Multiple sequence alignment - TraesCS3A01G489000

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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 TraesCS3A01G489000 chr3A 100.000 4572 0 0 1 4572 716755676 716760247 0.000000e+00 8444.0
1 TraesCS3A01G489000 chr3D 94.673 4618 129 35 1 4572 581117130 581112584 0.000000e+00 7057.0
2 TraesCS3A01G489000 chr3D 88.265 196 18 5 1 192 555272132 555271938 3.560000e-56 230.0
3 TraesCS3A01G489000 chr3D 97.297 37 1 0 1109 1145 417738712 417738748 3.820000e-06 63.9
4 TraesCS3A01G489000 chr3B 93.810 4443 173 52 180 4572 777577879 777582269 0.000000e+00 6588.0
5 TraesCS3A01G489000 chr3B 97.297 37 1 0 1109 1145 544109566 544109602 3.820000e-06 63.9
6 TraesCS3A01G489000 chr5D 79.095 751 127 28 2575 3313 222739328 222740060 1.480000e-134 490.0
7 TraesCS3A01G489000 chr5D 88.462 182 19 2 1 181 553900928 553900748 7.700000e-53 219.0
8 TraesCS3A01G489000 chr5D 90.566 159 15 0 1004 1162 222737951 222738109 1.290000e-50 211.0
9 TraesCS3A01G489000 chr5A 78.961 751 128 28 2575 3313 304539225 304538493 6.880000e-133 484.0
10 TraesCS3A01G489000 chr5A 92.667 150 11 0 1013 1162 304540594 304540445 2.770000e-52 217.0
11 TraesCS3A01G489000 chr5B 78.296 751 133 28 2575 3313 250234455 250233723 1.500000e-124 457.0
12 TraesCS3A01G489000 chr5B 92.000 150 12 0 1013 1162 250235826 250235677 1.290000e-50 211.0
13 TraesCS3A01G489000 chrUn 89.130 184 17 3 1 182 101935619 101935801 4.600000e-55 226.0
14 TraesCS3A01G489000 chr2A 88.649 185 18 3 1 183 557392562 557392379 5.950000e-54 222.0
15 TraesCS3A01G489000 chr1B 90.116 172 14 3 1 170 26825956 26826126 2.140000e-53 220.0
16 TraesCS3A01G489000 chr1B 87.500 184 20 3 1 182 413503329 413503511 4.630000e-50 209.0
17 TraesCS3A01G489000 chr6D 89.205 176 15 4 9 182 459843239 459843066 2.770000e-52 217.0
18 TraesCS3A01G489000 chr4B 87.568 185 20 3 1 183 147722551 147722734 1.290000e-50 211.0


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 TraesCS3A01G489000 chr3A 716755676 716760247 4571 False 8444.0 8444 100.0000 1 4572 1 chr3A.!!$F1 4571
1 TraesCS3A01G489000 chr3D 581112584 581117130 4546 True 7057.0 7057 94.6730 1 4572 1 chr3D.!!$R2 4571
2 TraesCS3A01G489000 chr3B 777577879 777582269 4390 False 6588.0 6588 93.8100 180 4572 1 chr3B.!!$F2 4392
3 TraesCS3A01G489000 chr5D 222737951 222740060 2109 False 350.5 490 84.8305 1004 3313 2 chr5D.!!$F1 2309
