Multiple sequence alignment - TraesCS1B01G103000

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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 TraesCS1B01G103000 chr1B 100.000 2762 0 0 1 2762 113214054 113211293 0.000000e+00 5101.0
1 TraesCS1B01G103000 chr1B 99.273 2614 19 0 149 2762 113316267 113313654 0.000000e+00 4723.0
2 TraesCS1B01G103000 chr1B 99.120 2614 20 1 149 2762 113499055 113496445 0.000000e+00 4697.0
3 TraesCS1B01G103000 chr1B 84.248 2133 272 41 218 2312 113516577 113514471 0.000000e+00 2019.0
4 TraesCS1B01G103000 chr1B 98.795 1079 9 1 1684 2762 113407767 113406693 0.000000e+00 1917.0
5 TraesCS1B01G103000 chr1B 78.452 1615 279 46 216 1799 113026218 113024642 0.000000e+00 990.0
6 TraesCS1B01G103000 chr1B 79.561 1458 241 31 213 1640 50992406 50993836 0.000000e+00 989.0
7 TraesCS1B01G103000 chr1B 95.205 146 7 0 2 147 40413947 40414092 5.950000e-57 231.0
8 TraesCS1B01G103000 chr1B 87.500 144 11 6 2273 2411 51003231 51003372 2.850000e-35 159.0
9 TraesCS1B01G103000 chrUn 99.408 1690 10 0 149 1838 372932518 372934207 0.000000e+00 3066.0
10 TraesCS1B01G103000 chrUn 84.507 71 11 0 251 321 102692429 102692359 1.370000e-08 71.3
11 TraesCS1B01G103000 chr1D 93.939 1980 93 12 171 2123 72435570 72433591 0.000000e+00 2966.0
12 TraesCS1B01G103000 chr1D 80.619 1873 275 51 564 2392 72443223 72441395 0.000000e+00 1367.0
13 TraesCS1B01G103000 chr1D 80.556 1872 277 49 564 2392 72459630 72457803 0.000000e+00 1360.0
14 TraesCS1B01G103000 chr1D 79.128 1605 273 40 216 1799 71769954 71768391 0.000000e+00 1051.0
15 TraesCS1B01G103000 chr1A 79.224 1805 320 43 171 1947 32191021 32192798 0.000000e+00 1205.0
16 TraesCS1B01G103000 chr1A 75.369 203 37 9 251 445 570787900 570787703 4.900000e-13 86.1
17 TraesCS1B01G103000 chr5B 78.261 1196 231 25 618 1800 411744253 411743074 0.000000e+00 741.0
18 TraesCS1B01G103000 chr5B 95.547 247 11 0 2509 2755 523959543 523959297 1.990000e-106 396.0
19 TraesCS1B01G103000 chr5B 97.931 145 3 0 1 145 685306561 685306417 4.570000e-63 252.0
20 TraesCS1B01G103000 chr5D 78.932 1030 180 26 216 1220 350689176 350688159 0.000000e+00 665.0
21 TraesCS1B01G103000 chr4D 97.083 240 7 0 2516 2755 10756004 10756243 3.310000e-109 405.0
22 TraesCS1B01G103000 chr7B 96.281 242 9 0 2514 2755 125853926 125854167 5.540000e-107 398.0
23 TraesCS1B01G103000 chr7B 95.868 242 10 0 2514 2755 145817346 145817105 2.580000e-105 392.0
