Multiple sequence alignment - TraesCS5D01G360700

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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 TraesCS5D01G360700 chr5D 100.000 3872 0 0 1 3872 440364649 440368520 0.000000e+00 7151.0
1 TraesCS5D01G360700 chr5B 92.349 3686 164 65 255 3872 535699040 535702675 0.000000e+00 5136.0
2 TraesCS5D01G360700 chr5B 96.947 262 7 1 1 262 535698733 535698993 4.590000e-119 438.0
3 TraesCS5D01G360700 chr5A 91.263 3342 161 72 620 3872 556524383 556527682 0.000000e+00 4433.0
4 TraesCS5D01G360700 chr5A 94.889 587 27 2 1 584 556523444 556524030 0.000000e+00 915.0
5 TraesCS5D01G360700 chr5A 90.323 310 21 4 3010 3314 450226294 450225989 7.790000e-107 398.0
6 TraesCS5D01G360700 chr7A 89.041 292 16 8 3072 3349 114354345 114354634 7.960000e-92 348.0
7 TraesCS5D01G360700 chr3D 74.064 374 61 32 1015 1376 515776450 515776799 1.890000e-23 121.0
8 TraesCS5D01G360700 chr3B 73.569 367 63 27 1015 1368 678548307 678548652 4.090000e-20 110.0
9 TraesCS5D01G360700 chr3A 78.523 149 28 4 1015 1161 650056198 650056344 1.150000e-15 95.3
10 TraesCS5D01G360700 chr1D 92.857 56 4 0 1016 1071 359666063 359666008 8.920000e-12 82.4
11 TraesCS5D01G360700 chr1A 92.857 56 4 0 1016 1071 459188395 459188340 8.920000e-12 82.4
12 TraesCS5D01G360700 chr1A 84.615 78 8 4 1455 1530 343675275 343675350 1.490000e-09 75.0
13 TraesCS5D01G360700 chr6D 77.083 144 29 4 1019 1160 60487872 60487731 3.210000e-11 80.5
14 TraesCS5D01G360700 chr2D 88.525 61 5 2 1016 1075 175331281 175331340 5.370000e-09 73.1


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 TraesCS5D01G360700 chr5D 440364649 440368520 3871 False 7151 7151 100.000 1 3872 1 chr5D.!!$F1 3871
1 TraesCS5D01G360700 chr5B 535698733 535702675 3942 False 2787 5136 94.648 1 3872 2 chr5B.!!$F1 3871
2 TraesCS5D01G360700 chr5A 556523444 556527682 4238 False 2674 4433 93.076 1 3872 2 chr5A.!!$F1 3871

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 1379 0.905357 ACCTACCAACCTAGCTGCTG 59.095 55.0 13.43 0.0 0.0 4.41 F
1621 2057 0.392863 CCCGTCATGCAAGGTGATCA 60.393 55.0 0.00 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2657 0.758123 TGCATATGGCCATGACTCGA 59.242 50.0 29.04 7.36 43.89 4.04 R
3245 3749 0.908198 AAGCCTCCAATCGAGAAGCT 59.092 50.0 0.00 0.00 41.63 3.74 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
189 190 1.204704 TGACACACTTATCGAGGCTGG 59.795 52.381 0.00 0.00 0.00 4.85
264 265 7.233144 TGGCTCCACAATGCACATATATATTTT 59.767 33.333 0.00 0.00 0.00 1.82
333 389 4.748892 CTCAGCTTTTAACTCTCGGATCA 58.251 43.478 0.00 0.00 0.00 2.92
