Multiple sequence alignment - TraesCS1D01G220800

Loading Multiple Alignment...

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 TraesCS1D01G220800 chr1D 100.000 3323 0 0 1 3323 308453926 308457248 0.000000e+00 6137.0
1 TraesCS1D01G220800 chr1D 94.444 126 5 2 2485 2610 116548463 116548340 3.380000e-45 193.0
2 TraesCS1D01G220800 chr1D 84.848 132 14 5 2877 3003 110771038 110771168 9.680000e-26 128.0
3 TraesCS1D01G220800 chr1B 95.333 2507 92 13 1 2496 418069181 418071673 0.000000e+00 3958.0
4 TraesCS1D01G220800 chr1B 92.504 667 33 4 2666 3323 418071753 418072411 0.000000e+00 939.0
5 TraesCS1D01G220800 chr1B 95.968 124 4 1 2493 2615 8855984 8855861 2.020000e-47 200.0
6 TraesCS1D01G220800 chr1B 98.333 60 1 0 2607 2666 418071668 418071727 4.530000e-19 106.0
7 TraesCS1D01G220800 chr1A 94.670 2514 97 18 1 2492 387833692 387836190 0.000000e+00 3866.0
8 TraesCS1D01G220800 chr1A 91.246 674 32 15 2666 3323 387836255 387836917 0.000000e+00 893.0
9 TraesCS1D01G220800 chr1A 96.694 121 4 0 2493 2613 208212650 208212530 5.620000e-48 202.0
10 TraesCS1D01G220800 chr1A 100.000 57 0 0 2607 2663 387836170 387836226 4.530000e-19 106.0
11 TraesCS1D01G220800 chr3A 96.000 125 5 0 2492 2616 602271378 602271254 1.560000e-48 204.0
12 TraesCS1D01G220800 chr3A 80.420 143 25 2 2864 3003 549622936 549622794 4.530000e-19 106.0
13 TraesCS1D01G220800 chr3A 88.462 52 5 1 2888 2939 454516782 454516832 9.950000e-06 62.1
14 TraesCS1D01G220800 chr2B 96.639 119 4 0 2493 2611 657072231 657072113 7.270000e-47 198.0
15 TraesCS1D01G220800 chr2B 100.000 30 0 0 2974 3003 310496375 310496404 4.630000e-04 56.5
16 TraesCS1D01G220800 chr2A 96.639 119 4 0 2492 2610 606523805 606523687 7.270000e-47 198.0
17 TraesCS1D01G220800 chr2A 93.939 132 7 1 2490 2620 634616322 634616453 7.270000e-47 198.0
18 TraesCS1D01G220800 chr5D 93.893 131 7 1 2480 2610 118840439 118840568 2.620000e-46 196.0
19 TraesCS1D01G220800 chr2D 93.130 131 7 2 2493 2622 12692357 12692228 1.220000e-44 191.0
20 TraesCS1D01G220800 chr6B 86.607 112 9 4 2866 2971 549621289 549621400 5.820000e-23 119.0
21 TraesCS1D01G220800 chr6B 100.000 30 0 0 2974 3003 201412053 201412024 4.630000e-04 56.5
22 TraesCS1D01G220800 chr6B 96.875 32 1 0 2974 3005 82158003 82157972 2.000000e-03 54.7
23 TraesCS1D01G220800 chr3B 86.047 86 7 3 2874 2955 434987205 434987289 1.640000e-13 87.9
24 TraesCS1D01G220800 chr6A 100.000 30 0 0 2974 3003 137379742 137379713 4.630000e-04 56.5
25 TraesCS1D01G220800 chr5B 100.000 30 0 0 2974 3003 98663301 98663330 4.630000e-04 56.5


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 TraesCS1D01G220800 chr1D 308453926 308457248 3322 False 6137.000000 6137 100.000000 1 3323 1 chr1D.!!$F2 3322
1 TraesCS1D01G220800 chr1B 418069181 418072411 3230 False 1667.666667 3958 95.390000 1 3323 3 chr1B.!!$F1 3322
2 TraesCS1D01G220800 chr1A 387833692 387836917 3225 False 1621.666667 3866 95.305333 1 3323 3 chr1A.!!$F1 3322

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
