Multiple sequence alignment - TraesCS4A01G141200

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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 TraesCS4A01G141200 chr4A 100.000 2529 0 0 1 2529 219339886 219337358 0.000000e+00 4671
1 TraesCS4A01G141200 chr4A 97.959 98 1 1 2433 2529 524928226 524928323 4.330000e-38 169
2 TraesCS4A01G141200 chr2D 95.700 1837 66 8 1 1824 630270277 630272113 0.000000e+00 2942
3 TraesCS4A01G141200 chr2D 95.647 1838 66 8 1 1824 33933800 33935637 0.000000e+00 2939
4 TraesCS4A01G141200 chr2D 94.839 1182 43 9 1 1171 272801674 272800500 0.000000e+00 1829
5 TraesCS4A01G141200 chr2D 93.659 615 37 2 1824 2437 111174651 111175264 0.000000e+00 918
6 TraesCS4A01G141200 chr2D 93.627 612 38 1 1827 2437 299610078 299610689 0.000000e+00 913
7 TraesCS4A01G141200 chr2D 93.627 612 38 1 1827 2437 391963227 391963838 0.000000e+00 913
8 TraesCS4A01G141200 chr3A 95.225 1843 67 10 1 1824 672878448 672876608 0.000000e+00 2896
9 TraesCS4A01G141200 chr3A 97.938 97 2 0 2433 2529 577722 577818 4.330000e-38 169
10 TraesCS4A01G141200 chr3B 95.062 1843 72 13 1 1824 201560790 201558948 0.000000e+00 2881
11 TraesCS4A01G141200 chr3B 98.958 96 1 0 2434 2529 88070993 88071088 3.340000e-39 172
12 TraesCS4A01G141200 chr3B 98.947 95 1 0 2435 2529 12815448 12815354 1.200000e-38 171
13 TraesCS4A01G141200 chr1B 94.574 1843 80 10 1 1824 633728880 633727039 0.000000e+00 2832
14 TraesCS4A01G141200 chr5D 94.038 1845 86 13 1 1824 432292734 432290893 0.000000e+00 2776
15 TraesCS4A01G141200 chr5D 93.954 612 36 1 1827 2437 251066784 251067395 0.000000e+00 924
16 TraesCS4A01G141200 chr5B 93.597 1843 86 11 1 1824 432876708 432878537 0.000000e+00 2721
17 TraesCS4A01G141200 chr5B 93.966 1243 53 10 604 1824 413608022 413609264 0.000000e+00 1860
18 TraesCS4A01G141200 chr7A 91.798 1841 121 22 1 1824 352677461 352675634 0.000000e+00 2536
19 TraesCS4A01G141200 chr7A 98.947 95 1 0 2435 2529 87888869 87888775 1.200000e-38 171
20 TraesCS4A01G141200 chr4D 93.682 1646 85 8 197 1824 245648863 245650507 0.000000e+00 2446
21 TraesCS4A01G141200 chr4D 93.496 615 39 1 1824 2437 391944776 391945390 0.000000e+00 913
22 TraesCS4A01G141200 chrUn 94.839 1182 43 9 1 1171 327663320 327662146 0.000000e+00 1829
23 TraesCS4A01G141200 chrUn 95.854 989 36 3 841 1824 371049286 371050274 0.000000e+00 1594
24 TraesCS4A01G141200 chr7D 93.638 613 37 2 1827 2437 425494302 425493690 0.000000e+00 915
