Multiple sequence alignment - TraesCS3A01G293500

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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 TraesCS3A01G293500 chr3A 100.000 2732 0 0 1 2732 525627498 525630229 0.000000e+00 5046.0
1 TraesCS3A01G293500 chr3A 93.576 1401 64 15 560 1951 525297210 525298593 0.000000e+00 2065.0
2 TraesCS3A01G293500 chr3A 83.447 441 38 17 138 557 525296741 525297167 7.140000e-101 377.0
3 TraesCS3A01G293500 chr3A 94.231 104 6 0 370 473 525291719 525291822 2.820000e-35 159.0
4 TraesCS3A01G293500 chr3A 100.000 31 0 0 1935 1965 525298605 525298635 1.060000e-04 58.4
5 TraesCS3A01G293500 chr3B 93.493 1675 77 10 560 2228 529796644 529798292 0.000000e+00 2460.0
6 TraesCS3A01G293500 chr3B 91.184 397 27 5 2209 2601 529799816 529800208 1.440000e-147 532.0
7 TraesCS3A01G293500 chr3B 87.750 400 31 12 169 551 529796197 529796595 4.150000e-123 451.0
8 TraesCS3A01G293500 chr3B 83.210 405 41 11 166 556 529725849 529726240 2.010000e-91 346.0
9 TraesCS3A01G293500 chr3B 94.643 112 2 4 2623 2732 529800269 529800378 1.300000e-38 171.0
10 TraesCS3A01G293500 chr3B 89.583 48 5 0 4 51 457204878 457204831 8.170000e-06 62.1
11 TraesCS3A01G293500 chr3D 91.837 1666 85 16 560 2210 403693115 403694744 0.000000e+00 2276.0
12 TraesCS3A01G293500 chr3D 93.477 1395 63 12 560 1947 403352156 403353529 0.000000e+00 2047.0
13 TraesCS3A01G293500 chr3D 92.731 509 14 6 68 557 403692568 403693072 0.000000e+00 713.0
14 TraesCS3A01G293500 chr3D 86.692 526 29 13 2232 2727 403694727 403695241 1.850000e-151 545.0
15 TraesCS3A01G293500 chr3D 88.473 347 27 6 2280 2621 403674577 403674915 9.110000e-110 407.0
16 TraesCS3A01G293500 chr3D 85.504 407 37 13 169 557 403351528 403351930 3.280000e-109 405.0
17 TraesCS3A01G293500 chr3D 83.969 262 27 9 166 413 403330639 403330899 1.260000e-58 237.0
18 TraesCS3A01G293500 chr3D 88.442 199 17 3 1950 2148 403674175 403674367 4.550000e-58 235.0
19 TraesCS3A01G293500 chr3D 96.154 78 3 0 2 79 403675283 403675360 7.940000e-26 128.0
20 TraesCS3A01G293500 chr6D 85.000 80 6 6 2276 2354 193557842 193557916 2.920000e-10 76.8
21 TraesCS3A01G293500 chr6B 85.714 77 5 6 2279 2354 300953184 300953113 2.920000e-10 76.8
22 TraesCS3A01G293500 chr6A 85.000 80 6 6 2276 2354 268571932 268572006 2.920000e-10 76.8
23 TraesCS3A01G293500 chr2D 95.349 43 2 0 2279 2321 336480117 336480075 4.880000e-08 69.4
24 TraesCS3A01G293500 chr2A 93.617 47 2 1 2279 2324 446589734 446589688 4.880000e-08 69.4