657 661 0.035458 CCCTCGGCAAGAAGAACAGT 59.965 55.0 0.00 0.00 0.00 3.55 F
840 862 0.037447 TTGATGTCCGTGGCATGGAA 59.963 50.0 29.24 19.07 34.53 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 1778 0.035317 TCGCTGCATTGGTTCACTCT 59.965 50.0 0.0 0.0 0.0 3.24 R
2592 2617 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.0 0.0 0.0 0.0 3.46 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
21 22 2.919494 CGCAAAACCTCACCCAGCC 61.919 63.158 0.00 0.00 0.00 4.85
29 30 2.745884 TCACCCAGCCGCATTTCG 60.746 61.111 0.00 0.00 38.08 3.46
49 53 2.163010 CGTCTTCTTGCATTTGCCTGAT 59.837 45.455 0.00 0.00 41.18 2.90
50 54 3.366679 CGTCTTCTTGCATTTGCCTGATT 60.367 43.478 0.00 0.00 41.18 2.57
51 55 4.142622 CGTCTTCTTGCATTTGCCTGATTA 60.143 41.667 0.00 0.00 41.18 1.75
52 56 5.449588 CGTCTTCTTGCATTTGCCTGATTAT 60.450 40.000 0.00 0.00 41.18 1.28
53 57 6.335777 GTCTTCTTGCATTTGCCTGATTATT 58.664 36.000 0.00 0.00 41.18 1.40
390 394 2.713770 GAGAGCATCGCGTCCGTA 59.286 61.111 5.77 0.00 42.67 4.02
492 496 0.249398 ATTTCCTCCGGACCTTCGTG 59.751 55.000 0.00 0.00 0.00 4.35
584 588 1.339631 GGTGAACATCGGGTCCATCAA 60.340 52.381 0.00 0.00 0.00 2.57
609 613 2.918131 GCTCAACTGGTGCAAATTCGTC 60.918 50.000 0.00 0.00 36.06 4.20
657 661 0.035458 CCCTCGGCAAGAAGAACAGT 59.965 55.000 0.00 0.00 0.00 3.55
666 670 0.768221 AGAAGAACAGTGCAGGGGGA 60.768 55.000 0.00 0.00 0.00 4.81
736 744 9.063615 TCATGAGACAAGGAATATGAATGAATG 57.936 33.333 0.00 0.00 0.00 2.67
780 800 6.474751 ACACTGAAGTTAGTCTAACACGTTTC 59.525 38.462 21.92 16.60 41.07 2.78
781 801 6.474427 CACTGAAGTTAGTCTAACACGTTTCA 59.526 38.462 21.92 19.39 41.07 2.69
782 802 7.169308 CACTGAAGTTAGTCTAACACGTTTCAT 59.831 37.037 21.92 11.09 41.07 2.57
783 803 8.355169 ACTGAAGTTAGTCTAACACGTTTCATA 58.645 33.333 21.92 4.65 41.07 2.15
840 862 0.037447 TTGATGTCCGTGGCATGGAA 59.963 50.000 29.24 19.07 34.53 3.53
966 988 7.787725 TGTAAGTTCTTCTCTTGGAGTTTTC 57.212 36.000 0.00 0.00 0.00 2.29
1119 1144 2.811317 CTGCTTGGCGACGTCTCC 60.811 66.667 17.77 17.77 0.00 3.71
1214 1239 6.507958 TGTGCGAAAATTATCTTCATTGGA 57.492 33.333 0.00 0.00 0.00 3.53
1356 1381 0.247460 TCATGCGTGAAGTCTCTGGG 59.753 55.000 6.04 0.00 0.00 4.45
1463 1488 2.202756 GGATGTCGACACGCTCCC 60.203 66.667 22.71 13.00 0.00 4.30
1515 1540 1.239296 TGGAAGACACGTCGGTCGAT 61.239 55.000 0.92 0.00 42.62 3.59
1781 1806 1.468565 CCAATGCAGCGAAGAACATGG 60.469 52.381 0.00 0.00 0.00 3.66
1831 1856 5.635278 TGTTCATGAGGATGTGATGGTAT 57.365 39.130 0.00 0.00 0.00 2.73
1836 1861 5.130809 TCATGAGGATGTGATGGTATCAACA 59.869 40.000 0.00 0.00 41.69 3.33
1857 1882 1.550327 TGGTTGTTTCACAGGCAACA 58.450 45.000 8.56 0.00 42.84 3.33
1878 1903 4.177026 CAGAAGAACCTGGAGATGTAACG 58.823 47.826 0.00 0.00 0.00 3.18
1942 1967 2.461110 GGCATAGTGAACCGGTGCG 61.461 63.158 8.52 0.00 36.70 5.34
1972 1997 4.523813 AGAACATGTAAACGTCGCAAAAG 58.476 39.130 0.00 0.00 0.00 2.27
2034 2059 1.895707 AGCTGTGTCACTGCCAAGC 60.896 57.895 25.87 15.68 43.01 4.01
2064 2089 3.853671 GCACACAACAGAAAAACACTGAG 59.146 43.478 0.00 0.00 38.55 3.35
