Multiple sequence alignment - TraesCS1D01G237200

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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 TraesCS1D01G237200 chr1D 100.000 3940 0 0 1 3940 326284746 326288685 0.000000e+00 7276.0
1 TraesCS1D01G237200 chr1A 96.530 3948 90 16 1 3940 412457425 412461333 0.000000e+00 6488.0
2 TraesCS1D01G237200 chr1A 95.918 49 1 1 2980 3028 576281393 576281346 1.170000e-10 78.7
3 TraesCS1D01G237200 chr1B 97.420 3488 56 13 1 3487 439844510 439847964 0.000000e+00 5912.0
4 TraesCS1D01G237200 chr1B 93.933 478 8 5 3469 3938 439848534 439848998 0.000000e+00 702.0
5 TraesCS1D01G237200 chr1B 97.826 46 1 0 2981 3026 671563332 671563377 3.260000e-11 80.5
6 TraesCS1D01G237200 chr3B 96.154 52 2 0 2982 3033 597475715 597475664 7.010000e-13 86.1
7 TraesCS1D01G237200 chr6B 90.476 63 4 2 2970 3030 679977476 679977538 9.070000e-12 82.4
8 TraesCS1D01G237200 chr7A 86.301 73 8 2 2956 3027 635683666 635683737 1.170000e-10 78.7
9 TraesCS1D01G237200 chr4D 94.231 52 2 1 2984 3035 47511185 47511135 1.170000e-10 78.7
10 TraesCS1D01G237200 chr3A 84.146 82 11 2 2981 3061 446317993 446317913 1.170000e-10 78.7


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 TraesCS1D01G237200 chr1D 326284746 326288685 3939 False 7276 7276 100.0000 1 3940 1 chr1D.!!$F1 3939
1 TraesCS1D01G237200 chr1A 412457425 412461333 3908 False 6488 6488 96.5300 1 3940 1 chr1A.!!$F1 3939
2 TraesCS1D01G237200 chr1B 439844510 439848998 4488 False 3307 5912 95.6765 1 3938 2 chr1B.!!$F2 3937

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
927 930 0.109723 TTGCAGTGAACCACTACCCC 59.890 55.000 0.0 0.0 43.43 4.95 F
932 935 0.828677 GTGAACCACTACCCCGCTAT 59.171 55.000 0.0 0.0 0.00 2.97 F
1718 1721 2.092968 ACTTGCTCACCAGAACAGAACA 60.093 45.455 0.0 0.0 0.00 3.18 F
2711 2727 1.505151 TAGGCCCCCACAGCATCAAA 61.505 55.000 0.0 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2297 0.108520 TCCGTGTGGAATAAGGACGC 60.109 55.00 0.00 0.0 42.85 5.19 R
2414 2417 0.108585 TGGACAGTGCTTCTTGGGAC 59.891 55.00 0.00 0.0 0.00 4.46 R
2870 2886 0.835941 CTGGAGCTAGGATTGCCAGT 59.164 55.00 7.11 0.0 40.88 4.00 R
3645 4259 5.165961 AGTTAGATGCAGCCTTTACTTCA 57.834 39.13 0.00 0.0 0.00 3.02 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
332 334 8.461222 CAAATCCAAAAGCACAGAGATAACATA 58.539 33.333 0.00 0.00 0.00 2.29
340 342 6.830912 AGCACAGAGATAACATATTGGCTTA 58.169 36.000 0.00 0.00 0.00 3.09
524 527 7.283127 TCTGTTAACTGCTCTGTTTCATCTTTT 59.717 33.333 7.22 0.00 0.00 2.27
628 631 4.329638 TCATTTTGCCCTTCCTCCATAA 57.670 40.909 0.00 0.00 0.00 1.90
