Multiple sequence alignment - TraesCS5D01G489800

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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 TraesCS5D01G489800 chr5D 100.000 2474 0 0 1 2474 524911670 524909197 0.000000e+00 4569.0
1 TraesCS5D01G489800 chr5A 94.846 912 39 4 1566 2474 651324980 651324074 0.000000e+00 1417.0
2 TraesCS5D01G489800 chr5A 91.993 587 24 6 966 1540 651325547 651324972 0.000000e+00 802.0
3 TraesCS5D01G489800 chr5A 87.709 358 24 9 1 341 651326794 651326440 1.380000e-107 399.0
4 TraesCS5D01G489800 chr5A 84.309 376 26 23 458 818 651326182 651325825 1.100000e-88 337.0
5 TraesCS5D01G489800 chr5A 88.571 70 8 0 1135 1204 651564234 651564165 4.380000e-13 86.1
6 TraesCS5D01G489800 chr5A 87.143 70 9 0 1135 1204 651555849 651555780 2.040000e-11 80.5
7 TraesCS5D01G489800 chr5A 87.143 70 9 0 1141 1210 651569546 651569477 2.040000e-11 80.5
8 TraesCS5D01G489800 chr5B 89.569 719 23 20 863 1540 659403733 659403026 0.000000e+00 865.0
9 TraesCS5D01G489800 chr5B 86.126 382 23 18 450 819 659404113 659403750 3.860000e-103 385.0
10 TraesCS5D01G489800 chr5B 94.167 240 12 2 1 239 659404674 659404436 5.030000e-97 364.0
11 TraesCS5D01G489800 chr5B 82.192 73 7 3 1135 1204 659505977 659505908 9.560000e-05 58.4
12 TraesCS5D01G489800 chr2D 89.268 615 44 13 1870 2470 556318908 556319514 0.000000e+00 750.0
13 TraesCS5D01G489800 chr2D 85.385 260 21 8 1869 2116 556333028 556333282 1.140000e-63 254.0
14 TraesCS5D01G489800 chr2D 95.745 47 2 0 1885 1931 620924071 620924117 2.640000e-10 76.8
15 TraesCS5D01G489800 chr4A 88.980 608 49 9 1875 2470 43270037 43269436 0.000000e+00 736.0
16 TraesCS5D01G489800 chr4A 84.553 369 52 5 2106 2471 649015759 649015393 6.500000e-96 361.0
17 TraesCS5D01G489800 chr4A 97.872 47 0 1 1885 1931 597216202 597216157 2.040000e-11 80.5
18 TraesCS5D01G489800 chr6B 87.745 612 59 7 1870 2470 35309935 35310541 0.000000e+00 701.0
19 TraesCS5D01G489800 chr1D 91.877 357 26 3 2116 2470 7858851 7859206 1.710000e-136 496.0
20 TraesCS5D01G489800 chr3D 83.978 362 53 5 2111 2470 325995643 325996001 2.360000e-90 342.0
21 TraesCS5D01G489800 chrUn 83.469 369 56 5 2106 2471 40876945 40876579 3.050000e-89 339.0
22 TraesCS5D01G489800 chr4D 82.353 391 59 10 2088 2471 15817230 15817617 5.100000e-87 331.0
23 TraesCS5D01G489800 chr6D 97.872 47 0 1 1885 1931 10047534 10047489 2.040000e-11 80.5
24 TraesCS5D01G489800 chr3A 97.872 47 0 1 1885 1931 41168040 41167995 2.040000e-11 80.5
25 TraesCS5D01G489800 chr3A 97.872 47 0 1 1885 1931 41173049 41173004 2.040000e-11 80.5
26 TraesCS5D01G489800 chr3A 97.872 47 0 1 1885 1931 713964294 713964339 2.040000e-11 80.5
27 TraesCS5D01G489800 chr3A 97.778 45 0 1 1885 1929 713969327 713969370 2.640000e-10 76.8
