Multiple sequence alignment - TraesCS4A01G047500

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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 TraesCS4A01G047500 chr4A 100.000 5526 0 0 1 5526 38709993 38715518 0.000000e+00 10205
1 TraesCS4A01G047500 chr4A 98.911 918 10 0 3 920 38703089 38704006 0.000000e+00 1640
2 TraesCS4A01G047500 chr4A 94.884 430 16 3 5092 5518 331467395 331467821 0.000000e+00 667
3 TraesCS4A01G047500 chr4A 92.405 237 17 1 2164 2399 658151895 658151659 2.470000e-88 337
4 TraesCS4A01G047500 chr2A 96.730 4618 122 15 915 5526 628528655 628524061 0.000000e+00 7664
5 TraesCS4A01G047500 chr2A 92.618 1016 56 9 988 1988 16577733 16578744 0.000000e+00 1443
6 TraesCS4A01G047500 chr5B 96.768 4362 128 9 1076 5430 382951917 382956272 0.000000e+00 7262
7 TraesCS4A01G047500 chr5B 91.090 2458 183 24 2402 4852 576795717 576798145 0.000000e+00 3293
8 TraesCS4A01G047500 chr7A 98.177 4004 71 2 1112 5115 676285967 676281966 0.000000e+00 6988
9 TraesCS4A01G047500 chr7A 92.552 2457 147 22 2402 4852 145450250 145452676 0.000000e+00 3491
10 TraesCS4A01G047500 chr7A 98.249 914 16 0 3 916 8346200 8345287 0.000000e+00 1600
11 TraesCS4A01G047500 chr7D 92.843 2445 147 17 2411 4852 38015089 38012670 0.000000e+00 3520
12 TraesCS4A01G047500 chr7D 89.278 1912 173 16 2406 4309 277901561 277903448 0.000000e+00 2366
13 TraesCS4A01G047500 chr7D 94.550 422 18 2 5075 5493 38012380 38011961 0.000000e+00 647
14 TraesCS4A01G047500 chr3A 92.434 2445 151 19 2411 4851 714573222 714570808 0.000000e+00 3459
15 TraesCS4A01G047500 chr3A 98.472 916 14 0 5 920 700674347 700673432 0.000000e+00 1615
16 TraesCS4A01G047500 chr3A 98.257 918 15 1 3 920 67819035 67819951 0.000000e+00 1605
17 TraesCS4A01G047500 chr3A 98.357 913 15 0 3 915 667542028 667541116 0.000000e+00 1604
18 TraesCS4A01G047500 chr3A 98.148 918 17 0 3 920 599952367 599951450 0.000000e+00 1602
19 TraesCS4A01G047500 chr3A 98.046 921 18 0 3 923 700667433 700666513 0.000000e+00 1602
20 TraesCS4A01G047500 chr5D 97.443 1916 46 3 915 2828 80206070 80207984 0.000000e+00 3264
21 TraesCS4A01G047500 chr5D 97.143 1365 35 3 2868 4230 80207976 80209338 0.000000e+00 2302
22 TraesCS4A01G047500 chr5D 97.660 641 11 2 4882 5519 80212709 80213348 0.000000e+00 1098
23 TraesCS4A01G047500 chr5D 87.586 290 22 3 1988 2264 365178531 365178819 1.920000e-84 324
24 TraesCS4A01G047500 chr5D 85.666 293 24 3 1988 2263 366751919 366752210 5.410000e-75 292
25 TraesCS4A01G047500 chr3D 96.967 1912 42 4 918 2827 65439449 65437552 0.000000e+00 3195
26 TraesCS4A01G047500 chr3D 97.123 1460 40 2 915 2374 535486852 535485395 0.000000e+00 2462
27 TraesCS4A01G047500 chr3D 96.857 1368 38 3 2868 4233 65437559 65436195 0.000000e+00 2283
28 TraesCS4A01G047500 chr3D 97.273 1247 25 6 4277 5519 65436205 65434964 0.000000e+00 2106
29 TraesCS4A01G047500 chr3D 90.580 276 21 5 4845 5118 480829053 480828781 1.460000e-95 361
30 TraesCS4A01G047500 chr4B 91.993 1761 116 13 3766 5521 116736316 116738056 0.000000e+00 2447
