Multiple sequence alignment - TraesCS5B01G100900

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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 TraesCS5B01G100900 chr5B 100.000 2312 0 0 1 2312 134025912 134023601 0.000000e+00 4270
1 TraesCS5B01G100900 chr5D 89.471 2308 122 44 99 2312 120889613 120887333 0.000000e+00 2804
2 TraesCS5B01G100900 chr5A 94.378 1583 50 15 99 1649 131787135 131785560 0.000000e+00 2394
3 TraesCS5B01G100900 chr5A 85.196 331 20 11 1956 2258 131785066 131784737 1.720000e-81 313


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 TraesCS5B01G100900 chr5B 134023601 134025912 2311 True 4270.0 4270 100.000 1 2312 1 chr5B.!!$R1 2311
1 TraesCS5B01G100900 chr5D 120887333 120889613 2280 True 2804.0 2804 89.471 99 2312 1 chr5D.!!$R1 2213
2 TraesCS5B01G100900 chr5A 131784737 131787135 2398 True 1353.5 2394 89.787 99 2258 2 chr5A.!!$R1 2159

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
77 78 0.171007 CGCACTTCCGGCATCAAAAT 59.829 50.0 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1401 0.322322 ATTTTGCCGAGTGGTACCGA 59.678 50.0 7.57 0.0 37.67 4.69 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
17 18 3.960237 CAAAACGAGCAGGCGGTA 58.040 55.556 0.00 0.00 35.12 4.02
18 19 1.787847 CAAAACGAGCAGGCGGTAG 59.212 57.895 0.00 0.00 35.12 3.18
19 20 1.375523 AAAACGAGCAGGCGGTAGG 60.376 57.895 0.00 0.00 35.12 3.18
20 21 1.823169 AAAACGAGCAGGCGGTAGGA 61.823 55.000 0.00 0.00 35.12 2.94
21 22 2.502692 AAACGAGCAGGCGGTAGGAC 62.503 60.000 0.00 0.00 35.12 3.85
22 23 3.141488 CGAGCAGGCGGTAGGACT 61.141 66.667 0.00 0.00 0.00 3.85
23 24 2.711922 CGAGCAGGCGGTAGGACTT 61.712 63.158 0.00 0.00 0.00 3.01
24 25 1.153549 GAGCAGGCGGTAGGACTTG 60.154 63.158 0.00 0.00 0.00 3.16
25 26 2.125106 GCAGGCGGTAGGACTTGG 60.125 66.667 0.00 0.00 0.00 3.61
26 27 2.125106 CAGGCGGTAGGACTTGGC 60.125 66.667 0.00 0.00 0.00 4.52
27 28 2.606519 AGGCGGTAGGACTTGGCA 60.607 61.111 0.00 0.00 0.00 4.92
28 29 2.125106 GGCGGTAGGACTTGGCAG 60.125 66.667 0.00 0.00 0.00 4.85
29 30 2.125106 GCGGTAGGACTTGGCAGG 60.125 66.667 0.00 0.00 0.00 4.85
30 31 2.955881 GCGGTAGGACTTGGCAGGT 61.956 63.158 0.23 0.23 0.00 4.00
31 32 1.079127 CGGTAGGACTTGGCAGGTG 60.079 63.158 7.11 0.00 0.00 4.00
32 33 1.541310 CGGTAGGACTTGGCAGGTGA 61.541 60.000 7.11 0.00 0.00 4.02
33 34 0.250513 GGTAGGACTTGGCAGGTGAG 59.749 60.000 7.11 0.00 0.00 3.51
34 35 0.977395 GTAGGACTTGGCAGGTGAGT 59.023 55.000 7.11 0.00 0.00 3.41
35 36 0.976641 TAGGACTTGGCAGGTGAGTG 59.023 55.000 7.11 0.00 0.00 3.51
36 37 1.056700 AGGACTTGGCAGGTGAGTGT 61.057 55.000 7.11 0.00 0.00 3.55
37 38 0.179018 GGACTTGGCAGGTGAGTGTT 60.179 55.000 7.11 0.00 0.00 3.32
38 39 1.230324 GACTTGGCAGGTGAGTGTTC 58.770 55.000 7.11 0.00 0.00 3.18
39 40 0.179018 ACTTGGCAGGTGAGTGTTCC 60.179 55.000 0.00 0.00 0.00 3.62
40 41 0.890996 CTTGGCAGGTGAGTGTTCCC 60.891 60.000 0.00 0.00 0.00 3.97
41 42 2.358737 GGCAGGTGAGTGTTCCCG 60.359 66.667 0.00 0.00 0.00 5.14
42 43 3.050275 GCAGGTGAGTGTTCCCGC 61.050 66.667 0.00 0.00 0.00 6.13
