Multiple sequence alignment - TraesCS7D01G063400

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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 TraesCS7D01G063400 chr7D 100.000 4865 0 0 1 4865 34469428 34474292 0.000000e+00 8985.0
1 TraesCS7D01G063400 chr7D 92.144 1502 78 11 2123 3614 34374779 34376250 0.000000e+00 2084.0
2 TraesCS7D01G063400 chr7D 92.465 1075 54 7 2123 3196 34755200 34754152 0.000000e+00 1511.0
3 TraesCS7D01G063400 chr7D 89.298 841 64 8 3194 4029 34754060 34753241 0.000000e+00 1031.0
4 TraesCS7D01G063400 chr7D 92.022 727 42 7 1090 1812 34371596 34372310 0.000000e+00 1007.0
5 TraesCS7D01G063400 chr7D 87.882 883 63 23 1042 1910 34758924 34758072 0.000000e+00 998.0
6 TraesCS7D01G063400 chr7D 93.827 486 25 2 3539 4024 34376251 34376731 0.000000e+00 726.0
7 TraesCS7D01G063400 chr7D 94.278 367 15 2 4049 4415 34377241 34377601 1.530000e-154 556.0
8 TraesCS7D01G063400 chr7D 88.009 442 31 6 4446 4865 34752399 34751958 2.020000e-138 503.0
9 TraesCS7D01G063400 chr7D 86.224 392 24 5 1952 2313 34372361 34372752 9.810000e-107 398.0
10 TraesCS7D01G063400 chr7D 89.320 309 29 1 2009 2313 34758036 34757728 7.640000e-103 385.0
11 TraesCS7D01G063400 chr7D 88.298 188 20 2 4050 4236 34752580 34752394 1.760000e-54 224.0
12 TraesCS7D01G063400 chr4A 90.966 1915 116 14 2123 4029 690620232 690618367 0.000000e+00 2525.0
13 TraesCS7D01G063400 chr4A 91.745 1708 106 13 2332 4025 690412915 690414601 0.000000e+00 2340.0
14 TraesCS7D01G063400 chr4A 83.424 2395 214 88 6 2313 690624625 690622327 0.000000e+00 2054.0
15 TraesCS7D01G063400 chr4A 86.644 876 62 33 1059 1910 690409545 690410389 0.000000e+00 918.0
16 TraesCS7D01G063400 chr4A 82.421 859 69 35 4050 4865 690415049 690415868 0.000000e+00 675.0
17 TraesCS7D01G063400 chr4A 87.686 471 27 14 4418 4865 690617276 690616814 2.010000e-143 520.0
18 TraesCS7D01G063400 chr4A 87.784 352 37 4 4066 4415 690617953 690617606 1.630000e-109 407.0
19 TraesCS7D01G063400 chr4A 90.508 295 24 1 2023 2313 690410431 690410725 2.120000e-103 387.0
20 TraesCS7D01G063400 chr4A 84.098 327 39 11 632 952 690409092 690409411 2.200000e-78 303.0
21 TraesCS7D01G063400 chr4A 100.000 32 0 0 1031 1062 690409530 690409561 5.260000e-05 60.2
22 TraesCS7D01G063400 chr4A 92.500 40 3 0 4615 4654 488530082 488530043 1.890000e-04 58.4
23 TraesCS7D01G063400 chr4A 94.595 37 0 2 544 580 62354767 62354733 6.800000e-04 56.5
24 TraesCS7D01G063400 chr7A 89.155 1918 122 36 2123 4029 35001806 34999964 0.000000e+00 2311.0
25 TraesCS7D01G063400 chr7A 94.498 1236 56 4 2009 3236 34744362 34745593 0.000000e+00 1895.0
