Multiple sequence alignment - TraesCS5D01G318200

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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 TraesCS5D01G318200 chr5D 100.000 2873 0 0 1 2873 411150483 411147611 0.000000e+00 5306
1 TraesCS5D01G318200 chr5D 93.882 850 50 2 1880 2728 23823086 23822238 0.000000e+00 1280
2 TraesCS5D01G318200 chr5D 91.495 823 60 2 1069 1881 410953039 410952217 0.000000e+00 1123
3 TraesCS5D01G318200 chr5D 82.586 781 76 26 280 1039 410953890 410953149 4.040000e-178 634
4 TraesCS5D01G318200 chr5D 86.000 350 43 5 1179 1528 411225760 411225417 1.260000e-98 370
5 TraesCS5D01G318200 chr5B 93.581 1667 53 14 179 1813 493517693 493516049 0.000000e+00 2436
6 TraesCS5D01G318200 chr5B 91.495 823 60 4 1069 1881 493481200 493480378 0.000000e+00 1123
7 TraesCS5D01G318200 chr5B 83.811 593 67 18 466 1039 493481872 493481290 1.170000e-148 536
8 TraesCS5D01G318200 chr5B 84.857 350 47 5 1179 1528 493695441 493695098 5.890000e-92 348
9 TraesCS5D01G318200 chr5B 84.874 357 37 13 1181 1533 492619510 492619853 7.620000e-91 344
10 TraesCS5D01G318200 chr7D 96.196 999 33 4 1878 2873 165633456 165632460 0.000000e+00 1629
11 TraesCS5D01G318200 chr2D 95.687 997 42 1 1878 2873 608365634 608364638 0.000000e+00 1602
12 TraesCS5D01G318200 chr2D 95.323 1005 42 3 1873 2873 532423046 532422043 0.000000e+00 1591
13 TraesCS5D01G318200 chr2D 94.700 1000 45 4 1880 2873 475894451 475895448 0.000000e+00 1546
14 TraesCS5D01G318200 chr1D 95.025 1005 46 3 1870 2873 244916265 244915264 0.000000e+00 1576
15 TraesCS5D01G318200 chr4D 94.584 997 51 3 1878 2873 32936757 32935763 0.000000e+00 1539
16 TraesCS5D01G318200 chr1A 94.489 998 49 5 1878 2873 26202324 26203317 0.000000e+00 1533
17 TraesCS5D01G318200 chr3A 93.769 995 60 2 1880 2873 44691165 44690172 0.000000e+00 1493
18 TraesCS5D01G318200 chr5A 95.023 864 34 1 1025 1879 522956907 522956044 0.000000e+00 1349
19 TraesCS5D01G318200 chr5A 91.383 824 60 3 1069 1881 522883472 522882649 0.000000e+00 1118
20 TraesCS5D01G318200 chr5A 89.893 653 37 6 156 788 522977204 522976561 0.000000e+00 813
21 TraesCS5D01G318200 chr5A 85.143 350 46 5 1179 1528 523148706 523148363 1.270000e-93 353
22 TraesCS5D01G318200 chr5A 82.609 207 16 6 833 1039 522884028 522883842 6.370000e-37 165
23 TraesCS5D01G318200 chr6B 88.825 519 31 11 2352 2867 650060834 650061328 1.890000e-171 612


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 TraesCS5D01G318200 chr5D 411147611 411150483 2872 True 5306.0 5306 100.0000 1 2873 1 chr5D.!!$R2 2872
1 TraesCS5D01G318200 chr5D 23822238 23823086 848 True 1280.0 1280 93.8820 1880 2728 1 chr5D.!!$R1 848
2 TraesCS5D01G318200 chr5D 410952217 410953890 1673 True 878.5 1123 87.0405 280 1881 2 chr5D.!!$R4 1601
3 TraesCS5D01G318200 chr5B 493516049 493517693 1644 True 2436.0 2436 93.5810 179 1813 1 chr5B.!!$R1 1634
4 TraesCS5D01G318200 chr5B 493480378 493481872 1494 True 829.5 1123 87.6530 466 1881 2 chr5B.!!$R3 1415
5 TraesCS5D01G318200 chr7D 165632460 165633456 996 True 1629.0 1629 96.1960 1878 2873 1 chr7D.!!$R1 995
6 TraesCS5D01G318200 chr2D 608364638 608365634 996 True 1602.0 1602 95.6870 1878 2873 1 chr2D.!!$R2 995
7 TraesCS5D01G318200 chr2D 532422043 532423046 1003 True 1591.0 1591 95.3230 1873 2873 1 chr2D.!!$R1 1000
