Multiple sequence alignment - TraesCS1D01G185900

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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 TraesCS1D01G185900 chr1D 100.000 3245 0 0 1 3245 256970830 256974074 0.000000e+00 5993.0
1 TraesCS1D01G185900 chr1B 94.044 1847 77 11 628 2469 356282955 356281137 0.000000e+00 2771.0
2 TraesCS1D01G185900 chr1B 93.393 560 36 1 1 560 356300873 356300315 0.000000e+00 828.0
3 TraesCS1D01G185900 chr1B 81.143 700 112 12 2507 3188 589133243 589132546 7.920000e-151 544.0
4 TraesCS1D01G185900 chr1B 95.890 73 3 0 568 640 356296431 356296359 5.690000e-23 119.0
5 TraesCS1D01G185900 chr1B 100.000 39 0 0 868 906 356282672 356282710 4.490000e-09 73.1
6 TraesCS1D01G185900 chr1A 91.610 1907 72 21 605 2469 330686524 330688384 0.000000e+00 2555.0
7 TraesCS1D01G185900 chr1A 91.248 617 47 5 1 610 330680936 330681552 0.000000e+00 833.0
8 TraesCS1D01G185900 chr1A 100.000 39 0 0 868 906 330686863 330686825 4.490000e-09 73.1
9 TraesCS1D01G185900 chr4D 80.237 759 125 15 2504 3245 82568498 82567748 6.120000e-152 547.0
10 TraesCS1D01G185900 chr4D 79.869 765 125 20 2499 3245 346204516 346203763 1.710000e-147 532.0
11 TraesCS1D01G185900 chr4D 82.682 537 86 3 2650 3179 37603507 37604043 1.360000e-128 470.0
12 TraesCS1D01G185900 chr2B 80.401 699 119 13 2507 3188 175453813 175454510 1.730000e-142 516.0
13 TraesCS1D01G185900 chr2B 78.547 289 51 7 2492 2771 571996893 571997179 2.570000e-41 180.0
14 TraesCS1D01G185900 chr2B 78.201 289 52 7 2492 2771 789408869 789409155 1.200000e-39 174.0
15 TraesCS1D01G185900 chr2B 77.778 297 54 8 2485 2771 571966236 571966530 4.300000e-39 172.0
16 TraesCS1D01G185900 chr2B 78.491 265 48 5 2514 2771 571836138 571836400 7.200000e-37 165.0
17 TraesCS1D01G185900 chr2B 77.474 293 55 7 2488 2771 789298900 789299190 7.200000e-37 165.0
18 TraesCS1D01G185900 chr2B 77.163 289 55 7 2492 2771 571853947 571854233 1.210000e-34 158.0
19 TraesCS1D01G185900 chr6D 80.401 699 118 13 2507 3188 50670608 50669912 6.210000e-142 514.0
20 TraesCS1D01G185900 chr6D 78.934 394 65 12 2499 2882 448655051 448654666 5.370000e-63 252.0
21 TraesCS1D01G185900 chr6B 80.142 705 115 17 2507 3188 7959631 7958929 1.340000e-138 503.0
22 TraesCS1D01G185900 chr6B 82.784 546 86 4 2651 3188 41028118 41027573 6.300000e-132 481.0
