Multiple sequence alignment - TraesCS5A01G106800

Loading Multiple Alignment...

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 TraesCS5A01G106800 chr5A 100.000 3088 0 0 1 3088 177592821 177595908 0.000000e+00 5703.0
1 TraesCS5A01G106800 chr2D 92.229 2046 109 17 667 2698 642016702 642018711 0.000000e+00 2852.0
2 TraesCS5A01G106800 chr2D 95.561 383 16 1 2322 2703 585949079 585948697 2.040000e-171 612.0
3 TraesCS5A01G106800 chr2D 91.084 415 35 2 450 864 642016455 642016867 7.480000e-156 560.0
4 TraesCS5A01G106800 chr2D 89.408 321 21 6 142 450 642014923 642015242 2.890000e-105 392.0
5 TraesCS5A01G106800 chr2D 89.116 147 7 5 4 150 642014759 642014896 1.140000e-39 174.0
6 TraesCS5A01G106800 chr5B 92.146 2050 109 17 667 2700 565906335 565908348 0.000000e+00 2846.0
7 TraesCS5A01G106800 chr5B 92.139 2048 109 17 667 2698 565833731 565835742 0.000000e+00 2843.0
8 TraesCS5A01G106800 chr5B 93.199 397 21 6 2697 3088 166811486 166811881 2.060000e-161 579.0
9 TraesCS5A01G106800 chr5B 91.084 415 35 2 450 864 565833484 565833896 7.480000e-156 560.0
10 TraesCS5A01G106800 chr5B 91.084 415 35 2 450 864 565906088 565906500 7.480000e-156 560.0
11 TraesCS5A01G106800 chr5B 89.408 321 21 6 142 450 565831952 565832271 2.890000e-105 392.0
12 TraesCS5A01G106800 chr5B 89.408 321 21 6 142 450 565904556 565904875 2.890000e-105 392.0
13 TraesCS5A01G106800 chr5B 89.116 147 7 5 4 150 565831788 565831925 1.140000e-39 174.0
14 TraesCS5A01G106800 chr5B 89.116 147 7 5 4 150 565904392 565904529 1.140000e-39 174.0
15 TraesCS5A01G106800 chr6B 92.143 2049 109 17 667 2699 485534011 485531999 0.000000e+00 2844.0
16 TraesCS5A01G106800 chr6B 91.084 415 35 2 450 864 485534258 485533846 7.480000e-156 560.0
17 TraesCS5A01G106800 chr6B 89.408 321 21 6 142 450 485535790 485535471 2.890000e-105 392.0
18 TraesCS5A01G106800 chr6B 85.638 188 26 1 106 292 102262208 102262021 2.430000e-46 196.0
19 TraesCS5A01G106800 chr6B 89.116 147 7 5 4 150 485535954 485535817 1.140000e-39 174.0
20 TraesCS5A01G106800 chr2A 92.139 2048 109 17 667 2698 294767212 294769223 0.000000e+00 2843.0
21 TraesCS5A01G106800 chr2A 91.084 415 35 2 450 864 294766965 294767377 7.480000e-156 560.0
22 TraesCS5A01G106800 chr2A 89.408 321 21 6 142 450 294765433 294765752 2.890000e-105 392.0
23 TraesCS5A01G106800 chr2A 89.116 147 7 5 4 150 294765269 294765406 1.140000e-39 174.0
24 TraesCS5A01G106800 chr1B 91.200 1250 73 14 1454 2699 626501697 626500481 0.000000e+00 1664.0
25 TraesCS5A01G106800 chr1B 90.031 321 19 10 142 450 626502893 626502574 1.330000e-108 403.0
26 TraesCS5A01G106800 chr1B 90.717 237 22 0 1248 1484 626501871 626501635 1.790000e-82 316.0
27 TraesCS5A01G106800 chr1B 92.562 121 8 1 30 150 626503039 626502920 4.090000e-39 172.0
28 TraesCS5A01G106800 chr1B 93.750 64 4 0 1377 1440 626501835 626501772 2.530000e-16 97.1
29 TraesCS5A01G106800 chr1A 82.962 1661 206 45 662 2266 18495078 18493439 0.000000e+00 1428.0
