Multiple sequence alignment - TraesCS6D01G220000

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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 TraesCS6D01G220000 chr6D 100.000 2591 0 0 1 2591 310126689 310124099 0.000000e+00 4785.0
1 TraesCS6D01G220000 chr6D 87.097 155 10 7 1788 1934 310124699 310124547 1.590000e-37 167.0
2 TraesCS6D01G220000 chr6D 87.013 154 12 6 1991 2143 310124902 310124756 1.590000e-37 167.0
3 TraesCS6D01G220000 chr6A 87.379 1347 71 34 879 2178 446755992 446754698 0.000000e+00 1454.0
4 TraesCS6D01G220000 chr6A 92.955 440 14 7 1 434 446756797 446756369 2.190000e-175 625.0
5 TraesCS6D01G220000 chr6A 89.051 274 20 7 2243 2513 446750162 446749896 5.340000e-87 331.0
6 TraesCS6D01G220000 chr6A 82.474 194 6 8 615 780 446756240 446756047 7.470000e-31 145.0
7 TraesCS6D01G220000 chr6A 94.118 85 5 0 527 611 446756368 446756284 2.090000e-26 130.0
8 TraesCS6D01G220000 chr6A 92.727 55 2 2 2538 2591 446749712 446749659 7.690000e-11 78.7
9 TraesCS6D01G220000 chr6B 87.343 1114 51 21 782 1856 477828076 477827014 0.000000e+00 1194.0
10 TraesCS6D01G220000 chr6B 92.214 822 22 12 1 786 477830859 477830044 0.000000e+00 1125.0
11 TraesCS6D01G220000 chr6B 84.000 650 39 28 1855 2494 477826901 477826307 4.840000e-157 564.0
12 TraesCS6D01G220000 chr6B 91.358 81 6 1 2064 2143 477826901 477826821 2.730000e-20 110.0
13 TraesCS6D01G220000 chr4B 80.230 435 46 20 2 421 122220978 122221387 9.070000e-75 291.0
14 TraesCS6D01G220000 chr4B 77.314 551 68 33 901 1426 122221880 122222398 3.290000e-69 272.0
15 TraesCS6D01G220000 chr4A 80.324 432 42 21 2 421 498701537 498701937 1.170000e-73 287.0
16 TraesCS6D01G220000 chr4A 78.894 398 46 24 901 1283 498702440 498702814 4.310000e-58 235.0
17 TraesCS6D01G220000 chr4D 79.720 429 53 19 2 421 85010536 85010939 1.960000e-71 279.0
18 TraesCS6D01G220000 chr4D 77.949 390 40 26 901 1274 85011440 85011799 4.370000e-48 202.0
19 TraesCS6D01G220000 chr2D 95.960 99 1 3 2228 2325 73267928 73267832 9.600000e-35 158.0
20 TraesCS6D01G220000 chr2A 95.918 98 2 2 2227 2324 72755709 72755804 9.600000e-35 158.0
21 TraesCS6D01G220000 chr2A 87.342 79 6 3 1174 1250 520308222 520308298 1.280000e-13 87.9
22 TraesCS6D01G220000 chr7D 94.949 99 4 1 2227 2325 583409425 583409522 1.240000e-33 154.0
