Multiple sequence alignment - TraesCS4B01G027900

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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 TraesCS4B01G027900 chr4B 100.000 4560 0 0 1 4560 20742909 20747468 0.000000e+00 8421
1 TraesCS4B01G027900 chr4D 95.147 3709 139 22 855 4560 10988016 10991686 0.000000e+00 5814
2 TraesCS4B01G027900 chr4D 82.889 637 52 28 52 641 10987070 10987696 1.880000e-143 520
3 TraesCS4B01G027900 chr4A 94.791 3763 128 27 826 4560 591874725 591878447 0.000000e+00 5801
4 TraesCS4B01G027900 chr4A 86.047 516 36 20 17 507 591873647 591874151 5.230000e-144 521
5 TraesCS4B01G027900 chr1B 97.490 478 12 0 2617 3094 252980368 252979891 0.000000e+00 817


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 TraesCS4B01G027900 chr4B 20742909 20747468 4559 False 8421 8421 100.000 1 4560 1 chr4B.!!$F1 4559
1 TraesCS4B01G027900 chr4D 10987070 10991686 4616 False 3167 5814 89.018 52 4560 2 chr4D.!!$F1 4508
2 TraesCS4B01G027900 chr4A 591873647 591878447 4800 False 3161 5801 90.419 17 4560 2 chr4A.!!$F1 4543

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
316 320 0.039472 TGTTGCATAGTGGCATGGGT 59.961 50.000 0.00 0.00 44.48 4.51 F
347 354 0.250727 GTACCAACTTGGGAGCTGCA 60.251 55.000 12.62 0.00 43.37 4.41 F
838 1203 0.317854 TGACTTGACGAGACTGCGTG 60.318 55.000 0.00 0.00 45.72 5.34 F
913 1278 2.126346 CCGTAACCGTCACGTCCC 60.126 66.667 0.00 0.00 37.71 4.46 F
2350 2733 0.523335 GTCGAAATGCATGGAACGGC 60.523 55.000 0.00 1.83 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2307 3.157087 GGGGAAATCCAATGCACGATAT 58.843 45.455 1.22 0.0 37.91 1.63 R
2259 2642 5.302568 TCATTTGCTGTCAGGATTTCAACTT 59.697 36.000 1.14 0.0 0.00 2.66 R
2350 2733 1.153369 AAGGTGATGGGATCGTGCG 60.153 57.895 0.00 0.0 0.00 5.34 R
2506 2889 1.247419 TTGCACCAATAAGCCCACCG 61.247 55.000 0.00 0.0 0.00 4.94 R
3682 4082 0.037590 ACAAACGGGCAGCAGGATAA 59.962 50.000 0.00 0.0 0.00 1.75 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
61 62 1.593006 GTTGGATTCGTAGCCGATGTG 59.407 52.381 0.00 0.00 43.80 3.21
209 213 9.832445 GATAGGAAGATATTGTAAAAGACCACA 57.168 33.333 0.00 0.00 0.00 4.17
210 214 9.838339 ATAGGAAGATATTGTAAAAGACCACAG 57.162 33.333 0.00 0.00 0.00 3.66
211 215 6.599638 AGGAAGATATTGTAAAAGACCACAGC 59.400 38.462 0.00 0.00 0.00 4.40
212 216 6.374333 GGAAGATATTGTAAAAGACCACAGCA 59.626 38.462 0.00 0.00 0.00 4.41
214 218 5.648092 AGATATTGTAAAAGACCACAGCACC 59.352 40.000 0.00 0.00 0.00 5.01
215 219 1.588674 TGTAAAAGACCACAGCACCG 58.411 50.000 0.00 0.00 0.00 4.94
216 220 1.134340 TGTAAAAGACCACAGCACCGT 60.134 47.619 0.00 0.00 0.00 4.83
217 221 1.944709 GTAAAAGACCACAGCACCGTT 59.055 47.619 0.00 0.00 0.00 4.44
223 227 2.721231 CACAGCACCGTTTGTGGG 59.279 61.111 5.40 0.00 45.55 4.61
267 271 7.882179 ACTGTAAATAAAGCGGTTTTGATCTT 58.118 30.769 18.81 7.33 0.00 2.40
268 272 7.807907 ACTGTAAATAAAGCGGTTTTGATCTTG 59.192 33.333 18.81 7.20 0.00 3.02
297 301 3.565482 GGCACGTATGGATTCATGACATT 59.435 43.478 0.00 0.00 34.96 2.71
