Multiple sequence alignment - TraesCS2D01G453100

Loading Multiple Alignment...

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 TraesCS2D01G453100 chr2D 100.000 1942 0 0 392 2333 562231459 562233400 0.000000e+00 3587
1 TraesCS2D01G453100 chr2D 88.889 126 14 0 1069 1194 562895846 562895971 3.100000e-34 156
2 TraesCS2D01G453100 chr2D 100.000 73 0 0 1 73 562231068 562231140 4.040000e-28 135
3 TraesCS2D01G453100 chr2A 89.657 1750 98 49 392 2120 702936660 702938347 0.000000e+00 2152
4 TraesCS2D01G453100 chr2A 83.636 220 14 13 1001 1218 702940274 702940473 1.100000e-43 187
5 TraesCS2D01G453100 chr2A 90.083 121 12 0 1075 1195 703382096 703382216 8.630000e-35 158
6 TraesCS2D01G453100 chr2B 88.269 1381 75 53 818 2151 671901281 671902621 0.000000e+00 1572
7 TraesCS2D01G453100 chr2B 97.744 133 3 0 392 524 671900744 671900876 1.800000e-56 230


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 TraesCS2D01G453100 chr2D 562231068 562233400 2332 False 1861.0 3587 100.0000 1 2333 2 chr2D.!!$F2 2332
1 TraesCS2D01G453100 chr2A 702936660 702940473 3813 False 1169.5 2152 86.6465 392 2120 2 chr2A.!!$F2 1728
2 TraesCS2D01G453100 chr2B 671900744 671902621 1877 False 901.0 1572 93.0065 392 2151 2 chr2B.!!$F1 1759

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
780 785 0.391661 TTCGCCCAAGCATCTCTCAC 60.392 55.0 0.0 0.0 39.83 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2408 0.748367 GATTTCCTCCACCTTCGGCC 60.748 60.0 0.0 0.0 0.0 6.13 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
24 25 4.774503 GCTTGGGCTGCGCTCTCT 62.775 66.667 17.81 0.00 35.22 3.10
25 26 2.046507 CTTGGGCTGCGCTCTCTT 60.047 61.111 17.81 0.00 0.00 2.85
26 27 1.673665 CTTGGGCTGCGCTCTCTTT 60.674 57.895 17.81 0.00 0.00 2.52
27 28 1.642952 CTTGGGCTGCGCTCTCTTTC 61.643 60.000 17.81 0.00 0.00 2.62
28 29 3.191539 GGGCTGCGCTCTCTTTCG 61.192 66.667 9.73 0.00 0.00 3.46
33 34 3.694527 GCGCTCTCTTTCGCCTAC 58.305 61.111 0.00 0.00 45.01 3.18
34 35 1.153823 GCGCTCTCTTTCGCCTACA 60.154 57.895 0.00 0.00 45.01 2.74
35 36 0.528684 GCGCTCTCTTTCGCCTACAT 60.529 55.000 0.00 0.00 45.01 2.29
36 37 1.927895 CGCTCTCTTTCGCCTACATT 58.072 50.000 0.00 0.00 0.00 2.71
37 38 1.855360 CGCTCTCTTTCGCCTACATTC 59.145 52.381 0.00 0.00 0.00 2.67
