Multiple sequence alignment - TraesCS2D01G326100

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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 TraesCS2D01G326100 chr2D 100.000 2876 0 0 1 2876 419672778 419675653 0.000000e+00 5312.0
1 TraesCS2D01G326100 chr2D 91.692 999 58 10 805 1803 419479732 419480705 0.000000e+00 1362.0
2 TraesCS2D01G326100 chr2D 93.182 44 3 0 8 51 584666812 584666855 6.650000e-07 65.8
3 TraesCS2D01G326100 chr2B 94.683 2351 97 12 409 2747 492087438 492089772 0.000000e+00 3624.0
4 TraesCS2D01G326100 chr2B 90.396 1010 65 10 804 1803 491961683 491962670 0.000000e+00 1299.0
5 TraesCS2D01G326100 chr2B 87.302 189 14 5 58 245 492087165 492087344 1.040000e-49 207.0
6 TraesCS2D01G326100 chr2B 95.876 97 2 2 2744 2839 383927839 383927934 3.840000e-34 156.0
7 TraesCS2D01G326100 chr2B 93.421 76 4 1 671 746 491961391 491961465 8.420000e-21 111.0
8 TraesCS2D01G326100 chr2B 86.420 81 9 2 271 351 492087346 492087424 1.420000e-13 87.9
9 TraesCS2D01G326100 chr2B 100.000 42 0 0 2835 2876 492089891 492089932 8.540000e-11 78.7
10 TraesCS2D01G326100 chr2A 95.729 2084 64 10 522 2593 570269095 570267025 0.000000e+00 3332.0
11 TraesCS2D01G326100 chr2A 92.417 989 70 1 815 1803 570502713 570501730 0.000000e+00 1406.0
12 TraesCS2D01G326100 chr2A 87.654 405 38 8 49 449 570269725 570269329 7.260000e-126 460.0
13 TraesCS2D01G326100 chr2A 97.714 175 4 0 2573 2747 570266858 570266684 4.660000e-78 302.0
14 TraesCS2D01G326100 chr2A 82.979 94 13 3 311 403 5456781 5456872 6.600000e-12 82.4
15 TraesCS2D01G326100 chr2A 87.719 57 5 2 15 71 16862951 16862897 6.650000e-07 65.8
16 TraesCS2D01G326100 chr2A 89.796 49 4 1 22 70 642203040 642202993 8.600000e-06 62.1
17 TraesCS2D01G326100 chr4A 97.826 92 2 0 2743 2834 707025577 707025486 2.970000e-35 159.0
18 TraesCS2D01G326100 chr7B 95.876 97 2 2 2745 2839 713437706 713437610 3.840000e-34 156.0
19 TraesCS2D01G326100 chr7B 83.333 90 13 2 312 400 747594287 747594375 6.600000e-12 82.4
20 TraesCS2D01G326100 chr7B 87.719 57 5 2 16 71 301630653 301630598 6.650000e-07 65.8
21 TraesCS2D01G326100 chr7A 95.833 96 3 1 2738 2833 46720554 46720460 1.380000e-33 154.0
22 TraesCS2D01G326100 chr7A 93.069 101 6 1 2733 2833 134734022 134734121 2.310000e-31 147.0
23 TraesCS2D01G326100 chr7A 86.458 96 10 3 306 400 25645874 25645781 5.070000e-18 102.0
24 TraesCS2D01G326100 chr7A 87.719 57 4 3 16 71 83791064 83791118 2.390000e-06 63.9
25 TraesCS2D01G326100 chr5A 95.789 95 4 0 2744 2838 225248509 225248415 1.380000e-33 154.0