298 302 4.530388 GCACGTATGGATTCATGACATTG 58.470 43.478 0.00 0.00 34.96 2.82
299 303 4.035558 GCACGTATGGATTCATGACATTGT 59.964 41.667 0.00 0.00 34.96 2.71
300 304 5.449041 GCACGTATGGATTCATGACATTGTT 60.449 40.000 0.00 0.00 34.96 2.83
301 305 5.967088 CACGTATGGATTCATGACATTGTTG 59.033 40.000 0.00 0.00 34.96 3.33
302 306 4.971830 CGTATGGATTCATGACATTGTTGC 59.028 41.667 0.00 0.00 34.96 4.17
303 307 5.448904 CGTATGGATTCATGACATTGTTGCA 60.449 40.000 0.00 0.00 34.96 4.08
305 309 6.718522 ATGGATTCATGACATTGTTGCATA 57.281 33.333 0.00 0.00 31.34 3.14
306 310 6.139048 TGGATTCATGACATTGTTGCATAG 57.861 37.500 0.00 0.00 0.00 2.23
310 314 3.129113 TCATGACATTGTTGCATAGTGGC 59.871 43.478 0.00 0.00 0.00 5.01
311 315 2.512705 TGACATTGTTGCATAGTGGCA 58.487 42.857 0.00 0.00 43.19 4.92
314 318 2.166870 ACATTGTTGCATAGTGGCATGG 59.833 45.455 0.00 0.00 44.48 3.66
315 319 1.184431 TTGTTGCATAGTGGCATGGG 58.816 50.000 0.00 0.00 44.48 4.00
316 320 0.039472 TGTTGCATAGTGGCATGGGT 59.961 50.000 0.00 0.00 44.48 4.51
317 321 1.185315 GTTGCATAGTGGCATGGGTT 58.815 50.000 0.00 0.00 44.48 4.11
318 322 1.135024 GTTGCATAGTGGCATGGGTTG 60.135 52.381 0.00 0.00 44.48 3.77
345 352 3.249687 GGTACCAACTTGGGAGCTG 57.750 57.895 14.19 0.00 45.30 4.24
346 353 0.960861 GGTACCAACTTGGGAGCTGC 60.961 60.000 14.19 0.00 45.30 5.25
347 354 0.250727 GTACCAACTTGGGAGCTGCA 60.251 55.000 12.62 0.00 43.37 4.41
348 355 0.476338 TACCAACTTGGGAGCTGCAA 59.524 50.000 12.62 0.00 43.37 4.08
349 356 1.109323 ACCAACTTGGGAGCTGCAAC 61.109 55.000 12.62 0.00 43.37 4.17
362 385 1.372582 CTGCAACTCACACGCCATAT 58.627 50.000 0.00 0.00 0.00 1.78
363 386 2.549926 CTGCAACTCACACGCCATATA 58.450 47.619 0.00 0.00 0.00 0.86
364 387 3.133691 CTGCAACTCACACGCCATATAT 58.866 45.455 0.00 0.00 0.00 0.86
365 388 2.871633 TGCAACTCACACGCCATATATG 59.128 45.455 5.68 5.68 0.00 1.78
366 389 2.349817 GCAACTCACACGCCATATATGC 60.350 50.000 7.24 2.52 0.00 3.14
384 407 3.829886 TGCGAAGGAGCAAGTATTTTG 57.170 42.857 0.00 0.00 45.06 2.44
438 462 3.277715 GAGCTGAGAAGGGAAAATCTGG 58.722 50.000 0.00 0.00 0.00 3.86
494 538 6.446781 AATTCATGTGACATGTCCAGAATC 57.553 37.500 23.39 7.22 0.00 2.52
507 551 3.766051 GTCCAGAATCCCATTTTTGCTCT 59.234 43.478 0.00 0.00 0.00 4.09
516 560 2.036217 CCATTTTTGCTCTGCCTTGACA 59.964 45.455 0.00 0.00 0.00 3.58
517 561 3.314553 CATTTTTGCTCTGCCTTGACAG 58.685 45.455 0.00 0.00 39.12 3.51
519 563 1.311859 TTTGCTCTGCCTTGACAGTG 58.688 50.000 0.00 0.00 38.84 3.66
526 570 2.687935 TCTGCCTTGACAGTGTTTTTCC 59.312 45.455 0.00 0.00 38.84 3.13
535 579 4.095782 TGACAGTGTTTTTCCTTTTCCTCG 59.904 41.667 0.00 0.00 0.00 4.63
554 598 0.804989 GTACTGTGCTCATGGTTGCC 59.195 55.000 0.00 0.00 0.00 4.52
611 656 2.496899 ATCATCCAAAACCTGCGACT 57.503 45.000 0.00 0.00 0.00 4.18
659 711 2.380084 ACTCTCTTCGCCGCAAAATA 57.620 45.000 0.00 0.00 0.00 1.40
665 717 2.225491 TCTTCGCCGCAAAATATATGGC 59.775 45.455 1.71 1.71 42.29 4.40
694 746 7.615403 TGCTGAGACAAGTCTTTAACTGATAT 58.385 34.615 3.96 0.00 40.61 1.63
695 747 8.749354 TGCTGAGACAAGTCTTTAACTGATATA 58.251 33.333 3.96 0.00 40.61 0.86
