Multiple sequence alignment - TraesCS3A01G531500

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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 TraesCS3A01G531500 chr3A 100.000 2535 0 0 1 2535 744305630 744303096 0.000000e+00 4682
1 TraesCS3A01G531500 chr3A 93.976 2042 85 14 1 2012 744281366 744279333 0.000000e+00 3055
2 TraesCS3A01G531500 chr3A 93.659 410 19 4 2002 2404 744279316 744278907 7.760000e-170 606
3 TraesCS3A01G531500 chr3A 94.853 136 7 0 2400 2535 744270349 744270214 1.980000e-51 213
4 TraesCS3A01G531500 chr3D 89.588 1287 107 17 548 1823 610194906 610193636 0.000000e+00 1609
5 TraesCS3A01G531500 chr3D 89.848 394 32 7 7 398 610197397 610197010 1.350000e-137 499
6 TraesCS3A01G531500 chr3B 84.049 815 85 21 1490 2287 822101826 822101040 0.000000e+00 743
7 TraesCS3A01G531500 chr3B 91.095 539 39 8 686 1217 822102781 822102245 0.000000e+00 721
8 TraesCS3A01G531500 chr3B 92.748 262 18 1 1222 1483 822102214 822101954 6.620000e-101 377


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 TraesCS3A01G531500 chr3A 744303096 744305630 2534 True 4682.000000 4682 100.000000 1 2535 1 chr3A.!!$R2 2534
1 TraesCS3A01G531500 chr3A 744278907 744281366 2459 True 1830.500000 3055 93.817500 1 2404 2 chr3A.!!$R3 2403
2 TraesCS3A01G531500 chr3D 610193636 610197397 3761 True 1054.000000 1609 89.718000 7 1823 2 chr3D.!!$R1 1816
3 TraesCS3A01G531500 chr3B 822101040 822102781 1741 True 613.666667 743 89.297333 686 2287 3 chr3B.!!$R1 1601

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
553 2509 1.203038 TGACATTGCATTGTCCCAGGT 60.203 47.619 29.34 4.41 44.37 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 4592 0.03213 CCCGGTCGTCCATGTATCTG 59.968 60.0 0.0 0.0 0.0 2.9 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
67 68 7.259161 TGTAGTTACCATTTGTTGTTTTGGTC 58.741 34.615 0.00 0.00 41.46 4.02
88 89 1.675483 TGCTGTGAACTCATTTGCGTT 59.325 42.857 0.00 0.00 0.00 4.84
323 326 1.339438 ACCCACTGTGAAGCATGCTAG 60.339 52.381 23.00 17.04 0.00 3.42
495 605 2.757099 GCATGGGCCCAACTCAGG 60.757 66.667 32.58 15.08 0.00 3.86
553 2509 1.203038 TGACATTGCATTGTCCCAGGT 60.203 47.619 29.34 4.41 44.37 4.00
576 2541 2.535166 CCGTGCAAATTGACACAGTTTG 59.465 45.455 16.35 12.85 41.69 2.93
600 2565 4.032960 ACATTGTCTAGCCAAACATGGA 57.967 40.909 0.00 0.00 0.00 3.41
630 2595 5.864474 AGTCAACTCGAGACAACATACAATC 59.136 40.000 21.68 0.00 38.46 2.67
644 2609 9.502091 ACAACATACAATCTTAGTTTTAGCTGA 57.498 29.630 0.00 0.00 0.00 4.26
701 2667 9.693157 GTTTTGTTGAAGTCAATTGAATTTCAG 57.307 29.630 20.94 0.00 38.24 3.02
776 2745 3.940209 TTTTGATCAATGTCACCAGCC 57.060 42.857 9.40 0.00 0.00 4.85
783 2752 2.100584 TCAATGTCACCAGCCACAAAAC 59.899 45.455 0.00 0.00 0.00 2.43
797 2766 4.795962 GCCACAAAACGATGACTCCATTTT 60.796 41.667 0.00 0.00 32.09 1.82
948 2922 6.459923 GTGTGACTCACCTCTATCTCTTTTT 58.540 40.000 6.72 0.00 40.84 1.94