26 TraesCS2D01G326100 chr5A 92.381 105 6 2 2731 2835 635512577 635512475 6.420000e-32 148.0
27 TraesCS2D01G326100 chr5B 91.589 107 6 2 2728 2832 689944095 689943990 8.310000e-31 145.0
28 TraesCS2D01G326100 chr1A 92.157 102 6 2 2745 2846 548488446 548488347 2.990000e-30 143.0
29 TraesCS2D01G326100 chr1A 89.130 46 4 1 96 141 577767282 577767238 4.000000e-04 56.5
30 TraesCS2D01G326100 chr3B 83.333 102 15 2 304 404 237977239 237977339 3.050000e-15 93.5
31 TraesCS2D01G326100 chr6A 83.838 99 13 3 301 397 1139513 1139610 1.100000e-14 91.6
32 TraesCS2D01G326100 chr5D 88.732 71 8 0 71 141 406171119 406171189 1.420000e-13 87.9
33 TraesCS2D01G326100 chr4B 87.671 73 7 2 328 399 87686947 87686876 1.840000e-12 84.2
34 TraesCS2D01G326100 chr4B 82.796 93 11 5 306 397 585726737 585726649 8.540000e-11 78.7
35 TraesCS2D01G326100 chr4B 89.286 56 5 1 16 71 159603783 159603837 5.140000e-08 69.4
36 TraesCS2D01G326100 chr3D 82.955 88 13 2 313 399 483523882 483523968 8.540000e-11 78.7
37 TraesCS2D01G326100 chr3D 89.091 55 4 2 17 71 135380748 135380800 1.850000e-07 67.6
38 TraesCS2D01G326100 chr4D 93.478 46 3 0 15 60 134142513 134142468 5.140000e-08 69.4
39 TraesCS2D01G326100 chr1B 89.091 55 4 2 16 70 262095520 262095468 1.850000e-07 67.6
40 TraesCS2D01G326100 chrUn 97.059 34 0 1 1000 1033 33171779 33171747 4.000000e-04 56.5


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 TraesCS2D01G326100 chr2D 419672778 419675653 2875 False 5312.000000 5312 100.00000 1 2876 1 chr2D.!!$F2 2875
1 TraesCS2D01G326100 chr2D 419479732 419480705 973 False 1362.000000 1362 91.69200 805 1803 1 chr2D.!!$F1 998
2 TraesCS2D01G326100 chr2B 492087165 492089932 2767 False 999.400000 3624 92.10125 58 2876 4 chr2B.!!$F3 2818
3 TraesCS2D01G326100 chr2B 491961391 491962670 1279 False 705.000000 1299 91.90850 671 1803 2 chr2B.!!$F2 1132
4 TraesCS2D01G326100 chr2A 570501730 570502713 983 True 1406.000000 1406 92.41700 815 1803 1 chr2A.!!$R2 988
5 TraesCS2D01G326100 chr2A 570266684 570269725 3041 True 1364.666667 3332 93.69900 49 2747 3 chr2A.!!$R4 2698

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
546 739 0.178995 CTCCCGGACCTAGTACTCCC 60.179 65.0 0.73 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2770 0.54851 AATAGCTGAACCCTCCCTGC 59.451 55.0 0.0 0.0 0.0 4.85 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 8.055279 TGGATGATTCTGAAAAACAATACTCC 57.945 34.615 0.00 1.31 0.00 3.85
27 28 7.122650 TGGATGATTCTGAAAAACAATACTCCC 59.877 37.037 0.00 0.00 0.00 4.30
28 29 7.340487 GGATGATTCTGAAAAACAATACTCCCT 59.660 37.037 0.00 0.00 0.00 4.20
