Multiple sequence alignment - TraesCS1B01G035100

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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 TraesCS1B01G035100 chr1B 100.000 2225 0 0 1 2225 16692377 16694601 0.000000e+00 4109.0
1 TraesCS1B01G035100 chr1B 93.590 1560 85 14 131 1685 16477793 16479342 0.000000e+00 2313.0
2 TraesCS1B01G035100 chr1B 93.290 775 49 1 910 1684 16645423 16646194 0.000000e+00 1140.0
3 TraesCS1B01G035100 chr1B 90.207 531 39 4 1708 2225 16844102 16844632 0.000000e+00 680.0
4 TraesCS1B01G035100 chr1B 89.850 532 39 7 1708 2225 16894821 16895351 0.000000e+00 669.0
5 TraesCS1B01G035100 chr1B 87.266 534 42 13 1708 2225 17344836 17345359 8.850000e-164 586.0
6 TraesCS1B01G035100 chr1A 92.219 1568 107 12 125 1685 22634701 22633142 0.000000e+00 2206.0
7 TraesCS1B01G035100 chr1A 93.025 1061 70 4 606 1664 12698839 12697781 0.000000e+00 1546.0
8 TraesCS1B01G035100 chr1A 77.305 423 56 20 1794 2208 13573995 13574385 1.730000e-51 213.0
9 TraesCS1B01G035100 chr1A 86.413 184 19 2 1744 1925 13343072 13343251 1.740000e-46 196.0
10 TraesCS1B01G035100 chr1A 73.380 432 68 24 1775 2193 13457376 13457773 1.400000e-22 117.0
11 TraesCS1B01G035100 chr1A 94.340 53 2 1 800 852 508104020 508104071 1.830000e-11 80.5
12 TraesCS1B01G035100 chr1D 91.002 1567 105 17 133 1685 11123164 11124708 0.000000e+00 2080.0
13 TraesCS1B01G035100 chr1D 88.092 697 64 11 133 817 11040474 11041163 0.000000e+00 809.0
14 TraesCS1B01G035100 chr1D 86.514 697 60 15 133 817 11089200 11089874 0.000000e+00 736.0
15 TraesCS1B01G035100 chr1D 76.471 527 82 24 1719 2219 11322290 11322800 4.740000e-62 248.0
16 TraesCS1B01G035100 chr1D 82.520 246 36 4 1714 1958 11458265 11458504 2.240000e-50 209.0
17 TraesCS1B01G035100 chr1D 79.522 293 36 15 491 761 11197339 11197629 1.050000e-43 187.0
18 TraesCS1B01G035100 chr1D 89.552 67 6 1 133 198 11009281 11009347 1.420000e-12 84.2
19 TraesCS1B01G035100 chrUn 86.891 534 44 13 1708 2225 385679491 385678968 1.920000e-160 575.0
20 TraesCS1B01G035100 chr2D 90.741 54 4 1 799 851 306253807 306253754 1.100000e-08 71.3
21 TraesCS1B01G035100 chr2D 91.111 45 4 0 799 843 633255945 633255989 6.630000e-06 62.1
22 TraesCS1B01G035100 chr2D 91.111 45 4 0 799 843 633283301 633283345 6.630000e-06 62.1
23 TraesCS1B01G035100 chr3B 90.566 53 4 1 799 851 528659641 528659692 3.960000e-08 69.4


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 TraesCS1B01G035100 chr1B 16692377 16694601 2224 False 4109 4109 100.000 1 2225 1 chr1B.!!$F3 2224
1 TraesCS1B01G035100 chr1B 16477793 16479342 1549 False 2313 2313 93.590 131 1685 1 chr1B.!!$F1 1554
2 TraesCS1B01G035100 chr1B 16645423 16646194 771 False 1140 1140 93.290 910 1684 1 chr1B.!!$F2 774
3 TraesCS1B01G035100 chr1B 16844102 16844632 530 False 680 680 90.207 1708 2225 1 chr1B.!!$F4 517
4 TraesCS1B01G035100 chr1B 16894821 16895351 530 False 669 669 89.850 1708 2225 1 chr1B.!!$F5 517
5 TraesCS1B01G035100 chr1B 17344836 17345359 523 False 586 586 87.266 1708 2225 1 chr1B.!!$F6 517
6 TraesCS1B01G035100 chr1A 22633142 22634701 1559 True 2206 2206 92.219 125 1685 1 chr1A.!!$R2 1560