30 TraesCS5A01G106800 chr1A 82.147 1658 216 44 662 2266 518795350 518793720 0.000000e+00 1349.0
31 TraesCS5A01G106800 chr1A 78.316 392 57 20 450 822 18495357 18494975 8.610000e-56 228.0
32 TraesCS5A01G106800 chr4B 90.710 915 49 13 1787 2698 647588434 647589315 0.000000e+00 1186.0
33 TraesCS5A01G106800 chr3B 89.583 816 83 2 1436 2250 137598575 137599389 0.000000e+00 1035.0
34 TraesCS5A01G106800 chr7B 88.312 693 45 13 2009 2698 682740753 682741412 0.000000e+00 798.0
35 TraesCS5A01G106800 chr3A 94.866 448 20 2 3 448 128545766 128546212 0.000000e+00 697.0
36 TraesCS5A01G106800 chr3A 83.186 565 82 11 696 1250 104460255 104460816 3.550000e-139 505.0
37 TraesCS5A01G106800 chr3A 78.962 366 53 17 450 799 416041888 416042245 8.610000e-56 228.0
38 TraesCS5A01G106800 chr3D 84.875 562 74 8 696 1249 87943142 87943700 9.670000e-155 556.0
39 TraesCS5A01G106800 chr3D 80.340 412 67 13 450 854 432090257 432090661 1.800000e-77 300.0
40 TraesCS5A01G106800 chr6D 82.087 642 78 26 854 1483 156256308 156255692 5.900000e-142 514.0
41 TraesCS5A01G106800 chr5D 88.986 345 23 9 2697 3037 169974029 169973696 2.220000e-111 412.0
42 TraesCS5A01G106800 chr5D 98.305 59 1 0 3030 3088 169972898 169972840 1.510000e-18 104.0
43 TraesCS5A01G106800 chr6A 78.689 366 54 17 450 799 607379382 607379739 4.010000e-54 222.0
44 TraesCS5A01G106800 chr4D 87.845 181 19 3 104 282 259488189 259488010 3.120000e-50 209.0
45 TraesCS5A01G106800 chr7A 100.000 35 0 0 414 448 287611451 287611485 7.150000e-07 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 TraesCS5A01G106800 chr5A 177592821 177595908 3087 False 5703.00 5703 100.00000 1 3088 1 chr5A.!!$F1 3087
1 TraesCS5A01G106800 chr2D 642014759 642018711 3952 False 994.50 2852 90.45925 4 2698 4 chr2D.!!$F1 2694
2 TraesCS5A01G106800 chr5B 565904392 565908348 3956 False 993.00 2846 90.43850 4 2700 4 chr5B.!!$F3 2696
3 TraesCS5A01G106800 chr5B 565831788 565835742 3954 False 992.25 2843 90.43675 4 2698 4 chr5B.!!$F2 2694
4 TraesCS5A01G106800 chr6B 485531999 485535954 3955 True 992.50 2844 90.43775 4 2699 4 chr6B.!!$R2 2695
5 TraesCS5A01G106800 chr2A 294765269 294769223 3954 False 992.25 2843 90.43675 4 2698 4 chr2A.!!$F1 2694
6 TraesCS5A01G106800 chr1B 626500481 626503039 2558 True 530.42 1664 91.65200 30 2699 5 chr1B.!!$R1 2669
7 TraesCS5A01G106800 chr1A 518793720 518795350 1630 True 1349.00 1349 82.14700 662 2266 1 chr1A.!!$R1 1604
8 TraesCS5A01G106800 chr1A 18493439 18495357 1918 True 828.00 1428 80.63900 450 2266 2 chr1A.!!$R2 1816
9 TraesCS5A01G106800 chr4B 647588434 647589315 881 False 1186.00 1186 90.71000 1787 2698 1 chr4B.!!$F1 911
10 TraesCS5A01G106800 chr3B 137598575 137599389 814 False 1035.00 1035 89.58300 1436 2250 1 chr3B.!!$F1 814
11 TraesCS5A01G106800 chr7B 682740753 682741412 659 False 798.00 798 88.31200 2009 2698 1 chr7B.!!$F1 689
12 TraesCS5A01G106800 chr3A 104460255 104460816 561 False 505.00 505 83.18600 696 1250 1 chr3A.!!$F1 554
