Multiple sequence alignment - TraesCS2A01G164500

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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 TraesCS2A01G164500 chr2A 100.000 2567 0 0 1 2567 116832541 116829975 0.000000e+00 4741.0
1 TraesCS2A01G164500 chr2A 92.135 2492 181 10 82 2567 116699594 116697112 0.000000e+00 3502.0
2 TraesCS2A01G164500 chr2A 90.566 53 5 0 870 922 116698751 116698699 1.270000e-08 71.3
3 TraesCS2A01G164500 chr2D 92.043 2501 176 12 80 2567 115150830 115148340 0.000000e+00 3494.0
4 TraesCS2A01G164500 chr2D 83.985 1561 225 16 921 2470 44139949 44138403 0.000000e+00 1474.0
5 TraesCS2A01G164500 chr2D 85.166 573 72 9 284 854 245074935 245075496 2.220000e-160 575.0
6 TraesCS2A01G164500 chr2D 90.566 53 5 0 870 922 115149991 115149939 1.270000e-08 71.3
7 TraesCS2A01G164500 chr2B 91.270 2497 193 20 80 2567 165779651 165777171 0.000000e+00 3380.0
8 TraesCS2A01G164500 chr2B 91.182 2495 198 19 80 2567 165929330 165926851 0.000000e+00 3369.0
9 TraesCS2A01G164500 chr2B 95.745 47 2 0 876 922 165778805 165778759 2.740000e-10 76.8
10 TraesCS2A01G164500 chr2B 92.453 53 4 0 870 922 165928493 165928441 2.740000e-10 76.8
11 TraesCS2A01G164500 chr4A 87.347 735 91 2 921 1654 735146447 735147180 0.000000e+00 841.0
12 TraesCS2A01G164500 chr4A 86.803 735 95 2 921 1654 735936559 735937292 0.000000e+00 819.0
13 TraesCS2A01G164500 chr4A 84.647 736 89 10 921 1654 736968624 736969337 0.000000e+00 712.0
14 TraesCS2A01G164500 chr4A 84.647 736 89 10 921 1654 736995739 736996452 0.000000e+00 712.0
15 TraesCS2A01G164500 chr4A 79.627 697 112 24 126 807 703779338 703778657 8.310000e-130 473.0
16 TraesCS2A01G164500 chr7D 85.029 688 80 16 127 807 375036864 375037535 0.000000e+00 678.0
17 TraesCS2A01G164500 chr7A 84.157 688 89 16 127 807 421486631 421487305 0.000000e+00 649.0
18 TraesCS2A01G164500 chr7A 91.250 80 7 0 1 80 116729245 116729324 2.700000e-20 110.0
19 TraesCS2A01G164500 chr7A 91.250 80 7 0 1 80 483492895 483492974 2.700000e-20 110.0
20 TraesCS2A01G164500 chr7A 91.250 80 5 2 1 79 597660487 597660565 9.710000e-20 108.0
21 TraesCS2A01G164500 chr4B 80.576 695 104 24 126 807 139634585 139635261 8.200000e-140 507.0
22 TraesCS2A01G164500 chr3A 91.250 80 7 0 1 80 256623996 256623917 2.700000e-20 110.0
23 TraesCS2A01G164500 chr3A 91.139 79 7 0 1 79 207121826 207121904 9.710000e-20 108.0
24 TraesCS2A01G164500 chr3A 91.935 62 5 0 795 856 696406773 696406834 1.270000e-13 87.9
25 TraesCS2A01G164500 chr5A 91.139 79 7 0 1 79 319951581 319951503 9.710000e-20 108.0
26 TraesCS2A01G164500 chr6A 89.873 79 8 0 1 79 277561681 277561759 4.520000e-18 102.0
27 TraesCS2A01G164500 chr6A 89.873 79 8 0 1 79 590382584 590382662 4.520000e-18 102.0
