Multiple sequence alignment - TraesCS5B01G051400

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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 TraesCS5B01G051400 chr5B 100.000 5567 0 0 1 5567 56196313 56190747 0.000000e+00 10281.0
1 TraesCS5B01G051400 chr5B 88.460 3397 282 52 1271 4627 37072738 37069412 0.000000e+00 4000.0
2 TraesCS5B01G051400 chr5B 80.547 329 57 6 549 872 101432093 101431767 4.310000e-61 246.0
3 TraesCS5B01G051400 chr5B 100.000 31 0 0 2051 2081 710948743 710948713 2.170000e-04 58.4
4 TraesCS5B01G051400 chr2B 95.249 3410 111 19 1257 4627 705192277 705195674 0.000000e+00 5352.0
5 TraesCS5B01G051400 chr2B 83.486 109 13 5 1097 1201 50481578 50481471 4.590000e-16 97.1
6 TraesCS5B01G051400 chr2B 79.310 116 17 7 545 657 47507691 47507580 2.150000e-09 75.0
7 TraesCS5B01G051400 chr5D 99.316 2485 14 1 2143 4627 53028334 53025853 0.000000e+00 4492.0
8 TraesCS5B01G051400 chr5D 88.918 3393 268 43 1271 4627 42542789 42546109 0.000000e+00 4084.0
9 TraesCS5B01G051400 chr5D 94.910 1218 35 11 1 1200 53030619 53029411 0.000000e+00 1881.0
10 TraesCS5B01G051400 chr5D 87.482 1358 121 20 2626 3958 15373511 15374844 0.000000e+00 1520.0
11 TraesCS5B01G051400 chr5D 90.356 1068 71 13 1453 2515 15372471 15373511 0.000000e+00 1373.0
12 TraesCS5B01G051400 chr5D 95.309 810 10 2 1248 2057 53029112 53028331 0.000000e+00 1260.0
13 TraesCS5B01G051400 chr5D 84.974 579 61 15 1368 1937 14980823 14980262 1.050000e-156 564.0
14 TraesCS5B01G051400 chr5D 88.937 461 36 9 1552 2005 15347496 15347044 6.300000e-154 555.0
15 TraesCS5B01G051400 chr5D 85.902 305 22 8 1355 1659 15366619 15366902 7.010000e-79 305.0
16 TraesCS5B01G051400 chr5D 86.634 202 19 3 2004 2205 15346772 15346579 3.380000e-52 217.0
17 TraesCS5B01G051400 chr5D 85.119 168 17 7 60 220 88773407 88773241 1.240000e-36 165.0
18 TraesCS5B01G051400 chr5D 75.519 241 49 8 639 872 508290732 508290495 5.900000e-20 110.0
19 TraesCS5B01G051400 chr5D 78.065 155 18 5 1099 1237 520440371 520440217 3.570000e-12 84.2
20 TraesCS5B01G051400 chr2A 96.191 1759 53 5 2582 4326 718947716 718949474 0.000000e+00 2865.0
21 TraesCS5B01G051400 chr2A 95.152 1279 43 9 1253 2531 718946456 718947715 0.000000e+00 2001.0
22 TraesCS5B01G051400 chr2A 95.973 149 3 2 4481 4627 718958596 718958743 7.210000e-59 239.0
23 TraesCS5B01G051400 chr2A 97.778 90 2 0 4392 4481 718958553 718958642 7.470000e-34 156.0
24 TraesCS5B01G051400 chr2A 93.056 72 2 1 4323 4394 718953816 718953884 9.870000e-18 102.0
25 TraesCS5B01G051400 chr6B 93.031 947 33 13 4631 5567 493515654 493514731 0.000000e+00 1352.0
26 TraesCS5B01G051400 chr5A 88.110 328 35 2 545 872 595045948 595046271 2.430000e-103 387.0
27 TraesCS5B01G051400 chr7B 87.500 328 39 2 545 872 508143270 508143595 1.460000e-100 377.0
