Multiple sequence alignment - TraesCS2A01G411100

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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 TraesCS2A01G411100 chr2A 100.000 3003 0 0 1 3003 669113716 669110714 0.000000e+00 5546.0
1 TraesCS2A01G411100 chr2A 98.136 3004 54 2 1 3003 668918774 668921776 0.000000e+00 5236.0
2 TraesCS2A01G411100 chr2A 81.312 701 108 7 1715 2415 668926411 668927088 5.660000e-152 547.0
3 TraesCS2A01G411100 chr2A 81.022 685 107 11 1731 2415 669106003 669105342 9.540000e-145 523.0
4 TraesCS2A01G411100 chr2A 90.854 164 11 3 464 627 668925855 668926014 1.810000e-52 217.0
5 TraesCS2A01G411100 chr2A 90.854 164 11 3 464 627 669106633 669106474 1.810000e-52 217.0
6 TraesCS2A01G411100 chr2A 95.455 44 2 0 2891 2934 610177916 610177959 1.490000e-08 71.3
7 TraesCS2A01G411100 chr2D 93.644 1479 58 12 1532 3003 523361277 523359828 0.000000e+00 2178.0
8 TraesCS2A01G411100 chr2D 81.223 703 104 15 1715 2415 523310332 523309656 2.630000e-150 542.0
9 TraesCS2A01G411100 chr2D 80.577 381 30 20 700 1050 523310717 523310351 1.380000e-63 254.0
10 TraesCS2A01G411100 chr2D 88.415 164 18 1 464 626 523310892 523310729 2.360000e-46 196.0
11 TraesCS2A01G411100 chr2D 81.696 224 17 7 954 1176 523361480 523361280 6.660000e-37 165.0
12 TraesCS2A01G411100 chr2D 97.727 44 1 0 2891 2934 462241351 462241394 3.210000e-10 76.8
13 TraesCS2A01G411100 chr2D 87.879 66 6 2 505 570 523393095 523393032 3.210000e-10 76.8
14 TraesCS2A01G411100 chr2D 95.455 44 2 0 2891 2934 131641944 131641901 1.490000e-08 71.3
15 TraesCS2A01G411100 chr2D 93.617 47 3 0 2893 2939 645724406 645724452 1.490000e-08 71.3
16 TraesCS2A01G411100 chr2D 93.617 47 3 0 2893 2939 645815359 645815313 1.490000e-08 71.3
17 TraesCS2A01G411100 chr7B 94.168 463 25 1 1 461 217303475 217303937 0.000000e+00 704.0
18 TraesCS2A01G411100 chr6B 93.534 464 27 2 1 461 719411518 719411981 0.000000e+00 688.0
19 TraesCS2A01G411100 chr5B 93.534 464 27 2 1 461 682361068 682360605 0.000000e+00 688.0
20 TraesCS2A01G411100 chr3B 93.521 463 27 2 1 460 650614010 650614472 0.000000e+00 686.0
21 TraesCS2A01G411100 chr1B 93.521 463 27 2 1 460 330837987 330838449 0.000000e+00 686.0
22 TraesCS2A01G411100 chrUn 93.162 468 27 4 1 464 8241300 8241766 0.000000e+00 682.0
23 TraesCS2A01G411100 chrUn 93.162 468 27 4 1 464 375362677 375363143 0.000000e+00 682.0
24 TraesCS2A01G411100 chrUn 93.162 468 27 4 1 464 426590932 426591398 0.000000e+00 682.0
25 TraesCS2A01G411100 chr2B 80.599 701 113 8 1715 2415 617528599 617527922 1.230000e-143 520.0
26 TraesCS2A01G411100 chr2B 78.412 403 42 22 681 1052 617529004 617528616 1.400000e-53 220.0
27 TraesCS2A01G411100 chr2B 87.805 164 16 3 464 627 617529152 617528993 3.950000e-44 189.0
28 TraesCS2A01G411100 chr2B 97.727 44 1 0 2891 2934 545153677 545153720 3.210000e-10 76.8
29 TraesCS2A01G411100 chr2B 93.617 47 3 0 2893 2939 790228203 790228157 1.490000e-08 71.3


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 TraesCS2A01G411100 chr2A 669110714 669113716 3002 True 5546.000000 5546 100.000 1 3003 1 chr2A.!!$R1 3002
