Multiple sequence alignment - TraesCS7D01G259100

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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 TraesCS7D01G259100 chr7D 100.000 2636 0 0 1 2636 234793377 234796012 0 4868
1 TraesCS7D01G259100 chr7A 94.826 2474 103 14 179 2636 249580379 249582843 0 3836
2 TraesCS7D01G259100 chr7B 92.160 2398 122 33 258 2636 210805865 210808215 0 3326


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 TraesCS7D01G259100 chr7D 234793377 234796012 2635 False 4868 4868 100.000 1 2636 1 chr7D.!!$F1 2635
1 TraesCS7D01G259100 chr7A 249580379 249582843 2464 False 3836 3836 94.826 179 2636 1 chr7A.!!$F1 2457
2 TraesCS7D01G259100 chr7B 210805865 210808215 2350 False 3326 3326 92.160 258 2636 1 chr7B.!!$F1 2378

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
75 76 0.035598 TGCGGACGGATGAGGAAAAA 59.964 50.0 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 1770 0.85353 AAATGGGTATCCTGAGCCCC 59.146 55.0 0.0 0.0 41.66 5.8 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
22 23 4.739195 TCAAATGCGGGTTTAAAGTATGC 58.261 39.130 0.00 0.00 0.00 3.14
23 24 4.218635 TCAAATGCGGGTTTAAAGTATGCA 59.781 37.500 6.75 6.75 35.10 3.96
24 25 4.370364 AATGCGGGTTTAAAGTATGCAG 57.630 40.909 9.34 0.00 33.99 4.41
25 26 3.060736 TGCGGGTTTAAAGTATGCAGA 57.939 42.857 0.00 0.00 0.00 4.26
26 27 3.006940 TGCGGGTTTAAAGTATGCAGAG 58.993 45.455 0.00 0.00 0.00 3.35
27 28 3.267483 GCGGGTTTAAAGTATGCAGAGA 58.733 45.455 0.00 0.00 0.00 3.10
28 29 3.309954 GCGGGTTTAAAGTATGCAGAGAG 59.690 47.826 0.00 0.00 0.00 3.20
29 30 3.309954 CGGGTTTAAAGTATGCAGAGAGC 59.690 47.826 0.00 0.00 45.96 4.09
39 40 1.427020 GCAGAGAGCGTTGAATGGC 59.573 57.895 0.00 0.00 0.00 4.40
40 41 1.712081 CAGAGAGCGTTGAATGGCG 59.288 57.895 0.00 0.00 0.00 5.69
41 42 1.448540 AGAGAGCGTTGAATGGCGG 60.449 57.895 0.00 0.00 0.00 6.13
42 43 3.100862 GAGAGCGTTGAATGGCGGC 62.101 63.158 0.00 0.00 0.00 6.53
43 44 4.179579 GAGCGTTGAATGGCGGCC 62.180 66.667 13.32 13.32 0.00 6.13
44 45 4.722700 AGCGTTGAATGGCGGCCT 62.723 61.111 21.46 0.00 0.00 5.19
45 46 4.179579 GCGTTGAATGGCGGCCTC 62.180 66.667 21.46 11.00 0.00 4.70
46 47 3.508840 CGTTGAATGGCGGCCTCC 61.509 66.667 21.46 4.25 0.00 4.30
47 48 2.044946 GTTGAATGGCGGCCTCCT 60.045 61.111 21.46 4.04 0.00 3.69
48 49 1.678970 GTTGAATGGCGGCCTCCTT 60.679 57.895 21.46 10.95 0.00 3.36
49 50 1.378514 TTGAATGGCGGCCTCCTTC 60.379 57.895 21.46 18.80 0.00 3.46
50 51 2.517166 GAATGGCGGCCTCCTTCC 60.517 66.667 21.46 0.61 0.00 3.46
56 57 3.382832 CGGCCTCCTTCCGTGTCT 61.383 66.667 0.00 0.00 41.85 3.41
57 58 2.266055 GGCCTCCTTCCGTGTCTG 59.734 66.667 0.00 0.00 0.00 3.51
58 59 2.435059 GCCTCCTTCCGTGTCTGC 60.435 66.667 0.00 0.00 0.00 4.26
59 60 2.125912 CCTCCTTCCGTGTCTGCG 60.126 66.667 0.00 0.00 0.00 5.18
67 68 2.880879 CGTGTCTGCGGACGGATG 60.881 66.667 20.49 6.04 44.83 3.51
68 69 2.571757 GTGTCTGCGGACGGATGA 59.428 61.111 20.49 0.00 44.83 2.92
69 70 1.517257 GTGTCTGCGGACGGATGAG 60.517 63.158 20.49 0.00 44.83 2.90