31 TraesCS4A01G047500 chr2D 92.633 1656 93 11 3673 5318 602412432 602410796 0.000000e+00 2355
32 TraesCS4A01G047500 chr2D 93.611 1080 58 8 2597 3675 602413986 602412917 0.000000e+00 1602
33 TraesCS4A01G047500 chr1A 98.043 920 18 0 1 920 379720594 379719675 0.000000e+00 1600
34 TraesCS4A01G047500 chr1A 98.148 918 16 1 3 920 521207034 521207950 0.000000e+00 1600
35 TraesCS4A01G047500 chr3B 92.527 1017 59 8 988 1988 749158749 749157734 0.000000e+00 1441
36 TraesCS4A01G047500 chr3B 92.827 237 16 1 2164 2399 749157534 749157298 5.300000e-90 342
37 TraesCS4A01G047500 chr6B 91.937 1017 64 8 988 1988 52458811 52457797 0.000000e+00 1408
38 TraesCS4A01G047500 chr5A 95.444 417 14 2 5092 5505 398259256 398258842 0.000000e+00 660
39 TraesCS4A01G047500 chr4D 91.304 276 20 4 4845 5118 211032225 211032498 1.880000e-99 374
40 TraesCS4A01G047500 chrUn 92.405 237 12 2 2164 2399 357639591 357639822 3.190000e-87 333


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 TraesCS4A01G047500 chr4A 38709993 38715518 5525 False 10205.000000 10205 100.000000 1 5526 1 chr4A.!!$F2 5525
1 TraesCS4A01G047500 chr4A 38703089 38704006 917 False 1640.000000 1640 98.911000 3 920 1 chr4A.!!$F1 917
2 TraesCS4A01G047500 chr2A 628524061 628528655 4594 True 7664.000000 7664 96.730000 915 5526 1 chr2A.!!$R1 4611
3 TraesCS4A01G047500 chr2A 16577733 16578744 1011 False 1443.000000 1443 92.618000 988 1988 1 chr2A.!!$F1 1000
4 TraesCS4A01G047500 chr5B 382951917 382956272 4355 False 7262.000000 7262 96.768000 1076 5430 1 chr5B.!!$F1 4354
5 TraesCS4A01G047500 chr5B 576795717 576798145 2428 False 3293.000000 3293 91.090000 2402 4852 1 chr5B.!!$F2 2450
6 TraesCS4A01G047500 chr7A 676281966 676285967 4001 True 6988.000000 6988 98.177000 1112 5115 1 chr7A.!!$R2 4003
7 TraesCS4A01G047500 chr7A 145450250 145452676 2426 False 3491.000000 3491 92.552000 2402 4852 1 chr7A.!!$F1 2450
8 TraesCS4A01G047500 chr7A 8345287 8346200 913 True 1600.000000 1600 98.249000 3 916 1 chr7A.!!$R1 913
9 TraesCS4A01G047500 chr7D 277901561 277903448 1887 False 2366.000000 2366 89.278000 2406 4309 1 chr7D.!!$F1 1903
10 TraesCS4A01G047500 chr7D 38011961 38015089 3128 True 2083.500000 3520 93.696500 2411 5493 2 chr7D.!!$R1 3082
11 TraesCS4A01G047500 chr3A 714570808 714573222 2414 True 3459.000000 3459 92.434000 2411 4851 1 chr3A.!!$R5 2440
12 TraesCS4A01G047500 chr3A 700673432 700674347 915 True 1615.000000 1615 98.472000 5 920 1 chr3A.!!$R4 915
13 TraesCS4A01G047500 chr3A 67819035 67819951 916 False 1605.000000 1605 98.257000 3 920 1 chr3A.!!$F1 917
14 TraesCS4A01G047500 chr3A 667541116 667542028 912 True 1604.000000 1604 98.357000 3 915 1 chr3A.!!$R2 912
15 TraesCS4A01G047500 chr3A 599951450 599952367 917 True 1602.000000 1602 98.148000 3 920 1 chr3A.!!$R1 917
16 TraesCS4A01G047500 chr3A 700666513 700667433 920 True 1602.000000 1602 98.046000 3 923 1 chr3A.!!$R3 920
17 TraesCS4A01G047500 chr5D 80206070 80213348 7278 False 2221.333333 3264 97.415333 915 5519 3 chr5D.!!$F3 4604
