Multiple sequence alignment - TraesCS7B01G052500

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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 TraesCS7B01G052500 chr7B 100.000 2587 0 0 1 2587 54924857 54922271 0.000000e+00 4778.0
1 TraesCS7B01G052500 chr7B 99.070 860 5 3 1 858 54933852 54932994 0.000000e+00 1541.0
2 TraesCS7B01G052500 chr7B 97.454 864 14 7 2 862 577095817 577096675 0.000000e+00 1467.0
3 TraesCS7B01G052500 chr7B 97.442 860 18 3 2 858 577086833 577087691 0.000000e+00 1463.0
4 TraesCS7B01G052500 chr3B 95.872 969 39 1 1619 2587 672251091 672250124 0.000000e+00 1567.0
5 TraesCS7B01G052500 chr3B 97.442 860 17 5 2 857 252453911 252453053 0.000000e+00 1461.0
6 TraesCS7B01G052500 chr3B 93.085 752 26 2 857 1608 672276984 672276259 0.000000e+00 1077.0
7 TraesCS7B01G052500 chr6B 94.650 972 47 5 1619 2587 431423121 431424090 0.000000e+00 1502.0
8 TraesCS7B01G052500 chr6B 95.000 600 24 2 1000 1599 431405253 431405846 0.000000e+00 937.0
9 TraesCS7B01G052500 chr6B 94.845 97 4 1 857 953 431405148 431405243 1.600000e-32 150.0
10 TraesCS7B01G052500 chr5A 97.677 861 17 3 1 858 274628287 274629147 0.000000e+00 1476.0
11 TraesCS7B01G052500 chr5A 97.332 862 18 4 1 857 274637284 274638145 0.000000e+00 1459.0
12 TraesCS7B01G052500 chr4A 97.567 863 15 6 1 858 413491793 413492654 0.000000e+00 1472.0
13 TraesCS7B01G052500 chr3A 97.672 859 16 4 2 858 636060582 636061438 0.000000e+00 1472.0
14 TraesCS7B01G052500 chr2B 97.448 862 17 4 1 857 126038192 126039053 0.000000e+00 1465.0
15 TraesCS7B01G052500 chr5D 92.086 973 72 5 1619 2587 306248517 306249488 0.000000e+00 1365.0
16 TraesCS7B01G052500 chr7D 91.984 973 72 6 1619 2587 71618896 71619866 0.000000e+00 1360.0
17 TraesCS7B01G052500 chr7D 90.339 973 80 9 1619 2587 135507429 135508391 0.000000e+00 1264.0
18 TraesCS7B01G052500 chr7D 91.024 635 43 8 972 1599 135503137 135503764 0.000000e+00 845.0
19 TraesCS7B01G052500 chr7D 90.363 633 48 7 972 1599 71587265 71587889 0.000000e+00 819.0
20 TraesCS7B01G052500 chr7D 83.276 586 70 15 2004 2587 370972666 370973225 4.940000e-142 514.0
21 TraesCS7B01G052500 chr7D 82.794 587 72 16 2003 2587 209094217 209094776 4.970000e-137 497.0
22 TraesCS7B01G052500 chr7A 91.496 976 74 8 1619 2587 80558167 80557194 0.000000e+00 1334.0
23 TraesCS7B01G052500 chr7A 90.701 613 46 5 1000 1608 80562487 80561882 0.000000e+00 806.0
24 TraesCS7B01G052500 chr6A 90.881 976 81 7 1619 2587 535297167 535298141 0.000000e+00 1303.0
25 TraesCS7B01G052500 chr6A 90.536 634 46 9 972 1599 535279026 535279651 0.000000e+00 826.0
26 TraesCS7B01G052500 chr1D 90.442 973 67 14 1619 2585 267990797 267989845 0.000000e+00 1258.0
27 TraesCS7B01G052500 chr1D 91.790 609 44 2 1000 1608 267994588 267993986 0.000000e+00 843.0
28 TraesCS7B01G052500 chr1D 92.027 602 39 4 1000 1599 18171927 18171333 0.000000e+00 837.0
29 TraesCS7B01G052500 chr1D 97.222 36 1 0 897 932 267994654 267994619 7.730000e-06 62.1
30 TraesCS7B01G052500 chr1B 90.741 648 54 6 1619 2263 52804918 52804274 0.000000e+00 859.0
31 TraesCS7B01G052500 chr1B 88.419 639 64 7 972 1608 52847993 52847363 0.000000e+00 761.0


