Multiple sequence alignment - TraesCS4B01G051800

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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 TraesCS4B01G051800 chr4B 100.000 4538 0 0 1 4538 40492286 40496823 0.000000e+00 8381
1 TraesCS4B01G051800 chr4B 96.981 3577 88 10 866 4432 120262228 120258662 0.000000e+00 5989
2 TraesCS4B01G051800 chr4B 96.672 3576 103 8 866 4432 222595378 222598946 0.000000e+00 5930
3 TraesCS4B01G051800 chr4B 97.454 864 20 2 1 863 120270290 120269428 0.000000e+00 1472
4 TraesCS4B01G051800 chr4B 99.057 106 1 0 4433 4538 9292477 9292372 1.670000e-44 191
5 TraesCS4B01G051800 chr4B 99.057 106 1 0 4433 4538 9299537 9299432 1.670000e-44 191
6 TraesCS4B01G051800 chr4B 99.057 106 1 0 4433 4538 27097077 27097182 1.670000e-44 191
7 TraesCS4B01G051800 chr4B 99.057 106 1 0 4433 4538 530482422 530482527 1.670000e-44 191
8 TraesCS4B01G051800 chr4B 99.057 106 1 0 4433 4538 642491263 642491158 1.670000e-44 191
9 TraesCS4B01G051800 chr6B 96.616 3576 104 8 866 4432 706416279 706412712 0.000000e+00 5917
10 TraesCS4B01G051800 chr6B 97.798 863 17 2 1 863 706365446 706364586 0.000000e+00 1487
11 TraesCS4B01G051800 chr6B 97.567 863 17 3 1 863 122831873 122831015 0.000000e+00 1474
12 TraesCS4B01G051800 chr6B 97.451 863 20 1 1 863 129733677 129732817 0.000000e+00 1471
13 TraesCS4B01G051800 chr3A 96.589 3577 97 10 866 4432 91838725 91842286 0.000000e+00 5906
14 TraesCS4B01G051800 chr3A 98.030 863 15 2 1 863 91830648 91831508 0.000000e+00 1498
15 TraesCS4B01G051800 chr4A 96.508 3551 107 6 867 4409 531952862 531956403 0.000000e+00 5854
16 TraesCS4B01G051800 chr5B 96.857 3404 91 8 1041 4432 10418338 10414939 0.000000e+00 5679
17 TraesCS4B01G051800 chr5B 99.057 106 1 0 4433 4538 168992891 168992996 1.670000e-44 191
18 TraesCS4B01G051800 chr2D 95.339 3583 139 13 866 4432 340331543 340327973 0.000000e+00 5666
19 TraesCS4B01G051800 chr7A 98.045 2916 55 2 866 3779 492427037 492424122 0.000000e+00 5068
20 TraesCS4B01G051800 chr7A 97.798 863 18 1 1 863 492435447 492434586 0.000000e+00 1487
21 TraesCS4B01G051800 chr5A 93.138 3308 195 17 1146 4432 220265038 220268334 0.000000e+00 4822
22 TraesCS4B01G051800 chr2A 88.391 1809 166 21 2652 4432 724964671 724962879 0.000000e+00 2137
23 TraesCS4B01G051800 chr1B 98.148 864 14 2 1 863 666895897 666895035 0.000000e+00 1506
24 TraesCS4B01G051800 chr7B 97.685 864 19 1 1 863 504093326 504092463 0.000000e+00 1483
25 TraesCS4B01G051800 chr2B 97.451 863 20 2 1 863 758263716 758262856 0.000000e+00 1471