7 TraesCS1B01G035100 chr1A 12697781 12698839 1058 True 1546 1546 93.025 606 1664 1 chr1A.!!$R1 1058
8 TraesCS1B01G035100 chr1D 11123164 11124708 1544 False 2080 2080 91.002 133 1685 1 chr1D.!!$F4 1552
9 TraesCS1B01G035100 chr1D 11040474 11041163 689 False 809 809 88.092 133 817 1 chr1D.!!$F2 684
10 TraesCS1B01G035100 chr1D 11089200 11089874 674 False 736 736 86.514 133 817 1 chr1D.!!$F3 684
11 TraesCS1B01G035100 chr1D 11322290 11322800 510 False 248 248 76.471 1719 2219 1 chr1D.!!$F6 500
12 TraesCS1B01G035100 chrUn 385678968 385679491 523 True 575 575 86.891 1708 2225 1 chrUn.!!$R1 517

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
98 99 0.04394 AGCTCCCTCCTGACCAATCT 59.956 55.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1685 0.821711 TGTCGGCAAAGGGTTTGAGG 60.822 55.0 3.56 0.0 43.26 3.86 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
23 24 5.366460 GACCCAGTTAGGTTATAAAGCTCC 58.634 45.833 0.00 0.00 41.42 4.70
24 25 4.141779 ACCCAGTTAGGTTATAAAGCTCCG 60.142 45.833 0.00 0.00 36.44 4.63
25 26 3.808174 CCAGTTAGGTTATAAAGCTCCGC 59.192 47.826 0.00 0.00 40.27 5.54
26 27 4.443034 CCAGTTAGGTTATAAAGCTCCGCT 60.443 45.833 0.00 0.00 42.56 5.52
27 28 8.807153 CCCAGTTAGGTTATAAAGCTCCGCTT 62.807 46.154 0.00 0.00 43.20 4.68
37 38 2.579410 AGCTCCGCTTTCCCTTAAAA 57.421 45.000 0.00 0.00 33.89 1.52
38 39 3.087370 AGCTCCGCTTTCCCTTAAAAT 57.913 42.857 0.00 0.00 33.89 1.82
39 40 4.230745 AGCTCCGCTTTCCCTTAAAATA 57.769 40.909 0.00 0.00 33.89 1.40
40 41 4.595986 AGCTCCGCTTTCCCTTAAAATAA 58.404 39.130 0.00 0.00 33.89 1.40
41 42 5.014202 AGCTCCGCTTTCCCTTAAAATAAA 58.986 37.500 0.00 0.00 33.89 1.40
42 43 5.656859 AGCTCCGCTTTCCCTTAAAATAAAT 59.343 36.000 0.00 0.00 33.89 1.40
43 44 5.977725 GCTCCGCTTTCCCTTAAAATAAATC 59.022 40.000 0.00 0.00 0.00 2.17
44 45 6.183360 GCTCCGCTTTCCCTTAAAATAAATCT 60.183 38.462 0.00 0.00 0.00 2.40
45 46 7.012989 GCTCCGCTTTCCCTTAAAATAAATCTA 59.987 37.037 0.00 0.00 0.00 1.98
46 47 8.446599 TCCGCTTTCCCTTAAAATAAATCTAG 57.553 34.615 0.00 0.00 0.00 2.43
47 48 8.269317 TCCGCTTTCCCTTAAAATAAATCTAGA 58.731 33.333 0.00 0.00 0.00 2.43
48 49 8.899771 CCGCTTTCCCTTAAAATAAATCTAGAA 58.100 33.333 0.00 0.00 0.00 2.10
49 50 9.717892 CGCTTTCCCTTAAAATAAATCTAGAAC 57.282 33.333 0.00 0.00 0.00 3.01
50 51 9.717892 GCTTTCCCTTAAAATAAATCTAGAACG 57.282 33.333 0.00 0.00 0.00 3.95
52 53 9.962809 TTTCCCTTAAAATAAATCTAGAACGGA 57.037 29.630 0.00 0.00 0.00 4.69
53 54 9.609346 TTCCCTTAAAATAAATCTAGAACGGAG 57.391 33.333 0.00 0.00 0.00 4.63
54 55 8.208903 TCCCTTAAAATAAATCTAGAACGGAGG 58.791 37.037 0.00 0.00 0.00 4.30
55 56 7.991460 CCCTTAAAATAAATCTAGAACGGAGGT 59.009 37.037 0.00 0.00 0.00 3.85
56 57 8.827677 CCTTAAAATAAATCTAGAACGGAGGTG 58.172 37.037 0.00 0.00 0.00 4.00
57 58 8.726870 TTAAAATAAATCTAGAACGGAGGTGG 57.273 34.615 0.00 0.00 0.00 4.61
58 59 5.952347 AATAAATCTAGAACGGAGGTGGT 57.048 39.130 0.00 0.00 0.00 4.16
59 60 7.427989 AAATAAATCTAGAACGGAGGTGGTA 57.572 36.000 0.00 0.00 0.00 3.25
60 61 4.732672 AAATCTAGAACGGAGGTGGTAC 57.267 45.455 0.00 0.00 0.00 3.34
61 62 3.666345 ATCTAGAACGGAGGTGGTACT 57.334 47.619 0.00 0.00 0.00 2.73
62 63 4.785346 ATCTAGAACGGAGGTGGTACTA 57.215 45.455 0.00 0.00 0.00 1.82