8 TraesCS5D01G318200 chr2D 475894451 475895448 997 False 1546.0 1546 94.7000 1880 2873 1 chr2D.!!$F1 993
9 TraesCS5D01G318200 chr1D 244915264 244916265 1001 True 1576.0 1576 95.0250 1870 2873 1 chr1D.!!$R1 1003
10 TraesCS5D01G318200 chr4D 32935763 32936757 994 True 1539.0 1539 94.5840 1878 2873 1 chr4D.!!$R1 995
11 TraesCS5D01G318200 chr1A 26202324 26203317 993 False 1533.0 1533 94.4890 1878 2873 1 chr1A.!!$F1 995
12 TraesCS5D01G318200 chr3A 44690172 44691165 993 True 1493.0 1493 93.7690 1880 2873 1 chr3A.!!$R1 993
13 TraesCS5D01G318200 chr5A 522956044 522956907 863 True 1349.0 1349 95.0230 1025 1879 1 chr5A.!!$R1 854
14 TraesCS5D01G318200 chr5A 522976561 522977204 643 True 813.0 813 89.8930 156 788 1 chr5A.!!$R2 632
15 TraesCS5D01G318200 chr5A 522882649 522884028 1379 True 641.5 1118 86.9960 833 1881 2 chr5A.!!$R4 1048

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
732 768 0.248949 GCCCATCGGTCGACTAGAAC 60.249 60.0 16.46 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 2349 0.174845 TCAAATTCGCTCCGACGGAT 59.825 50.0 18.71 0.0 34.89 4.18 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
40 41 8.657074 TGTTTTAATATTGACCGATAGAGTGG 57.343 34.615 0.00 0.00 39.76 4.00
41 42 8.262227 TGTTTTAATATTGACCGATAGAGTGGT 58.738 33.333 0.00 0.00 42.42 4.16
42 43 9.754382 GTTTTAATATTGACCGATAGAGTGGTA 57.246 33.333 0.00 0.00 38.99 3.25
43 44 9.754382 TTTTAATATTGACCGATAGAGTGGTAC 57.246 33.333 0.00 0.00 38.99 3.34
44 45 8.701908 TTAATATTGACCGATAGAGTGGTACT 57.298 34.615 0.00 0.00 38.99 2.73
45 46 4.920640 ATTGACCGATAGAGTGGTACTG 57.079 45.455 0.00 0.00 38.99 2.74
46 47 3.639672 TGACCGATAGAGTGGTACTGA 57.360 47.619 0.00 0.00 38.99 3.41
47 48 3.276857 TGACCGATAGAGTGGTACTGAC 58.723 50.000 0.00 0.00 38.99 3.51
48 49 2.286872 ACCGATAGAGTGGTACTGACG 58.713 52.381 0.00 0.00 36.50 4.35
49 50 1.002684 CCGATAGAGTGGTACTGACGC 60.003 57.143 0.00 0.00 39.76 5.19
50 51 1.669265 CGATAGAGTGGTACTGACGCA 59.331 52.381 0.00 0.00 39.76 5.24
51 52 2.096980 CGATAGAGTGGTACTGACGCAA 59.903 50.000 0.00 0.00 39.76 4.85
52 53 3.436496 GATAGAGTGGTACTGACGCAAC 58.564 50.000 0.00 0.00 0.00 4.17
53 54 1.037493 AGAGTGGTACTGACGCAACA 58.963 50.000 0.00 0.00 0.00 3.33
54 55 1.137513 GAGTGGTACTGACGCAACAC 58.862 55.000 0.00 0.00 0.00 3.32
55 56 0.750850 AGTGGTACTGACGCAACACT 59.249 50.000 0.00 0.00 34.63 3.55
56 57 1.958579 AGTGGTACTGACGCAACACTA 59.041 47.619 0.00 0.00 37.41 2.74
57 58 2.363038 AGTGGTACTGACGCAACACTAA 59.637 45.455 0.00 0.00 37.41 2.24
58 59 3.125316 GTGGTACTGACGCAACACTAAA 58.875 45.455 0.00 0.00 0.00 1.85
59 60 3.183775 GTGGTACTGACGCAACACTAAAG 59.816 47.826 0.00 0.00 0.00 1.85
60 61 2.157085 GGTACTGACGCAACACTAAAGC 59.843 50.000 0.00 0.00 0.00 3.51
61 62 2.240493 ACTGACGCAACACTAAAGCT 57.760 45.000 0.00 0.00 0.00 3.74
62 63 2.561569 ACTGACGCAACACTAAAGCTT 58.438 42.857 0.00 0.00 0.00 3.74
63 64 2.287915 ACTGACGCAACACTAAAGCTTG 59.712 45.455 0.00 0.00 0.00 4.01
64 65 2.543848 CTGACGCAACACTAAAGCTTGA 59.456 45.455 0.00 0.00 0.00 3.02
65 66 3.138304 TGACGCAACACTAAAGCTTGAT 58.862 40.909 0.00 0.00 0.00 2.57
66 67 3.058983 TGACGCAACACTAAAGCTTGATG 60.059 43.478 0.00 1.14 0.00 3.07
67 68 2.878406 ACGCAACACTAAAGCTTGATGT 59.122 40.909 0.00 1.85 0.00 3.06