28 TraesCS2A01G164500 chr1A 89.873 79 8 0 1 79 398391177 398391255 4.520000e-18 102.0
29 TraesCS2A01G164500 chr7B 93.548 62 4 0 795 856 187599568 187599629 2.720000e-15 93.5


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 TraesCS2A01G164500 chr2A 116829975 116832541 2566 True 4741.00 4741 100.0000 1 2567 1 chr2A.!!$R1 2566
1 TraesCS2A01G164500 chr2A 116697112 116699594 2482 True 1786.65 3502 91.3505 82 2567 2 chr2A.!!$R2 2485
2 TraesCS2A01G164500 chr2D 115148340 115150830 2490 True 1782.65 3494 91.3045 80 2567 2 chr2D.!!$R2 2487
3 TraesCS2A01G164500 chr2D 44138403 44139949 1546 True 1474.00 1474 83.9850 921 2470 1 chr2D.!!$R1 1549
4 TraesCS2A01G164500 chr2D 245074935 245075496 561 False 575.00 575 85.1660 284 854 1 chr2D.!!$F1 570
5 TraesCS2A01G164500 chr2B 165777171 165779651 2480 True 1728.40 3380 93.5075 80 2567 2 chr2B.!!$R1 2487
6 TraesCS2A01G164500 chr2B 165926851 165929330 2479 True 1722.90 3369 91.8175 80 2567 2 chr2B.!!$R2 2487
7 TraesCS2A01G164500 chr4A 735146447 735147180 733 False 841.00 841 87.3470 921 1654 1 chr4A.!!$F1 733
8 TraesCS2A01G164500 chr4A 735936559 735937292 733 False 819.00 819 86.8030 921 1654 1 chr4A.!!$F2 733
9 TraesCS2A01G164500 chr4A 736968624 736969337 713 False 712.00 712 84.6470 921 1654 1 chr4A.!!$F3 733
10 TraesCS2A01G164500 chr4A 736995739 736996452 713 False 712.00 712 84.6470 921 1654 1 chr4A.!!$F4 733
11 TraesCS2A01G164500 chr4A 703778657 703779338 681 True 473.00 473 79.6270 126 807 1 chr4A.!!$R1 681
12 TraesCS2A01G164500 chr7D 375036864 375037535 671 False 678.00 678 85.0290 127 807 1 chr7D.!!$F1 680
13 TraesCS2A01G164500 chr7A 421486631 421487305 674 False 649.00 649 84.1570 127 807 1 chr7A.!!$F2 680
14 TraesCS2A01G164500 chr4B 139634585 139635261 676 False 507.00 507 80.5760 126 807 1 chr4B.!!$F1 681

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
27 28 0.102844 GCAAGCAACTGACAAGGCAA 59.897 50.0 0.00 0.0 0.0 4.52 F
55 56 0.179029 AAACACCGGAAGACACCTGG 60.179 55.0 9.46 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1416 0.390124 CTGCAGGCCACAACACATTT 59.610 50.0 5.01 0.0 0.0 2.32 R
1690 1722 0.981183 ATTAGGGCTCACGGTCACAA 59.019 50.0 0.00 0.0 0.0 3.33 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
19 20 3.318875 CGACACGCAAGCAACTGA 58.681 55.556 0.00 0.00 45.62 3.41
20 21 1.083401 CGACACGCAAGCAACTGAC 60.083 57.895 0.00 0.00 45.62 3.51
21 22 1.761244 CGACACGCAAGCAACTGACA 61.761 55.000 0.00 0.00 45.62 3.58
22 23 0.376852 GACACGCAAGCAACTGACAA 59.623 50.000 0.00 0.00 45.62 3.18
23 24 0.378257 ACACGCAAGCAACTGACAAG 59.622 50.000 0.00 0.00 45.62 3.16