23 TraesCS1D01G185900 chr5B 78.266 796 138 21 2472 3242 693880470 693881255 2.260000e-131 479.0
24 TraesCS1D01G185900 chr2D 78.360 744 127 16 2502 3215 544501083 544501822 4.940000e-123 451.0
25 TraesCS1D01G185900 chr5D 80.000 340 58 9 234 569 469721814 469722147 3.230000e-60 243.0
26 TraesCS1D01G185900 chr4B 79.221 154 31 1 2499 2651 517006340 517006187 4.430000e-19 106.0


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 TraesCS1D01G185900 chr1D 256970830 256974074 3244 False 5993.0 5993 100.0000 1 3245 1 chr1D.!!$F1 3244
1 TraesCS1D01G185900 chr1B 356281137 356282955 1818 True 2771.0 2771 94.0440 628 2469 1 chr1B.!!$R1 1841
2 TraesCS1D01G185900 chr1B 589132546 589133243 697 True 544.0 544 81.1430 2507 3188 1 chr1B.!!$R2 681
3 TraesCS1D01G185900 chr1B 356296359 356300873 4514 True 473.5 828 94.6415 1 640 2 chr1B.!!$R3 639
4 TraesCS1D01G185900 chr1A 330686524 330688384 1860 False 2555.0 2555 91.6100 605 2469 1 chr1A.!!$F2 1864
5 TraesCS1D01G185900 chr1A 330680936 330681552 616 False 833.0 833 91.2480 1 610 1 chr1A.!!$F1 609
6 TraesCS1D01G185900 chr4D 82567748 82568498 750 True 547.0 547 80.2370 2504 3245 1 chr4D.!!$R1 741
7 TraesCS1D01G185900 chr4D 346203763 346204516 753 True 532.0 532 79.8690 2499 3245 1 chr4D.!!$R2 746
8 TraesCS1D01G185900 chr4D 37603507 37604043 536 False 470.0 470 82.6820 2650 3179 1 chr4D.!!$F1 529
9 TraesCS1D01G185900 chr2B 175453813 175454510 697 False 516.0 516 80.4010 2507 3188 1 chr2B.!!$F1 681
10 TraesCS1D01G185900 chr6D 50669912 50670608 696 True 514.0 514 80.4010 2507 3188 1 chr6D.!!$R1 681
11 TraesCS1D01G185900 chr6B 7958929 7959631 702 True 503.0 503 80.1420 2507 3188 1 chr6B.!!$R1 681
12 TraesCS1D01G185900 chr6B 41027573 41028118 545 True 481.0 481 82.7840 2651 3188 1 chr6B.!!$R2 537
13 TraesCS1D01G185900 chr5B 693880470 693881255 785 False 479.0 479 78.2660 2472 3242 1 chr5B.!!$F1 770
14 TraesCS1D01G185900 chr2D 544501083 544501822 739 False 451.0 451 78.3600 2502 3215 1 chr2D.!!$F1 713

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
585 4461 0.600255 AAGCACGCACCAGTACAGAC 60.6 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 6163 0.890683 ACAGGCTTAACAATGCTGGC 59.109 50.0 0.0 0.0 0.0 4.85 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
102 103 4.619227 ACCGGCGTCAACACCCAG 62.619 66.667 6.01 0.00 0.00 4.45
139 140 3.347216 CCTAATTGTTGGAGGTCACCTG 58.653 50.000 0.00 0.00 31.76 4.00
