Multiple sequence alignment - TraesCS7D01G195300

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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 TraesCS7D01G195300 chr7D 100.000 2946 0 0 1 2946 151857458 151854513 0.000000e+00 5441.0
1 TraesCS7D01G195300 chr7D 95.212 1671 66 10 446 2108 152099381 152097717 0.000000e+00 2630.0
2 TraesCS7D01G195300 chr7D 97.851 1489 29 2 1461 2946 151940053 151938565 0.000000e+00 2569.0
3 TraesCS7D01G195300 chr7D 96.630 1454 33 7 1 1446 151941482 151940037 0.000000e+00 2399.0
4 TraesCS7D01G195300 chr7D 94.486 399 13 7 27 420 152100952 152100558 9.030000e-170 606.0
5 TraesCS7D01G195300 chr7D 82.512 629 74 20 805 1421 152120440 152121044 1.210000e-143 520.0
6 TraesCS7D01G195300 chr7D 85.650 446 54 5 1530 1973 152121128 152121565 7.440000e-126 460.0
7 TraesCS7D01G195300 chr7D 78.750 160 32 2 1241 1399 538895309 538895151 4.020000e-19 106.0
8 TraesCS7D01G195300 chr7D 96.491 57 2 0 2783 2839 18445276 18445332 8.690000e-16 95.3
9 TraesCS7D01G195300 chr7B 91.099 1101 59 18 351 1431 113770024 113771105 0.000000e+00 1454.0
10 TraesCS7D01G195300 chr7B 93.438 640 34 2 1499 2134 113771140 113771775 0.000000e+00 942.0
11 TraesCS7D01G195300 chr7B 79.665 895 115 41 573 1431 114178290 114179153 1.520000e-162 582.0
12 TraesCS7D01G195300 chr7B 85.938 448 51 5 1530 1973 114179216 114179655 4.450000e-128 468.0
13 TraesCS7D01G195300 chr7B 86.012 336 32 10 1738 2059 113772649 113772983 2.170000e-91 346.0
14 TraesCS7D01G195300 chr7B 78.125 160 33 2 1241 1399 581395682 581395524 1.870000e-17 100.0
15 TraesCS7D01G195300 chrUn 89.988 809 50 17 1 787 85641956 85641157 0.000000e+00 1016.0
16 TraesCS7D01G195300 chrUn 82.429 387 48 10 2410 2781 85640052 85639671 1.320000e-83 320.0
17 TraesCS7D01G195300 chr7A 82.889 637 75 18 805 1431 152540367 152540979 2.580000e-150 542.0
18 TraesCS7D01G195300 chr7A 85.714 462 53 10 1530 1987 152541041 152541493 2.660000e-130 475.0
19 TraesCS7D01G195300 chr7A 78.750 160 32 2 1241 1399 620412451 620412293 4.020000e-19 106.0
20 TraesCS7D01G195300 chr7A 98.148 54 1 0 2783 2836 211399408 211399461 8.690000e-16 95.3
21 TraesCS7D01G195300 chr5A 98.246 57 1 0 2783 2839 238841563 238841619 1.870000e-17 100.0
22 TraesCS7D01G195300 chr4D 100.000 31 0 0 2809 2839 307152798 307152828 1.140000e-04 58.4


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 TraesCS7D01G195300 chr7D 151854513 151857458 2945 True 5441.0 5441 100.0000 1 2946 1 chr7D.!!$R1 2945
1 TraesCS7D01G195300 chr7D 151938565 151941482 2917 True 2484.0 2569 97.2405 1 2946 2 chr7D.!!$R3 2945
2 TraesCS7D01G195300 chr7D 152097717 152100952 3235 True 1618.0 2630 94.8490 27 2108 2 chr7D.!!$R4 2081
3 TraesCS7D01G195300 chr7D 152120440 152121565 1125 False 490.0 520 84.0810 805 1973 2 chr7D.!!$F2 1168
4 TraesCS7D01G195300 chr7B 113770024 113772983 2959 False 914.0 1454 90.1830 351 2134 3 chr7B.!!$F1 1783
5 TraesCS7D01G195300 chr7B 114178290 114179655 1365 False 525.0 582 82.8015 573 1973 2 chr7B.!!$F2 1400
6 TraesCS7D01G195300 chrUn 85639671 85641956 2285 True 668.0 1016 86.2085 1 2781 2 chrUn.!!$R1 2780
7 TraesCS7D01G195300 chr7A 152540367 152541493 1126 False 508.5 542 84.3015 805 1987 2 chr7A.!!$F2 1182

