Multiple sequence alignment - TraesCS4B01G219500

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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 TraesCS4B01G219500 chr4B 100.000 2276 0 0 1 2276 462216963 462214688 0.000000e+00 4204
1 TraesCS4B01G219500 chr4D 93.177 1920 91 15 376 2276 375123935 375122037 0.000000e+00 2784
2 TraesCS4B01G219500 chr4D 93.557 357 21 2 1 356 375124475 375124120 4.300000e-147 531
3 TraesCS4B01G219500 chr4A 90.968 2004 138 25 1 1993 89443704 89445675 0.000000e+00 2658
4 TraesCS4B01G219500 chr4A 91.781 292 11 3 1986 2276 89445867 89446146 5.890000e-106 394
5 TraesCS4B01G219500 chr5B 86.802 394 36 11 1892 2276 74990745 74991131 2.090000e-115 425
6 TraesCS4B01G219500 chr5D 84.130 460 43 17 1825 2275 69098223 69098661 3.500000e-113 418
7 TraesCS4B01G219500 chr5A 84.017 463 42 18 1825 2276 59702715 59703156 1.260000e-112 416


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 TraesCS4B01G219500 chr4B 462214688 462216963 2275 True 4204.0 4204 100.0000 1 2276 1 chr4B.!!$R1 2275
1 TraesCS4B01G219500 chr4D 375122037 375124475 2438 True 1657.5 2784 93.3670 1 2276 2 chr4D.!!$R1 2275
2 TraesCS4B01G219500 chr4A 89443704 89446146 2442 False 1526.0 2658 91.3745 1 2276 2 chr4A.!!$F1 2275

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
910 1082 0.179045 AGCAAACCTCGACTTGTGCT 60.179 50.0 0.98 0.98 37.5 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2553 0.396695 CCCAAGCTGGCATCCTGATT 60.397 55.0 0.0 0.0 35.79 2.57 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
194 198 6.097981 ACTGTGCATCATTCTTCAGATAGAGA 59.902 38.462 3.95 0.00 0.00 3.10
211 215 9.688592 CAGATAGAGAAAAAGAACAAAAATGCT 57.311 29.630 0.00 0.00 0.00 3.79
252 256 4.023193 GGTTATGGCATATTACACAGCACC 60.023 45.833 8.24 5.79 0.00 5.01
261 265 3.688694 TTACACAGCACCGGAATACTT 57.311 42.857 9.46 0.00 0.00 2.24
441 611 0.531974 ACACAATGCCCGCGTATAGG 60.532 55.000 4.92 0.00 0.00 2.57
608 778 2.735772 GCCCTCCATCTTCTCGCCA 61.736 63.158 0.00 0.00 0.00 5.69
626 796 1.144093 CCAGTATCTCCCTCCTCGACT 59.856 57.143 0.00 0.00 0.00 4.18
714 884 1.194781 AGAGCCCATCGTTCACACCT 61.195 55.000 0.00 0.00 0.00 4.00
731 901 3.997064 CTCGCCCAAGAGCCGAGTG 62.997 68.421 0.00 0.00 42.41 3.51
789 960 1.677633 GCACATAACCCCGCCAACT 60.678 57.895 0.00 0.00 0.00 3.16
