Multiple sequence alignment - TraesCS2A01G314700

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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 TraesCS2A01G314700 chr2A 100.000 2950 0 0 1 2950 539653028 539650079 0.000000e+00 5448.0
1 TraesCS2A01G314700 chr2D 91.901 2704 91 47 296 2950 402552751 402550127 0.000000e+00 3663.0
2 TraesCS2A01G314700 chr2D 95.745 94 4 0 1 94 402554248 402554155 5.090000e-33 152.0
3 TraesCS2A01G314700 chr2B 90.019 2094 124 23 1 2052 476042666 476044716 0.000000e+00 2630.0
4 TraesCS2A01G314700 chr2B 92.604 649 36 8 2304 2947 476044877 476045518 0.000000e+00 922.0
5 TraesCS2A01G314700 chr2B 92.029 138 7 2 2121 2257 476044742 476044876 1.080000e-44 191.0
6 TraesCS2A01G314700 chr4A 84.158 101 9 4 2762 2856 37060207 37060108 1.130000e-14 91.6
7 TraesCS2A01G314700 chr3A 84.000 100 11 2 2759 2853 12778803 12778902 1.130000e-14 91.6
8 TraesCS2A01G314700 chr7B 85.185 81 6 3 2775 2855 533304518 533304592 8.770000e-11 78.7
9 TraesCS2A01G314700 chr3B 82.979 94 8 4 2762 2854 423807013 423807099 8.770000e-11 78.7
10 TraesCS2A01G314700 chr5D 82.759 87 9 3 2762 2848 264494445 264494525 4.080000e-09 73.1
11 TraesCS2A01G314700 chr3D 81.720 93 11 2 2762 2854 326696955 326697041 4.080000e-09 73.1
12 TraesCS2A01G314700 chr6B 79.612 103 16 2 2757 2854 10714978 10714876 5.280000e-08 69.4


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 TraesCS2A01G314700 chr2A 539650079 539653028 2949 True 5448.000000 5448 100.000000 1 2950 1 chr2A.!!$R1 2949
1 TraesCS2A01G314700 chr2D 402550127 402554248 4121 True 1907.500000 3663 93.823000 1 2950 2 chr2D.!!$R1 2949
2 TraesCS2A01G314700 chr2B 476042666 476045518 2852 False 1247.666667 2630 91.550667 1 2947 3 chr2B.!!$F1 2946

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
104 105 0.385751 TCGAAGCTCCCAATCTAGCG 59.614 55.0 0.0 0.0 43.63 4.26 F
606 1864 0.669077 CCTATACGGAACAGCGAGCT 59.331 55.0 0.0 0.0 33.16 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 3056 1.033746 TGCCCATCTAAGCAAGCAGC 61.034 55.0 0.0 0.0 46.19 5.25 R
2320 3605 0.240945 CACGACATGCCCTTTCAACC 59.759 55.0 0.0 0.0 0.00 3.77 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
25 26 0.887247 TGCAATCACCCATGAAACCG 59.113 50.000 0.00 0.00 38.69 4.44
104 105 0.385751 TCGAAGCTCCCAATCTAGCG 59.614 55.000 0.00 0.00 43.63 4.26
127 128 7.339732 CGAAGCATACTTTATGTCTATGGAC 57.660 40.000 1.56 1.56 38.41 4.02
177 178 5.169295 CCGAAGATCTTCTTTTCGTACCTT 58.831 41.667 28.28 0.00 41.39 3.50
