Multiple sequence alignment - TraesCS3A01G066200

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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 TraesCS3A01G066200 chr3A 100.000 3152 0 0 1 3152 39573244 39576395 0.000000e+00 5821.0
1 TraesCS3A01G066200 chr3A 95.540 2489 107 4 667 3152 39858350 39860837 0.000000e+00 3978.0
2 TraesCS3A01G066200 chr3A 95.141 2511 93 8 666 3152 39307250 39309755 0.000000e+00 3934.0
3 TraesCS3A01G066200 chr3A 95.102 2511 94 8 666 3152 39323982 39326487 0.000000e+00 3928.0
4 TraesCS3A01G066200 chr3A 94.134 2506 127 13 666 3152 39185132 39187636 0.000000e+00 3795.0
5 TraesCS3A01G066200 chr3A 93.945 2527 105 8 666 3152 39677988 39680506 0.000000e+00 3775.0
6 TraesCS3A01G066200 chr3A 93.814 2522 111 23 666 3150 39658329 39660842 0.000000e+00 3751.0
7 TraesCS3A01G066200 chr3A 93.793 2497 122 17 666 3150 38692162 38694637 0.000000e+00 3722.0
8 TraesCS3A01G066200 chr3A 94.459 1534 56 7 871 2385 39698449 39699972 0.000000e+00 2335.0
9 TraesCS3A01G066200 chr3A 94.925 670 28 4 2 666 39857647 39858315 0.000000e+00 1044.0
10 TraesCS3A01G066200 chr3A 94.318 528 23 5 2 527 38690981 38691503 0.000000e+00 802.0
11 TraesCS3A01G066200 chr3A 93.762 529 27 3 2 527 39183959 39184484 0.000000e+00 789.0
12 TraesCS3A01G066200 chr3A 93.762 529 19 3 2 516 39248320 39248848 0.000000e+00 782.0
13 TraesCS3A01G066200 chr3A 95.096 469 19 3 12 476 39442573 39443041 0.000000e+00 736.0
14 TraesCS3A01G066200 chr3A 94.154 479 24 4 2 476 39657777 39658255 0.000000e+00 726.0
15 TraesCS3A01G066200 chr3A 94.351 478 19 4 2 476 39697668 39698140 0.000000e+00 726.0
16 TraesCS3A01G066200 chr3A 93.305 478 29 2 2 476 39677437 39677914 0.000000e+00 702.0
17 TraesCS3A01G066200 chr3A 93.103 232 16 0 666 897 39698214 39698445 1.080000e-89 340.0
18 TraesCS3A01G066200 chr3A 95.631 206 9 0 666 871 39443115 39443320 6.520000e-87 331.0
19 TraesCS3A01G066200 chr3A 97.744 133 3 0 533 665 38691995 38692127 2.450000e-56 230.0
20 TraesCS3A01G066200 chr3A 96.241 133 3 2 533 665 39184967 39185097 1.900000e-52 217.0
21 TraesCS3A01G066200 chr3A 96.471 85 3 0 581 665 39307131 39307215 1.180000e-29 141.0
22 TraesCS3A01G066200 chr3A 96.471 85 3 0 581 665 39323863 39323947 1.180000e-29 141.0
23 TraesCS3A01G066200 chr3D 88.484 1537 144 14 1586 3091 29371740 29373274 0.000000e+00 1827.0
24 TraesCS3A01G066200 chr3D 88.346 532 49 9 932 1452 29361723 29362252 7.420000e-176 627.0
25 TraesCS3A01G066200 chr3D 87.273 330 29 9 534 851 29285188 29285516 6.420000e-97 364.0
26 TraesCS3A01G066200 chr3D 81.281 203 14 7 5 183 29361077 29361279 3.280000e-30 143.0
27 TraesCS3A01G066200 chr3B 87.322 1191 135 10 1939 3116 50061612 50062799 0.000000e+00 1349.0