791 962 1.677633 ACATAACCCCGCCAACTGC 60.678 57.895 0.00 0.00 0.00 4.40
801 972 1.202405 CCGCCAACTGCAGTTTTCTTT 60.202 47.619 29.23 4.82 41.33 2.52
803 974 1.594397 GCCAACTGCAGTTTTCTTTGC 59.406 47.619 29.23 19.04 40.77 3.68
826 997 0.337428 AGGTCCCCGAGGCTTTACTA 59.663 55.000 0.00 0.00 0.00 1.82
829 1000 0.632835 TCCCCGAGGCTTTACTAGGA 59.367 55.000 0.00 0.00 35.51 2.94
830 1001 0.751452 CCCCGAGGCTTTACTAGGAC 59.249 60.000 0.00 0.00 35.51 3.85
841 1012 4.654724 GCTTTACTAGGACAAGGGGTATCT 59.345 45.833 0.00 0.00 0.00 1.98
842 1013 5.837438 GCTTTACTAGGACAAGGGGTATCTA 59.163 44.000 0.00 0.00 0.00 1.98
843 1014 6.239261 GCTTTACTAGGACAAGGGGTATCTAC 60.239 46.154 0.00 0.00 0.00 2.59
844 1015 3.830121 ACTAGGACAAGGGGTATCTACG 58.170 50.000 0.00 0.00 0.00 3.51
845 1016 2.083628 AGGACAAGGGGTATCTACGG 57.916 55.000 0.00 0.00 0.00 4.02
860 1032 7.093858 GGGTATCTACGGAATAAGCTTCATAGT 60.094 40.741 0.00 0.83 0.00 2.12
869 1041 6.017026 GGAATAAGCTTCATAGTAAAGGGTGC 60.017 42.308 0.00 0.00 0.00 5.01
876 1048 3.376859 TCATAGTAAAGGGTGCATTTGCG 59.623 43.478 0.00 0.00 45.83 4.85
880 1052 2.368655 AAAGGGTGCATTTGCGAATC 57.631 45.000 0.00 0.00 45.83 2.52
887 1059 3.563808 GGTGCATTTGCGAATCTACCATA 59.436 43.478 18.05 0.00 45.83 2.74
888 1060 4.319766 GGTGCATTTGCGAATCTACCATAG 60.320 45.833 18.05 0.00 45.83 2.23
889 1061 3.250762 TGCATTTGCGAATCTACCATAGC 59.749 43.478 0.00 0.00 45.83 2.97
890 1062 3.250762 GCATTTGCGAATCTACCATAGCA 59.749 43.478 0.00 0.00 0.00 3.49
898 1070 4.260784 CGAATCTACCATAGCAAGCAAACC 60.261 45.833 0.00 0.00 0.00 3.27
908 1080 1.597937 GCAAGCAAACCTCGACTTGTG 60.598 52.381 11.44 0.00 41.22 3.33
909 1081 0.663153 AAGCAAACCTCGACTTGTGC 59.337 50.000 0.00 0.00 0.00 4.57
910 1082 0.179045 AGCAAACCTCGACTTGTGCT 60.179 50.000 0.98 0.98 37.50 4.40
911 1083 1.070134 AGCAAACCTCGACTTGTGCTA 59.930 47.619 4.63 0.00 40.40 3.49
912 1084 1.194772 GCAAACCTCGACTTGTGCTAC 59.805 52.381 0.00 0.00 0.00 3.58
913 1085 1.798813 CAAACCTCGACTTGTGCTACC 59.201 52.381 0.00 0.00 0.00 3.18
914 1086 1.339097 AACCTCGACTTGTGCTACCT 58.661 50.000 0.00 0.00 0.00 3.08
987 1160 1.150567 CTTCTCCAGCCTTCATCGCG 61.151 60.000 0.00 0.00 0.00 5.87
1319 1495 0.464554 CCCGCCATCTCCTCCTTTTC 60.465 60.000 0.00 0.00 0.00 2.29
1321 1497 0.543749 CGCCATCTCCTCCTTTTCCT 59.456 55.000 0.00 0.00 0.00 3.36
1353 1529 5.348997 GGTCTGTGCTCTTTTATGTACTGTC 59.651 44.000 0.00 0.00 0.00 3.51