25 TraesCS3A01G293500 chr2B 93.023 43 3 0 2279 2321 404115980 404115938 2.270000e-06 63.9
26 TraesCS3A01G293500 chr7D 94.444 36 2 0 3 38 386844340 386844375 3.800000e-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 TraesCS3A01G293500 chr3A 525627498 525630229 2731 False 5046.000000 5046 100.0000 1 2732 1 chr3A.!!$F2 2731
1 TraesCS3A01G293500 chr3A 525296741 525298635 1894 False 833.466667 2065 92.3410 138 1965 3 chr3A.!!$F3 1827
2 TraesCS3A01G293500 chr3B 529796197 529800378 4181 False 903.500000 2460 91.7675 169 2732 4 chr3B.!!$F2 2563
3 TraesCS3A01G293500 chr3D 403351528 403353529 2001 False 1226.000000 2047 89.4905 169 1947 2 chr3D.!!$F2 1778
4 TraesCS3A01G293500 chr3D 403692568 403695241 2673 False 1178.000000 2276 90.4200 68 2727 3 chr3D.!!$F4 2659
5 TraesCS3A01G293500 chr3D 403674175 403675360 1185 False 256.666667 407 91.0230 2 2621 3 chr3D.!!$F3 2619

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
52 53 0.036765 ATCCAACTTAACCGCGCAGA 60.037 50.0 8.75 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 2166 0.253044 GGGTGAGCTCCAAGCACATA 59.747 55.0 12.15 0.0 43.3 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
26 27 9.990868 ACCCCATTTAACTCTATCATAAGTTTT 57.009 29.630 0.00 0.00 37.02 2.43
46 47 7.985476 AGTTTTCATCATATCCAACTTAACCG 58.015 34.615 0.00 0.00 0.00 4.44
47 48 6.371809 TTTCATCATATCCAACTTAACCGC 57.628 37.500 0.00 0.00 0.00 5.68
48 49 4.055360 TCATCATATCCAACTTAACCGCG 58.945 43.478 0.00 0.00 0.00 6.46
49 50 2.206750 TCATATCCAACTTAACCGCGC 58.793 47.619 0.00 0.00 0.00 6.86
50 51 1.937223 CATATCCAACTTAACCGCGCA 59.063 47.619 8.75 0.00 0.00 6.09
51 52 1.647346 TATCCAACTTAACCGCGCAG 58.353 50.000 8.75 0.00 0.00 5.18
52 53 0.036765 ATCCAACTTAACCGCGCAGA 60.037 50.000 8.75 0.00 0.00 4.26
53 54 0.249953 TCCAACTTAACCGCGCAGAA 60.250 50.000 8.75 0.00 0.00 3.02
54 55 0.165944 CCAACTTAACCGCGCAGAAG 59.834 55.000 8.75 7.12 0.00 2.85
55 56 0.452784 CAACTTAACCGCGCAGAAGC 60.453 55.000 8.75 0.00 37.42 3.86
56 57 1.574702 AACTTAACCGCGCAGAAGCC 61.575 55.000 8.75 0.00 37.52 4.35
57 58 2.031314 TTAACCGCGCAGAAGCCA 59.969 55.556 8.75 0.00 37.52 4.75
58 59 1.369091 CTTAACCGCGCAGAAGCCAT 61.369 55.000 8.75 0.00 37.52 4.40
59 60 0.958382 TTAACCGCGCAGAAGCCATT 60.958 50.000 8.75 0.00 37.52 3.16
60 61 0.108089 TAACCGCGCAGAAGCCATTA 60.108 50.000 8.75 0.00 37.52 1.90
61 62 1.369091 AACCGCGCAGAAGCCATTAG 61.369 55.000 8.75 0.00 37.52 1.73