1044 3018 5.355350 AGCACTCCAAGACATAAACATTAGC 59.645 40.000 0.00 0.00 0.00 3.09
1091 3065 7.807680 ACGAAGAGAACACATATTTTTCCTTC 58.192 34.615 0.00 0.00 0.00 3.46
1294 3298 2.923020 GTTTTGTTGGTGTTGTGCAGAG 59.077 45.455 0.00 0.00 0.00 3.35
1426 3431 2.414481 CTGTGAGAAGAAGAACGCCATG 59.586 50.000 0.00 0.00 0.00 3.66
1793 3921 4.540099 AGGGATTGGACTAGATTGGTTTCA 59.460 41.667 0.00 0.00 0.00 2.69
1797 3925 6.603201 GGATTGGACTAGATTGGTTTCATCAA 59.397 38.462 0.00 0.00 0.00 2.57
1895 4023 6.663734 TCTGGTTCATCTCATACTCTACTCA 58.336 40.000 0.00 0.00 0.00 3.41
1903 4031 8.821817 TCATCTCATACTCTACTCATAGTAGCT 58.178 37.037 8.87 0.00 45.93 3.32
1963 4107 2.755103 GGATTGGATTGTCAGTTGACCC 59.245 50.000 9.60 4.77 44.15 4.46
1996 4140 1.135315 CAATCTTGGGTGGCAATCACG 60.135 52.381 0.00 0.00 46.96 4.35
2035 4206 7.148069 GGATATATAATGCACTTACTTTGGCCC 60.148 40.741 0.00 0.00 0.00 5.80
2065 4236 7.234988 TCAAACTCTACTCCTAGTAGCCTTTTT 59.765 37.037 8.87 3.83 45.93 1.94
2130 4301 9.049523 CAACTGTAAGCATCATTCATATGTAGT 57.950 33.333 1.90 0.00 37.60 2.73
2174 4345 3.066291 ACAATTCGGTGCATAGGAACA 57.934 42.857 0.00 0.00 0.00 3.18
2239 4414 7.012607 TCTTTCTTTCTTTGGATCAAGGGAAT 58.987 34.615 0.00 0.00 0.00 3.01
2250 4425 4.442472 GGATCAAGGGAATGCCAATTTCAG 60.442 45.833 0.00 0.00 35.15 3.02
2280 4456 2.291209 TGGGTACACCACTCTCGTTA 57.709 50.000 0.00 0.00 46.80 3.18
2339 4518 3.431626 CGTGATGTGAATACAAGGGGCTA 60.432 47.826 0.00 0.00 40.84 3.93
2369 4548 4.082733 CGTCATACTATGTCGGATGATGGT 60.083 45.833 7.55 0.00 37.98 3.55
2404 4583 8.296211 AGTAAGATAAAGTGGAGGAGTCTAAC 57.704 38.462 0.00 0.00 0.00 2.34
2405 4584 7.894364 AGTAAGATAAAGTGGAGGAGTCTAACA 59.106 37.037 0.00 0.00 0.00 2.41
2406 4585 6.532988 AGATAAAGTGGAGGAGTCTAACAC 57.467 41.667 0.00 0.00 33.66 3.32
2407 4586 6.257586 AGATAAAGTGGAGGAGTCTAACACT 58.742 40.000 7.88 7.88 40.65 3.55
2408 4587 6.726764 AGATAAAGTGGAGGAGTCTAACACTT 59.273 38.462 15.95 15.95 45.23 3.16
2409 4588 4.875561 AAGTGGAGGAGTCTAACACTTC 57.124 45.455 15.95 0.00 42.49 3.01
2410 4589 4.120946 AGTGGAGGAGTCTAACACTTCT 57.879 45.455 7.88 0.00 44.79 2.85
2411 4590 3.829601 AGTGGAGGAGTCTAACACTTCTG 59.170 47.826 7.88 0.00 41.71 3.02
2412 4591 3.827302 GTGGAGGAGTCTAACACTTCTGA 59.173 47.826 0.00 0.00 41.71 3.27
2413 4592 3.827302 TGGAGGAGTCTAACACTTCTGAC 59.173 47.826 0.00 0.00 41.71 3.51
2414 4593 3.827302 GGAGGAGTCTAACACTTCTGACA 59.173 47.826 0.00 0.00 41.71 3.58
2415 4594 4.082463 GGAGGAGTCTAACACTTCTGACAG 60.082 50.000 0.00 0.00 41.71 3.51
2416 4595 4.730966 AGGAGTCTAACACTTCTGACAGA 58.269 43.478 0.00 0.00 39.87 3.41
2417 4596 5.329399 AGGAGTCTAACACTTCTGACAGAT 58.671 41.667 5.87 0.00 39.87 2.90
2418 4597 6.486056 AGGAGTCTAACACTTCTGACAGATA 58.514 40.000 5.87 0.00 39.87 1.98
2419 4598 6.376018 AGGAGTCTAACACTTCTGACAGATAC 59.624 42.308 5.87 0.00 39.87 2.24
2420 4599 6.151312 GGAGTCTAACACTTCTGACAGATACA 59.849 42.308 5.87 0.00 34.41 2.29
