Multiple sequence alignment - TraesCS6B01G290000

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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 TraesCS6B01G290000 chr6B 100.000 2498 0 0 1 2498 521521317 521518820 0.000000e+00 4614.0
1 TraesCS6B01G290000 chr6A 93.935 2226 52 27 304 2498 486012519 486010346 0.000000e+00 3286.0
2 TraesCS6B01G290000 chr6D 93.602 1563 63 20 303 1842 345396443 345394895 0.000000e+00 2298.0
3 TraesCS6B01G290000 chr6D 92.269 802 24 11 1722 2498 345394871 345394083 0.000000e+00 1103.0
4 TraesCS6B01G290000 chr1B 92.188 256 17 2 1 255 511433593 511433846 2.360000e-95 359.0
5 TraesCS6B01G290000 chr1B 89.844 256 23 2 1 255 599249649 599249902 2.400000e-85 326.0
6 TraesCS6B01G290000 chr1B 89.453 256 26 1 1 255 612923434 612923179 3.100000e-84 322.0
7 TraesCS6B01G290000 chr4B 90.347 259 20 4 1 257 673172796 673172541 3.980000e-88 335.0
8 TraesCS6B01G290000 chr4B 100.000 29 0 0 253 281 652824859 652824887 1.000000e-03 54.7
9 TraesCS6B01G290000 chr5B 90.272 257 21 3 1 255 572967987 572967733 1.430000e-87 333.0
10 TraesCS6B01G290000 chr7B 89.922 258 21 3 1 255 14722359 14722614 6.660000e-86 327.0
11 TraesCS6B01G290000 chr7B 89.062 256 24 4 1 255 146907360 146907612 5.190000e-82 315.0
12 TraesCS6B01G290000 chr7B 88.803 259 25 3 1 257 167580846 167580590 5.190000e-82 315.0
13 TraesCS6B01G290000 chr7B 100.000 29 0 0 253 281 713681046 713681018 1.000000e-03 54.7
14 TraesCS6B01G290000 chr4A 89.494 257 24 3 1 255 596868667 596868412 3.100000e-84 322.0
15 TraesCS6B01G290000 chr1D 83.621 232 26 9 9 235 291082845 291083069 9.060000e-50 207.0
16 TraesCS6B01G290000 chr1D 84.360 211 21 10 27 233 356882245 356882043 1.960000e-46 196.0
17 TraesCS6B01G290000 chr1D 79.574 235 26 14 1 233 63624767 63624553 5.570000e-32 148.0
18 TraesCS6B01G290000 chr1D 100.000 28 0 0 253 280 253349850 253349823 4.000000e-03 52.8
19 TraesCS6B01G290000 chr1D 100.000 28 0 0 253 280 299573299 299573326 4.000000e-03 52.8
20 TraesCS6B01G290000 chr1D 100.000 28 0 0 253 280 332944148 332944175 4.000000e-03 52.8
21 TraesCS6B01G290000 chr5D 100.000 29 0 0 252 280 387602685 387602713 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 TraesCS6B01G290000 chr6B 521518820 521521317 2497 True 4614.0 4614 100.0000 1 2498 1 chr6B.!!$R1 2497
1 TraesCS6B01G290000 chr6A 486010346 486012519 2173 True 3286.0 3286 93.9350 304 2498 1 chr6A.!!$R1 2194
2 TraesCS6B01G290000 chr6D 345394083 345396443 2360 True 1700.5 2298 92.9355 303 2498 2 chr6D.!!$R1 2195

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
918 934 0.037232 CGTCTGTTCCCTTGGTCTCC 60.037 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 2380 0.741221 GGTGATGAGCCGTTGGAGAC 60.741 60.0 0.0 0.0 0.0 3.36 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
37 38 3.666883 TTAAATGCTAATGTGGACGCG 57.333 42.857 3.53 3.53 0.00 6.01
38 39 1.448985 AAATGCTAATGTGGACGCGT 58.551 45.000 13.85 13.85 0.00 6.01