29 30 7.687941 TGATTCTGAAAAACAATACTCCCTC 57.312 36.000 0.00 0.00 0.00 4.30
30 31 6.659242 TGATTCTGAAAAACAATACTCCCTCC 59.341 38.462 0.00 0.00 0.00 4.30
31 32 5.576563 TCTGAAAAACAATACTCCCTCCA 57.423 39.130 0.00 0.00 0.00 3.86
32 33 6.139679 TCTGAAAAACAATACTCCCTCCAT 57.860 37.500 0.00 0.00 0.00 3.41
33 34 6.180472 TCTGAAAAACAATACTCCCTCCATC 58.820 40.000 0.00 0.00 0.00 3.51
34 35 5.261216 TGAAAAACAATACTCCCTCCATCC 58.739 41.667 0.00 0.00 0.00 3.51
35 36 3.953542 AAACAATACTCCCTCCATCCC 57.046 47.619 0.00 0.00 0.00 3.85
36 37 2.587060 ACAATACTCCCTCCATCCCA 57.413 50.000 0.00 0.00 0.00 4.37
37 38 3.080660 ACAATACTCCCTCCATCCCAT 57.919 47.619 0.00 0.00 0.00 4.00
38 39 4.228237 ACAATACTCCCTCCATCCCATA 57.772 45.455 0.00 0.00 0.00 2.74
39 40 4.577096 ACAATACTCCCTCCATCCCATAA 58.423 43.478 0.00 0.00 0.00 1.90
40 41 5.173246 ACAATACTCCCTCCATCCCATAAT 58.827 41.667 0.00 0.00 0.00 1.28
41 42 6.339220 ACAATACTCCCTCCATCCCATAATA 58.661 40.000 0.00 0.00 0.00 0.98
42 43 6.974247 ACAATACTCCCTCCATCCCATAATAT 59.026 38.462 0.00 0.00 0.00 1.28
43 44 8.135586 ACAATACTCCCTCCATCCCATAATATA 58.864 37.037 0.00 0.00 0.00 0.86
44 45 9.003145 CAATACTCCCTCCATCCCATAATATAA 57.997 37.037 0.00 0.00 0.00 0.98
45 46 8.805145 ATACTCCCTCCATCCCATAATATAAG 57.195 38.462 0.00 0.00 0.00 1.73
46 47 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
47 48 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
48 49 5.667626 TCCCTCCATCCCATAATATAAGAGC 59.332 44.000 0.00 0.00 0.00 4.09
49 50 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
50 51 5.129485 CCTCCATCCCATAATATAAGAGCGT 59.871 44.000 0.00 0.00 0.00 5.07
51 52 6.323996 CCTCCATCCCATAATATAAGAGCGTA 59.676 42.308 0.00 0.00 0.00 4.42
52 53 7.348080 TCCATCCCATAATATAAGAGCGTAG 57.652 40.000 0.00 0.00 0.00 3.51
53 54 6.895756 TCCATCCCATAATATAAGAGCGTAGT 59.104 38.462 0.00 0.00 0.00 2.73
54 55 7.399191 TCCATCCCATAATATAAGAGCGTAGTT 59.601 37.037 0.00 0.00 0.00 2.24
55 56 7.492669 CCATCCCATAATATAAGAGCGTAGTTG 59.507 40.741 0.00 0.00 0.00 3.16
56 57 7.770366 TCCCATAATATAAGAGCGTAGTTGA 57.230 36.000 0.00 0.00 0.00 3.18
65 66 3.318017 AGAGCGTAGTTGACACATTCAC 58.682 45.455 0.00 0.00 32.26 3.18
143 145 5.463061 GCAATAGCAACATGTCAACAAACTT 59.537 36.000 0.00 0.00 41.58 2.66
170 172 8.721478 GCAATAGTATATCAACCGATCAACAAT 58.279 33.333 0.00 0.00 32.73 2.71
322 325 9.280174 CACAAATTTAAACTACTACTCCTTCCA 57.720 33.333 0.00 0.00 0.00 3.53
391 396 9.886132 AAAAACGTCTTATATCATAGGACAAGT 57.114 29.630 8.56 0.00 0.00 3.16
393 398 7.818997 ACGTCTTATATCATAGGACAAGTGA 57.181 36.000 8.56 0.00 0.00 3.41
394 399 7.877003 ACGTCTTATATCATAGGACAAGTGAG 58.123 38.462 8.56 0.00 0.00 3.51
