Multiple sequence alignment - TraesCS2D01G261200

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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 TraesCS2D01G261200 chr2D 100.000 2432 0 0 1 2432 317943387 317940956 0.000000e+00 4492.0
1 TraesCS2D01G261200 chr2D 88.372 430 34 3 2010 2432 610708929 610709349 1.000000e-138 503.0
2 TraesCS2D01G261200 chr2D 92.593 216 16 0 1268 1483 610707318 610707533 6.530000e-81 311.0
3 TraesCS2D01G261200 chr2D 92.810 153 9 1 1480 1632 610708710 610708860 1.130000e-53 220.0
4 TraesCS2D01G261200 chr2D 94.595 37 2 0 1222 1258 12523790 12523826 9.390000e-05 58.4
5 TraesCS2D01G261200 chr2B 95.199 2458 73 15 1 2432 385563374 385560936 0.000000e+00 3843.0
6 TraesCS2D01G261200 chr2A 95.549 1595 48 10 849 2432 415062088 415063670 0.000000e+00 2531.0
7 TraesCS2D01G261200 chr2A 90.147 1492 104 24 976 2432 750149895 750148412 0.000000e+00 1901.0
8 TraesCS2D01G261200 chr2A 93.174 879 39 6 1 863 414994531 414995404 0.000000e+00 1271.0
9 TraesCS2D01G261200 chr7D 89.540 1501 92 24 964 2432 498275151 498273684 0.000000e+00 1842.0
10 TraesCS2D01G261200 chr5D 75.899 556 101 25 1900 2431 472627578 472627032 1.120000e-63 254.0
11 TraesCS2D01G261200 chr5B 75.681 551 105 22 1900 2431 580073981 580073441 5.190000e-62 248.0
12 TraesCS2D01G261200 chr5B 75.446 505 105 15 1102 1601 579810053 579809563 6.760000e-56 228.0
13 TraesCS2D01G261200 chrUn 77.368 190 37 6 1229 1415 293161165 293161351 9.190000e-20 108.0
14 TraesCS2D01G261200 chrUn 77.368 190 37 6 1229 1415 409868967 409868781 9.190000e-20 108.0
15 TraesCS2D01G261200 chr6D 75.130 193 38 9 1229 1416 97520251 97520438 5.570000e-12 82.4


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 TraesCS2D01G261200 chr2D 317940956 317943387 2431 True 4492.000000 4492 100.000000 1 2432 1 chr2D.!!$R1 2431
1 TraesCS2D01G261200 chr2D 610707318 610709349 2031 False 344.666667 503 91.258333 1268 2432 3 chr2D.!!$F2 1164
2 TraesCS2D01G261200 chr2B 385560936 385563374 2438 True 3843.000000 3843 95.199000 1 2432 1 chr2B.!!$R1 2431
3 TraesCS2D01G261200 chr2A 415062088 415063670 1582 False 2531.000000 2531 95.549000 849 2432 1 chr2A.!!$F2 1583
4 TraesCS2D01G261200 chr2A 750148412 750149895 1483 True 1901.000000 1901 90.147000 976 2432 1 chr2A.!!$R1 1456
5 TraesCS2D01G261200 chr2A 414994531 414995404 873 False 1271.000000 1271 93.174000 1 863 1 chr2A.!!$F1 862
6 TraesCS2D01G261200 chr7D 498273684 498275151 1467 True 1842.000000 1842 89.540000 964 2432 1 chr7D.!!$R1 1468
7 TraesCS2D01G261200 chr5D 472627032 472627578 546 True 254.000000 254 75.899000 1900 2431 1 chr5D.!!$R1 531
8 TraesCS2D01G261200 chr5B 580073441 580073981 540 True 248.000000 248 75.681000 1900 2431 1 chr5B.!!$R2 531

