Multiple sequence alignment - TraesCS3A01G519400

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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 TraesCS3A01G519400 chr3A 100.000 2393 0 0 1 2393 737170473 737172865 0.000000e+00 4420.0
1 TraesCS3A01G519400 chr3A 89.664 803 72 7 52 850 672063315 672062520 0.000000e+00 1013.0
2 TraesCS3A01G519400 chr3A 83.043 690 92 11 853 1539 737140573 737141240 9.460000e-169 603.0
3 TraesCS3A01G519400 chr3A 85.385 130 18 1 1692 1820 737125105 737125234 1.490000e-27 134.0
4 TraesCS3A01G519400 chr3A 98.039 51 1 0 1 51 737150588 737150638 3.280000e-14 89.8
5 TraesCS3A01G519400 chr3A 94.118 51 3 0 1 51 537565498 537565448 7.090000e-11 78.7
6 TraesCS3A01G519400 chr3A 94.118 51 3 0 1 51 540773923 540773973 7.090000e-11 78.7
7 TraesCS3A01G519400 chr3A 95.349 43 2 0 851 893 737133108 737133150 4.270000e-08 69.4
8 TraesCS3A01G519400 chr3B 88.622 1582 121 20 853 2391 813880497 813882062 0.000000e+00 1869.0
9 TraesCS3A01G519400 chr3B 79.408 709 104 24 854 1539 813765028 813764339 1.680000e-126 462.0
10 TraesCS3A01G519400 chr5D 89.900 802 74 4 52 852 563636989 563636194 0.000000e+00 1026.0
11 TraesCS3A01G519400 chr5D 89.664 803 73 8 52 852 72934611 72933817 0.000000e+00 1014.0
12 TraesCS3A01G519400 chr4D 89.950 796 73 4 56 850 449041567 449040778 0.000000e+00 1020.0
13 TraesCS3A01G519400 chr7B 89.664 803 74 6 52 852 710378733 710377938 0.000000e+00 1014.0
14 TraesCS3A01G519400 chr2D 89.651 802 76 5 52 852 179114716 179115511 0.000000e+00 1014.0
15 TraesCS3A01G519400 chr2D 89.664 803 74 6 52 852 303346136 303345341 0.000000e+00 1014.0
16 TraesCS3A01G519400 chr7D 89.664 803 72 8 52 852 267101710 267102503 0.000000e+00 1013.0
17 TraesCS3A01G519400 chr6D 89.539 803 76 5 52 852 316106294 316107090 0.000000e+00 1011.0
18 TraesCS3A01G519400 chrUn 91.148 610 35 11 853 1446 46178425 46179031 0.000000e+00 809.0
19 TraesCS3A01G519400 chrUn 81.631 969 125 26 869 1820 46160963 46161895 0.000000e+00 754.0
20 TraesCS3A01G519400 chr4A 96.078 51 2 0 1 51 254981530 254981580 1.520000e-12 84.2
21 TraesCS3A01G519400 chr7A 94.231 52 3 0 1 52 191258045 191258096 1.970000e-11 80.5
22 TraesCS3A01G519400 chr6A 94.118 51 3 0 1 51 105249612 105249562 7.090000e-11 78.7
23 TraesCS3A01G519400 chr5A 94.118 51 3 0 1 51 160222344 160222294 7.090000e-11 78.7
24 TraesCS3A01G519400 chr5A 94.118 51 3 0 1 51 517213312 517213262 7.090000e-11 78.7
25 TraesCS3A01G519400 chr2A 94.118 51 3 0 1 51 515742423 515742373 7.090000e-11 78.7


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 TraesCS3A01G519400 chr3A 737170473 737172865 2392 False 4420 4420 100.000 1 2393 1 chr3A.!!$F6 2392
