Multiple sequence alignment - TraesCS5A01G077100

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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 TraesCS5A01G077100 chr5A 100.000 5769 0 0 1 5769 93196119 93201887 0.000000e+00 10654
1 TraesCS5A01G077100 chr5A 91.871 1267 83 7 1937 3194 599811773 599810518 0.000000e+00 1751
2 TraesCS5A01G077100 chr5A 95.477 619 27 1 5146 5763 643462122 643462740 0.000000e+00 987
3 TraesCS5A01G077100 chr5A 95.200 625 26 3 5146 5769 149271439 149272060 0.000000e+00 985
4 TraesCS5A01G077100 chr5A 95.185 623 28 2 5148 5769 565470031 565470652 0.000000e+00 983
5 TraesCS5A01G077100 chr5A 95.738 610 25 1 2 610 494270568 494269959 0.000000e+00 981
6 TraesCS5A01G077100 chr5A 95.574 610 25 2 2 610 51865060 51864452 0.000000e+00 976
7 TraesCS5A01G077100 chr5A 90.034 582 33 6 610 1175 268558905 268559477 0.000000e+00 730
8 TraesCS5A01G077100 chr5A 80.851 329 48 11 1490 1815 435634760 435635076 1.610000e-60 244
9 TraesCS5A01G077100 chr5A 75.200 250 54 7 611 856 396985117 396984872 1.700000e-20 111
10 TraesCS5A01G077100 chr3A 99.176 3885 29 3 610 4491 606012511 606016395 0.000000e+00 6994
11 TraesCS5A01G077100 chr3A 99.199 624 5 0 4522 5145 606016386 606017009 0.000000e+00 1125
12 TraesCS5A01G077100 chr3A 95.048 626 29 2 5146 5769 635447954 635448579 0.000000e+00 983
13 TraesCS5A01G077100 chr3A 78.098 799 129 31 4383 5146 357347003 357346216 1.130000e-126 464
14 TraesCS5A01G077100 chr3A 79.936 314 48 13 1506 1815 737014493 737014795 3.500000e-52 217
15 TraesCS5A01G077100 chr5B 92.842 964 59 3 2231 3194 589125903 589124950 0.000000e+00 1389
16 TraesCS5A01G077100 chr5B 89.299 271 19 5 1962 2223 589126238 589125969 1.200000e-86 331
17 TraesCS5A01G077100 chr5D 92.654 912 56 4 2283 3194 480712185 480711285 0.000000e+00 1303
18 TraesCS5A01G077100 chr5D 80.048 421 61 11 610 1013 133540783 133541197 2.030000e-74 291
19 TraesCS5A01G077100 chr5D 82.927 328 46 8 610 933 124722644 124722965 2.630000e-73 287
20 TraesCS5A01G077100 chr5D 80.615 325 48 13 1487 1808 542184123 542184435 2.690000e-58 237
21 TraesCS5A01G077100 chr6A 95.360 625 28 1 5146 5769 526785098 526784474 0.000000e+00 992
22 TraesCS5A01G077100 chr6A 95.200 625 29 1 5146 5769 462104346 462103722 0.000000e+00 987
23 TraesCS5A01G077100 chr6A 95.574 610 26 1 2 610 155265391 155266000 0.000000e+00 976
24 TraesCS5A01G077100 chr6A 95.574 610 26 1 2 610 537711575 537712184 0.000000e+00 976
25 TraesCS5A01G077100 chr6A 81.875 800 97 32 4382 5156 19821220 19820444 1.050000e-176 630