43 44 2.425592 CAGGTGAGTGTTCCCGCA 59.574 61.111 0.00 0.00 0.00 5.69
44 45 1.961277 CAGGTGAGTGTTCCCGCAC 60.961 63.158 0.00 0.00 39.51 5.34
52 53 3.756933 AGTGTTCCCGCACTTAAGTAA 57.243 42.857 8.04 0.00 46.45 2.24
53 54 4.281898 AGTGTTCCCGCACTTAAGTAAT 57.718 40.909 8.04 0.00 46.45 1.89
54 55 4.648651 AGTGTTCCCGCACTTAAGTAATT 58.351 39.130 8.04 0.00 46.45 1.40
55 56 4.454504 AGTGTTCCCGCACTTAAGTAATTG 59.545 41.667 8.04 0.00 46.45 2.32
56 57 4.214758 GTGTTCCCGCACTTAAGTAATTGT 59.785 41.667 8.04 0.00 36.51 2.71
57 58 4.214545 TGTTCCCGCACTTAAGTAATTGTG 59.785 41.667 8.04 2.65 0.00 3.33
61 62 3.196007 GCACTTAAGTAATTGTGCGCA 57.804 42.857 5.66 5.66 44.60 6.09
62 63 2.908626 GCACTTAAGTAATTGTGCGCAC 59.091 45.455 33.11 33.11 44.60 5.34
63 64 3.364964 GCACTTAAGTAATTGTGCGCACT 60.365 43.478 37.59 22.54 44.60 4.40
64 65 4.783242 CACTTAAGTAATTGTGCGCACTT 58.217 39.130 37.59 27.27 35.50 3.16
65 66 4.846137 CACTTAAGTAATTGTGCGCACTTC 59.154 41.667 37.59 22.61 33.47 3.01
66 67 2.989422 AAGTAATTGTGCGCACTTCC 57.011 45.000 37.59 18.17 0.00 3.46
67 68 0.796312 AGTAATTGTGCGCACTTCCG 59.204 50.000 37.59 0.00 0.00 4.30
68 69 0.179200 GTAATTGTGCGCACTTCCGG 60.179 55.000 37.59 0.00 0.00 5.14
69 70 1.917782 TAATTGTGCGCACTTCCGGC 61.918 55.000 37.59 13.47 0.00 6.13
72 73 4.166011 GTGCGCACTTCCGGCATC 62.166 66.667 32.55 1.96 39.14 3.91
73 74 4.695993 TGCGCACTTCCGGCATCA 62.696 61.111 5.66 0.00 0.00 3.07
74 75 3.430862 GCGCACTTCCGGCATCAA 61.431 61.111 0.30 0.00 0.00 2.57
75 76 2.976840 GCGCACTTCCGGCATCAAA 61.977 57.895 0.30 0.00 0.00 2.69
76 77 1.578926 CGCACTTCCGGCATCAAAA 59.421 52.632 0.00 0.00 0.00 2.44
77 78 0.171007 CGCACTTCCGGCATCAAAAT 59.829 50.000 0.00 0.00 0.00 1.82
78 79 1.632422 GCACTTCCGGCATCAAAATG 58.368 50.000 0.00 0.00 35.87 2.32
79 80 1.202114 GCACTTCCGGCATCAAAATGA 59.798 47.619 0.00 0.00 34.61 2.57
80 81 2.159198 GCACTTCCGGCATCAAAATGAT 60.159 45.455 0.00 0.00 37.65 2.45
81 82 3.066621 GCACTTCCGGCATCAAAATGATA 59.933 43.478 0.00 0.00 34.28 2.15
82 83 4.601019 CACTTCCGGCATCAAAATGATAC 58.399 43.478 0.00 0.00 34.28 2.24
83 84 4.096231 CACTTCCGGCATCAAAATGATACA 59.904 41.667 0.00 0.00 34.28 2.29
84 85 4.704540 ACTTCCGGCATCAAAATGATACAA 59.295 37.500 0.00 0.00 34.28 2.41
85 86 5.184864 ACTTCCGGCATCAAAATGATACAAA 59.815 36.000 0.00 0.00 34.28 2.83
86 87 5.247507 TCCGGCATCAAAATGATACAAAG 57.752 39.130 0.00 0.00 34.28 2.77
87 88 3.798337 CCGGCATCAAAATGATACAAAGC 59.202 43.478 0.00 0.00 34.28 3.51
88 89 4.422840 CGGCATCAAAATGATACAAAGCA 58.577 39.130 0.00 0.00 34.28 3.91
89 90 5.045215 CGGCATCAAAATGATACAAAGCAT 58.955 37.500 0.00 0.00 34.28 3.79
90 91 6.207928 CGGCATCAAAATGATACAAAGCATA 58.792 36.000 0.00 0.00 34.28 3.14
91 92 6.696583 CGGCATCAAAATGATACAAAGCATAA 59.303 34.615 0.00 0.00 34.28 1.90
92 93 7.383029 CGGCATCAAAATGATACAAAGCATAAT 59.617 33.333 0.00 0.00 34.28 1.28
93 94 8.492748 GGCATCAAAATGATACAAAGCATAATG 58.507 33.333 0.00 0.00 34.28 1.90
94 95 9.251792 GCATCAAAATGATACAAAGCATAATGA 57.748 29.630 0.00 0.00 34.28 2.57
96 97 8.861033 TCAAAATGATACAAAGCATAATGAGC 57.139 30.769 0.00 0.00 29.71 4.26