443 501 6.182039 TGTATAAACATGTGCTCAGCTTTC 57.818 37.500 0.00 0.00 0.00 2.62
622 1011 2.356432 CCATTCACTTGCCAGGATGAGA 60.356 50.000 0.00 0.00 39.69 3.27
623 1012 2.775911 TTCACTTGCCAGGATGAGAG 57.224 50.000 0.00 0.00 39.69 3.20
624 1013 1.942776 TCACTTGCCAGGATGAGAGA 58.057 50.000 0.00 0.00 39.69 3.10
625 1014 1.829849 TCACTTGCCAGGATGAGAGAG 59.170 52.381 0.00 0.00 39.69 3.20
626 1015 1.829849 CACTTGCCAGGATGAGAGAGA 59.170 52.381 0.00 0.00 39.69 3.10
627 1016 2.109774 ACTTGCCAGGATGAGAGAGAG 58.890 52.381 0.00 0.00 39.69 3.20
628 1017 2.292126 ACTTGCCAGGATGAGAGAGAGA 60.292 50.000 0.00 0.00 39.69 3.10
629 1018 2.070305 TGCCAGGATGAGAGAGAGAG 57.930 55.000 0.00 0.00 39.69 3.20
630 1019 1.568123 TGCCAGGATGAGAGAGAGAGA 59.432 52.381 0.00 0.00 39.69 3.10
631 1020 2.233271 GCCAGGATGAGAGAGAGAGAG 58.767 57.143 0.00 0.00 39.69 3.20
644 1033 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
659 1048 5.172934 AGAGAGAGTGTTACACGTCTAGAG 58.827 45.833 18.68 0.00 39.64 2.43
710 1108 2.159462 GGAAAAGGATGAAGCTTGCGAG 60.159 50.000 2.10 0.00 0.00 5.03
719 1118 1.028868 AAGCTTGCGAGGGAATCTGC 61.029 55.000 0.00 0.00 0.00 4.26
957 1363 4.148825 CCGCCGAAGCAGCTACCT 62.149 66.667 0.00 0.00 39.83 3.08
961 1367 1.956629 GCCGAAGCAGCTACCTACCA 61.957 60.000 0.00 0.00 39.53 3.25
963 1369 1.641577 CGAAGCAGCTACCTACCAAC 58.358 55.000 0.00 0.00 0.00 3.77
966 1372 2.544844 AGCAGCTACCTACCAACCTA 57.455 50.000 0.00 0.00 0.00 3.08
967 1373 2.389715 AGCAGCTACCTACCAACCTAG 58.610 52.381 0.00 0.00 0.00 3.02
969 1375 2.389715 CAGCTACCTACCAACCTAGCT 58.610 52.381 0.00 0.00 42.16 3.32
970 1376 2.389715 AGCTACCTACCAACCTAGCTG 58.610 52.381 0.00 0.00 40.35 4.24
971 1377 1.202545 GCTACCTACCAACCTAGCTGC 60.203 57.143 0.00 0.00 30.81 5.25
972 1378 2.389715 CTACCTACCAACCTAGCTGCT 58.610 52.381 7.57 7.57 0.00 4.24
973 1379 0.905357 ACCTACCAACCTAGCTGCTG 59.095 55.000 13.43 0.00 0.00 4.41
1584 2012 7.256655 CCATCCAGGTATGTATAATCACCTTCA 60.257 40.741 0.00 0.00 39.40 3.02
1591 2019 9.429359 GGTATGTATAATCACCTTCATTCTCTG 57.571 37.037 0.00 0.00 0.00 3.35
1594 2022 8.311395 TGTATAATCACCTTCATTCTCTGAGT 57.689 34.615 4.32 0.00 34.68 3.41
1595 2023 8.200120 TGTATAATCACCTTCATTCTCTGAGTG 58.800 37.037 4.32 0.00 34.68 3.51
1596 2024 5.752036 AATCACCTTCATTCTCTGAGTGA 57.248 39.130 4.32 0.00 40.97 3.41
1597 2025 4.527509 TCACCTTCATTCTCTGAGTGAC 57.472 45.455 4.32 0.00 35.36 3.67
1598 2026 3.259374 TCACCTTCATTCTCTGAGTGACC 59.741 47.826 4.32 0.00 35.36 4.02
1599 2027 3.260380 CACCTTCATTCTCTGAGTGACCT 59.740 47.826 4.32 0.00 33.83 3.85
1600 2028 4.464244 CACCTTCATTCTCTGAGTGACCTA 59.536 45.833 4.32 0.00 33.83 3.08
