Multiple sequence alignment - TraesCS5D01G478800

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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 TraesCS5D01G478800 chr5D 100.000 2234 0 0 1 2234 517361106 517358873 0.000000e+00 4126.0
1 TraesCS5D01G478800 chr5D 82.663 721 86 24 354 1063 517270066 517270758 8.830000e-169 603.0
2 TraesCS5D01G478800 chr5D 80.309 777 104 29 303 1063 517317191 517317934 1.950000e-150 542.0
3 TraesCS5D01G478800 chr5D 86.559 372 29 6 1060 1415 517317967 517318333 7.480000e-105 390.0
4 TraesCS5D01G478800 chr5D 84.533 375 35 12 1061 1415 517270792 517271163 1.270000e-92 350.0
5 TraesCS5D01G478800 chr5B 87.545 1662 89 56 636 2234 649829178 649827572 0.000000e+00 1814.0
6 TraesCS5D01G478800 chr5B 89.906 743 35 23 631 1349 649859562 649858836 0.000000e+00 920.0
7 TraesCS5D01G478800 chr5B 89.579 451 44 2 614 1061 649729406 649729856 8.950000e-159 569.0
8 TraesCS5D01G478800 chr5B 80.984 752 105 21 320 1059 649539889 649540614 1.500000e-156 562.0
9 TraesCS5D01G478800 chr5B 83.696 368 31 12 1061 1413 649729892 649730245 9.950000e-84 320.0
10 TraesCS5D01G478800 chr5B 86.239 109 11 1 316 424 649859871 649859767 5.040000e-22 115.0
11 TraesCS5D01G478800 chr5B 85.714 63 5 3 248 307 649729072 649729133 1.850000e-06 63.9
12 TraesCS5D01G478800 chr5B 86.207 58 6 1 248 303 649539802 649539859 6.660000e-06 62.1
13 TraesCS5D01G478800 chr5A 89.600 375 22 5 247 604 644506621 644506247 5.620000e-126 460.0
14 TraesCS5D01G478800 chr5A 85.811 444 31 10 631 1066 644456299 644455880 2.040000e-120 442.0
15 TraesCS5D01G478800 chr5A 84.516 465 37 10 614 1063 644358422 644358866 5.700000e-116 427.0
16 TraesCS5D01G478800 chr5A 93.151 292 9 4 1061 1342 644444900 644444610 3.430000e-113 418.0
17 TraesCS5D01G478800 chr5A 90.415 313 14 5 308 606 644487720 644487410 4.470000e-107 398.0
18 TraesCS5D01G478800 chr5A 84.492 374 36 8 1060 1415 644358899 644359268 1.270000e-92 350.0
19 TraesCS5D01G478800 chr5A 98.851 174 2 0 1061 1234 644455843 644455670 5.990000e-81 311.0
20 TraesCS5D01G478800 chr5A 81.019 432 45 17 636 1066 644445326 644444931 2.150000e-80 309.0
21 TraesCS5D01G478800 chr5A 97.126 174 5 0 1061 1234 644501458 644501285 6.030000e-76 294.0
22 TraesCS5D01G478800 chr5A 96.129 155 6 0 103 257 644488002 644487848 1.020000e-63 254.0
23 TraesCS5D01G478800 chr5A 85.200 250 12 10 824 1066 644501720 644501489 1.330000e-57 233.0
24 TraesCS5D01G478800 chr5A 87.097 155 17 2 604 755 644487336 644487182 2.950000e-39 172.0
