Multiple sequence alignment - TraesCS5D01G514200

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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 TraesCS5D01G514200 chr5D 100.000 4838 0 0 974 5811 537969710 537964873 0.000000e+00 8935.0
1 TraesCS5D01G514200 chr5D 100.000 611 0 0 1 611 537970683 537970073 0.000000e+00 1129.0
2 TraesCS5D01G514200 chr5B 95.405 4287 110 22 1003 5268 678622534 678618314 0.000000e+00 6745.0
3 TraesCS5D01G514200 chr5B 97.980 297 4 1 5517 5811 678618309 678618013 1.120000e-141 514.0
4 TraesCS5D01G514200 chr5B 90.120 334 30 3 1 332 678624916 678624584 1.160000e-116 431.0
5 TraesCS5D01G514200 chr5B 85.294 102 14 1 5138 5238 602342924 602343025 2.860000e-18 104.0
6 TraesCS5D01G514200 chr5B 83.333 90 14 1 5171 5259 626439066 626438977 1.340000e-11 82.4
7 TraesCS5D01G514200 chr4A 97.497 2437 48 2 3341 5776 632151809 632149385 0.000000e+00 4150.0
8 TraesCS5D01G514200 chr4A 97.808 2327 36 4 974 3293 632155354 632153036 0.000000e+00 4000.0
9 TraesCS5D01G514200 chr4A 80.829 1278 143 46 4397 5614 631381382 631380147 0.000000e+00 909.0
10 TraesCS5D01G514200 chr4A 90.496 484 24 5 1 462 632156344 632155861 2.300000e-173 619.0
11 TraesCS5D01G514200 chr4A 97.333 75 2 0 3286 3360 632152044 632151970 1.700000e-25 128.0
12 TraesCS5D01G514200 chr4A 98.551 69 0 1 450 518 632155820 632155753 2.840000e-23 121.0
13 TraesCS5D01G514200 chr6D 83.105 219 28 4 4239 4456 63927231 63927021 2.140000e-44 191.0
14 TraesCS5D01G514200 chr6A 83.412 211 20 9 4251 4456 81192598 81192398 1.290000e-41 182.0
15 TraesCS5D01G514200 chr3D 84.483 174 24 2 4935 5105 6864157 6863984 1.000000e-37 169.0
16 TraesCS5D01G514200 chr7D 87.097 93 9 3 4120 4211 575488373 575488463 1.030000e-17 102.0
17 TraesCS5D01G514200 chr5A 89.189 74 6 2 5165 5238 628920176 628920105 2.230000e-14 91.6
18 TraesCS5D01G514200 chr1A 87.500 80 8 2 5159 5238 428477938 428478015 2.230000e-14 91.6
19 TraesCS5D01G514200 chr2A 87.671 73 3 4 5145 5217 139889431 139889497 4.830000e-11 80.5
20 TraesCS5D01G514200 chr3A 88.889 63 5 2 5162 5223 535796704 535796643 6.240000e-10 76.8


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 TraesCS5D01G514200 chr5D 537964873 537970683 5810 True 5032.000000 8935 100.000000 1 5811 2 chr5D.!!$R1 5810
1 TraesCS5D01G514200 chr5B 678618013 678624916 6903 True 2563.333333 6745 94.501667 1 5811 3 chr5B.!!$R2 5810
2 TraesCS5D01G514200 chr4A 632149385 632156344 6959 True 1803.600000 4150 96.337000 1 5776 5 chr4A.!!$R2 5775