26 TraesCS4B01G051800 chrUn 99.057 106 1 0 4433 4538 325019619 325019724 1.670000e-44 191
27 TraesCS4B01G051800 chr6A 99.057 106 1 0 4433 4538 155653333 155653228 1.670000e-44 191
28 TraesCS4B01G051800 chr1A 99.057 106 1 0 4433 4538 503717752 503717857 1.670000e-44 191


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 TraesCS4B01G051800 chr4B 40492286 40496823 4537 False 8381 8381 100.000 1 4538 1 chr4B.!!$F2 4537
1 TraesCS4B01G051800 chr4B 120258662 120262228 3566 True 5989 5989 96.981 866 4432 1 chr4B.!!$R3 3566
2 TraesCS4B01G051800 chr4B 222595378 222598946 3568 False 5930 5930 96.672 866 4432 1 chr4B.!!$F3 3566
3 TraesCS4B01G051800 chr4B 120269428 120270290 862 True 1472 1472 97.454 1 863 1 chr4B.!!$R4 862
4 TraesCS4B01G051800 chr6B 706412712 706416279 3567 True 5917 5917 96.616 866 4432 1 chr6B.!!$R4 3566
5 TraesCS4B01G051800 chr6B 706364586 706365446 860 True 1487 1487 97.798 1 863 1 chr6B.!!$R3 862
6 TraesCS4B01G051800 chr6B 122831015 122831873 858 True 1474 1474 97.567 1 863 1 chr6B.!!$R1 862
7 TraesCS4B01G051800 chr6B 129732817 129733677 860 True 1471 1471 97.451 1 863 1 chr6B.!!$R2 862
8 TraesCS4B01G051800 chr3A 91838725 91842286 3561 False 5906 5906 96.589 866 4432 1 chr3A.!!$F2 3566
9 TraesCS4B01G051800 chr3A 91830648 91831508 860 False 1498 1498 98.030 1 863 1 chr3A.!!$F1 862
10 TraesCS4B01G051800 chr4A 531952862 531956403 3541 False 5854 5854 96.508 867 4409 1 chr4A.!!$F1 3542
11 TraesCS4B01G051800 chr5B 10414939 10418338 3399 True 5679 5679 96.857 1041 4432 1 chr5B.!!$R1 3391
12 TraesCS4B01G051800 chr2D 340327973 340331543 3570 True 5666 5666 95.339 866 4432 1 chr2D.!!$R1 3566
13 TraesCS4B01G051800 chr7A 492424122 492427037 2915 True 5068 5068 98.045 866 3779 1 chr7A.!!$R1 2913
14 TraesCS4B01G051800 chr7A 492434586 492435447 861 True 1487 1487 97.798 1 863 1 chr7A.!!$R2 862
15 TraesCS4B01G051800 chr5A 220265038 220268334 3296 False 4822 4822 93.138 1146 4432 1 chr5A.!!$F1 3286
16 TraesCS4B01G051800 chr2A 724962879 724964671 1792 True 2137 2137 88.391 2652 4432 1 chr2A.!!$R1 1780
17 TraesCS4B01G051800 chr1B 666895035 666895897 862 True 1506 1506 98.148 1 863 1 chr1B.!!$R1 862
18 TraesCS4B01G051800 chr7B 504092463 504093326 863 True 1483 1483 97.685 1 863 1 chr7B.!!$R1 862
19 TraesCS4B01G051800 chr2B 758262856 758263716 860 True 1471 1471 97.451 1 863 1 chr2B.!!$R1 862

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
960 965 0.900182 CTTGGGGAAGTTTCTGGGCC 60.900 60.000 0.0 0.00 0.0 5.80 F