39 40 0.726827 AATGCTAATGTGGACGCGTG 59.273 50.000 20.70 0.00 0.00 5.34
40 41 1.089481 ATGCTAATGTGGACGCGTGG 61.089 55.000 20.70 0.00 0.00 4.94
41 42 1.447140 GCTAATGTGGACGCGTGGA 60.447 57.895 20.70 0.00 0.00 4.02
42 43 1.693083 GCTAATGTGGACGCGTGGAC 61.693 60.000 20.70 13.83 0.00 4.02
43 44 0.108804 CTAATGTGGACGCGTGGACT 60.109 55.000 20.70 0.02 0.00 3.85
44 45 0.108992 TAATGTGGACGCGTGGACTC 60.109 55.000 20.70 8.41 0.00 3.36
45 46 2.781595 AATGTGGACGCGTGGACTCC 62.782 60.000 20.70 12.48 0.00 3.85
46 47 3.681835 GTGGACGCGTGGACTCCT 61.682 66.667 20.70 0.00 0.00 3.69
47 48 3.680786 TGGACGCGTGGACTCCTG 61.681 66.667 20.70 0.00 0.00 3.86
53 54 4.436998 CGTGGACTCCTGCCGGAC 62.437 72.222 5.05 0.00 34.92 4.79
54 55 2.997897 GTGGACTCCTGCCGGACT 60.998 66.667 5.05 0.00 34.92 3.85
55 56 2.203788 TGGACTCCTGCCGGACTT 60.204 61.111 5.05 0.00 34.92 3.01
56 57 2.283529 TGGACTCCTGCCGGACTTC 61.284 63.158 5.05 0.00 34.92 3.01
57 58 2.182030 GACTCCTGCCGGACTTCG 59.818 66.667 5.05 0.00 34.92 3.79
58 59 2.600769 ACTCCTGCCGGACTTCGT 60.601 61.111 5.05 0.00 34.92 3.85
59 60 2.125912 CTCCTGCCGGACTTCGTG 60.126 66.667 5.05 0.00 34.92 4.35
60 61 3.649277 CTCCTGCCGGACTTCGTGG 62.649 68.421 5.05 0.00 34.92 4.94
67 68 4.699522 GGACTTCGTGGCCGGCTT 62.700 66.667 28.56 1.49 31.76 4.35
68 69 2.668550 GACTTCGTGGCCGGCTTT 60.669 61.111 28.56 2.29 33.95 3.51
69 70 1.375013 GACTTCGTGGCCGGCTTTA 60.375 57.895 28.56 10.66 33.95 1.85
70 71 0.952010 GACTTCGTGGCCGGCTTTAA 60.952 55.000 28.56 14.43 33.95 1.52
71 72 0.322187 ACTTCGTGGCCGGCTTTAAT 60.322 50.000 28.56 3.16 33.95 1.40
72 73 0.098728 CTTCGTGGCCGGCTTTAATG 59.901 55.000 28.56 14.81 33.95 1.90
73 74 0.606944 TTCGTGGCCGGCTTTAATGT 60.607 50.000 28.56 0.00 33.95 2.71
74 75 0.606944 TCGTGGCCGGCTTTAATGTT 60.607 50.000 28.56 0.00 33.95 2.71
75 76 0.242555 CGTGGCCGGCTTTAATGTTT 59.757 50.000 28.56 0.00 0.00 2.83
76 77 1.469308 CGTGGCCGGCTTTAATGTTTA 59.531 47.619 28.56 0.00 0.00 2.01
77 78 2.095161 CGTGGCCGGCTTTAATGTTTAA 60.095 45.455 28.56 0.00 0.00 1.52
78 79 3.428316 CGTGGCCGGCTTTAATGTTTAAT 60.428 43.478 28.56 0.00 0.00 1.40
79 80 4.500127 GTGGCCGGCTTTAATGTTTAATT 58.500 39.130 28.56 0.00 0.00 1.40
80 81 5.652518 GTGGCCGGCTTTAATGTTTAATTA 58.347 37.500 28.56 0.00 0.00 1.40
81 82 6.100668 GTGGCCGGCTTTAATGTTTAATTAA 58.899 36.000 28.56 0.00 0.00 1.40
82 83 6.759356 GTGGCCGGCTTTAATGTTTAATTAAT 59.241 34.615 28.56 0.00 0.00 1.40
83 84 7.279090 GTGGCCGGCTTTAATGTTTAATTAATT 59.721 33.333 28.56 5.89 0.00 1.40
84 85 7.824779 TGGCCGGCTTTAATGTTTAATTAATTT 59.175 29.630 28.56 0.00 0.00 1.82
85 86 9.315525 GGCCGGCTTTAATGTTTAATTAATTTA 57.684 29.630 28.56 0.00 0.00 1.40
116 117 9.902196 TTATGTTAAATATGCATGCATTCTGAG 57.098 29.630 36.23 0.00 37.82 3.35
117 118 7.337480 TGTTAAATATGCATGCATTCTGAGT 57.663 32.000 36.23 16.45 37.82 3.41
118 119 7.774134 TGTTAAATATGCATGCATTCTGAGTT 58.226 30.769 36.23 24.68 37.82 3.01
