Multiple sequence alignment - TraesCS5D01G557300

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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 TraesCS5D01G557300 chr5D 100.000 3454 0 0 1 3454 559895651 559899104 0.000000e+00 6379.0
1 TraesCS5D01G557300 chr5B 94.291 2610 127 11 850 3454 694172589 694175181 0.000000e+00 3975.0
2 TraesCS5D01G557300 chr5B 91.919 495 20 6 88 581 694171066 694171541 0.000000e+00 675.0
3 TraesCS5D01G557300 chr5B 91.279 172 10 4 598 768 694171848 694172015 2.680000e-56 230.0
4 TraesCS5D01G557300 chr4A 90.243 2224 134 31 852 3045 613417735 613419905 0.000000e+00 2828.0
5 TraesCS5D01G557300 chr4A 91.925 483 27 9 88 568 613415994 613416466 0.000000e+00 665.0
6 TraesCS5D01G557300 chr4A 93.888 409 23 2 3047 3454 613419991 613420398 1.760000e-172 616.0
7 TraesCS5D01G557300 chr4A 86.364 88 8 3 1 86 613415873 613415958 3.670000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G557300 chr5D 559895651 559899104 3453 False 6379.000000 6379 100.000000 1 3454 1 chr5D.!!$F1 3453
1 TraesCS5D01G557300 chr5B 694171066 694175181 4115 False 1626.666667 3975 92.496333 88 3454 3 chr5B.!!$F1 3366
2 TraesCS5D01G557300 chr4A 613415873 613420398 4525 False 1050.625000 2828 90.605000 1 3454 4 chr4A.!!$F1 3453

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
591 629 0.112995 TCAAACCAGAGCTGCCCATT 59.887 50.0 0.0 0.0 0.00 3.16 F
593 631 0.112995 AAACCAGAGCTGCCCATTGA 59.887 50.0 0.0 0.0 0.00 2.57 F
1398 2627 0.322648 TCTCCGTCTACGTCAGGTCA 59.677 55.0 0.0 0.0 37.74 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 3182 0.376152 CACATGCTTCGACTCCATGC 59.624 55.0 15.26 2.19 39.86 4.06 R
1954 3183 1.012086 CCACATGCTTCGACTCCATG 58.988 55.0 14.25 14.25 41.49 3.66 R
2649 3901 0.445436 GTTCAGGTTGAGATGCAGCG 59.555 55.0 0.00 0.00 0.00 5.18 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
27 30 6.127310 GGTATTCTGACTGTGTACTCCTGATT 60.127 42.308 0.00 0.00 0.00 2.57
34 37 5.482908 ACTGTGTACTCCTGATTGTCATTC 58.517 41.667 0.00 0.00 0.00 2.67
35 38 5.012046 ACTGTGTACTCCTGATTGTCATTCA 59.988 40.000 0.00 0.00 0.00 2.57
36 39 5.237815 TGTGTACTCCTGATTGTCATTCAC 58.762 41.667 0.00 0.00 0.00 3.18
86 89 9.851686 ATTGACTCATAAATCTGCAGGTATTTA 57.148 29.630 15.13 16.91 33.39 1.40
127 164 3.266772 TCTTTCAGGGTATGATTGCTGGT 59.733 43.478 0.00 0.00 37.89 4.00
136 173 4.273480 GGTATGATTGCTGGTCATGTGTAC 59.727 45.833 8.62 0.00 36.96 2.90
151 188 5.958380 TCATGTGTACTACTTCCTGGAAGAT 59.042 40.000 36.38 23.94 41.71 2.40
263 300 2.721231 CACCCAACGCTGGTGTTG 59.279 61.111 17.02 17.02 46.62 3.33
416 453 6.677076 AGTATAATTCTCAGTTAGGGGTTGGT 59.323 38.462 0.00 0.00 0.00 3.67