23 TraesCS6D01G220000 chr7D 100.000 28 0 0 421 448 540712605 540712578 5.000000e-03 52.8
24 TraesCS6D01G220000 chr7A 90.909 110 7 3 2219 2325 731279165 731279056 7.470000e-31 145.0
25 TraesCS6D01G220000 chr7A 90.909 110 7 3 2219 2325 731294493 731294384 7.470000e-31 145.0
26 TraesCS6D01G220000 chr3A 87.805 123 10 3 2206 2325 107048943 107049063 3.480000e-29 139.0
27 TraesCS6D01G220000 chr7B 84.247 146 12 8 2229 2364 23439292 23439436 5.820000e-27 132.0
28 TraesCS6D01G220000 chr2B 91.803 61 4 1 1174 1234 456024111 456024170 1.650000e-12 84.2


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 TraesCS6D01G220000 chr6D 310124099 310126689 2590 True 1706.333333 4785 91.37000 1 2591 3 chr6D.!!$R1 2590
1 TraesCS6D01G220000 chr6A 446754698 446756797 2099 True 588.500000 1454 89.23150 1 2178 4 chr6A.!!$R2 2177
2 TraesCS6D01G220000 chr6A 446749659 446750162 503 True 204.850000 331 90.88900 2243 2591 2 chr6A.!!$R1 348
3 TraesCS6D01G220000 chr6B 477826307 477830859 4552 True 748.250000 1194 88.72875 1 2494 4 chr6B.!!$R1 2493
4 TraesCS6D01G220000 chr4B 122220978 122222398 1420 False 281.500000 291 78.77200 2 1426 2 chr4B.!!$F1 1424
5 TraesCS6D01G220000 chr4A 498701537 498702814 1277 False 261.000000 287 79.60900 2 1283 2 chr4A.!!$F1 1281
6 TraesCS6D01G220000 chr4D 85010536 85011799 1263 False 240.500000 279 78.83450 2 1274 2 chr4D.!!$F1 1272

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
838 3168 0.099613 CGACTATCTGCACTGCTCGT 59.9 55.0 1.98 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2542 5251 0.324368 AGACTGGCGGAGGTATGTCA 60.324 55.0 0.0 0.0 0.0 3.58 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
75 76 2.425312 ACAAGAGAGCGAGACAGGTATG 59.575 50.000 0.00 0.00 0.00 2.39
79 82 0.457851 GAGCGAGACAGGTATGTGCT 59.542 55.000 0.00 0.00 40.68 4.40
80 83 1.676529 GAGCGAGACAGGTATGTGCTA 59.323 52.381 0.00 0.00 40.68 3.49
81 84 2.099263 GAGCGAGACAGGTATGTGCTAA 59.901 50.000 0.00 0.00 40.68 3.09
82 85 2.159226 AGCGAGACAGGTATGTGCTAAC 60.159 50.000 0.00 0.00 40.68 2.34
83 86 2.416836 GCGAGACAGGTATGTGCTAACA 60.417 50.000 0.00 0.00 40.68 2.41
84 87 3.439293 CGAGACAGGTATGTGCTAACAG 58.561 50.000 0.00 0.00 40.68 3.16
162 172 5.129634 TGGATGAGTTTGTGCAGAAACTTA 58.870 37.500 34.33 31.26 44.46 2.24
287 297 6.316513 AGAAGGTATGTAGATTAGAGGTCCC 58.683 44.000 0.00 0.00 0.00 4.46
