Multiple sequence alignment - TraesCS5D01G230400

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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 TraesCS5D01G230400 chr5D 100.000 3737 0 0 1 3737 337329347 337325611 0.000000e+00 6902
1 TraesCS5D01G230400 chr5A 93.570 1773 89 10 1073 2833 438776343 438774584 0.000000e+00 2619
2 TraesCS5D01G230400 chr5A 91.195 636 39 8 3012 3633 438774094 438773462 0.000000e+00 848
3 TraesCS5D01G230400 chr5A 91.837 294 19 4 8 298 438778431 438778140 4.490000e-109 405
4 TraesCS5D01G230400 chr5A 90.244 164 13 2 484 644 438778105 438777942 1.050000e-50 211
5 TraesCS5D01G230400 chr5A 89.928 139 9 3 692 825 438776473 438776335 1.380000e-39 174
6 TraesCS5D01G230400 chr5A 88.710 124 12 2 429 551 521662951 521663073 2.330000e-32 150
7 TraesCS5D01G230400 chr5A 88.785 107 8 3 3633 3737 438773397 438773293 1.090000e-25 128
8 TraesCS5D01G230400 chr5B 88.599 1956 127 35 7 1917 396056297 396054393 0.000000e+00 2289
9 TraesCS5D01G230400 chr5B 94.077 878 41 4 1914 2784 396046962 396046089 0.000000e+00 1323
10 TraesCS5D01G230400 chr5B 90.514 875 37 13 2879 3737 396045279 396044435 0.000000e+00 1114
11 TraesCS5D01G230400 chr5B 87.823 657 59 8 7 644 396069388 396068734 0.000000e+00 750
12 TraesCS5D01G230400 chr5B 80.685 642 44 28 639 1247 396068700 396068106 3.450000e-115 425
13 TraesCS5D01G230400 chr7B 90.083 121 10 1 424 542 324138594 324138714 5.000000e-34 156
14 TraesCS5D01G230400 chr3D 91.892 111 9 0 429 539 292030939 292031049 5.000000e-34 156
15 TraesCS5D01G230400 chr3B 85.906 149 18 3 398 544 431580330 431580183 5.000000e-34 156
16 TraesCS5D01G230400 chr2A 89.344 122 10 3 429 548 57999205 57999325 2.330000e-32 150
17 TraesCS5D01G230400 chr2D 87.692 130 11 5 429 556 78903249 78903375 3.010000e-31 147


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 TraesCS5D01G230400 chr5D 337325611 337329347 3736 True 6902.000000 6902 100.0000 1 3737 1 chr5D.!!$R1 3736
1 TraesCS5D01G230400 chr5A 438773293 438778431 5138 True 730.833333 2619 90.9265 8 3737 6 chr5A.!!$R1 3729
2 TraesCS5D01G230400 chr5B 396054393 396056297 1904 True 2289.000000 2289 88.5990 7 1917 1 chr5B.!!$R1 1910
3 TraesCS5D01G230400 chr5B 396044435 396046962 2527 True 1218.500000 1323 92.2955 1914 3737 2 chr5B.!!$R2 1823
