Multiple sequence alignment - TraesCS7A01G047600

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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 TraesCS7A01G047600 chr7A 100.000 2519 0 0 1 2519 21597760 21595242 0.000000e+00 4652.0
1 TraesCS7A01G047600 chr7A 97.589 2530 43 4 1 2519 21986573 21984051 0.000000e+00 4318.0
2 TraesCS7A01G047600 chr7A 94.424 1112 54 5 390 1494 21959082 21957972 0.000000e+00 1703.0
3 TraesCS7A01G047600 chr7A 90.805 1131 64 14 390 1494 21712690 21711574 0.000000e+00 1476.0
4 TraesCS7A01G047600 chr7A 82.056 574 70 18 1103 1652 21609282 21609846 2.280000e-125 459.0
5 TraesCS7A01G047600 chr7A 81.707 574 73 17 1103 1652 22017950 22018515 1.370000e-122 449.0
6 TraesCS7A01G047600 chr7A 89.458 332 23 9 390 713 21561374 21561047 2.330000e-110 409.0
7 TraesCS7A01G047600 chr7A 84.915 411 41 9 1 392 21713162 21712754 1.820000e-106 396.0
8 TraesCS7A01G047600 chr7A 80.263 304 33 15 789 1081 22017566 22017853 1.180000e-48 204.0
9 TraesCS7A01G047600 chr7A 82.305 243 23 7 169 392 21959387 21959146 2.560000e-45 193.0
10 TraesCS7A01G047600 chr7A 83.854 192 11 9 775 958 21608910 21609089 5.570000e-37 165.0
11 TraesCS7A01G047600 chr4A 88.410 1346 91 23 434 1756 712733793 712735096 0.000000e+00 1561.0
12 TraesCS7A01G047600 chr4A 87.741 1346 99 24 434 1756 712764452 712765754 0.000000e+00 1511.0
13 TraesCS7A01G047600 chr4A 92.628 624 30 7 872 1479 669044103 669044726 0.000000e+00 883.0
14 TraesCS7A01G047600 chr4A 85.484 434 45 15 390 817 669043683 669044104 1.070000e-118 436.0
15 TraesCS7A01G047600 chr4A 88.379 327 30 4 69 392 712733274 712733595 1.090000e-103 387.0
16 TraesCS7A01G047600 chr4A 88.379 327 30 4 69 392 712763942 712764263 1.090000e-103 387.0
17 TraesCS7A01G047600 chr4A 88.037 326 32 4 69 392 669043299 669043619 1.830000e-101 379.0
18 TraesCS7A01G047600 chr4A 88.106 227 20 7 1795 2017 712735097 712735320 1.920000e-66 263.0
19 TraesCS7A01G047600 chr4A 88.106 227 20 7 1795 2017 712765755 712765978 1.920000e-66 263.0
20 TraesCS7A01G047600 chr4A 85.714 84 8 3 498 581 712591804 712591883 4.460000e-13 86.1
21 TraesCS7A01G047600 chr7D 87.477 1102 71 23 390 1479 21121651 21122697 0.000000e+00 1208.0
22 TraesCS7A01G047600 chr7D 87.198 1117 76 23 390 1494 21485964 21484903 0.000000e+00 1208.0
23 TraesCS7A01G047600 chr6A 97.753 89 2 0 2431 2519 298969534 298969622 1.210000e-33 154.0
24 TraesCS7A01G047600 chr6A 93.023 86 6 0 2432 2517 539160668 539160753 2.630000e-25 126.0
25 TraesCS7A01G047600 chr2A 93.258 89 6 0 2431 2519 66094646 66094734 5.650000e-27 132.0
26 TraesCS7A01G047600 chr2A 92.135 89 7 0 2431 2519 66089254 66089342 2.630000e-25 126.0
27 TraesCS7A01G047600 chr5A 92.222 90 5 2 2431 2519 447545055 447545143 2.630000e-25 126.0
28 TraesCS7A01G047600 chr5A 91.209 91 6 2 2430 2519 92437138 92437049 3.400000e-24 122.0
29 TraesCS7A01G047600 chr4D 91.111 90 6 2 2431 2519 47982124 47982036 1.220000e-23 121.0
30 TraesCS7A01G047600 chr6B 89.474 95 8 2 2426 2519 713382737 713382830 4.400000e-23 119.0


