Multiple sequence alignment - TraesCS5D01G537800

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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 TraesCS5D01G537800 chr5D 100.000 3083 0 0 1 3083 550302056 550298974 0.000000e+00 5694.0
1 TraesCS5D01G537800 chr5D 85.402 1466 170 20 992 2423 550374514 550373059 0.000000e+00 1482.0
2 TraesCS5D01G537800 chr5D 87.104 1264 139 15 790 2049 550402753 550401510 0.000000e+00 1410.0
3 TraesCS5D01G537800 chr5D 96.045 177 6 1 2683 2859 300760461 300760636 1.400000e-73 287.0
4 TraesCS5D01G537800 chr5D 81.884 138 15 7 91 225 550375258 550375128 1.170000e-19 108.0
5 TraesCS5D01G537800 chr5D 90.909 77 5 1 1 77 432290882 432290956 5.440000e-18 102.0
6 TraesCS5D01G537800 chr5B 95.975 2236 70 6 469 2695 702479933 702477709 0.000000e+00 3613.0
7 TraesCS5D01G537800 chr5B 83.260 1828 234 39 828 2599 702552821 702551010 0.000000e+00 1615.0
8 TraesCS5D01G537800 chr5B 82.500 1720 198 45 790 2471 702558101 702556447 0.000000e+00 1413.0
9 TraesCS5D01G537800 chr5B 90.376 426 29 6 7 428 702480343 702479926 1.620000e-152 549.0
10 TraesCS5D01G537800 chr5B 89.300 243 4 11 2863 3083 702477646 702477404 5.030000e-73 285.0
11 TraesCS5D01G537800 chr5B 100.000 32 0 0 45 76 143268943 143268912 3.320000e-05 60.2
12 TraesCS5D01G537800 chr4A 92.526 1659 81 16 831 2477 617360181 617361808 0.000000e+00 2337.0
13 TraesCS5D01G537800 chr4A 84.355 1713 216 28 748 2423 617288745 617290442 0.000000e+00 1631.0
14 TraesCS5D01G537800 chr4A 83.845 1758 226 26 748 2468 617348814 617350550 0.000000e+00 1620.0
15 TraesCS5D01G537800 chr4A 86.767 1466 162 19 790 2239 617281329 617282778 0.000000e+00 1604.0
16 TraesCS5D01G537800 chr4A 87.879 759 48 18 80 822 617359187 617359917 0.000000e+00 852.0
17 TraesCS5D01G537800 chr4A 94.545 110 5 1 2975 3083 617362123 617362232 5.290000e-38 169.0
18 TraesCS5D01G537800 chr4A 77.311 357 32 25 91 415 617288190 617288529 6.840000e-37 165.0
19 TraesCS5D01G537800 chr4A 77.311 357 32 25 91 415 617348259 617348598 6.840000e-37 165.0
20 TraesCS5D01G537800 chr4A 100.000 31 0 0 2873 2903 617362060 617362090 1.190000e-04 58.4
21 TraesCS5D01G537800 chr4D 97.619 168 4 0 2693 2860 28982881 28983048 3.890000e-74 289.0
22 TraesCS5D01G537800 chr6D 97.605 167 4 0 2692 2858 336841791 336841625 1.400000e-73 287.0
23 TraesCS5D01G537800 chr5A 96.512 172 6 0 2691 2862 519947502 519947331 5.030000e-73 285.0
24 TraesCS5D01G537800 chr7D 97.576 165 4 0 2693 2857 530406900 530406736 1.810000e-72 283.0
25 TraesCS5D01G537800 chr1A 97.576 165 4 0 2693 2857 480758749 480758913 1.810000e-72 283.0
26 TraesCS5D01G537800 chr1A 93.506 77 3 1 1 77 371922972 371922898 2.510000e-21 113.0