28 TraesCS3A01G066200 chr3B 89.489 333 32 2 196 527 828240561 828240231 4.860000e-113 418.0
29 TraesCS3A01G066200 chr3B 94.400 125 6 1 538 662 50061322 50061445 1.150000e-44 191.0
30 TraesCS3A01G066200 chr3B 80.769 130 7 11 932 1061 50186249 50186360 5.600000e-13 86.1


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 TraesCS3A01G066200 chr3A 39573244 39576395 3151 False 5821.000000 5821 100.000000 1 3152 1 chr3A.!!$F2 3151
1 TraesCS3A01G066200 chr3A 39857647 39860837 3190 False 2511.000000 3978 95.232500 2 3152 2 chr3A.!!$F11 3150
2 TraesCS3A01G066200 chr3A 39657777 39660842 3065 False 2238.500000 3751 93.984000 2 3150 2 chr3A.!!$F8 3148
3 TraesCS3A01G066200 chr3A 39677437 39680506 3069 False 2238.500000 3775 93.625000 2 3152 2 chr3A.!!$F9 3150
4 TraesCS3A01G066200 chr3A 39307131 39309755 2624 False 2037.500000 3934 95.806000 581 3152 2 chr3A.!!$F5 2571
5 TraesCS3A01G066200 chr3A 39323863 39326487 2624 False 2034.500000 3928 95.786500 581 3152 2 chr3A.!!$F6 2571
6 TraesCS3A01G066200 chr3A 39183959 39187636 3677 False 1600.333333 3795 94.712333 2 3152 3 chr3A.!!$F4 3150
7 TraesCS3A01G066200 chr3A 38690981 38694637 3656 False 1584.666667 3722 95.285000 2 3150 3 chr3A.!!$F3 3148
8 TraesCS3A01G066200 chr3A 39697668 39699972 2304 False 1133.666667 2335 93.971000 2 2385 3 chr3A.!!$F10 2383
9 TraesCS3A01G066200 chr3A 39248320 39248848 528 False 782.000000 782 93.762000 2 516 1 chr3A.!!$F1 514
10 TraesCS3A01G066200 chr3A 39442573 39443320 747 False 533.500000 736 95.363500 12 871 2 chr3A.!!$F7 859
11 TraesCS3A01G066200 chr3D 29371740 29373274 1534 False 1827.000000 1827 88.484000 1586 3091 1 chr3D.!!$F2 1505
12 TraesCS3A01G066200 chr3D 29361077 29362252 1175 False 385.000000 627 84.813500 5 1452 2 chr3D.!!$F3 1447
13 TraesCS3A01G066200 chr3B 50061322 50062799 1477 False 770.000000 1349 90.861000 538 3116 2 chr3B.!!$F2 2578

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
198 223 1.408702 ACAAAGCTGAAATGGCAACGT 59.591 42.857 0.0 0.0 42.51 3.99 F
1128 1793 1.004440 GCTGAAGAAGGGCACGAGT 60.004 57.895 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1168 1833 1.273324 GGAGGAGAGAAGAAGGGTGGA 60.273 57.143 0.0 0.0 0.00 4.02 R
3052 3778 3.436243 AGTTTGGTGGGTGAAGTTTCAA 58.564 40.909 0.0 0.0 39.21 2.69 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
198 223 1.408702 ACAAAGCTGAAATGGCAACGT 59.591 42.857 0.00 0.0 42.51 3.99
254 281 9.391006 TCCGTGCATATCTTTAATTCTAGTTTT 57.609 29.630 0.00 0.0 0.00 2.43
344 371 9.394767 GAAAAAGGGGAATAATTTATGTGCATT 57.605 29.630 0.00 0.0 0.00 3.56
519 558 1.623542 AAGGTGGAGATGCGGGGTAC 61.624 60.000 0.00 0.0 0.00 3.34
1128 1793 1.004440 GCTGAAGAAGGGCACGAGT 60.004 57.895 0.00 0.0 0.00 4.18
1194 1859 1.405105 CTTCTTCTCTCCTCCTGCGAG 59.595 57.143 0.00 0.0 35.72 5.03
