Multiple sequence alignment - TraesCS6D01G215800

Loading Multiple Alignment...

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 TraesCS6D01G215800 chr6D 100.000 3353 0 0 1 3353 306026720 306023368 0.000000e+00 6192.0
1 TraesCS6D01G215800 chr6D 94.413 698 31 3 2661 3353 2534124 2534818 0.000000e+00 1066.0
2 TraesCS6D01G215800 chr6B 94.401 1929 60 18 733 2661 470808726 470810606 0.000000e+00 2920.0
3 TraesCS6D01G215800 chr6B 90.674 579 36 7 1 574 470803453 470804018 0.000000e+00 754.0
4 TraesCS6D01G215800 chr6B 91.667 168 11 2 578 745 470806370 470806534 2.600000e-56 230.0
5 TraesCS6D01G215800 chr6A 95.843 1780 54 8 889 2661 440427578 440425812 0.000000e+00 2859.0
6 TraesCS6D01G215800 chr6A 91.696 566 41 4 16 577 440528028 440527465 0.000000e+00 780.0
7 TraesCS6D01G215800 chr6A 92.123 292 21 2 582 872 440427983 440427693 8.660000e-111 411.0
8 TraesCS6D01G215800 chr5D 94.971 696 28 3 2659 3353 256208715 256209404 0.000000e+00 1085.0
9 TraesCS6D01G215800 chr2D 94.699 698 29 4 2661 3353 574564183 574563489 0.000000e+00 1077.0
10 TraesCS6D01G215800 chr2D 94.579 701 27 4 2661 3353 553417654 553418351 0.000000e+00 1074.0
11 TraesCS6D01G215800 chr1D 94.699 698 29 3 2661 3353 79934405 79933711 0.000000e+00 1077.0
12 TraesCS6D01G215800 chr1D 94.294 701 30 4 2660 3353 411245299 411245996 0.000000e+00 1064.0
13 TraesCS6D01G215800 chr7D 94.524 694 32 3 2661 3353 64807407 64806719 0.000000e+00 1066.0
14 TraesCS6D01G215800 chr7D 94.286 700 32 3 2659 3353 617126096 617126792 0.000000e+00 1064.0
15 TraesCS6D01G215800 chr7D 90.385 52 2 2 690 741 242407358 242407310 7.770000e-07 65.8
16 TraesCS6D01G215800 chr3B 94.380 694 30 6 2661 3348 42782479 42781789 0.000000e+00 1057.0


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 TraesCS6D01G215800 chr6D 306023368 306026720 3352 True 6192.000000 6192 100.000000 1 3353 1 chr6D.!!$R1 3352
1 TraesCS6D01G215800 chr6D 2534124 2534818 694 False 1066.000000 1066 94.413000 2661 3353 1 chr6D.!!$F1 692
2 TraesCS6D01G215800 chr6B 470803453 470810606 7153 False 1301.333333 2920 92.247333 1 2661 3 chr6B.!!$F1 2660
3 TraesCS6D01G215800 chr6A 440425812 440427983 2171 True 1635.000000 2859 93.983000 582 2661 2 chr6A.!!$R2 2079
4 TraesCS6D01G215800 chr6A 440527465 440528028 563 True 780.000000 780 91.696000 16 577 1 chr6A.!!$R1 561
5 TraesCS6D01G215800 chr5D 256208715 256209404 689 False 1085.000000 1085 94.971000 2659 3353 1 chr5D.!!$F1 694