1 TraesCS3A01G519400 chr3A 672062520 672063315 795 True 1013 1013 89.664 52 850 1 chr3A.!!$R2 798
2 TraesCS3A01G519400 chr3A 737140573 737141240 667 False 603 603 83.043 853 1539 1 chr3A.!!$F4 686
3 TraesCS3A01G519400 chr3B 813880497 813882062 1565 False 1869 1869 88.622 853 2391 1 chr3B.!!$F1 1538
4 TraesCS3A01G519400 chr3B 813764339 813765028 689 True 462 462 79.408 854 1539 1 chr3B.!!$R1 685
5 TraesCS3A01G519400 chr5D 563636194 563636989 795 True 1026 1026 89.900 52 852 1 chr5D.!!$R2 800
6 TraesCS3A01G519400 chr5D 72933817 72934611 794 True 1014 1014 89.664 52 852 1 chr5D.!!$R1 800
7 TraesCS3A01G519400 chr4D 449040778 449041567 789 True 1020 1020 89.950 56 850 1 chr4D.!!$R1 794
8 TraesCS3A01G519400 chr7B 710377938 710378733 795 True 1014 1014 89.664 52 852 1 chr7B.!!$R1 800
9 TraesCS3A01G519400 chr2D 179114716 179115511 795 False 1014 1014 89.651 52 852 1 chr2D.!!$F1 800
10 TraesCS3A01G519400 chr2D 303345341 303346136 795 True 1014 1014 89.664 52 852 1 chr2D.!!$R1 800
11 TraesCS3A01G519400 chr7D 267101710 267102503 793 False 1013 1013 89.664 52 852 1 chr7D.!!$F1 800
12 TraesCS3A01G519400 chr6D 316106294 316107090 796 False 1011 1011 89.539 52 852 1 chr6D.!!$F1 800
13 TraesCS3A01G519400 chrUn 46178425 46179031 606 False 809 809 91.148 853 1446 1 chrUn.!!$F2 593
14 TraesCS3A01G519400 chrUn 46160963 46161895 932 False 754 754 81.631 869 1820 1 chrUn.!!$F1 951

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
726 731 0.116342 TCACTCCCCCTCTTAGTGCA 59.884 55.0 0.0 0.0 40.34 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1721 0.107945 GAGATGGAGCACACAGGACC 60.108 60.0 0.0 0.0 0.0 4.46 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
20 21 1.722011 ACGGCAAGAGTTGGAATACG 58.278 50.000 0.00 0.00 0.00 3.06
21 22 1.274167 ACGGCAAGAGTTGGAATACGA 59.726 47.619 0.00 0.00 0.00 3.43
22 23 2.289195 ACGGCAAGAGTTGGAATACGAA 60.289 45.455 0.00 0.00 0.00 3.85
23 24 2.936498 CGGCAAGAGTTGGAATACGAAT 59.064 45.455 0.00 0.00 0.00 3.34
24 25 4.116961 CGGCAAGAGTTGGAATACGAATA 58.883 43.478 0.00 0.00 0.00 1.75
25 26 4.569162 CGGCAAGAGTTGGAATACGAATAA 59.431 41.667 0.00 0.00 0.00 1.40
26 27 5.276868 CGGCAAGAGTTGGAATACGAATAAG 60.277 44.000 0.00 0.00 0.00 1.73
27 28 5.007724 GGCAAGAGTTGGAATACGAATAAGG 59.992 44.000 0.00 0.00 0.00 2.69
28 29 5.585047 GCAAGAGTTGGAATACGAATAAGGT 59.415 40.000 0.00 0.00 0.00 3.50
29 30 6.759827 GCAAGAGTTGGAATACGAATAAGGTA 59.240 38.462 0.00 0.00 0.00 3.08
30 31 7.279313 GCAAGAGTTGGAATACGAATAAGGTAA 59.721 37.037 0.00 0.00 0.00 2.85
31 32 9.158233 CAAGAGTTGGAATACGAATAAGGTAAA 57.842 33.333 0.00 0.00 0.00 2.01
32 33 9.901172 AAGAGTTGGAATACGAATAAGGTAAAT 57.099 29.630 0.00 0.00 0.00 1.40
33 34 9.901172 AGAGTTGGAATACGAATAAGGTAAATT 57.099 29.630 0.00 0.00 0.00 1.82