97 98 7.644945 TCAAAATGATACAAAGCATAATGAGCG 59.355 33.333 0.00 0.00 37.01 5.03
104 105 3.533606 AAGCATAATGAGCGACAGTCT 57.466 42.857 0.00 0.00 37.01 3.24
295 306 7.731882 TTCGGTAAAGATGTGTCACATAAAA 57.268 32.000 18.42 2.47 39.27 1.52
296 307 7.915293 TCGGTAAAGATGTGTCACATAAAAT 57.085 32.000 18.42 8.07 39.27 1.82
297 308 7.747888 TCGGTAAAGATGTGTCACATAAAATG 58.252 34.615 18.42 6.19 39.27 2.32
298 309 6.468956 CGGTAAAGATGTGTCACATAAAATGC 59.531 38.462 18.42 5.31 39.27 3.56
301 312 9.190858 GTAAAGATGTGTCACATAAAATGCAAA 57.809 29.630 18.42 0.00 39.27 3.68
303 314 8.659925 AAGATGTGTCACATAAAATGCAAAAA 57.340 26.923 18.42 0.00 39.27 1.94
305 316 9.275398 AGATGTGTCACATAAAATGCAAAAATT 57.725 25.926 18.42 0.00 39.27 1.82
419 432 6.643388 TCTAAATATGCACTCAGAAAGCAGA 58.357 36.000 0.00 0.00 42.14 4.26
487 500 9.213799 GAGATATCTGGATGTTATTCTGAAACC 57.786 37.037 10.74 0.00 0.00 3.27
553 566 1.373246 GCACTGGCCGTACGTACAA 60.373 57.895 24.50 6.84 0.00 2.41
559 572 1.055338 GGCCGTACGTACAATATCGC 58.945 55.000 24.50 14.30 0.00 4.58
608 621 3.758023 CAGCAGAATTGTGGGACAACATA 59.242 43.478 4.57 0.00 44.16 2.29
638 651 9.254133 CTATTTGACTGATCTCGTCAATATTGT 57.746 33.333 22.75 13.60 46.95 2.71
639 652 6.892310 TTGACTGATCTCGTCAATATTGTG 57.108 37.500 20.09 9.28 44.03 3.33
809 835 4.954202 AGGTTGATCTCCTGAATACGTACA 59.046 41.667 0.00 0.00 33.62 2.90
852 878 2.354821 CAGCGCTATAAAAGGAACCCAC 59.645 50.000 10.99 0.00 0.00 4.61
853 879 1.329599 GCGCTATAAAAGGAACCCACG 59.670 52.381 0.00 0.00 0.00 4.94
870 896 0.537188 ACGGACTCCATGCTACCAAG 59.463 55.000 0.00 0.00 0.00 3.61
885 911 1.133199 ACCAAGCCATCCCAAGTTTCA 60.133 47.619 0.00 0.00 0.00 2.69
958 991 1.009829 GCAAGCTCGTTGATACCAGG 58.990 55.000 0.00 0.00 38.60 4.45
983 1016 2.955660 CCTCGAGGTTCTTGATCTAGCT 59.044 50.000 24.04 0.00 0.00 3.32
984 1017 4.138290 CCTCGAGGTTCTTGATCTAGCTA 58.862 47.826 24.04 0.00 0.00 3.32
985 1018 4.215399 CCTCGAGGTTCTTGATCTAGCTAG 59.785 50.000 24.04 15.01 0.00 3.42
986 1019 4.783055 TCGAGGTTCTTGATCTAGCTAGT 58.217 43.478 20.10 8.00 0.00 2.57
988 1021 4.336993 CGAGGTTCTTGATCTAGCTAGTGT 59.663 45.833 20.10 10.51 0.00 3.55
989 1022 5.504994 CGAGGTTCTTGATCTAGCTAGTGTC 60.505 48.000 20.10 18.14 0.00 3.67
990 1023 5.265191 AGGTTCTTGATCTAGCTAGTGTCA 58.735 41.667 20.10 20.20 0.00 3.58
1160 1193 1.283029 CAAGGGCAAGGAGATGGAGAA 59.717 52.381 0.00 0.00 0.00 2.87
1227 1260 1.522668 TCATCGGTGGAAAGCTTGTG 58.477 50.000 0.00 0.00 0.00 3.33
1275 1308 1.151450 CCTTGGTGGTGAGCTGGTT 59.849 57.895 0.00 0.00 0.00 3.67
1368 1401 7.454225 GGATGGATATTTACAGAGCCTAACTT 58.546 38.462 0.00 0.00 0.00 2.66
1407 1440 7.464358 CAAAATAAATAGTCGAAGAGTGTGGG 58.536 38.462 0.00 0.00 42.12 4.61
1409 1442 3.870633 AATAGTCGAAGAGTGTGGGAC 57.129 47.619 0.00 0.00 42.12 4.46
1410 1443 1.162698 TAGTCGAAGAGTGTGGGACG 58.837 55.000 0.00 0.00 42.12 4.79
1411 1444 0.822532 AGTCGAAGAGTGTGGGACGT 60.823 55.000 0.00 0.00 39.65 4.34
1412 1445 0.386985 GTCGAAGAGTGTGGGACGTC 60.387 60.000 7.13 7.13 36.95 4.34
1413 1446 1.442184 CGAAGAGTGTGGGACGTCG 60.442 63.158 9.92 0.00 0.00 5.12
