Multiple sequence alignment - TraesCS2A01G581200

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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 TraesCS2A01G581200 chr2A 100.000 3221 0 0 1 3221 773341674 773338454 0.000000e+00 5949
1 TraesCS2A01G581200 chr2A 96.923 975 25 3 2247 3221 738095017 738094048 0.000000e+00 1629
2 TraesCS2A01G581200 chr2A 96.814 973 29 2 2251 3221 733127565 733126593 0.000000e+00 1624
3 TraesCS2A01G581200 chr2A 96.502 972 31 2 2251 3221 45174635 45173666 0.000000e+00 1604
4 TraesCS2A01G581200 chr2A 96.421 978 26 4 2247 3221 613238381 613237410 0.000000e+00 1604
5 TraesCS2A01G581200 chr2A 96.395 971 31 2 2251 3221 762526629 762527595 0.000000e+00 1596
6 TraesCS2A01G581200 chr2A 98.876 801 9 0 1 801 773361267 773360467 0.000000e+00 1430
7 TraesCS2A01G581200 chr2A 90.099 808 77 1 1 805 13346139 13346946 0.000000e+00 1046
8 TraesCS2A01G581200 chr2A 90.363 799 74 1 1 796 15984077 15984875 0.000000e+00 1046
9 TraesCS2A01G581200 chr2A 90.363 799 74 1 1 796 48942334 48941536 0.000000e+00 1046
10 TraesCS2A01G581200 chr2A 90.363 799 74 1 1 796 137190510 137191308 0.000000e+00 1046
11 TraesCS2A01G581200 chr1A 96.571 1458 36 6 796 2250 572001222 571999776 0.000000e+00 2403
12 TraesCS2A01G581200 chr1A 96.923 975 25 3 2247 3221 581110849 581111818 0.000000e+00 1629
13 TraesCS2A01G581200 chr7A 96.377 1463 42 6 796 2250 689936577 689938036 0.000000e+00 2398
14 TraesCS2A01G581200 chr7A 96.910 971 25 4 2251 3221 648904501 648905466 0.000000e+00 1622
15 TraesCS2A01G581200 chr7A 93.665 805 51 0 1 805 525994473 525993669 0.000000e+00 1205
16 TraesCS2A01G581200 chr7A 89.864 809 78 2 1 806 546151784 546150977 0.000000e+00 1037
17 TraesCS2A01G581200 chr5A 96.025 1459 52 4 795 2250 573012042 573010587 0.000000e+00 2368
18 TraesCS2A01G581200 chr5A 95.953 1458 46 5 796 2250 634624343 634625790 0.000000e+00 2353
19 TraesCS2A01G581200 chr5A 96.126 981 29 3 2244 3221 477790194 477791168 0.000000e+00 1592
20 TraesCS2A01G581200 chr5A 93.197 147 9 1 796 941 634632146 634632000 7.000000e-52 215
21 TraesCS2A01G581200 chr6A 96.091 1458 45 5 796 2250 116690212 116691660 0.000000e+00 2366
22 TraesCS2A01G581200 chr6A 96.608 973 25 2 2251 3221 37537900 37536934 0.000000e+00 1607
23 TraesCS2A01G581200 chr6A 88.177 812 86 5 1 806 514578372 514579179 0.000000e+00 959
24 TraesCS2A01G581200 chr1D 94.441 1475 60 12 795 2250 42897082 42895611 0.000000e+00 2250
25 TraesCS2A01G581200 chr1D 88.519 810 87 4 1 806 248013730 248012923 0.000000e+00 976
26 TraesCS2A01G581200 chr2B 92.575 1468 81 9 798 2250 80552484 80551030 0.000000e+00 2082
27 TraesCS2A01G581200 chr4D 92.657 1430 72 15 837 2250 488848778 488850190 0.000000e+00 2028
28 TraesCS2A01G581200 chr5D 91.774 1471 90 16 796 2250 388593347 388594802 0.000000e+00 2017