26 TraesCS7D01G063400 chr7A 91.754 764 47 4 3266 4029 34745589 34746336 0.000000e+00 1048.0
27 TraesCS7D01G063400 chr7A 86.338 893 63 22 979 1869 34743354 34744189 0.000000e+00 918.0
28 TraesCS7D01G063400 chr7A 88.140 801 45 21 3232 4029 34963791 34963038 0.000000e+00 907.0
29 TraesCS7D01G063400 chr7A 90.045 663 48 13 4066 4719 34962693 34962040 0.000000e+00 843.0
30 TraesCS7D01G063400 chr7A 85.732 799 64 22 1024 1812 35003041 35002283 0.000000e+00 798.0
31 TraesCS7D01G063400 chr7A 90.191 367 33 3 4050 4415 34746816 34747180 4.410000e-130 475.0
32 TraesCS7D01G063400 chr7A 85.000 480 41 13 4415 4865 34747250 34747727 4.440000e-125 459.0
33 TraesCS7D01G063400 chr7A 89.071 366 38 1 4050 4415 34999509 34999146 2.060000e-123 453.0
34 TraesCS7D01G063400 chr7A 84.067 477 45 12 4418 4865 34999073 34998599 9.670000e-117 431.0
35 TraesCS7D01G063400 chr7A 83.042 401 30 15 1775 2143 35002231 35001837 3.630000e-86 329.0
36 TraesCS7D01G063400 chr7A 84.266 286 30 10 9 288 34741482 34741758 1.040000e-66 265.0
37 TraesCS7D01G063400 chr7A 86.166 253 24 8 375 625 34742587 34742830 3.730000e-66 263.0
38 TraesCS7D01G063400 chr7A 80.967 331 30 17 633 957 34742911 34743214 1.050000e-56 231.0
39 TraesCS7D01G063400 chr7A 97.414 116 3 0 4750 4865 34961893 34961778 1.070000e-46 198.0
40 TraesCS7D01G063400 chr2B 90.264 493 46 2 2241 2733 704812642 704813132 1.140000e-180 643.0
41 TraesCS7D01G063400 chr2B 89.021 337 35 2 1308 1644 704812300 704812634 2.710000e-112 416.0
42 TraesCS7D01G063400 chr5D 82.796 93 10 5 488 580 418077210 418077124 1.450000e-10 78.7
43 TraesCS7D01G063400 chr5B 82.353 85 12 2 489 573 505562367 505562286 2.430000e-08 71.3
44 TraesCS7D01G063400 chr5B 94.595 37 2 0 544 580 565538967 565539003 1.890000e-04 58.4
45 TraesCS7D01G063400 chr2A 92.857 42 3 0 4613 4654 160778898 160778939 1.460000e-05 62.1
46 TraesCS7D01G063400 chr2A 88.000 50 6 0 4605 4654 278920349 278920398 5.260000e-05 60.2
47 TraesCS7D01G063400 chr2A 100.000 31 0 0 543 573 718912005 718911975 1.890000e-04 58.4
48 TraesCS7D01G063400 chr1B 76.336 131 21 9 447 573 668711206 668711082 1.460000e-05 62.1
49 TraesCS7D01G063400 chr4D 92.500 40 3 0 4615 4654 93455893 93455932 1.890000e-04 58.4
50 TraesCS7D01G063400 chr3A 94.737 38 1 1 545 582 581391922 581391886 1.890000e-04 58.4
51 TraesCS7D01G063400 chr3A 100.000 28 0 0 4627 4654 645393140 645393167 9.000000e-03 52.8
52 TraesCS7D01G063400 chrUn 92.308 39 3 0 4616 4654 126679316 126679354 6.800000e-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 TraesCS7D01G063400 chr7D 34469428 34474292 4864 False 8985.000000 8985 100.000000 1 4865 1 chr7D.!!$F1 4864
