Multiple sequence alignment - TraesCS2D01G215900

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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 TraesCS2D01G215900 chr2D 100.000 2693 0 0 1 2693 178778384 178775692 0.000000e+00 4974.0
1 TraesCS2D01G215900 chr2D 96.892 1255 22 7 607 1849 178287749 178286500 0.000000e+00 2085.0
2 TraesCS2D01G215900 chr2D 95.455 748 21 6 1019 1755 178612287 178611542 0.000000e+00 1181.0
3 TraesCS2D01G215900 chr2D 94.675 770 24 6 1932 2691 178286500 178285738 0.000000e+00 1179.0
4 TraesCS2D01G215900 chr2D 91.766 668 37 10 1991 2644 178284131 178283468 0.000000e+00 913.0
5 TraesCS2D01G215900 chr2D 92.123 457 33 2 1967 2420 178611279 178610823 2.260000e-180 641.0
6 TraesCS2D01G215900 chr2D 87.845 362 33 6 253 606 185370909 185370551 5.360000e-112 414.0
7 TraesCS2D01G215900 chr2D 94.118 204 9 2 2443 2644 178605979 178605777 9.370000e-80 307.0
8 TraesCS2D01G215900 chr2D 91.960 199 16 0 836 1034 178616985 178616787 2.040000e-71 279.0
9 TraesCS2D01G215900 chr2D 96.053 152 3 1 1559 1710 178284614 178284466 7.450000e-61 244.0
10 TraesCS2D01G215900 chr2D 88.235 119 10 3 609 723 178620470 178620352 3.620000e-29 139.0
11 TraesCS2D01G215900 chr2D 97.959 49 1 0 1754 1802 178611510 178611462 4.780000e-13 86.1
12 TraesCS2D01G215900 chr2D 97.727 44 1 0 609 652 178307918 178307875 2.880000e-10 76.8
13 TraesCS2D01G215900 chr2B 94.540 934 34 8 841 1758 235578820 235577888 0.000000e+00 1426.0
14 TraesCS2D01G215900 chr2B 91.235 251 16 4 2397 2644 235577097 235576850 1.190000e-88 337.0
15 TraesCS2D01G215900 chr1D 94.669 619 25 3 4 615 58876587 58875970 0.000000e+00 953.0
16 TraesCS2D01G215900 chr1D 94.023 619 20 7 4 607 379490094 379489478 0.000000e+00 922.0
17 TraesCS2D01G215900 chr1D 86.481 503 46 9 1 485 386914872 386915370 1.420000e-147 532.0
18 TraesCS2D01G215900 chr1D 90.361 332 31 1 276 606 110021044 110021375 4.120000e-118 435.0
19 TraesCS2D01G215900 chr1D 81.391 489 55 20 4 482 426922243 426921781 1.520000e-97 366.0
20 TraesCS2D01G215900 chr1D 97.826 92 2 0 1846 1937 437574306 437574215 2.780000e-35 159.0
21 TraesCS2D01G215900 chr4D 92.512 641 28 8 4 629 6559557 6560192 0.000000e+00 900.0
22 TraesCS2D01G215900 chr4D 93.355 617 23 7 4 606 453056715 453057327 0.000000e+00 896.0
23 TraesCS2D01G215900 chr4D 90.826 109 7 3 1826 1934 23978629 23978734 2.790000e-30 143.0
24 TraesCS2D01G215900 chr1A 91.351 659 49 6 1991 2644 34174183 34173528 0.000000e+00 894.0
25 TraesCS2D01G215900 chr1A 80.938 341 34 11 838 1178 34174720 34174411 9.630000e-60 241.0
26 TraesCS2D01G215900 chr1A 94.444 108 4 2 1828 1934 486046059 486046165 5.960000e-37 165.0