119 120 8.252417 TGTTAAATATGCATGCATTCTGAGTTT 58.748 29.630 36.23 25.00 37.82 2.66
120 121 9.090692 GTTAAATATGCATGCATTCTGAGTTTT 57.909 29.630 36.23 22.94 37.82 2.43
121 122 9.656040 TTAAATATGCATGCATTCTGAGTTTTT 57.344 25.926 36.23 20.00 37.82 1.94
139 140 3.984508 TTTTTACGCCGTCAAAATGGA 57.015 38.095 5.30 0.00 32.79 3.41
140 141 4.506886 TTTTTACGCCGTCAAAATGGAT 57.493 36.364 5.30 0.00 32.79 3.41
141 142 3.750639 TTTACGCCGTCAAAATGGATC 57.249 42.857 0.00 0.00 32.79 3.36
142 143 1.282817 TACGCCGTCAAAATGGATCG 58.717 50.000 0.00 0.00 32.79 3.69
143 144 1.297598 CGCCGTCAAAATGGATCGC 60.298 57.895 0.00 0.00 32.79 4.58
144 145 1.297598 GCCGTCAAAATGGATCGCG 60.298 57.895 0.00 0.00 32.79 5.87
145 146 1.297598 CCGTCAAAATGGATCGCGC 60.298 57.895 0.00 0.00 32.79 6.86
146 147 1.297598 CGTCAAAATGGATCGCGCC 60.298 57.895 0.00 0.00 0.00 6.53
147 148 1.800032 GTCAAAATGGATCGCGCCA 59.200 52.632 7.94 7.94 43.23 5.69
148 149 0.248215 GTCAAAATGGATCGCGCCAG 60.248 55.000 11.18 0.00 42.15 4.85
149 150 1.587088 CAAAATGGATCGCGCCAGC 60.587 57.895 11.18 0.00 42.15 4.85
173 174 3.345808 CACACGCACCGACCCAAG 61.346 66.667 0.00 0.00 0.00 3.61
212 213 4.794648 CCGCCTGGCCGATCCAAA 62.795 66.667 14.12 0.00 46.01 3.28
213 214 3.508840 CGCCTGGCCGATCCAAAC 61.509 66.667 14.12 0.00 46.01 2.93
214 215 3.508840 GCCTGGCCGATCCAAACG 61.509 66.667 7.66 0.00 46.01 3.60
224 225 2.657184 CGATCCAAACGGACAAAAACC 58.343 47.619 0.00 0.00 34.62 3.27
230 231 4.030821 CGGACAAAAACCGGACGA 57.969 55.556 9.46 0.00 45.65 4.20
231 232 2.309326 CGGACAAAAACCGGACGAA 58.691 52.632 9.46 0.00 45.65 3.85
232 233 0.656785 CGGACAAAAACCGGACGAAA 59.343 50.000 9.46 0.00 45.65 3.46
233 234 1.264826 CGGACAAAAACCGGACGAAAT 59.735 47.619 9.46 0.00 45.65 2.17
234 235 2.663606 CGGACAAAAACCGGACGAAATC 60.664 50.000 9.46 0.00 45.65 2.17
235 236 2.291190 GGACAAAAACCGGACGAAATCA 59.709 45.455 9.46 0.00 0.00 2.57
236 237 3.294102 GACAAAAACCGGACGAAATCAC 58.706 45.455 9.46 0.00 0.00 3.06
237 238 2.033675 ACAAAAACCGGACGAAATCACC 59.966 45.455 9.46 0.00 0.00 4.02
238 239 0.869730 AAAACCGGACGAAATCACCG 59.130 50.000 9.46 0.00 45.24 4.94
239 240 0.249996 AAACCGGACGAAATCACCGT 60.250 50.000 9.46 0.00 44.34 4.83
240 241 0.249996 AACCGGACGAAATCACCGTT 60.250 50.000 9.46 0.00 44.34 4.44
241 242 0.668401 ACCGGACGAAATCACCGTTC 60.668 55.000 9.46 0.00 44.34 3.95
247 248 1.945207 CGAAATCACCGTTCGTTTGG 58.055 50.000 0.00 0.00 42.23 3.28
248 249 1.399215 CGAAATCACCGTTCGTTTGGG 60.399 52.381 0.00 0.00 42.23 4.12
249 250 1.605232 GAAATCACCGTTCGTTTGGGT 59.395 47.619 0.00 0.00 33.37 4.51
250 251 1.232119 AATCACCGTTCGTTTGGGTC 58.768 50.000 0.00 0.00 29.82 4.46
251 252 0.947180 ATCACCGTTCGTTTGGGTCG 60.947 55.000 0.00 0.00 29.82 4.79
252 253 2.280321 ACCGTTCGTTTGGGTCGG 60.280 61.111 0.00 0.00 45.53 4.79
253 254 3.719144 CCGTTCGTTTGGGTCGGC 61.719 66.667 0.00 0.00 35.01 5.54
254 255 3.719144 CGTTCGTTTGGGTCGGCC 61.719 66.667 0.00 0.00 0.00 6.13
