Multiple sequence alignment - TraesCS7A01G425100

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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 TraesCS7A01G425100 chr7A 100.000 3872 0 0 1 3872 618108868 618112739 0.000000e+00 7151
1 TraesCS7A01G425100 chr4B 98.930 2898 29 2 1 2896 612336091 612338988 0.000000e+00 5179
2 TraesCS7A01G425100 chr5A 98.930 2897 29 2 1 2896 10295370 10298265 0.000000e+00 5177
3 TraesCS7A01G425100 chr5A 92.604 338 23 1 3268 3605 631533871 631533536 5.820000e-133 484
4 TraesCS7A01G425100 chr5A 91.768 328 25 2 3268 3594 607289582 607289256 4.560000e-124 455
5 TraesCS7A01G425100 chr5A 90.549 328 31 0 3268 3595 591086078 591085751 5.940000e-118 435
6 TraesCS7A01G425100 chr5B 98.792 2898 33 2 1 2896 660693880 660690983 0.000000e+00 5156
7 TraesCS7A01G425100 chr3B 97.447 2899 70 4 1 2896 818056383 818059280 0.000000e+00 4940
8 TraesCS7A01G425100 chr4A 99.000 2601 23 3 299 2896 597729891 597727291 0.000000e+00 4656
9 TraesCS7A01G425100 chr4A 97.746 976 22 0 2897 3872 429434190 429435165 0.000000e+00 1681
10 TraesCS7A01G425100 chr4A 91.768 328 26 1 3268 3594 467244479 467244806 4.560000e-124 455
11 TraesCS7A01G425100 chr5D 95.179 2904 135 5 1 2899 15724998 15727901 0.000000e+00 4582
12 TraesCS7A01G425100 chr2B 94.959 2896 136 5 1 2894 12280405 12283292 0.000000e+00 4530
13 TraesCS7A01G425100 chr2B 91.100 2910 248 8 1 2907 142214398 142217299 0.000000e+00 3928
14 TraesCS7A01G425100 chr2B 94.675 169 9 0 185 353 731730092 731730260 2.970000e-66 263
15 TraesCS7A01G425100 chr1B 94.686 2898 147 4 1 2897 526384839 526381948 0.000000e+00 4492
16 TraesCS7A01G425100 chr1B 93.233 266 16 1 3607 3872 169650821 169650558 1.300000e-104 390
17 TraesCS7A01G425100 chr1B 94.366 142 8 0 3099 3240 169650975 169650834 6.510000e-53 219
18 TraesCS7A01G425100 chr1B 91.667 120 7 1 2929 3045 169651294 169651175 3.100000e-36 163
19 TraesCS7A01G425100 chr6A 96.209 976 26 2 2897 3872 593281194 593280230 0.000000e+00 1587
20 TraesCS7A01G425100 chr6A 92.966 327 23 0 3268 3594 493558143 493557817 9.730000e-131 477
21 TraesCS7A01G425100 chr6A 92.073 328 26 0 3268 3595 203524317 203523990 2.730000e-126 462
22 TraesCS7A01G425100 chr4D 91.354 347 27 1 2897 3240 211167428 211167774 4.530000e-129 472
23 TraesCS7A01G425100 chr3A 91.159 328 28 1 3268 3594 36138141 36137814 9.870000e-121 444


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 TraesCS7A01G425100 chr7A 618108868 618112739 3871 False 7151.000000 7151 100.000000 1 3872 1 chr7A.!!$F1 3871
1 TraesCS7A01G425100 chr4B 612336091 612338988 2897 False 5179.000000 5179 98.930000 1 2896 1 chr4B.!!$F1 2895
2 TraesCS7A01G425100 chr5A 10295370 10298265 2895 False 5177.000000 5177 98.930000 1 2896 1 chr5A.!!$F1 2895
3 TraesCS7A01G425100 chr5B 660690983 660693880 2897 True 5156.000000 5156 98.792000 1 2896 1 chr5B.!!$R1 2895
4 TraesCS7A01G425100 chr3B 818056383 818059280 2897 False 4940.000000 4940 97.447000 1 2896 1 chr3B.!!$F1 2895
5 TraesCS7A01G425100 chr4A 597727291 597729891 2600 True 4656.000000 4656 99.000000 299 2896 1 chr4A.!!$R1 2597
6 TraesCS7A01G425100 chr4A 429434190 429435165 975 False 1681.000000 1681 97.746000 2897 3872 1 chr4A.!!$F1 975
7 TraesCS7A01G425100 chr5D 15724998 15727901 2903 False 4582.000000 4582 95.179000 1 2899 1 chr5D.!!$F1 2898
8 TraesCS7A01G425100 chr2B 12280405 12283292 2887 False 4530.000000 4530 94.959000 1 2894 1 chr2B.!!$F1 2893
9 TraesCS7A01G425100 chr2B 142214398 142217299 2901 False 3928.000000 3928 91.100000 1 2907 1 chr2B.!!$F2 2906
10 TraesCS7A01G425100 chr1B 526381948 526384839 2891 True 4492.000000 4492 94.686000 1 2897 1 chr1B.!!$R1 2896
11 TraesCS7A01G425100 chr1B 169650558 169651294 736 True 257.333333 390 93.088667 2929 3872 3 chr1B.!!$R2 943
12 TraesCS7A01G425100 chr6A 593280230 593281194 964 True 1587.000000 1587 96.209000 2897 3872 1 chr6A.!!$R3 975