2249 2259 0.974010 ATCCCACCCTTTGCATGCAG 60.974 55.000 21.5 11.84 0.0 4.41 F
2332 2342 2.271800 GGTATTTCTCGCTCACCAGTG 58.728 52.381 0.0 0.00 0.0 3.66 F
2602 2615 3.081061 GTGTCATGGAACTATGTTGGCA 58.919 45.455 0.0 0.00 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2595 2608 1.992538 TGACATCATGGTTGCCAACA 58.007 45.000 10.18 0.00 36.95 3.33 R
3409 3453 1.466851 AAAGCTGAAGGCCAGGCAAC 61.467 55.000 15.19 4.23 43.13 4.17 R
3433 3477 4.715534 TGTGGAAGGGAAGATTGTAACA 57.284 40.909 0.00 0.00 0.00 2.41 R
4436 4497 0.475475 CATCCCCTATGCTTCAGCCA 59.525 55.000 0.00 0.00 41.18 4.75 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
859 864 6.631016 TCTCCATACGGCATAATGTTATCTC 58.369 40.000 0.00 0.00 0.00 2.75
863 868 9.416284 TCCATACGGCATAATGTTATCTCTATA 57.584 33.333 0.00 0.00 0.00 1.31
864 869 9.464714 CCATACGGCATAATGTTATCTCTATAC 57.535 37.037 0.00 0.00 0.00 1.47
960 965 0.900182 CTTGGGGAAGTTTCTGGGCC 60.900 60.000 0.00 0.00 0.00 5.80
1047 1052 8.109634 AGAATAGTGGTGAGGAAACAATATTGT 58.890 33.333 15.47 15.47 44.72 2.71
1165 1173 6.051717 GTGGTCTGCATGTCTATTTACATCT 58.948 40.000 0.00 0.00 38.01 2.90
1435 1445 9.817809 GGTAATGAATGAGATACTGTACTTTCA 57.182 33.333 0.00 0.00 33.44 2.69
1517 1527 6.128486 TGATTACATCATAACATGCCCTTGT 58.872 36.000 0.00 0.00 33.59 3.16
1718 1728 1.691976 ACGACCACACAGATCAAAGGA 59.308 47.619 0.00 0.00 0.00 3.36
1868 1878 9.317936 TCTAACTAGTGTATGCATGATTCTTTG 57.682 33.333 10.16 2.79 0.00 2.77
2249 2259 0.974010 ATCCCACCCTTTGCATGCAG 60.974 55.000 21.50 11.84 0.00 4.41
2268 2278 8.616076 GCATGCAGTTCTATCAATAGTTTACTT 58.384 33.333 14.21 0.00 0.00 2.24
2332 2342 2.271800 GGTATTTCTCGCTCACCAGTG 58.728 52.381 0.00 0.00 0.00 3.66
2595 2608 5.183713 CACCATTGTTGTGTCATGGAACTAT 59.816 40.000 4.41 0.00 36.33 2.12
2602 2615 3.081061 GTGTCATGGAACTATGTTGGCA 58.919 45.455 0.00 0.00 0.00 4.92
2893 2919 8.797438 GTTCTTCTTCCATCAAGGTAAAGATTT 58.203 33.333 0.00 0.00 39.02 2.17
3433 3477 2.450476 CCTGGCCTTCAGCTTTTGTAT 58.550 47.619 3.32 0.00 42.05 2.29
3817 3866 6.978080 ACGAATTTTTGTATGTGTTCTGCTTT 59.022 30.769 0.00 0.00 0.00 3.51
3822 3871 9.816354 ATTTTTGTATGTGTTCTGCTTTAGTTT 57.184 25.926 0.00 0.00 0.00 2.66
4160 4218 5.353394 ACATGTTACCACCGATGTTCTAT 57.647 39.130 0.00 0.00 0.00 1.98
4240 4299 3.490155 TGTTCGGTAACACATAACACACG 59.510 43.478 0.00 0.00 40.69 4.49
4257 4316 6.788684 ACACACGTGTTACTATAATGCAAA 57.211 33.333 20.79 0.00 41.83 3.68
4363 4423 8.458843 ACATTTGAAACTGTGTTACTATATGGC 58.541 33.333 0.00 0.00 0.00 4.40
4432 4493 1.896465 AGGTCTGTCCTCTTGTAGTGC 59.104 52.381 0.00 0.00 44.42 4.40
