Multiple sequence alignment - TraesCS5D01G482000

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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 TraesCS5D01G482000 chr5D 100.000 5354 0 0 1 5354 519654522 519649169 0.000000e+00 9888.0
1 TraesCS5D01G482000 chr5B 92.450 4980 219 62 13 4905 654498623 654493714 0.000000e+00 6968.0
2 TraesCS5D01G482000 chr5B 92.601 446 22 5 4910 5351 654493557 654493119 9.790000e-177 630.0
3 TraesCS5D01G482000 chr5A 91.173 3886 225 43 10 3844 646213938 646210120 0.000000e+00 5168.0
4 TraesCS5D01G482000 chr5A 89.111 1552 96 40 3860 5354 646210029 646208494 0.000000e+00 1862.0
5 TraesCS5D01G482000 chr7B 83.582 804 87 17 2764 3527 576427712 576428510 0.000000e+00 712.0
6 TraesCS5D01G482000 chr4A 84.017 463 58 6 2762 3212 654154638 654155096 1.070000e-116 431.0
7 TraesCS5D01G482000 chr4A 83.726 467 62 4 2757 3212 654184063 654184526 3.830000e-116 429.0
8 TraesCS5D01G482000 chr1B 81.930 487 55 10 2873 3330 684585931 684585449 1.090000e-101 381.0
9 TraesCS5D01G482000 chrUn 79.783 554 74 13 2811 3330 34342080 34342629 8.470000e-98 368.0
10 TraesCS5D01G482000 chrUn 96.970 33 1 0 3441 3473 108217465 108217433 7.490000e-04 56.5
11 TraesCS5D01G482000 chr3B 79.783 554 74 13 2811 3330 5471286 5471835 8.470000e-98 368.0
12 TraesCS5D01G482000 chr3B 79.422 554 76 13 2811 3330 5487286 5486737 1.830000e-94 357.0
13 TraesCS5D01G482000 chr4B 96.970 33 1 0 3441 3473 666057148 666057180 7.490000e-04 56.5


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 TraesCS5D01G482000 chr5D 519649169 519654522 5353 True 9888 9888 100.0000 1 5354 1 chr5D.!!$R1 5353
1 TraesCS5D01G482000 chr5B 654493119 654498623 5504 True 3799 6968 92.5255 13 5351 2 chr5B.!!$R1 5338
2 TraesCS5D01G482000 chr5A 646208494 646213938 5444 True 3515 5168 90.1420 10 5354 2 chr5A.!!$R1 5344
3 TraesCS5D01G482000 chr7B 576427712 576428510 798 False 712 712 83.5820 2764 3527 1 chr7B.!!$F1 763
4 TraesCS5D01G482000 chrUn 34342080 34342629 549 False 368 368 79.7830 2811 3330 1 chrUn.!!$F1 519
5 TraesCS5D01G482000 chr3B 5471286 5471835 549 False 368 368 79.7830 2811 3330 1 chr3B.!!$F1 519
6 TraesCS5D01G482000 chr3B 5486737 5487286 549 True 357 357 79.4220 2811 3330 1 chr3B.!!$R1 519

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
489 512 0.178975 ATTTCGCCCACCAACTTCCA 60.179 50.000 0.00 0.00 0.00 3.53 F
578 604 0.851332 CCCCTCCCCTTCCTTCCTTT 60.851 60.000 0.00 0.00 0.00 3.11 F
1326 1374 0.908180 ACGGGAAGGTCTACAAGGGG 60.908 60.000 0.00 0.00 0.00 4.79 F
1651 1709 0.249398 TGAGAGCCGCTTTAGGGTTC 59.751 55.000 0.00 0.00 42.85 3.62 F
1668 1727 1.005975 GTTCTCATTGAATCGACGGCG 60.006 52.381 2.87 2.87 36.99 6.46 F
