Multiple sequence alignment - TraesCS5D01G537500

Loading Multiple Alignment...

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 TraesCS5D01G537500 chr5D 100.000 4788 0 0 1 4788 550150653 550155440 0.000000e+00 8842
1 TraesCS5D01G537500 chr5B 93.380 3837 163 35 449 4219 702267823 702271634 0.000000e+00 5594
2 TraesCS5D01G537500 chr5B 82.020 812 87 27 2979 3750 702274438 702275230 1.880000e-178 636
3 TraesCS5D01G537500 chr5B 93.165 395 23 3 3 396 702267137 702267528 1.160000e-160 577
4 TraesCS5D01G537500 chr5B 78.906 256 46 8 4036 4287 256375797 256376048 2.960000e-37 167
5 TraesCS5D01G537500 chr4A 95.039 2681 108 5 2123 4787 617654281 617651610 0.000000e+00 4191
6 TraesCS5D01G537500 chr4A 93.260 2359 88 14 1058 3402 617545094 617542793 0.000000e+00 3410
7 TraesCS5D01G537500 chr4A 92.163 1378 69 15 487 1854 617655628 617654280 0.000000e+00 1910
8 TraesCS5D01G537500 chr4A 83.149 724 82 23 4027 4744 617649075 617648386 4.070000e-175 625
9 TraesCS5D01G537500 chr4A 93.566 373 22 2 1 372 617656526 617656155 5.410000e-154 555
10 TraesCS5D01G537500 chr4A 75.527 617 113 29 3880 4469 599590951 599590346 7.900000e-68 268
11 TraesCS5D01G537500 chr4A 96.721 61 2 0 423 483 617655858 617655798 8.480000e-18 102
12 TraesCS5D01G537500 chr2B 78.152 682 113 26 2669 3320 729628906 729629581 7.460000e-108 401
13 TraesCS5D01G537500 chr6D 77.508 618 109 18 3889 4494 332491384 332490785 1.280000e-90 344
14 TraesCS5D01G537500 chr1D 80.537 447 81 6 4026 4469 251992595 251992152 5.940000e-89 339
15 TraesCS5D01G537500 chr1D 73.259 359 63 18 4142 4497 144937955 144937627 3.050000e-17 100
16 TraesCS5D01G537500 chr6B 76.329 583 124 12 3903 4477 487844929 487845505 2.800000e-77 300
17 TraesCS5D01G537500 chr6A 77.755 481 90 11 4027 4498 471536361 471535889 3.650000e-71 279
18 TraesCS5D01G537500 chr3D 78.716 296 58 4 4027 4320 45101157 45100865 4.890000e-45 193


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 TraesCS5D01G537500 chr5D 550150653 550155440 4787 False 8842.0 8842 100.000000 1 4788 1 chr5D.!!$F1 4787
1 TraesCS5D01G537500 chr5B 702267137 702275230 8093 False 2269.0 5594 89.521667 3 4219 3 chr5B.!!$F2 4216
2 TraesCS5D01G537500 chr4A 617542793 617545094 2301 True 3410.0 3410 93.260000 1058 3402 1 chr4A.!!$R2 2344
3 TraesCS5D01G537500 chr4A 617648386 617656526 8140 True 1476.6 4191 92.127600 1 4787 5 chr4A.!!$R3 4786
4 TraesCS5D01G537500 chr4A 599590346 599590951 605 True 268.0 268 75.527000 3880 4469 1 chr4A.!!$R1 589
5 TraesCS5D01G537500 chr2B 729628906 729629581 675 False 401.0 401 78.152000 2669 3320 1 chr2B.!!$F1 651
6 TraesCS5D01G537500 chr6D 332490785 332491384 599 True 344.0 344 77.508000 3889 4494 1 chr6D.!!$R1 605
7 TraesCS5D01G537500 chr6B 487844929 487845505 576 False 300.0 300 76.329000 3903 4477 1 chr6B.!!$F1 574

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
404 406 0.243636 CGAACTCCATTTTGGCACCC 59.756 55.000 0.0 0.0 37.47 4.61 F
405 407 0.608130 GAACTCCATTTTGGCACCCC 59.392 55.000 0.0 0.0 37.47 4.95 F
