Multiple sequence alignment - TraesCS1D01G106100

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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 TraesCS1D01G106100 chr1D 100.000 4123 0 0 1 4123 97925399 97921277 0.000000e+00 7614
1 TraesCS1D01G106100 chr1A 92.617 3860 171 56 47 3834 93404527 93400710 0.000000e+00 5445
2 TraesCS1D01G106100 chr1A 93.388 121 8 0 4003 4123 93400659 93400539 3.270000e-41 180
3 TraesCS1D01G106100 chr1B 94.337 3479 146 31 1 3444 155403553 155407015 0.000000e+00 5286
4 TraesCS1D01G106100 chr1B 91.537 898 57 14 2952 3840 155407026 155407913 0.000000e+00 1219
5 TraesCS1D01G106100 chr1B 88.000 200 17 5 3927 4123 155407949 155408144 3.210000e-56 230
6 TraesCS1D01G106100 chr7B 96.364 110 4 0 3831 3940 683101574 683101465 9.100000e-42 182
7 TraesCS1D01G106100 chr3D 95.413 109 5 0 3831 3939 536331031 536331139 1.520000e-39 174
8 TraesCS1D01G106100 chr3D 90.833 120 11 0 3829 3948 43996205 43996324 1.190000e-35 161
9 TraesCS1D01G106100 chr5D 95.370 108 5 0 3832 3939 365693410 365693303 5.480000e-39 172
10 TraesCS1D01G106100 chr5A 95.370 108 5 0 3832 3939 467377559 467377452 5.480000e-39 172
11 TraesCS1D01G106100 chr6A 93.805 113 7 0 3827 3939 170017878 170017766 1.970000e-38 171
12 TraesCS1D01G106100 chr4B 94.444 108 6 0 3832 3939 87405224 87405117 2.550000e-37 167
13 TraesCS1D01G106100 chr2B 92.241 116 9 0 3830 3945 142916537 142916422 9.170000e-37 165
14 TraesCS1D01G106100 chr6B 90.909 121 9 2 3821 3939 454733020 454733140 1.190000e-35 161


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 TraesCS1D01G106100 chr1D 97921277 97925399 4122 True 7614.0 7614 100.000000 1 4123 1 chr1D.!!$R1 4122
1 TraesCS1D01G106100 chr1A 93400539 93404527 3988 True 2812.5 5445 93.002500 47 4123 2 chr1A.!!$R1 4076
2 TraesCS1D01G106100 chr1B 155403553 155408144 4591 False 2245.0 5286 91.291333 1 4123 3 chr1B.!!$F1 4122

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
566 572 1.338769 ACATGTTTCGCCACTCCTACC 60.339 52.381 0.00 0.00 0.0 3.18 F
1003 1068 0.534203 TCGCTCTGTTTTCGCCCTTT 60.534 50.000 0.00 0.00 0.0 3.11 F
1633 1701 0.311790 AGTTCTTGCGGTTCGTACGA 59.688 50.000 15.28 15.28 0.0 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 1678 0.461339 ACGAACCGCAAGAACTGTGT 60.461 50.0 0.0 0.0 43.02 3.72 R
2344 2435 1.174783 TGTTGTCGAGACCTAGCTCC 58.825 55.0 0.0 0.0 0.00 4.70 R
3396 3504 0.320771 AGCAGTAGCCTGAACCAACG 60.321 55.0 0.0 0.0 41.50 4.10 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
151 152 4.777463 AGAAAGAAAAGAGACCGAACCAA 58.223 39.130 0.00 0.00 0.00 3.67
266 267 7.445900 TCGATTTTTGTCGTACTAGCAATAG 57.554 36.000 0.00 0.00 42.07 1.73