349 350 4.095483 GCAGTGGTTGAAGATTATGACCTG 59.905 45.833 0.00 0.00 0.00 4.00
365 366 1.228367 CTGCTTGGGTCTGGTTGCT 60.228 57.895 0.00 0.00 0.00 3.91
383 384 5.451242 GGTTGCTGATTTTTGTGTTGTAGGA 60.451 40.000 0.00 0.00 0.00 2.94
411 412 3.278574 TCGCAAGGTTCAGGAATAATGG 58.721 45.455 0.00 0.00 38.47 3.16
429 430 0.678048 GGCACAAAGCTCCCGAGATT 60.678 55.000 0.00 0.00 44.79 2.40
473 474 5.656859 AGTTTTAGGGTGCTTCTGTTTTTCT 59.343 36.000 0.00 0.00 0.00 2.52
475 476 2.310538 AGGGTGCTTCTGTTTTTCTGG 58.689 47.619 0.00 0.00 0.00 3.86
485 486 5.975693 TCTGTTTTTCTGGTTCTTTGTGT 57.024 34.783 0.00 0.00 0.00 3.72
496 497 4.634004 TGGTTCTTTGTGTGTGTCTTAGTG 59.366 41.667 0.00 0.00 0.00 2.74
515 516 5.591643 AGTGTGTGCTTGTACGAATTAAG 57.408 39.130 0.00 0.00 0.00 1.85
585 4461 0.600255 AAGCACGCACCAGTACAGAC 60.600 55.000 0.00 0.00 0.00 3.51
590 4466 1.663739 GCACCAGTACAGACGGTGA 59.336 57.895 21.18 0.00 45.37 4.02
595 4471 2.433239 ACCAGTACAGACGGTGAACTTT 59.567 45.455 0.00 0.00 33.18 2.66
714 4603 3.254060 CCCATCGCATATAGAAACTCGG 58.746 50.000 0.00 0.00 0.00 4.63
868 4782 3.608073 CCAAATTCTTTCCGTCGAAATGC 59.392 43.478 0.00 0.00 37.36 3.56
869 4783 3.487563 AATTCTTTCCGTCGAAATGCC 57.512 42.857 0.00 0.00 37.36 4.40
871 4785 1.226018 CTTTCCGTCGAAATGCCGC 60.226 57.895 0.00 0.00 37.36 6.53
872 4786 1.635663 CTTTCCGTCGAAATGCCGCT 61.636 55.000 0.00 0.00 37.36 5.52
873 4787 1.231958 TTTCCGTCGAAATGCCGCTT 61.232 50.000 0.00 0.00 32.96 4.68
874 4788 1.231958 TTCCGTCGAAATGCCGCTTT 61.232 50.000 0.00 0.00 0.00 3.51
875 4789 1.511887 CCGTCGAAATGCCGCTTTG 60.512 57.895 0.00 0.00 0.00 2.77
886 4800 4.082523 CGCTTTGGCTCCCTCCGA 62.083 66.667 0.00 0.00 36.09 4.55
887 4801 2.436824 GCTTTGGCTCCCTCCGAC 60.437 66.667 0.00 0.00 35.22 4.79
888 4802 2.125512 CTTTGGCTCCCTCCGACG 60.126 66.667 0.00 0.00 0.00 5.12
889 4803 3.665675 CTTTGGCTCCCTCCGACGG 62.666 68.421 7.84 7.84 0.00 4.79
895 4809 2.039951 TCCCTCCGACGGGGATTT 59.960 61.111 17.53 0.00 46.99 2.17
896 4810 1.614226 TCCCTCCGACGGGGATTTT 60.614 57.895 17.53 0.00 46.99 1.82
899 4813 2.435234 TCCGACGGGGATTTTGCG 60.435 61.111 15.25 0.00 40.94 4.85
900 4814 3.505184 CCGACGGGGATTTTGCGG 61.505 66.667 5.81 0.00 38.47 5.69
901 4815 2.744709 CGACGGGGATTTTGCGGT 60.745 61.111 0.00 0.00 0.00 5.68
902 4816 2.874751 GACGGGGATTTTGCGGTG 59.125 61.111 0.00 0.00 0.00 4.94