28 TraesCS5B01G051400 chr7B 82.888 187 31 1 653 838 350473698 350473884 3.450000e-37 167.0
29 TraesCS5B01G051400 chr7B 83.962 106 13 4 1099 1200 570439499 570439394 1.280000e-16 99.0
30 TraesCS5B01G051400 chr3B 86.970 330 40 2 545 872 183059160 183058832 8.810000e-98 368.0
31 TraesCS5B01G051400 chr3B 81.967 122 17 5 1084 1201 803917240 803917360 1.280000e-16 99.0
32 TraesCS5B01G051400 chr4A 85.671 328 41 4 545 872 58108798 58108477 1.920000e-89 340.0
33 TraesCS5B01G051400 chr4A 86.034 179 17 5 56 226 604560156 604559978 9.520000e-43 185.0
34 TraesCS5B01G051400 chr3D 89.655 145 14 1 57 200 613235219 613235363 3.430000e-42 183.0
35 TraesCS5B01G051400 chr3D 85.577 104 12 1 1101 1201 579298377 579298274 7.630000e-19 106.0
36 TraesCS5B01G051400 chr1D 85.000 180 17 6 57 227 205598 205776 2.060000e-39 174.0
37 TraesCS5B01G051400 chr1A 88.652 141 16 0 57 197 7804391 7804531 7.410000e-39 172.0
38 TraesCS5B01G051400 chr4D 84.971 173 19 6 60 225 397514779 397514951 9.590000e-38 169.0
39 TraesCS5B01G051400 chr4D 82.967 182 20 9 54 227 360865775 360865953 2.690000e-33 154.0
40 TraesCS5B01G051400 chr2D 82.353 204 27 8 1539 1739 583233843 583233646 9.590000e-38 169.0
41 TraesCS5B01G051400 chr2D 100.000 29 0 0 295 323 358965493 358965521 3.000000e-03 54.7
42 TraesCS5B01G051400 chr6A 82.418 182 24 8 54 228 481999141 481999321 9.660000e-33 152.0
43 TraesCS5B01G051400 chr1B 84.906 106 12 4 1099 1200 1346451 1346346 2.740000e-18 104.0
44 TraesCS5B01G051400 chr7D 84.259 108 14 3 1099 1204 602823976 602823870 9.870000e-18 102.0
45 TraesCS5B01G051400 chrUn 82.143 112 16 4 1098 1206 89802980 89803090 5.940000e-15 93.5
46 TraesCS5B01G051400 chr7A 82.143 112 16 4 1098 1206 17210298 17210408 5.940000e-15 93.5


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 TraesCS5B01G051400 chr5B 56190747 56196313 5566 True 10281.000000 10281 100.000000 1 5567 1 chr5B.!!$R2 5566
1 TraesCS5B01G051400 chr5B 37069412 37072738 3326 True 4000.000000 4000 88.460000 1271 4627 1 chr5B.!!$R1 3356
2 TraesCS5B01G051400 chr2B 705192277 705195674 3397 False 5352.000000 5352 95.249000 1257 4627 1 chr2B.!!$F1 3370
3 TraesCS5B01G051400 chr5D 42542789 42546109 3320 False 4084.000000 4084 88.918000 1271 4627 1 chr5D.!!$F2 3356
4 TraesCS5B01G051400 chr5D 53025853 53030619 4766 True 2544.333333 4492 96.511667 1 4627 3 chr5D.!!$R6 4626
5 TraesCS5B01G051400 chr5D 15372471 15374844 2373 False 1446.500000 1520 88.919000 1453 3958 2 chr5D.!!$F3 2505
6 TraesCS5B01G051400 chr5D 14980262 14980823 561 True 564.000000 564 84.974000 1368 1937 1 chr5D.!!$R1 569
7 TraesCS5B01G051400 chr5D 15346579 15347496 917 True 386.000000 555 87.785500 1552 2205 2 chr5D.!!$R5 653
8 TraesCS5B01G051400 chr2A 718946456 718949474 3018 False 2433.000000 2865 95.671500 1253 4326 2 chr2A.!!$F2 3073
