Multiple sequence alignment - TraesCS2B01G373700

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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 TraesCS2B01G373700 chr2B 100.000 2754 0 0 1 2754 532226424 532223671 0.000000e+00 5086.0
1 TraesCS2B01G373700 chr2B 91.736 121 9 1 1283 1403 532225076 532224957 1.700000e-37 167.0
2 TraesCS2B01G373700 chr2B 91.736 121 9 1 1349 1468 532225142 532225022 1.700000e-37 167.0
3 TraesCS2B01G373700 chr2D 98.721 1407 16 2 1349 2754 452406362 452404957 0.000000e+00 2497.0
4 TraesCS2B01G373700 chr2D 96.530 634 15 3 777 1403 452406875 452406242 0.000000e+00 1042.0
5 TraesCS2B01G373700 chr2D 90.441 272 17 5 919 1189 545732040 545732303 1.570000e-92 350.0
6 TraesCS2B01G373700 chr7D 90.162 1423 88 24 1349 2754 366750096 366751483 0.000000e+00 1805.0
7 TraesCS2B01G373700 chr7D 90.441 272 17 5 919 1189 488118261 488117998 1.570000e-92 350.0
8 TraesCS2B01G373700 chr7D 91.255 263 14 5 927 1189 613848687 613848940 1.570000e-92 350.0
9 TraesCS2B01G373700 chr7D 85.390 308 25 7 1109 1403 366749910 366750210 4.460000e-78 302.0
10 TraesCS2B01G373700 chr3D 90.091 1423 86 26 1349 2754 135170045 135168661 0.000000e+00 1796.0
11 TraesCS2B01G373700 chr3D 89.466 1424 93 23 1349 2754 159121838 159123222 0.000000e+00 1746.0
12 TraesCS2B01G373700 chr3D 88.148 405 30 7 795 1189 53826751 53826355 1.490000e-127 466.0
13 TraesCS2B01G373700 chr3D 85.246 305 25 8 1112 1403 135170228 135169931 2.070000e-76 296.0
14 TraesCS2B01G373700 chrUn 90.134 1419 85 23 1352 2754 291715394 291714015 0.000000e+00 1794.0
15 TraesCS2B01G373700 chrUn 90.134 1419 85 23 1352 2754 291932931 291931552 0.000000e+00 1794.0
16 TraesCS2B01G373700 chrUn 90.134 1419 85 23 1352 2754 302329290 302327911 0.000000e+00 1794.0
17 TraesCS2B01G373700 chrUn 91.538 780 54 9 1 776 49014580 49013809 0.000000e+00 1064.0
18 TraesCS2B01G373700 chrUn 84.918 305 26 8 1112 1403 291715581 291715284 9.650000e-75 291.0
19 TraesCS2B01G373700 chrUn 84.918 305 26 8 1112 1403 291933118 291932821 9.650000e-75 291.0
20 TraesCS2B01G373700 chrUn 84.918 305 26 8 1112 1403 302329477 302329180 9.650000e-75 291.0
21 TraesCS2B01G373700 chr7A 89.993 1419 87 24 1352 2754 299410770 299409391 0.000000e+00 1783.0
22 TraesCS2B01G373700 chr7A 92.455 782 48 9 1 777 130300592 130299817 0.000000e+00 1107.0
23 TraesCS2B01G373700 chr7A 88.603 272 22 5 919 1189 648678978 648678715 3.420000e-84 322.0
24 TraesCS2B01G373700 chr7A 82.951 305 32 9 1112 1403 299410957 299410660 9.790000e-65 257.0
25 TraesCS2B01G373700 chr5D 90.029 1384 86 23 1391 2754 22452337 22453688 0.000000e+00 1744.0
26 TraesCS2B01G373700 chr3B 90.809 1001 83 3 1762 2754 295256845 295257844 0.000000e+00 1330.0