395 400 7.502895 ACGTCTTATATCATAGGACAAGTGAGT 59.497 37.037 8.56 0.00 0.00 3.41
396 401 9.000486 CGTCTTATATCATAGGACAAGTGAGTA 58.000 37.037 8.56 0.00 0.00 2.59
440 445 7.725251 TCATATAAAGATCCCCAAAATTGCAC 58.275 34.615 0.00 0.00 0.00 4.57
463 656 7.062839 GCACGATTTTGTTTCATAAATAGCCAA 59.937 33.333 0.00 0.00 0.00 4.52
501 694 0.655733 CCGCTCGTTCAAAACACACT 59.344 50.000 0.00 0.00 0.00 3.55
507 700 1.871039 CGTTCAAAACACACTCCCGAT 59.129 47.619 0.00 0.00 0.00 4.18
543 736 0.998145 ACACTCCCGGACCTAGTACT 59.002 55.000 0.73 0.00 0.00 2.73
546 739 0.178995 CTCCCGGACCTAGTACTCCC 60.179 65.000 0.73 0.00 0.00 4.30
964 1339 3.503748 CCCCAATCAGAATTCTATTCGCC 59.496 47.826 7.86 0.00 0.00 5.54
965 1340 4.392940 CCCAATCAGAATTCTATTCGCCT 58.607 43.478 7.86 0.00 0.00 5.52
966 1341 4.214971 CCCAATCAGAATTCTATTCGCCTG 59.785 45.833 7.86 0.00 0.00 4.85
967 1342 5.059161 CCAATCAGAATTCTATTCGCCTGA 58.941 41.667 7.86 0.00 35.48 3.86
968 1343 5.528690 CCAATCAGAATTCTATTCGCCTGAA 59.471 40.000 7.86 0.00 38.76 3.02
969 1344 6.206243 CCAATCAGAATTCTATTCGCCTGAAT 59.794 38.462 7.86 0.00 46.41 2.57
970 1345 7.296660 CAATCAGAATTCTATTCGCCTGAATC 58.703 38.462 7.86 0.00 43.70 2.52
971 1346 4.984785 TCAGAATTCTATTCGCCTGAATCG 59.015 41.667 7.86 0.00 43.70 3.34
972 1347 4.151335 CAGAATTCTATTCGCCTGAATCGG 59.849 45.833 7.86 0.00 43.70 4.18
973 1348 4.039245 AGAATTCTATTCGCCTGAATCGGA 59.961 41.667 6.06 0.00 43.70 4.55
974 1349 3.371102 TTCTATTCGCCTGAATCGGAG 57.629 47.619 0.00 0.00 43.70 4.63
975 1350 1.000163 TCTATTCGCCTGAATCGGAGC 60.000 52.381 0.00 0.00 43.70 4.70
976 1351 0.750249 TATTCGCCTGAATCGGAGCA 59.250 50.000 0.00 0.00 43.70 4.26
977 1352 0.531532 ATTCGCCTGAATCGGAGCAG 60.532 55.000 0.00 4.24 40.90 4.24
1240 1631 0.454600 GCTCGTCGTAATGTCCCTGA 59.545 55.000 0.00 0.00 0.00 3.86
1248 1639 4.030913 TCGTAATGTCCCTGATCTTCCTT 58.969 43.478 0.00 0.00 0.00 3.36
1459 1850 1.901650 CTCCGACAAGCCTGTTTCGC 61.902 60.000 0.00 0.00 35.30 4.70
1780 2171 2.095461 TCGAGTCTCTTCAGTGGATGG 58.905 52.381 0.00 0.00 0.00 3.51
1812 2203 3.099170 ATGCAATCCGGGGAGCCT 61.099 61.111 0.00 0.00 0.00 4.58
1895 2286 1.488393 GATCCTGCTTCCTGGTAGCTT 59.512 52.381 23.25 8.22 39.38 3.74
1896 2287 0.615331 TCCTGCTTCCTGGTAGCTTG 59.385 55.000 23.25 16.13 39.38 4.01
1903 2294 2.254152 TCCTGGTAGCTTGATGGAGT 57.746 50.000 0.00 0.00 0.00 3.85
2163 2554 3.952323 ACAAATGCTCAATGCTATCTGCT 59.048 39.130 0.00 0.00 43.37 4.24
2228 2621 9.298774 GTGTACTAGTCTTTTGGTACATGATAC 57.701 37.037 0.00 0.00 43.73 2.24
2261 2654 8.420222 TCTAAATGCAAAAATCTTCCAGTTTCA 58.580 29.630 0.00 0.00 0.00 2.69
