Multiple sequence alignment - TraesCS5B01G445000

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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 TraesCS5B01G445000 chr5B 100.000 2372 0 0 1 2372 617231776 617234147 0.000000e+00 4381
1 TraesCS5B01G445000 chr5B 88.281 128 15 0 446 573 91191098 91191225 1.140000e-33 154
2 TraesCS5B01G445000 chr5B 83.333 114 18 1 114 227 91190739 91190851 1.160000e-18 104
3 TraesCS5B01G445000 chr5D 92.519 655 24 9 668 1310 497942272 497942913 0.000000e+00 915
4 TraesCS5B01G445000 chr5D 90.144 416 15 8 1628 2022 497943240 497943650 3.490000e-143 518
5 TraesCS5B01G445000 chr5D 91.453 351 29 1 2022 2372 497943699 497944048 4.590000e-132 481
6 TraesCS5B01G445000 chr5D 91.148 305 17 7 1303 1604 497942951 497943248 2.840000e-109 405
7 TraesCS5B01G445000 chr5A 91.603 655 30 9 668 1310 622106534 622107175 0.000000e+00 881
8 TraesCS5B01G445000 chr5A 89.713 418 19 7 1623 2021 622107499 622107911 1.630000e-141 512
9 TraesCS5B01G445000 chr5A 92.810 306 14 7 1303 1605 622107213 622107513 1.010000e-118 436
10 TraesCS5B01G445000 chr5A 82.996 247 37 4 2058 2302 564748404 564748647 3.970000e-53 219
11 TraesCS5B01G445000 chr5A 82.759 203 29 5 2090 2290 690785154 690785352 2.420000e-40 176
12 TraesCS5B01G445000 chr3A 89.465 598 42 7 1 578 22610104 22610700 0.000000e+00 736
13 TraesCS5B01G445000 chr3A 88.293 410 48 0 1 410 713538101 713538510 2.120000e-135 492
14 TraesCS5B01G445000 chr6A 89.562 594 41 7 1 574 468473044 468473636 0.000000e+00 734
15 TraesCS5B01G445000 chr6A 85.897 156 22 0 121 276 76579959 76580114 1.460000e-37 167
16 TraesCS5B01G445000 chr6A 85.938 128 17 1 446 573 76580321 76580447 4.110000e-28 135
17 TraesCS5B01G445000 chr7A 84.800 625 38 14 1 579 688374923 688375536 2.040000e-160 575
18 TraesCS5B01G445000 chr7A 95.588 136 6 0 2 137 729678535 729678400 3.970000e-53 219
19 TraesCS5B01G445000 chr4A 89.234 418 44 1 1 418 19174058 19174474 2.700000e-144 521
20 TraesCS5B01G445000 chr4A 83.951 243 30 7 2055 2297 604640711 604640944 8.530000e-55 224
21 TraesCS5B01G445000 chr4A 92.754 138 10 0 440 577 19177861 19177998 1.440000e-47 200
22 TraesCS5B01G445000 chr4A 88.806 134 15 0 446 579 590315661 590315528 5.240000e-37 165
23 TraesCS5B01G445000 chr4A 88.806 134 15 0 446 579 590327032 590326899 5.240000e-37 165
24 TraesCS5B01G445000 chr7B 85.294 238 30 4 2058 2293 633254582 633254816 8.470000e-60 241
25 TraesCS5B01G445000 chr7B 82.591 247 33 7 2058 2295 33421925 33422170 2.390000e-50 209
26 TraesCS5B01G445000 chr3D 82.906 234 40 0 2060 2293 49449428 49449195 6.640000e-51 211
27 TraesCS5B01G445000 chr3D 83.810 210 33 1 2087 2295 549450738 549450947 5.170000e-47 198
28 TraesCS5B01G445000 chr1A 86.772 189 23 2 2108 2295 488075198 488075011 2.390000e-50 209
29 TraesCS5B01G445000 chr2A 84.615 156 24 0 121 276 607838719 607838564 3.160000e-34 156
30 TraesCS5B01G445000 chr2A 86.154 130 17 1 446 575 607838357 607838229 3.180000e-29 139
31 TraesCS5B01G445000 chr1B 83.660 153 24 1 114 266 164284 164435 2.460000e-30 143