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 TraesCS7B01G052500 chr7B 54922271 54924857 2586 True 4778.000000 4778 100.000000 1 2587 1 chr7B.!!$R1 2586
1 TraesCS7B01G052500 chr7B 54932994 54933852 858 True 1541.000000 1541 99.070000 1 858 1 chr7B.!!$R2 857
2 TraesCS7B01G052500 chr7B 577095817 577096675 858 False 1467.000000 1467 97.454000 2 862 1 chr7B.!!$F2 860
3 TraesCS7B01G052500 chr7B 577086833 577087691 858 False 1463.000000 1463 97.442000 2 858 1 chr7B.!!$F1 856
4 TraesCS7B01G052500 chr3B 672250124 672251091 967 True 1567.000000 1567 95.872000 1619 2587 1 chr3B.!!$R2 968
5 TraesCS7B01G052500 chr3B 252453053 252453911 858 True 1461.000000 1461 97.442000 2 857 1 chr3B.!!$R1 855
6 TraesCS7B01G052500 chr3B 672276259 672276984 725 True 1077.000000 1077 93.085000 857 1608 1 chr3B.!!$R3 751
7 TraesCS7B01G052500 chr6B 431423121 431424090 969 False 1502.000000 1502 94.650000 1619 2587 1 chr6B.!!$F1 968
8 TraesCS7B01G052500 chr6B 431405148 431405846 698 False 543.500000 937 94.922500 857 1599 2 chr6B.!!$F2 742
9 TraesCS7B01G052500 chr5A 274628287 274629147 860 False 1476.000000 1476 97.677000 1 858 1 chr5A.!!$F1 857
10 TraesCS7B01G052500 chr5A 274637284 274638145 861 False 1459.000000 1459 97.332000 1 857 1 chr5A.!!$F2 856
11 TraesCS7B01G052500 chr4A 413491793 413492654 861 False 1472.000000 1472 97.567000 1 858 1 chr4A.!!$F1 857
12 TraesCS7B01G052500 chr3A 636060582 636061438 856 False 1472.000000 1472 97.672000 2 858 1 chr3A.!!$F1 856
13 TraesCS7B01G052500 chr2B 126038192 126039053 861 False 1465.000000 1465 97.448000 1 857 1 chr2B.!!$F1 856
14 TraesCS7B01G052500 chr5D 306248517 306249488 971 False 1365.000000 1365 92.086000 1619 2587 1 chr5D.!!$F1 968
15 TraesCS7B01G052500 chr7D 71618896 71619866 970 False 1360.000000 1360 91.984000 1619 2587 1 chr7D.!!$F2 968
16 TraesCS7B01G052500 chr7D 135503137 135508391 5254 False 1054.500000 1264 90.681500 972 2587 2 chr7D.!!$F5 1615
17 TraesCS7B01G052500 chr7D 71587265 71587889 624 False 819.000000 819 90.363000 972 1599 1 chr7D.!!$F1 627
18 TraesCS7B01G052500 chr7D 370972666 370973225 559 False 514.000000 514 83.276000 2004 2587 1 chr7D.!!$F4 583
19 TraesCS7B01G052500 chr7D 209094217 209094776 559 False 497.000000 497 82.794000 2003 2587 1 chr7D.!!$F3 584
20 TraesCS7B01G052500 chr7A 80557194 80562487 5293 True 1070.000000 1334 91.098500 1000 2587 2 chr7A.!!$R1 1587
21 TraesCS7B01G052500 chr6A 535297167 535298141 974 False 1303.000000 1303 90.881000 1619 2587 1 chr6A.!!$F2 968
22 TraesCS7B01G052500 chr6A 535279026 535279651 625 False 826.000000 826 90.536000 972 1599 1 chr6A.!!$F1 627
23 TraesCS7B01G052500 chr1D 18171333 18171927 594 True 837.000000 837 92.027000 1000 1599 1 chr1D.!!$R1 599
24 TraesCS7B01G052500 chr1D 267989845 267994654 4809 True 721.033333 1258 93.151333 897 2585 3 chr1D.!!$R2 1688
25 TraesCS7B01G052500 chr1B 52804274 52804918 644 True 859.000000 859 90.741000 1619 2263 1 chr1B.!!$R1 644
26 TraesCS7B01G052500 chr1B 52847363 52847993 630 True 761.000000 761 88.419000 972 1608 1 chr1B.!!$R2 636

