Multiple sequence alignment - TraesCS2A01G055100

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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 TraesCS2A01G055100 chr2A 100.000 1475 0 0 820 2294 23796207 23797681 0.000000e+00 2724.0
1 TraesCS2A01G055100 chr2A 96.962 1481 38 3 820 2294 600113411 600111932 0.000000e+00 2479.0
2 TraesCS2A01G055100 chr2A 96.932 1434 41 3 862 2294 571019198 571020629 0.000000e+00 2401.0
3 TraesCS2A01G055100 chr2A 100.000 569 0 0 1 569 23795388 23795956 0.000000e+00 1051.0
4 TraesCS2A01G055100 chr2A 93.642 519 29 3 1 518 571018393 571018908 0.000000e+00 773.0
5 TraesCS2A01G055100 chr2A 90.802 511 30 7 1 508 600114358 600113862 0.000000e+00 667.0
6 TraesCS2A01G055100 chr7A 97.290 1476 39 1 820 2294 707844413 707845888 0.000000e+00 2503.0
7 TraesCS2A01G055100 chr7A 97.019 1476 43 1 820 2294 650324537 650323062 0.000000e+00 2481.0
8 TraesCS2A01G055100 chr7A 96.542 1475 50 1 820 2294 650260721 650259248 0.000000e+00 2440.0
9 TraesCS2A01G055100 chr7A 92.897 535 36 2 1 534 650261628 650261095 0.000000e+00 776.0
10 TraesCS2A01G055100 chr7A 93.058 533 33 4 1 532 707843478 707844007 0.000000e+00 776.0
11 TraesCS2A01G055100 chr7A 90.549 455 40 3 7 459 650325298 650324845 1.170000e-167 599.0
12 TraesCS2A01G055100 chr1A 96.949 1475 44 1 820 2293 380400835 380402309 0.000000e+00 2473.0
13 TraesCS2A01G055100 chr1A 96.003 1476 57 2 820 2294 531840028 531838554 0.000000e+00 2398.0
14 TraesCS2A01G055100 chr1A 94.406 572 27 5 1 569 11027064 11026495 0.000000e+00 874.0
15 TraesCS2A01G055100 chr1A 92.199 423 30 3 1 421 504201296 504201717 1.520000e-166 595.0
16 TraesCS2A01G055100 chr1A 97.403 77 2 0 493 569 380400719 380400795 5.140000e-27 132.0
17 TraesCS2A01G055100 chr1A 95.238 63 2 1 508 569 10358619 10358681 5.220000e-17 99.0
18 TraesCS2A01G055100 chr1B 96.070 1476 56 2 820 2294 658504109 658502635 0.000000e+00 2403.0
19 TraesCS2A01G055100 chr4A 94.516 1477 76 5 820 2294 382145499 382146972 0.000000e+00 2274.0
20 TraesCS2A01G055100 chr5A 94.066 573 26 5 1 569 603018455 603019023 0.000000e+00 863.0
21 TraesCS2A01G055100 chr5A 93.202 559 35 3 1 558 507566463 507565907 0.000000e+00 819.0
22 TraesCS2A01G055100 chr5B 98.387 62 1 0 508 569 61755074 61755135 2.410000e-20 110.0
23 TraesCS2A01G055100 chrUn 93.548 62 4 0 508 569 79780483 79780544 2.430000e-15 93.5