68 69 4.062293 ACGCAACACTAAAGCTTGATGTA 58.938 39.130 0.00 0.00 0.00 2.29
69 70 4.152402 ACGCAACACTAAAGCTTGATGTAG 59.848 41.667 0.00 0.00 0.00 2.74
70 71 4.388773 CGCAACACTAAAGCTTGATGTAGA 59.611 41.667 0.00 0.00 0.00 2.59
71 72 5.063944 CGCAACACTAAAGCTTGATGTAGAT 59.936 40.000 0.00 0.00 0.00 1.98
72 73 6.253746 GCAACACTAAAGCTTGATGTAGATG 58.746 40.000 0.00 2.20 0.00 2.90
73 74 6.128172 GCAACACTAAAGCTTGATGTAGATGT 60.128 38.462 0.00 3.05 0.00 3.06
74 75 7.064609 GCAACACTAAAGCTTGATGTAGATGTA 59.935 37.037 0.00 0.00 0.00 2.29
75 76 8.598924 CAACACTAAAGCTTGATGTAGATGTAG 58.401 37.037 0.00 0.00 0.00 2.74
76 77 8.067751 ACACTAAAGCTTGATGTAGATGTAGA 57.932 34.615 0.00 0.00 0.00 2.59
77 78 8.194104 ACACTAAAGCTTGATGTAGATGTAGAG 58.806 37.037 0.00 0.00 0.00 2.43
78 79 8.409371 CACTAAAGCTTGATGTAGATGTAGAGA 58.591 37.037 0.00 0.00 0.00 3.10
79 80 8.972127 ACTAAAGCTTGATGTAGATGTAGAGAA 58.028 33.333 0.00 0.00 0.00 2.87
80 81 9.809096 CTAAAGCTTGATGTAGATGTAGAGAAA 57.191 33.333 0.00 0.00 0.00 2.52
112 113 9.130312 GGTATTACTCTACAAATGAATAGCTCG 57.870 37.037 0.00 0.00 0.00 5.03
113 114 9.894783 GTATTACTCTACAAATGAATAGCTCGA 57.105 33.333 0.00 0.00 0.00 4.04
115 116 8.803201 TTACTCTACAAATGAATAGCTCGATG 57.197 34.615 0.00 0.00 0.00 3.84
116 117 6.810911 ACTCTACAAATGAATAGCTCGATGT 58.189 36.000 0.00 0.00 0.00 3.06
117 118 7.941919 ACTCTACAAATGAATAGCTCGATGTA 58.058 34.615 0.00 0.00 0.00 2.29
118 119 8.079203 ACTCTACAAATGAATAGCTCGATGTAG 58.921 37.037 8.50 8.50 37.86 2.74
119 120 8.166422 TCTACAAATGAATAGCTCGATGTAGA 57.834 34.615 11.98 11.98 40.30 2.59
120 121 8.797438 TCTACAAATGAATAGCTCGATGTAGAT 58.203 33.333 11.98 0.00 39.11 1.98
121 122 7.881643 ACAAATGAATAGCTCGATGTAGATC 57.118 36.000 0.00 0.00 0.00 2.75
122 123 7.665690 ACAAATGAATAGCTCGATGTAGATCT 58.334 34.615 0.00 0.00 0.00 2.75
123 124 7.812191 ACAAATGAATAGCTCGATGTAGATCTC 59.188 37.037 0.00 0.00 0.00 2.75
124 125 7.459795 AATGAATAGCTCGATGTAGATCTCA 57.540 36.000 0.00 0.00 0.00 3.27
125 126 6.884280 TGAATAGCTCGATGTAGATCTCAA 57.116 37.500 0.00 0.00 0.00 3.02
126 127 6.673106 TGAATAGCTCGATGTAGATCTCAAC 58.327 40.000 0.00 0.00 0.00 3.18
127 128 6.263168 TGAATAGCTCGATGTAGATCTCAACA 59.737 38.462 0.00 0.00 0.00 3.33
128 129 4.991153 AGCTCGATGTAGATCTCAACAA 57.009 40.909 0.00 0.00 0.00 2.83
129 130 5.330455 AGCTCGATGTAGATCTCAACAAA 57.670 39.130 0.00 0.00 0.00 2.83
130 131 5.911752 AGCTCGATGTAGATCTCAACAAAT 58.088 37.500 0.00 0.00 0.00 2.32
131 132 6.344500 AGCTCGATGTAGATCTCAACAAATT 58.656 36.000 0.00 0.00 0.00 1.82
132 133 7.492524 AGCTCGATGTAGATCTCAACAAATTA 58.507 34.615 0.00 0.00 0.00 1.40
133 134 7.436673 AGCTCGATGTAGATCTCAACAAATTAC 59.563 37.037 0.00 0.00 0.00 1.89
134 135 7.436673 GCTCGATGTAGATCTCAACAAATTACT 59.563 37.037 0.00 0.00 0.00 2.24
135 136 8.858003 TCGATGTAGATCTCAACAAATTACTC 57.142 34.615 0.00 0.00 0.00 2.59
136 137 7.921214 TCGATGTAGATCTCAACAAATTACTCC 59.079 37.037 0.00 0.00 0.00 3.85
137 138 7.923344 CGATGTAGATCTCAACAAATTACTCCT 59.077 37.037 0.00 0.00 0.00 3.69
138 139 9.255304 GATGTAGATCTCAACAAATTACTCCTC 57.745 37.037 0.00 0.00 0.00 3.71
139 140 8.134202 TGTAGATCTCAACAAATTACTCCTCA 57.866 34.615 0.00 0.00 0.00 3.86
140 141 8.035394 TGTAGATCTCAACAAATTACTCCTCAC 58.965 37.037 0.00 0.00 0.00 3.51