4 TraesCS5D01G230400 chr5B 396068106 396069388 1282 True 587.500000 750 84.2540 7 1247 2 chr5B.!!$R3 1240

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
646 671 0.621571 TGAGGCCTCCCACTAGCATT 60.622 55.0 29.95 0.0 0.0 3.56 F
1534 3070 0.179092 GCCTTATAGTGGACGCCGTT 60.179 55.0 0.00 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2521 4068 0.106708 TCCACTTGCTTCGCAGAGTT 59.893 50.000 0.00 0.0 40.61 3.01 R
3059 5385 2.108952 AGAACTCCATCAGGCCAAAACT 59.891 45.455 5.01 0.0 33.74 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
74 77 7.288810 ACATCAGGAACATGTTTTTGTACAT 57.711 32.000 13.36 2.10 39.27 2.29
162 165 9.632807 TTTTTCCATACACACTGTATATTTTGC 57.367 29.630 0.00 0.00 41.28 3.68
346 362 9.643693 ACATATTTAAGACTTTCCAAATGCTTG 57.356 29.630 0.00 0.00 0.00 4.01
422 439 7.147932 ACCTCGTTCCTAAGTATAAGACCTTTC 60.148 40.741 0.00 0.00 0.00 2.62
441 458 3.510388 TCAGAGAACATACGGAGCAAG 57.490 47.619 0.00 0.00 0.00 4.01
442 459 2.826128 TCAGAGAACATACGGAGCAAGT 59.174 45.455 0.00 0.00 0.00 3.16
503 520 9.908152 CATCCGTATGTAGTTCATAGTGAAATA 57.092 33.333 0.00 0.00 38.22 1.40
592 610 8.435430 ACGAAAAGAAAAAGCAAAGAAGAAAAG 58.565 29.630 0.00 0.00 0.00 2.27
640 665 1.305718 GAGACTGAGGCCTCCCACT 60.306 63.158 29.95 23.24 0.00 4.00
644 669 1.687146 CTGAGGCCTCCCACTAGCA 60.687 63.158 29.95 8.35 0.00 3.49
645 670 1.003442 TGAGGCCTCCCACTAGCAT 59.997 57.895 29.95 0.00 0.00 3.79
646 671 0.621571 TGAGGCCTCCCACTAGCATT 60.622 55.000 29.95 0.00 0.00 3.56
655 719 1.398390 CCCACTAGCATTCAAACTCGC 59.602 52.381 0.00 0.00 0.00 5.03
761 2255 4.995058 TTCCTTCCCCTGCCCCGT 62.995 66.667 0.00 0.00 0.00 5.28
873 2409 1.404717 GGTGAGAGCAAGCAAGATCGA 60.405 52.381 0.00 0.00 0.00 3.59
887 2423 1.935873 AGATCGATTCGACGACGGTAA 59.064 47.619 11.56 0.00 44.84 2.85
898 2434 1.078637 GACGGTAACCCCTTGCCTC 60.079 63.158 0.00 0.00 30.04 4.70
934 2470 1.300697 GCTCACCAAGTCCGACGTT 60.301 57.895 0.00 0.00 0.00 3.99
962 2498 3.323979 GGAGACCATCCGAAATTAGGCTA 59.676 47.826 0.00 0.00 38.67 3.93
1004 2540 2.098680 GACGTCTCAGTCTCGCGG 59.901 66.667 8.70 0.00 38.09 6.46
1005 2541 2.358369 ACGTCTCAGTCTCGCGGA 60.358 61.111 6.13 0.00 0.00 5.54
1006 2542 2.299294 GACGTCTCAGTCTCGCGGAG 62.299 65.000 8.70 4.40 40.15 4.63
1019 2555 3.479269 CGGAGCAAAGTCGCCGTC 61.479 66.667 0.00 0.00 43.04 4.79
