Multiple sequence alignment - TraesCS5A01G492100

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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 TraesCS5A01G492100 chr5A 100.000 2988 0 0 1 2988 661150484 661147497 0.000000e+00 5518
1 TraesCS5A01G492100 chr5A 84.768 151 5 12 1575 1716 661148856 661148715 5.200000e-28 135
2 TraesCS5A01G492100 chr5A 84.768 151 5 12 1629 1770 661148910 661148769 5.200000e-28 135
3 TraesCS5A01G492100 chr4D 89.501 1924 73 49 1106 2988 481547728 481549563 0.000000e+00 2314
4 TraesCS5A01G492100 chr4D 84.158 707 44 37 435 1111 481547032 481547700 9.100000e-175 623
5 TraesCS5A01G492100 chr4D 83.535 413 28 15 1 385 481546542 481546942 1.700000e-92 350
6 TraesCS5A01G492100 chr4D 84.459 148 11 8 1626 1770 481548174 481548312 5.200000e-28 135
7 TraesCS5A01G492100 chr4B 91.347 1121 42 24 1106 2219 610562394 610563466 0.000000e+00 1482
8 TraesCS5A01G492100 chr4B 88.410 673 46 18 2294 2961 610564153 610564798 0.000000e+00 782
9 TraesCS5A01G492100 chr4B 84.591 636 45 20 390 1001 610561680 610562286 1.540000e-162 582
10 TraesCS5A01G492100 chr4B 83.042 401 33 10 1 383 610561235 610561618 6.170000e-87 331
11 TraesCS5A01G492100 chr4B 84.459 148 11 8 1626 1770 610562830 610562968 5.200000e-28 135
12 TraesCS5A01G492100 chr1D 81.404 285 33 12 1408 1688 262475299 262475567 6.490000e-52 215
13 TraesCS5A01G492100 chr1B 81.206 282 32 14 1408 1685 348479120 348479384 1.090000e-49 207
14 TraesCS5A01G492100 chr1A 82.072 251 27 12 1408 1649 336476443 336476684 6.530000e-47 198


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 TraesCS5A01G492100 chr5A 661147497 661150484 2987 True 1929.333333 5518 89.845333 1 2988 3 chr5A.!!$R1 2987
1 TraesCS5A01G492100 chr4D 481546542 481549563 3021 False 855.500000 2314 85.413250 1 2988 4 chr4D.!!$F1 2987
2 TraesCS5A01G492100 chr4B 610561235 610564798 3563 False 662.400000 1482 86.369800 1 2961 5 chr4B.!!$F1 2960

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
249 279 0.316204 TTGGTTTCGTCTCGGAGGAC 59.684 55.0 4.96 1.74 0.00 3.85 F
888 1043 0.967887 CTCACCTTCTCCCTGCGAGA 60.968 60.0 0.00 0.00 46.29 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1568 0.179067 AACAACGCGGAACAGAGGAA 60.179 50.0 12.47 0.00 0.00 3.36 R
2599 3413 0.178767 AAGTGCGATGCATCCAGCTA 59.821 50.0 20.87 7.65 45.94 3.32 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
154 167 2.722487 CCCGGAATCGACCTCTCG 59.278 66.667 0.73 0.00 41.65 4.04
249 279 0.316204 TTGGTTTCGTCTCGGAGGAC 59.684 55.000 4.96 1.74 0.00 3.85
275 309 1.542108 CCGGGAATCAGAATCAGAGGC 60.542 57.143 0.00 0.00 0.00 4.70
276 310 1.542108 CGGGAATCAGAATCAGAGGCC 60.542 57.143 0.00 0.00 0.00 5.19
277 311 1.542108 GGGAATCAGAATCAGAGGCCG 60.542 57.143 0.00 0.00 0.00 6.13
278 312 1.139853 GGAATCAGAATCAGAGGCCGT 59.860 52.381 0.00 0.00 0.00 5.68
315 349 4.168291 GGCAGCCGAGGAGGGAAG 62.168 72.222 0.00 0.00 41.48 3.46
316 350 4.847444 GCAGCCGAGGAGGGAAGC 62.847 72.222 0.00 0.00 41.48 3.86
317 351 3.080121 CAGCCGAGGAGGGAAGCT 61.080 66.667 0.00 0.00 41.48 3.74
320 354 3.133946 CCGAGGAGGGAAGCTAGC 58.866 66.667 6.62 6.62 35.97 3.42
