.01
342 349 1.962822 GGGGTTCCGTTGGTTCGTC 60.963 63.158 0.00 0.00 0.00 4.20
441 448 4.456535 CGACTCTTTCTCTCCTCCAGATA 58.543 47.826 0.00 0.00 0.00 1.98
456 464 5.008118 CCTCCAGATATTTCGCTTTCCTTTC 59.992 44.000 0.00 0.00 0.00 2.62
466 474 1.680249 GCTTTCCTTTCCGCTCCAGAT 60.680 52.381 0.00 0.00 0.00 2.90
487 495 2.945456 AGAAAACTCCCTTTCCCACAC 58.055 47.619 0.00 0.00 36.18 3.82
488 496 1.607148 GAAAACTCCCTTTCCCACACG 59.393 52.381 0.00 0.00 30.44 4.49
491 499 3.234630 CTCCCTTTCCCACACGCGA 62.235 63.158 15.93 0.00 0.00 5.87
642 653 0.036858 GCCTCGCTGTTTCTTCCTCT 60.037 55.000 0.00 0.00 0.00 3.69
646 657 3.249917 CTCGCTGTTTCTTCCTCTTCTC 58.750 50.000 0.00 0.00 0.00 2.87
837 856 6.202937 CCGTCGATCTATATATTCTCTTGCC 58.797 44.000 0.00 0.00 0.00 4.52
1236 1263 1.742880 GAACAGAGGCATCAGCGCA 60.743 57.895 11.47 0.00 43.41 6.09
1362 1389 1.228552 GGGCCTCAAGAACAAGCCA 60.229 57.895 0.84 0.00 45.72 4.75
1410 1437 2.975799 GCGTGCCGGTTCCTCAAA 60.976 61.111 1.90 0.00 0.00 2.69
1521 1548 3.057337 CTGGAGTTCCGGTCCGTT 58.943 61.111 11.06 0.00 39.43 4.44
1675 1702 4.419921 CCACCAACCCCTACCGCC 62.420 72.222 0.00 0.00 0.00 6.13
1947 1975 1.596260 CATGAGCTCTGCAATGGTACG 59.404 52.381 16.19 0.00 0.00 3.67
1971 1999 4.027458 CGCTGTTGATTCTTGTTGTGTTTG 60.027 41.667 0.00 0.00 0.00 2.93
2106 2134 2.890371 GACGTGCGGGACAGGTAT 59.110 61.111 0.00 0.00 46.99 2.73
2124 2152 2.627515 ATGCGCATGTCAAGGACTAT 57.372 45.000 24.69 0.00 33.15 2.12
2159 2187 2.868583 TCATCGAGGTACGTACACTAGC 59.131 50.000 26.02 9.22 43.13 3.42
2161 2189 3.801114 TCGAGGTACGTACACTAGCTA 57.199 47.619 26.02 0.00 43.13 3.32
2163 2191 3.131223 TCGAGGTACGTACACTAGCTACT 59.869 47.826 26.02 11.72 43.13 2.57
2164 2192 3.868077 CGAGGTACGTACACTAGCTACTT 59.132 47.826 26.02 0.00 37.22 2.24
2168 2196 6.352516 AGGTACGTACACTAGCTACTTACAT 58.647 40.000 26.02 6.65 0.00 2.29
2169 2197 7.500992 AGGTACGTACACTAGCTACTTACATA 58.499 38.462 26.02 0.00 0.00 2.29
2170 2198 8.153550 AGGTACGTACACTAGCTACTTACATAT 58.846 37.037 26.02 0.00 0.00 1.78
2397 2425 3.057596 GTGCTCGTGATTTGATTTGGGAA 60.058 43.478 0.00 0.00 0.00 3.97
2407 2435 6.496565 TGATTTGATTTGGGAATTACTGGTGT 59.503 34.615 0.00 0.00 0.00 4.16
2416 2444 2.515996 ATTACTGGTGTCCGGTGGCG 62.516 60.000 0.00 0.00 43.80 5.69
2469 2497 2.426023 GCGTGGTGAAGGAGGTGT 59.574 61.111 0.00 0.00 0.00 4.16
2648 2676 0.508641 CTCCACGAAACACAGCGAAG 59.491 55.000 0.00 0.00 0.00 3.79
