Multiple sequence alignment - TraesCS2B01G122600

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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 TraesCS2B01G122600 chr2B 100.000 2549 0 0 1 2549 89839476 89842024 0 4708
1 TraesCS2B01G122600 chr2B 95.010 1984 93 6 568 2549 692955896 692957875 0 3110
2 TraesCS2B01G122600 chr2B 94.874 1990 90 9 568 2549 492636664 492638649 0 3099
3 TraesCS2B01G122600 chr2B 94.808 1984 96 6 568 2549 458657422 458659400 0 3086
4 TraesCS2B01G122600 chr2B 92.820 571 31 6 1 568 704105662 704106225 0 819
5 TraesCS2B01G122600 chr4A 95.209 1983 89 6 569 2549 705529252 705527274 0 3131
6 TraesCS2B01G122600 chr1B 95.121 1988 88 6 568 2549 581717562 581715578 0 3125
7 TraesCS2B01G122600 chr1B 94.861 1985 96 5 566 2549 561526127 561528106 0 3096
8 TraesCS2B01G122600 chr1B 94.854 1982 96 6 569 2549 520844119 520842143 0 3090
9 TraesCS2B01G122600 chr1B 91.944 571 41 3 1 568 630217728 630217160 0 795
10 TraesCS2B01G122600 chr7B 94.816 1987 97 5 566 2549 720989193 720987210 0 3094
11 TraesCS2B01G122600 chr3B 94.763 1986 97 6 568 2549 108092313 108090331 0 3085
12 TraesCS2B01G122600 chr3B 92.782 568 39 1 1 568 635336054 635335489 0 821
13 TraesCS2B01G122600 chr5D 93.531 572 30 3 1 568 467755058 467754490 0 845
14 TraesCS2B01G122600 chr3D 92.794 569 40 1 1 568 8734488 8735056 0 822
15 TraesCS2B01G122600 chr3D 92.606 568 38 3 1 568 332022587 332023150 0 813
16 TraesCS2B01G122600 chr3D 92.254 568 43 1 1 568 403158956 403158390 0 804
17 TraesCS2B01G122600 chr7D 92.632 570 40 2 1 568 67408143 67408712 0 819
18 TraesCS2B01G122600 chr5B 92.430 568 40 2 1 568 563015009 563014445 0 808


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 TraesCS2B01G122600 chr2B 89839476 89842024 2548 False 4708 4708 100.000 1 2549 1 chr2B.!!$F1 2548
1 TraesCS2B01G122600 chr2B 692955896 692957875 1979 False 3110 3110 95.010 568 2549 1 chr2B.!!$F4 1981
2 TraesCS2B01G122600 chr2B 492636664 492638649 1985 False 3099 3099 94.874 568 2549 1 chr2B.!!$F3 1981
3 TraesCS2B01G122600 chr2B 458657422 458659400 1978 False 3086 3086 94.808 568 2549 1 chr2B.!!$F2 1981
4 TraesCS2B01G122600 chr2B 704105662 704106225 563 False 819 819 92.820 1 568 1 chr2B.!!$F5 567
5 TraesCS2B01G122600 chr4A 705527274 705529252 1978 True 3131 3131 95.209 569 2549 1 chr4A.!!$R1 1980
6 TraesCS2B01G122600 chr1B 581715578 581717562 1984 True 3125 3125 95.121 568 2549 1 chr1B.!!$R2 1981
7 TraesCS2B01G122600 chr1B 561526127 561528106 1979 False 3096 3096 94.861 566 2549 1 chr1B.!!$F1 1983
8 TraesCS2B01G122600 chr1B 520842143 520844119 1976 True 3090 3090 94.854 569 2549 1 chr1B.!!$R1 1980
9 TraesCS2B01G122600 chr1B 630217160 630217728 568 True 795 795 91.944 1 568 1 chr1B.!!$R3 567
