Multiple sequence alignment - TraesCS5A01G307200

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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 TraesCS5A01G307200 chr5A 100.000 3033 0 0 1 3033 519903250 519906282 0.000000e+00 5602.0
1 TraesCS5A01G307200 chr5A 100.000 99 0 0 3327 3425 519906576 519906674 2.100000e-42 183.0
2 TraesCS5A01G307200 chr5A 92.857 42 1 2 1182 1222 674169182 674169222 3.690000e-05 60.2
3 TraesCS5A01G307200 chr5D 89.938 3041 182 58 2 3010 408851625 408854573 0.000000e+00 3807.0
4 TraesCS5A01G307200 chr5B 94.663 2080 61 17 605 2668 490769315 490771360 0.000000e+00 3181.0
5 TraesCS5A01G307200 chr5B 91.860 258 15 3 2755 3010 490771406 490771659 4.200000e-94 355.0
6 TraesCS5A01G307200 chr5B 94.186 86 5 0 2925 3010 490772688 490772773 7.710000e-27 132.0
7 TraesCS5A01G307200 chr3A 83.391 1439 189 31 1018 2425 516239586 516238167 0.000000e+00 1288.0
8 TraesCS5A01G307200 chr3D 83.287 1436 190 31 1018 2425 396673535 396672122 0.000000e+00 1277.0
9 TraesCS5A01G307200 chr3B 82.790 1441 191 30 1018 2425 522031764 522030348 0.000000e+00 1234.0
10 TraesCS5A01G307200 chr4D 84.397 141 20 2 1182 1321 494833352 494833213 1.660000e-28 137.0
11 TraesCS5A01G307200 chr4B 82.424 165 21 3 1158 1321 634344339 634344182 1.660000e-28 137.0
12 TraesCS5A01G307200 chr1B 80.128 156 24 6 1158 1311 11182346 11182196 3.610000e-20 110.0


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 TraesCS5A01G307200 chr5A 519903250 519906674 3424 False 2892.500000 5602 100.000000 1 3425 2 chr5A.!!$F2 3424
1 TraesCS5A01G307200 chr5D 408851625 408854573 2948 False 3807.000000 3807 89.938000 2 3010 1 chr5D.!!$F1 3008
2 TraesCS5A01G307200 chr5B 490769315 490772773 3458 False 1222.666667 3181 93.569667 605 3010 3 chr5B.!!$F1 2405
3 TraesCS5A01G307200 chr3A 516238167 516239586 1419 True 1288.000000 1288 83.391000 1018 2425 1 chr3A.!!$R1 1407
4 TraesCS5A01G307200 chr3D 396672122 396673535 1413 True 1277.000000 1277 83.287000 1018 2425 1 chr3D.!!$R1 1407
5 TraesCS5A01G307200 chr3B 522030348 522031764 1416 True 1234.000000 1234 82.790000 1018 2425 1 chr3B.!!$R1 1407

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
945 984 0.109039 TCGCACGCTGCAACATACTA 60.109 50.0 0.0 0.0 45.36 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2593 2688 0.171455 ATGTCTTCGTCCTCTCGTGC 59.829 55.0 0.0 0.0 0.0 5.34 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
20 21 1.948144 GCCCCAACTTCTCTCAGCTTC 60.948 57.143 0.00 0.00 0.00 3.86
21 22 1.674221 CCCCAACTTCTCTCAGCTTCG 60.674 57.143 0.00 0.00 0.00 3.79
23 24 0.712775 CAACTTCTCTCAGCTTCGCG 59.287 55.000 0.00 0.00 0.00 5.87
24 25 0.598562 AACTTCTCTCAGCTTCGCGA 59.401 50.000 3.71 3.71 0.00 5.87
25 26 0.598562 ACTTCTCTCAGCTTCGCGAA 59.401 50.000 22.01 22.01 0.00 4.70
28 29 1.702886 TCTCTCAGCTTCGCGAAAAG 58.297 50.000 23.54 13.39 0.00 2.27
38 39 0.608035 TCGCGAAAAGATGGCCCTTT 60.608 50.000 6.20 0.00 37.94 3.11
42 43 1.474077 CGAAAAGATGGCCCTTTCCAG 59.526 52.381 0.00 0.00 39.89 3.86
43 44 2.807676 GAAAAGATGGCCCTTTCCAGA 58.192 47.619 0.00 0.00 39.89 3.86
49 50 5.930209 AGATGGCCCTTTCCAGATATTTA 57.070 39.130 0.00 0.00 39.89 1.40
