Multiple sequence alignment - TraesCS1A01G152900

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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 TraesCS1A01G152900 chr1A 100.000 6350 0 0 1 6350 265020906 265027255 0.000000e+00 11727.0
1 TraesCS1A01G152900 chr1A 93.537 5029 283 21 497 5511 541472767 541467767 0.000000e+00 7448.0
2 TraesCS1A01G152900 chr1A 97.212 538 8 2 5815 6350 108758272 108757740 0.000000e+00 904.0
3 TraesCS1A01G152900 chr1B 97.732 5819 91 15 1 5816 302205384 302211164 0.000000e+00 9976.0
4 TraesCS1A01G152900 chr1B 93.472 5147 297 22 498 5634 608471068 608465951 0.000000e+00 7607.0
5 TraesCS1A01G152900 chr1B 85.517 145 12 4 5667 5802 608465952 608465808 6.640000e-30 143.0
6 TraesCS1A01G152900 chr1D 98.214 5096 82 6 724 5816 206494935 206500024 0.000000e+00 8898.0
7 TraesCS1A01G152900 chr1D 93.524 5142 297 15 497 5634 445395270 445390161 0.000000e+00 7618.0
8 TraesCS1A01G152900 chr1D 92.363 694 26 12 1 693 206494268 206494935 0.000000e+00 963.0
9 TraesCS1A01G152900 chr2D 88.028 4260 497 13 1149 5403 361258880 361254629 0.000000e+00 5029.0
10 TraesCS1A01G152900 chr2D 88.095 84 10 0 1001 1084 361259278 361259195 4.050000e-17 100.0
11 TraesCS1A01G152900 chr2A 87.938 4253 501 11 1149 5396 486212121 486207876 0.000000e+00 5001.0
12 TraesCS1A01G152900 chr2A 98.507 536 7 1 5815 6350 656260223 656259689 0.000000e+00 944.0
13 TraesCS1A01G152900 chr2A 97.774 539 9 2 5814 6350 598969793 598969256 0.000000e+00 926.0
14 TraesCS1A01G152900 chr2A 86.207 87 12 0 998 1084 486212511 486212425 1.880000e-15 95.3
15 TraesCS1A01G152900 chr2B 87.708 4263 508 15 1149 5403 429490127 429485873 0.000000e+00 4955.0
16 TraesCS1A01G152900 chr2B 91.943 1117 78 9 4521 5634 161023907 161025014 0.000000e+00 1554.0
17 TraesCS1A01G152900 chr2B 86.331 139 13 4 5667 5802 161025013 161025148 5.130000e-31 147.0
18 TraesCS1A01G152900 chr3A 98.895 543 5 1 5808 6350 519223536 519222995 0.000000e+00 968.0
19 TraesCS1A01G152900 chr3A 97.222 540 13 1 5813 6350 575336790 575336251 0.000000e+00 913.0
20 TraesCS1A01G152900 chr5A 97.948 536 11 0 5815 6350 611122792 611123327 0.000000e+00 929.0
21 TraesCS1A01G152900 chr5A 97.403 539 12 1 5814 6350 197224389 197223851 0.000000e+00 917.0
22 TraesCS1A01G152900 chr4A 97.575 536 13 0 5815 6350 517317624 517317089 0.000000e+00 918.0
23 TraesCS1A01G152900 chr7A 97.217 539 13 1 5814 6350 83018944 83019482 0.000000e+00 911.0
24 TraesCS1A01G152900 chr4B 93.574 249 11 4 1 249 533504586 533504829 3.620000e-97 366.0


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 TraesCS1A01G152900 chr1A 265020906 265027255 6349 False 11727.00 11727 100.0000 1 6350 1 chr1A.!!$F1 6349