3412 3534 0.304705 CTGTCACACTTCAACGTGGC 59.695 55.000 0.00 0.00 39.19 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 1613 0.325933 TCAGGCACAGTTGGAGATGG 59.674 55.000 0.00 0.0 0.00 3.51 R
1651 1709 0.806102 ACCGCCGTCGATTCAATGAG 60.806 55.000 0.00 0.0 38.10 2.90 R
3265 3382 4.574828 GTGAACTCTAGAAACAACAGCCAA 59.425 41.667 0.00 0.0 0.00 4.52 R
3330 3452 1.134699 GGAATCACGGAGATCAGTGCA 60.135 52.381 8.07 0.0 40.93 4.57 R
3436 3558 2.352715 GCCAAAGCTGTAAACATCCACC 60.353 50.000 0.00 0.0 35.50 4.61 R
5090 5480 1.303799 GCATCACCTCACCTGTGCTG 61.304 60.000 0.00 0.0 34.00 4.41 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
74 76 4.630069 GTGTAAATGCATCACCGTTACTCT 59.370 41.667 15.64 0.00 0.00 3.24
78 80 0.721718 GCATCACCGTTACTCTGCAC 59.278 55.000 0.00 0.00 0.00 4.57
87 89 5.753438 CACCGTTACTCTGCACATACATATT 59.247 40.000 0.00 0.00 0.00 1.28
117 119 0.319555 ATATTCGGCCGATCCACACG 60.320 55.000 31.56 0.00 34.01 4.49
164 166 6.654582 ACAGATACATATCACACAAGCAAACA 59.345 34.615 1.88 0.00 35.17 2.83
165 167 7.337689 ACAGATACATATCACACAAGCAAACAT 59.662 33.333 1.88 0.00 35.17 2.71
167 169 8.830580 AGATACATATCACACAAGCAAACATAC 58.169 33.333 1.88 0.00 35.17 2.39
184 188 4.619973 ACATACAAAACACACTGCCATTG 58.380 39.130 0.00 0.00 0.00 2.82
192 196 2.434884 ACTGCCATTGCTCGACGG 60.435 61.111 0.00 0.00 38.71 4.79
194 198 1.522355 CTGCCATTGCTCGACGGAT 60.522 57.895 0.00 0.00 38.71 4.18
241 246 4.951254 TCTCGTCCAATCTACACACAAAA 58.049 39.130 0.00 0.00 0.00 2.44
257 262 4.397730 ACACAAAATGCATCGCCATTACTA 59.602 37.500 0.00 0.00 34.50 1.82
268 273 6.447162 CATCGCCATTACTAGACAGATACAA 58.553 40.000 0.00 0.00 0.00 2.41
288 293 4.922692 ACAACACACAACAATCAACACAAG 59.077 37.500 0.00 0.00 0.00 3.16
292 297 5.863397 ACACACAACAATCAACACAAGAAAG 59.137 36.000 0.00 0.00 0.00 2.62
364 370 1.298906 ATCAATGGTGGGGGCTGGAT 61.299 55.000 0.00 0.00 0.00 3.41
366 372 3.012775 AATGGTGGGGGCTGGATGG 62.013 63.158 0.00 0.00 0.00 3.51
415 438 5.163258 TGAGAGAGGGAAGAGATATTTTGGC 60.163 44.000 0.00 0.00 0.00 4.52
489 512 0.178975 ATTTCGCCCACCAACTTCCA 60.179 50.000 0.00 0.00 0.00 3.53
578 604 0.851332 CCCCTCCCCTTCCTTCCTTT 60.851 60.000 0.00 0.00 0.00 3.11
582 608 1.996291 CTCCCCTTCCTTCCTTTCCTT 59.004 52.381 0.00 0.00 0.00 3.36
583 609 2.380249 CTCCCCTTCCTTCCTTTCCTTT 59.620 50.000 0.00 0.00 0.00 3.11
767 795 3.004734 CCCACTTTTCAGCTCAAAATCGT 59.995 43.478 0.00 0.00 0.00 3.73
870 899 2.529389 ACTGGGGCTTTCCGAGGT 60.529 61.111 0.00 0.00 44.56 3.85
1326 1374 0.908180 ACGGGAAGGTCTACAAGGGG 60.908 60.000 0.00 0.00 0.00 4.79
1331 1379 2.027100 GGAAGGTCTACAAGGGGAAGTG 60.027 54.545 0.00 0.00 0.00 3.16
1339 1387 1.630878 ACAAGGGGAAGTGAGTGGATC 59.369 52.381 0.00 0.00 0.00 3.36
1343 1391 1.630878 GGGGAAGTGAGTGGATCAACT 59.369 52.381 1.12 1.12 40.43 3.16
