Multiple sequence alignment - TraesCS3A01G013000

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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 TraesCS3A01G013000 chr3A 100.000 4139 0 0 1 4139 9612250 9616388 0.000000e+00 7644.0
1 TraesCS3A01G013000 chr3A 95.673 2450 87 4 773 3216 9780258 9777822 0.000000e+00 3919.0
2 TraesCS3A01G013000 chr3A 99.791 478 1 0 1 478 9781352 9780875 0.000000e+00 878.0
3 TraesCS3A01G013000 chr3A 98.113 265 3 1 468 730 9780517 9780253 1.050000e-125 460.0
4 TraesCS3A01G013000 chr3A 91.667 276 15 3 3285 3560 9777825 9777558 3.910000e-100 375.0
5 TraesCS3A01G013000 chr3A 86.029 272 20 8 3882 4137 9777113 9776844 4.080000e-70 276.0
6 TraesCS3A01G013000 chr3A 94.737 38 2 0 3595 3632 9777562 9777525 4.470000e-05 60.2
7 TraesCS3A01G013000 chr3D 96.106 3236 98 7 6 3216 4170259 4167027 0.000000e+00 5252.0
8 TraesCS3A01G013000 chr3D 90.797 1869 116 8 1809 3632 4076805 4078662 0.000000e+00 2447.0
9 TraesCS3A01G013000 chr3D 86.037 1769 172 35 1 1748 4074996 4076710 0.000000e+00 1829.0
10 TraesCS3A01G013000 chr3D 94.068 354 14 2 3285 3632 4167030 4166678 7.880000e-147 531.0
11 TraesCS3A01G013000 chr3D 93.471 291 16 2 3718 4005 4078832 4079122 2.960000e-116 429.0
12 TraesCS3A01G013000 chr3D 85.556 270 18 9 3878 4139 4166352 4166096 3.170000e-66 263.0
13 TraesCS3A01G013000 chr3D 98.438 64 0 1 3660 3722 4078744 4078807 1.220000e-20 111.0
14 TraesCS3A01G013000 chr3D 97.368 38 1 0 3718 3755 4166493 4166456 9.600000e-07 65.8
15 TraesCS3A01G013000 chr3D 94.737 38 2 0 4084 4121 4079153 4079190 4.470000e-05 60.2
16 TraesCS3A01G013000 chr3B 93.076 2123 91 17 1146 3212 6667670 6665548 0.000000e+00 3055.0
17 TraesCS3A01G013000 chr3B 85.992 2984 253 70 747 3623 6393441 6396366 0.000000e+00 3042.0
18 TraesCS3A01G013000 chr3B 93.481 767 40 5 2161 2918 13937795 13937030 0.000000e+00 1131.0
19 TraesCS3A01G013000 chr3B 93.164 746 42 5 1 740 6392655 6393397 0.000000e+00 1086.0
20 TraesCS3A01G013000 chr3B 88.079 604 36 20 1611 2180 13939279 13938678 0.000000e+00 684.0
21 TraesCS3A01G013000 chr3B 91.694 301 14 3 2928 3217 13936989 13936689 1.390000e-109 407.0
22 TraesCS3A01G013000 chr3B 96.154 234 9 0 988 1221 13939516 13939283 2.330000e-102 383.0
23 TraesCS3A01G013000 chr3B 84.384 333 32 11 3304 3632 13936576 13936260 4.020000e-80 309.0
24 TraesCS3A01G013000 chr3B 89.767 215 10 4 890 1104 6667864 6667662 8.820000e-67 265.0
25 TraesCS3A01G013000 chr3B 82.569 327 26 8 3289 3587 6665556 6665233 4.100000e-65 259.0
26 TraesCS3A01G013000 chr3B 84.462 251 24 10 3902 4139 6352524 6352276 2.490000e-57 233.0
27 TraesCS3A01G013000 chr3B 80.451 266 22 13 3902 4139 6422284 6422021 4.250000e-40 176.0
28 TraesCS3A01G013000 chr3B 94.737 76 4 0 4064 4139 6662440 6662365 7.270000e-23 119.0
29 TraesCS3A01G013000 chr3B 87.156 109 2 4 3824 3932 6664979 6664883 3.380000e-21 113.0
30 TraesCS3A01G013000 chr3B 96.721 61 1 1 790 849 6667916 6667856 2.630000e-17 100.0