25 TraesCS5D01G478800 chr5A 95.918 98 4 0 87 184 644506840 644506743 2.300000e-35 159.0
26 TraesCS5D01G478800 chr5A 85.811 148 17 1 316 459 644456622 644456475 1.070000e-33 154.0
27 TraesCS5D01G478800 chr5A 100.000 38 0 0 220 257 644506743 644506706 1.110000e-08 71.3
28 TraesCS5D01G478800 chr2B 86.555 119 15 1 1856 1973 570123248 570123366 1.800000e-26 130.0
29 TraesCS5D01G478800 chr2B 85.593 118 17 0 1856 1973 570162776 570162893 8.380000e-25 124.0
30 TraesCS5D01G478800 chr2B 92.308 78 6 0 1 78 6470418 6470495 6.520000e-21 111.0
31 TraesCS5D01G478800 chr2B 89.041 73 6 1 1 73 45569751 45569681 3.060000e-14 89.8
32 TraesCS5D01G478800 chr2B 93.750 48 3 0 1931 1978 45140696 45140649 3.080000e-09 73.1
33 TraesCS5D01G478800 chr2D 83.607 122 18 2 1856 1976 485583893 485584013 1.810000e-21 113.0
34 TraesCS5D01G478800 chr7A 88.158 76 7 1 1 76 520789734 520789661 3.060000e-14 89.8


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 TraesCS5D01G478800 chr5D 517358873 517361106 2233 True 4126.000000 4126 100.000000 1 2234 1 chr5D.!!$R1 2233
1 TraesCS5D01G478800 chr5D 517270066 517271163 1097 False 476.500000 603 83.598000 354 1415 2 chr5D.!!$F1 1061
2 TraesCS5D01G478800 chr5D 517317191 517318333 1142 False 466.000000 542 83.434000 303 1415 2 chr5D.!!$F2 1112
3 TraesCS5D01G478800 chr5B 649827572 649829178 1606 True 1814.000000 1814 87.545000 636 2234 1 chr5B.!!$R1 1598
4 TraesCS5D01G478800 chr5B 649858836 649859871 1035 True 517.500000 920 88.072500 316 1349 2 chr5B.!!$R2 1033
5 TraesCS5D01G478800 chr5B 649729072 649730245 1173 False 317.633333 569 86.329667 248 1413 3 chr5B.!!$F2 1165
6 TraesCS5D01G478800 chr5B 649539802 649540614 812 False 312.050000 562 83.595500 248 1059 2 chr5B.!!$F1 811
7 TraesCS5D01G478800 chr5A 644358422 644359268 846 False 388.500000 427 84.504000 614 1415 2 chr5A.!!$F1 801
8 TraesCS5D01G478800 chr5A 644444610 644445326 716 True 363.500000 418 87.085000 636 1342 2 chr5A.!!$R1 706
9 TraesCS5D01G478800 chr5A 644455670 644456622 952 True 302.333333 442 90.157667 316 1234 3 chr5A.!!$R2 918
10 TraesCS5D01G478800 chr5A 644487182 644488002 820 True 274.666667 398 91.213667 103 755 3 chr5A.!!$R3 652
11 TraesCS5D01G478800 chr5A 644506247 644506840 593 True 230.100000 460 95.172667 87 604 3 chr5A.!!$R5 517

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
759 1050 0.100503 AGTCAAAAAGCACCACGCAC 59.899 50.0 0.0 0.0 46.13 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 2445 0.317854 GAAGGCGACAACAAGGCAAC 60.318 55.0 0.0 0.0 35.18 4.17 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
