Multiple sequence alignment - TraesCS2D01G449000

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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 TraesCS2D01G449000 chr2D 100.000 2471 0 0 1 2471 558906497 558904027 0.000000e+00 4564.0
1 TraesCS2D01G449000 chr2D 97.024 840 12 6 1645 2471 545012493 545013332 0.000000e+00 1400.0
2 TraesCS2D01G449000 chr2D 79.124 776 120 34 896 1654 558957104 558956354 4.750000e-137 497.0
3 TraesCS2D01G449000 chr2D 86.364 66 7 2 791 855 558957187 558957123 1.230000e-08 71.3
4 TraesCS2D01G449000 chr2A 92.633 1113 53 13 578 1665 699536463 699535355 0.000000e+00 1574.0
5 TraesCS2D01G449000 chr2A 92.561 820 45 8 1668 2471 778784159 778783340 0.000000e+00 1162.0
6 TraesCS2D01G449000 chr2A 83.575 1035 87 39 668 1665 699556055 699555067 0.000000e+00 893.0
7 TraesCS2D01G449000 chr2B 87.582 1369 85 39 373 1665 667426392 667425033 0.000000e+00 1507.0
8 TraesCS2D01G449000 chr2B 83.298 1401 162 43 186 1541 668013228 668011855 0.000000e+00 1225.0
9 TraesCS2D01G449000 chr2B 79.474 380 68 8 896 1270 668023099 668022725 6.780000e-66 261.0
10 TraesCS2D01G449000 chr2B 89.809 157 15 1 2310 2465 718975040 718974884 1.500000e-47 200.0
11 TraesCS2D01G449000 chr7A 92.831 823 41 9 1666 2471 611732160 611731339 0.000000e+00 1177.0
12 TraesCS2D01G449000 chr7A 87.636 461 47 8 1853 2306 706085687 706086144 6.050000e-146 527.0
13 TraesCS2D01G449000 chr3D 93.040 819 36 13 1665 2463 580920089 580920906 0.000000e+00 1177.0
14 TraesCS2D01G449000 chr6A 92.019 827 46 10 1664 2471 615481561 615480736 0.000000e+00 1144.0
15 TraesCS2D01G449000 chr1D 96.902 581 10 4 1664 2237 488618280 488618859 0.000000e+00 966.0
16 TraesCS2D01G449000 chr4A 88.509 818 55 14 1665 2471 691703152 691703941 0.000000e+00 953.0
17 TraesCS2D01G449000 chr5A 94.366 568 27 2 1903 2465 51750551 51751118 0.000000e+00 867.0
18 TraesCS2D01G449000 chr5A 88.976 254 16 7 1663 1904 51750137 51750390 1.110000e-78 303.0
19 TraesCS2D01G449000 chr5A 81.609 87 8 5 14 98 413189022 413189102 5.700000e-07 65.8
20 TraesCS2D01G449000 chr3A 100.000 29 0 0 67 95 645757554 645757582 1.000000e-03 54.7


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 TraesCS2D01G449000 chr2D 558904027 558906497 2470 True 4564.00 4564 100.000 1 2471 1 chr2D.!!$R1 2470
1 TraesCS2D01G449000 chr2D 545012493 545013332 839 False 1400.00 1400 97.024 1645 2471 1 chr2D.!!$F1 826
2 TraesCS2D01G449000 chr2D 558956354 558957187 833 True 284.15 497 82.744 791 1654 2 chr2D.!!$R2 863
3 TraesCS2D01G449000 chr2A 699535355 699536463 1108 True 1574.00 1574 92.633 578 1665 1 chr2A.!!$R1 1087
4 TraesCS2D01G449000 chr2A 778783340 778784159 819 True 1162.00 1162 92.561 1668 2471 1 chr2A.!!$R3 803
5 TraesCS2D01G449000 chr2A 699555067 699556055 988 True 893.00 893 83.575 668 1665 1 chr2A.!!$R2 997
6 TraesCS2D01G449000 chr2B 667425033 667426392 1359 True 1507.00 1507 87.582 373 1665 1 chr2B.!!$R1 1292