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
853 854 2.423892 GACAACTATGAGAGAGCCACGA 59.576 50.0 0.00 0.0 0.00 4.35 F
1738 1747 0.106967 TTATATTGCGTGGCAGCCCA 60.107 50.0 9.64 0.0 40.61 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2612 2625 2.357034 GCGCCTTTGTCACCGAGA 60.357 61.111 0.0 0.0 0.0 4.04 R
3315 3496 1.053424 AGTAACCAAACGCTCCCTGA 58.947 50.000 0.0 0.0 0.0 3.86 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
80 81 2.989639 CGCAGATGGGTTCCCTGA 59.010 61.111 9.43 0.00 0.00 3.86
208 209 8.229253 TGTTATAGTGCTAATACCGAAGAAGA 57.771 34.615 0.00 0.00 0.00 2.87
852 853 2.480416 GGACAACTATGAGAGAGCCACG 60.480 54.545 0.00 0.00 0.00 4.94
853 854 2.423892 GACAACTATGAGAGAGCCACGA 59.576 50.000 0.00 0.00 0.00 4.35
921 922 3.708403 TGCTCACAAGAAGATGGACAT 57.292 42.857 0.00 0.00 0.00 3.06
1118 1120 4.956075 ACTAATTAAATCAGTGGCCCAAGG 59.044 41.667 0.00 0.00 0.00 3.61
1317 1321 7.891498 TCTTAAAGTTTTTAACCAGGCTCTT 57.109 32.000 0.00 0.00 0.00 2.85
1619 1624 1.142748 CAGACCTCATCGACCAGGC 59.857 63.158 10.81 5.03 32.32 4.85
1738 1747 0.106967 TTATATTGCGTGGCAGCCCA 60.107 50.000 9.64 0.00 40.61 5.36
1942 1953 6.433093 ACTGGCGGTTCAAACTAATAGATTTT 59.567 34.615 0.00 0.00 0.00 1.82
2079 2090 1.856873 ATGGAACCTGCCCCCTGAA 60.857 57.895 0.00 0.00 0.00 3.02
2328 2339 7.309194 CGAAAAGGGAAAAGTCTGATGGTTAAT 60.309 37.037 0.00 0.00 0.00 1.40
2462 2474 1.993653 CCTGGGGAGCTGTGATTCA 59.006 57.895 0.00 0.00 0.00 2.57
2612 2625 2.827800 ATCATCGAGACGGATTGCAT 57.172 45.000 0.00 0.00 0.00 3.96
2702 2715 2.956132 TCAAGCCATGAAAGGGAACAA 58.044 42.857 0.00 0.00 43.46 2.83
2707 2720 3.966665 AGCCATGAAAGGGAACAAAGAAA 59.033 39.130 0.00 0.00 43.46 2.52
3033 3052 2.877168 CTGAAGCCTTATCTCATGTGGC 59.123 50.000 0.00 0.00 43.52 5.01
3093 3112 5.401972 CGAGCATGAAGAATGTGAGATACTC 59.598 44.000 0.00 0.00 38.65 2.59
3231 3412 1.737355 GCCTCCAAAAGTGTGCAGCA 61.737 55.000 0.00 0.00 0.00 4.41
3286 3467 4.407551 GCCATTGCTTTGATCCGC 57.592 55.556 0.00 0.00 33.53 5.54
3338 3519 1.154197 GGAGCGTTTGGTTACTGGAC 58.846 55.000 0.00 0.00 0.00 4.02
3373 3554 2.799126 TGGTTGCACGGGATATCTTT 57.201 45.000 2.05 0.00 0.00 2.52
3510 3691 7.639113 TGTTTGAGAATTTTAGACTGGTGTT 57.361 32.000 0.00 0.00 0.00 3.32
3511 3692 8.740123 TGTTTGAGAATTTTAGACTGGTGTTA 57.260 30.769 0.00 0.00 0.00 2.41
3570 3751 2.178876 TTTTCGATGCAGAGGCCGGA 62.179 55.000 5.05 0.00 40.13 5.14