1020 2556 3.119096 GGAGCAAAGTCGCCGTCC 61.119 66.667 0.00 0.00 0.00 4.79
1021 2557 2.357034 GAGCAAAGTCGCCGTCCA 60.357 61.111 0.00 0.00 0.00 4.02
1022 2558 2.665185 AGCAAAGTCGCCGTCCAC 60.665 61.111 0.00 0.00 0.00 4.02
1023 2559 2.970324 GCAAAGTCGCCGTCCACA 60.970 61.111 0.00 0.00 0.00 4.17
1024 2560 2.539338 GCAAAGTCGCCGTCCACAA 61.539 57.895 0.00 0.00 0.00 3.33
1025 2561 1.852067 GCAAAGTCGCCGTCCACAAT 61.852 55.000 0.00 0.00 0.00 2.71
1026 2562 0.591170 CAAAGTCGCCGTCCACAATT 59.409 50.000 0.00 0.00 0.00 2.32
1031 2567 2.034999 GCCGTCCACAATTCCCCA 59.965 61.111 0.00 0.00 0.00 4.96
1032 2568 2.340328 GCCGTCCACAATTCCCCAC 61.340 63.158 0.00 0.00 0.00 4.61
1041 2577 2.092914 CACAATTCCCCACCCTCTACTC 60.093 54.545 0.00 0.00 0.00 2.59
1065 2601 2.022764 TGCGATCCACGAATTCACAT 57.977 45.000 6.22 0.00 45.77 3.21
1074 2610 3.058016 CCACGAATTCACATGAGCTTTGT 60.058 43.478 6.22 0.00 0.00 2.83
1086 2622 2.363038 TGAGCTTTGTTGCTGCTGAATT 59.637 40.909 0.00 0.00 44.17 2.17
1171 2707 1.379977 CCCTGACGACCTGCTCCTA 60.380 63.158 0.00 0.00 0.00 2.94
1275 2811 2.705826 CGCGCTGGATCTCAAAGC 59.294 61.111 5.56 0.00 0.00 3.51
1344 2880 4.521062 AGCCACGAGATCGCTGCC 62.521 66.667 11.49 0.00 44.43 4.85
1500 3036 4.561105 GAGATCTTCGAAGACAACACCTT 58.439 43.478 29.24 11.57 37.98 3.50
1534 3070 0.179092 GCCTTATAGTGGACGCCGTT 60.179 55.000 0.00 0.00 0.00 4.44
1629 3165 1.379843 ATTTCCCCCATGGTCGCAC 60.380 57.895 11.73 0.00 34.77 5.34
1834 3370 0.387239 GCTGCGGGTACAAAAGCAAG 60.387 55.000 0.00 0.00 39.26 4.01
1858 3394 1.067693 TTGCACTGATACTCAACGCG 58.932 50.000 3.53 3.53 0.00 6.01
1963 3502 3.357079 GTTCTGCACGCCACCCTG 61.357 66.667 0.00 0.00 0.00 4.45
2040 3579 1.066143 TGATCAGCGGGAAGGTTCTTC 60.066 52.381 0.00 0.00 0.00 2.87
2041 3580 1.208293 GATCAGCGGGAAGGTTCTTCT 59.792 52.381 7.47 0.00 0.00 2.85
2042 3581 1.056660 TCAGCGGGAAGGTTCTTCTT 58.943 50.000 7.47 0.00 0.00 2.52
2054 3593 3.135167 AGGTTCTTCTTTCCGGTACAACA 59.865 43.478 0.00 0.00 0.00 3.33
2070 3617 1.407656 AACACGGAGCTGGAGACCAA 61.408 55.000 0.00 0.00 30.80 3.67
2100 3647 1.135575 CCTCATGCGGTTCTTTCAAGC 60.136 52.381 0.00 0.00 0.00 4.01
2275 3822 1.083806 TCATCGACGCTGCACCATTC 61.084 55.000 0.00 0.00 0.00 2.67
2521 4068 2.364973 TGCGGCTGGGAGATGGTA 60.365 61.111 0.00 0.00 0.00 3.25
2605 4152 0.678950 CGGCCCAAATTGAAGTGGTT 59.321 50.000 0.00 0.00 32.60 3.67