7 TraesCS2D01G449000 chr2B 668011855 668013228 1373 True 1225.00 1225 83.298 186 1541 1 chr2B.!!$R2 1355
8 TraesCS2D01G449000 chr7A 611731339 611732160 821 True 1177.00 1177 92.831 1666 2471 1 chr7A.!!$R1 805
9 TraesCS2D01G449000 chr3D 580920089 580920906 817 False 1177.00 1177 93.040 1665 2463 1 chr3D.!!$F1 798
10 TraesCS2D01G449000 chr6A 615480736 615481561 825 True 1144.00 1144 92.019 1664 2471 1 chr6A.!!$R1 807
11 TraesCS2D01G449000 chr1D 488618280 488618859 579 False 966.00 966 96.902 1664 2237 1 chr1D.!!$F1 573
12 TraesCS2D01G449000 chr4A 691703152 691703941 789 False 953.00 953 88.509 1665 2471 1 chr4A.!!$F1 806
13 TraesCS2D01G449000 chr5A 51750137 51751118 981 False 585.00 867 91.671 1663 2465 2 chr5A.!!$F2 802

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
706 750 0.108207 CTCATGGACCTGATGCCTCC 59.892 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2360 2.543012 CACAAATTTGCACGAATTGGCA 59.457 40.909 18.12 0.0 38.46 4.92 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
33 34 6.505039 AAAATCTAAAAAGCCGAAAACACG 57.495 33.333 0.00 0.00 0.00 4.49
34 35 4.823790 ATCTAAAAAGCCGAAAACACGT 57.176 36.364 0.00 0.00 0.00 4.49
35 36 3.942739 TCTAAAAAGCCGAAAACACGTG 58.057 40.909 15.48 15.48 0.00 4.49
36 37 1.273688 AAAAAGCCGAAAACACGTGC 58.726 45.000 17.22 0.00 0.00 5.34
37 38 0.863957 AAAAGCCGAAAACACGTGCG 60.864 50.000 17.22 10.98 35.71 5.34
38 39 1.707239 AAAGCCGAAAACACGTGCGA 61.707 50.000 17.22 0.00 35.71 5.10
39 40 1.707239 AAGCCGAAAACACGTGCGAA 61.707 50.000 17.22 0.00 35.71 4.70
40 41 1.297745 GCCGAAAACACGTGCGAAA 60.298 52.632 17.22 0.00 0.00 3.46
41 42 0.862283 GCCGAAAACACGTGCGAAAA 60.862 50.000 17.22 0.00 0.00 2.29
42 43 1.536149 CCGAAAACACGTGCGAAAAA 58.464 45.000 17.22 0.00 0.00 1.94
63 64 2.438868 AACAAAATTGAAGGGAGCGC 57.561 45.000 0.00 0.00 0.00 5.92
64 65 0.603065 ACAAAATTGAAGGGAGCGCC 59.397 50.000 2.29 0.00 0.00 6.53
65 66 0.890683 CAAAATTGAAGGGAGCGCCT 59.109 50.000 2.29 0.00 0.00 5.52
66 67 2.091541 CAAAATTGAAGGGAGCGCCTA 58.908 47.619 2.29 0.00 0.00 3.93
67 68 2.044123 AAATTGAAGGGAGCGCCTAG 57.956 50.000 2.29 0.00 0.00 3.02
68 69 1.204146 AATTGAAGGGAGCGCCTAGA 58.796 50.000 2.29 0.00 0.00 2.43
69 70 0.755686 ATTGAAGGGAGCGCCTAGAG 59.244 55.000 2.29 0.00 0.00 2.43
70 71 1.961180 TTGAAGGGAGCGCCTAGAGC 61.961 60.000 2.29 0.00 38.52 4.09
79 80 2.105128 GCCTAGAGCGCGACACAT 59.895 61.111 12.10 0.00 0.00 3.21
80 81 1.359117 GCCTAGAGCGCGACACATA 59.641 57.895 12.10 0.00 0.00 2.29
81 82 0.661780 GCCTAGAGCGCGACACATAG 60.662 60.000 12.10 3.74 0.00 2.23
82 83 0.661780 CCTAGAGCGCGACACATAGC 60.662 60.000 12.10 0.00 0.00 2.97
105 106 3.123620 CTGAGAGCGCCAGCCAAC 61.124 66.667 2.29 0.00 46.67 3.77
106 107 4.704833 TGAGAGCGCCAGCCAACC 62.705 66.667 2.29 0.00 46.67 3.77
113 114 3.384532 GCCAGCCAACCCCATGTG 61.385 66.667 0.00 0.00 0.00 3.21
114 115 2.440147 CCAGCCAACCCCATGTGA 59.560 61.111 0.00 0.00 0.00 3.58
