Multiple sequence alignment - TraesCS2A01G040600

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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 TraesCS2A01G040600 chr2A 100.000 3326 0 0 1 3326 16618569 16615244 0.000000e+00 6143.0
1 TraesCS2A01G040600 chr2A 92.477 1409 78 15 1420 2824 16630000 16628616 0.000000e+00 1989.0
2 TraesCS2A01G040600 chr2A 87.859 906 60 11 4 885 16631464 16630585 0.000000e+00 1018.0
3 TraesCS2A01G040600 chr2A 96.192 499 19 0 930 1428 16630589 16630091 0.000000e+00 817.0
4 TraesCS2A01G040600 chr2A 82.933 416 68 1 1020 1435 733656389 733656801 4.050000e-99 372.0
5 TraesCS2A01G040600 chr2A 80.529 416 64 9 1919 2326 733657771 733658177 1.500000e-78 303.0
6 TraesCS2A01G040600 chr2A 88.679 212 19 2 2939 3145 16628629 16628418 1.530000e-63 254.0
7 TraesCS2A01G040600 chr2A 87.845 181 21 1 3146 3326 65817171 65816992 9.350000e-51 211.0
8 TraesCS2A01G040600 chr2A 87.097 186 22 2 3142 3326 756137047 756137231 3.360000e-50 209.0
9 TraesCS2A01G040600 chr2D 89.232 2749 198 47 21 2732 14372381 14375068 0.000000e+00 3347.0
10 TraesCS2A01G040600 chr2D 91.216 148 9 1 2980 3123 14377047 14377194 7.280000e-47 198.0
11 TraesCS2A01G040600 chr2D 91.912 136 9 2 2815 2950 20689725 20689858 4.380000e-44 189.0
12 TraesCS2A01G040600 chr6D 83.664 655 98 7 1025 1677 344058913 344058266 2.840000e-170 608.0
13 TraesCS2A01G040600 chr6D 82.747 597 89 11 1719 2313 344058258 344057674 1.370000e-143 520.0
14 TraesCS2A01G040600 chr6A 83.051 649 101 6 1031 1677 484409982 484409341 6.190000e-162 580.0
15 TraesCS2A01G040600 chr6A 93.182 132 9 0 2820 2951 135929012 135929143 9.420000e-46 195.0
16 TraesCS2A01G040600 chr6B 82.669 652 104 5 1025 1674 519330915 519330271 1.340000e-158 569.0
17 TraesCS2A01G040600 chr6B 81.271 598 96 10 1719 2313 519323878 519323294 1.400000e-128 470.0
18 TraesCS2A01G040600 chr6B 88.172 186 20 2 3142 3326 632816282 632816098 1.550000e-53 220.0
19 TraesCS2A01G040600 chr6B 87.097 186 22 2 3142 3326 632820164 632819980 3.360000e-50 209.0
20 TraesCS2A01G040600 chr6B 93.130 131 9 0 2819 2949 356112663 356112793 3.390000e-45 193.0
21 TraesCS2A01G040600 chr3B 75.887 564 104 22 1072 1617 732110691 732111240 3.290000e-65 259.0
22 TraesCS2A01G040600 chr3B 83.471 121 10 5 2576 2693 817027927 817027814 1.630000e-18 104.0
23 TraesCS2A01G040600 chr2B 91.304 184 15 1 3141 3324 794223289 794223107 1.980000e-62 250.0
24 TraesCS2A01G040600 chr2B 90.217 184 17 1 3141 3324 683779060 683779242 4.290000e-59 239.0
25 TraesCS2A01G040600 chr2B 85.345 116 11 4 2583 2696 761700260 761700149 7.540000e-22 115.0
26 TraesCS2A01G040600 chr1B 88.172 186 20 2 3142 3326 484213641 484213457 1.550000e-53 220.0
27 TraesCS2A01G040600 chr1B 87.701 187 21 2 3141 3326 14822371 14822556 2.010000e-52 217.0
28 TraesCS2A01G040600 chr1B 93.233 133 8 1 2818 2949 626227011 626226879 9.420000e-46 195.0