2653 4204 6.542370 AGTGTATGCAGGAATTATTACGCTTT 59.458 34.615 0.00 0.00 0.00 3.51
2658 4209 4.359706 CAGGAATTATTACGCTTTTGGGC 58.640 43.478 0.00 0.00 35.59 5.36
2661 4212 4.803613 GGAATTATTACGCTTTTGGGCTTG 59.196 41.667 0.00 0.00 35.59 4.01
2666 4217 5.652994 ATTACGCTTTTGGGCTTGATTTA 57.347 34.783 0.00 0.00 35.59 1.40
2677 4228 5.007034 TGGGCTTGATTTATGTTCTTCGAA 58.993 37.500 0.00 0.00 0.00 3.71
2725 4280 8.040132 TGGTTTCTGGATTTTGCTAATAAATGG 58.960 33.333 0.00 0.00 0.00 3.16
2731 4286 7.781056 TGGATTTTGCTAATAAATGGGAAGAC 58.219 34.615 0.00 0.00 0.00 3.01
2740 4295 8.352942 GCTAATAAATGGGAAGACGAAAATGAT 58.647 33.333 0.00 0.00 0.00 2.45
2741 4296 9.884465 CTAATAAATGGGAAGACGAAAATGATC 57.116 33.333 0.00 0.00 0.00 2.92
2743 4298 2.006888 TGGGAAGACGAAAATGATCGC 58.993 47.619 0.00 0.00 46.51 4.58
2789 4707 4.211125 TGTAACTGAAATGTTTCCTGCCA 58.789 39.130 3.26 0.00 36.36 4.92
2799 4717 2.162681 GTTTCCTGCCATACTTGCTGT 58.837 47.619 0.00 0.00 0.00 4.40
2811 4729 5.914635 CCATACTTGCTGTTGTTTTGTACTG 59.085 40.000 0.00 0.00 0.00 2.74
2845 4763 7.602753 CGAGGTCAATATGTTGGAGTATCATA 58.397 38.462 2.06 0.00 36.25 2.15
2848 4766 9.104713 AGGTCAATATGTTGGAGTATCATATCA 57.895 33.333 2.06 0.00 34.85 2.15
2865 4783 5.302568 TCATATCAAATTTAGCAAGGCCCTG 59.697 40.000 0.00 0.00 0.00 4.45
2867 4785 2.825532 TCAAATTTAGCAAGGCCCTGAC 59.174 45.455 5.23 0.00 0.00 3.51
2869 4787 1.839424 ATTTAGCAAGGCCCTGACAC 58.161 50.000 5.23 0.00 0.00 3.67
2870 4788 0.771127 TTTAGCAAGGCCCTGACACT 59.229 50.000 5.23 0.00 0.00 3.55
2871 4789 0.324943 TTAGCAAGGCCCTGACACTC 59.675 55.000 5.23 0.00 0.00 3.51
2872 4790 1.553690 TAGCAAGGCCCTGACACTCC 61.554 60.000 5.23 0.00 0.00 3.85
2873 4791 2.352805 CAAGGCCCTGACACTCCC 59.647 66.667 0.00 0.00 0.00 4.30
2876 4794 2.930562 GGCCCTGACACTCCCTGT 60.931 66.667 0.00 0.00 34.96 4.00
2877 4795 1.612442 GGCCCTGACACTCCCTGTA 60.612 63.158 0.00 0.00 31.03 2.74
2966 5246 3.249091 CTTGACACTGCAGCTGTACTAG 58.751 50.000 15.27 11.15 0.00 2.57
2994 5274 8.480643 AGGTCAGATGTTAATTCTTACTTTCG 57.519 34.615 0.00 0.00 0.00 3.46
3230 5562 2.544685 CAGCTACTCCAAACTCCATCG 58.455 52.381 0.00 0.00 0.00 3.84
3349 5681 1.479323 CCAGCTTGCTGCCATGTATTT 59.521 47.619 16.37 0.00 44.23 1.40
3394 5726 6.271488 TGTTTCCATGAAATCACCAAGATC 57.729 37.500 0.00 0.00 35.39 2.75