115 116 1.978617 CCAGCCAACCCCATGTGAC 60.979 63.158 0.00 0.00 0.00 3.67
116 117 1.978617 CAGCCAACCCCATGTGACC 60.979 63.158 0.00 0.00 0.00 4.02
117 118 2.162906 AGCCAACCCCATGTGACCT 61.163 57.895 0.00 0.00 0.00 3.85
118 119 1.228862 GCCAACCCCATGTGACCTT 60.229 57.895 0.00 0.00 0.00 3.50
119 120 0.831711 GCCAACCCCATGTGACCTTT 60.832 55.000 0.00 0.00 0.00 3.11
120 121 0.968405 CCAACCCCATGTGACCTTTG 59.032 55.000 0.00 0.00 0.00 2.77
121 122 0.968405 CAACCCCATGTGACCTTTGG 59.032 55.000 0.00 0.00 0.00 3.28
123 124 4.440145 CCCATGTGACCTTTGGGG 57.560 61.111 7.29 0.00 45.37 4.96
124 125 1.773635 CCCATGTGACCTTTGGGGA 59.226 57.895 7.29 0.00 45.37 4.81
125 126 0.323725 CCCATGTGACCTTTGGGGAG 60.324 60.000 7.29 0.00 45.37 4.30
126 127 0.323725 CCATGTGACCTTTGGGGAGG 60.324 60.000 0.00 0.00 42.75 4.30
127 128 0.967380 CATGTGACCTTTGGGGAGGC 60.967 60.000 0.00 0.00 40.65 4.70
128 129 1.142688 ATGTGACCTTTGGGGAGGCT 61.143 55.000 0.00 0.00 40.65 4.58
129 130 1.002011 GTGACCTTTGGGGAGGCTC 60.002 63.158 5.78 5.78 40.65 4.70
130 131 2.231380 TGACCTTTGGGGAGGCTCC 61.231 63.158 25.80 25.80 40.65 4.70
131 132 3.330720 ACCTTTGGGGAGGCTCCG 61.331 66.667 26.54 14.28 40.65 4.63
138 139 4.821589 GGGAGGCTCCGCAACGAG 62.822 72.222 26.54 0.00 37.43 4.18
148 149 2.744709 GCAACGAGCGCCCCTTAA 60.745 61.111 2.29 0.00 0.00 1.85
149 150 2.112815 GCAACGAGCGCCCCTTAAT 61.113 57.895 2.29 0.00 0.00 1.40
150 151 1.654023 GCAACGAGCGCCCCTTAATT 61.654 55.000 2.29 0.00 0.00 1.40
151 152 1.658994 CAACGAGCGCCCCTTAATTA 58.341 50.000 2.29 0.00 0.00 1.40
152 153 1.597663 CAACGAGCGCCCCTTAATTAG 59.402 52.381 2.29 0.00 0.00 1.73
153 154 0.828677 ACGAGCGCCCCTTAATTAGT 59.171 50.000 2.29 0.00 0.00 2.24
154 155 1.208776 ACGAGCGCCCCTTAATTAGTT 59.791 47.619 2.29 0.00 0.00 2.24
155 156 1.597663 CGAGCGCCCCTTAATTAGTTG 59.402 52.381 2.29 0.00 0.00 3.16
156 157 1.333931 GAGCGCCCCTTAATTAGTTGC 59.666 52.381 2.29 0.00 0.00 4.17
157 158 1.064685 AGCGCCCCTTAATTAGTTGCT 60.065 47.619 2.29 0.00 0.00 3.91
158 159 1.333931 GCGCCCCTTAATTAGTTGCTC 59.666 52.381 0.00 0.00 0.00 4.26
159 160 2.919228 CGCCCCTTAATTAGTTGCTCT 58.081 47.619 0.00 0.00 0.00 4.09
160 161 2.872858 CGCCCCTTAATTAGTTGCTCTC 59.127 50.000 0.00 0.00 0.00 3.20
161 162 3.215151 GCCCCTTAATTAGTTGCTCTCC 58.785 50.000 0.00 0.00 0.00 3.71
162 163 3.371595 GCCCCTTAATTAGTTGCTCTCCA 60.372 47.826 0.00 0.00 0.00 3.86
163 164 4.855340 CCCCTTAATTAGTTGCTCTCCAA 58.145 43.478 0.00 0.00 0.00 3.53
164 165 5.449553 CCCCTTAATTAGTTGCTCTCCAAT 58.550 41.667 0.00 0.00 35.55 3.16
165 166 5.300286 CCCCTTAATTAGTTGCTCTCCAATG 59.700 44.000 0.00 0.00 35.55 2.82
166 167 5.888161 CCCTTAATTAGTTGCTCTCCAATGT 59.112 40.000 0.00 0.00 35.55 2.71
167 168 6.378280 CCCTTAATTAGTTGCTCTCCAATGTT 59.622 38.462 0.00 0.00 35.55 2.71
168 169 7.093771 CCCTTAATTAGTTGCTCTCCAATGTTT 60.094 37.037 0.00 0.00 35.55 2.83
