Multiple sequence alignment - TraesCS4D01G333200

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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 TraesCS4D01G333200 chr4D 100.000 3763 0 0 1 3763 490414437 490410675 0.000000e+00 6950.0
1 TraesCS4D01G333200 chr4D 81.105 2117 294 56 948 2984 490405348 490403258 0.000000e+00 1596.0
2 TraesCS4D01G333200 chr4D 90.546 952 57 13 2237 3160 490376654 490377600 0.000000e+00 1229.0
3 TraesCS4D01G333200 chr4D 86.476 525 37 8 1657 2165 490375969 490376475 2.560000e-151 545.0
4 TraesCS4D01G333200 chr4D 83.624 574 63 19 3185 3748 490377789 490378341 9.320000e-141 510.0
5 TraesCS4D01G333200 chr4D 81.313 594 92 14 3185 3763 490403193 490402604 7.360000e-127 464.0
6 TraesCS4D01G333200 chr4D 77.567 263 51 8 425 683 468404513 468404771 6.510000e-33 152.0
7 TraesCS4D01G333200 chr4B 95.990 1596 27 6 1612 3180 630043770 630042185 0.000000e+00 2558.0
8 TraesCS4D01G333200 chr4B 81.949 2022 289 48 1044 3009 630015834 630013833 0.000000e+00 1642.0
9 TraesCS4D01G333200 chr4B 94.844 931 22 10 673 1587 630044983 630044063 0.000000e+00 1430.0
10 TraesCS4D01G333200 chr4B 97.531 567 11 2 106 672 630045742 630045179 0.000000e+00 966.0
11 TraesCS4D01G333200 chr4B 94.218 588 24 6 3179 3762 630042118 630041537 0.000000e+00 889.0
12 TraesCS4D01G333200 chr4B 83.227 942 114 21 1044 1951 630099823 630098892 0.000000e+00 824.0
13 TraesCS4D01G333200 chr4B 76.962 1198 182 55 2026 3178 630098746 630097598 6.960000e-167 597.0
14 TraesCS4D01G333200 chr4B 80.936 598 90 15 3185 3763 630013789 630013197 5.730000e-123 451.0
15 TraesCS4D01G333200 chr4B 97.273 110 3 0 1 110 630045972 630045863 1.780000e-43 187.0
16 TraesCS4D01G333200 chr5A 98.716 1324 12 4 2444 3763 671988880 671987558 0.000000e+00 2346.0
17 TraesCS4D01G333200 chr5A 80.795 1963 278 54 1046 2933 671978712 671976774 0.000000e+00 1445.0
18 TraesCS4D01G333200 chr5A 95.405 914 22 10 673 1570 671990953 671990044 0.000000e+00 1437.0
19 TraesCS4D01G333200 chr5A 96.907 776 23 1 1646 2420 671989643 671988868 0.000000e+00 1299.0
20 TraesCS4D01G333200 chr5A 90.167 956 55 17 2237 3160 671956110 671957058 0.000000e+00 1208.0
21 TraesCS4D01G333200 chr5A 90.021 932 68 7 1257 2165 671955002 671955931 0.000000e+00 1182.0
22 TraesCS4D01G333200 chr5A 94.659 674 33 3 1 672 671991818 671991146 0.000000e+00 1042.0
23 TraesCS4D01G333200 chr5A 78.878 1444 207 53 1571 2989 672028044 672026674 0.000000e+00 887.0
24 TraesCS4D01G333200 chr5A 90.802 424 32 3 1257 1673 675734148 675734571 9.130000e-156 560.0
25 TraesCS4D01G333200 chr5A 83.826 575 61 19 3185 3748 671957247 671957800 5.570000e-143 518.0
26 TraesCS4D01G333200 chr5A 79.868 606 80 23 3185 3763 671976646 671976056 4.530000e-109 405.0
27 TraesCS4D01G333200 chr5A 89.103 312 34 0 1014 1325 672028509 672028198 4.560000e-104 388.0
28 TraesCS4D01G333200 chr5A 79.104 469 66 18 982 1435 533283034 533282583 1.020000e-75 294.0
29 TraesCS4D01G333200 chr5A 77.273 264 49 10 425 683 290923249 290922992 1.090000e-30 145.0
30 TraesCS4D01G333200 chr5A 90.667 75 6 1 599 673 357053129 357053202 8.600000e-17 99.0
31 TraesCS4D01G333200 chr5B 80.412 776 88 24 848 1587 505779631 505778884 1.990000e-147 532.0
32 TraesCS4D01G333200 chr5B 75.341 1026 161 50 2187 3178 505778062 505777095 3.500000e-110 409.0
33 TraesCS4D01G333200 chr6A 85.161 155 21 2 1018 1171 3310064 3310217 1.400000e-34 158.0
34 TraesCS4D01G333200 chr6A 86.420 81 7 2 1865 1942 3001744 3001823 6.700000e-13 86.1
35 TraesCS4D01G333200 chr6D 87.000 100 13 0 563 662 386229 386328 3.070000e-21 113.0
36 TraesCS4D01G333200 chr6D 86.420 81 7 2 1865 1942 4266596 4266517 6.700000e-13 86.1
37 TraesCS4D01G333200 chr6D 85.366 82 9 1 1864 1942 4643250 4643331 8.660000e-12 82.4
38 TraesCS4D01G333200 chr6B 87.654 81 6 2 1865 1942 8423878 8423957 1.440000e-14 91.6