2277 2670 4.214332 CAGTTTCAAGTAAGTCCCAGCTTC 59.786 45.833 0.00 0.00 0.00 3.86
2377 2770 4.698780 TCATGATCAGGCTGAACTTGAAAG 59.301 41.667 28.91 12.57 32.97 2.62
2477 2878 6.600032 TCTTGGTTTGCTAGTTTTTCTGTGTA 59.400 34.615 0.00 0.00 0.00 2.90
2494 2895 6.209361 TCTGTGTATGATTCGTGCTTCTATC 58.791 40.000 0.00 0.00 0.00 2.08
2537 2940 5.065218 GGCACTATTACTTCACTGGTTGATG 59.935 44.000 0.00 0.00 32.84 3.07
2646 3236 8.956533 TTCACCATATGAAGATATTTTCGTCA 57.043 30.769 3.65 0.00 45.09 4.35
2757 3354 3.432326 GCAAATCTCATACTCCCTCCGTT 60.432 47.826 0.00 0.00 0.00 4.44
2759 3356 2.068834 TCTCATACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
2760 3357 1.286849 TCTCATACTCCCTCCGTTCCA 59.713 52.381 0.00 0.00 0.00 3.53
2766 3363 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2767 3364 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2770 3367 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2772 3369 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2773 3370 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2775 3372 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2776 3373 6.414732 TCCGTTCCAAAATAGATGACTCAAT 58.585 36.000 0.00 0.00 0.00 2.57
2777 3374 6.884295 TCCGTTCCAAAATAGATGACTCAATT 59.116 34.615 0.00 0.00 0.00 2.32
2778 3375 7.393234 TCCGTTCCAAAATAGATGACTCAATTT 59.607 33.333 0.00 0.00 0.00 1.82
2781 3378 9.696917 GTTCCAAAATAGATGACTCAATTTTGT 57.303 29.630 18.01 0.00 43.14 2.83
2829 3457 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2830 3458 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2831 3459 3.629142 ATTTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
2832 3460 2.314071 TTTGGAACGGAGGGAGTAGA 57.686 50.000 0.00 0.00 0.00 2.59
2833 3461 2.544844 TTGGAACGGAGGGAGTAGAT 57.455 50.000 0.00 0.00 0.00 1.98
2834 3462 3.675348 TTGGAACGGAGGGAGTAGATA 57.325 47.619 0.00 0.00 0.00 1.98
2835 3463 3.225177 TGGAACGGAGGGAGTAGATAG 57.775 52.381 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.689972 GGAGTATTGTTTTTCAGAATCATCCAT 58.310 33.333 0.00 0.00 0.00 3.41
1 2 7.122650 GGGAGTATTGTTTTTCAGAATCATCCA 59.877 37.037 0.00 0.00 0.00 3.41
2 3 7.340487 AGGGAGTATTGTTTTTCAGAATCATCC 59.660 37.037 0.00 0.00 0.00 3.51
3 4 8.286191 AGGGAGTATTGTTTTTCAGAATCATC 57.714 34.615 0.00 0.00 0.00 2.92
4 5 7.340487 GGAGGGAGTATTGTTTTTCAGAATCAT 59.660 37.037 0.00 0.00 0.00 2.45
7 8 6.552008 TGGAGGGAGTATTGTTTTTCAGAAT 58.448 36.000 0.00 0.00 0.00 2.40
8 9 5.947663 TGGAGGGAGTATTGTTTTTCAGAA 58.052 37.500 0.00 0.00 0.00 3.02