18 TraesCS4A01G047500 chr3D 65434964 65439449 4485 True 2528.000000 3195 97.032333 918 5519 3 chr3D.!!$R3 4601
19 TraesCS4A01G047500 chr3D 535485395 535486852 1457 True 2462.000000 2462 97.123000 915 2374 1 chr3D.!!$R2 1459
20 TraesCS4A01G047500 chr4B 116736316 116738056 1740 False 2447.000000 2447 91.993000 3766 5521 1 chr4B.!!$F1 1755
21 TraesCS4A01G047500 chr2D 602410796 602413986 3190 True 1978.500000 2355 93.122000 2597 5318 2 chr2D.!!$R1 2721
22 TraesCS4A01G047500 chr1A 379719675 379720594 919 True 1600.000000 1600 98.043000 1 920 1 chr1A.!!$R1 919
23 TraesCS4A01G047500 chr1A 521207034 521207950 916 False 1600.000000 1600 98.148000 3 920 1 chr1A.!!$F1 917
24 TraesCS4A01G047500 chr3B 749157298 749158749 1451 True 891.500000 1441 92.677000 988 2399 2 chr3B.!!$R1 1411
25 TraesCS4A01G047500 chr6B 52457797 52458811 1014 True 1408.000000 1408 91.937000 988 1988 1 chr6B.!!$R1 1000

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
936 937 0.196118 TCCACCCCTTTCTCTTCCCT 59.804 55.000 0.00 0.00 0.00 4.20 F
1596 1615 2.598907 CGTTACCAGTTGACGCACAAAG 60.599 50.000 0.00 0.00 40.36 2.77 F
2175 2226 0.515564 AATTAAGTGTGCGCGTCCAC 59.484 50.000 18.55 18.55 36.28 4.02 F
2934 2999 2.176798 TCATGGGTTGGTTCAGGACTTT 59.823 45.455 0.00 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2060 1.067669 TCTTCAATCTCGAGATGCCCG 59.932 52.381 27.93 16.37 34.49 6.13 R
3107 3172 1.384989 GGCATCCTCGGTCTTCTCGA 61.385 60.000 0.00 0.00 35.24 4.04 R
3288 3353 2.622436 CTAGGTTTCCTTTCCGAGCTG 58.378 52.381 0.00 0.00 34.61 4.24 R
4632 5190 0.456628 CATGCGTTGCAATGGGATGA 59.543 50.000 22.07 0.00 43.62 2.92 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 2.126467 TCGAACAACTTTCGGGTTACG 58.874 47.619 6.57 0.00 41.78 3.18
118 119 2.948979 GACATGACCGAGATGACTCTCT 59.051 50.000 0.00 0.00 44.92 3.10
782 783 1.141053 GGCTTACTAGGGACATGGTGG 59.859 57.143 0.00 0.00 0.00 4.61
927 928 1.786441 TCCAACAATCTCCACCCCTTT 59.214 47.619 0.00 0.00 0.00 3.11
933 934 3.009584 ACAATCTCCACCCCTTTCTCTTC 59.990 47.826 0.00 0.00 0.00 2.87
936 937 0.196118 TCCACCCCTTTCTCTTCCCT 59.804 55.000 0.00 0.00 0.00 4.20
1410 1429 4.191544 CCCAAGCAAGATGAACTCGATTA 58.808 43.478 0.00 0.00 0.00 1.75
1596 1615 2.598907 CGTTACCAGTTGACGCACAAAG 60.599 50.000 0.00 0.00 40.36 2.77
1927 1950 4.464008 TGCAATTTGTGAAGAGAAGAGGT 58.536 39.130 0.00 0.00 0.00 3.85
2016 2043 6.347696 TCATCAATTTTTGCCAACAGAAACT 58.652 32.000 0.00 0.00 33.19 2.66
2175 2226 0.515564 AATTAAGTGTGCGCGTCCAC 59.484 50.000 18.55 18.55 36.28 4.02
2380 2433 5.201243 TCGGGATCTAGAGTTCATGAAGAA 58.799 41.667 8.80 0.00 0.00 2.52
2503 2559 3.991773 GTGTTCATGTGCGTTAGAAGGTA 59.008 43.478 0.00 0.00 0.00 3.08
2607 2663 6.014669 ACATTGTTATTGGTAAACCTGCATGT 60.015 34.615 0.02 0.00 36.82 3.21
2934 2999 2.176798 TCATGGGTTGGTTCAGGACTTT 59.823 45.455 0.00 0.00 0.00 2.66
2948 3013 9.091220 GGTTCAGGACTTTAGGTATATATCACT 57.909 37.037 0.00 0.00 0.00 3.41
3185 3250 4.159693 TCTGTTACGACTTATGGTGATGCT 59.840 41.667 0.00 0.00 0.00 3.79
3288 3353 3.235369 GAGATCCTCCAGCCACCC 58.765 66.667 0.00 0.00 0.00 4.61
