Multiple sequence alignment - TraesCS4B01G326300

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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 TraesCS4B01G326300 chr4B 100.000 6314 0 0 1 6314 617327184 617333497 0.000000e+00 11660
1 TraesCS4B01G326300 chr4B 99.517 414 2 0 5340 5753 617327734 617328147 0.000000e+00 754
2 TraesCS4B01G326300 chr4B 99.517 414 2 0 551 964 617332523 617332936 0.000000e+00 754
3 TraesCS4B01G326300 chr1B 99.483 5218 15 4 551 5757 14048388 14053604 0.000000e+00 9478
4 TraesCS4B01G326300 chr1B 99.570 4652 20 0 1110 5761 634418280 634413629 0.000000e+00 8480
5 TraesCS4B01G326300 chr1B 99.517 414 2 0 551 964 634414050 634413637 0.000000e+00 754
6 TraesCS4B01G326300 chr1B 98.807 419 3 2 5336 5753 14048385 14048802 0.000000e+00 745
7 TraesCS4B01G326300 chr1B 99.036 415 3 1 551 964 14053187 14053601 0.000000e+00 743
8 TraesCS4B01G326300 chr1B 98.837 86 1 0 4153 4238 634418363 634418278 3.050000e-33 154
9 TraesCS4B01G326300 chr6A 99.616 2084 7 1 3674 5756 83348846 83346763 0.000000e+00 3803
10 TraesCS4B01G326300 chr6A 99.433 1058 4 1 551 1608 83352231 83351176 0.000000e+00 1919
11 TraesCS4B01G326300 chr6A 99.275 414 3 0 551 964 83347180 83346767 0.000000e+00 749
12 TraesCS4B01G326300 chr6A 99.510 408 2 0 3113 3520 83350546 83350139 0.000000e+00 743
13 TraesCS4B01G326300 chr6A 98.792 414 3 1 5340 5753 83352231 83351820 0.000000e+00 736
14 TraesCS4B01G326300 chr4D 93.617 564 23 3 1 551 484686382 484686945 0.000000e+00 830
15 TraesCS4B01G326300 chr4D 95.968 496 17 1 5822 6314 484686994 484687489 0.000000e+00 802
16 TraesCS4B01G326300 chr5A 95.335 493 15 2 5830 6314 665609678 665610170 0.000000e+00 776
17 TraesCS4B01G326300 chr5A 96.897 419 11 2 5336 5753 628565342 628564925 0.000000e+00 701
18 TraesCS4B01G326300 chr5A 97.108 415 11 1 551 965 628565337 628564924 0.000000e+00 699
19 TraesCS4B01G326300 chr5A 90.505 495 29 4 75 551 665609087 665609581 6.900000e-179 638
20 TraesCS4B01G326300 chr5A 96.774 62 2 0 1 62 665608697 665608758 3.110000e-18 104
21 TraesCS4B01G326300 chr7B 87.027 370 40 7 5339 5705 733749074 733748710 1.640000e-110 411
22 TraesCS4B01G326300 chr7B 86.992 369 40 7 551 916 733749073 733748710 5.890000e-110 409
23 TraesCS4B01G326300 chr7B 82.418 455 63 9 113 551 495720625 495721078 1.280000e-101 381
24 TraesCS4B01G326300 chr7B 92.278 259 20 0 6025 6283 495721478 495721736 1.000000e-97 368
25 TraesCS4B01G326300 chr7D 79.623 584 82 22 1 551 471868490 471869069 9.930000e-103 385
26 TraesCS4B01G326300 chr7D 92.278 259 20 0 6025 6283 471869465 471869723 1.000000e-97 368
27 TraesCS4B01G326300 chr7A 79.245 583 82 23 1 551 524701073 524700498 2.780000e-98 370
28 TraesCS4B01G326300 chr7A 85.906 149 16 3 5610 5754 28453268 28453415 3.050000e-33 154
29 TraesCS4B01G326300 chr7A 85.811 148 16 3 821 964 28453268 28453414 1.100000e-32 152
30 TraesCS4B01G326300 chr3B 86.957 115 11 2 5336 5446 52834708 52834822 6.650000e-25 126
31 TraesCS4B01G326300 chr3B 86.486 111 11 1 551 657 52834712 52834822 1.110000e-22 119


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 TraesCS4B01G326300 chr4B 617327184 617333497 6313 False 11660.000000 11660 100.000000 1 6314 1 chr4B.!!$F1 6313
1 TraesCS4B01G326300 chr1B 634413629 634418280 4651 True 8480.000000 8480 99.570000 1110 5761 1 chr1B.!!$R1 4651
2 TraesCS4B01G326300 chr1B 14048385 14053604 5219 False 3655.333333 9478 99.108667 551 5757 3 chr1B.!!$F1 5206
3 TraesCS4B01G326300 chr6A 83346763 83352231 5468 True 1590.000000 3803 99.325200 551 5756 5 chr6A.!!$R1 5205
4 TraesCS4B01G326300 chr4D 484686382 484687489 1107 False 816.000000 830 94.792500 1 6314 2 chr4D.!!$F1 6313
5 TraesCS4B01G326300 chr5A 665608697 665610170 1473 False 506.000000 776 94.204667 1 6314 3 chr5A.!!$F1 6313
6 TraesCS4B01G326300 chr7B 495720625 495721736 1111 False 374.500000 381 87.348000 113 6283 2 chr7B.!!$F1 6170
7 TraesCS4B01G326300 chr7D 471868490 471869723 1233 False 376.500000 385 85.950500 1 6283 2 chr7D.!!$F1 6282
8 TraesCS4B01G326300 chr7A 524700498 524701073 575 True 370.000000 370 79.245000 1 551 1 chr7A.!!$R1 550

