Multiple sequence alignment - TraesCS7A01G239900

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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 TraesCS7A01G239900 chr7A 100.000 3986 0 0 1 3986 214436506 214432521 0.000000e+00 7361
1 TraesCS7A01G239900 chr7B 96.707 3492 79 10 1 3487 165533266 165529806 0.000000e+00 5779
2 TraesCS7A01G239900 chr7B 95.355 409 15 3 3578 3986 165529630 165529226 0.000000e+00 647
3 TraesCS7A01G239900 chr7B 92.568 148 8 2 3448 3594 165529791 165529646 4.040000e-50 209
4 TraesCS7A01G239900 chr7D 96.404 3476 103 9 18 3487 202059485 202056026 0.000000e+00 5707
5 TraesCS7A01G239900 chr7D 92.844 545 31 5 3449 3986 202055985 202055442 0.000000e+00 784
6 TraesCS7A01G239900 chr7D 94.425 287 16 0 3700 3986 201979084 201978798 3.660000e-120 442
7 TraesCS7A01G239900 chr6D 76.006 1863 390 46 1138 2979 375028608 375030434 0.000000e+00 911
8 TraesCS7A01G239900 chr6B 75.612 1919 411 45 1082 2979 561701016 561702898 0.000000e+00 898


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 TraesCS7A01G239900 chr7A 214432521 214436506 3985 True 7361.000000 7361 100.000000 1 3986 1 chr7A.!!$R1 3985
1 TraesCS7A01G239900 chr7B 165529226 165533266 4040 True 2211.666667 5779 94.876667 1 3986 3 chr7B.!!$R1 3985
2 TraesCS7A01G239900 chr7D 202055442 202059485 4043 True 3245.500000 5707 94.624000 18 3986 2 chr7D.!!$R2 3968
3 TraesCS7A01G239900 chr6D 375028608 375030434 1826 False 911.000000 911 76.006000 1138 2979 1 chr6D.!!$F1 1841
4 TraesCS7A01G239900 chr6B 561701016 561702898 1882 False 898.000000 898 75.612000 1082 2979 1 chr6B.!!$F1 1897

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
705 711 0.660488 TGGTTGCACTGCGTTAGTTG 59.340 50.0 0.0 0.0 37.60 3.16 F
1431 1438 1.538047 ATCTGCCTGTCATGCGTTTT 58.462 45.0 0.0 0.0 0.00 2.43 F
2689 2705 0.671472 TGTCCTGCTGATGCTTGTCG 60.671 55.0 0.0 0.0 40.48 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1620 0.905357 AGACATCCCCTTCTTGTCCG 59.095 55.0 0.00 0.0 40.46 4.79 R
2775 2791 0.975040 AGAGAGCAACAGAGCCCGAT 60.975 55.0 0.00 0.0 34.23 4.18 R
3809 3945 0.400213 TCTGGGCCAAGAACGTGAAT 59.600 50.0 7.63 0.0 0.00 2.57 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
36 37 2.904866 GAAACGGCAGCACCACCA 60.905 61.111 0.00 0.00 39.03 4.17
37 38 3.194272 GAAACGGCAGCACCACCAC 62.194 63.158 0.00 0.00 39.03 4.16
163 164 2.348998 CGCCTGCCCTCCCATATC 59.651 66.667 0.00 0.00 0.00 1.63
255 256 1.867363 ACCTTCCTCCGCAGTTCTAT 58.133 50.000 0.00 0.00 0.00 1.98
257 258 2.959707 ACCTTCCTCCGCAGTTCTATAG 59.040 50.000 0.00 0.00 0.00 1.31
258 259 3.223435 CCTTCCTCCGCAGTTCTATAGA 58.777 50.000 0.00 0.00 0.00 1.98
