Multiple sequence alignment - TraesCS6A01G194000

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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 TraesCS6A01G194000 chr6A 100.000 4098 0 0 1 4098 271185204 271181107 0.000000e+00 7568
1 TraesCS6A01G194000 chr6A 95.915 3011 97 9 344 3350 260125388 260128376 0.000000e+00 4855
2 TraesCS6A01G194000 chr6A 96.286 754 28 0 3345 4098 313497496 313498249 0.000000e+00 1238
3 TraesCS6A01G194000 chr6A 96.286 754 28 0 3345 4098 490238736 490239489 0.000000e+00 1238
4 TraesCS6A01G194000 chrUn 97.625 3369 61 11 1 3350 93416581 93419949 0.000000e+00 5760
5 TraesCS6A01G194000 chr5D 97.624 3367 62 10 1 3350 560880234 560876869 0.000000e+00 5758
6 TraesCS6A01G194000 chr5D 96.760 3364 63 14 1 3350 503213639 503210308 0.000000e+00 5566
7 TraesCS6A01G194000 chr3B 97.118 3366 77 15 1 3350 201522439 201519078 0.000000e+00 5661
8 TraesCS6A01G194000 chr1A 96.095 3355 111 17 1 3350 168442865 168446204 0.000000e+00 5452
9 TraesCS6A01G194000 chr1A 96.154 754 29 0 3345 4098 217657623 217658376 0.000000e+00 1232
10 TraesCS6A01G194000 chr1D 97.843 3060 52 12 1 3048 144238468 144235411 0.000000e+00 5273
11 TraesCS6A01G194000 chr3A 96.663 2427 63 9 1 2418 672914576 672916993 0.000000e+00 4017
12 TraesCS6A01G194000 chr3A 96.444 2137 64 10 389 2520 692573171 692571042 0.000000e+00 3515
13 TraesCS6A01G194000 chr3A 96.154 754 29 0 3345 4098 162831139 162831892 0.000000e+00 1232
14 TraesCS6A01G194000 chr3A 94.627 335 13 2 1 330 471793317 471792983 7.850000e-142 514
15 TraesCS6A01G194000 chr3A 94.393 107 6 0 2724 2830 38285988 38286094 9.110000e-37 165
16 TraesCS6A01G194000 chr2A 96.286 754 27 1 3345 4098 331506409 331507161 0.000000e+00 1236
17 TraesCS6A01G194000 chr2A 97.787 497 11 0 2500 2996 771308040 771308536 0.000000e+00 857
18 TraesCS6A01G194000 chr2A 97.037 135 4 0 2651 2785 65287526 65287660 1.150000e-55 228
19 TraesCS6A01G194000 chr2A 87.692 195 18 5 3144 3334 713871661 713871853 5.330000e-54 222
20 TraesCS6A01G194000 chr2A 97.479 119 3 0 173 291 187060399 187060281 1.930000e-48 204
21 TraesCS6A01G194000 chr2A 96.721 122 4 0 170 291 187105846 187105967 1.930000e-48 204
22 TraesCS6A01G194000 chr2A 81.308 214 29 4 5 216 605912462 605912258 3.280000e-36 163
23 TraesCS6A01G194000 chr7A 96.154 754 29 0 3345 4098 309606775 309607528 0.000000e+00 1232
24 TraesCS6A01G194000 chr7A 96.154 754 28 1 3345 4098 445073106 445072354 0.000000e+00 1230
25 TraesCS6A01G194000 chr7A 96.154 754 28 1 3345 4098 456302439 456303191 0.000000e+00 1230
26 TraesCS6A01G194000 chr7A 94.304 474 21 2 1 468 352186367 352186840 0.000000e+00 721
27 TraesCS6A01G194000 chr4A 96.154 754 29 0 3345 4098 7970827 7971580 0.000000e+00 1232
28 TraesCS6A01G194000 chr4A 88.378 370 24 3 1 359 114912550 114912189 1.050000e-115 427
29 TraesCS6A01G194000 chr4A 93.103 261 16 1 2984 3242 949438 949698 8.310000e-102 381