24 TraesCS1B01G103000 chr4B 95.868 242 10 0 2514 2755 532585978 532585737 2.580000e-105 392.0
25 TraesCS1B01G103000 chr3B 95.851 241 7 2 2516 2755 160148111 160148349 1.200000e-103 387.0
26 TraesCS1B01G103000 chr5A 98.639 147 2 0 1 147 553150127 553150273 7.590000e-66 261.0
27 TraesCS1B01G103000 chr5A 95.105 143 7 0 2 144 36172704 36172846 2.770000e-55 226.0
28 TraesCS1B01G103000 chr5A 95.105 143 7 0 2 144 87418856 87418714 2.770000e-55 226.0
29 TraesCS1B01G103000 chr5A 95.105 143 7 0 2 144 687142541 687142399 2.770000e-55 226.0
30 TraesCS1B01G103000 chr6A 97.279 147 4 0 1 147 592013425 592013279 1.640000e-62 250.0
31 TraesCS1B01G103000 chr6A 95.139 144 5 2 2 144 102118208 102118066 2.770000e-55 226.0
32 TraesCS1B01G103000 chr2B 95.105 143 7 0 2 144 733460796 733460654 2.770000e-55 226.0
33 TraesCS1B01G103000 chr6B 81.481 135 25 0 220 354 82958228 82958094 8.090000e-21 111.0


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 TraesCS1B01G103000 chr1B 113211293 113214054 2761 True 5101 5101 100.000 1 2762 1 chr1B.!!$R2 2761
1 TraesCS1B01G103000 chr1B 113313654 113316267 2613 True 4723 4723 99.273 149 2762 1 chr1B.!!$R3 2613
2 TraesCS1B01G103000 chr1B 113496445 113499055 2610 True 4697 4697 99.120 149 2762 1 chr1B.!!$R5 2613
3 TraesCS1B01G103000 chr1B 113514471 113516577 2106 True 2019 2019 84.248 218 2312 1 chr1B.!!$R6 2094
4 TraesCS1B01G103000 chr1B 113406693 113407767 1074 True 1917 1917 98.795 1684 2762 1 chr1B.!!$R4 1078
5 TraesCS1B01G103000 chr1B 113024642 113026218 1576 True 990 990 78.452 216 1799 1 chr1B.!!$R1 1583
6 TraesCS1B01G103000 chr1B 50992406 50993836 1430 False 989 989 79.561 213 1640 1 chr1B.!!$F2 1427
7 TraesCS1B01G103000 chrUn 372932518 372934207 1689 False 3066 3066 99.408 149 1838 1 chrUn.!!$F1 1689
8 TraesCS1B01G103000 chr1D 72433591 72435570 1979 True 2966 2966 93.939 171 2123 1 chr1D.!!$R2 1952
9 TraesCS1B01G103000 chr1D 72441395 72443223 1828 True 1367 1367 80.619 564 2392 1 chr1D.!!$R3 1828
10 TraesCS1B01G103000 chr1D 72457803 72459630 1827 True 1360 1360 80.556 564 2392 1 chr1D.!!$R4 1828
11 TraesCS1B01G103000 chr1D 71768391 71769954 1563 True 1051 1051 79.128 216 1799 1 chr1D.!!$R1 1583
12 TraesCS1B01G103000 chr1A 32191021 32192798 1777 False 1205 1205 79.224 171 1947 1 chr1A.!!$F1 1776
13 TraesCS1B01G103000 chr5B 411743074 411744253 1179 True 741 741 78.261 618 1800 1 chr5B.!!$R1 1182