24 25 0.317269 CACGCAAGCAACTGACAAGG 60.317 55.000 0.00 0.00 45.62 3.61
25 26 1.370900 CGCAAGCAACTGACAAGGC 60.371 57.895 0.00 0.00 0.00 4.35
26 27 1.735360 GCAAGCAACTGACAAGGCA 59.265 52.632 0.00 0.00 0.00 4.75
27 28 0.102844 GCAAGCAACTGACAAGGCAA 59.897 50.000 0.00 0.00 0.00 4.52
28 29 1.843992 CAAGCAACTGACAAGGCAAC 58.156 50.000 0.00 0.00 0.00 4.17
29 30 1.134753 CAAGCAACTGACAAGGCAACA 59.865 47.619 0.00 0.00 41.41 3.33
30 31 1.473258 AGCAACTGACAAGGCAACAA 58.527 45.000 0.00 0.00 41.41 2.83
31 32 1.134946 AGCAACTGACAAGGCAACAAC 59.865 47.619 0.00 0.00 41.41 3.32
32 33 1.135141 GCAACTGACAAGGCAACAACA 60.135 47.619 0.00 0.00 41.41 3.33
33 34 2.673610 GCAACTGACAAGGCAACAACAA 60.674 45.455 0.00 0.00 41.41 2.83
34 35 2.923020 CAACTGACAAGGCAACAACAAC 59.077 45.455 0.00 0.00 41.41 3.32
35 36 1.132262 ACTGACAAGGCAACAACAACG 59.868 47.619 0.00 0.00 41.41 4.10
36 37 1.400142 CTGACAAGGCAACAACAACGA 59.600 47.619 0.00 0.00 41.41 3.85
37 38 1.813178 TGACAAGGCAACAACAACGAA 59.187 42.857 0.00 0.00 41.41 3.85
38 39 2.229062 TGACAAGGCAACAACAACGAAA 59.771 40.909 0.00 0.00 41.41 3.46
39 40 2.596862 GACAAGGCAACAACAACGAAAC 59.403 45.455 0.00 0.00 41.41 2.78
40 41 2.029828 ACAAGGCAACAACAACGAAACA 60.030 40.909 0.00 0.00 41.41 2.83
41 42 2.271821 AGGCAACAACAACGAAACAC 57.728 45.000 0.00 0.00 41.41 3.32
42 43 1.135228 AGGCAACAACAACGAAACACC 60.135 47.619 0.00 0.00 41.41 4.16
43 44 0.911184 GCAACAACAACGAAACACCG 59.089 50.000 0.00 0.00 0.00 4.94
44 45 1.540407 CAACAACAACGAAACACCGG 58.460 50.000 0.00 0.00 0.00 5.28
45 46 1.130749 CAACAACAACGAAACACCGGA 59.869 47.619 9.46 0.00 0.00 5.14
46 47 1.451067 ACAACAACGAAACACCGGAA 58.549 45.000 9.46 0.00 0.00 4.30
47 48 1.399089 ACAACAACGAAACACCGGAAG 59.601 47.619 9.46 1.96 0.00 3.46
48 49 1.666700 CAACAACGAAACACCGGAAGA 59.333 47.619 9.46 0.00 0.00 2.87
49 50 1.292992 ACAACGAAACACCGGAAGAC 58.707 50.000 9.46 0.00 0.00 3.01
50 51 1.292061 CAACGAAACACCGGAAGACA 58.708 50.000 9.46 0.00 0.00 3.41
51 52 1.004292 CAACGAAACACCGGAAGACAC 60.004 52.381 9.46 0.00 0.00 3.67
52 53 0.531311 ACGAAACACCGGAAGACACC 60.531 55.000 9.46 0.00 0.00 4.16
53 54 0.249741 CGAAACACCGGAAGACACCT 60.250 55.000 9.46 0.00 0.00 4.00
54 55 1.226746 GAAACACCGGAAGACACCTG 58.773 55.000 9.46 0.00 0.00 4.00
55 56 0.179029 AAACACCGGAAGACACCTGG 60.179 55.000 9.46 0.00 0.00 4.45
56 57 2.358737 CACCGGAAGACACCTGGC 60.359 66.667 9.46 0.00 0.00 4.85
57 58 2.847234 ACCGGAAGACACCTGGCA 60.847 61.111 9.46 0.00 0.00 4.92
58 59 2.358737 CCGGAAGACACCTGGCAC 60.359 66.667 0.00 0.00 0.00 5.01
59 60 2.425592 CGGAAGACACCTGGCACA 59.574 61.111 0.00 0.00 0.00 4.57
60 61 1.003355 CGGAAGACACCTGGCACAT 60.003 57.895 0.00 0.00 38.20 3.21
61 62 1.021390 CGGAAGACACCTGGCACATC 61.021 60.000 0.00 0.00 38.20 3.06
