Multiple sequence alignment - TraesCS1A01G353500

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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 TraesCS1A01G353500 chr1A 100.000 3046 0 0 1 3046 537043954 537040909 0.000000e+00 5626
1 TraesCS1A01G353500 chr1A 88.809 1117 85 18 709 1810 221812302 221811211 0.000000e+00 1334
2 TraesCS1A01G353500 chr2A 97.271 3078 44 11 1 3046 520056924 520053855 0.000000e+00 5182
3 TraesCS1A01G353500 chr2A 92.288 1984 118 15 1094 3046 309469119 309471098 0.000000e+00 2784
4 TraesCS1A01G353500 chr2A 87.195 164 20 1 1503 1665 401088876 401089039 5.190000e-43 185
5 TraesCS1A01G353500 chr3A 98.515 2222 28 3 828 3046 679891840 679889621 0.000000e+00 3916
6 TraesCS1A01G353500 chr3A 94.296 859 20 6 1 831 679905979 679905122 0.000000e+00 1288
7 TraesCS1A01G353500 chr4A 92.446 2224 94 40 1 2184 535950817 535948628 0.000000e+00 3109
8 TraesCS1A01G353500 chr4A 94.461 1354 50 5 1379 2707 311931881 311933234 0.000000e+00 2061
9 TraesCS1A01G353500 chr4A 91.874 923 46 14 2146 3046 535948628 535947713 0.000000e+00 1262
10 TraesCS1A01G353500 chr4A 94.630 540 17 10 709 1240 311931351 311931886 0.000000e+00 826
11 TraesCS1A01G353500 chr2D 94.967 1987 68 10 1089 3046 341958782 341960765 0.000000e+00 3086
12 TraesCS1A01G353500 chr6B 93.639 1069 37 10 1 1040 4738747 4739813 0.000000e+00 1568
13 TraesCS1A01G353500 chr6B 93.277 1071 39 10 1 1040 4735744 4736812 0.000000e+00 1548
14 TraesCS1A01G353500 chr6B 92.530 1071 47 11 1 1040 4741749 4742817 0.000000e+00 1504
15 TraesCS1A01G353500 chr6B 94.215 121 6 1 595 714 663597299 663597179 1.870000e-42 183
16 TraesCS1A01G353500 chr7A 91.711 1134 57 13 709 1812 347426638 347425512 0.000000e+00 1539
17 TraesCS1A01G353500 chr7A 90.463 1122 85 14 709 1815 401657022 401655908 0.000000e+00 1459
18 TraesCS1A01G353500 chr7A 92.017 689 44 7 777 1460 339108819 339109501 0.000000e+00 957
19 TraesCS1A01G353500 chr7B 91.242 1119 81 9 709 1812 289287107 289288223 0.000000e+00 1507
20 TraesCS1A01G353500 chr7B 91.482 587 34 9 710 1283 235123305 235122722 0.000000e+00 793
21 TraesCS1A01G353500 chr1B 92.359 1047 50 13 1 1019 295052458 295051414 0.000000e+00 1463
22 TraesCS1A01G353500 chr1B 95.000 620 18 7 1015 1626 295009819 295009205 0.000000e+00 961
23 TraesCS1A01G353500 chr5D 89.921 1141 69 15 1813 2913 364369942 364368808 0.000000e+00 1428
24 TraesCS1A01G353500 chr5B 89.753 1132 72 21 1813 2910 429930649 429929528 0.000000e+00 1408
25 TraesCS1A01G353500 chr5B 93.548 124 7 1 592 714 51553230 51553107 1.870000e-42 183
26 TraesCS1A01G353500 chr5A 88.676 1042 69 25 1813 2812 139787705 139786671 0.000000e+00 1225
27 TraesCS1A01G353500 chr5A 84.891 1006 110 14 2076 3046 207740255 207741253 0.000000e+00 977
