Multiple sequence alignment - TraesCS4A01G079800

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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 TraesCS4A01G079800 chr4A 100.000 7065 0 0 1 7065 81823248 81816184 0.000000e+00 13047.0
1 TraesCS4A01G079800 chr4D 96.164 3259 71 16 1693 4920 381879364 381882599 0.000000e+00 5276.0
2 TraesCS4A01G079800 chr4D 92.308 1911 100 21 4919 6785 381882680 381884587 0.000000e+00 2671.0
3 TraesCS4A01G079800 chr4D 95.468 1633 52 9 1 1619 381877756 381879380 0.000000e+00 2586.0
4 TraesCS4A01G079800 chr4D 84.483 290 9 7 6790 7065 381884640 381884907 3.270000e-63 254.0
5 TraesCS4A01G079800 chr4B 94.962 1727 73 8 2358 4072 469012650 469014374 0.000000e+00 2695.0
6 TraesCS4A01G079800 chr4B 94.906 1433 42 8 198 1619 469010610 469012022 0.000000e+00 2213.0
7 TraesCS4A01G079800 chr4B 93.784 1271 62 8 4767 6026 469015424 469016688 0.000000e+00 1893.0
8 TraesCS4A01G079800 chr4B 96.600 647 16 3 1682 2323 469012007 469012652 0.000000e+00 1068.0
9 TraesCS4A01G079800 chr4B 92.275 712 29 4 4071 4764 469014536 469015239 0.000000e+00 987.0
10 TraesCS4A01G079800 chr4B 87.015 593 30 14 6216 6788 469016682 469017247 6.020000e-175 625.0
11 TraesCS4A01G079800 chr4B 88.406 276 11 8 6790 7065 469025661 469025915 5.320000e-81 313.0
12 TraesCS4A01G079800 chr4B 100.000 32 0 0 1 32 469010177 469010208 7.650000e-05 60.2
13 TraesCS4A01G079800 chr5D 91.789 1364 77 18 3354 4702 497781841 497780498 0.000000e+00 1866.0


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 TraesCS4A01G079800 chr4A 81816184 81823248 7064 True 13047.000000 13047 100.000000 1 7065 1 chr4A.!!$R1 7064
1 TraesCS4A01G079800 chr4D 381877756 381884907 7151 False 2696.750000 5276 92.105750 1 7065 4 chr4D.!!$F1 7064
2 TraesCS4A01G079800 chr4B 469010177 469017247 7070 False 1363.028571 2695 94.220286 1 6788 7 chr4B.!!$F2 6787
3 TraesCS4A01G079800 chr5D 497780498 497781841 1343 True 1866.000000 1866 91.789000 3354 4702 1 chr5D.!!$R1 1348

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
618 861 0.398522 ATACGTGGGAGGAGATGGCA 60.399 55.0 0.00 0.00 0.00 4.92 F
1616 1880 0.450983 TGCATGTGTGTGTGTGTGTG 59.549 50.0 0.00 0.00 0.00 3.82 F
1617 1881 0.451383 GCATGTGTGTGTGTGTGTGT 59.549 50.0 0.00 0.00 0.00 3.72 F
2760 3030 0.239347 GCTTCCAGTGTGCATGTCAC 59.761 55.0 11.79 11.79 45.82 3.67 F
3762 4040 2.349886 GCGTGGTAAAGAGAGCAATGAG 59.650 50.0 0.00 0.00 0.00 2.90 F
5078 5819 0.252761 TTCGAAGCCAGCATCATCCA 59.747 50.0 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1955 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.0 0.00 4.16 R
2642 2912 0.963962 CCACTTGCTGCATCCTTGTT 59.036 50.000 1.84 0.0 0.00 2.83 R
3352 3626 1.750206 TGCACAGCACTGTTGTTCATT 59.250 42.857 0.00 0.0 42.83 2.57 R
4101 4552 0.758734 CTGGACCTCAACCACTGACA 59.241 55.000 0.00 0.0 33.57 3.58 R
5546 6290 0.036010 TCCCTTGCTAGCTGACTTGC 60.036 55.000 17.23 0.0 43.86 4.01 R
6902 7753 0.385390 CCACAAGTTGACAACTGGGC 59.615 55.000 23.64 0.0 41.91 5.36 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
50 51 7.284716 AGGAAACGAACAAATTATTATCCCCTC 59.715 37.037 0.00 0.00 0.00 4.30
73 74 1.687123 CGTACGATTCCTTCCATCCCT 59.313 52.381 10.44 0.00 0.00 4.20
484 726 5.975344 GTGGTTGTGATGATCATGCTTTATG 59.025 40.000 14.30 0.00 38.17 1.90
596 839 0.855349 GCTCCGCTGATGATAACACG 59.145 55.000 0.00 0.00 0.00 4.49
617 860 0.759346 AATACGTGGGAGGAGATGGC 59.241 55.000 0.00 0.00 0.00 4.40
618 861 0.398522 ATACGTGGGAGGAGATGGCA 60.399 55.000 0.00 0.00 0.00 4.92