903 4817 3.336715 GACGGGGATTTTGCGGTGC 62.337 63.158 0.00 0.00 0.00 5.01
905 4819 2.679996 GGGGATTTTGCGGTGCCT 60.680 61.111 0.00 0.00 0.00 4.75
909 4823 2.916703 ATTTTGCGGTGCCTGGCA 60.917 55.556 19.30 19.30 37.39 4.92
1351 5268 4.361971 TCGTGCTCTCCGACCCCT 62.362 66.667 0.00 0.00 0.00 4.79
1544 5461 1.094073 ATCGCGTACTACAGCTCCGT 61.094 55.000 5.77 0.00 0.00 4.69
1605 5522 3.537874 GCCGGGGTCGAGCACTAT 61.538 66.667 15.90 0.00 39.00 2.12
1665 5582 0.605083 TCATCTGCGAGCTTGAGTGT 59.395 50.000 4.70 0.00 0.00 3.55
1764 5681 3.710722 CCAGGAAGCGGCAGGTCT 61.711 66.667 1.45 0.00 0.00 3.85
1767 5684 2.032681 GGAAGCGGCAGGTCTGTT 59.967 61.111 1.45 0.00 0.00 3.16
1863 5780 4.818417 GACAACGACATTGGCGTG 57.182 55.556 19.93 14.74 43.20 5.34
1865 5782 2.182614 GACAACGACATTGGCGTGGG 62.183 60.000 22.91 17.90 43.20 4.61
1866 5783 2.671619 AACGACATTGGCGTGGGG 60.672 61.111 19.93 0.00 41.75 4.96
1867 5784 4.715523 ACGACATTGGCGTGGGGG 62.716 66.667 18.40 0.00 40.94 5.40
2246 6163 5.733373 GCTGGTTCTTCCCAAATTATTAGCG 60.733 44.000 0.00 0.00 33.07 4.26
2265 6182 0.890683 GCCAGCATTGTTAAGCCTGT 59.109 50.000 0.00 0.00 0.00 4.00
2266 6183 2.091541 GCCAGCATTGTTAAGCCTGTA 58.908 47.619 0.00 0.00 0.00 2.74
2267 6184 2.159379 GCCAGCATTGTTAAGCCTGTAC 60.159 50.000 0.00 0.00 0.00 2.90
2305 6222 8.955061 ATCGTTTCAACATTCATACTTCAAAG 57.045 30.769 0.00 0.00 0.00 2.77
2307 6224 8.402472 TCGTTTCAACATTCATACTTCAAAGTT 58.598 29.630 0.00 0.00 40.37 2.66
2308 6225 9.019764 CGTTTCAACATTCATACTTCAAAGTTT 57.980 29.630 0.00 0.00 40.37 2.66
2334 6251 6.190954 ACTACAATTTTTGCGAGGGTTATC 57.809 37.500 0.00 0.00 0.00 1.75
2431 6348 2.148768 ACCACTCGATTCCGGTTTTTC 58.851 47.619 0.00 0.00 36.24 2.29
2434 6351 2.064014 ACTCGATTCCGGTTTTTCGAC 58.936 47.619 0.00 0.00 35.85 4.20
2444 6361 3.907788 CCGGTTTTTCGACGTATTTTTCC 59.092 43.478 0.00 0.00 0.00 3.13
2456 6373 8.394877 TCGACGTATTTTTCCTTTAGACGTATA 58.605 33.333 0.00 0.00 41.65 1.47
2457 6374 9.173939 CGACGTATTTTTCCTTTAGACGTATAT 57.826 33.333 0.00 0.00 41.65 0.86
2459 6376 9.173939 ACGTATTTTTCCTTTAGACGTATATCG 57.826 33.333 0.00 0.00 39.99 2.92
2543 6467 1.679977 CCCTCCACCGTCGACCTTA 60.680 63.158 10.58 0.00 0.00 2.69
2615 6548 7.732996 TCTAGACCAAAGTAGCTTAGTGTTTT 58.267 34.615 0.00 0.00 0.00 2.43
2618 6551 5.442391 ACCAAAGTAGCTTAGTGTTTTGGA 58.558 37.500 17.73 0.00 44.46 3.53
2619 6552 5.889289 ACCAAAGTAGCTTAGTGTTTTGGAA 59.111 36.000 17.73 0.00 44.46 3.53
