Multiple sequence alignment - TraesCS4B01G326500

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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 TraesCS4B01G326500 chr4B 100.000 2375 0 0 1 2375 617405128 617402754 0.000000e+00 4386.0
1 TraesCS4B01G326500 chr4B 92.950 1234 57 12 360 1582 617425031 617423817 0.000000e+00 1770.0
2 TraesCS4B01G326500 chr4B 90.784 727 45 12 1663 2375 617423816 617423098 0.000000e+00 952.0
3 TraesCS4B01G326500 chr4B 91.761 352 24 3 1 351 617425415 617425068 3.550000e-133 484.0
4 TraesCS4B01G326500 chr5A 88.527 1595 92 33 1 1569 665763505 665761976 0.000000e+00 1847.0
5 TraesCS4B01G326500 chr5A 77.778 243 46 8 497 734 429255323 429255562 2.460000e-30 143.0
6 TraesCS4B01G326500 chr4D 89.482 1217 54 23 360 1571 484722033 484720886 0.000000e+00 1471.0
7 TraesCS4B01G326500 chr4D 88.571 525 53 6 1611 2132 484716698 484716178 4.310000e-177 630.0
8 TraesCS4B01G326500 chr4D 94.068 354 19 2 1 353 484722424 484722072 9.660000e-149 536.0
9 TraesCS4B01G326500 chr4D 94.326 141 8 0 2124 2264 484716073 484715933 1.430000e-52 217.0
10 TraesCS4B01G326500 chr4D 78.970 233 43 6 507 734 445481342 445481573 1.140000e-33 154.0
11 TraesCS4B01G326500 chr4D 95.455 44 2 0 229 272 50887348 50887391 1.180000e-08 71.3
12 TraesCS4B01G326500 chr4A 82.677 254 30 9 507 750 602178682 602178931 1.850000e-51 213.0
13 TraesCS4B01G326500 chr5D 80.905 199 32 6 508 702 514920468 514920664 4.090000e-33 152.0
14 TraesCS4B01G326500 chr6D 80.402 199 33 6 507 701 57787197 57787393 1.900000e-31 147.0
15 TraesCS4B01G326500 chr6B 79.602 201 35 6 505 701 659589548 659589746 3.180000e-29 139.0
16 TraesCS4B01G326500 chr2D 82.178 101 13 4 2158 2257 273475097 273475001 5.440000e-12 82.4
17 TraesCS4B01G326500 chr2B 76.515 132 25 6 15 145 569016094 569015968 1.520000e-07 67.6
18 TraesCS4B01G326500 chr1A 95.238 42 2 0 231 272 99148197 99148238 1.520000e-07 67.6


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 TraesCS4B01G326500 chr4B 617402754 617405128 2374 True 4386.000000 4386 100.000000 1 2375 1 chr4B.!!$R1 2374
1 TraesCS4B01G326500 chr4B 617423098 617425415 2317 True 1068.666667 1770 91.831667 1 2375 3 chr4B.!!$R2 2374
2 TraesCS4B01G326500 chr5A 665761976 665763505 1529 True 1847.000000 1847 88.527000 1 1569 1 chr5A.!!$R1 1568
3 TraesCS4B01G326500 chr4D 484720886 484722424 1538 True 1003.500000 1471 91.775000 1 1571 2 chr4D.!!$R2 1570
4 TraesCS4B01G326500 chr4D 484715933 484716698 765 True 423.500000 630 91.448500 1611 2264 2 chr4D.!!$R1 653

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