3396 5728 3.544684 TCCATGAAATCACCAAGATCGG 58.455 45.455 0.00 0.00 35.39 4.18
3404 5736 3.887621 TCACCAAGATCGGGTCTAAAG 57.112 47.619 8.91 0.00 36.19 1.85
3413 5745 5.205056 AGATCGGGTCTAAAGATCTGAAGT 58.795 41.667 5.88 0.00 46.40 3.01
3415 5747 3.700038 TCGGGTCTAAAGATCTGAAGTCC 59.300 47.826 0.00 4.25 37.60 3.85
3469 5801 1.750778 CGCATTTAGAGGGCCAATGTT 59.249 47.619 6.18 0.00 31.60 2.71
3577 5916 3.774766 TGTAGGCATAAAAGCTCCTCTCA 59.225 43.478 0.00 0.00 34.17 3.27
3588 5927 2.246067 AGCTCCTCTCAGGGTCTGAATA 59.754 50.000 0.00 0.00 40.18 1.75
3603 5942 6.239887 GGGTCTGAATACCATAGGCATAGAAA 60.240 42.308 0.00 0.00 41.67 2.52
3624 5963 1.137479 CCCCTTCTGAACGCCGTAATA 59.863 52.381 0.00 0.00 0.00 0.98
3625 5964 2.419021 CCCCTTCTGAACGCCGTAATAA 60.419 50.000 0.00 0.00 0.00 1.40
3657 6064 1.000938 CCTGCTTCCTTTGTGCACTTC 60.001 52.381 19.41 0.00 32.91 3.01
3658 6065 1.952296 CTGCTTCCTTTGTGCACTTCT 59.048 47.619 19.41 0.00 32.91 2.85
3659 6066 2.360165 CTGCTTCCTTTGTGCACTTCTT 59.640 45.455 19.41 0.00 32.91 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
332 348 7.951530 AAATGTTACTCAAGCATTTGGAAAG 57.048 32.000 0.00 0.00 40.14 2.62
399 416 7.613022 TCTGAAAGGTCTTATACTTAGGAACGA 59.387 37.037 0.00 0.00 0.00 3.85
422 439 3.238108 ACTTGCTCCGTATGTTCTCTG 57.762 47.619 0.00 0.00 0.00 3.35
567 584 8.647226 TCTTTTCTTCTTTGCTTTTTCTTTTCG 58.353 29.630 0.00 0.00 0.00 3.46
625 650 1.687493 GCTAGTGGGAGGCCTCAGT 60.687 63.158 33.29 19.68 0.00 3.41
690 2184 1.073548 GGCCCACCCTTAAACGTGA 59.926 57.895 0.00 0.00 31.36 4.35
857 2393 2.159184 TCGAATCGATCTTGCTTGCTCT 60.159 45.455 0.00 0.00 0.00 4.09
860 2396 1.331507 CGTCGAATCGATCTTGCTTGC 60.332 52.381 9.10 0.00 38.42 4.01
873 2409 0.967380 AGGGGTTACCGTCGTCGAAT 60.967 55.000 2.98 0.00 46.96 3.34
898 2434 3.019545 GCGAGCGAGATTCCGTCG 61.020 66.667 0.00 0.00 40.50 5.12
947 2483 1.070134 TGCGCTAGCCTAATTTCGGAT 59.930 47.619 9.73 0.00 44.33 4.18
962 2498 1.072331 CTAGGGTTAATGGGATGCGCT 59.928 52.381 9.73 0.00 0.00 5.92
993 2529 1.080501 CTTTGCTCCGCGAGACTGA 60.081 57.895 8.23 0.00 0.00 3.41
995 2531 1.080434 GACTTTGCTCCGCGAGACT 60.080 57.895 8.23 0.00 0.00 3.24
996 2532 2.437343 CGACTTTGCTCCGCGAGAC 61.437 63.158 8.23 0.00 0.00 3.36
997 2533 2.126463 CGACTTTGCTCCGCGAGA 60.126 61.111 8.23 1.68 0.00 4.04
