Multiple sequence alignment - TraesCS5D01G102300

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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 TraesCS5D01G102300 chr5D 100.000 6108 0 0 1 6108 115412142 115406035 0.000000e+00 11280.0
1 TraesCS5D01G102300 chr5B 97.427 5480 74 17 517 5959 126610006 126604557 0.000000e+00 9276.0
2 TraesCS5D01G102300 chr5B 89.981 539 21 9 1 508 126617345 126616809 0.000000e+00 665.0
3 TraesCS5D01G102300 chr5B 81.790 324 44 6 3 312 544412977 544412655 2.180000e-64 257.0
4 TraesCS5D01G102300 chr5B 87.611 113 14 0 481 593 617233963 617234075 1.380000e-26 132.0
5 TraesCS5D01G102300 chr5A 91.030 3980 225 42 308 4245 121421273 121417384 0.000000e+00 5251.0
6 TraesCS5D01G102300 chr5A 93.793 725 39 2 4453 5171 121417384 121416660 0.000000e+00 1085.0
7 TraesCS5D01G102300 chr5A 91.401 314 23 2 5170 5479 121416499 121416186 1.570000e-115 427.0
8 TraesCS5D01G102300 chr5A 90.184 326 15 7 1 311 121421662 121421339 5.700000e-110 409.0
9 TraesCS5D01G102300 chr5A 93.191 235 13 3 5510 5743 121416187 121415955 5.860000e-90 342.0
10 TraesCS5D01G102300 chrUn 100.000 386 0 0 1929 2314 480650113 480650498 0.000000e+00 713.0
11 TraesCS5D01G102300 chr4A 86.503 326 30 5 1 312 621134044 621133719 4.530000e-91 346.0
12 TraesCS5D01G102300 chr4A 86.196 326 30 6 1 312 531256728 531257052 7.580000e-89 339.0
13 TraesCS5D01G102300 chr3A 86.196 326 31 3 1 312 687982641 687982316 2.110000e-89 340.0
14 TraesCS5D01G102300 chr3A 80.899 267 28 8 308 551 726299930 726299664 8.080000e-44 189.0
15 TraesCS5D01G102300 chr3A 77.524 307 43 11 308 589 615097929 615097624 1.760000e-35 161.0
16 TraesCS5D01G102300 chr7A 85.890 326 32 5 1 312 217947364 217947689 9.810000e-88 335.0
17 TraesCS5D01G102300 chr7A 82.822 326 42 2 1 312 724313444 724313119 4.660000e-71 279.0
18 TraesCS5D01G102300 chr3D 86.111 324 30 7 2 311 22686624 22686302 9.810000e-88 335.0
19 TraesCS5D01G102300 chr3D 80.357 280 32 8 314 570 22686252 22685973 2.250000e-44 191.0
20 TraesCS5D01G102300 chr2D 85.890 326 32 6 1 312 651564999 651565324 9.810000e-88 335.0
21 TraesCS5D01G102300 chr4D 85.627 327 31 7 1 312 385674501 385674176 4.560000e-86 329.0
22 TraesCS5D01G102300 chr4D 78.808 302 39 8 308 586 385610360 385610061 4.860000e-41 180.0
23 TraesCS5D01G102300 chr4D 78.477 302 40 8 308 586 385674110 385673811 2.260000e-39 174.0
24 TraesCS5D01G102300 chr2B 85.065 308 31 7 1 294 691812436 691812130 3.580000e-77 300.0
25 TraesCS5D01G102300 chr3B 80.000 300 34 11 308 585 429387241 429386946 1.340000e-46 198.0