273 274 7.801547 TTGTCGTACTAGCAATAGTAACAAC 57.198 36.000 7.90 3.90 32.63 3.32
461 466 2.025155 ACGCATTAACACCAACACCAA 58.975 42.857 0.00 0.00 0.00 3.67
477 482 1.831736 ACCAACAGATAAGGAGGGACG 59.168 52.381 0.00 0.00 0.00 4.79
556 562 8.786937 ACATATAATCAAATCACATGTTTCGC 57.213 30.769 0.00 0.00 0.00 4.70
566 572 1.338769 ACATGTTTCGCCACTCCTACC 60.339 52.381 0.00 0.00 0.00 3.18
590 598 3.339253 AAAGGCCAAGCATTCATTTCC 57.661 42.857 5.01 0.00 28.96 3.13
681 714 8.684386 TGATGGAACTTTCAACTATGTTGTTA 57.316 30.769 9.78 0.00 0.00 2.41
691 724 8.456904 TTCAACTATGTTGTTACTACGATGTC 57.543 34.615 9.78 0.00 0.00 3.06
768 817 4.955811 ACAATGTGTGTTCTCCACTCTA 57.044 40.909 0.00 0.00 44.81 2.43
871 935 4.578516 TGGGCATGTATTGAACTTATTCGG 59.421 41.667 0.00 0.00 37.69 4.30
873 937 4.211389 GCATGTATTGAACTTATTCGGCG 58.789 43.478 0.00 0.00 37.69 6.46
876 940 5.954434 TGTATTGAACTTATTCGGCGTAC 57.046 39.130 6.85 0.00 37.69 3.67
879 943 6.535865 TGTATTGAACTTATTCGGCGTACAAT 59.464 34.615 6.85 1.72 37.69 2.71
936 1001 5.067805 GGATCCATTTTTCTCTGGCGTAATT 59.932 40.000 6.95 0.00 32.30 1.40
938 1003 5.007034 TCCATTTTTCTCTGGCGTAATTCA 58.993 37.500 0.00 0.00 32.30 2.57
939 1004 5.652014 TCCATTTTTCTCTGGCGTAATTCAT 59.348 36.000 0.00 0.00 32.30 2.57
983 1048 4.604114 CCGAAACGGGGGTACTTC 57.396 61.111 2.00 0.00 44.15 3.01
990 1055 1.753463 CGGGGGTACTTCTCGCTCT 60.753 63.158 0.00 0.00 0.00 4.09
1003 1068 0.534203 TCGCTCTGTTTTCGCCCTTT 60.534 50.000 0.00 0.00 0.00 3.11
1034 1099 5.394333 GCAACGGATAAGGAGACTAAGAACT 60.394 44.000 0.00 0.00 42.68 3.01
1156 1221 1.618343 GGCTGCTATCTCTTCTCCTCC 59.382 57.143 0.00 0.00 0.00 4.30
1159 1224 1.862911 TGCTATCTCTTCTCCTCCCCT 59.137 52.381 0.00 0.00 0.00 4.79
1163 1231 0.556380 TCTCTTCTCCTCCCCTCCCT 60.556 60.000 0.00 0.00 0.00 4.20
1240 1308 1.517832 CACGACACCCTCATCTCCC 59.482 63.158 0.00 0.00 0.00 4.30
1536 1604 1.229853 TTCCCCACTTCTCCCCTCC 60.230 63.158 0.00 0.00 0.00 4.30
1610 1678 1.075212 TGTCAACCATGGCCTGATCAA 59.925 47.619 13.04 2.87 0.00 2.57
1628 1696 0.655733 AACACAGTTCTTGCGGTTCG 59.344 50.000 0.00 0.00 0.00 3.95
1632 1700 0.433492 CAGTTCTTGCGGTTCGTACG 59.567 55.000 9.53 9.53 0.00 3.67
1633 1701 0.311790 AGTTCTTGCGGTTCGTACGA 59.688 50.000 15.28 15.28 0.00 3.43
1634 1702 1.068055 AGTTCTTGCGGTTCGTACGAT 60.068 47.619 20.27 0.00 0.00 3.73
1635 1703 1.319669 GTTCTTGCGGTTCGTACGATC 59.680 52.381 20.27 18.01 0.00 3.69
1636 1704 0.521867 TCTTGCGGTTCGTACGATCG 60.522 55.000 26.43 26.43 0.00 3.69
1684 1760 0.665835 AGCTGTTCCTAGAGCGATCG 59.334 55.000 11.69 11.69 44.91 3.69
1736 1814 7.241628 TGGCAGAGTAAGATCATAAGATAGGA 58.758 38.462 0.00 0.00 33.72 2.94
