Multiple sequence alignment - TraesCS3A01G491500

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 TraesCS3A01G491500 chr3A 100.000 2846 0 0 1 2846 718837861 718835016 0.000000e+00 5256.0
1 TraesCS3A01G491500 chr3D 94.871 2047 54 15 825 2846 588489492 588487472 0.000000e+00 3151.0
2 TraesCS3A01G491500 chr3B 94.181 1203 34 16 827 2014 786970774 786969593 0.000000e+00 1801.0
3 TraesCS3A01G491500 chr3B 91.842 809 27 18 2063 2843 786969594 786968797 0.000000e+00 1092.0
4 TraesCS3A01G491500 chr1A 100.000 827 0 0 1 827 136932522 136931696 0.000000e+00 1528.0
5 TraesCS3A01G491500 chr1A 99.637 827 3 0 1 827 456384312 456383486 0.000000e+00 1511.0
6 TraesCS3A01G491500 chr1A 82.934 334 27 16 2206 2536 513850741 513850435 1.000000e-69 274.0
7 TraesCS3A01G491500 chr1A 94.118 68 2 2 2259 2324 513851930 513851863 5.020000e-18 102.0
8 TraesCS3A01G491500 chr2B 99.758 827 2 0 1 827 656970196 656971022 0.000000e+00 1517.0
9 TraesCS3A01G491500 chr2B 89.855 69 5 2 2258 2324 62783237 62783305 1.400000e-13 87.9
10 TraesCS3A01G491500 chr6B 99.638 828 2 1 1 827 58829647 58830474 0.000000e+00 1511.0
11 TraesCS3A01G491500 chr6B 99.637 827 3 0 1 827 410235094 410234268 0.000000e+00 1511.0
12 TraesCS3A01G491500 chr5D 99.637 827 3 0 1 827 565525517 565526343 0.000000e+00 1511.0
13 TraesCS3A01G491500 chr5D 86.486 148 18 2 1042 1188 417040864 417040718 8.160000e-36 161.0
14 TraesCS3A01G491500 chr1B 99.637 827 3 0 1 827 69840764 69841590 0.000000e+00 1511.0
15 TraesCS3A01G491500 chr1B 99.637 827 3 0 1 827 564892630 564891804 0.000000e+00 1511.0
16 TraesCS3A01G491500 chr1B 99.637 827 3 0 1 827 655769655 655770481 0.000000e+00 1511.0
17 TraesCS3A01G491500 chr5A 83.891 329 27 6 2204 2532 654420156 654419854 9.970000e-75 291.0
18 TraesCS3A01G491500 chr5A 87.162 148 17 2 1042 1188 530302403 530302257 1.750000e-37 167.0
19 TraesCS3A01G491500 chr1D 83.333 336 27 10 2204 2536 416536470 416536161 1.670000e-72 283.0
20 TraesCS3A01G491500 chr2D 82.738 336 29 9 2204 2536 34675695 34675386 3.610000e-69 272.0
21 TraesCS3A01G491500 chr2D 94.118 68 2 2 2259 2324 34676892 34676825 5.020000e-18 102.0
22 TraesCS3A01G491500 chr2D 91.304 69 4 2 2258 2324 607796278 607796346 3.020000e-15 93.5
23 TraesCS3A01G491500 chr5B 82.282 333 31 11 2204 2536 618772712 618773016 2.170000e-66 263.0
24 TraesCS3A01G491500 chr5B 87.162 148 17 2 1042 1188 504307103 504306957 1.750000e-37 167.0
25 TraesCS3A01G491500 chr7D 82.143 336 27 10 2204 2536 45485965 45485660 1.010000e-64 257.0
26 TraesCS3A01G491500 chr7D 90.385 156 15 0 1035 1190 259840854 259840699 3.720000e-49 206.0
27 TraesCS3A01G491500 chr6D 81.602 337 28 11 2204 2536 68976253 68976559 6.090000e-62 248.0
28 TraesCS3A01G491500 chr7B 88.957 163 18 0 1028 1190 239362948 239363110 4.810000e-48 202.0
29 TraesCS3A01G491500 chr7B 90.090 111 8 2 2200 2309 692189204 692189312 1.060000e-29 141.0
30 TraesCS3A01G491500 chr7A 89.744 156 16 0 1035 1190 282369265 282369110 1.730000e-47 200.0
31 TraesCS3A01G491500 chr6A 93.939 66 2 2 2261 2324 525286775 525286710 6.490000e-17 99.0