4433 4494 1.066787 GGTCTGTCCTCTTGTAGTGCC 60.067 57.143 0.00 0.00 0.00 5.01
4434 4495 1.896465 GTCTGTCCTCTTGTAGTGCCT 59.104 52.381 0.00 0.00 0.00 4.75
4435 4496 3.090037 GTCTGTCCTCTTGTAGTGCCTA 58.910 50.000 0.00 0.00 0.00 3.93
4436 4497 3.702045 GTCTGTCCTCTTGTAGTGCCTAT 59.298 47.826 0.00 0.00 0.00 2.57
4437 4498 3.701542 TCTGTCCTCTTGTAGTGCCTATG 59.298 47.826 0.00 0.00 0.00 2.23
4438 4499 2.766263 TGTCCTCTTGTAGTGCCTATGG 59.234 50.000 0.00 0.00 0.00 2.74
4450 4511 1.818642 GCCTATGGCTGAAGCATAGG 58.181 55.000 22.97 22.97 46.69 2.57
4451 4512 1.612726 GCCTATGGCTGAAGCATAGGG 60.613 57.143 25.55 15.49 46.69 3.53
4452 4513 1.004044 CCTATGGCTGAAGCATAGGGG 59.996 57.143 21.23 8.54 42.25 4.79
4453 4514 1.980765 CTATGGCTGAAGCATAGGGGA 59.019 52.381 4.43 0.00 44.36 4.81
4454 4515 1.453633 ATGGCTGAAGCATAGGGGAT 58.546 50.000 4.43 0.00 44.36 3.85
4455 4516 0.475475 TGGCTGAAGCATAGGGGATG 59.525 55.000 4.43 0.00 44.36 3.51
4456 4517 0.767375 GGCTGAAGCATAGGGGATGA 59.233 55.000 4.43 0.00 44.36 2.92
4457 4518 1.544314 GGCTGAAGCATAGGGGATGAC 60.544 57.143 4.43 0.00 44.36 3.06
4458 4519 1.141657 GCTGAAGCATAGGGGATGACA 59.858 52.381 0.00 0.00 41.59 3.58
4459 4520 2.843701 CTGAAGCATAGGGGATGACAC 58.156 52.381 0.00 0.00 37.82 3.67
4460 4521 2.437281 CTGAAGCATAGGGGATGACACT 59.563 50.000 0.00 0.00 37.82 3.55
4461 4522 2.435805 TGAAGCATAGGGGATGACACTC 59.564 50.000 0.00 0.00 37.82 3.51
4462 4523 2.180946 AGCATAGGGGATGACACTCA 57.819 50.000 0.00 0.00 37.82 3.41
4463 4524 2.699160 AGCATAGGGGATGACACTCAT 58.301 47.619 0.00 0.00 40.34 2.90
4479 4540 9.956640 ATGACACTCATCTCTTCTTTATCTTTT 57.043 29.630 0.00 0.00 29.59 2.27
4480 4541 9.212641 TGACACTCATCTCTTCTTTATCTTTTG 57.787 33.333 0.00 0.00 0.00 2.44
4481 4542 9.429359 GACACTCATCTCTTCTTTATCTTTTGA 57.571 33.333 0.00 0.00 0.00 2.69
4482 4543 9.213799 ACACTCATCTCTTCTTTATCTTTTGAC 57.786 33.333 0.00 0.00 0.00 3.18
4483 4544 8.379161 CACTCATCTCTTCTTTATCTTTTGACG 58.621 37.037 0.00 0.00 0.00 4.35
4484 4545 8.091449 ACTCATCTCTTCTTTATCTTTTGACGT 58.909 33.333 0.00 0.00 0.00 4.34
4485 4546 8.244494 TCATCTCTTCTTTATCTTTTGACGTG 57.756 34.615 0.00 0.00 0.00 4.49
4486 4547 7.331934 TCATCTCTTCTTTATCTTTTGACGTGG 59.668 37.037 0.00 0.00 0.00 4.94
4487 4548 6.522054 TCTCTTCTTTATCTTTTGACGTGGT 58.478 36.000 0.00 0.00 0.00 4.16
4488 4549 6.645415 TCTCTTCTTTATCTTTTGACGTGGTC 59.355 38.462 0.00 0.00 0.00 4.02
4489 4550 5.404366 TCTTCTTTATCTTTTGACGTGGTCG 59.596 40.000 0.00 0.00 43.34 4.79
4490 4551 3.991773 TCTTTATCTTTTGACGTGGTCGG 59.008 43.478 0.00 0.00 41.85 4.79