4 TraesCS3A01G489000 chr5A 304538493 304540594 2101 True 350.5 484 85.8140 1013 3313 2 chr5A.!!$R1 2300
5 TraesCS3A01G489000 chr5B 250233723 250235826 2103 True 334.0 457 85.1480 1013 3313 2 chr5B.!!$R1 2300

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
647 662 0.793617 ACTGGGGAGAAAGGGAGAGA 59.206 55.0 0.00 0.0 0.00 3.10 F
1557 1659 0.464452 CCGTCCTCACCCAGGTAATC 59.536 60.0 0.00 0.0 43.95 1.75 F
1799 1916 0.248134 GCTACTCGAGTGTGGTAGCG 60.248 60.0 28.12 6.9 45.35 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1809 0.179067 GCCGATCCCAACATAACCGA 60.179 55.000 0.0 0.0 0.00 4.69 R
3556 4086 0.394762 TGTCTCATGGGAAGCCATGC 60.395 55.000 0.0 0.0 44.95 4.06 R
3658 4189 4.814771 TGATCATGCATTCTCATCACTGAC 59.185 41.667 0.0 0.0 0.00 3.51 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
57 58 5.422214 AAAAGATACAGACAATCGGGAGT 57.578 39.130 0.00 0.00 0.00 3.85
59 60 3.632333 AGATACAGACAATCGGGAGTGA 58.368 45.455 2.84 0.00 0.00 3.41
91 92 2.879103 TTTCTGGAGGGCTAACAAGG 57.121 50.000 0.00 0.00 0.00 3.61
102 103 3.630312 GGGCTAACAAGGAAATTATGCGA 59.370 43.478 0.00 0.00 0.00 5.10
131 132 7.330900 AGAAGAAATGCATCTTACATTCTGG 57.669 36.000 9.28 0.00 39.70 3.86
138 139 8.937634 AATGCATCTTACATTCTGGAATTTTC 57.062 30.769 0.00 0.00 32.28 2.29
141 142 9.241919 TGCATCTTACATTCTGGAATTTTCTTA 57.758 29.630 0.00 0.00 0.00 2.10
192 193 4.772886 TGAGGAAGTATAAAGGAAGCCC 57.227 45.455 0.00 0.00 0.00 5.19
208 209 2.565841 AGCCCTGCATCGTCTTTAATC 58.434 47.619 0.00 0.00 0.00 1.75
216 217 5.660460 TGCATCGTCTTTAATCTTGCTCTA 58.340 37.500 0.00 0.00 0.00 2.43
234 235 3.366396 TCTACTCTCCTACAAGGCAAGG 58.634 50.000 0.00 0.00 34.61 3.61
495 500 0.949582 TCCTACCTAGCTCCCCCAAT 59.050 55.000 0.00 0.00 0.00 3.16
505 510 1.999634 CTCCCCCAATACAGGCCCAG 62.000 65.000 0.00 0.00 0.00 4.45
522 527 2.558350 CCCAGAAAAATCTCAAGCCCCT 60.558 50.000 0.00 0.00 0.00 4.79
562 577 2.497675 GAGAGAGAATGGGTGTGTGCTA 59.502 50.000 0.00 0.00 0.00 3.49
563 578 2.499289 AGAGAGAATGGGTGTGTGCTAG 59.501 50.000 0.00 0.00 0.00 3.42
646 661 1.662686 AACTGGGGAGAAAGGGAGAG 58.337 55.000 0.00 0.00 0.00 3.20
647 662 0.793617 ACTGGGGAGAAAGGGAGAGA 59.206 55.000 0.00 0.00 0.00 3.10
648 663 1.273552 ACTGGGGAGAAAGGGAGAGAG 60.274 57.143 0.00 0.00 0.00 3.20
649 664 1.007721 CTGGGGAGAAAGGGAGAGAGA 59.992 57.143 0.00 0.00 0.00 3.10
