Multiple sequence alignment - TraesCS2D01G509400

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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 TraesCS2D01G509400 chr2D 100.000 2582 0 0 1 2582 601718537 601715956 0.000000e+00 4769
1 TraesCS2D01G509400 chr2D 97.794 544 11 1 1 544 337389995 337390537 0.000000e+00 937
2 TraesCS2D01G509400 chr2D 100.000 449 0 0 2901 3349 601715637 601715189 0.000000e+00 830
3 TraesCS2D01G509400 chrUn 96.055 2053 73 4 530 2582 15307561 15309605 0.000000e+00 3336
4 TraesCS2D01G509400 chrUn 95.714 2053 80 4 530 2582 247977797 247975753 0.000000e+00 3297
5 TraesCS2D01G509400 chrUn 95.789 1401 51 2 670 2070 15288273 15289665 0.000000e+00 2254
6 TraesCS2D01G509400 chrUn 87.249 1890 203 27 534 2401 258621215 258623088 0.000000e+00 2121
7 TraesCS2D01G509400 chrUn 87.190 1897 204 28 534 2407 296303085 296301205 0.000000e+00 2121
8 TraesCS2D01G509400 chrUn 93.750 640 35 2 530 1169 375647795 375648429 0.000000e+00 955
9 TraesCS2D01G509400 chrUn 92.428 449 32 2 2901 3349 15309664 15310110 1.010000e-179 640
10 TraesCS2D01G509400 chrUn 92.428 449 32 2 2901 3349 247975694 247975248 1.010000e-179 640
11 TraesCS2D01G509400 chrUn 92.428 449 32 2 2901 3349 308935678 308935232 1.010000e-179 640
12 TraesCS2D01G509400 chr2B 92.442 1839 133 3 534 2370 732040543 732038709 0.000000e+00 2621
13 TraesCS2D01G509400 chr2B 88.043 1773 157 29 774 2532 732046374 732044643 0.000000e+00 2049
14 TraesCS2D01G509400 chr2B 86.020 1867 214 33 544 2384 733071985 733073830 0.000000e+00 1958
15 TraesCS2D01G509400 chr2B 84.864 1916 252 24 534 2421 732014268 732012363 0.000000e+00 1897
16 TraesCS2D01G509400 chr2B 85.992 257 27 7 534 783 732046653 732046399 1.980000e-67 267
17 TraesCS2D01G509400 chr2A 87.114 1521 177 14 901 2408 734894154 734892640 0.000000e+00 1705
18 TraesCS2D01G509400 chr2A 92.428 449 32 2 2901 3349 734919156 734918710 1.010000e-179 640
19 TraesCS2D01G509400 chr7D 98.507 536 7 1 1 535 185108005 185108540 0.000000e+00 944
20 TraesCS2D01G509400 chr7D 97.967 541 10 1 1 541 169367850 169368389 0.000000e+00 937
21 TraesCS2D01G509400 chr7D 97.967 541 10 1 1 540 616176882 616176342 0.000000e+00 937
22 TraesCS2D01G509400 chr6D 98.505 535 7 1 1 534 63772665 63772131 0.000000e+00 942
23 TraesCS2D01G509400 chr6D 98.493 531 8 0 1 531 315086592 315087122 0.000000e+00 937
24 TraesCS2D01G509400 chr5D 98.505 535 7 1 1 534 390247902 390248436 0.000000e+00 942
25 TraesCS2D01G509400 chr3D 98.505 535 7 1 1 534 301384182 301383648 0.000000e+00 942
