Multiple sequence alignment - TraesCS1D01G377900

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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 TraesCS1D01G377900 chr1D 100.000 3998 0 0 1 3998 454171660 454167663 0.000000e+00 7384.0
1 TraesCS1D01G377900 chr1D 95.122 82 4 0 3462 3543 454168090 454168009 3.240000e-26 130.0
2 TraesCS1D01G377900 chr1D 95.122 82 4 0 3571 3652 454168199 454168118 3.240000e-26 130.0
3 TraesCS1D01G377900 chr1D 97.297 37 1 0 2832 2868 454168758 454168722 3.340000e-06 63.9
4 TraesCS1D01G377900 chr1B 96.728 3178 70 10 1 3154 624667606 624664439 0.000000e+00 5262.0
5 TraesCS1D01G377900 chr1B 99.647 851 2 1 3148 3998 624664407 624663558 0.000000e+00 1554.0
6 TraesCS1D01G377900 chr1B 95.122 82 4 0 3462 3543 624663985 624663904 3.240000e-26 130.0
7 TraesCS1D01G377900 chr1B 95.122 82 4 0 3571 3652 624664094 624664013 3.240000e-26 130.0
8 TraesCS1D01G377900 chr1B 97.297 37 1 0 2832 2868 624664693 624664657 3.340000e-06 63.9
9 TraesCS1D01G377900 chr2B 89.888 1790 125 30 1080 2839 554720553 554722316 0.000000e+00 2252.0
10 TraesCS1D01G377900 chr2B 93.182 528 32 4 1 526 5440964 5441489 0.000000e+00 773.0
11 TraesCS1D01G377900 chr2B 92.642 530 35 4 1 527 768457922 768457394 0.000000e+00 760.0
12 TraesCS1D01G377900 chr2B 92.235 528 37 4 1 526 5017456 5017981 0.000000e+00 745.0
13 TraesCS1D01G377900 chr2B 92.677 396 23 3 3154 3543 42146071 42146466 2.090000e-157 566.0
14 TraesCS1D01G377900 chr2B 87.970 266 23 6 3732 3996 42146483 42146740 5.020000e-79 305.0
15 TraesCS1D01G377900 chr2B 89.627 241 18 6 2872 3108 42145694 42145931 2.340000e-77 300.0
16 TraesCS1D01G377900 chr2B 93.137 102 7 0 3568 3669 42146382 42146483 2.490000e-32 150.0
17 TraesCS1D01G377900 chr4A 86.460 1226 109 21 1623 2806 48299315 48300525 0.000000e+00 1291.0
18 TraesCS1D01G377900 chr4A 93.573 529 32 2 2 528 618919724 618919196 0.000000e+00 787.0
19 TraesCS1D01G377900 chr4D 85.915 994 100 11 1623 2579 415294103 415293113 0.000000e+00 1024.0
20 TraesCS1D01G377900 chr4D 94.737 228 10 2 2578 2805 415293009 415292784 1.770000e-93 353.0
21 TraesCS1D01G377900 chr6B 88.776 686 59 7 2157 2839 462685559 462684889 0.000000e+00 824.0
22 TraesCS1D01G377900 chr6B 94.180 378 17 4 1557 1931 462685934 462685559 4.480000e-159 571.0
23 TraesCS1D01G377900 chr6B 80.529 529 62 20 630 1152 252085509 252085016 6.310000e-98 368.0
24 TraesCS1D01G377900 chr6B 84.615 325 42 7 2298 2617 192915669 192915990 2.320000e-82 316.0
25 TraesCS1D01G377900 chr2D 94.151 530 28 3 1 527 199131883 199131354 0.000000e+00 804.0
26 TraesCS1D01G377900 chr2D 93.639 393 18 3 3154 3543 26767403 26767791 7.450000e-162 580.0
27 TraesCS1D01G377900 chr2D 88.346 266 25 4 3732 3996 26767808 26768068 8.340000e-82 315.0
28 TraesCS1D01G377900 chr2D 89.627 241 18 6 2872 3108 26767026 26767263 2.340000e-77 300.0
29 TraesCS1D01G377900 chr2D 92.157 102 8 0 3568 3669 26767707 26767808 1.160000e-30 145.0
30 TraesCS1D01G377900 chrUn 93.409 531 31 4 1 528 26663293 26663822 0.000000e+00 784.0