32 TraesCS3A01G491500 chr2A 89.855 69 5 2 2258 2324 41736590 41736658 1.400000e-13 87.9


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 TraesCS3A01G491500 chr3A 718835016 718837861 2845 True 5256.0 5256 100.0000 1 2846 1 chr3A.!!$R1 2845
1 TraesCS3A01G491500 chr3D 588487472 588489492 2020 True 3151.0 3151 94.8710 825 2846 1 chr3D.!!$R1 2021
2 TraesCS3A01G491500 chr3B 786968797 786970774 1977 True 1446.5 1801 93.0115 827 2843 2 chr3B.!!$R1 2016
3 TraesCS3A01G491500 chr1A 136931696 136932522 826 True 1528.0 1528 100.0000 1 827 1 chr1A.!!$R1 826
4 TraesCS3A01G491500 chr1A 456383486 456384312 826 True 1511.0 1511 99.6370 1 827 1 chr1A.!!$R2 826
5 TraesCS3A01G491500 chr2B 656970196 656971022 826 False 1517.0 1517 99.7580 1 827 1 chr2B.!!$F2 826
6 TraesCS3A01G491500 chr6B 58829647 58830474 827 False 1511.0 1511 99.6380 1 827 1 chr6B.!!$F1 826
7 TraesCS3A01G491500 chr6B 410234268 410235094 826 True 1511.0 1511 99.6370 1 827 1 chr6B.!!$R1 826
8 TraesCS3A01G491500 chr5D 565525517 565526343 826 False 1511.0 1511 99.6370 1 827 1 chr5D.!!$F1 826
9 TraesCS3A01G491500 chr1B 69840764 69841590 826 False 1511.0 1511 99.6370 1 827 1 chr1B.!!$F1 826
10 TraesCS3A01G491500 chr1B 564891804 564892630 826 True 1511.0 1511 99.6370 1 827 1 chr1B.!!$R1 826
11 TraesCS3A01G491500 chr1B 655769655 655770481 826 False 1511.0 1511 99.6370 1 827 1 chr1B.!!$F2 826

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
968 982 1.226542 GCAACCCTAACCCTAGCCC 59.773 63.158 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2576 2623 0.251073 AAGCCAATGCCAAGAATGCC 59.749 50.0 0.0 0.0 38.69 4.4 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
968 982 1.226542 GCAACCCTAACCCTAGCCC 59.773 63.158 0.00 0.00 0.00 5.19
969 983 1.525442 CAACCCTAACCCTAGCCCG 59.475 63.158 0.00 0.00 0.00 6.13
984 998 2.306384 CCCGGGCCCCTTCTACTTT 61.306 63.158 18.66 0.00 0.00 2.66
998 1012 3.167485 TCTACTTTAAGAAGCCCGTCCA 58.833 45.455 0.00 0.00 36.29 4.02
1009 1023 2.278206 CCGTCCAGATGCTCGACG 60.278 66.667 7.46 7.46 46.79 5.12
1345 1364 0.038744 CACCTCCAGCCATCAAGGTT 59.961 55.000 0.00 0.00 40.13 3.50
1346 1365 0.779997 ACCTCCAGCCATCAAGGTTT 59.220 50.000 0.00 0.00 39.05 3.27
1347 1366 1.180029 CCTCCAGCCATCAAGGTTTG 58.820 55.000 0.00 0.00 40.61 2.93
1348 1367 1.548582 CCTCCAGCCATCAAGGTTTGT 60.549 52.381 0.00 0.00 40.61 2.83
1349 1368 2.290896 CCTCCAGCCATCAAGGTTTGTA 60.291 50.000 0.00 0.00 40.61 2.41
1413 1438 2.407361 CGTGCGTAATTCGAGACAGTTT 59.593 45.455 2.15 0.00 42.86 2.66
1635 1660 2.277692 CGCGCCAGCAATGACATG 60.278 61.111 0.00 0.00 45.49 3.21
1963 1991 4.181010 CTCTCATGGCCGGGGTGG 62.181 72.222 2.18 0.00 42.50 4.61
2028 2056 5.856126 TGACATCAAGTGTTAATCGTTCC 57.144 39.130 0.00 0.00 42.36 3.62
2042 2070 2.641305 TCGTTCCTAGTCTAGTCCAGC 58.359 52.381 6.15 0.00 0.00 4.85
2067 2095 2.166664 GTCCTCCTAGTAGCACCAGTTG 59.833 54.545 0.00 0.00 0.00 3.16
2232 2264 3.149196 TGGTTTCTTCTTGTCTCATGCC 58.851 45.455 0.00 0.00 0.00 4.40
2420 2457 4.496895 CAGAAAAGTTTGACTCTTGCAACG 59.503 41.667 0.00 0.00 0.00 4.10
2515 2552 0.244721 CACTCACTCATCGGAGCACA 59.755 55.000 0.00 0.00 45.42 4.57
