Multiple sequence alignment - TraesCS5D01G324200

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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 TraesCS5D01G324200 chr5D 100.000 9081 0 0 1 9081 416078856 416069776 0.000000e+00 16770.0
1 TraesCS5D01G324200 chr5D 92.063 126 7 1 5845 5967 416072964 416072839 3.370000e-39 174.0
2 TraesCS5D01G324200 chr5D 92.063 126 7 1 5893 6018 416073012 416072890 3.370000e-39 174.0
3 TraesCS5D01G324200 chr5B 98.456 4599 48 7 839 5431 502508583 502504002 0.000000e+00 8078.0
4 TraesCS5D01G324200 chr5B 98.366 3549 48 6 5428 8974 502503910 502500370 0.000000e+00 6224.0
5 TraesCS5D01G324200 chr5B 87.500 184 10 2 662 845 502634342 502634172 5.560000e-47 200.0
6 TraesCS5D01G324200 chr5B 95.536 112 5 0 8969 9080 502500212 502500101 7.240000e-41 180.0
7 TraesCS5D01G324200 chr5B 92.063 126 7 1 5893 6018 502503494 502503372 3.370000e-39 174.0
8 TraesCS5D01G324200 chr5B 92.784 97 4 3 6940 7035 411034768 411034862 4.420000e-28 137.0
9 TraesCS5D01G324200 chr5A 98.528 3804 39 7 834 4624 528587743 528583944 0.000000e+00 6698.0
10 TraesCS5D01G324200 chr5A 98.226 2368 30 4 4621 6983 528583745 528581385 0.000000e+00 4130.0
11 TraesCS5D01G324200 chr5A 95.846 1998 43 7 6982 8972 528581281 528579317 0.000000e+00 3193.0
12 TraesCS5D01G324200 chr5A 100.000 47 0 0 769 815 528587786 528587740 4.520000e-13 87.9
13 TraesCS5D01G324200 chr5A 97.500 40 1 0 5469 5508 38014671 38014710 1.640000e-07 69.4
14 TraesCS5D01G324200 chr5A 92.500 40 3 0 662 701 528600500 528600461 3.540000e-04 58.4
15 TraesCS5D01G324200 chr7D 98.156 2169 31 3 2138 4297 603364970 603362802 0.000000e+00 3775.0
16 TraesCS5D01G324200 chr7D 88.467 1448 123 19 1968 3401 574037751 574039168 0.000000e+00 1709.0
17 TraesCS5D01G324200 chr7D 93.856 1058 41 9 4390 5441 603362808 603361769 0.000000e+00 1572.0
18 TraesCS5D01G324200 chr7D 92.067 1021 54 11 5501 6519 603361772 603360777 0.000000e+00 1411.0
19 TraesCS5D01G324200 chr7D 91.235 810 34 12 870 1655 603376086 603375290 0.000000e+00 1068.0
20 TraesCS5D01G324200 chr7D 89.353 742 47 10 7582 8322 603359851 603359141 0.000000e+00 904.0
21 TraesCS5D01G324200 chr7D 97.125 487 14 0 1651 2137 603368916 603368430 0.000000e+00 822.0
22 TraesCS5D01G324200 chr7D 94.278 367 17 3 6549 6914 603360786 603360423 7.960000e-155 558.0
23 TraesCS5D01G324200 chr7D 87.500 312 27 5 8779 9080 603358603 603358294 5.220000e-92 350.0
24 TraesCS5D01G324200 chr7D 87.029 239 14 9 8320 8547 603358980 603358748 4.210000e-63 254.0
25 TraesCS5D01G324200 chr7D 95.890 146 6 0 990 1135 574036778 574036923 4.240000e-58 237.0
26 TraesCS5D01G324200 chr7D 90.226 133 10 1 5845 5974 603361389 603361257 4.360000e-38 171.0
27 TraesCS5D01G324200 chr7D 95.876 97 4 0 769 865 603376240 603376144 3.390000e-34 158.0
28 TraesCS5D01G324200 chr7D 92.208 77 4 1 1892 1966 574037552 574037628 3.470000e-19 108.0
