Multiple sequence alignment - TraesCS3A01G031700

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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 TraesCS3A01G031700 chr3A 100.000 2993 0 0 1 2993 17453967 17450975 0.000000e+00 5528
1 TraesCS3A01G031700 chr3A 88.142 565 52 6 2423 2981 17509396 17508841 0.000000e+00 658
2 TraesCS3A01G031700 chr3D 96.176 2275 47 17 1 2250 10803078 10805337 0.000000e+00 3683
3 TraesCS3A01G031700 chr3D 95.522 670 27 2 2327 2993 10805376 10806045 0.000000e+00 1068
4 TraesCS3A01G031700 chr3D 95.522 670 27 2 2327 2993 10818703 10819372 0.000000e+00 1068
5 TraesCS3A01G031700 chr3B 84.532 2586 308 56 24 2559 15096480 15099023 0.000000e+00 2475
6 TraesCS3A01G031700 chr3B 85.209 2488 263 51 26 2456 15168104 15165665 0.000000e+00 2459
7 TraesCS3A01G031700 chr3B 84.377 2586 313 55 24 2559 15142703 15140159 0.000000e+00 2453
8 TraesCS3A01G031700 chr3B 85.363 2439 274 46 68 2453 26398475 26400883 0.000000e+00 2449
9 TraesCS3A01G031700 chr3B 85.199 2439 278 47 68 2453 26056308 26058716 0.000000e+00 2427
10 TraesCS3A01G031700 chr3B 85.135 2442 278 47 68 2453 26429131 26431543 0.000000e+00 2420
11 TraesCS3A01G031700 chr3B 85.062 2430 288 45 68 2453 25920195 25922593 0.000000e+00 2407
12 TraesCS3A01G031700 chr3B 85.879 2259 255 38 68 2281 26245306 26247545 0.000000e+00 2346
13 TraesCS3A01G031700 chr3B 85.988 835 69 18 153 943 15164997 15164167 0.000000e+00 850
14 TraesCS3A01G031700 chr3B 85.676 754 61 19 151 860 26432195 26432945 0.000000e+00 750
15 TraesCS3A01G031700 chr3B 88.858 359 31 3 151 500 26401541 26401899 1.650000e-117 433
16 TraesCS3A01G031700 chr3B 88.579 359 32 3 151 500 26059374 26059732 7.670000e-116 427
17 TraesCS3A01G031700 chr3B 88.301 359 33 3 151 500 26248443 26248801 3.570000e-114 422
18 TraesCS3A01G031700 chrUn 95.235 1448 32 14 14 1437 43590217 43591651 0.000000e+00 2257
19 TraesCS3A01G031700 chrUn 95.522 670 27 2 2327 2993 314619723 314620392 0.000000e+00 1068
20 TraesCS3A01G031700 chr1D 85.525 1658 173 36 68 1673 447664724 447666366 0.000000e+00 1670


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 TraesCS3A01G031700 chr3A 17450975 17453967 2992 True 5528.0 5528 100.0000 1 2993 1 chr3A.!!$R1 2992
1 TraesCS3A01G031700 chr3A 17508841 17509396 555 True 658.0 658 88.1420 2423 2981 1 chr3A.!!$R2 558
2 TraesCS3A01G031700 chr3D 10803078 10806045 2967 False 2375.5 3683 95.8490 1 2993 2 chr3D.!!$F2 2992
3 TraesCS3A01G031700 chr3D 10818703 10819372 669 False 1068.0 1068 95.5220 2327 2993 1 chr3D.!!$F1 666
4 TraesCS3A01G031700 chr3B 15096480 15099023 2543 False 2475.0 2475 84.5320 24 2559 1 chr3B.!!$F1 2535
5 TraesCS3A01G031700 chr3B 15140159 15142703 2544 True 2453.0 2453 84.3770 24 2559 1 chr3B.!!$R1 2535
6 TraesCS3A01G031700 chr3B 25920195 25922593 2398 False 2407.0 2407 85.0620 68 2453 1 chr3B.!!$F2 2385
7 TraesCS3A01G031700 chr3B 15164167 15168104 3937 True 1654.5 2459 85.5985 26 2456 2 chr3B.!!$R2 2430
8 TraesCS3A01G031700 chr3B 26429131 26432945 3814 False 1585.0 2420 85.4055 68 2453 2 chr3B.!!$F6 2385
9 TraesCS3A01G031700 chr3B 26398475 26401899 3424 False 1441.0 2449 87.1105 68 2453 2 chr3B.!!$F5 2385
10 TraesCS3A01G031700 chr3B 26056308 26059732 3424 False 1427.0 2427 86.8890 68 2453 2 chr3B.!!$F3 2385
11 TraesCS3A01G031700 chr3B 26245306 26248801 3495 False 1384.0 2346 87.0900 68 2281 2 chr3B.!!$F4 2213
12 TraesCS3A01G031700 chrUn 43590217 43591651 1434 False 2257.0 2257 95.2350 14 1437 1 chrUn.!!$F1 1423
13 TraesCS3A01G031700 chrUn 314619723 314620392 669 False 1068.0 1068 95.5220 2327 2993 1 chrUn.!!$F2 666
14 TraesCS3A01G031700 chr1D 447664724 447666366 1642 False 1670.0 1670 85.5250 68 1673 1 chr1D.!!$F1 1605