51 52 4.453480 TGGCCCTTTCCAGATATTTAGG 57.547 45.455 0.00 0.00 0.00 2.69
52 53 3.157881 GGCCCTTTCCAGATATTTAGGC 58.842 50.000 0.00 0.00 37.14 3.93
53 54 2.814336 GCCCTTTCCAGATATTTAGGCG 59.186 50.000 0.00 0.00 0.00 5.52
64 65 0.808755 ATTTAGGCGGGCAGAAAACG 59.191 50.000 3.78 0.00 0.00 3.60
76 77 2.481276 GCAGAAAACGGCCTGAAAGTTT 60.481 45.455 0.00 0.00 39.45 2.66
77 78 3.243267 GCAGAAAACGGCCTGAAAGTTTA 60.243 43.478 0.00 0.00 37.13 2.01
81 82 0.769247 ACGGCCTGAAAGTTTAGGGT 59.231 50.000 0.00 0.00 34.58 4.34
85 86 1.880646 GCCTGAAAGTTTAGGGTGCGA 60.881 52.381 4.23 0.00 34.58 5.10
140 146 4.309950 ACCACTCGCCGAACCACC 62.310 66.667 0.00 0.00 0.00 4.61
149 155 1.876714 CCGAACCACCGCTGATACG 60.877 63.158 0.00 0.00 0.00 3.06
171 177 4.269523 GCCCTGCACCACCACTCA 62.270 66.667 0.00 0.00 0.00 3.41
174 180 2.510411 CTGCACCACCACTCACCA 59.490 61.111 0.00 0.00 0.00 4.17
175 181 1.073722 CTGCACCACCACTCACCAT 59.926 57.895 0.00 0.00 0.00 3.55
185 191 2.187946 CTCACCATCGTGCCTCCC 59.812 66.667 0.00 0.00 40.04 4.30
187 193 3.716195 CACCATCGTGCCTCCCCA 61.716 66.667 0.00 0.00 32.04 4.96
203 209 4.430423 CAAGCCGCGTCGTTGCTC 62.430 66.667 4.92 0.00 33.36 4.26
215 221 3.241530 TTGCTCGCCCCTGTCACT 61.242 61.111 0.00 0.00 0.00 3.41
247 253 3.701040 CCTAGGCCATTTGTATGCTTGTT 59.299 43.478 5.01 0.00 0.00 2.83
251 257 6.107901 AGGCCATTTGTATGCTTGTTTAAA 57.892 33.333 5.01 0.00 0.00 1.52
290 298 3.422796 ACTTTAGAGAGCGGAACTGAGA 58.577 45.455 0.00 0.00 0.00 3.27
298 306 2.668945 GAGCGGAACTGAGAAAAGTAGC 59.331 50.000 0.00 0.00 0.00 3.58
309 317 5.050490 TGAGAAAAGTAGCTGTGAGACAAC 58.950 41.667 0.00 0.00 0.00 3.32
313 321 7.445945 AGAAAAGTAGCTGTGAGACAACTTAT 58.554 34.615 0.00 0.00 29.47 1.73
323 331 8.604890 GCTGTGAGACAACTTATCCTAAATTAC 58.395 37.037 0.00 0.00 0.00 1.89
325 333 9.431887 TGTGAGACAACTTATCCTAAATTACAC 57.568 33.333 0.00 0.00 0.00 2.90
334 342 5.623956 ATCCTAAATTACACGGACATCCA 57.376 39.130 0.00 0.00 35.14 3.41
339 347 6.819649 CCTAAATTACACGGACATCCAGTAAA 59.180 38.462 13.75 5.34 38.65 2.01
345 353 2.036217 ACGGACATCCAGTAAAACGACA 59.964 45.455 0.00 0.00 35.14 4.35
352 360 4.650545 TCCAGTAAAACGACATTTACGC 57.349 40.909 13.42 0.00 45.87 4.42
353 361 3.121611 TCCAGTAAAACGACATTTACGCG 59.878 43.478 3.53 3.53 45.87 6.01
378 388 3.536570 GGTTGGAGAGCTATTGGAGTTC 58.463 50.000 0.00 0.00 35.69 3.01
394 404 6.139679 TGGAGTTCTTCTAACCATCCAATT 57.860 37.500 0.00 0.00 32.62 2.32
396 406 7.872138 TGGAGTTCTTCTAACCATCCAATTAT 58.128 34.615 0.00 0.00 32.62 1.28
443 453 5.869753 CTGTTTTCAGTCTGAACATAGGG 57.130 43.478 14.98 0.86 42.48 3.53
447 457 2.265367 TCAGTCTGAACATAGGGCCAA 58.735 47.619 6.18 0.00 0.00 4.52
475 485 3.685836 AACGGTTTTTACACTCTGCAC 57.314 42.857 0.00 0.00 0.00 4.57
476 486 2.914059 ACGGTTTTTACACTCTGCACT 58.086 42.857 0.00 0.00 0.00 4.40
477 487 2.870411 ACGGTTTTTACACTCTGCACTC 59.130 45.455 0.00 0.00 0.00 3.51
478 488 3.131396 CGGTTTTTACACTCTGCACTCT 58.869 45.455 0.00 0.00 0.00 3.24
479 489 3.059597 CGGTTTTTACACTCTGCACTCTG 60.060 47.826 0.00 0.00 0.00 3.35
480 490 3.304057 GGTTTTTACACTCTGCACTCTGC 60.304 47.826 0.00 0.00 45.29 4.26
493 503 4.802876 GCACTCTGCAGGTGAATAATAC 57.197 45.455 28.64 12.52 44.26 1.89