255 256 3.719144 GTTCGTTTGGGTCGGCCG 61.719 66.667 22.12 22.12 34.97 6.13
256 257 4.238654 TTCGTTTGGGTCGGCCGT 62.239 61.111 27.15 0.00 34.97 5.68
257 258 4.668118 TCGTTTGGGTCGGCCGTC 62.668 66.667 27.15 20.62 34.97 4.79
287 288 3.636231 CCCGTTGGAGCAGGGTGA 61.636 66.667 0.00 0.00 40.27 4.02
288 289 2.429930 CCGTTGGAGCAGGGTGAA 59.570 61.111 0.00 0.00 0.00 3.18
289 290 1.228124 CCGTTGGAGCAGGGTGAAA 60.228 57.895 0.00 0.00 0.00 2.69
290 291 1.237285 CCGTTGGAGCAGGGTGAAAG 61.237 60.000 0.00 0.00 0.00 2.62
291 292 0.250295 CGTTGGAGCAGGGTGAAAGA 60.250 55.000 0.00 0.00 0.00 2.52
292 293 1.528129 GTTGGAGCAGGGTGAAAGAG 58.472 55.000 0.00 0.00 0.00 2.85
293 294 1.072331 GTTGGAGCAGGGTGAAAGAGA 59.928 52.381 0.00 0.00 0.00 3.10
294 295 0.979665 TGGAGCAGGGTGAAAGAGAG 59.020 55.000 0.00 0.00 0.00 3.20
295 296 1.270907 GGAGCAGGGTGAAAGAGAGA 58.729 55.000 0.00 0.00 0.00 3.10
296 297 1.625818 GGAGCAGGGTGAAAGAGAGAA 59.374 52.381 0.00 0.00 0.00 2.87
297 298 2.354604 GGAGCAGGGTGAAAGAGAGAAG 60.355 54.545 0.00 0.00 0.00 2.85
298 299 1.627834 AGCAGGGTGAAAGAGAGAAGG 59.372 52.381 0.00 0.00 0.00 3.46
299 300 1.948144 GCAGGGTGAAAGAGAGAAGGC 60.948 57.143 0.00 0.00 0.00 4.35
300 301 1.349026 CAGGGTGAAAGAGAGAAGGCA 59.651 52.381 0.00 0.00 0.00 4.75
301 302 2.026449 CAGGGTGAAAGAGAGAAGGCAT 60.026 50.000 0.00 0.00 0.00 4.40
302 303 3.198635 CAGGGTGAAAGAGAGAAGGCATA 59.801 47.826 0.00 0.00 0.00 3.14
303 304 4.043596 AGGGTGAAAGAGAGAAGGCATAT 58.956 43.478 0.00 0.00 0.00 1.78
304 305 4.133078 GGGTGAAAGAGAGAAGGCATATG 58.867 47.826 0.00 0.00 0.00 1.78
305 306 4.384647 GGGTGAAAGAGAGAAGGCATATGT 60.385 45.833 4.29 0.00 0.00 2.29
306 307 4.813697 GGTGAAAGAGAGAAGGCATATGTC 59.186 45.833 0.00 0.00 0.00 3.06
307 308 4.813697 GTGAAAGAGAGAAGGCATATGTCC 59.186 45.833 3.04 5.90 0.00 4.02
308 309 4.718774 TGAAAGAGAGAAGGCATATGTCCT 59.281 41.667 3.04 8.22 34.90 3.85
309 310 5.190528 TGAAAGAGAGAAGGCATATGTCCTT 59.809 40.000 23.24 23.24 45.98 3.36
335 336 0.454600 CAAGCCATGGACAGACATGC 59.545 55.000 18.40 0.00 45.29 4.06
521 522 2.123033 GGCCTCTCCCCTCCTCTC 60.123 72.222 0.00 0.00 0.00 3.20
620 621 0.178903 TAAGGACACTGCCACCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
715 716 5.059833 GGTGTCAGAGACTTCTTCAATGTT 58.940 41.667 0.00 0.00 33.15 2.71
864 868 4.922103 CGGTGTTCTTCTCCAAGTAGTTAC 59.078 45.833 0.00 0.00 0.00 2.50
918 934 0.037232 CGTCTGTTCCCTTGGTCTCC 60.037 60.000 0.00 0.00 0.00 3.71
925 941 0.848053 TCCCTTGGTCTCCGGTTTTT 59.152 50.000 0.00 0.00 0.00 1.94
972 988 8.954950 TTTCATTCTCATTCACTAGATCTTCC 57.045 34.615 0.00 0.00 0.00 3.46
1213 1237 2.485657 GGAGGCAAGGAATACTACCAGC 60.486 54.545 0.00 0.00 0.00 4.85
1214 1238 2.170607 GAGGCAAGGAATACTACCAGCA 59.829 50.000 0.00 0.00 34.20 4.41
1215 1239 2.171448 AGGCAAGGAATACTACCAGCAG 59.829 50.000 0.00 0.00 34.20 4.24
1311 1335 4.606071 CCTGACGGCAAAGAGAGG 57.394 61.111 0.00 0.00 0.00 3.69
1339 1363 0.249573 TCGAAAGGACGGTGACAACC 60.250 55.000 0.00 0.00 43.76 3.77