27 TraesCS2B01G373700 chr3B 92.980 755 45 8 1 750 437812593 437813344 0.000000e+00 1094.0
28 TraesCS2B01G373700 chr3B 91.255 789 58 9 1 784 728973584 728974366 0.000000e+00 1064.0
29 TraesCS2B01G373700 chr1B 92.658 790 47 8 1 786 634500849 634500067 0.000000e+00 1127.0
30 TraesCS2B01G373700 chr3A 93.122 756 46 6 1 750 738659261 738658506 0.000000e+00 1103.0
31 TraesCS2B01G373700 chr3A 88.971 272 20 6 919 1189 543675660 543675922 7.350000e-86 327.0
32 TraesCS2B01G373700 chr3A 84.906 265 27 7 1113 1364 214466011 214465747 3.520000e-64 255.0
33 TraesCS2B01G373700 chr2A 91.834 796 51 12 1 789 24395192 24395980 0.000000e+00 1098.0
34 TraesCS2B01G373700 chr2A 88.722 266 22 3 798 1059 34792240 34792501 4.430000e-83 318.0
35 TraesCS2B01G373700 chr4A 91.508 789 52 13 1 784 668744834 668744056 0.000000e+00 1072.0
36 TraesCS2B01G373700 chr4A 91.582 784 55 9 1 780 704758042 704757266 0.000000e+00 1072.0
37 TraesCS2B01G373700 chr4A 87.719 285 25 6 919 1202 23399018 23398743 9.510000e-85 324.0
38 TraesCS2B01G373700 chr4A 84.118 170 18 5 794 959 23399175 23399011 3.670000e-34 156.0
39 TraesCS2B01G373700 chr6D 86.667 645 69 10 1379 2008 15515485 15516127 0.000000e+00 699.0
40 TraesCS2B01G373700 chr6B 84.116 724 90 13 1379 2081 27328941 27329660 0.000000e+00 676.0
41 TraesCS2B01G373700 chr6A 84.866 674 79 10 1379 2030 16227030 16227702 0.000000e+00 658.0
42 TraesCS2B01G373700 chr6A 87.500 56 7 0 1283 1338 16227065 16227120 6.370000e-07 65.8


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 TraesCS2B01G373700 chr2B 532223671 532226424 2753 True 1806.666667 5086 94.490667 1 2754 3 chr2B.!!$R1 2753
1 TraesCS2B01G373700 chr2D 452404957 452406875 1918 True 1769.500000 2497 97.625500 777 2754 2 chr2D.!!$R1 1977
2 TraesCS2B01G373700 chr7D 366749910 366751483 1573 False 1053.500000 1805 87.776000 1109 2754 2 chr7D.!!$F2 1645
3 TraesCS2B01G373700 chr3D 159121838 159123222 1384 False 1746.000000 1746 89.466000 1349 2754 1 chr3D.!!$F1 1405
4 TraesCS2B01G373700 chr3D 135168661 135170228 1567 True 1046.000000 1796 87.668500 1112 2754 2 chr3D.!!$R2 1642
5 TraesCS2B01G373700 chrUn 49013809 49014580 771 True 1064.000000 1064 91.538000 1 776 1 chrUn.!!$R1 775
6 TraesCS2B01G373700 chrUn 291714015 291715581 1566 True 1042.500000 1794 87.526000 1112 2754 2 chrUn.!!$R2 1642
7 TraesCS2B01G373700 chrUn 291931552 291933118 1566 True 1042.500000 1794 87.526000 1112 2754 2 chrUn.!!$R3 1642
8 TraesCS2B01G373700 chrUn 302327911 302329477 1566 True 1042.500000 1794 87.526000 1112 2754 2 chrUn.!!$R4 1642
9 TraesCS2B01G373700 chr7A 130299817 130300592 775 True 1107.000000 1107 92.455000 1 777 1 chr7A.!!$R1 776
10 TraesCS2B01G373700 chr7A 299409391 299410957 1566 True 1020.000000 1783 86.472000 1112 2754 2 chr7A.!!$R3 1642