321 355 2.503382 CCGAGGAGGGAAGCTAGCC 61.503 68.421 12.13 0.00 35.97 3.93
407 496 2.329690 CCAGATCGCCTCGACTCG 59.670 66.667 0.00 0.00 39.18 4.18
428 517 3.003568 CTGTACTGTGCGCGCTGTG 62.004 63.158 34.59 22.36 0.00 3.66
429 518 3.777925 GTACTGTGCGCGCTGTGG 61.778 66.667 34.59 20.48 0.00 4.17
494 595 2.032071 AAAAGGCGGGGAGACGTG 59.968 61.111 0.00 0.00 35.98 4.49
545 650 8.303780 ACACATCCACATCAGATAGATATAGG 57.696 38.462 0.00 0.00 34.43 2.57
570 675 1.747709 AGATAGACGTACGCACTGGT 58.252 50.000 16.72 8.54 0.00 4.00
676 792 3.188873 CCGCTAGTCTCTATTTAGGACCG 59.811 52.174 0.00 0.00 0.00 4.79
815 960 1.194781 CCCACACACCCTCACTAGCT 61.195 60.000 0.00 0.00 0.00 3.32
821 966 3.024547 CACACCCTCACTAGCTTAGCTA 58.975 50.000 13.70 13.70 40.44 3.32
826 972 2.550606 CCTCACTAGCTTAGCTACTCCG 59.449 54.545 10.21 3.32 40.44 4.63
829 975 3.377485 TCACTAGCTTAGCTACTCCGTTG 59.623 47.826 10.21 1.49 40.44 4.10
839 985 2.490903 GCTACTCCGTTGTTCTCACCTA 59.509 50.000 0.00 0.00 0.00 3.08
845 991 2.170607 CCGTTGTTCTCACCTATCCCAT 59.829 50.000 0.00 0.00 0.00 4.00
858 1009 5.762218 CACCTATCCCATTTGATCTTCTGAC 59.238 44.000 0.00 0.00 0.00 3.51
880 1031 1.677637 CCTACCCGCTCACCTTCTCC 61.678 65.000 0.00 0.00 0.00 3.71
887 1042 1.515020 CTCACCTTCTCCCTGCGAG 59.485 63.158 0.00 0.00 40.30 5.03
888 1043 0.967887 CTCACCTTCTCCCTGCGAGA 60.968 60.000 0.00 0.00 46.29 4.04
893 1048 2.438614 TCTCCCTGCGAGAGACGG 60.439 66.667 0.00 0.00 42.97 4.79
894 1049 2.752238 CTCCCTGCGAGAGACGGT 60.752 66.667 0.00 0.00 41.63 4.83
895 1050 3.057547 CTCCCTGCGAGAGACGGTG 62.058 68.421 0.00 0.00 41.63 4.94
896 1051 3.374402 CCCTGCGAGAGACGGTGT 61.374 66.667 0.00 0.00 42.83 4.16
900 1055 2.355837 GCGAGAGACGGTGTGCAA 60.356 61.111 0.00 0.00 42.83 4.08
932 1087 1.003355 CATGTCGGCCAAGGTGAGT 60.003 57.895 2.24 0.00 0.00 3.41
933 1088 1.003355 ATGTCGGCCAAGGTGAGTG 60.003 57.895 2.24 0.00 0.00 3.51
936 1091 2.743928 CGGCCAAGGTGAGTGAGC 60.744 66.667 2.24 0.00 0.00 4.26
939 1094 1.239968 GGCCAAGGTGAGTGAGCAAG 61.240 60.000 0.00 0.00 0.00 4.01
940 1095 1.860484 GCCAAGGTGAGTGAGCAAGC 61.860 60.000 0.00 0.00 0.00 4.01
941 1096 1.572085 CCAAGGTGAGTGAGCAAGCG 61.572 60.000 0.00 0.00 0.00 4.68
952 1107 1.905922 GAGCAAGCGCGCTTCTTCTT 61.906 55.000 41.23 24.33 44.01 2.52
955 1110 2.035442 AAGCGCGCTTCTTCTTCCC 61.035 57.895 38.88 1.64 0.00 3.97
1038 1193 3.305398 TCTTTGCTCGAGGTTCTCTTC 57.695 47.619 15.58 0.00 0.00 2.87
1091 1246 1.509703 GGGAACGCGTTTCTCTCTTT 58.490 50.000 28.26 1.50 31.04 2.52
1092 1247 1.871676 GGGAACGCGTTTCTCTCTTTT 59.128 47.619 28.26 0.65 31.04 2.27
1093 1248 3.062042 GGGAACGCGTTTCTCTCTTTTA 58.938 45.455 28.26 0.00 31.04 1.52
1094 1249 3.683340 GGGAACGCGTTTCTCTCTTTTAT 59.317 43.478 28.26 0.00 31.04 1.40
1133 1321 3.072915 TCCAAATGTCTTCCTCTGCTTCA 59.927 43.478 0.00 0.00 0.00 3.02
1149 1337 6.448006 TCTGCTTCAGACTGTAAACTAACTC 58.552 40.000 1.59 0.00 35.39 3.01
1288 1477 4.873129 CCGCACCCATCTCGTCCG 62.873 72.222 0.00 0.00 0.00 4.79
1290 1479 4.451150 GCACCCATCTCGTCCGCA 62.451 66.667 0.00 0.00 0.00 5.69
1291 1480 2.202797 CACCCATCTCGTCCGCAG 60.203 66.667 0.00 0.00 0.00 5.18
1293 1482 2.105128 CCCATCTCGTCCGCAGTC 59.895 66.667 0.00 0.00 0.00 3.51