1 TraesCS7D01G063400 chr7D 34371596 34377601 6005 False 954.200000 2084 91.699000 1090 4415 5 chr7D.!!$F2 3325
2 TraesCS7D01G063400 chr7D 34751958 34758924 6966 True 775.333333 1511 89.212000 1042 4865 6 chr7D.!!$R1 3823
3 TraesCS7D01G063400 chr4A 690616814 690624625 7811 True 1376.500000 2525 87.465000 6 4865 4 chr4A.!!$R3 4859
4 TraesCS7D01G063400 chr4A 690409092 690415868 6776 False 780.533333 2340 89.236000 632 4865 6 chr4A.!!$F1 4233
5 TraesCS7D01G063400 chr7A 34998599 35003041 4442 True 864.400000 2311 86.213400 1024 4865 5 chr7A.!!$R2 3841
6 TraesCS7D01G063400 chr7A 34741482 34747727 6245 False 694.250000 1895 87.397500 9 4865 8 chr7A.!!$F1 4856
7 TraesCS7D01G063400 chr7A 34961778 34963791 2013 True 649.333333 907 91.866333 3232 4865 3 chr7A.!!$R1 1633
8 TraesCS7D01G063400 chr2B 704812300 704813132 832 False 529.500000 643 89.642500 1308 2733 2 chr2B.!!$F1 1425

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
973 1851 0.319083 TTCTCGCTCCCGCAAAGTTA 59.681 50.000 0.0 0.00 35.30 2.24 F
1280 2299 0.807496 GCTGGAACAAGCATCAGGTC 59.193 55.000 0.0 0.00 38.70 3.85 F
1284 2303 0.807496 GAACAAGCATCAGGTCAGCC 59.193 55.000 0.0 0.00 0.00 4.85 F
1483 2528 1.827399 AAGACCGAGGTTCGTGCCAT 61.827 55.000 0.0 0.00 38.40 4.40 F
1509 2554 1.923864 CGCCAGGTGTTTGTGTTTTTC 59.076 47.619 0.0 0.00 0.00 2.29 F
3318 9841 1.190833 ACCAGTCTCAGCTCTGTGGG 61.191 60.000 8.5 1.89 30.07 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2694 9119 0.251297 CCAAGTCACCATGCCCTTCA 60.251 55.000 0.00 0.0 0.00 3.02 R
2749 9174 1.760613 GATATGGACACCAACGGAGGA 59.239 52.381 2.13 0.0 36.95 3.71 R
2874 9299 3.177487 GCTGCAGATTTTAGAAGCAAGC 58.823 45.455 20.43 0.0 34.45 4.01 R
3301 9824 0.246086 GACCCACAGAGCTGAGACTG 59.754 60.000 4.21 0.0 39.65 3.51 R
3541 10067 7.907214 AAACCAGCCATCGATAAATATCTAC 57.093 36.000 0.00 0.0 0.00 2.59 R
4242 11738 0.687427 TGCGTGATCCTCCCTCATGA 60.687 55.000 0.00 0.0 32.46 3.07 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
286 296 4.021925 ACTCAAGGCCTGCGGTCC 62.022 66.667 5.69 0.00 0.00 4.46
292 302 4.660938 GGCCTGCGGTCCCTGTTT 62.661 66.667 0.00 0.00 0.00 2.83
297 307 3.047877 GCGGTCCCTGTTTGTCCG 61.048 66.667 0.00 0.00 43.37 4.79
298 308 2.738480 CGGTCCCTGTTTGTCCGA 59.262 61.111 0.00 0.00 43.22 4.55
307 317 2.154462 CTGTTTGTCCGAGCCATTCTT 58.846 47.619 0.00 0.00 0.00 2.52
326 336 2.738521 GCGTTGCTTGAGGCGAGA 60.739 61.111 0.00 0.00 45.43 4.04
346 1057 5.242795 AGATTGCACTAAACCCTTACAGT 57.757 39.130 0.00 0.00 0.00 3.55