31 32 3.827784 CGTTGCGCGACGAGGAAG 61.828 66.667 40.23 13.75 45.47 3.46
32 33 3.479269 GTTGCGCGACGAGGAAGG 61.479 66.667 12.10 0.00 0.00 3.46
33 34 3.676605 TTGCGCGACGAGGAAGGA 61.677 61.111 12.10 0.00 0.00 3.36
34 35 3.909258 TTGCGCGACGAGGAAGGAC 62.909 63.158 12.10 0.00 0.00 3.85
36 37 4.831307 CGCGACGAGGAAGGACCG 62.831 72.222 0.00 0.00 44.74 4.79
37 38 4.493747 GCGACGAGGAAGGACCGG 62.494 72.222 0.00 0.00 44.74 5.28
38 39 4.493747 CGACGAGGAAGGACCGGC 62.494 72.222 0.00 0.00 44.74 6.13
39 40 4.144703 GACGAGGAAGGACCGGCC 62.145 72.222 0.00 3.58 44.74 6.13
42 43 3.787001 GAGGAAGGACCGGCCCAG 61.787 72.222 10.37 0.00 44.74 4.45
43 44 4.658786 AGGAAGGACCGGCCCAGT 62.659 66.667 10.37 0.00 44.74 4.00
44 45 3.647771 GGAAGGACCGGCCCAGTT 61.648 66.667 10.37 0.00 37.37 3.16
45 46 2.434774 GAAGGACCGGCCCAGTTT 59.565 61.111 10.37 0.00 37.37 2.66
46 47 1.674651 GAAGGACCGGCCCAGTTTC 60.675 63.158 10.37 0.00 37.37 2.78
47 48 3.546714 AAGGACCGGCCCAGTTTCG 62.547 63.158 10.37 0.00 37.37 3.46
68 69 3.861263 GGTGCGCCGAACCGAATC 61.861 66.667 4.18 0.00 0.00 2.52
69 70 4.204891 GTGCGCCGAACCGAATCG 62.205 66.667 4.18 0.00 42.37 3.34
70 71 4.728102 TGCGCCGAACCGAATCGT 62.728 61.111 4.18 0.00 41.16 3.73
71 72 3.484547 GCGCCGAACCGAATCGTT 61.485 61.111 0.82 0.00 41.16 3.85
72 73 3.018840 GCGCCGAACCGAATCGTTT 62.019 57.895 0.82 0.00 41.16 3.60
73 74 1.058284 CGCCGAACCGAATCGTTTC 59.942 57.895 2.76 2.76 41.16 2.78
74 75 1.422662 GCCGAACCGAATCGTTTCC 59.577 57.895 7.33 0.00 41.16 3.13
75 76 1.974249 GCCGAACCGAATCGTTTCCC 61.974 60.000 7.33 0.00 41.16 3.97
76 77 0.390735 CCGAACCGAATCGTTTCCCT 60.391 55.000 7.33 0.00 41.16 4.20
77 78 1.435577 CGAACCGAATCGTTTCCCTT 58.564 50.000 7.33 0.00 38.01 3.95
78 79 1.802365 CGAACCGAATCGTTTCCCTTT 59.198 47.619 7.33 0.00 38.01 3.11
79 80 2.412325 CGAACCGAATCGTTTCCCTTTG 60.412 50.000 7.33 0.00 38.01 2.77
80 81 2.265589 ACCGAATCGTTTCCCTTTGT 57.734 45.000 0.82 0.00 0.00 2.83
81 82 1.877443 ACCGAATCGTTTCCCTTTGTG 59.123 47.619 0.82 0.00 0.00 3.33
82 83 2.147958 CCGAATCGTTTCCCTTTGTGA 58.852 47.619 0.82 0.00 0.00 3.58
83 84 2.747446 CCGAATCGTTTCCCTTTGTGAT 59.253 45.455 0.82 0.00 0.00 3.06
84 85 3.936453 CCGAATCGTTTCCCTTTGTGATA 59.064 43.478 0.82 0.00 0.00 2.15
85 86 4.201783 CCGAATCGTTTCCCTTTGTGATAC 60.202 45.833 0.82 0.00 0.00 2.24
89 90 4.824289 TCGTTTCCCTTTGTGATACTACC 58.176 43.478 0.00 0.00 0.00 3.18
120 121 0.391793 GCCACCAGGTTAGTCAGCTC 60.392 60.000 0.00 0.00 37.19 4.09
149 150 5.189180 GTGAATATGAAGAGGCCTTGTTCT 58.811 41.667 22.71 8.16 31.62 3.01
