Multiple sequence alignment - TraesCS5A01G405100

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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 TraesCS5A01G405100 chr5A 100.000 4066 0 0 1 4066 596564201 596568266 0.000000e+00 7509.0
1 TraesCS5A01G405100 chr5D 95.430 3392 106 8 709 4066 477377707 477381083 0.000000e+00 5360.0
2 TraesCS5A01G405100 chr5D 92.011 751 42 7 68 817 477377012 477377745 0.000000e+00 1038.0
3 TraesCS5A01G405100 chr5D 94.595 74 4 0 744 817 477377637 477377710 9.240000e-22 115.0
4 TraesCS5A01G405100 chr5B 96.030 2418 63 5 1169 3580 585005290 585007680 0.000000e+00 3903.0
5 TraesCS5A01G405100 chr5B 91.878 788 37 9 34 820 585004119 585004880 0.000000e+00 1075.0
6 TraesCS5A01G405100 chr5B 91.813 513 16 2 3577 4063 585007996 585008508 0.000000e+00 691.0
7 TraesCS5A01G405100 chr5B 93.291 313 18 1 825 1134 585004978 585005290 3.700000e-125 459.0
8 TraesCS5A01G405100 chr5B 97.436 39 1 0 779 817 585004769 585004807 2.620000e-07 67.6
9 TraesCS5A01G405100 chr1B 78.912 2390 376 74 1022 3346 676151227 676148901 0.000000e+00 1504.0
10 TraesCS5A01G405100 chr1B 81.040 1366 208 26 2018 3374 676118986 676120309 0.000000e+00 1040.0
11 TraesCS5A01G405100 chr1B 73.510 755 166 25 2263 3001 676391187 676390451 5.220000e-64 255.0
12 TraesCS5A01G405100 chr1B 85.268 224 30 2 268 491 570270420 570270640 1.140000e-55 228.0
13 TraesCS5A01G405100 chr1B 81.315 289 38 9 226 510 676161721 676161445 1.900000e-53 220.0
14 TraesCS5A01G405100 chr1B 88.462 78 7 1 3425 3500 676120458 676120535 4.330000e-15 93.5
15 TraesCS5A01G405100 chr1A 81.292 1502 222 35 1882 3373 583115843 583117295 0.000000e+00 1162.0
16 TraesCS5A01G405100 chr1A 81.095 1169 180 28 2130 3286 583130792 583129653 0.000000e+00 896.0
17 TraesCS5A01G405100 chr1A 75.533 891 178 32 1988 2856 583297450 583296578 6.330000e-108 401.0
18 TraesCS5A01G405100 chr1A 81.015 532 72 18 1556 2080 583131401 583130892 2.950000e-106 396.0
19 TraesCS5A01G405100 chr1A 81.849 292 34 10 226 510 583132624 583132345 1.140000e-55 228.0
20 TraesCS5A01G405100 chr1A 84.906 212 23 3 268 470 517408893 517409104 5.330000e-49 206.0
21 TraesCS5A01G405100 chr1A 84.270 178 23 2 350 522 583299354 583299177 6.990000e-38 169.0
22 TraesCS5A01G405100 chr1A 80.822 219 33 5 3400 3616 583117297 583117508 3.250000e-36 163.0
23 TraesCS5A01G405100 chr1D 74.382 890 174 41 1988 2856 485712178 485711322 8.420000e-87 331.0