70 71 2.105128 GTCTGCGGACGGATGAGG 59.895 66.667 10.53 0.00 32.57 3.86
71 72 2.044352 TCTGCGGACGGATGAGGA 60.044 61.111 0.00 0.00 0.00 3.71
72 73 1.680989 TCTGCGGACGGATGAGGAA 60.681 57.895 0.00 0.00 0.00 3.36
73 74 1.218047 CTGCGGACGGATGAGGAAA 59.782 57.895 0.00 0.00 0.00 3.13
74 75 0.391130 CTGCGGACGGATGAGGAAAA 60.391 55.000 0.00 0.00 0.00 2.29
75 76 0.035598 TGCGGACGGATGAGGAAAAA 59.964 50.000 0.00 0.00 0.00 1.94
94 95 2.565046 AAATTGTGGGTTGCCATTGG 57.435 45.000 0.00 0.00 0.00 3.16
95 96 1.727062 AATTGTGGGTTGCCATTGGA 58.273 45.000 6.95 0.00 0.00 3.53
96 97 1.269012 ATTGTGGGTTGCCATTGGAG 58.731 50.000 6.95 0.00 0.00 3.86
97 98 0.187117 TTGTGGGTTGCCATTGGAGA 59.813 50.000 6.95 0.00 0.00 3.71
98 99 0.409092 TGTGGGTTGCCATTGGAGAT 59.591 50.000 6.95 0.00 0.00 2.75
99 100 0.819582 GTGGGTTGCCATTGGAGATG 59.180 55.000 6.95 0.00 0.00 2.90
100 101 0.971959 TGGGTTGCCATTGGAGATGC 60.972 55.000 6.95 0.00 0.00 3.91
101 102 0.685458 GGGTTGCCATTGGAGATGCT 60.685 55.000 6.95 0.00 0.00 3.79
102 103 1.188863 GGTTGCCATTGGAGATGCTT 58.811 50.000 6.95 0.00 0.00 3.91
103 104 1.551883 GGTTGCCATTGGAGATGCTTT 59.448 47.619 6.95 0.00 0.00 3.51
104 105 2.760092 GGTTGCCATTGGAGATGCTTTA 59.240 45.455 6.95 0.00 0.00 1.85
105 106 3.181483 GGTTGCCATTGGAGATGCTTTAG 60.181 47.826 6.95 0.00 0.00 1.85
106 107 3.650281 TGCCATTGGAGATGCTTTAGA 57.350 42.857 6.95 0.00 0.00 2.10
107 108 3.548770 TGCCATTGGAGATGCTTTAGAG 58.451 45.455 6.95 0.00 0.00 2.43
108 109 3.200605 TGCCATTGGAGATGCTTTAGAGA 59.799 43.478 6.95 0.00 0.00 3.10
109 110 3.563390 GCCATTGGAGATGCTTTAGAGAC 59.437 47.826 6.95 0.00 0.00 3.36
110 111 4.774124 CCATTGGAGATGCTTTAGAGACA 58.226 43.478 0.00 0.00 0.00 3.41
111 112 4.574013 CCATTGGAGATGCTTTAGAGACAC 59.426 45.833 0.00 0.00 0.00 3.67
112 113 3.510388 TGGAGATGCTTTAGAGACACG 57.490 47.619 0.00 0.00 0.00 4.49
113 114 2.197577 GGAGATGCTTTAGAGACACGC 58.802 52.381 0.00 0.00 0.00 5.34
114 115 2.159170 GGAGATGCTTTAGAGACACGCT 60.159 50.000 0.00 0.00 0.00 5.07
115 116 3.066900 GGAGATGCTTTAGAGACACGCTA 59.933 47.826 0.00 0.00 0.00 4.26
116 117 4.440250 GGAGATGCTTTAGAGACACGCTAA 60.440 45.833 0.00 0.00 0.00 3.09
117 118 4.425520 AGATGCTTTAGAGACACGCTAAC 58.574 43.478 0.00 0.00 0.00 2.34
118 119 2.955614 TGCTTTAGAGACACGCTAACC 58.044 47.619 0.00 0.00 0.00 2.85
119 120 1.918609 GCTTTAGAGACACGCTAACCG 59.081 52.381 0.00 0.00 44.21 4.44
120 121 2.415090 GCTTTAGAGACACGCTAACCGA 60.415 50.000 0.00 0.00 41.02 4.69
121 122 3.829948 CTTTAGAGACACGCTAACCGAA 58.170 45.455 0.00 0.00 41.02 4.30
122 123 2.907910 TAGAGACACGCTAACCGAAC 57.092 50.000 0.00 0.00 41.02 3.95
123 124 0.956633 AGAGACACGCTAACCGAACA 59.043 50.000 0.00 0.00 41.02 3.18
124 125 1.068472 AGAGACACGCTAACCGAACAG 60.068 52.381 0.00 0.00 41.02 3.16
125 126 0.956633 AGACACGCTAACCGAACAGA 59.043 50.000 0.00 0.00 41.02 3.41
126 127 1.544691 AGACACGCTAACCGAACAGAT 59.455 47.619 0.00 0.00 41.02 2.90
127 128 2.029290 AGACACGCTAACCGAACAGATT 60.029 45.455 0.00 0.00 41.02 2.40
