Multiple sequence alignment - TraesCS6D01G156300

Loading Multiple Alignment...

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 TraesCS6D01G156300 chr6D 100.000 6142 0 0 1 6142 132415323 132409182 0.000000e+00 11343.0
1 TraesCS6D01G156300 chr6D 98.169 2950 31 5 2033 4981 132312212 132309285 0.000000e+00 5127.0
2 TraesCS6D01G156300 chr6D 98.138 2041 28 3 1 2031 132314549 132312509 0.000000e+00 3550.0
3 TraesCS6D01G156300 chr6D 97.278 845 18 4 5142 5983 132303006 132302164 0.000000e+00 1428.0
4 TraesCS6D01G156300 chr6D 87.234 188 8 5 5955 6142 132289857 132289686 3.750000e-47 200.0
5 TraesCS6D01G156300 chr6A 97.579 3552 67 8 2033 5575 171459338 171455797 0.000000e+00 6065.0
6 TraesCS6D01G156300 chr6A 96.919 2045 42 12 1 2029 171461676 171459637 0.000000e+00 3408.0
7 TraesCS6D01G156300 chr6A 95.059 506 15 7 5505 6004 171455795 171455294 0.000000e+00 787.0
8 TraesCS6D01G156300 chr6A 90.845 142 8 1 6001 6142 171455257 171455121 1.050000e-42 185.0
9 TraesCS6D01G156300 chr6B 92.864 2074 83 26 1 2031 229730418 229728367 0.000000e+00 2950.0
10 TraesCS6D01G156300 chr6B 88.575 2197 140 49 3392 5532 229726803 229724662 0.000000e+00 2564.0
11 TraesCS6D01G156300 chr6B 96.299 1270 43 4 2033 3302 229728067 229726802 0.000000e+00 2082.0
12 TraesCS6D01G156300 chr6B 100.000 30 0 0 5944 5973 229724559 229724530 8.600000e-04 56.5
13 TraesCS6D01G156300 chr6B 100.000 28 0 0 2078 2105 265978782 265978755 1.100000e-02 52.8
14 TraesCS6D01G156300 chr5A 89.333 375 34 3 5548 5918 1951099 1950727 3.350000e-127 466.0
15 TraesCS6D01G156300 chr5A 77.154 499 101 11 1134 1625 69103998 69103506 1.690000e-70 278.0
16 TraesCS6D01G156300 chr4A 89.516 372 32 3 5551 5918 626320216 626319848 1.210000e-126 464.0
17 TraesCS6D01G156300 chr4A 78.041 296 54 11 193 485 516487625 516487912 6.330000e-40 176.0
18 TraesCS6D01G156300 chr5D 88.889 378 31 8 5548 5918 370117039 370117412 7.260000e-124 455.0
19 TraesCS6D01G156300 chr5D 78.643 501 92 13 1136 1625 74090878 74090382 9.930000e-83 318.0
20 TraesCS6D01G156300 chr3D 88.859 377 33 5 5548 5918 94246284 94245911 7.260000e-124 455.0
21 TraesCS6D01G156300 chr2D 87.173 382 40 7 5545 5918 618123866 618123486 5.690000e-115 425.0
22 TraesCS6D01G156300 chr3B 87.268 377 39 5 5548 5918 13423064 13422691 7.360000e-114 422.0
23 TraesCS6D01G156300 chr1D 87.200 375 40 5 5548 5918 143544923 143545293 2.650000e-113 420.0
24 TraesCS6D01G156300 chr5B 79.810 421 75 8 1134 1551 78420696 78421109 1.290000e-76 298.0
