Multiple sequence alignment - TraesCS5A01G305900

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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 TraesCS5A01G305900 chr5A 100.000 3833 0 0 1 3833 514409239 514405407 0.000000e+00 7079.0
1 TraesCS5A01G305900 chr5A 94.364 621 32 3 3168 3787 118591330 118591948 0.000000e+00 950.0
2 TraesCS5A01G305900 chr5A 93.182 616 38 4 3168 3782 80356626 80357238 0.000000e+00 902.0
3 TraesCS5A01G305900 chr5A 80.147 272 42 10 2403 2668 381686388 381686653 3.910000e-45 193.0
4 TraesCS5A01G305900 chr5D 92.538 2975 166 29 231 3173 408483992 408481042 0.000000e+00 4213.0
5 TraesCS5A01G305900 chr5D 86.528 193 25 1 13 205 408485168 408484977 1.080000e-50 211.0
6 TraesCS5A01G305900 chr5D 77.544 285 43 11 1664 1945 408482755 408482489 6.630000e-33 152.0
7 TraesCS5A01G305900 chr5D 96.226 53 1 1 3782 3833 408481045 408480993 6.820000e-13 86.1
8 TraesCS5A01G305900 chr5D 91.379 58 5 0 167 224 408484578 408484521 3.170000e-11 80.5
9 TraesCS5A01G305900 chr5B 91.871 2940 179 27 253 3173 490053192 490050294 0.000000e+00 4050.0
10 TraesCS5A01G305900 chr5B 95.455 154 7 0 2972 3125 567240455 567240302 2.960000e-61 246.0
11 TraesCS5A01G305900 chr5B 95.105 143 7 0 2983 3125 567295821 567295963 3.850000e-55 226.0
12 TraesCS5A01G305900 chr5B 85.128 195 27 2 10 203 490054192 490053999 8.400000e-47 198.0
13 TraesCS5A01G305900 chr5B 79.710 276 40 13 2406 2672 466687236 466686968 6.540000e-43 185.0
14 TraesCS5A01G305900 chr4A 93.492 630 37 4 3167 3795 351534726 351534100 0.000000e+00 933.0
15 TraesCS5A01G305900 chr4A 93.258 623 37 3 3166 3786 107598588 107599207 0.000000e+00 913.0
16 TraesCS5A01G305900 chr3A 93.841 617 36 2 3166 3782 209023864 209023250 0.000000e+00 928.0
17 TraesCS5A01G305900 chr3A 93.831 616 33 4 3168 3782 503172780 503173391 0.000000e+00 922.0
18 TraesCS5A01G305900 chr3A 92.960 625 41 3 3161 3782 294213063 294212439 0.000000e+00 907.0
19 TraesCS5A01G305900 chr6A 93.517 617 37 3 3166 3782 284945880 284946493 0.000000e+00 915.0
20 TraesCS5A01G305900 chr6A 79.928 279 40 13 2402 2669 46549127 46548854 1.410000e-44 191.0
21 TraesCS5A01G305900 chr7A 92.628 624 45 1 3170 3793 103133655 103133033 0.000000e+00 896.0
22 TraesCS5A01G305900 chr2B 95.031 161 8 0 2965 3125 391174738 391174578 1.770000e-63 254.0
