Multiple sequence alignment - TraesCS6D01G085600

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 TraesCS6D01G085600 chr6D 100.000 2642 0 0 1 2642 50955656 50958297 0.000000e+00 4879
1 TraesCS6D01G085600 chr6D 95.606 2663 81 14 1 2642 53176716 53174069 0.000000e+00 4237
2 TraesCS6D01G085600 chr6D 88.492 2520 206 42 173 2642 51342392 51344877 0.000000e+00 2970
3 TraesCS6D01G085600 chr6D 88.374 2503 207 23 173 2642 51067702 51070153 0.000000e+00 2933
4 TraesCS6D01G085600 chr6D 85.544 2511 246 49 173 2630 51348306 51350752 0.000000e+00 2518
5 TraesCS6D01G085600 chr6D 85.470 2512 250 51 173 2630 51073523 51075973 0.000000e+00 2510
6 TraesCS6D01G085600 chr6D 86.689 2111 228 23 541 2630 50948978 50951056 0.000000e+00 2292
7 TraesCS6D01G085600 chr6D 95.946 74 1 1 54 125 51073374 51073447 4.620000e-23 119
8 TraesCS6D01G085600 chr6D 95.946 74 1 1 54 125 51348157 51348230 4.620000e-23 119
9 TraesCS6D01G085600 chr6A 93.794 2288 129 8 361 2640 64168198 64165916 0.000000e+00 3426
10 TraesCS6D01G085600 chr6A 82.759 638 58 26 173 782 64175644 64175031 3.010000e-144 521
11 TraesCS6D01G085600 chr6A 95.431 197 8 1 173 368 64168561 64168365 1.970000e-81 313
12 TraesCS6D01G085600 chr6A 92.025 163 10 2 1 163 64168760 64168601 2.650000e-55 226
13 TraesCS6D01G085600 chr6B 94.157 1968 96 7 677 2642 120317474 120315524 0.000000e+00 2979
14 TraesCS6D01G085600 chr6B 87.609 2518 236 35 173 2642 120595960 120593471 0.000000e+00 2852
15 TraesCS6D01G085600 chr6B 88.904 2280 197 22 397 2642 120355400 120353143 0.000000e+00 2758
16 TraesCS6D01G085600 chr6B 87.911 2068 209 18 602 2642 120132997 120130944 0.000000e+00 2396
17 TraesCS6D01G085600 chr6B 96.104 231 9 0 173 403 120355732 120355502 6.900000e-101 377
18 TraesCS6D01G085600 chr6B 84.615 260 18 7 336 575 120133428 120133171 3.400000e-59 239
19 TraesCS6D01G085600 chr6B 90.184 163 13 3 1 163 120355941 120355782 2.660000e-50 209
20 TraesCS6D01G085600 chr6B 75.359 418 37 30 54 446 120318237 120317861 9.860000e-30 141
21 TraesCS6D01G085600 chr6B 94.737 76 4 0 173 248 120133762 120133687 4.620000e-23 119
22 TraesCS6D01G085600 chr3D 86.902 2382 219 44 332 2642 560025277 560022918 0.000000e+00 2584
23 TraesCS6D01G085600 chr1B 87.126 2338 227 33 331 2607 4519389 4517065 0.000000e+00 2582
24 TraesCS6D01G085600 chr7A 85.992 2520 222 56 173 2615 631983864 631986329 0.000000e+00 2577
25 TraesCS6D01G085600 chr7B 85.748 2533 218 55 173 2615 591461056 591463535 0.000000e+00 2545
26 TraesCS6D01G085600 chr7B 88.889 117 8 3 590 705 216661810 216661922 3.550000e-29 139
27 TraesCS6D01G085600 chr7D 85.573 2523 227 59 173 2615 548230522 548232987 0.000000e+00 2516
28 TraesCS6D01G085600 chr5D 87.977 2096 188 25 594 2642 57819423 57821501 0.000000e+00 2416
29 TraesCS6D01G085600 chr5B 87.937 2089 195 18 599 2642 60826096 60824020 0.000000e+00 2409
30 TraesCS6D01G085600 chr3B 81.423 253 23 7 340 568 318290231 318290483 4.490000e-43 185


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 TraesCS6D01G085600 chr6D 50955656 50958297 2641 False 4879.000000 4879 100.000000 1 2642 1 chr6D.!!$F2 2641