371 1082 4.196778 TTGCGGCTGGGGTTGTGA 62.197 61.111 0.00 0.00 0.00 3.58
372 1083 4.641645 TGCGGCTGGGGTTGTGAG 62.642 66.667 0.00 0.00 0.00 3.51
376 1142 2.360475 GCTGGGGTTGTGAGCCTC 60.360 66.667 0.00 0.00 43.15 4.70
420 1186 9.382244 CCACACGTTTTCTTCTCTTTATTTTAG 57.618 33.333 0.00 0.00 0.00 1.85
484 1253 6.486320 TCTTTATTTCTCTGCAACACATGTCA 59.514 34.615 0.00 0.00 0.00 3.58
493 1262 3.803231 TGCAACACATGTCAGCATTTTTC 59.197 39.130 11.19 0.00 35.19 2.29
854 1726 9.974980 ACATTGTATAAACCGTTTCAGAAAATT 57.025 25.926 0.00 0.00 0.00 1.82
888 1760 9.057365 CATATTTTTGCAACATTTGAGCATTTC 57.943 29.630 0.00 0.00 38.19 2.17
973 1851 0.319083 TTCTCGCTCCCGCAAAGTTA 59.681 50.000 0.00 0.00 35.30 2.24
977 1855 2.396157 GCTCCCGCAAAGTTACCCG 61.396 63.158 0.00 0.00 35.78 5.28
1007 2006 3.659183 ATGCTTATGGATAGGCCCATC 57.341 47.619 2.00 2.00 43.07 3.51
1011 2010 3.559171 GCTTATGGATAGGCCCATCGAAA 60.559 47.826 5.01 0.00 43.07 3.46
1014 2013 4.533832 ATGGATAGGCCCATCGAAAGGC 62.534 54.545 18.31 18.31 43.07 4.35
1029 2028 2.343484 AAGGCCCTTTTAGTATCCGC 57.657 50.000 0.00 0.00 0.00 5.54
1278 2297 1.651240 CCGCTGGAACAAGCATCAGG 61.651 60.000 2.08 0.00 38.70 3.86
1279 2298 0.957395 CGCTGGAACAAGCATCAGGT 60.957 55.000 2.08 0.00 38.70 4.00
1280 2299 0.807496 GCTGGAACAAGCATCAGGTC 59.193 55.000 0.00 0.00 38.70 3.85
1281 2300 1.883638 GCTGGAACAAGCATCAGGTCA 60.884 52.381 0.00 0.00 38.70 4.02
1282 2301 2.082231 CTGGAACAAGCATCAGGTCAG 58.918 52.381 0.00 0.00 38.70 3.51
1283 2302 0.807496 GGAACAAGCATCAGGTCAGC 59.193 55.000 0.00 0.00 0.00 4.26
1284 2303 0.807496 GAACAAGCATCAGGTCAGCC 59.193 55.000 0.00 0.00 0.00 4.85
1483 2528 1.827399 AAGACCGAGGTTCGTGCCAT 61.827 55.000 0.00 0.00 38.40 4.40
1509 2554 1.923864 CGCCAGGTGTTTGTGTTTTTC 59.076 47.619 0.00 0.00 0.00 2.29
1510 2555 2.416701 CGCCAGGTGTTTGTGTTTTTCT 60.417 45.455 0.00 0.00 0.00 2.52
1516 2561 3.699538 GGTGTTTGTGTTTTTCTCTCCCT 59.300 43.478 0.00 0.00 0.00 4.20
1533 2578 4.697756 TGAGCCCGGCCGTTCAAG 62.698 66.667 26.12 8.02 0.00 3.02
1611 2657 3.235481 TCCACGGTTCGGCCTCAA 61.235 61.111 0.00 0.00 34.25 3.02
1739 2785 2.480416 GCATCTTCTCTGTCTACACGGG 60.480 54.545 0.00 0.00 0.00 5.28
1760 2806 4.922103 GGGTCTCTTTGTTCGTACTTACTG 59.078 45.833 0.00 0.00 0.00 2.74
1795 2841 7.278646 TGTCAATTGATCATGTAACTCACTAGC 59.721 37.037 12.12 0.00 0.00 3.42
1798 2844 5.011090 TGATCATGTAACTCACTAGCCAC 57.989 43.478 0.00 0.00 0.00 5.01
1821 2867 3.527533 TGCATAGTCGTGGTGGATAAAC 58.472 45.455 0.00 0.00 0.00 2.01
1886 2932 4.018490 TCACTAGGCGTTTGGATACTGTA 58.982 43.478 0.00 0.00 37.61 2.74
