Multiple sequence alignment - TraesCS4A01G303700

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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 TraesCS4A01G303700 chr4A 100.000 2282 0 0 1 2282 599585672 599587953 0 4215
1 TraesCS4A01G303700 chr1A 96.953 2035 55 6 254 2282 554513923 554511890 0 3408
2 TraesCS4A01G303700 chr5D 96.904 2035 56 6 254 2282 503219893 503217860 0 3402
3 TraesCS4A01G303700 chr5D 96.658 2035 61 6 254 2282 503276551 503278584 0 3374
4 TraesCS4A01G303700 chr5D 96.314 2035 68 4 254 2282 6190615 6188582 0 3336
5 TraesCS4A01G303700 chr3B 96.855 2035 57 6 254 2282 201528699 201526666 0 3397
6 TraesCS4A01G303700 chr6D 96.708 2035 60 6 254 2282 168256601 168254568 0 3380
7 TraesCS4A01G303700 chr3D 96.708 2035 57 8 254 2282 589277870 589279900 0 3378
8 TraesCS4A01G303700 chrUn 96.629 2017 61 6 254 2264 346594819 346596834 0 3341
9 TraesCS4A01G303700 chr3A 96.265 2035 67 8 254 2282 672908334 672910365 0 3328


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 TraesCS4A01G303700 chr4A 599585672 599587953 2281 False 4215 4215 100.000 1 2282 1 chr4A.!!$F1 2281
1 TraesCS4A01G303700 chr1A 554511890 554513923 2033 True 3408 3408 96.953 254 2282 1 chr1A.!!$R1 2028
2 TraesCS4A01G303700 chr5D 503217860 503219893 2033 True 3402 3402 96.904 254 2282 1 chr5D.!!$R2 2028
3 TraesCS4A01G303700 chr5D 503276551 503278584 2033 False 3374 3374 96.658 254 2282 1 chr5D.!!$F1 2028
4 TraesCS4A01G303700 chr5D 6188582 6190615 2033 True 3336 3336 96.314 254 2282 1 chr5D.!!$R1 2028
5 TraesCS4A01G303700 chr3B 201526666 201528699 2033 True 3397 3397 96.855 254 2282 1 chr3B.!!$R1 2028
6 TraesCS4A01G303700 chr6D 168254568 168256601 2033 True 3380 3380 96.708 254 2282 1 chr6D.!!$R1 2028
7 TraesCS4A01G303700 chr3D 589277870 589279900 2030 False 3378 3378 96.708 254 2282 1 chr3D.!!$F1 2028
8 TraesCS4A01G303700 chrUn 346594819 346596834 2015 False 3341 3341 96.629 254 2264 1 chrUn.!!$F1 2010
9 TraesCS4A01G303700 chr3A 672908334 672910365 2031 False 3328 3328 96.265 254 2282 1 chr3A.!!$F1 2028

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
149 150 0.033503 TGACCTCTCCTACGATGGCA 60.034 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 1921 0.838987 AAGGGGTGCTTCCGGTTCTA 60.839 55.0 0.0 0.0 37.0 2.1 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 2.182030 GAGGCCTCGGACGACAAG 59.818 66.667 19.06 0.00 0.00 3.16
20 21 3.358076 GAGGCCTCGGACGACAAGG 62.358 68.421 19.06 0.00 0.00 3.61
21 22 3.692406 GGCCTCGGACGACAAGGT 61.692 66.667 0.00 0.00 32.49 3.50
22 23 2.432628 GCCTCGGACGACAAGGTG 60.433 66.667 0.00 0.00 32.49 4.00
23 24 2.432628 CCTCGGACGACAAGGTGC 60.433 66.667 0.00 0.00 0.00 5.01
24 25 2.432628 CTCGGACGACAAGGTGCC 60.433 66.667 0.00 0.00 0.00 5.01
25 26 4.351938 TCGGACGACAAGGTGCCG 62.352 66.667 0.00 0.00 43.11 5.69
27 28 3.998672 GGACGACAAGGTGCCGGA 61.999 66.667 5.05 0.00 0.00 5.14
