Multiple sequence alignment - TraesCS1D01G151400

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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 TraesCS1D01G151400 chr1D 100.000 3560 0 0 1 3560 209754598 209758157 0.000000e+00 6575.0
1 TraesCS1D01G151400 chr1D 94.686 207 10 1 1 207 374378740 374378535 1.590000e-83 320.0
2 TraesCS1D01G151400 chr1D 86.730 211 20 3 3346 3548 20713624 20713834 9.940000e-56 228.0
3 TraesCS1D01G151400 chr1D 80.667 150 20 9 3199 3341 365974909 365974762 1.350000e-19 108.0
4 TraesCS1D01G151400 chr5B 95.722 3436 111 12 1 3432 202893739 202890336 0.000000e+00 5498.0
5 TraesCS1D01G151400 chr5B 94.631 149 6 1 3414 3560 202890322 202890174 2.760000e-56 230.0
6 TraesCS1D01G151400 chr5B 89.172 157 10 3 1 150 32128864 32129020 4.690000e-44 189.0
7 TraesCS1D01G151400 chr5B 85.799 169 12 1 3346 3502 687208506 687208674 6.110000e-38 169.0
8 TraesCS1D01G151400 chr6B 94.915 2399 101 16 588 2981 643872925 643870543 0.000000e+00 3735.0
9 TraesCS1D01G151400 chr6B 94.752 2382 101 11 592 2964 643647842 643650208 0.000000e+00 3685.0
10 TraesCS1D01G151400 chr6B 94.315 2357 125 4 592 2944 664684777 664687128 0.000000e+00 3602.0
11 TraesCS1D01G151400 chr6B 86.047 215 10 1 3346 3560 9195847 9196041 2.780000e-51 213.0
12 TraesCS1D01G151400 chr6B 85.542 166 22 2 3180 3343 48433737 48433902 4.730000e-39 172.0
13 TraesCS1D01G151400 chr7D 92.926 2403 108 24 592 2967 621161669 621164036 0.000000e+00 3439.0
14 TraesCS1D01G151400 chr7D 87.081 209 20 2 3346 3553 638588769 638588971 2.760000e-56 230.0
15 TraesCS1D01G151400 chr1B 94.952 2179 93 8 789 2964 311136417 311134253 0.000000e+00 3398.0
16 TraesCS1D01G151400 chr1B 92.948 865 59 2 592 1455 619144422 619143559 0.000000e+00 1258.0
17 TraesCS1D01G151400 chr1B 92.090 847 60 7 592 1436 676889979 676889138 0.000000e+00 1186.0
18 TraesCS1D01G151400 chr3B 91.952 2398 158 18 592 2964 200854333 200856720 0.000000e+00 3326.0
19 TraesCS1D01G151400 chr3B 91.743 2398 163 18 592 2964 200829424 200831811 0.000000e+00 3299.0
20 TraesCS1D01G151400 chr3B 86.294 197 25 1 3346 3542 596828981 596828787 2.780000e-51 213.0
21 TraesCS1D01G151400 chr3B 84.862 218 12 5 3343 3560 574267865 574268061 2.170000e-47 200.0
22 TraesCS1D01G151400 chr3B 95.283 106 3 1 3346 3449 574290742 574290847 2.200000e-37 167.0
23 TraesCS1D01G151400 chr3B 95.192 104 5 0 3346 3449 220739061 220739164 7.910000e-37 165.0
24 TraesCS1D01G151400 chr2B 91.486 2396 167 20 592 2964 464670822 464673203 0.000000e+00 3260.0
25 TraesCS1D01G151400 chr2B 85.714 217 10 2 1 217 28241838 28241643 3.600000e-50 209.0
26 TraesCS1D01G151400 chr2B 94.872 39 2 0 3284 3322 600628 600590 1.070000e-05 62.1
27 TraesCS1D01G151400 chr7B 94.097 2016 84 16 950 2964 639855661 639857642 0.000000e+00 3031.0