441 479 2.404789 CCAATGCGCTGCTAACCG 59.595 61.111 9.73 0.00 0.00 4.44
444 482 0.378257 CAATGCGCTGCTAACCGAAT 59.622 50.000 9.73 0.00 0.00 3.34
457 495 4.809426 GCTAACCGAATTGTATGTAGCTGT 59.191 41.667 0.00 0.00 0.00 4.40
462 500 3.865164 CGAATTGTATGTAGCTGTGCTCA 59.135 43.478 0.00 0.00 40.44 4.26
467 505 3.701040 TGTATGTAGCTGTGCTCATGAGA 59.299 43.478 27.04 8.75 40.44 3.27
468 506 2.955477 TGTAGCTGTGCTCATGAGAG 57.045 50.000 27.04 15.47 44.96 3.20
469 507 1.479730 TGTAGCTGTGCTCATGAGAGG 59.520 52.381 27.04 12.56 42.33 3.69
470 508 0.463204 TAGCTGTGCTCATGAGAGGC 59.537 55.000 27.04 20.55 42.33 4.70
471 509 1.818785 GCTGTGCTCATGAGAGGCC 60.819 63.158 27.04 8.96 42.33 5.19
472 510 1.600638 CTGTGCTCATGAGAGGCCA 59.399 57.895 27.04 11.61 42.33 5.36
494 532 6.109359 CCATTGGTTGTTGGTTAACTTTGAA 58.891 36.000 5.42 0.00 37.68 2.69
523 561 0.250252 TTGTCTCATCTTGCGTGGCA 60.250 50.000 0.00 0.00 36.47 4.92
524 562 0.671472 TGTCTCATCTTGCGTGGCAG 60.671 55.000 0.00 0.00 40.61 4.85
525 563 0.671781 GTCTCATCTTGCGTGGCAGT 60.672 55.000 0.00 0.00 40.61 4.40
527 565 1.642037 CTCATCTTGCGTGGCAGTGG 61.642 60.000 0.00 0.00 40.61 4.00
528 566 3.058160 ATCTTGCGTGGCAGTGGC 61.058 61.111 10.30 10.30 40.61 5.01
529 567 3.848301 ATCTTGCGTGGCAGTGGCA 62.848 57.895 16.56 16.56 40.61 4.92
581 619 1.609208 GCTGAAGCCTTCAAACCAGA 58.391 50.000 8.74 0.00 39.58 3.86
582 620 1.538950 GCTGAAGCCTTCAAACCAGAG 59.461 52.381 8.74 0.00 39.58 3.35
584 622 1.143684 TGAAGCCTTCAAACCAGAGCT 59.856 47.619 4.27 0.00 36.59 4.09
585 623 1.538950 GAAGCCTTCAAACCAGAGCTG 59.461 52.381 0.00 0.00 0.00 4.24
586 624 0.892814 AGCCTTCAAACCAGAGCTGC 60.893 55.000 0.00 0.00 0.00 5.25
587 625 1.871126 GCCTTCAAACCAGAGCTGCC 61.871 60.000 0.00 0.00 0.00 4.85
588 626 1.246737 CCTTCAAACCAGAGCTGCCC 61.247 60.000 0.00 0.00 0.00 5.36
589 627 0.538057 CTTCAAACCAGAGCTGCCCA 60.538 55.000 0.00 0.00 0.00 5.36
591 629 0.112995 TCAAACCAGAGCTGCCCATT 59.887 50.000 0.00 0.00 0.00 3.16
593 631 0.112995 AAACCAGAGCTGCCCATTGA 59.887 50.000 0.00 0.00 0.00 2.57
594 632 0.112995 AACCAGAGCTGCCCATTGAA 59.887 50.000 0.00 0.00 0.00 2.69
703 1373 9.111613 TCTAAGCTTTGCTTCTACTAGTAGTAG 57.888 37.037 25.55 25.55 46.77 2.57
704 1374 7.706100 AAGCTTTGCTTCTACTAGTAGTAGT 57.294 36.000 28.50 14.57 46.77 2.73
706 1376 8.804912 AGCTTTGCTTCTACTAGTAGTAGTAA 57.195 34.615 28.50 25.53 46.31 2.24
708 1378 9.852091 GCTTTGCTTCTACTAGTAGTAGTAAAA 57.148 33.333 32.16 27.32 46.31 1.52
736 1406 5.106277 CGAAAGGAGAAACATTTAAGGGTCC 60.106 44.000 0.00 0.00 32.54 4.46
747 1417 5.843969 ACATTTAAGGGTCCCTTTGATTTGT 59.156 36.000 28.48 19.65 41.69 2.83
748 1418 7.013834 ACATTTAAGGGTCCCTTTGATTTGTA 58.986 34.615 28.48 4.86 41.69 2.41
