Multiple sequence alignment - TraesCS2D01G522000

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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 TraesCS2D01G522000 chr2D 100.000 2879 0 0 1 2879 610423624 610420746 0.000000e+00 5317.0
1 TraesCS2D01G522000 chr7D 95.088 2769 116 12 117 2879 570676731 570673977 0.000000e+00 4342.0
2 TraesCS2D01G522000 chr5D 91.159 2805 180 44 119 2879 432777116 432774336 0.000000e+00 3744.0
3 TraesCS2D01G522000 chr5D 91.001 2778 176 44 153 2879 432781644 432778890 0.000000e+00 3677.0
4 TraesCS2D01G522000 chr5D 98.684 228 3 0 117 344 421865313 421865540 3.450000e-109 405.0
5 TraesCS2D01G522000 chr7A 92.311 2367 169 9 520 2879 711983215 711985575 0.000000e+00 3350.0
6 TraesCS2D01G522000 chr7A 90.354 311 19 5 114 416 711982848 711983155 5.780000e-107 398.0
7 TraesCS2D01G522000 chr2A 90.736 1889 168 5 995 2879 25355017 25353132 0.000000e+00 2512.0
8 TraesCS2D01G522000 chr1A 90.058 1911 162 12 995 2879 536289658 536291566 0.000000e+00 2451.0
9 TraesCS2D01G522000 chr3D 90.031 1906 167 9 995 2879 209669558 209671461 0.000000e+00 2446.0
10 TraesCS2D01G522000 chr6A 90.021 1894 175 10 995 2879 282151792 282149904 0.000000e+00 2438.0
11 TraesCS2D01G522000 chr2B 89.852 1892 176 9 995 2879 667803197 667805079 0.000000e+00 2416.0
12 TraesCS2D01G522000 chr6B 89.364 1824 138 39 470 2258 694393949 694395751 0.000000e+00 2242.0
13 TraesCS2D01G522000 chr6B 91.154 667 32 9 118 763 60082178 60081518 0.000000e+00 880.0
14 TraesCS2D01G522000 chr6B 88.623 334 21 10 113 437 694379926 694380251 9.670000e-105 390.0
15 TraesCS2D01G522000 chr3B 94.211 691 34 5 117 806 540480649 540479964 0.000000e+00 1050.0
16 TraesCS2D01G522000 chr3B 91.581 677 31 10 110 763 71115364 71114691 0.000000e+00 911.0
17 TraesCS2D01G522000 chr3B 100.000 38 0 0 2842 2879 540479584 540479547 1.430000e-08 71.3


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 TraesCS2D01G522000 chr2D 610420746 610423624 2878 True 5317.00 5317 100.0000 1 2879 1 chr2D.!!$R1 2878
1 TraesCS2D01G522000 chr7D 570673977 570676731 2754 True 4342.00 4342 95.0880 117 2879 1 chr7D.!!$R1 2762
2 TraesCS2D01G522000 chr5D 432774336 432781644 7308 True 3710.50 3744 91.0800 119 2879 2 chr5D.!!$R1 2760
3 TraesCS2D01G522000 chr7A 711982848 711985575 2727 False 1874.00 3350 91.3325 114 2879 2 chr7A.!!$F1 2765
4 TraesCS2D01G522000 chr2A 25353132 25355017 1885 True 2512.00 2512 90.7360 995 2879 1 chr2A.!!$R1 1884
5 TraesCS2D01G522000 chr1A 536289658 536291566 1908 False 2451.00 2451 90.0580 995 2879 1 chr1A.!!$F1 1884
