Multiple sequence alignment - TraesCS3D01G357600

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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 TraesCS3D01G357600 chr3D 100.000 3820 0 0 1 3820 470884104 470887923 0.000000e+00 7055.0
1 TraesCS3D01G357600 chr3D 95.833 48 1 1 289 336 470884321 470884367 4.090000e-10 76.8
2 TraesCS3D01G357600 chr3D 95.833 48 1 1 218 264 470884392 470884439 4.090000e-10 76.8
3 TraesCS3D01G357600 chr3B 90.392 3320 169 56 1 3252 625328358 625331595 0.000000e+00 4226.0
4 TraesCS3D01G357600 chr3B 90.773 466 26 10 3231 3682 625331609 625332071 1.170000e-169 606.0
5 TraesCS3D01G357600 chr3B 90.503 179 14 1 3641 3819 625332076 625332251 2.290000e-57 233.0
6 TraesCS3D01G357600 chr3A 93.299 1761 79 20 2089 3819 613168860 613170611 0.000000e+00 2562.0
7 TraesCS3D01G357600 chr3A 90.570 1718 89 31 401 2104 613167189 613168847 0.000000e+00 2207.0
8 TraesCS3D01G357600 chr3A 85.612 417 30 14 52 455 613166787 613167186 9.880000e-111 411.0
9 TraesCS3D01G357600 chr3A 79.135 532 69 21 3287 3807 35434913 35435413 2.840000e-86 329.0
10 TraesCS3D01G357600 chr7D 80.151 398 41 21 3415 3801 69089109 69088739 2.930000e-66 263.0
11 TraesCS3D01G357600 chr7D 80.634 284 25 14 2703 2980 69119484 69119225 3.890000e-45 193.0
12 TraesCS3D01G357600 chr7D 89.831 59 6 0 2704 2762 1859790 1859732 4.090000e-10 76.8
13 TraesCS3D01G357600 chr2B 91.667 60 5 0 2703 2762 632396454 632396513 2.450000e-12 84.2


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 TraesCS3D01G357600 chr3D 470884104 470887923 3819 False 2402.866667 7055 97.222 1 3820 3 chr3D.!!$F1 3819
1 TraesCS3D01G357600 chr3B 625328358 625332251 3893 False 1688.333333 4226 90.556 1 3819 3 chr3B.!!$F1 3818
2 TraesCS3D01G357600 chr3A 613166787 613170611 3824 False 1726.666667 2562 89.827 52 3819 3 chr3A.!!$F2 3767
3 TraesCS3D01G357600 chr3A 35434913 35435413 500 False 329.000000 329 79.135 3287 3807 1 chr3A.!!$F1 520

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
171 181 0.029300 CGTTCAGTGCAACCAACCTG 59.971 55.0 0.0 0.0 37.80 4.00 F
1194 1274 0.245539 CGGTGTTATGTCTCCGTGGT 59.754 55.0 0.0 0.0 38.92 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1914 0.034337 AACGCTTCCTCGGCACTAAA 59.966 50.000 0.00 0.00 0.00 1.85 R
3049 3221 1.195448 GAACAGCATCTGTGAACACGG 59.805 52.381 7.38 7.38 44.62 4.94 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
42 43 1.133792 ACCACACTTCAACCCTCCTTG 60.134 52.381 0.00 0.00 0.00 3.61