2185 2210 3.425162 AGGAAGACAAGAACATGGACC 57.575 47.619 0.00 0.00 0.00 4.46
2499 2524 9.490083 ACTATTTACATGAAGTAAGTACTCCCT 57.510 33.333 0.00 0.00 43.20 4.20
2500 2525 9.968870 CTATTTACATGAAGTAAGTACTCCCTC 57.031 37.037 0.00 0.00 43.20 4.30
2501 2526 6.786967 TTACATGAAGTAAGTACTCCCTCC 57.213 41.667 0.00 0.00 37.77 4.30
2502 2527 3.700038 ACATGAAGTAAGTACTCCCTCCG 59.300 47.826 0.00 0.00 34.99 4.63
2503 2528 3.446442 TGAAGTAAGTACTCCCTCCGT 57.554 47.619 0.00 0.00 34.99 4.69
2504 2529 3.350833 TGAAGTAAGTACTCCCTCCGTC 58.649 50.000 0.00 0.00 34.99 4.79
2505 2530 2.433662 AGTAAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2506 2531 1.064091 AGTAAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
2507 2532 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2508 2533 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
2509 2534 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2510 2535 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2511 2536 1.348696 GTACTCCCTCCGTCCCAAAAA 59.651 52.381 0.00 0.00 0.00 1.94
2530 2555 5.692115 AAAAACTTGTCCCTCAAATGGTT 57.308 34.783 0.00 0.00 35.48 3.67
2531 2556 4.670896 AAACTTGTCCCTCAAATGGTTG 57.329 40.909 0.00 0.00 35.48 3.77
2532 2557 3.312736 ACTTGTCCCTCAAATGGTTGT 57.687 42.857 0.00 0.00 36.07 3.32
2533 2558 4.447138 ACTTGTCCCTCAAATGGTTGTA 57.553 40.909 0.00 0.00 36.07 2.41
2534 2559 4.998051 ACTTGTCCCTCAAATGGTTGTAT 58.002 39.130 0.00 0.00 36.07 2.29
2535 2560 5.010282 ACTTGTCCCTCAAATGGTTGTATC 58.990 41.667 0.00 0.00 36.07 2.24
2536 2561 4.927267 TGTCCCTCAAATGGTTGTATCT 57.073 40.909 0.00 0.00 36.07 1.98
2537 2562 6.012858 ACTTGTCCCTCAAATGGTTGTATCTA 60.013 38.462 0.00 0.00 36.07 1.98
2538 2563 5.989477 TGTCCCTCAAATGGTTGTATCTAG 58.011 41.667 0.00 0.00 36.07 2.43
2539 2564 4.816925 GTCCCTCAAATGGTTGTATCTAGC 59.183 45.833 0.00 0.00 36.07 3.42
2540 2565 4.473196 TCCCTCAAATGGTTGTATCTAGCA 59.527 41.667 0.00 0.00 36.07 3.49
2541 2566 4.576463 CCCTCAAATGGTTGTATCTAGCAC 59.424 45.833 0.00 0.00 36.07 4.40
2542 2567 4.576463 CCTCAAATGGTTGTATCTAGCACC 59.424 45.833 0.00 0.00 36.07 5.01
2543 2568 5.172687 TCAAATGGTTGTATCTAGCACCA 57.827 39.130 0.00 0.00 36.07 4.17
2544 2569 5.565509 TCAAATGGTTGTATCTAGCACCAA 58.434 37.500 0.00 0.00 36.07 3.67
2545 2570 5.647658 TCAAATGGTTGTATCTAGCACCAAG 59.352 40.000 0.00 0.00 36.07 3.61
2546 2571 4.844349 ATGGTTGTATCTAGCACCAAGT 57.156 40.909 0.00 0.00 0.00 3.16
2547 2572 4.634012 TGGTTGTATCTAGCACCAAGTT 57.366 40.909 0.00 0.00 0.00 2.66
2548 2573 5.748670 TGGTTGTATCTAGCACCAAGTTA 57.251 39.130 0.00 0.00 0.00 2.24
2549 2574 5.730550 TGGTTGTATCTAGCACCAAGTTAG 58.269 41.667 0.00 0.00 32.79 2.34
2550 2575 5.247564 TGGTTGTATCTAGCACCAAGTTAGT 59.752 40.000 0.00 0.00 33.25 2.24
2551 2576 5.581085 GGTTGTATCTAGCACCAAGTTAGTG 59.419 44.000 0.00 0.00 38.30 2.74
2563 2588 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
2564 2589 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
2565 2590 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
