Multiple sequence alignment - TraesCS5D01G311200

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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 TraesCS5D01G311200 chr5D 100.000 1999 0 0 678 2676 407755114 407757112 0.000000e+00 3692.0
1 TraesCS5D01G311200 chr5D 100.000 462 0 0 1 462 407754437 407754898 0.000000e+00 854.0
2 TraesCS5D01G311200 chr5D 84.818 606 75 7 2075 2676 407773493 407774085 6.380000e-166 593.0
3 TraesCS5D01G311200 chr5D 91.131 327 25 4 1324 1648 407772629 407772953 8.790000e-120 440.0
4 TraesCS5D01G311200 chr5A 97.475 713 15 2 1964 2676 513227017 513227726 0.000000e+00 1214.0
5 TraesCS5D01G311200 chr5A 89.111 900 62 22 764 1639 513225774 513226661 0.000000e+00 1086.0
6 TraesCS5D01G311200 chr5A 80.586 273 27 8 19 277 654410663 654410923 1.260000e-43 187.0
7 TraesCS5D01G311200 chr5A 85.714 70 7 2 679 748 2831206 2831272 1.330000e-08 71.3
8 TraesCS5D01G311200 chr5A 92.857 42 3 0 70 111 654410930 654410971 8.000000e-06 62.1
9 TraesCS5D01G311200 chr5B 92.533 750 48 5 904 1647 488820037 488820784 0.000000e+00 1068.0
10 TraesCS5D01G311200 chr5B 95.245 673 29 1 2005 2674 488821132 488821804 0.000000e+00 1062.0
11 TraesCS5D01G311200 chr2D 94.600 463 23 2 1 461 120489475 120489013 0.000000e+00 715.0
12 TraesCS5D01G311200 chr7B 94.384 463 19 4 1 461 471913048 471913505 0.000000e+00 704.0
13 TraesCS5D01G311200 chr7B 93.421 76 4 1 678 753 471913605 471913679 7.830000e-21 111.0
14 TraesCS5D01G311200 chr6A 91.145 463 31 8 1 460 552300744 552301199 1.050000e-173 619.0
15 TraesCS5D01G311200 chr6B 87.037 162 21 0 297 458 42426280 42426441 1.640000e-42 183.0
16 TraesCS5D01G311200 chr7D 85.507 69 6 4 686 753 93620071 93620006 4.780000e-08 69.4


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 TraesCS5D01G311200 chr5D 407754437 407757112 2675 False 2273.0 3692 100.0000 1 2676 2 chr5D.!!$F1 2675
1 TraesCS5D01G311200 chr5D 407772629 407774085 1456 False 516.5 593 87.9745 1324 2676 2 chr5D.!!$F2 1352
2 TraesCS5D01G311200 chr5A 513225774 513227726 1952 False 1150.0 1214 93.2930 764 2676 2 chr5A.!!$F2 1912
3 TraesCS5D01G311200 chr5B 488820037 488821804 1767 False 1065.0 1068 93.8890 904 2674 2 chr5B.!!$F1 1770
4 TraesCS5D01G311200 chr7B 471913048 471913679 631 False 407.5 704 93.9025 1 753 2 chr7B.!!$F1 752

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