4491 4552 2.373540 TATCTTTTGACGTGGTCGGG 57.626 50.000 0.00 0.00 41.85 5.14
4492 4553 0.953960 ATCTTTTGACGTGGTCGGGC 60.954 55.000 0.00 0.00 41.85 6.13
4493 4554 1.890041 CTTTTGACGTGGTCGGGCA 60.890 57.895 0.00 0.00 41.85 5.36
4494 4555 1.228003 TTTTGACGTGGTCGGGCAT 60.228 52.632 0.00 0.00 41.85 4.40
4495 4556 0.820074 TTTTGACGTGGTCGGGCATT 60.820 50.000 0.00 0.00 41.85 3.56
4496 4557 1.511318 TTTGACGTGGTCGGGCATTG 61.511 55.000 0.00 0.00 41.85 2.82
4497 4558 2.047655 GACGTGGTCGGGCATTGA 60.048 61.111 0.00 0.00 41.85 2.57
4498 4559 2.047274 ACGTGGTCGGGCATTGAG 60.047 61.111 0.00 0.00 41.85 3.02
4499 4560 3.499737 CGTGGTCGGGCATTGAGC 61.500 66.667 0.00 0.00 44.65 4.26
4500 4561 2.045926 GTGGTCGGGCATTGAGCT 60.046 61.111 0.00 0.00 44.79 4.09
4501 4562 2.046023 TGGTCGGGCATTGAGCTG 60.046 61.111 0.00 0.00 44.79 4.24
4502 4563 2.268920 GGTCGGGCATTGAGCTGA 59.731 61.111 0.00 0.00 44.79 4.26
4503 4564 1.817099 GGTCGGGCATTGAGCTGAG 60.817 63.158 0.00 0.00 44.79 3.35
4504 4565 2.124983 TCGGGCATTGAGCTGAGC 60.125 61.111 0.00 0.00 44.79 4.26
4505 4566 2.124819 CGGGCATTGAGCTGAGCT 60.125 61.111 6.69 6.69 44.79 4.09
4516 4577 2.383368 AGCTGAGCTCAATCTCACAC 57.617 50.000 18.85 0.20 38.11 3.82
4517 4578 1.066286 AGCTGAGCTCAATCTCACACC 60.066 52.381 18.85 0.00 38.11 4.16
4518 4579 1.066286 GCTGAGCTCAATCTCACACCT 60.066 52.381 18.85 0.00 38.11 4.00
4519 4580 2.614987 GCTGAGCTCAATCTCACACCTT 60.615 50.000 18.85 0.00 38.11 3.50
4520 4581 3.001414 CTGAGCTCAATCTCACACCTTG 58.999 50.000 18.85 0.00 38.11 3.61
4521 4582 1.736681 GAGCTCAATCTCACACCTTGC 59.263 52.381 9.40 0.00 33.41 4.01
4522 4583 1.072806 AGCTCAATCTCACACCTTGCA 59.927 47.619 0.00 0.00 0.00 4.08
4523 4584 1.881973 GCTCAATCTCACACCTTGCAA 59.118 47.619 0.00 0.00 0.00 4.08
4524 4585 2.490903 GCTCAATCTCACACCTTGCAAT 59.509 45.455 0.00 0.00 0.00 3.56
4525 4586 3.691118 GCTCAATCTCACACCTTGCAATA 59.309 43.478 0.00 0.00 0.00 1.90
4526 4587 4.437930 GCTCAATCTCACACCTTGCAATAC 60.438 45.833 0.00 0.00 0.00 1.89
4527 4588 4.650734 TCAATCTCACACCTTGCAATACA 58.349 39.130 0.00 0.00 0.00 2.29
4528 4589 4.696877 TCAATCTCACACCTTGCAATACAG 59.303 41.667 0.00 0.00 0.00 2.74
4529 4590 3.057969 TCTCACACCTTGCAATACAGG 57.942 47.619 0.00 0.00 0.00 4.00
4530 4591 1.470098 CTCACACCTTGCAATACAGGC 59.530 52.381 0.00 0.00 0.00 4.85
4531 4592 1.202867 TCACACCTTGCAATACAGGCA 60.203 47.619 0.00 0.00 40.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 118 4.973168 TGGTTCAAAGCTCATGTAAGTCT 58.027 39.130 0.00 0.00 0.00 3.24
