Multiple sequence alignment - TraesCS2D01G225400

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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 TraesCS2D01G225400 chr2D 100.000 4064 0 0 1 4064 193116836 193120899 0.000000e+00 7505
1 TraesCS2D01G225400 chr2A 92.138 4172 139 59 1 4064 207052419 207056509 0.000000e+00 5712
2 TraesCS2D01G225400 chr2B 90.285 2522 108 54 1611 4064 249263398 249265850 0.000000e+00 3173
3 TraesCS2D01G225400 chr2B 91.259 1430 48 28 1 1379 249261689 249263092 0.000000e+00 1877
4 TraesCS2D01G225400 chr2B 94.241 191 6 2 1420 1610 249263184 249263369 1.850000e-73 287


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 TraesCS2D01G225400 chr2D 193116836 193120899 4063 False 7505 7505 100.000000 1 4064 1 chr2D.!!$F1 4063
1 TraesCS2D01G225400 chr2A 207052419 207056509 4090 False 5712 5712 92.138000 1 4064 1 chr2A.!!$F1 4063
2 TraesCS2D01G225400 chr2B 249261689 249265850 4161 False 1779 3173 91.928333 1 4064 3 chr2B.!!$F1 4063

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
298 325 0.10852 AGCCGCCATCTTTGCATTTG 60.109 50.0 0.00 0.0 0.0 2.32 F
1218 1277 0.17910 CACCGCCTTGATCGATGTCT 60.179 55.0 0.54 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2157 0.034896 TTTCCGTCCAGCAGACTTCC 59.965 55.0 5.5 0.0 43.91 3.46 R
3073 3298 0.034059 GTCCCATCGCCTATCACTGG 59.966 60.0 0.0 0.0 0.00 4.00 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
86 90 7.630242 TTATTAGCAAGTCCTTGGAGAAATG 57.370 36.000 8.97 0.00 40.74 2.32
239 247 1.268778 GCGAGCCGTGCAAAAACTTC 61.269 55.000 0.00 0.00 0.00 3.01
286 298 0.534877 CCAGCATATGTTAGCCGCCA 60.535 55.000 4.29 0.00 0.00 5.69
287 299 1.527034 CAGCATATGTTAGCCGCCAT 58.473 50.000 4.29 0.00 0.00 4.40
298 325 0.108520 AGCCGCCATCTTTGCATTTG 60.109 50.000 0.00 0.00 0.00 2.32
313 340 5.178096 TGCATTTGAGAGGTAAAGATGGA 57.822 39.130 0.00 0.00 0.00 3.41
779 821 1.406898 GCTTTCTTCTAGCCCCATTGC 59.593 52.381 0.00 0.00 32.45 3.56
982 1033 0.321671 ACAGAGCTAGCCGCAGAAAA 59.678 50.000 12.13 0.00 42.61 2.29
984 1035 1.129437 CAGAGCTAGCCGCAGAAAAAC 59.871 52.381 12.13 0.00 42.61 2.43
987 1038 0.875059 GCTAGCCGCAGAAAAACACT 59.125 50.000 2.29 0.00 38.92 3.55
1218 1277 0.179100 CACCGCCTTGATCGATGTCT 60.179 55.000 0.54 0.00 0.00 3.41