26 TraesCS5D01G102300 chr7B 86.239 109 15 0 481 589 394941806 394941698 1.080000e-22 119.0
27 TraesCS5D01G102300 chr7B 90.541 74 7 0 1789 1862 143337671 143337598 1.400000e-16 99.0
28 TraesCS5D01G102300 chr6D 87.368 95 7 2 1766 1860 24823336 24823425 3.010000e-18 104.0
29 TraesCS5D01G102300 chr6D 91.549 71 6 0 1789 1859 263008860 263008790 1.400000e-16 99.0
30 TraesCS5D01G102300 chr7D 92.857 70 5 0 1789 1858 401536756 401536687 1.080000e-17 102.0
31 TraesCS5D01G102300 chr7D 90.667 75 6 1 1789 1863 56941307 56941234 1.400000e-16 99.0
32 TraesCS5D01G102300 chr6A 91.549 71 6 0 1789 1859 358151021 358150951 1.400000e-16 99.0
33 TraesCS5D01G102300 chr2A 90.541 74 7 0 1789 1862 569278877 569278804 1.400000e-16 99.0
34 TraesCS5D01G102300 chr2A 83.824 68 11 0 590 657 14694032 14694099 1.420000e-06 65.8


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 TraesCS5D01G102300 chr5D 115406035 115412142 6107 True 11280.0 11280 100.0000 1 6108 1 chr5D.!!$R1 6107
1 TraesCS5D01G102300 chr5B 126604557 126610006 5449 True 9276.0 9276 97.4270 517 5959 1 chr5B.!!$R1 5442
2 TraesCS5D01G102300 chr5B 126616809 126617345 536 True 665.0 665 89.9810 1 508 1 chr5B.!!$R2 507
3 TraesCS5D01G102300 chr5A 121415955 121421662 5707 True 1502.8 5251 91.9198 1 5743 5 chr5A.!!$R1 5742
4 TraesCS5D01G102300 chr3D 22685973 22686624 651 True 263.0 335 83.2340 2 570 2 chr3D.!!$R1 568
5 TraesCS5D01G102300 chr4D 385673811 385674501 690 True 251.5 329 82.0520 1 586 2 chr4D.!!$R2 585

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
565 677 0.039256 TTAGCACGCTTCGTAACCGT 60.039 50.000 0.00 0.00 38.32 4.83 F
770 882 1.615814 CGGAGAGGGAGAGGAGGAA 59.384 63.158 0.00 0.00 0.00 3.36 F
2717 2882 0.179092 GCAGGATCCCAAAAGCATGC 60.179 55.000 10.51 10.51 0.00 4.06 F
4417 4591 0.694444 TGGATGGGAGGGCTCTTACC 60.694 60.000 1.45 1.45 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1505 1658 7.162761 TGCAGAATGTCAATGGAATTTGAAAT 58.837 30.769 0.00 0.0 37.36 2.17 R
3131 3296 1.812571 GAACACCTGCATCCGTTGATT 59.187 47.619 0.00 0.0 0.00 2.57 R
4645 4825 1.536766 CCTGAAAATTCGTCTGCAGCA 59.463 47.619 9.47 0.0 0.00 4.41 R
6063 6414 0.108424 ACTGCGCCTCTGTCTCAATC 60.108 55.000 4.18 0.0 0.00 2.67 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 5.249393 AGGAAAGATGTGGAGAGAGCTTTTA 59.751 40.000 0.00 0.00 0.00 1.52
242 258 2.629656 CCCGCTTTGTTGCCTCCTG 61.630 63.158 0.00 0.00 0.00 3.86
312 376 4.460948 AATTGAGAAATGGTGGTCATGC 57.539 40.909 0.00 0.00 35.99 4.06
329 416 3.927758 TCATGCACTATTTGTTGCATTGC 59.072 39.130 6.33 0.46 39.52 3.56
432 531 7.120579 TGAATGAGAAGTGTTGTTTGTGTTAGT 59.879 33.333 0.00 0.00 0.00 2.24
