Multiple sequence alignment - TraesCS3B01G509400

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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 TraesCS3B01G509400 chr3B 100.000 2712 0 0 1 2712 753580214 753577503 0.000000e+00 5009.0
1 TraesCS3B01G509400 chr3B 89.337 2035 131 38 1 1998 753677052 753675067 0.000000e+00 2477.0
2 TraesCS3B01G509400 chr3B 81.044 728 89 29 466 1167 701122801 701122097 3.970000e-148 534.0
3 TraesCS3B01G509400 chr3B 81.206 564 67 21 2178 2711 753674908 753674354 4.180000e-113 418.0
4 TraesCS3B01G509400 chr3B 82.937 252 22 12 2178 2414 752047945 752048190 9.840000e-50 207.0
5 TraesCS3B01G509400 chr3B 82.996 247 25 8 2178 2414 752077993 752078232 9.840000e-50 207.0
6 TraesCS3B01G509400 chr3B 82.645 242 25 8 2178 2414 752038870 752039099 5.920000e-47 198.0
7 TraesCS3B01G509400 chr3B 84.653 202 24 6 1619 1817 751953302 751953499 7.660000e-46 195.0
8 TraesCS3B01G509400 chr3B 83.571 140 19 1 1843 1982 752038573 752038708 7.880000e-26 128.0
9 TraesCS3B01G509400 chr3D 95.788 2730 79 21 1 2712 565561765 565559054 0.000000e+00 4372.0
10 TraesCS3B01G509400 chr3D 88.409 2036 136 30 1 1998 565608512 565606539 0.000000e+00 2361.0
11 TraesCS3B01G509400 chr3D 83.594 256 25 10 2178 2423 565606380 565606132 9.770000e-55 224.0
12 TraesCS3B01G509400 chr3D 84.689 209 25 6 1612 1817 564202914 564203118 4.580000e-48 202.0
13 TraesCS3B01G509400 chr3D 86.429 140 19 0 1843 1982 564305980 564306119 1.300000e-33 154.0
14 TraesCS3B01G509400 chr3A 97.143 1855 47 4 1 1854 699754826 699752977 0.000000e+00 3127.0
15 TraesCS3B01G509400 chr3A 88.389 2024 147 41 8 1998 699767394 699765426 0.000000e+00 2355.0
16 TraesCS3B01G509400 chr3A 91.063 884 45 14 1849 2712 699752933 699752064 0.000000e+00 1164.0
17 TraesCS3B01G509400 chr3A 77.752 436 52 21 2037 2439 699765428 699765005 2.720000e-55 226.0
18 TraesCS3B01G509400 chr3A 85.167 209 24 6 1612 1817 698762328 698762532 9.840000e-50 207.0
19 TraesCS3B01G509400 chr3A 82.645 242 25 8 2178 2414 698856091 698856320 5.920000e-47 198.0
20 TraesCS3B01G509400 chr3A 87.313 134 17 0 1849 1982 698855796 698855929 1.300000e-33 154.0
21 TraesCS3B01G509400 chr6D 81.514 1796 239 60 1 1764 30096908 30095174 0.000000e+00 1391.0
22 TraesCS3B01G509400 chr6D 78.560 1819 254 73 1 1760 31472702 31474443 0.000000e+00 1074.0
23 TraesCS3B01G509400 chr6B 81.473 1792 246 52 1 1764 57418153 57419886 0.000000e+00 1391.0
24 TraesCS3B01G509400 chr6B 81.425 1755 230 43 36 1760 57733243 57731555 0.000000e+00 1347.0
25 TraesCS3B01G509400 chr6B 80.679 1796 236 49 1 1760 79878360 79880080 0.000000e+00 1291.0
26 TraesCS3B01G509400 chr6A 81.504 1795 240 57 1 1764 32742199 32743932 0.000000e+00 1391.0
