Multiple sequence alignment - TraesCS2D01G369300

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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 TraesCS2D01G369300 chr2D 100.000 3999 0 0 1 3999 473584006 473588004 0.000000e+00 7385
1 TraesCS2D01G369300 chr2B 92.831 2748 119 31 3 2688 553975444 553978175 0.000000e+00 3912
2 TraesCS2D01G369300 chr2B 86.376 712 44 19 3312 3999 553978757 553979439 0.000000e+00 728
3 TraesCS2D01G369300 chr2B 92.363 419 25 3 2779 3197 553978174 553978585 1.240000e-164 590
4 TraesCS2D01G369300 chr2B 80.089 447 52 20 23 456 553973920 553974342 8.400000e-77 298
5 TraesCS2D01G369300 chr2A 92.035 2737 132 32 309 2999 615519670 615522366 0.000000e+00 3768
6 TraesCS2D01G369300 chr2A 90.704 710 38 18 3291 3982 615522664 615523363 0.000000e+00 920
7 TraesCS2D01G369300 chr2A 78.261 207 21 9 3029 3225 615522362 615522554 1.170000e-20 111
8 TraesCS2D01G369300 chrUn 88.458 1239 89 24 1917 3137 75461788 75460586 0.000000e+00 1447
9 TraesCS2D01G369300 chrUn 94.861 934 34 7 1002 1929 75463745 75462820 0.000000e+00 1447
10 TraesCS2D01G369300 chrUn 91.287 746 35 12 246 973 75464477 75463744 0.000000e+00 990
11 TraesCS2D01G369300 chr3B 78.601 243 37 10 967 1195 756671570 756671811 3.220000e-31 147
12 TraesCS2D01G369300 chr3A 79.130 230 33 9 979 1195 702574616 702574843 1.160000e-30 145


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 TraesCS2D01G369300 chr2D 473584006 473588004 3998 False 7385.000000 7385 100.000000 1 3999 1 chr2D.!!$F1 3998
1 TraesCS2D01G369300 chr2B 553973920 553979439 5519 False 1382.000000 3912 87.914750 3 3999 4 chr2B.!!$F1 3996
2 TraesCS2D01G369300 chr2A 615519670 615523363 3693 False 1599.666667 3768 87.000000 309 3982 3 chr2A.!!$F1 3673
3 TraesCS2D01G369300 chrUn 75460586 75464477 3891 True 1294.666667 1447 91.535333 246 3137 3 chrUn.!!$R1 2891

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
464 2013 0.036010 ATCGCCCCTCAACTTGAGTG 60.036 55.000 16.10 6.21 42.8 3.51 F
668 2231 0.719465 GTGTGCCGAGGTGAAATACG 59.281 55.000 0.00 0.00 0.0 3.06 F
679 2242 1.017177 TGAAATACGTCGTGGGCAGC 61.017 55.000 8.47 0.00 0.0 5.25 F
1053 2638 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 3368 3.502356 CCCCTTAACTGGGCAAGTAAAA 58.498 45.455 0.0 0.0 45.78 1.52 R
2651 5307 0.179189 GCTATGTGTGAACAAGGCGC 60.179 55.000 0.0 0.0 0.00 6.53 R
2652 5308 1.155889 TGCTATGTGTGAACAAGGCG 58.844 50.000 0.0 0.0 0.00 5.52 R
3016 5681 0.660300 GCGTCAAACAAGGGAAAGCG 60.660 55.000 0.0 0.0 0.00 4.68 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
