Multiple sequence alignment - TraesCS6D01G223500

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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 TraesCS6D01G223500 chr6D 100.000 3994 0 0 1 3994 315626708 315622715 0.000000e+00 7376
1 TraesCS6D01G223500 chr6D 94.895 901 34 3 3105 3994 464213697 464214596 0.000000e+00 1399
2 TraesCS6D01G223500 chr6D 92.786 901 27 3 3104 3994 379092415 379093287 0.000000e+00 1269
3 TraesCS6D01G223500 chr6D 97.159 176 3 2 2528 2703 392897145 392896972 3.020000e-76 296
4 TraesCS6D01G223500 chr6A 96.392 2550 46 11 1 2536 452777670 452775153 0.000000e+00 4157
5 TraesCS6D01G223500 chr6A 95.620 411 9 2 2696 3105 452775156 452774754 0.000000e+00 651
6 TraesCS6D01G223500 chr6B 95.531 2573 61 17 1 2536 511566506 511569061 0.000000e+00 4065
7 TraesCS6D01G223500 chr6B 96.594 411 13 1 2696 3105 511569058 511569468 0.000000e+00 680
8 TraesCS6D01G223500 chr3D 95.560 901 29 2 3104 3994 214959732 214958833 0.000000e+00 1432
9 TraesCS6D01G223500 chr7D 95.551 899 29 2 3106 3994 114468339 114467442 0.000000e+00 1428
10 TraesCS6D01G223500 chr7D 95.117 901 31 3 3104 3994 151541137 151540240 0.000000e+00 1408
11 TraesCS6D01G223500 chr7D 97.674 172 4 0 2531 2702 45837346 45837517 3.020000e-76 296
12 TraesCS6D01G223500 chr3A 95.238 903 30 4 3104 3994 660860781 660861682 0.000000e+00 1417
13 TraesCS6D01G223500 chr2D 95.333 900 28 10 3106 3994 70391946 70391050 0.000000e+00 1417
14 TraesCS6D01G223500 chr2D 94.889 900 34 3 3106 3994 101660883 101659985 0.000000e+00 1397
15 TraesCS6D01G223500 chr2D 94.772 899 35 3 3106 3994 161898505 161897609 0.000000e+00 1389
16 TraesCS6D01G223500 chr2D 95.130 883 32 2 3123 3994 484919097 484919979 0.000000e+00 1382
17 TraesCS6D01G223500 chr2D 94.333 900 34 11 3106 3994 623950340 623949447 0.000000e+00 1363
18 TraesCS6D01G223500 chr5D 94.615 910 35 5 3096 3994 422449114 422448208 0.000000e+00 1397
19 TraesCS6D01G223500 chr5D 93.333 900 27 4 3105 3994 404193743 404194619 0.000000e+00 1299
20 TraesCS6D01G223500 chr5D 93.264 193 8 4 2527 2718 245718446 245718258 3.040000e-71 279
21 TraesCS6D01G223500 chr1D 94.673 901 38 1 3104 3994 84728838 84729738 0.000000e+00 1389
22 TraesCS6D01G223500 chr1D 97.000 400 11 1 3595 3994 464937376 464937774 0.000000e+00 671
23 TraesCS6D01G223500 chr1D 97.688 173 4 0 2532 2704 423269504 423269676 8.390000e-77 298
24 TraesCS6D01G223500 chr1D 97.126 174 4 1 2526 2699 238940208 238940380 3.900000e-75 292
25 TraesCS6D01G223500 chr1D 96.067 178 7 0 2529 2706 345368849 345368672 1.400000e-74 291
26 TraesCS6D01G223500 chr1A 93.021 874 40 8 3106 3959 579858169 579859041 0.000000e+00 1256
27 TraesCS6D01G223500 chr4B 96.154 182 6 1 2519 2700 113961102 113961282 3.020000e-76 296
28 TraesCS6D01G223500 chr4B 93.717 191 10 2 2514 2703 592024214 592024403 6.530000e-73 285
29 TraesCS6D01G223500 chr5A 98.214 168 2 1 2532 2699 362179015 362179181 3.900000e-75 292


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 TraesCS6D01G223500 chr6D 315622715 315626708 3993 True 7376.0 7376 100.0000 1 3994 1 chr6D.!!$R1 3993
1 TraesCS6D01G223500 chr6D 464213697 464214596 899 False 1399.0 1399 94.8950 3105 3994 1 chr6D.!!$F2 889
2 TraesCS6D01G223500 chr6D 379092415 379093287 872 False 1269.0 1269 92.7860 3104 3994 1 chr6D.!!$F1 890
3 TraesCS6D01G223500 chr6A 452774754 452777670 2916 True 2404.0 4157 96.0060 1 3105 2 chr6A.!!$R1 3104
4 TraesCS6D01G223500 chr6B 511566506 511569468 2962 False 2372.5 4065 96.0625 1 3105 2 chr6B.!!$F1 3104
