Multiple sequence alignment - TraesCS4A01G026400

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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 TraesCS4A01G026400 chr4A 100.000 1597 0 0 936 2532 18141696 18140100 0.000000e+00 2950.0
1 TraesCS4A01G026400 chr4A 95.677 1573 47 7 960 2530 616105995 616104442 0.000000e+00 2508.0
2 TraesCS4A01G026400 chr4A 100.000 441 0 0 1 441 18142631 18142191 0.000000e+00 815.0
3 TraesCS4A01G026400 chr7A 96.932 1532 42 5 936 2464 70819726 70821255 0.000000e+00 2564.0
4 TraesCS4A01G026400 chr7A 91.396 709 35 8 1825 2530 697767883 697768568 0.000000e+00 948.0
5 TraesCS4A01G026400 chr2A 96.932 1532 42 5 936 2464 719256628 719258157 0.000000e+00 2564.0
6 TraesCS4A01G026400 chr2A 91.925 1610 55 19 943 2530 605196765 605195209 0.000000e+00 2183.0
7 TraesCS4A01G026400 chr3A 95.526 1587 40 11 950 2530 24905393 24903832 0.000000e+00 2508.0
8 TraesCS4A01G026400 chr1A 95.343 1589 47 11 947 2530 21872694 21871128 0.000000e+00 2499.0
9 TraesCS4A01G026400 chr2D 96.029 1536 46 10 936 2464 645195048 645196575 0.000000e+00 2484.0
10 TraesCS4A01G026400 chr2D 93.182 704 22 10 1829 2530 72385559 72384880 0.000000e+00 1011.0
11 TraesCS4A01G026400 chr2D 98.354 243 4 0 199 441 645194645 645194887 6.470000e-116 427.0
12 TraesCS4A01G026400 chr2D 97.925 241 5 0 201 441 576925654 576925414 3.900000e-113 418.0
13 TraesCS4A01G026400 chr3D 96.084 1532 45 10 939 2464 512508899 512510421 0.000000e+00 2483.0
14 TraesCS4A01G026400 chr3D 97.925 241 5 0 201 441 512508439 512508679 3.900000e-113 418.0
15 TraesCS4A01G026400 chr6D 94.950 1604 46 14 936 2530 100359262 100360839 0.000000e+00 2481.0
16 TraesCS4A01G026400 chr6D 89.958 707 23 11 1829 2530 431131238 431130575 0.000000e+00 869.0
17 TraesCS4A01G026400 chr6D 98.340 241 4 0 201 441 17067058 17067298 8.370000e-115 424.0
18 TraesCS4A01G026400 chr6D 97.510 241 6 0 201 441 100358866 100359106 1.810000e-111 412.0
19 TraesCS4A01G026400 chr7D 95.896 1535 47 11 936 2464 3770421 3771945 0.000000e+00 2471.0
20 TraesCS4A01G026400 chr6A 92.175 1623 60 25 951 2530 41485869 41487467 0.000000e+00 2231.0
21 TraesCS4A01G026400 chrUn 91.515 495 14 8 2040 2530 295753673 295753203 0.000000e+00 656.0
22 TraesCS4A01G026400 chrUn 91.515 495 14 8 2040 2530 349182529 349182999 0.000000e+00 656.0
23 TraesCS4A01G026400 chr5D 98.340 241 4 0 201 441 79126812 79126572 8.370000e-115 424.0
24 TraesCS4A01G026400 chr5D 97.925 241 5 0 201 441 543865238 543865478 3.900000e-113 418.0
