Multiple sequence alignment - TraesCS1D01G338000

Loading Multiple Alignment...

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 TraesCS1D01G338000 chr1D 100.000 3284 0 0 1 3284 427373282 427369999 0.000000e+00 6065
1 TraesCS1D01G338000 chr1D 83.153 1662 229 36 955 2596 427332244 427330614 0.000000e+00 1471
2 TraesCS1D01G338000 chr1D 82.961 1479 200 33 915 2373 427319559 427318113 0.000000e+00 1288
3 TraesCS1D01G338000 chr1D 87.674 860 104 2 948 1805 427596922 427596063 0.000000e+00 1000
4 TraesCS1D01G338000 chr1A 97.003 2302 50 10 908 3195 522535977 522533681 0.000000e+00 3851
5 TraesCS1D01G338000 chr1A 84.177 1422 186 21 960 2368 522510855 522509460 0.000000e+00 1343
6 TraesCS1D01G338000 chr1A 83.488 1399 182 31 959 2336 522516329 522514959 0.000000e+00 1258
7 TraesCS1D01G338000 chr1B 94.338 1307 52 5 1335 2639 579001936 579000650 0.000000e+00 1984
8 TraesCS1D01G338000 chr1B 84.330 1672 211 34 955 2596 577913147 577911497 0.000000e+00 1589
9 TraesCS1D01G338000 chr1B 84.605 1442 176 32 955 2371 578045436 578044016 0.000000e+00 1391
10 TraesCS1D01G338000 chr1B 86.765 884 108 8 968 1850 577829257 577828382 0.000000e+00 976
11 TraesCS1D01G338000 chr1B 90.566 424 29 7 2645 3062 579000591 579000173 4.790000e-153 551
12 TraesCS1D01G338000 chr1B 82.202 545 65 19 2519 3039 578052756 578052220 1.080000e-119 440
13 TraesCS1D01G338000 chr1B 81.200 250 18 16 3064 3284 579000076 578999827 1.210000e-39 174
14 TraesCS1D01G338000 chr6D 97.677 904 20 1 1 904 452111336 452110434 0.000000e+00 1552
15 TraesCS1D01G338000 chr6D 90.608 905 83 2 1 903 70785470 70784566 0.000000e+00 1199
16 TraesCS1D01G338000 chr7D 96.681 904 30 0 1 904 84171029 84170126 0.000000e+00 1504
17 TraesCS1D01G338000 chr7D 96.822 881 26 2 26 905 23073144 23072265 0.000000e+00 1471
18 TraesCS1D01G338000 chr5D 84.676 1527 198 22 941 2442 523187595 523186080 0.000000e+00 1491
19 TraesCS1D01G338000 chr5D 84.630 1529 195 23 941 2442 523314784 523313269 0.000000e+00 1485
20 TraesCS1D01G338000 chr6A 96.128 904 35 0 1 904 13362171 13361268 0.000000e+00 1476
21 TraesCS1D01G338000 chr6A 93.031 287 20 0 1 287 596548261 596547975 1.410000e-113 420
22 TraesCS1D01G338000 chr7A 96.013 903 36 0 1 903 730798916 730799818 0.000000e+00 1469
23 TraesCS1D01G338000 chr2D 97.455 668 17 0 237 904 537439264 537438597 0.000000e+00 1140
24 TraesCS1D01G338000 chr2A 92.661 654 42 2 255 904 4364959 4365610 0.000000e+00 937
25 TraesCS1D01G338000 chr2B 81.498 908 157 10 2 904 104021003 104020102 0.000000e+00 736


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 TraesCS1D01G338000 chr1D 427369999 427373282 3283 True 6065 6065 100.000000 1 3284 1 chr1D.!!$R3 3283
1 TraesCS1D01G338000 chr1D 427330614 427332244 1630 True 1471 1471 83.153000 955 2596 1 chr1D.!!$R2 1641
2 TraesCS1D01G338000 chr1D 427318113 427319559 1446 True 1288 1288 82.961000 915 2373 1 chr1D.!!$R1 1458
3 TraesCS1D01G338000 chr1D 427596063 427596922 859 True 1000 1000 87.674000 948 1805 1 chr1D.!!$R4 857