63 64 4.574674 TCTAGAACGGAGGTGGTACTAA 57.425 45.455 0.00 0.00 0.00 2.24
64 65 4.922206 TCTAGAACGGAGGTGGTACTAAA 58.078 43.478 0.00 0.00 0.00 1.85
65 66 3.949842 AGAACGGAGGTGGTACTAAAC 57.050 47.619 0.00 0.00 0.00 2.01
66 67 3.233507 AGAACGGAGGTGGTACTAAACA 58.766 45.455 0.00 0.00 0.00 2.83
67 68 3.642848 AGAACGGAGGTGGTACTAAACAA 59.357 43.478 0.00 0.00 0.00 2.83
68 69 3.672767 ACGGAGGTGGTACTAAACAAG 57.327 47.619 0.00 0.00 0.00 3.16
69 70 2.967887 ACGGAGGTGGTACTAAACAAGT 59.032 45.455 0.00 0.00 42.62 3.16
70 71 3.006217 ACGGAGGTGGTACTAAACAAGTC 59.994 47.826 0.00 0.00 39.80 3.01
71 72 3.615834 CGGAGGTGGTACTAAACAAGTCC 60.616 52.174 0.00 0.00 39.80 3.85
72 73 3.581770 GGAGGTGGTACTAAACAAGTCCT 59.418 47.826 0.00 0.00 39.80 3.85
73 74 4.041321 GGAGGTGGTACTAAACAAGTCCTT 59.959 45.833 0.00 0.00 39.80 3.36
74 75 5.224821 AGGTGGTACTAAACAAGTCCTTC 57.775 43.478 0.00 0.00 39.80 3.46
75 76 4.041321 AGGTGGTACTAAACAAGTCCTTCC 59.959 45.833 0.00 0.00 39.80 3.46
76 77 4.202388 GGTGGTACTAAACAAGTCCTTCCA 60.202 45.833 0.00 0.00 39.80 3.53
77 78 4.753610 GTGGTACTAAACAAGTCCTTCCAC 59.246 45.833 0.00 0.00 39.80 4.02
78 79 4.202388 TGGTACTAAACAAGTCCTTCCACC 60.202 45.833 0.00 0.00 39.80 4.61
79 80 4.202388 GGTACTAAACAAGTCCTTCCACCA 60.202 45.833 0.00 0.00 39.80 4.17
80 81 4.086706 ACTAAACAAGTCCTTCCACCAG 57.913 45.455 0.00 0.00 30.33 4.00
81 82 1.692411 AAACAAGTCCTTCCACCAGC 58.308 50.000 0.00 0.00 0.00 4.85
82 83 0.846693 AACAAGTCCTTCCACCAGCT 59.153 50.000 0.00 0.00 0.00 4.24
83 84 0.398318 ACAAGTCCTTCCACCAGCTC 59.602 55.000 0.00 0.00 0.00 4.09
84 85 0.322008 CAAGTCCTTCCACCAGCTCC 60.322 60.000 0.00 0.00 0.00 4.70
85 86 1.492993 AAGTCCTTCCACCAGCTCCC 61.493 60.000 0.00 0.00 0.00 4.30
86 87 1.920835 GTCCTTCCACCAGCTCCCT 60.921 63.158 0.00 0.00 0.00 4.20
87 88 1.613630 TCCTTCCACCAGCTCCCTC 60.614 63.158 0.00 0.00 0.00 4.30
88 89 2.674220 CCTTCCACCAGCTCCCTCC 61.674 68.421 0.00 0.00 0.00 4.30
89 90 1.614824 CTTCCACCAGCTCCCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
90 91 1.908340 CTTCCACCAGCTCCCTCCTG 61.908 65.000 0.00 0.00 0.00 3.86
91 92 2.284921 CCACCAGCTCCCTCCTGA 60.285 66.667 0.00 0.00 32.03 3.86
92 93 2.664081 CCACCAGCTCCCTCCTGAC 61.664 68.421 0.00 0.00 32.03 3.51
93 94 2.284995 ACCAGCTCCCTCCTGACC 60.285 66.667 0.00 0.00 32.03 4.02
94 95 2.284921 CCAGCTCCCTCCTGACCA 60.285 66.667 0.00 0.00 32.03 4.02
95 96 1.920325 CCAGCTCCCTCCTGACCAA 60.920 63.158 0.00 0.00 32.03 3.67
96 97 1.277580 CCAGCTCCCTCCTGACCAAT 61.278 60.000 0.00 0.00 32.03 3.16
97 98 0.179936 CAGCTCCCTCCTGACCAATC 59.820 60.000 0.00 0.00 32.03 2.67
98 99 0.043940 AGCTCCCTCCTGACCAATCT 59.956 55.000 0.00 0.00 0.00 2.40
99 100 0.179936 GCTCCCTCCTGACCAATCTG 59.820 60.000 0.00 0.00 0.00 2.90
100 101 0.835941 CTCCCTCCTGACCAATCTGG 59.164 60.000 0.00 0.00 45.02 3.86
104 105 3.087343 TCCTGACCAATCTGGAGCA 57.913 52.632 0.00 0.00 45.37 4.26
105 106 1.588239 TCCTGACCAATCTGGAGCAT 58.412 50.000 0.00 0.00 45.37 3.79
106 107 1.487976 TCCTGACCAATCTGGAGCATC 59.512 52.381 0.00 0.00 45.37 3.91
121 122 4.935885 GAGCATCCATTCGATATCCAAC 57.064 45.455 0.00 0.00 0.00 3.77
122 123 3.329386 AGCATCCATTCGATATCCAACG 58.671 45.455 0.00 0.00 0.00 4.10