1 TraesCS1A01G152900 chr1A 541467767 541472767 5000 True 7448.00 7448 93.5370 497 5511 1 chr1A.!!$R2 5014
2 TraesCS1A01G152900 chr1A 108757740 108758272 532 True 904.00 904 97.2120 5815 6350 1 chr1A.!!$R1 535
3 TraesCS1A01G152900 chr1B 302205384 302211164 5780 False 9976.00 9976 97.7320 1 5816 1 chr1B.!!$F1 5815
4 TraesCS1A01G152900 chr1B 608465808 608471068 5260 True 3875.00 7607 89.4945 498 5802 2 chr1B.!!$R1 5304
5 TraesCS1A01G152900 chr1D 445390161 445395270 5109 True 7618.00 7618 93.5240 497 5634 1 chr1D.!!$R1 5137
6 TraesCS1A01G152900 chr1D 206494268 206500024 5756 False 4930.50 8898 95.2885 1 5816 2 chr1D.!!$F1 5815
7 TraesCS1A01G152900 chr2D 361254629 361259278 4649 True 2564.50 5029 88.0615 1001 5403 2 chr2D.!!$R1 4402
8 TraesCS1A01G152900 chr2A 486207876 486212511 4635 True 2548.15 5001 87.0725 998 5396 2 chr2A.!!$R3 4398
9 TraesCS1A01G152900 chr2A 656259689 656260223 534 True 944.00 944 98.5070 5815 6350 1 chr2A.!!$R2 535
10 TraesCS1A01G152900 chr2A 598969256 598969793 537 True 926.00 926 97.7740 5814 6350 1 chr2A.!!$R1 536
11 TraesCS1A01G152900 chr2B 429485873 429490127 4254 True 4955.00 4955 87.7080 1149 5403 1 chr2B.!!$R1 4254
12 TraesCS1A01G152900 chr2B 161023907 161025148 1241 False 850.50 1554 89.1370 4521 5802 2 chr2B.!!$F1 1281
13 TraesCS1A01G152900 chr3A 519222995 519223536 541 True 968.00 968 98.8950 5808 6350 1 chr3A.!!$R1 542
14 TraesCS1A01G152900 chr3A 575336251 575336790 539 True 913.00 913 97.2220 5813 6350 1 chr3A.!!$R2 537
15 TraesCS1A01G152900 chr5A 611122792 611123327 535 False 929.00 929 97.9480 5815 6350 1 chr5A.!!$F1 535
16 TraesCS1A01G152900 chr5A 197223851 197224389 538 True 917.00 917 97.4030 5814 6350 1 chr5A.!!$R1 536
17 TraesCS1A01G152900 chr4A 517317089 517317624 535 True 918.00 918 97.5750 5815 6350 1 chr4A.!!$R1 535
18 TraesCS1A01G152900 chr7A 83018944 83019482 538 False 911.00 911 97.2170 5814 6350 1 chr7A.!!$F1 536

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
387 390 3.391296 TCCTCACTGTTAACTTTGAGCCT 59.609 43.478 22.14 0.0 35.18 4.58 F
462 465 3.632643 TGCTGAACCTATGCTGAATCA 57.367 42.857 0.00 0.0 0.00 2.57 F
1321 1600 0.179073 CGCAGTATCCAGGGGAGTTG 60.179 60.000 0.00 0.0 34.05 3.16 F
2829 3108 5.412594 AGAGCTCGATTTTAATGCAGTTCAA 59.587 36.000 8.37 0.0 0.00 2.69 F
2877 3156 5.489792 AATTATATCGTGTGATCAGGGCT 57.510 39.130 0.00 0.0 35.99 5.19 F
4510 4789 1.434555 TACGCCCAAATTCACAGACG 58.565 50.000 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1321 1600 6.070881 ACAGATGCCTCTATCAATGGACTATC 60.071 42.308 0.0 0.0 0.00 2.08 R