406 408 0.835971 AACTCCATTTTGGCACCCCC 60.836 55.000 0.0 0.0 37.47 5.40 F
1274 1747 0.951558 CCACGTTTCCCTCACTTTGG 59.048 55.000 0.0 0.0 0.00 3.28 F
2568 3048 1.469079 GGCCGAATGGAAACCGAAATG 60.469 52.381 0.0 0.0 37.49 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1864 1.212935 ACTACTCACATGGATTGGGGC 59.787 52.381 0.0 0.0 0.00 5.80 R
1874 2352 1.343789 CATCACGGAGAGGCAGATGAT 59.656 52.381 0.0 0.0 38.62 2.45 R
1912 2390 1.522569 GAGTAGCCGCCCAATGTCT 59.477 57.895 0.0 0.0 0.00 3.41 R
3268 3775 2.194212 GGAGAGCGCGATGACCCTA 61.194 63.158 12.1 0.0 0.00 3.53 R
4169 4715 0.322546 GGATTCCACCATATCCCCGC 60.323 60.000 0.0 0.0 35.33 6.13 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
51 52 4.910585 GCTCCGTGCCCATACCCG 62.911 72.222 0.00 0.00 35.15 5.28
100 102 4.343526 AGACACTCCCATAGTATCTTGCAG 59.656 45.833 0.00 0.00 38.94 4.41
184 186 7.633621 AGAGTATGTTATTGTTCATGATTGCG 58.366 34.615 0.00 0.00 0.00 4.85
187 189 3.120025 TGTTATTGTTCATGATTGCGCGT 60.120 39.130 8.43 0.00 0.00 6.01
188 190 2.178474 ATTGTTCATGATTGCGCGTC 57.822 45.000 8.43 4.01 0.00 5.19
250 252 4.021192 GGATCCAAAGATGAAAAACAGGCA 60.021 41.667 6.95 0.00 30.90 4.75
256 258 4.843220 AGATGAAAAACAGGCACAAGAG 57.157 40.909 0.00 0.00 0.00 2.85
269 271 2.877300 GCACAAGAGGAGATTTCAGGCA 60.877 50.000 0.00 0.00 0.00 4.75
340 342 8.260818 AGAGATCGAAATCCAAAGAACATTAGA 58.739 33.333 0.00 0.00 31.78 2.10
396 398 2.094338 GTCCCTCGTACGAACTCCATTT 60.094 50.000 20.00 0.00 0.00 2.32
397 399 2.564062 TCCCTCGTACGAACTCCATTTT 59.436 45.455 20.00 0.00 0.00 1.82
398 400 2.671396 CCCTCGTACGAACTCCATTTTG 59.329 50.000 20.00 3.18 0.00 2.44
399 401 2.671396 CCTCGTACGAACTCCATTTTGG 59.329 50.000 20.00 8.84 39.43 3.28
400 402 2.070783 TCGTACGAACTCCATTTTGGC 58.929 47.619 17.11 0.00 37.47 4.52
401 403 1.801771 CGTACGAACTCCATTTTGGCA 59.198 47.619 10.44 0.00 37.47 4.92
402 404 2.412325 CGTACGAACTCCATTTTGGCAC 60.412 50.000 10.44 0.00 37.47 5.01
403 405 0.958822 ACGAACTCCATTTTGGCACC 59.041 50.000 0.00 0.00 37.47 5.01
404 406 0.243636 CGAACTCCATTTTGGCACCC 59.756 55.000 0.00 0.00 37.47 4.61
405 407 0.608130 GAACTCCATTTTGGCACCCC 59.392 55.000 0.00 0.00 37.47 4.95
406 408 0.835971 AACTCCATTTTGGCACCCCC 60.836 55.000 0.00 0.00 37.47 5.40
515 929 3.129113 TCTCGCATGGAAAAATGGATGTG 59.871 43.478 0.00 0.00 0.00 3.21
517 931 4.013050 TCGCATGGAAAAATGGATGTGTA 58.987 39.130 0.00 0.00 0.00 2.90
536 950 5.883115 TGTGTACTTCTCTCTGATCCACTAG 59.117 44.000 0.00 0.00 0.00 2.57
546 960 4.072839 TCTGATCCACTAGCCTATACACG 58.927 47.826 0.00 0.00 0.00 4.49
550 964 4.160642 TCCACTAGCCTATACACGAGAA 57.839 45.455 0.00 0.00 0.00 2.87
569 983 8.899776 CACGAGAATTTTTGAGAATTTCTTCTG 58.100 33.333 0.00 0.00 41.87 3.02
688 1105 7.702348 GGGATTTTTCTTGAACGAATGAATAGG 59.298 37.037 0.00 0.00 0.00 2.57
706 1156 3.297134 AGGTCATATTGGGCGTGAATT 57.703 42.857 0.00 0.00 0.00 2.17
766 1218 8.803397 AACATAGGAACAGTAATTAGGAAACC 57.197 34.615 0.00 0.00 0.00 3.27
788 1240 8.587952 AACCAAAATATATAGCCAATTTTCGC 57.412 30.769 0.00 0.00 32.05 4.70