34 1557 6.881065 TCCTCTTCTCATCTATTGTGTTTTGG 59.119 38.462 0.00 0.00 0.00 3.28
53 1576 4.686191 TGGACTGAAATTTTGTGGCAAT 57.314 36.364 0.00 0.00 0.00 3.56
64 1587 9.101655 GAAATTTTGTGGCAATGCTAGATAATT 57.898 29.630 10.14 10.14 29.67 1.40
149 1680 3.568007 TGCTGGTAGCTAAAACAGGTTTG 59.432 43.478 17.84 0.61 42.97 2.93
220 1751 4.202030 TGTTGGTGTCCGTTCCAAAAATAC 60.202 41.667 0.00 0.00 43.89 1.89
305 1837 0.526954 AGTATAACCTTCGTGCGCCG 60.527 55.000 4.18 8.64 38.13 6.46
330 1862 4.517934 CCATCCCAGCCCAGCCAG 62.518 72.222 0.00 0.00 0.00 4.85
459 2008 0.546598 CCCTAATCGCCCCTCAACTT 59.453 55.000 0.00 0.00 0.00 2.66
460 2009 1.668419 CCTAATCGCCCCTCAACTTG 58.332 55.000 0.00 0.00 0.00 3.16
464 2013 0.036010 ATCGCCCCTCAACTTGAGTG 60.036 55.000 16.10 6.21 42.80 3.51
582 2131 4.377897 TCTCTTTCCTTTGTTCCTTCGTC 58.622 43.478 0.00 0.00 0.00 4.20
668 2231 0.719465 GTGTGCCGAGGTGAAATACG 59.281 55.000 0.00 0.00 0.00 3.06
679 2242 1.017177 TGAAATACGTCGTGGGCAGC 61.017 55.000 8.47 0.00 0.00 5.25
717 2280 4.076394 TGAGGGTATTTGGTGTAAACAGC 58.924 43.478 5.37 5.37 44.06 4.40
755 2319 5.321927 TCCACCTTCCCTTAAAAGATGTTC 58.678 41.667 0.00 0.00 0.00 3.18
884 2457 2.004583 TGTGTATTCGCCTACTGCAC 57.995 50.000 0.00 0.00 41.33 4.57
1035 2608 6.393171 AGCTGAGAAAGATAAACAAATTGCC 58.607 36.000 0.00 0.00 0.00 4.52
1053 2638 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1156 2741 1.153208 CATCTCCCAGTCTGCAGCC 60.153 63.158 9.47 0.00 0.00 4.85
1181 2766 3.692690 TGGTACAAAAGGACATTAGGCC 58.307 45.455 0.00 0.00 31.92 5.19
1228 2813 6.656693 AGATGTGGTGTCTCTAAATTTTCCTG 59.343 38.462 0.00 0.00 0.00 3.86
1491 3083 5.841810 TCAGATTTGTTTTTAGGTTGCCAG 58.158 37.500 0.00 0.00 0.00 4.85
1562 3154 3.394674 TGCCTGTTTCGTAGATTCACA 57.605 42.857 0.00 0.00 35.04 3.58
1745 3338 1.555075 TGGCCTGAAGATGGTGAGTAC 59.445 52.381 3.32 0.00 0.00 2.73
1775 3368 6.371809 TGTTAATGTTCGCTTTTGAAGACT 57.628 33.333 0.00 0.00 0.00 3.24
1786 3379 4.745125 GCTTTTGAAGACTTTTACTTGCCC 59.255 41.667 0.00 0.00 0.00 5.36
1845 3447 6.592870 AGTTAAAGGGCACTATTCTATGGTC 58.407 40.000 0.00 0.00 0.00 4.02
1858 3460 9.148104 ACTATTCTATGGTCGTTTGAAGTTTAC 57.852 33.333 0.00 0.00 0.00 2.01
1886 3488 4.431809 TGAACTTTTGGCACTGATGTTTG 58.568 39.130 0.00 0.00 0.00 2.93
2132 4781 6.472887 ACACCCATTTATCCGGATATGTTAG 58.527 40.000 24.55 15.43 0.00 2.34
2145 4794 9.893634 TCCGGATATGTTAGAACTTTTTCATAA 57.106 29.630 0.00 0.00 33.72 1.90
2287 4938 4.451096 GCTTTAGCACTAACAAGCACTGTA 59.549 41.667 8.54 0.00 38.01 2.74
