Multiple sequence alignment - TraesCS2A01G252400

Loading Multiple Alignment...

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 TraesCS2A01G252400 chr2A 100.000 4636 0 0 1 4636 383614847 383610212 0.000000e+00 8562.0
1 TraesCS2A01G252400 chr2D 96.119 3917 103 22 734 4633 304997751 304993867 0.000000e+00 6346.0
2 TraesCS2A01G252400 chr2D 91.000 600 33 6 120 708 304998339 304997750 0.000000e+00 789.0
3 TraesCS2A01G252400 chr2B 93.927 2371 100 14 113 2460 373501565 373499216 0.000000e+00 3541.0
4 TraesCS2A01G252400 chr2B 96.382 1520 39 4 2460 3963 373495830 373494311 0.000000e+00 2488.0
5 TraesCS2A01G252400 chr2B 97.479 119 3 0 1 119 216950764 216950882 2.190000e-48 204.0
6 TraesCS2A01G252400 chr2B 94.958 119 6 0 1 119 4333777 4333659 2.200000e-43 187.0
7 TraesCS2A01G252400 chr2B 94.118 119 7 0 1 119 122704126 122704008 1.020000e-41 182.0
8 TraesCS2A01G252400 chr2B 95.161 62 2 1 4572 4633 373494017 373493957 3.820000e-16 97.1
9 TraesCS2A01G252400 chr5A 79.506 1376 236 27 904 2249 670826646 670828005 0.000000e+00 937.0
10 TraesCS2A01G252400 chr5A 84.746 236 36 0 3384 3619 670834330 670834565 2.160000e-58 237.0
11 TraesCS2A01G252400 chr4B 83.475 236 39 0 3384 3619 627541787 627542022 2.170000e-53 220.0
12 TraesCS2A01G252400 chr7B 97.479 119 3 0 1 119 75064132 75064014 2.190000e-48 204.0
13 TraesCS2A01G252400 chr7B 97.479 119 3 0 1 119 649151239 649151121 2.190000e-48 204.0
14 TraesCS2A01G252400 chr7A 97.479 119 3 0 1 119 697949178 697949296 2.190000e-48 204.0
15 TraesCS2A01G252400 chr1B 96.639 119 4 0 1 119 191943559 191943441 1.020000e-46 198.0
16 TraesCS2A01G252400 chr1D 89.916 119 12 0 1 119 480406342 480406224 2.230000e-33 154.0
17 TraesCS2A01G252400 chr1D 74.330 261 46 15 4369 4625 480557296 480557053 1.780000e-14 91.6
18 TraesCS2A01G252400 chr1A 90.588 85 7 1 23 106 576669787 576669703 1.360000e-20 111.0


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 TraesCS2A01G252400 chr2A 383610212 383614847 4635 True 8562.000000 8562 100.000000 1 4636 1 chr2A.!!$R1 4635
1 TraesCS2A01G252400 chr2D 304993867 304998339 4472 True 3567.500000 6346 93.559500 120 4633 2 chr2D.!!$R1 4513
2 TraesCS2A01G252400 chr2B 373493957 373501565 7608 True 2042.033333 3541 95.156667 113 4633 3 chr2B.!!$R3 4520
3 TraesCS2A01G252400 chr5A 670826646 670828005 1359 False 937.000000 937 79.506000 904 2249 1 chr5A.!!$F1 1345

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
381 396 0.035820 TCGCGGTTCCTTGCCTATTT 60.036 50.0 6.13 0.00 0.00 1.40 F
500 523 0.383949 TTTCCGTTCTTTGCTGTGGC 59.616 50.0 0.00 0.00 39.26 5.01 F
1154 1187 0.462759 CCGCTCTGCCTAGGGAAAAG 60.463 60.0 11.72 9.34 0.00 2.27 F