591 595 5.050490 GTCCTGAAGTCATATGTGCGTAAT 58.950 41.667 1.90 0.00 0.00 1.89
859 864 2.878406 CCCTTTGGCATGTTCCGTATAG 59.122 50.000 0.00 0.00 0.00 1.31
863 868 1.606313 CCCCTTTGGCATGTTCCGT 60.606 57.895 0.00 0.00 0.00 4.69
864 869 3.287445 CCCCTTTGGCATGTTCCG 58.713 61.111 0.00 0.00 0.00 4.30
960 965 3.475566 TCCTCCATTTCTAGCAATCGG 57.524 47.619 0.00 0.00 0.00 4.18
1047 1052 3.148412 TGTGAAGTACCTGTACGCACTA 58.852 45.455 23.71 14.59 41.85 2.74
1086 1094 8.482852 AAATAGAAGGGCAGCAAATAACATAT 57.517 30.769 0.00 0.00 0.00 1.78
1087 1095 7.896383 AAATAGAAGGGCAGCAAATAACATA 57.104 32.000 0.00 0.00 0.00 2.29
1088 1096 6.796785 AAATAGAAGGGCAGCAAATAACAT 57.203 33.333 0.00 0.00 0.00 2.71
1123 1131 5.658634 AGACCACACTACATCTCATGTACAT 59.341 40.000 1.41 1.41 44.38 2.29
1517 1527 7.548075 GGGAACGACTAATTATGTTCTTCTCAA 59.452 37.037 17.63 0.00 40.34 3.02
1718 1728 8.734386 CCTTCTTCTTGTGAGTTGCTAAATAAT 58.266 33.333 0.00 0.00 0.00 1.28
1810 1820 7.445402 CCATAACTTGATCCCGAGAACAATTAT 59.555 37.037 0.00 0.00 34.65 1.28
1868 1878 6.872920 AGATTCTCCAATCGATCCTATAAGC 58.127 40.000 0.00 0.00 43.05 3.09
2190 2200 8.439971 ACCTCTTCTATGCCATTATTGACATAA 58.560 33.333 0.00 0.00 0.00 1.90
2268 2278 9.498176 GGTTTTCCTACAGAACTAACAAATCTA 57.502 33.333 0.00 0.00 32.95 1.98
2332 2342 3.452755 ACCTTTGTTTTACCAAGCAGC 57.547 42.857 0.00 0.00 0.00 5.25
2564 2577 2.618241 GACACAACAATGGTGAGCAAGA 59.382 45.455 4.82 0.00 39.53 3.02
2571 2584 3.318839 AGTTCCATGACACAACAATGGTG 59.681 43.478 0.00 0.00 41.95 4.17
2595 2608 1.992538 TGACATCATGGTTGCCAACA 58.007 45.000 10.18 0.00 36.95 3.33
2602 2615 6.662865 TTGTAATTGGTTGACATCATGGTT 57.337 33.333 0.00 0.00 0.00 3.67
2893 2919 4.258543 GCAGTAAACCATGCTACTTGGTA 58.741 43.478 5.67 0.00 46.75 3.25
3066 3099 7.886446 CCCTAAGAAACTAAATAAACTGGACCA 59.114 37.037 0.00 0.00 0.00 4.02
3409 3453 1.466851 AAAGCTGAAGGCCAGGCAAC 61.467 55.000 15.19 4.23 43.13 4.17
3433 3477 4.715534 TGTGGAAGGGAAGATTGTAACA 57.284 40.909 0.00 0.00 0.00 2.41
3586 3631 8.943909 ATGTAAACTACAACTATTGGTAGCTC 57.056 34.615 0.00 0.00 42.76 4.09
4160 4218 9.524106 CACCGTAGTAACATATTTTGATAGACA 57.476 33.333 0.00 0.00 0.00 3.41
4343 4403 7.498443 ACTAGGCCATATAGTAACACAGTTTC 58.502 38.462 5.01 0.00 31.71 2.78
4363 4423 4.755123 CAGGTCCAAAAGTGTGTTACTAGG 59.245 45.833 0.00 0.00 39.18 3.02
4432 4493 1.004044 CCCCTATGCTTCAGCCATAGG 59.996 57.143 19.99 19.99 43.69 2.57
4433 4494 1.980765 TCCCCTATGCTTCAGCCATAG 59.019 52.381 0.00 4.29 41.18 2.23
4434 4495 2.116869 TCCCCTATGCTTCAGCCATA 57.883 50.000 0.00 0.00 41.18 2.74