6 TraesCS6D01G215800 chr2D 574563489 574564183 694 True 1077.000000 1077 94.699000 2661 3353 1 chr2D.!!$R1 692
7 TraesCS6D01G215800 chr2D 553417654 553418351 697 False 1074.000000 1074 94.579000 2661 3353 1 chr2D.!!$F1 692
8 TraesCS6D01G215800 chr1D 79933711 79934405 694 True 1077.000000 1077 94.699000 2661 3353 1 chr1D.!!$R1 692
9 TraesCS6D01G215800 chr1D 411245299 411245996 697 False 1064.000000 1064 94.294000 2660 3353 1 chr1D.!!$F1 693
10 TraesCS6D01G215800 chr7D 64806719 64807407 688 True 1066.000000 1066 94.524000 2661 3353 1 chr7D.!!$R1 692
11 TraesCS6D01G215800 chr7D 617126096 617126792 696 False 1064.000000 1064 94.286000 2659 3353 1 chr7D.!!$F1 694
12 TraesCS6D01G215800 chr3B 42781789 42782479 690 True 1057.000000 1057 94.380000 2661 3348 1 chr3B.!!$R1 687

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
181 184 0.096976 GTCATGGTCCAAACGCATCG 59.903 55.0 0.0 0.0 0.00 3.84 F
1913 6570 0.317103 CGTTCTATGGCCGACGAGAG 60.317 60.0 0.0 0.0 37.69 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 6611 1.458777 TTCCTCCCCGTGTGTCTGT 60.459 57.895 0.0 0.0 0.00 3.41 R
3259 7942 0.035056 CCATGTGGACCCTGAGTTCC 60.035 60.000 0.0 0.0 37.39 3.62 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
168 171 6.754675 TGTATTACAATAGTGTCGTGTCATGG 59.245 38.462 0.00 0.00 39.30 3.66
181 184 0.096976 GTCATGGTCCAAACGCATCG 59.903 55.000 0.00 0.00 0.00 3.84
464 470 2.233431 TGTGCCCACCTATGAATTTTGC 59.767 45.455 0.00 0.00 0.00 3.68
481 487 8.366401 TGAATTTTGCAGGTATCTGATTTTTGA 58.634 29.630 7.33 0.00 43.49 2.69
538 544 4.207891 AGGAATACATTGCACGAGTCTT 57.792 40.909 0.00 0.00 0.00 3.01
540 546 5.352284 AGGAATACATTGCACGAGTCTTAG 58.648 41.667 0.00 0.00 0.00 2.18
543 549 6.480320 GGAATACATTGCACGAGTCTTAGAAT 59.520 38.462 0.00 0.00 0.00 2.40
578 584 8.888579 ACAGTTGATACCTTTATGCTACATAC 57.111 34.615 0.00 0.00 0.00 2.39
579 585 7.931948 ACAGTTGATACCTTTATGCTACATACC 59.068 37.037 0.00 0.00 0.00 2.73
580 586 8.150945 CAGTTGATACCTTTATGCTACATACCT 58.849 37.037 0.00 0.00 0.00 3.08
590 2943 7.946655 TTATGCTACATACCTCGAATTTGAG 57.053 36.000 14.94 14.94 35.70 3.02
714 3068 1.575132 CGCTGCAAATCGAACGTCG 60.575 57.895 0.00 0.00 42.10 5.12
723 3077 4.490890 GCAAATCGAACGTCGGATTTTTAG 59.509 41.667 18.66 11.96 40.88 1.85
765 5323 4.153958 TCGTGACACCAAATTATGTTGC 57.846 40.909 0.00 0.00 0.00 4.17
788 5346 4.058124 CGCGAGGATATCAATTTTCTCCA 58.942 43.478 0.00 0.00 0.00 3.86
864 5422 4.217754 TGTCACGCCAGATTTTTAACAC 57.782 40.909 0.00 0.00 0.00 3.32