24 TraesCS5A01G405100 chr1D 84.141 227 33 1 268 491 421031409 421031635 2.460000e-52 217.0
25 TraesCS5A01G405100 chr2B 86.829 205 23 3 3827 4029 712911915 712912117 4.090000e-55 226.0
26 TraesCS5A01G405100 chr7A 81.614 223 26 8 272 491 498945011 498944801 1.940000e-38 171.0
27 TraesCS5A01G405100 chr7A 81.043 211 39 1 3830 4040 498940890 498940681 2.510000e-37 167.0
28 TraesCS5A01G405100 chr4A 83.537 164 19 6 3044 3207 46639290 46639135 3.270000e-31 147.0
29 TraesCS5A01G405100 chr4A 84.536 97 14 1 3449 3545 46625581 46625486 1.200000e-15 95.3
30 TraesCS5A01G405100 chr4A 91.803 61 5 0 2792 2852 46639418 46639478 7.240000e-13 86.1
31 TraesCS5A01G405100 chr4D 83.178 107 17 1 3439 3545 418208253 418208358 3.350000e-16 97.1


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 TraesCS5A01G405100 chr5A 596564201 596568266 4065 False 7509.000000 7509 100.000000 1 4066 1 chr5A.!!$F1 4065
1 TraesCS5A01G405100 chr5D 477377012 477381083 4071 False 2171.000000 5360 94.012000 68 4066 3 chr5D.!!$F1 3998
2 TraesCS5A01G405100 chr5B 585004119 585008508 4389 False 1239.120000 3903 94.089600 34 4063 5 chr5B.!!$F1 4029
3 TraesCS5A01G405100 chr1B 676148901 676151227 2326 True 1504.000000 1504 78.912000 1022 3346 1 chr1B.!!$R1 2324
4 TraesCS5A01G405100 chr1B 676118986 676120535 1549 False 566.750000 1040 84.751000 2018 3500 2 chr1B.!!$F2 1482
5 TraesCS5A01G405100 chr1B 676390451 676391187 736 True 255.000000 255 73.510000 2263 3001 1 chr1B.!!$R3 738
6 TraesCS5A01G405100 chr1A 583115843 583117508 1665 False 662.500000 1162 81.057000 1882 3616 2 chr1A.!!$F2 1734
7 TraesCS5A01G405100 chr1A 583129653 583132624 2971 True 506.666667 896 81.319667 226 3286 3 chr1A.!!$R1 3060
8 TraesCS5A01G405100 chr1A 583296578 583299354 2776 True 285.000000 401 79.901500 350 2856 2 chr1A.!!$R2 2506
9 TraesCS5A01G405100 chr1D 485711322 485712178 856 True 331.000000 331 74.382000 1988 2856 1 chr1D.!!$R1 868

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
502 513 1.001406 CGAGGTATCATCTCTTGCCCC 59.999 57.143 0.0 0.0 0.00 5.80 F
1054 1866 1.411651 GCTCCCCCTATTCTTCGCCT 61.412 60.000 0.0 0.0 0.00 5.52 F
2249 3258 0.748450 TTATCCGTACTTGAGGGGCG 59.252 55.000 0.0 0.0 33.56 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2871 0.398239 TCAGGCTCTCATCCTCCAGG 60.398 60.0 0.00 0.00 0.00 4.45 R
2461 3470 0.807496 GTAGGGCAGCAGAAGCAAAG 59.193 55.0 0.00 0.00 45.49 2.77 R