696 748 9.587772 GCTGAGACAAGTCTTTAACTGATATAA 57.412 33.333 3.96 0.00 40.61 0.98
780 837 5.349817 AGTGAATCTAGCGACAATTGTGAAG 59.650 40.000 17.58 8.30 0.00 3.02
785 842 2.571212 AGCGACAATTGTGAAGACCAA 58.429 42.857 17.58 0.00 0.00 3.67
790 847 5.090757 CGACAATTGTGAAGACCAATGATG 58.909 41.667 17.58 0.00 33.01 3.07
792 849 6.409524 ACAATTGTGAAGACCAATGATGTT 57.590 33.333 11.07 0.00 33.01 2.71
793 850 6.218019 ACAATTGTGAAGACCAATGATGTTG 58.782 36.000 11.07 0.00 33.01 3.33
794 851 6.183360 ACAATTGTGAAGACCAATGATGTTGT 60.183 34.615 11.07 0.00 33.01 3.32
795 852 4.834357 TGTGAAGACCAATGATGTTGTG 57.166 40.909 0.00 0.00 0.00 3.33
796 853 4.459330 TGTGAAGACCAATGATGTTGTGA 58.541 39.130 0.00 0.00 0.00 3.58
797 854 4.886489 TGTGAAGACCAATGATGTTGTGAA 59.114 37.500 0.00 0.00 0.00 3.18
798 855 5.359292 TGTGAAGACCAATGATGTTGTGAAA 59.641 36.000 0.00 0.00 0.00 2.69
810 867 7.509141 TGATGTTGTGAAATGTGAATAGTGT 57.491 32.000 0.00 0.00 0.00 3.55
820 877 4.446994 TGTGAATAGTGTGAGCTCTCTG 57.553 45.455 16.19 0.00 0.00 3.35
821 878 4.082125 TGTGAATAGTGTGAGCTCTCTGA 58.918 43.478 16.19 1.52 0.00 3.27
822 879 4.082517 TGTGAATAGTGTGAGCTCTCTGAC 60.083 45.833 16.19 5.06 0.00 3.51
823 880 4.157656 GTGAATAGTGTGAGCTCTCTGACT 59.842 45.833 16.19 13.62 0.00 3.41
824 881 4.769488 TGAATAGTGTGAGCTCTCTGACTT 59.231 41.667 16.19 4.84 0.00 3.01
838 1203 0.317854 TGACTTGACGAGACTGCGTG 60.318 55.000 0.00 0.00 45.72 5.34
913 1278 2.126346 CCGTAACCGTCACGTCCC 60.126 66.667 0.00 0.00 37.71 4.46
915 1280 2.806621 GTAACCGTCACGTCCCGC 60.807 66.667 0.00 0.00 0.00 6.13
1538 1921 2.830370 CCTGCCGGCCATCTTTCC 60.830 66.667 26.77 0.00 0.00 3.13
1657 2040 2.301009 AGACGAAGAACCCCGTTACATT 59.699 45.455 0.00 0.00 39.30 2.71
2259 2642 7.335924 GTCTGGCCATAGTATTAAAGTGTTCAA 59.664 37.037 5.51 0.00 0.00 2.69
2263 2646 8.520351 GGCCATAGTATTAAAGTGTTCAAAGTT 58.480 33.333 0.00 0.00 0.00 2.66
2350 2733 0.523335 GTCGAAATGCATGGAACGGC 60.523 55.000 0.00 1.83 0.00 5.68
2491 2874 6.205464 ACATGTTTTATGGAGTCACTCTGTTG 59.795 38.462 4.40 0.00 0.00 3.33
2506 2889 3.919216 TCTGTTGCTAGTTCTTCTGCTC 58.081 45.455 0.00 0.00 0.00 4.26
2560 2943 0.738762 CACTCAGATGGTGTGCTCCG 60.739 60.000 0.00 0.00 34.59 4.63
2565 2948 0.761187 AGATGGTGTGCTCCGCATAT 59.239 50.000 0.00 0.00 41.91 1.78
2585 2968 0.032952 TGAGAAACGGGGTGACTTCG 59.967 55.000 0.00 0.00 0.00 3.79
2815 3198 4.069312 TCCAATCAAGGGTAGGTACTCA 57.931 45.455 0.00 0.00 41.75 3.41
3159 3542 2.515996 TACTACCCACGCCTTGCTGC 62.516 60.000 0.00 0.00 0.00 5.25
3166 3549 3.127533 CGCCTTGCTGCAGGTACC 61.128 66.667 17.12 2.73 36.15 3.34
3221 3604 4.947388 GGCAACAAGGAGGTTATAACATGA 59.053 41.667 17.16 0.00 0.00 3.07
3337 3720 4.005650 TCTTCAATTGTGAGGATGTGCTC 58.994 43.478 5.13 0.00 35.11 4.26
3526 3909 5.710099 TGGGAACTTATCTGCTAAAAGGTTG 59.290 40.000 0.00 0.00 0.00 3.77
3546 3929 0.901827 TTTAGCAGCCGAGGTGATGA 59.098 50.000 7.19 0.00 30.67 2.92
3562 3945 6.013379 AGGTGATGACTGGGATGTATAGTAG 58.987 44.000 0.00 0.00 0.00 2.57