27 TraesCS2D01G215900 chr7D 93.042 618 27 6 4 606 503800244 503799628 0.000000e+00 889.0
28 TraesCS2D01G215900 chr7D 85.571 499 50 12 4 485 88025215 88024722 1.110000e-138 503.0
29 TraesCS2D01G215900 chr7D 95.876 97 4 0 1842 1938 540399156 540399252 9.980000e-35 158.0
30 TraesCS2D01G215900 chr1B 91.311 610 44 7 2040 2644 54888157 54887552 0.000000e+00 824.0
31 TraesCS2D01G215900 chr1B 95.000 100 4 1 1837 1935 513248406 513248505 3.590000e-34 156.0
32 TraesCS2D01G215900 chr5D 85.060 502 56 9 1 485 546070505 546071004 6.700000e-136 494.0
33 TraesCS2D01G215900 chrUn 90.826 327 28 2 276 601 108529336 108529011 1.140000e-118 436.0
34 TraesCS2D01G215900 chr5A 90.060 332 31 2 276 606 409354368 409354698 1.920000e-116 429.0
35 TraesCS2D01G215900 chr2A 94.444 108 3 3 1825 1930 90521833 90521727 2.150000e-36 163.0
36 TraesCS2D01G215900 chr2A 95.876 97 2 2 1845 1939 71560835 71560739 3.590000e-34 156.0
37 TraesCS2D01G215900 chr6D 92.793 111 4 4 1831 1941 149721762 149721656 9.980000e-35 158.0
38 TraesCS2D01G215900 chr3D 95.876 97 3 1 1848 1944 923028 923123 3.590000e-34 156.0


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 TraesCS2D01G215900 chr2D 178775692 178778384 2692 True 4974.000000 4974 100.0000 1 2693 1 chr2D.!!$R3 2692
1 TraesCS2D01G215900 chr2D 178283468 178287749 4281 True 1105.250000 2085 94.8465 607 2691 4 chr2D.!!$R5 2084
2 TraesCS2D01G215900 chr2D 178610823 178612287 1464 True 636.033333 1181 95.1790 1019 2420 3 chr2D.!!$R6 1401
3 TraesCS2D01G215900 chr2D 178616787 178620470 3683 True 209.000000 279 90.0975 609 1034 2 chr2D.!!$R7 425
4 TraesCS2D01G215900 chr2B 235576850 235578820 1970 True 881.500000 1426 92.8875 841 2644 2 chr2B.!!$R1 1803
5 TraesCS2D01G215900 chr1D 58875970 58876587 617 True 953.000000 953 94.6690 4 615 1 chr1D.!!$R1 611
6 TraesCS2D01G215900 chr1D 379489478 379490094 616 True 922.000000 922 94.0230 4 607 1 chr1D.!!$R2 603
7 TraesCS2D01G215900 chr4D 6559557 6560192 635 False 900.000000 900 92.5120 4 629 1 chr4D.!!$F1 625
8 TraesCS2D01G215900 chr4D 453056715 453057327 612 False 896.000000 896 93.3550 4 606 1 chr4D.!!$F3 602
9 TraesCS2D01G215900 chr1A 34173528 34174720 1192 True 567.500000 894 86.1445 838 2644 2 chr1A.!!$R1 1806
10 TraesCS2D01G215900 chr7D 503799628 503800244 616 True 889.000000 889 93.0420 4 606 1 chr7D.!!$R2 602
11 TraesCS2D01G215900 chr1B 54887552 54888157 605 True 824.000000 824 91.3110 2040 2644 1 chr1B.!!$R1 604

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
873 4216 0.109458 TACGACATGAGACGCGCTTT 60.109 50.0 5.73 0.0 36.39 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2654 8767 0.105709 TAGCAGATCCATCCCCGTGA 60.106 55.0 0.0 0.0 0.0 4.35 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
