Multiple sequence alignment - TraesCS5B01G420000

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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 TraesCS5B01G420000 chr5B 100.000 4171 0 0 1 4171 595651712 595655882 0.000000e+00 7703.0
1 TraesCS5B01G420000 chr5B 82.786 761 77 33 2578 3301 595626963 595627706 7.610000e-177 630.0
2 TraesCS5B01G420000 chr5B 86.652 457 40 12 971 1412 595624697 595625147 1.740000e-133 486.0
3 TraesCS5B01G420000 chr5B 79.022 777 112 29 1638 2392 595625144 595625891 6.270000e-133 484.0
4 TraesCS5B01G420000 chr5A 91.973 3675 160 52 564 4171 606153034 606156640 0.000000e+00 5027.0
5 TraesCS5B01G420000 chr5A 82.993 1370 172 38 971 2303 606053295 606054640 0.000000e+00 1182.0
6 TraesCS5B01G420000 chr5A 84.030 789 81 23 2548 3303 606054863 606055639 0.000000e+00 717.0
7 TraesCS5B01G420000 chr5A 76.565 559 71 25 3418 3949 606056469 606056994 6.920000e-63 252.0
8 TraesCS5B01G420000 chr5A 82.422 256 39 6 449 701 606063043 606063295 7.020000e-53 219.0
9 TraesCS5B01G420000 chr5D 92.899 2887 126 28 1345 4167 484567979 484570850 0.000000e+00 4122.0
10 TraesCS5B01G420000 chr5D 83.356 1478 200 27 971 2410 484415714 484417183 0.000000e+00 1325.0
11 TraesCS5B01G420000 chr5D 84.861 720 67 16 2586 3274 484417338 484418046 0.000000e+00 688.0
12 TraesCS5B01G420000 chr5D 87.652 494 27 13 809 1302 484567158 484567617 1.020000e-150 544.0
13 TraesCS5B01G420000 chr6A 87.500 184 17 6 1045 1224 30422633 30422814 1.520000e-49 207.0
14 TraesCS5B01G420000 chr6A 74.172 453 78 23 1046 1492 30716027 30716446 7.220000e-33 152.0
15 TraesCS5B01G420000 chrUn 82.432 222 24 11 1026 1242 27073107 27073318 3.310000e-41 180.0
16 TraesCS5B01G420000 chrUn 81.651 218 33 4 1026 1242 27965099 27964888 1.540000e-39 174.0
17 TraesCS5B01G420000 chrUn 77.381 168 25 9 1330 1492 76751521 76751362 2.070000e-13 87.9
18 TraesCS5B01G420000 chrUn 85.714 70 9 1 1425 1494 327372201 327372133 5.780000e-09 73.1
19 TraesCS5B01G420000 chrUn 90.000 50 4 1 376 425 32986809 32986857 3.480000e-06 63.9
20 TraesCS5B01G420000 chr6B 82.432 222 24 11 1026 1242 82004627 82004838 3.310000e-41 180.0
21 TraesCS5B01G420000 chr6B 83.133 166 26 2 1054 1218 51098529 51098365 2.600000e-32 150.0
22 TraesCS5B01G420000 chr6B 87.692 65 6 2 1428 1491 76153008 76152945 1.610000e-09 75.0
23 TraesCS5B01G420000 chr6D 81.364 220 37 2 1028 1246 29094600 29094384 4.290000e-40 176.0
24 TraesCS5B01G420000 chr6D 73.770 244 41 15 1425 1661 29932850 29933077 1.610000e-09 75.0


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 TraesCS5B01G420000 chr5B 595651712 595655882 4170 False 7703.000000 7703 100.0000 1 4171 1 chr5B.!!$F1 4170
1 TraesCS5B01G420000 chr5B 595624697 595627706 3009 False 533.333333 630 82.8200 971 3301 3 chr5B.!!$F2 2330
2 TraesCS5B01G420000 chr5A 606153034 606156640 3606 False 5027.000000 5027 91.9730 564 4171 1 chr5A.!!$F2 3607
3 TraesCS5B01G420000 chr5A 606053295 606056994 3699 False 717.000000 1182 81.1960 971 3949 3 chr5A.!!$F3 2978