1251 1314 2.284417 CGGCTCGCTGTTTTATAACCTC 59.716 50.000 0.00 0.00 33.15 3.85
1252 1315 3.532542 GGCTCGCTGTTTTATAACCTCT 58.467 45.455 0.00 0.00 33.15 3.69
1253 1316 4.690122 GGCTCGCTGTTTTATAACCTCTA 58.310 43.478 0.00 0.00 33.15 2.43
1283 1346 7.604164 ACTTAGTGTACCATGATTCTCTTGTTG 59.396 37.037 0.00 0.00 0.00 3.33
1524 1643 5.429130 TCAATATAAATACGGGCACACACA 58.571 37.500 0.00 0.00 0.00 3.72
1525 1644 5.294799 TCAATATAAATACGGGCACACACAC 59.705 40.000 0.00 0.00 0.00 3.82
1721 1893 3.128068 GTGGCGTCTTATTTAACCTTGGG 59.872 47.826 0.00 0.00 0.00 4.12
1772 1944 2.606065 GGCGTTGTACAATGTTCAACCC 60.606 50.000 24.88 21.07 39.49 4.11
1837 2013 8.624776 CAAGTGTTATTTCTTTTCTGACCTCTT 58.375 33.333 0.00 0.00 0.00 2.85
1846 2022 4.377839 TTTCTGACCTCTTGCTCGATAG 57.622 45.455 0.00 0.00 0.00 2.08
1868 2044 5.246307 AGTTGTCCTGTAACTAAGCATTCC 58.754 41.667 0.00 0.00 36.66 3.01
1871 2047 4.192317 GTCCTGTAACTAAGCATTCCTGG 58.808 47.826 0.00 0.00 0.00 4.45
1929 2114 9.495572 TTTTGTTGTCTTACCAAATCAAAAACT 57.504 25.926 0.00 0.00 32.23 2.66
1933 2118 9.313118 GTTGTCTTACCAAATCAAAAACTGAAT 57.687 29.630 0.00 0.00 37.67 2.57
1959 2156 8.172484 TGATTTACACGTAACATGCACTTAATC 58.828 33.333 0.00 0.00 0.00 1.75
1960 2157 4.577687 ACACGTAACATGCACTTAATCG 57.422 40.909 0.00 0.00 0.00 3.34
1961 2158 3.369756 ACACGTAACATGCACTTAATCGG 59.630 43.478 0.00 0.00 0.00 4.18
1962 2159 3.615056 CACGTAACATGCACTTAATCGGA 59.385 43.478 0.00 0.00 0.00 4.55
1964 2161 4.328983 ACGTAACATGCACTTAATCGGAAG 59.671 41.667 0.00 0.00 0.00 3.46
1965 2162 4.328983 CGTAACATGCACTTAATCGGAAGT 59.671 41.667 0.00 0.00 40.35 3.01
1966 2163 4.946784 AACATGCACTTAATCGGAAGTC 57.053 40.909 0.00 0.00 37.57 3.01
1967 2164 4.207891 ACATGCACTTAATCGGAAGTCT 57.792 40.909 0.00 0.00 37.57 3.24
1968 2165 3.935203 ACATGCACTTAATCGGAAGTCTG 59.065 43.478 0.00 0.00 37.57 3.51
2001 2198 1.670674 GCTACAATGTCGGTCGGTTCA 60.671 52.381 0.00 0.00 0.00 3.18
2007 2204 0.320946 TGTCGGTCGGTTCATTTCCC 60.321 55.000 0.00 0.00 0.00 3.97
2027 2225 3.011257 CCCTCCCCTAAGAACAAATTCCA 59.989 47.826 0.00 0.00 35.18 3.53
2287 2488 1.616159 TTTTAGCAGGCTTGTGGACC 58.384 50.000 0.00 0.00 0.00 4.46
2327 2529 6.403866 TGCATACACTCAAAATTCAGGTTT 57.596 33.333 0.00 0.00 0.00 3.27