2144 2222 4.848357 CACCCATCAACCAGTAATCTCTT 58.152 43.478 0.00 0.00 0.00 2.85
2200 2278 7.453393 TCTCTGATCTGAAAAGTAACAATGGT 58.547 34.615 3.72 0.00 0.00 3.55
2256 2346 8.725148 AGAACTGAATGTGTATTGAACATCTTC 58.275 33.333 0.00 0.00 41.10 2.87
2292 2383 9.180678 GTGTATTGAACATTTTTCACTTCGATT 57.819 29.630 0.00 0.00 41.10 3.34
2344 2435 1.274712 ACAGGAAGAAGAGGAGGCAG 58.725 55.000 0.00 0.00 0.00 4.85
2745 2845 1.687368 GGATGGAGCAGCAGGGAAATT 60.687 52.381 0.00 0.00 0.00 1.82
2781 2881 3.004419 GCTGATGATGTTGATGTGATGGG 59.996 47.826 0.00 0.00 0.00 4.00
2964 3071 7.339466 ACTGTGATTAGTCCAGAGTTTGTTTTT 59.661 33.333 9.60 0.00 34.99 1.94
3151 3258 6.039605 TCAATCAGTGCAAATCAAGACAGAAA 59.960 34.615 0.00 0.00 0.00 2.52
3305 3413 4.832266 TCATGCCAAAGTGATAACCTTTGT 59.168 37.500 10.84 0.00 44.61 2.83
3396 3504 0.321671 TCAGCCCTACTGCAGTTGAC 59.678 55.000 27.06 17.51 46.76 3.18
3555 4165 3.089284 CCTATGGTTTTGGGAGTGGTTC 58.911 50.000 0.00 0.00 0.00 3.62
3617 4231 0.314935 CAACATGTCACAGGGTTGCC 59.685 55.000 11.05 0.00 34.86 4.52
3670 4284 1.649664 CCAGTTCAGCTTCCTCATCG 58.350 55.000 0.00 0.00 0.00 3.84
3741 4355 1.708341 AGTTTGTGAAGCCTGCCAAT 58.292 45.000 0.00 0.00 0.00 3.16
3744 4358 0.469705 TTGTGAAGCCTGCCAATGGT 60.470 50.000 0.00 0.00 0.00 3.55
3753 4367 3.331591 AGCCTGCCAATGGTGATATATCA 59.668 43.478 11.49 11.49 0.00 2.15
3763 4377 8.824781 CCAATGGTGATATATCAATCGAAGATC 58.175 37.037 16.97 1.74 45.12 2.75
3800 4414 2.220653 AGCAAGCTGGGCATAAGAAA 57.779 45.000 12.59 0.00 0.00 2.52
3840 4455 6.325286 ACAGATTCTTGAATAGTACTCCCTCC 59.675 42.308 0.00 0.00 0.00 4.30
3843 4458 4.607239 TCTTGAATAGTACTCCCTCCGTT 58.393 43.478 0.00 0.00 0.00 4.44
3844 4459 5.021458 TCTTGAATAGTACTCCCTCCGTTT 58.979 41.667 0.00 0.00 0.00 3.60
3845 4460 4.730949 TGAATAGTACTCCCTCCGTTTG 57.269 45.455 0.00 0.00 0.00 2.93
3848 4463 5.012354 TGAATAGTACTCCCTCCGTTTGTTT 59.988 40.000 0.00 0.00 0.00 2.83
3849 4464 3.851458 AGTACTCCCTCCGTTTGTTTT 57.149 42.857 0.00 0.00 0.00 2.43
3858 4473 5.409214 TCCCTCCGTTTGTTTTTATAAGACG 59.591 40.000 0.00 0.00 0.00 4.18
3859 4474 5.179929 CCCTCCGTTTGTTTTTATAAGACGT 59.820 40.000 0.00 0.00 0.00 4.34
3860 4475 6.293571 CCCTCCGTTTGTTTTTATAAGACGTT 60.294 38.462 0.00 0.00 0.00 3.99
3862 4477 7.321984 CCTCCGTTTGTTTTTATAAGACGTTTC 59.678 37.037 0.00 0.00 0.00 2.78
3863 4478 7.692088 TCCGTTTGTTTTTATAAGACGTTTCA 58.308 30.769 0.00 0.00 0.00 2.69
3864 4479 7.851963 TCCGTTTGTTTTTATAAGACGTTTCAG 59.148 33.333 0.00 0.00 0.00 3.02
3865 4480 7.851963 CCGTTTGTTTTTATAAGACGTTTCAGA 59.148 33.333 0.00 0.00 0.00 3.27
3866 4481 8.667204 CGTTTGTTTTTATAAGACGTTTCAGAC 58.333 33.333 0.00 0.00 0.00 3.51