28 29 2.432628 GACGACAAGGTGCCGGAG 60.433 66.667 5.05 0.00 0.00 4.63
29 30 4.681978 ACGACAAGGTGCCGGAGC 62.682 66.667 5.05 0.00 40.48 4.70
39 40 4.819761 GCCGGAGCAGCATGACGA 62.820 66.667 5.05 0.00 39.69 4.20
40 41 2.887568 CCGGAGCAGCATGACGAC 60.888 66.667 0.00 0.00 39.69 4.34
41 42 2.125952 CGGAGCAGCATGACGACA 60.126 61.111 0.00 0.00 39.69 4.35
42 43 1.737735 CGGAGCAGCATGACGACAA 60.738 57.895 0.00 0.00 39.69 3.18
43 44 1.086067 CGGAGCAGCATGACGACAAT 61.086 55.000 0.00 0.00 39.69 2.71
44 45 0.376152 GGAGCAGCATGACGACAATG 59.624 55.000 0.00 0.00 39.69 2.82
45 46 0.247974 GAGCAGCATGACGACAATGC 60.248 55.000 12.60 12.60 39.69 3.56
46 47 1.226491 GCAGCATGACGACAATGCC 60.226 57.895 14.85 1.88 41.88 4.40
47 48 1.925415 GCAGCATGACGACAATGCCA 61.925 55.000 14.85 0.00 41.88 4.92
48 49 0.522626 CAGCATGACGACAATGCCAA 59.477 50.000 14.85 0.00 41.88 4.52
49 50 1.068402 CAGCATGACGACAATGCCAAA 60.068 47.619 14.85 0.00 41.88 3.28
50 51 1.200716 AGCATGACGACAATGCCAAAG 59.799 47.619 14.85 0.00 41.88 2.77
51 52 1.733389 GCATGACGACAATGCCAAAGG 60.733 52.381 0.00 0.00 35.44 3.11
52 53 1.135315 CATGACGACAATGCCAAAGGG 60.135 52.381 0.00 0.00 37.18 3.95
53 54 0.893270 TGACGACAATGCCAAAGGGG 60.893 55.000 0.00 0.00 40.85 4.79
54 55 0.608035 GACGACAATGCCAAAGGGGA 60.608 55.000 0.00 0.00 40.01 4.81
55 56 0.178975 ACGACAATGCCAAAGGGGAA 60.179 50.000 0.00 0.00 38.38 3.97
56 57 0.527565 CGACAATGCCAAAGGGGAAG 59.472 55.000 0.00 0.00 38.38 3.46
57 58 0.897621 GACAATGCCAAAGGGGAAGG 59.102 55.000 0.00 0.00 38.38 3.46
63 64 2.289840 CCAAAGGGGAAGGCATTGG 58.710 57.895 0.00 0.00 40.01 3.16
64 65 0.252193 CCAAAGGGGAAGGCATTGGA 60.252 55.000 0.00 0.00 42.46 3.53
65 66 1.643310 CAAAGGGGAAGGCATTGGAA 58.357 50.000 0.00 0.00 0.00 3.53
66 67 1.551883 CAAAGGGGAAGGCATTGGAAG 59.448 52.381 0.00 0.00 0.00 3.46
67 68 0.615827 AAGGGGAAGGCATTGGAAGC 60.616 55.000 0.00 0.00 0.00 3.86
68 69 1.000866 GGGGAAGGCATTGGAAGCT 59.999 57.895 0.00 0.00 0.00 3.74
69 70 0.615827 GGGGAAGGCATTGGAAGCTT 60.616 55.000 0.00 0.00 0.00 3.74
70 71 0.820226 GGGAAGGCATTGGAAGCTTC 59.180 55.000 18.54 18.54 0.00 3.86
71 72 0.453390 GGAAGGCATTGGAAGCTTCG 59.547 55.000 19.91 7.50 0.00 3.79
72 73 0.453390 GAAGGCATTGGAAGCTTCGG 59.547 55.000 19.91 10.44 0.00 4.30
73 74 0.038166 AAGGCATTGGAAGCTTCGGA 59.962 50.000 19.91 11.24 0.00 4.55
74 75 0.257039 AGGCATTGGAAGCTTCGGAT 59.743 50.000 19.91 12.99 0.00 4.18
75 76 0.665298 GGCATTGGAAGCTTCGGATC 59.335 55.000 19.91 6.92 0.00 3.36
76 77 0.305922 GCATTGGAAGCTTCGGATCG 59.694 55.000 19.91 8.49 0.00 3.69
77 78 1.656652 CATTGGAAGCTTCGGATCGT 58.343 50.000 19.91 0.46 0.00 3.73
78 79 2.009774 CATTGGAAGCTTCGGATCGTT 58.990 47.619 19.91 0.00 0.00 3.85
79 80 1.722011 TTGGAAGCTTCGGATCGTTC 58.278 50.000 19.91 4.39 0.00 3.95
80 81 0.457853 TGGAAGCTTCGGATCGTTCG 60.458 55.000 19.91 0.00 0.00 3.95
81 82 1.631595 GAAGCTTCGGATCGTTCGC 59.368 57.895 11.40 0.00 0.00 4.70
82 83 2.067453 GAAGCTTCGGATCGTTCGCG 62.067 60.000 11.40 0.00 42.98 5.87