1266 1932 4.160252 GCAGAAGATTAAGGGCATTTCCAA 59.840 41.667 0.00 0.0 36.21 3.53
1942 2638 4.389992 CACACGATGCAAGTCTTTCTACAT 59.610 41.667 0.00 0.0 0.00 2.29
1993 2692 3.589735 TGTTCCCATTTAGCCCTGTAAGA 59.410 43.478 0.00 0.0 34.07 2.10
2159 2861 6.100424 TGTTGGAGTTTCCCCACAATAAAAAT 59.900 34.615 0.00 0.0 35.03 1.82
2395 3109 5.926542 TCTTCAACAAGGTTCTATTGAGTCG 59.073 40.000 0.00 0.0 32.90 4.18
2489 3203 7.955324 CGAACAATTTGTACTACACATAACCTG 59.045 37.037 1.76 0.0 36.90 4.00
2553 3267 9.438228 TCAATTCGTACCTTATTTGTATTCACA 57.562 29.630 0.00 0.0 0.00 3.58
2604 3318 3.209410 GCTCTACCACCATCCATTCTTG 58.791 50.000 0.00 0.0 0.00 3.02
3025 3746 2.959707 ACGAAATCTCCTCGCTATTCCT 59.040 45.455 0.00 0.0 39.97 3.36
3052 3778 2.851263 TTCATTCCACGGTTGCTAGT 57.149 45.000 0.00 0.0 0.00 2.57
3085 3811 3.432046 CCCACCAAACTTCTGCACAAAAT 60.432 43.478 0.00 0.0 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 223 9.484806 AGCTACTACTACTTAATTACCTTGGAA 57.515 33.333 0.00 0.00 0.00 3.53
344 371 5.237815 AGTGAATGTTCTCGCAAACATAGA 58.762 37.500 13.40 3.73 46.49 1.98
519 558 6.398918 ACTATTGCAGTAAGGGATATTAGCG 58.601 40.000 0.00 0.00 34.98 4.26
654 1187 2.607499 TCACCAATGGGATGCTTTTGT 58.393 42.857 3.55 0.00 38.05 2.83
1128 1793 1.525077 GGCCACGAAACACAGGACA 60.525 57.895 0.00 0.00 0.00 4.02
1168 1833 1.273324 GGAGGAGAGAAGAAGGGTGGA 60.273 57.143 0.00 0.00 0.00 4.02
1194 1859 2.507407 TATCAACCTCTTTGTGGGCC 57.493 50.000 0.00 0.00 36.49 5.80
1539 2207 6.012745 AGCTCCCAGATCAAAAACAATTACT 58.987 36.000 0.00 0.00 0.00 2.24
1942 2638 4.766373 ACATTAATGAACATGCACTGGACA 59.234 37.500 22.16 0.00 0.00 4.02
2022 2721 6.392354 ACTCAATTGGCACATACATTTTGAG 58.608 36.000 5.42 7.56 40.52 3.02
2159 2861 4.295870 GACTTCTCGACACACACATGTAA 58.704 43.478 0.00 0.00 36.72 2.41
2364 3078 8.717821 CAATAGAACCTTGTTGAAGAACGATTA 58.282 33.333 0.00 0.00 34.49 1.75
2395 3109 6.223138 TCAGTGTGACAATTTATGACGTTC 57.777 37.500 0.00 0.00 0.00 3.95
2489 3203 9.607285 TTGCTAAATTATGAGAAACTTCGAAAC 57.393 29.630 0.00 0.00 0.00 2.78
2604 3318 4.621034 CGGTTAAATTTGTGTGATGCCTTC 59.379 41.667 0.00 0.00 0.00 3.46
2709 3424 6.624423 AGCTTTTCAGTCGAATGCATATTTT 58.376 32.000 8.24 0.00 35.01 1.82
2710 3425 6.199937 AGCTTTTCAGTCGAATGCATATTT 57.800 33.333 8.24 0.00 35.01 1.40
2711 3426 5.824904 AGCTTTTCAGTCGAATGCATATT 57.175 34.783 8.24 0.00 35.01 1.28
2712 3427 6.017605 CCTTAGCTTTTCAGTCGAATGCATAT 60.018 38.462 8.24 0.00 35.01 1.78
3025 3746 4.142859 GCAACCGTGGAATGAATACGTAAA 60.143 41.667 0.00 0.00 36.17 2.01
3052 3778 3.436243 AGTTTGGTGGGTGAAGTTTCAA 58.564 40.909 0.00 0.00 39.21 2.69
3085 3811 8.038944 AGTTATTATCTGCTCGTCACCTTTTTA 58.961 33.333 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.