Multiple sequence alignment - TraesCS3D01G426000

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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 TraesCS3D01G426000 chr3D 100.000 2261 0 0 1 2261 538575056 538572796 0.000000e+00 4176.0
1 TraesCS3D01G426000 chr3D 84.016 757 91 18 870 1619 538699667 538698934 0.000000e+00 701.0
2 TraesCS3D01G426000 chr3D 82.968 775 89 27 865 1619 538687549 538686798 0.000000e+00 660.0
3 TraesCS3D01G426000 chr3D 78.054 925 107 47 731 1586 538516019 538515122 1.560000e-136 496.0
4 TraesCS3D01G426000 chr3D 95.122 41 2 0 1631 1671 566387212 566387252 5.210000e-07 65.8
5 TraesCS3D01G426000 chr3B 92.476 1236 48 16 397 1621 713493427 713492226 0.000000e+00 1725.0
6 TraesCS3D01G426000 chr3B 82.772 772 92 24 870 1619 713968897 713968145 0.000000e+00 651.0
7 TraesCS3D01G426000 chr3B 85.179 614 70 12 865 1470 713988339 713987739 5.340000e-171 610.0
8 TraesCS3D01G426000 chr3B 78.381 976 105 57 725 1621 713392247 713391299 9.190000e-149 536.0
9 TraesCS3D01G426000 chr3B 93.388 242 11 2 67 303 713495390 713495149 9.930000e-94 353.0
10 TraesCS3D01G426000 chr3A 86.650 809 47 12 859 1612 674018123 674017321 0.000000e+00 839.0
11 TraesCS3D01G426000 chr3A 80.807 917 114 32 725 1619 674061434 674060558 0.000000e+00 662.0
12 TraesCS3D01G426000 chr3A 82.654 761 99 22 870 1619 674025640 674024902 0.000000e+00 643.0
13 TraesCS3D01G426000 chr3A 92.537 67 5 0 1 67 536887887 536887953 1.850000e-16 97.1
14 TraesCS3D01G426000 chr6A 87.336 608 71 4 1636 2242 256897338 256897940 0.000000e+00 691.0
15 TraesCS3D01G426000 chr6A 91.304 69 5 1 1 68 593455081 593455013 2.390000e-15 93.5
16 TraesCS3D01G426000 chr5B 83.099 639 99 3 1619 2257 391011137 391011766 7.000000e-160 573.0
17 TraesCS3D01G426000 chr5D 82.426 643 108 3 1620 2261 114589625 114588987 7.050000e-155 556.0
18 TraesCS3D01G426000 chr5D 69.737 608 172 10 1635 2238 334993357 334993956 2.390000e-15 93.5
19 TraesCS3D01G426000 chr1B 78.816 642 122 9 1617 2257 533229945 533230573 9.660000e-114 420.0
20 TraesCS3D01G426000 chr4D 75.094 530 118 11 1676 2201 215495571 215496090 3.750000e-58 235.0
21 TraesCS3D01G426000 chr7D 92.537 67 5 0 1 67 515404802 515404868 1.850000e-16 97.1
22 TraesCS3D01G426000 chr7D 92.537 67 5 0 1 67 626756446 626756512 1.850000e-16 97.1
23 TraesCS3D01G426000 chr7B 92.537 67 5 0 1 67 741101725 741101659 1.850000e-16 97.1
24 TraesCS3D01G426000 chr2B 92.537 67 5 0 1 67 392650458 392650524 1.850000e-16 97.1
25 TraesCS3D01G426000 chr6B 91.304 69 5 1 2 69 645094981 645095049 2.390000e-15 93.5
26 TraesCS3D01G426000 chr4B 91.304 69 4 2 1 67 591929147 591929079 2.390000e-15 93.5
27 TraesCS3D01G426000 chr4A 91.176 68 5 1 1 67 700456679 700456746 8.600000e-15 91.6