4 TraesCS5B01G420000 chr5D 484567158 484570850 3692 False 2333.000000 4122 90.2755 809 4167 2 chr5D.!!$F2 3358
5 TraesCS5B01G420000 chr5D 484415714 484418046 2332 False 1006.500000 1325 84.1085 971 3274 2 chr5D.!!$F1 2303

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
185 186 0.248702 GTTCACCGCGCCTTCAAAAA 60.249 50.0 0.00 0.0 0.0 1.94 F
1943 2320 0.391263 AAAAGGGAGATCGACCGTGC 60.391 55.0 7.67 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2333 0.111639 TAGTTTTCCCCAGCACCCAC 59.888 55.0 0.0 0.0 0.0 4.61 R
3402 5680 0.040958 GTGGAGCAAGACAAACAGCG 60.041 55.0 0.0 0.0 0.0 5.18 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
39 40 8.907222 AATTTTAGAAAATGTTCATTGTGCCT 57.093 26.923 0.00 0.00 38.53 4.75
40 41 8.907222 ATTTTAGAAAATGTTCATTGTGCCTT 57.093 26.923 0.00 0.00 37.24 4.35
41 42 7.945033 TTTAGAAAATGTTCATTGTGCCTTC 57.055 32.000 0.00 0.10 36.09 3.46
42 43 5.534207 AGAAAATGTTCATTGTGCCTTCA 57.466 34.783 0.00 0.00 36.09 3.02
43 44 5.916318 AGAAAATGTTCATTGTGCCTTCAA 58.084 33.333 0.00 0.00 36.09 2.69
44 45 6.347696 AGAAAATGTTCATTGTGCCTTCAAA 58.652 32.000 0.00 0.00 36.09 2.69
45 46 6.822676 AGAAAATGTTCATTGTGCCTTCAAAA 59.177 30.769 0.00 0.00 36.09 2.44
46 47 6.998968 AAATGTTCATTGTGCCTTCAAAAA 57.001 29.167 0.00 0.00 0.00 1.94
75 76 9.836864 TGTGAATGCACTGTAATATAGATTTCT 57.163 29.630 5.18 0.00 45.36 2.52
175 176 8.609478 ATTATTACTTTTAAATGTTCACCGCG 57.391 30.769 11.52 0.00 0.00 6.46
176 177 2.657184 ACTTTTAAATGTTCACCGCGC 58.343 42.857 0.00 0.00 0.00 6.86
177 178 1.982913 CTTTTAAATGTTCACCGCGCC 59.017 47.619 0.00 0.00 0.00 6.53
178 179 1.240256 TTTAAATGTTCACCGCGCCT 58.760 45.000 0.00 0.00 0.00 5.52
179 180 1.240256 TTAAATGTTCACCGCGCCTT 58.760 45.000 0.00 0.00 0.00 4.35
180 181 0.800012 TAAATGTTCACCGCGCCTTC 59.200 50.000 0.00 0.00 0.00 3.46
181 182 1.169661 AAATGTTCACCGCGCCTTCA 61.170 50.000 0.00 0.00 0.00 3.02
182 183 1.169661 AATGTTCACCGCGCCTTCAA 61.170 50.000 0.00 0.00 0.00 2.69
183 184 1.169661 ATGTTCACCGCGCCTTCAAA 61.170 50.000 0.00 0.00 0.00 2.69
184 185 1.357334 GTTCACCGCGCCTTCAAAA 59.643 52.632 0.00 0.00 0.00 2.44
185 186 0.248702 GTTCACCGCGCCTTCAAAAA 60.249 50.000 0.00 0.00 0.00 1.94
213 214 9.486497 TGTTAATGCTTTAAAAAGAATCATGCA 57.514 25.926 6.64 0.00 33.04 3.96
308 309 9.829507 TTTTGATCATAACAATTTCCAAACTGT 57.170 25.926 0.00 0.00 0.00 3.55
309 310 9.829507 TTTGATCATAACAATTTCCAAACTGTT 57.170 25.926 0.00 4.47 36.11 3.16
310 311 9.474920 TTGATCATAACAATTTCCAAACTGTTC 57.525 29.630 2.33 0.00 34.08 3.18
311 312 8.637099 TGATCATAACAATTTCCAAACTGTTCA 58.363 29.630 2.33 0.00 34.08 3.18
312 313 9.643693 GATCATAACAATTTCCAAACTGTTCAT 57.356 29.630 2.33 0.00 34.08 2.57
377 378 9.730705 AGTTCTTATCAGTCAGAAAAATCATGA 57.269 29.630 0.00 0.00 30.76 3.07
378 379 9.766277 GTTCTTATCAGTCAGAAAAATCATGAC 57.234 33.333 0.00 0.00 42.91 3.06
379 380 9.506018 TTCTTATCAGTCAGAAAAATCATGACA 57.494 29.630 0.00 0.00 44.59 3.58
380 381 9.676861 TCTTATCAGTCAGAAAAATCATGACAT 57.323 29.630 0.00 0.00 44.59 3.06
440 441 9.801714 CATGACATTTTAGAAAATTGTTCTTGC 57.198 29.630 0.00 0.00 36.52 4.01