169 170 8.956426 CCTTAATTAGTTGCTCTCCAATGTTTA 58.044 33.333 0.00 0.00 35.55 2.01
170 171 9.994432 CTTAATTAGTTGCTCTCCAATGTTTAG 57.006 33.333 0.00 0.00 35.55 1.85
171 172 7.396540 AATTAGTTGCTCTCCAATGTTTAGG 57.603 36.000 0.00 0.00 35.55 2.69
172 173 4.373156 AGTTGCTCTCCAATGTTTAGGT 57.627 40.909 0.00 0.00 35.55 3.08
173 174 4.074970 AGTTGCTCTCCAATGTTTAGGTG 58.925 43.478 0.00 0.00 35.55 4.00
174 175 3.788227 TGCTCTCCAATGTTTAGGTGT 57.212 42.857 0.00 0.00 0.00 4.16
175 176 4.098914 TGCTCTCCAATGTTTAGGTGTT 57.901 40.909 0.00 0.00 0.00 3.32
176 177 4.469657 TGCTCTCCAATGTTTAGGTGTTT 58.530 39.130 0.00 0.00 0.00 2.83
177 178 4.518970 TGCTCTCCAATGTTTAGGTGTTTC 59.481 41.667 0.00 0.00 0.00 2.78
178 179 4.378459 GCTCTCCAATGTTTAGGTGTTTCG 60.378 45.833 0.00 0.00 0.00 3.46
179 180 4.710324 TCTCCAATGTTTAGGTGTTTCGT 58.290 39.130 0.00 0.00 0.00 3.85
180 181 4.513692 TCTCCAATGTTTAGGTGTTTCGTG 59.486 41.667 0.00 0.00 0.00 4.35
181 182 3.003897 TCCAATGTTTAGGTGTTTCGTGC 59.996 43.478 0.00 0.00 0.00 5.34
182 183 3.004315 CCAATGTTTAGGTGTTTCGTGCT 59.996 43.478 0.00 0.00 0.00 4.40
183 184 4.214545 CCAATGTTTAGGTGTTTCGTGCTA 59.785 41.667 0.00 0.00 0.00 3.49
184 185 5.382303 CAATGTTTAGGTGTTTCGTGCTAG 58.618 41.667 0.00 0.00 0.00 3.42
192 193 1.235724 GTTTCGTGCTAGGCTGGTTT 58.764 50.000 0.00 0.00 0.00 3.27
199 200 1.450312 CTAGGCTGGTTTGGGCTCG 60.450 63.158 0.00 0.00 40.13 5.03
224 225 3.157750 TGGTATGTTTAGCCGGGTTTT 57.842 42.857 13.43 0.00 0.00 2.43
235 236 1.822371 GCCGGGTTTTGTTACATCCAT 59.178 47.619 2.18 0.00 0.00 3.41
253 254 2.290577 CCATCCCAAATCCTAGCCTAGC 60.291 54.545 0.00 0.00 0.00 3.42
259 260 0.568192 AATCCTAGCCTAGCCTGGGA 59.432 55.000 8.36 8.36 45.07 4.37
263 264 2.387160 TCCTAGCCTAGCCTGGGATATT 59.613 50.000 1.12 0.00 37.54 1.28
274 275 4.070716 GCCTGGGATATTCTCATGTCTTG 58.929 47.826 0.00 0.00 0.00 3.02
278 279 5.684704 TGGGATATTCTCATGTCTTGTTCC 58.315 41.667 0.00 0.00 0.00 3.62
280 281 5.762218 GGGATATTCTCATGTCTTGTTCCAG 59.238 44.000 0.00 0.00 0.00 3.86
296 297 1.071699 TCCAGTGGCTGTAGGTGAAAC 59.928 52.381 3.51 0.00 0.00 2.78
407 408 6.844696 ATAACACAGCTTATGATGTAACCG 57.155 37.500 0.00 0.00 41.28 4.44
410 411 3.242944 CACAGCTTATGATGTAACCGACG 59.757 47.826 0.00 0.00 41.28 5.12
480 482 2.530460 AATGGGACCTGCTTGCATTA 57.470 45.000 0.00 0.00 0.00 1.90
481 483 2.761786 ATGGGACCTGCTTGCATTAT 57.238 45.000 0.00 0.00 0.00 1.28
482 484 2.530460 TGGGACCTGCTTGCATTATT 57.470 45.000 0.00 0.00 0.00 1.40
483 485 3.660970 TGGGACCTGCTTGCATTATTA 57.339 42.857 0.00 0.00 0.00 0.98
663 699 2.289195 TGTCTCCATGAACAACCGTACC 60.289 50.000 0.00 0.00 0.00 3.34
684 724 3.276857 CTGTAGCATCTGCAGGTTCATT 58.723 45.455 15.13 0.00 45.16 2.57
687 727 1.203994 AGCATCTGCAGGTTCATTTGC 59.796 47.619 15.13 5.13 45.16 3.68
706 750 0.108207 CTCATGGACCTGATGCCTCC 59.892 60.000 0.00 0.00 0.00 4.30
1012 1080 2.125147 CGAAGATGGGAAGCGCCA 60.125 61.111 2.29 0.00 38.95 5.69
1169 1237 2.183555 CTTCTACACGCCCCCGAC 59.816 66.667 0.00 0.00 38.29 4.79