2666 2694 1.064621 GCACATAGCATTGGTGGCG 59.935 57.895 0.00 0.00 44.79 5.69
3207 3240 5.197451 TGTTTCCTCTTGAGTAAGGCAAAA 58.803 37.500 0.00 0.00 34.59 2.44
3295 3330 6.415280 TCATTTCCAACGTTGTGAAAAATACG 59.585 34.615 30.68 21.69 39.71 3.06
3296 3331 5.481200 TTCCAACGTTGTGAAAAATACGA 57.519 34.783 25.63 9.63 37.44 3.43
3345 3380 1.383456 AAGCCAAAAGTGCACTGCGA 61.383 50.000 22.49 0.00 0.00 5.10
3434 3470 3.194005 ACAAATCCCTACATGGCTACG 57.806 47.619 0.00 0.00 0.00 3.51
3461 3497 7.492524 ACTTTCTTTCTGGTGGATTTCTTTTC 58.507 34.615 0.00 0.00 0.00 2.29
3482 3518 5.047566 TCTGAACTTTTTCTGGTGGATCA 57.952 39.130 0.00 0.00 32.81 2.92
3500 3545 5.423290 TGGATCAGTCTAGAACATGTCACAT 59.577 40.000 0.00 0.00 0.00 3.21
3502 3547 4.498241 TCAGTCTAGAACATGTCACATGC 58.502 43.478 18.19 2.36 0.00 4.06
3524 3569 3.030291 TCAAAAGCACCCTCAACATTGT 58.970 40.909 0.00 0.00 0.00 2.71
3525 3570 3.450457 TCAAAAGCACCCTCAACATTGTT 59.550 39.130 0.00 0.00 0.00 2.83
3528 3573 1.956477 AGCACCCTCAACATTGTTGAC 59.044 47.619 24.66 15.92 0.00 3.18
3529 3574 1.956477 GCACCCTCAACATTGTTGACT 59.044 47.619 24.66 10.07 0.00 3.41
3530 3575 2.287788 GCACCCTCAACATTGTTGACTG 60.288 50.000 24.66 19.97 0.00 3.51
3533 3578 3.632145 ACCCTCAACATTGTTGACTGTTC 59.368 43.478 24.66 0.00 33.45 3.18
3534 3579 3.885297 CCCTCAACATTGTTGACTGTTCT 59.115 43.478 24.66 0.00 33.45 3.01
3535 3580 5.063204 CCCTCAACATTGTTGACTGTTCTA 58.937 41.667 24.66 5.77 33.45 2.10
3536 3581 5.049405 CCCTCAACATTGTTGACTGTTCTAC 60.049 44.000 24.66 0.00 33.45 2.59
3537 3582 5.333339 CCTCAACATTGTTGACTGTTCTACG 60.333 44.000 24.66 13.34 33.45 3.51
3539 3584 5.233476 TCAACATTGTTGACTGTTCTACGTC 59.767 40.000 24.66 0.00 33.45 4.34
3541 3586 2.410785 TGTTGACTGTTCTACGTCCG 57.589 50.000 0.00 0.00 30.77 4.79
3543 3588 2.049228 GTTGACTGTTCTACGTCCGTG 58.951 52.381 1.98 0.00 0.00 4.94
3544 3589 0.039798 TGACTGTTCTACGTCCGTGC 60.040 55.000 1.98 0.00 0.00 5.34
3545 3590 0.039798 GACTGTTCTACGTCCGTGCA 60.040 55.000 1.98 0.00 0.00 4.57
3546 3591 0.386476 ACTGTTCTACGTCCGTGCAA 59.614 50.000 1.98 0.00 0.00 4.08
3548 3593 2.066262 CTGTTCTACGTCCGTGCAAAT 58.934 47.619 1.98 0.00 0.00 2.32
3549 3594 2.478894 CTGTTCTACGTCCGTGCAAATT 59.521 45.455 1.98 0.00 0.00 1.82
3550 3595 2.873472 TGTTCTACGTCCGTGCAAATTT 59.127 40.909 1.98 0.00 0.00 1.82
3551 3596 3.312973 TGTTCTACGTCCGTGCAAATTTT 59.687 39.130 1.98 0.00 0.00 1.82