13 TraesCS5A01G106800 chr3D 87943142 87943700 558 False 556.00 556 84.87500 696 1249 1 chr3D.!!$F1 553
14 TraesCS5A01G106800 chr6D 156255692 156256308 616 True 514.00 514 82.08700 854 1483 1 chr6D.!!$R1 629
15 TraesCS5A01G106800 chr5D 169972840 169974029 1189 True 258.00 412 93.64550 2697 3088 2 chr5D.!!$R1 391

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
109 110 0.461870 TGAGAGCAAGTGTTGTGCGT 60.462 50.000 0.00 0.00 46.86 5.24 F
935 2304 2.168521 ACATGCTAGCGAACCTATGTGT 59.831 45.455 13.55 3.86 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 3209 0.249489 GCTGACTCACCACAAGTCGT 60.249 55.0 0.0 0.0 44.96 4.34 R
2516 3979 0.109723 GTTGGTGGGTGAGGTTAGCA 59.890 55.0 0.0 0.0 0.00 3.49 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
109 110 0.461870 TGAGAGCAAGTGTTGTGCGT 60.462 50.000 0.00 0.00 46.86 5.24
179 215 2.547855 GCGGACCATATGTACTGATGCA 60.548 50.000 1.24 0.00 0.00 3.96
182 218 4.561326 CGGACCATATGTACTGATGCATGA 60.561 45.833 2.46 0.00 32.77 3.07
295 342 6.778559 GTCAGGGACTACTACATCTTCCTATT 59.221 42.308 0.00 0.00 36.02 1.73
318 365 6.100404 TGTTGATTTTCTCCCCAAAATCTG 57.900 37.500 15.93 0.00 46.45 2.90
322 369 2.514458 TTCTCCCCAAAATCTGAGGC 57.486 50.000 0.00 0.00 0.00 4.70
346 393 6.072452 GCAACTTGTTAACTGCTTCTCCTATT 60.072 38.462 7.22 0.00 0.00 1.73
359 406 5.643777 GCTTCTCCTATTTACTGCTTGACAA 59.356 40.000 0.00 0.00 0.00 3.18
362 409 7.004555 TCTCCTATTTACTGCTTGACAAAGA 57.995 36.000 0.00 0.00 35.19 2.52
399 446 7.330946 TGACTTGTTCCTGTTGAAGTTATATCG 59.669 37.037 0.00 0.00 32.37 2.92
406 453 9.661563 TTCCTGTTGAAGTTATATCGTTTGTAT 57.338 29.630 0.00 0.00 0.00 2.29
583 1843 6.513180 TGTAGTAGCTACCATGTCATTTAGC 58.487 40.000 20.31 12.59 36.24 3.09
716 2051 4.858692 CCAAATACTTGCTGAATTGGTTCG 59.141 41.667 0.00 0.00 37.15 3.95
724 2059 4.832248 TGCTGAATTGGTTCGTTATCTCT 58.168 39.130 0.00 0.00 37.15 3.10
746 2113 7.064609 TCTCTAAATACTTGCTGAATTGGTTCG 59.935 37.037 0.00 0.00 37.15 3.95
935 2304 2.168521 ACATGCTAGCGAACCTATGTGT 59.831 45.455 13.55 3.86 0.00 3.72
1023 2392 7.658575 GCCATGGCTATGAATGAACATTTTAAT 59.341 33.333 29.98 0.65 36.36 1.40
1080 2452 4.020128 ACAAGGACATGGAAGAGGAAGTAC 60.020 45.833 0.00 0.00 0.00 2.73
1090 2462 7.311092 TGGAAGAGGAAGTACAAACAGATAA 57.689 36.000 0.00 0.00 0.00 1.75
1272 2662 4.095483 AGCTATTTCTTTGCTGGAATGACG 59.905 41.667 0.00 0.00 35.54 4.35
1327 2721 5.711506 TCAAAATCCTTGCTGAAATGAGCTA 59.288 36.000 0.00 0.00 39.90 3.32
1351 2745 2.425668 TCATGCATCATCACTTGCTTGG 59.574 45.455 0.00 0.00 41.65 3.61
1388 2782 9.959721 ACTCTATTTTCTTGCTGGAATAAGTAA 57.040 29.630 0.00 0.00 0.00 2.24
1443 2897 6.890663 TTTTCATGCATTATAACTTGCTGC 57.109 33.333 11.34 6.79 39.60 5.25
1463 2917 6.036626 TGCTGCAATTTATTCTTTCATGCATG 59.963 34.615 21.07 21.07 41.00 4.06
1703 3157 7.383102 AGGTACAAATGTGATTGATCTTGAC 57.617 36.000 0.00 0.00 34.38 3.18
1708 3162 6.205464 ACAAATGTGATTGATCTTGACGAACT 59.795 34.615 0.00 0.00 34.38 3.01
