Multiple sequence alignment - TraesCS3A01G122700

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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 TraesCS3A01G122700 chr3A 100.000 2525 0 0 1 2525 98508555 98506031 0.000000e+00 4663.0
1 TraesCS3A01G122700 chr3A 92.494 1652 86 8 806 2442 637963466 637965094 0.000000e+00 2329.0
2 TraesCS3A01G122700 chr3A 91.589 749 54 5 66 807 637962586 637963332 0.000000e+00 1026.0
3 TraesCS3A01G122700 chr3A 82.994 835 120 13 828 1644 11068290 11067460 0.000000e+00 736.0
4 TraesCS3A01G122700 chr3A 82.874 835 120 14 828 1644 11074498 11073669 0.000000e+00 728.0
5 TraesCS3A01G122700 chr3A 80.678 295 42 6 1648 1940 11067414 11067133 5.470000e-52 215.0
6 TraesCS3A01G122700 chr3A 96.629 89 3 0 2437 2525 637966823 637966911 5.630000e-32 148.0
7 TraesCS3A01G122700 chr2A 93.026 1735 83 7 806 2525 133573906 133572195 0.000000e+00 2499.0
8 TraesCS3A01G122700 chr2A 91.856 749 55 5 66 810 133574783 133574037 0.000000e+00 1040.0
9 TraesCS3A01G122700 chr1A 92.512 1736 92 4 806 2525 177479179 177480892 0.000000e+00 2451.0
10 TraesCS3A01G122700 chr1A 90.933 750 58 6 66 807 177477744 177478491 0.000000e+00 1000.0
11 TraesCS3A01G122700 chr7D 79.739 844 140 21 824 1644 574055939 574056774 1.300000e-162 582.0
12 TraesCS3A01G122700 chr7B 79.621 844 140 22 824 1644 415339536 415340370 6.060000e-161 577.0
13 TraesCS3A01G122700 chr7B 78.947 133 28 0 1894 2026 680669161 680669029 9.620000e-15 91.6
14 TraesCS3A01G122700 chr2D 79.584 818 134 18 849 1644 88606830 88607636 2.840000e-154 555.0
15 TraesCS3A01G122700 chr2D 79.462 818 138 17 849 1644 88690620 88691429 1.020000e-153 553.0
16 TraesCS3A01G122700 chr2D 86.270 488 42 7 1642 2125 485099549 485099083 8.060000e-140 507.0
17 TraesCS3A01G122700 chr3D 85.391 486 48 6 1642 2125 443312957 443313421 1.360000e-132 483.0
18 TraesCS3A01G122700 chr1D 88.889 387 41 2 1642 2026 126866011 126865625 2.270000e-130 475.0
19 TraesCS3A01G122700 chr1D 86.207 87 12 0 2039 2125 126865632 126865546 7.440000e-16 95.3
20 TraesCS3A01G122700 chr4B 84.633 436 44 6 1691 2125 377156396 377155983 1.810000e-111 412.0
21 TraesCS3A01G122700 chr4D 81.614 223 36 4 1806 2026 278185657 278185438 2.000000e-41 180.0


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 TraesCS3A01G122700 chr3A 98506031 98508555 2524 True 4663.000000 4663 100.000000 1 2525 1 chr3A.!!$R2 2524