88 89 6.979817 GCATGTATAGGCAATTGAACATCAAA 59.020 34.615 10.34 0.00 35.23 2.69
208 209 8.020819 TGAATTGCTTTTGTATGTAGCACTAAC 58.979 33.333 0.00 0.00 43.96 2.34
213 228 4.914312 TTGTATGTAGCACTAACGTTGC 57.086 40.909 11.99 6.85 0.00 4.17
290 305 7.598869 CCAAAAAGAAAAGTTGCTTCCCTATAC 59.401 37.037 0.00 0.00 0.00 1.47
476 493 7.732222 TTTTTGATCCCCTAATAAATGCAGT 57.268 32.000 0.00 0.00 0.00 4.40
721 742 2.890808 TTCGGGATCAGATACTGTGC 57.109 50.000 0.99 0.00 32.61 4.57
760 4103 0.835740 CCGAGTTATTACGACGCGTG 59.164 55.000 20.70 12.18 41.39 5.34
778 4121 2.660802 CCTAAACCACGCGTCCCT 59.339 61.111 9.86 0.00 0.00 4.20
780 4123 1.740296 CTAAACCACGCGTCCCTGG 60.740 63.158 9.86 10.92 0.00 4.45
873 4216 0.109458 TACGACATGAGACGCGCTTT 60.109 50.000 5.73 0.00 36.39 3.51
935 4278 7.602753 TGATGATTCGACTCCATATATTTCGT 58.397 34.615 0.00 0.00 0.00 3.85
954 4297 0.677731 TCAAAGCCTTGATCCAGCCG 60.678 55.000 0.00 0.00 36.62 5.52
1453 4803 1.305201 GGAAGCTTTGGACACGTTCA 58.695 50.000 0.00 0.00 0.00 3.18
1854 5498 9.830186 ACATATGACAATATTACTACTCCCTCT 57.170 33.333 10.38 0.00 0.00 3.69
1856 5500 9.830186 ATATGACAATATTACTACTCCCTCTGT 57.170 33.333 0.00 0.00 0.00 3.41
1857 5501 7.584122 TGACAATATTACTACTCCCTCTGTC 57.416 40.000 0.00 0.00 0.00 3.51
1858 5502 6.550108 TGACAATATTACTACTCCCTCTGTCC 59.450 42.308 0.00 0.00 30.78 4.02
1859 5503 5.839606 ACAATATTACTACTCCCTCTGTCCC 59.160 44.000 0.00 0.00 0.00 4.46
1860 5504 5.681494 ATATTACTACTCCCTCTGTCCCA 57.319 43.478 0.00 0.00 0.00 4.37
1861 5505 3.839323 TTACTACTCCCTCTGTCCCAA 57.161 47.619 0.00 0.00 0.00 4.12
1862 5506 2.715763 ACTACTCCCTCTGTCCCAAA 57.284 50.000 0.00 0.00 0.00 3.28
1863 5507 2.986050 ACTACTCCCTCTGTCCCAAAA 58.014 47.619 0.00 0.00 0.00 2.44
1864 5508 3.532102 ACTACTCCCTCTGTCCCAAAAT 58.468 45.455 0.00 0.00 0.00 1.82
1865 5509 4.695606 ACTACTCCCTCTGTCCCAAAATA 58.304 43.478 0.00 0.00 0.00 1.40
1866 5510 5.289510 ACTACTCCCTCTGTCCCAAAATAT 58.710 41.667 0.00 0.00 0.00 1.28
1867 5511 6.449956 ACTACTCCCTCTGTCCCAAAATATA 58.550 40.000 0.00 0.00 0.00 0.86
1868 5512 6.906901 ACTACTCCCTCTGTCCCAAAATATAA 59.093 38.462 0.00 0.00 0.00 0.98
1869 5513 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
1870 5514 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
1871 5515 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
1872 5516 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
1873 5517 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
1874 5518 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
1875 5519 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