26 TraesCS5A01G077100 chr4A 95.908 611 23 2 2 610 578369784 578370394 0.000000e+00 989
27 TraesCS5A01G077100 chr4A 95.738 610 25 1 2 610 46102491 46103100 0.000000e+00 981
28 TraesCS5A01G077100 chr4A 81.533 796 111 21 4380 5145 520438292 520437503 1.770000e-174 623
29 TraesCS5A01G077100 chr4A 88.816 304 31 1 4652 4955 642139331 642139631 2.540000e-98 370
30 TraesCS5A01G077100 chr4A 87.554 233 23 5 4398 4626 642139108 642139338 1.230000e-66 265
31 TraesCS5A01G077100 chr4A 80.573 314 44 12 1506 1815 196693638 196693938 5.820000e-55 226
32 TraesCS5A01G077100 chr4A 83.969 131 20 1 1814 1943 642137431 642137561 2.180000e-24 124
33 TraesCS5A01G077100 chr1A 95.484 620 26 2 5146 5763 24169368 24169987 0.000000e+00 989
34 TraesCS5A01G077100 chr1A 82.595 316 49 5 603 916 222915790 222916101 2.050000e-69 274
35 TraesCS5A01G077100 chr1A 80.192 313 47 12 1506 1815 509944136 509943836 2.710000e-53 220
36 TraesCS5A01G077100 chr7A 95.200 625 29 1 5146 5769 287432016 287432640 0.000000e+00 987
37 TraesCS5A01G077100 chr7A 95.192 624 29 1 5146 5768 120709370 120709993 0.000000e+00 985
38 TraesCS5A01G077100 chr7A 95.745 611 23 3 2 610 247017453 247018062 0.000000e+00 981
39 TraesCS5A01G077100 chr7A 84.519 478 60 11 1335 1806 587998058 587998527 1.460000e-125 460
40 TraesCS5A01G077100 chr7A 84.342 479 60 12 1335 1806 16760900 16760430 6.810000e-124 455
41 TraesCS5A01G077100 chr7A 88.391 379 31 7 3626 3995 587998673 587999047 1.480000e-120 444
42 TraesCS5A01G077100 chr7A 87.958 382 33 7 3626 3998 16760284 16759907 6.860000e-119 438
43 TraesCS5A01G077100 chr7A 80.128 312 49 10 1506 1815 554919847 554919547 2.710000e-53 220
44 TraesCS5A01G077100 chr2A 95.738 610 25 1 2 610 211264847 211264238 0.000000e+00 981
45 TraesCS5A01G077100 chr2A 95.738 610 25 1 2 610 392888821 392889430 0.000000e+00 981
46 TraesCS5A01G077100 chr2A 77.930 802 133 28 4374 5145 32968636 32967849 1.460000e-125 460
47 TraesCS5A01G077100 chr2A 81.201 383 63 9 4766 5145 91497502 91497878 3.380000e-77 300
48 TraesCS5A01G077100 chr2D 89.229 752 76 4 4401 5148 645355097 645354347 0.000000e+00 935
49 TraesCS5A01G077100 chr2D 89.027 401 33 7 3604 3998 645356588 645356193 2.420000e-133 486
50 TraesCS5A01G077100 chr2D 82.968 411 40 13 609 1013 645358375 645357989 1.540000e-90 344
51 TraesCS5A01G077100 chr2D 86.364 132 18 0 611 742 548751415 548751546 1.680000e-30 145
52 TraesCS5A01G077100 chr2D 83.969 131 20 1 1814 1943 645356753 645356623 2.180000e-24 124
53 TraesCS5A01G077100 chr3B 88.533 750 79 6 4401 5145 87945683 87944936 0.000000e+00 902
