Multiple sequence alignment - TraesCS2A01G049200

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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 TraesCS2A01G049200 chr2A 100.000 2695 0 0 1 2695 19035316 19032622 0.000000e+00 4977.0
1 TraesCS2A01G049200 chr2A 83.748 1046 140 17 5 1030 19055108 19054073 0.000000e+00 963.0
2 TraesCS2A01G049200 chr2A 82.301 791 102 18 1005 1778 19054064 19053295 0.000000e+00 651.0
3 TraesCS2A01G049200 chr2A 81.048 248 31 11 2439 2671 24210391 24210145 1.650000e-42 183.0
4 TraesCS2A01G049200 chr2D 97.292 2696 67 5 3 2695 17613103 17610411 0.000000e+00 4569.0
5 TraesCS2A01G049200 chr2D 97.218 2696 69 5 3 2695 17640474 17637782 0.000000e+00 4558.0
6 TraesCS2A01G049200 chr2D 83.059 1700 242 26 5 1672 17775473 17773788 0.000000e+00 1502.0
7 TraesCS2A01G049200 chr2D 83.516 91 12 3 2604 2694 5421035 5420948 6.180000e-12 82.4
8 TraesCS2A01G049200 chr2B 94.817 2701 125 12 3 2695 29549005 29551698 0.000000e+00 4198.0
9 TraesCS2A01G049200 chr2B 83.900 1795 241 35 5 1770 29262883 29264658 0.000000e+00 1670.0
10 TraesCS2A01G049200 chr2B 83.677 1795 245 35 5 1770 29318120 29319895 0.000000e+00 1648.0
11 TraesCS2A01G049200 chr2B 83.686 1796 243 37 5 1770 29349239 29351014 0.000000e+00 1648.0
12 TraesCS2A01G049200 chr2B 87.330 442 50 5 10 451 29218019 29218454 4.010000e-138 501.0
13 TraesCS2A01G049200 chr3B 94.418 1451 75 4 361 1810 765017784 765019229 0.000000e+00 2226.0
14 TraesCS2A01G049200 chr3B 92.958 355 22 2 1802 2155 765019255 765019607 5.150000e-142 514.0
15 TraesCS2A01G049200 chr3D 85.897 234 19 5 2439 2659 11779940 11780172 1.250000e-58 237.0
16 TraesCS2A01G049200 chr3A 83.268 257 26 8 2441 2681 25240766 25240511 1.260000e-53 220.0
17 TraesCS2A01G049200 chr3A 83.478 230 22 7 2441 2657 25304334 25304108 1.640000e-47 200.0
18 TraesCS2A01G049200 chr6D 83.197 244 28 11 2410 2647 455832707 455832943 7.560000e-51 211.0
19 TraesCS2A01G049200 chrUn 81.707 246 30 6 2435 2667 49171909 49172152 9.850000e-45 191.0
20 TraesCS2A01G049200 chrUn 81.707 246 30 6 2435 2667 252588779 252589022 9.850000e-45 191.0
21 TraesCS2A01G049200 chrUn 78.512 242 36 7 2439 2667 240151185 240151423 7.780000e-31 145.0
22 TraesCS2A01G049200 chr6B 83.182 220 24 5 2440 2647 693072443 693072661 3.540000e-44 189.0
23 TraesCS2A01G049200 chr4A 80.000 270 26 16 2440 2695 645949766 645949511 9.920000e-40 174.0
24 TraesCS2A01G049200 chr4D 89.908 109 9 2 2116 2222 414999661 414999553 3.620000e-29 139.0
25 TraesCS2A01G049200 chr4B 89.815 108 10 1 2116 2222 511163807 511163700 1.300000e-28 137.0
26 TraesCS2A01G049200 chr5D 90.816 98 8 1 2117 2213 481427105 481427202 2.180000e-26 130.0
27 TraesCS2A01G049200 chr7D 90.000 100 9 1 2118 2216 580850179 580850080 7.830000e-26 128.0
28 TraesCS2A01G049200 chr7B 89.109 101 9 2 2118 2216 648660021 648659921 1.010000e-24 124.0
29 TraesCS2A01G049200 chr6A 89.691 97 9 1 2118 2213 93798350 93798446 3.640000e-24 122.0