38 39 2.480416 CGCTCTCTTTCGCCTACATTCT 60.480 50.000 0.00 0.00 0.00 2.40
39 40 2.863137 GCTCTCTTTCGCCTACATTCTG 59.137 50.000 0.00 0.00 0.00 3.02
40 41 3.677424 GCTCTCTTTCGCCTACATTCTGT 60.677 47.826 0.00 0.00 0.00 3.41
41 42 4.109050 CTCTCTTTCGCCTACATTCTGTC 58.891 47.826 0.00 0.00 0.00 3.51
42 43 3.764434 TCTCTTTCGCCTACATTCTGTCT 59.236 43.478 0.00 0.00 0.00 3.41
43 44 3.849911 TCTTTCGCCTACATTCTGTCTG 58.150 45.455 0.00 0.00 0.00 3.51
44 45 3.258372 TCTTTCGCCTACATTCTGTCTGT 59.742 43.478 0.00 0.00 0.00 3.41
45 46 2.654749 TCGCCTACATTCTGTCTGTG 57.345 50.000 0.00 0.00 0.00 3.66
46 47 1.002366 CGCCTACATTCTGTCTGTGC 58.998 55.000 0.00 0.00 0.00 4.57
47 48 1.672737 CGCCTACATTCTGTCTGTGCA 60.673 52.381 0.00 0.00 0.00 4.57
48 49 2.636830 GCCTACATTCTGTCTGTGCAT 58.363 47.619 0.00 0.00 0.00 3.96
49 50 2.353889 GCCTACATTCTGTCTGTGCATG 59.646 50.000 0.00 0.00 0.00 4.06
50 51 2.941064 CCTACATTCTGTCTGTGCATGG 59.059 50.000 0.00 0.00 0.00 3.66
51 52 1.830279 ACATTCTGTCTGTGCATGGG 58.170 50.000 0.00 0.00 0.00 4.00
52 53 0.454600 CATTCTGTCTGTGCATGGGC 59.545 55.000 0.00 0.00 41.68 5.36
68 69 3.418068 GCACTGTGCCAGCGAGAC 61.418 66.667 21.78 0.00 37.42 3.36
69 70 3.108289 CACTGTGCCAGCGAGACG 61.108 66.667 0.00 0.00 34.37 4.18
70 71 3.606662 ACTGTGCCAGCGAGACGT 61.607 61.111 0.00 0.00 34.37 4.34
71 72 2.265904 ACTGTGCCAGCGAGACGTA 61.266 57.895 0.00 0.00 34.37 3.57
72 73 1.801913 CTGTGCCAGCGAGACGTAC 60.802 63.158 0.00 0.00 0.00 3.67
486 487 3.501040 TTCCCCCGCACACTTTCCC 62.501 63.158 0.00 0.00 0.00 3.97
608 612 2.026301 CCCGGATCTCGTCGCTTC 59.974 66.667 0.73 0.00 37.11 3.86
610 614 2.026301 CGGATCTCGTCGCTTCCC 59.974 66.667 0.00 0.00 0.00 3.97
648 652 2.123769 GCTGCACCATGGGCCATA 60.124 61.111 20.73 1.61 0.00 2.74
649 653 2.492773 GCTGCACCATGGGCCATAC 61.493 63.158 20.73 9.75 0.00 2.39
651 655 2.906897 GCACCATGGGCCATACCG 60.907 66.667 20.73 12.07 40.62 4.02
748 753 2.747855 CCGCCCACAGCCTTCTTC 60.748 66.667 0.00 0.00 38.78 2.87
777 782 1.457346 CTTTTCGCCCAAGCATCTCT 58.543 50.000 0.00 0.00 39.83 3.10
780 785 0.391661 TTCGCCCAAGCATCTCTCAC 60.392 55.000 0.00 0.00 39.83 3.51
815 929 4.660938 ACTTTCCGCCCAGGCACC 62.661 66.667 9.78 0.00 42.06 5.01
816 930 4.659172 CTTTCCGCCCAGGCACCA 62.659 66.667 9.78 0.00 42.06 4.17
