Multiple sequence alignment - TraesCS1A01G209800

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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 TraesCS1A01G209800 chr1A 100.000 2435 0 0 1 2435 372288593 372286159 0.000000e+00 4497.0
1 TraesCS1A01G209800 chr1A 91.379 1218 72 23 397 1603 372316668 372315473 0.000000e+00 1637.0
2 TraesCS1A01G209800 chr1D 90.720 1347 82 25 320 1650 298604973 298603654 0.000000e+00 1755.0
3 TraesCS1A01G209800 chr1D 91.532 496 28 5 1900 2389 464928797 464928310 0.000000e+00 671.0
4 TraesCS1A01G209800 chr1D 91.816 391 23 4 622 1010 298599204 298598821 9.910000e-149 536.0
5 TraesCS1A01G209800 chr1D 90.549 328 19 8 1555 1877 298598799 298598479 8.050000e-115 424.0
6 TraesCS1A01G209800 chr1D 85.656 244 25 6 1634 1877 298603600 298603367 5.200000e-62 248.0
7 TraesCS1A01G209800 chr1D 97.479 119 2 1 509 627 298599949 298599832 4.110000e-48 202.0
8 TraesCS1A01G209800 chr1B 89.629 1427 68 19 289 1678 401764299 401762916 0.000000e+00 1742.0
9 TraesCS1A01G209800 chr1B 91.392 1092 58 16 597 1678 401992767 401991702 0.000000e+00 1463.0
10 TraesCS1A01G209800 chr1B 89.379 998 59 23 638 1622 402039924 402038961 0.000000e+00 1212.0
11 TraesCS1A01G209800 chr1B 92.238 554 19 2 3 532 401993318 401992765 0.000000e+00 763.0
12 TraesCS1A01G209800 chr1B 94.606 241 12 1 54 293 401765702 401765462 2.960000e-99 372.0
13 TraesCS1A01G209800 chr1B 85.294 238 26 6 1634 1871 402003774 402003546 1.130000e-58 237.0
14 TraesCS1A01G209800 chr1B 88.060 201 19 5 320 519 402040119 402039923 1.460000e-57 233.0
15 TraesCS1A01G209800 chr1B 92.308 65 5 0 1 65 401766179 401766115 2.580000e-15 93.5
16 TraesCS1A01G209800 chr4B 82.154 1003 122 34 624 1600 603037675 603038646 0.000000e+00 808.0
17 TraesCS1A01G209800 chr4B 81.322 1044 116 48 624 1639 603148095 603149087 0.000000e+00 774.0
18 TraesCS1A01G209800 chr4B 83.148 629 81 12 854 1478 603026250 603025643 3.540000e-153 551.0
19 TraesCS1A01G209800 chr4D 83.787 882 81 35 624 1478 477558660 477559506 0.000000e+00 780.0
20 TraesCS1A01G209800 chr4D 91.129 248 14 4 1885 2132 423981016 423981255 1.800000e-86 329.0
21 TraesCS1A01G209800 chr4D 92.891 211 12 1 2225 2432 423981254 423981464 1.090000e-78 303.0
22 TraesCS1A01G209800 chr4D 86.000 150 15 3 2292 2435 205903439 205903588 3.240000e-34 156.0
23 TraesCS1A01G209800 chr3B 89.408 557 40 5 1885 2435 810628909 810628366 0.000000e+00 684.0
24 TraesCS1A01G209800 chr3B 90.608 362 28 5 1958 2319 472653954 472654309 2.190000e-130 475.0
25 TraesCS1A01G209800 chr3B 79.419 413 56 22 1889 2291 335834249 335834642 5.160000e-67 265.0
26 TraesCS1A01G209800 chr3B 90.698 129 8 2 2307 2432 472660408 472660535 4.160000e-38 169.0
27 TraesCS1A01G209800 chr5B 89.493 552 41 9 1889 2435 267667697 267667158 0.000000e+00 682.0