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
982 2191 1.15145 CACCTTGTCAACCAGGGCT 59.849 57.895 5.37 0.0 44.06 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2855 5275 0.257039 GGTGGCACCTTGGAGATCAT 59.743 55.0 29.22 0.0 34.73 2.45 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
248 253 8.911662 GCAGTTAAAAACATGTATCGAAATGTT 58.088 29.630 15.03 15.03 46.35 2.71
301 306 6.110033 TCCAATATGAACTAAGTGCGCTTTA 58.890 36.000 19.18 3.47 36.22 1.85
440 1597 4.336713 TGTTCGTCACCATGAATCACAAAA 59.663 37.500 0.00 0.00 30.00 2.44
444 1601 5.067153 TCGTCACCATGAATCACAAAACTTT 59.933 36.000 0.00 0.00 0.00 2.66
571 1745 2.420022 CTGGATTAGCAAACCACGAAGG 59.580 50.000 0.00 0.00 45.67 3.46
607 1786 4.944962 TGTGATCATTAAGCAAAGACCG 57.055 40.909 0.00 0.00 0.00 4.79
982 2191 1.151450 CACCTTGTCAACCAGGGCT 59.849 57.895 5.37 0.00 44.06 5.19
1043 2252 0.039437 TTCTGCTCCAAGTCGACGTC 60.039 55.000 10.46 5.18 0.00 4.34
1152 2365 3.546407 GCATGCTTGCTGCTCATAC 57.454 52.632 16.80 0.00 45.77 2.39
1153 2366 1.022735 GCATGCTTGCTGCTCATACT 58.977 50.000 16.80 0.00 45.77 2.12
1154 2367 1.404391 GCATGCTTGCTGCTCATACTT 59.596 47.619 16.80 0.00 45.77 2.24
1155 2368 2.541178 GCATGCTTGCTGCTCATACTTC 60.541 50.000 16.80 0.00 45.77 3.01
1157 2370 0.654683 GCTTGCTGCTCATACTTCCG 59.345 55.000 0.00 0.00 38.95 4.30
1189 2409 7.389330 TCGTTAAAATCTGTGATGTGGTGTAAT 59.611 33.333 0.00 0.00 0.00 1.89
1448 2738 2.742774 CAAAGTTTGGGCACACTTAGC 58.257 47.619 7.78 0.00 32.74 3.09
1449 2739 2.362077 CAAAGTTTGGGCACACTTAGCT 59.638 45.455 7.78 0.00 32.74 3.32
1450 2740 2.364972 AGTTTGGGCACACTTAGCTT 57.635 45.000 0.00 0.00 0.00 3.74
1451 2741 2.230660 AGTTTGGGCACACTTAGCTTC 58.769 47.619 0.00 0.00 0.00 3.86
1452 2742 1.953686 GTTTGGGCACACTTAGCTTCA 59.046 47.619 0.00 0.00 0.00 3.02
1453 2743 2.356665 TTGGGCACACTTAGCTTCAA 57.643 45.000 0.00 0.00 0.00 2.69
1454 2744 2.356665 TGGGCACACTTAGCTTCAAA 57.643 45.000 0.00 0.00 0.00 2.69
1455 2745 2.660572 TGGGCACACTTAGCTTCAAAA 58.339 42.857 0.00 0.00 0.00 2.44
1456 2746 3.027412 TGGGCACACTTAGCTTCAAAAA 58.973 40.909 0.00 0.00 0.00 1.94
1903 3201 2.104111 AGATCGGTTCAAGAACACCACA 59.896 45.455 14.25 0.00 42.85 4.17
1926 3224 2.610694 CGGTTGAGTGCAGCCACAG 61.611 63.158 0.00 0.00 44.85 3.66
2488 4892 8.420222 GTGATATACTCCCTCCATCTGATAATG 58.580 40.741 0.00 0.00 0.00 1.90
2545 4952 2.541346 GCGGAGGGCGTAACTTTTATAC 59.459 50.000 0.00 0.00 0.00 1.47