29 TraesCS2A01G040600 chr7A 86.885 183 23 1 3144 3326 709340152 709339971 1.560000e-48 204.0
30 TraesCS2A01G040600 chr3D 93.893 131 8 0 2819 2949 540540559 540540689 7.280000e-47 198.0
31 TraesCS2A01G040600 chr3D 86.087 115 9 4 2580 2692 515824950 515824841 2.100000e-22 117.0
32 TraesCS2A01G040600 chr3D 86.364 66 7 2 141 205 70113732 70113668 1.660000e-08 71.3
33 TraesCS2A01G040600 chr7D 95.122 123 6 0 2829 2951 117761498 117761376 9.420000e-46 195.0
34 TraesCS2A01G040600 chr7B 93.182 132 8 1 2818 2949 89668136 89668006 3.390000e-45 193.0
35 TraesCS2A01G040600 chr7B 93.182 132 7 1 2818 2949 726453958 726454087 3.390000e-45 193.0
36 TraesCS2A01G040600 chr7B 85.593 118 11 4 2577 2692 573927669 573927782 5.830000e-23 119.0
37 TraesCS2A01G040600 chr5B 89.933 149 11 4 2818 2964 547075843 547075697 4.380000e-44 189.0
38 TraesCS2A01G040600 chr5B 80.769 104 18 2 1209 1311 396160580 396160682 2.750000e-11 80.5
39 TraesCS2A01G040600 chr4B 86.325 117 10 4 2583 2697 650743780 650743668 4.510000e-24 122.0
40 TraesCS2A01G040600 chr3A 85.714 112 10 3 2583 2692 650197533 650197426 2.710000e-21 113.0
41 TraesCS2A01G040600 chr5D 84.956 113 11 2 2582 2692 542310170 542310278 3.510000e-20 110.0
42 TraesCS2A01G040600 chr5A 85.185 108 10 3 2589 2694 371025718 371025615 4.540000e-19 106.0
43 TraesCS2A01G040600 chr5A 79.048 105 18 4 1209 1311 438787090 438787192 5.950000e-08 69.4


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 TraesCS2A01G040600 chr2A 16615244 16618569 3325 True 6143.0 6143 100.00000 1 3326 1 chr2A.!!$R1 3325
1 TraesCS2A01G040600 chr2A 16628418 16631464 3046 True 1019.5 1989 91.30175 4 3145 4 chr2A.!!$R3 3141
2 TraesCS2A01G040600 chr2A 733656389 733658177 1788 False 337.5 372 81.73100 1020 2326 2 chr2A.!!$F2 1306
3 TraesCS2A01G040600 chr2D 14372381 14377194 4813 False 1772.5 3347 90.22400 21 3123 2 chr2D.!!$F2 3102
4 TraesCS2A01G040600 chr6D 344057674 344058913 1239 True 564.0 608 83.20550 1025 2313 2 chr6D.!!$R1 1288
5 TraesCS2A01G040600 chr6A 484409341 484409982 641 True 580.0 580 83.05100 1031 1677 1 chr6A.!!$R1 646
6 TraesCS2A01G040600 chr6B 519330271 519330915 644 True 569.0 569 82.66900 1025 1674 1 chr6B.!!$R2 649
7 TraesCS2A01G040600 chr6B 519323294 519323878 584 True 470.0 470 81.27100 1719 2313 1 chr6B.!!$R1 594
8 TraesCS2A01G040600 chr6B 632816098 632820164 4066 True 214.5 220 87.63450 3142 3326 2 chr6B.!!$R3 184
9 TraesCS2A01G040600 chr3B 732110691 732111240 549 False 259.0 259 75.88700 1072 1617 1 chr3B.!!$F1 545

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
973 1023 0.248949 GTAGTCGTCGATCCCCTTGC 60.249 60.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2931 5465 0.251297 TGTACTCCCTTCGTCCGGAA 60.251 55.0 5.23 0.0 0.0 4.3 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
157 160 0.251916 TAGGGCATCTTCAACGTGGG 59.748 55.000 0.00 0.00 0.00 4.61