3321 4373 0.169009 GGAGAGCACGTGCCAAAATC 59.831 55.0 35.51 25.29 43.38 2.17 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 4.852138 TCCGAGATAAGTAATTCCGAACG 58.148 43.478 0.00 0.00 0.00 3.95
24 25 3.979495 CCGAGATAAGTAATTCCGAACGG 59.021 47.826 6.94 6.94 0.00 4.44
25 26 4.261322 CCGAGATAAGTAATTCCGAACGGA 60.261 45.833 12.04 12.04 43.52 4.69
26 27 5.458891 CGAGATAAGTAATTCCGAACGGAT 58.541 41.667 16.57 5.74 44.74 4.18
27 28 5.342525 CGAGATAAGTAATTCCGAACGGATG 59.657 44.000 16.57 0.00 44.74 3.51
28 29 6.401047 AGATAAGTAATTCCGAACGGATGA 57.599 37.500 16.57 3.46 44.74 2.92
29 30 6.812998 AGATAAGTAATTCCGAACGGATGAA 58.187 36.000 16.57 2.72 44.74 2.57
30 31 6.924060 AGATAAGTAATTCCGAACGGATGAAG 59.076 38.462 16.57 0.00 44.74 3.02
31 32 4.467198 AGTAATTCCGAACGGATGAAGT 57.533 40.909 16.57 4.39 44.74 3.01
32 33 5.587388 AGTAATTCCGAACGGATGAAGTA 57.413 39.130 16.57 3.44 44.74 2.24
33 34 6.158023 AGTAATTCCGAACGGATGAAGTAT 57.842 37.500 16.57 3.63 44.74 2.12
34 35 6.579865 AGTAATTCCGAACGGATGAAGTATT 58.420 36.000 16.57 13.53 44.74 1.89
35 36 7.719483 AGTAATTCCGAACGGATGAAGTATTA 58.281 34.615 16.57 12.65 44.74 0.98
36 37 8.199449 AGTAATTCCGAACGGATGAAGTATTAA 58.801 33.333 16.57 0.00 44.74 1.40
37 38 7.478520 AATTCCGAACGGATGAAGTATTAAG 57.521 36.000 16.57 0.00 44.74 1.85
55 56 6.754702 ATTAAGCATAGCAGCTCCAATATG 57.245 37.500 0.00 0.00 45.89 1.78
56 57 3.069079 AGCATAGCAGCTCCAATATGG 57.931 47.619 0.00 0.00 42.18 2.74
65 66 4.262808 GCAGCTCCAATATGGTAGAGTGAT 60.263 45.833 0.00 0.00 39.03 3.06
192 193 1.323271 TTCACGGCCCTGCACAAAAA 61.323 50.000 0.00 0.00 0.00 1.94
203 204 1.657181 CACAAAAACCTCACCGCGC 60.657 57.895 0.00 0.00 0.00 6.86
219 220 2.331451 GCCACGGAAGTTGTGTGC 59.669 61.111 0.00 0.00 46.40 4.57
502 513 1.001406 CGAGGTATCATCTCTTGCCCC 59.999 57.143 0.00 0.00 0.00 5.80
588 705 2.168496 GCCATGATTGATCCCCTCATG 58.832 52.381 16.53 16.53 43.71 3.07
620 1253 2.103601 GGTATGGGGCGCTTAGTTCTTA 59.896 50.000 7.64 0.00 0.00 2.10
630 1266 7.201794 GGGGCGCTTAGTTCTTATTCTATTTTT 60.202 37.037 7.64 0.00 0.00 1.94
655 1291 7.821652 TGATATCGTCTAGATTCATCTGGTTC 58.178 38.462 0.00 0.00 40.66 3.62
752 1388 3.560025 CCCCTTCTGCAGTGTAAGATTGT 60.560 47.826 14.67 0.00 0.00 2.71
763 1399 6.374333 GCAGTGTAAGATTGTCAGGGAAAATA 59.626 38.462 0.00 0.00 0.00 1.40
877 1686 7.345422 TGAACTCATTTTCAGTTCCATTTCA 57.655 32.000 9.50 0.00 46.35 2.69
896 1705 6.809630 TTTCAATGTGATACCGATGTTGAA 57.190 33.333 0.00 0.00 33.72 2.69
949 1761 2.283529 AACCGCGACATCTCCACCT 61.284 57.895 8.23 0.00 0.00 4.00