128 129 2.334838 ACACGCTAACCGAACAGATTC 58.665 47.619 0.00 0.00 41.02 2.52
129 130 2.029290 ACACGCTAACCGAACAGATTCT 60.029 45.455 0.00 0.00 41.02 2.40
130 131 2.599082 CACGCTAACCGAACAGATTCTC 59.401 50.000 0.00 0.00 41.02 2.87
131 132 2.194271 CGCTAACCGAACAGATTCTCC 58.806 52.381 0.00 0.00 40.02 3.71
132 133 2.159226 CGCTAACCGAACAGATTCTCCT 60.159 50.000 0.00 0.00 40.02 3.69
133 134 3.066342 CGCTAACCGAACAGATTCTCCTA 59.934 47.826 0.00 0.00 40.02 2.94
134 135 4.439700 CGCTAACCGAACAGATTCTCCTAA 60.440 45.833 0.00 0.00 40.02 2.69
135 136 5.602628 GCTAACCGAACAGATTCTCCTAAT 58.397 41.667 0.00 0.00 32.12 1.73
136 137 5.463724 GCTAACCGAACAGATTCTCCTAATG 59.536 44.000 0.00 0.00 32.12 1.90
137 138 3.798202 ACCGAACAGATTCTCCTAATGC 58.202 45.455 0.00 0.00 32.12 3.56
138 139 3.197766 ACCGAACAGATTCTCCTAATGCA 59.802 43.478 0.00 0.00 32.12 3.96
139 140 4.191544 CCGAACAGATTCTCCTAATGCAA 58.808 43.478 0.00 0.00 32.12 4.08
140 141 4.818546 CCGAACAGATTCTCCTAATGCAAT 59.181 41.667 0.00 0.00 32.12 3.56
141 142 5.277683 CCGAACAGATTCTCCTAATGCAATG 60.278 44.000 0.00 0.00 32.12 2.82
142 143 5.511234 AACAGATTCTCCTAATGCAATGC 57.489 39.130 0.00 0.00 0.00 3.56
143 144 3.562973 ACAGATTCTCCTAATGCAATGCG 59.437 43.478 0.00 0.00 0.00 4.73
144 145 3.811497 CAGATTCTCCTAATGCAATGCGA 59.189 43.478 0.00 0.00 0.00 5.10
145 146 4.063689 AGATTCTCCTAATGCAATGCGAG 58.936 43.478 0.00 0.51 0.00 5.03
146 147 3.541996 TTCTCCTAATGCAATGCGAGA 57.458 42.857 0.00 3.15 0.00 4.04
147 148 3.103447 TCTCCTAATGCAATGCGAGAG 57.897 47.619 0.00 2.33 0.00 3.20
160 161 2.145225 CGAGAGCAATTATCCCGCG 58.855 57.895 0.00 0.00 0.00 6.46
161 162 0.597637 CGAGAGCAATTATCCCGCGT 60.598 55.000 4.92 0.00 0.00 6.01
162 163 0.861837 GAGAGCAATTATCCCGCGTG 59.138 55.000 4.92 0.00 0.00 5.34
163 164 0.178068 AGAGCAATTATCCCGCGTGT 59.822 50.000 4.92 0.00 0.00 4.49
164 165 0.582005 GAGCAATTATCCCGCGTGTC 59.418 55.000 4.92 0.00 0.00 3.67
165 166 1.151777 AGCAATTATCCCGCGTGTCG 61.152 55.000 4.92 0.00 38.08 4.35
174 175 4.978773 CGCGTGTCGGTTTTTGAA 57.021 50.000 0.00 0.00 33.78 2.69
175 176 3.221834 CGCGTGTCGGTTTTTGAAA 57.778 47.368 0.00 0.00 33.78 2.69
176 177 1.536149 CGCGTGTCGGTTTTTGAAAA 58.464 45.000 0.00 0.00 33.78 2.29
177 178 1.912110 CGCGTGTCGGTTTTTGAAAAA 59.088 42.857 0.00 0.00 33.78 1.94
235 236 2.526304 ATATGGTGCTTACGTCGCAT 57.474 45.000 14.42 3.31 39.89 4.73
305 307 4.202010 CGCTTTTCCTTGAGAAACCTTTCA 60.202 41.667 0.78 0.00 44.20 2.69
346 348 2.172483 AACGCCAGCAACGATCTCCT 62.172 55.000 0.00 0.00 0.00 3.69
386 388 2.514458 TCTCCATTTCTTCCCTTGCC 57.486 50.000 0.00 0.00 0.00 4.52
387 389 1.995542 TCTCCATTTCTTCCCTTGCCT 59.004 47.619 0.00 0.00 0.00 4.75
390 392 2.097825 CCATTTCTTCCCTTGCCTCTG 58.902 52.381 0.00 0.00 0.00 3.35
604 613 3.850273 GTCGCAAGCAATCTTCAAGAATG 59.150 43.478 0.00 0.00 37.18 2.67
788 808 4.262808 CCACAATTCCACAAATGGCCTAAA 60.263 41.667 3.32 0.00 46.80 1.85
794 814 7.732222 ATTCCACAAATGGCCTAAAAATAGA 57.268 32.000 3.32 0.00 46.80 1.98
796 816 6.252995 TCCACAAATGGCCTAAAAATAGACT 58.747 36.000 3.32 0.00 46.80 3.24
