Multiple sequence alignment - TraesCS1A01G038500

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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 TraesCS1A01G038500 chr1A 100.000 4050 0 0 1 4050 21064629 21068678 0 7480
1 TraesCS1A01G038500 chr1A 95.500 4089 127 22 1 4050 255468331 255472401 0 6479
2 TraesCS1A01G038500 chr6A 96.192 4097 103 6 4 4050 494434264 494430171 0 6652
3 TraesCS1A01G038500 chr6A 95.875 4097 120 14 1 4050 184597153 184601247 0 6584
4 TraesCS1A01G038500 chr6A 95.594 4085 125 23 1 4050 480634613 480638677 0 6495
5 TraesCS1A01G038500 chr6A 95.335 4094 119 33 1 4050 40637881 40641946 0 6436
6 TraesCS1A01G038500 chr3A 95.915 4088 128 9 1 4050 653950010 653945924 0 6588
7 TraesCS1A01G038500 chr3A 95.635 4078 121 21 1 4050 42782739 42786787 0 6492
8 TraesCS1A01G038500 chr3A 95.360 4116 118 21 1 4050 450966035 450961927 0 6475
9 TraesCS1A01G038500 chr3A 96.252 3815 104 9 217 3994 745765190 745761378 0 6216
10 TraesCS1A01G038500 chr3B 95.913 4086 115 18 1 4050 462502532 462498463 0 6573
11 TraesCS1A01G038500 chr4A 95.892 4090 111 14 1 4050 578198828 578202900 0 6569
12 TraesCS1A01G038500 chr4A 96.336 3412 89 12 1 3378 37337904 37334495 0 5576
13 TraesCS1A01G038500 chr2B 95.903 4076 120 18 1 4050 99562167 99566221 0 6558
14 TraesCS1A01G038500 chr2B 95.439 4078 119 23 1 4050 608463256 608459218 0 6438
15 TraesCS1A01G038500 chr6B 95.664 4082 126 22 1 4050 21367753 21363691 0 6510
16 TraesCS1A01G038500 chr4B 95.588 4080 129 24 1 4050 14715047 14710989 0 6490
17 TraesCS1A01G038500 chr7B 95.541 4082 130 26 1 4050 194124486 194128547 0 6482
18 TraesCS1A01G038500 chr2A 95.500 4089 126 23 1 4050 389212619 389208550 0 6479
19 TraesCS1A01G038500 chr2A 95.608 3415 97 9 1 3378 733079588 733076190 0 5426
20 TraesCS1A01G038500 chr5A 95.296 4082 116 25 1 4050 17462226 17466263 0 6405
21 TraesCS1A01G038500 chr5A 95.015 1364 43 7 1 1340 396399890 396401252 0 2119
22 TraesCS1A01G038500 chr7A 96.798 2124 41 2 1 2097 722678496 722680619 0 3520
23 TraesCS1A01G038500 chr7A 97.416 1974 40 5 2086 4050 722689149 722691120 0 3352


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 TraesCS1A01G038500 chr1A 21064629 21068678 4049 False 7480 7480 100.000 1 4050 1 chr1A.!!$F1 4049
1 TraesCS1A01G038500 chr1A 255468331 255472401 4070 False 6479 6479 95.500 1 4050 1 chr1A.!!$F2 4049
2 TraesCS1A01G038500 chr6A 494430171 494434264 4093 True 6652 6652 96.192 4 4050 1 chr6A.!!$R1 4046