2421 4600 7.147983 GGAGTCTAACACTTCTGACAGATACAT 60.148 40.741 5.87 0.00 34.41 2.29
2422 4601 7.542890 AGTCTAACACTTCTGACAGATACATG 58.457 38.462 5.87 5.27 32.41 3.21
2423 4602 6.754209 GTCTAACACTTCTGACAGATACATGG 59.246 42.308 5.87 0.00 0.00 3.66
2424 4603 5.745312 AACACTTCTGACAGATACATGGA 57.255 39.130 5.87 0.00 0.00 3.41
2425 4604 5.078411 ACACTTCTGACAGATACATGGAC 57.922 43.478 5.87 0.00 0.00 4.02
2426 4605 4.108336 CACTTCTGACAGATACATGGACG 58.892 47.826 5.87 0.00 0.00 4.79
2427 4606 4.017126 ACTTCTGACAGATACATGGACGA 58.983 43.478 5.87 0.00 0.00 4.20
2428 4607 4.142359 ACTTCTGACAGATACATGGACGAC 60.142 45.833 5.87 0.00 0.00 4.34
2429 4608 2.688446 TCTGACAGATACATGGACGACC 59.312 50.000 0.00 0.00 0.00 4.79
2430 4609 1.404035 TGACAGATACATGGACGACCG 59.596 52.381 0.00 0.00 39.42 4.79
2431 4610 0.744874 ACAGATACATGGACGACCGG 59.255 55.000 0.00 0.00 39.42 5.28
2432 4611 0.032130 CAGATACATGGACGACCGGG 59.968 60.000 6.32 0.00 39.42 5.73
2433 4612 1.113517 AGATACATGGACGACCGGGG 61.114 60.000 6.32 0.00 39.42 5.73
2434 4613 1.382146 ATACATGGACGACCGGGGT 60.382 57.895 6.32 2.45 39.42 4.95
2435 4614 0.106066 ATACATGGACGACCGGGGTA 60.106 55.000 6.32 2.35 39.42 3.69
2436 4615 0.752743 TACATGGACGACCGGGGTAG 60.753 60.000 6.32 0.00 39.42 3.18
2437 4616 2.056223 CATGGACGACCGGGGTAGT 61.056 63.158 6.32 3.11 39.42 2.73
2438 4617 2.056223 ATGGACGACCGGGGTAGTG 61.056 63.158 6.32 0.00 39.42 2.74
2439 4618 3.455469 GGACGACCGGGGTAGTGG 61.455 72.222 6.32 0.00 34.26 4.00
2440 4619 2.361610 GACGACCGGGGTAGTGGA 60.362 66.667 6.32 0.00 34.26 4.02
2441 4620 1.755783 GACGACCGGGGTAGTGGAT 60.756 63.158 6.32 0.00 34.26 3.41
2442 4621 1.305549 ACGACCGGGGTAGTGGATT 60.306 57.895 6.32 0.00 32.94 3.01
2443 4622 0.033208 ACGACCGGGGTAGTGGATTA 60.033 55.000 6.32 0.00 32.94 1.75
2444 4623 0.672342 CGACCGGGGTAGTGGATTAG 59.328 60.000 6.32 0.00 0.00 1.73
2445 4624 1.046204 GACCGGGGTAGTGGATTAGG 58.954 60.000 6.32 0.00 0.00 2.69
2446 4625 0.399519 ACCGGGGTAGTGGATTAGGG 60.400 60.000 6.32 0.00 0.00 3.53
2447 4626 0.399519 CCGGGGTAGTGGATTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
2448 4627 1.503800 CGGGGTAGTGGATTAGGGTT 58.496 55.000 0.00 0.00 0.00 4.11
2449 4628 1.140252 CGGGGTAGTGGATTAGGGTTG 59.860 57.143 0.00 0.00 0.00 3.77
2450 4629 1.493446 GGGGTAGTGGATTAGGGTTGG 59.507 57.143 0.00 0.00 0.00 3.77
2451 4630 1.493446 GGGTAGTGGATTAGGGTTGGG 59.507 57.143 0.00 0.00 0.00 4.12
2452 4631 2.484602 GGTAGTGGATTAGGGTTGGGA 58.515 52.381 0.00 0.00 0.00 4.37
2453 4632 2.848071 GGTAGTGGATTAGGGTTGGGAA 59.152 50.000 0.00 0.00 0.00 3.97
2454 4633 3.118000 GGTAGTGGATTAGGGTTGGGAAG 60.118 52.174 0.00 0.00 0.00 3.46
2455 4634 1.923148 AGTGGATTAGGGTTGGGAAGG 59.077 52.381 0.00 0.00 0.00 3.46
2456 4635 1.920351 GTGGATTAGGGTTGGGAAGGA 59.080 52.381 0.00 0.00 0.00 3.36
2457 4636 2.514160 GTGGATTAGGGTTGGGAAGGAT 59.486 50.000 0.00 0.00 0.00 3.24