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 TraesCS4D01G333200 chr4D 490410675 490414437 3762 True 6950.000000 6950 100.000000 1 3763 1 chr4D.!!$R1 3762
1 TraesCS4D01G333200 chr4D 490402604 490405348 2744 True 1030.000000 1596 81.209000 948 3763 2 chr4D.!!$R2 2815
2 TraesCS4D01G333200 chr4D 490375969 490378341 2372 False 761.333333 1229 86.882000 1657 3748 3 chr4D.!!$F2 2091
3 TraesCS4D01G333200 chr4B 630041537 630045972 4435 True 1206.000000 2558 95.971200 1 3762 5 chr4B.!!$R2 3761
4 TraesCS4D01G333200 chr4B 630013197 630015834 2637 True 1046.500000 1642 81.442500 1044 3763 2 chr4B.!!$R1 2719
5 TraesCS4D01G333200 chr4B 630097598 630099823 2225 True 710.500000 824 80.094500 1044 3178 2 chr4B.!!$R3 2134
6 TraesCS4D01G333200 chr5A 671987558 671991818 4260 True 1531.000000 2346 96.421750 1 3763 4 chr5A.!!$R4 3762
7 TraesCS4D01G333200 chr5A 671955002 671957800 2798 False 969.333333 1208 88.004667 1257 3748 3 chr5A.!!$F3 2491
8 TraesCS4D01G333200 chr5A 671976056 671978712 2656 True 925.000000 1445 80.331500 1046 3763 2 chr5A.!!$R3 2717
9 TraesCS4D01G333200 chr5A 672026674 672028509 1835 True 637.500000 887 83.990500 1014 2989 2 chr5A.!!$R5 1975
10 TraesCS4D01G333200 chr5B 505777095 505779631 2536 True 470.500000 532 77.876500 848 3178 2 chr5B.!!$R1 2330

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
512 639 3.199508 CAGTGACCTGGATTCCTCATCTT 59.800 47.826 0.0 0.0 34.9 2.40 F
1246 1614 1.074775 AAGCCGCCCATCTTCAACA 59.925 52.632 0.0 0.0 0.0 3.33 F
2008 2783 0.902531 AGGGTACAATGAGGACACCG 59.097 55.000 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2771 0.465705 ATCGCATCGGTGTCCTCATT 59.534 50.0 0.0 0.0 0.00 2.57 R
2146 3004 5.304357 TGACAGACAGAGACAAGGAATTACA 59.696 40.0 0.0 0.0 0.00 2.41 R
3255 4593 1.194121 ATTCCCCAAAGCACAAGCCC 61.194 55.0 0.0 0.0 43.56 5.19 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
143 269 3.702045 GAGTACCAGTTCAGCTCCAGTAT 59.298 47.826 0.00 0.0 0.00 2.12
512 639 3.199508 CAGTGACCTGGATTCCTCATCTT 59.800 47.826 0.00 0.0 34.90 2.40
1246 1614 1.074775 AAGCCGCCCATCTTCAACA 59.925 52.632 0.00 0.0 0.00 3.33
1587 1992 1.135139 GCATGCCTCTACGAGTCAGAA 59.865 52.381 6.36 0.0 0.00 3.02
1590 1995 2.723273 TGCCTCTACGAGTCAGAATCA 58.277 47.619 0.00 0.0 0.00 2.57
1996 2771 1.406751 CGGTGATGATGCAAGGGTACA 60.407 52.381 0.00 0.0 0.00 2.90
2008 2783 0.902531 AGGGTACAATGAGGACACCG 59.097 55.000 0.00 0.0 0.00 4.94
3255 4593 7.387673 TGCAACTAACATGATATCCTTATTCCG 59.612 37.037 0.00 0.0 0.00 4.30
3579 4931 4.814771 GTCCTAGCAAGTGTGTACTGTTTT 59.185 41.667 0.00 0.0 37.19 2.43
3634 4986 6.712547 TCTTTCAGATTTGAACTCCTTCCTTC 59.287 38.462 0.00 0.0 42.79 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
398 524 2.427506 GGAACGTGAGCTTTGGATCTT 58.572 47.619 0.0 0.0 0.00 2.40
428 554 3.771160 GACGGAGGGTGGCATCGT 61.771 66.667 0.0 0.0 36.74 3.73
512 639 2.342279 CGCAAGAACAGGGTCCGA 59.658 61.111 0.0 0.0 43.02 4.55
1996 2771 0.465705 ATCGCATCGGTGTCCTCATT 59.534 50.000 0.0 0.0 0.00 2.57
2008 2783 9.439537 GAAAAAGGTAGATAAGAAAATCGCATC 57.560 33.333 0.0 0.0 0.00 3.91
2146 3004 5.304357 TGACAGACAGAGACAAGGAATTACA 59.696 40.000 0.0 0.0 0.00 2.41
2379 3377 7.989416 TTCGGGTTGAATGAAACTAGTAATT 57.011 32.000 0.0 0.0 0.00 1.40
2395 3393 6.570692 ACAATACTCACTACTATTCGGGTTG 58.429 40.000 0.0 0.0 0.00 3.77
3255 4593 1.194121 ATTCCCCAAAGCACAAGCCC 61.194 55.000 0.0 0.0 43.56 5.19
3579 4931 5.880332 GCAGTTCCACTCATTACTCCATTAA 59.120 40.000 0.0 0.0 0.00 1.40


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

AutoCloner maintained by Alex Coulton.