3 TraesCS1A01G038500 chr6A 184597153 184601247 4094 False 6584 6584 95.875 1 4050 1 chr6A.!!$F2 4049
4 TraesCS1A01G038500 chr6A 480634613 480638677 4064 False 6495 6495 95.594 1 4050 1 chr6A.!!$F3 4049
5 TraesCS1A01G038500 chr6A 40637881 40641946 4065 False 6436 6436 95.335 1 4050 1 chr6A.!!$F1 4049
6 TraesCS1A01G038500 chr3A 653945924 653950010 4086 True 6588 6588 95.915 1 4050 1 chr3A.!!$R2 4049
7 TraesCS1A01G038500 chr3A 42782739 42786787 4048 False 6492 6492 95.635 1 4050 1 chr3A.!!$F1 4049
8 TraesCS1A01G038500 chr3A 450961927 450966035 4108 True 6475 6475 95.360 1 4050 1 chr3A.!!$R1 4049
9 TraesCS1A01G038500 chr3A 745761378 745765190 3812 True 6216 6216 96.252 217 3994 1 chr3A.!!$R3 3777
10 TraesCS1A01G038500 chr3B 462498463 462502532 4069 True 6573 6573 95.913 1 4050 1 chr3B.!!$R1 4049
11 TraesCS1A01G038500 chr4A 578198828 578202900 4072 False 6569 6569 95.892 1 4050 1 chr4A.!!$F1 4049
12 TraesCS1A01G038500 chr4A 37334495 37337904 3409 True 5576 5576 96.336 1 3378 1 chr4A.!!$R1 3377
13 TraesCS1A01G038500 chr2B 99562167 99566221 4054 False 6558 6558 95.903 1 4050 1 chr2B.!!$F1 4049
14 TraesCS1A01G038500 chr2B 608459218 608463256 4038 True 6438 6438 95.439 1 4050 1 chr2B.!!$R1 4049
15 TraesCS1A01G038500 chr6B 21363691 21367753 4062 True 6510 6510 95.664 1 4050 1 chr6B.!!$R1 4049
16 TraesCS1A01G038500 chr4B 14710989 14715047 4058 True 6490 6490 95.588 1 4050 1 chr4B.!!$R1 4049
17 TraesCS1A01G038500 chr7B 194124486 194128547 4061 False 6482 6482 95.541 1 4050 1 chr7B.!!$F1 4049
18 TraesCS1A01G038500 chr2A 389208550 389212619 4069 True 6479 6479 95.500 1 4050 1 chr2A.!!$R1 4049
19 TraesCS1A01G038500 chr2A 733076190 733079588 3398 True 5426 5426 95.608 1 3378 1 chr2A.!!$R2 3377
20 TraesCS1A01G038500 chr5A 17462226 17466263 4037 False 6405 6405 95.296 1 4050 1 chr5A.!!$F1 4049
21 TraesCS1A01G038500 chr5A 396399890 396401252 1362 False 2119 2119 95.015 1 1340 1 chr5A.!!$F2 1339
22 TraesCS1A01G038500 chr7A 722678496 722680619 2123 False 3520 3520 96.798 1 2097 1 chr7A.!!$F1 2096
23 TraesCS1A01G038500 chr7A 722689149 722691120 1971 False 3352 3352 97.416 2086 4050 1 chr7A.!!$F2 1964

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
994 1138 0.746659 GCAGTTGCCTCAAACCAAGT 59.253 50.0 0.00 0.00 34.31 3.16 F