1348 1627 8.599624 ATCCTTGAAACTAATTCCATGTCATT 57.400 30.769 0.0 0.0 37.22 2.57 R
2877 3156 0.776810 TCTCCCCCATTTCTGCACAA 59.223 50.000 0.0 0.0 0.00 3.33 R
4459 4738 1.318576 CATAAAGGGGATGTTCGGCC 58.681 55.000 0.0 0.0 0.00 6.13 R
4669 4948 1.762708 AATGCGATCCCACGGAATTT 58.237 45.000 0.0 0.0 37.15 1.82 R
5495 5779 2.066262 CGCCATTTACAGAACGAGTGT 58.934 47.619 0.0 0.0 0.00 3.55 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
66 69 5.695851 ATAGAAAGACTTTGCACAGTTGG 57.304 39.130 7.01 0.00 0.00 3.77
183 186 9.277783 GAAAGATCCAGTAAATGCTACATGTAT 57.722 33.333 5.91 0.00 0.00 2.29
185 188 7.390027 AGATCCAGTAAATGCTACATGTATCC 58.610 38.462 5.91 1.50 0.00 2.59
186 189 6.493189 TCCAGTAAATGCTACATGTATCCA 57.507 37.500 5.91 7.37 0.00 3.41
187 190 6.524734 TCCAGTAAATGCTACATGTATCCAG 58.475 40.000 5.91 0.00 0.00 3.86
263 266 7.523293 TTGAATCTTTTGCTAAACAGATCCA 57.477 32.000 0.00 0.00 0.00 3.41
264 267 7.523293 TGAATCTTTTGCTAAACAGATCCAA 57.477 32.000 0.00 0.00 0.00 3.53
265 268 7.950512 TGAATCTTTTGCTAAACAGATCCAAA 58.049 30.769 0.00 0.00 0.00 3.28
266 269 8.587608 TGAATCTTTTGCTAAACAGATCCAAAT 58.412 29.630 0.00 0.00 0.00 2.32
267 270 9.428097 GAATCTTTTGCTAAACAGATCCAAATT 57.572 29.630 0.00 0.00 0.00 1.82
268 271 9.783081 AATCTTTTGCTAAACAGATCCAAATTT 57.217 25.926 0.00 0.00 0.00 1.82
269 272 9.783081 ATCTTTTGCTAAACAGATCCAAATTTT 57.217 25.926 0.00 0.00 0.00 1.82
334 337 6.919721 TCTCGGAAAATTTGACCTTATTTGG 58.080 36.000 11.26 0.00 0.00 3.28
354 357 7.745620 TTTGGACTAAAGGATTGAGAGAAAC 57.254 36.000 0.00 0.00 0.00 2.78
387 390 3.391296 TCCTCACTGTTAACTTTGAGCCT 59.609 43.478 22.14 0.00 35.18 4.58
449 452 4.048504 GTTGGTAATGTGGTTTGCTGAAC 58.951 43.478 0.00 0.00 37.53 3.18
460 463 4.708726 GTTTGCTGAACCTATGCTGAAT 57.291 40.909 0.00 0.00 31.85 2.57
461 464 4.666237 GTTTGCTGAACCTATGCTGAATC 58.334 43.478 0.00 0.00 31.85 2.52
462 465 3.632643 TGCTGAACCTATGCTGAATCA 57.367 42.857 0.00 0.00 0.00 2.57
474 477 5.541953 ATGCTGAATCACTCATGTAGCTA 57.458 39.130 0.00 0.00 32.14 3.32
475 478 5.541953 TGCTGAATCACTCATGTAGCTAT 57.458 39.130 0.00 0.00 32.14 2.97
491 494 7.603180 TGTAGCTATGGTTGAACTATCTGAT 57.397 36.000 0.00 0.00 0.00 2.90
725 735 7.397221 TCATGTCCTGAGAAATATTTGTGACT 58.603 34.615 5.17 0.00 0.00 3.41
772 782 8.599624 ATTTCTATCCTGGAACAATGAACAAT 57.400 30.769 0.00 0.00 38.70 2.71
796 806 7.194112 TCATATTGACCTTGGTCTTGACATA 57.806 36.000 19.11 9.05 0.00 2.29
1112 1379 9.295825 TCAACTAAATATGCTTCTCTTTTTGGA 57.704 29.630 0.00 0.00 0.00 3.53
1138 1405 8.674263 ATGTAATCATTCTCATGTTCTTCTCC 57.326 34.615 0.00 0.00 0.00 3.71
