Multiple sequence alignment - TraesCS4A01G371300

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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 TraesCS4A01G371300 chr4A 100.000 2399 0 0 1 2399 644923845 644921447 0.000000e+00 4431
1 TraesCS4A01G371300 chr7D 94.125 2417 122 4 1 2399 180439622 180442036 0.000000e+00 3659
2 TraesCS4A01G371300 chr3A 93.877 2417 129 4 1 2399 703853572 703851157 0.000000e+00 3626
3 TraesCS4A01G371300 chr3A 93.722 1115 52 3 654 1752 171150784 171151896 0.000000e+00 1655
4 TraesCS4A01G371300 chr3A 93.286 1117 53 6 654 1752 545675769 545674657 0.000000e+00 1628
5 TraesCS4A01G371300 chr6D 93.546 2417 133 5 1 2399 150886679 150884268 0.000000e+00 3578
6 TraesCS4A01G371300 chr3D 93.380 2417 138 7 1 2399 86081407 86078995 0.000000e+00 3557
7 TraesCS4A01G371300 chr2B 92.450 2318 150 10 103 2399 696855918 696858231 0.000000e+00 3288
8 TraesCS4A01G371300 chr3B 90.194 2417 181 18 1 2399 702151889 702149511 0.000000e+00 3099
9 TraesCS4A01G371300 chr7B 92.348 1895 126 4 1 1878 30075426 30073534 0.000000e+00 2678
10 TraesCS4A01G371300 chr5A 91.414 1619 90 13 147 1748 241459561 241457975 0.000000e+00 2174
11 TraesCS4A01G371300 chr5A 93.168 805 51 2 1598 2399 667565205 667566008 0.000000e+00 1179
12 TraesCS4A01G371300 chr2A 90.859 1619 95 16 147 1748 111272867 111271285 0.000000e+00 2121
13 TraesCS4A01G371300 chr2A 94.828 406 20 1 1995 2399 545065869 545066274 1.210000e-177 632
14 TraesCS4A01G371300 chr6B 91.294 873 57 4 1151 2006 65426128 65425258 0.000000e+00 1173
15 TraesCS4A01G371300 chr1B 89.595 519 44 7 1 509 624881302 624881820 0.000000e+00 651
16 TraesCS4A01G371300 chr1A 89.648 512 46 6 1 509 548669992 548670499 0.000000e+00 645
17 TraesCS4A01G371300 chr4B 95.050 404 19 1 1997 2399 145028664 145029067 3.360000e-178 634
18 TraesCS4A01G371300 chr5D 81.407 398 30 10 1583 1957 483324111 483324487 3.900000e-73 285


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 TraesCS4A01G371300 chr4A 644921447 644923845 2398 True 4431 4431 100.000 1 2399 1 chr4A.!!$R1 2398
1 TraesCS4A01G371300 chr7D 180439622 180442036 2414 False 3659 3659 94.125 1 2399 1 chr7D.!!$F1 2398
2 TraesCS4A01G371300 chr3A 703851157 703853572 2415 True 3626 3626 93.877 1 2399 1 chr3A.!!$R2 2398
3 TraesCS4A01G371300 chr3A 171150784 171151896 1112 False 1655 1655 93.722 654 1752 1 chr3A.!!$F1 1098
4 TraesCS4A01G371300 chr3A 545674657 545675769 1112 True 1628 1628 93.286 654 1752 1 chr3A.!!$R1 1098
5 TraesCS4A01G371300 chr6D 150884268 150886679 2411 True 3578 3578 93.546 1 2399 1 chr6D.!!$R1 2398
6 TraesCS4A01G371300 chr3D 86078995 86081407 2412 True 3557 3557 93.380 1 2399 1 chr3D.!!$R1 2398
7 TraesCS4A01G371300 chr2B 696855918 696858231 2313 False 3288 3288 92.450 103 2399 1 chr2B.!!$F1 2296
