Multiple sequence alignment - TraesCS3D01G416700

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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 TraesCS3D01G416700 chr3D 100.000 2459 0 0 1 2459 528093859 528096317 0.000000e+00 4542.0
1 TraesCS3D01G416700 chr3D 83.302 1593 127 76 167 1695 527734841 527736358 0.000000e+00 1339.0
2 TraesCS3D01G416700 chr3D 88.653 802 57 13 408 1179 528083170 528083967 0.000000e+00 946.0
3 TraesCS3D01G416700 chr3D 82.950 522 40 14 1175 1695 528084506 528084979 2.260000e-115 425.0
4 TraesCS3D01G416700 chr3D 90.865 208 18 1 197 403 528072287 528072494 6.700000e-71 278.0
5 TraesCS3D01G416700 chr3D 85.083 181 16 2 197 375 527891460 527891631 9.040000e-40 174.0
6 TraesCS3D01G416700 chr3A 85.584 1970 179 63 516 2457 662519718 662521610 0.000000e+00 1967.0
7 TraesCS3D01G416700 chr3A 78.158 380 43 23 151 509 662513108 662513468 3.210000e-49 206.0
8 TraesCS3D01G416700 chr3B 88.793 1276 77 28 222 1483 698121516 698122739 0.000000e+00 1504.0
9 TraesCS3D01G416700 chr3B 83.677 1311 107 52 425 1695 697982675 697983918 0.000000e+00 1136.0
10 TraesCS3D01G416700 chr3B 87.671 949 64 24 753 1695 698194640 698195541 0.000000e+00 1055.0
11 TraesCS3D01G416700 chr3B 84.110 1095 79 43 425 1483 697999627 698000662 0.000000e+00 970.0
12 TraesCS3D01G416700 chr3B 87.462 662 35 18 112 756 698193160 698193790 0.000000e+00 719.0
13 TraesCS3D01G416700 chr5A 86.813 91 10 2 7 96 419213900 419213811 1.560000e-17 100.0
14 TraesCS3D01G416700 chr6B 81.818 99 8 7 1 94 281226165 281226258 9.430000e-10 75.0
15 TraesCS3D01G416700 chr6B 87.719 57 5 2 1 55 126302333 126302277 5.680000e-07 65.8
16 TraesCS3D01G416700 chr6B 91.111 45 2 2 1 43 281219072 281219028 2.640000e-05 60.2
17 TraesCS3D01G416700 chr2B 80.952 84 16 0 1 84 764914009 764914092 1.580000e-07 67.6
18 TraesCS3D01G416700 chr6A 80.220 91 15 3 5 94 76710413 76710501 5.680000e-07 65.8
19 TraesCS3D01G416700 chr1D 90.000 50 5 0 6 55 6590220 6590269 5.680000e-07 65.8
20 TraesCS3D01G416700 chr5B 79.775 89 15 3 7 94 523526434 523526348 7.340000e-06 62.1
21 TraesCS3D01G416700 chr5B 97.222 36 0 1 7 41 559189004 559188969 2.640000e-05 60.2


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 TraesCS3D01G416700 chr3D 528093859 528096317 2458 False 4542.0 4542 100.0000 1 2459 1 chr3D.!!$F4 2458
1 TraesCS3D01G416700 chr3D 527734841 527736358 1517 False 1339.0 1339 83.3020 167 1695 1 chr3D.!!$F1 1528
2 TraesCS3D01G416700 chr3D 528083170 528084979 1809 False 685.5 946 85.8015 408 1695 2 chr3D.!!$F5 1287
3 TraesCS3D01G416700 chr3A 662519718 662521610 1892 False 1967.0 1967 85.5840 516 2457 1 chr3A.!!$F2 1941
4 TraesCS3D01G416700 chr3B 698121516 698122739 1223 False 1504.0 1504 88.7930 222 1483 1 chr3B.!!$F3 1261
5 TraesCS3D01G416700 chr3B 697982675 697983918 1243 False 1136.0 1136 83.6770 425 1695 1 chr3B.!!$F1 1270