1485 1531 7.497925 AGTCCTACTCTGACAACAAATTTTC 57.502 36.000 0.00 0.00 35.15 2.29
1518 1587 4.816392 TGTAGTAAGCTATGTGTGTGGTG 58.184 43.478 0.00 0.00 0.00 4.17
1638 1711 6.936900 GCTATTGGATATGTGTATGGAGTGTT 59.063 38.462 0.00 0.00 0.00 3.32
1722 1795 4.520179 TGTGATGATCCCAGTGATTCAAG 58.480 43.478 0.00 0.00 32.41 3.02
1730 1803 3.588842 TCCCAGTGATTCAAGTGGAAGAT 59.411 43.478 15.07 0.00 42.44 2.40
1781 1859 5.343307 AAAAATGCATGGGAGGTCATAAC 57.657 39.130 0.00 0.00 0.00 1.89
1788 1866 4.142381 GCATGGGAGGTCATAACACTTTTC 60.142 45.833 0.00 0.00 0.00 2.29
1807 1885 4.345859 TTCTGATAGTGTCGGTTTGGTT 57.654 40.909 0.00 0.00 34.65 3.67
1820 1898 6.037391 TGTCGGTTTGGTTGTAGTTCTTTTAG 59.963 38.462 0.00 0.00 0.00 1.85
1847 1925 3.250040 GCACGTTTAGGTCTCATTTGTGT 59.750 43.478 0.00 0.00 0.00 3.72
1855 1933 9.918630 GTTTAGGTCTCATTTGTGTAGTAAGTA 57.081 33.333 0.00 0.00 0.00 2.24
1864 1942 4.261578 TGTGTAGTAAGTAGCCCAACAC 57.738 45.455 0.00 0.00 37.00 3.32
1912 1990 1.066215 ACCTGCTCGCATGACACATTA 60.066 47.619 0.00 0.00 0.00 1.90
1914 1992 2.223112 CCTGCTCGCATGACACATTAAC 60.223 50.000 0.00 0.00 0.00 2.01
1915 1993 2.416202 CTGCTCGCATGACACATTAACA 59.584 45.455 0.00 0.00 0.00 2.41
1918 1996 3.261580 CTCGCATGACACATTAACAGGA 58.738 45.455 0.00 0.00 0.00 3.86
1921 1999 2.684881 GCATGACACATTAACAGGAGGG 59.315 50.000 0.00 0.00 0.00 4.30
1923 2001 1.702401 TGACACATTAACAGGAGGGCA 59.298 47.619 0.00 0.00 0.00 5.36
1924 2002 2.290260 TGACACATTAACAGGAGGGCAG 60.290 50.000 0.00 0.00 0.00 4.85
1925 2003 1.705186 ACACATTAACAGGAGGGCAGT 59.295 47.619 0.00 0.00 0.00 4.40
1926 2004 2.086869 CACATTAACAGGAGGGCAGTG 58.913 52.381 0.00 0.00 0.00 3.66
1927 2005 1.004745 ACATTAACAGGAGGGCAGTGG 59.995 52.381 0.00 0.00 0.00 4.00
1928 2006 0.034089 ATTAACAGGAGGGCAGTGGC 60.034 55.000 8.47 8.47 40.13 5.01
1929 2007 1.422977 TTAACAGGAGGGCAGTGGCA 61.423 55.000 19.48 0.00 43.71 4.92
2020 2317 5.604650 CACTCTCCATTCCCTAGGTTATCTT 59.395 44.000 8.29 0.00 0.00 2.40
2023 2320 6.453476 TCTCCATTCCCTAGGTTATCTTTCT 58.547 40.000 8.29 0.00 0.00 2.52
2070 2385 1.454847 GGGTTGTTGGCACTGACCA 60.455 57.895 12.64 0.00 38.16 4.02
2084 2399 2.159043 ACTGACCAGCCAAGACATATCG 60.159 50.000 0.00 0.00 0.00 2.92
2100 2415 0.603569 ATCGTCGTTGAGTTGCCTCT 59.396 50.000 0.00 0.00 38.61 3.69
2113 2428 0.770499 TGCCTCTGACCCATGAACAA 59.230 50.000 0.00 0.00 0.00 2.83
2117 2432 3.875369 GCCTCTGACCCATGAACAATTCT 60.875 47.826 0.00 0.00 0.00 2.40
2273 2610 3.186205 TCACGCATGCATATGGTAATTCG 59.814 43.478 19.57 0.00 34.79 3.34
2283 2620 8.404889 TGCATATGGTAATTCGACAAATTTTG 57.595 30.769 7.59 7.59 38.53 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.635663 CCTACCGCCTGCTCGTTTTG 61.636 60.000 0.00 0.00 0.00 2.44
1 2 1.375523 CCTACCGCCTGCTCGTTTT 60.376 57.895 0.00 0.00 0.00 2.43
2 3 2.264794 CCTACCGCCTGCTCGTTT 59.735 61.111 0.00 0.00 0.00 3.60
3 4 2.678934 TCCTACCGCCTGCTCGTT 60.679 61.111 0.00 0.00 0.00 3.85
4 5 3.450115 GTCCTACCGCCTGCTCGT 61.450 66.667 0.00 0.00 0.00 4.18
5 6 2.711922 AAGTCCTACCGCCTGCTCG 61.712 63.158 0.00 0.00 0.00 5.03