28 TraesCS5D01G489800 chr3B 95.745 47 2 0 1885 1931 134062417 134062463 2.640000e-10 76.8
29 TraesCS5D01G489800 chr7A 100.000 33 0 0 1174 1206 722898946 722898978 7.390000e-06 62.1
30 TraesCS5D01G489800 chr7A 100.000 33 0 0 1174 1206 722938490 722938522 7.390000e-06 62.1
31 TraesCS5D01G489800 chr7A 100.000 33 0 0 1174 1206 722988457 722988489 7.390000e-06 62.1


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 TraesCS5D01G489800 chr5D 524909197 524911670 2473 True 4569.00 4569 100.00000 1 2474 1 chr5D.!!$R1 2473
1 TraesCS5D01G489800 chr5A 651324074 651326794 2720 True 738.75 1417 89.71425 1 2474 4 chr5A.!!$R4 2473
2 TraesCS5D01G489800 chr5B 659403026 659404674 1648 True 538.00 865 89.95400 1 1540 3 chr5B.!!$R2 1539
3 TraesCS5D01G489800 chr2D 556318908 556319514 606 False 750.00 750 89.26800 1870 2470 1 chr2D.!!$F1 600
4 TraesCS5D01G489800 chr4A 43269436 43270037 601 True 736.00 736 88.98000 1875 2470 1 chr4A.!!$R1 595
5 TraesCS5D01G489800 chr6B 35309935 35310541 606 False 701.00 701 87.74500 1870 2470 1 chr6B.!!$F1 600

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
527 707 0.111061 TGGGTGCAGCAGTCAGATTT 59.889 50.0 19.06 0.0 0.0 2.17 F
624 813 0.179018 AGTCAACTCCCACAACTGCC 60.179 55.0 0.00 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1824 0.616111 GCCCAGAGAGAGAGGTCCAA 60.616 60.000 0.0 0.0 0.0 3.53 R
1988 2370 1.906574 TCCCTCGCATGTACCTTTCTT 59.093 47.619 0.0 0.0 0.0 2.52 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
37 38 3.024547 TCGGAGGAGGACAGAACAATAG 58.975 50.000 0.00 0.00 0.00 1.73
50 54 3.008049 AGAACAATAGAAAGGACGGCAGT 59.992 43.478 0.00 0.00 0.00 4.40
53 57 4.504858 ACAATAGAAAGGACGGCAGTTAG 58.495 43.478 0.00 0.00 0.00 2.34
196 202 5.520748 AAGAAGATAAACATCCACAGGGT 57.479 39.130 0.00 0.00 34.93 4.34
280 298 5.005971 CCGCATTTCAATTGCTTAATTGGAG 59.994 40.000 11.51 0.00 39.84 3.86
304 322 4.150098 CACCGTTGACTAGAGCAAAACTAC 59.850 45.833 0.00 0.00 0.00 2.73
305 323 4.202182 ACCGTTGACTAGAGCAAAACTACA 60.202 41.667 0.00 0.00 0.00 2.74
306 324 4.386049 CCGTTGACTAGAGCAAAACTACAG 59.614 45.833 0.00 0.00 0.00 2.74
318 336 5.770162 AGCAAAACTACAGAAATGGCTAACT 59.230 36.000 0.00 0.00 0.00 2.24
348 371 7.977904 TGCACATAATTATGCATATAGAGCAC 58.022 34.615 22.66 0.00 46.63 4.40
349 372 7.825761 TGCACATAATTATGCATATAGAGCACT 59.174 33.333 22.66 0.00 46.63 4.40
350 373 8.671921 GCACATAATTATGCATATAGAGCACTT 58.328 33.333 22.66 0.00 45.95 3.16
355 378 8.694975 AATTATGCATATAGAGCACTTAGACG 57.305 34.615 7.36 0.00 45.95 4.18
356 379 5.966742 ATGCATATAGAGCACTTAGACGA 57.033 39.130 0.00 0.00 45.95 4.20
357 380 5.767816 TGCATATAGAGCACTTAGACGAA 57.232 39.130 0.00 0.00 37.02 3.85