1565 1709 1.463553 AAACCTTCAAGGCCGCCAAG 61.464 55.0 13.15 6.59 39.63 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 2047 0.663153 GAACTGCTCGTGCCAAGTTT 59.337 50.0 14.08 2.12 36.14 2.66 R
3318 3552 0.040067 GCCACTGTGCAACTGCTTAC 60.040 55.0 1.29 0.00 39.67 2.34 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
123 127 1.000827 GATGCTGACGACGATGAGGAT 60.001 52.381 0.00 0.36 0.00 3.24
153 159 3.519667 GGATGAATCAGAGGAGGAGGAT 58.480 50.000 0.00 0.00 0.00 3.24
337 460 1.458588 GGGGACAAAGGGGCAACAA 60.459 57.895 0.00 0.00 39.74 2.83
519 642 0.763035 GTTCTGGTGGTACAGGTGGT 59.237 55.000 0.00 0.00 41.80 4.16
630 774 5.205759 AGGATTTGCCAAAGTCAAAGAAG 57.794 39.130 0.00 0.00 40.02 2.85
823 967 4.346730 TCAAATTGACATGGAGGAAGCAT 58.653 39.130 0.00 0.00 0.00 3.79
994 1138 0.746659 GCAGTTGCCTCAAACCAAGT 59.253 50.000 0.00 0.00 34.31 3.16
1548 1692 6.874664 TGTTCGACATTATAAGTAGGTGCAAA 59.125 34.615 0.00 0.00 0.00 3.68
1565 1709 1.463553 AAACCTTCAAGGCCGCCAAG 61.464 55.000 13.15 6.59 39.63 3.61
1579 1723 2.418628 CCGCCAAGTACAACACTATTGG 59.581 50.000 0.00 0.00 37.95 3.16
1903 2047 0.813610 CCCGATATGCGCAGAACCAA 60.814 55.000 18.32 0.00 39.11 3.67
1995 2139 5.824421 ACATCTCAAAGGTCTCCATTCATT 58.176 37.500 0.00 0.00 0.00 2.57
2409 2565 9.515020 GTTGTCAAAAATTGTTATTGAGACTGA 57.485 29.630 0.00 0.00 34.02 3.41
2477 2633 4.469657 TGTTATGCCACTGAGGTTTTCTT 58.530 39.130 0.00 0.00 40.61 2.52
2621 2781 6.183360 TGCAGATAAAATTACAGCAAGGGATG 60.183 38.462 0.00 0.00 36.23 3.51
2890 3057 2.341543 CTGCCAGTGCTCGAGTGT 59.658 61.111 15.13 0.00 38.71 3.55
3309 3543 1.083489 TGGCGCATAAGTAGTTGCAC 58.917 50.000 10.83 0.00 38.80 4.57
3310 3544 1.083489 GGCGCATAAGTAGTTGCACA 58.917 50.000 10.83 0.00 38.80 4.57
3311 3545 1.202031 GGCGCATAAGTAGTTGCACAC 60.202 52.381 10.83 0.00 38.80 3.82
3312 3546 1.732259 GCGCATAAGTAGTTGCACACT 59.268 47.619 0.30 6.74 38.80 3.55
3313 3547 2.474526 GCGCATAAGTAGTTGCACACTG 60.475 50.000 0.30 0.00 38.80 3.66
3314 3548 2.094258 CGCATAAGTAGTTGCACACTGG 59.906 50.000 10.59 0.39 38.80 4.00
3315 3549 2.159517 GCATAAGTAGTTGCACACTGGC 60.160 50.000 10.59 5.43 38.72 4.85
3316 3550 2.920724 TAAGTAGTTGCACACTGGCA 57.079 45.000 10.59 0.00 43.19 4.92
3317 3551 1.308998 AAGTAGTTGCACACTGGCAC 58.691 50.000 10.59 3.27 44.86 5.01
3318 3552 0.880278 AGTAGTTGCACACTGGCACG 60.880 55.000 10.59 0.00 44.86 5.34
3319 3553 1.145156 TAGTTGCACACTGGCACGT 59.855 52.632 10.59 0.00 44.86 4.49
3320 3554 0.389757 TAGTTGCACACTGGCACGTA 59.610 50.000 10.59 0.00 44.86 3.57