25 TraesCS4A01G141200 chr7D 93.627 612 37 2 1827 2437 129737079 129736469 0.000000e+00 913
26 TraesCS4A01G141200 chr7D 93.627 612 38 1 1827 2437 184435101 184434490 0.000000e+00 913
27 TraesCS4A01G141200 chr1D 93.475 613 36 4 1827 2437 392927374 392927984 0.000000e+00 907
28 TraesCS4A01G141200 chr2B 97.980 99 1 1 2432 2529 93898790 93898888 1.200000e-38 171
29 TraesCS4A01G141200 chr2B 93.878 98 4 2 1729 1824 794832935 794832838 2.030000e-31 147
30 TraesCS4A01G141200 chr6A 97.000 100 3 0 2430 2529 102183348 102183249 4.330000e-38 169
31 TraesCS4A01G141200 chr2A 97.959 98 1 1 2433 2529 188261406 188261503 4.330000e-38 169
32 TraesCS4A01G141200 chr7B 96.078 102 3 1 2428 2529 17175283 17175383 5.600000e-37 165


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 TraesCS4A01G141200 chr4A 219337358 219339886 2528 True 4671 4671 100.000 1 2529 1 chr4A.!!$R1 2528
1 TraesCS4A01G141200 chr2D 630270277 630272113 1836 False 2942 2942 95.700 1 1824 1 chr2D.!!$F5 1823
2 TraesCS4A01G141200 chr2D 33933800 33935637 1837 False 2939 2939 95.647 1 1824 1 chr2D.!!$F1 1823
3 TraesCS4A01G141200 chr2D 272800500 272801674 1174 True 1829 1829 94.839 1 1171 1 chr2D.!!$R1 1170
4 TraesCS4A01G141200 chr2D 111174651 111175264 613 False 918 918 93.659 1824 2437 1 chr2D.!!$F2 613
5 TraesCS4A01G141200 chr2D 299610078 299610689 611 False 913 913 93.627 1827 2437 1 chr2D.!!$F3 610
6 TraesCS4A01G141200 chr2D 391963227 391963838 611 False 913 913 93.627 1827 2437 1 chr2D.!!$F4 610
7 TraesCS4A01G141200 chr3A 672876608 672878448 1840 True 2896 2896 95.225 1 1824 1 chr3A.!!$R1 1823
8 TraesCS4A01G141200 chr3B 201558948 201560790 1842 True 2881 2881 95.062 1 1824 1 chr3B.!!$R2 1823
9 TraesCS4A01G141200 chr1B 633727039 633728880 1841 True 2832 2832 94.574 1 1824 1 chr1B.!!$R1 1823
10 TraesCS4A01G141200 chr5D 432290893 432292734 1841 True 2776 2776 94.038 1 1824 1 chr5D.!!$R1 1823
11 TraesCS4A01G141200 chr5D 251066784 251067395 611 False 924 924 93.954 1827 2437 1 chr5D.!!$F1 610
12 TraesCS4A01G141200 chr5B 432876708 432878537 1829 False 2721 2721 93.597 1 1824 1 chr5B.!!$F2 1823
13 TraesCS4A01G141200 chr5B 413608022 413609264 1242 False 1860 1860 93.966 604 1824 1 chr5B.!!$F1 1220
14 TraesCS4A01G141200 chr7A 352675634 352677461 1827 True 2536 2536 91.798 1 1824 1 chr7A.!!$R2 1823
15 TraesCS4A01G141200 chr4D 245648863 245650507 1644 False 2446 2446 93.682 197 1824 1 chr4D.!!$F1 1627