1354 1530 5.926542 GTCTGTGCTCTTTTATGTACTGTCA 59.073 40.000 0.00 0.00 0.00 3.58
1368 1544 5.500234 TGTACTGTCATAGTAGGGTTACGT 58.500 41.667 0.00 0.00 42.37 3.57
1377 1556 3.818180 AGTAGGGTTACGTCGATCTGAT 58.182 45.455 0.00 0.00 34.88 2.90
1381 1560 2.292569 GGGTTACGTCGATCTGATGCTA 59.707 50.000 0.00 0.00 37.08 3.49
1388 1567 6.260870 ACGTCGATCTGATGCTAATAGAAT 57.739 37.500 0.00 0.00 37.08 2.40
1395 1575 7.308169 CGATCTGATGCTAATAGAATTTTGCCA 60.308 37.037 0.00 0.00 0.00 4.92
1421 1601 3.825143 ATGTTTGCTGGATAATTGCCC 57.175 42.857 0.00 0.00 0.00 5.36
1506 1686 4.870991 TCGCATACCGATTTTACATGTGAA 59.129 37.500 9.11 3.21 41.89 3.18
1507 1687 5.351740 TCGCATACCGATTTTACATGTGAAA 59.648 36.000 17.02 17.02 41.89 2.69
1508 1688 6.037720 TCGCATACCGATTTTACATGTGAAAT 59.962 34.615 24.01 24.01 41.89 2.17
1509 1689 6.690957 CGCATACCGATTTTACATGTGAAATT 59.309 34.615 24.42 14.34 40.02 1.82
1545 1725 9.998106 ATTGTGGCTTTAGAATTATCGTATAGT 57.002 29.630 0.00 0.00 0.00 2.12
1567 1747 1.529244 GCCCTGGTGTTCTTGCAGT 60.529 57.895 0.00 0.00 0.00 4.40
1598 1778 5.163195 ACCTTTGGCTATTACTACATCCCAG 60.163 44.000 0.00 0.00 0.00 4.45
1606 1786 6.814146 GCTATTACTACATCCCAGTAGCATTC 59.186 42.308 0.00 0.00 44.14 2.67
1628 1808 2.100197 TGCGCTACTCCATACTTGTCT 58.900 47.619 9.73 0.00 0.00 3.41
1706 1886 4.553938 CGTGTTACCCATCAACTGTTTGAC 60.554 45.833 0.00 0.00 44.66 3.18
1719 1899 6.526325 TCAACTGTTTGACGAAATGTTGAAAG 59.474 34.615 16.11 0.00 40.44 2.62
1731 1911 1.670730 TTGAAAGCGCGCATCCTCA 60.671 52.632 35.10 24.52 0.00 3.86
1814 1995 1.954382 CTGGCTATGCACCGAGTAGTA 59.046 52.381 0.00 0.00 0.00 1.82
1838 2019 1.909302 ACCAGAATGTCCTGATCCGTT 59.091 47.619 0.00 0.00 36.29 4.44
1862 2043 6.690530 TCAAGAAAAGGATAACATTGCAAGG 58.309 36.000 10.01 10.01 0.00 3.61
2077 2468 4.102210 AGCATTGCCACACTGAGACTATAT 59.898 41.667 4.70 0.00 0.00 0.86
2162 2553 1.042003 TGGTTGCTTCTTGCTTGCCA 61.042 50.000 0.00 0.00 43.37 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 176 7.783090 TTTCTCTATCTGAAGAATGATGCAC 57.217 36.000 0.00 0.00 0.00 4.57
209 213 8.827677 CATAACCTGTTACATTAGGAAGTAAGC 58.172 37.037 0.00 0.00 37.52 3.09
211 215 7.771826 GCCATAACCTGTTACATTAGGAAGTAA 59.228 37.037 0.00 0.00 37.52 2.24
212 216 7.092802 TGCCATAACCTGTTACATTAGGAAGTA 60.093 37.037 0.00 0.00 37.52 2.24