358 381 5.763088 TGCATATAGAGCACTTAGACGAAG 58.237 41.667 0.00 0.00 41.37 3.79
389 452 2.472861 CGTAACAAGTGTCAGTCAGCTG 59.527 50.000 7.63 7.63 43.87 4.24
407 470 3.525199 AGCTGTGAAGGATGGGTTTATCT 59.475 43.478 0.00 0.00 0.00 1.98
408 471 3.629398 GCTGTGAAGGATGGGTTTATCTG 59.371 47.826 0.00 0.00 0.00 2.90
417 480 7.272144 AGGATGGGTTTATCTGTCTAAAGTT 57.728 36.000 0.00 0.00 0.00 2.66
456 634 8.410141 GGATACTCAGGTAATGCAGATATACTC 58.590 40.741 0.00 0.00 0.00 2.59
499 677 6.366315 ACTAAACACTATAGTCGCTCTCAG 57.634 41.667 1.26 0.00 0.00 3.35
500 678 3.701532 AACACTATAGTCGCTCTCAGC 57.298 47.619 1.26 0.00 38.02 4.26
524 704 2.427320 GTGGGTGCAGCAGTCAGA 59.573 61.111 19.06 0.00 0.00 3.27
525 705 1.002868 GTGGGTGCAGCAGTCAGAT 60.003 57.895 19.06 0.00 0.00 2.90
526 706 0.607489 GTGGGTGCAGCAGTCAGATT 60.607 55.000 19.06 0.00 0.00 2.40
527 707 0.111061 TGGGTGCAGCAGTCAGATTT 59.889 50.000 19.06 0.00 0.00 2.17
528 708 0.807496 GGGTGCAGCAGTCAGATTTC 59.193 55.000 19.06 0.00 0.00 2.17
529 709 1.527034 GGTGCAGCAGTCAGATTTCA 58.473 50.000 11.86 0.00 0.00 2.69
530 710 1.198637 GGTGCAGCAGTCAGATTTCAC 59.801 52.381 11.86 0.00 0.00 3.18
532 712 3.329386 GTGCAGCAGTCAGATTTCACTA 58.671 45.455 0.00 0.00 0.00 2.74
533 713 3.124297 GTGCAGCAGTCAGATTTCACTAC 59.876 47.826 0.00 0.00 0.00 2.73
537 717 2.027192 GCAGTCAGATTTCACTACCCCA 60.027 50.000 0.00 0.00 0.00 4.96
538 718 3.600388 CAGTCAGATTTCACTACCCCAC 58.400 50.000 0.00 0.00 0.00 4.61
556 738 3.276857 CCACAGCTGCAAACTCATCTAT 58.723 45.455 15.27 0.00 0.00 1.98
557 739 3.064958 CCACAGCTGCAAACTCATCTATG 59.935 47.826 15.27 0.00 0.00 2.23
558 740 3.688185 CACAGCTGCAAACTCATCTATGT 59.312 43.478 15.27 0.00 0.00 2.29
559 741 4.872124 CACAGCTGCAAACTCATCTATGTA 59.128 41.667 15.27 0.00 0.00 2.29
560 742 5.352293 CACAGCTGCAAACTCATCTATGTAA 59.648 40.000 15.27 0.00 0.00 2.41
563 751 7.225538 ACAGCTGCAAACTCATCTATGTAATAC 59.774 37.037 15.27 0.00 0.00 1.89
573 761 8.723365 ACTCATCTATGTAATACCATCCCAAAA 58.277 33.333 0.00 0.00 0.00 2.44
587 775 7.746703 ACCATCCCAAAATAATAGGAGTACTC 58.253 38.462 14.87 14.87 0.00 2.59
603 792 8.124808 AGGAGTACTCGATCTAAAATTATCCC 57.875 38.462 16.56 0.00 0.00 3.85
615 804 7.116736 TCTAAAATTATCCCAAGTCAACTCCC 58.883 38.462 0.00 0.00 0.00 4.30
616 805 4.946160 AATTATCCCAAGTCAACTCCCA 57.054 40.909 0.00 0.00 0.00 4.37
617 806 3.713826 TTATCCCAAGTCAACTCCCAC 57.286 47.619 0.00 0.00 0.00 4.61
618 807 1.444933 ATCCCAAGTCAACTCCCACA 58.555 50.000 0.00 0.00 0.00 4.17
620 809 1.133915 TCCCAAGTCAACTCCCACAAC 60.134 52.381 0.00 0.00 0.00 3.32
621 810 1.133792 CCCAAGTCAACTCCCACAACT 60.134 52.381 0.00 0.00 0.00 3.16
622 811 1.949525 CCAAGTCAACTCCCACAACTG 59.050 52.381 0.00 0.00 0.00 3.16
623 812 1.334869 CAAGTCAACTCCCACAACTGC 59.665 52.381 0.00 0.00 0.00 4.40
