Multiple sequence alignment - TraesCS6A01G387500

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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 TraesCS6A01G387500 chr6A 100.000 2381 0 0 499 2879 603905440 603907820 0.000000e+00 4397
1 TraesCS6A01G387500 chr6A 100.000 170 0 0 1 170 603904942 603905111 5.990000e-82 315
2 TraesCS6A01G387500 chr7A 97.140 2343 50 10 539 2879 542714340 542716667 0.000000e+00 3940
3 TraesCS6A01G387500 chr7A 92.453 159 10 1 12 170 542713806 542713962 2.890000e-55 226
4 TraesCS6A01G387500 chr1A 97.570 2305 41 8 577 2879 564160204 564157913 0.000000e+00 3932
5 TraesCS6A01G387500 chr3A 96.851 2350 59 4 531 2879 144697447 144699782 0.000000e+00 3916
6 TraesCS6A01G387500 chr3A 96.735 1807 41 5 1074 2879 126051593 126053382 0.000000e+00 2994
7 TraesCS6A01G387500 chr3A 92.453 159 10 1 12 170 144697018 144697174 2.890000e-55 226
8 TraesCS6A01G387500 chr7B 96.191 2363 82 6 519 2879 660101519 660103875 0.000000e+00 3858
9 TraesCS6A01G387500 chr7B 90.789 152 12 2 20 170 660101455 660101605 4.860000e-48 202
10 TraesCS6A01G387500 chr3B 95.851 2362 71 12 519 2879 228014551 228016886 0.000000e+00 3794
11 TraesCS6A01G387500 chr3B 90.728 151 14 0 20 170 228014487 228014637 4.860000e-48 202
12 TraesCS6A01G387500 chr6B 96.932 1923 51 5 962 2879 18463701 18461782 0.000000e+00 3217
13 TraesCS6A01G387500 chr6B 96.674 1924 54 7 962 2879 18465676 18467595 0.000000e+00 3190
14 TraesCS6A01G387500 chr6B 89.017 173 12 2 1 166 18464208 18464036 1.050000e-49 207
15 TraesCS6A01G387500 chr6B 90.972 144 12 1 23 166 18465199 18465341 2.930000e-45 193
16 TraesCS6A01G387500 chr2D 96.830 1893 32 3 988 2879 618324321 618322456 0.000000e+00 3138
17 TraesCS6A01G387500 chr6D 96.836 1675 43 7 501 2173 39065771 39064105 0.000000e+00 2791
18 TraesCS6A01G387500 chr4B 96.354 1673 55 4 501 2172 167378520 167376853 0.000000e+00 2747
19 TraesCS6A01G387500 chr4B 95.131 1335 58 5 519 1852 273959156 273960484 0.000000e+00 2098
20 TraesCS6A01G387500 chr4B 89.017 173 12 2 1 166 167378643 167378471 1.050000e-49 207
21 TraesCS6A01G387500 chr2B 95.685 1576 62 4 501 2075 311925679 311924109 0.000000e+00 2529
22 TraesCS6A01G387500 chr2B 87.861 173 14 2 1 166 311925802 311925630 2.260000e-46 196
23 TraesCS6A01G387500 chr4A 96.289 1482 30 2 501 1982 147536198 147534742 0.000000e+00 2409
24 TraesCS6A01G387500 chr4A 93.289 149 10 0 22 170 147536344 147536196 1.340000e-53 220


