Multiple sequence alignment - TraesCS3A01G252100

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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 TraesCS3A01G252100 chr3A 100.000 2333 0 0 1 2333 472415631 472413299 0.000000e+00 4309
1 TraesCS3A01G252100 chrUn 84.014 1714 155 51 720 2333 289488053 289486359 0.000000e+00 1537
2 TraesCS3A01G252100 chrUn 88.349 1193 98 27 1165 2333 296683781 296682606 0.000000e+00 1395
3 TraesCS3A01G252100 chrUn 87.033 509 40 18 1833 2333 41271516 41271026 3.390000e-153 551
4 TraesCS3A01G252100 chrUn 88.976 127 11 1 720 846 470554884 470554761 1.120000e-33 154
5 TraesCS3A01G252100 chr5A 97.905 716 15 0 1 716 4721845 4722560 0.000000e+00 1240
6 TraesCS3A01G252100 chr4B 98.034 712 14 0 5 716 597294318 597295029 0.000000e+00 1238
7 TraesCS3A01G252100 chr7A 96.508 716 20 2 1 716 191840950 191840240 0.000000e+00 1179
8 TraesCS3A01G252100 chr7A 96.229 716 22 2 1 716 736105575 736106285 0.000000e+00 1168
9 TraesCS3A01G252100 chr7A 94.693 603 19 7 716 1317 170890179 170890769 0.000000e+00 924
10 TraesCS3A01G252100 chr7A 98.466 326 5 0 1642 1967 170891365 170891690 2.010000e-160 575
11 TraesCS3A01G252100 chr7A 95.455 352 8 5 1989 2333 170891681 170892031 2.620000e-154 555
12 TraesCS3A01G252100 chr7A 98.319 238 4 0 1140 1377 170890768 170891005 3.590000e-113 418
13 TraesCS3A01G252100 chr7A 96.121 232 1 3 1412 1635 170891005 170891236 2.830000e-99 372
14 TraesCS3A01G252100 chr6A 96.089 716 23 2 1 716 565050248 565049538 0.000000e+00 1162
15 TraesCS3A01G252100 chr2B 95.955 717 23 3 1 716 98127537 98126826 0.000000e+00 1158
16 TraesCS3A01G252100 chr2B 95.531 716 27 2 1 716 4920065 4920775 0.000000e+00 1140
17 TraesCS3A01G252100 chr2B 85.882 510 42 19 1833 2333 518558538 518558050 1.240000e-142 516
18 TraesCS3A01G252100 chr6B 95.950 716 23 3 1 716 558915021 558914312 0.000000e+00 1157
19 TraesCS3A01G252100 chr6B 94.429 718 35 2 1 716 149037177 149037891 0.000000e+00 1099
20 TraesCS3A01G252100 chr3B 87.033 509 45 13 1833 2333 17914948 17915443 2.620000e-154 555
21 TraesCS3A01G252100 chr3B 87.033 509 40 18 1833 2333 69612747 69612257 3.390000e-153 551


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 TraesCS3A01G252100 chr3A 472413299 472415631 2332 True 4309.0 4309 100.0000 1 2333 1 chr3A.!!$R1 2332
1 TraesCS3A01G252100 chrUn 289486359 289488053 1694 True 1537.0 1537 84.0140 720 2333 1 chrUn.!!$R2 1613
2 TraesCS3A01G252100 chrUn 296682606 296683781 1175 True 1395.0 1395 88.3490 1165 2333 1 chrUn.!!$R3 1168