28 TraesCS1D01G151400 chr7B 85.897 156 21 1 44 198 328084337 328084182 7.910000e-37 165.0
29 TraesCS1D01G151400 chr7B 96.552 87 3 0 3346 3432 379427145 379427231 1.030000e-30 145.0
30 TraesCS1D01G151400 chr4B 93.572 1338 64 10 592 1924 429036069 429037389 0.000000e+00 1975.0
31 TraesCS1D01G151400 chr4B 85.909 220 21 1 3340 3549 52592582 52592801 3.580000e-55 226.0
32 TraesCS1D01G151400 chr4B 86.250 160 4 1 3344 3503 522341640 522341499 1.320000e-34 158.0
33 TraesCS1D01G151400 chr6A 94.608 204 11 0 1 204 20234553 20234350 2.060000e-82 316.0
34 TraesCS1D01G151400 chr3A 84.454 238 32 5 3106 3340 428461631 428461396 2.760000e-56 230.0
35 TraesCS1D01G151400 chr1A 84.416 231 32 4 3113 3340 2233019 2232790 1.290000e-54 224.0
36 TraesCS1D01G151400 chr4A 92.617 149 9 1 3414 3560 675654584 675654732 2.780000e-51 213.0
37 TraesCS1D01G151400 chr4A 79.839 124 17 7 3203 3319 37772194 37772316 2.280000e-12 84.2
38 TraesCS1D01G151400 chr6D 90.909 132 8 3 3414 3541 122414114 122414245 1.310000e-39 174.0
39 TraesCS1D01G151400 chr5D 80.537 149 21 8 3199 3341 33670391 33670537 1.350000e-19 108.0
40 TraesCS1D01G151400 chr5D 92.308 39 3 0 3284 3322 543212076 543212114 4.960000e-04 56.5


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 TraesCS1D01G151400 chr1D 209754598 209758157 3559 False 6575 6575 100.0000 1 3560 1 chr1D.!!$F2 3559
1 TraesCS1D01G151400 chr5B 202890174 202893739 3565 True 2864 5498 95.1765 1 3560 2 chr5B.!!$R1 3559
2 TraesCS1D01G151400 chr6B 643870543 643872925 2382 True 3735 3735 94.9150 588 2981 1 chr6B.!!$R1 2393
3 TraesCS1D01G151400 chr6B 643647842 643650208 2366 False 3685 3685 94.7520 592 2964 1 chr6B.!!$F3 2372
4 TraesCS1D01G151400 chr6B 664684777 664687128 2351 False 3602 3602 94.3150 592 2944 1 chr6B.!!$F4 2352
5 TraesCS1D01G151400 chr7D 621161669 621164036 2367 False 3439 3439 92.9260 592 2967 1 chr7D.!!$F1 2375
6 TraesCS1D01G151400 chr1B 311134253 311136417 2164 True 3398 3398 94.9520 789 2964 1 chr1B.!!$R1 2175
7 TraesCS1D01G151400 chr1B 619143559 619144422 863 True 1258 1258 92.9480 592 1455 1 chr1B.!!$R2 863
8 TraesCS1D01G151400 chr1B 676889138 676889979 841 True 1186 1186 92.0900 592 1436 1 chr1B.!!$R3 844
9 TraesCS1D01G151400 chr3B 200854333 200856720 2387 False 3326 3326 91.9520 592 2964 1 chr3B.!!$F2 2372
10 TraesCS1D01G151400 chr3B 200829424 200831811 2387 False 3299 3299 91.7430 592 2964 1 chr3B.!!$F1 2372
11 TraesCS1D01G151400 chr2B 464670822 464673203 2381 False 3260 3260 91.4860 592 2964 1 chr2B.!!$F1 2372
12 TraesCS1D01G151400 chr7B 639855661 639857642 1981 False 3031 3031 94.0970 950 2964 1 chr7B.!!$F2 2014
13 TraesCS1D01G151400 chr4B 429036069 429037389 1320 False 1975 1975 93.5720 592 1924 1 chr4B.!!$F2 1332

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