14 TraesCS1B01G103000 chr5D 350688159 350689176 1017 True 665 665 78.932 216 1220 1 chr5D.!!$R1 1004

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
131 132 0.319469 AAATCCACTTTTTGCGGCCG 60.319 50.0 24.05 24.05 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2142 4.05605 ACTAGGTTTACTTTGCACAGTCG 58.944 43.478 9.19 0.0 0.0 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
23 24 6.998968 AACCAAATTTTGACTGCAATTTGA 57.001 29.167 17.00 0.00 46.58 2.69
24 25 6.362210 ACCAAATTTTGACTGCAATTTGAC 57.638 33.333 17.00 0.00 46.58 3.18
25 26 6.114767 ACCAAATTTTGACTGCAATTTGACT 58.885 32.000 17.00 3.44 46.58 3.41
26 27 6.598850 ACCAAATTTTGACTGCAATTTGACTT 59.401 30.769 17.00 2.96 46.58 3.01
27 28 7.768120 ACCAAATTTTGACTGCAATTTGACTTA 59.232 29.630 17.00 0.00 46.58 2.24
28 29 8.610896 CCAAATTTTGACTGCAATTTGACTTAA 58.389 29.630 17.00 0.00 46.58 1.85
29 30 9.985318 CAAATTTTGACTGCAATTTGACTTAAA 57.015 25.926 12.01 0.00 46.58 1.52
33 34 9.985318 TTTTGACTGCAATTTGACTTAAATTTG 57.015 25.926 0.00 0.00 44.49 2.32
34 35 8.939201 TTGACTGCAATTTGACTTAAATTTGA 57.061 26.923 0.00 0.00 44.49 2.69
35 36 9.545105 TTGACTGCAATTTGACTTAAATTTGAT 57.455 25.926 0.00 0.00 44.49 2.57
36 37 9.195411 TGACTGCAATTTGACTTAAATTTGATC 57.805 29.630 0.00 0.00 44.49 2.92
37 38 9.195411 GACTGCAATTTGACTTAAATTTGATCA 57.805 29.630 0.00 0.00 44.49 2.92
38 39 9.199982 ACTGCAATTTGACTTAAATTTGATCAG 57.800 29.630 0.00 0.00 44.49 2.90
39 40 9.414295 CTGCAATTTGACTTAAATTTGATCAGA 57.586 29.630 0.00 0.00 44.49 3.27
40 41 9.761504 TGCAATTTGACTTAAATTTGATCAGAA 57.238 25.926 0.00 0.00 44.49 3.02
56 57 8.592105 TTGATCAGAATTTGTCAAATTTCACC 57.408 30.769 21.51 10.95 40.97 4.02
57 58 7.724287 TGATCAGAATTTGTCAAATTTCACCA 58.276 30.769 21.51 14.03 40.97 4.17
58 59 8.202811 TGATCAGAATTTGTCAAATTTCACCAA 58.797 29.630 21.51 7.38 40.97 3.67
59 60 9.211485 GATCAGAATTTGTCAAATTTCACCAAT 57.789 29.630 21.51 11.38 40.97 3.16
60 61 8.961294 TCAGAATTTGTCAAATTTCACCAATT 57.039 26.923 21.51 4.28 40.97 2.32
61 62 9.393512 TCAGAATTTGTCAAATTTCACCAATTT 57.606 25.926 21.51 0.00 44.60 1.82
62 63 9.654417 CAGAATTTGTCAAATTTCACCAATTTC 57.346 29.630 21.51 8.42 42.28 2.17
63 64 8.550376 AGAATTTGTCAAATTTCACCAATTTCG 58.450 29.630 21.51 0.00 42.28 3.46
64 65 6.595772 TTTGTCAAATTTCACCAATTTCGG 57.404 33.333 0.00 0.00 42.28 4.30
65 66 4.054671 TGTCAAATTTCACCAATTTCGGC 58.945 39.130 0.00 0.00 42.28 5.54
