Multiple sequence alignment - TraesCS2B01G131000

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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 TraesCS2B01G131000 chr2B 100.000 1660 0 0 848 2507 98079737 98078078 0 3066
1 TraesCS2B01G131000 chr2B 93.438 1661 105 3 848 2506 76226447 76224789 0 2460
2 TraesCS2B01G131000 chr2B 92.775 1661 115 4 848 2506 128444136 128445793 0 2398
3 TraesCS2B01G131000 chr2B 100.000 556 0 0 1 556 98080584 98080029 0 1027
4 TraesCS2B01G131000 chr1B 95.247 1662 75 3 848 2507 337030502 337032161 0 2628
5 TraesCS2B01G131000 chr1B 94.054 555 31 2 3 556 337029869 337030422 0 841
6 TraesCS2B01G131000 chr1B 93.153 555 36 2 4 556 284374172 284373618 0 813
7 TraesCS2B01G131000 chr5B 95.247 1662 72 4 848 2507 98129221 98130877 0 2625
8 TraesCS2B01G131000 chr5B 92.359 1662 122 4 848 2507 219667041 219668699 0 2361
9 TraesCS2B01G131000 chr5B 95.176 539 25 1 1 538 98128419 98128957 0 850
10 TraesCS2B01G131000 chr5B 93.514 555 34 2 1 553 219666407 219666961 0 824
11 TraesCS2B01G131000 chr4B 93.746 1663 98 5 848 2507 522871941 522870282 0 2490
12 TraesCS2B01G131000 chr4B 93.321 1662 107 3 848 2507 129556308 129557967 0 2451
13 TraesCS2B01G131000 chr4B 92.960 1662 113 3 848 2507 520047112 520045453 0 2418
14 TraesCS2B01G131000 chr4B 92.460 557 39 3 1 556 5673292 5672738 0 793
15 TraesCS2B01G131000 chr4B 92.460 557 38 4 1 554 515461145 515461700 0 793
16 TraesCS2B01G131000 chr4B 92.157 561 37 6 1 556 478388330 478388888 0 785
17 TraesCS2B01G131000 chr7B 93.081 1662 111 3 848 2507 162199187 162200846 0 2429
18 TraesCS2B01G131000 chr6B 92.652 558 38 3 1 556 607375416 607375972 0 800
19 TraesCS2B01G131000 chr6B 92.487 559 39 3 1 556 240984434 240983876 0 797


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 TraesCS2B01G131000 chr2B 98078078 98080584 2506 True 2046.5 3066 100.0000 1 2507 2 chr2B.!!$R2 2506
1 TraesCS2B01G131000 chr2B 76224789 76226447 1658 True 2460.0 2460 93.4380 848 2506 1 chr2B.!!$R1 1658
2 TraesCS2B01G131000 chr2B 128444136 128445793 1657 False 2398.0 2398 92.7750 848 2506 1 chr2B.!!$F1 1658
3 TraesCS2B01G131000 chr1B 337029869 337032161 2292 False 1734.5 2628 94.6505 3 2507 2 chr1B.!!$F1 2504
4 TraesCS2B01G131000 chr1B 284373618 284374172 554 True 813.0 813 93.1530 4 556 1 chr1B.!!$R1 552
5 TraesCS2B01G131000 chr5B 98128419 98130877 2458 False 1737.5 2625 95.2115 1 2507 2 chr5B.!!$F1 2506
6 TraesCS2B01G131000 chr5B 219666407 219668699 2292 False 1592.5 2361 92.9365 1 2507 2 chr5B.!!$F2 2506
7 TraesCS2B01G131000 chr4B 522870282 522871941 1659 True 2490.0 2490 93.7460 848 2507 1 chr4B.!!$R3 1659