54 TraesCS5A01G077100 chr3B 78.983 747 110 30 4440 5154 53599506 53600237 3.150000e-127 466
55 TraesCS5A01G077100 chr3B 87.599 379 33 9 3626 3995 53597442 53597815 1.490000e-115 427
56 TraesCS5A01G077100 chr3B 82.014 139 24 1 1806 1943 87947146 87947008 3.650000e-22 117
57 TraesCS5A01G077100 chrUn 100.000 399 0 0 2946 3344 478806836 478807234 0.000000e+00 737
58 TraesCS5A01G077100 chr4B 87.435 382 34 8 3626 3998 163903347 163902971 1.490000e-115 427
59 TraesCS5A01G077100 chr3D 80.048 421 59 14 611 1013 46512464 46512051 7.310000e-74 289


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 TraesCS5A01G077100 chr5A 93196119 93201887 5768 False 10654.00 10654 100.000000 1 5769 1 chr5A.!!$F1 5768
1 TraesCS5A01G077100 chr5A 599810518 599811773 1255 True 1751.00 1751 91.871000 1937 3194 1 chr5A.!!$R4 1257
2 TraesCS5A01G077100 chr5A 643462122 643462740 618 False 987.00 987 95.477000 5146 5763 1 chr5A.!!$F6 617
3 TraesCS5A01G077100 chr5A 149271439 149272060 621 False 985.00 985 95.200000 5146 5769 1 chr5A.!!$F2 623
4 TraesCS5A01G077100 chr5A 565470031 565470652 621 False 983.00 983 95.185000 5148 5769 1 chr5A.!!$F5 621
5 TraesCS5A01G077100 chr5A 494269959 494270568 609 True 981.00 981 95.738000 2 610 1 chr5A.!!$R3 608
6 TraesCS5A01G077100 chr5A 51864452 51865060 608 True 976.00 976 95.574000 2 610 1 chr5A.!!$R1 608
7 TraesCS5A01G077100 chr5A 268558905 268559477 572 False 730.00 730 90.034000 610 1175 1 chr5A.!!$F3 565
8 TraesCS5A01G077100 chr3A 606012511 606017009 4498 False 4059.50 6994 99.187500 610 5145 2 chr3A.!!$F3 4535
9 TraesCS5A01G077100 chr3A 635447954 635448579 625 False 983.00 983 95.048000 5146 5769 1 chr3A.!!$F1 623
10 TraesCS5A01G077100 chr3A 357346216 357347003 787 True 464.00 464 78.098000 4383 5146 1 chr3A.!!$R1 763
11 TraesCS5A01G077100 chr5B 589124950 589126238 1288 True 860.00 1389 91.070500 1962 3194 2 chr5B.!!$R1 1232
12 TraesCS5A01G077100 chr5D 480711285 480712185 900 True 1303.00 1303 92.654000 2283 3194 1 chr5D.!!$R1 911
13 TraesCS5A01G077100 chr6A 526784474 526785098 624 True 992.00 992 95.360000 5146 5769 1 chr6A.!!$R3 623
14 TraesCS5A01G077100 chr6A 462103722 462104346 624 True 987.00 987 95.200000 5146 5769 1 chr6A.!!$R2 623
15 TraesCS5A01G077100 chr6A 155265391 155266000 609 False 976.00 976 95.574000 2 610 1 chr6A.!!$F1 608
16 TraesCS5A01G077100 chr6A 537711575 537712184 609 False 976.00 976 95.574000 2 610 1 chr6A.!!$F2 608
17 TraesCS5A01G077100 chr6A 19820444 19821220 776 True 630.00 630 81.875000 4382 5156 1 chr6A.!!$R1 774