6 TraesCS2D01G522000 chr3D 209669558 209671461 1903 False 2446.00 2446 90.0310 995 2879 1 chr3D.!!$F1 1884
7 TraesCS2D01G522000 chr6A 282149904 282151792 1888 True 2438.00 2438 90.0210 995 2879 1 chr6A.!!$R1 1884
8 TraesCS2D01G522000 chr2B 667803197 667805079 1882 False 2416.00 2416 89.8520 995 2879 1 chr2B.!!$F1 1884
9 TraesCS2D01G522000 chr6B 694393949 694395751 1802 False 2242.00 2242 89.3640 470 2258 1 chr6B.!!$F2 1788
10 TraesCS2D01G522000 chr6B 60081518 60082178 660 True 880.00 880 91.1540 118 763 1 chr6B.!!$R1 645
11 TraesCS2D01G522000 chr3B 71114691 71115364 673 True 911.00 911 91.5810 110 763 1 chr3B.!!$R1 653
12 TraesCS2D01G522000 chr3B 540479547 540480649 1102 True 560.65 1050 97.1055 117 2879 2 chr3B.!!$R2 2762

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
46 47 0.041576 GGGTCGAACGTTGTCTTTGC 60.042 55.0 5.0 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 6554 0.03467 ATTCTCCTCAAGTGCAGCCC 60.035 55.0 0.0 0.0 0.0 5.19 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 4.043168 CTCCGAACGTGCCAGTTT 57.957 55.556 0.00 0.00 34.00 2.66
19 20 0.661020 CTCCGAACGTGCCAGTTTTT 59.339 50.000 0.00 0.00 34.00 1.94
21 22 2.482721 CTCCGAACGTGCCAGTTTTTAT 59.517 45.455 0.00 0.00 34.00 1.40
22 23 2.879646 TCCGAACGTGCCAGTTTTTATT 59.120 40.909 0.00 0.00 34.00 1.40
23 24 3.315749 TCCGAACGTGCCAGTTTTTATTT 59.684 39.130 0.00 0.00 34.00 1.40
24 25 4.045783 CCGAACGTGCCAGTTTTTATTTT 58.954 39.130 0.00 0.00 34.00 1.82
25 26 4.504826 CCGAACGTGCCAGTTTTTATTTTT 59.495 37.500 0.00 0.00 34.00 1.94
27 28 5.606515 CGAACGTGCCAGTTTTTATTTTTCG 60.607 40.000 0.00 0.00 34.00 3.46
28 29 4.045783 ACGTGCCAGTTTTTATTTTTCGG 58.954 39.130 0.00 0.00 0.00 4.30
29 30 3.427193 CGTGCCAGTTTTTATTTTTCGGG 59.573 43.478 0.00 0.00 0.00 5.14
30 31 4.373527 GTGCCAGTTTTTATTTTTCGGGT 58.626 39.130 0.00 0.00 0.00 5.28
31 32 4.446385 GTGCCAGTTTTTATTTTTCGGGTC 59.554 41.667 0.00 0.00 0.00 4.46
33 34 4.557097 GCCAGTTTTTATTTTTCGGGTCGA 60.557 41.667 0.00 0.00 0.00 4.20
34 35 5.521544 CCAGTTTTTATTTTTCGGGTCGAA 58.478 37.500 0.00 0.00 44.28 3.71
35 36 5.400188 CCAGTTTTTATTTTTCGGGTCGAAC 59.600 40.000 2.04 0.00 45.64 3.95
36 37 5.114423 CAGTTTTTATTTTTCGGGTCGAACG 59.886 40.000 2.04 4.54 45.64 3.95
37 38 4.809815 TTTTATTTTTCGGGTCGAACGT 57.190 36.364 10.09 0.00 45.64 3.99
38 39 4.809815 TTTATTTTTCGGGTCGAACGTT 57.190 36.364 0.00 0.00 45.64 3.99
39 40 2.673976 ATTTTTCGGGTCGAACGTTG 57.326 45.000 5.00 0.00 45.64 4.10