3563 3946 5.775701 GGTGATGACTGGGATGTATAGTAGT 59.224 44.000 0.00 0.00 0.00 2.73
3564 3947 6.946583 GGTGATGACTGGGATGTATAGTAGTA 59.053 42.308 0.00 0.00 0.00 1.82
3569 3952 6.776116 TGACTGGGATGTATAGTAGTAACAGG 59.224 42.308 0.00 0.00 0.00 4.00
3633 4033 7.940137 TGATTAGCTAAGTTTCCAAGTTGGTAA 59.060 33.333 21.35 15.47 39.03 2.85
3634 4034 8.700439 ATTAGCTAAGTTTCCAAGTTGGTAAA 57.300 30.769 21.35 16.25 39.03 2.01
3635 4035 6.635030 AGCTAAGTTTCCAAGTTGGTAAAG 57.365 37.500 21.35 13.09 39.03 1.85
3636 4036 5.009710 AGCTAAGTTTCCAAGTTGGTAAAGC 59.990 40.000 21.35 20.83 39.03 3.51
3637 4037 5.221165 GCTAAGTTTCCAAGTTGGTAAAGCA 60.221 40.000 22.02 9.32 39.03 3.91
3638 4038 4.918810 AGTTTCCAAGTTGGTAAAGCAG 57.081 40.909 21.35 0.00 39.03 4.24
3639 4039 4.532834 AGTTTCCAAGTTGGTAAAGCAGA 58.467 39.130 21.35 0.00 39.03 4.26
3640 4040 4.580580 AGTTTCCAAGTTGGTAAAGCAGAG 59.419 41.667 21.35 0.00 39.03 3.35
3641 4041 3.140325 TCCAAGTTGGTAAAGCAGAGG 57.860 47.619 21.35 0.00 39.03 3.69
3642 4042 2.162681 CCAAGTTGGTAAAGCAGAGGG 58.837 52.381 14.21 0.00 31.35 4.30
3643 4043 1.541588 CAAGTTGGTAAAGCAGAGGGC 59.458 52.381 0.00 0.00 45.30 5.19
3644 4044 5.958690 CCAAGTTGGTAAAGCAGAGGGCT 62.959 52.174 14.21 0.00 44.01 5.19
3690 4090 3.754188 CACTGAAGTGCTTTATCCTGC 57.246 47.619 0.00 0.00 39.39 4.85
3691 4091 3.341823 CACTGAAGTGCTTTATCCTGCT 58.658 45.455 0.00 0.00 39.39 4.24
3692 4092 3.126514 CACTGAAGTGCTTTATCCTGCTG 59.873 47.826 0.00 0.00 39.39 4.41
3693 4093 2.086869 TGAAGTGCTTTATCCTGCTGC 58.913 47.619 0.00 0.00 0.00 5.25
3694 4094 1.403323 GAAGTGCTTTATCCTGCTGCC 59.597 52.381 0.00 0.00 0.00 4.85
3695 4095 0.394899 AGTGCTTTATCCTGCTGCCC 60.395 55.000 0.00 0.00 0.00 5.36
3696 4096 1.451927 TGCTTTATCCTGCTGCCCG 60.452 57.895 0.00 0.00 0.00 6.13
3697 4097 1.452108 GCTTTATCCTGCTGCCCGT 60.452 57.895 0.00 0.00 0.00 5.28
3698 4098 1.032114 GCTTTATCCTGCTGCCCGTT 61.032 55.000 0.00 0.00 0.00 4.44
3699 4099 1.463674 CTTTATCCTGCTGCCCGTTT 58.536 50.000 0.00 0.00 0.00 3.60
3700 4100 1.133025 CTTTATCCTGCTGCCCGTTTG 59.867 52.381 0.00 0.00 0.00 2.93
3701 4101 0.037590 TTATCCTGCTGCCCGTTTGT 59.962 50.000 0.00 0.00 0.00 2.83
3702 4102 0.906066 TATCCTGCTGCCCGTTTGTA 59.094 50.000 0.00 0.00 0.00 2.41
3703 4103 0.255890 ATCCTGCTGCCCGTTTGTAT 59.744 50.000 0.00 0.00 0.00 2.29
3704 4104 0.906066 TCCTGCTGCCCGTTTGTATA 59.094 50.000 0.00 0.00 0.00 1.47
3711 4111 4.760715 TGCTGCCCGTTTGTATAAGTTAAA 59.239 37.500 0.00 0.00 0.00 1.52
3712 4112 5.241064 TGCTGCCCGTTTGTATAAGTTAAAA 59.759 36.000 0.00 0.00 0.00 1.52
3847 4247 2.920647 GCATCGGGTTTGCAAACTGTAC 60.921 50.000 34.39 21.14 39.90 2.90
3855 4255 4.798387 GGTTTGCAAACTGTACTTTGTCAG 59.202 41.667 34.39 0.00 38.89 3.51
3901 4301 1.890876 TGGTCCAGAACGAATGGTTG 58.109 50.000 0.00 0.00 39.50 3.77
3902 4302 1.142060 TGGTCCAGAACGAATGGTTGT 59.858 47.619 0.00 0.00 39.50 3.32
3903 4303 2.369203 TGGTCCAGAACGAATGGTTGTA 59.631 45.455 0.00 0.00 39.50 2.41
3959 4361 8.068977 TGAAATGTTTTATTTGTCATTTGCAGC 58.931 29.630 6.69 0.00 39.52 5.25
4084 4487 1.744522 TGGCGTGAACCATGATCAATG 59.255 47.619 0.00 0.00 33.75 2.82