4435 4496 1.075050 CATCCCCTATGCTTCAGCCAT 59.925 52.381 0.00 0.00 41.18 4.40
4436 4497 0.475475 CATCCCCTATGCTTCAGCCA 59.525 55.000 0.00 0.00 41.18 4.75
4437 4498 0.767375 TCATCCCCTATGCTTCAGCC 59.233 55.000 0.00 0.00 41.18 4.85
4438 4499 1.141657 TGTCATCCCCTATGCTTCAGC 59.858 52.381 0.00 0.00 42.50 4.26
4439 4500 2.437281 AGTGTCATCCCCTATGCTTCAG 59.563 50.000 0.00 0.00 35.38 3.02
4440 4501 2.435805 GAGTGTCATCCCCTATGCTTCA 59.564 50.000 0.00 0.00 35.38 3.02
4441 4502 2.435805 TGAGTGTCATCCCCTATGCTTC 59.564 50.000 0.00 0.00 35.38 3.86
4442 4503 2.481441 TGAGTGTCATCCCCTATGCTT 58.519 47.619 0.00 0.00 35.38 3.91
4443 4504 2.180946 TGAGTGTCATCCCCTATGCT 57.819 50.000 0.00 0.00 35.38 3.79
4444 4505 3.051081 GATGAGTGTCATCCCCTATGC 57.949 52.381 5.72 0.00 45.66 3.14
4453 4514 9.956640 AAAAGATAAAGAAGAGATGAGTGTCAT 57.043 29.630 0.00 0.00 40.34 3.06
4454 4515 9.212641 CAAAAGATAAAGAAGAGATGAGTGTCA 57.787 33.333 0.00 0.00 0.00 3.58
4455 4516 9.429359 TCAAAAGATAAAGAAGAGATGAGTGTC 57.571 33.333 0.00 0.00 0.00 3.67
4456 4517 9.213799 GTCAAAAGATAAAGAAGAGATGAGTGT 57.786 33.333 0.00 0.00 0.00 3.55
4457 4518 8.379161 CGTCAAAAGATAAAGAAGAGATGAGTG 58.621 37.037 0.00 0.00 0.00 3.51
4458 4519 8.091449 ACGTCAAAAGATAAAGAAGAGATGAGT 58.909 33.333 0.00 0.00 0.00 3.41
4459 4520 8.379161 CACGTCAAAAGATAAAGAAGAGATGAG 58.621 37.037 0.00 0.00 0.00 2.90
4460 4521 7.331934 CCACGTCAAAAGATAAAGAAGAGATGA 59.668 37.037 0.00 0.00 0.00 2.92
4461 4522 7.118390 ACCACGTCAAAAGATAAAGAAGAGATG 59.882 37.037 0.00 0.00 0.00 2.90
4462 4523 7.162082 ACCACGTCAAAAGATAAAGAAGAGAT 58.838 34.615 0.00 0.00 0.00 2.75
4463 4524 6.522054 ACCACGTCAAAAGATAAAGAAGAGA 58.478 36.000 0.00 0.00 0.00 3.10
4464 4525 6.400091 CGACCACGTCAAAAGATAAAGAAGAG 60.400 42.308 0.00 0.00 32.09 2.85
4465 4526 5.404366 CGACCACGTCAAAAGATAAAGAAGA 59.596 40.000 0.00 0.00 32.09 2.87
4466 4527 5.389516 CCGACCACGTCAAAAGATAAAGAAG 60.390 44.000 0.00 0.00 37.88 2.85
4467 4528 4.449743 CCGACCACGTCAAAAGATAAAGAA 59.550 41.667 0.00 0.00 37.88 2.52
4468 4529 3.991773 CCGACCACGTCAAAAGATAAAGA 59.008 43.478 0.00 0.00 37.88 2.52
4469 4530 3.124636 CCCGACCACGTCAAAAGATAAAG 59.875 47.826 0.00 0.00 37.88 1.85
4470 4531 3.068560 CCCGACCACGTCAAAAGATAAA 58.931 45.455 0.00 0.00 37.88 1.40
4471 4532 2.690786 CCCGACCACGTCAAAAGATAA 58.309 47.619 0.00 0.00 37.88 1.75
4472 4533 1.673626 GCCCGACCACGTCAAAAGATA 60.674 52.381 0.00 0.00 37.88 1.98
4473 4534 0.953960 GCCCGACCACGTCAAAAGAT 60.954 55.000 0.00 0.00 37.88 2.40