494 504 4.191544 GCACTCTGCAGGTGAATAATACA 58.808 43.478 28.64 1.98 44.26 2.29
496 506 5.297776 GCACTCTGCAGGTGAATAATACAAT 59.702 40.000 28.64 0.00 44.26 2.71
504 543 7.388776 TGCAGGTGAATAATACAATAGATGAGC 59.611 37.037 0.00 0.00 0.00 4.26
538 577 4.768130 AAAAGAAGATGACGAGTCGAGA 57.232 40.909 21.50 5.03 0.00 4.04
539 578 4.349663 AAAGAAGATGACGAGTCGAGAG 57.650 45.455 21.50 0.00 0.00 3.20
540 579 3.254470 AGAAGATGACGAGTCGAGAGA 57.746 47.619 21.50 0.00 38.16 3.10
558 597 7.095270 TCGAGAGACTAAACTTAATTTCACCC 58.905 38.462 0.00 0.00 33.31 4.61
559 598 6.034683 CGAGAGACTAAACTTAATTTCACCCG 59.965 42.308 0.00 0.00 0.00 5.28
560 599 5.642491 AGAGACTAAACTTAATTTCACCCGC 59.358 40.000 0.00 0.00 0.00 6.13
561 600 5.310451 AGACTAAACTTAATTTCACCCGCA 58.690 37.500 0.00 0.00 0.00 5.69
562 601 5.766174 AGACTAAACTTAATTTCACCCGCAA 59.234 36.000 0.00 0.00 0.00 4.85
563 602 6.263617 AGACTAAACTTAATTTCACCCGCAAA 59.736 34.615 0.00 0.00 0.00 3.68
564 603 6.807789 ACTAAACTTAATTTCACCCGCAAAA 58.192 32.000 0.00 0.00 0.00 2.44
565 604 7.266400 ACTAAACTTAATTTCACCCGCAAAAA 58.734 30.769 0.00 0.00 0.00 1.94
590 629 9.802039 AAAAGAGAGAGAGAGAGACTAAACTTA 57.198 33.333 0.00 0.00 0.00 2.24
637 676 5.684550 AGTGTTTTTAAACGGTCAGGATC 57.315 39.130 1.35 0.00 41.74 3.36
650 689 3.209410 GTCAGGATCGCATCTTTGGAAT 58.791 45.455 0.00 0.00 0.00 3.01
652 691 3.118298 TCAGGATCGCATCTTTGGAATCA 60.118 43.478 0.00 0.00 0.00 2.57
711 750 2.159421 TCGCGAGGTTACTTCTCATCAC 60.159 50.000 3.71 0.00 0.00 3.06
718 757 2.921754 GTTACTTCTCATCACCGTTCGG 59.078 50.000 9.81 9.81 0.00 4.30
732 771 3.919973 TTCGGGCAAGCGGACGTAC 62.920 63.158 0.00 0.00 0.00 3.67
778 817 2.269241 GGGCTCTCCGGAAACCAG 59.731 66.667 16.55 7.10 0.00 4.00
810 849 2.094659 GTGATCAGTGACCGCACCG 61.095 63.158 0.00 0.00 46.32 4.94
811 850 3.188786 GATCAGTGACCGCACCGC 61.189 66.667 0.00 0.00 46.32 5.68
812 851 3.932580 GATCAGTGACCGCACCGCA 62.933 63.158 0.00 0.00 46.32 5.69
813 852 4.961511 TCAGTGACCGCACCGCAC 62.962 66.667 0.00 0.00 46.32 5.34
834 873 3.064958 ACCTCTCGTACATATGTCGTGTG 59.935 47.826 12.68 15.11 0.00 3.82
835 874 3.036633 CTCTCGTACATATGTCGTGTGC 58.963 50.000 12.68 0.00 0.00 4.57
857 896 2.044860 CGCCGTTCATCTCGATAAGAC 58.955 52.381 0.00 0.00 36.65 3.01
859 898 2.862921 GCCGTTCATCTCGATAAGACCC 60.863 54.545 0.00 0.00 36.65 4.46
902 941 2.355756 CCGGCAGATTTGTTACATCTGG 59.644 50.000 15.16 2.90 45.45 3.86
943 982 1.059369 CTCGCACGCTGCAACATAC 59.941 57.895 0.00 0.00 45.36 2.39
944 983 1.354337 CTCGCACGCTGCAACATACT 61.354 55.000 0.00 0.00 45.36 2.12
945 984 0.109039 TCGCACGCTGCAACATACTA 60.109 50.000 0.00 0.00 45.36 1.82
963 1002 4.154347 GCTGCCTCCACTCCTCCG 62.154 72.222 0.00 0.00 0.00 4.63
1104 1166 0.905337 CGGGGAAGGAGAGGAACACT 60.905 60.000 0.00 0.00 0.00 3.55
1584 1646 4.073200 GGGTACACCGTCCCCGTG 62.073 72.222 0.00 0.00 37.89 4.94
2459 2548 3.499737 CCACTCCGTTGCCATCGC 61.500 66.667 0.00 0.00 0.00 4.58
2523 2616 7.647907 ACCGTATGTATAATTCGATTTGGAC 57.352 36.000 2.86 2.00 0.00 4.02
2585 2680 2.572191 ATTGATTGAAGTGCCATGCG 57.428 45.000 0.00 0.00 0.00 4.73
2586 2681 0.109179 TTGATTGAAGTGCCATGCGC 60.109 50.000 0.00 0.00 39.59 6.09