650 665 1.007721 TGGGGAGAAAGGGAGAGAGAG 59.992 57.143 0.00 0.00 0.00 3.20
651 666 1.289530 GGGGAGAAAGGGAGAGAGAGA 59.710 57.143 0.00 0.00 0.00 3.10
936 957 2.360801 CTCTCCCTCTCCGAATTGACTC 59.639 54.545 0.00 0.00 0.00 3.36
951 972 4.609866 TTGACTCATAGAGGAGGAGGAA 57.390 45.455 0.00 0.00 40.42 3.36
963 984 4.214327 GAGGAAGAGGAGGCGGCG 62.214 72.222 0.51 0.51 0.00 6.46
974 995 3.953887 GGCGGCGGATTAGCAAGC 61.954 66.667 9.78 1.26 40.05 4.01
1557 1659 0.464452 CCGTCCTCACCCAGGTAATC 59.536 60.000 0.00 0.00 43.95 1.75
1564 1666 4.785914 TCCTCACCCAGGTAATCAATTACA 59.214 41.667 13.37 0.00 43.95 2.41
1567 1669 6.710744 CCTCACCCAGGTAATCAATTACATAC 59.289 42.308 13.37 0.00 43.33 2.39
1568 1670 7.420214 CCTCACCCAGGTAATCAATTACATACT 60.420 40.741 13.37 1.21 43.33 2.12
1604 1709 2.169144 CCCAATTCCCAATTCTTGCTCC 59.831 50.000 0.00 0.00 0.00 4.70
1608 1713 1.275666 TCCCAATTCTTGCTCCTCGA 58.724 50.000 0.00 0.00 0.00 4.04
1617 1722 1.002544 CTTGCTCCTCGACCCTCTTTT 59.997 52.381 0.00 0.00 0.00 2.27
1622 1727 1.198759 CCTCGACCCTCTTTTCCCCA 61.199 60.000 0.00 0.00 0.00 4.96
1623 1728 0.912486 CTCGACCCTCTTTTCCCCAT 59.088 55.000 0.00 0.00 0.00 4.00
1624 1729 0.618458 TCGACCCTCTTTTCCCCATG 59.382 55.000 0.00 0.00 0.00 3.66
1626 1731 1.004277 CGACCCTCTTTTCCCCATGAA 59.996 52.381 0.00 0.00 0.00 2.57
1630 1736 2.827921 CCCTCTTTTCCCCATGAACAAG 59.172 50.000 0.00 0.00 31.05 3.16
1640 1746 5.012239 TCCCCATGAACAAGAATCAAGAAG 58.988 41.667 0.00 0.00 0.00 2.85
1643 1749 5.649395 CCCATGAACAAGAATCAAGAAGCTA 59.351 40.000 0.00 0.00 0.00 3.32
1644 1750 6.151648 CCCATGAACAAGAATCAAGAAGCTAA 59.848 38.462 0.00 0.00 0.00 3.09
1662 1770 5.710646 AGCTAATAATCTCTCACTCCTGGA 58.289 41.667 0.00 0.00 0.00 3.86
1698 1807 0.630673 TTGTGGGGATCAAGATGGGG 59.369 55.000 0.00 0.00 0.00 4.96
1699 1808 1.288508 TGTGGGGATCAAGATGGGGG 61.289 60.000 0.00 0.00 0.00 5.40
1700 1809 1.086565 TGGGGATCAAGATGGGGGT 59.913 57.895 0.00 0.00 0.00 4.95
1701 1810 0.993509 TGGGGATCAAGATGGGGGTC 60.994 60.000 0.00 0.00 0.00 4.46
1760 1869 3.632604 AGCAGCATTGATTTGATCTCTGG 59.367 43.478 0.00 0.00 0.00 3.86
1781 1898 4.171005 GGCCGTACCTTTTTAAATGAAGC 58.829 43.478 0.00 0.00 34.51 3.86
1799 1916 0.248134 GCTACTCGAGTGTGGTAGCG 60.248 60.000 28.12 6.90 45.35 4.26
1923 2218 0.742635 GCTTTCTTCCTCCTCCTGCG 60.743 60.000 0.00 0.00 0.00 5.18
1925 2220 1.553690 TTTCTTCCTCCTCCTGCGGG 61.554 60.000 4.71 4.71 0.00 6.13
