Multiple sequence alignment - TraesCS3B01G016800

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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 TraesCS3B01G016800 chr3B 100.000 3275 0 0 1 3275 6956005 6959279 0.000000e+00 6048.0
1 TraesCS3B01G016800 chr3B 88.159 1385 137 10 921 2279 6966906 6968289 0.000000e+00 1624.0
2 TraesCS3B01G016800 chr3B 86.441 59 7 1 267 325 6965768 6965825 2.730000e-06 63.9
3 TraesCS3B01G016800 chr3D 96.802 1501 46 1 794 2292 6456290 6454790 0.000000e+00 2505.0
4 TraesCS3B01G016800 chr3D 89.508 1382 121 14 921 2279 6425956 6424576 0.000000e+00 1727.0
5 TraesCS3B01G016800 chr3D 92.377 774 44 9 1 769 6457427 6456664 0.000000e+00 1088.0
6 TraesCS3B01G016800 chr3D 90.767 769 48 11 2525 3273 6434178 6433413 0.000000e+00 1005.0
7 TraesCS3B01G016800 chr3D 89.474 209 8 6 2320 2521 6454696 6454495 5.420000e-63 252.0
8 TraesCS3B01G016800 chr3A 89.237 1310 120 13 982 2279 13852225 13853525 0.000000e+00 1618.0
9 TraesCS3B01G016800 chr3A 82.222 135 22 2 2670 2803 63827529 63827662 7.430000e-22 115.0
10 TraesCS3B01G016800 chr3A 89.831 59 5 1 267 325 13851348 13851405 1.260000e-09 75.0
11 TraesCS3B01G016800 chr7D 87.628 1366 149 6 923 2284 40118701 40120050 0.000000e+00 1568.0
12 TraesCS3B01G016800 chr7B 73.966 411 92 11 1134 1540 666554718 666554319 5.660000e-33 152.0
13 TraesCS3B01G016800 chr7B 76.596 141 23 7 2662 2797 645408849 645408714 5.860000e-08 69.4
14 TraesCS3B01G016800 chr2D 79.245 106 22 0 2701 2806 3009772 3009667 1.260000e-09 75.0
15 TraesCS3B01G016800 chr1A 95.238 42 2 0 2765 2806 5515886 5515927 2.110000e-07 67.6


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 TraesCS3B01G016800 chr3B 6956005 6959279 3274 False 6048.000000 6048 100.000000 1 3275 1 chr3B.!!$F1 3274
1 TraesCS3B01G016800 chr3B 6965768 6968289 2521 False 843.950000 1624 87.300000 267 2279 2 chr3B.!!$F2 2012
2 TraesCS3B01G016800 chr3D 6424576 6425956 1380 True 1727.000000 1727 89.508000 921 2279 1 chr3D.!!$R1 1358
3 TraesCS3B01G016800 chr3D 6454495 6457427 2932 True 1281.666667 2505 92.884333 1 2521 3 chr3D.!!$R3 2520
4 TraesCS3B01G016800 chr3D 6433413 6434178 765 True 1005.000000 1005 90.767000 2525 3273 1 chr3D.!!$R2 748
5 TraesCS3B01G016800 chr3A 13851348 13853525 2177 False 846.500000 1618 89.534000 267 2279 2 chr3A.!!$F2 2012
6 TraesCS3B01G016800 chr7D 40118701 40120050 1349 False 1568.000000 1568 87.628000 923 2284 1 chr7D.!!$F1 1361

