Multiple sequence alignment - TraesCS3A01G324700

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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 TraesCS3A01G324700 chr3A 100.000 2817 0 0 1 2817 569389657 569386841 0.000000e+00 5203.0
1 TraesCS3A01G324700 chr3A 93.921 806 43 3 2018 2817 696213937 696214742 0.000000e+00 1212.0
2 TraesCS3A01G324700 chr3D 92.602 1987 103 24 49 2010 432021537 432019570 0.000000e+00 2815.0
3 TraesCS3A01G324700 chr3D 88.889 54 6 0 3 56 586434063 586434116 1.810000e-07 67.6
4 TraesCS3A01G324700 chr3D 87.273 55 5 2 4 57 475933864 475933917 8.430000e-06 62.1
5 TraesCS3A01G324700 chr3B 91.998 1912 108 22 49 1928 564203795 564201897 0.000000e+00 2641.0
6 TraesCS3A01G324700 chr3B 88.406 69 5 2 141 209 19881233 19881168 2.330000e-11 80.5
7 TraesCS3A01G324700 chr1A 94.293 806 39 6 2018 2817 279702975 279703779 0.000000e+00 1227.0
8 TraesCS3A01G324700 chr1A 93.696 809 47 3 2013 2817 497100109 497100917 0.000000e+00 1208.0
9 TraesCS3A01G324700 chr4A 94.161 805 42 4 2018 2817 632834205 632833401 0.000000e+00 1221.0
10 TraesCS3A01G324700 chr7A 94.140 802 45 2 2018 2817 610893401 610894202 0.000000e+00 1219.0
11 TraesCS3A01G324700 chr7A 88.000 50 6 0 4 53 670301437 670301388 3.030000e-05 60.2
12 TraesCS3A01G324700 chr6A 94.154 804 42 3 2016 2817 520170497 520169697 0.000000e+00 1219.0
13 TraesCS3A01G324700 chr6A 94.147 803 42 4 2018 2817 604376479 604377279 0.000000e+00 1218.0
14 TraesCS3A01G324700 chr6A 88.889 54 5 1 3 56 185326993 185327045 6.510000e-07 65.8
15 TraesCS3A01G324700 chr6A 87.273 55 6 1 4 58 505351588 505351535 8.430000e-06 62.1
16 TraesCS3A01G324700 chr2A 93.921 806 43 6 2018 2817 748358614 748359419 0.000000e+00 1212.0
17 TraesCS3A01G324700 chr2A 93.204 824 46 8 2004 2817 720453695 720454518 0.000000e+00 1203.0
18 TraesCS3A01G324700 chr4D 87.931 58 4 3 2 57 123953002 123953058 6.510000e-07 65.8
19 TraesCS3A01G324700 chr6D 87.037 54 5 2 4 56 27532772 27532824 3.030000e-05 60.2
20 TraesCS3A01G324700 chr1D 88.235 51 4 2 4 53 32539708 32539757 3.030000e-05 60.2
21 TraesCS3A01G324700 chr6B 85.455 55 7 1 1 54 681238686 681238632 3.920000e-04 56.5


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 TraesCS3A01G324700 chr3A 569386841 569389657 2816 True 5203 5203 100.000 1 2817 1 chr3A.!!$R1 2816
1 TraesCS3A01G324700 chr3A 696213937 696214742 805 False 1212 1212 93.921 2018 2817 1 chr3A.!!$F1 799