2336 4987 2.319025 TCATTGGTTTTCCTTCCCCC 57.681 50.000 0.00 0.00 41.38 5.40
2411 5067 5.298347 AGTTGTTAACCTAGTTGCTGAGTC 58.702 41.667 2.48 0.00 0.00 3.36
2561 5217 5.415701 ACATTTCGCATGTCCTGTTAAATCT 59.584 36.000 0.00 0.00 0.00 2.40
2649 5305 3.932710 TCCATGCTTGTTTCGTATGAGAC 59.067 43.478 0.00 0.00 0.00 3.36
2702 5364 1.415672 AACTTGTCGGGAAGGCAGGA 61.416 55.000 0.00 0.00 34.89 3.86
2703 5365 1.201429 ACTTGTCGGGAAGGCAGGAT 61.201 55.000 0.00 0.00 34.89 3.24
2718 5380 4.389890 GCAGGATAACATTGCCATTCAA 57.610 40.909 0.00 0.00 39.32 2.69
2732 5394 3.873801 GCCATTCAAGAGGAACCTTGCTA 60.874 47.826 0.00 0.00 42.34 3.49
2734 5396 4.566488 CCATTCAAGAGGAACCTTGCTACT 60.566 45.833 0.00 0.00 42.34 2.57
2736 5398 2.567615 TCAAGAGGAACCTTGCTACTCC 59.432 50.000 0.00 0.00 42.34 3.85
2738 5400 2.183679 AGAGGAACCTTGCTACTCCTG 58.816 52.381 0.00 0.00 38.45 3.86
2739 5401 0.615850 AGGAACCTTGCTACTCCTGC 59.384 55.000 0.00 0.00 36.92 4.85
2740 5402 0.615850 GGAACCTTGCTACTCCTGCT 59.384 55.000 0.00 0.00 0.00 4.24
2742 5404 1.276421 GAACCTTGCTACTCCTGCTCA 59.724 52.381 0.00 0.00 0.00 4.26
2743 5405 0.610687 ACCTTGCTACTCCTGCTCAC 59.389 55.000 0.00 0.00 0.00 3.51
2746 5408 0.545309 TTGCTACTCCTGCTCACCCT 60.545 55.000 0.00 0.00 0.00 4.34
2747 5409 0.335019 TGCTACTCCTGCTCACCCTA 59.665 55.000 0.00 0.00 0.00 3.53
2748 5410 1.036707 GCTACTCCTGCTCACCCTAG 58.963 60.000 0.00 0.00 0.00 3.02
2749 5411 1.686741 GCTACTCCTGCTCACCCTAGT 60.687 57.143 0.00 0.00 0.00 2.57
2751 5413 2.031495 ACTCCTGCTCACCCTAGTTT 57.969 50.000 0.00 0.00 0.00 2.66
2820 5485 3.944250 ATGCTCCACCAAAGCCCGG 62.944 63.158 0.00 0.00 39.05 5.73
2832 5497 1.557269 AAGCCCGGTCATGAAGAGCT 61.557 55.000 0.00 0.00 42.56 4.09
2868 5533 1.484038 AACAAGGACAAGCAAGGCAA 58.516 45.000 0.00 0.00 0.00 4.52
2878 5543 4.260170 ACAAGCAAGGCAAAAACATCAAA 58.740 34.783 0.00 0.00 0.00 2.69
2941 5606 3.009033 ACAAGATCCTCAAATTCCGGTCA 59.991 43.478 0.00 0.00 0.00 4.02
2953 5618 2.358737 CGGTCAACCAGTGAGGGC 60.359 66.667 0.00 0.00 43.89 5.19
3016 5681 3.641437 TGAAACACAATGCTTGTAGCC 57.359 42.857 1.95 0.00 43.23 3.93
3020 5685 0.523072 CACAATGCTTGTAGCCGCTT 59.477 50.000 0.00 0.00 43.23 4.68
3029 5694 0.109723 TGTAGCCGCTTTCCCTTGTT 59.890 50.000 0.00 0.00 0.00 2.83
3033 5698 0.318699 GCCGCTTTCCCTTGTTTGAC 60.319 55.000 0.00 0.00 0.00 3.18
3051 5722 1.296755 ACGCTTCTGATGCACAGCAG 61.297 55.000 9.58 9.58 43.65 4.24
3153 5829 2.503943 GGTAACTCGCAATTGTGACG 57.496 50.000 17.57 15.12 0.00 4.35