632 635 3.825908 TTGCCCTTCCTCCATAAACTT 57.174 42.857 0.00 0.00 0.00 2.66
633 636 3.366052 TGCCCTTCCTCCATAAACTTC 57.634 47.619 0.00 0.00 0.00 3.01
634 637 2.025321 TGCCCTTCCTCCATAAACTTCC 60.025 50.000 0.00 0.00 0.00 3.46
635 638 2.242452 GCCCTTCCTCCATAAACTTCCT 59.758 50.000 0.00 0.00 0.00 3.36
636 639 3.891049 CCCTTCCTCCATAAACTTCCTG 58.109 50.000 0.00 0.00 0.00 3.86
637 640 3.523564 CCCTTCCTCCATAAACTTCCTGA 59.476 47.826 0.00 0.00 0.00 3.86
638 641 4.384647 CCCTTCCTCCATAAACTTCCTGAG 60.385 50.000 0.00 0.00 0.00 3.35
676 679 4.601019 CAGGATGCTTAAAACATAAGCCG 58.399 43.478 15.39 0.00 46.78 5.52
927 930 0.109723 TTGCAGTGAACCACTACCCC 59.890 55.000 0.00 0.00 43.43 4.95
932 935 0.828677 GTGAACCACTACCCCGCTAT 59.171 55.000 0.00 0.00 0.00 2.97
1500 1503 2.174360 GACTACCTCCACCTTACGGTT 58.826 52.381 0.00 0.00 42.13 4.44
1718 1721 2.092968 ACTTGCTCACCAGAACAGAACA 60.093 45.455 0.00 0.00 0.00 3.18
1719 1722 2.708216 TGCTCACCAGAACAGAACAA 57.292 45.000 0.00 0.00 0.00 2.83
1765 1768 4.523083 GTGGTCTAGGTCAATTTGGCATA 58.477 43.478 3.03 0.00 0.00 3.14
1823 1826 6.677913 CCACAAATGGTAAATCGAAAGAACT 58.322 36.000 0.00 0.00 42.28 3.01
2294 2297 4.790765 TCTCAACTCAGATACACACCAG 57.209 45.455 0.00 0.00 0.00 4.00
2414 2417 2.810274 CACCCATGGCTTAATCTCATCG 59.190 50.000 6.09 0.00 0.00 3.84
2594 2610 9.671279 ACATCATGTCATAGTATTTTCAAGTGA 57.329 29.630 0.00 0.00 0.00 3.41
2683 2699 2.316677 TCTACCTGGTGGGATTCCTACA 59.683 50.000 19.53 7.71 38.76 2.74
2711 2727 1.505151 TAGGCCCCCACAGCATCAAA 61.505 55.000 0.00 0.00 0.00 2.69
2870 2886 3.655777 AGAGGAAAAACACCTATGACCCA 59.344 43.478 0.00 0.00 37.93 4.51
3206 3222 2.738846 CCTTTGAGTTGTGTCTGATCCG 59.261 50.000 0.00 0.00 0.00 4.18
3399 3423 8.783093 TGATTAACAAATAAAGGTGTCTGACAG 58.217 33.333 11.41 0.00 0.00 3.51
3400 3424 8.918202 ATTAACAAATAAAGGTGTCTGACAGA 57.082 30.769 11.41 0.00 0.00 3.41
3401 3425 6.619801 AACAAATAAAGGTGTCTGACAGAC 57.380 37.500 25.76 25.76 45.26 3.51
3402 3426 5.930135 ACAAATAAAGGTGTCTGACAGACT 58.070 37.500 30.51 16.15 45.27 3.24
3403 3427 5.760253 ACAAATAAAGGTGTCTGACAGACTG 59.240 40.000 30.51 20.64 45.27 3.51
3404 3428 5.808366 AATAAAGGTGTCTGACAGACTGA 57.192 39.130 30.51 13.39 45.27 3.41
3405 3429 3.460857 AAAGGTGTCTGACAGACTGAC 57.539 47.619 30.51 22.40 45.27 3.51
3426 3450 7.039011 ACTGACATGTGAAAGAGACCTGTATAA 60.039 37.037 1.15 0.00 0.00 0.98
3450 3474 3.250762 TGCAGAAAATGAACTGAGTTCCG 59.749 43.478 21.45 3.92 41.35 4.30
3631 4245 7.390162 TGACATGAGCGAAATAATGCCAATATA 59.610 33.333 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 4.836125 AAATCGTATGGACATGGATTGC 57.164 40.909 11.56 0.00 30.78 3.56