28 TraesCS1A01G209800 chr7A 89.358 545 36 12 1889 2432 514818312 514818835 0.000000e+00 665.0
29 TraesCS1A01G209800 chr4A 82.230 816 91 33 846 1645 684449413 684448636 0.000000e+00 654.0
30 TraesCS1A01G209800 chr4A 93.878 49 1 1 2250 2296 467262360 467262312 3.360000e-09 73.1
31 TraesCS1A01G209800 chr5D 83.289 377 40 14 1874 2239 224874039 224874403 2.330000e-85 326.0
32 TraesCS1A01G209800 chr6B 81.383 376 45 19 1887 2253 126289028 126289387 1.430000e-72 283.0
33 TraesCS1A01G209800 chr7B 79.529 425 58 23 1885 2296 106803712 106803304 2.380000e-70 276.0
34 TraesCS1A01G209800 chr5A 92.045 176 11 3 1886 2061 26523378 26523550 6.730000e-61 244.0


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 TraesCS1A01G209800 chr1A 372286159 372288593 2434 True 4497.000000 4497 100.0000 1 2435 1 chr1A.!!$R1 2434
1 TraesCS1A01G209800 chr1A 372315473 372316668 1195 True 1637.000000 1637 91.3790 397 1603 1 chr1A.!!$R2 1206
2 TraesCS1A01G209800 chr1D 298598479 298604973 6494 True 633.000000 1755 91.2440 320 1877 5 chr1D.!!$R2 1557
3 TraesCS1A01G209800 chr1B 401991702 401993318 1616 True 1113.000000 1463 91.8150 3 1678 2 chr1B.!!$R3 1675
4 TraesCS1A01G209800 chr1B 401762916 401766179 3263 True 735.833333 1742 92.1810 1 1678 3 chr1B.!!$R2 1677
5 TraesCS1A01G209800 chr1B 402038961 402040119 1158 True 722.500000 1212 88.7195 320 1622 2 chr1B.!!$R4 1302
6 TraesCS1A01G209800 chr4B 603037675 603038646 971 False 808.000000 808 82.1540 624 1600 1 chr4B.!!$F1 976
7 TraesCS1A01G209800 chr4B 603148095 603149087 992 False 774.000000 774 81.3220 624 1639 1 chr4B.!!$F2 1015
8 TraesCS1A01G209800 chr4B 603025643 603026250 607 True 551.000000 551 83.1480 854 1478 1 chr4B.!!$R1 624
9 TraesCS1A01G209800 chr4D 477558660 477559506 846 False 780.000000 780 83.7870 624 1478 1 chr4D.!!$F2 854
10 TraesCS1A01G209800 chr3B 810628366 810628909 543 True 684.000000 684 89.4080 1885 2435 1 chr3B.!!$R1 550
11 TraesCS1A01G209800 chr5B 267667158 267667697 539 True 682.000000 682 89.4930 1889 2435 1 chr5B.!!$R1 546
12 TraesCS1A01G209800 chr7A 514818312 514818835 523 False 665.000000 665 89.3580 1889 2432 1 chr7A.!!$F1 543
13 TraesCS1A01G209800 chr4A 684448636 684449413 777 True 654.000000 654 82.2300 846 1645 1 chr4A.!!$R2 799

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
534 2241 0.459585 TATTTCCGTGTCCTCTGCGC 60.46 55.0 0.0 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 8626 0.035598 TGCCAAACGCAGCCTTAGTA 59.964 50.0 0.0 0.0 44.64 1.82 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 28 6.767902 ACCTCATTATCTCGCAAATTATGTGT 59.232 34.615 0.00 0.00 40.52 3.72
65 66 1.185315 CTTGTTGGTTGCATAGGGGG 58.815 55.000 0.00 0.00 0.00 5.40
106 532 8.622948 AAATTATACTAGCAGATTGTAAGCCC 57.377 34.615 0.00 0.00 0.00 5.19
131 557 6.747280 CGTTGCTATGGAATAAAACTCTTTGG 59.253 38.462 0.00 0.00 0.00 3.28