1876 5520 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
1877 5521 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
1878 5522 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
1892 5536 8.707938 AAGAACGTTTTTAACACTACACTAGT 57.292 30.769 0.46 0.00 40.28 2.57
1905 5549 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
1906 5550 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
1907 5551 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
1908 5552 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
1909 5553 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
1910 5554 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
1911 5555 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
1921 5565 9.632969 CAAAAACGTTCTTATATTATGAGACGG 57.367 33.333 0.00 8.31 0.00 4.79
1922 5566 9.590451 AAAAACGTTCTTATATTATGAGACGGA 57.410 29.630 0.00 0.00 0.00 4.69
1923 5567 8.798748 AAACGTTCTTATATTATGAGACGGAG 57.201 34.615 0.00 6.40 0.00 4.63
1924 5568 6.910995 ACGTTCTTATATTATGAGACGGAGG 58.089 40.000 16.71 6.29 0.00 4.30
1925 5569 6.072064 ACGTTCTTATATTATGAGACGGAGGG 60.072 42.308 16.71 2.79 0.00 4.30
1926 5570 6.150641 CGTTCTTATATTATGAGACGGAGGGA 59.849 42.308 0.00 0.00 0.00 4.20
1927 5571 7.540299 GTTCTTATATTATGAGACGGAGGGAG 58.460 42.308 0.00 0.00 0.00 4.30
1928 5572 6.791371 TCTTATATTATGAGACGGAGGGAGT 58.209 40.000 0.00 0.00 0.00 3.85
1929 5573 7.925622 TCTTATATTATGAGACGGAGGGAGTA 58.074 38.462 0.00 0.00 0.00 2.59
1930 5574 8.558312 TCTTATATTATGAGACGGAGGGAGTAT 58.442 37.037 0.00 0.00 0.00 2.12
2055 5736 9.757227 TTACACGAAAATGAAATCAAAATCCTT 57.243 25.926 0.00 0.00 0.00 3.36
2114 5795 6.547141 TGAGTTCATGAAATCAAAAGTGGACT 59.453 34.615 30.42 11.27 41.62 3.85
2165 8167 4.571580 ACATTGCAAACCACAACAAATGAG 59.428 37.500 1.71 0.00 0.00 2.90
2186 8188 5.181811 TGAGTGCGAAAAATCACATTGATCT 59.818 36.000 0.00 0.00 35.76 2.75
2242 8245 5.737063 GCATCAGTTCTGAAACCACACAAAT 60.737 40.000 6.60 0.00 35.92 2.32
2331 8334 7.510675 AGGGTAAGACATCTAAATCTTTCCA 57.489 36.000 10.57 0.00 41.66 3.53
2354 8357 5.010719 CAGGGCAGAAGCAATCAATCAATAT 59.989 40.000 0.00 0.00 44.61 1.28
2442 8551 2.866762 CAAGATACGCTTCCTAGGTTGC 59.133 50.000 9.08 13.04 33.60 4.17
2443 8552 2.108168 AGATACGCTTCCTAGGTTGCA 58.892 47.619 21.83 9.31 0.00 4.08
2454 8565 1.476845 TAGGTTGCACAAGGCCGAGA 61.477 55.000 0.00 0.00 43.89 4.04
2477 8588 5.534207 ACCGTTCCATCCGTTATATGTAA 57.466 39.130 0.00 0.00 0.00 2.41
2479 8590 4.687483 CCGTTCCATCCGTTATATGTAACC 59.313 45.833 6.76 0.00 37.49 2.85
2482 8593 6.145048 CGTTCCATCCGTTATATGTAACCTTC 59.855 42.308 6.76 0.00 37.49 3.46
