Multiple sequence alignment - TraesCS1D01G257800

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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 TraesCS1D01G257800 chr1D 100.000 2910 0 0 1 2910 350655056 350652147 0.000000e+00 5374
1 TraesCS1D01G257800 chr1A 92.044 2627 114 42 258 2831 451619709 451617125 0.000000e+00 3605
2 TraesCS1D01G257800 chr1A 96.629 89 3 0 2822 2910 451616548 451616460 6.500000e-32 148
3 TraesCS1D01G257800 chr1B 92.501 1947 78 34 991 2910 473286179 473284274 0.000000e+00 2724
4 TraesCS1D01G257800 chr1B 94.023 686 28 6 258 942 473286853 473286180 0.000000e+00 1027
5 TraesCS1D01G257800 chr1B 96.721 61 2 0 1 61 194531600 194531660 5.130000e-18 102
6 TraesCS1D01G257800 chr4D 95.238 252 12 0 1 252 373813275 373813024 1.620000e-107 399
7 TraesCS1D01G257800 chr6A 95.161 248 12 0 1 248 601959714 601959961 2.720000e-105 392
8 TraesCS1D01G257800 chr6A 86.420 243 33 0 1 243 447583851 447584093 1.720000e-67 267
9 TraesCS1D01G257800 chr6B 94.024 251 12 2 1 248 647845744 647845994 7.610000e-101 377


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 TraesCS1D01G257800 chr1D 350652147 350655056 2909 True 5374.0 5374 100.0000 1 2910 1 chr1D.!!$R1 2909
1 TraesCS1D01G257800 chr1A 451616460 451619709 3249 True 1876.5 3605 94.3365 258 2910 2 chr1A.!!$R1 2652
2 TraesCS1D01G257800 chr1B 473284274 473286853 2579 True 1875.5 2724 93.2620 258 2910 2 chr1B.!!$R1 2652

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
750 770 0.333652 TCTCACCGTCTCCACCCATA 59.666 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 2589 0.0414 CAAACGCACGCACTGATGAA 60.041 50.0 0.0 0.0 0.0 2.57 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
18 19 4.373116 GGGAGAACGGCGACTGCA 62.373 66.667 16.62 0.00 45.35 4.41
19 20 2.811317 GGAGAACGGCGACTGCAG 60.811 66.667 16.62 13.48 45.35 4.41
20 21 3.482783 GAGAACGGCGACTGCAGC 61.483 66.667 16.62 5.81 45.35 5.25
21 22 4.299547 AGAACGGCGACTGCAGCA 62.300 61.111 16.62 0.00 45.35 4.41
22 23 3.782244 GAACGGCGACTGCAGCAG 61.782 66.667 21.54 21.54 45.35 4.24
31 32 3.429141 CTGCAGCAGCGGTGGAAG 61.429 66.667 17.54 0.15 46.23 3.46
32 33 3.889134 CTGCAGCAGCGGTGGAAGA 62.889 63.158 17.54 0.00 46.23 2.87
33 34 3.426568 GCAGCAGCGGTGGAAGAC 61.427 66.667 17.54 0.00 0.00 3.01
34 35 3.114616 CAGCAGCGGTGGAAGACG 61.115 66.667 17.54 0.00 0.00 4.18
35 36 3.303135 AGCAGCGGTGGAAGACGA 61.303 61.111 17.54 0.00 0.00 4.20
36 37 3.112709 GCAGCGGTGGAAGACGAC 61.113 66.667 17.54 0.00 0.00 4.34
37 38 2.805353 CAGCGGTGGAAGACGACG 60.805 66.667 6.74 0.00 0.00 5.12