29 TraesCS5D01G324200 chr7D 83.065 124 7 7 8616 8728 603358737 603358617 5.800000e-17 100.0
30 TraesCS5D01G324200 chr7A 95.136 2282 85 15 1361 3634 696031306 696029043 0.000000e+00 3576.0
31 TraesCS5D01G324200 chr7A 91.387 1846 94 16 3634 5441 696025716 696023898 0.000000e+00 2468.0
32 TraesCS5D01G324200 chr7A 86.171 1533 113 45 7582 9080 696022036 696020569 0.000000e+00 1565.0
33 TraesCS5D01G324200 chr7A 87.055 1406 109 32 2826 4181 663809398 663808016 0.000000e+00 1520.0
34 TraesCS5D01G324200 chr7A 91.773 1021 62 10 5501 6519 696023901 696022901 0.000000e+00 1400.0
35 TraesCS5D01G324200 chr7A 88.810 983 66 15 4465 5441 663807838 663806894 0.000000e+00 1166.0
36 TraesCS5D01G324200 chr7A 95.652 368 12 3 6548 6914 696022911 696022547 1.020000e-163 588.0
37 TraesCS5D01G324200 chr7A 87.595 395 42 5 1884 2277 663810408 663810020 1.390000e-122 451.0
38 TraesCS5D01G324200 chr7A 84.223 431 33 15 5501 5926 663806897 663806497 3.980000e-103 387.0
39 TraesCS5D01G324200 chr7A 91.039 279 13 9 867 1139 696031645 696031373 5.180000e-97 366.0
40 TraesCS5D01G324200 chr7A 93.133 233 16 0 4 236 699036135 699035903 8.730000e-90 342.0
41 TraesCS5D01G324200 chr7A 88.462 260 22 5 6059 6310 663806497 663806238 3.180000e-79 307.0
42 TraesCS5D01G324200 chr7A 95.238 147 7 0 993 1139 663811195 663811049 5.480000e-57 233.0
43 TraesCS5D01G324200 chr7A 84.158 202 16 4 662 860 696033347 696033159 2.010000e-41 182.0
44 TraesCS5D01G324200 chr7A 89.600 125 13 0 4180 4304 663807987 663807863 9.440000e-35 159.0
45 TraesCS5D01G324200 chr7A 84.932 73 8 2 5439 5508 9329374 9329302 4.550000e-08 71.3
46 TraesCS5D01G324200 chr7B 89.577 1631 95 26 3846 5441 684485438 684483848 0.000000e+00 2001.0
47 TraesCS5D01G324200 chr7B 97.702 1088 20 4 6170 7254 684472556 684471471 0.000000e+00 1866.0
48 TraesCS5D01G324200 chr7B 87.623 913 86 15 2732 3626 684486474 684485571 0.000000e+00 1035.0
49 TraesCS5D01G324200 chr7B 92.135 712 41 7 7243 7952 684471317 684470619 0.000000e+00 990.0
50 TraesCS5D01G324200 chr7B 88.378 826 52 23 8260 9080 684461546 684460760 0.000000e+00 953.0
51 TraesCS5D01G324200 chr7B 86.329 907 69 18 676 1554 684549406 684548527 0.000000e+00 937.0
52 TraesCS5D01G324200 chr7B 91.412 687 47 7 5501 6183 684483847 684483169 0.000000e+00 931.0
53 TraesCS5D01G324200 chr7B 92.994 471 25 2 7805 8274 684462055 684461592 0.000000e+00 680.0
54 TraesCS5D01G324200 chr7B 92.126 381 19 3 7946 8322 684469662 684469289 2.250000e-145 527.0
55 TraesCS5D01G324200 chr7B 91.957 373 21 6 769 1138 684487272 684486906 1.750000e-141 514.0
56 TraesCS5D01G324200 chr7B 93.478 230 13 2 7582 7811 684465941 684465714 3.140000e-89 340.0
57 TraesCS5D01G324200 chr7B 85.938 256 27 5 7031 7285 684466442 684466195 1.940000e-66 265.0
58 TraesCS5D01G324200 chr7B 99.270 137 1 0 3675 3811 684485575 684485439 1.960000e-61 248.0