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 TraesCS5B01G445000 chr5B 617231776 617234147 2371 False 4381.000000 4381 100.000000 1 2372 1 chr5B.!!$F1 2371
1 TraesCS5B01G445000 chr5D 497942272 497944048 1776 False 579.750000 915 91.316000 668 2372 4 chr5D.!!$F1 1704
2 TraesCS5B01G445000 chr5A 622106534 622107911 1377 False 609.666667 881 91.375333 668 2021 3 chr5A.!!$F3 1353
3 TraesCS5B01G445000 chr3A 22610104 22610700 596 False 736.000000 736 89.465000 1 578 1 chr3A.!!$F1 577
4 TraesCS5B01G445000 chr6A 468473044 468473636 592 False 734.000000 734 89.562000 1 574 1 chr6A.!!$F1 573
5 TraesCS5B01G445000 chr7A 688374923 688375536 613 False 575.000000 575 84.800000 1 579 1 chr7A.!!$F1 578
6 TraesCS5B01G445000 chr4A 19174058 19177998 3940 False 360.500000 521 90.994000 1 577 2 chr4A.!!$F2 576

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
870 4263 0.028242 CGTAAAACACAGGCGCAACA 59.972 50.0 10.83 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 5572 0.233848 CCTTGTTTACCGTGCACGAC 59.766 55.0 39.1 27.99 43.02 4.34 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
45 46 2.023673 CTTGGGAACTTGCAGTGTCAA 58.976 47.619 0.00 0.00 0.00 3.18
53 54 5.009610 GGAACTTGCAGTGTCAATTCCTTTA 59.990 40.000 19.47 0.00 32.96 1.85
297 324 4.426313 GAAGCGGGGTGAAGGGGG 62.426 72.222 0.00 0.00 0.00 5.40
355 383 6.599638 AGAATTGGAGTAGGATTTACAAGTGC 59.400 38.462 0.00 0.00 0.00 4.40
382 410 3.635373 GACCTGTAGATTGTCCGGTGATA 59.365 47.826 0.00 0.00 0.00 2.15
385 413 4.524714 CCTGTAGATTGTCCGGTGATATCT 59.475 45.833 0.00 8.64 32.66 1.98
414 442 1.124780 TGGTTGTTCTTCCTCGACCA 58.875 50.000 0.00 0.00 43.37 4.02
433 461 4.309950 GTCGTGGCCTGACCCGTT 62.310 66.667 15.41 0.00 37.83 4.44
434 462 3.998672 TCGTGGCCTGACCCGTTC 61.999 66.667 3.32 0.00 37.83 3.95
437 465 1.905512 GTGGCCTGACCCGTTCTAT 59.094 57.895 3.32 0.00 37.83 1.98
438 466 0.252197 GTGGCCTGACCCGTTCTATT 59.748 55.000 3.32 0.00 37.83 1.73
442 3835 2.007608 GCCTGACCCGTTCTATTGTTC 58.992 52.381 0.00 0.00 0.00 3.18
470 3863 0.603065 ATACAGCGACAGACAGTGCA 59.397 50.000 0.00 0.00 0.00 4.57
504 3897 4.236935 GTTTTGGACATACAAGTGGCATG 58.763 43.478 0.00 0.00 0.00 4.06
579 3972 6.354130 TGCTAAATAGACAGTCCCATAAACC 58.646 40.000 0.00 0.00 0.00 3.27
580 3973 6.157994 TGCTAAATAGACAGTCCCATAAACCT 59.842 38.462 0.00 0.00 0.00 3.50
581 3974 7.054751 GCTAAATAGACAGTCCCATAAACCTT 58.945 38.462 0.00 0.00 0.00 3.50
582 3975 8.208903 GCTAAATAGACAGTCCCATAAACCTTA 58.791 37.037 0.00 0.00 0.00 2.69
589 3982 9.990868 AGACAGTCCCATAAACCTTAATAAAAT 57.009 29.630 0.00 0.00 0.00 1.82
596 3989 9.804758 CCCATAAACCTTAATAAAATAAACGCA 57.195 29.630 0.00 0.00 0.00 5.24
601 3994 9.581099 AAACCTTAATAAAATAAACGCATGAGG 57.419 29.630 0.00 0.00 0.00 3.86
602 3995 7.200455 ACCTTAATAAAATAAACGCATGAGGC 58.800 34.615 0.00 0.00 39.90 4.70
603 3996 6.640907 CCTTAATAAAATAAACGCATGAGGCC 59.359 38.462 0.00 0.00 40.31 5.19
604 3997 2.559998 AAAATAAACGCATGAGGCCG 57.440 45.000 0.00 0.00 40.31 6.13
605 3998 0.738389 AAATAAACGCATGAGGCCGG 59.262 50.000 0.00 0.00 40.31 6.13
606 3999 1.101049 AATAAACGCATGAGGCCGGG 61.101 55.000 2.18 0.00 40.31 5.73
607 4000 2.958578 ATAAACGCATGAGGCCGGGG 62.959 60.000 2.18 0.00 40.31 5.73
