Multiple sequence alignment - TraesCS4A01G144600

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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 TraesCS4A01G144600 chr4A 100.000 3728 0 0 1 3728 245406559 245402832 0.000000e+00 6885.0
1 TraesCS4A01G144600 chr5A 97.802 3730 68 7 1 3726 489013859 489010140 0.000000e+00 6421.0
2 TraesCS4A01G144600 chr3D 89.433 3085 272 34 628 3682 220634961 220638021 0.000000e+00 3842.0
3 TraesCS4A01G144600 chr3D 90.926 1642 123 18 549 2173 204073336 204074968 0.000000e+00 2183.0
4 TraesCS4A01G144600 chr3D 89.279 1511 144 15 2177 3682 204088041 204089538 0.000000e+00 1877.0
5 TraesCS4A01G144600 chr3D 90.813 566 46 4 1 562 204072515 204073078 0.000000e+00 752.0
6 TraesCS4A01G144600 chr3D 90.283 566 48 5 1 562 220634082 220634644 0.000000e+00 734.0
7 TraesCS4A01G144600 chr3D 94.231 52 3 0 549 600 220634913 220634964 3.090000e-11 80.5
8 TraesCS4A01G144600 chr6A 92.802 2334 141 16 549 2856 180857153 180859485 0.000000e+00 3354.0
9 TraesCS4A01G144600 chr6A 89.952 826 64 7 2909 3728 180859495 180860307 0.000000e+00 1048.0
10 TraesCS4A01G144600 chr6A 92.229 489 35 2 1 486 180856435 180856923 0.000000e+00 689.0
11 TraesCS4A01G144600 chr6A 89.855 414 33 7 3317 3726 180860342 180860750 1.190000e-144 523.0
12 TraesCS4A01G144600 chr3B 92.433 2326 146 17 560 2856 496830430 496832754 0.000000e+00 3293.0
13 TraesCS4A01G144600 chr3B 90.191 836 60 13 2904 3728 496836599 496837423 0.000000e+00 1070.0
14 TraesCS4A01G144600 chr3B 90.615 309 22 6 2554 2856 496836288 496836595 1.610000e-108 403.0
15 TraesCS4A01G144600 chr3B 92.063 126 10 0 3603 3728 496835894 496836019 1.060000e-40 178.0
16 TraesCS4A01G144600 chr4B 91.628 2341 159 21 549 2856 224358096 224355760 0.000000e+00 3203.0
17 TraesCS4A01G144600 chr4B 92.000 375 22 5 4 370 224358778 224358404 1.530000e-143 520.0
18 TraesCS4A01G144600 chr4B 92.857 126 9 0 3603 3728 224354322 224354197 2.290000e-42 183.0
19 TraesCS4A01G144600 chr2B 92.974 1523 89 15 1352 2856 77373277 77371755 0.000000e+00 2204.0
20 TraesCS4A01G144600 chr2B 90.283 813 73 5 549 1356 77386606 77385795 0.000000e+00 1059.0
21 TraesCS4A01G144600 chr2B 89.234 836 64 13 2904 3728 77371751 77370931 0.000000e+00 1022.0
22 TraesCS4A01G144600 chr2B 90.508 453 32 8 4 448 77395968 77395519 4.150000e-164 588.0
23 TraesCS4A01G144600 chr2B 88.889 342 25 9 3317 3648 77370896 77370558 3.470000e-110 409.0
24 TraesCS4A01G144600 chr2D 88.399 1112 101 26 549 1640 257213949 257215052 0.000000e+00 1314.0
25 TraesCS4A01G144600 chr2D 88.639 801 79 11 1689 2480 257215055 257215852 0.000000e+00 965.0
26 TraesCS4A01G144600 chr2D 88.142 565 53 9 5 562 257202871 257203428 0.000000e+00 660.0
27 TraesCS4A01G144600 chr1B 87.320 1112 114 22 549 1640 386621333 386620229 0.000000e+00 1247.0
28 TraesCS4A01G144600 chr1B 88.639 801 81 9 1689 2480 86703928 86703129 0.000000e+00 966.0
29 TraesCS4A01G144600 chr1B 86.972 568 55 15 5 562 386622156 386621598 4.090000e-174 621.0
30 TraesCS4A01G144600 chr1B 86.620 568 56 14 5 562 86705871 86705314 8.850000e-171 610.0