39 40 4.719369 GCGGTGGAAGACGACGCT 62.719 66.667 0.00 0.00 46.02 5.07
40 41 2.805353 CGGTGGAAGACGACGCTG 60.805 66.667 0.00 0.00 0.00 5.18
41 42 2.432628 GGTGGAAGACGACGCTGG 60.433 66.667 0.00 0.00 0.00 4.85
42 43 2.649034 GTGGAAGACGACGCTGGA 59.351 61.111 0.00 0.00 0.00 3.86
43 44 1.215647 GTGGAAGACGACGCTGGAT 59.784 57.895 0.00 0.00 0.00 3.41
44 45 0.802607 GTGGAAGACGACGCTGGATC 60.803 60.000 0.00 0.00 0.00 3.36
45 46 1.586564 GGAAGACGACGCTGGATCG 60.587 63.158 0.00 0.00 45.17 3.69
46 47 1.586564 GAAGACGACGCTGGATCGG 60.587 63.158 0.00 0.00 43.95 4.18
72 73 4.122515 GCAGACGTTCGCGACAGC 62.123 66.667 9.15 1.43 44.71 4.40
82 83 3.857854 GCGACAGCGGCATCACTG 61.858 66.667 1.45 0.00 39.86 3.66
83 84 3.190849 CGACAGCGGCATCACTGG 61.191 66.667 1.45 0.00 38.25 4.00
84 85 2.821366 GACAGCGGCATCACTGGG 60.821 66.667 1.45 0.00 38.25 4.45
92 93 4.147449 CATCACTGGGCGAGCCGA 62.147 66.667 8.14 3.04 36.85 5.54
93 94 3.842923 ATCACTGGGCGAGCCGAG 61.843 66.667 21.84 21.84 45.71 4.63
95 96 4.504916 CACTGGGCGAGCCGAGAG 62.505 72.222 28.47 18.87 43.43 3.20
96 97 4.742649 ACTGGGCGAGCCGAGAGA 62.743 66.667 28.47 1.40 43.43 3.10
97 98 4.200283 CTGGGCGAGCCGAGAGAC 62.200 72.222 19.41 0.00 43.43 3.36
125 126 2.745100 CGAGTCCGTCGTGGGAGA 60.745 66.667 0.00 0.00 44.20 3.71
126 127 2.751913 CGAGTCCGTCGTGGGAGAG 61.752 68.421 0.00 0.00 44.20 3.20
127 128 3.053849 GAGTCCGTCGTGGGAGAGC 62.054 68.421 0.00 0.00 36.58 4.09
128 129 3.371063 GTCCGTCGTGGGAGAGCA 61.371 66.667 0.00 0.00 36.58 4.26
129 130 3.371063 TCCGTCGTGGGAGAGCAC 61.371 66.667 0.00 0.00 38.76 4.40
130 131 4.778415 CCGTCGTGGGAGAGCACG 62.778 72.222 0.00 0.00 45.09 5.34
148 149 4.292178 CCGCGGGGAGCTCAGATC 62.292 72.222 20.10 0.00 45.59 2.75
149 150 4.292178 CGCGGGGAGCTCAGATCC 62.292 72.222 17.19 0.00 45.59 3.36
150 151 4.292178 GCGGGGAGCTCAGATCCG 62.292 72.222 23.48 23.48 44.04 4.18
151 152 3.610669 CGGGGAGCTCAGATCCGG 61.611 72.222 17.19 7.93 37.75 5.14
152 153 2.444895 GGGGAGCTCAGATCCGGT 60.445 66.667 17.19 0.00 37.75 5.28
153 154 2.801631 GGGGAGCTCAGATCCGGTG 61.802 68.421 17.19 0.00 37.75 4.94
154 155 2.060980 GGGAGCTCAGATCCGGTGT 61.061 63.158 17.19 0.00 37.75 4.16
155 156 1.439644 GGAGCTCAGATCCGGTGTC 59.560 63.158 17.19 0.79 0.00 3.67
156 157 1.064946 GAGCTCAGATCCGGTGTCG 59.935 63.158 9.40 0.00 0.00 4.35
179 180 4.796231 CGCAACGGAGGTCGGAGG 62.796 72.222 0.00 0.00 44.45 4.30
191 192 3.610669 CGGAGGCCGGAGATCCAG 61.611 72.222 5.05 1.73 44.15 3.86
192 193 3.237741 GGAGGCCGGAGATCCAGG 61.238 72.222 5.05 2.86 35.14 4.45