3 TraesCS5D01G514200 chr4A 631380147 631381382 1235 True 909.000000 909 80.829000 4397 5614 1 chr4A.!!$R1 1217

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
566 1940 0.106519 ATTCCCCATCGGCCTTCTTG 60.107 55.000 0.00 0.00 0.00 3.02 F
584 2223 0.547712 TGCTGAGGAAACCCTAGCCT 60.548 55.000 0.00 0.00 33.42 4.58 F
587 2226 0.976073 TGAGGAAACCCTAGCCTCCG 60.976 60.000 9.95 0.00 46.01 4.63 F
1014 2653 1.153107 TTCCATGGATCTGCCGCAG 60.153 57.895 17.06 14.62 40.66 5.18 F
1703 3357 2.045926 CAACCCCGGCCTCTTCAG 60.046 66.667 0.00 0.00 0.00 3.02 F
3211 4873 1.456705 ACCAAACCACCGGTTGCAT 60.457 52.632 2.97 0.00 46.20 3.96 F
3692 6535 1.899437 TAAGCAAGTGGGGGCGAGAG 61.899 60.000 0.00 0.00 34.54 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 3094 2.721231 CCATAATTGGGGCGCACG 59.279 61.111 10.83 0.0 39.56 5.34 R
2240 3894 2.767972 TGATGATGTCAGGAGGGATGT 58.232 47.619 0.00 0.0 31.80 3.06 R
2685 4339 7.558161 TGCATATAGAAGTTGAATGGACTTG 57.442 36.000 0.00 0.0 37.46 3.16 R
2990 4652 2.108250 AGGTGGCCAAGTACTGAATGTT 59.892 45.455 7.24 0.0 0.00 2.71 R
3692 6535 0.678048 CTCCTTGTAAGCCCAGTGCC 60.678 60.000 0.00 0.0 42.71 5.01 R
4309 7152 3.006430 TGTCTCAAGCACCACTATTCGAA 59.994 43.478 0.00 0.0 0.00 3.71 R
4944 7809 4.737765 GTCGCTCATCTCTGAAGTATCAAC 59.262 45.833 0.00 0.0 34.49 3.18 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
98 101 1.649271 GGATGTGCCAAGGGGAGGAT 61.649 60.000 0.00 0.00 35.59 3.24
151 154 2.110352 GCGTCCATACAAACCCGGG 61.110 63.158 22.25 22.25 0.00 5.73
201 206 1.849097 AACTGACACTCGTCCGTTTC 58.151 50.000 0.00 0.00 44.30 2.78
226 231 2.732016 GGGTTGGGCCGTGTTTTC 59.268 61.111 0.00 0.00 38.44 2.29
554 1928 6.240263 CCCATACATCTCATCTTTATTCCCCA 60.240 42.308 0.00 0.00 0.00 4.96
555 1929 7.408543 CCATACATCTCATCTTTATTCCCCAT 58.591 38.462 0.00 0.00 0.00 4.00
556 1930 7.555554 CCATACATCTCATCTTTATTCCCCATC 59.444 40.741 0.00 0.00 0.00 3.51
557 1931 5.555017 ACATCTCATCTTTATTCCCCATCG 58.445 41.667 0.00 0.00 0.00 3.84
558 1932 4.623932 TCTCATCTTTATTCCCCATCGG 57.376 45.455 0.00 0.00 0.00 4.18
559 1933 3.077359 CTCATCTTTATTCCCCATCGGC 58.923 50.000 0.00 0.00 0.00 5.54
560 1934 2.162681 CATCTTTATTCCCCATCGGCC 58.837 52.381 0.00 0.00 0.00 6.13
561 1935 1.518367 TCTTTATTCCCCATCGGCCT 58.482 50.000 0.00 0.00 0.00 5.19
562 1936 1.850345 TCTTTATTCCCCATCGGCCTT 59.150 47.619 0.00 0.00 0.00 4.35
563 1937 2.158667 TCTTTATTCCCCATCGGCCTTC 60.159 50.000 0.00 0.00 0.00 3.46
564 1938 1.518367 TTATTCCCCATCGGCCTTCT 58.482 50.000 0.00 0.00 0.00 2.85
565 1939 1.518367 TATTCCCCATCGGCCTTCTT 58.482 50.000 0.00 0.00 0.00 2.52
