Multiple sequence alignment - TraesCS1D01G143700

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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 TraesCS1D01G143700 chr1D 100.000 3662 0 0 1 3662 199336994 199333333 0.000000e+00 6763.0
1 TraesCS1D01G143700 chr1A 93.045 3695 171 36 1 3662 250529056 250525415 0.000000e+00 5321.0
2 TraesCS1D01G143700 chr1B 94.498 2490 69 13 466 2946 279574031 279571601 0.000000e+00 3777.0
3 TraesCS1D01G143700 chr1B 84.783 460 32 13 1 435 279574479 279574033 9.400000e-116 427.0
4 TraesCS1D01G143700 chr2D 72.666 889 204 34 1523 2388 199762502 199761630 3.630000e-65 259.0
5 TraesCS1D01G143700 chr2A 72.448 911 208 37 1523 2408 220015380 220014488 6.070000e-63 252.0
6 TraesCS1D01G143700 chr2B 72.241 879 205 34 1523 2378 376014961 376014099 6.110000e-58 235.0
7 TraesCS1D01G143700 chr5D 81.992 261 33 14 3369 3620 232249579 232249834 3.710000e-50 209.0
8 TraesCS1D01G143700 chr4D 78.409 88 15 4 3368 3454 1302030 1301946 2.000000e-03 54.7


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 TraesCS1D01G143700 chr1D 199333333 199336994 3661 True 6763 6763 100.0000 1 3662 1 chr1D.!!$R1 3661
1 TraesCS1D01G143700 chr1A 250525415 250529056 3641 True 5321 5321 93.0450 1 3662 1 chr1A.!!$R1 3661
2 TraesCS1D01G143700 chr1B 279571601 279574479 2878 True 2102 3777 89.6405 1 2946 2 chr1B.!!$R1 2945
3 TraesCS1D01G143700 chr2D 199761630 199762502 872 True 259 259 72.6660 1523 2388 1 chr2D.!!$R1 865
4 TraesCS1D01G143700 chr2A 220014488 220015380 892 True 252 252 72.4480 1523 2408 1 chr2A.!!$R1 885
5 TraesCS1D01G143700 chr2B 376014099 376014961 862 True 235 235 72.2410 1523 2378 1 chr2B.!!$R1 855

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
780 818 1.202639 TCTCATGTGCACGTTCCTTGT 60.203 47.619 9.37 0.0 0.0 3.16 F
1617 1660 2.438795 GACTCCTCCCTCGCGTCT 60.439 66.667 5.77 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1862 0.846693 AGCTTGTTTCCCCACTCAGT 59.153 50.000 0.0 0.0 0.0 3.41 R
2917 2970 2.275318 GATCCTCGCCTCAACAGAAAG 58.725 52.381 0.0 0.0 0.0 2.62 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
355 382 3.659786 CAATACGGGTCACTCAACTCAA 58.340 45.455 0.00 0.00 0.00 3.02
362 389 4.058817 GGGTCACTCAACTCAAGTAAGTG 58.941 47.826 14.77 14.77 38.91 3.16
422 449 3.068732 TGATCGCTGGGTATCTCAAAGAG 59.931 47.826 0.00 0.00 0.00 2.85
442 469 4.133078 GAGGTGGATGGTTGATCTGATTC 58.867 47.826 0.00 0.00 0.00 2.52
693 725 3.252701 GCATTCTGCCATCCTATCAACTG 59.747 47.826 0.00 0.00 37.42 3.16
694 726 3.565764 TTCTGCCATCCTATCAACTGG 57.434 47.619 0.00 0.00 0.00 4.00
695 727 1.770658 TCTGCCATCCTATCAACTGGG 59.229 52.381 0.00 0.00 0.00 4.45
696 728 1.492176 CTGCCATCCTATCAACTGGGT 59.508 52.381 0.00 0.00 0.00 4.51
697 729 1.212688 TGCCATCCTATCAACTGGGTG 59.787 52.381 0.00 0.00 34.39 4.61
698 730 1.212935 GCCATCCTATCAACTGGGTGT 59.787 52.381 0.00 0.00 32.81 4.16