27 TraesCS5D01G537800 chr2A 95.954 173 7 0 2693 2865 389221007 389221179 6.510000e-72 281.0
28 TraesCS5D01G537800 chr6A 94.915 177 9 0 2684 2860 420829330 420829506 8.420000e-71 278.0
29 TraesCS5D01G537800 chr6A 92.308 78 4 1 1 78 235058329 235058254 3.250000e-20 110.0
30 TraesCS5D01G537800 chr2D 96.407 167 6 0 2693 2859 420278157 420278323 3.030000e-70 276.0
31 TraesCS5D01G537800 chr3D 92.208 77 4 1 1 77 182097368 182097294 1.170000e-19 108.0
32 TraesCS5D01G537800 chr7B 89.333 75 6 1 1 75 89559376 89559304 3.270000e-15 93.5


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 TraesCS5D01G537800 chr5D 550298974 550302056 3082 True 5694.000000 5694 100.000000 1 3083 1 chr5D.!!$R1 3082
1 TraesCS5D01G537800 chr5D 550401510 550402753 1243 True 1410.000000 1410 87.104000 790 2049 1 chr5D.!!$R2 1259
2 TraesCS5D01G537800 chr5D 550373059 550375258 2199 True 795.000000 1482 83.643000 91 2423 2 chr5D.!!$R3 2332
3 TraesCS5D01G537800 chr5B 702551010 702558101 7091 True 1514.000000 1615 82.880000 790 2599 2 chr5B.!!$R3 1809
4 TraesCS5D01G537800 chr5B 702477404 702480343 2939 True 1482.333333 3613 91.883667 7 3083 3 chr5B.!!$R2 3076
5 TraesCS5D01G537800 chr4A 617281329 617282778 1449 False 1604.000000 1604 86.767000 790 2239 1 chr4A.!!$F1 1449
6 TraesCS5D01G537800 chr4A 617288190 617290442 2252 False 898.000000 1631 80.833000 91 2423 2 chr4A.!!$F2 2332
7 TraesCS5D01G537800 chr4A 617348259 617350550 2291 False 892.500000 1620 80.578000 91 2468 2 chr4A.!!$F3 2377
8 TraesCS5D01G537800 chr4A 617359187 617362232 3045 False 854.100000 2337 93.737500 80 3083 4 chr4A.!!$F4 3003

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
268 298 0.383949 GGAACGAGCTAGCTGGAGAG 59.616 60.0 30.57 14.7 0.0 3.20 F
615 724 0.823769 TCGCCTAGCCACATCGATCT 60.824 55.0 0.00 0.0 0.0 2.75 F
1738 2191 0.827507 GAAGTGGCAATGGTGGTGGT 60.828 55.0 0.00 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 2021 0.393808 GTACCATCACCACCGGCAAT 60.394 55.000 0.0 0.0 0.0 3.56 R
1894 7599 2.055689 CTCCACCACTGCCAGTTCCA 62.056 60.000 0.0 0.0 0.0 3.53 R
2841 8617 1.288335 AGATGTACTCCCTCCGTTCCT 59.712 52.381 0.0 0.0 0.0 3.36 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
25 26 2.680339 GAGCTCTAACCATGTTTCAGCC 59.320 50.000 6.43 0.00 0.00 4.85
27 28 3.519510 AGCTCTAACCATGTTTCAGCCTA 59.480 43.478 3.93 0.00 0.00 3.93
33 34 4.508551 ACCATGTTTCAGCCTATGATCA 57.491 40.909 0.00 0.00 37.89 2.92
36 37 5.533903 ACCATGTTTCAGCCTATGATCAATC 59.466 40.000 0.00 0.00 37.89 2.67
37 38 5.048224 CCATGTTTCAGCCTATGATCAATCC 60.048 44.000 0.00 0.00 37.89 3.01
40 41 6.840527 TGTTTCAGCCTATGATCAATCCATA 58.159 36.000 0.00 0.00 37.89 2.74
41 42 6.938596 TGTTTCAGCCTATGATCAATCCATAG 59.061 38.462 0.00 0.00 41.76 2.23