4086 4489 2.423185 GGCGTGAACCATGATCAATGAA 59.577 45.455 0.00 0.00 38.72 2.57
4099 4502 9.320352 CCATGATCAATGAAAATTATGAAGCAA 57.680 29.630 0.00 0.00 38.72 3.91
4218 4622 5.833406 TGTATGCCACAGGTTTGATAATG 57.167 39.130 0.00 0.00 31.89 1.90
4250 4657 2.892852 CAAGAATCAGGAAAAGCCACCA 59.107 45.455 0.00 0.00 40.02 4.17
4278 4685 6.753279 TGAATCAAAACTTGCAGTTCTTCTTG 59.247 34.615 2.65 4.32 37.47 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.069204 TGTCAGACTGTCACTGAAGGC 59.931 52.381 10.88 0.00 44.29 4.35
1 2 2.625314 TCTGTCAGACTGTCACTGAAGG 59.375 50.000 10.88 3.14 44.29 3.46
2 3 3.067320 TGTCTGTCAGACTGTCACTGAAG 59.933 47.826 28.67 6.71 45.27 3.02
3 4 3.023832 TGTCTGTCAGACTGTCACTGAA 58.976 45.455 28.67 7.09 45.27 3.02
4 5 2.359214 GTGTCTGTCAGACTGTCACTGA 59.641 50.000 28.67 7.75 45.27 3.41
5 6 2.544694 GGTGTCTGTCAGACTGTCACTG 60.545 54.545 28.67 4.89 45.27 3.66
6 7 1.683917 GGTGTCTGTCAGACTGTCACT 59.316 52.381 28.67 0.00 45.27 3.41
7 8 1.683917 AGGTGTCTGTCAGACTGTCAC 59.316 52.381 28.67 21.60 45.27 3.67
8 9 1.683385 CAGGTGTCTGTCAGACTGTCA 59.317 52.381 28.67 10.18 45.27 3.58
9 10 1.604185 GCAGGTGTCTGTCAGACTGTC 60.604 57.143 28.67 19.42 45.27 3.51
10 11 0.390860 GCAGGTGTCTGTCAGACTGT 59.609 55.000 28.67 13.69 45.27 3.55
11 12 0.320247 GGCAGGTGTCTGTCAGACTG 60.320 60.000 28.67 20.90 45.27 3.51
12 13 1.810606 CGGCAGGTGTCTGTCAGACT 61.811 60.000 28.67 10.47 45.40 3.24
13 14 1.373497 CGGCAGGTGTCTGTCAGAC 60.373 63.158 23.67 23.67 45.40 3.51
14 15 2.574018 CCGGCAGGTGTCTGTCAGA 61.574 63.158 0.00 0.00 45.40 3.27
15 16 2.047844 CCGGCAGGTGTCTGTCAG 60.048 66.667 0.00 0.00 45.40 3.51
34 35 1.488527 CTACGAATCCAACGGCTAGC 58.511 55.000 6.04 6.04 34.93 3.42
64 65 5.806654 ACTGTCAAACAAAAAGGGCATAT 57.193 34.783 0.00 0.00 0.00 1.78
72 73 6.927294 AACAAACCAACTGTCAAACAAAAA 57.073 29.167 0.00 0.00 0.00 1.94
74 75 6.238484 CCAAAACAAACCAACTGTCAAACAAA 60.238 34.615 0.00 0.00 0.00 2.83
209 213 1.671054 CGATCCCACAAACGGTGCT 60.671 57.895 0.00 0.00 46.50 4.40
210 214 2.867472 CGATCCCACAAACGGTGC 59.133 61.111 0.00 0.00 46.50 5.01
212 216 1.546589 TAGGCGATCCCACAAACGGT 61.547 55.000 3.45 0.00 35.39 4.83
214 218 0.174845 TCTAGGCGATCCCACAAACG 59.825 55.000 3.45 0.00 35.39 3.60
215 219 2.396590 TTCTAGGCGATCCCACAAAC 57.603 50.000 3.45 0.00 35.39 2.93
216 220 3.199946 AGATTTCTAGGCGATCCCACAAA 59.800 43.478 3.45 0.45 35.39 2.83
217 221 2.771943 AGATTTCTAGGCGATCCCACAA 59.228 45.455 3.45 0.00 35.39 3.33
223 227 6.079424 ACAGTTCTAGATTTCTAGGCGATC 57.921 41.667 13.31 0.00 44.60 3.69
267 271 0.613572 TCCATACGTGCCTCCAGACA 60.614 55.000 0.00 0.00 0.00 3.41
268 272 0.753262 ATCCATACGTGCCTCCAGAC 59.247 55.000 0.00 0.00 0.00 3.51
297 301 0.039472 ACCCATGCCACTATGCAACA 59.961 50.000 0.00 0.00 45.84 3.33
298 302 1.135024 CAACCCATGCCACTATGCAAC 60.135 52.381 0.00 0.00 45.84 4.17
299 303 1.184431 CAACCCATGCCACTATGCAA 58.816 50.000 0.00 0.00 45.84 4.08
300 304 2.884976 CAACCCATGCCACTATGCA 58.115 52.632 0.00 0.00 46.94 3.96