2063 2112 0.737715 GATGCAGGAAGACGCTCGTT 60.738 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1524 1.280421 GAGTGATCAGTCTGGCCCTTT 59.720 52.381 21.17 0.0 0.00 3.11 R
2224 2276 6.855763 AATAGCATTGGAGGAAACATGAAA 57.144 33.333 0.00 0.0 0.00 2.69 R
2676 6115 1.202382 GCAGATTCCATGGCTTCAAGC 60.202 52.381 6.96 0.0 41.46 4.01 R
3662 7112 1.817740 GCCACAGGCCAGAAACTACAA 60.818 52.381 5.01 0.0 44.06 2.41 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 2.677875 GCTGGCTTCAGTTGGGGG 60.678 66.667 0.00 0.00 40.51 5.40
18 19 2.677875 CTGGCTTCAGTTGGGGGC 60.678 66.667 0.00 0.00 33.96 5.80
19 20 4.659172 TGGCTTCAGTTGGGGGCG 62.659 66.667 0.00 0.00 0.00 6.13
20 21 4.660938 GGCTTCAGTTGGGGGCGT 62.661 66.667 0.00 0.00 0.00 5.68
21 22 3.365265 GCTTCAGTTGGGGGCGTG 61.365 66.667 0.00 0.00 0.00 5.34
22 23 3.365265 CTTCAGTTGGGGGCGTGC 61.365 66.667 0.00 0.00 0.00 5.34
27 28 4.992511 GTTGGGGGCGTGCGTGTA 62.993 66.667 0.00 0.00 0.00 2.90
28 29 4.690719 TTGGGGGCGTGCGTGTAG 62.691 66.667 0.00 0.00 0.00 2.74
32 33 4.675029 GGGCGTGCGTGTAGGTGT 62.675 66.667 0.00 0.00 0.00 4.16
33 34 2.259204 GGCGTGCGTGTAGGTGTA 59.741 61.111 0.00 0.00 0.00 2.90
34 35 1.373246 GGCGTGCGTGTAGGTGTAA 60.373 57.895 0.00 0.00 0.00 2.41
35 36 0.945265 GGCGTGCGTGTAGGTGTAAA 60.945 55.000 0.00 0.00 0.00 2.01
36 37 0.860533 GCGTGCGTGTAGGTGTAAAA 59.139 50.000 0.00 0.00 0.00 1.52
37 38 1.461897 GCGTGCGTGTAGGTGTAAAAT 59.538 47.619 0.00 0.00 0.00 1.82
38 39 2.096119 GCGTGCGTGTAGGTGTAAAATT 60.096 45.455 0.00 0.00 0.00 1.82
39 40 3.123284 GCGTGCGTGTAGGTGTAAAATTA 59.877 43.478 0.00 0.00 0.00 1.40
40 41 4.631036 CGTGCGTGTAGGTGTAAAATTAC 58.369 43.478 0.00 0.00 0.00 1.89
41 42 4.386652 CGTGCGTGTAGGTGTAAAATTACT 59.613 41.667 5.05 0.00 34.77 2.24
42 43 5.572511 CGTGCGTGTAGGTGTAAAATTACTA 59.427 40.000 5.05 0.00 34.77 1.82
43 44 6.452872 CGTGCGTGTAGGTGTAAAATTACTAC 60.453 42.308 5.05 0.00 35.71 2.73
44 45 6.365789 GTGCGTGTAGGTGTAAAATTACTACA 59.634 38.462 5.05 0.00 40.99 2.74
45 46 6.927936 TGCGTGTAGGTGTAAAATTACTACAA 59.072 34.615 0.00 0.00 43.69 2.41
46 47 7.440556 TGCGTGTAGGTGTAAAATTACTACAAA 59.559 33.333 0.00 0.00 43.69 2.83
47 48 8.281893 GCGTGTAGGTGTAAAATTACTACAAAA 58.718 33.333 0.00 0.00 43.69 2.44
64 65 8.821147 ACTACAAAATCTATTAACACACACGA 57.179 30.769 0.00 0.00 0.00 4.35
65 66 9.431887 ACTACAAAATCTATTAACACACACGAT 57.568 29.630 0.00 0.00 0.00 3.73
68 69 9.959749 ACAAAATCTATTAACACACACGATTTT 57.040 25.926 0.00 0.00 39.05 1.82
72 73 9.988350 AATCTATTAACACACACGATTTTGATC 57.012 29.630 0.00 0.00 0.00 2.92
80 81 2.780595 CGATTTTGATCGTGGGGCT 58.219 52.632 0.91 0.00 39.07 5.19
81 82 0.378257 CGATTTTGATCGTGGGGCTG 59.622 55.000 0.91 0.00 39.07 4.85