5 TraesCS6D01G223500 chr3D 214958833 214959732 899 True 1432.0 1432 95.5600 3104 3994 1 chr3D.!!$R1 890
6 TraesCS6D01G223500 chr7D 114467442 114468339 897 True 1428.0 1428 95.5510 3106 3994 1 chr7D.!!$R1 888
7 TraesCS6D01G223500 chr7D 151540240 151541137 897 True 1408.0 1408 95.1170 3104 3994 1 chr7D.!!$R2 890
8 TraesCS6D01G223500 chr3A 660860781 660861682 901 False 1417.0 1417 95.2380 3104 3994 1 chr3A.!!$F1 890
9 TraesCS6D01G223500 chr2D 70391050 70391946 896 True 1417.0 1417 95.3330 3106 3994 1 chr2D.!!$R1 888
10 TraesCS6D01G223500 chr2D 101659985 101660883 898 True 1397.0 1397 94.8890 3106 3994 1 chr2D.!!$R2 888
11 TraesCS6D01G223500 chr2D 161897609 161898505 896 True 1389.0 1389 94.7720 3106 3994 1 chr2D.!!$R3 888
12 TraesCS6D01G223500 chr2D 484919097 484919979 882 False 1382.0 1382 95.1300 3123 3994 1 chr2D.!!$F1 871
13 TraesCS6D01G223500 chr2D 623949447 623950340 893 True 1363.0 1363 94.3330 3106 3994 1 chr2D.!!$R4 888
14 TraesCS6D01G223500 chr5D 422448208 422449114 906 True 1397.0 1397 94.6150 3096 3994 1 chr5D.!!$R2 898
15 TraesCS6D01G223500 chr5D 404193743 404194619 876 False 1299.0 1299 93.3330 3105 3994 1 chr5D.!!$F1 889
16 TraesCS6D01G223500 chr1D 84728838 84729738 900 False 1389.0 1389 94.6730 3104 3994 1 chr1D.!!$F1 890
17 TraesCS6D01G223500 chr1A 579858169 579859041 872 False 1256.0 1256 93.0210 3106 3959 1 chr1A.!!$F1 853

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
721 724 2.591133 CCCAAAATAAACCGAACTGCG 58.409 47.619 0.0 0.0 40.47 5.18 F
2436 2481 0.179181 CGGCTGATGTCACAACATGC 60.179 55.000 0.0 0.0 46.20 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2578 2623 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.0 0.0 44.79 4.02 R
3415 3466 1.153353 CGACATGGCAACCGTAGTTT 58.847 50.000 0.0 0.0 32.45 2.66 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
262 265 7.044181 TGAAAAGTTCCATTTTTATGCACACA 58.956 30.769 0.00 0.00 32.62 3.72
413 416 9.400638 GATTGTCCGAGAGTTCTTAATATACAG 57.599 37.037 0.00 0.00 0.00 2.74
518 521 2.740981 GTGCATCAGAGAGACCTTGTTG 59.259 50.000 0.00 0.00 0.00 3.33
585 588 9.241919 TGCACATGAAGATATTCCTTTTCTAAA 57.758 29.630 0.00 0.00 0.00 1.85
718 721 4.650131 TGAAACCCCAAAATAAACCGAACT 59.350 37.500 0.00 0.00 0.00 3.01
721 724 2.591133 CCCAAAATAAACCGAACTGCG 58.409 47.619 0.00 0.00 40.47 5.18
1095 1102 1.743252 GGAGCCACAGGAAGCTTCG 60.743 63.158 19.91 9.89 40.11 3.79
1128 1135 1.000486 TCCTCCCCTCGACCTTCTG 60.000 63.158 0.00 0.00 0.00 3.02
1414 1421 1.883544 CTCCAGATGCTGCTGCTCG 60.884 63.158 17.00 8.01 40.48 5.03
1443 1450 7.708752 CACTTGGTCTCTGAACTAATCTTATCC 59.291 40.741 0.00 0.00 0.00 2.59
1547 1554 1.664659 CATCCAGAAGCTTCTTCGCTG 59.335 52.381 26.44 16.13 40.79 5.18
1692 1699 5.415701 AGATTATGCACTTTCGGAATTGTGT 59.584 36.000 18.74 8.45 33.44 3.72
1961 1968 6.841119 TGTACTTGTATGTGTCATGATTTGC 58.159 36.000 0.00 0.00 0.00 3.68
1962 1969 5.963176 ACTTGTATGTGTCATGATTTGCA 57.037 34.783 0.00 0.00 0.00 4.08
1963 1970 5.702865 ACTTGTATGTGTCATGATTTGCAC 58.297 37.500 0.00 2.73 34.76 4.57
2063 2070 7.221828 TGATTCTACACGATCATTTCTTTCG 57.778 36.000 0.00 0.00 38.76 3.46
2158 2165 6.442112 TCACACGATTGTCAATTTGCATTTA 58.558 32.000 0.00 0.00 31.66 1.40
2375 2420 8.475639 AGGTACTATGTCGTTGAATTATGTTCT 58.524 33.333 0.00 0.00 36.02 3.01
2376 2421 8.540492 GGTACTATGTCGTTGAATTATGTTCTG 58.460 37.037 0.00 0.00 0.00 3.02
2377 2422 9.084164 GTACTATGTCGTTGAATTATGTTCTGT 57.916 33.333 0.00 0.00 0.00 3.41