8 TraesCS2B01G131000 chr4B 129556308 129557967 1659 False 2451.0 2451 93.3210 848 2507 1 chr4B.!!$F1 1659
9 TraesCS2B01G131000 chr4B 520045453 520047112 1659 True 2418.0 2418 92.9600 848 2507 1 chr4B.!!$R2 1659
10 TraesCS2B01G131000 chr4B 5672738 5673292 554 True 793.0 793 92.4600 1 556 1 chr4B.!!$R1 555
11 TraesCS2B01G131000 chr4B 515461145 515461700 555 False 793.0 793 92.4600 1 554 1 chr4B.!!$F3 553
12 TraesCS2B01G131000 chr4B 478388330 478388888 558 False 785.0 785 92.1570 1 556 1 chr4B.!!$F2 555
13 TraesCS2B01G131000 chr7B 162199187 162200846 1659 False 2429.0 2429 93.0810 848 2507 1 chr7B.!!$F1 1659
14 TraesCS2B01G131000 chr6B 607375416 607375972 556 False 800.0 800 92.6520 1 556 1 chr6B.!!$F1 555
15 TraesCS2B01G131000 chr6B 240983876 240984434 558 True 797.0 797 92.4870 1 556 1 chr6B.!!$R1 555

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
199 200 1.304952 CCCAAAATAGGGCACGGGA 59.695 57.895 0.0 0.0 43.1 5.14 F
1134 1138 1.221840 CCGCCACTACTTCATGCCT 59.778 57.895 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1271 1275 0.679640 GGTGAATGGTTGCGGATCCA 60.680 55.000 13.41 9.31 38.14 3.41 R
2279 2285 1.153429 GGTACCCTTTCTGCGCGAT 60.153 57.895 12.10 0.00 0.00 4.58 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
199 200 1.304952 CCCAAAATAGGGCACGGGA 59.695 57.895 0.00 0.00 43.10 5.14
864 868 4.486887 TTCTGGTCGACGGAGACA 57.513 55.556 13.81 3.71 42.62 3.41
921 925 2.631418 CTTCTACTTCGAAGCGGTGA 57.369 50.000 24.86 14.14 34.59 4.02
982 986 3.567579 CTCTGCCCGCCCTTTTCCA 62.568 63.158 0.00 0.00 0.00 3.53
990 994 2.612721 CCCGCCCTTTTCCAATTTCTTG 60.613 50.000 0.00 0.00 0.00 3.02
1076 1080 3.959520 CGGTTTTCGCGCATCTTTA 57.040 47.368 8.75 0.00 0.00 1.85
1134 1138 1.221840 CCGCCACTACTTCATGCCT 59.778 57.895 0.00 0.00 0.00 4.75
1209 1213 2.330216 GGCAAGAAGGAGGCCTATCTA 58.670 52.381 4.42 0.00 44.32 1.98
1271 1275 1.673920 GTGGTGTTGGATTGTTGACGT 59.326 47.619 0.00 0.00 0.00 4.34
1281 1285 0.533085 TTGTTGACGTGGATCCGCAA 60.533 50.000 24.60 14.21 0.00 4.85
1316 1320 2.125106 CCAAGCCCGAGTAGTGCC 60.125 66.667 0.00 0.00 0.00 5.01
1365 1369 3.243234 CGGACGATGCTAGACTGAAGATT 60.243 47.826 0.00 0.00 0.00 2.40
1422 1426 1.202099 TCAATGTAGGGGCCGTTGGA 61.202 55.000 3.09 0.00 31.26 3.53
1423 1427 0.106719 CAATGTAGGGGCCGTTGGAT 60.107 55.000 3.09 0.00 0.00 3.41
1424 1428 0.106719 AATGTAGGGGCCGTTGGATG 60.107 55.000 3.09 0.00 0.00 3.51
1562 1567 1.002069 TGGAGTTGGATGGGATGCTT 58.998 50.000 0.00 0.00 0.00 3.91
1739 1745 1.237285 ACAGGTCGTGCAGCAATTCC 61.237 55.000 0.00 0.00 0.00 3.01