797 817 6.152661 TCCACAAATGGCCTAAAAATAGACTG 59.847 38.462 3.32 0.00 46.80 3.51
900 920 3.733337 CTCCTATATTTCGCAGCACCTT 58.267 45.455 0.00 0.00 0.00 3.50
931 951 2.572104 ACAATCACCCAGAGGAGTTACC 59.428 50.000 0.00 0.00 36.73 2.85
954 974 5.467705 CAATCAAGAAGGCAGGAGAAAAAG 58.532 41.667 0.00 0.00 0.00 2.27
1074 1096 3.186047 GTGTTCGTGGCGATCCCG 61.186 66.667 0.00 0.00 35.23 5.14
1606 1628 1.121240 GTACGTCGGCAAGATCATCG 58.879 55.000 0.00 0.00 0.00 3.84
2006 2031 4.207891 TGATACAGAGAAGCCAAGGAAC 57.792 45.455 0.00 0.00 0.00 3.62
2111 2136 2.837291 GTGTGCCCCAAGGTTGCA 60.837 61.111 0.00 0.00 34.57 4.08
2159 2184 1.349627 CGTAGCCAGCTGCATTTCG 59.650 57.895 8.66 5.24 44.83 3.46
2171 2196 3.426695 GCTGCATTTCGAAACATGCTACT 60.427 43.478 27.57 4.60 45.21 2.57
2196 2221 7.050377 TGGTTAAAATGGATTTTTGCTTGACA 58.950 30.769 2.79 0.00 40.24 3.58
2205 2230 5.232838 GGATTTTTGCTTGACAACAGACAAG 59.767 40.000 0.00 0.00 44.05 3.16
2226 2251 3.323403 AGTTGGGAATTTGATTGCGGAAA 59.677 39.130 0.00 0.00 0.00 3.13
2232 2257 4.388773 GGAATTTGATTGCGGAAAGGAAAC 59.611 41.667 0.00 0.00 32.72 2.78
2343 2368 7.730364 AGTCATAAATAAAGCCGTTGATAGG 57.270 36.000 0.00 0.00 0.00 2.57
2406 2434 6.682423 CAAGCATTGTATATGGACAGTTGA 57.318 37.500 0.00 0.00 42.34 3.18
2407 2435 7.268199 CAAGCATTGTATATGGACAGTTGAT 57.732 36.000 0.00 0.00 42.34 2.57
2413 2441 7.848223 TTGTATATGGACAGTTGATGTGAAG 57.152 36.000 0.00 0.00 44.17 3.02
2430 2458 9.647918 TGATGTGAAGAGAAATATACTACTCCT 57.352 33.333 0.00 0.00 0.00 3.69
2434 2462 9.849166 GTGAAGAGAAATATACTACTCCTATGC 57.151 37.037 0.00 0.00 0.00 3.14
2435 2463 9.588096 TGAAGAGAAATATACTACTCCTATGCA 57.412 33.333 0.00 0.00 0.00 3.96
2446 2477 6.879400 ACTACTCCTATGCAAAAGACTAAGG 58.121 40.000 0.00 0.00 0.00 2.69
2448 2479 6.374417 ACTCCTATGCAAAAGACTAAGGAA 57.626 37.500 0.00 0.00 31.57 3.36
2452 2483 6.012858 TCCTATGCAAAAGACTAAGGAAGGAA 60.013 38.462 0.00 0.00 0.00 3.36
2457 2488 6.152379 GCAAAAGACTAAGGAAGGAATTGTG 58.848 40.000 0.00 0.00 0.00 3.33
2459 2490 7.588512 CAAAAGACTAAGGAAGGAATTGTGAG 58.411 38.462 0.00 0.00 0.00 3.51
2465 2496 6.887002 ACTAAGGAAGGAATTGTGAGATTTCC 59.113 38.462 0.00 0.00 34.29 3.13
2472 2503 4.100035 GGAATTGTGAGATTTCCCAATCCC 59.900 45.833 0.00 0.00 39.95 3.85
2481 2512 8.526147 GTGAGATTTCCCAATCCCATATAATTG 58.474 37.037 0.00 0.00 39.95 2.32
2482 2513 8.233820 TGAGATTTCCCAATCCCATATAATTGT 58.766 33.333 0.00 0.00 39.95 2.71
2596 2627 9.668497 AAAATAGGAGTACATAACCTTGAGAAC 57.332 33.333 0.00 0.00 35.52 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.218635 TGCATACTTTAAACCCGCATTTGA 59.781 37.500 0.00 0.00 0.00 2.69
1 2 4.489810 TGCATACTTTAAACCCGCATTTG 58.510 39.130 0.00 0.00 0.00 2.32
2 3 4.461081 TCTGCATACTTTAAACCCGCATTT 59.539 37.500 0.00 0.00 0.00 2.32
3 4 4.013728 TCTGCATACTTTAAACCCGCATT 58.986 39.130 0.00 0.00 0.00 3.56
4 5 3.616219 TCTGCATACTTTAAACCCGCAT 58.384 40.909 0.00 0.00 0.00 4.73
5 6 3.006940 CTCTGCATACTTTAAACCCGCA 58.993 45.455 0.00 0.00 0.00 5.69