6 TraesCS3D01G416700 chr3B 697999627 698000662 1035 False 970.0 970 84.1100 425 1483 1 chr3B.!!$F2 1058
7 TraesCS3D01G416700 chr3B 698193160 698195541 2381 False 887.0 1055 87.5665 112 1695 2 chr3B.!!$F4 1583

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
21 22 0.108472 CCGACGGTAGGAAAAGGGTC 60.108 60.0 5.48 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 3140 0.666274 CCGCCGCATCGTACATACAT 60.666 55.0 0.0 0.0 0.0 2.29 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.926207 CCCCGACGGTAGGAAAAG 57.074 61.111 13.94 0.00 0.00 2.27
18 19 1.219935 CCCCGACGGTAGGAAAAGG 59.780 63.158 13.94 0.00 0.00 3.11
19 20 1.219935 CCCGACGGTAGGAAAAGGG 59.780 63.158 13.94 0.00 0.00 3.95
20 21 1.547472 CCCGACGGTAGGAAAAGGGT 61.547 60.000 13.94 0.00 33.00 4.34
21 22 0.108472 CCGACGGTAGGAAAAGGGTC 60.108 60.000 5.48 0.00 0.00 4.46
22 23 0.604578 CGACGGTAGGAAAAGGGTCA 59.395 55.000 0.00 0.00 0.00 4.02
23 24 1.403780 CGACGGTAGGAAAAGGGTCAG 60.404 57.143 0.00 0.00 0.00 3.51
24 25 1.897802 GACGGTAGGAAAAGGGTCAGA 59.102 52.381 0.00 0.00 0.00 3.27
25 26 2.500504 GACGGTAGGAAAAGGGTCAGAT 59.499 50.000 0.00 0.00 0.00 2.90
26 27 2.500504 ACGGTAGGAAAAGGGTCAGATC 59.499 50.000 0.00 0.00 0.00 2.75
27 28 2.158943 CGGTAGGAAAAGGGTCAGATCC 60.159 54.545 0.00 0.00 0.00 3.36
28 29 3.116174 GGTAGGAAAAGGGTCAGATCCT 58.884 50.000 0.00 0.00 42.89 3.24
29 30 3.118223 GGTAGGAAAAGGGTCAGATCCTG 60.118 52.174 1.77 0.00 40.62 3.86
30 31 2.921221 AGGAAAAGGGTCAGATCCTGA 58.079 47.619 1.77 0.00 39.03 3.86
31 32 3.260205 AGGAAAAGGGTCAGATCCTGAA 58.740 45.455 1.77 0.00 42.46 3.02
32 33 3.657727 AGGAAAAGGGTCAGATCCTGAAA 59.342 43.478 1.77 0.00 42.46 2.69
33 34 4.293368 AGGAAAAGGGTCAGATCCTGAAAT 59.707 41.667 1.77 0.00 42.46 2.17
34 35 5.492524 AGGAAAAGGGTCAGATCCTGAAATA 59.507 40.000 1.77 0.00 42.46 1.40
35 36 6.161170 AGGAAAAGGGTCAGATCCTGAAATAT 59.839 38.462 1.77 0.00 42.46 1.28
36 37 6.836007 GGAAAAGGGTCAGATCCTGAAATATT 59.164 38.462 1.77 0.00 42.46 1.28
37 38 7.343057 GGAAAAGGGTCAGATCCTGAAATATTT 59.657 37.037 1.77 0.00 42.46 1.40
38 39 8.670521 AAAAGGGTCAGATCCTGAAATATTTT 57.329 30.769 1.77 0.00 42.46 1.82
39 40 7.888250 AAGGGTCAGATCCTGAAATATTTTC 57.112 36.000 1.77 0.00 42.46 2.29
40 41 6.973642 AGGGTCAGATCCTGAAATATTTTCA 58.026 36.000 0.00 2.96 42.46 2.69
41 42 7.413446 AGGGTCAGATCCTGAAATATTTTCAA 58.587 34.615 0.00 0.00 42.46 2.69
42 43 7.895429 AGGGTCAGATCCTGAAATATTTTCAAA 59.105 33.333 0.00 0.00 42.46 2.69
43 44 8.699130 GGGTCAGATCCTGAAATATTTTCAAAT 58.301 33.333 1.43 1.94 42.46 2.32
61 62 9.840427 TTTTCAAATTAGGATCAGATTTCGAAC 57.160 29.630 0.00 0.00 0.00 3.95
62 63 8.560355 TTCAAATTAGGATCAGATTTCGAACA 57.440 30.769 0.00 0.00 0.00 3.18
63 64 8.560355 TCAAATTAGGATCAGATTTCGAACAA 57.440 30.769 0.00 0.00 0.00 2.83