1926 2221 4.168291 CTTCCTCCTCCTGCGGGC 62.168 72.222 6.73 0.00 0.00 6.13
1927 2222 4.722535 TTCCTCCTCCTGCGGGCT 62.723 66.667 6.73 0.00 0.00 5.19
2113 2432 4.972733 ATGGCCGCCACTGTTGCA 62.973 61.111 16.16 0.00 35.80 4.08
2231 2732 4.394439 TTTTGCGCTAGGGTTTTCTTTT 57.606 36.364 9.73 0.00 0.00 2.27
2232 2733 3.636282 TTGCGCTAGGGTTTTCTTTTC 57.364 42.857 9.73 0.00 0.00 2.29
2233 2734 2.858745 TGCGCTAGGGTTTTCTTTTCT 58.141 42.857 9.73 0.00 0.00 2.52
2234 2735 3.219281 TGCGCTAGGGTTTTCTTTTCTT 58.781 40.909 9.73 0.00 0.00 2.52
2235 2736 3.634910 TGCGCTAGGGTTTTCTTTTCTTT 59.365 39.130 9.73 0.00 0.00 2.52
2241 2742 6.039382 GCTAGGGTTTTCTTTTCTTTGTGAGA 59.961 38.462 0.00 0.00 0.00 3.27
2242 2743 6.456795 AGGGTTTTCTTTTCTTTGTGAGAG 57.543 37.500 0.00 0.00 35.37 3.20
2416 2919 8.849168 CACATCTCATATATGGGTAGAGATCTC 58.151 40.741 15.29 15.29 42.43 2.75
2434 2937 8.383175 AGAGATCTCTTCCTTTATATCGTCTCT 58.617 37.037 19.92 0.00 36.31 3.10
2436 2939 8.792633 AGATCTCTTCCTTTATATCGTCTCTTG 58.207 37.037 0.00 0.00 0.00 3.02
2439 2942 9.404848 TCTCTTCCTTTATATCGTCTCTTGTTA 57.595 33.333 0.00 0.00 0.00 2.41
2440 2943 9.672086 CTCTTCCTTTATATCGTCTCTTGTTAG 57.328 37.037 0.00 0.00 0.00 2.34
2441 2944 8.136165 TCTTCCTTTATATCGTCTCTTGTTAGC 58.864 37.037 0.00 0.00 0.00 3.09
2443 2946 8.008513 TCCTTTATATCGTCTCTTGTTAGCTT 57.991 34.615 0.00 0.00 0.00 3.74
2444 2947 7.921214 TCCTTTATATCGTCTCTTGTTAGCTTG 59.079 37.037 0.00 0.00 0.00 4.01
2445 2948 7.306866 CCTTTATATCGTCTCTTGTTAGCTTGC 60.307 40.741 0.00 0.00 0.00 4.01
2447 2950 2.947852 TCGTCTCTTGTTAGCTTGCTC 58.052 47.619 0.00 0.00 0.00 4.26
2473 2980 1.541452 CGCTCTCTCGGTCTCTCCATA 60.541 57.143 0.00 0.00 35.57 2.74
2761 3273 1.298413 CGTCGTCGCCAAGATCGAT 60.298 57.895 0.00 0.00 38.29 3.59
3265 3795 2.981302 CTCACCCACATCGAGCCA 59.019 61.111 0.00 0.00 0.00 4.75
3373 3903 1.188871 TGTACAGCGACCACCATCCA 61.189 55.000 0.00 0.00 0.00 3.41
3405 3935 2.357396 TGGCGTGTACAGCAGCAG 60.357 61.111 16.50 0.00 36.08 4.24
3487 4017 1.134098 GGGATGGACGTGATGAACCAT 60.134 52.381 4.01 4.01 44.40 3.55
3556 4086 0.389948 CCTCTTCGTTGTTCTCCCCG 60.390 60.000 0.00 0.00 0.00 5.73
3707 4244 8.140677 GATCAGATGATCCTTTTAGACTGTTG 57.859 38.462 11.08 0.00 43.85 3.33
3850 4391 4.981806 TTGGTGGTGTTCTTTTGAGAAG 57.018 40.909 0.00 0.00 0.00 2.85
3856 4397 5.800438 GTGGTGTTCTTTTGAGAAGTTTGAC 59.200 40.000 0.00 0.00 0.00 3.18
