Multiple sequence alignment - TraesCS1A01G002800

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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 TraesCS1A01G002800 chr1A 100.000 3258 0 0 1 3258 1568220 1564963 0.000000e+00 6017
1 TraesCS1A01G002800 chr1A 98.776 3185 39 0 74 3258 1619085 1615901 0.000000e+00 5666
2 TraesCS1A01G002800 chr1A 96.196 3207 89 15 74 3258 12274991 12278186 0.000000e+00 5216
3 TraesCS1A01G002800 chr1A 96.515 2324 66 4 74 2396 9662501 9664810 0.000000e+00 3829
4 TraesCS1A01G002800 chrUn 97.559 3196 66 4 74 3258 264694343 264697537 0.000000e+00 5459
5 TraesCS1A01G002800 chr7A 97.208 3188 75 6 74 3258 724220204 724217028 0.000000e+00 5382
6 TraesCS1A01G002800 chr7A 97.010 1438 38 2 74 1508 2039066 2037631 0.000000e+00 2412
7 TraesCS1A01G002800 chr6A 96.678 3191 89 5 74 3258 575506585 575509764 0.000000e+00 5289
8 TraesCS1A01G002800 chr6A 96.552 87 1 2 1 86 333726367 333726282 3.390000e-30 143
9 TraesCS1A01G002800 chr4A 96.520 3190 93 11 74 3258 17861106 17864282 0.000000e+00 5260
10 TraesCS1A01G002800 chr4A 96.793 3118 84 6 147 3258 631535399 631532292 0.000000e+00 5190
11 TraesCS1A01G002800 chr4A 97.085 2504 70 3 758 3258 618493194 618490691 0.000000e+00 4217
12 TraesCS1A01G002800 chr4A 92.172 396 13 4 2880 3258 734635605 734635999 7.950000e-151 544
13 TraesCS1A01G002800 chr7B 96.394 3189 98 6 74 3258 643692672 643689497 0.000000e+00 5236
14 TraesCS1A01G002800 chr7B 97.619 84 1 1 1 84 10388922 10389004 3.390000e-30 143
15 TraesCS1A01G002800 chr4B 96.255 3204 90 9 74 3258 664138354 664141546 0.000000e+00 5225
16 TraesCS1A01G002800 chr4B 98.780 82 1 0 1 82 160199072 160198991 2.620000e-31 147
17 TraesCS1A01G002800 chr4B 97.619 84 1 1 1 84 198999736 198999818 3.390000e-30 143
18 TraesCS1A01G002800 chr2B 96.308 3196 92 12 74 3258 737152774 737149594 0.000000e+00 5225
19 TraesCS1A01G002800 chr2B 100.000 79 0 0 1 79 535090659 535090737 2.620000e-31 147
20 TraesCS1A01G002800 chr5B 96.067 3204 94 7 74 3258 127791067 127787877 0.000000e+00 5190
21 TraesCS1A01G002800 chr2A 95.443 3204 97 8 74 3258 772273995 772277168 0.000000e+00 5062
22 TraesCS1A01G002800 chr2A 97.082 2947 73 7 315 3258 32430655 32427719 0.000000e+00 4953
23 TraesCS1A01G002800 chr6B 96.528 144 4 1 3116 3258 37736597 37736740 1.510000e-58 237
24 TraesCS1A01G002800 chr6B 92.079 101 5 3 1 100 386531279 386531181 4.380000e-29 139
25 TraesCS1A01G002800 chr1B 100.000 80 0 0 1 80 432480716 432480795 7.280000e-32 148
26 TraesCS1A01G002800 chr3B 97.619 84 2 0 1 84 694607573 694607490 9.420000e-31 145
27 TraesCS1A01G002800 chr5A 96.512 86 1 2 1 86 6231687 6231770 1.220000e-29 141


