Multiple sequence alignment - TraesCS5B01G557800

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 TraesCS5B01G557800 chr5B 100.000 1896 0 0 719 2614 705458365 705460260 0.000000e+00 3502.0
1 TraesCS5B01G557800 chr5B 100.000 401 0 0 1 401 705457647 705458047 0.000000e+00 741.0
2 TraesCS5B01G557800 chr7D 93.968 1575 90 5 719 2290 61668648 61667076 0.000000e+00 2377.0
3 TraesCS5B01G557800 chr7D 95.285 403 15 3 1 401 61669072 61668672 1.020000e-178 636.0
4 TraesCS5B01G557800 chr5A 93.714 1575 94 5 719 2290 338458166 338456594 0.000000e+00 2355.0
5 TraesCS5B01G557800 chr5A 90.135 223 20 2 2291 2511 435332954 435332732 3.290000e-74 289.0
6 TraesCS5B01G557800 chr5A 92.000 75 6 0 2539 2613 410550460 410550534 3.560000e-19 106.0
7 TraesCS5B01G557800 chr1D 93.166 1595 82 14 719 2290 419053986 419055576 0.000000e+00 2316.0
8 TraesCS5B01G557800 chr1D 92.163 1595 97 10 719 2290 34230152 34231741 0.000000e+00 2228.0
9 TraesCS5B01G557800 chr1D 95.455 396 14 4 1 396 419053568 419053959 1.710000e-176 628.0
10 TraesCS5B01G557800 chr1D 90.090 222 21 1 2291 2511 26658489 26658710 1.180000e-73 287.0
11 TraesCS5B01G557800 chr4B 93.526 1560 72 9 754 2290 642269512 642271065 0.000000e+00 2294.0
12 TraesCS5B01G557800 chr4B 96.717 396 11 1 1 396 642269068 642269461 0.000000e+00 658.0
13 TraesCS5B01G557800 chr4B 92.063 63 5 0 2551 2613 486262096 486262034 3.580000e-14 89.8
14 TraesCS5B01G557800 chr2D 92.816 1573 89 14 719 2290 459634506 459632957 0.000000e+00 2257.0
15 TraesCS5B01G557800 chr2D 95.262 401 15 3 4 401 302021912 302021513 1.320000e-177 632.0
16 TraesCS5B01G557800 chr2D 90.135 223 19 3 2291 2511 75608846 75608625 1.180000e-73 287.0
17 TraesCS5B01G557800 chr2D 94.737 76 4 0 2539 2614 641377778 641377853 4.570000e-23 119.0
18 TraesCS5B01G557800 chr2D 90.000 70 7 0 2544 2613 649069205 649069274 9.960000e-15 91.6
19 TraesCS5B01G557800 chr3A 91.830 1579 118 7 719 2290 717430087 717431661 0.000000e+00 2191.0
20 TraesCS5B01G557800 chr3A 95.466 397 16 2 1 396 717429671 717430066 1.320000e-177 632.0
21 TraesCS5B01G557800 chr2B 91.335 1581 127 6 719 2292 83722893 83724470 0.000000e+00 2152.0
22 TraesCS5B01G557800 chr2B 95.250 400 15 2 1 396 83722472 83722871 4.750000e-177 630.0
23 TraesCS5B01G557800 chr2B 83.471 121 18 2 2171 2290 64111905 64112024 7.650000e-21 111.0
24 TraesCS5B01G557800 chr2B 77.483 151 29 5 2144 2291 786080556 786080408 4.640000e-13 86.1
25 TraesCS5B01G557800 chrUn 95.762 1227 50 2 757 1981 57104323 57103097 0.000000e+00 1977.0
26 TraesCS5B01G557800 chrUn 95.691 1230 51 2 754 1981 294652931 294654160 0.000000e+00 1977.0
27 TraesCS5B01G557800 chrUn 96.030 403 12 2 1 401 57104784 57104384 0.000000e+00 652.0
28 TraesCS5B01G557800 chr3B 93.230 1359 55 7 969 2290 43256504 43257862 0.000000e+00 1965.0
29 TraesCS5B01G557800 chr4A 95.545 404 13 4 1 401 601692606 601692205 2.190000e-180 641.0
30 TraesCS5B01G557800 chr1A 95.718 397 15 2 1 396 14735783 14736178 2.840000e-179 638.0