159 162 1.971167 GGCATCTTCAACGTGGGCA 60.971 57.895 0.00 0.00 0.00 5.36
256 259 2.267642 CCGAAATCCCCGCACTCA 59.732 61.111 0.00 0.00 0.00 3.41
272 275 2.103094 CACTCAGCCCCTAAATCGATGA 59.897 50.000 0.00 0.00 0.00 2.92
338 349 2.495227 GGTTACTTTCCCCTCCCCATA 58.505 52.381 0.00 0.00 0.00 2.74
396 421 2.583441 CGTGCTTCACCCCTCCTCA 61.583 63.158 0.00 0.00 0.00 3.86
474 503 1.153765 CATCGTCCTGAAGCGAGCA 60.154 57.895 0.00 0.00 40.56 4.26
539 572 0.535780 CTCATGGCACCTGTGTGTGT 60.536 55.000 0.00 0.00 44.65 3.72
541 574 1.102809 CATGGCACCTGTGTGTGTGT 61.103 55.000 0.00 0.00 44.65 3.72
586 619 0.737804 TGTGCTTGTTGTCATTGCGT 59.262 45.000 0.00 0.00 0.00 5.24
681 714 3.953612 GCAATTTGGATGGACACATAGGA 59.046 43.478 0.00 0.00 37.47 2.94
754 799 9.961266 CGAACATGTCTACGAACATTTATTAAA 57.039 29.630 0.00 0.00 37.78 1.52
790 835 0.466739 TGCTCTTATCGTCGCCCCTA 60.467 55.000 0.00 0.00 0.00 3.53
799 844 2.284331 TCGCCCCTACTGCCTTGA 60.284 61.111 0.00 0.00 0.00 3.02
829 874 1.978580 TGTGAGGAAGAAGGGAGAACC 59.021 52.381 0.00 0.00 40.67 3.62
878 928 2.569404 GGAGACAGGTGGAAAGAGATGT 59.431 50.000 0.00 0.00 0.00 3.06
879 929 3.008485 GGAGACAGGTGGAAAGAGATGTT 59.992 47.826 0.00 0.00 0.00 2.71
885 935 5.067805 ACAGGTGGAAAGAGATGTTTGTTTC 59.932 40.000 0.00 0.00 0.00 2.78
897 947 8.383175 AGAGATGTTTGTTTCTCTTATTACCCA 58.617 33.333 0.00 0.00 44.90 4.51
898 948 8.336801 AGATGTTTGTTTCTCTTATTACCCAC 57.663 34.615 0.00 0.00 0.00 4.61
900 950 6.607019 TGTTTGTTTCTCTTATTACCCACCT 58.393 36.000 0.00 0.00 0.00 4.00
901 951 6.488683 TGTTTGTTTCTCTTATTACCCACCTG 59.511 38.462 0.00 0.00 0.00 4.00
902 952 4.585879 TGTTTCTCTTATTACCCACCTGC 58.414 43.478 0.00 0.00 0.00 4.85
973 1023 0.248949 GTAGTCGTCGATCCCCTTGC 60.249 60.000 0.00 0.00 0.00 4.01
1008 1058 2.586079 CGCCGCGACATGGATTCT 60.586 61.111 8.23 0.00 0.00 2.40
1050 1100 2.992689 TCCTGCCTCGTAACGCCA 60.993 61.111 0.00 0.00 0.00 5.69
1709 2328 2.202146 GTCGTCGACCGTCGTGAG 60.202 66.667 19.89 12.42 41.35 3.51
1710 2329 2.662857 TCGTCGACCGTCGTGAGT 60.663 61.111 19.89 0.00 41.35 3.41
1715 2334 2.941333 GACCGTCGTGAGTCGTGA 59.059 61.111 0.00 0.00 40.95 4.35
1716 2335 1.440023 GACCGTCGTGAGTCGTGAC 60.440 63.158 4.85 4.85 40.95 3.67
1749 2368 1.379977 TCTCCAGGGACCAGCTACG 60.380 63.158 0.00 0.00 0.00 3.51
2158 2859 4.473520 AGCTGGTTCCGCATCCCG 62.474 66.667 0.00 0.00 0.00 5.14
2242 2943 1.004200 CGGGTGGGTGTACCTGTTC 60.004 63.158 0.44 0.00 41.32 3.18
2356 3057 1.996191 CTTCTTCTAGCCACTGAACGC 59.004 52.381 0.00 0.00 0.00 4.84
2380 3081 5.481824 CCCTAAGCTGTGACCATATATCAGA 59.518 44.000 0.00 0.00 0.00 3.27
2455 3163 0.871163 TTCAGCTTGCTTTTGTGCGC 60.871 50.000 0.00 0.00 35.36 6.09
2468 3176 1.317613 TGTGCGCTTTGGTTGAATCT 58.682 45.000 9.73 0.00 0.00 2.40
2525 3233 7.148738 CGACTGAGATTTGGATGTTATATTCGG 60.149 40.741 0.00 0.00 0.00 4.30
2562 3272 5.302357 AGATCCGTGCAATTTTTCTCTTC 57.698 39.130 0.00 0.00 0.00 2.87
2601 3315 4.216902 TCTTCGTCTGGAATTACTTGTCGA 59.783 41.667 0.00 0.00 33.26 4.20