2458 4637 3.720002 GTGGATTAGGGTTGGGAAGGATA 59.280 47.826 0.00 0.00 0.00 2.59
2459 4638 3.720002 TGGATTAGGGTTGGGAAGGATAC 59.280 47.826 0.00 0.00 0.00 2.24
2460 4639 3.244457 GGATTAGGGTTGGGAAGGATACG 60.244 52.174 0.00 0.00 46.39 3.06
2461 4640 2.852714 TAGGGTTGGGAAGGATACGA 57.147 50.000 0.00 0.00 46.39 3.43
2462 4641 1.961133 AGGGTTGGGAAGGATACGAA 58.039 50.000 0.00 0.00 46.39 3.85
2463 4642 2.488836 AGGGTTGGGAAGGATACGAAT 58.511 47.619 0.00 0.00 46.39 3.34
2464 4643 3.660959 AGGGTTGGGAAGGATACGAATA 58.339 45.455 0.00 0.00 46.39 1.75
2465 4644 3.390311 AGGGTTGGGAAGGATACGAATAC 59.610 47.826 0.00 0.00 46.39 1.89
2466 4645 3.495629 GGGTTGGGAAGGATACGAATACC 60.496 52.174 0.00 0.00 46.39 2.73
2467 4646 3.390311 GGTTGGGAAGGATACGAATACCT 59.610 47.826 0.00 0.00 46.39 3.08
2468 4647 4.502777 GGTTGGGAAGGATACGAATACCTC 60.503 50.000 0.00 0.00 46.39 3.85
2469 4648 3.236896 TGGGAAGGATACGAATACCTCC 58.763 50.000 0.00 0.00 46.39 4.30
2470 4649 3.236896 GGGAAGGATACGAATACCTCCA 58.763 50.000 0.00 0.00 46.39 3.86
2471 4650 3.644738 GGGAAGGATACGAATACCTCCAA 59.355 47.826 0.00 0.00 46.39 3.53
2472 4651 4.102054 GGGAAGGATACGAATACCTCCAAA 59.898 45.833 0.00 0.00 46.39 3.28
2473 4652 5.055144 GGAAGGATACGAATACCTCCAAAC 58.945 45.833 0.00 0.00 46.39 2.93
2474 4653 5.395990 GGAAGGATACGAATACCTCCAAACA 60.396 44.000 0.00 0.00 46.39 2.83
2475 4654 5.687166 AGGATACGAATACCTCCAAACAA 57.313 39.130 0.00 0.00 46.39 2.83
2476 4655 5.671493 AGGATACGAATACCTCCAAACAAG 58.329 41.667 0.00 0.00 46.39 3.16
2477 4656 5.189145 AGGATACGAATACCTCCAAACAAGT 59.811 40.000 0.00 0.00 46.39 3.16
2478 4657 5.522824 GGATACGAATACCTCCAAACAAGTC 59.477 44.000 0.00 0.00 0.00 3.01
2479 4658 3.323243 ACGAATACCTCCAAACAAGTCG 58.677 45.455 0.00 0.00 0.00 4.18
2480 4659 2.093783 CGAATACCTCCAAACAAGTCGC 59.906 50.000 0.00 0.00 0.00 5.19
2481 4660 2.851263 ATACCTCCAAACAAGTCGCA 57.149 45.000 0.00 0.00 0.00 5.10
2482 4661 1.873698 TACCTCCAAACAAGTCGCAC 58.126 50.000 0.00 0.00 0.00 5.34
2483 4662 0.180406 ACCTCCAAACAAGTCGCACT 59.820 50.000 0.00 0.00 0.00 4.40
2484 4663 1.414919 ACCTCCAAACAAGTCGCACTA 59.585 47.619 0.00 0.00 0.00 2.74
2485 4664 2.069273 CCTCCAAACAAGTCGCACTAG 58.931 52.381 0.00 0.00 0.00 2.57
2486 4665 1.461127 CTCCAAACAAGTCGCACTAGC 59.539 52.381 0.00 0.00 37.42 3.42
2487 4666 0.517316 CCAAACAAGTCGCACTAGCC 59.483 55.000 0.00 0.00 37.52 3.93
2488 4667 0.163788 CAAACAAGTCGCACTAGCCG 59.836 55.000 0.00 0.00 37.52 5.52
2489 4668 1.566018 AAACAAGTCGCACTAGCCGC 61.566 55.000 0.00 0.00 37.52 6.53
2490 4669 3.188786 CAAGTCGCACTAGCCGCC 61.189 66.667 0.00 0.00 37.52 6.13
2491 4670 3.691342 AAGTCGCACTAGCCGCCA 61.691 61.111 0.00 0.00 37.52 5.69
2492 4671 3.019003 AAGTCGCACTAGCCGCCAT 62.019 57.895 0.00 0.00 37.52 4.40
2493 4672 3.264897 GTCGCACTAGCCGCCATG 61.265 66.667 0.00 0.00 37.52 3.66
2494 4673 4.529219 TCGCACTAGCCGCCATGG 62.529 66.667 7.63 7.63 42.50 3.66
2502 4681 3.827634 GCCGCCATGGGTTTCTAG 58.172 61.111 15.13 0.00 38.63 2.43
