Multiple sequence alignment - TraesCS5D01G100500

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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 TraesCS5D01G100500 chr5D 100.000 4676 0 0 1 4676 113382833 113387508 0.000000e+00 8636.0
1 TraesCS5D01G100500 chr5D 85.350 157 20 2 1738 1891 504792195 504792351 4.840000e-35 159.0
2 TraesCS5D01G100500 chr5A 94.407 4720 148 44 1 4673 118662212 118666862 0.000000e+00 7147.0
3 TraesCS5D01G100500 chr5A 83.648 159 26 0 1888 2046 670398858 670399016 2.910000e-32 150.0
4 TraesCS5D01G100500 chr5A 84.615 156 17 6 1743 1893 370244585 370244738 1.050000e-31 148.0
5 TraesCS5D01G100500 chr5A 92.381 105 5 3 3979 4082 136393613 136393715 3.770000e-31 147.0
6 TraesCS5D01G100500 chr5B 95.452 2067 59 8 1798 3855 123753460 123755500 0.000000e+00 3264.0
7 TraesCS5D01G100500 chr5B 93.729 1754 54 14 7 1723 123751643 123753377 0.000000e+00 2579.0
8 TraesCS5D01G100500 chr5B 90.999 711 47 9 3954 4658 123755629 123756328 0.000000e+00 942.0
9 TraesCS5D01G100500 chr5B 85.235 149 19 2 1739 1886 675426345 675426199 2.910000e-32 150.0
10 TraesCS5D01G100500 chr5B 94.505 91 5 0 3992 4082 136410449 136410539 1.750000e-29 141.0
11 TraesCS5D01G100500 chr5B 85.950 121 7 5 1631 1748 527760625 527760512 2.290000e-23 121.0
12 TraesCS5D01G100500 chr5B 96.364 55 1 1 152 205 123751004 123751058 6.440000e-14 89.8
13 TraesCS5D01G100500 chr4D 90.226 133 9 3 1746 1876 215174021 215173891 2.240000e-38 171.0
14 TraesCS5D01G100500 chr4D 93.878 98 3 2 3988 4083 216545578 216545674 1.360000e-30 145.0
15 TraesCS5D01G100500 chr4D 100.000 71 0 0 4010 4080 92221653 92221583 1.060000e-26 132.0
16 TraesCS5D01G100500 chr4D 91.026 78 5 2 3988 4064 92222381 92222305 2.300000e-18 104.0
17 TraesCS5D01G100500 chr6B 96.842 95 2 1 3988 4081 720559363 720559457 1.740000e-34 158.0
18 TraesCS5D01G100500 chr6B 85.616 146 15 5 1743 1886 347459980 347460121 1.050000e-31 148.0
19 TraesCS5D01G100500 chr6B 85.135 148 16 5 1743 1886 474319983 474320128 3.770000e-31 147.0
20 TraesCS5D01G100500 chr7D 92.593 108 7 1 3974 4081 634675044 634675150 2.250000e-33 154.0
21 TraesCS5D01G100500 chr7D 93.939 99 4 2 3988 4086 583409432 583409528 1.050000e-31 148.0
22 TraesCS5D01G100500 chr7D 94.000 100 2 4 3989 4086 583594810 583594907 1.050000e-31 148.0
23 TraesCS5D01G100500 chr7D 95.652 92 2 2 3989 4080 634667237 634667326 3.770000e-31 147.0
24 TraesCS5D01G100500 chr7D 90.141 71 7 0 1969 2039 489601542 489601612 4.980000e-15 93.5
25 TraesCS5D01G100500 chr7D 79.570 93 15 2 1934 2024 583594028 583593938 3.910000e-06 63.9
26 TraesCS5D01G100500 chr6A 96.774 93 1 2 3990 4082 615434020 615433930 2.250000e-33 154.0
