Multiple sequence alignment - TraesCS4D01G213200

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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 TraesCS4D01G213200 chr4D 100.000 2930 0 0 1 2930 366044689 366047618 0.000000e+00 5411
1 TraesCS4D01G213200 chr7D 95.880 2063 43 13 903 2930 311619101 311621156 0.000000e+00 3301
2 TraesCS4D01G213200 chr7D 100.000 55 0 0 843 897 311619009 311619063 5.170000e-18 102
3 TraesCS4D01G213200 chr3B 95.201 2063 61 4 903 2930 371039616 371037557 0.000000e+00 3227
4 TraesCS4D01G213200 chr3B 94.501 491 18 2 2449 2930 279756457 279756947 0.000000e+00 749
5 TraesCS4D01G213200 chr3B 90.591 372 25 6 6 368 380277850 380277480 4.390000e-133 484
6 TraesCS4D01G213200 chr3B 85.000 500 25 9 2394 2843 363586967 363586468 2.060000e-126 462
7 TraesCS4D01G213200 chr3B 100.000 55 0 0 843 897 371039708 371039654 5.170000e-18 102
8 TraesCS4D01G213200 chr3B 98.214 56 1 0 842 897 363588541 363588486 6.680000e-17 99
9 TraesCS4D01G213200 chr6A 95.941 1971 59 4 903 2864 197861134 197859176 0.000000e+00 3177
10 TraesCS4D01G213200 chr6A 98.439 897 13 1 1 897 197862067 197861172 0.000000e+00 1578
11 TraesCS4D01G213200 chr6A 85.401 411 49 6 371 770 563261670 563262080 1.620000e-112 416
12 TraesCS4D01G213200 chr6A 87.624 202 24 1 146 347 563710949 563711149 1.760000e-57 233
13 TraesCS4D01G213200 chr4B 94.697 1867 58 12 1100 2930 149993379 149995240 0.000000e+00 2861
14 TraesCS4D01G213200 chr4B 96.558 1627 50 4 903 2528 175308689 175307068 0.000000e+00 2689
15 TraesCS4D01G213200 chr4B 93.220 649 22 5 2290 2930 338503422 338502788 0.000000e+00 935
16 TraesCS4D01G213200 chr4B 100.000 55 0 0 843 897 531340100 531340154 5.170000e-18 102
17 TraesCS4D01G213200 chr3A 98.155 1626 29 1 903 2528 361576773 361575149 0.000000e+00 2835
18 TraesCS4D01G213200 chr3A 98.662 897 12 0 1 897 361577707 361576811 0.000000e+00 1591
19 TraesCS4D01G213200 chr3A 95.904 293 11 1 2639 2930 361575140 361574848 9.500000e-130 473
20 TraesCS4D01G213200 chr3A 96.390 277 10 0 2654 2930 171064946 171065222 9.570000e-125 457
21 TraesCS4D01G213200 chr5B 97.856 1586 34 0 903 2488 209633761 209632176 0.000000e+00 2741
22 TraesCS4D01G213200 chr5B 92.633 638 25 5 2301 2930 277765866 277766489 0.000000e+00 898
23 TraesCS4D01G213200 chr5B 100.000 55 0 0 843 897 209633853 209633799 5.170000e-18 102
24 TraesCS4D01G213200 chr5D 97.107 1590 41 4 903 2488 199084397 199085985 0.000000e+00 2676
25 TraesCS4D01G213200 chr5A 97.042 1589 44 3 903 2488 216692119 216693707 0.000000e+00 2671
26 TraesCS4D01G213200 chr5A 100.000 55 0 0 843 897 216692026 216692080 5.170000e-18 102