1 TraesCS3A01G122700 chr3A 637962586 637966911 4325 False 1167.666667 2329 93.570667 66 2525 3 chr3A.!!$F1 2459
2 TraesCS3A01G122700 chr3A 11073669 11074498 829 True 728.000000 728 82.874000 828 1644 1 chr3A.!!$R1 816
3 TraesCS3A01G122700 chr3A 11067133 11068290 1157 True 475.500000 736 81.836000 828 1940 2 chr3A.!!$R3 1112
4 TraesCS3A01G122700 chr2A 133572195 133574783 2588 True 1769.500000 2499 92.441000 66 2525 2 chr2A.!!$R1 2459
5 TraesCS3A01G122700 chr1A 177477744 177480892 3148 False 1725.500000 2451 91.722500 66 2525 2 chr1A.!!$F1 2459
6 TraesCS3A01G122700 chr7D 574055939 574056774 835 False 582.000000 582 79.739000 824 1644 1 chr7D.!!$F1 820
7 TraesCS3A01G122700 chr7B 415339536 415340370 834 False 577.000000 577 79.621000 824 1644 1 chr7B.!!$F1 820
8 TraesCS3A01G122700 chr2D 88606830 88607636 806 False 555.000000 555 79.584000 849 1644 1 chr2D.!!$F1 795
9 TraesCS3A01G122700 chr2D 88690620 88691429 809 False 553.000000 553 79.462000 849 1644 1 chr2D.!!$F2 795

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
778 790 0.104855 TTCTTCAGCGTGTGACTGCT 59.895 50.0 0.0 0.0 43.58 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2916 0.393537 CCGCTTGCTCCTTGGATTCT 60.394 55.0 0.0 0.0 0.0 2.4 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
17 18 4.513519 CGGTTTAGGCGCTCATGA 57.486 55.556 7.64 0.00 0.00 3.07
18 19 2.301505 CGGTTTAGGCGCTCATGAG 58.698 57.895 18.84 18.84 0.00 2.90
32 33 4.991153 CTCATGAGCCTACTACTGTTGA 57.009 45.455 10.38 0.00 0.00 3.18
33 34 5.330455 CTCATGAGCCTACTACTGTTGAA 57.670 43.478 10.38 0.00 0.00 2.69
34 35 5.724328 CTCATGAGCCTACTACTGTTGAAA 58.276 41.667 10.38 0.00 0.00 2.69
35 36 6.109156 TCATGAGCCTACTACTGTTGAAAA 57.891 37.500 0.00 0.00 0.00 2.29
36 37 6.711277 TCATGAGCCTACTACTGTTGAAAAT 58.289 36.000 0.00 0.00 0.00 1.82
37 38 6.595326 TCATGAGCCTACTACTGTTGAAAATG 59.405 38.462 0.00 0.00 0.00 2.32
38 39 4.695455 TGAGCCTACTACTGTTGAAAATGC 59.305 41.667 0.00 0.00 0.00 3.56
39 40 4.010349 AGCCTACTACTGTTGAAAATGCC 58.990 43.478 0.00 0.00 0.00 4.40
40 41 3.128764 GCCTACTACTGTTGAAAATGCCC 59.871 47.826 0.00 0.00 0.00 5.36
41 42 4.331968 CCTACTACTGTTGAAAATGCCCA 58.668 43.478 0.00 0.00 0.00 5.36
42 43 4.764823 CCTACTACTGTTGAAAATGCCCAA 59.235 41.667 0.00 0.00 0.00 4.12
43 44 5.242838 CCTACTACTGTTGAAAATGCCCAAA 59.757 40.000 0.00 0.00 0.00 3.28
44 45 5.806654 ACTACTGTTGAAAATGCCCAAAT 57.193 34.783 0.00 0.00 0.00 2.32
