Multiple sequence alignment - TraesCS2B01G142800

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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 TraesCS2B01G142800 chr2B 100.000 3922 0 0 1 3922 109873077 109869156 0.000000e+00 7243
1 TraesCS2B01G142800 chr2B 97.184 3942 87 6 1 3922 109184702 109180765 0.000000e+00 6643
2 TraesCS2B01G142800 chr2B 95.822 2633 99 7 4 2630 109093674 109091047 0.000000e+00 4242
3 TraesCS2B01G142800 chr2B 94.769 1147 51 2 2785 3922 109085401 109084255 0.000000e+00 1777
4 TraesCS2B01G142800 chr2B 92.490 972 69 4 2626 3595 109359520 109358551 0.000000e+00 1387
5 TraesCS2B01G142800 chr2B 86.687 323 33 7 3597 3919 109336808 109336496 2.240000e-92 350
6 TraesCS2B01G142800 chr2B 78.248 331 65 4 1911 2239 109935566 109935241 5.140000e-49 206
7 TraesCS2B01G142800 chrUn 95.583 2649 90 7 1 2630 235541337 235543977 0.000000e+00 4218
8 TraesCS2B01G142800 chrUn 95.583 2649 90 7 1 2630 256966702 256964062 0.000000e+00 4218
9 TraesCS2B01G142800 chrUn 95.583 2649 90 7 1 2630 271157747 271155107 0.000000e+00 4218
10 TraesCS2B01G142800 chrUn 92.952 2639 143 18 1 2630 289663197 289660593 0.000000e+00 3803
11 TraesCS2B01G142800 chrUn 93.841 1721 73 16 571 2290 379030677 379032365 0.000000e+00 2560
12 TraesCS2B01G142800 chrUn 93.598 1312 68 5 2626 3922 289660540 289659230 0.000000e+00 1943
13 TraesCS2B01G142800 chr2A 93.066 2639 140 23 1 2630 71214831 71212227 0.000000e+00 3819
14 TraesCS2B01G142800 chr2A 91.701 2639 154 26 1 2630 71162049 71159467 0.000000e+00 3600
15 TraesCS2B01G142800 chr2A 94.699 1528 75 5 1105 2630 71315305 71313782 0.000000e+00 2368
16 TraesCS2B01G142800 chr2A 96.528 1296 40 2 2627 3922 71115661 71114371 0.000000e+00 2139
17 TraesCS2B01G142800 chr2A 93.674 1312 67 3 2626 3922 71212174 71210864 0.000000e+00 1949
18 TraesCS2B01G142800 chr2A 93.445 1312 70 3 2626 3922 71159414 71158104 0.000000e+00 1932
19 TraesCS2B01G142800 chr2A 93.064 1312 73 4 2626 3922 71313729 71312421 0.000000e+00 1903
20 TraesCS2B01G142800 chr2A 90.057 1056 77 17 3 1046 71316359 71315320 0.000000e+00 1343
21 TraesCS2B01G142800 chr2D 94.136 2507 110 9 157 2630 72376580 72374078 0.000000e+00 3781
22 TraesCS2B01G142800 chr2D 93.777 2523 105 9 157 2630 72657078 72654559 0.000000e+00 3742
23 TraesCS2B01G142800 chr2D 96.762 1297 41 1 2626 3922 72654506 72653211 0.000000e+00 2161
24 TraesCS2B01G142800 chr2D 96.754 1294 40 2 2626 3919 72374025 72372734 0.000000e+00 2156


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 TraesCS2B01G142800 chr2B 109869156 109873077 3921 True 7243.000000 7243 100.000000 1 3922 1 chr2B.!!$R6 3921
1 TraesCS2B01G142800 chr2B 109180765 109184702 3937 True 6643.000000 6643 97.184000 1 3922 1 chr2B.!!$R3 3921
2 TraesCS2B01G142800 chr2B 109091047 109093674 2627 True 4242.000000 4242 95.822000 4 2630 1 chr2B.!!$R2 2626
3 TraesCS2B01G142800 chr2B 109084255 109085401 1146 True 1777.000000 1777 94.769000 2785 3922 1 chr2B.!!$R1 1137
4 TraesCS2B01G142800 chr2B 109358551 109359520 969 True 1387.000000 1387 92.490000 2626 3595 1 chr2B.!!$R5 969
5 TraesCS2B01G142800 chrUn 235541337 235543977 2640 False 4218.000000 4218 95.583000 1 2630 1 chrUn.!!$F1 2629
6 TraesCS2B01G142800 chrUn 256964062 256966702 2640 True 4218.000000 4218 95.583000 1 2630 1 chrUn.!!$R1 2629