1395 1434 1.344953 ACAGGCACACCAGGTTCTCA 61.345 55.000 0.00 0.00 39.06 3.27
1627 1671 6.183361 GGAATGTATCCCTCATTGTTAGGAGT 60.183 42.308 0.00 0.00 43.00 3.85
1698 1742 3.054434 CCATAGTGTTCTCCCATGGTTGA 60.054 47.826 11.73 5.38 33.03 3.18
1699 1743 2.867109 AGTGTTCTCCCATGGTTGAG 57.133 50.000 11.73 11.22 0.00 3.02
1700 1744 1.352352 AGTGTTCTCCCATGGTTGAGG 59.648 52.381 11.73 0.00 0.00 3.86
1701 1745 1.073923 GTGTTCTCCCATGGTTGAGGT 59.926 52.381 11.73 0.00 0.00 3.85
1702 1746 1.780309 TGTTCTCCCATGGTTGAGGTT 59.220 47.619 11.73 0.00 0.00 3.50
1703 1747 2.162681 GTTCTCCCATGGTTGAGGTTG 58.837 52.381 11.73 0.00 0.00 3.77
1704 1748 1.741028 TCTCCCATGGTTGAGGTTGA 58.259 50.000 11.73 0.00 0.00 3.18
1705 1749 1.351017 TCTCCCATGGTTGAGGTTGAC 59.649 52.381 11.73 0.00 0.00 3.18
1706 1750 0.404040 TCCCATGGTTGAGGTTGACC 59.596 55.000 11.73 0.00 36.45 4.02
1746 1792 2.105821 AGTAGGGTTAACTGTTGCTGCA 59.894 45.455 5.42 0.00 0.00 4.41
1783 1971 8.833493 ACTGCAACCTTCGGTTATTATTATTAC 58.167 33.333 0.00 0.00 45.01 1.89
1825 2013 0.313043 ACTGTTGCTTGCATGCAGAC 59.687 50.000 24.21 22.75 44.27 3.51
1842 2030 3.603532 CAGACCTTGCAATCTTCTGCTA 58.396 45.455 15.31 0.00 43.07 3.49
1843 2031 3.373439 CAGACCTTGCAATCTTCTGCTAC 59.627 47.826 15.31 0.00 43.07 3.58
1900 2111 1.205893 ACAAGCTACACTCTAGCCAGC 59.794 52.381 0.00 0.00 41.25 4.85
1998 2211 7.386025 GTCAAATTAATTGCCTTCTGCTTCTTT 59.614 33.333 0.39 0.00 42.00 2.52
2112 2325 2.291475 TGAGGCCCACATGCAATCTTTA 60.291 45.455 0.00 0.00 0.00 1.85
2156 2370 5.559417 GCATTTCAGCAAACCAAATCACTTG 60.559 40.000 0.00 0.00 34.52 3.16
2166 2380 4.190772 ACCAAATCACTTGTTTGCCTTTG 58.809 39.130 0.00 0.00 35.71 2.77
2364 2583 4.631131 ACCTTGGCTTGAAGTAATTTTGC 58.369 39.130 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.854291 CGCGTCCACATTAGCATTTAAAAA 59.146 37.500 0.00 0.00 0.00 1.94
15 16 4.083217 ACGCGTCCACATTAGCATTTAAAA 60.083 37.500 5.58 0.00 0.00 1.52
16 17 3.437395 ACGCGTCCACATTAGCATTTAAA 59.563 39.130 5.58 0.00 0.00 1.52
17 18 3.004171 ACGCGTCCACATTAGCATTTAA 58.996 40.909 5.58 0.00 0.00 1.52
18 19 2.350192 CACGCGTCCACATTAGCATTTA 59.650 45.455 9.86 0.00 0.00 1.40
19 20 1.130373 CACGCGTCCACATTAGCATTT 59.870 47.619 9.86 0.00 0.00 2.32
20 21 0.726827 CACGCGTCCACATTAGCATT 59.273 50.000 9.86 0.00 0.00 3.56
21 22 1.089481 CCACGCGTCCACATTAGCAT 61.089 55.000 9.86 0.00 0.00 3.79
22 23 1.739929 CCACGCGTCCACATTAGCA 60.740 57.895 9.86 0.00 0.00 3.49
23 24 1.447140 TCCACGCGTCCACATTAGC 60.447 57.895 9.86 0.00 0.00 3.09
24 25 0.108804 AGTCCACGCGTCCACATTAG 60.109 55.000 9.86 0.00 0.00 1.73
25 26 0.108992 GAGTCCACGCGTCCACATTA 60.109 55.000 9.86 0.00 0.00 1.90
26 27 1.374252 GAGTCCACGCGTCCACATT 60.374 57.895 9.86 0.00 0.00 2.71
27 28 2.261671 GAGTCCACGCGTCCACAT 59.738 61.111 9.86 0.00 0.00 3.21
28 29 3.986006 GGAGTCCACGCGTCCACA 61.986 66.667 9.86 0.00 0.00 4.17
29 30 3.681835 AGGAGTCCACGCGTCCAC 61.682 66.667 9.86 9.15 32.23 4.02