622 865 2.359169 TGGGAGGAGATGGCACGAC 61.359 63.158 0.00 0.00 0.00 4.34
629 872 0.661552 GAGATGGCACGACTACGCTA 59.338 55.000 0.00 0.00 43.96 4.26
696 948 8.609176 TGATCGGTGTTTATAAGCTTAACATTC 58.391 33.333 10.85 8.16 34.63 2.67
780 1034 7.996098 TCCAATATACTTGCCTTATTAAGCC 57.004 36.000 0.00 0.00 0.00 4.35
847 1101 4.875536 TGCTTGCGTATGACATTACTTCAT 59.124 37.500 0.00 0.00 37.47 2.57
1119 1373 4.163441 TCCACCTGAAATTGAGTTGTCA 57.837 40.909 0.00 0.00 0.00 3.58
1257 1511 2.712057 ATTTCTGCGCAAAAGGACTG 57.288 45.000 13.05 0.00 0.00 3.51
1266 1520 3.074412 CGCAAAAGGACTGAGGTGTATT 58.926 45.455 0.00 0.00 0.00 1.89
1293 1547 5.555017 ACCAAATGGATAATCGAGATCCTG 58.445 41.667 22.99 15.63 43.00 3.86
1356 1610 9.902684 TTTTTATATGTTGATTGGAATGCCATT 57.097 25.926 0.00 0.00 45.46 3.16
1613 1877 1.391577 ACATGCATGTGTGTGTGTGT 58.608 45.000 30.92 3.77 40.03 3.72
1614 1878 1.065851 ACATGCATGTGTGTGTGTGTG 59.934 47.619 30.92 2.24 40.03 3.82
1615 1879 1.065851 CATGCATGTGTGTGTGTGTGT 59.934 47.619 18.91 0.00 0.00 3.72
1616 1880 0.450983 TGCATGTGTGTGTGTGTGTG 59.549 50.000 0.00 0.00 0.00 3.82
1617 1881 0.451383 GCATGTGTGTGTGTGTGTGT 59.549 50.000 0.00 0.00 0.00 3.72
1618 1882 1.794800 GCATGTGTGTGTGTGTGTGTG 60.795 52.381 0.00 0.00 0.00 3.82
1619 1883 0.451383 ATGTGTGTGTGTGTGTGTGC 59.549 50.000 0.00 0.00 0.00 4.57
1620 1884 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
1621 1885 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
1622 1886 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
1623 1887 3.860125 GTGTGTGTGTGTGCGCGT 61.860 61.111 8.43 0.00 0.00 6.01
1624 1888 3.858989 TGTGTGTGTGTGCGCGTG 61.859 61.111 8.43 0.00 0.00 5.34
1656 1920 3.935872 CGTGTGCGTGTGGGTGTG 61.936 66.667 0.00 0.00 0.00 3.82
1657 1921 3.582120 GTGTGCGTGTGGGTGTGG 61.582 66.667 0.00 0.00 0.00 4.17
1658 1922 4.866224 TGTGCGTGTGGGTGTGGG 62.866 66.667 0.00 0.00 0.00 4.61
1659 1923 4.868116 GTGCGTGTGGGTGTGGGT 62.868 66.667 0.00 0.00 0.00 4.51
1660 1924 4.866224 TGCGTGTGGGTGTGGGTG 62.866 66.667 0.00 0.00 0.00 4.61
1661 1925 4.868116 GCGTGTGGGTGTGGGTGT 62.868 66.667 0.00 0.00 0.00 4.16
1662 1926 2.899838 CGTGTGGGTGTGGGTGTG 60.900 66.667 0.00 0.00 0.00 3.82
1663 1927 2.518349 GTGTGGGTGTGGGTGTGG 60.518 66.667 0.00 0.00 0.00 4.17
1664 1928 3.814906 TGTGGGTGTGGGTGTGGG 61.815 66.667 0.00 0.00 0.00 4.61
1665 1929 3.816090 GTGGGTGTGGGTGTGGGT 61.816 66.667 0.00 0.00 0.00 4.51
1666 1930 3.814906 TGGGTGTGGGTGTGGGTG 61.815 66.667 0.00 0.00 0.00 4.61
1667 1931 3.816090 GGGTGTGGGTGTGGGTGT 61.816 66.667 0.00 0.00 0.00 4.16
1668 1932 2.518349 GGTGTGGGTGTGGGTGTG 60.518 66.667 0.00 0.00 0.00 3.82
1669 1933 2.518349 GTGTGGGTGTGGGTGTGG 60.518 66.667 0.00 0.00 0.00 4.17
1670 1934 3.814906 TGTGGGTGTGGGTGTGGG 61.815 66.667 0.00 0.00 0.00 4.61
1671 1935 3.816090 GTGGGTGTGGGTGTGGGT 61.816 66.667 0.00 0.00 0.00 4.51
1672 1936 3.814906 TGGGTGTGGGTGTGGGTG 61.815 66.667 0.00 0.00 0.00 4.61
1673 1937 3.816090 GGGTGTGGGTGTGGGTGT 61.816 66.667 0.00 0.00 0.00 4.16
1674 1938 2.518349 GGTGTGGGTGTGGGTGTG 60.518 66.667 0.00 0.00 0.00 3.82
1675 1939 2.518349 GTGTGGGTGTGGGTGTGG 60.518 66.667 0.00 0.00 0.00 4.17
1676 1940 3.814906 TGTGGGTGTGGGTGTGGG 61.815 66.667 0.00 0.00 0.00 4.61
1677 1941 3.816090 GTGGGTGTGGGTGTGGGT 61.816 66.667 0.00 0.00 0.00 4.51
1678 1942 3.814906 TGGGTGTGGGTGTGGGTG 61.815 66.667 0.00 0.00 0.00 4.61
1679 1943 3.816090 GGGTGTGGGTGTGGGTGT 61.816 66.667 0.00 0.00 0.00 4.16
1680 1944 2.518349 GGTGTGGGTGTGGGTGTG 60.518 66.667 0.00 0.00 0.00 3.82
1681 1945 2.274104 GTGTGGGTGTGGGTGTGT 59.726 61.111 0.00 0.00 0.00 3.72