441 442 8.939201 TGACATTTTAGAAAATTGTTCTTGCA 57.061 26.923 0.00 0.00 36.52 4.08
442 443 9.376075 TGACATTTTAGAAAATTGTTCTTGCAA 57.624 25.926 0.00 0.00 36.52 4.08
496 497 4.927978 ATGTTCGTGACATTTTCCCAAA 57.072 36.364 2.13 0.00 46.80 3.28
497 498 4.720649 TGTTCGTGACATTTTCCCAAAA 57.279 36.364 0.00 0.00 32.00 2.44
498 499 5.269505 TGTTCGTGACATTTTCCCAAAAT 57.730 34.783 0.00 0.00 41.57 1.82
499 500 6.392625 TGTTCGTGACATTTTCCCAAAATA 57.607 33.333 0.00 0.00 38.97 1.40
500 501 6.987386 TGTTCGTGACATTTTCCCAAAATAT 58.013 32.000 0.00 0.00 38.97 1.28
501 502 7.437748 TGTTCGTGACATTTTCCCAAAATATT 58.562 30.769 0.00 0.00 38.97 1.28
502 503 7.596995 TGTTCGTGACATTTTCCCAAAATATTC 59.403 33.333 0.00 0.00 38.97 1.75
503 504 7.461182 TCGTGACATTTTCCCAAAATATTCT 57.539 32.000 0.00 0.00 38.97 2.40
504 505 8.568676 TCGTGACATTTTCCCAAAATATTCTA 57.431 30.769 0.00 0.00 38.97 2.10
505 506 8.673711 TCGTGACATTTTCCCAAAATATTCTAG 58.326 33.333 0.00 0.00 38.97 2.43
506 507 7.432252 CGTGACATTTTCCCAAAATATTCTAGC 59.568 37.037 0.00 0.00 38.97 3.42
507 508 8.250332 GTGACATTTTCCCAAAATATTCTAGCA 58.750 33.333 0.00 0.00 38.97 3.49
508 509 8.250332 TGACATTTTCCCAAAATATTCTAGCAC 58.750 33.333 0.00 0.00 38.97 4.40
509 510 8.366359 ACATTTTCCCAAAATATTCTAGCACT 57.634 30.769 0.00 0.00 38.97 4.40
510 511 8.815912 ACATTTTCCCAAAATATTCTAGCACTT 58.184 29.630 0.00 0.00 38.97 3.16
511 512 9.657419 CATTTTCCCAAAATATTCTAGCACTTT 57.343 29.630 0.00 0.00 38.97 2.66
515 516 8.871629 TCCCAAAATATTCTAGCACTTTAACA 57.128 30.769 0.00 0.00 0.00 2.41
516 517 8.956426 TCCCAAAATATTCTAGCACTTTAACAG 58.044 33.333 0.00 0.00 0.00 3.16
517 518 8.956426 CCCAAAATATTCTAGCACTTTAACAGA 58.044 33.333 0.00 0.00 0.00 3.41
527 528 8.343366 TCTAGCACTTTAACAGATATCTACACG 58.657 37.037 4.54 0.00 0.00 4.49
528 529 6.864342 AGCACTTTAACAGATATCTACACGT 58.136 36.000 4.54 0.00 0.00 4.49
529 530 7.321153 AGCACTTTAACAGATATCTACACGTT 58.679 34.615 4.54 8.03 0.00 3.99
530 531 7.817962 AGCACTTTAACAGATATCTACACGTTT 59.182 33.333 4.54 0.00 0.00 3.60
531 532 8.440833 GCACTTTAACAGATATCTACACGTTTT 58.559 33.333 4.54 0.00 0.00 2.43
549 550 9.906660 ACACGTTTTAAACAATATTCATGTCAT 57.093 25.926 8.61 0.00 0.00 3.06
668 672 9.965824 AAAATGTTCAACAGGTATCTTAAACAG 57.034 29.630 0.00 0.00 0.00 3.16
679 683 8.576442 CAGGTATCTTAAACAGGTTTGATTTGT 58.424 33.333 7.63 0.00 34.23 2.83
680 684 9.802039 AGGTATCTTAAACAGGTTTGATTTGTA 57.198 29.630 7.63 0.00 34.23 2.41
688 692 7.655328 TAAACAGGTTTGATTTGTATGGCAAAG 59.345 33.333 7.63 0.00 40.53 2.77
818 829 4.429854 AAGCACAGAGAAAAGAAGAGGT 57.570 40.909 0.00 0.00 0.00 3.85
819 830 5.552870 AAGCACAGAGAAAAGAAGAGGTA 57.447 39.130 0.00 0.00 0.00 3.08
820 831 4.888917 AGCACAGAGAAAAGAAGAGGTAC 58.111 43.478 0.00 0.00 0.00 3.34
821 832 4.345257 AGCACAGAGAAAAGAAGAGGTACA 59.655 41.667 0.00 0.00 0.00 2.90
822 833 5.057149 GCACAGAGAAAAGAAGAGGTACAA 58.943 41.667 0.00 0.00 0.00 2.41
838 849 4.590226 GGTACAACACCGTGTTTTTACTG 58.410 43.478 21.62 12.42 38.77 2.74
863 884 1.270678 GGCGTTCTGACCCAGTTAAGT 60.271 52.381 0.00 0.00 32.61 2.24
