Multiple sequence alignment - TraesCS7A01G459000

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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 TraesCS7A01G459000 chr7A 100.000 2923 0 0 1 2923 654048949 654051871 0.000000e+00 5398
1 TraesCS7A01G459000 chr7A 97.095 1446 40 2 574 2018 730331767 730330323 0.000000e+00 2436
2 TraesCS7A01G459000 chr7A 96.819 1446 43 3 574 2018 730379035 730377592 0.000000e+00 2412
3 TraesCS7A01G459000 chr7A 96.346 903 28 5 2011 2912 653711162 653712060 0.000000e+00 1480
4 TraesCS7A01G459000 chr7A 95.415 916 36 5 2011 2923 573512739 573513651 0.000000e+00 1454
5 TraesCS7A01G459000 chr7A 95.154 908 37 5 2019 2923 93746884 93747787 0.000000e+00 1426
6 TraesCS7A01G459000 chr7A 94.009 918 46 7 2008 2923 93753865 93754775 0.000000e+00 1382
7 TraesCS7A01G459000 chr7A 97.742 620 14 0 1330 1949 68795494 68796113 0.000000e+00 1068
8 TraesCS7A01G459000 chr7A 92.250 671 39 8 3 667 648156280 648155617 0.000000e+00 939
9 TraesCS7A01G459000 chr7A 91.172 691 52 8 1 682 14529754 14529064 0.000000e+00 929
10 TraesCS7A01G459000 chr4B 91.634 2044 118 13 1 2018 7100718 7102734 0.000000e+00 2778
11 TraesCS7A01G459000 chr4B 93.048 187 13 0 683 869 576736100 576735914 1.030000e-69 274
12 TraesCS7A01G459000 chr2B 90.102 2051 153 36 1 2018 692693937 692691904 0.000000e+00 2617
13 TraesCS7A01G459000 chr4A 90.409 1689 116 24 355 2015 670764585 670766255 0.000000e+00 2180
14 TraesCS7A01G459000 chr4A 91.979 187 14 1 683 869 3776864 3776679 8.030000e-66 261
15 TraesCS7A01G459000 chr5A 93.276 1041 56 1 992 2018 437594020 437592980 0.000000e+00 1522
16 TraesCS7A01G459000 chr5A 90.379 686 55 9 1 682 246343513 246342835 0.000000e+00 891
17 TraesCS7A01G459000 chr5A 94.156 308 18 0 683 990 437449040 437449347 1.230000e-128 470
18 TraesCS7A01G459000 chr5A 91.444 187 16 0 683 869 433438109 433438295 1.040000e-64 257
19 TraesCS7A01G459000 chr3A 95.815 908 33 4 2019 2923 566471544 566472449 0.000000e+00 1461
20 TraesCS7A01G459000 chr3A 94.438 917 43 6 2011 2923 66146430 66145518 0.000000e+00 1404
21 TraesCS7A01G459000 chr3A 94.336 918 44 7 2010 2923 658666422 658667335 0.000000e+00 1400
22 TraesCS7A01G459000 chr3A 97.656 768 17 1 1252 2018 21307079 21307846 0.000000e+00 1317
23 TraesCS7A01G459000 chr3A 94.469 687 33 4 1 682 631786443 631787129 0.000000e+00 1053
24 TraesCS7A01G459000 chr3A 91.266 687 48 9 1 681 129251391 129250711 0.000000e+00 926
25 TraesCS7A01G459000 chr3A 92.784 194 5 2 681 865 689948287 689948094 3.710000e-69 272
26 TraesCS7A01G459000 chr3A 91.919 198 7 2 681 869 547726937 547727134 4.800000e-68 268
27 TraesCS7A01G459000 chr1A 95.082 915 36 3 2011 2923 556075587 556074680 0.000000e+00 1432
28 TraesCS7A01G459000 chr2A 94.923 906 40 4 2019 2923 160996467 160997367 0.000000e+00 1413
29 TraesCS7A01G459000 chr2A 97.653 767 18 0 1252 2018 22312388 22311622 0.000000e+00 1317
30 TraesCS7A01G459000 chr2A 97.132 767 22 0 1252 2018 746144550 746143784 0.000000e+00 1295
31 TraesCS7A01G459000 chr2A 91.753 194 7 2 681 865 92989966 92990159 8.030000e-66 261
32 TraesCS7A01G459000 chr1B 85.349 1174 110 29 869 2018 637833316 637832181 0.000000e+00 1158
33 TraesCS7A01G459000 chr6A 93.869 685 37 4 1 682 546014561 546015243 0.000000e+00 1027
34 TraesCS7A01G459000 chr6B 92.878 688 42 4 1 682 669952404 669953090 0.000000e+00 992