23 TraesCS5A01G305900 chr2B 97.826 46 0 1 3128 3173 474342099 474342055 1.140000e-10 78.7
24 TraesCS5A01G305900 chr1D 81.560 282 40 9 2403 2676 14667395 14667672 4.980000e-54 222.0
25 TraesCS5A01G305900 chr1D 80.074 271 44 8 2403 2667 408464573 408464307 3.910000e-45 193.0
26 TraesCS5A01G305900 chr2A 90.625 160 15 0 2965 3124 25257640 25257799 3.000000e-51 213.0
27 TraesCS5A01G305900 chr2A 90.625 160 15 0 2965 3124 25324101 25324260 3.000000e-51 213.0
28 TraesCS5A01G305900 chr2A 90.000 160 16 0 2965 3124 25306908 25307067 1.400000e-49 207.0
29 TraesCS5A01G305900 chr2A 92.969 128 9 0 2997 3124 25275701 25275828 1.820000e-43 187.0
30 TraesCS5A01G305900 chr3D 79.927 274 42 10 2403 2668 79555367 79555099 5.050000e-44 189.0
31 TraesCS5A01G305900 chr3D 94.340 53 2 1 3782 3833 6755620 6755568 3.170000e-11 80.5
32 TraesCS5A01G305900 chr1A 79.705 271 47 8 2403 2669 100041463 100041197 5.050000e-44 189.0
33 TraesCS5A01G305900 chr3B 94.643 56 2 1 3779 3833 665462387 665462442 6.820000e-13 86.1
34 TraesCS5A01G305900 chrUn 94.340 53 2 1 3782 3833 86517385 86517333 3.170000e-11 80.5
35 TraesCS5A01G305900 chrUn 94.340 53 2 1 3782 3833 206784903 206784851 3.170000e-11 80.5
36 TraesCS5A01G305900 chrUn 92.857 56 3 1 3779 3833 345388392 345388447 3.170000e-11 80.5
37 TraesCS5A01G305900 chrUn 95.652 46 1 1 3128 3173 86517426 86517382 5.310000e-09 73.1
38 TraesCS5A01G305900 chrUn 95.652 46 1 1 3128 3173 206784944 206784900 5.310000e-09 73.1
39 TraesCS5A01G305900 chrUn 95.652 46 1 1 3128 3173 345388354 345388398 5.310000e-09 73.1
40 TraesCS5A01G305900 chr6D 94.340 53 2 1 3782 3833 124503779 124503727 3.170000e-11 80.5
41 TraesCS5A01G305900 chr6D 95.652 46 1 1 3128 3173 124503820 124503776 5.310000e-09 73.1
42 TraesCS5A01G305900 chr4D 92.857 56 3 1 3779 3833 6759381 6759436 3.170000e-11 80.5
43 TraesCS5A01G305900 chr4D 94.340 53 2 1 3782 3833 123289960 123289908 3.170000e-11 80.5
44 TraesCS5A01G305900 chr4D 95.652 46 1 1 3128 3173 6759343 6759387 5.310000e-09 73.1
45 TraesCS5A01G305900 chr4D 95.652 46 1 1 3128 3173 123290001 123289957 5.310000e-09 73.1


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 TraesCS5A01G305900 chr5A 514405407 514409239 3832 True 7079.00 7079 100.0000 1 3833 1 chr5A.!!$R1 3832
1 TraesCS5A01G305900 chr5A 118591330 118591948 618 False 950.00 950 94.3640 3168 3787 1 chr5A.!!$F2 619