3868 4483 9.710979 TTTGTTTTTATAAGACGTTTCAGACAG 57.289 29.630 0.00 0.00 0.00 3.51
3869 4484 7.857569 TGTTTTTATAAGACGTTTCAGACAGG 58.142 34.615 0.00 0.00 0.00 4.00
3870 4485 7.496591 TGTTTTTATAAGACGTTTCAGACAGGT 59.503 33.333 0.00 0.00 0.00 4.00
3871 4486 8.340443 GTTTTTATAAGACGTTTCAGACAGGTT 58.660 33.333 0.00 0.00 0.00 3.50
3873 4488 1.583054 AGACGTTTCAGACAGGTTGC 58.417 50.000 0.00 0.00 0.00 4.17
3874 4489 1.139058 AGACGTTTCAGACAGGTTGCT 59.861 47.619 0.00 0.00 0.00 3.91
3875 4490 1.940613 GACGTTTCAGACAGGTTGCTT 59.059 47.619 0.00 0.00 0.00 3.91
3876 4491 2.354821 GACGTTTCAGACAGGTTGCTTT 59.645 45.455 0.00 0.00 0.00 3.51
3877 4492 2.097466 ACGTTTCAGACAGGTTGCTTTG 59.903 45.455 0.00 0.00 0.00 2.77
3878 4493 2.097466 CGTTTCAGACAGGTTGCTTTGT 59.903 45.455 0.00 0.00 0.00 2.83
3879 4494 3.311322 CGTTTCAGACAGGTTGCTTTGTA 59.689 43.478 0.00 0.00 0.00 2.41
3880 4495 4.598062 GTTTCAGACAGGTTGCTTTGTAC 58.402 43.478 0.00 0.00 0.00 2.90
3881 4496 3.838244 TCAGACAGGTTGCTTTGTACT 57.162 42.857 0.00 0.00 0.00 2.73
3882 4497 3.466836 TCAGACAGGTTGCTTTGTACTG 58.533 45.455 0.00 0.00 35.40 2.74
3883 4498 3.118408 TCAGACAGGTTGCTTTGTACTGT 60.118 43.478 0.00 0.00 44.34 3.55
3884 4499 3.002656 CAGACAGGTTGCTTTGTACTGTG 59.997 47.826 0.00 0.00 41.98 3.66
3885 4500 2.943033 GACAGGTTGCTTTGTACTGTGT 59.057 45.455 0.00 0.00 41.98 3.72
3886 4501 3.352648 ACAGGTTGCTTTGTACTGTGTT 58.647 40.909 0.00 0.00 40.56 3.32
3887 4502 3.128589 ACAGGTTGCTTTGTACTGTGTTG 59.871 43.478 0.00 0.00 40.56 3.33
3888 4503 3.376859 CAGGTTGCTTTGTACTGTGTTGA 59.623 43.478 0.00 0.00 0.00 3.18
3889 4504 4.013728 AGGTTGCTTTGTACTGTGTTGAA 58.986 39.130 0.00 0.00 0.00 2.69
3890 4505 4.102649 GGTTGCTTTGTACTGTGTTGAAC 58.897 43.478 0.00 0.00 0.00 3.18
3891 4506 4.380023 GGTTGCTTTGTACTGTGTTGAACA 60.380 41.667 0.00 0.00 37.22 3.18
3902 4517 4.880886 TGTGTTGAACAGTGTCTGAATG 57.119 40.909 0.00 0.00 35.18 2.67
3903 4518 4.260985 TGTGTTGAACAGTGTCTGAATGT 58.739 39.130 0.00 0.00 35.18 2.71
3904 4519 4.332543 TGTGTTGAACAGTGTCTGAATGTC 59.667 41.667 0.00 0.00 35.18 3.06
3905 4520 4.572389 GTGTTGAACAGTGTCTGAATGTCT 59.428 41.667 0.00 0.00 35.18 3.41
3906 4521 5.753438 GTGTTGAACAGTGTCTGAATGTCTA 59.247 40.000 0.00 0.00 35.18 2.59
3907 4522 6.257849 GTGTTGAACAGTGTCTGAATGTCTAA 59.742 38.462 0.00 0.00 35.18 2.10
3908 4523 6.821160 TGTTGAACAGTGTCTGAATGTCTAAA 59.179 34.615 0.00 0.00 35.18 1.85
3909 4524 7.335673 TGTTGAACAGTGTCTGAATGTCTAAAA 59.664 33.333 0.00 0.00 35.18 1.52
3910 4525 8.345565 GTTGAACAGTGTCTGAATGTCTAAAAT 58.654 33.333 0.00 0.00 35.18 1.82
3911 4526 7.864686 TGAACAGTGTCTGAATGTCTAAAATG 58.135 34.615 0.00 0.00 35.18 2.32