1204 1272 1.419374 CGAGGTGAAGAAGGTTGACG 58.581 55.000 0.00 0.00 0.00 4.35
1270 1338 4.373116 GCCCCGTGAAGCTCGTCA 62.373 66.667 0.00 0.00 0.00 4.35
1392 1499 3.936203 TTCTGCACGGCCGGACTT 61.936 61.111 31.76 4.77 0.00 3.01
1524 1636 1.826024 CCGGTGAAGGAGATGGAGG 59.174 63.158 0.00 0.00 0.00 4.30
1526 1638 0.978146 CGGTGAAGGAGATGGAGGGT 60.978 60.000 0.00 0.00 0.00 4.34
1541 1653 3.205056 TGGAGGGTTCATGGCAGAATAAT 59.795 43.478 0.00 0.00 0.00 1.28
1542 1654 4.415179 TGGAGGGTTCATGGCAGAATAATA 59.585 41.667 0.00 0.00 0.00 0.98
1790 1942 2.909965 ACACGGCCGGCATGTTTT 60.910 55.556 31.76 12.12 0.00 2.43
2066 2403 2.311463 TGCATTTCCTTTTTCCGGTCA 58.689 42.857 0.00 0.00 0.00 4.02
2082 2422 5.172934 TCCGGTCACAACATTCTGTATTAC 58.827 41.667 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.532302 ACGTGTTTTCGGCTTTTTAGATTTTT 59.468 30.769 0.00 0.00 34.94 1.94
10 11 6.020201 CACGTGTTTTCGGCTTTTTAGATTTT 60.020 34.615 7.58 0.00 34.94 1.82
11 12 5.457473 CACGTGTTTTCGGCTTTTTAGATTT 59.543 36.000 7.58 0.00 34.94 2.17
12 13 4.973663 CACGTGTTTTCGGCTTTTTAGATT 59.026 37.500 7.58 0.00 34.94 2.40
13 14 4.533222 CACGTGTTTTCGGCTTTTTAGAT 58.467 39.130 7.58 0.00 34.94 1.98
14 15 3.789459 GCACGTGTTTTCGGCTTTTTAGA 60.789 43.478 18.38 0.00 34.94 2.10
15 16 2.466205 GCACGTGTTTTCGGCTTTTTAG 59.534 45.455 18.38 0.00 34.94 1.85
16 17 2.452105 GCACGTGTTTTCGGCTTTTTA 58.548 42.857 18.38 0.00 34.94 1.52
17 18 1.273688 GCACGTGTTTTCGGCTTTTT 58.726 45.000 18.38 0.00 34.94 1.94
18 19 0.863957 CGCACGTGTTTTCGGCTTTT 60.864 50.000 18.38 0.00 34.94 2.27
19 20 1.298041 CGCACGTGTTTTCGGCTTT 60.298 52.632 18.38 0.00 34.94 3.51
20 21 1.707239 TTCGCACGTGTTTTCGGCTT 61.707 50.000 18.38 0.00 34.94 4.35
21 22 1.707239 TTTCGCACGTGTTTTCGGCT 61.707 50.000 18.38 0.00 34.94 5.52
22 23 0.862283 TTTTCGCACGTGTTTTCGGC 60.862 50.000 18.38 0.00 34.94 5.54
23 24 1.536149 TTTTTCGCACGTGTTTTCGG 58.464 45.000 18.38 0.25 34.94 4.30
41 42 3.559655 GCGCTCCCTTCAATTTTGTTTTT 59.440 39.130 0.00 0.00 0.00 1.94
42 43 3.130633 GCGCTCCCTTCAATTTTGTTTT 58.869 40.909 0.00 0.00 0.00 2.43
43 44 2.547855 GGCGCTCCCTTCAATTTTGTTT 60.548 45.455 7.64 0.00 0.00 2.83
44 45 1.000843 GGCGCTCCCTTCAATTTTGTT 59.999 47.619 7.64 0.00 0.00 2.83
45 46 0.603065 GGCGCTCCCTTCAATTTTGT 59.397 50.000 7.64 0.00 0.00 2.83
46 47 0.890683 AGGCGCTCCCTTCAATTTTG 59.109 50.000 7.64 0.00 43.06 2.44
47 48 2.026262 TCTAGGCGCTCCCTTCAATTTT 60.026 45.455 7.64 0.00 43.06 1.82
48 49 1.559682 TCTAGGCGCTCCCTTCAATTT 59.440 47.619 7.64 0.00 43.06 1.82
49 50 1.139853 CTCTAGGCGCTCCCTTCAATT 59.860 52.381 7.64 0.00 43.06 2.32
50 51 0.755686 CTCTAGGCGCTCCCTTCAAT 59.244 55.000 7.64 0.00 43.06 2.57
51 52 1.961180 GCTCTAGGCGCTCCCTTCAA 61.961 60.000 7.64 0.00 43.06 2.69
52 53 2.427245 GCTCTAGGCGCTCCCTTCA 61.427 63.158 7.64 0.00 43.06 3.02
53 54 2.419620 GCTCTAGGCGCTCCCTTC 59.580 66.667 7.64 0.00 43.06 3.46