1715 3169 2.731451 TGATCTTGACGAACTGAAAGCG 59.269 45.455 0.00 0.00 37.60 4.68
1755 3209 2.673775 TGAAGAGGTTGCCCAATCAA 57.326 45.000 0.00 0.00 0.00 2.57
1757 3211 1.200020 GAAGAGGTTGCCCAATCAACG 59.800 52.381 0.00 0.00 45.33 4.10
1801 3256 4.408596 TCCCAAGTTGAAGAAAGCCAAAAT 59.591 37.500 3.87 0.00 0.00 1.82
1856 3311 5.324409 ACCATAATGGCTTCAAGTGAAAGA 58.676 37.500 0.00 0.00 42.67 2.52
1954 3409 4.907269 ACTCCCTGGTTTTGATTTGGATTT 59.093 37.500 0.00 0.00 0.00 2.17
1979 3434 7.513856 TCCTTGCACATTACTATGCCTATTTA 58.486 34.615 0.00 0.00 41.33 1.40
2149 3606 4.046286 ACCAAAACAATGGAGCTATGGA 57.954 40.909 0.00 0.00 43.54 3.41
2299 3760 3.703286 TCATGCATTATCACTTGCTGC 57.297 42.857 0.00 0.00 39.60 5.25
2310 3771 4.389890 TCACTTGCTGCAATTTGTTCTT 57.610 36.364 16.38 0.00 0.00 2.52
2311 3772 4.757594 TCACTTGCTGCAATTTGTTCTTT 58.242 34.783 16.38 0.00 0.00 2.52
2312 3773 4.805192 TCACTTGCTGCAATTTGTTCTTTC 59.195 37.500 16.38 0.00 0.00 2.62
2313 3774 4.567558 CACTTGCTGCAATTTGTTCTTTCA 59.432 37.500 16.38 0.00 0.00 2.69
2314 3775 5.235616 CACTTGCTGCAATTTGTTCTTTCAT 59.764 36.000 16.38 0.00 0.00 2.57
2315 3776 5.235616 ACTTGCTGCAATTTGTTCTTTCATG 59.764 36.000 16.38 1.37 0.00 3.07
2316 3777 4.059511 TGCTGCAATTTGTTCTTTCATGG 58.940 39.130 0.00 0.00 0.00 3.66
2317 3778 4.202233 TGCTGCAATTTGTTCTTTCATGGA 60.202 37.500 0.00 0.00 0.00 3.41
2318 3779 4.933400 GCTGCAATTTGTTCTTTCATGGAT 59.067 37.500 0.00 0.00 0.00 3.41
2319 3780 5.410439 GCTGCAATTTGTTCTTTCATGGATT 59.590 36.000 0.00 0.00 0.00 3.01
2320 3781 6.591062 GCTGCAATTTGTTCTTTCATGGATTA 59.409 34.615 0.00 0.00 0.00 1.75
2321 3782 7.279313 GCTGCAATTTGTTCTTTCATGGATTAT 59.721 33.333 0.00 0.00 0.00 1.28
2322 3783 9.806203 CTGCAATTTGTTCTTTCATGGATTATA 57.194 29.630 0.00 0.00 0.00 0.98
2323 3784 9.585099 TGCAATTTGTTCTTTCATGGATTATAC 57.415 29.630 0.00 0.00 0.00 1.47
2324 3785 9.807649 GCAATTTGTTCTTTCATGGATTATACT 57.192 29.630 0.00 0.00 0.00 2.12
2327 3788 9.807649 ATTTGTTCTTTCATGGATTATACTTGC 57.192 29.630 0.00 0.00 0.00 4.01
2328 3789 8.579850 TTGTTCTTTCATGGATTATACTTGCT 57.420 30.769 0.00 0.00 0.00 3.91
2329 3790 7.988737 TGTTCTTTCATGGATTATACTTGCTG 58.011 34.615 0.00 0.00 0.00 4.41
2330 3791 7.828717 TGTTCTTTCATGGATTATACTTGCTGA 59.171 33.333 0.00 0.00 0.00 4.26
2331 3792 8.677300 GTTCTTTCATGGATTATACTTGCTGAA 58.323 33.333 0.00 0.00 0.00 3.02
2332 3793 8.806429 TCTTTCATGGATTATACTTGCTGAAA 57.194 30.769 0.00 0.00 32.33 2.69
2333 3794 9.412460 TCTTTCATGGATTATACTTGCTGAAAT 57.588 29.630 0.00 0.00 32.71 2.17
2336 3797 9.806203 TTCATGGATTATACTTGCTGAAATTTG 57.194 29.630 0.00 0.00 0.00 2.32
2337 3798 8.970020 TCATGGATTATACTTGCTGAAATTTGT 58.030 29.630 0.00 0.00 0.00 2.83
2338 3799 9.590451 CATGGATTATACTTGCTGAAATTTGTT 57.410 29.630 0.00 0.00 0.00 2.83
2339 3800 9.807649 ATGGATTATACTTGCTGAAATTTGTTC 57.192 29.630 0.00 0.00 0.00 3.18
2340 3801 8.250332 TGGATTATACTTGCTGAAATTTGTTCC 58.750 33.333 0.00 0.00 0.00 3.62