624 813 0.179018 AGTCAACTCCCACAACTGCC 60.179 55.000 0.00 0.00 0.00 4.85
628 817 1.352622 AACTCCCACAACTGCCCTCA 61.353 55.000 0.00 0.00 0.00 3.86
645 834 3.599343 CCTCAATCGATCTCAACCAACA 58.401 45.455 0.00 0.00 0.00 3.33
655 844 2.158827 TCTCAACCAACAAGCAGTAGCA 60.159 45.455 0.00 0.00 45.49 3.49
656 845 2.221169 TCAACCAACAAGCAGTAGCAG 58.779 47.619 0.00 0.00 45.49 4.24
657 846 1.949525 CAACCAACAAGCAGTAGCAGT 59.050 47.619 0.00 0.00 45.49 4.40
658 847 1.884235 ACCAACAAGCAGTAGCAGTC 58.116 50.000 0.00 0.00 45.49 3.51
659 848 1.417890 ACCAACAAGCAGTAGCAGTCT 59.582 47.619 0.00 0.00 45.49 3.24
660 849 2.632996 ACCAACAAGCAGTAGCAGTCTA 59.367 45.455 0.00 0.00 45.49 2.59
661 850 3.257393 CCAACAAGCAGTAGCAGTCTAG 58.743 50.000 0.00 0.00 45.49 2.43
662 851 2.663826 ACAAGCAGTAGCAGTCTAGC 57.336 50.000 0.00 0.00 45.49 3.42
663 852 1.895798 ACAAGCAGTAGCAGTCTAGCA 59.104 47.619 0.00 0.00 45.49 3.49
744 933 5.739161 GTCCAAACGAACAGATAATGATTGC 59.261 40.000 0.00 0.00 0.00 3.56
822 1011 9.696572 TGAAAGGTCTACAAGTAGTATAGATGT 57.303 33.333 7.09 0.00 34.84 3.06
823 1012 9.953697 GAAAGGTCTACAAGTAGTATAGATGTG 57.046 37.037 7.09 0.00 34.84 3.21
824 1013 9.476928 AAAGGTCTACAAGTAGTATAGATGTGT 57.523 33.333 7.09 0.00 34.84 3.72
842 1031 3.670625 GTGTAATACACTCTGGTTGCCA 58.329 45.455 15.68 0.00 45.27 4.92
845 1034 4.759693 TGTAATACACTCTGGTTGCCAAAG 59.240 41.667 0.00 0.00 30.80 2.77
850 1039 3.513515 ACACTCTGGTTGCCAAAGAAAAA 59.486 39.130 0.00 0.00 30.80 1.94
851 1040 4.114794 CACTCTGGTTGCCAAAGAAAAAG 58.885 43.478 0.00 0.00 30.80 2.27
852 1041 3.769300 ACTCTGGTTGCCAAAGAAAAAGT 59.231 39.130 0.00 0.00 30.80 2.66
853 1042 4.953579 ACTCTGGTTGCCAAAGAAAAAGTA 59.046 37.500 0.00 0.00 30.80 2.24
859 1188 9.573133 CTGGTTGCCAAAGAAAAAGTATATAAG 57.427 33.333 0.00 0.00 30.80 1.73
860 1189 9.084533 TGGTTGCCAAAGAAAAAGTATATAAGT 57.915 29.630 0.00 0.00 0.00 2.24
907 1236 8.986847 CATATCATTCTCCAAGCTAACTAACTG 58.013 37.037 0.00 0.00 0.00 3.16
908 1237 5.178797 TCATTCTCCAAGCTAACTAACTGC 58.821 41.667 0.00 0.00 0.00 4.40
909 1238 4.891992 TTCTCCAAGCTAACTAACTGCT 57.108 40.909 0.00 0.00 38.87 4.24
944 1273 1.337384 TACATGAGTGGATGCGGCCT 61.337 55.000 0.00 0.00 0.00 5.19
990 1337 2.765250 GAACGCGAAGAGCTCCACCA 62.765 60.000 15.93 0.00 45.59 4.17
1020 1376 1.140312 TGAAGAGGCTGAGGTTTGGT 58.860 50.000 0.00 0.00 0.00 3.67
1348 1722 3.465403 CCCACGAGCAGGAGGAGG 61.465 72.222 0.00 0.00 0.00 4.30
1349 1723 2.363018 CCACGAGCAGGAGGAGGA 60.363 66.667 0.00 0.00 0.00 3.71
1350 1724 2.422231 CCACGAGCAGGAGGAGGAG 61.422 68.421 0.00 0.00 0.00 3.69
1352 1726 2.837291 CGAGCAGGAGGAGGAGGG 60.837 72.222 0.00 0.00 0.00 4.30
1353 1727 3.160748 GAGCAGGAGGAGGAGGGC 61.161 72.222 0.00 0.00 0.00 5.19