3868 4409 6.353323 TGAGAAGTTTGACAGGTGATGTTTA 58.647 36.000 0.00 0.00 44.17 2.01
4042 4584 4.384940 TGAAATCACACAAGGTCGATTGA 58.615 39.130 5.78 0.00 31.82 2.57
4108 4653 3.938963 CCCGCTGTACACAAATGTAAGAT 59.061 43.478 0.00 0.00 42.99 2.40
4162 4707 7.618117 TGTGAACAGAGGGAGTATTACTTATCA 59.382 37.037 0.00 0.00 0.00 2.15
4371 4919 7.187824 ACCTTTTGCTATCTCAACTGATAGA 57.812 36.000 13.68 0.00 45.19 1.98
4442 4992 4.195416 GGGAGTTATTTGAGGCTGAGAAG 58.805 47.826 0.00 0.00 0.00 2.85
4459 5009 8.680903 GGCTGAGAAGATTTTGAGATTATTTGA 58.319 33.333 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.764524 TGTAGCAAAAGAAGAAAGTATCTCTC 57.235 34.615 0.00 0.00 37.42 3.20
36 37 4.466370 TCACTCCCGATTGTCTGTATCTTT 59.534 41.667 0.00 0.00 0.00 2.52
37 38 4.023980 TCACTCCCGATTGTCTGTATCTT 58.976 43.478 0.00 0.00 0.00 2.40
52 53 4.846168 AAAGGGAAAGTATCTCACTCCC 57.154 45.455 0.00 0.00 40.30 4.30
57 58 5.045578 CCTCCAGAAAAGGGAAAGTATCTCA 60.046 44.000 0.00 0.00 33.11 3.27
59 60 5.443230 CCTCCAGAAAAGGGAAAGTATCT 57.557 43.478 0.00 0.00 33.11 1.98
171 172 4.164221 CAGGGCTTCCTTTATACTTCCTCA 59.836 45.833 0.00 0.00 39.29 3.86
192 193 4.569966 AGAGCAAGATTAAAGACGATGCAG 59.430 41.667 0.00 0.00 34.89 4.41
208 209 3.181480 GCCTTGTAGGAGAGTAGAGCAAG 60.181 52.174 0.00 0.00 37.67 4.01
216 217 2.327325 TCCTTGCCTTGTAGGAGAGT 57.673 50.000 0.00 0.00 37.67 3.24
495 500 4.335416 CTTGAGATTTTTCTGGGCCTGTA 58.665 43.478 4.53 0.00 0.00 2.74
505 510 7.945109 AGGTTATATAGGGGCTTGAGATTTTTC 59.055 37.037 0.00 0.00 0.00 2.29
562 577 0.998928 TGGTGCCTCTCTCTCTCTCT 59.001 55.000 0.00 0.00 0.00 3.10
563 578 1.392589 CTGGTGCCTCTCTCTCTCTC 58.607 60.000 0.00 0.00 0.00 3.20
646 661 4.646945 TCTGTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
647 662 4.614475 TCTGTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
648 663 5.105146 ACTTCTGTCTCTCTCTCTCTCTCTC 60.105 48.000 0.00 0.00 0.00 3.20
649 664 4.780021 ACTTCTGTCTCTCTCTCTCTCTCT 59.220 45.833 0.00 0.00 0.00 3.10
650 665 4.872691 CACTTCTGTCTCTCTCTCTCTCTC 59.127 50.000 0.00 0.00 0.00 3.20
651 666 4.532126 TCACTTCTGTCTCTCTCTCTCTCT 59.468 45.833 0.00 0.00 0.00 3.10
850 871 2.301583 GAGCTTGAAGAAGAGGAGTGGT 59.698 50.000 0.00 0.00 0.00 4.16
936 957 3.500289 CCTCCTCTTCCTCCTCCTCTATG 60.500 56.522 0.00 0.00 0.00 2.23
951 972 2.123425 TAATCCGCCGCCTCCTCT 60.123 61.111 0.00 0.00 0.00 3.69