18 TraesCS5A01G077100 chr4A 578369784 578370394 610 False 989.00 989 95.908000 2 610 1 chr4A.!!$F3 608
19 TraesCS5A01G077100 chr4A 46102491 46103100 609 False 981.00 981 95.738000 2 610 1 chr4A.!!$F1 608
20 TraesCS5A01G077100 chr4A 520437503 520438292 789 True 623.00 623 81.533000 4380 5145 1 chr4A.!!$R1 765
21 TraesCS5A01G077100 chr4A 642137431 642139631 2200 False 253.00 370 86.779667 1814 4955 3 chr4A.!!$F4 3141
22 TraesCS5A01G077100 chr1A 24169368 24169987 619 False 989.00 989 95.484000 5146 5763 1 chr1A.!!$F1 617
23 TraesCS5A01G077100 chr7A 287432016 287432640 624 False 987.00 987 95.200000 5146 5769 1 chr7A.!!$F3 623
24 TraesCS5A01G077100 chr7A 120709370 120709993 623 False 985.00 985 95.192000 5146 5768 1 chr7A.!!$F1 622
25 TraesCS5A01G077100 chr7A 247017453 247018062 609 False 981.00 981 95.745000 2 610 1 chr7A.!!$F2 608
26 TraesCS5A01G077100 chr7A 587998058 587999047 989 False 452.00 460 86.455000 1335 3995 2 chr7A.!!$F4 2660
27 TraesCS5A01G077100 chr7A 16759907 16760900 993 True 446.50 455 86.150000 1335 3998 2 chr7A.!!$R2 2663
28 TraesCS5A01G077100 chr2A 211264238 211264847 609 True 981.00 981 95.738000 2 610 1 chr2A.!!$R2 608
29 TraesCS5A01G077100 chr2A 392888821 392889430 609 False 981.00 981 95.738000 2 610 1 chr2A.!!$F2 608
30 TraesCS5A01G077100 chr2A 32967849 32968636 787 True 460.00 460 77.930000 4374 5145 1 chr2A.!!$R1 771
31 TraesCS5A01G077100 chr2D 645354347 645358375 4028 True 472.25 935 86.298250 609 5148 4 chr2D.!!$R1 4539
32 TraesCS5A01G077100 chr3B 87944936 87947146 2210 True 509.50 902 85.273500 1806 5145 2 chr3B.!!$R1 3339
33 TraesCS5A01G077100 chr3B 53597442 53600237 2795 False 446.50 466 83.291000 3626 5154 2 chr3B.!!$F1 1528

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
719 723 0.033228 CCGGCAAAAATGCACAAGGA 59.967 50.0 2.97 0.0 36.33 3.36 F
1403 1440 1.680522 GCATCGGGCTCCTCTTCTCA 61.681 60.0 0.00 0.0 40.25 3.27 F
2537 3167 7.430760 AGAGGTTACTTCTCTGCTATTTCAT 57.569 36.0 0.00 0.0 39.83 2.57 F
4340 7014 1.877637 TTTCCATATCCGGCATCGTG 58.122 50.0 0.00 0.0 33.95 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2537 3167 5.710099 TGTCATCACTAGTACATGTGTGAGA 59.290 40.00 18.25 13.61 41.77 3.27 R
3344 3978 8.031864 TGTCACAAAGAGCAGAAAACATAAAAA 58.968 29.63 0.00 0.00 0.00 1.94 R
4445 7365 1.308069 AATCATGTGCACCGCTCCAC 61.308 55.00 15.69 0.00 0.00 4.02 R
5210 8176 0.102300 CCACACATCGACCGCTATCA 59.898 55.00 0.00 0.00 0.00 2.15 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