2381 2583 4.278419 AGGGAATAACTGCAACTTGTTGAC 59.722 41.667 16.57 8.78 0.00 3.18
2384 2586 0.100503 AACTGCAACTTGTTGACGGC 59.899 50.000 16.57 2.61 0.00 5.68
2439 2641 4.100344 TCCAAGCTTATGAATACCACGCTA 59.900 41.667 0.00 0.00 0.00 4.26
2448 2650 3.003378 TGAATACCACGCTACAGATCTCG 59.997 47.826 0.00 0.00 0.00 4.04
2460 2662 4.415332 ATCTCGTGCGCGTCGGTT 62.415 61.111 20.50 3.98 39.49 4.44
2724 2928 2.124612 CTCGCCATGTCCATGCCA 60.125 61.111 1.64 0.00 37.49 4.92
2795 2999 2.030371 AGTTAGCCTAGGAAGGTACGC 58.970 52.381 14.75 0.00 45.64 4.42
2808 3016 3.192230 TACGCGCGCCCAGAATTG 61.192 61.111 32.58 11.44 0.00 2.32
2816 3024 1.097232 CGCCCAGAATTGCTCATGAA 58.903 50.000 0.00 0.00 0.00 2.57
3073 3298 1.000938 CAAAGGTCTGAGCCAAGCAAC 60.001 52.381 2.76 0.00 0.00 4.17
3081 3306 1.350684 TGAGCCAAGCAACCAGTGATA 59.649 47.619 0.00 0.00 0.00 2.15
3146 3371 1.608590 CGGACTGTGTTGGAAAGCAAT 59.391 47.619 0.00 0.00 0.00 3.56
3287 3516 2.288729 CGTCTCCCGTCGATGTTGTATA 59.711 50.000 3.52 0.00 0.00 1.47
3289 3518 4.227538 GTCTCCCGTCGATGTTGTATATG 58.772 47.826 3.52 0.00 0.00 1.78
3290 3519 3.887110 TCTCCCGTCGATGTTGTATATGT 59.113 43.478 3.52 0.00 0.00 2.29
3291 3520 5.049198 GTCTCCCGTCGATGTTGTATATGTA 60.049 44.000 3.52 0.00 0.00 2.29
3292 3521 5.049198 TCTCCCGTCGATGTTGTATATGTAC 60.049 44.000 3.52 0.00 0.00 2.90
3293 3522 4.022935 TCCCGTCGATGTTGTATATGTACC 60.023 45.833 3.52 0.00 0.00 3.34
3294 3523 3.910170 CCGTCGATGTTGTATATGTACCG 59.090 47.826 3.52 0.00 0.00 4.02
3295 3524 4.319694 CCGTCGATGTTGTATATGTACCGA 60.320 45.833 3.52 0.00 0.00 4.69
3296 3525 5.207033 CGTCGATGTTGTATATGTACCGAA 58.793 41.667 0.00 0.00 0.00 4.30
3297 3526 5.854866 CGTCGATGTTGTATATGTACCGAAT 59.145 40.000 0.00 0.00 0.00 3.34
3298 3527 6.032146 CGTCGATGTTGTATATGTACCGAATC 59.968 42.308 0.00 0.00 0.00 2.52
3341 3570 4.759782 TGCTTTTAGTGAGCTCCTATGTC 58.240 43.478 12.15 3.66 40.75 3.06
3342 3571 4.467795 TGCTTTTAGTGAGCTCCTATGTCT 59.532 41.667 12.15 2.96 40.75 3.41
3343 3572 5.656859 TGCTTTTAGTGAGCTCCTATGTCTA 59.343 40.000 12.15 2.04 40.75 2.59
3346 3575 7.661536 TTTTAGTGAGCTCCTATGTCTATGT 57.338 36.000 12.15 0.00 0.00 2.29
3347 3576 6.641169 TTAGTGAGCTCCTATGTCTATGTG 57.359 41.667 12.15 0.00 0.00 3.21
3348 3577 3.894427 AGTGAGCTCCTATGTCTATGTGG 59.106 47.826 12.15 0.00 0.00 4.17
