Multiple sequence alignment - TraesCS7B01G255100

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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 TraesCS7B01G255100 chr7B 100.000 4578 0 0 1 4578 472331570 472326993 0.000000e+00 8455.0
1 TraesCS7B01G255100 chr7B 99.528 3177 10 3 1403 4578 472397037 472393865 0.000000e+00 5779.0
2 TraesCS7B01G255100 chr7B 95.353 2109 63 6 1881 3988 651341432 651339358 0.000000e+00 3319.0
3 TraesCS7B01G255100 chr7B 81.276 1442 234 24 2064 3488 651408917 651410339 0.000000e+00 1134.0
4 TraesCS7B01G255100 chr7B 95.994 649 24 2 2544 3191 651443712 651444359 0.000000e+00 1053.0
5 TraesCS7B01G255100 chr7B 79.840 1503 247 27 1930 3401 651454045 651452568 0.000000e+00 1046.0
6 TraesCS7B01G255100 chr7B 79.439 1498 249 27 1930 3396 651336460 651337929 0.000000e+00 1005.0
7 TraesCS7B01G255100 chr7B 98.095 525 10 0 4054 4578 651450505 651451029 0.000000e+00 915.0
8 TraesCS7B01G255100 chr7B 95.194 541 18 2 3187 3727 651445085 651445617 0.000000e+00 848.0
9 TraesCS7B01G255100 chr7B 89.708 651 47 7 764 1405 701324933 701325572 0.000000e+00 813.0
10 TraesCS7B01G255100 chr7B 95.434 438 16 1 1419 1852 651341866 651341429 0.000000e+00 695.0
11 TraesCS7B01G255100 chr7B 88.694 513 36 5 24 535 701319367 701319858 1.410000e-169 606.0
12 TraesCS7B01G255100 chr7B 94.611 334 15 2 3722 4055 651450089 651450419 8.780000e-142 514.0
13 TraesCS7B01G255100 chr7B 87.277 393 46 4 1014 1403 701319757 701319366 3.250000e-121 446.0
14 TraesCS7B01G255100 chr7B 86.189 391 52 2 1014 1402 472331157 472331547 5.480000e-114 422.0
15 TraesCS7B01G255100 chr7B 94.872 234 12 0 529 762 701324105 701324338 2.600000e-97 366.0
16 TraesCS7B01G255100 chr7B 89.200 250 12 4 4054 4290 651339242 651338995 9.630000e-77 298.0
17 TraesCS7B01G255100 chr7B 92.529 174 10 1 4319 4492 651338618 651338448 3.540000e-61 246.0
18 TraesCS7B01G255100 chr5B 97.262 1388 27 4 23 1402 420375178 420373794 0.000000e+00 2342.0
19 TraesCS7B01G255100 chr5B 96.472 1247 32 6 164 1402 529227398 529228640 0.000000e+00 2049.0
20 TraesCS7B01G255100 chr5B 88.354 1391 95 19 24 1400 592856647 592855310 0.000000e+00 1609.0
21 TraesCS7B01G255100 chr5B 86.957 391 48 3 24 414 420373794 420374181 1.960000e-118 436.0
22 TraesCS7B01G255100 chr5B 86.076 395 52 3 1014 1405 592856257 592856651 5.480000e-114 422.0
23 TraesCS7B01G255100 chr1B 96.900 1387 32 4 23 1400 593493799 593492415 0.000000e+00 2313.0
24 TraesCS7B01G255100 chr1B 86.701 391 50 2 1014 1402 593493408 593493798 2.530000e-117 433.0
25 TraesCS7B01G255100 chr7D 95.851 1398 50 2 2657 4054 583986488 583985099 0.000000e+00 2254.0
26 TraesCS7B01G255100 chr7D 86.005 2015 255 14 1404 3402 583479191 583477188 0.000000e+00 2134.0