3321 3555 0.462937 AGTTGCACACTGGCACGTAA 60.463 50.000 0.00 0.00 44.86 3.18
3322 3556 0.041312 GTTGCACACTGGCACGTAAG 60.041 55.000 0.00 0.00 44.86 2.34
3323 3557 1.781025 TTGCACACTGGCACGTAAGC 61.781 55.000 0.00 0.00 44.86 3.09
3324 3558 2.250939 GCACACTGGCACGTAAGCA 61.251 57.895 0.00 0.00 45.62 3.91
3325 3559 1.862123 CACACTGGCACGTAAGCAG 59.138 57.895 0.00 0.00 45.62 4.24
3326 3560 0.880278 CACACTGGCACGTAAGCAGT 60.880 55.000 0.00 0.00 45.62 4.40
3327 3561 0.179056 ACACTGGCACGTAAGCAGTT 60.179 50.000 0.00 0.00 45.62 3.16
3328 3562 0.235665 CACTGGCACGTAAGCAGTTG 59.764 55.000 0.00 0.00 45.62 3.16
3329 3563 1.207593 CTGGCACGTAAGCAGTTGC 59.792 57.895 0.00 0.00 45.62 4.17
3330 3564 1.506309 CTGGCACGTAAGCAGTTGCA 61.506 55.000 6.90 0.00 45.16 4.08
3473 3742 0.179032 TGAGTGTGGGTTGTTCGCAT 60.179 50.000 0.00 0.00 40.92 4.73
3493 3762 1.373748 GCTTAACGCCACCGAGTGA 60.374 57.895 5.71 0.00 35.23 3.41
3616 3885 3.119101 GGAGGAAGTTGCTGAGATACGAA 60.119 47.826 0.00 0.00 0.00 3.85
3905 4195 3.721035 TCATAGATGCTGAATGTGTCCG 58.279 45.455 0.00 0.00 0.00 4.79
3913 4203 0.396435 TGAATGTGTCCGCTTGGTCT 59.604 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 127 3.006217 CCTCTGATTCATCCGCATCTGTA 59.994 47.826 0.00 0.00 0.00 2.74
153 159 6.813293 TCTTCATTGTCATCCTCATCCTTA 57.187 37.500 0.00 0.00 0.00 2.69
337 460 0.549950 CCCCTCTCACTGCCATCAAT 59.450 55.000 0.00 0.00 0.00 2.57
519 642 3.031736 GCTAGTCCTCCTGGATGTGTTA 58.968 50.000 0.00 0.00 45.29 2.41
630 774 3.178267 CTGAGACTCTGCTTCGTCATTC 58.822 50.000 3.68 0.00 32.68 2.67
823 967 1.518367 ACCCAGTCAAGACCCTTTCA 58.482 50.000 0.00 0.00 0.00 2.69
994 1138 4.344390 AGCATCTGCACTCATCATCTTCTA 59.656 41.667 4.79 0.00 45.16 2.10
1192 1336 5.014018 ACCCCAAATCTTTTGTGGCATATTT 59.986 36.000 0.00 0.00 0.00 1.40
1246 1390 1.380246 GCACCCCTGCATCAATGGA 60.380 57.895 0.00 0.00 43.62 3.41
1548 1692 1.774894 TACTTGGCGGCCTTGAAGGT 61.775 55.000 21.46 8.78 37.80 3.50
1565 1709 5.067954 ACTTGGTTCCCAATAGTGTTGTAC 58.932 41.667 0.00 0.00 43.07 2.90
1579 1723 3.119708 GCATCATTCACTGACTTGGTTCC 60.120 47.826 0.00 0.00 36.48 3.62
1762 1906 3.069158 TCACACTCATCGATGCTGATCAT 59.931 43.478 20.81 0.00 38.32 2.45
1903 2047 0.663153 GAACTGCTCGTGCCAAGTTT 59.337 50.000 14.08 2.12 36.14 2.66
1995 2139 7.327975 TGAAAGTCTTCTTCTTGTTGTAGTCA 58.672 34.615 0.00 0.00 32.90 3.41
2197 2341 3.316868 GTGTGCAACTAAAAGCCCTGTTA 59.683 43.478 0.00 0.00 38.04 2.41
