Multiple sequence alignment - TraesCS4A01G388100

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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 TraesCS4A01G388100 chr4A 100.000 4042 0 0 1 4042 665637796 665633755 0.000000e+00 7465
1 TraesCS4A01G388100 chr4A 87.156 218 24 3 563 779 638429949 638430163 1.120000e-60 244
2 TraesCS4A01G388100 chr3B 99.540 3480 14 2 563 4042 83505016 83501539 0.000000e+00 6336
3 TraesCS4A01G388100 chr3B 95.213 564 26 1 1 564 139465071 139464509 0.000000e+00 891
4 TraesCS4A01G388100 chr7A 93.132 1587 100 3 2441 4027 126092230 126090653 0.000000e+00 2318
5 TraesCS4A01G388100 chr7A 87.638 1545 105 36 562 2050 126093741 126092227 0.000000e+00 1716
6 TraesCS4A01G388100 chr1A 92.376 1587 98 4 2441 4027 28662341 28660778 0.000000e+00 2239
7 TraesCS4A01G388100 chr1A 92.060 1587 105 6 2441 4027 10114599 10116164 0.000000e+00 2213
8 TraesCS4A01G388100 chr1A 87.792 1540 110 33 562 2050 28663850 28662338 0.000000e+00 1731
9 TraesCS4A01G388100 chr1A 86.198 797 75 16 561 1324 10089312 10090106 0.000000e+00 830
10 TraesCS4A01G388100 chr1A 89.706 408 24 7 1320 1726 10095253 10095643 4.660000e-139 505
11 TraesCS4A01G388100 chr1A 93.421 304 18 2 1748 2050 10114300 10114602 2.220000e-122 449
12 TraesCS4A01G388100 chr4D 85.389 1451 162 17 2542 3951 4632554 4633995 0.000000e+00 1459
13 TraesCS4A01G388100 chr4D 82.244 811 84 32 1748 2538 4631706 4632476 0.000000e+00 645
14 TraesCS4A01G388100 chr1B 92.972 996 61 5 2441 3436 572903775 572902789 0.000000e+00 1443
15 TraesCS4A01G388100 chr1B 95.390 564 24 2 1 564 635346978 635347539 0.000000e+00 896
16 TraesCS4A01G388100 chr1B 88.245 638 54 15 1359 1993 572904434 572903815 0.000000e+00 743
17 TraesCS4A01G388100 chr1B 93.502 277 18 0 3670 3946 572902792 572902516 2.910000e-111 412
18 TraesCS4A01G388100 chr7B 86.083 1085 121 13 2969 4027 74324861 74323781 0.000000e+00 1140
19 TraesCS4A01G388100 chr7B 79.634 820 113 38 562 1356 74332364 74331574 1.280000e-149 540
20 TraesCS4A01G388100 chr7B 86.250 480 48 6 2466 2931 74325340 74324865 4.660000e-139 505
21 TraesCS4A01G388100 chr7B 89.118 340 32 5 1748 2085 74328354 74328018 6.250000e-113 418
22 TraesCS4A01G388100 chr7B 89.527 296 25 5 2181 2473 74328017 74327725 1.770000e-98 370
23 TraesCS4A01G388100 chr2B 85.161 1085 127 13 2969 4027 34343016 34341940 0.000000e+00 1081
24 TraesCS4A01G388100 chr2B 96.631 564 18 1 1 564 39240416 39239854 0.000000e+00 935
25 TraesCS4A01G388100 chr2B 95.390 564 24 2 1 564 553891091 553891652 0.000000e+00 896
26 TraesCS4A01G388100 chr2B 95.213 564 26 1 1 564 25492937 25492375 0.000000e+00 891
27 TraesCS4A01G388100 chr2B 86.358 777 74 13 2181 2931 34343790 34343020 0.000000e+00 819
28 TraesCS4A01G388100 chr2B 79.415 821 120 36 562 1356 34345175 34344378 5.950000e-148 534