72 74 4.977963 GCAAAATCGTATGGACATGGATTG 59.022 41.667 11.56 6.02 30.78 2.67
73 75 4.644234 TGCAAAATCGTATGGACATGGATT 59.356 37.500 0.00 7.27 31.25 3.01
340 342 3.003394 TCAATTGATGTTCGGCAGGAT 57.997 42.857 3.38 0.00 0.00 3.24
452 454 3.969312 TGATGTGGATCTCAGCAGGATTA 59.031 43.478 5.57 0.00 0.00 1.75
524 527 5.243730 GGGAGAAAGAAAACAATGACATGGA 59.756 40.000 0.00 0.00 0.00 3.41
628 631 2.964209 TCTGTCAGGACTCAGGAAGTT 58.036 47.619 0.00 0.00 38.74 2.66
632 635 2.451490 GACATCTGTCAGGACTCAGGA 58.549 52.381 5.46 0.00 44.18 3.86
633 636 1.133982 CGACATCTGTCAGGACTCAGG 59.866 57.143 10.69 0.00 44.99 3.86
634 637 1.468908 GCGACATCTGTCAGGACTCAG 60.469 57.143 10.69 0.00 44.99 3.35
635 638 0.528017 GCGACATCTGTCAGGACTCA 59.472 55.000 10.69 0.00 44.99 3.41
636 639 0.528017 TGCGACATCTGTCAGGACTC 59.472 55.000 10.69 0.00 44.99 3.36
637 640 0.529833 CTGCGACATCTGTCAGGACT 59.470 55.000 10.69 0.00 44.99 3.85
638 641 0.459237 CCTGCGACATCTGTCAGGAC 60.459 60.000 10.96 0.00 44.99 3.85
676 679 5.074584 AGAGTCTGGTATTCGTTCTTTCC 57.925 43.478 0.00 0.00 0.00 3.13
717 720 6.839124 TGGATCAAAGATTATGTTGCAGTT 57.161 33.333 0.00 0.00 0.00 3.16
927 930 7.116090 CAGGAGAAAGATGAAAGATGTATAGCG 59.884 40.741 0.00 0.00 0.00 4.26
932 935 9.003658 GTTTTCAGGAGAAAGATGAAAGATGTA 57.996 33.333 0.00 0.00 44.03 2.29
1245 1248 2.356535 GGAGTGCTCACCCATCAAGAAT 60.357 50.000 1.41 0.00 0.00 2.40
1500 1503 1.152652 ATTTGACAACGTGCCCCCA 60.153 52.632 0.00 0.00 0.00 4.96
1718 1721 3.136809 AGAGCAGCATGGAAGAGATCATT 59.863 43.478 0.00 0.00 35.86 2.57
1719 1722 2.706723 AGAGCAGCATGGAAGAGATCAT 59.293 45.455 0.00 0.00 35.86 2.45
1765 1768 0.393077 CGATCCTGGCCCGAGTAATT 59.607 55.000 0.00 0.00 0.00 1.40
1823 1826 2.303890 AGCATGGAGTTGTCACAGATGA 59.696 45.455 0.00 0.00 0.00 2.92
2294 2297 0.108520 TCCGTGTGGAATAAGGACGC 60.109 55.000 0.00 0.00 42.85 5.19
2414 2417 0.108585 TGGACAGTGCTTCTTGGGAC 59.891 55.000 0.00 0.00 0.00 4.46
2590 2606 7.033791 GCATGAAACAAGATGAATCATTCACT 58.966 34.615 0.98 0.00 43.48 3.41
2591 2607 6.809689 TGCATGAAACAAGATGAATCATTCAC 59.190 34.615 0.98 0.00 43.48 3.18
2592 2608 6.926313 TGCATGAAACAAGATGAATCATTCA 58.074 32.000 1.59 1.59 45.01 2.57
2593 2609 7.255569 TCTGCATGAAACAAGATGAATCATTC 58.744 34.615 0.00 0.00 29.03 2.67
2594 2610 7.165460 TCTGCATGAAACAAGATGAATCATT 57.835 32.000 0.00 0.00 29.03 2.57
2595 2611 6.769134 TCTGCATGAAACAAGATGAATCAT 57.231 33.333 0.00 0.00 30.62 2.45
2596 2612 6.405397 CCATCTGCATGAAACAAGATGAATCA 60.405 38.462 17.29 0.00 36.28 2.57
2597 2613 5.977725 CCATCTGCATGAAACAAGATGAATC 59.022 40.000 17.29 0.00 36.28 2.52
2598 2614 5.163447 CCCATCTGCATGAAACAAGATGAAT 60.163 40.000 17.29 0.00 36.28 2.57