83 84 4.267013 GCTTCGGATCGTTCGCGC 62.267 66.667 0.00 0.00 41.05 6.86
84 85 3.617538 CTTCGGATCGTTCGCGCC 61.618 66.667 0.00 0.00 41.05 6.53
108 109 4.813526 CGACGACGGCGAGGTCAG 62.814 72.222 22.49 17.57 41.64 3.51
111 112 4.838486 CGACGGCGAGGTCAGCTC 62.838 72.222 16.62 0.00 40.82 4.09
112 113 4.500116 GACGGCGAGGTCAGCTCC 62.500 72.222 16.62 0.00 36.91 4.70
118 119 3.844090 GAGGTCAGCTCCTCCGGC 61.844 72.222 9.85 0.00 45.84 6.13
119 120 4.390556 AGGTCAGCTCCTCCGGCT 62.391 66.667 0.00 0.00 41.07 5.52
120 121 3.844090 GGTCAGCTCCTCCGGCTC 61.844 72.222 0.00 0.00 38.03 4.70
121 122 3.071206 GTCAGCTCCTCCGGCTCA 61.071 66.667 0.00 0.00 38.03 4.26
122 123 2.757508 TCAGCTCCTCCGGCTCAG 60.758 66.667 0.00 0.00 38.03 3.35
123 124 3.847602 CAGCTCCTCCGGCTCAGG 61.848 72.222 0.00 0.00 38.03 3.86
126 127 4.787280 CTCCTCCGGCTCAGGGGT 62.787 72.222 7.78 0.00 0.00 4.95
127 128 4.779733 TCCTCCGGCTCAGGGGTC 62.780 72.222 7.78 0.00 0.00 4.46
131 132 4.760047 CCGGCTCAGGGGTCGTTG 62.760 72.222 0.00 0.00 0.00 4.10
132 133 3.691342 CGGCTCAGGGGTCGTTGA 61.691 66.667 0.00 0.00 0.00 3.18
133 134 2.047179 GGCTCAGGGGTCGTTGAC 60.047 66.667 0.00 0.00 0.00 3.18
143 144 3.992636 GTCGTTGACCTCTCCTACG 57.007 57.895 0.00 0.00 0.00 3.51
144 145 1.446907 GTCGTTGACCTCTCCTACGA 58.553 55.000 0.00 0.00 38.72 3.43
145 146 2.015587 GTCGTTGACCTCTCCTACGAT 58.984 52.381 0.00 0.00 42.31 3.73
146 147 2.014857 TCGTTGACCTCTCCTACGATG 58.985 52.381 0.00 0.00 36.44 3.84
147 148 1.065701 CGTTGACCTCTCCTACGATGG 59.934 57.143 0.00 0.00 34.36 3.51
148 149 1.112113 TTGACCTCTCCTACGATGGC 58.888 55.000 0.00 0.00 0.00 4.40
149 150 0.033503 TGACCTCTCCTACGATGGCA 60.034 55.000 0.00 0.00 0.00 4.92
150 151 0.671251 GACCTCTCCTACGATGGCAG 59.329 60.000 0.00 0.00 0.00 4.85
151 152 0.757188 ACCTCTCCTACGATGGCAGG 60.757 60.000 0.00 2.32 34.74 4.85
152 153 0.468214 CCTCTCCTACGATGGCAGGA 60.468 60.000 0.00 0.00 38.66 3.86
153 154 1.403814 CTCTCCTACGATGGCAGGAA 58.596 55.000 0.00 0.00 40.43 3.36
154 155 1.967066 CTCTCCTACGATGGCAGGAAT 59.033 52.381 0.00 0.00 40.43 3.01
155 156 3.157881 CTCTCCTACGATGGCAGGAATA 58.842 50.000 0.00 0.00 40.43 1.75
156 157 2.891580 TCTCCTACGATGGCAGGAATAC 59.108 50.000 0.00 0.00 40.43 1.89
157 158 2.628178 CTCCTACGATGGCAGGAATACA 59.372 50.000 0.00 0.00 40.43 2.29
158 159 3.239449 TCCTACGATGGCAGGAATACAT 58.761 45.455 0.00 0.00 38.02 2.29
159 160 3.646162 TCCTACGATGGCAGGAATACATT 59.354 43.478 0.00 0.00 38.02 2.71
160 161 4.102524 TCCTACGATGGCAGGAATACATTT 59.897 41.667 0.00 0.00 38.02 2.32
161 162 4.821805 CCTACGATGGCAGGAATACATTTT 59.178 41.667 0.00 0.00 33.42 1.82
162 163 5.995282 CCTACGATGGCAGGAATACATTTTA 59.005 40.000 0.00 0.00 33.42 1.52
163 164 6.147821 CCTACGATGGCAGGAATACATTTTAG 59.852 42.308 0.00 0.00 33.42 1.85
164 165 5.437060 ACGATGGCAGGAATACATTTTAGT 58.563 37.500 0.00 0.00 0.00 2.24
165 166 6.588204 ACGATGGCAGGAATACATTTTAGTA 58.412 36.000 0.00 0.00 0.00 1.82