123 124 2.416547 GCATCCATTCGATATCCAACGG 59.583 50.000 0.00 0.00 0.00 4.44
129 130 1.954146 CGATATCCAACGGCCCGTG 60.954 63.158 10.80 3.91 39.99 4.94
145 146 4.439563 GGCCCGTGGTAATTATTGTCAAAG 60.440 45.833 0.00 0.00 0.00 2.77
226 228 8.145767 TGTGAATTCTCTTTTGAATGCAAATCT 58.854 29.630 7.05 0.00 41.93 2.40
232 234 8.528917 TCTCTTTTGAATGCAAATCTTCAATG 57.471 30.769 12.63 9.58 43.07 2.82
279 282 7.761651 ATATTACATGTGACTGCGCTATATG 57.238 36.000 9.73 9.04 0.00 1.78
286 289 4.248859 GTGACTGCGCTATATGGATGATT 58.751 43.478 9.73 0.00 0.00 2.57
484 505 1.443872 GAGCCACGTCGTGTACCAG 60.444 63.158 23.01 9.17 0.00 4.00
561 583 4.260620 GCACAATGAAACAAGTAGTCGTGT 60.261 41.667 0.00 0.00 37.84 4.49
644 667 4.501433 AGCATCCTATCCCATCTTCTCTT 58.499 43.478 0.00 0.00 0.00 2.85
672 695 8.129001 TGATAGATCTTCCCTATAAATAGGCCA 58.871 37.037 5.01 0.00 46.88 5.36
712 735 7.238486 ACTCATATCAGTCAAGTTCAGAGTT 57.762 36.000 0.00 0.00 29.12 3.01
718 741 4.584743 TCAGTCAAGTTCAGAGTTAGCTCA 59.415 41.667 9.43 0.00 44.00 4.26
937 969 3.320541 TGAACTATTTGGGCCAACTGTTG 59.679 43.478 25.39 13.50 0.00 3.33
1201 1233 1.468224 GCATCATCGTCGACACTGTCT 60.468 52.381 17.16 2.03 0.00 3.41
1234 1266 3.230134 TCCATTGGTTAGCAAGCTTTGT 58.770 40.909 0.00 0.00 0.00 2.83
1288 1320 7.130917 GCATGCTGATGAATAAGTAGTTTCAG 58.869 38.462 11.37 5.05 35.47 3.02
1407 1439 4.096532 TCGGCTTGTTGTTCATGTGTTTAA 59.903 37.500 0.00 0.00 0.00 1.52
1472 1505 8.335532 TGGATTATTTCAACAACTTAGACCTG 57.664 34.615 0.00 0.00 0.00 4.00
1595 1628 7.000472 TGGACAAACTTCTGAGATGAGAATTT 59.000 34.615 2.06 0.00 31.51 1.82
1671 1705 1.028905 CTCAAACCCTTTGCCGACAA 58.971 50.000 0.00 0.00 40.43 3.18
1685 1719 5.041951 TGCCGACAAATAAGAAACATGAC 57.958 39.130 0.00 0.00 0.00 3.06
1686 1720 4.083003 TGCCGACAAATAAGAAACATGACC 60.083 41.667 0.00 0.00 0.00 4.02
1687 1721 4.674362 GCCGACAAATAAGAAACATGACCC 60.674 45.833 0.00 0.00 0.00 4.46
1688 1722 4.142469 CCGACAAATAAGAAACATGACCCC 60.142 45.833 0.00 0.00 0.00 4.95
1689 1723 4.436852 CGACAAATAAGAAACATGACCCCG 60.437 45.833 0.00 0.00 0.00 5.73
1690 1724 4.403734 ACAAATAAGAAACATGACCCCGT 58.596 39.130 0.00 0.00 0.00 5.28
1691 1725 4.217550 ACAAATAAGAAACATGACCCCGTG 59.782 41.667 0.00 0.00 35.46 4.94
1692 1726 1.816074 TAAGAAACATGACCCCGTGC 58.184 50.000 0.00 0.00 32.58 5.34
1693 1727 0.893727 AAGAAACATGACCCCGTGCC 60.894 55.000 0.00 0.00 32.58 5.01
1694 1728 1.303317 GAAACATGACCCCGTGCCT 60.303 57.895 0.00 0.00 32.58 4.75
1695 1729 0.035820 GAAACATGACCCCGTGCCTA 60.036 55.000 0.00 0.00 32.58 3.93
1696 1730 0.623723 AAACATGACCCCGTGCCTAT 59.376 50.000 0.00 0.00 32.58 2.57
1697 1731 0.180406 AACATGACCCCGTGCCTATC 59.820 55.000 0.00 0.00 32.58 2.08
1698 1732 0.980754 ACATGACCCCGTGCCTATCA 60.981 55.000 0.00 0.00 32.58 2.15
1699 1733 0.180171 CATGACCCCGTGCCTATCAA 59.820 55.000 0.00 0.00 0.00 2.57
1700 1734 0.180406 ATGACCCCGTGCCTATCAAC 59.820 55.000 0.00 0.00 0.00 3.18
1701 1735 1.195442 TGACCCCGTGCCTATCAACA 61.195 55.000 0.00 0.00 0.00 3.33
1702 1736 0.180406 GACCCCGTGCCTATCAACAT 59.820 55.000 0.00 0.00 0.00 2.71
1703 1737 0.623723 ACCCCGTGCCTATCAACATT 59.376 50.000 0.00 0.00 0.00 2.71
1704 1738 1.841277 ACCCCGTGCCTATCAACATTA 59.159 47.619 0.00 0.00 0.00 1.90