66 67 3.431912 GTCAAATTTCACCAATTTCGGCC 59.568 43.478 0.00 0.00 42.28 6.13
67 68 3.323403 TCAAATTTCACCAATTTCGGCCT 59.677 39.130 0.00 0.00 42.28 5.19
68 69 4.524714 TCAAATTTCACCAATTTCGGCCTA 59.475 37.500 0.00 0.00 42.28 3.93
69 70 4.450082 AATTTCACCAATTTCGGCCTAC 57.550 40.909 0.00 0.00 30.09 3.18
70 71 2.570415 TTCACCAATTTCGGCCTACA 57.430 45.000 0.00 0.00 0.00 2.74
71 72 2.799126 TCACCAATTTCGGCCTACAT 57.201 45.000 0.00 0.00 0.00 2.29
72 73 3.916359 TCACCAATTTCGGCCTACATA 57.084 42.857 0.00 0.00 0.00 2.29
73 74 4.431416 TCACCAATTTCGGCCTACATAT 57.569 40.909 0.00 0.00 0.00 1.78
74 75 5.554437 TCACCAATTTCGGCCTACATATA 57.446 39.130 0.00 0.00 0.00 0.86
75 76 5.302360 TCACCAATTTCGGCCTACATATAC 58.698 41.667 0.00 0.00 0.00 1.47
76 77 5.071250 TCACCAATTTCGGCCTACATATACT 59.929 40.000 0.00 0.00 0.00 2.12
77 78 5.763204 CACCAATTTCGGCCTACATATACTT 59.237 40.000 0.00 0.00 0.00 2.24
78 79 6.262273 CACCAATTTCGGCCTACATATACTTT 59.738 38.462 0.00 0.00 0.00 2.66
79 80 6.831868 ACCAATTTCGGCCTACATATACTTTT 59.168 34.615 0.00 0.00 0.00 2.27
80 81 7.012989 ACCAATTTCGGCCTACATATACTTTTC 59.987 37.037 0.00 0.00 0.00 2.29
81 82 6.780706 ATTTCGGCCTACATATACTTTTCG 57.219 37.500 0.00 0.00 0.00 3.46
82 83 3.645884 TCGGCCTACATATACTTTTCGC 58.354 45.455 0.00 0.00 0.00 4.70
83 84 2.735134 CGGCCTACATATACTTTTCGCC 59.265 50.000 0.00 0.00 0.00 5.54
84 85 3.554337 CGGCCTACATATACTTTTCGCCT 60.554 47.826 0.00 0.00 0.00 5.52
85 86 3.995048 GGCCTACATATACTTTTCGCCTC 59.005 47.826 0.00 0.00 0.00 4.70
86 87 4.502604 GGCCTACATATACTTTTCGCCTCA 60.503 45.833 0.00 0.00 0.00 3.86
87 88 4.686554 GCCTACATATACTTTTCGCCTCAG 59.313 45.833 0.00 0.00 0.00 3.35
88 89 5.230942 CCTACATATACTTTTCGCCTCAGG 58.769 45.833 0.00 0.00 0.00 3.86
89 90 3.467803 ACATATACTTTTCGCCTCAGGC 58.532 45.455 5.22 5.22 46.75 4.85
107 108 1.934463 CCGAGATGGCCGAAATTCG 59.066 57.895 8.62 8.62 40.07 3.34
117 118 3.526825 CGAAATTCGGCCGAAATCC 57.473 52.632 41.31 29.08 37.69 3.01
118 119 0.730265 CGAAATTCGGCCGAAATCCA 59.270 50.000 41.31 22.04 37.69 3.41
119 120 1.531058 CGAAATTCGGCCGAAATCCAC 60.531 52.381 41.31 27.17 37.69 4.02
120 121 1.743394 GAAATTCGGCCGAAATCCACT 59.257 47.619 41.31 23.27 37.69 4.00
121 122 1.834188 AATTCGGCCGAAATCCACTT 58.166 45.000 41.31 27.41 37.69 3.16
122 123 1.834188 ATTCGGCCGAAATCCACTTT 58.166 45.000 41.31 21.74 37.69 2.66