2600 5007 6.418057 TGTTCAAACCCAAGCTTGAAATAT 57.582 33.333 28.05 6.94 41.79 1.28
2855 5275 4.165372 ACGAGCCCCTTTTAAATATGGAGA 59.835 41.667 0.00 0.00 0.00 3.71
2891 5311 6.027749 GTGCCACCTTCATCGTTATTTTAAG 58.972 40.000 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 253 3.633986 TGTACACAATGGTTCACAATGCA 59.366 39.130 0.00 0.00 33.12 3.96
391 397 3.049912 GAGTGGTTCCGCACAAAATTTC 58.950 45.455 5.19 0.00 0.00 2.17
440 1597 4.202212 GGTTTTTCTACCATGCACCAAAGT 60.202 41.667 0.00 0.00 38.12 2.66
444 1601 2.950781 TGGTTTTTCTACCATGCACCA 58.049 42.857 0.00 0.00 43.14 4.17
571 1745 2.417339 TCACAACTCACGAGCACTAC 57.583 50.000 0.00 0.00 0.00 2.73
607 1786 0.371645 CGATGTCTTCTTCGGCTTGC 59.628 55.000 0.00 0.00 37.51 4.01
982 2191 1.000843 CATGGTGAGACGAACCTGTGA 59.999 52.381 0.00 0.00 38.60 3.58
1043 2252 2.269241 GGAAGAACCCCGAGCCAG 59.731 66.667 0.00 0.00 0.00 4.85
1157 2370 7.230222 CACATCACAGATTTTAACGAGAAGTC 58.770 38.462 0.00 0.00 0.00 3.01
1189 2409 0.594540 GCTGCATGCACGTCAAACAA 60.595 50.000 18.46 0.00 42.31 2.83
1458 2748 4.278975 TGAAAGTGTGCCCAAACTTTTT 57.721 36.364 15.60 0.00 44.53 1.94
1459 2749 3.971245 TGAAAGTGTGCCCAAACTTTT 57.029 38.095 15.60 2.94 44.53 2.27
1460 2750 3.181466 GGATGAAAGTGTGCCCAAACTTT 60.181 43.478 14.66 14.66 46.56 2.66
1461 2751 2.365293 GGATGAAAGTGTGCCCAAACTT 59.635 45.455 0.00 0.00 38.25 2.66
1462 2752 1.963515 GGATGAAAGTGTGCCCAAACT 59.036 47.619 0.00 0.00 0.00 2.66
1463 2753 1.686052 TGGATGAAAGTGTGCCCAAAC 59.314 47.619 0.00 0.00 0.00 2.93
1464 2754 2.079170 TGGATGAAAGTGTGCCCAAA 57.921 45.000 0.00 0.00 0.00 3.28
1465 2755 2.079170 TTGGATGAAAGTGTGCCCAA 57.921 45.000 0.00 0.00 0.00 4.12
1466 2756 1.962807 CTTTGGATGAAAGTGTGCCCA 59.037 47.619 0.00 0.00 36.96 5.36
1467 2757 2.730550 CTTTGGATGAAAGTGTGCCC 57.269 50.000 0.00 0.00 36.96 5.36
1539 2837 0.179192 CGGCACATCGTCCACAAATG 60.179 55.000 0.00 0.00 0.00 2.32
1856 3154 1.530646 GGCGCAGTAGTCGTAGTACAC 60.531 57.143 10.83 0.00 0.00 2.90
1903 3201 2.629656 GCTGCACTCAACCGGCATT 61.630 57.895 0.00 0.00 36.87 3.56
2585 4992 9.739276 TGGTCTAATATATATTTCAAGCTTGGG 57.261 33.333 25.73 1.60 0.00 4.12
2813 5233 5.333875 GCTCGTTTCACTCGAATTTAAAGGT 60.334 40.000 0.00 0.00 36.89 3.50
2855 5275 0.257039 GGTGGCACCTTGGAGATCAT 59.743 55.000 29.22 0.00 34.73 2.45


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

AutoCloner maintained by Alex Coulton.