3154 5830 1.463528 GGTAACTCGCAATTGTGACGC 60.464 52.381 17.57 7.92 0.00 5.19
3155 5831 1.459592 GTAACTCGCAATTGTGACGCT 59.540 47.619 17.57 7.61 0.00 5.07
3156 5832 0.235665 AACTCGCAATTGTGACGCTG 59.764 50.000 17.57 10.54 0.00 5.18
3157 5833 0.599991 ACTCGCAATTGTGACGCTGA 60.600 50.000 17.57 0.00 0.00 4.26
3158 5834 0.179240 CTCGCAATTGTGACGCTGAC 60.179 55.000 17.57 0.00 0.00 3.51
3173 5849 2.040213 CTGACGCATGATTCCGGTGC 62.040 60.000 0.00 1.91 35.59 5.01
3200 5876 8.138928 TCTTGTCCTCTCTTTCTGAATTATGA 57.861 34.615 0.00 0.00 0.00 2.15
3202 5878 7.487822 TGTCCTCTCTTTCTGAATTATGAGT 57.512 36.000 0.00 0.00 0.00 3.41
3203 5879 7.551585 TGTCCTCTCTTTCTGAATTATGAGTC 58.448 38.462 0.00 0.00 0.00 3.36
3245 6050 2.094894 GTGAACTCATGCAGACCATTCG 59.905 50.000 0.00 0.00 29.71 3.34
3289 6094 4.240881 CGGCACCCGGTACTACTA 57.759 61.111 0.00 0.00 44.15 1.82
3322 6127 0.883370 AAGTCGTTGGCTTCCGGTTC 60.883 55.000 0.00 0.00 0.00 3.62
3385 6195 1.807981 CTCACGCGCAACCGGAATA 60.808 57.895 9.46 0.00 34.32 1.75
3414 6224 9.635404 TCTGGAATTCTAAAACCTCTTTAAACA 57.365 29.630 5.23 0.00 0.00 2.83
3423 6233 3.053826 ACCTCTTTAAACACCAGGACCT 58.946 45.455 0.00 0.00 0.00 3.85
3440 6250 4.407296 AGGACCTGGAATCTTGATAGTGAC 59.593 45.833 0.00 0.00 0.00 3.67
3461 6271 9.303116 AGTGACTCCCATGTAATATAAGAGTAG 57.697 37.037 0.00 0.00 33.46 2.57
3492 6302 2.558359 GCCACTTGCACCATAGAAAACT 59.442 45.455 0.00 0.00 40.77 2.66
3505 6317 1.003233 AAAACTCCGAGCTCCTGCC 60.003 57.895 8.47 0.00 40.80 4.85
3526 6338 2.047274 CTGCCGTGAACGTGGGAT 60.047 61.111 1.75 0.00 37.74 3.85
3531 6347 2.949909 CGTGAACGTGGGATGGGGA 61.950 63.158 0.00 0.00 34.11 4.81
3554 6370 1.577328 CCAAAGACCAATCGCAGCGT 61.577 55.000 15.93 0.00 0.00 5.07
3555 6371 1.075542 CAAAGACCAATCGCAGCGTA 58.924 50.000 15.93 1.65 0.00 4.42
3556 6372 1.463056 CAAAGACCAATCGCAGCGTAA 59.537 47.619 15.93 0.00 0.00 3.18
3557 6373 1.076332 AAGACCAATCGCAGCGTAAC 58.924 50.000 15.93 2.21 0.00 2.50
3558 6374 0.037697 AGACCAATCGCAGCGTAACA 60.038 50.000 15.93 0.00 0.00 2.41
3560 6376 1.195900 GACCAATCGCAGCGTAACAAA 59.804 47.619 15.93 0.00 0.00 2.83
3561 6377 1.069500 ACCAATCGCAGCGTAACAAAC 60.069 47.619 15.93 0.00 0.00 2.93
3562 6378 1.196808 CCAATCGCAGCGTAACAAACT 59.803 47.619 15.93 0.00 0.00 2.66
3564 6380 3.120477 CCAATCGCAGCGTAACAAACTAA 60.120 43.478 15.93 0.00 0.00 2.24
3565 6381 4.436852 CCAATCGCAGCGTAACAAACTAAT 60.437 41.667 15.93 0.00 0.00 1.73
3568 6384 5.444586 TCGCAGCGTAACAAACTAATTAG 57.555 39.130 15.93 11.05 0.00 1.73
3569 6385 4.925054 TCGCAGCGTAACAAACTAATTAGT 59.075 37.500 15.93 12.50 38.39 2.24