310 314 3.569701 GGTACCAATATCAGCAACCCATG 59.430 47.826 7.15 0.00 0.00 3.66
311 315 3.204158 TGGTACCAATATCAGCAACCCAT 59.796 43.478 13.60 0.00 0.00 4.00
314 318 4.270008 AGTTGGTACCAATATCAGCAACC 58.730 43.478 29.40 12.80 46.59 3.77
315 319 5.393027 CCAAGTTGGTACCAATATCAGCAAC 60.393 44.000 29.40 14.37 46.06 4.17
316 320 4.704540 CCAAGTTGGTACCAATATCAGCAA 59.295 41.667 29.40 1.39 38.28 3.91
317 321 4.269183 CCAAGTTGGTACCAATATCAGCA 58.731 43.478 29.40 2.20 38.28 4.41
318 322 3.632145 CCCAAGTTGGTACCAATATCAGC 59.368 47.826 29.40 15.63 38.28 4.26
319 323 5.110814 TCCCAAGTTGGTACCAATATCAG 57.889 43.478 29.40 18.05 38.28 2.90
320 324 4.627741 GCTCCCAAGTTGGTACCAATATCA 60.628 45.833 29.40 4.69 38.28 2.15
321 325 3.883489 GCTCCCAAGTTGGTACCAATATC 59.117 47.826 29.40 17.06 38.28 1.63
322 326 3.527665 AGCTCCCAAGTTGGTACCAATAT 59.472 43.478 29.40 18.52 38.28 1.28
323 327 2.916934 AGCTCCCAAGTTGGTACCAATA 59.083 45.455 29.40 6.38 38.28 1.90
324 328 1.710809 AGCTCCCAAGTTGGTACCAAT 59.289 47.619 29.40 12.78 38.28 3.16
327 331 0.960861 GCAGCTCCCAAGTTGGTACC 60.961 60.000 20.54 4.43 35.17 3.34
328 332 0.250727 TGCAGCTCCCAAGTTGGTAC 60.251 55.000 20.54 9.28 35.17 3.34
343 350 1.372582 ATATGGCGTGTGAGTTGCAG 58.627 50.000 0.00 0.00 0.00 4.41
344 351 2.682155 TATATGGCGTGTGAGTTGCA 57.318 45.000 0.00 0.00 0.00 4.08
345 352 2.349817 GCATATATGGCGTGTGAGTTGC 60.350 50.000 14.51 0.00 0.00 4.17
346 353 3.526385 GCATATATGGCGTGTGAGTTG 57.474 47.619 14.51 0.00 0.00 3.16
362 385 4.941263 ACAAAATACTTGCTCCTTCGCATA 59.059 37.500 0.00 0.00 40.04 3.14
363 386 3.758554 ACAAAATACTTGCTCCTTCGCAT 59.241 39.130 0.00 0.00 40.04 4.73
364 387 3.058293 CACAAAATACTTGCTCCTTCGCA 60.058 43.478 0.00 0.00 38.31 5.10
365 388 3.492313 CACAAAATACTTGCTCCTTCGC 58.508 45.455 0.00 0.00 0.00 4.70
366 389 3.189287 AGCACAAAATACTTGCTCCTTCG 59.811 43.478 0.00 0.00 43.14 3.79
367 390 4.773323 AGCACAAAATACTTGCTCCTTC 57.227 40.909 0.00 0.00 43.14 3.46
384 407 2.162681 ACATTCCCAGCAAAGTAGCAC 58.837 47.619 0.00 0.00 36.85 4.40
480 523 5.413499 CAAAAATGGGATTCTGGACATGTC 58.587 41.667 17.91 17.91 0.00 3.06
494 538 1.619827 TCAAGGCAGAGCAAAAATGGG 59.380 47.619 0.00 0.00 0.00 4.00
507 551 2.733956 AGGAAAAACACTGTCAAGGCA 58.266 42.857 0.00 0.00 0.00 4.75
516 560 5.296035 CAGTACGAGGAAAAGGAAAAACACT 59.704 40.000 0.00 0.00 0.00 3.55
517 561 5.065602 ACAGTACGAGGAAAAGGAAAAACAC 59.934 40.000 0.00 0.00 0.00 3.32
519 563 5.507974 CACAGTACGAGGAAAAGGAAAAAC 58.492 41.667 0.00 0.00 0.00 2.43
526 570 3.026630 TGAGCACAGTACGAGGAAAAG 57.973 47.619 0.00 0.00 0.00 2.27
535 579 0.804989 GGCAACCATGAGCACAGTAC 59.195 55.000 0.00 0.00 0.00 2.73
554 598 2.036556 AAACATGAGCAGCGAAAACG 57.963 45.000 0.00 0.00 0.00 3.60
605 650 1.552792 TGTCATTATCACCCAGTCGCA 59.447 47.619 0.00 0.00 0.00 5.10
611 656 3.719268 AGTGCTTGTCATTATCACCCA 57.281 42.857 0.00 0.00 0.00 4.51
659 711 1.070445 GTCTCAGCAGCCGCCATAT 59.930 57.895 0.00 0.00 39.83 1.78
665 717 0.320247 AAGACTTGTCTCAGCAGCCG 60.320 55.000 3.58 0.00 0.00 5.52
718 770 9.283768 TCACTTATGTTGTGATTTACATTCACT 57.716 29.630 5.52 0.00 43.12 3.41