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 TraesCS6A01G387500 chr6A 603904942 603907820 2878 False 2356.0 4397 100.0000 1 2879 2 chr6A.!!$F1 2878
1 TraesCS6A01G387500 chr7A 542713806 542716667 2861 False 2083.0 3940 94.7965 12 2879 2 chr7A.!!$F1 2867
2 TraesCS6A01G387500 chr1A 564157913 564160204 2291 True 3932.0 3932 97.5700 577 2879 1 chr1A.!!$R1 2302
3 TraesCS6A01G387500 chr3A 126051593 126053382 1789 False 2994.0 2994 96.7350 1074 2879 1 chr3A.!!$F1 1805
4 TraesCS6A01G387500 chr3A 144697018 144699782 2764 False 2071.0 3916 94.6520 12 2879 2 chr3A.!!$F2 2867
5 TraesCS6A01G387500 chr7B 660101455 660103875 2420 False 2030.0 3858 93.4900 20 2879 2 chr7B.!!$F1 2859
6 TraesCS6A01G387500 chr3B 228014487 228016886 2399 False 1998.0 3794 93.2895 20 2879 2 chr3B.!!$F1 2859
7 TraesCS6A01G387500 chr6B 18461782 18464208 2426 True 1712.0 3217 92.9745 1 2879 2 chr6B.!!$R1 2878
8 TraesCS6A01G387500 chr6B 18465199 18467595 2396 False 1691.5 3190 93.8230 23 2879 2 chr6B.!!$F1 2856
9 TraesCS6A01G387500 chr2D 618322456 618324321 1865 True 3138.0 3138 96.8300 988 2879 1 chr2D.!!$R1 1891
10 TraesCS6A01G387500 chr6D 39064105 39065771 1666 True 2791.0 2791 96.8360 501 2173 1 chr6D.!!$R1 1672
11 TraesCS6A01G387500 chr4B 273959156 273960484 1328 False 2098.0 2098 95.1310 519 1852 1 chr4B.!!$F1 1333
12 TraesCS6A01G387500 chr4B 167376853 167378643 1790 True 1477.0 2747 92.6855 1 2172 2 chr4B.!!$R1 2171
13 TraesCS6A01G387500 chr2B 311924109 311925802 1693 True 1362.5 2529 91.7730 1 2075 2 chr2B.!!$R1 2074
14 TraesCS6A01G387500 chr4A 147534742 147536344 1602 True 1314.5 2409 94.7890 22 1982 2 chr4A.!!$R1 1960

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
737 1433 2.093973 CGGAGCAAGGTCAAGTATCACT 60.094 50.0 1.42 0.0 0.00 3.41 F
1553 2314 0.174389 GAGGCTGAGAGCGATGTTGA 59.826 55.0 0.00 0.0 43.62 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 2318 0.240678 CATCCTCGCTCTCATCCTCG 59.759 60.000 0.00 0.00 0.00 4.63 R
2399 3197 1.144936 GGTAGCACTAGCCAGCTGG 59.855 63.158 29.34 29.34 41.97 4.85 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
140 148 3.547787 AACTCCTGGAGGACGGGCT 62.548 63.158 26.56 1.69 45.92 5.19
517 525 3.706373 GCGGCCAACTCCCTGAGA 61.706 66.667 2.24 0.00 33.32 3.27
541 794 4.424711 GAGGCGGCCATTGTGGGA 62.425 66.667 23.09 0.00 38.19 4.37
651 1347 2.378634 CCATGGTGGGGAGGAGGAC 61.379 68.421 2.57 0.00 32.67 3.85
726 1422 2.594592 GCAACACCGGAGCAAGGT 60.595 61.111 9.46 0.00 43.97 3.50