45 46 6.909550 ACTACTGTTGAAAATGCCCAAATA 57.090 33.333 0.00 0.00 0.00 1.40
46 47 7.296628 ACTACTGTTGAAAATGCCCAAATAA 57.703 32.000 0.00 0.00 0.00 1.40
47 48 7.731054 ACTACTGTTGAAAATGCCCAAATAAA 58.269 30.769 0.00 0.00 0.00 1.40
48 49 8.374743 ACTACTGTTGAAAATGCCCAAATAAAT 58.625 29.630 0.00 0.00 0.00 1.40
49 50 9.218440 CTACTGTTGAAAATGCCCAAATAAATT 57.782 29.630 0.00 0.00 0.00 1.82
50 51 7.873910 ACTGTTGAAAATGCCCAAATAAATTG 58.126 30.769 0.00 0.00 38.84 2.32
51 52 7.501892 ACTGTTGAAAATGCCCAAATAAATTGT 59.498 29.630 0.00 0.00 37.32 2.71
52 53 8.908786 TGTTGAAAATGCCCAAATAAATTGTA 57.091 26.923 0.00 0.00 37.32 2.41
53 54 8.778358 TGTTGAAAATGCCCAAATAAATTGTAC 58.222 29.630 0.00 0.00 37.32 2.90
54 55 7.913674 TGAAAATGCCCAAATAAATTGTACC 57.086 32.000 0.00 0.00 37.32 3.34
55 56 6.591834 TGAAAATGCCCAAATAAATTGTACCG 59.408 34.615 0.00 0.00 37.32 4.02
56 57 5.923733 AATGCCCAAATAAATTGTACCGA 57.076 34.783 0.00 0.00 37.32 4.69
57 58 4.705337 TGCCCAAATAAATTGTACCGAC 57.295 40.909 0.00 0.00 37.32 4.79
58 59 3.444388 TGCCCAAATAAATTGTACCGACC 59.556 43.478 0.00 0.00 37.32 4.79
59 60 3.181484 GCCCAAATAAATTGTACCGACCC 60.181 47.826 0.00 0.00 37.32 4.46
60 61 4.274978 CCCAAATAAATTGTACCGACCCT 58.725 43.478 0.00 0.00 37.32 4.34
61 62 5.438833 CCCAAATAAATTGTACCGACCCTA 58.561 41.667 0.00 0.00 37.32 3.53
62 63 5.297527 CCCAAATAAATTGTACCGACCCTAC 59.702 44.000 0.00 0.00 37.32 3.18
63 64 5.881443 CCAAATAAATTGTACCGACCCTACA 59.119 40.000 0.00 0.00 37.32 2.74
64 65 6.183360 CCAAATAAATTGTACCGACCCTACAC 60.183 42.308 0.00 0.00 37.32 2.90
71 72 2.260434 CGACCCTACACACACCCG 59.740 66.667 0.00 0.00 0.00 5.28
118 119 1.681264 GGCCCAGGTATGTGCAATTAC 59.319 52.381 0.00 0.00 30.39 1.89
133 134 5.121768 GTGCAATTACAATGGTAGTCTCGTT 59.878 40.000 0.00 0.00 0.00 3.85
138 139 7.598759 ATTACAATGGTAGTCTCGTTCCTAT 57.401 36.000 0.00 0.00 0.00 2.57
151 152 7.068839 AGTCTCGTTCCTATCACACTCATAAAT 59.931 37.037 0.00 0.00 0.00 1.40
206 207 5.049680 CGCAGGCTTAAGTAGAAGAAAACAA 60.050 40.000 4.02 0.00 0.00 2.83
277 281 4.278419 ACAAAGGAAAAAGATTCGGTGGAG 59.722 41.667 0.00 0.00 0.00 3.86
294 298 3.551915 GCCGTTCGCTACCGCTTC 61.552 66.667 0.00 0.00 0.00 3.86
310 314 2.611473 CGCTTCATATTCGGCTCCTCAT 60.611 50.000 0.00 0.00 0.00 2.90
328 332 4.752879 GGGCCACAAGCGTCGCTA 62.753 66.667 22.04 0.00 45.17 4.26
420 424 0.179081 GATGGCGGTAACTCTCACCC 60.179 60.000 0.00 0.00 31.96 4.61
509 521 1.751351 CACACTCTTCCTCATCGCCTA 59.249 52.381 0.00 0.00 0.00 3.93