10 TraesCS2B01G122600 chr7B 720987210 720989193 1983 True 3094 3094 94.816 566 2549 1 chr7B.!!$R1 1983
11 TraesCS2B01G122600 chr3B 108090331 108092313 1982 True 3085 3085 94.763 568 2549 1 chr3B.!!$R1 1981
12 TraesCS2B01G122600 chr3B 635335489 635336054 565 True 821 821 92.782 1 568 1 chr3B.!!$R2 567
13 TraesCS2B01G122600 chr5D 467754490 467755058 568 True 845 845 93.531 1 568 1 chr5D.!!$R1 567
14 TraesCS2B01G122600 chr3D 8734488 8735056 568 False 822 822 92.794 1 568 1 chr3D.!!$F1 567
15 TraesCS2B01G122600 chr3D 332022587 332023150 563 False 813 813 92.606 1 568 1 chr3D.!!$F2 567
16 TraesCS2B01G122600 chr3D 403158390 403158956 566 True 804 804 92.254 1 568 1 chr3D.!!$R1 567
17 TraesCS2B01G122600 chr7D 67408143 67408712 569 False 819 819 92.632 1 568 1 chr7D.!!$F1 567
18 TraesCS2B01G122600 chr5B 563014445 563015009 564 True 808 808 92.430 1 568 1 chr5B.!!$R1 567

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
991 1010 0.391263 GTTGAGATCCCGTTCGGCTT 60.391 55.0 5.66 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 2439 1.531149 CACTAAACCAAGTGCCACTCG 59.469 52.381 0.0 0.0 40.4 4.18 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
180 181 6.909550 AACTTATGGCAAGGTTTACATCAA 57.090 33.333 0.00 0.00 0.00 2.57
260 261 8.553459 TGACACTCATCTTTTCTCTATTTTCC 57.447 34.615 0.00 0.00 0.00 3.13
262 263 7.386851 ACACTCATCTTTTCTCTATTTTCCGA 58.613 34.615 0.00 0.00 0.00 4.55
264 265 7.547370 CACTCATCTTTTCTCTATTTTCCGACT 59.453 37.037 0.00 0.00 0.00 4.18
384 385 3.347216 AGGTATGCGCTTTGTGAAAGAT 58.653 40.909 9.73 0.00 41.02 2.40
449 450 8.424918 CCTAATATGTAAGAAGCTTCTCCAAGA 58.575 37.037 28.58 18.67 36.28 3.02
451 452 8.674263 AATATGTAAGAAGCTTCTCCAAGATG 57.326 34.615 28.58 0.00 36.28 2.90
459 460 4.030134 GCTTCTCCAAGATGCTTCATTG 57.970 45.455 2.07 4.13 40.85 2.82
674 689 2.177531 GCGCACCGACTCGTTCTA 59.822 61.111 0.30 0.00 0.00 2.10
719 734 1.200020 CAACATTTTGACTCGGCCCTC 59.800 52.381 0.00 0.00 34.24 4.30
735 750 1.536418 CTCACAGGTGGGACCAGGA 60.536 63.158 0.00 0.00 41.95 3.86
746 761 4.704103 ACCAGGAGGCAGAGGCGA 62.704 66.667 0.00 0.00 42.47 5.54
926 945 1.301293 GGCAGTGGGAAGCTAGCTT 59.699 57.895 29.71 29.71 39.23 3.74
991 1010 0.391263 GTTGAGATCCCGTTCGGCTT 60.391 55.000 5.66 0.00 0.00 4.35
1109 1128 1.672881 GAGCATTGATCGGAGGGTTTG 59.327 52.381 0.00 0.00 0.00 2.93
1133 1152 0.762418 ACACCGAGGAACCACAATCA 59.238 50.000 0.00 0.00 0.00 2.57
1159 1178 0.917259 CTACGTGTGCAGCGAGAATC 59.083 55.000 16.16 0.00 0.00 2.52
1193 1212 2.142319 GGCAATTGCACCATTTTCGTT 58.858 42.857 30.32 0.00 44.36 3.85
1202 1221 1.810151 ACCATTTTCGTTGTCGGGATG 59.190 47.619 0.00 0.00 37.69 3.51
1264 1283 2.297033 GCATGCTTCTTTCTTTGGGTCA 59.703 45.455 11.37 0.00 0.00 4.02
1310 1329 1.538512 TGAACTGCAAGAAGAGCATGC 59.461 47.619 10.51 10.51 41.82 4.06