737 1433 2.093973 CGGAGCAAGGTCAAGTATCACT 60.094 50.000 1.42 0.00 0.00 3.41
889 1585 6.478344 CCTCTCTTCTAGATTTGTCGAAATGG 59.522 42.308 0.00 0.00 31.58 3.16
1170 1886 2.295253 ACTCGCCTCGTTATTTGGAG 57.705 50.000 0.00 0.00 0.00 3.86
1328 2047 6.408548 CCATCGGAACCATATGAGCCTATAAT 60.409 42.308 3.65 0.00 0.00 1.28
1385 2110 8.797350 AACAACATAGAACAAGATGATGATGA 57.203 30.769 0.00 0.00 32.06 2.92
1386 2111 8.975663 ACAACATAGAACAAGATGATGATGAT 57.024 30.769 0.00 0.00 32.06 2.45
1387 2112 8.837389 ACAACATAGAACAAGATGATGATGATG 58.163 33.333 0.00 0.00 32.06 3.07
1403 2128 5.614308 TGATGATGATTATCTTCGCAACCT 58.386 37.500 8.31 0.00 39.24 3.50
1548 2309 2.832661 AGCGAGGCTGAGAGCGAT 60.833 61.111 0.00 0.00 43.62 4.58
1549 2310 2.657944 GCGAGGCTGAGAGCGATG 60.658 66.667 0.00 0.00 43.62 3.84
1550 2311 2.804167 CGAGGCTGAGAGCGATGT 59.196 61.111 0.00 0.00 43.62 3.06
1551 2312 1.140589 CGAGGCTGAGAGCGATGTT 59.859 57.895 0.00 0.00 43.62 2.71
1552 2313 1.144565 CGAGGCTGAGAGCGATGTTG 61.145 60.000 0.00 0.00 43.62 3.33
1553 2314 0.174389 GAGGCTGAGAGCGATGTTGA 59.826 55.000 0.00 0.00 43.62 3.18
1554 2315 0.175302 AGGCTGAGAGCGATGTTGAG 59.825 55.000 0.00 0.00 43.62 3.02
1555 2316 0.174389 GGCTGAGAGCGATGTTGAGA 59.826 55.000 0.00 0.00 43.62 3.27
1556 2317 1.558741 GCTGAGAGCGATGTTGAGAG 58.441 55.000 0.00 0.00 0.00 3.20
1557 2318 1.558741 CTGAGAGCGATGTTGAGAGC 58.441 55.000 0.00 0.00 0.00 4.09
1558 2319 0.179153 TGAGAGCGATGTTGAGAGCG 60.179 55.000 0.00 0.00 34.34 5.03
1559 2320 0.099613 GAGAGCGATGTTGAGAGCGA 59.900 55.000 0.00 0.00 34.34 4.93
1600 2397 3.929610 GAGCATGTCAGAGGTTGAAGTAC 59.070 47.826 0.00 0.00 37.61 2.73
1698 2495 8.996651 ACGAAGGAAGAAAATATCCCAATATT 57.003 30.769 0.00 0.00 39.29 1.28
2124 2922 2.145958 AGAGCATCATGGAATCGACG 57.854 50.000 0.00 0.00 37.82 5.12
2387 3185 3.177228 AGATAGCACCTTCTTGACAGGT 58.823 45.455 0.00 0.00 46.35 4.00
2399 3197 0.690762 TGACAGGTAGGTTCAAGGGC 59.309 55.000 0.00 0.00 0.00 5.19
2595 3394 5.112129 ACAGGTGTAAAAGAAGTGTTCCT 57.888 39.130 0.00 0.00 0.00 3.36
2819 3619 6.588373 GTCTAGGAGTCAGTTCTCAACAATTC 59.412 42.308 0.00 0.00 36.30 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 135 3.541713 GCCTAGCCCGTCCTCCAG 61.542 72.222 0.00 0.00 0.00 3.86
500 508 2.543067 ATTCTCAGGGAGTTGGCCGC 62.543 60.000 0.00 0.00 0.00 6.53
501 509 0.745845 CATTCTCAGGGAGTTGGCCG 60.746 60.000 0.00 0.00 0.00 6.13
502 510 0.394899 CCATTCTCAGGGAGTTGGCC 60.395 60.000 0.00 0.00 31.54 5.36