114 117 1.956477 ACTTTTGGAGACCATGTGCAC 59.044 47.619 10.75 10.75 31.53 4.57
122 125 4.009675 GGAGACCATGTGCACTAATTTCA 58.990 43.478 19.41 0.00 0.00 2.69
160 165 5.556690 AAACGCGATCGACTATTATTGAC 57.443 39.130 21.57 0.00 39.41 3.18
268 298 0.383949 GGAACGAGCTAGCTGGAGAG 59.616 60.000 30.57 14.70 0.00 3.20
283 313 1.953686 GGAGAGTCTAATGCGAGCTCT 59.046 52.381 12.85 0.00 39.00 4.09
364 406 3.631686 TGTTAATTTGCATGCGCCTAGAT 59.368 39.130 14.09 0.00 37.32 1.98
428 473 2.260247 GGTTAAACCCAAGGTCGCC 58.740 57.895 0.00 0.00 33.12 5.54
429 474 1.579964 GGTTAAACCCAAGGTCGCCG 61.580 60.000 0.00 0.00 33.12 6.46
430 475 1.967494 TTAAACCCAAGGTCGCCGC 60.967 57.895 0.00 0.00 33.12 6.53
431 476 3.905437 TAAACCCAAGGTCGCCGCC 62.905 63.158 0.00 0.00 33.12 6.13
454 499 4.166011 GCAGTGTTCCGGCGATGC 62.166 66.667 9.30 4.93 0.00 3.91
455 500 2.741985 CAGTGTTCCGGCGATGCA 60.742 61.111 9.30 0.01 0.00 3.96
456 501 2.742372 AGTGTTCCGGCGATGCAC 60.742 61.111 9.30 13.68 0.00 4.57
457 502 4.147322 GTGTTCCGGCGATGCACG 62.147 66.667 9.30 0.00 45.66 5.34
458 503 4.365505 TGTTCCGGCGATGCACGA 62.366 61.111 9.30 0.00 45.77 4.35
459 504 2.890474 GTTCCGGCGATGCACGAT 60.890 61.111 9.30 0.00 45.77 3.73
460 505 2.889988 TTCCGGCGATGCACGATG 60.890 61.111 9.30 4.00 45.77 3.84
466 511 3.863543 CGATGCACGATGCCGCAA 61.864 61.111 0.00 0.00 44.23 4.85
467 512 2.023741 GATGCACGATGCCGCAAG 59.976 61.111 0.00 0.00 44.23 4.01
471 516 2.703409 CACGATGCCGCAAGTAGC 59.297 61.111 0.00 0.00 39.95 3.58
512 613 9.229784 CAACACACTATGCTTAATTCATCATTC 57.770 33.333 0.00 0.00 0.00 2.67
540 641 6.092807 CACTGCCAGAAGATTAACTTAACTCC 59.907 42.308 0.00 0.00 39.13 3.85
554 655 7.690952 AACTTAACTCCGTAAAATGCCAATA 57.309 32.000 0.00 0.00 0.00 1.90
570 671 4.137543 GCCAATATCAAAGGATCCGAGTT 58.862 43.478 5.98 0.00 34.89 3.01
615 724 0.823769 TCGCCTAGCCACATCGATCT 60.824 55.000 0.00 0.00 0.00 2.75
681 790 1.519758 ACACTTACGCGTTCTTTCACG 59.480 47.619 20.78 0.00 43.36 4.35
690 836 1.583054 GTTCTTTCACGTGTCAGGCT 58.417 50.000 16.51 0.00 0.00 4.58
777 923 6.650807 TGATCTGCCTCGATCAATAAATTACC 59.349 38.462 7.68 0.00 44.88 2.85
797 970 2.757868 CCGACTGGAATCAAGAGAGAGT 59.242 50.000 0.00 0.00 37.49 3.24
977 1414 4.038763 GGATCACCGTAAGATATGTCACCA 59.961 45.833 0.00 0.00 43.02 4.17
1127 1574 0.895100 TGTCCTTGTGAGCATTGGGC 60.895 55.000 0.00 0.00 45.30 5.36
1568 2021 2.047655 CAAACGCACCGGCTCCTA 60.048 61.111 0.00 0.00 38.10 2.94
1738 2191 0.827507 GAAGTGGCAATGGTGGTGGT 60.828 55.000 0.00 0.00 0.00 4.16
2157 7882 7.312154 GTTTGTGCCAATAGACATATGTGAAA 58.688 34.615 14.43 0.00 0.00 2.69
2181 7907 6.543735 AGAGTACCTCATTTGTAGCCTTTTT 58.456 36.000 0.00 0.00 32.06 1.94