444 466 4.753186 ACTCCCTCCGATCCATAATAAGT 58.247 43.478 0.00 0.00 0.00 2.24
453 475 8.165239 TCCGATCCATAATAAGTTTTTGGATG 57.835 34.615 12.92 7.28 35.14 3.51
469 491 5.633473 TTGGATGGGAGGGAGTAGTATAT 57.367 43.478 0.00 0.00 0.00 0.86
555 583 3.554752 GGTGTCATTTGTCCACCATTTGG 60.555 47.826 13.56 0.00 46.33 3.28
637 927 5.248248 TGATTGTACTGAAAGATGTCTCCCA 59.752 40.000 0.00 0.00 37.43 4.37
705 1011 6.532302 CACTATGTTGGCATTACGTACTGTTA 59.468 38.462 13.66 1.84 36.58 2.41
706 1012 7.063662 CACTATGTTGGCATTACGTACTGTTAA 59.936 37.037 13.66 7.18 36.58 2.01
707 1013 6.995511 ATGTTGGCATTACGTACTGTTAAT 57.004 33.333 13.66 0.00 29.54 1.40
710 1016 5.804692 TGGCATTACGTACTGTTAATTGG 57.195 39.130 13.66 0.00 0.00 3.16
711 1017 5.489249 TGGCATTACGTACTGTTAATTGGA 58.511 37.500 13.66 0.00 0.00 3.53
802 3132 4.556104 CGTAAGACTCAACTTCTCGAACCA 60.556 45.833 0.00 0.00 43.02 3.67
835 3165 1.403679 GAGTCGACTATCTGCACTGCT 59.596 52.381 20.09 0.00 0.00 4.24
836 3166 1.403679 AGTCGACTATCTGCACTGCTC 59.596 52.381 18.46 0.00 0.00 4.26
837 3167 0.378610 TCGACTATCTGCACTGCTCG 59.621 55.000 1.98 2.31 0.00 5.03
838 3168 0.099613 CGACTATCTGCACTGCTCGT 59.900 55.000 1.98 0.00 0.00 4.18
839 3169 1.833860 GACTATCTGCACTGCTCGTC 58.166 55.000 1.98 0.00 0.00 4.20
840 3170 1.133216 GACTATCTGCACTGCTCGTCA 59.867 52.381 1.98 0.00 0.00 4.35
866 3196 0.797249 GAATCCGACACCGACTCGTG 60.797 60.000 0.00 0.00 39.75 4.35
872 3202 0.575390 GACACCGACTCGTGTTTGTG 59.425 55.000 14.84 14.84 46.85 3.33
966 3314 1.849219 GTCGAGCTACATCGCTTCAAG 59.151 52.381 0.00 0.00 41.08 3.02
1158 3533 2.435410 CAGCAGCAGATGACGCCA 60.435 61.111 0.00 0.00 31.30 5.69
1161 3536 2.747822 GCAGCAGATGACGCCACAG 61.748 63.158 0.00 0.00 0.00 3.66
1311 3692 1.000993 ATTTGCATTACCCCGGCCA 59.999 52.632 2.24 0.00 0.00 5.36
1359 3740 2.863153 CAGCGCTTCGGGTTTCTG 59.137 61.111 7.50 0.00 0.00 3.02
1462 3864 3.499737 CGTTGCATCCAGGACGGC 61.500 66.667 7.83 7.83 33.14 5.68
1570 3978 0.321564 CTCCCAGATGAACCAACGCA 60.322 55.000 0.00 0.00 0.00 5.24
1572 3980 1.176527 CCCAGATGAACCAACGCAAT 58.823 50.000 0.00 0.00 0.00 3.56
1574 3982 1.621107 CAGATGAACCAACGCAATGC 58.379 50.000 0.00 0.00 0.00 3.56
1675 4090 5.600484 ACTCTGTAGGCTGCTATTCAGTATT 59.400 40.000 3.77 0.00 44.66 1.89
1676 4091 6.090483 TCTGTAGGCTGCTATTCAGTATTC 57.910 41.667 3.77 0.00 44.66 1.75