11 TraesCS2B01G373700 chr5D 22452337 22453688 1351 False 1744.000000 1744 90.029000 1391 2754 1 chr5D.!!$F1 1363
12 TraesCS2B01G373700 chr3B 295256845 295257844 999 False 1330.000000 1330 90.809000 1762 2754 1 chr3B.!!$F1 992
13 TraesCS2B01G373700 chr3B 437812593 437813344 751 False 1094.000000 1094 92.980000 1 750 1 chr3B.!!$F2 749
14 TraesCS2B01G373700 chr3B 728973584 728974366 782 False 1064.000000 1064 91.255000 1 784 1 chr3B.!!$F3 783
15 TraesCS2B01G373700 chr1B 634500067 634500849 782 True 1127.000000 1127 92.658000 1 786 1 chr1B.!!$R1 785
16 TraesCS2B01G373700 chr3A 738658506 738659261 755 True 1103.000000 1103 93.122000 1 750 1 chr3A.!!$R2 749
17 TraesCS2B01G373700 chr2A 24395192 24395980 788 False 1098.000000 1098 91.834000 1 789 1 chr2A.!!$F1 788
18 TraesCS2B01G373700 chr4A 668744056 668744834 778 True 1072.000000 1072 91.508000 1 784 1 chr4A.!!$R1 783
19 TraesCS2B01G373700 chr4A 704757266 704758042 776 True 1072.000000 1072 91.582000 1 780 1 chr4A.!!$R2 779
20 TraesCS2B01G373700 chr6D 15515485 15516127 642 False 699.000000 699 86.667000 1379 2008 1 chr6D.!!$F1 629
21 TraesCS2B01G373700 chr6B 27328941 27329660 719 False 676.000000 676 84.116000 1379 2081 1 chr6B.!!$F1 702
22 TraesCS2B01G373700 chr6A 16227030 16227702 672 False 361.900000 658 86.183000 1283 2030 2 chr6A.!!$F1 747

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
472 482 0.578211 GTGCACTGCAAAACACATGC 59.422 50.0 10.32 0.0 41.47 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 2022 4.039603 ACAAAAGGAGGATAAGCTGCTT 57.96 40.909 19.93 19.93 32.69 3.91 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
38 39 0.819259 AACTGCAGTTGCCATGTCGT 60.819 50.000 30.66 2.58 41.18 4.34
40 41 1.155889 CTGCAGTTGCCATGTCGTTA 58.844 50.000 5.25 0.00 41.18 3.18
127 128 5.891451 TGGTCTGATCTAATGTAGTTGACG 58.109 41.667 0.00 0.00 0.00 4.35
404 413 3.811083 ACACATGACAACTCGGGTAAAA 58.189 40.909 0.00 0.00 0.00 1.52
405 414 4.200874 ACACATGACAACTCGGGTAAAAA 58.799 39.130 0.00 0.00 0.00 1.94
440 450 6.538742 GCCACATTCTTATAAAGCACACTAGA 59.461 38.462 0.00 0.00 0.00 2.43
472 482 0.578211 GTGCACTGCAAAACACATGC 59.422 50.000 10.32 0.00 41.47 4.06
604 619 3.252284 CCACACACCAGCCCCTCT 61.252 66.667 0.00 0.00 0.00 3.69
613 628 2.526873 AGCCCCTCTCGTGTGGTT 60.527 61.111 5.01 0.00 0.00 3.67
619 634 1.000060 CCCTCTCGTGTGGTTAAACGA 60.000 52.381 5.01 0.64 45.86 3.85
669 684 1.982395 CCAGGCCAGTCCTACGTGA 60.982 63.158 5.01 0.00 45.52 4.35
750 765 4.341502 ATGCAAACGCCCACACGC 62.342 61.111 0.00 0.00 36.19 5.34
752 767 4.341502 GCAAACGCCCACACGCAT 62.342 61.111 0.00 0.00 36.19 4.73
753 768 2.972144 GCAAACGCCCACACGCATA 61.972 57.895 0.00 0.00 36.19 3.14
754 769 1.154301 CAAACGCCCACACGCATAC 60.154 57.895 0.00 0.00 36.19 2.39