137 563 5.459505 TGGAATAAAACTCTTTGGTTCCCA 58.540 37.500 0.00 0.00 38.54 4.37
138 564 5.303333 TGGAATAAAACTCTTTGGTTCCCAC 59.697 40.000 0.00 0.00 38.54 4.61
249 675 2.301870 TCCGTCAAGCTTAATCTGTGGT 59.698 45.455 0.00 0.00 0.00 4.16
262 688 5.853572 AATCTGTGGTAAAGTTCCCCTTA 57.146 39.130 0.00 0.00 31.48 2.69
318 1912 4.002316 TCGAAATGACAATGATGAGCACA 58.998 39.130 0.00 0.00 0.00 4.57
327 1921 8.002984 TGACAATGATGAGCACATGATTAATT 57.997 30.769 8.34 0.00 38.02 1.40
370 1964 4.649692 ACCAGATGACTATCAATGGATGC 58.350 43.478 16.27 0.00 38.73 3.91
532 2239 2.213499 CCATATTTCCGTGTCCTCTGC 58.787 52.381 0.00 0.00 0.00 4.26
533 2240 1.860950 CATATTTCCGTGTCCTCTGCG 59.139 52.381 0.00 0.00 0.00 5.18
534 2241 0.459585 TATTTCCGTGTCCTCTGCGC 60.460 55.000 0.00 0.00 0.00 6.09
535 2242 3.756288 TATTTCCGTGTCCTCTGCGCC 62.756 57.143 4.18 0.00 0.00 6.53
557 2264 3.492421 CGTACCGCTAACTAAGTCCAA 57.508 47.619 0.00 0.00 0.00 3.53
558 2265 3.432782 CGTACCGCTAACTAAGTCCAAG 58.567 50.000 0.00 0.00 0.00 3.61
559 2266 2.381725 ACCGCTAACTAAGTCCAAGC 57.618 50.000 0.00 0.00 0.00 4.01
563 2270 3.993508 GCTAACTAAGTCCAAGCGTTC 57.006 47.619 0.00 0.00 0.00 3.95
564 2271 3.323243 GCTAACTAAGTCCAAGCGTTCA 58.677 45.455 0.00 0.00 0.00 3.18
565 2272 3.123116 GCTAACTAAGTCCAAGCGTTCAC 59.877 47.826 0.00 0.00 0.00 3.18
566 2273 2.902705 ACTAAGTCCAAGCGTTCACA 57.097 45.000 0.00 0.00 0.00 3.58
567 2274 2.480845 ACTAAGTCCAAGCGTTCACAC 58.519 47.619 0.00 0.00 0.00 3.82
568 2275 1.798813 CTAAGTCCAAGCGTTCACACC 59.201 52.381 0.00 0.00 0.00 4.16
569 2276 0.818040 AAGTCCAAGCGTTCACACCC 60.818 55.000 0.00 0.00 0.00 4.61
570 2277 2.112297 TCCAAGCGTTCACACCCC 59.888 61.111 0.00 0.00 0.00 4.95
571 2278 2.203280 CCAAGCGTTCACACCCCA 60.203 61.111 0.00 0.00 0.00 4.96
572 2279 1.603455 CCAAGCGTTCACACCCCAT 60.603 57.895 0.00 0.00 0.00 4.00
573 2280 1.580942 CAAGCGTTCACACCCCATG 59.419 57.895 0.00 0.00 0.00 3.66
574 2281 1.603455 AAGCGTTCACACCCCATGG 60.603 57.895 4.14 4.14 37.80 3.66
576 2283 1.901464 GCGTTCACACCCCATGGTT 60.901 57.895 11.73 0.00 44.75 3.67
577 2284 0.606944 GCGTTCACACCCCATGGTTA 60.607 55.000 11.73 0.00 44.75 2.85
578 2285 1.898902 CGTTCACACCCCATGGTTAA 58.101 50.000 11.73 0.00 44.75 2.01
579 2286 2.442413 CGTTCACACCCCATGGTTAAT 58.558 47.619 11.73 0.00 44.75 1.40
580 2287 2.823154 CGTTCACACCCCATGGTTAATT 59.177 45.455 11.73 0.00 44.75 1.40
581 2288 4.011023 CGTTCACACCCCATGGTTAATTA 58.989 43.478 11.73 0.00 44.75 1.40
582 2289 4.642885 CGTTCACACCCCATGGTTAATTAT 59.357 41.667 11.73 0.00 44.75 1.28
583 2290 5.126384 CGTTCACACCCCATGGTTAATTATT 59.874 40.000 11.73 0.00 44.75 1.40
584 2291 6.337356 GTTCACACCCCATGGTTAATTATTG 58.663 40.000 11.73 0.00 44.75 1.90
585 2292 4.404073 TCACACCCCATGGTTAATTATTGC 59.596 41.667 11.73 0.00 44.75 3.56