1044 1856 2.365635 GGTCTGCTGCTCCCCCTA 60.366 66.667 0.00 0.00 0.00 3.53
1054 1866 1.411651 GCTCCCCCTATTCTTCGCCT 61.412 60.000 0.00 0.00 0.00 5.52
1110 1922 1.599047 CCTCTGGACATGGCGTCTT 59.401 57.895 0.00 0.00 44.70 3.01
1151 1963 3.779759 CTCAAGTGCACCATCTACTCTC 58.220 50.000 14.63 0.00 0.00 3.20
1164 1976 3.249752 TCTACTCTCCCTACGCCTATCT 58.750 50.000 0.00 0.00 0.00 1.98
1246 2102 3.912496 TTGCTGTAGCTCCATATGTGT 57.088 42.857 5.38 0.00 42.66 3.72
1297 2159 3.075148 GAGAGCCAGGAGTTTTGGTTAC 58.925 50.000 0.00 0.00 38.02 2.50
1379 2252 9.717942 ATCATTGCTTCTCAACTAATATCCTAC 57.282 33.333 0.00 0.00 37.53 3.18
1653 2570 3.576078 TGGTCACATGGAAGAAACTGT 57.424 42.857 0.00 0.00 0.00 3.55
1703 2623 7.132213 CGATGTTAAACTCTTTGCTTCTTTCA 58.868 34.615 0.00 0.00 0.00 2.69
1870 2795 7.709947 AGTTGCTATGCTAACGTAGTATGTTA 58.290 34.615 13.16 13.16 45.00 2.41
1943 2871 2.649331 TGTAGCTTAGTTGCGTCCTC 57.351 50.000 0.00 0.00 38.13 3.71
2122 3050 2.703416 TGGTCAACATCATGTCTCAGC 58.297 47.619 0.00 0.00 0.00 4.26
2187 3190 8.798975 ACTTCTACCCTTCTAATTGGATATGA 57.201 34.615 0.00 0.00 0.00 2.15
2235 3244 2.917933 TGCTGTGGTGCATACTTATCC 58.082 47.619 0.00 0.00 38.12 2.59
2249 3258 0.748450 TTATCCGTACTTGAGGGGCG 59.252 55.000 0.00 0.00 33.56 6.13
2440 3449 1.963515 GCAACAATGTCCCAGAGGTTT 59.036 47.619 0.00 0.00 0.00 3.27
2461 3470 8.037166 AGGTTTAATTTTCTGATTGCTTCATCC 58.963 33.333 0.00 0.00 32.72 3.51
2497 3506 3.541632 CCTACATTGGCTTATTGGACGT 58.458 45.455 0.00 0.00 0.00 4.34
2510 3519 6.477360 GCTTATTGGACGTTCCTTTTTGAAAA 59.523 34.615 0.00 0.00 37.46 2.29
2547 3556 9.793259 ATTATTCAGACTTCTTCACAAGGTAAA 57.207 29.630 0.00 0.00 0.00 2.01
2550 3559 8.603242 TTCAGACTTCTTCACAAGGTAAATAC 57.397 34.615 0.00 0.00 0.00 1.89
2618 3644 5.453587 GTGACGCAGAAAATAATTCATGAGC 59.546 40.000 0.00 0.00 0.00 4.26
3065 4104 1.287146 GAGAGGGTAGTGGGGTACTGA 59.713 57.143 0.00 0.00 40.65 3.41
3164 4203 4.258543 ACGAATGGTAAACACCCATACTG 58.741 43.478 0.00 0.00 41.87 2.74
3211 4250 4.187694 CAGTCAGCCCTGATTTTAGTCTC 58.812 47.826 0.77 0.00 42.18 3.36
3321 4373 4.497300 CCATTCTTGTAAAATGGCCAGTG 58.503 43.478 13.05 0.00 44.81 3.66
3617 4994 5.895636 TGCTGACAATTTGGTACTTATGG 57.104 39.130 0.78 0.00 0.00 2.74
3691 5069 4.599041 TGCAATATGGTTCAAGTAGGCTT 58.401 39.130 0.00 0.00 34.82 4.35
3882 5285 5.112220 TGCTGCTGTTCAAACAATTCTAG 57.888 39.130 0.00 0.00 38.66 2.43
3885 5288 3.058293 TGCTGTTCAAACAATTCTAGGCG 60.058 43.478 0.00 0.00 38.66 5.52