25 TraesCS4A01G026400 chr1D 97.925 241 5 0 201 441 10554226 10554466 3.900000e-113 418.0
26 TraesCS4A01G026400 chr4D 97.510 241 6 0 201 441 36561616 36561376 1.810000e-111 412.0
27 TraesCS4A01G026400 chr4D 93.548 62 3 1 2470 2530 471281706 471281767 9.650000e-15 91.6
28 TraesCS4A01G026400 chr5B 82.653 98 16 1 2 99 108525183 108525087 4.490000e-13 86.1


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 TraesCS4A01G026400 chr4A 18140100 18142631 2531 True 1882.5 2950 100.0000 1 2532 2 chr4A.!!$R2 2531
1 TraesCS4A01G026400 chr4A 616104442 616105995 1553 True 2508.0 2508 95.6770 960 2530 1 chr4A.!!$R1 1570
2 TraesCS4A01G026400 chr7A 70819726 70821255 1529 False 2564.0 2564 96.9320 936 2464 1 chr7A.!!$F1 1528
3 TraesCS4A01G026400 chr7A 697767883 697768568 685 False 948.0 948 91.3960 1825 2530 1 chr7A.!!$F2 705
4 TraesCS4A01G026400 chr2A 719256628 719258157 1529 False 2564.0 2564 96.9320 936 2464 1 chr2A.!!$F1 1528
5 TraesCS4A01G026400 chr2A 605195209 605196765 1556 True 2183.0 2183 91.9250 943 2530 1 chr2A.!!$R1 1587
6 TraesCS4A01G026400 chr3A 24903832 24905393 1561 True 2508.0 2508 95.5260 950 2530 1 chr3A.!!$R1 1580
7 TraesCS4A01G026400 chr1A 21871128 21872694 1566 True 2499.0 2499 95.3430 947 2530 1 chr1A.!!$R1 1583
8 TraesCS4A01G026400 chr2D 645194645 645196575 1930 False 1455.5 2484 97.1915 199 2464 2 chr2D.!!$F1 2265
9 TraesCS4A01G026400 chr2D 72384880 72385559 679 True 1011.0 1011 93.1820 1829 2530 1 chr2D.!!$R1 701
10 TraesCS4A01G026400 chr3D 512508439 512510421 1982 False 1450.5 2483 97.0045 201 2464 2 chr3D.!!$F1 2263
11 TraesCS4A01G026400 chr6D 100358866 100360839 1973 False 1446.5 2481 96.2300 201 2530 2 chr6D.!!$F2 2329
12 TraesCS4A01G026400 chr6D 431130575 431131238 663 True 869.0 869 89.9580 1829 2530 1 chr6D.!!$R1 701
13 TraesCS4A01G026400 chr7D 3770421 3771945 1524 False 2471.0 2471 95.8960 936 2464 1 chr7D.!!$F1 1528
14 TraesCS4A01G026400 chr6A 41485869 41487467 1598 False 2231.0 2231 92.1750 951 2530 1 chr6A.!!$F1 1579

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
45 46 0.108138 GGCACTGGTAGTACAGGCAG 60.108 60.0 2.06 3.28 42.75 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1859 1.131928 AAGTTAGAGGTGGGCCGGTT 61.132 55.0 1.9 0.0 40.5 4.44 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
17 18 3.179284 ACACATCCCCATGCACCA 58.821 55.556 0.00 0.00 32.57 4.17
18 19 1.000521 ACACATCCCCATGCACCAG 60.001 57.895 0.00 0.00 32.57 4.00
19 20 1.755395 CACATCCCCATGCACCAGG 60.755 63.158 0.00 0.00 32.57 4.45
20 21 2.240918 ACATCCCCATGCACCAGGT 61.241 57.895 0.00 0.00 32.57 4.00