31 TraesCS5B01G557800 chr5D 90.135 223 20 2 2291 2511 38328898 38328676 3.290000e-74 289.0
32 TraesCS5B01G557800 chr5D 90.135 223 19 3 2291 2511 26989248 26989469 1.180000e-73 287.0
33 TraesCS5B01G557800 chr4D 90.455 220 19 2 2293 2511 4685912 4686130 3.290000e-74 289.0
34 TraesCS5B01G557800 chr4D 90.090 222 21 1 2291 2511 11387963 11388184 1.180000e-73 287.0
35 TraesCS5B01G557800 chr3D 90.090 222 21 1 2291 2511 19222761 19222540 1.180000e-73 287.0
36 TraesCS5B01G557800 chr3D 90.090 222 20 2 2291 2511 595816845 595817065 1.180000e-73 287.0
37 TraesCS5B01G557800 chr3D 94.667 75 4 0 2539 2613 520075213 520075139 1.640000e-22 117.0
38 TraesCS5B01G557800 chr1B 91.781 73 5 1 2541 2613 213918055 213917984 1.660000e-17 100.0
39 TraesCS5B01G557800 chr7A 88.750 80 6 2 2535 2613 131938440 131938363 7.700000e-16 95.3
40 TraesCS5B01G557800 chr2A 91.304 69 6 0 2541 2609 765296438 765296506 7.700000e-16 95.3


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 TraesCS5B01G557800 chr5B 705457647 705460260 2613 False 2121.5 3502 100.0000 1 2614 2 chr5B.!!$F1 2613
1 TraesCS5B01G557800 chr7D 61667076 61669072 1996 True 1506.5 2377 94.6265 1 2290 2 chr7D.!!$R1 2289
2 TraesCS5B01G557800 chr5A 338456594 338458166 1572 True 2355.0 2355 93.7140 719 2290 1 chr5A.!!$R1 1571
3 TraesCS5B01G557800 chr1D 34230152 34231741 1589 False 2228.0 2228 92.1630 719 2290 1 chr1D.!!$F2 1571
4 TraesCS5B01G557800 chr1D 419053568 419055576 2008 False 1472.0 2316 94.3105 1 2290 2 chr1D.!!$F3 2289
5 TraesCS5B01G557800 chr4B 642269068 642271065 1997 False 1476.0 2294 95.1215 1 2290 2 chr4B.!!$F1 2289
6 TraesCS5B01G557800 chr2D 459632957 459634506 1549 True 2257.0 2257 92.8160 719 2290 1 chr2D.!!$R3 1571
7 TraesCS5B01G557800 chr3A 717429671 717431661 1990 False 1411.5 2191 93.6480 1 2290 2 chr3A.!!$F1 2289
8 TraesCS5B01G557800 chr2B 83722472 83724470 1998 False 1391.0 2152 93.2925 1 2292 2 chr2B.!!$F2 2291
9 TraesCS5B01G557800 chrUn 294652931 294654160 1229 False 1977.0 1977 95.6910 754 1981 1 chrUn.!!$F1 1227
10 TraesCS5B01G557800 chrUn 57103097 57104784 1687 True 1314.5 1977 95.8960 1 1981 2 chrUn.!!$R1 1980
11 TraesCS5B01G557800 chr3B 43256504 43257862 1358 False 1965.0 1965 93.2300 969 2290 1 chr3B.!!$F1 1321

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
958 966 4.202253 TGTCTTCTCTGCTTGTGCTTAAGA 60.202 41.667 6.67 0.0 40.48 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2261 0.58873 CGCGTCATAATTTGCCCACG 60.589 55.0 0.0 0.0 0.0 4.94 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
62 64 7.790823 TTTACCTTTTTGCGTACTAGAACTT 57.209 32.000 0.00 0.00 0.00 2.66
165 169 9.043079 GTTCACTTAACTATCTTGTAATAGCCC 57.957 37.037 0.00 0.00 35.05 5.19
168 172 7.709613 CACTTAACTATCTTGTAATAGCCCGTT 59.290 37.037 0.00 0.00 33.33 4.44
229 236 8.280909 TGATAAGTTTTGAAGCGATTGAAAAC 57.719 30.769 26.55 26.55 38.17 2.43
255 262 8.299570 CCATCAGTTTTGATTTAGTATATGGCC 58.700 37.037 0.00 0.00 42.12 5.36
304 311 5.562917 CATAATCACTTTGACATGTGACCG 58.437 41.667 1.15 0.00 44.52 4.79