1 TraesCS2A01G411100 chr2A 668918774 668921776 3002 False 5236.000000 5236 98.136 1 3003 1 chr2A.!!$F2 3002
2 TraesCS2A01G411100 chr2A 668925855 668927088 1233 False 382.000000 547 86.083 464 2415 2 chr2A.!!$F3 1951
3 TraesCS2A01G411100 chr2A 669105342 669106633 1291 True 370.000000 523 85.938 464 2415 2 chr2A.!!$R2 1951
4 TraesCS2A01G411100 chr2D 523359828 523361480 1652 True 1171.500000 2178 87.670 954 3003 2 chr2D.!!$R5 2049
5 TraesCS2A01G411100 chr2D 523309656 523310892 1236 True 330.666667 542 83.405 464 2415 3 chr2D.!!$R4 1951
6 TraesCS2A01G411100 chr2B 617527922 617529152 1230 True 309.666667 520 82.272 464 2415 3 chr2B.!!$R2 1951

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
59 60 0.887387 TAGGACCAGCGCACCAAAAC 60.887 55.000 11.47 0.0 0.0 2.43 F
66 67 1.226945 GCGCACCAAAACAGCAACT 60.227 52.632 0.30 0.0 0.0 3.16 F
1230 1275 1.009389 GGAGGAAGCACGTGAAGTCG 61.009 60.000 22.23 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1178 1223 0.469917 GATGCCCTTCCTGGATTCGA 59.530 55.0 0.0 0.0 38.35 3.71 R
1253 1298 0.603707 CTCAGCCGCAACCTTCTTCA 60.604 55.0 0.0 0.0 0.00 3.02 R
2540 2592 0.529773 AGAAACAACTGCGCGAGACA 60.530 50.0 12.1 0.0 0.00 3.41 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
56 57 2.345991 GTAGGACCAGCGCACCAA 59.654 61.111 11.47 0.0 0.00 3.67
59 60 0.887387 TAGGACCAGCGCACCAAAAC 60.887 55.000 11.47 0.0 0.00 2.43
66 67 1.226945 GCGCACCAAAACAGCAACT 60.227 52.632 0.30 0.0 0.00 3.16
67 68 1.481819 GCGCACCAAAACAGCAACTG 61.482 55.000 0.30 0.0 37.52 3.16
238 239 4.387343 AACGGGGGCTAGACGGGA 62.387 66.667 0.00 0.0 0.00 5.14
269 270 2.688666 ATCTTCAGGGAGCCGCCA 60.689 61.111 0.00 0.0 38.95 5.69
270 271 3.036429 ATCTTCAGGGAGCCGCCAC 62.036 63.158 0.00 0.0 38.95 5.01
442 444 3.506455 GGAGGCAGAAACCCTAACTTTTC 59.494 47.826 0.00 0.0 31.41 2.29
467 469 3.139211 GGAGGAAGGAGGAGGCAATAATT 59.861 47.826 0.00 0.0 0.00 1.40
534 536 5.769662 ACTCATTGTCAGGAAAATAAGCACA 59.230 36.000 0.00 0.0 0.00 4.57
951 986 6.377327 AATCGAAAAGAAAAGAGAACAGCA 57.623 33.333 0.00 0.0 0.00 4.41
952 987 5.156804 TCGAAAAGAAAAGAGAACAGCAC 57.843 39.130 0.00 0.0 0.00 4.40
988 1023 2.048127 GGCAGCGGAAAGACGAGT 60.048 61.111 0.00 0.0 35.47 4.18
1018 1063 1.753368 GATGGAAGGAGAGGCGGAGG 61.753 65.000 0.00 0.0 0.00 4.30
1048 1093 1.446272 GCGAGGGGAAAGAGTGTCG 60.446 63.158 0.00 0.0 0.00 4.35
1060 1105 1.305297 AGTGTCGGAGAGGGCATCA 60.305 57.895 0.58 0.0 36.95 3.07
1178 1223 2.048127 GGTGAAGCGGAAGAGCGT 60.048 61.111 0.00 0.0 43.00 5.07
1230 1275 1.009389 GGAGGAAGCACGTGAAGTCG 61.009 60.000 22.23 0.0 0.00 4.18
1248 1293 3.945921 AGTCGTTATCGGAGATCAAGTCA 59.054 43.478 0.00 0.0 45.12 3.41
1253 1298 1.393603 TCGGAGATCAAGTCAGCGAT 58.606 50.000 0.00 0.0 0.00 4.58
1445 1490 1.144503 GGTGATGGAATGGCTGGAGAT 59.855 52.381 0.00 0.0 0.00 2.75
1848 1893 2.110006 GATGGGAGAGGAAGGCGC 59.890 66.667 0.00 0.0 0.00 6.53
1865 1910 2.359169 GCGGTGAGGGATGAGGTGA 61.359 63.158 0.00 0.0 0.00 4.02
1886 1931 6.378280 GGTGACAAAGTTGGATATTGAGGAAT 59.622 38.462 0.00 0.0 0.00 3.01