1380 1399 1.689575 CCGGAAGAAGAGATGGAGGGA 60.690 57.143 0.00 0.00 0.00 4.20
1486 1505 6.878389 ACCAATACCCATTTGCAAATACTTTG 59.122 34.615 23.69 19.50 43.44 2.77
1579 1598 9.087871 TGGAGGAATTTGTAATCTTGAAAATCA 57.912 29.630 0.00 0.00 0.00 2.57
1761 1785 7.595130 CAGAGCCAAACAATTAAGGTTAGAAAC 59.405 37.037 0.00 0.00 0.00 2.78
2034 2059 1.599797 GTGGTGTTTAGGGCTGCGT 60.600 57.895 0.00 0.00 0.00 5.24
2062 2087 1.069823 CGCTAGGACAGATGGCAAGAT 59.930 52.381 0.00 0.00 0.00 2.40
2106 2131 6.422100 GCAATGTATACATAGTGAGACTGTGG 59.578 42.308 18.56 0.00 40.99 4.17
2113 2138 6.114187 ACATAGTGAGACTGTGGAATTTGA 57.886 37.500 5.60 0.00 40.99 2.69
2224 2251 0.248289 GCCAGTAACCGCTAGGACAA 59.752 55.000 0.00 0.00 41.02 3.18
2263 2290 5.914716 ACATGGGTAGGGAAGGAATGTATAA 59.085 40.000 0.00 0.00 0.00 0.98
2351 2379 5.046950 AGTGGTTTTCCTTTGTTTTGCACTA 60.047 36.000 0.00 0.00 41.38 2.74
2355 2383 7.228706 TGGTTTTCCTTTGTTTTGCACTAAAAA 59.771 29.630 0.00 0.00 39.18 1.94
2363 2391 6.356757 TGTTTTGCACTAAAAATTTGGAGC 57.643 33.333 5.07 5.07 39.79 4.70
2364 2392 6.112058 TGTTTTGCACTAAAAATTTGGAGCT 58.888 32.000 11.50 0.00 39.79 4.09
2371 2399 6.427853 GCACTAAAAATTTGGAGCTTTGGAAT 59.572 34.615 4.83 0.00 33.74 3.01
2376 2404 3.749665 TTTGGAGCTTTGGAATGTTGG 57.250 42.857 0.00 0.00 0.00 3.77
2411 2439 0.248866 CTGCCACGTGGTTTTGGTTC 60.249 55.000 33.92 16.16 37.57 3.62
2448 2476 1.072331 AGTGTTAGAGTGGCACTTGGG 59.928 52.381 22.98 0.00 40.13 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.134818 AGGATTACGTCGATGCTTGCA 60.135 47.619 4.06 0.00 0.00 4.08
27 28 2.753452 ACGAAGAGCTCATCGTAAAGGA 59.247 45.455 37.21 0.00 46.47 3.36
37 38 0.539669 TGGAGGTGACGAAGAGCTCA 60.540 55.000 17.77 0.00 39.29 4.26
180 181 0.036010 GCCATGCTGTGTACCAGACT 60.036 55.000 13.57 0.00 44.49 3.24
262 263 1.600916 GCTCAAAGCCCGACCAAGT 60.601 57.895 0.00 0.00 34.48 3.16
370 371 4.260538 GCCTCATAGATCTTTCACAAAGCG 60.261 45.833 0.00 0.00 38.39 4.68
384 385 2.552599 AGATCGAGACGCCTCATAGA 57.447 50.000 0.00 0.00 39.39 1.98
449 450 3.659183 AGGCCTACTTCAATGAAGCAT 57.341 42.857 21.69 7.09 42.79 3.79
451 452 5.734503 GCATAAAGGCCTACTTCAATGAAGC 60.735 44.000 21.69 9.41 42.79 3.86
456 457 5.360999 GGAAAGCATAAAGGCCTACTTCAAT 59.639 40.000 5.16 0.00 38.85 2.57
457 458 4.705023 GGAAAGCATAAAGGCCTACTTCAA 59.295 41.667 5.16 0.00 38.85 2.69
458 459 4.263727 TGGAAAGCATAAAGGCCTACTTCA 60.264 41.667 5.16 0.00 38.85 3.02
459 460 4.270008 TGGAAAGCATAAAGGCCTACTTC 58.730 43.478 5.16 1.31 38.85 3.01
538 553 4.528076 AAGTGAGTGGGAGCTCTATAGA 57.472 45.455 14.64 1.69 36.51 1.98
542 557 3.176924 AGAAAGTGAGTGGGAGCTCTA 57.823 47.619 14.64 0.00 36.51 2.43
719 734 2.596851 CCTCCTGGTCCCACCTGTG 61.597 68.421 0.00 0.00 39.58 3.66
735 750 0.251341 AAAATTGGTCGCCTCTGCCT 60.251 50.000 0.00 0.00 0.00 4.75