43 44 7.333323 ACGAATAAGGTAAATTATATCCGGGG 58.667 38.462 0.00 0.00 0.00 5.73
44 45 7.038088 ACGAATAAGGTAAATTATATCCGGGGT 60.038 37.037 0.00 0.00 0.00 4.95
45 46 7.279313 CGAATAAGGTAAATTATATCCGGGGTG 59.721 40.741 0.00 0.00 0.00 4.61
46 47 5.917545 AAGGTAAATTATATCCGGGGTGT 57.082 39.130 0.00 0.00 0.00 4.16
47 48 5.917545 AGGTAAATTATATCCGGGGTGTT 57.082 39.130 0.00 0.00 0.00 3.32
48 49 7.391388 AAGGTAAATTATATCCGGGGTGTTA 57.609 36.000 0.00 0.00 0.00 2.41
49 50 6.772605 AGGTAAATTATATCCGGGGTGTTAC 58.227 40.000 0.00 1.98 0.00 2.50
50 51 6.329723 AGGTAAATTATATCCGGGGTGTTACA 59.670 38.462 0.00 0.00 0.00 2.41
126 127 5.067674 CCACACAAGATCACCTTCTTCAAAA 59.932 40.000 0.00 0.00 33.69 2.44
157 158 4.097892 TCTTTCTTCCCTTGTTTGCTTGTC 59.902 41.667 0.00 0.00 0.00 3.18
204 205 6.818644 TCTCAATATTTTCCTTGGTCTTCTCG 59.181 38.462 0.00 0.00 0.00 4.04
213 214 5.130350 TCCTTGGTCTTCTCGTGAATTTTT 58.870 37.500 0.00 0.00 0.00 1.94
238 240 4.457834 AGAAGTCAGCACGCTTACTTAT 57.542 40.909 16.41 11.88 39.66 1.73
265 267 2.472695 TTAGTTCGCTCCTGCAATGT 57.527 45.000 0.00 0.00 39.64 2.71
272 274 2.083774 CGCTCCTGCAATGTTAAAGGA 58.916 47.619 0.00 0.00 39.64 3.36
320 323 7.621102 GTTTGAAACCATAAACAGCTTCAAAG 58.379 34.615 7.76 0.00 41.11 2.77
326 329 4.082571 CCATAAACAGCTTCAAAGGGACAG 60.083 45.833 0.00 0.00 0.00 3.51
335 338 6.655003 CAGCTTCAAAGGGACAGAATTTAGTA 59.345 38.462 0.00 0.00 0.00 1.82
365 368 2.672098 ACCACCCTGTTGTATGCAAAA 58.328 42.857 0.00 0.00 36.22 2.44
374 377 3.565902 TGTTGTATGCAAAATCCACGTGA 59.434 39.130 19.30 3.36 36.22 4.35
395 398 1.630878 GGGAGACACTCTTCCCACATT 59.369 52.381 4.71 0.00 36.06 2.71
398 401 4.145052 GGAGACACTCTTCCCACATTTTT 58.855 43.478 0.00 0.00 0.00 1.94
403 406 8.250143 AGACACTCTTCCCACATTTTTAATTT 57.750 30.769 0.00 0.00 0.00 1.82
404 407 8.143835 AGACACTCTTCCCACATTTTTAATTTG 58.856 33.333 0.00 0.00 0.00 2.32
462 465 2.490115 TGCGGTTGACAACTTCAGTTTT 59.510 40.909 17.52 0.00 35.83 2.43
468 471 6.106003 GGTTGACAACTTCAGTTTTTCCATT 58.894 36.000 17.52 0.00 35.83 3.16
507 510 3.998099 AGTGGAAAAGAGAAGCTTTGC 57.002 42.857 0.00 0.00 45.85 3.68
512 515 3.571828 GGAAAAGAGAAGCTTTGCTCCTT 59.428 43.478 10.68 3.05 45.85 3.36
513 516 4.762251 GGAAAAGAGAAGCTTTGCTCCTTA 59.238 41.667 10.68 0.00 45.85 2.69
519 522 4.464947 AGAAGCTTTGCTCCTTACTTTGT 58.535 39.130 0.00 0.00 38.25 2.83
525 528 3.788227 TGCTCCTTACTTTGTCCACAT 57.212 42.857 0.00 0.00 0.00 3.21
553 556 8.755941 GTTTTCCAAAAATAGCTCAGAAACTTC 58.244 33.333 0.00 0.00 0.00 3.01
562 565 1.787155 CTCAGAAACTTCGTGTCACGG 59.213 52.381 24.33 12.30 42.81 4.94
582 585 4.055360 CGGTCTGAAACAATAGTGTGTGA 58.945 43.478 0.00 0.00 38.27 3.58
593 596 6.108687 ACAATAGTGTGTGATACTCCATGTG 58.891 40.000 0.00 0.00 36.31 3.21