943 948 0.905337 AGAGGAAGAAGACCACCGGG 60.905 60.0 6.32 0.0 41.29 5.73 F
1448 1478 0.469331 TTAGACTCCCCGCCGATGAT 60.469 55.0 0.00 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2536 0.460109 CGACCTCAATGCCATCGTCA 60.460 55.0 0.00 0.00 0.0 4.35 R
3256 3318 0.100861 GTAGTAGGTCGCAGCTCCAC 59.899 60.0 6.32 3.35 0.0 4.02 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
160 161 1.066430 TCGGATGGCCACAAACTAGTC 60.066 52.381 8.16 0.00 0.00 2.59
292 293 2.590092 GGCCGGTCCTGCACTAAT 59.410 61.111 1.90 0.00 0.00 1.73
369 370 6.138702 GCGCTTTTATACTTATCGCTTTTGTC 59.861 38.462 0.00 0.00 38.29 3.18
399 400 4.417426 TTTGTCGTCTTTTCTCTTCCCT 57.583 40.909 0.00 0.00 0.00 4.20
406 407 5.480772 TCGTCTTTTCTCTTCCCTGTTCTAT 59.519 40.000 0.00 0.00 0.00 1.98
427 428 2.041891 TCGTTTTCCCCTCTCTCTCTCT 59.958 50.000 0.00 0.00 0.00 3.10
428 429 2.425668 CGTTTTCCCCTCTCTCTCTCTC 59.574 54.545 0.00 0.00 0.00 3.20
943 948 0.905337 AGAGGAAGAAGACCACCGGG 60.905 60.000 6.32 0.00 41.29 5.73
1175 1204 4.014406 AGCAGTTCATTCATGCAAGATCA 58.986 39.130 0.00 0.00 42.45 2.92
1448 1478 0.469331 TTAGACTCCCCGCCGATGAT 60.469 55.000 0.00 0.00 0.00 2.45
1637 1667 1.277557 AGGAATCAGCGTCTTCAGCTT 59.722 47.619 0.00 0.00 44.06 3.74
1689 1719 2.819984 ATTCGTTCTGCATGGCCGGT 62.820 55.000 1.90 0.00 0.00 5.28
1949 1990 4.072131 AGTGACAGTCATGCCGTTTTAAT 58.928 39.130 6.51 0.00 0.00 1.40
2108 2149 1.291588 CTGACGAGGTTGAGCTGCT 59.708 57.895 0.00 0.00 0.00 4.24
2198 2240 3.109547 CAAGCGCCGCAACTACGA 61.110 61.111 13.36 0.00 34.06 3.43
2300 2342 1.269257 GGACTTCACCAAGCACTTTGC 60.269 52.381 0.00 0.00 45.46 3.68
2493 2536 3.070734 CCCTCAAGGTCATCATCTTCGAT 59.929 47.826 0.00 0.00 0.00 3.59
2615 2676 5.050972 GCTATGGTTTATGCGTAGAACTGTC 60.051 44.000 9.40 0.00 0.00 3.51
2702 2764 2.268762 TGATGTGTGCTGCCAAAGTA 57.731 45.000 0.00 0.00 0.00 2.24
2772 2834 3.932545 TGCATACAACCAAACACCATC 57.067 42.857 0.00 0.00 0.00 3.51
2969 3031 1.743321 AACCAAACACGCCCATGGTG 61.743 55.000 11.73 5.04 45.15 4.17
3042 3104 2.031245 CACCGTTTTGCTACATGCTTCA 60.031 45.455 0.00 0.00 43.37 3.02
3083 3145 1.836166 ACCAGCATCACACTCTGCTAT 59.164 47.619 0.00 0.00 46.62 2.97
3092 3154 3.629855 TCACACTCTGCTATAGCTCAGAC 59.370 47.826 24.61 0.00 42.66 3.51
3123 3185 3.289836 CCAAGCATCACCATGGAATACA 58.710 45.455 21.47 0.00 34.82 2.29
3158 3220 4.742201 GCTCCACTTCGGCGAGCA 62.742 66.667 10.46 0.00 46.63 4.26
3256 3318 2.549754 GGATTTGCTACATCCATCACGG 59.450 50.000 4.92 0.00 40.21 4.94
3276 3338 0.323087 TGGAGCTGCGACCTACTACA 60.323 55.000 16.74 0.00 0.00 2.74
3283 3345 1.930908 GCGACCTACTACAGCGGTGT 61.931 60.000 25.12 25.12 41.06 4.16
3320 3383 3.114065 CGTCTCGGATTTTGCTACTACC 58.886 50.000 0.00 0.00 0.00 3.18
3323 3386 3.635373 TCTCGGATTTTGCTACTACCGAT 59.365 43.478 0.00 0.00 46.11 4.18
3334 3397 5.833082 TGCTACTACCGATGAGAGATTTTC 58.167 41.667 0.00 0.00 0.00 2.29