871 874 0.390866 AACAGTCAGATGCAGAGGCG 60.391 55.0 0.0 0.0 45.35 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1781 0.168788 CGCAGCAAAACGATGACCAT 59.831 50.0 0.0 0.0 30.38 3.55 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
51 52 2.565391 TGGCAGAGTGTTCGGATTTAGA 59.435 45.455 0.00 0.00 0.00 2.10
55 56 4.677584 CAGAGTGTTCGGATTTAGAGAGG 58.322 47.826 0.00 0.00 0.00 3.69
59 60 6.436532 AGAGTGTTCGGATTTAGAGAGGTAAA 59.563 38.462 0.00 0.00 0.00 2.01
114 115 6.713792 GAGAATAGTTGTCTCTTTGTGGAC 57.286 41.667 0.00 0.00 38.80 4.02
209 210 2.224499 TGTCACTGTTGAGCATAGGCAA 60.224 45.455 0.67 0.00 44.61 4.52
271 273 8.071967 TCATAATTGAGCAGCTTCATATTTTCG 58.928 33.333 0.00 0.00 0.00 3.46
281 283 7.170658 GCAGCTTCATATTTTCGTAGAAGATCT 59.829 37.037 0.00 0.00 45.90 2.75
282 284 9.684448 CAGCTTCATATTTTCGTAGAAGATCTA 57.316 33.333 0.00 0.00 45.90 1.98
299 301 8.986847 AGAAGATCTAAATAAGCATTCATGTCG 58.013 33.333 0.00 0.00 0.00 4.35
316 318 2.482336 TGTCGTCACCAATTATGTGTGC 59.518 45.455 7.06 2.60 35.25 4.57
380 383 2.038033 TCCACCCAGTTAGAAAACTCCG 59.962 50.000 0.00 0.00 44.28 4.63
381 384 1.804748 CACCCAGTTAGAAAACTCCGC 59.195 52.381 0.00 0.00 44.28 5.54
382 385 1.418637 ACCCAGTTAGAAAACTCCGCA 59.581 47.619 0.00 0.00 44.28 5.69
386 389 4.698304 CCCAGTTAGAAAACTCCGCATAAA 59.302 41.667 0.00 0.00 44.28 1.40
403 406 6.472163 CCGCATAAATTTTGTCACTTATGGTC 59.528 38.462 0.00 0.00 33.99 4.02
415 418 8.084985 TGTCACTTATGGTCCAACTATTATGA 57.915 34.615 0.00 0.00 0.00 2.15
461 464 7.566760 TTGTGTTGCAGAGAAAAGAGATTAA 57.433 32.000 0.00 0.00 0.00 1.40
714 717 5.326069 ACTAGGCTAGGACATCGTCATATT 58.674 41.667 24.57 0.00 33.68 1.28
715 718 5.775701 ACTAGGCTAGGACATCGTCATATTT 59.224 40.000 24.57 0.00 33.68 1.40
757 760 3.593247 GCATGTTTGCGAGTGCTAG 57.407 52.632 0.00 0.00 43.34 3.42
758 761 0.798776 GCATGTTTGCGAGTGCTAGT 59.201 50.000 0.00 0.00 43.34 2.57
759 762 1.999735 GCATGTTTGCGAGTGCTAGTA 59.000 47.619 0.00 0.00 43.34 1.82
760 763 2.609459 GCATGTTTGCGAGTGCTAGTAT 59.391 45.455 0.00 0.00 43.34 2.12
761 764 3.802139 GCATGTTTGCGAGTGCTAGTATA 59.198 43.478 0.00 0.00 43.34 1.47
762 765 4.449068 GCATGTTTGCGAGTGCTAGTATAT 59.551 41.667 0.00 0.00 43.34 0.86
763 766 5.633601 GCATGTTTGCGAGTGCTAGTATATA 59.366 40.000 0.00 0.00 43.34 0.86
764 767 6.145534 GCATGTTTGCGAGTGCTAGTATATAA 59.854 38.462 0.00 0.00 43.34 0.98