749 1419 7.178451 ACATTTAAGGGTCCCTTTGATTTGTAG 59.822 37.037 28.48 11.97 41.69 2.74
750 1420 6.457159 TTAAGGGTCCCTTTGATTTGTAGA 57.543 37.500 28.48 3.28 41.69 2.59
751 1421 5.333566 AAGGGTCCCTTTGATTTGTAGAA 57.666 39.130 18.29 0.00 41.69 2.10
752 1422 5.536497 AGGGTCCCTTTGATTTGTAGAAT 57.464 39.130 3.85 0.00 0.00 2.40
753 1423 5.903923 AGGGTCCCTTTGATTTGTAGAATT 58.096 37.500 3.85 0.00 0.00 2.17
754 1424 5.952347 AGGGTCCCTTTGATTTGTAGAATTC 59.048 40.000 3.85 0.00 0.00 2.17
755 1425 5.952347 GGGTCCCTTTGATTTGTAGAATTCT 59.048 40.000 13.56 13.56 0.00 2.40
756 1426 6.095580 GGGTCCCTTTGATTTGTAGAATTCTC 59.904 42.308 12.24 4.68 0.00 2.87
757 1427 6.659242 GGTCCCTTTGATTTGTAGAATTCTCA 59.341 38.462 12.24 7.33 0.00 3.27
758 1428 7.176690 GGTCCCTTTGATTTGTAGAATTCTCAA 59.823 37.037 12.24 12.82 0.00 3.02
759 1429 8.576442 GTCCCTTTGATTTGTAGAATTCTCAAA 58.424 33.333 23.31 23.31 35.92 2.69
760 1430 9.142014 TCCCTTTGATTTGTAGAATTCTCAAAA 57.858 29.630 24.15 19.78 35.28 2.44
761 1431 9.196552 CCCTTTGATTTGTAGAATTCTCAAAAC 57.803 33.333 24.15 22.36 35.28 2.43
762 1432 8.905702 CCTTTGATTTGTAGAATTCTCAAAACG 58.094 33.333 24.15 13.12 35.28 3.60
763 1433 9.450807 CTTTGATTTGTAGAATTCTCAAAACGT 57.549 29.630 24.15 15.04 35.28 3.99
766 1436 8.717821 TGATTTGTAGAATTCTCAAAACGTAGG 58.282 33.333 24.15 0.00 35.28 3.18
767 1437 8.842358 ATTTGTAGAATTCTCAAAACGTAGGA 57.158 30.769 24.15 9.91 35.28 2.94
768 1438 7.647907 TTGTAGAATTCTCAAAACGTAGGAC 57.352 36.000 12.24 0.39 0.00 3.85
769 1439 6.751157 TGTAGAATTCTCAAAACGTAGGACA 58.249 36.000 12.24 3.22 0.00 4.02
770 1440 7.383687 TGTAGAATTCTCAAAACGTAGGACAT 58.616 34.615 12.24 0.00 0.00 3.06
771 1441 6.727824 AGAATTCTCAAAACGTAGGACATG 57.272 37.500 0.88 0.00 0.00 3.21
774 1444 3.734463 TCTCAAAACGTAGGACATGCAA 58.266 40.909 0.00 0.00 0.00 4.08
787 1457 4.828939 AGGACATGCAAGATTCTCAAAACA 59.171 37.500 0.00 0.00 0.00 2.83
796 1466 8.677300 TGCAAGATTCTCAAAACATAGGAATAC 58.323 33.333 0.00 0.00 0.00 1.89
812 1529 6.710597 AGGAATACGATTAGCAGAGTTGTA 57.289 37.500 0.00 0.00 0.00 2.41
813 1530 7.108841 AGGAATACGATTAGCAGAGTTGTAA 57.891 36.000 0.00 0.00 0.00 2.41
814 1531 7.553334 AGGAATACGATTAGCAGAGTTGTAAA 58.447 34.615 0.00 0.00 0.00 2.01
815 1532 8.038944 AGGAATACGATTAGCAGAGTTGTAAAA 58.961 33.333 0.00 0.00 0.00 1.52
818 1535 8.997621 ATACGATTAGCAGAGTTGTAAAAGAA 57.002 30.769 0.00 0.00 0.00 2.52
819 1536 7.118422 ACGATTAGCAGAGTTGTAAAAGAAC 57.882 36.000 0.00 0.00 0.00 3.01
820 1537 6.147328 ACGATTAGCAGAGTTGTAAAAGAACC 59.853 38.462 0.00 0.00 0.00 3.62
822 1539 4.439253 AGCAGAGTTGTAAAAGAACCCT 57.561 40.909 0.00 0.00 0.00 4.34
823 1540 4.137543 AGCAGAGTTGTAAAAGAACCCTG 58.862 43.478 0.00 0.00 33.53 4.45
831 1697 7.523415 AGTTGTAAAAGAACCCTGATAAGGAA 58.477 34.615 0.00 0.00 0.00 3.36