62 63 1.021390 GGAAGACACCTGGCACATCG 61.021 60.000 0.00 0.00 38.20 3.84
63 64 1.003355 AAGACACCTGGCACATCGG 60.003 57.895 0.00 0.00 38.20 4.18
64 65 1.768684 AAGACACCTGGCACATCGGT 61.769 55.000 0.00 0.00 38.20 4.69
65 66 1.741770 GACACCTGGCACATCGGTC 60.742 63.158 0.00 0.00 38.20 4.79
66 67 2.347114 CACCTGGCACATCGGTCA 59.653 61.111 0.00 0.00 38.20 4.02
67 68 1.302431 CACCTGGCACATCGGTCAA 60.302 57.895 0.00 0.00 38.20 3.18
68 69 1.302511 ACCTGGCACATCGGTCAAC 60.303 57.895 0.00 0.00 38.20 3.18
69 70 2.390599 CCTGGCACATCGGTCAACG 61.391 63.158 0.00 0.00 46.11 4.10
70 71 2.358125 TGGCACATCGGTCAACGG 60.358 61.111 0.00 0.00 44.45 4.44
71 72 3.124921 GGCACATCGGTCAACGGG 61.125 66.667 0.00 0.00 44.45 5.28
72 73 3.799755 GCACATCGGTCAACGGGC 61.800 66.667 0.00 0.00 44.45 6.13
73 74 3.487202 CACATCGGTCAACGGGCG 61.487 66.667 0.00 0.00 44.45 6.13
76 77 3.454573 ATCGGTCAACGGGCGCTA 61.455 61.111 7.64 0.00 44.45 4.26
77 78 3.711541 ATCGGTCAACGGGCGCTAC 62.712 63.158 7.64 0.00 44.45 3.58
78 79 4.728102 CGGTCAACGGGCGCTACA 62.728 66.667 7.64 0.00 39.42 2.74
92 93 2.602878 CGCTACATCGTTGTACCAGTT 58.397 47.619 2.17 0.00 37.28 3.16
116 117 3.005554 CAGACTACCAACTGCTCCATTG 58.994 50.000 0.00 0.00 0.00 2.82
145 147 6.513180 AGAGATTTTGCATGAATGGCTATTG 58.487 36.000 0.00 0.00 0.00 1.90
170 172 1.071633 CGACGACGACTACCGAGTATG 60.072 57.143 0.00 0.00 42.66 2.39
573 578 7.332557 ACATGGTGCATGACATTAATGATTTT 58.667 30.769 22.16 0.00 43.81 1.82
720 732 2.479566 AGAATGAATCCACACGTGCT 57.520 45.000 17.22 0.00 0.00 4.40
756 770 6.595716 CGAAACAAGATCTCCCTTTAATGAGT 59.404 38.462 0.00 0.00 0.00 3.41
837 859 2.028385 CGGAGTACCAGGCTAACAAGTT 60.028 50.000 0.00 0.00 35.59 2.66
865 887 8.383175 TCCATTAGGAGTAGAGAAAACAACATT 58.617 33.333 0.00 0.00 39.61 2.71
867 889 5.948992 AGGAGTAGAGAAAACAACATTGC 57.051 39.130 0.00 0.00 0.00 3.56
874 896 3.694734 AGAAAACAACATTGCGTCACAG 58.305 40.909 0.00 0.00 0.00 3.66
884 906 6.530913 ACATTGCGTCACAGATATATTGAC 57.469 37.500 6.11 6.11 36.99 3.18
1103 1125 4.324254 GGAACCCTCAATGTGACAATCCTA 60.324 45.833 0.00 0.00 0.00 2.94
1141 1163 4.521146 CTCATGCCACTCCATTTAGTTCT 58.479 43.478 0.00 0.00 0.00 3.01
1198 1226 9.013229 AGAACAATGCACTTCTTTAATGTATGA 57.987 29.630 0.00 0.00 0.00 2.15
1278 1306 8.561738 TCTTTTGTCCCTTCAGAATATTGTAC 57.438 34.615 0.00 0.00 0.00 2.90
1298 1327 2.095768 ACGATCTGGTTTTTCATGCACG 60.096 45.455 0.00 0.00 0.00 5.34
1350 1379 0.947244 CCAAGACGTGCAAAGAGCTT 59.053 50.000 0.00 0.00 45.94 3.74
1372 1401 3.402628 GTGGGACATATACCGCTTCAT 57.597 47.619 0.00 0.00 44.52 2.57
1374 1403 2.076863 GGGACATATACCGCTTCATGC 58.923 52.381 0.00 0.00 38.57 4.06