2626 6559 6.715347 AGCTTAGTGTTTTGGAAGTTCATT 57.285 33.333 5.01 0.00 0.00 2.57
2629 6562 6.756542 GCTTAGTGTTTTGGAAGTTCATTGTT 59.243 34.615 5.01 0.00 0.00 2.83
2636 6575 2.690497 TGGAAGTTCATTGTTTTGGCGA 59.310 40.909 5.01 0.00 0.00 5.54
2640 6579 1.025812 TTCATTGTTTTGGCGACGGT 58.974 45.000 0.00 0.00 0.00 4.83
2644 6583 1.025812 TTGTTTTGGCGACGGTGATT 58.974 45.000 0.00 0.00 0.00 2.57
2656 6595 1.851021 CGGTGATTGCGGTGCTGAAA 61.851 55.000 0.00 0.00 0.00 2.69
2678 6617 5.648330 AAAAGTTTCTCCAGGTCCTACTT 57.352 39.130 0.00 0.00 0.00 2.24
2704 6643 0.963962 GGCGATCGGTCCTATGGTTA 59.036 55.000 18.30 0.00 0.00 2.85
2706 6645 1.884579 GCGATCGGTCCTATGGTTAGA 59.115 52.381 18.30 0.00 0.00 2.10
2781 6720 0.603065 CTCGTGGTGGATCTGTGTCA 59.397 55.000 0.00 0.00 0.00 3.58
2791 6730 0.977627 ATCTGTGTCATCGGGCTCCA 60.978 55.000 0.00 0.00 0.00 3.86
2792 6731 1.191489 TCTGTGTCATCGGGCTCCAA 61.191 55.000 0.00 0.00 0.00 3.53
2815 6754 1.132640 GCGACGACATTTGCTCCAC 59.867 57.895 0.00 0.00 0.00 4.02
2818 6757 0.798776 GACGACATTTGCTCCACCAG 59.201 55.000 0.00 0.00 0.00 4.00
2849 6789 2.040606 GGGGGTAGTCCAGGAGCA 59.959 66.667 0.00 0.00 37.22 4.26
2854 6794 1.490574 GGTAGTCCAGGAGCAGATGT 58.509 55.000 0.00 0.00 0.00 3.06
2865 6805 6.501805 TCCAGGAGCAGATGTATATTATGGTT 59.498 38.462 0.00 0.00 0.00 3.67
2889 6840 1.884464 CGGTGGCATCTGTGGATCG 60.884 63.158 0.00 0.00 0.00 3.69
2892 6843 0.391661 GTGGCATCTGTGGATCGTGT 60.392 55.000 0.00 0.00 0.00 4.49
2899 6850 2.167662 TCTGTGGATCGTGTGCTAGAA 58.832 47.619 0.00 0.00 0.00 2.10
2950 6902 0.466739 TCCTCCGGCGCTTAGTCATA 60.467 55.000 7.64 0.00 0.00 2.15
2985 6937 0.904649 TGGAGTTCGATGGCATGTCT 59.095 50.000 3.81 0.00 0.00 3.41
3023 6975 4.624024 GTCTGATTCGTTCAACGGTAATGA 59.376 41.667 10.69 1.13 42.81 2.57
3024 6976 5.119588 GTCTGATTCGTTCAACGGTAATGAA 59.880 40.000 10.69 0.00 42.81 2.57
3044 7000 2.652382 TTCGCCTTTGACGAGCCACA 62.652 55.000 0.00 0.00 41.18 4.17
3048 7004 1.522668 CCTTTGACGAGCCACATTGA 58.477 50.000 0.00 0.00 0.00 2.57
3054 7010 0.687354 ACGAGCCACATTGAAGGTCT 59.313 50.000 0.00 0.00 0.00 3.85
3058 7014 0.524862 GCCACATTGAAGGTCTGCAG 59.475 55.000 7.63 7.63 0.00 4.41
3060 7016 2.507484 CCACATTGAAGGTCTGCAGAA 58.493 47.619 20.19 1.13 0.00 3.02
3064 7020 3.144506 CATTGAAGGTCTGCAGAACTGT 58.855 45.455 34.18 22.91 42.17 3.55
3137 7093 2.877097 TTCCTTTGATGGCTGCTGTA 57.123 45.000 0.00 0.00 0.00 2.74