209 210 4.084718 GTGACGAATTAACAAAGTTTCGCG 59.915 41.667 0.00 0.00 43.43 5.87
211 212 4.835344 ACGAATTAACAAAGTTTCGCGAA 58.165 34.783 19.38 19.38 43.43 4.70
224 225 6.969669 AGTTTCGCGAAATTGTCTAAAAAG 57.030 33.333 34.19 0.00 32.36 2.27
225 226 6.721321 AGTTTCGCGAAATTGTCTAAAAAGA 58.279 32.000 34.19 6.78 32.36 2.52
227 229 5.025986 TCGCGAAATTGTCTAAAAAGACC 57.974 39.130 6.20 0.00 37.99 3.85
250 252 8.281212 ACCTATGTTCGCTCATTTTCTATTTT 57.719 30.769 0.00 0.00 0.00 1.82
302 305 1.813786 AGCTCAACACGTCTCCTCTAC 59.186 52.381 0.00 0.00 0.00 2.59
307 1544 1.306642 ACACGTCTCCTCTACGCAGG 61.307 60.000 0.00 0.00 44.04 4.85
310 1547 1.339438 ACGTCTCCTCTACGCAGGTTA 60.339 52.381 0.00 0.00 44.04 2.85
336 1573 2.253758 CCGCCACAACACTCCACAG 61.254 63.158 0.00 0.00 0.00 3.66
355 1592 2.360475 GACCCTGCCTTGGCTCAC 60.360 66.667 13.18 0.00 0.00 3.51
404 1641 2.798847 GGTTCTTCGCGACTACACTTTT 59.201 45.455 9.15 0.00 0.00 2.27
454 1691 3.718815 AGAACAAAAGAGACCGTGACTC 58.281 45.455 0.00 0.00 34.95 3.36
456 1693 1.407979 ACAAAAGAGACCGTGACTCGT 59.592 47.619 0.00 0.00 39.12 4.18
492 1729 2.815657 CACAACAACGTGTAGTGCAA 57.184 45.000 0.00 0.00 32.00 4.08
504 1741 4.611355 CGTGTAGTGCAAAACTCAATCAGG 60.611 45.833 0.00 0.00 40.56 3.86
507 1744 2.694628 AGTGCAAAACTCAATCAGGCAA 59.305 40.909 0.00 0.00 31.64 4.52
512 1749 4.053295 CAAAACTCAATCAGGCAACCAAG 58.947 43.478 0.00 0.00 37.17 3.61
571 1829 1.779569 AAACAGTAGCGACTTCCACG 58.220 50.000 0.00 0.00 31.73 4.94
606 1864 0.669077 CCTATACGGAACAGCGAGCT 59.331 55.000 0.00 0.00 33.16 4.09
607 1865 1.335142 CCTATACGGAACAGCGAGCTC 60.335 57.143 2.73 2.73 33.16 4.09
724 1982 2.717011 CCGTAACGTTGTTGTTGATTGC 59.283 45.455 11.99 0.00 33.32 3.56
725 1983 3.355270 CGTAACGTTGTTGTTGATTGCA 58.645 40.909 11.99 0.00 33.32 4.08
728 1986 3.338818 ACGTTGTTGTTGATTGCAGAG 57.661 42.857 0.00 0.00 0.00 3.35
884 2142 3.007920 CCAGCCTCCCACAGCTCT 61.008 66.667 0.00 0.00 37.18 4.09
885 2143 2.583520 CAGCCTCCCACAGCTCTC 59.416 66.667 0.00 0.00 37.18 3.20
935 2193 3.551846 CTCCTCCCTCTACACTTCTCTC 58.448 54.545 0.00 0.00 0.00 3.20
936 2194 3.194620 TCCTCCCTCTACACTTCTCTCT 58.805 50.000 0.00 0.00 0.00 3.10
937 2195 3.201266 TCCTCCCTCTACACTTCTCTCTC 59.799 52.174 0.00 0.00 0.00 3.20
938 2196 3.551846 CTCCCTCTACACTTCTCTCTCC 58.448 54.545 0.00 0.00 0.00 3.71
986 2244 2.507484 CAGATTTGTTGCCTCACCTCA 58.493 47.619 0.00 0.00 0.00 3.86
991 2249 1.053835 TGTTGCCTCACCTCACCTCA 61.054 55.000 0.00 0.00 0.00 3.86
1118 2376 3.742248 CTCCTCCCCGTCCCTCTCC 62.742 73.684 0.00 0.00 0.00 3.71