2685 2787 1.731720 GTCGAGACCACGTACCTAGT 58.268 55.000 0.00 0.00 34.70 2.57
2731 2839 1.428448 CGAAAACAGACGAGCCATGA 58.572 50.000 0.00 0.00 0.00 3.07
2732 2840 1.391485 CGAAAACAGACGAGCCATGAG 59.609 52.381 0.00 0.00 0.00 2.90
2770 2878 3.195825 ACCCCATTCTCTTCTCGTACTTG 59.804 47.826 0.00 0.00 0.00 3.16
2808 2918 6.149474 CGGATGGGTATGAATGAAGATAAACC 59.851 42.308 0.00 0.00 0.00 3.27
2819 2929 5.880164 TGAAGATAAACCGGGATGACATA 57.120 39.130 6.32 0.00 0.00 2.29
2988 3098 7.790823 AAAATGGTTCTATTGCATTAATGGC 57.209 32.000 17.02 9.73 0.00 4.40
2990 3100 3.640967 TGGTTCTATTGCATTAATGGCCC 59.359 43.478 17.02 1.36 0.00 5.80
2993 3103 5.538433 GGTTCTATTGCATTAATGGCCCTAA 59.462 40.000 17.02 0.00 0.00 2.69
3010 3120 4.084171 GCCCTAAGTTTTACGTGACACTTC 60.084 45.833 14.29 0.00 31.83 3.01
3011 3121 4.450080 CCCTAAGTTTTACGTGACACTTCC 59.550 45.833 14.29 0.00 31.83 3.46
3013 3123 3.832615 AGTTTTACGTGACACTTCCCT 57.167 42.857 0.00 0.00 0.00 4.20
3014 3124 3.725490 AGTTTTACGTGACACTTCCCTC 58.275 45.455 0.00 0.00 0.00 4.30
3015 3125 2.427232 TTTACGTGACACTTCCCTCG 57.573 50.000 0.00 0.00 0.00 4.63
3016 3126 0.038892 TTACGTGACACTTCCCTCGC 60.039 55.000 0.00 0.00 0.00 5.03
3344 3657 3.914860 AGTCCCTCCTTCCTTCCAA 57.085 52.632 0.00 0.00 0.00 3.53
3345 3658 1.363246 AGTCCCTCCTTCCTTCCAAC 58.637 55.000 0.00 0.00 0.00 3.77
3346 3659 1.132365 AGTCCCTCCTTCCTTCCAACT 60.132 52.381 0.00 0.00 0.00 3.16
3347 3660 1.003696 GTCCCTCCTTCCTTCCAACTG 59.996 57.143 0.00 0.00 0.00 3.16
3348 3661 0.322906 CCCTCCTTCCTTCCAACTGC 60.323 60.000 0.00 0.00 0.00 4.40
3349 3662 0.322906 CCTCCTTCCTTCCAACTGCC 60.323 60.000 0.00 0.00 0.00 4.85
3351 3664 1.073199 CCTTCCTTCCAACTGCCGT 59.927 57.895 0.00 0.00 0.00 5.68
3353 3666 0.250295 CTTCCTTCCAACTGCCGTCA 60.250 55.000 0.00 0.00 0.00 4.35
3366 3679 1.205064 CCGTCAGCAAAAGCTCGTG 59.795 57.895 0.00 0.00 0.00 4.35
3367 3680 1.439365 CGTCAGCAAAAGCTCGTGC 60.439 57.895 12.51 12.51 41.22 5.34
3370 3683 2.591715 AGCAAAAGCTCGTGCGGT 60.592 55.556 14.06 0.00 45.62 5.68
3371 3684 2.127232 GCAAAAGCTCGTGCGGTC 60.127 61.111 3.48 0.00 45.42 4.79
3372 3685 2.170985 CAAAAGCTCGTGCGGTCG 59.829 61.111 3.48 0.00 45.42 4.79
3373 3686 3.041940 AAAAGCTCGTGCGGTCGG 61.042 61.111 3.48 0.00 45.42 4.79
3393 3706 4.803426 GCCCTCGTCAGCGTCTGG 62.803 72.222 6.95 0.00 39.49 3.86
3394 3707 3.374402 CCCTCGTCAGCGTCTGGT 61.374 66.667 6.95 0.00 39.49 4.00
3395 3708 2.651361 CCTCGTCAGCGTCTGGTT 59.349 61.111 6.95 0.00 39.49 3.67
3397 3710 1.009389 CCTCGTCAGCGTCTGGTTTC 61.009 60.000 6.95 0.00 39.49 2.78
3398 3711 0.039074 CTCGTCAGCGTCTGGTTTCT 60.039 55.000 6.95 0.00 39.49 2.52
3399 3712 0.039437 TCGTCAGCGTCTGGTTTCTC 60.039 55.000 6.95 0.00 39.49 2.87
3400 3713 1.009389 CGTCAGCGTCTGGTTTCTCC 61.009 60.000 6.95 0.00 31.51 3.71
3401 3714 0.670854 GTCAGCGTCTGGTTTCTCCC 60.671 60.000 6.95 0.00 34.77 4.30
3402 3715 1.738099 CAGCGTCTGGTTTCTCCCG 60.738 63.158 0.00 0.00 34.77 5.14
3403 3716 3.119096 GCGTCTGGTTTCTCCCGC 61.119 66.667 0.00 0.00 37.27 6.13
3404 3717 2.809601 CGTCTGGTTTCTCCCGCG 60.810 66.667 0.00 0.00 34.77 6.46
3406 3719 1.005394 GTCTGGTTTCTCCCGCGAA 60.005 57.895 8.23 0.00 34.77 4.70
3407 3720 1.005394 TCTGGTTTCTCCCGCGAAC 60.005 57.895 8.23 2.80 34.77 3.95