27 TraesCS5D01G100500 chr6A 91.667 108 4 5 3979 4086 146548613 146548511 1.360000e-30 145.0
28 TraesCS5D01G100500 chr6A 82.222 90 14 1 1934 2021 146550587 146550676 5.020000e-10 76.8
29 TraesCS5D01G100500 chr7B 93.333 105 4 3 3979 4081 741621201 741621098 8.100000e-33 152.0
30 TraesCS5D01G100500 chr1A 95.789 95 2 2 3988 4082 119739106 119739014 8.100000e-33 152.0
31 TraesCS5D01G100500 chr3D 86.861 137 15 2 1753 1886 583290927 583290791 2.910000e-32 150.0
32 TraesCS5D01G100500 chr3D 84.868 152 18 3 1747 1893 53830422 53830573 1.050000e-31 148.0
33 TraesCS5D01G100500 chr3D 93.000 100 4 3 3982 4080 90781605 90781702 4.880000e-30 143.0
34 TraesCS5D01G100500 chr3D 87.500 120 7 3 1630 1748 613606637 613606525 1.060000e-26 132.0
35 TraesCS5D01G100500 chr3D 91.667 96 4 4 3988 4081 90783782 90783875 3.800000e-26 130.0
36 TraesCS5D01G100500 chr1B 85.135 148 16 5 1743 1886 560743583 560743438 3.770000e-31 147.0
37 TraesCS5D01G100500 chr1B 98.765 81 1 0 4002 4082 172256302 172256222 1.360000e-30 145.0
38 TraesCS5D01G100500 chr7A 88.095 126 9 6 3957 4081 731131869 731131989 1.360000e-30 145.0
39 TraesCS5D01G100500 chr7A 88.095 126 9 6 3957 4081 731161577 731161697 1.360000e-30 145.0
40 TraesCS5D01G100500 chr7A 88.095 126 9 6 3957 4081 731190535 731190655 1.360000e-30 145.0
41 TraesCS5D01G100500 chr7A 87.395 119 7 3 1631 1748 150586755 150586866 3.800000e-26 130.0
42 TraesCS5D01G100500 chr6D 98.750 80 1 0 4003 4082 470603302 470603223 4.880000e-30 143.0
43 TraesCS5D01G100500 chr6D 91.089 101 5 2 3979 4079 310124461 310124365 2.940000e-27 134.0
44 TraesCS5D01G100500 chr1D 92.929 99 5 2 3980 4078 112632866 112632770 4.880000e-30 143.0
45 TraesCS5D01G100500 chr1D 97.059 34 1 0 1888 1921 398368516 398368483 1.820000e-04 58.4
46 TraesCS5D01G100500 chr2A 88.889 117 5 3 1633 1748 194713136 194713245 2.270000e-28 137.0
47 TraesCS5D01G100500 chr4B 87.200 125 7 4 1625 1748 467460770 467460654 2.940000e-27 134.0
48 TraesCS5D01G100500 chr4B 92.188 64 5 0 1969 2032 362776524 362776587 1.790000e-14 91.6
49 TraesCS5D01G100500 chr4A 87.288 118 7 3 1632 1748 352482007 352481897 1.370000e-25 128.0
50 TraesCS5D01G100500 chr4A 85.950 121 7 9 1629 1747 578766400 578766288 2.290000e-23 121.0
51 TraesCS5D01G100500 chr4A 88.462 52 2 3 1984 2035 585234728 585234681 5.050000e-05 60.2
52 TraesCS5D01G100500 chr3B 83.133 83 14 0 1950 2032 143572647 143572729 5.020000e-10 76.8


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 TraesCS5D01G100500 chr5D 113382833 113387508 4675 False 8636.0 8636 100.000 1 4676 1 chr5D.!!$F1 4675