30 TraesCS6A01G194000 chr4A 97.297 148 4 0 3176 3323 700661455 700661602 6.800000e-63 252
31 TraesCS6A01G194000 chr4A 92.857 98 6 1 2645 2741 547290845 547290942 1.540000e-29 141
32 TraesCS6A01G194000 chr7B 93.190 558 27 7 2767 3321 459813610 459813061 0.000000e+00 809
33 TraesCS6A01G194000 chr7B 97.980 99 2 0 289 387 366254565 366254663 5.450000e-39 172
34 TraesCS6A01G194000 chr7B 81.776 214 28 4 5 216 698140575 698140779 7.040000e-38 169
35 TraesCS6A01G194000 chr4D 91.255 526 37 6 1 520 349797499 349798021 0.000000e+00 708


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 TraesCS6A01G194000 chr6A 271181107 271185204 4097 True 7568 7568 100.000 1 4098 1 chr6A.!!$R1 4097
1 TraesCS6A01G194000 chr6A 260125388 260128376 2988 False 4855 4855 95.915 344 3350 1 chr6A.!!$F1 3006
2 TraesCS6A01G194000 chr6A 313497496 313498249 753 False 1238 1238 96.286 3345 4098 1 chr6A.!!$F2 753
3 TraesCS6A01G194000 chr6A 490238736 490239489 753 False 1238 1238 96.286 3345 4098 1 chr6A.!!$F3 753
4 TraesCS6A01G194000 chrUn 93416581 93419949 3368 False 5760 5760 97.625 1 3350 1 chrUn.!!$F1 3349
5 TraesCS6A01G194000 chr5D 560876869 560880234 3365 True 5758 5758 97.624 1 3350 1 chr5D.!!$R2 3349
6 TraesCS6A01G194000 chr5D 503210308 503213639 3331 True 5566 5566 96.760 1 3350 1 chr5D.!!$R1 3349
7 TraesCS6A01G194000 chr3B 201519078 201522439 3361 True 5661 5661 97.118 1 3350 1 chr3B.!!$R1 3349
8 TraesCS6A01G194000 chr1A 168442865 168446204 3339 False 5452 5452 96.095 1 3350 1 chr1A.!!$F1 3349
9 TraesCS6A01G194000 chr1A 217657623 217658376 753 False 1232 1232 96.154 3345 4098 1 chr1A.!!$F2 753
10 TraesCS6A01G194000 chr1D 144235411 144238468 3057 True 5273 5273 97.843 1 3048 1 chr1D.!!$R1 3047
11 TraesCS6A01G194000 chr3A 672914576 672916993 2417 False 4017 4017 96.663 1 2418 1 chr3A.!!$F3 2417
12 TraesCS6A01G194000 chr3A 692571042 692573171 2129 True 3515 3515 96.444 389 2520 1 chr3A.!!$R2 2131
13 TraesCS6A01G194000 chr3A 162831139 162831892 753 False 1232 1232 96.154 3345 4098 1 chr3A.!!$F2 753
14 TraesCS6A01G194000 chr2A 331506409 331507161 752 False 1236 1236 96.286 3345 4098 1 chr2A.!!$F3 753
15 TraesCS6A01G194000 chr7A 309606775 309607528 753 False 1232 1232 96.154 3345 4098 1 chr7A.!!$F1 753
16 TraesCS6A01G194000 chr7A 445072354 445073106 752 True 1230 1230 96.154 3345 4098 1 chr7A.!!$R1 753
17 TraesCS6A01G194000 chr7A 456302439 456303191 752 False 1230 1230 96.154 3345 4098 1 chr7A.!!$F3 753
18 TraesCS6A01G194000 chr4A 7970827 7971580 753 False 1232 1232 96.154 3345 4098 1 chr4A.!!$F2 753
19 TraesCS6A01G194000 chr7B 459813061 459813610 549 True 809 809 93.190 2767 3321 1 chr7B.!!$R1 554
20 TraesCS6A01G194000 chr4D 349797499 349798021 522 False 708 708 91.255 1 520 1 chr4D.!!$F1 519

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
387 404 7.120923 ACTAACCTCTATAAGAAATGCGGAA 57.879 36.000 0.0 0.0 0.00 4.30 F
1336 1386 1.067212 GACTGATTCGTAGGCGTGGAT 59.933 52.381 0.0 0.0 39.49 3.41 F