3912 4527 7.498900 TGAACAGTGTCTGAATGTCTAAAATGT 59.501 33.333 0.00 0.00 35.18 2.71
3913 4528 7.426929 ACAGTGTCTGAATGTCTAAAATGTC 57.573 36.000 3.70 0.00 35.18 3.06
3914 4529 7.220030 ACAGTGTCTGAATGTCTAAAATGTCT 58.780 34.615 3.70 0.00 35.18 3.41
3915 4530 7.716998 ACAGTGTCTGAATGTCTAAAATGTCTT 59.283 33.333 3.70 0.00 35.18 3.01
3916 4531 9.208022 CAGTGTCTGAATGTCTAAAATGTCTTA 57.792 33.333 0.00 0.00 32.44 2.10
3917 4532 9.950496 AGTGTCTGAATGTCTAAAATGTCTTAT 57.050 29.630 0.00 0.00 0.00 1.73
3948 4563 3.700038 ACAGAGGAAGTACCAGATAACCG 59.300 47.826 0.00 0.00 42.04 4.44
3952 4567 2.093341 GGAAGTACCAGATAACCGGCAA 60.093 50.000 0.00 0.00 38.79 4.52
3969 4587 3.438087 CGGCAATCTAGCTATCAAATGGG 59.562 47.826 0.00 0.00 34.17 4.00
3975 4593 0.468771 AGCTATCAAATGGGCAGCCC 60.469 55.000 25.54 25.54 45.71 5.19
3984 4602 0.178924 ATGGGCAGCCCTTTTCACTT 60.179 50.000 31.51 3.21 45.70 3.16
4009 4627 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4010 4628 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4011 4629 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4012 4630 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4013 4631 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4023 4641 2.289133 ACACACACACACACACACACTA 60.289 45.455 0.00 0.00 0.00 2.74
4024 4642 2.935849 CACACACACACACACACACTAT 59.064 45.455 0.00 0.00 0.00 2.12
4041 4659 4.040952 ACACTATGAGCTGTTCCAAGAAGT 59.959 41.667 0.00 0.00 0.00 3.01
4059 4677 0.312102 GTGGGAAGCAAAGCACTGAC 59.688 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.554490 ACTACCTCTACCAAAATATGAGATGT 57.446 34.615 0.00 0.00 0.00 3.06
72 73 5.084519 AGTTCCCTGATTTTAAACCCTTCC 58.915 41.667 0.00 0.00 0.00 3.46
110 111 5.487153 TTCTTTTTGTTGCTACTAACGCA 57.513 34.783 0.00 0.00 33.28 5.24
151 152 7.653713 CCTTATCTGCTGACGTTAGTGATAATT 59.346 37.037 23.63 8.67 31.63 1.40
231 232 7.186021 ACGACAAAAATCGAACTCATAGTTT 57.814 32.000 1.63 0.00 45.13 2.66
266 267 7.757624 TGTGTTCCATCTTTTTCTTGTTGTTAC 59.242 33.333 0.00 0.00 0.00 2.50
273 274 8.870160 TGTTAATGTGTTCCATCTTTTTCTTG 57.130 30.769 0.00 0.00 31.75 3.02
461 466 2.544844 TTCCGTCCCTCCTTATCTGT 57.455 50.000 0.00 0.00 0.00 3.41
477 482 1.464997 CTACTTTGCTCACCGCTTTCC 59.535 52.381 0.00 0.00 40.11 3.13
544 550 0.396435 AGGAGTGGCGAAACATGTGA 59.604 50.000 0.00 0.00 0.00 3.58
576 584 1.473677 TGGAGCGGAAATGAATGCTTG 59.526 47.619 0.00 0.00 37.91 4.01
577 585 1.838112 TGGAGCGGAAATGAATGCTT 58.162 45.000 0.00 0.00 37.91 3.91
681 714 7.433708 TGAAATTTGTTGATGACATCGTAGT 57.566 32.000 10.79 0.00 38.26 2.73
832 881 7.042797 ACATGCCCATTTAAAGTTGCTATAG 57.957 36.000 0.00 0.00 0.00 1.31