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 TraesCS2A01G055100 chr2A 23795388 23797681 2293 False 1887.5 2724 100.0000 1 2294 2 chr2A.!!$F1 2293
1 TraesCS2A01G055100 chr2A 571018393 571020629 2236 False 1587.0 2401 95.2870 1 2294 2 chr2A.!!$F2 2293
2 TraesCS2A01G055100 chr2A 600111932 600114358 2426 True 1573.0 2479 93.8820 1 2294 2 chr2A.!!$R1 2293
3 TraesCS2A01G055100 chr7A 707843478 707845888 2410 False 1639.5 2503 95.1740 1 2294 2 chr7A.!!$F1 2293
4 TraesCS2A01G055100 chr7A 650259248 650261628 2380 True 1608.0 2440 94.7195 1 2294 2 chr7A.!!$R1 2293
5 TraesCS2A01G055100 chr7A 650323062 650325298 2236 True 1540.0 2481 93.7840 7 2294 2 chr7A.!!$R2 2287
6 TraesCS2A01G055100 chr1A 531838554 531840028 1474 True 2398.0 2398 96.0030 820 2294 1 chr1A.!!$R2 1474
7 TraesCS2A01G055100 chr1A 380400719 380402309 1590 False 1302.5 2473 97.1760 493 2293 2 chr1A.!!$F3 1800
8 TraesCS2A01G055100 chr1A 11026495 11027064 569 True 874.0 874 94.4060 1 569 1 chr1A.!!$R1 568
9 TraesCS2A01G055100 chr1B 658502635 658504109 1474 True 2403.0 2403 96.0700 820 2294 1 chr1B.!!$R1 1474
10 TraesCS2A01G055100 chr4A 382145499 382146972 1473 False 2274.0 2274 94.5160 820 2294 1 chr4A.!!$F1 1474
11 TraesCS2A01G055100 chr5A 603018455 603019023 568 False 863.0 863 94.0660 1 569 1 chr5A.!!$F1 568
12 TraesCS2A01G055100 chr5A 507565907 507566463 556 True 819.0 819 93.2020 1 558 1 chr5A.!!$R1 557