2 TraesCS5A01G305900 chr5A 80356626 80357238 612 False 902.00 902 93.1820 3168 3782 1 chr5A.!!$F1 614
3 TraesCS5A01G305900 chr5D 408480993 408485168 4175 True 948.52 4213 88.8430 13 3833 5 chr5D.!!$R1 3820
4 TraesCS5A01G305900 chr5B 490050294 490054192 3898 True 2124.00 4050 88.4995 10 3173 2 chr5B.!!$R3 3163
5 TraesCS5A01G305900 chr4A 351534100 351534726 626 True 933.00 933 93.4920 3167 3795 1 chr4A.!!$R1 628
6 TraesCS5A01G305900 chr4A 107598588 107599207 619 False 913.00 913 93.2580 3166 3786 1 chr4A.!!$F1 620
7 TraesCS5A01G305900 chr3A 209023250 209023864 614 True 928.00 928 93.8410 3166 3782 1 chr3A.!!$R1 616
8 TraesCS5A01G305900 chr3A 503172780 503173391 611 False 922.00 922 93.8310 3168 3782 1 chr3A.!!$F1 614
9 TraesCS5A01G305900 chr3A 294212439 294213063 624 True 907.00 907 92.9600 3161 3782 1 chr3A.!!$R2 621
10 TraesCS5A01G305900 chr6A 284945880 284946493 613 False 915.00 915 93.5170 3166 3782 1 chr6A.!!$F1 616
11 TraesCS5A01G305900 chr7A 103133033 103133655 622 True 896.00 896 92.6280 3170 3793 1 chr7A.!!$R1 623

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
902 2607 0.467804 GATCCAGCAGGAACCTCCTC 59.532 60.0 0.32 0.0 45.66 3.71 F
2125 3839 0.676782 GGTCAGTGGCGCCTAACATT 60.677 55.0 29.70 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2499 4217 1.004595 TGTAGTCGACGGAGACATCG 58.995 55.0 10.46 0.24 43.24 3.84 R
3632 5366 0.465460 TGCCGGGCATAATCTTCCAC 60.465 55.0 19.77 0.00 31.71 4.02 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
87 88 4.346129 CGGACCTACACACTAAATACGAC 58.654 47.826 0.00 0.00 0.00 4.34
91 92 3.378112 CCTACACACTAAATACGACCGGA 59.622 47.826 9.46 0.00 0.00 5.14
95 96 3.795101 CACACTAAATACGACCGGACATC 59.205 47.826 9.46 0.00 0.00 3.06
96 97 3.698040 ACACTAAATACGACCGGACATCT 59.302 43.478 9.46 0.00 0.00 2.90
98 99 5.107133 CACTAAATACGACCGGACATCTTT 58.893 41.667 9.46 0.00 0.00 2.52
101 102 4.402056 AATACGACCGGACATCTTTCAT 57.598 40.909 9.46 0.00 0.00 2.57
160 161 9.307121 CATAGAAACTGTACTATGAGGAAACTG 57.693 37.037 20.36 2.64 44.80 3.16
217 656 5.679638 GCCCATGTTGTTGAGGATAATGTTC 60.680 44.000 0.00 0.00 0.00 3.18
224 1185 2.821546 TGAGGATAATGTTCGGCTTCG 58.178 47.619 0.00 0.00 0.00 3.79
226 1187 1.139058 AGGATAATGTTCGGCTTCGCT 59.861 47.619 0.00 0.00 0.00 4.93
245 1206 3.394719 GCTAGCCTACTTGTAGAATGGC 58.605 50.000 2.29 5.25 40.54 4.40