3349 3578 3.006323 GTGAGCTCCTATGTCTATGTGGG 59.994 52.174 12.15 0.00 0.00 4.61
3350 3579 3.235200 GAGCTCCTATGTCTATGTGGGT 58.765 50.000 0.87 0.00 0.00 4.51
3351 3580 4.141018 TGAGCTCCTATGTCTATGTGGGTA 60.141 45.833 12.15 0.00 0.00 3.69
3393 3622 4.154296 GCATCAGATCAGGTGCCC 57.846 61.111 12.10 0.00 0.00 5.36
3402 3631 0.971386 ATCAGGTGCCCTTGCTTTTG 59.029 50.000 0.00 0.00 38.71 2.44
3421 3650 1.166531 GGGGTCACTGCTGTGTGTTC 61.167 60.000 21.35 11.37 44.14 3.18
3473 3706 4.845598 TGACGGCGAAATATATTACGTACG 59.154 41.667 16.62 15.01 35.70 3.67
3516 3755 6.591935 TGACTGGTTAGGATTGACAATATCC 58.408 40.000 0.00 0.00 41.59 2.59
3561 3800 0.392729 AGCTCCAGATCAGTGCAAGC 60.393 55.000 11.03 0.00 0.00 4.01
3579 3818 1.842562 AGCAAGTGGAGCACATAGGAT 59.157 47.619 0.00 0.00 36.74 3.24
3580 3819 3.041211 AGCAAGTGGAGCACATAGGATA 58.959 45.455 0.00 0.00 36.74 2.59
3581 3820 3.070734 AGCAAGTGGAGCACATAGGATAG 59.929 47.826 0.00 0.00 36.74 2.08
3583 3822 3.619900 AGTGGAGCACATAGGATAGGA 57.380 47.619 0.00 0.00 36.74 2.94
3584 3823 3.505386 AGTGGAGCACATAGGATAGGAG 58.495 50.000 0.00 0.00 36.74 3.69
3585 3824 3.116939 AGTGGAGCACATAGGATAGGAGT 60.117 47.826 0.00 0.00 36.74 3.85
3586 3825 4.106502 AGTGGAGCACATAGGATAGGAGTA 59.893 45.833 0.00 0.00 36.74 2.59
3587 3826 4.461081 GTGGAGCACATAGGATAGGAGTAG 59.539 50.000 0.00 0.00 34.08 2.57
3625 3871 7.695480 AAAGGAAAGAATTAAGAAGCTCTCC 57.305 36.000 0.00 0.00 0.00 3.71
3755 4004 4.566488 CCTGAGTTGGAATTAGGAACTGCT 60.566 45.833 0.00 0.00 41.52 4.24
3756 4005 4.326826 TGAGTTGGAATTAGGAACTGCTG 58.673 43.478 0.00 0.00 41.52 4.41
3815 4066 1.391485 GACTCGTGCATGTCATGTCAC 59.609 52.381 21.05 21.05 35.45 3.67
3958 4227 3.343972 CACTGTTGCAAGGTCGGG 58.656 61.111 0.00 0.00 0.00 5.14
4051 4320 2.870372 GCACGTCCATGCCTGTTC 59.130 61.111 0.00 0.00 39.86 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 90 4.759183 AGATGCAGAAGAAAGGAAGTGTTC 59.241 41.667 0.00 0.00 0.00 3.18
156 160 0.610174 AAGATTGCTCCGCTGAGACA 59.390 50.000 9.60 3.92 41.42 3.41
172 176 5.836024 AACTATACTGGGTTCCAACAAGA 57.164 39.130 0.00 0.00 30.80 3.02
239 247 3.003689 AGGTTCTTGTTGAGACAAATGCG 59.996 43.478 0.00 0.00 44.65 4.73
286 298 7.147949 CCATCTTTACCTCTCAAATGCAAAGAT 60.148 37.037 0.00 0.00 40.21 2.40