380 387 9.875708 TTATATATTGTAGTTTTGGCCATCCTT 57.124 29.630 6.09 0.00 0.00 3.36
396 403 7.502226 TGGCCATCCTTAGTGTCTTATATTTTG 59.498 37.037 0.00 0.00 0.00 2.44
397 404 7.502561 GGCCATCCTTAGTGTCTTATATTTTGT 59.497 37.037 0.00 0.00 0.00 2.83
886 894 6.278363 TCACAAGTGTCTAGTTGTAAAGGAC 58.722 40.000 0.00 0.00 46.12 3.85
958 966 4.202253 TGTCTTCTCTGCTTGTGCTTAAGA 60.202 41.667 6.67 0.00 40.48 2.10
1020 1029 5.308825 GAGATGGAAAACAAGGTCTCTCAA 58.691 41.667 0.00 0.00 32.82 3.02
1061 1070 2.963371 GAACTCTGCGACGGAGGT 59.037 61.111 16.74 10.25 39.81 3.85
1272 1281 2.367894 CAGGCAAGATGAGGAGCATAGA 59.632 50.000 0.00 0.00 37.34 1.98
1286 1295 4.588528 GGAGCATAGAAAGAGAGATGAGGT 59.411 45.833 0.00 0.00 0.00 3.85
1530 1541 0.961019 TTGCTGCTCCATTGTTGGTC 59.039 50.000 0.00 0.00 44.06 4.02
1744 1758 1.569708 AAAAACACAAGTGCCGCATG 58.430 45.000 0.00 0.00 0.00 4.06
1769 1783 5.710513 TTTAATGGGCTGATGTGCATATC 57.289 39.130 15.93 15.93 34.04 1.63
1857 1877 1.477923 GCGGTAAAATGGGCCCATAGA 60.478 52.381 37.59 22.07 35.31 1.98
1959 1979 2.821366 CGCCACATCAGCTCCACC 60.821 66.667 0.00 0.00 0.00 4.61
1983 2080 2.821366 CCACATCAGCTCCACGCC 60.821 66.667 0.00 0.00 40.39 5.68
2002 2099 2.409055 GGCGCCACATCAGATTGCA 61.409 57.895 24.80 0.00 0.00 4.08
2003 2100 1.507630 GCGCCACATCAGATTGCAA 59.492 52.632 0.00 0.00 0.00 4.08
2164 2261 4.778143 ACCGTCAAGGATGGGCGC 62.778 66.667 0.00 0.00 42.60 6.53
2292 2389 8.548721 CAGATTAACGACTTTCTTGTAGTGTTT 58.451 33.333 0.00 0.00 0.00 2.83
2293 2390 9.106070 AGATTAACGACTTTCTTGTAGTGTTTT 57.894 29.630 0.00 0.00 0.00 2.43
2418 2515 9.573133 AATGCCTTTCTAACAGATAAATTTTCG 57.427 29.630 0.00 0.00 0.00 3.46
2419 2516 8.106247 TGCCTTTCTAACAGATAAATTTTCGT 57.894 30.769 0.00 0.00 0.00 3.85
2420 2517 8.573035 TGCCTTTCTAACAGATAAATTTTCGTT 58.427 29.630 0.00 6.09 0.00 3.85
2421 2518 9.406828 GCCTTTCTAACAGATAAATTTTCGTTT 57.593 29.630 0.00 0.00 0.00 3.60
2429 2526 8.797266 ACAGATAAATTTTCGTTTGAAACTCC 57.203 30.769 6.49 0.00 43.54 3.85
2430 2527 7.589954 ACAGATAAATTTTCGTTTGAAACTCCG 59.410 33.333 6.49 0.00 43.54 4.63
2431 2528 7.801315 CAGATAAATTTTCGTTTGAAACTCCGA 59.199 33.333 6.49 0.00 43.54 4.55
2432 2529 8.512138 AGATAAATTTTCGTTTGAAACTCCGAT 58.488 29.630 6.49 0.00 43.54 4.18
2433 2530 9.763465 GATAAATTTTCGTTTGAAACTCCGATA 57.237 29.630 6.49 0.00 43.54 2.92
2434 2531 7.847166 AAATTTTCGTTTGAAACTCCGATAC 57.153 32.000 6.49 0.00 43.54 2.24
2435 2532 6.796705 ATTTTCGTTTGAAACTCCGATACT 57.203 33.333 6.49 0.00 43.54 2.12
2436 2533 6.607735 TTTTCGTTTGAAACTCCGATACTT 57.392 33.333 6.49 0.00 43.54 2.24
2437 2534 5.834239 TTCGTTTGAAACTCCGATACTTC 57.166 39.130 6.49 0.00 0.00 3.01
2438 2535 3.916172 TCGTTTGAAACTCCGATACTTCG 59.084 43.478 6.49 0.00 45.08 3.79
2439 2536 7.224513 TTTCGTTTGAAACTCCGATACTTCGA 61.225 38.462 6.49 0.00 42.22 3.71
2440 2537 8.627429 TTTCGTTTGAAACTCCGATACTTCGAA 61.627 37.037 6.49 0.00 42.22 3.71
2484 2581 5.410067 ACGAAGTGCATCCAATTTTTATGG 58.590 37.500 0.00 0.00 42.51 2.74