3552 3597 4.201930 TGTTCTACGTCCGTGCAAATTTTT 60.202 37.500 1.98 0.00 0.00 1.94
3553 3598 3.879427 TCTACGTCCGTGCAAATTTTTG 58.121 40.909 1.98 0.00 41.03 2.44
3554 3599 2.570442 ACGTCCGTGCAAATTTTTGT 57.430 40.000 5.05 0.00 40.24 2.83
3555 3600 2.189342 ACGTCCGTGCAAATTTTTGTG 58.811 42.857 5.05 0.00 40.24 3.33
3556 3601 2.159366 ACGTCCGTGCAAATTTTTGTGA 60.159 40.909 5.05 0.00 40.24 3.58
3558 3603 3.489047 CGTCCGTGCAAATTTTTGTGAAT 59.511 39.130 5.05 0.00 40.24 2.57
3614 3672 9.403110 CTGATTTTAGGAATGTTTGTTCTTCAG 57.597 33.333 0.00 0.00 0.00 3.02
3626 3684 7.267128 TGTTTGTTCTTCAGAGAATTTTGCAT 58.733 30.769 0.00 0.00 43.41 3.96
3645 3703 8.655651 TTTGCATGTATATAGAACATTCGACA 57.344 30.769 0.00 0.00 35.39 4.35
3646 3704 8.655651 TTGCATGTATATAGAACATTCGACAA 57.344 30.769 0.00 2.87 35.39 3.18
3647 3705 8.831715 TGCATGTATATAGAACATTCGACAAT 57.168 30.769 0.00 0.00 35.39 2.71
3648 3706 8.711457 TGCATGTATATAGAACATTCGACAATG 58.289 33.333 0.00 0.00 44.57 2.82
3656 3714 2.610974 CATTCGACAATGTACGAGCG 57.389 50.000 7.66 0.00 39.59 5.03
3657 3715 2.182014 CATTCGACAATGTACGAGCGA 58.818 47.619 0.00 0.06 39.59 4.93
3658 3716 2.334971 TTCGACAATGTACGAGCGAA 57.665 45.000 3.29 3.29 39.59 4.70
3659 3717 1.609932 TCGACAATGTACGAGCGAAC 58.390 50.000 0.00 0.00 34.49 3.95
3660 3718 1.069091 TCGACAATGTACGAGCGAACA 60.069 47.619 0.00 0.00 34.49 3.18
3669 3727 3.743911 TGTACGAGCGAACATTCAACAAT 59.256 39.130 0.00 0.00 0.00 2.71
3731 3789 3.387374 TGTTCACAAGGGTGCATTTGAAT 59.613 39.130 13.37 0.00 44.87 2.57
3732 3790 3.940209 TCACAAGGGTGCATTTGAATC 57.060 42.857 13.37 0.00 44.87 2.52
3740 3798 3.489738 GGGTGCATTTGAATCCAAGATCG 60.490 47.826 0.00 0.00 33.23 3.69
3744 3802 4.142403 TGCATTTGAATCCAAGATCGGAAC 60.142 41.667 0.00 0.00 38.95 3.62
3754 3817 3.563808 CCAAGATCGGAACAACACTTTCA 59.436 43.478 0.00 0.00 0.00 2.69
3764 3827 6.750039 CGGAACAACACTTTCACAAAATTAGT 59.250 34.615 0.00 0.00 0.00 2.24
3766 3829 8.931775 GGAACAACACTTTCACAAAATTAGTTT 58.068 29.630 0.00 0.00 0.00 2.66
3803 3866 3.965470 AAACCACCACCCTAGAAAGTT 57.035 42.857 0.00 0.00 0.00 2.66
3806 3870 2.781174 ACCACCACCCTAGAAAGTTGAA 59.219 45.455 0.00 0.00 0.00 2.69
3812 3876 4.827284 CCACCCTAGAAAGTTGAATTGTGT 59.173 41.667 0.00 0.00 0.00 3.72
3836 5289 4.562082 ACAATCATTTGCATTGGTGACAG 58.438 39.130 2.33 0.00 37.83 3.51
3849 5302 1.302431 TGACAGGATTGGTGCCACG 60.302 57.895 0.00 0.00 0.00 4.94
3882 5336 2.290323 TGTCTTTGCTTCTTCCCTAGCC 60.290 50.000 0.00 0.00 36.56 3.93