62 63 1.815421 CCGCGCAGAAGCCATTAGT 60.815 57.895 8.75 0.00 37.52 2.24
63 64 1.349627 CGCGCAGAAGCCATTAGTG 59.650 57.895 8.75 0.00 37.52 2.74
64 65 1.063166 GCGCAGAAGCCATTAGTGC 59.937 57.895 0.30 0.00 37.52 4.40
65 66 1.723870 CGCAGAAGCCATTAGTGCC 59.276 57.895 0.00 0.00 37.52 5.01
66 67 1.718757 CGCAGAAGCCATTAGTGCCC 61.719 60.000 0.00 0.00 37.52 5.36
67 68 0.394899 GCAGAAGCCATTAGTGCCCT 60.395 55.000 0.00 0.00 33.58 5.19
68 69 1.386533 CAGAAGCCATTAGTGCCCTG 58.613 55.000 0.00 0.00 0.00 4.45
69 70 1.065199 CAGAAGCCATTAGTGCCCTGA 60.065 52.381 0.00 0.00 34.05 3.86
70 71 1.211457 AGAAGCCATTAGTGCCCTGAG 59.789 52.381 0.00 0.00 0.00 3.35
71 72 0.995024 AAGCCATTAGTGCCCTGAGT 59.005 50.000 0.00 0.00 0.00 3.41
72 73 0.543749 AGCCATTAGTGCCCTGAGTC 59.456 55.000 0.00 0.00 0.00 3.36
107 108 3.881688 GCATGAAAGCACTCATAGGTCAT 59.118 43.478 0.00 0.00 34.20 3.06
108 109 4.024218 GCATGAAAGCACTCATAGGTCATC 60.024 45.833 0.00 0.00 34.20 2.92
109 110 4.824479 TGAAAGCACTCATAGGTCATCA 57.176 40.909 0.00 0.00 0.00 3.07
110 111 5.164620 TGAAAGCACTCATAGGTCATCAA 57.835 39.130 0.00 0.00 0.00 2.57
118 119 6.586344 CACTCATAGGTCATCAACACCTTAT 58.414 40.000 0.00 0.00 41.95 1.73
200 201 2.234908 GCATGACAGTACAGGAGGTTCT 59.765 50.000 0.00 0.00 0.00 3.01
231 232 7.042456 GCAGTCATAATCGATCAAACTGTACAT 60.042 37.037 21.29 0.00 36.05 2.29
233 234 9.684448 AGTCATAATCGATCAAACTGTACATAG 57.316 33.333 0.00 0.00 0.00 2.23
238 239 7.609760 ATCGATCAAACTGTACATAGCAAAA 57.390 32.000 0.00 0.00 0.00 2.44
429 440 2.132517 TAGTTGCCGAGCGTCACGAA 62.133 55.000 0.00 0.00 0.00 3.85
552 588 5.594926 ACTATACTAAGCACGCCGTTAATT 58.405 37.500 0.00 0.00 0.00 1.40
557 593 2.983930 GCACGCCGTTAATTGCCCA 61.984 57.895 0.00 0.00 0.00 5.36
589 848 0.968405 GCTAGGGGCAGAGAGATCTG 59.032 60.000 0.00 0.83 41.35 2.90
613 873 8.631480 TGGAGAGTTAAAAATAAAGGAACCTC 57.369 34.615 0.00 0.00 0.00 3.85
875 1140 1.216178 GCCAACTGCGCCATCATTT 59.784 52.632 4.18 0.00 0.00 2.32
968 1235 0.750182 ACCCACCAACCAACGACAAG 60.750 55.000 0.00 0.00 0.00 3.16
1170 1437 1.053264 CCCTGCTCCTGCACCTCTAT 61.053 60.000 0.00 0.00 45.31 1.98
1689 1956 1.142748 GCATGTCGAGGACCTGGAG 59.857 63.158 6.43 0.00 30.79 3.86
1692 1959 0.333312 ATGTCGAGGACCTGGAGAGT 59.667 55.000 6.43 0.00 0.00 3.24
1698 1965 0.902516 AGGACCTGGAGAGTCAGCAC 60.903 60.000 0.00 0.00 35.89 4.40
1735 2002 6.173339 CACTCTGTGGATACCAATTAGTGTT 58.827 40.000 14.16 0.00 35.58 3.32
1829 2110 4.130118 GCCGATTCAGAGGTGTGAAATAT 58.870 43.478 0.00 0.00 39.84 1.28