1 TraesCS5D01G100500 chr5A 118662212 118666862 4650 False 7147.0 7147 94.407 1 4673 1 chr5A.!!$F1 4672
2 TraesCS5D01G100500 chr5B 123751004 123756328 5324 False 1718.7 3264 94.136 7 4658 4 chr5B.!!$F2 4651

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
724 1368 1.722011 AGGTGACGAGCCATTAAACG 58.278 50.000 0.0 0.0 0.00 3.60 F
1142 1789 1.153647 TGCCTCCAAGCGTATCACG 60.154 57.895 0.0 0.0 45.88 4.35 F
1761 2468 2.915869 ACAAATACTCCCTCTGTCCCA 58.084 47.619 0.0 0.0 0.00 4.37 F
3351 4061 1.204786 TCCCTCCCCGCATTTGAGAA 61.205 55.000 0.0 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 3153 0.321671 CCTGCTCCGGTCTTTCTTCA 59.678 55.000 0.00 0.0 0.0 3.02 R
3005 3712 2.384382 CGCCTGCAGTTAACACTTTTG 58.616 47.619 13.81 0.0 0.0 2.44 R
3355 4065 0.388907 GGCGCACATTTGTTGCTGAT 60.389 50.000 10.83 0.0 0.0 2.90 R
4547 5336 0.108585 TGCTCCCCTAAATCATCGCC 59.891 55.000 0.00 0.0 0.0 5.54 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
69 703 1.798626 ACATGAGCAGGGAGAGCATA 58.201 50.000 0.00 0.00 0.00 3.14
125 759 7.578169 ACTAAGTTTAGCGACATGTTCTTAC 57.422 36.000 0.00 3.42 34.09 2.34
260 904 2.289444 GGCTAACTACCTGTTGCTGACA 60.289 50.000 0.00 0.00 39.55 3.58
276 920 3.363970 GCTGACACAACTTGATGTTACCG 60.364 47.826 0.00 0.00 37.07 4.02
455 1099 3.959535 TGGCCATTCTCATTTCCAAAC 57.040 42.857 0.00 0.00 0.00 2.93
723 1367 3.751698 AGAAAGGTGACGAGCCATTAAAC 59.248 43.478 0.00 0.00 0.00 2.01
724 1368 1.722011 AGGTGACGAGCCATTAAACG 58.278 50.000 0.00 0.00 0.00 3.60
907 1551 6.119536 TGACTTACACTCAACATTTCCAGTT 58.880 36.000 0.00 0.00 0.00 3.16
1127 1774 4.410400 CCTTCCCTGGACCGTGCC 62.410 72.222 0.00 0.00 0.00 5.01
1142 1789 1.153647 TGCCTCCAAGCGTATCACG 60.154 57.895 0.00 0.00 45.88 4.35
1453 2100 5.897377 AAGCATGGTAATCAGGTAAACAC 57.103 39.130 0.00 0.00 0.00 3.32
1568 2238 5.421277 TGGTTGGTGTTATTAGGACATACG 58.579 41.667 0.00 0.00 0.00 3.06
1674 2344 5.365021 ACTCTGCATATTAGCTTTGACCT 57.635 39.130 0.00 0.00 34.99 3.85
1755 2462 8.164070 ACTTTCACAATAACAAATACTCCCTCT 58.836 33.333 0.00 0.00 0.00 3.69
1761 2468 2.915869 ACAAATACTCCCTCTGTCCCA 58.084 47.619 0.00 0.00 0.00 4.37
1795 2502 9.421399 TGTCTTAGATTTGTCTAGATACATCCA 57.579 33.333 10.91 0.00 0.00 3.41
1801 2508 9.553064 AGATTTGTCTAGATACATCCATTTGTC 57.447 33.333 10.91 0.00 0.00 3.18
1802 2509 9.553064 GATTTGTCTAGATACATCCATTTGTCT 57.447 33.333 4.69 0.00 0.00 3.41
1805 2512 8.996651 TGTCTAGATACATCCATTTGTCTAGA 57.003 34.615 0.00 5.97 33.80 2.43
1806 2513 9.593565 TGTCTAGATACATCCATTTGTCTAGAT 57.406 33.333 11.65 0.00 36.37 1.98
1809 2516 9.995957 CTAGATACATCCATTTGTCTAGATACG 57.004 37.037 0.00 0.00 30.90 3.06
1810 2517 7.831753 AGATACATCCATTTGTCTAGATACGG 58.168 38.462 0.00 0.00 0.00 4.02