1601 2029 5.128499 CACCTTCATTCTCTGAGTGACCTAT 59.872 44.000 4.32 0.00 33.83 2.57
1602 2030 5.362430 ACCTTCATTCTCTGAGTGACCTATC 59.638 44.000 4.32 0.00 34.68 2.08
1603 2031 5.221422 CCTTCATTCTCTGAGTGACCTATCC 60.221 48.000 4.32 0.00 34.68 2.59
1604 2032 4.219115 TCATTCTCTGAGTGACCTATCCC 58.781 47.826 4.32 0.00 0.00 3.85
1605 2033 2.350057 TCTCTGAGTGACCTATCCCG 57.650 55.000 4.32 0.00 0.00 5.14
1606 2034 1.564818 TCTCTGAGTGACCTATCCCGT 59.435 52.381 4.32 0.00 0.00 5.28
1607 2035 1.950909 CTCTGAGTGACCTATCCCGTC 59.049 57.143 0.00 0.00 0.00 4.79
1608 2036 1.283905 TCTGAGTGACCTATCCCGTCA 59.716 52.381 0.00 0.00 37.91 4.35
1613 2049 1.134521 GTGACCTATCCCGTCATGCAA 60.135 52.381 0.00 0.00 41.99 4.08
1621 2057 0.392863 CCCGTCATGCAAGGTGATCA 60.393 55.000 0.00 0.00 0.00 2.92
1622 2058 1.671979 CCGTCATGCAAGGTGATCAT 58.328 50.000 0.00 0.00 0.00 2.45
1623 2059 1.332686 CCGTCATGCAAGGTGATCATG 59.667 52.381 0.00 0.00 39.02 3.07
1624 2060 1.268386 CGTCATGCAAGGTGATCATGC 60.268 52.381 11.97 11.97 37.93 4.06
1628 2064 0.458260 TGCAAGGTGATCATGCATGC 59.542 50.000 22.25 11.82 44.52 4.06
1629 2065 0.458260 GCAAGGTGATCATGCATGCA 59.542 50.000 25.04 25.04 39.81 3.96
1630 2066 1.068588 GCAAGGTGATCATGCATGCAT 59.931 47.619 27.46 27.46 39.81 3.96
1648 2084 5.028549 TGCATGTCTAATCTTCTCCTTCC 57.971 43.478 0.00 0.00 0.00 3.46
1652 2088 5.620738 TGTCTAATCTTCTCCTTCCATGG 57.379 43.478 4.97 4.97 0.00 3.66
1656 2092 3.505480 ATCTTCTCCTTCCATGGATGC 57.495 47.619 17.06 0.00 35.30 3.91
1659 2095 3.203710 TCTTCTCCTTCCATGGATGCAAT 59.796 43.478 17.06 0.00 35.30 3.56
1660 2096 2.940158 TCTCCTTCCATGGATGCAATG 58.060 47.619 17.06 5.33 35.30 2.82
1661 2097 1.961394 CTCCTTCCATGGATGCAATGG 59.039 52.381 17.06 9.30 45.13 3.16
1666 2102 2.234300 CCATGGATGCAATGGAAAGC 57.766 50.000 5.56 0.00 46.44 3.51
1668 2104 2.960384 CCATGGATGCAATGGAAAGCTA 59.040 45.455 5.56 0.00 46.44 3.32
1669 2105 3.576982 CCATGGATGCAATGGAAAGCTAT 59.423 43.478 5.56 0.00 46.44 2.97
1672 2108 6.239373 CCATGGATGCAATGGAAAGCTATTTA 60.239 38.462 5.56 0.00 46.44 1.40
1673 2109 6.395426 TGGATGCAATGGAAAGCTATTTAG 57.605 37.500 0.00 0.00 0.00 1.85
1745 2207 4.574599 AGAAAATTTTCTGCTTGCGTCT 57.425 36.364 28.35 4.45 45.27 4.18
1746 2208 5.689383 AGAAAATTTTCTGCTTGCGTCTA 57.311 34.783 28.35 0.00 45.27 2.59
1757 2219 3.818210 TGCTTGCGTCTAAAATGAAAGGA 59.182 39.130 0.00 0.00 30.90 3.36
1759 2221 4.853743 GCTTGCGTCTAAAATGAAAGGAAG 59.146 41.667 0.00 0.00 30.90 3.46
1761 2223 5.607119 TGCGTCTAAAATGAAAGGAAGAC 57.393 39.130 0.00 0.00 0.00 3.01
1763 2225 5.840940 CGTCTAAAATGAAAGGAAGACGT 57.159 39.130 13.00 0.00 46.74 4.34