871 935 4.030529 GCATGAAAACATGTGATTGTACGC 59.969 41.667 0.00 0.00 35.16 4.42
873 937 6.380995 TGAGCATGAAAACATGTGATTGTAC 58.619 36.000 0.00 0.00 35.16 2.90
876 940 5.692654 TGTTGAGCATGAAAACATGTGATTG 59.307 36.000 0.00 0.00 35.16 2.67
879 943 4.915158 TGTTGAGCATGAAAACATGTGA 57.085 36.364 0.00 0.00 35.16 3.58
951 1016 3.552699 CGTTTCGGGTAAATATGAAGCGA 59.447 43.478 4.42 0.00 44.33 4.93
983 1048 0.951040 AAGGGCGAAAACAGAGCGAG 60.951 55.000 0.00 0.00 0.00 5.03
990 1055 2.544903 GCTAGCAAAAAGGGCGAAAACA 60.545 45.455 10.63 0.00 36.08 2.83
1003 1068 3.196901 TCTCCTTATCCGTTGCTAGCAAA 59.803 43.478 30.83 16.87 37.70 3.68
1138 1203 2.158325 AGGGGAGGAGAAGAGATAGCAG 60.158 54.545 0.00 0.00 0.00 4.24
1156 1221 0.691413 GAGTAGTTGGGGAGGGAGGG 60.691 65.000 0.00 0.00 0.00 4.30
1159 1224 1.160289 AGGGAGTAGTTGGGGAGGGA 61.160 60.000 0.00 0.00 0.00 4.20
1163 1231 1.394963 GGGAGGGAGTAGTTGGGGA 59.605 63.158 0.00 0.00 0.00 4.81
1240 1308 1.811266 CTCGGCGGTGATCTTGGTG 60.811 63.158 7.21 0.00 0.00 4.17
1536 1604 6.591448 AGCACAAACAAGAAAGAAAGGAAAAG 59.409 34.615 0.00 0.00 0.00 2.27
1610 1678 0.461339 ACGAACCGCAAGAACTGTGT 60.461 50.000 0.00 0.00 43.02 3.72
1634 1702 2.492019 ATCAAGAATCGATCGCACGA 57.508 45.000 11.09 6.28 46.04 4.35
1635 1703 4.893036 ATAATCAAGAATCGATCGCACG 57.107 40.909 11.09 0.00 0.00 5.34
1636 1704 6.251589 ACGATATAATCAAGAATCGATCGCAC 59.748 38.462 11.09 4.10 42.88 5.34
1684 1760 5.221422 ACAGAGGCTCTAATGATTCTAGCAC 60.221 44.000 18.26 6.87 34.85 4.40
1736 1814 2.358322 ACCCGGATTAAAATCGCCAT 57.642 45.000 0.73 0.00 36.27 4.40
2151 2229 5.528043 ACATATCACTTTTGCCAACAACA 57.472 34.783 0.00 0.00 34.87 3.33
2152 2230 6.701400 AGAAACATATCACTTTTGCCAACAAC 59.299 34.615 0.00 0.00 34.87 3.32
2153 2231 6.815089 AGAAACATATCACTTTTGCCAACAA 58.185 32.000 0.00 0.00 0.00 2.83
2154 2232 6.265196 AGAGAAACATATCACTTTTGCCAACA 59.735 34.615 0.00 0.00 0.00 3.33
2165 2243 9.160496 ACTTTTCAGATCAGAGAAACATATCAC 57.840 33.333 7.30 0.00 33.82 3.06
2200 2278 6.250711 TGTTATCAGACTAGGACCACTAACA 58.749 40.000 0.00 0.00 0.00 2.41
2263 2353 8.802856 CGAAGTGAAAAATGTTCAATACACAAA 58.197 29.630 0.00 0.00 40.19 2.83
2292 2383 1.567537 GCGTTGCAAAGCGTCTACA 59.432 52.632 21.24 0.00 0.00 2.74
2344 2435 1.174783 TGTTGTCGAGACCTAGCTCC 58.825 55.000 0.00 0.00 0.00 4.70
2745 2845 5.129980 ACATCATCAGCCTGAAAGAGACATA 59.870 40.000 0.00 0.00 34.07 2.29
2781 2881 2.170397 CCAAATACAAAATCCAGCCCCC 59.830 50.000 0.00 0.00 0.00 5.40
2964 3071 8.956426 GGAACACATTGAATCAGGAGTAAAATA 58.044 33.333 0.00 0.00 0.00 1.40
2972 3079 5.715439 ATAGGGAACACATTGAATCAGGA 57.285 39.130 0.00 0.00 0.00 3.86
