Multiple sequence alignment - TraesCS2A01G356100

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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 TraesCS2A01G356100 chr2A 100.000 1528 0 0 767 2294 600113463 600111936 0.000000e+00 2822
1 TraesCS2A01G356100 chr2A 96.953 1477 38 3 819 2294 23796207 23797677 0.000000e+00 2471
2 TraesCS2A01G356100 chr2A 96.722 1434 41 2 861 2294 571019198 571020625 0.000000e+00 2383
3 TraesCS2A01G356100 chr2A 100.000 368 0 0 1 368 600114229 600113862 0.000000e+00 680
4 TraesCS2A01G356100 chr2A 91.821 379 15 7 3 368 571018523 571018898 4.370000e-142 514
5 TraesCS2A01G356100 chr2A 90.052 382 22 6 1 368 23795516 23795895 4.430000e-132 481
6 TraesCS2A01G356100 chr2A 87.667 300 19 11 67 366 725037725 725037444 1.310000e-87 333
7 TraesCS2A01G356100 chr7A 96.962 1514 40 3 782 2294 650324574 650323066 0.000000e+00 2536
8 TraesCS2A01G356100 chr7A 97.002 1501 39 2 795 2294 707844389 707845884 0.000000e+00 2518
9 TraesCS2A01G356100 chr7A 96.697 1514 42 5 782 2294 650260758 650259252 0.000000e+00 2512
10 TraesCS2A01G356100 chr7A 91.864 381 15 5 1 368 707843606 707843983 3.380000e-143 518
11 TraesCS2A01G356100 chr7A 90.645 310 16 11 67 366 622694565 622694259 1.280000e-107 399
12 TraesCS2A01G356100 chr1A 96.896 1514 41 2 782 2294 380400798 380402306 0.000000e+00 2531
13 TraesCS2A01G356100 chr1A 95.578 1515 58 5 782 2294 531840065 531838558 0.000000e+00 2418
14 TraesCS2A01G356100 chr1A 92.147 382 14 5 1 368 11026935 11026556 2.020000e-145 525
15 TraesCS2A01G356100 chr1A 87.500 336 32 9 1 334 504201424 504201751 1.660000e-101 379
16 TraesCS2A01G356100 chr5A 95.376 1514 47 6 782 2294 507565720 507564229 0.000000e+00 2386
17 TraesCS2A01G356100 chr5A 91.623 382 14 6 1 368 603018585 603018962 1.570000e-141 512
18 TraesCS2A01G356100 chr5A 94.521 146 5 2 767 912 603019017 603019159 2.970000e-54 222
19 TraesCS2A01G356100 chr1B 95.439 1491 59 5 806 2294 658504122 658502639 0.000000e+00 2368
20 TraesCS2A01G356100 chr4A 94.411 1485 75 4 810 2293 382145490 382146967 0.000000e+00 2276
21 TraesCS2A01G356100 chrUn 91.243 354 17 4 1 341 248381224 248380872 9.590000e-129 470
22 TraesCS2A01G356100 chrUn 91.083 314 13 5 67 366 24704758 24705070 5.900000e-111 411


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 TraesCS2A01G356100 chr2A 600111936 600114229 2293 True 1751.0 2822 100.0000 1 2294 2 chr2A.!!$R2 2293
1 TraesCS2A01G356100 chr2A 23795516 23797677 2161 False 1476.0 2471 93.5025 1 2294 2 chr2A.!!$F1 2293
2 TraesCS2A01G356100 chr2A 571018523 571020625 2102 False 1448.5 2383 94.2715 3 2294 2 chr2A.!!$F2 2291
3 TraesCS2A01G356100 chr7A 650323066 650324574 1508 True 2536.0 2536 96.9620 782 2294 1 chr7A.!!$R3 1512
4 TraesCS2A01G356100 chr7A 650259252 650260758 1506 True 2512.0 2512 96.6970 782 2294 1 chr7A.!!$R2 1512
5 TraesCS2A01G356100 chr7A 707843606 707845884 2278 False 1518.0 2518 94.4330 1 2294 2 chr7A.!!$F1 2293
6 TraesCS2A01G356100 chr1A 380400798 380402306 1508 False 2531.0 2531 96.8960 782 2294 1 chr1A.!!$F1 1512
7 TraesCS2A01G356100 chr1A 531838558 531840065 1507 True 2418.0 2418 95.5780 782 2294 1 chr1A.!!$R2 1512
8 TraesCS2A01G356100 chr5A 507564229 507565720 1491 True 2386.0 2386 95.3760 782 2294 1 chr5A.!!$R1 1512
9 TraesCS2A01G356100 chr5A 603018585 603019159 574 False 367.0 512 93.0720 1 912 2 chr5A.!!$F1 911
10 TraesCS2A01G356100 chr1B 658502639 658504122 1483 True 2368.0 2368 95.4390 806 2294 1 chr1B.!!$R1 1488
11 TraesCS2A01G356100 chr4A 382145490 382146967 1477 False 2276.0 2276 94.4110 810 2293 1 chr4A.!!$F1 1483

