Multiple sequence alignment - TraesCS7D01G084000

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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 TraesCS7D01G084000 chr7D 100.000 2375 0 0 1 2375 51238841 51236467 0 4386
1 TraesCS7D01G084000 chr7D 93.795 2353 91 10 1 2349 79226633 79228934 0 3485
2 TraesCS7D01G084000 chr5D 95.835 2353 81 8 1 2350 384512075 384509737 0 3786
3 TraesCS7D01G084000 chr5D 94.135 2370 111 17 1 2350 29767644 29765283 0 3581
4 TraesCS7D01G084000 chr5D 93.639 1682 87 9 686 2350 140952538 140950860 0 2495
5 TraesCS7D01G084000 chr5D 95.712 1516 57 7 834 2346 401783433 401784943 0 2433
6 TraesCS7D01G084000 chr5D 95.465 838 35 3 1 836 401780346 401781182 0 1334
7 TraesCS7D01G084000 chr1D 94.898 2352 88 8 1 2349 336730165 336727843 0 3650
8 TraesCS7D01G084000 chr6D 93.993 2364 89 17 4 2349 297171452 297169124 0 3530
9 TraesCS7D01G084000 chr6D 93.554 2358 92 33 1 2349 446364371 446362065 0 3458
10 TraesCS7D01G084000 chr3A 91.953 2361 141 31 1 2349 702240713 702243036 0 3262
11 TraesCS7D01G084000 chr3A 92.087 1428 72 12 925 2349 615135803 615134414 0 1973
12 TraesCS7D01G084000 chr3A 94.927 887 43 2 1 885 615136676 615135790 0 1387
13 TraesCS7D01G084000 chr2D 94.907 1551 52 2 1 1550 239256910 239258434 0 2401
14 TraesCS7D01G084000 chr2D 92.967 1436 73 21 925 2349 645235747 645234329 0 2067
15 TraesCS7D01G084000 chr2D 94.820 888 42 4 1 885 645236620 645235734 0 1382
16 TraesCS7D01G084000 chr2D 92.469 810 45 10 1549 2349 239258381 239259183 0 1144
17 TraesCS7D01G084000 chr2A 92.503 1454 59 17 901 2349 610790142 610791550 0 2036
18 TraesCS7D01G084000 chr4D 94.112 1019 39 7 857 1855 125802883 125801866 0 1530
19 TraesCS7D01G084000 chr4A 95.147 886 42 1 1 885 129030567 129031452 0 1397
20 TraesCS7D01G084000 chr5A 92.212 886 57 4 1 885 235675138 235676012 0 1243


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 TraesCS7D01G084000 chr7D 51236467 51238841 2374 True 4386.0 4386 100.0000 1 2375 1 chr7D.!!$R1 2374
1 TraesCS7D01G084000 chr7D 79226633 79228934 2301 False 3485.0 3485 93.7950 1 2349 1 chr7D.!!$F1 2348
2 TraesCS7D01G084000 chr5D 384509737 384512075 2338 True 3786.0 3786 95.8350 1 2350 1 chr5D.!!$R3 2349
3 TraesCS7D01G084000 chr5D 29765283 29767644 2361 True 3581.0 3581 94.1350 1 2350 1 chr5D.!!$R1 2349
4 TraesCS7D01G084000 chr5D 140950860 140952538 1678 True 2495.0 2495 93.6390 686 2350 1 chr5D.!!$R2 1664
5 TraesCS7D01G084000 chr5D 401780346 401784943 4597 False 1883.5 2433 95.5885 1 2346 2 chr5D.!!$F1 2345
6 TraesCS7D01G084000 chr1D 336727843 336730165 2322 True 3650.0 3650 94.8980 1 2349 1 chr1D.!!$R1 2348
7 TraesCS7D01G084000 chr6D 297169124 297171452 2328 True 3530.0 3530 93.9930 4 2349 1 chr6D.!!$R1 2345
8 TraesCS7D01G084000 chr6D 446362065 446364371 2306 True 3458.0 3458 93.5540 1 2349 1 chr6D.!!$R2 2348
9 TraesCS7D01G084000 chr3A 702240713 702243036 2323 False 3262.0 3262 91.9530 1 2349 1 chr3A.!!$F1 2348
10 TraesCS7D01G084000 chr3A 615134414 615136676 2262 True 1680.0 1973 93.5070 1 2349 2 chr3A.!!$R1 2348
11 TraesCS7D01G084000 chr2D 239256910 239259183 2273 False 1772.5 2401 93.6880 1 2349 2 chr2D.!!$F1 2348
12 TraesCS7D01G084000 chr2D 645234329 645236620 2291 True 1724.5 2067 93.8935 1 2349 2 chr2D.!!$R1 2348
13 TraesCS7D01G084000 chr2A 610790142 610791550 1408 False 2036.0 2036 92.5030 901 2349 1 chr2A.!!$F1 1448
14 TraesCS7D01G084000 chr4D 125801866 125802883 1017 True 1530.0 1530 94.1120 857 1855 1 chr4D.!!$R1 998
15 TraesCS7D01G084000 chr4A 129030567 129031452 885 False 1397.0 1397 95.1470 1 885 1 chr4A.!!$F1 884
16 TraesCS7D01G084000 chr5A 235675138 235676012 874 False 1243.0 1243 92.2120 1 885 1 chr5A.!!$F1 884