62 63 0.661780 CTATGTGTCGCGCTCTAGGC 60.662 60.000 5.56 0.00 37.64 3.93
63 64 0.661780 GCTATGTGTCGCGCTCTAGG 60.662 60.000 5.56 0.00 0.00 3.02
64 65 0.994241 CGCTATGTGTCGCGCTCTAG 60.994 60.000 5.56 0.00 43.01 2.43
65 66 1.010013 CGCTATGTGTCGCGCTCTA 60.010 57.895 5.56 0.00 43.01 2.43
66 67 2.278206 CGCTATGTGTCGCGCTCT 60.278 61.111 5.56 0.00 43.01 4.09
72 73 4.873129 AGCCGCCGCTATGTGTCG 62.873 66.667 0.00 0.00 46.08 4.35
73 74 3.264897 CAGCCGCCGCTATGTGTC 61.265 66.667 0.00 0.00 46.25 3.67
74 75 3.723235 CTCAGCCGCCGCTATGTGT 62.723 63.158 0.00 0.00 46.25 3.72
75 76 2.963854 CTCAGCCGCCGCTATGTG 60.964 66.667 0.00 0.00 46.25 3.21
76 77 3.144120 CTCTCAGCCGCCGCTATGT 62.144 63.158 0.00 0.00 46.25 2.29
77 78 2.355599 CTCTCAGCCGCCGCTATG 60.356 66.667 0.00 0.00 46.25 2.23
78 79 4.292178 GCTCTCAGCCGCCGCTAT 62.292 66.667 0.00 0.00 46.25 2.97
88 89 3.123620 GTTGGCTGGCGCTCTCAG 61.124 66.667 7.64 7.66 36.09 3.35
89 90 4.704833 GGTTGGCTGGCGCTCTCA 62.705 66.667 7.64 0.00 36.09 3.27
96 97 3.384532 CACATGGGGTTGGCTGGC 61.385 66.667 0.00 0.00 0.00 4.85
97 98 1.978617 GTCACATGGGGTTGGCTGG 60.979 63.158 0.00 0.00 0.00 4.85
98 99 1.978617 GGTCACATGGGGTTGGCTG 60.979 63.158 0.00 0.00 0.00 4.85
99 100 1.729267 AAGGTCACATGGGGTTGGCT 61.729 55.000 0.00 0.00 0.00 4.75
100 101 0.831711 AAAGGTCACATGGGGTTGGC 60.832 55.000 0.00 0.00 0.00 4.52
101 102 0.968405 CAAAGGTCACATGGGGTTGG 59.032 55.000 0.00 0.00 0.00 3.77
102 103 0.968405 CCAAAGGTCACATGGGGTTG 59.032 55.000 0.00 0.00 0.00 3.77
103 104 3.455737 CCAAAGGTCACATGGGGTT 57.544 52.632 0.00 0.00 0.00 4.11
107 108 0.323725 CCTCCCCAAAGGTCACATGG 60.324 60.000 0.00 0.00 36.75 3.66
108 109 0.967380 GCCTCCCCAAAGGTCACATG 60.967 60.000 0.00 0.00 38.79 3.21
109 110 1.142688 AGCCTCCCCAAAGGTCACAT 61.143 55.000 0.00 0.00 38.79 3.21
110 111 1.774217 AGCCTCCCCAAAGGTCACA 60.774 57.895 0.00 0.00 38.79 3.58
111 112 1.002011 GAGCCTCCCCAAAGGTCAC 60.002 63.158 0.00 0.00 38.79 3.67
112 113 2.231380 GGAGCCTCCCCAAAGGTCA 61.231 63.158 0.00 0.00 38.79 4.02
113 114 2.677848 GGAGCCTCCCCAAAGGTC 59.322 66.667 0.00 0.00 38.79 3.85
114 115 3.330720 CGGAGCCTCCCCAAAGGT 61.331 66.667 4.85 0.00 38.79 3.50
131 132 1.654023 AATTAAGGGGCGCTCGTTGC 61.654 55.000 24.68 0.00 38.57 4.17
132 133 1.597663 CTAATTAAGGGGCGCTCGTTG 59.402 52.381 24.68 4.01 0.00 4.10
133 134 1.208776 ACTAATTAAGGGGCGCTCGTT 59.791 47.619 20.26 20.26 0.00 3.85
134 135 0.828677 ACTAATTAAGGGGCGCTCGT 59.171 50.000 7.64 0.00 0.00 4.18
135 136 1.597663 CAACTAATTAAGGGGCGCTCG 59.402 52.381 7.64 0.00 0.00 5.03
136 137 1.333931 GCAACTAATTAAGGGGCGCTC 59.666 52.381 7.64 1.18 0.00 5.03
137 138 1.064685 AGCAACTAATTAAGGGGCGCT 60.065 47.619 7.64 0.00 34.58 5.92
138 139 1.333931 GAGCAACTAATTAAGGGGCGC 59.666 52.381 0.00 0.00 34.58 6.53
139 140 2.872858 GAGAGCAACTAATTAAGGGGCG 59.127 50.000 0.00 0.00 34.58 6.13
140 141 3.215151 GGAGAGCAACTAATTAAGGGGC 58.785 50.000 0.00 0.00 0.00 5.80