1811 2518 7.670140 AGATACATCCATTTGTCTAGATACGGA 59.330 37.037 0.00 0.00 0.00 4.69
1900 2607 9.529823 TTGAGTCGGAGGTAATATATAAGATGT 57.470 33.333 0.00 0.00 0.00 3.06
2072 2779 6.570186 GCAAGTCATGATGTTATGTTGGTTCA 60.570 38.462 0.00 0.00 0.00 3.18
2446 3153 5.339282 GGAGTAACCCTAAGAAGAATGCCTT 60.339 44.000 0.00 0.00 37.93 4.35
2959 3666 4.215399 CGAGGTTGGAGAAACATTTGCTTA 59.785 41.667 0.00 0.00 40.86 3.09
2981 3688 7.444487 GCTTACTCTCTTTTAAACTTCCTGGAA 59.556 37.037 9.14 9.14 0.00 3.53
3005 3712 4.090819 AGGTTCAGTTCCTAGGAGTTCTC 58.909 47.826 12.26 2.86 33.04 2.87
3025 3732 2.032799 TCAAAAGTGTTAACTGCAGGCG 59.967 45.455 19.93 0.00 36.51 5.52
3122 3829 4.159135 AGAAGGTCCATTGCATCATTTGAC 59.841 41.667 0.00 0.00 0.00 3.18
3157 3867 4.498323 CACTCGCGTTTCTACTACCATTAC 59.502 45.833 5.77 0.00 0.00 1.89
3179 3889 5.885465 ACCTTCTGACAGAATCATTCCTTT 58.115 37.500 18.04 0.00 36.48 3.11
3329 4039 1.408822 CCTGCAGGTAACCAATCCTCC 60.409 57.143 25.53 0.00 37.17 4.30
3341 4051 2.991167 AATCCTCCCATCCCTCCCCG 62.991 65.000 0.00 0.00 0.00 5.73
3351 4061 1.204786 TCCCTCCCCGCATTTGAGAA 61.205 55.000 0.00 0.00 0.00 2.87
3353 4063 1.686115 CCCTCCCCGCATTTGAGAAAT 60.686 52.381 0.00 0.00 0.00 2.17
3354 4064 1.678101 CCTCCCCGCATTTGAGAAATC 59.322 52.381 0.00 0.00 0.00 2.17
3355 4065 2.368439 CTCCCCGCATTTGAGAAATCA 58.632 47.619 0.00 0.00 0.00 2.57
3356 4066 2.954318 CTCCCCGCATTTGAGAAATCAT 59.046 45.455 0.00 0.00 0.00 2.45
3357 4067 2.951642 TCCCCGCATTTGAGAAATCATC 59.048 45.455 0.00 0.00 0.00 2.92
3358 4068 2.689471 CCCCGCATTTGAGAAATCATCA 59.311 45.455 0.00 0.00 0.00 3.07
3359 4069 3.243301 CCCCGCATTTGAGAAATCATCAG 60.243 47.826 0.00 0.00 0.00 2.90
3360 4070 3.369385 CCGCATTTGAGAAATCATCAGC 58.631 45.455 0.00 0.00 0.00 4.26
3361 4071 3.181494 CCGCATTTGAGAAATCATCAGCA 60.181 43.478 0.00 0.00 0.00 4.41
3362 4072 4.417506 CGCATTTGAGAAATCATCAGCAA 58.582 39.130 0.00 0.00 0.00 3.91
3363 4073 4.264614 CGCATTTGAGAAATCATCAGCAAC 59.735 41.667 0.00 0.00 0.00 4.17
3549 4263 1.806542 GAGCGCTTGATTTTGAGGACA 59.193 47.619 13.26 0.00 0.00 4.02
3551 4265 1.537202 GCGCTTGATTTTGAGGACACT 59.463 47.619 0.00 0.00 0.00 3.55
3655 4373 2.815478 TGCAAATTTGTTCGTTGGTCC 58.185 42.857 19.03 0.00 0.00 4.46
3672 4390 4.250464 TGGTCCAATAAGCGAGTTACAAG 58.750 43.478 0.00 0.00 0.00 3.16
3753 4471 3.577649 ACACCGTTGAGATGTACTGAG 57.422 47.619 0.00 0.00 0.00 3.35
3768 4486 1.977854 ACTGAGCCAGTGATGTTACCA 59.022 47.619 7.00 0.00 43.63 3.25
3856 4574 5.776173 TTATTTTTCCTGGCGAGTTTTCA 57.224 34.783 0.00 0.00 0.00 2.69
3918 4694 2.892374 AGCAAGAAACAAAAGGCACAC 58.108 42.857 0.00 0.00 0.00 3.82