64 65 8.450964 TCAAATTAGGATCAGATTTCGAACAAC 58.549 33.333 0.00 0.00 0.00 3.32
65 66 8.454106 CAAATTAGGATCAGATTTCGAACAACT 58.546 33.333 0.00 0.00 0.00 3.16
66 67 8.567285 AATTAGGATCAGATTTCGAACAACTT 57.433 30.769 0.00 0.00 0.00 2.66
67 68 7.596749 TTAGGATCAGATTTCGAACAACTTC 57.403 36.000 0.00 0.00 0.00 3.01
68 69 5.799213 AGGATCAGATTTCGAACAACTTCT 58.201 37.500 0.00 0.00 0.00 2.85
69 70 6.234177 AGGATCAGATTTCGAACAACTTCTT 58.766 36.000 0.00 0.00 0.00 2.52
70 71 6.370166 AGGATCAGATTTCGAACAACTTCTTC 59.630 38.462 0.00 0.00 0.00 2.87
71 72 5.576337 TCAGATTTCGAACAACTTCTTCG 57.424 39.130 0.00 0.00 41.55 3.79
72 73 4.447724 TCAGATTTCGAACAACTTCTTCGG 59.552 41.667 0.00 0.00 40.75 4.30
73 74 4.447724 CAGATTTCGAACAACTTCTTCGGA 59.552 41.667 0.00 0.00 40.75 4.55
74 75 5.050363 CAGATTTCGAACAACTTCTTCGGAA 60.050 40.000 0.00 0.00 41.64 4.30
84 85 3.898517 CTTCTTCGGAAGGGTCAAAAC 57.101 47.619 17.19 0.00 45.52 2.43
85 86 3.211045 CTTCTTCGGAAGGGTCAAAACA 58.789 45.455 17.19 0.00 45.52 2.83
86 87 2.567985 TCTTCGGAAGGGTCAAAACAC 58.432 47.619 17.19 0.00 0.00 3.32
87 88 1.263217 CTTCGGAAGGGTCAAAACACG 59.737 52.381 9.93 0.00 32.44 4.49
88 89 0.464870 TCGGAAGGGTCAAAACACGA 59.535 50.000 0.00 0.00 32.44 4.35
89 90 1.134461 TCGGAAGGGTCAAAACACGAA 60.134 47.619 0.00 0.00 32.44 3.85
90 91 1.671845 CGGAAGGGTCAAAACACGAAA 59.328 47.619 0.00 0.00 32.44 3.46
91 92 2.292292 CGGAAGGGTCAAAACACGAAAT 59.708 45.455 0.00 0.00 32.44 2.17
92 93 3.243267 CGGAAGGGTCAAAACACGAAATT 60.243 43.478 0.00 0.00 32.44 1.82
93 94 4.689071 GGAAGGGTCAAAACACGAAATTT 58.311 39.130 0.00 0.00 32.44 1.82
94 95 5.505985 CGGAAGGGTCAAAACACGAAATTTA 60.506 40.000 0.00 0.00 32.44 1.40
95 96 5.918576 GGAAGGGTCAAAACACGAAATTTAG 59.081 40.000 0.00 0.00 32.44 1.85
96 97 6.459670 AAGGGTCAAAACACGAAATTTAGT 57.540 33.333 0.00 0.00 32.44 2.24
97 98 6.068473 AGGGTCAAAACACGAAATTTAGTC 57.932 37.500 0.44 0.00 32.44 2.59
98 99 5.009310 AGGGTCAAAACACGAAATTTAGTCC 59.991 40.000 0.44 0.00 32.44 3.85
99 100 5.221087 GGGTCAAAACACGAAATTTAGTCCA 60.221 40.000 0.44 0.00 0.00 4.02
100 101 6.443792 GGTCAAAACACGAAATTTAGTCCAT 58.556 36.000 0.44 0.00 0.00 3.41
101 102 6.581166 GGTCAAAACACGAAATTTAGTCCATC 59.419 38.462 0.44 0.00 0.00 3.51
102 103 7.136119 GTCAAAACACGAAATTTAGTCCATCA 58.864 34.615 0.44 0.00 0.00 3.07
103 104 7.807907 GTCAAAACACGAAATTTAGTCCATCAT 59.192 33.333 0.44 0.00 0.00 2.45
104 105 7.807433 TCAAAACACGAAATTTAGTCCATCATG 59.193 33.333 0.44 0.00 0.00 3.07
105 106 5.818136 ACACGAAATTTAGTCCATCATGG 57.182 39.130 0.00 0.00 39.43 3.66
106 107 5.253330 ACACGAAATTTAGTCCATCATGGT 58.747 37.500 2.79 0.00 39.03 3.55
107 108 6.411376 ACACGAAATTTAGTCCATCATGGTA 58.589 36.000 2.79 0.00 39.03 3.25
108 109 6.538742 ACACGAAATTTAGTCCATCATGGTAG 59.461 38.462 2.79 0.00 39.03 3.18
109 110 6.017934 CACGAAATTTAGTCCATCATGGTAGG 60.018 42.308 2.79 0.00 39.03 3.18