1251 1272 3.797353 GGGGAAGAGGCGGATGCA 61.797 66.667 0.00 0.00 45.35 3.96
1486 1586 3.319198 GAGGGTGTCGAGGGCCAA 61.319 66.667 6.18 0.00 0.00 4.52
1564 1666 8.539856 AATTGGGGATTAATTAGGGAGAGTAT 57.460 34.615 0.00 0.00 0.00 2.12
1567 1669 6.249192 GGAATTGGGGATTAATTAGGGAGAG 58.751 44.000 0.00 0.00 0.00 3.20
1568 1670 5.075900 GGGAATTGGGGATTAATTAGGGAGA 59.924 44.000 0.00 0.00 0.00 3.71
1604 1709 0.912486 ATGGGGAAAAGAGGGTCGAG 59.088 55.000 0.00 0.00 0.00 4.04
1608 1713 1.786441 TGTTCATGGGGAAAAGAGGGT 59.214 47.619 0.00 0.00 37.23 4.34
1617 1722 4.656100 TCTTGATTCTTGTTCATGGGGA 57.344 40.909 0.00 0.00 0.00 4.81
1630 1736 9.762933 AGTGAGAGATTATTAGCTTCTTGATTC 57.237 33.333 0.00 0.00 0.00 2.52
1640 1746 5.566627 GCTCCAGGAGTGAGAGATTATTAGC 60.567 48.000 18.37 0.00 31.26 3.09
1643 1749 4.344679 CAGCTCCAGGAGTGAGAGATTATT 59.655 45.833 18.37 0.00 31.26 1.40
1644 1750 3.896888 CAGCTCCAGGAGTGAGAGATTAT 59.103 47.826 18.37 0.00 31.26 1.28
1654 1760 1.383803 GATCCCCAGCTCCAGGAGT 60.384 63.158 18.37 2.06 31.94 3.85
1662 1770 0.319728 CAATCGATCGATCCCCAGCT 59.680 55.000 29.48 10.59 33.08 4.24
1698 1807 1.578583 CGATCCCAACATAACCGACC 58.421 55.000 0.00 0.00 0.00 4.79
1699 1808 1.578583 CCGATCCCAACATAACCGAC 58.421 55.000 0.00 0.00 0.00 4.79
1700 1809 0.179067 GCCGATCCCAACATAACCGA 60.179 55.000 0.00 0.00 0.00 4.69
1701 1810 1.495584 CGCCGATCCCAACATAACCG 61.496 60.000 0.00 0.00 0.00 4.44
1760 1869 5.055642 AGCTTCATTTAAAAAGGTACGGC 57.944 39.130 3.15 0.00 31.81 5.68
1781 1898 0.377554 CCGCTACCACACTCGAGTAG 59.622 60.000 19.57 12.81 37.20 2.57
1799 1916 4.560151 GACGACGTCGACGATACC 57.440 61.111 41.52 24.56 43.02 2.73
2113 2432 4.240103 TGGTGTGCTGCTCGTGCT 62.240 61.111 11.19 0.00 40.48 4.40
2231 2732 5.321927 GGGAAATTAACCCTCTCACAAAGA 58.678 41.667 11.90 0.00 43.65 2.52
2232 2733 5.644977 GGGAAATTAACCCTCTCACAAAG 57.355 43.478 11.90 0.00 43.65 2.77
2416 2919 8.138712 AGCTAACAAGAGACGATATAAAGGAAG 58.861 37.037 0.00 0.00 0.00 3.46
2434 2937 1.604604 GGTGGTGAGCAAGCTAACAA 58.395 50.000 11.50 0.00 0.00 2.83
2436 2939 1.912371 GCGGTGGTGAGCAAGCTAAC 61.912 60.000 0.66 0.66 0.00 2.34
2439 2942 3.890936 GAGCGGTGGTGAGCAAGCT 62.891 63.158 14.15 14.15 37.69 3.74
2440 2943 3.426568 GAGCGGTGGTGAGCAAGC 61.427 66.667 0.00 5.41 35.48 4.01
2441 2944 1.739562 GAGAGCGGTGGTGAGCAAG 60.740 63.158 0.00 0.00 35.48 4.01