123 124 1.611519 TTCGGCCGAAATCCACTTTT 58.388 45.000 37.13 0.00 0.00 2.27
124 125 1.611519 TCGGCCGAAATCCACTTTTT 58.388 45.000 28.99 0.00 0.00 1.94
125 126 1.268352 TCGGCCGAAATCCACTTTTTG 59.732 47.619 28.99 0.00 0.00 2.44
126 127 1.428448 GGCCGAAATCCACTTTTTGC 58.572 50.000 0.00 0.00 0.00 3.68
127 128 1.059942 GCCGAAATCCACTTTTTGCG 58.940 50.000 0.00 0.00 0.00 4.85
128 129 1.696988 CCGAAATCCACTTTTTGCGG 58.303 50.000 0.00 0.00 0.00 5.69
129 130 1.059942 CGAAATCCACTTTTTGCGGC 58.940 50.000 0.00 0.00 0.00 6.53
130 131 1.428448 GAAATCCACTTTTTGCGGCC 58.572 50.000 0.00 0.00 0.00 6.13
131 132 0.319469 AAATCCACTTTTTGCGGCCG 60.319 50.000 24.05 24.05 0.00 6.13
132 133 1.175983 AATCCACTTTTTGCGGCCGA 61.176 50.000 33.48 11.82 0.00 5.54
133 134 1.175983 ATCCACTTTTTGCGGCCGAA 61.176 50.000 33.48 19.06 0.00 4.30
134 135 1.066587 CCACTTTTTGCGGCCGAAA 59.933 52.632 33.48 25.41 0.00 3.46
135 136 0.528684 CCACTTTTTGCGGCCGAAAA 60.529 50.000 33.48 30.41 34.13 2.29
136 137 1.496934 CACTTTTTGCGGCCGAAAAT 58.503 45.000 31.40 14.84 34.63 1.82
137 138 1.455408 CACTTTTTGCGGCCGAAAATC 59.545 47.619 31.40 12.64 34.63 2.17
138 139 1.067821 ACTTTTTGCGGCCGAAAATCA 59.932 42.857 31.40 19.65 34.63 2.57
139 140 2.131183 CTTTTTGCGGCCGAAAATCAA 58.869 42.857 31.40 21.75 34.63 2.57
140 141 2.225068 TTTTGCGGCCGAAAATCAAA 57.775 40.000 31.40 24.80 0.00 2.69
141 142 2.225068 TTTGCGGCCGAAAATCAAAA 57.775 40.000 33.48 5.17 0.00 2.44
142 143 1.492720 TTGCGGCCGAAAATCAAAAC 58.507 45.000 33.48 7.30 0.00 2.43
143 144 0.385751 TGCGGCCGAAAATCAAAACA 59.614 45.000 33.48 10.37 0.00 2.83
144 145 1.059942 GCGGCCGAAAATCAAAACAG 58.940 50.000 33.48 0.00 0.00 3.16
145 146 1.601914 GCGGCCGAAAATCAAAACAGT 60.602 47.619 33.48 0.00 0.00 3.55
146 147 2.050691 CGGCCGAAAATCAAAACAGTG 58.949 47.619 24.07 0.00 0.00 3.66
147 148 2.542824 CGGCCGAAAATCAAAACAGTGT 60.543 45.455 24.07 0.00 0.00 3.55
686 699 3.173953 TGGCTCCTGTGATTTTCCAAT 57.826 42.857 0.00 0.00 0.00 3.16
813 827 7.540474 TGTCTTGGAGAACTTATACTTGTCT 57.460 36.000 0.00 0.00 0.00 3.41
2029 2142 9.601971 TGTGATTTATTTTTACTGCGAGTTAAC 57.398 29.630 0.00 0.00 0.00 2.01
2202 2342 8.408601 GCATGAATGTTATATTTCTGGACACTT 58.591 33.333 0.00 0.00 0.00 3.16
2252 2395 9.941664 CATGTGTAGAATAAATCACATTTCTCC 57.058 33.333 6.86 0.00 45.30 3.71
2523 2670 3.945285 ACTTCTCTTTGTCGAAAAAGGCA 59.055 39.130 24.49 11.07 37.67 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.598850 AGTCAAATTGCAGTCAAAATTTGGTT 59.401 30.769 15.66 5.52 46.53 3.67