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
830 1050 0.53065 CCCCGATTCAGACCACATCG 60.531 60.0 0.0 0.0 39.63 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 1992 6.594788 ACACAGGTGCATTAAAGAATGAAT 57.405 33.333 0.0 0.0 44.59 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
140 142 2.432300 CGGATCACCCCCGTAAGCT 61.432 63.158 0.00 0.00 41.91 3.74
208 210 2.558066 TGGCCAACCAAACCCTAGA 58.442 52.632 0.61 0.00 45.37 2.43
209 211 1.080638 TGGCCAACCAAACCCTAGAT 58.919 50.000 0.61 0.00 45.37 1.98
210 212 1.005450 TGGCCAACCAAACCCTAGATC 59.995 52.381 0.61 0.00 45.37 2.75
211 213 1.285078 GGCCAACCAAACCCTAGATCT 59.715 52.381 0.00 0.00 35.26 2.75
265 280 4.400251 CCACCCTCTCCCCGACCT 62.400 72.222 0.00 0.00 0.00 3.85
284 299 0.701659 TAGATCTCCCTCCCCGACCT 60.702 60.000 0.00 0.00 0.00 3.85
287 302 1.731324 ATCTCCCTCCCCGACCTAGG 61.731 65.000 7.41 7.41 0.00 3.02
361 376 1.303799 CGCTGCTCTTGACCTGCAAT 61.304 55.000 0.00 0.00 35.59 3.56
830 1050 0.530650 CCCCGATTCAGACCACATCG 60.531 60.000 0.00 0.00 39.63 3.84
871 1091 3.124088 CCTCCTCCTCCCCTCCTT 58.876 66.667 0.00 0.00 0.00 3.36
1073 1294 1.608717 ATCCGCCTCGTCAAGAGCTT 61.609 55.000 0.00 0.00 45.54 3.74
1136 1357 1.022735 GCTCGTCTAGATCCGGTTCA 58.977 55.000 14.83 0.63 0.00 3.18
1230 1451 0.604511 GGTTCGTCGTCATGGGGTTT 60.605 55.000 0.00 0.00 0.00 3.27
1334 1555 2.314071 TCCCGTCTCCCTCTTGTTTA 57.686 50.000 0.00 0.00 0.00 2.01
1770 1992 5.427036 TCGTGCTATGTGTCGATGTATTA 57.573 39.130 0.00 0.00 0.00 0.98
1911 2134 6.785488 ATATTGTAGGACACATGTTATGCG 57.215 37.500 0.00 0.00 36.90 4.73
2109 2334 1.419381 TGCTGGTGGTGTCTTCTACA 58.581 50.000 0.00 0.00 35.06 2.74
2110 2335 1.765904 TGCTGGTGGTGTCTTCTACAA 59.234 47.619 0.00 0.00 40.63 2.41
2111 2336 2.371841 TGCTGGTGGTGTCTTCTACAAT 59.628 45.455 0.00 0.00 40.63 2.71
2112 2337 3.580895 TGCTGGTGGTGTCTTCTACAATA 59.419 43.478 0.00 0.00 40.63 1.90
2113 2338 4.225042 TGCTGGTGGTGTCTTCTACAATAT 59.775 41.667 0.00 0.00 40.63 1.28
2252 2477 8.684386 TGTCAATAGTCTTTTGGTTCATACAA 57.316 30.769 3.57 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 7.442062 GGTCCAAGAAATGTGTCATTTTGAAAT 59.558 33.333 8.72 0.00 0.00 2.17
134 135 1.537135 GGACGGCTCAGATCAGCTTAC 60.537 57.143 5.15 0.00 39.58 2.34
140 142 1.591703 GTGTGGACGGCTCAGATCA 59.408 57.895 0.00 0.00 0.00 2.92
208 210 0.330431 AGAGGGAGAGGGAGGGAGAT 60.330 60.000 0.00 0.00 0.00 2.75
209 211 0.996762 GAGAGGGAGAGGGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
210 212 1.541672 GAGAGGGAGAGGGAGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
211 213 2.015726 GGAGAGGGAGAGGGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
250 265 1.000041 ATCTAGGTCGGGGAGAGGGT 61.000 60.000 0.00 0.00 0.00 4.34
265 280 0.701659 AGGTCGGGGAGGGAGATCTA 60.702 60.000 0.00 0.00 0.00 1.98
284 299 4.541648 GGCGGAGAGGGAGGCCTA 62.542 72.222 4.42 0.00 42.29 3.93
830 1050 2.109181 GGCGAGCTATGGTGGGAC 59.891 66.667 0.00 0.00 0.00 4.46
871 1091 3.519107 TGGATTTGTGCTCTGGATCTACA 59.481 43.478 0.00 0.00 0.00 2.74
1034 1255 1.006102 CTGTCCTTGGCGAACTCGT 60.006 57.895 0.51 0.00 42.22 4.18
1136 1357 3.944015 CAGATCTGGCGAAAGAGGAAAAT 59.056 43.478 15.38 0.00 0.00 1.82
1230 1451 0.944311 GCTTGACGAAGAAGCCGACA 60.944 55.000 0.00 0.00 40.03 4.35
1334 1555 3.389002 ACCCAAGTCTAACTAAACCGTGT 59.611 43.478 0.00 0.00 0.00 4.49
1770 1992 6.594788 ACACAGGTGCATTAAAGAATGAAT 57.405 33.333 0.00 0.00 44.59 2.57
1911 2134 7.499232 AGGTGCATTAAAGTATAGATCAACACC 59.501 37.037 0.00 0.00 41.20 4.16
2252 2477 7.013823 AGCATTCATATATGAGGCACTAAGT 57.986 36.000 28.53 14.07 41.55 2.24


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

AutoCloner maintained by Alex Coulton.