4 TraesCS1D01G338000 chr1A 522533681 522535977 2296 True 3851 3851 97.003000 908 3195 1 chr1A.!!$R3 2287
5 TraesCS1D01G338000 chr1A 522509460 522510855 1395 True 1343 1343 84.177000 960 2368 1 chr1A.!!$R1 1408
6 TraesCS1D01G338000 chr1A 522514959 522516329 1370 True 1258 1258 83.488000 959 2336 1 chr1A.!!$R2 1377
7 TraesCS1D01G338000 chr1B 577911497 577913147 1650 True 1589 1589 84.330000 955 2596 1 chr1B.!!$R2 1641
8 TraesCS1D01G338000 chr1B 578044016 578045436 1420 True 1391 1391 84.605000 955 2371 1 chr1B.!!$R3 1416
9 TraesCS1D01G338000 chr1B 577828382 577829257 875 True 976 976 86.765000 968 1850 1 chr1B.!!$R1 882
10 TraesCS1D01G338000 chr1B 578999827 579001936 2109 True 903 1984 88.701333 1335 3284 3 chr1B.!!$R5 1949
11 TraesCS1D01G338000 chr1B 578052220 578052756 536 True 440 440 82.202000 2519 3039 1 chr1B.!!$R4 520
12 TraesCS1D01G338000 chr6D 452110434 452111336 902 True 1552 1552 97.677000 1 904 1 chr6D.!!$R2 903
13 TraesCS1D01G338000 chr6D 70784566 70785470 904 True 1199 1199 90.608000 1 903 1 chr6D.!!$R1 902
14 TraesCS1D01G338000 chr7D 84170126 84171029 903 True 1504 1504 96.681000 1 904 1 chr7D.!!$R2 903
15 TraesCS1D01G338000 chr7D 23072265 23073144 879 True 1471 1471 96.822000 26 905 1 chr7D.!!$R1 879
16 TraesCS1D01G338000 chr5D 523186080 523187595 1515 True 1491 1491 84.676000 941 2442 1 chr5D.!!$R1 1501
17 TraesCS1D01G338000 chr5D 523313269 523314784 1515 True 1485 1485 84.630000 941 2442 1 chr5D.!!$R2 1501
18 TraesCS1D01G338000 chr6A 13361268 13362171 903 True 1476 1476 96.128000 1 904 1 chr6A.!!$R1 903
19 TraesCS1D01G338000 chr7A 730798916 730799818 902 False 1469 1469 96.013000 1 903 1 chr7A.!!$F1 902
20 TraesCS1D01G338000 chr2D 537438597 537439264 667 True 1140 1140 97.455000 237 904 1 chr2D.!!$R1 667
21 TraesCS1D01G338000 chr2A 4364959 4365610 651 False 937 937 92.661000 255 904 1 chr2A.!!$F1 649
22 TraesCS1D01G338000 chr2B 104020102 104021003 901 True 736 736 81.498000 2 904 1 chr2B.!!$R1 902

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
747 749 0.038343 GGCACATTGGTCGTTTGCAT 60.038 50.0 0.0 0.0 34.76 3.96 F
1285 1302 0.468226 AGCCACGTCAAACAAGGAGA 59.532 50.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2023 0.034337 CACAGCAGCAGCCCAAAAAT 59.966 50.0 0.0 0.0 43.56 1.82 R
3067 3335 0.104120 CGGTTGACAGACACCACTGA 59.896 55.0 0.0 0.0 40.63 3.41 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
24 25 2.132352 TGCTGTTGTTGCATGCCCA 61.132 52.632 16.68 9.27 35.31 5.36
108 109 1.160137 GGAACACTGGTGATGAGTGC 58.840 55.000 7.78 0.00 44.01 4.40
120 121 4.424626 GTGATGAGTGCTTGTTCGATCTA 58.575 43.478 0.00 0.00 0.00 1.98
136 137 3.257375 CGATCTATTGGTAACCATCCGGA 59.743 47.826 6.61 6.61 31.53 5.14
207 208 5.506151 GCTTCGTAATGATTCCATGCATGAA 60.506 40.000 28.31 18.94 32.36 2.57
271 272 7.775093 TGCAAAGCTATATGGTCTCACTAAATT 59.225 33.333 0.00 0.00 0.00 1.82
439 440 1.447838 GACGGCTCCTTTGATGCGA 60.448 57.895 0.00 0.00 0.00 5.10
519 520 1.275856 TCGGCGTGTTGGTTTATACCT 59.724 47.619 6.85 0.00 45.27 3.08