2351 3812 7.118101 TGCTGAAATTTGTTCCTTTATGCATTC 59.882 33.333 3.54 0.00 0.00 2.67
2540 4003 0.560688 ACCTCACCCACCAACCAAAT 59.439 50.000 0.00 0.00 0.00 2.32
2593 4056 9.720769 TTTAACCTTCAAACCAAACAAAACATA 57.279 25.926 0.00 0.00 0.00 2.29
2671 4135 3.850098 GATGCCCATAGCCACCCCG 62.850 68.421 0.00 0.00 42.71 5.73
2683 4147 2.933287 ACCCCGGCATGTCCTTCA 60.933 61.111 0.00 0.00 0.00 3.02
2685 4149 1.304052 CCCCGGCATGTCCTTCAAA 60.304 57.895 0.00 0.00 0.00 2.69
2692 4156 2.102252 GGCATGTCCTTCAAACCAAACA 59.898 45.455 0.00 0.00 0.00 2.83
2711 4175 4.396357 ACACATCCTAAATTTGTCCCCA 57.604 40.909 0.00 0.00 0.00 4.96
2725 4189 0.251832 TCCCCAGACACTCCAGACTC 60.252 60.000 0.00 0.00 0.00 3.36
2728 4192 0.962489 CCAGACACTCCAGACTCGTT 59.038 55.000 0.00 0.00 0.00 3.85
2729 4193 1.068194 CCAGACACTCCAGACTCGTTC 60.068 57.143 0.00 0.00 0.00 3.95
2760 4226 2.821969 GTGTGTCCATTTTGAGATGGCT 59.178 45.455 0.00 0.00 45.07 4.75
2781 4248 1.460255 CTCCCCAAAAGCTGTCCCA 59.540 57.895 0.00 0.00 0.00 4.37
2798 4265 1.881973 CCCAAACAGACATGTCCACAG 59.118 52.381 22.21 12.16 39.29 3.66
2811 4278 1.131126 GTCCACAGACATTTGATGCGG 59.869 52.381 0.00 0.00 42.99 5.69
2819 4286 2.348660 ACATTTGATGCGGCCATTTTG 58.651 42.857 2.24 0.00 0.00 2.44
2823 4290 1.184431 TGATGCGGCCATTTTGATGT 58.816 45.000 2.24 0.00 0.00 3.06
2841 4308 3.423539 TGTATAGCATTGGAGATGCCC 57.576 47.619 7.33 0.00 45.59 5.36
2882 4349 2.038387 ACCAACGGAGCACATTATCC 57.962 50.000 0.00 0.00 0.00 2.59
2908 4375 7.764141 ACATGTGATAATTATAGCCATGCAA 57.236 32.000 20.57 0.00 33.31 4.08
2922 4389 6.468333 AGCCATGCAAATACAATATTGTCA 57.532 33.333 24.00 15.54 42.35 3.58
2923 4390 7.058023 AGCCATGCAAATACAATATTGTCAT 57.942 32.000 24.00 16.99 42.35 3.06
2924 4391 7.149973 AGCCATGCAAATACAATATTGTCATC 58.850 34.615 24.00 10.07 42.35 2.92
2925 4392 6.088483 GCCATGCAAATACAATATTGTCATCG 59.912 38.462 24.00 14.00 42.35 3.84
2926 4393 6.088483 CCATGCAAATACAATATTGTCATCGC 59.912 38.462 24.00 20.76 42.35 4.58
2927 4394 6.375945 TGCAAATACAATATTGTCATCGCT 57.624 33.333 24.00 1.09 42.35 4.93
2928 4395 6.429624 TGCAAATACAATATTGTCATCGCTC 58.570 36.000 24.00 9.56 42.35 5.03
2929 4396 6.038050 TGCAAATACAATATTGTCATCGCTCA 59.962 34.615 24.00 11.72 42.35 4.26
2960 4427 1.955778 CCACATGCCAGACACAAAAGA 59.044 47.619 0.00 0.00 0.00 2.52
2961 4428 2.361757 CCACATGCCAGACACAAAAGAA 59.638 45.455 0.00 0.00 0.00 2.52
3024 4491 2.229784 CCTTGCCAAACTCATCCTTGTC 59.770 50.000 0.00 0.00 0.00 3.18
3025 4492 1.522668 TGCCAAACTCATCCTTGTCG 58.477 50.000 0.00 0.00 0.00 4.35
3026 4493 0.169009 GCCAAACTCATCCTTGTCGC 59.831 55.000 0.00 0.00 0.00 5.19
3027 4494 1.522668 CCAAACTCATCCTTGTCGCA 58.477 50.000 0.00 0.00 0.00 5.10
3038 5311 3.246619 TCCTTGTCGCAAAACACAAAAC 58.753 40.909 0.00 0.00 32.16 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.315142 GACAGATGCAGGGCCGACA 62.315 63.158 0.00 0.00 0.00 4.35
46 47 3.785859 GGACAGATGCAGGGCCGA 61.786 66.667 0.00 0.00 0.00 5.54
87 88 0.583438 CACAACACTTGCTCTCACGG 59.417 55.000 0.00 0.00 0.00 4.94