198 199 4.598894 CGGAGATCCAGGCGGCAG 62.599 72.222 13.08 2.03 35.14 4.85
199 200 4.247380 GGAGATCCAGGCGGCAGG 62.247 72.222 14.79 14.79 35.64 4.85
200 201 4.247380 GAGATCCAGGCGGCAGGG 62.247 72.222 20.47 16.40 0.00 4.45
249 250 1.221414 GCAAGAGCGCCATAGTTAGG 58.779 55.000 2.29 0.00 0.00 2.69
250 251 1.871080 CAAGAGCGCCATAGTTAGGG 58.129 55.000 2.29 0.00 0.00 3.53
251 252 0.759346 AAGAGCGCCATAGTTAGGGG 59.241 55.000 2.29 0.00 41.62 4.79
256 257 3.095922 GCCATAGTTAGGGGCACAC 57.904 57.895 0.00 0.00 46.92 3.82
257 258 0.546598 GCCATAGTTAGGGGCACACT 59.453 55.000 0.00 0.00 46.92 3.55
258 259 1.064685 GCCATAGTTAGGGGCACACTT 60.065 52.381 0.00 0.00 46.92 3.16
259 260 2.643551 CCATAGTTAGGGGCACACTTG 58.356 52.381 0.00 0.00 0.00 3.16
260 261 2.026262 CCATAGTTAGGGGCACACTTGT 60.026 50.000 0.00 0.00 0.00 3.16
261 262 3.270877 CATAGTTAGGGGCACACTTGTC 58.729 50.000 0.00 0.00 0.00 3.18
262 263 1.435256 AGTTAGGGGCACACTTGTCT 58.565 50.000 0.00 0.00 0.00 3.41
263 264 2.616524 AGTTAGGGGCACACTTGTCTA 58.383 47.619 0.00 0.00 0.00 2.59
264 265 2.567615 AGTTAGGGGCACACTTGTCTAG 59.432 50.000 0.00 0.00 0.00 2.43
265 266 2.565834 GTTAGGGGCACACTTGTCTAGA 59.434 50.000 0.00 0.00 0.00 2.43
266 267 0.977395 AGGGGCACACTTGTCTAGAC 59.023 55.000 16.32 16.32 0.00 2.59
267 268 0.977395 GGGGCACACTTGTCTAGACT 59.023 55.000 23.01 0.58 0.00 3.24
297 298 8.504815 CATCTGTCATATTTCACCATCTTGATC 58.495 37.037 0.00 0.00 0.00 2.92
358 359 0.687757 TCTCCCCACCATTCTCTCCG 60.688 60.000 0.00 0.00 0.00 4.63
393 394 3.628646 GACCTGGCCGGATTGTGCT 62.629 63.158 15.09 0.00 36.31 4.40
749 769 0.972983 CTCTCACCGTCTCCACCCAT 60.973 60.000 0.00 0.00 0.00 4.00
750 770 0.333652 TCTCACCGTCTCCACCCATA 59.666 55.000 0.00 0.00 0.00 2.74
846 866 1.462432 TGGAGCCCACCTAACACCA 60.462 57.895 0.00 0.00 0.00 4.17
847 867 1.002502 GGAGCCCACCTAACACCAC 60.003 63.158 0.00 0.00 0.00 4.16
872 892 4.345854 CGCTCTATATAAACCCTCTCCCT 58.654 47.826 0.00 0.00 0.00 4.20
944 964 4.026640 CACTGCAAGCAACAATACAAACAC 60.027 41.667 0.00 0.00 37.60 3.32
947 967 3.245048 GCAAGCAACAATACAAACACCAC 59.755 43.478 0.00 0.00 0.00 4.16
948 968 4.681744 CAAGCAACAATACAAACACCACT 58.318 39.130 0.00 0.00 0.00 4.00
969 989 1.609072 CGAGCATCCTAAGATCGACCA 59.391 52.381 0.00 0.00 46.76 4.02
1029 1053 3.774702 GCGGAGAACGTTGACGCC 61.775 66.667 22.58 12.90 46.52 5.68
1197 1221 2.582436 CGCCACAACCCCGTCTAT 59.418 61.111 0.00 0.00 0.00 1.98
1371 1395 2.369629 CGACAAGGTACGCACACGG 61.370 63.158 0.00 0.00 46.04 4.94
1372 1396 1.300388 GACAAGGTACGCACACGGT 60.300 57.895 0.00 0.00 46.04 4.83