1677 4092 5.835819 TCTGTAGGCTGCTATTCAGTATTCT 59.164 40.000 3.77 0.00 44.66 2.40
1678 4093 6.325028 TCTGTAGGCTGCTATTCAGTATTCTT 59.675 38.462 3.77 0.00 44.66 2.52
1679 4094 6.516718 TGTAGGCTGCTATTCAGTATTCTTC 58.483 40.000 3.77 0.00 44.66 2.87
1680 4095 5.620738 AGGCTGCTATTCAGTATTCTTCA 57.379 39.130 0.00 0.00 44.66 3.02
1681 4096 5.363939 AGGCTGCTATTCAGTATTCTTCAC 58.636 41.667 0.00 0.00 44.66 3.18
1682 4097 5.130145 AGGCTGCTATTCAGTATTCTTCACT 59.870 40.000 0.00 0.00 44.66 3.41
1683 4098 5.819901 GGCTGCTATTCAGTATTCTTCACTT 59.180 40.000 0.00 0.00 44.66 3.16
1684 4099 6.018343 GGCTGCTATTCAGTATTCTTCACTTC 60.018 42.308 0.00 0.00 44.66 3.01
1685 4100 6.018343 GCTGCTATTCAGTATTCTTCACTTCC 60.018 42.308 0.00 0.00 44.66 3.46
1686 4101 7.187824 TGCTATTCAGTATTCTTCACTTCCT 57.812 36.000 0.00 0.00 0.00 3.36
1687 4102 7.624549 TGCTATTCAGTATTCTTCACTTCCTT 58.375 34.615 0.00 0.00 0.00 3.36
1688 4103 8.103305 TGCTATTCAGTATTCTTCACTTCCTTT 58.897 33.333 0.00 0.00 0.00 3.11
1689 4104 8.951243 GCTATTCAGTATTCTTCACTTCCTTTT 58.049 33.333 0.00 0.00 0.00 2.27
1691 4106 7.745620 TTCAGTATTCTTCACTTCCTTTTCC 57.254 36.000 0.00 0.00 0.00 3.13
1692 4107 7.079451 TCAGTATTCTTCACTTCCTTTTCCT 57.921 36.000 0.00 0.00 0.00 3.36
1693 4108 7.518188 TCAGTATTCTTCACTTCCTTTTCCTT 58.482 34.615 0.00 0.00 0.00 3.36
1694 4109 7.445402 TCAGTATTCTTCACTTCCTTTTCCTTG 59.555 37.037 0.00 0.00 0.00 3.61
1714 4129 5.221126 CCTTGTCTTCACTTCCTTTTCCTTG 60.221 44.000 0.00 0.00 0.00 3.61
1716 4131 4.881850 TGTCTTCACTTCCTTTTCCTTGTC 59.118 41.667 0.00 0.00 0.00 3.18
1724 4139 5.656416 ACTTCCTTTTCCTTGTCATTGTCAA 59.344 36.000 0.00 0.00 0.00 3.18
1739 4154 7.041576 TGTCATTGTCAAAGAACTCTGAATCTG 60.042 37.037 0.00 0.00 0.00 2.90
1774 4193 1.746220 CTTCGGACTGTCTTCGAGGAT 59.254 52.381 7.85 0.00 32.89 3.24
1775 4194 2.704464 TCGGACTGTCTTCGAGGATA 57.296 50.000 7.85 0.00 0.00 2.59
1776 4195 3.210232 TCGGACTGTCTTCGAGGATAT 57.790 47.619 7.85 0.00 0.00 1.63
1777 4196 4.347360 TCGGACTGTCTTCGAGGATATA 57.653 45.455 7.85 0.00 0.00 0.86
1778 4197 4.316645 TCGGACTGTCTTCGAGGATATAG 58.683 47.826 7.85 2.94 0.00 1.31
1779 4198 3.120130 CGGACTGTCTTCGAGGATATAGC 60.120 52.174 7.85 0.00 0.00 2.97
1780 4199 3.821600 GGACTGTCTTCGAGGATATAGCA 59.178 47.826 7.85 0.00 0.00 3.49
1781 4200 4.083003 GGACTGTCTTCGAGGATATAGCAG 60.083 50.000 7.85 5.58 0.00 4.24
