Multiple sequence alignment - TraesCS1B01G159000

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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 TraesCS1B01G159000 chr1B 100.000 3191 0 0 1 3191 269305849 269302659 0.000000e+00 5893.0
1 TraesCS1B01G159000 chr1B 85.118 1485 214 7 1710 3191 403121376 403122856 0.000000e+00 1511.0
2 TraesCS1B01G159000 chr6A 95.174 3129 134 5 1 3123 129345497 129348614 0.000000e+00 4926.0
3 TraesCS1B01G159000 chr7A 95.201 2542 116 3 656 3191 30219623 30217082 0.000000e+00 4013.0
4 TraesCS1B01G159000 chr7A 95.377 1752 81 0 1440 3191 482197540 482199291 0.000000e+00 2787.0
5 TraesCS1B01G159000 chr7A 93.804 581 33 1 1 578 30220206 30219626 0.000000e+00 870.0
6 TraesCS1B01G159000 chr1A 95.479 2057 88 3 1136 3191 392523219 392521167 0.000000e+00 3278.0
7 TraesCS1B01G159000 chr1A 93.904 2034 99 5 1 2028 316893476 316895490 0.000000e+00 3046.0
8 TraesCS1B01G159000 chr1A 95.858 1183 49 0 2009 3191 316896803 316897985 0.000000e+00 1914.0
9 TraesCS1B01G159000 chr3B 98.215 1793 30 2 1400 3191 772140624 772138833 0.000000e+00 3133.0
10 TraesCS1B01G159000 chr3B 84.029 1509 227 12 1687 3191 473725747 473727245 0.000000e+00 1439.0
11 TraesCS1B01G159000 chr3B 88.462 52 6 0 1200 1251 439338939 439338888 2.660000e-06 63.9
12 TraesCS1B01G159000 chr5D 89.048 2237 216 9 1 2224 555478547 555480767 0.000000e+00 2747.0
13 TraesCS1B01G159000 chr7B 84.916 1485 217 7 1710 3191 229833476 229834956 0.000000e+00 1495.0
14 TraesCS1B01G159000 chr2B 76.298 751 151 23 5 746 412776531 412775799 3.010000e-100 375.0
15 TraesCS1B01G159000 chr5A 74.968 787 165 22 1 780 328954594 328955355 1.830000e-87 333.0
16 TraesCS1B01G159000 chr5A 89.583 48 5 0 1196 1243 328955834 328955881 9.560000e-06 62.1
17 TraesCS1B01G159000 chr4B 75.210 714 162 11 73 780 94512215 94511511 1.100000e-84 324.0
18 TraesCS1B01G159000 chr4B 87.500 56 7 0 1196 1251 94511059 94511004 7.390000e-07 65.8


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 TraesCS1B01G159000 chr1B 269302659 269305849 3190 True 5893.0 5893 100.0000 1 3191 1 chr1B.!!$R1 3190
1 TraesCS1B01G159000 chr1B 403121376 403122856 1480 False 1511.0 1511 85.1180 1710 3191 1 chr1B.!!$F1 1481
2 TraesCS1B01G159000 chr6A 129345497 129348614 3117 False 4926.0 4926 95.1740 1 3123 1 chr6A.!!$F1 3122
3 TraesCS1B01G159000 chr7A 482197540 482199291 1751 False 2787.0 2787 95.3770 1440 3191 1 chr7A.!!$F1 1751
4 TraesCS1B01G159000 chr7A 30217082 30220206 3124 True 2441.5 4013 94.5025 1 3191 2 chr7A.!!$R1 3190
5 TraesCS1B01G159000 chr1A 392521167 392523219 2052 True 3278.0 3278 95.4790 1136 3191 1 chr1A.!!$R1 2055
6 TraesCS1B01G159000 chr1A 316893476 316897985 4509 False 2480.0 3046 94.8810 1 3191 2 chr1A.!!$F1 3190
7 TraesCS1B01G159000 chr3B 772138833 772140624 1791 True 3133.0 3133 98.2150 1400 3191 1 chr3B.!!$R2 1791