630 706 0.523072 CGGAGGGCTCAACATGTTTG 59.477 55.0 8.77 6.17 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1917 0.102481 GTGTATCGCACTCCCGACAT 59.898 55.0 0.0 0.0 44.41 3.06 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
108 110 1.971481 TGCTTGAGTGTGTGATGCTT 58.029 45.000 0.00 0.00 0.00 3.91
133 135 8.177119 TGTGCTAAATTTGGTGAAGTTTAGAT 57.823 30.769 11.74 0.00 36.66 1.98
216 225 8.902040 AAACTTTCTCGCATATCTGAATTTTC 57.098 30.769 0.00 0.00 0.00 2.29
252 261 5.537674 AGCTTCTCAAATGTCCAAACTTCAT 59.462 36.000 0.00 0.00 0.00 2.57
294 304 4.393062 CCGCACTCAAACATCTTTCACTAT 59.607 41.667 0.00 0.00 0.00 2.12
448 493 5.505654 GCCACCCTAACATACATCAATTTCG 60.506 44.000 0.00 0.00 0.00 3.46
612 688 5.618056 ATGACCTATATTGCTTCAATGCG 57.382 39.130 2.57 0.00 35.54 4.73
630 706 0.523072 CGGAGGGCTCAACATGTTTG 59.477 55.000 8.77 6.17 0.00 2.93
788 873 1.884004 CGCGTACCCGGGGTAATTG 60.884 63.158 27.12 19.59 40.12 2.32
798 883 0.661020 GGGGTAATTGCCATCGAACG 59.339 55.000 14.98 0.00 0.00 3.95
799 884 1.375551 GGGTAATTGCCATCGAACGT 58.624 50.000 14.98 0.00 0.00 3.99
800 885 2.553086 GGGTAATTGCCATCGAACGTA 58.447 47.619 14.98 0.00 0.00 3.57
801 886 2.286025 GGGTAATTGCCATCGAACGTAC 59.714 50.000 14.98 0.00 0.00 3.67
802 887 3.192466 GGTAATTGCCATCGAACGTACT 58.808 45.455 7.82 0.00 0.00 2.73
803 888 3.244579 GGTAATTGCCATCGAACGTACTC 59.755 47.826 7.82 0.00 0.00 2.59
804 889 1.935933 ATTGCCATCGAACGTACTCC 58.064 50.000 0.00 0.00 0.00 3.85
870 955 0.610687 AAGGGGAGCTTCAACTCTCG 59.389 55.000 0.00 0.00 38.11 4.04
906 991 8.596293 TCTATATAAGCACAACATCATCCATCA 58.404 33.333 0.00 0.00 0.00 3.07
926 1011 1.043116 TCCTGGACATACTCTGCCCG 61.043 60.000 0.00 0.00 27.83 6.13
948 1044 2.231478 TCTCTGGTCCTAGCAAACGAAG 59.769 50.000 0.00 0.00 0.00 3.79
973 1069 4.101119 CCAAAACTATCTACCCATCCTCGT 59.899 45.833 0.00 0.00 0.00 4.18
988 1084 5.414454 CCATCCTCGTGGTTTATCAAGAAAA 59.586 40.000 2.99 0.00 34.46 2.29
1067 1163 1.405526 GCACGGAAATCCTACTGCAGA 60.406 52.381 23.35 2.95 32.25 4.26
1182 1280 8.994170 TCATTAACATTTTCGTGTGTTGAGATA 58.006 29.630 1.34 0.00 38.84 1.98
1266 1365 1.400142 CAGGACGTTTTGTGCAAGACA 59.600 47.619 6.44 0.00 42.22 3.41
1395 1501 0.674895 CCTTCTGAAGGTTCCAGCCG 60.675 60.000 25.13 0.00 43.95 5.52
1589 1700 2.590092 CGGCCCCTTCGGATTTCT 59.410 61.111 0.00 0.00 0.00 2.52
1590 1701 1.827394 CGGCCCCTTCGGATTTCTA 59.173 57.895 0.00 0.00 0.00 2.10
1591 1702 0.396811 CGGCCCCTTCGGATTTCTAT 59.603 55.000 0.00 0.00 0.00 1.98
1592 1703 1.608283 CGGCCCCTTCGGATTTCTATC 60.608 57.143 0.00 0.00 0.00 2.08
1593 1704 1.271434 GGCCCCTTCGGATTTCTATCC 60.271 57.143 0.00 0.00 45.89 2.59
1594 1705 1.700186 GCCCCTTCGGATTTCTATCCT 59.300 52.381 0.00 0.00 46.97 3.24