16 TraesCS4A01G141200 chr4D 391944776 391945390 614 False 913 913 93.496 1824 2437 1 chr4D.!!$F2 613
17 TraesCS4A01G141200 chrUn 327662146 327663320 1174 True 1829 1829 94.839 1 1171 1 chrUn.!!$R1 1170
18 TraesCS4A01G141200 chrUn 371049286 371050274 988 False 1594 1594 95.854 841 1824 1 chrUn.!!$F1 983
19 TraesCS4A01G141200 chr7D 425493690 425494302 612 True 915 915 93.638 1827 2437 1 chr7D.!!$R3 610
20 TraesCS4A01G141200 chr7D 129736469 129737079 610 True 913 913 93.627 1827 2437 1 chr7D.!!$R1 610
21 TraesCS4A01G141200 chr7D 184434490 184435101 611 True 913 913 93.627 1827 2437 1 chr7D.!!$R2 610
22 TraesCS4A01G141200 chr1D 392927374 392927984 610 False 907 907 93.475 1827 2437 1 chr1D.!!$F1 610

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
234 235 3.658705 TGTTCCCTATGGTAACTGGGTTT 59.341 43.478 0.0 0.0 41.11 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2008 2.12457 GATCGCACACAGCCCCAT 60.125 61.111 0.0 0.0 41.38 4.0 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
29 30 4.056740 CGAGGATGAGAATGGATCAGTTG 58.943 47.826 0.00 0.00 0.00 3.16
186 187 9.003658 TCTCAAACAAGAGAAAGAAACATATCC 57.996 33.333 0.00 0.00 41.45 2.59
234 235 3.658705 TGTTCCCTATGGTAACTGGGTTT 59.341 43.478 0.00 0.00 41.11 3.27
260 261 7.809546 TGAGTTATGGTCAACAAACAATACA 57.190 32.000 0.00 0.00 0.00 2.29
269 270 7.090173 GGTCAACAAACAATACATGCTACAAT 58.910 34.615 0.00 0.00 0.00 2.71
339 340 6.655078 TTACCTATAACGATTCACTACCCC 57.345 41.667 0.00 0.00 0.00 4.95
433 434 6.462073 GTGAAGTATGTGTTCACGTATGTT 57.538 37.500 7.91 5.64 43.17 2.71
440 441 4.417506 TGTGTTCACGTATGTTCGATAGG 58.582 43.478 0.00 0.00 34.70 2.57
474 475 5.243730 TGTGGATTGGAGATTTGAAAAGGAC 59.756 40.000 0.00 0.00 0.00 3.85
563 564 4.100344 TGTTGAGTACTGTCCAACAAGCTA 59.900 41.667 20.40 3.51 44.66 3.32
636 637 9.384682 GAATTGAATTACAACCAAATTGCTTTG 57.615 29.630 0.00 4.61 42.62 2.77
1046 1065 5.072741 TGAGATTCTTATGCTATTTGGGGC 58.927 41.667 0.00 0.00 0.00 5.80
1185 1210 3.000727 ACTTTGTAGCTATCGCACAACC 58.999 45.455 0.00 0.00 37.10 3.77
1204 1229 5.044846 ACAACCTCTTATTTATGTGGGAGCT 60.045 40.000 0.00 0.00 0.00 4.09
1240 1275 8.192068 TGATCATATTCGTTGTAATGTTCGTT 57.808 30.769 0.00 0.00 0.00 3.85
1304 1339 2.224523 GGACATGGGTTCACTTCACTCA 60.225 50.000 0.00 0.00 0.00 3.41
1354 1389 9.467796 CTAATGACTACTATCCCAGATACATCA 57.532 37.037 0.00 0.00 0.00 3.07
1358 1393 4.833478 ACTATCCCAGATACATCATGGC 57.167 45.455 0.00 0.00 32.46 4.40