2378 2423 8.547967 ACTATGTCGTTGAATTATGTTCTGTT 57.452 30.769 0.00 0.00 0.00 3.16
2379 2424 8.999431 ACTATGTCGTTGAATTATGTTCTGTTT 58.001 29.630 0.00 0.00 0.00 2.83
2380 2425 9.478019 CTATGTCGTTGAATTATGTTCTGTTTC 57.522 33.333 0.00 0.00 0.00 2.78
2389 2434 9.904198 TGAATTATGTTCTGTTTCTGGATGATA 57.096 29.630 0.00 0.00 0.00 2.15
2436 2481 0.179181 CGGCTGATGTCACAACATGC 60.179 55.000 0.00 0.00 46.20 4.06
2547 2592 5.180367 GTACATAAGTACTCCCTCCGTTC 57.820 47.826 0.00 0.00 45.66 3.95
2548 2593 3.029570 ACATAAGTACTCCCTCCGTTCC 58.970 50.000 0.00 0.00 0.00 3.62
2549 2594 3.297736 CATAAGTACTCCCTCCGTTCCT 58.702 50.000 0.00 0.00 0.00 3.36
2550 2595 4.079558 ACATAAGTACTCCCTCCGTTCCTA 60.080 45.833 0.00 0.00 0.00 2.94
2551 2596 3.463048 AAGTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
2552 2597 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2553 2598 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2554 2599 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2555 2600 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2556 2601 6.141790 AGTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2557 2602 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2558 2603 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2559 2604 5.427481 ACTCCCTCCGTTCCTAAATATTTGA 59.573 40.000 11.05 0.00 0.00 2.69
2560 2605 5.677567 TCCCTCCGTTCCTAAATATTTGAC 58.322 41.667 11.05 3.92 0.00 3.18
2561 2606 5.427481 TCCCTCCGTTCCTAAATATTTGACT 59.573 40.000 11.05 0.00 0.00 3.41
2562 2607 6.069847 TCCCTCCGTTCCTAAATATTTGACTT 60.070 38.462 11.05 0.00 0.00 3.01
2563 2608 6.602009 CCCTCCGTTCCTAAATATTTGACTTT 59.398 38.462 11.05 0.00 0.00 2.66
2564 2609 7.122204 CCCTCCGTTCCTAAATATTTGACTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2565 2610 8.520351 CCTCCGTTCCTAAATATTTGACTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2582 2627 9.965824 TTGACTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2583 2628 9.354673 TGACTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
2599 2644 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2600 2645 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2601 2646 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2602 2647 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
2603 2648 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2604 2649 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
2605 2650 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
2606 2651 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
2607 2652 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
2608 2653 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2610 2655 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2638 2683 9.944376 TTAGAGTGTAGATTCACTTATTTTGCT 57.056 29.630 0.98 0.00 46.81 3.91
2639 2684 8.485976 AGAGTGTAGATTCACTTATTTTGCTC 57.514 34.615 0.98 0.00 46.81 4.26
2640 2685 7.550906 AGAGTGTAGATTCACTTATTTTGCTCC 59.449 37.037 0.98 0.00 46.81 4.70
2641 2686 6.313905 AGTGTAGATTCACTTATTTTGCTCCG 59.686 38.462 0.00 0.00 44.92 4.63
2642 2687 6.092259 GTGTAGATTCACTTATTTTGCTCCGT 59.908 38.462 0.00 0.00 35.68 4.69
2643 2688 7.277098 GTGTAGATTCACTTATTTTGCTCCGTA 59.723 37.037 0.00 0.00 35.68 4.02
2644 2689 7.985184 TGTAGATTCACTTATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
2645 2690 7.251704 AGATTCACTTATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