1519 1893 2.573462 TGTTCCTTCTGCAATAGCTCCT 59.427 45.455 0.00 0.00 42.74 3.69
1522 1896 3.916035 TCCTTCTGCAATAGCTCCTCTA 58.084 45.455 0.00 0.00 42.74 2.43
1530 1907 5.450453 TGCAATAGCTCCTCTACTACTCTT 58.550 41.667 0.00 0.00 42.74 2.85
1531 1908 5.894393 TGCAATAGCTCCTCTACTACTCTTT 59.106 40.000 0.00 0.00 42.74 2.52
1532 1909 6.381420 TGCAATAGCTCCTCTACTACTCTTTT 59.619 38.462 0.00 0.00 42.74 2.27
1533 1910 6.921307 GCAATAGCTCCTCTACTACTCTTTTC 59.079 42.308 0.00 0.00 37.91 2.29
1534 1911 7.201875 GCAATAGCTCCTCTACTACTCTTTTCT 60.202 40.741 0.00 0.00 37.91 2.52
1535 1912 8.349983 CAATAGCTCCTCTACTACTCTTTTCTC 58.650 40.741 0.00 0.00 0.00 2.87
1536 1913 6.074698 AGCTCCTCTACTACTCTTTTCTCT 57.925 41.667 0.00 0.00 0.00 3.10
1537 1914 7.202972 AGCTCCTCTACTACTCTTTTCTCTA 57.797 40.000 0.00 0.00 0.00 2.43
1538 1915 7.635648 AGCTCCTCTACTACTCTTTTCTCTAA 58.364 38.462 0.00 0.00 0.00 2.10
1539 1916 7.555195 AGCTCCTCTACTACTCTTTTCTCTAAC 59.445 40.741 0.00 0.00 0.00 2.34
1540 1917 7.555195 GCTCCTCTACTACTCTTTTCTCTAACT 59.445 40.741 0.00 0.00 0.00 2.24
1541 1918 9.457436 CTCCTCTACTACTCTTTTCTCTAACTT 57.543 37.037 0.00 0.00 0.00 2.66
1542 1919 9.452287 TCCTCTACTACTCTTTTCTCTAACTTC 57.548 37.037 0.00 0.00 0.00 3.01
1543 1920 9.457436 CCTCTACTACTCTTTTCTCTAACTTCT 57.543 37.037 0.00 0.00 0.00 2.85
1548 1925 9.357161 ACTACTCTTTTCTCTAACTTCTTCTCA 57.643 33.333 0.00 0.00 0.00 3.27
1551 1928 9.892130 ACTCTTTTCTCTAACTTCTTCTCAAAA 57.108 29.630 0.00 0.00 0.00 2.44
1606 1983 7.642586 GTGTGGTGTTTCTTTCTTGTACAATAC 59.357 37.037 9.13 0.00 0.00 1.89
1613 1990 5.001232 TCTTTCTTGTACAATACTGGTGGC 58.999 41.667 9.13 0.00 0.00 5.01
1673 2052 8.620116 AAGATTTATTTGGGTTTGTGAATTGG 57.380 30.769 0.00 0.00 0.00 3.16
1825 2205 2.223044 GCGAATGGATTCCTCGTGTTTC 60.223 50.000 13.86 3.78 35.06 2.78
1852 2232 1.480205 CACTCTTTGCAAAACAGCCG 58.520 50.000 13.84 0.21 0.00 5.52
1873 2253 4.143556 CCGAAAGAATTGTTCGCAATGTTG 60.144 41.667 13.07 0.00 46.23 3.33
1995 2377 2.154389 CGTACGAACGTCCAAAGAAAGG 59.846 50.000 10.44 0.00 44.21 3.11
2013 2395 3.176924 AGGTACATGCGAGGGATAGAT 57.823 47.619 0.00 0.00 0.00 1.98
2022 2404 6.545666 ACATGCGAGGGATAGATAGATAAGAG 59.454 42.308 0.00 0.00 0.00 2.85
2061 2453 9.575957 AATATCTAACTAAACCCTGGCCTATAT 57.424 33.333 3.32 0.00 0.00 0.86
2112 2504 9.095065 GGTACGTGACATACAAGAGAATATTTT 57.905 33.333 0.00 0.00 0.00 1.82
2128 2520 9.620259 GAGAATATTTTCAACACTCTCCCTTAT 57.380 33.333 1.22 0.00 34.08 1.73
2129 2521 9.401058 AGAATATTTTCAACACTCTCCCTTATG 57.599 33.333 0.00 0.00 34.08 1.90
2172 2564 8.974238 TGAGATTATGCCTGAATTCTTCAAAAT 58.026 29.630 7.05 0.32 39.58 1.82
2385 2778 2.288763 GGGGGTTGCACTTGTGTAATTG 60.289 50.000 7.47 0.00 0.00 2.32
