Multiple sequence alignment - TraesCS4D01G289000

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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 TraesCS4D01G289000 chr4D 100.000 3772 0 0 1 3772 460049366 460045595 0 6966
1 TraesCS4D01G289000 chr4A 95.854 2967 93 14 825 3772 8203967 8206922 0 4771
2 TraesCS4D01G289000 chr4A 93.484 798 24 8 15 795 8202900 8203686 0 1160


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 TraesCS4D01G289000 chr4D 460045595 460049366 3771 True 6966.0 6966 100.000 1 3772 1 chr4D.!!$R1 3771
1 TraesCS4D01G289000 chr4A 8202900 8206922 4022 False 2965.5 4771 94.669 15 3772 2 chr4A.!!$F1 3757

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
802 828 0.032912 TATGTAGGACAGGCACGGGA 60.033 55.0 0.00 0.0 0.00 5.14 F
823 849 0.958822 GAACTCCCCAACAACGCAAT 59.041 50.0 0.00 0.0 0.00 3.56 F
1931 2208 0.107066 TCGAGCACCGGTCCTACATA 60.107 55.0 2.59 0.0 39.14 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 2018 0.818296 AGCATCTACACGGTGACTCC 59.182 55.000 16.29 0.0 0.00 3.85 R
2063 2340 1.069978 TGATGCACTGACAGGACGAAA 59.930 47.619 7.51 0.0 0.00 3.46 R
3023 3317 1.211703 TCCTGAAGCAGTGGTGAAACA 59.788 47.619 0.00 0.0 39.98 2.83 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
111 112 4.988598 CTCACCACCGGCAAGCGT 62.989 66.667 0.00 0.00 0.00 5.07
199 210 2.430610 GGCATCCTCAGCGTCCTCT 61.431 63.158 0.00 0.00 0.00 3.69
281 292 4.404098 GTGGGAATGCCGGGTCGT 62.404 66.667 2.18 0.00 33.83 4.34
394 405 3.222354 GAGTGGACGAGGTGGCGTT 62.222 63.158 0.00 0.00 45.72 4.84
396 407 4.308458 TGGACGAGGTGGCGTTGG 62.308 66.667 0.00 0.00 45.72 3.77
526 552 0.108898 GTCGACACAGCTGCTCATCT 60.109 55.000 15.27 0.00 0.00 2.90
599 625 1.073964 CTGTGGCGATTGTGTCTGAG 58.926 55.000 0.00 0.00 0.00 3.35
620 646 7.824289 TCTGAGGACAATAAGGTGAAATTACAG 59.176 37.037 0.00 0.00 0.00 2.74
654 680 2.437180 TTCTGATGGCTGCCGCAG 60.437 61.111 26.26 26.26 38.10 5.18
795 821 7.041030 CCGTGCTCTATATATATGTAGGACAGG 60.041 44.444 20.59 18.45 0.00 4.00
796 822 7.520776 CGTGCTCTATATATATGTAGGACAGGC 60.521 44.444 20.59 11.63 0.00 4.85
797 823 7.285629 GTGCTCTATATATATGTAGGACAGGCA 59.714 40.741 18.05 13.34 0.00 4.75
801 827 1.048601 ATATGTAGGACAGGCACGGG 58.951 55.000 0.00 0.00 0.00 5.28
802 828 0.032912 TATGTAGGACAGGCACGGGA 60.033 55.000 0.00 0.00 0.00 5.14
803 829 1.330655 ATGTAGGACAGGCACGGGAG 61.331 60.000 0.00 0.00 0.00 4.30