166 167 7.224297 ACGATGGCAGGAATACATTTTAGTAT 58.776 34.615 0.00 0.00 36.29 2.12
167 168 7.719633 ACGATGGCAGGAATACATTTTAGTATT 59.280 33.333 0.00 0.00 44.90 1.89
168 169 8.567948 CGATGGCAGGAATACATTTTAGTATTT 58.432 33.333 0.00 0.00 42.93 1.40
234 235 8.746052 TCTAAATATGAATGAAAATCCGGTGT 57.254 30.769 0.00 0.00 0.00 4.16
235 236 8.836413 TCTAAATATGAATGAAAATCCGGTGTC 58.164 33.333 0.00 0.00 0.00 3.67
236 237 6.391227 AATATGAATGAAAATCCGGTGTCC 57.609 37.500 0.00 0.00 0.00 4.02
237 238 2.442413 TGAATGAAAATCCGGTGTCCC 58.558 47.619 0.00 0.00 0.00 4.46
238 239 2.224892 TGAATGAAAATCCGGTGTCCCA 60.225 45.455 0.00 0.00 0.00 4.37
239 240 2.595750 ATGAAAATCCGGTGTCCCAA 57.404 45.000 0.00 0.00 0.00 4.12
240 241 2.366640 TGAAAATCCGGTGTCCCAAA 57.633 45.000 0.00 0.00 0.00 3.28
241 242 2.667470 TGAAAATCCGGTGTCCCAAAA 58.333 42.857 0.00 0.00 0.00 2.44
242 243 3.235200 TGAAAATCCGGTGTCCCAAAAT 58.765 40.909 0.00 0.00 0.00 1.82
243 244 4.408276 TGAAAATCCGGTGTCCCAAAATA 58.592 39.130 0.00 0.00 0.00 1.40
244 245 5.020132 TGAAAATCCGGTGTCCCAAAATAT 58.980 37.500 0.00 0.00 0.00 1.28
245 246 5.482175 TGAAAATCCGGTGTCCCAAAATATT 59.518 36.000 0.00 0.00 0.00 1.28
246 247 6.014156 TGAAAATCCGGTGTCCCAAAATATTT 60.014 34.615 0.00 0.00 0.00 1.40
247 248 5.337578 AATCCGGTGTCCCAAAATATTTG 57.662 39.130 0.00 0.00 0.00 2.32
248 249 3.093057 TCCGGTGTCCCAAAATATTTGG 58.907 45.455 13.67 13.67 39.25 3.28
249 250 2.829120 CCGGTGTCCCAAAATATTTGGT 59.171 45.455 17.91 0.00 37.88 3.67
250 251 3.367910 CCGGTGTCCCAAAATATTTGGTG 60.368 47.826 17.91 10.98 37.88 4.17
251 252 3.508012 CGGTGTCCCAAAATATTTGGTGA 59.492 43.478 17.91 12.69 37.88 4.02
252 253 4.159506 CGGTGTCCCAAAATATTTGGTGAT 59.840 41.667 17.91 0.00 37.88 3.06
256 257 7.287696 GGTGTCCCAAAATATTTGGTGATCTAT 59.712 37.037 17.91 0.00 37.88 1.98
342 343 7.178573 TGGTACATGAAAATGATTAGTCCCAA 58.821 34.615 0.00 0.00 0.00 4.12
541 542 7.440556 TGCTAAAGAGAAATGATCACTATGAGC 59.559 37.037 0.00 2.57 32.94 4.26
586 587 5.765182 CCATTCCAAATAGCGAGAATTAGGT 59.235 40.000 0.00 0.00 0.00 3.08
629 630 4.125703 CTCTTTCAATTCGAGGATCCAGG 58.874 47.826 15.82 5.01 0.00 4.45
650 651 3.871594 GGGAGGTGTTTTCATAGTCATCG 59.128 47.826 0.00 0.00 0.00 3.84
662 663 5.778862 TCATAGTCATCGCCGAATATTTGA 58.221 37.500 4.10 0.00 0.00 2.69
669 670 4.053469 TCGCCGAATATTTGACATCTCA 57.947 40.909 4.10 0.00 0.00 3.27
751 752 3.383505 TGATGTACGGTGATCCCTGTTAG 59.616 47.826 0.00 0.00 0.00 2.34
778 779 1.904287 TGGCTGAATGGTTAAAGCGT 58.096 45.000 0.00 0.00 36.50 5.07
798 799 5.885912 AGCGTCCAACTCATAATTGGTAAAT 59.114 36.000 3.81 0.00 45.83 1.40
818 819 1.698506 TTTGCGGGTTCAATTCCTGT 58.301 45.000 0.00 0.00 34.14 4.00
888 889 4.708909 TCTCTATCCATGGAATCTCATCCG 59.291 45.833 20.67 0.95 42.76 4.18
983 985 5.073428 TCGATACTGGAACTCAGAGCATAT 58.927 41.667 0.00 0.00 46.18 1.78
1147 1149 4.594062 TCTTTGGTGTTAAGGTGGTAGCTA 59.406 41.667 0.00 0.00 0.00 3.32
1216 1218 1.952990 TGGGCCATACAATGCATTACG 59.047 47.619 12.53 3.20 0.00 3.18