2483 8594 5.775686 TCCATCCGTTATATGTAACCTTCG 58.224 41.667 6.76 0.00 37.49 3.79
2484 8595 5.535783 TCCATCCGTTATATGTAACCTTCGA 59.464 40.000 6.76 0.00 37.49 3.71
2486 8597 5.443185 TCCGTTATATGTAACCTTCGAGG 57.557 43.478 6.76 1.99 42.49 4.63
2487 8598 5.132502 TCCGTTATATGTAACCTTCGAGGA 58.867 41.667 6.76 4.10 37.67 3.71
2488 8599 5.240183 TCCGTTATATGTAACCTTCGAGGAG 59.760 44.000 6.76 0.00 37.67 3.69
2490 8601 5.913514 CGTTATATGTAACCTTCGAGGAGTG 59.086 44.000 6.76 0.00 37.67 3.51
2589 8702 4.338012 TGTCTGAATCATTTCTGTGGCAT 58.662 39.130 0.00 0.00 33.75 4.40
2594 8707 5.508567 TGAATCATTTCTGTGGCATAGGAA 58.491 37.500 7.48 7.48 32.78 3.36
2617 8730 1.425066 TCAGCAGGGTTTTGGAGTCAT 59.575 47.619 0.00 0.00 0.00 3.06
2644 8757 1.207791 TTTGCTTTTGCCCCCTTGAA 58.792 45.000 0.00 0.00 46.87 2.69
2645 8758 1.433121 TTGCTTTTGCCCCCTTGAAT 58.567 45.000 0.00 0.00 46.87 2.57
2646 8759 0.975887 TGCTTTTGCCCCCTTGAATC 59.024 50.000 0.00 0.00 46.87 2.52
2647 8760 0.975887 GCTTTTGCCCCCTTGAATCA 59.024 50.000 0.00 0.00 40.15 2.57
2648 8761 1.066645 GCTTTTGCCCCCTTGAATCAG 60.067 52.381 0.00 0.00 40.15 2.90
2649 8762 1.551883 CTTTTGCCCCCTTGAATCAGG 59.448 52.381 0.00 0.00 0.00 3.86
2650 8763 0.904394 TTTGCCCCCTTGAATCAGGC 60.904 55.000 4.49 4.49 44.13 4.85
2651 8764 1.803453 TTGCCCCCTTGAATCAGGCT 61.803 55.000 11.67 0.00 44.19 4.58
2652 8765 1.454663 GCCCCCTTGAATCAGGCTC 60.455 63.158 4.24 0.00 40.57 4.70
2653 8766 1.153086 CCCCCTTGAATCAGGCTCG 60.153 63.158 0.00 0.00 31.69 5.03
2654 8767 1.604378 CCCCTTGAATCAGGCTCGT 59.396 57.895 0.00 0.00 31.69 4.18
2655 8768 0.462759 CCCCTTGAATCAGGCTCGTC 60.463 60.000 0.00 0.00 31.69 4.20
2656 8769 0.250234 CCCTTGAATCAGGCTCGTCA 59.750 55.000 0.00 0.00 31.69 4.35
2657 8770 1.363744 CCTTGAATCAGGCTCGTCAC 58.636 55.000 0.00 0.00 0.00 3.67
2658 8771 0.994995 CTTGAATCAGGCTCGTCACG 59.005 55.000 0.00 0.00 0.00 4.35
2659 8772 0.389817 TTGAATCAGGCTCGTCACGG 60.390 55.000 0.00 0.00 0.00 4.94
2660 8773 1.519455 GAATCAGGCTCGTCACGGG 60.519 63.158 0.00 0.00 0.00 5.28
2661 8774 2.907897 GAATCAGGCTCGTCACGGGG 62.908 65.000 0.00 0.00 0.00 5.73
2662 8775 3.957435 ATCAGGCTCGTCACGGGGA 62.957 63.158 0.00 0.00 0.00 4.81
2663 8776 3.461773 CAGGCTCGTCACGGGGAT 61.462 66.667 0.00 0.00 0.00 3.85
2664 8777 3.461773 AGGCTCGTCACGGGGATG 61.462 66.667 0.00 0.00 0.00 3.51
2665 8778 4.530857 GGCTCGTCACGGGGATGG 62.531 72.222 0.00 0.00 33.11 3.51
2666 8779 3.458163 GCTCGTCACGGGGATGGA 61.458 66.667 0.00 0.00 33.11 3.41
2667 8780 2.797278 GCTCGTCACGGGGATGGAT 61.797 63.158 0.00 0.00 33.11 3.41
2668 8781 1.364171 CTCGTCACGGGGATGGATC 59.636 63.158 0.00 0.00 33.11 3.36
2669 8782 1.076265 TCGTCACGGGGATGGATCT 60.076 57.895 0.00 0.00 33.11 2.75