1374 1398 0.877213 ACAAGGTACGCACACGGTTC 60.877 55.000 0.00 0.00 46.04 3.62
1384 1414 2.590575 CACGGTTCCACGGCACTT 60.591 61.111 0.00 0.00 38.39 3.16
1397 1427 1.667724 CGGCACTTGTGATGATTCTCC 59.332 52.381 4.79 0.00 0.00 3.71
1444 1475 0.401356 TCTGTGGAATGCAGCTTGGA 59.599 50.000 0.00 0.00 34.21 3.53
1447 1478 1.304381 TGGAATGCAGCTTGGACCC 60.304 57.895 0.00 0.00 0.00 4.46
1912 1948 0.533032 TCGCCGTTGACATATGACCA 59.467 50.000 10.38 4.12 0.00 4.02
1913 1949 1.138069 TCGCCGTTGACATATGACCAT 59.862 47.619 10.38 0.00 0.00 3.55
2278 2319 3.181466 TGGATCACTAGTGCGCATTACAT 60.181 43.478 15.91 3.61 0.00 2.29
2279 2320 4.038642 TGGATCACTAGTGCGCATTACATA 59.961 41.667 15.91 0.00 0.00 2.29
2310 2351 2.582978 GGGTAACTCTGGCGGACC 59.417 66.667 0.00 0.00 0.00 4.46
2320 2361 0.176219 CTGGCGGACCGGTATTACAA 59.824 55.000 17.22 0.00 39.70 2.41
2456 2504 0.035820 TAAACGTGGGTCAGGATGGC 60.036 55.000 0.00 0.00 42.54 4.40
2494 2542 7.342581 TGGTAACCATTTAATGCTACTGATCA 58.657 34.615 0.00 0.00 0.00 2.92
2530 2580 8.276252 TGCTTCTGTTAAAGTGTAAACTTCTT 57.724 30.769 0.00 0.00 0.00 2.52
2531 2581 8.181573 TGCTTCTGTTAAAGTGTAAACTTCTTG 58.818 33.333 0.00 0.00 0.00 3.02
2532 2582 8.182227 GCTTCTGTTAAAGTGTAAACTTCTTGT 58.818 33.333 0.00 0.00 0.00 3.16
2534 2584 9.834628 TTCTGTTAAAGTGTAAACTTCTTGTTG 57.165 29.630 0.00 0.00 39.13 3.33
2536 2586 9.490663 CTGTTAAAGTGTAAACTTCTTGTTGAG 57.509 33.333 0.00 0.00 39.13 3.02
2537 2587 9.221933 TGTTAAAGTGTAAACTTCTTGTTGAGA 57.778 29.630 0.00 0.00 39.13 3.27
2689 2755 4.503910 TCCCTATCACAAAACACGATCAG 58.496 43.478 0.00 0.00 0.00 2.90
2709 2775 8.333908 CGATCAGAGAAACTTATCTCCAAAATG 58.666 37.037 0.90 0.00 45.70 2.32
2717 2783 9.358872 GAAACTTATCTCCAAAATGAATCCAAC 57.641 33.333 0.00 0.00 0.00 3.77
2722 2788 6.729690 TCTCCAAAATGAATCCAACAAACT 57.270 33.333 0.00 0.00 0.00 2.66
2728 2796 9.270640 CCAAAATGAATCCAACAAACTCAAATA 57.729 29.630 0.00 0.00 0.00 1.40
2736 2804 8.742554 ATCCAACAAACTCAAATATCGTTTTC 57.257 30.769 0.00 0.00 0.00 2.29
2738 2806 6.087555 CCAACAAACTCAAATATCGTTTTCCG 59.912 38.462 0.00 0.00 38.13 4.30
2740 2808 5.239963 ACAAACTCAAATATCGTTTTCCGGT 59.760 36.000 0.00 0.00 37.11 5.28
2813 2882 0.106918 AAGAGTGCACCGGGACAAAA 60.107 50.000 14.63 0.00 37.91 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.373116 TGCAGTCGCCGTTCTCCC 62.373 66.667 0.00 0.00 37.32 4.30
3 4 3.482783 GCTGCAGTCGCCGTTCTC 61.483 66.667 16.64 0.00 37.32 2.87
4 5 4.299547 TGCTGCAGTCGCCGTTCT 62.300 61.111 16.64 0.00 37.32 3.01