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
461 478 0.110688 CGCACATGACGGAACAACAG 60.111 55.0 0.00 0.0 0.0 3.16 F
480 497 0.454196 GACCCAAATAACGGCGCAAT 59.546 50.0 10.83 0.0 0.0 3.56 F
837 1292 0.893727 GGCCTTGAATCACCCACGTT 60.894 55.0 0.00 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 3174 1.222113 GCCAGGTACCTGCTCCTTC 59.778 63.158 32.98 14.49 42.35 3.46 R
1999 3196 1.475403 TCTACTTCTTCTCCGGCCAG 58.525 55.000 2.24 0.00 0.00 4.85 R
2522 3815 0.179100 ATCATCGGTCAGAAGTGGCG 60.179 55.000 0.00 0.00 0.00 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
39 40 9.825972 CTCACAATAACAGTTTAACCAATACTG 57.174 33.333 3.25 3.25 43.72 2.74
57 58 4.605640 ACTGATTTCCACACAAAATGGG 57.394 40.909 0.00 0.00 37.85 4.00
129 130 6.212791 AGTGTATGAAGTAGCAGTTTTAGGGA 59.787 38.462 0.00 0.00 0.00 4.20
133 134 5.497474 TGAAGTAGCAGTTTTAGGGAATCC 58.503 41.667 0.00 0.00 0.00 3.01
154 155 7.636150 ATCCAACTTTCCACATAATCTCTTG 57.364 36.000 0.00 0.00 0.00 3.02
213 215 0.251341 AAGGGCTGCCTTTTCGACAT 60.251 50.000 19.68 0.00 0.00 3.06
330 344 2.768253 TGAGCAATAGTCACACCTGG 57.232 50.000 0.00 0.00 0.00 4.45
331 345 2.256306 TGAGCAATAGTCACACCTGGA 58.744 47.619 0.00 0.00 0.00 3.86
332 346 2.637382 TGAGCAATAGTCACACCTGGAA 59.363 45.455 0.00 0.00 0.00 3.53
333 347 3.265791 GAGCAATAGTCACACCTGGAAG 58.734 50.000 0.00 0.00 0.00 3.46
353 367 2.252976 GCTGGAAAGCCTAGAGATGG 57.747 55.000 0.00 0.00 34.31 3.51
433 450 8.711457 CCAAAATGTTTACAATGATCTTGAACC 58.289 33.333 10.61 0.02 0.00 3.62
443 460 0.744414 ATCTTGAACCGCCCACATCG 60.744 55.000 0.00 0.00 0.00 3.84
445 462 3.834013 TTGAACCGCCCACATCGCA 62.834 57.895 0.00 0.00 0.00 5.10
451 468 2.793946 GCCCACATCGCACATGAC 59.206 61.111 0.00 0.00 0.00 3.06
460 477 0.530870 TCGCACATGACGGAACAACA 60.531 50.000 0.00 0.00 0.00 3.33
461 478 0.110688 CGCACATGACGGAACAACAG 60.111 55.000 0.00 0.00 0.00 3.16
462 479 1.225855 GCACATGACGGAACAACAGA 58.774 50.000 0.00 0.00 0.00 3.41
472 489 3.566742 ACGGAACAACAGACCCAAATAAC 59.433 43.478 0.00 0.00 0.00 1.89
476 493 1.135803 CAACAGACCCAAATAACGGCG 60.136 52.381 4.80 4.80 0.00 6.46
479 496 0.606944 AGACCCAAATAACGGCGCAA 60.607 50.000 10.83 0.00 0.00 4.85
480 497 0.454196 GACCCAAATAACGGCGCAAT 59.546 50.000 10.83 0.00 0.00 3.56
507 524 6.555315 CCTTTATGCAAACCATACTGTTCTC 58.445 40.000 0.00 0.00 36.18 2.87