998 2534 3.843240 GCGACTTTGCTCCGCGAG 61.843 66.667 8.23 4.18 39.54 5.03
1002 2538 3.479269 GACGGCGACTTTGCTCCG 61.479 66.667 16.62 0.00 46.61 4.63
1003 2539 3.119096 GGACGGCGACTTTGCTCC 61.119 66.667 16.62 3.88 34.52 4.70
1004 2540 2.357034 TGGACGGCGACTTTGCTC 60.357 61.111 16.62 0.00 34.52 4.26
1005 2541 2.665185 GTGGACGGCGACTTTGCT 60.665 61.111 16.62 0.00 34.52 3.91
1006 2542 1.852067 ATTGTGGACGGCGACTTTGC 61.852 55.000 16.62 0.00 0.00 3.68
1007 2543 0.591170 AATTGTGGACGGCGACTTTG 59.409 50.000 16.62 0.00 0.00 2.77
1008 2544 0.872388 GAATTGTGGACGGCGACTTT 59.128 50.000 16.62 0.00 0.00 2.66
1009 2545 0.953960 GGAATTGTGGACGGCGACTT 60.954 55.000 16.62 0.00 0.00 3.01
1010 2546 1.375523 GGAATTGTGGACGGCGACT 60.376 57.895 16.62 0.00 0.00 4.18
1011 2547 2.396157 GGGAATTGTGGACGGCGAC 61.396 63.158 16.62 7.58 0.00 5.19
1012 2548 2.046700 GGGAATTGTGGACGGCGA 60.047 61.111 16.62 0.00 0.00 5.54
1013 2549 3.131478 GGGGAATTGTGGACGGCG 61.131 66.667 4.80 4.80 0.00 6.46
1014 2550 2.034999 TGGGGAATTGTGGACGGC 59.965 61.111 0.00 0.00 0.00 5.68
1015 2551 1.677633 GGTGGGGAATTGTGGACGG 60.678 63.158 0.00 0.00 0.00 4.79
1016 2552 1.677633 GGGTGGGGAATTGTGGACG 60.678 63.158 0.00 0.00 0.00 4.79
1017 2553 0.323451 GAGGGTGGGGAATTGTGGAC 60.323 60.000 0.00 0.00 0.00 4.02
1018 2554 0.477597 AGAGGGTGGGGAATTGTGGA 60.478 55.000 0.00 0.00 0.00 4.02
1019 2555 1.064685 GTAGAGGGTGGGGAATTGTGG 60.065 57.143 0.00 0.00 0.00 4.17
1020 2556 1.916181 AGTAGAGGGTGGGGAATTGTG 59.084 52.381 0.00 0.00 0.00 3.33
1021 2557 2.197465 GAGTAGAGGGTGGGGAATTGT 58.803 52.381 0.00 0.00 0.00 2.71
1022 2558 1.490910 GGAGTAGAGGGTGGGGAATTG 59.509 57.143 0.00 0.00 0.00 2.32
1023 2559 1.628327 GGGAGTAGAGGGTGGGGAATT 60.628 57.143 0.00 0.00 0.00 2.17
1024 2560 0.029989 GGGAGTAGAGGGTGGGGAAT 60.030 60.000 0.00 0.00 0.00 3.01
1025 2561 1.394963 GGGAGTAGAGGGTGGGGAA 59.605 63.158 0.00 0.00 0.00 3.97
1026 2562 1.236026 ATGGGAGTAGAGGGTGGGGA 61.236 60.000 0.00 0.00 0.00 4.81
1031 2567 0.325296 TCGCAATGGGAGTAGAGGGT 60.325 55.000 0.00 0.00 0.00 4.34
1032 2568 1.001406 GATCGCAATGGGAGTAGAGGG 59.999 57.143 6.12 0.00 0.00 4.30
1041 2577 1.002468 GAATTCGTGGATCGCAATGGG 60.002 52.381 0.00 0.00 39.67 4.00
1065 2601 1.391577 TTCAGCAGCAACAAAGCTCA 58.608 45.000 0.00 0.00 44.54 4.26
1074 2610 2.613474 GCCATTGGAAATTCAGCAGCAA 60.613 45.455 6.95 0.00 0.00 3.91