26 TraesCS2D01G509400 chr3D 97.970 542 9 2 1 541 484276388 484275848 0.000000e+00 939


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 TraesCS2D01G509400 chr2D 601715189 601718537 3348 True 2799.5 4769 100.0000 1 3349 2 chr2D.!!$R1 3348
1 TraesCS2D01G509400 chr2D 337389995 337390537 542 False 937.0 937 97.7940 1 544 1 chr2D.!!$F1 543
2 TraesCS2D01G509400 chrUn 15288273 15289665 1392 False 2254.0 2254 95.7890 670 2070 1 chrUn.!!$F1 1400
3 TraesCS2D01G509400 chrUn 258621215 258623088 1873 False 2121.0 2121 87.2490 534 2401 1 chrUn.!!$F2 1867
4 TraesCS2D01G509400 chrUn 296301205 296303085 1880 True 2121.0 2121 87.1900 534 2407 1 chrUn.!!$R1 1873
5 TraesCS2D01G509400 chrUn 15307561 15310110 2549 False 1988.0 3336 94.2415 530 3349 2 chrUn.!!$F4 2819
6 TraesCS2D01G509400 chrUn 247975248 247977797 2549 True 1968.5 3297 94.0710 530 3349 2 chrUn.!!$R3 2819
7 TraesCS2D01G509400 chrUn 375647795 375648429 634 False 955.0 955 93.7500 530 1169 1 chrUn.!!$F3 639
8 TraesCS2D01G509400 chr2B 732038709 732040543 1834 True 2621.0 2621 92.4420 534 2370 1 chr2B.!!$R2 1836
9 TraesCS2D01G509400 chr2B 733071985 733073830 1845 False 1958.0 1958 86.0200 544 2384 1 chr2B.!!$F1 1840
10 TraesCS2D01G509400 chr2B 732012363 732014268 1905 True 1897.0 1897 84.8640 534 2421 1 chr2B.!!$R1 1887
11 TraesCS2D01G509400 chr2B 732044643 732046653 2010 True 1158.0 2049 87.0175 534 2532 2 chr2B.!!$R3 1998
12 TraesCS2D01G509400 chr2A 734892640 734894154 1514 True 1705.0 1705 87.1140 901 2408 1 chr2A.!!$R1 1507
13 TraesCS2D01G509400 chr7D 185108005 185108540 535 False 944.0 944 98.5070 1 535 1 chr7D.!!$F2 534
14 TraesCS2D01G509400 chr7D 169367850 169368389 539 False 937.0 937 97.9670 1 541 1 chr7D.!!$F1 540
15 TraesCS2D01G509400 chr7D 616176342 616176882 540 True 937.0 937 97.9670 1 540 1 chr7D.!!$R1 539
16 TraesCS2D01G509400 chr6D 63772131 63772665 534 True 942.0 942 98.5050 1 534 1 chr6D.!!$R1 533
17 TraesCS2D01G509400 chr6D 315086592 315087122 530 False 937.0 937 98.4930 1 531 1 chr6D.!!$F1 530
18 TraesCS2D01G509400 chr5D 390247902 390248436 534 False 942.0 942 98.5050 1 534 1 chr5D.!!$F1 533
19 TraesCS2D01G509400 chr3D 301383648 301384182 534 True 942.0 942 98.5050 1 534 1 chr3D.!!$R1 533
20 TraesCS2D01G509400 chr3D 484275848 484276388 540 True 939.0 939 97.9700 1 541 1 chr3D.!!$R2 540

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
150 151 0.169230 GTTGTGACGTTTGGCACACA 59.831 50.000 2.92 4.5 43.97 3.72 F