3883 5337 1.066143 TCTTTGCTTCTTCCCTAGCCG 60.066 52.381 0.00 0.00 36.56 5.52
3886 5340 1.227002 GCTTCTTCCCTAGCCGACG 60.227 63.158 0.00 0.00 0.00 5.12
3887 5341 1.437986 CTTCTTCCCTAGCCGACGG 59.562 63.158 10.29 10.29 0.00 4.79
3888 5342 1.304713 TTCTTCCCTAGCCGACGGT 60.305 57.895 16.73 4.97 0.00 4.83
3890 5344 3.718210 CTTCCCTAGCCGACGGTGC 62.718 68.421 16.73 1.30 0.00 5.01
3892 5346 4.208686 CCCTAGCCGACGGTGCTC 62.209 72.222 16.73 0.00 40.23 4.26
3893 5347 3.141488 CCTAGCCGACGGTGCTCT 61.141 66.667 16.73 6.36 40.23 4.09
3894 5348 1.822613 CCTAGCCGACGGTGCTCTA 60.823 63.158 16.73 7.24 40.23 2.43
3895 5349 1.381928 CCTAGCCGACGGTGCTCTAA 61.382 60.000 16.73 0.00 40.23 2.10
3896 5350 0.669077 CTAGCCGACGGTGCTCTAAT 59.331 55.000 16.73 0.00 40.23 1.73
3897 5351 1.067212 CTAGCCGACGGTGCTCTAATT 59.933 52.381 16.73 0.00 40.23 1.40
3898 5352 1.108776 AGCCGACGGTGCTCTAATTA 58.891 50.000 16.73 0.00 32.41 1.40
3899 5353 1.687123 AGCCGACGGTGCTCTAATTAT 59.313 47.619 16.73 0.00 32.41 1.28
3900 5354 2.102588 AGCCGACGGTGCTCTAATTATT 59.897 45.455 16.73 0.00 32.41 1.40
3901 5355 2.221055 GCCGACGGTGCTCTAATTATTG 59.779 50.000 16.73 0.00 0.00 1.90
3902 5356 2.221055 CCGACGGTGCTCTAATTATTGC 59.779 50.000 5.48 3.69 0.00 3.56
3903 5357 2.221055 CGACGGTGCTCTAATTATTGCC 59.779 50.000 7.18 0.00 0.00 4.52
3904 5358 3.202906 GACGGTGCTCTAATTATTGCCA 58.797 45.455 7.18 0.00 0.00 4.92
3905 5359 3.206150 ACGGTGCTCTAATTATTGCCAG 58.794 45.455 7.18 3.69 0.00 4.85
3906 5360 2.031682 CGGTGCTCTAATTATTGCCAGC 60.032 50.000 7.18 0.00 0.00 4.85
3907 5361 2.951642 GGTGCTCTAATTATTGCCAGCA 59.048 45.455 7.18 4.03 34.54 4.41
3909 5363 2.951642 TGCTCTAATTATTGCCAGCACC 59.048 45.455 0.00 0.00 32.00 5.01
3934 5388 1.340600 GCAGGTGGCCATTAGGTTGTA 60.341 52.381 9.72 0.00 37.19 2.41
3950 5404 2.744202 GTTGTATTGGTCAGGTGCTCAG 59.256 50.000 0.00 0.00 0.00 3.35
3951 5405 1.977854 TGTATTGGTCAGGTGCTCAGT 59.022 47.619 0.00 0.00 0.00 3.41
3959 5413 0.964700 CAGGTGCTCAGTGTCTCTCA 59.035 55.000 0.00 0.00 0.00 3.27
3971 5425 4.087892 CTCTCAGGGTGGTGGCGG 62.088 72.222 0.00 0.00 0.00 6.13
3972 5426 4.954118 TCTCAGGGTGGTGGCGGT 62.954 66.667 0.00 0.00 0.00 5.68
4053 6435 4.290711 TCTGACTGCATTGGATGAAGAA 57.709 40.909 2.96 0.00 38.25 2.52
4057 6439 3.350833 ACTGCATTGGATGAAGAAGACC 58.649 45.455 2.96 0.00 38.25 3.85
4061 6443 3.698040 GCATTGGATGAAGAAGACCACAT 59.302 43.478 0.00 0.00 31.87 3.21