891 1005 2.760385 CCCCGTCCACCTCCTCTC 60.760 72.222 0.00 0.00 0.00 3.20
1314 1434 1.303317 GGTGTCCAACAAGGCCGAT 60.303 57.895 0.00 0.00 37.29 4.18
1329 1449 2.261671 GATGTGTCCGTGGCGAGT 59.738 61.111 0.00 0.00 0.00 4.18
1342 1462 3.109547 CGAGTTAGTTGCGCCGCA 61.110 61.111 8.16 8.16 36.47 5.69
1345 1465 3.350612 GTTAGTTGCGCCGCACCA 61.351 61.111 13.21 0.00 38.71 4.17
1396 1520 2.433970 CCTTTTTGCCTTGGGTTGAAGA 59.566 45.455 0.00 0.00 0.00 2.87
1489 1617 0.387622 CTGCAAACACTGGGCAATCG 60.388 55.000 0.00 0.00 37.06 3.34
1578 1706 1.301716 GAGAGCGGGTGTGCAAGAA 60.302 57.895 0.00 0.00 37.31 2.52
1598 1726 2.331194 ACACCGTCGCTGTGTAATTAC 58.669 47.619 8.75 8.75 44.73 1.89
1704 1832 1.737838 TGAACCGGCAGATGTTGATC 58.262 50.000 0.00 0.00 0.00 2.92
1705 1833 0.652592 GAACCGGCAGATGTTGATCG 59.347 55.000 0.00 0.00 33.34 3.69
1706 1834 1.369091 AACCGGCAGATGTTGATCGC 61.369 55.000 0.00 0.00 33.34 4.58
1707 1835 1.522355 CCGGCAGATGTTGATCGCT 60.522 57.895 0.00 0.00 33.34 4.93
1708 1836 1.493950 CCGGCAGATGTTGATCGCTC 61.494 60.000 0.00 0.00 33.34 5.03
1739 1867 4.768968 ACAATTGACAATTCTTAGCCAGCT 59.231 37.500 13.59 0.00 0.00 4.24
1749 1877 8.031277 ACAATTCTTAGCCAGCTAAATTTTCTG 58.969 33.333 12.83 4.69 37.97 3.02
1762 1891 9.985730 AGCTAAATTTTCTGAAATGATGAAACA 57.014 25.926 3.31 0.00 35.69 2.83
1774 1903 8.646356 TGAAATGATGAAACAAATATTTGACGC 58.354 29.630 30.18 18.85 40.55 5.19
1776 1905 6.266168 TGATGAAACAAATATTTGACGCCT 57.734 33.333 30.18 13.96 40.55 5.52
1797 1929 4.946157 CCTAAGAATCAGAGGCACAATTGT 59.054 41.667 4.92 4.92 0.00 2.71
1809 1941 3.622612 GGCACAATTGTTTTTCACTTGCT 59.377 39.130 8.77 0.00 39.34 3.91
1827 1988 2.044860 GCTAGTATTACAGCTCGTGCG 58.955 52.381 3.48 2.02 45.42 5.34
1835 1996 1.437089 CAGCTCGTGCGACAAAACG 60.437 57.895 3.48 0.00 45.42 3.60
1940 2103 4.553547 GCAGTTCGCCATGATTATGTTCTC 60.554 45.833 0.00 0.00 32.21 2.87
1941 2104 4.813161 CAGTTCGCCATGATTATGTTCTCT 59.187 41.667 0.00 0.00 32.21 3.10
2105 2275 4.998979 GATTTTCATTTGGCGAATCGAC 57.001 40.909 6.91 3.27 34.27 4.20
2114 2284 4.398549 TTGGCGAATCGACTAAACAAAG 57.601 40.909 10.78 0.00 35.04 2.77
2126 2374 0.180171 AAACAAAGGGCCAAGGCAAC 59.820 50.000 13.87 5.17 44.11 4.17
2127 2375 1.695114 AACAAAGGGCCAAGGCAACC 61.695 55.000 13.87 5.84 44.11 3.77
