Multiple sequence alignment - TraesCS2D01G215700

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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 TraesCS2D01G215700 chr2D 100.000 2762 0 0 1 2762 178527974 178530735 0.000000e+00 5101
1 TraesCS2D01G215700 chr2D 96.287 1616 42 7 139 1752 178695844 178697443 0.000000e+00 2636
2 TraesCS2D01G215700 chr2D 88.800 375 36 3 1231 1602 315425059 315425430 3.240000e-124 455
3 TraesCS2D01G215700 chr2D 83.884 242 35 2 3 242 178868817 178869056 7.700000e-56 228
4 TraesCS2D01G215700 chr2D 97.321 112 3 0 3 114 178695741 178695852 1.010000e-44 191
5 TraesCS2D01G215700 chr7D 98.037 1019 19 1 1745 2762 224462467 224463485 0.000000e+00 1770
6 TraesCS2D01G215700 chr7D 98.030 1015 18 2 1750 2762 101141704 101142718 0.000000e+00 1762
7 TraesCS2D01G215700 chr7D 98.121 1011 18 1 1753 2762 89273734 89272724 0.000000e+00 1760
8 TraesCS2D01G215700 chr7D 85.781 429 53 5 422 849 257511699 257512120 5.430000e-122 448
9 TraesCS2D01G215700 chr3D 98.221 1012 17 1 1752 2762 481549368 481548357 0.000000e+00 1768
10 TraesCS2D01G215700 chr3D 98.220 1011 16 2 1753 2762 297461381 297460372 0.000000e+00 1766
11 TraesCS2D01G215700 chr5D 98.124 1013 18 1 1751 2762 99339096 99338084 0.000000e+00 1764
12 TraesCS2D01G215700 chr5D 98.123 1012 18 1 1752 2762 533563168 533562157 0.000000e+00 1762
13 TraesCS2D01G215700 chr1D 98.121 1011 17 2 1753 2762 460321192 460320183 0.000000e+00 1760
14 TraesCS2D01G215700 chr1D 86.824 425 52 4 428 851 10334447 10334868 3.220000e-129 472
15 TraesCS2D01G215700 chr4D 98.026 1013 19 1 1751 2762 442161775 442160763 0.000000e+00 1759
16 TraesCS2D01G215700 chr2B 95.283 848 28 6 907 1752 235062474 235063311 0.000000e+00 1334
17 TraesCS2D01G215700 chr2B 90.047 854 70 4 3 856 235903547 235904385 0.000000e+00 1092
18 TraesCS2D01G215700 chr2B 88.876 845 81 9 3 846 235060617 235061449 0.000000e+00 1027
19 TraesCS2D01G215700 chr2B 89.481 770 31 14 925 1687 235905910 235906636 0.000000e+00 928
20 TraesCS2D01G215700 chr2B 89.227 427 40 3 1189 1609 383355488 383355914 1.880000e-146 529
21 TraesCS2D01G215700 chr2A 92.099 886 40 10 869 1752 193584749 193585606 0.000000e+00 1221
22 TraesCS2D01G215700 chr2A 88.396 879 81 13 3 877 193579493 193580354 0.000000e+00 1038
23 TraesCS2D01G215700 chr6D 86.806 432 49 6 422 849 18193030 18192603 2.490000e-130 475
24 TraesCS2D01G215700 chr6A 86.374 433 53 6 422 853 8866564 8866991 4.170000e-128 468