1595 1706 2.106684 GCCCCTTCGGATTTCTATCCTT 59.893 50.000 0.00 0.00 46.97 3.36
1596 1707 3.807561 GCCCCTTCGGATTTCTATCCTTC 60.808 52.174 0.00 0.00 46.97 3.46
1597 1708 3.244596 CCCCTTCGGATTTCTATCCTTCC 60.245 52.174 0.00 0.00 46.97 3.46
1598 1709 3.244596 CCCTTCGGATTTCTATCCTTCCC 60.245 52.174 0.00 0.00 46.97 3.97
1599 1710 3.648545 CCTTCGGATTTCTATCCTTCCCT 59.351 47.826 0.00 0.00 46.97 4.20
1600 1711 4.103311 CCTTCGGATTTCTATCCTTCCCTT 59.897 45.833 0.00 0.00 46.97 3.95
1601 1712 4.689612 TCGGATTTCTATCCTTCCCTTG 57.310 45.455 0.00 0.00 46.97 3.61
1602 1713 3.142174 CGGATTTCTATCCTTCCCTTGC 58.858 50.000 0.00 0.00 46.97 4.01
1603 1714 3.142174 GGATTTCTATCCTTCCCTTGCG 58.858 50.000 0.00 0.00 45.88 4.85
1604 1715 3.433740 GGATTTCTATCCTTCCCTTGCGT 60.434 47.826 0.00 0.00 45.88 5.24
1605 1716 4.202326 GGATTTCTATCCTTCCCTTGCGTA 60.202 45.833 0.00 0.00 45.88 4.42
1606 1717 3.814005 TTCTATCCTTCCCTTGCGTAC 57.186 47.619 0.00 0.00 0.00 3.67
1607 1718 2.037144 TCTATCCTTCCCTTGCGTACC 58.963 52.381 0.00 0.00 0.00 3.34
1608 1719 1.760613 CTATCCTTCCCTTGCGTACCA 59.239 52.381 0.00 0.00 0.00 3.25
1609 1720 1.213296 ATCCTTCCCTTGCGTACCAT 58.787 50.000 0.00 0.00 0.00 3.55
1687 1798 5.213891 TGCACATATGAACCATCTACGAT 57.786 39.130 10.38 0.00 0.00 3.73
1688 1799 4.990426 TGCACATATGAACCATCTACGATG 59.010 41.667 10.38 0.00 0.00 3.84
1692 1803 7.708322 GCACATATGAACCATCTACGATGATAT 59.292 37.037 10.38 0.00 0.00 1.63
1697 1808 7.049799 TGAACCATCTACGATGATATTGTGA 57.950 36.000 5.46 0.00 0.00 3.58
1701 1812 5.346011 CCATCTACGATGATATTGTGAACCG 59.654 44.000 5.46 0.00 0.00 4.44
1717 1828 0.033796 ACCGTAATCTCCCGTCCAGA 60.034 55.000 0.00 0.00 0.00 3.86
1773 1885 4.054825 GTGTACCCCGGCGTCGAA 62.055 66.667 12.93 0.00 39.00 3.71
1809 1921 4.783621 TGCCGGAGCAGCCATGTC 62.784 66.667 5.05 0.00 46.52 3.06
1815 1927 3.005539 AGCAGCCATGTCGGGAGT 61.006 61.111 0.00 0.00 34.06 3.85
1837 1949 0.657840 GATACACAAGACATGCCGGC 59.342 55.000 22.73 22.73 0.00 6.13
1855 1967 3.568430 CCGGCAAGAACTTTTAAGAACCT 59.432 43.478 0.00 0.00 0.00 3.50
1864 1976 6.260271 AGAACTTTTAAGAACCTGAAACCTCG 59.740 38.462 0.00 0.00 0.00 4.63
1893 2005 0.686769 GAGGGACCCTGTATGGACGT 60.687 60.000 20.90 0.00 38.35 4.34
1925 2037 1.624391 GGGCTTCCCTAGGTCAACCTA 60.624 57.143 8.29 8.58 42.23 3.08
1951 2063 1.392710 CCTATGGCCTCGAGGTTCGT 61.393 60.000 31.43 24.82 41.35 3.85
1968 2080 2.215196 TCGTTACCCTGCAACAAGAAC 58.785 47.619 0.00 0.00 0.00 3.01
2163 2389 8.170553 CCAAAAAGCAAATTAATCCATTTCGAG 58.829 33.333 0.00 0.00 0.00 4.04
2164 2390 7.832503 AAAAGCAAATTAATCCATTTCGAGG 57.167 32.000 0.00 0.00 0.00 4.63