566 1940 0.106519 ATTCCCCATCGGCCTTCTTG 60.107 55.000 0.00 0.00 0.00 3.02
567 1941 2.830370 CCCCATCGGCCTTCTTGC 60.830 66.667 0.00 0.00 0.00 4.01
568 1942 2.273449 CCCATCGGCCTTCTTGCT 59.727 61.111 0.00 0.00 0.00 3.91
569 1943 2.117156 CCCATCGGCCTTCTTGCTG 61.117 63.158 0.00 0.00 39.04 4.41
572 1946 2.665000 TCGGCCTTCTTGCTGAGG 59.335 61.111 0.00 0.00 41.60 3.86
573 1947 1.913262 TCGGCCTTCTTGCTGAGGA 60.913 57.895 0.00 0.00 41.60 3.71
574 1948 1.003355 CGGCCTTCTTGCTGAGGAA 60.003 57.895 0.00 0.00 40.15 3.36
575 1949 0.606401 CGGCCTTCTTGCTGAGGAAA 60.606 55.000 0.00 0.00 40.15 3.13
579 2218 1.074566 CCTTCTTGCTGAGGAAACCCT 59.925 52.381 0.00 0.00 36.57 4.34
581 2220 3.604582 CTTCTTGCTGAGGAAACCCTAG 58.395 50.000 0.00 0.00 33.25 3.02
584 2223 0.547712 TGCTGAGGAAACCCTAGCCT 60.548 55.000 0.00 0.00 33.42 4.58
587 2226 0.976073 TGAGGAAACCCTAGCCTCCG 60.976 60.000 9.95 0.00 46.01 4.63
588 2227 2.189784 GGAAACCCTAGCCTCCGC 59.810 66.667 0.00 0.00 0.00 5.54
590 2229 3.735037 GAAACCCTAGCCTCCGCCG 62.735 68.421 0.00 0.00 34.57 6.46
1014 2653 1.153107 TTCCATGGATCTGCCGCAG 60.153 57.895 17.06 14.62 40.66 5.18
1201 2840 2.555199 GCTATGCCACTGAGGTAGTTG 58.445 52.381 0.00 0.00 37.60 3.16
1455 3094 2.094494 TCTCACTGTTCGCCTTCTCATC 60.094 50.000 0.00 0.00 0.00 2.92
1703 3357 2.045926 CAACCCCGGCCTCTTCAG 60.046 66.667 0.00 0.00 0.00 3.02
2094 3748 4.142038 TCAGCCCAAATGATCATGAGATG 58.858 43.478 9.46 7.59 33.72 2.90
2240 3894 6.411376 TCGCTGACTATTTTGGAAATCCTAA 58.589 36.000 0.44 0.00 36.82 2.69
2578 4232 8.418662 ACATCCATTTTGTCCATGAATATTCAG 58.581 33.333 21.97 13.96 41.08 3.02
2837 4491 2.693591 TCCTCTTAGTTCATCGCGGAAT 59.306 45.455 6.13 0.00 0.00 3.01
3061 4723 3.906720 TCAGTCACCTGCTTTATACCC 57.093 47.619 0.00 0.00 38.66 3.69
3211 4873 1.456705 ACCAAACCACCGGTTGCAT 60.457 52.632 2.97 0.00 46.20 3.96
3247 4909 6.977213 TGGTTTCTCCATGTTTAAGTAAAGC 58.023 36.000 0.00 0.00 41.93 3.51
3248 4910 6.547880 TGGTTTCTCCATGTTTAAGTAAAGCA 59.452 34.615 0.00 0.00 41.93 3.91
3249 4911 7.084486 GGTTTCTCCATGTTTAAGTAAAGCAG 58.916 38.462 0.00 0.00 35.97 4.24
3265 4927 9.736023 AAGTAAAGCAGAACAAAGTAGAATTTG 57.264 29.630 1.14 1.14 44.14 2.32
3325 5986 9.229784 CTCAATTTTTATGCTGCATACAGTTAG 57.770 33.333 21.19 10.88 46.30 2.34
3393 6234 7.538334 TGCGTGAAATGATTTCTTTCATACAAG 59.462 33.333 17.76 1.05 42.68 3.16
3692 6535 1.899437 TAAGCAAGTGGGGGCGAGAG 61.899 60.000 0.00 0.00 34.54 3.20
4152 6995 7.557358 TCCTGTGATTGTTTTATATGTGCTGAT 59.443 33.333 0.00 0.00 0.00 2.90
4237 7080 6.540914 GGATCGGTATTAAACATCTTGTTCCA 59.459 38.462 0.00 0.00 40.14 3.53