2606 3320 5.004821 CGTCTGGAATTACTTGTCGAAGATG 59.995 44.000 0.00 0.00 40.67 2.90
2676 3390 7.360361 ACAACCATTTCTTCGACAAGTATTTC 58.640 34.615 0.00 0.00 0.00 2.17
2711 3427 6.586844 GGAGTACTTGTTATGTCACTTGACTC 59.413 42.308 10.63 0.00 44.99 3.36
2718 3434 7.703058 TGTTATGTCACTTGACTCAGATCTA 57.297 36.000 10.63 0.00 44.99 1.98
2719 3435 7.766283 TGTTATGTCACTTGACTCAGATCTAG 58.234 38.462 10.63 0.00 44.99 2.43
2732 3448 5.717178 ACTCAGATCTAGCCACACTCTTTTA 59.283 40.000 0.00 0.00 0.00 1.52
2736 3452 9.588096 TCAGATCTAGCCACACTCTTTTATATA 57.412 33.333 0.00 0.00 0.00 0.86
2758 5292 2.158696 GGAGCAAACCTGATCATAGGCT 60.159 50.000 0.00 1.40 39.86 4.58
2837 5371 8.707796 AAAGGATATATACTTTCTCCGTCTGA 57.292 34.615 16.02 0.00 36.18 3.27
2838 5372 8.707796 AAGGATATATACTTTCTCCGTCTGAA 57.292 34.615 4.19 0.00 0.00 3.02
2839 5373 8.707796 AGGATATATACTTTCTCCGTCTGAAA 57.292 34.615 0.00 0.00 33.15 2.69
2840 5374 9.144298 AGGATATATACTTTCTCCGTCTGAAAA 57.856 33.333 0.00 0.00 33.70 2.29
2841 5375 9.930693 GGATATATACTTTCTCCGTCTGAAAAT 57.069 33.333 0.00 0.00 33.70 1.82
2846 5380 6.787085 ACTTTCTCCGTCTGAAAATACTTG 57.213 37.500 0.00 0.00 33.70 3.16
2847 5381 6.289064 ACTTTCTCCGTCTGAAAATACTTGT 58.711 36.000 0.00 0.00 33.70 3.16
2848 5382 6.424207 ACTTTCTCCGTCTGAAAATACTTGTC 59.576 38.462 0.00 0.00 33.70 3.18
2849 5383 5.462530 TCTCCGTCTGAAAATACTTGTCA 57.537 39.130 0.00 0.00 0.00 3.58
2850 5384 6.037786 TCTCCGTCTGAAAATACTTGTCAT 57.962 37.500 0.00 0.00 0.00 3.06
2851 5385 6.464222 TCTCCGTCTGAAAATACTTGTCATT 58.536 36.000 0.00 0.00 0.00 2.57
2852 5386 7.608153 TCTCCGTCTGAAAATACTTGTCATTA 58.392 34.615 0.00 0.00 0.00 1.90
2853 5387 8.092068 TCTCCGTCTGAAAATACTTGTCATTAA 58.908 33.333 0.00 0.00 0.00 1.40
2854 5388 8.610248 TCCGTCTGAAAATACTTGTCATTAAA 57.390 30.769 0.00 0.00 0.00 1.52
2855 5389 9.058174 TCCGTCTGAAAATACTTGTCATTAAAA 57.942 29.630 0.00 0.00 0.00 1.52
2856 5390 9.840427 CCGTCTGAAAATACTTGTCATTAAAAT 57.160 29.630 0.00 0.00 0.00 1.82
2914 5448 9.132923 ACGTCTAGATACATCTCTTTTTATCCA 57.867 33.333 0.00 0.00 38.32 3.41
2928 5462 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
2935 5469 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2936 5470 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2937 5471 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2938 5472 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2939 5473 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2940 5474 3.193903 TGATGACAAGTATTTCCGGACGA 59.806 43.478 1.83 0.00 0.00 4.20
2941 5475 3.663995 TGACAAGTATTTCCGGACGAA 57.336 42.857 1.83 0.00 0.00 3.85
2942 5476 3.581755 TGACAAGTATTTCCGGACGAAG 58.418 45.455 1.83 0.00 0.00 3.79
2943 5477 2.928116 GACAAGTATTTCCGGACGAAGG 59.072 50.000 1.83 0.00 0.00 3.46
2944 5478 2.277084 CAAGTATTTCCGGACGAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