6 7 1.153549 CAAGTCCTACCGCCTGCTC 60.154 63.158 0.00 0.00 0.00 4.26
7 8 2.660064 CCAAGTCCTACCGCCTGCT 61.660 63.158 0.00 0.00 0.00 4.24
8 9 2.125106 CCAAGTCCTACCGCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
9 10 2.125106 GCCAAGTCCTACCGCCTG 60.125 66.667 0.00 0.00 0.00 4.85
10 11 2.606519 TGCCAAGTCCTACCGCCT 60.607 61.111 0.00 0.00 0.00 5.52
11 12 2.125106 CTGCCAAGTCCTACCGCC 60.125 66.667 0.00 0.00 0.00 6.13
12 13 2.125106 CCTGCCAAGTCCTACCGC 60.125 66.667 0.00 0.00 0.00 5.68
13 14 1.079127 CACCTGCCAAGTCCTACCG 60.079 63.158 0.00 0.00 0.00 4.02
14 15 0.250513 CTCACCTGCCAAGTCCTACC 59.749 60.000 0.00 0.00 0.00 3.18
15 16 0.977395 ACTCACCTGCCAAGTCCTAC 59.023 55.000 0.00 0.00 0.00 3.18
16 17 0.976641 CACTCACCTGCCAAGTCCTA 59.023 55.000 0.00 0.00 0.00 2.94
17 18 1.056700 ACACTCACCTGCCAAGTCCT 61.057 55.000 0.00 0.00 0.00 3.85
18 19 0.179018 AACACTCACCTGCCAAGTCC 60.179 55.000 0.00 0.00 0.00 3.85
19 20 1.230324 GAACACTCACCTGCCAAGTC 58.770 55.000 0.00 0.00 0.00 3.01
20 21 0.179018 GGAACACTCACCTGCCAAGT 60.179 55.000 0.00 0.00 0.00 3.16
21 22 0.890996 GGGAACACTCACCTGCCAAG 60.891 60.000 0.00 0.00 0.00 3.61
22 23 1.150536 GGGAACACTCACCTGCCAA 59.849 57.895 0.00 0.00 0.00 4.52
23 24 2.836154 GGGAACACTCACCTGCCA 59.164 61.111 0.00 0.00 0.00 4.92
24 25 2.358737 CGGGAACACTCACCTGCC 60.359 66.667 0.00 0.00 0.00 4.85
26 27 1.961277 GTGCGGGAACACTCACCTG 60.961 63.158 0.00 0.00 37.58 4.00
27 28 2.426023 GTGCGGGAACACTCACCT 59.574 61.111 0.00 0.00 37.58 4.00
33 34 4.214758 ACAATTACTTAAGTGCGGGAACAC 59.785 41.667 18.56 0.00 41.02 3.32
34 35 4.214545 CACAATTACTTAAGTGCGGGAACA 59.785 41.667 18.56 0.00 34.90 3.18
35 36 4.719040 CACAATTACTTAAGTGCGGGAAC 58.281 43.478 18.56 0.00 34.90 3.62
36 37 3.189702 GCACAATTACTTAAGTGCGGGAA 59.810 43.478 18.56 4.31 46.35 3.97
37 38 2.745281 GCACAATTACTTAAGTGCGGGA 59.255 45.455 18.56 0.00 46.35 5.14
38 39 3.131240 GCACAATTACTTAAGTGCGGG 57.869 47.619 18.56 7.83 46.35 6.13
42 43 4.404507 AGTGCGCACAATTACTTAAGTG 57.595 40.909 39.21 3.83 37.30 3.16
43 44 4.083484 GGAAGTGCGCACAATTACTTAAGT 60.083 41.667 39.21 13.68 33.46 2.24
44 45 4.403453 GGAAGTGCGCACAATTACTTAAG 58.597 43.478 39.21 0.00 33.46 1.85
45 46 3.120477 CGGAAGTGCGCACAATTACTTAA 60.120 43.478 39.21 0.00 32.38 1.85
46 47 2.413796 CGGAAGTGCGCACAATTACTTA 59.586 45.455 39.21 0.00 32.38 2.24
47 48 1.196808 CGGAAGTGCGCACAATTACTT 59.803 47.619 39.21 24.75 32.38 2.24
48 49 0.796312 CGGAAGTGCGCACAATTACT 59.204 50.000 39.21 17.54 32.38 2.24
49 50 0.179200 CCGGAAGTGCGCACAATTAC 60.179 55.000 39.21 25.90 33.46 1.89
50 51 1.917782 GCCGGAAGTGCGCACAATTA 61.918 55.000 39.21 0.00 33.46 1.40
51 52 2.953821 CCGGAAGTGCGCACAATT 59.046 55.556 39.21 26.96 36.65 2.32
52 53 3.737172 GCCGGAAGTGCGCACAAT 61.737 61.111 39.21 28.33 0.00 2.71
55 56 4.166011 GATGCCGGAAGTGCGCAC 62.166 66.667 32.79 32.79 34.87 5.34
56 57 4.695993 TGATGCCGGAAGTGCGCA 62.696 61.111 5.66 5.66 36.84 6.09
57 58 2.470801 TTTTGATGCCGGAAGTGCGC 62.471 55.000 5.05 0.00 0.00 6.09