59 TraesCS5D01G324200 chr7B 93.684 95 5 1 6943 7037 639796290 639796197 3.420000e-29 141.0
60 TraesCS5D01G324200 chr7B 98.701 77 1 0 1552 1628 684546807 684546731 4.420000e-28 137.0
61 TraesCS5D01G324200 chr7B 90.476 105 6 4 6933 7035 741667088 741667190 1.590000e-27 135.0
62 TraesCS5D01G324200 chr7B 97.500 40 1 0 5469 5508 203031494 203031455 1.640000e-07 69.4
63 TraesCS5D01G324200 chr2D 91.916 668 51 2 2 666 122708367 122707700 0.000000e+00 931.0
64 TraesCS5D01G324200 chr2A 92.535 576 42 1 1 575 73201455 73202030 0.000000e+00 824.0
65 TraesCS5D01G324200 chr2A 89.091 110 8 4 6936 7043 4139204 4139311 5.720000e-27 134.0
66 TraesCS5D01G324200 chr3A 88.253 664 75 2 6 666 33447995 33447332 0.000000e+00 791.0
67 TraesCS5D01G324200 chr3A 88.793 116 8 3 6927 7041 489193190 489193079 4.420000e-28 137.0
68 TraesCS5D01G324200 chr4A 87.256 667 82 2 3 666 37292084 37291418 0.000000e+00 758.0
69 TraesCS5D01G324200 chr4A 90.411 219 18 3 7584 7801 311930845 311931061 1.490000e-72 285.0
70 TraesCS5D01G324200 chr1A 87.218 665 82 2 2 663 31132049 31132713 0.000000e+00 754.0
71 TraesCS5D01G324200 chr6D 79.237 655 125 10 6 654 163934294 163934943 6.470000e-121 446.0
72 TraesCS5D01G324200 chr6D 100.000 28 0 0 7549 7576 8551061 8551034 1.600000e-02 52.8
73 TraesCS5D01G324200 chr3D 78.955 651 133 4 6 654 454668462 454667814 3.010000e-119 440.0
74 TraesCS5D01G324200 chr2B 90.045 221 19 3 7584 7803 88674451 88674669 5.370000e-72 283.0
75 TraesCS5D01G324200 chr2B 93.333 45 1 2 5469 5513 790630080 790630038 2.120000e-06 65.8
76 TraesCS5D01G324200 chr3B 87.931 116 9 3 6927 7041 478078460 478078349 2.060000e-26 132.0
77 TraesCS5D01G324200 chr3B 93.333 45 2 1 5469 5512 472309405 472309449 2.120000e-06 65.8
78 TraesCS5D01G324200 chr3B 96.875 32 0 1 7549 7580 214558344 214558314 1.600000e-02 52.8
79 TraesCS5D01G324200 chr1D 93.478 46 2 1 5469 5513 100882936 100882891 5.880000e-07 67.6
80 TraesCS5D01G324200 chr6B 93.333 45 2 1 5469 5512 564059857 564059813 2.120000e-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 TraesCS5D01G324200 chr5D 416069776 416078856 9080 True 16770.000000 16770 100.000000 1 9081 1 chr5D.!!$R1 9080
1 TraesCS5D01G324200 chr5B 502500101 502508583 8482 True 3664.000000 8078 96.105250 839 9080 4 chr5B.!!$R2 8241
2 TraesCS5D01G324200 chr5A 528579317 528587786 8469 True 3527.225000 6698 98.150000 769 8972 4 chr5A.!!$R2 8203
3 TraesCS5D01G324200 chr7D 603358294 603368916 10622 True 991.700000 3775 91.265500 1651 9080 10 chr7D.!!$R1 7429
4 TraesCS5D01G324200 chr7D 574036778 574039168 2390 False 684.666667 1709 92.188333 990 3401 3 chr7D.!!$F1 2411
5 TraesCS5D01G324200 chr7D 603375290 603376240 950 True 613.000000 1068 93.555500 769 1655 2 chr7D.!!$R2 886
6 TraesCS5D01G324200 chr7A 696020569 696033347 12778 True 1449.285714 3576 90.759429 662 9080 7 chr7A.!!$R4 8418