804 830 2.363795 TAGGACAGGCACGGGAGG 60.364 66.667 0.00 0.00 0.00 4.30
805 831 2.926326 TAGGACAGGCACGGGAGGA 61.926 63.158 0.00 0.00 0.00 3.71
806 832 2.449967 TAGGACAGGCACGGGAGGAA 62.450 60.000 0.00 0.00 0.00 3.36
807 833 2.047179 GACAGGCACGGGAGGAAC 60.047 66.667 0.00 0.00 0.00 3.62
820 846 1.228154 AGGAACTCCCCAACAACGC 60.228 57.895 0.00 0.00 36.42 4.84
821 847 1.527380 GGAACTCCCCAACAACGCA 60.527 57.895 0.00 0.00 0.00 5.24
823 849 0.958822 GAACTCCCCAACAACGCAAT 59.041 50.000 0.00 0.00 0.00 3.56
1083 1360 1.680338 GATCCCCGTTTCTTGATGGG 58.320 55.000 0.00 0.00 44.21 4.00
1194 1471 1.269448 CCGTTTCTTGATGGGTGTTGG 59.731 52.381 0.00 0.00 0.00 3.77
1287 1564 2.956964 GCTGATCGAACGAGCCGG 60.957 66.667 9.81 0.00 0.00 6.13
1341 1618 1.298859 GGTGCGCTCGAATTGGTCTT 61.299 55.000 9.73 0.00 0.00 3.01
1389 1666 5.831525 ACCCCTTCTCGTAATGTTTTCTTTT 59.168 36.000 0.00 0.00 0.00 2.27
1425 1702 2.566036 CGTGCTTAATCGCGTTTCAAA 58.434 42.857 5.77 0.00 35.47 2.69
1434 1711 1.117234 CGCGTTTCAAAACTTTCCCG 58.883 50.000 0.00 0.00 36.77 5.14
1452 1729 2.610232 CCCGCTAATTGCTGTTTGCTTT 60.610 45.455 0.00 0.00 43.37 3.51
1499 1776 5.947503 TGTTTCAATTTCTTTTGCAGACG 57.052 34.783 0.00 0.00 0.00 4.18
1517 1794 2.031870 ACGGAGATCGACATGGAATCA 58.968 47.619 0.00 0.00 42.43 2.57
1521 1798 3.812053 GGAGATCGACATGGAATCAAAGG 59.188 47.826 0.00 0.00 0.00 3.11
1531 1808 2.084546 GGAATCAAAGGGGTCGTCAAG 58.915 52.381 0.00 0.00 0.00 3.02
1568 1845 1.306141 TGACCTCCCCGAGCAGATT 60.306 57.895 0.00 0.00 0.00 2.40
1644 1921 2.555757 GTCTGCAAATCTTGGCTCAACT 59.444 45.455 0.00 0.00 0.00 3.16
1715 1992 1.448540 GCACCTGATCGTCCCAGTG 60.449 63.158 0.00 0.00 0.00 3.66
1732 2009 1.774254 AGTGGATCCAGACAACACCAA 59.226 47.619 16.81 0.00 32.71 3.67
1741 2018 3.438087 CCAGACAACACCAAGCATAAGAG 59.562 47.826 0.00 0.00 0.00 2.85
1770 2047 3.242091 CCGTGTAGATGCTGTTGATTTCG 60.242 47.826 0.00 0.00 0.00 3.46
1784 2061 1.338136 ATTTCGAGCACCCCGAGGAT 61.338 55.000 0.00 0.00 37.35 3.24
1803 2080 3.181454 GGATGGTGTCCGTTCCATAATCT 60.181 47.826 0.00 0.00 43.45 2.40
1831 2108 3.019564 CCAGCTTTGGACTATTTGAGGG 58.980 50.000 0.00 0.00 0.00 4.30
1851 2128 3.631227 GGGCTTTGATCCAGATGAAGAAG 59.369 47.826 0.00 0.00 0.00 2.85
1860 2137 0.901124 AGATGAAGAAGCCGCAGAGT 59.099 50.000 0.00 0.00 0.00 3.24
1880 2157 5.828747 GAGTATCTAATGTCTGCCGTACAA 58.171 41.667 0.00 0.00 0.00 2.41
1920 2197 1.137825 CTCGTCTCCTTCGAGCACC 59.862 63.158 2.59 0.00 45.77 5.01
