Multiple sequence alignment - TraesCS4D01G117300

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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 TraesCS4D01G117300 chr4D 100.000 3494 0 0 250 3743 97970931 97967438 0.000000e+00 6453.0
1 TraesCS4D01G117300 chr4D 87.116 2018 204 27 900 2870 97962503 97960495 0.000000e+00 2235.0
2 TraesCS4D01G117300 chr4D 81.844 716 100 20 1587 2283 374041175 374040471 3.240000e-160 575.0
3 TraesCS4D01G117300 chr4D 100.000 41 0 0 1 41 97971180 97971140 4.010000e-10 76.8
4 TraesCS4D01G117300 chr4B 97.007 2005 47 2 900 2892 139572242 139570239 0.000000e+00 3358.0
5 TraesCS4D01G117300 chr4B 86.670 2033 200 32 900 2870 139549281 139547258 0.000000e+00 2187.0
6 TraesCS4D01G117300 chr4B 80.519 1232 192 23 1381 2575 139593660 139592440 0.000000e+00 902.0
7 TraesCS4D01G117300 chr4B 82.410 921 136 19 1381 2283 460156617 460155705 0.000000e+00 780.0
8 TraesCS4D01G117300 chr1D 86.244 1970 222 16 969 2892 363861164 363863130 0.000000e+00 2091.0
9 TraesCS4D01G117300 chr1D 98.709 852 11 0 2892 3743 421870105 421870956 0.000000e+00 1513.0
10 TraesCS4D01G117300 chr1D 98.592 852 12 0 2892 3743 387523683 387522832 0.000000e+00 1507.0
11 TraesCS4D01G117300 chr1D 98.476 853 13 0 2891 3743 334243601 334244453 0.000000e+00 1504.0
12 TraesCS4D01G117300 chr1B 85.637 2040 236 23 901 2892 487405524 487407554 0.000000e+00 2091.0
13 TraesCS4D01G117300 chr1A 84.306 2039 264 21 901 2892 463218534 463220563 0.000000e+00 1941.0
14 TraesCS4D01G117300 chr5D 99.061 852 8 0 2892 3743 29141759 29142610 0.000000e+00 1530.0
15 TraesCS4D01G117300 chr5D 85.321 654 93 2 250 900 491568209 491568862 0.000000e+00 673.0
16 TraesCS4D01G117300 chr5D 85.168 654 93 2 250 899 365346218 365346871 0.000000e+00 667.0
17 TraesCS4D01G117300 chr7D 98.828 853 10 0 2891 3743 56882162 56881310 0.000000e+00 1520.0
18 TraesCS4D01G117300 chr7D 98.828 853 9 1 2891 3743 612267960 612267109 0.000000e+00 1519.0
19 TraesCS4D01G117300 chr7D 98.593 853 11 1 2891 3743 93993863 93994714 0.000000e+00 1507.0
20 TraesCS4D01G117300 chr7D 85.758 653 87 4 250 899 615562663 615562014 0.000000e+00 686.0
21 TraesCS4D01G117300 chr4A 87.389 1356 127 19 917 2234 478209508 478210857 0.000000e+00 1517.0
22 TraesCS4D01G117300 chr4A 83.808 667 78 16 2230 2870 478216299 478216961 1.150000e-169 606.0
23 TraesCS4D01G117300 chr2D 98.710 853 11 0 2891 3743 520046748 520045896 0.000000e+00 1515.0
24 TraesCS4D01G117300 chr2D 98.592 852 12 0 2892 3743 22833716 22834567 0.000000e+00 1507.0
25 TraesCS4D01G117300 chr2D 84.940 664 94 5 250 909 586955873 586956534 0.000000e+00 667.0
26 TraesCS4D01G117300 chr2D 100.000 41 0 0 1 41 71925030 71924990 4.010000e-10 76.8
27 TraesCS4D01G117300 chr6D 95.552 652 26 2 250 898 94685436 94684785 0.000000e+00 1040.0
28 TraesCS4D01G117300 chr6D 82.597 724 83 20 900 1612 61002837 61003528 1.920000e-167 599.0