1897 3099 7.328737 GCGTTTGGATACTGTAGTGGATAATAG 59.671 40.741 0.00 0.00 37.61 1.73
1928 3213 6.951778 AGCTATTTGTTTATACTTGGGGTTGT 59.048 34.615 0.00 0.00 0.00 3.32
1936 3221 2.417719 ACTTGGGGTTGTCTCTACCT 57.582 50.000 0.00 0.00 35.92 3.08
1996 3281 3.678056 ATCGTGCTCCTAAAGTTCACA 57.322 42.857 0.00 0.00 0.00 3.58
2048 3353 8.067784 TCGTGTTCAGCTCAAAATTTAAGTTAG 58.932 33.333 0.00 0.00 0.00 2.34
2223 3558 3.181455 CCTATACTAGCCCACAATGCACA 60.181 47.826 0.00 0.00 0.00 4.57
2245 6347 4.602340 ATTCAGTACACGTCTGGTTCTT 57.398 40.909 3.21 0.00 34.15 2.52
2350 8775 8.879759 AGATTTTATCATTTTGCTCATGCTTTG 58.120 29.630 0.00 0.00 40.48 2.77
2384 8809 4.643387 GCGCAGGTCAGTGGGGTT 62.643 66.667 0.30 0.00 0.00 4.11
2403 8828 4.275936 GGGTTTCCAGATGCATGTATACAC 59.724 45.833 7.96 0.00 0.00 2.90
2673 9098 4.036027 CAGATTCATTTTCATCCAGACCCG 59.964 45.833 0.00 0.00 0.00 5.28
2694 9119 5.826208 CCCGCCTTCAGTAATATTTAAAGGT 59.174 40.000 14.31 0.00 36.48 3.50
2874 9299 7.551617 ACCAAGAATTATCCTACAGGTAAAACG 59.448 37.037 0.00 0.00 36.34 3.60
2880 9305 2.038033 TCCTACAGGTAAAACGCTTGCT 59.962 45.455 0.00 0.00 36.34 3.91
2881 9306 2.812011 CCTACAGGTAAAACGCTTGCTT 59.188 45.455 0.00 0.00 0.00 3.91
3124 9552 3.063704 CAGCCAAGCCGGATTGCA 61.064 61.111 26.87 0.00 36.56 4.08
3177 9606 7.308229 GGAGGATGATTAAAGGACAAATGATCG 60.308 40.741 0.00 0.00 29.58 3.69
3204 9727 7.003402 AGCATGTATTGTAATTTTGTTGGGT 57.997 32.000 0.00 0.00 0.00 4.51
3246 9769 7.226918 GGTCTAGCTTTTTCTTCAGTAGTTGTT 59.773 37.037 0.00 0.00 0.00 2.83
3288 9811 9.548208 GCATTCTTTTTCTGTCTAATGACTTAC 57.452 33.333 0.00 0.00 43.29 2.34
3301 9824 8.854312 GTCTAATGACTTACGTTGTAAACTACC 58.146 37.037 0.00 0.00 41.41 3.18
3318 9841 1.190833 ACCAGTCTCAGCTCTGTGGG 61.191 60.000 8.50 1.89 30.07 4.61
3389 9912 1.339055 TGCCATCGTCCTTCTTCCTTG 60.339 52.381 0.00 0.00 0.00 3.61
3400 9923 4.012374 CCTTCTTCCTTGCAAATGAGCTA 58.988 43.478 0.00 0.00 34.99 3.32
3422 9945 7.818930 AGCTACATTTGAATTGTTACCATTTGG 59.181 33.333 0.00 0.00 42.17 3.28
3425 9949 7.504403 ACATTTGAATTGTTACCATTTGGACA 58.496 30.769 3.01 0.00 38.94 4.02
3507 10033 5.467399 TGGAGTACAAAAACTATTGACACGG 59.533 40.000 0.00 0.00 34.38 4.94
3541 10067 6.040729 TGAGCCCCAAATATGTGTATCATTTG 59.959 38.462 0.00 0.00 38.69 2.32
3752 10354 5.199723 TGAGCTCATTATGTCTCTGTCTCT 58.800 41.667 13.74 0.00 0.00 3.10
3755 10357 5.655974 AGCTCATTATGTCTCTGTCTCTTCA 59.344 40.000 0.00 0.00 0.00 3.02
3788 10390 0.394899 CTCTCAACAGGCCCCCAATC 60.395 60.000 0.00 0.00 0.00 2.67
3793 10395 0.325577 AACAGGCCCCCAATCAATCC 60.326 55.000 0.00 0.00 0.00 3.01