925 2154 7.831193 TCAAACCAAATTCAAATTCCCAAAAGA 59.169 29.630 0.00 0.00 0.00 2.52
942 2171 6.868339 CCCAAAAGATTTTAAGCCACAGTTAG 59.132 38.462 0.00 0.00 0.00 2.34
974 2203 2.162906 TCAAGCTTGGGCCCTCCTT 61.163 57.895 25.70 18.72 39.73 3.36
976 2205 2.923910 AAGCTTGGGCCCTCCTTCC 61.924 63.158 25.70 5.33 39.73 3.46
983 2212 2.298661 GGCCCTCCTTCCCTCGAAA 61.299 63.158 0.00 0.00 0.00 3.46
987 2216 0.690762 CCTCCTTCCCTCGAAAACCA 59.309 55.000 0.00 0.00 0.00 3.67
991 2220 1.265905 CCTTCCCTCGAAAACCAAACG 59.734 52.381 0.00 0.00 0.00 3.60
992 2221 1.265905 CTTCCCTCGAAAACCAAACGG 59.734 52.381 0.00 0.00 0.00 4.44
993 2222 0.469070 TCCCTCGAAAACCAAACGGA 59.531 50.000 0.00 0.00 0.00 4.69
1047 2276 2.046892 CTGACCAAGGCCCTGACG 60.047 66.667 1.80 0.00 0.00 4.35
1097 2326 4.760047 GCTCGCCTTCTTCGCCCA 62.760 66.667 0.00 0.00 0.00 5.36
1290 2519 2.883468 CGCGCTCGTCGTCTCCTAT 61.883 63.158 5.56 0.00 41.07 2.57
1299 2528 1.137086 GTCGTCTCCTATGGTGCATGT 59.863 52.381 0.00 0.00 0.00 3.21
1347 2576 1.298859 GCCTGTTCGACGAATTGCCT 61.299 55.000 14.27 0.00 0.00 4.75
1393 2622 1.947456 CCATGATCTCCGTCTACGTCA 59.053 52.381 0.00 0.00 37.74 4.35
1398 2627 0.322648 TCTCCGTCTACGTCAGGTCA 59.677 55.000 0.00 0.00 37.74 4.02
1408 2637 2.675423 TCAGGTCAGGGGACGTCG 60.675 66.667 9.92 0.00 45.28 5.12
1476 2705 1.347707 TCCTGCTTCAACTCGGTGATT 59.652 47.619 0.00 0.00 0.00 2.57
1500 2729 4.083862 GTGGCGGAGTCTGGGGAC 62.084 72.222 0.05 0.00 42.41 4.46
1532 2761 4.592936 CGTCGAGCTCTACCGGCG 62.593 72.222 12.85 8.78 46.93 6.46
1553 2782 4.864334 GCAGGGGATGGGCGTCAG 62.864 72.222 0.00 0.00 0.00 3.51
1596 2825 2.357517 CTCGTCCCTGTGTGCACC 60.358 66.667 15.69 6.37 0.00 5.01
1633 2862 3.625897 CGGTCAGGGAGGTGCACA 61.626 66.667 20.43 0.00 0.00 4.57
1641 2870 2.666190 GAGGTGCACAGCTTCGCA 60.666 61.111 20.43 2.65 39.57 5.10
1642 2871 2.033141 AGGTGCACAGCTTCGCAT 59.967 55.556 20.43 0.00 40.89 4.73
1671 2900 1.154413 CATGTTCGCGAGTTGCCAC 60.154 57.895 9.59 3.86 42.08 5.01
1687 2916 4.704103 ACCTCGGCAGCTCCCTCA 62.704 66.667 0.00 0.00 0.00 3.86
1703 2932 4.201679 CATCGAGGCGTACGGGCA 62.202 66.667 18.39 0.00 45.36 5.36
1737 2966 2.954611 GGCGCACAGAGGGTTTTC 59.045 61.111 10.83 0.00 0.00 2.29
1774 3003 2.022129 GACGTGGTTGTCTGGAGCG 61.022 63.158 0.00 0.00 35.95 5.03
1848 3077 0.760567 TCAGGCGTATGGAGCTGGAT 60.761 55.000 0.00 0.00 34.52 3.41
1920 3149 3.260483 GCTGGTCGCGCAGATGAG 61.260 66.667 16.55 7.09 0.00 2.90
1932 3161 2.349886 CGCAGATGAGGCTTTGAAGTAC 59.650 50.000 0.00 0.00 0.00 2.73
1935 3164 4.457257 GCAGATGAGGCTTTGAAGTACTTT 59.543 41.667 10.02 0.00 0.00 2.66
1953 3182 5.418310 ACTTTGATGTGTTAACCAAGACG 57.582 39.130 2.48 0.00 30.62 4.18