287 299 6.151648 CCATCTTTACCTCTCAAATGCAAAGA 59.848 38.462 0.00 0.00 35.64 2.52
376 407 0.947244 CAAAGTGTGCACCAGGTCTC 59.053 55.000 15.69 0.00 0.00 3.36
779 821 1.534163 CCTAATCAGTGATGCATGCGG 59.466 52.381 14.09 0.00 0.00 5.69
856 907 2.313172 GCTCCTGTGTCTGTGTGCG 61.313 63.158 0.00 0.00 0.00 5.34
982 1033 5.243730 CACCCATCCTGATTTTGTAAGTGTT 59.756 40.000 0.00 0.00 0.00 3.32
984 1035 4.158394 CCACCCATCCTGATTTTGTAAGTG 59.842 45.833 0.00 0.00 0.00 3.16
987 1038 4.085733 CACCACCCATCCTGATTTTGTAA 58.914 43.478 0.00 0.00 0.00 2.41
1218 1277 2.343758 GAGCCGGACAAGCAGACA 59.656 61.111 5.05 0.00 0.00 3.41
1283 1346 0.596082 TTTAGTCTTTTGCCTGCGCC 59.404 50.000 4.18 0.00 0.00 6.53
1513 1632 1.372838 TTGTGAAGTGTGTGTGCCCG 61.373 55.000 0.00 0.00 0.00 6.13
1524 1643 3.469008 TCGGACACTTGATTGTGAAGT 57.531 42.857 1.47 0.00 40.12 3.01
1525 1644 3.061295 CGATCGGACACTTGATTGTGAAG 59.939 47.826 7.38 0.00 40.12 3.02
1672 1844 4.211920 TGTTACCCTGGGAACAAGAAAAG 58.788 43.478 22.23 0.00 42.06 2.27
1721 1893 2.860628 CGCGGACGCATAGTTGAGC 61.861 63.158 17.35 0.00 42.06 4.26
1772 1944 1.737793 GCCAGAATGAAGGTAACCACG 59.262 52.381 0.00 0.00 39.69 4.94
1825 2001 3.764434 ACTATCGAGCAAGAGGTCAGAAA 59.236 43.478 0.00 0.00 42.32 2.52
1837 2013 3.762288 AGTTACAGGACAACTATCGAGCA 59.238 43.478 0.00 0.00 34.50 4.26
1846 2022 5.122396 CAGGAATGCTTAGTTACAGGACAAC 59.878 44.000 0.00 0.00 0.00 3.32
1868 2044 8.567285 ACTAGTTGATTTAGATGGAAAACCAG 57.433 34.615 0.00 0.00 0.00 4.00
1903 2088 9.495572 AGTTTTTGATTTGGTAAGACAACAAAA 57.504 25.926 0.00 0.00 37.60 2.44
1905 2090 8.307483 TCAGTTTTTGATTTGGTAAGACAACAA 58.693 29.630 0.00 0.00 0.00 2.83
1929 2114 6.148645 AGTGCATGTTACGTGTAAATCATTCA 59.851 34.615 6.43 0.00 0.00 2.57
1933 2118 5.933187 AAGTGCATGTTACGTGTAAATCA 57.067 34.783 6.43 0.00 0.00 2.57
1937 2122 5.062433 CCGATTAAGTGCATGTTACGTGTAA 59.938 40.000 6.43 0.00 0.00 2.41
1959 2156 2.125912 CCGTCCAGCAGACTTCCG 60.126 66.667 5.50 0.00 43.91 4.30
1960 2157 0.034896 TTTCCGTCCAGCAGACTTCC 59.965 55.000 5.50 0.00 43.91 3.46
1961 2158 1.801178 CTTTTCCGTCCAGCAGACTTC 59.199 52.381 5.50 0.00 43.91 3.01
1962 2159 1.884235 CTTTTCCGTCCAGCAGACTT 58.116 50.000 5.50 0.00 43.91 3.01