864 885 2.067013 GCGTTCTGACCCAGTTAAGTC 58.933 52.381 0.00 0.00 32.61 3.01
865 886 2.288886 GCGTTCTGACCCAGTTAAGTCT 60.289 50.000 0.00 0.00 34.02 3.24
866 887 3.576648 CGTTCTGACCCAGTTAAGTCTC 58.423 50.000 0.00 0.00 34.02 3.36
867 888 3.256136 CGTTCTGACCCAGTTAAGTCTCT 59.744 47.826 0.00 0.00 34.02 3.10
868 889 4.561105 GTTCTGACCCAGTTAAGTCTCTG 58.439 47.826 0.00 0.00 34.02 3.35
870 891 2.900546 CTGACCCAGTTAAGTCTCTGGT 59.099 50.000 8.56 0.85 46.79 4.00
871 892 3.314693 TGACCCAGTTAAGTCTCTGGTT 58.685 45.455 8.56 0.00 46.79 3.67
872 893 3.071023 TGACCCAGTTAAGTCTCTGGTTG 59.929 47.826 8.56 0.00 46.79 3.77
873 894 2.372172 ACCCAGTTAAGTCTCTGGTTGG 59.628 50.000 8.56 0.00 46.79 3.77
874 895 2.372172 CCCAGTTAAGTCTCTGGTTGGT 59.628 50.000 8.56 0.00 46.79 3.67
875 896 3.403038 CCAGTTAAGTCTCTGGTTGGTG 58.597 50.000 2.38 0.00 44.19 4.17
876 897 3.403038 CAGTTAAGTCTCTGGTTGGTGG 58.597 50.000 0.00 0.00 0.00 4.61
877 898 2.372172 AGTTAAGTCTCTGGTTGGTGGG 59.628 50.000 0.00 0.00 0.00 4.61
922 943 3.691049 TTGAAAACGAAACCTCTGCTG 57.309 42.857 0.00 0.00 0.00 4.41
927 948 3.971032 AACGAAACCTCTGCTGAAAAG 57.029 42.857 0.00 0.00 0.00 2.27
928 949 1.604278 ACGAAACCTCTGCTGAAAAGC 59.396 47.619 0.00 0.00 0.00 3.51
930 951 2.227388 CGAAACCTCTGCTGAAAAGCAT 59.773 45.455 0.11 0.00 44.47 3.79
933 954 5.562696 CGAAACCTCTGCTGAAAAGCATAAA 60.563 40.000 0.11 0.00 44.47 1.40
934 955 5.789643 AACCTCTGCTGAAAAGCATAAAA 57.210 34.783 0.11 0.00 44.47 1.52
1704 2066 2.526993 CGTTCGCACCACGGTTTCA 61.527 57.895 0.00 0.00 43.89 2.69
1771 2142 0.886490 GAATGGGGATACTGCTGCCG 60.886 60.000 0.00 0.00 0.00 5.69
1839 2216 3.442996 ACTGGATAAGTGCAGCGAC 57.557 52.632 0.00 0.00 46.66 5.19
1943 2320 0.391263 AAAAGGGAGATCGACCGTGC 60.391 55.000 7.67 0.00 0.00 5.34
1956 2333 2.052590 CGTGCCGGTGTTGTTTCG 60.053 61.111 1.90 0.00 0.00 3.46
1997 2374 7.769220 ACTATTGAATTGGATCAGCTTCTTTG 58.231 34.615 0.00 0.00 0.00 2.77
2064 2441 5.390885 CGAGGTCAATAATGTGGTGTTTCTG 60.391 44.000 0.00 0.00 0.00 3.02
2120 2497 3.484407 AGTCATTGAAGTTCAGCAAGCT 58.516 40.909 5.56 0.19 0.00 3.74
2121 2498 4.645535 AGTCATTGAAGTTCAGCAAGCTA 58.354 39.130 5.56 0.00 0.00 3.32
2307 2697 5.286082 CCGCTAAATGTGCTATTGAACAAAC 59.714 40.000 0.00 0.00 34.97 2.93
2372 2785 2.482142 GGGATTGAAGTCAGAGGTAGCG 60.482 54.545 0.00 0.00 0.00 4.26
2540 3971 5.397142 AGATGGAAAACAGCTGGAAATTC 57.603 39.130 19.93 15.08 45.73 2.17
2564 4019 3.947910 AGCTGAAATGTCCAAATGGTG 57.052 42.857 0.00 0.00 36.34 4.17
2700 4192 7.479980 TCATTTTTACCACTTGTTGAAGACTG 58.520 34.615 0.00 0.00 32.98 3.51
2737 4229 9.352191 GAGTCTACTTGTACCAGAGGATAAATA 57.648 37.037 0.08 0.00 0.00 1.40
2881 4393 7.043325 CGGGAATAACTTTAGATCACTTCTTCG 60.043 40.741 0.00 0.00 35.79 3.79
3034 4548 8.912988 ACATGTGTTTTTCCTCTCTCAATTTTA 58.087 29.630 0.00 0.00 0.00 1.52
3322 5571 0.531974 TTCTCACTGTGGTTCACGCC 60.532 55.000 8.11 0.00 37.14 5.68
3332 5581 1.084289 GGTTCACGCCACCTATTGTC 58.916 55.000 0.00 0.00 0.00 3.18
3333 5582 0.719465 GTTCACGCCACCTATTGTCG 59.281 55.000 0.00 0.00 0.00 4.35
