Multiple sequence alignment - TraesCS7A01G079400

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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 TraesCS7A01G079400 chr7A 100.000 2409 0 0 1 2409 45068527 45066119 0.000000e+00 4449.0
1 TraesCS7A01G079400 chr7A 98.921 2410 23 3 1 2409 45021710 45019303 0.000000e+00 4303.0
2 TraesCS7A01G079400 chr7A 97.901 953 19 1 1458 2409 41020042 41020994 0.000000e+00 1648.0
3 TraesCS7A01G079400 chr7A 97.077 958 25 3 1454 2409 45372615 45371659 0.000000e+00 1611.0
4 TraesCS7A01G079400 chr7A 97.254 947 25 1 1464 2409 45310769 45311715 0.000000e+00 1604.0
5 TraesCS7A01G079400 chr7A 95.469 949 27 5 1462 2409 45273103 45272170 0.000000e+00 1500.0
6 TraesCS7A01G079400 chr7A 96.648 716 22 2 1694 2408 31643941 31643227 0.000000e+00 1188.0
7 TraesCS7A01G079400 chr7A 87.846 650 56 16 818 1463 43439348 43438718 0.000000e+00 741.0
8 TraesCS7A01G079400 chr7A 87.846 650 56 16 818 1463 43458024 43457394 0.000000e+00 741.0
9 TraesCS7A01G079400 chr7A 95.216 439 11 2 716 1145 44885052 44884615 0.000000e+00 686.0
10 TraesCS7A01G079400 chr7A 85.540 657 64 16 818 1463 45602868 45602232 0.000000e+00 658.0
11 TraesCS7A01G079400 chr7A 85.258 658 66 16 818 1463 45574167 45573529 0.000000e+00 649.0
12 TraesCS7A01G079400 chr7A 85.191 655 72 16 818 1463 45593857 45593219 0.000000e+00 649.0
13 TraesCS7A01G079400 chr7A 97.640 339 8 0 76 414 44885391 44885053 1.240000e-162 582.0
14 TraesCS7A01G079400 chr7A 96.273 322 12 0 1143 1464 44877557 44877236 1.640000e-146 529.0
15 TraesCS7A01G079400 chr7A 98.333 240 4 0 1466 1705 31644491 31644252 2.860000e-114 422.0
16 TraesCS7A01G079400 chr7A 84.615 312 26 8 817 1117 45186373 45186073 8.420000e-75 291.0
17 TraesCS7A01G079400 chr7A 88.966 145 10 2 272 413 45186568 45186427 8.850000e-40 174.0
18 TraesCS7A01G079400 chr7A 94.118 51 3 0 713 763 43260033 43259983 7.140000e-11 78.7
19 TraesCS7A01G079400 chr7A 96.875 32 1 0 793 824 41021460 41021429 1.000000e-03 54.7
20 TraesCS7A01G079400 chr4A 94.118 646 28 4 818 1463 651986045 651985410 0.000000e+00 974.0
21 TraesCS7A01G079400 chr4A 92.628 312 20 3 407 715 628560847 628561158 1.700000e-121 446.0
22 TraesCS7A01G079400 chr4A 97.934 242 5 0 1464 1705 714595418 714595659 1.030000e-113 420.0
23 TraesCS7A01G079400 chr4A 87.463 335 36 6 82 411 651638932 651638599 4.860000e-102 381.0
24 TraesCS7A01G079400 chr4A 88.163 245 22 4 818 1059 651638543 651638303 3.920000e-73 285.0
25 TraesCS7A01G079400 chr4A 96.078 51 1 1 713 763 651986101 651986052 5.520000e-12 82.4
26 TraesCS7A01G079400 chr4A 96.078 51 1 1 713 763 652002303 652002254 5.520000e-12 82.4
27 TraesCS7A01G079400 chr4A 97.222 36 1 0 1462 1497 666818919 666818884 7.190000e-06 62.1
28 TraesCS7A01G079400 chr7D 84.985 646 62 8 818 1459 43384707 43384093 7.310000e-175 623.0
29 TraesCS7A01G079400 chr7D 87.625 501 39 18 969 1463 43430106 43429623 5.820000e-156 560.0
30 TraesCS7A01G079400 chr7D 88.393 336 33 6 82 411 43385099 43384764 1.340000e-107 399.0
31 TraesCS7A01G079400 chr7D 81.093 439 49 16 1 411 43430714 43430282 1.070000e-83 320.0
32 TraesCS7A01G079400 chr7D 91.045 67 1 2 758 819 185138062 185137996 4.270000e-13 86.1
33 TraesCS7A01G079400 chr5A 93.528 309 17 3 412 718 36016528 36016835 7.850000e-125 457.0
34 TraesCS7A01G079400 chr5A 92.834 307 20 2 411 715 487399245 487398939 6.110000e-121 444.0
35 TraesCS7A01G079400 chr3A 92.212 321 20 4 407 723 545355081 545354762 1.310000e-122 449.0
36 TraesCS7A01G079400 chr3A 92.532 308 21 2 409 714 713982634 713982327 7.910000e-120 440.0
37 TraesCS7A01G079400 chr3A 86.275 255 31 4 1460 1713 687926877 687926626 8.480000e-70 274.0
38 TraesCS7A01G079400 chr4D 92.834 307 20 2 411 715 444466644 444466338 6.110000e-121 444.0
39 TraesCS7A01G079400 chr6B 92.810 306 20 2 412 715 47429698 47430003 2.200000e-120 442.0
40 TraesCS7A01G079400 chr6B 84.375 64 5 5 760 820 504603096 504603157 9.300000e-05 58.4
41 TraesCS7A01G079400 chr3B 92.233 309 22 2 410 716 803634561 803634253 1.020000e-118 436.0
42 TraesCS7A01G079400 chr1B 80.086 467 72 13 1698 2144 20386090 20386555 6.420000e-86 327.0
43 TraesCS7A01G079400 chr7B 77.043 257 45 9 1464 1713 652736303 652736054 4.180000e-28 135.0
44 TraesCS7A01G079400 chr7B 76.824 233 40 9 1488 1713 652776540 652776315 4.210000e-23 119.0
45 TraesCS7A01G079400 chr7B 75.107 233 44 9 1488 1713 652830467 652830242 1.970000e-16 97.1
46 TraesCS7A01G079400 chr6D 95.000 60 2 1 760 818 466735551 466735610 2.550000e-15 93.5
47 TraesCS7A01G079400 chr2B 90.625 64 4 2 762 823 291851477 291851540 1.530000e-12 84.2
48 TraesCS7A01G079400 chr1A 89.062 64 4 3 760 820 164458518 164458455 2.570000e-10 76.8
49 TraesCS7A01G079400 chr1A 86.154 65 3 5 761 820 399497137 399497074 5.560000e-07 65.8
50 TraesCS7A01G079400 chr1A 89.583 48 5 0 744 791 435966313 435966266 7.190000e-06 62.1
51 TraesCS7A01G079400 chr5B 90.000 50 4 1 1458 1507 475345646 475345598 2.000000e-06 63.9