3800 10402 2.310538 CCCCCAATCAATCCAGCTTAC 58.689 52.381 0.00 0.00 0.00 2.34
3801 10403 2.358090 CCCCCAATCAATCCAGCTTACA 60.358 50.000 0.00 0.00 0.00 2.41
3850 10465 2.902486 TGGCCCATTGTTCAATTGCTAA 59.098 40.909 0.00 0.00 0.00 3.09
4025 10640 4.947388 ACAAAACGTGTGGATTGGCTATAT 59.053 37.500 0.00 0.00 39.72 0.86
4029 10644 7.435068 AAACGTGTGGATTGGCTATATATTC 57.565 36.000 0.00 0.00 0.00 1.75
4030 10645 5.488341 ACGTGTGGATTGGCTATATATTCC 58.512 41.667 0.00 0.00 0.00 3.01
4031 10646 4.566759 CGTGTGGATTGGCTATATATTCCG 59.433 45.833 0.00 0.00 0.00 4.30
4032 10647 5.623596 CGTGTGGATTGGCTATATATTCCGA 60.624 44.000 0.00 0.00 0.00 4.55
4035 10650 7.985184 GTGTGGATTGGCTATATATTCCGATTA 59.015 37.037 7.49 0.91 0.00 1.75
4036 10651 8.713971 TGTGGATTGGCTATATATTCCGATTAT 58.286 33.333 7.49 0.00 0.00 1.28
4073 11567 0.537188 AGTGACCCGCGAGATGATTT 59.463 50.000 8.23 0.00 0.00 2.17
4164 11658 1.134521 TCTTATGACCGCGAAATGGCT 60.135 47.619 8.23 0.00 0.00 4.75
4242 11738 5.614324 TCGATGTTTCCAAGATATCCACT 57.386 39.130 0.00 0.00 0.00 4.00
4296 11792 1.350351 AGCAGCCCCTATTCTATGCAG 59.650 52.381 0.00 0.00 36.15 4.41
4317 11813 2.887152 GTGAAGGTGATGTGGCTCTTTT 59.113 45.455 0.00 0.00 0.00 2.27
4552 12409 2.839486 ACATGACAGGACGAACACAT 57.161 45.000 0.00 0.00 0.00 3.21
4568 12425 5.560183 CGAACACATAGTTGGGTGAAGAAAC 60.560 44.000 0.00 0.00 39.02 2.78
4594 12451 5.007136 GCTACCTTCTCTGCATTTGTACATC 59.993 44.000 0.00 0.00 0.00 3.06
4595 12452 4.910195 ACCTTCTCTGCATTTGTACATCA 58.090 39.130 0.00 0.00 0.00 3.07
4649 12507 8.821686 TGATCCATAATAAGTGTCATGGTTTT 57.178 30.769 0.00 0.00 39.21 2.43
4738 12701 0.340208 AAGGGGTCTAGGTCCTGAGG 59.660 60.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 204 8.211629 TCTTCTTTACTTTTGCTTAGTCTTCCT 58.788 33.333 0.00 0.00 0.00 3.36
237 243 4.968812 TCCTTTCGGTTTTTCGTTTTCT 57.031 36.364 0.00 0.00 0.00 2.52
238 244 6.392353 TTTTCCTTTCGGTTTTTCGTTTTC 57.608 33.333 0.00 0.00 0.00 2.29
264 274 1.455383 CCGCAGGCCTTGAGTGTTTT 61.455 55.000 0.00 0.00 46.14 2.43
286 296 0.804989 GAATGGCTCGGACAAACAGG 59.195 55.000 0.00 0.00 0.00 4.00
307 317 4.617520 TCGCCTCAAGCAACGCCA 62.618 61.111 0.00 0.00 44.04 5.69
326 336 4.980573 TCACTGTAAGGGTTTAGTGCAAT 58.019 39.130 0.00 0.00 39.54 3.56
371 1082 3.026694 ACAAACAAAGCAGAAAGAGGCT 58.973 40.909 0.00 0.00 43.46 4.58
372 1083 3.443099 ACAAACAAAGCAGAAAGAGGC 57.557 42.857 0.00 0.00 0.00 4.70
455 1224 8.506437 CATGTGTTGCAGAGAAATAAAGAAGTA 58.494 33.333 0.00 0.00 0.00 2.24
456 1225 6.942532 TGTGTTGCAGAGAAATAAAGAAGT 57.057 33.333 0.00 0.00 0.00 3.01