2183 2409 4.026475 CGAGGAGACGAATAACTTTCATGC 60.026 45.833 0.00 0.00 35.09 4.06
2284 2511 1.886542 GGAAAATGTTCGGCCTTCAGT 59.113 47.619 0.00 0.00 34.28 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 110 7.575414 TCTAAACTTCACCAAATTTAGCACA 57.425 32.000 0.00 0.00 35.51 4.57
133 135 0.106868 TCTCACGGGCTCCTCGAATA 60.107 55.000 0.00 0.00 0.00 1.75
216 225 2.233271 TGAGAAGCTCTTGGCCAAAAG 58.767 47.619 20.91 17.84 43.05 2.27
252 261 1.543802 GGATGTCCGTGCCAAATTTGA 59.456 47.619 19.86 0.00 0.00 2.69
525 588 9.466497 TGCTCCTTTGAGTCTTTTTATATTGAT 57.534 29.630 0.00 0.00 40.95 2.57
570 645 5.284660 GTCATTGAATTGACGCTGTTTGATC 59.715 40.000 0.00 0.00 36.93 2.92
612 688 0.890683 CCAAACATGTTGAGCCCTCC 59.109 55.000 12.82 0.00 0.00 4.30
782 867 3.244579 GGAGTACGTTCGATGGCAATTAC 59.755 47.826 0.00 0.00 0.00 1.89
788 873 3.993103 CGGAGTACGTTCGATGGC 58.007 61.111 0.00 0.00 37.93 4.40
800 885 9.521841 TCAGATCATATCTTTTAGATACGGAGT 57.478 33.333 0.00 0.00 39.76 3.85
802 887 8.462811 GCTCAGATCATATCTTTTAGATACGGA 58.537 37.037 0.00 1.69 39.76 4.69
803 888 7.430793 CGCTCAGATCATATCTTTTAGATACGG 59.569 40.741 0.00 0.00 39.76 4.02
804 889 7.965655 ACGCTCAGATCATATCTTTTAGATACG 59.034 37.037 0.00 0.00 39.76 3.06
870 955 3.675698 GTGCTTATATAGAGTTCCTGCGC 59.324 47.826 0.00 0.00 0.00 6.09
926 1011 1.544691 TCGTTTGCTAGGACCAGAGAC 59.455 52.381 0.00 0.00 0.00 3.36
948 1044 3.138468 AGGATGGGTAGATAGTTTTGGGC 59.862 47.826 0.00 0.00 0.00 5.36
973 1069 8.519526 GGTATGTGATGTTTTCTTGATAAACCA 58.480 33.333 0.00 0.00 35.20 3.67
988 1084 1.475034 GGCGTCCATGGTATGTGATGT 60.475 52.381 12.58 0.00 0.00 3.06
1067 1163 2.156051 GAGAGAACACGAACCGGCCT 62.156 60.000 0.00 0.00 0.00 5.19
1157 1255 9.605955 TTATCTCAACACACGAAAATGTTAATG 57.394 29.630 0.00 0.00 36.92 1.90
1193 1292 3.612479 GCAATCCTCTGCACGAAAACAAT 60.612 43.478 0.00 0.00 42.17 2.71
1382 1481 2.815647 CGCTCGGCTGGAACCTTC 60.816 66.667 0.00 0.00 0.00 3.46
1395 1501 2.586792 AGGATGGCCTTGACGCTC 59.413 61.111 3.32 0.00 43.90 5.03
1583 1694 3.809905 ACGCAAGGGAAGGATAGAAATC 58.190 45.455 0.00 0.00 46.39 2.17
1584 1695 3.933861 ACGCAAGGGAAGGATAGAAAT 57.066 42.857 0.00 0.00 46.39 2.17
1585 1696 3.118519 GGTACGCAAGGGAAGGATAGAAA 60.119 47.826 0.00 0.00 46.39 2.52
1586 1697 2.433239 GGTACGCAAGGGAAGGATAGAA 59.567 50.000 0.00 0.00 46.39 2.10
1587 1698 2.037144 GGTACGCAAGGGAAGGATAGA 58.963 52.381 0.00 0.00 46.39 1.98
1588 1699 1.760613 TGGTACGCAAGGGAAGGATAG 59.239 52.381 0.00 0.00 46.39 2.08
1589 1700 1.868713 TGGTACGCAAGGGAAGGATA 58.131 50.000 0.00 0.00 46.39 2.59
1590 1701 1.134098 CATGGTACGCAAGGGAAGGAT 60.134 52.381 0.00 0.00 46.39 3.24
1591 1702 0.251916 CATGGTACGCAAGGGAAGGA 59.748 55.000 0.00 0.00 46.39 3.36