2646 2691 6.823689 AGATTCACTTATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
2647 2692 7.985184 AGATTCACTTATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
2648 2693 7.534085 TTCACTTATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
2649 2694 6.636705 TCACTTATTTTGCTCCGTATGTAGT 58.363 36.000 0.00 0.00 0.00 2.73
2650 2695 6.755141 TCACTTATTTTGCTCCGTATGTAGTC 59.245 38.462 0.00 0.00 0.00 2.59
2651 2696 6.533723 CACTTATTTTGCTCCGTATGTAGTCA 59.466 38.462 0.00 0.00 0.00 3.41
2652 2697 6.534079 ACTTATTTTGCTCCGTATGTAGTCAC 59.466 38.462 0.00 0.00 0.00 3.67
2653 2698 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2654 2699 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2655 2700 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2656 2701 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2657 2702 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2658 2703 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2659 2704 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2660 2705 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2661 2706 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2662 2707 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2663 2708 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2664 2709 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2665 2710 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2666 2711 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2667 2712 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2675 2720 9.996554 TCACTTGTTGAAATCTCTATAAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
2693 2738 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2694 2739 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2695 2740 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2696 2741 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2697 2742 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2698 2743 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2899 2944 8.842358 ATTGAAAAATTTGAGAACAGCATCAT 57.158 26.923 0.00 0.00 0.00 2.45
2981 3026 6.858993 GCAAGAAGGTCTACGATATCTGTAAG 59.141 42.308 0.34 1.19 0.00 2.34
3075 3121 7.490079 CCTTTGGTTGTAACAAGGAACTAAAAC 59.510 37.037 7.68 0.00 38.49 2.43
3282 3332 3.192466 GTGTGGGCGAAATAGATAACGT 58.808 45.455 0.00 0.00 0.00 3.99
3311 3361 2.412605 GGTACGTCAGGCCTCGTAT 58.587 57.895 24.50 6.17 42.81 3.06
3412 3463 2.268762 TAAGTGCAGTTGCCATGTCA 57.731 45.000 17.21 0.00 41.18 3.58
3415 3466 1.072173 AGTGCAGTTGCCATGTCACTA 59.928 47.619 1.06 0.00 41.18 2.74
3484 3535 0.035630 GCAGTTGCCATCTCAGGTCT 60.036 55.000 0.00 0.00 34.31 3.85
3725 3811 2.444624 ATCTGCTTACGTGCACGCG 61.445 57.895 37.35 25.82 44.43 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
316 319 9.399403 GCTTAAAAACACTTAAAGATCCAAGAG 57.601 33.333 6.38 2.05 0.00 2.85
413 416 0.814010 ATGTTATCAAGACGCCGGCC 60.814 55.000 23.46 7.92 0.00 6.13
518 521 3.118592 ACCAAGAGGAAGCATACAGCTAC 60.119 47.826 0.00 0.00 46.53 3.58
718 721 1.002403 TCCCTCCCTATCAACCGCA 59.998 57.895 0.00 0.00 0.00 5.69
721 724 0.267960 TCCCTCCCTCCCTATCAACC 59.732 60.000 0.00 0.00 0.00 3.77
1095 1102 2.250741 GAGGAGGAGGAAGCAGCACC 62.251 65.000 0.00 0.00 0.00 5.01
1128 1135 0.455815 CTACGAAATTTGGGGGCTGC 59.544 55.000 5.14 0.00 0.00 5.25
1414 1421 2.246719 AGTTCAGAGACCAAGTGTGC 57.753 50.000 0.00 0.00 0.00 4.57
1692 1699 8.686334 ACTTTCTCAAGTTTTTGCTCATCTTTA 58.314 29.630 0.00 0.00 40.66 1.85