7 TraesCS5D01G324200 chr7A 663806238 663811195 4957 True 603.285714 1520 88.711857 993 6310 7 chr7A.!!$R3 5317
8 TraesCS5D01G324200 chr7B 684483169 684487272 4103 True 945.800000 2001 91.967800 769 6183 5 chr7B.!!$R4 5414
9 TraesCS5D01G324200 chr7B 684460760 684472556 11796 True 803.000000 1866 91.821571 6170 9080 7 chr7B.!!$R3 2910
10 TraesCS5D01G324200 chr7B 684546731 684549406 2675 True 537.000000 937 92.515000 676 1628 2 chr7B.!!$R5 952
11 TraesCS5D01G324200 chr2D 122707700 122708367 667 True 931.000000 931 91.916000 2 666 1 chr2D.!!$R1 664
12 TraesCS5D01G324200 chr2A 73201455 73202030 575 False 824.000000 824 92.535000 1 575 1 chr2A.!!$F2 574
13 TraesCS5D01G324200 chr3A 33447332 33447995 663 True 791.000000 791 88.253000 6 666 1 chr3A.!!$R1 660
14 TraesCS5D01G324200 chr4A 37291418 37292084 666 True 758.000000 758 87.256000 3 666 1 chr4A.!!$R1 663
15 TraesCS5D01G324200 chr1A 31132049 31132713 664 False 754.000000 754 87.218000 2 663 1 chr1A.!!$F1 661
16 TraesCS5D01G324200 chr6D 163934294 163934943 649 False 446.000000 446 79.237000 6 654 1 chr6D.!!$F1 648
17 TraesCS5D01G324200 chr3D 454667814 454668462 648 True 440.000000 440 78.955000 6 654 1 chr3D.!!$R1 648

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
290 291 0.405198 TGGGTCAGTGCACATTGGAT 59.595 50.000 21.04 0.0 0.00 3.41 F
333 334 1.034838 TATGCGCCCACATGGTTTCC 61.035 55.000 4.18 0.0 36.04 3.13 F
667 671 1.629043 AGTACTGAGAGCAAACCGGA 58.371 50.000 9.46 0.0 0.00 5.14 F
724 730 1.681076 GCCCCCGAGTTGGACTAAA 59.319 57.895 0.00 0.0 42.00 1.85 F
2747 9754 3.880047 AAATGTTCCACTGGATGCATG 57.120 42.857 2.46 0.0 31.56 4.06 F
4336 15040 4.890158 AAAATAAAGGCTGAGGGGTTTG 57.110 40.909 0.00 0.0 0.00 2.93 F
4715 15630 5.966742 ATCGATCTCAAACGATGGATCTA 57.033 39.130 0.00 0.0 45.38 1.98 F
5245 16172 3.758554 GGCAAATTTGGACTCTCAGCTAA 59.241 43.478 19.47 0.0 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 9290 5.125100 TCAATGACAGAAATGCTCCAAAC 57.875 39.130 0.00 0.0 0.00 2.93 R
2563 9557 0.259938 GGGCCAGATCCATTTCCTGT 59.740 55.000 4.39 0.0 0.00 4.00 R
3558 10842 3.550842 GGAAGTGGCAAAAACAGTGCTAG 60.551 47.826 0.00 0.0 41.88 3.42 R
4336 15040 1.821216 TTTCCAAGAGAACCCGCATC 58.179 50.000 0.00 0.0 32.95 3.91 R
4715 15630 1.216678 TGAGAACCCACCAACAACCAT 59.783 47.619 0.00 0.0 0.00 3.55 R
5245 16172 5.972327 AGATCCATTCTCTCCTTGTGAAT 57.028 39.130 0.00 0.0 38.84 2.57 R
8029 28141 4.625607 AAGATTCCTCCGAGAAAACTGT 57.374 40.909 0.00 0.0 0.00 3.55 R
8692 29042 3.660111 GCAGGGTGCACAACGGTC 61.660 66.667 20.43 0.0 44.26 4.79 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
121 122 1.633852 GCAGCTGCTTGACTTCCTCG 61.634 60.000 31.33 0.00 38.21 4.63
123 124 0.681733 AGCTGCTTGACTTCCTCGAA 59.318 50.000 0.00 0.00 0.00 3.71
162 163 5.626116 GCGACAAATCCTTCCCTTTACTCTA 60.626 44.000 0.00 0.00 0.00 2.43
278 279 0.668706 CTCAACTGTCGCTGGGTCAG 60.669 60.000 15.21 15.21 35.60 3.51