1682 1946 2.118404 GTGTGGGTGTGGGTGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
1683 1947 2.274104 GTGGGTGTGGGTGTGTGT 59.726 61.111 0.00 0.00 0.00 3.72
1684 1948 2.118404 GTGGGTGTGGGTGTGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
1685 1949 2.518349 GGGTGTGGGTGTGTGTGG 60.518 66.667 0.00 0.00 0.00 4.17
1686 1950 2.518349 GGTGTGGGTGTGTGTGGG 60.518 66.667 0.00 0.00 0.00 4.61
1687 1951 2.274104 GTGTGGGTGTGTGTGGGT 59.726 61.111 0.00 0.00 0.00 4.51
1688 1952 2.118404 GTGTGGGTGTGTGTGGGTG 61.118 63.158 0.00 0.00 0.00 4.61
1689 1953 2.274104 GTGGGTGTGTGTGGGTGT 59.726 61.111 0.00 0.00 0.00 4.16
1690 1954 2.118404 GTGGGTGTGTGTGGGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
1691 1955 2.518349 GGGTGTGTGTGGGTGTGG 60.518 66.667 0.00 0.00 0.00 4.17
2269 2539 2.291741 CTCAAGCAAGAAACACACCCTC 59.708 50.000 0.00 0.00 0.00 4.30
2276 2546 1.168714 GAAACACACCCTCCATCAGC 58.831 55.000 0.00 0.00 0.00 4.26
2412 2682 8.713737 ATATGTAGTTACTGATGCAGCATATG 57.286 34.615 8.22 6.71 34.37 1.78
2642 2912 1.084018 AAGGCTTGGATTGAGGGGAA 58.916 50.000 0.00 0.00 0.00 3.97
2671 2941 2.029288 AGCAAGTGGTCACGATGCG 61.029 57.895 20.44 0.00 46.33 4.73
2697 2967 7.380423 AGGATACATTGCCTTAGATGTTAGT 57.620 36.000 0.00 0.00 37.62 2.24
2760 3030 0.239347 GCTTCCAGTGTGCATGTCAC 59.761 55.000 11.79 11.79 45.82 3.67
2826 3097 5.566627 CGGCTCCATAGATTTTGTTTGGTTT 60.567 40.000 0.00 0.00 0.00 3.27
2827 3098 6.230472 GGCTCCATAGATTTTGTTTGGTTTT 58.770 36.000 0.00 0.00 0.00 2.43
2828 3099 6.710295 GGCTCCATAGATTTTGTTTGGTTTTT 59.290 34.615 0.00 0.00 0.00 1.94
3137 3408 4.653341 AGGTAGCTTCTCATGCATAACTCT 59.347 41.667 0.00 0.00 0.00 3.24
3352 3626 6.897966 AGGTAGACCATTTCTTCAGACATAGA 59.102 38.462 0.66 0.00 38.89 1.98
3565 3843 9.994432 CTCTTACATTTTATGCACCTTCTAAAG 57.006 33.333 0.00 0.00 0.00 1.85
3603 3881 6.504398 ACTTTTGAAGATTTTCGGAAGGAAC 58.496 36.000 12.63 0.00 36.04 3.62
3762 4040 2.349886 GCGTGGTAAAGAGAGCAATGAG 59.650 50.000 0.00 0.00 0.00 2.90
3982 4267 7.986889 ACAATGTTGAGCTTCCAAGTTTTTATT 59.013 29.630 0.00 0.00 0.00 1.40
4011 4296 8.758829 TCTCTTTCAGCTAAAGGTTGATACATA 58.241 33.333 12.67 0.00 44.10 2.29
4138 4589 3.327757 TCCAGGATATGTCTGTATTGGCC 59.672 47.826 0.00 0.00 0.00 5.36
4143 4594 5.547666 AGGATATGTCTGTATTGGCCATGTA 59.452 40.000 6.09 0.00 0.00 2.29
4230 4682 9.311916 CATAGTAATGCTATTAGAAGAGATGGC 57.688 37.037 0.00 0.00 38.28 4.40
4296 4750 5.763876 AAGGTAATGGTCTGAACTAGCTT 57.236 39.130 0.00 0.00 0.00 3.74
4315 4769 8.263640 ACTAGCTTGATGAATGTGTTTCTCTAT 58.736 33.333 1.04 0.00 35.23 1.98
4318 4772 8.263640 AGCTTGATGAATGTGTTTCTCTATAGT 58.736 33.333 0.00 0.00 35.23 2.12
4319 4773 8.887717 GCTTGATGAATGTGTTTCTCTATAGTT 58.112 33.333 0.00 0.00 35.23 2.24
4465 4919 7.386851 TGAAGTCTCTTCGGAATTTATGTTCT 58.613 34.615 5.28 0.00 0.00 3.01
4471 4925 6.234920 TCTTCGGAATTTATGTTCTGACCAA 58.765 36.000 0.00 0.00 41.79 3.67
4472 4926 6.371548 TCTTCGGAATTTATGTTCTGACCAAG 59.628 38.462 0.00 0.00 41.79 3.61
4544 4998 6.384258 TGCTGTGTTTCAATAGTTTAAGCA 57.616 33.333 0.00 0.00 34.77 3.91
4869 5521 8.395633 ACAGTGTGTATTTTCAACACTTAGTTC 58.604 33.333 5.00 0.00 45.95 3.01
4893 5552 5.119898 CGGCAATTCAATATAGCAGAGAGTC 59.880 44.000 0.00 0.00 0.00 3.36
4901 5560 8.083828 TCAATATAGCAGAGAGTCCTTTTCTT 57.916 34.615 0.00 0.00 0.00 2.52
5008 5749 7.588488 CGGTGTTATTTTGTTAGTGTTACCTTG 59.412 37.037 0.00 0.00 0.00 3.61
5067 5808 3.009723 TGATCCTGTGATTTTCGAAGCC 58.990 45.455 0.00 0.00 0.00 4.35
5078 5819 0.252761 TTCGAAGCCAGCATCATCCA 59.747 50.000 0.00 0.00 0.00 3.41