141 142 7.251321 AGATCTCAACAAATTACTCCTCACT 57.749 36.000 0.00 0.00 0.00 3.41
142 143 8.367660 AGATCTCAACAAATTACTCCTCACTA 57.632 34.615 0.00 0.00 0.00 2.74
143 144 8.986991 AGATCTCAACAAATTACTCCTCACTAT 58.013 33.333 0.00 0.00 0.00 2.12
144 145 8.954950 ATCTCAACAAATTACTCCTCACTATG 57.045 34.615 0.00 0.00 0.00 2.23
145 146 8.134202 TCTCAACAAATTACTCCTCACTATGA 57.866 34.615 0.00 0.00 0.00 2.15
146 147 8.035394 TCTCAACAAATTACTCCTCACTATGAC 58.965 37.037 0.00 0.00 0.00 3.06
147 148 7.103641 TCAACAAATTACTCCTCACTATGACC 58.896 38.462 0.00 0.00 0.00 4.02
148 149 6.620877 ACAAATTACTCCTCACTATGACCA 57.379 37.500 0.00 0.00 0.00 4.02
149 150 6.644347 ACAAATTACTCCTCACTATGACCAG 58.356 40.000 0.00 0.00 0.00 4.00
150 151 4.946478 ATTACTCCTCACTATGACCAGC 57.054 45.455 0.00 0.00 0.00 4.85
151 152 1.490574 ACTCCTCACTATGACCAGCC 58.509 55.000 0.00 0.00 0.00 4.85
152 153 1.007721 ACTCCTCACTATGACCAGCCT 59.992 52.381 0.00 0.00 0.00 4.58
153 154 2.245028 ACTCCTCACTATGACCAGCCTA 59.755 50.000 0.00 0.00 0.00 3.93
154 155 2.890311 CTCCTCACTATGACCAGCCTAG 59.110 54.545 0.00 0.00 0.00 3.02
213 216 4.262635 CCACTAATCGAGGCCAGTGATATT 60.263 45.833 17.79 5.80 40.67 1.28
218 221 1.001406 CGAGGCCAGTGATATTCTCCC 59.999 57.143 5.01 0.00 0.00 4.30
251 254 7.449247 AGAAACATATAAAAAGCAAAGGCCAA 58.551 30.769 5.01 0.00 42.56 4.52
380 404 2.416202 CACGTATCATGCAGCAGAAACA 59.584 45.455 0.00 0.00 0.00 2.83
531 555 2.668457 CCGGACGTTGAATCTTCTTCAG 59.332 50.000 0.00 0.00 0.00 3.02
545 569 7.684937 ATCTTCTTCAGATTTCCTGTCAAAG 57.315 36.000 0.00 0.00 39.47 2.77
553 581 5.641209 CAGATTTCCTGTCAAAGTCCTAGTG 59.359 44.000 0.00 0.00 38.10 2.74
732 768 0.248949 GCCCATCGGTCGACTAGAAC 60.249 60.000 16.46 0.00 0.00 3.01
888 928 1.876156 GCAGGAGCGAAAATATCAGGG 59.124 52.381 0.00 0.00 0.00 4.45
981 1034 6.749216 CGTCACGCATAACTATAAATGAGT 57.251 37.500 0.00 0.00 36.70 3.41
985 1038 6.771188 ACGCATAACTATAAATGAGTGAGC 57.229 37.500 0.00 0.00 35.25 4.26
986 1039 5.402568 ACGCATAACTATAAATGAGTGAGCG 59.597 40.000 0.00 0.00 42.72 5.03
987 1040 5.612865 GCATAACTATAAATGAGTGAGCGC 58.387 41.667 0.00 0.00 0.00 5.92
988 1041 5.177511 GCATAACTATAAATGAGTGAGCGCA 59.822 40.000 11.47 0.00 0.00 6.09
989 1042 6.584954 CATAACTATAAATGAGTGAGCGCAC 58.415 40.000 13.22 13.22 45.49 5.34
997 1050 2.340078 GTGAGCGCACTCTGGACA 59.660 61.111 13.84 0.00 43.85 4.02
998 1051 2.024319 GTGAGCGCACTCTGGACAC 61.024 63.158 13.84 2.91 43.85 3.67
999 1052 2.433318 GAGCGCACTCTGGACACC 60.433 66.667 11.47 0.00 40.03 4.16
1000 1053 3.226429 GAGCGCACTCTGGACACCA 62.226 63.158 11.47 0.00 40.03 4.17
1016 1083 1.069513 CACCACACTCGACTACCCAAA 59.930 52.381 0.00 0.00 0.00 3.28
1053 1120 2.047274 CACGTACCCCAGTGGCAG 60.047 66.667 2.61 0.00 37.83 4.85
1579 2004 2.683933 CTCCCCCGTGTACCTGCT 60.684 66.667 0.00 0.00 0.00 4.24
1683 2108 1.306633 GGGGAAATGGACCTGGACC 59.693 63.158 8.34 8.34 0.00 4.46
1902 2337 4.814234 GTCATTTTACAGTGCATCCGGATA 59.186 41.667 18.63 0.00 0.00 2.59
1912 2349 2.909662 TGCATCCGGATAATATGGACCA 59.090 45.455 18.63 0.00 33.91 4.02
1970 2407 2.251869 TACGCTGATGTCACGTGTAC 57.748 50.000 16.51 12.72 40.78 2.90
1983 2420 3.811497 TCACGTGTACTATATCAGACCCG 59.189 47.826 16.51 0.00 0.00 5.28
1999 2436 4.432601 CGGAGGGGCATTTTTGGA 57.567 55.556 0.00 0.00 0.00 3.53