9 10 5.576563 TGGAGGGAGTATTGTTTTTCAGA 57.423 39.130 0.00 0.00 0.00 3.27
10 11 5.358160 GGATGGAGGGAGTATTGTTTTTCAG 59.642 44.000 0.00 0.00 0.00 3.02
11 12 5.261216 GGATGGAGGGAGTATTGTTTTTCA 58.739 41.667 0.00 0.00 0.00 2.69
12 13 4.645136 GGGATGGAGGGAGTATTGTTTTTC 59.355 45.833 0.00 0.00 0.00 2.29
13 14 4.045334 TGGGATGGAGGGAGTATTGTTTTT 59.955 41.667 0.00 0.00 0.00 1.94
14 15 3.596046 TGGGATGGAGGGAGTATTGTTTT 59.404 43.478 0.00 0.00 0.00 2.43
15 16 3.197983 TGGGATGGAGGGAGTATTGTTT 58.802 45.455 0.00 0.00 0.00 2.83
16 17 2.858644 TGGGATGGAGGGAGTATTGTT 58.141 47.619 0.00 0.00 0.00 2.83
17 18 2.587060 TGGGATGGAGGGAGTATTGT 57.413 50.000 0.00 0.00 0.00 2.71
18 19 5.786121 ATTATGGGATGGAGGGAGTATTG 57.214 43.478 0.00 0.00 0.00 1.90
19 20 9.230477 CTTATATTATGGGATGGAGGGAGTATT 57.770 37.037 0.00 0.00 0.00 1.89
20 21 8.587244 TCTTATATTATGGGATGGAGGGAGTAT 58.413 37.037 0.00 0.00 0.00 2.12
21 22 7.961940 TCTTATATTATGGGATGGAGGGAGTA 58.038 38.462 0.00 0.00 0.00 2.59
22 23 6.826727 TCTTATATTATGGGATGGAGGGAGT 58.173 40.000 0.00 0.00 0.00 3.85
23 24 6.183361 GCTCTTATATTATGGGATGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
24 25 5.667626 GCTCTTATATTATGGGATGGAGGGA 59.332 44.000 0.00 0.00 0.00 4.20
25 26 5.453903 CGCTCTTATATTATGGGATGGAGGG 60.454 48.000 0.00 0.00 0.00 4.30
26 27 5.129485 ACGCTCTTATATTATGGGATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
27 28 6.227298 ACGCTCTTATATTATGGGATGGAG 57.773 41.667 0.00 0.00 0.00 3.86
28 29 6.895756 ACTACGCTCTTATATTATGGGATGGA 59.104 38.462 0.00 0.00 0.00 3.41
29 30 7.113658 ACTACGCTCTTATATTATGGGATGG 57.886 40.000 0.00 0.00 0.00 3.51
30 31 8.251026 TCAACTACGCTCTTATATTATGGGATG 58.749 37.037 0.00 0.00 0.00 3.51
31 32 8.251721 GTCAACTACGCTCTTATATTATGGGAT 58.748 37.037 0.00 0.00 0.00 3.85
32 33 7.231925 TGTCAACTACGCTCTTATATTATGGGA 59.768 37.037 0.00 0.00 0.00 4.37
33 34 7.328737 GTGTCAACTACGCTCTTATATTATGGG 59.671 40.741 0.00 0.00 35.62 4.00
34 35 7.865889 TGTGTCAACTACGCTCTTATATTATGG 59.134 37.037 0.00 0.00 39.46 2.74
35 36 8.797266 TGTGTCAACTACGCTCTTATATTATG 57.203 34.615 0.00 0.00 39.46 1.90
36 37 9.982651 AATGTGTCAACTACGCTCTTATATTAT 57.017 29.630 0.00 0.00 39.46 1.28
37 38 9.459640 GAATGTGTCAACTACGCTCTTATATTA 57.540 33.333 0.00 0.00 39.46 0.98
38 39 7.979537 TGAATGTGTCAACTACGCTCTTATATT 59.020 33.333 0.00 0.00 39.46 1.28
39 40 7.435488 GTGAATGTGTCAACTACGCTCTTATAT 59.565 37.037 0.00 0.00 38.23 0.86
40 41 6.750501 GTGAATGTGTCAACTACGCTCTTATA 59.249 38.462 0.00 0.00 38.23 0.98
41 42 5.577164 GTGAATGTGTCAACTACGCTCTTAT 59.423 40.000 0.00 0.00 38.23 1.73
42 43 4.921515 GTGAATGTGTCAACTACGCTCTTA 59.078 41.667 0.00 0.00 38.23 2.10
