Multiple sequence alignment - TraesCS4A01G497000

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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 TraesCS4A01G497000 chr4A 100.000 3764 0 0 1 3764 743229594 743225831 0.000000e+00 6951.0
1 TraesCS4A01G497000 chr4A 99.309 3764 4 1 1 3764 743186325 743182584 0.000000e+00 6787.0
2 TraesCS4A01G497000 chr4A 100.000 1672 0 0 3868 5539 743225727 743224056 0.000000e+00 3088.0
3 TraesCS4A01G497000 chr4A 99.880 1672 2 0 3868 5539 743182582 743180911 0.000000e+00 3077.0
4 TraesCS4A01G497000 chr4A 86.297 956 99 14 3868 4818 743136837 743135909 0.000000e+00 1011.0
5 TraesCS4A01G497000 chr4A 85.714 539 69 7 2411 2947 743139318 743138786 3.750000e-156 562.0
6 TraesCS4A01G497000 chr4A 84.152 448 59 5 1818 2259 743139743 743139302 1.840000e-114 424.0
7 TraesCS4A01G497000 chr4A 86.786 280 29 6 2948 3220 743138896 743138618 6.970000e-79 305.0
8 TraesCS4A01G497000 chr4A 78.908 403 45 9 3367 3764 743137206 743136839 2.580000e-58 237.0
9 TraesCS4A01G497000 chr4A 89.714 175 13 3 1645 1815 743139958 743139785 9.340000e-53 219.0
10 TraesCS4A01G497000 chr4A 95.506 89 3 1 4891 4978 642603540 642603628 2.080000e-29 141.0
11 TraesCS4A01G497000 chrUn 100.000 1093 0 0 1 1093 367891948 367893040 0.000000e+00 2019.0
12 TraesCS4A01G497000 chrUn 88.641 1074 104 8 1300 2362 89039541 89038475 0.000000e+00 1291.0
13 TraesCS4A01G497000 chrUn 86.823 812 78 17 2958 3764 89038025 89037238 0.000000e+00 880.0
14 TraesCS4A01G497000 chrUn 84.393 865 123 6 3874 4738 89037230 89036378 0.000000e+00 839.0
15 TraesCS4A01G497000 chrUn 89.655 551 52 3 2401 2947 89038474 89037925 0.000000e+00 697.0
16 TraesCS4A01G497000 chrUn 87.805 287 25 4 688 964 89040100 89039814 1.490000e-85 327.0
17 TraesCS4A01G497000 chrUn 80.519 77 15 0 5463 5539 471497733 471497809 5.990000e-05 60.2
18 TraesCS4A01G497000 chr7D 88.553 926 102 4 3874 4799 1126250 1125329 0.000000e+00 1120.0
19 TraesCS4A01G497000 chr7D 89.051 822 88 2 3868 4689 2194531 2193712 0.000000e+00 1018.0
20 TraesCS4A01G497000 chr7D 83.816 828 104 17 2948 3764 1127066 1126258 0.000000e+00 760.0
21 TraesCS4A01G497000 chr7D 81.775 834 90 38 2948 3764 2195321 2194533 4.680000e-180 641.0
22 TraesCS4A01G497000 chr7D 88.867 512 46 7 2440 2947 1127460 1126956 2.190000e-173 619.0
23 TraesCS4A01G497000 chr7D 87.619 525 59 2 2423 2947 2195729 2195211 6.140000e-169 604.0
24 TraesCS4A01G497000 chr7D 82.969 458 57 12 1818 2260 1127905 1127454 1.450000e-105 394.0
25 TraesCS4A01G497000 chr7D 80.543 442 48 17 1818 2255 1807119 1807526 6.970000e-79 305.0
26 TraesCS4A01G497000 chr7D 92.105 152 10 2 1656 1807 2210165 2210016 4.350000e-51 213.0
27 TraesCS4A01G497000 chr7D 91.096 146 13 0 1655 1800 1128113 1127968 1.220000e-46 198.0
28 TraesCS4A01G497000 chr7D 83.981 206 26 3 2423 2628 1807703 1807901 2.040000e-44 191.0
29 TraesCS4A01G497000 chr7D 83.482 224 15 4 4684 4885 2171992 2171769 7.330000e-44 189.0
30 TraesCS4A01G497000 chr7D 91.045 134 8 2 4982 5111 1106958 1106825 1.590000e-40 178.0
31 TraesCS4A01G497000 chr7D 92.174 115 8 1 5029 5142 2171717 2171603 1.600000e-35 161.0
32 TraesCS4A01G497000 chr7D 95.402 87 3 1 4895 4980 428885095 428885181 2.690000e-28 137.0
33 TraesCS4A01G497000 chr7D 95.122 41 1 1 1381 1421 1128218 1128179 4.630000e-06 63.9
34 TraesCS4A01G497000 chr7A 84.844 739 76 18 3038 3764 945041 944327 0.000000e+00 712.0
35 TraesCS4A01G497000 chr7A 86.253 371 51 0 3874 4244 944319 943949 2.400000e-108 403.0
36 TraesCS4A01G497000 chr7A 100.000 28 0 0 2920 2947 945048 945021 1.000000e-02 52.8
37 TraesCS4A01G497000 chr4D 82.582 643 104 4 3915 4550 74358675 74358034 1.350000e-155 560.0
38 TraesCS4A01G497000 chr4D 84.977 426 58 3 2525 2947 74359859 74359437 1.430000e-115 427.0
39 TraesCS4A01G497000 chr4D 80.987 547 76 15 2962 3500 74359533 74359007 5.170000e-110 409.0
40 TraesCS4A01G497000 chr4D 83.673 441 62 3 1818 2258 74365957 74365527 1.860000e-109 407.0
41 TraesCS4A01G497000 chr4D 94.898 98 2 3 4892 4988 492602239 492602144 3.460000e-32 150.0
42 TraesCS4A01G497000 chr4D 96.552 87 2 1 4895 4980 50531445 50531359 5.780000e-30 143.0
43 TraesCS4A01G497000 chr4B 81.659 458 72 6 4012 4461 106826630 106826177 2.440000e-98 370.0
44 TraesCS4A01G497000 chr6B 76.965 547 66 32 5 526 343005221 343004710 1.980000e-64 257.0
45 TraesCS4A01G497000 chr6D 85.106 188 17 5 5 187 218424319 218424500 1.230000e-41 182.0
46 TraesCS4A01G497000 chr6D 97.674 86 1 1 4895 4979 142846397 142846312 4.470000e-31 147.0
47 TraesCS4A01G497000 chr3B 91.964 112 5 4 4879 4987 729205869 729205979 2.670000e-33 154.0
48 TraesCS4A01G497000 chr3B 98.810 84 0 1 4896 4978 71400462 71400379 1.240000e-31 148.0
49 TraesCS4A01G497000 chr3D 95.604 91 3 1 4891 4980 145198715 145198805 1.610000e-30 145.0
50 TraesCS4A01G497000 chr3D 83.448 145 22 2 5395 5539 581075119 581075261 3.480000e-27 134.0
51 TraesCS4A01G497000 chr3D 76.389 144 30 4 5398 5539 595873539 595873398 2.140000e-09 75.0
52 TraesCS4A01G497000 chr6A 77.966 118 25 1 5423 5539 10381520 10381637 7.700000e-09 73.1


