Multiple sequence alignment - TraesCS7B01G411700

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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 TraesCS7B01G411700 chr7B 100.000 2237 0 0 1 2237 680073713 680075949 0.000000e+00 4132.0
1 TraesCS7B01G411700 chr7B 94.304 1071 40 10 1 1058 707879521 707880583 0.000000e+00 1620.0
2 TraesCS7B01G411700 chr7B 92.609 663 34 9 1309 1969 707881132 707881781 0.000000e+00 939.0
3 TraesCS7B01G411700 chr7B 91.366 637 46 3 1601 2237 707883198 707883825 0.000000e+00 863.0
4 TraesCS7B01G411700 chr7B 95.789 190 7 1 1051 1239 707880730 707880919 2.790000e-79 305.0
5 TraesCS7B01G411700 chr7D 95.151 1258 39 5 1 1253 600863754 600864994 0.000000e+00 1965.0
6 TraesCS7B01G411700 chr7D 92.197 833 40 7 1256 2087 600865088 600865896 0.000000e+00 1155.0
7 TraesCS7B01G411700 chr6D 84.447 1871 211 47 415 2237 471112251 471114089 0.000000e+00 1770.0
8 TraesCS7B01G411700 chr6D 85.182 1073 102 25 359 1393 471277080 471276027 0.000000e+00 1048.0
9 TraesCS7B01G411700 chr6D 86.979 768 61 19 494 1253 459552023 459551287 0.000000e+00 828.0
10 TraesCS7B01G411700 chr6D 81.205 979 135 30 1280 2237 459550642 459549692 0.000000e+00 743.0
11 TraesCS7B01G411700 chr6D 84.916 716 88 9 1530 2237 471275863 471275160 0.000000e+00 706.0
12 TraesCS7B01G411700 chr6D 88.250 400 30 10 1256 1639 459551180 459550782 1.570000e-126 462.0
13 TraesCS7B01G411700 chr6D 78.571 168 20 10 78 238 459552417 459552259 1.830000e-16 97.1
14 TraesCS7B01G411700 chr6B 83.880 1706 196 44 574 2237 719425313 719423645 0.000000e+00 1554.0
15 TraesCS7B01G411700 chr6B 87.149 996 101 13 356 1337 719307903 719308885 0.000000e+00 1105.0
16 TraesCS7B01G411700 chr7A 92.439 820 39 6 1256 2074 692784956 692785753 0.000000e+00 1149.0
17 TraesCS7B01G411700 chr7A 96.997 333 6 1 910 1242 692784569 692784897 6.980000e-155 556.0
18 TraesCS7B01G411700 chr2B 86.053 760 66 13 517 1253 771415462 771416204 0.000000e+00 780.0
19 TraesCS7B01G411700 chr2B 80.962 977 143 26 1277 2237 771416835 771417784 0.000000e+00 734.0
20 TraesCS7B01G411700 chr2B 88.689 389 27 10 1258 1639 771416318 771416696 2.020000e-125 459.0
21 TraesCS7B01G411700 chr2B 87.949 390 32 7 1256 1639 771480347 771480727 1.580000e-121 446.0
22 TraesCS7B01G411700 chr2B 95.455 44 2 0 428 471 771415396 771415439 1.110000e-08 71.3
23 TraesCS7B01G411700 chr3A 81.358 987 137 28 1280 2237 574280179 574279211 0.000000e+00 760.0
24 TraesCS7B01G411700 chr3A 92.636 258 16 2 704 958 574319003 574319260 3.510000e-98 368.0