9 TraesCS5B01G051400 chr6B 493514731 493515654 923 True 1352.000000 1352 93.031000 4631 5567 1 chr6B.!!$R1 936

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
197 200 1.001181 GCTGCATCATCCTCTCCTCTC 59.999 57.143 0.00 0.00 0.00 3.20 F
1041 1057 0.588730 CGTCCACGTGTGCAAAACTG 60.589 55.000 15.65 0.00 34.11 3.16 F
1246 1516 0.165295 TACGAGTCGCGAGTTCAGTG 59.835 55.000 19.09 8.49 44.57 3.66 F
2134 2719 0.036875 CTTCTTCACCTTCGCCCCTT 59.963 55.000 0.00 0.00 0.00 3.95 F
2782 3394 0.469705 TGCAACACCAAGAAGGGCAT 60.470 50.000 0.00 0.00 43.89 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1274 0.036010 ATCCGACTGGCTTTCCACTG 60.036 55.000 0.0 0.0 37.47 3.66 R
2094 2679 1.021390 CGCGGTCTTGCTTCAAGGAT 61.021 55.000 0.0 0.0 41.33 3.24 R
3098 3730 0.950836 CGGTGTTGCATTGAAGGACA 59.049 50.000 0.0 0.0 0.00 4.02 R
3267 3902 2.036217 ACATAACACGACGGTTGGAGAA 59.964 45.455 0.0 0.0 32.29 2.87 R
4633 5301 2.369860 TGACAGTTCTGCATCTCAACCT 59.630 45.455 0.0 0.0 0.00 3.50 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
104 107 6.016527 TGTTTTGTGTGTAGGTGTTGTTTACA 60.017 34.615 0.00 0.00 0.00 2.41
121 124 5.009210 TGTTTACATAGTGTTGCTTGGTTCC 59.991 40.000 0.00 0.00 0.00 3.62
129 132 2.304761 TGTTGCTTGGTTCCCCTACTAG 59.695 50.000 0.00 0.00 0.00 2.57
197 200 1.001181 GCTGCATCATCCTCTCCTCTC 59.999 57.143 0.00 0.00 0.00 3.20
198 201 1.270274 CTGCATCATCCTCTCCTCTCG 59.730 57.143 0.00 0.00 0.00 4.04
294 299 3.312504 CGCGTGTAGCCGATCGTG 61.313 66.667 15.09 6.80 44.76 4.35
398 404 2.990994 GATGGGAATGGGAGGCAGGC 62.991 65.000 0.00 0.00 0.00 4.85
413 419 2.046604 GGCTTACGCGGGAGGTTT 60.047 61.111 12.47 0.00 36.88 3.27
436 442 2.550830 TTCTTGCTTTTCTCTCGGCT 57.449 45.000 0.00 0.00 0.00 5.52
491 497 5.512473 TGCGTGTTGAATACCTAAAACAAC 58.488 37.500 0.00 0.00 40.44 3.32
499 505 8.364894 GTTGAATACCTAAAACAACAGGGATTT 58.635 33.333 0.00 0.00 44.14 2.17
519 525 8.124199 GGGATTTTTATGTAAAATTAGCGACGA 58.876 33.333 0.00 0.00 44.46 4.20
539 545 3.185594 CGAACGGTCAAAAGCACTAATGA 59.814 43.478 0.00 0.00 0.00 2.57
602 608 8.421249 AATATCTGAAGAACCACAAAAATCCA 57.579 30.769 0.00 0.00 0.00 3.41
765 771 4.988540 CACCGGCTCGAGAAAATATATCAA 59.011 41.667 18.75 0.00 0.00 2.57
817 823 7.932491 TCATTCAAGAAAGGATTTGCAATTGAA 59.068 29.630 17.90 17.90 39.27 2.69
848 854 4.142038 CCTAAACTTGTTGCCTAACCACT 58.858 43.478 0.00 0.00 35.92 4.00
978 984 3.886505 TGGAGGCTTTAAAAATGACGTGT 59.113 39.130 0.00 0.00 0.00 4.49
1001 1017 4.281941 TCACTGGCTTATAGGATGTGCTAG 59.718 45.833 0.00 0.00 38.05 3.42
1017 1033 7.547370 GGATGTGCTAGTATTAACCATGATCTC 59.453 40.741 0.00 0.00 0.00 2.75
1039 1055 4.278609 CGTCCACGTGTGCAAAAC 57.721 55.556 15.65 2.02 34.11 2.43
1040 1056 1.719117 CGTCCACGTGTGCAAAACT 59.281 52.632 15.65 0.00 34.11 2.66
1041 1057 0.588730 CGTCCACGTGTGCAAAACTG 60.589 55.000 15.65 0.00 34.11 3.16