2485 2582 5.047377 ACGAAGTGCATCCAATTTTTATGGT 60.047 36.000 0.00 0.00 42.51 3.55
2486 2583 6.151985 ACGAAGTGCATCCAATTTTTATGGTA 59.848 34.615 0.00 0.00 42.51 3.25
2487 2584 7.032580 CGAAGTGCATCCAATTTTTATGGTAA 58.967 34.615 0.00 0.00 39.09 2.85
2488 2585 7.009174 CGAAGTGCATCCAATTTTTATGGTAAC 59.991 37.037 0.00 0.00 39.09 2.50
2489 2586 6.639563 AGTGCATCCAATTTTTATGGTAACC 58.360 36.000 0.00 0.00 39.09 2.85
2490 2587 6.440328 AGTGCATCCAATTTTTATGGTAACCT 59.560 34.615 0.00 0.00 39.09 3.50
2491 2588 6.756542 GTGCATCCAATTTTTATGGTAACCTC 59.243 38.462 0.00 0.00 39.09 3.85
2492 2589 6.667414 TGCATCCAATTTTTATGGTAACCTCT 59.333 34.615 0.00 0.00 39.09 3.69
2493 2590 7.147915 TGCATCCAATTTTTATGGTAACCTCTC 60.148 37.037 0.00 0.00 39.09 3.20
2494 2591 7.147915 GCATCCAATTTTTATGGTAACCTCTCA 60.148 37.037 0.00 0.00 39.09 3.27
2495 2592 8.748412 CATCCAATTTTTATGGTAACCTCTCAA 58.252 33.333 0.00 0.00 39.09 3.02
2496 2593 8.893563 TCCAATTTTTATGGTAACCTCTCAAT 57.106 30.769 0.00 0.00 39.09 2.57
2497 2594 9.320295 TCCAATTTTTATGGTAACCTCTCAATT 57.680 29.630 0.00 0.00 39.09 2.32
2498 2595 9.942850 CCAATTTTTATGGTAACCTCTCAATTT 57.057 29.630 0.00 0.00 33.08 1.82
2548 2645 9.793259 TCTGAAAAATCCCATGTAATCTATACC 57.207 33.333 0.00 0.00 0.00 2.73
2549 2646 9.573166 CTGAAAAATCCCATGTAATCTATACCA 57.427 33.333 0.00 0.00 0.00 3.25
2550 2647 9.928618 TGAAAAATCCCATGTAATCTATACCAA 57.071 29.630 0.00 0.00 0.00 3.67
2570 2667 7.687941 ACCAATATAACAAGACACAAAGAGG 57.312 36.000 0.00 0.00 0.00 3.69
2571 2668 6.151144 ACCAATATAACAAGACACAAAGAGGC 59.849 38.462 0.00 0.00 0.00 4.70
2572 2669 6.150976 CCAATATAACAAGACACAAAGAGGCA 59.849 38.462 0.00 0.00 0.00 4.75
2573 2670 6.992063 ATATAACAAGACACAAAGAGGCAG 57.008 37.500 0.00 0.00 0.00 4.85
2574 2671 3.281727 AACAAGACACAAAGAGGCAGA 57.718 42.857 0.00 0.00 0.00 4.26
2575 2672 3.498774 ACAAGACACAAAGAGGCAGAT 57.501 42.857 0.00 0.00 0.00 2.90
2576 2673 3.406764 ACAAGACACAAAGAGGCAGATC 58.593 45.455 0.00 0.00 0.00 2.75
2577 2674 2.746362 CAAGACACAAAGAGGCAGATCC 59.254 50.000 0.00 0.00 0.00 3.36
2578 2675 1.980765 AGACACAAAGAGGCAGATCCA 59.019 47.619 0.00 0.00 37.29 3.41
2579 2676 2.373169 AGACACAAAGAGGCAGATCCAA 59.627 45.455 0.00 0.00 37.29 3.53
2580 2677 3.009916 AGACACAAAGAGGCAGATCCAAT 59.990 43.478 0.00 0.00 37.29 3.16
2581 2678 3.760684 GACACAAAGAGGCAGATCCAATT 59.239 43.478 0.00 0.00 37.29 2.32
2582 2679 4.922206 ACACAAAGAGGCAGATCCAATTA 58.078 39.130 0.00 0.00 37.29 1.40
2583 2680 5.324409 ACACAAAGAGGCAGATCCAATTAA 58.676 37.500 0.00 0.00 37.29 1.40
2584 2681 5.954150 ACACAAAGAGGCAGATCCAATTAAT 59.046 36.000 0.00 0.00 37.29 1.40
2585 2682 6.096001 ACACAAAGAGGCAGATCCAATTAATC 59.904 38.462 0.00 0.00 37.29 1.75
2586 2683 6.320672 CACAAAGAGGCAGATCCAATTAATCT 59.679 38.462 0.00 0.00 37.29 2.40
2587 2684 6.545298 ACAAAGAGGCAGATCCAATTAATCTC 59.455 38.462 0.62 0.00 37.29 2.75
2588 2685 4.892433 AGAGGCAGATCCAATTAATCTCG 58.108 43.478 0.62 0.00 37.29 4.04
2589 2686 4.590647 AGAGGCAGATCCAATTAATCTCGA 59.409 41.667 0.62 0.00 37.29 4.04