5317 6061 1.336125 GCATCAGGCTTTGTGGATAGC 59.664 52.381 0.00 0.00 40.25 2.97
5350 6094 7.878621 AAGGGATGATATCTTCCATCAACTA 57.121 36.000 29.25 0.00 40.75 2.24
5407 6151 4.105577 TCCCACCTGCTGGTTATAACTTA 58.894 43.478 13.36 4.56 46.05 2.24
5416 6160 6.591935 TGCTGGTTATAACTTAGATCCCTTG 58.408 40.000 15.05 0.00 0.00 3.61
5429 6173 0.846427 TCCCTTGGGATTGCTGGACT 60.846 55.000 3.91 0.00 0.00 3.85
5446 6190 5.589452 GCTGGACTCAGATCAAAGAATTCAT 59.411 40.000 8.44 0.00 43.49 2.57
5476 6220 4.415881 TCTGGATTGGTATTACATGCGT 57.584 40.909 0.00 0.00 0.00 5.24
5546 6290 0.671781 CCTTGAGGCTGGTCAGAACG 60.672 60.000 0.00 0.00 0.00 3.95
5575 6319 2.941720 GCTAGCAAGGGAAACATCTGAG 59.058 50.000 10.63 0.00 0.00 3.35
5590 6334 8.859236 AAACATCTGAGATTGAAGAAGATGAA 57.141 30.769 15.74 0.00 44.53 2.57
5796 6543 8.057011 AGCATTTGGATATCATAATATGGCAGA 58.943 33.333 4.83 0.00 0.00 4.26
5800 6547 9.585369 TTTGGATATCATAATATGGCAGACAAA 57.415 29.630 4.83 5.21 0.00 2.83
5824 6574 2.240414 TCATTCCAGCCATCACAGTGAT 59.760 45.455 10.53 10.53 37.65 3.06
5848 6598 0.556258 TATCAGAGGGAAGCGAGGGA 59.444 55.000 0.00 0.00 0.00 4.20
5983 6733 2.028476 TCATTTCACCGATGAACGACCT 60.028 45.455 0.00 0.00 44.66 3.85
5986 6736 0.896479 TCACCGATGAACGACCTGGA 60.896 55.000 0.00 0.00 45.77 3.86
6078 6828 3.399330 CAGTGTAGGCTCGAAAAAGGAA 58.601 45.455 0.00 0.00 0.00 3.36
6121 6874 4.017877 GCTTGCTCGTGCGCTGTT 62.018 61.111 9.73 0.00 43.34 3.16
6127 6880 1.491563 CTCGTGCGCTGTTGTAACC 59.508 57.895 9.73 0.00 0.00 2.85
6149 6902 2.935955 GTGTGAACCACGCCTTCG 59.064 61.111 0.00 0.00 38.73 3.79
6378 7136 2.028020 ACTTTCCTGAGAGGGTTTAGCG 60.028 50.000 0.00 0.00 35.59 4.26
6383 7141 2.496470 CCTGAGAGGGTTTAGCGTTAGT 59.504 50.000 0.00 0.00 0.00 2.24
6398 7156 5.479306 AGCGTTAGTTGTCACATAATGAGT 58.521 37.500 0.00 0.00 38.28 3.41
6399 7157 6.627243 AGCGTTAGTTGTCACATAATGAGTA 58.373 36.000 0.00 0.00 38.28 2.59
6400 7158 6.530534 AGCGTTAGTTGTCACATAATGAGTAC 59.469 38.462 0.00 0.00 38.28 2.73
6423 7226 5.958380 ACTAGTAACTGTTGATCCCATGAGA 59.042 40.000 2.69 0.00 0.00 3.27
6431 7234 2.052468 TGATCCCATGAGATGTGGAGG 58.948 52.381 0.00 0.00 39.12 4.30
6479 7282 2.185004 TTGGTAGCAAGTTCTGGAGC 57.815 50.000 2.54 0.00 0.00 4.70
6535 7338 1.734465 CCTCAGCATCCTTGTCGAAAC 59.266 52.381 0.00 0.00 0.00 2.78
6537 7340 1.347707 TCAGCATCCTTGTCGAAACCT 59.652 47.619 0.00 0.00 0.00 3.50
6538 7341 2.154462 CAGCATCCTTGTCGAAACCTT 58.846 47.619 0.00 0.00 0.00 3.50
6593 7396 2.027100 AGTAGGTAGGCAAAAGCAGGTC 60.027 50.000 0.00 0.00 0.00 3.85
6614 7417 2.164663 ATACGCGACATGTGCACCG 61.165 57.895 15.93 11.67 0.00 4.94
6640 7443 4.391869 GTCGAGACCAAAACCCCC 57.608 61.111 0.00 0.00 0.00 5.40
6685 7488 2.586792 GGGCCGCTTCAGATCTGT 59.413 61.111 21.92 0.00 0.00 3.41
6716 7519 3.775654 CAGGAGCCCCTCGACACC 61.776 72.222 0.00 0.00 42.02 4.16
6736 7539 1.669999 GCCACTCAATGCCACCCATC 61.670 60.000 0.00 0.00 31.43 3.51
6739 7542 1.456331 CTCAATGCCACCCATCCCC 60.456 63.158 0.00 0.00 31.43 4.81
6742 7545 3.684369 AATGCCACCCATCCCCAGC 62.684 63.158 0.00 0.00 31.43 4.85
6747 7550 3.402681 ACCCATCCCCAGCACGAG 61.403 66.667 0.00 0.00 0.00 4.18
6768 7571 2.592287 TTTCCCCCAACGCACGAC 60.592 61.111 0.00 0.00 0.00 4.34
6830 7681 9.705290 GTAACCAACCATGATTTTACATTTTCT 57.295 29.630 0.00 0.00 0.00 2.52
6831 7682 8.606040 AACCAACCATGATTTTACATTTTCTG 57.394 30.769 0.00 0.00 0.00 3.02
6832 7683 7.961351 ACCAACCATGATTTTACATTTTCTGA 58.039 30.769 0.00 0.00 0.00 3.27
6860 7711 2.504367 GTAACCAACCATGACAGCAGT 58.496 47.619 0.00 0.00 0.00 4.40