6 7 3.267483 TCTCTGCATACTTTAAACCCGC 58.733 45.455 0.00 0.00 0.00 6.13
7 8 3.309954 GCTCTCTGCATACTTTAAACCCG 59.690 47.826 0.00 0.00 42.31 5.28
8 9 3.309954 CGCTCTCTGCATACTTTAAACCC 59.690 47.826 0.00 0.00 43.06 4.11
9 10 3.933332 ACGCTCTCTGCATACTTTAAACC 59.067 43.478 0.00 0.00 43.06 3.27
10 11 5.120208 TCAACGCTCTCTGCATACTTTAAAC 59.880 40.000 0.00 0.00 43.06 2.01
11 12 5.234752 TCAACGCTCTCTGCATACTTTAAA 58.765 37.500 0.00 0.00 43.06 1.52
12 13 4.816392 TCAACGCTCTCTGCATACTTTAA 58.184 39.130 0.00 0.00 43.06 1.52
13 14 4.450082 TCAACGCTCTCTGCATACTTTA 57.550 40.909 0.00 0.00 43.06 1.85
14 15 3.319137 TCAACGCTCTCTGCATACTTT 57.681 42.857 0.00 0.00 43.06 2.66
15 16 3.319137 TTCAACGCTCTCTGCATACTT 57.681 42.857 0.00 0.00 43.06 2.24
16 17 3.193263 CATTCAACGCTCTCTGCATACT 58.807 45.455 0.00 0.00 43.06 2.12
17 18 2.286294 CCATTCAACGCTCTCTGCATAC 59.714 50.000 0.00 0.00 43.06 2.39
18 19 2.554142 CCATTCAACGCTCTCTGCATA 58.446 47.619 0.00 0.00 43.06 3.14
19 20 1.376543 CCATTCAACGCTCTCTGCAT 58.623 50.000 0.00 0.00 43.06 3.96
20 21 1.300971 GCCATTCAACGCTCTCTGCA 61.301 55.000 0.00 0.00 43.06 4.41
21 22 1.427020 GCCATTCAACGCTCTCTGC 59.573 57.895 0.00 0.00 38.57 4.26
22 23 1.699656 CCGCCATTCAACGCTCTCTG 61.700 60.000 0.00 0.00 0.00 3.35
23 24 1.448540 CCGCCATTCAACGCTCTCT 60.449 57.895 0.00 0.00 0.00 3.10
24 25 3.093278 CCGCCATTCAACGCTCTC 58.907 61.111 0.00 0.00 0.00 3.20
25 26 3.127533 GCCGCCATTCAACGCTCT 61.128 61.111 0.00 0.00 0.00 4.09
26 27 4.179579 GGCCGCCATTCAACGCTC 62.180 66.667 3.91 0.00 0.00 5.03
27 28 4.722700 AGGCCGCCATTCAACGCT 62.723 61.111 13.15 0.00 0.00 5.07
28 29 4.179579 GAGGCCGCCATTCAACGC 62.180 66.667 13.15 0.00 0.00 4.84
29 30 3.508840 GGAGGCCGCCATTCAACG 61.509 66.667 22.24 0.00 0.00 4.10
30 31 1.657751 GAAGGAGGCCGCCATTCAAC 61.658 60.000 28.68 7.95 0.00 3.18
31 32 1.378514 GAAGGAGGCCGCCATTCAA 60.379 57.895 28.68 0.00 0.00 2.69
32 33 2.272146 GAAGGAGGCCGCCATTCA 59.728 61.111 28.68 0.00 0.00 2.57
33 34 2.517166 GGAAGGAGGCCGCCATTC 60.517 66.667 28.68 24.21 0.00 2.67
34 35 4.489771 CGGAAGGAGGCCGCCATT 62.490 66.667 28.68 18.06 42.55 3.16
40 41 2.266055 CAGACACGGAAGGAGGCC 59.734 66.667 0.00 0.00 0.00 5.19
41 42 2.435059 GCAGACACGGAAGGAGGC 60.435 66.667 0.00 0.00 0.00 4.70
42 43 2.125912 CGCAGACACGGAAGGAGG 60.126 66.667 0.00 0.00 0.00 4.30
50 51 2.880879 CATCCGTCCGCAGACACG 60.881 66.667 0.20 0.00 43.73 4.49
51 52 1.517257 CTCATCCGTCCGCAGACAC 60.517 63.158 0.20 0.00 43.73 3.67
52 53 2.710902 CCTCATCCGTCCGCAGACA 61.711 63.158 0.20 0.00 43.73 3.41
53 54 1.945354 TTCCTCATCCGTCCGCAGAC 61.945 60.000 0.00 0.00 39.83 3.51
54 55 1.254975 TTTCCTCATCCGTCCGCAGA 61.255 55.000 0.00 0.00 0.00 4.26
55 56 0.391130 TTTTCCTCATCCGTCCGCAG 60.391 55.000 0.00 0.00 0.00 5.18
56 57 0.035598 TTTTTCCTCATCCGTCCGCA 59.964 50.000 0.00 0.00 0.00 5.69
57 58 2.849081 TTTTTCCTCATCCGTCCGC 58.151 52.632 0.00 0.00 0.00 5.54
73 74 3.117738 TCCAATGGCAACCCACAATTTTT 60.118 39.130 0.00 0.00 45.77 1.94
74 75 2.441001 TCCAATGGCAACCCACAATTTT 59.559 40.909 0.00 0.00 45.77 1.82