27 TraesCS3B01G509400 chr6A 81.554 1789 224 50 6 1760 32811746 32810030 0.000000e+00 1378.0
28 TraesCS3B01G509400 chr6A 93.220 59 4 0 1702 1760 31750666 31750608 1.340000e-13 87.9
29 TraesCS3B01G509400 chrUn 80.902 1796 230 51 1 1760 27474040 27475758 0.000000e+00 1312.0
30 TraesCS3B01G509400 chrUn 80.554 1409 175 60 1 1353 137912886 137911521 0.000000e+00 992.0


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 TraesCS3B01G509400 chr3B 753577503 753580214 2711 True 5009.0 5009 100.0000 1 2712 1 chr3B.!!$R2 2711
1 TraesCS3B01G509400 chr3B 753674354 753677052 2698 True 1447.5 2477 85.2715 1 2711 2 chr3B.!!$R3 2710
2 TraesCS3B01G509400 chr3B 701122097 701122801 704 True 534.0 534 81.0440 466 1167 1 chr3B.!!$R1 701
3 TraesCS3B01G509400 chr3D 565559054 565561765 2711 True 4372.0 4372 95.7880 1 2712 1 chr3D.!!$R1 2711
4 TraesCS3B01G509400 chr3D 565606132 565608512 2380 True 1292.5 2361 86.0015 1 2423 2 chr3D.!!$R2 2422
5 TraesCS3B01G509400 chr3A 699752064 699754826 2762 True 2145.5 3127 94.1030 1 2712 2 chr3A.!!$R1 2711
6 TraesCS3B01G509400 chr3A 699765005 699767394 2389 True 1290.5 2355 83.0705 8 2439 2 chr3A.!!$R2 2431
7 TraesCS3B01G509400 chr6D 30095174 30096908 1734 True 1391.0 1391 81.5140 1 1764 1 chr6D.!!$R1 1763
8 TraesCS3B01G509400 chr6D 31472702 31474443 1741 False 1074.0 1074 78.5600 1 1760 1 chr6D.!!$F1 1759
9 TraesCS3B01G509400 chr6B 57418153 57419886 1733 False 1391.0 1391 81.4730 1 1764 1 chr6B.!!$F1 1763
10 TraesCS3B01G509400 chr6B 57731555 57733243 1688 True 1347.0 1347 81.4250 36 1760 1 chr6B.!!$R1 1724
11 TraesCS3B01G509400 chr6B 79878360 79880080 1720 False 1291.0 1291 80.6790 1 1760 1 chr6B.!!$F2 1759
12 TraesCS3B01G509400 chr6A 32742199 32743932 1733 False 1391.0 1391 81.5040 1 1764 1 chr6A.!!$F1 1763
13 TraesCS3B01G509400 chr6A 32810030 32811746 1716 True 1378.0 1378 81.5540 6 1760 1 chr6A.!!$R2 1754
14 TraesCS3B01G509400 chrUn 27474040 27475758 1718 False 1312.0 1312 80.9020 1 1760 1 chrUn.!!$F1 1759
15 TraesCS3B01G509400 chrUn 137911521 137912886 1365 True 992.0 992 80.5540 1 1353 1 chrUn.!!$R1 1352

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
359 364 1.204704 CATGAGGAACACCGTCTGCTA 59.795 52.381 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2245 2.229543 CCAATTCGTATCATGCCCATGG 59.77 50.0 4.14 4.14 39.24 3.66 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
114 116 8.773033 AGTAAGAAAGTATTATCGGGTTCCTA 57.227 34.615 0.00 0.00 0.00 2.94
359 364 1.204704 CATGAGGAACACCGTCTGCTA 59.795 52.381 0.00 0.00 0.00 3.49
524 600 2.486472 ACACTTCAAGCTGGATCTGG 57.514 50.000 0.00 0.00 0.00 3.86
800 904 6.256539 CACTGTTGTGTTCCTATGCTATAGTG 59.743 42.308 0.84 0.00 39.24 2.74
971 1076 6.932356 TCAGGCATTTAAGAAGCTGATTAG 57.068 37.500 0.00 0.00 0.00 1.73