35 TraesCS7A01G459000 chr3B 92.526 669 48 2 1 667 620325996 620325328 0.000000e+00 957
36 TraesCS7A01G459000 chr7B 89.444 701 64 7 1 700 154312552 154311861 0.000000e+00 876


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 TraesCS7A01G459000 chr7A 654048949 654051871 2922 False 5398 5398 100.000 1 2923 1 chr7A.!!$F6 2922
1 TraesCS7A01G459000 chr7A 730330323 730331767 1444 True 2436 2436 97.095 574 2018 1 chr7A.!!$R3 1444
2 TraesCS7A01G459000 chr7A 730377592 730379035 1443 True 2412 2412 96.819 574 2018 1 chr7A.!!$R4 1444
3 TraesCS7A01G459000 chr7A 653711162 653712060 898 False 1480 1480 96.346 2011 2912 1 chr7A.!!$F5 901
4 TraesCS7A01G459000 chr7A 573512739 573513651 912 False 1454 1454 95.415 2011 2923 1 chr7A.!!$F4 912
5 TraesCS7A01G459000 chr7A 93746884 93747787 903 False 1426 1426 95.154 2019 2923 1 chr7A.!!$F2 904
6 TraesCS7A01G459000 chr7A 93753865 93754775 910 False 1382 1382 94.009 2008 2923 1 chr7A.!!$F3 915
7 TraesCS7A01G459000 chr7A 68795494 68796113 619 False 1068 1068 97.742 1330 1949 1 chr7A.!!$F1 619
8 TraesCS7A01G459000 chr7A 648155617 648156280 663 True 939 939 92.250 3 667 1 chr7A.!!$R2 664
9 TraesCS7A01G459000 chr7A 14529064 14529754 690 True 929 929 91.172 1 682 1 chr7A.!!$R1 681
10 TraesCS7A01G459000 chr4B 7100718 7102734 2016 False 2778 2778 91.634 1 2018 1 chr4B.!!$F1 2017
11 TraesCS7A01G459000 chr2B 692691904 692693937 2033 True 2617 2617 90.102 1 2018 1 chr2B.!!$R1 2017
12 TraesCS7A01G459000 chr4A 670764585 670766255 1670 False 2180 2180 90.409 355 2015 1 chr4A.!!$F1 1660
13 TraesCS7A01G459000 chr5A 437592980 437594020 1040 True 1522 1522 93.276 992 2018 1 chr5A.!!$R2 1026
14 TraesCS7A01G459000 chr5A 246342835 246343513 678 True 891 891 90.379 1 682 1 chr5A.!!$R1 681
15 TraesCS7A01G459000 chr3A 566471544 566472449 905 False 1461 1461 95.815 2019 2923 1 chr3A.!!$F3 904
16 TraesCS7A01G459000 chr3A 66145518 66146430 912 True 1404 1404 94.438 2011 2923 1 chr3A.!!$R1 912
17 TraesCS7A01G459000 chr3A 658666422 658667335 913 False 1400 1400 94.336 2010 2923 1 chr3A.!!$F5 913
18 TraesCS7A01G459000 chr3A 21307079 21307846 767 False 1317 1317 97.656 1252 2018 1 chr3A.!!$F1 766
19 TraesCS7A01G459000 chr3A 631786443 631787129 686 False 1053 1053 94.469 1 682 1 chr3A.!!$F4 681
20 TraesCS7A01G459000 chr3A 129250711 129251391 680 True 926 926 91.266 1 681 1 chr3A.!!$R2 680
21 TraesCS7A01G459000 chr1A 556074680 556075587 907 True 1432 1432 95.082 2011 2923 1 chr1A.!!$R1 912
22 TraesCS7A01G459000 chr2A 160996467 160997367 900 False 1413 1413 94.923 2019 2923 1 chr2A.!!$F2 904
23 TraesCS7A01G459000 chr2A 22311622 22312388 766 True 1317 1317 97.653 1252 2018 1 chr2A.!!$R1 766
24 TraesCS7A01G459000 chr2A 746143784 746144550 766 True 1295 1295 97.132 1252 2018 1 chr2A.!!$R2 766
25 TraesCS7A01G459000 chr1B 637832181 637833316 1135 True 1158 1158 85.349 869 2018 1 chr1B.!!$R1 1149
26 TraesCS7A01G459000 chr6A 546014561 546015243 682 False 1027 1027 93.869 1 682 1 chr6A.!!$F1 681
27 TraesCS7A01G459000 chr6B 669952404 669953090 686 False 992 992 92.878 1 682 1 chr6B.!!$F1 681
28 TraesCS7A01G459000 chr3B 620325328 620325996 668 True 957 957 92.526 1 667 1 chr3B.!!$R1 666
29 TraesCS7A01G459000 chr7B 154311861 154312552 691 True 876 876 89.444 1 700 1 chr7B.!!$R1 699

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