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 TraesCS7A01G047600 chr7A 21595242 21597760 2518 True 4652.000000 4652 100.000000 1 2519 1 chr7A.!!$R2 2518
1 TraesCS7A01G047600 chr7A 21984051 21986573 2522 True 4318.000000 4318 97.589000 1 2519 1 chr7A.!!$R3 2518
2 TraesCS7A01G047600 chr7A 21957972 21959387 1415 True 948.000000 1703 88.364500 169 1494 2 chr7A.!!$R5 1325
3 TraesCS7A01G047600 chr7A 21711574 21713162 1588 True 936.000000 1476 87.860000 1 1494 2 chr7A.!!$R4 1493
4 TraesCS7A01G047600 chr7A 22017566 22018515 949 False 326.500000 449 80.985000 789 1652 2 chr7A.!!$F2 863
5 TraesCS7A01G047600 chr7A 21608910 21609846 936 False 312.000000 459 82.955000 775 1652 2 chr7A.!!$F1 877
6 TraesCS7A01G047600 chr4A 712733274 712735320 2046 False 737.000000 1561 88.298333 69 2017 3 chr4A.!!$F3 1948
7 TraesCS7A01G047600 chr4A 712763942 712765978 2036 False 720.333333 1511 88.075333 69 2017 3 chr4A.!!$F4 1948
8 TraesCS7A01G047600 chr4A 669043299 669044726 1427 False 566.000000 883 88.716333 69 1479 3 chr4A.!!$F2 1410
9 TraesCS7A01G047600 chr7D 21121651 21122697 1046 False 1208.000000 1208 87.477000 390 1479 1 chr7D.!!$F1 1089
10 TraesCS7A01G047600 chr7D 21484903 21485964 1061 True 1208.000000 1208 87.198000 390 1494 1 chr7D.!!$R1 1104