594 602 2.482864 CCCTTGTTTCCAACATTGTGC 58.517 47.619 0.00 0.0 41.79 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1767 1.616159 TAGCCCTTGCAGTTTCCAAC 58.384 50.000 0.00 0.00 41.13 3.77 R
2428 2512 4.000988 CCTAATTTACACTCGGCTGTTGT 58.999 43.478 7.54 7.54 0.00 3.32 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
102 103 2.761208 CAGACACTTTCGGAGATACCCT 59.239 50.000 0.00 0.00 35.04 4.34
150 151 0.169230 GTTGTGACGTTTGGCACACA 59.831 50.000 2.92 4.50 43.97 3.72
165 166 2.554032 GCACACACAAAGCACTCCTATT 59.446 45.455 0.00 0.00 0.00 1.73
423 424 4.875536 TGTGGTCTATGTATTCACACATGC 59.124 41.667 0.00 0.00 39.46 4.06
451 452 6.954944 ACGATTTCCGGATAACACAATTATG 58.045 36.000 4.15 0.00 43.93 1.90
594 602 2.482864 CCCTTGTTTCCAACATTGTGC 58.517 47.619 0.00 0.00 41.79 4.57
604 612 2.896685 CCAACATTGTGCTTTTCCCCTA 59.103 45.455 0.00 0.00 0.00 3.53
798 844 6.446318 TCATGTTTTGTTCCTCAACTATTGC 58.554 36.000 0.00 0.00 35.61 3.56
940 1001 7.712639 TCTCTAATGCTTACTCAAATCATGACC 59.287 37.037 0.00 0.00 33.47 4.02
1329 1407 5.747197 TCTTCGAACAAAGATATAGCCGAAC 59.253 40.000 0.00 0.00 32.48 3.95
2040 2122 6.463360 TCACACTTTGTATCACTAATGAGCA 58.537 36.000 0.00 0.00 38.57 4.26
2116 2198 0.242017 GATGCTGAGGTGGTTGCAAC 59.758 55.000 21.59 21.59 38.96 4.17
2290 2372 0.536460 GGGAACAAAGGCGGTGAAGA 60.536 55.000 0.00 0.00 0.00 2.87
2312 2394 6.879400 AGAAACTAGGTTATACAGCTTGGAG 58.121 40.000 0.00 0.00 34.13 3.86
2428 2512 7.157347 TGCATGCCACATGTAAATTTCTTAAA 58.843 30.769 16.68 0.00 0.00 1.52
2439 2523 7.136119 TGTAAATTTCTTAAACAACAGCCGAG 58.864 34.615 0.00 0.00 0.00 4.63
2948 3034 4.040339 TCACATAGGTTTTGAGAGCACTGA 59.960 41.667 0.00 0.00 0.00 3.41
2965 3051 6.241207 GCACTGAGCTAACTTGTGAAATTA 57.759 37.500 0.00 0.00 41.15 1.40
2968 3054 8.616076 GCACTGAGCTAACTTGTGAAATTATAT 58.384 33.333 0.00 0.00 41.15 0.86
3040 3126 4.997395 ACAATAAGTTGCTACACCACTCTG 59.003 41.667 0.13 0.00 38.96 3.35
3063 3149 0.100682 TGTTACTCGCTCCTCATCGC 59.899 55.000 0.00 0.00 0.00 4.58
3088 3174 5.394115 GCATCGGTCCATTAACCTTTTTGAT 60.394 40.000 0.00 0.00 37.15 2.57
3089 3175 5.637006 TCGGTCCATTAACCTTTTTGATG 57.363 39.130 0.00 0.00 37.15 3.07
3095 3181 7.308710 GGTCCATTAACCTTTTTGATGTCGTTA 60.309 37.037 0.00 0.00 36.32 3.18
3103 3189 8.347729 ACCTTTTTGATGTCGTTATTTTTGTC 57.652 30.769 0.00 0.00 0.00 3.18
3109 3195 2.612672 TGTCGTTATTTTTGTCGTGCCA 59.387 40.909 0.00 0.00 0.00 4.92
3131 3217 2.373169 AGGAAGCTCAGGTTGATTGACA 59.627 45.455 0.00 0.00 0.00 3.58