3919 4695 2.233431 AGCAAGAAACAAAAGGCACACA 59.767 40.909 0.00 0.00 0.00 3.72
3933 4709 7.622893 AAAGGCACACAAACAAATTTATTGT 57.377 28.000 13.11 13.11 37.76 2.71
3938 4714 6.194325 GCACACAAACAAATTTATTGTTGCAC 59.806 34.615 25.95 14.26 41.30 4.57
3960 4736 5.050634 CACATGTGAAGGAAATTTGTGCAAG 60.051 40.000 21.64 0.00 0.00 4.01
3964 4740 6.347696 TGTGAAGGAAATTTGTGCAAGAAAT 58.652 32.000 0.00 0.00 42.13 2.17
3973 4749 1.406898 TGTGCAAGAAATTTGCCACGA 59.593 42.857 9.15 0.00 44.32 4.35
3976 4752 2.035704 TGCAAGAAATTTGCCACGATGT 59.964 40.909 9.15 0.00 44.32 3.06
4088 4864 2.678471 CAAATGCCCTTTGGATGACC 57.322 50.000 1.84 0.00 40.52 4.02
4231 5020 3.217231 GTTTCCGCAAAAACGCCG 58.783 55.556 0.00 0.00 30.16 6.46
4350 5139 4.069232 CCGCTCGAACCTGCTCCA 62.069 66.667 0.00 0.00 0.00 3.86
4370 5159 1.200519 TTCAATCGATCCCTCGGGTT 58.799 50.000 0.00 0.00 45.10 4.11
4500 5289 3.141398 GCCTGAATGATCCATTTCGCTA 58.859 45.455 0.00 0.00 33.90 4.26
4504 5293 3.136443 TGAATGATCCATTTCGCTAGGGT 59.864 43.478 6.70 0.00 33.90 4.34
4508 5297 2.871096 TCCATTTCGCTAGGGTTGTT 57.129 45.000 6.70 0.00 0.00 2.83
4510 5299 2.159382 CCATTTCGCTAGGGTTGTTGT 58.841 47.619 6.70 0.00 0.00 3.32
4511 5300 2.556622 CCATTTCGCTAGGGTTGTTGTT 59.443 45.455 6.70 0.00 0.00 2.83
4512 5301 3.005367 CCATTTCGCTAGGGTTGTTGTTT 59.995 43.478 6.70 0.00 0.00 2.83
4523 5312 0.309302 TTGTTGTTTGCATCGACCGG 59.691 50.000 0.00 0.00 0.00 5.28
4524 5313 0.533085 TGTTGTTTGCATCGACCGGA 60.533 50.000 9.46 0.00 0.00 5.14
4546 5335 6.631766 CGGAGGACTAGAAATTTGGGATGTTA 60.632 42.308 0.00 0.00 0.00 2.41
4547 5336 6.768381 GGAGGACTAGAAATTTGGGATGTTAG 59.232 42.308 0.00 0.00 0.00 2.34
4593 5382 0.251916 TGTGATTTGCGAGGGGGTAG 59.748 55.000 0.00 0.00 0.00 3.18
4619 5409 0.862490 TTGTGTGTGTGAATACGGCG 59.138 50.000 4.80 4.80 0.00 6.46
4622 5412 0.032267 TGTGTGTGAATACGGCGTCA 59.968 50.000 19.21 5.64 0.00 4.35
4632 5422 1.616620 TACGGCGTCATGTTCGTAAC 58.383 50.000 19.21 0.00 35.56 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 703 6.903534 TGGAGACTTGGAGTAGAATAAATCCT 59.096 38.462 0.00 0.00 31.66 3.24
125 759 6.144402 GTCAGCAACAATGTTAAAAGGACATG 59.856 38.462 0.00 0.00 37.76 3.21
131 765 7.063308 ACAACAAGTCAGCAACAATGTTAAAAG 59.937 33.333 0.00 0.00 37.80 2.27
260 904 8.626526 AGAAAAATTACGGTAACATCAAGTTGT 58.373 29.630 2.10 0.00 41.50 3.32
455 1099 1.003355 ACCTCCATGAAGTGTGGCG 60.003 57.895 0.00 0.00 36.66 5.69
864 1508 9.719355 GTAAGTCAAAAATGTTGGGGAAAATAT 57.281 29.630 0.00 0.00 0.00 1.28
865 1509 8.705594 TGTAAGTCAAAAATGTTGGGGAAAATA 58.294 29.630 0.00 0.00 0.00 1.40
866 1510 7.497579 GTGTAAGTCAAAAATGTTGGGGAAAAT 59.502 33.333 0.00 0.00 0.00 1.82