2695 8471 2.101582 GTGATCGGTCTTGGCTGATACT 59.898 50.000 0.00 0.00 34.85 2.12
2696 8472 2.362397 TGATCGGTCTTGGCTGATACTC 59.638 50.000 0.00 0.00 34.85 2.59
2698 8474 0.105039 CGGTCTTGGCTGATACTCCC 59.895 60.000 0.00 0.00 0.00 4.30
2700 8476 1.414550 GGTCTTGGCTGATACTCCCTC 59.585 57.143 0.00 0.00 0.00 4.30
2701 8477 1.414550 GTCTTGGCTGATACTCCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
2703 8479 0.325296 TTGGCTGATACTCCCTCCGT 60.325 55.000 0.00 0.00 0.00 4.69
2705 8481 0.389757 GGCTGATACTCCCTCCGTTC 59.610 60.000 0.00 0.00 0.00 3.95
2706 8482 0.389757 GCTGATACTCCCTCCGTTCC 59.610 60.000 0.00 0.00 0.00 3.62
2707 8483 2.030045 GCTGATACTCCCTCCGTTCCT 61.030 57.143 0.00 0.00 0.00 3.36
2708 8484 2.752154 GCTGATACTCCCTCCGTTCCTA 60.752 54.545 0.00 0.00 0.00 2.94
2709 8485 3.563223 CTGATACTCCCTCCGTTCCTAA 58.437 50.000 0.00 0.00 0.00 2.69
2710 8486 3.958798 CTGATACTCCCTCCGTTCCTAAA 59.041 47.826 0.00 0.00 0.00 1.85
2711 8487 4.553678 TGATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
2712 8488 5.708544 TGATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
2713 8489 6.320518 TGATACTCCCTCCGTTCCTAAATAT 58.679 40.000 0.00 0.00 0.00 1.28
2714 8490 7.472741 TGATACTCCCTCCGTTCCTAAATATA 58.527 38.462 0.00 0.00 0.00 0.86
2717 8493 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2718 8494 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2719 8495 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2720 8496 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2722 8498 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2740 8516 9.750125 AAGTCTTTTTAGACATTTCAAATGGAC 57.250 29.630 14.70 8.92 41.02 4.02
2743 8519 9.528018 TCTTTTTAGACATTTCAAATGGACAAC 57.472 29.630 14.70 1.26 0.00 3.32
2747 8523 6.219417 AGACATTTCAAATGGACAACAACA 57.781 33.333 14.70 0.00 0.00 3.33
2749 8525 7.950512 AGACATTTCAAATGGACAACAACATA 58.049 30.769 14.70 0.00 0.00 2.29
2751 8527 6.640499 ACATTTCAAATGGACAACAACATACG 59.360 34.615 14.70 0.00 0.00 3.06
2752 8528 4.757799 TCAAATGGACAACAACATACGG 57.242 40.909 0.00 0.00 0.00 4.02
2753 8529 4.390264 TCAAATGGACAACAACATACGGA 58.610 39.130 0.00 0.00 0.00 4.69
2758 8534 5.092554 TGGACAACAACATACGGATGTAT 57.907 39.130 15.10 2.23 45.93 2.29
2798 8574 7.516198 AGTGTAGATTCACTCATTTTGCTTT 57.484 32.000 0.00 0.00 44.07 3.51
2799 8575 7.365741 AGTGTAGATTCACTCATTTTGCTTTG 58.634 34.615 0.00 0.00 44.07 2.77
2800 8576 7.013655 AGTGTAGATTCACTCATTTTGCTTTGT 59.986 33.333 0.00 0.00 44.07 2.83
2801 8577 8.289618 GTGTAGATTCACTCATTTTGCTTTGTA 58.710 33.333 0.00 0.00 35.68 2.41
2802 8578 9.013229 TGTAGATTCACTCATTTTGCTTTGTAT 57.987 29.630 0.00 0.00 0.00 2.29
2809 8585 9.665719 TCACTCATTTTGCTTTGTATATAGTCA 57.334 29.630 0.00 0.00 0.00 3.41