1376 1424 3.620427 ACCCGTGCATAGTGTTTCATA 57.380 42.857 0.00 0.00 0.00 2.15
1377 1425 3.267483 ACCCGTGCATAGTGTTTCATAC 58.733 45.455 0.00 0.00 0.00 2.39
1460 1518 4.856509 TCCTCAGCTTTAGTACTAGCAGA 58.143 43.478 17.76 14.29 39.85 4.26
1467 1525 5.068460 AGCTTTAGTACTAGCAGATGTCCAG 59.932 44.000 17.76 0.00 39.85 3.86
1486 1544 4.351407 TCCAGTCCAAACTAATGGGTGTTA 59.649 41.667 0.00 0.00 41.05 2.41
1525 1583 7.201794 CCAGGAGTTATGTATCAACGAAGTAGA 60.202 40.741 0.00 0.00 45.00 2.59
1612 1670 1.790623 ACGTACAGACACAACAATCGC 59.209 47.619 0.00 0.00 0.00 4.58
1651 1709 0.249398 TGAGAGCCGCTTTAGGGTTC 59.751 55.000 0.00 0.00 42.85 3.62
1657 1716 1.401905 GCCGCTTTAGGGTTCTCATTG 59.598 52.381 0.00 0.00 0.00 2.82
1668 1727 1.005975 GTTCTCATTGAATCGACGGCG 60.006 52.381 2.87 2.87 36.99 6.46
1672 1731 1.135053 TCATTGAATCGACGGCGGTAA 60.135 47.619 12.58 0.00 38.28 2.85
1727 1786 6.720112 AATTTAGATATGCCAGCATGTTGT 57.280 33.333 15.29 4.19 37.82 3.32
1781 1840 9.546428 AGGATTCTGAAATTTGTTTTAGTTTGG 57.454 29.630 0.00 0.00 0.00 3.28
2139 2201 6.659776 AGAAAAAGTAACACTTGAAGATCGC 58.340 36.000 0.00 0.00 38.66 4.58
2211 2273 2.789409 AGGTACATCCTTGCCTGAAC 57.211 50.000 0.00 0.00 45.67 3.18
2235 2297 3.694072 GCAACATTACTGTGCCTAATCCA 59.306 43.478 0.00 0.00 35.22 3.41
2243 2305 8.902806 CATTACTGTGCCTAATCCAATTTTAGA 58.097 33.333 0.00 0.00 0.00 2.10
2556 2619 3.624326 TTGACTTTTCCTGTTGCATCG 57.376 42.857 0.00 0.00 0.00 3.84
2633 2706 2.616842 CGGGTGGCATATTTACCAAGAC 59.383 50.000 0.00 0.00 37.79 3.01
2659 2733 3.156293 TGGAAGATGACAAACATGGGTG 58.844 45.455 0.00 0.00 39.56 4.61
2670 2744 4.769488 ACAAACATGGGTGCACAATATACA 59.231 37.500 20.43 7.54 0.00 2.29
2970 3050 3.884895 TCCTTTCTGTCAAAGCTGTTCA 58.115 40.909 0.00 0.00 0.00 3.18
2972 3052 3.549625 CCTTTCTGTCAAAGCTGTTCAGC 60.550 47.826 15.88 15.88 0.00 4.26
2976 3056 1.312815 GTCAAAGCTGTTCAGCCACT 58.687 50.000 19.28 3.91 34.90 4.00
2998 3078 7.041098 CCACTCTCTTTATGCTTTTACAGTGTT 60.041 37.037 0.00 0.00 0.00 3.32
3210 3309 6.707440 TTATGAACTGAAGCCAGAACAAAA 57.293 33.333 0.00 0.00 43.02 2.44
3211 3310 5.796424 ATGAACTGAAGCCAGAACAAAAT 57.204 34.783 0.00 0.00 43.02 1.82
3212 3311 5.186996 TGAACTGAAGCCAGAACAAAATC 57.813 39.130 0.00 0.00 43.02 2.17
3265 3382 7.716799 TTTGTATGCCCACTTGATAATTTCT 57.283 32.000 0.00 0.00 0.00 2.52
3273 3390 5.047092 CCCACTTGATAATTTCTTGGCTGTT 60.047 40.000 0.00 0.00 0.00 3.16
3330 3452 9.545105 CTATACAAAGAGAAATCAGATGCTCTT 57.455 33.333 17.31 17.31 46.46 2.85
3342 3464 3.849002 TGCTCTTGCACTGATCTCC 57.151 52.632 0.00 0.00 45.31 3.71
3360 3482 3.009033 TCTCCGTGATTCCAAAACCTGAT 59.991 43.478 0.00 0.00 0.00 2.90
3412 3534 0.304705 CTGTCACACTTCAACGTGGC 59.695 55.000 0.00 0.00 39.19 5.01