21 22 1.755395 CATCCCCATGCACCAGGTG 60.755 63.158 16.16 16.16 36.51 4.00
37 38 3.238497 TGCGGTGGCACTGGTAGT 61.238 61.111 26.71 0.00 46.21 2.73
38 39 1.909287 TGCGGTGGCACTGGTAGTA 60.909 57.895 26.71 6.46 46.21 1.82
39 40 1.447314 GCGGTGGCACTGGTAGTAC 60.447 63.158 26.71 6.18 39.62 2.73
40 41 1.969085 CGGTGGCACTGGTAGTACA 59.031 57.895 18.87 0.00 0.00 2.90
41 42 0.108804 CGGTGGCACTGGTAGTACAG 60.109 60.000 18.87 0.85 44.03 2.74
42 43 0.249398 GGTGGCACTGGTAGTACAGG 59.751 60.000 18.45 0.00 42.75 4.00
43 44 0.391263 GTGGCACTGGTAGTACAGGC 60.391 60.000 11.13 2.24 42.75 4.85
44 45 0.834261 TGGCACTGGTAGTACAGGCA 60.834 55.000 2.06 4.75 42.75 4.75
45 46 0.108138 GGCACTGGTAGTACAGGCAG 60.108 60.000 2.06 3.28 42.75 4.85
46 47 0.741221 GCACTGGTAGTACAGGCAGC 60.741 60.000 2.06 0.00 42.75 5.25
47 48 0.108138 CACTGGTAGTACAGGCAGCC 60.108 60.000 1.84 1.84 42.75 4.85
48 49 1.141881 CTGGTAGTACAGGCAGCCG 59.858 63.158 5.55 3.56 34.84 5.52
49 50 2.202892 GGTAGTACAGGCAGCCGC 60.203 66.667 5.55 0.00 37.44 6.53
50 51 2.722201 GGTAGTACAGGCAGCCGCT 61.722 63.158 5.55 5.97 38.60 5.52
51 52 1.519455 GTAGTACAGGCAGCCGCTG 60.519 63.158 16.47 16.47 38.60 5.18
52 53 1.982395 TAGTACAGGCAGCCGCTGT 60.982 57.895 21.29 10.98 38.60 4.40
53 54 1.945354 TAGTACAGGCAGCCGCTGTC 61.945 60.000 17.51 17.51 36.18 3.51
54 55 4.435436 TACAGGCAGCCGCTGTCG 62.435 66.667 21.29 16.69 41.46 4.35
56 57 4.435436 CAGGCAGCCGCTGTCGTA 62.435 66.667 21.29 0.00 41.46 3.43
57 58 4.436998 AGGCAGCCGCTGTCGTAC 62.437 66.667 21.29 4.42 41.46 3.67
60 61 4.063967 CAGCCGCTGTCGTACCCA 62.064 66.667 12.54 0.00 0.00 4.51
61 62 3.760035 AGCCGCTGTCGTACCCAG 61.760 66.667 0.00 3.40 0.00 4.45
62 63 3.755628 GCCGCTGTCGTACCCAGA 61.756 66.667 10.56 0.00 31.38 3.86
63 64 3.077519 GCCGCTGTCGTACCCAGAT 62.078 63.158 10.56 0.00 31.38 2.90
64 65 1.226974 CCGCTGTCGTACCCAGATG 60.227 63.158 10.56 3.23 31.38 2.90
65 66 1.511305 CGCTGTCGTACCCAGATGT 59.489 57.895 10.56 0.00 31.38 3.06
66 67 0.802222 CGCTGTCGTACCCAGATGTG 60.802 60.000 10.56 0.00 31.38 3.21
67 68 0.530744 GCTGTCGTACCCAGATGTGA 59.469 55.000 10.56 0.00 31.38 3.58
68 69 1.736032 GCTGTCGTACCCAGATGTGAC 60.736 57.143 10.56 0.00 31.38 3.67
69 70 0.524414 TGTCGTACCCAGATGTGACG 59.476 55.000 0.00 0.00 34.90 4.35
70 71 0.801067 GTCGTACCCAGATGTGACGC 60.801 60.000 0.00 0.00 33.64 5.19
71 72 0.963856 TCGTACCCAGATGTGACGCT 60.964 55.000 0.00 0.00 33.64 5.07
72 73 0.802222 CGTACCCAGATGTGACGCTG 60.802 60.000 0.00 0.00 0.00 5.18
73 74 1.084370 GTACCCAGATGTGACGCTGC 61.084 60.000 0.00 0.00 0.00 5.25