2590 2687 4.636249 AGGCAGATCCAATTAATCTCGAC 58.364 43.478 0.62 0.69 37.29 4.20
2591 2688 3.748568 GGCAGATCCAATTAATCTCGACC 59.251 47.826 0.62 0.77 31.05 4.79
2592 2689 4.503991 GGCAGATCCAATTAATCTCGACCT 60.504 45.833 0.62 0.00 31.05 3.85
2593 2690 5.059833 GCAGATCCAATTAATCTCGACCTT 58.940 41.667 0.62 0.00 31.05 3.50
2594 2691 5.178438 GCAGATCCAATTAATCTCGACCTTC 59.822 44.000 0.62 0.00 31.05 3.46
2595 2692 6.283694 CAGATCCAATTAATCTCGACCTTCA 58.716 40.000 0.62 0.00 31.05 3.02
2596 2693 6.763135 CAGATCCAATTAATCTCGACCTTCAA 59.237 38.462 0.62 0.00 31.05 2.69
2597 2694 7.280876 CAGATCCAATTAATCTCGACCTTCAAA 59.719 37.037 0.62 0.00 31.05 2.69
2598 2695 7.995488 AGATCCAATTAATCTCGACCTTCAAAT 59.005 33.333 0.00 0.00 0.00 2.32
2599 2696 7.553881 TCCAATTAATCTCGACCTTCAAATC 57.446 36.000 0.00 0.00 0.00 2.17
2600 2697 7.109501 TCCAATTAATCTCGACCTTCAAATCA 58.890 34.615 0.00 0.00 0.00 2.57
2601 2698 7.775093 TCCAATTAATCTCGACCTTCAAATCAT 59.225 33.333 0.00 0.00 0.00 2.45
2602 2699 7.859377 CCAATTAATCTCGACCTTCAAATCATG 59.141 37.037 0.00 0.00 0.00 3.07
2603 2700 8.400947 CAATTAATCTCGACCTTCAAATCATGT 58.599 33.333 0.00 0.00 0.00 3.21
2604 2701 7.539712 TTAATCTCGACCTTCAAATCATGTC 57.460 36.000 0.00 0.00 0.00 3.06
2605 2702 4.535526 TCTCGACCTTCAAATCATGTCA 57.464 40.909 0.00 0.00 0.00 3.58
2606 2703 4.893608 TCTCGACCTTCAAATCATGTCAA 58.106 39.130 0.00 0.00 0.00 3.18
2607 2704 5.491070 TCTCGACCTTCAAATCATGTCAAT 58.509 37.500 0.00 0.00 0.00 2.57
2608 2705 5.582269 TCTCGACCTTCAAATCATGTCAATC 59.418 40.000 0.00 0.00 0.00 2.67
2609 2706 5.491070 TCGACCTTCAAATCATGTCAATCT 58.509 37.500 0.00 0.00 0.00 2.40
2610 2707 6.639563 TCGACCTTCAAATCATGTCAATCTA 58.360 36.000 0.00 0.00 0.00 1.98
2611 2708 7.102993 TCGACCTTCAAATCATGTCAATCTAA 58.897 34.615 0.00 0.00 0.00 2.10
2612 2709 7.064609 TCGACCTTCAAATCATGTCAATCTAAC 59.935 37.037 0.00 0.00 0.00 2.34
2613 2710 7.148423 CGACCTTCAAATCATGTCAATCTAACA 60.148 37.037 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 8.141298 TCTGGTGGAGTAACTCAAACAATATA 57.859 34.615 0.00 0.00 29.89 0.86
229 236 8.299570 GGCCATATACTAAATCAAAACTGATGG 58.700 37.037 0.00 0.00 33.59 3.51
255 262 8.526681 GCGCTTTTATTAAAGTCATTTCATCTG 58.473 33.333 0.00 0.00 42.25 2.90
304 311 7.573968 ATTCTGTAATTTTAGGTGGCTGATC 57.426 36.000 0.00 0.00 0.00 2.92
774 782 7.514721 TCTACAACAAAGTGGACTATTTCCTT 58.485 34.615 0.00 0.00 46.10 3.36
856 864 9.602568 TTTACAACTAGACACTTGTGATAACAA 57.397 29.630 7.83 0.00 32.77 2.83
886 894 5.294306 TCTTTGTAAGGAAAGCTATCATGCG 59.706 40.000 0.00 0.00 38.13 4.73
958 966 5.472137 AGCAACAAACATGGTTATAAGACGT 59.528 36.000 0.00 0.00 0.00 4.34
1020 1029 3.474798 TCCTGTCCATCTTCTGTAGGT 57.525 47.619 0.00 0.00 0.00 3.08
1061 1070 2.260844 AGCAAGCACTTCAGCTACAA 57.739 45.000 0.00 0.00 45.89 2.41
1272 1281 4.163427 TCCTGTTCACCTCATCTCTCTTT 58.837 43.478 0.00 0.00 0.00 2.52
1286 1295 2.158769 TCAGCTTGCTTCTTCCTGTTCA 60.159 45.455 0.00 0.00 0.00 3.18
1342 1353 3.065510 CCTTGAGATGATCTTGCTTGCAG 59.934 47.826 0.00 0.00 0.00 4.41