1119 2377 3.756783 CCTCCCCGTCCCTCTCCT 61.757 72.222 0.00 0.00 0.00 3.69
1120 2378 2.364961 CTCCCCGTCCCTCTCCTT 59.635 66.667 0.00 0.00 0.00 3.36
1292 2556 1.213013 GCTCAACTTCGGCGAGAGA 59.787 57.895 23.02 13.27 0.00 3.10
1522 2795 0.678048 AGGAAGGAAGCCATGAACGC 60.678 55.000 0.00 0.00 0.00 4.84
1653 2927 2.996249 AGTAGACAGGCCATGTGATG 57.004 50.000 5.01 0.00 44.17 3.07
1654 2928 1.134280 AGTAGACAGGCCATGTGATGC 60.134 52.381 5.01 1.82 44.17 3.91
1699 2976 8.493547 GTGTCTGTTTTATTTGTGAGTAGGTAC 58.506 37.037 0.00 0.00 0.00 3.34
1733 3010 2.985896 TCCAGATTCCGAAATGGTGAC 58.014 47.619 12.96 0.00 39.52 3.67
1772 3049 1.630878 GGGGCTGGGACTGATTATAGG 59.369 57.143 0.00 0.00 0.00 2.57
1773 3050 1.003696 GGGCTGGGACTGATTATAGGC 59.996 57.143 0.00 0.00 0.00 3.93
1774 3051 1.981495 GGCTGGGACTGATTATAGGCT 59.019 52.381 0.00 0.00 0.00 4.58
1775 3052 2.373502 GGCTGGGACTGATTATAGGCTT 59.626 50.000 0.00 0.00 0.00 4.35
1776 3053 3.583086 GGCTGGGACTGATTATAGGCTTA 59.417 47.826 0.00 0.00 0.00 3.09
1777 3054 4.226168 GGCTGGGACTGATTATAGGCTTAT 59.774 45.833 0.00 0.00 0.00 1.73
1778 3055 5.425539 GGCTGGGACTGATTATAGGCTTATA 59.574 44.000 0.00 0.00 0.00 0.98
1779 3056 6.407525 GGCTGGGACTGATTATAGGCTTATAG 60.408 46.154 0.00 0.00 0.00 1.31
1888 3172 4.092675 GTGCTAGCACTTCAGAGAATCAAC 59.907 45.833 35.25 7.76 43.12 3.18
1890 3174 4.874966 GCTAGCACTTCAGAGAATCAACAT 59.125 41.667 10.63 0.00 37.82 2.71
1891 3175 5.353678 GCTAGCACTTCAGAGAATCAACATT 59.646 40.000 10.63 0.00 37.82 2.71
1892 3176 5.624344 AGCACTTCAGAGAATCAACATTG 57.376 39.130 0.00 0.00 37.82 2.82
1893 3177 4.082895 AGCACTTCAGAGAATCAACATTGC 60.083 41.667 0.00 0.00 37.82 3.56
1959 3243 2.375174 TGCACTTATGAACCTTGGTCCT 59.625 45.455 0.00 0.00 0.00 3.85
2052 3336 5.993441 GGCTGTACCTGTACTTTGTTTTCTA 59.007 40.000 8.75 0.00 37.00 2.10
2053 3337 6.073385 GGCTGTACCTGTACTTTGTTTTCTAC 60.073 42.308 8.75 0.00 37.00 2.59
2054 3338 6.704937 GCTGTACCTGTACTTTGTTTTCTACT 59.295 38.462 8.75 0.00 37.00 2.57
2055 3339 7.869429 GCTGTACCTGTACTTTGTTTTCTACTA 59.131 37.037 8.75 0.00 37.00 1.82
2056 3340 9.189723 CTGTACCTGTACTTTGTTTTCTACTAC 57.810 37.037 8.75 0.00 37.00 2.73
2057 3341 8.917088 TGTACCTGTACTTTGTTTTCTACTACT 58.083 33.333 8.75 0.00 37.00 2.57
2058 3342 9.404348 GTACCTGTACTTTGTTTTCTACTACTC 57.596 37.037 0.21 0.00 33.45 2.59
2059 3343 7.440198 ACCTGTACTTTGTTTTCTACTACTCC 58.560 38.462 0.00 0.00 0.00 3.85
2060 3344 7.289549 ACCTGTACTTTGTTTTCTACTACTCCT 59.710 37.037 0.00 0.00 0.00 3.69