58 59 0.171007 ATTTTGATGCCGGAAGTGCG 59.829 50.000 5.05 0.00 0.00 5.34
59 60 1.202114 TCATTTTGATGCCGGAAGTGC 59.798 47.619 5.05 0.00 0.00 4.40
60 61 3.788333 ATCATTTTGATGCCGGAAGTG 57.212 42.857 5.05 0.00 35.43 3.16
61 62 4.269183 TGTATCATTTTGATGCCGGAAGT 58.731 39.130 5.05 0.00 38.48 3.01
62 63 4.898829 TGTATCATTTTGATGCCGGAAG 57.101 40.909 5.05 0.00 38.48 3.46
63 64 5.649557 CTTTGTATCATTTTGATGCCGGAA 58.350 37.500 5.05 0.00 38.48 4.30
64 65 4.439974 GCTTTGTATCATTTTGATGCCGGA 60.440 41.667 5.05 0.00 38.48 5.14
65 66 3.798337 GCTTTGTATCATTTTGATGCCGG 59.202 43.478 0.00 0.00 38.48 6.13
66 67 4.422840 TGCTTTGTATCATTTTGATGCCG 58.577 39.130 0.30 0.00 38.48 5.69
67 68 8.492748 CATTATGCTTTGTATCATTTTGATGCC 58.507 33.333 0.30 0.00 38.48 4.40
68 69 9.251792 TCATTATGCTTTGTATCATTTTGATGC 57.748 29.630 0.30 0.00 37.70 3.91
70 71 9.472361 GCTCATTATGCTTTGTATCATTTTGAT 57.528 29.630 0.00 0.00 40.72 2.57
71 72 7.644945 CGCTCATTATGCTTTGTATCATTTTGA 59.355 33.333 0.00 0.00 0.00 2.69
72 73 7.644945 TCGCTCATTATGCTTTGTATCATTTTG 59.355 33.333 0.00 0.00 0.00 2.44
73 74 7.645340 GTCGCTCATTATGCTTTGTATCATTTT 59.355 33.333 0.00 0.00 0.00 1.82
74 75 7.134815 GTCGCTCATTATGCTTTGTATCATTT 58.865 34.615 0.00 0.00 0.00 2.32
75 76 6.260714 TGTCGCTCATTATGCTTTGTATCATT 59.739 34.615 0.00 0.00 0.00 2.57
76 77 5.759763 TGTCGCTCATTATGCTTTGTATCAT 59.240 36.000 0.00 0.00 0.00 2.45
77 78 5.115480 TGTCGCTCATTATGCTTTGTATCA 58.885 37.500 0.00 0.00 0.00 2.15
78 79 5.235186 ACTGTCGCTCATTATGCTTTGTATC 59.765 40.000 0.00 0.00 0.00 2.24
79 80 5.118990 ACTGTCGCTCATTATGCTTTGTAT 58.881 37.500 0.00 0.00 0.00 2.29
80 81 4.503910 ACTGTCGCTCATTATGCTTTGTA 58.496 39.130 0.00 0.00 0.00 2.41
81 82 3.338249 ACTGTCGCTCATTATGCTTTGT 58.662 40.909 0.00 0.00 0.00 2.83
82 83 3.620374 AGACTGTCGCTCATTATGCTTTG 59.380 43.478 1.52 0.00 0.00 2.77
83 84 3.866651 AGACTGTCGCTCATTATGCTTT 58.133 40.909 1.52 0.00 0.00 3.51
84 85 3.533606 AGACTGTCGCTCATTATGCTT 57.466 42.857 1.52 0.00 0.00 3.91
85 86 4.142160 TGTTAGACTGTCGCTCATTATGCT 60.142 41.667 1.52 0.00 0.00 3.79
86 87 4.026475 GTGTTAGACTGTCGCTCATTATGC 60.026 45.833 1.52 0.00 0.00 3.14
87 88 5.102313 TGTGTTAGACTGTCGCTCATTATG 58.898 41.667 1.52 0.00 0.00 1.90
88 89 5.324784 TGTGTTAGACTGTCGCTCATTAT 57.675 39.130 1.52 0.00 0.00 1.28
89 90 4.776795 TGTGTTAGACTGTCGCTCATTA 57.223 40.909 1.52 0.00 0.00 1.90
90 91 3.660501 TGTGTTAGACTGTCGCTCATT 57.339 42.857 1.52 0.00 0.00 2.57
91 92 3.660501 TTGTGTTAGACTGTCGCTCAT 57.339 42.857 1.52 0.00 0.00 2.90
92 93 3.120792 GTTTGTGTTAGACTGTCGCTCA 58.879 45.455 1.52 0.43 0.00 4.26
93 94 3.120792 TGTTTGTGTTAGACTGTCGCTC 58.879 45.455 1.52 0.00 0.00 5.03
94 95 3.123804 CTGTTTGTGTTAGACTGTCGCT 58.876 45.455 1.52 0.00 0.00 4.93
95 96 2.864343 ACTGTTTGTGTTAGACTGTCGC 59.136 45.455 1.52 0.00 0.00 5.19
96 97 4.207224 CAGACTGTTTGTGTTAGACTGTCG 59.793 45.833 1.52 0.00 43.02 4.35
97 98 5.232414 GTCAGACTGTTTGTGTTAGACTGTC 59.768 44.000 1.59 0.00 40.42 3.51
104 105 5.912892 TCTCATGTCAGACTGTTTGTGTTA 58.087 37.500 1.59 0.00 0.00 2.41
146 148 7.969536 ACATCAAATTTCGGTCCTATATCTG 57.030 36.000 0.00 0.00 0.00 2.90