2566 2591 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
2567 2592 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
2568 2593 8.554528 CAAGTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
2569 2594 8.023021 AGTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
2570 2595 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
2571 2596 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
2572 2597 5.604231 AGTGCTAGATACATCCATTTGAGGA 59.396 40.000 0.00 0.00 43.01 3.71
2573 2598 6.100279 AGTGCTAGATACATCCATTTGAGGAA 59.900 38.462 0.00 0.00 41.92 3.36
2574 2599 6.203723 GTGCTAGATACATCCATTTGAGGAAC 59.796 42.308 0.00 0.00 41.92 3.62
2575 2600 6.126796 TGCTAGATACATCCATTTGAGGAACA 60.127 38.462 0.00 0.00 41.92 3.18
2576 2601 6.767902 GCTAGATACATCCATTTGAGGAACAA 59.232 38.462 0.00 0.00 41.92 2.83
2577 2602 7.041508 GCTAGATACATCCATTTGAGGAACAAG 60.042 40.741 0.00 0.00 41.92 3.16
2578 2603 5.591877 AGATACATCCATTTGAGGAACAAGC 59.408 40.000 0.00 0.00 41.92 4.01
2579 2604 3.771216 ACATCCATTTGAGGAACAAGCT 58.229 40.909 0.00 0.00 41.92 3.74
2580 2605 4.154942 ACATCCATTTGAGGAACAAGCTT 58.845 39.130 0.00 0.00 41.92 3.74
2581 2606 4.021719 ACATCCATTTGAGGAACAAGCTTG 60.022 41.667 24.84 24.84 41.92 4.01
2582 2607 2.892852 TCCATTTGAGGAACAAGCTTGG 59.107 45.455 29.18 12.28 39.77 3.61
2583 2608 2.028748 CCATTTGAGGAACAAGCTTGGG 60.029 50.000 29.18 13.19 39.77 4.12
2584 2609 2.746279 TTTGAGGAACAAGCTTGGGA 57.254 45.000 29.18 4.51 39.77 4.37
2585 2610 1.981256 TTGAGGAACAAGCTTGGGAC 58.019 50.000 29.18 17.88 34.20 4.46
2586 2611 0.843309 TGAGGAACAAGCTTGGGACA 59.157 50.000 29.18 17.71 0.00 4.02
2587 2612 2.357673 TTGAGGAACAAGCTTGGGACAA 60.358 45.455 29.18 21.59 37.48 3.18
2588 2613 4.249028 TTGAGGAACAAGCTTGGGACAAG 61.249 47.826 29.18 3.71 37.48 3.16
2589 2614 6.701067 TTGAGGAACAAGCTTGGGACAAGT 62.701 45.833 29.18 4.47 37.48 3.16
2608 2633 2.444281 TTTTTCGGACGGAGGGAGT 58.556 52.632 0.00 0.00 0.00 3.85
2609 2634 1.631405 TTTTTCGGACGGAGGGAGTA 58.369 50.000 0.00 0.00 0.00 2.59
2610 2635 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
2690 2741 8.306038 TGCATAATATTGGTGGAAATATTCAGC 58.694 33.333 0.00 10.42 40.33 4.26
2710 2761 0.391793 CCTTCCACTTCCTCCTTCGC 60.392 60.000 0.00 0.00 0.00 4.70
2711 2762 0.737715 CTTCCACTTCCTCCTTCGCG 60.738 60.000 0.00 0.00 0.00 5.87
2721 2772 0.438830 CTCCTTCGCGTTGCTGTTAC 59.561 55.000 5.77 0.00 0.00 2.50
2760 2812 3.744238 TCTTGTCATCGTTCCTGAACA 57.256 42.857 10.38 0.00 41.20 3.18
2821 2873 4.213482 TCTTTTCCTTGCGAGTTAAAGCTC 59.787 41.667 15.37 0.00 0.00 4.09
2932 2988 9.825972 CATACGAACTAAAATGAGTGAACAAAT 57.174 29.630 0.00 0.00 0.00 2.32
2933 2989 9.825972 ATACGAACTAAAATGAGTGAACAAATG 57.174 29.630 0.00 0.00 0.00 2.32
2941 2997 5.571784 ATGAGTGAACAAATGCACTATGG 57.428 39.130 0.00 0.00 44.77 2.74
2958 3014 6.459848 GCACTATGGGTCTATATACATCCGAC 60.460 46.154 0.00 0.00 0.00 4.79
3004 3061 2.134789 TAGTGAACGGAGGGAGTACC 57.865 55.000 0.00 0.00 40.67 3.34
3028 3085 3.058639 GGCACTTGTTCTGACTTTGCTAG 60.059 47.826 0.00 0.00 0.00 3.42