3 TraesCS3A01G252100 chr5A 4721845 4722560 715 False 1240.0 1240 97.9050 1 716 1 chr5A.!!$F1 715
4 TraesCS3A01G252100 chr4B 597294318 597295029 711 False 1238.0 1238 98.0340 5 716 1 chr4B.!!$F1 711
5 TraesCS3A01G252100 chr7A 191840240 191840950 710 True 1179.0 1179 96.5080 1 716 1 chr7A.!!$R1 715
6 TraesCS3A01G252100 chr7A 736105575 736106285 710 False 1168.0 1168 96.2290 1 716 1 chr7A.!!$F1 715
7 TraesCS3A01G252100 chr7A 170890179 170892031 1852 False 568.8 924 96.6108 716 2333 5 chr7A.!!$F2 1617
8 TraesCS3A01G252100 chr6A 565049538 565050248 710 True 1162.0 1162 96.0890 1 716 1 chr6A.!!$R1 715
9 TraesCS3A01G252100 chr2B 98126826 98127537 711 True 1158.0 1158 95.9550 1 716 1 chr2B.!!$R1 715
10 TraesCS3A01G252100 chr2B 4920065 4920775 710 False 1140.0 1140 95.5310 1 716 1 chr2B.!!$F1 715
11 TraesCS3A01G252100 chr6B 558914312 558915021 709 True 1157.0 1157 95.9500 1 716 1 chr6B.!!$R1 715
12 TraesCS3A01G252100 chr6B 149037177 149037891 714 False 1099.0 1099 94.4290 1 716 1 chr6B.!!$F1 715

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
49 50 3.693807 TCAATACACCGGACTGTCTACT 58.306 45.455 9.46 0.0 0.0 2.57 F
704 710 6.276847 TCAATTTTCTGGTACGCATTTGTTT 58.723 32.000 0.00 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1086 2.358737 GTGCTCTCCCCAACCGTG 60.359 66.667 0.0 0.0 0.0 4.94 R
1965 2347 2.768253 TCATCATGCAAGGAAGTCGT 57.232 45.000 0.0 0.0 0.0 4.34 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
49 50 3.693807 TCAATACACCGGACTGTCTACT 58.306 45.455 9.46 0.0 0.00 2.57
307 312 9.559958 CAATAATCTGTGAACTCCATAAACAAC 57.440 33.333 0.00 0.0 0.00 3.32
632 638 9.323985 CCTTAGTTTTGAAAATGAACAAATCCA 57.676 29.630 0.00 0.0 36.21 3.41
644 650 8.542497 AATGAACAAATCCATCTCAAAACATG 57.458 30.769 0.00 0.0 0.00 3.21
704 710 6.276847 TCAATTTTCTGGTACGCATTTGTTT 58.723 32.000 0.00 0.0 0.00 2.83
1047 1098 2.511600 GCGATCACGGTTGGGGAG 60.512 66.667 0.00 0.0 40.15 4.30
1054 1110 4.760047 CGGTTGGGGAGAGCACCG 62.760 72.222 0.00 0.0 45.75 4.94
1376 1611 4.082026 TCTCATCATCGACGCATGGATATT 60.082 41.667 0.00 0.0 0.00 1.28
1378 1613 3.942130 TCATCGACGCATGGATATTCT 57.058 42.857 0.00 0.0 0.00 2.40
1379 1614 4.257267 TCATCGACGCATGGATATTCTT 57.743 40.909 0.00 0.0 0.00 2.52
1380 1615 3.989817 TCATCGACGCATGGATATTCTTG 59.010 43.478 0.00 0.0 0.00 3.02
1385 1633 5.405269 TCGACGCATGGATATTCTTGTATTG 59.595 40.000 0.00 0.0 0.00 1.90
1392 1640 8.579006 GCATGGATATTCTTGTATTGATTTCCA 58.421 33.333 0.00 0.0 34.33 3.53