2599 2615 4.158949 CCCATCTGCATGAAACAAGATGAA 59.841 41.667 17.29 0.00 36.28 2.57
2600 2616 3.697542 CCCATCTGCATGAAACAAGATGA 59.302 43.478 17.29 0.00 36.28 2.92
2601 2617 3.697542 TCCCATCTGCATGAAACAAGATG 59.302 43.478 0.00 6.37 34.61 2.90
2602 2618 3.698040 GTCCCATCTGCATGAAACAAGAT 59.302 43.478 0.00 0.00 30.57 2.40
2649 2665 5.316987 CACCAGGTAGAAAACTTCCTCATT 58.683 41.667 0.00 0.00 0.00 2.57
2711 2727 3.192466 GTTGTTCAGGTTCAGTGTACGT 58.808 45.455 0.00 0.00 0.00 3.57
2773 2789 4.947388 TGGTGTAGTTTGGAAGATATTGCC 59.053 41.667 0.00 0.00 0.00 4.52
2870 2886 0.835941 CTGGAGCTAGGATTGCCAGT 59.164 55.000 7.11 0.00 40.88 4.00
3166 3182 7.337938 TCAAAGGTATGTCATTGCTGATCTTA 58.662 34.615 0.00 0.00 32.98 2.10
3228 3244 6.205464 CAGCTGTTTCATGGACCGATATAATT 59.795 38.462 5.25 0.00 0.00 1.40
3399 3423 3.993081 CAGGTCTCTTTCACATGTCAGTC 59.007 47.826 0.00 0.00 0.00 3.51
3400 3424 3.389329 ACAGGTCTCTTTCACATGTCAGT 59.611 43.478 0.00 0.00 33.62 3.41
3401 3425 4.000331 ACAGGTCTCTTTCACATGTCAG 58.000 45.455 0.00 0.00 33.62 3.51
3402 3426 5.745312 ATACAGGTCTCTTTCACATGTCA 57.255 39.130 0.00 0.00 39.40 3.58
3403 3427 8.607459 CATTTATACAGGTCTCTTTCACATGTC 58.393 37.037 0.00 0.00 39.40 3.06
3404 3428 7.066284 GCATTTATACAGGTCTCTTTCACATGT 59.934 37.037 0.00 0.00 41.44 3.21
3405 3429 7.066163 TGCATTTATACAGGTCTCTTTCACATG 59.934 37.037 0.00 0.00 0.00 3.21
3406 3430 7.112122 TGCATTTATACAGGTCTCTTTCACAT 58.888 34.615 0.00 0.00 0.00 3.21
3426 3450 5.563475 CGGAACTCAGTTCATTTTCTGCATT 60.563 40.000 19.37 0.00 43.54 3.56
3579 4193 8.669571 AGTATATATTACAGGCCATTCACCTTT 58.330 33.333 5.01 0.00 34.42 3.11
3631 4245 7.995488 AGCCTTTACTTCATATGCATCTTACTT 59.005 33.333 0.19 0.00 0.00 2.24
3642 4256 7.512992 AGTTAGATGCAGCCTTTACTTCATAT 58.487 34.615 0.00 0.00 0.00 1.78
3643 4257 6.889198 AGTTAGATGCAGCCTTTACTTCATA 58.111 36.000 0.00 0.00 0.00 2.15
3644 4258 5.749462 AGTTAGATGCAGCCTTTACTTCAT 58.251 37.500 0.00 0.00 0.00 2.57
3645 4259 5.165961 AGTTAGATGCAGCCTTTACTTCA 57.834 39.130 0.00 0.00 0.00 3.02
3646 4260 6.574350 TCTAGTTAGATGCAGCCTTTACTTC 58.426 40.000 0.00 0.00 0.00 3.01
3699 4318 6.513806 TCATGGTGGAAAGTGATTACAATG 57.486 37.500 0.00 0.00 32.26 2.82
3822 4441 9.436957 CCTTTGTTAAGACTGATGTGTATAACT 57.563 33.333 0.00 0.00 32.92 2.24
3823 4442 8.665685 CCCTTTGTTAAGACTGATGTGTATAAC 58.334 37.037 0.00 0.00 32.92 1.89
3824 4443 7.827236 CCCCTTTGTTAAGACTGATGTGTATAA 59.173 37.037 0.00 0.00 32.92 0.98
3825 4444 7.335627 CCCCTTTGTTAAGACTGATGTGTATA 58.664 38.462 0.00 0.00 32.92 1.47
3912 4537 7.096230 CGTATATGCTGATGTGAACGATTTACA 60.096 37.037 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.