290 291 0.405198 TGGGTCAGTGCACATTGGAT 59.595 50.000 21.04 0.00 0.00 3.41
333 334 1.034838 TATGCGCCCACATGGTTTCC 61.035 55.000 4.18 0.00 36.04 3.13
391 392 2.224305 GGCCGTAGCTCCATCTACATTT 60.224 50.000 0.00 0.00 39.01 2.32
420 421 2.689034 CCCCTCCTCTGGTGGACC 60.689 72.222 6.30 0.00 38.51 4.46
505 507 5.701224 TCCCCATTAAGTTGACAACTCTTT 58.299 37.500 20.81 8.62 41.91 2.52
518 520 3.250040 ACAACTCTTTTTGCTATCGCGTT 59.750 39.130 5.77 0.00 39.65 4.84
519 521 4.219033 CAACTCTTTTTGCTATCGCGTTT 58.781 39.130 5.77 0.00 39.65 3.60
591 593 2.798145 CGCATACGCATCCTGTACAAGA 60.798 50.000 0.00 0.00 38.40 3.02
667 671 1.629043 AGTACTGAGAGCAAACCGGA 58.371 50.000 9.46 0.00 0.00 5.14
674 678 1.810030 GAGCAAACCGGAGTAGGCG 60.810 63.158 9.46 0.00 32.14 5.52
678 682 3.600898 AAACCGGAGTAGGCGGTGC 62.601 63.158 9.46 0.00 36.03 5.01
722 728 2.686106 GGCCCCCGAGTTGGACTA 60.686 66.667 0.00 0.00 42.00 2.59
724 730 1.681076 GCCCCCGAGTTGGACTAAA 59.319 57.895 0.00 0.00 42.00 1.85
2246 9170 5.105877 GGGCAAGGAAGGTATTTGTAGTTTC 60.106 44.000 0.00 0.00 0.00 2.78
2563 9557 9.627123 ACTTATTGTTCTGCCTGCTATAATTTA 57.373 29.630 0.00 0.00 0.00 1.40
2747 9754 3.880047 AAATGTTCCACTGGATGCATG 57.120 42.857 2.46 0.00 31.56 4.06
3815 14426 5.163642 GCAAGAAACTCTCTCGTAGTATGGA 60.164 44.000 0.00 0.00 31.02 3.41
3944 14571 8.948631 CTGTTATCTTAAGAACAGGAATGCTA 57.051 34.615 22.00 1.40 46.31 3.49
4336 15040 4.890158 AAAATAAAGGCTGAGGGGTTTG 57.110 40.909 0.00 0.00 0.00 2.93
4715 15630 5.966742 ATCGATCTCAAACGATGGATCTA 57.033 39.130 0.00 0.00 45.38 1.98
4881 15799 7.403421 CAAAAACATGTTAGTCGTTCTACACA 58.597 34.615 12.39 0.00 0.00 3.72
5245 16172 3.758554 GGCAAATTTGGACTCTCAGCTAA 59.241 43.478 19.47 0.00 0.00 3.09
5414 16341 7.604164 TCATCTTCAGATTCAACAAGTAAGGTC 59.396 37.037 0.00 0.00 31.21 3.85
6279 17319 5.741040 GTGTTGCATAGCTTTCTAATTCTGC 59.259 40.000 0.00 0.00 31.21 4.26
7016 18187 7.011669 AGAGTAGTGATCTAAACGCTCTTAGAC 59.988 40.741 6.54 3.41 39.98 2.59
8344 28683 8.316214 TGTAAAAGGTAGTAGTCACAAATAGGG 58.684 37.037 0.00 0.00 0.00 3.53
8451 28790 2.125350 GGTCTGAAGGAGCTGCCG 60.125 66.667 0.00 0.00 43.43 5.69
8612 28962 6.183360 GCTTGTGCCATTTTGTATCCTATTCT 60.183 38.462 0.00 0.00 0.00 2.40
8692 29042 1.800586 CTTCATGATGCCGAATACCCG 59.199 52.381 0.00 0.00 0.00 5.28
8771 29131 1.655350 GCGCCGCAATATGTTCTGC 60.655 57.895 3.15 0.00 35.14 4.26
9033 29579 3.367743 TCGTCCTACCGTGCGCTT 61.368 61.111 9.73 0.00 0.00 4.68
9053 29599 2.959516 TCATCACAGGTTCGCAACTAG 58.040 47.619 0.00 0.00 0.00 2.57
9066 29612 2.732282 CGCAACTAGCATCTCTCGTTCA 60.732 50.000 0.00 0.00 46.13 3.18
9071 29617 5.181690 ACTAGCATCTCTCGTTCAGATTC 57.818 43.478 0.00 0.00 0.00 2.52
9080 29626 8.538856 CATCTCTCGTTCAGATTCTTGTTTATC 58.461 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 1.007154 GCCGCTAGGACCGATCTTC 60.007 63.158 0.00 0.00 41.02 2.87
123 124 3.288290 CGCCGCTAGGACCGATCT 61.288 66.667 0.00 0.00 41.02 2.75