249 1927 2.880890 GCCTACTTGTAGAATGGCATGG 59.119 50.000 0.00 0.00 40.04 3.66
251 1929 2.814805 ACTTGTAGAATGGCATGGCT 57.185 45.000 21.08 4.46 0.00 4.75
267 1946 4.754114 GCATGGCTGTGGTTAATTCAAAAA 59.246 37.500 0.00 0.00 0.00 1.94
322 2001 1.470285 GCCGACCGTGCTAATTGAGTA 60.470 52.381 0.00 0.00 0.00 2.59
379 2058 8.806429 TCAATAATGACAGAAAAAGGAGCATA 57.194 30.769 0.00 0.00 0.00 3.14
517 2209 3.598019 ACCGCTGGATAAGTAACGAAA 57.402 42.857 1.50 0.00 0.00 3.46
575 2267 7.306205 TGTATGTGTGTCATTGATGTATGTG 57.694 36.000 0.00 0.00 37.91 3.21
597 2289 6.163476 GTGTGTGTTTCTGTCTCCATGTATA 58.837 40.000 0.00 0.00 0.00 1.47
598 2290 6.818644 GTGTGTGTTTCTGTCTCCATGTATAT 59.181 38.462 0.00 0.00 0.00 0.86
599 2291 7.979537 GTGTGTGTTTCTGTCTCCATGTATATA 59.020 37.037 0.00 0.00 0.00 0.86
600 2292 7.979537 TGTGTGTTTCTGTCTCCATGTATATAC 59.020 37.037 5.89 5.89 0.00 1.47
601 2293 7.979537 GTGTGTTTCTGTCTCCATGTATATACA 59.020 37.037 17.65 17.65 40.98 2.29
723 2416 3.978687 ACAACTACCAATCGATCGATCC 58.021 45.455 29.48 2.50 33.08 3.36
902 2607 0.467804 GATCCAGCAGGAACCTCCTC 59.532 60.000 0.32 0.00 45.66 3.71
956 2661 5.064071 GTCTTTGCATAGTTAACTCTGGCTC 59.936 44.000 19.25 6.63 0.00 4.70
958 2663 2.496070 TGCATAGTTAACTCTGGCTCGT 59.504 45.455 19.25 0.00 0.00 4.18
983 2688 2.616376 CACACGATCTAGTCTCCTCCTG 59.384 54.545 0.00 0.00 0.00 3.86
984 2689 2.240160 ACACGATCTAGTCTCCTCCTGT 59.760 50.000 0.00 0.00 0.00 4.00
985 2690 3.455177 ACACGATCTAGTCTCCTCCTGTA 59.545 47.826 0.00 0.00 0.00 2.74
996 2701 2.175069 CTCCTCCTGTACTGGTAGGCTA 59.825 54.545 21.89 11.90 34.00 3.93
997 2702 2.175069 TCCTCCTGTACTGGTAGGCTAG 59.825 54.545 21.89 11.76 34.00 3.42
998 2703 2.588620 CTCCTGTACTGGTAGGCTAGG 58.411 57.143 17.42 1.46 34.00 3.02
1637 3351 4.803426 CAGCAGCCGAGACGACCC 62.803 72.222 0.00 0.00 0.00 4.46
1649 3363 4.715130 CGACCCCCTCCCCACAGA 62.715 72.222 0.00 0.00 0.00 3.41
1966 3680 0.966179 TGCCTACAAGTTCGAGCTCA 59.034 50.000 15.40 0.00 0.00 4.26
2125 3839 0.676782 GGTCAGTGGCGCCTAACATT 60.677 55.000 29.70 0.00 0.00 2.71
2378 4096 2.411904 CAGCATAAGAATCGGAGGAGC 58.588 52.381 0.00 0.00 0.00 4.70
2419 4137 8.812972 TGTTTACTAACAGTGATATCTCCAGTT 58.187 33.333 3.98 10.44 39.29 3.16
2426 4144 5.896106 ACAGTGATATCTCCAGTTCATCAGA 59.104 40.000 3.98 0.00 0.00 3.27
2484 4202 4.502171 TTTCAGAATTTTCAGCGATGCA 57.498 36.364 0.00 0.00 0.00 3.96
2489 4207 2.704725 ATTTTCAGCGATGCACGTTT 57.295 40.000 0.00 0.00 44.60 3.60