2061 3345 7.599245 CCTGTACTTTGTTTTCTACTACTCCTG 59.401 40.741 0.00 0.00 0.00 3.86
2062 3346 7.439381 TGTACTTTGTTTTCTACTACTCCTGG 58.561 38.462 0.00 0.00 0.00 4.45
2063 3347 6.496144 ACTTTGTTTTCTACTACTCCTGGT 57.504 37.500 0.00 0.00 0.00 4.00
2064 3348 6.522946 ACTTTGTTTTCTACTACTCCTGGTC 58.477 40.000 0.00 0.00 0.00 4.02
2065 3349 6.326843 ACTTTGTTTTCTACTACTCCTGGTCT 59.673 38.462 0.00 0.00 0.00 3.85
2066 3350 7.508296 ACTTTGTTTTCTACTACTCCTGGTCTA 59.492 37.037 0.00 0.00 0.00 2.59
2067 3351 7.463961 TTGTTTTCTACTACTCCTGGTCTAG 57.536 40.000 0.00 0.00 0.00 2.43
2068 3352 6.550163 TGTTTTCTACTACTCCTGGTCTAGT 58.450 40.000 9.83 9.83 0.00 2.57
2069 3353 6.658391 TGTTTTCTACTACTCCTGGTCTAGTC 59.342 42.308 8.65 0.00 0.00 2.59
2070 3354 6.639590 TTTCTACTACTCCTGGTCTAGTCT 57.360 41.667 8.65 0.00 0.00 3.24
2071 3355 5.617528 TCTACTACTCCTGGTCTAGTCTG 57.382 47.826 8.65 5.38 0.00 3.51
2072 3356 5.031495 TCTACTACTCCTGGTCTAGTCTGT 58.969 45.833 8.65 4.46 0.00 3.41
2073 3357 6.200852 TCTACTACTCCTGGTCTAGTCTGTA 58.799 44.000 8.65 5.17 0.00 2.74
2074 3358 5.979656 ACTACTCCTGGTCTAGTCTGTAT 57.020 43.478 0.00 0.00 0.00 2.29
2075 3359 6.330178 ACTACTCCTGGTCTAGTCTGTATT 57.670 41.667 0.00 0.00 0.00 1.89
2076 3360 6.733509 ACTACTCCTGGTCTAGTCTGTATTT 58.266 40.000 0.00 0.00 0.00 1.40
2077 3361 6.829811 ACTACTCCTGGTCTAGTCTGTATTTC 59.170 42.308 0.00 0.00 0.00 2.17
2078 3362 5.833340 ACTCCTGGTCTAGTCTGTATTTCT 58.167 41.667 0.00 0.00 0.00 2.52
2079 3363 6.257586 ACTCCTGGTCTAGTCTGTATTTCTT 58.742 40.000 0.00 0.00 0.00 2.52
2080 3364 6.726764 ACTCCTGGTCTAGTCTGTATTTCTTT 59.273 38.462 0.00 0.00 0.00 2.52
2081 3365 7.093684 ACTCCTGGTCTAGTCTGTATTTCTTTC 60.094 40.741 0.00 0.00 0.00 2.62
2082 3366 6.954684 TCCTGGTCTAGTCTGTATTTCTTTCT 59.045 38.462 0.00 0.00 0.00 2.52
2083 3367 8.114102 TCCTGGTCTAGTCTGTATTTCTTTCTA 58.886 37.037 0.00 0.00 0.00 2.10
2084 3368 8.919145 CCTGGTCTAGTCTGTATTTCTTTCTAT 58.081 37.037 0.00 0.00 0.00 1.98
2085 3369 9.959749 CTGGTCTAGTCTGTATTTCTTTCTATC 57.040 37.037 0.00 0.00 0.00 2.08
2088 3372 9.458374 GTCTAGTCTGTATTTCTTTCTATCTGC 57.542 37.037 0.00 0.00 0.00 4.26
2102 3386 9.155975 TCTTTCTATCTGCACTGTATTTCTTTC 57.844 33.333 0.00 0.00 0.00 2.62
2129 3413 2.374184 CACTGTCCTCTCCTGGTCTAG 58.626 57.143 0.00 0.00 0.00 2.43
2169 3453 7.117523 ACGCTATCATGATAGAAAATTCAGAGC 59.882 37.037 36.28 22.27 42.55 4.09
2208 3492 4.789012 TCATGGAAAATCAGCAAACTCC 57.211 40.909 0.00 0.00 0.00 3.85
2227 3512 6.374417 ACTCCAGATGTATGGTTAACTGTT 57.626 37.500 5.42 0.00 41.43 3.16