141 142 4.503714 TGGAGAGCAACTAATTAAGGGG 57.496 45.455 0.00 0.00 0.00 4.79
142 143 5.888161 ACATTGGAGAGCAACTAATTAAGGG 59.112 40.000 0.00 0.00 0.00 3.95
143 144 7.396540 AACATTGGAGAGCAACTAATTAAGG 57.603 36.000 0.00 0.00 0.00 2.69
144 145 9.994432 CTAAACATTGGAGAGCAACTAATTAAG 57.006 33.333 0.00 0.00 0.00 1.85
145 146 8.956426 CCTAAACATTGGAGAGCAACTAATTAA 58.044 33.333 0.00 0.00 0.00 1.40
146 147 8.107095 ACCTAAACATTGGAGAGCAACTAATTA 58.893 33.333 0.00 0.00 0.00 1.40
147 148 6.948309 ACCTAAACATTGGAGAGCAACTAATT 59.052 34.615 0.00 0.00 0.00 1.40
148 149 6.375455 CACCTAAACATTGGAGAGCAACTAAT 59.625 38.462 0.00 0.00 0.00 1.73
149 150 5.705441 CACCTAAACATTGGAGAGCAACTAA 59.295 40.000 0.00 0.00 0.00 2.24
150 151 5.221843 ACACCTAAACATTGGAGAGCAACTA 60.222 40.000 0.00 0.00 0.00 2.24
151 152 4.074970 CACCTAAACATTGGAGAGCAACT 58.925 43.478 0.00 0.00 0.00 3.16
152 153 3.821033 ACACCTAAACATTGGAGAGCAAC 59.179 43.478 0.00 0.00 0.00 4.17
153 154 4.098914 ACACCTAAACATTGGAGAGCAA 57.901 40.909 0.00 0.00 0.00 3.91
154 155 3.788227 ACACCTAAACATTGGAGAGCA 57.212 42.857 0.00 0.00 0.00 4.26
155 156 4.378459 CGAAACACCTAAACATTGGAGAGC 60.378 45.833 0.00 0.00 0.00 4.09
156 157 4.755123 ACGAAACACCTAAACATTGGAGAG 59.245 41.667 0.00 0.00 0.00 3.20
157 158 4.513692 CACGAAACACCTAAACATTGGAGA 59.486 41.667 0.00 0.00 0.00 3.71
158 159 4.783242 CACGAAACACCTAAACATTGGAG 58.217 43.478 0.00 0.00 0.00 3.86
159 160 3.003897 GCACGAAACACCTAAACATTGGA 59.996 43.478 0.00 0.00 0.00 3.53
160 161 3.004315 AGCACGAAACACCTAAACATTGG 59.996 43.478 0.00 0.00 0.00 3.16
161 162 4.223320 AGCACGAAACACCTAAACATTG 57.777 40.909 0.00 0.00 0.00 2.82
162 163 4.454504 CCTAGCACGAAACACCTAAACATT 59.545 41.667 0.00 0.00 0.00 2.71
163 164 4.000988 CCTAGCACGAAACACCTAAACAT 58.999 43.478 0.00 0.00 0.00 2.71
164 165 3.395639 CCTAGCACGAAACACCTAAACA 58.604 45.455 0.00 0.00 0.00 2.83
165 166 2.159037 GCCTAGCACGAAACACCTAAAC 59.841 50.000 0.00 0.00 0.00 2.01
166 167 2.038033 AGCCTAGCACGAAACACCTAAA 59.962 45.455 0.00 0.00 0.00 1.85
167 168 1.621814 AGCCTAGCACGAAACACCTAA 59.378 47.619 0.00 0.00 0.00 2.69
168 169 1.067142 CAGCCTAGCACGAAACACCTA 60.067 52.381 0.00 0.00 0.00 3.08
169 170 0.320771 CAGCCTAGCACGAAACACCT 60.321 55.000 0.00 0.00 0.00 4.00
170 171 1.298859 CCAGCCTAGCACGAAACACC 61.299 60.000 0.00 0.00 0.00 4.16
171 172 0.602905 ACCAGCCTAGCACGAAACAC 60.603 55.000 0.00 0.00 0.00 3.32
172 173 0.107831 AACCAGCCTAGCACGAAACA 59.892 50.000 0.00 0.00 0.00 2.83
173 174 1.069227 CAAACCAGCCTAGCACGAAAC 60.069 52.381 0.00 0.00 0.00 2.78
174 175 1.234821 CAAACCAGCCTAGCACGAAA 58.765 50.000 0.00 0.00 0.00 3.46
175 176 0.605319 CCAAACCAGCCTAGCACGAA 60.605 55.000 0.00 0.00 0.00 3.85
176 177 1.003839 CCAAACCAGCCTAGCACGA 60.004 57.895 0.00 0.00 0.00 4.35
177 178 2.040544 CCCAAACCAGCCTAGCACG 61.041 63.158 0.00 0.00 0.00 5.34
178 179 2.343426 GCCCAAACCAGCCTAGCAC 61.343 63.158 0.00 0.00 0.00 4.40