5 6 3.782244 CTGCTGCAGTCGCCGTTC 61.782 66.667 21.21 0.00 37.32 3.95
12 13 4.687215 TCCACCGCTGCTGCAGTC 62.687 66.667 28.50 19.70 39.64 3.51
13 14 4.254709 TTCCACCGCTGCTGCAGT 62.255 61.111 28.50 9.31 39.64 4.40
14 15 3.429141 CTTCCACCGCTGCTGCAG 61.429 66.667 24.80 24.80 39.64 4.41
15 16 3.939939 TCTTCCACCGCTGCTGCA 61.940 61.111 16.29 0.88 39.64 4.41
16 17 3.426568 GTCTTCCACCGCTGCTGC 61.427 66.667 5.34 5.34 0.00 5.25
17 18 3.114616 CGTCTTCCACCGCTGCTG 61.115 66.667 0.00 0.00 0.00 4.41
18 19 3.303135 TCGTCTTCCACCGCTGCT 61.303 61.111 0.00 0.00 0.00 4.24
19 20 3.112709 GTCGTCTTCCACCGCTGC 61.113 66.667 0.00 0.00 0.00 5.25
20 21 2.805353 CGTCGTCTTCCACCGCTG 60.805 66.667 0.00 0.00 0.00 5.18
21 22 4.719369 GCGTCGTCTTCCACCGCT 62.719 66.667 0.00 0.00 41.06 5.52
22 23 4.719369 AGCGTCGTCTTCCACCGC 62.719 66.667 0.00 0.00 44.35 5.68
23 24 2.805353 CAGCGTCGTCTTCCACCG 60.805 66.667 0.00 0.00 0.00 4.94
24 25 2.227089 ATCCAGCGTCGTCTTCCACC 62.227 60.000 0.00 0.00 0.00 4.61
25 26 0.802607 GATCCAGCGTCGTCTTCCAC 60.803 60.000 0.00 0.00 0.00 4.02
26 27 1.511305 GATCCAGCGTCGTCTTCCA 59.489 57.895 0.00 0.00 0.00 3.53
27 28 1.586564 CGATCCAGCGTCGTCTTCC 60.587 63.158 0.00 0.00 34.56 3.46
28 29 1.586564 CCGATCCAGCGTCGTCTTC 60.587 63.158 0.00 0.00 37.39 2.87
29 30 2.490217 CCGATCCAGCGTCGTCTT 59.510 61.111 0.00 0.00 37.39 3.01
30 31 4.194720 GCCGATCCAGCGTCGTCT 62.195 66.667 0.00 0.00 37.39 4.18
55 56 4.122515 GCTGTCGCGAACGTCTGC 62.123 66.667 12.06 10.62 42.52 4.26
65 66 3.857854 CAGTGATGCCGCTGTCGC 61.858 66.667 0.00 0.00 43.88 5.19
66 67 3.190849 CCAGTGATGCCGCTGTCG 61.191 66.667 0.00 0.00 46.61 4.35
67 68 2.821366 CCCAGTGATGCCGCTGTC 60.821 66.667 0.00 0.00 46.61 3.51
75 76 4.147449 TCGGCTCGCCCAGTGATG 62.147 66.667 1.72 0.00 0.00 3.07
76 77 3.842923 CTCGGCTCGCCCAGTGAT 61.843 66.667 1.72 0.00 0.00 3.06
78 79 4.504916 CTCTCGGCTCGCCCAGTG 62.505 72.222 1.72 0.00 0.00 3.66
79 80 4.742649 TCTCTCGGCTCGCCCAGT 62.743 66.667 1.72 0.00 0.00 4.00
80 81 4.200283 GTCTCTCGGCTCGCCCAG 62.200 72.222 1.72 0.00 0.00 4.45
109 110 3.053849 GCTCTCCCACGACGGACTC 62.054 68.421 0.00 0.00 36.56 3.36
110 111 3.063084 GCTCTCCCACGACGGACT 61.063 66.667 0.00 0.00 36.56 3.85
111 112 3.371063 TGCTCTCCCACGACGGAC 61.371 66.667 0.00 0.00 36.56 4.79
112 113 3.371063 GTGCTCTCCCACGACGGA 61.371 66.667 0.00 0.00 36.56 4.69
131 132 4.292178 GATCTGAGCTCCCCGCGG 62.292 72.222 21.04 21.04 45.59 6.46
132 133 4.292178 GGATCTGAGCTCCCCGCG 62.292 72.222 12.15 0.00 45.59 6.46
133 134 4.292178 CGGATCTGAGCTCCCCGC 62.292 72.222 12.15 0.00 39.57 6.13