98 99 4.021650 CGTACCACGCACAACACT 57.978 55.556 0.00 0.00 33.65 3.55
154 155 0.032130 AGTACATATGGTCCGCGCAG 59.968 55.000 8.75 0.00 0.00 5.18
155 156 0.249280 CAGTACATATGGTCCGCGCA 60.249 55.000 8.75 0.00 0.00 6.09
156 157 0.031585 TCAGTACATATGGTCCGCGC 59.968 55.000 7.80 0.00 0.00 6.86
157 158 2.328473 CATCAGTACATATGGTCCGCG 58.672 52.381 7.80 0.00 0.00 6.46
160 161 4.898320 TCATGCATCAGTACATATGGTCC 58.102 43.478 7.80 0.00 0.00 4.46
161 162 7.389884 AGAAATCATGCATCAGTACATATGGTC 59.610 37.037 7.80 0.00 0.00 4.02
162 163 7.229308 AGAAATCATGCATCAGTACATATGGT 58.771 34.615 7.80 0.00 0.00 3.55
179 215 9.650714 TGGATAGAAAATCAATGGAGAAATCAT 57.349 29.630 0.00 0.00 0.00 2.45
182 218 9.258629 TGTTGGATAGAAAATCAATGGAGAAAT 57.741 29.630 0.00 0.00 0.00 2.17
244 280 1.004560 TCGCCTTTGACCTGAGCTG 60.005 57.895 0.00 0.00 0.00 4.24
318 365 3.565902 AGAAGCAGTTAACAAGTTGCCTC 59.434 43.478 8.61 8.05 37.26 4.70
322 369 7.440523 AATAGGAGAAGCAGTTAACAAGTTG 57.559 36.000 8.61 0.00 0.00 3.16
338 385 7.004555 TCTTTGTCAAGCAGTAAATAGGAGA 57.995 36.000 0.00 0.00 0.00 3.71
346 393 7.228507 ACATGTACATTCTTTGTCAAGCAGTAA 59.771 33.333 5.37 0.00 39.87 2.24
359 406 6.772716 AGGAACAAGTCAACATGTACATTCTT 59.227 34.615 5.37 3.82 0.00 2.52
362 409 5.827797 ACAGGAACAAGTCAACATGTACATT 59.172 36.000 5.37 0.00 0.00 2.71
505 1765 2.041485 TCCCACATTTGATCAGCAAGGA 59.959 45.455 0.00 0.00 37.87 3.36
583 1843 2.196749 ACAATAGATCGTCGCAGCAAG 58.803 47.619 0.00 0.00 0.00 4.01
724 2059 6.811253 ACGAACCAATTCAGCAAGTATTTA 57.189 33.333 0.00 0.00 34.14 1.40
746 2113 9.294030 CCAATTCAGCAAGTATTTGAAGATAAC 57.706 33.333 1.56 0.00 36.36 1.89
935 2304 4.572571 GGCCACCGGTCACCACAA 62.573 66.667 16.07 0.00 0.00 3.33
1023 2392 1.595929 GGTTCCAAAGTCGGTGCGA 60.596 57.895 0.00 0.00 0.00 5.10
1080 2452 6.623486 TGATTTGAGGTGCATTATCTGTTTG 58.377 36.000 0.00 0.00 0.00 2.93
1272 2662 5.648092 AGTACTTATTCCAACAGTGAATGGC 59.352 40.000 12.93 0.37 36.62 4.40
1327 2721 5.109210 CAAGCAAGTGATGATGCATGAAAT 58.891 37.500 2.46 0.00 0.00 2.17
1338 2732 4.843220 AAAGAAGTCCAAGCAAGTGATG 57.157 40.909 0.00 0.00 0.00 3.07
1388 2782 8.537728 TTTCAGCAAGGATTTGGATATAACAT 57.462 30.769 0.00 0.00 34.79 2.71
1390 2784 8.632679 TCATTTCAGCAAGGATTTGGATATAAC 58.367 33.333 0.00 0.00 34.79 1.89
1443 2897 9.692749 AGCTATCATGCATGAAAGAATAAATTG 57.307 29.630 31.79 14.34 40.69 2.32
1463 2917 8.408601 TGAAAGAATAAATTCCAGCAAGCTATC 58.591 33.333 0.00 0.00 37.51 2.08
1545 2999 7.637709 CTTTGTGGTCCTTTATAAACAAAGC 57.362 36.000 18.30 7.97 44.12 3.51
1625 3079 0.469917 TAGCCATGCTAGCTCCAACC 59.530 55.000 17.23 0.00 41.83 3.77
1703 3157 2.036933 GCTTTGTTCGCTTTCAGTTCG 58.963 47.619 0.00 0.00 0.00 3.95
1708 3162 1.024271 AGCAGCTTTGTTCGCTTTCA 58.976 45.000 0.00 0.00 35.07 2.69
1715 3169 1.871126 GAGGGGCAGCAGCTTTGTTC 61.871 60.000 0.00 0.00 41.70 3.18
1755 3209 0.249489 GCTGACTCACCACAAGTCGT 60.249 55.000 0.00 0.00 44.96 4.34