4071 6453 3.037549 AGAAGACCACATGGAGATCCTC 58.962 50.000 4.53 0.00 38.94 3.71
4072 6454 2.557555 AGACCACATGGAGATCCTCA 57.442 50.000 4.53 0.00 38.94 3.86
4118 6500 4.096003 CATCCCCACGGGCGACTT 62.096 66.667 0.00 0.00 43.94 3.01
4123 6505 3.697747 CCACGGGCGACTTGGGTA 61.698 66.667 1.68 0.00 31.88 3.69
4125 6507 2.602568 ACGGGCGACTTGGGTAGT 60.603 61.111 0.00 0.00 40.71 2.73
4131 6513 1.375523 CGACTTGGGTAGTGGCACC 60.376 63.158 15.27 0.00 37.17 5.01
4135 6517 2.129555 CTTGGGTAGTGGCACCAGCT 62.130 60.000 15.27 0.00 40.65 4.24
4155 6537 3.787001 CCCACGCCTTCTCCCCTC 61.787 72.222 0.00 0.00 0.00 4.30
4156 6538 3.787001 CCACGCCTTCTCCCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
4157 6539 3.787001 CACGCCTTCTCCCCTCCC 61.787 72.222 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.153549 CGTAGCTTCAGGGTCAGGC 60.154 63.158 0.00 0.00 0.00 4.85
22 23 1.021968 GCATGACCGTAAACCCATCC 58.978 55.000 0.00 0.00 0.00 3.51
53 54 3.622166 AAATGGGACGGAACTACGATT 57.378 42.857 0.00 0.00 37.61 3.34
56 57 2.968675 AGAAAATGGGACGGAACTACG 58.031 47.619 0.00 0.00 40.31 3.51
59 60 4.070009 GTTGTAGAAAATGGGACGGAACT 58.930 43.478 0.00 0.00 0.00 3.01
281 288 1.582610 GGATCCGCGGTTGAGCAAAA 61.583 55.000 27.15 1.58 36.85 2.44
282 289 2.038269 GGATCCGCGGTTGAGCAAA 61.038 57.895 27.15 2.48 36.85 3.68
441 448 1.468914 GAGCGGAAAGGAAAGCGAAAT 59.531 47.619 0.00 0.00 34.34 2.17
456 464 2.483889 GGGAGTTTTCTATCTGGAGCGG 60.484 54.545 0.00 0.00 0.00 5.52
466 474 3.495453 CGTGTGGGAAAGGGAGTTTTCTA 60.495 47.826 0.00 0.00 37.26 2.10
642 653 0.809385 CCGACGCACTAGAAGGAGAA 59.191 55.000 0.00 0.00 0.00 2.87
646 657 2.579787 CGCCGACGCACTAGAAGG 60.580 66.667 0.00 0.00 34.03 3.46
763 778 5.190132 AGAGACCACTAGCTACTAGAACAGA 59.810 44.000 8.57 0.00 37.49 3.41
837 856 3.717830 CATAGAAACCGACGACAAAACG 58.282 45.455 0.00 0.00 39.31 3.60
1203 1230 0.175760 TGTTCTGGCCGTAGAGATGC 59.824 55.000 0.00 0.00 0.00 3.91
1410 1437 3.681835 GCGGAGGTGTCCACGTCT 61.682 66.667 16.83 0.00 44.18 4.18
1675 1702 1.541310 TTGTCGTAGGCCACCCTGAG 61.541 60.000 5.01 0.00 42.90 3.35
1716 1743 2.035442 GTTGAAGGTGAGCGGCTCC 61.035 63.158 26.00 16.91 0.00 4.70
1947 1975 2.046313 CACAACAAGAATCAACAGCGC 58.954 47.619 0.00 0.00 0.00 5.92
1971 1999 2.079925 GACAGGCCTGTTGATTCAGAC 58.920 52.381 37.98 18.83 45.05 3.51
2106 2134 1.066215 ACATAGTCCTTGACATGCGCA 60.066 47.619 14.96 14.96 34.60 6.09