82 83 1.750193 GATTTTGATCGTGGGGCTGA 58.250 50.000 0.00 0.00 0.00 4.26
83 84 1.672881 GATTTTGATCGTGGGGCTGAG 59.327 52.381 0.00 0.00 0.00 3.35
84 85 0.690192 TTTTGATCGTGGGGCTGAGA 59.310 50.000 0.00 0.00 0.00 3.27
85 86 0.250234 TTTGATCGTGGGGCTGAGAG 59.750 55.000 0.00 0.00 0.00 3.20
86 87 2.107953 GATCGTGGGGCTGAGAGC 59.892 66.667 0.00 0.00 41.46 4.09
87 88 2.685017 ATCGTGGGGCTGAGAGCA 60.685 61.111 0.00 0.00 44.75 4.26
88 89 2.244117 GATCGTGGGGCTGAGAGCAA 62.244 60.000 0.00 0.00 44.75 3.91
89 90 1.841302 ATCGTGGGGCTGAGAGCAAA 61.841 55.000 0.00 0.00 44.75 3.68
90 91 2.037136 CGTGGGGCTGAGAGCAAAG 61.037 63.158 0.00 0.00 44.75 2.77
91 92 1.676967 GTGGGGCTGAGAGCAAAGG 60.677 63.158 0.00 0.00 44.75 3.11
92 93 2.044551 GGGGCTGAGAGCAAAGGG 60.045 66.667 0.00 0.00 44.75 3.95
93 94 2.606587 GGGGCTGAGAGCAAAGGGA 61.607 63.158 0.00 0.00 44.75 4.20
94 95 1.377856 GGGCTGAGAGCAAAGGGAC 60.378 63.158 0.00 0.00 44.75 4.46
95 96 1.376466 GGCTGAGAGCAAAGGGACA 59.624 57.895 0.00 0.00 44.75 4.02
96 97 0.957888 GGCTGAGAGCAAAGGGACAC 60.958 60.000 0.00 0.00 44.75 3.67
97 98 0.250467 GCTGAGAGCAAAGGGACACA 60.250 55.000 0.00 0.00 41.89 3.72
98 99 1.517242 CTGAGAGCAAAGGGACACAC 58.483 55.000 0.00 0.00 0.00 3.82
99 100 0.249868 TGAGAGCAAAGGGACACACG 60.250 55.000 0.00 0.00 0.00 4.49
100 101 0.951040 GAGAGCAAAGGGACACACGG 60.951 60.000 0.00 0.00 0.00 4.94
101 102 1.070786 GAGCAAAGGGACACACGGA 59.929 57.895 0.00 0.00 0.00 4.69
102 103 0.321653 GAGCAAAGGGACACACGGAT 60.322 55.000 0.00 0.00 0.00 4.18
103 104 0.981183 AGCAAAGGGACACACGGATA 59.019 50.000 0.00 0.00 0.00 2.59
104 105 1.084289 GCAAAGGGACACACGGATAC 58.916 55.000 0.00 0.00 0.00 2.24
105 106 1.609580 GCAAAGGGACACACGGATACA 60.610 52.381 0.00 0.00 0.00 2.29
106 107 2.773487 CAAAGGGACACACGGATACAA 58.227 47.619 0.00 0.00 0.00 2.41
107 108 2.467566 AAGGGACACACGGATACAAC 57.532 50.000 0.00 0.00 0.00 3.32
108 109 1.344065 AGGGACACACGGATACAACA 58.656 50.000 0.00 0.00 0.00 3.33
109 110 1.906574 AGGGACACACGGATACAACAT 59.093 47.619 0.00 0.00 0.00 2.71
110 111 2.006888 GGGACACACGGATACAACATG 58.993 52.381 0.00 0.00 0.00 3.21
111 112 1.396996 GGACACACGGATACAACATGC 59.603 52.381 0.00 0.00 0.00 4.06
116 117 2.307363 CGGATACAACATGCCGGAC 58.693 57.895 5.05 0.00 40.08 4.79
118 119 1.157870 GGATACAACATGCCGGACGG 61.158 60.000 5.05 6.35 38.57 4.79
137 138 3.199289 ACGGGAAGGGGTTAAGTAAGATG 59.801 47.826 0.00 0.00 0.00 2.90
174 178 3.356290 CCCATCAAAATTCCTCCGTTCT 58.644 45.455 0.00 0.00 0.00 3.01
228 233 3.054802 TCAGCCCTTCTTCTCTGATTTCC 60.055 47.826 0.00 0.00 31.35 3.13
312 327 2.436417 CCGGATTTGCTTCTTCCTTCA 58.564 47.619 0.00 0.00 0.00 3.02
371 386 2.412323 GGGGGATTTTCGCGGTTCC 61.412 63.158 6.13 7.62 0.00 3.62