1874 2157 6.602009 GTCCTATGTTTTAATTAGGCACTGGT 59.398 38.462 0.00 0.00 41.52 4.00
1899 2183 2.813754 TGTTTATGTGCTTGGAGCTCAC 59.186 45.455 17.19 5.76 45.84 3.51
1912 2197 1.899142 GAGCTCACCCCATATCTCTCC 59.101 57.143 9.40 0.00 0.00 3.71
1972 2285 3.201708 AGCTCTGTTTTCTCTGGCCATAT 59.798 43.478 5.51 0.00 0.00 1.78
1983 2296 0.465460 TGGCCATATCGCTTGTTCCC 60.465 55.000 0.00 0.00 0.00 3.97
1984 2297 0.179018 GGCCATATCGCTTGTTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
2003 2321 5.123227 TCCCTTGATGATTTCGTTATGACC 58.877 41.667 0.00 0.00 0.00 4.02
2006 2324 4.131649 TGATGATTTCGTTATGACCGGT 57.868 40.909 6.92 6.92 0.00 5.28
2036 2354 0.463654 AACGAAGGACAAGCTGTGCA 60.464 50.000 9.65 0.00 41.46 4.57
2099 2417 6.461640 AGAATGCTTGAATGAAGGGAAAAAG 58.538 36.000 0.00 0.00 31.56 2.27
2171 2493 4.285292 GGTACCATGTTCTATGTACGACG 58.715 47.826 7.15 0.00 0.00 5.12
2195 2517 3.263170 TGTCTTGTGCTTGCTTAGGGATA 59.737 43.478 0.00 0.00 0.00 2.59
2228 4232 8.969260 ATGGCATTCTTTTCTTTCTTCTTTTT 57.031 26.923 0.00 0.00 0.00 1.94
2263 4267 1.338674 TGGCATTCTAACCACACGGAG 60.339 52.381 0.00 0.00 35.59 4.63
2330 4334 7.584122 ACGATGATTTAGGTCTTTAGCTCTA 57.416 36.000 0.00 0.00 34.60 2.43
2331 4335 7.427214 ACGATGATTTAGGTCTTTAGCTCTAC 58.573 38.462 0.00 0.00 34.60 2.59
2365 4370 8.575649 AAAAGGTACATAATTCAGAAACGGAT 57.424 30.769 0.00 0.00 0.00 4.18
2366 4371 7.553881 AAGGTACATAATTCAGAAACGGATG 57.446 36.000 0.00 0.00 0.00 3.51
2413 4422 8.750515 TCAATCATTGTGAAAATGAGCCTATA 57.249 30.769 4.17 0.00 39.69 1.31
2448 4457 1.080569 GGGCTGAACATTTGCACCG 60.081 57.895 0.00 0.00 0.00 4.94
2537 4546 2.643232 GCTCCCACGTAAGACCCGT 61.643 63.158 0.00 0.00 43.62 5.28
2571 4585 2.953188 TGGAGGGACACCAGGAAAA 58.047 52.632 0.00 0.00 46.01 2.29
2573 4587 0.771755 GGAGGGACACCAGGAAAAGT 59.228 55.000 0.00 0.00 39.49 2.66
2578 4592 1.067060 GGACACCAGGAAAAGTTGTGC 59.933 52.381 0.00 0.00 0.00 4.57
2616 4642 2.614829 TAAAGACATAGGAAGCGGGC 57.385 50.000 0.00 0.00 0.00 6.13
2665 4718 3.031736 ACTACTGGTGGAAGATACGCAT 58.968 45.455 0.00 0.00 0.00 4.73
2666 4719 2.604046 ACTGGTGGAAGATACGCATC 57.396 50.000 0.00 0.00 0.00 3.91
2667 4720 2.111384 ACTGGTGGAAGATACGCATCT 58.889 47.619 0.00 0.00 43.67 2.90
2668 4721 2.159043 ACTGGTGGAAGATACGCATCTG 60.159 50.000 0.00 0.00 40.81 2.90
2669 4722 1.221414 GGTGGAAGATACGCATCTGC 58.779 55.000 0.00 0.00 40.81 4.26
2670 4723 1.473257 GGTGGAAGATACGCATCTGCA 60.473 52.381 5.96 0.00 40.81 4.41
2671 4724 1.594862 GTGGAAGATACGCATCTGCAC 59.405 52.381 5.96 5.26 40.81 4.57