29 TraesCS4D01G117300 chr6D 76.169 663 110 28 1666 2287 61003519 61004174 4.700000e-79 305.0
30 TraesCS4D01G117300 chr6D 100.000 41 0 0 1 41 94687158 94687118 4.010000e-10 76.8
31 TraesCS4D01G117300 chr6B 79.033 1407 212 50 905 2268 134838207 134839573 0.000000e+00 887.0
32 TraesCS4D01G117300 chr2B 89.433 653 66 2 250 899 105813819 105813167 0.000000e+00 821.0
33 TraesCS4D01G117300 chr2B 89.264 652 65 4 250 898 547007324 547006675 0.000000e+00 811.0
34 TraesCS4D01G117300 chr3B 78.531 1239 197 42 1381 2579 706028707 706027498 0.000000e+00 750.0
35 TraesCS4D01G117300 chr3B 81.564 358 63 3 900 1256 772133629 772133984 3.660000e-75 292.0
36 TraesCS4D01G117300 chr3D 78.243 1241 194 47 1381 2579 533959905 533958699 0.000000e+00 726.0
37 TraesCS4D01G117300 chr3D 85.518 656 89 5 250 901 32310285 32310938 0.000000e+00 680.0
38 TraesCS4D01G117300 chr3A 85.561 651 89 4 250 897 523541382 523540734 0.000000e+00 676.0


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 TraesCS4D01G117300 chr4D 97967438 97971180 3742 True 3264.9 6453 100.000 1 3743 2 chr4D.!!$R3 3742
1 TraesCS4D01G117300 chr4D 97960495 97962503 2008 True 2235.0 2235 87.116 900 2870 1 chr4D.!!$R1 1970
2 TraesCS4D01G117300 chr4D 374040471 374041175 704 True 575.0 575 81.844 1587 2283 1 chr4D.!!$R2 696
3 TraesCS4D01G117300 chr4B 139570239 139572242 2003 True 3358.0 3358 97.007 900 2892 1 chr4B.!!$R2 1992
4 TraesCS4D01G117300 chr4B 139547258 139549281 2023 True 2187.0 2187 86.670 900 2870 1 chr4B.!!$R1 1970
5 TraesCS4D01G117300 chr4B 139592440 139593660 1220 True 902.0 902 80.519 1381 2575 1 chr4B.!!$R3 1194
6 TraesCS4D01G117300 chr4B 460155705 460156617 912 True 780.0 780 82.410 1381 2283 1 chr4B.!!$R4 902
7 TraesCS4D01G117300 chr1D 363861164 363863130 1966 False 2091.0 2091 86.244 969 2892 1 chr1D.!!$F2 1923
8 TraesCS4D01G117300 chr1D 421870105 421870956 851 False 1513.0 1513 98.709 2892 3743 1 chr1D.!!$F3 851
9 TraesCS4D01G117300 chr1D 387522832 387523683 851 True 1507.0 1507 98.592 2892 3743 1 chr1D.!!$R1 851
10 TraesCS4D01G117300 chr1D 334243601 334244453 852 False 1504.0 1504 98.476 2891 3743 1 chr1D.!!$F1 852
11 TraesCS4D01G117300 chr1B 487405524 487407554 2030 False 2091.0 2091 85.637 901 2892 1 chr1B.!!$F1 1991
12 TraesCS4D01G117300 chr1A 463218534 463220563 2029 False 1941.0 1941 84.306 901 2892 1 chr1A.!!$F1 1991
13 TraesCS4D01G117300 chr5D 29141759 29142610 851 False 1530.0 1530 99.061 2892 3743 1 chr5D.!!$F1 851
14 TraesCS4D01G117300 chr5D 491568209 491568862 653 False 673.0 673 85.321 250 900 1 chr5D.!!$F3 650
15 TraesCS4D01G117300 chr5D 365346218 365346871 653 False 667.0 667 85.168 250 899 1 chr5D.!!$F2 649
16 TraesCS4D01G117300 chr7D 56881310 56882162 852 True 1520.0 1520 98.828 2891 3743 1 chr7D.!!$R1 852
17 TraesCS4D01G117300 chr7D 612267109 612267960 851 True 1519.0 1519 98.828 2891 3743 1 chr7D.!!$R2 852