1592 1703 0.251916 TCATGGTACGCAAGGGAAGG 59.748 55.000 0.00 0.00 46.39 3.46
1593 1704 1.066143 ACTCATGGTACGCAAGGGAAG 60.066 52.381 0.00 0.00 46.39 3.46
1594 1705 0.981183 ACTCATGGTACGCAAGGGAA 59.019 50.000 0.00 0.00 46.39 3.97
1595 1706 0.981183 AACTCATGGTACGCAAGGGA 59.019 50.000 0.00 0.00 46.39 4.20
1596 1707 1.821216 AAACTCATGGTACGCAAGGG 58.179 50.000 0.00 0.00 46.39 3.95
1597 1708 3.938963 ACATAAACTCATGGTACGCAAGG 59.061 43.478 0.00 0.00 46.39 3.61
1643 1754 6.308524 TGCAACAAAATCATAAAATGCTCGAG 59.691 34.615 8.45 8.45 33.87 4.04
1687 1798 5.607477 GGGAGATTACGGTTCACAATATCA 58.393 41.667 0.00 0.00 0.00 2.15
1688 1799 4.684703 CGGGAGATTACGGTTCACAATATC 59.315 45.833 0.00 0.00 0.00 1.63
1692 1803 1.619827 ACGGGAGATTACGGTTCACAA 59.380 47.619 0.00 0.00 0.00 3.33
1697 1808 0.822164 CTGGACGGGAGATTACGGTT 59.178 55.000 0.00 0.00 0.00 4.44
1701 1812 3.821421 ATTGTCTGGACGGGAGATTAC 57.179 47.619 0.00 0.00 0.00 1.89
1717 1828 6.038271 GTGTGAACACTTTCCTACAGAATTGT 59.962 38.462 6.33 0.00 43.25 2.71
1773 1885 1.154093 CGTGTCCTGCGTATCACGT 60.154 57.895 14.04 0.00 44.73 4.49
1805 1917 0.102481 GTGTATCGCACTCCCGACAT 59.898 55.000 0.00 0.00 44.41 3.06
1806 1918 1.509463 GTGTATCGCACTCCCGACA 59.491 57.895 0.00 0.00 44.41 4.35
1815 1927 1.368641 GGCATGTCTTGTGTATCGCA 58.631 50.000 0.00 0.00 0.00 5.10
1826 1938 0.250901 AAGTTCTTGCCGGCATGTCT 60.251 50.000 33.70 28.51 0.00 3.41
1831 1943 2.577700 TCTTAAAAGTTCTTGCCGGCA 58.422 42.857 29.03 29.03 0.00 5.69
1837 1949 7.772166 AGGTTTCAGGTTCTTAAAAGTTCTTG 58.228 34.615 0.00 0.00 0.00 3.02
1855 1967 1.290955 CCGGCAGTACGAGGTTTCA 59.709 57.895 0.00 0.00 35.47 2.69
1864 1976 3.468140 GGTCCCTCCCGGCAGTAC 61.468 72.222 0.00 0.00 0.00 2.73
1883 1995 2.961893 GCCCCCACACGTCCATACA 61.962 63.158 0.00 0.00 0.00 2.29
1893 2005 2.616893 AAGCCCATAGCCCCCACA 60.617 61.111 0.00 0.00 45.47 4.17
1951 2063 3.357203 TGTTGTTCTTGTTGCAGGGTAA 58.643 40.909 0.00 0.00 0.00 2.85
1991 2103 4.899457 CCCTTTCTTCTTTACCCCAGTTTT 59.101 41.667 0.00 0.00 0.00 2.43
1992 2104 4.078805 ACCCTTTCTTCTTTACCCCAGTTT 60.079 41.667 0.00 0.00 0.00 2.66
2107 2220 4.529769 TCCATCTGAGATCATATGTGACCC 59.470 45.833 1.90 0.00 37.14 4.46
2163 2389 4.870426 TCAGCATGAAAGTTATTCGTCTCC 59.130 41.667 0.00 0.00 45.97 3.71
2183 2409 8.815141 ATGATCTTGAATCGAGAACTATTCAG 57.185 34.615 4.04 0.00 41.68 3.02
2264 2490 1.886542 ACTGAAGGCCGAACATTTTCC 59.113 47.619 0.00 0.00 0.00 3.13
2266 2492 1.535462 CGACTGAAGGCCGAACATTTT 59.465 47.619 0.00 0.00 0.00 1.82
2273 2500 0.106868 TAGATCCGACTGAAGGCCGA 60.107 55.000 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.