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 TraesCS1A01G002800 chr1A 1564963 1568220 3257 True 6017 6017 100.000 1 3258 1 chr1A.!!$R1 3257
1 TraesCS1A01G002800 chr1A 1615901 1619085 3184 True 5666 5666 98.776 74 3258 1 chr1A.!!$R2 3184
2 TraesCS1A01G002800 chr1A 12274991 12278186 3195 False 5216 5216 96.196 74 3258 1 chr1A.!!$F2 3184
3 TraesCS1A01G002800 chr1A 9662501 9664810 2309 False 3829 3829 96.515 74 2396 1 chr1A.!!$F1 2322
4 TraesCS1A01G002800 chrUn 264694343 264697537 3194 False 5459 5459 97.559 74 3258 1 chrUn.!!$F1 3184
5 TraesCS1A01G002800 chr7A 724217028 724220204 3176 True 5382 5382 97.208 74 3258 1 chr7A.!!$R2 3184
6 TraesCS1A01G002800 chr7A 2037631 2039066 1435 True 2412 2412 97.010 74 1508 1 chr7A.!!$R1 1434
7 TraesCS1A01G002800 chr6A 575506585 575509764 3179 False 5289 5289 96.678 74 3258 1 chr6A.!!$F1 3184
8 TraesCS1A01G002800 chr4A 17861106 17864282 3176 False 5260 5260 96.520 74 3258 1 chr4A.!!$F1 3184
9 TraesCS1A01G002800 chr4A 631532292 631535399 3107 True 5190 5190 96.793 147 3258 1 chr4A.!!$R2 3111
10 TraesCS1A01G002800 chr4A 618490691 618493194 2503 True 4217 4217 97.085 758 3258 1 chr4A.!!$R1 2500
11 TraesCS1A01G002800 chr7B 643689497 643692672 3175 True 5236 5236 96.394 74 3258 1 chr7B.!!$R1 3184
12 TraesCS1A01G002800 chr4B 664138354 664141546 3192 False 5225 5225 96.255 74 3258 1 chr4B.!!$F2 3184
13 TraesCS1A01G002800 chr2B 737149594 737152774 3180 True 5225 5225 96.308 74 3258 1 chr2B.!!$R1 3184
14 TraesCS1A01G002800 chr5B 127787877 127791067 3190 True 5190 5190 96.067 74 3258 1 chr5B.!!$R1 3184
15 TraesCS1A01G002800 chr2A 772273995 772277168 3173 False 5062 5062 95.443 74 3258 1 chr2A.!!$F1 3184
16 TraesCS1A01G002800 chr2A 32427719 32430655 2936 True 4953 4953 97.082 315 3258 1 chr2A.!!$R1 2943

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
24 25 0.739462 CGTGAGGCCGCAAAGTGATA 60.739 55.000 12.05 0.0 0.00 2.15 F
29 30 0.947244 GGCCGCAAAGTGATATGAGG 59.053 55.000 0.00 0.0 39.25 3.86 F
31 32 1.331756 GCCGCAAAGTGATATGAGGTG 59.668 52.381 0.00 0.0 38.58 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1735 6.524734 TGCATCTACTTCAGAACTTCAGAAA 58.475 36.000 0.00 0.0 36.67 2.52 R
1712 1886 7.010923 CAGAACTTCAGAACTAGTATTGCATCC 59.989 40.741 0.00 0.0 0.00 3.51 R
2373 2547 8.996024 ACTACATAACAAAAGCAAACTTGTTT 57.004 26.923 5.59 0.0 41.77 2.83 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
22 23 2.664851 CGTGAGGCCGCAAAGTGA 60.665 61.111 12.05 0.00 0.00 3.41
23 24 2.034879 CGTGAGGCCGCAAAGTGAT 61.035 57.895 12.05 0.00 0.00 3.06
24 25 0.739462 CGTGAGGCCGCAAAGTGATA 60.739 55.000 12.05 0.00 0.00 2.15