671 674 1.597663 GACACGGGATAAAATGAGCCG 59.402 52.381 0.00 0.00 0.00 5.52
677 680 2.618709 GGGATAAAATGAGCCGTCTTGG 59.381 50.000 0.00 0.00 42.50 3.61
702 705 6.493189 AAACCTATCAACCACCACAAAAAT 57.507 33.333 0.00 0.00 0.00 1.82
726 731 0.116342 TCACTCCCCCTCTTAGTGCA 59.884 55.000 0.00 0.00 40.34 4.57
770 775 7.699709 TCCATACAAATATCTTCCCAAGGTA 57.300 36.000 0.00 0.00 0.00 3.08
771 776 8.287904 TCCATACAAATATCTTCCCAAGGTAT 57.712 34.615 0.00 0.00 36.38 2.73
772 777 9.400208 TCCATACAAATATCTTCCCAAGGTATA 57.600 33.333 0.00 0.00 33.75 1.47
825 830 6.056884 AGTTCATAAGGGTTTAAACGTGACA 58.943 36.000 12.07 0.00 0.00 3.58
834 839 5.278120 GGGTTTAAACGTGACATAGCTTTGT 60.278 40.000 9.75 9.75 0.00 2.83
921 936 0.955428 AGTTGTGCAATGCGATCGGT 60.955 50.000 18.30 0.00 0.00 4.69
933 949 0.365523 CGATCGGTGTTGTAACTGCG 59.634 55.000 7.38 0.00 0.00 5.18
941 963 3.424829 GGTGTTGTAACTGCGATCACATG 60.425 47.826 0.00 0.00 0.00 3.21
955 977 9.573133 CTGCGATCACATGATATATACTTAACA 57.427 33.333 0.00 0.00 34.37 2.41
1013 1056 4.488136 TGCCATGGCTGCCTACCG 62.488 66.667 35.53 5.78 42.51 4.02
1023 1066 2.303549 CTGCCTACCGCCTCCTCTTG 62.304 65.000 0.00 0.00 36.24 3.02
1299 1354 3.755628 GACGACCGCAGTAGGGCA 61.756 66.667 0.00 0.00 40.05 5.36
1400 1455 6.204688 GGAATCGGTGATCTGTAAAATGCATA 59.795 38.462 0.00 0.00 0.00 3.14
1401 1456 7.094634 GGAATCGGTGATCTGTAAAATGCATAT 60.095 37.037 0.00 0.00 0.00 1.78
1509 1566 4.662961 CCCGTCTGTGCACTGCGA 62.663 66.667 28.16 16.87 0.00 5.10
1525 1590 2.643272 GACCTGTCGCAGTCGTCA 59.357 61.111 6.19 0.00 36.96 4.35
1539 1604 0.318441 TCGTCAGAGCTCCACCTTTG 59.682 55.000 10.93 0.47 0.00 2.77
1540 1605 1.294659 CGTCAGAGCTCCACCTTTGC 61.295 60.000 10.93 0.00 0.00 3.68
1541 1606 0.957888 GTCAGAGCTCCACCTTTGCC 60.958 60.000 10.93 0.00 0.00 4.52
1542 1607 1.130054 TCAGAGCTCCACCTTTGCCT 61.130 55.000 10.93 0.00 0.00 4.75
1543 1608 0.251077 CAGAGCTCCACCTTTGCCTT 60.251 55.000 10.93 0.00 0.00 4.35
1555 1620 2.488153 CCTTTGCCTTACTTTCCTTCCG 59.512 50.000 0.00 0.00 0.00 4.30
1629 1696 6.409704 CCGTGTTCCTCCATGAATATATGAT 58.590 40.000 0.00 0.00 0.00 2.45
1654 1721 2.646930 TGAAGCTGCATAGATGGTTGG 58.353 47.619 1.02 0.00 0.00 3.77
1658 1725 1.972872 CTGCATAGATGGTTGGGTCC 58.027 55.000 0.00 0.00 0.00 4.46
1676 1743 1.911357 TCCTGTGTGCTCCATCTCATT 59.089 47.619 0.00 0.00 0.00 2.57
1687 1755 4.202121 GCTCCATCTCATTTAGGACGTACA 60.202 45.833 0.00 0.00 0.00 2.90
1723 1803 6.719370 AGATAGTCTTATCCTAAGCCTGACAG 59.281 42.308 0.00 0.00 37.05 3.51
1800 1881 7.161404 CCTTATCATTAGTAACTAGCATGCCA 58.839 38.462 15.66 0.00 0.00 4.92
1827 1908 4.207891 TGTGGTGAGAGATAAGCCTTTC 57.792 45.455 0.00 0.00 0.00 2.62
1833 1914 5.361285 GGTGAGAGATAAGCCTTTCTCTACA 59.639 44.000 14.85 12.50 46.67 2.74