43 44 3.741344 GTGAATGTGTCAACTACGCTCTT 59.259 43.478 0.00 0.00 38.23 2.85
44 45 3.005897 AGTGAATGTGTCAACTACGCTCT 59.994 43.478 0.00 0.00 38.23 4.09
45 46 3.121944 CAGTGAATGTGTCAACTACGCTC 59.878 47.826 0.00 0.00 38.23 5.03
46 47 3.059884 CAGTGAATGTGTCAACTACGCT 58.940 45.455 0.00 0.00 38.23 5.07
47 48 2.157668 CCAGTGAATGTGTCAACTACGC 59.842 50.000 0.00 0.00 38.23 4.42
48 49 3.184379 CACCAGTGAATGTGTCAACTACG 59.816 47.826 0.00 0.00 38.23 3.51
49 50 3.498397 CCACCAGTGAATGTGTCAACTAC 59.502 47.826 0.00 0.00 38.23 2.73
50 51 3.389656 TCCACCAGTGAATGTGTCAACTA 59.610 43.478 0.00 0.00 38.23 2.24
51 52 2.172505 TCCACCAGTGAATGTGTCAACT 59.827 45.455 0.00 0.00 38.23 3.16
52 53 2.549754 CTCCACCAGTGAATGTGTCAAC 59.450 50.000 0.00 0.00 38.23 3.18
53 54 2.849942 CTCCACCAGTGAATGTGTCAA 58.150 47.619 0.00 0.00 38.23 3.18
54 55 1.543208 GCTCCACCAGTGAATGTGTCA 60.543 52.381 0.00 0.00 0.00 3.58
55 56 1.160137 GCTCCACCAGTGAATGTGTC 58.840 55.000 0.00 0.00 0.00 3.67
56 57 0.250901 GGCTCCACCAGTGAATGTGT 60.251 55.000 0.00 0.00 38.86 3.72
143 145 7.213678 TGTTGATCGGTTGATATACTATTGCA 58.786 34.615 0.00 0.00 34.09 4.08
211 213 0.747255 ACTCATAGCTACTGTGCCCG 59.253 55.000 0.00 0.00 0.00 6.13
267 269 9.071276 TCTCAAAATCAAGAATCAATATAGCCC 57.929 33.333 0.00 0.00 0.00 5.19
437 442 6.529829 TGGCTATTTATGAAACAAAATCGTGC 59.470 34.615 0.00 0.00 0.00 5.34
451 644 6.094048 CGGATGGGAGTATTTGGCTATTTATG 59.906 42.308 0.00 0.00 0.00 1.90
463 656 1.625818 GGATCTGCGGATGGGAGTATT 59.374 52.381 14.17 0.00 35.27 1.89
501 694 0.107800 AGACGAGTTCGAGATCGGGA 60.108 55.000 20.81 0.00 43.12 5.14
507 700 4.320057 GGAGTGTTTTAGACGAGTTCGAGA 60.320 45.833 8.72 0.00 43.02 4.04
543 736 0.179067 GACTGTGACGTGGTTTGGGA 60.179 55.000 0.00 0.00 0.00 4.37
546 739 0.179056 AGGGACTGTGACGTGGTTTG 60.179 55.000 0.00 0.00 37.18 2.93
964 1339 3.359194 CAGTCCTGCTCCGATTCAG 57.641 57.895 0.00 0.00 0.00 3.02
1240 1631 4.326255 CTTGGCGGCAAGGAAGAT 57.674 55.556 36.64 0.00 0.00 2.40
1347 1738 2.203001 CCACACACGGTGCAGACA 60.203 61.111 8.30 0.00 46.50 3.41
1385 1776 0.667487 CGAGCTGCCGTTCTTGAGAA 60.667 55.000 0.00 0.00 0.00 2.87
1459 1850 2.507992 CTCAGAAGCCAGCGACCG 60.508 66.667 0.00 0.00 0.00 4.79
1780 2171 4.567959 GGATTGCATGCCAAACTTATTGAC 59.432 41.667 16.68 0.00 36.92 3.18
1812 2203 1.996292 CTCGCTCGGATGAAAACTCA 58.004 50.000 0.00 0.00 0.00 3.41
1870 2261 2.114616 ACCAGGAAGCAGGATCTACAG 58.885 52.381 0.00 0.00 0.00 2.74
1895 2286 2.614481 GGCCAACGTTTCTACTCCATCA 60.614 50.000 0.00 0.00 0.00 3.07
1896 2287 2.007608 GGCCAACGTTTCTACTCCATC 58.992 52.381 0.00 0.00 0.00 3.51