6861 7712 2.949177 AACCAACCATGACAGCAGTA 57.051 45.000 0.00 0.00 0.00 2.74
6872 7723 2.422479 TGACAGCAGTAGTACGATCCAC 59.578 50.000 0.00 0.00 0.00 4.02
6873 7724 2.683867 GACAGCAGTAGTACGATCCACT 59.316 50.000 0.00 0.71 0.00 4.00
6902 7753 0.744281 GGAGAGAGAGAGGCCTTTCG 59.256 60.000 17.11 0.00 0.00 3.46
6937 7788 6.653526 ACTTGTGGTTGATTGATTCATTGA 57.346 33.333 0.00 0.00 33.34 2.57
6938 7789 7.235935 ACTTGTGGTTGATTGATTCATTGAT 57.764 32.000 0.00 0.00 33.34 2.57
6939 7790 7.673180 ACTTGTGGTTGATTGATTCATTGATT 58.327 30.769 0.00 0.00 33.34 2.57
6940 7791 8.805175 ACTTGTGGTTGATTGATTCATTGATTA 58.195 29.630 0.00 0.00 33.34 1.75
6997 7848 2.141517 CCATTTCCTCGCTCATGCTAG 58.858 52.381 0.00 0.00 36.97 3.42
6999 7850 0.826715 TTTCCTCGCTCATGCTAGCT 59.173 50.000 17.23 0.00 40.49 3.32
7000 7851 0.103755 TTCCTCGCTCATGCTAGCTG 59.896 55.000 17.23 11.65 40.49 4.24
7001 7852 1.039785 TCCTCGCTCATGCTAGCTGT 61.040 55.000 17.23 1.42 40.49 4.40
7002 7853 0.670706 CCTCGCTCATGCTAGCTGTA 59.329 55.000 17.23 0.00 40.49 2.74
7019 7883 3.231160 CTGTAAATTTCCCGCACGTTTC 58.769 45.455 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.756903 ATGGAAGGAATCGTACGGGG 59.243 55.000 16.52 0.00 0.00 5.73
73 74 0.675837 AAGAGACGTGACGGGATCGA 60.676 55.000 10.66 0.00 40.11 3.59
114 115 2.534042 AGACGATGAGAGGGGAAGAA 57.466 50.000 0.00 0.00 0.00 2.52
141 143 3.659089 AAGGGGAATCGGACGCACG 62.659 63.158 0.00 0.00 0.00 5.34
456 698 4.880120 AGCATGATCATCACAACCACTAAG 59.120 41.667 4.86 0.00 0.00 2.18
504 747 3.802948 ACTTGTAGCAGAATCCCTACG 57.197 47.619 4.85 0.00 37.36 3.51
514 757 3.741344 ACGTTTGAGCTAACTTGTAGCAG 59.259 43.478 8.00 0.00 42.68 4.24
596 839 1.344763 CCATCTCCTCCCACGTATTCC 59.655 57.143 0.00 0.00 0.00 3.01
617 860 1.096386 AGAGGCCTAGCGTAGTCGTG 61.096 60.000 4.42 0.00 39.49 4.35
618 861 0.394080 AAGAGGCCTAGCGTAGTCGT 60.394 55.000 4.42 0.00 39.49 4.34
696 948 4.495472 CAGTTAGGCGCAAATCAATTAACG 59.505 41.667 10.83 0.00 0.00 3.18
780 1034 0.879765 CAAGGGCAAGCTCTGAACAG 59.120 55.000 0.00 0.00 0.00 3.16
847 1101 5.490159 ACGGGTATGGTAAATCGAAGAAAA 58.510 37.500 0.00 0.00 43.58 2.29
1119 1373 2.567615 ACTTGGCAATCTTCGGTAGTCT 59.432 45.455 0.00 0.00 0.00 3.24
1266 1520 6.934645 GGATCTCGATTATCCATTTGGTAACA 59.065 38.462 17.78 0.00 43.62 2.41
1293 1547 3.744426 AGCACACCGTAAACAGTACATTC 59.256 43.478 0.00 0.00 0.00 2.67
1604 1868 2.277247 GCGCACACACACACACAC 60.277 61.111 0.30 0.00 0.00 3.82
1605 1869 3.858989 CGCGCACACACACACACA 61.859 61.111 8.75 0.00 0.00 3.72
1606 1870 3.860125 ACGCGCACACACACACAC 61.860 61.111 5.73 0.00 0.00 3.82
1607 1871 3.858989 CACGCGCACACACACACA 61.859 61.111 5.73 0.00 0.00 3.72
1633 1897 4.918060 CACACGCACACGCACACG 62.918 66.667 0.00 0.00 45.53 4.49
1634 1898 4.589700 CCACACGCACACGCACAC 62.590 66.667 0.00 0.00 45.53 3.82
1640 1904 3.582120 CCACACCCACACGCACAC 61.582 66.667 0.00 0.00 0.00 3.82
1641 1905 4.866224 CCCACACCCACACGCACA 62.866 66.667 0.00 0.00 0.00 4.57
1642 1906 4.868116 ACCCACACCCACACGCAC 62.868 66.667 0.00 0.00 0.00 5.34
1643 1907 4.866224 CACCCACACCCACACGCA 62.866 66.667 0.00 0.00 0.00 5.24
1644 1908 4.868116 ACACCCACACCCACACGC 62.868 66.667 0.00 0.00 0.00 5.34
1645 1909 2.899838 CACACCCACACCCACACG 60.900 66.667 0.00 0.00 0.00 4.49
1646 1910 2.518349 CCACACCCACACCCACAC 60.518 66.667 0.00 0.00 0.00 3.82
1647 1911 3.814906 CCCACACCCACACCCACA 61.815 66.667 0.00 0.00 0.00 4.17
1648 1912 3.816090 ACCCACACCCACACCCAC 61.816 66.667 0.00 0.00 0.00 4.61
1649 1913 3.814906 CACCCACACCCACACCCA 61.815 66.667 0.00 0.00 0.00 4.51