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
548 921 0.747255 GTTGCTCTCGCCATCCTCTA 59.253 55.000 0.00 0.0 34.43 2.43 F
814 1188 3.069872 TGTGTCGCTGGTTTAGTAAAGGA 59.930 43.478 0.00 0.0 0.00 3.36 F
4493 6015 0.318955 GGCATTGAAGTTGCGCAAGT 60.319 50.000 25.78 25.1 41.07 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3185 3568 7.589958 TTCCAAGCTTCATAAGGTGTTTTTA 57.410 32.000 0.00 0.0 39.57 1.52 R
4493 6015 3.192001 GCAGAGTGAAATGCCATCTTCAA 59.808 43.478 4.58 0.0 36.41 2.69 R
6013 7546 2.821366 CCACTGCGTCCAGATGGC 60.821 66.667 0.00 0.0 41.77 4.40 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 3.500642 CTCGCGGCTCTCTCGACA 61.501 66.667 6.13 0.00 0.00 4.35
104 450 2.042104 AGCTGTACGTACGTGTTGTC 57.958 50.000 30.25 14.76 0.00 3.18
336 691 1.444553 CTGGCTCTTCGTGTCGGTC 60.445 63.158 0.00 0.00 0.00 4.79
382 740 2.855770 AATGGCCTGGCAAGGGACA 61.856 57.895 22.05 3.48 46.92 4.02
546 919 1.522580 GGTTGCTCTCGCCATCCTC 60.523 63.158 0.00 0.00 34.43 3.71
547 920 1.519719 GTTGCTCTCGCCATCCTCT 59.480 57.895 0.00 0.00 34.43 3.69
548 921 0.747255 GTTGCTCTCGCCATCCTCTA 59.253 55.000 0.00 0.00 34.43 2.43
549 922 0.747255 TTGCTCTCGCCATCCTCTAC 59.253 55.000 0.00 0.00 34.43 2.59
768 1141 3.942748 GTGGTGTTGGTTTCTGTAACTGA 59.057 43.478 0.00 0.00 36.93 3.41
814 1188 3.069872 TGTGTCGCTGGTTTAGTAAAGGA 59.930 43.478 0.00 0.00 0.00 3.36
4493 6015 0.318955 GGCATTGAAGTTGCGCAAGT 60.319 50.000 25.78 25.10 41.07 3.16
4774 6296 1.137872 TGGCAGCGGTGAAACAAATTT 59.862 42.857 20.69 0.00 39.98 1.82
5386 6908 1.071071 TGGTCGTGGTAAAACCTGGAG 59.929 52.381 0.00 0.00 39.58 3.86
5773 7296 1.749634 TCTACTTCTCCGTGCTAAGGC 59.250 52.381 0.00 0.00 39.26 4.35
5793 7322 6.959639 AGGCAATTCATTTACGGATACAAT 57.040 33.333 0.00 0.00 0.00 2.71
6297 7950 1.000233 TACGCACGCTCGTGTCTTTC 61.000 55.000 21.30 5.75 46.90 2.62
6304 7957 0.449022 GCTCGTGTCTTTCGTTTCGC 60.449 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.968901 TCAGTATGGTTCCGGCGAGT 60.969 55.000 9.30 0.0 36.16 4.18
104 450 1.164041 TGCATCATCGCAGCCATCAG 61.164 55.000 0.00 0.0 36.86 2.90
240 595 0.109272 TCGACACGAAGCTGATCACC 60.109 55.000 0.00 0.0 31.06 4.02
366 721 4.284550 GTGTCCCTTGCCAGGCCA 62.285 66.667 9.64 0.0 39.20 5.36
410 780 4.742201 CCTGACCGTGACCCTGCG 62.742 72.222 0.00 0.0 0.00 5.18
546 919 7.279313 ACAACAGGTTTACACAACTAACAGTAG 59.721 37.037 0.00 0.0 0.00 2.57
547 920 7.104939 ACAACAGGTTTACACAACTAACAGTA 58.895 34.615 0.00 0.0 0.00 2.74
548 921 5.941647 ACAACAGGTTTACACAACTAACAGT 59.058 36.000 0.00 0.0 0.00 3.55
549 922 6.431198 ACAACAGGTTTACACAACTAACAG 57.569 37.500 0.00 0.0 0.00 3.16
768 1141 3.260884 TCCGGCTCTACTCTTTTGATGTT 59.739 43.478 0.00 0.0 0.00 2.71
3185 3568 7.589958 TTCCAAGCTTCATAAGGTGTTTTTA 57.410 32.000 0.00 0.0 39.57 1.52
4493 6015 3.192001 GCAGAGTGAAATGCCATCTTCAA 59.808 43.478 4.58 0.0 36.41 2.69
4774 6296 5.655090 TCAGAGTTCCACGGATATACTTCAA 59.345 40.000 0.00 0.0 0.00 2.69
5825 7354 5.117592 CAGCAACGGAAACAAGATCAAAATC 59.882 40.000 0.00 0.0 0.00 2.17
6013 7546 2.821366 CCACTGCGTCCAGATGGC 60.821 66.667 0.00 0.0 41.77 4.40


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

AutoCloner maintained by Alex Coulton.