2705 4758 1.158434 GTGGCGATTCCGGTAAAACA 58.842 50.000 0.00 0.00 37.80 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.990868 AAAACTTATGATAGAGTTAAATGGGGT 57.009 29.630 0.00 0.00 35.17 4.95
20 21 8.458843 CGGTTAAGTTGGATATGATGAAAACTT 58.541 33.333 0.00 0.00 40.11 2.66
21 22 7.415206 GCGGTTAAGTTGGATATGATGAAAACT 60.415 37.037 0.00 0.00 0.00 2.66
22 23 6.691388 GCGGTTAAGTTGGATATGATGAAAAC 59.309 38.462 0.00 0.00 0.00 2.43
23 24 6.457663 CGCGGTTAAGTTGGATATGATGAAAA 60.458 38.462 0.00 0.00 0.00 2.29
24 25 5.007234 CGCGGTTAAGTTGGATATGATGAAA 59.993 40.000 0.00 0.00 0.00 2.69
25 26 4.509970 CGCGGTTAAGTTGGATATGATGAA 59.490 41.667 0.00 0.00 0.00 2.57
26 27 4.055360 CGCGGTTAAGTTGGATATGATGA 58.945 43.478 0.00 0.00 0.00 2.92
27 28 3.363970 GCGCGGTTAAGTTGGATATGATG 60.364 47.826 8.83 0.00 0.00 3.07
28 29 2.806244 GCGCGGTTAAGTTGGATATGAT 59.194 45.455 8.83 0.00 0.00 2.45
29 30 2.206750 GCGCGGTTAAGTTGGATATGA 58.793 47.619 8.83 0.00 0.00 2.15
30 31 1.937223 TGCGCGGTTAAGTTGGATATG 59.063 47.619 8.83 0.00 0.00 1.78
31 32 2.159014 TCTGCGCGGTTAAGTTGGATAT 60.159 45.455 17.37 0.00 0.00 1.63
32 33 1.205179 TCTGCGCGGTTAAGTTGGATA 59.795 47.619 17.37 0.00 0.00 2.59
33 34 0.036765 TCTGCGCGGTTAAGTTGGAT 60.037 50.000 17.37 0.00 0.00 3.41
34 35 0.249953 TTCTGCGCGGTTAAGTTGGA 60.250 50.000 17.37 0.00 0.00 3.53
35 36 0.165944 CTTCTGCGCGGTTAAGTTGG 59.834 55.000 17.37 0.00 0.00 3.77
36 37 0.452784 GCTTCTGCGCGGTTAAGTTG 60.453 55.000 17.37 1.29 0.00 3.16
37 38 1.574702 GGCTTCTGCGCGGTTAAGTT 61.575 55.000 17.37 0.00 40.82 2.66
38 39 2.033194 GGCTTCTGCGCGGTTAAGT 61.033 57.895 17.37 0.00 40.82 2.24
39 40 1.369091 ATGGCTTCTGCGCGGTTAAG 61.369 55.000 17.37 14.38 40.82 1.85
40 41 0.958382 AATGGCTTCTGCGCGGTTAA 60.958 50.000 17.37 2.84 40.82 2.01
41 42 0.108089 TAATGGCTTCTGCGCGGTTA 60.108 50.000 17.37 3.25 40.82 2.85
42 43 1.369091 CTAATGGCTTCTGCGCGGTT 61.369 55.000 17.37 4.33 40.82 4.44
43 44 1.815421 CTAATGGCTTCTGCGCGGT 60.815 57.895 17.37 0.00 40.82 5.68
44 45 1.815421 ACTAATGGCTTCTGCGCGG 60.815 57.895 10.86 10.86 40.82 6.46
45 46 1.349627 CACTAATGGCTTCTGCGCG 59.650 57.895 0.00 0.00 40.82 6.86
46 47 1.063166 GCACTAATGGCTTCTGCGC 59.937 57.895 0.00 0.00 40.82 6.09
55 56 2.503356 AGAAGACTCAGGGCACTAATGG 59.497 50.000 0.00 0.00 0.00 3.16
56 57 3.902881 AGAAGACTCAGGGCACTAATG 57.097 47.619 0.00 0.00 0.00 1.90
57 58 4.917906 AAAGAAGACTCAGGGCACTAAT 57.082 40.909 0.00 0.00 0.00 1.73