1784 2246 9.152595 AGACGTAAAATTTTCTGAGAGGATTAC 57.847 33.333 6.72 0.00 0.00 1.89
1796 2258 5.324409 TGAGAGGATTACAACATGGCTTTT 58.676 37.500 0.00 0.00 0.00 2.27
1797 2259 5.415701 TGAGAGGATTACAACATGGCTTTTC 59.584 40.000 0.00 0.00 0.00 2.29
1800 2263 4.706962 AGGATTACAACATGGCTTTTCTCC 59.293 41.667 0.00 0.00 0.00 3.71
1820 2283 1.574134 CGTCTGTAAAACGGTGTGGT 58.426 50.000 0.00 0.00 36.51 4.16
1821 2284 2.741612 CGTCTGTAAAACGGTGTGGTA 58.258 47.619 0.00 0.00 36.51 3.25
1823 2286 3.721035 GTCTGTAAAACGGTGTGGTAGT 58.279 45.455 0.00 0.00 0.00 2.73
1824 2287 4.556501 CGTCTGTAAAACGGTGTGGTAGTA 60.557 45.833 0.00 0.00 36.51 1.82
1844 2324 5.003804 AGTAGTATGGGTCACTTTGCTTTG 58.996 41.667 0.00 0.00 0.00 2.77
1845 2325 2.558359 AGTATGGGTCACTTTGCTTTGC 59.442 45.455 0.00 0.00 0.00 3.68
1854 2334 1.882623 ACTTTGCTTTGCTCCAGCTAC 59.117 47.619 0.00 0.00 42.66 3.58
1855 2335 2.157738 CTTTGCTTTGCTCCAGCTACT 58.842 47.619 0.00 0.00 42.66 2.57
1856 2336 3.244561 ACTTTGCTTTGCTCCAGCTACTA 60.245 43.478 0.00 0.00 42.66 1.82
1857 2337 2.386661 TGCTTTGCTCCAGCTACTAC 57.613 50.000 0.00 0.00 42.66 2.73
1858 2338 1.902508 TGCTTTGCTCCAGCTACTACT 59.097 47.619 0.00 0.00 42.66 2.57
1859 2339 2.093973 TGCTTTGCTCCAGCTACTACTC 60.094 50.000 0.00 0.00 42.66 2.59
1860 2340 2.167487 GCTTTGCTCCAGCTACTACTCT 59.833 50.000 0.00 0.00 42.66 3.24
1861 2341 3.779759 CTTTGCTCCAGCTACTACTCTG 58.220 50.000 0.00 0.00 42.66 3.35
1862 2342 2.808906 TGCTCCAGCTACTACTCTGA 57.191 50.000 0.00 0.00 42.66 3.27
1863 2343 3.304911 TGCTCCAGCTACTACTCTGAT 57.695 47.619 0.00 0.00 42.66 2.90
1864 2344 2.954989 TGCTCCAGCTACTACTCTGATG 59.045 50.000 0.00 0.00 42.66 3.07
1865 2345 3.218453 GCTCCAGCTACTACTCTGATGA 58.782 50.000 0.00 0.00 38.21 2.92
1866 2346 3.253188 GCTCCAGCTACTACTCTGATGAG 59.747 52.174 0.00 0.00 40.99 2.90
1867 2347 4.713553 CTCCAGCTACTACTCTGATGAGA 58.286 47.826 0.00 0.00 42.73 3.27
2084 2575 2.159268 AGTCTGCACTGATCATGAGACG 60.159 50.000 0.09 0.00 35.93 4.18
2164 2659 3.156401 GAGATAGCAGCTCGTGTCG 57.844 57.895 0.00 0.00 0.00 4.35
2165 2660 0.658368 GAGATAGCAGCTCGTGTCGA 59.342 55.000 0.00 0.00 0.00 4.20
2240 2735 3.244805 GCTGAATCCCATCATCATCCTCA 60.245 47.826 0.00 0.00 0.00 3.86
2254 2749 3.588842 TCATCCTCACACCCTTCTGATTT 59.411 43.478 0.00 0.00 0.00 2.17
2303 2798 2.779755 TCTCCCGCTTTGCTTTGATA 57.220 45.000 0.00 0.00 0.00 2.15
2317 2812 3.862642 GCTTTGATAATCGATCGGCCTCT 60.863 47.826 16.41 0.00 37.38 3.69
2469 2964 5.826601 TCAGTGTGTGCATAAACTTTCAA 57.173 34.783 3.07 0.00 0.00 2.69
2519 3014 7.570161 CAGATGGATCTTGTTTTTGCTTTTTC 58.430 34.615 0.00 0.00 34.22 2.29
2521 3016 5.988287 TGGATCTTGTTTTTGCTTTTTCCT 58.012 33.333 0.00 0.00 0.00 3.36