349 362 0.389391 AATCGATCGACGGCCTGATT 59.611 50.000 22.06 5.15 42.82 2.57
408 421 3.627577 GGTTCAAGTTGTCTGCTTTCTGA 59.372 43.478 2.11 0.00 0.00 3.27
410 423 2.614057 CGGTTCAAGTTGTCTGCTTTCT 59.386 45.455 2.11 0.00 0.00 2.52
419 432 2.290641 GCACAGAATCGGTTCAAGTTGT 59.709 45.455 11.72 3.08 36.79 3.32
553 566 5.183228 CGGGGAATACCAAATTAGCGATAT 58.817 41.667 0.00 0.00 42.91 1.63
559 572 3.800531 ACGACGGGGAATACCAAATTAG 58.199 45.455 0.00 0.00 42.91 1.73
608 621 4.158579 TGACGAGATCAGTCAAATAGCTGT 59.841 41.667 17.93 0.00 44.56 4.40
639 652 4.799824 ATTTGGCCATGTGCGCGC 62.800 61.111 27.26 27.26 42.61 6.86
722 743 5.978814 ACTTCGGAATATTAGCTTGTGTCT 58.021 37.500 0.00 0.00 0.00 3.41
809 835 2.024414 GCAGGTTGGTTGAAAGAGTGT 58.976 47.619 0.00 0.00 0.00 3.55
852 878 0.811616 GCTTGGTAGCATGGAGTCCG 60.812 60.000 4.30 0.00 46.95 4.79
853 879 3.086733 GCTTGGTAGCATGGAGTCC 57.913 57.895 0.73 0.73 46.95 3.85
870 896 1.114627 GGGATGAAACTTGGGATGGC 58.885 55.000 0.00 0.00 0.00 4.40
885 911 2.664402 AGTTTGTGCTTCTGTGGGAT 57.336 45.000 0.00 0.00 0.00 3.85
958 991 2.003301 GATCAAGAACCTCGAGGCAAC 58.997 52.381 31.56 21.05 39.32 4.17
983 1016 1.489481 CATCTCTGCCCCTGACACTA 58.511 55.000 0.00 0.00 0.00 2.74
984 1017 1.270414 CCATCTCTGCCCCTGACACT 61.270 60.000 0.00 0.00 0.00 3.55
985 1018 1.222936 CCATCTCTGCCCCTGACAC 59.777 63.158 0.00 0.00 0.00 3.67
986 1019 1.080907 TCCATCTCTGCCCCTGACA 59.919 57.895 0.00 0.00 0.00 3.58
988 1021 1.690633 GGTCCATCTCTGCCCCTGA 60.691 63.158 0.00 0.00 0.00 3.86
989 1022 2.914289 GGTCCATCTCTGCCCCTG 59.086 66.667 0.00 0.00 0.00 4.45
990 1023 2.765807 CGGTCCATCTCTGCCCCT 60.766 66.667 0.00 0.00 0.00 4.79
1275 1308 1.072173 CCTGCATTCCGTATCATGGGA 59.928 52.381 0.00 0.00 0.00 4.37
1368 1401 0.322322 ATTTTGCCGAGTGGTACCGA 59.678 50.000 7.57 0.00 37.67 4.69
1407 1440 5.204101 GCTCTTAGGTTATTCTACGACGTC 58.796 45.833 2.43 5.18 0.00 4.34
1409 1442 4.275443 AGGCTCTTAGGTTATTCTACGACG 59.725 45.833 0.00 0.00 0.00 5.12
1410 1443 5.771153 AGGCTCTTAGGTTATTCTACGAC 57.229 43.478 0.00 0.00 0.00 4.34
1411 1444 7.059156 ACTTAGGCTCTTAGGTTATTCTACGA 58.941 38.462 0.00 0.00 0.00 3.43
1412 1445 7.274603 ACTTAGGCTCTTAGGTTATTCTACG 57.725 40.000 0.00 0.00 0.00 3.51
1413 1446 9.353431 ACTACTTAGGCTCTTAGGTTATTCTAC 57.647 37.037 0.00 0.00 0.00 2.59
1485 1531 9.709600 CACATAGCTTACTACATATAGTGATCG 57.290 37.037 0.00 0.00 41.92 3.69
1512 1581 4.838423 ACCTAGCTATATGCATACACCACA 59.162 41.667 8.99 0.00 45.94 4.17
1513 1582 5.407407 ACCTAGCTATATGCATACACCAC 57.593 43.478 8.99 0.00 45.94 4.16
1518 1587 7.301054 CAAAAGCAACCTAGCTATATGCATAC 58.699 38.462 20.79 0.00 45.89 2.39
1673 1746 3.616560 GCTCTTGACAAGGTTCCACGATA 60.617 47.826 15.13 0.00 0.00 2.92
1674 1747 2.872038 GCTCTTGACAAGGTTCCACGAT 60.872 50.000 15.13 0.00 0.00 3.73
1675 1748 1.540363 GCTCTTGACAAGGTTCCACGA 60.540 52.381 15.13 0.00 0.00 4.35
1676 1749 0.868406 GCTCTTGACAAGGTTCCACG 59.132 55.000 15.13 0.00 0.00 4.94
1677 1750 1.967319 TGCTCTTGACAAGGTTCCAC 58.033 50.000 15.13 0.31 0.00 4.02