1042 1058 0.865639 GTCCACGTGTGCAAAACTGC 60.866 55.000 15.65 0.00 0.00 4.40
1043 1059 1.138459 CCACGTGTGCAAAACTGCA 59.862 52.632 15.65 0.00 43.22 4.41
1103 1119 5.695851 AGAATGAAGACAACAAAGCGAAT 57.304 34.783 0.00 0.00 0.00 3.34
1108 1124 4.335315 TGAAGACAACAAAGCGAATCAACT 59.665 37.500 0.00 0.00 0.00 3.16
1214 1246 2.840651 GGATTTCTCAGTGGGAGGAGAA 59.159 50.000 0.00 0.00 45.63 2.87
1218 1250 2.977808 TCTCAGTGGGAGGAGAAGTTT 58.022 47.619 0.00 0.00 44.19 2.66
1222 1254 0.685660 GTGGGAGGAGAAGTTTCCGT 59.314 55.000 0.00 0.00 42.29 4.69
1242 1274 3.201741 GACTACGAGTCGCGAGTTC 57.798 57.895 19.09 13.81 44.57 3.01
1243 1275 0.441533 GACTACGAGTCGCGAGTTCA 59.558 55.000 19.09 5.45 44.57 3.18
1246 1516 0.165295 TACGAGTCGCGAGTTCAGTG 59.835 55.000 19.09 8.49 44.57 3.66
1351 1633 2.284699 CGGAGGGGGAGGACTTGT 60.285 66.667 0.00 0.00 0.00 3.16
1597 1894 1.080025 GTCCTACGGCTCAAACGCT 60.080 57.895 0.00 0.00 34.00 5.07
1903 2215 1.214589 GCTGGCCACATCTTTGCTG 59.785 57.895 0.00 0.00 0.00 4.41
2094 2679 1.536418 CGGCCCCCTCATCCTCATA 60.536 63.158 0.00 0.00 0.00 2.15
2134 2719 0.036875 CTTCTTCACCTTCGCCCCTT 59.963 55.000 0.00 0.00 0.00 3.95
2138 2723 2.282462 CACCTTCGCCCCTTGCTT 60.282 61.111 0.00 0.00 38.05 3.91
2205 2790 1.887198 CCGCGAGACTACATCCCTATT 59.113 52.381 8.23 0.00 0.00 1.73
2207 2792 2.678324 GCGAGACTACATCCCTATTGC 58.322 52.381 0.00 0.00 0.00 3.56
2782 3394 0.469705 TGCAACACCAAGAAGGGCAT 60.470 50.000 0.00 0.00 43.89 4.40
3220 3855 3.031736 AGTCATCTACCATACAGGCGTT 58.968 45.455 0.00 0.00 43.14 4.84
3267 3902 2.992114 AGGAGACGACGGCAAGCT 60.992 61.111 2.19 0.00 0.00 3.74
3367 4005 0.244450 TACACGCCGTTTCGAGGAAT 59.756 50.000 0.00 0.00 0.00 3.01
4627 5295 4.084171 GGCTTGACAAGAAAACGGTACTAC 60.084 45.833 19.51 0.00 0.00 2.73
4628 5296 4.748600 GCTTGACAAGAAAACGGTACTACT 59.251 41.667 19.51 0.00 0.00 2.57
4629 5297 5.107568 GCTTGACAAGAAAACGGTACTACTC 60.108 44.000 19.51 0.00 0.00 2.59
4630 5298 5.518848 TGACAAGAAAACGGTACTACTCA 57.481 39.130 0.00 0.00 0.00 3.41
4631 5299 6.092955 TGACAAGAAAACGGTACTACTCAT 57.907 37.500 0.00 0.00 0.00 2.90
4632 5300 7.218228 TGACAAGAAAACGGTACTACTCATA 57.782 36.000 0.00 0.00 0.00 2.15
4633 5301 7.660112 TGACAAGAAAACGGTACTACTCATAA 58.340 34.615 0.00 0.00 0.00 1.90
4634 5302 7.811236 TGACAAGAAAACGGTACTACTCATAAG 59.189 37.037 0.00 0.00 0.00 1.73
4635 5303 7.095270 ACAAGAAAACGGTACTACTCATAAGG 58.905 38.462 0.00 0.00 0.00 2.69
4636 5304 6.847421 AGAAAACGGTACTACTCATAAGGT 57.153 37.500 0.00 0.00 0.00 3.50
4651 5319 5.181009 TCATAAGGTTGAGATGCAGAACTG 58.819 41.667 0.00 0.00 0.00 3.16
4652 5320 3.498774 AAGGTTGAGATGCAGAACTGT 57.501 42.857 0.00 0.00 0.00 3.55
4674 5342 4.220602 GTCACCTAATTTGGGAACTGCATT 59.779 41.667 10.77 0.00 0.00 3.56
4706 5374 1.067071 GCGGCTGTAGGTTTAGTCTGT 60.067 52.381 0.00 0.00 0.00 3.41