8 TraesCS4A01G371300 chr3B 702149511 702151889 2378 True 3099 3099 90.194 1 2399 1 chr3B.!!$R1 2398
9 TraesCS4A01G371300 chr7B 30073534 30075426 1892 True 2678 2678 92.348 1 1878 1 chr7B.!!$R1 1877
10 TraesCS4A01G371300 chr5A 241457975 241459561 1586 True 2174 2174 91.414 147 1748 1 chr5A.!!$R1 1601
11 TraesCS4A01G371300 chr5A 667565205 667566008 803 False 1179 1179 93.168 1598 2399 1 chr5A.!!$F1 801
12 TraesCS4A01G371300 chr2A 111271285 111272867 1582 True 2121 2121 90.859 147 1748 1 chr2A.!!$R1 1601
13 TraesCS4A01G371300 chr6B 65425258 65426128 870 True 1173 1173 91.294 1151 2006 1 chr6B.!!$R1 855
14 TraesCS4A01G371300 chr1B 624881302 624881820 518 False 651 651 89.595 1 509 1 chr1B.!!$F1 508
15 TraesCS4A01G371300 chr1A 548669992 548670499 507 False 645 645 89.648 1 509 1 chr1A.!!$F1 508

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
309 316 0.105964 ACACTGAAGTTGCGTGGCTA 59.894 50.0 6.20 0.0 33.13 3.93 F
1329 1344 1.051008 TTCTCTCTGCTGCTGGTTCA 58.949 50.0 6.69 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1409 0.326927 TAGCACACAAGGGGGCTAAC 59.673 55.0 3.32 0.0 36.03 2.34 R
2143 2176 1.035139 GGGAACGGCGAGGTTATAGA 58.965 55.0 16.62 0.0 0.00 1.98 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
95 102 1.451387 CCCCGGCAGGATGTACAAC 60.451 63.158 3.68 0.00 41.02 3.32
96 103 1.602237 CCCGGCAGGATGTACAACT 59.398 57.895 3.68 0.00 41.02 3.16
111 118 3.050354 AACTGGACCCGCCACAACA 62.050 57.895 0.00 0.00 43.33 3.33
152 159 1.442769 TTCAGGATCACGCTTTGCTC 58.557 50.000 0.00 0.00 0.00 4.26
273 280 3.146066 ACTGCAATTTTCTGAAGCCGTA 58.854 40.909 0.00 0.00 0.00 4.02
309 316 0.105964 ACACTGAAGTTGCGTGGCTA 59.894 50.000 6.20 0.00 33.13 3.93
400 413 6.995686 TGATACTACAAACTCTTGGCTTTCAA 59.004 34.615 0.00 0.00 36.82 2.69
449 462 7.490657 TGTGATTAGTTGAACTATACCCTGT 57.509 36.000 5.81 0.00 29.64 4.00
542 555 3.011517 ACGCCCCAGCAAGATCCT 61.012 61.111 0.00 0.00 39.83 3.24
556 569 3.254024 ATCCTGGCCGTCACGCTTT 62.254 57.895 0.00 0.00 0.00 3.51
558 571 3.777925 CTGGCCGTCACGCTTTCG 61.778 66.667 0.00 0.00 42.43 3.46
663 677 4.329545 GCCTCGTTGACCCCAGCA 62.330 66.667 0.00 0.00 0.00 4.41
677 691 2.285969 AGCAGCAGGACTCCCCAT 60.286 61.111 0.00 0.00 37.41 4.00
714 728 4.790962 CCAGGGAGCATGCGCAGT 62.791 66.667 23.18 6.35 42.27 4.40
718 732 2.590007 GGAGCATGCGCAGTAGGG 60.590 66.667 23.18 3.75 42.27 3.53
758 772 8.783093 CATCTAGTTACTGAATACTCCTCTGAG 58.217 40.741 0.00 0.00 44.62 3.35
835 849 6.389278 ACCTCCTGTCTAGTATAGGACAAGTA 59.611 42.308 7.86 0.00 40.36 2.24
1029 1043 5.163301 GGAAGATATGTTCCTGACCAAGCTA 60.163 44.000 21.51 0.00 42.57 3.32
1187 1202 1.468127 TGATTTGTTCGATGTGCGCAT 59.532 42.857 15.91 13.71 40.61 4.73
1235 1250 3.019799 AGAAGATGGCGAGTAAGGAGA 57.980 47.619 0.00 0.00 0.00 3.71
1237 1252 3.131400 AGAAGATGGCGAGTAAGGAGAAC 59.869 47.826 0.00 0.00 0.00 3.01