1650 1914 3.816090 ACACCCACACCCACACCC 61.816 66.667 0.00 0.00 0.00 4.61
1651 1915 2.518349 CACACCCACACCCACACC 60.518 66.667 0.00 0.00 0.00 4.16
1652 1916 2.518349 CCACACCCACACCCACAC 60.518 66.667 0.00 0.00 0.00 3.82
1653 1917 3.814906 CCCACACCCACACCCACA 61.815 66.667 0.00 0.00 0.00 4.17
1654 1918 3.816090 ACCCACACCCACACCCAC 61.816 66.667 0.00 0.00 0.00 4.61
1655 1919 3.814906 CACCCACACCCACACCCA 61.815 66.667 0.00 0.00 0.00 4.51
1656 1920 3.816090 ACACCCACACCCACACCC 61.816 66.667 0.00 0.00 0.00 4.61
1657 1921 2.518349 CACACCCACACCCACACC 60.518 66.667 0.00 0.00 0.00 4.16
1658 1922 2.518349 CCACACCCACACCCACAC 60.518 66.667 0.00 0.00 0.00 3.82
1659 1923 3.814906 CCCACACCCACACCCACA 61.815 66.667 0.00 0.00 0.00 4.17
1660 1924 3.816090 ACCCACACCCACACCCAC 61.816 66.667 0.00 0.00 0.00 4.61
1661 1925 3.814906 CACCCACACCCACACCCA 61.815 66.667 0.00 0.00 0.00 4.51
1662 1926 3.816090 ACACCCACACCCACACCC 61.816 66.667 0.00 0.00 0.00 4.61
1663 1927 2.518349 CACACCCACACCCACACC 60.518 66.667 0.00 0.00 0.00 4.16
1664 1928 2.118404 CACACACCCACACCCACAC 61.118 63.158 0.00 0.00 0.00 3.82
1665 1929 2.273776 CACACACCCACACCCACA 59.726 61.111 0.00 0.00 0.00 4.17
1666 1930 2.118404 CACACACACCCACACCCAC 61.118 63.158 0.00 0.00 0.00 4.61
1667 1931 2.273776 CACACACACCCACACCCA 59.726 61.111 0.00 0.00 0.00 4.51
1668 1932 2.518349 CCACACACACCCACACCC 60.518 66.667 0.00 0.00 0.00 4.61
1669 1933 2.518349 CCCACACACACCCACACC 60.518 66.667 0.00 0.00 0.00 4.16
1670 1934 2.118404 CACCCACACACACCCACAC 61.118 63.158 0.00 0.00 0.00 3.82
1671 1935 2.273776 CACCCACACACACCCACA 59.726 61.111 0.00 0.00 0.00 4.17
1672 1936 2.118404 CACACCCACACACACCCAC 61.118 63.158 0.00 0.00 0.00 4.61
1673 1937 2.273776 CACACCCACACACACCCA 59.726 61.111 0.00 0.00 0.00 4.51
1674 1938 2.518349 CCACACCCACACACACCC 60.518 66.667 0.00 0.00 0.00 4.61
1675 1939 2.518349 CCCACACCCACACACACC 60.518 66.667 0.00 0.00 0.00 4.16
1676 1940 2.118404 CACCCACACCCACACACAC 61.118 63.158 0.00 0.00 0.00 3.82
1677 1941 2.273776 CACCCACACCCACACACA 59.726 61.111 0.00 0.00 0.00 3.72
1678 1942 2.118404 CACACCCACACCCACACAC 61.118 63.158 0.00 0.00 0.00 3.82
1679 1943 2.273776 CACACCCACACCCACACA 59.726 61.111 0.00 0.00 0.00 3.72
1680 1944 2.118404 CACACACCCACACCCACAC 61.118 63.158 0.00 0.00 0.00 3.82
1681 1945 2.273776 CACACACCCACACCCACA 59.726 61.111 0.00 0.00 0.00 4.17
1682 1946 2.118404 CACACACACCCACACCCAC 61.118 63.158 0.00 0.00 0.00 4.61
1683 1947 2.273776 CACACACACCCACACCCA 59.726 61.111 0.00 0.00 0.00 4.51
1684 1948 2.118404 CACACACACACCCACACCC 61.118 63.158 0.00 0.00 0.00 4.61
1685 1949 1.377987 ACACACACACACCCACACC 60.378 57.895 0.00 0.00 0.00 4.16
1686 1950 0.958382 ACACACACACACACCCACAC 60.958 55.000 0.00 0.00 0.00 3.82
1687 1951 0.957888 CACACACACACACACCCACA 60.958 55.000 0.00 0.00 0.00 4.17
1688 1952 0.958382 ACACACACACACACACCCAC 60.958 55.000 0.00 0.00 0.00 4.61
1689 1953 0.957888 CACACACACACACACACCCA 60.958 55.000 0.00 0.00 0.00 4.51
1690 1954 0.958382 ACACACACACACACACACCC 60.958 55.000 0.00 0.00 0.00 4.61
1691 1955 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
2269 2539 3.815133 AGCTTACATGGGCTGATGG 57.185 52.632 8.83 0.00 37.41 3.51
2276 2546 2.423538 GTGGCTTAACAGCTTACATGGG 59.576 50.000 0.00 0.00 46.44 4.00
2642 2912 0.963962 CCACTTGCTGCATCCTTGTT 59.036 50.000 1.84 0.00 0.00 2.83
2671 2941 8.368668 ACTAACATCTAAGGCAATGTATCCTAC 58.631 37.037 0.00 0.00 35.10 3.18
2697 2967 3.026707 TGCATCTGTAGCCTGTAGGTA 57.973 47.619 0.00 0.00 37.57 3.08
2737 3007 2.192711 TGCACACTGGAAGCTGCA 59.807 55.556 1.02 0.00 45.55 4.41