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
332 334 1.803922 CGTGCAGATGTTCGCGGTA 60.804 57.895 6.13 0.0 33.14 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 2887 0.099613 CCGTGAGTCTCTGTCATCGG 59.9 60.0 0.65 2.85 34.56 4.18 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
143 145 7.012610 TGTGGCTTTACTTTTTGAACTACTACC 59.987 37.037 0.00 0.00 0.00 3.18
228 230 6.729295 GCTTAATTTTCGGTAATACGCGTATC 59.271 38.462 30.32 19.08 0.00 2.24
263 265 7.108194 TCATCTCACTTTGATGAGCAGTAAAT 58.892 34.615 2.72 0.00 44.94 1.40
332 334 1.803922 CGTGCAGATGTTCGCGGTA 60.804 57.895 6.13 0.00 33.14 4.02
409 412 7.087639 TCTTTTTCGAAGTTTCTTTTGAAGCA 58.912 30.769 0.00 0.00 41.30 3.91
437 447 5.514274 TTTTGTCACAACCTCCTCAAATC 57.486 39.130 0.00 0.00 0.00 2.17
439 449 4.437682 TGTCACAACCTCCTCAAATCTT 57.562 40.909 0.00 0.00 0.00 2.40
478 488 3.405823 TGCACTCACATCACTCATTCA 57.594 42.857 0.00 0.00 0.00 2.57
488 498 2.362736 TCACTCATTCAGGCATCTTGC 58.637 47.619 0.00 0.00 44.08 4.01
681 691 8.658499 ACATTATACTTTCGGTAAGTGATTCC 57.342 34.615 9.90 0.00 46.46 3.01
695 705 5.712152 AGTGATTCCTTTGTTGGTCATTC 57.288 39.130 0.00 0.00 0.00 2.67
831 850 9.541143 TGCGAAGATATATTCACAAGAACATTA 57.459 29.630 10.52 0.00 36.39 1.90
1410 1435 2.125952 CACAGCCGCATCGTCTCA 60.126 61.111 0.00 0.00 0.00 3.27
1411 1436 1.520120 CACAGCCGCATCGTCTCAT 60.520 57.895 0.00 0.00 0.00 2.90
1651 2861 8.000780 AGATTAGTTTGAAATAATCAGGGCAC 57.999 34.615 19.76 0.00 44.20 5.01
1677 2887 2.418976 GGTAACGGAGCTTGAATGGAAC 59.581 50.000 0.00 0.00 0.00 3.62
1679 2889 0.673644 ACGGAGCTTGAATGGAACCG 60.674 55.000 0.00 0.00 43.61 4.44
1681 2891 1.743772 CGGAGCTTGAATGGAACCGAT 60.744 52.381 0.00 0.00 41.09 4.18
1684 2894 2.352960 GAGCTTGAATGGAACCGATGAC 59.647 50.000 0.00 0.00 0.00 3.06
1717 2943 2.588877 CGAGGGCGGCGATGAAAT 60.589 61.111 12.98 0.00 0.00 2.17
1860 3104 0.970937 AGATGAAGGCGTTCCTCCGA 60.971 55.000 16.06 0.00 43.40 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.847467 GCATACGCAACTGATTCATCTGC 60.847 47.826 9.12 9.12 38.36 4.26
70 72 8.825667 TCCAAATTAAAAATGAGTTTACAGCC 57.174 30.769 0.00 0.00 0.00 4.85
100 102 3.198068 CCACATTCAGGATCGTAACTGG 58.802 50.000 0.00 0.00 35.47 4.00
143 145 4.918810 ACAAACTCAAGGGCTTAACTTG 57.081 40.909 0.00 0.00 45.08 3.16
290 292 0.610174 TCGAGCACCTGAGCATCTTT 59.390 50.000 0.00 0.00 36.85 2.52
320 322 2.004017 TGTCCAAATACCGCGAACATC 58.996 47.619 8.23 0.00 0.00 3.06
332 334 6.443849 TGTCTAAGGTCCTAGAATGTCCAAAT 59.556 38.462 0.00 0.00 29.74 2.32
437 447 4.201485 GCAAAACTTCGTGTGTGTTTGAAG 60.201 41.667 0.00 0.00 42.66 3.02
439 449 3.238441 GCAAAACTTCGTGTGTGTTTGA 58.762 40.909 0.00 0.00 34.63 2.69
488 498 6.956299 AAGAATCTGAAATTTTTCGGCATG 57.044 33.333 6.94 0.00 42.05 4.06
695 705 4.439563 GCCATATTACTTTCCCGTGGTTTG 60.440 45.833 0.00 0.00 0.00 2.93
789 808 5.115480 TCTTCGCAGATGCACATTGTATAA 58.885 37.500 5.55 0.00 42.21 0.98
831 850 6.649557 GCATAGTTTGTACTACCTTTCACAGT 59.350 38.462 0.00 0.00 39.59 3.55
1410 1435 4.458397 CTTACCTCCACTGCATCATCAAT 58.542 43.478 0.00 0.00 0.00 2.57
1411 1436 3.370846 CCTTACCTCCACTGCATCATCAA 60.371 47.826 0.00 0.00 0.00 2.57
1651 2861 0.387622 TCAAGCTCCGTTACCGTTCG 60.388 55.000 0.00 0.00 0.00 3.95
1677 2887 0.099613 CCGTGAGTCTCTGTCATCGG 59.900 60.000 0.65 2.85 34.56 4.18
1679 2889 0.524392 CGCCGTGAGTCTCTGTCATC 60.524 60.000 0.65 0.00 0.00 2.92
1681 2891 1.599797 TCGCCGTGAGTCTCTGTCA 60.600 57.895 0.65 0.00 0.00 3.58
1684 2894 2.202362 CGTCGCCGTGAGTCTCTG 60.202 66.667 0.65 0.00 0.00 3.35
1816 3060 2.069465 CTCATCGACAGGGAGAGGCG 62.069 65.000 0.00 0.00 0.00 5.52
1860 3104 2.111043 CTGGCGGACACAACCAGT 59.889 61.111 0.00 0.00 44.91 4.00


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

AutoCloner maintained by Alex Coulton.