586 2293 3.709141 ACACCCCATGGTTAATTATTGCC 59.291 43.478 11.73 0.00 44.75 4.52
587 2294 3.966665 CACCCCATGGTTAATTATTGCCT 59.033 43.478 11.73 0.00 44.75 4.75
588 2295 5.144100 CACCCCATGGTTAATTATTGCCTA 58.856 41.667 11.73 0.00 44.75 3.93
589 2296 5.600484 CACCCCATGGTTAATTATTGCCTAA 59.400 40.000 11.73 0.00 44.75 2.69
590 2297 6.098982 CACCCCATGGTTAATTATTGCCTAAA 59.901 38.462 11.73 0.00 44.75 1.85
591 2298 6.674419 ACCCCATGGTTAATTATTGCCTAAAA 59.326 34.615 11.73 0.00 44.75 1.52
592 2299 7.182930 ACCCCATGGTTAATTATTGCCTAAAAA 59.817 33.333 11.73 0.00 44.75 1.94
593 2300 8.217111 CCCCATGGTTAATTATTGCCTAAAAAT 58.783 33.333 11.73 0.00 0.00 1.82
727 2440 5.591877 ACTTGTTGCCATATCTCCAGAATTC 59.408 40.000 0.00 0.00 0.00 2.17
765 2494 6.344500 TGCTTAAATCTTGTCTCATCTCTCC 58.656 40.000 0.00 0.00 0.00 3.71
878 2616 2.047679 ACTACGTCAAACAGCTCGAC 57.952 50.000 0.00 0.00 0.00 4.20
886 2629 2.198304 AAACAGCTCGACCCCATCCC 62.198 60.000 0.00 0.00 0.00 3.85
938 2685 2.888212 ACAACTCTCTCCAAGCTCTCT 58.112 47.619 0.00 0.00 0.00 3.10
961 2708 1.001181 CATCCCAAACCCAAAGCACTG 59.999 52.381 0.00 0.00 0.00 3.66
962 2709 0.758685 TCCCAAACCCAAAGCACTGG 60.759 55.000 0.00 0.00 36.10 4.00
963 2710 0.758685 CCCAAACCCAAAGCACTGGA 60.759 55.000 5.68 0.00 38.96 3.86
964 2711 0.675633 CCAAACCCAAAGCACTGGAG 59.324 55.000 5.68 0.00 38.96 3.86
965 2712 1.402787 CAAACCCAAAGCACTGGAGT 58.597 50.000 5.68 0.10 38.96 3.85
974 2721 5.233988 CCAAAGCACTGGAGTAGCTATATC 58.766 45.833 0.00 0.00 38.96 1.63
976 2723 6.462500 CAAAGCACTGGAGTAGCTATATCAT 58.538 40.000 0.00 0.00 37.70 2.45
1006 2753 1.337074 CCCACACAATCACAATGGCAC 60.337 52.381 0.00 0.00 0.00 5.01
1011 2758 1.259609 CAATCACAATGGCACCCAGT 58.740 50.000 0.00 0.00 36.75 4.00
1024 2771 2.752358 CCAGTGCTGCCCTCTTCA 59.248 61.111 0.00 0.00 0.00 3.02
1219 2980 2.202946 TGTGCGCCAACGTTCTCA 60.203 55.556 4.18 0.00 42.83 3.27
1436 3201 0.114168 ACTTGCCCAGCCCATTAACA 59.886 50.000 0.00 0.00 0.00 2.41
1439 3206 0.407528 TGCCCAGCCCATTAACAGAA 59.592 50.000 0.00 0.00 0.00 3.02
1444 3211 3.279434 CCAGCCCATTAACAGAAGTACC 58.721 50.000 0.00 0.00 0.00 3.34
1496 3283 5.390567 GCTTTCCGTACTTCGTTTTCATGAT 60.391 40.000 0.00 0.00 37.94 2.45
1497 3284 5.524511 TTCCGTACTTCGTTTTCATGATG 57.475 39.130 0.00 0.00 37.94 3.07
1551 3342 8.868522 ATTGTGTAACCAGTACTACTACAGTA 57.131 34.615 9.85 4.15 35.50 2.74
1552 3343 8.868522 TTGTGTAACCAGTACTACTACAGTAT 57.131 34.615 9.85 0.00 37.89 2.12
1553 3344 8.868522 TGTGTAACCAGTACTACTACAGTATT 57.131 34.615 9.85 0.00 37.89 1.89
1554 3345 9.300681 TGTGTAACCAGTACTACTACAGTATTT 57.699 33.333 9.85 0.00 37.89 1.40
1687 8427 6.029346 ATTTGTACAAAATAGCTTGCAGCT 57.971 33.333 23.97 13.86 43.32 4.24
1747 8490 0.170339 GGGAAAAAGGCGATCAACGG 59.830 55.000 0.00 0.00 42.83 4.44
1748 8491 0.170339 GGAAAAAGGCGATCAACGGG 59.830 55.000 0.00 0.00 42.83 5.28