2945 5479 1.856629 AGTATTTCCGGACGAAGGGA 58.143 50.000 1.83 0.00 0.00 4.20
2946 5480 1.755380 AGTATTTCCGGACGAAGGGAG 59.245 52.381 1.83 0.00 33.01 4.30
2947 5481 1.479730 GTATTTCCGGACGAAGGGAGT 59.520 52.381 1.83 0.00 33.01 3.85
2948 5482 1.856629 ATTTCCGGACGAAGGGAGTA 58.143 50.000 1.83 0.00 33.01 2.59
2949 5483 0.890683 TTTCCGGACGAAGGGAGTAC 59.109 55.000 1.83 0.00 33.01 2.73
2950 5484 0.251297 TTCCGGACGAAGGGAGTACA 60.251 55.000 1.83 0.00 33.01 2.90
2951 5485 0.679002 TCCGGACGAAGGGAGTACAG 60.679 60.000 0.00 0.00 0.00 2.74
2959 5493 2.033372 GAAGGGAGTACAGACTAGGCC 58.967 57.143 0.00 0.00 35.45 5.19
2972 5506 3.019564 GACTAGGCCTGGACTACGTTTA 58.980 50.000 24.81 0.00 0.00 2.01
2984 5518 5.821470 TGGACTACGTTTACAACATTTTGGA 59.179 36.000 0.00 0.00 37.00 3.53
2999 5572 0.402504 TTGGACCGGGCTTACACATT 59.597 50.000 7.57 0.00 0.00 2.71
3005 5578 3.606687 ACCGGGCTTACACATTTTAGAG 58.393 45.455 6.32 0.00 0.00 2.43
3010 5583 3.309954 GGCTTACACATTTTAGAGCGGAG 59.690 47.826 0.00 0.00 0.00 4.63
3075 5648 2.156917 TCAGGCTGAAGAACAAGCATG 58.843 47.619 16.28 3.10 36.54 4.06
3076 5649 2.156917 CAGGCTGAAGAACAAGCATGA 58.843 47.619 9.42 0.00 36.96 3.07
3162 9621 3.822607 GAGCATCTCCAACAGACGT 57.177 52.632 0.00 0.00 32.26 4.34
3197 9656 6.183360 CGACGAGCTAAAATAGTTTTACAGCA 60.183 38.462 10.51 0.00 36.32 4.41
3198 9657 7.464178 CGACGAGCTAAAATAGTTTTACAGCAT 60.464 37.037 10.51 0.00 36.32 3.79
3201 9660 8.338259 CGAGCTAAAATAGTTTTACAGCATCAT 58.662 33.333 10.51 0.00 36.32 2.45
3228 9687 1.241315 AATTTTAGCGCACCGTGGCT 61.241 50.000 11.47 15.82 43.12 4.75
3237 9696 1.639298 GCACCGTGGCTGATTCAGTC 61.639 60.000 11.39 11.39 36.52 3.51
3238 9697 1.021390 CACCGTGGCTGATTCAGTCC 61.021 60.000 15.39 15.69 34.88 3.85
3296 9755 1.133253 CAACAATCCAGCAGACGCG 59.867 57.895 3.53 3.53 45.49 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.663523 TGCTTTGATATCGTGATAGATCCCTA 59.336 38.462 0.00 0.00 32.39 3.53
4 5 5.481824 TGCTTTGATATCGTGATAGATCCCT 59.518 40.000 0.00 0.00 32.39 4.20
5 6 5.724328 TGCTTTGATATCGTGATAGATCCC 58.276 41.667 0.00 0.00 32.39 3.85
6 7 7.547019 TGATTGCTTTGATATCGTGATAGATCC 59.453 37.037 0.00 0.00 32.39 3.36
7 8 8.471361 TGATTGCTTTGATATCGTGATAGATC 57.529 34.615 0.00 0.00 32.39 2.75
157 160 5.941948 ACATATAAGGGCGAAATAAGTGC 57.058 39.130 0.00 0.00 0.00 4.40
159 162 5.699458 CCGAACATATAAGGGCGAAATAAGT 59.301 40.000 0.00 0.00 0.00 2.24
209 212 4.576463 AGTACGGTATTCGGATTAACGAGT 59.424 41.667 20.36 5.37 44.47 4.18
256 259 3.644966 TGTTTCATCGATTTAGGGGCT 57.355 42.857 0.00 0.00 0.00 5.19
272 275 6.306987 AGACATCCAGACAACCTTATTGTTT 58.693 36.000 0.00 0.00 31.96 2.83
321 332 2.062636 GCATATGGGGAGGGGAAAGTA 58.937 52.381 4.56 0.00 0.00 2.24
338 349 1.070445 GCCAGCTCGGTAGATGCAT 59.930 57.895 0.00 0.00 37.82 3.96
369 394 4.182433 TGAAGCACGGTGTGGGCA 62.182 61.111 10.24 0.92 33.64 5.36
374 399 3.168528 AGGGGTGAAGCACGGTGT 61.169 61.111 10.24 0.00 34.83 4.16