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 TraesCS2A01G049200 chr2A 19032622 19035316 2694 True 4977 4977 100.0000 1 2695 1 chr2A.!!$R1 2694
1 TraesCS2A01G049200 chr2A 19053295 19055108 1813 True 807 963 83.0245 5 1778 2 chr2A.!!$R3 1773
2 TraesCS2A01G049200 chr2D 17610411 17613103 2692 True 4569 4569 97.2920 3 2695 1 chr2D.!!$R2 2692
3 TraesCS2A01G049200 chr2D 17637782 17640474 2692 True 4558 4558 97.2180 3 2695 1 chr2D.!!$R3 2692
4 TraesCS2A01G049200 chr2D 17773788 17775473 1685 True 1502 1502 83.0590 5 1672 1 chr2D.!!$R4 1667
5 TraesCS2A01G049200 chr2B 29549005 29551698 2693 False 4198 4198 94.8170 3 2695 1 chr2B.!!$F5 2692
6 TraesCS2A01G049200 chr2B 29262883 29264658 1775 False 1670 1670 83.9000 5 1770 1 chr2B.!!$F2 1765
7 TraesCS2A01G049200 chr2B 29318120 29319895 1775 False 1648 1648 83.6770 5 1770 1 chr2B.!!$F3 1765
8 TraesCS2A01G049200 chr2B 29349239 29351014 1775 False 1648 1648 83.6860 5 1770 1 chr2B.!!$F4 1765
9 TraesCS2A01G049200 chr3B 765017784 765019607 1823 False 1370 2226 93.6880 361 2155 2 chr3B.!!$F1 1794