1381 1416 5.393461 GCATGGAATTCTTTGGACTACAAGG 60.393 44.000 5.23 0.00 40.82 3.61
1521 1556 3.931907 AGGTGCAATTACTATGGCTCA 57.068 42.857 0.00 0.00 31.51 4.26
1667 1702 9.698309 TTTTCTCTTTTGTTGTGTAATTGTTCA 57.302 25.926 0.00 0.00 0.00 3.18
1719 1754 6.834969 TCTTGCCCTCATATTGAAATGAATCA 59.165 34.615 0.00 0.00 35.51 2.57
1722 1757 6.041182 TGCCCTCATATTGAAATGAATCAAGG 59.959 38.462 0.00 0.00 42.21 3.61
1851 1887 4.634443 GGTACAGCGACATCCTAAACAAAT 59.366 41.667 0.00 0.00 0.00 2.32
1946 1983 1.548719 ACACGACCCAGAAATCATCGA 59.451 47.619 0.00 0.00 36.64 3.59
2000 2038 4.592192 CGATCGGGCGAGGCATGT 62.592 66.667 7.38 0.00 0.00 3.21
2047 2085 0.253044 CATCCCACACGGTGAATCCT 59.747 55.000 16.29 0.00 35.23 3.24
2169 2207 5.464069 TCTGTAGGTATGTACATCCCACAT 58.536 41.667 18.71 9.51 39.82 3.21
2173 2211 4.562767 AGGTATGTACATCCCACATGGTA 58.437 43.478 18.71 0.00 37.22 3.25
2214 2252 5.209818 CGTAGGTATGTACATCCCACATT 57.790 43.478 18.71 1.64 37.74 2.71
2312 2350 1.263217 CCTAACGCAAACAGTTCGCTT 59.737 47.619 0.00 0.00 33.42 4.68
2315 2353 1.092921 ACGCAAACAGTTCGCTTCCA 61.093 50.000 0.00 0.00 0.00 3.53
2319 2357 2.223479 GCAAACAGTTCGCTTCCAGAAA 60.223 45.455 0.00 0.00 0.00 2.52
2423 2461 7.176515 TGTTGTCTGAGTAACCATTTGCAATAT 59.823 33.333 0.00 0.00 0.00 1.28
2437 2475 8.835439 CCATTTGCAATATAAAACCCCAATAAC 58.165 33.333 0.00 0.00 0.00 1.89
2438 2476 9.388506 CATTTGCAATATAAAACCCCAATAACA 57.611 29.630 0.00 0.00 0.00 2.41
2439 2477 8.779354 TTTGCAATATAAAACCCCAATAACAC 57.221 30.769 0.00 0.00 0.00 3.32
2440 2478 7.726033 TGCAATATAAAACCCCAATAACACT 57.274 32.000 0.00 0.00 0.00 3.55
2441 2479 8.824756 TGCAATATAAAACCCCAATAACACTA 57.175 30.769 0.00 0.00 0.00 2.74
2442 2480 8.908903 TGCAATATAAAACCCCAATAACACTAG 58.091 33.333 0.00 0.00 0.00 2.57
2443 2481 8.909923 GCAATATAAAACCCCAATAACACTAGT 58.090 33.333 0.00 0.00 0.00 2.57
2445 2483 6.769134 ATAAAACCCCAATAACACTAGTGC 57.231 37.500 22.90 0.00 0.00 4.40
2446 2484 3.799432 AACCCCAATAACACTAGTGCA 57.201 42.857 22.90 11.37 0.00 4.57
2447 2485 3.350219 ACCCCAATAACACTAGTGCAG 57.650 47.619 22.90 8.03 0.00 4.41
2448 2486 2.910319 ACCCCAATAACACTAGTGCAGA 59.090 45.455 22.90 8.53 0.00 4.26
2449 2487 3.329520 ACCCCAATAACACTAGTGCAGAA 59.670 43.478 22.90 6.17 0.00 3.02
2450 2488 3.689649 CCCCAATAACACTAGTGCAGAAC 59.310 47.826 22.90 0.00 0.00 3.01
2451 2489 3.689649 CCCAATAACACTAGTGCAGAACC 59.310 47.826 22.90 0.00 0.00 3.62
2452 2490 3.370978 CCAATAACACTAGTGCAGAACCG 59.629 47.826 22.90 5.66 0.00 4.44