508 618 1.686587 GGTAAAGCAAAACACCAGCCT 59.313 47.619 0.00 0.00 0.00 4.58
565 677 0.039256 TTAGCACGCTTCGTAACCGT 60.039 50.000 0.00 0.00 38.32 4.83
770 882 1.615814 CGGAGAGGGAGAGGAGGAA 59.384 63.158 0.00 0.00 0.00 3.36
861 976 3.542602 ACTCCCCACTCCCCACCT 61.543 66.667 0.00 0.00 0.00 4.00
1633 1786 2.846827 ACCTTAGCTAATTCCAGTGGCT 59.153 45.455 6.64 0.00 37.08 4.75
2717 2882 0.179092 GCAGGATCCCAAAAGCATGC 60.179 55.000 10.51 10.51 0.00 4.06
3131 3296 1.352083 CACTCCCTTCAAGGACCTCA 58.648 55.000 4.43 0.00 37.67 3.86
3396 3565 9.132521 CAAAAGATCAAACAACAGATACATTCC 57.867 33.333 0.00 0.00 0.00 3.01
3513 3684 0.987081 ATCTCAGGATGCAGGCCAGT 60.987 55.000 5.01 0.00 34.76 4.00
3612 3783 6.214191 TCTTGCTTTGGTTTCACAAACATA 57.786 33.333 1.78 0.00 43.15 2.29
4226 4400 2.222227 ATGAAGCCCAAGGGAAGTTC 57.778 50.000 9.92 8.62 37.50 3.01
4329 4503 0.899717 GGGGATTGCTCAAACTGGCA 60.900 55.000 0.00 0.00 36.62 4.92
4417 4591 0.694444 TGGATGGGAGGGCTCTTACC 60.694 60.000 1.45 1.45 0.00 2.85
4515 4689 9.632807 GTTGGTCTATAATCTGTCATCTGATAC 57.367 37.037 0.00 0.00 33.11 2.24
4645 4825 2.045926 GTCACGCTCCATTGCCCT 60.046 61.111 0.00 0.00 0.00 5.19
5360 5707 6.976636 ATTTTACTGAACTAGCTGCTCTTC 57.023 37.500 4.91 9.15 0.00 2.87
5361 5708 5.468540 TTTACTGAACTAGCTGCTCTTCA 57.531 39.130 4.91 13.30 0.00 3.02
5574 5921 1.996191 GTTTCTAAGAGCTGGCAGTCG 59.004 52.381 17.16 0.00 0.00 4.18
5600 5947 5.224888 CACAGGAATGAACCACAAAGATTG 58.775 41.667 0.00 0.00 0.00 2.67
5710 6060 1.134037 GTACAGGGTGGTTTGTGTCCA 60.134 52.381 0.00 0.00 0.00 4.02
5841 6192 8.568794 CATTGAGATCAGTGCAAGATTTCATAT 58.431 33.333 18.40 13.56 36.76 1.78
5876 6227 8.165397 ACTAAGAGAGAAAACACTAGTACTCCT 58.835 37.037 0.00 0.00 0.00 3.69
5877 6228 7.457024 AAGAGAGAAAACACTAGTACTCCTC 57.543 40.000 0.00 0.00 0.00 3.71
5878 6229 5.947566 AGAGAGAAAACACTAGTACTCCTCC 59.052 44.000 0.00 0.00 0.00 4.30
5879 6230 4.701171 AGAGAAAACACTAGTACTCCTCCG 59.299 45.833 0.00 0.00 0.00 4.63
5880 6231 4.405548 AGAAAACACTAGTACTCCTCCGT 58.594 43.478 0.00 0.00 0.00 4.69
5881 6232 4.458642 AGAAAACACTAGTACTCCTCCGTC 59.541 45.833 0.00 0.00 0.00 4.79
5882 6233 2.416680 ACACTAGTACTCCTCCGTCC 57.583 55.000 0.00 0.00 0.00 4.79
5883 6234 1.064832 ACACTAGTACTCCTCCGTCCC 60.065 57.143 0.00 0.00 0.00 4.46
5884 6235 1.064906 CACTAGTACTCCTCCGTCCCA 60.065 57.143 0.00 0.00 0.00 4.37
5951 6302 6.061022 ACAGGTTATGTCATGGTGAACATA 57.939 37.500 0.00 1.82 37.75 2.29
5955 6306 8.469200 CAGGTTATGTCATGGTGAACATATTTT 58.531 33.333 5.96 0.00 37.84 1.82
6007 6358 6.817765 ATTTTCATAACACGGTGAACATCT 57.182 33.333 16.29 0.00 34.34 2.90
