Multiple sequence alignment - TraesCS4A01G343000

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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 TraesCS4A01G343000 chr4A 100.000 2495 0 0 1 2495 622486253 622483759 0.000000e+00 4608.0
1 TraesCS4A01G343000 chr4A 99.279 2495 17 1 1 2495 622520645 622518152 0.000000e+00 4506.0
2 TraesCS4A01G343000 chr4A 98.878 2495 9 1 1 2495 622452137 622449662 0.000000e+00 4434.0
3 TraesCS4A01G343000 chr4A 100.000 662 0 0 2551 3212 622483703 622483042 0.000000e+00 1223.0
4 TraesCS4A01G343000 chr4A 98.941 661 7 0 2552 3212 622449643 622448983 0.000000e+00 1182.0
5 TraesCS4A01G343000 chr4A 98.792 662 8 0 2551 3212 622518133 622517472 0.000000e+00 1179.0
6 TraesCS4A01G343000 chr4A 87.001 877 66 25 1000 1847 622185174 622186031 0.000000e+00 944.0
7 TraesCS4A01G343000 chr4A 84.433 758 70 18 1115 1845 622444544 622443808 0.000000e+00 702.0
8 TraesCS4A01G343000 chr4A 95.307 277 10 3 228 502 511884606 511884331 1.370000e-118 436.0
9 TraesCS4A01G343000 chr4A 89.933 149 13 2 76 224 602785803 602785657 1.180000e-44 191.0
10 TraesCS4A01G343000 chr4A 97.143 35 1 0 2988 3022 696019840 696019806 3.460000e-05 60.2
11 TraesCS4A01G343000 chr4A 100.000 28 0 0 699 726 736819663 736819690 6.000000e-03 52.8
12 TraesCS4A01G343000 chr5D 86.879 1227 91 24 807 2004 546472885 546474070 0.000000e+00 1310.0
13 TraesCS4A01G343000 chr5D 86.747 996 85 22 1000 1985 546454852 546455810 0.000000e+00 1064.0
14 TraesCS4A01G343000 chr5D 87.542 594 64 7 1016 1607 546460823 546461408 0.000000e+00 678.0
15 TraesCS4A01G343000 chr5D 85.714 105 14 1 2894 2997 556685187 556685083 3.390000e-20 110.0
16 TraesCS4A01G343000 chr5D 82.645 121 10 5 843 958 546358210 546358324 2.640000e-16 97.1
17 TraesCS4A01G343000 chr5B 89.171 1062 75 16 806 1841 689653116 689654163 0.000000e+00 1288.0
18 TraesCS4A01G343000 chr5B 87.145 1128 94 26 906 2004 689658692 689659797 0.000000e+00 1232.0
19 TraesCS4A01G343000 chr5B 88.163 1056 76 24 810 1835 689600788 689601824 0.000000e+00 1212.0
20 TraesCS4A01G343000 chr5B 87.406 1064 84 22 806 1845 689632492 689633529 0.000000e+00 1177.0
21 TraesCS4A01G343000 chr5B 87.182 866 69 17 1004 1854 689666379 689667217 0.000000e+00 946.0
22 TraesCS4A01G343000 chr5B 88.264 622 61 7 2553 3164 689660424 689661043 0.000000e+00 734.0
23 TraesCS4A01G343000 chr5B 88.073 545 38 10 1004 1539 689913691 689914217 3.520000e-174 621.0
24 TraesCS4A01G343000 chr5B 87.500 432 45 7 1421 1847 689914258 689914685 1.040000e-134 490.0
25 TraesCS4A01G343000 chr5B 88.184 347 27 9 2088 2432 689659799 689660133 4.990000e-108 401.0
26 TraesCS4A01G343000 chr5B 83.871 155 22 1 521 672 689458413 689458567 9.290000e-31 145.0
27 TraesCS4A01G343000 chr5B 88.764 89 9 1 1916 2004 689654157 689654244 1.220000e-19 108.0
28 TraesCS4A01G343000 chr5B 92.754 69 4 1 2005 2072 642230868 642230936 7.330000e-17 99.0
29 TraesCS4A01G343000 chr5B 100.000 46 0 0 3166 3211 16107281 16107326 5.710000e-13 86.1
30 TraesCS4A01G343000 chr5B 85.366 82 7 5 904 980 689596440 689596521 2.660000e-11 80.5
31 TraesCS4A01G343000 chr1A 96.029 277 9 2 228 502 398249691 398249967 1.760000e-122 449.0
32 TraesCS4A01G343000 chr1A 86.228 167 18 5 62 225 5131725 5131561 3.290000e-40 176.0
33 TraesCS4A01G343000 chr3A 96.337 273 9 1 233 504 312039477 312039205 6.320000e-122 448.0
34 TraesCS4A01G343000 chr3A 94.982 279 12 2 226 502 108372823 108372545 1.370000e-118 436.0
35 TraesCS4A01G343000 chr3A 95.604 273 11 1 233 504 333491722 333491450 1.370000e-118 436.0
36 TraesCS4A01G343000 chr3A 100.000 37 0 0 3166 3202 112379190 112379226 5.750000e-08 69.4
37 TraesCS4A01G343000 chr6A 94.464 289 13 3 226 512 562065419 562065706 2.940000e-120 442.0
38 TraesCS4A01G343000 chr6A 89.189 148 15 1 77 224 85700383 85700237 1.970000e-42 183.0
39 TraesCS4A01G343000 chr6B 95.307 277 10 3 231 505 499154194 499153919 1.370000e-118 436.0
40 TraesCS4A01G343000 chr6B 95.652 46 2 0 3166 3211 643573524 643573479 1.240000e-09 75.0
41 TraesCS4A01G343000 chr4D 92.466 146 10 1 77 222 481856471 481856615 1.170000e-49 207.0
42 TraesCS4A01G343000 chr6D 90.604 149 13 1 77 225 468870242 468870389 2.530000e-46 196.0
43 TraesCS4A01G343000 chr7D 88.889 153 11 4 75 225 13796454 13796602 1.970000e-42 183.0
44 TraesCS4A01G343000 chr7D 88.667 150 16 1 76 225 6747408 6747260 7.080000e-42 182.0
45 TraesCS4A01G343000 chr7D 88.889 72 7 1 2004 2074 627215537 627215466 1.590000e-13 87.9
46 TraesCS4A01G343000 chr7D 85.000 80 7 4 2005 2079 56649441 56649520 3.440000e-10 76.8
47 TraesCS4A01G343000 chr7D 95.349 43 2 0 3169 3211 276516112 276516070 5.750000e-08 69.4
48 TraesCS4A01G343000 chr5A 92.405 79 4 1 2010 2088 180368260 180368336 9.420000e-21 111.0
49 TraesCS4A01G343000 chr2B 89.412 85 8 1 2005 2088 749303482 749303566 4.380000e-19 106.0
50 TraesCS4A01G343000 chr7A 79.439 107 16 3 2923 3028 717238877 717238776 1.600000e-08 71.3
51 TraesCS4A01G343000 chr1D 100.000 38 0 0 3166 3203 319684976 319685013 1.600000e-08 71.3
52 TraesCS4A01G343000 chr4B 90.000 50 5 0 2042 2091 636680457 636680408 7.440000e-07 65.8