514 531 5.449304 CAAACCATACTGTTCTCCGAAAAC 58.551 41.667 0.00 0.00 0.00 2.43
530 547 8.367911 TCTCCGAAAACTGCATTATAGTATGAT 58.632 33.333 0.00 0.00 0.00 2.45
589 606 9.392021 CTGTTTTTGCATTTGTTTTACTTTGTT 57.608 25.926 0.00 0.00 0.00 2.83
664 682 7.614494 TGGATCTGAAAAAGAAATTCAATCCC 58.386 34.615 17.67 9.05 39.90 3.85
668 686 7.444299 TCTGAAAAAGAAATTCAATCCCTTGG 58.556 34.615 0.00 0.00 36.43 3.61
669 687 5.997129 TGAAAAAGAAATTCAATCCCTTGGC 59.003 36.000 0.00 0.00 34.04 4.52
676 694 4.677673 ATTCAATCCCTTGGCTATTTGC 57.322 40.909 0.00 0.00 41.94 3.68
710 728 8.743714 AGGATTTTTCTTATTTCTTGCTCGATT 58.256 29.630 0.00 0.00 0.00 3.34
711 729 8.801913 GGATTTTTCTTATTTCTTGCTCGATTG 58.198 33.333 0.00 0.00 0.00 2.67
728 746 6.144724 GCTCGATTGAGGAATAATAGTCACAC 59.855 42.308 12.06 0.00 42.79 3.82
729 747 7.107639 TCGATTGAGGAATAATAGTCACACA 57.892 36.000 0.00 0.00 0.00 3.72
744 762 2.079925 CACACAGAAAAGCCTAGAGCC 58.920 52.381 0.00 0.00 45.47 4.70
762 780 4.098196 AGAGCCGAGTTTAAGATAGTGACC 59.902 45.833 0.00 0.00 0.00 4.02
769 787 7.119262 CCGAGTTTAAGATAGTGACCACAAATT 59.881 37.037 2.78 0.00 0.00 1.82
782 1237 6.481644 GTGACCACAAATTGCCTTTTCATTAA 59.518 34.615 0.00 0.00 0.00 1.40
783 1238 6.481644 TGACCACAAATTGCCTTTTCATTAAC 59.518 34.615 0.00 0.00 0.00 2.01
784 1239 5.762711 ACCACAAATTGCCTTTTCATTAACC 59.237 36.000 0.00 0.00 0.00 2.85
785 1240 5.181056 CCACAAATTGCCTTTTCATTAACCC 59.819 40.000 0.00 0.00 0.00 4.11
786 1241 4.994217 ACAAATTGCCTTTTCATTAACCCG 59.006 37.500 0.00 0.00 0.00 5.28
787 1242 5.221541 ACAAATTGCCTTTTCATTAACCCGA 60.222 36.000 0.00 0.00 0.00 5.14
788 1243 3.926821 TTGCCTTTTCATTAACCCGAC 57.073 42.857 0.00 0.00 0.00 4.79
789 1244 2.164338 TGCCTTTTCATTAACCCGACC 58.836 47.619 0.00 0.00 0.00 4.79
790 1245 2.164338 GCCTTTTCATTAACCCGACCA 58.836 47.619 0.00 0.00 0.00 4.02
791 1246 2.559231 GCCTTTTCATTAACCCGACCAA 59.441 45.455 0.00 0.00 0.00 3.67
792 1247 3.194755 GCCTTTTCATTAACCCGACCAAT 59.805 43.478 0.00 0.00 0.00 3.16
793 1248 4.399934 GCCTTTTCATTAACCCGACCAATA 59.600 41.667 0.00 0.00 0.00 1.90
794 1249 5.068591 GCCTTTTCATTAACCCGACCAATAT 59.931 40.000 0.00 0.00 0.00 1.28
795 1250 6.406512 GCCTTTTCATTAACCCGACCAATATT 60.407 38.462 0.00 0.00 0.00 1.28
796 1251 6.978080 CCTTTTCATTAACCCGACCAATATTG 59.022 38.462 8.58 8.58 0.00 1.90
801 1256 6.485313 TCATTAACCCGACCAATATTGCTTAG 59.515 38.462 10.11 0.00 0.00 2.18
837 1292 0.893727 GGCCTTGAATCACCCACGTT 60.894 55.000 0.00 0.00 0.00 3.99