1237 1239 4.100498 ACGGACGTATGATCATTACCCTTT 59.900 41.667 14.65 0.00 0.00 3.11
1239 1241 6.014840 ACGGACGTATGATCATTACCCTTTAT 60.015 38.462 14.65 0.00 0.00 1.40
1241 1243 7.577046 CGGACGTATGATCATTACCCTTTATCT 60.577 40.741 14.65 0.00 0.00 1.98
1323 1326 7.954788 ACGGCAAAACATTTATACAAAACAT 57.045 28.000 0.00 0.00 0.00 2.71
1393 1396 5.914635 CCAATCCACGAAATAATTTGATCCG 59.085 40.000 0.00 0.00 0.00 4.18
1400 1403 4.269123 CGAAATAATTTGATCCGTGGACGA 59.731 41.667 0.00 0.00 43.02 4.20
1403 1406 2.691409 ATTTGATCCGTGGACGACAT 57.309 45.000 0.00 0.00 43.02 3.06
1416 1423 2.232941 GGACGACATCTGGTAAAGGTCA 59.767 50.000 0.00 0.00 0.00 4.02
1425 1432 7.586349 ACATCTGGTAAAGGTCATAATTCCAT 58.414 34.615 0.00 0.00 0.00 3.41
1475 1482 2.415625 GGAGGTCATAAGCGCCTATACG 60.416 54.545 2.29 0.00 39.49 3.06
1476 1483 2.486982 GAGGTCATAAGCGCCTATACGA 59.513 50.000 2.29 0.00 34.06 3.43
1584 1591 4.814967 TGTCTCATACACTATGGGGATGA 58.185 43.478 0.00 0.00 37.26 2.92
1593 1600 5.161135 ACACTATGGGGATGATGAGAAGAT 58.839 41.667 0.00 0.00 0.00 2.40
1689 1698 3.421844 GAAATGCCCTACCTTTGAGTGT 58.578 45.455 0.00 0.00 0.00 3.55
1844 1853 6.017605 CAGCAAGTGATTGAGTTCAGTAGTTT 60.018 38.462 0.00 0.00 0.00 2.66
1912 1921 3.870419 ACAAAATTGTTTGAAGCACGCAT 59.130 34.783 6.21 0.00 45.99 4.73
1951 1960 4.444876 CCTTGTTTCAAAGAGAGGAGGACA 60.445 45.833 0.00 0.00 0.00 4.02
2019 2028 2.025699 GCAGTGGTAATTAAGACCCCCA 60.026 50.000 6.83 0.00 35.99 4.96
2096 2105 7.323895 ACGTAATTTCATAGAGTCATTCGATCG 59.676 37.037 9.36 9.36 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.182030 CTTGTCGTCCGAGGCCTC 59.818 66.667 23.79 23.79 0.00 4.70
3 4 3.382832 CCTTGTCGTCCGAGGCCT 61.383 66.667 3.86 3.86 37.93 5.19
7 8 2.432628 GGCACCTTGTCGTCCGAG 60.433 66.667 0.00 0.00 0.00 4.63
8 9 4.351938 CGGCACCTTGTCGTCCGA 62.352 66.667 0.00 0.00 41.12 4.55
10 11 3.934391 CTCCGGCACCTTGTCGTCC 62.934 68.421 0.00 0.00 45.14 4.79
11 12 2.432628 CTCCGGCACCTTGTCGTC 60.433 66.667 0.00 0.00 45.14 4.20
12 13 4.681978 GCTCCGGCACCTTGTCGT 62.682 66.667 0.00 0.00 45.14 4.34
13 14 4.680237 TGCTCCGGCACCTTGTCG 62.680 66.667 0.00 0.00 46.34 4.35
14 15 2.743928 CTGCTCCGGCACCTTGTC 60.744 66.667 0.00 0.00 44.28 3.18
22 23 4.819761 TCGTCATGCTGCTCCGGC 62.820 66.667 0.00 0.00 39.26 6.13
23 24 2.887568 GTCGTCATGCTGCTCCGG 60.888 66.667 0.00 0.00 0.00 5.14
24 25 1.086067 ATTGTCGTCATGCTGCTCCG 61.086 55.000 0.00 0.00 0.00 4.63
25 26 0.376152 CATTGTCGTCATGCTGCTCC 59.624 55.000 0.00 0.00 0.00 4.70
26 27 0.247974 GCATTGTCGTCATGCTGCTC 60.248 55.000 0.00 0.00 38.22 4.26
27 28 1.651240 GGCATTGTCGTCATGCTGCT 61.651 55.000 13.36 0.00 40.82 4.24
28 29 1.226491 GGCATTGTCGTCATGCTGC 60.226 57.895 13.36 9.04 40.82 5.25
29 30 0.522626 TTGGCATTGTCGTCATGCTG 59.477 50.000 13.36 1.22 40.82 4.41
30 31 1.200716 CTTTGGCATTGTCGTCATGCT 59.799 47.619 13.36 0.00 40.82 3.79
31 32 1.621107 CTTTGGCATTGTCGTCATGC 58.379 50.000 7.43 7.43 40.34 4.06