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
991 1068 1.67392 GTTGTGAAGTTTCGAGGGCAA 59.326 47.619 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2767 3106 0.107897 TGTTGTATGCTGGCCTACCG 60.108 55.0 3.32 0.0 39.7 4.02 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
130 136 9.905713 AATATAATACTGAAATCGCATGGGTAT 57.094 29.630 9.86 0.00 0.00 2.73
149 155 5.529060 GGGTATCTCCTGTTCTTTAATGCAG 59.471 44.000 0.00 0.00 36.25 4.41
452 470 6.446318 TCTGTGCACATTTTCTGATTTTACC 58.554 36.000 22.00 0.00 0.00 2.85
501 519 2.752354 CTGGTTTGGCATCCATTACGAA 59.248 45.455 11.36 0.00 31.53 3.85
502 520 3.360867 TGGTTTGGCATCCATTACGAAT 58.639 40.909 7.66 0.00 31.53 3.34
503 521 3.766591 TGGTTTGGCATCCATTACGAATT 59.233 39.130 7.66 0.00 31.53 2.17
504 522 4.221703 TGGTTTGGCATCCATTACGAATTT 59.778 37.500 7.66 0.00 31.53 1.82
505 523 5.419155 TGGTTTGGCATCCATTACGAATTTA 59.581 36.000 7.66 0.00 31.53 1.40
506 524 5.746721 GGTTTGGCATCCATTACGAATTTAC 59.253 40.000 0.00 0.00 31.53 2.01
507 525 4.804608 TGGCATCCATTACGAATTTACG 57.195 40.909 0.00 0.00 39.31 3.18
508 526 4.443621 TGGCATCCATTACGAATTTACGA 58.556 39.130 0.00 0.00 37.03 3.43
511 529 5.408604 GGCATCCATTACGAATTTACGATCT 59.591 40.000 0.00 0.00 37.03 2.75
567 610 7.873719 TGTCGACCATACATTAAAAATGGAT 57.126 32.000 14.12 0.00 42.36 3.41
647 690 3.057526 CGACCTAATCATCAGATACCGCA 60.058 47.826 0.00 0.00 33.08 5.69
731 794 5.521544 TGTGTCTGCGCATACGTAAATATA 58.478 37.500 19.40 0.00 42.83 0.86
991 1068 1.673920 GTTGTGAAGTTTCGAGGGCAA 59.326 47.619 0.00 0.00 0.00 4.52
1197 1279 5.354513 TCACGCCACTATATCTATCTAGTGC 59.645 44.000 9.05 5.52 42.19 4.40
1676 1759 7.172342 ACTTTTTCTATACCACTGCCATACAA 58.828 34.615 0.00 0.00 0.00 2.41
1800 1883 5.379187 TCGATCAAATCCATGGATGTCAAT 58.621 37.500 27.97 17.05 34.70 2.57
1820 1903 6.317642 GTCAATAGCTCTGACTCTGAAGACTA 59.682 42.308 17.57 0.00 40.10 2.59
1920 2003 4.365514 AACCAACACAGATGGACATACA 57.634 40.909 0.00 0.00 40.56 2.29
1933 2016 7.334171 CAGATGGACATACACTTGTGTTCAATA 59.666 37.037 11.80 0.00 36.05 1.90
2051 2135 8.850156 GGCAAGTGATGGATTTGTAATAACTAT 58.150 33.333 0.00 0.00 0.00 2.12
2264 2350 9.967451 TTCATTCTGTTCCTATGTATGGTAAAA 57.033 29.630 0.00 0.00 0.00 1.52
2304 2475 9.695526 GCATATAAAATATCCATGCAGAAAACA 57.304 29.630 0.00 0.00 41.25 2.83
2434 2605 7.298854 GTTGCTTATCTTGGACAGTTTAAGAC 58.701 38.462 3.34 0.00 33.69 3.01
2529 2704 8.954729 TGATTATAATTCTAATCCAACCCTCCA 58.045 33.333 16.66 0.00 37.32 3.86
2712 2923 1.077005 TGGCCCCTTACAAAGCAGATT 59.923 47.619 0.00 0.00 0.00 2.40
2727 3066 8.703743 ACAAAGCAGATTCTGAGATAACTAGAT 58.296 33.333 17.87 0.00 32.44 1.98