1329 1344 1.051008 TTCTCTCTGCTGCTGGTTCA 58.949 50.000 6.69 0.00 0.00 3.18
1394 1409 2.980568 TGGTAATCAGGTTGCCGTTAG 58.019 47.619 0.00 0.00 44.74 2.34
1462 1477 6.844696 TTGCATATTTCCTTCGTGTATCTC 57.155 37.500 0.00 0.00 0.00 2.75
1501 1532 9.719355 AAACAACTCCAGTTAGAATTTTTGTTT 57.281 25.926 0.00 0.00 38.92 2.83
1555 1586 5.655090 TGGTGTTGAGAAATCGATAGGTAGA 59.345 40.000 0.00 0.00 0.00 2.59
1657 1689 8.845413 ATGGAAGAACTTATATCAATCTGCTC 57.155 34.615 0.00 0.00 0.00 4.26
1694 1726 9.225682 TCTATGTACTCCCTCCTTAATTCAAAT 57.774 33.333 0.00 0.00 0.00 2.32
1726 1758 6.480320 CACTTATTTTTGATCGGAGGGAGTAG 59.520 42.308 0.00 0.00 0.00 2.57
1776 1808 9.985318 GTCATTTCAGAATTCAGATAGAAACTG 57.015 33.333 8.44 9.39 41.59 3.16
1811 1843 7.231722 GGAGCCTTCTATTCAGTCATAGACTTA 59.768 40.741 0.00 0.00 41.37 2.24
1813 1845 8.982723 AGCCTTCTATTCAGTCATAGACTTAAA 58.017 33.333 0.00 0.00 41.37 1.52
1855 1887 6.918022 CCTCTGTGTTTTTCAGGTACAAAATC 59.082 38.462 0.00 0.00 34.15 2.17
1856 1888 6.801575 TCTGTGTTTTTCAGGTACAAAATCC 58.198 36.000 0.00 0.00 34.15 3.01
1903 1935 4.365514 TGGTGCATCTCTTTTCAGGTAA 57.634 40.909 0.00 0.00 0.00 2.85
1973 2006 1.217942 AGAACCTTGCCCTCAACCTTT 59.782 47.619 0.00 0.00 0.00 3.11
2086 2119 0.456628 GTGAGGTTCTCCTAGGTCGC 59.543 60.000 9.08 0.34 45.24 5.19
2120 2153 2.224233 CGACATGAAGCTCAGGGATGAT 60.224 50.000 0.00 0.00 31.56 2.45
2142 2175 3.516981 TTGAGAGGCTCAAGAAGATCG 57.483 47.619 18.26 0.00 44.27 3.69
2143 2176 2.451490 TGAGAGGCTCAAGAAGATCGT 58.549 47.619 18.26 0.00 37.57 3.73
2144 2177 2.425312 TGAGAGGCTCAAGAAGATCGTC 59.575 50.000 18.26 0.00 37.57 4.20
2264 2300 3.134804 AGGACTAGCAGTTTGTGTCTTGT 59.865 43.478 0.00 0.00 0.00 3.16
2334 2370 7.554118 TGATAGACTTAATTTTCTGCTGGAAGG 59.446 37.037 0.00 0.00 35.16 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 54 1.504359 CGACGAACAACCAAGGCTTA 58.496 50.000 0.00 0.00 0.00 3.09
53 60 1.595929 GAGCCCGACGAACAACCAA 60.596 57.895 0.00 0.00 0.00 3.67
57 64 4.367023 CCCGAGCCCGACGAACAA 62.367 66.667 0.00 0.00 38.22 2.83
96 103 0.322098 CTTATGTTGTGGCGGGTCCA 60.322 55.000 0.00 0.00 44.18 4.02
136 143 0.737715 GACGAGCAAAGCGTGATCCT 60.738 55.000 0.00 0.00 42.77 3.24
152 159 2.120232 CGCATAGCTCCTTACAAGACG 58.880 52.381 0.00 0.00 0.00 4.18
168 175 0.804989 GCTACCAGCTGAAAACGCAT 59.195 50.000 17.39 0.00 38.45 4.73
243 250 9.578439 GCTTCAGAAAATTGCAGTAATTTCTAT 57.422 29.630 9.39 0.00 45.74 1.98
273 280 9.998106 ACTTCAGTGTTTGTAGACATAGTTAAT 57.002 29.630 0.00 0.00 0.00 1.40
309 316 4.775236 CATCAAGCCTACTTAGCCTTTCT 58.225 43.478 0.00 0.00 33.74 2.52
400 413 1.820519 TCGGGACAGTACGCAGTTAAT 59.179 47.619 0.00 0.00 37.78 1.40
478 491 8.165239 TGTATGCAATAACAGAATGATTACCC 57.835 34.615 0.00 0.00 39.69 3.69
494 507 4.825634 CCATCTCATCAACCTGTATGCAAT 59.174 41.667 0.00 0.00 0.00 3.56