520 532 3.689161 CCTCATCGCCTACTCAGATCTAG 59.311 52.174 0.00 0.00 0.00 2.43
588 600 1.089920 CTGCCAATTGACTCTTCCCG 58.910 55.000 7.12 0.00 0.00 5.14
594 606 0.246635 ATTGACTCTTCCCGACGGTG 59.753 55.000 13.94 4.52 0.00 4.94
621 633 1.064357 CCGCACCGTTGTGTTTTACTT 59.936 47.619 0.00 0.00 44.65 2.24
626 638 3.379057 CACCGTTGTGTTTTACTTCCCTT 59.621 43.478 0.00 0.00 37.72 3.95
641 653 3.939740 TCCCTTTGATCCCTTCTCATG 57.060 47.619 0.00 0.00 0.00 3.07
653 665 2.012673 CTTCTCATGCCTTTTCCCTCG 58.987 52.381 0.00 0.00 0.00 4.63
679 691 5.582665 GCTTGTTCTAGATCCACGATTTCTT 59.417 40.000 0.00 0.00 0.00 2.52
712 724 4.785453 CGCCCCTTCTCCCACTGC 62.785 72.222 0.00 0.00 0.00 4.40
714 726 2.673523 CCCCTTCTCCCACTGCTG 59.326 66.667 0.00 0.00 0.00 4.41
718 730 0.671781 CCTTCTCCCACTGCTGAACG 60.672 60.000 0.00 0.00 0.00 3.95
740 752 1.993370 CGTCTTTCTCGGCAGGTAAAG 59.007 52.381 5.80 5.80 0.00 1.85
778 790 0.104855 TTCTTCAGCGTGTGACTGCT 59.895 50.000 0.00 0.00 43.58 4.24
818 1526 6.860023 GCATGATGCACCTATAGAAAATTGAC 59.140 38.462 13.36 0.00 44.26 3.18
1124 1849 6.663523 ACCATTACCTTTTACCCAATCAAGAG 59.336 38.462 0.00 0.00 0.00 2.85
1155 1880 3.541632 GAGGTCACCTGTCAAAGTTTCA 58.458 45.455 0.00 0.00 31.76 2.69
1156 1881 3.945285 GAGGTCACCTGTCAAAGTTTCAA 59.055 43.478 0.00 0.00 31.76 2.69
1244 1969 0.179045 ATGGATGCTTACGAGGGTGC 60.179 55.000 0.00 0.00 0.00 5.01
1297 2022 2.817258 CGGACTGTGGAAAAGGCAAATA 59.183 45.455 0.00 0.00 20.01 1.40
1376 2103 1.954258 GCTGAAAGAGAGCCTTGGCAT 60.954 52.381 14.54 1.60 34.07 4.40
1389 2116 2.424956 CCTTGGCATAAACAAGCTCCTC 59.575 50.000 0.00 0.00 42.98 3.71
1522 2249 9.624373 AGCTCAATAATGTTCTTCTCAATGTAT 57.376 29.630 0.00 0.00 0.00 2.29
1590 2318 3.694072 TCAACCTTCAAGAAACTGGTGTG 59.306 43.478 0.00 0.00 0.00 3.82
1591 2319 3.366052 ACCTTCAAGAAACTGGTGTGT 57.634 42.857 0.00 0.00 0.00 3.72
1592 2320 4.497291 ACCTTCAAGAAACTGGTGTGTA 57.503 40.909 0.00 0.00 0.00 2.90
1615 2343 0.257039 CCTTATGGCCAGGAGCAGTT 59.743 55.000 13.05 0.00 46.50 3.16
1680 2452 3.935203 GCAGATCTTCGACAATGAAGGAA 59.065 43.478 0.00 0.00 44.38 3.36
1714 2486 8.002984 TGATTTATGTGTCGTACCTGAAGATA 57.997 34.615 0.00 0.00 0.00 1.98
1861 2633 3.528597 GGTTCTTCCGAAGCTATCTGT 57.471 47.619 3.00 0.00 42.75 3.41
1876 2648 7.308450 AGCTATCTGTTGAGCCTTAATGATA 57.692 36.000 0.00 0.00 39.65 2.15
1954 2726 6.043127 TCTCCATTATGCCAAATCTACTGCTA 59.957 38.462 0.00 0.00 0.00 3.49