27 TraesCS4D01G213200 chr2A 97.996 898 17 1 1 897 381733159 381732262 0.000000e+00 1557
28 TraesCS4D01G213200 chr2A 95.567 812 16 4 2125 2927 381722309 381721509 0.000000e+00 1282
29 TraesCS4D01G213200 chr7B 92.912 649 24 5 2290 2930 195988135 195987501 0.000000e+00 924
30 TraesCS4D01G213200 chr1B 90.541 370 28 4 6 368 514931815 514932184 1.580000e-132 483
31 TraesCS4D01G213200 chr7A 96.727 275 8 1 2657 2930 430765921 430765647 9.570000e-125 457
32 TraesCS4D01G213200 chr6D 88.186 237 24 4 146 379 420748599 420748834 2.220000e-71 279
33 TraesCS4D01G213200 chr6B 87.660 235 27 2 146 379 633915710 633915943 3.720000e-69 272


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 TraesCS4D01G213200 chr4D 366044689 366047618 2929 False 5411.0 5411 100.000000 1 2930 1 chr4D.!!$F1 2929
1 TraesCS4D01G213200 chr7D 311619009 311621156 2147 False 1701.5 3301 97.940000 843 2930 2 chr7D.!!$F1 2087
2 TraesCS4D01G213200 chr3B 371037557 371039708 2151 True 1664.5 3227 97.600500 843 2930 2 chr3B.!!$R3 2087
3 TraesCS4D01G213200 chr3B 363586468 363588541 2073 True 280.5 462 91.607000 842 2843 2 chr3B.!!$R2 2001
4 TraesCS4D01G213200 chr6A 197859176 197862067 2891 True 2377.5 3177 97.190000 1 2864 2 chr6A.!!$R1 2863
5 TraesCS4D01G213200 chr4B 149993379 149995240 1861 False 2861.0 2861 94.697000 1100 2930 1 chr4B.!!$F1 1830
6 TraesCS4D01G213200 chr4B 175307068 175308689 1621 True 2689.0 2689 96.558000 903 2528 1 chr4B.!!$R1 1625
7 TraesCS4D01G213200 chr4B 338502788 338503422 634 True 935.0 935 93.220000 2290 2930 1 chr4B.!!$R2 640
8 TraesCS4D01G213200 chr3A 361574848 361577707 2859 True 1633.0 2835 97.573667 1 2930 3 chr3A.!!$R1 2929
9 TraesCS4D01G213200 chr5B 209632176 209633853 1677 True 1421.5 2741 98.928000 843 2488 2 chr5B.!!$R1 1645
10 TraesCS4D01G213200 chr5B 277765866 277766489 623 False 898.0 898 92.633000 2301 2930 1 chr5B.!!$F1 629
11 TraesCS4D01G213200 chr5D 199084397 199085985 1588 False 2676.0 2676 97.107000 903 2488 1 chr5D.!!$F1 1585
12 TraesCS4D01G213200 chr5A 216692026 216693707 1681 False 1386.5 2671 98.521000 843 2488 2 chr5A.!!$F1 1645
13 TraesCS4D01G213200 chr2A 381732262 381733159 897 True 1557.0 1557 97.996000 1 897 1 chr2A.!!$R2 896
14 TraesCS4D01G213200 chr2A 381721509 381722309 800 True 1282.0 1282 95.567000 2125 2927 1 chr2A.!!$R1 802
15 TraesCS4D01G213200 chr7B 195987501 195988135 634 True 924.0 924 92.912000 2290 2930 1 chr7B.!!$R1 640

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