3914 5317 1.135489 GCATGGTTGACTGCTGTGATG 60.135 52.381 0.00 0.00 35.49 3.07
4032 5435 7.770433 CCAATGGTAAATGACTGTTCAGAGATA 59.230 37.037 6.83 0.00 34.35 1.98
4041 5444 6.351711 TGACTGTTCAGAGATAATCATTGGG 58.648 40.000 6.83 0.00 0.00 4.12
4060 5463 3.582208 TGGGCTTGCAATGGAAGTAAATT 59.418 39.130 15.64 0.00 0.00 1.82
4063 5466 5.106594 GGGCTTGCAATGGAAGTAAATTTTG 60.107 40.000 15.64 0.00 0.00 2.44
4064 5467 5.700373 GGCTTGCAATGGAAGTAAATTTTGA 59.300 36.000 15.64 0.00 0.00 2.69
4065 5468 6.372381 GGCTTGCAATGGAAGTAAATTTTGAT 59.628 34.615 15.64 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.979495 CCGTTCGGAATTACTTATCTCGG 59.021 47.826 5.19 0.00 0.00 4.63
3 4 4.852138 TCCGTTCGGAATTACTTATCTCG 58.148 43.478 11.66 0.00 0.00 4.04
5 6 6.401047 TCATCCGTTCGGAATTACTTATCT 57.599 37.500 17.72 0.00 37.88 1.98
6 7 6.700520 ACTTCATCCGTTCGGAATTACTTATC 59.299 38.462 17.72 0.00 37.88 1.75
8 9 5.969423 ACTTCATCCGTTCGGAATTACTTA 58.031 37.500 17.72 0.00 37.88 2.24
9 10 4.828829 ACTTCATCCGTTCGGAATTACTT 58.171 39.130 17.72 0.00 37.88 2.24
10 11 4.467198 ACTTCATCCGTTCGGAATTACT 57.533 40.909 17.72 0.00 37.88 2.24
11 12 6.839820 AATACTTCATCCGTTCGGAATTAC 57.160 37.500 17.72 0.00 37.88 1.89
12 13 7.170320 GCTTAATACTTCATCCGTTCGGAATTA 59.830 37.037 17.72 12.36 37.88 1.40
13 14 6.018180 GCTTAATACTTCATCCGTTCGGAATT 60.018 38.462 17.72 13.24 37.88 2.17
14 15 5.465724 GCTTAATACTTCATCCGTTCGGAAT 59.534 40.000 17.72 3.28 37.88 3.01
15 16 4.807304 GCTTAATACTTCATCCGTTCGGAA 59.193 41.667 17.72 0.00 37.88 4.30
16 17 4.142116 TGCTTAATACTTCATCCGTTCGGA 60.142 41.667 16.22 16.22 38.82 4.55
17 18 4.116961 TGCTTAATACTTCATCCGTTCGG 58.883 43.478 4.74 4.74 0.00 4.30
18 19 5.907197 ATGCTTAATACTTCATCCGTTCG 57.093 39.130 0.00 0.00 0.00 3.95
19 20 6.423905 TGCTATGCTTAATACTTCATCCGTTC 59.576 38.462 0.00 0.00 0.00 3.95
20 21 6.288294 TGCTATGCTTAATACTTCATCCGTT 58.712 36.000 0.00 0.00 0.00 4.44
21 22 5.853936 TGCTATGCTTAATACTTCATCCGT 58.146 37.500 0.00 0.00 0.00 4.69
22 23 5.163913 GCTGCTATGCTTAATACTTCATCCG 60.164 44.000 0.00 0.00 0.00 4.18
23 24 5.936956 AGCTGCTATGCTTAATACTTCATCC 59.063 40.000 0.00 0.00 40.93 3.51
24 25 6.091986 GGAGCTGCTATGCTTAATACTTCATC 59.908 42.308 0.15 0.00 44.17 2.92
25 26 5.936956 GGAGCTGCTATGCTTAATACTTCAT 59.063 40.000 0.15 0.00 44.17 2.57
26 27 5.163311 TGGAGCTGCTATGCTTAATACTTCA 60.163 40.000 6.82 0.00 44.17 3.02
27 28 5.300752 TGGAGCTGCTATGCTTAATACTTC 58.699 41.667 6.82 0.00 44.17 3.01