618 4011 4.209866 GCCGGGGCCATCATCCTT 62.210 66.667 4.39 0.00 34.56 3.36
619 4012 2.603008 CCGGGGCCATCATCCTTT 59.397 61.111 4.39 0.00 0.00 3.11
620 4013 1.076044 CCGGGGCCATCATCCTTTT 60.076 57.895 4.39 0.00 0.00 2.27
621 4014 1.109323 CCGGGGCCATCATCCTTTTC 61.109 60.000 4.39 0.00 0.00 2.29
622 4015 1.109323 CGGGGCCATCATCCTTTTCC 61.109 60.000 4.39 0.00 0.00 3.13
623 4016 0.032217 GGGGCCATCATCCTTTTCCA 60.032 55.000 4.39 0.00 0.00 3.53
624 4017 1.622173 GGGGCCATCATCCTTTTCCAA 60.622 52.381 4.39 0.00 0.00 3.53
625 4018 2.187100 GGGCCATCATCCTTTTCCAAA 58.813 47.619 4.39 0.00 0.00 3.28
626 4019 2.571202 GGGCCATCATCCTTTTCCAAAA 59.429 45.455 4.39 0.00 0.00 2.44
627 4020 3.008923 GGGCCATCATCCTTTTCCAAAAA 59.991 43.478 4.39 0.00 0.00 1.94
641 4034 3.051479 AAAAAGGTACCGGCGCCG 61.051 61.111 41.00 41.00 39.44 6.46
654 4047 4.891727 CGCCGGGGGACTTCATCG 62.892 72.222 11.42 0.00 0.00 3.84
656 4049 3.470888 CCGGGGGACTTCATCGCT 61.471 66.667 0.00 0.00 40.16 4.93
657 4050 2.202932 CGGGGGACTTCATCGCTG 60.203 66.667 0.00 0.00 40.16 5.18
658 4051 2.190578 GGGGGACTTCATCGCTGG 59.809 66.667 0.00 0.00 40.16 4.85
659 4052 2.514824 GGGGACTTCATCGCTGGC 60.515 66.667 0.00 0.00 40.16 4.85
660 4053 2.268920 GGGACTTCATCGCTGGCA 59.731 61.111 0.00 0.00 37.30 4.92
661 4054 2.109126 GGGACTTCATCGCTGGCAC 61.109 63.158 0.00 0.00 37.30 5.01
662 4055 1.078848 GGACTTCATCGCTGGCACT 60.079 57.895 0.00 0.00 0.00 4.40
663 4056 0.175760 GGACTTCATCGCTGGCACTA 59.824 55.000 0.00 0.00 0.00 2.74
664 4057 1.405526 GGACTTCATCGCTGGCACTAA 60.406 52.381 0.00 0.00 0.00 2.24
665 4058 2.555199 GACTTCATCGCTGGCACTAAT 58.445 47.619 0.00 0.00 0.00 1.73
666 4059 3.492656 GGACTTCATCGCTGGCACTAATA 60.493 47.826 0.00 0.00 0.00 0.98
710 4103 2.994995 ATGCTGTCCACGTCCGGA 60.995 61.111 0.00 0.00 0.00 5.14
736 4129 4.268405 GGACTAGAAGTCTAGAACTCGTCG 59.732 50.000 19.82 0.00 46.80 5.12
745 4138 1.513586 GAACTCGTCGCCGTGTAGG 60.514 63.158 0.00 0.00 39.65 3.18
750 4143 1.599071 CTCGTCGCCGTGTAGGTATAA 59.401 52.381 0.00 0.00 43.70 0.98
862 4255 8.301730 TCAAAGTAATACTCCGTAAAACACAG 57.698 34.615 0.00 0.00 0.00 3.66
863 4256 7.385752 TCAAAGTAATACTCCGTAAAACACAGG 59.614 37.037 0.00 0.00 0.00 4.00
864 4257 5.173664 AGTAATACTCCGTAAAACACAGGC 58.826 41.667 0.00 0.00 0.00 4.85
865 4258 2.068837 TACTCCGTAAAACACAGGCG 57.931 50.000 0.00 0.00 0.00 5.52
866 4259 1.226030 ACTCCGTAAAACACAGGCGC 61.226 55.000 0.00 0.00 0.00 6.53
867 4260 1.225376 CTCCGTAAAACACAGGCGCA 61.225 55.000 10.83 0.00 0.00 6.09
868 4261 0.814410 TCCGTAAAACACAGGCGCAA 60.814 50.000 10.83 0.00 0.00 4.85
869 4262 0.659123 CCGTAAAACACAGGCGCAAC 60.659 55.000 10.83 0.00 0.00 4.17
870 4263 0.028242 CGTAAAACACAGGCGCAACA 59.972 50.000 10.83 0.00 0.00 3.33
871 4264 1.753956 GTAAAACACAGGCGCAACAG 58.246 50.000 10.83 0.00 0.00 3.16
873 4266 2.627510 AAAACACAGGCGCAACAGGC 62.628 55.000 10.83 0.00 39.90 4.85
890 4283 3.052082 CGCCTGTTGCCCTCTGTG 61.052 66.667 0.00 0.00 36.24 3.66
891 4284 2.113986 GCCTGTTGCCCTCTGTGT 59.886 61.111 0.00 0.00 0.00 3.72
922 4315 3.430218 CGACATCAAGATCGATTAAGGCC 59.570 47.826 0.00 0.00 40.86 5.19
960 4353 4.615815 ATCGATCCAGCAGGCCGC 62.616 66.667 11.02 11.02 42.91 6.53