789 1241 7.721402 ACCAAAATATATAGCCAATTTTCGCA 58.279 30.769 0.00 0.00 32.05 5.10
790 1242 8.200792 ACCAAAATATATAGCCAATTTTCGCAA 58.799 29.630 0.00 0.00 32.05 4.85
791 1243 9.039870 CCAAAATATATAGCCAATTTTCGCAAA 57.960 29.630 0.00 0.00 32.05 3.68
808 1260 9.862371 TTTTCGCAAAAGAAAAATATATAGCCA 57.138 25.926 2.83 0.00 44.25 4.75
809 1261 9.862371 TTTCGCAAAAGAAAAATATATAGCCAA 57.138 25.926 0.00 0.00 37.20 4.52
971 1429 3.894547 AACCACCGCATCCGTGTCC 62.895 63.158 0.00 0.00 0.00 4.02
1272 1745 1.675552 CACCACGTTTCCCTCACTTT 58.324 50.000 0.00 0.00 0.00 2.66
1274 1747 0.951558 CCACGTTTCCCTCACTTTGG 59.048 55.000 0.00 0.00 0.00 3.28
1327 1800 2.781757 TGCCATCTCTTCTCATCCCATT 59.218 45.455 0.00 0.00 0.00 3.16
1328 1801 3.975982 TGCCATCTCTTCTCATCCCATTA 59.024 43.478 0.00 0.00 0.00 1.90
1329 1802 4.413189 TGCCATCTCTTCTCATCCCATTAA 59.587 41.667 0.00 0.00 0.00 1.40
1456 1929 6.005198 TGTCATATCTGCATGCATTTATCCA 58.995 36.000 22.97 15.11 0.00 3.41
1556 2029 3.706600 TCCGGTTTATTAGGCACACTT 57.293 42.857 0.00 0.00 0.00 3.16
1561 2034 5.151389 CGGTTTATTAGGCACACTTGTTTC 58.849 41.667 0.00 0.00 0.00 2.78
1782 2260 4.502171 ACATGCGTGTGAAATGATTCAA 57.498 36.364 11.65 0.00 46.66 2.69
1874 2352 2.119029 ATCGTCGCCGGATGTCTCA 61.119 57.895 5.05 0.00 33.95 3.27
1912 2390 2.496341 CTCATCGGCTTCTCGGCA 59.504 61.111 0.00 0.00 38.27 5.69
2053 2531 4.680237 CAAGGTCCGGCTCGTGCA 62.680 66.667 12.07 0.00 41.91 4.57
2407 2885 8.827832 TTCAAAGATTTCACTCATTCCCATAT 57.172 30.769 0.00 0.00 0.00 1.78
2516 2996 8.681806 TCGAATTATTTGGTTGCATTTCTATCA 58.318 29.630 0.00 0.00 0.00 2.15
2517 2997 8.961092 CGAATTATTTGGTTGCATTTCTATCAG 58.039 33.333 0.00 0.00 0.00 2.90
2568 3048 1.469079 GGCCGAATGGAAACCGAAATG 60.469 52.381 0.00 0.00 37.49 2.32
2772 3252 2.956987 GCCGTGGATGCATATGCC 59.043 61.111 24.54 10.19 41.18 4.40
2869 3349 3.645687 ACCTGGGTAATGTTTTGTGCATT 59.354 39.130 0.00 0.00 39.55 3.56
2944 3451 7.615403 ACTATTCTGACATGTTTTCTCAGCTA 58.385 34.615 0.00 0.00 32.88 3.32
3184 3691 5.051409 TCATCCTATTTGGCATCATGACA 57.949 39.130 0.00 0.00 30.30 3.58
3268 3775 3.984732 GGCCCTGACCCCAAGCTT 61.985 66.667 0.00 0.00 0.00 3.74
3394 3901 1.746615 CCTCGCCATTGGTGTCCTG 60.747 63.158 15.63 5.50 34.40 3.86
3484 3991 4.286291 CCTCAGGGTGTTAGTTTACCTTCT 59.714 45.833 0.00 0.00 37.15 2.85
3649 4156 0.809241 CAGTCCTTGCGCTCATCCTC 60.809 60.000 9.73 0.00 0.00 3.71
4087 4633 4.330620 TCCGCGTAGATCCAATTTTTGTAC 59.669 41.667 4.92 0.00 0.00 2.90
4290 4837 5.172934 GTGAAGTCAACCGTCCAACATATA 58.827 41.667 0.00 0.00 0.00 0.86
4298 4845 6.039717 TCAACCGTCCAACATATACCTACTAC 59.960 42.308 0.00 0.00 0.00 2.73
4307 4854 8.145767 CCAACATATACCTACTACGGATGAAAA 58.854 37.037 0.00 0.00 0.00 2.29
4346 4893 1.522668 TGGTGAATTTGCAGAGGTCG 58.477 50.000 0.00 0.00 0.00 4.79
4356 4903 1.367471 CAGAGGTCGGCACTGACAA 59.633 57.895 11.53 0.00 40.72 3.18
4357 4904 0.036952 CAGAGGTCGGCACTGACAAT 60.037 55.000 11.53 0.00 40.72 2.71
4374 4921 3.942115 GACAATGCTTACCTCCCTCTTTC 59.058 47.826 0.00 0.00 0.00 2.62