3590 3718 4.102524 TGGCGGAATGATACCACTTTCTAT 59.897 41.667 0.00 0.00 0.00 1.98
3653 3781 5.615925 AGTTACAACTCTCCTGTTTCACT 57.384 39.130 0.00 0.00 32.86 3.41
3700 3828 6.203723 GCAGGCCATTAGTAATGTCTCTTTAG 59.796 42.308 19.18 5.02 37.18 1.85
3701 3829 7.275920 CAGGCCATTAGTAATGTCTCTTTAGT 58.724 38.462 19.18 0.00 37.18 2.24
3702 3830 7.439655 CAGGCCATTAGTAATGTCTCTTTAGTC 59.560 40.741 19.18 5.36 37.18 2.59
3703 3831 7.345914 AGGCCATTAGTAATGTCTCTTTAGTCT 59.654 37.037 19.18 7.29 37.18 3.24
3704 3832 7.988028 GGCCATTAGTAATGTCTCTTTAGTCTT 59.012 37.037 19.18 0.00 37.18 3.01
3705 3833 9.384764 GCCATTAGTAATGTCTCTTTAGTCTTT 57.615 33.333 19.18 0.00 37.18 2.52
3758 3888 8.535690 AGTAGAAGTACTGTATGTTTTGAAGC 57.464 34.615 0.00 0.00 38.14 3.86
3820 3950 9.362539 GAATGATAGCAAAATTGTGAGACAAAT 57.637 29.630 0.00 0.00 41.96 2.32
3823 3953 8.143193 TGATAGCAAAATTGTGAGACAAATTGT 58.857 29.630 0.00 0.00 41.96 2.71
3847 3977 1.962807 CACATTTGTGGGAAGAAGGCA 59.037 47.619 2.69 0.00 42.10 4.75
3856 3986 3.191371 GTGGGAAGAAGGCAACACATTAG 59.809 47.826 0.00 0.00 41.41 1.73
4031 4251 9.158233 TCTTACCCATATTTTCTCTTGTTTACG 57.842 33.333 0.00 0.00 0.00 3.18
4168 4388 3.036429 ATGCTGGACGCCTTCCTCC 62.036 63.158 0.88 0.00 46.10 4.30
4169 4389 3.394836 GCTGGACGCCTTCCTCCT 61.395 66.667 0.88 0.00 46.10 3.69
4213 4433 3.343788 GAGGCAGACGAGGACACGG 62.344 68.421 0.00 0.00 37.61 4.94
4332 4552 0.762418 TGTTTGCCTCGAAGAAGGGA 59.238 50.000 0.00 0.00 34.09 4.20
4511 4739 7.038048 TGCTTGTTTTGTGTTTTGATGATACA 58.962 30.769 0.00 0.00 0.00 2.29
4631 4863 1.610522 CCCCTCTTGTTTTCACTGCAG 59.389 52.381 13.48 13.48 0.00 4.41
4633 4865 2.033801 CCCTCTTGTTTTCACTGCAGTG 59.966 50.000 36.07 36.07 46.91 3.66
4678 4910 4.080356 TGATCCAAACAGACTTGATAGGGG 60.080 45.833 0.00 0.00 0.00 4.79
4681 4913 4.105697 TCCAAACAGACTTGATAGGGGTTT 59.894 41.667 0.00 0.00 0.00 3.27
4683 4915 5.414765 CCAAACAGACTTGATAGGGGTTTAC 59.585 44.000 0.00 0.00 0.00 2.01
4684 4916 4.838904 ACAGACTTGATAGGGGTTTACC 57.161 45.455 0.00 0.00 39.11 2.85
4739 4971 8.012241 CACTGACTCTTGAGCTAACATTTTAAC 58.988 37.037 0.00 0.00 0.00 2.01
4825 5057 6.940298 CCAAGTTACTCACAATTTCTTCCCTA 59.060 38.462 0.00 0.00 0.00 3.53
4839 5071 7.812690 TTTCTTCCCTAAACAGAAAGTTACC 57.187 36.000 0.00 0.00 40.26 2.85
4841 5073 4.276058 TCCCTAAACAGAAAGTTACCCG 57.724 45.455 0.00 0.00 40.26 5.28
4905 5139 5.620206 ACGAATAGATGCCCATGAATTGTA 58.380 37.500 0.00 0.00 0.00 2.41
4907 5141 6.017109 ACGAATAGATGCCCATGAATTGTAAC 60.017 38.462 0.00 0.00 0.00 2.50
4908 5142 6.017192 CGAATAGATGCCCATGAATTGTAACA 60.017 38.462 0.00 0.00 0.00 2.41
4913 5299 3.505680 TGCCCATGAATTGTAACACTGAC 59.494 43.478 0.00 0.00 0.00 3.51