457 1226 7.365741 ACATGTGTTGCAGAGAAATAAAGAAG 58.634 34.615 0.00 0.00 0.00 2.85
463 1232 4.154737 GCTGACATGTGTTGCAGAGAAATA 59.845 41.667 14.63 0.00 33.78 1.40
745 1616 7.929785 AGCATCTGAAACAAATTTTCTGTGATT 59.070 29.630 0.00 0.00 0.00 2.57
746 1617 7.439381 AGCATCTGAAACAAATTTTCTGTGAT 58.561 30.769 0.00 0.00 0.00 3.06
882 1754 6.599437 TGTTCGCTCTACTTTTAAGAAATGC 58.401 36.000 0.00 0.00 0.00 3.56
934 1810 7.165812 GCGAGAATATGTTCATTGCGTATTTTT 59.834 33.333 4.92 0.00 36.79 1.94
977 1855 6.374613 GCCTATCCATAAGCATTTACCCTTAC 59.625 42.308 0.00 0.00 0.00 2.34
1007 2006 2.870411 CGGATACTAAAAGGGCCTTTCG 59.130 50.000 30.54 24.70 31.99 3.46
1011 2010 0.106149 CGCGGATACTAAAAGGGCCT 59.894 55.000 0.00 0.00 0.00 5.19
1014 2013 0.883370 GGCCGCGGATACTAAAAGGG 60.883 60.000 33.48 0.00 0.00 3.95
1311 2335 0.548989 CGGAGGAGAGGAGAGGAGAA 59.451 60.000 0.00 0.00 0.00 2.87
1516 2561 4.697756 CTTGAACGGCCGGGCTCA 62.698 66.667 31.76 24.53 0.00 4.26
1530 2575 2.558359 GGTCAATCCCCACTGAAACTTG 59.442 50.000 0.00 0.00 0.00 3.16
1533 2578 1.165270 CGGTCAATCCCCACTGAAAC 58.835 55.000 0.00 0.00 0.00 2.78
1739 2785 9.831737 TTATACAGTAAGTACGAACAAAGAGAC 57.168 33.333 0.00 0.00 35.05 3.36
1798 2844 2.315925 ATCCACCACGACTATGCAAG 57.684 50.000 0.00 0.00 0.00 4.01
1821 2867 7.977293 TCCAAAGATCATAAATCACAAATGCAG 59.023 33.333 0.00 0.00 0.00 4.41
1914 3198 5.216665 AGGTAGAGACAACCCCAAGTATA 57.783 43.478 0.00 0.00 37.77 1.47
2011 3316 2.224079 GCTGAACACGAAGCTCAAATGA 59.776 45.455 0.00 0.00 36.47 2.57
2048 3353 8.993121 CACATTACTTACATCCATATCCAGAAC 58.007 37.037 0.00 0.00 0.00 3.01
2223 3558 4.602340 AGAACCAGACGTGTACTGAATT 57.398 40.909 0.00 0.00 37.54 2.17
2350 8775 2.739913 TGCGCTTGTGTTACCAGAATAC 59.260 45.455 9.73 0.00 0.00 1.89
2403 8828 4.437930 GGAATTCTGGTTCTGATTTCTGCG 60.438 45.833 5.23 0.00 0.00 5.18
2673 9098 8.406297 CCTTCACCTTTAAATATTACTGAAGGC 58.594 37.037 9.54 0.00 43.91 4.35
2694 9119 0.251297 CCAAGTCACCATGCCCTTCA 60.251 55.000 0.00 0.00 0.00 3.02
2749 9174 1.760613 GATATGGACACCAACGGAGGA 59.239 52.381 2.13 0.00 36.95 3.71
2751 9176 4.665833 TTAGATATGGACACCAACGGAG 57.334 45.455 0.00 0.00 36.95 4.63
2824 9249 5.645067 TCACACTGGAATGCAATTAGAAGAG 59.355 40.000 0.00 0.00 36.07 2.85
2874 9299 3.177487 GCTGCAGATTTTAGAAGCAAGC 58.823 45.455 20.43 0.00 34.45 4.01
3124 9552 6.258160 CGGCTTCACAAAGAATTCGATAAAT 58.742 36.000 0.00 0.00 35.25 1.40
3177 9606 7.222611 CCCAACAAAATTACAATACATGCTAGC 59.777 37.037 8.10 8.10 0.00 3.42
3204 9727 4.824537 GCTAGACCTCATAGATGACACAGA 59.175 45.833 0.00 0.00 32.50 3.41
3246 9769 4.922206 AGAATGCCATCACCTTCAGTTTA 58.078 39.130 0.00 0.00 0.00 2.01