3409 3722 0.673644 CTGGTTTCTCCCGCGAACAT 60.674 55.000 8.23 0.00 34.77 2.71
3410 3723 0.953471 TGGTTTCTCCCGCGAACATG 60.953 55.000 8.23 0.00 34.77 3.21
3411 3724 0.953960 GGTTTCTCCCGCGAACATGT 60.954 55.000 8.23 0.00 0.00 3.21
3413 3726 0.953471 TTTCTCCCGCGAACATGTGG 60.953 55.000 8.23 0.00 39.29 4.17
3417 3730 4.287580 CCGCGAACATGTGGGTAA 57.712 55.556 8.23 0.00 35.83 2.85
3418 3731 2.775351 CCGCGAACATGTGGGTAAT 58.225 52.632 8.23 0.00 35.83 1.89
3419 3732 1.942677 CCGCGAACATGTGGGTAATA 58.057 50.000 8.23 0.00 35.83 0.98
3420 3733 1.864711 CCGCGAACATGTGGGTAATAG 59.135 52.381 8.23 0.00 35.83 1.73
3421 3734 1.864711 CGCGAACATGTGGGTAATAGG 59.135 52.381 0.00 0.00 0.00 2.57
3423 3736 2.420967 GCGAACATGTGGGTAATAGGGT 60.421 50.000 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.037447 AAGCTGAGAGAAGTTGGGGC 59.963 55.000 0.00 0.00 0.00 5.80
20 21 0.179163 GAAAGGGCCATCTTTTCGCG 60.179 55.000 6.18 0.00 37.13 5.87
21 22 0.173481 GGAAAGGGCCATCTTTTCGC 59.827 55.000 6.18 0.00 37.13 4.70
23 24 2.807676 TCTGGAAAGGGCCATCTTTTC 58.192 47.619 6.18 6.88 37.13 2.29
24 25 2.999185 TCTGGAAAGGGCCATCTTTT 57.001 45.000 6.18 0.00 37.13 2.27
25 26 4.821532 ATATCTGGAAAGGGCCATCTTT 57.178 40.909 6.18 5.79 39.41 2.52
28 29 5.012893 CCTAAATATCTGGAAAGGGCCATC 58.987 45.833 6.18 3.11 37.30 3.51
38 39 1.347707 CTGCCCGCCTAAATATCTGGA 59.652 52.381 0.00 0.00 0.00 3.86
42 43 3.303791 CGTTTTCTGCCCGCCTAAATATC 60.304 47.826 0.00 0.00 0.00 1.63
43 44 2.616842 CGTTTTCTGCCCGCCTAAATAT 59.383 45.455 0.00 0.00 0.00 1.28
64 65 0.888619 GCACCCTAAACTTTCAGGCC 59.111 55.000 0.00 0.00 0.00 5.19
76 77 3.138798 GACGAGGCTCGCACCCTA 61.139 66.667 34.76 0.00 45.12 3.53
122 123 3.041940 GTGGTTCGGCGAGTGGTG 61.042 66.667 10.46 0.00 0.00 4.17
123 124 4.309950 GGTGGTTCGGCGAGTGGT 62.310 66.667 10.46 0.00 0.00 4.16
131 132 1.876714 CGTATCAGCGGTGGTTCGG 60.877 63.158 17.65 1.17 0.00 4.30
154 160 4.269523 TGAGTGGTGGTGCAGGGC 62.270 66.667 0.00 0.00 0.00 5.19
171 177 2.933287 TTGGGGAGGCACGATGGT 60.933 61.111 0.00 0.00 0.00 3.55
198 204 3.241530 AGTGACAGGGGCGAGCAA 61.242 61.111 0.00 0.00 0.00 3.91
231 237 8.600449 TTTCCTTTAAACAAGCATACAAATGG 57.400 30.769 0.00 0.00 33.38 3.16
270 278 4.442375 TTCTCAGTTCCGCTCTCTAAAG 57.558 45.455 0.00 0.00 0.00 1.85
279 287 2.413453 CAGCTACTTTTCTCAGTTCCGC 59.587 50.000 0.00 0.00 0.00 5.54
280 288 3.430218 CACAGCTACTTTTCTCAGTTCCG 59.570 47.826 0.00 0.00 0.00 4.30
290 298 6.651225 GGATAAGTTGTCTCACAGCTACTTTT 59.349 38.462 0.00 0.00 38.76 2.27
298 306 9.653287 TGTAATTTAGGATAAGTTGTCTCACAG 57.347 33.333 0.00 0.00 0.00 3.66
309 317 7.214381 TGGATGTCCGTGTAATTTAGGATAAG 58.786 38.462 0.00 0.00 39.43 1.73
313 321 4.468510 ACTGGATGTCCGTGTAATTTAGGA 59.531 41.667 0.00 0.00 39.43 2.94
323 331 2.410730 GTCGTTTTACTGGATGTCCGTG 59.589 50.000 6.75 0.17 39.43 4.94
325 333 2.679450 TGTCGTTTTACTGGATGTCCG 58.321 47.619 0.00 0.00 39.43 4.79
334 342 4.143263 CCTTCGCGTAAATGTCGTTTTACT 60.143 41.667 5.77 0.00 39.06 2.24
339 347 1.073177 CCCTTCGCGTAAATGTCGTT 58.927 50.000 5.77 0.00 0.00 3.85
345 353 1.276989 TCTCCAACCCTTCGCGTAAAT 59.723 47.619 5.77 0.00 0.00 1.40
352 360 2.555199 CAATAGCTCTCCAACCCTTCG 58.445 52.381 0.00 0.00 0.00 3.79