1840 1921 8.317776 AGATAAGCCTTTCTCTACATTCTCTT 57.682 34.615 0.00 0.00 0.00 2.85
1841 1922 8.203485 AGATAAGCCTTTCTCTACATTCTCTTG 58.797 37.037 0.00 0.00 0.00 3.02
1842 1923 5.753721 AGCCTTTCTCTACATTCTCTTGT 57.246 39.130 0.00 0.00 0.00 3.16
1855 1936 0.764890 CTCTTGTCACCCCCTCAACA 59.235 55.000 0.00 0.00 0.00 3.33
1856 1937 1.352352 CTCTTGTCACCCCCTCAACAT 59.648 52.381 0.00 0.00 0.00 2.71
1862 1943 3.288092 GTCACCCCCTCAACATTTATCC 58.712 50.000 0.00 0.00 0.00 2.59
1867 1948 6.797540 TCACCCCCTCAACATTTATCCTATAT 59.202 38.462 0.00 0.00 0.00 0.86
1868 1949 6.886459 CACCCCCTCAACATTTATCCTATATG 59.114 42.308 0.00 0.00 0.00 1.78
1889 1970 3.003480 GTGGCACTCTTAAGATGTCACC 58.997 50.000 25.87 19.08 41.95 4.02
1909 1990 5.943416 TCACCATTGTACACATCCTTAAAGG 59.057 40.000 0.00 0.00 36.46 3.11
1931 2012 2.223572 CCCGGAAGCACAAGCATTAATC 60.224 50.000 0.73 0.00 45.49 1.75
1939 2020 6.290294 AGCACAAGCATTAATCCTTTGAAT 57.710 33.333 9.07 0.00 45.49 2.57
1942 2023 6.400568 CACAAGCATTAATCCTTTGAATGGT 58.599 36.000 9.07 0.00 41.67 3.55
1964 2053 0.393808 GCCACGGTACCATGGTCAAT 60.394 55.000 26.98 2.47 38.34 2.57
1985 2074 1.811645 GATCGGGAGGCTCTAGGTGC 61.812 65.000 15.23 0.00 0.00 5.01
1991 2081 0.391228 GAGGCTCTAGGTGCTTAGGC 59.609 60.000 7.40 0.00 39.26 3.93
2016 2107 2.807878 TTTTTCGCTCGCCATTTGC 58.192 47.368 0.00 0.00 0.00 3.68
2024 2115 0.462581 CTCGCCATTTGCTCCTGCTA 60.463 55.000 0.00 0.00 40.48 3.49
2033 2124 0.686789 TGCTCCTGCTACTTTGCTCA 59.313 50.000 0.00 0.00 40.48 4.26
2072 2163 8.818057 CCACACGGTATTTTTGTTAATTTTGAA 58.182 29.630 0.00 0.00 0.00 2.69
2251 2351 9.269453 TGCACAAATTAATGTTCATGAATTTCA 57.731 25.926 12.12 5.54 30.91 2.69
2252 2352 9.749490 GCACAAATTAATGTTCATGAATTTCAG 57.251 29.630 12.12 11.81 30.91 3.02
2311 2411 9.328845 CAAAGAAGAAAAATGGGAAAAGAATGA 57.671 29.630 0.00 0.00 0.00 2.57
2376 2476 0.909133 TGAGCCCATCTACACCAGCA 60.909 55.000 0.00 0.00 0.00 4.41
2379 2479 1.285962 AGCCCATCTACACCAGCAATT 59.714 47.619 0.00 0.00 0.00 2.32
2382 2482 2.947652 CCCATCTACACCAGCAATTCAG 59.052 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.073816 CGTATTCCAACTCTTGCCGTT 58.926 47.619 0.00 0.00 0.00 4.44
1 2 1.274167 TCGTATTCCAACTCTTGCCGT 59.726 47.619 0.00 0.00 0.00 5.68
2 3 2.004583 TCGTATTCCAACTCTTGCCG 57.995 50.000 0.00 0.00 0.00 5.69
3 4 5.007724 CCTTATTCGTATTCCAACTCTTGCC 59.992 44.000 0.00 0.00 0.00 4.52
4 5 5.585047 ACCTTATTCGTATTCCAACTCTTGC 59.415 40.000 0.00 0.00 0.00 4.01
5 6 8.712285 TTACCTTATTCGTATTCCAACTCTTG 57.288 34.615 0.00 0.00 0.00 3.02
6 7 9.901172 ATTTACCTTATTCGTATTCCAACTCTT 57.099 29.630 0.00 0.00 0.00 2.85
7 8 9.901172 AATTTACCTTATTCGTATTCCAACTCT 57.099 29.630 0.00 0.00 0.00 3.24