1294 1483 2.105128 CCATCTCGTCCGCAGTCC 59.895 66.667 0.00 0.00 0.00 3.85
1295 1484 2.278206 CATCTCGTCCGCAGTCCG 60.278 66.667 0.00 0.00 0.00 4.79
1306 1495 3.117171 CAGTCCGCACTGCTCTGC 61.117 66.667 0.00 0.00 43.77 4.26
1307 1496 4.385405 AGTCCGCACTGCTCTGCC 62.385 66.667 0.00 0.00 33.18 4.85
1308 1497 4.385405 GTCCGCACTGCTCTGCCT 62.385 66.667 0.00 0.00 33.18 4.75
1309 1498 3.630013 TCCGCACTGCTCTGCCTT 61.630 61.111 0.00 0.00 33.18 4.35
1310 1499 2.670934 CCGCACTGCTCTGCCTTT 60.671 61.111 0.00 0.00 33.18 3.11
1311 1500 2.263741 CCGCACTGCTCTGCCTTTT 61.264 57.895 0.00 0.00 33.18 2.27
1312 1501 1.656441 CGCACTGCTCTGCCTTTTT 59.344 52.632 0.00 0.00 33.18 1.94
1345 1534 4.927267 ATCCATTAGTCAAAGACCACCA 57.073 40.909 0.00 0.00 32.18 4.17
1349 1538 4.399303 CCATTAGTCAAAGACCACCAATCC 59.601 45.833 0.00 0.00 32.18 3.01
1351 1540 2.863809 AGTCAAAGACCACCAATCCAC 58.136 47.619 0.00 0.00 32.18 4.02
1381 1570 3.491652 GCCGACGGCTCTGCTTTC 61.492 66.667 31.30 0.00 46.69 2.62
1391 1580 1.719600 CTCTGCTTTCCTCTGTTCCG 58.280 55.000 0.00 0.00 0.00 4.30
1395 1584 1.228657 GCTTTCCTCTGTTCCGCGTT 61.229 55.000 4.92 0.00 0.00 4.84
1585 1775 0.178861 AGGAGGAGGCCAAGAAGGAA 60.179 55.000 5.01 0.00 41.22 3.36
1648 1838 2.047179 AAGAAGGAAGGCGACGGC 60.047 61.111 14.41 14.41 38.90 5.68
1681 1871 2.901042 GGGAAGAAGGACGGCGAT 59.099 61.111 16.62 0.00 0.00 4.58
1682 1872 1.521681 GGGAAGAAGGACGGCGATG 60.522 63.158 16.62 0.00 0.00 3.84
1683 1873 1.521681 GGAAGAAGGACGGCGATGG 60.522 63.158 16.62 0.00 0.00 3.51
1997 2187 4.489810 CGTCATCTGCTAAGTCAAAGTCT 58.510 43.478 0.00 0.00 0.00 3.24
2113 2307 5.821204 AGTTTGCAAGATGAAACTGTACAC 58.179 37.500 0.00 0.00 40.19 2.90
2122 2316 7.393841 AGATGAAACTGTACACCTAGTAGTC 57.606 40.000 0.00 0.00 32.19 2.59
2139 2333 5.341407 GTAGTCGTCTACTATAGCACCAC 57.659 47.826 11.87 0.00 42.63 4.16
2140 2334 2.871022 AGTCGTCTACTATAGCACCACG 59.129 50.000 0.00 3.92 36.36 4.94
2141 2335 1.600957 TCGTCTACTATAGCACCACGC 59.399 52.381 0.00 0.00 42.91 5.34
2184 2378 7.337150 ACATTTGTAATGTGAAAATTGCGAG 57.663 32.000 4.37 0.00 0.00 5.03
2194 2392 1.648504 AAATTGCGAGGCTACGTACC 58.351 50.000 0.00 0.00 35.59 3.34
2264 2860 7.068839 ACAACAGAGAACAAAACTAGAGAGAGA 59.931 37.037 0.00 0.00 0.00 3.10
2266 2862 7.657336 ACAGAGAACAAAACTAGAGAGAGAAG 58.343 38.462 0.00 0.00 0.00 2.85
2269 2865 7.724061 AGAGAACAAAACTAGAGAGAGAAGAGT 59.276 37.037 0.00 0.00 0.00 3.24
2271 2867 6.339587 ACAAAACTAGAGAGAGAAGAGTGG 57.660 41.667 0.00 0.00 0.00 4.00
2272 2868 5.836358 ACAAAACTAGAGAGAGAAGAGTGGT 59.164 40.000 0.00 0.00 0.00 4.16
2273 2869 6.325286 ACAAAACTAGAGAGAGAAGAGTGGTT 59.675 38.462 0.00 0.00 0.00 3.67
2274 2870 6.987403 AAACTAGAGAGAGAAGAGTGGTTT 57.013 37.500 0.00 0.00 0.00 3.27
2275 2871 8.361139 CAAAACTAGAGAGAGAAGAGTGGTTTA 58.639 37.037 0.00 0.00 0.00 2.01
2276 2872 7.457024 AACTAGAGAGAGAAGAGTGGTTTAC 57.543 40.000 0.00 0.00 0.00 2.01
2277 2873 6.544650 ACTAGAGAGAGAAGAGTGGTTTACA 58.455 40.000 0.00 0.00 0.00 2.41
2279 2875 5.636123 AGAGAGAGAAGAGTGGTTTACAGA 58.364 41.667 0.00 0.00 0.00 3.41
2280 2876 5.710099 AGAGAGAGAAGAGTGGTTTACAGAG 59.290 44.000 0.00 0.00 0.00 3.35