2006 4548 6.570672 AGGATACCACATATGTGTAGTACG 57.429 41.667 29.25 17.56 44.21 3.67
2053 4596 9.194972 TGGTGGCAAATTATTGAGATGTTATTA 57.805 29.630 0.00 0.00 38.94 0.98
2054 4597 9.683069 GGTGGCAAATTATTGAGATGTTATTAG 57.317 33.333 0.00 0.00 38.94 1.73
2097 4640 3.425359 GGAATGCACGTTTCTGATCACAG 60.425 47.826 0.00 0.00 44.66 3.66
2159 4703 9.813826 ATGGGGTTCTTATCAAGGATTTAATAG 57.186 33.333 0.00 0.00 0.00 1.73
2184 4728 0.827368 GGTAGGAGACTCCTTGCCTG 59.173 60.000 28.86 0.00 46.91 4.85
2196 4740 5.826643 ACTCCTTGCCTGAATAATGGTTAA 58.173 37.500 0.00 0.00 0.00 2.01
2326 4870 1.683011 CCACTAGACCAAATGCCCTGG 60.683 57.143 0.00 0.00 40.05 4.45
2399 4943 4.098960 TGACTTCAAGTGACCTAAACGACT 59.901 41.667 0.00 0.00 0.00 4.18
2424 4973 3.276857 CACACATCCCCTCATTCAAGAG 58.723 50.000 0.00 0.00 35.39 2.85
2425 4974 3.054875 CACACATCCCCTCATTCAAGAGA 60.055 47.826 0.00 0.00 37.87 3.10
2505 5056 2.228822 CACGCCACCTTCTATGCTTTTT 59.771 45.455 0.00 0.00 0.00 1.94
2507 5058 4.076394 ACGCCACCTTCTATGCTTTTTAA 58.924 39.130 0.00 0.00 0.00 1.52
2508 5059 4.705023 ACGCCACCTTCTATGCTTTTTAAT 59.295 37.500 0.00 0.00 0.00 1.40
2509 5060 5.883673 ACGCCACCTTCTATGCTTTTTAATA 59.116 36.000 0.00 0.00 0.00 0.98
2510 5061 6.038271 ACGCCACCTTCTATGCTTTTTAATAG 59.962 38.462 0.00 0.00 0.00 1.73
2511 5062 6.260050 CGCCACCTTCTATGCTTTTTAATAGA 59.740 38.462 0.00 0.00 0.00 1.98
2512 5063 7.418408 GCCACCTTCTATGCTTTTTAATAGAC 58.582 38.462 0.00 0.00 0.00 2.59
2513 5064 7.283354 GCCACCTTCTATGCTTTTTAATAGACT 59.717 37.037 0.00 0.00 0.00 3.24
2514 5065 9.178758 CCACCTTCTATGCTTTTTAATAGACTT 57.821 33.333 0.00 0.00 0.00 3.01
2558 5267 1.066143 ACTTTGACATACCTCCGCCAG 60.066 52.381 0.00 0.00 0.00 4.85
2559 5268 0.981183 TTTGACATACCTCCGCCAGT 59.019 50.000 0.00 0.00 0.00 4.00
2560 5269 0.535335 TTGACATACCTCCGCCAGTC 59.465 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 5.122512 TCAGAGTCTGTTACTGTTAGCAC 57.877 43.478 19.53 0.00 39.07 4.40
79 82 4.526650 TGGCATCAGAGTCTGTTACTGTTA 59.473 41.667 19.53 0.00 39.07 2.41
80 83 3.324846 TGGCATCAGAGTCTGTTACTGTT 59.675 43.478 19.53 0.00 39.07 3.16
81 84 2.899900 TGGCATCAGAGTCTGTTACTGT 59.100 45.455 19.53 0.00 39.07 3.55
82 85 3.599730 TGGCATCAGAGTCTGTTACTG 57.400 47.619 19.53 13.32 39.07 2.74
83 86 5.939764 TTATGGCATCAGAGTCTGTTACT 57.060 39.130 19.53 4.40 42.80 2.24