353 361 2.505819 TCCAATAGCTCTCCAACCCTTC 59.494 50.000 0.00 0.00 0.00 3.46
399 409 8.553459 ACAGTTTGATACAGAGAACCAAATAG 57.447 34.615 0.00 0.00 0.00 1.73
400 410 8.918202 AACAGTTTGATACAGAGAACCAAATA 57.082 30.769 0.00 0.00 0.00 1.40
401 411 7.823745 AACAGTTTGATACAGAGAACCAAAT 57.176 32.000 0.00 0.00 0.00 2.32
402 412 7.639113 AAACAGTTTGATACAGAGAACCAAA 57.361 32.000 0.00 0.00 0.00 3.28
403 413 7.338196 TGAAAACAGTTTGATACAGAGAACCAA 59.662 33.333 0.00 0.00 0.00 3.67
404 414 6.826231 TGAAAACAGTTTGATACAGAGAACCA 59.174 34.615 0.00 0.00 0.00 3.67
405 415 7.012421 ACTGAAAACAGTTTGATACAGAGAACC 59.988 37.037 19.95 0.00 29.93 3.62
406 416 7.920738 ACTGAAAACAGTTTGATACAGAGAAC 58.079 34.615 19.95 0.00 29.93 3.01
413 423 7.693952 TGTTCAGACTGAAAACAGTTTGATAC 58.306 34.615 19.32 18.15 43.02 2.24
432 442 3.768757 TGGATTTTTGGCCCTATGTTCAG 59.231 43.478 0.00 0.00 0.00 3.02
443 453 4.624336 AAAAACCGTTTGGATTTTTGGC 57.376 36.364 0.00 0.00 44.96 4.52
475 485 8.933807 CATCTATTGTATTATTCACCTGCAGAG 58.066 37.037 17.39 8.04 0.00 3.35
476 486 8.650490 TCATCTATTGTATTATTCACCTGCAGA 58.350 33.333 17.39 0.00 0.00 4.26
477 487 8.837788 TCATCTATTGTATTATTCACCTGCAG 57.162 34.615 6.78 6.78 0.00 4.41
478 488 7.388776 GCTCATCTATTGTATTATTCACCTGCA 59.611 37.037 0.00 0.00 0.00 4.41
479 489 7.148340 GGCTCATCTATTGTATTATTCACCTGC 60.148 40.741 0.00 0.00 0.00 4.85
480 490 7.063898 CGGCTCATCTATTGTATTATTCACCTG 59.936 40.741 0.00 0.00 0.00 4.00
481 491 7.039011 TCGGCTCATCTATTGTATTATTCACCT 60.039 37.037 0.00 0.00 0.00 4.00
493 503 2.389059 CGAGTGTCGGCTCATCTATTG 58.611 52.381 0.00 0.00 36.00 1.90
494 504 1.269309 GCGAGTGTCGGCTCATCTATT 60.269 52.381 0.00 0.00 40.84 1.73
496 506 1.029947 TGCGAGTGTCGGCTCATCTA 61.030 55.000 0.00 0.00 40.84 1.98
532 571 7.063191 GGGTGAAATTAAGTTTAGTCTCTCGAC 59.937 40.741 0.00 0.00 40.54 4.20
537 576 5.410439 TGCGGGTGAAATTAAGTTTAGTCTC 59.590 40.000 0.00 0.00 0.00 3.36
538 577 5.310451 TGCGGGTGAAATTAAGTTTAGTCT 58.690 37.500 0.00 0.00 0.00 3.24
539 578 5.616488 TGCGGGTGAAATTAAGTTTAGTC 57.384 39.130 0.00 0.00 0.00 2.59
540 579 6.394025 TTTGCGGGTGAAATTAAGTTTAGT 57.606 33.333 0.00 0.00 0.00 2.24
541 580 7.701809 TTTTTGCGGGTGAAATTAAGTTTAG 57.298 32.000 0.00 0.00 0.00 1.85
563 602 8.706322 AGTTTAGTCTCTCTCTCTCTCTTTTT 57.294 34.615 0.00 0.00 0.00 1.94
564 603 8.706322 AAGTTTAGTCTCTCTCTCTCTCTTTT 57.294 34.615 0.00 0.00 0.00 2.27
565 604 9.802039 TTAAGTTTAGTCTCTCTCTCTCTCTTT 57.198 33.333 0.00 0.00 0.00 2.52
566 605 9.975218 ATTAAGTTTAGTCTCTCTCTCTCTCTT 57.025 33.333 0.00 0.00 0.00 2.85
567 606 9.975218 AATTAAGTTTAGTCTCTCTCTCTCTCT 57.025 33.333 0.00 0.00 0.00 3.10
582 621 7.120726 CCCCCGCCATATTCTAATTAAGTTTAG 59.879 40.741 0.00 0.00 0.00 1.85
586 625 4.600111 TCCCCCGCCATATTCTAATTAAGT 59.400 41.667 0.00 0.00 0.00 2.24
590 629 3.397955 ACTTCCCCCGCCATATTCTAATT 59.602 43.478 0.00 0.00 0.00 1.40
599 638 2.231380 ACTTCACTTCCCCCGCCAT 61.231 57.895 0.00 0.00 0.00 4.40
637 676 3.130633 TCCGTATGATTCCAAAGATGCG 58.869 45.455 0.00 0.00 0.00 4.73
650 689 2.285083 CCCGCAATTTTCTCCGTATGA 58.715 47.619 0.00 0.00 0.00 2.15
652 691 1.675552 CCCCGCAATTTTCTCCGTAT 58.324 50.000 0.00 0.00 0.00 3.06