2494 4212 2.342179 TCAGCGATGCACGTTTAATGA 58.658 42.857 0.00 5.23 44.60 2.57
2499 4217 4.209288 AGCGATGCACGTTTAATGAGATAC 59.791 41.667 9.76 0.00 44.60 2.24
2553 4271 6.750501 CGGTGACTTCGTAAAATCTCAAGATA 59.249 38.462 0.00 0.00 33.73 1.98
2581 4299 0.603569 GCTCAGTCTTTCGGAGGTGA 59.396 55.000 0.00 0.00 38.48 4.02
2601 4319 5.538813 GGTGATCATATGAGTAGGGTGTGTA 59.461 44.000 11.78 0.00 0.00 2.90
2617 4338 5.057149 GGTGTGTATGCTTAATAGAGGTGG 58.943 45.833 0.00 0.00 0.00 4.61
2641 4362 7.766738 TGGGTGTATGCATGTATATATAAACGG 59.233 37.037 10.16 0.00 0.00 4.44
2642 4363 7.254658 GGGTGTATGCATGTATATATAAACGGC 60.255 40.741 10.16 0.00 0.00 5.68
2646 4367 5.241662 TGCATGTATATATAAACGGCTGCA 58.758 37.500 0.50 5.24 33.89 4.41
2654 4375 1.635844 TAAACGGCTGCATCTGTACG 58.364 50.000 1.75 0.00 0.00 3.67
2668 4389 7.872881 TGCATCTGTACGGTGTTAAATAAAAA 58.127 30.769 0.64 0.00 0.00 1.94
2675 4396 7.856894 TGTACGGTGTTAAATAAAAAGCTTGAC 59.143 33.333 0.00 0.00 0.00 3.18
2682 4403 7.755822 TGTTAAATAAAAAGCTTGACAACGTGT 59.244 29.630 0.00 0.00 0.00 4.49
2687 4408 2.024176 AGCTTGACAACGTGTTGACT 57.976 45.000 18.87 5.68 42.93 3.41
2688 4409 1.933853 AGCTTGACAACGTGTTGACTC 59.066 47.619 18.87 7.88 42.93 3.36
2689 4410 1.663643 GCTTGACAACGTGTTGACTCA 59.336 47.619 18.87 10.25 42.93 3.41
2694 4415 5.303747 TGACAACGTGTTGACTCATTTTT 57.696 34.783 18.87 0.00 42.93 1.94
2876 4605 6.920817 ACAATGAGTACACATTCGACTTCTA 58.079 36.000 14.65 0.00 38.25 2.10
2877 4606 6.807230 ACAATGAGTACACATTCGACTTCTAC 59.193 38.462 14.65 0.00 38.25 2.59
2885 4614 9.778993 GTACACATTCGACTTCTACATAGTTAA 57.221 33.333 0.00 0.00 0.00 2.01
2959 4688 7.228308 GCAAAATCATATAAGACTCCTGCTCTT 59.772 37.037 0.00 0.00 0.00 2.85
2960 4689 9.118300 CAAAATCATATAAGACTCCTGCTCTTT 57.882 33.333 0.00 0.00 0.00 2.52
2994 4723 3.499745 GGATACCCACCCACAGAAAAGTT 60.500 47.826 0.00 0.00 0.00 2.66
3009 4738 9.106070 CACAGAAAAGTTAGTACCTTACTTGTT 57.894 33.333 5.84 3.93 40.14 2.83
3028 4757 4.318332 TGTTCTTGAGCTGGTCAACTATG 58.682 43.478 17.52 8.86 40.45 2.23
3036 4765 1.825474 CTGGTCAACTATGTCCTCCGT 59.175 52.381 0.00 0.00 35.96 4.69
3108 4837 4.646492 GCATCATAACATGGAAGAAACCCT 59.354 41.667 0.00 0.00 0.00 4.34
3113 4842 2.519013 ACATGGAAGAAACCCTTGAGC 58.481 47.619 0.00 0.00 34.68 4.26
3130 4859 0.773644 AGCAATATCGGAATGGCCCT 59.226 50.000 0.00 0.00 0.00 5.19
