Multiple sequence alignment - TraesCS1D01G311600

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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 TraesCS1D01G311600 chr1D 100.000 2648 0 0 1 2648 407694879 407697526 0.000000e+00 4891.0
1 TraesCS1D01G311600 chr1D 83.874 986 101 30 802 1754 407807711 407808671 0.000000e+00 887.0
2 TraesCS1D01G311600 chr1D 80.622 996 113 36 846 1811 407823179 407824124 0.000000e+00 697.0
3 TraesCS1D01G311600 chr1D 81.154 260 32 9 1984 2227 161036257 161035999 2.690000e-45 193.0
4 TraesCS1D01G311600 chr1D 92.437 119 8 1 2461 2579 252593181 252593064 4.530000e-38 169.0
5 TraesCS1D01G311600 chr1B 91.228 1254 72 19 750 1979 548278482 548279721 0.000000e+00 1672.0
6 TraesCS1D01G311600 chr1B 82.490 988 109 27 806 1754 548300391 548301353 0.000000e+00 808.0
7 TraesCS1D01G311600 chr1B 83.524 874 110 22 846 1689 548292758 548293627 0.000000e+00 785.0
8 TraesCS1D01G311600 chr1B 80.267 1049 141 37 846 1866 548390900 548391910 0.000000e+00 730.0
9 TraesCS1D01G311600 chr1B 82.573 482 57 16 1070 1529 548202917 548203393 1.480000e-107 399.0
10 TraesCS1D01G311600 chr1A 87.898 942 64 27 842 1754 503325233 503326153 0.000000e+00 1062.0
11 TraesCS1D01G311600 chr1A 83.630 281 28 11 1978 2242 52534111 52534389 5.660000e-62 248.0
12 TraesCS1D01G311600 chr1A 86.145 166 15 5 2296 2453 52534371 52534536 3.500000e-39 172.0
13 TraesCS1D01G311600 chr1A 91.736 121 9 1 2460 2579 445505065 445505185 1.630000e-37 167.0
14 TraesCS1D01G311600 chr1A 84.571 175 17 5 2296 2460 445504742 445504916 5.860000e-37 165.0
15 TraesCS1D01G311600 chr3D 86.866 769 56 20 1 753 596879336 596878597 0.000000e+00 819.0
16 TraesCS1D01G311600 chr3D 80.370 703 110 21 983 1680 519710291 519709612 2.350000e-140 508.0
17 TraesCS1D01G311600 chr3D 87.156 436 34 13 327 754 468765593 468765172 2.390000e-130 475.0
18 TraesCS1D01G311600 chr3D 88.034 351 21 10 7 341 500634616 500634271 1.910000e-106 396.0
19 TraesCS1D01G311600 chr3D 86.612 366 40 8 1326 1689 519947647 519947289 1.910000e-106 396.0
20 TraesCS1D01G311600 chr3D 89.231 65 3 3 841 901 519876861 519876797 7.860000e-11 78.7
21 TraesCS1D01G311600 chr3D 90.000 50 4 1 751 800 519877212 519877164 2.200000e-06 63.9
22 TraesCS1D01G311600 chr6D 96.945 491 6 3 1978 2460 9826770 9827259 0.000000e+00 815.0
23 TraesCS1D01G311600 chr6D 88.736 435 26 12 1 413 24895039 24894606 6.540000e-141 510.0
24 TraesCS1D01G311600 chr6D 98.438 192 3 0 2457 2648 9827383 9827574 3.260000e-89 339.0
25 TraesCS1D01G311600 chr6D 91.597 119 9 1 2461 2579 21104571 21104454 2.110000e-36 163.0
26 TraesCS1D01G311600 chr6D 97.727 44 1 0 2583 2626 17134723 17134680 2.830000e-10 76.8