25 TraesCS7B01G411700 chr3A 90.909 77 6 1 284 360 574318475 574318550 3.930000e-18 102.0
26 TraesCS7B01G411700 chr6A 87.152 467 48 4 359 818 616057203 616056742 9.160000e-144 520.0
27 TraesCS7B01G411700 chr6A 86.364 462 38 10 812 1253 616056291 616055835 4.320000e-132 481.0
28 TraesCS7B01G411700 chr6A 82.323 198 30 5 6 199 616094440 616094244 1.370000e-37 167.0


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 TraesCS7B01G411700 chr7B 680073713 680075949 2236 False 4132.000 4132 100.00000 1 2237 1 chr7B.!!$F1 2236
1 TraesCS7B01G411700 chr7B 707879521 707883825 4304 False 931.750 1620 93.51700 1 2237 4 chr7B.!!$F2 2236
2 TraesCS7B01G411700 chr7D 600863754 600865896 2142 False 1560.000 1965 93.67400 1 2087 2 chr7D.!!$F1 2086
3 TraesCS7B01G411700 chr6D 471112251 471114089 1838 False 1770.000 1770 84.44700 415 2237 1 chr6D.!!$F1 1822
4 TraesCS7B01G411700 chr6D 471275160 471277080 1920 True 877.000 1048 85.04900 359 2237 2 chr6D.!!$R2 1878
5 TraesCS7B01G411700 chr6D 459549692 459552417 2725 True 532.525 828 83.75125 78 2237 4 chr6D.!!$R1 2159
6 TraesCS7B01G411700 chr6B 719423645 719425313 1668 True 1554.000 1554 83.88000 574 2237 1 chr6B.!!$R1 1663
7 TraesCS7B01G411700 chr6B 719307903 719308885 982 False 1105.000 1105 87.14900 356 1337 1 chr6B.!!$F1 981
8 TraesCS7B01G411700 chr7A 692784569 692785753 1184 False 852.500 1149 94.71800 910 2074 2 chr7A.!!$F1 1164
9 TraesCS7B01G411700 chr2B 771415396 771417784 2388 False 511.075 780 87.78975 428 2237 4 chr2B.!!$F2 1809
10 TraesCS7B01G411700 chr3A 574279211 574280179 968 True 760.000 760 81.35800 1280 2237 1 chr3A.!!$R1 957
11 TraesCS7B01G411700 chr3A 574318475 574319260 785 False 235.000 368 91.77250 284 958 2 chr3A.!!$F1 674
12 TraesCS7B01G411700 chr6A 616055835 616057203 1368 True 500.500 520 86.75800 359 1253 2 chr6A.!!$R2 894

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
137 141 1.369091 CTGACAAGGCGGCATGTACC 61.369 60.0 20.23 9.32 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 5475 0.037139 CGGTGTCCGGGTAATCAACA 60.037 55.0 0.0 0.0 44.15 3.33 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
40 43 7.278424 TGCTATATTTTTCCAAGCATGAAAAGC 59.722 33.333 0.00 8.00 41.30 3.51
43 46 4.669206 TTTTCCAAGCATGAAAAGCTGA 57.331 36.364 0.00 0.00 42.53 4.26
53 56 5.243283 AGCATGAAAAGCTGATCTGTTTCTT 59.757 36.000 0.00 7.35 41.61 2.52
59 62 7.172190 TGAAAAGCTGATCTGTTTCTTGTAGAG 59.828 37.037 13.32 0.00 32.41 2.43
70 73 8.208224 TCTGTTTCTTGTAGAGGTATTGTTTCA 58.792 33.333 0.00 0.00 0.00 2.69