75 76 2.038820 CTCCAATGGCAACCCACAATTT 59.961 45.455 0.00 0.00 45.77 1.82
76 77 1.624813 CTCCAATGGCAACCCACAATT 59.375 47.619 0.00 0.00 45.77 2.32
77 78 1.203162 TCTCCAATGGCAACCCACAAT 60.203 47.619 0.00 0.00 45.77 2.71
78 79 0.187117 TCTCCAATGGCAACCCACAA 59.813 50.000 0.00 0.00 45.77 3.33
79 80 0.409092 ATCTCCAATGGCAACCCACA 59.591 50.000 0.00 0.00 45.77 4.17
80 81 0.819582 CATCTCCAATGGCAACCCAC 59.180 55.000 0.00 0.00 45.77 4.61
82 83 0.685458 AGCATCTCCAATGGCAACCC 60.685 55.000 0.00 0.00 0.00 4.11
83 84 1.188863 AAGCATCTCCAATGGCAACC 58.811 50.000 0.00 0.00 0.00 3.77
84 85 3.696051 TCTAAAGCATCTCCAATGGCAAC 59.304 43.478 0.00 0.00 0.00 4.17
85 86 3.949754 CTCTAAAGCATCTCCAATGGCAA 59.050 43.478 0.00 0.00 0.00 4.52
86 87 3.200605 TCTCTAAAGCATCTCCAATGGCA 59.799 43.478 0.00 0.00 0.00 4.92
87 88 3.563390 GTCTCTAAAGCATCTCCAATGGC 59.437 47.826 0.00 0.00 0.00 4.40
88 89 4.574013 GTGTCTCTAAAGCATCTCCAATGG 59.426 45.833 0.00 0.00 0.00 3.16
89 90 4.269603 CGTGTCTCTAAAGCATCTCCAATG 59.730 45.833 0.00 0.00 0.00 2.82
90 91 4.437239 CGTGTCTCTAAAGCATCTCCAAT 58.563 43.478 0.00 0.00 0.00 3.16
91 92 3.849911 CGTGTCTCTAAAGCATCTCCAA 58.150 45.455 0.00 0.00 0.00 3.53
92 93 2.417379 GCGTGTCTCTAAAGCATCTCCA 60.417 50.000 0.00 0.00 0.00 3.86
93 94 2.159170 AGCGTGTCTCTAAAGCATCTCC 60.159 50.000 0.00 0.00 0.00 3.71
94 95 3.157932 AGCGTGTCTCTAAAGCATCTC 57.842 47.619 0.00 0.00 0.00 2.75
95 96 4.425520 GTTAGCGTGTCTCTAAAGCATCT 58.574 43.478 0.00 0.00 0.00 2.90
96 97 3.552294 GGTTAGCGTGTCTCTAAAGCATC 59.448 47.826 0.00 0.00 0.00 3.91
97 98 3.522553 GGTTAGCGTGTCTCTAAAGCAT 58.477 45.455 0.00 0.00 0.00 3.79
98 99 2.670229 CGGTTAGCGTGTCTCTAAAGCA 60.670 50.000 0.00 0.00 0.00 3.91
99 100 1.918609 CGGTTAGCGTGTCTCTAAAGC 59.081 52.381 0.00 0.00 0.00 3.51
100 101 3.482722 TCGGTTAGCGTGTCTCTAAAG 57.517 47.619 3.21 0.00 0.00 1.85
101 102 3.004629 TGTTCGGTTAGCGTGTCTCTAAA 59.995 43.478 3.21 0.00 0.00 1.85
102 103 2.553602 TGTTCGGTTAGCGTGTCTCTAA 59.446 45.455 3.21 0.00 0.00 2.10
103 104 2.153645 TGTTCGGTTAGCGTGTCTCTA 58.846 47.619 3.21 0.00 0.00 2.43
104 105 0.956633 TGTTCGGTTAGCGTGTCTCT 59.043 50.000 3.21 0.00 0.00 3.10
105 106 1.068748 TCTGTTCGGTTAGCGTGTCTC 60.069 52.381 3.21 0.00 0.00 3.36
106 107 0.956633 TCTGTTCGGTTAGCGTGTCT 59.043 50.000 3.21 0.00 0.00 3.41
107 108 1.992170 ATCTGTTCGGTTAGCGTGTC 58.008 50.000 3.21 0.00 0.00 3.67
108 109 2.029290 AGAATCTGTTCGGTTAGCGTGT 60.029 45.455 3.21 0.00 39.38 4.49
109 110 2.599082 GAGAATCTGTTCGGTTAGCGTG 59.401 50.000 3.21 0.00 39.38 5.34
110 111 2.416972 GGAGAATCTGTTCGGTTAGCGT 60.417 50.000 3.21 0.00 39.38 5.07
111 112 2.159226 AGGAGAATCTGTTCGGTTAGCG 60.159 50.000 0.00 0.00 39.38 4.26
112 113 3.528597 AGGAGAATCTGTTCGGTTAGC 57.471 47.619 0.00 0.00 39.38 3.09
113 114 5.463724 GCATTAGGAGAATCTGTTCGGTTAG 59.536 44.000 0.00 0.00 39.38 2.34
114 115 5.105106 TGCATTAGGAGAATCTGTTCGGTTA 60.105 40.000 0.00 0.00 39.38 2.85
115 116 4.192317 GCATTAGGAGAATCTGTTCGGTT 58.808 43.478 0.00 0.00 39.38 4.44
