Multiple sequence alignment - TraesCS3A01G212500

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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 TraesCS3A01G212500 chr3A 100.000 3900 0 0 1 3900 382441773 382437874 0.000000e+00 7203
1 TraesCS3A01G212500 chr1A 96.525 3396 107 7 510 3900 255202939 255206328 0.000000e+00 5607
2 TraesCS3A01G212500 chr1A 95.439 3245 143 5 1 3243 423234904 423231663 0.000000e+00 5168
3 TraesCS3A01G212500 chr1A 95.376 3244 147 3 1 3243 423171209 423167968 0.000000e+00 5156
4 TraesCS3A01G212500 chr1A 95.035 3283 152 4 1 3274 423107789 423104509 0.000000e+00 5149
5 TraesCS3A01G212500 chr1A 94.926 3291 144 9 1 3274 423296793 423293509 0.000000e+00 5131
6 TraesCS3A01G212500 chr1A 97.306 2079 54 2 1822 3900 272648540 272650616 0.000000e+00 3528
7 TraesCS3A01G212500 chr1A 96.167 574 22 0 3327 3900 423293513 423292940 0.000000e+00 939
8 TraesCS3A01G212500 chr1A 97.066 409 11 1 1 408 244180393 244179985 0.000000e+00 688
9 TraesCS3A01G212500 chr1A 93.913 115 5 2 417 530 272649240 272649353 5.180000e-39 172
10 TraesCS3A01G212500 chr4A 95.903 3271 117 9 631 3900 138467241 138463987 0.000000e+00 5282
11 TraesCS3A01G212500 chr4A 91.847 834 56 7 510 1339 146401639 146402464 0.000000e+00 1153
12 TraesCS3A01G212500 chr4D 97.414 2591 61 3 1310 3900 349448342 349445758 0.000000e+00 4409
13 TraesCS3A01G212500 chr4D 93.913 115 5 2 417 530 349447135 349447022 5.180000e-39 172
14 TraesCS3A01G212500 chr7A 96.922 2079 60 2 1822 3900 269297622 269299696 0.000000e+00 3482
15 TraesCS3A01G212500 chr7A 95.844 409 15 2 1 408 298539954 298540361 0.000000e+00 660
16 TraesCS3A01G212500 chr3B 92.083 1162 82 8 510 1667 309750348 309751503 0.000000e+00 1628
17 TraesCS3A01G212500 chr6A 91.487 834 60 6 510 1339 279747071 279747897 0.000000e+00 1136
18 TraesCS3A01G212500 chr6A 93.913 115 5 2 417 530 553596877 553596764 5.180000e-39 172
19 TraesCS3A01G212500 chr1B 96.806 407 11 2 1 406 358391771 358391366 0.000000e+00 678
20 TraesCS3A01G212500 chr1B 93.077 130 8 1 1539 1668 512137362 512137234 5.140000e-44 189
21 TraesCS3A01G212500 chr4B 94.866 409 19 2 1 408 404626311 404625904 4.250000e-179 638
22 TraesCS3A01G212500 chr4B 93.913 115 5 2 417 530 373353529 373353642 5.180000e-39 172
23 TraesCS3A01G212500 chr6D 84.578 415 44 15 1 406 445403546 445403949 1.020000e-105 394
24 TraesCS3A01G212500 chr2A 90.608 181 16 1 1667 1847 305388487 305388666 5.040000e-59 239
25 TraesCS3A01G212500 chr5A 90.411 146 13 1 1663 1808 425253889 425254033 1.430000e-44 191
26 TraesCS3A01G212500 chrUn 93.913 115 5 2 417 530 325925322 325925209 5.180000e-39 172