29 TraesCS2A01G581200 chr3A 96.491 798 28 0 1 798 46781756 46782553 0.000000e+00 1319
30 TraesCS2A01G581200 chr3A 93.540 805 52 0 1 805 355914874 355915678 0.000000e+00 1199
31 TraesCS2A01G581200 chr3A 92.707 809 54 3 1 806 694616623 694617429 0.000000e+00 1162
32 TraesCS2A01G581200 chr4A 88.614 808 89 1 1 805 65879805 65880612 0.000000e+00 979
33 TraesCS2A01G581200 chr3B 88.243 808 92 1 1 805 783059731 783060538 0.000000e+00 963
34 TraesCS2A01G581200 chr6D 90.248 646 41 14 796 1427 45676096 45676733 0.000000e+00 824
35 TraesCS2A01G581200 chr3D 79.449 1017 137 48 794 1770 388399408 388400392 0.000000e+00 654


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 TraesCS2A01G581200 chr2A 773338454 773341674 3220 True 5949 5949 100.000 1 3221 1 chr2A.!!$R6 3220
1 TraesCS2A01G581200 chr2A 738094048 738095017 969 True 1629 1629 96.923 2247 3221 1 chr2A.!!$R5 974
2 TraesCS2A01G581200 chr2A 733126593 733127565 972 True 1624 1624 96.814 2251 3221 1 chr2A.!!$R4 970
3 TraesCS2A01G581200 chr2A 45173666 45174635 969 True 1604 1604 96.502 2251 3221 1 chr2A.!!$R1 970
4 TraesCS2A01G581200 chr2A 613237410 613238381 971 True 1604 1604 96.421 2247 3221 1 chr2A.!!$R3 974
5 TraesCS2A01G581200 chr2A 762526629 762527595 966 False 1596 1596 96.395 2251 3221 1 chr2A.!!$F4 970
6 TraesCS2A01G581200 chr2A 773360467 773361267 800 True 1430 1430 98.876 1 801 1 chr2A.!!$R7 800
7 TraesCS2A01G581200 chr2A 13346139 13346946 807 False 1046 1046 90.099 1 805 1 chr2A.!!$F1 804
8 TraesCS2A01G581200 chr2A 15984077 15984875 798 False 1046 1046 90.363 1 796 1 chr2A.!!$F2 795
9 TraesCS2A01G581200 chr2A 48941536 48942334 798 True 1046 1046 90.363 1 796 1 chr2A.!!$R2 795
10 TraesCS2A01G581200 chr2A 137190510 137191308 798 False 1046 1046 90.363 1 796 1 chr2A.!!$F3 795
11 TraesCS2A01G581200 chr1A 571999776 572001222 1446 True 2403 2403 96.571 796 2250 1 chr1A.!!$R1 1454
12 TraesCS2A01G581200 chr1A 581110849 581111818 969 False 1629 1629 96.923 2247 3221 1 chr1A.!!$F1 974
13 TraesCS2A01G581200 chr7A 689936577 689938036 1459 False 2398 2398 96.377 796 2250 1 chr7A.!!$F2 1454
14 TraesCS2A01G581200 chr7A 648904501 648905466 965 False 1622 1622 96.910 2251 3221 1 chr7A.!!$F1 970
15 TraesCS2A01G581200 chr7A 525993669 525994473 804 True 1205 1205 93.665 1 805 1 chr7A.!!$R1 804
16 TraesCS2A01G581200 chr7A 546150977 546151784 807 True 1037 1037 89.864 1 806 1 chr7A.!!$R2 805
17 TraesCS2A01G581200 chr5A 573010587 573012042 1455 True 2368 2368 96.025 795 2250 1 chr5A.!!$R1 1455
18 TraesCS2A01G581200 chr5A 634624343 634625790 1447 False 2353 2353 95.953 796 2250 1 chr5A.!!$F2 1454
19 TraesCS2A01G581200 chr5A 477790194 477791168 974 False 1592 1592 96.126 2244 3221 1 chr5A.!!$F1 977
20 TraesCS2A01G581200 chr6A 116690212 116691660 1448 False 2366 2366 96.091 796 2250 1 chr6A.!!$F1 1454
21 TraesCS2A01G581200 chr6A 37536934 37537900 966 True 1607 1607 96.608 2251 3221 1 chr6A.!!$R1 970
