Multiple sequence alignment - TraesCS5A01G524900

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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 TraesCS5A01G524900 chr5A 100.000 3281 0 0 1 3281 685539684 685536404 0.000000e+00 6059
1 TraesCS5A01G524900 chr4D 93.017 2463 122 27 1 2428 502413840 502411393 0.000000e+00 3550
2 TraesCS5A01G524900 chr4D 95.122 861 31 8 2428 3279 502411365 502410507 0.000000e+00 1347
3 TraesCS5A01G524900 chr4B 91.815 2468 132 40 1 2428 646660696 646658259 0.000000e+00 3374
4 TraesCS5A01G524900 chr4B 84.848 264 37 3 2147 2410 50251790 50252050 2.510000e-66 263
5 TraesCS5A01G524900 chr4B 88.889 81 8 1 3184 3263 50251370 50251290 7.490000e-17 99
6 TraesCS5A01G524900 chr2A 89.760 1416 141 4 984 2399 536623633 536625044 0.000000e+00 1808
7 TraesCS5A01G524900 chr2B 88.744 1457 147 16 984 2432 472898477 472899924 0.000000e+00 1766
8 TraesCS5A01G524900 chr2D 89.511 1392 138 8 1008 2399 398780042 398781425 0.000000e+00 1755
9 TraesCS5A01G524900 chr3D 85.859 99 13 1 3184 3281 93831804 93831902 1.610000e-18 104


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 TraesCS5A01G524900 chr5A 685536404 685539684 3280 True 6059.0 6059 100.0000 1 3281 1 chr5A.!!$R1 3280
1 TraesCS5A01G524900 chr4D 502410507 502413840 3333 True 2448.5 3550 94.0695 1 3279 2 chr4D.!!$R1 3278
2 TraesCS5A01G524900 chr4B 646658259 646660696 2437 True 3374.0 3374 91.8150 1 2428 1 chr4B.!!$R2 2427
3 TraesCS5A01G524900 chr2A 536623633 536625044 1411 False 1808.0 1808 89.7600 984 2399 1 chr2A.!!$F1 1415
4 TraesCS5A01G524900 chr2B 472898477 472899924 1447 False 1766.0 1766 88.7440 984 2432 1 chr2B.!!$F1 1448
5 TraesCS5A01G524900 chr2D 398780042 398781425 1383 False 1755.0 1755 89.5110 1008 2399 1 chr2D.!!$F1 1391

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
602 636 0.031585 ACGCTGTTGAGACGCACTTA 59.968 50.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2481 2567 0.040514 CACAAAAGAATGTCGCGGCA 60.041 50.0 19.03 19.03 0.0 5.69 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
90 105 2.125269 CCGGCCTTTCAGGTACGG 60.125 66.667 0.00 11.83 45.94 4.02
118 133 0.663568 CCGTCCGCCGATTAGCTAAG 60.664 60.000 12.54 0.00 39.56 2.18
210 227 2.885644 CCGATCTGCCGACGTTGG 60.886 66.667 18.24 18.24 0.00 3.77
212 229 2.444624 CGATCTGCCGACGTTGGTG 61.445 63.158 22.97 15.66 0.00 4.17
291 309 2.085320 TCAGCGTAGAGAGAACTGGAC 58.915 52.381 0.00 0.00 0.00 4.02
297 315 0.980423 AGAGAGAACTGGACCTTGCC 59.020 55.000 0.00 0.00 0.00 4.52