4377 4924 1.286248 GCTTACCTCCCTCTTTCCCA 58.714 55.000 0.00 0.00 0.00 4.37
4401 4948 2.126467 CATTGCAACAAGGGACAAACG 58.874 47.619 0.00 0.00 0.00 3.60
4424 4971 1.228063 CCGCCTTAGCTGCATCCAT 60.228 57.895 1.02 0.00 36.60 3.41
4433 8267 2.474112 AGCTGCATCCATGGGAAAAAT 58.526 42.857 13.02 0.00 34.34 1.82
4494 8329 2.158219 AGTGACGTATGGGATATGGGGA 60.158 50.000 0.00 0.00 0.00 4.81
4500 8335 3.371917 CGTATGGGATATGGGGATGCAAT 60.372 47.826 0.00 0.00 0.00 3.56
4502 8337 3.737559 TGGGATATGGGGATGCAATAC 57.262 47.619 0.00 0.00 0.00 1.89
4514 8349 6.770785 TGGGGATGCAATACATAAGTAACTTC 59.229 38.462 0.00 0.00 39.84 3.01
4565 8403 9.461312 TGAAAAGTGATAAGTAAATGCCATAGT 57.539 29.630 0.00 0.00 0.00 2.12
4569 8407 9.547753 AAGTGATAAGTAAATGCCATAGTAGTG 57.452 33.333 0.00 0.00 0.00 2.74
4570 8408 8.924303 AGTGATAAGTAAATGCCATAGTAGTGA 58.076 33.333 0.00 0.00 0.00 3.41
4571 8409 9.542462 GTGATAAGTAAATGCCATAGTAGTGAA 57.458 33.333 0.00 0.00 0.00 3.18
4574 8412 7.865706 AAGTAAATGCCATAGTAGTGAAAGG 57.134 36.000 0.00 0.00 0.00 3.11
4577 8415 2.985896 TGCCATAGTAGTGAAAGGCAC 58.014 47.619 0.00 0.00 46.25 5.01
4588 8426 4.224715 GTGAAAGGCACTACAAGAAACC 57.775 45.455 0.00 0.00 44.27 3.27
4589 8427 3.630312 GTGAAAGGCACTACAAGAAACCA 59.370 43.478 0.00 0.00 44.27 3.67
4590 8428 3.882888 TGAAAGGCACTACAAGAAACCAG 59.117 43.478 0.00 0.00 38.49 4.00
4593 8431 1.604604 GCACTACAAGAAACCAGCCA 58.395 50.000 0.00 0.00 0.00 4.75
4594 8432 1.266989 GCACTACAAGAAACCAGCCAC 59.733 52.381 0.00 0.00 0.00 5.01
4595 8433 2.851195 CACTACAAGAAACCAGCCACT 58.149 47.619 0.00 0.00 0.00 4.00
4596 8434 2.549754 CACTACAAGAAACCAGCCACTG 59.450 50.000 0.00 0.00 0.00 3.66
4656 8494 2.813754 CACCACATGTACTTGGGTCAAG 59.186 50.000 12.86 6.15 45.85 3.02
4657 8495 1.812571 CCACATGTACTTGGGTCAAGC 59.187 52.381 12.86 0.00 44.43 4.01
4668 8506 4.980805 GTCAAGCCCGCGTGGTCA 62.981 66.667 15.14 0.00 36.04 4.02
4685 8523 4.269183 TGGTCAAAATACCGCATTCTGAT 58.731 39.130 0.00 0.00 42.91 2.90
4705 8543 0.419865 TGGTCTTCCATACCCTCCCA 59.580 55.000 0.00 0.00 39.03 4.37
4724 8562 2.274437 CACGGATTGATGAGGTGACTG 58.726 52.381 0.00 0.00 44.43 3.51
4725 8563 2.094026 CACGGATTGATGAGGTGACTGA 60.094 50.000 0.00 0.00 44.43 3.41
4733 8571 2.015456 TGAGGTGACTGACATCCACT 57.985 50.000 7.13 0.00 44.43 4.00
4734 8572 1.895798 TGAGGTGACTGACATCCACTC 59.104 52.381 7.13 0.00 44.43 3.51
4747 8585 1.991121 TCCACTCGTCCACAACTAGT 58.009 50.000 0.00 0.00 34.40 2.57
4748 8586 2.313317 TCCACTCGTCCACAACTAGTT 58.687 47.619 1.12 1.12 31.88 2.24
4749 8587 2.696707 TCCACTCGTCCACAACTAGTTT 59.303 45.455 5.07 0.00 31.88 2.66
4750 8588 3.133362 TCCACTCGTCCACAACTAGTTTT 59.867 43.478 5.07 0.00 31.88 2.43
4753 8591 3.311596 ACTCGTCCACAACTAGTTTTTGC 59.688 43.478 5.07 0.00 30.07 3.68
4754 8592 3.271729 TCGTCCACAACTAGTTTTTGCA 58.728 40.909 5.07 0.00 0.00 4.08
4755 8593 3.064271 TCGTCCACAACTAGTTTTTGCAC 59.936 43.478 5.07 1.80 0.00 4.57
4756 8594 3.181505 CGTCCACAACTAGTTTTTGCACA 60.182 43.478 5.07 0.00 0.00 4.57
4757 8595 4.102649 GTCCACAACTAGTTTTTGCACAC 58.897 43.478 5.07 0.46 0.00 3.82