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 TraesCS4A01G144600 chr4A 245402832 245406559 3727 True 6885.000000 6885 100.000000 1 3728 1 chr4A.!!$R1 3727
1 TraesCS4A01G144600 chr5A 489010140 489013859 3719 True 6421.000000 6421 97.802000 1 3726 1 chr5A.!!$R1 3725
2 TraesCS4A01G144600 chr3D 204088041 204089538 1497 False 1877.000000 1877 89.279000 2177 3682 1 chr3D.!!$F1 1505
3 TraesCS4A01G144600 chr3D 220634082 220638021 3939 False 1552.166667 3842 91.315667 1 3682 3 chr3D.!!$F3 3681
4 TraesCS4A01G144600 chr3D 204072515 204074968 2453 False 1467.500000 2183 90.869500 1 2173 2 chr3D.!!$F2 2172
5 TraesCS4A01G144600 chr6A 180856435 180860750 4315 False 1403.500000 3354 91.209500 1 3728 4 chr6A.!!$F1 3727
6 TraesCS4A01G144600 chr3B 496830430 496837423 6993 False 1236.000000 3293 91.325500 560 3728 4 chr3B.!!$F1 3168
7 TraesCS4A01G144600 chr4B 224354197 224358778 4581 True 1302.000000 3203 92.161667 4 3728 3 chr4B.!!$R1 3724
8 TraesCS4A01G144600 chr2B 77370558 77373277 2719 True 1211.666667 2204 90.365667 1352 3728 3 chr2B.!!$R3 2376
9 TraesCS4A01G144600 chr2B 77385795 77386606 811 True 1059.000000 1059 90.283000 549 1356 1 chr2B.!!$R1 807
10 TraesCS4A01G144600 chr2D 257213949 257215852 1903 False 1139.500000 1314 88.519000 549 2480 2 chr2D.!!$F2 1931
11 TraesCS4A01G144600 chr2D 257202871 257203428 557 False 660.000000 660 88.142000 5 562 1 chr2D.!!$F1 557
12 TraesCS4A01G144600 chr1B 386620229 386622156 1927 True 934.000000 1247 87.146000 5 1640 2 chr1B.!!$R2 1635
13 TraesCS4A01G144600 chr1B 86703129 86705871 2742 True 788.000000 966 87.629500 5 2480 2 chr1B.!!$R1 2475