162 163 1.364626 CGAGATCGCCTGCAAGCTTT 61.365 55.000 5.63 0.00 0.00 3.51
278 279 3.056678 TGTCATTTCCATCCAATGTGCAC 60.057 43.478 10.75 10.75 33.91 4.57
290 291 0.889994 GGTGCAGCATGTCATTTCCA 59.110 50.000 11.86 0.00 39.31 3.53
391 392 0.195096 AGGAGGGGTGGGTGAAAGTA 59.805 55.000 0.00 0.00 0.00 2.24
420 421 2.440409 CTGTGGTGAAGGAGAAATGGG 58.560 52.381 0.00 0.00 0.00 4.00
518 520 2.418746 GGCCAGAAGATAGAAGACGCAA 60.419 50.000 0.00 0.00 0.00 4.85
519 521 1.137086 GGCCAGAAGATAGAAGACGCA 59.863 52.381 0.00 0.00 0.00 5.24
579 581 2.563179 ACGAGCTGTTCTTGTACAGGAT 59.437 45.455 8.68 0.00 44.50 3.24
580 582 1.961394 ACGAGCTGTTCTTGTACAGGA 59.039 47.619 3.11 3.11 44.50 3.86
591 593 3.599730 TCAGATGATGAACGAGCTGTT 57.400 42.857 0.00 0.00 45.61 3.16
615 617 1.743958 CTCCTGTCGTGGTTCGTAGAT 59.256 52.381 0.00 0.00 40.80 1.98
674 678 0.315886 CCGGGTTGTAAAAAGGCACC 59.684 55.000 0.00 0.00 0.00 5.01
678 682 2.433436 CTCCTCCGGGTTGTAAAAAGG 58.567 52.381 0.00 0.00 0.00 3.11
707 713 0.390735 CGTTTAGTCCAACTCGGGGG 60.391 60.000 0.00 0.00 34.36 5.40
712 718 2.712057 TCCGACGTTTAGTCCAACTC 57.288 50.000 0.00 0.00 46.92 3.01
722 728 1.790623 CGACTTGTGAATCCGACGTTT 59.209 47.619 0.00 0.00 0.00 3.60
724 730 0.594602 TCGACTTGTGAATCCGACGT 59.405 50.000 0.00 0.00 0.00 4.34
765 772 4.351938 TTCACACGGGCCGAGTCG 62.352 66.667 35.78 23.37 0.00 4.18
767 774 4.657824 CGTTCACACGGGCCGAGT 62.658 66.667 35.78 29.33 43.16 4.18
2298 9290 5.125100 TCAATGACAGAAATGCTCCAAAC 57.875 39.130 0.00 0.00 0.00 2.93
2563 9557 0.259938 GGGCCAGATCCATTTCCTGT 59.740 55.000 4.39 0.00 0.00 4.00
3558 10842 3.550842 GGAAGTGGCAAAAACAGTGCTAG 60.551 47.826 0.00 0.00 41.88 3.42
4336 15040 1.821216 TTTCCAAGAGAACCCGCATC 58.179 50.000 0.00 0.00 32.95 3.91
4715 15630 1.216678 TGAGAACCCACCAACAACCAT 59.783 47.619 0.00 0.00 0.00 3.55
4881 15799 6.623549 CGGAACAGAAACATCAGCAATATGTT 60.624 38.462 5.73 5.73 46.77 2.71
5245 16172 5.972327 AGATCCATTCTCTCCTTGTGAAT 57.028 39.130 0.00 0.00 38.84 2.57
6279 17319 7.067728 CGCACAATGATGTCTATTCAATACAG 58.932 38.462 0.00 0.00 37.82 2.74
7016 18187 6.712179 ACTAATACTCCCTCCGTAAAGAAG 57.288 41.667 0.00 0.00 0.00 2.85
7369 18730 6.478673 GGAAACAGTGGTTAAAACATGGAAAG 59.521 38.462 0.00 0.00 35.82 2.62
8029 28141 4.625607 AAGATTCCTCCGAGAAAACTGT 57.374 40.909 0.00 0.00 0.00 3.55
8120 28234 8.255905 GCTACTTACAGTCAAAACTAAGGGATA 58.744 37.037 0.00 0.00 33.25 2.59
8344 28683 3.983344 GCATCAACCAAGTGTTCATGTTC 59.017 43.478 0.00 0.00 37.71 3.18
8612 28962 7.499563 GTCCAGATGTCTGACAGATAGTAGTAA 59.500 40.741 16.46 0.00 46.59 2.24
8692 29042 3.660111 GCAGGGTGCACAACGGTC 61.660 66.667 20.43 0.00 44.26 4.79
9033 29579 2.930887 GCTAGTTGCGAACCTGTGATGA 60.931 50.000 0.00 0.00 0.00 2.92
9053 29599 4.180057 ACAAGAATCTGAACGAGAGATGC 58.820 43.478 0.00 0.00 32.80 3.91


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

AutoCloner maintained by Alex Coulton.