1924 2201 2.182030 CTCCTTCGAGCACCGGTC 59.818 66.667 2.59 0.00 39.14 4.79
1928 2205 1.139095 CTTCGAGCACCGGTCCTAC 59.861 63.158 2.59 0.00 39.14 3.18
1931 2208 0.107066 TCGAGCACCGGTCCTACATA 60.107 55.000 2.59 0.00 39.14 2.29
1937 2214 2.810400 GCACCGGTCCTACATATGCAAT 60.810 50.000 2.59 0.00 0.00 3.56
1986 2263 2.014857 CACAGCTGGATGACCATGAAG 58.985 52.381 19.93 0.00 45.87 3.02
2009 2286 1.072266 TGGGACTTTACATGCTGGGT 58.928 50.000 0.00 0.00 0.00 4.51
2033 2310 5.835819 TGATGAGTTTAGGGTCCTCTATCTG 59.164 44.000 0.00 0.00 0.00 2.90
2056 2333 2.022625 AGGAAGATGAGGAGGGTGATGA 60.023 50.000 0.00 0.00 0.00 2.92
2057 2334 2.978278 GGAAGATGAGGAGGGTGATGAT 59.022 50.000 0.00 0.00 0.00 2.45
2063 2340 4.868172 TGAGGAGGGTGATGATGAATTT 57.132 40.909 0.00 0.00 0.00 1.82
2086 2363 2.079158 CGTCCTGTCAGTGCATCAATT 58.921 47.619 0.00 0.00 0.00 2.32
2152 2432 2.672874 CGAATCAGCGAGAAAATGGACA 59.327 45.455 0.00 0.00 0.00 4.02
2153 2433 3.484229 CGAATCAGCGAGAAAATGGACAC 60.484 47.826 0.00 0.00 0.00 3.67
2163 2443 3.005155 AGAAAATGGACACAAGAAGCTGC 59.995 43.478 0.00 0.00 0.00 5.25
2248 2528 3.695606 GACGGAGCTGTGGCCAGA 61.696 66.667 5.11 2.89 41.50 3.86
2249 2529 3.941657 GACGGAGCTGTGGCCAGAC 62.942 68.421 5.11 0.00 41.50 3.51
2266 2549 5.634859 GGCCAGACATTACAGTTTTTGATTG 59.365 40.000 0.00 0.00 0.00 2.67
2314 2597 0.695347 CTTCCCAAGACCAAGGAGCT 59.305 55.000 0.00 0.00 0.00 4.09
2316 2599 0.473694 TCCCAAGACCAAGGAGCTCA 60.474 55.000 17.19 0.00 0.00 4.26
2317 2600 0.622665 CCCAAGACCAAGGAGCTCAT 59.377 55.000 17.19 5.25 0.00 2.90
2336 2619 1.220529 TCAAGAGCAACGACAGCAAG 58.779 50.000 0.00 0.00 0.00 4.01
2351 2634 2.670414 CAGCAAGACGATGAAGGTTCTC 59.330 50.000 0.00 0.00 30.38 2.87
2642 2925 3.922640 GGAGAGCTAGCGCCTGGG 61.923 72.222 15.37 0.00 36.60 4.45
2829 3123 6.161855 ACCGAGCTATGTTTCTGAATATCA 57.838 37.500 0.00 0.00 0.00 2.15
2908 3202 3.364366 GCTTTTCTCATCACACGTTCAGG 60.364 47.826 0.00 0.00 0.00 3.86
2925 3219 4.655762 TCAGGTATACTCATCACTGTGC 57.344 45.455 2.12 0.00 0.00 4.57
2927 3221 4.711846 TCAGGTATACTCATCACTGTGCTT 59.288 41.667 2.12 0.00 0.00 3.91
3023 3317 1.419387 GTGCATAAGGAGGAGGATGCT 59.581 52.381 7.18 0.00 44.05 3.79
3068 3362 2.093764 GCAGATCACAGCTCCTACTTGT 60.094 50.000 0.00 0.00 0.00 3.16
3092 3386 3.954258 GTGCTTTCTTGTATATTGGGCCT 59.046 43.478 4.53 0.00 0.00 5.19
3103 3397 0.396695 ATTGGGCCTTCTGATGCTGG 60.397 55.000 4.53 0.00 0.00 4.85
3106 3400 1.751927 GGCCTTCTGATGCTGGTGG 60.752 63.158 0.00 0.00 0.00 4.61