165 166 2.031870 GTTCTCCCTGTGCACCTTTTT 58.968 47.619 15.69 0.00 0.00 1.94
332 487 7.434307 CGAATACGTACATTTCAACTCCTGTAT 59.566 37.037 0.00 0.00 34.56 2.29
358 513 4.782156 TGATTGTACGCAAGAATGTTGTG 58.218 39.130 1.98 1.98 38.10 3.33
361 516 2.546368 TGTACGCAAGAATGTTGTGGAC 59.454 45.455 11.56 11.56 42.48 4.02
374 529 4.992688 TGTTGTGGACTTGACAAATTCAC 58.007 39.130 0.95 0.95 35.15 3.18
452 611 0.322456 CCAACTCGGCCTTTCCATGA 60.322 55.000 0.00 0.00 34.01 3.07
608 809 6.839124 TCAAATAGATTGATTGGTGCACTT 57.161 33.333 17.98 1.66 43.08 3.16
609 810 6.623486 TCAAATAGATTGATTGGTGCACTTG 58.377 36.000 17.98 8.43 43.08 3.16
624 905 1.676006 CACTTGCCTTTTTGTCGTCCT 59.324 47.619 0.00 0.00 0.00 3.85
707 991 5.533154 ACCGTGGATTCACTAAACAAATGAA 59.467 36.000 1.86 0.00 41.53 2.57
757 1048 0.594796 CCAGTCAAAAAGCACCACGC 60.595 55.000 0.00 0.00 42.91 5.34
759 1050 0.100503 AGTCAAAAAGCACCACGCAC 59.899 50.000 0.00 0.00 46.13 5.34
813 1122 1.134401 CACTCGCCTAACCATCCACAT 60.134 52.381 0.00 0.00 0.00 3.21
817 1126 1.680338 GCCTAACCATCCACATGACC 58.320 55.000 0.00 0.00 30.57 4.02
973 1293 0.237235 TTTTGCAACGGAGCTAAGCG 59.763 50.000 0.00 0.00 31.38 4.68
1008 1335 3.186390 GATTTGCGCGATGGGGAGC 62.186 63.158 12.10 0.00 0.00 4.70
1070 1439 2.149578 GAACAAGAGACAGCAGCATGT 58.850 47.619 0.00 0.00 39.31 3.21
1300 1692 0.531311 TAGATCGTGCATGCAGGCTG 60.531 55.000 30.59 16.69 34.04 4.85
1356 1788 6.033341 GTGTGTGTGTGTGTGTGATTAATTT 58.967 36.000 0.00 0.00 0.00 1.82
1437 1877 5.810587 GTGTAATTAGACCATGATGACGTGT 59.189 40.000 0.00 0.00 0.00 4.49
1438 1878 6.976349 GTGTAATTAGACCATGATGACGTGTA 59.024 38.462 0.00 0.00 0.00 2.90
1439 1879 6.976349 TGTAATTAGACCATGATGACGTGTAC 59.024 38.462 0.00 0.00 0.00 2.90
1440 1880 5.592104 ATTAGACCATGATGACGTGTACA 57.408 39.130 0.00 0.00 0.00 2.90
1448 1888 1.060553 GATGACGTGTACATGTTGCCG 59.939 52.381 21.31 10.67 0.00 5.69
1452 1892 0.162933 CGTGTACATGTTGCCGTGTC 59.837 55.000 2.30 0.00 41.12 3.67
1458 1898 1.018752 CATGTTGCCGTGTCCGATGA 61.019 55.000 0.00 0.00 35.63 2.92
1465 1905 1.335689 GCCGTGTCCGATGATAGGTAC 60.336 57.143 0.00 0.00 35.63 3.34
1467 1907 2.031069 CCGTGTCCGATGATAGGTACTG 60.031 54.545 0.00 0.00 35.74 2.74
1468 1908 2.617308 CGTGTCCGATGATAGGTACTGT 59.383 50.000 0.00 0.00 35.74 3.55
1469 1909 3.811497 CGTGTCCGATGATAGGTACTGTA 59.189 47.826 0.00 0.00 35.74 2.74
1471 1911 5.048921 CGTGTCCGATGATAGGTACTGTATT 60.049 44.000 0.00 0.00 35.74 1.89
1472 1912 6.514541 CGTGTCCGATGATAGGTACTGTATTT 60.515 42.308 0.00 0.00 35.74 1.40