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 TraesCS3A01G212500 chr3A 382437874 382441773 3899 True 7203.0 7203 100.0000 1 3900 1 chr3A.!!$R1 3899
1 TraesCS3A01G212500 chr1A 255202939 255206328 3389 False 5607.0 5607 96.5250 510 3900 1 chr1A.!!$F1 3390
2 TraesCS3A01G212500 chr1A 423231663 423234904 3241 True 5168.0 5168 95.4390 1 3243 1 chr1A.!!$R4 3242
3 TraesCS3A01G212500 chr1A 423167968 423171209 3241 True 5156.0 5156 95.3760 1 3243 1 chr1A.!!$R3 3242
4 TraesCS3A01G212500 chr1A 423104509 423107789 3280 True 5149.0 5149 95.0350 1 3274 1 chr1A.!!$R2 3273
5 TraesCS3A01G212500 chr1A 423292940 423296793 3853 True 3035.0 5131 95.5465 1 3900 2 chr1A.!!$R5 3899
6 TraesCS3A01G212500 chr1A 272648540 272650616 2076 False 1850.0 3528 95.6095 417 3900 2 chr1A.!!$F2 3483
7 TraesCS3A01G212500 chr4A 138463987 138467241 3254 True 5282.0 5282 95.9030 631 3900 1 chr4A.!!$R1 3269
8 TraesCS3A01G212500 chr4A 146401639 146402464 825 False 1153.0 1153 91.8470 510 1339 1 chr4A.!!$F1 829
9 TraesCS3A01G212500 chr4D 349445758 349448342 2584 True 2290.5 4409 95.6635 417 3900 2 chr4D.!!$R1 3483
10 TraesCS3A01G212500 chr7A 269297622 269299696 2074 False 3482.0 3482 96.9220 1822 3900 1 chr7A.!!$F1 2078
11 TraesCS3A01G212500 chr3B 309750348 309751503 1155 False 1628.0 1628 92.0830 510 1667 1 chr3B.!!$F1 1157
12 TraesCS3A01G212500 chr6A 279747071 279747897 826 False 1136.0 1136 91.4870 510 1339 1 chr6A.!!$F1 829

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
408 410 0.466124 AGAATTCGCCCCTGCTACTC 59.534 55.000 0.00 0.0 34.43 2.59 F
983 995 1.758122 TGCAGCGAGCTGGATAGGA 60.758 57.895 24.25 0.0 45.94 2.94 F
2405 2435 2.583143 GTGTTTAGGGGTTTCAGTGCT 58.417 47.619 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1443 2.743752 CCAACGTGCTCTCGCCATG 61.744 63.158 0.0 0.0 34.43 3.66 R
2700 2730 2.623889 GCTTAGAGAATCCGTCCTGCTA 59.376 50.000 0.0 0.0 33.66 3.49 R
3288 3328 6.240549 AGAGATTGGTAGGAATCGAAACAT 57.759 37.500 0.0 0.0 37.41 2.71 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
79 80 7.522542 ACAAGGTGAGCTCTATCTCTAATCTA 58.477 38.462 16.19 0.00 34.29 1.98
207 209 9.360093 CTTGGTTATTTACTACTCTCACTTCAG 57.640 37.037 0.00 0.00 0.00 3.02
224 226 5.048224 CACTTCAGGATGCTTGTTCATTCTT 60.048 40.000 0.00 0.00 29.99 2.52
272 274 3.346426 AGGCAATGGGACTGTTGAC 57.654 52.632 0.00 0.00 28.97 3.18
300 302 3.137360 ACCAGAGCTTCTTCAGAAAACCT 59.863 43.478 0.00 0.00 33.07 3.50
304 306 6.169094 CAGAGCTTCTTCAGAAAACCTATGA 58.831 40.000 0.00 0.00 33.07 2.15
343 345 6.183360 CGCAATTTTGTTCAAGGTAAAACCAA 60.183 34.615 0.00 0.00 41.95 3.67
408 410 0.466124 AGAATTCGCCCCTGCTACTC 59.534 55.000 0.00 0.00 34.43 2.59