7 TraesCS2B01G142800 chrUn 271155107 271157747 2640 True 4218.000000 4218 95.583000 1 2630 1 chrUn.!!$R2 2629
8 TraesCS2B01G142800 chrUn 289659230 289663197 3967 True 2873.000000 3803 93.275000 1 3922 2 chrUn.!!$R3 3921
9 TraesCS2B01G142800 chrUn 379030677 379032365 1688 False 2560.000000 2560 93.841000 571 2290 1 chrUn.!!$F2 1719
10 TraesCS2B01G142800 chr2A 71210864 71214831 3967 True 2884.000000 3819 93.370000 1 3922 2 chr2A.!!$R3 3921
11 TraesCS2B01G142800 chr2A 71158104 71162049 3945 True 2766.000000 3600 92.573000 1 3922 2 chr2A.!!$R2 3921
12 TraesCS2B01G142800 chr2A 71114371 71115661 1290 True 2139.000000 2139 96.528000 2627 3922 1 chr2A.!!$R1 1295
13 TraesCS2B01G142800 chr2A 71312421 71316359 3938 True 1871.333333 2368 92.606667 3 3922 3 chr2A.!!$R4 3919
14 TraesCS2B01G142800 chr2D 72372734 72376580 3846 True 2968.500000 3781 95.445000 157 3919 2 chr2D.!!$R1 3762
15 TraesCS2B01G142800 chr2D 72653211 72657078 3867 True 2951.500000 3742 95.269500 157 3922 2 chr2D.!!$R2 3765

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
994 1051 0.031857 ATGCAGATCTTCGGCTCGAG 59.968 55.000 8.45 8.45 38.41 4.04 F
995 1052 1.948635 GCAGATCTTCGGCTCGAGC 60.949 63.158 29.38 29.38 37.14 5.03 F
1497 1554 2.113860 AGTTGTCGTATGCCATGCTT 57.886 45.000 0.00 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2384 2464 1.202879 TGTGCCTTTCTAACCAGGTGG 60.203 52.381 0.0 0.0 42.17 4.61 R
2864 3004 5.190528 AGTCATACACCATTCACCAAGAGAT 59.809 40.000 0.0 0.0 0.00 2.75 R
3364 3506 1.142060 TCAGGGAAAGCGGAACAAGAA 59.858 47.619 0.0 0.0 0.00 2.52 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
23 24 6.406692 GTAATAGTCCTAGCACTGATTGGA 57.593 41.667 0.00 0.00 0.00 3.53
148 149 1.601663 GCACAACACTAATTGCGGCAA 60.602 47.619 18.85 18.85 34.82 4.52
172 173 1.970092 TTTGGTTTGATCCGACGGTT 58.030 45.000 14.79 5.25 0.00 4.44
304 308 2.103263 GGATTTGCTCCCGTGATAGTCT 59.897 50.000 0.00 0.00 38.19 3.24
336 340 2.192861 CCCTTGTTGCTTCACGGCA 61.193 57.895 0.00 0.00 40.74 5.69
542 551 4.758692 CGCTTCCGGCACATCTAT 57.241 55.556 0.00 0.00 41.91 1.98
728 747 3.794564 CAGTTTCCTTAACAAACGGCAAC 59.205 43.478 0.00 0.00 38.54 4.17
819 840 1.202867 TGCATGCTTGTACAGGAACCA 60.203 47.619 20.33 0.00 0.00 3.67
994 1051 0.031857 ATGCAGATCTTCGGCTCGAG 59.968 55.000 8.45 8.45 38.41 4.04
995 1052 1.948635 GCAGATCTTCGGCTCGAGC 60.949 63.158 29.38 29.38 37.14 5.03
1125 1182 4.157105 CACATCATGTCATTCTTGAAGGCA 59.843 41.667 0.00 0.00 34.65 4.75
1497 1554 2.113860 AGTTGTCGTATGCCATGCTT 57.886 45.000 0.00 0.00 0.00 3.91
1638 1695 2.654749 TCGAATGCGAGATCAGTTGT 57.345 45.000 0.00 0.00 42.51 3.32
1875 1932 4.159321 ACAGAGAGCTCGAAGATTCATGAA 59.841 41.667 11.26 11.26 33.89 2.57
1967 2024 5.508567 TGAAGGAATTTACAGGCATGATCA 58.491 37.500 4.84 0.00 0.00 2.92
1973 2030 5.762825 ATTTACAGGCATGATCATCACAC 57.237 39.130 4.84 0.00 0.00 3.82
2125 2182 8.149631 TGGTGGATATAGAGAATGCAATGATA 57.850 34.615 0.00 0.00 0.00 2.15
2142 2199 6.038271 GCAATGATACGAAGATTTTAGGTGGT 59.962 38.462 0.00 0.00 0.00 4.16
2200 2257 4.350368 TTGGAGTTGTTGACTGATGCTA 57.650 40.909 0.00 0.00 39.19 3.49
2209 2266 4.642437 TGTTGACTGATGCTAGAGAGGTAG 59.358 45.833 0.00 0.00 0.00 3.18