1705 1739 2.441750 ACCCCGTGCCTATCAACATTAT 59.558 45.455 0.00 0.00 0.00 1.28
1706 1740 3.117663 ACCCCGTGCCTATCAACATTATT 60.118 43.478 0.00 0.00 0.00 1.40
1931 1968 4.753233 TGATTGTGAAGGTTTTTGTGTGG 58.247 39.130 0.00 0.00 0.00 4.17
1984 2044 3.690475 AGAGACGAACGGGGTATTTTT 57.310 42.857 0.00 0.00 0.00 1.94
1985 2045 3.332034 AGAGACGAACGGGGTATTTTTG 58.668 45.455 0.00 0.00 0.00 2.44
1986 2046 3.007182 AGAGACGAACGGGGTATTTTTGA 59.993 43.478 0.00 0.00 0.00 2.69
1987 2047 3.332034 AGACGAACGGGGTATTTTTGAG 58.668 45.455 0.00 0.00 0.00 3.02
1988 2048 3.069289 GACGAACGGGGTATTTTTGAGT 58.931 45.455 0.00 0.00 0.00 3.41
2026 2087 2.995466 TGAAAGCTCGGCAAATGAAG 57.005 45.000 0.00 0.00 0.00 3.02
2027 2088 1.068333 TGAAAGCTCGGCAAATGAAGC 60.068 47.619 0.00 0.00 0.00 3.86
2043 2104 5.551760 ATGAAGCGACCTTGTAGAAAATG 57.448 39.130 0.00 0.00 0.00 2.32
2100 2161 4.829064 TTCTTTGGTGAACATTCGGAAG 57.171 40.909 0.00 0.00 0.00 3.46
2108 2169 5.048507 GGTGAACATTCGGAAGTAGTATCC 58.951 45.833 0.00 0.00 0.00 2.59
2150 2219 8.731605 AGAATCATATATAGTCGTAGTGTGGTG 58.268 37.037 0.00 0.00 0.00 4.17
2162 2231 2.387757 AGTGTGGTGCAGGAAAATTGT 58.612 42.857 0.00 0.00 0.00 2.71
2192 2268 3.239449 TGCAGTAGAAAAGAGTCAGGGA 58.761 45.455 0.00 0.00 0.00 4.20
2208 2284 9.391227 AGAGTCAGGGAATCATATCTTCTTTAT 57.609 33.333 0.00 0.00 0.00 1.40
2210 2286 9.163894 AGTCAGGGAATCATATCTTCTTTATGA 57.836 33.333 0.00 0.00 39.64 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.366460 GGAGCTTTATAACCTAACTGGGTC 58.634 45.833 0.00 0.00 38.87 4.46
1 2 4.141779 CGGAGCTTTATAACCTAACTGGGT 60.142 45.833 0.00 0.00 42.05 4.51
2 3 4.377897 CGGAGCTTTATAACCTAACTGGG 58.622 47.826 0.00 0.00 41.11 4.45
20 21 7.334844 AGATTTATTTTAAGGGAAAGCGGAG 57.665 36.000 0.00 0.00 0.00 4.63
21 22 8.269317 TCTAGATTTATTTTAAGGGAAAGCGGA 58.731 33.333 0.00 0.00 0.00 5.54
22 23 8.446599 TCTAGATTTATTTTAAGGGAAAGCGG 57.553 34.615 0.00 0.00 0.00 5.52
23 24 9.717892 GTTCTAGATTTATTTTAAGGGAAAGCG 57.282 33.333 0.00 0.00 0.00 4.68
24 25 9.717892 CGTTCTAGATTTATTTTAAGGGAAAGC 57.282 33.333 0.00 0.00 0.00 3.51
26 27 9.962809 TCCGTTCTAGATTTATTTTAAGGGAAA 57.037 29.630 0.00 0.00 0.00 3.13
27 28 9.609346 CTCCGTTCTAGATTTATTTTAAGGGAA 57.391 33.333 0.00 0.00 31.34 3.97
28 29 8.208903 CCTCCGTTCTAGATTTATTTTAAGGGA 58.791 37.037 0.00 0.00 0.00 4.20
29 30 7.991460 ACCTCCGTTCTAGATTTATTTTAAGGG 59.009 37.037 0.00 0.00 0.00 3.95
30 31 8.827677 CACCTCCGTTCTAGATTTATTTTAAGG 58.172 37.037 0.00 0.00 0.00 2.69
31 32 8.827677 CCACCTCCGTTCTAGATTTATTTTAAG 58.172 37.037 0.00 0.00 0.00 1.85
32 33 8.323567 ACCACCTCCGTTCTAGATTTATTTTAA 58.676 33.333 0.00 0.00 0.00 1.52
33 34 7.854337 ACCACCTCCGTTCTAGATTTATTTTA 58.146 34.615 0.00 0.00 0.00 1.52
34 35 6.718294 ACCACCTCCGTTCTAGATTTATTTT 58.282 36.000 0.00 0.00 0.00 1.82
35 36 6.309389 ACCACCTCCGTTCTAGATTTATTT 57.691 37.500 0.00 0.00 0.00 1.40
36 37 5.952347 ACCACCTCCGTTCTAGATTTATT 57.048 39.130 0.00 0.00 0.00 1.40
37 38 6.134754 AGTACCACCTCCGTTCTAGATTTAT 58.865 40.000 0.00 0.00 0.00 1.40
38 39 5.513233 AGTACCACCTCCGTTCTAGATTTA 58.487 41.667 0.00 0.00 0.00 1.40
39 40 4.351127 AGTACCACCTCCGTTCTAGATTT 58.649 43.478 0.00 0.00 0.00 2.17