2155 2403 8.451687 AAATCAAATCAAACATGATACACACG 57.548 30.769 0.00 0.00 33.60 4.49
2160 2408 1.737838 AACATGATACACACGCCAGG 58.262 50.000 0.00 0.00 0.00 4.45
2194 2442 8.853126 GTGGAGGAAATCAAATCAATCATGATA 58.147 33.333 9.04 0.00 45.60 2.15
2202 2450 5.598005 TCAAATCAATCATGATACCCCAACC 59.402 40.000 9.04 0.00 45.60 3.77
2224 2472 3.407967 AATCCCCCGGCGTCACAT 61.408 61.111 6.01 0.00 0.00 3.21
2229 2477 3.186047 CCCGGCGTCACATTCGTC 61.186 66.667 6.01 0.00 0.00 4.20
2235 2483 1.441515 CGTCACATTCGTCGGACGT 60.442 57.895 27.53 9.08 45.73 4.34
2286 2535 3.295273 ACTCAGCGCCGAGTCACA 61.295 61.111 20.44 0.00 42.70 3.58
2316 2565 1.059942 GGAACATTTCCGCGCAAAAG 58.940 50.000 8.75 0.00 40.59 2.27
2318 2567 2.389998 GAACATTTCCGCGCAAAAGAA 58.610 42.857 8.75 1.16 0.00 2.52
2321 2570 2.538037 ACATTTCCGCGCAAAAGAAAAC 59.462 40.909 8.75 0.00 33.53 2.43
2322 2571 1.192793 TTTCCGCGCAAAAGAAAACG 58.807 45.000 8.75 0.00 0.00 3.60
2323 2572 0.099082 TTCCGCGCAAAAGAAAACGT 59.901 45.000 8.75 0.00 0.00 3.99
2324 2573 0.099082 TCCGCGCAAAAGAAAACGTT 59.901 45.000 8.75 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.855360 GAATGTAGGCGAAAGAGAGCG 59.145 52.381 0.00 0.00 0.00 5.03
18 19 2.863137 CAGAATGTAGGCGAAAGAGAGC 59.137 50.000 0.00 0.00 0.00 4.09
30 31 4.786127 GCCCATGCACAGACAGAATGTAG 61.786 52.174 0.00 0.00 44.54 2.74
31 32 2.940971 GCCCATGCACAGACAGAATGTA 60.941 50.000 0.00 0.00 44.54 2.29
32 33 2.223928 GCCCATGCACAGACAGAATGT 61.224 52.381 0.00 0.00 46.53 2.71
33 34 0.454600 GCCCATGCACAGACAGAATG 59.545 55.000 0.00 0.00 39.08 2.67
34 35 0.038599 TGCCCATGCACAGACAGAAT 59.961 50.000 0.00 0.00 44.23 2.40
35 36 1.455412 TGCCCATGCACAGACAGAA 59.545 52.632 0.00 0.00 44.23 3.02
36 37 3.159615 TGCCCATGCACAGACAGA 58.840 55.556 0.00 0.00 44.23 3.41
55 56 2.257371 GTACGTCTCGCTGGCACA 59.743 61.111 0.00 0.00 0.00 4.57
486 487 2.256117 AGGTTTGGAGTCTTTCACGG 57.744 50.000 0.00 0.00 0.00 4.94
648 652 3.219281 ACTTTATGTTTGTTCTGCCGGT 58.781 40.909 1.90 0.00 0.00 5.28
649 653 3.915437 ACTTTATGTTTGTTCTGCCGG 57.085 42.857 0.00 0.00 0.00 6.13
651 655 8.986477 AATCATTACTTTATGTTTGTTCTGCC 57.014 30.769 0.00 0.00 0.00 4.85
794 799 1.045911 TGCCTGGGCGGAAAGTTTTT 61.046 50.000 7.14 0.00 45.51 1.94
815 929 3.834447 TTCGAGGCCGTGACGTGTG 62.834 63.158 3.64 0.00 37.05 3.82