44 45 1.133792 CACACTTCAACCCTCCTTGGT 60.134 52.381 0.00 0.00 41.55 3.67
47 48 2.105821 CACTTCAACCCTCCTTGGTACA 59.894 50.000 0.00 0.00 37.76 2.90
112 113 5.610398 AGCCCCTTTTCACTTTATTTTGTG 58.390 37.500 0.00 0.00 35.68 3.33
157 167 8.802856 CACTCAAAATATTTGTTTGTTCGTTCA 58.197 29.630 0.39 0.00 37.28 3.18
171 181 0.029300 CGTTCAGTGCAACCAACCTG 59.971 55.000 0.00 0.00 37.80 4.00
194 206 5.659463 GCCTTGTGCAAATCCAATTACATA 58.341 37.500 0.00 0.00 40.77 2.29
238 250 8.689972 ACATGACATTAATTTTGGATCTTCTCC 58.310 33.333 0.00 0.00 45.19 3.71
251 263 5.069318 GGATCTTCTCCATTCAAGGATTCC 58.931 45.833 0.00 0.00 44.26 3.01
252 264 5.398353 GGATCTTCTCCATTCAAGGATTCCA 60.398 44.000 5.29 0.00 44.26 3.53
253 265 5.722172 TCTTCTCCATTCAAGGATTCCAT 57.278 39.130 5.29 0.00 36.99 3.41
254 266 6.083487 TCTTCTCCATTCAAGGATTCCATT 57.917 37.500 5.29 0.00 36.99 3.16
255 267 6.496743 TCTTCTCCATTCAAGGATTCCATTT 58.503 36.000 5.29 0.00 36.99 2.32
256 268 6.955851 TCTTCTCCATTCAAGGATTCCATTTT 59.044 34.615 5.29 0.00 36.99 1.82
257 269 6.780457 TCTCCATTCAAGGATTCCATTTTC 57.220 37.500 5.29 0.00 36.99 2.29
274 286 4.367039 TTTTCTTCCCGAATCCTCTGTT 57.633 40.909 0.00 0.00 0.00 3.16
383 396 3.281395 CCCGAACGCCGTTTGGTT 61.281 61.111 29.33 0.00 43.58 3.67
402 415 1.859302 TTTTGCACAGAACCCCAACT 58.141 45.000 0.00 0.00 0.00 3.16
485 557 1.302033 CAGCTTCCCGTCAGCACTT 60.302 57.895 0.00 0.00 39.99 3.16
851 925 4.415332 GAGCGCCACGAGTCGGAA 62.415 66.667 18.30 0.00 0.00 4.30
932 1006 2.807895 CCTACGACACAACCGCCG 60.808 66.667 0.00 0.00 0.00 6.46
1189 1269 2.618053 CCTGTTCGGTGTTATGTCTCC 58.382 52.381 0.00 0.00 0.00 3.71
1193 1273 0.528924 TCGGTGTTATGTCTCCGTGG 59.471 55.000 0.00 0.00 42.59 4.94
1194 1274 0.245539 CGGTGTTATGTCTCCGTGGT 59.754 55.000 0.00 0.00 38.92 4.16
1262 1353 4.803426 CGGTGCAGACGGCTCTCC 62.803 72.222 0.00 0.00 45.15 3.71
1263 1354 3.386237 GGTGCAGACGGCTCTCCT 61.386 66.667 0.00 0.00 45.15 3.69
1264 1355 2.183046 GTGCAGACGGCTCTCCTC 59.817 66.667 0.00 0.00 45.15 3.71
1265 1356 3.443925 TGCAGACGGCTCTCCTCG 61.444 66.667 0.00 0.00 45.15 4.63
1266 1357 4.863925 GCAGACGGCTCTCCTCGC 62.864 72.222 0.00 0.00 40.25 5.03
1267 1358 4.544689 CAGACGGCTCTCCTCGCG 62.545 72.222 0.00 0.00 0.00 5.87
1301 1392 3.246619 GTCGATTGCTAGATCGGATTCC 58.753 50.000 12.39 0.00 46.63 3.01
1302 1393 2.231478 TCGATTGCTAGATCGGATTCCC 59.769 50.000 12.39 0.00 46.63 3.97
1309 1400 3.433740 GCTAGATCGGATTCCCCTTGTTT 60.434 47.826 0.00 0.00 0.00 2.83