780 818 1.202639 TCTCATGTGCACGTTCCTTGT 60.203 47.619 9.37 0.00 0.00 3.16
786 824 2.490115 TGTGCACGTTCCTTGTTTCTTT 59.510 40.909 13.13 0.00 0.00 2.52
1016 1059 2.627945 GGGTATGATGAAGCGACACAA 58.372 47.619 0.00 0.00 0.00 3.33
1617 1660 2.438795 GACTCCTCCCTCGCGTCT 60.439 66.667 5.77 0.00 0.00 4.18
1625 1668 3.506096 CCTCGCGTCTGCCGTCTA 61.506 66.667 5.77 0.00 39.32 2.59
1878 1921 0.248743 GGAACATGACCGCGATCGTA 60.249 55.000 17.81 0.00 0.00 3.43
2491 2543 1.334992 CGTGAATGACGCGTTCGACT 61.335 55.000 15.53 0.00 45.77 4.18
2589 2641 5.957771 AGCCAGAGATGTATAGTTGGAAA 57.042 39.130 0.00 0.00 0.00 3.13
2672 2724 3.563390 GCCTTCAATTAGCTTAGCTCCTG 59.437 47.826 11.09 6.89 40.44 3.86
2677 2729 2.403252 TTAGCTTAGCTCCTGGTTGC 57.597 50.000 11.09 6.38 40.44 4.17
2815 2868 6.670027 AGTACATAGATCAGGGGGTAATCATC 59.330 42.308 0.00 0.00 0.00 2.92
2817 2870 5.486775 ACATAGATCAGGGGGTAATCATCTG 59.513 44.000 0.00 0.00 0.00 2.90
2847 2900 9.838975 TCATTTAAACTTTATGTAGCACATGTG 57.161 29.630 21.83 21.83 39.53 3.21
2911 2964 1.391933 CCAGGCTGTGCATGCATCAT 61.392 55.000 25.64 11.12 39.11 2.45
2952 3005 1.918262 AGGATCAAGGTCTCAATGCCA 59.082 47.619 0.00 0.00 0.00 4.92
2967 3020 4.050553 CAATGCCAAAATATAACGGCCTG 58.949 43.478 0.00 0.00 44.22 4.85
2976 3029 7.262048 CAAAATATAACGGCCTGTAAAATGGT 58.738 34.615 0.00 0.00 0.00 3.55
2983 3036 3.674955 CGGCCTGTAAAATGGTTTAAGGC 60.675 47.826 0.00 16.09 43.63 4.35
2986 3039 5.128008 GGCCTGTAAAATGGTTTAAGGCATA 59.872 40.000 20.96 0.00 44.66 3.14
2998 3051 8.871629 TGGTTTAAGGCATAAAATCTAGAACA 57.128 30.769 0.00 0.00 35.33 3.18
2999 3052 9.474313 TGGTTTAAGGCATAAAATCTAGAACAT 57.526 29.630 0.00 0.00 35.33 2.71
3311 3410 7.954788 TTTGGGAACATTTTTAGAAAATCGG 57.045 32.000 0.00 0.00 42.32 4.18
3371 3471 8.034215 ACAGAATTGTTTTCAAACTCATGAACA 58.966 29.630 0.00 0.00 43.39 3.18
3372 3472 9.037737 CAGAATTGTTTTCAAACTCATGAACAT 57.962 29.630 0.00 0.00 43.39 2.71
3373 3473 9.603921 AGAATTGTTTTCAAACTCATGAACATT 57.396 25.926 0.00 0.00 43.39 2.71
3378 3478 9.212641 TGTTTTCAAACTCATGAACATTTTTCA 57.787 25.926 0.00 0.00 38.95 2.69
3387 3487 9.767228 ACTCATGAACATTTTTCAAAATCATGA 57.233 25.926 19.07 19.07 43.01 3.07
3423 3523 6.205784 TGATCGAACAGTTTTCCAAAATCAC 58.794 36.000 0.00 0.00 0.00 3.06
3424 3524 5.568685 TCGAACAGTTTTCCAAAATCACA 57.431 34.783 0.00 0.00 0.00 3.58
3431 3531 7.973601 ACAGTTTTCCAAAATCACAAACATTC 58.026 30.769 0.00 0.00 31.06 2.67
3435 3535 9.276397 GTTTTCCAAAATCACAAACATTCTTTG 57.724 29.630 0.00 0.00 35.64 2.77
3436 3536 8.558973 TTTCCAAAATCACAAACATTCTTTGT 57.441 26.923 0.00 0.00 42.75 2.83
3582 3682 7.928167 AGAAATTTGGACTTTTGTGAAATCCTC 59.072 33.333 0.00 0.00 0.00 3.71
3586 3686 6.729690 TGGACTTTTGTGAAATCCTCAATT 57.270 33.333 0.00 0.00 35.22 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
355 382 2.351726 GCGCGATTTGAATCCACTTACT 59.648 45.455 12.10 0.00 31.68 2.24
362 389 0.581529 TGATCGCGCGATTTGAATCC 59.418 50.000 41.80 28.07 34.60 3.01