816 930 3.598715 TTCGAGGCCGTGACGTGT 61.599 61.111 3.64 0.00 37.05 4.49
891 1005 0.603707 TTCCGCTTGAGCTGAGGTTG 60.604 55.000 0.00 0.00 35.75 3.77
985 1102 2.500165 CATGAGGCAGAGCTCGCT 59.500 61.111 23.23 13.32 0.00 4.93
986 1103 2.588314 CCATGAGGCAGAGCTCGC 60.588 66.667 18.35 18.35 0.00 5.03
1293 1413 2.203294 GCCTTGTTGGACACCGGT 60.203 61.111 0.00 0.00 38.35 5.28
1303 1423 1.671054 CGGACACATCGGCCTTGTT 60.671 57.895 0.00 0.00 0.00 2.83
1304 1424 2.047274 CGGACACATCGGCCTTGT 60.047 61.111 0.00 1.01 0.00 3.16
1314 1434 1.287815 CTAACTCGCCACGGACACA 59.712 57.895 0.00 0.00 0.00 3.72
1342 1462 0.543646 ACTAGCTAACCCGGTGTGGT 60.544 55.000 0.00 0.00 41.55 4.16
1345 1465 1.285962 TCCTACTAGCTAACCCGGTGT 59.714 52.381 0.00 0.00 0.00 4.16
1348 1468 2.664015 AGTTCCTACTAGCTAACCCGG 58.336 52.381 0.00 0.00 31.21 5.73
1396 1520 1.208165 AAGAACCCCGCATCCTCCTT 61.208 55.000 0.00 0.00 0.00 3.36
1475 1603 1.675641 GCTCCGATTGCCCAGTGTT 60.676 57.895 0.00 0.00 0.00 3.32
1477 1605 2.046023 TGCTCCGATTGCCCAGTG 60.046 61.111 0.00 0.00 0.00 3.66
1478 1606 2.270205 CTGCTCCGATTGCCCAGT 59.730 61.111 0.00 0.00 0.00 4.00
1479 1607 2.335092 ATCCTGCTCCGATTGCCCAG 62.335 60.000 0.00 0.00 0.00 4.45
1480 1608 2.329539 GATCCTGCTCCGATTGCCCA 62.330 60.000 0.00 0.00 0.00 5.36
1489 1617 4.899239 CCGCGGTGATCCTGCTCC 62.899 72.222 19.50 0.00 33.49 4.70
1533 1661 2.090719 TCATACCCAAACCCAAACCCAA 60.091 45.455 0.00 0.00 0.00 4.12
1534 1662 1.503784 TCATACCCAAACCCAAACCCA 59.496 47.619 0.00 0.00 0.00 4.51
1535 1663 2.176045 CTCATACCCAAACCCAAACCC 58.824 52.381 0.00 0.00 0.00 4.11
1536 1664 3.089284 CTCTCATACCCAAACCCAAACC 58.911 50.000 0.00 0.00 0.00 3.27
1537 1665 3.089284 CCTCTCATACCCAAACCCAAAC 58.911 50.000 0.00 0.00 0.00 2.93
1538 1666 2.990284 TCCTCTCATACCCAAACCCAAA 59.010 45.455 0.00 0.00 0.00 3.28
1598 1726 2.095853 ACTTTACATCGATTGCCTTGCG 59.904 45.455 0.00 0.00 0.00 4.85
1681 1809 2.690497 TCAACATCTGCCGGTTCAAAAA 59.310 40.909 1.90 0.00 0.00 1.94
1691 1819 1.493950 CCGAGCGATCAACATCTGCC 61.494 60.000 0.00 0.00 32.31 4.85
1704 1832 1.593006 GTCAATTGTACCATCCGAGCG 59.407 52.381 5.13 0.00 0.00 5.03
1705 1833 2.627945 TGTCAATTGTACCATCCGAGC 58.372 47.619 5.13 0.00 0.00 5.03
1706 1834 5.586243 AGAATTGTCAATTGTACCATCCGAG 59.414 40.000 15.52 0.00 0.00 4.63