1903 2294 1.071699 AGCTTCAGGCCAACGTTTCTA 59.928 47.619 5.01 0.00 43.05 2.10
1989 2380 6.822676 CCAGCTATCAAAATTTGGGCAATTTA 59.177 34.615 5.83 0.00 43.20 1.40
1992 2383 4.225717 ACCAGCTATCAAAATTTGGGCAAT 59.774 37.500 5.83 0.00 0.00 3.56
1993 2384 3.582208 ACCAGCTATCAAAATTTGGGCAA 59.418 39.130 5.83 0.00 0.00 4.52
2163 2554 8.153221 TCACATAATAAGACTTAAAGGGTCCA 57.847 34.615 0.00 0.00 34.56 4.02
2228 2621 8.876790 GGAAGATTTTTGCATTTAGAAATCCAG 58.123 33.333 12.41 0.00 38.59 3.86
2261 2654 1.640917 TCCGAAGCTGGGACTTACTT 58.359 50.000 2.70 0.00 0.00 2.24
2277 2670 4.718940 AAATGCCTTTTGAGGTATTCCG 57.281 40.909 8.83 0.00 42.15 4.30
2377 2770 0.548510 AATAGCTGAACCCTCCCTGC 59.451 55.000 0.00 0.00 0.00 4.85
2477 2878 2.224042 TGCCGATAGAAGCACGAATCAT 60.224 45.455 0.00 0.00 33.08 2.45
2558 2961 8.375608 ACAGCTGACTTTATAGCATCTTAATG 57.624 34.615 23.35 0.00 42.29 1.90
2641 3231 6.148948 CCACTGCAAAAATATCTTTTGACGA 58.851 36.000 18.90 7.69 40.73 4.20
2791 3388 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2792 3389 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2793 3390 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2794 3391 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2795 3392 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2797 3394 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2798 3395 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2799 3396 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2801 3398 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2803 3400 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2804 3401 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2806 3403 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2808 3405 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2809 3406 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2816 3444 3.226682 ACTATCTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
2829 3457 9.363401 ACCAGCACAGTAAATATGTACTATCTA 57.637 33.333 5.21 0.00 32.92 1.98
2830 3458 8.144478 CACCAGCACAGTAAATATGTACTATCT 58.856 37.037 5.21 1.14 32.92 1.98
2831 3459 8.141909 TCACCAGCACAGTAAATATGTACTATC 58.858 37.037 5.21 0.00 32.92 2.08
2832 3460 7.926555 GTCACCAGCACAGTAAATATGTACTAT 59.073 37.037 5.21 0.00 32.92 2.12
2833 3461 7.262772 GTCACCAGCACAGTAAATATGTACTA 58.737 38.462 5.21 0.00 32.92 1.82
2834 3462 6.106673 GTCACCAGCACAGTAAATATGTACT 58.893 40.000 0.00 0.00 34.56 2.73
2835 3463 5.005394 CGTCACCAGCACAGTAAATATGTAC 59.995 44.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.