2281 2877 5.636123 AGAGAGAAGAGTGGTTTACAGAGA 58.364 41.667 0.00 0.00 0.00 3.10
2282 2878 5.710099 AGAGAGAAGAGTGGTTTACAGAGAG 59.290 44.000 0.00 0.00 0.00 3.20
2283 2879 5.636123 AGAGAAGAGTGGTTTACAGAGAGA 58.364 41.667 0.00 0.00 0.00 3.10
2284 2880 5.710099 AGAGAAGAGTGGTTTACAGAGAGAG 59.290 44.000 0.00 0.00 0.00 3.20
2285 2881 5.636123 AGAAGAGTGGTTTACAGAGAGAGA 58.364 41.667 0.00 0.00 0.00 3.10
2286 2882 5.710099 AGAAGAGTGGTTTACAGAGAGAGAG 59.290 44.000 0.00 0.00 0.00 3.20
2287 2883 5.249780 AGAGTGGTTTACAGAGAGAGAGA 57.750 43.478 0.00 0.00 0.00 3.10
2288 2884 5.253330 AGAGTGGTTTACAGAGAGAGAGAG 58.747 45.833 0.00 0.00 0.00 3.20
2320 3134 3.378512 AGAGAGAGAGAGAGAGAGCAGA 58.621 50.000 0.00 0.00 0.00 4.26
2321 3135 3.387374 AGAGAGAGAGAGAGAGAGCAGAG 59.613 52.174 0.00 0.00 0.00 3.35
2322 3136 2.158842 AGAGAGAGAGAGAGAGCAGAGC 60.159 54.545 0.00 0.00 0.00 4.09
2323 3137 1.561076 AGAGAGAGAGAGAGCAGAGCA 59.439 52.381 0.00 0.00 0.00 4.26
2324 3138 1.945394 GAGAGAGAGAGAGCAGAGCAG 59.055 57.143 0.00 0.00 0.00 4.24
2343 3157 4.197498 GTGCGGTGCATGATGGGC 62.197 66.667 0.00 0.00 41.91 5.36
2394 3208 5.791336 ACTTTGCTTTCTAGAAAAAGGGG 57.209 39.130 22.89 12.61 36.86 4.79
2397 3211 6.382859 ACTTTGCTTTCTAGAAAAAGGGGAAA 59.617 34.615 22.89 19.42 36.86 3.13
2398 3212 6.800072 TTGCTTTCTAGAAAAAGGGGAAAA 57.200 33.333 18.25 3.48 36.86 2.29
2435 3249 5.360591 ACGGTTATTTTTGGCATTTTGTCA 58.639 33.333 0.00 0.00 0.00 3.58
2491 3305 7.827015 GCAACGCCATTGTACAGAATACTGTA 61.827 42.308 6.07 6.07 46.11 2.74
2585 3399 2.173569 GGAATTATGCTCACCCTGACCT 59.826 50.000 0.00 0.00 0.00 3.85
2590 3404 1.915769 GCTCACCCTGACCTGACCT 60.916 63.158 0.00 0.00 0.00 3.85
2591 3405 1.978473 CTCACCCTGACCTGACCTG 59.022 63.158 0.00 0.00 0.00 4.00
2592 3406 0.542938 CTCACCCTGACCTGACCTGA 60.543 60.000 0.00 0.00 0.00 3.86
2593 3407 0.832135 TCACCCTGACCTGACCTGAC 60.832 60.000 0.00 0.00 0.00 3.51
2594 3408 1.536662 ACCCTGACCTGACCTGACC 60.537 63.158 0.00 0.00 0.00 4.02
2595 3409 2.294078 CCCTGACCTGACCTGACCC 61.294 68.421 0.00 0.00 0.00 4.46
2596 3410 1.536418 CCTGACCTGACCTGACCCA 60.536 63.158 0.00 0.00 0.00 4.51
2597 3411 1.548357 CCTGACCTGACCTGACCCAG 61.548 65.000 0.00 0.00 0.00 4.45
2598 3412 2.177594 CTGACCTGACCTGACCCAGC 62.178 65.000 0.00 0.00 0.00 4.85
2599 3413 1.915769 GACCTGACCTGACCCAGCT 60.916 63.158 0.00 0.00 0.00 4.24
2624 3438 4.675510 CTGGATGCATCGCACTTATTTTT 58.324 39.130 20.15 0.00 43.04 1.94
2626 3440 4.082300 TGGATGCATCGCACTTATTTTTGT 60.082 37.500 20.15 0.00 43.04 2.83
2630 3444 5.153513 TGCATCGCACTTATTTTTGTTCTC 58.846 37.500 0.00 0.00 31.71 2.87
2635 3449 6.791303 TCGCACTTATTTTTGTTCTCTGTTT 58.209 32.000 0.00 0.00 0.00 2.83
2639 3453 8.321005 GCACTTATTTTTGTTCTCTGTTTGTTC 58.679 33.333 0.00 0.00 0.00 3.18
2650 3464 6.377327 TCTCTGTTTGTTCTTTGATCAACC 57.623 37.500 7.89 0.00 0.00 3.77
2651 3465 5.885352 TCTCTGTTTGTTCTTTGATCAACCA 59.115 36.000 7.89 0.00 0.00 3.67
2724 3565 2.670905 TCCGTTGCACGTCAGAATAATG 59.329 45.455 7.68 0.00 40.58 1.90
2727 3568 3.124466 CGTTGCACGTCAGAATAATGGAA 59.876 43.478 0.00 0.00 36.74 3.53
2728 3569 4.651994 GTTGCACGTCAGAATAATGGAAG 58.348 43.478 0.00 0.00 0.00 3.46