27 TraesCS1D01G311600 chr2D 84.948 764 72 25 1 750 323088803 323088069 0.000000e+00 734.0
28 TraesCS1D01G311600 chr2D 87.524 521 32 11 5 492 101870780 101870260 2.960000e-159 571.0
29 TraesCS1D01G311600 chr2D 87.472 439 35 11 324 755 391101934 391101509 3.060000e-134 488.0
30 TraesCS1D01G311600 chr2D 89.796 294 19 4 1 283 557687387 557687680 1.500000e-97 366.0
31 TraesCS1D01G311600 chr2D 85.625 160 13 5 1980 2130 70028292 70028134 2.730000e-35 159.0
32 TraesCS1D01G311600 chr3B 84.416 770 73 26 1 752 237322176 237321436 0.000000e+00 713.0
33 TraesCS1D01G311600 chr3B 82.254 772 85 38 1 752 237320387 237319648 1.040000e-173 619.0
34 TraesCS1D01G311600 chr3B 82.583 666 88 19 983 1642 684268917 684268274 1.780000e-156 562.0
35 TraesCS1D01G311600 chr3B 81.324 680 96 21 983 1654 684413235 684412579 8.400000e-145 523.0
36 TraesCS1D01G311600 chr3B 89.474 76 4 3 830 901 684462392 684462317 2.810000e-15 93.5
37 TraesCS1D01G311600 chr3B 97.872 47 1 0 2249 2295 156652899 156652853 6.070000e-12 82.4
38 TraesCS1D01G311600 chr3B 90.196 51 4 1 751 801 684460749 684460700 6.120000e-07 65.8
39 TraesCS1D01G311600 chr5A 83.679 772 78 23 1 754 665825155 665825896 0.000000e+00 684.0
40 TraesCS1D01G311600 chr5A 82.513 589 62 18 179 752 632820347 632819785 1.840000e-131 479.0
41 TraesCS1D01G311600 chr5A 91.935 124 9 1 2457 2579 11243493 11243616 3.500000e-39 172.0
42 TraesCS1D01G311600 chr5A 92.647 68 3 2 2394 2460 444553850 444553784 2.170000e-16 97.1
43 TraesCS1D01G311600 chr7D 96.535 404 6 2 2064 2460 536156252 536156654 0.000000e+00 662.0
44 TraesCS1D01G311600 chr7D 85.092 436 32 17 322 750 414276120 414276529 5.270000e-112 414.0
45 TraesCS1D01G311600 chr7D 98.438 192 3 0 2457 2648 536156778 536156969 3.260000e-89 339.0
46 TraesCS1D01G311600 chr7D 83.333 192 15 9 1978 2153 616928847 616928657 7.590000e-36 161.0
47 TraesCS1D01G311600 chr7D 93.878 49 2 1 2574 2621 519676524 519676572 3.660000e-09 73.1
48 TraesCS1D01G311600 chr7D 95.556 45 1 1 2583 2627 506139837 506139794 1.320000e-08 71.3
49 TraesCS1D01G311600 chr7D 86.765 68 1 5 2394 2460 23087963 23087903 4.730000e-08 69.4
50 TraesCS1D01G311600 chr7B 83.051 767 72 30 1 754 514054640 514055361 0.000000e+00 643.0
51 TraesCS1D01G311600 chr7B 93.878 49 2 1 2574 2621 553057475 553057523 3.660000e-09 73.1
52 TraesCS1D01G311600 chr7B 93.750 48 1 2 2577 2624 552775278 552775323 1.320000e-08 71.3
53 TraesCS1D01G311600 chr7B 89.796 49 4 1 2574 2621 552789834 552789882 7.910000e-06 62.1
54 TraesCS1D01G311600 chr5D 89.841 502 27 7 1 492 444716551 444716064 8.050000e-175 623.0
55 TraesCS1D01G311600 chr5D 88.544 515 32 10 1 490 39094668 39095180 1.360000e-167 599.0