25 TraesCS6D01G156300 chr4B 77.663 291 50 14 193 475 99430382 99430665 4.930000e-36 163.0
26 TraesCS6D01G156300 chr4D 74.930 359 75 14 192 543 67358128 67357778 3.840000e-32 150.0


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 TraesCS6D01G156300 chr6D 132409182 132415323 6141 True 11343.000 11343 100.0000 1 6142 1 chr6D.!!$R3 6141
1 TraesCS6D01G156300 chr6D 132309285 132314549 5264 True 4338.500 5127 98.1535 1 4981 2 chr6D.!!$R4 4980
2 TraesCS6D01G156300 chr6D 132302164 132303006 842 True 1428.000 1428 97.2780 5142 5983 1 chr6D.!!$R2 841
3 TraesCS6D01G156300 chr6A 171455121 171461676 6555 True 2611.250 6065 95.1005 1 6142 4 chr6A.!!$R1 6141
4 TraesCS6D01G156300 chr6B 229724530 229730418 5888 True 1913.125 2950 94.4345 1 5973 4 chr6B.!!$R2 5972

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
475 481 3.485947 TGTTGGATCGTTAAGCATTGC 57.514 42.857 0.00 0.0 0.00 3.56 F
1600 1636 7.134815 CGAGGAGGTGCAAATTATGAATTTAG 58.865 38.462 0.00 0.0 38.97 1.85 F
2853 3198 0.539051 CAGGCTTTCCGGATGACTCT 59.461 55.000 4.15 0.0 37.47 3.24 F
4416 4763 1.388174 TATTTCCTTTCCCCTGGGCA 58.612 50.000 7.39 0.0 34.68 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 1910 1.737793 GTACAGGGTGCAATGCAGTAC 59.262 52.381 8.73 13.54 40.08 2.73 R
3361 3707 1.523758 CGTGTAGGCCAAAGAAGCTT 58.476 50.000 5.01 0.00 0.00 3.74 R
4807 5182 1.777878 TCAAAAGGGTGGCTGTTCCTA 59.222 47.619 0.00 0.00 35.26 2.94 R
5815 6376 2.120232 CTGCGTACATCTCGACATTCC 58.880 52.381 0.00 0.00 0.00 3.01 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
169 171 8.116651 AGATAGAAGATGCGTATGTACTGAAT 57.883 34.615 0.00 0.00 0.00 2.57
337 343 9.807649 ATATTTTTGATGTCTTGAAGGTATTGC 57.192 29.630 0.00 0.00 0.00 3.56
413 419 6.263344 TGATTTGGTACTCTTTCGTATCTCG 58.737 40.000 0.00 0.00 41.41 4.04
475 481 3.485947 TGTTGGATCGTTAAGCATTGC 57.514 42.857 0.00 0.00 0.00 3.56
497 503 8.459521 TTGCGTTTAAATTCTACATTCATTGG 57.540 30.769 0.00 0.00 0.00 3.16
1117 1150 8.943594 TTATTAATTTACCGGCCTCCATTAAT 57.056 30.769 0.00 11.32 33.48 1.40
1600 1636 7.134815 CGAGGAGGTGCAAATTATGAATTTAG 58.865 38.462 0.00 0.00 38.97 1.85
1907 1953 1.651987 ACTGGTCACAAAGTCACACG 58.348 50.000 0.00 0.00 0.00 4.49
2031 2079 5.357742 AGGCTACATGACAATACACATGA 57.642 39.130 12.90 0.00 44.28 3.07
2032 2080 5.118990 AGGCTACATGACAATACACATGAC 58.881 41.667 12.90 3.62 44.28 3.06
2033 2081 4.875536 GGCTACATGACAATACACATGACA 59.124 41.667 12.90 1.63 44.28 3.58
2034 2082 5.353956 GGCTACATGACAATACACATGACAA 59.646 40.000 12.90 0.00 44.28 3.18