27 TraesCS7B01G255100 chr7D 90.860 744 67 1 2637 3380 583965477 583964735 0.000000e+00 996.0
28 TraesCS7B01G255100 chr7D 81.012 1206 195 21 2304 3493 583994676 583993489 0.000000e+00 928.0
29 TraesCS7B01G255100 chr7D 96.964 527 11 3 4054 4578 583985013 583984490 0.000000e+00 880.0
30 TraesCS7B01G255100 chr7D 82.692 728 96 12 1971 2680 583973408 583974123 1.810000e-173 619.0
31 TraesCS7B01G255100 chr7D 85.569 589 51 13 1930 2509 583989146 583988583 1.840000e-163 586.0
32 TraesCS7B01G255100 chr7D 87.941 340 24 9 4055 4390 583870699 583870373 7.180000e-103 385.0
33 TraesCS7B01G255100 chr7D 94.578 166 8 1 1473 1638 583989673 583989509 5.880000e-64 255.0
34 TraesCS7B01G255100 chr7A 85.990 2020 253 11 1403 3402 675115557 675113548 0.000000e+00 2135.0
35 TraesCS7B01G255100 chr7A 98.182 55 1 0 4054 4108 124795692 124795746 3.770000e-16 97.1
36 TraesCS7B01G255100 chr5A 94.432 1383 56 13 24 1402 687295449 687294084 0.000000e+00 2108.0
37 TraesCS7B01G255100 chr5A 96.644 1043 22 5 370 1402 652659972 652658933 0.000000e+00 1720.0
38 TraesCS7B01G255100 chr5A 93.333 345 23 0 24 368 652660281 652659937 1.140000e-140 510.0
39 TraesCS7B01G255100 chr3B 89.414 1228 82 13 24 1241 782681729 782682918 0.000000e+00 1504.0
40 TraesCS7B01G255100 chr6A 79.811 1268 222 17 2147 3401 146501916 146500670 0.000000e+00 893.0
41 TraesCS7B01G255100 chr6A 84.115 661 55 20 1413 2033 146502656 146502006 1.100000e-165 593.0
42 TraesCS7B01G255100 chr6A 84.830 501 41 19 3554 4054 146497156 146497621 5.360000e-129 472.0
43 TraesCS7B01G255100 chr6A 88.187 364 25 2 3162 3524 146496821 146497167 7.080000e-113 418.0
44 TraesCS7B01G255100 chr6A 91.103 281 15 7 4293 4571 146497887 146498159 5.590000e-99 372.0
45 TraesCS7B01G255100 chr6A 83.654 312 25 13 412 702 566430831 566431137 2.100000e-68 270.0
46 TraesCS7B01G255100 chr6A 87.817 197 19 5 4054 4247 146497685 146497879 4.610000e-55 226.0
47 TraesCS7B01G255100 chrUn 100.000 390 0 0 4174 4563 479953204 479953593 0.000000e+00 721.0
48 TraesCS7B01G255100 chr6B 84.509 581 43 20 487 1024 637862621 637863197 8.720000e-147 531.0
49 TraesCS7B01G255100 chr6D 85.283 265 11 12 412 650 423170691 423170429 9.840000e-62 248.0
50 TraesCS7B01G255100 chr2D 95.238 63 2 1 4053 4114 35210496 35210434 1.050000e-16 99.0
51 TraesCS7B01G255100 chr4D 93.548 62 3 1 4054 4114 370369298 370369237 1.750000e-14 91.6


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 TraesCS7B01G255100 chr7B 472326993 472331570 4577 True 8455.0 8455 100.00000 1 4578 1 chr7B.!!$R1 4577
1 TraesCS7B01G255100 chr7B 472393865 472397037 3172 True 5779.0 5779 99.52800 1403 4578 1 chr7B.!!$R2 3175
2 TraesCS7B01G255100 chr7B 651338448 651341866 3418 True 1139.5 3319 93.12900 1419 4492 4 chr7B.!!$R5 3073