2072 2510 6.070424 AGGGTATTCTCGGTACAAATTTCAGA 60.070 38.462 0.00 0.00 0.00 3.27
2221 2664 4.523282 GCCCCTCCCTCCCTCCAT 62.523 72.222 0.00 0.00 0.00 3.41
2242 2685 0.941463 CCAATTCCCTCGCGATCTCG 60.941 60.000 10.36 0.00 43.27 4.04
2375 2819 2.442413 GCCACAAGGTTATAGGCAACA 58.558 47.619 0.00 0.00 44.59 3.33
2428 2872 0.395724 TCTACGCCTCTCTGCCATGA 60.396 55.000 0.00 0.00 0.00 3.07
2450 2894 3.245229 ACCACAACTTTGATCTGGCCATA 60.245 43.478 5.51 0.00 0.00 2.74
2478 2922 1.890041 CGAAGGCAACGTGGTTGGA 60.890 57.895 10.19 0.00 42.99 3.53
2557 3001 1.274703 ATTCATCCAGCCCCGACTGT 61.275 55.000 0.00 0.00 35.83 3.55
2558 3002 2.124983 CATCCAGCCCCGACTGTG 60.125 66.667 0.00 0.00 35.83 3.66
2570 3014 2.619177 CCCGACTGTGAGATCTACGAAT 59.381 50.000 0.00 0.00 0.00 3.34
2654 3098 5.459536 TGATAGGTGAGATTTGGAGATCG 57.540 43.478 0.00 0.00 0.00 3.69
2797 3246 8.477984 TTGGCATGTGCTTTATAAGAAAAATC 57.522 30.769 4.84 0.00 41.70 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.273016 CCACTCTATCGGTCAATATTAAAACAT 57.727 33.333 0.00 0.00 0.00 2.71
15 16 8.262227 ACCACTCTATCGGTCAATATTAAAACA 58.738 33.333 0.00 0.00 0.00 2.83
16 17 8.658499 ACCACTCTATCGGTCAATATTAAAAC 57.342 34.615 0.00 0.00 0.00 2.43
17 18 9.754382 GTACCACTCTATCGGTCAATATTAAAA 57.246 33.333 0.00 0.00 36.69 1.52
18 19 9.139734 AGTACCACTCTATCGGTCAATATTAAA 57.860 33.333 0.00 0.00 36.69 1.52
19 20 8.573885 CAGTACCACTCTATCGGTCAATATTAA 58.426 37.037 0.00 0.00 36.69 1.40
20 21 7.940688 TCAGTACCACTCTATCGGTCAATATTA 59.059 37.037 0.00 0.00 36.69 0.98
21 22 6.776116 TCAGTACCACTCTATCGGTCAATATT 59.224 38.462 0.00 0.00 36.69 1.28
22 23 6.207025 GTCAGTACCACTCTATCGGTCAATAT 59.793 42.308 0.00 0.00 36.69 1.28
23 24 5.530171 GTCAGTACCACTCTATCGGTCAATA 59.470 44.000 0.00 0.00 36.69 1.90
24 25 4.338682 GTCAGTACCACTCTATCGGTCAAT 59.661 45.833 0.00 0.00 36.69 2.57
25 26 3.693085 GTCAGTACCACTCTATCGGTCAA 59.307 47.826 0.00 0.00 36.69 3.18
26 27 3.276857 GTCAGTACCACTCTATCGGTCA 58.723 50.000 0.00 0.00 36.69 4.02
27 28 2.287373 CGTCAGTACCACTCTATCGGTC 59.713 54.545 0.00 0.00 36.69 4.79
28 29 2.286872 CGTCAGTACCACTCTATCGGT 58.713 52.381 0.00 0.00 39.41 4.69
29 30 1.002684 GCGTCAGTACCACTCTATCGG 60.003 57.143 0.00 0.00 0.00 4.18
30 31 1.669265 TGCGTCAGTACCACTCTATCG 59.331 52.381 0.00 0.00 0.00 2.92
31 32 3.119602 TGTTGCGTCAGTACCACTCTATC 60.120 47.826 0.00 0.00 0.00 2.08
32 33 2.823747 TGTTGCGTCAGTACCACTCTAT 59.176 45.455 0.00 0.00 0.00 1.98
33 34 2.030540 GTGTTGCGTCAGTACCACTCTA 60.031 50.000 0.00 0.00 0.00 2.43
34 35 1.037493 TGTTGCGTCAGTACCACTCT 58.963 50.000 0.00 0.00 0.00 3.24
35 36 1.137513 GTGTTGCGTCAGTACCACTC 58.862 55.000 0.00 0.00 0.00 3.51
36 37 0.750850 AGTGTTGCGTCAGTACCACT 59.249 50.000 0.00 0.00 0.00 4.00
37 38 2.427232 TAGTGTTGCGTCAGTACCAC 57.573 50.000 0.00 0.00 0.00 4.16
38 39 3.386486 CTTTAGTGTTGCGTCAGTACCA 58.614 45.455 0.00 0.00 0.00 3.25
39 40 2.157085 GCTTTAGTGTTGCGTCAGTACC 59.843 50.000 0.00 0.00 0.00 3.34
40 41 3.057734 AGCTTTAGTGTTGCGTCAGTAC 58.942 45.455 0.00 0.00 0.00 2.73
41 42 3.380479 AGCTTTAGTGTTGCGTCAGTA 57.620 42.857 0.00 0.00 0.00 2.74
42 43 2.240493 AGCTTTAGTGTTGCGTCAGT 57.760 45.000 0.00 0.00 0.00 3.41
43 44 2.543848 TCAAGCTTTAGTGTTGCGTCAG 59.456 45.455 0.00 0.00 0.00 3.51