74 75 1.257750 TACCCAGATGTGACGCTGCT 61.258 55.000 0.00 0.00 0.00 4.24
75 76 2.104859 CCCAGATGTGACGCTGCTG 61.105 63.158 0.00 0.00 0.00 4.41
76 77 2.747822 CCAGATGTGACGCTGCTGC 61.748 63.158 5.34 5.34 0.00 5.25
77 78 2.030958 CAGATGTGACGCTGCTGCA 61.031 57.895 16.29 0.88 39.64 4.41
78 79 1.078637 AGATGTGACGCTGCTGCAT 60.079 52.632 16.29 0.00 39.64 3.96
79 80 1.062047 GATGTGACGCTGCTGCATG 59.938 57.895 16.29 1.14 39.64 4.06
80 81 1.363885 GATGTGACGCTGCTGCATGA 61.364 55.000 16.29 0.00 39.64 3.07
81 82 1.642037 ATGTGACGCTGCTGCATGAC 61.642 55.000 16.29 5.27 39.64 3.06
82 83 2.031516 GTGACGCTGCTGCATGACT 61.032 57.895 16.29 0.00 39.64 3.41
83 84 0.737367 GTGACGCTGCTGCATGACTA 60.737 55.000 16.29 0.00 39.64 2.59
84 85 0.459063 TGACGCTGCTGCATGACTAG 60.459 55.000 16.29 0.00 39.64 2.57
85 86 1.760268 GACGCTGCTGCATGACTAGC 61.760 60.000 16.29 3.32 39.64 3.42
86 87 1.812507 CGCTGCTGCATGACTAGCA 60.813 57.895 16.29 15.77 46.79 3.49
90 91 1.949465 TGCTGCATGACTAGCATCTG 58.051 50.000 13.54 0.00 44.36 2.90
91 92 1.227639 GCTGCATGACTAGCATCTGG 58.772 55.000 0.00 0.00 41.82 3.86
92 93 1.202615 GCTGCATGACTAGCATCTGGA 60.203 52.381 0.00 0.00 41.82 3.86
93 94 2.550423 GCTGCATGACTAGCATCTGGAT 60.550 50.000 0.00 0.00 41.82 3.41
94 95 3.327626 CTGCATGACTAGCATCTGGATC 58.672 50.000 0.00 0.00 41.82 3.36
95 96 2.038164 TGCATGACTAGCATCTGGATCC 59.962 50.000 4.20 4.20 37.02 3.36
96 97 2.930023 GCATGACTAGCATCTGGATCCG 60.930 54.545 7.39 2.06 34.15 4.18
97 98 0.676184 TGACTAGCATCTGGATCCGC 59.324 55.000 7.39 4.08 0.00 5.54
98 99 0.676184 GACTAGCATCTGGATCCGCA 59.324 55.000 7.39 0.00 0.00 5.69
99 100 0.678395 ACTAGCATCTGGATCCGCAG 59.322 55.000 7.39 0.00 0.00 5.18
100 101 0.669932 CTAGCATCTGGATCCGCAGC 60.670 60.000 7.39 8.64 0.00 5.25
101 102 2.426122 TAGCATCTGGATCCGCAGCG 62.426 60.000 8.18 8.18 0.00 5.18
117 118 3.870606 CGGAGCCCAGTGTTAACG 58.129 61.111 0.26 0.00 0.00 3.18
118 119 1.740296 CGGAGCCCAGTGTTAACGG 60.740 63.158 0.26 0.00 0.00 4.44
119 120 1.373812 GGAGCCCAGTGTTAACGGT 59.626 57.895 0.26 0.00 0.00 4.83
120 121 0.953960 GGAGCCCAGTGTTAACGGTG 60.954 60.000 0.26 0.65 0.00 4.94
121 122 1.574702 GAGCCCAGTGTTAACGGTGC 61.575 60.000 0.26 2.93 0.00 5.01
122 123 2.622962 GCCCAGTGTTAACGGTGCC 61.623 63.158 0.26 0.00 0.00 5.01
123 124 1.228003 CCCAGTGTTAACGGTGCCA 60.228 57.895 0.26 0.00 0.00 4.92
124 125 1.512156 CCCAGTGTTAACGGTGCCAC 61.512 60.000 0.26 0.00 0.00 5.01
125 126 1.567537 CAGTGTTAACGGTGCCACG 59.432 57.895 0.26 0.00 40.31 4.94