1322 1413 5.722290 TCCCCTTGTTTTTAATCCTTCCTT 58.278 37.500 0.00 0.00 0.00 3.36
1324 1415 5.237815 CCCTTGTTTTTAATCCTTCCTTGC 58.762 41.667 0.00 0.00 0.00 4.01
1347 1438 3.369756 TCGCGCGATGATTTTAGTTTTCT 59.630 39.130 31.40 0.00 0.00 2.52
1348 1439 3.714498 CGCGCGATGATTTTAGTTTTCTC 59.286 43.478 28.94 0.00 0.00 2.87
1349 1440 3.714498 GCGCGATGATTTTAGTTTTCTCG 59.286 43.478 12.10 0.00 0.00 4.04
1350 1441 3.714498 CGCGATGATTTTAGTTTTCTCGC 59.286 43.478 0.00 0.00 44.78 5.03
1355 1446 3.124636 TGATTTTAGTTTTCTCGCGAGGC 59.875 43.478 33.98 21.09 0.00 4.70
1396 1488 7.047891 TGAATATGCGAGAATTTTGGTAGACT 58.952 34.615 0.00 0.00 0.00 3.24
1416 1508 5.364157 AGACTTTTTGATCTAGATACGCCCT 59.636 40.000 4.89 0.00 0.00 5.19
1462 1556 5.936686 TCTTGAGTATCCCGTCGTAATAG 57.063 43.478 0.00 0.00 0.00 1.73
1475 1569 7.178274 TCCCGTCGTAATAGGCCTTATTAATTA 59.822 37.037 12.58 5.59 36.30 1.40
1509 1603 0.800012 GCGATGTTTTCTTACGGGCA 59.200 50.000 0.00 0.00 0.00 5.36
1536 1630 6.015688 AGGATTCATATTGTGATGTTGCCATC 60.016 38.462 0.00 0.00 46.41 3.51
1537 1631 6.015688 GGATTCATATTGTGATGTTGCCATCT 60.016 38.462 4.83 0.00 46.38 2.90
1538 1632 7.175467 GGATTCATATTGTGATGTTGCCATCTA 59.825 37.037 4.83 0.00 46.38 1.98
1681 1775 1.099689 CAACTCCCTCCTCTCGTCTC 58.900 60.000 0.00 0.00 0.00 3.36
1682 1776 0.393267 AACTCCCTCCTCTCGTCTCG 60.393 60.000 0.00 0.00 0.00 4.04
1683 1777 1.222387 CTCCCTCCTCTCGTCTCGT 59.778 63.158 0.00 0.00 0.00 4.18
1684 1778 0.812412 CTCCCTCCTCTCGTCTCGTC 60.812 65.000 0.00 0.00 0.00 4.20
1685 1779 1.222387 CCCTCCTCTCGTCTCGTCT 59.778 63.158 0.00 0.00 0.00 4.18
1686 1780 0.812412 CCCTCCTCTCGTCTCGTCTC 60.812 65.000 0.00 0.00 0.00 3.36
1687 1781 1.149361 CCTCCTCTCGTCTCGTCTCG 61.149 65.000 0.00 0.00 0.00 4.04
1688 1782 0.458889 CTCCTCTCGTCTCGTCTCGT 60.459 60.000 0.00 0.00 0.00 4.18
1689 1783 0.458197 TCCTCTCGTCTCGTCTCGTC 60.458 60.000 0.00 0.00 0.00 4.20
1690 1784 0.458889 CCTCTCGTCTCGTCTCGTCT 60.459 60.000 0.00 0.00 0.00 4.18
1774 1870 7.014115 CGGAATAGTACGTCACACATCTATAC 58.986 42.308 0.00 0.00 0.00 1.47
1782 1878 6.042777 ACGTCACACATCTATACCAATGAAG 58.957 40.000 0.00 0.00 0.00 3.02
1783 1879 6.127451 ACGTCACACATCTATACCAATGAAGA 60.127 38.462 0.00 0.00 0.00 2.87
1784 1880 6.756542 CGTCACACATCTATACCAATGAAGAA 59.243 38.462 0.00 0.00 0.00 2.52
1785 1881 7.043125 CGTCACACATCTATACCAATGAAGAAG 60.043 40.741 0.00 0.00 0.00 2.85
1786 1882 7.981789 GTCACACATCTATACCAATGAAGAAGA 59.018 37.037 0.00 0.00 0.00 2.87