4918 5304 6.304126 CCATGAATTGTAACACTGACGTAAC 58.696 40.000 0.00 0.00 0.00 2.50
4922 5308 6.535865 TGAATTGTAACACTGACGTAACACTT 59.464 34.615 0.00 0.00 0.00 3.16
4923 5309 5.954434 TTGTAACACTGACGTAACACTTC 57.046 39.130 0.00 0.00 0.00 3.01
5025 5415 5.990668 ACAATACAAAGATGTCCTACCTCC 58.009 41.667 0.00 0.00 41.05 4.30
5028 5418 2.237392 ACAAAGATGTCCTACCTCCAGC 59.763 50.000 0.00 0.00 33.41 4.85
5041 5431 7.442666 GTCCTACCTCCAGCTATTTCAAATTAG 59.557 40.741 0.00 0.00 0.00 1.73
5045 5435 6.768381 ACCTCCAGCTATTTCAAATTAGTAGC 59.232 38.462 0.00 0.00 38.37 3.58
5129 5526 0.885879 TACCACTCTACCAGCACACG 59.114 55.000 0.00 0.00 0.00 4.49
5149 5546 2.181021 GTACTGCAGTCCCGGTCG 59.819 66.667 25.56 0.00 0.00 4.79
5317 5726 2.106683 CGTTCCTCCGGCATCAACC 61.107 63.158 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.651704 TGACGTGTGTGATATATTTATGGAGTG 59.348 37.037 0.00 0.00 0.00 3.51
1 2 7.722363 TGACGTGTGTGATATATTTATGGAGT 58.278 34.615 0.00 0.00 0.00 3.85
2 3 8.587952 TTGACGTGTGTGATATATTTATGGAG 57.412 34.615 0.00 0.00 0.00 3.86
3 4 8.950208 TTTGACGTGTGTGATATATTTATGGA 57.050 30.769 0.00 0.00 0.00 3.41
4 5 9.597999 CATTTGACGTGTGTGATATATTTATGG 57.402 33.333 0.00 0.00 0.00 2.74
5 6 9.597999 CCATTTGACGTGTGTGATATATTTATG 57.402 33.333 0.00 0.00 0.00 1.90
6 7 8.289618 GCCATTTGACGTGTGTGATATATTTAT 58.710 33.333 0.00 0.00 0.00 1.40
7 8 7.517575 CGCCATTTGACGTGTGTGATATATTTA 60.518 37.037 0.00 0.00 0.00 1.40
8 9 6.494842 GCCATTTGACGTGTGTGATATATTT 58.505 36.000 0.00 0.00 0.00 1.40
74 76 3.873952 TGCTTACGCAATATGTATGTGCA 59.126 39.130 0.00 0.00 44.62 4.57
87 89 1.332375 GGCCGAATATTTGCTTACGCA 59.668 47.619 9.82 0.00 46.24 5.24
117 119 2.785679 GAGTAACGGTGATGCATTTGC 58.214 47.619 0.00 0.00 42.50 3.68
164 166 3.321682 AGCAATGGCAGTGTGTTTTGTAT 59.678 39.130 16.96 0.00 44.61 2.29
165 167 2.692557 AGCAATGGCAGTGTGTTTTGTA 59.307 40.909 16.96 0.00 44.61 2.41
167 169 2.129607 GAGCAATGGCAGTGTGTTTTG 58.870 47.619 16.96 3.58 44.61 2.44
184 188 4.106197 GGAATGTGATATATCCGTCGAGC 58.894 47.826 10.25 0.00 0.00 5.03
192 196 5.700832 TGCCGTTTGAGGAATGTGATATATC 59.299 40.000 5.73 5.73 0.00 1.63
194 198 5.029807 TGCCGTTTGAGGAATGTGATATA 57.970 39.130 0.00 0.00 0.00 0.86
241 246 3.321968 TCTGTCTAGTAATGGCGATGCAT 59.678 43.478 0.00 0.00 0.00 3.96
257 262 6.054941 TGATTGTTGTGTGTTGTATCTGTCT 58.945 36.000 0.00 0.00 0.00 3.41
268 273 5.384063 TTCTTGTGTTGATTGTTGTGTGT 57.616 34.783 0.00 0.00 0.00 3.72
288 293 5.394553 CCAAATCTCCTGGTTATTGGCTTTC 60.395 44.000 9.22 0.00 31.86 2.62
292 297 3.631250 TCCAAATCTCCTGGTTATTGGC 58.369 45.455 14.22 0.00 37.74 4.52
364 370 1.616327 CCACCATGGTCCTCCTCCA 60.616 63.158 16.53 0.00 39.41 3.86
366 372 1.341156 CCTCCACCATGGTCCTCCTC 61.341 65.000 16.53 0.00 39.03 3.71