6008 6359 6.627395 TTTTCATAACACGGTGAACATCTT 57.373 33.333 16.29 0.00 34.34 2.40
6009 6360 6.627395 TTTCATAACACGGTGAACATCTTT 57.373 33.333 16.29 0.00 34.34 2.52
6010 6361 6.627395 TTCATAACACGGTGAACATCTTTT 57.373 33.333 16.29 0.00 29.93 2.27
6011 6362 6.627395 TCATAACACGGTGAACATCTTTTT 57.373 33.333 16.29 0.00 0.00 1.94
6012 6363 6.434596 TCATAACACGGTGAACATCTTTTTG 58.565 36.000 16.29 2.75 0.00 2.44
6013 6364 4.974368 AACACGGTGAACATCTTTTTGA 57.026 36.364 16.29 0.00 0.00 2.69
6014 6365 5.514274 AACACGGTGAACATCTTTTTGAT 57.486 34.783 16.29 0.00 35.40 2.57
6015 6366 5.514274 ACACGGTGAACATCTTTTTGATT 57.486 34.783 16.29 0.00 32.05 2.57
6016 6367 5.901552 ACACGGTGAACATCTTTTTGATTT 58.098 33.333 16.29 0.00 32.05 2.17
6017 6368 7.033530 ACACGGTGAACATCTTTTTGATTTA 57.966 32.000 16.29 0.00 32.05 1.40
6018 6369 7.657336 ACACGGTGAACATCTTTTTGATTTAT 58.343 30.769 16.29 0.00 32.05 1.40
6019 6370 8.788806 ACACGGTGAACATCTTTTTGATTTATA 58.211 29.630 16.29 0.00 32.05 0.98
6020 6371 9.787532 CACGGTGAACATCTTTTTGATTTATAT 57.212 29.630 0.74 0.00 32.05 0.86
6021 6372 9.787532 ACGGTGAACATCTTTTTGATTTATATG 57.212 29.630 0.00 0.00 32.05 1.78
6044 6395 8.915871 ATGAATCGATTTGTAAAAATGACAGG 57.084 30.769 12.81 0.00 0.00 4.00
6045 6396 7.312154 TGAATCGATTTGTAAAAATGACAGGG 58.688 34.615 12.81 0.00 0.00 4.45
6046 6397 6.834168 ATCGATTTGTAAAAATGACAGGGT 57.166 33.333 0.00 0.00 0.00 4.34
6047 6398 7.931578 ATCGATTTGTAAAAATGACAGGGTA 57.068 32.000 0.00 0.00 0.00 3.69
6048 6399 7.931578 TCGATTTGTAAAAATGACAGGGTAT 57.068 32.000 0.00 0.00 0.00 2.73
6049 6400 9.621629 ATCGATTTGTAAAAATGACAGGGTATA 57.378 29.630 0.00 0.00 0.00 1.47
6050 6401 9.621629 TCGATTTGTAAAAATGACAGGGTATAT 57.378 29.630 0.00 0.00 0.00 0.86
6063 6414 9.658799 ATGACAGGGTATATTAATTCTCAATCG 57.341 33.333 0.00 0.00 0.00 3.34
6064 6415 8.866093 TGACAGGGTATATTAATTCTCAATCGA 58.134 33.333 0.00 0.00 0.00 3.59
6065 6416 9.877178 GACAGGGTATATTAATTCTCAATCGAT 57.123 33.333 0.00 0.00 0.00 3.59
6077 6428 3.170791 TCAATCGATTGAGACAGAGGC 57.829 47.619 31.83 0.00 41.51 4.70
6078 6429 1.857217 CAATCGATTGAGACAGAGGCG 59.143 52.381 30.12 0.86 40.14 5.52
6079 6430 0.249238 ATCGATTGAGACAGAGGCGC 60.249 55.000 0.00 0.00 0.00 6.53
6080 6431 1.153765 CGATTGAGACAGAGGCGCA 60.154 57.895 10.83 0.00 0.00 6.09
6081 6432 1.144565 CGATTGAGACAGAGGCGCAG 61.145 60.000 10.83 0.00 0.00 5.18
6082 6433 0.108424 GATTGAGACAGAGGCGCAGT 60.108 55.000 10.83 0.91 0.00 4.40
6083 6434 0.390866 ATTGAGACAGAGGCGCAGTG 60.391 55.000 10.83 5.42 0.00 3.66
6084 6435 2.813042 GAGACAGAGGCGCAGTGC 60.813 66.667 10.83 4.58 45.38 4.40