2159 2187 6.195428 CGAGATGCATGCGTATATGTAAGTAG 59.805 42.308 13.55 0.00 0.00 2.57
2161 2189 4.859245 CGAGATGCATGCGTATATGTAAGT 59.141 41.667 13.55 0.00 0.00 2.24
2163 2191 5.054390 TCGAGATGCATGCGTATATGTAA 57.946 39.130 13.55 0.00 0.00 2.41
2164 2192 4.695217 TCGAGATGCATGCGTATATGTA 57.305 40.909 13.55 0.00 0.00 2.29
2168 2196 4.809673 AGAATTCGAGATGCATGCGTATA 58.190 39.130 13.55 0.00 0.00 1.47
2169 2197 3.657634 AGAATTCGAGATGCATGCGTAT 58.342 40.909 13.55 10.18 0.00 3.06
2170 2198 3.052745 GAGAATTCGAGATGCATGCGTA 58.947 45.455 13.55 1.78 0.00 4.42
2334 2362 7.421530 TTGAGTATACAAGAACTGTTTCTGC 57.578 36.000 5.50 0.00 41.56 4.26
2397 2425 1.298667 GCCACCGGACACCAGTAAT 59.701 57.895 9.46 0.00 0.00 1.89
2416 2444 2.452813 CCGTACTGCACACGCCATC 61.453 63.158 9.98 0.00 38.07 3.51
2549 2577 0.882474 CGAGGGACTTGACGAACTCT 59.118 55.000 0.00 0.00 44.22 3.24
2648 2676 1.064621 CGCCACCAATGCTATGTGC 59.935 57.895 0.00 0.00 43.25 4.57
2666 2694 4.271049 CCATGTCACATGTTCGGTTAGATC 59.729 45.833 16.74 0.00 0.00 2.75
2965 2994 4.388499 ACCAGCGCCTTGTACCGG 62.388 66.667 2.29 0.00 0.00 5.28
2992 3021 0.250295 CCTTGGCGTCCTTGTTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
3134 3163 1.865865 CCGATCCTTGTATTGTCCCG 58.134 55.000 0.00 0.00 0.00 5.14
3181 3210 4.287067 TGCCTTACTCAAGAGGAAACAGAT 59.713 41.667 1.73 0.00 34.91 2.90
3207 3240 3.474570 GCCAGCATCTCGTCCCCT 61.475 66.667 0.00 0.00 0.00 4.79
3295 3330 3.910648 AGGAGTAAGTGTTGCGTACTTC 58.089 45.455 3.70 0.00 41.32 3.01
3296 3331 4.522022 ACTAGGAGTAAGTGTTGCGTACTT 59.478 41.667 0.00 5.56 41.32 2.24
3434 3470 7.511959 AAGAAATCCACCAGAAAGAAAGTAC 57.488 36.000 0.00 0.00 0.00 2.73
3461 3497 4.823989 ACTGATCCACCAGAAAAAGTTCAG 59.176 41.667 0.00 0.00 37.59 3.02
3482 3518 4.221482 TGAGCATGTGACATGTTCTAGACT 59.779 41.667 32.21 18.07 31.73 3.24
3500 3545 1.032014 GTTGAGGGTGCTTTTGAGCA 58.968 50.000 0.00 0.00 43.22 4.26
3502 3547 3.068590 ACAATGTTGAGGGTGCTTTTGAG 59.931 43.478 0.00 0.00 0.00 3.02
3516 3561 5.403897 ACGTAGAACAGTCAACAATGTTG 57.596 39.130 19.23 19.23 39.66 3.33
3517 3562 4.510340 GGACGTAGAACAGTCAACAATGTT 59.490 41.667 0.00 0.00 42.17 2.71
3518 3563 4.056050 GGACGTAGAACAGTCAACAATGT 58.944 43.478 0.00 0.00 39.01 2.71
3519 3564 3.121279 CGGACGTAGAACAGTCAACAATG 59.879 47.826 0.00 0.00 39.01 2.82
3521 3566 2.099592 ACGGACGTAGAACAGTCAACAA 59.900 45.455 0.00 0.00 39.01 2.83