2528 2873 4.265904 TCTCTTCAACGTATTTCTGGCA 57.734 40.909 0.00 0.00 0.00 4.92
2572 2917 2.688507 TCTGCTTCTTCGGTCATGTTC 58.311 47.619 0.00 0.00 0.00 3.18
2853 3198 0.539051 CAGGCTTTCCGGATGACTCT 59.461 55.000 4.15 0.00 37.47 3.24
3161 3507 1.611491 GAAAAACCGTTGATCCAGGCA 59.389 47.619 0.00 0.00 0.00 4.75
3213 3559 6.601332 TCCCCAATTACTCAATTAGGACATC 58.399 40.000 0.00 0.00 35.58 3.06
3361 3707 2.505819 GTTAAGAATCCTGAGGCCTCCA 59.494 50.000 29.95 16.48 0.00 3.86
3949 4296 5.527582 GGCAGTTTAGATTAATCACCGACAT 59.472 40.000 17.56 0.00 0.00 3.06
4416 4763 1.388174 TATTTCCTTTCCCCTGGGCA 58.612 50.000 7.39 0.00 34.68 5.36
4445 4792 5.163602 TGGAAGCAAGTATGTTGTCGTTTTT 60.164 36.000 0.00 0.00 0.00 1.94
4673 5028 5.701290 GGATTACATGAGCTTATGGTGGTAC 59.299 44.000 21.26 8.27 32.32 3.34
4749 5107 5.448654 TGCATTCAGTAGCCCATCTTTTAT 58.551 37.500 0.00 0.00 0.00 1.40
4892 5279 6.613755 AGTGTAGAATTTTGTTTGCTACGT 57.386 33.333 0.00 0.00 35.41 3.57
4893 5280 7.718272 AGTGTAGAATTTTGTTTGCTACGTA 57.282 32.000 0.00 0.00 35.41 3.57
4894 5281 7.570161 AGTGTAGAATTTTGTTTGCTACGTAC 58.430 34.615 0.00 0.00 35.41 3.67
4947 5334 7.406553 TGAGTGTTTGTTCTAGAAAAATGTCG 58.593 34.615 8.93 0.00 0.00 4.35
5047 5434 6.630444 AGTTGCTTTGCAGGATATTATGAG 57.370 37.500 0.00 0.00 40.61 2.90
5748 6307 6.374333 TGTCTCATGAAAAGCCTATTAACACC 59.626 38.462 0.00 0.00 0.00 4.16
5759 6318 7.539034 AGCCTATTAACACCAAATTTTGTCT 57.461 32.000 8.26 0.00 0.00 3.41
5812 6373 2.192624 GCGAAACAAGTTTGTGTGCAT 58.807 42.857 2.45 0.00 41.31 3.96
5815 6376 3.000872 CGAAACAAGTTTGTGTGCATGTG 60.001 43.478 2.45 0.00 41.31 3.21
5831 6392 3.246226 GCATGTGGAATGTCGAGATGTAC 59.754 47.826 0.00 0.00 30.48 2.90
5850 6411 3.837213 ACGCAGGAATCATTTTGTCAG 57.163 42.857 0.00 0.00 0.00 3.51
5908 6469 6.014327 ACATTTTGAAAACCAGGAGCATATGT 60.014 34.615 4.29 0.00 0.00 2.29
5990 6552 8.874816 TCTTTGCAGTTTTTACCATTTAACAAC 58.125 29.630 0.00 0.00 0.00 3.32
6027 6630 2.910482 CTCCATTCATTTTCGTTGCACG 59.090 45.455 0.00 0.00 44.19 5.34
6070 6673 4.700365 TCGAGTGCCACGTCAGCG 62.700 66.667 2.87 0.00 44.93 5.18
6125 6728 2.432628 CGAACGGCCACTCTCCAC 60.433 66.667 2.24 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
337 343 3.341823 CTGATCAACAGTGGAAGGAAGG 58.658 50.000 0.00 0.00 41.30 3.46
475 481 7.032580 TGCCCAATGAATGTAGAATTTAAACG 58.967 34.615 0.00 0.00 0.00 3.60
683 713 3.004734 GCTCAACCTATGCACACAAACTT 59.995 43.478 0.00 0.00 0.00 2.66
1561 1597 4.695455 CACCTCCTCGTTGAACAAATACAT 59.305 41.667 0.00 0.00 0.00 2.29