2 TraesCS3A01G324700 chr3D 432019570 432021537 1967 True 2815 2815 92.602 49 2010 1 chr3D.!!$R1 1961
3 TraesCS3A01G324700 chr3B 564201897 564203795 1898 True 2641 2641 91.998 49 1928 1 chr3B.!!$R2 1879
4 TraesCS3A01G324700 chr1A 279702975 279703779 804 False 1227 1227 94.293 2018 2817 1 chr1A.!!$F1 799
5 TraesCS3A01G324700 chr1A 497100109 497100917 808 False 1208 1208 93.696 2013 2817 1 chr1A.!!$F2 804
6 TraesCS3A01G324700 chr4A 632833401 632834205 804 True 1221 1221 94.161 2018 2817 1 chr4A.!!$R1 799
7 TraesCS3A01G324700 chr7A 610893401 610894202 801 False 1219 1219 94.140 2018 2817 1 chr7A.!!$F1 799
8 TraesCS3A01G324700 chr6A 520169697 520170497 800 True 1219 1219 94.154 2016 2817 1 chr6A.!!$R2 801
9 TraesCS3A01G324700 chr6A 604376479 604377279 800 False 1218 1218 94.147 2018 2817 1 chr6A.!!$F2 799
10 TraesCS3A01G324700 chr2A 748358614 748359419 805 False 1212 1212 93.921 2018 2817 1 chr2A.!!$F2 799
11 TraesCS3A01G324700 chr2A 720453695 720454518 823 False 1203 1203 93.204 2004 2817 1 chr2A.!!$F1 813

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
117 118 0.031585 TAGATCGTGTATGGGCGCAC 59.968 55.0 10.83 6.04 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2013 0.033011 AGGACTAGCTGACGGATGGT 60.033 55.0 0.0 0.0 0.0 3.55 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 4.841441 AAAAATGGCCTGGCGAGA 57.159 50.000 13.40 0.00 0.00 4.04
21 22 2.267045 AAAAATGGCCTGGCGAGAC 58.733 52.632 13.40 0.00 0.00 3.36
22 23 1.250840 AAAAATGGCCTGGCGAGACC 61.251 55.000 13.40 0.00 39.84 3.85
23 24 2.142292 AAAATGGCCTGGCGAGACCT 62.142 55.000 13.40 0.00 40.22 3.85
24 25 1.271840 AAATGGCCTGGCGAGACCTA 61.272 55.000 13.40 0.00 40.22 3.08
25 26 1.056700 AATGGCCTGGCGAGACCTAT 61.057 55.000 13.40 0.00 40.22 2.57
26 27 1.056700 ATGGCCTGGCGAGACCTATT 61.057 55.000 13.40 0.00 40.22 1.73
27 28 0.397957 TGGCCTGGCGAGACCTATTA 60.398 55.000 13.40 0.00 40.22 0.98
28 29 0.318762 GGCCTGGCGAGACCTATTAG 59.681 60.000 13.40 0.00 40.22 1.73
29 30 0.318762 GCCTGGCGAGACCTATTAGG 59.681 60.000 1.35 8.25 42.49 2.69
30 31 0.969894 CCTGGCGAGACCTATTAGGG 59.030 60.000 14.26 0.00 40.58 3.53
31 32 0.969894 CTGGCGAGACCTATTAGGGG 59.030 60.000 14.26 2.04 40.58 4.79
32 33 1.119574 TGGCGAGACCTATTAGGGGC 61.120 60.000 14.26 10.72 40.58 5.80
33 34 1.289380 GCGAGACCTATTAGGGGCG 59.711 63.158 14.26 13.79 40.58 6.13
34 35 1.289380 CGAGACCTATTAGGGGCGC 59.711 63.158 14.26 0.00 40.58 6.53
35 36 1.289380 GAGACCTATTAGGGGCGCG 59.711 63.158 14.26 0.00 40.58 6.86