1 2 6.114767 AGTCAAATTGCAGTCAAAATTTGGT 58.885 32.000 15.66 5.01 46.53 3.67
7 8 9.985318 CAAATTTAAGTCAAATTGCAGTCAAAA 57.015 25.926 0.00 0.00 44.37 2.44
8 9 9.376075 TCAAATTTAAGTCAAATTGCAGTCAAA 57.624 25.926 0.00 0.00 44.37 2.69
9 10 8.939201 TCAAATTTAAGTCAAATTGCAGTCAA 57.061 26.923 0.00 0.00 44.37 3.18
10 11 9.195411 GATCAAATTTAAGTCAAATTGCAGTCA 57.805 29.630 0.00 0.00 44.37 3.41
11 12 9.195411 TGATCAAATTTAAGTCAAATTGCAGTC 57.805 29.630 0.00 0.00 44.37 3.51
12 13 9.199982 CTGATCAAATTTAAGTCAAATTGCAGT 57.800 29.630 0.00 0.00 44.37 4.40
13 14 9.414295 TCTGATCAAATTTAAGTCAAATTGCAG 57.586 29.630 0.00 0.00 44.37 4.41
14 15 9.761504 TTCTGATCAAATTTAAGTCAAATTGCA 57.238 25.926 0.00 0.00 44.37 4.08
30 31 9.044150 GGTGAAATTTGACAAATTCTGATCAAA 57.956 29.630 22.98 3.30 43.23 2.69
31 32 8.202811 TGGTGAAATTTGACAAATTCTGATCAA 58.797 29.630 22.98 9.09 40.05 2.57
32 33 7.724287 TGGTGAAATTTGACAAATTCTGATCA 58.276 30.769 22.98 19.35 40.05 2.92
33 34 8.592105 TTGGTGAAATTTGACAAATTCTGATC 57.408 30.769 22.98 17.42 40.05 2.92
34 35 9.563748 AATTGGTGAAATTTGACAAATTCTGAT 57.436 25.926 22.98 10.26 40.05 2.90
35 36 8.961294 AATTGGTGAAATTTGACAAATTCTGA 57.039 26.923 22.98 9.89 40.05 3.27
36 37 9.654417 GAAATTGGTGAAATTTGACAAATTCTG 57.346 29.630 22.98 0.00 46.29 3.02
37 38 8.550376 CGAAATTGGTGAAATTTGACAAATTCT 58.450 29.630 22.98 14.55 46.29 2.40
38 39 7.798052 CCGAAATTGGTGAAATTTGACAAATTC 59.202 33.333 22.98 16.93 46.29 2.17
39 40 7.638134 CCGAAATTGGTGAAATTTGACAAATT 58.362 30.769 18.41 18.41 46.29 1.82
40 41 6.293353 GCCGAAATTGGTGAAATTTGACAAAT 60.293 34.615 10.02 7.62 46.29 2.32
41 42 5.007136 GCCGAAATTGGTGAAATTTGACAAA 59.993 36.000 10.02 5.07 46.29 2.83
42 43 4.509600 GCCGAAATTGGTGAAATTTGACAA 59.490 37.500 10.02 5.81 46.29 3.18
43 44 4.054671 GCCGAAATTGGTGAAATTTGACA 58.945 39.130 10.02 0.00 46.29 3.58
44 45 3.431912 GGCCGAAATTGGTGAAATTTGAC 59.568 43.478 0.00 0.00 46.29 3.18
45 46 3.323403 AGGCCGAAATTGGTGAAATTTGA 59.677 39.130 0.00 0.00 46.29 2.69
46 47 3.663025 AGGCCGAAATTGGTGAAATTTG 58.337 40.909 0.00 0.00 46.29 2.32
48 49 3.829601 TGTAGGCCGAAATTGGTGAAATT 59.170 39.130 0.00 0.00 40.32 1.82
49 50 3.426615 TGTAGGCCGAAATTGGTGAAAT 58.573 40.909 0.00 0.00 0.00 2.17
50 51 2.865079 TGTAGGCCGAAATTGGTGAAA 58.135 42.857 0.00 0.00 0.00 2.69
51 52 2.570415 TGTAGGCCGAAATTGGTGAA 57.430 45.000 0.00 0.00 0.00 3.18