179 180 2.035626 GCCCAAACCAGCCTAGCA 59.964 61.111 0.00 0.00 0.00 3.49
180 181 1.750780 GAGCCCAAACCAGCCTAGC 60.751 63.158 0.00 0.00 0.00 3.42
181 182 1.450312 CGAGCCCAAACCAGCCTAG 60.450 63.158 0.00 0.00 0.00 3.02
182 183 1.899437 CTCGAGCCCAAACCAGCCTA 61.899 60.000 0.00 0.00 0.00 3.93
183 184 3.249189 TCGAGCCCAAACCAGCCT 61.249 61.111 0.00 0.00 0.00 4.58
184 185 2.747855 CTCGAGCCCAAACCAGCC 60.748 66.667 0.00 0.00 0.00 4.85
192 193 1.264749 ACATACCAAGCTCGAGCCCA 61.265 55.000 32.94 14.43 43.38 5.36
199 200 1.940613 CCGGCTAAACATACCAAGCTC 59.059 52.381 0.00 0.00 35.30 4.09
224 225 4.879295 AGGATTTGGGATGGATGTAACA 57.121 40.909 0.00 0.00 0.00 2.41
235 236 1.061346 AGGCTAGGCTAGGATTTGGGA 60.061 52.381 18.73 0.00 0.00 4.37
253 254 5.301835 ACAAGACATGAGAATATCCCAGG 57.698 43.478 0.00 0.00 0.00 4.45
259 260 6.118170 CCACTGGAACAAGACATGAGAATAT 58.882 40.000 0.00 0.00 38.70 1.28
263 264 2.550855 GCCACTGGAACAAGACATGAGA 60.551 50.000 0.00 0.00 38.70 3.27
274 275 0.685097 TCACCTACAGCCACTGGAAC 59.315 55.000 0.00 0.00 35.51 3.62
278 279 1.202758 TGGTTTCACCTACAGCCACTG 60.203 52.381 0.00 0.00 39.58 3.66
280 281 1.975660 TTGGTTTCACCTACAGCCAC 58.024 50.000 0.00 0.00 39.58 5.01
296 297 0.394216 TCTGCCCATGTCCGATTTGG 60.394 55.000 0.00 0.00 40.09 3.28
299 300 1.135094 ATCTCTGCCCATGTCCGATT 58.865 50.000 0.00 0.00 0.00 3.34
341 342 6.798427 ACAGGAATGAGTATATATCCGCAT 57.202 37.500 0.00 0.00 35.31 4.73
385 386 5.808540 GTCGGTTACATCATAAGCTGTGTTA 59.191 40.000 0.00 0.00 0.00 2.41
392 393 4.084537 CCATTCGTCGGTTACATCATAAGC 60.085 45.833 0.00 0.00 0.00 3.09
407 408 2.218953 TTAGTGATCGCCCATTCGTC 57.781 50.000 1.76 0.00 0.00 4.20
410 411 1.537202 GCCATTAGTGATCGCCCATTC 59.463 52.381 1.76 0.00 0.00 2.67
663 699 2.391616 TGAACCTGCAGATGCTACAG 57.608 50.000 17.39 0.00 42.66 2.74
684 724 0.394762 GGCATCAGGTCCATGAGCAA 60.395 55.000 0.00 0.00 31.44 3.91
687 727 0.108207 GGAGGCATCAGGTCCATGAG 59.892 60.000 0.00 0.00 31.44 2.90
706 750 4.814294 GGGTGTAGTGAGCGCCCG 62.814 72.222 2.29 0.00 45.38 6.13
1184 1252 1.149148 GTCAACCTTCTTCACCTCGC 58.851 55.000 0.00 0.00 0.00 5.03
1392 1499 5.981088 TTAAGTGGTACGTGGATTAGACA 57.019 39.130 0.00 0.00 0.00 3.41
1541 1653 5.173673 CACGCGCGGACTTTATTTATAGTTA 59.826 40.000 35.22 0.00 0.00 2.24
1542 1654 4.026310 CACGCGCGGACTTTATTTATAGTT 60.026 41.667 35.22 2.79 0.00 2.24
1570 1694 4.024698 GCTCACTAGCTCGGCATG 57.975 61.111 0.00 0.00 45.85 4.06
1591 1717 7.072030 GCAGATTACATTTTATGACGATGACC 58.928 38.462 0.00 0.00 0.00 4.02
1658 1798 8.225777 ACTGATTTTTAGTCGTTCCGTTTATTC 58.774 33.333 0.00 0.00 0.00 1.75
1685 1827 7.901029 ACTGAGACTTCAATAGAAATCAGTCA 58.099 34.615 11.47 0.00 42.43 3.41
1810 1968 6.129009 GCACTTTGCACAGTCTATTTTCAATG 60.129 38.462 1.59 0.00 44.26 2.82
2023 2360 2.543012 CACAAATTTGCACGAATTGGCA 59.457 40.909 18.12 0.00 38.46 4.92


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

AutoCloner maintained by Alex Coulton.