877 954 0.107312 GCTGCTCTGACCATCCACAT 60.107 55.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2567 2725 0.341609 CCCCCTCTCTCTCTTTCCCT 59.658 60.0 0.0 0.0 0.0 4.2 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
25 26 4.323257 CCGTTCCTACCTAGTGGTTGAATT 60.323 45.833 0.00 0.00 46.05 2.17
35 36 5.989168 CCTAGTGGTTGAATTTTGGAAAACC 59.011 40.000 0.00 0.00 40.59 3.27
120 122 1.004044 AGCAAACTATGAGGCAGCTGT 59.996 47.619 16.64 0.00 0.00 4.40
168 172 3.316868 TGAACCGGTGGAAATTTGTCTTC 59.683 43.478 8.52 0.00 0.00 2.87
340 346 9.884465 CTCGGAAAATGATTAAAAATAGCTAGG 57.116 33.333 0.00 0.00 0.00 3.02
408 414 8.496751 GTGGTCTAACTCTAGTGAAAATTTGTC 58.503 37.037 0.00 0.00 0.00 3.18
419 425 4.978580 GTGAAAATTTGTCTGGTGCTCTTC 59.021 41.667 0.00 0.00 0.00 2.87
572 584 1.271434 CCATCCATCTCTGCATCCCAG 60.271 57.143 0.00 0.00 43.17 4.45
589 601 2.648304 CCCAGATCCATCCATCCATCTT 59.352 50.000 0.00 0.00 0.00 2.40
726 795 2.549282 GCGACATGCGAACGTGTT 59.451 55.556 12.67 0.00 46.14 3.32
865 942 4.218578 CATCGCCCTCGCTGCTCT 62.219 66.667 0.00 0.00 35.26 4.09
877 954 0.107312 GCTGCTCTGACCATCCACAT 60.107 55.000 0.00 0.00 0.00 3.21
888 965 2.502492 ATCCACATCTCGAGCCCGG 61.502 63.158 7.81 5.63 36.24 5.73
1017 1100 1.487976 GCCATGGAGAACCTGATCTCA 59.512 52.381 18.40 0.00 46.24 3.27
1106 1189 3.449227 CTGGGACTCGCTGCCGTA 61.449 66.667 0.00 0.00 31.12 4.02
1415 1563 5.655974 GGAAGCTAGGTACTACTACCACTTT 59.344 44.000 0.00 0.00 44.75 2.66
1571 1720 6.516739 TGTGGTTCTGTGTTTTGACATTTA 57.483 33.333 0.00 0.00 0.00 1.40
1694 1844 2.036346 GCAAGAGCTTGTCCATTTTGGT 59.964 45.455 11.47 0.00 42.31 3.67
1760 1910 2.089980 GATTCTGCAGGCATTGTCACT 58.910 47.619 15.13 0.00 0.00 3.41
1819 1969 2.106566 AGACAGGGAGTATGCAGAGTG 58.893 52.381 0.00 0.00 0.00 3.51
1937 2087 0.755079 CATGATTGAGGGGCTCTCGA 59.245 55.000 6.82 6.82 45.32 4.04
2567 2725 3.775316 GTTGGAATAGGACTCCTTGAGGA 59.225 47.826 1.94 0.00 43.08 3.71
2755 2921 5.755849 ACTCCGGTAAAATCCTGATTTCAT 58.244 37.500 0.00 0.00 39.88 2.57
2892 3058 7.807907 CCTTCGGTATATCAAAATGCATAAACC 59.192 37.037 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.989168 GGTTTTCCAAAATTCAACCACTAGG 59.011 40.000 0.00 0.00 37.44 3.02
25 26 5.247337 AGAGAAACACCAAAGGTTTTCCAAA 59.753 36.000 14.47 0.00 43.73 3.28
120 122 4.888239 TGGAAACGGGTCAAATTTGAACTA 59.112 37.500 30.02 4.78 44.25 2.24
168 172 3.319137 TTTGATCCACCTCTCGTGAAG 57.681 47.619 0.00 0.00 46.20 3.02
340 346 7.977853 ACCAATTTGTATGCATTTCTGATCTTC 59.022 33.333 3.54 0.00 0.00 2.87
408 414 8.822652 AAAAATATTTTTCAGAAGAGCACCAG 57.177 30.769 18.40 0.00 35.61 4.00
572 584 6.013898 TCTGTAGAAAGATGGATGGATGGATC 60.014 42.308 0.00 0.00 0.00 3.36
849 926 4.218578 CAGAGCAGCGAGGGCGAT 62.219 66.667 0.00 0.00 46.35 4.58
865 942 0.461548 GCTCGAGATGTGGATGGTCA 59.538 55.000 18.75 0.00 0.00 4.02
966 1049 1.533994 ATCTGGCCGGATCCGATCA 60.534 57.895 35.42 27.41 42.83 2.92
1017 1100 1.363744 GCTGCAGCTTATTGACGAGT 58.636 50.000 31.33 0.00 38.21 4.18
1082 1165 2.997897 GCGAGTCCCAGAGGGTGT 60.998 66.667 1.36 0.00 44.74 4.16
1415 1563 0.846015 CATGCCCCCTAGTTGATCCA 59.154 55.000 0.00 0.00 0.00 3.41
1571 1720 2.143876 ACAGTGTGCCAAAGGAGTTT 57.856 45.000 0.00 0.00 0.00 2.66
1694 1844 4.230657 CGTCACAAAAACAAAACAGGACA 58.769 39.130 0.00 0.00 0.00 4.02
1819 1969 1.380246 TTCCTGGGGACATGCATGC 60.380 57.895 26.53 18.01 41.51 4.06
2567 2725 0.341609 CCCCCTCTCTCTCTTTCCCT 59.658 60.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.