28 29 5.296151 TGGAGCTGCTATGCTTAATACTT 57.704 39.130 6.82 0.00 44.17 2.24
29 30 4.963318 TGGAGCTGCTATGCTTAATACT 57.037 40.909 6.82 0.00 44.17 2.12
30 31 7.201679 CCATATTGGAGCTGCTATGCTTAATAC 60.202 40.741 12.16 0.00 44.17 1.89
31 32 6.825213 CCATATTGGAGCTGCTATGCTTAATA 59.175 38.462 12.16 3.74 44.17 0.98
32 33 5.651139 CCATATTGGAGCTGCTATGCTTAAT 59.349 40.000 12.16 1.57 44.17 1.40
33 34 5.005740 CCATATTGGAGCTGCTATGCTTAA 58.994 41.667 12.16 0.00 44.17 1.85
34 35 4.042062 ACCATATTGGAGCTGCTATGCTTA 59.958 41.667 12.16 0.00 44.17 3.09
35 36 3.181436 ACCATATTGGAGCTGCTATGCTT 60.181 43.478 12.16 0.00 44.17 3.91
37 38 2.787994 ACCATATTGGAGCTGCTATGC 58.212 47.619 12.16 0.00 40.96 3.14
55 56 3.195825 CCCCGATAATCCATCACTCTACC 59.804 52.174 0.00 0.00 32.71 3.18
56 57 3.368531 GCCCCGATAATCCATCACTCTAC 60.369 52.174 0.00 0.00 32.71 2.59
65 66 1.048601 GACAGAGCCCCGATAATCCA 58.951 55.000 0.00 0.00 0.00 3.41
203 204 2.892334 CGGCACACAACTTCCGTGG 61.892 63.158 0.00 0.00 38.74 4.94
588 705 1.253100 CCCCATACCACACCAACAAC 58.747 55.000 0.00 0.00 0.00 3.32
630 1266 7.448469 TGAACCAGATGAATCTAGACGATATCA 59.552 37.037 3.12 0.00 34.85 2.15
634 1270 5.596361 ACTGAACCAGATGAATCTAGACGAT 59.404 40.000 0.00 0.00 34.85 3.73
655 1291 1.189524 TGGGGTGAAGGTCGGTACTG 61.190 60.000 0.00 0.00 0.00 2.74
661 1297 2.781681 AGTAAATGGGGTGAAGGTCG 57.218 50.000 0.00 0.00 0.00 4.79
664 1300 7.574607 AGTTCTAATAGTAAATGGGGTGAAGG 58.425 38.462 0.00 0.00 0.00 3.46
668 1304 9.490379 GACATAGTTCTAATAGTAAATGGGGTG 57.510 37.037 0.00 0.00 0.00 4.61
698 1334 1.469079 GGCAATCATACCAACGCCAAC 60.469 52.381 0.00 0.00 39.38 3.77
741 1377 7.931275 GGATATTTTCCCTGACAATCTTACAC 58.069 38.462 0.00 0.00 38.75 2.90
763 1399 1.843851 TCTTACATTGCGGAAGGGGAT 59.156 47.619 6.23 0.00 0.00 3.85
837 1636 4.826733 TGAGTTCAACATAACCACAGCAAT 59.173 37.500 0.00 0.00 0.00 3.56
877 1686 5.245531 ACACTTCAACATCGGTATCACATT 58.754 37.500 0.00 0.00 0.00 2.71
896 1705 8.457261 GCAATGATAAGAAAAAGATCAGACACT 58.543 33.333 0.00 0.00 33.29 3.55
949 1761 2.360726 TGCGGCGTAGAGAGGACA 60.361 61.111 9.37 0.00 0.00 4.02
1017 1829 0.807496 GCAGCAGACCCATGAGTTTC 59.193 55.000 0.00 0.00 0.00 2.78
1020 1832 1.601171 GAGCAGCAGACCCATGAGT 59.399 57.895 0.00 0.00 0.00 3.41
1044 1856 1.000955 ACGACACAGAAGGCGAAGAAT 59.999 47.619 0.00 0.00 0.00 2.40
1054 1866 2.680841 CAAACTCCCAAACGACACAGAA 59.319 45.455 0.00 0.00 0.00 3.02
1151 1963 0.674534 GGTCACAGATAGGCGTAGGG 59.325 60.000 0.00 0.00 0.00 3.53