3334 5583 0.604073 TTCACGCCACCTATTGTCGA 59.396 50.000 0.00 0.00 0.00 4.20
3335 5584 0.604073 TCACGCCACCTATTGTCGAA 59.396 50.000 0.00 0.00 0.00 3.71
3336 5585 1.001068 TCACGCCACCTATTGTCGAAA 59.999 47.619 0.00 0.00 0.00 3.46
3337 5586 1.127951 CACGCCACCTATTGTCGAAAC 59.872 52.381 0.00 0.00 0.00 2.78
3338 5587 1.001633 ACGCCACCTATTGTCGAAACT 59.998 47.619 0.00 0.00 0.00 2.66
3388 5666 4.838423 TCCACTTTGATCTTGGTACTCTCA 59.162 41.667 0.00 0.00 0.00 3.27
3402 5680 1.066787 ACTCTCACCTTAGAAAGCGCC 60.067 52.381 2.29 0.00 0.00 6.53
3591 5893 0.035036 CCATCTCCTGATGCTGCGAT 59.965 55.000 0.00 0.00 46.43 4.58
3656 5959 1.102809 TGTTGCCTGTTGACAGCCAG 61.103 55.000 5.62 0.00 42.47 4.85
3677 5981 0.682209 AGCGATGCTGAAGGGCAAAT 60.682 50.000 0.00 0.00 45.68 2.32
3703 6007 1.740025 GAAGAACCGGCATTTCAGAGG 59.260 52.381 0.00 0.00 0.00 3.69
3894 6209 7.982224 AGTAAACGGCTATTTCTTACATTTCC 58.018 34.615 0.00 0.00 0.00 3.13
3952 6286 2.034939 TGCTTTCAACACCATGAAGCAG 59.965 45.455 10.66 0.00 40.21 4.24
4125 6466 5.069251 TCATCAACCGGTGGTACAAATTTTT 59.931 36.000 8.52 0.00 44.16 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.341078 AGGCACAATGAACATTTTCTAAAATTT 57.659 25.926 0.00 0.00 36.52 1.82
14 15 8.907222 AGGCACAATGAACATTTTCTAAAATT 57.093 26.923 0.00 0.00 36.52 1.82
15 16 8.907222 AAGGCACAATGAACATTTTCTAAAAT 57.093 26.923 0.00 0.00 39.07 1.82
16 17 7.984050 TGAAGGCACAATGAACATTTTCTAAAA 59.016 29.630 0.00 0.00 32.36 1.52
17 18 7.495901 TGAAGGCACAATGAACATTTTCTAAA 58.504 30.769 0.00 0.00 32.36 1.85
18 19 7.048629 TGAAGGCACAATGAACATTTTCTAA 57.951 32.000 0.00 0.00 32.36 2.10
19 20 6.647334 TGAAGGCACAATGAACATTTTCTA 57.353 33.333 0.00 0.00 32.36 2.10
20 21 5.534207 TGAAGGCACAATGAACATTTTCT 57.466 34.783 0.00 0.00 32.36 2.52
21 22 6.601741 TTTGAAGGCACAATGAACATTTTC 57.398 33.333 0.00 0.83 0.00 2.29
22 23 6.998968 TTTTGAAGGCACAATGAACATTTT 57.001 29.167 0.00 0.00 0.00 1.82
23 24 6.998968 TTTTTGAAGGCACAATGAACATTT 57.001 29.167 0.00 0.00 0.00 2.32
49 50 9.836864 AGAAATCTATATTACAGTGCATTCACA 57.163 29.630 0.00 0.00 45.49 3.58
149 150 9.068008 CGCGGTGAACATTTAAAAGTAATAATT 57.932 29.630 0.00 0.00 0.00 1.40
150 151 7.219344 GCGCGGTGAACATTTAAAAGTAATAAT 59.781 33.333 8.83 0.00 0.00 1.28
151 152 6.523893 GCGCGGTGAACATTTAAAAGTAATAA 59.476 34.615 8.83 0.00 0.00 1.40
152 153 6.022821 GCGCGGTGAACATTTAAAAGTAATA 58.977 36.000 8.83 0.00 0.00 0.98
153 154 4.854839 GCGCGGTGAACATTTAAAAGTAAT 59.145 37.500 8.83 0.00 0.00 1.89
154 155 4.220572 GCGCGGTGAACATTTAAAAGTAA 58.779 39.130 8.83 0.00 0.00 2.24
155 156 3.365164 GGCGCGGTGAACATTTAAAAGTA 60.365 43.478 8.83 0.00 0.00 2.24
156 157 2.606065 GGCGCGGTGAACATTTAAAAGT 60.606 45.455 8.83 0.00 0.00 2.66
157 158 1.982913 GGCGCGGTGAACATTTAAAAG 59.017 47.619 8.83 0.00 0.00 2.27
158 159 1.609555 AGGCGCGGTGAACATTTAAAA 59.390 42.857 8.83 0.00 0.00 1.52
159 160 1.240256 AGGCGCGGTGAACATTTAAA 58.760 45.000 8.83 0.00 0.00 1.52
160 161 1.198178 GAAGGCGCGGTGAACATTTAA 59.802 47.619 8.83 0.00 0.00 1.52
161 162 0.800012 GAAGGCGCGGTGAACATTTA 59.200 50.000 8.83 0.00 0.00 1.40