1938 1983 4.406326 TGGGCCGTTCTTTGATATGTACTA 59.594 41.667 0.00 0.0 0.00 1.82
2254 2303 1.604593 GTCATTGCCAGCACCCTGT 60.605 57.895 0.00 0.0 37.38 4.00
2386 2438 1.267121 TCTCTTCCTCCGTGAAAGGG 58.733 55.000 0.00 0.0 45.09 3.95
2503 2555 7.804614 TGTTGTTTTGTTGATTGTAGTTGTC 57.195 32.000 0.00 0.0 0.00 3.18
2540 2592 0.395586 TGTTTGCAGTTGACTGGCCT 60.396 50.000 12.65 0.0 43.94 5.19
2651 2703 5.248248 TGATCCATCAGACCTTCAACTACAA 59.752 40.000 0.00 0.0 32.11 2.41
2679 2731 2.890945 TGAGACCACTCTGTCGAATGAA 59.109 45.455 0.00 0.0 42.99 2.57
2775 2828 8.803235 GTTACTAATTGGAGGAAAAGGAAATGT 58.197 33.333 0.00 0.0 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 239 5.492524 TCCCTGAAGATGGAATAAAGGTCTT 59.507 40.000 0.00 0.00 32.23 3.01
269 270 1.587933 GCTCAGGAAGACGAGACGGT 61.588 60.000 0.00 0.00 0.00 4.83
270 271 1.137825 GCTCAGGAAGACGAGACGG 59.862 63.158 0.00 0.00 0.00 4.79
442 444 2.726351 GCCTCCTCCTTCCTCCACG 61.726 68.421 0.00 0.00 0.00 4.94
467 469 9.436957 GGAGTGTAGAGACTATCAAATGAAAAA 57.563 33.333 0.00 0.00 0.00 1.94
775 782 1.887707 CTCGGGATAGCGCAAACCC 60.888 63.158 20.63 20.63 39.02 4.11
988 1023 1.285078 TCCTTCCATCTCAGGAGACGA 59.715 52.381 0.22 0.00 40.75 4.20
1018 1063 4.821589 CCTCGCCTCCGCTTCCAC 62.822 72.222 0.00 0.00 0.00 4.02
1048 1093 2.716814 CATGCTTGATGCCCTCTCC 58.283 57.895 0.00 0.00 42.00 3.71
1060 1105 2.676471 GGTTCCCGTGGCATGCTT 60.676 61.111 18.92 0.00 0.00 3.91
1178 1223 0.469917 GATGCCCTTCCTGGATTCGA 59.530 55.000 0.00 0.00 38.35 3.71
1230 1275 3.046390 CGCTGACTTGATCTCCGATAAC 58.954 50.000 0.00 0.00 0.00 1.89
1248 1293 1.021390 CCGCAACCTTCTTCATCGCT 61.021 55.000 0.00 0.00 0.00 4.93
1253 1298 0.603707 CTCAGCCGCAACCTTCTTCA 60.604 55.000 0.00 0.00 0.00 3.02
1337 1382 1.937924 GCCCCTGGCCTCCATAAACT 61.938 60.000 3.32 0.00 44.06 2.66
1445 1490 2.317900 TCCTAAATCTGGACCCTCCTCA 59.682 50.000 0.00 0.00 37.46 3.86
1820 1865 1.140652 CTCTCCCATCTCCTTGGCTTC 59.859 57.143 0.00 0.00 35.29 3.86
1848 1893 1.257750 TGTCACCTCATCCCTCACCG 61.258 60.000 0.00 0.00 0.00 4.94
1865 1910 7.405292 TCAGATTCCTCAATATCCAACTTTGT 58.595 34.615 0.00 0.00 0.00 2.83
1886 1931 1.018840 TTCTCCTCCATCCCCTCAGA 58.981 55.000 0.00 0.00 0.00 3.27
1958 2003 0.689623 CTGCTGAAGAACCAGGACCT 59.310 55.000 0.00 0.00 34.82 3.85
2133 2178 7.985752 AGGAAGATTTAGATAATTCGTTCGGTT 59.014 33.333 0.00 0.00 0.00 4.44
2228 2277 1.211969 CTGGCAATGACAGCAGCAC 59.788 57.895 1.91 0.00 29.34 4.40
2254 2303 6.481976 TCTGCGACTTTGACAAAGAAAATCTA 59.518 34.615 30.01 10.14 41.02 1.98
2386 2438 4.009675 TGAGTCAGTATTTGGCAATCACC 58.990 43.478 0.00 0.00 32.36 4.02
2503 2555 1.027357 CAAGGATCCTGCATTTCCCG 58.973 55.000 17.02 0.00 0.00 5.14
2540 2592 0.529773 AGAAACAACTGCGCGAGACA 60.530 50.000 12.10 0.00 0.00 3.41
2651 2703 3.181482 CGACAGAGTGGTCTCATTAGCAT 60.181 47.826 0.00 0.00 42.66 3.79
2679 2731 6.806249 CACACCGTAACATAATTTTGCAGAAT 59.194 34.615 0.00 0.00 0.00 2.40
2775 2828 9.667107 CTAACTCTACCATCATGTTTAAAAGGA 57.333 33.333 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.