29 TraesCS4A01G388100 chr2B 81.818 154 24 4 994 1145 714134159 714134310 4.240000e-25 126
30 TraesCS4A01G388100 chr4B 85.046 983 121 12 2991 3951 7517545 7518523 0.000000e+00 977
31 TraesCS4A01G388100 chr4B 82.490 731 85 24 1748 2467 7516821 7517519 5.780000e-168 601
32 TraesCS4A01G388100 chr4B 87.558 217 22 4 562 777 570151222 570151010 3.120000e-61 246
33 TraesCS4A01G388100 chr5B 95.752 565 21 3 1 564 595045277 595045839 0.000000e+00 907
34 TraesCS4A01G388100 chr5B 95.552 562 25 0 1 562 507355224 507354663 0.000000e+00 900
35 TraesCS4A01G388100 chr5B 95.699 558 21 3 7 564 458015331 458014777 0.000000e+00 894
36 TraesCS4A01G388100 chr5B 95.213 564 26 1 1 564 574665704 574666266 0.000000e+00 891
37 TraesCS4A01G388100 chr5B 87.963 216 21 4 563 777 672101089 672101300 2.410000e-62 250
38 TraesCS4A01G388100 chrUn 86.797 765 96 5 3191 3954 400056316 400055556 0.000000e+00 848
39 TraesCS4A01G388100 chrUn 82.627 731 85 23 1748 2467 436443129 436443828 3.450000e-170 608
40 TraesCS4A01G388100 chr5D 88.468 607 61 8 1770 2373 503614763 503614163 0.000000e+00 725
41 TraesCS4A01G388100 chr5D 83.117 154 15 3 2396 2538 503613846 503613693 3.280000e-26 130
42 TraesCS4A01G388100 chr2D 81.818 154 24 4 994 1145 589979476 589979627 4.240000e-25 126
43 TraesCS4A01G388100 chr2A 81.818 154 24 4 994 1145 724303403 724303554 4.240000e-25 126


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 TraesCS4A01G388100 chr4A 665633755 665637796 4041 True 7465.000000 7465 100.000000 1 4042 1 chr4A.!!$R1 4041
1 TraesCS4A01G388100 chr3B 83501539 83505016 3477 True 6336.000000 6336 99.540000 563 4042 1 chr3B.!!$R1 3479
2 TraesCS4A01G388100 chr3B 139464509 139465071 562 True 891.000000 891 95.213000 1 564 1 chr3B.!!$R2 563
3 TraesCS4A01G388100 chr7A 126090653 126093741 3088 True 2017.000000 2318 90.385000 562 4027 2 chr7A.!!$R1 3465
4 TraesCS4A01G388100 chr1A 28660778 28663850 3072 True 1985.000000 2239 90.084000 562 4027 2 chr1A.!!$R1 3465
5 TraesCS4A01G388100 chr1A 10114300 10116164 1864 False 1331.000000 2213 92.740500 1748 4027 2 chr1A.!!$F3 2279
6 TraesCS4A01G388100 chr1A 10089312 10090106 794 False 830.000000 830 86.198000 561 1324 1 chr1A.!!$F1 763
7 TraesCS4A01G388100 chr4D 4631706 4633995 2289 False 1052.000000 1459 83.816500 1748 3951 2 chr4D.!!$F1 2203
8 TraesCS4A01G388100 chr1B 635346978 635347539 561 False 896.000000 896 95.390000 1 564 1 chr1B.!!$F1 563
9 TraesCS4A01G388100 chr1B 572902516 572904434 1918 True 866.000000 1443 91.573000 1359 3946 3 chr1B.!!$R1 2587
10 TraesCS4A01G388100 chr7B 74323781 74332364 8583 True 594.600000 1140 86.122400 562 4027 5 chr7B.!!$R1 3465
11 TraesCS4A01G388100 chr2B 39239854 39240416 562 True 935.000000 935 96.631000 1 564 1 chr2B.!!$R2 563
12 TraesCS4A01G388100 chr2B 553891091 553891652 561 False 896.000000 896 95.390000 1 564 1 chr2B.!!$F1 563