58 59 7.891183 TCAAATACAGAGCCAAAACCCTAATTA 59.109 33.333 0.00 0.0 0.00 1.40
115 117 2.347490 GGCCTGTTTCGGAGCTCA 59.653 61.111 17.19 0.0 0.00 4.26
226 228 6.342111 GGGTCCATAGTTATTAGCTAGATGC 58.658 44.000 0.00 0.0 43.29 3.91
235 237 8.028652 AGTTATTAGCTAGATGCCTTCTTCTT 57.971 34.615 0.00 0.0 44.23 2.52
329 333 3.059597 GTGTGTTTGTTGAGACCGATGAG 60.060 47.826 0.00 0.0 0.00 2.90
418 422 6.258230 TGATTGGTTATCTTTGCAAGTCTG 57.742 37.500 0.00 0.0 34.17 3.51
419 423 5.335897 TGATTGGTTATCTTTGCAAGTCTGC 60.336 40.000 0.00 0.0 40.37 4.26
552 556 7.411274 GCAACAAGGCACGTATTGTATTATTA 58.589 34.615 11.86 0.0 38.66 0.98
647 651 5.046663 CACTAAATTGGGGGCAATTAACTGT 60.047 40.000 0.00 0.0 34.06 3.55
719 723 0.033228 CCGGCAAAAATGCACAAGGA 59.967 50.000 2.97 0.0 36.33 3.36
792 796 4.768968 GCAATGATATGCCCATCTTAGGTT 59.231 41.667 0.00 0.0 40.49 3.50
1403 1440 1.680522 GCATCGGGCTCCTCTTCTCA 61.681 60.000 0.00 0.0 40.25 3.27
2332 2962 9.107367 GCTGATTAATGCATACTTATTTTCGAC 57.893 33.333 0.00 0.0 0.00 4.20
2537 3167 7.430760 AGAGGTTACTTCTCTGCTATTTCAT 57.569 36.000 0.00 0.0 39.83 2.57
3344 3978 3.411446 TGTTGAGATTGCGGTCTTCATT 58.589 40.909 0.00 0.0 0.00 2.57
3527 4161 8.047911 TCCCCGTTGTTAATATACAAGAAATCA 58.952 33.333 0.00 0.0 38.60 2.57
3698 4332 4.006989 ACACAGTTTTCGCCAGCATTATA 58.993 39.130 0.00 0.0 0.00 0.98
4340 7014 1.877637 TTTCCATATCCGGCATCGTG 58.122 50.000 0.00 0.0 33.95 4.35
4467 7390 1.368641 GAGCGGTGCACATGATTGTA 58.631 50.000 20.43 0.0 33.76 2.41
4468 7391 1.328680 GAGCGGTGCACATGATTGTAG 59.671 52.381 20.43 0.0 33.76 2.74
4869 7835 6.043706 AGAGTGCAATAGCCTTATAGATTGGT 59.956 38.462 0.00 0.0 41.13 3.67
4971 7937 2.039216 TGCCGGGAGAACTTTGAACATA 59.961 45.455 2.18 0.0 0.00 2.29
4972 7938 3.279434 GCCGGGAGAACTTTGAACATAT 58.721 45.455 2.18 0.0 0.00 1.78
5173 8139 4.513442 TGTCATCTTGCTTAAGGCGTTAT 58.487 39.130 4.29 0.0 45.43 1.89
5356 8322 6.696583 TGTCAATTGCTCAACAGTAATTTGTG 59.303 34.615 0.00 0.0 40.85 3.33
5607 8576 4.201485 CGCGAGGATTTATTTGTTTTGTGC 60.201 41.667 0.00 0.0 0.00 4.57
5678 8648 6.072452 GGTTCTCAAAACTGAGGGAAATACTG 60.072 42.308 2.47 0.0 36.62 2.74
5687 8657 3.380637 TGAGGGAAATACTGACGCTACTC 59.619 47.826 0.00 0.0 0.00 2.59
5704 8674 0.825010 CTCTGCTGCACCACCCTTTT 60.825 55.000 0.00 0.0 0.00 2.27
5763 8733 1.457346 CAAGAAGGATTTCTGGCGCT 58.543 50.000 7.64 0.0 42.80 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.000840 GGGGTACGTAGGTATATATAGGAGC 58.999 48.000 0.00 0.00 0.00 4.70
58 59 0.105408 ACAGAAAGTTACGGCGGTGT 59.895 50.000 13.24 0.00 0.00 4.16