3029 3086 3.561725 GCACTTGTTCTGACTTTGCTAGT 59.438 43.478 0.00 0.00 40.71 2.57
3030 3087 4.750098 GCACTTGTTCTGACTTTGCTAGTA 59.250 41.667 0.00 0.00 37.17 1.82
3072 3130 4.624452 GCTCTGCATGTTTTGAATTTCCTC 59.376 41.667 0.00 0.00 0.00 3.71
3074 3132 6.349611 GCTCTGCATGTTTTGAATTTCCTCTA 60.350 38.462 0.00 0.00 0.00 2.43
3125 3183 7.504403 ACCTAATCACATATGTTCTCTTCCAG 58.496 38.462 5.37 0.00 0.00 3.86
3126 3184 7.345653 ACCTAATCACATATGTTCTCTTCCAGA 59.654 37.037 5.37 0.00 0.00 3.86
3127 3185 8.373981 CCTAATCACATATGTTCTCTTCCAGAT 58.626 37.037 5.37 0.00 0.00 2.90
3185 3243 0.104304 ACTGTCGAAAACGGTCTGCT 59.896 50.000 0.00 0.00 44.48 4.24
3189 3247 2.954611 GAAAACGGTCTGCTGGGC 59.045 61.111 0.00 0.00 0.00 5.36
3217 3283 2.169978 TGATCAGTGCCTGAGAATCCAG 59.830 50.000 10.13 0.00 44.08 3.86
3223 3289 3.009916 AGTGCCTGAGAATCCAGTTGAAT 59.990 43.478 0.00 0.00 32.43 2.57
3283 3358 1.674221 CCTAGCTGGCACTGTGAACTC 60.674 57.143 12.86 0.00 0.00 3.01
3284 3359 0.321671 TAGCTGGCACTGTGAACTCC 59.678 55.000 12.86 3.53 0.00 3.85
3285 3360 2.320587 GCTGGCACTGTGAACTCCG 61.321 63.158 12.86 1.57 0.00 4.63
3286 3361 1.069765 CTGGCACTGTGAACTCCGT 59.930 57.895 12.86 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.440914 GCAAATGCAAGAAGACGAAATGCG 62.441 45.833 0.00 0.00 43.10 4.73
29 30 3.863142 ATCAGGCAAATGCAAGAAGAC 57.137 42.857 7.80 0.00 44.36 3.01
49 53 8.582657 TGGATTGGGATTTCTCGTTAAAATAA 57.417 30.769 0.00 0.00 0.00 1.40
50 54 7.284489 CCTGGATTGGGATTTCTCGTTAAAATA 59.716 37.037 0.00 0.00 0.00 1.40
51 55 6.096846 CCTGGATTGGGATTTCTCGTTAAAAT 59.903 38.462 0.00 0.00 0.00 1.82
52 56 5.417580 CCTGGATTGGGATTTCTCGTTAAAA 59.582 40.000 0.00 0.00 0.00 1.52
53 57 4.947388 CCTGGATTGGGATTTCTCGTTAAA 59.053 41.667 0.00 0.00 0.00 1.52
186 190 2.268280 CACTGGAGCCTCAGCAGG 59.732 66.667 0.00 0.00 43.56 4.85
251 255 2.750637 GCTCGGAGGAGTCGGTGA 60.751 66.667 7.20 0.00 42.53 4.02
390 394 4.235762 ACGCCGTGCTTGTCCAGT 62.236 61.111 0.00 0.00 0.00 4.00
420 424 3.746949 CTCCAGGCTCGCCATGGAC 62.747 68.421 18.40 5.97 37.98 4.02
450 454 1.215647 GTCCGCCGACTTCATCAGT 59.784 57.895 0.00 0.00 39.07 3.41
492 496 1.587613 GGACGAGAGCACGAGCATC 60.588 63.158 7.77 3.84 45.49 3.91
584 588 0.183492 TTTGCACCAGTTGAGCTCCT 59.817 50.000 12.15 0.00 0.00 3.69
609 613 1.515952 CTTCTCGAGCTGCTCCACG 60.516 63.158 22.97 13.04 0.00 4.94
657 661 2.614969 AAGAGGCATCCCCCTGCA 60.615 61.111 0.00 0.00 44.12 4.41
666 670 3.776969 TCACCACAAGATAGAAGAGGCAT 59.223 43.478 0.00 0.00 0.00 4.40
702 706 9.063615 CATATTCCTTGTCTCATGAATCAATCA 57.936 33.333 11.07 0.00 43.67 2.57
703 707 9.281371 TCATATTCCTTGTCTCATGAATCAATC 57.719 33.333 11.07 0.00 0.00 2.67
704 708 9.636789 TTCATATTCCTTGTCTCATGAATCAAT 57.363 29.630 11.07 2.37 29.84 2.57
705 709 9.636789 ATTCATATTCCTTGTCTCATGAATCAA 57.363 29.630 0.00 4.60 38.21 2.57
752 763 6.150318 CGTGTTAGACTAACTTCAGTGTGAT 58.850 40.000 22.65 0.00 39.38 3.06
753 764 5.066893 ACGTGTTAGACTAACTTCAGTGTGA 59.933 40.000 22.65 0.42 39.38 3.58