25 TraesCS2D01G215700 chr6B 86.190 420 53 5 421 840 681080036 681080450 1.510000e-122 449
26 TraesCS2D01G215700 chr6B 84.527 433 37 12 1189 1600 79797877 79797454 4.280000e-108 401
27 TraesCS2D01G215700 chrUn 85.648 432 34 12 1189 1600 27634952 27635375 1.970000e-116 429


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 TraesCS2D01G215700 chr2D 178527974 178530735 2761 False 5101.0 5101 100.0000 1 2762 1 chr2D.!!$F1 2761
1 TraesCS2D01G215700 chr2D 178695741 178697443 1702 False 1413.5 2636 96.8040 3 1752 2 chr2D.!!$F4 1749
2 TraesCS2D01G215700 chr7D 224462467 224463485 1018 False 1770.0 1770 98.0370 1745 2762 1 chr7D.!!$F2 1017
3 TraesCS2D01G215700 chr7D 101141704 101142718 1014 False 1762.0 1762 98.0300 1750 2762 1 chr7D.!!$F1 1012
4 TraesCS2D01G215700 chr7D 89272724 89273734 1010 True 1760.0 1760 98.1210 1753 2762 1 chr7D.!!$R1 1009
5 TraesCS2D01G215700 chr3D 481548357 481549368 1011 True 1768.0 1768 98.2210 1752 2762 1 chr3D.!!$R2 1010
6 TraesCS2D01G215700 chr3D 297460372 297461381 1009 True 1766.0 1766 98.2200 1753 2762 1 chr3D.!!$R1 1009
7 TraesCS2D01G215700 chr5D 99338084 99339096 1012 True 1764.0 1764 98.1240 1751 2762 1 chr5D.!!$R1 1011
8 TraesCS2D01G215700 chr5D 533562157 533563168 1011 True 1762.0 1762 98.1230 1752 2762 1 chr5D.!!$R2 1010
9 TraesCS2D01G215700 chr1D 460320183 460321192 1009 True 1760.0 1760 98.1210 1753 2762 1 chr1D.!!$R1 1009
10 TraesCS2D01G215700 chr4D 442160763 442161775 1012 True 1759.0 1759 98.0260 1751 2762 1 chr4D.!!$R1 1011
11 TraesCS2D01G215700 chr2B 235060617 235063311 2694 False 1180.5 1334 92.0795 3 1752 2 chr2B.!!$F2 1749
12 TraesCS2D01G215700 chr2B 235903547 235906636 3089 False 1010.0 1092 89.7640 3 1687 2 chr2B.!!$F3 1684
13 TraesCS2D01G215700 chr2A 193584749 193585606 857 False 1221.0 1221 92.0990 869 1752 1 chr2A.!!$F2 883
14 TraesCS2D01G215700 chr2A 193579493 193580354 861 False 1038.0 1038 88.3960 3 877 1 chr2A.!!$F1 874

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
291 293 0.394080 TCCGTTGGTTGGTCGGTTTT 60.394 50.0 0.0 0.0 43.94 2.43 F
1623 4077 0.992802 GCTTCTTTCTAGCCACGACG 59.007 55.0 0.0 0.0 32.45 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 4164 1.065636 AGGTAGACACGACGGAGATGA 60.066 52.381 0.00 0.0 0.00 2.92 R
2585 5048 3.697747 CGGCTACCGGTGAACCCA 61.698 66.667 19.93 0.0 44.15 4.51 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
87 88 2.953020 GCTATAAGCAGAGATCCACCG 58.047 52.381 0.00 0.00 41.89 4.94