40 41 1.367659 TTTTTCGGGTCGAACGTTGT 58.632 45.000 5.00 0.00 45.64 3.32
41 42 0.929615 TTTTCGGGTCGAACGTTGTC 59.070 50.000 5.00 0.00 45.64 3.18
42 43 0.102844 TTTCGGGTCGAACGTTGTCT 59.897 50.000 5.00 0.00 45.64 3.41
43 44 0.102844 TTCGGGTCGAACGTTGTCTT 59.897 50.000 5.00 0.00 41.05 3.01
44 45 0.102844 TCGGGTCGAACGTTGTCTTT 59.897 50.000 5.00 0.00 31.06 2.52
45 46 0.231279 CGGGTCGAACGTTGTCTTTG 59.769 55.000 5.00 0.00 0.00 2.77
46 47 0.041576 GGGTCGAACGTTGTCTTTGC 60.042 55.000 5.00 0.00 0.00 3.68
48 49 0.382636 GTCGAACGTTGTCTTTGCCG 60.383 55.000 5.00 0.00 0.00 5.69
49 50 0.806884 TCGAACGTTGTCTTTGCCGT 60.807 50.000 5.00 0.00 34.56 5.68
51 52 1.530236 CGAACGTTGTCTTTGCCGTTT 60.530 47.619 5.00 0.00 42.89 3.60
52 53 1.843753 GAACGTTGTCTTTGCCGTTTG 59.156 47.619 5.00 0.00 42.89 2.93
53 54 1.088306 ACGTTGTCTTTGCCGTTTGA 58.912 45.000 0.00 0.00 0.00 2.69
54 55 1.673920 ACGTTGTCTTTGCCGTTTGAT 59.326 42.857 0.00 0.00 0.00 2.57
55 56 2.098443 ACGTTGTCTTTGCCGTTTGATT 59.902 40.909 0.00 0.00 0.00 2.57
56 57 2.719046 CGTTGTCTTTGCCGTTTGATTC 59.281 45.455 0.00 0.00 0.00 2.52
57 58 3.049912 GTTGTCTTTGCCGTTTGATTCC 58.950 45.455 0.00 0.00 0.00 3.01
59 60 2.293122 TGTCTTTGCCGTTTGATTCCTG 59.707 45.455 0.00 0.00 0.00 3.86
60 61 1.885887 TCTTTGCCGTTTGATTCCTGG 59.114 47.619 0.00 0.00 0.00 4.45
63 64 1.212751 GCCGTTTGATTCCTGGCAC 59.787 57.895 0.00 0.00 45.06 5.01
64 65 1.244019 GCCGTTTGATTCCTGGCACT 61.244 55.000 0.00 0.00 45.06 4.40
65 66 1.948611 GCCGTTTGATTCCTGGCACTA 60.949 52.381 0.00 0.00 45.06 2.74
66 67 2.432444 CCGTTTGATTCCTGGCACTAA 58.568 47.619 0.00 0.00 0.00 2.24
67 68 3.016736 CCGTTTGATTCCTGGCACTAAT 58.983 45.455 0.00 0.00 0.00 1.73
69 70 3.941483 CGTTTGATTCCTGGCACTAATCT 59.059 43.478 14.70 0.00 32.12 2.40
70 71 4.396166 CGTTTGATTCCTGGCACTAATCTT 59.604 41.667 14.70 0.00 32.12 2.40
71 72 5.644644 GTTTGATTCCTGGCACTAATCTTG 58.355 41.667 14.70 0.00 32.12 3.02
72 73 3.889815 TGATTCCTGGCACTAATCTTGG 58.110 45.455 14.70 0.00 32.12 3.61
73 74 3.523157 TGATTCCTGGCACTAATCTTGGA 59.477 43.478 14.70 2.00 32.12 3.53
74 75 3.634397 TTCCTGGCACTAATCTTGGAG 57.366 47.619 0.00 0.00 0.00 3.86
75 76 1.210478 TCCTGGCACTAATCTTGGAGC 59.790 52.381 0.00 0.00 0.00 4.70
76 77 1.065199 CCTGGCACTAATCTTGGAGCA 60.065 52.381 0.00 0.00 0.00 4.26
78 79 2.617308 CTGGCACTAATCTTGGAGCATG 59.383 50.000 0.00 0.00 0.00 4.06
79 80 1.952296 GGCACTAATCTTGGAGCATGG 59.048 52.381 0.00 0.00 0.00 3.66
80 81 2.421952 GGCACTAATCTTGGAGCATGGA 60.422 50.000 0.00 0.00 0.00 3.41
82 83 3.432749 GCACTAATCTTGGAGCATGGAGA 60.433 47.826 0.00 0.00 0.00 3.71