36 37 2.156051 GAGACCTATTAGGGGCGCGG 62.156 65.000 14.26 0.00 40.58 6.46
37 38 3.878374 GACCTATTAGGGGCGCGGC 62.878 68.421 26.39 26.39 40.58 6.53
38 39 3.626924 CCTATTAGGGGCGCGGCT 61.627 66.667 32.30 16.42 0.00 5.52
39 40 2.357517 CTATTAGGGGCGCGGCTG 60.358 66.667 32.30 9.89 0.00 4.85
40 41 3.883744 CTATTAGGGGCGCGGCTGG 62.884 68.421 32.30 10.36 0.00 4.85
63 64 3.369381 GCTCTTAGCATCTTGGCGA 57.631 52.632 0.00 0.00 41.89 5.54
78 79 1.867615 GCGATCAGCTCCATCATGC 59.132 57.895 0.00 0.00 44.04 4.06
80 81 1.880271 CGATCAGCTCCATCATGCTT 58.120 50.000 0.00 0.00 37.44 3.91
82 83 2.573369 GATCAGCTCCATCATGCTTGT 58.427 47.619 0.00 0.00 37.44 3.16
99 100 2.031314 TTTGCTCCGGCGCAGTTA 59.969 55.556 19.90 1.58 41.55 2.24
117 118 0.031585 TAGATCGTGTATGGGCGCAC 59.968 55.000 10.83 6.04 0.00 5.34
125 126 3.284133 TATGGGCGCACGACACGAA 62.284 57.895 10.83 0.00 0.00 3.85
135 136 1.372004 CGACACGAACGGGCAGTAA 60.372 57.895 0.00 0.00 0.00 2.24
145 146 0.107410 CGGGCAGTAACATGGGCTTA 60.107 55.000 0.00 0.00 0.00 3.09
158 159 1.754621 GGCTTAAAGCTCCCCTGCC 60.755 63.158 0.00 0.00 41.99 4.85
183 184 6.694445 AAGGAAGAAGAAGAAATCCTCAGA 57.306 37.500 0.00 0.00 39.56 3.27
187 188 4.831107 AGAAGAAGAAATCCTCAGACTGC 58.169 43.478 0.00 0.00 0.00 4.40
200 201 1.068264 CAGACTGCTGAGTTCGCTACA 60.068 52.381 0.00 0.00 45.17 2.74
210 211 6.592220 TGCTGAGTTCGCTACATTGTAAAATA 59.408 34.615 0.00 0.00 0.00 1.40
211 212 7.279981 TGCTGAGTTCGCTACATTGTAAAATAT 59.720 33.333 0.00 0.00 0.00 1.28
212 213 7.584123 GCTGAGTTCGCTACATTGTAAAATATG 59.416 37.037 0.00 0.00 0.00 1.78
252 272 9.914131 GAAAATAATAACAAGCCTGAAGAAACT 57.086 29.630 0.00 0.00 0.00 2.66
271 291 4.758251 TGACATGACCTGGCGGCG 62.758 66.667 0.51 0.51 34.57 6.46
307 336 4.409588 CGAACACTTGGACGCGCG 62.410 66.667 30.96 30.96 0.00 6.86
390 419 2.024871 CATCTCCGTCGTCCTCGC 59.975 66.667 0.00 0.00 36.96 5.03
429 458 2.242572 CCCGATCGCACATGCTCTG 61.243 63.158 10.32 0.00 39.32 3.35
430 459 2.242572 CCGATCGCACATGCTCTGG 61.243 63.158 10.32 0.00 39.32 3.86
431 460 1.227060 CGATCGCACATGCTCTGGA 60.227 57.895 0.26 0.00 39.32 3.86
464 493 1.534175 GCTCTCGAGTGTTCCATACCG 60.534 57.143 13.13 0.00 0.00 4.02
492 521 3.390521 ACGCTCTTGGCCGGATCA 61.391 61.111 5.05 0.00 37.74 2.92
778 807 0.603172 AGAGATGCATGATCGGCTGC 60.603 55.000 2.46 8.80 36.04 5.25
808 837 1.594833 GGACGTATGCACAGGGTGA 59.405 57.895 0.00 0.00 35.23 4.02
809 838 0.178068 GGACGTATGCACAGGGTGAT 59.822 55.000 0.00 0.00 35.23 3.06