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
276 284 0.760945 CCCCCTAAGCCGATCTGAGT 60.761 60.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2330 1.021202 CCTTTTTGAGGTCACACGCA 58.979 50.0 0.0 0.0 40.95 5.24 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
58 59 3.367292 GCCATTGATTTCCACACGTGATT 60.367 43.478 25.01 0.00 0.00 2.57
138 141 2.174639 CCTGGGAACTTGGCCACATATA 59.825 50.000 3.88 0.00 0.00 0.86
145 148 5.536161 GGAACTTGGCCACATATAATGACAT 59.464 40.000 3.88 0.00 0.00 3.06
148 151 8.710749 AACTTGGCCACATATAATGACATAAT 57.289 30.769 3.88 0.00 0.00 1.28
159 162 9.546909 CATATAATGACATAATGCGAAGGTTTC 57.453 33.333 0.00 0.00 0.00 2.78
160 163 4.900635 ATGACATAATGCGAAGGTTTCC 57.099 40.909 0.00 0.00 0.00 3.13
163 166 3.426615 ACATAATGCGAAGGTTTCCCAA 58.573 40.909 0.00 0.00 0.00 4.12
220 226 6.713762 TCAAAATGACACATTTCTTGGACT 57.286 33.333 9.60 0.00 0.00 3.85
232 238 3.914426 TCTTGGACTAATCAGAAGGCC 57.086 47.619 0.00 0.00 43.12 5.19
255 261 1.522569 CTCCCTTCCCACGGATCAC 59.477 63.158 0.00 0.00 0.00 3.06
256 262 1.972660 CTCCCTTCCCACGGATCACC 61.973 65.000 0.00 0.00 0.00 4.02
276 284 0.760945 CCCCCTAAGCCGATCTGAGT 60.761 60.000 0.00 0.00 0.00 3.41
295 303 2.166459 AGTCGTCCACACCATACAGATG 59.834 50.000 0.00 0.00 0.00 2.90
514 522 1.282248 CTGCAACGACCAACGACGAT 61.282 55.000 0.00 0.00 45.77 3.73
944 1297 3.000819 TCCATTCCCCTCACGCGT 61.001 61.111 5.58 5.58 0.00 6.01
979 1333 2.899044 CGTCGGCTCGGAGATCTCC 61.899 68.421 29.15 29.15 46.18 3.71
1302 1656 2.992689 TCCGGCTAGGTGCGAACA 60.993 61.111 0.00 0.00 44.05 3.18
1368 1722 2.705658 AGACTTGGGTCATGTTGTCTCA 59.294 45.455 0.00 0.00 44.36 3.27
1569 1924 1.026182 CATTGCCGCTAGTTGCCTCA 61.026 55.000 3.63 0.00 38.78 3.86
1973 2330 2.749621 GCCAGCTTTATGTAGCAGTGTT 59.250 45.455 0.00 0.00 43.68 3.32
2066 2424 3.304928 GGAACATTGTGTTTCCTGAGCTG 60.305 47.826 0.00 0.00 41.28 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.779922 CCAAATGATCAATCTTATGGCCAG 58.220 41.667 13.05 0.00 0.00 4.85
45 46 0.249699 ACGAGCAATCACGTGTGGAA 60.250 50.000 16.51 0.00 41.17 3.53
58 59 2.890808 AGTGTTCTCAGAAACGAGCA 57.109 45.000 0.00 0.00 32.75 4.26
108 111 4.225042 GGCCAAGTTCCCAGGAAAAATAAT 59.775 41.667 0.00 0.00 35.75 1.28
120 123 4.278419 GTCATTATATGTGGCCAAGTTCCC 59.722 45.833 7.24 0.00 0.00 3.97
138 141 5.248870 GGAAACCTTCGCATTATGTCATT 57.751 39.130 0.00 0.00 0.00 2.57
180 183 9.597999 GTCATTTTGAAACAGGCATAAAAATTC 57.402 29.630 0.00 0.00 0.00 2.17
181 184 9.118300 TGTCATTTTGAAACAGGCATAAAAATT 57.882 25.926 0.00 0.00 0.00 1.82
185 191 6.577103 TGTGTCATTTTGAAACAGGCATAAA 58.423 32.000 0.00 0.00 39.54 1.40
232 238 2.264794 CGTGGGAAGGGAGGTTCG 59.735 66.667 0.00 0.00 0.00 3.95
276 284 1.134818 GCATCTGTATGGTGTGGACGA 60.135 52.381 0.00 0.00 33.38 4.20
295 303 0.163146 GTGCGTTTAGGAGACGTTGC 59.837 55.000 0.00 0.00 42.22 4.17
387 395 2.781406 GGTCAGGGAGAGGGAGGT 59.219 66.667 0.00 0.00 0.00 3.85
486 494 0.249911 GGTCGTTGCAGGTCAAGAGT 60.250 55.000 0.00 0.00 34.91 3.24
921 1273 3.502875 GAGGGGAATGGAGGGGGC 61.503 72.222 0.00 0.00 0.00 5.80
1302 1656 2.516460 CGGGATCGGAGGAGACGT 60.516 66.667 0.00 0.00 0.00 4.34
1392 1746 1.446099 CAGGACTGTACGCGCACAT 60.446 57.895 13.46 3.37 0.00 3.21
1401 1755 1.103803 GGTCAGATCGCAGGACTGTA 58.896 55.000 0.82 0.00 33.93 2.74
1569 1924 1.304134 GCCCCCAATTCGTCCTGTT 60.304 57.895 0.00 0.00 0.00 3.16
1885 2242 9.236691 GCATAACATGTGTCCTACAATATTTTG 57.763 33.333 0.00 0.00 43.77 2.44
1889 2246 7.227314 CACTGCATAACATGTGTCCTACAATAT 59.773 37.037 0.00 0.00 43.77 1.28
1973 2330 1.021202 CCTTTTTGAGGTCACACGCA 58.979 50.000 0.00 0.00 40.95 5.24
2066 2424 7.645058 TGGATTCTAAGAAATGGATTGGAAC 57.355 36.000 0.00 0.00 30.13 3.62


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

AutoCloner maintained by Alex Coulton.