503 511 3.181526 CCATTCTCAGGGAGTTGGC 57.818 57.895 0.00 0.00 31.54 4.52
512 520 2.587194 CGCCTCGCCCATTCTCAG 60.587 66.667 0.00 0.00 0.00 3.35
513 521 4.161295 CCGCCTCGCCCATTCTCA 62.161 66.667 0.00 0.00 0.00 3.27
726 1422 2.101415 CGCATCCCTCAGTGATACTTGA 59.899 50.000 0.00 0.00 0.00 3.02
737 1433 1.748403 GATGTAGCCGCATCCCTCA 59.252 57.895 6.80 0.00 39.33 3.86
889 1585 7.617041 ATGAAACTCCTAAGTAATCTGTTGC 57.383 36.000 0.00 0.00 33.48 4.17
917 1632 8.255206 TCAGATTTTGCAGCAAATTATCATCTT 58.745 29.630 24.80 12.19 33.19 2.40
1170 1886 4.935205 TCATAGTACTGAACATGTGCAACC 59.065 41.667 8.18 0.00 34.36 3.77
1385 2110 6.267928 AGGTACTAGGTTGCGAAGATAATCAT 59.732 38.462 0.00 0.00 36.02 2.45
1386 2111 5.597182 AGGTACTAGGTTGCGAAGATAATCA 59.403 40.000 0.00 0.00 36.02 2.57
1387 2112 5.921408 CAGGTACTAGGTTGCGAAGATAATC 59.079 44.000 0.00 0.00 36.02 1.75
1403 2128 5.395657 CCAACATGCTCATTCTCAGGTACTA 60.396 44.000 0.00 0.00 36.02 1.82
1548 2309 1.747924 CTCTCATCCTCGCTCTCAACA 59.252 52.381 0.00 0.00 0.00 3.33
1549 2310 1.535860 GCTCTCATCCTCGCTCTCAAC 60.536 57.143 0.00 0.00 0.00 3.18
1550 2311 0.743688 GCTCTCATCCTCGCTCTCAA 59.256 55.000 0.00 0.00 0.00 3.02
1551 2312 1.443322 CGCTCTCATCCTCGCTCTCA 61.443 60.000 0.00 0.00 0.00 3.27
1552 2313 1.163420 TCGCTCTCATCCTCGCTCTC 61.163 60.000 0.00 0.00 0.00 3.20
1553 2314 1.153066 TCGCTCTCATCCTCGCTCT 60.153 57.895 0.00 0.00 0.00 4.09
1554 2315 1.282570 CTCGCTCTCATCCTCGCTC 59.717 63.158 0.00 0.00 0.00 5.03
1555 2316 2.192861 CCTCGCTCTCATCCTCGCT 61.193 63.158 0.00 0.00 0.00 4.93
1556 2317 1.523154 ATCCTCGCTCTCATCCTCGC 61.523 60.000 0.00 0.00 0.00 5.03
1557 2318 0.240678 CATCCTCGCTCTCATCCTCG 59.759 60.000 0.00 0.00 0.00 4.63
1558 2319 1.541147 CTCATCCTCGCTCTCATCCTC 59.459 57.143 0.00 0.00 0.00 3.71
1559 2320 1.144708 TCTCATCCTCGCTCTCATCCT 59.855 52.381 0.00 0.00 0.00 3.24
1600 2397 5.459536 TCGTGATATTCCTCATCTTCCTG 57.540 43.478 0.00 0.00 0.00 3.86
1698 2495 1.885887 AGCGCCAATTTAAACTCTGCA 59.114 42.857 2.29 0.00 0.00 4.41
1836 2634 4.331168 GTGCACTCATCTTCCATTGTAGAC 59.669 45.833 10.32 0.00 0.00 2.59
2387 3185 1.685224 CAGCTGGCCCTTGAACCTA 59.315 57.895 5.57 0.00 0.00 3.08
2399 3197 1.144936 GGTAGCACTAGCCAGCTGG 59.855 63.158 29.34 29.34 41.97 4.85
2595 3394 4.298626 ACATTCCCTATGTTCAGCCTCTA 58.701 43.478 0.00 0.00 45.19 2.43
2819 3619 5.478679 TGTTTGTAACATAATCCACCTTGGG 59.521 40.000 0.00 0.00 35.68 4.12


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

AutoCloner maintained by Alex Coulton.