1 TraesCS6D01G085600 chr6D 53174069 53176716 2647 True 4237.000000 4237 95.606000 1 2642 1 chr6D.!!$R1 2641
2 TraesCS6D01G085600 chr6D 50948978 50951056 2078 False 2292.000000 2292 86.689000 541 2630 1 chr6D.!!$F1 2089
3 TraesCS6D01G085600 chr6D 51342392 51350752 8360 False 1869.000000 2970 89.994000 54 2642 3 chr6D.!!$F4 2588
4 TraesCS6D01G085600 chr6D 51067702 51075973 8271 False 1854.000000 2933 89.930000 54 2642 3 chr6D.!!$F3 2588
5 TraesCS6D01G085600 chr6A 64165916 64168760 2844 True 1321.666667 3426 93.750000 1 2640 3 chr6A.!!$R2 2639
6 TraesCS6D01G085600 chr6A 64175031 64175644 613 True 521.000000 521 82.759000 173 782 1 chr6A.!!$R1 609
7 TraesCS6D01G085600 chr6B 120593471 120595960 2489 True 2852.000000 2852 87.609000 173 2642 1 chr6B.!!$R1 2469
8 TraesCS6D01G085600 chr6B 120315524 120318237 2713 True 1560.000000 2979 84.758000 54 2642 2 chr6B.!!$R3 2588
9 TraesCS6D01G085600 chr6B 120353143 120355941 2798 True 1114.666667 2758 91.730667 1 2642 3 chr6B.!!$R4 2641
10 TraesCS6D01G085600 chr6B 120130944 120133762 2818 True 918.000000 2396 89.087667 173 2642 3 chr6B.!!$R2 2469
11 TraesCS6D01G085600 chr3D 560022918 560025277 2359 True 2584.000000 2584 86.902000 332 2642 1 chr3D.!!$R1 2310
12 TraesCS6D01G085600 chr1B 4517065 4519389 2324 True 2582.000000 2582 87.126000 331 2607 1 chr1B.!!$R1 2276
13 TraesCS6D01G085600 chr7A 631983864 631986329 2465 False 2577.000000 2577 85.992000 173 2615 1 chr7A.!!$F1 2442
14 TraesCS6D01G085600 chr7B 591461056 591463535 2479 False 2545.000000 2545 85.748000 173 2615 1 chr7B.!!$F2 2442
15 TraesCS6D01G085600 chr7D 548230522 548232987 2465 False 2516.000000 2516 85.573000 173 2615 1 chr7D.!!$F1 2442
16 TraesCS6D01G085600 chr5D 57819423 57821501 2078 False 2416.000000 2416 87.977000 594 2642 1 chr5D.!!$F1 2048
17 TraesCS6D01G085600 chr5B 60824020 60826096 2076 True 2409.000000 2409 87.937000 599 2642 1 chr5B.!!$R1 2043

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
653 1490 1.269988 GCTTGCATCGATCCTAGCTCA 60.27 52.381 14.47 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2868 0.103755 TGCTGCAGCTCCGAGATAAG 59.896 55.0 36.61 0.0 42.66 1.73 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
47 48 2.764269 CCCCACATCTTCCTTCCTCTA 58.236 52.381 0.00 0.0 0.00 2.43
125 133 3.531538 CTCCGATCCCGAATCAAAGAAA 58.468 45.455 0.00 0.0 38.22 2.52
136 144 5.180117 CCGAATCAAAGAAAGAGAGAAGCAA 59.820 40.000 0.00 0.0 0.00 3.91
138 146 7.303998 CGAATCAAAGAAAGAGAGAAGCAATT 58.696 34.615 0.00 0.0 0.00 2.32
286 401 5.058492 CACGCTTTCTTTTAGATTCGCTTTG 59.942 40.000 0.00 0.0 0.00 2.77
617 1450 1.795768 GGTTCAGATTCAGCACGTGA 58.204 50.000 22.23 0.0 0.00 4.35
653 1490 1.269988 GCTTGCATCGATCCTAGCTCA 60.270 52.381 14.47 0.0 0.00 4.26
696 1625 6.325028 ACAGCTAGTTCATTATTCAGGCTCTA 59.675 38.462 0.00 0.0 0.00 2.43
863 1851 9.323985 GCTCAAAGTTCATCAGTATATTCTTCT 57.676 33.333 0.00 0.0 0.00 2.85
1037 2044 0.452184 GCTCTCGTGACGGAGATTCA 59.548 55.000 21.71 0.0 41.92 2.57
1352 2359 1.239347 GACTCTGGGCTTGGTTGTTC 58.761 55.000 0.00 0.0 0.00 3.18