134 135 3.610669 CCGGATCTGAGCTCCCCG 61.611 72.222 20.16 20.16 39.85 5.73
135 136 2.444895 ACCGGATCTGAGCTCCCC 60.445 66.667 9.46 6.38 0.00 4.81
136 137 2.022240 GACACCGGATCTGAGCTCCC 62.022 65.000 9.46 3.78 0.00 4.30
137 138 1.439644 GACACCGGATCTGAGCTCC 59.560 63.158 9.46 0.00 0.00 4.70
138 139 1.064946 CGACACCGGATCTGAGCTC 59.935 63.158 9.46 6.82 0.00 4.09
139 140 3.201494 CGACACCGGATCTGAGCT 58.799 61.111 9.46 0.00 0.00 4.09
162 163 4.796231 CCTCCGACCTCCGTTGCG 62.796 72.222 0.00 0.00 36.31 4.85
164 165 4.452733 GGCCTCCGACCTCCGTTG 62.453 72.222 0.00 0.00 36.31 4.10
175 176 3.237741 CCTGGATCTCCGGCCTCC 61.238 72.222 0.00 0.00 41.13 4.30
176 177 3.934962 GCCTGGATCTCCGGCCTC 61.935 72.222 16.45 0.00 44.35 4.70
181 182 4.598894 CTGCCGCCTGGATCTCCG 62.599 72.222 0.00 0.00 39.43 4.63
182 183 4.247380 CCTGCCGCCTGGATCTCC 62.247 72.222 0.00 0.00 37.49 3.71
183 184 4.247380 CCCTGCCGCCTGGATCTC 62.247 72.222 0.00 0.00 37.49 2.75
230 231 1.221414 CCTAACTATGGCGCTCTTGC 58.779 55.000 7.64 0.00 0.00 4.01
231 232 1.541233 CCCCTAACTATGGCGCTCTTG 60.541 57.143 7.64 0.00 0.00 3.02
232 233 0.759346 CCCCTAACTATGGCGCTCTT 59.241 55.000 7.64 0.00 0.00 2.85
233 234 1.759459 GCCCCTAACTATGGCGCTCT 61.759 60.000 7.64 0.00 35.08 4.09
234 235 1.301795 GCCCCTAACTATGGCGCTC 60.302 63.158 7.64 0.00 35.08 5.03
235 236 2.829592 GCCCCTAACTATGGCGCT 59.170 61.111 7.64 0.00 35.08 5.92
238 239 0.546598 AGTGTGCCCCTAACTATGGC 59.453 55.000 0.00 0.00 45.56 4.40
239 240 2.026262 ACAAGTGTGCCCCTAACTATGG 60.026 50.000 0.00 0.00 0.00 2.74
240 241 3.055094 AGACAAGTGTGCCCCTAACTATG 60.055 47.826 0.00 0.00 0.00 2.23
241 242 3.182152 AGACAAGTGTGCCCCTAACTAT 58.818 45.455 0.00 0.00 0.00 2.12
242 243 2.616524 AGACAAGTGTGCCCCTAACTA 58.383 47.619 0.00 0.00 0.00 2.24
243 244 1.435256 AGACAAGTGTGCCCCTAACT 58.565 50.000 0.00 0.00 0.00 2.24
244 245 2.565834 TCTAGACAAGTGTGCCCCTAAC 59.434 50.000 0.00 0.00 0.00 2.34
245 246 2.565834 GTCTAGACAAGTGTGCCCCTAA 59.434 50.000 18.20 0.00 0.00 2.69
246 247 2.176889 GTCTAGACAAGTGTGCCCCTA 58.823 52.381 18.20 0.00 0.00 3.53
247 248 0.977395 GTCTAGACAAGTGTGCCCCT 59.023 55.000 18.20 0.00 0.00 4.79
248 249 0.977395 AGTCTAGACAAGTGTGCCCC 59.023 55.000 24.44 0.00 0.00 5.80
249 250 2.841442 AAGTCTAGACAAGTGTGCCC 57.159 50.000 24.44 0.00 0.00 5.36
250 251 5.073311 TGATAAGTCTAGACAAGTGTGCC 57.927 43.478 24.44 6.03 0.00 5.01
251 252 6.475076 CAGATGATAAGTCTAGACAAGTGTGC 59.525 42.308 24.44 8.99 0.00 4.57
252 253 7.542890 ACAGATGATAAGTCTAGACAAGTGTG 58.457 38.462 24.44 13.70 0.00 3.82