3171 7139 2.029369 GTGACGGGCGTTGGTGTA 59.971 61.111 0.00 0.00 0.00 2.90
3179 7147 0.948678 GGCGTTGGTGTAAAGCTCAA 59.051 50.000 0.00 0.00 42.43 3.02
3200 7168 5.881443 TCAAAGGTTTCTTCGGTCTTGTTTA 59.119 36.000 0.00 0.00 31.82 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 1.221840 CGCCTATCTGCTGGGTGTT 59.778 57.895 0.00 0.00 31.62 3.32
102 103 0.756903 TAGGGTTTCCGCCTATCTGC 59.243 55.000 0.00 0.00 38.33 4.26
139 140 2.234168 GTGTGTTTCCCTCCTCCTCTAC 59.766 54.545 0.00 0.00 0.00 2.59
245 246 2.881513 ACATGTGCATCCAACACGTTTA 59.118 40.909 0.00 0.00 41.03 2.01
270 271 0.098728 CAGCGCCGAAAATACAAGGG 59.901 55.000 2.29 0.00 0.00 3.95
349 350 0.610232 ATCAGCAACCAGACCCAAGC 60.610 55.000 0.00 0.00 0.00 4.01
365 366 7.054124 AGAAGACTCCTACAACACAAAAATCA 58.946 34.615 0.00 0.00 0.00 2.57
383 384 1.001406 CCTGAACCTTGCGAGAAGACT 59.999 52.381 1.22 0.00 0.00 3.24
411 412 1.168714 AAATCTCGGGAGCTTTGTGC 58.831 50.000 0.00 0.00 43.29 4.57
424 425 5.924825 ACCAGTAGTAACACACGAAAATCTC 59.075 40.000 0.00 0.00 0.00 2.75
429 430 5.772825 ACTACCAGTAGTAACACACGAAA 57.227 39.130 8.71 0.00 43.98 3.46
473 474 4.634004 CACTAAGACACACACAAAGAACCA 59.366 41.667 0.00 0.00 0.00 3.67
475 476 5.121768 ACACACTAAGACACACACAAAGAAC 59.878 40.000 0.00 0.00 0.00 3.01
485 486 3.260475 ACAAGCACACACTAAGACACA 57.740 42.857 0.00 0.00 0.00 3.72
496 497 6.224420 AGTTCTTAATTCGTACAAGCACAC 57.776 37.500 0.00 0.00 0.00 3.82
585 4461 0.872881 ACCGTCGTCAAAGTTCACCG 60.873 55.000 0.00 0.00 0.00 4.94
590 4466 3.551659 GGACTCTTACCGTCGTCAAAGTT 60.552 47.826 0.00 0.00 32.24 2.66
595 4471 1.162698 CTGGACTCTTACCGTCGTCA 58.837 55.000 0.00 0.00 32.24 4.35
646 4522 2.175811 GGGTCATTGACGTTGCGC 59.824 61.111 10.56 0.00 32.65 6.09
869 4783 4.082523 TCGGAGGGAGCCAAAGCG 62.083 66.667 0.00 0.00 46.67 4.68
871 4785 2.125512 CGTCGGAGGGAGCCAAAG 60.126 66.667 0.00 0.00 0.00 2.77
872 4786 3.702048 CCGTCGGAGGGAGCCAAA 61.702 66.667 11.23 0.00 0.00 3.28
879 4793 1.451387 CAAAATCCCCGTCGGAGGG 60.451 63.158 14.39 9.75 46.60 4.30
880 4794 2.112815 GCAAAATCCCCGTCGGAGG 61.113 63.158 14.39 12.61 46.60 4.30
881 4795 2.461110 CGCAAAATCCCCGTCGGAG 61.461 63.158 14.39 0.00 46.60 4.63
885 4799 2.874751 CACCGCAAAATCCCCGTC 59.125 61.111 0.00 0.00 0.00 4.79
886 4800 3.370231 GCACCGCAAAATCCCCGT 61.370 61.111 0.00 0.00 0.00 5.28