1473 1913 6.862090 GTGTCCGATGATAGGTACTGTATTTC 59.138 42.308 0.00 0.00 41.52 2.17
1474 1914 6.084925 GTCCGATGATAGGTACTGTATTTCG 58.915 44.000 0.00 4.55 41.52 3.46
1475 1915 5.766670 TCCGATGATAGGTACTGTATTTCGT 59.233 40.000 0.00 0.00 41.52 3.85
1478 1918 7.536622 CCGATGATAGGTACTGTATTTCGTAAC 59.463 40.741 0.00 0.00 41.52 2.50
1487 1927 8.589629 GGTACTGTATTTCGTAACTTACATGTG 58.410 37.037 9.11 0.00 0.00 3.21
1489 1929 6.091713 ACTGTATTTCGTAACTTACATGTGCC 59.908 38.462 9.11 0.00 0.00 5.01
1490 1930 4.957759 ATTTCGTAACTTACATGTGCCC 57.042 40.909 9.11 0.00 0.00 5.36
1498 1938 6.238266 CGTAACTTACATGTGCCCGAAATATT 60.238 38.462 9.11 0.00 0.00 1.28
1630 2073 2.899900 TCTAATGCACACCAGTCTCACT 59.100 45.455 0.00 0.00 0.00 3.41
1650 2101 9.996554 TCTCACTAATGTTCTTTCATCTAAACA 57.003 29.630 0.00 0.00 36.19 2.83
1653 2110 9.778993 CACTAATGTTCTTTCATCTAAACATGG 57.221 33.333 0.00 1.21 40.46 3.66
1766 2223 3.920231 AGATTCACTGCTAGGATTGCA 57.080 42.857 0.00 0.00 38.81 4.08
1820 2277 5.529430 TCGTGTGGTCTAAACATCAAAACAT 59.471 36.000 0.00 0.00 0.00 2.71
1834 2291 8.899427 ACATCAAAACATATAGAGAGGTGATG 57.101 34.615 7.97 7.97 43.38 3.07
1881 2338 3.616956 TTGGTGGTGTTGCAAATTTGA 57.383 38.095 22.31 4.41 0.00 2.69
1923 2381 6.506538 AGGACATCTATTGGAGCACTATTT 57.493 37.500 0.00 0.00 0.00 1.40
1927 2385 9.289782 GGACATCTATTGGAGCACTATTTTAAT 57.710 33.333 0.00 0.00 0.00 1.40
1987 2445 3.497584 GGAGATGCTCTAATCCAAAGGGG 60.498 52.174 0.00 0.00 38.37 4.79
2001 2459 1.106944 AAGGGGTTGCCTTGTTGTCG 61.107 55.000 0.00 0.00 0.00 4.35
2051 2509 2.266055 GGAGACCTCAGGCAACGG 59.734 66.667 0.00 0.00 46.39 4.44
2107 2569 2.423577 CTAGGGTTTCAAGTGGGTTCG 58.576 52.381 0.00 0.00 0.00 3.95
2108 2570 0.841289 AGGGTTTCAAGTGGGTTCGA 59.159 50.000 0.00 0.00 0.00 3.71
2137 2599 2.295909 AGCGACTCTGAATGGCTCTATC 59.704 50.000 0.00 0.00 0.00 2.08
2141 2603 4.377943 CGACTCTGAATGGCTCTATCTACG 60.378 50.000 0.00 0.00 0.00 3.51
2144 2606 5.240623 ACTCTGAATGGCTCTATCTACGAAG 59.759 44.000 0.00 0.00 0.00 3.79
2158 2620 5.769484 TCTACGAAGAAAAGTGACTGACT 57.231 39.130 0.00 0.00 35.94 3.41
2199 2661 0.035458 GCCAATAGAGGGTCCCGATG 59.965 60.000 0.99 0.00 0.00 3.84
2216 2678 2.293122 CGATGAATTGTGGGTTGTGTGT 59.707 45.455 0.00 0.00 0.00 3.72
2217 2679 3.500299 CGATGAATTGTGGGTTGTGTGTA 59.500 43.478 0.00 0.00 0.00 2.90
2218 2680 4.612712 CGATGAATTGTGGGTTGTGTGTAC 60.613 45.833 0.00 0.00 0.00 2.90
2219 2681 3.621558 TGAATTGTGGGTTGTGTGTACA 58.378 40.909 0.00 0.00 34.31 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.827784 CTTCCTCGTCGCGCAACG 61.828 66.667 16.11 16.11 43.92 4.10