489 512 2.445983 CGGGGTATAAAGCGGGGGT 61.446 63.158 0.00 0.00 0.00 4.95
578 604 3.961414 GTGGTGCGGGGGAAAGGA 61.961 66.667 0.00 0.00 0.00 3.36
748 776 3.607078 GCGACGATTTTGAGCTGAAAAGT 60.607 43.478 16.18 9.68 0.00 2.66
767 795 2.025418 GAACCGAGCGGAAAAGCGA 61.025 57.895 16.83 0.00 43.00 4.93
850 878 2.920912 TCGGAAAGCCCCAGTCGT 60.921 61.111 0.00 0.00 0.00 4.34
854 882 1.915078 ATCACCTCGGAAAGCCCCAG 61.915 60.000 0.00 0.00 0.00 4.45
855 883 1.497309 AATCACCTCGGAAAGCCCCA 61.497 55.000 0.00 0.00 0.00 4.96
870 899 1.523154 GGCGGACAAAGCACCAATCA 61.523 55.000 0.00 0.00 36.08 2.57
919 964 0.248621 CGCTCATGGAAAAATCGGCC 60.249 55.000 0.00 0.00 0.00 6.13
1311 1359 2.904434 TCACTTCCCCTTGTAGACCTTC 59.096 50.000 0.00 0.00 0.00 3.46
1326 1374 7.173218 TGTCATAAAAGTTGATCCACTCACTTC 59.827 37.037 0.00 0.00 32.17 3.01
1331 1379 9.774742 GTTATTGTCATAAAAGTTGATCCACTC 57.225 33.333 0.00 0.00 0.00 3.51
1339 1387 5.571357 GCACGGGTTATTGTCATAAAAGTTG 59.429 40.000 0.00 0.00 0.00 3.16
1343 1391 5.906113 ATGCACGGGTTATTGTCATAAAA 57.094 34.783 0.00 0.00 0.00 1.52
1376 1424 1.238439 CCTTCGGCTGAAACATGTGT 58.762 50.000 9.73 0.00 32.66 3.72
1377 1425 1.197721 GACCTTCGGCTGAAACATGTG 59.802 52.381 9.73 0.00 32.66 3.21
1460 1518 3.333680 ACCCATTAGTTTGGACTGGACAT 59.666 43.478 0.00 0.00 39.25 3.06
1467 1525 5.867174 GCAATTAACACCCATTAGTTTGGAC 59.133 40.000 0.00 0.00 39.25 4.02
1486 1544 6.041979 ACATAACTCCTGGACTTTTTGCAATT 59.958 34.615 0.00 0.00 0.00 2.32
1525 1583 9.990868 AATTAAAATCATACCAACTCTTACCCT 57.009 29.630 0.00 0.00 0.00 4.34
1555 1613 0.325933 TCAGGCACAGTTGGAGATGG 59.674 55.000 0.00 0.00 0.00 3.51
1558 1616 1.421268 ACATTCAGGCACAGTTGGAGA 59.579 47.619 0.00 0.00 0.00 3.71
1590 1648 3.426191 GCGATTGTTGTGTCTGTACGTAA 59.574 43.478 0.00 0.00 0.00 3.18
1594 1652 2.139917 TGGCGATTGTTGTGTCTGTAC 58.860 47.619 0.00 0.00 0.00 2.90
1599 1657 3.362888 GCAATTTTGGCGATTGTTGTGTC 60.363 43.478 8.98 0.00 36.96 3.67
1600 1658 2.543430 GCAATTTTGGCGATTGTTGTGT 59.457 40.909 8.98 0.00 36.96 3.72
1601 1659 2.543012 TGCAATTTTGGCGATTGTTGTG 59.457 40.909 8.98 0.00 36.96 3.33
1602 1660 2.831333 TGCAATTTTGGCGATTGTTGT 58.169 38.095 8.98 0.00 36.96 3.32
1651 1709 0.806102 ACCGCCGTCGATTCAATGAG 60.806 55.000 0.00 0.00 38.10 2.90
1657 1716 1.000938 AGGTATTACCGCCGTCGATTC 60.001 52.381 7.21 0.00 44.90 2.52
1668 1727 9.965902 ATAAATCAGATCATTGGAGGTATTACC 57.034 33.333 4.57 4.57 38.99 2.85
1711 1770 6.822170 CAGATATCTACAACATGCTGGCATAT 59.178 38.462 4.54 0.00 34.91 1.78
1727 1786 7.128751 ACCATAGCAGGAATAGCAGATATCTA 58.871 38.462 4.54 0.00 0.00 1.98
1781 1840 7.173390 ACTCTTTGCAAGTATTAGAACAAGACC 59.827 37.037 0.00 0.00 0.00 3.85
1822 1881 9.041354 ACCCATGGTGTACATTTAAACATAAAT 57.959 29.630 11.73 0.00 37.84 1.40