40 41 3.978610 AGTACCACCTCCGTTCTAGATT 58.021 45.455 0.00 0.00 0.00 2.40
41 42 3.666345 AGTACCACCTCCGTTCTAGAT 57.334 47.619 0.00 0.00 0.00 1.98
42 43 4.574674 TTAGTACCACCTCCGTTCTAGA 57.425 45.455 0.00 0.00 0.00 2.43
43 44 4.460382 TGTTTAGTACCACCTCCGTTCTAG 59.540 45.833 0.00 0.00 0.00 2.43
44 45 4.406456 TGTTTAGTACCACCTCCGTTCTA 58.594 43.478 0.00 0.00 0.00 2.10
45 46 3.233507 TGTTTAGTACCACCTCCGTTCT 58.766 45.455 0.00 0.00 0.00 3.01
46 47 3.665745 TGTTTAGTACCACCTCCGTTC 57.334 47.619 0.00 0.00 0.00 3.95
47 48 3.389002 ACTTGTTTAGTACCACCTCCGTT 59.611 43.478 0.00 0.00 34.56 4.44
48 49 2.967887 ACTTGTTTAGTACCACCTCCGT 59.032 45.455 0.00 0.00 34.56 4.69
49 50 3.582780 GACTTGTTTAGTACCACCTCCG 58.417 50.000 0.00 0.00 37.17 4.63
50 51 3.581770 AGGACTTGTTTAGTACCACCTCC 59.418 47.826 0.00 0.00 38.62 4.30
51 52 4.886496 AGGACTTGTTTAGTACCACCTC 57.114 45.455 0.00 0.00 38.62 3.85
52 53 4.041321 GGAAGGACTTGTTTAGTACCACCT 59.959 45.833 0.00 0.00 38.62 4.00
53 54 4.202388 TGGAAGGACTTGTTTAGTACCACC 60.202 45.833 0.00 0.00 38.62 4.61
54 55 4.753610 GTGGAAGGACTTGTTTAGTACCAC 59.246 45.833 0.00 0.00 38.62 4.16
55 56 4.202388 GGTGGAAGGACTTGTTTAGTACCA 60.202 45.833 0.00 0.00 38.62 3.25
56 57 4.202388 TGGTGGAAGGACTTGTTTAGTACC 60.202 45.833 0.00 0.00 38.62 3.34
57 58 4.964593 TGGTGGAAGGACTTGTTTAGTAC 58.035 43.478 0.00 0.00 37.17 2.73
58 59 4.504340 GCTGGTGGAAGGACTTGTTTAGTA 60.504 45.833 0.00 0.00 37.17 1.82
59 60 3.747708 GCTGGTGGAAGGACTTGTTTAGT 60.748 47.826 0.00 0.00 40.71 2.24
60 61 2.814336 GCTGGTGGAAGGACTTGTTTAG 59.186 50.000 0.00 0.00 0.00 1.85
61 62 2.441750 AGCTGGTGGAAGGACTTGTTTA 59.558 45.455 0.00 0.00 0.00 2.01
62 63 1.215423 AGCTGGTGGAAGGACTTGTTT 59.785 47.619 0.00 0.00 0.00 2.83
63 64 0.846693 AGCTGGTGGAAGGACTTGTT 59.153 50.000 0.00 0.00 0.00 2.83
64 65 0.398318 GAGCTGGTGGAAGGACTTGT 59.602 55.000 0.00 0.00 0.00 3.16
65 66 0.322008 GGAGCTGGTGGAAGGACTTG 60.322 60.000 0.00 0.00 0.00 3.16
66 67 1.492993 GGGAGCTGGTGGAAGGACTT 61.493 60.000 0.00 0.00 0.00 3.01
67 68 1.920835 GGGAGCTGGTGGAAGGACT 60.921 63.158 0.00 0.00 0.00 3.85
68 69 1.904990 GAGGGAGCTGGTGGAAGGAC 61.905 65.000 0.00 0.00 0.00 3.85
69 70 1.613630 GAGGGAGCTGGTGGAAGGA 60.614 63.158 0.00 0.00 0.00 3.36
70 71 2.674220 GGAGGGAGCTGGTGGAAGG 61.674 68.421 0.00 0.00 0.00 3.46
71 72 1.614824 AGGAGGGAGCTGGTGGAAG 60.615 63.158 0.00 0.00 0.00 3.46
72 73 1.920325 CAGGAGGGAGCTGGTGGAA 60.920 63.158 0.00 0.00 0.00 3.53
73 74 2.284921 CAGGAGGGAGCTGGTGGA 60.285 66.667 0.00 0.00 0.00 4.02
74 75 2.284921 TCAGGAGGGAGCTGGTGG 60.285 66.667 0.00 0.00 0.00 4.61
75 76 2.664081 GGTCAGGAGGGAGCTGGTG 61.664 68.421 0.00 0.00 32.68 4.17
76 77 2.284995 GGTCAGGAGGGAGCTGGT 60.285 66.667 0.00 0.00 32.68 4.00
77 78 1.277580 ATTGGTCAGGAGGGAGCTGG 61.278 60.000 0.00 0.00 36.30 4.85
78 79 0.179936 GATTGGTCAGGAGGGAGCTG 59.820 60.000 0.00 0.00 36.30 4.24
79 80 0.043940 AGATTGGTCAGGAGGGAGCT 59.956 55.000 0.00 0.00 36.30 4.09
80 81 0.179936 CAGATTGGTCAGGAGGGAGC 59.820 60.000 0.00 0.00 35.89 4.70
81 82 0.835941 CCAGATTGGTCAGGAGGGAG 59.164 60.000 0.00 0.00 33.04 4.30
82 83 0.417437 TCCAGATTGGTCAGGAGGGA 59.583 55.000 0.00 0.00 39.03 4.20