13 TraesCS4A01G388100 chr2B 25492375 25492937 562 True 891.000000 891 95.213000 1 564 1 chr2B.!!$R1 563
14 TraesCS4A01G388100 chr2B 34341940 34345175 3235 True 811.333333 1081 83.644667 562 4027 3 chr2B.!!$R3 3465
15 TraesCS4A01G388100 chr4B 7516821 7518523 1702 False 789.000000 977 83.768000 1748 3951 2 chr4B.!!$F1 2203
16 TraesCS4A01G388100 chr5B 595045277 595045839 562 False 907.000000 907 95.752000 1 564 1 chr5B.!!$F2 563
17 TraesCS4A01G388100 chr5B 507354663 507355224 561 True 900.000000 900 95.552000 1 562 1 chr5B.!!$R2 561
18 TraesCS4A01G388100 chr5B 458014777 458015331 554 True 894.000000 894 95.699000 7 564 1 chr5B.!!$R1 557
19 TraesCS4A01G388100 chr5B 574665704 574666266 562 False 891.000000 891 95.213000 1 564 1 chr5B.!!$F1 563
20 TraesCS4A01G388100 chrUn 400055556 400056316 760 True 848.000000 848 86.797000 3191 3954 1 chrUn.!!$R1 763
21 TraesCS4A01G388100 chrUn 436443129 436443828 699 False 608.000000 608 82.627000 1748 2467 1 chrUn.!!$F1 719
22 TraesCS4A01G388100 chr5D 503613693 503614763 1070 True 427.500000 725 85.792500 1770 2538 2 chr5D.!!$R1 768

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
20 21 0.176680 CCCAGAACAGGATCCGACTG 59.823 60.000 5.98 13.47 41.64 3.51 F
318 319 4.901250 AGGTGATTTGTTTGGAAGGTGATT 59.099 37.500 0.00 0.00 0.00 2.57 F
484 485 5.077564 GGAGGGAGACAAAATAAAACCAGT 58.922 41.667 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 8450 7.120726 GGTGCTACCTCTAAAAGCAAGAATTTA 59.879 37.037 0.0 0.00 47.00 1.40 R
2634 8485 6.552008 TCATAATACAGGAAAATGGATCCCC 58.448 40.000 9.9 2.15 37.71 4.81 R
3370 9283 3.857157 TTGGTTGGTCTTACTCTGCTT 57.143 42.857 0.0 0.00 0.00 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
20 21 0.176680 CCCAGAACAGGATCCGACTG 59.823 60.000 5.98 13.47 41.64 3.51
318 319 4.901250 AGGTGATTTGTTTGGAAGGTGATT 59.099 37.500 0.00 0.00 0.00 2.57
484 485 5.077564 GGAGGGAGACAAAATAAAACCAGT 58.922 41.667 0.00 0.00 0.00 4.00
2599 8450 7.831193 GGACAATATATCCTCATAATGGCTGTT 59.169 37.037 0.00 0.00 33.03 3.16
3370 9283 7.890127 AGATCATTCATTTGGGACTTTTCACTA 59.110 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.751924 GTAGCAGTCGGATCCTGTTCT 59.248 52.381 10.75 3.16 32.41 3.01
242 243 8.757982 TCTCCTTCCATACTAATAAAGTACGT 57.242 34.615 0.00 0.00 43.47 3.57
484 485 7.841956 TCACCACTTTCTTTGGTTTTATTTCA 58.158 30.769 0.00 0.00 45.62 2.69
534 537 0.683828 TGGTGAATAGTCCGCCGGTA 60.684 55.000 1.63 0.00 37.01 4.02
986 1035 3.399181 GCATCGTCTCCACCCCCA 61.399 66.667 0.00 0.00 0.00 4.96
2599 8450 7.120726 GGTGCTACCTCTAAAAGCAAGAATTTA 59.879 37.037 0.00 0.00 47.00 1.40
2634 8485 6.552008 TCATAATACAGGAAAATGGATCCCC 58.448 40.000 9.90 2.15 37.71 4.81
3370 9283 3.857157 TTGGTTGGTCTTACTCTGCTT 57.143 42.857 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.