44 45 2.556257 TCAAGCTTTAGTGTTGCGTCA 58.444 42.857 0.00 0.00 0.00 4.35
45 46 3.058914 ACATCAAGCTTTAGTGTTGCGTC 60.059 43.478 0.00 0.00 0.00 5.19
46 47 2.878406 ACATCAAGCTTTAGTGTTGCGT 59.122 40.909 0.00 0.00 0.00 5.24
47 48 3.542712 ACATCAAGCTTTAGTGTTGCG 57.457 42.857 0.00 0.00 0.00 4.85
48 49 5.862924 TCTACATCAAGCTTTAGTGTTGC 57.137 39.130 11.91 0.00 0.00 4.17
49 50 7.369803 ACATCTACATCAAGCTTTAGTGTTG 57.630 36.000 11.91 10.52 0.00 3.33
50 51 8.531982 TCTACATCTACATCAAGCTTTAGTGTT 58.468 33.333 11.91 0.00 0.00 3.32
51 52 8.067751 TCTACATCTACATCAAGCTTTAGTGT 57.932 34.615 0.00 4.79 0.00 3.55
52 53 8.409371 TCTCTACATCTACATCAAGCTTTAGTG 58.591 37.037 0.00 0.00 0.00 2.74
53 54 8.526667 TCTCTACATCTACATCAAGCTTTAGT 57.473 34.615 0.00 0.00 0.00 2.24
54 55 9.809096 TTTCTCTACATCTACATCAAGCTTTAG 57.191 33.333 0.00 0.00 0.00 1.85
86 87 9.130312 CGAGCTATTCATTTGTAGAGTAATACC 57.870 37.037 0.00 0.00 0.00 2.73
87 88 9.894783 TCGAGCTATTCATTTGTAGAGTAATAC 57.105 33.333 0.00 0.00 0.00 1.89
89 90 9.416794 CATCGAGCTATTCATTTGTAGAGTAAT 57.583 33.333 0.00 0.00 0.00 1.89
90 91 8.414003 ACATCGAGCTATTCATTTGTAGAGTAA 58.586 33.333 0.00 0.00 0.00 2.24
91 92 7.941919 ACATCGAGCTATTCATTTGTAGAGTA 58.058 34.615 0.00 0.00 0.00 2.59
92 93 6.810911 ACATCGAGCTATTCATTTGTAGAGT 58.189 36.000 0.00 0.00 0.00 3.24
93 94 8.293157 TCTACATCGAGCTATTCATTTGTAGAG 58.707 37.037 11.98 0.00 36.86 2.43
94 95 8.166422 TCTACATCGAGCTATTCATTTGTAGA 57.834 34.615 11.98 11.98 38.04 2.59
95 96 8.978564 ATCTACATCGAGCTATTCATTTGTAG 57.021 34.615 8.50 8.50 35.54 2.74
96 97 8.797438 AGATCTACATCGAGCTATTCATTTGTA 58.203 33.333 0.00 0.00 33.75 2.41
97 98 7.665690 AGATCTACATCGAGCTATTCATTTGT 58.334 34.615 0.00 0.00 33.75 2.83
98 99 7.811713 TGAGATCTACATCGAGCTATTCATTTG 59.188 37.037 0.00 0.00 33.75 2.32
99 100 7.890515 TGAGATCTACATCGAGCTATTCATTT 58.109 34.615 0.00 0.00 33.75 2.32
100 101 7.459795 TGAGATCTACATCGAGCTATTCATT 57.540 36.000 0.00 0.00 33.75 2.57
101 102 7.040132 TGTTGAGATCTACATCGAGCTATTCAT 60.040 37.037 0.00 0.00 33.75 2.57
102 103 6.263168 TGTTGAGATCTACATCGAGCTATTCA 59.737 38.462 0.00 0.00 33.75 2.57
103 104 6.673106 TGTTGAGATCTACATCGAGCTATTC 58.327 40.000 0.00 0.00 33.75 1.75
104 105 6.641169 TGTTGAGATCTACATCGAGCTATT 57.359 37.500 0.00 0.00 33.75 1.73
105 106 6.641169 TTGTTGAGATCTACATCGAGCTAT 57.359 37.500 0.00 0.00 33.75 2.97
106 107 6.451064 TTTGTTGAGATCTACATCGAGCTA 57.549 37.500 0.00 0.00 33.75 3.32
107 108 4.991153 TTGTTGAGATCTACATCGAGCT 57.009 40.909 0.00 0.00 33.75 4.09
108 109 6.595772 AATTTGTTGAGATCTACATCGAGC 57.404 37.500 0.00 0.00 33.75 5.03
109 110 8.864069 AGTAATTTGTTGAGATCTACATCGAG 57.136 34.615 0.00 0.00 33.75 4.04
110 111 7.921214 GGAGTAATTTGTTGAGATCTACATCGA 59.079 37.037 0.00 0.00 33.75 3.59
111 112 7.923344 AGGAGTAATTTGTTGAGATCTACATCG 59.077 37.037 0.00 0.00 33.75 3.84
112 113 9.255304 GAGGAGTAATTTGTTGAGATCTACATC 57.745 37.037 0.00 0.00 32.18 3.06
113 114 8.762645 TGAGGAGTAATTTGTTGAGATCTACAT 58.237 33.333 0.00 0.00 32.18 2.29
114 115 8.035394 GTGAGGAGTAATTTGTTGAGATCTACA 58.965 37.037 0.00 0.00 0.00 2.74
115 116 8.254508 AGTGAGGAGTAATTTGTTGAGATCTAC 58.745 37.037 0.00 0.00 0.00 2.59
116 117 8.367660 AGTGAGGAGTAATTTGTTGAGATCTA 57.632 34.615 0.00 0.00 0.00 1.98
117 118 7.251321 AGTGAGGAGTAATTTGTTGAGATCT 57.749 36.000 0.00 0.00 0.00 2.75