887 4801 4.128388 GGCACCGCAAAATCCCCG 62.128 66.667 0.00 0.00 0.00 5.73
888 4802 2.679996 AGGCACCGCAAAATCCCC 60.680 61.111 0.00 0.00 0.00 4.81
889 4803 2.573340 CAGGCACCGCAAAATCCC 59.427 61.111 0.00 0.00 0.00 3.85
893 4807 3.150335 TTGCCAGGCACCGCAAAA 61.150 55.556 15.89 0.00 40.41 2.44
894 4808 3.910490 GTTGCCAGGCACCGCAAA 61.910 61.111 15.89 0.00 43.96 3.68
970 4887 4.950475 TGTGTGTGTGACCCTTGATAAAAA 59.050 37.500 0.00 0.00 0.00 1.94
971 4888 4.527944 TGTGTGTGTGACCCTTGATAAAA 58.472 39.130 0.00 0.00 0.00 1.52
1320 5237 2.283388 ACGAGGTAGCCGTGGGAA 60.283 61.111 7.49 0.00 38.97 3.97
1605 5522 2.053865 CACGTAGAACCGCCCCCTA 61.054 63.158 0.00 0.00 0.00 3.53
2050 5967 4.373116 GCACGCCGGGAAGTCTGA 62.373 66.667 2.18 0.00 0.00 3.27
2246 6163 0.890683 ACAGGCTTAACAATGCTGGC 59.109 50.000 0.00 0.00 0.00 4.85
2265 6182 9.642327 TGTTGAAACGATAGCAGTTAATTAGTA 57.358 29.630 0.00 0.00 42.67 1.82
2266 6183 8.542497 TGTTGAAACGATAGCAGTTAATTAGT 57.458 30.769 0.00 0.00 42.67 2.24
2267 6184 9.988350 AATGTTGAAACGATAGCAGTTAATTAG 57.012 29.630 0.00 0.00 42.67 1.73
2305 6222 6.698329 ACCCTCGCAAAAATTGTAGTTTAAAC 59.302 34.615 10.47 10.47 0.00 2.01
2307 6224 6.394025 ACCCTCGCAAAAATTGTAGTTTAA 57.606 33.333 0.00 0.00 0.00 1.52
2308 6225 6.394025 AACCCTCGCAAAAATTGTAGTTTA 57.606 33.333 0.00 0.00 0.00 2.01
2309 6226 4.929819 ACCCTCGCAAAAATTGTAGTTT 57.070 36.364 0.00 0.00 0.00 2.66
2311 6228 5.708230 TGATAACCCTCGCAAAAATTGTAGT 59.292 36.000 0.00 0.00 0.00 2.73
2316 6233 4.816392 GGTTGATAACCCTCGCAAAAATT 58.184 39.130 0.00 0.00 46.12 1.82
2334 6251 4.298332 GGTGTTAACAATGCTCAAGGTTG 58.702 43.478 10.51 0.00 0.00 3.77
2410 6327 1.804601 AAAACCGGAATCGAGTGGTC 58.195 50.000 9.46 0.00 39.00 4.02
2431 6348 5.752098 ACGTCTAAAGGAAAAATACGTCG 57.248 39.130 0.00 0.00 37.53 5.12
2456 6373 1.482593 AGATCGCCAGGAAAGAACGAT 59.517 47.619 0.00 0.00 45.37 3.73
2457 6374 0.895530 AGATCGCCAGGAAAGAACGA 59.104 50.000 0.00 0.00 37.15 3.85
2458 6375 1.281899 GAGATCGCCAGGAAAGAACG 58.718 55.000 0.00 0.00 0.00 3.95
2459 6376 1.281899 CGAGATCGCCAGGAAAGAAC 58.718 55.000 0.00 0.00 0.00 3.01
2460 6377 3.741029 CGAGATCGCCAGGAAAGAA 57.259 52.632 0.00 0.00 0.00 2.52
2481 6398 4.741239 ACCTCCTGATGGGGCGGT 62.741 66.667 0.00 0.00 35.50 5.68
2484 6401 2.367512 AGGACCTCCTGATGGGGC 60.368 66.667 0.00 0.00 46.55 5.80
2543 6467 1.990060 CCCCTCACCACCGATGACT 60.990 63.158 0.00 0.00 0.00 3.41