2729 3570 4.200838 TGCACGTCAGAATAATGGAAGA 57.799 40.909 0.00 0.00 0.00 2.87
2730 3571 4.769688 TGCACGTCAGAATAATGGAAGAT 58.230 39.130 0.00 0.00 0.00 2.40
2731 3572 4.811024 TGCACGTCAGAATAATGGAAGATC 59.189 41.667 0.00 0.00 0.00 2.75
2732 3573 4.212214 GCACGTCAGAATAATGGAAGATCC 59.788 45.833 0.00 0.00 36.96 3.36
2750 3591 5.665459 AGATCCATTTAGTCAGTGTGCTAC 58.335 41.667 0.00 0.00 0.00 3.58
2755 3596 6.714810 TCCATTTAGTCAGTGTGCTACAATTT 59.285 34.615 0.00 0.00 0.00 1.82
2756 3597 7.023575 CCATTTAGTCAGTGTGCTACAATTTC 58.976 38.462 0.00 0.00 0.00 2.17
2757 3598 7.308529 CCATTTAGTCAGTGTGCTACAATTTCA 60.309 37.037 0.00 0.00 0.00 2.69
2767 3608 5.711506 TGTGCTACAATTTCATCACTGGATT 59.288 36.000 0.00 0.00 0.00 3.01
2772 3613 8.623903 GCTACAATTTCATCACTGGATTAATGA 58.376 33.333 0.00 0.00 0.00 2.57
2774 3615 8.812513 ACAATTTCATCACTGGATTAATGAGA 57.187 30.769 0.00 0.00 30.39 3.27
2775 3616 8.900781 ACAATTTCATCACTGGATTAATGAGAG 58.099 33.333 0.00 0.00 30.39 3.20
2786 3627 6.333416 TGGATTAATGAGAGAACGTCTTGAG 58.667 40.000 0.00 0.00 34.71 3.02
2808 3649 4.022849 AGGAAACTAAAACTGCACATGAGC 60.023 41.667 8.32 8.32 40.61 4.26
2823 3664 0.321210 TGAGCATCTTCCCGCGAAAA 60.321 50.000 8.23 0.00 34.92 2.29
2854 3695 1.019673 CATGAACATCTTCCCGCCAG 58.980 55.000 0.00 0.00 0.00 4.85
2898 3739 2.180432 AACCCTAACTGGCTCGTTTC 57.820 50.000 0.00 0.00 0.00 2.78
2947 3793 2.466982 CGATGCACGCAGCCATCTT 61.467 57.895 1.07 0.00 44.83 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 107 3.712881 GGTTCGTGTCTGCCGTGC 61.713 66.667 0.00 0.00 0.00 5.34
154 167 1.301009 CGCTCGCTTTATCTCCCCC 60.301 63.158 0.00 0.00 0.00 5.40
249 279 4.063689 CTGATTCTGATTCCCGGATGAAG 58.936 47.826 0.73 0.00 0.00 3.02
304 338 1.743321 CTGGCTAGCTTCCCTCCTCG 61.743 65.000 15.72 0.00 0.00 4.63
392 481 3.587933 GGCGAGTCGAGGCGATCT 61.588 66.667 18.61 0.00 38.42 2.75
514 615 0.911769 TGATGTGGATGTGTCCCTCC 59.088 55.000 0.00 0.00 44.41 4.30
518 623 4.944619 TCTATCTGATGTGGATGTGTCC 57.055 45.455 0.00 0.00 45.31 4.02
545 650 5.163972 CCAGTGCGTACGTCTATCTATCTAC 60.164 48.000 17.90 0.87 0.00 2.59
552 657 1.669779 AGACCAGTGCGTACGTCTATC 59.330 52.381 17.90 14.71 0.00 2.08
554 659 0.800631 CAGACCAGTGCGTACGTCTA 59.199 55.000 17.90 0.79 0.00 2.59
557 662 2.049433 GCAGACCAGTGCGTACGT 60.049 61.111 17.90 0.00 32.74 3.57
630 746 1.222567 GAGAGGAGAGGAGAGGAGGT 58.777 60.000 0.00 0.00 0.00 3.85
676 792 2.715624 GAATTGGTGATCGCGGGC 59.284 61.111 6.13 0.00 0.00 6.13
815 960 3.057033 GGTGAGAACAACGGAGTAGCTAA 60.057 47.826 0.00 0.00 45.00 3.09
826 972 5.253330 TCAAATGGGATAGGTGAGAACAAC 58.747 41.667 0.00 0.00 0.00 3.32
829 975 5.934781 AGATCAAATGGGATAGGTGAGAAC 58.065 41.667 0.00 0.00 0.00 3.01
839 985 3.813443 CGGTCAGAAGATCAAATGGGAT 58.187 45.455 0.00 0.00 0.00 3.85
845 991 2.093658 GGTAGGCGGTCAGAAGATCAAA 60.094 50.000 0.00 0.00 0.00 2.69
880 1031 2.126307 CACACCGTCTCTCGCAGG 60.126 66.667 0.00 0.00 38.35 4.85
939 1094 3.854459 CGGGAAGAAGAAGCGCGC 61.854 66.667 26.66 26.66 0.00 6.86
940 1095 0.734942 TTACGGGAAGAAGAAGCGCG 60.735 55.000 0.00 0.00 42.59 6.86
941 1096 1.327764 CATTACGGGAAGAAGAAGCGC 59.672 52.381 0.00 0.00 0.00 5.92