83 84 4.125703 CACTAATCTTGGAGCATGGAGAC 58.874 47.826 0.00 0.00 0.00 3.36
94 95 3.791640 TGGAGACAGCCACGTCAT 58.208 55.556 0.00 0.00 38.43 3.06
95 96 1.293179 TGGAGACAGCCACGTCATG 59.707 57.895 0.00 0.00 38.43 3.07
96 97 1.293498 GGAGACAGCCACGTCATGT 59.707 57.895 0.00 0.00 38.43 3.21
97 98 0.320771 GGAGACAGCCACGTCATGTT 60.321 55.000 0.00 0.00 38.43 2.71
99 100 1.195448 GAGACAGCCACGTCATGTTTG 59.805 52.381 0.00 0.00 38.43 2.93
100 101 0.944386 GACAGCCACGTCATGTTTGT 59.056 50.000 0.00 0.00 35.88 2.83
102 103 1.333619 ACAGCCACGTCATGTTTGTTC 59.666 47.619 0.00 0.00 0.00 3.18
104 105 1.873591 AGCCACGTCATGTTTGTTCTC 59.126 47.619 0.00 0.00 0.00 2.87
105 106 1.069227 GCCACGTCATGTTTGTTCTCC 60.069 52.381 0.00 0.00 0.00 3.71
108 109 2.286833 CACGTCATGTTTGTTCTCCGTT 59.713 45.455 0.00 0.00 0.00 4.44
109 110 2.542595 ACGTCATGTTTGTTCTCCGTTC 59.457 45.455 0.00 0.00 0.00 3.95
110 111 2.409752 CGTCATGTTTGTTCTCCGTTCG 60.410 50.000 0.00 0.00 0.00 3.95
111 112 2.096417 GTCATGTTTGTTCTCCGTTCGG 60.096 50.000 4.74 4.74 0.00 4.30
112 113 2.139917 CATGTTTGTTCTCCGTTCGGA 58.860 47.619 13.34 13.34 0.00 4.55
113 114 2.312722 TGTTTGTTCTCCGTTCGGAA 57.687 45.000 14.79 4.13 33.41 4.30
114 115 2.630158 TGTTTGTTCTCCGTTCGGAAA 58.370 42.857 14.79 9.36 33.41 3.13
115 116 3.008330 TGTTTGTTCTCCGTTCGGAAAA 58.992 40.909 14.79 5.66 33.41 2.29
326 4744 3.433173 CCCCCGGTAAACCTAAAGAGATG 60.433 52.174 0.00 0.00 0.00 2.90
327 4745 3.453353 CCCCGGTAAACCTAAAGAGATGA 59.547 47.826 0.00 0.00 0.00 2.92
328 4746 4.443034 CCCCGGTAAACCTAAAGAGATGAG 60.443 50.000 0.00 0.00 0.00 2.90
376 4819 2.040278 CTCCTCCCAGCCCACTCT 59.960 66.667 0.00 0.00 0.00 3.24
377 4820 2.039624 TCCTCCCAGCCCACTCTC 59.960 66.667 0.00 0.00 0.00 3.20
445 4892 1.306997 CCCTCCCCTAGCTTGACCA 60.307 63.158 0.00 0.00 0.00 4.02
651 5109 2.259818 CAGCAGCTTCCGACTCGT 59.740 61.111 0.00 0.00 0.00 4.18
716 5203 6.557568 ACCTTGTATGATTTTCCCCTGTTAA 58.442 36.000 0.00 0.00 0.00 2.01
719 5206 7.832187 CCTTGTATGATTTTCCCCTGTTAACTA 59.168 37.037 7.22 0.00 0.00 2.24
753 5241 2.585330 TCAAGTGCAGCAAATCCTTGA 58.415 42.857 17.89 17.89 39.21 3.02
1200 5710 6.418101 CATTTGGTATGGATCCGGAGATAAT 58.582 40.000 11.34 3.58 30.90 1.28
1329 5839 1.277557 GAACCTGCTCCTGTCATGACT 59.722 52.381 25.55 1.94 0.00 3.41
1348 5858 3.926198 ACTGAGGAGATGGATGATCAGT 58.074 45.455 0.09 0.01 41.79 3.41
1395 5905 4.951825 GCCGAAGCAAGCCTATGAAGGA 62.952 54.545 0.00 0.00 41.73 3.36
1425 5935 0.477204 ATGATGAGCCTGTGGGATGG 59.523 55.000 0.00 0.00 33.58 3.51