325 343 4.060667 CGGTTTCCCCCATGCCCT 62.061 66.667 0.00 0.00 0.00 5.19
327 345 1.685765 GGTTTCCCCCATGCCCTTC 60.686 63.158 0.00 0.00 0.00 3.46
329 347 0.972471 GTTTCCCCCATGCCCTTCTG 60.972 60.000 0.00 0.00 0.00 3.02
330 348 2.166957 TTTCCCCCATGCCCTTCTGG 62.167 60.000 0.00 0.00 37.09 3.86
342 364 1.668419 CCTTCTGGCAGTTTATCCCG 58.332 55.000 15.27 0.00 0.00 5.14
346 368 2.518587 GGCAGTTTATCCCGGGGC 60.519 66.667 23.50 14.31 0.00 5.80
362 389 0.542333 GGGCTAGGGTTCTTCTGGTC 59.458 60.000 0.00 0.00 0.00 4.02
441 468 3.616821 TCGATTCTACTGCCGATTTGTTG 59.383 43.478 0.00 0.00 0.00 3.33
445 476 2.037902 TCTACTGCCGATTTGTTGGACA 59.962 45.455 0.00 0.00 0.00 4.02
447 478 0.240945 CTGCCGATTTGTTGGACACC 59.759 55.000 0.00 0.00 0.00 4.16
460 491 2.027625 GACACCGGTGTAGCACAGC 61.028 63.158 38.93 21.32 45.05 4.40
475 506 2.724839 GCACAGCGTTTCACCGATTTAG 60.725 50.000 0.00 0.00 0.00 1.85
478 509 3.185797 ACAGCGTTTCACCGATTTAGTTC 59.814 43.478 0.00 0.00 0.00 3.01
479 510 3.185594 CAGCGTTTCACCGATTTAGTTCA 59.814 43.478 0.00 0.00 0.00 3.18
481 512 4.088648 GCGTTTCACCGATTTAGTTCATG 58.911 43.478 0.00 0.00 0.00 3.07
482 513 4.378046 GCGTTTCACCGATTTAGTTCATGT 60.378 41.667 0.00 0.00 0.00 3.21
483 514 5.685841 CGTTTCACCGATTTAGTTCATGTT 58.314 37.500 0.00 0.00 0.00 2.71
484 515 5.788531 CGTTTCACCGATTTAGTTCATGTTC 59.211 40.000 0.00 0.00 0.00 3.18
485 516 6.565060 CGTTTCACCGATTTAGTTCATGTTCA 60.565 38.462 0.00 0.00 0.00 3.18
486 517 6.480524 TTCACCGATTTAGTTCATGTTCAG 57.519 37.500 0.00 0.00 0.00 3.02
487 518 5.789521 TCACCGATTTAGTTCATGTTCAGA 58.210 37.500 0.00 0.00 0.00 3.27
488 519 5.869344 TCACCGATTTAGTTCATGTTCAGAG 59.131 40.000 0.00 0.00 0.00 3.35
489 520 5.869344 CACCGATTTAGTTCATGTTCAGAGA 59.131 40.000 0.00 0.00 0.00 3.10
490 521 6.368791 CACCGATTTAGTTCATGTTCAGAGAA 59.631 38.462 0.00 0.00 0.00 2.87
493 524 7.118390 CCGATTTAGTTCATGTTCAGAGAAACT 59.882 37.037 0.00 0.00 0.00 2.66
494 525 7.954248 CGATTTAGTTCATGTTCAGAGAAACTG 59.046 37.037 0.00 0.00 46.97 3.16
513 544 5.836821 ACTGATACGTCTAGCTGAATTGA 57.163 39.130 0.00 0.00 0.00 2.57
525 556 6.988580 TCTAGCTGAATTGAACACCATATCTG 59.011 38.462 0.00 0.00 0.00 2.90
600 634 1.661821 GACGCTGTTGAGACGCACT 60.662 57.895 0.00 0.00 0.00 4.40
601 635 1.215655 GACGCTGTTGAGACGCACTT 61.216 55.000 0.00 0.00 0.00 3.16
602 636 0.031585 ACGCTGTTGAGACGCACTTA 59.968 50.000 0.00 0.00 0.00 2.24
638 691 8.109634 AGGTGTTGTCCTGTAAATCTGAATAAT 58.890 33.333 0.00 0.00 36.35 1.28
639 692 9.391006 GGTGTTGTCCTGTAAATCTGAATAATA 57.609 33.333 0.00 0.00 0.00 0.98