2503 4682 1.223487 GCCGCCATGGGTTTCTAGA 59.777 57.895 15.13 0.00 38.63 2.43
2504 4683 0.815615 GCCGCCATGGGTTTCTAGAG 60.816 60.000 15.13 0.00 38.63 2.43
2505 4684 0.815615 CCGCCATGGGTTTCTAGAGC 60.816 60.000 15.13 0.00 0.00 4.09
2506 4685 1.154205 CGCCATGGGTTTCTAGAGCG 61.154 60.000 15.13 2.33 36.06 5.03
2507 4686 1.440145 GCCATGGGTTTCTAGAGCGC 61.440 60.000 15.13 0.00 0.00 5.92
2508 4687 0.179000 CCATGGGTTTCTAGAGCGCT 59.821 55.000 11.27 11.27 0.00 5.92
2509 4688 1.576356 CATGGGTTTCTAGAGCGCTC 58.424 55.000 30.01 30.01 0.00 5.03
2510 4689 0.103208 ATGGGTTTCTAGAGCGCTCG 59.897 55.000 30.39 18.17 34.09 5.03
2511 4690 1.248785 TGGGTTTCTAGAGCGCTCGT 61.249 55.000 30.39 20.74 34.09 4.18
2512 4691 0.108756 GGGTTTCTAGAGCGCTCGTT 60.109 55.000 30.39 17.64 34.09 3.85
2513 4692 1.133790 GGGTTTCTAGAGCGCTCGTTA 59.866 52.381 30.39 17.83 34.09 3.18
2514 4693 2.223758 GGGTTTCTAGAGCGCTCGTTAT 60.224 50.000 30.39 16.51 34.09 1.89
2515 4694 3.004106 GGGTTTCTAGAGCGCTCGTTATA 59.996 47.826 30.39 16.76 34.09 0.98
2516 4695 4.321082 GGGTTTCTAGAGCGCTCGTTATAT 60.321 45.833 30.39 15.37 34.09 0.86
2517 4696 5.221130 GGTTTCTAGAGCGCTCGTTATATT 58.779 41.667 30.39 14.63 34.09 1.28
2518 4697 5.690857 GGTTTCTAGAGCGCTCGTTATATTT 59.309 40.000 30.39 13.88 34.09 1.40
2519 4698 6.200475 GGTTTCTAGAGCGCTCGTTATATTTT 59.800 38.462 30.39 13.14 34.09 1.82
2520 4699 7.254353 GGTTTCTAGAGCGCTCGTTATATTTTT 60.254 37.037 30.39 12.40 34.09 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.441410 TCACAGCAGACCAAAACAACA 58.559 42.857 0.00 0.00 0.00 3.33
67 68 1.265095 ACGCAAATGAGTTCACAGCAG 59.735 47.619 0.00 0.00 0.00 4.24
129 130 8.803799 CAACATTTGTGTTAGGACTTACAAAAC 58.196 33.333 0.00 0.00 43.59 2.43
158 159 6.494893 AACTAACGTATGCAACAATGTGAT 57.505 33.333 0.00 0.00 0.00 3.06
161 162 6.554334 AGAAACTAACGTATGCAACAATGT 57.446 33.333 0.00 0.00 0.00 2.71
323 326 8.604035 CAATATTATATAGACCCATCGCAACAC 58.396 37.037 0.00 0.00 0.00 3.32
432 542 9.316594 TCCACCTCGAAATCTATACCAATATAA 57.683 33.333 0.00 0.00 0.00 0.98
440 550 3.306818 GCGTCCACCTCGAAATCTATAC 58.693 50.000 0.00 0.00 0.00 1.47
467 577 2.757099 CCCATGCCTCTTGCCACC 60.757 66.667 0.00 0.00 40.16 4.61
468 578 3.455469 GCCCATGCCTCTTGCCAC 61.455 66.667 0.00 0.00 40.16 5.01
495 605 4.584327 AAACCACCACAAGATAAGCAAC 57.416 40.909 0.00 0.00 0.00 4.17
553 2509 0.030504 CTGTGTCAATTTGCACGGCA 59.969 50.000 15.14 0.00 38.36 5.69
576 2541 5.048083 TCCATGTTTGGCTAGACAATGTTTC 60.048 40.000 12.92 1.85 43.29 2.78
600 2565 6.085555 TGTTGTCTCGAGTTGACTAAATCT 57.914 37.500 13.13 0.00 35.63 2.40
714 2680 5.627499 TGTCTAGCCACTTTAATTGCAAG 57.373 39.130 4.94 0.00 0.00 4.01
747 2714 8.396390 TGGTGACATTGATCAAAAATGTTTTTG 58.604 29.630 19.71 19.71 45.81 2.44
756 2725 3.005684 GTGGCTGGTGACATTGATCAAAA 59.994 43.478 13.09 0.00 41.51 2.44
797 2766 9.421806 CTACAAAATAAGCATGACCATTCAAAA 57.578 29.630 0.00 0.00 34.61 2.44