28 TraesCS3D01G426000 chr1D 94.872 39 2 0 1631 1669 18735740 18735778 6.740000e-06 62.1


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 TraesCS3D01G426000 chr3D 538572796 538575056 2260 True 4176 4176 100.000 1 2261 1 chr3D.!!$R2 2260
1 TraesCS3D01G426000 chr3D 538698934 538699667 733 True 701 701 84.016 870 1619 1 chr3D.!!$R4 749
2 TraesCS3D01G426000 chr3D 538686798 538687549 751 True 660 660 82.968 865 1619 1 chr3D.!!$R3 754
3 TraesCS3D01G426000 chr3D 538515122 538516019 897 True 496 496 78.054 731 1586 1 chr3D.!!$R1 855
4 TraesCS3D01G426000 chr3B 713492226 713495390 3164 True 1039 1725 92.932 67 1621 2 chr3B.!!$R4 1554
5 TraesCS3D01G426000 chr3B 713968145 713968897 752 True 651 651 82.772 870 1619 1 chr3B.!!$R2 749
6 TraesCS3D01G426000 chr3B 713987739 713988339 600 True 610 610 85.179 865 1470 1 chr3B.!!$R3 605
7 TraesCS3D01G426000 chr3B 713391299 713392247 948 True 536 536 78.381 725 1621 1 chr3B.!!$R1 896
8 TraesCS3D01G426000 chr3A 674017321 674018123 802 True 839 839 86.650 859 1612 1 chr3A.!!$R1 753
9 TraesCS3D01G426000 chr3A 674060558 674061434 876 True 662 662 80.807 725 1619 1 chr3A.!!$R3 894
10 TraesCS3D01G426000 chr3A 674024902 674025640 738 True 643 643 82.654 870 1619 1 chr3A.!!$R2 749
11 TraesCS3D01G426000 chr6A 256897338 256897940 602 False 691 691 87.336 1636 2242 1 chr6A.!!$F1 606
12 TraesCS3D01G426000 chr5B 391011137 391011766 629 False 573 573 83.099 1619 2257 1 chr5B.!!$F1 638
13 TraesCS3D01G426000 chr5D 114588987 114589625 638 True 556 556 82.426 1620 2261 1 chr5D.!!$R1 641
14 TraesCS3D01G426000 chr1B 533229945 533230573 628 False 420 420 78.816 1617 2257 1 chr1B.!!$F1 640
15 TraesCS3D01G426000 chr4D 215495571 215496090 519 False 235 235 75.094 1676 2201 1 chr4D.!!$F1 525

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
27 28 0.030638 AAAATGGCCGTATGCATCGC 59.969 50.0 0.19 3.34 43.89 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 3005 0.033011 TCTCTCCTGTAGCCTGGACC 60.033 60.0 0.0 0.0 35.15 4.46 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
26 27 3.829886 ATAAAATGGCCGTATGCATCG 57.170 42.857 0.19 7.03 43.89 3.84
27 28 0.030638 AAAATGGCCGTATGCATCGC 59.969 50.000 0.19 3.34 43.89 4.58
28 29 1.795170 AAATGGCCGTATGCATCGCC 61.795 55.000 20.23 20.23 43.89 5.54
29 30 2.680974 AATGGCCGTATGCATCGCCT 62.681 55.000 24.73 13.00 43.89 5.52
30 31 1.826340 ATGGCCGTATGCATCGCCTA 61.826 55.000 24.73 15.58 43.89 3.93
31 32 1.738099 GGCCGTATGCATCGCCTAG 60.738 63.158 19.92 6.63 43.89 3.02
32 33 1.289066 GCCGTATGCATCGCCTAGA 59.711 57.895 0.19 0.00 40.77 2.43
33 34 0.108615 GCCGTATGCATCGCCTAGAT 60.109 55.000 0.19 0.00 41.01 1.98