56 TraesCS1D01G311600 chr3A 82.101 676 91 18 983 1651 655080903 655080251 3.850000e-153 551.0
57 TraesCS1D01G311600 chr3A 81.445 609 93 12 1035 1642 655079389 655078800 5.130000e-132 481.0
58 TraesCS1D01G311600 chr3A 80.109 548 39 43 6 546 680986245 680986729 7.020000e-91 344.0
59 TraesCS1D01G311600 chr3A 87.500 160 10 4 1981 2130 718380786 718380945 2.710000e-40 176.0
60 TraesCS1D01G311600 chr3A 96.000 50 2 0 2246 2295 550498551 550498600 6.070000e-12 82.4
61 TraesCS1D01G311600 chr6B 84.703 353 36 7 1 349 657647516 657647178 1.170000e-88 337.0
62 TraesCS1D01G311600 chr6A 84.783 276 24 9 1984 2242 428726025 428725751 7.270000e-66 261.0
63 TraesCS1D01G311600 chr6A 91.534 189 15 1 2460 2648 428725472 428725285 2.610000e-65 259.0
64 TraesCS1D01G311600 chr4A 84.588 279 26 7 1980 2242 141117839 141117562 7.270000e-66 261.0
65 TraesCS1D01G311600 chr4A 94.495 109 5 1 2471 2579 713133750 713133857 1.630000e-37 167.0
66 TraesCS1D01G311600 chr7A 84.397 282 24 9 1980 2242 644711438 644711718 2.610000e-65 259.0
67 TraesCS1D01G311600 chr7A 87.356 174 13 3 2296 2460 150270248 150270421 9.670000e-45 191.0
68 TraesCS1D01G311600 chr7A 88.406 138 6 4 2333 2460 644711721 644711858 9.810000e-35 158.0
69 TraesCS1D01G311600 chr2A 87.654 162 10 3 1979 2130 744541207 744541046 2.090000e-41 180.0
70 TraesCS1D01G311600 chr2A 93.277 119 8 0 2461 2579 744540663 744540545 2.710000e-40 176.0
71 TraesCS1D01G311600 chr2A 86.364 88 8 4 2375 2460 49324133 49324218 2.810000e-15 93.5
72 TraesCS1D01G311600 chr2A 91.304 69 3 3 2394 2460 47350590 47350657 1.010000e-14 91.6


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 TraesCS1D01G311600 chr1D 407694879 407697526 2647 False 4891.0 4891 100.0000 1 2648 1 chr1D.!!$F1 2647
1 TraesCS1D01G311600 chr1D 407807711 407808671 960 False 887.0 887 83.8740 802 1754 1 chr1D.!!$F2 952
2 TraesCS1D01G311600 chr1D 407823179 407824124 945 False 697.0 697 80.6220 846 1811 1 chr1D.!!$F3 965
3 TraesCS1D01G311600 chr1B 548278482 548279721 1239 False 1672.0 1672 91.2280 750 1979 1 chr1B.!!$F2 1229
4 TraesCS1D01G311600 chr1B 548300391 548301353 962 False 808.0 808 82.4900 806 1754 1 chr1B.!!$F4 948
5 TraesCS1D01G311600 chr1B 548292758 548293627 869 False 785.0 785 83.5240 846 1689 1 chr1B.!!$F3 843
6 TraesCS1D01G311600 chr1B 548390900 548391910 1010 False 730.0 730 80.2670 846 1866 1 chr1B.!!$F5 1020
7 TraesCS1D01G311600 chr1A 503325233 503326153 920 False 1062.0 1062 87.8980 842 1754 1 chr1A.!!$F1 912
8 TraesCS1D01G311600 chr3D 596878597 596879336 739 True 819.0 819 86.8660 1 753 1 chr3D.!!$R5 752
9 TraesCS1D01G311600 chr3D 519709612 519710291 679 True 508.0 508 80.3700 983 1680 1 chr3D.!!$R3 697
10 TraesCS1D01G311600 chr6D 9826770 9827574 804 False 577.0 815 97.6915 1978 2648 2 chr6D.!!$F1 670