118 119 9.039870 CATAGTGAGGAGTAATTTGTTGAGATC 57.960 37.037 0.00 0.00 0.00 2.75
119 120 8.762645 TCATAGTGAGGAGTAATTTGTTGAGAT 58.237 33.333 0.00 0.00 0.00 2.75
120 121 8.035394 GTCATAGTGAGGAGTAATTTGTTGAGA 58.965 37.037 0.00 0.00 0.00 3.27
121 122 7.278868 GGTCATAGTGAGGAGTAATTTGTTGAG 59.721 40.741 0.00 0.00 0.00 3.02
122 123 7.103641 GGTCATAGTGAGGAGTAATTTGTTGA 58.896 38.462 0.00 0.00 0.00 3.18
123 124 6.878923 TGGTCATAGTGAGGAGTAATTTGTTG 59.121 38.462 0.00 0.00 0.00 3.33
124 125 7.016153 TGGTCATAGTGAGGAGTAATTTGTT 57.984 36.000 0.00 0.00 0.00 2.83
125 126 6.620877 TGGTCATAGTGAGGAGTAATTTGT 57.379 37.500 0.00 0.00 0.00 2.83
126 127 5.525378 GCTGGTCATAGTGAGGAGTAATTTG 59.475 44.000 0.00 0.00 0.00 2.32
127 128 5.396884 GGCTGGTCATAGTGAGGAGTAATTT 60.397 44.000 0.00 0.00 0.00 1.82
128 129 4.101741 GGCTGGTCATAGTGAGGAGTAATT 59.898 45.833 0.00 0.00 0.00 1.40
129 130 3.643792 GGCTGGTCATAGTGAGGAGTAAT 59.356 47.826 0.00 0.00 0.00 1.89
130 131 3.031736 GGCTGGTCATAGTGAGGAGTAA 58.968 50.000 0.00 0.00 0.00 2.24
131 132 2.245028 AGGCTGGTCATAGTGAGGAGTA 59.755 50.000 0.00 0.00 0.00 2.59
132 133 1.007721 AGGCTGGTCATAGTGAGGAGT 59.992 52.381 0.00 0.00 0.00 3.85
133 134 1.786937 AGGCTGGTCATAGTGAGGAG 58.213 55.000 0.00 0.00 0.00 3.69
134 135 2.245028 ACTAGGCTGGTCATAGTGAGGA 59.755 50.000 0.00 0.00 40.42 3.71
135 136 2.672098 ACTAGGCTGGTCATAGTGAGG 58.328 52.381 0.00 0.00 40.42 3.86
136 137 3.254657 GCTACTAGGCTGGTCATAGTGAG 59.745 52.174 6.84 0.00 41.79 3.51
137 138 3.117474 AGCTACTAGGCTGGTCATAGTGA 60.117 47.826 6.84 0.00 41.79 3.41
138 139 3.226777 AGCTACTAGGCTGGTCATAGTG 58.773 50.000 6.84 0.00 41.79 2.74
139 140 3.117474 TGAGCTACTAGGCTGGTCATAGT 60.117 47.826 6.84 0.00 43.79 2.12
140 141 3.254657 GTGAGCTACTAGGCTGGTCATAG 59.745 52.174 6.84 0.28 43.20 2.23
141 142 3.223435 GTGAGCTACTAGGCTGGTCATA 58.777 50.000 6.84 0.00 43.20 2.15
142 143 2.035632 GTGAGCTACTAGGCTGGTCAT 58.964 52.381 6.84 0.00 43.20 3.06
143 144 1.475403 GTGAGCTACTAGGCTGGTCA 58.525 55.000 6.84 3.33 43.20 4.02
144 145 0.747852 GGTGAGCTACTAGGCTGGTC 59.252 60.000 6.84 0.25 43.20 4.02
145 146 0.336737 AGGTGAGCTACTAGGCTGGT 59.663 55.000 9.01 9.01 43.20 4.00
146 147 1.036707 GAGGTGAGCTACTAGGCTGG 58.963 60.000 0.00 0.00 43.20 4.85
147 148 1.769026 TGAGGTGAGCTACTAGGCTG 58.231 55.000 0.00 0.00 43.20 4.85
148 149 2.534042 TTGAGGTGAGCTACTAGGCT 57.466 50.000 0.00 0.00 46.11 4.58
149 150 2.287909 CGATTGAGGTGAGCTACTAGGC 60.288 54.545 0.00 0.00 0.00 3.93
150 151 2.294791 CCGATTGAGGTGAGCTACTAGG 59.705 54.545 0.00 0.00 0.00 3.02
151 152 2.294791 CCCGATTGAGGTGAGCTACTAG 59.705 54.545 0.00 0.00 0.00 2.57
152 153 2.092049 TCCCGATTGAGGTGAGCTACTA 60.092 50.000 0.00 0.00 0.00 1.82
153 154 1.115467 CCCGATTGAGGTGAGCTACT 58.885 55.000 0.00 0.00 0.00 2.57
154 155 1.112113 TCCCGATTGAGGTGAGCTAC 58.888 55.000 0.00 0.00 0.00 3.58
218 221 9.825972 TTGCTTTTTATATGTTTCTCTCGAAAG 57.174 29.630 0.00 0.00 39.65 2.62
380 404 0.333993 TCTCCTACTACCGGTTGCCT 59.666 55.000 15.04 0.00 0.00 4.75
531 555 4.938226 CCACTAGGACTTTGACAGGAAATC 59.062 45.833 0.00 0.00 36.89 2.17
545 569 1.299468 CTCGCATCGCCACTAGGAC 60.299 63.158 0.00 0.00 36.89 3.85
680 716 3.625764 TGCGGAACAAATATCTAACCAGC 59.374 43.478 0.00 0.00 0.00 4.85