1961 1968 9.904647 GCAAATACAAATGCATTTACATAAGTG 57.095 29.630 23.69 15.73 42.12 3.16
1962 1969 9.650539 TGCAAATACAAATGCATTTACATAAGT 57.349 25.926 23.69 17.67 46.87 2.24
2063 2070 3.261137 ACCCAGTTCTTGTAACCTCTAGC 59.739 47.826 0.00 0.00 0.00 3.42
2436 2481 5.010012 GGAGGCAAAGTTATGTTATCCATGG 59.990 44.000 4.97 4.97 34.86 3.66
2536 2581 5.758784 GTCAAATATTTAGGAACGGAGGGAG 59.241 44.000 0.00 0.00 0.00 4.30
2537 2582 5.427481 AGTCAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2538 2583 5.681639 AGTCAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2539 2584 7.625828 AAAGTCAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2556 2601 9.965824 GTCCATTTGAAATCTCTAAAAAGTCAA 57.034 29.630 0.00 0.00 0.00 3.18
2557 2602 9.354673 AGTCCATTTGAAATCTCTAAAAAGTCA 57.645 29.630 0.00 0.00 0.00 3.41
2561 2606 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2562 2607 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2563 2608 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2564 2609 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2565 2610 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2566 2611 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2567 2612 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
2568 2613 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
2569 2614 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
2570 2615 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
2571 2616 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
2572 2617 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
2573 2618 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
2574 2619 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2575 2620 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2576 2621 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2577 2622 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2578 2623 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2579 2624 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2580 2625 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
2581 2626 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
2582 2627 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
2584 2629 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2617 2662 6.092259 ACGGAGCAAAATAAGTGAATCTACAC 59.908 38.462 0.00 0.00 40.60 2.90
2618 2663 6.170506 ACGGAGCAAAATAAGTGAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
2619 2664 6.663944 ACGGAGCAAAATAAGTGAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
2620 2665 7.985184 ACATACGGAGCAAAATAAGTGAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
2621 2666 6.823689 ACATACGGAGCAAAATAAGTGAATCT 59.176 34.615 0.00 0.00 0.00 2.40
2622 2667 7.016361 ACATACGGAGCAAAATAAGTGAATC 57.984 36.000 0.00 0.00 0.00 2.52
2623 2668 7.769044 ACTACATACGGAGCAAAATAAGTGAAT 59.231 33.333 0.00 0.00 0.00 2.57
2624 2669 7.101054 ACTACATACGGAGCAAAATAAGTGAA 58.899 34.615 0.00 0.00 0.00 3.18
2625 2670 6.636705 ACTACATACGGAGCAAAATAAGTGA 58.363 36.000 0.00 0.00 0.00 3.41
2626 2671 6.533723 TGACTACATACGGAGCAAAATAAGTG 59.466 38.462 0.00 0.00 0.00 3.16
2627 2672 6.534079 GTGACTACATACGGAGCAAAATAAGT 59.466 38.462 0.00 0.00 0.00 2.24
2628 2673 6.757010 AGTGACTACATACGGAGCAAAATAAG 59.243 38.462 0.00 0.00 0.00 1.73
2629 2674 6.636705 AGTGACTACATACGGAGCAAAATAA 58.363 36.000 0.00 0.00 0.00 1.40
2630 2675 6.216801 AGTGACTACATACGGAGCAAAATA 57.783 37.500 0.00 0.00 0.00 1.40