58 59 4.706842 AAAAGAAGACTCAGGGCACTAA 57.293 40.909 0.00 0.00 0.00 2.24
59 60 4.706842 AAAAAGAAGACTCAGGGCACTA 57.293 40.909 0.00 0.00 0.00 2.74
60 61 3.584733 AAAAAGAAGACTCAGGGCACT 57.415 42.857 0.00 0.00 0.00 4.40
61 62 5.335976 CCATTAAAAAGAAGACTCAGGGCAC 60.336 44.000 0.00 0.00 0.00 5.01
62 63 4.766891 CCATTAAAAAGAAGACTCAGGGCA 59.233 41.667 0.00 0.00 0.00 5.36
63 64 4.380973 GCCATTAAAAAGAAGACTCAGGGC 60.381 45.833 0.00 0.00 0.00 5.19
64 65 4.766891 TGCCATTAAAAAGAAGACTCAGGG 59.233 41.667 0.00 0.00 0.00 4.45
65 66 5.964958 TGCCATTAAAAAGAAGACTCAGG 57.035 39.130 0.00 0.00 0.00 3.86
66 67 7.149569 TCATGCCATTAAAAAGAAGACTCAG 57.850 36.000 0.00 0.00 0.00 3.35
67 68 7.523293 TTCATGCCATTAAAAAGAAGACTCA 57.477 32.000 0.00 0.00 0.00 3.41
68 69 7.062722 GCTTTCATGCCATTAAAAAGAAGACTC 59.937 37.037 7.71 0.00 0.00 3.36
69 70 6.870439 GCTTTCATGCCATTAAAAAGAAGACT 59.130 34.615 7.71 0.00 0.00 3.24
70 71 6.646240 TGCTTTCATGCCATTAAAAAGAAGAC 59.354 34.615 7.71 0.00 0.00 3.01
71 72 6.646240 GTGCTTTCATGCCATTAAAAAGAAGA 59.354 34.615 7.71 0.00 0.00 2.87
72 73 6.647895 AGTGCTTTCATGCCATTAAAAAGAAG 59.352 34.615 7.71 0.00 0.00 2.85
107 108 9.109393 GCAGATTAATAACTGATAAGGTGTTGA 57.891 33.333 8.05 0.00 36.38 3.18
108 109 8.345565 GGCAGATTAATAACTGATAAGGTGTTG 58.654 37.037 8.05 0.00 36.38 3.33
109 110 8.275040 AGGCAGATTAATAACTGATAAGGTGTT 58.725 33.333 8.05 0.00 36.38 3.32
110 111 7.716998 CAGGCAGATTAATAACTGATAAGGTGT 59.283 37.037 8.05 0.00 36.38 4.16
118 119 3.744214 CGGCCAGGCAGATTAATAACTGA 60.744 47.826 15.19 0.00 36.38 3.41
200 201 2.433970 TGATCGATTATGACTGCACCCA 59.566 45.455 0.00 0.00 0.00 4.51
231 232 4.772100 CCTCCTCCCATTTTCTTTTTGCTA 59.228 41.667 0.00 0.00 0.00 3.49
233 234 3.866066 GCCTCCTCCCATTTTCTTTTTGC 60.866 47.826 0.00 0.00 0.00 3.68
238 239 1.387119 AGGCCTCCTCCCATTTTCTT 58.613 50.000 0.00 0.00 0.00 2.52
297 302 1.332997 CAATGGCAGCGAAAGATCCTC 59.667 52.381 0.00 0.00 0.00 3.71
429 440 2.001361 CTCGGTTACTCGGCGATGGT 62.001 60.000 11.27 8.74 0.00 3.55
557 593 2.351276 CTAGCCGGGTGTTGCCTT 59.649 61.111 18.40 0.00 37.43 4.35
589 848 7.668469 TGGAGGTTCCTTTATTTTTAACTCTCC 59.332 37.037 0.00 0.00 37.46 3.71
613 873 2.146342 GCCGATACACCATGATCTTGG 58.854 52.381 22.73 22.73 42.82 3.61
875 1140 1.543944 TTGCGATGGAGCTGGTGAGA 61.544 55.000 0.00 0.00 38.13 3.27
1512 1779 1.376942 CTGCTTCTCCTGCACCCAG 60.377 63.158 0.00 0.00 38.85 4.45
1637 1904 4.293648 CGTGGTCACCCTGCGTCA 62.294 66.667 0.00 0.00 0.00 4.35