884 1339 6.403866 ACAAACCATCAGCTTTTACATTGA 57.596 33.333 0.00 0.00 0.00 2.57
1297 2494 4.980805 GCGTGGAGTTCGTGGCCA 62.981 66.667 0.00 0.00 0.00 5.36
1782 2979 2.029518 CTGTGGCAGTGTCGCTCA 59.970 61.111 10.07 0.00 0.00 4.26
1972 3169 1.482593 ACCTCGTTAAGCTGATCAGGG 59.517 52.381 23.89 15.40 0.00 4.45
1977 3174 1.983119 TTAAGCTGATCAGGGGCGGG 61.983 60.000 23.89 0.00 0.00 6.13
1999 3196 3.330720 AGCAGGTACCTGGCACCC 61.331 66.667 36.91 22.69 43.77 4.61
2281 3501 2.803817 AAGTTCACCTGACCGCCGT 61.804 57.895 0.00 0.00 0.00 5.68
2292 3512 2.742372 CCGCCGTGCAAAGCTAGT 60.742 61.111 7.54 0.00 0.00 2.57
2294 3514 1.132640 CGCCGTGCAAAGCTAGTTC 59.867 57.895 7.54 0.00 0.00 3.01
2295 3515 1.291877 CGCCGTGCAAAGCTAGTTCT 61.292 55.000 7.54 0.00 0.00 3.01
2297 3517 0.716108 CCGTGCAAAGCTAGTTCTCG 59.284 55.000 0.00 0.00 0.00 4.04
2298 3518 1.668919 CCGTGCAAAGCTAGTTCTCGA 60.669 52.381 0.00 0.00 0.00 4.04
2315 3559 6.313905 AGTTCTCGATCGAAGTTGCATTTTAT 59.686 34.615 19.92 0.00 0.00 1.40
2317 3561 7.161829 TCTCGATCGAAGTTGCATTTTATAC 57.838 36.000 19.92 0.00 0.00 1.47
2318 3562 6.754675 TCTCGATCGAAGTTGCATTTTATACA 59.245 34.615 19.92 0.00 0.00 2.29
2387 3673 2.165641 CACGTATTAGTCAGGTCAGGCA 59.834 50.000 0.00 0.00 0.00 4.75
2418 3705 5.674933 AAAAACTTTTGCGTCAACCAAAA 57.325 30.435 0.00 0.00 39.19 2.44
2490 3783 4.873129 CCGCCCGATCGACCACAG 62.873 72.222 18.66 0.00 0.00 3.66
2491 3784 4.129737 CGCCCGATCGACCACAGT 62.130 66.667 18.66 0.00 0.00 3.55
2492 3785 2.509336 GCCCGATCGACCACAGTG 60.509 66.667 18.66 0.00 0.00 3.66
2493 3786 2.970639 CCCGATCGACCACAGTGT 59.029 61.111 18.66 0.00 0.00 3.55
2494 3787 1.153823 CCCGATCGACCACAGTGTC 60.154 63.158 18.66 0.00 0.00 3.67
2495 3788 1.584495 CCGATCGACCACAGTGTCA 59.416 57.895 18.66 0.00 34.88 3.58
2496 3789 0.732880 CCGATCGACCACAGTGTCAC 60.733 60.000 18.66 0.00 34.88 3.67
2497 3790 0.241213 CGATCGACCACAGTGTCACT 59.759 55.000 10.26 0.00 34.88 3.41
2507 3800 4.059459 GTGTCACTTGCCGTCGCG 62.059 66.667 0.00 0.00 38.08 5.87
2530 3823 3.423154 CAACCGCCTCGCCACTTC 61.423 66.667 0.00 0.00 0.00 3.01
2557 3850 4.000325 CGATGATACCACACCAAAGTTCA 59.000 43.478 0.00 0.00 0.00 3.18
2564 3857 2.462889 CACACCAAAGTTCACATGCAC 58.537 47.619 0.00 0.00 0.00 4.57
2567 3860 0.664166 CCAAAGTTCACATGCACGGC 60.664 55.000 0.00 0.00 0.00 5.68
2569 3862 2.128853 AAAGTTCACATGCACGGCCG 62.129 55.000 26.86 26.86 0.00 6.13