1418 2425 4.707448 ACCAAAAATAACGTCATATGGGCA 59.293 37.500 2.13 0.0 0.00 5.36
1557 2564 4.503741 TGTAGTGAAGAATTGCAAAGGC 57.496 40.909 1.71 0.0 41.68 4.35
1641 2649 9.541143 GAGTTTGAGAGGAAAAGAGGAATATAG 57.459 37.037 0.00 0.0 0.00 1.31
1782 2793 3.844577 GAAGTAGGACTTCGTGCTGTA 57.155 47.619 3.74 0.0 44.22 2.74
1857 2868 5.981315 CCTAAATGACAATGACATGATTGCC 59.019 40.000 0.00 0.0 36.89 4.52
1941 2952 8.648698 ACTCTAGTGATATCAGCTATTGTGAT 57.351 34.615 5.42 0.0 38.26 3.06
2070 3081 7.094248 CCATCAGAAATAGGATTCACACAACAA 60.094 37.037 0.00 0.0 0.00 2.83
2160 3171 2.378634 CGAGGGGATGAAGGCCCTT 61.379 63.158 0.00 0.0 45.30 3.95
2239 3250 2.662866 CTGGGATGTGCTTCATTGGAT 58.337 47.619 0.00 0.0 36.83 3.41
2365 3377 5.068636 TCGAGTGTTGTAGTAAGGTCTCTT 58.931 41.667 0.00 0.0 37.03 2.85
2417 3429 4.381411 GTTCACTACTCCAGCAACTTCTT 58.619 43.478 0.00 0.0 0.00 2.52
2548 3566 1.681166 GGACAAGGCTGTGCATCATCT 60.681 52.381 0.00 0.0 43.07 2.90
2586 3606 8.107095 ACTTGTATGGACTTTCTATTGCCTTTA 58.893 33.333 0.00 0.0 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.772567 ATGTGGGGCCGGCCTATTA 60.773 57.895 42.70 27.15 36.10 0.98
47 48 0.610687 CTCTCTTTTCCAGCGGAGGT 59.389 55.000 0.00 0.00 41.48 3.85
125 133 3.258971 CGGAGGAAATTGCTTCTCTCT 57.741 47.619 0.00 0.00 34.38 3.10
163 171 3.574396 CGGGAGATAGAAACTATGGCTGA 59.426 47.826 0.00 0.00 0.00 4.26
168 176 3.568853 ACGACCGGGAGATAGAAACTATG 59.431 47.826 6.32 0.00 0.00 2.23
170 178 2.947652 CACGACCGGGAGATAGAAACTA 59.052 50.000 6.32 0.00 0.00 2.24
171 179 1.749634 CACGACCGGGAGATAGAAACT 59.250 52.381 6.32 0.00 0.00 2.66
286 401 6.424207 GTCGAGTTTCCCCTATCAATATCAAC 59.576 42.308 0.00 0.00 0.00 3.18
536 1193 5.824904 AACCAGAGCATGCAAATTACTAG 57.175 39.130 21.98 4.94 0.00 2.57
617 1450 2.416431 GCAAGCAATTCCGCAAGAAGAT 60.416 45.455 0.00 0.00 38.07 2.40
672 1515 5.609423 AGAGCCTGAATAATGAACTAGCTG 58.391 41.667 0.00 0.00 0.00 4.24
718 1665 6.121590 TGACACTACATGCCACATCATTAAT 58.878 36.000 0.00 0.00 0.00 1.40
1023 2030 2.254459 CTCTTGTGAATCTCCGTCACG 58.746 52.381 0.00 0.00 46.89 4.35
1037 2044 2.030027 TGTCCTGGTGATCCTCTTGT 57.970 50.000 0.00 0.00 34.23 3.16
1180 2187 2.364970 TCTGCAAATTTGTGAACCTGGG 59.635 45.455 19.03 0.00 0.00 4.45
1352 2359 3.395639 ACCAATTTCTTGCAATGCACTG 58.604 40.909 7.72 4.06 38.71 3.66
1418 2425 0.687354 ACCAACTGCAACCGAGAGAT 59.313 50.000 0.00 0.00 0.00 2.75
1557 2564 8.447924 ACTTTAGGAAGTCATGATGATTGATG 57.552 34.615 0.00 0.00 42.35 3.07
1641 2649 2.489329 CACATCACCTGGAACACAATCC 59.511 50.000 0.00 0.00 40.10 3.01
1782 2793 4.288626 TCCAATGCTTTACACTTCCCTAGT 59.711 41.667 0.00 0.00 37.68 2.57
1857 2868 0.103755 TGCTGCAGCTCCGAGATAAG 59.896 55.000 36.61 0.00 42.66 1.73
1941 2952 6.153170 TGTTATCAGTAAATGACGTCCTGGTA 59.847 38.462 14.12 10.12 41.91 3.25
2070 3081 3.152341 CTGAATGAGCACCAGAAAACCT 58.848 45.455 0.00 0.00 0.00 3.50
2239 3250 1.927487 TTACTCAAGCGTGGGGTCTA 58.073 50.000 4.07 0.00 0.00 2.59
2417 3429 6.064060 CCAATTGTCTTCATAAGGGCATCTA 58.936 40.000 4.43 0.00 0.00 1.98
2548 3566 7.973048 AGTCCATACAAGTAAATCTAGGTCA 57.027 36.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.