2443 2946 2.601666 AGAGAGCGGTGGTGAGCA 60.602 61.111 0.00 0.00 35.48 4.26
2444 2947 2.183046 GAGAGAGCGGTGGTGAGC 59.817 66.667 0.00 0.00 0.00 4.26
2445 2948 2.487428 CGAGAGAGCGGTGGTGAG 59.513 66.667 0.00 0.00 0.00 3.51
2473 2980 1.552337 CTCACAGCTCACAGGTATGGT 59.448 52.381 0.00 0.00 0.00 3.55
2876 3406 1.508632 CGGATCTTGTTGTGGTCGTT 58.491 50.000 0.00 0.00 0.00 3.85
3265 3795 1.166531 GGCACAGTCGGAGCTTGTTT 61.167 55.000 0.00 0.00 0.00 2.83
3277 3807 2.986413 ACGAGCTCGAGGCACAGT 60.986 61.111 40.58 14.59 44.79 3.55
3457 3987 1.006758 ACGTCCATCCCTAGGTTGAGA 59.993 52.381 8.29 0.00 0.00 3.27
3556 4086 0.394762 TGTCTCATGGGAAGCCATGC 60.395 55.000 0.00 0.00 44.95 4.06
3658 4189 4.814771 TGATCATGCATTCTCATCACTGAC 59.185 41.667 0.00 0.00 0.00 3.51
3699 4236 5.646577 AGACGCTACTTAATCAACAGTCT 57.353 39.130 0.00 0.00 0.00 3.24
3701 4238 6.482308 ACAAAAGACGCTACTTAATCAACAGT 59.518 34.615 0.00 0.00 0.00 3.55
3707 4244 8.182881 TCTCTCTACAAAAGACGCTACTTAATC 58.817 37.037 0.00 0.00 0.00 1.75
3876 4418 6.426328 TGCACAAAACAGAAACAGTTTTCATT 59.574 30.769 0.00 0.00 44.72 2.57
3877 4419 5.931146 TGCACAAAACAGAAACAGTTTTCAT 59.069 32.000 0.00 0.00 44.72 2.57
3884 4426 4.031991 CACACATGCACAAAACAGAAACAG 59.968 41.667 0.00 0.00 0.00 3.16
4060 4605 4.872664 ACTAGCGCATATAGGAAGACAAC 58.127 43.478 11.47 0.00 0.00 3.32
4128 4673 5.690865 ACTCCCTCTGTTCACAAATGTAAA 58.309 37.500 0.00 0.00 0.00 2.01
4190 4737 1.276844 GCTGCACGGCGCTAAATAG 59.723 57.895 6.90 2.08 43.06 1.73
4206 4753 9.313118 CAGTAAGGAAAAATAAAAACAAGTGCT 57.687 29.630 0.00 0.00 0.00 4.40
4207 4754 8.547894 CCAGTAAGGAAAAATAAAAACAAGTGC 58.452 33.333 0.00 0.00 41.22 4.40
4239 4787 7.764331 GCAGAAAATATGAATTTTGGCCAAAT 58.236 30.769 30.78 17.85 43.69 2.32
4276 4824 9.780186 ACTCTGCTACAAGTAAAATAAGTTCTT 57.220 29.630 0.00 0.00 0.00 2.52
4278 4826 7.958025 GCACTCTGCTACAAGTAAAATAAGTTC 59.042 37.037 0.00 0.00 40.96 3.01
4293 4841 6.284459 ACCTCTATTAAATGCACTCTGCTAC 58.716 40.000 0.00 0.00 45.31 3.58
4299 4847 7.443575 ACATGATGACCTCTATTAAATGCACTC 59.556 37.037 0.00 0.00 0.00 3.51
4349 4897 8.715191 ACTTCTATCAGTTGAGATAGCAAAAG 57.285 34.615 6.19 7.40 44.53 2.27
4442 4992 7.433131 TCATTGCGCTCAAATAATCTCAAAATC 59.567 33.333 9.73 0.00 35.56 2.17
4459 5009 1.684386 CCTCTCCCTCTCATTGCGCT 61.684 60.000 9.73 0.00 0.00 5.92


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

AutoCloner maintained by Alex Coulton.