872 5430 5.357032 CGCCAGATTTTTAACACTTCCCTAT 59.643 40.000 0.00 0.00 0.00 2.57
873 5431 6.458342 CGCCAGATTTTTAACACTTCCCTATC 60.458 42.308 0.00 0.00 0.00 2.08
874 5432 6.183360 GCCAGATTTTTAACACTTCCCTATCC 60.183 42.308 0.00 0.00 0.00 2.59
879 5452 9.642343 GATTTTTAACACTTCCCTATCCCTAAT 57.358 33.333 0.00 0.00 0.00 1.73
973 5630 1.367840 CCGATCCGATCAACTCCCC 59.632 63.158 9.07 0.00 0.00 4.81
1206 5863 2.588314 GGCAGGAGCAGCAGATCG 60.588 66.667 0.00 0.00 44.61 3.69
1477 6134 3.005539 ACCTGCGTCTCATGGGCT 61.006 61.111 0.00 0.00 0.00 5.19
1839 6496 3.201290 CGAATACCAGCTTCTCTGCAAT 58.799 45.455 0.00 0.00 41.50 3.56
1913 6570 0.317103 CGTTCTATGGCCGACGAGAG 60.317 60.000 0.00 0.00 37.69 3.20
1924 6587 2.678324 CCGACGAGAGCTTCTCTTTTT 58.322 47.619 0.00 0.00 41.35 1.94
1926 6589 2.664085 CGACGAGAGCTTCTCTTTTTCC 59.336 50.000 10.25 0.00 41.35 3.13
1948 6611 4.883585 CCTTGGCTTATCTTTCATGCAGTA 59.116 41.667 0.00 0.00 0.00 2.74
1957 6620 4.058124 TCTTTCATGCAGTACAGACACAC 58.942 43.478 0.00 0.00 0.00 3.82
1960 6623 0.037326 ATGCAGTACAGACACACGGG 60.037 55.000 0.00 0.00 0.00 5.28
1964 6635 0.898789 AGTACAGACACACGGGGAGG 60.899 60.000 0.00 0.00 0.00 4.30
1967 6638 1.293498 CAGACACACGGGGAGGAAG 59.707 63.158 0.00 0.00 0.00 3.46
1968 6639 1.155390 AGACACACGGGGAGGAAGA 59.845 57.895 0.00 0.00 0.00 2.87
1969 6640 0.471211 AGACACACGGGGAGGAAGAA 60.471 55.000 0.00 0.00 0.00 2.52
1970 6641 0.395312 GACACACGGGGAGGAAGAAA 59.605 55.000 0.00 0.00 0.00 2.52
1971 6642 0.396811 ACACACGGGGAGGAAGAAAG 59.603 55.000 0.00 0.00 0.00 2.62
1972 6643 0.955919 CACACGGGGAGGAAGAAAGC 60.956 60.000 0.00 0.00 0.00 3.51
1973 6644 1.374947 CACGGGGAGGAAGAAAGCA 59.625 57.895 0.00 0.00 0.00 3.91
1974 6645 0.250727 CACGGGGAGGAAGAAAGCAA 60.251 55.000 0.00 0.00 0.00 3.91
1975 6646 0.698818 ACGGGGAGGAAGAAAGCAAT 59.301 50.000 0.00 0.00 0.00 3.56
2042 6713 3.191162 CGAGGACATCAAGATTTGCCAAA 59.809 43.478 0.00 0.00 0.00 3.28
2097 6768 0.038892 GCGACTTGACCGGTGAAGTA 60.039 55.000 34.80 1.02 37.16 2.24
2139 6810 1.815003 CTGAACAATGCTCCCAACCTC 59.185 52.381 0.00 0.00 0.00 3.85
2190 6861 8.071235 AGGTACTTAGATATCTCCCCTTACTT 57.929 38.462 8.95 0.00 27.25 2.24
2319 6990 5.153950 AGTTTAGGGAGATCAACTGTCAC 57.846 43.478 0.00 0.00 0.00 3.67
2400 7071 0.811281 AAGACCGGCATTTGCTAAGC 59.189 50.000 0.00 0.00 41.70 3.09
2558 7229 1.209504 CCCCGAGGATTTGTAAGAGCA 59.790 52.381 0.00 0.00 33.47 4.26
2657 7328 4.744795 AGTTGGCTATTACTCTCACAGG 57.255 45.455 0.00 0.00 0.00 4.00