375 400 2.358737 GAGGGGTGAAGCACGGTG 60.359 66.667 3.15 3.15 34.83 4.94
411 440 2.265739 GCACTCGATGTCCAGCCA 59.734 61.111 0.00 0.00 0.00 4.75
456 485 0.529337 ATGCTCGCTTCAGGACGATG 60.529 55.000 0.00 0.00 37.72 3.84
457 486 0.529337 CATGCTCGCTTCAGGACGAT 60.529 55.000 0.00 0.00 37.72 3.73
481 510 1.271762 CCTGGCCTACATAGCATGCAT 60.272 52.381 21.98 8.63 0.00 3.96
484 513 0.399454 AGCCTGGCCTACATAGCATG 59.601 55.000 16.57 0.00 32.31 4.06
485 514 0.689623 GAGCCTGGCCTACATAGCAT 59.310 55.000 16.57 0.00 32.31 3.79
533 566 1.277842 CCTACATAGCCCACACACACA 59.722 52.381 0.00 0.00 0.00 3.72
534 567 2.012051 GCCTACATAGCCCACACACAC 61.012 57.143 0.00 0.00 0.00 3.82
539 572 1.417517 CAGATGCCTACATAGCCCACA 59.582 52.381 0.00 0.00 36.35 4.17
541 574 1.417517 CACAGATGCCTACATAGCCCA 59.582 52.381 0.00 0.00 36.35 5.36
681 714 5.616866 CGAGAACACCATCGCTTAAATGTTT 60.617 40.000 0.00 0.00 30.72 2.83
799 844 1.202330 CTTCCTCACATGGCCTCTCT 58.798 55.000 3.32 0.00 0.00 3.10
878 928 5.475564 GCAGGTGGGTAATAAGAGAAACAAA 59.524 40.000 0.00 0.00 0.00 2.83
879 929 5.007682 GCAGGTGGGTAATAAGAGAAACAA 58.992 41.667 0.00 0.00 0.00 2.83
885 935 1.810412 GCGGCAGGTGGGTAATAAGAG 60.810 57.143 0.00 0.00 0.00 2.85
889 939 1.524961 CAGCGGCAGGTGGGTAATA 59.475 57.895 8.26 0.00 41.81 0.98
890 940 2.272146 CAGCGGCAGGTGGGTAAT 59.728 61.111 8.26 0.00 41.81 1.89
973 1023 1.009829 CGGAAAGCTTGATTCTCGGG 58.990 55.000 0.00 0.00 0.00 5.14
1709 2328 2.478989 TGAGGATCCTCGTCACGAC 58.521 57.895 31.81 11.11 45.48 4.34
1713 2332 1.001269 ACGGTGAGGATCCTCGTCA 60.001 57.895 31.81 16.60 45.48 4.35
1714 2333 1.728672 GACGGTGAGGATCCTCGTC 59.271 63.158 31.81 29.93 46.16 4.20
1715 2334 0.748729 GAGACGGTGAGGATCCTCGT 60.749 60.000 31.81 27.29 45.48 4.18
1716 2335 1.448922 GGAGACGGTGAGGATCCTCG 61.449 65.000 31.81 24.52 45.48 4.63
1717 2336 0.395862 TGGAGACGGTGAGGATCCTC 60.396 60.000 31.59 31.59 43.01 3.71
1837 2456 4.394712 GTGGAGTCCGGGTGCAGG 62.395 72.222 0.00 0.00 0.00 4.85
2158 2859 2.279918 AAGTCCACGTCGTGCACC 60.280 61.111 20.01 9.16 31.34 5.01
2223 2924 2.459202 GAACAGGTACACCCACCCGG 62.459 65.000 0.00 0.00 39.62 5.73
2356 3057 5.481824 TCTGATATATGGTCACAGCTTAGGG 59.518 44.000 0.00 0.00 0.00 3.53
2525 3233 1.816224 GGATCTCGAGGTAGCATCTCC 59.184 57.143 13.56 0.00 0.00 3.71
2572 3282 6.591750 AGTAATTCCAGACGAAGAGAAAGA 57.408 37.500 0.00 0.00 32.78 2.52
2586 3298 5.414789 TCCATCTTCGACAAGTAATTCCA 57.585 39.130 0.00 0.00 0.00 3.53
2588 3300 8.873215 TTCTATCCATCTTCGACAAGTAATTC 57.127 34.615 0.00 0.00 0.00 2.17
2655 3369 5.447279 CCGGAAATACTTGTCGAAGAAATGG 60.447 44.000 0.00 0.00 39.69 3.16
2676 3390 1.346722 ACAAGTACTCCCTTTGTCCGG 59.653 52.381 0.00 0.00 29.55 5.14
2711 3427 9.853555 CTATATAAAAGAGTGTGGCTAGATCTG 57.146 37.037 5.18 0.00 0.00 2.90
2718 3434 5.366768 TGCTCCTATATAAAAGAGTGTGGCT 59.633 40.000 6.16 0.00 0.00 4.75
2719 3435 5.611374 TGCTCCTATATAAAAGAGTGTGGC 58.389 41.667 6.16 0.00 0.00 5.01