1386 1415 1.746470 CTTCATGCTGTGATCAGGCA 58.254 50.000 20.77 20.77 41.57 4.75
1387 1416 2.089201 CTTCATGCTGTGATCAGGCAA 58.911 47.619 21.87 8.54 41.57 4.52
1405 1434 0.829333 AAAATGTGTTGTGGCCTGCA 59.171 45.000 3.32 0.00 0.00 4.41
1527 1559 0.253044 TAAGGCTGTGGAGGATGTGC 59.747 55.000 0.00 0.00 0.00 4.57
1532 1564 1.134280 GCTGTGGAGGATGTGCTGTAT 60.134 52.381 0.00 0.00 0.00 2.29
1622 1654 6.076981 AGTTGTCTTTATGTTTTGGCTCAG 57.923 37.500 0.00 0.00 0.00 3.35
1702 1734 8.425577 AAATATTAGATTCTTGTGACCGTGAG 57.574 34.615 0.00 0.00 0.00 3.51
1764 1801 8.627208 AAATGATGTGTTCTTAGTGACTCATT 57.373 30.769 0.00 0.00 33.52 2.57
1768 1805 5.308014 TGTGTTCTTAGTGACTCATTGCAT 58.692 37.500 0.00 0.00 0.00 3.96
1778 1815 6.577103 AGTGACTCATTGCATATATATCCGG 58.423 40.000 0.00 0.00 0.00 5.14
1800 1837 7.447238 TCCGGAACAACAAGAATTTCTTAGATT 59.553 33.333 11.21 4.43 33.78 2.40
1823 1860 4.982241 TGAGACTCACTCCCTGATTTTT 57.018 40.909 0.00 0.00 44.34 1.94
1908 1945 7.822658 ACGAAGTATAGAGATATGAAAGAGGC 58.177 38.462 0.00 0.00 41.94 4.70
1978 2015 4.473477 ACTCTTATAAGTCTGGTGTGCC 57.527 45.455 12.19 0.00 0.00 5.01
2003 2040 3.810896 GACCGCGGCCAAATGGAC 61.811 66.667 28.58 0.00 40.84 4.02
2030 2067 7.687941 ATGAGGAGAACATTCGTTTTGTAAT 57.312 32.000 0.00 0.00 34.75 1.89
2140 2177 0.608130 TGATGGGTTGTGGACTCGAG 59.392 55.000 11.84 11.84 0.00 4.04
2151 2188 3.565902 TGTGGACTCGAGTGCAGATATAG 59.434 47.826 36.05 0.00 46.84 1.31
2178 2215 6.884295 AGACCATAGATTCAAATTGGAAACGA 59.116 34.615 0.00 0.00 0.00 3.85
2275 2312 8.201464 ACGTTTGAGAAGGGTTTAAAATTTCAT 58.799 29.630 0.00 0.00 0.00 2.57
2416 2453 3.931907 TCATAGTTGGGCATGCTAGTT 57.068 42.857 18.92 2.70 0.00 2.24
2419 2456 5.940617 TCATAGTTGGGCATGCTAGTTAAT 58.059 37.500 18.92 2.56 0.00 1.40
2422 2459 4.344104 AGTTGGGCATGCTAGTTAATTGT 58.656 39.130 18.92 0.00 0.00 2.71
2508 2545 9.793259 AAACAGATTATCCAGTTTGAAACTCTA 57.207 29.630 7.75 0.00 40.46 2.43
2553 2590 6.401394 TGGATAATCTGTATCTGCATGCTAC 58.599 40.000 20.33 13.50 0.00 3.58
2557 2594 4.677673 TCTGTATCTGCATGCTACATGT 57.322 40.909 20.33 2.69 28.49 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.083401 GTCAGTTGCTTGCGTGTCG 60.083 57.895 0.00 0.00 0.00 4.35
3 4 0.376852 TTGTCAGTTGCTTGCGTGTC 59.623 50.000 0.00 0.00 0.00 3.67
4 5 0.378257 CTTGTCAGTTGCTTGCGTGT 59.622 50.000 0.00 0.00 0.00 4.49
6 7 2.024918 CCTTGTCAGTTGCTTGCGT 58.975 52.632 0.00 0.00 0.00 5.24
7 8 1.370900 GCCTTGTCAGTTGCTTGCG 60.371 57.895 0.00 0.00 0.00 4.85
8 9 0.102844 TTGCCTTGTCAGTTGCTTGC 59.897 50.000 0.00 0.00 0.00 4.01
9 10 1.134753 TGTTGCCTTGTCAGTTGCTTG 59.865 47.619 0.00 0.00 0.00 4.01
10 11 1.473258 TGTTGCCTTGTCAGTTGCTT 58.527 45.000 0.00 0.00 0.00 3.91
11 12 1.134946 GTTGTTGCCTTGTCAGTTGCT 59.865 47.619 0.00 0.00 0.00 3.91