124 128 3.558931 TCTTTCAGTTGGAGCTGACAA 57.441 42.857 0.00 0.00 44.23 3.18
137 141 1.369091 CTGACAAGGCGGCATGTACC 61.369 60.000 20.23 9.32 0.00 3.34
222 233 4.333926 GCTCTGGTTCTAGTAATTGCAAGG 59.666 45.833 4.94 0.00 0.00 3.61
254 401 6.923508 TGTTGAATAAGTATCTCATACCGCAG 59.076 38.462 0.00 0.00 36.40 5.18
298 467 3.609853 TGGTTCTATTAGCAAGGCTGTG 58.390 45.455 0.07 0.00 40.10 3.66
332 501 3.237268 TCCATTGTTGGCTGTTAAGGT 57.763 42.857 0.00 0.00 43.29 3.50
357 567 5.169295 GGGATACTATATTCTGGCGTTGTC 58.831 45.833 0.00 0.00 0.00 3.18
1075 2051 1.202428 GGGAACTAGACCTGCGACATC 60.202 57.143 0.00 0.00 0.00 3.06
1134 2116 4.313020 AATCTCTTTGGCAGTTCCTCAT 57.687 40.909 0.00 0.00 35.26 2.90
1270 2366 8.697067 GTGAATTTGTGAGAATTCTTCATGTTG 58.303 33.333 9.87 0.00 43.28 3.33
1344 2972 0.110486 ACCAACAGGTAACAGCCCAG 59.890 55.000 0.00 0.00 41.41 4.45
1446 3154 5.175126 TCAGAAAAGTAGAAGCGAAGAAACG 59.825 40.000 0.00 0.00 0.00 3.60
1575 3291 5.431765 TCATGGCTTTTCCTCTATGAGTTC 58.568 41.667 0.00 0.00 35.26 3.01
1576 3292 4.908601 TGGCTTTTCCTCTATGAGTTCA 57.091 40.909 0.00 0.00 35.26 3.18
1626 3343 1.632589 GAAACAAGGGACCAGGCAAT 58.367 50.000 0.00 0.00 0.00 3.56
1645 3362 3.311110 GTGACCTCCACGGCTCCA 61.311 66.667 0.00 0.00 35.86 3.86
1646 3363 3.311110 TGACCTCCACGGCTCCAC 61.311 66.667 0.00 0.00 35.61 4.02
1794 3520 3.626924 GCCACCACGGAGACCACT 61.627 66.667 0.00 0.00 36.56 4.00
1806 3535 0.325765 AGACCACTAGCTTCCCCTCC 60.326 60.000 0.00 0.00 0.00 4.30
1871 3600 1.731433 CCGGTCGAAGGGCTAATCGA 61.731 60.000 0.00 5.89 45.01 3.59
1884 3613 2.034812 GCTAATCGACATCTTCCCGTCT 59.965 50.000 0.00 0.00 0.00 4.18
1970 5475 4.250170 ACCCTCCGTCCACACCCT 62.250 66.667 0.00 0.00 0.00 4.34
2132 5637 1.961277 CGAAGGCCAGCAACTCGTT 60.961 57.895 5.01 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 27 4.082408 CAGATCAGCTTTTCATGCTTGGAA 60.082 41.667 0.00 0.00 38.92 3.53
40 43 8.037758 ACAATACCTCTACAAGAAACAGATCAG 58.962 37.037 0.00 0.00 0.00 2.90
43 46 9.220767 GAAACAATACCTCTACAAGAAACAGAT 57.779 33.333 0.00 0.00 0.00 2.90
137 141 1.944709 TCATCTCTGGCAAATGCATCG 59.055 47.619 0.00 0.00 44.36 3.84
273 420 4.943705 CAGCCTTGCTAATAGAACCAAAGA 59.056 41.667 0.00 0.00 36.40 2.52
298 467 9.194101 AGCCAACAATGGATCTAATGACCAAAC 62.194 40.741 0.54 0.00 43.38 2.93
332 501 3.786553 ACGCCAGAATATAGTATCCCCA 58.213 45.455 0.00 0.00 0.00 4.96
357 567 3.289076 GCGGTTCTTTCAAAAAGAGTCG 58.711 45.455 15.57 15.57 0.00 4.18
952 1762 9.650714 ACAGGTTACAAGATACCTACATACATA 57.349 33.333 0.00 0.00 42.81 2.29
953 1763 8.421784 CACAGGTTACAAGATACCTACATACAT 58.578 37.037 0.00 0.00 42.81 2.29