1575 1611 5.505173 AATTCATAATTTGCACCTCCTCG 57.495 39.130 0.00 0.00 0.00 4.63
1869 1910 1.737793 GTACAGGGTGCAATGCAGTAC 59.262 52.381 8.73 13.54 40.08 2.73
1907 1953 9.495754 GCATAAAATCATGTCAGAGTTCTAAAC 57.504 33.333 0.00 0.00 0.00 2.01
2528 2873 4.778213 TGATAGCCTGGTAAAGCTGATT 57.222 40.909 0.00 0.00 40.28 2.57
2572 2917 4.172512 ATCCAGAGGCAGGCTGCG 62.173 66.667 31.22 18.13 46.21 5.18
2853 3198 1.683385 CCATCGAGTCTCAGTATGCCA 59.317 52.381 0.00 0.00 34.76 4.92
3161 3507 2.282180 ACGCGGTTTTGGCAGGAT 60.282 55.556 12.47 0.00 0.00 3.24
3213 3559 2.859032 GCTATCTTACTCGCTGGAACCG 60.859 54.545 0.00 0.00 0.00 4.44
3361 3707 1.523758 CGTGTAGGCCAAAGAAGCTT 58.476 50.000 5.01 0.00 0.00 3.74
3750 4096 2.664568 GCTTGTGCACAGCATATGTTTG 59.335 45.455 26.21 6.23 41.41 2.93
4416 4763 4.207165 ACAACATACTTGCTTCCAGTGTT 58.793 39.130 0.00 0.00 0.00 3.32
4446 4793 9.581289 TTTTAGAACTATCCATCCAGACAAAAA 57.419 29.630 0.00 0.00 0.00 1.94
4673 5028 7.128331 CACAATCCAGAGAATTAATTAGCACG 58.872 38.462 0.00 0.00 0.00 5.34
4749 5107 6.926826 TGCTTTTCTACTAACGACAATTCTCA 59.073 34.615 0.00 0.00 0.00 3.27
4807 5182 1.777878 TCAAAAGGGTGGCTGTTCCTA 59.222 47.619 0.00 0.00 35.26 2.94
4892 5279 7.831193 ACTCTGAACCCTTCGTTAATAGTAGTA 59.169 37.037 0.00 0.00 33.74 1.82
4893 5280 6.662663 ACTCTGAACCCTTCGTTAATAGTAGT 59.337 38.462 0.00 0.00 33.74 2.73
4894 5281 7.098074 ACTCTGAACCCTTCGTTAATAGTAG 57.902 40.000 0.00 0.00 33.74 2.57
4947 5334 6.194796 TGCTTTAGTTGCTATCAATTCACC 57.805 37.500 0.00 0.00 34.29 4.02
4990 5377 7.485418 TGATAAAAGAACTCGTAAACTTGCA 57.515 32.000 0.00 0.00 0.00 4.08
5047 5434 1.398960 GGCAGTATTTGATGCGATCGC 60.399 52.381 32.48 32.48 43.49 4.58
5115 5502 3.222603 AGTAAAAGTGGCACTTTCCAGG 58.777 45.455 37.46 0.00 46.78 4.45
5812 6373 2.734175 GCGTACATCTCGACATTCCACA 60.734 50.000 0.00 0.00 0.00 4.17
5815 6376 2.120232 CTGCGTACATCTCGACATTCC 58.880 52.381 0.00 0.00 0.00 3.01
5831 6392 4.424061 TTCTGACAAAATGATTCCTGCG 57.576 40.909 0.00 0.00 0.00 5.18
5928 6489 4.871933 ATAAAGGTTTTTCAGTGGCAGG 57.128 40.909 0.00 0.00 0.00 4.85
5990 6552 9.736414 AATGAATGGAGATCACTATCATTTAGG 57.264 33.333 0.00 0.00 35.13 2.69
6027 6630 2.937149 GGGGAGCAACGAAGTAAGATTC 59.063 50.000 0.00 0.00 45.00 2.52
6036 6639 3.249189 AGCCAGGGGAGCAACGAA 61.249 61.111 0.00 0.00 0.00 3.85
6039 6642 3.672295 CTCGAGCCAGGGGAGCAAC 62.672 68.421 0.00 0.00 0.00 4.17
6097 6700 3.737172 CCGTTCGGGCAAGGCAAG 61.737 66.667 3.04 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.