12 13 1.135141 TGTTGTTGCCTTGTCAGTTGC 60.135 47.619 0.00 0.00 0.00 4.17
13 14 2.923020 GTTGTTGTTGCCTTGTCAGTTG 59.077 45.455 0.00 0.00 0.00 3.16
14 15 2.415357 CGTTGTTGTTGCCTTGTCAGTT 60.415 45.455 0.00 0.00 0.00 3.16
15 16 1.132262 CGTTGTTGTTGCCTTGTCAGT 59.868 47.619 0.00 0.00 0.00 3.41
16 17 1.400142 TCGTTGTTGTTGCCTTGTCAG 59.600 47.619 0.00 0.00 0.00 3.51
17 18 1.454201 TCGTTGTTGTTGCCTTGTCA 58.546 45.000 0.00 0.00 0.00 3.58
18 19 2.553079 TTCGTTGTTGTTGCCTTGTC 57.447 45.000 0.00 0.00 0.00 3.18
19 20 2.029828 TGTTTCGTTGTTGTTGCCTTGT 60.030 40.909 0.00 0.00 0.00 3.16
20 21 2.344142 GTGTTTCGTTGTTGTTGCCTTG 59.656 45.455 0.00 0.00 0.00 3.61
21 22 2.601804 GTGTTTCGTTGTTGTTGCCTT 58.398 42.857 0.00 0.00 0.00 4.35
22 23 1.135228 GGTGTTTCGTTGTTGTTGCCT 60.135 47.619 0.00 0.00 0.00 4.75
23 24 1.273688 GGTGTTTCGTTGTTGTTGCC 58.726 50.000 0.00 0.00 0.00 4.52
24 25 0.911184 CGGTGTTTCGTTGTTGTTGC 59.089 50.000 0.00 0.00 0.00 4.17
25 26 1.130749 TCCGGTGTTTCGTTGTTGTTG 59.869 47.619 0.00 0.00 0.00 3.33
26 27 1.451067 TCCGGTGTTTCGTTGTTGTT 58.549 45.000 0.00 0.00 0.00 2.83
27 28 1.399089 CTTCCGGTGTTTCGTTGTTGT 59.601 47.619 0.00 0.00 0.00 3.32
28 29 1.666700 TCTTCCGGTGTTTCGTTGTTG 59.333 47.619 0.00 0.00 0.00 3.33
29 30 1.667212 GTCTTCCGGTGTTTCGTTGTT 59.333 47.619 0.00 0.00 0.00 2.83
30 31 1.292992 GTCTTCCGGTGTTTCGTTGT 58.707 50.000 0.00 0.00 0.00 3.32
31 32 1.004292 GTGTCTTCCGGTGTTTCGTTG 60.004 52.381 0.00 0.00 0.00 4.10
32 33 1.292992 GTGTCTTCCGGTGTTTCGTT 58.707 50.000 0.00 0.00 0.00 3.85
33 34 0.531311 GGTGTCTTCCGGTGTTTCGT 60.531 55.000 0.00 0.00 0.00 3.85
34 35 0.249741 AGGTGTCTTCCGGTGTTTCG 60.250 55.000 0.00 0.00 0.00 3.46
35 36 1.226746 CAGGTGTCTTCCGGTGTTTC 58.773 55.000 0.00 0.00 0.00 2.78
36 37 0.179029 CCAGGTGTCTTCCGGTGTTT 60.179 55.000 0.00 0.00 0.00 2.83
37 38 1.450211 CCAGGTGTCTTCCGGTGTT 59.550 57.895 0.00 0.00 0.00 3.32
38 39 3.148084 CCAGGTGTCTTCCGGTGT 58.852 61.111 0.00 0.00 0.00 4.16
39 40 2.358737 GCCAGGTGTCTTCCGGTG 60.359 66.667 0.00 0.00 0.00 4.94
40 41 2.847234 TGCCAGGTGTCTTCCGGT 60.847 61.111 0.00 0.00 0.00 5.28
41 42 2.358737 GTGCCAGGTGTCTTCCGG 60.359 66.667 0.00 0.00 0.00 5.14
42 43 1.003355 ATGTGCCAGGTGTCTTCCG 60.003 57.895 0.00 0.00 0.00 4.30
43 44 1.021390 CGATGTGCCAGGTGTCTTCC 61.021 60.000 0.00 0.00 0.00 3.46
44 45 1.021390 CCGATGTGCCAGGTGTCTTC 61.021 60.000 0.00 0.00 0.00 2.87
45 46 1.003355 CCGATGTGCCAGGTGTCTT 60.003 57.895 0.00 0.00 0.00 3.01
46 47 2.172483 GACCGATGTGCCAGGTGTCT 62.172 60.000 0.00 0.00 38.57 3.41
47 48 1.741770 GACCGATGTGCCAGGTGTC 60.742 63.158 0.00 0.00 38.57 3.67
48 49 2.050836 TTGACCGATGTGCCAGGTGT 62.051 55.000 0.00 0.00 38.57 4.16