2228 3513 7.490657 ACTCCAGATGTATGGTTAACTGTTA 57.509 36.000 5.42 0.00 41.43 2.41
2229 3514 7.328737 ACTCCAGATGTATGGTTAACTGTTAC 58.671 38.462 5.42 5.99 41.43 2.50
2252 3537 2.480419 AGCTGTTCGTGTTATCACAAGC 59.520 45.455 4.87 7.11 44.02 4.01
2263 3548 2.936919 ATCACAAGCTGTCCACTTCA 57.063 45.000 0.00 0.00 0.00 3.02
2320 3605 2.905075 TGATGCATAAACAGGGAGTCG 58.095 47.619 0.00 0.00 0.00 4.18
2398 3687 8.743714 AGGAAAGAAAAATAAGGAGCATAGTTG 58.256 33.333 0.00 0.00 0.00 3.16
2482 3771 4.122776 GCCAGATGGTCAGTAGTTACATG 58.877 47.826 0.00 0.00 37.57 3.21
2483 3772 4.697514 CCAGATGGTCAGTAGTTACATGG 58.302 47.826 0.00 0.00 0.00 3.66
2484 3773 4.162320 CCAGATGGTCAGTAGTTACATGGT 59.838 45.833 0.00 0.00 0.00 3.55
2625 3914 3.622163 CACTGAAGAGCAAGATGTGGATC 59.378 47.826 0.00 0.00 0.00 3.36
2727 4016 6.946229 TCAGTCTAAATAAGTTTCTGCGTC 57.054 37.500 0.00 0.00 0.00 5.19
2754 4043 3.065648 GTCCTCTTCTACTGTCACCGATC 59.934 52.174 0.00 0.00 0.00 3.69
2767 4056 4.466370 TGTCACCGATCAAATTCTACTCCT 59.534 41.667 0.00 0.00 0.00 3.69
2771 4061 4.469945 ACCGATCAAATTCTACTCCTTCCA 59.530 41.667 0.00 0.00 0.00 3.53
2811 4101 2.621526 AGTTTTGAACTAAGGCAACCCG 59.378 45.455 0.00 0.00 40.69 5.28
2813 4103 1.600023 TTGAACTAAGGCAACCCGTG 58.400 50.000 0.00 0.00 35.76 4.94
2816 4106 0.536460 AACTAAGGCAACCCGTGGTG 60.536 55.000 0.00 0.00 34.74 4.17
2884 4183 2.632512 CAATAGCAACAACAACCCCCTT 59.367 45.455 0.00 0.00 0.00 3.95
2906 4205 2.548920 GGAATAGCGGGGTCTTCATCAG 60.549 54.545 0.00 0.00 0.00 2.90
2909 4208 3.036429 GCGGGGTCTTCATCAGCCT 62.036 63.158 0.00 0.00 0.00 4.58
2910 4209 1.153289 CGGGGTCTTCATCAGCCTG 60.153 63.158 0.00 0.00 0.00 4.85
2915 4214 0.747283 GTCTTCATCAGCCTGCCAGG 60.747 60.000 6.32 6.32 38.80 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.937015 TGTAAAAACTATTGCCCCGTCTAC 59.063 41.667 0.00 0.00 0.00 2.59
61 62 7.043391 CGACATTCGAGCTACTAATTCATGAAA 60.043 37.037 13.09 0.00 43.74 2.69
94 95 6.425114 ACATAAAGTATGCTTCGCTAGATTGG 59.575 38.462 0.00 0.00 39.79 3.16
95 96 7.383572 AGACATAAAGTATGCTTCGCTAGATTG 59.616 37.037 0.00 0.00 39.79 2.67
104 105 7.095439 GCAGTCCATAGACATAAAGTATGCTTC 60.095 40.741 0.00 0.00 46.15 3.86
111 112 4.471386 ACAGGCAGTCCATAGACATAAAGT 59.529 41.667 0.00 0.00 46.15 2.66
126 127 2.071778 AACCAAACATGACAGGCAGT 57.928 45.000 0.00 0.00 0.00 4.40
127 128 3.612479 GCTTAACCAAACATGACAGGCAG 60.612 47.826 0.00 0.00 0.00 4.85
158 159 6.990349 TGTTTCAAGGTACGAAAAGAAGATCT 59.010 34.615 0.00 0.00 34.32 2.75
177 178 6.424176 TTGTTAATTCGTCACAGTGTTTCA 57.576 33.333 0.00 0.00 0.00 2.69
