Multiple sequence alignment - TraesCS1B01G353000

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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 TraesCS1B01G353000 chr1B 100.000 2342 0 0 1 2342 583550509 583552850 0 4325
1 TraesCS1B01G353000 chr7B 98.249 2341 40 1 2 2342 698126732 698124393 0 4095
2 TraesCS1B01G353000 chr7B 97.864 2341 50 0 2 2342 716795637 716793297 0 4047
3 TraesCS1B01G353000 chr7B 97.779 2341 48 2 2 2342 742937683 742940019 0 4032
4 TraesCS1B01G353000 chrUn 98.206 2341 42 0 2 2342 233525067 233522727 0 4091
5 TraesCS1B01G353000 chrUn 98.039 2346 41 1 2 2342 257944313 257946658 0 4072
6 TraesCS1B01G353000 chr7A 98.035 2341 46 0 2 2342 60095997 60093657 0 4069
7 TraesCS1B01G353000 chr1D 97.826 2346 46 1 2 2342 212429070 212431415 0 4045
8 TraesCS1B01G353000 chr6B 97.651 2341 55 0 2 2342 128889782 128887442 0 4019
9 TraesCS1B01G353000 chr4B 97.565 2341 57 0 2 2342 495537574 495535234 0 4008


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 TraesCS1B01G353000 chr1B 583550509 583552850 2341 False 4325 4325 100.000 1 2342 1 chr1B.!!$F1 2341
1 TraesCS1B01G353000 chr7B 698124393 698126732 2339 True 4095 4095 98.249 2 2342 1 chr7B.!!$R1 2340
2 TraesCS1B01G353000 chr7B 716793297 716795637 2340 True 4047 4047 97.864 2 2342 1 chr7B.!!$R2 2340
3 TraesCS1B01G353000 chr7B 742937683 742940019 2336 False 4032 4032 97.779 2 2342 1 chr7B.!!$F1 2340
4 TraesCS1B01G353000 chrUn 233522727 233525067 2340 True 4091 4091 98.206 2 2342 1 chrUn.!!$R1 2340
5 TraesCS1B01G353000 chrUn 257944313 257946658 2345 False 4072 4072 98.039 2 2342 1 chrUn.!!$F1 2340
6 TraesCS1B01G353000 chr7A 60093657 60095997 2340 True 4069 4069 98.035 2 2342 1 chr7A.!!$R1 2340
7 TraesCS1B01G353000 chr1D 212429070 212431415 2345 False 4045 4045 97.826 2 2342 1 chr1D.!!$F1 2340
8 TraesCS1B01G353000 chr6B 128887442 128889782 2340 True 4019 4019 97.651 2 2342 1 chr6B.!!$R1 2340
9 TraesCS1B01G353000 chr4B 495535234 495537574 2340 True 4008 4008 97.565 2 2342 1 chr4B.!!$R1 2340