840 862 2.125269 GGCGTGCCGTCAGGTATT 60.125 61.111 0.00 0.00 40.50 1.89
864 886 1.374758 CTTCCTGTCCCACGCAGAC 60.375 63.158 0.00 0.00 36.12 3.51
966 988 5.841957 AAAAGCATTGCTATTACAGAGGG 57.158 39.130 12.39 0.00 38.25 4.30
1119 1144 3.487536 TGACACAAAATTTGCTATCGCG 58.512 40.909 5.52 0.00 39.65 5.87
1210 1235 4.750941 AGAGGGGAAAATGTCAATTCCAA 58.249 39.130 17.78 0.00 45.64 3.53
1214 1239 8.613922 AATCATTAGAGGGGAAAATGTCAATT 57.386 30.769 0.00 0.00 33.35 2.32
1225 1250 5.255397 ACACACAAAATCATTAGAGGGGA 57.745 39.130 0.00 0.00 0.00 4.81
1329 1354 1.873591 ACTTCACGCATGAACTTGGTC 59.126 47.619 0.00 0.00 40.01 4.02
1330 1355 1.873591 GACTTCACGCATGAACTTGGT 59.126 47.619 0.00 0.00 40.01 3.67
1356 1381 4.112341 CCGCTGCAGCCTTCAAGC 62.112 66.667 32.07 6.68 37.91 4.01
1463 1488 3.181468 TGCCAGCTCTGAAGTATCATCTG 60.181 47.826 0.00 0.00 34.37 2.90
1515 1540 3.614092 GGAACTTCCATCTTCATGCTCA 58.386 45.455 2.62 0.00 36.28 4.26
1702 1727 1.909700 TCATTTCCTGAACCAGTGGC 58.090 50.000 9.78 0.00 0.00 5.01
1753 1778 0.035317 TCGCTGCATTGGTTCACTCT 59.965 50.000 0.00 0.00 0.00 3.24
1781 1806 3.119463 CGATGTTGGTTTTGCGACATTTC 59.881 43.478 0.00 0.00 33.21 2.17
1845 1870 2.092429 AGGTTCTTCTGTTGCCTGTGAA 60.092 45.455 0.00 0.00 0.00 3.18
1857 1882 4.082136 GTCGTTACATCTCCAGGTTCTTCT 60.082 45.833 0.00 0.00 0.00 2.85
1878 1903 2.560981 ACCATTTCCGGAAACATTGGTC 59.439 45.455 33.52 0.00 36.84 4.02
1904 1929 3.244387 GCCTTGATCTCCCTCTGGAATAC 60.244 52.174 0.00 0.00 41.17 1.89
1942 1967 3.185797 ACGTTTACATGTTCTTCTTCGCC 59.814 43.478 2.30 0.00 0.00 5.54
1972 1997 2.325583 TGACCGCTGGATGGATTTAC 57.674 50.000 1.50 0.00 0.00 2.01
2034 2059 2.820059 TCTGTTGTGTGCTAGGAGTG 57.180 50.000 0.00 0.00 0.00 3.51
2064 2089 1.343465 TCCTCAACGGAACACTCCTTC 59.657 52.381 0.00 0.00 39.40 3.46
2185 2210 4.573900 ACAAAGTTGATAGCAGGAGTCAG 58.426 43.478 0.00 0.00 0.00 3.51
2283 2308 1.734465 CCATTGACAGGAGAACGCTTC 59.266 52.381 0.00 0.00 0.00 3.86
2286 2311 1.648467 GGCCATTGACAGGAGAACGC 61.648 60.000 0.00 0.00 0.00 4.84
2508 2533 5.045942 ACAACCATTTGAGGGACAAGTTTTT 60.046 36.000 0.00 0.00 39.77 1.94
2509 2534 4.469586 ACAACCATTTGAGGGACAAGTTTT 59.530 37.500 0.00 0.00 39.77 2.43
2510 2535 4.030216 ACAACCATTTGAGGGACAAGTTT 58.970 39.130 0.00 0.00 39.77 2.66
2511 2536 3.642141 ACAACCATTTGAGGGACAAGTT 58.358 40.909 0.00 0.00 39.77 2.66
2512 2537 3.312736 ACAACCATTTGAGGGACAAGT 57.687 42.857 0.00 0.00 39.77 3.16
2513 2538 5.256474 AGATACAACCATTTGAGGGACAAG 58.744 41.667 0.00 0.00 39.77 3.16
2514 2539 5.255397 AGATACAACCATTTGAGGGACAA 57.745 39.130 0.00 0.00 36.48 3.18
2515 2540 4.927267 AGATACAACCATTTGAGGGACA 57.073 40.909 0.00 0.00 36.48 4.02
2516 2541 4.816925 GCTAGATACAACCATTTGAGGGAC 59.183 45.833 0.00 0.00 36.48 4.46
2517 2542 4.473196 TGCTAGATACAACCATTTGAGGGA 59.527 41.667 0.00 0.00 36.48 4.20
2518 2543 4.576463 GTGCTAGATACAACCATTTGAGGG 59.424 45.833 0.00 0.00 36.48 4.30
2519 2544 4.576463 GGTGCTAGATACAACCATTTGAGG 59.424 45.833 0.00 0.00 36.48 3.86