25 26 1.668419 GTGAGGCCGCAAAGTGATAT 58.332 50.000 12.05 0.00 0.00 1.63
26 27 1.331756 GTGAGGCCGCAAAGTGATATG 59.668 52.381 12.05 0.00 0.00 1.78
27 28 1.209261 TGAGGCCGCAAAGTGATATGA 59.791 47.619 6.75 0.00 0.00 2.15
28 29 1.869767 GAGGCCGCAAAGTGATATGAG 59.130 52.381 0.00 0.00 0.00 2.90
29 30 0.947244 GGCCGCAAAGTGATATGAGG 59.053 55.000 0.00 0.00 39.25 3.86
30 31 1.668419 GCCGCAAAGTGATATGAGGT 58.332 50.000 0.00 0.00 38.58 3.85
31 32 1.331756 GCCGCAAAGTGATATGAGGTG 59.668 52.381 0.00 0.00 38.58 4.00
32 33 2.632377 CCGCAAAGTGATATGAGGTGT 58.368 47.619 0.00 0.00 32.55 4.16
33 34 3.009723 CCGCAAAGTGATATGAGGTGTT 58.990 45.455 0.00 0.00 32.55 3.32
34 35 4.188462 CCGCAAAGTGATATGAGGTGTTA 58.812 43.478 0.00 0.00 32.55 2.41
35 36 4.034048 CCGCAAAGTGATATGAGGTGTTAC 59.966 45.833 0.00 0.00 32.55 2.50
36 37 4.034048 CGCAAAGTGATATGAGGTGTTACC 59.966 45.833 0.00 0.00 38.99 2.85
37 38 4.941263 GCAAAGTGATATGAGGTGTTACCA 59.059 41.667 0.28 0.00 41.95 3.25
38 39 5.065218 GCAAAGTGATATGAGGTGTTACCAG 59.935 44.000 0.28 0.00 41.95 4.00
39 40 4.408182 AGTGATATGAGGTGTTACCAGC 57.592 45.455 0.28 0.00 41.95 4.85
49 50 3.643763 GGTGTTACCAGCTAGATCGATG 58.356 50.000 0.54 0.00 38.42 3.84
50 51 3.068307 GGTGTTACCAGCTAGATCGATGT 59.932 47.826 0.54 0.00 38.42 3.06
51 52 4.045104 GTGTTACCAGCTAGATCGATGTG 58.955 47.826 0.54 0.00 0.00 3.21
52 53 3.951680 TGTTACCAGCTAGATCGATGTGA 59.048 43.478 0.54 0.00 0.00 3.58
53 54 4.202020 TGTTACCAGCTAGATCGATGTGAC 60.202 45.833 0.54 0.01 0.00 3.67
54 55 2.379005 ACCAGCTAGATCGATGTGACA 58.621 47.619 0.54 0.00 0.00 3.58
55 56 2.961741 ACCAGCTAGATCGATGTGACAT 59.038 45.455 0.54 0.00 0.00 3.06
56 57 3.005261 ACCAGCTAGATCGATGTGACATC 59.995 47.826 15.36 15.36 0.00 3.06
57 58 3.232771 CAGCTAGATCGATGTGACATCG 58.767 50.000 34.77 34.77 42.38 3.84
68 69 2.806237 GACATCGAGTCGGGGTCC 59.194 66.667 20.03 8.02 37.53 4.46
69 70 1.753463 GACATCGAGTCGGGGTCCT 60.753 63.158 20.03 0.00 37.53 3.85
70 71 2.005960 GACATCGAGTCGGGGTCCTG 62.006 65.000 20.03 9.27 37.53 3.86
71 72 1.753078 CATCGAGTCGGGGTCCTGA 60.753 63.158 13.54 0.00 0.00 3.86
467 468 4.221482 TGTCTATCTCACTGCACAGAACAT 59.779 41.667 4.31 0.00 0.00 2.71
1510 1684 8.915036 ACTAGTTCTGAAGTTCTGAAGTTTCTA 58.085 33.333 27.66 20.50 38.43 2.10
1561 1735 9.107177 CTGAAGTTTCTGAAGTAGATGCAATAT 57.893 33.333 0.00 0.00 34.80 1.28
1712 1886 6.203530 TGCAATAGTTCTGAAGTTCTGAAGTG 59.796 38.462 29.17 21.42 38.11 3.16
2219 2393 0.246635 GAAGTACTGGCAAGAGGCGA 59.753 55.000 0.00 0.00 46.16 5.54
2221 2395 0.905357 AGTACTGGCAAGAGGCGAAT 59.095 50.000 0.00 0.00 46.16 3.34
2373 2547 9.809096 TTGAACAAGTTTGCTTTTGTAATGATA 57.191 25.926 0.00 0.00 36.56 2.15