22 TraesCS2A01G581200 chr6A 514578372 514579179 807 False 959 959 88.177 1 806 1 chr6A.!!$F2 805
23 TraesCS2A01G581200 chr1D 42895611 42897082 1471 True 2250 2250 94.441 795 2250 1 chr1D.!!$R1 1455
24 TraesCS2A01G581200 chr1D 248012923 248013730 807 True 976 976 88.519 1 806 1 chr1D.!!$R2 805
25 TraesCS2A01G581200 chr2B 80551030 80552484 1454 True 2082 2082 92.575 798 2250 1 chr2B.!!$R1 1452
26 TraesCS2A01G581200 chr4D 488848778 488850190 1412 False 2028 2028 92.657 837 2250 1 chr4D.!!$F1 1413
27 TraesCS2A01G581200 chr5D 388593347 388594802 1455 False 2017 2017 91.774 796 2250 1 chr5D.!!$F1 1454
28 TraesCS2A01G581200 chr3A 46781756 46782553 797 False 1319 1319 96.491 1 798 1 chr3A.!!$F1 797
29 TraesCS2A01G581200 chr3A 355914874 355915678 804 False 1199 1199 93.540 1 805 1 chr3A.!!$F2 804
30 TraesCS2A01G581200 chr3A 694616623 694617429 806 False 1162 1162 92.707 1 806 1 chr3A.!!$F3 805
31 TraesCS2A01G581200 chr4A 65879805 65880612 807 False 979 979 88.614 1 805 1 chr4A.!!$F1 804
32 TraesCS2A01G581200 chr3B 783059731 783060538 807 False 963 963 88.243 1 805 1 chr3B.!!$F1 804
33 TraesCS2A01G581200 chr6D 45676096 45676733 637 False 824 824 90.248 796 1427 1 chr6D.!!$F1 631
34 TraesCS2A01G581200 chr3D 388399408 388400392 984 False 654 654 79.449 794 1770 1 chr3D.!!$F1 976

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
608 612 0.640768 GTTGTTACTGCGAGCTAGCG 59.359 55.0 14.36 11.1 40.67 4.26 F
929 936 0.780637 TCCTCACCACCTCACTCTCT 59.219 55.0 0.00 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 2269 2.354503 CCACTTCACTCCTCCATGACAG 60.355 54.545 0.0 0.0 0.0 3.51 R
2873 2955 1.482593 GACCACGTGATCCCTGAAGAT 59.517 52.381 19.3 0.0 0.0 2.40 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
608 612 0.640768 GTTGTTACTGCGAGCTAGCG 59.359 55.000 14.36 11.10 40.67 4.26
822 826 2.740714 GAGGCCGCGCTAACAACTG 61.741 63.158 5.56 0.00 0.00 3.16
929 936 0.780637 TCCTCACCACCTCACTCTCT 59.219 55.000 0.00 0.00 0.00 3.10
975 1005 2.566724 CTCCACTGCTCCTCTTCTTCTT 59.433 50.000 0.00 0.00 0.00 2.52
976 1006 2.564947 TCCACTGCTCCTCTTCTTCTTC 59.435 50.000 0.00 0.00 0.00 2.87
977 1007 2.354604 CCACTGCTCCTCTTCTTCTTCC 60.355 54.545 0.00 0.00 0.00 3.46
1033 1067 1.272490 CCAACAGCAACGAGACCTCTA 59.728 52.381 0.00 0.00 0.00 2.43
1050 1084 5.064558 ACCTCTAACGATGATGACGAGTAT 58.935 41.667 0.00 0.00 34.70 2.12
1060 1094 2.971430 TGACGAGTATATGAGCGAGC 57.029 50.000 0.00 0.00 0.00 5.03
1228 1284 0.963962 CCTGCTGCAACAAACTCCAT 59.036 50.000 3.02 0.00 0.00 3.41
1317 1373 2.446435 GAGAGGGCTGGCAAATTTGTA 58.554 47.619 19.03 8.31 0.00 2.41
1418 1475 7.059212 GTGATTGATTCTTTTTGTGCTTTTCG 58.941 34.615 0.00 0.00 0.00 3.46
1798 1873 4.961730 AGACAAAGAGGCTCATGAGATAGT 59.038 41.667 27.04 12.91 0.00 2.12
2060 2135 7.175467 AGTCAAGCTGATATCATTCAAAACACA 59.825 33.333 5.72 0.00 0.00 3.72