1429 5939 0.548031 TGAGCCTGTGGGATGGAATC 59.452 55.000 0.00 0.00 44.55 2.52
1448 5958 3.350219 TCAGGAGAACACCTATTTGCC 57.650 47.619 0.00 0.00 38.32 4.52
1474 5999 3.631227 GGAGAATGCTGAATCAAAGGAGG 59.369 47.826 0.00 0.00 0.00 4.30
1481 6006 2.686915 CTGAATCAAAGGAGGATGCCAC 59.313 50.000 0.00 0.00 0.00 5.01
1834 6363 7.094975 CGAACACTAAAACTTTCATGGTATGGA 60.095 37.037 0.00 0.00 0.00 3.41
2020 6554 2.425143 TGGCTTGCTGATAAAGGGAG 57.575 50.000 0.00 0.00 0.00 4.30
2189 6723 4.370364 TTTTCAGCAGTTGTGGAACTTC 57.630 40.909 0.00 0.00 40.68 3.01
2282 6818 3.134442 AGGGTGACATTGTGCATGTTTTT 59.866 39.130 0.00 0.00 46.96 1.94
2321 6857 2.146920 TCAAGCCATGCATTGATGGA 57.853 45.000 8.28 0.00 45.24 3.41
2336 6872 0.614812 ATGGATTTTTGGCAGGGTGC 59.385 50.000 0.00 0.00 44.08 5.01
2381 6917 7.775053 TGCAACTTTTCTTAGTGGGAAATAT 57.225 32.000 0.00 0.00 33.51 1.28
2400 6958 2.130821 TACCGGACAATTGGCAGCCA 62.131 55.000 11.22 11.22 0.00 4.75
2539 7097 1.143684 ACAAGGGCTTGCGATCCATAT 59.856 47.619 0.00 0.00 44.03 1.78
2704 7262 5.407995 GGACATATGAAGTAGAGAAGCATGC 59.592 44.000 10.51 10.51 0.00 4.06
2707 7265 7.052873 ACATATGAAGTAGAGAAGCATGCTTT 58.947 34.615 32.36 21.67 36.26 3.51
2822 7380 6.361481 CAGCAATGACAAAAGTTGAGTATGTG 59.639 38.462 0.00 0.00 0.00 3.21
2840 7398 4.597404 TGTGTGCAATAATTTGGCAGAA 57.403 36.364 0.00 0.00 33.22 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.950828 TAAAAACTGGCACGTTCGGA 58.049 45.000 1.90 0.00 0.00 4.55
2 3 2.981400 ATAAAAACTGGCACGTTCGG 57.019 45.000 0.00 0.00 0.00 4.30
3 4 5.606515 CGAAAAATAAAAACTGGCACGTTCG 60.607 40.000 0.00 0.00 0.00 3.95
4 5 5.331980 CCGAAAAATAAAAACTGGCACGTTC 60.332 40.000 0.00 0.00 0.00 3.95
5 6 4.504826 CCGAAAAATAAAAACTGGCACGTT 59.495 37.500 0.00 0.00 0.00 3.99
7 8 3.427193 CCCGAAAAATAAAAACTGGCACG 59.573 43.478 0.00 0.00 0.00 5.34
8 9 4.373527 ACCCGAAAAATAAAAACTGGCAC 58.626 39.130 0.00 0.00 0.00 5.01
9 10 4.623002 GACCCGAAAAATAAAAACTGGCA 58.377 39.130 0.00 0.00 0.00 4.92
10 11 3.671459 CGACCCGAAAAATAAAAACTGGC 59.329 43.478 0.00 0.00 0.00 4.85
11 12 5.110940 TCGACCCGAAAAATAAAAACTGG 57.889 39.130 0.00 0.00 31.06 4.00
24 25 0.102844 AAGACAACGTTCGACCCGAA 59.897 50.000 10.36 0.00 43.75 4.30
25 26 0.102844 AAAGACAACGTTCGACCCGA 59.897 50.000 10.36 0.00 0.00 5.14
27 28 0.041576 GCAAAGACAACGTTCGACCC 60.042 55.000 0.00 0.00 0.00 4.46
28 29 0.041576 GGCAAAGACAACGTTCGACC 60.042 55.000 0.00 0.00 0.00 4.79
29 30 0.382636 CGGCAAAGACAACGTTCGAC 60.383 55.000 0.00 0.00 0.00 4.20
30 31 0.806884 ACGGCAAAGACAACGTTCGA 60.807 50.000 0.00 0.00 35.90 3.71