867 1511 6.819146 GTGTAAGTCAAAAATGTTGGGGAAAA 59.181 34.615 0.00 0.00 0.00 2.29
871 1515 5.068460 TGAGTGTAAGTCAAAAATGTTGGGG 59.932 40.000 0.00 0.00 44.79 4.96
907 1551 7.651304 CACACATAAACAAAAGGCATGTCTTTA 59.349 33.333 24.78 10.03 36.09 1.85
1127 1774 0.249073 CCTCCGTGATACGCTTGGAG 60.249 60.000 0.00 0.00 44.65 3.86
1142 1789 3.078817 GGGGACAGAACACCCTCC 58.921 66.667 0.00 0.00 44.97 4.30
1409 2056 1.143838 CCGGTGCGATGAATCTCCA 59.856 57.895 0.00 0.00 0.00 3.86
1453 2100 7.530010 ACGAAACAAAAGATATGATCACTTGG 58.470 34.615 0.00 0.00 31.32 3.61
1606 2276 4.716784 TCAGAACAGGTATAGTGCCAAGAT 59.283 41.667 0.00 0.00 0.00 2.40
1755 2462 8.792633 CAAATCTAAGACAAGTAATTTGGGACA 58.207 33.333 0.00 0.00 41.25 4.02
1786 2493 7.827701 TCCGTATCTAGACAAATGGATGTATC 58.172 38.462 0.00 0.00 32.57 2.24
1791 2498 6.672266 ACATCCGTATCTAGACAAATGGAT 57.328 37.500 15.11 15.11 38.08 3.41
1792 2499 7.776618 ATACATCCGTATCTAGACAAATGGA 57.223 36.000 12.58 12.58 32.66 3.41
1806 2513 9.182214 ACTAAAACTTGTCTAGATACATCCGTA 57.818 33.333 0.00 0.00 0.00 4.02
1807 2514 7.974501 CACTAAAACTTGTCTAGATACATCCGT 59.025 37.037 0.00 0.00 0.00 4.69
1808 2515 7.974501 ACACTAAAACTTGTCTAGATACATCCG 59.025 37.037 0.00 0.00 0.00 4.18
1809 2516 9.654663 AACACTAAAACTTGTCTAGATACATCC 57.345 33.333 0.00 0.00 0.00 3.51
2032 2739 4.985538 TGACTTGCAAAATACTCCCTTCT 58.014 39.130 0.00 0.00 0.00 2.85
2446 3153 0.321671 CCTGCTCCGGTCTTTCTTCA 59.678 55.000 0.00 0.00 0.00 3.02
2981 3688 5.844601 AGAACTCCTAGGAACTGAACCTAT 58.155 41.667 13.77 0.00 41.52 2.57
3005 3712 2.384382 CGCCTGCAGTTAACACTTTTG 58.616 47.619 13.81 0.00 0.00 2.44
3025 3732 5.473846 GCCCAGTATTTTCCTTATAGCTTCC 59.526 44.000 0.00 0.00 0.00 3.46
3122 3829 2.475466 GCGAGTGTCATGGGCATGG 61.475 63.158 0.00 0.00 39.24 3.66
3157 3867 6.830873 AAAAGGAATGATTCTGTCAGAAGG 57.169 37.500 19.64 0.00 40.92 3.46
3179 3889 1.279271 GGCTGCCTTCTCCTGAGTAAA 59.721 52.381 12.43 0.00 0.00 2.01
3329 4039 1.829533 CAAATGCGGGGAGGGATGG 60.830 63.158 0.00 0.00 0.00 3.51
3341 4051 5.165676 TGTTGCTGATGATTTCTCAAATGC 58.834 37.500 0.00 0.00 34.37 3.56
3351 4061 3.247442 CGCACATTTGTTGCTGATGATT 58.753 40.909 0.00 0.00 0.00 2.57
3353 4063 1.666599 GCGCACATTTGTTGCTGATGA 60.667 47.619 0.30 0.00 0.00 2.92
3354 4064 0.711670 GCGCACATTTGTTGCTGATG 59.288 50.000 0.30 0.00 0.00 3.07
3355 4065 0.388907 GGCGCACATTTGTTGCTGAT 60.389 50.000 10.83 0.00 0.00 2.90
3356 4066 1.007502 GGCGCACATTTGTTGCTGA 60.008 52.632 10.83 0.00 0.00 4.26
3357 4067 1.005294 GAGGCGCACATTTGTTGCTG 61.005 55.000 10.83 0.00 0.00 4.41
3358 4068 1.286880 GAGGCGCACATTTGTTGCT 59.713 52.632 10.83 0.00 0.00 3.91
3359 4069 1.005294 CTGAGGCGCACATTTGTTGC 61.005 55.000 10.83 0.00 0.00 4.17