2732 3448 6.352565 GCCTATGATCAGGTTTGCTCCTATAT 60.353 42.308 0.09 0.00 38.05 0.86
2736 3452 2.158696 GCCTATGATCAGGTTTGCTCCT 60.159 50.000 0.09 0.00 38.05 3.69
2758 5292 1.338890 TGACAAACCCGGGTCAGACA 61.339 55.000 30.40 24.30 39.00 3.41
2824 5358 6.423905 TGACAAGTATTTTCAGACGGAGAAAG 59.576 38.462 0.00 0.00 36.45 2.62
2825 5359 6.285224 TGACAAGTATTTTCAGACGGAGAAA 58.715 36.000 0.00 0.00 33.48 2.52
2826 5360 5.849510 TGACAAGTATTTTCAGACGGAGAA 58.150 37.500 0.00 0.00 0.00 2.87
2827 5361 5.462530 TGACAAGTATTTTCAGACGGAGA 57.537 39.130 0.00 0.00 0.00 3.71
2828 5362 6.727824 AATGACAAGTATTTTCAGACGGAG 57.272 37.500 0.00 0.00 0.00 4.63
2829 5363 8.610248 TTTAATGACAAGTATTTTCAGACGGA 57.390 30.769 0.00 0.00 0.00 4.69
2830 5364 9.840427 ATTTTAATGACAAGTATTTTCAGACGG 57.160 29.630 0.00 0.00 0.00 4.79
2888 5422 9.132923 TGGATAAAAAGAGATGTATCTAGACGT 57.867 33.333 0.00 0.00 37.25 4.34
2902 5436 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
2909 5443 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
2910 5444 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2911 5445 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2912 5446 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2913 5447 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2914 5448 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2915 5449 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2916 5450 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2917 5451 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2918 5452 3.193903 TCGTCCGGAAATACTTGTCATCA 59.806 43.478 5.23 0.00 0.00 3.07
2919 5453 3.777478 TCGTCCGGAAATACTTGTCATC 58.223 45.455 5.23 0.00 0.00 2.92
2920 5454 3.880047 TCGTCCGGAAATACTTGTCAT 57.120 42.857 5.23 0.00 0.00 3.06
2921 5455 3.581755 CTTCGTCCGGAAATACTTGTCA 58.418 45.455 5.23 0.00 33.34 3.58
2922 5456 2.928116 CCTTCGTCCGGAAATACTTGTC 59.072 50.000 5.23 0.00 33.34 3.18
2923 5457 2.354403 CCCTTCGTCCGGAAATACTTGT 60.354 50.000 5.23 0.00 33.34 3.16
2924 5458 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
2925 5459 2.167900 CTCCCTTCGTCCGGAAATACTT 59.832 50.000 5.23 0.00 33.34 2.24
2926 5460 1.755380 CTCCCTTCGTCCGGAAATACT 59.245 52.381 5.23 0.00 33.34 2.12
2927 5461 1.479730 ACTCCCTTCGTCCGGAAATAC 59.520 52.381 5.23 0.00 33.34 1.89
2928 5462 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
2929 5463 1.479730 GTACTCCCTTCGTCCGGAAAT 59.520 52.381 5.23 0.00 33.34 2.17
2930 5464 0.890683 GTACTCCCTTCGTCCGGAAA 59.109 55.000 5.23 0.00 33.34 3.13
2931 5465 0.251297 TGTACTCCCTTCGTCCGGAA 60.251 55.000 5.23 0.00 0.00 4.30
2932 5466 0.679002 CTGTACTCCCTTCGTCCGGA 60.679 60.000 0.00 0.00 0.00 5.14
2933 5467 0.679002 TCTGTACTCCCTTCGTCCGG 60.679 60.000 0.00 0.00 0.00 5.14
2934 5468 0.450983 GTCTGTACTCCCTTCGTCCG 59.549 60.000 0.00 0.00 0.00 4.79
2935 5469 1.836802 AGTCTGTACTCCCTTCGTCC 58.163 55.000 0.00 0.00 0.00 4.79