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
46 47 3.573772 CTCCGTCTTGCGTGGCTCA 62.574 63.158 0.0 0.0 39.32 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 5846 0.541863 AGGTTTCACTATGGAGGGCG 59.458 55.0 0.0 0.0 0.0 6.13 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
46 47 3.573772 CTCCGTCTTGCGTGGCTCA 62.574 63.158 0.00 0.00 39.32 4.26
1040 1061 2.878429 GTCAGCTTCTCGAGGCGA 59.122 61.111 13.56 8.12 38.56 5.54
1245 1274 4.836825 TGATTCCTCACATGTCCTCTTTC 58.163 43.478 0.00 0.00 0.00 2.62
1261 1292 5.823045 TCCTCTTTCTCTCTGTTTTTGTTCC 59.177 40.000 0.00 0.00 0.00 3.62
1262 1293 5.590259 CCTCTTTCTCTCTGTTTTTGTTCCA 59.410 40.000 0.00 0.00 0.00 3.53
1474 1506 8.822652 AAGAAAAATGATTTGGTAGCAGAAAG 57.177 30.769 0.00 0.00 0.00 2.62
1526 1558 5.208463 TGCAGATGTACAAGTGTCTGTTA 57.792 39.130 20.07 10.72 40.08 2.41
1527 1559 5.793817 TGCAGATGTACAAGTGTCTGTTAT 58.206 37.500 20.07 0.00 40.08 1.89
1528 1560 6.230472 TGCAGATGTACAAGTGTCTGTTATT 58.770 36.000 20.07 0.00 40.08 1.40
1601 1633 9.688091 ATGTCTCAGTAGAGTTAGATGTTTCTA 57.312 33.333 0.00 0.00 42.66 2.10
1903 5846 6.012745 AGAGATGGCCCAATATGAATAAACC 58.987 40.000 0.00 0.00 0.00 3.27
2022 5969 6.699204 CCTACATTCAGTAATCTACAGTGCAG 59.301 42.308 0.00 0.00 30.92 4.41
2124 6076 4.165950 ACCTACAATCCATGTAAGGCATCA 59.834 41.667 0.00 0.00 43.75 3.07
2160 6112 0.544120 TTGGCCCCAAATCCTTCCAC 60.544 55.000 0.00 0.00 32.44 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.310373 CCCCCTCTACCTCCTCGTT 59.690 63.158 0.00 0.0 0.00 3.85
186 188 2.291540 CCCTCTCACTCTCTCTGTTCCT 60.292 54.545 0.00 0.0 0.00 3.36
187 189 2.099405 CCCTCTCACTCTCTCTGTTCC 58.901 57.143 0.00 0.0 0.00 3.62
188 190 2.802719 ACCCTCTCACTCTCTCTGTTC 58.197 52.381 0.00 0.0 0.00 3.18
189 191 2.990740 ACCCTCTCACTCTCTCTGTT 57.009 50.000 0.00 0.0 0.00 3.16
190 192 2.355310 CGTACCCTCTCACTCTCTCTGT 60.355 54.545 0.00 0.0 0.00 3.41
191 193 2.285083 CGTACCCTCTCACTCTCTCTG 58.715 57.143 0.00 0.0 0.00 3.35
1040 1061 2.285368 TCCTTCGGAGCCCACCAT 60.285 61.111 0.00 0.0 0.00 3.55
1261 1292 7.420002 TGACACAGAAAATTCAGAGTTTGATG 58.580 34.615 0.00 0.0 35.27 3.07
1262 1293 7.572523 TGACACAGAAAATTCAGAGTTTGAT 57.427 32.000 0.00 0.0 35.27 2.57
1903 5846 0.541863 AGGTTTCACTATGGAGGGCG 59.458 55.000 0.00 0.0 0.00 6.13
1967 5914 7.012704 ACCTGATTGCATATATGTGTTTCTGTC 59.987 37.037 14.14 3.3 0.00 3.51
2124 6076 5.457633 GGGGCCAAATACATACTAATGGACT 60.458 44.000 4.39 0.0 36.20 3.85
2160 6112 1.398390 GCGATTTAGTGGCCTGTTGAG 59.602 52.381 3.32 0.0 0.00 3.02
2362 6321 2.525629 TCTCCCCTGACGCACCAA 60.526 61.111 0.00 0.0 0.00 3.67


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

AutoCloner maintained by Alex Coulton.