2760 3030 1.808945 CTTGCTAAGCTTCACAGTGGG 59.191 52.381 0.00 0.00 0.00 4.61
2826 3097 4.647611 TCGCCAATAGAGAAAACTCCAAA 58.352 39.130 0.00 0.00 0.00 3.28
2827 3098 4.280436 TCGCCAATAGAGAAAACTCCAA 57.720 40.909 0.00 0.00 0.00 3.53
2828 3099 3.973206 TCGCCAATAGAGAAAACTCCA 57.027 42.857 0.00 0.00 0.00 3.86
3290 3564 4.270325 GCAGTTGAGTTTTAGAGACAACGT 59.730 41.667 0.00 0.00 43.36 3.99
3352 3626 1.750206 TGCACAGCACTGTTGTTCATT 59.250 42.857 0.00 0.00 42.83 2.57
3565 3843 9.696917 AATCTTCAAAAGTTATGGATGTGAAAC 57.303 29.630 0.00 0.00 37.35 2.78
3762 4040 3.915437 TCAAATTCTTTCCGAACCAGC 57.085 42.857 0.00 0.00 33.72 4.85
3970 4254 8.302438 AGCTGAAAGAGATGAATAAAAACTTGG 58.698 33.333 0.00 0.00 34.07 3.61
3982 4267 6.114187 TCAACCTTTAGCTGAAAGAGATGA 57.886 37.500 13.83 11.81 46.57 2.92
4011 4296 9.647797 CTAAACACCAAAACTAACCTTTCTTTT 57.352 29.630 0.00 0.00 0.00 2.27
4101 4552 0.758734 CTGGACCTCAACCACTGACA 59.241 55.000 0.00 0.00 33.57 3.58
4164 4616 8.589338 ACAATATAACAAGACACTTCTCAGAGT 58.411 33.333 0.00 0.00 0.00 3.24
4230 4682 5.178797 AGTAAGGAGTGATGAAAATGGACG 58.821 41.667 0.00 0.00 0.00 4.79
4315 4769 8.894731 TCACAGCTGTTACAAAATACAAAACTA 58.105 29.630 18.94 0.00 0.00 2.24
4318 4772 9.593134 AATTCACAGCTGTTACAAAATACAAAA 57.407 25.926 18.94 0.00 0.00 2.44
4319 4773 9.243637 GAATTCACAGCTGTTACAAAATACAAA 57.756 29.630 18.94 0.00 0.00 2.83
4320 4774 8.629158 AGAATTCACAGCTGTTACAAAATACAA 58.371 29.630 18.94 0.00 0.00 2.41
4321 4775 8.165239 AGAATTCACAGCTGTTACAAAATACA 57.835 30.769 18.94 0.00 0.00 2.29
4465 4919 5.013079 ACAAAGATAGATGGTCACTTGGTCA 59.987 40.000 0.00 0.00 0.00 4.02
4471 4925 5.181748 GCTCAACAAAGATAGATGGTCACT 58.818 41.667 0.00 0.00 0.00 3.41
4472 4926 4.333926 GGCTCAACAAAGATAGATGGTCAC 59.666 45.833 0.00 0.00 0.00 3.67
4544 4998 3.809832 CCGTGTCTTCTGAAGTCAAACAT 59.190 43.478 16.78 0.00 0.00 2.71
4869 5521 4.993584 ACTCTCTGCTATATTGAATTGCCG 59.006 41.667 0.00 0.00 0.00 5.69
4984 5725 9.228636 CACAAGGTAACACTAACAAAATAACAC 57.771 33.333 0.00 0.00 41.41 3.32
5008 5749 1.539827 GCATTGTCCCACTACAACCAC 59.460 52.381 0.00 0.00 41.89 4.16
5067 5808 6.206243 CCTAGTTAGGAAAATGGATGATGCTG 59.794 42.308 0.00 0.00 46.63 4.41
5078 5819 4.881157 ATGGTGGCCTAGTTAGGAAAAT 57.119 40.909 3.32 0.00 46.63 1.82
5156 5900 6.751157 TCTGAAAACTGCAAACAATCATGAT 58.249 32.000 1.18 1.18 0.00 2.45
5157 5901 6.146601 TCTGAAAACTGCAAACAATCATGA 57.853 33.333 0.00 0.00 0.00 3.07
5161 5905 5.343249 ACACTCTGAAAACTGCAAACAATC 58.657 37.500 0.00 0.00 0.00 2.67
5212 5956 6.280855 AGGTTATGTAAGAATTGTTTGCCC 57.719 37.500 0.00 0.00 0.00 5.36
5317 6061 5.301835 AGATATCATCCCTTTGACCTGTG 57.698 43.478 5.32 0.00 0.00 3.66
5350 6094 4.964262 TGGTTACGGATAATACTTGGGAGT 59.036 41.667 0.00 0.00 39.97 3.85
5416 6160 1.487976 TGATCTGAGTCCAGCAATCCC 59.512 52.381 0.00 0.00 40.20 3.85
5476 6220 4.532126 ACTCTATCCAAGTGTGGTGAATGA 59.468 41.667 0.00 0.00 46.11 2.57
5499 6243 1.885887 CGTCAAAATGGGGAGCTTCAA 59.114 47.619 0.00 0.00 0.00 2.69
5546 6290 0.036010 TCCCTTGCTAGCTGACTTGC 60.036 55.000 17.23 0.00 43.86 4.01
5554 6298 2.941720 CTCAGATGTTTCCCTTGCTAGC 59.058 50.000 8.10 8.10 0.00 3.42
5590 6334 8.693120 TTCCGTACAGATCAGAGTAATAATCT 57.307 34.615 0.00 0.00 0.00 2.40
5796 6543 3.256631 GTGATGGCTGGAATGACTTTTGT 59.743 43.478 0.00 0.00 0.00 2.83
5800 6547 2.040813 ACTGTGATGGCTGGAATGACTT 59.959 45.455 0.00 0.00 0.00 3.01
5824 6574 4.019858 CCTCGCTTCCCTCTGATATATCA 58.980 47.826 14.64 14.64 35.16 2.15
5848 6598 2.042537 TCGCCCTGCTCCAGATCT 60.043 61.111 0.00 0.00 32.44 2.75