1010 4403 1.065764 CCGCTAGCATGTACGAGCA 59.934 57.895 16.45 0.00 38.09 4.26
1058 4451 0.894184 TCGTCAAGGTCGAGGCTTCT 60.894 55.000 0.00 0.00 33.38 2.85
1066 4459 1.016653 GTCGAGGCTTCTCCAACAGC 61.017 60.000 0.00 0.00 37.29 4.40
1072 4465 0.391661 GCTTCTCCAACAGCCGATCA 60.392 55.000 0.00 0.00 0.00 2.92
1209 4602 1.267261 CCTTACACGCTATCTCCCGAG 59.733 57.143 0.00 0.00 0.00 4.63
1290 4692 1.228644 AGCAGTGCAGGCATTCCAA 60.229 52.632 19.20 0.00 33.74 3.53
1311 4713 3.479979 GGAGACCCCAAGACCGTT 58.520 61.111 0.00 0.00 34.14 4.44
1395 4845 0.770008 CGCACGCAACTAGTTTTTGC 59.230 50.000 17.38 17.38 44.94 3.68
1409 4859 8.879427 ACTAGTTTTTGCTAGGTATTCCAAAT 57.121 30.769 0.00 0.00 41.93 2.32
1414 4864 7.925043 TTTTGCTAGGTATTCCAAATCGTAA 57.075 32.000 0.00 0.00 35.89 3.18
1423 4873 8.248945 AGGTATTCCAAATCGTAATCCTATACG 58.751 37.037 0.69 0.69 41.89 3.06
1425 4875 7.884816 ATTCCAAATCGTAATCCTATACGTG 57.115 36.000 0.00 0.00 46.57 4.49
1525 4975 5.965922 TGGAGTCTATGTAATCATATGCCG 58.034 41.667 0.00 0.00 36.18 5.69
1534 4984 6.516739 TGTAATCATATGCCGGTTTCAAAA 57.483 33.333 1.90 0.00 0.00 2.44
1594 5044 8.231837 TGCCGTGTTTTTCTACAGATTAATTAC 58.768 33.333 0.00 0.00 0.00 1.89
1595 5045 8.231837 GCCGTGTTTTTCTACAGATTAATTACA 58.768 33.333 0.00 0.00 0.00 2.41
1596 5046 9.537848 CCGTGTTTTTCTACAGATTAATTACAC 57.462 33.333 0.00 0.00 0.00 2.90
1603 5053 7.751047 TCTACAGATTAATTACACTTGTCGC 57.249 36.000 0.00 0.00 0.00 5.19
1604 5054 5.796350 ACAGATTAATTACACTTGTCGCC 57.204 39.130 0.00 0.00 0.00 5.54
1605 5055 5.488341 ACAGATTAATTACACTTGTCGCCT 58.512 37.500 0.00 0.00 0.00 5.52
1606 5056 5.581085 ACAGATTAATTACACTTGTCGCCTC 59.419 40.000 0.00 0.00 0.00 4.70
1607 5057 5.006746 CAGATTAATTACACTTGTCGCCTCC 59.993 44.000 0.00 0.00 0.00 4.30
1608 5058 2.109425 AATTACACTTGTCGCCTCCC 57.891 50.000 0.00 0.00 0.00 4.30
1609 5059 0.252197 ATTACACTTGTCGCCTCCCC 59.748 55.000 0.00 0.00 0.00 4.81
1610 5060 0.834687 TTACACTTGTCGCCTCCCCT 60.835 55.000 0.00 0.00 0.00 4.79
1611 5061 0.040058 TACACTTGTCGCCTCCCCTA 59.960 55.000 0.00 0.00 0.00 3.53
1612 5062 0.834687 ACACTTGTCGCCTCCCCTAA 60.835 55.000 0.00 0.00 0.00 2.69
1613 5063 0.323629 CACTTGTCGCCTCCCCTAAA 59.676 55.000 0.00 0.00 0.00 1.85
1614 5064 1.061546 ACTTGTCGCCTCCCCTAAAA 58.938 50.000 0.00 0.00 0.00 1.52
1615 5065 1.422402 ACTTGTCGCCTCCCCTAAAAA 59.578 47.619 0.00 0.00 0.00 1.94
1738 5205 1.359117 GATCCGATCGCCGACAAGA 59.641 57.895 10.32 0.00 41.76 3.02
1740 5207 1.384989 ATCCGATCGCCGACAAGAGT 61.385 55.000 10.32 0.00 41.76 3.24
1764 5231 2.294074 TCTCGTTCCAACACTTTTGGG 58.706 47.619 3.25 0.00 39.96 4.12
1804 5273 6.935771 AGCATTGCAATAGATTTTTGTTTCCA 59.064 30.769 12.53 0.00 0.00 3.53
1830 5301 9.899226 ATGCTTTGTTTGTTTTCTATCTCTTAC 57.101 29.630 0.00 0.00 0.00 2.34
1831 5302 9.120538 TGCTTTGTTTGTTTTCTATCTCTTACT 57.879 29.630 0.00 0.00 0.00 2.24
1840 5311 9.640963 TGTTTTCTATCTCTTACTAGAAGTTGC 57.359 33.333 0.00 0.00 35.86 4.17
1873 5344 4.887655 AGAAAAATCGGTGGAAAGTTGAGT 59.112 37.500 0.00 0.00 0.00 3.41
1915 5386 6.261158 TCTCATAACCTTCACATAGAGACTCG 59.739 42.308 0.00 0.00 0.00 4.18
1919 5390 4.337145 ACCTTCACATAGAGACTCGAGTT 58.663 43.478 21.08 9.71 0.00 3.01