17 18 8.477256 CCCCGGATATAATTTACCTTATTCGTA 58.523 37.037 0.73 0.00 0.00 3.43
18 19 7.038088 ACCCCGGATATAATTTACCTTATTCGT 60.038 37.037 0.73 0.00 0.00 3.85
19 20 7.279313 CACCCCGGATATAATTTACCTTATTCG 59.721 40.741 0.73 0.00 0.00 3.34
20 21 8.105197 ACACCCCGGATATAATTTACCTTATTC 58.895 37.037 0.73 0.00 0.00 1.75
21 22 7.992295 ACACCCCGGATATAATTTACCTTATT 58.008 34.615 0.73 0.00 0.00 1.40
22 23 7.578458 ACACCCCGGATATAATTTACCTTAT 57.422 36.000 0.73 0.00 0.00 1.73
23 24 7.391388 AACACCCCGGATATAATTTACCTTA 57.609 36.000 0.73 0.00 0.00 2.69
24 25 5.917545 ACACCCCGGATATAATTTACCTT 57.082 39.130 0.73 0.00 0.00 3.50
25 26 5.917545 AACACCCCGGATATAATTTACCT 57.082 39.130 0.73 0.00 0.00 3.08
26 27 6.427853 GTGTAACACCCCGGATATAATTTACC 59.572 42.308 0.73 0.00 36.32 2.85
27 28 7.172019 CAGTGTAACACCCCGGATATAATTTAC 59.828 40.741 0.73 1.83 41.43 2.01
28 29 7.218614 CAGTGTAACACCCCGGATATAATTTA 58.781 38.462 0.73 0.00 41.43 1.40
29 30 6.059484 CAGTGTAACACCCCGGATATAATTT 58.941 40.000 0.73 0.00 41.43 1.82
30 31 5.617252 CAGTGTAACACCCCGGATATAATT 58.383 41.667 0.73 0.00 41.43 1.40
31 32 4.504340 GCAGTGTAACACCCCGGATATAAT 60.504 45.833 0.73 0.00 41.43 1.28
32 33 3.181463 GCAGTGTAACACCCCGGATATAA 60.181 47.826 0.73 0.00 41.43 0.98
33 34 2.366266 GCAGTGTAACACCCCGGATATA 59.634 50.000 0.73 0.00 41.43 0.86
34 35 1.140252 GCAGTGTAACACCCCGGATAT 59.860 52.381 0.73 0.00 41.43 1.63
35 36 0.538118 GCAGTGTAACACCCCGGATA 59.462 55.000 0.73 0.00 41.43 2.59
36 37 1.298667 GCAGTGTAACACCCCGGAT 59.701 57.895 0.73 0.00 41.43 4.18
37 38 1.697082 TTGCAGTGTAACACCCCGGA 61.697 55.000 0.73 0.00 41.43 5.14
38 39 1.228003 TTGCAGTGTAACACCCCGG 60.228 57.895 0.00 0.00 41.43 5.73
39 40 0.534203 AGTTGCAGTGTAACACCCCG 60.534 55.000 23.54 0.00 41.43 5.73
40 41 1.336755 CAAGTTGCAGTGTAACACCCC 59.663 52.381 23.54 0.00 41.43 4.95
41 42 1.269051 GCAAGTTGCAGTGTAACACCC 60.269 52.381 22.90 8.95 44.26 4.61
42 43 2.119671 GCAAGTTGCAGTGTAACACC 57.880 50.000 22.90 9.26 44.26 4.16
72 73 0.461516 GGAAGGATCGTTTCCCGGAC 60.462 60.000 0.73 0.00 46.81 4.79
126 127 4.610333 ACAAGGGAAGAAAGAAGGTGTTT 58.390 39.130 0.00 0.00 0.00 2.83
157 158 7.065443 TGAGAAGATGACTGAACAATATGCAAG 59.935 37.037 0.00 0.00 0.00 4.01
213 214 4.628074 AGTAAGCGTGCTGACTTCTAAAA 58.372 39.130 6.02 0.00 34.15 1.52
216 217 3.936372 AAGTAAGCGTGCTGACTTCTA 57.064 42.857 17.17 0.00 42.49 2.10
238 240 4.099419 TGCAGGAGCGAACTAATCTTGATA 59.901 41.667 0.00 0.00 46.23 2.15
277 280 4.721776 TCAAACCTGCTACTCCCATAGATT 59.278 41.667 0.00 0.00 0.00 2.40
312 315 5.966742 ACTAAATTCTGTCCCTTTGAAGC 57.033 39.130 0.00 0.00 0.00 3.86
313 316 7.063544 CGACTACTAAATTCTGTCCCTTTGAAG 59.936 40.741 0.00 0.00 0.00 3.02
320 323 6.338937 ACATTCGACTACTAAATTCTGTCCC 58.661 40.000 0.00 0.00 0.00 4.46