2570 3863 3.047280 GTTCACATGCACGGCCGA 61.047 61.111 35.90 10.61 0.00 5.54
2602 3895 0.037975 CTCAATGGGGCAAGTGCAAC 60.038 55.000 5.52 0.00 44.36 4.17
2616 3910 2.226330 GTGCAACATCAAGGTGTACCA 58.774 47.619 3.56 0.00 43.80 3.25
2646 3940 4.010349 GGTTACTCCCACCTTCTTTGATG 58.990 47.826 0.00 0.00 0.00 3.07
2647 3941 4.506802 GGTTACTCCCACCTTCTTTGATGT 60.507 45.833 0.00 0.00 0.00 3.06
2649 3943 1.815003 CTCCCACCTTCTTTGATGTGC 59.185 52.381 0.00 0.00 0.00 4.57
2650 3944 1.425066 TCCCACCTTCTTTGATGTGCT 59.575 47.619 0.00 0.00 0.00 4.40
2651 3945 2.158475 TCCCACCTTCTTTGATGTGCTT 60.158 45.455 0.00 0.00 0.00 3.91
2720 4014 9.847224 TCTCCTAAATGGTTTATCTATTGAACC 57.153 33.333 0.00 0.00 42.44 3.62
2727 4021 7.389803 TGGTTTATCTATTGAACCATGTGTG 57.610 36.000 3.24 0.00 45.69 3.82
2732 4026 5.119931 TCTATTGAACCATGTGTGCAAAC 57.880 39.130 10.62 0.00 45.73 2.93
2746 4040 4.024977 GTGTGCAAACCATGAACCATTTTC 60.025 41.667 0.00 0.00 36.66 2.29
2749 4043 3.498018 GCAAACCATGAACCATTTTCACC 59.502 43.478 0.00 0.00 0.00 4.02
2775 4069 0.813184 TTACCCGCGTCGAGATCTTT 59.187 50.000 4.92 0.00 0.00 2.52
2780 4074 2.864343 CCCGCGTCGAGATCTTTAAAAT 59.136 45.455 4.92 0.00 0.00 1.82
2856 4151 2.442424 TGAAACGAAAAACGAAAGCCG 58.558 42.857 0.00 0.00 45.77 5.52
2869 4164 2.469886 CGAAAGCCGTAAAACAAAAGCC 59.530 45.455 0.00 0.00 0.00 4.35
2879 4174 5.286558 CGTAAAACAAAAGCCGAGAAAACAA 59.713 36.000 0.00 0.00 0.00 2.83
2974 4275 4.100808 TGCTGTGCTTTTCTATTTTTGGGT 59.899 37.500 0.00 0.00 0.00 4.51
2999 4300 2.357009 GCAATTGTGCCTCTACTGGATG 59.643 50.000 7.40 0.00 45.68 3.51
3031 4332 2.930887 GCTTTTCCATTTTCGGGAAGCC 60.931 50.000 0.00 0.00 44.70 4.35
3041 4342 1.079197 CGGGAAGCCCAAATTTGCC 60.079 57.895 12.92 7.84 45.83 4.52
3049 4350 1.134610 GCCCAAATTTGCCTCTCATGG 60.135 52.381 12.92 7.02 0.00 3.66
3067 4368 1.087501 GGAAGAACGATTGTGCCTCC 58.912 55.000 0.00 0.00 0.00 4.30
3079 4380 3.025322 TGTGCCTCCTTTTCCTTTTCA 57.975 42.857 0.00 0.00 0.00 2.69
3103 4404 2.146342 AGACAATTGTGCTTCTCGTGG 58.854 47.619 17.58 0.00 0.00 4.94
3125 4426 4.318831 GGAAGAGTAGTTGTGCTTCGTTTG 60.319 45.833 0.00 0.00 38.05 2.93
3130 4431 2.953020 AGTTGTGCTTCGTTTGCAAAA 58.047 38.095 14.67 0.00 42.41 2.44
3144 4445 9.601971 TTCGTTTGCAAAATATAGTTGTTAGAC 57.398 29.630 14.67 0.00 0.00 2.59
3169 4470 7.648112 ACTGTAGAGTGTGTATATTGTATTGCG 59.352 37.037 0.00 0.00 0.00 4.85