52 53 2.799126 ATGTAGGCCGAAATTGGTGA 57.201 45.000 0.00 0.00 0.00 4.02
53 54 5.305585 AGTATATGTAGGCCGAAATTGGTG 58.694 41.667 0.00 0.00 0.00 4.17
54 55 5.562298 AGTATATGTAGGCCGAAATTGGT 57.438 39.130 0.00 0.00 0.00 3.67
55 56 6.877611 AAAGTATATGTAGGCCGAAATTGG 57.122 37.500 0.00 0.00 0.00 3.16
56 57 7.069569 CGAAAAGTATATGTAGGCCGAAATTG 58.930 38.462 0.00 0.00 0.00 2.32
57 58 6.293244 GCGAAAAGTATATGTAGGCCGAAATT 60.293 38.462 0.00 0.00 0.00 1.82
58 59 5.178809 GCGAAAAGTATATGTAGGCCGAAAT 59.821 40.000 0.00 0.00 0.00 2.17
59 60 4.508861 GCGAAAAGTATATGTAGGCCGAAA 59.491 41.667 0.00 0.00 0.00 3.46
60 61 4.053295 GCGAAAAGTATATGTAGGCCGAA 58.947 43.478 0.00 0.00 0.00 4.30
61 62 3.553508 GGCGAAAAGTATATGTAGGCCGA 60.554 47.826 0.00 0.00 0.00 5.54
62 63 2.735134 GGCGAAAAGTATATGTAGGCCG 59.265 50.000 0.00 0.00 0.00 6.13
63 64 3.995048 GAGGCGAAAAGTATATGTAGGCC 59.005 47.826 0.00 0.00 38.29 5.19
64 65 4.628074 TGAGGCGAAAAGTATATGTAGGC 58.372 43.478 0.00 0.00 0.00 3.93
65 66 5.230942 CCTGAGGCGAAAAGTATATGTAGG 58.769 45.833 0.00 0.00 0.00 3.18
66 67 4.686554 GCCTGAGGCGAAAAGTATATGTAG 59.313 45.833 8.16 0.00 39.62 2.74
67 68 4.628074 GCCTGAGGCGAAAAGTATATGTA 58.372 43.478 8.16 0.00 39.62 2.29
68 69 3.467803 GCCTGAGGCGAAAAGTATATGT 58.532 45.455 8.16 0.00 39.62 2.29
89 90 1.934463 CGAATTTCGGCCATCTCGG 59.066 57.895 10.95 0.00 36.00 4.63
99 100 0.730265 TGGATTTCGGCCGAATTTCG 59.270 50.000 38.89 11.81 40.07 3.46
100 101 1.743394 AGTGGATTTCGGCCGAATTTC 59.257 47.619 38.89 33.33 33.79 2.17
101 102 1.834188 AGTGGATTTCGGCCGAATTT 58.166 45.000 38.89 28.86 33.79 1.82
102 103 1.834188 AAGTGGATTTCGGCCGAATT 58.166 45.000 38.89 34.04 33.79 2.17
103 104 1.834188 AAAGTGGATTTCGGCCGAAT 58.166 45.000 38.89 27.72 33.79 3.34
104 105 1.611519 AAAAGTGGATTTCGGCCGAA 58.388 45.000 35.81 35.81 0.00 4.30
105 106 1.268352 CAAAAAGTGGATTTCGGCCGA 59.732 47.619 27.28 27.28 0.00 5.54
106 107 1.696988 CAAAAAGTGGATTTCGGCCG 58.303 50.000 22.12 22.12 0.00 6.13
107 108 1.428448 GCAAAAAGTGGATTTCGGCC 58.572 50.000 0.00 0.00 0.00 6.13
108 109 1.059942 CGCAAAAAGTGGATTTCGGC 58.940 50.000 0.00 0.00 0.00 5.54
117 118 1.455408 GATTTTCGGCCGCAAAAAGTG 59.545 47.619 26.06 0.00 0.00 3.16
118 119 1.067821 TGATTTTCGGCCGCAAAAAGT 59.932 42.857 26.06 15.45 0.00 2.66
119 120 1.777101 TGATTTTCGGCCGCAAAAAG 58.223 45.000 26.06 0.00 0.00 2.27
120 121 2.225068 TTGATTTTCGGCCGCAAAAA 57.775 40.000 26.06 24.01 0.00 1.94