4474 4535 1.595929 GCCCGACCACGTCAAAAGA 60.596 57.895 0.00 0.00 37.88 2.52
4475 4536 1.234615 ATGCCCGACCACGTCAAAAG 61.235 55.000 0.00 0.00 37.88 2.27
4476 4537 0.820074 AATGCCCGACCACGTCAAAA 60.820 50.000 0.00 0.00 37.88 2.44
4477 4538 1.228003 AATGCCCGACCACGTCAAA 60.228 52.632 0.00 0.00 37.88 2.69
4478 4539 1.963855 CAATGCCCGACCACGTCAA 60.964 57.895 0.00 0.00 37.88 3.18
4479 4540 2.358125 CAATGCCCGACCACGTCA 60.358 61.111 0.00 0.00 37.88 4.35
4480 4541 2.047655 TCAATGCCCGACCACGTC 60.048 61.111 0.00 0.00 37.88 4.34
4481 4542 2.047274 CTCAATGCCCGACCACGT 60.047 61.111 0.00 0.00 37.88 4.49
4482 4543 3.499737 GCTCAATGCCCGACCACG 61.500 66.667 0.00 0.00 39.43 4.94
4483 4544 2.045926 AGCTCAATGCCCGACCAC 60.046 61.111 0.00 0.00 44.23 4.16
4484 4545 2.046023 CAGCTCAATGCCCGACCA 60.046 61.111 0.00 0.00 44.23 4.02
4485 4546 1.817099 CTCAGCTCAATGCCCGACC 60.817 63.158 0.00 0.00 44.23 4.79
4486 4547 2.467826 GCTCAGCTCAATGCCCGAC 61.468 63.158 0.00 0.00 44.23 4.79
4487 4548 2.124983 GCTCAGCTCAATGCCCGA 60.125 61.111 0.00 0.00 44.23 5.14
4488 4549 2.124819 AGCTCAGCTCAATGCCCG 60.125 61.111 0.00 0.00 44.23 6.13
4497 4558 1.066286 GGTGTGAGATTGAGCTCAGCT 60.066 52.381 17.43 17.69 44.92 4.24
4498 4559 1.066286 AGGTGTGAGATTGAGCTCAGC 60.066 52.381 17.43 13.12 44.92 4.26
4499 4560 3.001414 CAAGGTGTGAGATTGAGCTCAG 58.999 50.000 17.43 0.00 44.92 3.35
4500 4561 2.873245 GCAAGGTGTGAGATTGAGCTCA 60.873 50.000 13.74 13.74 42.31 4.26
4501 4562 1.736681 GCAAGGTGTGAGATTGAGCTC 59.263 52.381 6.82 6.82 35.46 4.09
4502 4563 1.072806 TGCAAGGTGTGAGATTGAGCT 59.927 47.619 0.00 0.00 0.00 4.09
4503 4564 1.527034 TGCAAGGTGTGAGATTGAGC 58.473 50.000 0.00 0.00 0.00 4.26
4504 4565 4.696877 TGTATTGCAAGGTGTGAGATTGAG 59.303 41.667 4.94 0.00 0.00 3.02
4505 4566 4.650734 TGTATTGCAAGGTGTGAGATTGA 58.349 39.130 4.94 0.00 0.00 2.57
4506 4567 4.142534 CCTGTATTGCAAGGTGTGAGATTG 60.143 45.833 4.94 0.00 0.00 2.67
4507 4568 4.012374 CCTGTATTGCAAGGTGTGAGATT 58.988 43.478 4.94 0.00 0.00 2.40
4508 4569 3.614092 CCTGTATTGCAAGGTGTGAGAT 58.386 45.455 4.94 0.00 0.00 2.75
4509 4570 2.875672 GCCTGTATTGCAAGGTGTGAGA 60.876 50.000 4.94 0.00 0.00 3.27
4510 4571 1.470098 GCCTGTATTGCAAGGTGTGAG 59.530 52.381 4.94 0.00 0.00 3.51
4511 4572 1.202867 TGCCTGTATTGCAAGGTGTGA 60.203 47.619 4.94 0.00 35.40 3.58
4512 4573 1.246649 TGCCTGTATTGCAAGGTGTG 58.753 50.000 4.94 0.00 35.40 3.82
4513 4574 1.993956 TTGCCTGTATTGCAAGGTGT 58.006 45.000 4.94 0.00 43.36 4.16


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

AutoCloner maintained by Alex Coulton.