31 TraesCS3A01G013000 chr3B 97.368 38 1 0 3718 3755 6396587 6396624 9.600000e-07 65.8
32 TraesCS3A01G013000 chr3B 100.000 34 0 0 3718 3751 13936043 13936010 3.450000e-06 63.9
33 TraesCS3A01G013000 chrUn 85.992 2984 253 70 747 3623 246339341 246342266 0.000000e+00 3042.0
34 TraesCS3A01G013000 chrUn 93.164 746 42 5 1 740 246338555 246339297 0.000000e+00 1086.0
35 TraesCS3A01G013000 chrUn 97.368 38 1 0 3718 3755 246342487 246342524 9.600000e-07 65.8
36 TraesCS3A01G013000 chr6A 89.768 733 49 15 9 723 609885892 609886616 0.000000e+00 915.0
37 TraesCS3A01G013000 chr6A 93.659 410 18 3 3223 3632 609888433 609888834 1.270000e-169 606.0
38 TraesCS3A01G013000 chr6A 89.912 456 28 1 2725 3162 609887984 609888439 4.640000e-159 571.0
39 TraesCS3A01G013000 chr6A 89.082 403 27 10 3753 4139 609889052 609889453 6.220000e-133 484.0
40 TraesCS3A01G013000 chr2B 78.947 1026 180 24 2075 3072 752829810 752828793 0.000000e+00 665.0
41 TraesCS3A01G013000 chr5D 78.645 974 179 17 2079 3027 464078549 464079518 1.630000e-173 619.0
42 TraesCS3A01G013000 chr1B 78.195 133 27 2 1125 1256 9597342 9597473 2.650000e-12 84.2


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 TraesCS3A01G013000 chr3A 9612250 9616388 4138 False 7644.000000 7644 100.000000 1 4139 1 chr3A.!!$F1 4138
1 TraesCS3A01G013000 chr3A 9776844 9781352 4508 True 994.700000 3919 94.335000 1 4137 6 chr3A.!!$R1 4136
2 TraesCS3A01G013000 chr3D 4166096 4170259 4163 True 1527.950000 5252 93.274500 6 4139 4 chr3D.!!$R1 4133
3 TraesCS3A01G013000 chr3D 4074996 4079190 4194 False 975.240000 2447 92.696000 1 4121 5 chr3D.!!$F1 4120
4 TraesCS3A01G013000 chr3B 6392655 6396624 3969 False 1397.933333 3042 92.174667 1 3755 3 chr3B.!!$F1 3754
5 TraesCS3A01G013000 chr3B 6662365 6667916 5551 True 651.833333 3055 90.671000 790 4139 6 chr3B.!!$R3 3349
6 TraesCS3A01G013000 chr3B 13936010 13939516 3506 True 496.316667 1131 92.298667 988 3751 6 chr3B.!!$R4 2763
7 TraesCS3A01G013000 chrUn 246338555 246342524 3969 False 1397.933333 3042 92.174667 1 3755 3 chrUn.!!$F1 3754
8 TraesCS3A01G013000 chr6A 609885892 609889453 3561 False 644.000000 915 90.605250 9 4139 4 chr6A.!!$F1 4130
9 TraesCS3A01G013000 chr2B 752828793 752829810 1017 True 665.000000 665 78.947000 2075 3072 1 chr2B.!!$R1 997
10 TraesCS3A01G013000 chr5D 464078549 464079518 969 False 619.000000 619 78.645000 2079 3027 1 chr5D.!!$F1 948

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
508 880 3.409026 AATCGGATCTCTATTGTGCCC 57.591 47.619 0.0 0.0 0.00 5.36 F
1441 1933 2.159254 GCTGCCTTTGTCAGTTGTTCAA 60.159 45.455 0.0 0.0 34.21 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 2027 2.957402 AGGCTCAACATTCTGAACCA 57.043 45.0 0.00 0.0 34.53 3.67 R
3396 5174 0.108585 AGCGCCAACGGGATTATCAT 59.891 50.0 2.29 0.0 40.57 2.45 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
508 880 3.409026 AATCGGATCTCTATTGTGCCC 57.591 47.619 0.00 0.00 0.00 5.36