110 111 6.055588 CGAAATTTAGTCCATCATGGTAGGT 58.944 40.000 2.79 0.00 39.03 3.08
120 121 4.386761 CCATCATGGTAGGTCTCCCAATTT 60.387 45.833 0.00 0.00 33.66 1.82
132 133 1.140852 TCCCAATTTCCATCGAGCGAT 59.859 47.619 0.00 0.00 34.81 4.58
133 134 2.367241 TCCCAATTTCCATCGAGCGATA 59.633 45.455 4.93 0.00 32.93 2.92
134 135 2.738846 CCCAATTTCCATCGAGCGATAG 59.261 50.000 4.93 0.00 32.93 2.08
152 153 0.392998 AGACATTGCCCTTACCTGCG 60.393 55.000 0.00 0.00 0.00 5.18
160 161 1.026718 CCCTTACCTGCGAGCAAAGG 61.027 60.000 16.19 16.19 39.65 3.11
192 193 4.866682 GAGGGTCACTCGATTTTGAATC 57.133 45.455 0.00 0.00 36.29 2.52
249 255 0.460459 GCTTTAGCGACCTCTGGACC 60.460 60.000 0.00 0.00 0.00 4.46
262 268 2.760385 GGACCGAGCTAGGCAGGT 60.760 66.667 13.48 4.91 42.49 4.00
320 326 2.555757 ACTGCCTTCTTGCATTTGACTC 59.444 45.455 0.00 0.00 41.16 3.36
347 356 3.991536 GAGGCAACGGACGGAGAGC 62.992 68.421 0.00 0.00 46.39 4.09
368 377 2.719556 CGAGAACGCGTACTGAATATGG 59.280 50.000 14.46 0.00 0.00 2.74
370 379 2.100916 AGAACGCGTACTGAATATGGCT 59.899 45.455 14.46 0.00 0.00 4.75
371 380 2.135664 ACGCGTACTGAATATGGCTC 57.864 50.000 11.67 0.00 0.00 4.70
372 381 1.407618 ACGCGTACTGAATATGGCTCA 59.592 47.619 11.67 0.00 0.00 4.26
509 551 1.835483 CGACGCAGCTCAGCACTTTT 61.835 55.000 0.00 0.00 0.00 2.27
534 576 2.164219 CCTGCACAAGTGACACAAGTTT 59.836 45.455 8.59 0.00 0.00 2.66
684 752 1.088306 CGCTCTACGTGTCTCCTCTT 58.912 55.000 0.00 0.00 36.87 2.85
838 1782 2.335712 GCCTTTCCGTTCCCAGCAG 61.336 63.158 0.00 0.00 0.00 4.24
839 1783 1.675641 CCTTTCCGTTCCCAGCAGG 60.676 63.158 0.00 0.00 0.00 4.85
845 1789 4.666253 GTTCCCAGCAGGCCAGCA 62.666 66.667 23.38 0.00 36.85 4.41
846 1790 4.355720 TTCCCAGCAGGCCAGCAG 62.356 66.667 23.38 14.62 36.85 4.24
955 1911 5.125739 CCAGTACTAGTAAGTAGCAGCACTT 59.874 44.000 3.61 12.85 38.89 3.16
977 1945 7.595875 CACTTCATCATCAGTGATCTAGCTAAG 59.404 40.741 1.56 5.48 43.14 2.18
978 1946 7.505248 ACTTCATCATCAGTGATCTAGCTAAGA 59.495 37.037 1.56 0.00 43.14 2.10
1054 2030 1.670949 GCTCCTCGTCATCCTGCTCA 61.671 60.000 0.00 0.00 0.00 4.26
1500 3046 1.618640 GAGAACCGCTGCGTGTCTTC 61.619 60.000 21.59 14.43 0.00 2.87
1552 3103 3.733077 CGAATAACGGAGTGTGAGGTACC 60.733 52.174 2.73 2.73 45.00 3.34
1615 3176 1.083015 CGGCGGTCGAAGTTTTGTG 60.083 57.895 0.00 0.00 42.43 3.33
1724 3288 8.025445 CCCTGTATTTTGATTCTCTTTTCAGTG 58.975 37.037 0.00 0.00 0.00 3.66
1735 3299 4.704540 TCTCTTTTCAGTGTTTCCTTTGCA 59.295 37.500 0.00 0.00 0.00 4.08
1750 3314 9.428097 GTTTCCTTTGCATCTTTAAAGAATGAT 57.572 29.630 21.26 2.62 38.77 2.45
1932 3498 8.552083 AATTTGAAAATTGCTCCCATACTTTC 57.448 30.769 0.28 0.00 37.24 2.62
1985 3551 4.597079 TGAATTTCAAGAAAGTGCACGAC 58.403 39.130 12.01 7.02 33.32 4.34
1988 3554 3.673746 TTCAAGAAAGTGCACGACTTG 57.326 42.857 29.39 29.39 44.68 3.16
1995 3561 4.097892 AGAAAGTGCACGACTTGGAAAAAT 59.902 37.500 12.01 0.00 44.68 1.82