952 1107 4.495690 TCAATCCATGAACATTACGGGA 57.504 40.909 0.00 0.00 34.30 5.14
955 1110 7.250445 TCAGAATCAATCCATGAACATTACG 57.750 36.000 0.00 0.00 42.54 3.18
983 1138 3.198635 ACGCATATGGAATCAGGATAGGG 59.801 47.826 4.56 0.00 0.00 3.53
986 1141 3.837731 TGGACGCATATGGAATCAGGATA 59.162 43.478 4.56 0.00 0.00 2.59
1050 1205 3.623510 CGGGAAGGATTCTAAAGCAAGAC 59.376 47.826 0.00 0.00 46.56 3.01
1080 1235 8.231161 GGTGCAGAGTAAATAAAAGAGAGAAAC 58.769 37.037 0.00 0.00 0.00 2.78
1117 1305 2.298446 CAGTCTGAAGCAGAGGAAGACA 59.702 50.000 0.00 0.00 41.46 3.41
1133 1321 5.542779 CAAGCCAGAGTTAGTTTACAGTCT 58.457 41.667 0.00 0.00 0.00 3.24
1149 1337 3.515286 CCAGCATCGGCAAGCCAG 61.515 66.667 12.19 4.35 44.61 4.85
1278 1467 2.278206 CGGACTGCGGACGAGATG 60.278 66.667 0.00 0.00 0.00 2.90
1279 1468 4.194720 GCGGACTGCGGACGAGAT 62.195 66.667 16.32 0.00 0.00 2.75
1290 1479 4.385405 GGCAGAGCAGTGCGGACT 62.385 66.667 10.00 2.68 45.00 3.85
1291 1480 3.890936 AAGGCAGAGCAGTGCGGAC 62.891 63.158 10.00 5.81 45.00 4.79
1293 1482 1.799258 AAAAAGGCAGAGCAGTGCGG 61.799 55.000 10.00 4.76 45.00 5.69
1294 1483 1.656441 AAAAAGGCAGAGCAGTGCG 59.344 52.632 10.00 0.00 45.00 5.34
1309 1498 7.618907 TGACTAATGGATTCATCATGGGAAAAA 59.381 33.333 5.10 0.00 32.24 1.94
1310 1499 7.124721 TGACTAATGGATTCATCATGGGAAAA 58.875 34.615 5.10 0.00 32.24 2.29
1311 1500 6.671605 TGACTAATGGATTCATCATGGGAAA 58.328 36.000 5.10 0.00 32.24 3.13
1312 1501 6.264771 TGACTAATGGATTCATCATGGGAA 57.735 37.500 0.00 0.00 32.24 3.97
1313 1502 5.910355 TGACTAATGGATTCATCATGGGA 57.090 39.130 0.00 0.00 32.24 4.37
1314 1503 6.774170 TCTTTGACTAATGGATTCATCATGGG 59.226 38.462 0.00 0.00 32.24 4.00
1315 1504 7.255381 GGTCTTTGACTAATGGATTCATCATGG 60.255 40.741 0.00 0.00 30.99 3.66
1316 1505 7.283807 TGGTCTTTGACTAATGGATTCATCATG 59.716 37.037 0.00 0.00 30.99 3.07
1317 1506 7.284034 GTGGTCTTTGACTAATGGATTCATCAT 59.716 37.037 0.00 0.00 30.99 2.45
1318 1507 6.599244 GTGGTCTTTGACTAATGGATTCATCA 59.401 38.462 0.00 0.00 30.99 3.07
1319 1508 6.038714 GGTGGTCTTTGACTAATGGATTCATC 59.961 42.308 0.00 0.00 30.99 2.92
1320 1509 5.888161 GGTGGTCTTTGACTAATGGATTCAT 59.112 40.000 0.00 0.00 32.47 2.57
1321 1510 5.222027 TGGTGGTCTTTGACTAATGGATTCA 60.222 40.000 0.00 0.00 32.47 2.57
1322 1511 5.253330 TGGTGGTCTTTGACTAATGGATTC 58.747 41.667 0.00 0.00 32.47 2.52
1323 1512 5.255397 TGGTGGTCTTTGACTAATGGATT 57.745 39.130 0.00 0.00 32.47 3.01
1345 1534 1.337260 GCGTCAGTCAGTCAGTGGATT 60.337 52.381 0.00 0.00 0.00 3.01
1349 1538 1.730902 CGGCGTCAGTCAGTCAGTG 60.731 63.158 0.00 0.00 0.00 3.66
1351 1540 1.442857 GTCGGCGTCAGTCAGTCAG 60.443 63.158 6.85 0.00 0.00 3.51
1379 1568 0.179067 AACAACGCGGAACAGAGGAA 60.179 50.000 12.47 0.00 0.00 3.36
1381 1570 1.504359 TAAACAACGCGGAACAGAGG 58.496 50.000 12.47 0.00 0.00 3.69
1395 1584 1.400142 CGATGCCTGGCGAAATAAACA 59.600 47.619 14.98 0.00 0.00 2.83
1596 1786 2.751837 CGCCTTCCTTCTTGGCCC 60.752 66.667 0.00 0.00 43.42 5.80
1597 1787 2.751837 CCGCCTTCCTTCTTGGCC 60.752 66.667 0.00 0.00 43.42 5.36
1598 1788 3.443925 GCCGCCTTCCTTCTTGGC 61.444 66.667 0.00 0.00 42.94 4.52
1639 1829 3.311110 TCCTTCTTGCCGTCGCCT 61.311 61.111 0.00 0.00 0.00 5.52