11 TraesCS1D01G311600 chr2D 323088069 323088803 734 True 734.0 734 84.9480 1 750 1 chr2D.!!$R3 749
12 TraesCS1D01G311600 chr2D 101870260 101870780 520 True 571.0 571 87.5240 5 492 1 chr2D.!!$R2 487
13 TraesCS1D01G311600 chr3B 237319648 237322176 2528 True 666.0 713 83.3350 1 752 2 chr3B.!!$R4 751
14 TraesCS1D01G311600 chr3B 684268274 684268917 643 True 562.0 562 82.5830 983 1642 1 chr3B.!!$R2 659
15 TraesCS1D01G311600 chr3B 684412579 684413235 656 True 523.0 523 81.3240 983 1654 1 chr3B.!!$R3 671
16 TraesCS1D01G311600 chr5A 665825155 665825896 741 False 684.0 684 83.6790 1 754 1 chr5A.!!$F2 753
17 TraesCS1D01G311600 chr5A 632819785 632820347 562 True 479.0 479 82.5130 179 752 1 chr5A.!!$R2 573
18 TraesCS1D01G311600 chr7D 536156252 536156969 717 False 500.5 662 97.4865 2064 2648 2 chr7D.!!$F3 584
19 TraesCS1D01G311600 chr7B 514054640 514055361 721 False 643.0 643 83.0510 1 754 1 chr7B.!!$F1 753
20 TraesCS1D01G311600 chr5D 39094668 39095180 512 False 599.0 599 88.5440 1 490 1 chr5D.!!$F1 489
21 TraesCS1D01G311600 chr3A 655078800 655080903 2103 True 516.0 551 81.7730 983 1651 2 chr3A.!!$R1 668
22 TraesCS1D01G311600 chr6A 428725285 428726025 740 True 260.0 261 88.1585 1984 2648 2 chr6A.!!$R1 664

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
626 666 0.544833 TCGTGTTTACAGGGCCCCTA 60.545 55.0 21.43 5.21 29.64 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 5328 0.107214 GGGCACGAGAATCCCATGAA 60.107 55.0 0.0 0.0 39.82 2.57 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
66 68 2.436542 CAGACCCCGTATAATCAACCCA 59.563 50.000 0.00 0.00 0.00 4.51
146 151 1.134670 CCTCTTCCTCACGTCAATCCC 60.135 57.143 0.00 0.00 0.00 3.85
170 175 1.078426 CAGGCGGACGAGGGAAAAT 60.078 57.895 0.00 0.00 0.00 1.82
535 575 3.191371 GCAAAGATTCCTCAACCGTCAAT 59.809 43.478 0.00 0.00 0.00 2.57
548 588 4.685447 TCAATGTTGACCGGTCCG 57.315 55.556 31.19 12.67 31.01 4.79
564 604 2.589540 CGGTATGCAAGGCCCTGA 59.410 61.111 5.23 0.00 0.00 3.86
569 609 3.500343 GGTATGCAAGGCCCTGATAAAT 58.500 45.455 5.23 0.00 0.00 1.40
596 636 8.815565 TGCCCTCAAAACTGTATATTTATGAA 57.184 30.769 0.00 0.00 0.00 2.57
610 650 5.934935 ATTTATGAAGGTTTCGTGTTCGT 57.065 34.783 0.00 0.00 38.33 3.85
626 666 0.544833 TCGTGTTTACAGGGCCCCTA 60.545 55.000 21.43 5.21 29.64 3.53
722 2554 8.298854 AGTTATTTTACGGGTTTGACCATTTAC 58.701 33.333 0.00 0.00 41.02 2.01
725 2557 6.651975 TTTACGGGTTTGACCATTTACATT 57.348 33.333 0.00 0.00 41.02 2.71
726 2558 6.651975 TTACGGGTTTGACCATTTACATTT 57.348 33.333 0.00 0.00 41.02 2.32
727 2559 7.756395 TTACGGGTTTGACCATTTACATTTA 57.244 32.000 0.00 0.00 41.02 1.40
728 2560 6.844097 ACGGGTTTGACCATTTACATTTAT 57.156 33.333 0.00 0.00 41.02 1.40