32 33 1.135315 CCCTTTGGCATTGTCGTCATG 60.135 52.381 0.00 0.00 0.00 3.07
33 34 1.176527 CCCTTTGGCATTGTCGTCAT 58.823 50.000 0.00 0.00 0.00 3.06
34 35 0.893270 CCCCTTTGGCATTGTCGTCA 60.893 55.000 0.00 0.00 0.00 4.35
35 36 0.608035 TCCCCTTTGGCATTGTCGTC 60.608 55.000 0.00 0.00 0.00 4.20
36 37 0.178975 TTCCCCTTTGGCATTGTCGT 60.179 50.000 0.00 0.00 0.00 4.34
37 38 0.527565 CTTCCCCTTTGGCATTGTCG 59.472 55.000 0.00 0.00 0.00 4.35
38 39 0.897621 CCTTCCCCTTTGGCATTGTC 59.102 55.000 0.00 0.00 0.00 3.18
39 40 1.194121 GCCTTCCCCTTTGGCATTGT 61.194 55.000 0.00 0.00 45.46 2.71
40 41 1.598517 GCCTTCCCCTTTGGCATTG 59.401 57.895 0.00 0.00 45.46 2.82
41 42 4.135293 GCCTTCCCCTTTGGCATT 57.865 55.556 0.00 0.00 45.46 3.56
44 45 1.598517 CAATGCCTTCCCCTTTGGC 59.401 57.895 0.00 0.00 46.26 4.52
45 46 0.252193 TCCAATGCCTTCCCCTTTGG 60.252 55.000 0.00 0.00 38.29 3.28
46 47 1.551883 CTTCCAATGCCTTCCCCTTTG 59.448 52.381 0.00 0.00 0.00 2.77
47 48 1.942776 CTTCCAATGCCTTCCCCTTT 58.057 50.000 0.00 0.00 0.00 3.11
48 49 0.615827 GCTTCCAATGCCTTCCCCTT 60.616 55.000 0.00 0.00 0.00 3.95
49 50 1.000866 GCTTCCAATGCCTTCCCCT 59.999 57.895 0.00 0.00 0.00 4.79
50 51 0.615827 AAGCTTCCAATGCCTTCCCC 60.616 55.000 0.00 0.00 0.00 4.81
51 52 0.820226 GAAGCTTCCAATGCCTTCCC 59.180 55.000 15.97 0.00 0.00 3.97
52 53 0.453390 CGAAGCTTCCAATGCCTTCC 59.547 55.000 20.62 0.00 0.00 3.46
53 54 0.453390 CCGAAGCTTCCAATGCCTTC 59.547 55.000 20.62 0.00 0.00 3.46
54 55 0.038166 TCCGAAGCTTCCAATGCCTT 59.962 50.000 20.62 0.00 0.00 4.35
55 56 0.257039 ATCCGAAGCTTCCAATGCCT 59.743 50.000 20.62 0.00 0.00 4.75
56 57 0.665298 GATCCGAAGCTTCCAATGCC 59.335 55.000 20.62 2.10 0.00 4.40
57 58 0.305922 CGATCCGAAGCTTCCAATGC 59.694 55.000 20.62 5.98 0.00 3.56
58 59 1.656652 ACGATCCGAAGCTTCCAATG 58.343 50.000 20.62 9.44 0.00 2.82
59 60 2.280628 GAACGATCCGAAGCTTCCAAT 58.719 47.619 20.62 13.65 0.00 3.16
60 61 1.722011 GAACGATCCGAAGCTTCCAA 58.278 50.000 20.62 9.27 0.00 3.53
61 62 0.457853 CGAACGATCCGAAGCTTCCA 60.458 55.000 20.62 8.02 0.00 3.53
62 63 1.753468 GCGAACGATCCGAAGCTTCC 61.753 60.000 20.62 5.66 0.00 3.46
63 64 1.631595 GCGAACGATCCGAAGCTTC 59.368 57.895 16.84 16.84 0.00 3.86
64 65 2.158959 CGCGAACGATCCGAAGCTT 61.159 57.895 0.00 0.00 43.93 3.74
65 66 2.579787 CGCGAACGATCCGAAGCT 60.580 61.111 0.00 0.00 43.93 3.74
66 67 4.267013 GCGCGAACGATCCGAAGC 62.267 66.667 12.10 4.97 43.93 3.86
67 68 3.617538 GGCGCGAACGATCCGAAG 61.618 66.667 12.10 0.00 43.93 3.79
91 92 4.813526 CTGACCTCGCCGTCGTCG 62.814 72.222 0.00 0.00 35.40 5.12
94 95 4.838486 GAGCTGACCTCGCCGTCG 62.838 72.222 0.00 0.00 35.40 5.12
95 96 4.500116 GGAGCTGACCTCGCCGTC 62.500 72.222 0.00 0.00 41.71 4.79
97 98 4.200283 GAGGAGCTGACCTCGCCG 62.200 72.222 5.75 0.00 45.30 6.46
114 115 4.760047 CAACGACCCCTGAGCCGG 62.760 72.222 0.00 0.00 0.00 6.13
115 116 3.691342 TCAACGACCCCTGAGCCG 61.691 66.667 0.00 0.00 0.00 5.52
116 117 2.047179 GTCAACGACCCCTGAGCC 60.047 66.667 0.00 0.00 0.00 4.70