34 35 1.134367 GCCGTATGCATCGCCTAGATA 59.866 52.381 0.19 0.00 37.52 1.98
35 36 2.798680 CCGTATGCATCGCCTAGATAC 58.201 52.381 0.19 0.00 37.52 2.24
36 37 2.163613 CCGTATGCATCGCCTAGATACA 59.836 50.000 0.19 0.00 37.52 2.29
37 38 3.430008 CGTATGCATCGCCTAGATACAG 58.570 50.000 0.19 0.00 36.18 2.74
38 39 3.119814 CGTATGCATCGCCTAGATACAGT 60.120 47.826 0.19 0.00 36.18 3.55
39 40 2.800881 TGCATCGCCTAGATACAGTG 57.199 50.000 0.00 0.00 37.52 3.66
40 41 1.341209 TGCATCGCCTAGATACAGTGG 59.659 52.381 0.00 0.00 37.52 4.00
41 42 1.937108 GCATCGCCTAGATACAGTGGC 60.937 57.143 0.00 0.00 37.52 5.01
42 43 0.969894 ATCGCCTAGATACAGTGGCC 59.030 55.000 0.00 0.00 42.15 5.36
43 44 0.396556 TCGCCTAGATACAGTGGCCA 60.397 55.000 0.00 0.00 42.15 5.36
44 45 0.032678 CGCCTAGATACAGTGGCCAG 59.967 60.000 5.11 0.00 42.15 4.85
45 46 0.394565 GCCTAGATACAGTGGCCAGG 59.605 60.000 5.11 3.68 39.49 4.45
46 47 1.051812 CCTAGATACAGTGGCCAGGG 58.948 60.000 5.11 3.21 0.00 4.45
47 48 1.692762 CCTAGATACAGTGGCCAGGGT 60.693 57.143 5.11 10.50 0.00 4.34
48 49 1.689273 CTAGATACAGTGGCCAGGGTC 59.311 57.143 5.11 4.81 0.00 4.46
49 50 0.983378 AGATACAGTGGCCAGGGTCC 60.983 60.000 5.11 3.34 0.00 4.46
50 51 0.983378 GATACAGTGGCCAGGGTCCT 60.983 60.000 5.11 0.00 0.00 3.85
51 52 0.983378 ATACAGTGGCCAGGGTCCTC 60.983 60.000 5.11 0.00 0.00 3.71
52 53 3.721706 CAGTGGCCAGGGTCCTCC 61.722 72.222 5.11 0.00 0.00 4.30
54 55 3.403558 GTGGCCAGGGTCCTCCTC 61.404 72.222 5.11 0.00 46.12 3.71
55 56 4.741239 TGGCCAGGGTCCTCCTCC 62.741 72.222 0.00 0.00 46.12 4.30
56 57 4.423209 GGCCAGGGTCCTCCTCCT 62.423 72.222 0.00 0.00 46.12 3.69
57 58 2.285743 GCCAGGGTCCTCCTCCTT 60.286 66.667 0.00 0.00 46.12 3.36
58 59 1.925972 GCCAGGGTCCTCCTCCTTT 60.926 63.158 0.00 0.00 46.12 3.11
59 60 1.501654 GCCAGGGTCCTCCTCCTTTT 61.502 60.000 0.00 0.00 46.12 2.27
60 61 0.621082 CCAGGGTCCTCCTCCTTTTC 59.379 60.000 0.00 0.00 46.12 2.29
61 62 1.662686 CAGGGTCCTCCTCCTTTTCT 58.337 55.000 0.00 0.00 46.12 2.52
62 63 2.562214 CCAGGGTCCTCCTCCTTTTCTA 60.562 54.545 0.00 0.00 46.12 2.10
63 64 3.182152 CAGGGTCCTCCTCCTTTTCTAA 58.818 50.000 0.00 0.00 46.12 2.10
64 65 3.587506 CAGGGTCCTCCTCCTTTTCTAAA 59.412 47.826 0.00 0.00 46.12 1.85
65 66 4.042934 CAGGGTCCTCCTCCTTTTCTAAAA 59.957 45.833 0.00 0.00 46.12 1.52
66 67 4.668335 AGGGTCCTCCTCCTTTTCTAAAAA 59.332 41.667 0.00 0.00 44.06 1.94
67 68 5.316183 AGGGTCCTCCTCCTTTTCTAAAAAT 59.684 40.000 0.00 0.00 44.06 1.82
68 69 5.652891 GGGTCCTCCTCCTTTTCTAAAAATC 59.347 44.000 0.00 0.00 0.00 2.17
69 70 5.354513 GGTCCTCCTCCTTTTCTAAAAATCG 59.645 44.000 0.00 0.00 0.00 3.34
70 71 4.941873 TCCTCCTCCTTTTCTAAAAATCGC 59.058 41.667 0.00 0.00 0.00 4.58
71 72 4.096532 CCTCCTCCTTTTCTAAAAATCGCC 59.903 45.833 0.00 0.00 0.00 5.54