6121 6874 1.065636 TGGTTCACACAACCGGTTACA 60.066 47.619 21.79 6.31 43.15 2.41
6149 6902 3.808728 TGCCAGCTTATCATGAAGGTAC 58.191 45.455 0.00 0.00 35.44 3.34
6151 6904 3.370840 TTGCCAGCTTATCATGAAGGT 57.629 42.857 0.00 0.00 37.65 3.50
6152 6905 4.500887 CCATTTGCCAGCTTATCATGAAGG 60.501 45.833 0.00 0.00 0.00 3.46
6295 7048 6.591935 ACTTGTGAGGAAGTATCAAACAGAA 58.408 36.000 0.00 0.00 34.29 3.02
6329 7087 3.688272 CGTAGCAGATTGATTTTGCCTG 58.312 45.455 0.00 0.00 38.58 4.85
6398 7156 7.123383 TCTCATGGGATCAACAGTTACTAGTA 58.877 38.462 0.00 0.00 0.00 1.82
6399 7157 5.958380 TCTCATGGGATCAACAGTTACTAGT 59.042 40.000 0.00 0.00 0.00 2.57
6400 7158 6.471233 TCTCATGGGATCAACAGTTACTAG 57.529 41.667 0.00 0.00 0.00 2.57
6423 7226 3.828451 CCTTCAAAATGACACCTCCACAT 59.172 43.478 0.00 0.00 0.00 3.21
6431 7234 0.608130 GGGGGCCTTCAAAATGACAC 59.392 55.000 0.84 0.00 0.00 3.67
6490 7293 1.377856 GCTTCTTGTCTGGCCCTCC 60.378 63.158 0.00 0.00 0.00 4.30
6602 7405 1.571919 GGATACTCGGTGCACATGTC 58.428 55.000 20.43 8.33 0.00 3.06
6646 7449 1.863454 GCATGTCTATCAGCTTGTCCG 59.137 52.381 0.00 0.00 0.00 4.79
6739 7542 3.423154 GGGAAACCGCTCGTGCTG 61.423 66.667 7.97 3.47 43.64 4.41
6785 7588 3.895232 ACCATCAGCGAATTACAGACT 57.105 42.857 0.00 0.00 0.00 3.24
6786 7589 4.270325 GGTTACCATCAGCGAATTACAGAC 59.730 45.833 0.00 0.00 0.00 3.51
6788 7591 4.188462 TGGTTACCATCAGCGAATTACAG 58.812 43.478 0.00 0.00 0.00 2.74
6791 7642 3.942748 GGTTGGTTACCATCAGCGAATTA 59.057 43.478 4.38 0.00 46.92 1.40
6795 7646 3.543884 GGTTGGTTACCATCAGCGA 57.456 52.632 4.38 0.00 46.92 4.93
6815 7666 8.859090 ACCAACTCATCAGAAAATGTAAAATCA 58.141 29.630 0.00 0.00 0.00 2.57
6857 7708 3.503827 TTGCAGTGGATCGTACTACTG 57.496 47.619 17.64 17.64 46.85 2.74
6858 7709 4.737855 AATTGCAGTGGATCGTACTACT 57.262 40.909 1.46 0.00 32.04 2.57
6859 7710 4.494199 GCAAATTGCAGTGGATCGTACTAC 60.494 45.833 13.73 0.00 44.26 2.73
6860 7711 3.621268 GCAAATTGCAGTGGATCGTACTA 59.379 43.478 13.73 0.00 44.26 1.82
6861 7712 2.420022 GCAAATTGCAGTGGATCGTACT 59.580 45.455 13.73 0.00 44.26 2.73
6872 7723 1.664659 CTCTCTCTCCGCAAATTGCAG 59.335 52.381 18.65 6.83 45.36 4.41
6873 7724 1.276138 TCTCTCTCTCCGCAAATTGCA 59.724 47.619 18.65 0.00 45.36 4.08
6883 7734 0.744281 CGAAAGGCCTCTCTCTCTCC 59.256 60.000 5.23 0.00 0.00 3.71
6886 7737 4.825377 GCGAAAGGCCTCTCTCTC 57.175 61.111 5.23 0.00 34.80 3.20
6902 7753 0.385390 CCACAAGTTGACAACTGGGC 59.615 55.000 23.64 0.00 41.91 5.36
6934 7785 9.562583 GCCATCGTTACAGTTTAATTTAATCAA 57.437 29.630 0.00 0.00 0.00 2.57
6935 7786 8.952278 AGCCATCGTTACAGTTTAATTTAATCA 58.048 29.630 0.00 0.00 0.00 2.57
6936 7787 9.221775 CAGCCATCGTTACAGTTTAATTTAATC 57.778 33.333 0.00 0.00 0.00 1.75
6937 7788 7.700656 GCAGCCATCGTTACAGTTTAATTTAAT 59.299 33.333 0.00 0.00 0.00 1.40
6938 7789 7.024768 GCAGCCATCGTTACAGTTTAATTTAA 58.975 34.615 0.00 0.00 0.00 1.52
6939 7790 6.403855 GGCAGCCATCGTTACAGTTTAATTTA 60.404 38.462 6.55 0.00 0.00 1.40
6940 7791 5.399013 GCAGCCATCGTTACAGTTTAATTT 58.601 37.500 0.00 0.00 0.00 1.82
6949 7800 1.447140 GTCGGCAGCCATCGTTACA 60.447 57.895 13.30 0.00 0.00 2.41
6997 7848 0.519961 ACGTGCGGGAAATTTACAGC 59.480 50.000 17.57 17.57 0.00 4.40
6999 7850 2.349627 CGAAACGTGCGGGAAATTTACA 60.350 45.455 2.10 0.00 0.00 2.41
7000 7851 2.235855 CGAAACGTGCGGGAAATTTAC 58.764 47.619 3.40 0.00 0.00 2.01
7001 7852 1.399984 GCGAAACGTGCGGGAAATTTA 60.400 47.619 12.18 0.00 0.00 1.40
7002 7853 0.662077 GCGAAACGTGCGGGAAATTT 60.662 50.000 12.18 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.