1954 3183 3.889196 TTGATGTGTTAACCAAGACGC 57.111 42.857 2.48 0.00 30.62 5.19
1962 3191 2.380084 TAACCAAGACGCATGGAGTC 57.620 50.000 8.54 0.00 40.56 3.36
1971 3200 1.086067 CGCATGGAGTCGAAGCATGT 61.086 55.000 3.30 0.00 29.24 3.21
1986 3215 5.467735 CGAAGCATGTGGAGATCATTATTCA 59.532 40.000 0.00 0.00 0.00 2.57
2182 3411 2.490903 CCAGAGAATGCAGGGAACTTTG 59.509 50.000 0.00 0.00 40.21 2.77
2197 3426 4.508052 GAACTTTGTTTCGCTTGCAAATG 58.492 39.130 0.00 0.00 32.61 2.32
2649 3901 8.041919 GCCCTAACCCTAAATCTATCAGAATAC 58.958 40.741 0.00 0.00 0.00 1.89
2831 4085 7.616150 GTCCTAGCCTGATCTTATTACCATCTA 59.384 40.741 0.00 0.00 0.00 1.98
2895 4149 9.176460 TCAATCTGACACTGCATGAATTTATAA 57.824 29.630 0.00 0.00 0.00 0.98
3128 4472 4.759782 TCTAATGCCACTCTGCTCTAAAC 58.240 43.478 0.00 0.00 0.00 2.01
3143 4487 5.053145 GCTCTAAACTGCTATGCACATAGT 58.947 41.667 16.82 0.00 42.07 2.12
3356 4701 6.657117 TGATGCTAATGTTGGTGCTACTTTAA 59.343 34.615 0.00 0.00 0.00 1.52
3369 4714 4.083537 TGCTACTTTAACAAAGGCACATCG 60.084 41.667 3.88 0.00 42.82 3.84
3387 4732 8.774586 GGCACATCGTATTAGAAAACTGATATT 58.225 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.705507 TCAGGAGTACACAGTCAGAATACC 59.294 45.833 0.00 0.00 0.00 2.73
6 7 4.588951 ACAATCAGGAGTACACAGTCAGAA 59.411 41.667 0.00 0.00 0.00 3.02
11 12 5.012046 TGAATGACAATCAGGAGTACACAGT 59.988 40.000 0.00 0.00 0.00 3.55
14 15 5.237815 TGTGAATGACAATCAGGAGTACAC 58.762 41.667 0.00 0.00 0.00 2.90
15 16 5.482163 TGTGAATGACAATCAGGAGTACA 57.518 39.130 0.00 0.00 0.00 2.90
16 17 6.820656 AGAATGTGAATGACAATCAGGAGTAC 59.179 38.462 0.00 0.00 37.00 2.73
17 18 6.950842 AGAATGTGAATGACAATCAGGAGTA 58.049 36.000 0.00 0.00 37.00 2.59
18 19 5.813383 AGAATGTGAATGACAATCAGGAGT 58.187 37.500 0.00 0.00 37.00 3.85
27 30 8.134895 GTCCAAAAGTAAAGAATGTGAATGACA 58.865 33.333 0.00 0.00 39.53 3.58
86 89 8.177119 TGAAAGAAACATGGTTTAGCAGTTAT 57.823 30.769 0.00 0.00 0.00 1.89
93 130 7.393234 TCATACCCTGAAAGAAACATGGTTTAG 59.607 37.037 0.00 0.00 37.43 1.85
98 135 6.567050 CAATCATACCCTGAAAGAAACATGG 58.433 40.000 0.00 0.00 37.44 3.66
127 164 5.330233 TCTTCCAGGAAGTAGTACACATGA 58.670 41.667 25.92 2.48 40.24 3.07
136 173 4.141914 GGGTACACATCTTCCAGGAAGTAG 60.142 50.000 25.92 20.97 40.24 2.57
151 188 2.587080 GGTCATCCGAGGGTACACA 58.413 57.895 0.00 0.00 0.00 3.72
220 257 1.958715 CGCCACGACCACATTGTCA 60.959 57.895 0.00 0.00 34.88 3.58
416 453 1.015085 GCAGCGCATTGGCATCAAAA 61.015 50.000 11.47 0.00 41.24 2.44
441 479 5.525012 TCATGAGCACAGCTACATACAATTC 59.475 40.000 0.00 0.00 39.88 2.17
444 482 4.160252 TCTCATGAGCACAGCTACATACAA 59.840 41.667 18.36 0.00 39.88 2.41
457 495 0.106868 CCAATGGCCTCTCATGAGCA 60.107 55.000 18.36 10.35 38.93 4.26