3375 3440 2.943033 CAACTTCGTGAACTTCAACCCT 59.057 45.455 0.00 0.00 0.00 4.34
3600 3666 1.545841 TGACTACGTCCACAGCATCT 58.454 50.000 0.00 0.00 0.00 2.90
3604 3670 1.335182 CTACGTCCACAGCATCTCGAT 59.665 52.381 0.00 0.00 0.00 3.59
3912 4465 5.883503 TTTGTTTTCCGTTTCACACTAGT 57.116 34.783 0.00 0.00 0.00 2.57
3980 4535 5.180271 TGAGTACACGGTTCAAAGAAGTTT 58.820 37.500 0.00 0.00 0.00 2.66
4348 4904 0.324285 AGCTTGGCTCTTCCTGACTG 59.676 55.000 0.00 0.00 30.62 3.51
4508 5065 3.445096 GGAATCTGGTGTTTCTCCATTGG 59.555 47.826 0.00 0.00 34.26 3.16
4930 8272 3.197116 ACTTTCCCTACAACCTATGTCGG 59.803 47.826 0.00 0.00 42.70 4.79
5297 8761 2.742053 GCCAAGTACAATTCTGAAGCGA 59.258 45.455 0.00 0.00 0.00 4.93
5411 8875 6.577103 TGAAATTTTGTGGCAATTAGTGTGA 58.423 32.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
927 928 2.243736 GGAGAGAAGAGGAGGGAAGAGA 59.756 54.545 0.00 0.00 0.00 3.10
933 934 1.133482 GGAGAGGAGAGAAGAGGAGGG 60.133 61.905 0.00 0.00 0.00 4.30
936 937 1.994399 AGGGAGAGGAGAGAAGAGGA 58.006 55.000 0.00 0.00 0.00 3.71
1213 1232 5.806502 CACTCAGTGTTTTGAAAATCTGCAA 59.193 36.000 15.64 4.94 0.00 4.08
1596 1615 1.734465 GATCTAGCACCAGCACACAAC 59.266 52.381 0.00 0.00 45.49 3.32
2033 2060 1.067669 TCTTCAATCTCGAGATGCCCG 59.932 52.381 27.93 16.37 34.49 6.13
2175 2226 7.673180 ACATTCCCATATGCCTGAAAATATTG 58.327 34.615 0.00 0.00 0.00 1.90
2380 2433 4.319984 GGACCTTTTTAAATTCAGTCGCGT 60.320 41.667 5.77 0.00 0.00 6.01
2503 2559 8.691797 TGTTTAGGAAATTAGAAGCACAAACTT 58.308 29.630 0.00 0.00 0.00 2.66
2607 2663 2.093973 GGAAGAAGAGGCAGATCGACAA 60.094 50.000 0.00 0.00 0.00 3.18
2683 2739 9.178758 GATTCAATCAAAGAACCTGGTAATAGT 57.821 33.333 0.00 0.00 0.00 2.12
3107 3172 1.384989 GGCATCCTCGGTCTTCTCGA 61.385 60.000 0.00 0.00 35.24 4.04
3140 3205 4.866508 AAGAACACCATCGTACTTGAGA 57.133 40.909 0.00 0.00 0.00 3.27
3185 3250 7.226441 TCAAGATTGATCTCAAAACTCCTCAA 58.774 34.615 0.00 0.00 39.55 3.02
3288 3353 2.622436 CTAGGTTTCCTTTCCGAGCTG 58.378 52.381 0.00 0.00 34.61 4.24
3600 3666 4.020573 ACTTGGTCTTGAACATGGTATCGA 60.021 41.667 0.00 0.00 0.00 3.59
3604 3670 5.304686 AGAACTTGGTCTTGAACATGGTA 57.695 39.130 0.00 0.00 0.00 3.25
3912 4465 6.183360 GCCCACATGATAAATTCTGACATTCA 60.183 38.462 0.00 0.00 0.00 2.57
3965 4520 8.557029 ACTAAATGACTAAACTTCTTTGAACCG 58.443 33.333 0.00 0.00 0.00 4.44
4200 4756 5.155509 TCAATTTCGCAAAGATGATACCG 57.844 39.130 0.00 0.00 0.00 4.02
4269 4825 5.811399 TCTCGGTTAAGTGCATAAAATGG 57.189 39.130 0.00 0.00 0.00 3.16
4287 4843 5.751028 CCTCAACTATTAGAAAGCCTTCTCG 59.249 44.000 0.00 0.00 41.19 4.04
4348 4904 3.695606 TGAGCCTGGTGACGAGCC 61.696 66.667 0.00 0.00 0.00 4.70
4508 5065 1.329906 CTCTCAACATCGCATGCTTCC 59.670 52.381 17.13 0.00 0.00 3.46
4632 5190 0.456628 CATGCGTTGCAATGGGATGA 59.543 50.000 22.07 0.00 43.62 2.92
4746 5305 6.013379 ACTCTGCCATGTACTATATACAGCT 58.987 40.000 0.00 0.00 0.00 4.24
4930 8272 5.298527 GCAAAATCATTACAGTAGGTACCCC 59.701 44.000 8.74 0.00 0.00 4.95
5411 8875 9.832445 TTGAAACAAGAGTACATAGTTCTTTCT 57.168 29.630 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.