157 159 3.670637 GAGAGTGCGCATGGAGGCA 62.671 63.158 15.91 0.00 36.70 4.75
175 177 1.675714 GCAACAGTCGTGGGATGATCA 60.676 52.381 0.00 0.00 0.00 2.92
255 257 3.192844 GTCTCTCATTAGTTGTCGGGACA 59.807 47.826 0.00 0.00 39.98 4.02
291 293 0.394080 TCCGTTGGTTGGTCGGTTTT 60.394 50.000 0.00 0.00 43.94 2.43
426 430 5.932883 GGAACCAAGAAAAGATCGTAGACTT 59.067 40.000 0.00 0.00 42.51 3.01
439 443 4.832248 TCGTAGACTTGAATGGCAGATTT 58.168 39.130 0.00 0.00 0.00 2.17
882 3158 6.477253 AGAGTCCCTACAAAAAGAAAGATCC 58.523 40.000 0.00 0.00 0.00 3.36
1610 4064 1.457346 CCAGGATTTGAGCGCTTCTT 58.543 50.000 13.26 0.00 0.00 2.52
1612 4066 2.159462 CCAGGATTTGAGCGCTTCTTTC 60.159 50.000 13.26 7.10 0.00 2.62
1613 4067 2.746362 CAGGATTTGAGCGCTTCTTTCT 59.254 45.455 13.26 2.64 0.00 2.52
1614 4068 3.935203 CAGGATTTGAGCGCTTCTTTCTA 59.065 43.478 13.26 0.00 0.00 2.10
1615 4069 4.033817 CAGGATTTGAGCGCTTCTTTCTAG 59.966 45.833 13.26 0.00 0.00 2.43
1623 4077 0.992802 GCTTCTTTCTAGCCACGACG 59.007 55.000 0.00 0.00 32.45 5.12
1657 4118 2.493973 GCTGACTCCTGCGAGAGG 59.506 66.667 7.62 0.00 44.45 3.69
1670 4131 1.175983 CGAGAGGCGCCCTAGAGATT 61.176 60.000 26.15 0.00 31.76 2.40
1673 4134 2.628657 GAGAGGCGCCCTAGAGATTAAA 59.371 50.000 26.15 0.00 31.76 1.52
1700 4161 6.316140 GTGGAATTAGTATGTGTCTGATTGCA 59.684 38.462 0.00 0.00 37.09 4.08
1701 4162 7.012704 GTGGAATTAGTATGTGTCTGATTGCAT 59.987 37.037 7.55 0.00 39.66 3.96
1702 4163 7.227314 TGGAATTAGTATGTGTCTGATTGCATC 59.773 37.037 0.00 0.00 35.59 3.91
1703 4164 7.443575 GGAATTAGTATGTGTCTGATTGCATCT 59.556 37.037 0.00 0.00 32.60 2.90
1704 4165 7.959689 ATTAGTATGTGTCTGATTGCATCTC 57.040 36.000 0.00 0.00 0.00 2.75
1791 4254 7.466746 ACTGTTGCTTATAATGATTTGGTGT 57.533 32.000 0.00 0.00 0.00 4.16
1894 4357 7.076446 ACCATAATGACTACTCTAACATCCCT 58.924 38.462 0.00 0.00 0.00 4.20
2022 4485 1.523758 GAACATGAAGCACCCGAACT 58.476 50.000 0.00 0.00 0.00 3.01
2045 4508 4.724399 TGACCAAGAGCAACCTTTTCATA 58.276 39.130 0.00 0.00 0.00 2.15
2116 4579 4.030216 TGGATTGCTGGTCATGTAGACTA 58.970 43.478 0.00 0.00 46.72 2.59
2255 4718 2.181021 GGCCGACGAACGTGAGAT 59.819 61.111 4.19 0.00 40.78 2.75
2271 4734 5.820947 ACGTGAGATTGTAACCTGTCTTTTT 59.179 36.000 0.00 0.00 0.00 1.94
2507 4970 3.144506 AGAGACATGCTTGTTGAACAGG 58.855 45.455 6.70 2.77 35.79 4.00
2585 5048 5.562635 ACGATAGAGAGTAGGATCGGAAAT 58.437 41.667 7.88 0.00 44.20 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.744320 CGACATCCCAGGGCGTGATA 61.744 60.000 15.59 0.00 0.00 2.15