162 163 1.169661 TGAAGGCGCGGTGAACATTT 61.170 50.000 8.83 0.00 0.00 2.32
163 164 1.169661 TTGAAGGCGCGGTGAACATT 61.170 50.000 8.83 0.00 0.00 2.71
164 165 1.169661 TTTGAAGGCGCGGTGAACAT 61.170 50.000 8.83 0.00 0.00 2.71
165 166 1.377366 TTTTGAAGGCGCGGTGAACA 61.377 50.000 8.83 0.00 0.00 3.18
166 167 0.248702 TTTTTGAAGGCGCGGTGAAC 60.249 50.000 8.83 0.00 0.00 3.18
167 168 2.107705 TTTTTGAAGGCGCGGTGAA 58.892 47.368 8.83 0.00 0.00 3.18
168 169 3.829048 TTTTTGAAGGCGCGGTGA 58.171 50.000 8.83 0.00 0.00 4.02
187 188 9.486497 TGCATGATTCTTTTTAAAGCATTAACA 57.514 25.926 0.00 0.00 35.99 2.41
282 283 9.829507 ACAGTTTGGAAATTGTTATGATCAAAA 57.170 25.926 0.00 0.00 35.66 2.44
283 284 9.829507 AACAGTTTGGAAATTGTTATGATCAAA 57.170 25.926 10.31 0.00 43.90 2.69
284 285 9.474920 GAACAGTTTGGAAATTGTTATGATCAA 57.525 29.630 11.60 0.00 45.12 2.57
285 286 8.637099 TGAACAGTTTGGAAATTGTTATGATCA 58.363 29.630 11.60 0.00 45.12 2.92
286 287 9.643693 ATGAACAGTTTGGAAATTGTTATGATC 57.356 29.630 11.60 2.56 45.12 2.92
351 352 9.730705 TCATGATTTTTCTGACTGATAAGAACT 57.269 29.630 0.00 0.00 32.26 3.01
352 353 9.766277 GTCATGATTTTTCTGACTGATAAGAAC 57.234 33.333 0.00 0.00 37.04 3.01
353 354 9.506018 TGTCATGATTTTTCTGACTGATAAGAA 57.494 29.630 0.00 0.00 39.94 2.52
354 355 9.676861 ATGTCATGATTTTTCTGACTGATAAGA 57.323 29.630 0.00 0.00 39.94 2.10
414 415 9.801714 GCAAGAACAATTTTCTAAAATGTCATG 57.198 29.630 1.61 5.14 38.53 3.07
415 416 9.545105 TGCAAGAACAATTTTCTAAAATGTCAT 57.455 25.926 1.61 0.00 38.53 3.06
416 417 8.939201 TGCAAGAACAATTTTCTAAAATGTCA 57.061 26.923 1.61 0.00 38.53 3.58
476 477 4.720649 TTTTGGGAAAATGTCACGAACA 57.279 36.364 0.00 0.00 43.51 3.18
477 478 7.812669 AGAATATTTTGGGAAAATGTCACGAAC 59.187 33.333 4.84 0.00 41.01 3.95
478 479 7.891561 AGAATATTTTGGGAAAATGTCACGAA 58.108 30.769 4.84 0.00 41.01 3.85
479 480 7.461182 AGAATATTTTGGGAAAATGTCACGA 57.539 32.000 4.84 0.00 41.01 4.35
480 481 7.432252 GCTAGAATATTTTGGGAAAATGTCACG 59.568 37.037 0.00 0.00 41.01 4.35
481 482 8.250332 TGCTAGAATATTTTGGGAAAATGTCAC 58.750 33.333 0.00 0.00 41.01 3.67
482 483 8.250332 GTGCTAGAATATTTTGGGAAAATGTCA 58.750 33.333 0.00 0.00 41.01 3.58
483 484 8.470002 AGTGCTAGAATATTTTGGGAAAATGTC 58.530 33.333 0.00 3.09 41.01 3.06
484 485 8.366359 AGTGCTAGAATATTTTGGGAAAATGT 57.634 30.769 0.00 0.00 41.01 2.71
485 486 9.657419 AAAGTGCTAGAATATTTTGGGAAAATG 57.343 29.630 0.00 0.00 41.01 2.32
489 490 9.303116 TGTTAAAGTGCTAGAATATTTTGGGAA 57.697 29.630 0.00 0.00 0.00 3.97
490 491 8.871629 TGTTAAAGTGCTAGAATATTTTGGGA 57.128 30.769 0.00 0.00 0.00 4.37
491 492 8.956426 TCTGTTAAAGTGCTAGAATATTTTGGG 58.044 33.333 0.00 0.00 0.00 4.12
501 502 8.343366 CGTGTAGATATCTGTTAAAGTGCTAGA 58.657 37.037 15.79 0.00 0.00 2.43
502 503 8.129840 ACGTGTAGATATCTGTTAAAGTGCTAG 58.870 37.037 15.79 0.00 0.00 3.42
503 504 7.993101 ACGTGTAGATATCTGTTAAAGTGCTA 58.007 34.615 15.79 0.00 0.00 3.49
504 505 6.864342 ACGTGTAGATATCTGTTAAAGTGCT 58.136 36.000 15.79 0.00 0.00 4.40
505 506 7.521509 AACGTGTAGATATCTGTTAAAGTGC 57.478 36.000 15.79 0.00 0.00 4.40