18 TraesCS4D01G117300 chr7D 93993863 93994714 851 False 1507.0 1507 98.593 2891 3743 1 chr7D.!!$F1 852
19 TraesCS4D01G117300 chr7D 615562014 615562663 649 True 686.0 686 85.758 250 899 1 chr7D.!!$R3 649
20 TraesCS4D01G117300 chr4A 478209508 478210857 1349 False 1517.0 1517 87.389 917 2234 1 chr4A.!!$F1 1317
21 TraesCS4D01G117300 chr4A 478216299 478216961 662 False 606.0 606 83.808 2230 2870 1 chr4A.!!$F2 640
22 TraesCS4D01G117300 chr2D 520045896 520046748 852 True 1515.0 1515 98.710 2891 3743 1 chr2D.!!$R2 852
23 TraesCS4D01G117300 chr2D 22833716 22834567 851 False 1507.0 1507 98.592 2892 3743 1 chr2D.!!$F1 851
24 TraesCS4D01G117300 chr2D 586955873 586956534 661 False 667.0 667 84.940 250 909 1 chr2D.!!$F2 659
25 TraesCS4D01G117300 chr6D 94684785 94687158 2373 True 558.4 1040 97.776 1 898 2 chr6D.!!$R1 897
26 TraesCS4D01G117300 chr6D 61002837 61004174 1337 False 452.0 599 79.383 900 2287 2 chr6D.!!$F1 1387
27 TraesCS4D01G117300 chr6B 134838207 134839573 1366 False 887.0 887 79.033 905 2268 1 chr6B.!!$F1 1363
28 TraesCS4D01G117300 chr2B 105813167 105813819 652 True 821.0 821 89.433 250 899 1 chr2B.!!$R1 649
29 TraesCS4D01G117300 chr2B 547006675 547007324 649 True 811.0 811 89.264 250 898 1 chr2B.!!$R2 648
30 TraesCS4D01G117300 chr3B 706027498 706028707 1209 True 750.0 750 78.531 1381 2579 1 chr3B.!!$R1 1198
31 TraesCS4D01G117300 chr3D 533958699 533959905 1206 True 726.0 726 78.243 1381 2579 1 chr3D.!!$R1 1198
32 TraesCS4D01G117300 chr3D 32310285 32310938 653 False 680.0 680 85.518 250 901 1 chr3D.!!$F1 651
33 TraesCS4D01G117300 chr3A 523540734 523541382 648 True 676.0 676 85.561 250 897 1 chr3A.!!$R1 647

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
581 2058 0.035458 AAGGTATGGCGCTGGCTATC 59.965 55.000 7.64 0.0 39.85 2.08 F
1121 2619 1.306141 TGCTCTCCCGGATCCACTT 60.306 57.895 13.41 0.0 0.00 3.16 F
1185 2683 3.141488 CTCCTCCCCCACGACTCG 61.141 72.222 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 3468 0.030638 CTTCACCTTGGTGCAAACCG 59.969 55.0 14.49 0.0 0.00 4.44 R
2107 3734 0.396974 TGCTTGGGCTCACCTTTGTT 60.397 50.0 0.00 0.0 41.11 2.83 R
3061 4717 0.462759 GACGGAGCCAATCTTCCCAG 60.463 60.0 0.00 0.0 0.00 4.45 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
551 2028 3.190874 CTCTCTTGAGGCGGAATTACAC 58.809 50.000 0.00 0.0 36.70 2.90
581 2058 0.035458 AAGGTATGGCGCTGGCTATC 59.965 55.000 7.64 0.0 39.85 2.08
672 2149 2.419574 GCCCTCCAACGTTCAGCTTATA 60.420 50.000 0.00 0.0 0.00 0.98
674 2151 3.118738 CCCTCCAACGTTCAGCTTATAGT 60.119 47.826 0.00 0.0 0.00 2.12
689 2166 6.150976 CAGCTTATAGTCAATTGGTGTTGGAA 59.849 38.462 5.42 0.0 0.00 3.53
717 2194 8.508601 TCAAGTACTTATCTGGTATTAGGGAGA 58.491 37.037 8.04 0.0 0.00 3.71
718 2195 9.144298 CAAGTACTTATCTGGTATTAGGGAGAA 57.856 37.037 8.04 0.0 0.00 2.87
736 2216 6.498651 AGGGAGAATTCTCAGAAACTTAGTCA 59.501 38.462 31.29 0.0 44.60 3.41
753 2233 9.778741 AACTTAGTCATGTTCAAAATAGAGTGA 57.221 29.630 0.00 0.0 0.00 3.41