1757 3211 1.506493 CAGCTGACTCACCACAAGTC 58.494 55.000 8.42 0.00 42.83 3.01
1918 3373 3.008485 ACCAGGGAGTTCTTTCATCTCAC 59.992 47.826 0.00 0.00 32.45 3.51
1954 3409 3.931907 AGGCATAGTAATGTGCAAGGA 57.068 42.857 13.89 0.00 43.00 3.36
1979 3434 1.873591 GCAACACGAGGATTGTCAACT 59.126 47.619 0.00 0.00 0.00 3.16
2310 3771 9.806203 CAAATTTCAGCAAGTATAATCCATGAA 57.194 29.630 0.00 0.00 0.00 2.57
2311 3772 8.970020 ACAAATTTCAGCAAGTATAATCCATGA 58.030 29.630 0.00 0.00 0.00 3.07
2312 3773 9.590451 AACAAATTTCAGCAAGTATAATCCATG 57.410 29.630 0.00 0.00 0.00 3.66
2313 3774 9.807649 GAACAAATTTCAGCAAGTATAATCCAT 57.192 29.630 0.00 0.00 0.00 3.41
2314 3775 8.250332 GGAACAAATTTCAGCAAGTATAATCCA 58.750 33.333 0.00 0.00 0.00 3.41
2315 3776 8.470002 AGGAACAAATTTCAGCAAGTATAATCC 58.530 33.333 0.00 0.00 0.00 3.01
2316 3777 9.860898 AAGGAACAAATTTCAGCAAGTATAATC 57.139 29.630 0.00 0.00 0.00 1.75
2320 3781 9.643693 CATAAAGGAACAAATTTCAGCAAGTAT 57.356 29.630 0.00 0.00 0.00 2.12
2321 3782 7.598493 GCATAAAGGAACAAATTTCAGCAAGTA 59.402 33.333 0.00 0.00 0.00 2.24
2322 3783 6.424812 GCATAAAGGAACAAATTTCAGCAAGT 59.575 34.615 0.00 0.00 0.00 3.16
2323 3784 6.424509 TGCATAAAGGAACAAATTTCAGCAAG 59.575 34.615 0.00 0.00 30.37 4.01
2324 3785 6.286758 TGCATAAAGGAACAAATTTCAGCAA 58.713 32.000 0.00 0.00 30.37 3.91
2325 3786 5.851720 TGCATAAAGGAACAAATTTCAGCA 58.148 33.333 0.00 0.00 0.00 4.41
2326 3787 6.973229 ATGCATAAAGGAACAAATTTCAGC 57.027 33.333 0.00 0.00 0.00 4.26
2327 3788 8.767478 AGAATGCATAAAGGAACAAATTTCAG 57.233 30.769 0.00 0.00 0.00 3.02
2332 3793 9.643693 CAAGTTAGAATGCATAAAGGAACAAAT 57.356 29.630 0.00 0.00 0.00 2.32
2333 3794 7.598493 GCAAGTTAGAATGCATAAAGGAACAAA 59.402 33.333 0.00 0.00 42.12 2.83
2334 3795 7.039784 AGCAAGTTAGAATGCATAAAGGAACAA 60.040 33.333 0.00 0.00 44.95 2.83
2335 3796 6.434028 AGCAAGTTAGAATGCATAAAGGAACA 59.566 34.615 0.00 0.00 44.95 3.18
2336 3797 6.749118 CAGCAAGTTAGAATGCATAAAGGAAC 59.251 38.462 0.00 0.80 44.95 3.62
2337 3798 6.658816 TCAGCAAGTTAGAATGCATAAAGGAA 59.341 34.615 0.00 0.00 44.95 3.36
2338 3799 6.179756 TCAGCAAGTTAGAATGCATAAAGGA 58.820 36.000 0.00 0.00 44.95 3.36
2339 3800 6.441093 TCAGCAAGTTAGAATGCATAAAGG 57.559 37.500 0.00 0.00 44.95 3.11
2340 3801 8.922058 ATTTCAGCAAGTTAGAATGCATAAAG 57.078 30.769 0.00 0.00 44.95 1.85
2343 3804 8.306038 ACAAATTTCAGCAAGTTAGAATGCATA 58.694 29.630 0.00 0.00 44.95 3.14
2408 3870 6.153340 ACAAACTCCAGCAAGTTATAATGCAT 59.847 34.615 12.39 0.00 44.95 3.96
2410 3872 5.954335 ACAAACTCCAGCAAGTTATAATGC 58.046 37.500 3.31 3.31 38.52 3.56
2516 3979 0.109723 GTTGGTGGGTGAGGTTAGCA 59.890 55.000 0.00 0.00 0.00 3.49
2540 4003 3.832527 GCTGGGGATAGCCATTTTTCTA 58.167 45.455 0.00 0.00 37.73 2.10
2593 4056 3.718434 TGGTTGATGGATGAGATTAGCCT 59.282 43.478 0.00 0.00 0.00 4.58
2671 4135 2.102252 TGTTTGGTTTGAAGGACATGCC 59.898 45.455 0.00 0.00 0.00 4.40
2676 4140 3.636764 AGGATGTGTTTGGTTTGAAGGAC 59.363 43.478 0.00 0.00 0.00 3.85