2810 8586 9.708222 CACTCATTTTGCTTTGTATATAGTCAC 57.292 33.333 0.00 0.00 0.00 3.67
2811 8587 9.672673 ACTCATTTTGCTTTGTATATAGTCACT 57.327 29.630 0.00 0.00 0.00 3.41
2816 8592 9.891828 TTTTGCTTTGTATATAGTCACTTGTTG 57.108 29.630 0.00 0.00 0.00 3.33
2817 8593 8.840833 TTGCTTTGTATATAGTCACTTGTTGA 57.159 30.769 0.00 0.00 0.00 3.18
2818 8594 8.840833 TGCTTTGTATATAGTCACTTGTTGAA 57.159 30.769 0.00 0.00 35.39 2.69
2819 8595 9.278978 TGCTTTGTATATAGTCACTTGTTGAAA 57.721 29.630 0.00 0.00 35.39 2.69
2830 8606 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2831 8607 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2832 8608 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2833 8609 8.424918 TCACTTGTTGAAATCTCTAGAAAGACT 58.575 33.333 0.00 0.00 0.00 3.24
2834 8610 9.050601 CACTTGTTGAAATCTCTAGAAAGACTT 57.949 33.333 0.00 0.00 0.00 3.01
2851 8627 8.422566 AGAAAGACTTATATTTAGGAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
2852 8628 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2853 8629 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2854 8630 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2855 8631 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2856 8632 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2857 8633 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
2858 8634 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
2859 8635 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
2860 8636 1.777941 AGGAACGGAGGGAGTACATC 58.222 55.000 0.00 0.00 0.00 3.06
2861 8637 1.288335 AGGAACGGAGGGAGTACATCT 59.712 52.381 0.00 0.00 0.00 2.90
2870 8646 4.262249 GGAGGGAGTACATCTTATGAGCAC 60.262 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.383118 GGCTGAAACATGGTTAGAGCTCTA 60.383 45.833 19.72 19.72 0.00 2.43
3 4 3.604582 GCTGAAACATGGTTAGAGCTCT 58.395 45.455 22.17 22.17 0.00 4.09
4 5 2.680339 GGCTGAAACATGGTTAGAGCTC 59.320 50.000 20.77 5.27 0.00 4.09
5 6 2.307098 AGGCTGAAACATGGTTAGAGCT 59.693 45.455 20.77 8.98 0.00 4.09
9 10 6.057533 TGATCATAGGCTGAAACATGGTTAG 58.942 40.000 0.00 0.00 37.44 2.34
21 22 9.926158 GTATATCTATGGATTGATCATAGGCTG 57.074 37.037 0.00 0.00 42.44 4.85
22 23 9.099071 GGTATATCTATGGATTGATCATAGGCT 57.901 37.037 0.00 0.00 42.44 4.58
77 80 1.048724 AGTCCAAGGGCAGCGCTATA 61.049 55.000 10.99 0.00 0.00 1.31
78 81 1.915078 AAGTCCAAGGGCAGCGCTAT 61.915 55.000 10.99 0.37 0.00 2.97
114 117 4.328440 CGCAGGTCTGACTTCTGAAATTAG 59.672 45.833 15.42 0.00 0.00 1.73
122 125 1.603172 CGTTTCGCAGGTCTGACTTCT 60.603 52.381 7.85 0.00 0.00 2.85
187 195 3.230976 GCCGGGATCCCATCTTAATTTT 58.769 45.455 30.42 0.00 35.37 1.82
268 298 3.815337 TCGATAGAGCTCGCATTAGAC 57.185 47.619 8.37 0.00 42.67 2.59