2483 2657 8.870160 TTCAACTTTTGGTGATCATTTAGTTG 57.130 30.769 20.93 20.93 46.73 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.739462 TATCACTTTGCGGCCTCACG 60.739 55.000 0.00 0.00 0.00 4.35
6 7 1.331756 CATATCACTTTGCGGCCTCAC 59.668 52.381 0.00 0.00 0.00 3.51
7 8 1.209261 TCATATCACTTTGCGGCCTCA 59.791 47.619 0.00 0.00 0.00 3.86
8 9 1.869767 CTCATATCACTTTGCGGCCTC 59.130 52.381 0.00 0.00 0.00 4.70
9 10 1.475751 CCTCATATCACTTTGCGGCCT 60.476 52.381 0.00 0.00 0.00 5.19
10 11 0.947244 CCTCATATCACTTTGCGGCC 59.053 55.000 0.00 0.00 0.00 6.13
11 12 1.331756 CACCTCATATCACTTTGCGGC 59.668 52.381 0.00 0.00 0.00 6.53
12 13 2.632377 ACACCTCATATCACTTTGCGG 58.368 47.619 0.00 0.00 0.00 5.69
13 14 4.034048 GGTAACACCTCATATCACTTTGCG 59.966 45.833 0.00 0.00 34.73 4.85
14 15 4.941263 TGGTAACACCTCATATCACTTTGC 59.059 41.667 0.00 0.00 46.17 3.68
15 16 5.065218 GCTGGTAACACCTCATATCACTTTG 59.935 44.000 0.00 0.00 46.17 2.77
16 17 5.045578 AGCTGGTAACACCTCATATCACTTT 60.046 40.000 0.00 0.00 46.17 2.66
17 18 4.471386 AGCTGGTAACACCTCATATCACTT 59.529 41.667 0.00 0.00 46.17 3.16
18 19 4.033709 AGCTGGTAACACCTCATATCACT 58.966 43.478 0.00 0.00 46.17 3.41
19 20 4.408182 AGCTGGTAACACCTCATATCAC 57.592 45.455 0.00 0.00 46.17 3.06
20 21 5.454966 TCTAGCTGGTAACACCTCATATCA 58.545 41.667 0.00 0.00 46.17 2.15
21 22 6.597832 ATCTAGCTGGTAACACCTCATATC 57.402 41.667 0.00 0.00 46.17 1.63
22 23 5.184096 CGATCTAGCTGGTAACACCTCATAT 59.816 44.000 0.00 0.00 46.17 1.78
23 24 4.519350 CGATCTAGCTGGTAACACCTCATA 59.481 45.833 0.00 0.00 46.17 2.15
24 25 3.319405 CGATCTAGCTGGTAACACCTCAT 59.681 47.826 0.00 0.00 46.17 2.90
25 26 2.688446 CGATCTAGCTGGTAACACCTCA 59.312 50.000 0.00 0.00 46.17 3.86
26 27 2.950309 TCGATCTAGCTGGTAACACCTC 59.050 50.000 0.00 0.00 46.17 3.85
27 28 3.014304 TCGATCTAGCTGGTAACACCT 57.986 47.619 0.00 0.00 46.17 4.00
28 29 3.068307 ACATCGATCTAGCTGGTAACACC 59.932 47.826 0.00 0.00 46.17 4.16
29 30 4.045104 CACATCGATCTAGCTGGTAACAC 58.955 47.826 0.00 0.00 46.17 3.32
31 32 4.202020 TGTCACATCGATCTAGCTGGTAAC 60.202 45.833 0.00 0.00 0.00 2.50
32 33 3.951680 TGTCACATCGATCTAGCTGGTAA 59.048 43.478 0.00 0.00 0.00 2.85
33 34 3.551846 TGTCACATCGATCTAGCTGGTA 58.448 45.455 0.00 0.00 0.00 3.25
34 35 2.379005 TGTCACATCGATCTAGCTGGT 58.621 47.619 0.00 0.00 0.00 4.00
35 36 3.573598 GATGTCACATCGATCTAGCTGG 58.426 50.000 0.93 0.00 0.00 4.85
36 37 3.058639 TCGATGTCACATCGATCTAGCTG 60.059 47.826 33.92 7.87 44.42 4.24
37 38 3.142174 TCGATGTCACATCGATCTAGCT 58.858 45.455 33.92 0.00 44.42 3.32
38 39 3.544356 TCGATGTCACATCGATCTAGC 57.456 47.619 33.92 0.00 44.42 3.42