1321 1600 0.179073 CGCAGTATCCAGGGGAGTTG 60.179 60.000 0.00 0.00 34.05 3.16
2829 3108 5.412594 AGAGCTCGATTTTAATGCAGTTCAA 59.587 36.000 8.37 0.00 0.00 2.69
2877 3156 5.489792 AATTATATCGTGTGATCAGGGCT 57.510 39.130 0.00 0.00 35.99 5.19
3570 3849 6.359804 ACCGATAAAGGGTTTACTTAATCCC 58.640 40.000 6.95 6.95 42.83 3.85
4459 4738 6.324561 AGCTTGAGAAAGAAGGCTTAAAAG 57.675 37.500 0.00 0.00 32.98 2.27
4510 4789 1.434555 TACGCCCAAATTCACAGACG 58.565 50.000 0.00 0.00 0.00 4.18
4669 4948 4.471025 TGAACCAGAAGGCTGATCTAATGA 59.529 41.667 0.00 0.00 45.17 2.57
4976 5255 0.624500 ATCAGTGTGGCCATAGGGGT 60.625 55.000 9.72 0.00 39.65 4.95
5495 5779 3.562141 GCTGCTCTCGTCTACATCTAAGA 59.438 47.826 0.00 0.00 0.00 2.10
5501 5785 4.804665 TCTCGTCTACATCTAAGACACTCG 59.195 45.833 4.32 0.00 42.91 4.18
5606 5890 1.498865 AACACCGCTTCGTGCTTGAG 61.499 55.000 2.29 0.00 40.11 3.02
5754 6040 6.508030 TTGGTGCTAGGGATTGTATTATGA 57.492 37.500 0.00 0.00 0.00 2.15
5758 6044 7.678171 TGGTGCTAGGGATTGTATTATGATCTA 59.322 37.037 0.00 0.00 0.00 1.98
5759 6045 8.540388 GGTGCTAGGGATTGTATTATGATCTAA 58.460 37.037 0.00 0.00 0.00 2.10
5781 6076 8.350722 TCTAATATTCATGAGGTCTCGTACAAC 58.649 37.037 0.00 0.00 0.00 3.32
6082 6377 1.358152 CTACCACAAACCCCTCCTCA 58.642 55.000 0.00 0.00 0.00 3.86
6252 6556 1.152902 GCTGCATATGGGTGGCTCA 60.153 57.895 4.56 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.300681 AGAACAGAAATCAATTCATGGACTAAA 57.699 29.630 0.00 0.00 40.72 1.85
66 69 9.899226 AGAAAGACATTTGAATTACTAGCAAAC 57.101 29.630 0.00 0.00 34.72 2.93
292 295 5.185249 TCCGAGAATACTACTGGGAATATGC 59.815 44.000 0.00 0.00 38.82 3.14
296 299 6.555463 TTTTCCGAGAATACTACTGGGAAT 57.445 37.500 10.98 0.00 46.04 3.01
313 316 6.687604 AGTCCAAATAAGGTCAAATTTTCCG 58.312 36.000 0.00 0.00 0.00 4.30
330 333 7.445402 CAGTTTCTCTCAATCCTTTAGTCCAAA 59.555 37.037 0.00 0.00 0.00 3.28
334 337 5.352846 GCCAGTTTCTCTCAATCCTTTAGTC 59.647 44.000 0.00 0.00 0.00 2.59
387 390 1.631405 CAGGGTGAAAATTGAGGGCA 58.369 50.000 0.00 0.00 0.00 5.36
449 452 4.689812 GCTACATGAGTGATTCAGCATAGG 59.310 45.833 0.00 0.00 39.68 2.57
451 454 5.541953 AGCTACATGAGTGATTCAGCATA 57.458 39.130 0.00 0.00 39.68 3.14
452 455 4.418973 AGCTACATGAGTGATTCAGCAT 57.581 40.909 0.00 0.00 39.68 3.79
453 456 3.900966 AGCTACATGAGTGATTCAGCA 57.099 42.857 0.00 0.00 39.68 4.41
454 457 4.689812 CCATAGCTACATGAGTGATTCAGC 59.310 45.833 0.00 0.00 39.68 4.26
455 458 5.851720 ACCATAGCTACATGAGTGATTCAG 58.148 41.667 0.00 0.00 39.68 3.02
456 459 5.876651 ACCATAGCTACATGAGTGATTCA 57.123 39.130 0.00 0.00 40.85 2.57
457 460 6.283694 TCAACCATAGCTACATGAGTGATTC 58.716 40.000 0.00 0.00 0.00 2.52