422 424 7.495901 CCCCTGCTACTCAATCATGTATATAG 58.504 42.308 0.00 0.00 0.00 1.31
544 546 5.527951 TGAATTTTGTTCCGTTCCTTGATG 58.472 37.500 0.00 0.00 0.00 3.07
701 703 5.091552 TGGAGTTCTATTGGTCCTAACTGT 58.908 41.667 0.00 0.00 30.83 3.55
933 945 2.046314 CCTCGACCAATGCGGGTT 60.046 61.111 0.00 0.00 42.53 4.11
983 995 1.758122 TGCAGCGAGCTGGATAGGA 60.758 57.895 24.25 0.00 45.94 2.94
1074 1086 3.129502 CACCATGCTGCTGGTCCG 61.130 66.667 17.21 7.26 46.79 4.79
1179 1191 5.435686 AACTATGAACTGAATGGCCACTA 57.564 39.130 8.16 0.00 0.00 2.74
1376 1388 7.701539 TCATGGAAATAGCTTTTCTTTGCTA 57.298 32.000 15.98 0.00 44.47 3.49
1430 1443 6.404074 CCATTTCCTGTGATTAGCTTCAGAAC 60.404 42.308 0.00 0.00 0.00 3.01
1486 1499 9.806203 TGTTAATTTGATTCATATGCTTTGGAG 57.194 29.630 0.00 0.00 0.00 3.86
1492 1506 8.991243 TTGATTCATATGCTTTGGAGAAAAAG 57.009 30.769 0.00 0.00 39.66 2.27
1580 1596 3.523606 TTGTTTGTGCAGCAATCTTGT 57.476 38.095 0.00 0.00 36.89 3.16
1592 1608 4.106029 GCAATCTTGTTGCTGACATCAT 57.894 40.909 5.57 0.00 41.87 2.45
1703 1719 7.615757 TCATACTGAGATAACACTCTTCCAAGA 59.384 37.037 0.00 0.00 37.73 3.02
1704 1720 6.672266 ACTGAGATAACACTCTTCCAAGAA 57.328 37.500 0.00 0.00 37.73 2.52
2320 2350 2.936919 ATGTCAGTTGTTGCTGAGGA 57.063 45.000 0.00 0.00 45.03 3.71
2340 2370 6.950041 TGAGGATCCAGTTTCTCATTTTTCAT 59.050 34.615 15.82 0.00 32.10 2.57
2374 2404 9.154632 AGTACCAGTGATGTGTATAATATGGAA 57.845 33.333 0.00 0.00 0.00 3.53
2405 2435 2.583143 GTGTTTAGGGGTTTCAGTGCT 58.417 47.619 0.00 0.00 0.00 4.40
2406 2436 2.956333 GTGTTTAGGGGTTTCAGTGCTT 59.044 45.455 0.00 0.00 0.00 3.91
2555 2585 8.141268 GGCTGCTAAATTATTATGCTTTTGGTA 58.859 33.333 0.00 0.00 0.00 3.25
2700 2730 5.536538 GGAAGAGAACATTGGAGAAAAAGGT 59.463 40.000 0.00 0.00 0.00 3.50
2865 2895 5.772672 TGCACCATCCTATTACAGTTTGTTT 59.227 36.000 0.00 0.00 0.00 2.83
2939 2969 4.568152 ACTCCTTTGTGCATTGTTACAC 57.432 40.909 0.00 0.00 37.31 2.90
3160 3190 2.730550 TTAAACCGAGACCCGACTTC 57.269 50.000 0.00 0.00 41.76 3.01
3227 3257 2.612672 CAGCAATGCTATGACCTGACAG 59.387 50.000 7.70 0.00 36.40 3.51
3288 3328 3.694043 TGTGATTTGGTCAATCCTCGA 57.306 42.857 0.00 0.00 40.80 4.04
3830 3870 7.744087 ATTGTAGACAACTTTGTTGCTGATA 57.256 32.000 9.96 0.00 42.43 2.15
3853 3893 9.887629 GATATGAATATCTCTGGATGTGATGTT 57.112 33.333 3.50 0.00 36.94 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.975788 TCTTCTCTTCTTCGTTCGATCTG 58.024 43.478 0.00 0.00 0.00 2.90
207 209 5.649831 AGGTAAGAAGAATGAACAAGCATCC 59.350 40.000 0.00 0.00 0.00 3.51
224 226 3.055094 GTGAGGGAGAAATGCAGGTAAGA 60.055 47.826 0.00 0.00 0.00 2.10
272 274 0.175989 GAAGAAGCTCTGGTACCCGG 59.824 60.000 10.07 0.00 0.00 5.73