126 127 1.595929 AGTGTTAACGGTGCCACGG 60.596 57.895 0.27 0.27 38.39 4.94
127 128 2.973600 TGTTAACGGTGCCACGGC 60.974 61.111 0.00 0.00 42.35 5.68
128 129 3.729698 GTTAACGGTGCCACGGCC 61.730 66.667 5.42 0.00 41.09 6.13
129 130 4.251771 TTAACGGTGCCACGGCCA 62.252 61.111 2.24 0.00 41.09 5.36
130 131 3.554696 TTAACGGTGCCACGGCCAT 62.555 57.895 2.24 0.00 41.09 4.40
131 132 2.181445 TTAACGGTGCCACGGCCATA 62.181 55.000 2.24 0.00 41.09 2.74
132 133 2.581208 TAACGGTGCCACGGCCATAG 62.581 60.000 2.24 0.00 41.09 2.23
163 164 3.710722 CAGGCGTTGGGAGCTCCT 61.711 66.667 31.36 7.72 36.20 3.69
164 165 3.710722 AGGCGTTGGGAGCTCCTG 61.711 66.667 31.36 19.19 36.20 3.86
165 166 3.706373 GGCGTTGGGAGCTCCTGA 61.706 66.667 31.36 17.64 36.20 3.86
166 167 2.435059 GCGTTGGGAGCTCCTGAC 60.435 66.667 31.36 25.76 36.20 3.51
167 168 2.125912 CGTTGGGAGCTCCTGACG 60.126 66.667 31.70 31.70 38.58 4.35
168 169 2.435059 GTTGGGAGCTCCTGACGC 60.435 66.667 31.36 15.41 36.20 5.19
169 170 3.706373 TTGGGAGCTCCTGACGCC 61.706 66.667 31.36 14.67 36.20 5.68
176 177 4.504916 CTCCTGACGCCGGAGCAG 62.505 72.222 18.02 18.02 41.39 4.24
238 239 4.907010 GTGTGACGTTTTTCATGCGAATTA 59.093 37.500 0.00 0.00 0.00 1.40
295 296 5.801947 GTGATGCGATGTTTTAGAAGCAAAT 59.198 36.000 0.00 0.00 38.15 2.32
1145 1146 7.511371 TCCTATGGTCTAATTTCTCCCGATTTA 59.489 37.037 0.00 0.00 0.00 1.40
1207 1211 2.289945 GGATCTAGGATTCATGCGCCTT 60.290 50.000 4.18 0.00 33.28 4.35
1611 1619 2.990740 AGCCAGGGACCATTTGTTAA 57.009 45.000 0.00 0.00 0.00 2.01
1752 1761 6.597562 ACACACCCAAATTCAGTTTCTAGTA 58.402 36.000 0.00 0.00 0.00 1.82
2002 2011 9.549509 GTTAATTGTTTTTATGCATGTCTACGA 57.450 29.630 10.16 3.05 0.00 3.43
2088 2097 0.740737 GTTGCACCCATGTCCATAGC 59.259 55.000 0.00 0.00 0.00 2.97
2146 2172 6.172630 GGTTTGGCCAATATTTTGAAGATGT 58.827 36.000 21.26 0.00 34.60 3.06
2303 2329 8.372459 ACCCAACGATTATATAGAAGCATAACA 58.628 33.333 0.00 0.00 0.00 2.41
2531 2599 4.135153 CACCTCGCTCCTCGGGTG 62.135 72.222 9.34 9.34 45.71 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.000521 CTGGTGCATGGGGATGTGT 60.001 57.895 0.00 0.00 0.00 3.72
1 2 1.755395 CCTGGTGCATGGGGATGTG 60.755 63.158 0.00 0.00 0.00 3.21
2 3 2.240918 ACCTGGTGCATGGGGATGT 61.241 57.895 0.00 0.00 0.00 3.06
3 4 1.755395 CACCTGGTGCATGGGGATG 60.755 63.158 14.87 0.00 0.00 3.51
4 5 2.685366 CACCTGGTGCATGGGGAT 59.315 61.111 14.87 0.00 0.00 3.85
20 21 1.909287 TACTACCAGTGCCACCGCA 60.909 57.895 0.00 0.00 44.78 5.69
21 22 1.447314 GTACTACCAGTGCCACCGC 60.447 63.158 0.00 0.00 0.00 5.68
22 23 0.108804 CTGTACTACCAGTGCCACCG 60.109 60.000 0.00 0.00 29.18 4.94