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
706 924 0.533032 GGAGACAAAGACGGAGAGGG 59.467 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1979 0.251354 AGCGCATCATCTTGGTCAGT 59.749 50.0 11.47 0.0 0.0 3.41 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
583 779 7.174599 ACTTGATCAACCAGAGAAATCTTTGAG 59.825 37.037 3.38 0.00 30.38 3.02
706 924 0.533032 GGAGACAAAGACGGAGAGGG 59.467 60.000 0.00 0.00 0.00 4.30
858 1093 4.570663 CGGCTCGGCTAGGGTTCG 62.571 72.222 0.00 0.00 0.00 3.95
890 1129 9.914131 CTTTCCATGTTTATATAGATCGAGACA 57.086 33.333 0.00 0.00 0.00 3.41
1143 1496 1.887198 GAGGGTGACGAGTCAGAGAAA 59.113 52.381 6.13 0.00 40.75 2.52
1374 1727 1.678970 GGAAAGGAAGCGTGCCCAT 60.679 57.895 0.00 0.00 0.00 4.00
1498 1851 4.019174 TGAGGAGCTCATTTCCAAATTCC 58.981 43.478 17.19 0.00 35.39 3.01
1499 1852 4.019174 GAGGAGCTCATTTCCAAATTCCA 58.981 43.478 17.19 0.00 37.18 3.53
1500 1853 4.419282 AGGAGCTCATTTCCAAATTCCAA 58.581 39.130 17.19 0.00 37.18 3.53
1692 2060 2.235650 CTGCTTGAGGAAGACTGGATGA 59.764 50.000 0.00 0.00 0.00 2.92
1943 2314 4.530710 TTACAACCCAGCTGTACTACTG 57.469 45.455 13.81 8.29 0.00 2.74
1946 2317 3.899360 ACAACCCAGCTGTACTACTGTTA 59.101 43.478 13.81 0.00 31.76 2.41
1972 2343 2.747065 TGCTGCTGCGCTATTGCA 60.747 55.556 9.73 11.70 43.95 4.08
2072 2443 6.733145 TCTCTGTCTGTTGATGATATTCGAG 58.267 40.000 0.00 0.00 0.00 4.04
2086 2457 7.946655 TGATATTCGAGCTAAAATGAATCGT 57.053 32.000 0.00 0.00 35.05 3.73
2103 2474 5.065090 TGAATCGTCCTGTTCTGCATTTATG 59.935 40.000 0.00 0.00 0.00 1.90
2120 2493 6.581370 CATTTATGCGGTAAAGTATCTGTCG 58.419 40.000 1.45 0.00 35.83 4.35
2182 2555 2.293399 CCTACTTCTGTGTTGTTTGGGC 59.707 50.000 0.00 0.00 0.00 5.36
2183 2556 0.738389 ACTTCTGTGTTGTTTGGGCG 59.262 50.000 0.00 0.00 0.00 6.13
2185 2558 0.681564 TTCTGTGTTGTTTGGGCGGT 60.682 50.000 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.313690 TGTACATGGCTGCGTTATATCG 58.686 45.455 0.00 0.0 0.00 2.92
102 103 4.139859 TCGGTGTTTGTCTGAAAAGGTA 57.860 40.909 0.00 0.0 0.00 3.08
815 1050 0.538057 CCCTTCTTTGCTCTGCACCA 60.538 55.000 0.00 0.0 38.71 4.17
1143 1496 1.264749 TGTCAATCGCAGCTACCCCT 61.265 55.000 0.00 0.0 0.00 4.79
1374 1727 3.181466 TGAAAAGCTCTACACTGTCAGCA 60.181 43.478 13.20 0.0 34.08 4.41
1479 1832 4.021192 TGTTGGAATTTGGAAATGAGCTCC 60.021 41.667 12.15 0.0 0.00 4.70
1496 1849 0.183971 TTCGCCTTTTCCCTGTTGGA 59.816 50.000 0.00 0.0 43.18 3.53
1497 1850 1.067635 CATTCGCCTTTTCCCTGTTGG 60.068 52.381 0.00 0.0 0.00 3.77
1498 1851 1.885887 TCATTCGCCTTTTCCCTGTTG 59.114 47.619 0.00 0.0 0.00 3.33
1499 1852 2.162681 CTCATTCGCCTTTTCCCTGTT 58.837 47.619 0.00 0.0 0.00 3.16
1500 1853 1.073923 ACTCATTCGCCTTTTCCCTGT 59.926 47.619 0.00 0.0 0.00 4.00
1611 1979 0.251354 AGCGCATCATCTTGGTCAGT 59.749 50.000 11.47 0.0 0.00 3.41
1692 2060 1.202976 AGCAAGCTTGATCCCTTGTGT 60.203 47.619 30.39 0.0 40.34 3.72
1943 2314 0.588252 CAGCAGCACCACACTGTAAC 59.412 55.000 0.00 0.0 37.47 2.50
1946 2317 2.903855 GCAGCAGCACCACACTGT 60.904 61.111 0.00 0.0 41.58 3.55
2072 2443 5.563842 CAGAACAGGACGATTCATTTTAGC 58.436 41.667 0.00 0.0 0.00 3.09
2103 2474 1.852895 CAGCGACAGATACTTTACCGC 59.147 52.381 0.00 0.0 41.22 5.68
2105 2476 4.373348 AGACAGCGACAGATACTTTACC 57.627 45.455 0.00 0.0 0.00 2.85
2116 2489 2.926586 GCACACAAGATAGACAGCGACA 60.927 50.000 0.00 0.0 0.00 4.35
2120 2493 2.159599 GCAAGCACACAAGATAGACAGC 60.160 50.000 0.00 0.0 0.00 4.40
2182 2555 5.348164 AGAAAAAGATGGACAACAAAACCG 58.652 37.500 0.00 0.0 0.00 4.44
2183 2556 7.333174 TCAAAGAAAAAGATGGACAACAAAACC 59.667 33.333 0.00 0.0 0.00 3.27
2185 2558 8.093927 ACTCAAAGAAAAAGATGGACAACAAAA 58.906 29.630 0.00 0.0 0.00 2.44
2383 2756 8.573885 ACTATTTCTTTACCAAAGGCAAGTTAC 58.426 33.333 0.00 0.0 39.01 2.50
2453 2826 1.337387 CTACAAGCTACGCCCTAGACC 59.663 57.143 0.00 0.0 0.00 3.85


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

AutoCloner maintained by Alex Coulton.