954 1764 7.398047 ACACAGGTTACAAGATACCTACATACA 59.602 37.037 0.00 0.00 42.81 2.29
955 1765 7.705325 CACACAGGTTACAAGATACCTACATAC 59.295 40.741 0.00 0.00 42.81 2.39
1270 2366 3.494251 CCAGCAAAAACATAACACTTGCC 59.506 43.478 1.71 0.00 42.63 4.52
1344 2972 2.271944 AAACCTGTGTTGGCCTACTC 57.728 50.000 18.31 14.91 34.13 2.59
1446 3154 1.077915 GAGCTGCTCTTGTCTGCTTC 58.922 55.000 21.93 0.00 38.55 3.86
1588 3304 1.427020 GAGCTTGTGAATGAGCGGC 59.573 57.895 0.00 0.00 0.00 6.53
1590 3306 1.070821 TTCGAGCTTGTGAATGAGCG 58.929 50.000 0.00 0.00 0.00 5.03
1591 3307 2.224079 TGTTTCGAGCTTGTGAATGAGC 59.776 45.455 0.00 0.00 0.00 4.26
1592 3308 4.461405 CTTGTTTCGAGCTTGTGAATGAG 58.539 43.478 0.00 0.00 0.00 2.90
1593 3309 3.250762 CCTTGTTTCGAGCTTGTGAATGA 59.749 43.478 0.00 0.00 0.00 2.57
1594 3310 3.558505 CCTTGTTTCGAGCTTGTGAATG 58.441 45.455 0.00 0.00 0.00 2.67
1595 3311 2.554032 CCCTTGTTTCGAGCTTGTGAAT 59.446 45.455 0.00 0.00 0.00 2.57
1597 3313 1.140052 TCCCTTGTTTCGAGCTTGTGA 59.860 47.619 0.00 0.00 0.00 3.58
1626 3343 1.681327 GGAGCCGTGGAGGTCACTA 60.681 63.158 0.00 0.00 43.94 2.74
1639 3356 1.527433 GGTTTCTGCAAGGTGGAGCC 61.527 60.000 0.00 0.00 35.65 4.70
1640 3357 0.823356 TGGTTTCTGCAAGGTGGAGC 60.823 55.000 0.00 0.00 35.65 4.70
1641 3358 1.610522 CTTGGTTTCTGCAAGGTGGAG 59.389 52.381 0.00 0.00 37.15 3.86
1642 3359 1.214175 TCTTGGTTTCTGCAAGGTGGA 59.786 47.619 0.00 0.00 0.00 4.02
1643 3360 1.691196 TCTTGGTTTCTGCAAGGTGG 58.309 50.000 0.00 0.00 0.00 4.61
1644 3361 2.886523 TGATCTTGGTTTCTGCAAGGTG 59.113 45.455 0.00 0.00 0.00 4.00
1645 3362 3.228188 TGATCTTGGTTTCTGCAAGGT 57.772 42.857 0.00 0.00 0.00 3.50
1646 3363 4.337555 CCTATGATCTTGGTTTCTGCAAGG 59.662 45.833 0.00 0.00 0.00 3.61
1794 3520 1.307866 CAAGGGGGAGGGGAAGCTA 60.308 63.158 0.00 0.00 0.00 3.32
1806 3535 2.606519 TCGGTGGACCTCAAGGGG 60.607 66.667 0.29 0.00 40.27 4.79
1866 3595 1.065701 CGAGACGGGAAGATGTCGATT 59.934 52.381 0.00 0.00 40.05 3.34
1884 3613 2.031012 CTGCTGCTTGACACCCGA 59.969 61.111 0.00 0.00 0.00 5.14
1889 3618 0.179037 AGAGTTGCTGCTGCTTGACA 60.179 50.000 17.00 0.00 40.48 3.58
1893 3622 0.110104 AAGGAGAGTTGCTGCTGCTT 59.890 50.000 17.00 2.48 45.46 3.91
1961 3690 1.353022 GGGTAATCAACAGGGTGTGGA 59.647 52.381 0.00 0.00 34.31 4.02
1970 5475 0.037139 CGGTGTCCGGGTAATCAACA 60.037 55.000 0.00 0.00 44.15 3.33
2126 5631 1.249469 GGACCCCGAAGAGAACGAGT 61.249 60.000 0.00 0.00 0.00 4.18
2216 5721 3.760580 ATCCCTATCTGCTGCTAACAC 57.239 47.619 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.