765 768 7.307160 GCATGTTTGCGAGTGCTAGTATATAAA 60.307 37.037 0.00 0.00 43.34 1.40
766 769 8.547894 CATGTTTGCGAGTGCTAGTATATAAAA 58.452 33.333 0.00 0.00 43.34 1.52
767 770 8.481974 TGTTTGCGAGTGCTAGTATATAAAAA 57.518 30.769 0.00 0.00 43.34 1.94
788 791 1.389609 GGCATAGGACGTTCCTCCGA 61.390 60.000 9.44 0.00 45.66 4.55
805 808 1.323534 CCGACGATCCACAAATTCGAC 59.676 52.381 0.00 0.00 36.73 4.20
822 825 0.865769 GACGTGCAAATTCCGTCTGT 59.134 50.000 16.79 0.00 45.49 3.41
871 874 0.390866 AACAGTCAGATGCAGAGGCG 60.391 55.000 0.00 0.00 45.35 5.52
873 876 1.683707 AGTCAGATGCAGAGGCGGA 60.684 57.895 0.00 0.00 45.35 5.54
886 889 2.404186 GGCGGAAAAAGGCCCTACG 61.404 63.158 0.00 0.00 43.64 3.51
896 899 1.153765 GGCCCTACGTACGTGAACC 60.154 63.158 30.25 20.69 0.00 3.62
897 900 1.514873 GCCCTACGTACGTGAACCG 60.515 63.158 30.25 13.61 44.03 4.44
898 901 1.137404 CCCTACGTACGTGAACCGG 59.863 63.158 30.25 19.72 42.24 5.28
981 988 2.388232 GGAACGTGACATGACGCCC 61.388 63.158 0.00 1.51 43.33 6.13
982 989 2.726691 GAACGTGACATGACGCCCG 61.727 63.158 0.00 0.00 43.33 6.13
1014 1021 1.134068 GTCTATCTCCCACCCTTTGGC 60.134 57.143 0.00 0.00 45.37 4.52
1022 1029 0.901580 CCACCCTTTGGCTGCATCTT 60.902 55.000 0.50 0.00 39.07 2.40
1082 1092 3.806521 GGACTACATCATACAGCAGCAAG 59.193 47.826 0.00 0.00 0.00 4.01
1266 1279 4.754114 CCAACTGTCCTTTTTCTCTGAGAG 59.246 45.833 7.52 2.28 0.00 3.20
1268 1281 3.244387 ACTGTCCTTTTTCTCTGAGAGCC 60.244 47.826 4.17 0.00 0.00 4.70
1271 1284 2.083002 CCTTTTTCTCTGAGAGCCTGC 58.917 52.381 4.17 0.00 0.00 4.85
1279 1292 0.877743 CTGAGAGCCTGCGATCGATA 59.122 55.000 21.57 5.76 0.00 2.92
1459 1483 1.478916 GAGAAGGAGAAGAAGGACCCG 59.521 57.143 0.00 0.00 0.00 5.28
1553 1577 1.990060 CTGCGGGAGAAGGGGAAGA 60.990 63.158 0.00 0.00 0.00 2.87
1555 1579 0.914417 TGCGGGAGAAGGGGAAGAAT 60.914 55.000 0.00 0.00 0.00 2.40
1626 1650 2.028748 GGGCCGTTGTAGAGTGAGTTTA 60.029 50.000 0.00 0.00 0.00 2.01
1641 1666 1.967779 AGTTTATTTGGGTGCCGCTTT 59.032 42.857 0.00 0.00 0.00 3.51
1642 1667 2.367241 AGTTTATTTGGGTGCCGCTTTT 59.633 40.909 0.00 0.00 0.00 2.27
1669 1694 7.961325 TTCTTTTTGAGAATAATTTGGGTGC 57.039 32.000 0.00 0.00 39.44 5.01
1680 1705 2.447244 TTTGGGTGCCGCTTAATTTG 57.553 45.000 0.00 0.00 0.00 2.32
1692 1717 3.505836 GCTTAATTTGCCAGCTTCTCAC 58.494 45.455 0.00 0.00 0.00 3.51