4733 5402 4.876679 GCCCTCTAATTTCTAGGTGTTCAC 59.123 45.833 0.00 0.00 0.00 3.18
4777 5446 3.282021 GGCTTAGCATCAACTTCATCCA 58.718 45.455 6.53 0.00 0.00 3.41
4805 5474 2.892215 TCTGCTCCAATTGTTGCATTCA 59.108 40.909 18.56 7.33 34.79 2.57
4813 5482 4.418392 CAATTGTTGCATTCACCTAGCTC 58.582 43.478 0.00 0.00 0.00 4.09
4840 5509 8.877864 ATTAATTTGTCTGGTTGTCTCCATTA 57.122 30.769 0.00 0.00 36.84 1.90
4843 5512 2.028476 TGTCTGGTTGTCTCCATTACCG 60.028 50.000 0.00 0.00 36.84 4.02
4875 5545 9.959721 AGTGGACTAAATTTTCTAGCTTTCATA 57.040 29.630 0.00 0.00 0.00 2.15
4938 5608 3.577805 AGTTTTGCACTCCAGTACCTT 57.422 42.857 0.00 0.00 0.00 3.50
4939 5609 4.699925 AGTTTTGCACTCCAGTACCTTA 57.300 40.909 0.00 0.00 0.00 2.69
4943 5613 7.402862 AGTTTTGCACTCCAGTACCTTAATAT 58.597 34.615 0.00 0.00 0.00 1.28
4944 5614 8.545472 AGTTTTGCACTCCAGTACCTTAATATA 58.455 33.333 0.00 0.00 0.00 0.86
4945 5615 9.338622 GTTTTGCACTCCAGTACCTTAATATAT 57.661 33.333 0.00 0.00 0.00 0.86
4946 5616 9.914834 TTTTGCACTCCAGTACCTTAATATATT 57.085 29.630 2.97 2.97 0.00 1.28
4947 5617 9.555727 TTTGCACTCCAGTACCTTAATATATTC 57.444 33.333 0.00 0.00 0.00 1.75
4948 5618 8.257602 TGCACTCCAGTACCTTAATATATTCA 57.742 34.615 0.00 0.00 0.00 2.57
4949 5619 8.710239 TGCACTCCAGTACCTTAATATATTCAA 58.290 33.333 0.00 0.00 0.00 2.69
4950 5620 9.726438 GCACTCCAGTACCTTAATATATTCAAT 57.274 33.333 0.00 0.00 0.00 2.57
4975 5645 3.569701 ACCTTTTGCACATGTACCTTCTG 59.430 43.478 0.00 0.00 0.00 3.02
4984 5654 5.734720 CACATGTACCTTCTGGAAGTATGT 58.265 41.667 0.00 10.12 36.72 2.29
5000 5670 6.914757 GGAAGTATGTTGCATCTGAATTTAGC 59.085 38.462 0.00 0.00 0.00 3.09
5020 5690 2.923605 GCGGCATTTGCATCCATATGAC 60.924 50.000 3.65 0.00 44.36 3.06
5028 5698 8.680001 GCATTTGCATCCATATGACAGATAATA 58.320 33.333 3.65 0.00 41.59 0.98
5199 5876 6.491403 TGTATGCAACTCAGAGCTATGATAGA 59.509 38.462 12.21 0.00 0.00 1.98
5200 5877 5.859205 TGCAACTCAGAGCTATGATAGAA 57.141 39.130 12.21 0.00 0.00 2.10
5201 5878 5.595885 TGCAACTCAGAGCTATGATAGAAC 58.404 41.667 12.21 1.85 0.00 3.01
5202 5879 5.362143 TGCAACTCAGAGCTATGATAGAACT 59.638 40.000 12.21 0.00 0.00 3.01
5203 5880 5.920273 GCAACTCAGAGCTATGATAGAACTC 59.080 44.000 12.21 1.56 0.00 3.01
5214 5891 7.664731 AGCTATGATAGAACTCATGAAATTGGG 59.335 37.037 3.13 0.00 36.55 4.12
5223 5900 7.505585 AGAACTCATGAAATTGGGTTGTTTCTA 59.494 33.333 0.00 0.00 40.37 2.10
5338 6015 0.753867 TTAGAGGTCACAACGTGCCA 59.246 50.000 0.00 0.00 34.10 4.92
5347 6024 3.049674 AACGTGCCATGGACGCTG 61.050 61.111 26.38 17.13 40.56 5.18
5403 6080 8.539770 CATAGGTGCTGGTGTATTTCTAATAG 57.460 38.462 0.00 0.00 0.00 1.73
5430 6107 9.929180 TCATATCTCATAGGTGCTAATAACAAC 57.071 33.333 0.00 0.00 0.00 3.32
5442 6119 7.248437 GTGCTAATAACAACCTGGTGTATTTC 58.752 38.462 0.00 2.68 0.00 2.17