72 73 4.658063 TCCTCCTTTTCTAAAAATCGCCA 58.342 39.130 0.00 0.00 0.00 5.69
87 88 2.872557 CCACCGACTGCAAGCATG 59.127 61.111 0.00 0.00 37.60 4.06
106 107 1.294659 GCGCTTTCTGCTGCTAGTGT 61.295 55.000 0.00 0.00 40.11 3.55
117 118 1.810755 CTGCTAGTGTCCGTCAGTGTA 59.189 52.381 0.00 0.00 0.00 2.90
118 119 1.810755 TGCTAGTGTCCGTCAGTGTAG 59.189 52.381 0.00 0.00 0.00 2.74
119 120 1.467713 GCTAGTGTCCGTCAGTGTAGC 60.468 57.143 0.00 0.00 0.00 3.58
120 121 2.085320 CTAGTGTCCGTCAGTGTAGCT 58.915 52.381 0.00 0.00 0.00 3.32
121 122 0.882474 AGTGTCCGTCAGTGTAGCTC 59.118 55.000 0.00 0.00 0.00 4.09
123 124 0.887836 TGTCCGTCAGTGTAGCTCGT 60.888 55.000 0.00 0.00 0.00 4.18
124 125 0.179194 GTCCGTCAGTGTAGCTCGTC 60.179 60.000 0.00 0.00 0.00 4.20
125 126 1.226046 CCGTCAGTGTAGCTCGTCG 60.226 63.158 0.00 0.00 0.00 5.12
127 128 0.518764 CGTCAGTGTAGCTCGTCGTC 60.519 60.000 0.00 0.00 0.00 4.20
128 129 0.518764 GTCAGTGTAGCTCGTCGTCG 60.519 60.000 0.00 0.00 38.55 5.12
272 278 8.514594 TGCTAGAAAAATAAAATGTCTGGACAG 58.485 33.333 9.33 0.00 45.48 3.51
293 1901 2.770164 ACGTGGAAAAGATAGCAGCT 57.230 45.000 0.00 0.00 0.00 4.24
295 1903 3.786635 ACGTGGAAAAGATAGCAGCTAG 58.213 45.455 8.43 0.00 0.00 3.42
303 1911 0.607620 GATAGCAGCTAGAGGCCAGG 59.392 60.000 5.01 0.00 43.05 4.45
318 1926 1.134551 GCCAGGTGATCAGACTCTTCC 60.135 57.143 0.00 0.00 0.00 3.46
319 1927 1.135915 CCAGGTGATCAGACTCTTCCG 59.864 57.143 0.00 0.00 0.00 4.30
321 1929 2.096248 AGGTGATCAGACTCTTCCGAC 58.904 52.381 0.00 0.00 0.00 4.79
328 1936 5.652452 TGATCAGACTCTTCCGACTGATTTA 59.348 40.000 0.00 0.00 45.88 1.40
329 1937 6.322456 TGATCAGACTCTTCCGACTGATTTAT 59.678 38.462 0.00 0.00 45.88 1.40
330 1938 7.502561 TGATCAGACTCTTCCGACTGATTTATA 59.497 37.037 0.00 0.00 45.88 0.98
360 1968 1.621992 AAGAACTCCTCGTGCTCAGA 58.378 50.000 0.00 0.00 26.63 3.27
376 1984 1.277273 TCAGAGTGTGCCTTCATCTGG 59.723 52.381 0.00 0.00 38.32 3.86
383 1991 1.751927 GCCTTCATCTGGGCACTGG 60.752 63.158 0.00 0.00 46.84 4.00
394 2002 3.007614 TCTGGGCACTGGAAAACTAGTAC 59.992 47.826 0.00 0.00 0.00 2.73
463 2100 1.138883 GGCTCGTGCATACTCGTCA 59.861 57.895 12.07 0.00 41.91 4.35
465 2102 1.346365 GCTCGTGCATACTCGTCAAA 58.654 50.000 4.26 0.00 39.41 2.69
472 2112 2.672874 TGCATACTCGTCAAACAGCATC 59.327 45.455 0.00 0.00 0.00 3.91
542 2182 1.887198 ACAGGACGAGTTCGAGTTGAT 59.113 47.619 8.72 0.00 43.02 2.57
548 2188 4.438336 GGACGAGTTCGAGTTGATGTATGA 60.438 45.833 8.72 0.00 43.02 2.15
647 2287 1.152830 TGGAAAAGGCCAGTGGGAC 59.847 57.895 12.15 0.00 45.66 4.46
718 2358 5.867174 CGACCGTATATTATCTTGGCAATCA 59.133 40.000 0.00 0.00 0.00 2.57
785 2426 0.469331 TCTCCGGTCAGTGACACCTT 60.469 55.000 24.20 0.00 33.68 3.50
799 2440 4.214332 GTGACACCTTCCAGATTCACTTTC 59.786 45.833 0.00 0.00 32.38 2.62