705 758 8.332464 CACTTTGTACTGAAGATTTTTGTACGA 58.668 33.333 13.99 0.00 37.04 3.43
721 774 0.808453 ACGACGTGTGTGTTTCCTGG 60.808 55.000 0.00 0.00 0.00 4.45
739 792 4.104579 TCCTGGCATGTCATGGTATATGTT 59.895 41.667 14.64 0.00 0.00 2.71
751 804 6.894654 TCATGGTATATGTTGGGTTCATTTGT 59.105 34.615 0.00 0.00 0.00 2.83
753 806 5.355630 TGGTATATGTTGGGTTCATTTGTCG 59.644 40.000 0.00 0.00 0.00 4.35
756 809 1.678627 TGTTGGGTTCATTTGTCGTGG 59.321 47.619 0.00 0.00 0.00 4.94
777 830 4.079958 TGGTCAGCTACTCCAGATAGTGTA 60.080 45.833 0.00 0.00 0.00 2.90
778 831 4.888239 GGTCAGCTACTCCAGATAGTGTAA 59.112 45.833 0.00 0.00 0.00 2.41
779 832 5.536916 GGTCAGCTACTCCAGATAGTGTAAT 59.463 44.000 0.00 0.00 0.00 1.89
785 838 9.073475 AGCTACTCCAGATAGTGTAATTAGAAG 57.927 37.037 0.00 0.00 0.00 2.85
828 881 4.153475 TGTTGCTAAAGTAAACGGCATCTC 59.847 41.667 0.00 0.00 32.87 2.75
838 892 0.680280 ACGGCATCTCTAGTGGTCGT 60.680 55.000 0.00 0.00 0.00 4.34
901 955 1.795162 GCGCCGTGGAGAAAATTCATG 60.795 52.381 0.00 0.00 0.00 3.07
915 969 7.588512 AGAAAATTCATGAGTTCACTTAGCAC 58.411 34.615 3.69 0.00 0.00 4.40
916 970 5.886960 AATTCATGAGTTCACTTAGCACC 57.113 39.130 0.00 0.00 0.00 5.01
952 1008 7.891220 CGTGTGTTACTTTGATATTCTGTAACG 59.109 37.037 0.00 0.00 43.15 3.18
1236 1292 2.853542 TTGACCCAGCTGAGGCCA 60.854 61.111 17.39 10.74 39.73 5.36
1296 1352 1.334869 GTCCGTGGAATCATTGATGCC 59.665 52.381 15.93 15.93 38.23 4.40
1833 1889 4.940654 GCTGGAATAATCTCATCTAAGGCC 59.059 45.833 0.00 0.00 0.00 5.19
1896 1952 2.095668 CGTAGCGGATGCCTACTCTAAG 60.096 54.545 9.84 0.00 44.31 2.18
1934 1990 1.002201 TGAAACCGCCCTTCGTGATTA 59.998 47.619 0.00 0.00 36.19 1.75
1935 1991 2.285977 GAAACCGCCCTTCGTGATTAT 58.714 47.619 0.00 0.00 36.19 1.28
2091 2147 2.296752 TGAATTGCCAGTTGACCATGTG 59.703 45.455 0.00 0.00 0.00 3.21
2109 2165 2.170397 TGTGGAGAAGAAGCTGTCACAA 59.830 45.455 0.00 0.00 30.71 3.33
2142 2198 6.530120 TGACAAGAAATTTGCTGGTACTCTA 58.470 36.000 0.00 0.00 0.00 2.43
2262 2318 4.021016 GTGGACAGTCTTTACATGAGGTCT 60.021 45.833 0.00 0.00 0.00 3.85
2333 2391 7.957002 TGTTGGCTATGGTTTCATCTTTTAAA 58.043 30.769 0.00 0.00 34.96 1.52
2391 2449 6.060028 GTCAGTTTGACACTTTAATCTGCA 57.940 37.500 4.42 0.00 46.22 4.41
2436 2494 6.396829 AAAATCTACCTTGCTATGATTGGC 57.603 37.500 0.00 0.00 0.00 4.52
2444 2530 1.484653 TGCTATGATTGGCGTGTACCT 59.515 47.619 0.00 0.00 30.65 3.08
2461 2547 6.128634 CGTGTACCTTGAAAACTAGATGGTTC 60.129 42.308 0.00 0.00 0.00 3.62
2550 2646 5.063204 GGCCTGTGTATTGCTGAATATACA 58.937 41.667 0.00 6.32 41.36 2.29