209 210 9.543018 CGAACATAGGTCTTTTTAGACAATTTC 57.457 33.333 7.52 2.52 40.38 2.17
211 212 7.390718 AGCGAACATAGGTCTTTTTAGACAATT 59.609 33.333 7.52 0.00 40.38 2.32
224 225 7.484035 AATAGAAAATGAGCGAACATAGGTC 57.516 36.000 0.00 0.00 36.72 3.85
225 226 7.865706 AAATAGAAAATGAGCGAACATAGGT 57.134 32.000 0.00 0.00 0.00 3.08
250 252 9.709495 AACCGGTTCGCACTATATATAATAAAA 57.291 29.630 15.86 0.00 0.00 1.52
254 256 8.611654 AAAAACCGGTTCGCACTATATATAAT 57.388 30.769 22.53 0.00 0.00 1.28
281 284 2.201921 AGAGGAGACGTGTTGAGCTA 57.798 50.000 0.00 0.00 0.00 3.32
290 293 0.608582 AACCTGCGTAGAGGAGACGT 60.609 55.000 0.53 0.00 41.23 4.34
292 295 2.754002 AGTTAACCTGCGTAGAGGAGAC 59.246 50.000 0.53 0.00 41.23 3.36
302 305 1.787847 CGGCAAGAGTTAACCTGCG 59.212 57.895 15.01 9.21 0.00 5.18
307 1544 0.948678 TTGTGGCGGCAAGAGTTAAC 59.051 50.000 15.50 0.00 0.00 2.01
310 1547 1.453015 TGTTGTGGCGGCAAGAGTT 60.453 52.632 15.50 0.00 0.00 3.01
355 1592 1.069703 CATGACAAAGACGGTGCTGTG 60.070 52.381 0.00 0.00 0.00 3.66
404 1641 3.774734 TGTTTGGCAGAGTAGGACTAGA 58.225 45.455 0.00 0.00 0.00 2.43
485 1722 3.485394 TGCCTGATTGAGTTTTGCACTA 58.515 40.909 0.00 0.00 35.01 2.74
490 1727 3.731652 TGGTTGCCTGATTGAGTTTTG 57.268 42.857 0.00 0.00 0.00 2.44
492 1729 2.036346 GCTTGGTTGCCTGATTGAGTTT 59.964 45.455 0.00 0.00 0.00 2.66
504 1741 2.919328 AGGCAAGGGCTTGGTTGC 60.919 61.111 0.00 0.00 46.88 4.17
507 1744 3.570212 ACGAGGCAAGGGCTTGGT 61.570 61.111 11.22 2.52 42.94 3.67
586 1844 0.940047 GCTCGCTGTTCCGTATAGGC 60.940 60.000 0.00 0.00 40.77 3.93
724 1982 1.775039 CTCGCTCGCTCCTCTCTCTG 61.775 65.000 0.00 0.00 0.00 3.35
725 1983 1.523711 CTCGCTCGCTCCTCTCTCT 60.524 63.158 0.00 0.00 0.00 3.10
728 1986 2.407210 CACTCGCTCGCTCCTCTC 59.593 66.667 0.00 0.00 0.00 3.20
935 2193 0.535102 GGCGAGAGAGAGAGAGGGAG 60.535 65.000 0.00 0.00 0.00 4.30
936 2194 1.275421 TGGCGAGAGAGAGAGAGGGA 61.275 60.000 0.00 0.00 0.00 4.20
937 2195 1.101049 GTGGCGAGAGAGAGAGAGGG 61.101 65.000 0.00 0.00 0.00 4.30
938 2196 0.393673 TGTGGCGAGAGAGAGAGAGG 60.394 60.000 0.00 0.00 0.00 3.69
986 2244 1.362932 AGATACAGGTGGAGGTGAGGT 59.637 52.381 0.00 0.00 0.00 3.85
991 2249 2.700897 GCATACAGATACAGGTGGAGGT 59.299 50.000 0.00 0.00 0.00 3.85
1223 2484 4.514585 TGGTGGTGGTGGTGGTGC 62.515 66.667 0.00 0.00 0.00 5.01
1292 2556 4.208686 GCGAAGGCGATCCCGAGT 62.209 66.667 0.00 0.00 40.82 4.18
1522 2795 7.713734 ATGGAATTAATGGAGAATAGGCATG 57.286 36.000 0.00 0.00 0.00 4.06
1653 2927 1.077123 CACAGCTCTCACATCAGTGC 58.923 55.000 0.00 0.00 45.49 4.40