2621 2781 7.307694 TCTTGTTTATCTCATTCACATTGTGC 58.692 34.615 12.04 0.00 32.98 4.57
2890 3057 3.490249 CGTCCTTATCGGTTACATCTGCA 60.490 47.826 0.00 0.00 0.00 4.41
2989 3156 4.214971 GTGTTCATCAGCTCAATGTTGTCT 59.785 41.667 5.70 0.00 0.00 3.41
3049 3216 4.479158 TGAACTTTGGGTAATGCTTCCTT 58.521 39.130 0.00 0.00 0.00 3.36
3278 3445 1.021390 ATGCGCCACTCTGCAACTAC 61.021 55.000 4.18 0.00 45.45 2.73
3309 3543 0.235665 CAACTGCTTACGTGCCAGTG 59.764 55.000 15.23 8.34 0.00 3.66
3310 3544 1.507141 GCAACTGCTTACGTGCCAGT 61.507 55.000 0.00 4.99 38.21 4.00
3311 3545 1.207593 GCAACTGCTTACGTGCCAG 59.792 57.895 0.00 4.30 38.21 4.85
3312 3546 1.524849 TGCAACTGCTTACGTGCCA 60.525 52.632 0.00 0.00 42.66 4.92
3313 3547 1.082104 GTGCAACTGCTTACGTGCC 60.082 57.895 0.00 0.00 42.66 5.01
3314 3548 0.384725 CTGTGCAACTGCTTACGTGC 60.385 55.000 0.00 0.00 42.66 5.34
3315 3549 0.937304 ACTGTGCAACTGCTTACGTG 59.063 50.000 0.00 0.00 39.67 4.49
3316 3550 0.937304 CACTGTGCAACTGCTTACGT 59.063 50.000 2.95 0.00 39.67 3.57
3317 3551 0.235665 CCACTGTGCAACTGCTTACG 59.764 55.000 1.29 0.00 39.67 3.18
3318 3552 0.040067 GCCACTGTGCAACTGCTTAC 60.040 55.000 1.29 0.00 39.67 2.34
3319 3553 0.465278 TGCCACTGTGCAACTGCTTA 60.465 50.000 1.29 0.00 39.67 3.09
3320 3554 1.753848 TGCCACTGTGCAACTGCTT 60.754 52.632 1.29 0.00 39.67 3.91
3321 3555 2.124193 TGCCACTGTGCAACTGCT 60.124 55.556 1.29 0.00 39.67 4.24
3322 3556 2.026590 GTGCCACTGTGCAACTGC 59.973 61.111 1.29 0.49 44.11 4.40
3323 3557 1.237533 TATGTGCCACTGTGCAACTG 58.762 50.000 1.29 0.00 44.11 3.16
3324 3558 1.979855 TTATGTGCCACTGTGCAACT 58.020 45.000 1.29 0.00 44.11 3.16
3325 3559 2.228582 TCATTATGTGCCACTGTGCAAC 59.771 45.455 1.29 3.33 44.11 4.17
3326 3560 2.488937 CTCATTATGTGCCACTGTGCAA 59.511 45.455 1.29 0.00 44.11 4.08
3327 3561 2.086094 CTCATTATGTGCCACTGTGCA 58.914 47.619 1.29 1.51 39.37 4.57
3328 3562 2.086869 ACTCATTATGTGCCACTGTGC 58.913 47.619 1.29 0.00 0.00 4.57
3329 3563 3.671433 GCAACTCATTATGTGCCACTGTG 60.671 47.826 0.00 0.00 0.00 3.66
3330 3564 2.489329 GCAACTCATTATGTGCCACTGT 59.511 45.455 0.00 0.00 0.00 3.55
3448 3717 4.562082 CGAACAACCCACACTCATTACTA 58.438 43.478 0.00 0.00 0.00 1.82
3493 3762 0.114168 TGGGCAGTTGGCTACCATTT 59.886 50.000 5.63 0.00 44.01 2.32
3905 4195 4.503741 TTTAGCAATGTTGAGACCAAGC 57.496 40.909 0.00 0.00 32.06 4.01


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

AutoCloner maintained by Alex Coulton.