381 396 0.035820 TCGCGGTTCCTTGCCTATTT 60.036 50.000 6.13 0.00 0.00 1.40
405 420 1.837439 AGGTGCGAGTTAATCCATCCA 59.163 47.619 0.00 0.00 0.00 3.41
444 467 1.406069 CCACGGACAAGAGGAATCCAG 60.406 57.143 0.61 0.00 32.35 3.86
499 522 2.857748 GTTTTTCCGTTCTTTGCTGTGG 59.142 45.455 0.00 0.00 0.00 4.17
500 523 0.383949 TTTCCGTTCTTTGCTGTGGC 59.616 50.000 0.00 0.00 39.26 5.01
544 568 2.511218 CTCCAAATCATTCTCCCCTCCA 59.489 50.000 0.00 0.00 0.00 3.86
667 691 7.589958 ACAACACTGGGTGTAAATAAAATCA 57.410 32.000 3.69 0.00 46.79 2.57
673 697 7.975616 CACTGGGTGTAAATAAAATCATTCTGG 59.024 37.037 0.00 0.00 0.00 3.86
723 747 6.684686 CATCGACCCGATCCTTTTATTACTA 58.315 40.000 0.00 0.00 45.19 1.82
744 768 6.951971 ACTATTAGTCATTCCATGGATAGGC 58.048 40.000 17.06 12.80 0.00 3.93
751 775 2.071778 TCCATGGATAGGCTTTTGGC 57.928 50.000 11.44 0.00 46.43 4.52
802 826 3.181523 GGTCGCGTTTCTCATTTCCTAAC 60.182 47.826 5.77 0.00 0.00 2.34
811 835 9.460906 CGTTTCTCATTTCCTAACTAGTATACC 57.539 37.037 0.00 0.00 0.00 2.73
947 971 4.560128 TCAGTTGATAGCACTGACTGAAC 58.440 43.478 10.72 0.00 42.49 3.18
1074 1107 2.279582 ACAAGGACAAGATCTACGCG 57.720 50.000 3.53 3.53 0.00 6.01
1138 1171 3.682292 AAGATCTTCCGGTGCCCGC 62.682 63.158 0.88 0.00 46.86 6.13
1154 1187 0.462759 CCGCTCTGCCTAGGGAAAAG 60.463 60.000 11.72 9.34 0.00 2.27
1477 1510 1.073964 CAGACCATGCGAAGTCACTG 58.926 55.000 3.19 0.00 35.38 3.66
1491 1524 5.007626 CGAAGTCACTGTTCTTTTGGATTCA 59.992 40.000 0.00 0.00 0.00 2.57
1776 1812 5.888691 TTGCTCATTTTACTCGCCAAATA 57.111 34.783 0.00 0.00 0.00 1.40
1938 1983 6.983307 TGTTTTTGCTGCATTTTGTGTACTAT 59.017 30.769 1.84 0.00 0.00 2.12
1991 2040 4.818546 GGCAGCAGTAATATCATCTTGTGT 59.181 41.667 0.00 0.00 0.00 3.72
2063 2112 0.737715 GATGCAGGAAGACGCTCGTT 60.738 55.000 0.00 0.00 0.00 3.85
2676 6115 5.933463 AGAGCTGAAAGAGAAAGATGAACAG 59.067 40.000 0.00 0.00 34.07 3.16
2840 6279 5.029014 CCTTATATATCGCTTCGTCCTTCG 58.971 45.833 0.00 0.00 41.41 3.79
2913 6352 4.115516 CTCGATCCACTATTGGTGTCAAG 58.884 47.826 0.00 0.00 44.35 3.02
3245 6694 3.296322 TGATTTGATTTGACGGGCAAC 57.704 42.857 0.00 0.00 35.91 4.17
3446 6895 1.811359 CAAGCCCTGAAAGAAGAGCTG 59.189 52.381 0.00 0.00 34.07 4.24
3643 7092 4.941713 ACCTACTTCTCCTGAGTGAGATT 58.058 43.478 2.28 0.00 40.89 2.40
3662 7112 3.996921 TTGACGTCTCCTAGTCCTAGT 57.003 47.619 17.92 0.00 36.61 2.57
3697 7147 1.727880 TGTGGCGCTGTAAAATCGTAC 59.272 47.619 7.64 0.00 0.00 3.67
3730 7180 9.726438 AACAGTACTTGATGCTTAGTAAATTCT 57.274 29.630 0.00 0.00 0.00 2.40
3849 7304 1.268352 GTTGTTGCGTTTATGGCCTCA 59.732 47.619 3.32 0.00 0.00 3.86
3874 7329 1.760613 TCAAAGAGTGGACAGGTCGTT 59.239 47.619 0.00 0.00 0.00 3.85
4009 7465 7.473027 TTTAGGAAGTTTGTAGAACGTTCTG 57.527 36.000 35.24 0.00 38.19 3.02