2520 2545 5.185454 TGGTGCTAGATACAACCATTTGAG 58.815 41.667 0.00 0.00 36.48 3.02
2521 2546 5.172687 TGGTGCTAGATACAACCATTTGA 57.827 39.130 0.00 0.00 36.48 2.69
2522 2547 5.415701 ACTTGGTGCTAGATACAACCATTTG 59.584 40.000 0.00 0.00 38.83 2.32
2523 2548 5.570320 ACTTGGTGCTAGATACAACCATTT 58.430 37.500 0.00 0.00 0.00 2.32
2524 2549 5.179452 ACTTGGTGCTAGATACAACCATT 57.821 39.130 0.00 0.00 0.00 3.16
2525 2550 4.844349 ACTTGGTGCTAGATACAACCAT 57.156 40.909 0.00 0.00 0.00 3.55
2526 2551 4.634012 AACTTGGTGCTAGATACAACCA 57.366 40.909 0.00 0.00 0.00 3.67
2527 2552 5.581085 CACTAACTTGGTGCTAGATACAACC 59.419 44.000 0.00 0.00 0.00 3.77
2528 2553 6.648725 CACTAACTTGGTGCTAGATACAAC 57.351 41.667 0.00 0.00 0.00 3.32
2539 2564 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
2540 2565 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
2541 2566 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
2542 2567 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
2543 2568 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
2544 2569 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
2545 2570 7.386299 CCTCAAATGGATGTATCTAGCACTAAC 59.614 40.741 0.00 0.00 0.00 2.34
2546 2571 7.290014 TCCTCAAATGGATGTATCTAGCACTAA 59.710 37.037 0.00 0.00 0.00 2.24
2547 2572 6.782494 TCCTCAAATGGATGTATCTAGCACTA 59.218 38.462 0.00 0.00 0.00 2.74
2548 2573 5.604231 TCCTCAAATGGATGTATCTAGCACT 59.396 40.000 0.00 0.00 0.00 4.40
2549 2574 5.858381 TCCTCAAATGGATGTATCTAGCAC 58.142 41.667 0.00 0.00 0.00 4.40
2550 2575 6.126796 TGTTCCTCAAATGGATGTATCTAGCA 60.127 38.462 0.00 0.00 35.83 3.49
2551 2576 6.291377 TGTTCCTCAAATGGATGTATCTAGC 58.709 40.000 0.00 0.00 35.83 3.42
2552 2577 7.041508 GCTTGTTCCTCAAATGGATGTATCTAG 60.042 40.741 0.00 0.00 35.83 2.43
2553 2578 6.767902 GCTTGTTCCTCAAATGGATGTATCTA 59.232 38.462 0.00 0.00 35.83 1.98
2554 2579 5.591877 GCTTGTTCCTCAAATGGATGTATCT 59.408 40.000 0.00 0.00 35.83 1.98
2555 2580 5.591877 AGCTTGTTCCTCAAATGGATGTATC 59.408 40.000 0.00 0.00 35.83 2.24
2556 2581 5.513233 AGCTTGTTCCTCAAATGGATGTAT 58.487 37.500 0.00 0.00 35.83 2.29
2557 2582 4.922206 AGCTTGTTCCTCAAATGGATGTA 58.078 39.130 0.00 0.00 35.83 2.29
2558 2583 3.771216 AGCTTGTTCCTCAAATGGATGT 58.229 40.909 0.00 0.00 35.83 3.06
2559 2584 4.491676 CAAGCTTGTTCCTCAAATGGATG 58.508 43.478 18.65 0.00 35.83 3.51
2560 2585 3.512724 CCAAGCTTGTTCCTCAAATGGAT 59.487 43.478 24.35 0.00 36.92 3.41
2561 2586 2.892852 CCAAGCTTGTTCCTCAAATGGA 59.107 45.455 24.35 0.00 36.92 3.41
2562 2587 2.028748 CCCAAGCTTGTTCCTCAAATGG 60.029 50.000 24.35 10.71 35.48 3.16
2563 2588 2.892852 TCCCAAGCTTGTTCCTCAAATG 59.107 45.455 24.35 5.47 35.48 2.32
2564 2589 2.893489 GTCCCAAGCTTGTTCCTCAAAT 59.107 45.455 24.35 0.00 35.48 2.32
2565 2590 2.306847 GTCCCAAGCTTGTTCCTCAAA 58.693 47.619 24.35 0.00 35.48 2.69
2566 2591 1.214175 TGTCCCAAGCTTGTTCCTCAA 59.786 47.619 24.35 1.41 34.61 3.02
2567 2592 0.843309 TGTCCCAAGCTTGTTCCTCA 59.157 50.000 24.35 12.85 0.00 3.86
2568 2593 1.882623 CTTGTCCCAAGCTTGTTCCTC 59.117 52.381 24.35 10.65 0.00 3.71