719 771 9.891828 TTCACTTATGTTGTGATTTACATTCAC 57.108 29.630 0.00 0.00 42.95 3.18
743 800 9.035607 TCGCTAGATTCACTTTCAAAGATATTC 57.964 33.333 3.49 0.00 0.00 1.75
780 837 5.771469 TCACATTTCACAACATCATTGGTC 58.229 37.500 0.00 0.00 0.00 4.02
785 842 8.024865 CACACTATTCACATTTCACAACATCAT 58.975 33.333 0.00 0.00 0.00 2.45
790 847 5.853282 GCTCACACTATTCACATTTCACAAC 59.147 40.000 0.00 0.00 0.00 3.32
792 849 5.308014 AGCTCACACTATTCACATTTCACA 58.692 37.500 0.00 0.00 0.00 3.58
793 850 5.641209 AGAGCTCACACTATTCACATTTCAC 59.359 40.000 17.77 0.00 0.00 3.18
794 851 5.798132 AGAGCTCACACTATTCACATTTCA 58.202 37.500 17.77 0.00 0.00 2.69
795 852 6.035866 CAGAGAGCTCACACTATTCACATTTC 59.964 42.308 17.77 0.00 0.00 2.17
796 853 5.873712 CAGAGAGCTCACACTATTCACATTT 59.126 40.000 17.77 0.00 0.00 2.32
797 854 5.186603 TCAGAGAGCTCACACTATTCACATT 59.813 40.000 17.77 0.00 0.00 2.71
798 855 4.708909 TCAGAGAGCTCACACTATTCACAT 59.291 41.667 17.77 0.00 0.00 3.21
810 867 1.809547 CTCGTCAAGTCAGAGAGCTCA 59.190 52.381 17.77 0.00 34.13 4.26
820 877 0.317938 ACACGCAGTCTCGTCAAGTC 60.318 55.000 0.00 0.00 41.61 3.01
821 878 0.102481 AACACGCAGTCTCGTCAAGT 59.898 50.000 0.00 0.00 41.61 3.16
822 879 0.778815 GAACACGCAGTCTCGTCAAG 59.221 55.000 0.00 0.00 41.61 3.02
823 880 0.596600 GGAACACGCAGTCTCGTCAA 60.597 55.000 0.00 0.00 41.61 3.18
824 881 1.007734 GGAACACGCAGTCTCGTCA 60.008 57.895 0.00 0.00 41.61 4.35
893 1258 1.285641 GACGTGACGGTTACGGGAA 59.714 57.895 25.77 0.00 45.24 3.97
894 1259 2.625823 GGACGTGACGGTTACGGGA 61.626 63.158 25.77 0.00 45.24 5.14
971 1336 2.044946 GATGGGAGGTGGGTGTGC 60.045 66.667 0.00 0.00 0.00 4.57
972 1337 1.604378 GAGATGGGAGGTGGGTGTG 59.396 63.158 0.00 0.00 0.00 3.82
973 1338 1.616628 GGAGATGGGAGGTGGGTGT 60.617 63.158 0.00 0.00 0.00 4.16
1075 1452 4.779733 GACGAGGGCCAGGAGGGA 62.780 72.222 6.18 0.00 40.01 4.20
1538 1921 4.285807 TGGTCGTTGTCAAAATTCACAG 57.714 40.909 0.00 0.00 0.00 3.66
1924 2307 3.157087 GGGGAAATCCAATGCACGATAT 58.843 45.455 1.22 0.00 37.91 1.63
2259 2642 5.302568 TCATTTGCTGTCAGGATTTCAACTT 59.697 36.000 1.14 0.00 0.00 2.66
2263 2646 5.988310 ATTCATTTGCTGTCAGGATTTCA 57.012 34.783 1.14 0.00 0.00 2.69
2272 2655 7.814107 TCAATTTCCTTGTATTCATTTGCTGTC 59.186 33.333 0.00 0.00 36.20 3.51
2350 2733 1.153369 AAGGTGATGGGATCGTGCG 60.153 57.895 0.00 0.00 0.00 5.34
2491 2874 1.634702 CACCGAGCAGAAGAACTAGC 58.365 55.000 0.00 0.00 0.00 3.42
2506 2889 1.247419 TTGCACCAATAAGCCCACCG 61.247 55.000 0.00 0.00 0.00 4.94
2556 2939 1.867233 CCCGTTTCTCAATATGCGGAG 59.133 52.381 0.00 0.00 41.45 4.63
2560 2943 2.354821 GTCACCCCGTTTCTCAATATGC 59.645 50.000 0.00 0.00 0.00 3.14
2565 2948 1.539496 CGAAGTCACCCCGTTTCTCAA 60.539 52.381 0.00 0.00 0.00 3.02
2585 2968 2.555757 AGAACTGCTGCTTTGAATGGAC 59.444 45.455 0.00 0.00 0.00 4.02
2740 3123 2.545946 GCAGTGAGTTCCAAGACAAGTC 59.454 50.000 0.00 0.00 0.00 3.01
2946 3329 6.716628 AGGAACAGCTGACTTCAATTCATTTA 59.283 34.615 23.35 0.00 0.00 1.40
3077 3460 1.135373 ACGCTCTAAGTCGTCACATGG 60.135 52.381 0.00 0.00 33.09 3.66