31 TraesCS1D01G377900 chr7B 92.857 532 32 6 1 529 746356056 746355528 0.000000e+00 767.0
32 TraesCS1D01G377900 chr7B 87.179 312 27 8 3691 3996 21254307 21254611 3.830000e-90 342.0
33 TraesCS1D01G377900 chr7B 95.918 49 2 0 3645 3693 21254200 21254248 3.310000e-11 80.5
34 TraesCS1D01G377900 chr3B 92.600 527 35 4 1 524 126398130 126398655 0.000000e+00 754.0
35 TraesCS1D01G377900 chr4B 91.031 446 35 5 2361 2805 512164841 512164400 7.400000e-167 597.0
36 TraesCS1D01G377900 chr4B 86.875 480 52 6 1624 2093 512165576 512165098 9.840000e-146 527.0
37 TraesCS1D01G377900 chr2A 93.606 391 20 3 3154 3543 29098446 29098832 2.680000e-161 579.0
38 TraesCS1D01G377900 chr2A 87.784 352 35 7 2270 2617 32807487 32807140 4.810000e-109 405.0
39 TraesCS1D01G377900 chr2A 90.456 241 16 6 2872 3108 29098069 29098306 1.080000e-80 311.0
40 TraesCS1D01G377900 chr2A 87.970 266 26 4 3732 3996 29098849 29099109 3.880000e-80 309.0
41 TraesCS1D01G377900 chr5A 83.271 538 57 6 3434 3969 609634784 609634278 7.830000e-127 464.0
42 TraesCS1D01G377900 chr5A 87.749 351 34 8 2272 2617 362401251 362400905 6.220000e-108 401.0
43 TraesCS1D01G377900 chr5A 87.857 280 27 2 3154 3433 609635125 609634853 4.980000e-84 322.0
44 TraesCS1D01G377900 chr5A 85.892 241 26 6 2872 3108 609635499 609635263 2.390000e-62 250.0
45 TraesCS1D01G377900 chr7D 79.967 599 67 20 2028 2596 583281596 583281021 3.750000e-105 392.0
46 TraesCS1D01G377900 chr1A 90.717 237 16 5 2872 3104 537063252 537063018 1.080000e-80 311.0
47 TraesCS1D01G377900 chr1A 94.545 165 8 1 3154 3318 537062792 537062629 1.840000e-63 254.0
48 TraesCS1D01G377900 chr1A 97.222 36 1 0 2832 2867 537063223 537063188 1.200000e-05 62.1
49 TraesCS1D01G377900 chr3A 90.254 236 17 5 2873 3104 108028634 108028867 1.810000e-78 303.0
50 TraesCS1D01G377900 chr3A 89.212 241 19 6 2872 3108 611184864 611185101 1.090000e-75 294.0
51 TraesCS1D01G377900 chr3A 93.939 165 9 1 3154 3318 108029096 108029259 8.580000e-62 248.0
52 TraesCS1D01G377900 chr3A 84.848 99 9 1 3154 3252 611185397 611185489 1.180000e-15 95.3
53 TraesCS1D01G377900 chr3A 97.222 36 1 0 2832 2867 108028662 108028697 1.200000e-05 62.1
54 TraesCS1D01G377900 chr3A 100.000 30 0 0 1080 1109 703420483 703420512 5.580000e-04 56.5
55 TraesCS1D01G377900 chr5B 92.000 50 2 2 2872 2921 651227674 651227627 7.170000e-08 69.4


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 TraesCS1D01G377900 chr1D 454167663 454171660 3997 True 1926.975000 7384 96.885250 1 3998 4 chr1D.!!$R1 3997
1 TraesCS1D01G377900 chr1B 624663558 624667606 4048 True 1427.980000 5262 96.783200 1 3998 5 chr1B.!!$R1 3997
2 TraesCS1D01G377900 chr2B 554720553 554722316 1763 False 2252.000000 2252 89.888000 1080 2839 1 chr2B.!!$F3 1759
3 TraesCS1D01G377900 chr2B 5440964 5441489 525 False 773.000000 773 93.182000 1 526 1 chr2B.!!$F2 525
4 TraesCS1D01G377900 chr2B 768457394 768457922 528 True 760.000000 760 92.642000 1 527 1 chr2B.!!$R1 526
5 TraesCS1D01G377900 chr2B 5017456 5017981 525 False 745.000000 745 92.235000 1 526 1 chr2B.!!$F1 525