3171 4472 8.357402 TGTAGAGTGTGTATATTGTATTGCGAT 58.643 33.333 0.00 0.00 0.00 4.58
3245 4556 2.965831 ACAGTGAAAGAGCACACTCCTA 59.034 45.455 0.00 0.00 44.07 2.94
3273 4584 6.789268 TCTTTCCTGGTCATTTTCATTAGGA 58.211 36.000 0.00 0.00 0.00 2.94
3274 4585 7.413446 TCTTTCCTGGTCATTTTCATTAGGAT 58.587 34.615 0.00 0.00 33.29 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 7.890127 TCAAGAGATTATGTGGAAAGTTGGATT 59.110 33.333 0.00 0.00 0.00 3.01
133 134 7.605691 AGACTCAAGAGATTATGTGGAAAGTTG 59.394 37.037 3.73 0.00 0.00 3.16
177 179 7.415318 GGCAGCCCTTAAAAGTAATTAAGACTC 60.415 40.741 0.00 0.00 42.77 3.36
334 348 1.202746 CCCATCTCTAGGCTTTCCAGC 60.203 57.143 0.00 0.00 46.52 4.85
335 349 1.202746 GCCCATCTCTAGGCTTTCCAG 60.203 57.143 0.00 0.00 46.14 3.86
336 350 0.839946 GCCCATCTCTAGGCTTTCCA 59.160 55.000 0.00 0.00 46.14 3.53
337 351 3.715871 GCCCATCTCTAGGCTTTCC 57.284 57.895 0.00 0.00 46.14 3.13
353 367 2.561478 TGTTGTCACCCTCTTAAGCC 57.439 50.000 0.00 0.00 0.00 4.35
433 450 2.819154 TCATGTGCGATGTGGGCG 60.819 61.111 0.00 0.00 0.00 6.13
443 460 1.069906 GTCTGTTGTTCCGTCATGTGC 60.070 52.381 0.00 0.00 0.00 4.57
445 462 1.542547 GGGTCTGTTGTTCCGTCATGT 60.543 52.381 0.00 0.00 0.00 3.21
451 468 3.364565 CGTTATTTGGGTCTGTTGTTCCG 60.365 47.826 0.00 0.00 0.00 4.30
460 477 0.606944 TTGCGCCGTTATTTGGGTCT 60.607 50.000 4.18 0.00 0.00 3.85
461 478 0.454196 ATTGCGCCGTTATTTGGGTC 59.546 50.000 4.18 0.00 0.00 4.46
462 479 1.673920 CTATTGCGCCGTTATTTGGGT 59.326 47.619 4.18 0.00 0.00 4.51
476 493 4.122143 TGGTTTGCATAAAGGCTATTGC 57.878 40.909 8.74 8.74 38.76 3.56
479 496 6.129179 ACAGTATGGTTTGCATAAAGGCTAT 58.871 36.000 0.00 0.00 43.62 2.97
480 497 5.505780 ACAGTATGGTTTGCATAAAGGCTA 58.494 37.500 0.00 0.00 43.62 3.93
484 501 6.555315 GGAGAACAGTATGGTTTGCATAAAG 58.445 40.000 0.00 0.00 33.00 1.85
507 524 8.559536 ACAATCATACTATAATGCAGTTTTCGG 58.440 33.333 0.00 0.00 0.00 4.30
563 580 8.947304 ACAAAGTAAAACAAATGCAAAAACAG 57.053 26.923 0.00 0.00 0.00 3.16
637 655 9.662947 GGATTGAATTTCTTTTTCAGATCCATT 57.337 29.630 15.18 0.00 38.67 3.16
639 657 7.455638 AGGGATTGAATTTCTTTTTCAGATCCA 59.544 33.333 18.42 0.00 39.43 3.41
640 658 7.845037 AGGGATTGAATTTCTTTTTCAGATCC 58.155 34.615 13.40 13.40 38.44 3.36
651 669 6.631088 GCAAATAGCCAAGGGATTGAATTTCT 60.631 38.462 0.00 0.00 37.23 2.52
710 728 7.334421 GCTTTTCTGTGTGACTATTATTCCTCA 59.666 37.037 0.00 0.00 0.00 3.86