3288 9811 3.673809 GCTGAGACTGGTAGTTTACAACG 59.326 47.826 0.00 0.00 36.23 4.10
3301 9824 0.246086 GACCCACAGAGCTGAGACTG 59.754 60.000 4.21 0.00 39.65 3.51
3541 10067 7.907214 AAACCAGCCATCGATAAATATCTAC 57.093 36.000 0.00 0.00 0.00 2.59
3554 10080 6.942532 TTCATAGTCATTAAACCAGCCATC 57.057 37.500 0.00 0.00 0.00 3.51
3752 10354 0.833287 GAGCAGTGGGAGGCTATGAA 59.167 55.000 0.00 0.00 41.22 2.57
3755 10357 0.031716 TGAGAGCAGTGGGAGGCTAT 60.032 55.000 0.00 0.00 41.22 2.97
3800 10402 0.174162 GGCCTGGTTATTTGCAGCTG 59.826 55.000 10.11 10.11 0.00 4.24
3801 10403 0.251742 TGGCCTGGTTATTTGCAGCT 60.252 50.000 3.32 0.00 0.00 4.24
3850 10465 0.706433 ATGCCTCACTTGGGAATGGT 59.294 50.000 0.00 0.00 0.00 3.55
4029 10644 9.794685 CTCCATGATCGGAATATATATAATCGG 57.205 37.037 8.41 8.41 33.65 4.18
4035 10650 7.015682 GGGTCACTCCATGATCGGAATATATAT 59.984 40.741 0.00 0.00 39.64 0.86
4036 10651 6.323996 GGGTCACTCCATGATCGGAATATATA 59.676 42.308 0.00 0.00 39.64 0.86
4038 10653 4.466370 GGGTCACTCCATGATCGGAATATA 59.534 45.833 0.00 0.00 39.64 0.86
4039 10654 3.261897 GGGTCACTCCATGATCGGAATAT 59.738 47.826 0.00 0.00 39.64 1.28
4040 10655 2.632996 GGGTCACTCCATGATCGGAATA 59.367 50.000 0.00 0.00 39.64 1.75
4042 10657 0.830648 GGGTCACTCCATGATCGGAA 59.169 55.000 0.00 0.00 39.64 4.30
4044 10659 1.068083 CGGGTCACTCCATGATCGG 59.932 63.158 0.00 0.00 39.64 4.18
4046 10661 1.592669 CGCGGGTCACTCCATGATC 60.593 63.158 0.00 0.00 40.28 2.92
4073 11567 1.982395 CTCGGTACAGACCCTGCCA 60.982 63.158 0.00 0.00 43.64 4.92
4164 11658 6.630413 GCAGAGGACATTAGGTACATCAAGAA 60.630 42.308 0.00 0.00 30.17 2.52
4242 11738 0.687427 TGCGTGATCCTCCCTCATGA 60.687 55.000 0.00 0.00 32.46 3.07
4296 11792 2.191128 AAGAGCCACATCACCTTCAC 57.809 50.000 0.00 0.00 0.00 3.18
4317 11813 6.493116 TGTCTCGTTAATTGCGGTTTTAAAA 58.507 32.000 0.00 0.00 0.00 1.52
4552 12409 1.418637 AGCCGTTTCTTCACCCAACTA 59.581 47.619 0.00 0.00 0.00 2.24
4568 12425 1.667724 CAAATGCAGAGAAGGTAGCCG 59.332 52.381 0.00 0.00 0.00 5.52
4594 12451 8.487028 AGAGTAGTATTTTTCTCCTTATGGGTG 58.513 37.037 0.00 0.00 36.25 4.61
4595 12452 8.487028 CAGAGTAGTATTTTTCTCCTTATGGGT 58.513 37.037 0.00 0.00 36.25 4.51
4624 12481 8.821686 AAAACCATGACACTTATTATGGATCA 57.178 30.769 8.93 0.00 42.05 2.92
4704 12573 3.483421 ACCCCTTTAGTTAGCAACACAC 58.517 45.455 0.00 0.00 0.00 3.82
4738 12701 6.924060 GGTGACAGTGACCTATATAACATGTC 59.076 42.308 1.13 0.00 36.08 3.06
4740 12703 6.042093 AGGGTGACAGTGACCTATATAACATG 59.958 42.308 9.29 0.00 33.58 3.21


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

AutoCloner maintained by Alex Coulton.