2030 2802 9.881649 TCATATGTCTAATAGCATTCTTGGATC 57.118 33.333 1.90 0.00 0.00 3.36
2031 2803 9.887629 CATATGTCTAATAGCATTCTTGGATCT 57.112 33.333 0.00 0.00 0.00 2.75
2033 2805 7.609097 TGTCTAATAGCATTCTTGGATCTCT 57.391 36.000 0.00 0.00 0.00 3.10
2034 2806 8.712228 TGTCTAATAGCATTCTTGGATCTCTA 57.288 34.615 0.00 0.00 0.00 2.43
2035 2807 9.147732 TGTCTAATAGCATTCTTGGATCTCTAA 57.852 33.333 0.00 0.00 0.00 2.10
2040 2812 6.430962 AGCATTCTTGGATCTCTAATAGCA 57.569 37.500 0.00 0.00 0.00 3.49
2041 2813 7.018487 AGCATTCTTGGATCTCTAATAGCAT 57.982 36.000 0.00 0.00 0.00 3.79
2042 2814 7.460071 AGCATTCTTGGATCTCTAATAGCATT 58.540 34.615 0.00 0.00 0.00 3.56
2143 2916 2.700722 TATGCCACGTTATGCCTTCA 57.299 45.000 0.00 0.00 0.00 3.02
2152 2925 3.941483 ACGTTATGCCTTCAGAATCCAAG 59.059 43.478 0.00 0.00 0.00 3.61
2249 3022 5.025826 GTGGTTTATAATAACACACGCTGC 58.974 41.667 9.54 0.00 0.00 5.25
2258 3031 0.955428 ACACACGCTGCCACCTAATG 60.955 55.000 0.00 0.00 0.00 1.90
2308 3081 3.005554 AGATCTGCGAAAATCACACCAG 58.994 45.455 0.00 0.00 0.00 4.00
2313 3086 0.804989 CGAAAATCACACCAGAGCCC 59.195 55.000 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.766143 GCTCATGAGCGCCTAAACCG 61.766 60.000 30.64 0.00 45.29 4.44
1 2 2.017752 GCTCATGAGCGCCTAAACC 58.982 57.895 30.64 3.71 45.29 3.27
11 12 4.991153 TCAACAGTAGTAGGCTCATGAG 57.009 45.455 18.84 18.84 0.00 2.90
12 13 5.738619 TTTCAACAGTAGTAGGCTCATGA 57.261 39.130 0.00 0.00 0.00 3.07
13 14 6.676456 GCATTTTCAACAGTAGTAGGCTCATG 60.676 42.308 0.00 0.00 0.00 3.07
14 15 5.355350 GCATTTTCAACAGTAGTAGGCTCAT 59.645 40.000 0.00 0.00 0.00 2.90
15 16 4.695455 GCATTTTCAACAGTAGTAGGCTCA 59.305 41.667 0.00 0.00 0.00 4.26
16 17 4.095036 GGCATTTTCAACAGTAGTAGGCTC 59.905 45.833 0.00 0.00 0.00 4.70
17 18 4.010349 GGCATTTTCAACAGTAGTAGGCT 58.990 43.478 0.00 0.00 0.00 4.58
18 19 3.128764 GGGCATTTTCAACAGTAGTAGGC 59.871 47.826 0.00 0.00 0.00 3.93
19 20 4.331968 TGGGCATTTTCAACAGTAGTAGG 58.668 43.478 0.00 0.00 0.00 3.18
20 21 5.957842 TTGGGCATTTTCAACAGTAGTAG 57.042 39.130 0.00 0.00 0.00 2.57
21 22 6.909550 ATTTGGGCATTTTCAACAGTAGTA 57.090 33.333 0.00 0.00 0.00 1.82
22 23 5.806654 ATTTGGGCATTTTCAACAGTAGT 57.193 34.783 0.00 0.00 0.00 2.73
23 24 8.776376 ATTTATTTGGGCATTTTCAACAGTAG 57.224 30.769 0.00 0.00 0.00 2.57
24 25 8.997323 CAATTTATTTGGGCATTTTCAACAGTA 58.003 29.630 0.00 0.00 0.00 2.74
25 26 7.501892 ACAATTTATTTGGGCATTTTCAACAGT 59.498 29.630 0.00 0.00 39.80 3.55