3151 3445 1.929836 GATTAGAGCTTGTGCCTGTCG 59.070 52.381 0.00 0.00 40.80 4.35
3183 3477 1.386533 GAGAATGACCCTGCACATGG 58.613 55.000 0.00 0.00 0.00 3.66
3189 3483 1.228862 ACCCTGCACATGGTTTCCC 60.229 57.895 0.00 0.00 0.00 3.97
3192 3486 1.272425 CCCTGCACATGGTTTCCCTTA 60.272 52.381 0.00 0.00 0.00 2.69
3330 3624 6.152831 GGGTTTCTTTTGGTATGCAGTTATCT 59.847 38.462 0.00 0.00 0.00 1.98
3434 3728 5.721960 TCTTGGGTTCTAGAGCTAAACATCT 59.278 40.000 6.54 0.00 0.00 2.90
3587 3883 4.168479 ACCAGGTCACTTAAAACCCCTAAA 59.832 41.667 0.00 0.00 36.11 1.85
3590 3886 4.831155 AGGTCACTTAAAACCCCTAAAAGC 59.169 41.667 0.00 0.00 36.11 3.51
3604 3900 3.057946 CCTAAAAGCAACTCCAACAGCTC 60.058 47.826 0.00 0.00 36.07 4.09
3608 3904 1.905922 GCAACTCCAACAGCTCTCGC 61.906 60.000 0.00 0.00 0.00 5.03
3627 3923 6.936279 TCTCGCCCCTATCTCTAAAATAATG 58.064 40.000 0.00 0.00 0.00 1.90
3665 3961 0.961753 GCAAAAGACCCTCCCAACAG 59.038 55.000 0.00 0.00 0.00 3.16
3753 4049 6.103997 TGTATCTTTTTGACGGGCTAGTAAG 58.896 40.000 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.748798 AGAGGAGCAGGGGGTGGG 62.749 72.222 0.00 0.00 0.00 4.61
9 10 3.086600 GAGAGGAGCAGGGGGTGG 61.087 72.222 0.00 0.00 0.00 4.61
10 11 2.243774 TAGGAGAGGAGCAGGGGGTG 62.244 65.000 0.00 0.00 0.00 4.61
11 12 1.941820 TAGGAGAGGAGCAGGGGGT 60.942 63.158 0.00 0.00 0.00 4.95
12 13 1.458588 GTAGGAGAGGAGCAGGGGG 60.459 68.421 0.00 0.00 0.00 5.40
13 14 0.758685 CAGTAGGAGAGGAGCAGGGG 60.759 65.000 0.00 0.00 0.00 4.79
24 25 3.541713 GGGGCCTCGCAGTAGGAG 61.542 72.222 0.84 0.00 39.15 3.69
104 105 4.072088 CGACCAACCGACGCTTGC 62.072 66.667 0.00 0.00 0.00 4.01
111 112 4.595538 AAGCGCACGACCAACCGA 62.596 61.111 11.47 0.00 0.00 4.69
199 210 0.315886 TTGCAGACGAAGAAGGCGTA 59.684 50.000 0.00 0.00 42.77 4.42
443 454 2.663852 GCCGTGCCGTGTACAAGT 60.664 61.111 8.02 0.00 0.00 3.16
526 552 1.688884 TCCATGACCATGAGCCGGA 60.689 57.895 5.05 0.00 41.20 5.14
599 625 8.556213 TGTACTGTAATTTCACCTTATTGTCC 57.444 34.615 0.00 0.00 0.00 4.02
605 631 5.172934 CGGCTGTACTGTAATTTCACCTTA 58.827 41.667 1.46 0.00 0.00 2.69
610 636 4.219944 AGAGACGGCTGTACTGTAATTTCA 59.780 41.667 0.00 0.00 38.28 2.69
620 646 1.813786 AGAACAGAGAGACGGCTGTAC 59.186 52.381 0.00 0.00 44.06 2.90
801 827 1.235281 GCGTTGTTGGGGAGTTCCTC 61.235 60.000 0.00 0.00 36.90 3.71
802 828 1.228154 GCGTTGTTGGGGAGTTCCT 60.228 57.895 0.00 0.00 35.95 3.36