3235 4964 4.461431 AGTCCTTTTCGTTTGGTTTGAGTT 59.539 37.500 0.00 0.00 0.00 3.01
3245 4974 3.188159 TGGTTTGAGTTCACGCTAAGT 57.812 42.857 0.00 0.00 0.00 2.24
3307 5036 3.192466 GGCTTTTATAGAGACCGCGAAA 58.808 45.455 8.23 0.00 0.00 3.46
3317 5046 9.970395 TTATAGAGACCGCGAAAAATAATTAGA 57.030 29.630 8.23 0.00 0.00 2.10
3319 5048 7.787725 AGAGACCGCGAAAAATAATTAGATT 57.212 32.000 8.23 0.00 0.00 2.40
3397 5126 4.923893 TGTATCAACCAACGACCTATACG 58.076 43.478 0.00 0.00 0.00 3.06
3417 5146 9.424319 CTATACGCCATTCACATTTACTAATCT 57.576 33.333 0.00 0.00 0.00 2.40
3446 5175 7.050970 TCGTTCTAAATATATGAGTGGCAGT 57.949 36.000 0.00 0.00 0.00 4.40
3455 5184 0.538746 TGAGTGGCAGTCCTCGTGTA 60.539 55.000 19.21 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.766375 TCTTCTCTCACGAAGGTGTTTTT 58.234 39.130 0.00 0.00 44.68 1.94
12 13 4.372656 CTCTTCTCTCACGAAGGTGTTTT 58.627 43.478 0.00 0.00 44.68 2.43
13 14 3.800604 GCTCTTCTCTCACGAAGGTGTTT 60.801 47.826 0.00 0.00 44.68 2.83
14 15 2.288518 GCTCTTCTCTCACGAAGGTGTT 60.289 50.000 0.00 0.00 44.68 3.32
15 16 1.271102 GCTCTTCTCTCACGAAGGTGT 59.729 52.381 0.00 0.00 44.68 4.16
16 17 1.270826 TGCTCTTCTCTCACGAAGGTG 59.729 52.381 0.00 0.00 45.78 4.00
17 18 1.621992 TGCTCTTCTCTCACGAAGGT 58.378 50.000 0.00 0.00 40.56 3.50
23 24 3.181491 ACTCGCTTATGCTCTTCTCTCAC 60.181 47.826 0.00 0.00 36.97 3.51
24 25 3.020274 ACTCGCTTATGCTCTTCTCTCA 58.980 45.455 0.00 0.00 36.97 3.27
31 32 4.695217 GAGCTATACTCGCTTATGCTCT 57.305 45.455 0.00 0.00 41.26 4.09
66 67 4.676546 GGTCGTATTTAGTGTGTAGGTCC 58.323 47.826 0.00 0.00 0.00 4.46
87 88 2.103094 TGAGGCTATGAAAGATGTCCGG 59.897 50.000 0.00 0.00 0.00 5.14
91 92 7.568349 TCTAACATTGAGGCTATGAAAGATGT 58.432 34.615 4.31 0.00 0.00 3.06
95 96 7.856145 AACTCTAACATTGAGGCTATGAAAG 57.144 36.000 4.31 1.92 35.98 2.62
96 97 8.635765 AAAACTCTAACATTGAGGCTATGAAA 57.364 30.769 4.31 0.00 35.98 2.69
98 99 7.769044 GGTAAAACTCTAACATTGAGGCTATGA 59.231 37.037 4.31 0.00 35.98 2.15
101 102 7.011499 TGGTAAAACTCTAACATTGAGGCTA 57.989 36.000 0.00 0.00 35.98 3.93
160 161 8.175716 AGCTACTTCGATACAAAGTATTTTTGC 58.824 33.333 0.00 0.00 38.26 3.68
224 1185 3.181465 TGCCATTCTACAAGTAGGCTAGC 60.181 47.826 6.04 6.04 42.46 3.42
226 1187 4.202357 CCATGCCATTCTACAAGTAGGCTA 60.202 45.833 7.35 0.00 42.46 3.93
379 2058 4.471904 TGTTGCCATCGTCTCTTCTAAT 57.528 40.909 0.00 0.00 0.00 1.73