23 24 0.249398 CCTGTACTACCAGTGCCACC 59.751 60.000 0.00 0.00 29.18 4.61
24 25 0.391263 GCCTGTACTACCAGTGCCAC 60.391 60.000 0.00 0.00 29.18 5.01
25 26 0.834261 TGCCTGTACTACCAGTGCCA 60.834 55.000 0.00 0.00 31.59 4.92
26 27 0.108138 CTGCCTGTACTACCAGTGCC 60.108 60.000 0.00 0.00 31.59 5.01
27 28 0.741221 GCTGCCTGTACTACCAGTGC 60.741 60.000 0.00 0.00 32.58 4.40
28 29 0.108138 GGCTGCCTGTACTACCAGTG 60.108 60.000 12.43 0.00 0.00 3.66
29 30 1.605058 CGGCTGCCTGTACTACCAGT 61.605 60.000 17.92 0.00 0.00 4.00
30 31 1.141881 CGGCTGCCTGTACTACCAG 59.858 63.158 17.92 0.00 0.00 4.00
31 32 3.014085 GCGGCTGCCTGTACTACCA 62.014 63.158 17.92 0.00 33.98 3.25
32 33 2.202892 GCGGCTGCCTGTACTACC 60.203 66.667 17.92 0.00 33.98 3.18
33 34 1.519455 CAGCGGCTGCCTGTACTAC 60.519 63.158 18.16 0.00 44.31 2.73
34 35 1.945354 GACAGCGGCTGCCTGTACTA 61.945 60.000 28.80 0.00 44.31 1.82
35 36 3.302347 GACAGCGGCTGCCTGTACT 62.302 63.158 28.80 8.35 44.31 2.73
36 37 2.815647 GACAGCGGCTGCCTGTAC 60.816 66.667 28.80 10.32 44.31 2.90
37 38 4.435436 CGACAGCGGCTGCCTGTA 62.435 66.667 28.80 0.00 44.31 2.74
39 40 4.435436 TACGACAGCGGCTGCCTG 62.435 66.667 28.80 20.12 44.31 4.85
40 41 4.436998 GTACGACAGCGGCTGCCT 62.437 66.667 28.80 11.52 44.31 4.75
43 44 3.989698 CTGGGTACGACAGCGGCTG 62.990 68.421 27.43 27.43 43.17 4.85
44 45 3.760035 CTGGGTACGACAGCGGCT 61.760 66.667 0.00 0.00 43.17 5.52
45 46 3.077519 ATCTGGGTACGACAGCGGC 62.078 63.158 10.41 0.00 43.17 6.53
46 47 1.226974 CATCTGGGTACGACAGCGG 60.227 63.158 10.41 3.10 43.17 5.52
47 48 0.802222 CACATCTGGGTACGACAGCG 60.802 60.000 10.41 7.33 44.79 5.18
48 49 0.530744 TCACATCTGGGTACGACAGC 59.469 55.000 10.41 0.00 35.94 4.40
49 50 1.467543 CGTCACATCTGGGTACGACAG 60.468 57.143 9.28 9.28 35.66 3.51
50 51 0.524414 CGTCACATCTGGGTACGACA 59.476 55.000 0.00 0.00 35.66 4.35
51 52 0.801067 GCGTCACATCTGGGTACGAC 60.801 60.000 8.07 0.00 35.66 4.34
52 53 0.963856 AGCGTCACATCTGGGTACGA 60.964 55.000 8.07 0.00 35.66 3.43
53 54 0.802222 CAGCGTCACATCTGGGTACG 60.802 60.000 0.00 0.00 36.67 3.67
54 55 1.084370 GCAGCGTCACATCTGGGTAC 61.084 60.000 0.00 0.00 0.00 3.34
55 56 1.218047 GCAGCGTCACATCTGGGTA 59.782 57.895 0.00 0.00 0.00 3.69
56 57 2.046892 GCAGCGTCACATCTGGGT 60.047 61.111 0.00 0.00 0.00 4.51
57 58 2.104859 CAGCAGCGTCACATCTGGG 61.105 63.158 0.00 0.00 0.00 4.45
58 59 2.747822 GCAGCAGCGTCACATCTGG 61.748 63.158 0.00 0.00 0.00 3.86
59 60 1.366854 ATGCAGCAGCGTCACATCTG 61.367 55.000 0.00 0.00 46.23 2.90
60 61 1.078637 ATGCAGCAGCGTCACATCT 60.079 52.632 0.00 0.00 46.23 2.90