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
784 787 1.126488 ATCGCATGTCTCCAGGTCAT 58.874 50.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 4489 2.544686 CACAAACGTCAAATCCACCGTA 59.455 45.455 0.0 0.0 32.49 4.02 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
18 19 2.903404 AGTCTCCGGTTCCAGATCC 58.097 57.895 0.00 0.00 0.00 3.36
66 67 2.127708 GGAGATGTGGTCTACCCCAAT 58.872 52.381 0.00 0.00 37.29 3.16
196 198 8.405531 TCGAACAAGATGAATCAAGAAAAAGTT 58.594 29.630 0.00 0.00 0.00 2.66
261 263 5.359576 ACATTTTTGCCACTGTGAGAACTTA 59.640 36.000 9.86 0.00 0.00 2.24
262 264 5.906113 TTTTTGCCACTGTGAGAACTTAA 57.094 34.783 9.86 0.00 0.00 1.85
295 297 2.080286 ACCGTTTGATCCTCGTTGAG 57.920 50.000 0.00 0.00 0.00 3.02
446 448 2.427506 GTTTTCGGAGCCAGTCAAGAT 58.572 47.619 0.00 0.00 0.00 2.40
568 570 2.552315 GTTTGATTCGGAGCCACTCAAA 59.448 45.455 0.00 0.00 34.43 2.69
728 731 5.420409 GGGAAGCCATCTTATATAGAACCG 58.580 45.833 0.00 0.00 36.22 4.44
784 787 1.126488 ATCGCATGTCTCCAGGTCAT 58.874 50.000 0.00 0.00 0.00 3.06
842 3099 4.754114 AGTCTGCATCTTCTTCTGTTTGAC 59.246 41.667 0.00 0.00 0.00 3.18
843 3100 4.512944 GTCTGCATCTTCTTCTGTTTGACA 59.487 41.667 0.00 0.00 0.00 3.58
1092 3349 2.158957 AGTGCTCAAGACCGAAGTCAAA 60.159 45.455 0.00 0.00 46.15 2.69
1127 3384 2.912956 TCAGGAATGTTAGGCTCCAGTT 59.087 45.455 0.00 0.00 0.00 3.16
1175 3432 1.801332 CTGAAGTGGCTGCTCATGC 59.199 57.895 0.00 0.00 40.20 4.06
1412 3669 4.999950 GTCTTTGAACCTGTGATCTGATGT 59.000 41.667 0.00 0.00 0.00 3.06
1457 3714 5.754782 TGGGAAGTTATGTCGTAGTAGGTA 58.245 41.667 0.00 0.00 0.00 3.08
1520 3836 0.109342 CCTGGGAGCACTTGTGAACT 59.891 55.000 4.79 0.00 0.00 3.01
1613 3947 3.069443 GGCTCATTTTGGAACCAGTGAAA 59.931 43.478 0.00 0.00 0.00 2.69
1614 3948 4.051237 GCTCATTTTGGAACCAGTGAAAC 58.949 43.478 0.00 0.00 0.00 2.78
1630 3977 3.753272 GTGAAACTGTGATGGCTATGTGT 59.247 43.478 0.00 0.00 0.00 3.72
1903 4273 5.011227 GGCCCAAAACAATAGTGGACTTTTA 59.989 40.000 0.00 0.00 34.05 1.52
1904 4274 6.463190 GGCCCAAAACAATAGTGGACTTTTAA 60.463 38.462 0.00 0.00 34.05 1.52
1945 4316 4.281657 AGGCTCCATTCCCAGAAAATAAC 58.718 43.478 0.00 0.00 0.00 1.89
2072 4452 4.116961 CGGGCTGATTCTATTTTACGACA 58.883 43.478 0.00 0.00 0.00 4.35
2109 4489 0.679505 TTCTACCACGTCAGCTTGCT 59.320 50.000 0.00 0.00 0.00 3.91
2180 4562 6.385649 TGGTTGTTAAATCTGTGACCTTTC 57.614 37.500 0.00 0.00 0.00 2.62
2315 4698 7.141758 ACTATGACCATTCAGTGACCAATAT 57.858 36.000 0.00 0.00 34.35 1.28
2350 4733 6.408858 AGTTGACATATTTCTTGTAGTGCG 57.591 37.500 0.00 0.00 0.00 5.34
2351 4734 5.351465 AGTTGACATATTTCTTGTAGTGCGG 59.649 40.000 0.00 0.00 0.00 5.69
2352 4735 3.621268 TGACATATTTCTTGTAGTGCGGC 59.379 43.478 0.00 0.00 0.00 6.53
2353 4736 2.943033 ACATATTTCTTGTAGTGCGGCC 59.057 45.455 0.00 0.00 0.00 6.13