2001 3567 4.932200 TGCACGACTTGGAAAAATGTTTTT 59.068 33.333 3.30 3.30 42.60 1.94
2104 3693 8.735692 AAAATGTTCATGGTTTCAGAAAATGT 57.264 26.923 0.00 0.00 0.00 2.71
2108 3697 7.499292 TGTTCATGGTTTCAGAAAATGTTCAT 58.501 30.769 0.00 0.00 36.09 2.57
2270 3862 6.465084 TGATCATGATTTTGGCAAATGTTCA 58.535 32.000 14.29 16.31 32.35 3.18
2280 3872 9.819267 ATTTTGGCAAATGTTCATGAAATTTTT 57.181 22.222 14.29 7.59 30.89 1.94
2326 3918 9.853177 AAAGAAACAGGAAGATAAAAGAAGAGA 57.147 29.630 0.00 0.00 0.00 3.10
2327 3919 9.853177 AAGAAACAGGAAGATAAAAGAAGAGAA 57.147 29.630 0.00 0.00 0.00 2.87
2328 3920 9.853177 AGAAACAGGAAGATAAAAGAAGAGAAA 57.147 29.630 0.00 0.00 0.00 2.52
2339 3931 9.508567 GATAAAAGAAGAGAAAATTCCGAATGG 57.491 33.333 0.00 0.00 0.00 3.16
2368 3960 5.687285 CCTGAAGAAAATCAACTGAAAACGG 59.313 40.000 0.00 0.00 0.00 4.44
2381 3973 3.500014 TGAAAACGGAAAAACACGGTTC 58.500 40.909 0.00 0.00 39.36 3.62
2389 3981 4.214758 CGGAAAAACACGGTTCTAGGAAAT 59.785 41.667 0.00 0.00 0.00 2.17
2408 4000 8.721133 AGGAAATAGAAAATACCAAAACCAGT 57.279 30.769 0.00 0.00 0.00 4.00
2409 4001 8.585018 AGGAAATAGAAAATACCAAAACCAGTG 58.415 33.333 0.00 0.00 0.00 3.66
2412 4004 4.810345 AGAAAATACCAAAACCAGTGGGA 58.190 39.130 15.21 0.00 40.75 4.37
2415 4007 4.948341 AATACCAAAACCAGTGGGAAAC 57.052 40.909 15.21 0.00 40.75 2.78
2458 4051 4.530857 GGATGTGCGGTCGGGGAG 62.531 72.222 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.219935 CCTTTTCCTACCGTCGGGG 59.780 63.158 17.28 8.30 43.62 5.73
1 2 1.219935 CCCTTTTCCTACCGTCGGG 59.780 63.158 17.28 0.00 40.11 5.14
2 3 0.108472 GACCCTTTTCCTACCGTCGG 60.108 60.000 10.48 10.48 0.00 4.79
3 4 0.604578 TGACCCTTTTCCTACCGTCG 59.395 55.000 0.00 0.00 0.00 5.12
4 5 1.897802 TCTGACCCTTTTCCTACCGTC 59.102 52.381 0.00 0.00 0.00 4.79
5 6 2.019807 TCTGACCCTTTTCCTACCGT 57.980 50.000 0.00 0.00 0.00 4.83
6 7 2.158943 GGATCTGACCCTTTTCCTACCG 60.159 54.545 0.00 0.00 0.00 4.02
7 8 3.116174 AGGATCTGACCCTTTTCCTACC 58.884 50.000 0.00 0.00 35.07 3.18
8 9 3.775316 TCAGGATCTGACCCTTTTCCTAC 59.225 47.826 0.00 0.00 35.39 3.18
9 10 4.074799 TCAGGATCTGACCCTTTTCCTA 57.925 45.455 0.00 0.00 35.39 2.94
10 11 2.921221 TCAGGATCTGACCCTTTTCCT 58.079 47.619 0.00 0.00 35.39 3.36
11 12 3.721087 TTCAGGATCTGACCCTTTTCC 57.279 47.619 0.00 0.00 40.46 3.13
12 13 7.888250 AATATTTCAGGATCTGACCCTTTTC 57.112 36.000 0.00 0.00 40.46 2.29
13 14 8.670521 AAAATATTTCAGGATCTGACCCTTTT 57.329 30.769 0.10 0.00 40.46 2.27
14 15 7.895429 TGAAAATATTTCAGGATCTGACCCTTT 59.105 33.333 0.10 0.00 40.46 3.11
15 16 7.413446 TGAAAATATTTCAGGATCTGACCCTT 58.587 34.615 0.10 0.00 40.46 3.95
16 17 6.973642 TGAAAATATTTCAGGATCTGACCCT 58.026 36.000 0.10 0.00 40.46 4.34
17 18 7.645058 TTGAAAATATTTCAGGATCTGACCC 57.355 36.000 0.10 0.00 40.46 4.46
35 36 9.840427 GTTCGAAATCTGATCCTAATTTGAAAA 57.160 29.630 0.00 0.00 0.00 2.29