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 TraesCS4A01G497000 chr4A 743224056 743229594 5538 True 5019.500000 6951 100.000000 1 5539 2 chr4A.!!$R3 5538
1 TraesCS4A01G497000 chr4A 743180911 743186325 5414 True 4932.000000 6787 99.594500 1 5539 2 chr4A.!!$R2 5538
2 TraesCS4A01G497000 chr4A 743135909 743139958 4049 True 459.666667 1011 85.261833 1645 4818 6 chr4A.!!$R1 3173
3 TraesCS4A01G497000 chrUn 367891948 367893040 1092 False 2019.000000 2019 100.000000 1 1093 1 chrUn.!!$F1 1092
4 TraesCS4A01G497000 chrUn 89036378 89040100 3722 True 806.800000 1291 87.463400 688 4738 5 chrUn.!!$R1 4050
5 TraesCS4A01G497000 chr7D 2193712 2195729 2017 True 754.333333 1018 86.148333 2423 4689 3 chr7D.!!$R5 2266
6 TraesCS4A01G497000 chr7D 1125329 1128218 2889 True 525.816667 1120 88.403833 1381 4799 6 chr7D.!!$R3 3418
7 TraesCS4A01G497000 chr7D 1807119 1807901 782 False 248.000000 305 82.262000 1818 2628 2 chr7D.!!$F2 810
8 TraesCS4A01G497000 chr7A 943949 945048 1099 True 389.266667 712 90.365667 2920 4244 3 chr7A.!!$R1 1324
9 TraesCS4A01G497000 chr4D 74358034 74359859 1825 True 465.333333 560 82.848667 2525 4550 3 chr4D.!!$R4 2025
10 TraesCS4A01G497000 chr6B 343004710 343005221 511 True 257.000000 257 76.965000 5 526 1 chr6B.!!$R1 521

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
1683 1721 2.26892 GGATCTCCTTGTGGCGCA 59.731 61.111 10.83 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4600 6348 5.350365 TCTCACATACAAAAACGGTAGCATC 59.65 40.0 0.0 0.0 0.0 3.91 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
1683 1721 2.268920 GGATCTCCTTGTGGCGCA 59.731 61.111 10.83 0.0 0.0 6.09
4850 6602 5.593095 GGTTTTCTTTAGTTCCCTGTCAAGT 59.407 40.000 0.00 0.0 0.0 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1683 1721 7.764141 TGTTGCCATAATCATGCTGTATTAT 57.236 32.00 0.0 0.0 0.0 1.28
4600 6348 5.350365 TCTCACATACAAAAACGGTAGCATC 59.650 40.00 0.0 0.0 0.0 3.91
4850 6602 5.604758 AGCAGCAGAGAATATACAACAGA 57.395 39.13 0.0 0.0 0.0 3.41


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

AutoCloner maintained by Alex Coulton.