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 TraesCS7A01G079400 chr7A 45066119 45068527 2408 True 4449.0 4449 100.0000 1 2409 1 chr7A.!!$R7 2408
1 TraesCS7A01G079400 chr7A 45019303 45021710 2407 True 4303.0 4303 98.9210 1 2409 1 chr7A.!!$R6 2408
2 TraesCS7A01G079400 chr7A 41020042 41020994 952 False 1648.0 1648 97.9010 1458 2409 1 chr7A.!!$F1 951
3 TraesCS7A01G079400 chr7A 45371659 45372615 956 True 1611.0 1611 97.0770 1454 2409 1 chr7A.!!$R9 955
4 TraesCS7A01G079400 chr7A 45310769 45311715 946 False 1604.0 1604 97.2540 1464 2409 1 chr7A.!!$F2 945
5 TraesCS7A01G079400 chr7A 45272170 45273103 933 True 1500.0 1500 95.4690 1462 2409 1 chr7A.!!$R8 947
6 TraesCS7A01G079400 chr7A 31643227 31644491 1264 True 805.0 1188 97.4905 1466 2408 2 chr7A.!!$R13 942
7 TraesCS7A01G079400 chr7A 43438718 43439348 630 True 741.0 741 87.8460 818 1463 1 chr7A.!!$R3 645
8 TraesCS7A01G079400 chr7A 43457394 43458024 630 True 741.0 741 87.8460 818 1463 1 chr7A.!!$R4 645
9 TraesCS7A01G079400 chr7A 45602232 45602868 636 True 658.0 658 85.5400 818 1463 1 chr7A.!!$R12 645
10 TraesCS7A01G079400 chr7A 45573529 45574167 638 True 649.0 649 85.2580 818 1463 1 chr7A.!!$R10 645
11 TraesCS7A01G079400 chr7A 45593219 45593857 638 True 649.0 649 85.1910 818 1463 1 chr7A.!!$R11 645
12 TraesCS7A01G079400 chr7A 44884615 44885391 776 True 634.0 686 96.4280 76 1145 2 chr7A.!!$R14 1069
13 TraesCS7A01G079400 chr4A 651985410 651986101 691 True 528.2 974 95.0980 713 1463 2 chr4A.!!$R4 750
14 TraesCS7A01G079400 chr4A 651638303 651638932 629 True 333.0 381 87.8130 82 1059 2 chr4A.!!$R3 977
15 TraesCS7A01G079400 chr7D 43384093 43385099 1006 True 511.0 623 86.6890 82 1459 2 chr7D.!!$R2 1377
16 TraesCS7A01G079400 chr7D 43429623 43430714 1091 True 440.0 560 84.3590 1 1463 2 chr7D.!!$R3 1462