458 461 6.239217 TCAACCATAGCTACATGAGTGATT 57.761 37.500 0.00 0.00 0.00 2.57
459 462 5.876651 TCAACCATAGCTACATGAGTGAT 57.123 39.130 0.00 0.00 0.00 3.06
460 463 5.187772 AGTTCAACCATAGCTACATGAGTGA 59.812 40.000 0.00 0.00 0.00 3.41
461 464 5.423015 AGTTCAACCATAGCTACATGAGTG 58.577 41.667 0.00 0.00 0.00 3.51
462 465 5.683876 AGTTCAACCATAGCTACATGAGT 57.316 39.130 0.00 0.00 0.00 3.41
474 477 8.812513 TTTGAATGATCAGATAGTTCAACCAT 57.187 30.769 17.04 0.00 38.19 3.55
475 478 8.634335 TTTTGAATGATCAGATAGTTCAACCA 57.366 30.769 17.04 7.80 38.19 3.67
503 506 4.905429 TCAAATGCAAGGTAGTTCAGCTA 58.095 39.130 0.00 0.00 33.59 3.32
506 509 6.037610 GGTCTATCAAATGCAAGGTAGTTCAG 59.962 42.308 0.00 0.00 0.00 3.02
514 517 4.162040 AGAGGGTCTATCAAATGCAAGG 57.838 45.455 0.00 0.00 0.00 3.61
668 678 2.543653 GGCTGTGCAACGAGAAACAAAT 60.544 45.455 0.00 0.00 42.39 2.32
725 735 7.915293 AATCACGTTGGATGAAAATACAGTA 57.085 32.000 0.00 0.00 0.00 2.74
739 749 4.137116 TCCAGGATAGAAATCACGTTGG 57.863 45.455 0.00 0.00 33.41 3.77
772 782 5.497464 TGTCAAGACCAAGGTCAATATGA 57.503 39.130 20.52 14.91 46.76 2.15
1138 1405 5.128008 TCCTTTGTTTTCCCTGGTACAAAAG 59.872 40.000 11.89 8.20 39.26 2.27
1321 1600 6.070881 ACAGATGCCTCTATCAATGGACTATC 60.071 42.308 0.00 0.00 0.00 2.08
1348 1627 8.599624 ATCCTTGAAACTAATTCCATGTCATT 57.400 30.769 0.00 0.00 37.22 2.57
2829 3108 1.406065 CCATCTCAGCATCTCCCCGT 61.406 60.000 0.00 0.00 0.00 5.28
2877 3156 0.776810 TCTCCCCCATTTCTGCACAA 59.223 50.000 0.00 0.00 0.00 3.33
4459 4738 1.318576 CATAAAGGGGATGTTCGGCC 58.681 55.000 0.00 0.00 0.00 6.13
4510 4789 4.429108 GAGGATGCAGACAGTAGTTTCTC 58.571 47.826 0.00 0.00 0.00 2.87
4628 4907 3.251479 TCAAGAGATCCGACATTGTGG 57.749 47.619 0.00 0.00 0.00 4.17
4669 4948 1.762708 AATGCGATCCCACGGAATTT 58.237 45.000 0.00 0.00 37.15 1.82
5495 5779 2.066262 CGCCATTTACAGAACGAGTGT 58.934 47.619 0.00 0.00 0.00 3.55
5501 5785 4.251268 AGTAAGGACGCCATTTACAGAAC 58.749 43.478 9.20 0.00 31.38 3.01
5606 5890 8.638685 ATTATCACTGCATCAAATAACAAAGC 57.361 30.769 0.00 0.00 0.00 3.51
5754 6040 8.637196 TGTACGAGACCTCATGAATATTAGAT 57.363 34.615 0.00 0.00 0.00 1.98
5758 6044 6.757010 GTGTTGTACGAGACCTCATGAATATT 59.243 38.462 0.00 0.00 0.00 1.28
5759 6045 6.096987 AGTGTTGTACGAGACCTCATGAATAT 59.903 38.462 6.77 0.00 0.00 1.28
5781 6076 6.969366 TCCGAATATTTATTTCATGGCAGTG 58.031 36.000 0.00 0.00 0.00 3.66
5820 6115 6.823689 TCACCAACTCAGATTTTTATAGGAGC 59.176 38.462 0.00 0.00 0.00 4.70
6252 6556 2.358003 GCCAGTGCAGAACGAGCT 60.358 61.111 0.00 0.00 37.47 4.09


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

AutoCloner maintained by Alex Coulton.