31 32 0.027063 AACGGCAAAGACAACGTTCG 59.973 50.000 0.00 0.00 45.15 3.95
34 35 1.088306 TCAAACGGCAAAGACAACGT 58.912 45.000 0.00 0.00 41.88 3.99
35 36 2.399396 ATCAAACGGCAAAGACAACG 57.601 45.000 0.00 0.00 0.00 4.10
36 37 3.049912 GGAATCAAACGGCAAAGACAAC 58.950 45.455 0.00 0.00 0.00 3.32
37 38 2.955660 AGGAATCAAACGGCAAAGACAA 59.044 40.909 0.00 0.00 0.00 3.18
38 39 2.293122 CAGGAATCAAACGGCAAAGACA 59.707 45.455 0.00 0.00 0.00 3.41
39 40 2.351738 CCAGGAATCAAACGGCAAAGAC 60.352 50.000 0.00 0.00 0.00 3.01
40 41 1.885887 CCAGGAATCAAACGGCAAAGA 59.114 47.619 0.00 0.00 0.00 2.52
41 42 1.669795 GCCAGGAATCAAACGGCAAAG 60.670 52.381 0.00 0.00 42.50 2.77
42 43 0.316841 GCCAGGAATCAAACGGCAAA 59.683 50.000 0.00 0.00 42.50 3.68
43 44 1.963679 GCCAGGAATCAAACGGCAA 59.036 52.632 0.00 0.00 42.50 4.52
44 45 3.680156 GCCAGGAATCAAACGGCA 58.320 55.556 0.00 0.00 42.50 5.69
45 46 1.212751 GTGCCAGGAATCAAACGGC 59.787 57.895 0.00 0.00 43.28 5.68
46 47 2.107950 TAGTGCCAGGAATCAAACGG 57.892 50.000 0.00 0.00 0.00 4.44
48 49 5.393461 CCAAGATTAGTGCCAGGAATCAAAC 60.393 44.000 0.00 0.00 32.96 2.93
49 50 4.706476 CCAAGATTAGTGCCAGGAATCAAA 59.294 41.667 0.00 0.00 32.96 2.69
51 52 3.523157 TCCAAGATTAGTGCCAGGAATCA 59.477 43.478 0.00 0.00 32.96 2.57
52 53 4.133078 CTCCAAGATTAGTGCCAGGAATC 58.867 47.826 0.00 0.00 0.00 2.52
53 54 3.686691 GCTCCAAGATTAGTGCCAGGAAT 60.687 47.826 0.00 0.00 0.00 3.01
54 55 2.356125 GCTCCAAGATTAGTGCCAGGAA 60.356 50.000 0.00 0.00 0.00 3.36
55 56 1.210478 GCTCCAAGATTAGTGCCAGGA 59.790 52.381 0.00 0.00 0.00 3.86
56 57 1.065199 TGCTCCAAGATTAGTGCCAGG 60.065 52.381 0.00 0.00 0.00 4.45
57 58 2.408271 TGCTCCAAGATTAGTGCCAG 57.592 50.000 0.00 0.00 0.00 4.85
59 60 1.952296 CCATGCTCCAAGATTAGTGCC 59.048 52.381 0.00 0.00 0.00 5.01
60 61 2.877168 CTCCATGCTCCAAGATTAGTGC 59.123 50.000 0.00 0.00 0.00 4.40
63 64 4.378774 CTGTCTCCATGCTCCAAGATTAG 58.621 47.826 0.00 0.00 0.00 1.73
64 65 3.432749 GCTGTCTCCATGCTCCAAGATTA 60.433 47.826 0.00 0.00 0.00 1.75
65 66 2.683152 GCTGTCTCCATGCTCCAAGATT 60.683 50.000 0.00 0.00 0.00 2.40
66 67 1.134159 GCTGTCTCCATGCTCCAAGAT 60.134 52.381 0.00 0.00 0.00 2.40
67 68 0.251354 GCTGTCTCCATGCTCCAAGA 59.749 55.000 0.00 0.00 0.00 3.02
69 70 1.300963 GGCTGTCTCCATGCTCCAA 59.699 57.895 0.00 0.00 0.00 3.53
70 71 1.919816 TGGCTGTCTCCATGCTCCA 60.920 57.895 0.00 0.00 0.00 3.86
71 72 1.451028 GTGGCTGTCTCCATGCTCC 60.451 63.158 0.00 0.00 38.57 4.70
72 73 1.812922 CGTGGCTGTCTCCATGCTC 60.813 63.158 0.00 0.00 38.57 4.26