2567 2604 4.870636 TCTACGGGTAGGTAGGATTGAAA 58.129 43.478 6.04 0.00 40.22 2.69
2571 2608 4.081254 ACGGGTAGGTAGGATTGAAAGAAC 60.081 45.833 0.00 0.00 0.00 3.01
2576 2623 3.197983 AGGTAGGATTGAAAGAACGGGAG 59.802 47.826 0.00 0.00 0.00 4.30
2611 2658 3.221771 TGGCTTTGTGCTTTGTAGATGT 58.778 40.909 0.00 0.00 42.39 3.06
2633 2680 4.931661 AGCATCTTCTAATTGCATTGGG 57.068 40.909 0.00 0.00 38.84 4.12
2724 2778 8.001875 ACCATCTTATCTCACACTCATACTACT 58.998 37.037 0.00 0.00 0.00 2.57
2725 2779 9.508642 CCATCTTATCTCACACTCATACTACTA 57.491 37.037 0.00 0.00 0.00 1.82
2728 2782 9.549078 TCTTATCTCACACTCATACTACTACTG 57.451 37.037 0.00 0.00 0.00 2.74
2757 2814 9.926751 CATGTTAAACTATGTTAGCATCTTCAG 57.073 33.333 0.00 0.00 33.99 3.02
2794 2851 1.001068 TGCATGTTGGGAAGCATGTTG 59.999 47.619 6.43 0.00 43.04 3.33
2795 2852 1.001181 GCATGTTGGGAAGCATGTTGT 59.999 47.619 6.43 0.00 43.04 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
945 953 4.354162 GGGTTAGGGTTGCCGCCA 62.354 66.667 0.00 0.00 0.00 5.69
968 982 1.835531 TCTTAAAGTAGAAGGGGCCCG 59.164 52.381 18.95 0.00 0.00 6.13
969 983 3.887352 CTTCTTAAAGTAGAAGGGGCCC 58.113 50.000 17.12 17.12 44.75 5.80
982 996 2.939640 GCATCTGGACGGGCTTCTTAAA 60.940 50.000 0.00 0.00 0.00 1.52
984 998 0.178068 GCATCTGGACGGGCTTCTTA 59.822 55.000 0.00 0.00 0.00 2.10
1345 1364 0.797542 GCGGCGTGGTTACAATACAA 59.202 50.000 9.37 0.00 0.00 2.41
1346 1365 1.020333 GGCGGCGTGGTTACAATACA 61.020 55.000 9.37 0.00 0.00 2.29
1347 1366 1.708193 GGGCGGCGTGGTTACAATAC 61.708 60.000 9.37 0.00 0.00 1.89
1348 1367 1.449956 GGGCGGCGTGGTTACAATA 60.450 57.895 9.37 0.00 0.00 1.90
1349 1368 2.748647 GGGCGGCGTGGTTACAAT 60.749 61.111 9.37 0.00 0.00 2.71
1375 1394 0.524862 ACGCGTGAAGAGGATACGTT 59.475 50.000 12.93 0.00 46.39 3.99
1800 1828 3.876198 CCGCCGCCAAGTATGTGC 61.876 66.667 0.00 0.00 0.00 4.57
1801 1829 3.202001 CCCGCCGCCAAGTATGTG 61.202 66.667 0.00 0.00 0.00 3.21
1802 1830 3.675619 GACCCGCCGCCAAGTATGT 62.676 63.158 0.00 0.00 0.00 2.29
2042 2070 1.404843 GTGCTACTAGGAGGACTGGG 58.595 60.000 18.86 0.00 35.10 4.45
2232 2264 2.762327 AGGCATTGGGAACATAAGCAAG 59.238 45.455 0.00 0.00 42.32 4.01
2277 2309 0.827507 ACATGGTTTGCACCCCTGAC 60.828 55.000 12.16 0.00 43.49 3.51
2392 2428 5.677091 GCAAGAGTCAAACTTTTCTGCTCAA 60.677 40.000 0.00 0.00 0.00 3.02
2420 2457 0.670162 TGAAAGCCAAGCAAGTGAGC 59.330 50.000 0.00 0.00 0.00 4.26
2515 2552 3.199071 GGGGAAAACAAACAGGGAAAAGT 59.801 43.478 0.00 0.00 0.00 2.66
2571 2608 1.039233 AATGCCAAGAATGCCTCCCG 61.039 55.000 0.00 0.00 0.00 5.14
2576 2623 0.251073 AAGCCAATGCCAAGAATGCC 59.749 50.000 0.00 0.00 38.69 4.40
2611 2658 5.532406 GTCCCAATGCAATTAGAAGATGCTA 59.468 40.000 0.00 0.00 40.66 3.49
2725 2779 9.667107 ATGCTAACATAGTTTAACATGTACAGT 57.333 29.630 0.00 0.00 34.32 3.55
2727 2781 9.884636 AGATGCTAACATAGTTTAACATGTACA 57.115 29.630 0.00 0.00 36.35 2.90
2757 2814 2.697654 TGCATGCCAATTACCAAAAGC 58.302 42.857 16.68 0.00 0.00 3.51
2794 2851 4.007659 GCATCTCCTCTAGCCTCTACTAC 58.992 52.174 0.00 0.00 0.00 2.73
2795 2852 3.653352 TGCATCTCCTCTAGCCTCTACTA 59.347 47.826 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.