697 736 2.921754 CCGAACGGTGATGAGAAGTAAC 59.078 50.000 4.99 0.00 0.00 2.50
718 757 0.101759 TCATAGTACGTCCGCTTGCC 59.898 55.000 0.00 0.00 0.00 4.52
732 771 5.043903 ACAACCTCGATCGACAATTCATAG 58.956 41.667 15.15 0.64 0.00 2.23
777 816 2.496070 TGATCACGTAAGCTACTTGGCT 59.504 45.455 0.00 0.00 45.30 4.75
778 817 2.860735 CTGATCACGTAAGCTACTTGGC 59.139 50.000 0.00 0.00 45.62 4.52
810 849 2.033049 ACGACATATGTACGAGAGGTGC 59.967 50.000 24.62 4.77 0.00 5.01
811 850 3.064958 ACACGACATATGTACGAGAGGTG 59.935 47.826 24.62 17.63 0.00 4.00
812 851 3.064958 CACACGACATATGTACGAGAGGT 59.935 47.826 24.62 16.56 0.00 3.85
813 852 3.618698 CACACGACATATGTACGAGAGG 58.381 50.000 24.62 16.15 0.00 3.69
814 853 3.036633 GCACACGACATATGTACGAGAG 58.963 50.000 24.62 18.61 0.00 3.20
835 874 0.933047 TTATCGAGATGAACGGCGCG 60.933 55.000 6.90 0.00 0.00 6.86
857 896 1.218316 GCGTGAGGACCTAAGTGGG 59.782 63.158 0.00 0.00 41.11 4.61
859 898 0.888619 TGAGCGTGAGGACCTAAGTG 59.111 55.000 0.00 0.00 0.00 3.16
943 982 1.398958 GGAGGAGTGGAGGCAGCTAG 61.399 65.000 0.00 0.00 0.00 3.42
944 983 1.381872 GGAGGAGTGGAGGCAGCTA 60.382 63.158 0.00 0.00 0.00 3.32
945 984 2.686835 GGAGGAGTGGAGGCAGCT 60.687 66.667 0.00 0.00 0.00 4.24
1104 1166 1.216977 CCCCTTGACGTGCGTGATA 59.783 57.895 0.67 0.00 0.00 2.15
1690 1770 2.124151 GCCGTGCATGAAGGGGAT 60.124 61.111 14.40 0.00 0.00 3.85
1806 1886 2.263741 GGCCATGGTGATCGCCATC 61.264 63.158 33.23 23.75 45.47 3.51
2292 2381 1.513586 GGCGTACTCCGTCGTGAAG 60.514 63.158 0.00 0.00 39.32 3.02
2441 2530 2.047274 CGATGGCAACGGAGTGGT 60.047 61.111 9.50 0.00 45.00 4.16
2459 2548 5.519566 CGTAGGCAGTATATAGTACTCCGAG 59.480 48.000 0.00 0.00 0.00 4.63
2501 2594 7.148639 CCTGGTCCAAATCGAATTATACATACG 60.149 40.741 0.00 0.00 0.00 3.06
2523 2616 0.254178 ATGTGAACAGCTAGCCCTGG 59.746 55.000 12.13 1.14 37.16 4.45
2586 2681 4.056125 TCCTCTCGTGCGCTGGTG 62.056 66.667 9.73 1.18 0.00 4.17
2587 2682 4.057428 GTCCTCTCGTGCGCTGGT 62.057 66.667 9.73 0.00 0.00 4.00
2589 2684 3.610791 TTCGTCCTCTCGTGCGCTG 62.611 63.158 9.73 0.40 0.00 5.18
2590 2685 3.329688 CTTCGTCCTCTCGTGCGCT 62.330 63.158 9.73 0.00 0.00 5.92
2591 2686 2.876645 CTTCGTCCTCTCGTGCGC 60.877 66.667 0.00 0.00 0.00 6.09
2592 2687 1.512310 GTCTTCGTCCTCTCGTGCG 60.512 63.158 0.00 0.00 0.00 5.34
2593 2688 0.171455 ATGTCTTCGTCCTCTCGTGC 59.829 55.000 0.00 0.00 0.00 5.34
2677 2779 6.916387 TGTATGTAGACGTACGTACTAGGTAC 59.084 42.308 22.87 22.59 45.98 3.34
2678 2780 7.034685 TGTATGTAGACGTACGTACTAGGTA 57.965 40.000 22.87 14.80 45.98 3.08
2680 2782 5.980116 ACTGTATGTAGACGTACGTACTAGG 59.020 44.000 22.87 10.45 45.98 3.02
2685 2787 5.410924 ACTGACTGTATGTAGACGTACGTA 58.589 41.667 22.87 5.89 40.34 3.57
2696 2804 5.294356 TGTTTTCGCTAACTGACTGTATGT 58.706 37.500 0.00 0.00 0.00 2.29
2731 2839 1.270358 GGGTTGCTCACTCTTTCGTCT 60.270 52.381 0.00 0.00 0.00 4.18
2732 2840 1.149148 GGGTTGCTCACTCTTTCGTC 58.851 55.000 0.00 0.00 0.00 4.20
2785 2893 6.149474 CCGGTTTATCTTCATTCATACCCATC 59.851 42.308 0.00 0.00 0.00 3.51
2808 2918 5.077134 TCATAATCTGCTATGTCATCCCG 57.923 43.478 0.00 0.00 32.15 5.14
2819 2929 3.286329 TGCACACCATCATAATCTGCT 57.714 42.857 0.00 0.00 0.00 4.24