4014 7470 4.117685 AGTTTGTAGAACGTTCTGTGGAC 58.882 43.478 35.24 26.13 38.19 4.02
4035 7491 3.524346 GGTTTCCCCCTGTGTTTCA 57.476 52.632 0.00 0.00 0.00 2.69
4058 7514 5.722021 ATTTGCTGATTTTACGAGGGTTT 57.278 34.783 0.00 0.00 0.00 3.27
4111 7571 7.595311 ATTTTTGAACTTGTGAACACTTTCC 57.405 32.000 6.51 0.00 0.00 3.13
4118 7578 9.179909 TGAACTTGTGAACACTTTCCTAAAATA 57.820 29.630 6.51 0.00 0.00 1.40
4119 7579 9.447040 GAACTTGTGAACACTTTCCTAAAATAC 57.553 33.333 6.51 0.00 0.00 1.89
4122 7582 7.972832 TGTGAACACTTTCCTAAAATACGAT 57.027 32.000 6.51 0.00 0.00 3.73
4184 7644 7.231925 TGGGGAACTACTTTTCAAATCCTAAAC 59.768 37.037 0.00 0.00 0.00 2.01
4260 7724 8.860780 TTTTGGAGATTTGGGAAATATTTTGG 57.139 30.769 1.43 0.00 0.00 3.28
4359 7825 6.927933 AATTTCGCAAACTTTCTAATTCGG 57.072 33.333 0.00 0.00 0.00 4.30
4365 7831 5.564127 CGCAAACTTTCTAATTCGGAAACTC 59.436 40.000 0.00 0.00 0.00 3.01
4467 7933 4.018409 GCCAAAGGCCCAACTAGG 57.982 61.111 0.00 0.00 44.06 3.02
4491 7957 1.009829 CTAGCTAGCCAACCAAAGCG 58.990 55.000 12.13 0.00 39.94 4.68
4502 7970 0.541863 ACCAAAGCGAGTATCCTGGG 59.458 55.000 0.00 0.00 0.00 4.45
4515 7983 2.631428 CTGGGCGTGTGTGTTTCG 59.369 61.111 0.00 0.00 0.00 3.46
4620 8088 0.581529 CTGCTTCGTGCGTTTGAGAA 59.418 50.000 0.00 0.00 46.63 2.87
4633 8101 1.750341 TTGAGAAGGGGCGACGACAA 61.750 55.000 1.63 0.00 0.00 3.18
4634 8102 1.737008 GAGAAGGGGCGACGACAAC 60.737 63.158 1.63 0.00 0.00 3.32
4635 8103 2.741211 GAAGGGGCGACGACAACC 60.741 66.667 1.63 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.677875 CCCCCAACTGAAGCCAGC 60.678 66.667 0.00 0.00 44.16 4.85
1 2 2.677875 GCCCCCAACTGAAGCCAG 60.678 66.667 0.00 0.00 45.76 4.85
2 3 4.659172 CGCCCCCAACTGAAGCCA 62.659 66.667 0.00 0.00 0.00 4.75
3 4 4.660938 ACGCCCCCAACTGAAGCC 62.661 66.667 0.00 0.00 0.00 4.35
4 5 3.365265 CACGCCCCCAACTGAAGC 61.365 66.667 0.00 0.00 0.00 3.86
5 6 3.365265 GCACGCCCCCAACTGAAG 61.365 66.667 0.00 0.00 0.00 3.02
10 11 4.992511 TACACGCACGCCCCCAAC 62.993 66.667 0.00 0.00 0.00 3.77
11 12 4.690719 CTACACGCACGCCCCCAA 62.691 66.667 0.00 0.00 0.00 4.12
15 16 2.768503 TTACACCTACACGCACGCCC 62.769 60.000 0.00 0.00 0.00 6.13
16 17 0.945265 TTTACACCTACACGCACGCC 60.945 55.000 0.00 0.00 0.00 5.68
17 18 0.860533 TTTTACACCTACACGCACGC 59.139 50.000 0.00 0.00 0.00 5.34
18 19 3.799137 AATTTTACACCTACACGCACG 57.201 42.857 0.00 0.00 0.00 5.34
19 20 5.851047 AGTAATTTTACACCTACACGCAC 57.149 39.130 3.50 0.00 36.12 5.34
20 21 6.453943 TGTAGTAATTTTACACCTACACGCA 58.546 36.000 3.50 0.00 36.12 5.24
21 22 6.949578 TGTAGTAATTTTACACCTACACGC 57.050 37.500 3.50 0.00 36.12 5.34
38 39 9.911138 TCGTGTGTGTTAATAGATTTTGTAGTA 57.089 29.630 0.00 0.00 0.00 1.82