6 TraesCS1D01G377900 chr2B 42145694 42146740 1046 False 330.250000 566 90.852750 2872 3996 4 chr2B.!!$F4 1124
7 TraesCS1D01G377900 chr4A 48299315 48300525 1210 False 1291.000000 1291 86.460000 1623 2806 1 chr4A.!!$F1 1183
8 TraesCS1D01G377900 chr4A 618919196 618919724 528 True 787.000000 787 93.573000 2 528 1 chr4A.!!$R1 526
9 TraesCS1D01G377900 chr4D 415292784 415294103 1319 True 688.500000 1024 90.326000 1623 2805 2 chr4D.!!$R1 1182
10 TraesCS1D01G377900 chr6B 462684889 462685934 1045 True 697.500000 824 91.478000 1557 2839 2 chr6B.!!$R2 1282
11 TraesCS1D01G377900 chr2D 199131354 199131883 529 True 804.000000 804 94.151000 1 527 1 chr2D.!!$R1 526
12 TraesCS1D01G377900 chr2D 26767026 26768068 1042 False 335.000000 580 90.942250 2872 3996 4 chr2D.!!$F1 1124
13 TraesCS1D01G377900 chrUn 26663293 26663822 529 False 784.000000 784 93.409000 1 528 1 chrUn.!!$F1 527
14 TraesCS1D01G377900 chr7B 746355528 746356056 528 True 767.000000 767 92.857000 1 529 1 chr7B.!!$R1 528
15 TraesCS1D01G377900 chr3B 126398130 126398655 525 False 754.000000 754 92.600000 1 524 1 chr3B.!!$F1 523
16 TraesCS1D01G377900 chr4B 512164400 512165576 1176 True 562.000000 597 88.953000 1624 2805 2 chr4B.!!$R1 1181
17 TraesCS1D01G377900 chr2A 29098069 29099109 1040 False 399.666667 579 90.677333 2872 3996 3 chr2A.!!$F1 1124
18 TraesCS1D01G377900 chr5A 609634278 609635499 1221 True 345.333333 464 85.673333 2872 3969 3 chr5A.!!$R2 1097
19 TraesCS1D01G377900 chr7D 583281021 583281596 575 True 392.000000 392 79.967000 2028 2596 1 chr7D.!!$R1 568
20 TraesCS1D01G377900 chr1A 537062629 537063252 623 True 209.033333 311 94.161333 2832 3318 3 chr1A.!!$R1 486
21 TraesCS1D01G377900 chr3A 108028634 108029259 625 False 204.366667 303 93.805000 2832 3318 3 chr3A.!!$F2 486

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
329 331 0.396435 TTTGAAGGCTCGGAGCTTGA 59.604 50.000 27.47 12.45 41.99 3.02 F
931 943 1.026718 GCAATCTGGAGAACCGGTGG 61.027 60.000 8.52 0.00 42.77 4.61 F
1357 1369 1.228737 GGGAGAGGGAGAGGGATCG 60.229 68.421 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1737 0.372334 CTCGCGGAAAATAACACCGG 59.628 55.000 6.13 0.00 45.66 5.28 R
1807 1848 0.647410 CGGTCTTTGCATAGTCAGCG 59.353 55.000 4.00 3.88 33.85 5.18 R
2997 3228 2.633967 TCAGGCAAATGGAAGCATGTTT 59.366 40.909 0.00 0.00 42.56 2.83 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
142 143 3.612795 TGGGATCGGGAGAAATCTCTA 57.387 47.619 10.09 0.00 45.37 2.43
314 316 3.342377 TGATTGGTATCGGTGCTTTGA 57.658 42.857 0.00 0.00 33.23 2.69
329 331 0.396435 TTTGAAGGCTCGGAGCTTGA 59.604 50.000 27.47 12.45 41.99 3.02
335 337 2.586245 CTCGGAGCTTGATGGGCA 59.414 61.111 0.00 0.00 0.00 5.36
388 391 2.427232 TCGTTTCTTTGTCGATCCGT 57.573 45.000 0.00 0.00 0.00 4.69
456 460 2.031012 TGACTGTGCTGCTTCCGG 59.969 61.111 0.00 0.00 0.00 5.14
482 487 4.100035 AGCACCTATCATTGAATGTCTCGA 59.900 41.667 4.93 0.00 0.00 4.04
490 495 7.797038 ATCATTGAATGTCTCGATTGATTGA 57.203 32.000 4.93 0.00 0.00 2.57
567 573 2.095919 AGCCACGTCGATTTTACTTTGC 60.096 45.455 0.00 0.00 0.00 3.68