2453 2491 2.736144 TAACACTAGTGCAGAACCGG 57.264 50.000 22.90 0.00 0.00 5.28
2454 2492 0.034896 AACACTAGTGCAGAACCGGG 59.965 55.000 22.90 0.00 0.00 5.73
2455 2493 1.741770 CACTAGTGCAGAACCGGGC 60.742 63.158 10.54 0.00 0.00 6.13
2456 2494 2.214216 ACTAGTGCAGAACCGGGCA 61.214 57.895 6.32 1.81 37.77 5.36
2457 2495 1.003839 CTAGTGCAGAACCGGGCAA 60.004 57.895 6.32 0.00 42.45 4.52
2458 2496 0.392998 CTAGTGCAGAACCGGGCAAT 60.393 55.000 6.32 7.58 42.45 3.56
2459 2497 0.906066 TAGTGCAGAACCGGGCAATA 59.094 50.000 6.32 6.43 42.45 1.90
2460 2498 0.392998 AGTGCAGAACCGGGCAATAG 60.393 55.000 6.32 0.00 42.45 1.73
2461 2499 1.748879 TGCAGAACCGGGCAATAGC 60.749 57.895 6.32 2.35 37.03 2.97
2462 2500 1.748879 GCAGAACCGGGCAATAGCA 60.749 57.895 6.32 0.00 44.61 3.49
2463 2501 1.993369 GCAGAACCGGGCAATAGCAC 61.993 60.000 6.32 0.00 44.61 4.40
2464 2502 1.077716 AGAACCGGGCAATAGCACC 60.078 57.895 6.32 0.00 42.77 5.01
2468 2506 2.437716 CGGGCAATAGCACCGGTT 60.438 61.111 2.97 0.00 45.12 4.44
2469 2507 2.469516 CGGGCAATAGCACCGGTTC 61.470 63.158 2.97 0.00 45.12 3.62
2470 2508 2.469516 GGGCAATAGCACCGGTTCG 61.470 63.158 2.97 0.00 44.61 3.95
2471 2509 1.743995 GGCAATAGCACCGGTTCGT 60.744 57.895 2.97 0.00 44.61 3.85
2472 2510 0.460635 GGCAATAGCACCGGTTCGTA 60.461 55.000 2.97 0.00 44.61 3.43
2473 2511 1.361793 GCAATAGCACCGGTTCGTAA 58.638 50.000 2.97 0.00 41.58 3.18
2474 2512 1.326548 GCAATAGCACCGGTTCGTAAG 59.673 52.381 2.97 0.00 41.58 2.34
2475 2513 1.931172 CAATAGCACCGGTTCGTAAGG 59.069 52.381 2.97 0.00 38.47 2.69
2476 2514 0.179092 ATAGCACCGGTTCGTAAGGC 60.179 55.000 2.97 2.83 38.47 4.35
2477 2515 2.229690 TAGCACCGGTTCGTAAGGCC 62.230 60.000 2.97 0.00 38.47 5.19
2478 2516 2.435410 CACCGGTTCGTAAGGCCC 60.435 66.667 2.97 0.00 38.47 5.80
2479 2517 2.605601 ACCGGTTCGTAAGGCCCT 60.606 61.111 0.00 0.00 38.47 5.19
2480 2518 2.219164 ACCGGTTCGTAAGGCCCTT 61.219 57.895 0.00 0.00 38.47 3.95
2481 2519 1.002990 CCGGTTCGTAAGGCCCTTT 60.003 57.895 0.00 0.00 38.47 3.11
2482 2520 0.249955 CCGGTTCGTAAGGCCCTTTA 59.750 55.000 0.00 0.00 38.47 1.85
2483 2521 1.648504 CGGTTCGTAAGGCCCTTTAG 58.351 55.000 0.00 0.00 38.47 1.85
2484 2522 1.066645 CGGTTCGTAAGGCCCTTTAGT 60.067 52.381 0.00 0.00 38.47 2.24
2485 2523 2.353323 GGTTCGTAAGGCCCTTTAGTG 58.647 52.381 0.00 0.00 38.47 2.74
2486 2524 1.736126 GTTCGTAAGGCCCTTTAGTGC 59.264 52.381 0.00 0.00 38.47 4.40
2491 2529 2.035155 GGCCCTTTAGTGCCGGTT 59.965 61.111 1.90 0.00 38.00 4.44