1044 3018 6.488683 TCGTCTATTTTAATTTGGCTATGGGG 59.511 38.462 0.00 0.00 0.00 4.96
1264 3268 3.920446 ACACCAACAAAACAGAAACCAC 58.080 40.909 0.00 0.00 0.00 4.16
1271 3275 2.667481 CTGCACAACACCAACAAAACAG 59.333 45.455 0.00 0.00 0.00 3.16
1278 3282 3.374745 CAATTCTCTGCACAACACCAAC 58.625 45.455 0.00 0.00 0.00 3.77
1294 3298 1.509162 GTCAACGACCGCGCAATTC 60.509 57.895 8.75 0.00 42.48 2.17
1566 3692 5.404466 TCCACATGGCTTCCAAATAAAAG 57.596 39.130 0.00 0.00 36.95 2.27
1921 4065 8.597167 CAATCCCTGGTGTTCTATTATATCTCA 58.403 37.037 0.00 0.00 0.00 3.27
1924 4068 7.918076 TCCAATCCCTGGTGTTCTATTATATC 58.082 38.462 0.00 0.00 46.51 1.63
1963 4107 3.181497 CCCAAGATTGCAATAGAACACCG 60.181 47.826 12.97 0.00 0.00 4.94
2029 4200 2.375174 AGTAGAGTTTGACATGGGCCAA 59.625 45.455 11.89 0.00 0.00 4.52
2031 4202 2.633488 GAGTAGAGTTTGACATGGGCC 58.367 52.381 0.00 0.00 0.00 5.80
2130 4301 9.999660 TGTACACAACCAATAGTTTCTACATTA 57.000 29.630 0.00 0.00 36.18 1.90
2174 4345 2.452064 CCCCACACACACCTCCAGT 61.452 63.158 0.00 0.00 0.00 4.00
2219 4394 4.382362 GGCATTCCCTTGATCCAAAGAAAG 60.382 45.833 0.00 0.00 0.00 2.62
2239 4414 1.890573 GCACCCCTACTGAAATTGGCA 60.891 52.381 0.00 0.00 0.00 4.92
2250 4425 0.035725 GTGTACCCAAGCACCCCTAC 60.036 60.000 0.00 0.00 0.00 3.18
2305 4484 0.306533 ACATCACGCGGTGTTCAAAC 59.693 50.000 12.47 0.00 34.79 2.93
2317 4496 1.670811 GCCCCTTGTATTCACATCACG 59.329 52.381 0.00 0.00 33.76 4.35
2369 4548 8.603898 TCCACTTTATCTTACTCCTCACATTA 57.396 34.615 0.00 0.00 0.00 1.90
2404 4583 4.108336 CGTCCATGTATCTGTCAGAAGTG 58.892 47.826 6.64 3.77 0.00 3.16
2405 4584 4.017126 TCGTCCATGTATCTGTCAGAAGT 58.983 43.478 6.64 0.00 0.00 3.01
2406 4585 4.355437 GTCGTCCATGTATCTGTCAGAAG 58.645 47.826 6.64 0.00 0.00 2.85
2407 4586 3.130516 GGTCGTCCATGTATCTGTCAGAA 59.869 47.826 6.64 0.00 0.00 3.02
2408 4587 2.688446 GGTCGTCCATGTATCTGTCAGA 59.312 50.000 4.68 4.68 0.00 3.27
2409 4588 2.541794 CGGTCGTCCATGTATCTGTCAG 60.542 54.545 0.00 0.00 0.00 3.51
2410 4589 1.404035 CGGTCGTCCATGTATCTGTCA 59.596 52.381 0.00 0.00 0.00 3.58
2411 4590 1.269102 CCGGTCGTCCATGTATCTGTC 60.269 57.143 0.00 0.00 0.00 3.51
2412 4591 0.744874 CCGGTCGTCCATGTATCTGT 59.255 55.000 0.00 0.00 0.00 3.41
2413 4592 0.032130 CCCGGTCGTCCATGTATCTG 59.968 60.000 0.00 0.00 0.00 2.90
2414 4593 1.113517 CCCCGGTCGTCCATGTATCT 61.114 60.000 0.00 0.00 0.00 1.98
2415 4594 1.366366 CCCCGGTCGTCCATGTATC 59.634 63.158 0.00 0.00 0.00 2.24
2416 4595 0.106066 TACCCCGGTCGTCCATGTAT 60.106 55.000 0.00 0.00 0.00 2.29
2417 4596 0.752743 CTACCCCGGTCGTCCATGTA 60.753 60.000 0.00 0.00 0.00 2.29
2418 4597 2.037687 TACCCCGGTCGTCCATGT 59.962 61.111 0.00 0.00 0.00 3.21
2419 4598 2.056223 ACTACCCCGGTCGTCCATG 61.056 63.158 0.00 0.00 0.00 3.66
2420 4599 2.056223 CACTACCCCGGTCGTCCAT 61.056 63.158 0.00 0.00 0.00 3.41
2421 4600 2.677524 CACTACCCCGGTCGTCCA 60.678 66.667 0.00 0.00 0.00 4.02