1005 1486 4.186926 GCATCTGTAAAGCTCTCATGACA 58.813 43.478 0.00 0.00 0.00 3.58
1006 1487 4.815308 GCATCTGTAAAGCTCTCATGACAT 59.185 41.667 0.00 0.00 0.00 3.06
1393 1885 7.799081 TGGATTGAGATCAGATTACATGTTCT 58.201 34.615 2.30 0.00 33.77 3.01
1399 1891 9.371136 TGAGATCAGATTACATGTTCTTGTTAC 57.629 33.333 2.30 0.00 29.10 2.50
1441 1933 2.159254 GCTGCCTTTGTCAGTTGTTCAA 60.159 45.455 0.00 0.00 34.21 2.69
1535 2027 5.109903 GTTGAGTACCACGCAATCTTATCT 58.890 41.667 0.00 0.00 39.89 1.98
1963 2506 3.780902 TGTGTTGGTCATAGTATCTGCG 58.219 45.455 0.00 0.00 0.00 5.18
2077 2723 7.443879 TCTGTAATCTTGTTTATGCAGTGTTGA 59.556 33.333 0.00 0.00 0.00 3.18
2987 4616 0.106868 TGCATCCAGATGAAGCCAGG 60.107 55.000 11.81 0.00 41.20 4.45
3394 5172 4.695928 GGAGAGAACCGCTTTCTGTAAAAT 59.304 41.667 2.37 0.00 45.24 1.82
3395 5173 5.873164 GGAGAGAACCGCTTTCTGTAAAATA 59.127 40.000 2.37 0.00 45.24 1.40
3396 5174 6.370718 GGAGAGAACCGCTTTCTGTAAAATAA 59.629 38.462 2.37 0.00 45.24 1.40
3397 5175 7.065923 GGAGAGAACCGCTTTCTGTAAAATAAT 59.934 37.037 2.37 0.00 45.24 1.28
3398 5176 7.752695 AGAGAACCGCTTTCTGTAAAATAATG 58.247 34.615 2.37 0.00 45.24 1.90
3399 5177 7.606456 AGAGAACCGCTTTCTGTAAAATAATGA 59.394 33.333 2.37 0.00 45.24 2.57
3628 5465 4.518217 CTGCGAACGGATATGAAATGTTC 58.482 43.478 0.00 0.00 36.47 3.18
3632 5469 4.552767 CGAACGGATATGAAATGTTCTGCC 60.553 45.833 2.46 0.00 37.40 4.85
3634 5471 2.224079 CGGATATGAAATGTTCTGCCGG 59.776 50.000 0.00 0.00 33.13 6.13
3635 5472 2.554032 GGATATGAAATGTTCTGCCGGG 59.446 50.000 2.18 0.00 0.00 5.73
3637 5474 0.039618 ATGAAATGTTCTGCCGGGGT 59.960 50.000 2.18 0.00 0.00 4.95
3638 5475 0.178975 TGAAATGTTCTGCCGGGGTT 60.179 50.000 2.18 0.00 0.00 4.11
3639 5476 0.966179 GAAATGTTCTGCCGGGGTTT 59.034 50.000 2.18 0.00 0.00 3.27
3642 5479 0.039618 ATGTTCTGCCGGGGTTTCAT 59.960 50.000 2.18 0.00 0.00 2.57
3645 5515 0.034863 TTCTGCCGGGGTTTCATACC 60.035 55.000 2.18 0.00 46.99 2.73
3656 5526 5.450412 CGGGGTTTCATACCTTCATCATTTG 60.450 44.000 0.00 0.00 46.86 2.32
3657 5527 5.351458 GGGTTTCATACCTTCATCATTTGC 58.649 41.667 0.00 0.00 46.86 3.68
3658 5528 5.105392 GGGTTTCATACCTTCATCATTTGCA 60.105 40.000 0.00 0.00 46.86 4.08
3751 5774 3.131755 AGCTTTGCCATTCTTCTTATGCC 59.868 43.478 0.00 0.00 0.00 4.40
3775 5823 6.430000 CCCTGCTTGTTATTAAGTTACACACT 59.570 38.462 0.00 0.00 37.30 3.55
3838 5886 0.040514 TGCGACGCAAGGTTGATTTG 60.041 50.000 22.24 0.00 46.39 2.32
3932 6067 7.429633 TCTGTTTCAAACAAAAGTTCAGACAA 58.570 30.769 4.13 0.00 41.61 3.18
3944 6079 1.588239 TCAGACAATGAGGCAGGGAT 58.412 50.000 0.00 0.00 32.77 3.85
3953 6090 7.512058 AGACAATGAGGCAGGGATATATATAGG 59.488 40.741 0.00 0.00 0.00 2.57
4028 6165 1.369209 GTTTGTCGTCGTCGGTCGA 60.369 57.895 1.55 8.76 46.83 4.20
4043 6182 1.001764 TCGAGGTAGCTCCGGTGAA 60.002 57.895 16.06 0.00 41.99 3.18
4045 6184 1.817209 GAGGTAGCTCCGGTGAAGG 59.183 63.158 10.97 0.00 41.99 3.46
4048 6187 1.516423 GTAGCTCCGGTGAAGGGTC 59.484 63.158 7.92 0.00 0.00 4.46