2354 4737 1.647346 TATTTCTTGTAGTGCGGCCG 58.353 50.000 24.05 24.05 0.00 6.13
2355 4738 1.644786 ATTTCTTGTAGTGCGGCCGC 61.645 55.000 42.35 42.35 42.35 6.53
2356 4739 2.725203 TTTCTTGTAGTGCGGCCGCT 62.725 55.000 45.79 31.94 42.51 5.52
2357 4740 3.188786 CTTGTAGTGCGGCCGCTC 61.189 66.667 45.79 41.71 42.51 5.03
2358 4741 4.752879 TTGTAGTGCGGCCGCTCC 62.753 66.667 45.79 35.46 42.51 4.70
2371 4754 4.357947 GCTCCGACACTGGCGTGA 62.358 66.667 14.63 0.00 43.97 4.35
2372 4755 2.338620 CTCCGACACTGGCGTGAA 59.661 61.111 14.63 0.00 43.97 3.18
2373 4756 1.734477 CTCCGACACTGGCGTGAAG 60.734 63.158 14.63 8.47 43.97 3.02
2374 4757 2.029073 CCGACACTGGCGTGAAGT 59.971 61.111 14.63 0.00 43.97 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.887247 TTGCCATTCACCATCCGTTG 59.113 50.000 0.00 0.00 0.00 4.10
66 67 3.838244 AGCAGAGACAAACCTTGTGTA 57.162 42.857 0.00 0.00 45.52 2.90
196 198 4.955811 ACCAGTTCTCTGATTGTACACA 57.044 40.909 0.00 0.00 43.76 3.72
261 263 5.075493 TCAAACGGTAAGGTCTCTAGAGTT 58.925 41.667 19.21 9.22 0.00 3.01
262 264 4.660168 TCAAACGGTAAGGTCTCTAGAGT 58.340 43.478 19.21 2.76 0.00 3.24
446 448 5.363868 AGCATGGAGTGACTTACTATAGCAA 59.636 40.000 0.00 0.00 40.53 3.91
806 809 5.013547 AGATGCAGACTAGTACTTGACAGT 58.986 41.667 11.43 3.43 36.99 3.55
823 827 5.532032 TCAATGTCAAACAGAAGAAGATGCA 59.468 36.000 0.00 0.00 0.00 3.96
824 828 6.005583 TCAATGTCAAACAGAAGAAGATGC 57.994 37.500 0.00 0.00 0.00 3.91
1022 3279 3.097614 GGCTCTTCACCTTCTAGTACCA 58.902 50.000 0.00 0.00 0.00 3.25
1092 3349 2.957402 TCCTGAGGAATGTGCTTTGT 57.043 45.000 0.00 0.00 0.00 2.83
1117 3374 3.995636 TGTTCCTAGATAACTGGAGCCT 58.004 45.455 8.73 0.00 31.39 4.58
1127 3384 2.742348 TGCCGGAGTTGTTCCTAGATA 58.258 47.619 5.05 0.00 44.41 1.98
1175 3432 1.707632 CTTCTGCTCAAGGTCACGAG 58.292 55.000 0.00 0.00 0.00 4.18
1240 3497 1.065102 CGCCTTCATCTTGATTGCTGG 59.935 52.381 0.00 0.00 0.00 4.85
1242 3499 1.065199 TCCGCCTTCATCTTGATTGCT 60.065 47.619 0.00 0.00 0.00 3.91
1412 3669 4.748102 CAGCCTTCAAACTACGACAAACTA 59.252 41.667 0.00 0.00 0.00 2.24
1520 3836 1.075374 CCCAGGTTCACAAGATCCCAA 59.925 52.381 0.00 0.00 34.70 4.12
1613 3947 4.383118 GGAACTACACATAGCCATCACAGT 60.383 45.833 0.00 0.00 30.75 3.55
1614 3948 4.122776 GGAACTACACATAGCCATCACAG 58.877 47.826 0.00 0.00 30.75 3.66
1630 3977 3.825014 AGAACTACACAGCTTCGGAACTA 59.175 43.478 0.00 0.00 0.00 2.24
1822 4190 6.371595 TGGCCATTTTATTTTCTTGGATGT 57.628 33.333 0.00 0.00 0.00 3.06
2109 4489 2.544686 CACAAACGTCAAATCCACCGTA 59.455 45.455 0.00 0.00 32.49 4.02
2161 4542 6.605594 ACCAAAGAAAGGTCACAGATTTAACA 59.394 34.615 0.00 0.00 32.90 2.41
2276 4659 5.888724 TGGTCATAGTTTTCCTTTTGTGACA 59.111 36.000 0.00 0.00 37.15 3.58


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

AutoCloner maintained by Alex Coulton.