Multiple sequence alignment - TraesCS7D01G243100

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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 TraesCS7D01G243100 chr7D 100.000 2549 0 0 1 2549 208835145 208832597 0 4708
1 TraesCS7D01G243100 chr7A 92.913 2554 173 6 1 2549 221975595 221973045 0 3707
2 TraesCS7D01G243100 chrUn 91.738 2554 205 4 1 2549 86159505 86162057 0 3542
3 TraesCS7D01G243100 chr6D 89.754 2557 250 11 1 2549 326295847 326293295 0 3260
4 TraesCS7D01G243100 chr6B 89.467 2497 250 12 1 2486 496413122 496415616 0 3142


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 TraesCS7D01G243100 chr7D 208832597 208835145 2548 True 4708 4708 100.000 1 2549 1 chr7D.!!$R1 2548
1 TraesCS7D01G243100 chr7A 221973045 221975595 2550 True 3707 3707 92.913 1 2549 1 chr7A.!!$R1 2548
2 TraesCS7D01G243100 chrUn 86159505 86162057 2552 False 3542 3542 91.738 1 2549 1 chrUn.!!$F1 2548
3 TraesCS7D01G243100 chr6D 326293295 326295847 2552 True 3260 3260 89.754 1 2549 1 chr6D.!!$R1 2548
4 TraesCS7D01G243100 chr6B 496413122 496415616 2494 False 3142 3142 89.467 1 2486 1 chr6B.!!$F1 2485

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
670 673 0.040204 CCTCCTTGTCCTTGGCCATT 59.96 55.0 6.09 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1913 0.384309 GTGGAGACATGGCATGCATG 59.616 55.0 26.7 22.7 46.14 4.06 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
24 25 0.608640 GTCATCCTCGTGGTGGAACT 59.391 55.000 2.99 0.00 37.13 3.01
25 26 0.608130 TCATCCTCGTGGTGGAACTG 59.392 55.000 2.99 0.00 37.13 3.16
38 39 1.745489 GAACTGGCCCACGACCATC 60.745 63.158 0.00 0.00 36.36 3.51
54 55 2.585900 ACCATCCCCACTCTAGTCACTA 59.414 50.000 0.00 0.00 0.00 2.74
341 343 2.170166 GGACATTTTGTGCTCCCATGA 58.830 47.619 0.00 0.00 35.71 3.07
437 439 3.979101 TGACATTGCAGACTACATCCA 57.021 42.857 0.00 0.00 0.00 3.41
483 485 1.714794 GTGACTTCACTGATGACCCG 58.285 55.000 1.92 0.00 43.25 5.28
620 623 2.103263 ACATTGACTTCCCGGATCTAGC 59.897 50.000 0.73 0.00 0.00 3.42
627 630 2.511452 CCCGGATCTAGCCACCCAG 61.511 68.421 0.73 0.00 0.00 4.45
670 673 0.040204 CCTCCTTGTCCTTGGCCATT 59.960 55.000 6.09 0.00 0.00 3.16
691 694 3.720949 AGCGCACTAATACCATTCGTA 57.279 42.857 11.47 0.00 0.00 3.43
715 718 1.633432 TCCACCCATTCACTGGTAAGG 59.367 52.381 0.00 0.00 44.30 2.69
765 768 0.664761 CCACATTGAATAGGCGCCTG 59.335 55.000 38.98 22.97 0.00 4.85
784 787 1.291132 GCGAGTGAACTTATCTGCCC 58.709 55.000 0.00 0.00 0.00 5.36
802 805 4.321966 TCAACGGTGCCGGCATCA 62.322 61.111 37.18 17.18 44.69 3.07