121 122 2.225068 TTTGATTTTCGGCCGCAAAA 57.775 40.000 26.06 26.26 0.00 2.44
122 123 1.861575 GTTTTGATTTTCGGCCGCAAA 59.138 42.857 24.67 24.67 0.00 3.68
123 124 1.202417 TGTTTTGATTTTCGGCCGCAA 60.202 42.857 23.51 14.89 0.00 4.85
124 125 0.385751 TGTTTTGATTTTCGGCCGCA 59.614 45.000 23.51 6.92 0.00 5.69
125 126 1.059942 CTGTTTTGATTTTCGGCCGC 58.940 50.000 23.51 6.50 0.00 6.53
126 127 2.050691 CACTGTTTTGATTTTCGGCCG 58.949 47.619 22.12 22.12 0.00 6.13
127 128 3.092334 ACACTGTTTTGATTTTCGGCC 57.908 42.857 0.00 0.00 0.00 6.13
128 129 3.489416 GGAACACTGTTTTGATTTTCGGC 59.511 43.478 0.00 0.00 0.00 5.54
129 130 3.728718 CGGAACACTGTTTTGATTTTCGG 59.271 43.478 0.00 0.00 0.00 4.30
130 131 4.436523 GTCGGAACACTGTTTTGATTTTCG 59.563 41.667 0.00 0.00 0.00 3.46
131 132 4.436523 CGTCGGAACACTGTTTTGATTTTC 59.563 41.667 0.00 0.00 0.00 2.29
132 133 4.095185 TCGTCGGAACACTGTTTTGATTTT 59.905 37.500 0.00 0.00 0.00 1.82
133 134 3.623960 TCGTCGGAACACTGTTTTGATTT 59.376 39.130 0.00 0.00 0.00 2.17
134 135 3.199677 TCGTCGGAACACTGTTTTGATT 58.800 40.909 0.00 0.00 0.00 2.57
135 136 2.828877 TCGTCGGAACACTGTTTTGAT 58.171 42.857 0.00 0.00 0.00 2.57
136 137 2.296831 TCGTCGGAACACTGTTTTGA 57.703 45.000 0.00 0.00 0.00 2.69
137 138 2.849502 GCTTCGTCGGAACACTGTTTTG 60.850 50.000 0.00 0.00 0.00 2.44
138 139 1.329599 GCTTCGTCGGAACACTGTTTT 59.670 47.619 0.00 0.00 0.00 2.43
139 140 0.935196 GCTTCGTCGGAACACTGTTT 59.065 50.000 0.00 0.00 0.00 2.83
140 141 1.213094 CGCTTCGTCGGAACACTGTT 61.213 55.000 0.00 0.00 0.00 3.16
141 142 1.660575 CGCTTCGTCGGAACACTGT 60.661 57.895 0.00 0.00 0.00 3.55
142 143 1.606350 GACGCTTCGTCGGAACACTG 61.606 60.000 3.54 0.00 46.56 3.66
143 144 1.371389 GACGCTTCGTCGGAACACT 60.371 57.895 3.54 0.00 46.56 3.55
144 145 3.144605 GACGCTTCGTCGGAACAC 58.855 61.111 3.54 0.00 46.56 3.32
338 339 2.995872 GCGTCGAGGTTGAGAGGCT 61.996 63.158 7.01 0.00 42.75 4.58
686 699 0.674581 CAGCGCTGGTGAAATCTCCA 60.675 55.000 29.88 4.32 37.84 3.86
813 827 3.521560 GCAACCTACATCACGAATCTCA 58.478 45.455 0.00 0.00 0.00 3.27
2029 2142 4.056050 ACTAGGTTTACTTTGCACAGTCG 58.944 43.478 9.19 0.00 0.00 4.18
2202 2342 6.540551 TGCAAGAAGTTACACACTGTCATTAA 59.459 34.615 0.00 0.00 35.12 1.40
2523 2670 8.051901 GCTTTATAATATAAAGCGGGGTGAAT 57.948 34.615 30.20 0.00 46.31 2.57


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

AutoCloner maintained by Alex Coulton.