462 500 2.173519 CAACAACCAATGGCCTCTCAT 58.826 47.619 3.32 0.00 0.00 2.90
467 505 2.367241 GTTAACCAACAACCAATGGCCT 59.633 45.455 3.32 0.00 40.51 5.19
468 506 2.367241 AGTTAACCAACAACCAATGGCC 59.633 45.455 0.00 0.00 40.51 5.36
469 507 3.744238 AGTTAACCAACAACCAATGGC 57.256 42.857 0.00 0.00 40.51 4.40
470 508 5.665459 TCAAAGTTAACCAACAACCAATGG 58.335 37.500 0.88 0.00 42.60 3.16
471 509 7.784633 ATTCAAAGTTAACCAACAACCAATG 57.215 32.000 0.88 0.00 37.10 2.82
472 510 8.043710 TCAATTCAAAGTTAACCAACAACCAAT 58.956 29.630 0.88 0.00 37.10 3.16
494 532 4.627467 GCAAGATGAGACAAGTACGTCAAT 59.373 41.667 0.00 0.00 38.43 2.57
523 561 2.113986 GAAGGTGCCACTGCCACT 59.886 61.111 0.00 0.00 36.33 4.00
524 562 3.357079 CGAAGGTGCCACTGCCAC 61.357 66.667 0.00 0.00 36.33 5.01
525 563 2.046009 TAACGAAGGTGCCACTGCCA 62.046 55.000 0.00 0.00 36.33 4.92
527 565 1.165270 ATTAACGAAGGTGCCACTGC 58.835 50.000 0.00 0.00 38.26 4.40
528 566 3.374058 CCTAATTAACGAAGGTGCCACTG 59.626 47.826 0.00 0.00 0.00 3.66
529 567 3.606687 CCTAATTAACGAAGGTGCCACT 58.393 45.455 0.00 0.00 0.00 4.00
572 610 0.112995 AATGGGCAGCTCTGGTTTGA 59.887 50.000 0.00 0.00 0.00 2.69
581 619 1.551883 GTTGGAATTCAATGGGCAGCT 59.448 47.619 7.93 0.00 37.73 4.24
582 620 1.551883 AGTTGGAATTCAATGGGCAGC 59.448 47.619 7.93 0.00 37.73 5.25
584 622 2.886913 TGAGTTGGAATTCAATGGGCA 58.113 42.857 7.93 0.00 37.73 5.36
585 623 3.959535 TTGAGTTGGAATTCAATGGGC 57.040 42.857 7.93 0.00 37.73 5.36
586 624 5.122711 GCATTTTGAGTTGGAATTCAATGGG 59.877 40.000 7.93 0.00 35.09 4.00
587 625 5.935789 AGCATTTTGAGTTGGAATTCAATGG 59.064 36.000 7.93 0.00 35.09 3.16
588 626 6.647481 TCAGCATTTTGAGTTGGAATTCAATG 59.353 34.615 7.93 7.08 35.09 2.82
589 627 6.761312 TCAGCATTTTGAGTTGGAATTCAAT 58.239 32.000 7.93 0.00 35.09 2.57
591 629 5.787953 TCAGCATTTTGAGTTGGAATTCA 57.212 34.783 7.93 0.00 0.00 2.57
593 631 9.729281 ATTTAATCAGCATTTTGAGTTGGAATT 57.271 25.926 0.00 0.00 0.00 2.17
657 1327 8.703336 GCTTAGAAATTTGTTCCATGTCTTTTC 58.297 33.333 0.00 0.00 0.00 2.29
708 1378 8.053355 ACCCTTAAATGTTTCTCCTTTCGATAT 58.947 33.333 0.00 0.00 0.00 1.63
710 1380 6.246163 ACCCTTAAATGTTTCTCCTTTCGAT 58.754 36.000 0.00 0.00 0.00 3.59
711 1381 5.627135 ACCCTTAAATGTTTCTCCTTTCGA 58.373 37.500 0.00 0.00 0.00 3.71
712 1382 5.106277 GGACCCTTAAATGTTTCTCCTTTCG 60.106 44.000 0.00 0.00 0.00 3.46
713 1383 5.185249 GGGACCCTTAAATGTTTCTCCTTTC 59.815 44.000 2.09 0.00 0.00 2.62
714 1384 5.084519 GGGACCCTTAAATGTTTCTCCTTT 58.915 41.667 2.09 0.00 0.00 3.11
736 1406 8.905702 CGTTTTGAGAATTCTACAAATCAAAGG 58.094 33.333 22.45 13.85 37.78 3.11
747 1417 6.312918 GCATGTCCTACGTTTTGAGAATTCTA 59.687 38.462 8.25 0.00 0.00 2.10