1648 1838 2.809601 CCGTCGCCGTCCTTCTTG 60.810 66.667 0.00 0.00 0.00 3.02
1681 1871 2.606587 GCCCTCCTCCTTCTTGCCA 61.607 63.158 0.00 0.00 0.00 4.92
1682 1872 2.273776 GCCCTCCTCCTTCTTGCC 59.726 66.667 0.00 0.00 0.00 4.52
1683 1873 2.124942 CGCCCTCCTCCTTCTTGC 60.125 66.667 0.00 0.00 0.00 4.01
1997 2187 2.677979 CGCGAGCGATCGAGGGATA 61.678 63.158 29.29 0.00 42.83 2.59
2122 2316 1.659491 CGCGTGGTGCTATAGTAGACG 60.659 57.143 14.42 14.42 43.27 4.18
2174 2368 2.004733 GGTACGTAGCCTCGCAATTTT 58.995 47.619 13.80 0.00 0.00 1.82
2194 2392 0.249911 GGCATGTACTAGGGAAGGCG 60.250 60.000 0.00 0.00 0.00 5.52
2199 2397 0.830648 GCTGTGGCATGTACTAGGGA 59.169 55.000 0.00 0.00 38.54 4.20
2264 2860 5.636123 TCTCTCTCTCTGTAAACCACTCTT 58.364 41.667 0.00 0.00 0.00 2.85
2266 2862 5.250200 TCTCTCTCTCTCTGTAAACCACTC 58.750 45.833 0.00 0.00 0.00 3.51
2269 2865 5.249622 TCTCTCTCTCTCTCTCTGTAAACCA 59.750 44.000 0.00 0.00 0.00 3.67
2271 2867 6.640518 TCTCTCTCTCTCTCTCTCTGTAAAC 58.359 44.000 0.00 0.00 0.00 2.01
2272 2868 6.667848 TCTCTCTCTCTCTCTCTCTCTGTAAA 59.332 42.308 0.00 0.00 0.00 2.01
2273 2869 6.194967 TCTCTCTCTCTCTCTCTCTCTGTAA 58.805 44.000 0.00 0.00 0.00 2.41
2274 2870 5.766590 TCTCTCTCTCTCTCTCTCTCTGTA 58.233 45.833 0.00 0.00 0.00 2.74
2275 2871 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
2276 2872 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
2277 2873 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2279 2875 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2280 2876 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2281 2877 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2282 2878 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2283 2879 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2284 2880 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2285 2881 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2286 2882 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2287 2883 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2288 2884 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2320 3134 3.359523 CATGCACCGCACACTGCT 61.360 61.111 0.00 0.00 43.04 4.24
2321 3135 2.693762 ATCATGCACCGCACACTGC 61.694 57.895 0.00 0.00 43.04 4.40
2322 3136 1.135939 CATCATGCACCGCACACTG 59.864 57.895 0.00 0.00 43.04 3.66
2323 3137 2.042259 CCATCATGCACCGCACACT 61.042 57.895 0.00 0.00 43.04 3.55
2324 3138 2.486504 CCATCATGCACCGCACAC 59.513 61.111 0.00 0.00 43.04 3.82
2343 3157 2.795973 CCACATGCTGCATCACCG 59.204 61.111 13.10 4.07 0.00 4.94
2365 3179 9.358872 CTTTTTCTAGAAAGCAAAGTTTGAACT 57.641 29.630 19.82 12.88 33.83 3.01
2394 3208 3.311596 ACCGTATTATTGCGCCTCTTTTC 59.688 43.478 4.18 0.00 0.00 2.29
2397 3211 2.614829 ACCGTATTATTGCGCCTCTT 57.385 45.000 4.18 0.00 0.00 2.85
2398 3212 2.614829 AACCGTATTATTGCGCCTCT 57.385 45.000 4.18 0.00 0.00 3.69
2432 3246 1.202336 GCCTGGCTACAATTGCATGAC 60.202 52.381 12.43 0.00 0.00 3.06
2435 3249 2.008268 GCGCCTGGCTACAATTGCAT 62.008 55.000 17.92 0.00 39.11 3.96
2491 3305 8.328055 TGCTGATTCTCATGGTCCATATATAT 57.672 34.615 3.38 0.00 0.00 0.86