99 100 1.676678 GACACCGCTCCTCATGCCTA 61.677 60.000 0.00 0.00 0.00 3.93
157 159 2.179427 TCTGATCATCCCACGACTGTT 58.821 47.619 0.00 0.00 0.00 3.16
175 177 1.886542 GAAAACACTCCGCCCAAATCT 59.113 47.619 0.00 0.00 0.00 2.40
255 257 4.400529 ACGGAAACAAGCCAAGAAAAAT 57.599 36.364 0.00 0.00 0.00 1.82
291 293 8.842358 AATAATCCAGTAGAAACAAAACGAGA 57.158 30.769 0.00 0.00 0.00 4.04
426 430 1.469703 CTGCGACAAATCTGCCATTCA 59.530 47.619 0.00 0.00 0.00 2.57
439 443 2.046023 CCATTCCCTGCTGCGACA 60.046 61.111 0.00 0.00 0.00 4.35
577 581 8.877779 CGACTTTCATTCTTCATTGTCTCTATT 58.122 33.333 0.00 0.00 0.00 1.73
882 3158 2.675317 CGGGCTGTGTTCTTTCCTCTAG 60.675 54.545 0.00 0.00 0.00 2.43
1572 4026 2.586079 CATCTTGGGCGCGACGAT 60.586 61.111 12.10 1.61 0.00 3.73
1610 4064 2.229543 ACAATACACGTCGTGGCTAGAA 59.770 45.455 27.77 7.62 37.94 2.10
1612 4066 2.273370 ACAATACACGTCGTGGCTAG 57.727 50.000 27.77 17.02 37.94 3.42
1613 4067 3.500982 GTTACAATACACGTCGTGGCTA 58.499 45.455 27.77 13.49 37.94 3.93
1614 4068 2.331194 GTTACAATACACGTCGTGGCT 58.669 47.619 27.77 12.63 37.94 4.75
1615 4069 1.391144 GGTTACAATACACGTCGTGGC 59.609 52.381 27.77 8.20 37.94 5.01
1623 4077 2.026636 TCAGCCCTGGGTTACAATACAC 60.027 50.000 15.56 0.00 0.00 2.90
1657 4118 2.808543 CCACATTTAATCTCTAGGGCGC 59.191 50.000 0.00 0.00 0.00 6.53
1673 4134 7.012704 GCAATCAGACACATACTAATTCCACAT 59.987 37.037 0.00 0.00 0.00 3.21
1700 4161 2.045561 AGACACGACGGAGATGAGAT 57.954 50.000 0.00 0.00 0.00 2.75
1701 4162 2.277969 GTAGACACGACGGAGATGAGA 58.722 52.381 0.00 0.00 0.00 3.27
1702 4163 1.331138 GGTAGACACGACGGAGATGAG 59.669 57.143 0.00 0.00 0.00 2.90
1703 4164 1.065636 AGGTAGACACGACGGAGATGA 60.066 52.381 0.00 0.00 0.00 2.92
1704 4165 1.380524 AGGTAGACACGACGGAGATG 58.619 55.000 0.00 0.00 0.00 2.90
1791 4254 7.016914 ACCCTCTTATATACTCTTGTATGCCA 58.983 38.462 0.00 0.00 39.49 4.92
2022 4485 3.360867 TGAAAAGGTTGCTCTTGGTCAA 58.639 40.909 0.00 0.00 0.00 3.18
2116 4579 6.590234 TGTCTACTGTGACAACATATCAGT 57.410 37.500 9.56 0.00 43.08 3.41
2271 4734 8.141268 GGTAACAATTTGATTTCTTGGTCTTCA 58.859 33.333 2.79 0.00 0.00 3.02
2383 4846 6.126911 GGTCTCCACCTCAATAATTCTTCTCT 60.127 42.308 0.00 0.00 40.00 3.10
2507 4970 7.201565 CCATTACTCGTCCTGAAATCTCTTTTC 60.202 40.741 0.00 0.00 43.42 2.29
2585 5048 3.697747 CGGCTACCGGTGAACCCA 61.698 66.667 19.93 0.00 44.15 4.51


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

AutoCloner maintained by Alex Coulton.