1920 5391 4.396790 ACCTTCACATAGAGACTCGAGTTC 59.603 45.833 21.08 17.69 0.00 3.01
1939 5410 3.144657 TCTCTTCCAACACATGCATGT 57.855 42.857 26.61 26.61 42.84 3.21
1950 5421 3.378112 ACACATGCATGTTTCCGGAATAG 59.622 43.478 29.48 16.00 39.39 1.73
2034 5554 1.810853 CATCTCGTGCATGCGACCA 60.811 57.895 14.09 0.43 36.80 4.02
2042 5562 0.521291 TGCATGCGACCAAAAGTAGC 59.479 50.000 14.09 0.00 46.38 3.58
2046 5566 1.866925 GCGACCAAAAGTAGCGCTT 59.133 52.632 18.68 0.00 43.85 4.68
2052 5572 1.135859 CCAAAAGTAGCGCTTCAGCAG 60.136 52.381 18.68 2.00 42.21 4.24
2056 5576 1.444553 GTAGCGCTTCAGCAGTCGT 60.445 57.895 18.68 0.00 42.21 4.34
2083 5603 2.844122 AAACAAGGTTCAACACGCTC 57.156 45.000 0.00 0.00 0.00 5.03
2085 5605 0.179094 ACAAGGTTCAACACGCTCGA 60.179 50.000 0.00 0.00 0.00 4.04
2098 5618 0.024238 CGCTCGAGAAAACTGCATCG 59.976 55.000 18.75 1.63 36.54 3.84
2101 5621 0.666274 TCGAGAAAACTGCATCGCGT 60.666 50.000 5.77 0.00 39.42 6.01
2158 5678 1.565390 AATCTGGGCTGCTGCAGGTA 61.565 55.000 29.05 5.29 41.91 3.08
2161 5681 4.496336 GGGCTGCTGCAGGTAGGG 62.496 72.222 29.05 5.87 41.91 3.53
2177 5697 3.134127 GGCAGCGGGATTGGACAC 61.134 66.667 0.00 0.00 0.00 3.67
2189 5709 0.179161 TTGGACACCGTGTTTTTGCG 60.179 50.000 5.45 0.00 0.00 4.85
2190 5710 1.942223 GGACACCGTGTTTTTGCGC 60.942 57.895 5.45 0.00 0.00 6.09
2193 5713 0.524604 ACACCGTGTTTTTGCGCTTC 60.525 50.000 9.73 0.00 0.00 3.86
2213 5733 2.880963 TGGTAAAGCAAAACACCAGC 57.119 45.000 0.00 0.00 36.15 4.85
2239 5759 1.726659 CGCTAAAACGCTATTTCGGC 58.273 50.000 0.00 0.00 0.00 5.54
2265 5785 4.450955 AAAAATTAGTGCGCCGCG 57.549 50.000 8.83 8.83 0.00 6.46
2307 5827 8.296713 TGGAGATGCTCTTAACAAATAAAACAC 58.703 33.333 0.00 0.00 0.00 3.32
2351 5871 5.714047 TCGATGATATGCTAAACAGCCTAG 58.286 41.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 169 7.725251 ACTCTGGAATTACAGAAAATTTGCAA 58.275 30.769 20.85 0.00 46.05 4.08
297 324 4.036734 TCACCAGCTTCACAAATTCTTCAC 59.963 41.667 0.00 0.00 0.00 3.18
347 375 1.717032 ACAGGTCAGGAGCACTTGTA 58.283 50.000 0.97 0.00 32.65 2.41
350 378 2.310779 TCTACAGGTCAGGAGCACTT 57.689 50.000 0.97 0.00 0.00 3.16
355 383 2.099921 CGGACAATCTACAGGTCAGGAG 59.900 54.545 0.00 0.00 33.26 3.69
398 426 1.343465 GACCTGGTCGAGGAAGAACAA 59.657 52.381 11.71 0.00 46.33 2.83
423 451 3.611766 AGAACAATAGAACGGGTCAGG 57.388 47.619 0.00 0.00 0.00 3.86
425 453 6.703319 TCAAATAGAACAATAGAACGGGTCA 58.297 36.000 0.00 0.00 0.00 4.02
426 454 7.605410 TTCAAATAGAACAATAGAACGGGTC 57.395 36.000 0.00 0.00 0.00 4.46
427 455 7.989416 TTTCAAATAGAACAATAGAACGGGT 57.011 32.000 0.00 0.00 35.56 5.28
433 461 9.594478 TCGCTGTATTTCAAATAGAACAATAGA 57.406 29.630 0.00 0.00 35.56 1.98
434 462 9.638300 GTCGCTGTATTTCAAATAGAACAATAG 57.362 33.333 0.00 0.00 35.56 1.73
437 465 7.386573 TCTGTCGCTGTATTTCAAATAGAACAA 59.613 33.333 0.00 0.00 35.56 2.83
438 466 6.871492 TCTGTCGCTGTATTTCAAATAGAACA 59.129 34.615 0.00 0.00 35.56 3.18
442 3835 6.311445 ACTGTCTGTCGCTGTATTTCAAATAG 59.689 38.462 0.00 0.00 0.00 1.73
470 3863 0.266152 TCCAAAACCAACCCCCACAT 59.734 50.000 0.00 0.00 0.00 3.21
535 3928 9.809096 TTTAGCATTTGACTGTTTTACAATTGA 57.191 25.926 13.59 0.00 31.15 2.57