116 117 3.197766 TGCATTAGGAGAATCTGTTCGGT 59.802 43.478 0.00 0.00 39.38 4.69
117 118 3.797039 TGCATTAGGAGAATCTGTTCGG 58.203 45.455 0.00 0.00 39.38 4.30
118 119 5.745514 CATTGCATTAGGAGAATCTGTTCG 58.254 41.667 0.00 0.00 39.38 3.95
119 120 5.517904 GCATTGCATTAGGAGAATCTGTTC 58.482 41.667 3.15 0.00 33.73 3.18
120 121 4.036027 CGCATTGCATTAGGAGAATCTGTT 59.964 41.667 9.69 0.00 33.73 3.16
121 122 3.562973 CGCATTGCATTAGGAGAATCTGT 59.437 43.478 9.69 0.00 33.73 3.41
122 123 3.811497 TCGCATTGCATTAGGAGAATCTG 59.189 43.478 9.69 0.00 33.73 2.90
123 124 4.063689 CTCGCATTGCATTAGGAGAATCT 58.936 43.478 9.69 0.00 33.73 2.40
124 125 4.060900 TCTCGCATTGCATTAGGAGAATC 58.939 43.478 9.69 0.00 0.00 2.52
125 126 4.063689 CTCTCGCATTGCATTAGGAGAAT 58.936 43.478 9.69 0.00 30.90 2.40
126 127 3.461061 CTCTCGCATTGCATTAGGAGAA 58.539 45.455 9.69 0.00 30.90 2.87
127 128 2.804572 GCTCTCGCATTGCATTAGGAGA 60.805 50.000 9.69 10.59 35.78 3.71
128 129 1.530293 GCTCTCGCATTGCATTAGGAG 59.470 52.381 9.69 6.79 35.78 3.69
129 130 1.134431 TGCTCTCGCATTGCATTAGGA 60.134 47.619 9.69 0.54 42.25 2.94
130 131 1.302366 TGCTCTCGCATTGCATTAGG 58.698 50.000 9.69 0.00 42.25 2.69
140 141 3.289128 CGGGATAATTGCTCTCGCA 57.711 52.632 0.00 0.00 46.24 5.10
142 143 0.597637 ACGCGGGATAATTGCTCTCG 60.598 55.000 12.47 7.54 39.61 4.04
143 144 0.861837 CACGCGGGATAATTGCTCTC 59.138 55.000 12.47 0.00 0.00 3.20
144 145 0.178068 ACACGCGGGATAATTGCTCT 59.822 50.000 19.19 0.00 0.00 4.09
145 146 0.582005 GACACGCGGGATAATTGCTC 59.418 55.000 19.19 0.00 0.00 4.26
146 147 1.151777 CGACACGCGGGATAATTGCT 61.152 55.000 19.19 0.00 36.03 3.91
147 148 1.275657 CGACACGCGGGATAATTGC 59.724 57.895 19.19 0.00 36.03 3.56
157 158 1.536149 TTTTCAAAAACCGACACGCG 58.464 45.000 3.53 3.53 40.47 6.01
192 193 2.772568 TTGGGCGATGCGAATTTATG 57.227 45.000 0.00 0.00 0.00 1.90
235 236 8.758829 CCTATATATATGTGTTGGTAGCCTTGA 58.241 37.037 5.44 0.00 0.00 3.02
305 307 3.111484 GTTTCCAGGGAGAGAGAGGAAT 58.889 50.000 0.00 0.00 38.10 3.01
346 348 1.601477 GGAGGCGAACCGGGAAAAA 60.601 57.895 6.32 0.00 42.76 1.94
469 472 0.331278 ATTGGATTTGGCCGGAGTGA 59.669 50.000 5.05 0.00 0.00 3.41
615 624 0.744281 CCAAAACCGTCCTTGCTTGT 59.256 50.000 0.00 0.00 0.00 3.16
616 625 1.028905 TCCAAAACCGTCCTTGCTTG 58.971 50.000 0.00 0.00 0.00 4.01
617 626 1.407618 GTTCCAAAACCGTCCTTGCTT 59.592 47.619 0.00 0.00 0.00 3.91
618 627 1.029681 GTTCCAAAACCGTCCTTGCT 58.970 50.000 0.00 0.00 0.00 3.91
619 628 0.317519 CGTTCCAAAACCGTCCTTGC 60.318 55.000 0.00 0.00 31.27 4.01
620 629 0.317519 GCGTTCCAAAACCGTCCTTG 60.318 55.000 0.00 0.00 31.27 3.61
623 632 1.161563 TCTGCGTTCCAAAACCGTCC 61.162 55.000 0.00 0.00 31.27 4.79
624 633 0.234884 CTCTGCGTTCCAAAACCGTC 59.765 55.000 0.00 0.00 31.27 4.79
695 712 5.215160 CCAGAAGATCCAAAAGAAAACACG 58.785 41.667 0.00 0.00 0.00 4.49
708 725 4.697514 TCAATGATTCGACCAGAAGATCC 58.302 43.478 0.00 0.00 42.92 3.36
794 814 6.292150 GTGCTTATATTTAGAAGAGGGCAGT 58.708 40.000 0.00 0.00 0.00 4.40