1787 1883 8.539544 TCACACATCTATACCAATGAAGAAGAA 58.460 33.333 0.00 0.00 0.00 2.52
1804 1900 8.237267 TGAAGAAGAACTGTTTTCTCTTTCAAC 58.763 33.333 14.10 5.04 32.71 3.18
1809 1905 7.886338 AGAACTGTTTTCTCTTTCAACAAACT 58.114 30.769 0.00 0.00 30.15 2.66
1815 1911 2.358898 TCTCTTTCAACAAACTGCAGGC 59.641 45.455 19.93 0.00 0.00 4.85
1818 1914 4.144297 TCTTTCAACAAACTGCAGGCTAT 58.856 39.130 19.93 0.00 0.00 2.97
1920 2016 3.133003 AGCATGTATAACTCTTGTCCGCT 59.867 43.478 0.00 0.00 0.00 5.52
1921 2017 3.246226 GCATGTATAACTCTTGTCCGCTG 59.754 47.826 0.00 0.00 0.00 5.18
1928 2025 1.269831 ACTCTTGTCCGCTGAGTTGAC 60.270 52.381 0.00 0.00 37.76 3.18
1952 2049 2.443416 CAAAGCCCACCTACCTTTACC 58.557 52.381 0.00 0.00 0.00 2.85
2028 2125 3.572584 GAGCTTTCATCTTTGGTTGCAG 58.427 45.455 0.00 0.00 0.00 4.41
2030 2127 3.005155 AGCTTTCATCTTTGGTTGCAGTC 59.995 43.478 0.00 0.00 0.00 3.51
2049 2146 5.120830 GCAGTCTTCATACTTGTACAAGGTG 59.879 44.000 33.11 28.85 42.53 4.00
2070 2167 4.446385 GTGAAGTACAGCGTGAACATGTTA 59.554 41.667 11.95 0.00 0.00 2.41
2087 2184 6.476378 ACATGTTAGCTATCTTCAACCAACT 58.524 36.000 0.00 0.00 0.00 3.16
2096 2221 9.301897 AGCTATCTTCAACCAACTAGAAATTTT 57.698 29.630 0.00 0.00 0.00 1.82
2123 2248 7.610580 TTTCTTATTCTTGTCCCCACAAAAT 57.389 32.000 0.00 0.00 42.13 1.82
2230 2355 4.038402 AGGCCAGTTTCAATCAGAACAAAG 59.962 41.667 5.01 0.00 35.56 2.77
2271 2396 1.683917 ACTCTGCCGATAGTCATGTCC 59.316 52.381 0.00 0.00 0.00 4.02
2358 2483 2.143122 TCACTGAGAAATGCAACGACC 58.857 47.619 0.00 0.00 0.00 4.79
2468 2593 3.176708 CAAGTATGACTCGGTTGGTACG 58.823 50.000 0.00 0.00 0.00 3.67
2516 2641 4.929808 CACTATGGTGGCCGAGAATATTAC 59.070 45.833 0.32 0.00 39.59 1.89
2541 2666 0.321919 CTCTGCACCTAAGCAAGCCA 60.322 55.000 0.00 0.00 45.13 4.75
2565 2690 7.254455 CCACGGAATACAGTGATGTAAGAAATC 60.254 40.741 0.00 0.00 42.97 2.17
2580 2705 7.422399 TGTAAGAAATCGCTAAACAAAAAGCT 58.578 30.769 0.00 0.00 36.56 3.74
2626 2754 9.988350 ATATGTACTTTCACTTTTTAATCAGCG 57.012 29.630 0.00 0.00 0.00 5.18
2653 2781 2.276201 GCAACCAAGGTTTTGAACACC 58.724 47.619 0.79 0.00 36.36 4.16
2737 2866 3.583526 TGGTGGCAAGGTATAGTGTTGTA 59.416 43.478 0.00 0.00 0.00 2.41
2738 2867 4.226394 TGGTGGCAAGGTATAGTGTTGTAT 59.774 41.667 0.00 0.00 0.00 2.29
2739 2868 5.425862 TGGTGGCAAGGTATAGTGTTGTATA 59.574 40.000 0.00 0.00 0.00 1.47
2745 2904 7.040686 GGCAAGGTATAGTGTTGTATATTTGGG 60.041 40.741 0.00 0.00 0.00 4.12
2861 3020 5.297527 TCTCCCTTTTCGAACAAGGTAAAAC 59.702 40.000 24.70 0.00 39.50 2.43