4302 7145 6.614160 TGTTCAGTAAACTGCATTGATCATG 58.386 36.000 5.21 0.00 43.46 3.07
4438 7283 8.870116 ACCTTTCCTCTTTTGCTGTTTATTTAT 58.130 29.630 0.00 0.00 0.00 1.40
4593 7442 9.081997 GTCATGTCATGTTTTACTTTGTTGAAA 57.918 29.630 12.54 0.00 0.00 2.69
5705 8608 8.635765 TTGTCATTTTCTTTAGCAAGGATAGT 57.364 30.769 0.00 0.00 0.00 2.12
5776 8679 6.073981 TGTCCATCTCAAGAGTATATGCTCT 58.926 40.000 16.75 16.75 46.82 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 32 2.561956 CCACACTCGACACCTCCGT 61.562 63.158 0.00 0.00 0.00 4.69
115 118 1.934463 CAAACTCAGCACGAACGCT 59.066 52.632 0.00 0.00 45.21 5.07
151 154 1.595093 CGACCCAATTCTGGCCCAAC 61.595 60.000 0.00 0.00 41.99 3.77
210 215 2.333581 CGAAAACACGGCCCAACC 59.666 61.111 0.00 0.00 0.00 3.77
244 249 4.690719 ATTTGGTCCGCCGCGTCA 62.691 61.111 12.58 4.38 37.67 4.35
467 1764 0.112412 ACGGGAACTCATGGCCTTTT 59.888 50.000 3.32 0.00 0.00 2.27
522 1870 2.588877 AGATGTATGGGCGCGTGC 60.589 61.111 13.78 13.78 41.71 5.34
525 1873 0.037882 AGATGAGATGTATGGGCGCG 60.038 55.000 0.00 0.00 0.00 6.86
526 1874 2.175878 AAGATGAGATGTATGGGCGC 57.824 50.000 0.00 0.00 0.00 6.53
533 1907 6.295859 CCGATGGGGAATAAAGATGAGATGTA 60.296 42.308 0.00 0.00 38.47 2.29
554 1928 1.222936 CCTCAGCAAGAAGGCCGAT 59.777 57.895 0.00 0.00 0.00 4.18
555 1929 1.480212 TTCCTCAGCAAGAAGGCCGA 61.480 55.000 0.00 0.00 0.00 5.54
556 1930 0.606401 TTTCCTCAGCAAGAAGGCCG 60.606 55.000 0.00 0.00 0.00 6.13
557 1931 0.884514 GTTTCCTCAGCAAGAAGGCC 59.115 55.000 0.00 0.00 0.00 5.19
558 1932 0.884514 GGTTTCCTCAGCAAGAAGGC 59.115 55.000 0.00 0.00 0.00 4.35
559 1933 1.074566 AGGGTTTCCTCAGCAAGAAGG 59.925 52.381 0.00 0.00 39.80 3.46
560 1934 2.575805 AGGGTTTCCTCAGCAAGAAG 57.424 50.000 0.00 0.00 39.80 2.85
561 1935 2.290323 GCTAGGGTTTCCTCAGCAAGAA 60.290 50.000 0.00 0.00 43.66 2.52
562 1936 1.279271 GCTAGGGTTTCCTCAGCAAGA 59.721 52.381 0.00 0.00 43.66 3.02
563 1937 1.680249 GGCTAGGGTTTCCTCAGCAAG 60.680 57.143 11.75 0.00 43.66 4.01
564 1938 0.328258 GGCTAGGGTTTCCTCAGCAA 59.672 55.000 11.75 0.00 43.66 3.91
565 1939 0.547712 AGGCTAGGGTTTCCTCAGCA 60.548 55.000 11.75 0.00 43.66 4.41
566 1940 0.179234 GAGGCTAGGGTTTCCTCAGC 59.821 60.000 8.11 0.00 44.38 4.26
567 1941 0.833949 GGAGGCTAGGGTTTCCTCAG 59.166 60.000 13.41 0.00 46.24 3.35
568 1942 0.976073 CGGAGGCTAGGGTTTCCTCA 60.976 60.000 13.41 0.00 46.24 3.86
569 1943 1.823976 CGGAGGCTAGGGTTTCCTC 59.176 63.158 5.10 5.10 43.66 3.71
570 1944 2.368011 GCGGAGGCTAGGGTTTCCT 61.368 63.158 0.00 0.00 46.96 3.36
571 1945 2.189784 GCGGAGGCTAGGGTTTCC 59.810 66.667 0.00 0.00 35.83 3.13