811 840 0.107703 ACGTATGCACAGGGTGATGG 60.108 55.000 0.00 0.00 35.23 3.51
812 841 1.439353 CGTATGCACAGGGTGATGGC 61.439 60.000 0.00 0.00 35.23 4.40
852 881 5.172205 GGATCTGTTCTACTGGTTGTTCTC 58.828 45.833 0.00 0.00 0.00 2.87
881 910 0.323957 GCGTACCAACTCCTTCCCTT 59.676 55.000 0.00 0.00 0.00 3.95
882 911 1.944430 GCGTACCAACTCCTTCCCTTG 60.944 57.143 0.00 0.00 0.00 3.61
883 912 1.822506 GTACCAACTCCTTCCCTTGC 58.177 55.000 0.00 0.00 0.00 4.01
884 913 0.696501 TACCAACTCCTTCCCTTGCC 59.303 55.000 0.00 0.00 0.00 4.52
885 914 1.068352 ACCAACTCCTTCCCTTGCCT 61.068 55.000 0.00 0.00 0.00 4.75
937 966 2.253452 CTCTTGCACGCTGGTTGC 59.747 61.111 0.00 0.00 38.57 4.17
973 1002 3.075005 GCTCGGGGTGCACCTCTA 61.075 66.667 32.52 21.96 40.03 2.43
1290 1321 3.213506 ACTGTGCAGCATTCAAGTACAA 58.786 40.909 0.00 0.00 0.00 2.41
1292 1323 2.948315 TGTGCAGCATTCAAGTACAACA 59.052 40.909 0.00 0.00 0.00 3.33
1323 1354 2.742372 CCTTGAAGTGACCGCCGG 60.742 66.667 0.00 0.00 0.00 6.13
1336 1367 4.971125 GCCGGCGACTATGAGGCC 62.971 72.222 12.58 0.00 41.81 5.19
1342 1373 1.007964 CGACTATGAGGCCTGCTCG 60.008 63.158 12.00 4.75 0.00 5.03
1389 1420 4.697756 CGGCACCACCACCATCGT 62.698 66.667 0.00 0.00 39.03 3.73
1556 1587 2.261671 CACCGGTTCCGAGGACAG 59.738 66.667 2.97 0.00 0.00 3.51
1559 1590 2.995574 CGGTTCCGAGGACAGGGT 60.996 66.667 5.19 0.00 0.00 4.34
1874 1905 2.305927 ACATCCCTGTTCTCGTCCATTT 59.694 45.455 0.00 0.00 28.70 2.32
1915 1952 3.999663 GTGAGGTGAGATTTGTTGAGAGG 59.000 47.826 0.00 0.00 0.00 3.69
1932 1969 5.945310 TGAGAGGCCTGATAATAATTGCTT 58.055 37.500 12.00 0.00 0.00 3.91
1946 1983 7.880160 AATAATTGCTTGTTATGGTGAGCTA 57.120 32.000 0.00 0.00 36.16 3.32
1957 1994 4.970860 ATGGTGAGCTATATGCAGTCTT 57.029 40.909 0.00 0.00 45.94 3.01
1959 1996 4.445453 TGGTGAGCTATATGCAGTCTTTG 58.555 43.478 0.00 0.00 45.94 2.77
1962 1999 3.455910 TGAGCTATATGCAGTCTTTGGGT 59.544 43.478 0.00 0.00 45.94 4.51
1963 2000 4.080356 TGAGCTATATGCAGTCTTTGGGTT 60.080 41.667 0.00 0.00 45.94 4.11
1973 2010 4.393371 GCAGTCTTTGGGTTGAGATTACTC 59.607 45.833 0.00 0.00 42.88 2.59
1976 2013 3.007506 TCTTTGGGTTGAGATTACTCGCA 59.992 43.478 0.00 0.00 45.25 5.10
1978 2015 1.066430 TGGGTTGAGATTACTCGCACC 60.066 52.381 0.00 0.00 45.25 5.01
1979 2016 1.066430 GGGTTGAGATTACTCGCACCA 60.066 52.381 15.43 0.00 44.38 4.17
1980 2017 2.420129 GGGTTGAGATTACTCGCACCAT 60.420 50.000 15.43 0.00 44.38 3.55
1997 2037 1.686355 CATCCGTCAGCTAGTCCTCT 58.314 55.000 0.00 0.00 0.00 3.69