2150 2227 2.303890 TCATTGCTGAGCTCTTGAAGGA 59.696 45.455 16.19 8.62 0.00 3.36
2172 2249 3.242011 AGGTCATGGGTGCAAAGAAAAT 58.758 40.909 0.00 0.00 0.00 1.82
2183 2260 6.016276 GGGTGCAAAGAAAATCTAGACAAGAA 60.016 38.462 0.00 0.00 37.89 2.52
2192 2269 8.563732 AGAAAATCTAGACAAGAACAAAGAAGC 58.436 33.333 0.00 0.00 37.89 3.86
2245 2322 4.422073 TGGTAAGTGAATATGAGGCCTG 57.578 45.455 12.00 0.00 0.00 4.85
2467 2544 0.401738 CGGGACCAATAGGCATCCAT 59.598 55.000 0.00 0.00 39.06 3.41
2621 2703 0.821517 TATGTCCGTGCTTGGTCGAT 59.178 50.000 0.00 0.00 0.00 3.59
2700 2782 5.556570 GCAAACGAAGGAAATAGTAGATCGC 60.557 44.000 0.00 0.00 32.46 4.58
2801 2883 7.167924 TCTCGTATATCTATCCGACACTACT 57.832 40.000 0.00 0.00 0.00 2.57
2873 2955 3.967326 CAGGGTCCACATAGTATTCTCCA 59.033 47.826 0.00 0.00 0.00 3.86
2907 2989 1.879380 CGTGGTCAAGAAAGAATGCCA 59.121 47.619 0.00 0.00 0.00 4.92
3170 3260 4.996758 CACAAAAATCATTCCCTTGTTCCC 59.003 41.667 0.00 0.00 0.00 3.97
3189 3279 2.162809 CCCGCCACAACCACTTTATAAC 59.837 50.000 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
608 612 2.202676 CGCGGGAGAAGACAGCTC 60.203 66.667 0.00 0.00 0.00 4.09
929 936 1.679305 GGAGCAGAGTGAGTCGGGA 60.679 63.158 0.00 0.00 0.00 5.14
1033 1067 5.394802 GCTCATATACTCGTCATCATCGTT 58.605 41.667 0.00 0.00 0.00 3.85
1060 1094 9.499479 AAAATACTCCATATTCATGCTACTGAG 57.501 33.333 0.00 0.00 31.90 3.35
1228 1284 8.928448 AGAAAAGCTTGGATCTATCACAGTATA 58.072 33.333 0.00 0.00 0.00 1.47
1317 1373 1.610522 GTGTCAGTGCCTTCAAATGCT 59.389 47.619 0.00 0.00 0.00 3.79
1418 1475 4.142315 TGAGAAAAGCAGCAGCATTATTCC 60.142 41.667 3.17 0.00 45.49 3.01
1499 1570 3.648339 TGTTTCCATTGCTCTTTGCTC 57.352 42.857 0.00 0.00 43.37 4.26
1730 1801 6.296317 CCTCATGATACATATCCCAGAGCTTT 60.296 42.308 0.00 0.00 31.71 3.51
1798 1873 4.708177 CTCCTTCTTCAGTTTCTCAACCA 58.292 43.478 0.00 0.00 32.70 3.67
2060 2135 4.228210 TGTATCTCCTTCATGGCTTTCCTT 59.772 41.667 0.00 0.00 35.26 3.36
2150 2227 2.380064 TTCTTTGCACCCATGACCTT 57.620 45.000 0.00 0.00 0.00 3.50
2172 2249 5.918608 ACAGCTTCTTTGTTCTTGTCTAGA 58.081 37.500 0.00 0.00 0.00 2.43
2183 2260 2.373169 TCCTCCATGACAGCTTCTTTGT 59.627 45.455 0.00 0.00 0.00 2.83
2192 2269 2.354503 CCACTTCACTCCTCCATGACAG 60.355 54.545 0.00 0.00 0.00 3.51
2245 2322 4.880120 GGCCCTTTTTCTACCAGTGTATAC 59.120 45.833 0.00 0.00 0.00 1.47
2372 2449 2.362369 CGTGGAGGCCCATCTGTCT 61.362 63.158 0.00 0.00 45.68 3.41
2690 2772 7.147915 TGCATATATGTTCATGGCGATCTACTA 60.148 37.037 14.14 0.00 0.00 1.82
2700 2782 8.255905 TCTCTCTGTATGCATATATGTTCATGG 58.744 37.037 10.16 5.83 0.00 3.66
2873 2955 1.482593 GACCACGTGATCCCTGAAGAT 59.517 52.381 19.30 0.00 0.00 2.40
3087 3177 1.515954 CGGGGCTACACTGACGAAT 59.484 57.895 0.00 0.00 0.00 3.34
3170 3260 4.491234 TTGTTATAAAGTGGTTGTGGCG 57.509 40.909 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.