711 729 7.201652 GGCTTTTCTGTGTGACTATTATTCCTC 60.202 40.741 0.00 0.00 0.00 3.71
728 746 1.205893 ACTCGGCTCTAGGCTTTTCTG 59.794 52.381 0.00 0.00 41.46 3.02
729 747 1.562783 ACTCGGCTCTAGGCTTTTCT 58.437 50.000 0.00 0.00 41.46 2.52
744 762 7.596749 ATTTGTGGTCACTATCTTAAACTCG 57.403 36.000 2.66 0.00 0.00 4.18
762 780 5.107143 CGGGTTAATGAAAAGGCAATTTGTG 60.107 40.000 0.00 0.00 0.00 3.33
769 787 2.164338 GGTCGGGTTAATGAAAAGGCA 58.836 47.619 0.00 0.00 0.00 4.75
782 1237 2.572290 GCTAAGCAATATTGGTCGGGT 58.428 47.619 19.80 7.60 38.04 5.28
783 1238 1.880027 GGCTAAGCAATATTGGTCGGG 59.120 52.381 19.80 13.38 38.04 5.14
784 1239 2.571212 TGGCTAAGCAATATTGGTCGG 58.429 47.619 19.80 15.52 38.04 4.79
785 1240 5.940192 TTATGGCTAAGCAATATTGGTCG 57.060 39.130 19.80 14.61 38.04 4.79
793 1248 8.796475 CCACTGTAAATATTATGGCTAAGCAAT 58.204 33.333 0.00 0.00 0.00 3.56
794 1249 8.165239 CCACTGTAAATATTATGGCTAAGCAA 57.835 34.615 0.00 0.00 0.00 3.91
795 1250 7.744087 CCACTGTAAATATTATGGCTAAGCA 57.256 36.000 0.00 0.00 0.00 3.91
820 1275 0.240945 GCAACGTGGGTGATTCAAGG 59.759 55.000 0.00 0.00 0.00 3.61
822 1277 1.511318 CCGCAACGTGGGTGATTCAA 61.511 55.000 0.00 0.00 0.00 2.69
823 1278 1.963855 CCGCAACGTGGGTGATTCA 60.964 57.895 0.00 0.00 0.00 2.57
837 1292 3.948719 GGGTTGTCCAGTCCCGCA 61.949 66.667 0.00 0.00 35.00 5.69
884 1339 7.246171 ACTATCTTCAGTGACTGTATGGTTT 57.754 36.000 12.93 0.00 32.61 3.27
1075 2269 2.304180 AGGAGGAGACTTTGATGTGGTG 59.696 50.000 0.00 0.00 44.43 4.17
1579 2776 1.522580 GGAAGTCCGGCATGAGCTC 60.523 63.158 6.82 6.82 41.70 4.09
1647 2844 3.036819 GTCGAGGTAGGGGTAATCCTTT 58.963 50.000 0.00 0.00 38.30 3.11
1972 3169 3.081409 TACCTGCTCCTTCCCGCC 61.081 66.667 0.00 0.00 0.00 6.13
1977 3174 1.222113 GCCAGGTACCTGCTCCTTC 59.778 63.158 32.98 14.49 42.35 3.46
1999 3196 1.475403 TCTACTTCTTCTCCGGCCAG 58.525 55.000 2.24 0.00 0.00 4.85
2281 3501 2.163613 TCGATCGAGAACTAGCTTTGCA 59.836 45.455 15.15 0.00 0.00 4.08
2292 3512 6.662414 ATAAAATGCAACTTCGATCGAGAA 57.338 33.333 18.54 3.39 0.00 2.87
2294 3514 6.933130 TGTATAAAATGCAACTTCGATCGAG 58.067 36.000 18.54 14.40 0.00 4.04
2295 3515 6.895607 TGTATAAAATGCAACTTCGATCGA 57.104 33.333 15.15 15.15 0.00 3.59
2297 3517 9.162793 CTCAATGTATAAAATGCAACTTCGATC 57.837 33.333 0.00 0.00 0.00 3.69
2298 3518 8.677300 ACTCAATGTATAAAATGCAACTTCGAT 58.323 29.630 0.00 0.00 0.00 3.59
2418 3705 1.752694 CCATCCGACGGCCCAAAAT 60.753 57.895 9.66 0.00 0.00 1.82