2591 2687 0.321741 TTTCTTTGGCATCGGCGGTA 60.322 50.000 7.21 0.00 42.47 4.02
2618 2714 3.255395 TGTCGAATTTGTGCATGGATTGT 59.745 39.130 0.00 0.00 0.00 2.71
2670 2766 1.445871 CTGCACTGTTGATGCTGCTA 58.554 50.000 0.00 0.00 43.77 3.49
2681 2777 6.741109 TGTTGATGCTGCTATGAATATTTGG 58.259 36.000 0.00 0.00 0.00 3.28
2684 2780 6.301486 TGATGCTGCTATGAATATTTGGACT 58.699 36.000 0.00 0.00 0.00 3.85
2702 2798 7.490962 TTGGACTGATGTTTGTAGTTACAAG 57.509 36.000 5.03 0.00 45.77 3.16
2721 2817 3.064900 AGGCTCCTGTGTGATTTCTTC 57.935 47.619 0.00 0.00 0.00 2.87
2729 2825 2.821378 TGTGTGATTTCTTCATGCCCTG 59.179 45.455 0.00 0.00 36.54 4.45
2795 2891 7.550196 AGAGTTGTAGACGAAACCAAGTTAAAA 59.450 33.333 0.00 0.00 0.00 1.52
2798 2894 5.528320 TGTAGACGAAACCAAGTTAAAAGGG 59.472 40.000 0.00 0.00 0.00 3.95
2799 2895 4.529897 AGACGAAACCAAGTTAAAAGGGT 58.470 39.130 0.00 0.00 34.43 4.34
2800 2896 4.337274 AGACGAAACCAAGTTAAAAGGGTG 59.663 41.667 0.00 0.00 33.00 4.61
2927 3023 6.492772 ACAGTATAGTAAGCCACCAGGTATAC 59.507 42.308 0.00 0.00 37.19 1.47
2935 3031 2.485479 GCCACCAGGTATACACATGAGG 60.485 54.545 5.01 7.01 38.76 3.86
2954 3050 0.886563 GGCTTGTCATCAGCTTGCTT 59.113 50.000 0.00 0.00 0.00 3.91
2965 3061 6.200665 GTCATCAGCTTGCTTATTGTCTAGAG 59.799 42.308 0.00 0.00 0.00 2.43
2969 3065 4.405358 AGCTTGCTTATTGTCTAGAGCTCT 59.595 41.667 22.17 22.17 34.39 4.09
3045 3141 0.822532 TCTTAGGTCTCGGATCCGCC 60.823 60.000 29.62 23.50 39.59 6.13
3188 3284 6.522946 AGTCCTCATGATATGTGAATGTGAG 58.477 40.000 0.00 0.00 33.29 3.51
3248 3344 7.516198 AATCAAGTTCTGCAAAAGATGTAGT 57.484 32.000 0.00 0.00 41.94 2.73
3279 3375 8.675705 TTTCAGTGAATAAGACATTGTCTCAA 57.324 30.769 19.23 11.31 42.59 3.02
3280 3376 7.895975 TCAGTGAATAAGACATTGTCTCAAG 57.104 36.000 19.23 9.52 42.59 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 116 0.944788 GGCTTAGCTAATCGGCGGAC 60.945 60.000 7.21 0.00 37.29 4.79
194 210 2.126071 ACCAACGTCGGCAGATCG 60.126 61.111 0.00 7.13 0.00 3.69
235 252 2.100603 AGAACGCGCTAGCTCGAC 59.899 61.111 31.79 22.87 42.32 4.20
240 257 2.803713 GCTTCCAGAACGCGCTAGC 61.804 63.158 5.73 4.06 40.74 3.42
313 331 3.023116 CCAGAAGGGCATGGGGGA 61.023 66.667 0.00 0.00 32.63 4.81
323 341 1.668419 CGGGATAAACTGCCAGAAGG 58.332 55.000 0.00 0.00 34.29 3.46
324 342 1.668419 CCGGGATAAACTGCCAGAAG 58.332 55.000 0.00 0.00 34.29 2.85
325 343 0.254747 CCCGGGATAAACTGCCAGAA 59.745 55.000 18.48 0.00 34.29 3.02
327 345 1.152963 CCCCGGGATAAACTGCCAG 60.153 63.158 26.32 0.00 34.29 4.85
329 347 1.702022 TAGCCCCGGGATAAACTGCC 61.702 60.000 26.32 0.00 0.00 4.85