2734 7405 2.380365 GGGAACCGGGACTAAAGGT 58.620 57.895 6.32 0.00 40.86 3.50
2749 7420 4.529769 ACTAAAGGTTCGGTACTAAAGCCT 59.470 41.667 0.00 0.00 0.00 4.58
2848 7519 4.735358 GGGCCTTTGGTCCCGGTC 62.735 72.222 0.84 0.00 42.67 4.79
2861 7532 2.654877 CGGTCGGTAGCACCAACT 59.345 61.111 12.11 0.00 38.47 3.16
2862 7533 1.597797 CCGGTCGGTAGCACCAACTA 61.598 60.000 12.11 0.00 38.47 2.24
3091 7773 4.766404 AGTAAGCAAATGAAGGAAACCG 57.234 40.909 0.00 0.00 0.00 4.44
3185 7868 3.768468 TGGTCGAACAACAAGTTTTCC 57.232 42.857 0.00 0.00 41.51 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 83 5.345702 TGAAGCTGCATTTGAATCTATTGC 58.654 37.500 1.02 4.99 0.00 3.56
168 171 1.052287 CTTTTGCGATGCGTTTGGAC 58.948 50.000 0.00 0.00 0.00 4.02
181 184 9.626332 CATTTCAAAATTTTCAAATGCTTTTGC 57.374 25.926 22.07 0.00 41.66 3.68
330 336 7.935338 AGTTTGCACAAAGTATGAAATTCAG 57.065 32.000 1.10 0.00 32.58 3.02
438 444 7.274447 CAAAATTCATAGGTGGGCACAATTAT 58.726 34.615 0.00 0.00 0.00 1.28
464 470 8.059798 AGGATTTGTCAAAAATCAGATACCTG 57.940 34.615 1.31 0.00 41.74 4.00
479 485 7.465353 TTGATGCATCTTTTAGGATTTGTCA 57.535 32.000 26.32 0.00 0.00 3.58
481 487 7.124599 TCCATTGATGCATCTTTTAGGATTTGT 59.875 33.333 26.32 0.00 0.00 2.83
493 499 8.967918 CCTATATTTGAATCCATTGATGCATCT 58.032 33.333 26.32 5.39 36.39 2.90
543 549 4.323417 AGGTATCAACTGTTCGCATTTGA 58.677 39.130 3.54 3.54 46.11 2.69
564 570 8.365399 TCAAATTCGAGGTATGTAGCATAAAG 57.635 34.615 0.00 0.00 0.00 1.85
566 572 7.497595 ACTCAAATTCGAGGTATGTAGCATAA 58.502 34.615 0.00 0.00 37.34 1.90
578 584 6.648725 ACTTAATTCGACTCAAATTCGAGG 57.351 37.500 0.00 0.00 45.70 4.63
579 585 8.934973 AAAACTTAATTCGACTCAAATTCGAG 57.065 30.769 0.00 0.00 45.70 4.04
714 3068 7.262048 TCGATTTGCCATTTACCTAAAAATCC 58.738 34.615 0.00 0.00 0.00 3.01
723 3077 5.949233 GAATGTTCGATTTGCCATTTACC 57.051 39.130 0.00 0.00 0.00 2.85
765 5323 3.433615 GGAGAAAATTGATATCCTCGCGG 59.566 47.826 6.13 0.00 0.00 6.46
788 5346 1.074405 TCAGGATTTGTCAGGCTTGCT 59.926 47.619 0.00 0.00 0.00 3.91
864 5422 5.896073 ACTTGTCATTAGGGATAGGGAAG 57.104 43.478 0.00 0.00 0.00 3.46
872 5430 6.833041 TCTGTTTACAACTTGTCATTAGGGA 58.167 36.000 0.00 0.00 0.00 4.20
873 5431 7.504924 TTCTGTTTACAACTTGTCATTAGGG 57.495 36.000 0.00 0.00 0.00 3.53
874 5432 7.586300 CGTTTCTGTTTACAACTTGTCATTAGG 59.414 37.037 0.00 0.00 0.00 2.69
879 5452 5.163834 GGACGTTTCTGTTTACAACTTGTCA 60.164 40.000 0.00 0.00 0.00 3.58
915 5572 1.452953 TATCTTCCGATCCGCACGCT 61.453 55.000 0.00 0.00 0.00 5.07