4759 8597 4.104776 CCACAACTAGTTTTTGCACACAG 58.895 43.478 5.07 0.00 0.00 3.66
4760 8598 4.142491 CCACAACTAGTTTTTGCACACAGA 60.142 41.667 5.07 0.00 0.00 3.41
4761 8599 5.450412 CCACAACTAGTTTTTGCACACAGAT 60.450 40.000 5.07 0.00 0.00 2.90
4763 8601 5.215160 CAACTAGTTTTTGCACACAGATCC 58.785 41.667 5.07 0.00 0.00 3.36
4765 8603 4.887071 ACTAGTTTTTGCACACAGATCCAA 59.113 37.500 0.00 0.00 0.00 3.53
4766 8604 4.942761 AGTTTTTGCACACAGATCCAAT 57.057 36.364 0.00 0.00 0.00 3.16
4767 8605 4.874970 AGTTTTTGCACACAGATCCAATC 58.125 39.130 0.00 0.00 0.00 2.67
4768 8606 4.341806 AGTTTTTGCACACAGATCCAATCA 59.658 37.500 0.00 0.00 0.00 2.57
4769 8607 5.011329 AGTTTTTGCACACAGATCCAATCAT 59.989 36.000 0.00 0.00 0.00 2.45
4772 8610 3.538591 TGCACACAGATCCAATCATCTC 58.461 45.455 0.00 0.00 30.07 2.75
4773 8611 2.877168 GCACACAGATCCAATCATCTCC 59.123 50.000 0.00 0.00 30.07 3.71
4774 8612 3.474600 CACACAGATCCAATCATCTCCC 58.525 50.000 0.00 0.00 30.07 4.30
4775 8613 3.136077 CACACAGATCCAATCATCTCCCT 59.864 47.826 0.00 0.00 30.07 4.20
4777 8615 4.141528 ACACAGATCCAATCATCTCCCTTC 60.142 45.833 0.00 0.00 30.07 3.46
4779 8617 4.347583 ACAGATCCAATCATCTCCCTTCTC 59.652 45.833 0.00 0.00 30.07 2.87
4782 8620 5.307716 AGATCCAATCATCTCCCTTCTCTTC 59.692 44.000 0.00 0.00 0.00 2.87
4783 8621 4.629122 TCCAATCATCTCCCTTCTCTTCT 58.371 43.478 0.00 0.00 0.00 2.85
4784 8622 4.653341 TCCAATCATCTCCCTTCTCTTCTC 59.347 45.833 0.00 0.00 0.00 2.87
4786 8624 5.221501 CCAATCATCTCCCTTCTCTTCTCTC 60.222 48.000 0.00 0.00 0.00 3.20
4787 8625 4.879295 TCATCTCCCTTCTCTTCTCTCT 57.121 45.455 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 2.940410 TGGGAGTGTCTCAAAAACGTTC 59.060 45.455 0.00 0.00 31.08 3.95
184 186 2.915738 TTTCTTAGAGAGACGGACGC 57.084 50.000 0.00 0.00 33.02 5.19
187 189 6.812998 TGTTTTCTTTTCTTAGAGAGACGGA 58.187 36.000 0.00 0.00 33.02 4.69
188 190 7.478520 TTGTTTTCTTTTCTTAGAGAGACGG 57.521 36.000 0.00 0.00 33.02 4.79
226 228 4.021192 GCCTGTTTTTCATCTTTGGATCCA 60.021 41.667 11.44 11.44 0.00 3.41
250 252 2.026449 CCTGCCTGAAATCTCCTCTTGT 60.026 50.000 0.00 0.00 0.00 3.16
256 258 4.752146 CAATTTTCCTGCCTGAAATCTCC 58.248 43.478 0.00 0.00 34.41 3.71
269 271 1.267806 CGTGTGAGCTGCAATTTTCCT 59.732 47.619 1.02 0.00 0.00 3.36
340 342 1.927487 TGAAAGGCCTTCATGTGCAT 58.073 45.000 20.79 0.00 39.20 3.96
375 377 1.101331 ATGGAGTTCGTACGAGGGAC 58.899 55.000 18.64 13.90 0.00 4.46
410 412 1.113517 TCGAAAGATAGCCTCGGGGG 61.114 60.000 1.90 0.00 33.44 5.40
411 413 0.032267 GTCGAAAGATAGCCTCGGGG 59.968 60.000 0.00 0.00 45.19 5.73
412 414 0.032267 GGTCGAAAGATAGCCTCGGG 59.968 60.000 0.00 0.00 45.19 5.14
413 415 0.317938 CGGTCGAAAGATAGCCTCGG 60.318 60.000 0.00 0.00 45.19 4.63
414 416 0.661552 TCGGTCGAAAGATAGCCTCG 59.338 55.000 0.00 0.00 45.19 4.63
415 417 2.358267 TCTTCGGTCGAAAGATAGCCTC 59.642 50.000 7.23 0.00 45.19 4.70
416 418 2.376109 TCTTCGGTCGAAAGATAGCCT 58.624 47.619 7.23 0.00 45.19 4.58
417 419 2.865343 TCTTCGGTCGAAAGATAGCC 57.135 50.000 7.23 0.00 45.19 3.93