748 1418 5.122396 GCATGTCCTACGTTTTGAGAATTCT 59.878 40.000 7.95 7.95 0.00 2.40
749 1419 5.106712 TGCATGTCCTACGTTTTGAGAATTC 60.107 40.000 0.00 0.00 0.00 2.17
750 1420 4.759693 TGCATGTCCTACGTTTTGAGAATT 59.240 37.500 0.00 0.00 0.00 2.17
751 1421 4.323417 TGCATGTCCTACGTTTTGAGAAT 58.677 39.130 0.00 0.00 0.00 2.40
752 1422 3.734463 TGCATGTCCTACGTTTTGAGAA 58.266 40.909 0.00 0.00 0.00 2.87
753 1423 3.394674 TGCATGTCCTACGTTTTGAGA 57.605 42.857 0.00 0.00 0.00 3.27
754 1424 3.745975 TCTTGCATGTCCTACGTTTTGAG 59.254 43.478 0.00 0.00 0.00 3.02
755 1425 3.734463 TCTTGCATGTCCTACGTTTTGA 58.266 40.909 0.00 0.00 0.00 2.69
756 1426 4.685169 ATCTTGCATGTCCTACGTTTTG 57.315 40.909 0.00 0.00 0.00 2.44
757 1427 5.003804 AGAATCTTGCATGTCCTACGTTTT 58.996 37.500 0.00 0.00 0.00 2.43
758 1428 4.579869 AGAATCTTGCATGTCCTACGTTT 58.420 39.130 0.00 0.00 0.00 3.60
759 1429 4.184629 GAGAATCTTGCATGTCCTACGTT 58.815 43.478 0.00 0.00 0.00 3.99
760 1430 3.195610 TGAGAATCTTGCATGTCCTACGT 59.804 43.478 0.00 0.00 34.92 3.57
761 1431 3.785486 TGAGAATCTTGCATGTCCTACG 58.215 45.455 0.00 0.00 34.92 3.51
762 1432 6.072508 TGTTTTGAGAATCTTGCATGTCCTAC 60.073 38.462 0.00 0.00 34.92 3.18
763 1433 6.003326 TGTTTTGAGAATCTTGCATGTCCTA 58.997 36.000 0.00 0.00 34.92 2.94
764 1434 4.828939 TGTTTTGAGAATCTTGCATGTCCT 59.171 37.500 0.00 0.00 34.92 3.85
765 1435 5.125100 TGTTTTGAGAATCTTGCATGTCC 57.875 39.130 0.00 0.00 34.92 4.02
766 1436 6.971184 CCTATGTTTTGAGAATCTTGCATGTC 59.029 38.462 0.00 0.00 34.92 3.06
767 1437 6.660521 TCCTATGTTTTGAGAATCTTGCATGT 59.339 34.615 0.00 0.00 34.92 3.21
768 1438 7.092137 TCCTATGTTTTGAGAATCTTGCATG 57.908 36.000 0.00 0.00 34.92 4.06
769 1439 7.707624 TTCCTATGTTTTGAGAATCTTGCAT 57.292 32.000 0.00 0.00 34.92 3.96
770 1440 7.707624 ATTCCTATGTTTTGAGAATCTTGCA 57.292 32.000 0.00 0.00 34.92 4.08
771 1441 7.852945 CGTATTCCTATGTTTTGAGAATCTTGC 59.147 37.037 0.00 0.00 34.92 4.01
774 1444 9.838339 AATCGTATTCCTATGTTTTGAGAATCT 57.162 29.630 0.00 0.00 34.92 2.40
787 1457 7.291411 ACAACTCTGCTAATCGTATTCCTAT 57.709 36.000 0.00 0.00 0.00 2.57
796 1466 6.402226 GGGTTCTTTTACAACTCTGCTAATCG 60.402 42.308 0.00 0.00 0.00 3.34
860 2087 7.658982 AGGGCTCTTTGATTCAAAAGATTTTTC 59.341 33.333 12.62 0.17 43.41 2.29
861 2088 7.512130 AGGGCTCTTTGATTCAAAAGATTTTT 58.488 30.769 12.62 0.00 43.41 1.94
925 2154 5.534654 TGCTTCACTAACTGTGGCTTAAAAT 59.465 36.000 0.00 0.00 46.20 1.82
942 2171 0.093705 GCTTGACGACGATGCTTCAC 59.906 55.000 0.00 0.00 0.00 3.18
946 2175 1.016130 CCAAGCTTGACGACGATGCT 61.016 55.000 28.05 2.32 35.30 3.79
974 2203 0.469070 TCCGTTTGGTTTTCGAGGGA 59.531 50.000 0.00 0.00 36.30 4.20
976 2205 0.872388 CCTCCGTTTGGTTTTCGAGG 59.128 55.000 0.00 0.00 36.30 4.63