2862 3021 4.035441 TCCCTTTTCGAACAAGGTAAAACG 59.965 41.667 24.70 15.10 39.50 3.60
2922 3094 1.970640 TGGTCTTGCTCTCTGCTTACA 59.029 47.619 0.00 0.00 43.37 2.41
3011 3183 0.253044 TATGCCCACCTGAGCAACTC 59.747 55.000 0.00 0.00 43.36 3.01
3049 3221 1.929836 CTTCGCCTCTGCATCAGTTAC 59.070 52.381 0.00 0.00 37.32 2.50
3085 3257 4.389992 TGCTGTTCTTTATCAGAAAGCGAG 59.610 41.667 0.00 0.00 43.52 5.03
3095 3267 3.722147 TCAGAAAGCGAGCATATTCTCC 58.278 45.455 0.00 0.00 30.01 3.71
3378 3586 3.290710 AGGCTTTAATGTCAATGGCGAT 58.709 40.909 0.00 0.00 34.51 4.58
3381 3589 4.869861 GGCTTTAATGTCAATGGCGATTTT 59.130 37.500 0.00 0.00 0.00 1.82
3413 3630 2.304761 CTGTGGGGTTGGTGTACAGTAT 59.695 50.000 0.00 0.00 35.30 2.12
3466 3683 4.207165 CAAAGGTCACTGGGAAGAAAAGA 58.793 43.478 0.00 0.00 0.00 2.52
3495 3712 4.455533 CCTGGGTAAAAACCGTAGTTAACC 59.544 45.833 0.88 2.50 34.19 2.85
3665 3932 6.183360 TGTTCCTTTAAGTTGTATTGCTTGCA 60.183 34.615 0.00 0.00 0.00 4.08
3697 3964 6.927294 ACTTTCGTCTTGAGAAACAGAATT 57.073 33.333 0.00 0.00 34.36 2.17
3698 3965 9.537192 TTACTTTCGTCTTGAGAAACAGAATTA 57.463 29.630 0.00 0.00 34.36 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.609208 CAAGGAGGGTTGAAGTGTGG 58.391 55.000 0.00 0.00 0.00 4.17
42 43 7.605410 TCAAATTTCTACGATCCTTTGTACC 57.395 36.000 0.00 0.00 0.00 3.34
44 45 7.881232 ACCTTCAAATTTCTACGATCCTTTGTA 59.119 33.333 0.00 0.00 0.00 2.41
47 48 7.761038 AACCTTCAAATTTCTACGATCCTTT 57.239 32.000 0.00 0.00 0.00 3.11
76 77 7.295911 AGTGAAAAGGGGCTCTATAGGATTAAT 59.704 37.037 0.00 0.00 0.00 1.40
77 78 6.619852 AGTGAAAAGGGGCTCTATAGGATTAA 59.380 38.462 0.00 0.00 0.00 1.40
78 79 6.151049 AGTGAAAAGGGGCTCTATAGGATTA 58.849 40.000 0.00 0.00 0.00 1.75
128 129 8.402472 ACGAACAAACAAATATTTTGAGTGAGA 58.598 29.630 6.96 0.00 37.39 3.27
130 131 8.918961 AACGAACAAACAAATATTTTGAGTGA 57.081 26.923 6.96 0.00 37.39 3.41
132 133 8.918961 TGAACGAACAAACAAATATTTTGAGT 57.081 26.923 6.96 0.00 37.39 3.41
144 154 2.414824 GGTTGCACTGAACGAACAAACA 60.415 45.455 0.00 0.00 0.00 2.83
157 167 1.076044 AAGGCAGGTTGGTTGCACT 60.076 52.632 0.00 0.00 43.28 4.40
171 181 3.924144 TGTAATTGGATTTGCACAAGGC 58.076 40.909 0.00 0.00 45.13 4.35
194 206 6.325804 TGTCATGTCATATTCACTGGATCTCT 59.674 38.462 0.00 0.00 0.00 3.10
238 250 6.343703 GGGAAGAAAATGGAATCCTTGAATG 58.656 40.000 0.00 0.00 0.00 2.67
242 254 4.016444 TCGGGAAGAAAATGGAATCCTTG 58.984 43.478 0.00 0.00 0.00 3.61
245 257 5.188327 GATTCGGGAAGAAAATGGAATCC 57.812 43.478 0.00 0.00 42.91 3.01