3586 3767 0.984995 CGGAGAAGTCCCCCTTTTCT 59.015 55.000 0.00 0.00 40.20 2.52
3629 3810 2.485479 GGGCAGCGATTCCTTGATCTTA 60.485 50.000 0.00 0.00 0.00 2.10
3697 3878 5.528320 GGAATCATATGGGGCAAACAAAATG 59.472 40.000 2.13 0.00 0.00 2.32
3773 3954 5.217978 AGGGTGTGAACTATTTACGAACA 57.782 39.130 0.00 0.00 0.00 3.18
3840 4021 1.412343 GCCAATTTGCGTATCCCCATT 59.588 47.619 0.00 0.00 0.00 3.16
3854 4035 4.407329 TCCCCATTGCCATAATGATGAT 57.593 40.909 0.00 0.00 34.73 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 5.383476 CCCAATGCCTCTGATAAAATCTCT 58.617 41.667 0.00 0.00 0.00 3.10
208 209 2.963599 TTTAGGGAGCTCGGGTTTTT 57.036 45.000 7.83 0.00 0.00 1.94
745 746 4.804139 CGCGAATAAAAGGTGTGAGATACT 59.196 41.667 0.00 0.00 0.00 2.12
852 853 9.202273 CATTTAGATGGACTTATTAGCTGTCTC 57.798 37.037 0.00 0.00 0.00 3.36
853 854 7.659390 GCATTTAGATGGACTTATTAGCTGTCT 59.341 37.037 0.00 0.00 33.72 3.41
1118 1120 3.259123 ACTCATTGCAAAAGTGGGAATCC 59.741 43.478 14.94 0.00 0.00 3.01
1619 1624 0.734253 CTCCTTCCAAGCGTGACTCG 60.734 60.000 0.00 0.00 43.12 4.18
1942 1953 3.785859 GAGGCCTGGGATGCGACA 61.786 66.667 12.00 0.00 0.00 4.35
2079 2090 6.555360 CCCTTCCAGTATATTCTACTTCCTGT 59.445 42.308 0.00 0.00 0.00 4.00
2612 2625 2.357034 GCGCCTTTGTCACCGAGA 60.357 61.111 0.00 0.00 0.00 4.04
2895 2911 9.603189 ACCTAGTAGTACAGCCATTAGAAATAT 57.397 33.333 2.52 0.00 0.00 1.28
3054 3073 4.021456 TCATGCTCGGACGTCCAATAATAT 60.021 41.667 32.80 16.06 35.14 1.28
3286 3467 4.804139 GTCGGAGTGAGTAATAACCACATG 59.196 45.833 0.00 0.00 32.41 3.21
3315 3496 1.053424 AGTAACCAAACGCTCCCTGA 58.947 50.000 0.00 0.00 0.00 3.86
3338 3519 1.944177 ACCATCTCCCATCGGATAGG 58.056 55.000 0.00 0.00 37.60 2.57
3373 3554 2.124901 CGCCATCCAAACCGGCTA 60.125 61.111 0.00 0.00 43.95 3.93
3455 3636 3.498397 CACAGAGCGCTAAAGAAGGAAAA 59.502 43.478 11.50 0.00 0.00 2.29
3482 3663 8.190784 CACCAGTCTAAAATTCTCAAACAAAGT 58.809 33.333 0.00 0.00 0.00 2.66
3510 3691 9.974980 CCTTTATTAAACAAGCAAAGAGGTTTA 57.025 29.630 0.00 0.00 35.33 2.01
3511 3692 8.482943 ACCTTTATTAAACAAGCAAAGAGGTTT 58.517 29.630 0.00 0.00 35.33 3.27
3697 3878 4.145052 ACATGAAAAAGACTCCTTGGTCC 58.855 43.478 0.00 0.00 36.95 4.46
3773 3954 8.829373 AATTATCAAGAAAGACCTATTTGCCT 57.171 30.769 0.00 0.00 0.00 4.75
3840 4021 8.916062 ACTTGAATTAACATCATCATTATGGCA 58.084 29.630 0.00 0.00 33.61 4.92


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

AutoCloner maintained by Alex Coulton.