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
805 1151 0.524862 GTGTTGCAGATCTTGGGCTG 59.475 55.000 0.00 0.00 35.28 4.85 F
1876 2238 1.680735 CTGCAAACCTGGTTAGTGCAA 59.319 47.619 28.91 17.91 38.32 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2640 3032 1.355381 AGCAATGTCAACCATCTCCCA 59.645 47.619 0.00 0.00 31.75 4.37 R
3003 7244 3.251004 AGCAGTTAACTTGCTCGGAAAAG 59.749 43.478 20.13 2.76 32.98 2.27 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
711 1054 6.103997 TGTGGTCGTCCTATTTTATTCTCAC 58.896 40.000 0.00 0.00 34.23 3.51
805 1151 0.524862 GTGTTGCAGATCTTGGGCTG 59.475 55.000 0.00 0.00 35.28 4.85
838 1184 5.049680 TGAATTTAGTTTGTTCGAGAGCCAC 60.050 40.000 0.00 0.00 0.00 5.01
941 1287 3.007831 TGTGGAATCAAAATCAAAGGGGC 59.992 43.478 0.00 0.00 0.00 5.80
1107 1460 4.907188 TGATGATGATTTTGTTTTGCGC 57.093 36.364 0.00 0.00 0.00 6.09
1468 1825 8.275040 AGTTGATGCTAAATATCTGGTTACCTT 58.725 33.333 2.07 0.00 0.00 3.50
1876 2238 1.680735 CTGCAAACCTGGTTAGTGCAA 59.319 47.619 28.91 17.91 38.32 4.08
1901 2266 5.562501 GCCATTTTTGTTGCCAATTTACCTG 60.563 40.000 0.00 0.00 0.00 4.00
1902 2267 5.048852 CCATTTTTGTTGCCAATTTACCTGG 60.049 40.000 0.00 0.00 36.99 4.45
2079 2450 3.131223 CCATGACTCGTGGAGATACACTT 59.869 47.826 11.49 0.00 42.73 3.16
2453 2828 8.134895 GCGATGTAATTTTTCCTGGATCATTTA 58.865 33.333 0.00 0.00 0.00 1.40
2542 2930 8.413229 AGTAAAATGCTAACTGACACAACAATT 58.587 29.630 0.00 0.00 0.00 2.32
2827 7066 5.234752 TGTGTAGTTTACATTCGTGCATCT 58.765 37.500 0.00 0.00 41.34 2.90
2917 7156 5.284079 AGCAAAGCACACATTGAAGTTAAG 58.716 37.500 0.00 0.00 0.00 1.85
2964 7204 5.042463 TCATGTTGTGGAGGAAGTTAACA 57.958 39.130 8.61 0.00 33.26 2.41
3517 8231 6.208007 ACCTACATTTTGTAAAGGTGCTAACC 59.792 38.462 2.12 0.00 37.79 2.85
3682 8905 8.789825 TGCATGATTTGTTTTTATAGCCAAAT 57.210 26.923 0.00 0.00 39.51 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
471 486 9.926751 CGCAGGATATAATGATAAAAGCATTAG 57.073 33.333 4.23 0.00 40.39 1.73
711 1054 6.484364 AAAATATAGAAATGGGCCTTGTGG 57.516 37.500 4.53 0.00 0.00 4.17
805 1151 3.751698 ACAAACTAAATTCAGGCTCGTCC 59.248 43.478 0.00 0.00 0.00 4.79
838 1184 2.414481 CTGAATTTCTGGCGTCTCACAG 59.586 50.000 0.00 0.00 36.07 3.66
941 1287 1.560923 CTTCGGGATAGCACAAGTCG 58.439 55.000 0.00 0.00 0.00 4.18
1074 1421 6.600246 AAATCATCATCATCACTCAGAACG 57.400 37.500 0.00 0.00 0.00 3.95
1107 1460 2.128035 GTGAACACTGTTCTCTCACCG 58.872 52.381 20.18 0.00 32.10 4.94
1334 1690 9.261318 GAAGTAGCACAAAAACAAAAATGAAAC 57.739 29.630 0.00 0.00 0.00 2.78
1406 1763 4.074970 CAGTTGGAGGAGTGCACTTAAAT 58.925 43.478 22.65 7.29 0.00 1.40
1468 1825 1.455849 CAGCCAGTGGGACCAAAGA 59.544 57.895 12.15 0.00 35.59 2.52
1901 2266 4.392138 GCAGTTTAGATGACCACACTAACC 59.608 45.833 0.00 0.00 0.00 2.85
1902 2267 5.120830 CAGCAGTTTAGATGACCACACTAAC 59.879 44.000 0.00 0.00 0.00 2.34
2033 2404 3.657398 TCCAGGGACTCACGATACTTA 57.343 47.619 0.00 0.00 34.60 2.24
2079 2450 2.223745 GTTCCTTGAAAGGTTACGCCA 58.776 47.619 8.91 0.00 46.54 5.69
2542 2930 5.466058 CAGAATGTGGCTGCATAAAAACAAA 59.534 36.000 0.50 0.00 0.00 2.83
2640 3032 1.355381 AGCAATGTCAACCATCTCCCA 59.645 47.619 0.00 0.00 31.75 4.37
2827 7066 6.127054 ACAACATCCTCAATAGCAGCTAACTA 60.127 38.462 6.13 0.00 0.00 2.24
2917 7156 6.782150 AGTTACCATTTTTAAGATAGTGCGC 58.218 36.000 0.00 0.00 0.00 6.09
3003 7244 3.251004 AGCAGTTAACTTGCTCGGAAAAG 59.749 43.478 20.13 2.76 32.98 2.27
3419 7931 9.814899 AACATCTTGAGACAGAGAAGTTATATG 57.185 33.333 0.00 0.00 33.54 1.78
3682 8905 6.403855 GGCAAGTTAACTTCACTGTACAAACA 60.404 38.462 18.00 0.00 33.11 2.83


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

AutoCloner maintained by Alex Coulton.