2449 2843 3.577848 TGGCATTTGGTAGTGCTTTGATT 59.422 39.130 0.00 0.00 41.04 2.57
2459 2853 3.415212 AGTGCTTTGATTGCTGCTTCTA 58.585 40.909 0.00 0.00 0.00 2.10
2471 2865 5.263968 TGCTGCTTCTATACTTGACCTAC 57.736 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.001633 TGTCCTAACTGCCGTCCTTTC 59.998 52.381 0.00 0.00 0.00 2.62
50 54 7.334421 GCAGTCAGTGATTCTTATTTGTCCTAA 59.666 37.037 0.00 0.00 0.00 2.69
53 57 5.645497 AGCAGTCAGTGATTCTTATTTGTCC 59.355 40.000 0.00 0.00 0.00 4.02
140 146 6.980978 GCATTATTAGTTCTACTGAGCTCACA 59.019 38.462 13.74 2.43 35.40 3.58
230 239 4.459089 GTCCTGCCTGCCGTCCTC 62.459 72.222 0.00 0.00 0.00 3.71
239 248 0.108329 CGGTGTTATTCGTCCTGCCT 60.108 55.000 0.00 0.00 0.00 4.75
280 298 1.508632 TTTGCTCTAGTCAACGGTGC 58.491 50.000 0.00 0.00 0.00 5.01
324 342 8.206325 AGTGCTCTATATGCATAATTATGTGC 57.794 34.615 23.14 14.21 43.35 4.57
361 384 4.776743 ACTGACACTTGTTACGTACGTAG 58.223 43.478 25.56 19.15 31.71 3.51
362 385 4.272261 TGACTGACACTTGTTACGTACGTA 59.728 41.667 23.60 23.60 0.00 3.57
364 387 3.620761 TGACTGACACTTGTTACGTACG 58.379 45.455 15.01 15.01 0.00 3.67
389 452 5.104259 AGACAGATAAACCCATCCTTCAC 57.896 43.478 0.00 0.00 0.00 3.18
407 470 8.190326 TCCTTCACTAGATTGAACTTTAGACA 57.810 34.615 0.00 0.00 32.02 3.41
417 480 6.436027 ACCTGAGTATCCTTCACTAGATTGA 58.564 40.000 0.00 0.00 0.00 2.57
434 497 6.318913 AGGAGTATATCTGCATTACCTGAGT 58.681 40.000 0.00 0.00 36.95 3.41
435 498 6.663093 AGAGGAGTATATCTGCATTACCTGAG 59.337 42.308 0.00 0.00 36.95 3.35
436 499 6.556639 AGAGGAGTATATCTGCATTACCTGA 58.443 40.000 0.00 0.00 36.95 3.86
437 500 6.849085 AGAGGAGTATATCTGCATTACCTG 57.151 41.667 0.00 0.00 36.95 4.00
438 501 8.958060 TTTAGAGGAGTATATCTGCATTACCT 57.042 34.615 0.00 0.00 36.95 3.08
439 502 9.998106 TTTTTAGAGGAGTATATCTGCATTACC 57.002 33.333 0.00 0.00 36.95 2.85
471 649 9.810231 GAGAGCGACTATAGTGTTTAGTATAAC 57.190 37.037 10.90 0.00 30.15 1.89
507 685 0.607489 AATCTGACTGCTGCACCCAC 60.607 55.000 0.00 0.00 0.00 4.61
515 693 2.237392 GGGGTAGTGAAATCTGACTGCT 59.763 50.000 0.00 0.00 0.00 4.24
524 704 1.614317 GCAGCTGTGGGGTAGTGAAAT 60.614 52.381 16.64 0.00 0.00 2.17
525 705 0.250727 GCAGCTGTGGGGTAGTGAAA 60.251 55.000 16.64 0.00 0.00 2.69
526 706 1.374947 GCAGCTGTGGGGTAGTGAA 59.625 57.895 16.64 0.00 0.00 3.18
527 707 1.414866 TTGCAGCTGTGGGGTAGTGA 61.415 55.000 16.64 0.00 0.00 3.41
528 708 0.537143 TTTGCAGCTGTGGGGTAGTG 60.537 55.000 16.64 0.00 0.00 2.74
529 709 0.537371 GTTTGCAGCTGTGGGGTAGT 60.537 55.000 16.64 0.00 0.00 2.73
530 710 0.250901 AGTTTGCAGCTGTGGGGTAG 60.251 55.000 16.64 0.00 0.00 3.18
532 712 1.529244 GAGTTTGCAGCTGTGGGGT 60.529 57.895 16.64 0.00 0.00 4.95
533 713 0.896940 ATGAGTTTGCAGCTGTGGGG 60.897 55.000 16.64 0.00 0.00 4.96