981 1034 2.340078 GTGTCCAGAGTGCGCTCA 59.660 61.111 28.02 5.85 44.00 4.26
983 1036 3.233980 TGGTGTCCAGAGTGCGCT 61.234 61.111 9.73 0.00 0.00 5.92
984 1037 3.044305 GTGGTGTCCAGAGTGCGC 61.044 66.667 0.00 0.00 32.34 6.09
985 1038 1.956170 GTGTGGTGTCCAGAGTGCG 60.956 63.158 0.00 0.00 32.34 5.34
986 1039 0.601311 GAGTGTGGTGTCCAGAGTGC 60.601 60.000 0.00 0.00 30.23 4.40
987 1040 0.319040 CGAGTGTGGTGTCCAGAGTG 60.319 60.000 0.00 0.00 30.23 3.51
988 1041 0.467474 TCGAGTGTGGTGTCCAGAGT 60.467 55.000 0.00 0.00 32.90 3.24
989 1042 0.039074 GTCGAGTGTGGTGTCCAGAG 60.039 60.000 0.00 0.00 32.34 3.35
990 1043 0.467474 AGTCGAGTGTGGTGTCCAGA 60.467 55.000 0.00 0.00 32.34 3.86
991 1044 1.068472 GTAGTCGAGTGTGGTGTCCAG 60.068 57.143 2.10 0.00 32.34 3.86
992 1045 0.956633 GTAGTCGAGTGTGGTGTCCA 59.043 55.000 2.10 0.00 0.00 4.02
993 1046 0.243095 GGTAGTCGAGTGTGGTGTCC 59.757 60.000 2.10 0.00 0.00 4.02
994 1047 0.243095 GGGTAGTCGAGTGTGGTGTC 59.757 60.000 2.10 0.00 0.00 3.67
995 1048 0.468585 TGGGTAGTCGAGTGTGGTGT 60.469 55.000 2.10 0.00 0.00 4.16
996 1049 0.677288 TTGGGTAGTCGAGTGTGGTG 59.323 55.000 2.10 0.00 0.00 4.17
997 1050 1.343465 CTTTGGGTAGTCGAGTGTGGT 59.657 52.381 2.10 0.00 0.00 4.16
998 1051 1.939838 GCTTTGGGTAGTCGAGTGTGG 60.940 57.143 2.10 0.00 0.00 4.17
999 1052 1.429463 GCTTTGGGTAGTCGAGTGTG 58.571 55.000 2.10 0.00 0.00 3.82
1000 1053 0.320697 GGCTTTGGGTAGTCGAGTGT 59.679 55.000 2.10 0.00 0.00 3.55
1053 1120 2.174349 CTTTTGCTGGAGCGCGAC 59.826 61.111 12.10 1.97 45.83 5.19
1579 2004 2.358125 CATTGTCCACGGGCGACA 60.358 61.111 5.05 5.05 38.46 4.35
1804 2238 1.073199 CCCCAGTGTGAACCCACTC 59.927 63.158 0.00 0.00 43.70 3.51
1837 2272 3.096092 AGCAGTTTTGAGTTGGTCCAAA 58.904 40.909 5.69 0.00 0.00 3.28
1902 2337 1.618837 CTCCGACGGATGGTCCATATT 59.381 52.381 18.71 0.00 42.99 1.28
1912 2349 0.174845 TCAAATTCGCTCCGACGGAT 59.825 50.000 18.71 0.00 34.89 4.18
1970 2407 1.853963 CCCCTCCGGGTCTGATATAG 58.146 60.000 0.00 0.00 45.50 1.31
1983 2420 1.937191 TCTTCCAAAAATGCCCCTCC 58.063 50.000 0.00 0.00 0.00 4.30
2072 2510 8.406297 GGGATAAAAATCGAACTGAAAATAGCT 58.594 33.333 0.00 0.00 0.00 3.32
2131 2569 0.523966 CGGCGGCAAGGAATAAAACA 59.476 50.000 10.53 0.00 0.00 2.83
2221 2664 1.048724 AGATCGCGAGGGAATTGGGA 61.049 55.000 16.66 0.00 38.54 4.37
2242 2685 4.034742 TGTTCTTCGTTGAAAAGGTAGTGC 59.965 41.667 0.00 0.00 32.10 4.40
2243 2686 5.499047 GTGTTCTTCGTTGAAAAGGTAGTG 58.501 41.667 0.00 0.00 32.10 2.74
2245 2688 4.505191 TCGTGTTCTTCGTTGAAAAGGTAG 59.495 41.667 0.00 0.00 32.62 3.18
2375 2819 2.539302 CAATTGGGGTGTGGGAAAGAT 58.461 47.619 0.00 0.00 0.00 2.40
2428 2872 1.133513 TGGCCAGATCAAAGTTGTGGT 60.134 47.619 0.00 0.00 0.00 4.16
2450 2894 0.389948 GTTGCCTTCGGACGAGATGT 60.390 55.000 0.00 0.00 0.00 3.06
2478 2922 2.639347 TCCCGCAGAACATGATCCATAT 59.361 45.455 0.00 0.00 0.00 1.78
2557 3001 7.254556 GCAATGATTGAACATTCGTAGATCTCA 60.255 37.037 9.76 0.00 38.25 3.27
2558 3002 7.068341 GCAATGATTGAACATTCGTAGATCTC 58.932 38.462 9.76 0.00 38.25 2.75
2570 3014 7.160547 AGTGTATGAATGCAATGATTGAACA 57.839 32.000 9.76 0.00 0.00 3.18
2818 3267 7.033530 AGAATTAACACCAATGTTCAAACGA 57.966 32.000 0.00 0.00 46.46 3.85


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

AutoCloner maintained by Alex Coulton.