579 3972 6.359617 CGGCCTCATGCGTTTATTTTATTAAG 59.640 38.462 0.00 0.00 42.61 1.85
580 3973 6.202937 CGGCCTCATGCGTTTATTTTATTAA 58.797 36.000 0.00 0.00 42.61 1.40
581 3974 5.278071 CCGGCCTCATGCGTTTATTTTATTA 60.278 40.000 0.00 0.00 42.61 0.98
582 3975 4.499019 CCGGCCTCATGCGTTTATTTTATT 60.499 41.667 0.00 0.00 42.61 1.40
583 3976 3.004315 CCGGCCTCATGCGTTTATTTTAT 59.996 43.478 0.00 0.00 42.61 1.40
584 3977 2.356382 CCGGCCTCATGCGTTTATTTTA 59.644 45.455 0.00 0.00 42.61 1.52
585 3978 1.134175 CCGGCCTCATGCGTTTATTTT 59.866 47.619 0.00 0.00 42.61 1.82
586 3979 0.738389 CCGGCCTCATGCGTTTATTT 59.262 50.000 0.00 0.00 42.61 1.40
587 3980 1.101049 CCCGGCCTCATGCGTTTATT 61.101 55.000 0.00 0.00 42.61 1.40
588 3981 1.525995 CCCGGCCTCATGCGTTTAT 60.526 57.895 0.00 0.00 42.61 1.40
589 3982 2.124901 CCCGGCCTCATGCGTTTA 60.125 61.111 0.00 0.00 42.61 2.01
601 3994 3.738745 AAAGGATGATGGCCCCGGC 62.739 63.158 0.00 0.00 41.06 6.13
602 3995 1.076044 AAAAGGATGATGGCCCCGG 60.076 57.895 0.00 0.00 0.00 5.73
603 3996 1.109323 GGAAAAGGATGATGGCCCCG 61.109 60.000 0.00 0.00 0.00 5.73
604 3997 0.032217 TGGAAAAGGATGATGGCCCC 60.032 55.000 0.00 0.00 0.00 5.80
605 3998 1.864669 TTGGAAAAGGATGATGGCCC 58.135 50.000 0.00 0.00 0.00 5.80
606 3999 3.979101 TTTTGGAAAAGGATGATGGCC 57.021 42.857 0.00 0.00 0.00 5.36
624 4017 3.051479 CGGCGCCGGTACCTTTTT 61.051 61.111 40.50 0.00 35.56 1.94
637 4030 4.891727 CGATGAAGTCCCCCGGCG 62.892 72.222 0.00 0.00 0.00 6.46
639 4032 3.470888 AGCGATGAAGTCCCCCGG 61.471 66.667 0.00 0.00 0.00 5.73
640 4033 2.202932 CAGCGATGAAGTCCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
641 4034 2.190578 CCAGCGATGAAGTCCCCC 59.809 66.667 0.06 0.00 0.00 5.40
642 4035 2.514824 GCCAGCGATGAAGTCCCC 60.515 66.667 0.06 0.00 0.00 4.81
643 4036 2.109126 GTGCCAGCGATGAAGTCCC 61.109 63.158 0.06 0.00 0.00 4.46
644 4037 0.175760 TAGTGCCAGCGATGAAGTCC 59.824 55.000 0.06 0.00 0.00 3.85
645 4038 2.010145 TTAGTGCCAGCGATGAAGTC 57.990 50.000 0.06 0.00 0.00 3.01
646 4039 2.698855 ATTAGTGCCAGCGATGAAGT 57.301 45.000 0.06 0.00 0.00 3.01
647 4040 3.722147 ACTATTAGTGCCAGCGATGAAG 58.278 45.455 0.06 0.00 0.00 3.02
648 4041 3.819564 ACTATTAGTGCCAGCGATGAA 57.180 42.857 0.06 0.00 0.00 2.57
649 4042 3.492656 GGAACTATTAGTGCCAGCGATGA 60.493 47.826 15.11 0.00 43.85 2.92
650 4043 2.802816 GGAACTATTAGTGCCAGCGATG 59.197 50.000 15.11 0.00 43.85 3.84
651 4044 3.113260 GGAACTATTAGTGCCAGCGAT 57.887 47.619 15.11 0.00 43.85 4.58
652 4045 2.596904 GGAACTATTAGTGCCAGCGA 57.403 50.000 15.11 0.00 43.85 4.93
657 4050 1.867166 GCCGAGGAACTATTAGTGCC 58.133 55.000 12.47 12.47 44.82 5.01
658 4051 1.066605 TCGCCGAGGAACTATTAGTGC 59.933 52.381 0.00 0.00 41.55 4.40
659 4052 3.309388 CATCGCCGAGGAACTATTAGTG 58.691 50.000 0.00 0.00 41.55 2.74
660 4053 2.296471 CCATCGCCGAGGAACTATTAGT 59.704 50.000 0.00 0.00 41.55 2.24
661 4054 2.296471 ACCATCGCCGAGGAACTATTAG 59.704 50.000 0.00 0.00 41.55 1.73
662 4055 2.035449 CACCATCGCCGAGGAACTATTA 59.965 50.000 0.00 0.00 41.55 0.98
663 4056 1.120530 ACCATCGCCGAGGAACTATT 58.879 50.000 0.00 0.00 41.55 1.73
664 4057 0.389391 CACCATCGCCGAGGAACTAT 59.611 55.000 0.00 0.00 41.55 2.12