2422 4601 3.455469 CCACTACCCCGGTCGTCC 61.455 72.222 0.00 0.00 0.00 4.79
2423 4602 1.325476 AATCCACTACCCCGGTCGTC 61.325 60.000 0.00 0.00 0.00 4.20
2424 4603 0.033208 TAATCCACTACCCCGGTCGT 60.033 55.000 0.00 0.00 0.00 4.34
2425 4604 0.672342 CTAATCCACTACCCCGGTCG 59.328 60.000 0.00 0.00 0.00 4.79
2426 4605 1.046204 CCTAATCCACTACCCCGGTC 58.954 60.000 0.00 0.00 0.00 4.79
2427 4606 0.399519 CCCTAATCCACTACCCCGGT 60.400 60.000 0.00 0.00 0.00 5.28
2428 4607 0.399519 ACCCTAATCCACTACCCCGG 60.400 60.000 0.00 0.00 0.00 5.73
2429 4608 1.140252 CAACCCTAATCCACTACCCCG 59.860 57.143 0.00 0.00 0.00 5.73
2430 4609 1.493446 CCAACCCTAATCCACTACCCC 59.507 57.143 0.00 0.00 0.00 4.95
2431 4610 1.493446 CCCAACCCTAATCCACTACCC 59.507 57.143 0.00 0.00 0.00 3.69
2432 4611 2.484602 TCCCAACCCTAATCCACTACC 58.515 52.381 0.00 0.00 0.00 3.18
2433 4612 3.118000 CCTTCCCAACCCTAATCCACTAC 60.118 52.174 0.00 0.00 0.00 2.73
2434 4613 3.120108 CCTTCCCAACCCTAATCCACTA 58.880 50.000 0.00 0.00 0.00 2.74
2435 4614 1.923148 CCTTCCCAACCCTAATCCACT 59.077 52.381 0.00 0.00 0.00 4.00
2436 4615 1.920351 TCCTTCCCAACCCTAATCCAC 59.080 52.381 0.00 0.00 0.00 4.02
2437 4616 2.369668 TCCTTCCCAACCCTAATCCA 57.630 50.000 0.00 0.00 0.00 3.41
2438 4617 3.244457 CGTATCCTTCCCAACCCTAATCC 60.244 52.174 0.00 0.00 0.00 3.01
2439 4618 3.644738 TCGTATCCTTCCCAACCCTAATC 59.355 47.826 0.00 0.00 0.00 1.75
2440 4619 3.660959 TCGTATCCTTCCCAACCCTAAT 58.339 45.455 0.00 0.00 0.00 1.73
2441 4620 3.119009 TCGTATCCTTCCCAACCCTAA 57.881 47.619 0.00 0.00 0.00 2.69
2442 4621 2.852714 TCGTATCCTTCCCAACCCTA 57.147 50.000 0.00 0.00 0.00 3.53
2443 4622 1.961133 TTCGTATCCTTCCCAACCCT 58.039 50.000 0.00 0.00 0.00 4.34
2444 4623 3.495629 GGTATTCGTATCCTTCCCAACCC 60.496 52.174 0.00 0.00 0.00 4.11
2445 4624 3.390311 AGGTATTCGTATCCTTCCCAACC 59.610 47.826 0.00 0.00 0.00 3.77
2446 4625 4.502777 GGAGGTATTCGTATCCTTCCCAAC 60.503 50.000 0.00 0.00 0.00 3.77
2447 4626 3.644738 GGAGGTATTCGTATCCTTCCCAA 59.355 47.826 0.00 0.00 0.00 4.12
2448 4627 3.236896 GGAGGTATTCGTATCCTTCCCA 58.763 50.000 0.00 0.00 0.00 4.37
2449 4628 3.236896 TGGAGGTATTCGTATCCTTCCC 58.763 50.000 0.00 0.00 32.79 3.97
2450 4629 4.950205 TTGGAGGTATTCGTATCCTTCC 57.050 45.455 0.00 0.00 32.79 3.46
2451 4630 5.667466 TGTTTGGAGGTATTCGTATCCTTC 58.333 41.667 0.00 0.00 32.79 3.46
2452 4631 5.687166 TGTTTGGAGGTATTCGTATCCTT 57.313 39.130 0.00 0.00 32.79 3.36
2453 4632 5.189145 ACTTGTTTGGAGGTATTCGTATCCT 59.811 40.000 0.00 0.00 32.79 3.24
2454 4633 5.425630 ACTTGTTTGGAGGTATTCGTATCC 58.574 41.667 0.00 0.00 0.00 2.59
2455 4634 5.231568 CGACTTGTTTGGAGGTATTCGTATC 59.768 44.000 0.00 0.00 0.00 2.24
2456 4635 5.107133 CGACTTGTTTGGAGGTATTCGTAT 58.893 41.667 0.00 0.00 0.00 3.06
2457 4636 4.487948 CGACTTGTTTGGAGGTATTCGTA 58.512 43.478 0.00 0.00 0.00 3.43
2458 4637 3.323243 CGACTTGTTTGGAGGTATTCGT 58.677 45.455 0.00 0.00 0.00 3.85