36 37 9.008965 TGTTCGAAATCTGATCCTAATTTGAAA 57.991 29.630 0.00 0.00 0.00 2.69
37 38 8.560355 TGTTCGAAATCTGATCCTAATTTGAA 57.440 30.769 0.00 0.00 0.00 2.69
38 39 8.450964 GTTGTTCGAAATCTGATCCTAATTTGA 58.549 33.333 0.00 0.00 0.00 2.69
39 40 8.454106 AGTTGTTCGAAATCTGATCCTAATTTG 58.546 33.333 0.00 0.00 0.00 2.32
40 41 8.567285 AGTTGTTCGAAATCTGATCCTAATTT 57.433 30.769 0.00 0.00 0.00 1.82
41 42 8.567285 AAGTTGTTCGAAATCTGATCCTAATT 57.433 30.769 0.00 0.00 0.00 1.40
42 43 8.043710 AGAAGTTGTTCGAAATCTGATCCTAAT 58.956 33.333 0.00 0.00 37.79 1.73
43 44 7.386851 AGAAGTTGTTCGAAATCTGATCCTAA 58.613 34.615 0.00 0.00 37.79 2.69
44 45 6.936279 AGAAGTTGTTCGAAATCTGATCCTA 58.064 36.000 0.00 0.00 37.79 2.94
45 46 5.799213 AGAAGTTGTTCGAAATCTGATCCT 58.201 37.500 0.00 0.00 37.79 3.24
46 47 6.487689 AAGAAGTTGTTCGAAATCTGATCC 57.512 37.500 0.00 0.00 37.79 3.36
57 58 1.798813 CCCTTCCGAAGAAGTTGTTCG 59.201 52.381 24.00 24.00 46.93 3.95
58 59 2.806818 GACCCTTCCGAAGAAGTTGTTC 59.193 50.000 9.87 2.68 46.93 3.18
59 60 2.171870 TGACCCTTCCGAAGAAGTTGTT 59.828 45.455 9.87 0.00 46.93 2.83
60 61 1.766496 TGACCCTTCCGAAGAAGTTGT 59.234 47.619 9.87 0.00 46.93 3.32
61 62 2.543777 TGACCCTTCCGAAGAAGTTG 57.456 50.000 9.87 0.00 46.93 3.16
62 63 3.570912 TTTGACCCTTCCGAAGAAGTT 57.429 42.857 9.87 0.00 46.93 2.66
63 64 3.211865 GTTTTGACCCTTCCGAAGAAGT 58.788 45.455 9.87 6.60 46.93 3.01
65 66 2.946990 GTGTTTTGACCCTTCCGAAGAA 59.053 45.455 9.87 0.00 0.00 2.52
66 67 2.567985 GTGTTTTGACCCTTCCGAAGA 58.432 47.619 9.87 0.00 0.00 2.87
67 68 1.263217 CGTGTTTTGACCCTTCCGAAG 59.737 52.381 0.68 0.68 0.00 3.79
68 69 1.134461 TCGTGTTTTGACCCTTCCGAA 60.134 47.619 0.00 0.00 0.00 4.30
69 70 0.464870 TCGTGTTTTGACCCTTCCGA 59.535 50.000 0.00 0.00 0.00 4.55
70 71 1.301423 TTCGTGTTTTGACCCTTCCG 58.699 50.000 0.00 0.00 0.00 4.30
71 72 4.316205 AATTTCGTGTTTTGACCCTTCC 57.684 40.909 0.00 0.00 0.00 3.46
72 73 6.500910 ACTAAATTTCGTGTTTTGACCCTTC 58.499 36.000 0.00 0.00 0.00 3.46
73 74 6.459670 ACTAAATTTCGTGTTTTGACCCTT 57.540 33.333 0.00 0.00 0.00 3.95
74 75 5.009310 GGACTAAATTTCGTGTTTTGACCCT 59.991 40.000 0.00 0.00 0.00 4.34
75 76 5.217393 GGACTAAATTTCGTGTTTTGACCC 58.783 41.667 0.00 0.00 0.00 4.46
76 77 5.823353 TGGACTAAATTTCGTGTTTTGACC 58.177 37.500 0.00 0.00 31.25 4.02
77 78 7.136119 TGATGGACTAAATTTCGTGTTTTGAC 58.864 34.615 0.00 0.00 0.00 3.18
78 79 7.265647 TGATGGACTAAATTTCGTGTTTTGA 57.734 32.000 0.00 0.00 0.00 2.69
79 80 7.062138 CCATGATGGACTAAATTTCGTGTTTTG 59.938 37.037 5.27 0.00 40.96 2.44
80 81 7.090173 CCATGATGGACTAAATTTCGTGTTTT 58.910 34.615 5.27 0.00 40.96 2.43
81 82 6.208599 ACCATGATGGACTAAATTTCGTGTTT 59.791 34.615 20.11 0.00 40.96 2.83
82 83 5.710099 ACCATGATGGACTAAATTTCGTGTT 59.290 36.000 20.11 0.00 40.96 3.32
83 84 5.253330 ACCATGATGGACTAAATTTCGTGT 58.747 37.500 20.11 0.00 40.96 4.49