1998 2038 1.336440 CATCCGTCAGCTAGTCCTCTG 59.664 57.143 0.00 0.00 0.00 3.35
1999 2039 0.328592 TCCGTCAGCTAGTCCTCTGT 59.671 55.000 0.00 0.00 0.00 3.41
2000 2040 0.736053 CCGTCAGCTAGTCCTCTGTC 59.264 60.000 0.00 0.00 0.00 3.51
2001 2041 0.736053 CGTCAGCTAGTCCTCTGTCC 59.264 60.000 0.00 0.00 0.00 4.02
2002 2042 1.680555 CGTCAGCTAGTCCTCTGTCCT 60.681 57.143 0.00 0.00 0.00 3.85
2003 2043 2.420269 CGTCAGCTAGTCCTCTGTCCTA 60.420 54.545 0.00 0.00 0.00 2.94
2004 2044 3.622630 GTCAGCTAGTCCTCTGTCCTAA 58.377 50.000 0.00 0.00 0.00 2.69
2005 2045 4.017808 GTCAGCTAGTCCTCTGTCCTAAA 58.982 47.826 0.00 0.00 0.00 1.85
2006 2046 4.463186 GTCAGCTAGTCCTCTGTCCTAAAA 59.537 45.833 0.00 0.00 0.00 1.52
2007 2047 4.463186 TCAGCTAGTCCTCTGTCCTAAAAC 59.537 45.833 0.00 0.00 0.00 2.43
2008 2048 4.220821 CAGCTAGTCCTCTGTCCTAAAACA 59.779 45.833 0.00 0.00 0.00 2.83
2009 2049 5.026790 AGCTAGTCCTCTGTCCTAAAACAT 58.973 41.667 0.00 0.00 0.00 2.71
2014 2054 6.784031 AGTCCTCTGTCCTAAAACATTCATT 58.216 36.000 0.00 0.00 0.00 2.57
2052 2092 2.197875 CGGATCTCGGGTAGGGGT 59.802 66.667 0.00 0.00 34.75 4.95
2054 2094 1.047034 CGGATCTCGGGTAGGGGTTT 61.047 60.000 0.00 0.00 34.75 3.27
2070 2111 1.454653 GGTTTCGAACTGTGCGTCTAC 59.545 52.381 8.23 5.01 0.00 2.59
2071 2112 2.121786 GTTTCGAACTGTGCGTCTACA 58.878 47.619 8.23 0.00 0.00 2.74
2075 2116 0.039798 GAACTGTGCGTCTACACCGA 60.040 55.000 0.00 0.00 39.93 4.69
2103 2144 0.325296 AGAAGGCAGGGGACACGATA 60.325 55.000 0.00 0.00 0.00 2.92
2132 2173 1.602237 GTTCGGGCCCTCTTGATGA 59.398 57.895 22.43 4.41 0.00 2.92
2169 2210 9.639601 CTACGTCCTGCTTGATTAATATTGATA 57.360 33.333 0.00 0.00 0.00 2.15
2232 2277 2.434702 GGCTAAACCCTAGAAGCTAGCA 59.565 50.000 18.83 0.00 34.72 3.49
2332 2386 0.953003 GAGTCCTAGCCGAATACGCT 59.047 55.000 0.00 0.00 38.29 5.07
2355 2409 1.435563 TGGGGAGGAGTCCTTGTCTTA 59.564 52.381 14.41 0.00 43.36 2.10
2379 2435 2.554032 CGCCAAGTCTTGTGGAATCTTT 59.446 45.455 11.61 0.00 38.54 2.52
2400 2456 2.125147 GTATGCGGCAGCTGTCCA 60.125 61.111 21.86 16.98 45.42 4.02
2454 2512 2.894765 TCGGCCCAATATAACAGATCGA 59.105 45.455 0.00 0.00 0.00 3.59
2635 2695 3.541632 AGGATCGCCAAAATACATTCGT 58.458 40.909 0.00 0.00 36.29 3.85
2693 2753 3.697166 AGTTTCCGGCCTTTATCAATGT 58.303 40.909 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.250840 GGTCTCGCCAGGCCATTTTT 61.251 55.000 5.01 0.00 44.95 1.94
4 5 1.678970 GGTCTCGCCAGGCCATTTT 60.679 57.895 5.01 0.00 44.95 1.82