665 4058 1.672854 CCACCATCGCCGAGGAACTA 61.673 60.000 0.00 0.00 41.55 2.24
710 4103 6.181908 ACGAGTTCTAGACTTCTAGTCCAAT 58.818 40.000 12.11 0.00 46.18 3.16
736 4129 3.220940 AGGAGTCTTATACCTACACGGC 58.779 50.000 0.00 0.00 35.61 5.68
873 4266 3.052082 CACAGAGGGCAACAGGCG 61.052 66.667 0.00 0.00 46.16 5.52
874 4267 1.968540 GACACAGAGGGCAACAGGC 60.969 63.158 0.00 0.00 43.74 4.85
875 4268 1.302832 GGACACAGAGGGCAACAGG 60.303 63.158 0.00 0.00 39.74 4.00
878 4271 2.358737 CGGGACACAGAGGGCAAC 60.359 66.667 0.00 0.00 0.00 4.17
882 4275 4.742201 CACGCGGGACACAGAGGG 62.742 72.222 12.47 0.00 0.00 4.30
891 4284 4.365505 TTGATGTCGCACGCGGGA 62.366 61.111 15.48 1.68 40.25 5.14
922 4315 2.025969 CTCACGCCAGCTGACACAG 61.026 63.158 17.39 0.00 34.12 3.66
960 4353 2.457366 ACGACCAGGAAGCAAACTAG 57.543 50.000 0.00 0.00 0.00 2.57
964 4357 0.390124 ACGTACGACCAGGAAGCAAA 59.610 50.000 24.41 0.00 0.00 3.68
1010 4403 2.028385 GTGGAGTACTTTCCGATGGTGT 60.028 50.000 0.00 0.00 40.27 4.16
1058 4451 1.296392 CCACTGATCGGCTGTTGGA 59.704 57.895 0.00 0.00 0.00 3.53
1310 4712 2.675242 CCATACGGGCAGGGGACAA 61.675 63.158 0.00 0.00 0.00 3.18
1311 4713 3.087253 CCATACGGGCAGGGGACA 61.087 66.667 0.00 0.00 0.00 4.02
1409 4859 4.398988 ACACCAACACGTATAGGATTACGA 59.601 41.667 10.61 0.00 46.02 3.43
1414 4864 2.756760 ACGACACCAACACGTATAGGAT 59.243 45.455 6.37 0.00 38.47 3.24
1423 4873 2.735134 GACTATCCAACGACACCAACAC 59.265 50.000 0.00 0.00 0.00 3.32
1425 4875 3.314541 AGACTATCCAACGACACCAAC 57.685 47.619 0.00 0.00 0.00 3.77
1534 4984 8.500773 CGCACGGTATGACCTTTTTATATATTT 58.499 33.333 0.00 0.00 35.66 1.40
1537 4987 6.421501 CACGCACGGTATGACCTTTTTATATA 59.578 38.462 0.00 0.00 35.66 0.86
1539 4989 4.567558 CACGCACGGTATGACCTTTTTATA 59.432 41.667 0.00 0.00 35.66 0.98
1541 4991 2.737783 CACGCACGGTATGACCTTTTTA 59.262 45.455 0.00 0.00 35.66 1.52
1543 4993 1.153353 CACGCACGGTATGACCTTTT 58.847 50.000 0.00 0.00 35.66 2.27
1544 4994 0.034337 ACACGCACGGTATGACCTTT 59.966 50.000 0.00 0.00 35.66 3.11
1545 4995 0.669318 CACACGCACGGTATGACCTT 60.669 55.000 0.00 0.00 35.66 3.50
1546 4996 1.080093 CACACGCACGGTATGACCT 60.080 57.895 0.00 0.00 35.66 3.85
1547 4997 0.947180 AACACACGCACGGTATGACC 60.947 55.000 0.00 0.00 34.05 4.02
1548 4998 0.863144 AAACACACGCACGGTATGAC 59.137 50.000 0.00 0.00 0.00 3.06
1549 4999 1.261885 CAAAACACACGCACGGTATGA 59.738 47.619 0.00 0.00 0.00 2.15
1550 5000 1.669184 CAAAACACACGCACGGTATG 58.331 50.000 0.00 0.00 0.00 2.39
1594 5044 0.323629 TTTAGGGGAGGCGACAAGTG 59.676 55.000 0.00 0.00 0.00 3.16
1595 5045 1.061546 TTTTAGGGGAGGCGACAAGT 58.938 50.000 0.00 0.00 0.00 3.16
1596 5046 2.194201 TTTTTAGGGGAGGCGACAAG 57.806 50.000 0.00 0.00 0.00 3.16
1614 5064 6.539464 TCCGGCGACAAGTGTAATATATTTTT 59.461 34.615 9.30 0.00 0.00 1.94
1615 5065 6.050432 TCCGGCGACAAGTGTAATATATTTT 58.950 36.000 9.30 0.00 0.00 1.82
1616 5066 5.603596 TCCGGCGACAAGTGTAATATATTT 58.396 37.500 9.30 0.00 0.00 1.40
1617 5067 5.010314 TCTCCGGCGACAAGTGTAATATATT 59.990 40.000 9.30 2.97 0.00 1.28
1618 5068 4.521639 TCTCCGGCGACAAGTGTAATATAT 59.478 41.667 9.30 0.00 0.00 0.86
1619 5069 3.884693 TCTCCGGCGACAAGTGTAATATA 59.115 43.478 9.30 0.00 0.00 0.86