1164 1976 1.782201 AAGCAGGGATGCAGGTCACA 61.782 55.000 2.73 0.00 37.25 3.58
1246 2102 2.594303 CAGGCGTTGAACCCAGCA 60.594 61.111 5.79 0.00 0.00 4.41
1537 2444 2.588596 TGCTGTGCCACTGTGACG 60.589 61.111 9.86 0.00 0.00 4.35
1605 2522 7.807977 TTCAAGTCTTGCTTACATTTCTTCT 57.192 32.000 7.78 0.00 35.27 2.85
1606 2523 8.292448 TCATTCAAGTCTTGCTTACATTTCTTC 58.708 33.333 7.78 0.00 35.27 2.87
1703 2623 3.826729 GGAAGGCACAATTTCAAGGTAGT 59.173 43.478 0.00 0.00 0.00 2.73
1943 2871 0.398239 TCAGGCTCTCATCCTCCAGG 60.398 60.000 0.00 0.00 0.00 4.45
2122 3050 3.256383 TGACTTCATCCACATTGCCAAAG 59.744 43.478 0.00 0.00 0.00 2.77
2162 3165 8.798975 TCATATCCAATTAGAAGGGTAGAAGT 57.201 34.615 0.00 0.00 0.00 3.01
2187 3190 4.993028 TGCACCCACCTTAAAGATAAGTT 58.007 39.130 0.00 0.00 37.42 2.66
2235 3244 2.202756 GCTCGCCCCTCAAGTACG 60.203 66.667 0.00 0.00 0.00 3.67
2249 3258 1.891919 TTGTGACCACAAGGCGCTC 60.892 57.895 7.64 0.00 45.42 5.03
2440 3449 7.546667 GCAAAGGATGAAGCAATCAGAAAATTA 59.453 33.333 0.00 0.00 42.53 1.40
2461 3470 0.807496 GTAGGGCAGCAGAAGCAAAG 59.193 55.000 0.00 0.00 45.49 2.77
2497 3506 3.641906 TGGGGCGTATTTTCAAAAAGGAA 59.358 39.130 0.00 0.00 0.00 3.36
2510 3519 3.904339 AGTCTGAATAATCTGGGGCGTAT 59.096 43.478 0.00 0.00 0.00 3.06
2856 3893 2.103771 GAGTGAGCATAGATGGGCAGAA 59.896 50.000 0.00 0.00 0.00 3.02
3065 4104 2.639839 AGCCTGACCAGTAGTGACAAAT 59.360 45.455 0.00 0.00 0.00 2.32
3164 4203 2.238395 AGCTCCTCCCTGAGTGAAAATC 59.762 50.000 0.00 0.00 34.74 2.17
3211 4250 2.932614 CGTAGATTCAGTCTGGCCAAAG 59.067 50.000 7.01 0.00 37.83 2.77
3321 4373 0.169009 GGAGAGCACGTGCCAAAATC 59.831 55.000 35.51 25.29 43.38 2.17
3331 4383 1.546476 AGAGGTAAACAGGAGAGCACG 59.454 52.381 0.00 0.00 0.00 5.34
3386 4439 6.737254 TCCCTATGAAAGACGAACATTTTC 57.263 37.500 0.00 0.00 0.00 2.29
3392 4445 6.700520 ACGATAATTCCCTATGAAAGACGAAC 59.299 38.462 0.00 0.00 36.33 3.95
3656 5034 7.665559 TGAACCATATTGCAAGTTATCCCTATC 59.334 37.037 4.94 0.00 0.00 2.08
3691 5069 8.660295 TGTAATCTTCTAGTTCTGGAACCTAA 57.340 34.615 9.51 2.39 42.06 2.69
3871 5274 2.039879 AGGACCACGCCTAGAATTGTTT 59.960 45.455 0.00 0.00 36.22 2.83
3882 5285 2.203070 CCATGCTAGGACCACGCC 60.203 66.667 0.00 0.00 0.00 5.68
3885 5288 1.279271 AGTCAACCATGCTAGGACCAC 59.721 52.381 1.88 0.00 0.00 4.16
3914 5317 7.486232 GGAAACAAAAGCATAGCAGAATAGAAC 59.514 37.037 0.00 0.00 0.00 3.01
4041 5444 6.783892 TCAAAATTTACTTCCATTGCAAGC 57.216 33.333 4.94 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.