418 420 4.360563 TCATTCTTCGGTCGAAAGATAGC 58.639 43.478 7.23 0.00 45.19 2.97
419 421 5.340932 CGATCATTCTTCGGTCGAAAGATAG 59.659 44.000 7.23 5.63 45.19 2.08
420 422 5.008316 TCGATCATTCTTCGGTCGAAAGATA 59.992 40.000 7.23 0.00 38.25 1.98
421 423 4.045104 CGATCATTCTTCGGTCGAAAGAT 58.955 43.478 7.23 8.04 45.19 2.40
515 929 4.277423 GGCTAGTGGATCAGAGAGAAGTAC 59.723 50.000 0.00 0.00 0.00 2.73
517 931 3.052944 AGGCTAGTGGATCAGAGAGAAGT 60.053 47.826 0.00 0.00 0.00 3.01
536 950 6.903883 TCTCAAAAATTCTCGTGTATAGGC 57.096 37.500 0.00 0.00 0.00 3.93
546 960 8.807667 TGCAGAAGAAATTCTCAAAAATTCTC 57.192 30.769 0.00 0.00 0.00 2.87
639 1056 8.700051 TCCCATGTTTTTCAGAAGTAAATTTGA 58.300 29.630 0.00 0.00 0.00 2.69
688 1105 5.298276 TCCTAAAATTCACGCCCAATATGAC 59.702 40.000 0.00 0.00 0.00 3.06
743 1193 8.801882 TTGGTTTCCTAATTACTGTTCCTATG 57.198 34.615 0.00 0.00 0.00 2.23
762 1214 9.040939 GCGAAAATTGGCTATATATTTTGGTTT 57.959 29.630 0.00 0.00 33.08 3.27
798 1250 9.408648 GCCCTGTAATGTTAATTGGCTATATAT 57.591 33.333 0.00 0.00 31.50 0.86
799 1251 7.832187 GGCCCTGTAATGTTAATTGGCTATATA 59.168 37.037 0.00 0.00 33.61 0.86
800 1252 6.663523 GGCCCTGTAATGTTAATTGGCTATAT 59.336 38.462 0.00 0.00 33.61 0.86
801 1253 6.007703 GGCCCTGTAATGTTAATTGGCTATA 58.992 40.000 0.00 0.00 33.61 1.31
802 1254 4.832823 GGCCCTGTAATGTTAATTGGCTAT 59.167 41.667 0.00 0.00 33.61 2.97
803 1255 4.211920 GGCCCTGTAATGTTAATTGGCTA 58.788 43.478 0.00 0.00 33.61 3.93
804 1256 3.031013 GGCCCTGTAATGTTAATTGGCT 58.969 45.455 0.00 0.00 33.61 4.75
805 1257 2.763448 TGGCCCTGTAATGTTAATTGGC 59.237 45.455 0.00 0.00 32.75 4.52
806 1258 3.181491 CGTGGCCCTGTAATGTTAATTGG 60.181 47.826 0.00 0.00 0.00 3.16
807 1259 3.442273 ACGTGGCCCTGTAATGTTAATTG 59.558 43.478 0.00 0.00 0.00 2.32
808 1260 3.692690 ACGTGGCCCTGTAATGTTAATT 58.307 40.909 0.00 0.00 0.00 1.40
809 1261 3.359695 ACGTGGCCCTGTAATGTTAAT 57.640 42.857 0.00 0.00 0.00 1.40
810 1262 2.863132 ACGTGGCCCTGTAATGTTAA 57.137 45.000 0.00 0.00 0.00 2.01
811 1263 3.098377 TCTACGTGGCCCTGTAATGTTA 58.902 45.455 0.00 0.00 0.00 2.41
993 1451 4.097418 CTCCCTCCCTATCCATCGTTTAT 58.903 47.826 0.00 0.00 0.00 1.40
1327 1800 7.657306 TGGAAAGGGAAGGGAATGAATTATTA 58.343 34.615 0.00 0.00 0.00 0.98
1328 1801 6.511208 TGGAAAGGGAAGGGAATGAATTATT 58.489 36.000 0.00 0.00 0.00 1.40
1329 1802 6.103838 TGGAAAGGGAAGGGAATGAATTAT 57.896 37.500 0.00 0.00 0.00 1.28
1391 1864 1.212935 ACTACTCACATGGATTGGGGC 59.787 52.381 0.00 0.00 0.00 5.80
1425 1898 3.252701 GCATGCAGATATGACAAAGAGGG 59.747 47.826 14.21 0.00 0.00 4.30
1556 2029 8.112822 TGGTTAAATCATCAATCTAGGGAAACA 58.887 33.333 0.00 0.00 0.00 2.83
1615 2093 7.662604 AGAACAATTGAAATTTTCTCATGGC 57.337 32.000 13.59 4.20 0.00 4.40
1766 2244 2.095768 AGCCGTTGAATCATTTCACACG 60.096 45.455 12.31 12.31 41.50 4.49
1874 2352 1.343789 CATCACGGAGAGGCAGATGAT 59.656 52.381 0.00 0.00 38.62 2.45
1912 2390 1.522569 GAGTAGCCGCCCAATGTCT 59.477 57.895 0.00 0.00 0.00 3.41
2053 2531 2.040939 CCAGAGAGATCAGCCATGAGT 58.959 52.381 0.00 0.00 39.29 3.41