130 132 1.112113 GTAGAAGCCCTCCGTGATCA 58.888 55.000 0.00 0.00 0.00 2.92
226 228 7.516198 TGAGATCCAAAAAGAAAGAAGAAGG 57.484 36.000 0.00 0.00 0.00 3.46
235 237 9.965824 GAACTTTGTATTGAGATCCAAAAAGAA 57.034 29.630 17.36 7.05 38.43 2.52
282 285 6.250819 CGCAAAAGAAGATTACATCGAACAT 58.749 36.000 0.00 0.00 0.00 2.71
329 333 8.739972 AGATAAACTTGATCATAAACCCACAAC 58.260 33.333 0.00 0.00 0.00 3.32
418 422 5.095490 CCAAACCAAACTGATAATTCGAGC 58.905 41.667 0.00 0.00 0.00 5.03
419 423 5.095490 GCCAAACCAAACTGATAATTCGAG 58.905 41.667 0.00 0.00 0.00 4.04
647 651 5.280011 GCCCTTATTCTCATATTTCTCCCGA 60.280 44.000 0.00 0.00 0.00 5.14
719 723 3.454812 ACTTCTACCGGCAGTTTATCCAT 59.545 43.478 0.00 0.00 0.00 3.41
792 796 1.810151 GTTCTGCCGGCAGTTTTGATA 59.190 47.619 45.86 28.49 43.96 2.15
864 868 1.944709 ACGCGTTTGGGCCTAATTATC 59.055 47.619 5.58 0.00 0.00 1.75
2537 3167 5.710099 TGTCATCACTAGTACATGTGTGAGA 59.290 40.000 18.25 13.61 41.77 3.27
3344 3978 8.031864 TGTCACAAAGAGCAGAAAACATAAAAA 58.968 29.630 0.00 0.00 0.00 1.94
3564 4198 8.534778 CAAAGCAAATTAAGAACTTTCAGTGTC 58.465 33.333 0.00 0.00 0.00 3.67
3698 4332 4.464951 TGATTCCATCAAGCAGCTGAAAAT 59.535 37.500 20.43 1.42 36.11 1.82
3827 4466 5.186992 GGCTACATTTAACACCCTCCATTTT 59.813 40.000 0.00 0.00 0.00 1.82
4193 6859 1.383799 CCCCATTGGTTGCCTCTGA 59.616 57.895 1.20 0.00 0.00 3.27
4340 7014 3.059325 ACTGATACGGCGATACGAGTAAC 60.059 47.826 16.62 0.00 37.61 2.50
4445 7365 1.308069 AATCATGTGCACCGCTCCAC 61.308 55.000 15.69 0.00 0.00 4.02
4467 7390 9.394767 TGCATACATTGATTACAATACTCAACT 57.605 29.630 0.00 0.00 43.76 3.16
4468 7391 9.655769 CTGCATACATTGATTACAATACTCAAC 57.344 33.333 0.00 0.00 43.76 3.18
4869 7835 0.823769 TGCCACGGTTGCCAAATACA 60.824 50.000 1.40 0.00 0.00 2.29
5210 8176 0.102300 CCACACATCGACCGCTATCA 59.898 55.000 0.00 0.00 0.00 2.15
5310 8276 7.475015 TGACAAAATTGAGCATAGTTATGAGC 58.525 34.615 3.38 0.00 35.75 4.26
5356 8322 2.118313 AGGTATTTTACGGTGGGTGC 57.882 50.000 0.00 0.00 0.00 5.01
5517 8486 6.823182 ACGAGAGTGAGATCTGATAGATATGG 59.177 42.308 0.00 0.00 46.97 2.74
5551 8520 2.420058 GGGGTTGTCAATCCCTACAG 57.580 55.000 24.72 0.00 43.00 2.74
5584 8553 4.201485 GCACAAAACAAATAAATCCTCGCG 60.201 41.667 0.00 0.00 0.00 5.87
5678 8648 1.807573 GGTGCAGCAGAGTAGCGTC 60.808 63.158 11.86 0.00 40.15 5.19
5687 8657 0.825010 AGAAAAGGGTGGTGCAGCAG 60.825 55.000 20.85 0.00 33.07 4.24
5704 8674 3.211045 CGTTGGTTTTCCCTTGAAGAGA 58.789 45.455 0.00 0.00 39.73 3.10


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

AutoCloner maintained by Alex Coulton.