1742 1748 0.955428 GGTCGTGCAGCAATTCCTCA 60.955 55.000 0.00 0.00 0.00 3.86
1807 1813 4.295119 ACCCGCGACACCACTGAC 62.295 66.667 8.23 0.00 0.00 3.51
1826 1832 1.300156 GATGAGCTGCGGCGTATCA 60.300 57.895 23.60 17.89 44.37 2.15
1895 1901 2.048601 TGGTTTTACGTTGGAGGAGGA 58.951 47.619 0.00 0.00 0.00 3.71
2028 2034 2.360165 CCAGCAGTCTTCAAGCAACTTT 59.640 45.455 0.00 0.00 0.00 2.66
2279 2285 2.442272 GCCTACTCCTCCGCCTCA 60.442 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.721167 CGTCCGCCAAGATCCTCCA 61.721 63.158 0.00 0.00 0.00 3.86
84 85 2.460918 CTAGTATCCCGAACTTGTGCG 58.539 52.381 0.00 0.00 0.00 5.34
188 189 4.382320 GCGTGTTCCCGTGCCCTA 62.382 66.667 0.00 0.00 0.00 3.53
268 269 3.709880 CTCCCACGACGCCGCATTA 62.710 63.158 0.00 0.00 39.95 1.90
368 370 2.192861 CCGCAAGTGGCAAAGGTGA 61.193 57.895 0.00 0.00 45.17 4.02
921 925 5.045066 GGGGAAGAAGTAGTATCCTTTTGGT 60.045 44.000 0.00 0.00 41.38 3.67
982 986 6.582295 GTGTTCATAATGTCGCACAAGAAATT 59.418 34.615 0.00 0.00 33.09 1.82
990 994 3.538828 CGTACGTGTTCATAATGTCGCAC 60.539 47.826 7.22 0.00 0.00 5.34
1095 1099 2.990740 AAAGGGCTACATTTGGGTGA 57.009 45.000 0.00 0.00 0.00 4.02
1134 1138 1.313812 GCTCTCCTTTCTCGACCCGA 61.314 60.000 0.00 0.00 0.00 5.14
1209 1213 1.381463 GCTACGGAGTTCCCCCTCT 60.381 63.158 0.00 0.00 37.78 3.69
1271 1275 0.679640 GGTGAATGGTTGCGGATCCA 60.680 55.000 13.41 9.31 38.14 3.41
1281 1285 2.268076 GCGCAGGTTGGTGAATGGT 61.268 57.895 0.30 0.00 0.00 3.55
1365 1369 2.933287 AGAATCCGGGTGGTGGCA 60.933 61.111 0.00 0.00 36.30 4.92
1406 1410 1.531748 CATCCAACGGCCCCTACAT 59.468 57.895 0.00 0.00 0.00 2.29
1422 1426 2.203209 GCGGCGAAGGAATCCCAT 60.203 61.111 12.98 0.00 33.88 4.00
1423 1427 4.483243 GGCGGCGAAGGAATCCCA 62.483 66.667 12.98 0.00 33.88 4.37
1562 1567 3.057033 GGTCGTACTTGAACAGCTCCTTA 60.057 47.826 0.00 0.00 0.00 2.69
1739 1745 1.672356 CCTCCACCAAGCCGTTGAG 60.672 63.158 0.00 0.00 35.46 3.02
1742 1748 1.677552 CTACCTCCACCAAGCCGTT 59.322 57.895 0.00 0.00 0.00 4.44
1807 1813 2.355126 ATACGCCGCAGCTCATCG 60.355 61.111 0.00 0.00 36.60 3.84
1871 1877 4.279922 CCTCCTCCAACGTAAAACCAAAAT 59.720 41.667 0.00 0.00 0.00 1.82
1872 1878 3.633065 CCTCCTCCAACGTAAAACCAAAA 59.367 43.478 0.00 0.00 0.00 2.44
1928 1934 1.831652 CTCCCCGACAAGCTCCTGTT 61.832 60.000 0.00 0.00 0.00 3.16
2012 2018 4.464008 TCATGGAAAGTTGCTTGAAGACT 58.536 39.130 0.00 0.00 31.57 3.24
2028 2034 3.157252 GAGGGCTCCGCTCATGGA 61.157 66.667 4.65 0.00 42.00 3.41
2279 2285 1.153429 GGTACCCTTTCTGCGCGAT 60.153 57.895 12.10 0.00 0.00 4.58
2328 2334 2.003830 TCCTCCTCTTCTTCCTCCTCA 58.996 52.381 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.