1749 8492 1.161843 GAAAAAGGCGATCAACGGGA 58.838 50.000 0.00 0.00 42.83 5.14
1750 8493 0.879090 AAAAAGGCGATCAACGGGAC 59.121 50.000 0.00 0.00 42.83 4.46
1766 8509 0.376152 GGACGAACAGATGCAGCATG 59.624 55.000 14.22 3.05 40.87 4.06
1767 8510 1.362768 GACGAACAGATGCAGCATGA 58.637 50.000 14.22 0.00 39.69 3.07
1773 8516 1.212195 ACAGATGCAGCATGACCATCT 59.788 47.619 14.22 13.94 43.62 2.90
1785 8528 7.309012 GCAGCATGACCATCTACAATTAATGAT 60.309 37.037 0.00 0.00 39.69 2.45
1844 8587 5.139727 ACAACACCTCCATGAAAGAAATGA 58.860 37.500 0.00 0.00 0.00 2.57
1846 8589 3.753272 ACACCTCCATGAAAGAAATGACG 59.247 43.478 0.00 0.00 0.00 4.35
1847 8590 3.753272 CACCTCCATGAAAGAAATGACGT 59.247 43.478 0.00 0.00 0.00 4.34
1849 8592 4.216257 ACCTCCATGAAAGAAATGACGTTG 59.784 41.667 0.00 0.00 0.00 4.10
1858 8601 3.359654 AGAAATGACGTTGAAACAACGC 58.640 40.909 28.27 22.20 46.58 4.84
1859 8602 3.064820 AGAAATGACGTTGAAACAACGCT 59.935 39.130 28.27 18.80 46.58 5.07
1865 8608 1.062002 CGTTGAAACAACGCTGTCACT 59.938 47.619 20.54 0.00 36.82 3.41
1866 8609 2.283086 CGTTGAAACAACGCTGTCACTA 59.717 45.455 20.54 0.00 36.82 2.74
1874 8617 4.878439 ACAACGCTGTCACTAGATACAAA 58.122 39.130 0.00 0.00 0.00 2.83
1877 8620 6.752351 ACAACGCTGTCACTAGATACAAATAG 59.248 38.462 0.00 0.00 0.00 1.73
1878 8621 6.452494 ACGCTGTCACTAGATACAAATAGT 57.548 37.500 0.00 0.00 32.44 2.12
1879 8622 6.496571 ACGCTGTCACTAGATACAAATAGTC 58.503 40.000 0.00 0.00 29.77 2.59
1880 8623 6.095021 ACGCTGTCACTAGATACAAATAGTCA 59.905 38.462 0.00 0.00 29.77 3.41
1881 8624 6.972901 CGCTGTCACTAGATACAAATAGTCAA 59.027 38.462 0.00 0.00 29.77 3.18
1882 8625 7.488150 CGCTGTCACTAGATACAAATAGTCAAA 59.512 37.037 0.00 0.00 29.77 2.69
1883 8626 9.319143 GCTGTCACTAGATACAAATAGTCAAAT 57.681 33.333 0.00 0.00 29.77 2.32
1901 8644 1.379527 ATACTAAGGCTGCGTTTGGC 58.620 50.000 13.17 0.00 43.96 4.52
1911 8656 3.560826 GCGTTTGGCAGCAAAGTTA 57.439 47.368 0.00 0.00 42.87 2.24
1946 8692 0.800012 GCAATACCGCGGTTTCTGAA 59.200 50.000 38.94 18.62 0.00 3.02
1947 8693 1.198178 GCAATACCGCGGTTTCTGAAA 59.802 47.619 38.94 17.74 0.00 2.69
1948 8694 2.727916 GCAATACCGCGGTTTCTGAAAG 60.728 50.000 38.94 17.91 0.00 2.62
2106 8853 0.530870 GGAGAGAAAAGATCGGGGCG 60.531 60.000 0.00 0.00 0.00 6.13
2107 8854 0.460311 GAGAGAAAAGATCGGGGCGA 59.540 55.000 0.00 0.00 41.13 5.54
2126 8873 0.933097 ATCGCATCGCAGTTGACATC 59.067 50.000 0.00 0.00 0.00 3.06
2181 8929 6.915843 TGCGATCCTTTTTCTTTTTCTGTTAC 59.084 34.615 0.00 0.00 0.00 2.50
2258 9006 2.298610 CCACGTGCTAGTCTCCATCTA 58.701 52.381 10.91 0.00 0.00 1.98
2311 9060 6.015350 CACCAAGGGATAGACATATTCTACGT 60.015 42.308 0.00 0.00 39.78 3.57
2399 9151 5.566826 GCCGCTAATTACTCAGTCATCCATA 60.567 44.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.343758 GGTGCTTCGAGCTGTCCA 59.656 61.111 0.00 0.00 42.97 4.02