2492 2530 2.044555 GGCCCTTTAGTGCCGGTTC 61.045 63.158 1.90 0.00 38.00 3.62
2493 2531 2.044555 GCCCTTTAGTGCCGGTTCC 61.045 63.158 1.90 0.00 0.00 3.62
2494 2532 1.377229 CCCTTTAGTGCCGGTTCCA 59.623 57.895 1.90 0.00 0.00 3.53
2495 2533 0.034477 CCCTTTAGTGCCGGTTCCAT 60.034 55.000 1.90 0.00 0.00 3.41
2496 2534 1.210967 CCCTTTAGTGCCGGTTCCATA 59.789 52.381 1.90 0.00 0.00 2.74
2497 2535 2.356330 CCCTTTAGTGCCGGTTCCATAA 60.356 50.000 1.90 0.00 0.00 1.90
2498 2536 2.681344 CCTTTAGTGCCGGTTCCATAAC 59.319 50.000 1.90 0.00 34.66 1.89
2499 2537 3.606687 CTTTAGTGCCGGTTCCATAACT 58.393 45.455 1.90 0.00 35.81 2.24
2500 2538 2.684001 TAGTGCCGGTTCCATAACTG 57.316 50.000 1.90 0.00 41.01 3.16
2505 2543 3.551259 CGGTTCCATAACTGGCACT 57.449 52.632 0.00 0.00 42.80 4.40
2506 2544 2.684001 CGGTTCCATAACTGGCACTA 57.316 50.000 0.00 0.00 42.80 2.74
2507 2545 2.980568 CGGTTCCATAACTGGCACTAA 58.019 47.619 0.00 0.00 42.80 2.24
2508 2546 3.340034 CGGTTCCATAACTGGCACTAAA 58.660 45.455 0.00 0.00 42.80 1.85
2509 2547 3.374058 CGGTTCCATAACTGGCACTAAAG 59.626 47.826 0.00 0.00 42.80 1.85
2510 2548 4.332828 GGTTCCATAACTGGCACTAAAGT 58.667 43.478 0.00 0.00 42.80 2.66
2511 2549 4.156008 GGTTCCATAACTGGCACTAAAGTG 59.844 45.833 5.73 5.73 42.80 3.16
2512 2550 4.760204 GTTCCATAACTGGCACTAAAGTGT 59.240 41.667 11.54 0.00 42.80 3.55
2513 2551 5.334879 GTTCCATAACTGGCACTAAAGTGTG 60.335 44.000 11.54 5.46 42.80 3.82
2514 2552 8.221928 GTTCCATAACTGGCACTAAAGTGTGG 62.222 46.154 11.54 9.08 42.80 4.17
2527 2565 2.942641 GTGTGGTCACTAAAGGCCC 58.057 57.895 0.00 0.00 40.98 5.80
2528 2566 0.608308 GTGTGGTCACTAAAGGCCCC 60.608 60.000 0.00 0.00 40.98 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.821532 AAGAGATTGCCCAGGGAAATAT 57.178 40.909 12.45 9.21 0.00 1.28
234 235 9.508642 TGTATTGTTTGTTGACCATAACTCATA 57.491 29.630 0.00 0.00 0.00 2.15
260 261 7.338710 ACTTTGACCTATGTACATTGTAGCAT 58.661 34.615 14.77 13.01 0.00 3.79
339 340 7.641411 CGCTCTGGTGTAATTGATTTTTCATAG 59.359 37.037 0.00 0.00 0.00 2.23
433 434 3.833650 TCCACAACAGGTAAACCTATCGA 59.166 43.478 0.25 0.00 46.65 3.59
440 441 4.394729 TCTCCAATCCACAACAGGTAAAC 58.605 43.478 0.00 0.00 0.00 2.01
624 625 3.369546 AACCGACTCAAAGCAATTTGG 57.630 42.857 0.00 0.00 32.99 3.28
636 637 3.821421 ATGGAGATTGGTAACCGACTC 57.179 47.619 0.00 0.00 0.00 3.36
808 823 9.308318 TCCAATAAGCAGTAGTTTTTGTTTTTC 57.692 29.630 0.00 0.00 0.00 2.29
813 830 9.476202 GAATTTCCAATAAGCAGTAGTTTTTGT 57.524 29.630 0.00 0.00 0.00 2.83