9 10 0.318762 CTAATAGGTCTCGCCAGGCC 59.681 60.000 5.63 0.00 46.14 5.19
10 11 0.318762 CCTAATAGGTCTCGCCAGGC 59.681 60.000 0.00 0.00 40.61 4.85
11 12 0.969894 CCCTAATAGGTCTCGCCAGG 59.030 60.000 5.49 0.00 40.61 4.45
12 13 0.969894 CCCCTAATAGGTCTCGCCAG 59.030 60.000 5.49 0.00 40.61 4.85
13 14 1.119574 GCCCCTAATAGGTCTCGCCA 61.120 60.000 5.49 0.00 40.61 5.69
14 15 1.672320 GCCCCTAATAGGTCTCGCC 59.328 63.158 5.49 0.00 31.93 5.54
15 16 1.289380 CGCCCCTAATAGGTCTCGC 59.711 63.158 5.49 0.79 31.93 5.03
16 17 1.289380 GCGCCCCTAATAGGTCTCG 59.711 63.158 5.49 6.65 31.93 4.04
17 18 1.289380 CGCGCCCCTAATAGGTCTC 59.711 63.158 0.00 0.00 31.93 3.36
18 19 2.207924 CCGCGCCCCTAATAGGTCT 61.208 63.158 0.00 0.00 31.93 3.85
19 20 2.342648 CCGCGCCCCTAATAGGTC 59.657 66.667 0.00 0.00 31.93 3.85
20 21 3.937447 GCCGCGCCCCTAATAGGT 61.937 66.667 0.00 0.00 31.93 3.08
21 22 3.626924 AGCCGCGCCCCTAATAGG 61.627 66.667 0.00 0.00 34.30 2.57
22 23 2.357517 CAGCCGCGCCCCTAATAG 60.358 66.667 0.00 0.00 0.00 1.73
23 24 3.936203 CCAGCCGCGCCCCTAATA 61.936 66.667 0.00 0.00 0.00 0.98
45 46 1.797635 GATCGCCAAGATGCTAAGAGC 59.202 52.381 0.00 0.00 40.26 4.09
46 47 3.058450 CTGATCGCCAAGATGCTAAGAG 58.942 50.000 0.00 0.00 40.26 2.85
47 48 2.804572 GCTGATCGCCAAGATGCTAAGA 60.805 50.000 0.00 0.00 40.26 2.10
63 64 2.730934 ACAAGCATGATGGAGCTGAT 57.269 45.000 0.00 0.00 41.70 2.90
75 76 2.964978 GCCGGAGCAAACAAGCAT 59.035 55.556 5.05 0.00 39.53 3.79
78 79 3.659092 TGCGCCGGAGCAAACAAG 61.659 61.111 31.47 0.00 45.06 3.16
99 100 1.227263 GTGCGCCCATACACGATCT 60.227 57.895 4.18 0.00 0.00 2.75
117 118 1.372004 TTACTGCCCGTTCGTGTCG 60.372 57.895 0.00 0.00 0.00 4.35
125 126 2.045340 GCCCATGTTACTGCCCGT 60.045 61.111 0.00 0.00 0.00 5.28
135 136 0.033109 GGGGAGCTTTAAGCCCATGT 60.033 55.000 20.32 1.69 43.77 3.21
145 146 1.228988 CCTTTGGCAGGGGAGCTTT 60.229 57.895 2.22 0.00 39.39 3.51
158 159 6.939163 TCTGAGGATTTCTTCTTCTTCCTTTG 59.061 38.462 0.00 0.00 36.95 2.77
183 184 2.289072 ACAATGTAGCGAACTCAGCAGT 60.289 45.455 0.00 0.00 37.01 4.40
187 188 8.817100 TCATATTTTACAATGTAGCGAACTCAG 58.183 33.333 0.00 0.00 0.00 3.35
222 226 9.466497 TCTTCAGGCTTGTTATTATTTTCAGAT 57.534 29.630 0.00 0.00 0.00 2.90
225 229 9.691362 GTTTCTTCAGGCTTGTTATTATTTTCA 57.309 29.630 0.00 0.00 0.00 2.69
229 233 8.734386 CAGAGTTTCTTCAGGCTTGTTATTATT 58.266 33.333 0.00 0.00 0.00 1.40
230 234 8.103305 TCAGAGTTTCTTCAGGCTTGTTATTAT 58.897 33.333 0.00 0.00 0.00 1.28