15 16 3.479269 CCTTCCTCGTCGCGCAAC 61.479 66.667 8.75 0.00 0.00 4.17
16 17 3.676605 TCCTTCCTCGTCGCGCAA 61.677 61.111 8.75 0.00 0.00 4.85
17 18 4.415332 GTCCTTCCTCGTCGCGCA 62.415 66.667 8.75 0.00 0.00 6.09
19 20 4.831307 CGGTCCTTCCTCGTCGCG 62.831 72.222 0.00 0.00 0.00 5.87
20 21 4.493747 CCGGTCCTTCCTCGTCGC 62.494 72.222 0.00 0.00 0.00 5.19
21 22 4.493747 GCCGGTCCTTCCTCGTCG 62.494 72.222 1.90 0.00 0.00 5.12
22 23 4.144703 GGCCGGTCCTTCCTCGTC 62.145 72.222 1.90 0.00 0.00 4.20
25 26 3.787001 CTGGGCCGGTCCTTCCTC 61.787 72.222 28.64 0.00 34.39 3.71
26 27 4.658786 ACTGGGCCGGTCCTTCCT 62.659 66.667 28.64 2.18 34.39 3.36
27 28 3.205851 AAACTGGGCCGGTCCTTCC 62.206 63.158 28.64 6.57 34.39 3.46
28 29 1.674651 GAAACTGGGCCGGTCCTTC 60.675 63.158 28.64 18.26 34.39 3.46
29 30 2.434774 GAAACTGGGCCGGTCCTT 59.565 61.111 28.64 12.99 34.39 3.36
30 31 4.016706 CGAAACTGGGCCGGTCCT 62.017 66.667 28.64 5.14 34.39 3.85
51 52 3.861263 GATTCGGTTCGGCGCACC 61.861 66.667 18.96 18.96 0.00 5.01
52 53 4.204891 CGATTCGGTTCGGCGCAC 62.205 66.667 10.83 0.00 35.50 5.34
53 54 4.728102 ACGATTCGGTTCGGCGCA 62.728 61.111 10.83 0.00 43.33 6.09
54 55 2.875035 GAAACGATTCGGTTCGGCGC 62.875 60.000 19.93 0.00 43.48 6.53
55 56 1.058284 GAAACGATTCGGTTCGGCG 59.942 57.895 19.93 0.00 43.48 6.46
60 61 2.292292 CACAAAGGGAAACGATTCGGTT 59.708 45.455 9.49 9.49 40.41 4.44
61 62 1.877443 CACAAAGGGAAACGATTCGGT 59.123 47.619 11.29 0.00 36.36 4.69
62 63 2.147958 TCACAAAGGGAAACGATTCGG 58.852 47.619 11.29 0.00 36.36 4.30
63 64 4.630069 AGTATCACAAAGGGAAACGATTCG 59.370 41.667 4.14 4.14 36.36 3.34
64 65 6.036844 GGTAGTATCACAAAGGGAAACGATTC 59.963 42.308 0.00 0.00 34.66 2.52
65 66 5.878669 GGTAGTATCACAAAGGGAAACGATT 59.121 40.000 0.00 0.00 0.00 3.34
66 67 5.046159 TGGTAGTATCACAAAGGGAAACGAT 60.046 40.000 0.00 0.00 0.00 3.73
67 68 4.283978 TGGTAGTATCACAAAGGGAAACGA 59.716 41.667 0.00 0.00 0.00 3.85
68 69 4.390909 GTGGTAGTATCACAAAGGGAAACG 59.609 45.833 8.75 0.00 35.39 3.60
69 70 4.390909 CGTGGTAGTATCACAAAGGGAAAC 59.609 45.833 13.86 0.00 35.03 2.78
70 71 4.283978 TCGTGGTAGTATCACAAAGGGAAA 59.716 41.667 13.86 0.00 35.03 3.13
71 72 3.833650 TCGTGGTAGTATCACAAAGGGAA 59.166 43.478 13.86 0.00 35.03 3.97
72 73 3.433343 TCGTGGTAGTATCACAAAGGGA 58.567 45.455 13.86 0.00 35.03 4.20
73 74 3.194968 ACTCGTGGTAGTATCACAAAGGG 59.805 47.826 13.86 0.19 35.03 3.95
74 75 4.451629 ACTCGTGGTAGTATCACAAAGG 57.548 45.455 13.86 3.12 35.03 3.11
75 76 5.106038 TGGTACTCGTGGTAGTATCACAAAG 60.106 44.000 13.86 11.76 37.99 2.77
76 77 4.766373 TGGTACTCGTGGTAGTATCACAAA 59.234 41.667 13.86 0.40 37.99 2.83