1620 5070 2.691526 TCTCCGGCGACAAGTGTAATAT 59.308 45.455 9.30 0.00 0.00 1.28
1621 5071 2.093890 TCTCCGGCGACAAGTGTAATA 58.906 47.619 9.30 0.00 0.00 0.98
1622 5072 0.892755 TCTCCGGCGACAAGTGTAAT 59.107 50.000 9.30 0.00 0.00 1.89
1623 5073 0.892755 ATCTCCGGCGACAAGTGTAA 59.107 50.000 9.30 0.00 0.00 2.41
1624 5074 0.172578 CATCTCCGGCGACAAGTGTA 59.827 55.000 9.30 0.00 0.00 2.90
1625 5075 1.079819 CATCTCCGGCGACAAGTGT 60.080 57.895 9.30 0.00 0.00 3.55
1626 5076 1.078759 GTCATCTCCGGCGACAAGTG 61.079 60.000 9.30 0.30 0.00 3.16
1695 5145 2.358247 AACGCCGGTGCAACTAGG 60.358 61.111 16.69 0.00 37.32 3.02
1738 5205 3.261981 AGTGTTGGAACGAGAACAACT 57.738 42.857 14.32 0.00 43.54 3.16
1740 5207 4.380023 CCAAAAGTGTTGGAACGAGAACAA 60.380 41.667 6.16 0.00 42.06 2.83
1764 5231 3.796717 GCAATGCTAAAGGAATAAACGGC 59.203 43.478 0.00 0.00 0.00 5.68
1804 5273 9.899226 GTAAGAGATAGAAAACAAACAAAGCAT 57.101 29.630 0.00 0.00 0.00 3.79
1830 5301 6.377327 TTCTTTTGGACAAGCAACTTCTAG 57.623 37.500 0.00 0.00 0.00 2.43
1831 5302 6.767524 TTTCTTTTGGACAAGCAACTTCTA 57.232 33.333 0.00 0.00 0.00 2.10
1832 5303 5.659440 TTTCTTTTGGACAAGCAACTTCT 57.341 34.783 0.00 0.00 0.00 2.85
1840 5311 4.744631 CCACCGATTTTTCTTTTGGACAAG 59.255 41.667 0.00 0.00 0.00 3.16
1873 5344 9.778741 GGTTATGAGATGTATTTAATGGACTGA 57.221 33.333 0.00 0.00 0.00 3.41
1915 5386 3.141398 TGCATGTGTTGGAAGAGAACTC 58.859 45.455 0.00 0.00 0.00 3.01
1919 5390 3.144657 ACATGCATGTGTTGGAAGAGA 57.855 42.857 30.92 0.00 40.03 3.10
1920 5391 3.928727 AACATGCATGTGTTGGAAGAG 57.071 42.857 31.98 1.70 40.60 2.85
2026 5546 1.794222 GCGCTACTTTTGGTCGCAT 59.206 52.632 0.00 0.00 44.50 4.73
2034 5554 1.801178 GACTGCTGAAGCGCTACTTTT 59.199 47.619 12.05 0.00 45.83 2.27
2042 5562 3.037833 TGCACGACTGCTGAAGCG 61.038 61.111 0.00 0.88 44.57 4.68
2046 5566 2.077821 TTACCGTGCACGACTGCTGA 62.078 55.000 39.10 14.90 44.57 4.26
2052 5572 0.233848 CCTTGTTTACCGTGCACGAC 59.766 55.000 39.10 27.99 43.02 4.34
2056 5576 2.039818 TGAACCTTGTTTACCGTGCA 57.960 45.000 0.00 0.00 0.00 4.57
2083 5603 0.517132 CACGCGATGCAGTTTTCTCG 60.517 55.000 15.93 0.85 0.00 4.04
2101 5621 1.363145 GGCGCACCAAATACGTAGCA 61.363 55.000 10.83 0.00 35.26 3.49
2130 5650 0.963962 CAGCCCAGATTTTGCAGTGT 59.036 50.000 0.00 0.00 0.00 3.55
2132 5652 0.541296 AGCAGCCCAGATTTTGCAGT 60.541 50.000 0.00 0.00 38.97 4.40
2158 5678 4.115199 GTCCAATCCCGCTGCCCT 62.115 66.667 0.00 0.00 0.00 5.19
2161 5681 3.134127 GGTGTCCAATCCCGCTGC 61.134 66.667 0.00 0.00 0.00 5.25
2167 5687 2.738135 CAAAAACACGGTGTCCAATCC 58.262 47.619 15.09 0.00 0.00 3.01
2177 5697 0.934436 CCAGAAGCGCAAAAACACGG 60.934 55.000 11.47 0.00 0.00 4.94
2190 5710 4.647424 TGGTGTTTTGCTTTACCAGAAG 57.353 40.909 0.00 0.00 38.23 2.85
2271 5791 3.084579 CATCTCCAACAGACGCGC 58.915 61.111 5.73 0.00 32.26 6.86
2292 5812 7.009357 GTGTTTGAGCGGTGTTTTATTTGTTAA 59.991 33.333 0.00 0.00 0.00 2.01
2307 5827 0.804989 GATCCCTTGTGTTTGAGCGG 59.195 55.000 0.00 0.00 0.00 5.52
2351 5871 2.295885 CAGCTCATTGGGAGGATGAAC 58.704 52.381 0.00 0.00 44.22 3.18


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

AutoCloner maintained by Alex Coulton.