814 831 9.696917 AGAATTTCCAATAAGCAGTAGTTTTTG 57.303 29.630 0.00 0.00 0.00 2.44
1046 1065 5.189934 AGACCCCCTAGTAGAAGAACAAATG 59.810 44.000 0.00 0.00 0.00 2.32
1240 1275 6.560003 TCTTTAGACCATTCTGAGCCATTA 57.440 37.500 0.00 0.00 32.75 1.90
1286 1321 4.279169 ACAAATGAGTGAAGTGAACCCATG 59.721 41.667 0.00 0.00 0.00 3.66
1319 1354 8.822805 TGGGATAGTAGTCATTAGTGAAAAACT 58.177 33.333 0.00 0.00 43.40 2.66
1320 1355 9.099454 CTGGGATAGTAGTCATTAGTGAAAAAC 57.901 37.037 0.00 0.00 35.80 2.43
1354 1389 3.716431 AGTCCAAAGAATTCCATGCCAT 58.284 40.909 0.65 0.00 0.00 4.40
1358 1393 5.711976 ACCTTGTAGTCCAAAGAATTCCATG 59.288 40.000 0.65 1.42 31.20 3.66
1381 1416 6.002082 ACCCTGTTCTACTATTTGGTTTGAC 58.998 40.000 0.00 0.00 0.00 3.18
1784 1820 9.948964 CTTGTGATCAATCCATAGATACCAATA 57.051 33.333 0.00 0.00 32.82 1.90
1851 1887 2.291190 CGCGGAAAGGAGTTTTAAACCA 59.709 45.455 4.01 0.00 0.00 3.67
1970 2008 2.124570 GATCGCACACAGCCCCAT 60.125 61.111 0.00 0.00 41.38 4.00
2000 2038 5.182169 ACCTACGGAAATGATTGGGTTTA 57.818 39.130 0.00 0.00 0.00 2.01
2091 2129 9.778741 TGTACATACCTATGGAAATGATTTCTC 57.221 33.333 16.58 8.29 39.59 2.87
2169 2207 5.359576 CGGAAATGATTTCTGGGATTTACCA 59.640 40.000 17.00 0.00 41.33 3.25
2214 2252 5.105797 CGGAAATGATTTTCTGGGATTCACA 60.106 40.000 0.00 0.00 42.26 3.58
2312 2350 3.831323 ACAATCACACATGGTTTCTGGA 58.169 40.909 0.00 0.00 0.00 3.86
2315 2353 6.545666 TCAACTAACAATCACACATGGTTTCT 59.454 34.615 0.00 0.00 0.00 2.52
2319 2357 5.122239 CGATCAACTAACAATCACACATGGT 59.878 40.000 0.00 0.00 0.00 3.55
2423 2461 5.632118 TGCACTAGTGTTATTGGGGTTTTA 58.368 37.500 23.44 0.00 0.00 1.52
2437 2475 1.741770 GCCCGGTTCTGCACTAGTG 60.742 63.158 18.93 18.93 0.00 2.74
2438 2476 1.764571 TTGCCCGGTTCTGCACTAGT 61.765 55.000 0.00 0.00 37.18 2.57
2439 2477 0.392998 ATTGCCCGGTTCTGCACTAG 60.393 55.000 0.00 0.00 37.18 2.57
2440 2478 0.906066 TATTGCCCGGTTCTGCACTA 59.094 50.000 0.00 0.00 37.18 2.74
2441 2479 0.392998 CTATTGCCCGGTTCTGCACT 60.393 55.000 0.00 0.00 37.18 4.40
2442 2480 1.993369 GCTATTGCCCGGTTCTGCAC 61.993 60.000 0.00 0.00 37.18 4.57
2443 2481 1.748879 GCTATTGCCCGGTTCTGCA 60.749 57.895 0.00 0.00 35.27 4.41
2444 2482 1.748879 TGCTATTGCCCGGTTCTGC 60.749 57.895 0.00 0.00 38.71 4.26
2445 2483 1.376609 GGTGCTATTGCCCGGTTCTG 61.377 60.000 0.00 0.00 38.71 3.02
2446 2484 1.077716 GGTGCTATTGCCCGGTTCT 60.078 57.895 0.00 0.00 38.71 3.01
2447 2485 2.469516 CGGTGCTATTGCCCGGTTC 61.470 63.158 16.86 0.00 43.94 3.62