61 62 1.062047 CATGCAGCAGCGTCACATC 59.938 57.895 0.00 0.00 46.23 3.06
62 63 1.376295 TCATGCAGCAGCGTCACAT 60.376 52.632 0.00 0.00 46.23 3.21
63 64 2.030862 TCATGCAGCAGCGTCACA 59.969 55.556 0.00 0.00 46.23 3.58
64 65 0.737367 TAGTCATGCAGCAGCGTCAC 60.737 55.000 0.00 0.00 46.23 3.67
65 66 0.459063 CTAGTCATGCAGCAGCGTCA 60.459 55.000 0.00 0.00 46.23 4.35
66 67 1.760268 GCTAGTCATGCAGCAGCGTC 61.760 60.000 0.00 0.00 46.23 5.19
67 68 1.812922 GCTAGTCATGCAGCAGCGT 60.813 57.895 0.00 0.00 46.23 5.07
68 69 1.812507 TGCTAGTCATGCAGCAGCG 60.813 57.895 0.00 0.00 42.68 5.18
69 70 4.213666 TGCTAGTCATGCAGCAGC 57.786 55.556 0.00 0.00 42.68 5.25
72 73 1.202615 TCCAGATGCTAGTCATGCAGC 60.203 52.381 4.66 6.79 45.82 5.25
73 74 2.904697 TCCAGATGCTAGTCATGCAG 57.095 50.000 4.66 0.00 44.04 4.41
74 75 2.038164 GGATCCAGATGCTAGTCATGCA 59.962 50.000 6.95 0.00 44.95 3.96
75 76 2.697654 GGATCCAGATGCTAGTCATGC 58.302 52.381 6.95 0.00 35.05 4.06
76 77 2.930023 GCGGATCCAGATGCTAGTCATG 60.930 54.545 13.41 0.00 35.05 3.07
77 78 1.274728 GCGGATCCAGATGCTAGTCAT 59.725 52.381 13.41 0.06 38.32 3.06
78 79 0.676184 GCGGATCCAGATGCTAGTCA 59.324 55.000 13.41 0.00 0.00 3.41
79 80 0.676184 TGCGGATCCAGATGCTAGTC 59.324 55.000 13.41 0.00 0.00 2.59
80 81 0.678395 CTGCGGATCCAGATGCTAGT 59.322 55.000 13.41 0.00 34.77 2.57
81 82 0.669932 GCTGCGGATCCAGATGCTAG 60.670 60.000 13.41 8.17 34.77 3.42
82 83 1.368950 GCTGCGGATCCAGATGCTA 59.631 57.895 13.41 0.00 34.77 3.49
83 84 2.110627 GCTGCGGATCCAGATGCT 59.889 61.111 13.41 0.00 34.77 3.79
84 85 3.344215 CGCTGCGGATCCAGATGC 61.344 66.667 15.40 7.51 34.77 3.91
96 97 3.605749 TAACACTGGGCTCCGCTGC 62.606 63.158 0.00 0.00 0.00 5.25
97 98 1.003839 TTAACACTGGGCTCCGCTG 60.004 57.895 0.00 0.00 0.00 5.18
98 99 1.003718 GTTAACACTGGGCTCCGCT 60.004 57.895 0.00 0.00 0.00 5.52
99 100 2.388232 CGTTAACACTGGGCTCCGC 61.388 63.158 6.39 0.00 0.00 5.54
100 101 1.740296 CCGTTAACACTGGGCTCCG 60.740 63.158 6.39 0.00 0.00 4.63
101 102 0.953960 CACCGTTAACACTGGGCTCC 60.954 60.000 6.39 0.00 0.00 4.70
102 103 1.574702 GCACCGTTAACACTGGGCTC 61.575 60.000 6.39 0.00 33.86 4.70
103 104 1.599797 GCACCGTTAACACTGGGCT 60.600 57.895 6.39 0.00 33.86 5.19
104 105 2.622962 GGCACCGTTAACACTGGGC 61.623 63.158 6.39 5.97 35.85 5.36
105 106 1.228003 TGGCACCGTTAACACTGGG 60.228 57.895 6.39 0.99 0.00 4.45
106 107 1.837538 CGTGGCACCGTTAACACTGG 61.838 60.000 12.86 1.36 0.00 4.00
107 108 1.567537 CGTGGCACCGTTAACACTG 59.432 57.895 12.86 0.88 0.00 3.66
108 109 1.595929 CCGTGGCACCGTTAACACT 60.596 57.895 12.86 0.00 0.00 3.55