1637 1691 3.404224 TGGTTTACGTAGGAATGCACA 57.596 42.857 0.0 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2138 0.553819 ATCCTGCTACCTCCTCTCGT 59.446 55.000 0.0 0.0 0.0 4.18 R
2269 2324 1.526464 GCCACACTTCCAAATTTTGCG 59.474 47.619 3.5 0.0 0.0 4.85 R
3505 3569 5.258051 TGTTACAAGTCCCAGTTCAGTTTT 58.742 37.500 0.0 0.0 0.0 2.43 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
342 359 7.509659 GGAACCTAGAATTAGAGTCTTATGGGA 59.490 40.741 0.00 0.00 0.00 4.37
387 404 7.120923 ACTAACCTCTATAAGAAATGCGGAA 57.879 36.000 0.00 0.00 0.00 4.30
1004 1030 9.217278 GTCTAGTTCTATACGAATACTGATGGA 57.783 37.037 0.00 0.00 33.45 3.41
1051 1077 4.576463 GTCGTTATGATTCAAGCAAGGGAT 59.424 41.667 0.00 0.00 0.00 3.85
1165 1209 8.560903 AGGATACCAAAGATTCAAAGGATTAGT 58.439 33.333 0.00 0.00 37.17 2.24
1336 1386 1.067212 GACTGATTCGTAGGCGTGGAT 59.933 52.381 0.00 0.00 39.49 3.41
1356 1406 5.824624 TGGATGAATTAGAGTCATTTGCTCC 59.175 40.000 0.00 0.00 35.84 4.70
1362 1412 3.726557 AGAGTCATTTGCTCCAATCCA 57.273 42.857 0.00 0.00 33.69 3.41
1411 1462 8.816204 TCTTTCGAAAAAGAACTTTACTTTCG 57.184 30.769 12.41 18.31 46.09 3.46
1637 1691 3.404224 TGGTTTACGTAGGAATGCACA 57.596 42.857 0.00 0.00 0.00 4.57
1649 1703 7.173562 ACGTAGGAATGCACATTTTAGTTTACA 59.826 33.333 0.00 0.00 0.00 2.41
1853 1907 3.455990 TCGTACAGTAGGTTTGCAACA 57.544 42.857 0.00 0.00 0.00 3.33
1942 1996 6.346096 AGTGGTGTGCGATTAAGTTGTATAT 58.654 36.000 0.00 0.00 0.00 0.86
1957 2011 6.346096 AGTTGTATATGCGATGTAACACCTT 58.654 36.000 0.00 0.00 0.00 3.50
2038 2093 6.860023 CGCTTTCAACTTTCATTTCAAGAGAT 59.140 34.615 0.00 0.00 0.00 2.75
2147 2202 7.389053 GGAAGTGTGTTGAATCAAGAGTAGATT 59.611 37.037 0.00 0.00 38.35 2.40
2269 2324 3.262420 AGAAGGAACATGTATCACACGC 58.738 45.455 0.00 0.00 0.00 5.34
2281 2336 0.382158 TCACACGCGCAAAATTTGGA 59.618 45.000 5.73 0.00 0.00 3.53
2288 2343 1.526464 GCGCAAAATTTGGAAGTGTGG 59.474 47.619 0.30 0.00 0.00 4.17
2290 2345 2.559440 GCAAAATTTGGAAGTGTGGCA 58.441 42.857 7.89 0.00 0.00 4.92
2665 2720 7.016072 TCTGGTGGGAATGTAAATGAAAAACAT 59.984 33.333 0.00 0.00 41.45 2.71
3014 3070 8.688747 AGATCTTCTGAGAATTGACAGTTTTT 57.311 30.769 0.00 0.00 35.07 1.94
3570 3634 4.458989 ACGGATTAGTAACACGTGAACCTA 59.541 41.667 25.01 14.64 36.32 3.08
3698 3762 7.723616 CCACAATCAATTCCCCTACATATAACA 59.276 37.037 0.00 0.00 0.00 2.41
3727 3791 2.981898 TCTAGACTCGACATCGACCAA 58.018 47.619 0.00 0.00 44.22 3.67
3746 3810 3.443681 CCAATTTGGCTCAACGAACCTAT 59.556 43.478 1.71 0.00 0.00 2.57
3747 3811 4.082245 CCAATTTGGCTCAACGAACCTATT 60.082 41.667 1.71 0.00 0.00 1.73
3776 3840 0.867753 GCTCTGATACCGACGCTGTG 60.868 60.000 0.00 0.00 0.00 3.66
3925 3989 3.801114 ATATGACAGTGTCGCTAGCAA 57.199 42.857 18.17 0.00 34.95 3.91
3926 3990 2.455674 ATGACAGTGTCGCTAGCAAA 57.544 45.000 18.17 0.00 34.95 3.68
3946 4010 3.713826 ACATATGACAAAGAACCCGGT 57.286 42.857 10.38 0.00 0.00 5.28
4032 4096 0.179127 CGAGCATGTCGGTCATCAGT 60.179 55.000 9.07 0.00 45.58 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