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 TraesCS4A01G343000 chr4A 622483042 622486253 3211 True 2915.5 4608 100.000000 1 3212 2 chr4A.!!$R6 3211
1 TraesCS4A01G343000 chr4A 622517472 622520645 3173 True 2842.5 4506 99.035500 1 3212 2 chr4A.!!$R7 3211
2 TraesCS4A01G343000 chr4A 622448983 622452137 3154 True 2808.0 4434 98.909500 1 3212 2 chr4A.!!$R5 3211
3 TraesCS4A01G343000 chr4A 622185174 622186031 857 False 944.0 944 87.001000 1000 1847 1 chr4A.!!$F1 847
4 TraesCS4A01G343000 chr4A 622443808 622444544 736 True 702.0 702 84.433000 1115 1845 1 chr4A.!!$R3 730
5 TraesCS4A01G343000 chr5D 546472885 546474070 1185 False 1310.0 1310 86.879000 807 2004 1 chr5D.!!$F4 1197
6 TraesCS4A01G343000 chr5D 546454852 546455810 958 False 1064.0 1064 86.747000 1000 1985 1 chr5D.!!$F2 985
7 TraesCS4A01G343000 chr5D 546460823 546461408 585 False 678.0 678 87.542000 1016 1607 1 chr5D.!!$F3 591
8 TraesCS4A01G343000 chr5B 689600788 689601824 1036 False 1212.0 1212 88.163000 810 1835 1 chr5B.!!$F5 1025
9 TraesCS4A01G343000 chr5B 689632492 689633529 1037 False 1177.0 1177 87.406000 806 1845 1 chr5B.!!$F6 1039
10 TraesCS4A01G343000 chr5B 689666379 689667217 838 False 946.0 946 87.182000 1004 1854 1 chr5B.!!$F7 850
11 TraesCS4A01G343000 chr5B 689658692 689661043 2351 False 789.0 1232 87.864333 906 3164 3 chr5B.!!$F9 2258
12 TraesCS4A01G343000 chr5B 689653116 689654244 1128 False 698.0 1288 88.967500 806 2004 2 chr5B.!!$F8 1198
13 TraesCS4A01G343000 chr5B 689913691 689914685 994 False 555.5 621 87.786500 1004 1847 2 chr5B.!!$F10 843

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
138 139 6.947733 ACAAACAGATGGGTTATGATTGAAGA 59.052 34.615 2.1 0.0 32.8 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 2647 6.619744 TGTGTATGTCCTTGCATGTAATTTG 58.38 36.0 0.0 0.0 0.0 2.32 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
121 122 7.648039 AGTTTACATGGGTTTTACAAACAGA 57.352 32.000 0.0 0.0 0.00 3.41
138 139 6.947733 ACAAACAGATGGGTTATGATTGAAGA 59.052 34.615 2.1 0.0 32.80 2.87
2341 2647 8.655092 CATTAAGATGAGAGAGTGAACAAAGTC 58.345 37.037 0.0 0.0 35.16 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 7.510343 CCCCTTTAATCTTCAATCATAACCCAT 59.490 37.037 0.00 0.00 0.00 4.00
138 139 0.999493 GGCCCCTCCTCCCCTTTAAT 60.999 60.000 0.00 0.00 0.00 1.40
2341 2647 6.619744 TGTGTATGTCCTTGCATGTAATTTG 58.380 36.000 0.00 0.00 0.00 2.32
2598 3079 0.973632 TTACGGACAGATGTGGCACT 59.026 50.000 19.83 4.13 30.34 4.40


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

AutoCloner maintained by Alex Coulton.