Multiple sequence alignment - TraesCS2D01G509900

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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 TraesCS2D01G509900 chr2D 100.000 2549 0 0 1 2549 602009828 602007280 0.000000e+00 4708
1 TraesCS2D01G509900 chr2B 97.057 2548 71 4 3 2549 732224834 732222290 0.000000e+00 4287
2 TraesCS2D01G509900 chr2B 93.902 82 5 0 2 83 756556576 756556495 9.580000e-25 124
3 TraesCS2D01G509900 chr4B 87.930 2295 220 30 286 2549 654126335 654124067 0.000000e+00 2651
4 TraesCS2D01G509900 chr4B 87.784 1498 136 24 108 1561 654131805 654130311 0.000000e+00 1709
5 TraesCS2D01G509900 chr4B 87.295 1039 117 7 276 1303 638988443 638987409 0.000000e+00 1173
6 TraesCS2D01G509900 chr4B 81.496 1243 183 33 1323 2543 638987314 638986097 0.000000e+00 977
7 TraesCS2D01G509900 chr4B 81.000 800 107 28 1786 2549 654129568 654128778 6.070000e-166 593
8 TraesCS2D01G509900 chr4B 77.739 849 147 27 330 1166 431795281 431796099 1.370000e-132 483
9 TraesCS2D01G509900 chr5A 87.873 2243 228 25 276 2491 691814132 691811907 0.000000e+00 2595
10 TraesCS2D01G509900 chr5A 86.220 1045 123 9 276 1303 678082305 678083345 0.000000e+00 1112
11 TraesCS2D01G509900 chr5A 82.804 1227 178 24 1323 2534 678083440 678084648 0.000000e+00 1066
12 TraesCS2D01G509900 chr5A 86.667 165 18 1 108 268 691814348 691814184 2.010000e-41 180
13 TraesCS2D01G509900 chr4D 86.794 1045 117 11 276 1303 497667586 497666546 0.000000e+00 1146
14 TraesCS2D01G509900 chr4D 82.062 1232 188 24 1323 2539 497666451 497665238 0.000000e+00 1020
15 TraesCS2D01G509900 chr4D 76.152 868 136 56 325 1164 631004 630180 8.550000e-105 390
16 TraesCS2D01G509900 chr4A 83.130 1150 158 26 108 1243 731002619 731003746 0.000000e+00 1016
17 TraesCS2D01G509900 chr5B 82.162 925 135 21 325 1234 6918243 6919152 0.000000e+00 767
18 TraesCS2D01G509900 chr7D 93.976 83 5 0 1 83 31116283 31116201 2.660000e-25 126
19 TraesCS2D01G509900 chr2A 93.976 83 5 0 1 83 685632178 685632260 2.660000e-25 126
20 TraesCS2D01G509900 chr3D 92.683 82 6 0 2 83 578060025 578060106 4.450000e-23 119
21 TraesCS2D01G509900 chr3D 90.361 83 8 0 1 83 381169842 381169760 2.680000e-20 110
22 TraesCS2D01G509900 chrUn 91.566 83 7 0 1 83 27337344 27337426 5.760000e-22 115
23 TraesCS2D01G509900 chr7A 91.566 83 7 0 1 83 103049868 103049786 5.760000e-22 115
24 TraesCS2D01G509900 chr3A 91.463 82 7 0 2 83 648496396 648496477 2.070000e-21 113


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 TraesCS2D01G509900 chr2D 602007280 602009828 2548 True 4708.0 4708 100.000000 1 2549 1 chr2D.!!$R1 2548
1 TraesCS2D01G509900 chr2B 732222290 732224834 2544 True 4287.0 4287 97.057000 3 2549 1 chr2B.!!$R1 2546