429 2108 2.264480 CCGTGCCGTTGGATCTCA 59.736 61.111 0.00 0.00 0.00 3.27
517 2209 5.723672 TCGTTTGTCTCTCTATTTCACCT 57.276 39.130 0.00 0.00 0.00 4.00
902 2607 3.052036 CAGCCGAATTTTCAACTGGTTG 58.948 45.455 7.10 7.10 41.71 3.77
968 2673 3.789274 ACCAGTACAGGAGGAGACTAGAT 59.211 47.826 11.86 0.00 44.43 1.98
973 2678 2.657143 CCTACCAGTACAGGAGGAGAC 58.343 57.143 11.86 0.00 33.42 3.36
983 2688 6.777782 TCTTATACTCCTAGCCTACCAGTAC 58.222 44.000 0.00 0.00 0.00 2.73
984 2689 6.791466 TCTCTTATACTCCTAGCCTACCAGTA 59.209 42.308 0.00 0.00 0.00 2.74
985 2690 5.611835 TCTCTTATACTCCTAGCCTACCAGT 59.388 44.000 0.00 0.00 0.00 4.00
996 2701 3.833732 TCGCCATGTCTCTTATACTCCT 58.166 45.455 0.00 0.00 0.00 3.69
997 2702 4.021894 ACATCGCCATGTCTCTTATACTCC 60.022 45.833 0.00 0.00 39.15 3.85
998 2703 5.127693 ACATCGCCATGTCTCTTATACTC 57.872 43.478 0.00 0.00 39.15 2.59
1141 2846 3.237741 GGGCATCTCTCTCCCCCG 61.238 72.222 0.00 0.00 33.91 5.73
1637 3351 2.037367 TCTCGTCTGTGGGGAGGG 59.963 66.667 0.00 0.00 0.00 4.30
1642 3356 1.649390 CCTCTCGTCTCGTCTGTGGG 61.649 65.000 0.00 0.00 0.00 4.61
1649 3363 2.254737 ATCCCGTCCTCTCGTCTCGT 62.255 60.000 0.00 0.00 0.00 4.18
2125 3839 2.483876 CTCGACAGAAAGCAACAAGGA 58.516 47.619 0.00 0.00 0.00 3.36
2161 3875 1.595929 GGTTTCGCAACGGTCTGGA 60.596 57.895 0.00 0.00 33.13 3.86
2246 3960 6.925165 AGACACATTGATCAAACAATTGTTCC 59.075 34.615 23.47 13.37 38.25 3.62
2312 4030 2.920724 TCTTTTGTGGACCATCACGA 57.079 45.000 0.00 0.00 40.31 4.35
2419 4137 6.233434 AGCATCAACACTTAAACTCTGATGA 58.767 36.000 12.71 4.11 41.63 2.92
2426 4144 7.435068 AAATACGAGCATCAACACTTAAACT 57.565 32.000 0.00 0.00 33.17 2.66
2484 4202 6.207213 GGAGACATCGTATCTCATTAAACGT 58.793 40.000 12.93 0.00 43.80 3.99
2489 4207 4.151867 CGACGGAGACATCGTATCTCATTA 59.848 45.833 12.93 0.00 43.80 1.90
2494 4212 1.865970 GTCGACGGAGACATCGTATCT 59.134 52.381 0.00 0.00 41.22 1.98
2499 4217 1.004595 TGTAGTCGACGGAGACATCG 58.995 55.000 10.46 0.24 43.24 3.84
2553 4271 2.565841 GAAAGACTGAGCCGGCATATT 58.434 47.619 31.54 7.63 0.00 1.28
2581 4299 5.782331 AGCATACACACCCTACTCATATGAT 59.218 40.000 5.72 0.00 0.00 2.45
2601 4319 5.746065 GCATACACCCACCTCTATTAAGCAT 60.746 44.000 0.00 0.00 0.00 3.79
2617 4338 7.494625 AGCCGTTTATATATACATGCATACACC 59.505 37.037 0.00 0.00 0.00 4.16
2641 4362 2.004583 TAACACCGTACAGATGCAGC 57.995 50.000 0.00 0.00 0.00 5.25