3159 3245 0.674895 CCTCAAGACCGGGAGCAAAG 60.675 60.000 6.32 0.00 0.00 2.77
3166 3252 4.563140 AGACCGGGAGCAAAGTTTATTA 57.437 40.909 6.32 0.00 0.00 0.98
3208 3294 8.248253 TGACAGCTCGTGAACTAGAAATATTAA 58.752 33.333 0.00 0.00 0.00 1.40
3250 3336 4.468510 AGGTCGACACCAAAAGGATACATA 59.531 41.667 18.91 0.00 46.68 2.29
3262 3348 5.808366 AAGGATACATACATGGTCGACAT 57.192 39.130 18.91 6.28 39.17 3.06
3263 3349 5.392767 AGGATACATACATGGTCGACATC 57.607 43.478 18.91 7.95 36.87 3.06
3270 3356 3.685139 ACATGGTCGACATCAGAAGTT 57.315 42.857 18.91 0.00 37.84 2.66
3272 3358 3.997021 ACATGGTCGACATCAGAAGTTTC 59.003 43.478 18.91 0.00 37.84 2.78
3274 3360 5.047306 ACATGGTCGACATCAGAAGTTTCTA 60.047 40.000 18.91 0.00 37.84 2.10
3275 3361 5.661056 TGGTCGACATCAGAAGTTTCTAT 57.339 39.130 18.91 0.00 35.34 1.98
3286 3372 8.772705 CATCAGAAGTTTCTATGGCTAGAATTC 58.227 37.037 0.00 0.00 42.22 2.17
3300 3386 4.023365 GCTAGAATTCCATGAGGTTGATGC 60.023 45.833 0.65 0.00 35.89 3.91
3303 3389 1.838112 TTCCATGAGGTTGATGCCAC 58.162 50.000 0.00 0.00 35.89 5.01
3306 3392 0.813184 CATGAGGTTGATGCCACCAC 59.187 55.000 0.00 0.00 0.00 4.16
3309 3395 1.298859 GAGGTTGATGCCACCACGAC 61.299 60.000 0.00 0.00 0.00 4.34
3312 3398 3.816367 TTGATGCCACCACGACGCA 62.816 57.895 0.00 0.00 36.84 5.24
3333 3419 1.285641 GCAACACCACCATTCCACG 59.714 57.895 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 3.371166 GGGTGGCTATAAAGGTGCACTAA 60.371 47.826 17.98 0.00 0.00 2.24
150 151 4.442706 CGGATACAATAGGAGTGCTTTGT 58.557 43.478 13.58 13.58 36.37 2.83
165 166 0.687920 TTGTGCAACTCCCGGATACA 59.312 50.000 0.73 0.00 38.04 2.29
224 225 3.251729 TCGTGTAGTTCGTTTGCTAGAGT 59.748 43.478 0.00 0.00 0.00 3.24
423 424 5.977171 TGTGTTATCCGGAAATCGTAATG 57.023 39.130 9.01 0.00 37.11 1.90
451 452 8.570488 TCATGATAATTGTCTATTGTTCATGCC 58.430 33.333 18.84 0.00 41.74 4.40
557 561 3.732048 AGGGGGTTTTACATCGAATGT 57.268 42.857 0.00 0.00 46.92 2.71
594 602 6.015010 ACTCATCGATATCTGTAGGGGAAAAG 60.015 42.308 0.00 0.00 0.00 2.27
604 612 5.767269 CTGTAAGCACTCATCGATATCTGT 58.233 41.667 0.00 0.00 0.00 3.41
940 1001 4.641396 TGTTTGAGTGATCTACAACCCTG 58.359 43.478 0.00 0.00 0.00 4.45
1329 1407 8.489990 TCTTCTAAGCTGAAAATCTTCATCTG 57.510 34.615 0.00 0.00 40.78 2.90
1355 1433 5.852282 ATTTGTTGGTTGCTTGTTCTAGT 57.148 34.783 0.00 0.00 0.00 2.57
1685 1767 1.616159 TAGCCCTTGCAGTTTCCAAC 58.384 50.000 0.00 0.00 41.13 3.77
2040 2122 7.492524 TCTAGAATATCTGACAAGCGATTGTT 58.507 34.615 21.37 7.11 34.90 2.83
2290 2372 6.869206 TCTCCAAGCTGTATAACCTAGTTT 57.131 37.500 0.00 0.00 0.00 2.66