5443 6120 6.092944 TGCTAATAACAACCTGGTGTATTTCG 59.907 38.462 0.00 2.50 0.00 3.46
5548 6225 8.462016 GGTCTTGCTAGAAATTGTTTATGATGT 58.538 33.333 0.00 0.00 30.65 3.06
5549 6226 9.846248 GTCTTGCTAGAAATTGTTTATGATGTT 57.154 29.630 0.00 0.00 30.65 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 54 3.243569 CCTCACACCCAACGCAAATAAAA 60.244 43.478 0.00 0.00 0.00 1.52
52 55 2.294791 CCTCACACCCAACGCAAATAAA 59.705 45.455 0.00 0.00 0.00 1.40
121 124 6.749036 ACCAAGGTTATCAATCTAGTAGGG 57.251 41.667 0.00 0.00 0.00 3.53
129 132 6.156519 GGTTGTGAAACCAAGGTTATCAATC 58.843 40.000 4.68 7.77 42.38 2.67
197 200 4.212636 ACTTGTAATCTTCGTTGGTTTCCG 59.787 41.667 0.00 0.00 0.00 4.30
198 201 5.684550 ACTTGTAATCTTCGTTGGTTTCC 57.315 39.130 0.00 0.00 0.00 3.13
359 364 4.335647 CACCTCCTGCCACGCCTT 62.336 66.667 0.00 0.00 0.00 4.35
365 370 1.997311 CCATCTCCACCTCCTGCCA 60.997 63.158 0.00 0.00 0.00 4.92
436 442 3.862991 TCAACCCGAACCGGCACA 61.863 61.111 0.00 0.00 46.86 4.57
491 497 9.233232 GTCGCTAATTTTACATAAAAATCCCTG 57.767 33.333 1.14 0.00 45.12 4.45
499 505 6.090628 ACCGTTCGTCGCTAATTTTACATAAA 59.909 34.615 0.00 0.00 38.35 1.40
519 525 3.880490 TGTCATTAGTGCTTTTGACCGTT 59.120 39.130 9.92 0.00 38.12 4.44
539 545 9.753674 TCCAACAAAAGAGAGGAATAATAATGT 57.246 29.630 0.00 0.00 0.00 2.71
568 574 8.375506 TGTGGTTCTTCAGATATTTCTAACACT 58.624 33.333 3.69 0.00 0.00 3.55
602 608 8.328758 TCATAGTGGTTTCTATCTGGTTTCATT 58.671 33.333 0.00 0.00 0.00 2.57
702 708 4.823989 ACCAAACTCCATTTCACTCTCTTG 59.176 41.667 0.00 0.00 0.00 3.02
765 771 5.441718 TGCAAGATAAGAGAAGATGGGTT 57.558 39.130 0.00 0.00 0.00 4.11
817 823 4.022329 GGCAACAAGTTTAGGTGCAACTAT 60.022 41.667 13.35 0.00 33.12 2.12
834 840 3.901844 AGACTCTAAGTGGTTAGGCAACA 59.098 43.478 0.00 0.00 36.95 3.33
978 984 3.041211 AGCACATCCTATAAGCCAGTGA 58.959 45.455 0.00 0.00 0.00 3.41
1040 1056 0.603172 GCCATTGTGGTGCATTTGCA 60.603 50.000 0.05 0.05 43.11 4.08
1041 1057 1.300266 GGCCATTGTGGTGCATTTGC 61.300 55.000 0.00 0.00 40.46 3.68
1042 1058 0.674269 GGGCCATTGTGGTGCATTTG 60.674 55.000 4.39 0.00 40.46 2.32
1043 1059 1.678724 GGGCCATTGTGGTGCATTT 59.321 52.632 4.39 0.00 40.46 2.32
1044 1060 2.292559 GGGGCCATTGTGGTGCATT 61.293 57.895 4.39 0.00 40.46 3.56
1045 1061 2.684655 GGGGCCATTGTGGTGCAT 60.685 61.111 4.39 0.00 40.46 3.96
1052 1068 2.225496 TGTGGAAATAAGGGGCCATTGT 60.225 45.455 14.76 3.43 32.26 2.71
1108 1124 3.396276 TCCTTCTAACCATCCAACCACAA 59.604 43.478 0.00 0.00 0.00 3.33
1235 1267 0.884704 TGGCTTTCCACTGAACTCGC 60.885 55.000 0.00 0.00 37.47 5.03
1237 1269 2.147150 GACTGGCTTTCCACTGAACTC 58.853 52.381 0.00 0.00 37.47 3.01
1238 1270 1.541233 CGACTGGCTTTCCACTGAACT 60.541 52.381 0.00 0.00 37.47 3.01
1240 1272 0.250295 CCGACTGGCTTTCCACTGAA 60.250 55.000 0.00 0.00 37.47 3.02
1241 1273 1.118965 TCCGACTGGCTTTCCACTGA 61.119 55.000 0.00 0.00 37.47 3.41