280 282 6.169094 TCATAGGTTTTCTGAAGAAGCTCTG 58.831 40.000 15.24 15.29 35.45 3.35
300 302 9.585099 AAAATTGCGATTTAGAAAAGCATCATA 57.415 25.926 12.38 0.00 36.20 2.15
304 306 7.656707 ACAAAATTGCGATTTAGAAAAGCAT 57.343 28.000 12.38 0.00 36.20 3.79
343 345 1.272313 TGTAGTAGTCTCCGGCTTGGT 60.272 52.381 0.00 0.00 39.52 3.67
408 410 8.743085 ATTTAGCAGCCCTATATACATGATTG 57.257 34.615 0.00 0.00 0.00 2.67
422 424 6.424812 CCAAAAGCATAATAATTTAGCAGCCC 59.575 38.462 0.00 0.00 0.00 5.19
435 437 9.783081 AAATTCAGAAAAGACCAAAAGCATAAT 57.217 25.926 0.00 0.00 0.00 1.28
526 528 5.765677 TGTATTCATCAAGGAACGGAACAAA 59.234 36.000 0.00 0.00 0.00 2.83
544 546 4.051922 CAACCCTGTAGAGCGATGTATTC 58.948 47.826 0.00 0.00 0.00 1.75
983 995 1.081833 ATGGTCACCTCTCCTGCCT 59.918 57.895 0.00 0.00 0.00 4.75
1074 1086 0.040499 TGCCAATACCTTGTTCCCCC 59.960 55.000 0.00 0.00 0.00 5.40
1376 1388 6.808212 CGTAGAGCAAAAATCCAAATCACATT 59.192 34.615 0.00 0.00 0.00 2.71
1430 1443 2.743752 CCAACGTGCTCTCGCCATG 61.744 63.158 0.00 0.00 34.43 3.66
1492 1506 8.173775 GCATACAACATGATCTATGAACATAGC 58.826 37.037 14.69 5.19 40.37 2.97
1580 1596 9.368674 CCAAATTGTAAAATATGATGTCAGCAA 57.631 29.630 0.00 0.00 0.00 3.91
1592 1608 5.155905 ACCCACACCCCAAATTGTAAAATA 58.844 37.500 0.00 0.00 0.00 1.40
1881 1897 6.954102 TGCTAGGAGAGTAATATGCTTATGGA 59.046 38.462 0.00 0.00 0.00 3.41
2084 2108 7.297936 TCCAGACAATCTAACAGTTAGACAA 57.702 36.000 22.86 4.11 44.43 3.18
2352 2382 9.342308 AGTTTTCCATATTATACACATCACTGG 57.658 33.333 0.00 0.00 0.00 4.00
2374 2404 3.053170 ACCCCTAAACACCAGTTCAGTTT 60.053 43.478 0.00 0.00 36.84 2.66
2405 2435 9.622004 CTAACTAATCGAGAAAGTAACAGTCAA 57.378 33.333 0.00 0.00 0.00 3.18
2406 2436 9.006839 TCTAACTAATCGAGAAAGTAACAGTCA 57.993 33.333 0.00 0.00 0.00 3.41
2629 2659 4.213564 TGTTCCACAAACTGGCAAAATT 57.786 36.364 0.00 0.00 40.39 1.82
2700 2730 2.623889 GCTTAGAGAATCCGTCCTGCTA 59.376 50.000 0.00 0.00 33.66 3.49
2797 2827 2.906354 CGCATAGTACCTTCCAAAGCT 58.094 47.619 0.00 0.00 0.00 3.74
2865 2895 7.121168 GGAAGAACTGGTCAATTATGTCATCAA 59.879 37.037 0.00 0.00 0.00 2.57
2913 2943 3.424703 ACAATGCACAAAGGAGTAGCAT 58.575 40.909 0.00 0.00 46.86 3.79
2939 2969 9.383519 ACACACCTTCACAATTATATAACTCTG 57.616 33.333 0.00 0.00 0.00 3.35
3160 3190 9.286170 AGAATGGATGAGAATAGAAATGATGTG 57.714 33.333 0.00 0.00 0.00 3.21
3288 3328 6.240549 AGAGATTGGTAGGAATCGAAACAT 57.759 37.500 0.00 0.00 37.41 2.71
3800 3840 6.346040 GCAACAAAGTTGTCTACAATTCATGC 60.346 38.462 11.09 3.03 41.31 4.06
3830 3870 6.872547 CGAACATCACATCCAGAGATATTCAT 59.127 38.462 0.00 0.00 32.41 2.57


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

AutoCloner maintained by Alex Coulton.