2585 3399 1.079256 AGCTAGCTGGGTCAGGTCA 59.921 57.895 18.57 0.00 41.50 4.02
2595 3409 1.566882 GCGATGCATCCAGCTAGCTG 61.567 60.000 33.58 33.58 45.94 4.24
2596 3410 1.301558 GCGATGCATCCAGCTAGCT 60.302 57.895 20.87 12.68 45.94 3.32
2597 3411 1.596203 TGCGATGCATCCAGCTAGC 60.596 57.895 20.87 16.58 45.94 3.42
2598 3412 0.249784 AGTGCGATGCATCCAGCTAG 60.250 55.000 20.87 6.87 45.94 3.42
2599 3413 0.178767 AAGTGCGATGCATCCAGCTA 59.821 50.000 20.87 7.65 45.94 3.32
2607 3421 5.048782 AGAGAACAAAAATAAGTGCGATGCA 60.049 36.000 0.00 0.00 35.60 3.96
2624 3438 7.250569 GTTGATCAAAGAACAAACAGAGAACA 58.749 34.615 10.35 0.00 0.00 3.18
2626 3440 6.376864 TGGTTGATCAAAGAACAAACAGAGAA 59.623 34.615 10.35 0.00 37.17 2.87
2635 3449 3.305539 GCATGCTGGTTGATCAAAGAACA 60.306 43.478 10.35 7.29 0.00 3.18
2639 3453 3.186909 CATGCATGCTGGTTGATCAAAG 58.813 45.455 20.33 6.24 0.00 2.77
2651 3465 5.429658 CGTGAATCGTATGCATGCATGCT 62.430 47.826 42.08 31.31 43.32 3.79
2724 3565 4.333926 GCACACTGACTAAATGGATCTTCC 59.666 45.833 0.00 0.00 36.96 3.46
2727 3568 4.833478 AGCACACTGACTAAATGGATCT 57.167 40.909 0.00 0.00 0.00 2.75
2728 3569 5.419542 TGTAGCACACTGACTAAATGGATC 58.580 41.667 0.00 0.00 0.00 3.36
2729 3570 5.420725 TGTAGCACACTGACTAAATGGAT 57.579 39.130 0.00 0.00 0.00 3.41
2730 3571 4.882842 TGTAGCACACTGACTAAATGGA 57.117 40.909 0.00 0.00 0.00 3.41
2731 3572 6.500684 AATTGTAGCACACTGACTAAATGG 57.499 37.500 0.00 0.00 0.00 3.16
2732 3573 7.584108 TGAAATTGTAGCACACTGACTAAATG 58.416 34.615 0.00 0.00 0.00 2.32
2733 3574 7.744087 TGAAATTGTAGCACACTGACTAAAT 57.256 32.000 0.00 0.00 0.00 1.40
2734 3575 7.443879 TGATGAAATTGTAGCACACTGACTAAA 59.556 33.333 0.00 0.00 0.00 1.85
2735 3576 6.934083 TGATGAAATTGTAGCACACTGACTAA 59.066 34.615 0.00 0.00 0.00 2.24
2736 3577 6.368791 GTGATGAAATTGTAGCACACTGACTA 59.631 38.462 5.90 0.00 33.68 2.59
2737 3578 5.180117 GTGATGAAATTGTAGCACACTGACT 59.820 40.000 5.90 0.00 33.68 3.41
2738 3579 5.180117 AGTGATGAAATTGTAGCACACTGAC 59.820 40.000 11.59 0.00 35.78 3.51
2750 3591 9.117183 TCTCTCATTAATCCAGTGATGAAATTG 57.883 33.333 0.00 0.00 0.00 2.32
2755 3596 6.127338 ACGTTCTCTCATTAATCCAGTGATGA 60.127 38.462 0.00 0.00 0.00 2.92
2756 3597 6.045318 ACGTTCTCTCATTAATCCAGTGATG 58.955 40.000 0.00 0.00 0.00 3.07
2757 3598 6.097554 AGACGTTCTCTCATTAATCCAGTGAT 59.902 38.462 0.00 0.00 0.00 3.06
2767 3608 5.977489 TTCCTCAAGACGTTCTCTCATTA 57.023 39.130 0.00 0.00 0.00 1.90
2772 3613 5.786264 TTAGTTTCCTCAAGACGTTCTCT 57.214 39.130 0.00 0.00 0.00 3.10
2774 3615 6.258068 CAGTTTTAGTTTCCTCAAGACGTTCT 59.742 38.462 0.00 0.00 0.00 3.01
2775 3616 6.419771 CAGTTTTAGTTTCCTCAAGACGTTC 58.580 40.000 0.00 0.00 0.00 3.95
2786 3627 4.229876 GCTCATGTGCAGTTTTAGTTTCC 58.770 43.478 14.66 0.00 0.00 3.13
2823 3664 4.147321 AGATGTTCATGTGCACTTCCTTT 58.853 39.130 19.41 0.00 0.00 3.11
2828 3669 2.821969 GGGAAGATGTTCATGTGCACTT 59.178 45.455 19.41 9.21 33.93 3.16
2854 3695 2.159254 TGCTGGTGTGCAGTTCTTTTTC 60.159 45.455 0.00 0.00 38.12 2.29
2910 3751 0.322456 GCACTTGATGGCTACACCCA 60.322 55.000 0.00 0.00 39.65 4.51
2947 3793 9.607988 TTTCCTTGCGAGAACTGATTATAATTA 57.392 29.630 1.22 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.