729 2561 7.941431 ACGGGTTTGACCATTTACATTTATA 57.059 32.000 0.00 0.00 41.02 0.98
731 2563 6.908284 CGGGTTTGACCATTTACATTTATACG 59.092 38.462 0.00 0.00 41.02 3.06
732 2564 7.197703 GGGTTTGACCATTTACATTTATACGG 58.802 38.462 0.00 0.00 41.02 4.02
733 2565 7.197703 GGTTTGACCATTTACATTTATACGGG 58.802 38.462 0.00 0.00 38.42 5.28
734 2566 7.148035 GGTTTGACCATTTACATTTATACGGGT 60.148 37.037 0.00 0.00 38.42 5.28
761 2594 0.666913 GATGCTCTAAGGTCGCCGTA 59.333 55.000 0.00 0.00 0.00 4.02
767 2600 3.737355 GCTCTAAGGTCGCCGTAAGAAAT 60.737 47.826 0.00 0.00 43.02 2.17
794 2627 4.332819 GCCGACCATATTAAGATATGCACC 59.667 45.833 0.00 0.00 42.44 5.01
814 2647 2.224378 CCCATATGACATCAACCGCTCT 60.224 50.000 3.65 0.00 0.00 4.09
828 2661 2.229302 ACCGCTCTGTTAGTTGTCTCTC 59.771 50.000 0.00 0.00 0.00 3.20
829 2662 2.490115 CCGCTCTGTTAGTTGTCTCTCT 59.510 50.000 0.00 0.00 0.00 3.10
940 2797 4.360563 GGAATTCTCGAGAAATAGCGTGA 58.639 43.478 30.18 6.03 37.61 4.35
979 2860 1.000955 CTAGTGAACAAGTCGGCAGGT 59.999 52.381 0.00 0.00 0.00 4.00
1029 2936 3.943479 TTGCTTCCACCGCGCGTAT 62.943 57.895 29.95 14.09 0.00 3.06
1267 3174 0.663688 CGGAGCGCTGATGTACTACT 59.336 55.000 18.48 0.00 0.00 2.57
1455 3392 2.260434 GTCCTGGCGTACGAGCAA 59.740 61.111 21.65 0.00 39.27 3.91
1519 4916 1.911766 GTGGAGAAGGGGGACACGA 60.912 63.158 0.00 0.00 0.00 4.35
1711 5120 1.192146 TTGTCCAGGTCTCCCGGAAG 61.192 60.000 0.73 0.00 35.92 3.46
1712 5121 2.683933 TCCAGGTCTCCCGGAAGC 60.684 66.667 0.73 0.00 32.70 3.86
1713 5122 3.787001 CCAGGTCTCCCGGAAGCC 61.787 72.222 0.73 0.00 35.12 4.35
1748 5157 3.121030 GCATCTTGCGTCGTGGCT 61.121 61.111 0.00 0.00 31.71 4.75
1755 5164 1.781025 TTGCGTCGTGGCTTTTCCTG 61.781 55.000 0.00 0.00 35.26 3.86
1756 5165 2.556287 CGTCGTGGCTTTTCCTGC 59.444 61.111 0.00 0.00 35.26 4.85
1757 5166 2.250939 CGTCGTGGCTTTTCCTGCA 61.251 57.895 0.00 0.00 35.26 4.41
1797 5206 0.672401 GTCTTCGGTTGCGGATTCCA 60.672 55.000 3.09 0.00 0.00 3.53
1801 5210 2.398554 CGGTTGCGGATTCCACCAG 61.399 63.158 10.43 1.52 0.00 4.00
1802 5211 2.700773 GGTTGCGGATTCCACCAGC 61.701 63.158 3.09 1.48 0.00 4.85
1840 5249 2.692557 CTGAGACGGTGAATCTGGATCT 59.307 50.000 0.00 0.00 0.00 2.75
1902 5311 5.184287 GCTTTGCTATTGGGTTTTGGTAGTA 59.816 40.000 0.00 0.00 0.00 1.82
1916 5325 3.331150 TGGTAGTATGTGTTTTCCTGCG 58.669 45.455 0.00 0.00 0.00 5.18
1919 5328 2.846193 AGTATGTGTTTTCCTGCGTGT 58.154 42.857 0.00 0.00 0.00 4.49
1923 5332 2.020720 TGTGTTTTCCTGCGTGTTCAT 58.979 42.857 0.00 0.00 0.00 2.57
1940 5349 3.106986 ATGGGATTCTCGTGCCCCG 62.107 63.158 0.00 0.00 41.73 5.73
1950 5359 2.044352 GTGCCCCGCCCTATGTTT 60.044 61.111 0.00 0.00 0.00 2.83
1951 5360 2.044451 TGCCCCGCCCTATGTTTG 60.044 61.111 0.00 0.00 0.00 2.93