948 2623 1.536709 GGAAAGCAAAGGCACACACAG 60.537 52.381 0.00 0.00 44.61 3.66
1141 2855 1.604378 CAGCCCAGGTACCCTTCTG 59.396 63.158 8.74 7.43 0.00 3.02
1272 2986 2.622436 GTGATTTAGCTGAGCTCGGTT 58.378 47.619 23.36 20.04 40.44 4.44
1275 2989 2.370281 TTTAGCTGAGCTCGGTTGAG 57.630 50.000 23.36 8.95 45.49 3.02
1276 2990 0.532573 TTAGCTGAGCTCGGTTGAGG 59.467 55.000 23.36 2.03 42.79 3.86
1301 3020 3.712907 GCCGGTTGGTCCAGGCTA 61.713 66.667 12.39 0.00 45.46 3.93
1445 3189 3.267031 ACCATAAGAGTGGAAGAAAGGGG 59.733 47.826 0.00 0.00 42.02 4.79
1480 3253 3.524789 TCCCATTTCTGAGACCATGTGAT 59.475 43.478 0.00 0.00 0.00 3.06
1511 3284 5.106396 CCTCAATCAGAATGGAGTTTGTGTC 60.106 44.000 0.00 0.00 31.75 3.67
1553 3328 0.243907 CGTCCAACACTCCATCTCGT 59.756 55.000 0.00 0.00 0.00 4.18
1555 3330 0.526211 TCCAACACTCCATCTCGTCG 59.474 55.000 0.00 0.00 0.00 5.12
1597 3376 5.389859 TGCAGTTCCTTTTATGATGTTGG 57.610 39.130 0.00 0.00 0.00 3.77
1633 3412 3.413023 CGTTTTCCGCCGGCGTTA 61.413 61.111 43.12 30.03 37.81 3.18
1662 3441 4.554036 GCCCGCCTCAGTCATCCC 62.554 72.222 0.00 0.00 0.00 3.85
1734 3515 1.160137 AAACGGATGCTCACTCTTGC 58.840 50.000 0.00 0.00 0.00 4.01
1791 3572 7.038154 TCCTTTTAGTTTTTCATCCACAGTG 57.962 36.000 0.00 0.00 0.00 3.66
1847 3628 5.326900 TGTATGGACATCGCCTATACCTAA 58.673 41.667 0.00 0.00 0.00 2.69
1857 3638 6.540438 TCGCCTATACCTAATAATTCTGGG 57.460 41.667 0.00 0.00 0.00 4.45
1904 3686 6.533730 TGGATGATTACTCTCACTTTGTGTT 58.466 36.000 0.00 0.00 34.79 3.32
1985 3767 1.270094 CGTGTCTACTCAGTTTGGCCA 60.270 52.381 0.00 0.00 0.00 5.36
2013 3795 4.283363 ACATGCTCTTCAGACTGACAAT 57.717 40.909 4.15 0.00 0.00 2.71
2014 3796 4.001652 ACATGCTCTTCAGACTGACAATG 58.998 43.478 4.15 7.41 0.00 2.82
2015 3797 2.420642 TGCTCTTCAGACTGACAATGC 58.579 47.619 4.15 8.12 0.00 3.56
2016 3798 2.224354 TGCTCTTCAGACTGACAATGCA 60.224 45.455 4.15 10.53 0.00 3.96
2024 3806 3.256383 CAGACTGACAATGCATGGGAAAA 59.744 43.478 5.94 0.00 0.00 2.29
2085 3867 2.014128 CGGTACAATTTTCCGCCTCAT 58.986 47.619 0.00 0.00 37.90 2.90
2097 3879 1.345741 CCGCCTCATCTGTCCATACAT 59.654 52.381 0.00 0.00 34.37 2.29
2138 3920 2.793232 GCTGAACGTGTTCTTCGTACTT 59.207 45.455 13.40 0.00 40.69 2.24
2202 3984 0.609131 CCTCGGTTTTGGCCTGATGT 60.609 55.000 3.32 0.00 0.00 3.06
2211 3993 2.507944 GCCTGATGTCCTCGCCAT 59.492 61.111 0.00 0.00 0.00 4.40
2212 3994 1.748403 GCCTGATGTCCTCGCCATA 59.252 57.895 0.00 0.00 0.00 2.74
2242 4024 1.401905 CTCATTAACCTTCGCCCTTGC 59.598 52.381 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.806249 CGATGCATACGGCCATTTTATTAATT 59.194 34.615 2.24 0.00 43.89 1.40
2 3 6.321717 CGATGCATACGGCCATTTTATTAAT 58.678 36.000 2.24 0.00 43.89 1.40