1242 1274 0.036010 ATCCGACTGGCTTTCCACTG 60.036 55.000 0.00 0.00 37.47 3.66
1243 1275 0.250513 GATCCGACTGGCTTTCCACT 59.749 55.000 0.00 0.00 37.47 4.00
1246 1516 0.179070 GGAGATCCGACTGGCTTTCC 60.179 60.000 0.00 0.00 34.14 3.13
1346 1628 0.740868 CGCCATCATCGACCACAAGT 60.741 55.000 0.00 0.00 0.00 3.16
1351 1633 4.889856 CGCCGCCATCATCGACCA 62.890 66.667 0.00 0.00 0.00 4.02
1903 2215 2.902705 TATTCTACGATGGGGCACAC 57.097 50.000 0.00 0.00 0.00 3.82
2092 2677 2.565841 GCGGTCTTGCTTCAAGGATAT 58.434 47.619 6.71 0.00 41.33 1.63
2094 2679 1.021390 CGCGGTCTTGCTTCAAGGAT 61.021 55.000 0.00 0.00 41.33 3.24
2782 3394 3.445008 ACAGCTGGTTAGATCCTTCTCA 58.555 45.455 19.93 0.00 33.17 3.27
2892 3510 8.950208 ACTCACTAAGAAAGATGTAATAAGCC 57.050 34.615 0.00 0.00 0.00 4.35
3098 3730 0.950836 CGGTGTTGCATTGAAGGACA 59.049 50.000 0.00 0.00 0.00 4.02
3220 3855 4.020307 TGCAACAGTGAAGTCTCATCCATA 60.020 41.667 0.00 0.00 33.05 2.74
3267 3902 2.036217 ACATAACACGACGGTTGGAGAA 59.964 45.455 0.00 0.00 32.29 2.87
3367 4005 3.920231 AACTCAAGCATGCCATCTCTA 57.080 42.857 15.66 0.00 0.00 2.43
4627 5295 5.293814 CAGTTCTGCATCTCAACCTTATGAG 59.706 44.000 0.00 0.00 46.62 2.90
4628 5296 5.181009 CAGTTCTGCATCTCAACCTTATGA 58.819 41.667 0.00 0.00 0.00 2.15
4629 5297 4.940046 ACAGTTCTGCATCTCAACCTTATG 59.060 41.667 0.00 0.00 0.00 1.90
4630 5298 5.171339 ACAGTTCTGCATCTCAACCTTAT 57.829 39.130 0.00 0.00 0.00 1.73
4631 5299 4.040339 TGACAGTTCTGCATCTCAACCTTA 59.960 41.667 0.00 0.00 0.00 2.69
4632 5300 3.181451 TGACAGTTCTGCATCTCAACCTT 60.181 43.478 0.00 0.00 0.00 3.50
4633 5301 2.369860 TGACAGTTCTGCATCTCAACCT 59.630 45.455 0.00 0.00 0.00 3.50
4634 5302 2.481952 GTGACAGTTCTGCATCTCAACC 59.518 50.000 0.00 0.00 0.00 3.77
4635 5303 2.481952 GGTGACAGTTCTGCATCTCAAC 59.518 50.000 0.00 0.00 0.00 3.18
4636 5304 2.369860 AGGTGACAGTTCTGCATCTCAA 59.630 45.455 0.00 0.00 0.00 3.02
4651 5319 3.153919 TGCAGTTCCCAAATTAGGTGAC 58.846 45.455 0.00 0.00 0.00 3.67
4652 5320 3.517296 TGCAGTTCCCAAATTAGGTGA 57.483 42.857 0.00 0.00 0.00 4.02
4674 5342 4.345837 ACCTACAGCCGCACCTAATTAATA 59.654 41.667 0.00 0.00 0.00 0.98
4706 5374 4.288626 ACACCTAGAAATTAGAGGGCAACA 59.711 41.667 0.00 0.00 34.41 3.33
4752 5421 5.163478 GGATGAAGTTGATGCTAAGCCATTT 60.163 40.000 0.00 0.00 0.00 2.32
4777 5446 2.522185 ACAATTGGAGCAGAGCAATGT 58.478 42.857 10.83 0.00 0.00 2.71
4805 5474 6.485171 ACCAGACAAATTAATTGAGCTAGGT 58.515 36.000 0.39 0.00 41.85 3.08
4813 5482 6.980593 TGGAGACAACCAGACAAATTAATTG 58.019 36.000 0.39 0.00 40.74 2.32
4916 5586 3.214328 AGGTACTGGAGTGCAAAACTTG 58.786 45.455 0.00 0.00 36.66 3.16
4943 5613 7.225784 ACATGTGCAAAAGGTACATTGAATA 57.774 32.000 0.00 0.00 46.03 1.75
4944 5614 6.100404 ACATGTGCAAAAGGTACATTGAAT 57.900 33.333 0.00 0.00 46.03 2.57
4945 5615 5.528043 ACATGTGCAAAAGGTACATTGAA 57.472 34.783 0.00 0.00 46.03 2.69