39 40 8.821147 TCGTGTGTGTTAATAGATTTTGTAGT 57.179 30.769 0.00 0.00 0.00 2.73
42 43 9.959749 AAAATCGTGTGTGTTAATAGATTTTGT 57.040 25.926 11.02 0.00 41.94 2.83
46 47 9.988350 GATCAAAATCGTGTGTGTTAATAGATT 57.012 29.630 0.00 0.00 0.00 2.40
63 64 1.672881 CTCAGCCCCACGATCAAAATC 59.327 52.381 0.00 0.00 0.00 2.17
64 65 1.281867 TCTCAGCCCCACGATCAAAAT 59.718 47.619 0.00 0.00 0.00 1.82
65 66 0.690192 TCTCAGCCCCACGATCAAAA 59.310 50.000 0.00 0.00 0.00 2.44
66 67 0.250234 CTCTCAGCCCCACGATCAAA 59.750 55.000 0.00 0.00 0.00 2.69
67 68 1.900351 CTCTCAGCCCCACGATCAA 59.100 57.895 0.00 0.00 0.00 2.57
68 69 2.725312 GCTCTCAGCCCCACGATCA 61.725 63.158 0.00 0.00 34.48 2.92
69 70 2.107953 GCTCTCAGCCCCACGATC 59.892 66.667 0.00 0.00 34.48 3.69
70 71 1.841302 TTTGCTCTCAGCCCCACGAT 61.841 55.000 0.00 0.00 41.51 3.73
71 72 2.454832 CTTTGCTCTCAGCCCCACGA 62.455 60.000 0.00 0.00 41.51 4.35
72 73 2.032528 TTTGCTCTCAGCCCCACG 59.967 61.111 0.00 0.00 41.51 4.94
73 74 1.676967 CCTTTGCTCTCAGCCCCAC 60.677 63.158 0.00 0.00 41.51 4.61
74 75 2.759114 CCTTTGCTCTCAGCCCCA 59.241 61.111 0.00 0.00 41.51 4.96
75 76 2.044551 CCCTTTGCTCTCAGCCCC 60.045 66.667 0.00 0.00 41.51 5.80
76 77 1.377856 GTCCCTTTGCTCTCAGCCC 60.378 63.158 0.00 0.00 41.51 5.19
77 78 0.957888 GTGTCCCTTTGCTCTCAGCC 60.958 60.000 0.00 0.00 41.51 4.85
78 79 0.250467 TGTGTCCCTTTGCTCTCAGC 60.250 55.000 0.00 0.00 42.82 4.26
79 80 1.517242 GTGTGTCCCTTTGCTCTCAG 58.483 55.000 0.00 0.00 0.00 3.35
80 81 0.249868 CGTGTGTCCCTTTGCTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
81 82 0.951040 CCGTGTGTCCCTTTGCTCTC 60.951 60.000 0.00 0.00 0.00 3.20
82 83 1.071471 CCGTGTGTCCCTTTGCTCT 59.929 57.895 0.00 0.00 0.00 4.09
83 84 0.321653 ATCCGTGTGTCCCTTTGCTC 60.322 55.000 0.00 0.00 0.00 4.26
84 85 0.981183 TATCCGTGTGTCCCTTTGCT 59.019 50.000 0.00 0.00 0.00 3.91
85 86 1.084289 GTATCCGTGTGTCCCTTTGC 58.916 55.000 0.00 0.00 0.00 3.68
86 87 2.465860 TGTATCCGTGTGTCCCTTTG 57.534 50.000 0.00 0.00 0.00 2.77
87 88 2.105134 TGTTGTATCCGTGTGTCCCTTT 59.895 45.455 0.00 0.00 0.00 3.11
88 89 1.695242 TGTTGTATCCGTGTGTCCCTT 59.305 47.619 0.00 0.00 0.00 3.95
89 90 1.344065 TGTTGTATCCGTGTGTCCCT 58.656 50.000 0.00 0.00 0.00 4.20
90 91 2.006888 CATGTTGTATCCGTGTGTCCC 58.993 52.381 0.00 0.00 0.00 4.46
91 92 1.396996 GCATGTTGTATCCGTGTGTCC 59.603 52.381 0.00 0.00 0.00 4.02
92 93 1.396996 GGCATGTTGTATCCGTGTGTC 59.603 52.381 0.00 0.00 0.00 3.67
93 94 1.448985 GGCATGTTGTATCCGTGTGT 58.551 50.000 0.00 0.00 0.00 3.72
94 95 0.373370 CGGCATGTTGTATCCGTGTG 59.627 55.000 0.00 0.00 37.33 3.82
95 96 0.742990 CCGGCATGTTGTATCCGTGT 60.743 55.000 6.47 0.00 40.23 4.49
96 97 0.461163 TCCGGCATGTTGTATCCGTG 60.461 55.000 0.00 0.00 40.23 4.94