1402 1650 8.479689 TCTTGTATTGATTTCCATGCATTCATT 58.520 29.630 0.00 0.0 0.00 2.57
1694 2076 6.880484 AGCCAAATCATATTGCTTTTGATCA 58.120 32.000 0.00 0.0 32.17 2.92
1697 2079 7.254319 GCCAAATCATATTGCTTTTGATCAGTG 60.254 37.037 0.00 0.0 32.17 3.66
1704 2086 2.694628 TGCTTTTGATCAGTGGCAAAGT 59.305 40.909 15.01 0.0 35.64 2.66
1752 2134 7.889073 TCCTCTGATGATGGGTAGTAGTTATAC 59.111 40.741 0.00 0.0 0.00 1.47
1982 2364 7.233389 AGTATATACGACTTCCTTGCATGAT 57.767 36.000 7.23 0.0 0.00 2.45
2267 2655 7.123383 TGTTGTTGTATATACCCTCTCTCTCA 58.877 38.462 10.38 0.0 0.00 3.27
2270 2663 8.239038 TGTTGTATATACCCTCTCTCTCAAAG 57.761 38.462 10.38 0.0 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.711277 TGATAACTGGAGTTTAGTGCTCAAT 58.289 36.000 0.00 0.00 39.31 2.57
49 50 6.713276 TCTTAAATTAACCGGTTGGAGATCA 58.287 36.000 30.08 4.64 39.21 2.92
350 355 6.069323 TCTCCTGTAGACTACATCTCCTTCTT 60.069 42.308 15.58 0.00 39.04 2.52
402 407 3.396946 ACCGATGGTACTATGGAGAGGTA 59.603 47.826 12.42 0.00 32.11 3.08
669 675 4.456566 ACCAGAAAATTGAATTGGCAATGC 59.543 37.500 14.47 12.91 38.42 3.56
1030 1081 2.511600 CTCCCCAACCGTGATCGC 60.512 66.667 0.00 0.00 35.54 4.58
1035 1086 2.358737 GTGCTCTCCCCAACCGTG 60.359 66.667 0.00 0.00 0.00 4.94
1037 1088 4.760047 CGGTGCTCTCCCCAACCG 62.760 72.222 0.00 0.00 0.00 4.44
1174 1406 3.637273 GGTCAGGCCAAGGGACGT 61.637 66.667 5.01 0.00 34.63 4.34
1376 1611 7.407393 TGAATGCATGGAAATCAATACAAGA 57.593 32.000 0.00 0.00 0.00 3.02
1378 1613 8.041919 ACAATGAATGCATGGAAATCAATACAA 58.958 29.630 0.00 0.00 34.26 2.41
1379 1614 7.557724 ACAATGAATGCATGGAAATCAATACA 58.442 30.769 0.00 0.00 34.26 2.29
1380 1615 9.531942 TTACAATGAATGCATGGAAATCAATAC 57.468 29.630 0.00 0.00 34.26 1.89
1385 1633 8.651391 TCAATTACAATGAATGCATGGAAATC 57.349 30.769 0.00 0.00 34.26 2.17
1402 1650 7.511959 ACTAGCTCGTGAGATATCAATTACA 57.488 36.000 5.32 0.00 40.84 2.41
1635 1892 3.509575 ACAAGTCACAACCAACAACATGT 59.490 39.130 0.00 0.00 0.00 3.21
1638 2020 5.704888 CTTTACAAGTCACAACCAACAACA 58.295 37.500 0.00 0.00 0.00 3.33
1639 2021 4.561213 GCTTTACAAGTCACAACCAACAAC 59.439 41.667 0.00 0.00 0.00 3.32
1640 2022 4.461081 AGCTTTACAAGTCACAACCAACAA 59.539 37.500 0.00 0.00 0.00 2.83
1694 2076 7.834181 ACTTCCATTACATATAACTTTGCCACT 59.166 33.333 0.00 0.00 0.00 4.00
1752 2134 4.232221 TGAGGAGCTTTACTTACGTTTCG 58.768 43.478 0.00 0.00 0.00 3.46
1959 2341 7.090808 TCATCATGCAAGGAAGTCGTATATAC 58.909 38.462 2.53 2.53 0.00 1.47
1965 2347 2.768253 TCATCATGCAAGGAAGTCGT 57.232 45.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.