1086 2622 0.918983 ATCCTTCCGAGCCATTGGAA 59.081 50.000 6.95 0.00 45.30 3.53
1171 2707 1.437986 GAGACGGCGCAGGATAAGT 59.562 57.895 13.26 0.00 0.00 2.24
1275 2811 3.036084 GTGGCAGTGTGTCGGTCG 61.036 66.667 0.00 0.00 0.00 4.79
1344 2880 0.543277 TCTGGCATTCTGGGCTAGTG 59.457 55.000 0.00 0.00 40.35 2.74
1534 3070 2.609299 TGGACGCCCCAGGAATCA 60.609 61.111 0.00 0.00 40.82 2.57
1629 3165 3.437795 CGCCTGGCTTTCTGCTGG 61.438 66.667 17.92 0.00 42.39 4.85
1834 3370 2.113860 TGAGTATCAGTGCAAAGGCC 57.886 50.000 0.00 0.00 42.56 5.19
1858 3394 0.466922 CCCTGATTCCTGACATGGGC 60.467 60.000 0.00 0.00 0.00 5.36
1942 3478 2.633657 GTGGCGTGCAGAACAGTG 59.366 61.111 0.00 0.00 0.00 3.66
1991 3530 1.948138 CGAAGCTCGCATGCTCGAT 60.948 57.895 18.36 4.36 43.24 3.59
2001 3540 0.109689 AACGGAGAAGACGAAGCTCG 60.110 55.000 0.00 4.36 46.93 5.03
2054 3593 1.534235 AGTTGGTCTCCAGCTCCGT 60.534 57.895 0.00 0.00 41.11 4.69
2070 3617 1.145598 CGCATGAGGATGGCAGAGT 59.854 57.895 0.00 0.00 0.00 3.24
2137 3684 1.695114 CGATCCACATACCTGGCCCA 61.695 60.000 0.00 0.00 0.00 5.36
2254 3801 2.887568 GGTGCAGCGTCGATGAGG 60.888 66.667 15.87 0.00 0.00 3.86
2275 3822 1.338105 TGGACGTGAATGCTCTCAAGG 60.338 52.381 0.00 0.00 0.00 3.61
2358 3905 2.825836 CCTTCAGATGGCGGTGGC 60.826 66.667 0.00 0.00 38.90 5.01
2521 4068 0.106708 TCCACTTGCTTCGCAGAGTT 59.893 50.000 0.00 0.00 40.61 3.01
2605 4152 4.528206 TGCAGAGACTGAATTCAACCTAGA 59.472 41.667 9.88 0.00 32.44 2.43
2653 4204 5.007034 TCGAAGAACATAAATCAAGCCCAA 58.993 37.500 0.00 0.00 0.00 4.12
2666 4217 6.749139 TCGATCATCCTTATTCGAAGAACAT 58.251 36.000 3.35 0.00 45.90 2.71
2677 4228 6.042552 ACCAGAGAAACATCGATCATCCTTAT 59.957 38.462 0.00 0.00 0.00 1.73
2725 4280 2.673368 ACAGCGATCATTTTCGTCTTCC 59.327 45.455 0.00 0.00 41.16 3.46
2731 4286 3.181517 ACATCACACAGCGATCATTTTCG 60.182 43.478 0.00 0.00 41.99 3.46
2740 4295 3.592898 ACAGATTACATCACACAGCGA 57.407 42.857 0.00 0.00 0.00 4.93
2741 4296 4.318333 GCATACAGATTACATCACACAGCG 60.318 45.833 0.00 0.00 0.00 5.18
2743 4298 7.654923 ACATAGCATACAGATTACATCACACAG 59.345 37.037 0.00 0.00 0.00 3.66
2789 4707 5.507315 GGCAGTACAAAACAACAGCAAGTAT 60.507 40.000 0.00 0.00 0.00 2.12
2799 4717 3.435327 CGCTATGAGGCAGTACAAAACAA 59.565 43.478 0.00 0.00 0.00 2.83