931 943 1.026718 GCAATCTGGAGAACCGGTGG 61.027 60.000 8.52 0.00 42.77 4.61
1001 1013 2.264794 GACGGCGTTGACCAGGAT 59.735 61.111 16.19 0.00 0.00 3.24
1009 1021 3.950794 TTGACCAGGATGCCGTCGC 62.951 63.158 0.00 0.00 31.08 5.19
1051 1063 1.754226 GAGAGGAGCTCGTTGAGGATT 59.246 52.381 10.79 0.00 35.36 3.01
1272 1284 4.366684 GCCAGTTGTGGGGGAGGG 62.367 72.222 0.00 0.00 45.17 4.30
1353 1365 1.541672 GAGAGGGAGAGGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
1357 1369 1.228737 GGGAGAGGGAGAGGGATCG 60.229 68.421 0.00 0.00 0.00 3.69
1513 1549 2.053244 AGCCATCCAAGGATAGACTGG 58.947 52.381 0.40 1.34 32.93 4.00
1518 1554 5.221925 GCCATCCAAGGATAGACTGGATTTA 60.222 44.000 9.35 0.00 37.28 1.40
1525 1561 6.739331 AGGATAGACTGGATTTAGGTCTTG 57.261 41.667 0.00 0.00 40.29 3.02
1699 1737 2.596904 TGCACGACTCCTATTAAGGC 57.403 50.000 0.00 0.00 43.31 4.35
1807 1848 3.936453 TCCAATATGCAAACTACACGACC 59.064 43.478 0.00 0.00 0.00 4.79
1830 1871 3.334691 CTGACTATGCAAAGACCGGAAA 58.665 45.455 9.46 0.00 0.00 3.13
1922 1966 7.066163 CCTCTCAAATGTATGTACAAATGCTCA 59.934 37.037 0.00 0.00 39.99 4.26
2487 2610 2.029728 CAGAGCGACGGAAACATGAATC 59.970 50.000 0.00 0.00 0.00 2.52
2997 3228 3.793797 TCGATCGATTTCAGGTGCTAA 57.206 42.857 15.15 0.00 0.00 3.09
3983 4487 2.049767 TGACCGTCTAGATGGCGCA 61.050 57.895 27.87 22.68 43.31 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
314 316 1.222936 CCATCAAGCTCCGAGCCTT 59.777 57.895 16.99 7.86 43.77 4.35
329 331 2.597340 CCACCGGAGATTGCCCAT 59.403 61.111 9.46 0.00 0.00 4.00
335 337 2.671070 CTGCACCCACCGGAGATT 59.329 61.111 9.46 0.00 0.00 2.40
388 391 0.026544 GAAACAAACGCCGACAACGA 59.973 50.000 0.00 0.00 42.66 3.85
434 438 0.667487 GAAGCAGCACAGTCACGCTA 60.667 55.000 0.00 0.00 36.50 4.26
456 460 2.954318 ACATTCAATGATAGGTGCTGGC 59.046 45.455 3.79 0.00 0.00 4.85
482 487 7.978975 CCCCGTTTTGTATACAAATCAATCAAT 59.021 33.333 27.14 0.00 44.30 2.57
490 495 6.457355 GGTTTTCCCCGTTTTGTATACAAAT 58.543 36.000 27.14 0.00 44.30 2.32
567 573 1.554392 CTCGCTCTCCAATCAACGAG 58.446 55.000 0.00 0.00 40.70 4.18
1009 1021 0.596083 GACGGCATGACGAGGATCTG 60.596 60.000 31.27 0.00 37.61 2.90
1042 1054 1.657822 GAGAAGCGGGAATCCTCAAC 58.342 55.000 0.00 0.00 0.00 3.18
1069 1081 4.778415 CACCTCGCTCCGTCGTGG 62.778 72.222 8.01 8.01 45.48 4.94
1353 1365 2.224305 CCACAACCCTATCTTCCCGATC 60.224 54.545 0.00 0.00 33.48 3.69
1357 1369 3.555966 CATTCCACAACCCTATCTTCCC 58.444 50.000 0.00 0.00 0.00 3.97
1513 1549 2.239907 AGCAGGGGACAAGACCTAAATC 59.760 50.000 0.00 0.00 34.71 2.17
1518 1554 0.548682 ATCAGCAGGGGACAAGACCT 60.549 55.000 0.00 0.00 37.66 3.85
1699 1737 0.372334 CTCGCGGAAAATAACACCGG 59.628 55.000 6.13 0.00 45.66 5.28
1807 1848 0.647410 CGGTCTTTGCATAGTCAGCG 59.353 55.000 4.00 3.88 33.85 5.18
1830 1871 1.074566 CTGAAGCCTCAAGGACCCTTT 59.925 52.381 0.00 0.00 37.39 3.11
2511 2634 4.548451 AACCTGCAACTACTACCCTTAC 57.452 45.455 0.00 0.00 0.00 2.34
2997 3228 2.633967 TCAGGCAAATGGAAGCATGTTT 59.366 40.909 0.00 0.00 42.56 2.83


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

AutoCloner maintained by Alex Coulton.