248 260 4.018415 AGAGGATTCGGGAAGAAAATGGAA 60.018 41.667 0.00 0.00 42.91 3.53
249 261 3.523564 AGAGGATTCGGGAAGAAAATGGA 59.476 43.478 0.00 0.00 42.91 3.41
250 262 3.629398 CAGAGGATTCGGGAAGAAAATGG 59.371 47.826 0.00 0.00 42.91 3.16
251 263 4.265073 ACAGAGGATTCGGGAAGAAAATG 58.735 43.478 0.00 0.00 42.91 2.32
252 264 4.576330 ACAGAGGATTCGGGAAGAAAAT 57.424 40.909 0.00 0.00 42.91 1.82
253 265 4.367039 AACAGAGGATTCGGGAAGAAAA 57.633 40.909 0.00 0.00 42.91 2.29
254 266 5.247564 TCTTAACAGAGGATTCGGGAAGAAA 59.752 40.000 0.00 0.00 42.91 2.52
255 267 4.775780 TCTTAACAGAGGATTCGGGAAGAA 59.224 41.667 0.00 0.00 43.93 2.52
256 268 4.350245 TCTTAACAGAGGATTCGGGAAGA 58.650 43.478 0.00 0.00 0.00 2.87
257 269 4.688021 CTCTTAACAGAGGATTCGGGAAG 58.312 47.826 0.00 0.00 42.84 3.46
358 371 2.337246 CGGCGTTCGGGGGATTTTT 61.337 57.895 0.00 0.00 34.75 1.94
383 396 1.754226 GAGTTGGGGTTCTGTGCAAAA 59.246 47.619 0.00 0.00 0.00 2.44
442 513 0.386858 ACGGAACTGTGTCGATGACG 60.387 55.000 9.44 0.00 34.95 4.35
448 519 0.663568 GGACTGACGGAACTGTGTCG 60.664 60.000 0.00 2.27 37.94 4.35
485 557 1.740296 GAGGCTTTACGGCGCTGAA 60.740 57.895 25.98 10.16 44.22 3.02
562 634 1.299468 GATGCGCGACGGAAGAGAT 60.299 57.895 12.10 0.00 0.00 2.75
847 921 1.068472 ACTGCTCAACTACTCGTTCCG 60.068 52.381 0.00 0.00 32.27 4.30
848 922 2.726832 ACTGCTCAACTACTCGTTCC 57.273 50.000 0.00 0.00 32.27 3.62
849 923 3.172824 GCTACTGCTCAACTACTCGTTC 58.827 50.000 0.00 0.00 32.69 3.95
850 924 2.414293 CGCTACTGCTCAACTACTCGTT 60.414 50.000 0.00 0.00 36.97 3.85
851 925 1.130749 CGCTACTGCTCAACTACTCGT 59.869 52.381 0.00 0.00 36.97 4.18
932 1006 1.702491 GGATTAGGGCACGTGAACGC 61.702 60.000 22.23 11.00 44.43 4.84
1154 1234 2.685380 AGGGAGAAGGCGTGAGGG 60.685 66.667 0.00 0.00 0.00 4.30
1248 1339 3.443925 CGAGGAGAGCCGTCTGCA 61.444 66.667 0.00 0.00 43.50 4.41
1270 1361 3.257561 CAATCGACGCCCTGCTCG 61.258 66.667 0.00 0.00 33.22 5.03
1271 1362 2.629050 TAGCAATCGACGCCCTGCTC 62.629 60.000 17.59 0.00 43.85 4.26
1272 1363 2.635229 CTAGCAATCGACGCCCTGCT 62.635 60.000 17.98 17.98 46.50 4.24
1282 1373 2.611518 GGGAATCCGATCTAGCAATCG 58.388 52.381 6.81 6.81 46.28 3.34
1301 1392 5.012046 AGCAAGGAAGGATTAAAAACAAGGG 59.988 40.000 0.00 0.00 0.00 3.95
1302 1393 6.101650 AGCAAGGAAGGATTAAAAACAAGG 57.898 37.500 0.00 0.00 0.00 3.61
1309 1400 2.006888 CGCGAGCAAGGAAGGATTAAA 58.993 47.619 0.00 0.00 0.00 1.52
1324 1415 2.998668 AACTAAAATCATCGCGCGAG 57.001 45.000 36.99 26.95 0.00 5.03