1014 2653 4.326255 CCACCCAACATGGCTCTC 57.674 61.111 0.00 0.00 35.79 3.20
1455 3094 2.721231 CCATAATTGGGGCGCACG 59.279 61.111 10.83 0.00 39.56 5.34
1703 3357 4.216411 TCTTTATTGTGGAGCCCTGTAC 57.784 45.455 0.00 0.00 0.00 2.90
2094 3748 5.179182 CCATTCACCAAGTGCAAAATAAACC 59.821 40.000 0.00 0.00 32.98 3.27
2240 3894 2.767972 TGATGATGTCAGGAGGGATGT 58.232 47.619 0.00 0.00 31.80 3.06
2685 4339 7.558161 TGCATATAGAAGTTGAATGGACTTG 57.442 36.000 0.00 0.00 37.46 3.16
2990 4652 2.108250 AGGTGGCCAAGTACTGAATGTT 59.892 45.455 7.24 0.00 0.00 2.71
3170 4832 6.142320 GGTGTTTCGCTAAATGTTTTTCTGAG 59.858 38.462 0.00 0.00 0.00 3.35
3245 4907 7.121315 GGGATACAAATTCTACTTTGTTCTGCT 59.879 37.037 7.42 0.00 44.76 4.24
3246 4908 7.094377 TGGGATACAAATTCTACTTTGTTCTGC 60.094 37.037 7.42 2.49 44.76 4.26
3247 4909 8.335532 TGGGATACAAATTCTACTTTGTTCTG 57.664 34.615 7.42 0.00 44.76 3.02
3248 4910 8.793592 GTTGGGATACAAATTCTACTTTGTTCT 58.206 33.333 7.42 0.00 44.76 3.01
3249 4911 8.573035 TGTTGGGATACAAATTCTACTTTGTTC 58.427 33.333 7.42 5.75 44.76 3.18
3264 4926 8.703378 TCATATATGCAAAATGTTGGGATACA 57.297 30.769 7.92 0.00 35.10 2.29
3265 4927 9.979578 TTTCATATATGCAAAATGTTGGGATAC 57.020 29.630 7.92 0.00 35.10 2.24
3393 6234 4.234530 AGCTGCACTGAATTCTGAAAAC 57.765 40.909 18.13 5.76 0.00 2.43
3476 6317 9.432982 TGGAAATAATAGTTCCTAATTGCCATT 57.567 29.630 18.62 0.00 44.24 3.16
3477 6318 9.082313 CTGGAAATAATAGTTCCTAATTGCCAT 57.918 33.333 18.62 0.00 44.24 4.40
3489 6332 9.289782 GTAATGGATCAGCTGGAAATAATAGTT 57.710 33.333 15.13 0.00 0.00 2.24
3537 6380 6.595716 AGGAAGGTGATTTTAGTTCTTGATCG 59.404 38.462 0.00 0.00 0.00 3.69
3692 6535 0.678048 CTCCTTGTAAGCCCAGTGCC 60.678 60.000 0.00 0.00 42.71 5.01
4100 6943 7.771183 ACTAAAAATGCTTCAAAGTTCAGACA 58.229 30.769 0.00 0.00 0.00 3.41
4152 6995 4.206375 TGAAGAATCACAAACAGAGCCAA 58.794 39.130 0.00 0.00 0.00 4.52
4302 7145 3.877508 AGCACCACTATTCGAAATTAGGC 59.122 43.478 0.00 0.68 0.00 3.93
4309 7152 3.006430 TGTCTCAAGCACCACTATTCGAA 59.994 43.478 0.00 0.00 0.00 3.71
4438 7283 4.501229 GGCACATGAAAACATGAAAGGTGA 60.501 41.667 15.53 0.00 36.48 4.02
4593 7442 6.848562 AAGAATATACCCAACCCTCAGAAT 57.151 37.500 0.00 0.00 0.00 2.40
4726 7576 4.927978 AGGACAGTGATGATAGCTGTAC 57.072 45.455 0.00 3.68 42.71 2.90
4944 7809 4.737765 GTCGCTCATCTCTGAAGTATCAAC 59.262 45.833 0.00 0.00 34.49 3.18
5776 8679 5.824624 ACTGCAGTTCAGATTCAAGAAAAGA 59.175 36.000 15.25 0.00 45.72 2.52


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

AutoCloner maintained by Alex Coulton.