117 118 2.047179 GGTCAACGACCCCTGAGC 60.047 66.667 1.47 0.00 46.19 4.26
125 126 1.446907 TCGTAGGAGAGGTCAACGAC 58.553 55.000 0.00 0.00 37.57 4.34
126 127 2.014857 CATCGTAGGAGAGGTCAACGA 58.985 52.381 0.00 0.00 42.98 3.85
127 128 1.065701 CCATCGTAGGAGAGGTCAACG 59.934 57.143 0.00 0.00 35.82 4.10
128 129 1.202428 GCCATCGTAGGAGAGGTCAAC 60.202 57.143 8.08 0.00 0.00 3.18
129 130 1.112113 GCCATCGTAGGAGAGGTCAA 58.888 55.000 8.08 0.00 0.00 3.18
130 131 0.033503 TGCCATCGTAGGAGAGGTCA 60.034 55.000 8.08 4.90 0.00 4.02
131 132 0.671251 CTGCCATCGTAGGAGAGGTC 59.329 60.000 8.08 2.95 0.00 3.85
132 133 0.757188 CCTGCCATCGTAGGAGAGGT 60.757 60.000 8.08 0.00 44.30 3.85
133 134 0.468214 TCCTGCCATCGTAGGAGAGG 60.468 60.000 0.00 3.09 45.08 3.69
134 135 3.117657 TCCTGCCATCGTAGGAGAG 57.882 57.895 0.00 0.00 45.08 3.20
138 139 3.685139 ATGTATTCCTGCCATCGTAGG 57.315 47.619 0.00 0.00 42.97 3.18
139 140 6.706270 ACTAAAATGTATTCCTGCCATCGTAG 59.294 38.462 0.00 0.00 0.00 3.51
140 141 6.588204 ACTAAAATGTATTCCTGCCATCGTA 58.412 36.000 0.00 0.00 0.00 3.43
141 142 5.437060 ACTAAAATGTATTCCTGCCATCGT 58.563 37.500 0.00 0.00 0.00 3.73
142 143 7.672983 ATACTAAAATGTATTCCTGCCATCG 57.327 36.000 0.00 0.00 29.70 3.84
208 209 9.184523 ACACCGGATTTTCATTCATATTTAGAA 57.815 29.630 9.46 0.00 0.00 2.10
209 210 8.746052 ACACCGGATTTTCATTCATATTTAGA 57.254 30.769 9.46 0.00 0.00 2.10
210 211 8.076178 GGACACCGGATTTTCATTCATATTTAG 58.924 37.037 9.46 0.00 0.00 1.85
211 212 7.013846 GGGACACCGGATTTTCATTCATATTTA 59.986 37.037 9.46 0.00 0.00 1.40
212 213 6.183360 GGGACACCGGATTTTCATTCATATTT 60.183 38.462 9.46 0.00 0.00 1.40
213 214 5.301805 GGGACACCGGATTTTCATTCATATT 59.698 40.000 9.46 0.00 0.00 1.28
214 215 4.827284 GGGACACCGGATTTTCATTCATAT 59.173 41.667 9.46 0.00 0.00 1.78
215 216 4.204012 GGGACACCGGATTTTCATTCATA 58.796 43.478 9.46 0.00 0.00 2.15
216 217 3.023832 GGGACACCGGATTTTCATTCAT 58.976 45.455 9.46 0.00 0.00 2.57
217 218 2.224892 TGGGACACCGGATTTTCATTCA 60.225 45.455 9.46 0.00 40.75 2.57
218 219 2.442413 TGGGACACCGGATTTTCATTC 58.558 47.619 9.46 0.00 40.75 2.67
219 220 2.595750 TGGGACACCGGATTTTCATT 57.404 45.000 9.46 0.00 40.75 2.57
220 221 2.595750 TTGGGACACCGGATTTTCAT 57.404 45.000 9.46 0.00 39.29 2.57
221 222 2.366640 TTTGGGACACCGGATTTTCA 57.633 45.000 9.46 0.00 39.29 2.69
222 223 3.953712 ATTTTGGGACACCGGATTTTC 57.046 42.857 9.46 0.00 39.29 2.29
223 224 6.169800 CAAATATTTTGGGACACCGGATTTT 58.830 36.000 9.46 0.00 39.29 1.82
224 225 5.337975 CCAAATATTTTGGGACACCGGATTT 60.338 40.000 9.46 0.00 39.29 2.17
225 226 4.161377 CCAAATATTTTGGGACACCGGATT 59.839 41.667 9.46 0.00 39.29 3.01
226 227 3.704061 CCAAATATTTTGGGACACCGGAT 59.296 43.478 9.46 0.00 39.29 4.18
227 228 3.093057 CCAAATATTTTGGGACACCGGA 58.907 45.455 9.46 0.00 39.29 5.14
228 229 2.829120 ACCAAATATTTTGGGACACCGG 59.171 45.455 20.01 0.00 43.71 5.28
229 230 3.508012 TCACCAAATATTTTGGGACACCG 59.492 43.478 20.01 4.88 43.71 4.94