2407 2885 7.707624 ATGGAAAAGCAATCATTTCAGTAGA 57.292 32.000 0.00 0.00 37.29 2.59
2516 2996 5.875359 GGACCGAAATCTGTGACTTAAATCT 59.125 40.000 0.00 0.00 0.00 2.40
2517 2997 5.642063 TGGACCGAAATCTGTGACTTAAATC 59.358 40.000 0.00 0.00 0.00 2.17
2568 3048 7.373778 ACAATACTGGTTTAGAATTTCGGTC 57.626 36.000 0.00 0.00 0.00 4.79
2625 3105 7.503230 TGAATAAGCAGCCATTCATGAGATAAA 59.497 33.333 13.59 0.00 36.49 1.40
2869 3349 6.644592 GCATGCATTGTTTTAAGAGGTTGTTA 59.355 34.615 14.21 0.00 0.00 2.41
3268 3775 2.194212 GGAGAGCGCGATGACCCTA 61.194 63.158 12.10 0.00 0.00 3.53
3373 3880 1.971167 GACACCAATGGCGAGGCAA 60.971 57.895 0.00 0.00 0.00 4.52
3374 3881 2.359850 GACACCAATGGCGAGGCA 60.360 61.111 0.00 0.88 0.00 4.75
3394 3901 0.521242 GCACGACGATGGCAATGTTC 60.521 55.000 0.00 0.00 0.00 3.18
3480 3987 1.151668 CAAGACCAACGCAGGAGAAG 58.848 55.000 0.10 0.00 0.00 2.85
3484 3991 0.468226 AAGTCAAGACCAACGCAGGA 59.532 50.000 0.10 0.00 0.00 3.86
3649 4156 0.401738 TGCCTCTTGTCTTGGGAAGG 59.598 55.000 0.00 0.00 0.00 3.46
4169 4715 0.322546 GGATTCCACCATATCCCCGC 60.323 60.000 0.00 0.00 35.33 6.13
4290 4837 5.934402 ATGACTTTTCATCCGTAGTAGGT 57.066 39.130 0.00 0.00 38.08 3.08
4298 4845 7.553881 ACCAATACTAATGACTTTTCATCCG 57.446 36.000 0.00 0.00 42.00 4.18
4307 4854 8.262601 TCACCATCATACCAATACTAATGACT 57.737 34.615 0.00 0.00 31.56 3.41
4312 4859 8.629158 GCAAATTCACCATCATACCAATACTAA 58.371 33.333 0.00 0.00 0.00 2.24
4346 4893 1.740025 GAGGTAAGCATTGTCAGTGCC 59.260 52.381 15.99 2.03 43.50 5.01
4356 4903 1.847088 GGGAAAGAGGGAGGTAAGCAT 59.153 52.381 0.00 0.00 0.00 3.79
4357 4904 1.286248 GGGAAAGAGGGAGGTAAGCA 58.714 55.000 0.00 0.00 0.00 3.91
4374 4921 1.479323 CCCTTGTTGCAATGATCTGGG 59.521 52.381 0.59 5.52 0.00 4.45
4377 4924 3.159213 TGTCCCTTGTTGCAATGATCT 57.841 42.857 0.59 0.00 0.00 2.75
4401 4948 2.202946 GCAGCTAAGGCGGTCTCC 60.203 66.667 0.00 0.00 44.37 3.71
4412 4959 2.824689 TTTTCCCATGGATGCAGCTA 57.175 45.000 15.22 0.00 0.00 3.32
4424 4971 6.071278 CCAAACGGTATTAAGGATTTTTCCCA 60.071 38.462 0.00 0.00 0.00 4.37
4433 8267 4.502962 CGGTTACCAAACGGTATTAAGGA 58.497 43.478 1.13 0.00 38.83 3.36
4489 8324 6.260700 AGTTACTTATGTATTGCATCCCCA 57.739 37.500 0.00 0.00 38.94 4.96
4548 8386 9.561069 CCTTTCACTACTATGGCATTTACTTAT 57.439 33.333 4.78 0.00 0.00 1.73
4556 8394 3.931907 TGCCTTTCACTACTATGGCAT 57.068 42.857 4.88 4.88 44.35 4.40
4567 8405 3.630312 TGGTTTCTTGTAGTGCCTTTCAC 59.370 43.478 0.00 0.00 45.98 3.18
4568 8406 3.882888 CTGGTTTCTTGTAGTGCCTTTCA 59.117 43.478 0.00 0.00 0.00 2.69
4569 8407 3.304726 GCTGGTTTCTTGTAGTGCCTTTC 60.305 47.826 0.00 0.00 0.00 2.62
4570 8408 2.623416 GCTGGTTTCTTGTAGTGCCTTT 59.377 45.455 0.00 0.00 0.00 3.11
4571 8409 2.230660 GCTGGTTTCTTGTAGTGCCTT 58.769 47.619 0.00 0.00 0.00 4.35
4573 8411 0.881796 GGCTGGTTTCTTGTAGTGCC 59.118 55.000 0.00 0.00 0.00 5.01
4574 8412 1.266989 GTGGCTGGTTTCTTGTAGTGC 59.733 52.381 0.00 0.00 0.00 4.40
4576 8414 2.487265 CCAGTGGCTGGTTTCTTGTAGT 60.487 50.000 6.99 0.00 45.82 2.73
4577 8415 2.154462 CCAGTGGCTGGTTTCTTGTAG 58.846 52.381 6.99 0.00 45.82 2.74