1678 1751 2.957402 ATGCTCTTGACAAGGTTCCA 57.043 45.000 15.13 7.67 0.00 3.53
1686 1759 5.761726 GGATCATCACATTATGCTCTTGACA 59.238 40.000 0.00 0.00 0.00 3.58
1722 1795 4.124851 ACCGTGTCATTCTATCTTCCAC 57.875 45.455 0.00 0.00 0.00 4.02
1760 1833 4.160252 GTGTTATGACCTCCCATGCATTTT 59.840 41.667 0.00 0.00 0.00 1.82
1761 1834 3.701040 GTGTTATGACCTCCCATGCATTT 59.299 43.478 0.00 0.00 0.00 2.32
1762 1835 3.053395 AGTGTTATGACCTCCCATGCATT 60.053 43.478 0.00 0.00 0.00 3.56
1766 1839 5.124457 CAGAAAAGTGTTATGACCTCCCATG 59.876 44.000 0.00 0.00 0.00 3.66
1781 1859 5.334105 CCAAACCGACACTATCAGAAAAGTG 60.334 44.000 12.62 12.62 46.84 3.16
1788 1866 3.399330 ACAACCAAACCGACACTATCAG 58.601 45.455 0.00 0.00 0.00 2.90
1807 1885 6.854496 ACGTGCATTTCTAAAAGAACTACA 57.146 33.333 0.00 0.00 33.26 2.74
1820 1898 4.946784 ATGAGACCTAAACGTGCATTTC 57.053 40.909 0.00 0.00 0.00 2.17
1847 1925 4.020839 GGAACAGTGTTGGGCTACTTACTA 60.021 45.833 14.57 0.00 0.00 1.82
1855 1933 0.846693 AGAAGGAACAGTGTTGGGCT 59.153 50.000 14.57 2.47 0.00 5.19
1864 1942 1.901085 CTCGGGGGAGAAGGAACAG 59.099 63.158 0.00 0.00 0.00 3.16
1887 1965 1.080995 GTCATGCGAGCAGGTCAGAC 61.081 60.000 9.57 5.82 0.00 3.51
1912 1990 3.177884 TGCCACTGCCCTCCTGTT 61.178 61.111 0.00 0.00 36.33 3.16
1914 1992 4.421515 CCTGCCACTGCCCTCCTG 62.422 72.222 0.00 0.00 36.33 3.86
1915 1993 4.664267 TCCTGCCACTGCCCTCCT 62.664 66.667 0.00 0.00 36.33 3.69
1918 1996 2.011617 AAAACTCCTGCCACTGCCCT 62.012 55.000 0.00 0.00 36.33 5.19
1921 1999 1.527433 GGGAAAACTCCTGCCACTGC 61.527 60.000 0.00 0.00 38.26 4.40
1923 2001 1.073199 CGGGAAAACTCCTGCCACT 59.927 57.895 0.00 0.00 0.00 4.00
1924 2002 3.668386 CGGGAAAACTCCTGCCAC 58.332 61.111 0.00 0.00 0.00 5.01
2020 2317 0.325296 ACCGGAGTAGGGCATGAGAA 60.325 55.000 9.46 0.00 35.02 2.87
2023 2320 1.117150 GTTACCGGAGTAGGGCATGA 58.883 55.000 9.46 0.00 35.02 3.07
2070 2385 2.165641 TCAACGACGATATGTCTTGGCT 59.834 45.455 0.00 0.00 45.87 4.75
2076 2391 2.281762 GGCAACTCAACGACGATATGTC 59.718 50.000 0.00 0.00 44.53 3.06
2094 2409 0.770499 TTGTTCATGGGTCAGAGGCA 59.230 50.000 0.00 0.00 0.00 4.75
2100 2415 2.039746 ACCGAGAATTGTTCATGGGTCA 59.960 45.455 0.00 0.00 32.43 4.02
2113 2428 0.815734 ATTCGTCACCGACCGAGAAT 59.184 50.000 0.00 0.00 44.13 2.40
2117 2432 1.425031 CGTATTCGTCACCGACCGA 59.575 57.895 0.00 0.00 44.13 4.69
2149 2464 1.022735 ACCACTATCGGTCAGCTACG 58.977 55.000 0.00 0.00 32.11 3.51
2163 2478 1.435256 AAACTGACTAGGCCACCACT 58.565 50.000 5.01 0.00 0.00 4.00
2164 2479 3.270877 CATAAACTGACTAGGCCACCAC 58.729 50.000 5.01 0.00 0.00 4.16
2165 2480 2.238646 CCATAAACTGACTAGGCCACCA 59.761 50.000 5.01 0.00 0.00 4.17
2166 2481 2.504175 TCCATAAACTGACTAGGCCACC 59.496 50.000 5.01 0.00 0.00 4.61
2273 2610 8.357402 ACTACTTACACCAATCCAAAATTTGTC 58.643 33.333 4.92 0.00 0.00 3.18
2283 2620 7.438459 CACATAGCTTACTACTTACACCAATCC 59.562 40.741 0.00 0.00 0.00 3.01
2287 2624 5.186215 TGCACATAGCTTACTACTTACACCA 59.814 40.000 0.00 0.00 45.94 4.17


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

AutoCloner maintained by Alex Coulton.