84 87 6.595716 AGTTTTATGGCATCAGAGTCTGTTAC 59.404 38.462 19.53 6.47 32.61 2.50
162 172 1.132262 CTTCCCGTGCGTTGCAAATAT 59.868 47.619 0.00 0.00 41.47 1.28
287 297 4.574828 CCACTAATTTACATCAAGGACCGG 59.425 45.833 0.00 0.00 0.00 5.28
376 398 7.174946 ACCTCCAACAAAGTTCATACATACTTG 59.825 37.037 0.00 0.00 34.95 3.16
444 466 3.265489 ACTACTCCCTCCCATCCAAAAA 58.735 45.455 0.00 0.00 0.00 1.94
453 475 8.203681 ACATAAACAATATACTACTCCCTCCC 57.796 38.462 0.00 0.00 0.00 4.30
490 518 6.757947 CCTCAATGTCTCAAAACAAATTGTGT 59.242 34.615 0.00 0.00 44.64 3.72
555 583 1.880941 ACATTCCCTGTCCCCTCTAC 58.119 55.000 0.00 0.00 29.94 2.59
637 927 2.998316 GCTAGGGTGAGCTTGAGAAT 57.002 50.000 0.00 0.00 39.50 2.40
705 1011 8.502738 ACAAGGTAGACCAACATATATCCAATT 58.497 33.333 0.66 0.00 38.89 2.32
706 1012 8.045720 ACAAGGTAGACCAACATATATCCAAT 57.954 34.615 0.66 0.00 38.89 3.16
707 1013 7.419750 GGACAAGGTAGACCAACATATATCCAA 60.420 40.741 0.66 0.00 38.89 3.53
710 1016 7.062749 TGGACAAGGTAGACCAACATATATC 57.937 40.000 0.66 0.00 38.89 1.63
711 1017 6.464465 GCTGGACAAGGTAGACCAACATATAT 60.464 42.308 0.66 0.00 38.89 0.86
802 3132 2.997897 GACTCCCAGCCGGTGACT 60.998 66.667 1.90 0.00 0.00 3.41
835 3165 2.184322 GGATTCGCAGCCTGACGA 59.816 61.111 7.06 7.06 36.32 4.20
836 3166 3.257561 CGGATTCGCAGCCTGACG 61.258 66.667 0.00 0.00 0.00 4.35
837 3167 2.167861 GTCGGATTCGCAGCCTGAC 61.168 63.158 0.00 0.00 36.13 3.51
838 3168 2.184322 GTCGGATTCGCAGCCTGA 59.816 61.111 0.00 0.00 36.13 3.86
839 3169 2.125552 TGTCGGATTCGCAGCCTG 60.126 61.111 0.00 0.00 36.13 4.85
840 3170 2.125512 GTGTCGGATTCGCAGCCT 60.126 61.111 0.00 0.00 36.13 4.58
841 3171 3.195698 GGTGTCGGATTCGCAGCC 61.196 66.667 8.30 0.00 36.07 4.85
842 3172 3.554692 CGGTGTCGGATTCGCAGC 61.555 66.667 9.17 9.17 37.46 5.25
843 3173 2.158959 GTCGGTGTCGGATTCGCAG 61.159 63.158 0.00 0.00 36.95 5.18
866 3196 4.477302 TTTAAAGGCTCGTAGCACAAAC 57.523 40.909 8.71 0.00 44.75 2.93
872 3202 3.615496 TCGTGATTTTAAAGGCTCGTAGC 59.385 43.478 11.12 0.00 41.46 3.58
1158 3533 3.999285 ACCGCCTCCCTCCTCTGT 61.999 66.667 0.00 0.00 0.00 3.41
1207 3582 2.124151 GCCTATGGCCACCAGGTG 60.124 66.667 27.97 13.35 44.06 4.00
1286 3667 2.422235 CGGGGTAATGCAAATGGTCCTA 60.422 50.000 0.00 0.00 0.00 2.94
1296 3677 4.787286 CGTGGCCGGGGTAATGCA 62.787 66.667 2.18 0.00 0.00 3.96