803 829 1.104577 TTGCGTTGTTGGGGAGTTCC 61.105 55.000 0.00 0.00 0.00 3.62
804 830 0.958822 ATTGCGTTGTTGGGGAGTTC 59.041 50.000 0.00 0.00 0.00 3.01
805 831 0.958822 GATTGCGTTGTTGGGGAGTT 59.041 50.000 0.00 0.00 0.00 3.01
806 832 0.179004 TGATTGCGTTGTTGGGGAGT 60.179 50.000 0.00 0.00 0.00 3.85
807 833 0.240945 GTGATTGCGTTGTTGGGGAG 59.759 55.000 0.00 0.00 0.00 4.30
808 834 0.179004 AGTGATTGCGTTGTTGGGGA 60.179 50.000 0.00 0.00 0.00 4.81
811 837 2.384382 GTCAAGTGATTGCGTTGTTGG 58.616 47.619 0.00 0.00 0.00 3.77
812 838 2.036217 CGTCAAGTGATTGCGTTGTTG 58.964 47.619 0.00 0.00 0.00 3.33
813 839 1.002900 CCGTCAAGTGATTGCGTTGTT 60.003 47.619 0.00 0.00 0.00 2.83
814 840 0.586319 CCGTCAAGTGATTGCGTTGT 59.414 50.000 0.00 0.00 0.00 3.32
815 841 0.110238 CCCGTCAAGTGATTGCGTTG 60.110 55.000 0.00 0.00 0.00 4.10
816 842 1.234615 CCCCGTCAAGTGATTGCGTT 61.235 55.000 0.00 0.00 0.00 4.84
817 843 1.671054 CCCCGTCAAGTGATTGCGT 60.671 57.895 0.00 0.00 0.00 5.24
818 844 3.039202 GCCCCGTCAAGTGATTGCG 62.039 63.158 0.00 0.00 0.00 4.85
820 846 1.361668 CTCGCCCCGTCAAGTGATTG 61.362 60.000 0.00 0.00 0.00 2.67
821 847 1.079127 CTCGCCCCGTCAAGTGATT 60.079 57.895 0.00 0.00 0.00 2.57
823 849 4.373116 GCTCGCCCCGTCAAGTGA 62.373 66.667 0.00 0.00 0.00 3.41
852 1129 4.261801 CTGTAGTTGTTGGGGAAATCGAT 58.738 43.478 0.00 0.00 0.00 3.59
1194 1471 7.929941 AGAAAAAGATTCAGGAACTACCATC 57.070 36.000 0.00 0.00 42.04 3.51
1287 1564 3.756434 TGATGGGAACGAAATCTTGGTTC 59.244 43.478 5.91 5.91 44.50 3.62
1341 1618 3.830744 TTGAGAAACTCAAACGAGGGA 57.169 42.857 11.06 0.00 45.84 4.20
1389 1666 1.876416 GCACGGCCAGTTCTAAGAACA 60.876 52.381 2.24 0.00 0.00 3.18
1396 1673 1.739067 GATTAAGCACGGCCAGTTCT 58.261 50.000 2.24 0.00 0.00 3.01
1452 1729 4.245660 CAACTAGCCGATCAGTGAAAGAA 58.754 43.478 0.00 0.00 0.00 2.52
1499 1776 3.812053 CCTTTGATTCCATGTCGATCTCC 59.188 47.826 0.00 0.00 0.00 3.71
1517 1794 2.434774 GCCCTTGACGACCCCTTT 59.565 61.111 0.00 0.00 0.00 3.11
1568 1845 1.299648 CTCGAGGATTGCCCACCAA 59.700 57.895 3.91 0.00 37.41 3.67
1715 1992 1.168714 GCTTGGTGTTGTCTGGATCC 58.831 55.000 4.20 4.20 0.00 3.36
1732 2009 1.478510 CACGGTGACTCCTCTTATGCT 59.521 52.381 0.74 0.00 0.00 3.79
1741 2018 0.818296 AGCATCTACACGGTGACTCC 59.182 55.000 16.29 0.00 0.00 3.85
1770 2047 3.083997 ACCATCCTCGGGGTGCTC 61.084 66.667 0.00 0.00 35.67 4.26
1784 2061 2.679639 GCAGATTATGGAACGGACACCA 60.680 50.000 0.00 0.00 40.57 4.17
1788 2065 3.309954 GTGAAGCAGATTATGGAACGGAC 59.690 47.826 0.00 0.00 0.00 4.79