77 78 4.334552 TGGTACTCGTGGTAGTATCACAA 58.665 43.478 13.86 0.00 37.99 3.33
78 79 3.954200 TGGTACTCGTGGTAGTATCACA 58.046 45.455 13.86 0.70 37.99 3.58
79 80 4.732938 GCTTGGTACTCGTGGTAGTATCAC 60.733 50.000 3.24 3.24 41.61 3.06
80 81 3.379372 GCTTGGTACTCGTGGTAGTATCA 59.621 47.826 0.00 0.00 40.49 2.15
81 82 3.243334 GGCTTGGTACTCGTGGTAGTATC 60.243 52.174 0.00 0.00 34.59 2.24
82 83 2.692041 GGCTTGGTACTCGTGGTAGTAT 59.308 50.000 0.00 0.00 34.59 2.12
83 84 2.094675 GGCTTGGTACTCGTGGTAGTA 58.905 52.381 0.00 0.00 0.00 1.82
84 85 0.893447 GGCTTGGTACTCGTGGTAGT 59.107 55.000 0.00 0.00 0.00 2.73
85 86 0.892755 TGGCTTGGTACTCGTGGTAG 59.107 55.000 0.00 0.00 0.00 3.18
89 90 0.670546 CTGGTGGCTTGGTACTCGTG 60.671 60.000 0.00 0.00 0.00 4.35
120 121 3.209410 GCCTCTTCATATTCACACCCTG 58.791 50.000 0.00 0.00 0.00 4.45
149 150 2.151502 TTCAAAAAGGTGCACAGGGA 57.848 45.000 20.43 4.04 0.00 4.20
165 166 1.287503 GTCGCGGCCCAAAATTTCA 59.712 52.632 6.13 0.00 0.00 2.69
213 214 4.980805 GACGACCGGTTGGCTGCA 62.981 66.667 25.74 0.00 39.70 4.41
332 487 6.203915 ACAACATTCTTGCGTACAATCAACTA 59.796 34.615 0.00 0.00 34.61 2.24
358 513 3.636764 AGGGTTGTGAATTTGTCAAGTCC 59.363 43.478 0.00 0.00 38.23 3.85
361 516 4.499696 GGTCAGGGTTGTGAATTTGTCAAG 60.500 45.833 0.00 0.00 38.23 3.02
374 529 1.538204 CGATGGATACGGTCAGGGTTG 60.538 57.143 0.00 0.00 42.51 3.77
452 611 3.732219 CGTACGTACGGTATGAATGCATT 59.268 43.478 34.54 12.83 45.30 3.56
601 802 1.199624 CGACAAAAAGGCAAGTGCAC 58.800 50.000 9.40 9.40 44.36 4.57
606 807 2.222027 AGAGGACGACAAAAAGGCAAG 58.778 47.619 0.00 0.00 0.00 4.01
608 809 2.341846 AAGAGGACGACAAAAAGGCA 57.658 45.000 0.00 0.00 0.00 4.75
609 810 5.372547 AATTAAGAGGACGACAAAAAGGC 57.627 39.130 0.00 0.00 0.00 4.35
624 905 3.190535 GGAGCAAGCAACGGAAATTAAGA 59.809 43.478 0.00 0.00 0.00 2.10
707 991 1.362717 CGGGCCGTGTAATCGATCT 59.637 57.895 19.97 0.00 0.00 2.75
774 1065 5.525012 CGAGTGATTTGAATGATTAGAGGCA 59.475 40.000 0.00 0.00 0.00 4.75
973 1293 4.744631 GCAAATCTCTCTTGCTCTAGCTAC 59.255 45.833 3.26 0.00 44.66 3.58
1008 1335 4.840005 GCCGCCCTCTTCTTCCCG 62.840 72.222 0.00 0.00 0.00 5.14
1356 1788 7.595819 AACTGATACCCAATCAAAACAAAGA 57.404 32.000 0.00 0.00 44.05 2.52
1437 1877 0.248012 ATCGGACACGGCAACATGTA 59.752 50.000 0.00 0.00 41.39 2.29
1438 1878 1.003839 ATCGGACACGGCAACATGT 60.004 52.632 0.00 0.00 41.39 3.21
1439 1879 1.018752 TCATCGGACACGGCAACATG 61.019 55.000 0.00 0.00 41.39 3.21
1440 1880 0.107703 ATCATCGGACACGGCAACAT 60.108 50.000 0.00 0.00 41.39 2.71