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
1204 1307 2.159366 CGTAGATGTGGTGACAGAGGTC 60.159 54.545 0.0 0.0 44.46 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2766 7.533289 TTGTTATGCATGATGGATGATTCAT 57.467 32.0 10.16 0.0 33.31 2.57 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
1204 1307 2.159366 CGTAGATGTGGTGACAGAGGTC 60.159 54.545 0.00 0.00 44.46 3.85
1780 2207 8.887036 ATCAAAATGTGGTTCCTTAAGTTTTC 57.113 30.769 0.97 0.00 0.00 2.29
1816 2243 5.461526 CATGCATGATTGATCAATCTCACC 58.538 41.667 36.15 25.08 45.55 4.02
1992 2419 4.039488 ACCTGATTTCTTTTCTTGCATGCA 59.961 37.500 18.46 18.46 0.00 3.96
2338 2766 4.411869 TGGACACCCATATTCAGAATGCTA 59.588 41.667 5.85 0.00 37.58 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1007 1071 3.066342 GGCTAGTAGCATCGTGTAGAACA 59.934 47.826 23.24 0.00 44.75 3.18
1403 1506 1.446966 GCCTGCTCTCCGTTCAGTC 60.447 63.158 0.00 0.00 0.00 3.51
1780 2207 8.637281 TCAATCATGCATGCTAACTTAAAATG 57.363 30.769 22.25 10.63 0.00 2.32
1816 2243 0.393944 ATGTCCAGAGCATGCAGTGG 60.394 55.000 25.36 25.36 0.00 4.00
1992 2419 9.995003 GATACAATCTCCTCATATCAGAACTTT 57.005 33.333 0.00 0.00 0.00 2.66
2237 2665 9.405587 TGCTTAGTTAACAATTTGCAAGATAAC 57.594 29.630 8.61 4.42 0.00 1.89
2338 2766 7.533289 TTGTTATGCATGATGGATGATTCAT 57.467 32.000 10.16 0.00 33.31 2.57


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

AutoCloner maintained by Alex Coulton.