2235 2292 6.016276 AGCTGTCACCACCTTTTACTATTTTG 60.016 38.462 0.00 0.00 0.00 2.44
2384 2464 7.064609 TGAGCACATTTCTTACATAAGTAGCAC 59.935 37.037 0.00 0.00 34.93 4.40
2864 3004 1.440618 TTGGCAACCTGAAGACCCTA 58.559 50.000 0.00 0.00 0.00 3.53
2919 3059 7.658575 ACTTTGATGCATTAATTTTCTTGCTGT 59.341 29.630 4.56 0.00 36.10 4.40
3007 3147 7.085476 TGGGGCTTATGCTTACTTGATTATA 57.915 36.000 0.13 0.00 39.59 0.98
3094 3235 2.354259 CCAGAGAGGCATCAGAAACAC 58.646 52.381 0.00 0.00 0.00 3.32
3234 3376 8.548721 GGTATACCAGTCGAGAAAATTTATGTG 58.451 37.037 17.44 0.00 35.64 3.21
3364 3506 3.568430 TGACGGATATCGACTGCATACTT 59.432 43.478 0.00 0.00 42.43 2.24
3556 3714 0.603707 CTCCGCAACCAGAAGCAGAA 60.604 55.000 0.00 0.00 0.00 3.02
3572 3730 2.260822 CAGAAGAAGGAGTTCTGGGGA 58.739 52.381 5.14 0.00 44.87 4.81
3713 3871 0.179468 GTTGCCGGTGGGATAAGCTA 59.821 55.000 1.90 0.00 34.06 3.32
3895 4060 3.962718 AGTTATAGGCGGCTTTAGTACCA 59.037 43.478 19.76 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.825861 TTCGTTTCGCTACCTCCTTT 57.174 45.000 0.00 0.00 0.00 3.11
98 99 0.733150 GCCACCGCCTGTTATTTCTC 59.267 55.000 0.00 0.00 0.00 2.87
148 149 3.305064 CCGTCGGATCAAACCAAAAACAT 60.305 43.478 4.91 0.00 0.00 2.71
172 173 3.068691 CGCTCCCGGAAGACCTCA 61.069 66.667 0.73 0.00 0.00 3.86
304 308 2.837947 ACAAGGGAGATGGTCAGATGA 58.162 47.619 0.00 0.00 0.00 2.92
728 747 3.732212 TCATCAAAGGATATGGAGTGCG 58.268 45.455 0.00 0.00 30.87 5.34
819 840 3.055240 AGAGCTAGCAGAAGCACTTGATT 60.055 43.478 18.83 0.00 45.30 2.57
994 1051 4.179579 GCTCCGGTGCATTTCGGC 62.180 66.667 23.09 5.03 45.31 5.54
995 1052 2.745884 TGCTCCGGTGCATTTCGG 60.746 61.111 26.46 16.58 46.89 4.30
1125 1182 3.717294 GTGCGGACCACCTCCCAT 61.717 66.667 0.00 0.00 38.55 4.00
1293 1350 3.770040 CGGAGCATGACCACGGGA 61.770 66.667 0.00 0.00 0.00 5.14
1497 1554 1.007118 TGCCTGAGGATCCTGTAGTCA 59.993 52.381 22.02 10.62 0.00 3.41
1595 1652 7.063898 CGAGCATGATTAAAGTCTTCAAAGAGA 59.936 37.037 0.00 0.00 35.32 3.10
1638 1695 0.679002 GAGCAGCAATGGAGAAGGCA 60.679 55.000 0.00 0.00 0.00 4.75
1875 1932 6.865834 ACATTATCACTCAAGGAAGACTCT 57.134 37.500 0.00 0.00 0.00 3.24
2125 2182 3.006110 TGACGACCACCTAAAATCTTCGT 59.994 43.478 0.00 0.00 40.69 3.85
2142 2199 7.158099 TGAAAGACTCTGAAGAATATGACGA 57.842 36.000 0.00 0.00 0.00 4.20
2200 2257 1.356059 TGGTGACAGCTCTACCTCTCT 59.644 52.381 6.17 0.00 35.51 3.10
2384 2464 1.202879 TGTGCCTTTCTAACCAGGTGG 60.203 52.381 0.00 0.00 42.17 4.61
2864 3004 5.190528 AGTCATACACCATTCACCAAGAGAT 59.809 40.000 0.00 0.00 0.00 2.75
2919 3059 6.778069 AGCTTCTGTATATTAGGTGAGTGCTA 59.222 38.462 0.00 0.00 0.00 3.49
3007 3147 9.855021 ATGCGCTAAAATACTCAAAACTAAAAT 57.145 25.926 9.73 0.00 0.00 1.82
3094 3235 3.788333 TCTTCCCCGTAGTTTGATACG 57.212 47.619 0.00 0.00 46.28 3.06
3364 3506 1.142060 TCAGGGAAAGCGGAACAAGAA 59.858 47.619 0.00 0.00 0.00 2.52
3433 3575 8.066612 ACATACTTCCAATTTAACAGAATGGG 57.933 34.615 0.00 0.00 43.62 4.00
3556 3714 2.637165 ACATTCCCCAGAACTCCTTCT 58.363 47.619 0.00 0.00 37.19 2.85
3572 3730 8.737175 GCTCATGATGATGTTGGATATTACATT 58.263 33.333 0.00 0.00 35.24 2.71
3713 3871 9.841295 CTAGACCTACTACTAGATGAAGTTCTT 57.159 37.037 4.17 0.00 38.53 2.52
3895 4060 7.385752 CCTTTTACACAACATCAGAATTTGCAT 59.614 33.333 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.