1964 2161 0.603975 AGCTTTTCCGTCCAGCAGAC 60.604 55.000 0.00 0.00 42.54 3.51
1965 2162 0.973632 TAGCTTTTCCGTCCAGCAGA 59.026 50.000 0.00 0.00 35.88 4.26
1966 2163 1.079503 GTAGCTTTTCCGTCCAGCAG 58.920 55.000 0.00 0.00 35.88 4.24
1967 2164 0.394938 TGTAGCTTTTCCGTCCAGCA 59.605 50.000 0.00 0.00 35.88 4.41
1968 2165 1.519408 TTGTAGCTTTTCCGTCCAGC 58.481 50.000 0.00 0.00 0.00 4.85
2001 2198 5.552430 ATTTGTTCTTAGGGGAGGGAAAT 57.448 39.130 0.00 0.00 0.00 2.17
2007 2204 5.126061 CACATGGAATTTGTTCTTAGGGGAG 59.874 44.000 0.00 0.00 0.00 4.30
2027 2225 2.842496 ACTCCATCCTGTCACATCACAT 59.158 45.455 0.00 0.00 0.00 3.21
2287 2488 2.009051 TGCATATTCACCTGAAGCACG 58.991 47.619 0.00 0.00 37.48 5.34
2327 2529 4.074970 GGGTCTGAAGCTCTGAAAAATGA 58.925 43.478 0.00 0.00 0.00 2.57
2384 2586 4.362476 GTGGCCCCTGCGCAAAAG 62.362 66.667 13.05 3.38 38.85 2.27
2439 2641 2.202492 GACGCGCACGAGATCTGT 60.202 61.111 5.73 0.00 43.93 3.41
2460 2662 4.329545 GCCACCACGAAGGCCTGA 62.330 66.667 5.69 0.00 45.18 3.86
2724 2928 5.735285 TGATTGTGAAGATCAGAGTGAGT 57.265 39.130 0.00 0.00 0.00 3.41
2795 2999 2.475466 ATGAGCAATTCTGGGCGCG 61.475 57.895 0.00 0.00 32.14 6.86
2808 3016 6.094719 TGCACATTTATGAAGTTTCATGAGC 58.905 36.000 15.72 11.40 46.68 4.26
2816 3024 8.850156 AGAGTTTAGTTGCACATTTATGAAGTT 58.150 29.630 0.00 0.00 0.00 2.66
2869 3090 9.461312 ACTGCTCAGGAAATATAATAACACAAA 57.539 29.630 1.66 0.00 0.00 2.83
2913 3138 0.253044 TGTACAGGCCTCCAATCAGC 59.747 55.000 0.00 0.00 0.00 4.26
3004 3229 0.250467 TCCTTGTCTTGCAGCTCCAC 60.250 55.000 0.00 0.00 0.00 4.02
3005 3230 0.035881 CTCCTTGTCTTGCAGCTCCA 59.964 55.000 0.00 0.00 0.00 3.86
3073 3298 0.034059 GTCCCATCGCCTATCACTGG 59.966 60.000 0.00 0.00 0.00 4.00
3081 3306 0.984230 TCTTTTCTGTCCCATCGCCT 59.016 50.000 0.00 0.00 0.00 5.52
3146 3371 2.260154 CCAGTTCACGGTGCATGCA 61.260 57.895 18.46 18.46 0.00 3.96
3173 3402 1.204704 TCGTCCTGAGTCGATTGCATT 59.795 47.619 0.00 0.00 0.00 3.56
3174 3403 0.817654 TCGTCCTGAGTCGATTGCAT 59.182 50.000 0.00 0.00 0.00 3.96
3175 3404 0.817654 ATCGTCCTGAGTCGATTGCA 59.182 50.000 4.46 0.00 40.60 4.08
3176 3405 2.776312 TATCGTCCTGAGTCGATTGC 57.224 50.000 13.08 0.00 40.60 3.56
3177 3406 4.553756 TCTTATCGTCCTGAGTCGATTG 57.446 45.455 13.08 8.44 40.60 2.67