3570 6386 5.061311 TCGCAGCGTAACAAACTAATTAGTC 59.939 40.000 18.28 4.35 34.99 2.59
3571 6387 5.061808 CGCAGCGTAACAAACTAATTAGTCT 59.938 40.000 18.28 1.58 34.99 3.24
3573 6389 7.513196 CGCAGCGTAACAAACTAATTAGTCTAG 60.513 40.741 18.28 12.98 34.99 2.43
3592 6417 1.070758 AGCATACATAGACCCAAGCCG 59.929 52.381 0.00 0.00 0.00 5.52
3594 6419 2.484770 GCATACATAGACCCAAGCCGAA 60.485 50.000 0.00 0.00 0.00 4.30
3602 6427 0.467290 ACCCAAGCCGAAGCAAAAGA 60.467 50.000 0.00 0.00 43.56 2.52
3638 6464 3.954465 CTTGAGCTCCTGCGCTGCT 62.954 63.158 12.15 13.10 45.42 4.24
3639 6465 3.541950 TTGAGCTCCTGCGCTGCTT 62.542 57.895 12.15 0.00 45.42 3.91
3666 6492 4.270808 GCTAGATCTGAAGAGAAGCAAAGC 59.729 45.833 5.18 0.00 31.42 3.51
3711 6539 2.573369 CTAGACTAGCCCTTGAGCGTA 58.427 52.381 0.00 0.00 38.01 4.42
3723 6551 1.605753 TGAGCGTAGTAGCATCGGAT 58.394 50.000 0.00 0.00 40.15 4.18
3967 6805 7.401493 AGTCATCTTCTCTTCTTTCATTCCCTA 59.599 37.037 0.00 0.00 0.00 3.53
3970 6808 8.700051 CATCTTCTCTTCTTTCATTCCCTACTA 58.300 37.037 0.00 0.00 0.00 1.82
3974 6812 6.613271 TCTCTTCTTTCATTCCCTACTATGCT 59.387 38.462 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.931441 AGATGAGAAGAGGAACAAAAACG 57.069 39.130 0.00 0.00 0.00 3.60
1 2 8.787852 ACAATAGATGAGAAGAGGAACAAAAAC 58.212 33.333 0.00 0.00 0.00 2.43
4 5 7.453393 ACACAATAGATGAGAAGAGGAACAAA 58.547 34.615 0.00 0.00 0.00 2.83
6 7 6.611613 ACACAATAGATGAGAAGAGGAACA 57.388 37.500 0.00 0.00 0.00 3.18
7 8 7.913674 AAACACAATAGATGAGAAGAGGAAC 57.086 36.000 0.00 0.00 0.00 3.62
34 1557 4.060205 AGCATTGCCACAAAATTTCAGTC 58.940 39.130 4.70 0.00 0.00 3.51
149 1680 9.938670 ACCTGTTTTAGTTTTGTTTTTGAAAAC 57.061 25.926 11.41 11.41 46.40 2.43
305 1837 2.114838 GCTGGGATGGGCTGGATC 59.885 66.667 0.00 0.00 0.00 3.36
330 1862 4.500116 GAGTCGCAGAGGACGCCC 62.500 72.222 0.00 0.00 41.81 6.13
582 2131 0.714994 CCATTCGCCAAACAATTGCG 59.285 50.000 5.05 2.76 37.39 4.85
627 2176 2.021068 GCCGCTGCCAGTCAGAGATA 62.021 60.000 0.00 0.00 45.72 1.98
655 2204 1.265568 CCACGACGTATTTCACCTCG 58.734 55.000 0.00 0.00 40.28 4.63
668 2231 0.248289 TAACCTAAGCTGCCCACGAC 59.752 55.000 0.00 0.00 0.00 4.34
679 2242 8.980481 AATACCCTCATGTGAAATAACCTAAG 57.020 34.615 0.00 0.00 0.00 2.18
717 2280 1.756538 GGTGGATTTTACATGCCCCAG 59.243 52.381 0.00 0.00 0.00 4.45
755 2319 3.987547 TCGGGACTAGTACAGACGATAG 58.012 50.000 7.57 0.00 46.19 2.08
818 2385 5.382664 AAGTCCTTTCAGTCCCTTTGTAA 57.617 39.130 0.00 0.00 0.00 2.41
884 2457 7.554118 ACAAGATACAACTATCCAGGAAATGTG 59.446 37.037 0.00 0.00 30.40 3.21