2670 8783 1.068083 CGTCACGGGGATGGATCTG 59.932 63.158 0.00 0.00 0.00 2.90
2671 8784 1.227674 GTCACGGGGATGGATCTGC 60.228 63.158 0.00 0.00 0.00 4.26
2672 8785 1.383109 TCACGGGGATGGATCTGCT 60.383 57.895 0.00 0.00 0.00 4.24
2673 8786 0.105709 TCACGGGGATGGATCTGCTA 60.106 55.000 0.00 0.00 0.00 3.49
2674 8787 0.319728 CACGGGGATGGATCTGCTAG 59.680 60.000 0.00 0.00 0.00 3.42
2675 8788 1.294780 CGGGGATGGATCTGCTAGC 59.705 63.158 8.10 8.10 0.00 3.42
2676 8789 1.294780 GGGGATGGATCTGCTAGCG 59.705 63.158 10.77 5.22 0.00 4.26
2677 8790 1.375268 GGGATGGATCTGCTAGCGC 60.375 63.158 10.77 0.00 0.00 5.92
2678 8791 1.670590 GGATGGATCTGCTAGCGCT 59.329 57.895 17.26 17.26 36.97 5.92
2679 8792 0.389687 GGATGGATCTGCTAGCGCTC 60.390 60.000 16.34 0.00 36.97 5.03
2680 8793 0.732196 GATGGATCTGCTAGCGCTCG 60.732 60.000 16.34 9.56 36.97 5.03
2681 8794 2.732843 GGATCTGCTAGCGCTCGC 60.733 66.667 25.60 25.60 42.33 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.502091 CTTGCTATTGGTAATTAGTTGCCTATA 57.498 33.333 6.65 7.62 40.41 1.31
50 51 6.599244 TGCCTATACATGCTATAAATTGCCTC 59.401 38.462 0.00 0.00 0.00 4.70
88 89 4.908601 TGTTGATGGTCAGTTCCTACAT 57.091 40.909 0.00 0.00 0.00 2.29
336 352 6.270000 TCCCATATGAGTAGGTTTCGATGAAT 59.730 38.462 3.65 0.00 0.00 2.57
393 409 3.612472 TCAAATTCGTTTTCACCGTCC 57.388 42.857 0.00 0.00 0.00 4.79
476 493 1.218875 CGCGCGCATAACTATCCCAA 61.219 55.000 32.61 0.00 0.00 4.12
527 544 4.388499 AAGGATCACCCGCGCGTT 62.388 61.111 29.95 12.72 40.87 4.84
528 545 4.814294 GAAGGATCACCCGCGCGT 62.814 66.667 29.95 9.79 40.87 6.01
701 722 2.766263 AGCACAGTATCTGATCCCGAAA 59.234 45.455 3.70 0.00 35.18 3.46
760 4103 3.122971 GGGACGCGTGGTTTAGGC 61.123 66.667 20.70 0.00 36.84 3.93
774 4117 0.962356 GTCGTAAGTCGGTCCAGGGA 60.962 60.000 0.00 0.00 40.32 4.20
778 4121 0.448990 CGATGTCGTAAGTCGGTCCA 59.551 55.000 0.00 0.00 40.32 4.02
780 4123 2.532531 TTCGATGTCGTAAGTCGGTC 57.467 50.000 2.04 0.00 40.80 4.79
844 4187 2.163010 TCTCATGTCGTAAGTCGGTTCC 59.837 50.000 0.00 0.00 40.32 3.62
873 4216 0.677288 TCGGCGTCCTTTTTCTCTCA 59.323 50.000 6.85 0.00 0.00 3.27
935 4278 0.677731 CGGCTGGATCAAGGCTTTGA 60.678 55.000 20.59 14.17 46.67 2.69
954 4297 1.643832 GCCAAATGCGATCGAGACC 59.356 57.895 21.57 0.68 0.00 3.85
1121 4471 1.219393 GCGAGGTTGAAGGAGAGGG 59.781 63.158 0.00 0.00 0.00 4.30
1453 4803 4.394712 CTCGGGGCCGCAGTTCTT 62.395 66.667 21.08 0.00 39.59 2.52
1730 5084 5.560724 AGTACATGTACATGGAAGCAACTT 58.439 37.500 33.32 15.70 42.91 2.66
1849 5493 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
1850 5494 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
1851 5495 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