84 85 5.818136 ACCATGATGGACTAAATTTCGTG 57.182 39.130 20.11 0.00 40.96 4.35
85 86 6.055588 CCTACCATGATGGACTAAATTTCGT 58.944 40.000 20.11 0.00 40.96 3.85
86 87 6.055588 ACCTACCATGATGGACTAAATTTCG 58.944 40.000 20.11 0.00 40.96 3.46
87 88 7.283329 AGACCTACCATGATGGACTAAATTTC 58.717 38.462 20.11 3.41 40.96 2.17
88 89 7.213178 AGACCTACCATGATGGACTAAATTT 57.787 36.000 20.11 0.00 40.96 1.82
89 90 6.183361 GGAGACCTACCATGATGGACTAAATT 60.183 42.308 20.11 0.00 40.96 1.82
90 91 5.308237 GGAGACCTACCATGATGGACTAAAT 59.692 44.000 20.11 0.00 40.96 1.40
91 92 4.654262 GGAGACCTACCATGATGGACTAAA 59.346 45.833 20.11 0.00 40.96 1.85
92 93 4.223953 GGAGACCTACCATGATGGACTAA 58.776 47.826 20.11 0.00 40.96 2.24
93 94 3.845860 GGAGACCTACCATGATGGACTA 58.154 50.000 20.11 0.00 40.96 2.59
94 95 2.683768 GGAGACCTACCATGATGGACT 58.316 52.381 20.11 8.75 40.96 3.85
109 110 1.943340 GCTCGATGGAAATTGGGAGAC 59.057 52.381 0.00 0.00 0.00 3.36
110 111 1.473257 CGCTCGATGGAAATTGGGAGA 60.473 52.381 0.00 0.00 0.00 3.71
120 121 2.608016 GCAATGTCTATCGCTCGATGGA 60.608 50.000 13.10 13.10 39.30 3.41
132 133 1.134521 CGCAGGTAAGGGCAATGTCTA 60.135 52.381 0.00 0.00 0.00 2.59
133 134 0.392998 CGCAGGTAAGGGCAATGTCT 60.393 55.000 0.00 0.00 0.00 3.41
134 135 0.392461 TCGCAGGTAAGGGCAATGTC 60.392 55.000 0.00 0.00 0.00 3.06
152 153 1.639298 CGCACTGCCTACCTTTGCTC 61.639 60.000 0.00 0.00 0.00 4.26
160 161 2.184579 GACCCTCGCACTGCCTAC 59.815 66.667 0.00 0.00 0.00 3.18
249 255 2.029838 AATTTGACCTGCCTAGCTCG 57.970 50.000 0.00 0.00 0.00 5.03
262 268 1.309950 TGTTGGGTCGCGAAATTTGA 58.690 45.000 12.06 0.00 0.00 2.69
264 270 1.883275 TCATGTTGGGTCGCGAAATTT 59.117 42.857 12.06 0.00 0.00 1.82
336 344 2.100603 GTTCTCGCTCTCCGTCCG 59.899 66.667 0.00 0.00 38.35 4.79
347 356 2.719556 CCATATTCAGTACGCGTTCTCG 59.280 50.000 20.78 12.65 40.37 4.04
368 377 2.012673 CAAACCTGGATAGCAGTGAGC 58.987 52.381 0.00 0.00 46.19 4.26
370 379 2.353704 CGTCAAACCTGGATAGCAGTGA 60.354 50.000 0.00 0.00 0.00 3.41
371 380 2.002586 CGTCAAACCTGGATAGCAGTG 58.997 52.381 0.00 0.00 0.00 3.66
372 381 1.899814 TCGTCAAACCTGGATAGCAGT 59.100 47.619 0.00 0.00 0.00 4.40
447 484 2.291465 GTCACACTCACACACATGCATT 59.709 45.455 0.00 0.00 0.00 3.56
509 551 0.465460 GTGTCACTTGTGCAGGGGAA 60.465 55.000 0.00 0.00 0.00 3.97
534 576 0.920763 AGGCTGGGATGGATGGTTGA 60.921 55.000 0.00 0.00 0.00 3.18
631 691 2.506438 GGTGCCGCGTAGACAGAC 60.506 66.667 4.92 0.00 0.00 3.51
808 1752 1.138247 GAAAGGCATTGCTGGAGCG 59.862 57.895 8.82 0.00 45.83 5.03
955 1911 7.174772 GTCTCTTAGCTAGATCACTGATGATGA 59.825 40.741 0.00 0.00 46.01 2.92
1045 2021 2.515523 GCACGCCATGAGCAGGAT 60.516 61.111 0.00 0.00 44.04 3.24
1135 2111 4.112341 GTCCGTCACCTCCGTCCG 62.112 72.222 0.00 0.00 0.00 4.79
1425 2965 2.184322 GGCGCGAACCTGATCAGA 59.816 61.111 24.62 0.00 0.00 3.27
1500 3046 2.778679 GTACTCTGGCGCGCAAAG 59.221 61.111 34.42 27.89 0.00 2.77