2522 3017 5.816777 TGGATCTTGTTTTTGCTTTTTCCTG 59.183 36.000 0.00 0.00 0.00 3.86
2781 3277 4.738345 GACGCAGACGACGACGCT 62.738 66.667 7.30 2.80 43.93 5.07
3013 3512 3.433615 CCGAGTGTTGAAGGTGAAAGATC 59.566 47.826 0.00 0.00 0.00 2.75
3345 3854 1.136828 AGTTGTTGTGTGCCTCCCTA 58.863 50.000 0.00 0.00 0.00 3.53
3388 3897 6.320164 ACAAAAATGTAACTGCTTGTACCTGA 59.680 34.615 0.00 0.00 0.00 3.86
3442 3951 1.745653 GCACCTGGTTCTTATTGCCTC 59.254 52.381 0.00 0.00 0.00 4.70
3454 3963 7.068716 GGTTCTTATTGCCTCAGTAAATCCATT 59.931 37.037 0.00 0.00 0.00 3.16
3459 3968 6.618287 TTGCCTCAGTAAATCCATTATTCG 57.382 37.500 0.00 0.00 0.00 3.34
3461 3970 6.822442 TGCCTCAGTAAATCCATTATTCGTA 58.178 36.000 0.00 0.00 0.00 3.43
3519 4028 8.546597 ACTAAATTATGATTTTTGGCAACCAC 57.453 30.769 0.00 0.00 36.82 4.16
3526 4035 4.334759 TGATTTTTGGCAACCACATTTGTG 59.665 37.500 0.00 3.67 45.23 3.33
3543 4053 6.364706 ACATTTGTGCCGTAATTGTTTACATG 59.635 34.615 0.00 0.00 38.06 3.21
3547 4057 7.147143 TGTGCCGTAATTGTTTACATGTATT 57.853 32.000 6.36 1.11 38.06 1.89
3548 4058 8.265165 TGTGCCGTAATTGTTTACATGTATTA 57.735 30.769 6.36 0.09 38.06 0.98
3549 4059 8.176365 TGTGCCGTAATTGTTTACATGTATTAC 58.824 33.333 6.36 11.55 38.06 1.89
3551 4061 8.948145 TGCCGTAATTGTTTACATGTATTACTT 58.052 29.630 19.12 10.34 38.06 2.24
3552 4062 9.777575 GCCGTAATTGTTTACATGTATTACTTT 57.222 29.630 19.12 14.13 38.06 2.66
3738 4256 7.363705 CCTGTAAACATGGAAAATCCTATGCAA 60.364 37.037 0.00 0.00 37.46 4.08
3851 4369 7.954666 AGGAATACTATTCTAGATCAGAGGC 57.045 40.000 8.41 0.00 33.83 4.70
3866 4384 1.089920 GAGGCTACCACATGCTGTTG 58.910 55.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 208 1.902508 TCTTAGATCATCCGCATCCCC 59.097 52.381 0.00 0.00 0.00 4.81
269 325 7.466746 AGATGCCACTTACACACATTTTATT 57.533 32.000 0.00 0.00 0.00 1.40
333 389 5.421056 TCGGTATACACACCATCTTTCTCTT 59.579 40.000 5.01 0.00 38.61 2.85
433 491 3.187432 GTCCAACAGTTAGAAAGCTGAGC 59.813 47.826 0.00 0.00 36.62 4.26
443 501 5.661458 ACATAATCTCGGTCCAACAGTTAG 58.339 41.667 0.00 0.00 0.00 2.34
604 666 2.235650 CTCTCTCATCCTGGCAAGTGAA 59.764 50.000 0.00 0.00 0.00 3.18
622 1011 4.648762 CACTCTCTCTCTCTCTCTCTCTCT 59.351 50.000 0.00 0.00 0.00 3.10
623 1012 4.404073 ACACTCTCTCTCTCTCTCTCTCTC 59.596 50.000 0.00 0.00 0.00 3.20
624 1013 4.357325 ACACTCTCTCTCTCTCTCTCTCT 58.643 47.826 0.00 0.00 0.00 3.10
625 1014 4.744795 ACACTCTCTCTCTCTCTCTCTC 57.255 50.000 0.00 0.00 0.00 3.20
626 1015 5.483937 TGTAACACTCTCTCTCTCTCTCTCT 59.516 44.000 0.00 0.00 0.00 3.10
627 1016 5.581085 GTGTAACACTCTCTCTCTCTCTCTC 59.419 48.000 0.00 0.00 36.32 3.20