796 816 5.131977 TGGTGCTTATATTTAGAAGAGGGCA 59.868 40.000 0.00 0.00 0.00 5.36
797 817 5.621193 TGGTGCTTATATTTAGAAGAGGGC 58.379 41.667 0.00 0.00 0.00 5.19
879 899 3.393089 AGGTGCTGCGAAATATAGGAG 57.607 47.619 0.00 0.00 0.00 3.69
880 900 3.118408 ACAAGGTGCTGCGAAATATAGGA 60.118 43.478 0.00 0.00 0.00 2.94
900 920 0.537143 GGGTGATTGTGTGGCTGACA 60.537 55.000 0.00 0.00 0.00 3.58
931 951 5.458041 TTTTTCTCCTGCCTTCTTGATTG 57.542 39.130 0.00 0.00 0.00 2.67
954 974 9.397280 GCTAATTTATTATTATCAGGTCTCCCC 57.603 37.037 0.00 0.00 0.00 4.81
1074 1096 1.560923 CCACGAAGATGACGATGGAC 58.439 55.000 0.00 0.00 35.60 4.02
1494 1516 3.022981 GTCTCCGACGAGCTTCTTG 57.977 57.895 0.00 0.00 35.94 3.02
1695 1717 7.402054 TCTTGGACATGACCACTGTAAAATAT 58.598 34.615 16.76 0.00 39.85 1.28
1696 1718 6.774673 TCTTGGACATGACCACTGTAAAATA 58.225 36.000 16.76 0.00 39.85 1.40
1747 1770 0.853530 AAATGGGTATCCTGAGCCCC 59.146 55.000 0.00 0.00 41.66 5.80
2111 2136 0.036388 CTGTAGGTGTTGCCATCGGT 60.036 55.000 0.00 0.00 40.61 4.69
2114 2139 1.755179 ATGCTGTAGGTGTTGCCATC 58.245 50.000 0.00 0.00 40.61 3.51
2159 2184 6.919721 TCCATTTTAACCAGTAGCATGTTTC 58.080 36.000 0.00 0.00 0.00 2.78
2171 2196 7.050377 TGTCAAGCAAAAATCCATTTTAACCA 58.950 30.769 0.00 0.00 39.20 3.67
2196 2221 6.282930 CAATCAAATTCCCAACTTGTCTGTT 58.717 36.000 0.00 0.00 0.00 3.16
2205 2230 3.311486 TTCCGCAATCAAATTCCCAAC 57.689 42.857 0.00 0.00 0.00 3.77
2209 2234 3.866883 TCCTTTCCGCAATCAAATTCC 57.133 42.857 0.00 0.00 0.00 3.01
2226 2251 2.851263 TGCGGTATGACTTGTTTCCT 57.149 45.000 0.00 0.00 0.00 3.36
2232 2257 2.731968 GCCACAATTGCGGTATGACTTG 60.732 50.000 13.86 0.00 0.00 3.16
2398 2426 9.593134 AGTATATTTCTCTTCACATCAACTGTC 57.407 33.333 0.00 0.00 35.29 3.51
2426 2454 5.819901 CCTTCCTTAGTCTTTTGCATAGGAG 59.180 44.000 0.00 0.00 32.39 3.69
2427 2455 5.487488 TCCTTCCTTAGTCTTTTGCATAGGA 59.513 40.000 0.00 0.00 0.00 2.94
2429 2457 7.872113 ATTCCTTCCTTAGTCTTTTGCATAG 57.128 36.000 0.00 0.00 0.00 2.23
2430 2458 7.669722 ACAATTCCTTCCTTAGTCTTTTGCATA 59.330 33.333 0.00 0.00 0.00 3.14
2431 2459 6.494835 ACAATTCCTTCCTTAGTCTTTTGCAT 59.505 34.615 0.00 0.00 0.00 3.96
2432 2460 5.833131 ACAATTCCTTCCTTAGTCTTTTGCA 59.167 36.000 0.00 0.00 0.00 4.08
2433 2461 6.016276 TCACAATTCCTTCCTTAGTCTTTTGC 60.016 38.462 0.00 0.00 0.00 3.68
2434 2462 7.445402 TCTCACAATTCCTTCCTTAGTCTTTTG 59.555 37.037 0.00 0.00 0.00 2.44
2435 2463 7.518188 TCTCACAATTCCTTCCTTAGTCTTTT 58.482 34.615 0.00 0.00 0.00 2.27
2436 2464 7.079451 TCTCACAATTCCTTCCTTAGTCTTT 57.921 36.000 0.00 0.00 0.00 2.52
2445 2476 4.344104 TGGGAAATCTCACAATTCCTTCC 58.656 43.478 4.01 0.00 41.86 3.46
2446 2477 5.982890 TTGGGAAATCTCACAATTCCTTC 57.017 39.130 4.01 0.00 40.15 3.46
2457 2488 8.655935 ACAATTATATGGGATTGGGAAATCTC 57.344 34.615 10.88 0.00 37.53 2.75
2551 2582 3.732048 TTCTTGGAGGTACATTTCCCC 57.268 47.619 0.00 0.00 32.29 4.81
2596 2627 5.181245 AGGGAAATCAACATTTAGACGTGTG 59.819 40.000 0.00 0.00 31.94 3.82


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

AutoCloner maintained by Alex Coulton.