73 74 2.267006 CGTGGCTGTCTCCATGCT 59.733 61.111 0.00 0.00 38.57 3.79
74 75 2.046892 ACGTGGCTGTCTCCATGC 60.047 61.111 2.18 0.00 44.94 4.06
75 76 0.107993 ATGACGTGGCTGTCTCCATG 60.108 55.000 0.00 0.80 46.15 3.66
76 77 0.107993 CATGACGTGGCTGTCTCCAT 60.108 55.000 0.00 0.00 39.64 3.41
78 79 0.320771 AACATGACGTGGCTGTCTCC 60.321 55.000 0.00 0.00 39.64 3.71
79 80 1.195448 CAAACATGACGTGGCTGTCTC 59.805 52.381 0.00 0.00 39.64 3.36
80 81 1.229428 CAAACATGACGTGGCTGTCT 58.771 50.000 0.00 0.00 39.64 3.41
82 83 1.333619 GAACAAACATGACGTGGCTGT 59.666 47.619 0.00 0.00 0.00 4.40
83 84 1.603802 AGAACAAACATGACGTGGCTG 59.396 47.619 0.00 0.00 0.00 4.85
86 87 1.194547 CGGAGAACAAACATGACGTGG 59.805 52.381 0.00 0.00 0.00 4.94
87 88 1.864711 ACGGAGAACAAACATGACGTG 59.135 47.619 0.00 0.00 31.60 4.49
88 89 2.234300 ACGGAGAACAAACATGACGT 57.766 45.000 0.00 0.00 0.00 4.34
89 90 2.409752 CGAACGGAGAACAAACATGACG 60.410 50.000 0.00 0.00 0.00 4.35
90 91 2.096417 CCGAACGGAGAACAAACATGAC 60.096 50.000 7.53 0.00 37.50 3.06
91 92 2.139917 CCGAACGGAGAACAAACATGA 58.860 47.619 7.53 0.00 37.50 3.07
92 93 2.139917 TCCGAACGGAGAACAAACATG 58.860 47.619 12.04 0.00 39.76 3.21
94 95 2.312722 TTCCGAACGGAGAACAAACA 57.687 45.000 15.34 0.00 46.06 2.83
95 96 3.310501 TCTTTTCCGAACGGAGAACAAAC 59.689 43.478 15.34 0.00 46.06 2.93
96 97 3.533547 TCTTTTCCGAACGGAGAACAAA 58.466 40.909 15.34 11.96 46.06 2.83
97 98 3.128349 CTCTTTTCCGAACGGAGAACAA 58.872 45.455 15.34 5.18 46.06 2.83
99 100 2.987821 CTCTCTTTTCCGAACGGAGAAC 59.012 50.000 15.34 0.00 46.06 3.01
100 101 2.889045 TCTCTCTTTTCCGAACGGAGAA 59.111 45.455 15.34 15.75 46.06 2.87
102 103 3.299340 TTCTCTCTTTTCCGAACGGAG 57.701 47.619 15.34 5.48 46.06 4.63
104 105 3.424962 GCAATTCTCTCTTTTCCGAACGG 60.425 47.826 6.94 6.94 0.00 4.44
105 106 3.424962 GGCAATTCTCTCTTTTCCGAACG 60.425 47.826 0.00 0.00 0.00 3.95
108 109 3.074412 GTGGCAATTCTCTCTTTTCCGA 58.926 45.455 0.00 0.00 0.00 4.55
109 110 3.077359 AGTGGCAATTCTCTCTTTTCCG 58.923 45.455 0.00 0.00 0.00 4.30
110 111 6.261158 GGTATAGTGGCAATTCTCTCTTTTCC 59.739 42.308 0.00 0.00 0.00 3.13
111 112 6.823689 TGGTATAGTGGCAATTCTCTCTTTTC 59.176 38.462 0.00 0.00 0.00 2.29
112 113 6.599638 GTGGTATAGTGGCAATTCTCTCTTTT 59.400 38.462 0.00 0.00 0.00 2.27
113 114 6.069963 AGTGGTATAGTGGCAATTCTCTCTTT 60.070 38.462 0.00 0.00 0.00 2.52
114 115 5.426833 AGTGGTATAGTGGCAATTCTCTCTT 59.573 40.000 0.00 0.00 0.00 2.85
115 116 4.965532 AGTGGTATAGTGGCAATTCTCTCT 59.034 41.667 0.00 0.00 0.00 3.10
326 4744 2.614983 GGGAGAGATGTGTACGAGTCTC 59.385 54.545 11.23 11.23 37.86 3.36