2312 2394 5.611374 TCGGATGATTGGATAAACTCCTTC 58.389 41.667 0.00 0.00 45.21 3.46
2428 2512 4.000988 CCTAATTTACACTCGGCTGTTGT 58.999 43.478 7.54 7.54 0.00 3.32
2489 2573 5.393352 GCATATTTGGTTCTGCATGACTCAA 60.393 40.000 0.00 0.00 34.77 3.02
2490 2574 4.096833 GCATATTTGGTTCTGCATGACTCA 59.903 41.667 0.00 0.00 34.77 3.41
2555 2641 9.554395 TCAGAATTAAGTGTGACAAACTTCATA 57.446 29.630 14.43 2.77 38.73 2.15
2990 3076 5.473039 ACACTAAATTTGCATTGCCTTCTC 58.527 37.500 6.12 0.00 0.00 2.87
3016 3102 4.997395 AGAGTGGTGTAGCAACTTATTGTG 59.003 41.667 0.00 0.00 38.17 3.33
3017 3103 4.997395 CAGAGTGGTGTAGCAACTTATTGT 59.003 41.667 0.00 0.00 38.17 2.71
3018 3104 5.237815 TCAGAGTGGTGTAGCAACTTATTG 58.762 41.667 0.00 0.00 38.99 1.90
3040 3126 3.440228 GATGAGGAGCGAGTAACAACTC 58.560 50.000 0.00 0.00 0.00 3.01
3063 3149 1.663695 AAGGTTAATGGACCGATGCG 58.336 50.000 0.00 0.00 44.62 4.73
3088 3174 2.612672 TGGCACGACAAAAATAACGACA 59.387 40.909 0.00 0.00 0.00 4.35
3089 3175 3.256285 TGGCACGACAAAAATAACGAC 57.744 42.857 0.00 0.00 0.00 4.34
3095 3181 2.545742 GCTTCCTTGGCACGACAAAAAT 60.546 45.455 0.00 0.00 0.00 1.82
3103 3189 2.037136 CCTGAGCTTCCTTGGCACG 61.037 63.158 0.00 0.00 0.00 5.34
3109 3195 3.181440 TGTCAATCAACCTGAGCTTCCTT 60.181 43.478 0.00 0.00 0.00 3.36
3131 3217 0.035458 CGGTCTTGAGGCTTGGACTT 59.965 55.000 12.59 0.00 0.00 3.01
3166 3252 7.442364 ACGAGCTGTCAATTAGTTATATTGCAT 59.558 33.333 0.00 0.00 33.91 3.96
3208 3294 5.161943 ACCTCGTGGAATTTTAGCTAAGT 57.838 39.130 11.17 0.00 37.04 2.24
3223 3309 0.859232 CTTTTGGTGTCGACCTCGTG 59.141 55.000 14.12 0.00 43.58 4.35
3250 3336 3.685139 AACTTCTGATGTCGACCATGT 57.315 42.857 14.12 1.93 32.56 3.21
3270 3356 5.608437 ACCTCATGGAATTCTAGCCATAGAA 59.392 40.000 5.23 0.53 42.81 2.10
3272 3358 5.495926 ACCTCATGGAATTCTAGCCATAG 57.504 43.478 5.23 0.85 42.81 2.23
3274 3360 4.166725 TCAACCTCATGGAATTCTAGCCAT 59.833 41.667 5.23 0.00 45.47 4.40
3275 3361 3.523157 TCAACCTCATGGAATTCTAGCCA 59.477 43.478 5.23 0.00 38.78 4.75
3286 3372 0.323633 TGGTGGCATCAACCTCATGG 60.324 55.000 0.00 0.00 39.83 3.66
3303 3389 3.276091 TGTTGCCTTGCGTCGTGG 61.276 61.111 0.00 0.00 0.00 4.94
3306 3392 3.276091 TGGTGTTGCCTTGCGTCG 61.276 61.111 0.00 0.00 38.35 5.12
3309 3395 2.086251 AATGGTGGTGTTGCCTTGCG 62.086 55.000 0.00 0.00 38.35 4.85
3312 3398 0.105760 TGGAATGGTGGTGTTGCCTT 60.106 50.000 0.00 0.00 38.35 4.35


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

AutoCloner maintained by Alex Coulton.