330 348 0.250338 CTAGCCCCGGGATAAACTGC 60.250 60.000 26.32 15.55 0.00 4.40
331 349 0.396811 CCTAGCCCCGGGATAAACTG 59.603 60.000 26.32 3.67 0.00 3.16
332 350 0.767060 CCCTAGCCCCGGGATAAACT 60.767 60.000 26.32 13.42 44.90 2.66
333 351 1.058428 ACCCTAGCCCCGGGATAAAC 61.058 60.000 26.32 5.61 44.90 2.01
335 353 0.765519 GAACCCTAGCCCCGGGATAA 60.766 60.000 26.32 5.08 44.90 1.75
342 364 0.914902 ACCAGAAGAACCCTAGCCCC 60.915 60.000 0.00 0.00 0.00 5.80
346 368 2.420687 GCCATGACCAGAAGAACCCTAG 60.421 54.545 0.00 0.00 0.00 3.02
362 389 2.621998 CTCCTGAAGCCTAATTGCCATG 59.378 50.000 0.00 0.00 0.00 3.66
406 433 2.009774 AGAATCGACAATTGCCCTTCG 58.990 47.619 5.05 7.59 0.00 3.79
441 468 1.374252 CTGTGCTACACCGGTGTCC 60.374 63.158 41.97 31.64 43.74 4.02
445 476 2.653953 AAACGCTGTGCTACACCGGT 62.654 55.000 0.00 0.00 32.73 5.28
447 478 1.218875 TGAAACGCTGTGCTACACCG 61.219 55.000 0.00 0.00 32.73 4.94
460 491 5.277601 ACATGAACTAAATCGGTGAAACG 57.722 39.130 0.00 0.00 38.12 3.60
484 515 5.065346 TCAGCTAGACGTATCAGTTTCTCTG 59.935 44.000 0.00 0.00 44.85 3.35
485 516 5.186942 TCAGCTAGACGTATCAGTTTCTCT 58.813 41.667 0.00 0.00 0.00 3.10
486 517 5.487153 TCAGCTAGACGTATCAGTTTCTC 57.513 43.478 0.00 0.00 0.00 2.87
487 518 5.899120 TTCAGCTAGACGTATCAGTTTCT 57.101 39.130 0.00 0.00 0.00 2.52
488 519 6.752351 TCAATTCAGCTAGACGTATCAGTTTC 59.248 38.462 0.00 0.00 0.00 2.78
489 520 6.631016 TCAATTCAGCTAGACGTATCAGTTT 58.369 36.000 0.00 0.00 0.00 2.66
490 521 6.208988 TCAATTCAGCTAGACGTATCAGTT 57.791 37.500 0.00 0.00 0.00 3.16
493 524 5.805486 GTGTTCAATTCAGCTAGACGTATCA 59.195 40.000 0.00 0.00 0.00 2.15
494 525 5.232414 GGTGTTCAATTCAGCTAGACGTATC 59.768 44.000 0.00 0.00 0.00 2.24
496 527 4.021807 TGGTGTTCAATTCAGCTAGACGTA 60.022 41.667 0.00 0.00 34.86 3.57
504 535 5.824904 ACAGATATGGTGTTCAATTCAGC 57.175 39.130 0.00 0.00 0.00 4.26
513 544 7.981225 GGCATAAATCAAAACAGATATGGTGTT 59.019 33.333 0.00 0.00 39.89 3.32
525 556 6.090763 GGTGCTAAGTTGGCATAAATCAAAAC 59.909 38.462 17.47 0.16 41.86 2.43
654 707 3.422796 ACTAGTGTCCTGAGTCATCGTT 58.577 45.455 0.00 0.00 0.00 3.85
665 718 3.240302 ACAAAGTGGCTACTAGTGTCCT 58.760 45.455 1.97 0.00 35.69 3.85
667 720 5.048224 TCAGTACAAAGTGGCTACTAGTGTC 60.048 44.000 18.83 12.46 36.90 3.67
705 758 0.465460 ATGCCAGGAAACACACACGT 60.465 50.000 0.00 0.00 0.00 4.49
721 774 4.144297 ACCCAACATATACCATGACATGC 58.856 43.478 10.10 0.00 0.00 4.06
739 792 1.134068 TGACCACGACAAATGAACCCA 60.134 47.619 0.00 0.00 0.00 4.51