2 TraesCS2D01G509900 chr4B 654124067 654131805 7738 True 1651.0 2651 85.571333 108 2549 3 chr4B.!!$R2 2441
3 TraesCS2D01G509900 chr4B 638986097 638988443 2346 True 1075.0 1173 84.395500 276 2543 2 chr4B.!!$R1 2267
4 TraesCS2D01G509900 chr4B 431795281 431796099 818 False 483.0 483 77.739000 330 1166 1 chr4B.!!$F1 836
5 TraesCS2D01G509900 chr5A 691811907 691814348 2441 True 1387.5 2595 87.270000 108 2491 2 chr5A.!!$R1 2383
6 TraesCS2D01G509900 chr5A 678082305 678084648 2343 False 1089.0 1112 84.512000 276 2534 2 chr5A.!!$F1 2258
7 TraesCS2D01G509900 chr4D 497665238 497667586 2348 True 1083.0 1146 84.428000 276 2539 2 chr4D.!!$R2 2263
8 TraesCS2D01G509900 chr4D 630180 631004 824 True 390.0 390 76.152000 325 1164 1 chr4D.!!$R1 839
9 TraesCS2D01G509900 chr4A 731002619 731003746 1127 False 1016.0 1016 83.130000 108 1243 1 chr4A.!!$F1 1135
10 TraesCS2D01G509900 chr5B 6918243 6919152 909 False 767.0 767 82.162000 325 1234 1 chr5B.!!$F1 909

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
35 36 0.243636 ATGCCGCAAGTTTTAGCACC 59.756 50.0 0.0 0.0 36.06 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 7141 0.040204 CCCCAGGCCTGAACTTCAAT 59.96 55.0 34.91 0.0 0.0 2.57 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
21 22 2.031191 GTCACCGGTTTAATGTATGCCG 59.969 50.000 2.97 0.00 41.82 5.69
23 24 1.018148 CCGGTTTAATGTATGCCGCA 58.982 50.000 0.00 0.00 40.94 5.69
30 31 6.094061 GGTTTAATGTATGCCGCAAGTTTTA 58.906 36.000 0.00 0.00 0.00 1.52
35 36 0.243636 ATGCCGCAAGTTTTAGCACC 59.756 50.000 0.00 0.00 36.06 5.01
39 40 2.124122 CCGCAAGTTTTAGCACCAAAC 58.876 47.619 0.00 0.00 34.80 2.93
42 43 3.123050 GCAAGTTTTAGCACCAAACTGG 58.877 45.455 8.26 6.96 42.47 4.00
59 60 5.419760 AACTGGTTTTTCTCGCTAAGTTC 57.580 39.130 0.00 0.00 0.00 3.01
60 61 4.448210 ACTGGTTTTTCTCGCTAAGTTCA 58.552 39.130 0.00 0.00 0.00 3.18
61 62 4.511826 ACTGGTTTTTCTCGCTAAGTTCAG 59.488 41.667 0.00 0.00 0.00 3.02
62 63 4.699637 TGGTTTTTCTCGCTAAGTTCAGA 58.300 39.130 0.00 0.00 0.00 3.27
67 68 2.515854 TCTCGCTAAGTTCAGACACCT 58.484 47.619 0.00 0.00 0.00 4.00
69 70 1.961394 TCGCTAAGTTCAGACACCTGT 59.039 47.619 0.00 0.00 41.16 4.00
71 72 2.288213 CGCTAAGTTCAGACACCTGTGA 60.288 50.000 3.94 0.00 41.16 3.58
83 84 6.210584 TCAGACACCTGTGATGTAATTGACTA 59.789 38.462 3.94 0.00 41.16 2.59
84 85 6.873605 CAGACACCTGTGATGTAATTGACTAA 59.126 38.462 3.94 0.00 35.70 2.24
1170 6484 2.897207 CCCACGCCGATGAGGTTA 59.103 61.111 0.00 0.00 43.70 2.85
1228 6542 4.527157 GCGCGATGTGCAGCTTCC 62.527 66.667 12.10 0.00 46.97 3.46
1279 6593 1.186200 CTCTCTGGACCATCGGTTCA 58.814 55.000 0.00 0.00 39.18 3.18
1755 7156 2.613977 CGTGAGATTGAAGTTCAGGCCT 60.614 50.000 0.00 0.00 0.00 5.19