2444 3731 4.328983 CGGTTGAACATACATAGTGGTCAC 59.671 45.833 0.00 0.00 42.57 3.67
2490 3783 4.059459 CGCGACGGCAAGTGACAC 62.059 66.667 0.00 0.00 39.92 3.67
2518 3811 2.435059 GGTCAGAAGTGGCGAGGC 60.435 66.667 0.00 0.00 0.00 4.70
2521 3814 1.215382 CATCGGTCAGAAGTGGCGA 59.785 57.895 0.00 0.00 0.00 5.54
2522 3815 0.179100 ATCATCGGTCAGAAGTGGCG 60.179 55.000 0.00 0.00 0.00 5.69
2523 3816 2.474816 GTATCATCGGTCAGAAGTGGC 58.525 52.381 0.00 0.00 0.00 5.01
2530 3823 1.480545 TGGTGTGGTATCATCGGTCAG 59.519 52.381 0.00 0.00 0.00 3.51
2557 3850 2.742372 GAGTTCGGCCGTGCATGT 60.742 61.111 27.15 4.89 0.00 3.21
2616 3910 2.110011 AGGTGGGAGTAACCTTTGCAAT 59.890 45.455 0.00 0.00 46.14 3.56
2646 3940 6.648725 AACTAACAGATTACGATGAAGCAC 57.351 37.500 0.00 0.00 0.00 4.40
2647 3941 7.667043 AAAACTAACAGATTACGATGAAGCA 57.333 32.000 0.00 0.00 0.00 3.91
2695 3989 9.627123 TGGTTCAATAGATAAACCATTTAGGAG 57.373 33.333 2.19 0.00 45.62 3.69
2720 4014 2.223994 TGGTTCATGGTTTGCACACATG 60.224 45.455 14.93 14.93 42.44 3.21
2721 4015 2.037901 TGGTTCATGGTTTGCACACAT 58.962 42.857 5.20 0.00 0.00 3.21
2727 4021 3.498018 GGTGAAAATGGTTCATGGTTTGC 59.502 43.478 0.00 0.00 0.00 3.68
2732 4026 2.414029 CGACGGTGAAAATGGTTCATGG 60.414 50.000 0.00 0.00 0.00 3.66
2824 4119 5.432885 TTTTCGTTTCAGGCTTTTCCTAG 57.567 39.130 0.00 0.00 45.52 3.02
2836 4131 2.442424 CGGCTTTCGTTTTTCGTTTCA 58.558 42.857 0.00 0.00 40.80 2.69
2856 4151 6.635166 TTGTTTTCTCGGCTTTTGTTTTAC 57.365 33.333 0.00 0.00 0.00 2.01
2999 4300 6.544038 AAAATGGAAAAGCATAACTTGTGC 57.456 33.333 2.38 2.38 39.09 4.57
3031 4332 3.765511 TCTTCCATGAGAGGCAAATTTGG 59.234 43.478 19.47 0.47 0.00 3.28
3041 4342 3.063180 GCACAATCGTTCTTCCATGAGAG 59.937 47.826 0.00 0.00 0.00 3.20
3049 4350 2.100605 AGGAGGCACAATCGTTCTTC 57.899 50.000 0.00 0.00 0.00 2.87
3067 4368 8.598075 CACAATTGTCTTCTTGAAAAGGAAAAG 58.402 33.333 8.48 0.00 46.24 2.27
3079 4380 4.024556 CACGAGAAGCACAATTGTCTTCTT 60.025 41.667 31.47 23.98 39.86 2.52
3103 4404 4.762809 CAAACGAAGCACAACTACTCTTC 58.237 43.478 0.00 0.00 33.50 2.87
3130 4431 9.463902 ACACACTCTACAGTCTAACAACTATAT 57.536 33.333 0.00 0.00 0.00 0.86
3144 4445 7.860872 TCGCAATACAATATACACACTCTACAG 59.139 37.037 0.00 0.00 0.00 2.74
3152 4453 8.527810 TCCTATCATCGCAATACAATATACACA 58.472 33.333 0.00 0.00 0.00 3.72
3245 4556 9.933723 CTAATGAAAATGACCAGGAAAGAAAAT 57.066 29.630 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.