751 804 0.037734 TCTGGAGTAGCTGACCACGA 59.962 55.000 0.00 0.89 0.00 4.35
753 806 3.067461 CACTATCTGGAGTAGCTGACCAC 59.933 52.174 0.00 0.00 0.00 4.16
756 809 6.642707 ATTACACTATCTGGAGTAGCTGAC 57.357 41.667 0.00 0.00 0.00 3.51
808 861 4.202245 AGAGATGCCGTTTACTTTAGCA 57.798 40.909 0.00 0.00 37.94 3.49
828 881 1.732259 GCATGAAACCACGACCACTAG 59.268 52.381 0.00 0.00 0.00 2.57
838 892 1.039068 CAAGGGTGTGCATGAAACCA 58.961 50.000 12.32 0.00 35.56 3.67
901 955 5.065218 CCAATACATGGTGCTAAGTGAACTC 59.935 44.000 0.00 0.00 44.85 3.01
916 970 4.678509 AAGTAACACACGCCAATACATG 57.321 40.909 0.00 0.00 0.00 3.21
952 1008 3.282831 ACAAATGCCAAGTTACGAAGC 57.717 42.857 0.00 0.00 0.00 3.86
1145 1201 4.155280 GGTTGGTAATCGCAAGCTCTTTTA 59.845 41.667 0.00 0.00 37.18 1.52
1212 1268 2.768527 CCTCAGCTGGGTCAAGAGATTA 59.231 50.000 13.79 0.00 0.00 1.75
1236 1292 4.221482 GCCTTGGGAATCAGTGAGAAAAAT 59.779 41.667 0.00 0.00 0.00 1.82
1296 1352 0.391130 TTCCAGGAATCTTGGCGACG 60.391 55.000 6.52 0.00 0.00 5.12
1797 1853 0.250252 TTCCAGCAACATCGTCAGCA 60.250 50.000 0.00 0.00 0.00 4.41
1833 1889 1.407437 GGACCCACATACTTCAGGCTG 60.407 57.143 8.58 8.58 0.00 4.85
1875 1931 1.520494 TAGAGTAGGCATCCGCTACG 58.480 55.000 0.00 0.00 38.60 3.51
1881 1937 5.570320 AGAGATCTCTTAGAGTAGGCATCC 58.430 45.833 19.92 0.24 36.31 3.51
1896 1952 6.309251 CGGTTTCAAAGTACTTGAGAGATCTC 59.691 42.308 15.29 15.29 44.84 2.75
2061 2117 5.011586 TCAACTGGCAATTCAATCATCTGA 58.988 37.500 0.00 0.00 0.00 3.27
2091 2147 4.067896 TCATTTGTGACAGCTTCTTCTCC 58.932 43.478 0.00 0.00 0.00 3.71
2109 2165 6.872020 CAGCAAATTTCTTGTCAAGGATCATT 59.128 34.615 12.66 0.00 0.00 2.57
2142 2198 2.952714 GCAACCAGCACCTTGATCT 58.047 52.632 0.00 0.00 44.79 2.75
2179 2235 3.359950 GGAAGATGGCCTCTGTTTTCAT 58.640 45.455 3.32 0.00 33.29 2.57
2180 2236 2.555227 GGGAAGATGGCCTCTGTTTTCA 60.555 50.000 3.32 0.00 33.29 2.69
2262 2318 1.739466 GTTCAAGCCATGATCTTCGCA 59.261 47.619 0.00 0.00 38.03 5.10
2369 2427 6.691754 TTGCAGATTAAAGTGTCAAACTGA 57.308 33.333 0.00 0.00 39.81 3.41
2418 2476 2.545526 CACGCCAATCATAGCAAGGTAG 59.454 50.000 0.00 0.00 0.00 3.18
2428 2486 2.779755 TCAAGGTACACGCCAATCAT 57.220 45.000 0.00 0.00 0.00 2.45
2429 2487 2.552599 TTCAAGGTACACGCCAATCA 57.447 45.000 0.00 0.00 0.00 2.57
2430 2488 3.252458 AGTTTTCAAGGTACACGCCAATC 59.748 43.478 0.00 0.00 0.00 2.67
2432 2490 2.645802 AGTTTTCAAGGTACACGCCAA 58.354 42.857 0.00 0.00 0.00 4.52
2433 2491 2.335316 AGTTTTCAAGGTACACGCCA 57.665 45.000 0.00 0.00 0.00 5.69
2434 2492 3.656559 TCTAGTTTTCAAGGTACACGCC 58.343 45.455 0.00 0.00 0.00 5.68