259 260 3.637229 CCTTCCTCCGCAGTTCTATAGAA 59.363 47.826 11.24 11.24 0.00 2.10
276 277 0.708918 GAACTTTCTCGACGCTTCCG 59.291 55.000 0.00 0.00 41.14 4.30
287 288 1.153168 CGCTTCCGTCCATTCCCAT 60.153 57.895 0.00 0.00 0.00 4.00
361 362 2.542907 CGGATTTCATTCCCCCGCG 61.543 63.158 0.00 0.00 33.47 6.46
363 364 2.833121 ATTTCATTCCCCCGCGGC 60.833 61.111 22.85 0.00 0.00 6.53
446 451 4.033776 CGTGGTCATGGGGGCTGT 62.034 66.667 0.00 0.00 0.00 4.40
480 485 1.733912 CCATCGATGTGTCAACTGTGG 59.266 52.381 23.27 1.66 0.00 4.17
530 535 4.143389 CGATTTTAGGCGCGTAGGAAATAG 60.143 45.833 15.84 13.16 0.00 1.73
538 543 2.223377 CGCGTAGGAAATAGGGAATTGC 59.777 50.000 0.00 0.00 0.00 3.56
558 563 0.895530 TCGTCTGGTTAGAGGCAAGG 59.104 55.000 0.00 0.00 38.41 3.61
578 584 6.736519 GCAAGGTCGGTTGTATTTTAGGTTTT 60.737 38.462 0.00 0.00 0.00 2.43
642 648 2.158475 TGCCCTCTGTTTGTTGGAGAAT 60.158 45.455 0.00 0.00 0.00 2.40
705 711 0.660488 TGGTTGCACTGCGTTAGTTG 59.340 50.000 0.00 0.00 37.60 3.16
749 755 6.762702 TTGTTTAATCGGAGGGGAATTAAC 57.237 37.500 0.00 0.00 0.00 2.01
765 771 8.659491 GGGGAATTAACGTTTACTAGTAACTTG 58.341 37.037 14.96 9.99 0.00 3.16
773 779 7.436118 ACGTTTACTAGTAACTTGGATGTGAA 58.564 34.615 14.96 0.00 0.00 3.18
824 830 2.251409 TGCATGATCTTGCTCTAGGC 57.749 50.000 27.81 5.97 43.18 3.93
1031 1038 1.661112 GCTGCATAGTTCTCGTTGTCC 59.339 52.381 0.00 0.00 0.00 4.02
1431 1438 1.538047 ATCTGCCTGTCATGCGTTTT 58.462 45.000 0.00 0.00 0.00 2.43
1580 1587 9.675464 AGGAACAAATGTAGAAATAATCGGTAA 57.325 29.630 0.00 0.00 0.00 2.85
1613 1620 4.523943 AGGATCTGCTGTCATATCAGAGAC 59.476 45.833 0.00 0.00 39.82 3.36
2193 2200 4.940654 GCTTCAAGAGGAATGCTTCTTACT 59.059 41.667 0.00 0.00 38.27 2.24
2689 2705 0.671472 TGTCCTGCTGATGCTTGTCG 60.671 55.000 0.00 0.00 40.48 4.35
2712 2728 1.661112 GTTTGCGCTGAGGTATCTGTC 59.339 52.381 9.73 0.00 0.00 3.51
2718 2734 1.335496 GCTGAGGTATCTGTCGTCCTC 59.665 57.143 0.00 0.00 44.54 3.71
2775 2791 0.827507 GGTGGAAGGCCTTCTTTGCA 60.828 55.000 37.72 26.65 39.45 4.08
2949 2965 4.636206 GGCTTCTTGACGTCAATATCCTTT 59.364 41.667 29.79 0.00 35.02 3.11
3165 3181 3.303406 GCTGTTCAACTGCAGATGTTTC 58.697 45.455 23.35 13.49 41.83 2.78
3179 3196 8.268850 TGCAGATGTTTCCTTAGTAGATTTTC 57.731 34.615 0.00 0.00 0.00 2.29
3260 3277 7.691993 AGTGTTAAGGGGTAATGACTATGAT 57.308 36.000 0.00 0.00 0.00 2.45
3348 3365 6.378582 ACATTATTTGCTACGTGTTTCTTGG 58.621 36.000 0.00 0.00 0.00 3.61
3398 3415 6.027749 CGCTTTCTGTTTCTTTTACAGTGTT 58.972 36.000 0.00 0.00 42.77 3.32
3423 3440 2.397044 TCCTTCCAACCAAAAGCCAT 57.603 45.000 0.00 0.00 0.00 4.40