30 31 3.680786 CAGGAGTCCACGCGTCCA 61.681 66.667 9.86 0.00 32.23 4.02
43 44 3.691342 CCACGAAGTCCGGCAGGA 61.691 66.667 0.00 0.00 41.61 3.86
50 51 2.791501 TAAAGCCGGCCACGAAGTCC 62.792 60.000 26.15 0.00 41.61 3.85
51 52 0.952010 TTAAAGCCGGCCACGAAGTC 60.952 55.000 26.15 0.00 41.61 3.01
53 54 0.098728 CATTAAAGCCGGCCACGAAG 59.901 55.000 26.15 5.89 44.60 3.79
54 55 0.606944 ACATTAAAGCCGGCCACGAA 60.607 50.000 26.15 13.16 44.60 3.85
55 56 0.606944 AACATTAAAGCCGGCCACGA 60.607 50.000 26.15 7.86 44.60 4.35
56 57 0.242555 AAACATTAAAGCCGGCCACG 59.757 50.000 26.15 8.66 40.55 4.94
57 58 3.579335 TTAAACATTAAAGCCGGCCAC 57.421 42.857 26.15 0.00 0.00 5.01
58 59 4.810191 AATTAAACATTAAAGCCGGCCA 57.190 36.364 26.15 5.71 0.00 5.36
59 60 7.780008 AATTAATTAAACATTAAAGCCGGCC 57.220 32.000 26.15 5.07 0.00 6.13
90 91 9.902196 CTCAGAATGCATGCATATTTAACATAA 57.098 29.630 32.36 9.69 35.31 1.90
91 92 9.070179 ACTCAGAATGCATGCATATTTAACATA 57.930 29.630 32.36 10.88 35.31 2.29
92 93 7.948357 ACTCAGAATGCATGCATATTTAACAT 58.052 30.769 32.36 15.05 35.31 2.71
93 94 7.337480 ACTCAGAATGCATGCATATTTAACA 57.663 32.000 32.36 12.38 35.31 2.41
94 95 8.638685 AAACTCAGAATGCATGCATATTTAAC 57.361 30.769 32.36 18.21 35.31 2.01
95 96 9.656040 AAAAACTCAGAATGCATGCATATTTAA 57.344 25.926 32.36 16.10 35.31 1.52
119 120 3.984508 TCCATTTTGACGGCGTAAAAA 57.015 38.095 31.14 31.14 31.43 1.94
120 121 3.425094 CGATCCATTTTGACGGCGTAAAA 60.425 43.478 18.33 18.33 0.00 1.52
121 122 2.094575 CGATCCATTTTGACGGCGTAAA 59.905 45.455 14.74 9.87 0.00 2.01
122 123 1.661617 CGATCCATTTTGACGGCGTAA 59.338 47.619 14.74 0.91 0.00 3.18
123 124 1.282817 CGATCCATTTTGACGGCGTA 58.717 50.000 14.74 0.00 0.00 4.42
124 125 1.977594 GCGATCCATTTTGACGGCGT 61.978 55.000 14.65 14.65 0.00 5.68
125 126 1.297598 GCGATCCATTTTGACGGCG 60.298 57.895 4.80 4.80 0.00 6.46
126 127 1.297598 CGCGATCCATTTTGACGGC 60.298 57.895 0.00 0.00 0.00 5.68
127 128 1.297598 GCGCGATCCATTTTGACGG 60.298 57.895 12.10 0.00 0.00 4.79
128 129 1.297598 GGCGCGATCCATTTTGACG 60.298 57.895 12.10 0.00 0.00 4.35
129 130 0.248215 CTGGCGCGATCCATTTTGAC 60.248 55.000 12.10 0.00 35.22 3.18
130 131 1.992233 GCTGGCGCGATCCATTTTGA 61.992 55.000 12.10 0.00 35.22 2.69
131 132 1.587088 GCTGGCGCGATCCATTTTG 60.587 57.895 12.10 0.00 35.22 2.44
132 133 2.800736 GCTGGCGCGATCCATTTT 59.199 55.556 12.10 0.00 35.22 1.82
143 144 4.962122 GTGTGCACAACGCTGGCG 62.962 66.667 23.59 13.56 43.06 5.69
144 145 4.962122 CGTGTGCACAACGCTGGC 62.962 66.667 23.59 6.17 43.06 4.85
156 157 3.345808 CTTGGGTCGGTGCGTGTG 61.346 66.667 0.00 0.00 0.00 3.82
207 208 0.739561 CCGGTTTTTGTCCGTTTGGA 59.260 50.000 0.00 0.00 45.63 3.53
208 209 0.739561 TCCGGTTTTTGTCCGTTTGG 59.260 50.000 0.00 0.00 45.63 3.28
209 210 1.830086 GTCCGGTTTTTGTCCGTTTG 58.170 50.000 0.00 0.00 45.63 2.93
210 211 0.377905 CGTCCGGTTTTTGTCCGTTT 59.622 50.000 0.00 0.00 45.63 3.60
211 212 0.461693 TCGTCCGGTTTTTGTCCGTT 60.462 50.000 0.00 0.00 45.63 4.44