613 615 1.243902 ACGATTCGTGGCCATGTTTT 58.756 45.0 24.24 10.46 39.18 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2066 5.865552 CCAGTTTTCATCATGACCATCAAAC 59.134 40.0 0.0 3.84 0.0 2.93 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
369 371 8.617290 AAACTCCGAGTAAACAAAGAACATAT 57.383 30.769 0.26 0.00 0.00 1.78
613 615 1.243902 ACGATTCGTGGCCATGTTTT 58.756 45.000 24.24 10.46 39.18 2.43
763 765 9.722056 CTGTTTCTTAGCATTCAAATGGTATAC 57.278 33.333 13.63 10.57 45.50 1.47
897 899 6.265196 AGTTTGTGATGCTTCAGGTCAATAAA 59.735 34.615 1.91 0.00 30.85 1.40
898 900 5.627499 TGTGATGCTTCAGGTCAATAAAC 57.373 39.130 1.91 0.00 30.85 2.01
900 902 5.534278 TGTGATGCTTCAGGTCAATAAACAA 59.466 36.000 1.91 0.00 30.85 2.83
907 942 8.855110 TGCTTCAGGTCAATAAACAAATTTAGA 58.145 29.630 0.00 0.00 33.78 2.10
1094 1131 4.856801 CATGGGTCCCCTTCGCCG 62.857 72.222 5.13 0.00 36.94 6.46
1270 1308 6.421377 TCACATTGAATCTTCATACCGTTG 57.579 37.500 0.00 0.00 37.00 4.10
1365 1403 3.301835 CGAAGTGTTTGTGACGACTCAAG 60.302 47.826 2.94 0.00 32.45 3.02
1508 1547 5.528690 GTCAGTTTGAGCTGCCATTATATCA 59.471 40.000 0.00 0.00 36.49 2.15
1937 1978 6.692849 ACAAGATGGAATATGATCTAGGCA 57.307 37.500 0.00 0.00 0.00 4.75
2025 2066 2.118313 TGTTGACTGCATGATCAGGG 57.882 50.000 9.76 0.94 38.36 4.45
2256 2298 6.660521 AGCAATCTCCATTTGTTCAATCTGTA 59.339 34.615 0.00 0.00 0.00 2.74
2823 3004 8.482128 ACTTTGGAATATTTTTGTCCTTCACAA 58.518 29.630 0.00 0.00 43.68 3.33
2876 3057 6.531240 CAGGTTAAATGAGCATTGCGTAAAAT 59.469 34.615 2.38 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
369 371 6.364701 TCTTTCTTTGGAAGACAGAATTGGA 58.635 36.000 4.54 0.00 40.38 3.53
897 899 9.768662 ATTTGTTCTGAATGCTTCTAAATTTGT 57.231 25.926 0.00 0.00 0.00 2.83
907 942 7.664758 AGCTTCTAAATTTGTTCTGAATGCTT 58.335 30.769 0.00 0.00 0.00 3.91
973 1010 4.217118 ACCAATCTGCTCAAATTCAGTCAC 59.783 41.667 0.00 0.00 0.00 3.67
1094 1131 4.830600 TGGTTTGTAAAAGAGGGAACATCC 59.169 41.667 0.00 0.00 35.23 3.51
1270 1308 3.618690 ACAGAGAATAGGTTGGTGAGC 57.381 47.619 0.00 0.00 0.00 4.26
1508 1547 8.020819 CGGTGTGATTTGTAATACTTTGTTGAT 58.979 33.333 0.00 0.00 0.00 2.57
1937 1978 6.176183 GCATCCCTCAGTTATGTATGCTAAT 58.824 40.000 0.00 0.00 36.27 1.73
2025 2066 5.865552 CCAGTTTTCATCATGACCATCAAAC 59.134 40.000 0.00 3.84 0.00 2.93
2256 2298 7.454225 AGCTCTTTTCTCTTTACAACCTACAT 58.546 34.615 0.00 0.00 0.00 2.29
2799 2980 8.482128 ACTTGTGAAGGACAAAAATATTCCAAA 58.518 29.630 0.00 0.00 44.14 3.28
2800 2981 8.017418 ACTTGTGAAGGACAAAAATATTCCAA 57.983 30.769 0.00 0.00 44.14 3.53
2823 3004 3.323243 ACTACGCAATGCTCGTTTAACT 58.677 40.909 2.94 0.00 40.89 2.24
2830 3011 0.924090 GAAGGACTACGCAATGCTCG 59.076 55.000 2.94 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.