28 TraesCS1A01G353500 chr5A 86.170 940 75 22 2150 3046 384463490 384462563 0.000000e+00 965
29 TraesCS1A01G353500 chr7D 85.970 1005 100 14 2076 3046 289881161 289880164 0.000000e+00 1037
30 TraesCS1A01G353500 chr6D 86.277 940 70 25 2150 3046 248009003 248008080 0.000000e+00 966
31 TraesCS1A01G353500 chr2B 93.887 638 29 7 1 629 275148995 275148359 0.000000e+00 953
32 TraesCS1A01G353500 chr2B 90.550 582 39 8 710 1280 427753042 427753618 0.000000e+00 756
33 TraesCS1A01G353500 chr2B 94.759 477 19 6 709 1183 88674957 88675429 0.000000e+00 737
34 TraesCS1A01G353500 chr4B 89.402 736 43 9 1 705 341928093 341927362 0.000000e+00 894
35 TraesCS1A01G353500 chrUn 83.399 253 13 10 491 714 45365696 45365444 1.110000e-49 207


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 TraesCS1A01G353500 chr1A 537040909 537043954 3045 True 5626.0 5626 100.000000 1 3046 1 chr1A.!!$R2 3045
1 TraesCS1A01G353500 chr1A 221811211 221812302 1091 True 1334.0 1334 88.809000 709 1810 1 chr1A.!!$R1 1101
2 TraesCS1A01G353500 chr2A 520053855 520056924 3069 True 5182.0 5182 97.271000 1 3046 1 chr2A.!!$R1 3045
3 TraesCS1A01G353500 chr2A 309469119 309471098 1979 False 2784.0 2784 92.288000 1094 3046 1 chr2A.!!$F1 1952
4 TraesCS1A01G353500 chr3A 679889621 679891840 2219 True 3916.0 3916 98.515000 828 3046 1 chr3A.!!$R1 2218
5 TraesCS1A01G353500 chr3A 679905122 679905979 857 True 1288.0 1288 94.296000 1 831 1 chr3A.!!$R2 830
6 TraesCS1A01G353500 chr4A 535947713 535950817 3104 True 2185.5 3109 92.160000 1 3046 2 chr4A.!!$R1 3045
7 TraesCS1A01G353500 chr4A 311931351 311933234 1883 False 1443.5 2061 94.545500 709 2707 2 chr4A.!!$F1 1998
8 TraesCS1A01G353500 chr2D 341958782 341960765 1983 False 3086.0 3086 94.967000 1089 3046 1 chr2D.!!$F1 1957
9 TraesCS1A01G353500 chr6B 4735744 4742817 7073 False 1540.0 1568 93.148667 1 1040 3 chr6B.!!$F1 1039
10 TraesCS1A01G353500 chr7A 347425512 347426638 1126 True 1539.0 1539 91.711000 709 1812 1 chr7A.!!$R1 1103
11 TraesCS1A01G353500 chr7A 401655908 401657022 1114 True 1459.0 1459 90.463000 709 1815 1 chr7A.!!$R2 1106
12 TraesCS1A01G353500 chr7A 339108819 339109501 682 False 957.0 957 92.017000 777 1460 1 chr7A.!!$F1 683
13 TraesCS1A01G353500 chr7B 289287107 289288223 1116 False 1507.0 1507 91.242000 709 1812 1 chr7B.!!$F1 1103
14 TraesCS1A01G353500 chr7B 235122722 235123305 583 True 793.0 793 91.482000 710 1283 1 chr7B.!!$R1 573
15 TraesCS1A01G353500 chr1B 295051414 295052458 1044 True 1463.0 1463 92.359000 1 1019 1 chr1B.!!$R2 1018
16 TraesCS1A01G353500 chr1B 295009205 295009819 614 True 961.0 961 95.000000 1015 1626 1 chr1B.!!$R1 611
17 TraesCS1A01G353500 chr5D 364368808 364369942 1134 True 1428.0 1428 89.921000 1813 2913 1 chr5D.!!$R1 1100
18 TraesCS1A01G353500 chr5B 429929528 429930649 1121 True 1408.0 1408 89.753000 1813 2910 1 chr5B.!!$R2 1097