523 524 9.906660 ATGACATGAATATTGTTTAAAACGTGT 57.093 25.926 0.00 0.00 0.00 4.49
605 609 8.971321 GCTGGATATTAGTAAAAATGCACATTG 58.029 33.333 0.00 0.00 0.00 2.82
606 610 8.694540 TGCTGGATATTAGTAAAAATGCACATT 58.305 29.630 0.00 0.00 0.00 2.71
609 613 8.137437 ACATGCTGGATATTAGTAAAAATGCAC 58.863 33.333 0.00 0.00 0.00 4.57
610 614 8.236585 ACATGCTGGATATTAGTAAAAATGCA 57.763 30.769 0.00 0.00 0.00 3.96
650 654 7.504924 TCAAACCTGTTTAAGATACCTGTTG 57.495 36.000 0.00 0.00 0.00 3.33
654 658 8.706322 ACAAATCAAACCTGTTTAAGATACCT 57.294 30.769 0.00 0.00 0.00 3.08
659 663 7.014711 TGCCATACAAATCAAACCTGTTTAAGA 59.985 33.333 0.00 0.00 0.00 2.10
663 667 5.543507 TGCCATACAAATCAAACCTGTTT 57.456 34.783 0.00 0.00 0.00 2.83
666 670 5.782047 TCTTTGCCATACAAATCAAACCTG 58.218 37.500 0.00 0.00 46.90 4.00
667 671 6.418057 TTCTTTGCCATACAAATCAAACCT 57.582 33.333 0.00 0.00 46.90 3.50
668 672 7.489574 TTTTCTTTGCCATACAAATCAAACC 57.510 32.000 0.00 0.00 46.90 3.27
799 810 4.632153 TGTACCTCTTCTTTTCTCTGTGC 58.368 43.478 0.00 0.00 0.00 4.57
816 827 4.496175 CCAGTAAAAACACGGTGTTGTACC 60.496 45.833 27.55 18.01 40.14 3.34
818 829 3.065095 GCCAGTAAAAACACGGTGTTGTA 59.935 43.478 25.69 17.70 40.14 2.41
819 830 2.159352 GCCAGTAAAAACACGGTGTTGT 60.159 45.455 25.69 18.60 40.14 3.32
820 831 2.159366 TGCCAGTAAAAACACGGTGTTG 60.159 45.455 25.69 13.42 40.14 3.33
821 832 2.093106 TGCCAGTAAAAACACGGTGTT 58.907 42.857 20.23 20.23 43.41 3.32
822 833 1.402613 GTGCCAGTAAAAACACGGTGT 59.597 47.619 8.21 8.21 0.00 4.16
863 884 1.159905 TAGGCCCACCAACCAGAGA 59.840 57.895 0.00 0.00 39.06 3.10
864 885 1.299976 GTAGGCCCACCAACCAGAG 59.700 63.158 0.00 0.00 39.06 3.35
865 886 2.589157 CGTAGGCCCACCAACCAGA 61.589 63.158 0.00 0.00 39.06 3.86
866 887 2.046314 CGTAGGCCCACCAACCAG 60.046 66.667 0.00 0.00 39.06 4.00
867 888 4.338710 GCGTAGGCCCACCAACCA 62.339 66.667 0.00 0.00 39.06 3.67
888 909 4.573201 TCGTTTTCAAAGAACCGATCAAGT 59.427 37.500 0.00 0.00 0.00 3.16
903 924 2.912771 TCAGCAGAGGTTTCGTTTTCA 58.087 42.857 0.00 0.00 0.00 2.69
904 925 3.963383 TTCAGCAGAGGTTTCGTTTTC 57.037 42.857 0.00 0.00 0.00 2.29
942 963 9.937175 CGAGCTTTCTTATAATTTCTTTTAGGG 57.063 33.333 0.00 0.00 0.00 3.53
946 967 9.543018 CGAACGAGCTTTCTTATAATTTCTTTT 57.457 29.630 0.00 0.00 0.00 2.27
947 968 8.175716 CCGAACGAGCTTTCTTATAATTTCTTT 58.824 33.333 0.00 0.00 0.00 2.52
950 971 7.001695 ACCGAACGAGCTTTCTTATAATTTC 57.998 36.000 0.00 0.00 0.00 2.17
951 972 6.980051 ACCGAACGAGCTTTCTTATAATTT 57.020 33.333 0.00 0.00 0.00 1.82
952 973 6.980051 AACCGAACGAGCTTTCTTATAATT 57.020 33.333 0.00 0.00 0.00 1.40
953 974 6.980051 AAACCGAACGAGCTTTCTTATAAT 57.020 33.333 0.00 0.00 0.00 1.28
954 975 6.128472 GGAAAACCGAACGAGCTTTCTTATAA 60.128 38.462 0.00 0.00 0.00 0.98
955 976 5.349543 GGAAAACCGAACGAGCTTTCTTATA 59.650 40.000 0.00 0.00 0.00 0.98
956 977 4.153655 GGAAAACCGAACGAGCTTTCTTAT 59.846 41.667 0.00 0.00 0.00 1.73
957 978 3.495753 GGAAAACCGAACGAGCTTTCTTA 59.504 43.478 0.00 0.00 0.00 2.10
960 981 1.398071 CGGAAAACCGAACGAGCTTTC 60.398 52.381 2.30 0.00 34.88 2.62
969 990 0.179040 AACTGCTCCGGAAAACCGAA 60.179 50.000 5.23 0.00 34.88 4.30