1552 3103 2.202756 GCGCTCAACCCTACCTCG 60.203 66.667 0.00 0.00 0.00 4.63
1579 3136 2.408704 GCCGCATCGTACATACATTCTC 59.591 50.000 0.00 0.00 0.00 2.87
1582 3139 1.136690 CGCCGCATCGTACATACATT 58.863 50.000 0.00 0.00 0.00 2.71
1583 3140 0.666274 CCGCCGCATCGTACATACAT 60.666 55.000 0.00 0.00 0.00 2.29
1584 3141 1.299544 CCGCCGCATCGTACATACA 60.300 57.895 0.00 0.00 0.00 2.29
1585 3142 1.273455 GACCGCCGCATCGTACATAC 61.273 60.000 0.00 0.00 0.00 2.39
1586 3143 1.008194 GACCGCCGCATCGTACATA 60.008 57.895 0.00 0.00 0.00 2.29
1587 3144 2.279252 GACCGCCGCATCGTACAT 60.279 61.111 0.00 0.00 0.00 2.29
1703 3267 9.965824 GGAAACACTGAAAAGAGAATCAAAATA 57.034 29.630 0.00 0.00 37.82 1.40
1704 3268 8.699130 AGGAAACACTGAAAAGAGAATCAAAAT 58.301 29.630 0.00 0.00 37.82 1.82
1705 3269 8.066612 AGGAAACACTGAAAAGAGAATCAAAA 57.933 30.769 0.00 0.00 37.82 2.44
1713 3277 4.997565 TGCAAAGGAAACACTGAAAAGAG 58.002 39.130 0.00 0.00 0.00 2.85
1714 3278 5.360714 AGATGCAAAGGAAACACTGAAAAGA 59.639 36.000 0.00 0.00 0.00 2.52
1724 3288 8.816640 TCATTCTTTAAAGATGCAAAGGAAAC 57.183 30.769 18.37 0.00 34.49 2.78
1728 3292 6.694411 CCGATCATTCTTTAAAGATGCAAAGG 59.306 38.462 18.37 13.74 34.49 3.11
1735 3299 8.752005 TGAAATCCCGATCATTCTTTAAAGAT 57.248 30.769 18.37 3.75 34.49 2.40
1750 3314 7.852971 ACGATAACTATTTTTGAAATCCCGA 57.147 32.000 0.00 0.00 0.00 5.14
1913 3479 5.975693 TTCGAAAGTATGGGAGCAATTTT 57.024 34.783 0.00 0.00 0.00 1.82
1955 3521 6.703165 GCACTTTCTTGAAATTCATGAAGGTT 59.297 34.615 25.58 10.29 43.32 3.50
1956 3522 6.183360 TGCACTTTCTTGAAATTCATGAAGGT 60.183 34.615 23.74 23.74 45.15 3.50
1957 3523 6.145048 GTGCACTTTCTTGAAATTCATGAAGG 59.855 38.462 22.79 22.79 40.23 3.46
1958 3524 6.129273 CGTGCACTTTCTTGAAATTCATGAAG 60.129 38.462 19.08 16.10 40.23 3.02
1976 3542 2.687935 ACATTTTTCCAAGTCGTGCACT 59.312 40.909 16.19 0.00 36.64 4.40
2037 3603 6.972941 TGAAATTGCGAATATTTTACAACGC 58.027 32.000 9.33 9.33 44.95 4.84
2038 3604 9.784824 TTTTGAAATTGCGAATATTTTACAACG 57.215 25.926 0.00 0.00 0.00 4.10
2315 3907 8.630054 TCCATTCGGAATTTTCTCTTCTTTTA 57.370 30.769 0.00 0.00 38.83 1.52
2339 3931 8.702163 TTTCAGTTGATTTTCTTCAGGTTTTC 57.298 30.769 0.00 0.00 0.00 2.29
2344 3936 5.687285 CCGTTTTCAGTTGATTTTCTTCAGG 59.313 40.000 0.00 0.00 0.00 3.86
2345 3937 6.494842 TCCGTTTTCAGTTGATTTTCTTCAG 58.505 36.000 0.00 0.00 0.00 3.02
2368 3960 7.662604 TCTATTTCCTAGAACCGTGTTTTTC 57.337 36.000 0.00 0.00 33.40 2.29
2389 3981 5.954757 TCCCACTGGTTTTGGTATTTTCTA 58.045 37.500 0.00 0.00 31.46 2.10
2394 3986 4.100344 GTGTTTCCCACTGGTTTTGGTATT 59.900 41.667 0.00 0.00 41.11 1.89
2397 3989 1.828595 GTGTTTCCCACTGGTTTTGGT 59.171 47.619 0.00 0.00 41.11 3.67
2426 4019 2.660064 ATCCGGCTCAGTTCGGCTT 61.660 57.895 0.00 0.00 45.31 4.35


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

AutoCloner maintained by Alex Coulton.