283 313 4.583489 GTCCAAGTTGACCTAGGATCGATA 59.417 45.833 17.98 0.00 0.00 2.92
437 482 4.166011 GCATCGCCGGAACACTGC 62.166 66.667 5.05 1.94 0.00 4.40
438 483 2.741985 TGCATCGCCGGAACACTG 60.742 61.111 5.05 0.00 0.00 3.66
439 484 2.742372 GTGCATCGCCGGAACACT 60.742 61.111 5.05 0.00 33.10 3.55
440 485 4.147322 CGTGCATCGCCGGAACAC 62.147 66.667 5.05 4.02 32.73 3.32
441 486 3.657448 ATCGTGCATCGCCGGAACA 62.657 57.895 5.05 0.00 39.67 3.18
442 487 2.890474 ATCGTGCATCGCCGGAAC 60.890 61.111 5.05 0.00 39.67 3.62
443 488 2.889988 CATCGTGCATCGCCGGAA 60.890 61.111 5.05 0.00 39.67 4.30
453 498 2.703409 CTACTTGCGGCATCGTGC 59.297 61.111 2.28 1.92 44.08 5.34
454 499 2.703409 GCTACTTGCGGCATCGTG 59.297 61.111 2.28 0.00 38.89 4.35
457 502 3.861010 TAGCGAGCTACTTGCGGCATC 62.861 57.143 2.28 0.00 44.91 3.91
458 503 2.016393 TAGCGAGCTACTTGCGGCAT 62.016 55.000 2.28 0.00 44.91 4.40
459 504 2.220615 TTAGCGAGCTACTTGCGGCA 62.221 55.000 4.05 0.00 44.91 5.69
460 505 0.876342 ATTAGCGAGCTACTTGCGGC 60.876 55.000 4.05 0.00 44.91 6.53
461 506 1.132588 GATTAGCGAGCTACTTGCGG 58.867 55.000 4.05 0.00 44.91 5.69
462 507 1.132588 GGATTAGCGAGCTACTTGCG 58.867 55.000 4.05 0.00 44.91 4.85
463 508 2.225068 TGGATTAGCGAGCTACTTGC 57.775 50.000 4.05 0.00 40.93 4.01
464 509 3.786635 ACTTGGATTAGCGAGCTACTTG 58.213 45.455 4.05 0.00 0.00 3.16
465 510 3.447586 TGACTTGGATTAGCGAGCTACTT 59.552 43.478 4.05 0.00 0.00 2.24
466 511 3.024547 TGACTTGGATTAGCGAGCTACT 58.975 45.455 4.05 0.00 0.00 2.57
467 512 3.438297 TGACTTGGATTAGCGAGCTAC 57.562 47.619 4.05 0.00 0.00 3.58
471 516 3.123621 GTGTGTTGACTTGGATTAGCGAG 59.876 47.826 0.00 0.00 0.00 5.03
512 613 1.398390 GTTAATCTTCTGGCAGTGGCG 59.602 52.381 15.27 7.17 42.47 5.69
540 641 6.863126 GGATCCTTTGATATTGGCATTTTACG 59.137 38.462 3.84 0.00 0.00 3.18
554 655 4.440250 CGTACTGAACTCGGATCCTTTGAT 60.440 45.833 10.75 0.00 0.00 2.57
615 724 0.767375 GGCCTCAGCTGGATCCATAA 59.233 55.000 16.63 0.01 39.73 1.90
681 790 2.546795 CGAGATTCCCATAGCCTGACAC 60.547 54.545 0.00 0.00 0.00 3.67
777 923 4.448537 AACTCTCTCTTGATTCCAGTCG 57.551 45.455 0.00 0.00 0.00 4.18
861 1294 7.249147 CCAGCAGTACCGTTGACTATATATAC 58.751 42.308 0.00 0.00 0.00 1.47
862 1295 6.127814 GCCAGCAGTACCGTTGACTATATATA 60.128 42.308 0.00 0.00 0.00 0.86
863 1296 5.336531 GCCAGCAGTACCGTTGACTATATAT 60.337 44.000 0.00 0.00 0.00 0.86
864 1297 4.022589 GCCAGCAGTACCGTTGACTATATA 60.023 45.833 0.00 0.00 0.00 0.86
868 1301 0.245539 GCCAGCAGTACCGTTGACTA 59.754 55.000 0.00 0.00 0.00 2.59
1568 2021 0.393808 GTACCATCACCACCGGCAAT 60.394 55.000 0.00 0.00 0.00 3.56
1825 2278 2.288825 TGTAGCATAGCCTTCGCCATAC 60.289 50.000 0.00 0.00 34.57 2.39
1894 7599 2.055689 CTCCACCACTGCCAGTTCCA 62.056 60.000 0.00 0.00 0.00 3.53