3 4 5.694816 CGATGCATACGGCCATTTTATTAA 58.305 37.500 2.24 0.00 43.89 1.40
5 6 3.611530 GCGATGCATACGGCCATTTTATT 60.612 43.478 16.56 0.00 43.89 1.40
6 7 2.095263 GCGATGCATACGGCCATTTTAT 60.095 45.455 16.56 0.00 43.89 1.40
7 8 1.265635 GCGATGCATACGGCCATTTTA 59.734 47.619 16.56 0.00 43.89 1.52
8 9 0.030638 GCGATGCATACGGCCATTTT 59.969 50.000 16.56 0.00 43.89 1.82
9 10 1.654220 GCGATGCATACGGCCATTT 59.346 52.632 16.56 0.00 43.89 2.32
10 11 3.343972 GCGATGCATACGGCCATT 58.656 55.556 16.56 0.00 43.89 3.16
15 16 2.163613 TGTATCTAGGCGATGCATACGG 59.836 50.000 16.56 4.54 39.41 4.02
16 17 3.119814 ACTGTATCTAGGCGATGCATACG 60.120 47.826 0.00 6.68 42.63 3.06
17 18 4.169508 CACTGTATCTAGGCGATGCATAC 58.830 47.826 0.00 0.00 42.63 2.39
18 19 3.193479 CCACTGTATCTAGGCGATGCATA 59.807 47.826 0.00 0.00 42.63 3.14
19 20 2.028658 CCACTGTATCTAGGCGATGCAT 60.029 50.000 0.00 0.00 42.63 3.96
20 21 1.341209 CCACTGTATCTAGGCGATGCA 59.659 52.381 0.00 0.00 41.58 3.96
21 22 1.937108 GCCACTGTATCTAGGCGATGC 60.937 57.143 0.00 0.00 37.41 3.91
22 23 2.071688 GCCACTGTATCTAGGCGATG 57.928 55.000 0.00 0.00 37.41 3.84
26 27 0.394565 CCTGGCCACTGTATCTAGGC 59.605 60.000 0.00 0.00 46.28 3.93
27 28 1.051812 CCCTGGCCACTGTATCTAGG 58.948 60.000 0.00 0.00 0.00 3.02
28 29 1.689273 GACCCTGGCCACTGTATCTAG 59.311 57.143 0.00 0.00 0.00 2.43
29 30 1.691482 GGACCCTGGCCACTGTATCTA 60.691 57.143 0.00 0.00 0.00 1.98
30 31 0.983378 GGACCCTGGCCACTGTATCT 60.983 60.000 0.00 0.00 0.00 1.98
31 32 0.983378 AGGACCCTGGCCACTGTATC 60.983 60.000 0.00 0.00 0.00 2.24
32 33 0.983378 GAGGACCCTGGCCACTGTAT 60.983 60.000 0.00 0.00 0.00 2.29
33 34 1.612442 GAGGACCCTGGCCACTGTA 60.612 63.158 0.00 0.00 0.00 2.74
34 35 2.930562 GAGGACCCTGGCCACTGT 60.931 66.667 0.00 0.42 0.00 3.55
35 36 3.721706 GGAGGACCCTGGCCACTG 61.722 72.222 0.00 0.00 0.00 3.66
36 37 3.947041 AGGAGGACCCTGGCCACT 61.947 66.667 0.00 0.00 45.61 4.00
44 45 4.652679 TTTTAGAAAAGGAGGAGGACCC 57.347 45.455 0.00 0.00 36.73 4.46
45 46 5.354513 CGATTTTTAGAAAAGGAGGAGGACC 59.645 44.000 0.00 0.00 0.00 4.46
46 47 5.163744 GCGATTTTTAGAAAAGGAGGAGGAC 60.164 44.000 0.00 0.00 0.00 3.85
47 48 4.941873 GCGATTTTTAGAAAAGGAGGAGGA 59.058 41.667 0.00 0.00 0.00 3.71
48 49 4.096532 GGCGATTTTTAGAAAAGGAGGAGG 59.903 45.833 0.00 0.00 0.00 4.30
49 50 4.700213 TGGCGATTTTTAGAAAAGGAGGAG 59.300 41.667 0.00 0.00 0.00 3.69
50 51 4.457949 GTGGCGATTTTTAGAAAAGGAGGA 59.542 41.667 0.00 0.00 0.00 3.71
51 52 4.380550 GGTGGCGATTTTTAGAAAAGGAGG 60.381 45.833 0.00 0.00 0.00 4.30
52 53 4.671766 CGGTGGCGATTTTTAGAAAAGGAG 60.672 45.833 0.00 0.00 0.00 3.69
53 54 3.189702 CGGTGGCGATTTTTAGAAAAGGA 59.810 43.478 0.00 0.00 0.00 3.36
54 55 3.189702 TCGGTGGCGATTTTTAGAAAAGG 59.810 43.478 0.00 0.00 0.00 3.11