1699 2976 5.537188 GGAATCTGGATCACTTGCTAGTAG 58.463 45.833 0.00 0.00 31.96 2.57
1715 2992 3.691118 ACATGTCACCATTTCGGAATCTG 59.309 43.478 0.00 0.00 38.63 2.90
1733 3010 4.689071 CCCCACATGAATCAATCAACATG 58.311 43.478 0.00 0.00 42.54 3.21
1775 3052 8.967635 GATGCCCATCTAAGCAAGCAGCTATA 62.968 46.154 0.00 0.02 42.93 1.31
1779 3056 1.033746 TGCCCATCTAAGCAAGCAGC 61.034 55.000 0.00 0.00 46.19 5.25
1827 3111 1.943968 GCTAAGATCACGGCACCACAA 60.944 52.381 0.00 0.00 0.00 3.33
1888 3172 1.179152 TCCACATGGAGCAAGCAATG 58.821 50.000 0.00 0.00 39.78 2.82
1890 3174 1.546923 CATTCCACATGGAGCAAGCAA 59.453 47.619 0.00 0.00 46.36 3.91
1891 3175 1.179152 CATTCCACATGGAGCAAGCA 58.821 50.000 0.00 0.00 46.36 3.91
1892 3176 1.466856 TCATTCCACATGGAGCAAGC 58.533 50.000 0.00 0.00 46.36 4.01
1893 3177 3.697542 TCAATCATTCCACATGGAGCAAG 59.302 43.478 0.00 0.00 46.36 4.01
1959 3243 3.877559 CCATCATAGCAGGAGTGACAAA 58.122 45.455 0.00 0.00 0.00 2.83
2052 3336 5.979656 ATACAGACTAGACCAGGAGTAGT 57.020 43.478 0.00 0.00 0.00 2.73
2053 3337 7.057894 AGAAATACAGACTAGACCAGGAGTAG 58.942 42.308 0.00 0.00 0.00 2.57
2054 3338 6.971340 AGAAATACAGACTAGACCAGGAGTA 58.029 40.000 0.00 0.00 0.00 2.59
2055 3339 5.833340 AGAAATACAGACTAGACCAGGAGT 58.167 41.667 0.00 0.00 0.00 3.85
2056 3340 6.783708 AAGAAATACAGACTAGACCAGGAG 57.216 41.667 0.00 0.00 0.00 3.69
2057 3341 6.954684 AGAAAGAAATACAGACTAGACCAGGA 59.045 38.462 0.00 0.00 0.00 3.86
2058 3342 7.176589 AGAAAGAAATACAGACTAGACCAGG 57.823 40.000 0.00 0.00 0.00 4.45
2059 3343 9.959749 GATAGAAAGAAATACAGACTAGACCAG 57.040 37.037 0.00 0.00 0.00 4.00
2060 3344 9.702253 AGATAGAAAGAAATACAGACTAGACCA 57.298 33.333 0.00 0.00 0.00 4.02
2061 3345 9.959749 CAGATAGAAAGAAATACAGACTAGACC 57.040 37.037 0.00 0.00 0.00 3.85
2062 3346 9.458374 GCAGATAGAAAGAAATACAGACTAGAC 57.542 37.037 0.00 0.00 0.00 2.59
2063 3347 9.190317 TGCAGATAGAAAGAAATACAGACTAGA 57.810 33.333 0.00 0.00 0.00 2.43
2064 3348 9.243637 GTGCAGATAGAAAGAAATACAGACTAG 57.756 37.037 0.00 0.00 0.00 2.57
2065 3349 8.972127 AGTGCAGATAGAAAGAAATACAGACTA 58.028 33.333 0.00 0.00 0.00 2.59
2066 3350 7.763528 CAGTGCAGATAGAAAGAAATACAGACT 59.236 37.037 0.00 0.00 0.00 3.24
2067 3351 7.547370 ACAGTGCAGATAGAAAGAAATACAGAC 59.453 37.037 0.00 0.00 0.00 3.51
2068 3352 7.615403 ACAGTGCAGATAGAAAGAAATACAGA 58.385 34.615 0.00 0.00 0.00 3.41
2069 3353 7.840342 ACAGTGCAGATAGAAAGAAATACAG 57.160 36.000 0.00 0.00 0.00 2.74
2070 3354 9.890629 AATACAGTGCAGATAGAAAGAAATACA 57.109 29.630 0.00 0.00 0.00 2.29