19 TraesCS1A01G353500 chr5A 139786671 139787705 1034 True 1225.0 1225 88.676000 1813 2812 1 chr5A.!!$R1 999
20 TraesCS1A01G353500 chr5A 207740255 207741253 998 False 977.0 977 84.891000 2076 3046 1 chr5A.!!$F1 970
21 TraesCS1A01G353500 chr5A 384462563 384463490 927 True 965.0 965 86.170000 2150 3046 1 chr5A.!!$R2 896
22 TraesCS1A01G353500 chr7D 289880164 289881161 997 True 1037.0 1037 85.970000 2076 3046 1 chr7D.!!$R1 970
23 TraesCS1A01G353500 chr6D 248008080 248009003 923 True 966.0 966 86.277000 2150 3046 1 chr6D.!!$R1 896
24 TraesCS1A01G353500 chr2B 275148359 275148995 636 True 953.0 953 93.887000 1 629 1 chr2B.!!$R1 628
25 TraesCS1A01G353500 chr2B 427753042 427753618 576 False 756.0 756 90.550000 710 1280 1 chr2B.!!$F2 570
26 TraesCS1A01G353500 chr4B 341927362 341928093 731 True 894.0 894 89.402000 1 705 1 chr4B.!!$R1 704

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
607 3645 0.108329 CGTACTCCAGGCCGTTCAAT 60.108 55.000 0.0 0.0 0.0 2.57 F
822 3876 5.667539 TTCATCTTGTTTGTTCCAACCAA 57.332 34.783 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 7836 1.973138 CTCGTTGTCGTTGGACGTAT 58.027 50.0 0.0 0.0 46.49 3.06 R
2462 8674 3.546724 TGACAGGGTCTAAGAGAGATCG 58.453 50.0 0.0 0.0 35.96 3.69 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
496 505 5.044919 TGGGTGATGAATCAACTTCCTGTAT 60.045 40.000 8.19 0.00 43.90 2.29
528 537 2.660206 CATTGGACGACCCCGACA 59.340 61.111 0.34 0.00 39.50 4.35
607 3645 0.108329 CGTACTCCAGGCCGTTCAAT 60.108 55.000 0.00 0.00 0.00 2.57
822 3876 5.667539 TTCATCTTGTTTGTTCCAACCAA 57.332 34.783 0.00 0.00 0.00 3.67
1729 7836 0.399833 TGGCTATTGTGTGTGCAGGA 59.600 50.000 0.00 0.00 0.00 3.86
2163 8270 4.083324 CGCCTGCAATTCTTTTCTCTGTTA 60.083 41.667 0.00 0.00 0.00 2.41
2433 8641 8.924303 ACTACTTATTCAGTCATGCTATTACCA 58.076 33.333 0.00 0.00 36.88 3.25
2462 8674 6.690194 ATGGAGTGAAAGAGTATTGCAATC 57.310 37.500 16.86 7.93 0.00 2.67
2650 8866 4.873827 GTCGGTGTGGTGTATATGTCATTT 59.126 41.667 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
590 599 0.392461 GCATTGAACGGCCTGGAGTA 60.392 55.000 0.00 0.00 0.00 2.59
822 3876 3.603965 ACTAGTACTAGGCATCCAGCT 57.396 47.619 29.05 6.48 44.79 4.24
1542 7642 7.978925 AGAACTTATTATGATTTCCCTCCGAT 58.021 34.615 0.00 0.00 0.00 4.18
1729 7836 1.973138 CTCGTTGTCGTTGGACGTAT 58.027 50.000 0.00 0.00 46.49 3.06
2163 8270 3.837355 ACTGATGCTTTGGGAACTTTCT 58.163 40.909 0.00 0.00 0.00 2.52
2400 8608 9.066892 AGCATGACTGAATAAGTAGTTCAAAAA 57.933 29.630 0.00 0.00 40.07 1.94
2433 8641 6.150140 GCAATACTCTTTCACTCCATTCACTT 59.850 38.462 0.00 0.00 0.00 3.16
2462 8674 3.546724 TGACAGGGTCTAAGAGAGATCG 58.453 50.000 0.00 0.00 35.96 3.69
2650 8866 4.636648 ACCGACCGCAAATTTTCATACATA 59.363 37.500 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.