Multiple sequence alignment - TraesCS1D01G153700

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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 TraesCS1D01G153700 chr1D 100.000 2621 0 0 1 2621 214069450 214066830 0.000000e+00 4841.0
1 TraesCS1D01G153700 chr1B 96.098 2640 55 15 1 2621 307005665 307003055 0.000000e+00 4261.0
2 TraesCS1D01G153700 chr1A 96.579 2251 53 13 285 2523 271621082 271618844 0.000000e+00 3709.0
3 TraesCS1D01G153700 chr2D 86.150 426 56 2 1092 1517 483256332 483255910 8.550000e-125 457.0
4 TraesCS1D01G153700 chr2A 86.215 428 52 5 1092 1517 626589688 626589266 8.550000e-125 457.0
5 TraesCS1D01G153700 chr2B 85.948 427 55 4 1092 1517 568275131 568275553 3.980000e-123 451.0
6 TraesCS1D01G153700 chr6A 85.203 419 55 7 1102 1516 598619737 598619322 8.670000e-115 424.0
7 TraesCS1D01G153700 chr6A 85.149 404 60 0 1113 1516 422328668 422328265 5.220000e-112 414.0
8 TraesCS1D01G153700 chr6D 85.000 420 54 9 1102 1516 452722177 452721762 4.030000e-113 418.0
9 TraesCS1D01G153700 chr6D 84.901 404 61 0 1113 1516 296348047 296347644 2.430000e-110 409.0
10 TraesCS1D01G153700 chr3A 79.699 133 11 11 31 160 22222001 22222120 6.010000e-12 82.4
11 TraesCS1D01G153700 chr3B 100.000 35 0 0 76 110 615384172 615384206 6.050000e-07 65.8
12 TraesCS1D01G153700 chr3B 100.000 35 0 0 76 110 616435328 616435362 6.050000e-07 65.8


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 TraesCS1D01G153700 chr1D 214066830 214069450 2620 True 4841 4841 100.000 1 2621 1 chr1D.!!$R1 2620
1 TraesCS1D01G153700 chr1B 307003055 307005665 2610 True 4261 4261 96.098 1 2621 1 chr1B.!!$R1 2620
2 TraesCS1D01G153700 chr1A 271618844 271621082 2238 True 3709 3709 96.579 285 2523 1 chr1A.!!$R1 2238