231 235 7.387948 GTCAGAGTTTCTTCAGGCTTGTTATTA 59.612 37.037 0.00 0.00 0.00 0.98
232 236 6.205658 GTCAGAGTTTCTTCAGGCTTGTTATT 59.794 38.462 0.00 0.00 0.00 1.40
233 237 5.703130 GTCAGAGTTTCTTCAGGCTTGTTAT 59.297 40.000 0.00 0.00 0.00 1.89
252 272 2.981302 CCGCCAGGTCATGTCAGA 59.019 61.111 0.00 0.00 0.00 3.27
464 493 2.584391 AAGAGCGTGGGGAGTGGAC 61.584 63.158 0.00 0.00 0.00 4.02
492 521 1.595382 GGAATCTACGCTGGCGCAT 60.595 57.895 10.83 2.16 44.19 4.73
552 581 2.441378 CGTGTATGGTGGTCACGCG 61.441 63.158 3.53 3.53 45.66 6.01
622 651 9.349713 TGTAAAGTAACAGGAAAGAATGTTCAT 57.650 29.630 0.00 0.00 31.83 2.57
753 782 1.005275 ATCATGCATCTCTCGGGCG 60.005 57.895 0.00 0.00 0.00 6.13
778 807 0.734942 ATACGTCCGTTTCCTGCGTG 60.735 55.000 0.00 0.00 37.05 5.34
808 837 1.216178 GTTTTGGAGCATGCGCCAT 59.784 52.632 38.51 10.77 44.91 4.40
809 838 2.650196 GTTTTGGAGCATGCGCCA 59.350 55.556 35.67 35.67 43.94 5.69
811 840 2.082366 CACGTTTTGGAGCATGCGC 61.082 57.895 13.62 13.62 38.99 6.09
812 841 4.135570 CACGTTTTGGAGCATGCG 57.864 55.556 13.01 0.00 0.00 4.73
836 865 5.362717 TCACAGAAGAGAACAACCAGTAGAA 59.637 40.000 0.00 0.00 0.00 2.10
852 881 0.782384 GTTGGTACGCGTCACAGAAG 59.218 55.000 18.63 0.00 0.00 2.85
881 910 2.947532 CGGCAGACCAGAAGAGGCA 61.948 63.158 0.00 0.00 34.57 4.75
882 911 2.125350 CGGCAGACCAGAAGAGGC 60.125 66.667 0.00 0.00 34.57 4.70
883 912 1.216710 GTCGGCAGACCAGAAGAGG 59.783 63.158 5.60 0.00 41.41 3.69
884 913 0.389166 GTGTCGGCAGACCAGAAGAG 60.389 60.000 14.62 0.00 46.51 2.85
885 914 1.112916 TGTGTCGGCAGACCAGAAGA 61.113 55.000 14.62 0.00 46.51 2.87
962 991 1.141234 GTAGCCGTAGAGGTGCACC 59.859 63.158 29.22 29.22 43.70 5.01
971 1000 2.220313 GTCTGAGGTAGGTAGCCGTAG 58.780 57.143 0.00 0.00 0.00 3.51
972 1001 1.561076 TGTCTGAGGTAGGTAGCCGTA 59.439 52.381 0.00 0.00 0.00 4.02
973 1002 0.330604 TGTCTGAGGTAGGTAGCCGT 59.669 55.000 0.00 0.00 0.00 5.68
1062 1091 0.661020 CAACGTGGACCAGTGAAACC 59.339 55.000 0.00 0.00 37.80 3.27
1162 1191 2.173996 TGTCTCCGGGAAGAAAGGTTTT 59.826 45.455 0.00 0.00 0.00 2.43
1290 1321 0.108041 AAGGACGTTGTGGTTCGTGT 60.108 50.000 0.00 0.00 40.39 4.49
1292 1323 0.176219 TCAAGGACGTTGTGGTTCGT 59.824 50.000 7.69 0.00 43.00 3.85
1323 1354 1.300542 GAGCAGGCCTCATAGTCGC 60.301 63.158 0.00 0.25 40.45 5.19
1359 1390 3.422303 TGCCGCTGTTGTCGATGC 61.422 61.111 0.00 0.00 0.00 3.91
1444 1475 1.073923 ACCTCCAGCTTCATTCCGTTT 59.926 47.619 0.00 0.00 0.00 3.60
1591 1622 2.677524 TTGTGCCCTGCATGCCTC 60.678 61.111 16.68 0.88 41.91 4.70