1817 1958 3.117888 AGTTAGACATTGGGGTAGCCATG 60.118 47.826 14.06 11.26 0.00 3.66
1953 2169 8.420222 TGTGATCACATTCCAACTTGTTAATTT 58.580 29.630 24.56 0.00 36.21 1.82
2029 2245 1.464997 TGGTGGCGTTTTTGTTTTTGC 59.535 42.857 0.00 0.00 0.00 3.68
2057 2273 3.871006 GCATGATACGAATTGGTCTGTCA 59.129 43.478 0.00 1.45 0.00 3.58
2174 2402 4.020751 TCCTAGTGAAGCAGATATGCATCC 60.021 45.833 15.82 6.52 37.25 3.51
2176 2404 4.160642 AGTGAAGCAGATATGCATCCAA 57.839 40.909 15.82 0.00 37.25 3.53
2200 2461 8.385111 CAATGCTGGTGATTAAAACAATCATTC 58.615 33.333 3.23 1.20 38.71 2.67
2373 2649 4.698583 AGATTTGAGCAGCTGAACAATC 57.301 40.909 20.43 17.10 0.00 2.67
2390 2667 2.189191 ATCGCCCTGCACTGACACAT 62.189 55.000 0.00 0.00 0.00 3.21
2391 2668 1.079197 CGCCCTGCACTGACACATA 60.079 57.895 0.00 0.00 0.00 2.29
2392 2669 1.086067 CGCCCTGCACTGACACATAG 61.086 60.000 0.00 0.00 0.00 2.23
2575 2872 0.602638 CCGTTTGACCAGCAGTAGCA 60.603 55.000 0.00 0.00 45.49 3.49
2608 2907 1.667724 CTACGCAAGCAGGGAAATGAG 59.332 52.381 0.32 0.00 45.62 2.90
2695 2994 7.118680 TCGGCTTATCAGTAAAGGTTTTAGTTG 59.881 37.037 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 116 3.081804 CTCCTTGTCCCGTAGCAAAATT 58.918 45.455 0.00 0.00 0.00 1.82
359 364 5.468072 CACAGACACTCTTTTAACAGCATCT 59.532 40.000 0.00 0.00 0.00 2.90
472 540 5.032846 TGAAGAGAATCATCCCTTACAGGT 58.967 41.667 0.00 0.00 37.82 4.00
524 600 6.902341 TGACAAACAAAGATAGTGAGATTGC 58.098 36.000 0.00 0.00 0.00 3.56
971 1076 5.888161 TGCCTCTTCCATCTCTTTAATTTCC 59.112 40.000 0.00 0.00 0.00 3.13
1817 1958 4.396166 AGAATGCACAACTAAGTGTATGCC 59.604 41.667 0.00 0.00 42.74 4.40
1953 2169 9.857656 ATGATTAGAAGCATTAAAGATGGAAGA 57.142 29.630 0.00 0.00 29.30 2.87
1987 2203 5.069383 CCATGCCAACAAGGATGATATCAAA 59.931 40.000 9.99 0.00 36.75 2.69
2029 2245 2.229543 CCAATTCGTATCATGCCCATGG 59.770 50.000 4.14 4.14 39.24 3.66
2057 2273 7.106239 CCTGTGTCTTCCAGAAATAACATACT 58.894 38.462 0.00 0.00 31.38 2.12
2174 2402 7.837202 ATGATTGTTTTAATCACCAGCATTG 57.163 32.000 4.62 0.00 39.22 2.82
2176 2404 7.613585 TGAATGATTGTTTTAATCACCAGCAT 58.386 30.769 4.62 0.00 39.22 3.79
2278 2545 3.699038 AGTTCTAGAGCTAGTTCAGGCAG 59.301 47.826 7.41 1.05 34.84 4.85
2348 2624 3.261643 TGTTCAGCTGCTCAAATCTAGGA 59.738 43.478 9.47 0.00 0.00 2.94
2373 2649 1.079197 TATGTGTCAGTGCAGGGCG 60.079 57.895 0.00 0.00 0.00 6.13
2391 2668 9.830975 TCACTTGTTACATGCATATGTATTACT 57.169 29.630 3.23 0.00 46.22 2.24
2591 2888 1.167851 TTCTCATTTCCCTGCTTGCG 58.832 50.000 0.00 0.00 0.00 4.85
2600 2897 7.159372 TGTAACTACCAGACTTTCTCATTTCC 58.841 38.462 0.00 0.00 0.00 3.13
2608 2907 6.086785 AGACACTGTAACTACCAGACTTTC 57.913 41.667 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.