1439 3841 2.360350 CTGGATGCAACGGTGGCT 60.360 61.111 9.26 0.00 0.00 4.75
1570 3978 3.557898 CGCTAGAATACCATCTGGGCATT 60.558 47.826 0.54 0.01 42.05 3.56
1572 3980 1.344438 CGCTAGAATACCATCTGGGCA 59.656 52.381 0.54 0.00 42.05 5.36
1574 3982 3.753294 AACGCTAGAATACCATCTGGG 57.247 47.619 0.54 0.00 44.81 4.45
1675 4090 5.373812 AGACAAGGAAAAGGAAGTGAAGA 57.626 39.130 0.00 0.00 0.00 2.87
1676 4091 5.590259 TGAAGACAAGGAAAAGGAAGTGAAG 59.410 40.000 0.00 0.00 0.00 3.02
1677 4092 5.357032 GTGAAGACAAGGAAAAGGAAGTGAA 59.643 40.000 0.00 0.00 0.00 3.18
1678 4093 4.881850 GTGAAGACAAGGAAAAGGAAGTGA 59.118 41.667 0.00 0.00 0.00 3.41
1679 4094 4.884164 AGTGAAGACAAGGAAAAGGAAGTG 59.116 41.667 0.00 0.00 0.00 3.16
1680 4095 5.117406 AGTGAAGACAAGGAAAAGGAAGT 57.883 39.130 0.00 0.00 0.00 3.01
1681 4096 5.009110 GGAAGTGAAGACAAGGAAAAGGAAG 59.991 44.000 0.00 0.00 0.00 3.46
1682 4097 4.887655 GGAAGTGAAGACAAGGAAAAGGAA 59.112 41.667 0.00 0.00 0.00 3.36
1683 4098 4.166144 AGGAAGTGAAGACAAGGAAAAGGA 59.834 41.667 0.00 0.00 0.00 3.36
1684 4099 4.464947 AGGAAGTGAAGACAAGGAAAAGG 58.535 43.478 0.00 0.00 0.00 3.11
1685 4100 6.456795 AAAGGAAGTGAAGACAAGGAAAAG 57.543 37.500 0.00 0.00 0.00 2.27
1686 4101 6.127451 GGAAAAGGAAGTGAAGACAAGGAAAA 60.127 38.462 0.00 0.00 0.00 2.29
1687 4102 5.359860 GGAAAAGGAAGTGAAGACAAGGAAA 59.640 40.000 0.00 0.00 0.00 3.13
1688 4103 4.887655 GGAAAAGGAAGTGAAGACAAGGAA 59.112 41.667 0.00 0.00 0.00 3.36
1689 4104 4.166144 AGGAAAAGGAAGTGAAGACAAGGA 59.834 41.667 0.00 0.00 0.00 3.36
1690 4105 4.464947 AGGAAAAGGAAGTGAAGACAAGG 58.535 43.478 0.00 0.00 0.00 3.61
1691 4106 5.358160 ACAAGGAAAAGGAAGTGAAGACAAG 59.642 40.000 0.00 0.00 0.00 3.16
1692 4107 5.261216 ACAAGGAAAAGGAAGTGAAGACAA 58.739 37.500 0.00 0.00 0.00 3.18
1693 4108 4.855340 ACAAGGAAAAGGAAGTGAAGACA 58.145 39.130 0.00 0.00 0.00 3.41
1694 4109 4.881850 TGACAAGGAAAAGGAAGTGAAGAC 59.118 41.667 0.00 0.00 0.00 3.01
1714 4129 7.041508 ACAGATTCAGAGTTCTTTGACAATGAC 60.042 37.037 3.39 0.86 0.00 3.06
1716 4131 7.199541 ACAGATTCAGAGTTCTTTGACAATG 57.800 36.000 0.00 0.00 0.00 2.82
1724 4139 4.274459 GCACACAACAGATTCAGAGTTCTT 59.726 41.667 0.00 0.00 0.00 2.52
1774 4193 8.404107 TCTTACATATGTGTGCTACTGCTATA 57.596 34.615 18.81 0.00 39.39 1.31
1775 4194 7.290110 TCTTACATATGTGTGCTACTGCTAT 57.710 36.000 18.81 0.00 39.39 2.97