1530 1541 5.295292 ACATTGAGCTTACATCTCCAAATCG 59.705 40.000 0.00 0.00 0.00 3.34
1744 1758 4.389890 TGCACATCAGCCCATTAAAATC 57.610 40.909 0.00 0.00 0.00 2.17
1769 1783 2.478746 CCCATTTCCACGCGTTCG 59.521 61.111 10.22 2.04 42.43 3.95
1857 1877 6.719829 GCCCATTTATTTTAGTATAGCCAGGT 59.280 38.462 0.00 0.00 0.00 4.00
1915 1935 4.803426 AGCTGACGTGGCGCTAGC 62.803 66.667 7.64 4.06 44.18 3.42
1959 1979 1.748122 GAGCTGATGTGGCACCAGG 60.748 63.158 20.60 8.72 0.00 4.45
1983 2080 2.711311 CAATCTGATGTGGCGCCG 59.289 61.111 23.90 6.13 0.00 6.46
2002 2099 1.293062 AGTCCCATGTGGCATCTCTT 58.707 50.000 0.00 0.00 0.00 2.85
2003 2100 1.064906 CAAGTCCCATGTGGCATCTCT 60.065 52.381 0.00 0.00 0.00 3.10
2092 2189 3.083997 GTCACCGATCTGGCCCCT 61.084 66.667 0.00 0.00 43.94 4.79
2136 2233 5.278957 CCATCCTTGACGGTTTTTCATTTCT 60.279 40.000 0.00 0.00 0.00 2.52
2147 2244 4.778143 GCGCCCATCCTTGACGGT 62.778 66.667 0.00 0.00 0.00 4.83
2164 2261 0.588730 CGCGTCATAATTTGCCCACG 60.589 55.000 0.00 0.00 0.00 4.94
2219 2316 3.030291 TGCCAAAAACTGTCAAGGATGT 58.970 40.909 0.00 0.00 0.00 3.06
2392 2489 9.573133 CGAAAATTTATCTGTTAGAAAGGCATT 57.427 29.630 0.00 0.00 0.00 3.56
2393 2490 8.739972 ACGAAAATTTATCTGTTAGAAAGGCAT 58.260 29.630 0.00 0.00 0.00 4.40
2394 2491 8.106247 ACGAAAATTTATCTGTTAGAAAGGCA 57.894 30.769 0.00 0.00 0.00 4.75
2395 2492 8.965986 AACGAAAATTTATCTGTTAGAAAGGC 57.034 30.769 0.00 0.00 0.00 4.35
2403 2500 9.244799 GGAGTTTCAAACGAAAATTTATCTGTT 57.755 29.630 0.00 0.00 34.26 3.16
2404 2501 7.589954 CGGAGTTTCAAACGAAAATTTATCTGT 59.410 33.333 0.00 0.00 34.26 3.41
2405 2502 7.801315 TCGGAGTTTCAAACGAAAATTTATCTG 59.199 33.333 0.00 0.00 34.26 2.90
2406 2503 7.867752 TCGGAGTTTCAAACGAAAATTTATCT 58.132 30.769 0.00 0.00 34.26 1.98
2407 2504 8.669394 ATCGGAGTTTCAAACGAAAATTTATC 57.331 30.769 0.00 0.00 38.94 1.75
2408 2505 9.550811 GTATCGGAGTTTCAAACGAAAATTTAT 57.449 29.630 0.00 0.00 38.94 1.40
2409 2506 8.776470 AGTATCGGAGTTTCAAACGAAAATTTA 58.224 29.630 0.00 0.00 38.94 1.40
2410 2507 7.645402 AGTATCGGAGTTTCAAACGAAAATTT 58.355 30.769 0.00 0.00 38.94 1.82
2411 2508 7.198306 AGTATCGGAGTTTCAAACGAAAATT 57.802 32.000 0.00 0.00 38.94 1.82
2412 2509 6.796705 AGTATCGGAGTTTCAAACGAAAAT 57.203 33.333 0.00 0.00 38.94 1.82
2413 2510 6.562640 CGAAGTATCGGAGTTTCAAACGAAAA 60.563 38.462 0.00 0.00 45.32 2.29
2414 2511 5.107760 CGAAGTATCGGAGTTTCAAACGAAA 60.108 40.000 0.00 0.00 45.32 3.46
2415 2512 4.383649 CGAAGTATCGGAGTTTCAAACGAA 59.616 41.667 0.00 0.00 45.32 3.85
2416 2513 3.916172 CGAAGTATCGGAGTTTCAAACGA 59.084 43.478 0.00 0.00 45.32 3.85
2417 2514 4.227177 CGAAGTATCGGAGTTTCAAACG 57.773 45.455 0.00 0.00 45.32 3.60
2443 2540 8.774586 GCACTTCGTGTATAAAATGGATAATCT 58.225 33.333 0.00 0.00 35.75 2.40
2444 2541 8.556194 TGCACTTCGTGTATAAAATGGATAATC 58.444 33.333 0.00 0.00 35.75 1.75
2445 2542 8.445275 TGCACTTCGTGTATAAAATGGATAAT 57.555 30.769 0.00 0.00 35.75 1.28
2446 2543 7.851387 TGCACTTCGTGTATAAAATGGATAA 57.149 32.000 0.00 0.00 35.75 1.75