747 749 0.038343 GGCACATTGGTCGTTTGCAT 60.038 50.000 0.00 0.00 34.76 3.96
865 872 7.620880 TCTAGCAGGTGATTGTACAACTATTT 58.379 34.615 11.22 0.00 35.48 1.40
1031 1045 2.159184 TCCAAGACAAGCATAGCTCTCG 60.159 50.000 0.00 0.00 38.25 4.04
1273 1287 1.672356 GTTCATGAGGCAGCCACGT 60.672 57.895 15.80 5.87 0.00 4.49
1285 1302 0.468226 AGCCACGTCAAACAAGGAGA 59.532 50.000 0.00 0.00 0.00 3.71
1437 1457 2.389059 CTAGATGAGCATTCCACGTCG 58.611 52.381 0.00 0.00 0.00 5.12
1859 1885 7.227512 ACAATATGCTGTCATAACTCCTAAAGC 59.772 37.037 0.00 0.00 38.55 3.51
2217 2291 4.580167 TGGAAAAGGATATTCATGGAAGCG 59.420 41.667 0.00 0.00 0.00 4.68
2632 2745 2.654749 TGTGCTCATGAGGTCGTTAG 57.345 50.000 23.89 0.00 0.00 2.34
2727 2895 9.121517 GCTTGCATATAATCATTTCATGTGTAC 57.878 33.333 0.00 0.00 0.00 2.90
2760 2930 8.328758 AGTGTCATATTTTCCTGTCTATTTGGA 58.671 33.333 0.00 0.00 0.00 3.53
2977 3150 9.907229 CCTCTTTTGGAAGTTTATACCTAAGAT 57.093 33.333 0.00 0.00 34.41 2.40
3074 3342 5.932303 GTGTGTCTATATGTTTGTCAGTGGT 59.068 40.000 0.00 0.00 0.00 4.16
3076 3344 5.932303 GTGTCTATATGTTTGTCAGTGGTGT 59.068 40.000 0.00 0.00 0.00 4.16
3101 3369 4.202253 TGTCAACCGGATCAATGGAGATAG 60.202 45.833 9.46 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.060479 TCCCATATAGCACTGGAGGTT 57.940 47.619 0.00 0.00 34.24 3.50
108 109 6.202954 GGATGGTTACCAATAGATCGAACAAG 59.797 42.308 8.63 0.00 36.95 3.16
120 121 3.371595 CCTCTTTCCGGATGGTTACCAAT 60.372 47.826 8.63 0.00 36.95 3.16
136 137 4.511826 CAGAACTTTAGCACGTTCCTCTTT 59.488 41.667 0.00 0.00 40.18 2.52
439 440 1.671054 CTCCCGCCGTGTGTGATTT 60.671 57.895 0.00 0.00 0.00 2.17
905 912 9.988350 CAACATGTTTAAGACACATAATAGGTC 57.012 33.333 8.77 0.00 42.04 3.85
906 913 9.515226 ACAACATGTTTAAGACACATAATAGGT 57.485 29.630 8.77 0.00 42.04 3.08
912 919 9.332502 ACAAGTACAACATGTTTAAGACACATA 57.667 29.630 8.77 0.00 42.04 2.29
1859 1885 1.730064 ACACAAGCGGCTAAATACACG 59.270 47.619 1.35 0.00 0.00 4.49
1956 2023 0.034337 CACAGCAGCAGCCCAAAAAT 59.966 50.000 0.00 0.00 43.56 1.82
2217 2291 1.729284 TTTTGTAGTCGCCGAATCCC 58.271 50.000 0.00 0.00 0.00 3.85
2632 2745 7.148573 ACAGTATCACATCGAATGAACAGTTTC 60.149 37.037 6.81 0.00 0.00 2.78
2727 2895 7.335422 AGACAGGAAAATATGACACTGCTAAAG 59.665 37.037 0.00 0.00 0.00 1.85
2760 2930 5.009010 CCTGTAAAGTTGCAAGTCAATGACT 59.991 40.000 10.56 10.56 45.64 3.41
2842 3015 3.069079 AGAGCAATCTGAACACAGCAT 57.931 42.857 0.00 0.00 0.00 3.79
2977 3150 3.729862 TCACAATTGCTGCATGAACAA 57.270 38.095 10.01 0.00 0.00 2.83
3067 3335 0.104120 CGGTTGACAGACACCACTGA 59.896 55.000 0.00 0.00 40.63 3.41
3074 3342 2.615240 CCATTGATCCGGTTGACAGACA 60.615 50.000 0.00 0.00 0.00 3.41
3076 3344 1.905894 TCCATTGATCCGGTTGACAGA 59.094 47.619 0.00 0.00 0.00 3.41
3101 3369 5.489792 TGGGGACAATATATGCTTCTCTC 57.510 43.478 0.00 0.00 37.44 3.20
3231 3528 7.938490 ACCGGTGAAAAGAAACTATTACCTTAA 59.062 33.333 6.12 0.00 0.00 1.85
3232 3529 7.452562 ACCGGTGAAAAGAAACTATTACCTTA 58.547 34.615 6.12 0.00 0.00 2.69
3233 3530 6.301486 ACCGGTGAAAAGAAACTATTACCTT 58.699 36.000 6.12 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.