2642 4363 6.656314 TTATTTAACACCGTACAGATGCAG 57.344 37.500 0.00 0.00 0.00 4.41
2646 4367 8.331730 AGCTTTTTATTTAACACCGTACAGAT 57.668 30.769 0.00 0.00 0.00 2.90
2654 4375 7.221259 ACGTTGTCAAGCTTTTTATTTAACACC 59.779 33.333 0.00 0.00 0.00 4.16
2668 4389 1.933853 GAGTCAACACGTTGTCAAGCT 59.066 47.619 9.60 2.69 41.16 3.74
2675 4396 8.829514 TTAACTAAAAATGAGTCAACACGTTG 57.170 30.769 0.00 3.45 41.71 4.10
2741 4470 2.855963 CACATTCATCATTTTGCTCGCC 59.144 45.455 0.00 0.00 0.00 5.54
2876 4605 9.290988 TGTTGGATGTGTACATTTTAACTATGT 57.709 29.630 0.00 7.37 39.44 2.29
2886 4615 8.394877 CGTGTATTAATGTTGGATGTGTACATT 58.605 33.333 0.00 0.00 43.02 2.71
2890 4619 8.999220 TTACGTGTATTAATGTTGGATGTGTA 57.001 30.769 0.00 0.00 0.00 2.90
2931 4660 7.059156 AGCAGGAGTCTTATATGATTTTGCTT 58.941 34.615 13.31 4.59 33.66 3.91
2994 4723 6.295123 CCAGCTCAAGAACAAGTAAGGTACTA 60.295 42.308 0.00 0.00 38.49 1.82
3009 4738 3.055819 GGACATAGTTGACCAGCTCAAGA 60.056 47.826 0.00 0.00 39.69 3.02
3028 4757 1.744522 GGAGTCTTCACTACGGAGGAC 59.255 57.143 0.00 0.00 42.39 3.85
3108 4837 2.229792 GGCCATTCCGATATTGCTCAA 58.770 47.619 0.00 0.00 0.00 3.02
3113 4842 3.515502 TCTCTAGGGCCATTCCGATATTG 59.484 47.826 6.18 0.00 34.94 1.90
3130 4859 5.785423 TCTTGAAAGAATGGGGTTCTCTCTA 59.215 40.000 0.00 0.00 46.39 2.43
3199 4928 7.102847 ACGAAAAGGACTAAACCAAATCAAA 57.897 32.000 0.00 0.00 0.00 2.69
3245 4974 4.338400 CGTACAAGTACCTGGATCAGATCA 59.662 45.833 12.66 0.00 32.44 2.92
3252 4981 4.382685 CCATCAACGTACAAGTACCTGGAT 60.383 45.833 0.00 0.19 32.61 3.41
3253 4982 3.056393 CCATCAACGTACAAGTACCTGGA 60.056 47.826 0.00 0.00 32.61 3.86
3379 5108 1.135024 GGCGTATAGGTCGTTGGTTGA 60.135 52.381 0.00 0.00 0.00 3.18
3397 5126 7.989826 AGTTGAGATTAGTAAATGTGAATGGC 58.010 34.615 0.00 0.00 0.00 4.40
3417 5146 7.652105 GCCACTCATATATTTAGAACGAGTTGA 59.348 37.037 0.00 0.00 30.12 3.18
3455 5184 5.513267 CCTTCCTTTAATTAGCTCGCCCTAT 60.513 44.000 0.00 0.00 0.00 2.57
3519 5253 6.958767 AGTAGTCCAACACATTAAAGCCTAT 58.041 36.000 0.00 0.00 0.00 2.57
3632 5366 0.465460 TGCCGGGCATAATCTTCCAC 60.465 55.000 19.77 0.00 31.71 4.02
3739 5473 5.649557 CGTTGCAATGGGAAAAGAATGATA 58.350 37.500 11.00 0.00 0.00 2.15
3746 5480 1.139163 GTGCGTTGCAATGGGAAAAG 58.861 50.000 19.93 0.00 41.47 2.27
3793 5529 9.760077 CTCGCTTACTCCTATTTTCCTTATTTA 57.240 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.