8 TraesCS1B01G159000 chr3B 473725747 473727245 1498 False 1439.0 1439 84.0290 1687 3191 1 chr3B.!!$F1 1504
9 TraesCS1B01G159000 chr5D 555478547 555480767 2220 False 2747.0 2747 89.0480 1 2224 1 chr5D.!!$F1 2223
10 TraesCS1B01G159000 chr7B 229833476 229834956 1480 False 1495.0 1495 84.9160 1710 3191 1 chr7B.!!$F1 1481
11 TraesCS1B01G159000 chr2B 412775799 412776531 732 True 375.0 375 76.2980 5 746 1 chr2B.!!$R1 741

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
366 367 0.250209 CTAAGCTCATCCATGGCGCT 60.250 55.0 6.96 9.26 36.84 5.92 F
560 564 0.735632 GCTCTGTCTTCCAGTCTGCG 60.736 60.0 0.00 0.00 42.19 5.18 F
1930 1957 0.309922 GAACCGATCGACGCCTATCA 59.690 55.0 18.66 0.00 41.07 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1895 0.828022 ACGTCCCACTGTGAAACTGA 59.172 50.000 9.86 0.00 39.30 3.41 R
2065 3424 1.401552 GTCAAGCTTGAACAGTGCACA 59.598 47.619 29.99 1.63 39.21 4.57 R
2834 4194 6.034683 CTTCATTGCAAAAGAAGCTATCAAGC 59.965 38.462 23.53 0.00 43.47 4.01 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
333 334 1.004080 TGCTGCTGAAGACCTGCTC 60.004 57.895 0.00 0.00 40.01 4.26
366 367 0.250209 CTAAGCTCATCCATGGCGCT 60.250 55.000 6.96 9.26 36.84 5.92
501 505 0.955428 GTGTGGATGCAAGCTCGGAA 60.955 55.000 0.00 0.00 0.00 4.30
550 554 1.722034 TTGGTGGAGAGCTCTGTCTT 58.278 50.000 23.91 0.00 0.00 3.01
560 564 0.735632 GCTCTGTCTTCCAGTCTGCG 60.736 60.000 0.00 0.00 42.19 5.18
654 658 4.479993 ACCTGCCATCGCTGCCTC 62.480 66.667 0.00 0.00 35.36 4.70
675 679 2.604373 CGAGCGGAGACATCTCAAGATC 60.604 54.545 10.95 10.47 44.60 2.75
720 726 2.628178 TCTGATTTGTCGACAGAGTGGT 59.372 45.455 19.11 0.00 36.04 4.16
798 804 1.762222 CGCCGTCAATGATTCCGTCC 61.762 60.000 0.00 0.00 0.00 4.79
834 840 5.191323 AGAAGATGATGGAAGGATTCTGTGT 59.809 40.000 0.00 0.00 46.56 3.72
965 984 3.064987 GCCAAGGCTCTCGCTACGA 62.065 63.158 3.29 0.00 38.26 3.43
970 989 2.427740 GCTCTCGCTACGATCGGC 60.428 66.667 20.98 13.07 34.61 5.54
971 990 2.899044 GCTCTCGCTACGATCGGCT 61.899 63.158 20.98 1.14 34.61 5.52
987 1006 1.361993 GCTCCGAGATGACTGCGAT 59.638 57.895 0.00 0.00 0.00 4.58
990 1009 0.751643 TCCGAGATGACTGCGATGGA 60.752 55.000 0.00 0.00 0.00 3.41
995 1014 3.265791 GAGATGACTGCGATGGAAACTT 58.734 45.455 0.00 0.00 0.00 2.66
1117 1136 4.011517 GGAGGTCCCGAAACCGCA 62.012 66.667 10.94 0.00 44.49 5.69
1172 1191 4.087892 CAGCACTACCAGCCCGCT 62.088 66.667 0.00 0.00 0.00 5.52
1291 1310 1.002087 ACGAAAGATCACCGCCTTCTT 59.998 47.619 0.00 0.00 0.00 2.52
1391 1416 4.910585 GGGATTGCCGGCGTCGAT 62.911 66.667 23.90 13.03 39.00 3.59
1484 1510 2.745884 TTTGGGCGCGACTCCATG 60.746 61.111 13.91 0.00 32.48 3.66
1654 1680 3.072468 CCCCGACGCACCCTTCTA 61.072 66.667 0.00 0.00 0.00 2.10
1668 1694 1.137086 CCTTCTAGCTTGCTTCGCCTA 59.863 52.381 0.00 0.00 0.00 3.93
1868 1895 3.916989 AGGAAGACCTTGGTTGGTATCTT 59.083 43.478 0.00 0.00 45.36 2.40