2631 2676 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2632 2677 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2633 2678 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2634 2679 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2635 2680 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2636 2681 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2637 2682 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2638 2683 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2639 2684 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2640 2685 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2641 2686 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2649 2694 9.996554 TGTCTTTATAGAGATTTCAACAAGTGA 57.003 29.630 0.00 0.00 0.00 3.41
2667 2712 9.338622 CCTCCGTTCCTAAATATTTGTCTTTAT 57.661 33.333 11.05 0.00 0.00 1.40
2668 2713 7.771826 CCCTCCGTTCCTAAATATTTGTCTTTA 59.228 37.037 11.05 0.00 0.00 1.85
2669 2714 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2670 2715 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2671 2716 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2672 2717 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2673 2718 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2674 2719 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2675 2720 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2676 2721 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
2677 2722 7.628501 AATTACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
2678 2723 7.786464 ACTAATTACTCCCTCCGTTCCTAAATA 59.214 37.037 0.00 0.00 0.00 1.40
2679 2724 5.970501 AATTACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
2680 2725 5.960202 ACTAATTACTCCCTCCGTTCCTAAA 59.040 40.000 0.00 0.00 0.00 1.85
2681 2726 5.522641 ACTAATTACTCCCTCCGTTCCTAA 58.477 41.667 0.00 0.00 0.00 2.69
2682 2727 5.134725 ACTAATTACTCCCTCCGTTCCTA 57.865 43.478 0.00 0.00 0.00 2.94
2683 2728 3.991683 ACTAATTACTCCCTCCGTTCCT 58.008 45.455 0.00 0.00 0.00 3.36
2684 2729 5.362143 AGTTACTAATTACTCCCTCCGTTCC 59.638 44.000 0.00 0.00 0.00 3.62
2685 2730 6.096001 TCAGTTACTAATTACTCCCTCCGTTC 59.904 42.308 0.00 0.00 0.00 3.95
2686 2731 5.954150 TCAGTTACTAATTACTCCCTCCGTT 59.046 40.000 0.00 0.00 0.00 4.44
2687 2732 5.513233 TCAGTTACTAATTACTCCCTCCGT 58.487 41.667 0.00 0.00 0.00 4.69
2688 2733 5.009811 CCTCAGTTACTAATTACTCCCTCCG 59.990 48.000 0.00 0.00 0.00 4.63
2689 2734 5.898397 ACCTCAGTTACTAATTACTCCCTCC 59.102 44.000 0.00 0.00 0.00 4.30
2690 2735 6.606395 TGACCTCAGTTACTAATTACTCCCTC 59.394 42.308 0.00 0.00 0.00 4.30
2691 2736 6.500336 TGACCTCAGTTACTAATTACTCCCT 58.500 40.000 0.00 0.00 0.00 4.20
2692 2737 6.606395 TCTGACCTCAGTTACTAATTACTCCC 59.394 42.308 2.25 0.00 44.12 4.30
2693 2738 7.642082 TCTGACCTCAGTTACTAATTACTCC 57.358 40.000 2.25 0.00 44.12 3.85
2981 3026 1.005340 CGCTGCTTCAGTCTCCAATC 58.995 55.000 0.00 0.00 33.43 2.67
3037 3083 8.380099 TGTTACAACCAAAGGTATTGACTCTAT 58.620 33.333 0.00 0.00 33.12 1.98
3075 3121 2.412870 TGCTACCGAAACACATGACAG 58.587 47.619 0.00 0.00 0.00 3.51
3167 3213 1.073284 GTGTGGGCTGGTCCTTTTAGA 59.927 52.381 0.00 0.00 34.39 2.10
3235 3285 0.635009 ATGTAAGAGGGACCGGGAGA 59.365 55.000 6.32 0.00 0.00 3.71
3412 3463 3.332034 GACATGGCAACCGTAGTTTAGT 58.668 45.455 0.00 0.00 32.45 2.24
3415 3466 1.153353 CGACATGGCAACCGTAGTTT 58.847 50.000 0.00 0.00 32.45 2.66


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

AutoCloner maintained by Alex Coulton.