2569 2594 1.215423 ACTTGTCCCAAGCTTGTTCCT 59.785 47.619 24.35 0.00 0.00 3.36
2570 2595 1.692411 ACTTGTCCCAAGCTTGTTCC 58.308 50.000 24.35 11.81 0.00 3.62
2571 2596 3.801114 AAACTTGTCCCAAGCTTGTTC 57.199 42.857 24.35 14.17 0.00 3.18
2572 2597 4.551702 AAAAACTTGTCCCAAGCTTGTT 57.448 36.364 24.35 7.97 0.00 2.83
2590 2615 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
2591 2616 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
2592 2617 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
2593 2618 0.911769 TAGTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
2594 2619 1.135094 ATAGTACTCCCTCCGTCCGA 58.865 55.000 0.00 0.00 0.00 4.55
2595 2620 1.978454 AATAGTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
2596 2621 4.210331 TGTAAATAGTACTCCCTCCGTCC 58.790 47.826 0.00 0.00 0.00 4.79
2597 2622 5.533903 TCATGTAAATAGTACTCCCTCCGTC 59.466 44.000 0.00 0.00 0.00 4.79
2598 2623 5.452255 TCATGTAAATAGTACTCCCTCCGT 58.548 41.667 0.00 0.00 0.00 4.69
2599 2624 6.264744 TCTTCATGTAAATAGTACTCCCTCCG 59.735 42.308 0.00 0.00 0.00 4.63
2600 2625 7.598759 TCTTCATGTAAATAGTACTCCCTCC 57.401 40.000 0.00 0.00 0.00 4.30
2601 2626 8.915036 TCTTCTTCATGTAAATAGTACTCCCTC 58.085 37.037 0.00 0.00 0.00 4.30
2602 2627 8.840200 TCTTCTTCATGTAAATAGTACTCCCT 57.160 34.615 0.00 0.00 0.00 4.20
2603 2628 8.915036 TCTCTTCTTCATGTAAATAGTACTCCC 58.085 37.037 0.00 0.00 0.00 4.30
2604 2629 9.738832 GTCTCTTCTTCATGTAAATAGTACTCC 57.261 37.037 0.00 0.00 0.00 3.85
2690 2741 0.250513 CGAAGGAGGAAGTGGAAGGG 59.749 60.000 0.00 0.00 0.00 3.95
2710 2761 5.516090 ACTTGGTTAAATGTAACAGCAACG 58.484 37.500 8.06 2.10 41.31 4.10
2711 2762 7.200455 AGAACTTGGTTAAATGTAACAGCAAC 58.800 34.615 8.06 0.00 41.31 4.17
2721 2772 9.364989 TGACAAGAAAAAGAACTTGGTTAAATG 57.635 29.630 0.00 0.00 45.03 2.32
2760 2812 8.674607 GGATGACGTAAATGTTTTATCCTCTTT 58.325 33.333 0.00 0.00 32.20 2.52
2932 2988 5.359860 CGGATGTATATAGACCCATAGTGCA 59.640 44.000 0.00 0.00 0.00 4.57
2933 2989 5.593095 TCGGATGTATATAGACCCATAGTGC 59.407 44.000 0.00 0.00 0.00 4.40
2941 2997 7.450124 TTTCTGAGTCGGATGTATATAGACC 57.550 40.000 1.57 0.00 32.70 3.85
2958 3014 5.993106 AAGAGGTTCGAACTTTTTCTGAG 57.007 39.130 26.32 0.00 0.00 3.35
3004 3061 2.542411 GCAAAGTCAGAACAAGTGCCAG 60.542 50.000 0.00 0.00 0.00 4.85
3028 3085 3.059166 CAAAATGCCAGGTTTGCAGTAC 58.941 45.455 0.00 0.00 42.92 2.73
3029 3086 3.383620 CAAAATGCCAGGTTTGCAGTA 57.616 42.857 0.00 0.00 42.92 2.74
3030 3087 2.243602 CAAAATGCCAGGTTTGCAGT 57.756 45.000 0.00 0.00 42.92 4.40
3072 3130 2.677199 TGCTCAAACGCAGAGAAGTAG 58.323 47.619 3.82 0.00 34.44 2.57
3074 3132 1.802960 CATGCTCAAACGCAGAGAAGT 59.197 47.619 3.82 0.00 44.10 3.01
3185 3243 0.176449 CACTGATCATGTCTCGCCCA 59.824 55.000 0.00 0.00 0.00 5.36
3217 3283 9.288576 TGATGAAGATTATACCATGGATTCAAC 57.711 33.333 21.47 13.98 0.00 3.18
3223 3289 9.511272 CTGAAATGATGAAGATTATACCATGGA 57.489 33.333 21.47 2.01 0.00 3.41


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

AutoCloner maintained by Alex Coulton.