628 1017 5.488341 GTGTAACACTCTCTCTCTCTCTCT 58.512 45.833 0.00 0.00 36.32 3.10
629 1018 4.328983 CGTGTAACACTCTCTCTCTCTCTC 59.671 50.000 0.00 0.00 35.74 3.20
630 1019 4.250464 CGTGTAACACTCTCTCTCTCTCT 58.750 47.826 0.00 0.00 35.74 3.10
631 1020 3.998341 ACGTGTAACACTCTCTCTCTCTC 59.002 47.826 0.00 0.00 35.74 3.20
644 1033 6.653740 TCATTTCTCTCTCTAGACGTGTAACA 59.346 38.462 0.00 0.00 35.74 2.41
659 1048 0.179070 GACCGCCCCTCATTTCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
710 1108 2.291217 ACCTCCTCTTTTGCAGATTCCC 60.291 50.000 0.00 0.00 0.00 3.97
719 1118 5.599999 TTAGCTAGCTACCTCCTCTTTTG 57.400 43.478 24.09 0.00 0.00 2.44
1436 1860 2.515991 TTCATCCCGATTGCCCGC 60.516 61.111 0.00 0.00 0.00 6.13
1584 2012 3.226777 CGGGATAGGTCACTCAGAGAAT 58.773 50.000 3.79 0.00 0.00 2.40
1591 2019 1.269831 GCATGACGGGATAGGTCACTC 60.270 57.143 0.00 0.00 46.22 3.51
1592 2020 0.753262 GCATGACGGGATAGGTCACT 59.247 55.000 0.00 0.00 46.22 3.41
1593 2021 0.464036 TGCATGACGGGATAGGTCAC 59.536 55.000 0.00 0.00 46.22 3.67
1595 2023 1.541233 CCTTGCATGACGGGATAGGTC 60.541 57.143 0.00 0.00 34.99 3.85
1596 2024 0.469917 CCTTGCATGACGGGATAGGT 59.530 55.000 0.00 0.00 0.00 3.08
1597 2025 0.469917 ACCTTGCATGACGGGATAGG 59.530 55.000 0.00 0.00 0.00 2.57
1598 2026 1.138859 TCACCTTGCATGACGGGATAG 59.861 52.381 0.00 0.00 0.00 2.08
1599 2027 1.199615 TCACCTTGCATGACGGGATA 58.800 50.000 0.00 0.00 0.00 2.59
1600 2028 0.548031 ATCACCTTGCATGACGGGAT 59.452 50.000 0.00 0.00 0.00 3.85
1601 2029 0.107703 GATCACCTTGCATGACGGGA 60.108 55.000 0.00 0.00 0.00 5.14
1602 2030 0.392863 TGATCACCTTGCATGACGGG 60.393 55.000 0.00 0.00 0.00 5.28
1603 2031 1.332686 CATGATCACCTTGCATGACGG 59.667 52.381 0.00 0.00 41.35 4.79
1604 2032 1.268386 GCATGATCACCTTGCATGACG 60.268 52.381 13.62 0.00 43.22 4.35
1605 2033 1.746787 TGCATGATCACCTTGCATGAC 59.253 47.619 16.56 0.00 46.74 3.06
1606 2034 2.131776 TGCATGATCACCTTGCATGA 57.868 45.000 16.56 0.00 46.74 3.07
1621 2057 4.760715 GGAGAAGATTAGACATGCATGCAT 59.239 41.667 27.46 27.46 37.08 3.96
1622 2058 4.132336 GGAGAAGATTAGACATGCATGCA 58.868 43.478 26.53 25.04 0.00 3.96
1623 2059 4.387598 AGGAGAAGATTAGACATGCATGC 58.612 43.478 26.53 18.25 0.00 4.06
1624 2060 5.469421 GGAAGGAGAAGATTAGACATGCATG 59.531 44.000 25.09 25.09 0.00 4.06
1625 2061 5.131642 TGGAAGGAGAAGATTAGACATGCAT 59.868 40.000 0.00 0.00 0.00 3.96
1626 2062 4.471025 TGGAAGGAGAAGATTAGACATGCA 59.529 41.667 0.00 0.00 0.00 3.96
1627 2063 5.028549 TGGAAGGAGAAGATTAGACATGC 57.971 43.478 0.00 0.00 0.00 4.06
1628 2064 5.996513 CCATGGAAGGAGAAGATTAGACATG 59.003 44.000 5.56 0.00 33.66 3.21