4051 6190 3.771160 CTCCGGTGAAGGGTCGGG 61.771 72.222 0.00 0.00 43.54 5.14
4052 6191 4.304413 TCCGGTGAAGGGTCGGGA 62.304 66.667 0.00 0.00 43.54 5.14
4053 6192 3.771160 CCGGTGAAGGGTCGGGAG 61.771 72.222 0.00 0.00 40.07 4.30
4090 8594 1.537397 AGTGAGGAGGGAGCAGCAA 60.537 57.895 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
508 880 1.088340 CATCCAGGTGCAGCGAAGAG 61.088 60.000 10.78 0.00 0.00 2.85
1005 1486 2.006888 CGTGGAAATGCAACGGAGTAT 58.993 47.619 0.00 0.00 45.00 2.12
1006 1487 1.270412 ACGTGGAAATGCAACGGAGTA 60.270 47.619 12.10 0.00 45.00 2.59
1393 1885 6.957984 TTTAACCGTACGCATATGTAACAA 57.042 33.333 10.49 0.00 0.00 2.83
1399 1891 3.364565 GCCCATTTAACCGTACGCATATG 60.365 47.826 10.49 8.18 0.00 1.78
1535 2027 2.957402 AGGCTCAACATTCTGAACCA 57.043 45.000 0.00 0.00 34.53 3.67
1963 2506 9.029243 CCGATAATGAGCTTCATGATACTTATC 57.971 37.037 0.00 4.12 37.15 1.75
2077 2723 6.351117 GCAAAGACTAACCTGGATAGTACTGT 60.351 42.308 15.64 0.00 33.85 3.55
3149 4782 9.634163 GATAAAATTTGGTCCAAAACTACGATT 57.366 29.630 20.76 6.23 36.90 3.34
3394 5172 2.147958 GCGCCAACGGGATTATCATTA 58.852 47.619 0.00 0.00 40.57 1.90
3395 5173 0.951558 GCGCCAACGGGATTATCATT 59.048 50.000 0.00 0.00 40.57 2.57
3396 5174 0.108585 AGCGCCAACGGGATTATCAT 59.891 50.000 2.29 0.00 40.57 2.45
3397 5175 0.813610 CAGCGCCAACGGGATTATCA 60.814 55.000 2.29 0.00 40.57 2.15
3398 5176 0.814010 ACAGCGCCAACGGGATTATC 60.814 55.000 2.29 0.00 40.57 1.75
3399 5177 0.393808 AACAGCGCCAACGGGATTAT 60.394 50.000 2.29 0.00 40.57 1.28
3628 5465 4.235731 GGTATGAAACCCCGGCAG 57.764 61.111 0.00 0.00 43.16 4.85
3637 5474 6.839124 AGTGCAAATGATGAAGGTATGAAA 57.161 33.333 0.00 0.00 0.00 2.69
3638 5475 6.839124 AAGTGCAAATGATGAAGGTATGAA 57.161 33.333 0.00 0.00 0.00 2.57
3639 5476 6.318648 GGTAAGTGCAAATGATGAAGGTATGA 59.681 38.462 0.00 0.00 0.00 2.15
3642 5479 5.815581 AGGTAAGTGCAAATGATGAAGGTA 58.184 37.500 0.00 0.00 0.00 3.08
3645 5515 7.752239 CAGTTAAGGTAAGTGCAAATGATGAAG 59.248 37.037 0.00 0.00 32.89 3.02
3656 5526 5.061179 TGGAGTTTCAGTTAAGGTAAGTGC 58.939 41.667 0.00 0.00 38.64 4.40
3657 5527 8.311836 TCTATGGAGTTTCAGTTAAGGTAAGTG 58.688 37.037 0.00 0.00 39.81 3.16
3658 5528 8.431910 TCTATGGAGTTTCAGTTAAGGTAAGT 57.568 34.615 0.00 0.00 0.00 2.24
3751 5774 7.172532 TGAGTGTGTAACTTAATAACAAGCAGG 59.827 37.037 0.00 0.00 40.07 4.85
3814 5862 3.883744 AACCTTGCGTCGCAGGAGG 62.884 63.158 28.38 28.38 41.01 4.30
3838 5886 3.141398 TCTGTGTGAATGTTTGAGAGGC 58.859 45.455 0.00 0.00 0.00 4.70
3932 6067 5.730848 TGCCTATATATATCCCTGCCTCAT 58.269 41.667 0.00 0.00 0.00 2.90
3944 6079 5.019470 AGCACAGCACTCTGCCTATATATA 58.981 41.667 0.00 0.00 46.52 0.86
3953 6090 2.944429 CACAGCACAGCACTCTGC 59.056 61.111 0.00 0.00 44.10 4.26
4028 6165 1.686110 CCCTTCACCGGAGCTACCT 60.686 63.158 9.46 0.00 36.31 3.08
4053 6192 4.096003 TTACCCTGCTCCCGCTGC 62.096 66.667 0.00 0.00 36.97 5.25
4070 8574 1.685421 GCTGCTCCCTCCTCACTCT 60.685 63.158 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.