2459 4638 2.093783 GCGACTTGTTTGGAGGTATTCG 59.906 50.000 0.00 0.00 0.00 3.34
2460 4639 3.071479 TGCGACTTGTTTGGAGGTATTC 58.929 45.455 0.00 0.00 0.00 1.75
2461 4640 2.812011 GTGCGACTTGTTTGGAGGTATT 59.188 45.455 0.00 0.00 0.00 1.89
2462 4641 2.038557 AGTGCGACTTGTTTGGAGGTAT 59.961 45.455 0.00 0.00 0.00 2.73
2463 4642 1.414919 AGTGCGACTTGTTTGGAGGTA 59.585 47.619 0.00 0.00 0.00 3.08
2464 4643 0.180406 AGTGCGACTTGTTTGGAGGT 59.820 50.000 0.00 0.00 0.00 3.85
2465 4644 2.069273 CTAGTGCGACTTGTTTGGAGG 58.931 52.381 0.00 0.00 0.00 4.30
2466 4645 1.461127 GCTAGTGCGACTTGTTTGGAG 59.539 52.381 0.00 0.00 0.00 3.86
2467 4646 1.508632 GCTAGTGCGACTTGTTTGGA 58.491 50.000 0.00 0.00 0.00 3.53
2468 4647 0.517316 GGCTAGTGCGACTTGTTTGG 59.483 55.000 0.00 0.00 40.82 3.28
2469 4648 0.163788 CGGCTAGTGCGACTTGTTTG 59.836 55.000 0.00 0.00 40.82 2.93
2470 4649 1.566018 GCGGCTAGTGCGACTTGTTT 61.566 55.000 0.00 0.00 40.82 2.83
2471 4650 2.027625 GCGGCTAGTGCGACTTGTT 61.028 57.895 0.00 0.00 40.82 2.83
2472 4651 2.432628 GCGGCTAGTGCGACTTGT 60.433 61.111 0.00 0.00 40.82 3.16
2473 4652 3.188786 GGCGGCTAGTGCGACTTG 61.189 66.667 0.00 0.00 40.82 3.16
2474 4653 3.019003 ATGGCGGCTAGTGCGACTT 62.019 57.895 11.43 0.00 40.82 3.01
2475 4654 3.461773 ATGGCGGCTAGTGCGACT 61.462 61.111 11.43 0.00 40.82 4.18
2476 4655 3.264897 CATGGCGGCTAGTGCGAC 61.265 66.667 11.43 0.00 40.82 5.19
2477 4656 4.529219 CCATGGCGGCTAGTGCGA 62.529 66.667 11.43 0.42 40.82 5.10
2479 4658 3.995506 AACCCATGGCGGCTAGTGC 62.996 63.158 11.43 0.97 38.76 4.40
2480 4659 1.376609 GAAACCCATGGCGGCTAGTG 61.377 60.000 11.43 6.57 0.00 2.74
2481 4660 1.077716 GAAACCCATGGCGGCTAGT 60.078 57.895 11.43 0.00 0.00 2.57
2482 4661 0.468226 TAGAAACCCATGGCGGCTAG 59.532 55.000 11.43 1.99 0.00 3.42
2483 4662 0.468226 CTAGAAACCCATGGCGGCTA 59.532 55.000 11.43 4.11 0.00 3.93
2484 4663 1.224592 CTAGAAACCCATGGCGGCT 59.775 57.895 11.43 3.05 0.00 5.52
2485 4664 0.815615 CTCTAGAAACCCATGGCGGC 60.816 60.000 6.09 0.00 0.00 6.53
2486 4665 0.815615 GCTCTAGAAACCCATGGCGG 60.816 60.000 6.09 0.00 0.00 6.13
2487 4666 1.154205 CGCTCTAGAAACCCATGGCG 61.154 60.000 6.09 2.02 35.75 5.69
2488 4667 1.440145 GCGCTCTAGAAACCCATGGC 61.440 60.000 6.09 0.00 0.00 4.40
2489 4668 0.179000 AGCGCTCTAGAAACCCATGG 59.821 55.000 2.64 4.14 0.00 3.66
2490 4669 1.576356 GAGCGCTCTAGAAACCCATG 58.424 55.000 29.88 0.00 0.00 3.66
2491 4670 0.103208 CGAGCGCTCTAGAAACCCAT 59.897 55.000 32.88 0.00 0.00 4.00
2492 4671 1.248785 ACGAGCGCTCTAGAAACCCA 61.249 55.000 32.88 0.00 0.00 4.51
2493 4672 0.108756 AACGAGCGCTCTAGAAACCC 60.109 55.000 32.88 6.36 0.00 4.11
2494 4673 2.556534 TAACGAGCGCTCTAGAAACC 57.443 50.000 32.88 7.14 0.00 3.27
2495 4674 6.750775 AAATATAACGAGCGCTCTAGAAAC 57.249 37.500 32.88 7.93 0.00 2.78
2496 4675 7.766219 AAAAATATAACGAGCGCTCTAGAAA 57.234 32.000 32.88 16.98 0.00 2.52


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

AutoCloner maintained by Alex Coulton.