1703 1728 2.665537 CAGCTTCTCACTTGTCGATGAC 59.334 50.000 0.00 0.00 0.00 3.06
1730 1755 0.591659 TAACAGAGATCGATCCGCCG 59.408 55.000 21.66 10.49 0.00 6.46
1790 1824 1.742900 CTGCGTGCGATGAAGTACCG 61.743 60.000 0.00 0.00 0.00 4.02
1830 1869 5.431765 ACTATCTGTGAATAACCTGGCAAG 58.568 41.667 0.00 0.00 0.00 4.01
1882 1925 5.351458 AGATGAAGTTCACCAAGCAAAAAC 58.649 37.500 7.96 0.00 0.00 2.43
2040 2279 7.924412 TCTCGAGAGTACAAATAAACTTGTGTT 59.076 33.333 12.08 0.00 39.81 3.32
2234 2479 1.529010 CAGCACAAGGGACAAGCCA 60.529 57.895 0.00 0.00 38.95 4.75
2287 2532 3.384668 TCACTTCAAGTTTCTCGAGCAG 58.615 45.455 7.81 0.00 0.00 4.24
2321 2566 5.128205 CCATCCTTGATTTGTATGCTCTCA 58.872 41.667 0.00 0.00 0.00 3.27
2350 2595 4.671831 TCCATCCCTTCAATGTAAAGCAA 58.328 39.130 0.00 0.00 0.00 3.91
2432 2677 3.259374 CCCAGAGTGCAAGAAGAGTAAGA 59.741 47.826 0.00 0.00 0.00 2.10
2668 2913 4.517285 TCCAGATGAACAAGCCTTGATAC 58.483 43.478 12.25 2.70 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.859961 CGAACACTCTGCCAACTGTATAG 59.140 47.826 0.00 0.00 0.00 1.31
36 37 6.600882 TTTACCTCTCTAAATCCGAACACT 57.399 37.500 0.00 0.00 0.00 3.55
37 38 7.662604 TTTTTACCTCTCTAAATCCGAACAC 57.337 36.000 0.00 0.00 0.00 3.32
69 70 5.083122 TCTTTGTCTCCCAAAAATATGCCA 58.917 37.500 0.00 0.00 42.31 4.92
77 78 7.060421 ACAACTATTCTCTTTGTCTCCCAAAA 58.940 34.615 0.00 0.00 42.31 2.44
209 210 8.676401 AGAAAAATAAGCTTTTTGCAACACAAT 58.324 25.926 3.20 0.00 45.94 2.71
281 283 5.877564 TGGTGACGACATGAATGCTTATTTA 59.122 36.000 0.00 0.00 0.00 1.40
282 284 4.699735 TGGTGACGACATGAATGCTTATTT 59.300 37.500 0.00 0.00 0.00 1.40
299 301 2.489329 AGCTGCACACATAATTGGTGAC 59.511 45.455 16.18 9.64 39.53 3.67
380 383 7.319646 TGGACCATAAGTGACAAAATTTATGC 58.680 34.615 0.00 0.00 34.00 3.14
381 384 9.139174 GTTGGACCATAAGTGACAAAATTTATG 57.861 33.333 0.00 0.00 34.72 1.90
382 385 9.088987 AGTTGGACCATAAGTGACAAAATTTAT 57.911 29.630 0.00 0.00 0.00 1.40
386 389 8.650143 AATAGTTGGACCATAAGTGACAAAAT 57.350 30.769 0.00 0.00 0.00 1.82
430 433 6.310956 TCTTTTCTCTGCAACACAATTGTTTG 59.689 34.615 8.77 16.42 43.89 2.93
728 731 0.248990 CAAACATGCCTGTGCGTTGT 60.249 50.000 0.00 0.00 41.78 3.32
737 740 0.321564 TAGCACTCGCAAACATGCCT 60.322 50.000 0.00 0.00 42.27 4.75
779 782 0.245539 TTGTGGATCGTCGGAGGAAC 59.754 55.000 4.32 1.97 0.00 3.62