820 2300 1.488393 GTGGCTAGGCTCAATTCCTCT 59.512 52.381 18.18 0.0 35.21 3.69
1121 2619 1.306141 TGCTCTCCCGGATCCACTT 60.306 57.895 13.41 0.0 0.00 3.16
1185 2683 3.141488 CTCCTCCCCCACGACTCG 61.141 72.222 0.00 0.0 0.00 4.18
1848 3403 5.180304 GTCCTTCTTTGAAGAAATCGCTCTT 59.820 40.000 8.69 0.0 43.84 2.85
2029 3608 3.440173 GGTGCCTCATCTTTTCGATTTGA 59.560 43.478 0.00 0.0 0.00 2.69
2107 3734 1.372683 GACTGCACTGAAGGCTGGA 59.627 57.895 0.00 0.0 34.89 3.86
2472 4108 1.519234 CCGCTCGTGCATCAAGCTA 60.519 57.895 10.43 0.0 45.94 3.32
2677 4328 7.173907 CCTCAATCATGGTTGATACTAATGGAC 59.826 40.741 21.37 0.0 41.83 4.02
2720 4371 3.513515 AGAGCATCCGACTTTTCTCTTCT 59.486 43.478 0.00 0.0 33.66 2.85
2791 4443 5.336610 GGTCTCTACCTCTGGAAGTTGTTAC 60.337 48.000 0.00 0.0 43.08 2.50
3061 4717 1.702491 GGTCGTTAGTGGGCAATCGC 61.702 60.000 0.00 0.0 37.44 4.58
3523 5179 5.305585 AGACATATTCGTGTTGGAGTTTGT 58.694 37.500 0.00 0.0 31.16 2.83
3674 5330 1.194121 GGCCAGGGAGCATTTGGTTT 61.194 55.000 0.00 0.0 34.43 3.27
3738 5394 0.462937 CGGTTTGGATGGCGGTCATA 60.463 55.000 0.00 0.0 35.97 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
416 1890 1.596934 GTGGAAGGAGCCATCGACA 59.403 57.895 2.65 0.00 40.68 4.35
487 1963 2.019249 TGTATGCTGCAAAGAGGATGC 58.981 47.619 6.36 0.00 44.08 3.91
551 2028 0.514255 CCATACCTTGCATCATCGCG 59.486 55.000 0.00 0.00 33.35 5.87
592 2069 0.391130 TTGAAGAATCACCGGAGCCG 60.391 55.000 9.46 1.06 34.61 5.52
593 2070 1.943340 GATTGAAGAATCACCGGAGCC 59.057 52.381 9.46 0.00 38.33 4.70
672 2149 5.363580 ACTTGATTTCCAACACCAATTGACT 59.636 36.000 7.12 0.00 0.00 3.41
674 2151 5.867903 ACTTGATTTCCAACACCAATTGA 57.132 34.783 7.12 0.00 0.00 2.57
689 2166 9.670442 TCCCTAATACCAGATAAGTACTTGATT 57.330 33.333 18.56 2.90 0.00 2.57
717 2194 8.908786 TGAACATGACTAAGTTTCTGAGAATT 57.091 30.769 0.00 0.00 0.00 2.17
718 2195 8.908786 TTGAACATGACTAAGTTTCTGAGAAT 57.091 30.769 0.00 0.00 0.00 2.40
736 2216 5.520288 CGATCGGTCACTCTATTTTGAACAT 59.480 40.000 7.38 0.00 29.19 2.71
753 2233 2.172851 TAGTTTGCCAAACGATCGGT 57.827 45.000 20.98 10.86 45.88 4.69
820 2300 5.376625 GAGGCCATACATCCTCAATACAAA 58.623 41.667 5.01 0.00 46.24 2.83
1745 3300 1.194781 ATTCCCGTGGACACAGAGCT 61.195 55.000 3.12 0.00 0.00 4.09
1904 3468 0.030638 CTTCACCTTGGTGCAAACCG 59.969 55.000 14.49 0.00 0.00 4.44
2107 3734 0.396974 TGCTTGGGCTCACCTTTGTT 60.397 50.000 0.00 0.00 41.11 2.83
2377 4010 3.214328 GGCCACTTTCTTCAGACTGAAA 58.786 45.455 18.26 7.50 35.73 2.69
2472 4108 3.758554 CTCGGAAATCATGGAAAACCAGT 59.241 43.478 0.00 0.00 0.00 4.00
2677 4328 3.334691 TCTTGAAGTTCCCAATGCTACG 58.665 45.455 0.00 0.00 0.00 3.51
2791 4443 0.642291 CATACTGCGACAACAGAGCG 59.358 55.000 0.00 0.00 40.25 5.03
3061 4717 0.462759 GACGGAGCCAATCTTCCCAG 60.463 60.000 0.00 0.00 0.00 4.45
3523 5179 3.072330 TCCAGATAGTCCACAACAAAGCA 59.928 43.478 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.