3360 4070 0.592637 TCTGAGGCGCACATTTGTTG 59.407 50.000 10.83 0.00 0.00 3.33
3361 4071 1.538047 ATCTGAGGCGCACATTTGTT 58.462 45.000 10.83 0.00 0.00 2.83
3362 4072 2.401583 TATCTGAGGCGCACATTTGT 57.598 45.000 10.83 0.00 0.00 2.83
3363 4073 2.419673 TGTTATCTGAGGCGCACATTTG 59.580 45.455 10.83 0.00 0.00 2.32
3549 4263 3.314331 CTCTGACGCCACCCCAGT 61.314 66.667 0.00 0.00 0.00 4.00
3655 4373 9.297586 TGTAACTATCTTGTAACTCGCTTATTG 57.702 33.333 0.00 0.00 0.00 1.90
3794 4512 9.301897 TGCTGTCTTCTCTATATGTATGTATGT 57.698 33.333 0.00 0.00 0.00 2.29
3795 4513 9.786105 CTGCTGTCTTCTCTATATGTATGTATG 57.214 37.037 0.00 0.00 0.00 2.39
3796 4514 9.746457 TCTGCTGTCTTCTCTATATGTATGTAT 57.254 33.333 0.00 0.00 0.00 2.29
3797 4515 9.004717 GTCTGCTGTCTTCTCTATATGTATGTA 57.995 37.037 0.00 0.00 0.00 2.29
3883 4658 6.254589 TGTTTCTTGCTTCCAAAATACAAACG 59.745 34.615 0.00 0.00 0.00 3.60
3933 4709 4.809958 CACAAATTTCCTTCACATGTGCAA 59.190 37.500 21.38 14.30 31.53 4.08
3938 4714 5.291178 TCTTGCACAAATTTCCTTCACATG 58.709 37.500 0.00 0.00 0.00 3.21
3994 4770 3.307059 CGGAATGCCCCCAATTGTTTTTA 60.307 43.478 4.43 0.00 0.00 1.52
4000 4776 0.395586 TCTCGGAATGCCCCCAATTG 60.396 55.000 0.00 0.00 0.00 2.32
4103 4881 2.104792 GCATGCCCACCTATGTTAGAGA 59.895 50.000 6.36 0.00 0.00 3.10
4140 4929 4.504916 CTCTGAGCGAGTGGGCGG 62.505 72.222 0.00 0.00 38.18 6.13
4144 4933 2.282147 CTGAGGCTCTGAGCGAGTGG 62.282 65.000 22.25 8.39 43.62 4.00
4231 5020 2.004733 CTTCGATTTGTTACGGGGGAC 58.995 52.381 0.00 0.00 0.00 4.46
4350 5139 1.424638 ACCCGAGGGATCGATTGAAT 58.575 50.000 16.26 0.00 38.96 2.57
4370 5159 4.021650 GTGCGTCAGAACACGGAA 57.978 55.556 0.00 0.00 42.14 4.30
4484 5273 3.864789 ACCCTAGCGAAATGGATCATT 57.135 42.857 0.00 0.00 35.39 2.57
4500 5289 1.336755 GTCGATGCAAACAACAACCCT 59.663 47.619 0.00 0.00 0.00 4.34
4504 5293 0.309302 CCGGTCGATGCAAACAACAA 59.691 50.000 0.00 0.00 0.00 2.83
4508 5297 1.375396 CCTCCGGTCGATGCAAACA 60.375 57.895 0.00 0.00 0.00 2.83
4510 5299 1.079405 GTCCTCCGGTCGATGCAAA 60.079 57.895 0.00 0.00 0.00 3.68
4511 5300 0.681887 TAGTCCTCCGGTCGATGCAA 60.682 55.000 0.00 0.00 0.00 4.08
4512 5301 1.077285 TAGTCCTCCGGTCGATGCA 60.077 57.895 0.00 0.00 0.00 3.96
4523 5312 6.768381 CCTAACATCCCAAATTTCTAGTCCTC 59.232 42.308 0.00 0.00 0.00 3.71
4524 5313 6.663734 CCTAACATCCCAAATTTCTAGTCCT 58.336 40.000 0.00 0.00 0.00 3.85
4527 5316 4.881850 CGCCTAACATCCCAAATTTCTAGT 59.118 41.667 0.00 0.00 0.00 2.57
4546 5335 0.398318 GCTCCCCTAAATCATCGCCT 59.602 55.000 0.00 0.00 0.00 5.52
4547 5336 0.108585 TGCTCCCCTAAATCATCGCC 59.891 55.000 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.