2448 2486 2.437716 CGGTGCTATTGCCCGGTT 60.438 61.111 16.86 0.00 43.94 4.44
2451 2489 2.437716 AACCGGTGCTATTGCCCG 60.438 61.111 8.52 17.41 45.75 6.13
2452 2490 2.469516 CGAACCGGTGCTATTGCCC 61.470 63.158 8.52 0.00 38.71 5.36
2453 2491 0.460635 TACGAACCGGTGCTATTGCC 60.461 55.000 8.52 0.00 38.71 4.52
2454 2492 1.326548 CTTACGAACCGGTGCTATTGC 59.673 52.381 8.52 0.00 40.20 3.56
2455 2493 1.931172 CCTTACGAACCGGTGCTATTG 59.069 52.381 8.52 0.00 0.00 1.90
2456 2494 1.741394 GCCTTACGAACCGGTGCTATT 60.741 52.381 8.52 0.00 0.00 1.73
2457 2495 0.179092 GCCTTACGAACCGGTGCTAT 60.179 55.000 8.52 0.00 0.00 2.97
2458 2496 1.216178 GCCTTACGAACCGGTGCTA 59.784 57.895 8.52 0.00 0.00 3.49
2459 2497 2.047560 GCCTTACGAACCGGTGCT 60.048 61.111 8.52 0.00 0.00 4.40
2460 2498 3.122971 GGCCTTACGAACCGGTGC 61.123 66.667 8.52 4.53 0.00 5.01
2461 2499 2.435410 GGGCCTTACGAACCGGTG 60.435 66.667 8.52 0.00 0.00 4.94
2462 2500 1.771783 AAAGGGCCTTACGAACCGGT 61.772 55.000 21.25 0.00 0.00 5.28
2463 2501 0.249955 TAAAGGGCCTTACGAACCGG 59.750 55.000 21.25 0.00 0.00 5.28
2464 2502 1.066645 ACTAAAGGGCCTTACGAACCG 60.067 52.381 21.25 5.60 0.00 4.44
2465 2503 2.353323 CACTAAAGGGCCTTACGAACC 58.647 52.381 21.25 0.00 0.00 3.62
2466 2504 1.736126 GCACTAAAGGGCCTTACGAAC 59.264 52.381 21.25 5.99 0.00 3.95
2467 2505 1.339342 GGCACTAAAGGGCCTTACGAA 60.339 52.381 21.25 4.81 46.74 3.85
2468 2506 0.251073 GGCACTAAAGGGCCTTACGA 59.749 55.000 21.25 7.25 46.74 3.43
2469 2507 2.776659 GGCACTAAAGGGCCTTACG 58.223 57.895 21.25 15.66 46.74 3.18
2474 2512 2.035155 AACCGGCACTAAAGGGCC 59.965 61.111 13.51 13.51 46.80 5.80
2475 2513 2.044555 GGAACCGGCACTAAAGGGC 61.045 63.158 0.00 0.00 0.00 5.19
2476 2514 0.034477 ATGGAACCGGCACTAAAGGG 60.034 55.000 0.00 0.00 0.00 3.95
2477 2515 2.681344 GTTATGGAACCGGCACTAAAGG 59.319 50.000 0.00 0.00 0.00 3.11
2478 2516 3.374058 CAGTTATGGAACCGGCACTAAAG 59.626 47.826 0.00 0.00 36.08 1.85
2479 2517 3.340034 CAGTTATGGAACCGGCACTAAA 58.660 45.455 0.00 0.00 36.08 1.85
2480 2518 2.980568 CAGTTATGGAACCGGCACTAA 58.019 47.619 0.00 0.00 36.08 2.24
2481 2519 2.684001 CAGTTATGGAACCGGCACTA 57.316 50.000 0.00 0.00 36.08 2.74
2482 2520 3.551259 CAGTTATGGAACCGGCACT 57.449 52.632 0.00 0.00 36.08 4.40
2509 2547 0.608308 GGGGCCTTTAGTGACCACAC 60.608 60.000 0.84 0.00 46.24 3.82
2510 2548 1.765074 GGGGCCTTTAGTGACCACA 59.235 57.895 0.84 0.00 0.00 4.17
2511 2549 4.736739 GGGGCCTTTAGTGACCAC 57.263 61.111 0.84 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.