1035 2608 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1053 2638 6.945938 TCTAACTCTAGCAAGACATACTCC 57.054 41.667 0.00 0.00 0.00 3.85
1156 2741 5.585047 GCCTAATGTCCTTTTGTACCAGTAG 59.415 44.000 0.00 0.00 0.00 2.57
1304 2889 5.776358 TGGGACTCTATTGGCCATTTAAAT 58.224 37.500 6.09 0.00 0.00 1.40
1491 3083 6.085555 TCTGATAACGGTATCCATTGACTC 57.914 41.667 17.67 0.00 36.08 3.36
1562 3154 8.208903 ACGCATAATACTACCCAGATTTTTACT 58.791 33.333 0.00 0.00 0.00 2.24
1745 3338 8.894409 TCAAAAGCGAACATTAACATGAATAG 57.106 30.769 0.00 0.00 34.11 1.73
1775 3368 3.502356 CCCCTTAACTGGGCAAGTAAAA 58.498 45.455 0.00 0.00 45.78 1.52
1845 3447 9.511144 AAAGTTCAATAAGGTAAACTTCAAACG 57.489 29.630 0.00 0.00 40.16 3.60
1858 3460 5.452078 TCAGTGCCAAAAGTTCAATAAGG 57.548 39.130 0.00 0.00 0.00 2.69
1886 3488 7.775093 TGGTTTATTATAGATGGCAGCCATATC 59.225 37.037 27.75 16.88 45.26 1.63
2181 4830 3.624861 AGACACAAAGAACAGCTCACAAG 59.375 43.478 0.00 0.00 0.00 3.16
2239 4888 8.768955 GCTATCACAAATACTTATGGAGTTCAG 58.231 37.037 0.00 0.00 39.86 3.02
2252 4901 8.879759 TGTTAGTGCTAAAGCTATCACAAATAC 58.120 33.333 3.26 0.00 42.66 1.89
2287 4938 5.950544 TGGTACAGGTAACATCAGCTAAT 57.049 39.130 0.00 0.00 41.41 1.73
2561 5217 3.861276 ATGTACGAAACTCGGTCATGA 57.139 42.857 0.00 0.00 45.59 3.07
2649 5305 1.295357 TATGTGTGAACAAGGCGCCG 61.295 55.000 23.20 10.77 0.00 6.46
2651 5307 0.179189 GCTATGTGTGAACAAGGCGC 60.179 55.000 0.00 0.00 0.00 6.53
2652 5308 1.155889 TGCTATGTGTGAACAAGGCG 58.844 50.000 0.00 0.00 0.00 5.52
2702 5364 5.127682 GGTTCCTCTTGAATGGCAATGTTAT 59.872 40.000 0.00 0.00 35.59 1.89
2703 5365 4.462483 GGTTCCTCTTGAATGGCAATGTTA 59.538 41.667 0.00 0.00 35.59 2.41
2718 5380 2.183679 CAGGAGTAGCAAGGTTCCTCT 58.816 52.381 0.00 0.00 37.97 3.69
2732 5394 2.031495 AAACTAGGGTGAGCAGGAGT 57.969 50.000 0.00 0.00 0.00 3.85
2820 5485 1.028868 GGGTGCCAGCTCTTCATGAC 61.029 60.000 0.00 0.00 0.00 3.06
2868 5533 3.243401 GGACGGTGCTTCTTTGATGTTTT 60.243 43.478 0.00 0.00 0.00 2.43
2878 5543 1.674057 CTCCTTGGACGGTGCTTCT 59.326 57.895 0.31 0.00 0.00 2.85
2941 5606 2.847234 TGACGGCCCTCACTGGTT 60.847 61.111 0.00 0.00 0.00 3.67
2953 5618 2.125753 GCTCTGTGCTCCTGACGG 60.126 66.667 0.00 0.00 38.95 4.79
3016 5681 0.660300 GCGTCAAACAAGGGAAAGCG 60.660 55.000 0.00 0.00 0.00 4.68
3020 5685 1.946768 CAGAAGCGTCAAACAAGGGAA 59.053 47.619 1.61 0.00 0.00 3.97
3029 5694 1.150827 CTGTGCATCAGAAGCGTCAA 58.849 50.000 9.81 0.00 46.27 3.18
3033 5698 1.424240 CTGCTGTGCATCAGAAGCG 59.576 57.895 17.12 4.14 46.27 4.68