983 2212 0.673644 CATCGCTCCTCCGTTTGGTT 60.674 55.000 0.00 0.00 36.30 3.67
987 2216 1.218316 GTCCATCGCTCCTCCGTTT 59.782 57.895 0.00 0.00 0.00 3.60
991 2220 3.133946 GGAGTCCATCGCTCCTCC 58.866 66.667 3.60 0.00 46.71 4.30
1283 2512 0.181114 GGCACATGCACCATAGGAGA 59.819 55.000 6.15 0.00 44.36 3.71
1487 2716 3.450115 GACGGTCCCCAGACTCCG 61.450 72.222 0.00 0.00 46.98 4.63
1532 2761 4.962836 CGCCCATCCCCTGCATCC 62.963 72.222 0.00 0.00 0.00 3.51
1553 2782 4.554036 GGGTGATGAGCGAGGGCC 62.554 72.222 0.00 0.00 41.24 5.80
1612 2841 3.775654 CACCTCCCTGACCGAGCC 61.776 72.222 0.00 0.00 0.00 4.70
1641 2870 1.501741 GAACATGTCGTGCCGCAAT 59.498 52.632 0.00 0.00 0.00 3.56
1642 2871 2.942879 GAACATGTCGTGCCGCAA 59.057 55.556 0.00 0.00 0.00 4.85
1652 2881 1.596752 TGGCAACTCGCGAACATGT 60.597 52.632 11.33 0.55 43.84 3.21
1671 2900 3.160047 ATGAGGGAGCTGCCGAGG 61.160 66.667 19.62 0.00 37.63 4.63
1687 2916 3.900892 CTGCCCGTACGCCTCGAT 61.901 66.667 10.49 0.00 0.00 3.59
1703 2932 2.357517 CGACCAAAGAGCCGCACT 60.358 61.111 0.00 0.00 0.00 4.40
1737 2966 4.778415 CGCTCGTCCACCAGGTCG 62.778 72.222 0.00 0.00 45.88 4.79
1869 3098 1.686355 TCAACACGCCAAGGAACATT 58.314 45.000 0.00 0.00 0.00 2.71
1878 3107 2.594303 CAGGCCTTCAACACGCCA 60.594 61.111 0.00 0.00 45.56 5.69
1920 3149 5.438761 ACACATCAAAGTACTTCAAAGCC 57.561 39.130 8.95 0.00 0.00 4.35
1932 3161 4.219033 GCGTCTTGGTTAACACATCAAAG 58.781 43.478 8.10 1.78 0.00 2.77
1935 3164 2.839975 TGCGTCTTGGTTAACACATCA 58.160 42.857 8.10 0.00 0.00 3.07
1953 3182 0.376152 CACATGCTTCGACTCCATGC 59.624 55.000 15.26 2.19 39.86 4.06
1954 3183 1.012086 CCACATGCTTCGACTCCATG 58.988 55.000 14.25 14.25 41.49 3.66
1962 3191 5.467735 TGAATAATGATCTCCACATGCTTCG 59.532 40.000 0.00 0.00 0.00 3.79
1971 3200 5.698104 ACCAAGCATGAATAATGATCTCCA 58.302 37.500 0.00 0.00 38.72 3.86
1986 3215 2.173519 CCCAAGACATCAACCAAGCAT 58.826 47.619 0.00 0.00 0.00 3.79
2182 3411 4.260656 CGAATAGACATTTGCAAGCGAAAC 59.739 41.667 0.00 0.00 0.00 2.78
2197 3426 2.767505 CATACCCAAGCCCGAATAGAC 58.232 52.381 0.00 0.00 0.00 2.59
2334 3570 3.436243 ACAAGGAAGTGGTGGAAAAACA 58.564 40.909 0.00 0.00 0.00 2.83
2649 3901 0.445436 GTTCAGGTTGAGATGCAGCG 59.555 55.000 0.00 0.00 0.00 5.18
2968 4223 1.260544 GCTGTTGGCAGGAAGGAAAT 58.739 50.000 0.00 0.00 42.78 2.17
3143 4487 1.894466 CAGCAATGGGATTGTGGACAA 59.106 47.619 0.00 0.00 42.20 3.18
3187 4532 4.827692 TCAGTGCACGGATGTAATAAACT 58.172 39.130 16.07 0.00 0.00 2.66
3191 4536 4.081917 TGAGTTCAGTGCACGGATGTAATA 60.082 41.667 20.46 1.45 0.00 0.98
3356 4701 6.430000 AGTTTTCTAATACGATGTGCCTTTGT 59.570 34.615 0.00 0.00 0.00 2.83
3387 4732 6.242396 TGCACCTATTTGACTAGCCTTTTTA 58.758 36.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.