411 438 4.782691 TCAACCATCCACCTCTTTGAGATA 59.217 41.667 0.00 0.00 0.00 1.98
422 449 3.881688 CAGAATCAGATCAACCATCCACC 59.118 47.826 0.00 0.00 30.71 4.61
693 725 1.754234 GATGCATCCACCCACACCC 60.754 63.158 16.23 0.00 0.00 4.61
694 726 0.323725 AAGATGCATCCACCCACACC 60.324 55.000 23.06 0.00 0.00 4.16
695 727 1.549203 AAAGATGCATCCACCCACAC 58.451 50.000 23.06 0.00 0.00 3.82
696 728 2.170166 GAAAAGATGCATCCACCCACA 58.830 47.619 23.06 0.00 0.00 4.17
697 729 2.165030 CAGAAAAGATGCATCCACCCAC 59.835 50.000 23.06 10.01 0.00 4.61
698 730 2.041485 TCAGAAAAGATGCATCCACCCA 59.959 45.455 23.06 0.00 0.00 4.51
1445 1488 1.154225 GCCGTGTACTTGCACATGC 60.154 57.895 0.00 0.00 39.19 4.06
1448 1491 1.153147 TTGGCCGTGTACTTGCACA 60.153 52.632 0.00 0.00 39.19 4.57
1503 1546 4.803426 GTCTCCTGGAGCACGCCG 62.803 72.222 19.08 0.00 0.00 6.46
1659 1702 3.579302 TTGTGCCCCCAGAGGTGG 61.579 66.667 0.00 0.00 44.56 4.61
1819 1862 0.846693 AGCTTGTTTCCCCACTCAGT 59.153 50.000 0.00 0.00 0.00 3.41
2388 2440 1.826054 CCTCATCCTCTCGACGGCT 60.826 63.158 0.00 0.00 0.00 5.52
2556 2608 2.844654 TCTCTGGCTTCTCATCCTCT 57.155 50.000 0.00 0.00 0.00 3.69
2672 2724 4.021544 TCAAAACCACATAATCCAGCAACC 60.022 41.667 0.00 0.00 0.00 3.77
2677 2729 7.201732 GGAGTACATCAAAACCACATAATCCAG 60.202 40.741 0.00 0.00 0.00 3.86
2792 2845 6.669591 CAGATGATTACCCCCTGATCTATGTA 59.330 42.308 0.00 0.00 0.00 2.29
2847 2900 3.300009 CACTGTCTGAAAACGAAATGGC 58.700 45.455 0.00 0.00 0.00 4.40
2917 2970 2.275318 GATCCTCGCCTCAACAGAAAG 58.725 52.381 0.00 0.00 0.00 2.62
2952 3005 7.412853 ACCATTTTACAGGCCGTTATATTTT 57.587 32.000 5.57 0.00 0.00 1.82
3379 3479 9.642327 TCGATCATTCAAAACAATTCATGATTT 57.358 25.926 0.00 0.00 34.68 2.17
3380 3480 9.642327 TTCGATCATTCAAAACAATTCATGATT 57.358 25.926 0.00 0.00 32.68 2.57
3381 3481 9.079833 GTTCGATCATTCAAAACAATTCATGAT 57.920 29.630 0.00 0.00 34.72 2.45
3382 3482 8.081025 TGTTCGATCATTCAAAACAATTCATGA 58.919 29.630 0.00 0.00 29.21 3.07
3383 3483 8.230112 TGTTCGATCATTCAAAACAATTCATG 57.770 30.769 0.00 0.00 29.21 3.07
3384 3484 8.084073 ACTGTTCGATCATTCAAAACAATTCAT 58.916 29.630 0.00 0.00 30.90 2.57
3385 3485 7.424803 ACTGTTCGATCATTCAAAACAATTCA 58.575 30.769 0.00 0.00 30.90 2.57
3386 3486 7.858052 ACTGTTCGATCATTCAAAACAATTC 57.142 32.000 0.00 0.00 30.90 2.17
3387 3487 8.647143 AAACTGTTCGATCATTCAAAACAATT 57.353 26.923 0.00 0.00 30.90 2.32
3388 3488 8.647143 AAAACTGTTCGATCATTCAAAACAAT 57.353 26.923 0.00 0.00 30.90 2.71
3389 3489 7.221838 GGAAAACTGTTCGATCATTCAAAACAA 59.778 33.333 9.39 0.00 30.90 2.83
3543 3643 9.883142 AAGTCCAAATTTCTAAACAATTGTGAA 57.117 25.926 12.82 8.73 0.00 3.18
3549 3649 9.883142 TCACAAAAGTCCAAATTTCTAAACAAT 57.117 25.926 0.00 0.00 0.00 2.71
3550 3650 9.712305 TTCACAAAAGTCCAAATTTCTAAACAA 57.288 25.926 0.00 0.00 0.00 2.83
3551 3651 9.712305 TTTCACAAAAGTCCAAATTTCTAAACA 57.288 25.926 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.