109 110 2.940561 CCGTGGCACCGTTAACAC 59.059 61.111 12.86 0.00 0.00 3.32
110 111 2.973600 GCCGTGGCACCGTTAACA 60.974 61.111 12.86 0.00 41.49 2.41
111 112 3.729698 GGCCGTGGCACCGTTAAC 61.730 66.667 12.86 0.00 44.11 2.01
112 113 2.181445 TATGGCCGTGGCACCGTTAA 62.181 55.000 12.86 0.00 41.84 2.01
113 114 2.581208 CTATGGCCGTGGCACCGTTA 62.581 60.000 12.86 0.00 41.84 3.18
114 115 3.969250 CTATGGCCGTGGCACCGTT 62.969 63.158 12.86 0.00 41.84 4.44
115 116 4.467084 CTATGGCCGTGGCACCGT 62.467 66.667 12.86 2.03 41.84 4.83
146 147 3.710722 AGGAGCTCCCAACGCCTG 61.711 66.667 29.54 0.00 35.84 4.85
147 148 3.710722 CAGGAGCTCCCAACGCCT 61.711 66.667 29.54 5.79 37.90 5.52
148 149 3.706373 TCAGGAGCTCCCAACGCC 61.706 66.667 29.54 2.72 37.41 5.68
149 150 2.435059 GTCAGGAGCTCCCAACGC 60.435 66.667 29.54 11.51 37.41 4.84
150 151 2.125912 CGTCAGGAGCTCCCAACG 60.126 66.667 31.27 31.27 39.06 4.10
151 152 2.435059 GCGTCAGGAGCTCCCAAC 60.435 66.667 29.54 24.21 37.41 3.77
152 153 3.706373 GGCGTCAGGAGCTCCCAA 61.706 66.667 29.54 14.97 37.41 4.12
197 198 1.527844 CAGGAGCTATTGGCCCTGC 60.528 63.158 13.68 0.00 45.30 4.85
238 239 0.104304 AACAACGTCGCACTCCTTCT 59.896 50.000 0.00 0.00 0.00 2.85
295 296 3.402110 CCATGTCGCATTGGAGCTATTA 58.598 45.455 0.00 0.00 34.81 0.98
941 942 2.963101 CCATTCTGCATCCATGATTGGT 59.037 45.455 0.00 0.00 44.06 3.67
972 973 2.026641 CAATCGGGGCATCTTGTCAAT 58.973 47.619 0.00 0.00 0.00 2.57
1207 1211 1.228429 CTGAAAAACAGGGGGCCGA 60.228 57.895 0.00 0.00 42.39 5.54
1391 1396 7.011295 GCCAATTTTCTTCAATTCACACTTCAA 59.989 33.333 0.00 0.00 0.00 2.69
1611 1619 6.389091 TGCTTCACGCTAATTCAAATTCATT 58.611 32.000 0.00 0.00 40.11 2.57
1673 1681 4.019860 ACAGAGCATGAACACTGAATAGGT 60.020 41.667 0.00 0.00 33.15 3.08
1803 1812 3.769300 GGGCATGGTTATTTTCTCAAGGT 59.231 43.478 0.00 0.00 0.00 3.50
1850 1859 1.131928 AAGTTAGAGGTGGGCCGGTT 61.132 55.000 1.90 0.00 40.50 4.44
1854 1863 1.221021 CCGAAGTTAGAGGTGGGCC 59.779 63.158 0.00 0.00 0.00 5.80
2002 2011 6.839124 TGCAACTCATTTAGTTCATGGAAT 57.161 33.333 0.00 0.00 45.64 3.01
2088 2097 3.451894 GAGCCCCATGCAAACCCG 61.452 66.667 0.00 0.00 44.83 5.28
2146 2172 1.342474 ACCCCAATCACCACACACAAA 60.342 47.619 0.00 0.00 0.00 2.83
2273 2299 7.903145 TGCTTCTATATAATCGTTGGGTATGT 58.097 34.615 0.00 0.00 0.00 2.29
2443 2508 1.752694 CCGTTTGGTGCCCCCTATG 60.753 63.158 0.00 0.00 0.00 2.23
2468 2533 2.125202 GAAGAACCCGCGTTTGGTGG 62.125 60.000 4.92 0.00 46.36 4.61


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

AutoCloner maintained by Alex Coulton.