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
957 963 1.306642 AAGATGTCTCCGACGCGACT 61.307 55.0 15.93 0.0 34.95 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 1853 1.00432 AACGCGCCATCACCTACAA 60.004 52.632 5.73 0.0 0.0 2.41 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
91 92 6.808212 CGACCAAATTGAACAAATGATAGCTT 59.192 34.615 0.00 0.00 0.00 3.74
211 212 2.306255 ATCGCCCTTACGCGGTCAAT 62.306 55.000 12.47 0.00 43.50 2.57
215 216 1.663695 CCCTTACGCGGTCAATGAAT 58.336 50.000 12.47 0.00 0.00 2.57
453 454 4.742201 CGCCACTCCACGTCTGGG 62.742 72.222 0.00 0.00 38.25 4.45
475 476 1.412710 TGTCTTGGTCTCGCTCACTTT 59.587 47.619 0.00 0.00 0.00 2.66
884 890 1.698532 GGATGATGAGGATGAGCCAGT 59.301 52.381 0.00 0.00 40.02 4.00
913 919 3.644966 ACATAATTTTGGAGGAGCCGA 57.355 42.857 0.89 0.00 40.66 5.54
920 926 3.745803 GGAGGAGCCGAACGACGT 61.746 66.667 0.00 0.00 40.78 4.34
957 963 1.306642 AAGATGTCTCCGACGCGACT 61.307 55.000 15.93 0.00 34.95 4.18
1042 1048 1.403687 GCGGATACTCCCCAGCTTCT 61.404 60.000 0.00 0.00 31.13 2.85
1068 1074 2.158711 TCCGCTTACCGAGGAAGAGATA 60.159 50.000 0.00 0.00 38.77 1.98
1112 1118 3.216230 AGTTGGGTTGGGGTATAGAGT 57.784 47.619 0.00 0.00 0.00 3.24
1127 1133 3.332493 GAGTCGTAAGCGCGGTGGA 62.332 63.158 13.41 7.27 38.14 4.02
1349 1355 2.206223 GATCTTCCCCTAACCCAACCT 58.794 52.381 0.00 0.00 0.00 3.50
1360 1366 3.157680 CCAACCTGGGAACGGACT 58.842 61.111 0.00 0.00 39.98 3.85
1531 1537 0.981183 TGTCACTCACCGGCCTAAAT 59.019 50.000 0.00 0.00 0.00 1.40
1533 1539 0.251916 TCACTCACCGGCCTAAATGG 59.748 55.000 0.00 0.00 39.35 3.16
1642 1648 1.001406 CTTTCAGAGAAGTGGCGGTCT 59.999 52.381 0.00 0.00 0.00 3.85
1751 1757 1.524621 GGGTGACAGATCGGCCATG 60.525 63.158 2.24 0.00 0.00 3.66
1847 1853 3.330720 CCCGGCAGAGGAAAGGGT 61.331 66.667 0.00 0.00 37.36 4.34
1888 1894 3.620488 TGCTTCTTAGGGCGATGAAATT 58.380 40.909 0.00 0.00 0.00 1.82
1911 1917 1.441729 CTATGGGATCGTGCGTGGT 59.558 57.895 0.00 0.00 0.00 4.16
2070 2076 2.569404 GGAGCTAATATGGCTGGCTACT 59.431 50.000 7.99 0.00 40.40 2.57
2103 2109 3.283751 AGAAAGATGAGACGAGACGGAT 58.716 45.455 0.00 0.00 0.00 4.18
2269 2275 0.952280 CTCAGCCCACATGCATCATC 59.048 55.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 7.959658 ATTCCCAATGAACAACATGATCTTA 57.040 32.000 0.00 0.00 39.39 2.10
163 164 7.047271 TCTTGATGACGAATTCCATGATAACA 58.953 34.615 0.00 0.00 0.00 2.41
211 212 7.558161 CAGTCCTTGCATTAGTATGAATTCA 57.442 36.000 11.26 11.26 33.37 2.57
453 454 1.011451 GTGAGCGAGACCAAGACAGC 61.011 60.000 0.00 0.00 0.00 4.40
475 476 2.632544 CCGATACGATAGGCGGGCA 61.633 63.158 3.78 0.00 46.49 5.36
884 890 7.131907 TCCTCCAAAATTATGTTAGGATCGA 57.868 36.000 0.00 0.00 30.06 3.59
913 919 2.993899 CTGATTTTGAGGCTACGTCGTT 59.006 45.455 1.78 0.00 0.00 3.85
920 926 8.489489 AGACATCTTTATCTGATTTTGAGGCTA 58.511 33.333 0.00 0.00 0.00 3.93
957 963 7.147373 CCCCTATAAAAATCTAGTGGAAGTCCA 60.147 40.741 0.00 0.00 45.30 4.02
1112 1118 4.124351 CCTCCACCGCGCTTACGA 62.124 66.667 5.56 0.00 43.93 3.43
1127 1133 0.901124 GAGCACATCCTCTGTCACCT 59.099 55.000 0.00 0.00 35.29 4.00
1349 1355 2.606519 CCCTCCAGTCCGTTCCCA 60.607 66.667 0.00 0.00 0.00 4.37
1360 1366 3.329889 ATGCTGCGGTTCCCTCCA 61.330 61.111 0.00 0.00 0.00 3.86
1446 1452 2.706341 TACCAGGACCCTTGTGCCCT 62.706 60.000 0.00 0.00 32.35 5.19
1751 1757 4.009002 GGTGTATATCTCGGAGTACTCCC 58.991 52.174 31.78 17.61 46.96 4.30
1763 1769 5.369699 ACATTAGTTGCCCTGGTGTATATCT 59.630 40.000 0.00 0.00 0.00 1.98
1847 1853 1.004320 AACGCGCCATCACCTACAA 60.004 52.632 5.73 0.00 0.00 2.41
1911 1917 7.580302 GCCTTTCATCATCATCTATACCAGCTA 60.580 40.741 0.00 0.00 0.00 3.32
2070 2076 7.284716 TCGTCTCATCTTTCTTTGGCTATACTA 59.715 37.037 0.00 0.00 0.00 1.82
2103 2109 1.078918 CCGCTGCATCCTCTGACAA 60.079 57.895 0.00 0.00 0.00 3.18
2114 2120 3.390521 CCTGGTAGTCCCGCTGCA 61.391 66.667 0.00 0.00 35.15 4.41
2269 2275 2.289882 TGGACTGGAGTGCTTTCATCAG 60.290 50.000 0.00 0.00 37.28 2.90


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

AutoCloner maintained by Alex Coulton.