2447 2544 7.172532 GGATGCACTTCGTGTATAAAATGGATA 59.827 37.037 0.00 0.00 38.84 2.59
2448 2545 6.017109 GGATGCACTTCGTGTATAAAATGGAT 60.017 38.462 0.00 0.00 38.84 3.41
2449 2546 5.295787 GGATGCACTTCGTGTATAAAATGGA 59.704 40.000 0.00 0.00 38.84 3.41
2450 2547 5.065859 TGGATGCACTTCGTGTATAAAATGG 59.934 40.000 0.00 0.00 38.84 3.16
2451 2548 6.117911 TGGATGCACTTCGTGTATAAAATG 57.882 37.500 0.00 0.00 38.84 2.32
2452 2549 6.751514 TTGGATGCACTTCGTGTATAAAAT 57.248 33.333 0.00 0.00 38.84 1.82
2453 2550 6.751514 ATTGGATGCACTTCGTGTATAAAA 57.248 33.333 0.00 0.00 38.84 1.52
2454 2551 6.751514 AATTGGATGCACTTCGTGTATAAA 57.248 33.333 0.00 0.00 38.84 1.40
2455 2552 6.751514 AAATTGGATGCACTTCGTGTATAA 57.248 33.333 0.00 0.00 38.84 0.98
2456 2553 6.751514 AAAATTGGATGCACTTCGTGTATA 57.248 33.333 0.00 0.00 38.84 1.47
2457 2554 5.643379 AAAATTGGATGCACTTCGTGTAT 57.357 34.783 0.00 0.00 41.22 2.29
2458 2555 5.446143 AAAAATTGGATGCACTTCGTGTA 57.554 34.783 0.00 0.00 35.75 2.90
2459 2556 4.320608 AAAAATTGGATGCACTTCGTGT 57.679 36.364 0.00 0.00 35.75 4.49
2460 2557 5.289193 CCATAAAAATTGGATGCACTTCGTG 59.711 40.000 0.00 0.00 36.26 4.35
2461 2558 5.047377 ACCATAAAAATTGGATGCACTTCGT 60.047 36.000 0.00 0.00 37.69 3.85
2462 2559 5.410067 ACCATAAAAATTGGATGCACTTCG 58.590 37.500 0.00 0.00 37.69 3.79
2463 2560 7.277760 GGTTACCATAAAAATTGGATGCACTTC 59.722 37.037 0.00 0.00 37.69 3.01
2464 2561 7.038373 AGGTTACCATAAAAATTGGATGCACTT 60.038 33.333 3.51 0.00 37.69 3.16
2465 2562 6.440328 AGGTTACCATAAAAATTGGATGCACT 59.560 34.615 3.51 0.00 37.69 4.40
2466 2563 6.639563 AGGTTACCATAAAAATTGGATGCAC 58.360 36.000 3.51 0.00 37.69 4.57
2467 2564 6.667414 AGAGGTTACCATAAAAATTGGATGCA 59.333 34.615 3.51 0.00 37.69 3.96
2468 2565 7.112452 AGAGGTTACCATAAAAATTGGATGC 57.888 36.000 3.51 0.00 37.69 3.91
2469 2566 8.292444 TGAGAGGTTACCATAAAAATTGGATG 57.708 34.615 3.51 0.00 37.69 3.51
2470 2567 8.893563 TTGAGAGGTTACCATAAAAATTGGAT 57.106 30.769 3.51 0.00 37.69 3.41
2471 2568 8.893563 ATTGAGAGGTTACCATAAAAATTGGA 57.106 30.769 3.51 0.00 37.69 3.53
2472 2569 9.942850 AAATTGAGAGGTTACCATAAAAATTGG 57.057 29.630 3.51 0.00 40.26 3.16
2522 2619 9.793259 GGTATAGATTACATGGGATTTTTCAGA 57.207 33.333 0.00 0.00 0.00 3.27
2523 2620 9.573166 TGGTATAGATTACATGGGATTTTTCAG 57.427 33.333 0.00 0.00 0.00 3.02
2524 2621 9.928618 TTGGTATAGATTACATGGGATTTTTCA 57.071 29.630 0.00 0.00 0.00 2.69
2544 2641 9.396022 CCTCTTTGTGTCTTGTTATATTGGTAT 57.604 33.333 0.00 0.00 0.00 2.73
2545 2642 7.335924 GCCTCTTTGTGTCTTGTTATATTGGTA 59.664 37.037 0.00 0.00 0.00 3.25
2546 2643 6.151144 GCCTCTTTGTGTCTTGTTATATTGGT 59.849 38.462 0.00 0.00 0.00 3.67
2547 2644 6.150976 TGCCTCTTTGTGTCTTGTTATATTGG 59.849 38.462 0.00 0.00 0.00 3.16
2548 2645 7.119699 TCTGCCTCTTTGTGTCTTGTTATATTG 59.880 37.037 0.00 0.00 0.00 1.90
2549 2646 7.168219 TCTGCCTCTTTGTGTCTTGTTATATT 58.832 34.615 0.00 0.00 0.00 1.28
2550 2647 6.711277 TCTGCCTCTTTGTGTCTTGTTATAT 58.289 36.000 0.00 0.00 0.00 0.86
2551 2648 6.109156 TCTGCCTCTTTGTGTCTTGTTATA 57.891 37.500 0.00 0.00 0.00 0.98