49 50 1.302431 TTGACCGATGTGCCAGGTG 60.302 57.895 0.00 0.00 38.57 4.00
50 51 1.302511 GTTGACCGATGTGCCAGGT 60.303 57.895 0.00 0.00 41.63 4.00
51 52 2.390599 CGTTGACCGATGTGCCAGG 61.391 63.158 0.00 0.00 39.56 4.45
52 53 2.390599 CCGTTGACCGATGTGCCAG 61.391 63.158 0.00 0.00 39.56 4.85
53 54 2.358125 CCGTTGACCGATGTGCCA 60.358 61.111 0.00 0.00 39.56 4.92
54 55 3.124921 CCCGTTGACCGATGTGCC 61.125 66.667 0.00 0.00 39.56 5.01
55 56 3.799755 GCCCGTTGACCGATGTGC 61.800 66.667 0.00 0.00 39.56 4.57
56 57 3.487202 CGCCCGTTGACCGATGTG 61.487 66.667 0.00 0.00 39.56 3.21
58 59 3.709880 TAGCGCCCGTTGACCGATG 62.710 63.158 2.29 0.00 39.56 3.84
59 60 3.454573 TAGCGCCCGTTGACCGAT 61.455 61.111 2.29 0.00 39.56 4.18
60 61 4.424566 GTAGCGCCCGTTGACCGA 62.425 66.667 2.29 0.00 39.56 4.69
61 62 4.728102 TGTAGCGCCCGTTGACCG 62.728 66.667 2.29 0.00 0.00 4.79
62 63 2.125269 ATGTAGCGCCCGTTGACC 60.125 61.111 2.29 0.00 0.00 4.02
63 64 2.514013 CGATGTAGCGCCCGTTGAC 61.514 63.158 2.29 0.00 0.00 3.18
64 65 2.202690 CGATGTAGCGCCCGTTGA 60.203 61.111 2.29 0.00 0.00 3.18
65 66 2.098233 AACGATGTAGCGCCCGTTG 61.098 57.895 16.89 10.68 42.61 4.10
66 67 2.098233 CAACGATGTAGCGCCCGTT 61.098 57.895 2.29 9.95 44.67 4.44
67 68 1.936436 TACAACGATGTAGCGCCCGT 61.936 55.000 2.29 3.46 41.05 5.28
68 69 1.226745 TACAACGATGTAGCGCCCG 60.227 57.895 2.29 2.74 41.05 6.13
69 70 1.149964 GGTACAACGATGTAGCGCCC 61.150 60.000 17.45 6.83 46.84 6.13
70 71 2.294728 GGTACAACGATGTAGCGCC 58.705 57.895 17.45 7.16 46.84 6.53
74 75 5.063180 TGGTAACTGGTACAACGATGTAG 57.937 43.478 5.70 0.00 39.24 2.74
75 76 4.766373 TCTGGTAACTGGTACAACGATGTA 59.234 41.667 5.08 0.81 38.70 2.29
76 77 3.575256 TCTGGTAACTGGTACAACGATGT 59.425 43.478 5.08 3.12 38.70 3.06
77 78 3.924686 GTCTGGTAACTGGTACAACGATG 59.075 47.826 5.08 0.00 38.70 3.84
78 79 3.830755 AGTCTGGTAACTGGTACAACGAT 59.169 43.478 5.08 0.00 38.70 3.73
92 93 2.176889 GGAGCAGTTGGTAGTCTGGTA 58.823 52.381 0.00 0.00 41.47 3.25
116 117 4.038402 CCATTCATGCAAAATCTCTACCCC 59.962 45.833 0.00 0.00 0.00 4.95
145 147 1.860853 GGTAGTCGTCGTCGTTCGC 60.861 63.158 1.33 4.32 39.67 4.70
289 292 0.249322 AGACCGCCACATACATACGC 60.249 55.000 0.00 0.00 0.00 4.42
537 542 8.688747 TGTCATGCACCATGTCATTTATTATA 57.311 30.769 5.24 0.00 41.98 0.98
587 592 4.687901 AACCTTCCAAAACCAAATGAGG 57.312 40.909 0.00 0.00 0.00 3.86
624 633 9.542462 TGAGATCACCTTCCTAAAATATAAACG 57.458 33.333 0.00 0.00 0.00 3.60
702 712 4.651994 CTTTAGCACGTGTGGATTCATTC 58.348 43.478 18.38 0.00 0.00 2.67
720 732 6.128282 GGAGATCTTGTTTCGTGATTGCTTTA 60.128 38.462 0.00 0.00 0.00 1.85
856 878 3.988379 ATCTGTGACGCAATGTTGTTT 57.012 38.095 0.00 0.00 0.00 2.83
858 880 6.538381 TCAATATATCTGTGACGCAATGTTGT 59.462 34.615 7.89 0.00 0.00 3.32