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
199 200 2.245346 TAAAAGTTGCGCGTGCCGA 61.245 52.632 19.87 4.01 41.78 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2067 1.972795 TGGTTTGGACTAAGGTACGCT 59.027 47.619 0.0 0.0 0.0 5.07 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
41 42 9.503399 GAATAAACAATATCTTCGGATAACCCT 57.497 33.333 0.00 0.00 39.94 4.34
114 115 8.719560 TTGTTATATCGGTTACAAGTTATGCA 57.280 30.769 0.00 0.00 0.00 3.96
199 200 2.245346 TAAAAGTTGCGCGTGCCGA 61.245 52.632 19.87 4.01 41.78 5.54
297 299 3.765511 AGGTATGTTAACTGCACCGAGTA 59.234 43.478 7.22 0.00 34.36 2.59
611 627 9.295214 CATGTGTTTTACTTAATTGTGTGTCAA 57.705 29.630 0.00 0.00 40.53 3.18
633 649 6.663093 TCAACACATGGCCTTTTAATAGACAT 59.337 34.615 3.32 0.00 0.00 3.06
806 823 8.988064 TTGTTCGATCATATAGGATCTTTAGC 57.012 34.615 21.48 11.45 41.21 3.09
843 865 9.017509 TCTAGAATGCAGAAACAAATCTTTCAT 57.982 29.630 0.00 0.00 33.26 2.57
982 1008 9.237187 AGTATGTGACACCTCTATAGATACATG 57.763 37.037 2.11 2.48 0.00 3.21
1028 1092 3.067106 TGCTCGTGATCTTCAACCTTTC 58.933 45.455 0.00 0.00 0.00 2.62
1030 1094 3.664107 CTCGTGATCTTCAACCTTTCCA 58.336 45.455 0.00 0.00 0.00 3.53
1068 1132 7.333288 TGTCAATATTCTTGTCGCATATACG 57.667 36.000 0.00 0.00 0.00 3.06
1125 1191 3.950087 TCTAGCTTAATTGCATGCACG 57.050 42.857 22.58 7.77 34.99 5.34
1186 1253 2.421424 CAGGGAAATGGCGAAGAGAAAG 59.579 50.000 0.00 0.00 0.00 2.62
1634 1708 1.981256 ACCTGGATTGTGTGTTGGAC 58.019 50.000 0.00 0.00 0.00 4.02
1788 1872 8.305441 ACAAGTAAACCAACTTTCAAAAACTG 57.695 30.769 0.00 0.00 37.61 3.16
1837 1955 6.886459 AGCTGAAGCCTTTTCTGTCAATAATA 59.114 34.615 0.00 0.00 43.38 0.98
1879 1998 5.614308 AGTCAGTCATGTTTTGTCTCATCA 58.386 37.500 0.00 0.00 0.00 3.07
1948 2067 9.559732 GCTATCTTGATATAGAGCTAGAGATGA 57.440 37.037 0.00 0.00 32.13 2.92
1971 2090 2.301009 CGTACCTTAGTCCAAACCAGGT 59.699 50.000 0.00 0.00 40.84 4.00
2073 2192 4.761235 ACATGCACTTCAACAAGATGAG 57.239 40.909 0.00 0.00 33.34 2.90
2328 2448 4.801330 TGTCTTCGTATCATGAACCAGT 57.199 40.909 0.00 0.00 0.00 4.00
2336 2456 4.034394 CGTATCATGAACCAGTTGTGATGG 59.966 45.833 0.00 0.00 43.87 3.51
2405 2528 7.065923 GTCCCTACACTCTATGAAAAATGAACC 59.934 40.741 0.00 0.00 0.00 3.62
2406 2529 6.884295 CCCTACACTCTATGAAAAATGAACCA 59.116 38.462 0.00 0.00 0.00 3.67
2529 2654 4.932200 CGAGGAGCTCTACACAAGAAAAAT 59.068 41.667 14.64 0.00 32.46 1.82
2659 2784 7.441760 AGCATATTTGATGTTGCAAAGTTTCAA 59.558 29.630 0.00 5.65 40.68 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.474184 ACCACCTCAGTTTGTCAGGG 59.526 55.000 0.00 0.00 0.00 4.45
41 42 2.799126 ACAACCACCTCAGTTTGTCA 57.201 45.000 0.00 0.00 0.00 3.58
297 299 2.509548 TCCCTGCTGGCAAGTATGTAAT 59.490 45.455 3.63 0.00 0.00 1.89
611 627 8.766994 ATTATGTCTATTAAAAGGCCATGTGT 57.233 30.769 5.01 0.00 0.00 3.72
806 823 4.651503 TCTGCATTCTAGAACTCTAAGGGG 59.348 45.833 7.48 0.00 0.00 4.79
1186 1253 2.737252 GGCAAGTAGTAGCACAACAGTC 59.263 50.000 0.00 0.00 0.00 3.51
1549 1618 4.654091 AGTGTTGAAATCACCAAGTTGG 57.346 40.909 20.76 20.76 45.02 3.77
1634 1708 6.568869 AGTAGAGCAGTAAATAGCTTGACAG 58.431 40.000 0.00 0.00 42.04 3.51
1857 1975 5.106791 CCTGATGAGACAAAACATGACTGAC 60.107 44.000 0.00 0.00 34.10 3.51
1879 1998 6.281405 CACCGTAGCTAGAAAAATCATACCT 58.719 40.000 0.00 0.00 0.00 3.08
1948 2067 1.972795 TGGTTTGGACTAAGGTACGCT 59.027 47.619 0.00 0.00 0.00 5.07
1971 2090 3.330701 AGCATGTCAAGTTCCCTTTCCTA 59.669 43.478 0.00 0.00 0.00 2.94
2073 2192 8.992835 AATCATTTTCCTTGATACTTCTTTGC 57.007 30.769 0.00 0.00 33.52 3.68
2328 2448 8.765488 ATATATGGAATTGTTGACCATCACAA 57.235 30.769 0.00 0.00 42.44 3.33
2431 2554 8.523523 TTGACGTCGAAAAGTTTCATATTCTA 57.476 30.769 11.62 0.00 37.01 2.10


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

AutoCloner maintained by Alex Coulton.