1365 1457 5.998454 AAATTCTCGCATATTCAGTCCAG 57.002 39.130 0.00 0.00 0.00 3.86
1396 1488 6.098409 AGAGAAGGGCGTATCTAGATCAAAAA 59.902 38.462 8.95 0.00 0.00 1.94
1462 1556 5.899278 TGAATCCCCCTAATTAATAAGGCC 58.101 41.667 0.00 0.00 0.00 5.19
1475 1569 1.713005 ATCGCAGCATGAATCCCCCT 61.713 55.000 0.00 0.00 39.69 4.79
1509 1603 6.154877 TGGCAACATCACAATATGAATCCTTT 59.845 34.615 0.00 0.00 46.17 3.11
1681 1775 1.072116 AGACGAGACGAGACGAGACG 61.072 60.000 0.00 0.00 0.00 4.18
1682 1776 0.641783 GAGACGAGACGAGACGAGAC 59.358 60.000 0.00 0.00 0.00 3.36
1683 1777 0.243095 TGAGACGAGACGAGACGAGA 59.757 55.000 0.00 0.00 0.00 4.04
1684 1778 1.282817 ATGAGACGAGACGAGACGAG 58.717 55.000 0.00 0.00 0.00 4.18
1685 1779 2.573941 TATGAGACGAGACGAGACGA 57.426 50.000 0.00 0.00 0.00 4.20
1686 1780 3.491639 AGAATATGAGACGAGACGAGACG 59.508 47.826 0.00 0.00 0.00 4.18
1687 1781 4.084223 GGAGAATATGAGACGAGACGAGAC 60.084 50.000 0.00 0.00 0.00 3.36
1688 1782 4.059511 GGAGAATATGAGACGAGACGAGA 58.940 47.826 0.00 0.00 0.00 4.04
1689 1783 4.062293 AGGAGAATATGAGACGAGACGAG 58.938 47.826 0.00 0.00 0.00 4.18
1690 1784 4.074627 AGGAGAATATGAGACGAGACGA 57.925 45.455 0.00 0.00 0.00 4.20
1774 1870 7.269477 AGAGAAAACAGTTCTTCTTCATTGG 57.731 36.000 10.31 0.00 32.01 3.16
1782 1878 8.639428 GTTTGTTGAAAGAGAAAACAGTTCTTC 58.361 33.333 0.00 0.00 35.39 2.87
1783 1879 8.360390 AGTTTGTTGAAAGAGAAAACAGTTCTT 58.640 29.630 0.00 0.00 35.39 2.52
1784 1880 7.809806 CAGTTTGTTGAAAGAGAAAACAGTTCT 59.190 33.333 0.00 0.00 35.39 3.01
1785 1881 7.410835 GCAGTTTGTTGAAAGAGAAAACAGTTC 60.411 37.037 0.00 0.00 35.39 3.01
1786 1882 6.366061 GCAGTTTGTTGAAAGAGAAAACAGTT 59.634 34.615 0.00 0.00 35.39 3.16
1787 1883 5.863935 GCAGTTTGTTGAAAGAGAAAACAGT 59.136 36.000 0.00 0.00 35.39 3.55
1804 1900 3.762779 GCACTAAATAGCCTGCAGTTTG 58.237 45.455 13.81 3.55 0.00 2.93
1815 1911 2.128035 CGCTTCCTCGGCACTAAATAG 58.872 52.381 0.00 0.00 0.00 1.73
1818 1914 0.034337 AACGCTTCCTCGGCACTAAA 59.966 50.000 0.00 0.00 0.00 1.85
1920 2016 0.823356 GGGCTTTGCTGGTCAACTCA 60.823 55.000 0.00 0.00 33.73 3.41
1921 2017 0.823356 TGGGCTTTGCTGGTCAACTC 60.823 55.000 0.00 0.00 33.73 3.01
1928 2025 1.678970 GGTAGGTGGGCTTTGCTGG 60.679 63.158 0.00 0.00 0.00 4.85
1965 2062 6.715280 TCTGGCAGTGAAATTTTATCTCTCT 58.285 36.000 15.27 0.00 0.00 3.10
1966 2063 6.992063 TCTGGCAGTGAAATTTTATCTCTC 57.008 37.500 15.27 0.00 0.00 3.20
2049 2146 4.434330 GCTAACATGTTCACGCTGTACTTC 60.434 45.833 15.85 0.00 0.00 3.01
2062 2159 6.942576 AGTTGGTTGAAGATAGCTAACATGTT 59.057 34.615 16.68 16.68 0.00 2.71