55 56 4.083484 AGTCGGTGGCGATTTTTAGAAAAG 60.083 41.667 0.00 0.00 0.00 2.27
56 57 3.816523 AGTCGGTGGCGATTTTTAGAAAA 59.183 39.130 0.00 0.00 0.00 2.29
57 58 3.187637 CAGTCGGTGGCGATTTTTAGAAA 59.812 43.478 0.00 0.00 0.00 2.52
58 59 2.739913 CAGTCGGTGGCGATTTTTAGAA 59.260 45.455 0.00 0.00 0.00 2.10
59 60 2.343101 CAGTCGGTGGCGATTTTTAGA 58.657 47.619 0.00 0.00 0.00 2.10
60 61 1.202031 GCAGTCGGTGGCGATTTTTAG 60.202 52.381 0.00 0.00 0.00 1.85
61 62 0.800012 GCAGTCGGTGGCGATTTTTA 59.200 50.000 0.00 0.00 0.00 1.52
62 63 1.169661 TGCAGTCGGTGGCGATTTTT 61.170 50.000 0.00 0.00 0.00 1.94
63 64 1.169661 TTGCAGTCGGTGGCGATTTT 61.170 50.000 0.00 0.00 0.00 1.82
64 65 1.577328 CTTGCAGTCGGTGGCGATTT 61.577 55.000 0.00 0.00 0.00 2.17
65 66 2.031919 TTGCAGTCGGTGGCGATT 59.968 55.556 0.00 0.00 0.00 3.34
66 67 2.434884 CTTGCAGTCGGTGGCGAT 60.435 61.111 0.00 0.00 0.00 4.58
69 70 3.058160 ATGCTTGCAGTCGGTGGC 61.058 61.111 0.87 0.00 0.00 5.01
70 71 2.872557 CATGCTTGCAGTCGGTGG 59.127 61.111 0.87 0.00 0.00 4.61
89 90 1.082690 GGACACTAGCAGCAGAAAGC 58.917 55.000 0.00 0.00 46.19 3.51
106 107 1.632948 CGACGAGCTACACTGACGGA 61.633 60.000 0.00 0.00 0.00 4.69
118 119 4.838486 CTGGAGCCGACGACGAGC 62.838 72.222 9.28 10.50 42.66 5.03
119 120 4.180946 CCTGGAGCCGACGACGAG 62.181 72.222 9.28 0.00 42.66 4.18
120 121 4.710167 TCCTGGAGCCGACGACGA 62.710 66.667 9.28 0.00 42.66 4.20
121 122 3.277211 TTTCCTGGAGCCGACGACG 62.277 63.158 0.00 0.00 39.43 5.12
123 124 2.654877 GTTTCCTGGAGCCGACGA 59.345 61.111 0.00 0.00 0.00 4.20
124 125 2.434359 GGTTTCCTGGAGCCGACG 60.434 66.667 0.00 0.00 0.00 5.12
125 126 1.079057 GAGGTTTCCTGGAGCCGAC 60.079 63.158 11.93 8.10 31.76 4.79
127 128 0.175989 GTAGAGGTTTCCTGGAGCCG 59.824 60.000 11.93 0.00 31.76 5.52
128 129 1.208293 CAGTAGAGGTTTCCTGGAGCC 59.792 57.143 10.33 10.33 31.76 4.70
272 278 3.522553 AGCTGCTATCTTTTCCACGTAC 58.477 45.455 0.00 0.00 0.00 3.67
293 1901 1.289231 AGTCTGATCACCTGGCCTCTA 59.711 52.381 3.32 0.00 0.00 2.43
295 1903 0.463620 GAGTCTGATCACCTGGCCTC 59.536 60.000 3.32 0.00 0.00 4.70
303 1911 2.750166 TCAGTCGGAAGAGTCTGATCAC 59.250 50.000 0.00 0.00 43.20 3.06
336 1944 2.488545 GAGCACGAGGAGTTCTTACAGA 59.511 50.000 0.00 0.00 0.00 3.41
376 1984 3.251571 CGAGTACTAGTTTTCCAGTGCC 58.748 50.000 0.00 0.00 0.00 5.01
383 1991 7.968405 TCCGGTTAATAACGAGTACTAGTTTTC 59.032 37.037 23.72 11.34 31.14 2.29
424 2061 3.200825 CCTTGTACCATCCTGAACCTGAT 59.799 47.826 0.00 0.00 0.00 2.90
463 2100 3.683802 AGCAAAGCTCTAGATGCTGTTT 58.316 40.909 15.99 6.55 46.66 2.83
472 2112 4.947420 GTTTACACGAAGCAAAGCTCTAG 58.053 43.478 0.00 0.00 38.25 2.43
516 2156 2.743126 CTCGAACTCGTCCTGTAGTTCT 59.257 50.000 12.00 0.00 46.10 3.01