3522 3567 1.677576 ACGGACGTAGAACAGTCAACA 59.322 47.619 0.00 0.00 39.01 3.33
3524 3569 1.601162 GCACGGACGTAGAACAGTCAA 60.601 52.381 0.00 0.00 39.01 3.18
3525 3570 0.039798 GCACGGACGTAGAACAGTCA 60.040 55.000 0.00 0.00 39.01 3.41
3528 3573 1.493772 TTTGCACGGACGTAGAACAG 58.506 50.000 0.00 0.00 0.00 3.16
3529 3574 2.157834 ATTTGCACGGACGTAGAACA 57.842 45.000 0.00 0.00 0.00 3.18
3530 3575 3.531262 AAATTTGCACGGACGTAGAAC 57.469 42.857 0.00 0.00 0.00 3.01
3533 3578 3.420576 CACAAAAATTTGCACGGACGTAG 59.579 43.478 5.82 0.00 41.79 3.51
3534 3579 3.064958 TCACAAAAATTTGCACGGACGTA 59.935 39.130 5.82 0.00 41.79 3.57
3535 3580 2.159366 TCACAAAAATTTGCACGGACGT 60.159 40.909 5.82 0.00 41.79 4.34
3536 3581 2.455032 TCACAAAAATTTGCACGGACG 58.545 42.857 5.82 0.00 41.79 4.79
3537 3582 6.517914 TTATTCACAAAAATTTGCACGGAC 57.482 33.333 5.82 0.00 41.79 4.79
3539 3584 7.625553 TCTTTTATTCACAAAAATTTGCACGG 58.374 30.769 5.82 0.00 41.79 4.94
3639 3697 1.980844 GTTCGCTCGTACATTGTCGAA 59.019 47.619 6.27 6.27 35.69 3.71
3640 3698 1.069091 TGTTCGCTCGTACATTGTCGA 60.069 47.619 0.00 2.10 34.88 4.20
3641 3699 1.333115 TGTTCGCTCGTACATTGTCG 58.667 50.000 0.00 0.00 0.00 4.35
3642 3700 3.366724 TGAATGTTCGCTCGTACATTGTC 59.633 43.478 24.48 15.30 42.99 3.18
3643 3701 3.322369 TGAATGTTCGCTCGTACATTGT 58.678 40.909 24.48 8.43 42.99 2.71
3644 3702 3.989705 TGAATGTTCGCTCGTACATTG 57.010 42.857 24.48 0.00 42.99 2.82
3645 3703 3.743911 TGTTGAATGTTCGCTCGTACATT 59.256 39.130 21.26 21.26 44.67 2.71
3646 3704 3.322369 TGTTGAATGTTCGCTCGTACAT 58.678 40.909 8.38 8.38 37.65 2.29
3647 3705 2.745102 TGTTGAATGTTCGCTCGTACA 58.255 42.857 4.35 4.35 0.00 2.90
3648 3706 3.781341 TTGTTGAATGTTCGCTCGTAC 57.219 42.857 0.00 0.00 0.00 3.67
3649 3707 4.320667 CATTGTTGAATGTTCGCTCGTA 57.679 40.909 0.00 0.00 35.19 3.43
3650 3708 3.187478 CATTGTTGAATGTTCGCTCGT 57.813 42.857 0.00 0.00 35.19 4.18
3731 3789 3.485463 AAGTGTTGTTCCGATCTTGGA 57.515 42.857 0.00 0.00 35.83 3.53
3732 3790 3.563808 TGAAAGTGTTGTTCCGATCTTGG 59.436 43.478 0.00 0.00 0.00 3.61
3740 3798 8.474006 AACTAATTTTGTGAAAGTGTTGTTCC 57.526 30.769 0.00 0.00 0.00 3.62
3812 3876 4.038883 TGTCACCAATGCAAATGATTGTCA 59.961 37.500 4.54 3.44 38.85 3.58
3836 5289 3.124921 CCGACGTGGCACCAATCC 61.125 66.667 12.86 0.00 0.00 3.01
3849 5302 2.420022 AGCAAAGACACATTATGCCGAC 59.580 45.455 0.00 0.00 37.73 4.79
3855 5308 5.574188 AGGGAAGAAGCAAAGACACATTAT 58.426 37.500 0.00 0.00 0.00 1.28