97 98 0.461339 GTCCGGCATGTTGTATCCGT 60.461 55.000 0.00 0.00 40.23 4.69
98 99 1.487452 CGTCCGGCATGTTGTATCCG 61.487 60.000 0.00 0.00 41.41 4.18
99 100 1.157870 CCGTCCGGCATGTTGTATCC 61.158 60.000 0.00 0.00 0.00 2.59
100 101 1.157870 CCCGTCCGGCATGTTGTATC 61.158 60.000 0.00 0.00 0.00 2.24
101 102 1.153249 CCCGTCCGGCATGTTGTAT 60.153 57.895 0.00 0.00 0.00 2.29
102 103 1.828461 TTCCCGTCCGGCATGTTGTA 61.828 55.000 0.00 0.00 0.00 2.41
103 104 3.185299 TTCCCGTCCGGCATGTTGT 62.185 57.895 0.00 0.00 0.00 3.32
104 105 2.359354 TTCCCGTCCGGCATGTTG 60.359 61.111 0.00 0.00 0.00 3.33
105 106 2.046314 CTTCCCGTCCGGCATGTT 60.046 61.111 0.00 0.00 0.00 2.71
106 107 4.096003 CCTTCCCGTCCGGCATGT 62.096 66.667 0.00 0.00 0.00 3.21
107 108 4.856801 CCCTTCCCGTCCGGCATG 62.857 72.222 0.00 0.00 0.00 4.06
111 112 2.248086 CTTAACCCCTTCCCGTCCGG 62.248 65.000 0.00 0.00 0.00 5.14
116 117 3.199289 ACATCTTACTTAACCCCTTCCCG 59.801 47.826 0.00 0.00 0.00 5.14
118 119 6.896883 ACATACATCTTACTTAACCCCTTCC 58.103 40.000 0.00 0.00 0.00 3.46
137 138 4.850680 TGATGGGGTTTCACCTAACATAC 58.149 43.478 0.00 0.00 38.64 2.39
228 233 1.076044 AATGCGAGGGATTTGGGGG 60.076 57.895 0.00 0.00 0.00 5.40
381 396 4.202223 GGATGGATTAACTCGCACCTAAGA 60.202 45.833 0.00 0.00 0.00 2.10
392 407 6.493166 TCAAAGAATGGTGGATGGATTAACT 58.507 36.000 0.00 0.00 0.00 2.24
394 409 7.976414 AATCAAAGAATGGTGGATGGATTAA 57.024 32.000 0.00 0.00 0.00 1.40
405 420 6.435904 TCCGTGGAAAATAATCAAAGAATGGT 59.564 34.615 0.00 0.00 0.00 3.55
444 467 9.543018 GCAAAATTAACACTGATCAGTAGTAAC 57.457 33.333 27.44 11.97 40.20 2.50
500 523 3.181290 TTGATCGCTGCGACGCTG 61.181 61.111 28.41 21.43 39.18 5.18
501 524 3.181967 GTTGATCGCTGCGACGCT 61.182 61.111 28.41 12.13 39.18 5.07
502 525 4.210304 GGTTGATCGCTGCGACGC 62.210 66.667 28.41 21.61 39.18 5.19
503 526 3.554692 GGGTTGATCGCTGCGACG 61.555 66.667 28.41 0.00 39.18 5.12
504 527 2.032634 TTGGGTTGATCGCTGCGAC 61.033 57.895 28.41 20.19 39.18 5.19
505 528 2.032634 GTTGGGTTGATCGCTGCGA 61.033 57.895 28.01 28.01 41.13 5.10
506 529 1.970917 GAGTTGGGTTGATCGCTGCG 61.971 60.000 17.25 17.25 0.00 5.18
544 568 4.520492 GGGATCGGCAACTAAATCAATGAT 59.480 41.667 0.00 0.00 0.00 2.45
673 697 2.019984 GTGTGGATTTCCTCTGCCATC 58.980 52.381 0.00 0.00 36.82 3.51
744 768 4.513198 TCAGATAAAAACCGGCCAAAAG 57.487 40.909 0.00 0.00 0.00 2.27
957 985 2.631012 AAATGCCCCGAGGATGAGCC 62.631 60.000 0.00 0.00 33.47 4.70
968 996 4.279420 GGATGTTGAGAGATAAAATGCCCC 59.721 45.833 0.00 0.00 0.00 5.80
1083 1116 0.316841 TCAATTTTTGGGACCGCAGC 59.683 50.000 0.00 0.00 0.00 5.25
1138 1171 2.682269 GCTTCCTTTTCCCTAGGCAGAG 60.682 54.545 2.05 0.00 28.73 3.35
1154 1187 4.378459 CCTTGACGTTGTAATCTTGCTTCC 60.378 45.833 0.00 0.00 0.00 3.46