253 254 7.394641 TGACAGATGATAAGTCTAGACAAGTGT 59.605 37.037 24.44 14.35 33.56 3.55
254 255 7.766283 TGACAGATGATAAGTCTAGACAAGTG 58.234 38.462 24.44 11.66 33.56 3.16
255 256 7.946381 TGACAGATGATAAGTCTAGACAAGT 57.054 36.000 24.44 11.63 33.56 3.16
263 264 8.708378 TGGTGAAATATGACAGATGATAAGTCT 58.292 33.333 0.00 0.00 33.56 3.24
264 265 8.893219 TGGTGAAATATGACAGATGATAAGTC 57.107 34.615 0.00 0.00 0.00 3.01
265 266 9.499479 GATGGTGAAATATGACAGATGATAAGT 57.501 33.333 0.00 0.00 0.00 2.24
266 267 9.722184 AGATGGTGAAATATGACAGATGATAAG 57.278 33.333 0.00 0.00 0.00 1.73
297 298 3.337358 TGATCACTGTACAATGCACTGG 58.663 45.455 0.00 0.00 0.00 4.00
358 359 1.812922 TCGGTAGTCTCGTCTCCGC 60.813 63.158 0.00 0.00 40.81 5.54
364 365 2.045131 GCCAGGTCGGTAGTCTCGT 61.045 63.158 0.00 0.00 36.97 4.18
366 367 2.772691 CGGCCAGGTCGGTAGTCTC 61.773 68.421 5.20 0.00 36.97 3.36
393 394 0.609957 ATACTGCTTGCTGGCTTGCA 60.610 50.000 10.94 10.94 41.65 4.08
404 405 1.355720 ACTTGCTCCCCAATACTGCTT 59.644 47.619 0.00 0.00 31.91 3.91
632 633 0.890996 CTGGAAGTGTGAACCTGCCC 60.891 60.000 0.00 0.00 0.00 5.36
694 714 1.619807 GCTTCCCCGGCAAGGTAGTA 61.620 60.000 12.08 0.00 38.74 1.82
695 715 2.967946 GCTTCCCCGGCAAGGTAGT 61.968 63.158 12.08 0.00 38.74 2.73
696 716 2.124695 GCTTCCCCGGCAAGGTAG 60.125 66.667 12.08 5.69 38.74 3.18
731 751 0.333652 TATGGGTGGAGACGGTGAGA 59.666 55.000 0.00 0.00 0.00 3.27
749 769 1.611977 CGGAGAAGGACAGTGTGTGTA 59.388 52.381 0.00 0.00 40.56 2.90
750 770 0.389391 CGGAGAAGGACAGTGTGTGT 59.611 55.000 0.00 0.00 44.49 3.72
846 866 3.171528 GAGGGTTTATATAGAGCGGGGT 58.828 50.000 0.00 0.00 0.00 4.95
847 867 3.442076 AGAGGGTTTATATAGAGCGGGG 58.558 50.000 0.00 0.00 0.00 5.73
872 892 1.229496 TGTGGCTTGGAGCTAGGGA 60.229 57.895 0.00 0.00 41.99 4.20
944 964 2.351253 CGATCTTAGGATGCTCGAGTGG 60.351 54.545 15.13 0.00 31.46 4.00
947 967 2.095466 GGTCGATCTTAGGATGCTCGAG 60.095 54.545 8.45 8.45 30.25 4.04
948 968 1.880675 GGTCGATCTTAGGATGCTCGA 59.119 52.381 0.00 0.00 31.46 4.04
969 989 2.300437 CGTGAAAGGAAGGAAGGACTCT 59.700 50.000 0.00 0.00 0.00 3.24
1370 1394 0.889186 ATCACAAGTGCCGTGGAACC 60.889 55.000 0.00 0.00 35.03 3.62
1371 1395 0.238289 CATCACAAGTGCCGTGGAAC 59.762 55.000 0.00 0.00 35.03 3.62
1372 1396 0.107643 TCATCACAAGTGCCGTGGAA 59.892 50.000 0.00 0.00 35.03 3.53
1374 1398 1.131126 GAATCATCACAAGTGCCGTGG 59.869 52.381 0.00 0.00 35.03 4.94
1381 1411 2.881074 CGTCGGAGAATCATCACAAGT 58.119 47.619 0.00 0.00 39.69 3.16
1384 1414 0.179111 GGCGTCGGAGAATCATCACA 60.179 55.000 0.00 0.00 39.69 3.58