1922 1949 1.084370 CAGGCCAAGAACCGATCGAC 61.084 60.000 18.66 7.72 0.00 4.20
1930 1957 0.309922 GAACCGATCGACGCCTATCA 59.690 55.000 18.66 0.00 41.07 2.15
2369 3728 0.756442 AGGAAACCAAGCTTGCAGCA 60.756 50.000 21.43 0.00 45.56 4.41
2668 4028 0.175760 AGATGGATTGTCACCGACGG 59.824 55.000 13.61 13.61 34.95 4.79
2684 4044 2.338500 GACGGCTTCAACCAAGTCTAG 58.662 52.381 0.00 0.00 34.16 2.43
2834 4194 1.737793 GTAAACCCGACCATGAGCAAG 59.262 52.381 0.00 0.00 0.00 4.01
2984 4344 5.008911 GCCAAAATGCTTCCACTTTGAAAAT 59.991 36.000 0.00 0.00 39.76 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 1.518903 GCTGCGGGAAAAGCAAGAGT 61.519 55.000 0.00 0.00 44.67 3.24
469 473 2.047274 CACACCCAACGGCTCGAT 60.047 61.111 1.50 0.00 0.00 3.59
501 505 3.806949 TTAACAAGCATCCAACCCTCT 57.193 42.857 0.00 0.00 0.00 3.69
550 554 0.315251 CTTGACTGACGCAGACTGGA 59.685 55.000 12.77 0.00 35.18 3.86
560 564 2.230266 GAGGACCTCTGTCTTGACTGAC 59.770 54.545 14.72 0.00 41.47 3.51
654 658 0.735471 TCTTGAGATGTCTCCGCTCG 59.265 55.000 7.51 0.00 42.20 5.03
661 665 3.064682 CGACAGTCGATCTTGAGATGTCT 59.935 47.826 18.63 0.00 43.74 3.41
675 679 1.239296 TGTAGGGGTCACGACAGTCG 61.239 60.000 21.62 21.62 46.93 4.18
720 726 2.738139 CACTGGCGTGCACGATGA 60.738 61.111 41.19 22.17 43.02 2.92
804 810 2.172082 CCTTCCATCATCTTCTGCCAGA 59.828 50.000 0.00 0.00 0.00 3.86
815 821 3.801698 CGACACAGAATCCTTCCATCAT 58.198 45.455 0.00 0.00 0.00 2.45
898 907 0.400213 CTGGAGTGTTGGTTGCCCTA 59.600 55.000 0.00 0.00 0.00 3.53
970 989 0.318529 CCATCGCAGTCATCTCGGAG 60.319 60.000 0.00 0.00 0.00 4.63
971 990 0.751643 TCCATCGCAGTCATCTCGGA 60.752 55.000 0.00 0.00 0.00 4.55
987 1006 1.573829 GGCGCATGTCGAAGTTTCCA 61.574 55.000 10.83 0.00 41.67 3.53
1037 1056 2.103143 AGCCTCTGTCGATTCGCG 59.897 61.111 0.00 0.00 42.69 5.87
1122 1141 4.477975 CTCCTCGTCGGCGTGTCC 62.478 72.222 10.18 0.00 39.49 4.02
1172 1191 0.969149 ACCACGAGTCTCAATGCTGA 59.031 50.000 0.00 0.00 0.00 4.26
1291 1310 1.476891 GTCCTGGAATGTAGTGCGAGA 59.523 52.381 0.00 0.00 0.00 4.04
1668 1694 1.196012 GGGTCGGAGAAGTTCTGGAT 58.804 55.000 10.90 0.00 39.69 3.41
1868 1895 0.828022 ACGTCCCACTGTGAAACTGA 59.172 50.000 9.86 0.00 39.30 3.41
1922 1949 2.869801 TCCGCTAATTTTGTGATAGGCG 59.130 45.455 0.00 0.00 40.83 5.52
1930 1957 2.162408 GCAGCTTCTCCGCTAATTTTGT 59.838 45.455 0.00 0.00 38.41 2.83
2065 3424 1.401552 GTCAAGCTTGAACAGTGCACA 59.598 47.619 29.99 1.63 39.21 4.57
2369 3728 3.973425 AGCAGCAATAAAAGGATCCACT 58.027 40.909 15.82 0.00 0.00 4.00
2668 4028 1.079503 CCGCTAGACTTGGTTGAAGC 58.920 55.000 0.00 0.00 34.68 3.86
2684 4044 0.533085 GGTTCTTATCTCTGGCCCGC 60.533 60.000 0.00 0.00 0.00 6.13
2834 4194 6.034683 CTTCATTGCAAAAGAAGCTATCAAGC 59.965 38.462 23.53 0.00 43.47 4.01
2984 4344 6.493115 TGAAGTTAGGCATCTTGATCCAAAAA 59.507 34.615 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.