2139 2201 8.706936 CACATCATATTTACTTCTCGGATGAAG 58.293 37.037 0.00 12.59 46.33 3.02
2215 2277 7.480760 AAATTGGATTAGGCACAGTAATGTT 57.519 32.000 0.00 0.00 0.00 2.71
2633 2706 5.697633 CCCATGTTTGTCATCTTCCAAAAAG 59.302 40.000 0.00 0.00 34.09 2.27
2647 2720 4.769488 TGTATATTGTGCACCCATGTTTGT 59.231 37.500 15.69 0.00 0.00 2.83
2916 2996 6.743788 ACTACTGGAAGAACCTAGAAGGTAT 58.256 40.000 0.00 0.00 43.28 2.73
2970 3050 5.560724 TGTAAAAGCATAAAGAGAGTGGCT 58.439 37.500 0.00 0.00 0.00 4.75
2972 3052 6.428159 ACACTGTAAAAGCATAAAGAGAGTGG 59.572 38.462 0.00 0.00 33.06 4.00
2976 3056 9.772973 TTAGAACACTGTAAAAGCATAAAGAGA 57.227 29.630 0.00 0.00 0.00 3.10
2998 3078 7.935520 TCTGCACACACAAAACATTTATTAGA 58.064 30.769 0.00 0.00 0.00 2.10
3188 3286 6.489700 TGATTTTGTTCTGGCTTCAGTTCATA 59.510 34.615 0.00 0.00 39.45 2.15
3189 3287 5.302568 TGATTTTGTTCTGGCTTCAGTTCAT 59.697 36.000 0.00 0.00 39.45 2.57
3190 3288 4.644234 TGATTTTGTTCTGGCTTCAGTTCA 59.356 37.500 0.00 0.00 39.45 3.18
3210 3309 9.624373 AGTATAATTTCAAGCATCAACTCTGAT 57.376 29.630 0.00 0.00 43.40 2.90
3211 3310 9.453572 AAGTATAATTTCAAGCATCAACTCTGA 57.546 29.630 0.00 0.00 35.56 3.27
3212 3311 9.713740 GAAGTATAATTTCAAGCATCAACTCTG 57.286 33.333 0.00 0.00 0.00 3.35
3265 3382 4.574828 GTGAACTCTAGAAACAACAGCCAA 59.425 41.667 0.00 0.00 0.00 4.52
3273 3390 5.926542 CCGAAATCAGTGAACTCTAGAAACA 59.073 40.000 0.00 0.00 0.00 2.83
3330 3452 1.134699 GGAATCACGGAGATCAGTGCA 60.135 52.381 8.07 0.00 40.93 4.57
3342 3464 3.188460 ACGAATCAGGTTTTGGAATCACG 59.812 43.478 0.00 0.00 0.00 4.35
3360 3482 4.036262 ACTGCAAAAGCATAAGACAACGAA 59.964 37.500 0.00 0.00 0.00 3.85
3436 3558 2.352715 GCCAAAGCTGTAAACATCCACC 60.353 50.000 0.00 0.00 35.50 4.61
3569 3697 7.387948 ACATTATAGAAAGTGGTATCATTCCGC 59.612 37.037 0.00 0.00 35.90 5.54
3601 3729 5.822519 AGAGTCGCAGGATTTTATAATTGCA 59.177 36.000 4.25 0.00 30.36 4.08
3700 3828 7.549615 AGTAACAGTTTTGTCCAGTAAAGAC 57.450 36.000 0.00 0.00 36.23 3.01
3701 3829 8.480501 AGTAGTAACAGTTTTGTCCAGTAAAGA 58.519 33.333 0.00 0.00 36.23 2.52
3702 3830 8.548721 CAGTAGTAACAGTTTTGTCCAGTAAAG 58.451 37.037 0.00 0.00 36.23 1.85
3703 3831 7.011669 GCAGTAGTAACAGTTTTGTCCAGTAAA 59.988 37.037 0.00 0.00 36.23 2.01
3704 3832 6.480981 GCAGTAGTAACAGTTTTGTCCAGTAA 59.519 38.462 0.00 0.00 36.23 2.24
3705 3833 5.987347 GCAGTAGTAACAGTTTTGTCCAGTA 59.013 40.000 0.00 0.00 36.23 2.74
3706 3834 4.814771 GCAGTAGTAACAGTTTTGTCCAGT 59.185 41.667 0.00 0.00 36.23 4.00
3737 3865 6.803154 AGGCTTCAAAACATACAGTACTTC 57.197 37.500 0.00 0.00 0.00 3.01
3738 3866 6.016276 CCAAGGCTTCAAAACATACAGTACTT 60.016 38.462 0.00 0.00 0.00 2.24
3828 3958 2.365293 GTTGCCTTCTTCCCACAAATGT 59.635 45.455 0.00 0.00 0.00 2.71