2683 4147 6.989759 GGACAAATTTAGGATGTGTTTGGTTT 59.010 34.615 0.00 0.00 34.87 3.27
2685 4149 5.011635 GGGACAAATTTAGGATGTGTTTGGT 59.988 40.000 0.00 0.00 34.87 3.67
2692 4156 4.600062 GTCTGGGGACAAATTTAGGATGT 58.400 43.478 0.00 0.00 42.06 3.06
2711 4175 0.875728 CGAACGAGTCTGGAGTGTCT 59.124 55.000 0.00 0.00 0.00 3.41
2719 4183 1.136252 CCAAATGTGCGAACGAGTCTG 60.136 52.381 0.00 0.00 0.00 3.51
2760 4226 0.696501 GGACAGCTTTTGGGGAGGTA 59.303 55.000 0.00 0.00 0.00 3.08
2781 4248 3.558931 TGTCTGTGGACATGTCTGTTT 57.441 42.857 24.50 0.00 46.19 2.83
2798 4265 2.298411 AAATGGCCGCATCAAATGTC 57.702 45.000 0.00 0.00 0.00 3.06
2808 4275 2.293122 TGCTATACATCAAAATGGCCGC 59.707 45.455 0.00 0.00 37.19 6.53
2809 4276 4.771590 ATGCTATACATCAAAATGGCCG 57.228 40.909 0.00 0.00 37.19 6.13
2811 4278 6.016024 TCTCCAATGCTATACATCAAAATGGC 60.016 38.462 0.00 0.00 38.34 4.40
2819 4286 3.944015 GGGCATCTCCAATGCTATACATC 59.056 47.826 9.62 0.00 44.02 3.06
2823 4290 4.846367 ACTTAGGGCATCTCCAATGCTATA 59.154 41.667 9.62 1.45 44.02 1.31
2841 4308 6.077838 GGTAATTTGCGTTCAGTCAACTTAG 58.922 40.000 0.00 0.00 32.09 2.18
2882 4349 7.595604 TGCATGGCTATAATTATCACATGTTG 58.404 34.615 23.53 11.56 37.23 3.33
2901 4368 6.088483 GCGATGACAATATTGTATTTGCATGG 59.912 38.462 20.83 18.77 42.43 3.66
2902 4369 6.859508 AGCGATGACAATATTGTATTTGCATG 59.140 34.615 27.82 18.59 42.43 4.06
2908 4375 9.669353 GAAATTGAGCGATGACAATATTGTATT 57.331 29.630 20.83 11.28 42.43 1.89
2915 4382 5.005682 CGACAGAAATTGAGCGATGACAATA 59.994 40.000 0.00 0.00 35.99 1.90
2919 4386 2.535732 GCGACAGAAATTGAGCGATGAC 60.536 50.000 0.00 0.00 32.65 3.06
2922 4389 1.009829 GGCGACAGAAATTGAGCGAT 58.990 50.000 0.00 0.00 35.78 4.58
2923 4390 0.320334 TGGCGACAGAAATTGAGCGA 60.320 50.000 0.00 0.00 35.78 4.93
2924 4391 0.179215 GTGGCGACAGAAATTGAGCG 60.179 55.000 0.00 0.00 44.46 5.03
2925 4392 0.874390 TGTGGCGACAGAAATTGAGC 59.126 50.000 0.00 0.00 44.46 4.26
2926 4393 2.730090 GCATGTGGCGACAGAAATTGAG 60.730 50.000 7.82 0.00 44.46 3.02
2927 4394 1.199789 GCATGTGGCGACAGAAATTGA 59.800 47.619 7.82 0.00 44.46 2.57
2928 4395 1.621107 GCATGTGGCGACAGAAATTG 58.379 50.000 7.82 1.30 44.46 2.32
2929 4396 0.527565 GGCATGTGGCGACAGAAATT 59.472 50.000 7.82 0.00 46.16 1.82
2996 4463 6.435164 AGGATGAGTTTGGCAAGGTAAATAT 58.565 36.000 0.00 0.00 0.00 1.28
2997 4464 5.826643 AGGATGAGTTTGGCAAGGTAAATA 58.173 37.500 0.00 0.00 0.00 1.40
2998 4465 4.677182 AGGATGAGTTTGGCAAGGTAAAT 58.323 39.130 0.00 0.00 0.00 1.40
3018 4485 2.989840 TGTTTTGTGTTTTGCGACAAGG 59.010 40.909 0.00 0.00 33.73 3.61
3024 4491 5.117897 GGTGGTATATGTTTTGTGTTTTGCG 59.882 40.000 0.00 0.00 0.00 4.85
3025 4492 6.220201 AGGTGGTATATGTTTTGTGTTTTGC 58.780 36.000 0.00 0.00 0.00 3.68
3026 4493 8.353684 TGTAGGTGGTATATGTTTTGTGTTTTG 58.646 33.333 0.00 0.00 0.00 2.44
3027 4494 8.354426 GTGTAGGTGGTATATGTTTTGTGTTTT 58.646 33.333 0.00 0.00 0.00 2.43
3038 5311 6.315393 GTCAGTTTTGGTGTAGGTGGTATATG 59.685 42.308 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.