1821 2098 4.785301 TCTGGATCAAAGCCCTCAAATAG 58.215 43.478 0.00 0.00 0.00 1.73
1831 2108 3.066481 GGCTTCTTCATCTGGATCAAAGC 59.934 47.826 0.00 0.00 35.54 3.51
1851 2128 3.312828 CAGACATTAGATACTCTGCGGC 58.687 50.000 0.00 0.00 0.00 6.53
1860 2137 5.196341 CCTTGTACGGCAGACATTAGATA 57.804 43.478 0.00 0.00 0.00 1.98
1880 2157 1.611965 GAGGCCTCCAATTGAGCCT 59.388 57.895 26.81 26.81 44.92 4.58
1920 2197 3.329386 CTGGATTGCATATGTAGGACCG 58.671 50.000 4.29 0.00 0.00 4.79
1924 2201 5.227569 TGTACCTGGATTGCATATGTAGG 57.772 43.478 0.00 0.00 0.00 3.18
1928 2205 6.698008 TCTTTTGTACCTGGATTGCATATG 57.302 37.500 0.00 0.00 0.00 1.78
1931 2208 5.716228 TGATTCTTTTGTACCTGGATTGCAT 59.284 36.000 0.00 0.00 0.00 3.96
1937 2214 3.071479 GCGTGATTCTTTTGTACCTGGA 58.929 45.455 0.00 0.00 0.00 3.86
1986 2263 2.749621 CCAGCATGTAAAGTCCCAAGAC 59.250 50.000 0.00 0.00 43.89 3.01
1997 2274 3.719268 AACTCATCACCCAGCATGTAA 57.281 42.857 0.00 0.00 0.00 2.41
2009 2286 5.835819 CAGATAGAGGACCCTAAACTCATCA 59.164 44.000 0.00 0.00 33.76 3.07
2033 2310 2.472029 TCACCCTCCTCATCTTCCTTC 58.528 52.381 0.00 0.00 0.00 3.46
2056 2333 4.320494 GCACTGACAGGACGAAAAATTCAT 60.320 41.667 7.51 0.00 0.00 2.57
2057 2334 3.003275 GCACTGACAGGACGAAAAATTCA 59.997 43.478 7.51 0.00 0.00 2.57
2063 2340 1.069978 TGATGCACTGACAGGACGAAA 59.930 47.619 7.51 0.00 0.00 3.46
2086 2363 8.058847 AGTACCCAATGGATTTATTGCTAAGAA 58.941 33.333 0.00 0.00 36.86 2.52
2137 2414 3.126001 TCTTGTGTCCATTTTCTCGCT 57.874 42.857 0.00 0.00 0.00 4.93
2140 2417 4.791974 CAGCTTCTTGTGTCCATTTTCTC 58.208 43.478 0.00 0.00 0.00 2.87
2152 2432 2.621763 CTGAACCGCAGCTTCTTGT 58.378 52.632 0.00 0.00 37.90 3.16
2163 2443 1.294659 GAACTCTGCAGGCTGAACCG 61.295 60.000 20.86 5.72 46.52 4.44
2219 2499 1.520787 CTCCGTCGGTGCCCAATAC 60.521 63.158 11.88 0.00 0.00 1.89
2232 2512 4.008933 GTCTGGCCACAGCTCCGT 62.009 66.667 0.00 0.00 44.54 4.69
2233 2513 2.809861 AATGTCTGGCCACAGCTCCG 62.810 60.000 0.00 0.00 44.54 4.63
2247 2527 6.215845 ACTGGCAATCAAAAACTGTAATGTC 58.784 36.000 0.00 0.00 0.00 3.06
2248 2528 6.040842 AGACTGGCAATCAAAAACTGTAATGT 59.959 34.615 0.00 0.00 0.00 2.71
2249 2529 6.364165 CAGACTGGCAATCAAAAACTGTAATG 59.636 38.462 0.00 0.00 0.00 1.90
2266 2549 2.031333 CAGTGAAAAAGCTCAGACTGGC 60.031 50.000 1.81 5.25 0.00 4.85
2314 2597 1.270252 TGCTGTCGTTGCTCTTGATGA 60.270 47.619 0.00 0.00 0.00 2.92
2316 2599 1.802960 CTTGCTGTCGTTGCTCTTGAT 59.197 47.619 0.00 0.00 0.00 2.57