2767 3106 5.754778 ACTACGTTGCTGAAAAATAACACC 58.245 37.500 0.00 0.00 0.00 4.16
2886 4096 1.569479 GGAGAGCAGAACCACAACGC 61.569 60.000 0.00 0.00 0.00 4.84
2934 4144 2.125147 CATCACCACCGTCGGCAT 60.125 61.111 12.28 0.00 0.00 4.40
2982 4192 2.018727 TACTGGTGACACCACGCGTT 62.019 55.000 23.72 7.99 44.79 4.84
2984 4194 1.282248 CTGGTGACACCACGCGTTAG 61.282 60.000 23.72 6.78 44.79 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 136 5.182001 GCTTTCTGCATTAAAGAACAGGAGA 59.818 40.000 20.25 0.00 42.31 3.71
149 155 2.960819 TCCGCTTTAGAGTCAGCTTTC 58.039 47.619 0.00 0.00 33.52 2.62
501 519 6.814644 TCGGTTTGTTCATGTAGATCGTAAAT 59.185 34.615 0.00 0.00 0.00 1.40
502 520 6.157904 TCGGTTTGTTCATGTAGATCGTAAA 58.842 36.000 0.00 0.00 0.00 2.01
503 521 5.712004 TCGGTTTGTTCATGTAGATCGTAA 58.288 37.500 0.00 0.00 0.00 3.18
504 522 5.313520 TCGGTTTGTTCATGTAGATCGTA 57.686 39.130 0.00 0.00 0.00 3.43
505 523 4.182693 TCGGTTTGTTCATGTAGATCGT 57.817 40.909 0.00 0.00 0.00 3.73
506 524 4.803613 TCATCGGTTTGTTCATGTAGATCG 59.196 41.667 0.00 0.00 0.00 3.69
507 525 6.662414 TTCATCGGTTTGTTCATGTAGATC 57.338 37.500 0.00 0.00 0.00 2.75
508 526 8.908786 ATATTCATCGGTTTGTTCATGTAGAT 57.091 30.769 0.00 0.00 0.00 1.98
511 529 8.499403 TGAATATTCATCGGTTTGTTCATGTA 57.501 30.769 14.23 0.00 31.01 2.29
567 610 6.888088 CCATATGCATAGATCCTTTGAATCCA 59.112 38.462 12.79 0.00 0.00 3.41
685 738 8.135529 CACATTCCTTGAATCATACTACGAGTA 58.864 37.037 0.00 0.00 30.46 2.59
1007 1088 0.510359 CACTGCAACAACTCGAGCTC 59.490 55.000 13.61 2.73 0.00 4.09
1676 1759 1.301716 ACGCACGGAACTCTGCATT 60.302 52.632 0.00 0.00 32.57 3.56
1800 1883 5.685520 TCTAGTCTTCAGAGTCAGAGCTA 57.314 43.478 0.00 0.00 0.00 3.32
1920 2003 4.347813 GCACAACGTTATTGAACACAAGT 58.652 39.130 12.15 0.00 35.06 3.16
2254 2340 8.767085 TGCTTATATGTTAGCGTTTTACCATAC 58.233 33.333 0.00 0.00 40.26 2.39
2379 2550 3.766591 TCTCTCCTCATGACTTCTGTTCC 59.233 47.826 0.00 0.00 0.00 3.62
2519 2694 1.895131 CTGTTGGAAATGGAGGGTTGG 59.105 52.381 0.00 0.00 0.00 3.77
2529 2704 6.378280 ACTGACAAAGTTCTTCTGTTGGAAAT 59.622 34.615 0.00 0.00 34.57 2.17
2580 2790 7.863375 GCAATTAGCTCGATCGGTCTATTATAT 59.137 37.037 16.41 4.82 41.15 0.86
2666 2877 2.028130 CTACCTTGTGTTGTTTGGCCA 58.972 47.619 0.00 0.00 0.00 5.36
2727 3066 4.168014 CGTAGTCACGTGCCTTTATGTTA 58.832 43.478 11.67 0.00 43.31 2.41
2767 3106 0.107897 TGTTGTATGCTGGCCTACCG 60.108 55.000 3.32 0.00 39.70 4.02
2886 4096 0.814457 CACTCTCCTCTTGAGGACGG 59.186 60.000 14.79 12.27 41.76 4.79


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

AutoCloner maintained by Alex Coulton.