6093 6444 4.090057 GCGCAGTGCCCTCGAAAC 62.090 66.667 10.11 0.00 37.76 2.78
6094 6445 2.357517 CGCAGTGCCCTCGAAACT 60.358 61.111 10.11 0.00 0.00 2.66
6095 6446 2.383527 CGCAGTGCCCTCGAAACTC 61.384 63.158 10.11 0.00 0.00 3.01
6096 6447 1.004440 GCAGTGCCCTCGAAACTCT 60.004 57.895 2.85 0.00 0.00 3.24
6097 6448 1.016653 GCAGTGCCCTCGAAACTCTC 61.017 60.000 2.85 0.00 0.00 3.20
6098 6449 0.390472 CAGTGCCCTCGAAACTCTCC 60.390 60.000 0.00 0.00 0.00 3.71
6099 6450 1.079057 GTGCCCTCGAAACTCTCCC 60.079 63.158 0.00 0.00 0.00 4.30
6100 6451 1.229209 TGCCCTCGAAACTCTCCCT 60.229 57.895 0.00 0.00 0.00 4.20
6101 6452 1.258445 TGCCCTCGAAACTCTCCCTC 61.258 60.000 0.00 0.00 0.00 4.30
6102 6453 1.962321 GCCCTCGAAACTCTCCCTCC 61.962 65.000 0.00 0.00 0.00 4.30
6103 6454 1.331399 CCCTCGAAACTCTCCCTCCC 61.331 65.000 0.00 0.00 0.00 4.30
6104 6455 0.324830 CCTCGAAACTCTCCCTCCCT 60.325 60.000 0.00 0.00 0.00 4.20
6105 6456 1.107945 CTCGAAACTCTCCCTCCCTC 58.892 60.000 0.00 0.00 0.00 4.30
6106 6457 0.324460 TCGAAACTCTCCCTCCCTCC 60.324 60.000 0.00 0.00 0.00 4.30
6107 6458 1.331399 CGAAACTCTCCCTCCCTCCC 61.331 65.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.286808 AGCAAATTGGGCTTACAAAATCCT 59.713 37.500 0.00 0.00 38.81 3.24
242 258 1.390123 CACCACGTCGAATGACATGAC 59.610 52.381 0.00 0.00 40.66 3.06
261 278 2.777094 TGAAGGTCATCATGCGTTTCA 58.223 42.857 0.00 0.00 0.00 2.69
312 376 7.543172 AGTTTATCTGCAATGCAACAAATAGTG 59.457 33.333 9.92 0.00 38.41 2.74
432 531 0.098025 GCAGGCGCGCTAAATTACAA 59.902 50.000 32.29 0.00 0.00 2.41
556 668 0.935831 CAACAGACGCACGGTTACGA 60.936 55.000 7.26 0.00 44.60 3.43
565 677 2.280797 GCACCTCCAACAGACGCA 60.281 61.111 0.00 0.00 0.00 5.24
628 740 6.803807 GTCCTCAACTTAAAATTGATGCTCAC 59.196 38.462 3.04 0.00 35.57 3.51
648 760 2.696187 GTCCACTAGGATCCAAGTCCTC 59.304 54.545 15.82 0.00 45.51 3.71
663 775 4.498177 CGATGTGTGATATCTTCGTCCACT 60.498 45.833 3.98 0.00 0.00 4.00
664 776 3.731216 CGATGTGTGATATCTTCGTCCAC 59.269 47.826 3.98 2.61 0.00 4.02
757 869 0.988063 GCACTTTTCCTCCTCTCCCT 59.012 55.000 0.00 0.00 0.00 4.20
762 874 1.157585 GTTCCGCACTTTTCCTCCTC 58.842 55.000 0.00 0.00 0.00 3.71
763 875 0.472471 TGTTCCGCACTTTTCCTCCT 59.528 50.000 0.00 0.00 0.00 3.69
764 876 1.534729 ATGTTCCGCACTTTTCCTCC 58.465 50.000 0.00 0.00 0.00 4.30
861 976 1.948834 CAATGTGTGTGCTTCTGGTGA 59.051 47.619 0.00 0.00 0.00 4.02
1505 1658 7.162761 TGCAGAATGTCAATGGAATTTGAAAT 58.837 30.769 0.00 0.00 37.36 2.17
3131 3296 1.812571 GAACACCTGCATCCGTTGATT 59.187 47.619 0.00 0.00 0.00 2.57
3396 3565 4.328983 ACTGATTGAGGTTATACGTTTGCG 59.671 41.667 0.00 0.00 44.93 4.85