3118 3225 7.410800 TGATTTGCACTGATTGAATTGAAAC 57.589 32.000 0.00 0.00 0.00 2.78
3151 3258 5.953183 TCAATCAGCATAAGAAACGCAAAT 58.047 33.333 0.00 0.00 0.00 2.32
3305 3413 7.170393 TGCTGAGCTTGTCTCTAACTAATAA 57.830 36.000 5.83 0.00 42.38 1.40
3396 3504 0.320771 AGCAGTAGCCTGAACCAACG 60.321 55.000 0.00 0.00 41.50 4.10
3555 4165 4.737054 CATGAAAAGTCCCGGAGAATTTG 58.263 43.478 15.75 4.43 41.72 2.32
3670 4284 0.322816 TGGAGCAGGAGTTTGATGGC 60.323 55.000 0.00 0.00 0.00 4.40
3741 4355 8.367156 TGTTGATCTTCGATTGATATATCACCA 58.633 33.333 15.10 2.19 36.36 4.17
3744 4358 9.987272 ACTTGTTGATCTTCGATTGATATATCA 57.013 29.630 11.49 11.49 34.44 2.15
3753 4367 8.608844 AAAGAGTAACTTGTTGATCTTCGATT 57.391 30.769 12.25 0.39 38.98 3.34
3763 4377 7.166473 CAGCTTGCTTAAAAGAGTAACTTGTTG 59.834 37.037 0.00 0.00 38.98 3.33
3800 4414 4.708421 AGAATCTGTTGCCATTGCTATTGT 59.292 37.500 0.00 0.00 38.71 2.71
3840 4455 8.667204 GTCTGAAACGTCTTATAAAAACAAACG 58.333 33.333 0.00 0.00 35.00 3.60
3843 4458 8.339714 CCTGTCTGAAACGTCTTATAAAAACAA 58.660 33.333 0.00 0.00 0.00 2.83
3844 4459 7.496591 ACCTGTCTGAAACGTCTTATAAAAACA 59.503 33.333 0.00 0.00 0.00 2.83
3845 4460 7.858583 ACCTGTCTGAAACGTCTTATAAAAAC 58.141 34.615 0.00 0.00 0.00 2.43
3848 4463 6.073440 GCAACCTGTCTGAAACGTCTTATAAA 60.073 38.462 0.00 0.00 0.00 1.40
3849 4464 5.407387 GCAACCTGTCTGAAACGTCTTATAA 59.593 40.000 0.00 0.00 0.00 0.98
3858 4473 3.782889 ACAAAGCAACCTGTCTGAAAC 57.217 42.857 0.00 0.00 0.00 2.78
3859 4474 4.335315 CAGTACAAAGCAACCTGTCTGAAA 59.665 41.667 0.00 0.00 0.00 2.69
3860 4475 3.876914 CAGTACAAAGCAACCTGTCTGAA 59.123 43.478 0.00 0.00 0.00 3.02
3862 4477 3.002656 CACAGTACAAAGCAACCTGTCTG 59.997 47.826 0.00 0.00 34.31 3.51
3863 4478 3.206150 CACAGTACAAAGCAACCTGTCT 58.794 45.455 0.00 0.00 34.31 3.41
3864 4479 2.943033 ACACAGTACAAAGCAACCTGTC 59.057 45.455 0.00 0.00 34.31 3.51
3865 4480 2.999331 ACACAGTACAAAGCAACCTGT 58.001 42.857 0.00 0.00 36.85 4.00
3866 4481 3.376859 TCAACACAGTACAAAGCAACCTG 59.623 43.478 0.00 0.00 0.00 4.00
3868 4483 4.102649 GTTCAACACAGTACAAAGCAACC 58.897 43.478 0.00 0.00 0.00 3.77
3869 4484 4.728534 TGTTCAACACAGTACAAAGCAAC 58.271 39.130 0.00 0.00 0.00 4.17
3881 4496 4.260985 ACATTCAGACACTGTTCAACACA 58.739 39.130 0.00 0.00 32.61 3.72
3882 4497 4.572389 AGACATTCAGACACTGTTCAACAC 59.428 41.667 0.00 0.00 32.61 3.32
3883 4498 4.769688 AGACATTCAGACACTGTTCAACA 58.230 39.130 0.00 0.00 32.61 3.33
3884 4499 6.844696 TTAGACATTCAGACACTGTTCAAC 57.155 37.500 0.00 0.00 32.61 3.18
3885 4500 7.857734 TTTTAGACATTCAGACACTGTTCAA 57.142 32.000 0.00 0.00 32.61 2.69
3886 4501 7.498900 ACATTTTAGACATTCAGACACTGTTCA 59.501 33.333 0.00 0.00 32.61 3.18