2552 2649 4.973168 TCTGCCTCTTTGTGTCTTGTTAT 58.027 39.130 0.00 0.00 0.00 1.89
2553 2650 4.415881 TCTGCCTCTTTGTGTCTTGTTA 57.584 40.909 0.00 0.00 0.00 2.41
2554 2651 3.281727 TCTGCCTCTTTGTGTCTTGTT 57.718 42.857 0.00 0.00 0.00 2.83
2555 2652 3.406764 GATCTGCCTCTTTGTGTCTTGT 58.593 45.455 0.00 0.00 0.00 3.16
2556 2653 2.746362 GGATCTGCCTCTTTGTGTCTTG 59.254 50.000 0.00 0.00 0.00 3.02
2557 2654 2.373169 TGGATCTGCCTCTTTGTGTCTT 59.627 45.455 0.00 0.00 37.63 3.01
2558 2655 1.980765 TGGATCTGCCTCTTTGTGTCT 59.019 47.619 0.00 0.00 37.63 3.41
2559 2656 2.479566 TGGATCTGCCTCTTTGTGTC 57.520 50.000 0.00 0.00 37.63 3.67
2560 2657 2.957402 TTGGATCTGCCTCTTTGTGT 57.043 45.000 0.00 0.00 37.63 3.72
2561 2658 5.902613 TTAATTGGATCTGCCTCTTTGTG 57.097 39.130 0.00 0.00 37.63 3.33
2562 2659 6.430007 AGATTAATTGGATCTGCCTCTTTGT 58.570 36.000 5.62 0.00 37.63 2.83
2563 2660 6.293298 CGAGATTAATTGGATCTGCCTCTTTG 60.293 42.308 9.96 0.00 34.13 2.77
2564 2661 5.762218 CGAGATTAATTGGATCTGCCTCTTT 59.238 40.000 9.96 0.00 34.13 2.52
2565 2662 5.070981 TCGAGATTAATTGGATCTGCCTCTT 59.929 40.000 9.96 0.00 34.13 2.85
2566 2663 4.590647 TCGAGATTAATTGGATCTGCCTCT 59.409 41.667 9.96 0.00 34.13 3.69
2567 2664 4.688413 GTCGAGATTAATTGGATCTGCCTC 59.312 45.833 9.96 0.00 34.13 4.70
2568 2665 4.503991 GGTCGAGATTAATTGGATCTGCCT 60.504 45.833 9.96 0.00 34.13 4.75
2569 2666 3.748568 GGTCGAGATTAATTGGATCTGCC 59.251 47.826 9.96 6.75 34.13 4.85
2570 2667 4.636249 AGGTCGAGATTAATTGGATCTGC 58.364 43.478 9.96 3.47 34.13 4.26
2571 2668 6.283694 TGAAGGTCGAGATTAATTGGATCTG 58.716 40.000 9.96 4.73 34.13 2.90
2572 2669 6.485830 TGAAGGTCGAGATTAATTGGATCT 57.514 37.500 6.01 6.01 36.60 2.75
2573 2670 7.553881 TTTGAAGGTCGAGATTAATTGGATC 57.446 36.000 0.00 0.00 0.00 3.36
2574 2671 7.775093 TGATTTGAAGGTCGAGATTAATTGGAT 59.225 33.333 0.00 0.00 0.00 3.41
2575 2672 7.109501 TGATTTGAAGGTCGAGATTAATTGGA 58.890 34.615 0.00 0.00 0.00 3.53
2576 2673 7.320443 TGATTTGAAGGTCGAGATTAATTGG 57.680 36.000 0.00 0.00 0.00 3.16
2577 2674 8.400947 ACATGATTTGAAGGTCGAGATTAATTG 58.599 33.333 0.00 0.00 0.00 2.32
2578 2675 8.511604 ACATGATTTGAAGGTCGAGATTAATT 57.488 30.769 0.00 0.00 0.00 1.40
2579 2676 7.770433 TGACATGATTTGAAGGTCGAGATTAAT 59.230 33.333 0.00 0.00 0.00 1.40
2580 2677 7.102993 TGACATGATTTGAAGGTCGAGATTAA 58.897 34.615 0.00 0.00 0.00 1.40
2581 2678 6.639563 TGACATGATTTGAAGGTCGAGATTA 58.360 36.000 0.00 0.00 0.00 1.75
2582 2679 5.491070 TGACATGATTTGAAGGTCGAGATT 58.509 37.500 0.00 0.00 0.00 2.40
2583 2680 5.089970 TGACATGATTTGAAGGTCGAGAT 57.910 39.130 0.00 0.00 0.00 2.75
2584 2681 4.535526 TGACATGATTTGAAGGTCGAGA 57.464 40.909 0.00 0.00 0.00 4.04
2585 2682 5.583854 AGATTGACATGATTTGAAGGTCGAG 59.416 40.000 0.00 0.00 0.00 4.04
2586 2683 5.491070 AGATTGACATGATTTGAAGGTCGA 58.509 37.500 0.00 0.00 0.00 4.20
2587 2684 5.808042 AGATTGACATGATTTGAAGGTCG 57.192 39.130 0.00 0.00 0.00 4.79
2588 2685 8.044060 TGTTAGATTGACATGATTTGAAGGTC 57.956 34.615 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.