537 717 3.947868 ACATAGATGAGTTTGCAGCTGT 58.052 40.909 16.64 0.00 35.00 4.40
538 718 6.615264 ATTACATAGATGAGTTTGCAGCTG 57.385 37.500 10.11 10.11 35.00 4.24
560 742 9.406662 AGTACTCCTATTATTTTGGGATGGTAT 57.593 33.333 0.00 0.00 0.00 2.73
563 751 6.874134 CGAGTACTCCTATTATTTTGGGATGG 59.126 42.308 17.23 0.00 0.00 3.51
587 775 8.438676 AGTTGACTTGGGATAATTTTAGATCG 57.561 34.615 0.00 0.00 0.00 3.69
596 785 3.591527 TGTGGGAGTTGACTTGGGATAAT 59.408 43.478 0.00 0.00 0.00 1.28
597 786 2.983192 TGTGGGAGTTGACTTGGGATAA 59.017 45.455 0.00 0.00 0.00 1.75
603 792 1.334869 GCAGTTGTGGGAGTTGACTTG 59.665 52.381 0.00 0.00 0.00 3.16
615 804 1.667724 GATCGATTGAGGGCAGTTGTG 59.332 52.381 0.00 0.00 0.00 3.33
616 805 1.556911 AGATCGATTGAGGGCAGTTGT 59.443 47.619 0.00 0.00 0.00 3.32
617 806 2.208431 GAGATCGATTGAGGGCAGTTG 58.792 52.381 0.00 0.00 0.00 3.16
618 807 1.833630 TGAGATCGATTGAGGGCAGTT 59.166 47.619 0.00 0.00 0.00 3.16
620 809 2.208431 GTTGAGATCGATTGAGGGCAG 58.792 52.381 0.00 0.00 0.00 4.85
621 810 1.134401 GGTTGAGATCGATTGAGGGCA 60.134 52.381 0.00 0.00 0.00 5.36
622 811 1.134401 TGGTTGAGATCGATTGAGGGC 60.134 52.381 0.00 0.00 0.00 5.19
623 812 2.939103 GTTGGTTGAGATCGATTGAGGG 59.061 50.000 0.00 0.00 0.00 4.30
624 813 3.599343 TGTTGGTTGAGATCGATTGAGG 58.401 45.455 0.00 0.00 0.00 3.86
628 817 3.411446 TGCTTGTTGGTTGAGATCGATT 58.589 40.909 0.00 0.00 0.00 3.34
645 834 2.499289 ACATGCTAGACTGCTACTGCTT 59.501 45.455 0.00 0.00 40.48 3.91
655 844 3.378742 CGTAGGAGTTGACATGCTAGACT 59.621 47.826 0.00 0.00 0.00 3.24
656 845 3.377485 TCGTAGGAGTTGACATGCTAGAC 59.623 47.826 0.00 0.00 0.00 2.59
657 846 3.617284 TCGTAGGAGTTGACATGCTAGA 58.383 45.455 0.00 0.00 0.00 2.43
658 847 4.142359 ACTTCGTAGGAGTTGACATGCTAG 60.142 45.833 0.00 0.00 0.00 3.42
659 848 3.762288 ACTTCGTAGGAGTTGACATGCTA 59.238 43.478 0.00 0.00 0.00 3.49
660 849 2.563179 ACTTCGTAGGAGTTGACATGCT 59.437 45.455 0.00 0.00 0.00 3.79
661 850 2.924290 GACTTCGTAGGAGTTGACATGC 59.076 50.000 0.00 0.00 0.00 4.06
662 851 3.172050 CGACTTCGTAGGAGTTGACATG 58.828 50.000 0.00 0.00 34.11 3.21
663 852 2.415625 GCGACTTCGTAGGAGTTGACAT 60.416 50.000 0.00 0.00 42.22 3.06
819 1008 5.747545 TTGGCAACCAGAGTGTATTACACAT 60.748 40.000 24.80 12.76 42.48 3.21
820 1009 4.445019 TTGGCAACCAGAGTGTATTACACA 60.445 41.667 24.80 1.82 42.48 3.72
822 1011 4.359434 TTGGCAACCAGAGTGTATTACA 57.641 40.909 0.00 0.00 33.81 2.41
823 1012 5.001232 TCTTTGGCAACCAGAGTGTATTAC 58.999 41.667 0.00 0.00 37.10 1.89
824 1013 5.235850 TCTTTGGCAACCAGAGTGTATTA 57.764 39.130 0.00 0.00 37.10 0.98
827 1016 3.569194 TTCTTTGGCAACCAGAGTGTA 57.431 42.857 0.00 0.00 37.10 2.90
835 1024 9.569167 GACTTATATACTTTTTCTTTGGCAACC 57.431 33.333 0.00 0.00 0.00 3.77
838 1027 9.515226 ACAGACTTATATACTTTTTCTTTGGCA 57.485 29.630 0.00 0.00 0.00 4.92