2317 2600 1.202521 TCTTGCTGTCGTTGCTCTTGA 60.203 47.619 0.00 0.00 0.00 3.02
2328 2611 2.086054 ACCTTCATCGTCTTGCTGTC 57.914 50.000 0.00 0.00 0.00 3.51
2329 2612 2.037772 AGAACCTTCATCGTCTTGCTGT 59.962 45.455 0.00 0.00 0.00 4.40
2332 2615 1.656095 CGAGAACCTTCATCGTCTTGC 59.344 52.381 0.00 0.00 0.00 4.01
2336 2619 2.917971 CAACTCGAGAACCTTCATCGTC 59.082 50.000 21.68 0.00 37.69 4.20
2351 2634 2.049433 AACTCGCCGTCCAACTCG 60.049 61.111 0.00 0.00 0.00 4.18
2622 2905 3.213402 AGGCGCTAGCTCTCCGTC 61.213 66.667 13.93 0.00 44.37 4.79
2829 3123 4.265073 CTGCAACTAAAATACAGGGAGCT 58.735 43.478 0.00 0.00 0.00 4.09
2935 3229 4.985538 AGCAAATCACCTAGGAACAGAAA 58.014 39.130 17.98 0.00 0.00 2.52
2936 3230 4.640771 AGCAAATCACCTAGGAACAGAA 57.359 40.909 17.98 0.00 0.00 3.02
2938 3232 3.119708 GCAAGCAAATCACCTAGGAACAG 60.120 47.826 17.98 2.25 0.00 3.16
2940 3234 2.819608 TGCAAGCAAATCACCTAGGAAC 59.180 45.455 17.98 0.00 0.00 3.62
2941 3235 2.819608 GTGCAAGCAAATCACCTAGGAA 59.180 45.455 17.98 3.06 0.00 3.36
2943 3237 1.474077 GGTGCAAGCAAATCACCTAGG 59.526 52.381 7.41 7.41 45.04 3.02
2944 3238 2.927553 GGTGCAAGCAAATCACCTAG 57.072 50.000 0.00 0.00 45.04 3.02
3023 3317 1.211703 TCCTGAAGCAGTGGTGAAACA 59.788 47.619 0.00 0.00 39.98 2.83
3068 3362 3.625764 GCCCAATATACAAGAAAGCACGA 59.374 43.478 0.00 0.00 0.00 4.35
3106 3400 2.079925 GATCTTGGAACAGTGGTGAGC 58.920 52.381 0.00 0.00 42.39 4.26
3112 3406 7.776107 TCTAATCTACAGATCTTGGAACAGTG 58.224 38.462 0.00 0.00 34.24 3.66
3114 3408 6.922957 GCTCTAATCTACAGATCTTGGAACAG 59.077 42.308 0.00 0.00 34.24 3.16
3168 3462 1.549203 GAAACCATGTGCAGGGTCAT 58.451 50.000 9.04 1.81 45.89 3.06
3209 3503 5.699001 TGTCAACACTAGACGTTGCAATTAT 59.301 36.000 18.84 0.00 42.78 1.28
3330 3624 3.081061 AGCAATTTCCAGCATAACACGA 58.919 40.909 0.00 0.00 0.00 4.35
3408 3702 4.174762 GTTTAGCTCTAGAACCCAAGACG 58.825 47.826 0.00 0.00 0.00 4.18
3587 3883 1.875576 CGAGAGCTGTTGGAGTTGCTT 60.876 52.381 0.00 0.00 35.76 3.91
3604 3900 6.109359 CCATTATTTTAGAGATAGGGGCGAG 58.891 44.000 0.00 0.00 0.00 5.03
3608 3904 9.813826 AAATGACCATTATTTTAGAGATAGGGG 57.186 33.333 0.00 0.00 0.00 4.79
3627 3923 1.471287 GCCAACCTTCCGTAAATGACC 59.529 52.381 0.00 0.00 0.00 4.02
3665 3961 6.549912 AAGTTATGGACACTTTACGGAAAC 57.450 37.500 0.00 0.00 29.75 2.78
3711 4007 3.078891 ACAGGAAGATGAGAAAAGGCC 57.921 47.619 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.