3471 3488 7.803659 GGGAAAATTCTTTCTGTTTCTTCTACG 59.196 37.037 0.00 0.00 40.76 3.51
3519 3616 7.840342 AGAATATGATTCGAACAGCCATATC 57.160 36.000 17.13 13.02 31.45 1.63
3566 3663 0.178967 TTTCTTGGCATGCTGGTGGA 60.179 50.000 18.92 6.48 0.00 4.02
3576 3673 1.077212 GCTGGTGGATCTGTGGCAT 60.077 57.895 0.00 0.00 0.00 4.40
3597 3724 5.872635 CATAGTGACATGCAAAAGTACAGG 58.127 41.667 0.00 0.00 0.00 4.00
3678 3805 7.362662 TGCAGAAGCTGTTCTTTTATTACAAG 58.637 34.615 0.00 0.00 41.40 3.16
3727 3854 3.713288 TGAACAACAGAAGACGTAGGTG 58.287 45.455 0.00 0.00 0.00 4.00
3729 3856 2.313317 ACAACAGAAGACGTAGGTGGA 58.687 47.619 0.00 0.00 0.00 4.02
3741 3877 5.589452 AGACGTAGGTGGAAACAGATAGTAG 59.411 44.000 0.00 0.00 44.46 2.57
3742 3878 5.259632 ACGTAGGTGGAAACAGATAGTAGT 58.740 41.667 0.00 0.00 44.46 2.73
3743 3879 6.418101 ACGTAGGTGGAAACAGATAGTAGTA 58.582 40.000 0.00 0.00 44.46 1.82
3784 3920 2.813042 GCGAGACCACAGAGCTGC 60.813 66.667 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.031919 TGGTGCTGCCGTTTCGAT 59.968 55.556 0.00 0.00 41.21 3.59
36 37 2.087857 TTTCCATTTCCTGGCCCGGT 62.088 55.000 13.58 0.00 45.52 5.28
37 38 0.687427 ATTTCCATTTCCTGGCCCGG 60.687 55.000 6.92 6.92 45.52 5.73
38 39 0.746659 GATTTCCATTTCCTGGCCCG 59.253 55.000 0.00 0.00 45.52 6.13
163 164 4.172232 TGGATCCGGGGAGGGGAG 62.172 72.222 7.39 0.00 41.52 4.30
255 256 2.413765 CGGAAGCGTCGAGAAAGTTCTA 60.414 50.000 0.00 0.00 37.73 2.10
257 258 0.708918 CGGAAGCGTCGAGAAAGTTC 59.291 55.000 0.00 0.00 0.00 3.01
258 259 0.031721 ACGGAAGCGTCGAGAAAGTT 59.968 50.000 0.00 0.00 0.00 2.66
259 260 0.386985 GACGGAAGCGTCGAGAAAGT 60.387 55.000 0.00 0.00 0.00 2.66
260 261 1.071567 GGACGGAAGCGTCGAGAAAG 61.072 60.000 0.00 0.00 39.56 2.62
261 262 1.080974 GGACGGAAGCGTCGAGAAA 60.081 57.895 0.00 0.00 39.56 2.52
276 277 4.202050 CGAATTGAAGGAATGGGAATGGAC 60.202 45.833 0.00 0.00 0.00 4.02
287 288 0.323629 AGGGACGCGAATTGAAGGAA 59.676 50.000 15.93 0.00 0.00 3.36
363 364 3.638160 AGGAAGAGATCTAGAGCAAGCAG 59.362 47.826 11.20 0.00 0.00 4.24
446 451 1.032794 CGATGGCAGAGCAGGTACTA 58.967 55.000 0.00 0.00 36.02 1.82
480 485 1.234821 TCGGCAACCATGAAACACTC 58.765 50.000 0.00 0.00 0.00 3.51
530 535 2.093658 TCTAACCAGACGAGCAATTCCC 60.094 50.000 0.00 0.00 0.00 3.97
538 543 1.134965 CCTTGCCTCTAACCAGACGAG 60.135 57.143 0.00 0.00 0.00 4.18
558 563 8.724229 ACTATGAAAACCTAAAATACAACCGAC 58.276 33.333 0.00 0.00 0.00 4.79
578 584 8.026607 GCAAAATAGTGCAAAAGGTTACTATGA 58.973 33.333 0.00 0.00 44.29 2.15
642 648 4.868171 AGTATAGAAGCGCGATGACAAAAA 59.132 37.500 12.10 0.00 0.00 1.94
749 755 7.878477 TTCACATCCAAGTTACTAGTAAACG 57.122 36.000 16.82 8.27 0.00 3.60