342 359 8.947115 GTTAGTAAATCAGCAATAGTGTCCTTT 58.053 33.333 0.00 0.00 0.00 3.11
634 655 2.604139 TCCCATTCCACCCAAAACTTC 58.396 47.619 0.00 0.00 0.00 3.01
1004 1030 7.699878 ACTTACTTCAATTTTGACCCTATCCT 58.300 34.615 0.00 0.00 36.83 3.24
1336 1386 6.319658 GGATTGGAGCAAATGACTCTAATTCA 59.680 38.462 13.34 0.00 43.05 2.57
1356 1406 5.865552 CCTGTCTTTGTTATGCTTTGGATTG 59.134 40.000 0.00 0.00 0.00 2.67
1362 1412 3.844640 ACCCCTGTCTTTGTTATGCTTT 58.155 40.909 0.00 0.00 0.00 3.51
1411 1462 5.171874 CGCGGGTACTTGTTTTTACTTTTTC 59.828 40.000 0.00 0.00 0.00 2.29
1424 1476 1.129811 GAACATTTCCGCGGGTACTTG 59.870 52.381 27.83 17.68 0.00 3.16
1637 1691 6.482308 ACGTGCACTCTTCTGTAAACTAAAAT 59.518 34.615 16.19 0.00 0.00 1.82
1649 1703 5.386958 TGTTATTCTACGTGCACTCTTCT 57.613 39.130 16.19 0.00 0.00 2.85
1762 1816 5.376625 TGAGCTTTTGAATCCACAAGTACT 58.623 37.500 0.00 0.00 33.72 2.73
1853 1907 4.017126 GCCCTTTACCATAACTTCTGCTT 58.983 43.478 0.00 0.00 0.00 3.91
1907 1961 2.031245 CGCACACCACTTTTAGCAATGA 60.031 45.455 0.00 0.00 0.00 2.57
1942 1996 0.878416 GGCAAAGGTGTTACATCGCA 59.122 50.000 0.00 0.00 0.00 5.10
1957 2011 0.943673 CGACATCCATTATGCGGCAA 59.056 50.000 6.82 0.00 39.39 4.52
1996 2051 7.040473 TGAAAGCGGGTTAATTCTTTTACAA 57.960 32.000 0.00 0.00 0.00 2.41
2083 2138 0.553819 ATCCTGCTACCTCCTCTCGT 59.446 55.000 0.00 0.00 0.00 4.18
2147 2202 3.805422 CGACCATAATAAAGGCGCTTACA 59.195 43.478 7.64 0.00 0.00 2.41
2235 2290 6.656693 ACATGTTCCTTCTATTTCTCCAAGTG 59.343 38.462 0.00 0.00 0.00 3.16
2269 2324 1.526464 GCCACACTTCCAAATTTTGCG 59.474 47.619 3.50 0.00 0.00 4.85
2281 2336 2.037251 AGAATACTCGTGTGCCACACTT 59.963 45.455 24.29 12.21 46.46 3.16
2288 2343 5.041287 TGCTATTGTAGAATACTCGTGTGC 58.959 41.667 0.00 0.00 43.54 4.57
2290 2345 5.360144 ACCTGCTATTGTAGAATACTCGTGT 59.640 40.000 0.00 0.00 43.54 4.49
2642 2697 7.158021 TCATGTTTTTCATTTACATTCCCACC 58.842 34.615 0.00 0.00 34.09 4.61
3505 3569 5.258051 TGTTACAAGTCCCAGTTCAGTTTT 58.742 37.500 0.00 0.00 0.00 2.43
3570 3634 6.025793 AGGACTAGGCTCTCTTCTTCTATT 57.974 41.667 0.00 0.00 0.00 1.73
3698 3762 5.289675 CGATGTCGAGTCTAGAAATGCTTTT 59.710 40.000 0.00 0.00 43.02 2.27
3727 3791 3.443681 CCAATAGGTTCGTTGAGCCAAAT 59.556 43.478 2.51 0.00 35.33 2.32
3746 3810 0.975556 TATCAGAGCCGGACTGCCAA 60.976 55.000 19.63 7.53 35.61 4.52
3747 3811 1.381191 TATCAGAGCCGGACTGCCA 60.381 57.895 19.63 9.95 35.61 4.92
3768 3832 4.436998 CGGGGTCCTCACAGCGTC 62.437 72.222 0.00 0.00 0.00 5.19
3776 3840 1.153147 GCTTGGAATCGGGGTCCTC 60.153 63.158 0.00 0.00 36.03 3.71
3911 3975 3.865164 TCATATGTTTGCTAGCGACACTG 59.135 43.478 21.51 20.12 0.00 3.66
3925 3989 4.007659 GACCGGGTTCTTTGTCATATGTT 58.992 43.478 6.32 0.00 0.00 2.71
3926 3990 3.606687 GACCGGGTTCTTTGTCATATGT 58.393 45.455 6.32 0.00 0.00 2.29
4032 4096 0.824109 CTACAGCCCGGAATCACTCA 59.176 55.000 0.73 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.