106 532 6.747280 CCAAAGAGTTTTATTCCATAGCAACG 59.253 38.462 0.00 0.00 0.00 4.10
131 557 4.622933 GCCAGATTATTTTTGGGTGGGAAC 60.623 45.833 0.00 0.00 32.53 3.62
137 563 4.167319 ACCTTGCCAGATTATTTTTGGGT 58.833 39.130 0.00 0.00 32.53 4.51
138 564 4.824479 ACCTTGCCAGATTATTTTTGGG 57.176 40.909 0.00 0.00 32.53 4.12
198 624 1.355916 GTGTCCTAGCTAGGCGTCG 59.644 63.158 31.76 10.94 43.31 5.12
249 675 8.826293 TGAGTTTTCTTTTAAGGGGAACTTTA 57.174 30.769 0.00 0.00 40.64 1.85
262 688 6.460261 GCAGAGCTTTACCTGAGTTTTCTTTT 60.460 38.462 4.41 0.00 32.37 2.27
348 1942 4.103627 TGCATCCATTGATAGTCATCTGGT 59.896 41.667 8.18 0.00 33.64 4.00
370 1964 7.381323 TGTATGATATGCTGGTTCTACAGATG 58.619 38.462 0.00 0.00 40.97 2.90
538 2245 3.185330 GCTTGGACTTAGTTAGCGGTAC 58.815 50.000 0.00 0.00 0.00 3.34
539 2246 3.515330 GCTTGGACTTAGTTAGCGGTA 57.485 47.619 0.00 0.00 0.00 4.02
540 2247 2.381725 GCTTGGACTTAGTTAGCGGT 57.618 50.000 0.00 0.00 0.00 5.68
543 2250 3.123116 GTGAACGCTTGGACTTAGTTAGC 59.877 47.826 5.42 5.42 0.00 3.09
544 2251 4.150098 GTGTGAACGCTTGGACTTAGTTAG 59.850 45.833 0.00 0.00 0.00 2.34
545 2252 4.053295 GTGTGAACGCTTGGACTTAGTTA 58.947 43.478 0.00 0.00 0.00 2.24
546 2253 2.870411 GTGTGAACGCTTGGACTTAGTT 59.130 45.455 0.00 0.00 0.00 2.24
547 2254 2.480845 GTGTGAACGCTTGGACTTAGT 58.519 47.619 0.00 0.00 0.00 2.24
548 2255 1.798813 GGTGTGAACGCTTGGACTTAG 59.201 52.381 0.00 0.00 0.00 2.18
549 2256 1.541670 GGGTGTGAACGCTTGGACTTA 60.542 52.381 0.00 0.00 0.00 2.24
550 2257 0.818040 GGGTGTGAACGCTTGGACTT 60.818 55.000 0.00 0.00 0.00 3.01
551 2258 1.227853 GGGTGTGAACGCTTGGACT 60.228 57.895 0.00 0.00 0.00 3.85
552 2259 2.258726 GGGGTGTGAACGCTTGGAC 61.259 63.158 0.00 0.00 0.00 4.02
553 2260 2.063015 ATGGGGTGTGAACGCTTGGA 62.063 55.000 0.00 0.00 0.00 3.53
554 2261 1.603455 ATGGGGTGTGAACGCTTGG 60.603 57.895 0.00 0.00 0.00 3.61
555 2262 1.580942 CATGGGGTGTGAACGCTTG 59.419 57.895 0.00 0.00 0.00 4.01
556 2263 1.603455 CCATGGGGTGTGAACGCTT 60.603 57.895 2.85 0.00 0.00 4.68
557 2264 2.034066 CCATGGGGTGTGAACGCT 59.966 61.111 2.85 0.00 0.00 5.07
567 2274 6.739331 TTTAGGCAATAATTAACCATGGGG 57.261 37.500 18.09 0.00 41.29 4.96
577 2284 8.927411 AGCATCAGGTATTTTTAGGCAATAATT 58.073 29.630 0.00 0.00 0.00 1.40
578 2285 8.482852 AGCATCAGGTATTTTTAGGCAATAAT 57.517 30.769 0.00 0.00 0.00 1.28
579 2286 7.896383 AGCATCAGGTATTTTTAGGCAATAA 57.104 32.000 0.00 0.00 0.00 1.40
580 2287 7.896383 AAGCATCAGGTATTTTTAGGCAATA 57.104 32.000 0.00 0.00 0.00 1.90
581 2288 6.796785 AAGCATCAGGTATTTTTAGGCAAT 57.203 33.333 0.00 0.00 0.00 3.56
582 2289 6.437162 AGAAAGCATCAGGTATTTTTAGGCAA 59.563 34.615 0.00 0.00 0.00 4.52
583 2290 5.951747 AGAAAGCATCAGGTATTTTTAGGCA 59.048 36.000 0.00 0.00 0.00 4.75
584 2291 6.095440 TGAGAAAGCATCAGGTATTTTTAGGC 59.905 38.462 0.00 0.00 0.00 3.93
585 2292 7.630242 TGAGAAAGCATCAGGTATTTTTAGG 57.370 36.000 0.00 0.00 0.00 2.69