882 1211 7.659390 GCAGTTAGTTAGCTTGGAGAATGATAT 59.341 37.037 0.00 0.00 0.00 1.63
919 1248 4.486090 CCGCATCCACTCATGTAGTATAC 58.514 47.826 0.00 0.00 43.42 1.47
920 1249 3.056821 GCCGCATCCACTCATGTAGTATA 60.057 47.826 0.00 0.00 35.76 1.47
921 1250 2.289072 GCCGCATCCACTCATGTAGTAT 60.289 50.000 0.00 0.00 35.76 2.12
922 1251 1.068588 GCCGCATCCACTCATGTAGTA 59.931 52.381 0.00 0.00 35.76 1.82
923 1252 0.179073 GCCGCATCCACTCATGTAGT 60.179 55.000 0.00 0.00 39.81 2.73
924 1253 0.882042 GGCCGCATCCACTCATGTAG 60.882 60.000 0.00 0.00 0.00 2.74
925 1254 1.146041 GGCCGCATCCACTCATGTA 59.854 57.895 0.00 0.00 0.00 2.29
926 1255 2.124570 GGCCGCATCCACTCATGT 60.125 61.111 0.00 0.00 0.00 3.21
971 1318 2.095252 GGTGGAGCTCTTCGCGTTC 61.095 63.158 14.64 0.00 45.59 3.95
990 1337 3.005554 CAGCCTCTTCATTGTCGTGATT 58.994 45.455 0.00 0.00 0.00 2.57
1020 1376 3.992641 TCCACCTCCGCCTCCTCA 61.993 66.667 0.00 0.00 0.00 3.86
1450 1824 0.616111 GCCCAGAGAGAGAGGTCCAA 60.616 60.000 0.00 0.00 0.00 3.53
1522 1896 9.357161 TGAGAAGAAGTTAGAGAAAAGAGTAGT 57.643 33.333 0.00 0.00 0.00 2.73
1555 1932 7.232188 CCCCTAGGTTAGAGAAAAGAGTTTTT 58.768 38.462 8.29 0.00 39.16 1.94
1556 1933 6.780901 CCCCTAGGTTAGAGAAAAGAGTTTT 58.219 40.000 8.29 0.00 35.12 2.43
1557 1934 6.375830 CCCCTAGGTTAGAGAAAAGAGTTT 57.624 41.667 8.29 0.00 0.00 2.66
1606 1983 2.821378 TCAATCAATTGACAGCCACCAG 59.179 45.455 11.07 0.00 41.51 4.00
1613 1990 7.820386 TGGAAATCCAAATCAATCAATTGACAG 59.180 33.333 11.07 6.46 45.21 3.51
1654 2033 5.841237 TCCTTCCAATTCACAAACCCAAATA 59.159 36.000 0.00 0.00 0.00 1.40
1715 2094 5.178061 TGTTGTACATACTCAGGCAATCAG 58.822 41.667 0.00 0.00 0.00 2.90
1825 2205 3.781079 TTTGCAAAGAGTGGTCAACAG 57.219 42.857 8.05 0.00 0.00 3.16
1852 2232 5.914635 TCTCAACATTGCGAACAATTCTTTC 59.085 36.000 0.00 0.00 44.21 2.62
1873 2253 3.247006 TGAGACGCTTTACCCATTCTC 57.753 47.619 0.00 0.00 0.00 2.87
1988 2370 1.906574 TCCCTCGCATGTACCTTTCTT 59.093 47.619 0.00 0.00 0.00 2.52
1992 2374 2.958818 TCTATCCCTCGCATGTACCTT 58.041 47.619 0.00 0.00 0.00 3.50
1995 2377 7.499563 TCTTATCTATCTATCCCTCGCATGTAC 59.500 40.741 0.00 0.00 0.00 2.90
2061 2453 2.270850 GGGCGTGGGCATCAAGTA 59.729 61.111 0.00 0.00 42.47 2.24
2062 2454 3.965258 TGGGCGTGGGCATCAAGT 61.965 61.111 0.00 0.00 42.47 3.16
2112 2504 2.637382 TGTGCATAAGGGAGAGTGTTGA 59.363 45.455 0.00 0.00 0.00 3.18
2172 2564 7.695480 TCACAAAAGCATTGCCTACTATAAA 57.305 32.000 4.70 0.00 0.00 1.40
2175 2567 6.183360 GGATTCACAAAAGCATTGCCTACTAT 60.183 38.462 4.70 0.00 0.00 2.12
2385 2778 4.761739 TCCAGTCCATGTTGAAAGAACATC 59.238 41.667 0.00 0.00 38.69 3.06
2449 2843 4.709886 TGTAGGTCAAGTATAGAAGCAGCA 59.290 41.667 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.