4180 4354 7.335422 AGCCAGAGTATAACAAAGACAATTCTG 59.665 37.037 0.00 0.00 29.98 3.02
4329 4503 7.385894 AGGAAAGAGGATATTCTATTGCAGT 57.614 36.000 0.00 0.00 0.00 4.40
4417 4591 6.038603 TCTGTGTTCCTGTTTTGAAAGAGATG 59.961 38.462 2.52 0.00 31.45 2.90
4515 4689 3.990469 GGAGAGTACGATGCACATAATGG 59.010 47.826 0.00 0.00 0.00 3.16
4645 4825 1.536766 CCTGAAAATTCGTCTGCAGCA 59.463 47.619 9.47 0.00 0.00 4.41
5360 5707 9.699985 CAAGATCGAAATTCTTTCAGACTTATG 57.300 33.333 0.00 0.00 39.63 1.90
5361 5708 9.442047 ACAAGATCGAAATTCTTTCAGACTTAT 57.558 29.630 0.00 0.00 39.63 1.73
5574 5921 0.539438 TGTGGTTCATTCCTGTGCCC 60.539 55.000 0.00 0.00 0.00 5.36
5600 5947 6.765915 AAATCTCTGTGCTTTAGGAAATCC 57.234 37.500 0.00 0.00 0.00 3.01
5649 5999 9.590451 CAATAACAGAATGCCAATACAAGAATT 57.410 29.630 0.00 0.00 42.53 2.17
5695 6045 3.552132 AAAAATGGACACAAACCACCC 57.448 42.857 0.00 0.00 40.36 4.61
5876 6227 3.830744 CCATAATGTAAGTGGGACGGA 57.169 47.619 0.00 0.00 0.00 4.69
5882 6233 4.507335 CCCTCCATCCCATAATGTAAGTGG 60.507 50.000 0.00 0.00 0.00 4.00
5883 6234 4.350816 TCCCTCCATCCCATAATGTAAGTG 59.649 45.833 0.00 0.00 0.00 3.16
5884 6235 4.577096 TCCCTCCATCCCATAATGTAAGT 58.423 43.478 0.00 0.00 0.00 2.24
5981 6332 9.607988 AGATGTTCACCGTGTTATGAAAATATA 57.392 29.630 0.00 0.00 33.72 0.86
5982 6333 8.506168 AGATGTTCACCGTGTTATGAAAATAT 57.494 30.769 0.00 0.00 33.72 1.28
5983 6334 7.915293 AGATGTTCACCGTGTTATGAAAATA 57.085 32.000 0.00 0.00 33.72 1.40
5984 6335 6.817765 AGATGTTCACCGTGTTATGAAAAT 57.182 33.333 0.00 0.00 35.81 1.82
5985 6336 6.627395 AAGATGTTCACCGTGTTATGAAAA 57.373 33.333 0.00 0.00 36.62 2.29
5986 6337 6.627395 AAAGATGTTCACCGTGTTATGAAA 57.373 33.333 0.00 0.00 36.62 2.69
5987 6338 6.627395 AAAAGATGTTCACCGTGTTATGAA 57.373 33.333 0.00 0.00 32.44 2.57
5988 6339 6.261158 TCAAAAAGATGTTCACCGTGTTATGA 59.739 34.615 0.00 0.00 0.00 2.15
5989 6340 6.434596 TCAAAAAGATGTTCACCGTGTTATG 58.565 36.000 0.00 0.00 0.00 1.90
5990 6341 6.627395 TCAAAAAGATGTTCACCGTGTTAT 57.373 33.333 0.00 0.00 0.00 1.89
5991 6342 6.627395 ATCAAAAAGATGTTCACCGTGTTA 57.373 33.333 0.00 0.00 35.06 2.41
5992 6343 4.974368 TCAAAAAGATGTTCACCGTGTT 57.026 36.364 0.00 0.00 0.00 3.32
5993 6344 5.514274 AATCAAAAAGATGTTCACCGTGT 57.486 34.783 0.00 0.00 36.96 4.49
5994 6345 9.787532 ATATAAATCAAAAAGATGTTCACCGTG 57.212 29.630 0.00 0.00 36.96 4.94
5995 6346 9.787532 CATATAAATCAAAAAGATGTTCACCGT 57.212 29.630 0.00 0.00 36.96 4.83
6019 6370 7.975616 CCCTGTCATTTTTACAAATCGATTCAT 59.024 33.333 11.83 5.25 29.41 2.57
6020 6371 7.040062 ACCCTGTCATTTTTACAAATCGATTCA 60.040 33.333 11.83 0.00 29.41 2.57