326 329 6.478016 GGGTGGTACATTCGACTACTAAATTC 59.522 42.308 0.00 0.00 44.52 2.17
335 338 1.640917 ACAGGGTGGTACATTCGACT 58.359 50.000 0.00 0.00 44.52 4.18
365 368 0.251832 AGTGTCTCCCTCACGTGGAT 60.252 55.000 17.00 0.00 40.28 3.41
374 377 0.191064 TGTGGGAAGAGTGTCTCCCT 59.809 55.000 8.55 0.00 42.72 4.20
433 436 4.737855 AGTTGTCAACCGCATACTATCT 57.262 40.909 12.17 0.00 0.00 1.98
462 465 1.139853 GCCACCCACAAACAAATGGAA 59.860 47.619 0.00 0.00 38.34 3.53
468 471 1.959985 CTACATGCCACCCACAAACAA 59.040 47.619 0.00 0.00 0.00 2.83
507 510 3.926616 ACGATGTGGACAAAGTAAGGAG 58.073 45.455 0.00 0.00 0.00 3.69
512 515 4.452825 TGGAAAACGATGTGGACAAAGTA 58.547 39.130 0.00 0.00 0.00 2.24
513 516 3.283751 TGGAAAACGATGTGGACAAAGT 58.716 40.909 0.00 0.00 0.00 2.66
519 522 5.242838 AGCTATTTTTGGAAAACGATGTGGA 59.757 36.000 0.00 0.00 0.00 4.02
525 528 6.627395 TTCTGAGCTATTTTTGGAAAACGA 57.373 33.333 0.00 0.00 0.00 3.85
553 556 1.282817 TTGTTTCAGACCGTGACACG 58.717 50.000 21.02 21.02 38.51 4.49
562 565 7.063544 GGAGTATCACACACTATTGTTTCAGAC 59.936 40.741 0.00 0.00 36.25 3.51
582 585 1.831106 TCTTGCGACCACATGGAGTAT 59.169 47.619 4.53 0.00 38.94 2.12
593 596 0.603569 TCCAGAGAAGTCTTGCGACC 59.396 55.000 0.00 0.00 41.16 4.79
607 610 3.320541 ACATTGCCGATTTGTTTTCCAGA 59.679 39.130 0.00 0.00 0.00 3.86
611 614 4.047822 TCACACATTGCCGATTTGTTTTC 58.952 39.130 0.00 0.00 0.00 2.29
671 674 4.698780 GGTGGTTGATAGGTTTACCAAGAC 59.301 45.833 1.13 0.00 41.95 3.01
677 680 6.394025 TTTTGTGGTGGTTGATAGGTTTAC 57.606 37.500 0.00 0.00 0.00 2.01
702 705 3.519510 CACTAAGAGGGGGAGTGATTCAA 59.480 47.826 0.00 0.00 42.65 2.69
726 731 9.665719 GTATGGATTTTGTTTTTGGATTACCAT 57.334 29.630 0.00 0.00 46.34 3.55
786 791 9.063615 CCCTTATGAACTTTATACGCCTTTAAT 57.936 33.333 0.00 0.00 0.00 1.40
787 792 8.048514 ACCCTTATGAACTTTATACGCCTTTAA 58.951 33.333 0.00 0.00 0.00 1.52
804 809 6.314400 GCTATGTCACGTTTAAACCCTTATGA 59.686 38.462 12.66 6.34 0.00 2.15
808 813 4.648651 AGCTATGTCACGTTTAAACCCTT 58.351 39.130 12.66 0.00 0.00 3.95
825 830 3.054875 TGTGAGATCTGCCACAAAGCTAT 60.055 43.478 13.35 0.00 39.97 2.97
834 839 0.678950 TGACGTTGTGAGATCTGCCA 59.321 50.000 0.00 0.00 0.00 4.92
921 936 3.658709 TCATGTGATCGCAGTTACAACA 58.341 40.909 15.24 0.00 0.00 3.33
973 995 4.223032 AGCTAAGTACAGTGTGCACCTATT 59.777 41.667 15.69 1.40 0.00 1.73
981 1007 2.455674 TGGCAGCTAAGTACAGTGTG 57.544 50.000 5.88 0.00 0.00 3.82
1013 1056 1.528129 CACAAGGAACAAGAGGAGGC 58.472 55.000 0.00 0.00 0.00 4.70
1299 1354 3.941657 GAGCTCAGCGGACGCCTTT 62.942 63.158 13.63 0.00 43.17 3.11
1311 1366 3.154787 AGCAGCACCTTGAGCTCA 58.845 55.556 13.74 13.74 41.14 4.26
1498 1555 2.280119 GACAGGTCGCAGTGCACA 60.280 61.111 21.04 0.00 0.00 4.57