649 663 3.535629 CTGCTGCTGGGGTCAACGA 62.536 63.158 0.00 0.00 0.00 3.85
663 677 3.415087 GGCATGGGGAGTCCTGCT 61.415 66.667 18.41 0.00 38.69 4.24
706 720 3.866582 GAGGGCCCTACTGCGCAT 61.867 66.667 28.78 0.00 45.78 4.73
714 728 1.235756 TGAGATGAGAGAGGGCCCTA 58.764 55.000 28.78 9.57 0.00 3.53
718 732 3.766545 ACTAGATGAGATGAGAGAGGGC 58.233 50.000 0.00 0.00 0.00 5.19
758 772 7.377766 TCAGATTACAGGTGAAAAATAGCAC 57.622 36.000 0.00 0.00 0.00 4.40
835 849 8.848474 AGTAAAACACATACTAGCATTCACTT 57.152 30.769 0.00 0.00 31.96 3.16
934 948 1.959226 GTTCGACAAAGCAGGGCGA 60.959 57.895 0.00 0.00 0.00 5.54
1029 1043 2.816958 CTCTCGCGCATGCTGGTT 60.817 61.111 17.13 0.00 39.65 3.67
1039 1053 1.927608 TTCTCTGTGCTCCTCTCGCG 61.928 60.000 0.00 0.00 0.00 5.87
1101 1116 3.074412 CACAAACCAGCTGTAAGGGTAG 58.926 50.000 13.81 2.30 33.71 3.18
1187 1202 1.344438 AGCCTGACACTTCATCAACGA 59.656 47.619 0.00 0.00 0.00 3.85
1191 1206 2.540383 ACCTAGCCTGACACTTCATCA 58.460 47.619 0.00 0.00 0.00 3.07
1235 1250 0.395312 CACCGGTACTCAACAGGGTT 59.605 55.000 6.87 0.00 46.81 4.11
1237 1252 1.375523 GCACCGGTACTCAACAGGG 60.376 63.158 6.87 0.00 46.81 4.45
1276 1291 2.234908 CGAGGTGGAGATGTTCCTCTTT 59.765 50.000 8.16 0.00 46.92 2.52
1394 1409 0.326927 TAGCACACAAGGGGGCTAAC 59.673 55.000 3.32 0.00 36.03 2.34
1462 1477 5.063204 TGGAGTTGTTTCAGTTCATACAGG 58.937 41.667 0.00 0.00 0.00 4.00
1501 1532 6.980593 CAATCCTCAATTGGAAGTAACAACA 58.019 36.000 5.42 0.00 40.99 3.33
1648 1680 3.003689 AGAAACCAACAACGAGCAGATTG 59.996 43.478 0.00 0.00 0.00 2.67
1657 1689 4.390909 GGGAGTACATAGAAACCAACAACG 59.609 45.833 0.00 0.00 0.00 4.10
1694 1726 7.094805 CCTCCGATCAAAAATAAGTGTCTCAAA 60.095 37.037 0.00 0.00 0.00 2.69
1726 1758 3.503748 AGTTCAAGGCTGTTACAAGCATC 59.496 43.478 8.51 0.00 45.43 3.91
1776 1808 0.331616 TAGAAGGCTCCCCAAAAGGC 59.668 55.000 0.00 0.00 39.48 4.35
1855 1887 3.123804 GTCATGTACAGAACTATGGCGG 58.876 50.000 0.33 0.00 0.00 6.13
1856 1888 2.789339 CGTCATGTACAGAACTATGGCG 59.211 50.000 0.33 2.89 37.90 5.69
1922 1954 2.758089 CGATGCCAGCAAGACCAGC 61.758 63.158 0.00 0.00 0.00 4.85
1923 1955 2.758089 GCGATGCCAGCAAGACCAG 61.758 63.158 0.00 0.00 34.19 4.00
1973 2006 0.893727 GAGCAAAAAGGGAGCGGGAA 60.894 55.000 0.00 0.00 0.00 3.97
2054 2087 1.991121 ACCTCACGTCCTTGTAGTCA 58.009 50.000 0.00 0.00 0.00 3.41
2086 2119 0.949397 CATGTCGATGGCATTGGAGG 59.051 55.000 14.66 0.43 0.00 4.30
2142 2175 1.269465 GGGAACGGCGAGGTTATAGAC 60.269 57.143 16.62 0.00 0.00 2.59
2143 2176 1.035139 GGGAACGGCGAGGTTATAGA 58.965 55.000 16.62 0.00 0.00 1.98
2144 2177 1.038280 AGGGAACGGCGAGGTTATAG 58.962 55.000 16.62 0.00 0.00 1.31
2334 2370 6.458888 GGCATTCTAGTGTTTAGGAGATTTGC 60.459 42.308 0.00 0.00 31.58 3.68


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

AutoCloner maintained by Alex Coulton.