44 45 0.377203 CCGACTCGATGTCACATCGA 59.623 55.000 34.63 34.63 46.69 3.59
45 46 0.592500 CCCGACTCGATGTCACATCG 60.593 60.000 30.60 30.60 45.60 3.84
46 47 0.249073 CCCCGACTCGATGTCACATC 60.249 60.000 7.83 7.83 45.60 3.06
47 48 0.970937 ACCCCGACTCGATGTCACAT 60.971 55.000 13.14 0.00 45.60 3.21
48 49 1.592400 GACCCCGACTCGATGTCACA 61.592 60.000 13.14 0.00 45.60 3.58
49 50 1.139095 GACCCCGACTCGATGTCAC 59.861 63.158 13.14 0.00 45.60 3.67
50 51 2.050350 GGACCCCGACTCGATGTCA 61.050 63.158 16.91 0.00 45.60 3.58
51 52 1.753463 AGGACCCCGACTCGATGTC 60.753 63.158 0.00 5.96 42.06 3.06
52 53 2.052690 CAGGACCCCGACTCGATGT 61.053 63.158 0.00 0.00 0.00 3.06
53 54 1.753078 TCAGGACCCCGACTCGATG 60.753 63.158 0.00 0.00 0.00 3.84
54 55 1.753463 GTCAGGACCCCGACTCGAT 60.753 63.158 0.00 0.00 0.00 3.59
55 56 2.360852 GTCAGGACCCCGACTCGA 60.361 66.667 0.00 0.00 0.00 4.04
56 57 2.675423 TGTCAGGACCCCGACTCG 60.675 66.667 11.80 0.00 31.80 4.18
57 58 1.596895 GAGTGTCAGGACCCCGACTC 61.597 65.000 11.80 8.77 31.80 3.36
58 59 1.606889 GAGTGTCAGGACCCCGACT 60.607 63.158 11.80 0.00 31.80 4.18
59 60 2.647158 GGAGTGTCAGGACCCCGAC 61.647 68.421 4.95 4.95 0.00 4.79
60 61 2.283676 GGAGTGTCAGGACCCCGA 60.284 66.667 0.00 0.00 0.00 5.14
61 62 3.760035 CGGAGTGTCAGGACCCCG 61.760 72.222 9.44 9.44 33.83 5.73
62 63 3.391382 CCGGAGTGTCAGGACCCC 61.391 72.222 0.00 0.00 33.29 4.95
63 64 3.391382 CCCGGAGTGTCAGGACCC 61.391 72.222 0.73 0.00 33.29 4.46
64 65 1.911766 TTCCCGGAGTGTCAGGACC 60.912 63.158 0.73 0.00 33.29 4.46
65 66 1.292541 GTTCCCGGAGTGTCAGGAC 59.707 63.158 0.73 0.00 33.29 3.85
66 67 1.911766 GGTTCCCGGAGTGTCAGGA 60.912 63.158 0.73 0.00 33.29 3.86
67 68 1.481056 AAGGTTCCCGGAGTGTCAGG 61.481 60.000 0.73 0.00 0.00 3.86
68 69 1.067071 GTAAGGTTCCCGGAGTGTCAG 60.067 57.143 0.73 0.00 0.00 3.51
69 70 0.971386 GTAAGGTTCCCGGAGTGTCA 59.029 55.000 0.73 0.00 0.00 3.58
70 71 0.248565 GGTAAGGTTCCCGGAGTGTC 59.751 60.000 0.73 0.00 0.00 3.67
71 72 1.196766 GGGTAAGGTTCCCGGAGTGT 61.197 60.000 0.73 0.00 35.27 3.55
72 73 1.600638 GGGTAAGGTTCCCGGAGTG 59.399 63.158 0.73 0.00 35.27 3.51
1561 1735 6.524734 TGCATCTACTTCAGAACTTCAGAAA 58.475 36.000 0.00 0.00 36.67 2.52
1626 1800 7.663081 TGCATCTACTTGAGAAACTTCAGAAAT 59.337 33.333 0.00 0.00 37.85 2.17
1712 1886 7.010923 CAGAACTTCAGAACTAGTATTGCATCC 59.989 40.741 0.00 0.00 0.00 3.51
2373 2547 8.996024 ACTACATAACAAAAGCAAACTTGTTT 57.004 26.923 5.59 0.00 41.77 2.83
2483 2657 7.672983 TTCTGTATGATCTGACCAAAACTTC 57.327 36.000 0.00 0.00 0.00 3.01
2991 3170 3.080641 TCGGTGACTCGACCCCTA 58.919 61.111 0.00 0.00 33.92 3.53


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

AutoCloner maintained by Alex Coulton.