1776 4195 6.709018 TCTTACATATGTGTGCTACTGCTA 57.291 37.500 18.81 0.00 39.39 3.49
1777 4196 5.598416 TCTTACATATGTGTGCTACTGCT 57.402 39.130 18.81 0.00 39.39 4.24
1778 4197 6.090088 GCTATCTTACATATGTGTGCTACTGC 59.910 42.308 18.81 9.14 39.39 4.40
1779 4198 7.374272 AGCTATCTTACATATGTGTGCTACTG 58.626 38.462 18.81 3.45 39.39 2.74
1780 4199 7.531857 AGCTATCTTACATATGTGTGCTACT 57.468 36.000 18.81 5.10 39.39 2.57
1781 4200 8.297426 TGTAGCTATCTTACATATGTGTGCTAC 58.703 37.037 26.80 26.80 44.83 3.58
1913 4454 4.780021 AGCAGAACCCCATATAGTAGATGG 59.220 45.833 15.71 15.71 43.12 3.51
1914 4455 6.365970 AAGCAGAACCCCATATAGTAGATG 57.634 41.667 0.00 0.00 0.00 2.90
1970 4511 2.158957 TGGTATCCTCGAAGACAATGCC 60.159 50.000 0.00 0.00 31.69 4.40
2079 4622 0.867746 GCTGTGATCAGAAACGTGCA 59.132 50.000 0.00 0.00 43.76 4.57
2097 4640 3.366679 CCATGTGGTCATCTGTTCAAAGC 60.367 47.826 0.00 0.00 31.15 3.51
2356 4900 6.060788 AGTCAGCTCAATCTGGGAATATTTC 58.939 40.000 0.00 0.00 34.91 2.17
2359 4903 5.131642 TGAAGTCAGCTCAATCTGGGAATAT 59.868 40.000 0.00 0.00 34.91 1.28
2361 4905 3.265221 TGAAGTCAGCTCAATCTGGGAAT 59.735 43.478 0.00 0.00 34.91 3.01
2363 4907 2.259917 TGAAGTCAGCTCAATCTGGGA 58.740 47.619 0.00 0.00 34.91 4.37
2370 4914 2.435805 AGGTCACTTGAAGTCAGCTCAA 59.564 45.455 0.00 0.00 0.00 3.02
2372 4916 2.829741 AGGTCACTTGAAGTCAGCTC 57.170 50.000 0.00 0.00 0.00 4.09
2399 4943 1.508667 AATGAGGGGATGTGTGGCCA 61.509 55.000 0.00 0.00 0.00 5.36
2483 5034 1.026718 AAGCATAGAAGGTGGCGTGC 61.027 55.000 0.00 0.00 0.00 5.34
2484 5035 1.453155 AAAGCATAGAAGGTGGCGTG 58.547 50.000 0.00 0.00 0.00 5.34
2528 5079 9.158233 CGGAGGTATGTCAAAGTCTATTAAAAA 57.842 33.333 0.00 0.00 0.00 1.94
2531 5082 6.278363 GCGGAGGTATGTCAAAGTCTATTAA 58.722 40.000 0.00 0.00 0.00 1.40
2532 5083 5.221382 GGCGGAGGTATGTCAAAGTCTATTA 60.221 44.000 0.00 0.00 0.00 0.98
2533 5084 4.443034 GGCGGAGGTATGTCAAAGTCTATT 60.443 45.833 0.00 0.00 0.00 1.73
2542 5251 0.324368 AGACTGGCGGAGGTATGTCA 60.324 55.000 0.00 0.00 0.00 3.58
2549 5258 1.826385 AAAAATGAGACTGGCGGAGG 58.174 50.000 0.00 0.00 0.00 4.30
2558 5267 5.123979 ACCGAATGAAGCCTAAAAATGAGAC 59.876 40.000 0.00 0.00 0.00 3.36
2559 5268 5.253330 ACCGAATGAAGCCTAAAAATGAGA 58.747 37.500 0.00 0.00 0.00 3.27
2560 5269 5.567138 ACCGAATGAAGCCTAAAAATGAG 57.433 39.130 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.