3 TraesCS7B01G255100 chr7B 651408917 651410339 1422 False 1134.0 1134 81.27600 2064 3488 1 chr7B.!!$F3 1424
4 TraesCS7B01G255100 chr7B 651452568 651454045 1477 True 1046.0 1046 79.84000 1930 3401 1 chr7B.!!$R3 1471
5 TraesCS7B01G255100 chr7B 651336460 651337929 1469 False 1005.0 1005 79.43900 1930 3396 1 chr7B.!!$F2 1466
6 TraesCS7B01G255100 chr7B 651443712 651445617 1905 False 950.5 1053 95.59400 2544 3727 2 chr7B.!!$F5 1183
7 TraesCS7B01G255100 chr7B 651450089 651451029 940 False 714.5 915 96.35300 3722 4578 2 chr7B.!!$F6 856
8 TraesCS7B01G255100 chr7B 701324105 701325572 1467 False 589.5 813 92.29000 529 1405 2 chr7B.!!$F7 876
9 TraesCS7B01G255100 chr5B 420373794 420375178 1384 True 2342.0 2342 97.26200 23 1402 1 chr5B.!!$R1 1379
10 TraesCS7B01G255100 chr5B 529227398 529228640 1242 False 2049.0 2049 96.47200 164 1402 1 chr5B.!!$F2 1238
11 TraesCS7B01G255100 chr5B 592855310 592856647 1337 True 1609.0 1609 88.35400 24 1400 1 chr5B.!!$R2 1376
12 TraesCS7B01G255100 chr1B 593492415 593493799 1384 True 2313.0 2313 96.90000 23 1400 1 chr1B.!!$R1 1377
13 TraesCS7B01G255100 chr7D 583477188 583479191 2003 True 2134.0 2134 86.00500 1404 3402 1 chr7D.!!$R1 1998
14 TraesCS7B01G255100 chr7D 583964735 583965477 742 True 996.0 996 90.86000 2637 3380 1 chr7D.!!$R3 743
15 TraesCS7B01G255100 chr7D 583984490 583994676 10186 True 980.6 2254 90.79480 1473 4578 5 chr7D.!!$R4 3105
16 TraesCS7B01G255100 chr7D 583973408 583974123 715 False 619.0 619 82.69200 1971 2680 1 chr7D.!!$F1 709
17 TraesCS7B01G255100 chr7A 675113548 675115557 2009 True 2135.0 2135 85.99000 1403 3402 1 chr7A.!!$R1 1999
18 TraesCS7B01G255100 chr5A 687294084 687295449 1365 True 2108.0 2108 94.43200 24 1402 1 chr5A.!!$R1 1378
19 TraesCS7B01G255100 chr5A 652658933 652660281 1348 True 1115.0 1720 94.98850 24 1402 2 chr5A.!!$R2 1378
20 TraesCS7B01G255100 chr3B 782681729 782682918 1189 False 1504.0 1504 89.41400 24 1241 1 chr3B.!!$F1 1217
21 TraesCS7B01G255100 chr6A 146500670 146502656 1986 True 743.0 893 81.96300 1413 3401 2 chr6A.!!$R1 1988
22 TraesCS7B01G255100 chr6A 146496821 146498159 1338 False 372.0 472 87.98425 3162 4571 4 chr6A.!!$F2 1409
23 TraesCS7B01G255100 chr6B 637862621 637863197 576 False 531.0 531 84.50900 487 1024 1 chr6B.!!$F1 537

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
926 1559 0.752658 AGTGCCCATCGATCGATCAA 59.247 50.0 27.20 7.46 31.62 2.57 F
1425 2067 0.463116 AAACAGTGGTTCCGCTCGTT 60.463 50.0 1.58 7.84 35.82 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 5436 6.255670 CAGAACGAAACCAATAGATTCATCGA 59.744 38.462 0.0 0.0 33.61 3.59 R
3676 10108 7.282585 TGTTCATAGGCAGTGATATTTAGCTT 58.717 34.615 0.0 0.0 0.00 3.74 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