821 824 4.386867 TCAATGACTCGACTATTCCCAC 57.613 45.455 0.00 0.00 0.00 4.61
892 895 1.421646 AGCCTAGTGACAAGCTTTGGT 59.578 47.619 0.00 0.00 34.12 3.67
1008 1011 2.668457 GACATCGGACGGCATGATAATC 59.332 50.000 0.00 0.00 0.00 1.75
1167 1173 3.388676 TCTTTGGTACGAACCTTCTCCAA 59.611 43.478 0.00 0.00 46.91 3.53
1345 1351 4.540099 TGGTATCCACTGAGAAATTCCCTT 59.460 41.667 0.00 0.00 0.00 3.95
1379 1385 2.967362 TGCGGTGTACCTCAACTATTG 58.033 47.619 0.00 0.00 0.00 1.90
1419 1425 4.201724 CGTCATTTTGCTACCTACTGCTTC 60.202 45.833 0.00 0.00 0.00 3.86
1457 1463 1.581934 TCTGCAAGACACTTTCACGG 58.418 50.000 0.00 0.00 38.67 4.94
1582 1588 4.018870 TCACTAGTTGTGGCATTTATGGGA 60.019 41.667 4.86 0.00 46.20 4.37
1596 1602 7.190871 GCATTTATGGGAAATTCATTTGCTTG 58.809 34.615 4.07 0.00 38.07 4.01
1834 1842 4.527509 AGCCATATCTTACCATCGTGAG 57.472 45.455 0.00 0.00 0.00 3.51
1881 1889 8.875803 CATATGTCACATCCCAAAATTCAAAAG 58.124 33.333 0.00 0.00 0.00 2.27
2061 2070 4.837298 TGCATTGGGGCTGCAAATATATTA 59.163 37.500 0.50 0.00 46.06 0.98
2139 2148 8.837059 CGATTTGAGTTTGGAAATACTTAAACG 58.163 33.333 0.00 0.00 37.90 3.60
2161 2170 7.542534 ACGTAGTTCAAAACTCATAACACAA 57.457 32.000 0.00 0.00 37.78 3.33
2162 2171 7.404203 ACGTAGTTCAAAACTCATAACACAAC 58.596 34.615 0.00 0.00 37.78 3.32
2201 2214 6.699575 AAAAGCAGTATTCTTTATGCCGAT 57.300 33.333 0.00 0.00 39.51 4.18
2210 2223 1.452025 CTTTATGCCGATGACGTAGCG 59.548 52.381 0.00 0.00 38.07 4.26
2225 2238 0.529773 TAGCGCAATAGCACTTCCCG 60.530 55.000 11.47 0.00 42.27 5.14
2350 2363 2.124736 ACAACATGCCCGATCCCG 60.125 61.111 0.00 0.00 0.00 5.14
2408 2422 7.211573 TCATCAATCTTTTGTGATTTTGCAGT 58.788 30.769 0.00 0.00 34.77 4.40
2418 2432 2.889678 TGATTTTGCAGTGCATGTACCA 59.110 40.909 20.50 10.73 38.76 3.25
2489 2504 2.788807 ACCCCATGGTAAATAGCCATCA 59.211 45.455 11.73 0.00 45.45 3.07
2496 2511 2.562738 GGTAAATAGCCATCAATGCCCC 59.437 50.000 0.00 0.00 0.00 5.80
2543 2558 0.179020 CACTTCCACCAGGTTGCTCA 60.179 55.000 0.00 0.00 35.89 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.391263 GTTCCACCACGAGGATGACC 60.391 60.000 5.68 0.00 38.69 4.02
38 39 5.941555 AGAAAATAGTGACTAGAGTGGGG 57.058 43.478 0.00 0.00 0.00 4.96
70 71 4.202315 TGGAAGAGACGGTGAGAAATTGAA 60.202 41.667 0.00 0.00 0.00 2.69
210 211 8.365647 AGTTAGGTATACGATGGAATTTACTGG 58.634 37.037 0.00 0.00 0.00 4.00
341 343 3.144506 CAGTCTCTCCATTTTGTGCTGT 58.855 45.455 0.00 0.00 0.00 4.40
437 439 0.385390 CTTGCAAGTTGCCCGAAAGT 59.615 50.000 24.59 0.00 44.23 2.66
483 485 0.248336 CCATCGCATCACATGTGTGC 60.248 55.000 28.55 28.55 45.25 4.57