252 256 7.426929 AGATTGCTAGCATAAAAGTATTCCG 57.573 36.000 20.13 0.00 0.00 4.30
348 352 1.067516 CCCTTTGTTCAGCACAAGTGG 59.932 52.381 2.00 1.79 46.37 4.00
441 611 7.282450 ACTTGTTTATCGATTGACCCCTAATTC 59.718 37.037 1.71 0.00 0.00 2.17
533 703 2.044946 GGCCACTTCATCCGCCTT 60.045 61.111 0.00 0.00 38.41 4.35
608 778 2.938838 CAAGTCGAGGAGGGAGATACT 58.061 52.381 0.00 0.00 0.00 2.12
626 796 4.802051 GAGGATGCTGGGGCGCAA 62.802 66.667 10.83 0.00 44.06 4.85
731 901 2.962697 CTTTCGCTCCTAGGAGGCGC 62.963 65.000 34.75 23.01 42.48 6.53
736 906 0.968901 TTCCGCTTTCGCTCCTAGGA 60.969 55.000 11.98 11.98 0.00 2.94
757 927 2.437200 ATGTGCAAAACATCCGTTGG 57.563 45.000 0.00 0.00 44.51 3.77
758 928 3.672867 GGTTATGTGCAAAACATCCGTTG 59.327 43.478 9.32 0.00 44.51 4.10
789 960 0.248990 CTGCGGCAAAGAAAACTGCA 60.249 50.000 3.44 0.00 43.16 4.41
791 962 0.385390 ACCTGCGGCAAAGAAAACTG 59.615 50.000 3.44 0.00 0.00 3.16
809 980 0.751452 CCTAGTAAAGCCTCGGGGAC 59.249 60.000 4.80 0.00 33.58 4.46
814 985 2.159085 CCCTTGTCCTAGTAAAGCCTCG 60.159 54.545 0.00 0.00 0.00 4.63
826 997 1.572415 TCCGTAGATACCCCTTGTCCT 59.428 52.381 0.00 0.00 0.00 3.85
829 1000 4.040095 GCTTATTCCGTAGATACCCCTTGT 59.960 45.833 0.00 0.00 0.00 3.16
830 1001 4.283722 AGCTTATTCCGTAGATACCCCTTG 59.716 45.833 0.00 0.00 0.00 3.61
841 1012 7.070322 ACCCTTTACTATGAAGCTTATTCCGTA 59.930 37.037 0.00 0.00 0.00 4.02
842 1013 6.126854 ACCCTTTACTATGAAGCTTATTCCGT 60.127 38.462 0.00 0.00 0.00 4.69
843 1014 6.202954 CACCCTTTACTATGAAGCTTATTCCG 59.797 42.308 0.00 0.00 0.00 4.30
844 1015 6.017026 GCACCCTTTACTATGAAGCTTATTCC 60.017 42.308 0.00 0.00 0.00 3.01
845 1016 6.542370 TGCACCCTTTACTATGAAGCTTATTC 59.458 38.462 0.00 0.00 0.00 1.75
860 1032 3.088532 AGATTCGCAAATGCACCCTTTA 58.911 40.909 6.18 0.00 42.21 1.85
863 1035 2.017049 GTAGATTCGCAAATGCACCCT 58.983 47.619 6.18 0.00 42.21 4.34
869 1041 5.422666 TTGCTATGGTAGATTCGCAAATG 57.577 39.130 0.00 0.00 34.82 2.32
876 1048 4.884164 AGGTTTGCTTGCTATGGTAGATTC 59.116 41.667 0.00 0.00 0.00 2.52
880 1052 2.609459 CGAGGTTTGCTTGCTATGGTAG 59.391 50.000 0.00 0.00 0.00 3.18
887 1059 0.947244 CAAGTCGAGGTTTGCTTGCT 59.053 50.000 0.00 0.00 33.14 3.91
888 1060 0.663153 ACAAGTCGAGGTTTGCTTGC 59.337 50.000 10.20 0.00 41.22 4.01
889 1061 1.597937 GCACAAGTCGAGGTTTGCTTG 60.598 52.381 9.04 9.04 42.65 4.01
890 1062 0.663153 GCACAAGTCGAGGTTTGCTT 59.337 50.000 4.63 0.00 0.00 3.91