874 896 8.175716 TGACATATCTCGTGTCGTCAATATATC 58.824 37.037 0.00 0.00 46.89 1.63
930 952 8.417106 AGATATGACGTATCTTGTGTCTTCAAT 58.583 33.333 10.85 0.00 45.78 2.57
1103 1125 5.189736 TGGCATGAGGAGTAGAAAACATAGT 59.810 40.000 0.00 0.00 0.00 2.12
1198 1226 8.324306 ACACATATGGCTAGCAAATGTATAGAT 58.676 33.333 21.33 8.40 0.00 1.98
1243 1271 6.572519 TGAAGGGACAAAAGAAAAGAATGTG 58.427 36.000 0.00 0.00 0.00 3.21
1278 1306 2.159430 TCGTGCATGAAAAACCAGATCG 59.841 45.455 6.04 0.00 0.00 3.69
1350 1379 3.568443 TGAAGCGGTATATGTCCCACTA 58.432 45.455 0.00 0.00 0.00 2.74
1372 1401 2.029739 CACATTTTGCCTGATCACAGCA 60.030 45.455 10.86 10.86 42.25 4.41
1374 1403 3.928727 ACACATTTTGCCTGATCACAG 57.071 42.857 0.00 0.00 43.12 3.66
1386 1415 0.829333 TGCAGGCCACAACACATTTT 59.171 45.000 5.01 0.00 0.00 1.82
1387 1416 0.390124 CTGCAGGCCACAACACATTT 59.610 50.000 5.01 0.00 0.00 2.32
1587 1619 3.281727 AAGACAACTTGGCAGAGTCAA 57.718 42.857 0.00 0.00 34.80 3.18
1622 1654 8.479313 TGAGTTAGATATTCATGTGTGTGTTC 57.521 34.615 0.00 0.00 0.00 3.18
1690 1722 0.981183 ATTAGGGCTCACGGTCACAA 59.019 50.000 0.00 0.00 0.00 3.33
1702 1734 1.679559 CCAGGCTGGCAAATTAGGGC 61.680 60.000 22.68 0.00 0.00 5.19
1764 1801 6.764379 TCTTGTTGTTCCGGATATATATGCA 58.236 36.000 4.15 0.00 0.00 3.96
1800 1837 6.627087 AAAAATCAGGGAGTGAGTCTCATA 57.373 37.500 5.68 0.00 44.40 2.15
1823 1860 6.431543 TCTTTGTTCACTTGGTGTTACTTCAA 59.568 34.615 0.00 0.00 34.79 2.69
1884 1921 7.254852 GGCCTCTTTCATATCTCTATACTTCG 58.745 42.308 0.00 0.00 0.00 3.79
1888 1925 5.344884 GCGGCCTCTTTCATATCTCTATAC 58.655 45.833 0.00 0.00 0.00 1.47
1954 1991 5.337652 GGCACACCAGACTTATAAGAGTTCT 60.338 44.000 19.38 8.68 35.26 3.01
1975 2012 4.077184 CGCGGTCACTAAGGGGCA 62.077 66.667 0.00 0.00 0.00 5.36
1978 2015 4.832608 GGCCGCGGTCACTAAGGG 62.833 72.222 27.96 0.00 0.00 3.95
2003 2040 7.133891 ACAAAACGAATGTTCTCCTCATTAG 57.866 36.000 0.00 0.00 37.31 1.73
2030 2067 2.048601 TCCGTTTACACTCCAAAGGGA 58.951 47.619 5.41 5.41 43.84 4.20
2140 2177 5.651387 TCTATGGTCTGCTATATCTGCAC 57.349 43.478 0.00 0.00 36.37 4.57
2151 2188 6.455360 TTCCAATTTGAATCTATGGTCTGC 57.545 37.500 0.00 0.00 32.90 4.26
2170 2207 0.250295 CCAAGTCTGCCTCGTTTCCA 60.250 55.000 0.00 0.00 0.00 3.53
2178 2215 1.415672 TTTCCGGTCCAAGTCTGCCT 61.416 55.000 0.00 0.00 0.00 4.75
2275 2312 8.806429 TCTTAACTAATTGATTCATGCAAGGA 57.194 30.769 0.00 0.00 0.00 3.36
2406 2443 9.651718 GTTATCAAGTACAATTAACTAGCATGC 57.348 33.333 10.51 10.51 0.00 4.06
2484 2521 9.442047 CTTAGAGTTTCAAACTGGATAATCTGT 57.558 33.333 7.75 0.00 43.03 3.41
2528 2565 5.489249 AGCATGCAGATACAGATTATCCAG 58.511 41.667 21.98 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.