3051 5722 1.923356 TGAAGGGTCAAAGGATTGCC 58.077 50.000 0.00 0.00 36.45 4.52
3107 5779 5.279556 GGGATAGAGAATGCTAGTGGGTAAC 60.280 48.000 0.00 0.00 0.00 2.50
3141 5817 1.507713 CGTCAGCGTCACAATTGCG 60.508 57.895 5.05 2.27 0.00 4.85
3153 5829 1.815421 ACCGGAATCATGCGTCAGC 60.815 57.895 9.46 0.00 45.41 4.26
3154 5830 2.009108 CACCGGAATCATGCGTCAG 58.991 57.895 9.46 0.00 38.93 3.51
3155 5831 2.106074 GCACCGGAATCATGCGTCA 61.106 57.895 9.46 0.00 38.93 4.35
3156 5832 1.369091 AAGCACCGGAATCATGCGTC 61.369 55.000 9.46 0.00 44.25 5.19
3157 5833 1.369091 GAAGCACCGGAATCATGCGT 61.369 55.000 9.46 5.02 44.25 5.24
3158 5834 1.091771 AGAAGCACCGGAATCATGCG 61.092 55.000 9.46 0.00 44.25 4.73
3173 5849 8.881743 CATAATTCAGAAAGAGAGGACAAGAAG 58.118 37.037 0.00 0.00 0.00 2.85
3200 5876 5.450965 CCATTGTTGCAGAACTTCAAAGACT 60.451 40.000 0.00 0.00 32.79 3.24
3202 5878 4.402155 ACCATTGTTGCAGAACTTCAAAGA 59.598 37.500 0.00 0.00 32.79 2.52
3203 5879 4.505191 CACCATTGTTGCAGAACTTCAAAG 59.495 41.667 0.00 0.00 32.79 2.77
3210 5909 3.066621 TGAGTTCACCATTGTTGCAGAAC 59.933 43.478 3.68 3.68 36.32 3.01
3258 6063 3.521796 GCCGATGGCTTCTTGGGC 61.522 66.667 0.00 2.84 46.69 5.36
3273 6078 1.135721 CAAGTAGTAGTACCGGGTGCC 59.864 57.143 10.66 0.00 0.00 5.01
3275 6080 3.350833 ACTCAAGTAGTAGTACCGGGTG 58.649 50.000 10.66 0.00 36.36 4.61
3276 6081 3.728385 ACTCAAGTAGTAGTACCGGGT 57.272 47.619 6.32 4.46 36.36 5.28
3277 6082 5.431765 TCTAACTCAAGTAGTAGTACCGGG 58.568 45.833 6.32 0.00 37.50 5.73
3279 6084 9.339492 CTTTTTCTAACTCAAGTAGTAGTACCG 57.661 37.037 4.02 0.00 37.50 4.02
3283 6088 8.628280 ACGACTTTTTCTAACTCAAGTAGTAGT 58.372 33.333 0.00 0.00 37.50 2.73
3284 6089 9.460906 AACGACTTTTTCTAACTCAAGTAGTAG 57.539 33.333 0.00 0.00 37.50 2.57
3285 6090 9.241317 CAACGACTTTTTCTAACTCAAGTAGTA 57.759 33.333 0.00 0.00 37.50 1.82
3286 6091 7.224167 CCAACGACTTTTTCTAACTCAAGTAGT 59.776 37.037 0.00 0.00 41.49 2.73
3287 6092 7.564988 CCAACGACTTTTTCTAACTCAAGTAG 58.435 38.462 0.00 0.00 29.43 2.57
3288 6093 6.018507 GCCAACGACTTTTTCTAACTCAAGTA 60.019 38.462 0.00 0.00 29.43 2.24
3289 6094 5.220796 GCCAACGACTTTTTCTAACTCAAGT 60.221 40.000 0.00 0.00 32.02 3.16
3351 6161 3.803231 GCGTGAGATTCGTCTAGACTAGA 59.197 47.826 20.34 8.17 0.00 2.43
3352 6162 3.362207 CGCGTGAGATTCGTCTAGACTAG 60.362 52.174 20.34 2.81 0.00 2.57
3353 6163 2.538861 CGCGTGAGATTCGTCTAGACTA 59.461 50.000 20.34 7.19 0.00 2.59
3354 6164 1.328069 CGCGTGAGATTCGTCTAGACT 59.672 52.381 20.34 1.83 0.00 3.24