3178 3407 4.022762 CCATCTTATCGTCCTGAGTCGATT 60.023 45.833 13.08 0.00 40.60 3.34
3179 3408 3.504134 CCATCTTATCGTCCTGAGTCGAT 59.496 47.826 12.62 12.62 44.56 3.59
3180 3409 2.879026 CCATCTTATCGTCCTGAGTCGA 59.121 50.000 0.19 0.19 37.92 4.20
3181 3410 2.030717 CCCATCTTATCGTCCTGAGTCG 60.031 54.545 0.00 0.00 0.00 4.18
3182 3411 2.288518 GCCCATCTTATCGTCCTGAGTC 60.289 54.545 0.00 0.00 0.00 3.36
3183 3412 1.689273 GCCCATCTTATCGTCCTGAGT 59.311 52.381 0.00 0.00 0.00 3.41
3184 3413 1.688735 TGCCCATCTTATCGTCCTGAG 59.311 52.381 0.00 0.00 0.00 3.35
3185 3414 1.688735 CTGCCCATCTTATCGTCCTGA 59.311 52.381 0.00 0.00 0.00 3.86
3308 3537 6.072783 AGCTCACTAAAAGCATCTGAAACTTC 60.073 38.462 0.00 0.00 42.35 3.01
3341 3570 2.555199 GTGCTGAAGCTACCCACATAG 58.445 52.381 3.61 0.00 42.66 2.23
3342 3571 1.134818 CGTGCTGAAGCTACCCACATA 60.135 52.381 3.61 0.00 42.66 2.29
3343 3572 0.391661 CGTGCTGAAGCTACCCACAT 60.392 55.000 3.61 0.00 42.66 3.21
3346 3575 2.047274 GCGTGCTGAAGCTACCCA 60.047 61.111 3.61 0.00 42.66 4.51
3347 3576 2.047274 TGCGTGCTGAAGCTACCC 60.047 61.111 3.61 0.00 42.66 3.69
3348 3577 0.108804 TAGTGCGTGCTGAAGCTACC 60.109 55.000 3.61 0.00 42.66 3.18
3349 3578 1.927895 ATAGTGCGTGCTGAAGCTAC 58.072 50.000 3.61 0.00 42.66 3.58
3350 3579 2.672961 AATAGTGCGTGCTGAAGCTA 57.327 45.000 3.61 0.00 42.66 3.32
3351 3580 1.813513 AAATAGTGCGTGCTGAAGCT 58.186 45.000 3.61 0.00 42.66 3.74
3393 3622 0.032540 GCAGTGACCCCAAAAGCAAG 59.967 55.000 0.00 0.00 0.00 4.01
3421 3650 2.027325 CATCATGGACATGGTGGCG 58.973 57.895 15.96 0.00 44.17 5.69
3486 3719 4.872691 GTCAATCCTAACCAGTCATCAGTG 59.127 45.833 0.00 0.00 0.00 3.66
3516 3755 4.203950 TGCTACTTGTTTGTTTACGCAG 57.796 40.909 0.00 0.00 0.00 5.18
3561 3800 3.643320 TCCTATCCTATGTGCTCCACTTG 59.357 47.826 0.00 0.00 35.11 3.16
3601 3847 6.661377 GGGAGAGCTTCTTAATTCTTTCCTTT 59.339 38.462 0.00 0.00 32.33 3.11
3625 3871 1.865865 GTACATCCGTACTGGCATGG 58.134 55.000 0.00 0.00 43.97 3.66
3815 4066 0.448990 TGATCCGACGTGTAACCGAG 59.551 55.000 0.00 0.00 0.00 4.63
3913 4164 2.510238 GCGATCTTGAGCGGCAGT 60.510 61.111 10.23 0.00 0.00 4.40
3958 4227 4.210304 GCACTCGATCGGCGTTGC 62.210 66.667 16.41 14.26 40.73 4.17


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

AutoCloner maintained by Alex Coulton.