18 19 3.811031 TCGAAGCCAAGGAACCAAA 57.189 47.368 0.00 0.00 0.00 3.28
19 20 2.060050 TCGAAGCCAAGGAACCAAAA 57.940 45.000 0.00 0.00 0.00 2.44
20 21 2.379972 TCGAAGCCAAGGAACCAAAAA 58.620 42.857 0.00 0.00 0.00 1.94
650 671 2.093235 GCTTCCTCAACTATCCTGCAGT 60.093 50.000 13.81 0.00 0.00 4.40
926 1559 0.752658 AGTGCCCATCGATCGATCAA 59.247 50.000 27.20 7.46 31.62 2.57
1074 1713 4.832590 ACTGTATAGTGTAGCGCCTAAG 57.167 45.455 2.29 0.00 35.34 2.18
1241 1880 3.338250 GGGTCCAGGGATGCCACA 61.338 66.667 5.86 0.00 0.00 4.17
1425 2067 0.463116 AAACAGTGGTTCCGCTCGTT 60.463 50.000 1.58 7.84 35.82 3.85
2564 6481 4.308458 CCCTTCACCACGGCGTCA 62.308 66.667 10.85 0.00 0.00 4.35
3676 10108 2.625790 GGTTAGGTTTTGATGTGCACCA 59.374 45.455 15.69 2.55 0.00 4.17
3700 10132 7.308229 CCAAGCTAAATATCACTGCCTATGAAC 60.308 40.741 0.00 0.00 0.00 3.18
4172 10695 2.925578 TGCCATTTTCGAGCATCAAG 57.074 45.000 0.00 0.00 33.17 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.060050 TTTTGGTTCCTTGGCTTCGA 57.940 45.000 0.00 0.00 0.00 3.71
2 3 3.457234 CTGTTTTTGGTTCCTTGGCTTC 58.543 45.455 0.00 0.00 0.00 3.86
3 4 2.170397 CCTGTTTTTGGTTCCTTGGCTT 59.830 45.455 0.00 0.00 0.00 4.35
4 5 1.762370 CCTGTTTTTGGTTCCTTGGCT 59.238 47.619 0.00 0.00 0.00 4.75
5 6 1.810031 GCCTGTTTTTGGTTCCTTGGC 60.810 52.381 0.00 0.00 0.00 4.52
6 7 1.484240 TGCCTGTTTTTGGTTCCTTGG 59.516 47.619 0.00 0.00 0.00 3.61
7 8 2.430332 TCTGCCTGTTTTTGGTTCCTTG 59.570 45.455 0.00 0.00 0.00 3.61
8 9 2.745968 TCTGCCTGTTTTTGGTTCCTT 58.254 42.857 0.00 0.00 0.00 3.36
11 12 4.507756 GTGATTTCTGCCTGTTTTTGGTTC 59.492 41.667 0.00 0.00 0.00 3.62
13 14 3.706086 AGTGATTTCTGCCTGTTTTTGGT 59.294 39.130 0.00 0.00 0.00 3.67
14 15 4.053295 CAGTGATTTCTGCCTGTTTTTGG 58.947 43.478 0.00 0.00 0.00 3.28
16 17 5.127682 AGAACAGTGATTTCTGCCTGTTTTT 59.872 36.000 0.00 0.00 45.43 1.94
17 18 4.646492 AGAACAGTGATTTCTGCCTGTTTT 59.354 37.500 0.00 0.00 45.43 2.43
18 19 4.037208 CAGAACAGTGATTTCTGCCTGTTT 59.963 41.667 9.75 0.00 45.43 2.83
19 20 4.686944 TCAGAACAGTGATTTCTGCCTGTT 60.687 41.667 15.38 3.74 46.51 3.16
20 21 3.144506 CAGAACAGTGATTTCTGCCTGT 58.855 45.455 9.75 0.00 42.58 4.00
926 1559 3.530910 CTTTGGCCACTCGGTCGGT 62.531 63.158 3.88 0.00 41.18 4.69
1074 1713 3.418068 GTGTGCAGCGCCTGAGAC 61.418 66.667 2.29 3.43 32.44 3.36
1343 1984 5.924475 ATTCACAAACTAAACTGTCTCGG 57.076 39.130 0.00 0.00 0.00 4.63
1836 5436 6.255670 CAGAACGAAACCAATAGATTCATCGA 59.744 38.462 0.00 0.00 33.61 3.59
3676 10108 7.282585 TGTTCATAGGCAGTGATATTTAGCTT 58.717 34.615 0.00 0.00 0.00 3.74
3700 10132 9.487790 AACTTTTCTCTTAAGATCAGACTCTTG 57.512 33.333 5.44 0.00 36.21 3.02
4172 10695 7.900782 TGGTATCTTTGTAGAAAGTAAGTGC 57.099 36.000 11.74 2.16 39.79 4.40


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

AutoCloner maintained by Alex Coulton.