1448 1888 5.961396 ATACAGTACCTATCATCGGACAC 57.039 43.478 0.00 0.00 0.00 3.67
1452 1892 6.010294 ACGAAATACAGTACCTATCATCGG 57.990 41.667 14.39 0.00 0.00 4.18
1465 1905 6.456449 GGGCACATGTAAGTTACGAAATACAG 60.456 42.308 8.47 0.00 32.31 2.74
1467 1907 5.501252 CGGGCACATGTAAGTTACGAAATAC 60.501 44.000 8.47 0.00 0.00 1.89
1468 1908 4.567558 CGGGCACATGTAAGTTACGAAATA 59.432 41.667 8.47 0.00 0.00 1.40
1469 1909 3.372822 CGGGCACATGTAAGTTACGAAAT 59.627 43.478 8.47 0.00 0.00 2.17
1471 1911 2.029200 TCGGGCACATGTAAGTTACGAA 60.029 45.455 8.47 0.00 0.00 3.85
1472 1912 1.545136 TCGGGCACATGTAAGTTACGA 59.455 47.619 8.47 0.57 0.00 3.43
1473 1913 1.999048 TCGGGCACATGTAAGTTACG 58.001 50.000 8.47 0.00 0.00 3.18
1474 1914 4.957759 ATTTCGGGCACATGTAAGTTAC 57.042 40.909 6.06 6.06 0.00 2.50
1475 1915 7.633193 AAATATTTCGGGCACATGTAAGTTA 57.367 32.000 0.00 0.00 0.00 2.24
1478 1918 8.918961 TTTTAAATATTTCGGGCACATGTAAG 57.081 30.769 3.39 0.00 0.00 2.34
1552 1993 7.664731 CGGTGATAGTAAGAGAGGGAATACTTA 59.335 40.741 0.00 0.00 31.46 2.24
1555 1996 6.002704 TCGGTGATAGTAAGAGAGGGAATAC 58.997 44.000 0.00 0.00 0.00 1.89
1556 1997 6.196918 TCGGTGATAGTAAGAGAGGGAATA 57.803 41.667 0.00 0.00 0.00 1.75
1745 2202 4.226427 TGCAATCCTAGCAGTGAATCTT 57.774 40.909 0.00 0.00 37.02 2.40
1786 2243 0.388134 GACCACACGAGCTCGCTTAA 60.388 55.000 34.83 0.00 44.43 1.85
1791 2248 1.335597 TGTTTAGACCACACGAGCTCG 60.336 52.381 33.45 33.45 46.33 5.03
1923 2381 5.887754 AGGCAGGACCACTTTTTAGATTAA 58.112 37.500 0.00 0.00 43.14 1.40
1927 2385 3.876309 AAGGCAGGACCACTTTTTAGA 57.124 42.857 0.00 0.00 43.14 2.10
1930 2388 6.070824 CCAATAATAAGGCAGGACCACTTTTT 60.071 38.462 0.00 0.04 43.14 1.94
1935 2393 3.222603 CCCAATAATAAGGCAGGACCAC 58.777 50.000 0.00 0.00 43.14 4.16
1987 2445 0.317854 GAAGGCGACAACAAGGCAAC 60.318 55.000 0.00 0.00 35.18 4.17
2065 2523 4.096003 CACGGCCCCCTACCACTG 62.096 72.222 0.00 0.00 0.00 3.66
2107 2569 1.219393 CAGAGTCGCTCCCCCTTTC 59.781 63.158 3.66 0.00 0.00 2.62
2108 2570 0.836400 TTCAGAGTCGCTCCCCCTTT 60.836 55.000 3.66 0.00 0.00 3.11
2137 2599 5.977725 TCAAGTCAGTCACTTTTCTTCGTAG 59.022 40.000 0.00 0.00 43.38 3.51
2141 2603 6.610741 ACATCAAGTCAGTCACTTTTCTTC 57.389 37.500 0.00 0.00 43.38 2.87
2144 2606 7.220875 GGAAAAACATCAAGTCAGTCACTTTTC 59.779 37.037 0.00 0.00 43.38 2.29
2158 2620 4.275443 GCAAATTGCCTGGAAAAACATCAA 59.725 37.500 6.72 0.00 37.42 2.57
2199 2661 4.037446 ACATGTACACACAACCCACAATTC 59.963 41.667 0.00 0.00 38.42 2.17


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

AutoCloner maintained by Alex Coulton.