1046 5703 2.801631 CCCAGGGAGGAGACGATGC 61.802 68.421 0.00 0.00 41.22 3.91
1206 5863 2.716017 CCACTCCTCGAGCTCCACC 61.716 68.421 6.99 0.00 32.04 4.61
1386 6043 4.643387 AGGCAGCCGTGAACCCAC 62.643 66.667 5.55 0.00 39.86 4.61
1477 6134 1.740285 GGCTTAGATCGGAGCGGAA 59.260 57.895 14.48 0.00 39.78 4.30
1522 6179 4.530857 GCCGCCGCTGTGTAGGAT 62.531 66.667 3.81 0.00 0.00 3.24
1839 6496 7.499563 AGCTCTAATCTTGTCACGTTATAGAGA 59.500 37.037 9.90 0.00 38.11 3.10
1913 6570 5.417266 AGATAAGCCAAGGAAAAAGAGAAGC 59.583 40.000 0.00 0.00 0.00 3.86
1924 6587 3.949754 CTGCATGAAAGATAAGCCAAGGA 59.050 43.478 0.00 0.00 0.00 3.36
1926 6589 4.978083 ACTGCATGAAAGATAAGCCAAG 57.022 40.909 0.00 0.00 0.00 3.61
1948 6611 1.458777 TTCCTCCCCGTGTGTCTGT 60.459 57.895 0.00 0.00 0.00 3.41
1957 6620 1.839424 AATTGCTTTCTTCCTCCCCG 58.161 50.000 0.00 0.00 0.00 5.73
1991 6662 6.287589 TCCTAATCTGAAACAGAGAGGAAC 57.712 41.667 21.98 0.00 45.45 3.62
1999 6670 5.111989 TCGCTTCATCCTAATCTGAAACAG 58.888 41.667 0.00 0.00 31.40 3.16
2042 6713 7.831193 AGAGCAATGTAGTCAGGTTATGAAATT 59.169 33.333 0.00 0.00 40.43 1.82
2139 6810 5.852005 CAATTCTGCAGAGTAAGTTTCTCG 58.148 41.667 17.43 1.62 37.07 4.04
2190 6861 7.817418 AGCTTAACTGTTATTTCAAGTTGGA 57.183 32.000 2.34 0.00 0.00 3.53
2319 6990 1.339055 TGTTGAAGATCGCCCTCCTTG 60.339 52.381 0.00 0.00 0.00 3.61
2400 7071 0.881118 CCCACGTCCCTTCATTGTTG 59.119 55.000 0.00 0.00 0.00 3.33
2657 7328 5.099042 TGGCCCTTTTTCTACTAGTGATC 57.901 43.478 5.39 0.00 0.00 2.92
2734 7405 6.796785 AAGGTATAAGGCTTTAGTACCGAA 57.203 37.500 20.71 0.00 39.74 4.30
2749 7420 6.667414 TGTAAGAACCGGGACTAAAGGTATAA 59.333 38.462 6.32 0.00 37.26 0.98
2813 7484 4.337304 TCCTCCTGCCTGGGCTCA 62.337 66.667 13.05 0.00 42.51 4.26
2824 7495 1.925972 GACCAAAGGCCCTCCTCCT 60.926 63.158 0.00 0.00 43.40 3.69
2825 7496 2.677848 GACCAAAGGCCCTCCTCC 59.322 66.667 0.00 0.00 43.40 4.30
2826 7497 2.677848 GGACCAAAGGCCCTCCTC 59.322 66.667 0.00 0.00 43.40 3.71
2848 7519 1.153429 GGCCTAGTTGGTGCTACCG 60.153 63.158 0.00 0.00 42.58 4.02
3008 7690 0.454600 TCGACCAAGCACGGAGATAC 59.545 55.000 0.00 0.00 0.00 2.24
3052 7734 1.007580 CTAGCTAGCGTGTCGAGTCA 58.992 55.000 8.05 0.00 0.00 3.41
3091 7773 9.297586 TGTTCATGACGATATTCTGTACTTAAC 57.702 33.333 0.00 0.00 0.00 2.01
3185 7868 6.456447 GCTAGTAGCGTCGGATAGATATAG 57.544 45.833 6.36 0.00 0.00 1.31
3259 7942 0.035056 CCATGTGGACCCTGAGTTCC 60.035 60.000 0.00 0.00 37.39 3.62


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

AutoCloner maintained by Alex Coulton.