2845 4763 3.448660 GTCAGGGCCTTGCTAAATTTGAT 59.551 43.478 10.65 0.00 0.00 2.57
2848 4766 2.562738 GTGTCAGGGCCTTGCTAAATTT 59.437 45.455 10.65 0.00 0.00 1.82
2872 4790 3.633525 CCAATTGATGTGACCCATACAGG 59.366 47.826 7.12 0.00 32.56 4.00
2873 4791 4.272489 ACCAATTGATGTGACCCATACAG 58.728 43.478 7.12 0.00 32.56 2.74
2876 4794 8.278639 ACTAATTACCAATTGATGTGACCCATA 58.721 33.333 7.12 0.00 30.99 2.74
2877 4795 7.125391 ACTAATTACCAATTGATGTGACCCAT 58.875 34.615 7.12 0.00 32.45 4.00
2921 5201 5.319453 CACCAGATGCCATATTAGACCATT 58.681 41.667 0.00 0.00 0.00 3.16
2950 5230 3.193691 ACCTTACTAGTACAGCTGCAGTG 59.806 47.826 15.27 14.36 0.00 3.66
2985 5265 6.607689 TGGATTACACAATTGCGAAAGTAAG 58.392 36.000 5.05 0.00 39.59 2.34
3055 5381 3.181434 ACTCCATCAGGCCAAAACTTACA 60.181 43.478 5.01 0.00 33.74 2.41
3056 5382 3.421844 ACTCCATCAGGCCAAAACTTAC 58.578 45.455 5.01 0.00 33.74 2.34
3057 5383 3.806949 ACTCCATCAGGCCAAAACTTA 57.193 42.857 5.01 0.00 33.74 2.24
3058 5384 2.683211 ACTCCATCAGGCCAAAACTT 57.317 45.000 5.01 0.00 33.74 2.66
3059 5385 2.108952 AGAACTCCATCAGGCCAAAACT 59.891 45.455 5.01 0.00 33.74 2.66
3060 5386 2.489722 GAGAACTCCATCAGGCCAAAAC 59.510 50.000 5.01 0.00 33.74 2.43
3061 5387 2.376518 AGAGAACTCCATCAGGCCAAAA 59.623 45.455 5.01 0.00 33.74 2.44
3230 5562 3.067320 GGCTATCCTTTGATGTTTGGAGC 59.933 47.826 0.00 0.00 32.18 4.70
3369 5701 7.065120 ATCTTGGTGATTTCATGGAAACAAA 57.935 32.000 0.00 0.00 36.33 2.83
3394 5726 3.447586 TGGACTTCAGATCTTTAGACCCG 59.552 47.826 15.22 0.00 0.00 5.28
3396 5728 5.923733 TCTGGACTTCAGATCTTTAGACC 57.076 43.478 12.55 12.55 46.71 3.85
3413 5745 7.153985 GGTGAATTGTTTCAAATGAATCTGGA 58.846 34.615 0.00 0.00 43.29 3.86
3415 5747 7.654520 ACTGGTGAATTGTTTCAAATGAATCTG 59.345 33.333 0.00 0.00 43.29 2.90
3469 5801 7.671302 ACTCTAGCTTAGTGACTGAATGAAAA 58.329 34.615 0.00 0.00 0.00 2.29
3577 5916 3.060479 TGCCTATGGTATTCAGACCCT 57.940 47.619 0.00 0.00 38.89 4.34
3588 5927 2.789219 AGGGGTTTCTATGCCTATGGT 58.211 47.619 0.00 0.00 0.00 3.55
3603 5942 1.474332 TTACGGCGTTCAGAAGGGGT 61.474 55.000 21.24 0.00 0.00 4.95
3657 6064 0.890683 AAGAAGGGATTGCGCCAAAG 59.109 50.000 4.18 0.00 0.00 2.77
3658 6065 1.337118 AAAGAAGGGATTGCGCCAAA 58.663 45.000 4.18 0.00 0.00 3.28
3659 6066 2.208132 TAAAGAAGGGATTGCGCCAA 57.792 45.000 4.18 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.