6021 6372 7.312899 ACCCTGTCATTTTTACAAATCGATTC 58.687 34.615 11.83 0.00 29.41 2.52
6022 6373 7.227049 ACCCTGTCATTTTTACAAATCGATT 57.773 32.000 4.39 4.39 29.41 3.34
6023 6374 6.834168 ACCCTGTCATTTTTACAAATCGAT 57.166 33.333 0.00 0.00 29.41 3.59
6024 6375 7.931578 ATACCCTGTCATTTTTACAAATCGA 57.068 32.000 0.00 0.00 29.41 3.59
6037 6388 9.658799 CGATTGAGAATTAATATACCCTGTCAT 57.341 33.333 0.00 0.00 0.00 3.06
6038 6389 8.866093 TCGATTGAGAATTAATATACCCTGTCA 58.134 33.333 0.00 0.00 0.00 3.58
6039 6390 9.877178 ATCGATTGAGAATTAATATACCCTGTC 57.123 33.333 0.00 0.00 0.00 3.51
6057 6408 2.480244 CGCCTCTGTCTCAATCGATTGA 60.480 50.000 32.71 32.71 43.94 2.57
6058 6409 1.857217 CGCCTCTGTCTCAATCGATTG 59.143 52.381 28.48 28.48 39.10 2.67
6059 6410 1.804372 GCGCCTCTGTCTCAATCGATT 60.804 52.381 4.39 4.39 0.00 3.34
6060 6411 0.249238 GCGCCTCTGTCTCAATCGAT 60.249 55.000 0.00 0.00 0.00 3.59
6061 6412 1.139734 GCGCCTCTGTCTCAATCGA 59.860 57.895 0.00 0.00 0.00 3.59
6062 6413 1.144565 CTGCGCCTCTGTCTCAATCG 61.145 60.000 4.18 0.00 0.00 3.34
6063 6414 0.108424 ACTGCGCCTCTGTCTCAATC 60.108 55.000 4.18 0.00 0.00 2.67
6064 6415 0.390866 CACTGCGCCTCTGTCTCAAT 60.391 55.000 4.18 0.00 0.00 2.57
6065 6416 1.005748 CACTGCGCCTCTGTCTCAA 60.006 57.895 4.18 0.00 0.00 3.02
6066 6417 2.653115 CACTGCGCCTCTGTCTCA 59.347 61.111 4.18 0.00 0.00 3.27
6067 6418 2.813042 GCACTGCGCCTCTGTCTC 60.813 66.667 4.18 0.00 32.94 3.36
6076 6427 4.090057 GTTTCGAGGGCACTGCGC 62.090 66.667 10.03 10.03 41.91 6.09
6077 6428 2.357517 AGTTTCGAGGGCACTGCG 60.358 61.111 0.00 0.00 0.00 5.18
6078 6429 1.004440 AGAGTTTCGAGGGCACTGC 60.004 57.895 0.00 0.00 0.00 4.40
6079 6430 0.390472 GGAGAGTTTCGAGGGCACTG 60.390 60.000 0.00 0.00 0.00 3.66
6080 6431 1.545706 GGGAGAGTTTCGAGGGCACT 61.546 60.000 0.00 0.00 0.00 4.40
6081 6432 1.079057 GGGAGAGTTTCGAGGGCAC 60.079 63.158 0.00 0.00 0.00 5.01
6082 6433 1.229209 AGGGAGAGTTTCGAGGGCA 60.229 57.895 0.00 0.00 0.00 5.36
6083 6434 1.518302 GAGGGAGAGTTTCGAGGGC 59.482 63.158 0.00 0.00 0.00 5.19
6084 6435 1.331399 GGGAGGGAGAGTTTCGAGGG 61.331 65.000 0.00 0.00 0.00 4.30
6085 6436 0.324830 AGGGAGGGAGAGTTTCGAGG 60.325 60.000 0.00 0.00 0.00 4.63
6086 6437 1.107945 GAGGGAGGGAGAGTTTCGAG 58.892 60.000 0.00 0.00 0.00 4.04
6087 6438 0.324460 GGAGGGAGGGAGAGTTTCGA 60.324 60.000 0.00 0.00 0.00 3.71
6088 6439 1.331399 GGGAGGGAGGGAGAGTTTCG 61.331 65.000 0.00 0.00 0.00 3.46
6089 6440 2.610282 GGGAGGGAGGGAGAGTTTC 58.390 63.158 0.00 0.00 0.00 2.78
6090 6441 4.922067 GGGAGGGAGGGAGAGTTT 57.078 61.111 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.