788 791 1.724623 CACGTCGAATTTGTGGATCGT 59.275 47.619 0.00 0.00 37.79 3.73
805 808 0.586319 ACACAGACGGAATTTGCACG 59.414 50.000 0.00 0.00 0.00 5.34
822 825 0.682852 CACGTGGGTAAGGAAGGACA 59.317 55.000 7.95 0.00 0.00 4.02
856 859 0.391661 TTTCCGCCTCTGCATCTGAC 60.392 55.000 0.00 0.00 37.32 3.51
871 874 1.338105 ACGTACGTAGGGCCTTTTTCC 60.338 52.381 21.41 0.00 0.00 3.13
873 876 1.344114 TCACGTACGTAGGGCCTTTTT 59.656 47.619 22.34 0.00 0.00 1.94
886 889 2.084681 CGCAGTCCGGTTCACGTAC 61.085 63.158 0.00 0.00 42.24 3.67
896 899 2.513065 GATTGTTGTGCCGCAGTCCG 62.513 60.000 0.00 0.00 0.00 4.79
897 900 1.210155 GATTGTTGTGCCGCAGTCC 59.790 57.895 0.00 0.00 0.00 3.85
898 901 1.154413 CGATTGTTGTGCCGCAGTC 60.154 57.895 0.00 0.00 0.00 3.51
1014 1021 2.419324 GCCTCTGAAACTGAAGATGCAG 59.581 50.000 0.00 0.00 41.63 4.41
1022 1029 1.527034 GTGCATGCCTCTGAAACTGA 58.473 50.000 16.68 0.00 0.00 3.41
1061 1068 4.437239 ACTTGCTGCTGTATGATGTAGTC 58.563 43.478 0.00 0.00 0.00 2.59
1068 1075 1.065926 CCCTGACTTGCTGCTGTATGA 60.066 52.381 0.00 0.00 0.00 2.15
1082 1092 1.378250 AGCATTGCTCTGCCCTGAC 60.378 57.895 5.03 0.00 43.33 3.51
1235 1248 6.809869 AGAAAAAGGACAGTTGGAAATGAAG 58.190 36.000 0.00 0.00 0.00 3.02
1266 1279 1.135774 TGATACGTATCGATCGCAGGC 60.136 52.381 26.12 4.20 35.48 4.85
1268 1281 4.003519 TGATGATACGTATCGATCGCAG 57.996 45.455 26.12 3.88 35.48 5.18
1300 1313 3.520290 ACGATAAGAACGCATCAAGGA 57.480 42.857 0.00 0.00 0.00 3.36
1574 1598 1.674441 GGGCTTTATTCCGGTTACAGC 59.326 52.381 0.00 8.89 0.00 4.40
1576 1600 2.572556 TCTGGGCTTTATTCCGGTTACA 59.427 45.455 0.00 0.00 0.00 2.41
1647 1672 5.348451 CGGCACCCAAATTATTCTCAAAAAG 59.652 40.000 0.00 0.00 0.00 2.27
1648 1673 5.233988 CGGCACCCAAATTATTCTCAAAAA 58.766 37.500 0.00 0.00 0.00 1.94
1649 1674 4.815269 CGGCACCCAAATTATTCTCAAAA 58.185 39.130 0.00 0.00 0.00 2.44
1650 1675 3.367910 GCGGCACCCAAATTATTCTCAAA 60.368 43.478 0.00 0.00 0.00 2.69
1651 1676 2.165437 GCGGCACCCAAATTATTCTCAA 59.835 45.455 0.00 0.00 0.00 3.02
1652 1677 1.748493 GCGGCACCCAAATTATTCTCA 59.252 47.619 0.00 0.00 0.00 3.27
1653 1678 2.024414 AGCGGCACCCAAATTATTCTC 58.976 47.619 1.45 0.00 0.00 2.87
1654 1679 2.143876 AGCGGCACCCAAATTATTCT 57.856 45.000 1.45 0.00 0.00 2.40
1655 1680 2.959507 AAGCGGCACCCAAATTATTC 57.040 45.000 1.45 0.00 0.00 1.75
1656 1681 5.351948 AATTAAGCGGCACCCAAATTATT 57.648 34.783 1.45 0.00 0.00 1.40