1874 1905 5.469760 CCTCACAATCTGAACACACAATACA 59.530 40.000 0.00 0.00 0.00 2.29
1915 1952 7.596248 CACCATAACAAGCAATTATTATCAGGC 59.404 37.037 0.00 0.00 0.00 4.85
1932 1969 5.305386 AGACTGCATATAGCTCACCATAACA 59.695 40.000 0.00 0.00 45.94 2.41
1946 1983 4.574674 TCTCAACCCAAAGACTGCATAT 57.425 40.909 0.00 0.00 0.00 1.78
1957 1994 2.614481 GGTGCGAGTAATCTCAACCCAA 60.614 50.000 0.00 0.00 39.34 4.12
1959 1996 1.066430 TGGTGCGAGTAATCTCAACCC 60.066 52.381 0.00 0.00 42.05 4.11
1962 1999 2.481276 CGGATGGTGCGAGTAATCTCAA 60.481 50.000 0.00 0.00 40.44 3.02
1963 2000 1.067060 CGGATGGTGCGAGTAATCTCA 59.933 52.381 0.00 0.00 40.44 3.27
1973 2010 1.589993 CTAGCTGACGGATGGTGCG 60.590 63.158 0.00 0.00 37.19 5.34
1976 2013 0.033011 AGGACTAGCTGACGGATGGT 60.033 55.000 0.00 0.00 0.00 3.55
1978 2015 1.336440 CAGAGGACTAGCTGACGGATG 59.664 57.143 0.00 0.00 34.06 3.51
1979 2016 1.064314 ACAGAGGACTAGCTGACGGAT 60.064 52.381 0.00 0.00 36.07 4.18
1980 2017 0.328592 ACAGAGGACTAGCTGACGGA 59.671 55.000 0.00 0.00 36.07 4.69
2006 2046 3.210227 TGACACCGACAACAATGAATGT 58.790 40.909 0.00 0.00 46.82 2.71
2007 2047 3.894782 TGACACCGACAACAATGAATG 57.105 42.857 0.00 0.00 0.00 2.67
2008 2048 4.909696 TTTGACACCGACAACAATGAAT 57.090 36.364 0.00 0.00 0.00 2.57
2009 2049 4.416620 GTTTTGACACCGACAACAATGAA 58.583 39.130 0.00 0.00 0.00 2.57
2052 2092 2.121786 GTGTAGACGCACAGTTCGAAA 58.878 47.619 0.00 0.00 39.07 3.46
2054 2094 0.039798 GGTGTAGACGCACAGTTCGA 60.040 55.000 0.00 0.00 40.89 3.71
2075 2116 1.005924 CCCCTGCCTTCTGTTACCATT 59.994 52.381 0.00 0.00 0.00 3.16
2086 2127 1.213296 AATATCGTGTCCCCTGCCTT 58.787 50.000 0.00 0.00 0.00 4.35
2132 2173 2.289882 GCAGGACGTAGGGTTTTACCTT 60.290 50.000 0.00 0.00 42.09 3.50
2332 2386 1.538876 CAAGGACTCCTCCCCACCA 60.539 63.158 0.00 0.00 37.25 4.17
2355 2409 2.270352 TTCCACAAGACTTGGCGATT 57.730 45.000 19.16 0.00 33.71 3.34
2379 2435 0.740868 GACAGCTGCCGCATACAAGA 60.741 55.000 15.27 0.00 39.10 3.02
2400 2456 2.158813 CCGTATACTCATGGGCCAGTTT 60.159 50.000 13.78 2.35 0.00 2.66
2454 2512 1.155042 GTACTCACCACGTCGTCTCT 58.845 55.000 0.00 0.00 0.00 3.10
2628 2688 3.054878 GACGTGTAAACCTGACGAATGT 58.945 45.455 0.00 0.00 36.90 2.71
2635 2695 1.614996 TACCCGACGTGTAAACCTGA 58.385 50.000 0.00 0.00 0.00 3.86
2666 2726 4.157105 TGATAAAGGCCGGAAACTTAAAGC 59.843 41.667 5.05 1.92 0.00 3.51
2693 2753 9.104965 CCGAGGTGTGTCATAAAAATAATAAGA 57.895 33.333 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.