2936 5470 2.944349 CCTAGTCTGTACTCCCTTCGTC 59.056 54.545 0.00 0.00 37.15 4.20
2937 5471 2.944991 GCCTAGTCTGTACTCCCTTCGT 60.945 54.545 0.00 0.00 37.15 3.85
2938 5472 1.677052 GCCTAGTCTGTACTCCCTTCG 59.323 57.143 0.00 0.00 37.15 3.79
2939 5473 2.033372 GGCCTAGTCTGTACTCCCTTC 58.967 57.143 0.00 0.00 37.15 3.46
2940 5474 1.646977 AGGCCTAGTCTGTACTCCCTT 59.353 52.381 1.29 0.00 37.15 3.95
2941 5475 1.063567 CAGGCCTAGTCTGTACTCCCT 60.064 57.143 3.98 0.00 37.15 4.20
2942 5476 1.404843 CAGGCCTAGTCTGTACTCCC 58.595 60.000 3.98 0.00 37.15 4.30
2943 5477 1.063867 TCCAGGCCTAGTCTGTACTCC 60.064 57.143 3.98 0.00 37.15 3.85
2944 5478 2.025898 GTCCAGGCCTAGTCTGTACTC 58.974 57.143 3.98 0.00 37.15 2.59
2945 5479 1.641714 AGTCCAGGCCTAGTCTGTACT 59.358 52.381 3.98 0.00 39.91 2.73
2946 5480 2.146920 AGTCCAGGCCTAGTCTGTAC 57.853 55.000 3.98 0.00 32.80 2.90
2947 5481 2.421107 CGTAGTCCAGGCCTAGTCTGTA 60.421 54.545 3.98 0.00 32.80 2.74
2948 5482 1.682394 CGTAGTCCAGGCCTAGTCTGT 60.682 57.143 3.98 0.00 32.80 3.41
2949 5483 1.025812 CGTAGTCCAGGCCTAGTCTG 58.974 60.000 3.98 0.00 34.71 3.51
2950 5484 0.624785 ACGTAGTCCAGGCCTAGTCT 59.375 55.000 3.98 3.54 29.74 3.24
2951 5485 1.472188 AACGTAGTCCAGGCCTAGTC 58.528 55.000 3.98 0.00 45.00 2.59
2972 5506 0.469144 AGCCCGGTCCAAAATGTTGT 60.469 50.000 0.00 0.00 32.40 3.32
2984 5518 3.606687 CTCTAAAATGTGTAAGCCCGGT 58.393 45.455 0.00 0.00 0.00 5.28
2999 5572 5.421056 TCCAAACTCTATTCTCCGCTCTAAA 59.579 40.000 0.00 0.00 0.00 1.85
3005 5578 3.190874 CAGTCCAAACTCTATTCTCCGC 58.809 50.000 0.00 0.00 31.71 5.54
3010 5583 3.198853 AGAGCCCAGTCCAAACTCTATTC 59.801 47.826 0.00 0.00 35.99 1.75
3124 5701 0.863144 TAAGTTTTCGAGCCACGCAC 59.137 50.000 0.00 0.00 42.26 5.34
3171 9630 6.183360 GCTGTAAAACTATTTTAGCTCGTCGT 60.183 38.462 0.00 0.00 35.91 4.34
3197 9656 7.431084 CGGTGCGCTAAAATTACTAAAAATGAT 59.569 33.333 9.73 0.00 0.00 2.45
3198 9657 6.743627 CGGTGCGCTAAAATTACTAAAAATGA 59.256 34.615 9.73 0.00 0.00 2.57
3201 9660 5.852229 CACGGTGCGCTAAAATTACTAAAAA 59.148 36.000 9.73 0.00 0.00 1.94
3217 9676 2.741985 TGAATCAGCCACGGTGCG 60.742 61.111 1.68 0.00 36.02 5.34
3228 9687 0.390340 GCGTCTGCTGGACTGAATCA 60.390 55.000 8.31 0.00 42.44 2.57
3237 9696 2.987413 TATTTTTGTGCGTCTGCTGG 57.013 45.000 0.00 0.00 43.34 4.85
3238 9697 4.031028 GCTATATTTTTGTGCGTCTGCTG 58.969 43.478 0.00 0.00 43.34 4.41
3272 9731 0.167470 CTGCTGGATTGTTGTGAGCG 59.833 55.000 0.00 0.00 32.05 5.03
3275 9734 1.511850 CGTCTGCTGGATTGTTGTGA 58.488 50.000 0.00 0.00 0.00 3.58
3277 9736 1.568612 CGCGTCTGCTGGATTGTTGT 61.569 55.000 0.00 0.00 39.65 3.32
3280 9739 2.225791 TAGCGCGTCTGCTGGATTGT 62.226 55.000 8.43 0.00 46.70 2.71
3282 9741 0.391130 TTTAGCGCGTCTGCTGGATT 60.391 50.000 8.43 0.00 46.70 3.01
3283 9742 0.391130 TTTTAGCGCGTCTGCTGGAT 60.391 50.000 8.43 0.00 46.70 3.41


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

AutoCloner maintained by Alex Coulton.