1521 1586 1.294659 GCAAAGGTGGAGCTCTGACG 61.295 60.000 14.64 0.00 0.00 4.35
1525 1590 1.003696 GTAAGGCAAAGGTGGAGCTCT 59.996 52.381 14.64 0.00 0.00 4.09
1555 1620 2.159627 CACCACGCTGACTAATGAAACC 59.840 50.000 0.00 0.00 0.00 3.27
1629 1696 5.102953 ACCATCTATGCAGCTTCAACTTA 57.897 39.130 0.00 0.00 0.00 2.24
1654 1721 0.107945 GAGATGGAGCACACAGGACC 60.108 60.000 0.00 0.00 0.00 4.46
1658 1725 3.875727 CCTAAATGAGATGGAGCACACAG 59.124 47.826 0.00 0.00 0.00 3.66
1676 1743 1.913778 TGAGCCAGTGTACGTCCTAA 58.086 50.000 0.00 0.00 0.00 2.69
1687 1755 7.245292 AGGATAAGACTATCTTATGAGCCAGT 58.755 38.462 14.32 0.00 46.46 4.00
1772 1852 7.148507 GCATGCTAGTTACTAATGATAAGGCTG 60.149 40.741 11.37 1.80 0.00 4.85
1775 1855 7.161404 TGGCATGCTAGTTACTAATGATAAGG 58.839 38.462 18.92 0.00 0.00 2.69
1779 1859 7.880160 TTTTGGCATGCTAGTTACTAATGAT 57.120 32.000 18.92 0.00 0.00 2.45
1800 1881 6.904626 AGGCTTATCTCTCACCACATATTTT 58.095 36.000 0.00 0.00 0.00 1.82
1827 1908 3.118592 GGGGGTGACAAGAGAATGTAGAG 60.119 52.174 0.00 0.00 32.57 2.43
1833 1914 2.040412 GTTGAGGGGGTGACAAGAGAAT 59.960 50.000 0.00 0.00 0.00 2.40
1840 1921 3.308832 GGATAAATGTTGAGGGGGTGACA 60.309 47.826 0.00 0.00 0.00 3.58
1841 1922 3.053619 AGGATAAATGTTGAGGGGGTGAC 60.054 47.826 0.00 0.00 0.00 3.67
1842 1923 3.197983 AGGATAAATGTTGAGGGGGTGA 58.802 45.455 0.00 0.00 0.00 4.02
1855 1936 9.950496 CTTAAGAGTGCCACATATAGGATAAAT 57.050 33.333 0.00 0.00 0.00 1.40
1856 1937 9.154632 TCTTAAGAGTGCCACATATAGGATAAA 57.845 33.333 0.00 0.00 0.00 1.40
1862 1943 7.383572 GTGACATCTTAAGAGTGCCACATATAG 59.616 40.741 19.47 0.00 0.00 1.31
1867 1948 3.557054 GGTGACATCTTAAGAGTGCCACA 60.557 47.826 22.69 14.54 0.00 4.17
1868 1949 3.003480 GGTGACATCTTAAGAGTGCCAC 58.997 50.000 11.53 15.50 0.00 5.01
1889 1970 4.097892 GGGCCTTTAAGGATGTGTACAATG 59.902 45.833 16.18 0.00 37.67 2.82
1909 1990 1.312371 TAATGCTTGTGCTTCCGGGC 61.312 55.000 0.00 0.00 40.48 6.13
1942 2023 2.349376 CCATGGTACCGTGGCACA 59.651 61.111 34.89 4.11 44.87 4.57
1964 2053 1.153989 CCTAGAGCCTCCCGATCCA 59.846 63.158 0.00 0.00 0.00 3.41
2008 2099 1.467920 AAGTAGCAGGAGCAAATGGC 58.532 50.000 0.00 0.00 45.49 4.40
2016 2107 3.257469 TCATGAGCAAAGTAGCAGGAG 57.743 47.619 0.00 0.00 36.85 3.69
2041 2132 2.691011 ACAAAAATACCGTGTGGCTTGT 59.309 40.909 0.00 0.00 39.70 3.16
2042 2133 3.363341 ACAAAAATACCGTGTGGCTTG 57.637 42.857 0.00 0.00 39.70 4.01
2144 2237 9.874205 ATTTTCTTTCATGAACTTGTCTTCAAA 57.126 25.926 7.89 0.00 33.85 2.69
2349 2449 4.202357 GGTGTAGATGGGCTCATGACATAA 60.202 45.833 2.16 0.00 32.10 1.90
2351 2451 2.105477 GGTGTAGATGGGCTCATGACAT 59.895 50.000 2.16 0.00 32.10 3.06


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

AutoCloner maintained by Alex Coulton.