898 1070 2.743195 GCAGGTAGCACAAGTCGAG 58.257 57.895 0.00 0.00 44.79 4.04
1023 1199 2.526873 AGGGACAGCACCTCCGTT 60.527 61.111 0.00 0.00 31.01 4.44
1353 1529 4.753610 TCAGATCGACGTAACCCTACTATG 59.246 45.833 0.00 0.00 0.00 2.23
1354 1530 4.965814 TCAGATCGACGTAACCCTACTAT 58.034 43.478 0.00 0.00 0.00 2.12
1366 1542 7.573916 AAATTCTATTAGCATCAGATCGACG 57.426 36.000 0.00 0.00 0.00 5.12
1368 1544 7.095060 GGCAAAATTCTATTAGCATCAGATCGA 60.095 37.037 0.00 0.00 0.00 3.59
1388 1567 5.244851 TCCAGCAAACATAGTAATGGCAAAA 59.755 36.000 0.00 0.00 37.43 2.44
1395 1575 7.255942 GGGCAATTATCCAGCAAACATAGTAAT 60.256 37.037 0.00 0.00 0.00 1.89
1421 1601 3.531538 ACAATAGCAACCACCGTATCAG 58.468 45.455 0.00 0.00 0.00 2.90
1506 1686 8.107095 TCTAAAGCCACAATCAGGTAGTTAATT 58.893 33.333 0.00 0.00 0.00 1.40
1507 1687 7.630082 TCTAAAGCCACAATCAGGTAGTTAAT 58.370 34.615 0.00 0.00 0.00 1.40
1508 1688 7.011499 TCTAAAGCCACAATCAGGTAGTTAA 57.989 36.000 0.00 0.00 0.00 2.01
1509 1689 6.614694 TCTAAAGCCACAATCAGGTAGTTA 57.385 37.500 0.00 0.00 0.00 2.24
1545 1725 0.823356 GCAAGAACACCAGGGCAAGA 60.823 55.000 0.00 0.00 0.00 3.02
1567 1747 3.521937 AGTAATAGCCAAAGGTAGCACCA 59.478 43.478 7.86 0.00 41.95 4.17
1575 1755 5.163195 ACTGGGATGTAGTAATAGCCAAAGG 60.163 44.000 0.00 0.00 0.00 3.11
1606 1786 1.200483 CAAGTATGGAGTAGCGCACG 58.800 55.000 11.47 0.00 0.00 5.34
1628 1808 3.827876 ACACATTTGATCATGGTCAGCAA 59.172 39.130 9.00 1.95 0.00 3.91
1706 1886 0.996229 TGCGCGCTTTCAACATTTCG 60.996 50.000 33.29 0.00 0.00 3.46
1719 1899 1.358725 TTGTAACTGAGGATGCGCGC 61.359 55.000 27.26 27.26 0.00 6.86
1731 1911 3.181434 TGATCTGGTTTGGCCTTGTAACT 60.181 43.478 3.32 0.00 38.35 2.24
1814 1995 4.164221 ACGGATCAGGACATTCTGGTAAAT 59.836 41.667 0.00 0.00 35.58 1.40
1838 2019 6.690530 CCTTGCAATGTTATCCTTTTCTTGA 58.309 36.000 0.00 0.00 0.00 3.02
1855 2036 2.177394 TTATGACTCGTGCCTTGCAA 57.823 45.000 0.00 0.00 41.47 4.08
1862 2043 7.464830 AAGTTGTATACATTATGACTCGTGC 57.535 36.000 6.36 0.00 0.00 5.34
1898 2079 6.034898 GCCATATGCAGTTTGTGTTATTGAAC 59.965 38.462 0.00 0.00 40.77 3.18
2017 2400 4.017958 ACAGTATGAGAAGACCTCCTCTGA 60.018 45.833 0.00 0.00 41.25 3.27
2162 2553 0.396695 CCCAAGCTGGCATCCTGATT 60.397 55.000 0.00 0.00 35.79 2.57


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

AutoCloner maintained by Alex Coulton.