1852 5496 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
1866 5510 9.801873 ACTAGTGTAGTGTTAAAAACGTTCTTA 57.198 29.630 0.00 0.00 37.69 2.10
1867 5511 8.707938 ACTAGTGTAGTGTTAAAAACGTTCTT 57.292 30.769 0.00 0.00 37.69 2.52
1882 5526 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
1883 5527 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
1884 5528 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
1895 5539 9.632969 CCGTCTCATAATATAAGAACGTTTTTG 57.367 33.333 13.87 0.00 0.00 2.44
1896 5540 9.590451 TCCGTCTCATAATATAAGAACGTTTTT 57.410 29.630 9.22 9.22 0.00 1.94
1897 5541 9.245962 CTCCGTCTCATAATATAAGAACGTTTT 57.754 33.333 0.46 0.00 0.00 2.43
1898 5542 7.866393 CCTCCGTCTCATAATATAAGAACGTTT 59.134 37.037 0.46 0.00 0.00 3.60
1899 5543 7.368833 CCTCCGTCTCATAATATAAGAACGTT 58.631 38.462 0.00 0.00 0.00 3.99
1900 5544 6.072064 CCCTCCGTCTCATAATATAAGAACGT 60.072 42.308 0.00 0.00 0.00 3.99
1901 5545 6.150641 TCCCTCCGTCTCATAATATAAGAACG 59.849 42.308 0.00 0.00 0.00 3.95
1902 5546 7.177041 ACTCCCTCCGTCTCATAATATAAGAAC 59.823 40.741 0.00 0.00 0.00 3.01
1903 5547 7.239438 ACTCCCTCCGTCTCATAATATAAGAA 58.761 38.462 0.00 0.00 0.00 2.52
1904 5548 6.791371 ACTCCCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
1905 5549 8.754991 ATACTCCCTCCGTCTCATAATATAAG 57.245 38.462 0.00 0.00 0.00 1.73
1913 5557 9.716556 AAATATATAATACTCCCTCCGTCTCAT 57.283 33.333 0.00 0.00 0.00 2.90
1914 5558 8.967918 CAAATATATAATACTCCCTCCGTCTCA 58.032 37.037 0.00 0.00 0.00 3.27
1915 5559 8.968969 ACAAATATATAATACTCCCTCCGTCTC 58.031 37.037 0.00 0.00 0.00 3.36
1916 5560 8.896722 ACAAATATATAATACTCCCTCCGTCT 57.103 34.615 0.00 0.00 0.00 4.18
1917 5561 9.939802 AAACAAATATATAATACTCCCTCCGTC 57.060 33.333 0.00 0.00 0.00 4.79
1918 5562 9.939802 GAAACAAATATATAATACTCCCTCCGT 57.060 33.333 0.00 0.00 0.00 4.69
1919 5563 9.938280 TGAAACAAATATATAATACTCCCTCCG 57.062 33.333 0.00 0.00 0.00 4.63
2055 5736 1.352017 TCTGATTTGAAGCTCAGCCCA 59.648 47.619 0.00 0.00 38.99 5.36
2114 5795 9.968870 AGTGCGAACTTTATAAAATTGGTTTAA 57.031 25.926 0.00 0.00 35.33 1.52
2136 8138 3.090952 TGTGGTTTGCAATGTTAGTGC 57.909 42.857 0.00 0.00 42.55 4.40
2147 8149 2.284952 GCACTCATTTGTTGTGGTTTGC 59.715 45.455 0.00 0.00 32.85 3.68
2165 8167 7.201350 GGTTAAGATCAATGTGATTTTTCGCAC 60.201 37.037 0.00 0.00 37.20 5.34
2242 8245 3.843619 TGTCTGATGGGAATGTTGGTCTA 59.156 43.478 0.00 0.00 0.00 2.59
2331 8334 2.519771 TGATTGATTGCTTCTGCCCT 57.480 45.000 0.00 0.00 38.71 5.19
2354 8357 5.065914 GCTAGTTCTGATTCATGGGCATTA 58.934 41.667 0.00 0.00 0.00 1.90
2424 8533 2.202566 GTGCAACCTAGGAAGCGTATC 58.797 52.381 17.98 7.15 0.00 2.24