1952 5361 2.044352 GCCCCGCCCTATGTTTGT 60.044 61.111 0.00 0.00 0.00 2.83
1954 5363 1.752694 CCCCGCCCTATGTTTGTGG 60.753 63.158 0.00 0.00 0.00 4.17
1955 5364 1.301623 CCCGCCCTATGTTTGTGGA 59.698 57.895 0.00 0.00 0.00 4.02
1956 5365 0.748005 CCCGCCCTATGTTTGTGGAG 60.748 60.000 0.00 0.00 0.00 3.86
1960 5370 3.244561 CCGCCCTATGTTTGTGGAGATAT 60.245 47.826 0.00 0.00 0.00 1.63
1979 5389 8.966868 GGAGATATATGGGTTTCAACTTTCAAA 58.033 33.333 0.00 0.00 0.00 2.69
1981 5391 8.971073 AGATATATGGGTTTCAACTTTCAAAGG 58.029 33.333 1.31 0.00 0.00 3.11
1982 5392 8.893563 ATATATGGGTTTCAACTTTCAAAGGA 57.106 30.769 1.31 0.00 0.00 3.36
2203 5630 4.574674 AAAGCCTACTGATCCATCAACA 57.425 40.909 0.00 0.00 36.18 3.33
2242 5669 2.993899 CCATCAACGTACAGTCCACTTC 59.006 50.000 0.00 0.00 0.00 3.01
2444 5880 5.865085 ACAGTCAATTAGCACTGGAACTTA 58.135 37.500 13.27 0.00 43.78 2.24
2526 6089 8.134895 TGAAATTACAGTAAGAAAACCTTGCAG 58.865 33.333 0.00 0.00 39.56 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 125 1.819288 GACGTGAGGAAGAGGATGACA 59.181 52.381 0.00 0.00 0.00 3.58
124 129 2.432510 GGATTGACGTGAGGAAGAGGAT 59.567 50.000 0.00 0.00 0.00 3.24
295 313 2.209838 TTCGAATGGAGCTAGCGAAG 57.790 50.000 9.55 0.00 36.24 3.79
296 314 2.473816 CATTCGAATGGAGCTAGCGAA 58.526 47.619 27.09 5.25 43.78 4.70
297 315 2.140065 CATTCGAATGGAGCTAGCGA 57.860 50.000 27.09 0.00 32.78 4.93
308 344 2.928334 AGCAGCTCAATCCATTCGAAT 58.072 42.857 4.39 4.39 0.00 3.34
512 552 1.468914 GACGGTTGAGGAATCTTTGCC 59.531 52.381 0.00 0.00 0.00 4.52
545 585 2.690881 AGGGCCTTGCATACCGGA 60.691 61.111 9.46 0.00 0.00 5.14
546 586 2.343475 ATCAGGGCCTTGCATACCGG 62.343 60.000 10.65 0.00 0.00 5.28
547 587 0.396435 TATCAGGGCCTTGCATACCG 59.604 55.000 10.65 0.00 0.00 4.02
548 588 2.656947 TTATCAGGGCCTTGCATACC 57.343 50.000 10.65 0.00 0.00 2.73
549 589 5.291971 CAAATTTATCAGGGCCTTGCATAC 58.708 41.667 10.65 0.00 0.00 2.39
556 596 1.793414 GGGCAAATTTATCAGGGCCT 58.207 50.000 0.00 0.00 41.12 5.19
569 609 9.249053 TCATAAATATACAGTTTTGAGGGCAAA 57.751 29.630 0.00 0.00 41.97 3.68
590 630 4.121317 ACACGAACACGAAACCTTCATAA 58.879 39.130 0.00 0.00 0.00 1.90
591 631 3.719924 ACACGAACACGAAACCTTCATA 58.280 40.909 0.00 0.00 0.00 2.15
596 636 3.260740 TGTAAACACGAACACGAAACCT 58.739 40.909 0.00 0.00 0.00 3.50
604 644 0.535553 GGGCCCTGTAAACACGAACA 60.536 55.000 17.04 0.00 0.00 3.18
610 650 3.614568 TTTTTAGGGGCCCTGTAAACA 57.385 42.857 35.70 18.21 34.61 2.83
696 2528 6.904463 AATGGTCAAACCCGTAAAATAACT 57.096 33.333 0.00 0.00 37.50 2.24
722 2554 5.120830 GCATCTCTAGCAACCCGTATAAATG 59.879 44.000 0.00 0.00 0.00 2.32
725 2557 3.895656 AGCATCTCTAGCAACCCGTATAA 59.104 43.478 0.00 0.00 0.00 0.98