1707 1835 5.496556 AGAATTGTCAATTGTACCATCCGA 58.503 37.500 15.52 0.00 0.00 4.55
1708 1836 5.818136 AGAATTGTCAATTGTACCATCCG 57.182 39.130 15.52 0.00 0.00 4.18
1730 1858 8.121305 TCATTTCAGAAAATTTAGCTGGCTAA 57.879 30.769 16.48 10.53 36.81 3.09
1749 1877 8.110002 GGCGTCAAATATTTGTTTCATCATTTC 58.890 33.333 23.95 5.44 39.18 2.17
1761 1890 7.919690 TCTGATTCTTAGGCGTCAAATATTTG 58.080 34.615 20.13 20.13 39.48 2.32
1762 1891 7.227512 CCTCTGATTCTTAGGCGTCAAATATTT 59.772 37.037 0.00 0.00 0.00 1.40
1763 1892 6.708054 CCTCTGATTCTTAGGCGTCAAATATT 59.292 38.462 0.00 0.00 0.00 1.28
1764 1893 6.226787 CCTCTGATTCTTAGGCGTCAAATAT 58.773 40.000 0.00 0.00 0.00 1.28
1765 1894 5.601662 CCTCTGATTCTTAGGCGTCAAATA 58.398 41.667 0.00 0.00 0.00 1.40
1774 1903 4.946157 ACAATTGTGCCTCTGATTCTTAGG 59.054 41.667 11.07 0.00 0.00 2.69
1776 1905 6.899393 AAACAATTGTGCCTCTGATTCTTA 57.101 33.333 12.82 0.00 0.00 2.10
1797 1929 7.148639 CGAGCTGTAATACTAGCAAGTGAAAAA 60.149 37.037 14.07 0.00 42.29 1.94
1809 1941 2.679336 TGTCGCACGAGCTGTAATACTA 59.321 45.455 2.73 0.00 39.10 1.82
1827 1988 8.138365 TGAATAGATACATTAGCCGTTTTGTC 57.862 34.615 0.00 0.00 0.00 3.18
1864 2025 1.376609 CGCTAGCTCCCGGCAAAAAT 61.377 55.000 13.93 0.00 44.79 1.82
1997 2166 4.009675 GGTTCAGTACATGATTTGCTGGA 58.990 43.478 0.00 0.00 37.89 3.86
2105 2275 1.337118 TGCCTTGGCCCTTTGTTTAG 58.663 50.000 9.35 0.00 0.00 1.85
2114 2284 4.986708 TTCCGGTTGCCTTGGCCC 62.987 66.667 9.35 3.13 0.00 5.80
2126 2374 7.220683 GTGTATCATGTTTGATTTGATTTCCGG 59.779 37.037 0.00 0.00 42.61 5.14
2127 2375 7.754475 TGTGTATCATGTTTGATTTGATTTCCG 59.246 33.333 0.00 0.00 42.61 4.30
2160 2408 0.748367 GATTTCCTCCACCTTCGGCC 60.748 60.000 0.00 0.00 0.00 6.13
2194 2442 4.376170 GGATTGGCCGGTTGGGGT 62.376 66.667 1.90 0.00 35.78 4.95
2212 2460 3.186047 GACGAATGTGACGCCGGG 61.186 66.667 2.18 0.00 0.00 5.73
2224 2472 3.770263 ATAATTGAGACGTCCGACGAA 57.230 42.857 27.03 11.25 46.05 3.85
2229 2477 6.642683 ACAGTAAAATAATTGAGACGTCCG 57.357 37.500 13.01 0.00 0.00 4.79
2235 2483 9.677567 GCACAGAAAACAGTAAAATAATTGAGA 57.322 29.630 0.00 0.00 0.00 3.27
2257 2505 4.056125 CTGAGTCGCGAGGGCACA 62.056 66.667 10.24 1.58 39.92 4.57


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

AutoCloner maintained by Alex Coulton.