586 2293 8.734386 AGTTGAGAAAGCATCAGGTATTTTTAG 58.266 33.333 0.00 0.00 0.00 1.85
587 2294 8.635765 AGTTGAGAAAGCATCAGGTATTTTTA 57.364 30.769 0.00 0.00 0.00 1.52
588 2295 7.530426 AGTTGAGAAAGCATCAGGTATTTTT 57.470 32.000 0.00 0.00 0.00 1.94
589 2296 7.373493 CAAGTTGAGAAAGCATCAGGTATTTT 58.627 34.615 0.00 0.00 0.00 1.82
590 2297 6.571150 GCAAGTTGAGAAAGCATCAGGTATTT 60.571 38.462 7.16 0.00 0.00 1.40
591 2298 5.105997 GCAAGTTGAGAAAGCATCAGGTATT 60.106 40.000 7.16 0.00 0.00 1.89
592 2299 4.397417 GCAAGTTGAGAAAGCATCAGGTAT 59.603 41.667 7.16 0.00 0.00 2.73
593 2300 3.753272 GCAAGTTGAGAAAGCATCAGGTA 59.247 43.478 7.16 0.00 0.00 3.08
594 2301 2.555757 GCAAGTTGAGAAAGCATCAGGT 59.444 45.455 7.16 0.00 0.00 4.00
595 2302 2.818432 AGCAAGTTGAGAAAGCATCAGG 59.182 45.455 7.16 0.00 0.00 3.86
596 2303 4.500603 AAGCAAGTTGAGAAAGCATCAG 57.499 40.909 7.16 0.00 0.00 2.90
597 2304 6.654582 TGTATAAGCAAGTTGAGAAAGCATCA 59.345 34.615 7.16 0.00 0.00 3.07
598 2305 7.076842 TGTATAAGCAAGTTGAGAAAGCATC 57.923 36.000 7.16 0.00 0.00 3.91
691 2400 1.134946 GCAACAAGTTGAGCAACACCT 59.865 47.619 16.54 0.00 43.47 4.00
757 2486 7.854422 CGATGTATCATTTGTTTTGGAGAGATG 59.146 37.037 0.00 0.00 0.00 2.90
765 2494 7.148423 TGTCCTCTCGATGTATCATTTGTTTTG 60.148 37.037 0.00 0.00 0.00 2.44
878 2616 1.535444 ATGCATGCATGGGATGGGG 60.535 57.895 31.74 0.11 35.03 4.96
886 2629 2.823154 TGGTGATATGGATGCATGCATG 59.177 45.455 35.62 22.70 39.29 4.06
938 2685 0.396060 GCTTTGGGTTTGGGATGCAA 59.604 50.000 0.00 0.00 0.00 4.08
961 2708 7.254852 GTGTGCTAGAATGATATAGCTACTCC 58.745 42.308 0.00 0.00 44.78 3.85
962 2709 7.254852 GGTGTGCTAGAATGATATAGCTACTC 58.745 42.308 0.00 0.00 44.78 2.59
963 2710 6.153680 GGGTGTGCTAGAATGATATAGCTACT 59.846 42.308 0.00 0.00 44.78 2.57
964 2711 6.071334 TGGGTGTGCTAGAATGATATAGCTAC 60.071 42.308 0.00 8.85 44.78 3.58
965 2712 6.016555 TGGGTGTGCTAGAATGATATAGCTA 58.983 40.000 0.00 0.00 44.78 3.32
974 2721 2.183478 TGTGTGGGTGTGCTAGAATG 57.817 50.000 0.00 0.00 0.00 2.67
976 2723 2.105649 TGATTGTGTGGGTGTGCTAGAA 59.894 45.455 0.00 0.00 0.00 2.10
1006 2753 2.045536 GAAGAGGGCAGCACTGGG 60.046 66.667 0.00 0.00 0.00 4.45
1011 2758 2.124983 GCGATGAAGAGGGCAGCA 60.125 61.111 0.00 0.00 0.00 4.41
1024 2771 2.841988 GAGGAGGCTCAGGGCGAT 60.842 66.667 17.69 0.00 42.94 4.58
1219 2980 3.386237 GAGGCCGAGCAGTCCACT 61.386 66.667 0.00 0.00 0.00 4.00
1253 3014 3.364441 GGCAGCATTGGTCGTGCA 61.364 61.111 0.00 0.00 44.87 4.57
1436 3201 2.159382 CCCATGCAAAACGGTACTTCT 58.841 47.619 0.00 0.00 0.00 2.85
1439 3206 1.582610 CGCCCATGCAAAACGGTACT 61.583 55.000 0.00 0.00 37.32 2.73
1552 3343 9.674824 CATGCTTGTTTGCCAAAAATAAATAAA 57.325 25.926 0.00 0.00 31.20 1.40
1553 3344 8.844244 ACATGCTTGTTTGCCAAAAATAAATAA 58.156 25.926 0.00 0.00 29.55 1.40