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
761 770 0.681733 TGAGGTGAGGTGAGCTGAAC 59.318 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 1929 1.01058 TCATCACAAACAACGCACGT 58.989 45.0 0.0 0.0 0.0 4.49 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
40 41 4.687262 TTTCTCTTAGGTACTCCCTCCA 57.313 45.455 0.00 0.00 44.81 3.86
79 80 7.253422 AGTTCGAATATTGGCTTTGATTGAAG 58.747 34.615 0.00 0.00 0.00 3.02
89 90 8.954950 TTGGCTTTGATTGAAGTCAAATTTTA 57.045 26.923 2.50 0.00 45.31 1.52
411 412 1.072806 CCATCCATCCCGTCACATCAT 59.927 52.381 0.00 0.00 0.00 2.45
761 770 0.681733 TGAGGTGAGGTGAGCTGAAC 59.318 55.000 0.00 0.00 0.00 3.18
858 867 1.278127 CTTGTTCCATAGGACCACCGT 59.722 52.381 0.00 0.00 41.83 4.83
881 890 2.747855 GGCTCCCCAAGAAGCGTG 60.748 66.667 0.00 0.00 0.00 5.34
1014 1023 1.762957 AGATCAATGGACCTGGTACCG 59.237 52.381 6.60 1.95 0.00 4.02
1675 1684 2.231964 TGCAACGACTTTCCCTACGTAT 59.768 45.455 0.00 0.00 38.00 3.06
1676 1685 2.856557 GCAACGACTTTCCCTACGTATC 59.143 50.000 0.00 0.00 38.00 2.24
1677 1686 3.442100 CAACGACTTTCCCTACGTATCC 58.558 50.000 0.00 0.00 38.00 2.59
1678 1687 3.010200 ACGACTTTCCCTACGTATCCT 57.990 47.619 0.00 0.00 37.22 3.24
1679 1688 4.156455 ACGACTTTCCCTACGTATCCTA 57.844 45.455 0.00 0.00 37.22 2.94
1680 1689 4.723309 ACGACTTTCCCTACGTATCCTAT 58.277 43.478 0.00 0.00 37.22 2.57
1786 1799 1.470494 TGCAAGCGCGGATTAAATTCA 59.530 42.857 8.83 0.00 42.97 2.57
1914 1927 2.544844 TTCCCCACCCTCTACTACTG 57.455 55.000 0.00 0.00 0.00 2.74
1915 1928 1.390287 TCCCCACCCTCTACTACTGT 58.610 55.000 0.00 0.00 0.00 3.55
1916 1929 2.576841 TCCCCACCCTCTACTACTGTA 58.423 52.381 0.00 0.00 0.00 2.74
1917 1930 2.243221 TCCCCACCCTCTACTACTGTAC 59.757 54.545 0.00 0.00 0.00 2.90
1996 2015 8.375506 TGGCTCGATTTAATCCTCTATGTAATT 58.624 33.333 0.00 0.00 0.00 1.40
2038 2057 6.347859 AGTTTAGTCCTCTTGTAACCTCTG 57.652 41.667 0.00 0.00 0.00 3.35
2047 2066 2.113860 TGTAACCTCTGGCATCTTGC 57.886 50.000 0.00 0.00 44.08 4.01
2106 2127 4.002982 GTGATGTCCTGTTGCATCTTGTA 58.997 43.478 0.00 0.00 41.33 2.41
2174 2196 1.065709 TCCAGTTGGGGAATCTAACGC 60.066 52.381 0.00 0.00 37.22 4.84
2452 2474 3.893326 ACTGATGTACATGCAGCACTA 57.107 42.857 23.71 0.00 33.03 2.74
2546 2571 6.755206 AGTGTACTATGAGTGCAGTTTTGTA 58.245 36.000 0.00 0.00 40.79 2.41
2594 2620 4.471904 TTCACTCGTTGATGCTTAGGAT 57.528 40.909 0.00 0.00 32.84 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 235 5.979288 AATTCTATATACGTCCTCCGCTT 57.021 39.130 0.00 0.0 41.42 4.68
236 237 6.154445 TGAAAATTCTATATACGTCCTCCGC 58.846 40.000 0.00 0.0 41.42 5.54
411 412 1.971357 GAGACAGTGGGAGGTGAAAGA 59.029 52.381 0.00 0.0 0.00 2.52
1675 1684 5.733000 TGGTGGGAATACATAGGAATAGGA 58.267 41.667 0.00 0.0 0.00 2.94
1676 1685 6.445139 AGATGGTGGGAATACATAGGAATAGG 59.555 42.308 0.00 0.0 0.00 2.57
1677 1686 7.401493 AGAGATGGTGGGAATACATAGGAATAG 59.599 40.741 0.00 0.0 0.00 1.73
1678 1687 7.256399 AGAGATGGTGGGAATACATAGGAATA 58.744 38.462 0.00 0.0 0.00 1.75
1679 1688 6.094302 AGAGATGGTGGGAATACATAGGAAT 58.906 40.000 0.00 0.0 0.00 3.01
1680 1689 5.476983 AGAGATGGTGGGAATACATAGGAA 58.523 41.667 0.00 0.0 0.00 3.36
1803 1816 3.767902 ACTAGACTAGTAGGGGTAGCG 57.232 52.381 13.63 0.0 37.23 4.26
1914 1927 2.033577 TCATCACAAACAACGCACGTAC 60.034 45.455 0.00 0.0 0.00 3.67
1915 1928 2.202566 TCATCACAAACAACGCACGTA 58.797 42.857 0.00 0.0 0.00 3.57
1916 1929 1.010580 TCATCACAAACAACGCACGT 58.989 45.000 0.00 0.0 0.00 4.49
1917 1930 1.772966 GTTCATCACAAACAACGCACG 59.227 47.619 0.00 0.0 0.00 5.34
2038 2057 4.897140 AGAGATAGATCAAGCAAGATGCC 58.103 43.478 0.00 0.0 46.52 4.40
2047 2066 8.618702 ATTGCAATACCAAGAGATAGATCAAG 57.381 34.615 11.02 0.0 0.00 3.02
2083 2104 3.079578 CAAGATGCAACAGGACATCACT 58.920 45.455 5.84 0.0 44.16 3.41
2106 2127 2.576832 CGACCACACCGTACCCCTT 61.577 63.158 0.00 0.0 0.00 3.95
2174 2196 4.232905 TCCCCAGGGAGAACAGTG 57.767 61.111 7.25 0.0 39.76 3.66
2546 2571 4.607293 TGCAGAGACAGAAACATGTACT 57.393 40.909 0.00 0.0 32.25 2.73


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

AutoCloner maintained by Alex Coulton.