3887 4502 7.865707 ACATTTTAGACATTCAGACACTGTTC 58.134 34.615 0.00 0.00 32.61 3.18
3888 4503 7.716998 AGACATTTTAGACATTCAGACACTGTT 59.283 33.333 0.00 0.00 32.61 3.16
3889 4504 7.220030 AGACATTTTAGACATTCAGACACTGT 58.780 34.615 0.00 0.00 32.61 3.55
3890 4505 7.664082 AGACATTTTAGACATTCAGACACTG 57.336 36.000 0.00 0.00 0.00 3.66
3891 4506 9.950496 ATAAGACATTTTAGACATTCAGACACT 57.050 29.630 0.00 0.00 0.00 3.55
3910 4525 9.793259 ACTTCCTCTGTTCATTTTTATAAGACA 57.207 29.630 0.00 0.00 0.00 3.41
3915 4530 9.667107 CTGGTACTTCCTCTGTTCATTTTTATA 57.333 33.333 0.00 0.00 37.07 0.98
3916 4531 8.383175 TCTGGTACTTCCTCTGTTCATTTTTAT 58.617 33.333 0.00 0.00 37.07 1.40
3917 4532 7.741785 TCTGGTACTTCCTCTGTTCATTTTTA 58.258 34.615 0.00 0.00 37.07 1.52
3918 4533 6.601332 TCTGGTACTTCCTCTGTTCATTTTT 58.399 36.000 0.00 0.00 37.07 1.94
3919 4534 6.187727 TCTGGTACTTCCTCTGTTCATTTT 57.812 37.500 0.00 0.00 37.07 1.82
3920 4535 5.825593 TCTGGTACTTCCTCTGTTCATTT 57.174 39.130 0.00 0.00 37.07 2.32
3921 4536 7.331791 GTTATCTGGTACTTCCTCTGTTCATT 58.668 38.462 0.00 0.00 37.07 2.57
3922 4537 6.127026 GGTTATCTGGTACTTCCTCTGTTCAT 60.127 42.308 0.00 0.00 37.07 2.57
3923 4538 5.187186 GGTTATCTGGTACTTCCTCTGTTCA 59.813 44.000 0.00 0.00 37.07 3.18
3924 4539 5.662456 GGTTATCTGGTACTTCCTCTGTTC 58.338 45.833 0.00 0.00 37.07 3.18
3925 4540 4.159879 CGGTTATCTGGTACTTCCTCTGTT 59.840 45.833 0.00 0.00 37.07 3.16
3933 4548 3.454812 AGATTGCCGGTTATCTGGTACTT 59.545 43.478 16.54 0.00 41.89 2.24
3935 4550 3.470645 AGATTGCCGGTTATCTGGTAC 57.529 47.619 16.54 0.00 41.89 3.34
3948 4563 3.192212 GCCCATTTGATAGCTAGATTGCC 59.808 47.826 0.00 0.00 0.00 4.52
3952 4567 3.560882 GGCTGCCCATTTGATAGCTAGAT 60.561 47.826 7.66 0.00 34.89 1.98
3969 4587 2.360801 TGTGTTAAGTGAAAAGGGCTGC 59.639 45.455 0.00 0.00 0.00 5.25
3975 4593 5.567534 GTGTGTGTGTGTGTTAAGTGAAAAG 59.432 40.000 0.00 0.00 0.00 2.27
3984 4602 2.480802 GTGTGTGTGTGTGTGTGTGTTA 59.519 45.455 0.00 0.00 0.00 2.41
4009 4627 2.477754 CAGCTCATAGTGTGTGTGTGTG 59.522 50.000 0.00 0.00 0.00 3.82
4010 4628 2.103094 ACAGCTCATAGTGTGTGTGTGT 59.897 45.455 0.00 0.00 0.00 3.72
4011 4629 2.759191 ACAGCTCATAGTGTGTGTGTG 58.241 47.619 0.00 0.00 0.00 3.82
4012 4630 3.393800 GAACAGCTCATAGTGTGTGTGT 58.606 45.455 0.00 0.00 0.00 3.72
4013 4631 2.738846 GGAACAGCTCATAGTGTGTGTG 59.261 50.000 0.00 0.00 0.00 3.82
4041 4659 0.183492 AGTCAGTGCTTTGCTTCCCA 59.817 50.000 0.00 0.00 0.00 4.37
4047 4665 3.307242 CGAGGTAATAGTCAGTGCTTTGC 59.693 47.826 0.00 0.00 0.00 3.68
4059 4677 3.914312 CACTATGTGCCCGAGGTAATAG 58.086 50.000 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.