1083 1110 3.967335 CGGACGAGGATCTCCGGC 61.967 72.222 12.15 8.57 45.63 6.13
1656 2018 2.634940 AGAATCCACGGATACCCAGATG 59.365 50.000 0.00 0.00 33.97 2.90
1704 2066 1.659794 GGTGCTGGAAACACGCATT 59.340 52.632 0.00 0.00 43.12 3.56
1771 2142 2.627699 TGCCCAAATCAAACTGAAGGAC 59.372 45.455 0.00 0.00 0.00 3.85
1943 2320 1.820481 ACCCACGAAACAACACCGG 60.820 57.895 0.00 0.00 0.00 5.28
1956 2333 0.111639 TAGTTTTCCCCAGCACCCAC 59.888 55.000 0.00 0.00 0.00 4.61
1997 2374 0.394899 CATTCCCCTCTTGTCCAGGC 60.395 60.000 0.00 0.00 0.00 4.85
2064 2441 7.824779 ACCAAGAAAATACTGAATACTGTCCTC 59.175 37.037 0.00 0.00 0.00 3.71
2120 2497 5.216622 AGAAGTAAGATGCCTGTATGGGTA 58.783 41.667 0.00 0.00 36.00 3.69
2121 2498 4.040755 AGAAGTAAGATGCCTGTATGGGT 58.959 43.478 0.00 0.00 36.00 4.51
2207 2591 3.441572 AGGATGTGAAAAGCTTTCCATCG 59.558 43.478 24.85 0.00 32.17 3.84
2307 2697 6.694877 ATAATATCATAAGCAGCATGGCAG 57.305 37.500 0.00 0.00 35.86 4.85
2352 2758 2.427453 TCGCTACCTCTGACTTCAATCC 59.573 50.000 0.00 0.00 0.00 3.01
2540 3971 3.922240 CCATTTGGACATTTCAGCTTTCG 59.078 43.478 0.00 0.00 37.39 3.46
2673 4165 8.527810 AGTCTTCAACAAGTGGTAAAAATGAAA 58.472 29.630 0.00 0.00 0.00 2.69
2700 4192 3.321497 CAAGTAGACTCTGACACTTGCC 58.679 50.000 7.09 0.00 40.82 4.52
2881 4393 8.315391 TGCACATAATATTAGCTGATCAGAAC 57.685 34.615 27.04 9.56 0.00 3.01
3322 5571 6.300354 ACTTTCAAGTTTCGACAATAGGTG 57.700 37.500 0.00 0.00 35.21 4.00
3332 5581 1.136057 GCGGCCTACTTTCAAGTTTCG 60.136 52.381 0.00 0.00 40.37 3.46
3333 5582 1.199327 GGCGGCCTACTTTCAAGTTTC 59.801 52.381 12.87 0.00 40.37 2.78
3334 5583 1.244816 GGCGGCCTACTTTCAAGTTT 58.755 50.000 12.87 0.00 40.37 2.66
3335 5584 0.109723 TGGCGGCCTACTTTCAAGTT 59.890 50.000 21.46 0.00 40.37 2.66
3336 5585 0.328258 ATGGCGGCCTACTTTCAAGT 59.672 50.000 21.46 0.00 42.91 3.16
3337 5586 1.017387 GATGGCGGCCTACTTTCAAG 58.983 55.000 21.46 0.00 0.00 3.02
3338 5587 0.618458 AGATGGCGGCCTACTTTCAA 59.382 50.000 21.46 0.00 0.00 2.69
3388 5666 1.741770 CAGCGGCGCTTTCTAAGGT 60.742 57.895 34.51 4.87 36.40 3.50
3402 5680 0.040958 GTGGAGCAAGACAAACAGCG 60.041 55.000 0.00 0.00 0.00 5.18
3545 5847 1.327303 TTTTCCTGTGTGATGCCCAC 58.673 50.000 0.00 0.00 45.88 4.61
3591 5893 2.024369 TCTGGGCACATGTCCTCTACTA 60.024 50.000 3.79 0.00 41.34 1.82
3677 5981 3.571828 TGAAATGCCGGTTCTTCATTTGA 59.428 39.130 18.09 9.78 39.62 2.69
3703 6007 1.301677 CCTCTGGAAGGCGAAGTTGC 61.302 60.000 0.00 0.00 38.67 4.17
3764 6069 4.376146 GCCAAAATGGACACTGCTTTTTA 58.624 39.130 0.00 0.00 40.96 1.52
3894 6209 2.137523 GGCTCAAAGGCACATGTTTTG 58.862 47.619 13.12 13.12 40.97 2.44
3968 6302 7.516312 GCAGCAAAATCAGAAGAAGTTCAAAAG 60.516 37.037 5.50 0.00 34.82 2.27
4066 6407 7.255801 CCATTAAAGTTGTACCACCTCACAAAT 60.256 37.037 0.00 0.00 36.47 2.32
4081 6422 6.369340 TGATGATGCAAAAGCCATTAAAGTTG 59.631 34.615 0.00 0.00 0.00 3.16
4125 6466 3.064207 GCGAAACAGTCACTGGTCATAA 58.936 45.455 10.28 0.00 35.51 1.90


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

AutoCloner maintained by Alex Coulton.