83 84 3.012153 TCCAGATTGGTCAGGAGGG 57.988 57.895 0.00 0.00 39.03 4.30
86 87 1.487976 GATGCTCCAGATTGGTCAGGA 59.512 52.381 0.00 0.00 39.03 3.86
87 88 1.476471 GGATGCTCCAGATTGGTCAGG 60.476 57.143 0.00 0.00 39.03 3.86
88 89 1.211212 TGGATGCTCCAGATTGGTCAG 59.789 52.381 1.25 0.00 42.67 3.51
89 90 1.288188 TGGATGCTCCAGATTGGTCA 58.712 50.000 1.25 0.00 42.67 4.02
99 100 3.616956 TGGATATCGAATGGATGCTCC 57.383 47.619 0.00 3.06 38.14 4.70
100 101 3.369147 CGTTGGATATCGAATGGATGCTC 59.631 47.826 10.88 0.00 36.55 4.26
101 102 3.329386 CGTTGGATATCGAATGGATGCT 58.671 45.455 10.88 0.00 36.55 3.79
102 103 2.416547 CCGTTGGATATCGAATGGATGC 59.583 50.000 26.45 3.74 41.49 3.91
103 104 2.416547 GCCGTTGGATATCGAATGGATG 59.583 50.000 31.77 13.74 41.49 3.51
104 105 2.615493 GGCCGTTGGATATCGAATGGAT 60.615 50.000 31.77 0.00 41.49 3.41
105 106 1.270625 GGCCGTTGGATATCGAATGGA 60.271 52.381 31.77 0.00 41.49 3.41
106 107 1.156736 GGCCGTTGGATATCGAATGG 58.843 55.000 26.29 26.29 41.76 3.16
107 108 1.156736 GGGCCGTTGGATATCGAATG 58.843 55.000 11.59 11.59 0.00 2.67
108 109 0.320421 CGGGCCGTTGGATATCGAAT 60.320 55.000 19.97 0.00 0.00 3.34
109 110 1.068417 CGGGCCGTTGGATATCGAA 59.932 57.895 19.97 0.00 0.00 3.71
110 111 2.129146 ACGGGCCGTTGGATATCGA 61.129 57.895 28.83 0.00 36.35 3.59
111 112 1.954146 CACGGGCCGTTGGATATCG 60.954 63.158 32.12 12.03 38.32 2.92
112 113 1.597027 CCACGGGCCGTTGGATATC 60.597 63.158 32.12 0.00 38.32 1.63
113 114 1.049855 TACCACGGGCCGTTGGATAT 61.050 55.000 36.97 24.45 38.32 1.63
114 115 1.263342 TTACCACGGGCCGTTGGATA 61.263 55.000 36.97 26.26 38.32 2.59
115 116 1.917336 ATTACCACGGGCCGTTGGAT 61.917 55.000 36.97 25.94 38.32 3.41
116 117 2.127027 AATTACCACGGGCCGTTGGA 62.127 55.000 36.97 27.95 38.32 3.53
117 118 0.392729 TAATTACCACGGGCCGTTGG 60.393 55.000 32.09 32.09 38.32 3.77
118 119 1.670791 ATAATTACCACGGGCCGTTG 58.329 50.000 32.12 29.01 38.32 4.10
119 120 2.018515 CAATAATTACCACGGGCCGTT 58.981 47.619 32.12 19.51 38.32 4.44
120 121 1.065272 ACAATAATTACCACGGGCCGT 60.065 47.619 28.83 28.83 42.36 5.68
121 122 1.600485 GACAATAATTACCACGGGCCG 59.400 52.381 27.06 27.06 0.00 6.13
122 123 2.645802 TGACAATAATTACCACGGGCC 58.354 47.619 0.00 0.00 0.00 5.80
123 124 4.157105 ACTTTGACAATAATTACCACGGGC 59.843 41.667 0.00 0.00 0.00 6.13
199 201 8.842358 ATTTGCATTCAAAAGAGAATTCACAT 57.158 26.923 8.44 0.00 44.44 3.21
258 260 4.038642 TCCATATAGCGCAGTCACATGTAA 59.961 41.667 11.47 0.00 0.00 2.41
271 274 9.979270 GATCAAAAGTTAATCATCCATATAGCG 57.021 33.333 0.00 0.00 0.00 4.26
312 315 7.125391 TCCCTCGTTAAGGTTTATTAGACCTA 58.875 38.462 6.35 0.00 46.60 3.08
314 317 6.127225 ACTCCCTCGTTAAGGTTTATTAGACC 60.127 42.308 0.00 0.00 44.56 3.85
315 318 6.871844 ACTCCCTCGTTAAGGTTTATTAGAC 58.128 40.000 0.00 0.00 44.56 2.59
316 319 8.636213 CATACTCCCTCGTTAAGGTTTATTAGA 58.364 37.037 0.00 0.00 44.56 2.10
329 332 2.159085 GCTACTTGCATACTCCCTCGTT 60.159 50.000 0.00 0.00 42.31 3.85
419 438 2.110213 GACAACACGTGGGGCTGA 59.890 61.111 21.57 0.00 0.00 4.26
561 583 2.112928 ACACATGCAGGCGTGGAA 59.887 55.556 17.02 0.00 37.45 3.53
581 603 3.735240 GCACGAGAGAAGATAAGATGCTG 59.265 47.826 0.00 0.00 0.00 4.41