2591 6522 7.095187 CCAAAACACTAAGCTACTTTGGTCTAG 60.095 40.741 10.60 0.00 38.53 2.43
2595 6526 5.442391 TCCAAAACACTAAGCTACTTTGGT 58.558 37.500 15.15 0.00 42.16 3.67
2611 6544 5.568482 GCCAAAACAATGAACTTCCAAAAC 58.432 37.500 0.00 0.00 0.00 2.43
2615 6548 2.690497 TCGCCAAAACAATGAACTTCCA 59.310 40.909 0.00 0.00 0.00 3.53
2618 6551 2.542824 CCGTCGCCAAAACAATGAACTT 60.543 45.455 0.00 0.00 0.00 2.66
2619 6552 1.001815 CCGTCGCCAAAACAATGAACT 60.002 47.619 0.00 0.00 0.00 3.01
2626 6559 0.309302 CAATCACCGTCGCCAAAACA 59.691 50.000 0.00 0.00 0.00 2.83
2629 6562 2.950673 GCAATCACCGTCGCCAAA 59.049 55.556 0.00 0.00 0.00 3.28
2636 6575 3.049674 CAGCACCGCAATCACCGT 61.050 61.111 0.00 0.00 0.00 4.83
2656 6595 5.648330 AAGTAGGACCTGGAGAAACTTTT 57.352 39.130 3.53 0.00 0.00 2.27
2666 6605 1.204941 CCTCGTCAAAGTAGGACCTGG 59.795 57.143 3.53 0.00 31.64 4.45
2670 6609 0.524862 TCGCCTCGTCAAAGTAGGAC 59.475 55.000 0.00 0.00 31.64 3.85
2678 6617 2.488355 GACCGATCGCCTCGTCAA 59.512 61.111 10.32 0.00 46.18 3.18
2704 6643 4.229123 ACACTGGATTCCAAATCCATCTCT 59.771 41.667 18.98 3.22 46.12 3.10
2706 6645 4.264083 ACACACTGGATTCCAAATCCATCT 60.264 41.667 18.98 7.33 46.12 2.90
2726 6665 1.336240 GCACCATCCTTGCTTGAACAC 60.336 52.381 0.00 0.00 37.00 3.32
2781 6720 2.746277 GCAACGTTGGAGCCCGAT 60.746 61.111 28.33 0.00 0.00 4.18
2849 6789 7.119699 CACCGATGCAAACCATAATATACATCT 59.880 37.037 0.00 0.00 33.29 2.90
2854 6794 4.457603 GCCACCGATGCAAACCATAATATA 59.542 41.667 0.00 0.00 33.29 0.86
2865 6805 1.002257 ACAGATGCCACCGATGCAA 60.002 52.632 0.00 0.00 42.92 4.08
2889 6840 4.506654 CCACGTACCATAATTCTAGCACAC 59.493 45.833 0.00 0.00 0.00 3.82
2892 6843 5.303333 TCATCCACGTACCATAATTCTAGCA 59.697 40.000 0.00 0.00 0.00 3.49
2899 6850 5.808366 ATCTGTCATCCACGTACCATAAT 57.192 39.130 0.00 0.00 0.00 1.28
2950 6902 1.002017 CCAGATTTGGCACCCCCAT 59.998 57.895 0.00 0.00 44.89 4.00
3023 6975 0.605319 TGGCTCGTCAAAGGCGAATT 60.605 50.000 0.00 0.00 44.40 2.17
3024 6976 1.003839 TGGCTCGTCAAAGGCGAAT 60.004 52.632 0.00 0.00 44.40 3.34
3044 7000 3.498774 ACAGTTCTGCAGACCTTCAAT 57.501 42.857 18.03 0.00 0.00 2.57
3048 7004 5.911752 CTGATATACAGTTCTGCAGACCTT 58.088 41.667 18.03 8.41 41.30 3.50
3171 7139 3.288092 ACCGAAGAAACCTTTGAGCTTT 58.712 40.909 0.00 0.00 0.00 3.51
3179 7147 8.631480 ATTATAAACAAGACCGAAGAAACCTT 57.369 30.769 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.