620 623 1.153168 CCGAGGTAATGCTGGGTGG 60.153 63.158 0.00 0.00 0.00 4.61
627 630 3.573491 GCCGTGCCGAGGTAATGC 61.573 66.667 0.00 0.00 0.00 3.56
670 673 3.720949 ACGAATGGTATTAGTGCGCTA 57.279 42.857 9.73 1.99 0.00 4.26
691 694 2.814805 CCAGTGAATGGGTGGAGAAT 57.185 50.000 0.00 0.00 46.36 2.40
715 718 0.108585 TGTGAAGGGAACTCAGTGGC 59.891 55.000 0.00 0.00 42.68 5.01
765 768 1.134670 AGGGCAGATAAGTTCACTCGC 60.135 52.381 0.00 0.00 0.00 5.03
784 787 3.499737 GATGCCGGCACCGTTGAG 61.500 66.667 35.50 0.00 37.81 3.02
802 805 4.036498 CGTAGTGGGAATAGTCGAGTCATT 59.964 45.833 0.00 0.00 0.00 2.57
821 824 1.333931 TCAGGCTAATGACGAGCGTAG 59.666 52.381 0.00 0.00 41.06 3.51
892 895 2.742053 GGTCGATAGCTTGCACAAAAGA 59.258 45.455 0.00 0.00 0.00 2.52
1008 1011 1.826720 CCAGGGGTCAAATCCAATGTG 59.173 52.381 0.00 0.00 0.00 3.21
1167 1173 5.032846 TCTTCTTCATTGTATCCACCTCCT 58.967 41.667 0.00 0.00 0.00 3.69
1215 1221 0.462047 CAAGCACCTCCATACGGGAC 60.462 60.000 0.00 0.00 42.15 4.46
1251 1257 2.849942 TGTTGTGTCACCAATCTCCTG 58.150 47.619 0.00 0.00 0.00 3.86
1379 1385 6.604735 AATGACGAAATACTCCTTGCATAC 57.395 37.500 0.00 0.00 0.00 2.39
1419 1425 8.803201 TTGCAGATATAGTTGTCTTATCTTCG 57.197 34.615 0.00 0.00 31.84 3.79
1457 1463 2.971261 GAGTTTTTGCCAATTCGACGAC 59.029 45.455 0.00 0.00 0.00 4.34
1767 1775 8.403236 TGTGAAGCAGATTAATCAAATGATCTG 58.597 33.333 17.56 6.20 45.14 2.90
1834 1842 9.077674 CATATGGTCATCGACTTAATAGCTAAC 57.922 37.037 0.00 0.00 32.47 2.34
1905 1913 0.384309 GTGGAGACATGGCATGCATG 59.616 55.000 26.70 22.70 46.14 4.06
1919 1927 4.796038 AAAGATCCAAAATGCAGTGGAG 57.204 40.909 18.34 0.00 46.87 3.86
1921 1929 5.902613 TCTAAAGATCCAAAATGCAGTGG 57.097 39.130 7.40 7.40 36.13 4.00
2121 2130 9.934190 TTGAACTACGTTTAAGTATTTCCAAAC 57.066 29.630 0.00 0.00 36.22 2.93
2191 2204 1.483316 CGCTACGTCATCGGCATAAA 58.517 50.000 0.00 0.00 41.85 1.40
2192 2205 0.937699 GCGCTACGTCATCGGCATAA 60.938 55.000 0.00 0.00 41.85 1.90
2201 2214 2.660944 GTGCTATTGCGCTACGTCA 58.339 52.632 9.73 0.00 45.43 4.35
2210 2223 2.481471 GGCCGGGAAGTGCTATTGC 61.481 63.158 2.18 0.00 40.20 3.56
2283 2296 2.248487 CCTACAACTTAGTCGTGTCGC 58.752 52.381 0.00 0.00 0.00 5.19
2350 2363 2.738521 ACATGTCAGTGGTCGCGC 60.739 61.111 0.00 0.00 0.00 6.86
2418 2432 1.221840 GAGTGTGGGATCATGCGGT 59.778 57.895 0.00 0.00 0.00 5.68
2489 2504 1.202734 CGATGATCAGTCTGGGGCATT 60.203 52.381 0.09 0.00 0.00 3.56
2496 2511 0.390860 GGGTCCCGATGATCAGTCTG 59.609 60.000 0.09 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.