1554 3345 8.388484 ACATGCTTGTTTGCCAAAAATAAATA 57.612 26.923 0.00 0.00 29.55 1.40
1555 3346 7.274603 ACATGCTTGTTTGCCAAAAATAAAT 57.725 28.000 0.00 0.00 29.55 1.40
1556 3347 6.690194 ACATGCTTGTTTGCCAAAAATAAA 57.310 29.167 0.00 0.00 29.55 1.40
1559 3350 5.367302 AGTACATGCTTGTTTGCCAAAAAT 58.633 33.333 10.85 0.00 37.28 1.82
1712 8452 9.767228 GCCTTTTTCCCTTTTTGTTAATAACTA 57.233 29.630 4.67 0.00 0.00 2.24
1730 8470 1.135774 GTCCCGTTGATCGCCTTTTTC 60.136 52.381 0.00 0.00 38.35 2.29
1736 8476 2.125832 TTCGTCCCGTTGATCGCC 60.126 61.111 0.00 0.00 38.35 5.54
1747 8490 0.376152 CATGCTGCATCTGTTCGTCC 59.624 55.000 13.10 0.00 0.00 4.79
1748 8491 1.061711 GTCATGCTGCATCTGTTCGTC 59.938 52.381 13.10 0.00 0.00 4.20
1749 8492 1.081892 GTCATGCTGCATCTGTTCGT 58.918 50.000 13.10 0.00 0.00 3.85
1750 8493 0.376152 GGTCATGCTGCATCTGTTCG 59.624 55.000 13.10 0.27 0.00 3.95
1773 8516 6.068010 CCTAGGGTTGCCATCATTAATTGTA 58.932 40.000 0.00 0.00 0.00 2.41
1802 8545 1.073284 GTTGTTGGAGCACCTTCCCTA 59.927 52.381 0.71 0.00 36.35 3.53
1844 8587 1.080298 TGACAGCGTTGTTTCAACGT 58.920 45.000 27.17 16.05 44.69 3.99
1846 8589 2.825086 AGTGACAGCGTTGTTTCAAC 57.175 45.000 6.30 3.60 37.76 3.18
1847 8590 3.787785 TCTAGTGACAGCGTTGTTTCAA 58.212 40.909 6.30 0.00 37.76 2.69
1849 8592 4.921515 TGTATCTAGTGACAGCGTTGTTTC 59.078 41.667 6.30 3.11 37.76 2.78
1874 8617 5.277857 ACGCAGCCTTAGTATTTGACTAT 57.722 39.130 0.00 0.00 40.43 2.12
1877 8620 4.403453 CAAACGCAGCCTTAGTATTTGAC 58.597 43.478 0.00 0.00 0.00 3.18
1878 8621 3.438781 CCAAACGCAGCCTTAGTATTTGA 59.561 43.478 0.00 0.00 0.00 2.69
1879 8622 3.758300 CCAAACGCAGCCTTAGTATTTG 58.242 45.455 0.00 0.00 0.00 2.32
1880 8623 2.163613 GCCAAACGCAGCCTTAGTATTT 59.836 45.455 0.00 0.00 37.47 1.40
1881 8624 1.743394 GCCAAACGCAGCCTTAGTATT 59.257 47.619 0.00 0.00 37.47 1.89
1882 8625 1.339631 TGCCAAACGCAGCCTTAGTAT 60.340 47.619 0.00 0.00 44.64 2.12
1883 8626 0.035598 TGCCAAACGCAGCCTTAGTA 59.964 50.000 0.00 0.00 44.64 1.82
1911 8656 6.367695 GCGGTATTGCCAGAAAACTTTAAAAT 59.632 34.615 0.00 0.00 36.97 1.82
1964 8710 4.519540 AGCCAAACGCATCAAAGTATTT 57.480 36.364 0.00 0.00 38.61 1.40
2106 8853 0.933097 ATGTCAACTGCGATGCGATC 59.067 50.000 0.00 0.00 0.00 3.69
2107 8854 0.933097 GATGTCAACTGCGATGCGAT 59.067 50.000 0.00 0.00 0.00 4.58
2108 8855 1.413008 CGATGTCAACTGCGATGCGA 61.413 55.000 0.00 0.00 0.00 5.10
2109 8856 1.012998 CGATGTCAACTGCGATGCG 60.013 57.895 0.00 0.00 0.00 4.73
2110 8857 1.297158 GCGATGTCAACTGCGATGC 60.297 57.895 0.00 0.00 0.00 3.91
2126 8873 1.596260 TGTTATCTCGAGTAGACGGCG 59.404 52.381 13.13 4.80 36.93 6.46
2258 9006 5.608449 TGATTCGCTCATGATGAAGAGAAT 58.392 37.500 16.82 16.82 32.08 2.40
2311 9060 5.929415 CGCTCGATCTATAGATGCTAGGATA 59.071 44.000 20.05 0.00 34.37 2.59


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

AutoCloner maintained by Alex Coulton.