3382 3445 8.671384 TTGTAGCCTTATTGTGTAATCCATAC 57.329 34.615 0.00 0.00 34.92 2.39
3461 3558 1.540118 TGTGTGATAGGCCACCCCA 60.540 57.895 5.01 0.00 36.26 4.96
3494 3591 1.530323 CAGTTCCCCCAAAACCTACG 58.470 55.000 0.00 0.00 0.00 3.51
3528 3625 3.113824 TCGAGTCTAACCTAGGTCCTCT 58.886 50.000 16.64 11.33 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
369 370 5.916969 AGAAAAGACGACAAAAGCGATAAG 58.083 37.500 0.00 0.00 0.00 1.73
399 400 4.094476 AGAGAGGGGAAAACGATAGAACA 58.906 43.478 0.00 0.00 41.38 3.18
406 407 2.041891 AGAGAGAGAGAGGGGAAAACGA 59.958 50.000 0.00 0.00 0.00 3.85
427 428 1.786441 AGAGTTGGGGGAACAATTGGA 59.214 47.619 10.83 0.00 36.98 3.53
428 429 2.171003 GAGAGTTGGGGGAACAATTGG 58.829 52.381 10.83 0.00 36.98 3.16
492 493 2.124983 CCTCCATGTGGGCTGTCG 60.125 66.667 0.00 0.00 36.21 4.35
526 528 0.397187 TACCCTAACACCGCTTGCAA 59.603 50.000 0.00 0.00 0.00 4.08
1175 1204 4.311208 TCCCCCAATCCCTAAATCTACT 57.689 45.455 0.00 0.00 0.00 2.57
1212 1242 0.978907 TCCGTTCTGTACCCCCTTTC 59.021 55.000 0.00 0.00 0.00 2.62
1637 1667 3.432749 GCTCATGAAGGCCACTCAAGATA 60.433 47.826 5.01 0.00 0.00 1.98
1689 1719 0.102481 GCTCGAACTTCGGCTCCATA 59.898 55.000 11.21 0.00 40.88 2.74
1949 1990 3.156293 TGGCTAATTCAAGAGCTTGCAA 58.844 40.909 0.00 0.00 40.24 4.08
2198 2240 2.402564 CATCCTCCTGATGGTAGTGGT 58.597 52.381 0.00 0.00 45.99 4.16
2493 2536 0.460109 CGACCTCAATGCCATCGTCA 60.460 55.000 0.00 0.00 0.00 4.35
2615 2676 7.114106 CAGATATAAGCAGTACGACAGTTCATG 59.886 40.741 0.00 0.00 0.00 3.07
2772 2834 2.235891 GTTAGTCCACAAACCCAAGGG 58.764 52.381 2.91 2.91 42.03 3.95
3032 3094 1.348538 CGACGCGGTTGAAGCATGTA 61.349 55.000 12.47 0.00 34.19 2.29
3042 3104 2.428403 GCAAATTGCGACGCGGTT 60.428 55.556 16.14 9.49 31.71 4.44
3083 3145 4.129737 GGGCGTGCGTCTGAGCTA 62.130 66.667 0.00 0.00 38.13 3.32
3123 3185 3.172339 GAGCTAGATGGATGGATGGAGT 58.828 50.000 0.00 0.00 0.00 3.85
3158 3220 1.142688 ACCTCCAGGGATGCAGGTTT 61.143 55.000 0.00 0.00 40.27 3.27
3177 3239 1.042003 TTTGGCTCAGCTGGTTGCAA 61.042 50.000 15.13 7.06 45.94 4.08
3256 3318 0.100861 GTAGTAGGTCGCAGCTCCAC 59.899 60.000 6.32 3.35 0.00 4.02
3316 3379 6.392625 TGTAGGAAAATCTCTCATCGGTAG 57.607 41.667 0.00 0.00 0.00 3.18
3320 3383 9.703892 AATAGAATGTAGGAAAATCTCTCATCG 57.296 33.333 0.00 0.00 0.00 3.84
3353 3416 8.268605 TGGATTACACAATAAGGCTACAATACA 58.731 33.333 0.00 0.00 0.00 2.29
3382 3445 8.593679 TGTCATACAAGTCCTATACCAATATGG 58.406 37.037 0.00 0.00 45.02 2.74
3430 3523 2.106477 TCACACACACACACACACAT 57.894 45.000 0.00 0.00 0.00 3.21
3461 3558 2.291605 GGGAACTGGCTCAACCCTTTAT 60.292 50.000 0.00 0.00 37.83 1.40
3494 3591 7.263496 AGGTTAGACTCGATACCATGTAAAAC 58.737 38.462 0.00 0.00 33.02 2.43


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

AutoCloner maintained by Alex Coulton.