26 27 7.873910 ACAATTTATTTGGGCATTTTCAACAG 58.126 30.769 0.00 0.00 39.80 3.16
27 28 7.814264 ACAATTTATTTGGGCATTTTCAACA 57.186 28.000 0.00 0.00 39.80 3.33
28 29 8.233868 GGTACAATTTATTTGGGCATTTTCAAC 58.766 33.333 0.00 0.00 39.80 3.18
29 30 7.118390 CGGTACAATTTATTTGGGCATTTTCAA 59.882 33.333 0.00 0.00 39.80 2.69
30 31 6.591834 CGGTACAATTTATTTGGGCATTTTCA 59.408 34.615 0.00 0.00 39.80 2.69
31 32 6.814146 TCGGTACAATTTATTTGGGCATTTTC 59.186 34.615 0.00 0.00 39.80 2.29
32 33 6.592220 GTCGGTACAATTTATTTGGGCATTTT 59.408 34.615 0.00 0.00 39.80 1.82
33 34 6.103330 GTCGGTACAATTTATTTGGGCATTT 58.897 36.000 0.00 0.00 39.80 2.32
34 35 5.394773 GGTCGGTACAATTTATTTGGGCATT 60.395 40.000 0.00 0.00 39.80 3.56
35 36 4.098807 GGTCGGTACAATTTATTTGGGCAT 59.901 41.667 0.00 0.00 39.80 4.40
36 37 3.444388 GGTCGGTACAATTTATTTGGGCA 59.556 43.478 0.00 0.00 39.80 5.36
37 38 3.181484 GGGTCGGTACAATTTATTTGGGC 60.181 47.826 0.00 0.00 39.80 5.36
38 39 4.274978 AGGGTCGGTACAATTTATTTGGG 58.725 43.478 0.00 0.00 39.80 4.12
39 40 5.881443 TGTAGGGTCGGTACAATTTATTTGG 59.119 40.000 0.00 0.00 39.80 3.28
40 41 6.372103 TGTGTAGGGTCGGTACAATTTATTTG 59.628 38.462 0.00 0.00 41.36 2.32
41 42 6.372381 GTGTGTAGGGTCGGTACAATTTATTT 59.628 38.462 0.00 0.00 32.23 1.40
42 43 5.876460 GTGTGTAGGGTCGGTACAATTTATT 59.124 40.000 0.00 0.00 32.23 1.40
43 44 5.046448 TGTGTGTAGGGTCGGTACAATTTAT 60.046 40.000 0.00 0.00 32.23 1.40
44 45 4.282957 TGTGTGTAGGGTCGGTACAATTTA 59.717 41.667 0.00 0.00 32.23 1.40
45 46 3.071312 TGTGTGTAGGGTCGGTACAATTT 59.929 43.478 0.00 0.00 32.23 1.82
46 47 2.633967 TGTGTGTAGGGTCGGTACAATT 59.366 45.455 0.00 0.00 32.23 2.32
47 48 2.028748 GTGTGTGTAGGGTCGGTACAAT 60.029 50.000 0.00 0.00 32.23 2.71
48 49 1.340889 GTGTGTGTAGGGTCGGTACAA 59.659 52.381 0.00 0.00 32.23 2.41
49 50 0.961019 GTGTGTGTAGGGTCGGTACA 59.039 55.000 0.00 0.00 0.00 2.90
50 51 0.244721 GGTGTGTGTAGGGTCGGTAC 59.755 60.000 0.00 0.00 0.00 3.34
51 52 0.899717 GGGTGTGTGTAGGGTCGGTA 60.900 60.000 0.00 0.00 0.00 4.02
52 53 2.212110 GGGTGTGTGTAGGGTCGGT 61.212 63.158 0.00 0.00 0.00 4.69
53 54 2.660802 GGGTGTGTGTAGGGTCGG 59.339 66.667 0.00 0.00 0.00 4.79
54 55 2.260434 CGGGTGTGTGTAGGGTCG 59.740 66.667 0.00 0.00 0.00 4.79
55 56 2.660802 CCGGGTGTGTGTAGGGTC 59.339 66.667 0.00 0.00 0.00 4.46
56 57 3.633116 GCCGGGTGTGTGTAGGGT 61.633 66.667 2.18 0.00 0.00 4.34
57 58 2.406002 AAAGCCGGGTGTGTGTAGGG 62.406 60.000 7.07 0.00 0.00 3.53