4578 8416 2.270352 CCAGTGGCTGGTTTCTTGTA 57.730 50.000 6.99 0.00 45.82 2.41
4597 8435 4.992951 CCCGCCACTGGTAATATAGTTTAC 59.007 45.833 0.00 0.00 0.00 2.01
4599 8437 3.457012 ACCCGCCACTGGTAATATAGTTT 59.543 43.478 0.00 0.00 33.26 2.66
4600 8438 3.043418 ACCCGCCACTGGTAATATAGTT 58.957 45.455 0.00 0.00 33.26 2.24
4602 8440 2.367567 ACACCCGCCACTGGTAATATAG 59.632 50.000 0.00 0.00 33.84 1.31
4603 8441 2.400573 ACACCCGCCACTGGTAATATA 58.599 47.619 0.00 0.00 33.84 0.86
4604 8442 1.209621 ACACCCGCCACTGGTAATAT 58.790 50.000 0.00 0.00 33.84 1.28
4605 8443 1.481772 GTACACCCGCCACTGGTAATA 59.518 52.381 0.00 0.00 33.84 0.98
4610 8448 1.827399 AAGAGTACACCCGCCACTGG 61.827 60.000 0.00 0.00 0.00 4.00
4611 8449 0.670546 CAAGAGTACACCCGCCACTG 60.671 60.000 0.00 0.00 0.00 3.66
4614 8452 1.369692 CACAAGAGTACACCCGCCA 59.630 57.895 0.00 0.00 0.00 5.69
4615 8453 2.033194 GCACAAGAGTACACCCGCC 61.033 63.158 0.00 0.00 0.00 6.13
4616 8454 2.033194 GGCACAAGAGTACACCCGC 61.033 63.158 0.00 0.00 0.00 6.13
4617 8455 1.375523 GGGCACAAGAGTACACCCG 60.376 63.158 0.00 0.00 0.00 5.28
4656 8494 1.135939 GTATTTTGACCACGCGGGC 59.864 57.895 12.47 6.13 42.99 6.13
4657 8495 1.798087 GGTATTTTGACCACGCGGG 59.202 57.895 12.47 6.05 39.51 6.13
4667 8505 4.997565 ACCAATCAGAATGCGGTATTTTG 58.002 39.130 3.45 3.45 32.28 2.44
4668 8506 4.949856 AGACCAATCAGAATGCGGTATTTT 59.050 37.500 0.00 0.00 33.84 1.82
4705 8543 2.093973 GTCAGTCACCTCATCAATCCGT 60.094 50.000 0.00 0.00 0.00 4.69
4724 8562 1.000955 AGTTGTGGACGAGTGGATGTC 59.999 52.381 0.00 0.00 0.00 3.06
4725 8563 1.048601 AGTTGTGGACGAGTGGATGT 58.951 50.000 0.00 0.00 0.00 3.06
4733 8571 3.064271 GTGCAAAAACTAGTTGTGGACGA 59.936 43.478 20.85 0.00 0.00 4.20
4734 8572 3.181505 TGTGCAAAAACTAGTTGTGGACG 60.182 43.478 25.65 8.99 34.63 4.79
4747 8585 4.933505 TGATTGGATCTGTGTGCAAAAA 57.066 36.364 0.00 0.00 33.10 1.94
4748 8586 4.768448 AGATGATTGGATCTGTGTGCAAAA 59.232 37.500 0.00 0.00 33.10 2.44
4749 8587 4.338012 AGATGATTGGATCTGTGTGCAAA 58.662 39.130 0.00 0.00 33.10 3.68
4750 8588 3.943381 GAGATGATTGGATCTGTGTGCAA 59.057 43.478 0.00 0.00 32.57 4.08
4753 8591 3.136077 AGGGAGATGATTGGATCTGTGTG 59.864 47.826 0.00 0.00 32.57 3.82
4754 8592 3.391774 AGGGAGATGATTGGATCTGTGT 58.608 45.455 0.00 0.00 32.57 3.72
4755 8593 4.102838 AGAAGGGAGATGATTGGATCTGTG 59.897 45.833 0.00 0.00 32.57 3.66
4756 8594 4.305524 AGAAGGGAGATGATTGGATCTGT 58.694 43.478 0.00 0.00 32.57 3.41
4757 8595 4.594062 AGAGAAGGGAGATGATTGGATCTG 59.406 45.833 0.00 0.00 32.57 2.90
4759 8597 5.307716 AGAAGAGAAGGGAGATGATTGGATC 59.692 44.000 0.00 0.00 0.00 3.36
4760 8598 5.226015 AGAAGAGAAGGGAGATGATTGGAT 58.774 41.667 0.00 0.00 0.00 3.41
4761 8599 4.629122 AGAAGAGAAGGGAGATGATTGGA 58.371 43.478 0.00 0.00 0.00 3.53
4763 8601 5.599656 AGAGAGAAGAGAAGGGAGATGATTG 59.400 44.000 0.00 0.00 0.00 2.67
4765 8603 5.408079 AGAGAGAAGAGAAGGGAGATGAT 57.592 43.478 0.00 0.00 0.00 2.45
4766 8604 4.879295 AGAGAGAAGAGAAGGGAGATGA 57.121 45.455 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.