1629 2065 5.907662 TCCATGGAAGGAGAAGATTAGACAT 59.092 40.000 13.46 0.00 32.77 3.06
1630 2066 5.280499 TCCATGGAAGGAGAAGATTAGACA 58.720 41.667 13.46 0.00 32.77 3.41
1631 2067 5.878406 TCCATGGAAGGAGAAGATTAGAC 57.122 43.478 13.46 0.00 32.77 2.59
1632 2068 5.221803 GCATCCATGGAAGGAGAAGATTAGA 60.222 44.000 20.67 0.00 41.90 2.10
1633 2069 5.002516 GCATCCATGGAAGGAGAAGATTAG 58.997 45.833 20.67 0.00 41.90 1.73
1634 2070 4.413189 TGCATCCATGGAAGGAGAAGATTA 59.587 41.667 20.67 0.00 41.90 1.75
1635 2071 3.203710 TGCATCCATGGAAGGAGAAGATT 59.796 43.478 20.67 0.00 41.90 2.40
1636 2072 2.781757 TGCATCCATGGAAGGAGAAGAT 59.218 45.455 20.67 0.00 41.90 2.40
1639 2075 3.293337 CATTGCATCCATGGAAGGAGAA 58.707 45.455 20.67 10.63 41.42 2.87
1648 2084 4.866508 ATAGCTTTCCATTGCATCCATG 57.133 40.909 0.00 0.00 0.00 3.66
1691 2141 5.993441 CCAGCACAAAAGAAAAGGATCAATT 59.007 36.000 0.00 0.00 0.00 2.32
1692 2142 5.544650 CCAGCACAAAAGAAAAGGATCAAT 58.455 37.500 0.00 0.00 0.00 2.57
1757 2219 8.622948 AATCCTCTCAGAAAATTTTACGTCTT 57.377 30.769 2.75 0.00 0.00 3.01
1759 2221 8.932791 TGTAATCCTCTCAGAAAATTTTACGTC 58.067 33.333 2.75 0.00 0.00 4.34
1761 2223 9.543018 GTTGTAATCCTCTCAGAAAATTTTACG 57.457 33.333 2.75 0.00 0.00 3.18
1784 2246 1.200020 GACGGGAGAAAAGCCATGTTG 59.800 52.381 0.00 0.00 0.00 3.33
1816 2279 5.416947 CAAAGTGACCCATACTACTACCAC 58.583 45.833 0.00 0.00 0.00 4.16
1817 2280 4.081309 GCAAAGTGACCCATACTACTACCA 60.081 45.833 0.00 0.00 0.00 3.25
1819 2282 5.340439 AGCAAAGTGACCCATACTACTAC 57.660 43.478 0.00 0.00 0.00 2.73
1820 2283 6.170506 CAAAGCAAAGTGACCCATACTACTA 58.829 40.000 0.00 0.00 0.00 1.82
1821 2284 4.910458 AAGCAAAGTGACCCATACTACT 57.090 40.909 0.00 0.00 0.00 2.57
1823 2286 3.756434 GCAAAGCAAAGTGACCCATACTA 59.244 43.478 0.00 0.00 0.00 1.82
1824 2287 2.558359 GCAAAGCAAAGTGACCCATACT 59.442 45.455 0.00 0.00 0.00 2.12
1844 2324 3.218453 TCATCAGAGTAGTAGCTGGAGC 58.782 50.000 0.00 0.00 42.49 4.70
1845 2325 4.713553 TCTCATCAGAGTAGTAGCTGGAG 58.286 47.826 0.00 0.00 42.66 3.86
1854 2334 6.507958 TGTTTGTCTCTCTCATCAGAGTAG 57.492 41.667 0.00 0.00 45.92 2.57
1855 2335 6.435591 ACATGTTTGTCTCTCTCATCAGAGTA 59.564 38.462 0.00 0.00 45.92 2.59
1856 2336 5.245751 ACATGTTTGTCTCTCTCATCAGAGT 59.754 40.000 0.00 0.00 45.92 3.24
1857 2337 6.861144 TACATGTTTGTCTCTCTCATCAGAG 58.139 40.000 2.30 0.00 41.24 3.35
1858 2338 5.735285 ACATGTTTGTCTCTCTCATCAGA 57.265 39.130 0.00 0.00 0.00 3.27
1859 2339 6.041511 CCTACATGTTTGTCTCTCTCATCAG 58.958 44.000 2.30 0.00 37.28 2.90
1860 2340 5.625426 GCCTACATGTTTGTCTCTCTCATCA 60.625 44.000 2.30 0.00 37.28 3.07
1861 2341 4.808364 GCCTACATGTTTGTCTCTCTCATC 59.192 45.833 2.30 0.00 37.28 2.92