765 771 6.259608 CCTCACAATCTAGAACATTCACATCC 59.740 42.308 0.00 0.00 0.00 3.51
773 779 5.429762 TCCATTCCCTCACAATCTAGAACAT 59.570 40.000 0.00 0.00 0.00 2.71
824 830 8.429493 TGATAATTGCAGAAGACTAGTCATTG 57.571 34.615 24.44 18.28 0.00 2.82
827 833 9.534565 GTAATGATAATTGCAGAAGACTAGTCA 57.465 33.333 24.44 2.39 0.00 3.41
1031 1038 1.131126 CAGCCAACAATAACAGAGCCG 59.869 52.381 0.00 0.00 0.00 5.52
1218 1225 2.705826 GCGCTCTTCTTGATGCCG 59.294 61.111 0.00 0.00 0.00 5.69
1431 1438 2.236893 TGTGATACCATTCTGCTCAGCA 59.763 45.455 0.00 0.00 36.92 4.41
1580 1587 3.113824 ACAGCAGATCCTTCTTCTCCAT 58.886 45.455 0.00 0.00 0.00 3.41
1613 1620 0.905357 AGACATCCCCTTCTTGTCCG 59.095 55.000 0.00 0.00 40.46 4.79
2689 2705 2.076863 AGATACCTCAGCGCAAACAAC 58.923 47.619 11.47 0.00 0.00 3.32
2712 2728 4.981054 CAGAGATTCATGTATGTGAGGACG 59.019 45.833 0.00 0.00 0.00 4.79
2718 2734 6.036844 CCTCAACACAGAGATTCATGTATGTG 59.963 42.308 9.50 9.50 45.34 3.21
2775 2791 0.975040 AGAGAGCAACAGAGCCCGAT 60.975 55.000 0.00 0.00 34.23 4.18
2949 2965 1.080772 CGCGAAGAGGTAGTGCACA 60.081 57.895 21.04 1.84 0.00 4.57
3052 3068 4.495349 CCTCATTAAACTGCGCTTCTCATG 60.495 45.833 9.73 4.37 0.00 3.07
3165 3181 4.268884 GCAGCTGACGAAAATCTACTAAGG 59.731 45.833 20.43 0.00 0.00 2.69
3179 3196 3.511699 TGAATAAGTGTAGCAGCTGACG 58.488 45.455 20.43 0.00 0.00 4.35
3348 3365 6.445357 TTCCCGATAGTTTTGAAATTAGGC 57.555 37.500 0.00 0.00 0.00 3.93
3398 3415 4.257731 GCTTTTGGTTGGAAGGAAAAACA 58.742 39.130 0.00 0.00 0.00 2.83
3423 3440 5.598005 CCCAAGGAATATGGCAAAAGACATA 59.402 40.000 0.00 0.00 36.58 2.29
3471 3488 6.861065 TGTAGAAGAACAAAGTGACATTCC 57.139 37.500 0.00 0.00 0.00 3.01
3519 3616 1.445582 GGACCGCTGAAGTGTACCG 60.446 63.158 0.00 0.00 0.00 4.02
3561 3658 1.486310 TCACTATGCCACAGATCCACC 59.514 52.381 0.00 0.00 0.00 4.61
3566 3663 2.569059 GCATGTCACTATGCCACAGAT 58.431 47.619 0.00 0.00 45.93 2.90
3576 3673 4.202419 ACCCTGTACTTTTGCATGTCACTA 60.202 41.667 0.00 0.00 0.00 2.74
3597 3724 5.049267 TCGTATTCAACTGCCTACAAAAACC 60.049 40.000 0.00 0.00 0.00 3.27
3678 3805 4.687215 TGGTCACCAGAGCAGCGC 62.687 66.667 0.00 0.00 46.52 5.92
3705 3832 3.736252 CACCTACGTCTTCTGTTGTTCAG 59.264 47.826 0.00 0.00 44.85 3.02
3741 3877 7.359933 CCGGAACTAAGATCGATGTACTACTAC 60.360 44.444 0.54 0.00 0.00 2.73
3742 3878 6.648310 CCGGAACTAAGATCGATGTACTACTA 59.352 42.308 0.54 0.00 0.00 1.82
3743 3879 5.469421 CCGGAACTAAGATCGATGTACTACT 59.531 44.000 0.54 0.00 0.00 2.57
3809 3945 0.400213 TCTGGGCCAAGAACGTGAAT 59.600 50.000 7.63 0.00 0.00 2.57
3884 4020 0.605589 ACGTCTCCTTCAAGCTCCTG 59.394 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.