1397 1427 2.478746 CATTTTCCACGGGCGTCG 59.521 61.111 0.00 0.00 45.88 5.12
1567 1598 4.345962 TCGTCGCCGCCGAAGAAA 62.346 61.111 1.21 0.00 46.19 2.52
1900 1931 3.494924 GCACAGCCTATGGTCATATGTCA 60.495 47.826 1.90 3.47 0.00 3.58
1912 1948 2.047274 AACGCGTGCACAGCCTAT 60.047 55.556 14.98 5.89 0.00 2.57
1913 1949 2.980213 TTCAACGCGTGCACAGCCTA 62.980 55.000 14.98 3.28 0.00 3.93
2100 2140 4.677584 ACAAACACACAACGCATAACAAT 58.322 34.783 0.00 0.00 0.00 2.71
2263 2304 9.370126 GTTAAAAGAATATGTAATGCGCACTAG 57.630 33.333 14.90 0.00 0.00 2.57
2278 2319 6.592607 CAGAGTTACCCGCAGTTAAAAGAATA 59.407 38.462 0.00 0.00 0.00 1.75
2279 2320 5.411669 CAGAGTTACCCGCAGTTAAAAGAAT 59.588 40.000 0.00 0.00 0.00 2.40
2310 2351 8.504812 AAAACCGTTGTTAAATTGTAATACCG 57.495 30.769 0.00 0.00 33.30 4.02
2320 2361 5.125739 TGTGAGGTGAAAACCGTTGTTAAAT 59.874 36.000 0.00 0.00 33.30 1.40
2456 2504 1.082117 GTTACCATGTCGCTGGACCG 61.082 60.000 5.63 0.00 42.73 4.79
2466 2514 7.116075 TCAGTAGCATTAAATGGTTACCATGT 58.884 34.615 18.48 15.22 44.40 3.21
2494 2542 6.604795 ACTTTAACAGAAGCAGGCATTGATAT 59.395 34.615 0.00 0.00 0.00 1.63
2502 2550 5.008712 AGTTTACACTTTAACAGAAGCAGGC 59.991 40.000 0.00 0.00 0.00 4.85
2530 2580 3.187022 CACGCACTGATGAATTCTCAACA 59.813 43.478 7.05 1.37 34.49 3.33
2531 2581 3.740590 CACGCACTGATGAATTCTCAAC 58.259 45.455 7.05 1.11 34.49 3.18
2532 2582 2.160219 GCACGCACTGATGAATTCTCAA 59.840 45.455 7.05 0.00 34.49 3.02
2533 2583 1.733912 GCACGCACTGATGAATTCTCA 59.266 47.619 7.05 7.14 35.56 3.27
2534 2584 1.267235 CGCACGCACTGATGAATTCTC 60.267 52.381 7.05 2.78 0.00 2.87
2536 2586 0.443869 ACGCACGCACTGATGAATTC 59.556 50.000 0.00 0.00 0.00 2.17
2537 2587 0.874390 AACGCACGCACTGATGAATT 59.126 45.000 0.00 0.00 0.00 2.17
2538 2588 0.874390 AAACGCACGCACTGATGAAT 59.126 45.000 0.00 0.00 0.00 2.57
2539 2589 0.041400 CAAACGCACGCACTGATGAA 60.041 50.000 0.00 0.00 0.00 2.57
2689 2755 8.960591 TGGATTCATTTTGGAGATAAGTTTCTC 58.039 33.333 6.55 6.55 41.21 2.87
2709 2775 8.742554 AAACGATATTTGAGTTTGTTGGATTC 57.257 30.769 0.00 0.00 36.81 2.52
2736 2804 1.750399 CTGGAAATGGAGCCACCGG 60.750 63.158 0.00 0.00 42.61 5.28
2738 2806 2.409870 CGCTGGAAATGGAGCCACC 61.410 63.158 0.00 0.00 39.54 4.61
2740 2808 2.045045 CCGCTGGAAATGGAGCCA 60.045 61.111 0.00 0.00 30.98 4.75
2787 2855 1.569493 CGGTGCACTCTTTGGTTCG 59.431 57.895 17.98 4.30 0.00 3.95
2813 2882 2.512974 CGCCCGCGGTAGGAATTT 60.513 61.111 26.12 0.00 35.56 1.82
2835 3490 0.308993 GCGTATGAAATCTGCAGGCC 59.691 55.000 15.13 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.