327 4745 2.645802 GGGAGAGATGTGTACGAGTCT 58.354 52.381 0.00 0.00 0.00 3.24
328 4746 1.331138 CGGGAGAGATGTGTACGAGTC 59.669 57.143 0.00 0.00 0.00 3.36
439 4882 4.947147 GCGGTGCTGGGTGGTCAA 62.947 66.667 0.00 0.00 0.00 3.18
493 4950 3.637273 GGGTCGTTGGAGGCCAGT 61.637 66.667 5.01 0.00 33.81 4.00
651 5109 0.322975 GTTGAGCTGCTTGGGAGAGA 59.677 55.000 2.53 0.00 0.00 3.10
716 5203 9.683069 CTGCACTTGAAATGAAAAATACTTAGT 57.317 29.630 0.00 0.00 0.00 2.24
719 5206 6.985645 TGCTGCACTTGAAATGAAAAATACTT 59.014 30.769 0.00 0.00 0.00 2.24
753 5241 6.156602 TCCCATCCACTTGCAATGAAAAATAT 59.843 34.615 0.00 0.00 0.00 1.28
1200 5710 2.456577 TCAGAGATCAATGGGACGACA 58.543 47.619 0.00 0.00 0.00 4.35
1250 5760 8.985805 CGAACCTTAGTACTTTTGTGTTAGAAT 58.014 33.333 0.00 0.00 0.00 2.40
1267 5777 2.742053 CAATGGTCACACCGAACCTTAG 59.258 50.000 0.00 0.00 42.58 2.18
1329 5839 2.889678 CGACTGATCATCCATCTCCTCA 59.110 50.000 0.00 0.00 31.92 3.86
1348 5858 0.320374 AAGAATGGAGCGTGAACCGA 59.680 50.000 0.00 0.00 39.56 4.69
1395 5905 2.158534 AGGCTCATCATCCTCGTACTCT 60.159 50.000 0.00 0.00 0.00 3.24
1425 5935 4.336713 GGCAAATAGGTGTTCTCCTGATTC 59.663 45.833 3.99 0.00 38.41 2.52
1429 5939 3.012518 CAGGCAAATAGGTGTTCTCCTG 58.987 50.000 3.99 0.00 38.41 3.86
1448 5958 4.335874 CCTTTGATTCAGCATTCTCCTCAG 59.664 45.833 0.00 0.00 0.00 3.35
1474 5999 3.243839 ACATTTTTCTGTGGTGTGGCATC 60.244 43.478 0.00 0.00 0.00 3.91
1481 6006 2.350772 GGCTCGACATTTTTCTGTGGTG 60.351 50.000 0.00 0.00 0.00 4.17
1530 6058 5.491070 TCATAAGAGTTGTCAACATCCAGG 58.509 41.667 17.78 3.72 0.00 4.45
1834 6363 6.002062 GCAAGAAGCAAACAACTGTACTAT 57.998 37.500 0.00 0.00 44.79 2.12
2020 6554 0.034670 ATTCTCCTCAAGTGCAGCCC 60.035 55.000 0.00 0.00 0.00 5.19
2282 6818 6.350110 GCTTGAAGGCAATGAACAACCTATTA 60.350 38.462 0.00 0.00 32.68 0.98
2321 6857 0.681175 GTCTGCACCCTGCCAAAAAT 59.319 50.000 0.00 0.00 44.23 1.82
2336 6872 3.380471 TCAACCCCCAAATATGGTCTG 57.620 47.619 0.00 0.00 46.01 3.51
2381 6917 1.377987 GGCTGCCAATTGTCCGGTA 60.378 57.895 15.17 0.00 0.00 4.02
2400 6958 0.178938 TGCCCATCCACACCAATTGT 60.179 50.000 4.43 0.00 39.97 2.71
2539 7097 3.119319 TCCAACCCCTTACATGCATCTA 58.881 45.455 0.00 0.00 0.00 1.98
2704 7262 5.678107 GCTTGTATTTCTGCCATCCTGAAAG 60.678 44.000 0.00 0.00 42.28 2.62
2707 7265 3.282021 GCTTGTATTTCTGCCATCCTGA 58.718 45.455 0.00 0.00 0.00 3.86
2822 7380 6.202570 TGAAAACTTCTGCCAAATTATTGCAC 59.797 34.615 0.00 0.00 35.10 4.57


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

AutoCloner maintained by Alex Coulton.