2070 2167 8.870075 AAATTTCTAGTTGGTTGAAGATAGCT 57.130 30.769 0.00 0.00 0.00 3.32
2096 2221 8.713708 TTTGTGGGGACAAGAATAAGAAATAA 57.286 30.769 0.00 0.00 46.06 1.40
2123 2248 8.603181 GCTTTTGCACTTTCTCAAAGATTTTTA 58.397 29.630 8.59 0.00 46.58 1.52
2230 2355 2.530958 TAGCGCTTAGGGTTGTGGCC 62.531 60.000 18.68 0.00 0.00 5.36
2271 2396 5.629020 CGAAAGAAACAACCCATAATGTGTG 59.371 40.000 0.00 0.00 0.00 3.82
2468 2593 4.094442 ACAGAAGAACCAAAACAAGACGAC 59.906 41.667 0.00 0.00 0.00 4.34
2541 2666 6.475727 CGATTTCTTACATCACTGTATTCCGT 59.524 38.462 0.00 0.00 37.68 4.69
2565 2690 6.398935 GCATGAGTTAAGCTTTTTGTTTAGCG 60.399 38.462 3.20 0.00 42.18 4.26
2603 2728 6.017440 AGCGCTGATTAAAAAGTGAAAGTACA 60.017 34.615 10.39 0.00 0.00 2.90
2626 2754 3.130633 CAAAACCTTGGTTGCCTAAAGC 58.869 45.455 5.74 0.00 44.14 3.51
2653 2781 7.222611 CCACCTTGTACTGAAATGAACAAAAAG 59.777 37.037 0.00 0.00 31.90 2.27
2751 2910 9.770097 CAGTCAACCATATAACTCAGTCATAAT 57.230 33.333 0.00 0.00 0.00 1.28
2798 2957 2.381725 AGTAGTAAAACGAGCCTGGC 57.618 50.000 11.65 11.65 0.00 4.85
2861 3020 4.939052 ATGTCCAATAGTAAGGTCCTCG 57.061 45.455 0.00 0.00 0.00 4.63
2862 3021 5.104485 ACCAATGTCCAATAGTAAGGTCCTC 60.104 44.000 0.00 0.00 0.00 3.71
2957 3129 7.780008 TCGCTTTCCAGAAAATTATCGATTA 57.220 32.000 1.71 0.00 0.00 1.75
3011 3183 4.728882 GCGAAGTGAGCAAAAGTGGATATG 60.729 45.833 0.00 0.00 34.19 1.78
3049 3221 1.195448 GAACAGCATCTGTGAACACGG 59.805 52.381 7.38 7.38 44.62 4.94
3085 3257 7.283127 TCTGAAACAAAGTATGGGAGAATATGC 59.717 37.037 0.00 0.00 0.00 3.14
3095 3267 7.496529 TTCTGACTTCTGAAACAAAGTATGG 57.503 36.000 0.00 0.00 35.90 2.74
3381 3589 3.118592 CCAACCCCACAGCTTGTTAAAAA 60.119 43.478 0.00 0.00 0.00 1.94
3389 3606 0.179001 GTACACCAACCCCACAGCTT 60.179 55.000 0.00 0.00 0.00 3.74
3413 3630 9.599866 CTTATCTCAACCACAACTACATCATTA 57.400 33.333 0.00 0.00 0.00 1.90
3466 3683 3.568443 ACGGTTTTTACCCAGGACATTT 58.432 40.909 0.00 0.00 0.00 2.32
3495 3712 8.980481 AGTGATTATGACATAAAAAGTAGGGG 57.020 34.615 11.80 0.00 0.00 4.79
3523 3740 9.628500 CTAATTGCTTACCTAAAGTCCCTAAAT 57.372 33.333 0.00 0.00 37.53 1.40
3697 3964 5.601313 AGCCGTATCCTCTTTTGGAGTAATA 59.399 40.000 0.00 0.00 39.78 0.98
3698 3965 4.409247 AGCCGTATCCTCTTTTGGAGTAAT 59.591 41.667 0.00 0.00 39.78 1.89
3745 4012 8.744008 ATAATACAAAAGTATGACGATCCTCG 57.256 34.615 0.00 0.00 46.93 4.63


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

AutoCloner maintained by Alex Coulton.