1960 7364 2.729360 CACAGCGTGTCGTTCTCAATTA 59.271 45.455 1.24 0.00 0.00 1.40
2164 7577 1.302511 GTGACGTGGAAGTGGCCAT 60.303 57.895 9.72 0.00 40.68 4.40
2354 7779 0.959372 AGGACGAGGAATGACGACGT 60.959 55.000 0.00 0.00 39.82 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.031191 CGGCATACATTAAACCGGTGAC 59.969 50.000 8.52 0.00 40.18 3.67
1 2 2.281517 CGGCATACATTAAACCGGTGA 58.718 47.619 8.52 0.00 40.18 4.02
4 5 1.018148 TGCGGCATACATTAAACCGG 58.982 50.000 0.00 0.00 43.99 5.28
6 7 3.775661 ACTTGCGGCATACATTAAACC 57.224 42.857 2.28 0.00 0.00 3.27
7 8 6.237463 GCTAAAACTTGCGGCATACATTAAAC 60.237 38.462 2.28 0.00 0.00 2.01
8 9 5.802956 GCTAAAACTTGCGGCATACATTAAA 59.197 36.000 2.28 0.00 0.00 1.52
10 11 4.396478 TGCTAAAACTTGCGGCATACATTA 59.604 37.500 2.28 1.40 0.00 1.90
11 12 3.192422 TGCTAAAACTTGCGGCATACATT 59.808 39.130 2.28 0.16 0.00 2.71
18 19 0.031449 TTGGTGCTAAAACTTGCGGC 59.969 50.000 0.00 0.00 0.00 6.53
21 22 3.123050 CCAGTTTGGTGCTAAAACTTGC 58.877 45.455 8.61 0.00 43.60 4.01
35 36 5.169836 ACTTAGCGAGAAAAACCAGTTTG 57.830 39.130 0.00 0.00 32.36 2.93
39 40 4.750098 TCTGAACTTAGCGAGAAAAACCAG 59.250 41.667 0.00 0.00 0.00 4.00
42 43 5.433005 GTGTCTGAACTTAGCGAGAAAAAC 58.567 41.667 0.00 0.00 0.00 2.43
49 50 1.961394 ACAGGTGTCTGAACTTAGCGA 59.039 47.619 0.00 0.00 43.49 4.93
52 53 4.887748 ACATCACAGGTGTCTGAACTTAG 58.112 43.478 10.25 0.00 43.49 2.18
53 54 4.955811 ACATCACAGGTGTCTGAACTTA 57.044 40.909 10.25 0.00 43.49 2.24
59 60 5.240891 AGTCAATTACATCACAGGTGTCTG 58.759 41.667 0.00 1.93 46.10 3.51
60 61 5.489792 AGTCAATTACATCACAGGTGTCT 57.510 39.130 0.00 0.00 0.00 3.41
61 62 7.667043 TTTAGTCAATTACATCACAGGTGTC 57.333 36.000 0.00 0.00 0.00 3.67
62 63 8.458573 TTTTTAGTCAATTACATCACAGGTGT 57.541 30.769 0.00 0.00 0.00 4.16
93 94 3.124578 TGTTGCACAATACTCTGCAGA 57.875 42.857 17.19 17.19 44.05 4.26
291 298 0.386858 ACGAACTCGACGACATGGTG 60.387 55.000 6.05 0.00 43.02 4.17
395 447 3.672295 GAGAAGTGCCTGGCGGAGG 62.672 68.421 14.98 0.00 46.13 4.30
1170 6484 1.300697 GGACAACTTCCACGAGCGT 60.301 57.895 0.00 0.00 45.10 5.07
1228 6542 0.177604 GGGATGGAGAGTGTGAGCAG 59.822 60.000 0.00 0.00 0.00 4.24
1279 6593 1.378250 GCTGGGCTGAGCAGTTCAT 60.378 57.895 6.82 0.00 38.95 2.57
1552 6947 4.046462 CAGTCGAACGAGGTCTTTTACAA 58.954 43.478 0.00 0.00 0.00 2.41
1620 7021 2.592194 GTCTTCAACGTCTACATCGCA 58.408 47.619 0.00 0.00 0.00 5.10
1740 7141 0.040204 CCCCAGGCCTGAACTTCAAT 59.960 55.000 34.91 0.00 0.00 2.57
2063 7467 1.105759 GGAGATGCTGTGGAATGGCC 61.106 60.000 0.00 0.00 37.10 5.36
2314 7739 1.604915 GCCTCCACTTCTTCCCCTC 59.395 63.158 0.00 0.00 0.00 4.30
2375 7800 2.806237 CCTTCTCGTACCGCCTCC 59.194 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.