519 2159 2.181954 ACTCGAACTCGTCCTGTAGT 57.818 50.000 0.00 0.00 40.80 2.73
542 2182 7.565029 TCCTCTCTATCCTTTGTGAATCATACA 59.435 37.037 0.00 0.00 0.00 2.29
548 2188 7.443302 TGATTCCTCTCTATCCTTTGTGAAT 57.557 36.000 0.00 0.00 0.00 2.57
647 2287 2.742372 CTGCCAAGGTTCGGTCCG 60.742 66.667 4.39 4.39 0.00 4.79
651 2291 2.361610 ATGCCTGCCAAGGTTCGG 60.362 61.111 0.00 0.00 46.43 4.30
652 2292 2.879907 CATGCCTGCCAAGGTTCG 59.120 61.111 0.00 0.00 46.43 3.95
718 2358 0.248565 AGTGACACGATGAGCTGCAT 59.751 50.000 1.02 0.00 40.77 3.96
785 2426 1.974957 TCGTGGGAAAGTGAATCTGGA 59.025 47.619 0.00 0.00 0.00 3.86
948 2623 0.108898 TTGTGGTTGTGCACTTGTGC 60.109 50.000 19.41 17.73 0.00 4.57
1033 2719 2.198304 ATCGCCACCTTCCCCTTGAC 62.198 60.000 0.00 0.00 0.00 3.18
1290 3004 0.324738 CTCTCCTGTAGCCTGGACCA 60.325 60.000 0.00 0.00 35.15 4.02
1291 3005 0.033011 TCTCTCCTGTAGCCTGGACC 60.033 60.000 0.00 0.00 35.15 4.46
1337 3057 4.891992 ACTATGTATCCATGGCTACCAC 57.108 45.455 20.37 8.28 35.80 4.16
1338 3058 4.658435 ACAACTATGTATCCATGGCTACCA 59.342 41.667 20.37 10.68 38.24 3.25
1511 3284 5.390251 CGAACAAGAATGAACAGTGGAGATG 60.390 44.000 0.00 0.00 0.00 2.90
1553 3328 8.873215 TGCAATTTTAAATTTCTTTACACCGA 57.127 26.923 0.00 0.00 0.00 4.69
1584 3363 7.726291 TGTAAAGAGGTTCCCAACATCATAAAA 59.274 33.333 4.08 0.00 44.16 1.52
1633 3412 3.747976 GCGGGCGTGCCAAAGATT 61.748 61.111 13.76 0.00 37.98 2.40
1654 3433 2.362369 CGGTGGAGCTGGGATGACT 61.362 63.158 0.00 0.00 0.00 3.41
1734 3515 0.747644 TGCCCATACGACATGCTTGG 60.748 55.000 4.44 0.00 0.00 3.61
1778 3559 0.396435 AGACGCCACTGTGGATGAAA 59.604 50.000 30.23 0.00 40.96 2.69
1791 3572 5.978934 TTAATTCGAAAGGATAAGACGCC 57.021 39.130 0.00 0.00 0.00 5.68
1868 3650 7.271511 AGAGTAATCATCCAGAATGACAAGAC 58.728 38.462 0.00 0.00 47.00 3.01
1904 3686 1.614903 TCCTACGAAGCGGAAAAGTCA 59.385 47.619 0.00 0.00 0.00 3.41
1929 3711 1.296715 GAGTGTGGCGGGAACATCT 59.703 57.895 0.00 0.00 0.00 2.90
1985 3767 6.015519 GTCAGTCTGAAGAGCATGTATAGGAT 60.016 42.308 3.51 0.00 0.00 3.24
2024 3806 3.748048 CGGATGGTGATGCTATCGAATTT 59.252 43.478 0.00 0.00 36.12 1.82
2034 3816 3.211963 GGGTGCGGATGGTGATGC 61.212 66.667 0.00 0.00 0.00 3.91
2085 3867 5.482163 TTGTTGTGAGATGTATGGACAGA 57.518 39.130 0.00 0.00 39.50 3.41
2097 3879 3.942748 AGCTTTACCGTTTTGTTGTGAGA 59.057 39.130 0.00 0.00 0.00 3.27
2202 3984 3.161450 GGGTGGCTATGGCGAGGA 61.161 66.667 0.00 0.00 39.81 3.71
2211 3993 3.460825 AGGTTAATGAGAAGGGTGGCTA 58.539 45.455 0.00 0.00 0.00 3.93
2212 3994 2.279173 AGGTTAATGAGAAGGGTGGCT 58.721 47.619 0.00 0.00 0.00 4.75
2242 4024 1.798087 GTAATTCCAACGGGCACGG 59.202 57.895 15.46 0.00 46.48 4.94


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

AutoCloner maintained by Alex Coulton.