1657 1682 5.115480 CAAATTAAGCGGCACCCAAATTAT 58.885 37.500 1.45 0.00 0.00 1.28
1658 1683 4.499183 CAAATTAAGCGGCACCCAAATTA 58.501 39.130 1.45 0.00 0.00 1.40
1659 1684 3.333804 CAAATTAAGCGGCACCCAAATT 58.666 40.909 1.45 0.00 0.00 1.82
1660 1685 2.934801 GCAAATTAAGCGGCACCCAAAT 60.935 45.455 1.45 0.00 0.00 2.32
1661 1686 1.606737 GCAAATTAAGCGGCACCCAAA 60.607 47.619 1.45 0.00 0.00 3.28
1662 1687 0.037790 GCAAATTAAGCGGCACCCAA 60.038 50.000 1.45 0.00 0.00 4.12
1663 1688 1.589113 GCAAATTAAGCGGCACCCA 59.411 52.632 1.45 0.00 0.00 4.51
1664 1689 1.153647 GGCAAATTAAGCGGCACCC 60.154 57.895 1.45 0.00 0.00 4.61
1665 1690 0.458370 CTGGCAAATTAAGCGGCACC 60.458 55.000 1.45 0.00 0.00 5.01
1666 1691 1.078201 GCTGGCAAATTAAGCGGCAC 61.078 55.000 1.45 0.00 33.69 5.01
1667 1692 1.215117 GCTGGCAAATTAAGCGGCA 59.785 52.632 1.45 0.00 33.69 5.69
1668 1693 0.108662 AAGCTGGCAAATTAAGCGGC 60.109 50.000 0.00 0.00 41.88 6.53
1669 1694 1.474077 AGAAGCTGGCAAATTAAGCGG 59.526 47.619 0.00 0.00 41.88 5.52
1680 1705 0.319900 TCGACAAGTGAGAAGCTGGC 60.320 55.000 0.00 0.00 0.00 4.85
1692 1717 1.633561 ATGTGCTCGTCATCGACAAG 58.366 50.000 0.00 0.00 41.35 3.16
1703 1728 3.340337 TCGATCTCTGTTATGTGCTCG 57.660 47.619 0.00 0.00 0.00 5.03
1754 1779 2.253603 GCAGCAAAACGATGACCATTC 58.746 47.619 0.00 0.00 30.38 2.67
1756 1781 0.168788 CGCAGCAAAACGATGACCAT 59.831 50.000 0.00 0.00 30.38 3.55
1761 1786 2.419895 CGCACGCAGCAAAACGATG 61.420 57.895 0.00 0.00 46.13 3.84
1790 1824 4.752101 AGATAGTACGCATCAATTCAAGCC 59.248 41.667 11.57 0.00 0.00 4.35
1830 1869 0.682209 ATCATTGACTGGTGCTGGCC 60.682 55.000 0.00 0.00 0.00 5.36
1882 1925 3.244033 AGATCAAGTTCCAGAGCGAAG 57.756 47.619 0.00 0.00 0.00 3.79
2017 2256 7.847487 TGAACACAAGTTTATTTGTACTCTCG 58.153 34.615 0.00 0.00 39.17 4.04
2040 2279 5.896106 ACCTCTGTTCTGATGTAGATGATGA 59.104 40.000 0.00 0.00 34.80 2.92
2234 2479 5.733620 TTAACTTGGACGACAGTAAGGAT 57.266 39.130 0.00 0.00 0.00 3.24
2287 2532 0.458669 CAAGGATGGTGCATTGCCTC 59.541 55.000 6.12 0.00 0.00 4.70
2321 2566 4.939255 ACATTGAAGGGATGGAGAACATT 58.061 39.130 0.00 0.00 40.72 2.71
2350 2595 4.589908 AGGTACATTTCCGAAGCTCAAAT 58.410 39.130 0.00 0.00 0.00 2.32
2432 2677 2.043652 ATGGGGAAGCTGCGCAAT 60.044 55.556 13.05 1.10 33.90 3.56


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

AutoCloner maintained by Alex Coulton.