3882 5336 2.221055 GGCAATAATTAGAGCACCGTCG 59.779 50.000 12.33 0.00 0.00 5.12
3883 5337 3.202906 TGGCAATAATTAGAGCACCGTC 58.797 45.455 12.33 0.00 0.00 4.79
3886 5340 2.951642 TGCTGGCAATAATTAGAGCACC 59.048 45.455 12.33 1.44 31.66 5.01
3887 5341 3.957468 GTGCTGGCAATAATTAGAGCAC 58.043 45.455 15.00 15.00 46.66 4.40
3888 5342 2.951642 GGTGCTGGCAATAATTAGAGCA 59.048 45.455 12.33 0.00 34.16 4.26
3890 5344 2.549754 CGGGTGCTGGCAATAATTAGAG 59.450 50.000 0.00 0.00 0.00 2.43
3892 5346 2.571212 TCGGGTGCTGGCAATAATTAG 58.429 47.619 0.00 0.00 0.00 1.73
3893 5347 2.719531 TCGGGTGCTGGCAATAATTA 57.280 45.000 0.00 0.00 0.00 1.40
3894 5348 1.750778 CTTCGGGTGCTGGCAATAATT 59.249 47.619 0.00 0.00 0.00 1.40
3895 5349 1.392589 CTTCGGGTGCTGGCAATAAT 58.607 50.000 0.00 0.00 0.00 1.28
3896 5350 1.312371 GCTTCGGGTGCTGGCAATAA 61.312 55.000 0.00 0.00 0.00 1.40
3897 5351 1.748879 GCTTCGGGTGCTGGCAATA 60.749 57.895 0.00 0.00 0.00 1.90
3898 5352 3.064324 GCTTCGGGTGCTGGCAAT 61.064 61.111 0.00 0.00 0.00 3.56
3899 5353 4.577677 TGCTTCGGGTGCTGGCAA 62.578 61.111 0.00 0.00 0.00 4.52
3908 5362 2.550699 TAATGGCCACCTGCTTCGGG 62.551 60.000 8.16 0.00 40.92 5.14
3909 5363 1.077787 TAATGGCCACCTGCTTCGG 60.078 57.895 8.16 0.00 40.92 4.30
3917 5371 2.693074 CCAATACAACCTAATGGCCACC 59.307 50.000 8.16 0.00 36.63 4.61
3934 5388 0.767375 ACACTGAGCACCTGACCAAT 59.233 50.000 0.00 0.00 0.00 3.16
3950 5404 1.674057 CCACCACCCTGAGAGACAC 59.326 63.158 0.00 0.00 0.00 3.67
3951 5405 2.217038 GCCACCACCCTGAGAGACA 61.217 63.158 0.00 0.00 0.00 3.41
4027 6409 4.401022 TCATCCAATGCAGTCAGAAAAGT 58.599 39.130 0.00 0.00 0.00 2.66
4053 6435 2.557555 TGAGGATCTCCATGTGGTCT 57.442 50.000 0.00 0.00 38.89 3.85
4057 6439 5.303845 TCTCTTGTATGAGGATCTCCATGTG 59.696 44.000 9.57 0.00 38.89 3.21
4061 6443 4.078922 AGGTCTCTTGTATGAGGATCTCCA 60.079 45.833 0.00 0.00 38.89 3.86
4071 6453 2.224161 GGCTGGCTAGGTCTCTTGTATG 60.224 54.545 0.00 0.00 0.00 2.39
4072 6454 2.043227 GGCTGGCTAGGTCTCTTGTAT 58.957 52.381 0.00 0.00 0.00 2.29
4117 6499 0.838554 TAGCTGGTGCCACTACCCAA 60.839 55.000 0.00 0.00 40.09 4.12
4118 6500 1.229368 TAGCTGGTGCCACTACCCA 60.229 57.895 0.00 0.00 40.09 4.51
4131 6513 2.512515 GAAGGCGTGGGCTAGCTG 60.513 66.667 15.72 3.63 37.50 4.24
4135 6517 3.081409 GGGAGAAGGCGTGGGCTA 61.081 66.667 0.00 0.00 37.50 3.93


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

AutoCloner maintained by Alex Coulton.