3837 3967 4.762251 AGAACTAATGTGTTGCCTTCTTCC 59.238 41.667 0.00 0.00 0.00 3.46
3903 4113 4.448210 ACTATGACCAGTTCGTTTGTTGT 58.552 39.130 0.00 0.00 0.00 3.32
4125 4345 0.911045 TGATCTGGCTGAAGCTGGGA 60.911 55.000 1.74 0.00 41.70 4.37
4168 4388 1.517832 GTGGTGGAGGGATCGTCAG 59.482 63.158 0.00 0.00 0.00 3.51
4169 4389 1.987855 GGTGGTGGAGGGATCGTCA 60.988 63.158 0.00 0.00 0.00 4.35
4213 4433 1.444553 CTGTGTCTTCCGACTCCGC 60.445 63.158 0.00 0.00 40.86 5.54
4332 4552 2.363406 GCCTTCCCATTGCTGCCT 60.363 61.111 0.00 0.00 0.00 4.75
4631 4863 2.353704 GGATTGGCAAAGGGCTAAACAC 60.354 50.000 3.01 0.00 46.60 3.32
4633 4865 2.094026 CAGGATTGGCAAAGGGCTAAAC 60.094 50.000 3.01 0.00 46.60 2.01
4678 4910 7.659390 CCATCTCTAAGATCCATTGAGGTAAAC 59.341 40.741 7.41 0.00 39.02 2.01
4681 4913 6.385443 ACCATCTCTAAGATCCATTGAGGTA 58.615 40.000 7.41 0.00 39.02 3.08
4683 4915 5.822132 ACCATCTCTAAGATCCATTGAGG 57.178 43.478 7.41 0.00 31.32 3.86
4684 4916 7.871973 CAGTAACCATCTCTAAGATCCATTGAG 59.128 40.741 0.00 0.00 31.32 3.02
4739 4971 5.874831 TCGAAAATCCCAACAATGTAATCG 58.125 37.500 0.00 0.00 0.00 3.34
4776 5008 6.239629 GGTCACCCTAGAAATTGGTAGATAGG 60.240 46.154 0.00 0.00 0.00 2.57
4777 5009 6.326583 TGGTCACCCTAGAAATTGGTAGATAG 59.673 42.308 0.00 0.00 0.00 2.08
4778 5010 6.206787 TGGTCACCCTAGAAATTGGTAGATA 58.793 40.000 0.00 0.00 0.00 1.98
4825 5057 4.023193 CAGATTGCGGGTAACTTTCTGTTT 60.023 41.667 0.00 0.00 39.89 2.83
4841 5073 7.594758 TCAACTACTGCAAAATTTACAGATTGC 59.405 33.333 21.68 13.65 46.29 3.56
4889 5123 4.398988 TCAGTGTTACAATTCATGGGCATC 59.601 41.667 0.00 0.00 0.00 3.91
4905 5139 4.689071 TCATGAAGTGTTACGTCAGTGTT 58.311 39.130 0.00 0.00 39.76 3.32
4907 5141 5.651172 TTTCATGAAGTGTTACGTCAGTG 57.349 39.130 8.41 0.00 39.76 3.66
4908 5142 6.861065 ATTTTCATGAAGTGTTACGTCAGT 57.139 33.333 8.41 0.00 39.76 3.41
4913 5299 7.855409 TCTGTCAAATTTTCATGAAGTGTTACG 59.145 33.333 8.41 1.69 0.00 3.18
4918 5304 7.990541 TTGTCTGTCAAATTTTCATGAAGTG 57.009 32.000 8.41 6.26 32.64 3.16
4979 5365 7.877003 TGTATAAGGTTCGAAAATGCTTCAAA 58.123 30.769 0.00 0.00 0.00 2.69
4992 5379 8.548721 GGACATCTTTGTATTGTATAAGGTTCG 58.451 37.037 0.00 0.00 35.79 3.95
5025 5415 7.470289 AGACGCTACTAATTTGAAATAGCTG 57.530 36.000 0.00 5.33 36.85 4.24
5041 5431 6.573725 CACACAGAATTTGTAAAAGACGCTAC 59.426 38.462 0.00 0.00 38.16 3.58
5045 5435 7.962934 TTTCACACAGAATTTGTAAAAGACG 57.037 32.000 0.00 0.00 38.16 4.18
5090 5480 1.303799 GCATCACCTCACCTGTGCTG 61.304 60.000 0.00 0.00 34.00 4.41
5129 5526 4.814294 CCGGGACTGCAGTACGCC 62.814 72.222 28.31 21.68 41.33 5.68
5133 5530 3.066190 CCGACCGGGACTGCAGTA 61.066 66.667 21.73 0.00 38.47 2.74
5149 5546 1.606601 GGTGGGGAGAAGGTTTGCC 60.607 63.158 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.