58 59 0.536460 AAAAGCCGGGTGTGTGTAGG 60.536 55.000 7.07 0.00 0.00 3.18
59 60 0.872388 GAAAAGCCGGGTGTGTGTAG 59.128 55.000 7.07 0.00 0.00 2.74
60 61 0.535553 GGAAAAGCCGGGTGTGTGTA 60.536 55.000 7.07 0.00 0.00 2.90
61 62 1.826487 GGAAAAGCCGGGTGTGTGT 60.826 57.895 7.07 0.00 0.00 3.72
62 63 1.515521 GAGGAAAAGCCGGGTGTGTG 61.516 60.000 7.07 0.00 43.43 3.82
63 64 1.228154 GAGGAAAAGCCGGGTGTGT 60.228 57.895 7.07 0.00 43.43 3.72
64 65 2.325082 CGAGGAAAAGCCGGGTGTG 61.325 63.158 7.07 0.00 43.43 3.82
71 72 2.671963 AACGGCCGAGGAAAAGCC 60.672 61.111 35.90 0.00 43.53 4.35
118 119 5.163550 TGTGATAGGAACGAGACTACCATTG 60.164 44.000 0.00 0.00 0.00 2.82
133 134 8.588472 CATGTAGGATTTATGAGTGTGATAGGA 58.412 37.037 0.00 0.00 0.00 2.94
138 139 6.127083 TGAGCATGTAGGATTTATGAGTGTGA 60.127 38.462 0.00 0.00 0.00 3.58
151 152 9.769677 ATATATAGTTAGGTTGAGCATGTAGGA 57.230 33.333 0.00 0.00 0.00 2.94
183 184 5.941948 TGTTTTCTTCTACTTAAGCCTGC 57.058 39.130 1.29 0.00 0.00 4.85
243 247 4.911514 TTTTCCTTTGTCCCTTTCTTCG 57.088 40.909 0.00 0.00 0.00 3.79
287 291 0.249911 GGAGCCGAATATGAAGCGGT 60.250 55.000 0.00 0.00 46.38 5.68
294 298 1.947678 GCCCATGAGGAGCCGAATATG 60.948 57.143 0.00 0.00 38.24 1.78
328 332 1.899814 TCATTTAGTCAGCCCACGAGT 59.100 47.619 0.00 0.00 0.00 4.18
509 521 2.424474 CCGCAGGCTAGATCTGAGT 58.576 57.895 5.18 0.00 46.14 3.41
533 545 1.005037 ATGTTGAGCTTGGCGTCGA 60.005 52.632 0.00 0.00 0.00 4.20
574 586 0.974383 ACCGTCGGGAAGAGTCAATT 59.026 50.000 17.28 0.00 36.97 2.32
594 606 1.890510 ACAACGGTGCGGAAGGAAC 60.891 57.895 0.00 0.00 34.87 3.62
621 633 2.092212 GCATGAGAAGGGATCAAAGGGA 60.092 50.000 0.00 0.00 0.00 4.20
626 638 3.744940 AAAGGCATGAGAAGGGATCAA 57.255 42.857 0.00 0.00 0.00 2.57
641 653 1.172812 ACAAGCACGAGGGAAAAGGC 61.173 55.000 0.00 0.00 0.00 4.35
653 665 3.232213 TCGTGGATCTAGAACAAGCAC 57.768 47.619 0.00 0.00 0.00 4.40
679 691 4.680237 CGCTGGTCAGGTCGGCAA 62.680 66.667 0.00 0.00 36.37 4.52
710 722 1.767289 GAGAAAGACGACGTTCAGCA 58.233 50.000 14.60 0.00 37.07 4.41
712 724 1.328439 CCGAGAAAGACGACGTTCAG 58.672 55.000 14.60 8.58 37.07 3.02
714 726 0.662374 TGCCGAGAAAGACGACGTTC 60.662 55.000 0.13 5.53 35.39 3.95
718 730 0.524862 TACCTGCCGAGAAAGACGAC 59.475 55.000 0.00 0.00 0.00 4.34
740 752 3.055312 AGAAAAGTGGGACGGAATAGGAC 60.055 47.826 0.00 0.00 0.00 3.85
818 1526 2.614259 AGTAGATACAGATGCCCAGGG 58.386 52.381 0.00 0.00 0.00 4.45
1124 1849 2.435059 GTGACCTCCCGAGCTTGC 60.435 66.667 0.00 0.00 0.00 4.01