3166 3549 1.024271 CATTGCGGTATTCCAGTGGG 58.976 55.000 9.92 0.00 0.00 4.61
3221 3604 2.502947 TGAATGCTGCTCCAGTCAGTAT 59.497 45.455 0.00 0.00 38.27 2.12
3337 3720 4.083696 GCATTTGCAAACAGGAAATTCAGG 60.084 41.667 15.41 0.00 44.64 3.86
3375 3758 2.355716 GCTGGCTTTACATACTCCACCA 60.356 50.000 0.00 0.00 0.00 4.17
3406 3789 7.380065 GCTACTCCTGAAAACTTAGACATATCG 59.620 40.741 0.00 0.00 0.00 2.92
3526 3909 1.009829 CATCACCTCGGCTGCTAAAC 58.990 55.000 0.00 0.00 0.00 2.01
3535 3918 0.105593 CATCCCAGTCATCACCTCGG 59.894 60.000 0.00 0.00 0.00 4.63
3546 3929 6.075984 CCCTGTTACTACTATACATCCCAGT 58.924 44.000 0.00 0.00 0.00 4.00
3562 3945 8.803397 AAAAAGTATCCAGTTATCCCTGTTAC 57.197 34.615 0.00 0.00 0.00 2.50
3635 4035 1.410882 CTGGACTACTAAGCCCTCTGC 59.589 57.143 0.00 0.00 41.71 4.26
3636 4036 2.035632 CCTGGACTACTAAGCCCTCTG 58.964 57.143 0.00 0.00 0.00 3.35
3637 4037 1.062810 CCCTGGACTACTAAGCCCTCT 60.063 57.143 0.00 0.00 0.00 3.69
3638 4038 1.343176 ACCCTGGACTACTAAGCCCTC 60.343 57.143 0.00 0.00 0.00 4.30
3639 4039 0.717196 ACCCTGGACTACTAAGCCCT 59.283 55.000 0.00 0.00 0.00 5.19
3640 4040 0.831307 CACCCTGGACTACTAAGCCC 59.169 60.000 0.00 0.00 0.00 5.19
3641 4041 1.861982 TCACCCTGGACTACTAAGCC 58.138 55.000 0.00 0.00 0.00 4.35
3642 4042 4.650131 ACTAATCACCCTGGACTACTAAGC 59.350 45.833 0.00 0.00 0.00 3.09
3643 4043 5.452077 GCACTAATCACCCTGGACTACTAAG 60.452 48.000 0.00 0.00 0.00 2.18
3644 4044 4.404715 GCACTAATCACCCTGGACTACTAA 59.595 45.833 0.00 0.00 0.00 2.24
3645 4045 3.958798 GCACTAATCACCCTGGACTACTA 59.041 47.826 0.00 0.00 0.00 1.82
3646 4046 2.766828 GCACTAATCACCCTGGACTACT 59.233 50.000 0.00 0.00 0.00 2.57
3647 4047 2.500098 TGCACTAATCACCCTGGACTAC 59.500 50.000 0.00 0.00 0.00 2.73
3648 4048 2.827755 TGCACTAATCACCCTGGACTA 58.172 47.619 0.00 0.00 0.00 2.59
3649 4049 1.656587 TGCACTAATCACCCTGGACT 58.343 50.000 0.00 0.00 0.00 3.85
3652 4052 1.812571 GTGTTGCACTAATCACCCTGG 59.187 52.381 0.00 0.00 0.00 4.45
3657 4057 4.776743 CACTTCAGTGTTGCACTAATCAC 58.223 43.478 1.16 0.00 43.43 3.06
3680 4080 1.133025 CAAACGGGCAGCAGGATAAAG 59.867 52.381 0.00 0.00 0.00 1.85
3681 4081 1.173043 CAAACGGGCAGCAGGATAAA 58.827 50.000 0.00 0.00 0.00 1.40
3682 4082 0.037590 ACAAACGGGCAGCAGGATAA 59.962 50.000 0.00 0.00 0.00 1.75
3683 4083 0.906066 TACAAACGGGCAGCAGGATA 59.094 50.000 0.00 0.00 0.00 2.59
3684 4084 0.255890 ATACAAACGGGCAGCAGGAT 59.744 50.000 0.00 0.00 0.00 3.24
3686 4086 1.670811 CTTATACAAACGGGCAGCAGG 59.329 52.381 0.00 0.00 0.00 4.85
3687 4087 2.356135 ACTTATACAAACGGGCAGCAG 58.644 47.619 0.00 0.00 0.00 4.24
3847 4247 2.009051 TGCACACTGACACTGACAAAG 58.991 47.619 0.00 0.00 0.00 2.77
3855 4255 0.664761 AGTTGCATGCACACTGACAC 59.335 50.000 22.58 14.19 0.00 3.67
4003 4405 7.065216 AGTGTGATATTTCGACACAGAAATG 57.935 36.000 13.31 0.00 46.61 2.32
4099 4502 8.926092 AAAAGTAGTAGGAAAGAAGCTGATTT 57.074 30.769 0.00 0.00 0.00 2.17
4218 4622 6.764308 TTCCTGATTCTTGATGGTTTGATC 57.236 37.500 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.