2903 3013 1.806542 GCTCGCTTCAGTTGAATCCAA 59.193 47.619 0.00 0.00 33.01 3.53
2918 3028 5.343249 ACATATCCTGAAAATTTTGCTCGC 58.657 37.500 8.47 0.00 0.00 5.03
2982 3092 4.937015 GTCACGTAAAACTTAGGGCCATTA 59.063 41.667 6.18 0.00 0.00 1.90
2988 3098 4.450080 GGAAGTGTCACGTAAAACTTAGGG 59.550 45.833 0.00 0.00 33.14 3.53
2990 3100 5.295152 AGGGAAGTGTCACGTAAAACTTAG 58.705 41.667 0.00 0.00 33.14 2.18
2993 3103 3.725490 GAGGGAAGTGTCACGTAAAACT 58.275 45.455 0.00 0.00 29.76 2.66
3327 3640 1.003696 CAGTTGGAAGGAAGGAGGGAC 59.996 57.143 0.00 0.00 0.00 4.46
3328 3641 1.362224 CAGTTGGAAGGAAGGAGGGA 58.638 55.000 0.00 0.00 0.00 4.20
3329 3642 0.322906 GCAGTTGGAAGGAAGGAGGG 60.323 60.000 0.00 0.00 0.00 4.30
3330 3643 0.322906 GGCAGTTGGAAGGAAGGAGG 60.323 60.000 0.00 0.00 0.00 4.30
3331 3644 0.674895 CGGCAGTTGGAAGGAAGGAG 60.675 60.000 0.00 0.00 0.00 3.69
3332 3645 1.374947 CGGCAGTTGGAAGGAAGGA 59.625 57.895 0.00 0.00 0.00 3.36
3334 3647 0.250295 TGACGGCAGTTGGAAGGAAG 60.250 55.000 0.00 0.00 0.00 3.46
3335 3648 0.250295 CTGACGGCAGTTGGAAGGAA 60.250 55.000 11.12 0.00 37.37 3.36
3336 3649 1.371183 CTGACGGCAGTTGGAAGGA 59.629 57.895 11.12 0.00 37.37 3.36
3337 3650 2.328099 GCTGACGGCAGTTGGAAGG 61.328 63.158 21.75 0.00 44.17 3.46
3375 3688 4.803426 CAGACGCTGACGAGGGCC 62.803 72.222 0.00 0.00 43.93 5.80
3376 3689 4.803426 CCAGACGCTGACGAGGGC 62.803 72.222 8.20 0.00 43.93 5.19
3377 3690 2.436087 AAACCAGACGCTGACGAGGG 62.436 60.000 8.20 0.00 43.93 4.30
3378 3691 1.006102 AAACCAGACGCTGACGAGG 60.006 57.895 8.20 0.00 43.93 4.63
3379 3692 0.039074 AGAAACCAGACGCTGACGAG 60.039 55.000 8.20 0.00 43.93 4.18
3380 3693 0.039437 GAGAAACCAGACGCTGACGA 60.039 55.000 8.20 0.00 43.93 4.20
3381 3694 1.009389 GGAGAAACCAGACGCTGACG 61.009 60.000 8.20 0.00 41.34 4.35
3382 3695 0.670854 GGGAGAAACCAGACGCTGAC 60.671 60.000 8.20 0.00 41.20 3.51
3383 3696 1.671742 GGGAGAAACCAGACGCTGA 59.328 57.895 8.20 0.00 41.20 4.26
3384 3697 1.738099 CGGGAGAAACCAGACGCTG 60.738 63.158 0.52 0.52 41.20 5.18
3385 3698 2.657237 CGGGAGAAACCAGACGCT 59.343 61.111 0.00 0.00 41.20 5.07
3386 3699 3.119096 GCGGGAGAAACCAGACGC 61.119 66.667 0.00 0.00 41.20 5.19
3388 3701 1.005394 TTCGCGGGAGAAACCAGAC 60.005 57.895 6.13 0.00 41.20 3.51
3390 3703 0.673644 ATGTTCGCGGGAGAAACCAG 60.674 55.000 6.13 0.00 41.20 4.00
3391 3704 0.953471 CATGTTCGCGGGAGAAACCA 60.953 55.000 6.13 0.00 41.20 3.67
3393 3706 0.165944 CACATGTTCGCGGGAGAAAC 59.834 55.000 6.13 3.06 0.00 2.78
3394 3707 0.953471 CCACATGTTCGCGGGAGAAA 60.953 55.000 6.13 0.00 0.00 2.52
3395 3708 1.375396 CCACATGTTCGCGGGAGAA 60.375 57.895 6.13 0.00 0.00 2.87
3397 3710 2.233605 TACCCACATGTTCGCGGGAG 62.234 60.000 22.47 6.15 41.62 4.30
3398 3711 1.828461 TTACCCACATGTTCGCGGGA 61.828 55.000 22.47 0.00 41.62 5.14
3399 3712 0.746563 ATTACCCACATGTTCGCGGG 60.747 55.000 15.72 15.72 44.88 6.13
3400 3713 1.864711 CTATTACCCACATGTTCGCGG 59.135 52.381 6.13 0.00 0.00 6.46
3401 3714 1.864711 CCTATTACCCACATGTTCGCG 59.135 52.381 0.00 0.00 0.00 5.87
3402 3715 2.218603 CCCTATTACCCACATGTTCGC 58.781 52.381 0.00 0.00 0.00 4.70
3403 3716 3.553828 ACCCTATTACCCACATGTTCG 57.446 47.619 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.