1689 1956 3.618780 CTGCTGGGGGTGCTGACTC 62.619 68.421 0.00 0.00 0.00 3.36
1698 1965 2.674380 GAGTGTTGCTGCTGGGGG 60.674 66.667 0.00 0.00 0.00 5.40
1756 2027 1.135689 CGAATGGCGAGAACCCAAAAG 60.136 52.381 0.00 0.00 44.57 2.27
1829 2110 2.714250 ACACTTCAGGGGTGTATTTCCA 59.286 45.455 0.00 0.00 44.72 3.53
1874 2157 2.030007 GCTCCAAGCACATAAACAAGCA 60.030 45.455 0.00 0.00 41.89 3.91
1881 2165 1.340017 GGGTGAGCTCCAAGCACATAA 60.340 52.381 12.15 0.00 43.30 1.90
1882 2166 0.253044 GGGTGAGCTCCAAGCACATA 59.747 55.000 12.15 0.00 43.30 2.29
1899 2183 4.042062 TGCACAAATAGGAGAGATATGGGG 59.958 45.833 0.00 0.00 0.00 4.96
1912 2197 5.902613 TGATCCCTTCTTTGCACAAATAG 57.097 39.130 0.00 0.00 0.00 1.73
1972 2285 2.787473 ATCATCAAGGGAACAAGCGA 57.213 45.000 0.00 0.00 0.00 4.93
1983 2296 4.570772 ACCGGTCATAACGAAATCATCAAG 59.429 41.667 0.00 0.00 0.00 3.02
1984 2297 4.509616 ACCGGTCATAACGAAATCATCAA 58.490 39.130 0.00 0.00 0.00 2.57
2003 2321 3.082628 CGTTCAAACGCGCAACCG 61.083 61.111 5.73 0.00 46.06 4.44
2036 2354 2.148446 ACCATGGCTTATGCACATGT 57.852 45.000 13.04 0.00 41.70 3.21
2157 2479 3.754188 AGACACCGTCGTACATAGAAC 57.246 47.619 0.00 0.00 37.67 3.01
2171 2493 1.537202 CCTAAGCAAGCACAAGACACC 59.463 52.381 0.00 0.00 0.00 4.16
2195 2517 5.945144 AGAAAAGAATGCCATTGCCTATT 57.055 34.783 0.00 0.00 36.33 1.73
2228 4232 2.588027 TGCCATTGCGTATTCTCGTA 57.412 45.000 0.00 0.00 41.78 3.43
2238 4242 1.472082 TGTGGTTAGAATGCCATTGCG 59.528 47.619 0.00 0.00 41.78 4.85
2263 4267 2.841215 TGCTTACCAGTTACCACACAC 58.159 47.619 0.00 0.00 0.00 3.82
2307 4311 7.380065 GTGTAGAGCTAAAGACCTAAATCATCG 59.620 40.741 0.00 0.00 0.00 3.84
2413 4422 2.028876 GCCCCCGCACAGTAAATTTAT 58.971 47.619 0.31 0.00 34.03 1.40
2416 4425 0.965363 CAGCCCCCGCACAGTAAATT 60.965 55.000 0.00 0.00 37.52 1.82
2489 4498 1.921887 GCAATCGTGGTCATGCAATTG 59.078 47.619 0.00 0.00 38.63 2.32
2537 4546 2.023673 CTCCATGGCCGAATTGCTTTA 58.976 47.619 6.96 0.00 0.00 1.85
2567 4581 0.958822 ATGACCGGGCACAACTTTTC 59.041 50.000 15.41 0.00 0.00 2.29
2571 4585 2.159382 CTAAAATGACCGGGCACAACT 58.841 47.619 15.41 0.00 0.00 3.16
2573 4587 1.202952 ACCTAAAATGACCGGGCACAA 60.203 47.619 15.41 0.00 0.00 3.33
2578 4592 6.704937 GTCTTTATCTACCTAAAATGACCGGG 59.295 42.308 6.32 0.00 0.00 5.73
2616 4642 5.013236 GCTTACATTCGTGTTGTAACATCG 58.987 41.667 0.26 6.97 41.59 3.84
2705 4758 2.940410 ACGACGCCGGAATTATGAAATT 59.060 40.909 5.05 0.00 40.78 1.82


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

AutoCloner maintained by Alex Coulton.