1862 2342 4.383552 GGCCTACATGTTTGTCTCTCTCAT 60.384 45.833 2.30 0.00 37.28 2.90
1863 2343 3.055819 GGCCTACATGTTTGTCTCTCTCA 60.056 47.826 2.30 0.00 37.28 3.27
1864 2344 3.196685 AGGCCTACATGTTTGTCTCTCTC 59.803 47.826 1.29 0.00 37.28 3.20
1865 2345 3.177228 AGGCCTACATGTTTGTCTCTCT 58.823 45.455 1.29 0.00 37.28 3.10
1866 2346 3.526534 GAGGCCTACATGTTTGTCTCTC 58.473 50.000 4.42 8.83 37.28 3.20
1867 2347 2.093973 CGAGGCCTACATGTTTGTCTCT 60.094 50.000 20.13 6.59 37.28 3.10
2084 2575 2.094182 GCTTTGGTTAAGGCCCTTTAGC 60.094 50.000 0.00 2.40 33.18 3.09
2161 2656 1.151668 GCATATGGCCATGACTCGAC 58.848 55.000 29.04 6.72 36.11 4.20
2162 2657 0.758123 TGCATATGGCCATGACTCGA 59.242 50.000 29.04 7.36 43.89 4.04
2163 2658 1.467342 CATGCATATGGCCATGACTCG 59.533 52.381 29.04 12.27 43.89 4.18
2164 2659 2.486982 GACATGCATATGGCCATGACTC 59.513 50.000 29.04 14.29 43.89 3.36
2165 2660 2.511659 GACATGCATATGGCCATGACT 58.488 47.619 29.04 9.95 43.89 3.41
2240 2735 3.834231 CCATGGAAAAATCAGAAGGGTGT 59.166 43.478 5.56 0.00 0.00 4.16
2254 2749 1.223487 GACTAGCCGGCCATGGAAA 59.777 57.895 26.15 0.00 0.00 3.13
2303 2798 2.939103 CAGAAAAAGAGGCCGATCGATT 59.061 45.455 18.66 0.59 0.00 3.34
2469 2964 4.402056 TTGTGGTTTCTCGAGACTTTCT 57.598 40.909 16.36 0.00 0.00 2.52
2475 2970 3.509967 TCTGCTATTGTGGTTTCTCGAGA 59.490 43.478 12.08 12.08 0.00 4.04
2478 2973 3.310774 CCATCTGCTATTGTGGTTTCTCG 59.689 47.826 0.00 0.00 0.00 4.04
2519 3014 6.936335 TGCATGGTATATTAACTCATGACAGG 59.064 38.462 0.00 0.00 37.87 4.00
2521 3016 7.391275 CCATGCATGGTATATTAACTCATGACA 59.609 37.037 33.68 0.00 43.05 3.58
2522 3017 7.755591 CCATGCATGGTATATTAACTCATGAC 58.244 38.462 33.68 0.00 43.05 3.06
3245 3749 0.908198 AAGCCTCCAATCGAGAAGCT 59.092 50.000 0.00 0.00 41.63 3.74
3378 3887 4.614535 GCAAATTGAGCAGTCAGGTACAAG 60.615 45.833 0.00 0.00 32.98 3.16
3388 3897 4.744570 CAGATTGATGCAAATTGAGCAGT 58.255 39.130 10.98 1.40 46.36 4.40
3500 4009 6.769822 ACAAATGTGGTTGCCAAAAATCATAA 59.230 30.769 0.00 0.00 34.18 1.90
3519 4028 6.364706 ACATGTAAACAATTACGGCACAAATG 59.635 34.615 0.00 0.00 43.59 2.32
3526 4035 9.777575 AAAGTAATACATGTAAACAATTACGGC 57.222 29.630 10.14 0.00 43.59 5.68
3543 4053 9.333724 TGCTTGGCCTATTTACTAAAGTAATAC 57.666 33.333 3.32 0.00 39.89 1.89
3548 4058 9.726438 CTATATGCTTGGCCTATTTACTAAAGT 57.274 33.333 3.32 0.00 0.00 2.66
3549 4059 9.944376 TCTATATGCTTGGCCTATTTACTAAAG 57.056 33.333 3.32 0.00 0.00 1.85
3738 4256 2.151202 CAAGCATGTAACGGAACCTGT 58.849 47.619 0.00 0.00 0.00 4.00
3816 4334 7.308782 AGAATAGTATTCCTTCAACGCTTTG 57.691 36.000 17.52 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.