212 213 0.461693 TTCGTCCGGTTTTTGTCCGT 60.462 50.000 0.00 0.00 45.63 4.69
213 214 0.656785 TTTCGTCCGGTTTTTGTCCG 59.343 50.000 0.00 0.00 46.49 4.79
214 215 2.291190 TGATTTCGTCCGGTTTTTGTCC 59.709 45.455 0.00 0.00 0.00 4.02
215 216 3.294102 GTGATTTCGTCCGGTTTTTGTC 58.706 45.455 0.00 0.00 0.00 3.18
216 217 2.033675 GGTGATTTCGTCCGGTTTTTGT 59.966 45.455 0.00 0.00 0.00 2.83
217 218 2.657184 GGTGATTTCGTCCGGTTTTTG 58.343 47.619 0.00 0.00 0.00 2.44
218 219 1.264826 CGGTGATTTCGTCCGGTTTTT 59.735 47.619 0.00 0.00 40.49 1.94
219 220 0.869730 CGGTGATTTCGTCCGGTTTT 59.130 50.000 0.00 0.00 40.49 2.43
220 221 1.811176 AACGGTGATTTCGTCCGGTTT 60.811 47.619 0.00 3.07 42.18 3.27
221 222 0.249996 AACGGTGATTTCGTCCGGTT 60.250 50.000 0.00 7.16 42.18 4.44
229 230 1.605232 ACCCAAACGAACGGTGATTTC 59.395 47.619 0.00 0.00 0.00 2.17
230 231 1.605232 GACCCAAACGAACGGTGATTT 59.395 47.619 0.00 0.00 0.00 2.17
231 232 1.232119 GACCCAAACGAACGGTGATT 58.768 50.000 0.00 0.00 0.00 2.57
232 233 0.947180 CGACCCAAACGAACGGTGAT 60.947 55.000 0.00 0.00 0.00 3.06
233 234 1.592131 CGACCCAAACGAACGGTGA 60.592 57.895 0.00 0.00 0.00 4.02
234 235 2.600475 CCGACCCAAACGAACGGTG 61.600 63.158 0.00 0.00 38.97 4.94
235 236 2.280321 CCGACCCAAACGAACGGT 60.280 61.111 0.00 0.00 38.97 4.83
236 237 3.719144 GCCGACCCAAACGAACGG 61.719 66.667 0.00 0.00 45.26 4.44
237 238 3.719144 GGCCGACCCAAACGAACG 61.719 66.667 0.00 0.00 0.00 3.95
238 239 3.719144 CGGCCGACCCAAACGAAC 61.719 66.667 24.07 0.00 0.00 3.95
239 240 4.238654 ACGGCCGACCCAAACGAA 62.239 61.111 35.90 0.00 0.00 3.85
240 241 4.668118 GACGGCCGACCCAAACGA 62.668 66.667 35.90 0.00 0.00 3.85
270 271 2.690653 TTTCACCCTGCTCCAACGGG 62.691 60.000 0.00 0.00 43.79 5.28
271 272 1.228124 TTTCACCCTGCTCCAACGG 60.228 57.895 0.00 0.00 0.00 4.44
272 273 0.250295 TCTTTCACCCTGCTCCAACG 60.250 55.000 0.00 0.00 0.00 4.10
273 274 1.072331 TCTCTTTCACCCTGCTCCAAC 59.928 52.381 0.00 0.00 0.00 3.77
274 275 1.349026 CTCTCTTTCACCCTGCTCCAA 59.651 52.381 0.00 0.00 0.00 3.53
275 276 0.979665 CTCTCTTTCACCCTGCTCCA 59.020 55.000 0.00 0.00 0.00 3.86
276 277 1.270907 TCTCTCTTTCACCCTGCTCC 58.729 55.000 0.00 0.00 0.00 4.70
277 278 2.354604 CCTTCTCTCTTTCACCCTGCTC 60.355 54.545 0.00 0.00 0.00 4.26
278 279 1.627834 CCTTCTCTCTTTCACCCTGCT 59.372 52.381 0.00 0.00 0.00 4.24
279 280 1.948144 GCCTTCTCTCTTTCACCCTGC 60.948 57.143 0.00 0.00 0.00 4.85
280 281 1.349026 TGCCTTCTCTCTTTCACCCTG 59.651 52.381 0.00 0.00 0.00 4.45
281 282 1.734655 TGCCTTCTCTCTTTCACCCT 58.265 50.000 0.00 0.00 0.00 4.34
282 283 2.797177 ATGCCTTCTCTCTTTCACCC 57.203 50.000 0.00 0.00 0.00 4.61
283 284 4.775236 ACATATGCCTTCTCTCTTTCACC 58.225 43.478 1.58 0.00 0.00 4.02
284 285 4.813697 GGACATATGCCTTCTCTCTTTCAC 59.186 45.833 1.58 0.00 0.00 3.18
285 286 4.718774 AGGACATATGCCTTCTCTCTTTCA 59.281 41.667 11.55 0.00 29.44 2.69
286 287 5.289083 AGGACATATGCCTTCTCTCTTTC 57.711 43.478 11.55 0.00 29.44 2.62