1477 1510 3.070878 TGGCCCTTTGAATCCAAAAGAAC 59.929 43.478 0.00 0.00 41.28 3.01
1491 1524 1.280421 GAGTGATCAGTCTGGCCCTTT 59.720 52.381 21.17 0.00 0.00 3.11
1776 1812 9.950496 TCTTGTAAATGCTTATTCTTCTCTTCT 57.050 29.630 0.00 0.00 0.00 2.85
2224 2276 6.855763 AATAGCATTGGAGGAAACATGAAA 57.144 33.333 0.00 0.00 0.00 2.69
2676 6115 1.202382 GCAGATTCCATGGCTTCAAGC 60.202 52.381 6.96 0.00 41.46 4.01
2840 6279 1.267186 CGAGTAATTTGTTACCCGCGC 60.267 52.381 0.00 0.00 0.00 6.86
2913 6352 2.715046 TCATCAAGCACACCCATTCTC 58.285 47.619 0.00 0.00 0.00 2.87
3303 6752 6.753913 AGGACTCAAATCAGGATAGCAATA 57.246 37.500 0.00 0.00 0.00 1.90
3521 6970 3.164977 TTCCACAGCACGGGGACA 61.165 61.111 0.00 0.00 0.00 4.02
3643 7092 3.008813 ACAACTAGGACTAGGAGACGTCA 59.991 47.826 19.50 0.00 37.49 4.35
3662 7112 1.817740 GCCACAGGCCAGAAACTACAA 60.818 52.381 5.01 0.00 44.06 2.41
3697 7147 4.995124 AGCATCAAGTACTGTTACTACGG 58.005 43.478 0.00 0.00 37.59 4.02
3729 7179 6.088085 GTCGCAATTGTGTTTATTCCTTTCAG 59.912 38.462 18.08 0.00 0.00 3.02
3730 7180 5.918011 GTCGCAATTGTGTTTATTCCTTTCA 59.082 36.000 18.08 0.00 0.00 2.69
3849 7304 4.382040 CGACCTGTCCACTCTTTGACATAT 60.382 45.833 0.00 0.00 40.46 1.78
3928 7383 2.093973 CACACCTGCGAAGAGGTAATCT 60.094 50.000 0.00 0.00 45.15 2.40
4035 7491 5.722021 AACCCTCGTAAAATCAGCAAATT 57.278 34.783 0.00 0.00 0.00 1.82
4087 7546 7.386059 AGGAAAGTGTTCACAAGTTCAAAAAT 58.614 30.769 5.74 0.00 35.25 1.82
4096 7556 7.857569 TCGTATTTTAGGAAAGTGTTCACAAG 58.142 34.615 5.74 0.00 35.25 3.16
4222 7685 9.717942 CCAAATCTCCAAAAATGTACCAAATTA 57.282 29.630 0.00 0.00 0.00 1.40
4246 7710 6.942163 TCACAAATCCCAAAATATTTCCCA 57.058 33.333 0.10 0.00 0.00 4.37
4260 7724 8.140677 TGATTTTGTCAAATGTTCACAAATCC 57.859 30.769 0.00 0.00 39.23 3.01
4335 7799 7.808672 TCCGAATTAGAAAGTTTGCGAAATTA 58.191 30.769 0.00 0.00 0.00 1.40
4343 7807 9.516314 AAAAGAGTTTCCGAATTAGAAAGTTTG 57.484 29.630 10.55 0.00 37.09 2.93
4348 7812 9.511144 GTTTCAAAAGAGTTTCCGAATTAGAAA 57.489 29.630 0.16 0.16 0.00 2.52
4351 7815 9.463443 AATGTTTCAAAAGAGTTTCCGAATTAG 57.537 29.630 0.00 0.00 0.00 1.73
4353 7817 8.716646 AAATGTTTCAAAAGAGTTTCCGAATT 57.283 26.923 0.00 0.00 0.00 2.17
4354 7818 8.716646 AAAATGTTTCAAAAGAGTTTCCGAAT 57.283 26.923 0.00 0.00 25.38 3.34
4434 7900 0.968405 TGGCCATCCAAAGAAGCAAC 59.032 50.000 0.00 0.00 39.99 4.17
4467 7933 1.227292 GGTTGGCTAGCTAGTCGGC 60.227 63.158 20.02 14.36 0.00 5.54
4502 7970 0.505655 GGACTACGAAACACACACGC 59.494 55.000 0.00 0.00 0.00 5.34
4515 7983 0.386478 ACAACGCGTCGAAGGACTAC 60.386 55.000 14.44 0.00 41.16 2.73


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

AutoCloner maintained by Alex Coulton.