2181 7907 7.994425 TCAAGCAATTGACTATTTGAGGTAA 57.006 32.000 10.34 0.00 0.00 2.85
2184 7910 7.701078 CAGAATCAAGCAATTGACTATTTGAGG 59.299 37.037 10.34 0.14 33.23 3.86
2561 8337 4.481368 TGGGCGACATTCTGTTTACTAT 57.519 40.909 0.00 0.00 0.00 2.12
2695 8471 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2696 8472 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2714 8490 9.750125 GTCCATTTGAAATGTCTAAAAAGACTT 57.250 29.630 15.93 0.00 39.41 3.01
2717 8493 9.528018 GTTGTCCATTTGAAATGTCTAAAAAGA 57.472 29.630 15.93 1.84 0.00 2.52
2718 8494 9.311916 TGTTGTCCATTTGAAATGTCTAAAAAG 57.688 29.630 15.93 0.00 0.00 2.27
2719 8495 9.658799 TTGTTGTCCATTTGAAATGTCTAAAAA 57.341 25.926 15.93 6.88 0.00 1.94
2720 8496 9.092876 GTTGTTGTCCATTTGAAATGTCTAAAA 57.907 29.630 15.93 5.56 0.00 1.52
2722 8498 7.776107 TGTTGTTGTCCATTTGAAATGTCTAA 58.224 30.769 15.93 5.71 0.00 2.10
2725 8501 7.148983 CGTATGTTGTTGTCCATTTGAAATGTC 60.149 37.037 15.93 9.53 0.00 3.06
2727 8503 6.089283 CCGTATGTTGTTGTCCATTTGAAATG 59.911 38.462 10.84 10.84 0.00 2.32
2730 8506 4.822350 TCCGTATGTTGTTGTCCATTTGAA 59.178 37.500 0.00 0.00 0.00 2.69
2731 8507 4.390264 TCCGTATGTTGTTGTCCATTTGA 58.610 39.130 0.00 0.00 0.00 2.69
2736 8512 3.410631 ACATCCGTATGTTGTTGTCCA 57.589 42.857 0.00 0.00 44.07 4.02
2775 8551 7.141363 ACAAAGCAAAATGAGTGAATCTACAC 58.859 34.615 0.00 0.00 40.60 2.90
2776 8552 7.275888 ACAAAGCAAAATGAGTGAATCTACA 57.724 32.000 0.00 0.00 0.00 2.74
2783 8559 9.665719 TGACTATATACAAAGCAAAATGAGTGA 57.334 29.630 0.00 0.00 0.00 3.41
2784 8560 9.708222 GTGACTATATACAAAGCAAAATGAGTG 57.292 33.333 0.00 0.00 0.00 3.51
2785 8561 9.672673 AGTGACTATATACAAAGCAAAATGAGT 57.327 29.630 0.00 0.00 0.00 3.41
2790 8566 9.891828 CAACAAGTGACTATATACAAAGCAAAA 57.108 29.630 0.00 0.00 0.00 2.44
2791 8567 9.278978 TCAACAAGTGACTATATACAAAGCAAA 57.721 29.630 0.00 0.00 0.00 3.68
2792 8568 8.840833 TCAACAAGTGACTATATACAAAGCAA 57.159 30.769 0.00 0.00 0.00 3.91
2793 8569 8.840833 TTCAACAAGTGACTATATACAAAGCA 57.159 30.769 0.00 0.00 35.39 3.91
2804 8580 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2805 8581 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2806 8582 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2807 8583 8.424918 AGTCTTTCTAGAGATTTCAACAAGTGA 58.575 33.333 0.00 0.00 0.00 3.41
2808 8584 8.600449 AGTCTTTCTAGAGATTTCAACAAGTG 57.400 34.615 0.00 0.00 0.00 3.16
2825 8601 8.422566 CCTCCGTTCCTAAATATAAGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
2826 8602 7.656542 CCCTCCGTTCCTAAATATAAGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