712 735 3.118261 CCAGCTAAATGGACCTTGAGCTA 60.118 47.826 12.63 0.00 43.57 3.32
718 741 2.644798 ACTCACCAGCTAAATGGACCTT 59.355 45.455 0.00 0.00 43.57 3.50
804 834 3.285838 CTCTGCATGAGGACGATGG 57.714 57.895 0.00 0.00 39.08 3.51
902 934 7.260603 CCCAAATAGTTCACCAAATCATCTTC 58.739 38.462 0.00 0.00 0.00 2.87
937 969 6.844696 TCAGTTCAGACTACAAATGACAAC 57.155 37.500 0.00 0.00 33.90 3.32
969 1001 4.759693 TCCGTGAGCTGTAAACAATTGATT 59.240 37.500 13.59 9.50 0.00 2.57
981 1013 0.976641 TCCTTGATTCCGTGAGCTGT 59.023 50.000 0.00 0.00 0.00 4.40
1150 1182 2.182030 CCTGAAGTCGAGGGTCGC 59.818 66.667 0.00 0.00 40.21 5.19
1151 1183 1.507174 GTCCTGAAGTCGAGGGTCG 59.493 63.158 0.00 0.00 42.10 4.79
1201 1233 1.682849 CAATGGAAGGGGTGGTCGA 59.317 57.895 0.00 0.00 0.00 4.20
1234 1266 3.264947 CATCCATTTTGTCTCTCGCTCA 58.735 45.455 0.00 0.00 0.00 4.26
1288 1320 8.721478 AGCGTGTATTTATTCATCCATGATTAC 58.279 33.333 0.00 0.00 36.56 1.89
1374 1406 4.142609 ACAACAAGCCGACATCTCATAT 57.857 40.909 0.00 0.00 0.00 1.78
1472 1505 8.790718 AGCATATTTCATTCTAATGACACCATC 58.209 33.333 4.89 0.00 44.54 3.51
1496 1529 9.685828 CTCTAAGTAGATTAAGGTGTGATTAGC 57.314 37.037 0.00 0.00 0.00 3.09
1530 1563 6.479006 CATTTAAGATATCTCATGGGGCTCA 58.521 40.000 5.51 0.00 0.00 4.26
1595 1628 1.956297 CACGGGGTCACACTAAAACA 58.044 50.000 0.00 0.00 0.00 2.83
1651 1685 0.821711 TGTCGGCAAAGGGTTTGAGG 60.822 55.000 3.56 0.00 43.26 3.86
1671 1705 2.752903 GCACGGGGTCATGTTTCTTATT 59.247 45.455 0.00 0.00 0.00 1.40
1685 1719 2.631160 TAATGTTGATAGGCACGGGG 57.369 50.000 0.00 0.00 0.00 5.73
1686 1720 3.304659 GCAATAATGTTGATAGGCACGGG 60.305 47.826 0.00 0.00 0.00 5.28
1687 1721 3.565482 AGCAATAATGTTGATAGGCACGG 59.435 43.478 0.00 0.00 0.00 4.94
1688 1722 4.273235 TCAGCAATAATGTTGATAGGCACG 59.727 41.667 0.00 0.00 41.21 5.34
1689 1723 5.756195 TCAGCAATAATGTTGATAGGCAC 57.244 39.130 0.00 0.00 41.21 5.01
1697 1731 9.499585 CTAGTTCTTTCATCAGCAATAATGTTG 57.500 33.333 0.00 0.00 38.96 3.33
1698 1732 9.453572 TCTAGTTCTTTCATCAGCAATAATGTT 57.546 29.630 0.00 0.00 0.00 2.71
1699 1733 9.624373 ATCTAGTTCTTTCATCAGCAATAATGT 57.376 29.630 0.00 0.00 0.00 2.71
1704 1738 9.852091 GAAAAATCTAGTTCTTTCATCAGCAAT 57.148 29.630 0.00 0.00 0.00 3.56
1705 1739 8.849168 TGAAAAATCTAGTTCTTTCATCAGCAA 58.151 29.630 10.03 0.00 33.90 3.91
1706 1740 8.394971 TGAAAAATCTAGTTCTTTCATCAGCA 57.605 30.769 10.03 0.00 33.90 4.41
2026 2087 3.252458 ACCAACATTTTCTACAAGGTCGC 59.748 43.478 0.00 0.00 0.00 5.19
2027 2088 6.148811 ACATACCAACATTTTCTACAAGGTCG 59.851 38.462 0.00 0.00 0.00 4.79
2043 2104 9.485206 TCTTCAGTAGAACTTTTACATACCAAC 57.515 33.333 0.00 0.00 0.00 3.77
2083 2144 4.345859 ACTACTTCCGAATGTTCACCAA 57.654 40.909 0.00 0.00 0.00 3.67
2123 2192 9.298250 ACCACACTACGACTATATATGATTCTT 57.702 33.333 0.00 0.00 0.00 2.52
2124 2193 8.731605 CACCACACTACGACTATATATGATTCT 58.268 37.037 0.00 0.00 0.00 2.40
2132 2201 3.318275 CCTGCACCACACTACGACTATAT 59.682 47.826 0.00 0.00 0.00 0.86
2139 2208 1.588674 TTTTCCTGCACCACACTACG 58.411 50.000 0.00 0.00 0.00 3.51
2187 2263 9.790344 AACTCATAAAGAAGATATGATTCCCTG 57.210 33.333 0.00 0.00 38.66 4.45


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

AutoCloner maintained by Alex Coulton.