2073 3357 9.678260 AGAAATACAGTGCAGATAGAAAGAAAT 57.322 29.630 0.00 0.00 0.00 2.17
2074 3358 9.507329 AAGAAATACAGTGCAGATAGAAAGAAA 57.493 29.630 0.00 0.00 0.00 2.52
2075 3359 9.507329 AAAGAAATACAGTGCAGATAGAAAGAA 57.493 29.630 0.00 0.00 0.00 2.52
2076 3360 9.155975 GAAAGAAATACAGTGCAGATAGAAAGA 57.844 33.333 0.00 0.00 0.00 2.52
2077 3361 9.160496 AGAAAGAAATACAGTGCAGATAGAAAG 57.840 33.333 0.00 0.00 0.00 2.62
2080 3364 9.973450 GATAGAAAGAAATACAGTGCAGATAGA 57.027 33.333 0.00 0.00 0.00 1.98
2081 3365 9.979578 AGATAGAAAGAAATACAGTGCAGATAG 57.020 33.333 0.00 0.00 0.00 2.08
2082 3366 9.755804 CAGATAGAAAGAAATACAGTGCAGATA 57.244 33.333 0.00 0.00 0.00 1.98
2083 3367 7.226325 GCAGATAGAAAGAAATACAGTGCAGAT 59.774 37.037 0.00 0.00 0.00 2.90
2084 3368 6.536582 GCAGATAGAAAGAAATACAGTGCAGA 59.463 38.462 0.00 0.00 0.00 4.26
2085 3369 6.314648 TGCAGATAGAAAGAAATACAGTGCAG 59.685 38.462 0.00 0.00 32.56 4.41
2088 3372 7.332926 ACAGTGCAGATAGAAAGAAATACAGTG 59.667 37.037 0.00 0.00 0.00 3.66
2102 3386 2.361757 CAGGAGAGGACAGTGCAGATAG 59.638 54.545 0.00 0.00 0.00 2.08
2129 3413 1.996292 TAGCGTGATTGCACTCAGAC 58.004 50.000 7.05 2.73 42.93 3.51
2208 3492 8.198109 AGCTAGTAACAGTTAACCATACATCTG 58.802 37.037 0.88 0.00 0.00 2.90
2252 3537 4.543590 AGGTAACAGATGAAGTGGACAG 57.456 45.455 0.00 0.00 41.41 3.51
2320 3605 0.240945 CACGACATGCCCTTTCAACC 59.759 55.000 0.00 0.00 0.00 3.77
2378 3664 9.174166 TCCTAACAACTATGCTCCTTATTTTTC 57.826 33.333 0.00 0.00 0.00 2.29
2482 3771 6.980397 CCAAGATGCAAATTTTAGGACATACC 59.020 38.462 0.00 0.00 39.35 2.73
2483 3772 7.702348 GTCCAAGATGCAAATTTTAGGACATAC 59.298 37.037 14.24 0.00 41.88 2.39
2484 3773 7.395772 TGTCCAAGATGCAAATTTTAGGACATA 59.604 33.333 16.54 2.16 45.60 2.29
2625 3914 7.175641 ACAAAGATACCAAGAAGAACATTCCAG 59.824 37.037 0.00 0.00 0.00 3.86
2727 4016 4.477780 GTGACAGTAGAAGAGGACTTTCG 58.522 47.826 0.00 0.00 36.39 3.46
2754 4043 5.165961 TGGAGTGGAAGGAGTAGAATTTG 57.834 43.478 0.00 0.00 0.00 2.32
2786 4076 4.216731 GTTGCCTTAGTTCAAAACTACGC 58.783 43.478 0.00 5.44 43.30 4.42
2811 4101 1.472480 AGTGTCACAGTTTTGCACCAC 59.528 47.619 5.62 0.00 0.00 4.16
2813 4103 2.939460 AAGTGTCACAGTTTTGCACC 57.061 45.000 5.62 0.00 0.00 5.01
2816 4106 6.039616 TCCAAAATAAGTGTCACAGTTTTGC 58.960 36.000 22.14 0.00 36.03 3.68
2884 4183 1.416401 GATGAAGACCCCGCTATTCCA 59.584 52.381 0.00 0.00 0.00 3.53
2896 4195 0.747283 CCTGGCAGGCTGATGAAGAC 60.747 60.000 22.68 0.00 0.00 3.01
2915 4214 0.530288 ACATTGTACAATTGGGCGGC 59.470 50.000 18.50 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.