287 288 5.707066 AAGGACATATGCCTTCTCTCTTT 57.293 39.130 19.61 3.15 41.85 2.52
296 297 0.028642 AGGGGGAAGGACATATGCCT 60.029 55.000 11.55 11.55 37.35 4.75
297 298 0.402121 GAGGGGGAAGGACATATGCC 59.598 60.000 1.58 5.36 0.00 4.40
298 299 1.140312 TGAGGGGGAAGGACATATGC 58.860 55.000 1.58 0.00 0.00 3.14
299 300 2.487986 GCTTGAGGGGGAAGGACATATG 60.488 54.545 0.00 0.00 0.00 1.78
300 301 1.777272 GCTTGAGGGGGAAGGACATAT 59.223 52.381 0.00 0.00 0.00 1.78
301 302 1.213296 GCTTGAGGGGGAAGGACATA 58.787 55.000 0.00 0.00 0.00 2.29
302 303 1.575447 GGCTTGAGGGGGAAGGACAT 61.575 60.000 0.00 0.00 0.00 3.06
303 304 2.231380 GGCTTGAGGGGGAAGGACA 61.231 63.158 0.00 0.00 0.00 4.02
304 305 1.575447 ATGGCTTGAGGGGGAAGGAC 61.575 60.000 0.00 0.00 0.00 3.85
305 306 1.230281 ATGGCTTGAGGGGGAAGGA 60.230 57.895 0.00 0.00 0.00 3.36
306 307 1.076485 CATGGCTTGAGGGGGAAGG 60.076 63.158 0.00 0.00 0.00 3.46
307 308 1.076485 CCATGGCTTGAGGGGGAAG 60.076 63.158 0.00 0.00 0.00 3.46
308 309 1.543642 TCCATGGCTTGAGGGGGAA 60.544 57.895 6.96 0.00 0.00 3.97
309 310 2.127065 TCCATGGCTTGAGGGGGA 59.873 61.111 6.96 0.00 0.00 4.81
335 336 4.440127 GGGCATGCAAACGCAGGG 62.440 66.667 21.36 0.00 44.13 4.45
521 522 0.249868 TCTGTCTTGTCACCAAGCCG 60.250 55.000 0.00 0.00 46.33 5.52
620 621 2.999648 AGAGGAGAGCGGCTGCAA 61.000 61.111 21.93 0.00 46.23 4.08
715 716 4.177537 CTACATGAGGAGGAAGAGGAGA 57.822 50.000 0.00 0.00 0.00 3.71
864 868 5.360714 AGAAGTAGAGCAGAGAAGGAATGAG 59.639 44.000 0.00 0.00 0.00 2.90
918 934 3.796717 GCAGAAACAAGAAGGAAAAACCG 59.203 43.478 0.00 0.00 44.74 4.44
925 941 3.831323 TGGAATGCAGAAACAAGAAGGA 58.169 40.909 0.00 0.00 0.00 3.36
1213 1237 1.600957 GTTGTCATCGCCATCATCCTG 59.399 52.381 0.00 0.00 0.00 3.86
1214 1238 1.807755 CGTTGTCATCGCCATCATCCT 60.808 52.381 0.00 0.00 0.00 3.24
1215 1239 0.583438 CGTTGTCATCGCCATCATCC 59.417 55.000 0.00 0.00 0.00 3.51
1311 1335 1.803289 GTCCTTTCGATGGCCTTGC 59.197 57.895 3.32 0.00 0.00 4.01
1428 1467 2.689034 CCCTCGCCCCCTTTCTCT 60.689 66.667 0.00 0.00 0.00 3.10
1627 1671 3.658725 CCTTCCTCCCTCTTCTCCAATA 58.341 50.000 0.00 0.00 0.00 1.90
1656 1700 0.178961 AAGGCAAAACTGAGGACCCC 60.179 55.000 0.00 0.00 0.00 4.95
1746 1792 6.422776 CGAAGGTTGCAGTAGATTTACATT 57.577 37.500 0.00 0.00 31.96 2.71
1783 1971 4.996788 AAAGCAGGAAGGCATTGAATAG 57.003 40.909 0.00 0.00 35.83 1.73
1825 2013 3.693085 ACATGTAGCAGAAGATTGCAAGG 59.307 43.478 4.94 0.00 46.47 3.61
1842 2030 6.183361 TGCTCCATTAATAGCTAGGAACATGT 60.183 38.462 10.74 0.00 39.53 3.21
1843 2031 6.148480 GTGCTCCATTAATAGCTAGGAACATG 59.852 42.308 10.74 0.00 39.53 3.21
1900 2111 4.142622 TGTTTTGCTCGCAAATCTATCTGG 60.143 41.667 16.75 0.00 44.14 3.86
1998 2211 2.550277 TCTAGAGTCTGGGCAATGGA 57.450 50.000 1.86 0.00 0.00 3.41
2112 2325 2.348660 CCGTGCAAATGATTTTGGCAT 58.651 42.857 6.26 0.00 42.09 4.40
2166 2380 0.741221 GGTGATGAGCCGTTGGAGAC 60.741 60.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.