3355 6165 1.732528 CGCGTGAGATTCGTCTAGAC 58.267 55.000 13.18 13.18 0.00 2.59
3363 6173 2.395690 CGGTTGCGCGTGAGATTC 59.604 61.111 8.43 0.00 0.00 2.52
3366 6176 2.215465 TATTCCGGTTGCGCGTGAGA 62.215 55.000 8.43 0.00 0.00 3.27
3423 6233 4.361783 TGGGAGTCACTATCAAGATTCCA 58.638 43.478 0.00 0.00 41.07 3.53
3437 6247 7.094334 CGCTACTCTTATATTACATGGGAGTCA 60.094 40.741 0.00 0.00 34.88 3.41
3440 6250 6.037098 GCGCTACTCTTATATTACATGGGAG 58.963 44.000 0.00 0.00 0.00 4.30
3505 6317 3.403057 CACGTTCACGGCAGGACG 61.403 66.667 4.07 6.25 44.95 4.79
3526 6338 1.227249 TTGGTCTTTGGTCTTCCCCA 58.773 50.000 0.00 0.00 0.00 4.96
3531 6347 2.154462 CTGCGATTGGTCTTTGGTCTT 58.846 47.619 0.00 0.00 0.00 3.01
3560 6376 9.245481 GGGTCTATGTATGCTAGACTAATTAGT 57.755 37.037 18.05 18.05 43.00 2.24
3561 6377 9.244292 TGGGTCTATGTATGCTAGACTAATTAG 57.756 37.037 11.05 11.05 43.00 1.73
3562 6378 9.596308 TTGGGTCTATGTATGCTAGACTAATTA 57.404 33.333 14.90 0.00 43.00 1.40
3564 6380 7.310113 GCTTGGGTCTATGTATGCTAGACTAAT 60.310 40.741 14.90 0.00 43.00 1.73
3565 6381 6.015350 GCTTGGGTCTATGTATGCTAGACTAA 60.015 42.308 14.90 11.38 43.00 2.24
3568 6384 4.561105 GCTTGGGTCTATGTATGCTAGAC 58.439 47.826 0.00 10.04 42.81 2.59
3569 6385 3.578716 GGCTTGGGTCTATGTATGCTAGA 59.421 47.826 0.00 0.00 0.00 2.43
3570 6386 3.615110 CGGCTTGGGTCTATGTATGCTAG 60.615 52.174 0.00 0.00 0.00 3.42
3571 6387 2.299013 CGGCTTGGGTCTATGTATGCTA 59.701 50.000 0.00 0.00 0.00 3.49
3573 6389 1.070134 TCGGCTTGGGTCTATGTATGC 59.930 52.381 0.00 0.00 0.00 3.14
3592 6417 2.234143 ACTCCTGGCTTCTTTTGCTTC 58.766 47.619 0.00 0.00 0.00 3.86
3594 6419 1.959282 CAACTCCTGGCTTCTTTTGCT 59.041 47.619 0.00 0.00 0.00 3.91
3602 6427 3.152341 CAAGTGATTCAACTCCTGGCTT 58.848 45.455 0.00 0.00 0.00 4.35
3638 6464 4.428209 CTTCTCTTCAGATCTAGCGCAAA 58.572 43.478 11.47 0.00 0.00 3.68
3639 6465 3.736433 GCTTCTCTTCAGATCTAGCGCAA 60.736 47.826 11.47 0.00 0.00 4.85
3666 6492 0.945099 CAGGCTAGTGATGCTGCATG 59.055 55.000 21.53 6.19 31.15 4.06
3700 6528 1.600663 CGATGCTACTACGCTCAAGGG 60.601 57.143 0.00 0.00 0.00 3.95
3711 6539 1.982660 TCTCCGAATCCGATGCTACT 58.017 50.000 0.00 0.00 38.22 2.57
3723 6551 0.396556 TCATCCCCGTCATCTCCGAA 60.397 55.000 0.00 0.00 0.00 4.30
3790 6627 4.787280 CTCCTCCGGCTCCACCCT 62.787 72.222 0.00 0.00 33.26 4.34
3967 6805 2.366640 TAGCCGAGGAGAAGCATAGT 57.633 50.000 0.00 0.00 0.00 2.12
3970 6808 1.418334 ACATAGCCGAGGAGAAGCAT 58.582 50.000 0.00 0.00 0.00 3.79
3974 6812 3.366396 AGAGAAACATAGCCGAGGAGAA 58.634 45.455 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.