2442 8551 1.566018 GAACGGTTCTCGGCCTTGTG 61.566 60.000 13.49 0.00 44.45 3.33
2443 8552 1.301479 GAACGGTTCTCGGCCTTGT 60.301 57.895 13.49 0.00 44.45 3.16
2454 8565 4.411256 ACATATAACGGATGGAACGGTT 57.589 40.909 0.00 0.00 37.20 4.44
2477 8588 0.112606 TCTGGACACTCCTCGAAGGT 59.887 55.000 0.00 0.00 37.46 3.50
2479 8590 3.601443 AAATCTGGACACTCCTCGAAG 57.399 47.619 0.00 0.00 37.46 3.79
2482 8593 2.622436 GGAAAATCTGGACACTCCTCG 58.378 52.381 0.00 0.00 37.46 4.63
2483 8594 2.356227 GGGGAAAATCTGGACACTCCTC 60.356 54.545 0.00 0.00 37.46 3.71
2484 8595 1.636003 GGGGAAAATCTGGACACTCCT 59.364 52.381 0.00 0.00 37.46 3.69
2486 8597 1.003233 ACGGGGAAAATCTGGACACTC 59.997 52.381 0.00 0.00 0.00 3.51
2487 8598 1.064825 ACGGGGAAAATCTGGACACT 58.935 50.000 0.00 0.00 0.00 3.55
2488 8599 2.773993 TACGGGGAAAATCTGGACAC 57.226 50.000 0.00 0.00 0.00 3.67
2490 8601 4.266714 TGATTTACGGGGAAAATCTGGAC 58.733 43.478 9.27 0.00 41.72 4.02
2589 8702 3.494561 AACCCTGCTGAGGTTCCTA 57.505 52.632 9.63 0.00 44.42 2.94
2594 8707 0.111253 CTCCAAAACCCTGCTGAGGT 59.889 55.000 0.00 0.00 37.73 3.85
2617 8730 2.488952 GGGCAAAAGCAAATTCGGAAA 58.511 42.857 0.00 0.00 0.00 3.13
2644 8757 3.461773 CCCCGTGACGAGCCTGAT 61.462 66.667 6.54 0.00 0.00 2.90
2645 8758 3.957435 ATCCCCGTGACGAGCCTGA 62.957 63.158 6.54 0.00 0.00 3.86
2646 8759 3.461773 ATCCCCGTGACGAGCCTG 61.462 66.667 6.54 0.00 0.00 4.85
2647 8760 3.461773 CATCCCCGTGACGAGCCT 61.462 66.667 6.54 0.00 0.00 4.58
2648 8761 4.530857 CCATCCCCGTGACGAGCC 62.531 72.222 6.54 0.00 0.00 4.70
2649 8762 2.701163 GATCCATCCCCGTGACGAGC 62.701 65.000 6.54 0.00 0.00 5.03
2650 8763 1.109920 AGATCCATCCCCGTGACGAG 61.110 60.000 6.54 0.00 0.00 4.18
2651 8764 1.076265 AGATCCATCCCCGTGACGA 60.076 57.895 6.54 0.00 0.00 4.20
2652 8765 1.068083 CAGATCCATCCCCGTGACG 59.932 63.158 0.00 0.00 0.00 4.35
2653 8766 1.227674 GCAGATCCATCCCCGTGAC 60.228 63.158 0.00 0.00 0.00 3.67
2654 8767 0.105709 TAGCAGATCCATCCCCGTGA 60.106 55.000 0.00 0.00 0.00 4.35
2655 8768 0.319728 CTAGCAGATCCATCCCCGTG 59.680 60.000 0.00 0.00 0.00 4.94
2656 8769 1.476007 GCTAGCAGATCCATCCCCGT 61.476 60.000 10.63 0.00 0.00 5.28
2657 8770 1.294780 GCTAGCAGATCCATCCCCG 59.705 63.158 10.63 0.00 0.00 5.73
2658 8771 1.294780 CGCTAGCAGATCCATCCCC 59.705 63.158 16.45 0.00 0.00 4.81
2659 8772 1.375268 GCGCTAGCAGATCCATCCC 60.375 63.158 16.45 0.00 44.35 3.85
2660 8773 4.275524 GCGCTAGCAGATCCATCC 57.724 61.111 16.45 0.00 44.35 3.51
2671 8784 4.225340 AGACGACGCGAGCGCTAG 62.225 66.667 15.93 12.78 44.19 3.42
2672 8785 4.219846 GAGACGACGCGAGCGCTA 62.220 66.667 15.93 0.00 44.19 4.26


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

AutoCloner maintained by Alex Coulton.