2435 2493 4.092968 CCATCTAGTTTTCAAGGTACACGC 59.907 45.833 0.00 0.00 0.00 5.34
2436 2494 5.235516 ACCATCTAGTTTTCAAGGTACACG 58.764 41.667 0.00 0.00 0.00 4.49
2444 2530 8.690203 TTCATCTTGAACCATCTAGTTTTCAA 57.310 30.769 9.10 9.10 36.70 2.69
2461 2547 4.357142 GCAGCATAACATGGTTCATCTTG 58.643 43.478 0.00 0.00 39.29 3.02
2481 2567 0.040514 CACAAAAGAATGTCGCGGCA 60.041 50.000 19.03 19.03 0.00 5.69
2522 2608 2.961741 TCAGCAATACACAGGCCAAAAA 59.038 40.909 5.01 0.00 0.00 1.94
2523 2609 2.591923 TCAGCAATACACAGGCCAAAA 58.408 42.857 5.01 0.00 0.00 2.44
2527 2613 5.063204 TGTATATTCAGCAATACACAGGCC 58.937 41.667 0.00 0.00 34.47 5.19
2550 2646 2.240667 AGCCATACAACCTCTCAGCATT 59.759 45.455 0.00 0.00 0.00 3.56
2591 2687 6.206395 TCCATGCACAAATTCGACATATTT 57.794 33.333 0.00 0.00 0.00 1.40
2618 2714 0.755079 CGCAGATGAGAATCCCAGGA 59.245 55.000 0.00 0.00 0.00 3.86
2656 2752 6.861572 CCAAATATTCATAGCAGCATCAACAG 59.138 38.462 0.00 0.00 0.00 3.16
2670 2766 9.466497 ACTACAAACATCAGTCCAAATATTCAT 57.534 29.630 0.00 0.00 0.00 2.57
2681 2777 5.701290 AGCCTTGTAACTACAAACATCAGTC 59.299 40.000 4.01 0.00 44.67 3.51
2684 2780 5.001232 GGAGCCTTGTAACTACAAACATCA 58.999 41.667 4.01 0.00 44.67 3.07
2702 2798 2.783135 TGAAGAAATCACACAGGAGCC 58.217 47.619 0.00 0.00 31.50 4.70
2729 2825 2.086054 AGACAGAAATCACTGCCGAC 57.914 50.000 0.00 0.00 41.06 4.79
2795 2891 1.729586 TTGGAACTCTAGTGCACCCT 58.270 50.000 14.63 0.00 0.00 4.34
2831 2927 1.140852 CTATGATGCGGGTCCTTTCCA 59.859 52.381 0.00 0.00 0.00 3.53
2884 2980 7.913674 ATACTGTTAGAGGCTTTTTCAGAAG 57.086 36.000 13.16 0.00 0.00 2.85
2927 3023 2.014857 CTGATGACAAGCCCTCATGTG 58.985 52.381 0.00 0.00 0.00 3.21
2935 3031 0.886563 AAGCAAGCTGATGACAAGCC 59.113 50.000 0.00 0.00 0.00 4.35
2954 3050 8.845227 CACTTCTGATAAGAGCTCTAGACAATA 58.155 37.037 18.59 4.71 0.00 1.90
2965 3061 7.095691 GCATAAGATGACACTTCTGATAAGAGC 60.096 40.741 0.00 0.00 0.00 4.09
2969 3065 7.443272 CCATGCATAAGATGACACTTCTGATAA 59.557 37.037 0.00 0.00 0.00 1.75
3045 3141 3.325870 TCAGATAAGTGCCAACGACAAG 58.674 45.455 0.00 0.00 0.00 3.16
3161 3257 6.872547 CACATTCACATATCATGAGGACTAGG 59.127 42.308 0.09 0.00 0.00 3.02
3167 3263 6.764560 TCAACTCACATTCACATATCATGAGG 59.235 38.462 0.09 0.00 37.10 3.86
3188 3284 8.329203 AGAAGTTCTTGTAGGAAATGATCAAC 57.671 34.615 0.00 0.00 0.00 3.18
3248 3344 9.288576 ACAATGTCTTATTCACTGAAAAGATCA 57.711 29.630 14.31 13.79 36.38 2.92


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

AutoCloner maintained by Alex Coulton.