2827 8603 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2828 8604 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2829 8605 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2830 8606 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2831 8607 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2832 8608 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2833 8609 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
2834 8610 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
2835 8611 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2836 8612 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2837 8613 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2838 8614 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2839 8615 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2840 8616 2.512896 AGATGTACTCCCTCCGTTCCTA 59.487 50.000 0.00 0.00 0.00 2.94
2841 8617 1.288335 AGATGTACTCCCTCCGTTCCT 59.712 52.381 0.00 0.00 0.00 3.36
2842 8618 1.777941 AGATGTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
2843 8619 4.583489 TCATAAGATGTACTCCCTCCGTTC 59.417 45.833 0.00 0.00 0.00 3.95
2844 8620 4.543689 TCATAAGATGTACTCCCTCCGTT 58.456 43.478 0.00 0.00 0.00 4.44
2845 8621 4.145807 CTCATAAGATGTACTCCCTCCGT 58.854 47.826 0.00 0.00 0.00 4.69
2846 8622 3.057174 GCTCATAAGATGTACTCCCTCCG 60.057 52.174 0.00 0.00 0.00 4.63
2847 8623 3.898123 TGCTCATAAGATGTACTCCCTCC 59.102 47.826 0.00 0.00 0.00 4.30
2848 8624 4.557695 CGTGCTCATAAGATGTACTCCCTC 60.558 50.000 0.00 0.00 0.00 4.30
2849 8625 3.319405 CGTGCTCATAAGATGTACTCCCT 59.681 47.826 0.00 0.00 0.00 4.20
2850 8626 3.318275 TCGTGCTCATAAGATGTACTCCC 59.682 47.826 0.00 0.00 0.00 4.30
2851 8627 4.569761 TCGTGCTCATAAGATGTACTCC 57.430 45.455 0.00 0.00 0.00 3.85
2852 8628 6.669278 TGTATCGTGCTCATAAGATGTACTC 58.331 40.000 0.00 0.00 0.00 2.59
2853 8629 6.486993 TCTGTATCGTGCTCATAAGATGTACT 59.513 38.462 0.00 0.00 0.00 2.73
2854 8630 6.669278 TCTGTATCGTGCTCATAAGATGTAC 58.331 40.000 0.00 0.00 0.00 2.90
2855 8631 6.486993 ACTCTGTATCGTGCTCATAAGATGTA 59.513 38.462 0.00 0.00 0.00 2.29
2856 8632 5.300539 ACTCTGTATCGTGCTCATAAGATGT 59.699 40.000 0.00 0.00 0.00 3.06
2857 8633 5.767269 ACTCTGTATCGTGCTCATAAGATG 58.233 41.667 0.00 0.00 0.00 2.90
2858 8634 6.398234 AACTCTGTATCGTGCTCATAAGAT 57.602 37.500 0.00 0.00 0.00 2.40
2859 8635 5.836821 AACTCTGTATCGTGCTCATAAGA 57.163 39.130 0.00 0.00 0.00 2.10
2860 8636 6.730175 ACTAACTCTGTATCGTGCTCATAAG 58.270 40.000 0.00 0.00 0.00 1.73
2861 8637 6.694877 ACTAACTCTGTATCGTGCTCATAA 57.305 37.500 0.00 0.00 0.00 1.90
2870 8646 8.117988 GTCTGTCTCTAAACTAACTCTGTATCG 58.882 40.741 0.00 0.00 0.00 2.92
2969 8766 3.889520 AACGGAAAGACATCCTCCTAC 57.110 47.619 0.00 0.00 37.34 3.18


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

AutoCloner maintained by Alex Coulton.