4946 5616 5.048364 GGTACATGTGCAAAAGGTACATTGA 60.048 40.000 20.62 0.00 46.03 2.57
4947 5617 5.048083 AGGTACATGTGCAAAAGGTACATTG 60.048 40.000 20.62 0.00 46.03 2.82
4948 5618 5.076873 AGGTACATGTGCAAAAGGTACATT 58.923 37.500 20.62 10.18 46.03 2.71
4949 5619 4.662278 AGGTACATGTGCAAAAGGTACAT 58.338 39.130 20.62 14.35 46.03 2.29
4950 5620 4.093472 AGGTACATGTGCAAAAGGTACA 57.907 40.909 20.62 1.34 46.37 2.90
4951 5621 4.760204 AGAAGGTACATGTGCAAAAGGTAC 59.240 41.667 16.11 14.17 34.93 3.34
4952 5622 4.759693 CAGAAGGTACATGTGCAAAAGGTA 59.240 41.667 16.11 0.00 0.00 3.08
4953 5623 3.569701 CAGAAGGTACATGTGCAAAAGGT 59.430 43.478 16.11 0.00 0.00 3.50
4954 5624 3.057315 CCAGAAGGTACATGTGCAAAAGG 60.057 47.826 16.11 6.75 0.00 3.11
4955 5625 3.820467 TCCAGAAGGTACATGTGCAAAAG 59.180 43.478 16.11 1.54 35.89 2.27
4956 5626 3.826524 TCCAGAAGGTACATGTGCAAAA 58.173 40.909 16.11 0.00 35.89 2.44
4957 5627 3.500448 TCCAGAAGGTACATGTGCAAA 57.500 42.857 16.11 0.00 35.89 3.68
4958 5628 3.181445 ACTTCCAGAAGGTACATGTGCAA 60.181 43.478 16.11 0.00 42.53 4.08
4959 5629 2.371841 ACTTCCAGAAGGTACATGTGCA 59.628 45.455 16.11 0.00 42.53 4.57
4960 5630 3.059352 ACTTCCAGAAGGTACATGTGC 57.941 47.619 9.11 7.07 42.53 4.57
4961 5631 5.734720 ACATACTTCCAGAAGGTACATGTG 58.265 41.667 9.11 2.17 42.53 3.21
4962 5632 6.173339 CAACATACTTCCAGAAGGTACATGT 58.827 40.000 11.87 2.69 42.53 3.21
4963 5633 5.065218 GCAACATACTTCCAGAAGGTACATG 59.935 44.000 11.87 10.66 42.53 3.21
4975 5645 6.914757 GCTAAATTCAGATGCAACATACTTCC 59.085 38.462 0.00 0.00 0.00 3.46
4984 5654 2.090760 TGCCGCTAAATTCAGATGCAA 58.909 42.857 0.00 0.00 0.00 4.08
5000 5670 2.293955 TGTCATATGGATGCAAATGCCG 59.706 45.455 2.13 0.00 41.18 5.69
5020 5690 8.976353 AGTAAGCCACTCCATAGATATTATCTG 58.024 37.037 15.13 1.94 34.38 2.90
5199 5876 6.484364 AGAAACAACCCAATTTCATGAGTT 57.516 33.333 0.00 0.00 37.30 3.01
5200 5877 7.004086 TCTAGAAACAACCCAATTTCATGAGT 58.996 34.615 0.00 0.00 37.30 3.41
5201 5878 7.452880 TCTAGAAACAACCCAATTTCATGAG 57.547 36.000 0.00 0.00 37.30 2.90
5202 5879 7.505585 AGTTCTAGAAACAACCCAATTTCATGA 59.494 33.333 6.78 0.00 37.30 3.07
5203 5880 7.661040 AGTTCTAGAAACAACCCAATTTCATG 58.339 34.615 6.78 0.00 37.30 3.07
5257 5934 6.942532 TTCCAGCATACATAGTTCCATTTC 57.057 37.500 0.00 0.00 0.00 2.17
5338 6015 1.487976 AGGATTGTGATCAGCGTCCAT 59.512 47.619 17.70 5.28 33.77 3.41
5347 6024 4.272991 GTCATCTTGCTGAGGATTGTGATC 59.727 45.833 0.00 0.00 37.82 2.92
5403 6080 9.929180 TTGTTATTAGCACCTATGAGATATGAC 57.071 33.333 0.00 0.00 0.00 3.06
5450 6127 4.213270 TCAATATTATTTCTTCGCGCCCTG 59.787 41.667 0.00 0.00 0.00 4.45
5456 6133 8.895932 ACAACACTTCAATATTATTTCTTCGC 57.104 30.769 0.00 0.00 0.00 4.70
5510 6187 3.876309 AGCAAGACCTTTTTCCCTGTA 57.124 42.857 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.