1155 1880 1.977854 TGGTGCTGTGAGGTAGACATT 59.022 47.619 0.00 0.00 0.00 2.71
1156 1881 1.552337 CTGGTGCTGTGAGGTAGACAT 59.448 52.381 0.00 0.00 0.00 3.06
1244 1969 7.328277 TCATAATGGTAATCTTTTGGAACCG 57.672 36.000 0.00 0.00 32.69 4.44
1276 2001 1.028905 TTTGCCTTTTCCACAGTCCG 58.971 50.000 0.00 0.00 0.00 4.79
1297 2022 5.455326 CCTTAAGCTGCTGACCCAATAGTAT 60.455 44.000 1.35 0.00 0.00 2.12
1376 2103 3.149196 CCTTTGCTGAGGAGCTTGTTTA 58.851 45.455 0.13 0.00 46.39 2.01
1389 2116 2.236766 GATCCATCCCATCCTTTGCTG 58.763 52.381 0.00 0.00 0.00 4.41
1522 2249 3.585289 TGAAGGTATTCACAACTGGCCTA 59.415 43.478 3.32 0.00 40.54 3.93
1590 2318 3.519510 TGCTCCTGGCCATAAGGATATAC 59.480 47.826 5.51 0.69 42.94 1.47
1591 2319 3.776969 CTGCTCCTGGCCATAAGGATATA 59.223 47.826 5.51 0.00 42.94 0.86
1592 2320 2.575279 CTGCTCCTGGCCATAAGGATAT 59.425 50.000 5.51 0.00 42.94 1.63
1615 2343 1.741706 GGTCCTCATCGTCGTCTGTTA 59.258 52.381 0.00 0.00 0.00 2.41
1680 2452 7.385205 GGTACGACACATAAATCATTAGAGCAT 59.615 37.037 0.00 0.00 0.00 3.79
1714 2486 3.820557 TCTTGCAAGGCTGTTAGAAGTT 58.179 40.909 25.73 0.00 0.00 2.66
1876 2648 9.276590 CATCATTAGGTTCACATACACACATAT 57.723 33.333 0.00 0.00 0.00 1.78
1880 2652 6.985188 ACATCATTAGGTTCACATACACAC 57.015 37.500 0.00 0.00 0.00 3.82
2039 2811 8.896744 TGAGATAAACTTGGAAGCATAAGAATG 58.103 33.333 0.00 0.00 36.09 2.67
2040 2812 9.118300 CTGAGATAAACTTGGAAGCATAAGAAT 57.882 33.333 0.00 0.00 0.00 2.40
2041 2813 7.066284 GCTGAGATAAACTTGGAAGCATAAGAA 59.934 37.037 0.00 0.00 0.00 2.52
2042 2814 6.540189 GCTGAGATAAACTTGGAAGCATAAGA 59.460 38.462 0.00 0.00 0.00 2.10
2102 2875 7.967854 GCATAATTATTCAGTTAGCACACACAA 59.032 33.333 0.00 0.00 0.00 3.33
2143 2916 0.393537 CCGCTTGCTCCTTGGATTCT 60.394 55.000 0.00 0.00 0.00 2.40
2167 2940 2.286950 GCATGCACAGACTTCGTTTGAA 60.287 45.455 14.21 0.00 0.00 2.69
2174 2947 1.736681 GAAGAGGCATGCACAGACTTC 59.263 52.381 21.36 19.23 0.00 3.01
2227 3000 4.095185 GGCAGCGTGTGTTATTATAAACCA 59.905 41.667 0.00 0.00 0.00 3.67
2249 3022 3.117926 TGTGGGATGATGTCATTAGGTGG 60.118 47.826 0.00 0.00 36.57 4.61
2308 3081 2.177594 CTGACAGAGGTGGTGGGCTC 62.178 65.000 0.00 0.00 0.00 4.70
2313 3086 3.475566 TTTCTTCTGACAGAGGTGGTG 57.524 47.619 13.71 0.00 0.00 4.17
2348 3121 6.209391 AGGTGCATTTAGGATGTATAATTGCC 59.791 38.462 0.00 0.00 38.11 4.52
2481 4988 6.773976 AATGGAAACTCTGTGTGAAAGAAA 57.226 33.333 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.