726 2558 3.497332 AGCATCTCTAGCAACCCGTATA 58.503 45.455 0.00 0.00 0.00 1.47
727 2559 2.297597 GAGCATCTCTAGCAACCCGTAT 59.702 50.000 0.00 0.00 0.00 3.06
728 2560 1.681793 GAGCATCTCTAGCAACCCGTA 59.318 52.381 0.00 0.00 0.00 4.02
729 2561 0.461961 GAGCATCTCTAGCAACCCGT 59.538 55.000 0.00 0.00 0.00 5.28
761 2594 2.418368 TATGGTCGGCAGCATTTCTT 57.582 45.000 0.00 0.00 41.18 2.52
767 2600 3.769739 ATCTTAATATGGTCGGCAGCA 57.230 42.857 0.00 0.00 0.00 4.41
794 2627 2.804527 CAGAGCGGTTGATGTCATATGG 59.195 50.000 2.13 0.00 0.00 2.74
814 2647 3.506455 CGGAGGAAGAGAGACAACTAACA 59.494 47.826 0.00 0.00 0.00 2.41
828 2661 0.462759 GAGCCAACCATCGGAGGAAG 60.463 60.000 0.93 0.00 0.00 3.46
829 2662 1.602237 GAGCCAACCATCGGAGGAA 59.398 57.895 0.93 0.00 0.00 3.36
940 2797 1.315257 GCAATTCACTGGCCGATGGT 61.315 55.000 0.00 0.00 0.00 3.55
979 2860 2.525629 TTCCCGTGCCTCTGACCA 60.526 61.111 0.00 0.00 0.00 4.02
1029 2936 4.695993 TTGACGATGGCCAGCGCA 62.696 61.111 40.87 33.67 45.05 6.09
1258 3165 0.179119 GTGCGGCGGAAGTAGTACAT 60.179 55.000 9.78 0.00 0.00 2.29
1261 3168 2.486504 CGTGCGGCGGAAGTAGTA 59.513 61.111 9.78 0.00 36.85 1.82
1755 5164 1.948145 CTCCAAGATGATGCCTTCTGC 59.052 52.381 0.00 0.00 41.77 4.26
1756 5165 3.204526 GACTCCAAGATGATGCCTTCTG 58.795 50.000 0.00 0.00 0.00 3.02
1757 5166 2.158986 CGACTCCAAGATGATGCCTTCT 60.159 50.000 0.00 0.00 0.00 2.85
1801 5210 3.869272 CATCGCCACGGCAAGAGC 61.869 66.667 9.11 0.00 42.06 4.09
1802 5211 3.869272 GCATCGCCACGGCAAGAG 61.869 66.667 9.11 0.00 42.06 2.85
1814 5223 1.202348 AGATTCACCGTCTCAGCATCG 60.202 52.381 0.00 0.00 0.00 3.84
1840 5249 1.675310 CAAGAGGCCGCACCAATCA 60.675 57.895 9.88 0.00 43.14 2.57
1902 5311 2.020720 TGAACACGCAGGAAAACACAT 58.979 42.857 0.00 0.00 0.00 3.21
1916 5325 1.398390 GCACGAGAATCCCATGAACAC 59.602 52.381 0.00 0.00 0.00 3.32
1919 5328 0.107214 GGGCACGAGAATCCCATGAA 60.107 55.000 0.00 0.00 39.82 2.57
1940 5349 5.882557 CCATATATCTCCACAAACATAGGGC 59.117 44.000 0.00 0.00 0.00 5.19
1950 5359 6.575244 AGTTGAAACCCATATATCTCCACA 57.425 37.500 0.00 0.00 0.00 4.17
1951 5360 7.556275 TGAAAGTTGAAACCCATATATCTCCAC 59.444 37.037 0.00 0.00 0.00 4.02
1952 5361 7.638444 TGAAAGTTGAAACCCATATATCTCCA 58.362 34.615 0.00 0.00 0.00 3.86
1955 5364 8.971073 CCTTTGAAAGTTGAAACCCATATATCT 58.029 33.333 4.02 0.00 0.00 1.98
1956 5365 8.966868 TCCTTTGAAAGTTGAAACCCATATATC 58.033 33.333 4.02 0.00 0.00 1.63
1960 5370 6.609616 ACTTCCTTTGAAAGTTGAAACCCATA 59.390 34.615 4.02 0.00 0.00 2.74
2444 5880 9.528489 AATGGGTTCAGTACACTGTAATTTTAT 57.472 29.630 9.11 0.00 44.12 1.40
2526 6089 8.428063 TCTGTAGAAGACACTAGGTACTATACC 58.572 40.741 0.00 0.00 40.50 2.73


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

AutoCloner maintained by Alex Coulton.