230 231 5.422012 AGATCACCAAATATTTTGGGACACC 59.578 40.000 20.01 7.80 43.71 4.16
231 232 6.530019 AGATCACCAAATATTTTGGGACAC 57.470 37.500 20.01 4.85 43.71 3.67
232 233 9.573166 CTATAGATCACCAAATATTTTGGGACA 57.427 33.333 20.01 6.62 43.71 4.02
233 234 9.793259 TCTATAGATCACCAAATATTTTGGGAC 57.207 33.333 20.01 9.97 43.71 4.46
243 244 9.386122 AGTGATAGGTTCTATAGATCACCAAAT 57.614 33.333 21.64 15.60 44.85 2.32
244 245 8.783660 AGTGATAGGTTCTATAGATCACCAAA 57.216 34.615 21.64 12.59 44.85 3.28
245 246 9.877222 TTAGTGATAGGTTCTATAGATCACCAA 57.123 33.333 21.64 15.49 44.85 3.67
246 247 9.877222 TTTAGTGATAGGTTCTATAGATCACCA 57.123 33.333 21.64 11.58 44.85 4.17
256 257 8.716674 ATCGGGTATTTTAGTGATAGGTTCTA 57.283 34.615 0.00 0.00 0.00 2.10
322 323 6.851609 TCGTTTGGGACTAATCATTTTCATG 58.148 36.000 0.00 0.00 0.00 3.07
342 343 4.360951 TCACTTATTCCCAAACCTCGTT 57.639 40.909 0.00 0.00 0.00 3.85
541 542 5.933617 TGGATCCAATTCTATTGAGTCTGG 58.066 41.667 13.46 0.00 0.00 3.86
586 587 5.963253 AGAGAGATTGAGAGGGATCAAGAAA 59.037 40.000 0.00 0.00 42.20 2.52
629 630 3.309954 GCGATGACTATGAAAACACCTCC 59.690 47.826 0.00 0.00 0.00 4.30
650 651 5.991328 TTCTGAGATGTCAAATATTCGGC 57.009 39.130 0.00 0.00 30.14 5.54
729 730 1.860641 ACAGGGATCACCGTACATCA 58.139 50.000 0.00 0.00 46.96 3.07
751 752 0.757935 ACCATTCAGCCATGGATGCC 60.758 55.000 25.40 1.55 46.18 4.40
798 799 2.035632 ACAGGAATTGAACCCGCAAAA 58.964 42.857 0.00 0.00 0.00 2.44
818 819 1.963855 CCCGTTCGTGTGCATCCAA 60.964 57.895 0.00 0.00 0.00 3.53
888 889 6.861065 ACCAATTCGTTATGTATGGATGAC 57.139 37.500 0.00 0.00 0.00 3.06
983 985 5.368145 CATCCATAAATCGACTTTCCCTCA 58.632 41.667 0.00 0.00 0.00 3.86
1036 1038 5.952526 TTCTTTCCCAATAAACGAAGACC 57.047 39.130 0.00 0.00 0.00 3.85
1147 1149 3.259374 CCAGGTAGTCGATGGCTATTCAT 59.741 47.826 0.00 0.00 0.00 2.57
1216 1218 7.545965 CAGATAAAGGGTAATGATCATACGTCC 59.454 40.741 9.04 8.65 0.00 4.79
1239 1241 9.892444 TCTAGAAGTGGAATATAATAACCCAGA 57.108 33.333 0.00 0.00 0.00 3.86
1323 1326 1.600511 TTGCGTGTGCTCGGGATAGA 61.601 55.000 0.00 0.00 43.34 1.98
1350 1353 4.574674 TGGATTTCACTTGCCTGTCTAT 57.425 40.909 0.00 0.00 0.00 1.98
1393 1396 2.028385 ACCTTTACCAGATGTCGTCCAC 60.028 50.000 0.00 0.00 0.00 4.02
1400 1403 6.969043 TGGAATTATGACCTTTACCAGATGT 58.031 36.000 0.00 0.00 0.00 3.06
1403 1406 7.570982 TCCTATGGAATTATGACCTTTACCAGA 59.429 37.037 0.00 0.00 0.00 3.86
1425 1432 2.171659 TGCCTTGCGGTAATGATTCCTA 59.828 45.455 0.00 0.00 0.00 2.94
1523 1530 8.118976 TGATTAGGGTCGTATTCTATGGTTAG 57.881 38.462 0.00 0.00 0.00 2.34
1641 1648 9.184523 CCATTGATATAGGAACTTTTGTACCAA 57.815 33.333 0.00 0.00 41.75 3.67
1912 1921 0.838987 AAGGGGTGCTTCCGGTTCTA 60.839 55.000 0.00 0.00 37.00 2.10
2019 2028 3.056832 GGAGACATCCCTATTTTCCCCT 58.943 50.000 0.00 0.00 40.03 4.79
2096 2105 6.433766 GCTTATGTTCTTCATGTAGCATTCC 58.566 40.000 0.00 0.00 41.17 3.01


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

AutoCloner maintained by Alex Coulton.