796 811 4.687483 ACGAAAAGAAATACACCAGTACGG 59.313 41.667 0.00 2.71 42.50 4.02
943 965 1.605710 CTCCTGCAATATTCAAGCCCG 59.394 52.381 0.00 0.00 0.00 6.13
1094 1116 0.976641 AAGCAGAAGGTGATCCACGA 59.023 50.000 0.00 0.00 34.83 4.35
1098 1120 0.252284 AGAAGGTGATCCACGACCCT 60.252 55.000 0.00 0.00 34.83 4.34
1462 1489 3.637273 GGTTCTCCCACCGCCACT 61.637 66.667 0.00 0.00 0.00 4.00
1557 1611 2.282958 TCGCTGAACGGGACCTCT 60.283 61.111 0.00 0.00 43.89 3.69
1726 1823 4.336433 TGCTAATATGCTGTTGCTTTCTCC 59.664 41.667 0.00 0.00 40.48 3.71
2046 2149 0.176449 CATGGATGGTCACTCGCTCA 59.824 55.000 0.00 0.00 0.00 4.26
2324 2428 6.793349 GCTCAGAGCAAGATATTGAAAATGT 58.207 36.000 18.17 0.00 41.89 2.71
2450 2554 1.073284 AGGTGTATGAACGGGCAGTTT 59.927 47.619 4.14 0.00 44.35 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.737783 CGACATGGCAACCGTAGTTTAA 59.262 45.455 0.00 0.00 32.45 1.52
40 41 1.153353 CGACATGGCAACCGTAGTTT 58.847 50.000 0.00 0.00 32.45 2.66
127 128 6.420903 GGCAACTCCTAAAGTTTTGAAATCAC 59.579 38.462 0.00 0.00 46.26 3.06
208 209 4.469657 TCTTCCTTTTACATGGCAACTGT 58.530 39.130 0.00 0.00 37.61 3.55
404 413 8.635765 TTATAAGAATGTGGCAACTCTCTTTT 57.364 30.769 12.00 8.22 33.08 2.27
405 414 8.635765 TTTATAAGAATGTGGCAACTCTCTTT 57.364 30.769 12.00 5.38 33.08 2.52
420 429 6.889198 TGCCTCTAGTGTGCTTTATAAGAAT 58.111 36.000 0.00 0.00 0.00 2.40
482 492 1.229658 CTCCTCTCCCCACCCAAGT 60.230 63.158 0.00 0.00 0.00 3.16
560 575 1.600636 CAGTTCACCCACACGCCAT 60.601 57.895 0.00 0.00 0.00 4.40
604 619 0.102120 ACGGTCGTTTAACCACACGA 59.898 50.000 9.55 0.00 43.00 4.35
613 628 2.356075 CGCCCACACGGTCGTTTA 60.356 61.111 0.00 0.00 0.00 2.01
645 660 3.478780 GGACTGGCCTGGTGTGTA 58.521 61.111 14.82 0.00 0.00 2.90
669 684 4.393062 CGAATCTTGGCATGTTTCTAGTGT 59.607 41.667 17.10 0.00 0.00 3.55
723 738 1.787847 CGTTTGCATCTCGTCCACC 59.212 57.895 0.00 0.00 0.00 4.61
755 770 8.434661 TCTTTTCGTAAATGTTAACGTCCATAC 58.565 33.333 0.00 4.89 39.99 2.39
756 771 8.531622 TCTTTTCGTAAATGTTAACGTCCATA 57.468 30.769 0.00 0.00 39.99 2.74
757 772 7.424227 TCTTTTCGTAAATGTTAACGTCCAT 57.576 32.000 0.00 0.00 39.99 3.41
773 788 4.687483 CCGTACTGGTGTATTTCTTTTCGT 59.313 41.667 0.00 0.00 0.00 3.85
1462 1489 4.615795 CCCCGGGAGATAGCGGGA 62.616 72.222 26.32 0.00 43.92 5.14
1921 2022 4.039603 ACAAAAGGAGGATAAGCTGCTT 57.960 40.909 19.93 19.93 32.69 3.91
2046 2149 8.947055 AAGAAAATGTGCTAATCAAAACAAGT 57.053 26.923 0.00 0.00 0.00 3.16
2257 2361 7.192913 TGGCATTAGCATAAACTTGTTTATCG 58.807 34.615 13.82 11.21 44.61 2.92
2324 2428 4.858850 AGGAATGCATCATACACTTTCCA 58.141 39.130 0.00 0.00 39.10 3.53
2450 2554 6.058833 TGTCCACTGAATAAGTAACTGCAAA 58.941 36.000 0.00 0.00 36.83 3.68


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

AutoCloner maintained by Alex Coulton.