746 761 6.153756 GTGCAACGGTCTAAATAAAATTGGT 58.846 36.000 0.00 0.00 0.00 3.67
787 802 0.252479 CCTCAATGGCTCTCTGCTGT 59.748 55.000 0.00 0.00 42.39 4.40
800 815 1.539065 CGCAACGGCTCTATCCTCAAT 60.539 52.381 0.00 0.00 38.10 2.57
806 821 1.883084 CACCCGCAACGGCTCTATC 60.883 63.158 0.00 0.00 46.86 2.08
911 930 1.280421 CTCCAAAGCTAGCTTCCCACT 59.720 52.381 29.42 11.59 34.84 4.00
926 945 4.641645 CACCGCTGTGCCCTCCAA 62.642 66.667 0.00 0.00 35.31 3.53
991 1010 0.174389 GCAGAAGACATGGAGCTCGA 59.826 55.000 7.83 3.70 0.00 4.04
1093 1112 2.039746 TGTGACAAACCCTCCGATCAAT 59.960 45.455 0.00 0.00 0.00 2.57
1109 1128 0.878961 GTGGTTCCTCGGTGTGTGAC 60.879 60.000 0.00 0.00 0.00 3.67
1159 1178 0.179029 ATTGCCCCGATTCTTACCCG 60.179 55.000 0.00 0.00 0.00 5.28
1193 1212 2.083774 GATTGCTCAAACATCCCGACA 58.916 47.619 0.00 0.00 0.00 4.35
1202 1221 3.189287 ACAGATCAACCGATTGCTCAAAC 59.811 43.478 0.00 0.00 34.09 2.93
1264 1283 0.990374 AGAGTCTTGGCCAGAGCATT 59.010 50.000 5.11 0.00 42.56 3.56
1310 1329 2.580326 GCATGCGCAACCATTCGG 60.580 61.111 17.11 0.00 38.36 4.30
1380 1399 0.319383 CTCTGTCAGTGCGTGCTTCT 60.319 55.000 0.00 0.00 0.00 2.85
1459 1478 7.912778 AGTATTTGCAAATGGGTATTGGTAT 57.087 32.000 30.43 6.62 0.00 2.73
1486 1505 2.748209 ACCATACCTACAAATGCCCC 57.252 50.000 0.00 0.00 0.00 5.80
1583 1602 9.626045 CCAACATTTAAACTAGGTGAATTTCTC 57.374 33.333 0.00 0.00 0.00 2.87
1584 1603 9.143155 ACCAACATTTAAACTAGGTGAATTTCT 57.857 29.630 0.00 0.00 0.00 2.52
1585 1604 9.406828 GACCAACATTTAAACTAGGTGAATTTC 57.593 33.333 7.84 0.00 0.00 2.17
1586 1605 8.919145 TGACCAACATTTAAACTAGGTGAATTT 58.081 29.630 7.84 0.00 0.00 1.82
1796 1820 7.747888 TCACAGTGTATTTGAATTGGATTACG 58.252 34.615 0.00 0.00 0.00 3.18
2034 2059 1.927487 TCTGTCCTAGCGGTTACCAA 58.073 50.000 1.13 0.00 0.00 3.67
2062 2087 2.109128 TGCTTCCCTACCCATGTCAAAA 59.891 45.455 0.00 0.00 0.00 2.44
2207 2234 2.936498 CCATTTGTCCTAGCGGTTACTG 59.064 50.000 0.00 0.00 0.00 2.74
2208 2235 2.679930 GCCATTTGTCCTAGCGGTTACT 60.680 50.000 0.00 0.00 0.00 2.24
2224 2251 2.564062 CCCATGTCAAACTCTTGCCATT 59.436 45.455 0.00 0.00 28.75 3.16
2263 2290 8.450578 TTGACAAATTTCACAGTCTCACTATT 57.549 30.769 7.62 0.00 32.41 1.73
2351 2379 6.039605 CCAACATTCCAAAGCTCCAAATTTTT 59.960 34.615 0.00 0.00 0.00 1.94
2355 2383 3.903090 TCCAACATTCCAAAGCTCCAAAT 59.097 39.130 0.00 0.00 0.00 2.32
2363 2391 5.768317 ACATACGTTTCCAACATTCCAAAG 58.232 37.500 0.00 0.00 0.00 2.77
2364 2392 5.776173 ACATACGTTTCCAACATTCCAAA 57.224 34.783 0.00 0.00 0.00 3.28
2371 2399 3.378742 AGTGCAAACATACGTTTCCAACA 59.621 39.130 0.00 0.00 43.57 3.33
2376 2404 2.287308 TGGCAGTGCAAACATACGTTTC 60.287 45.455 18.61 0.00 43.57 2.78
2411 2439 1.531149 CACTAAACCAAGTGCCACTCG 59.469 52.381 0.00 0.00 40.40 4.18


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

AutoCloner maintained by Alex Coulton.