Multiple sequence alignment - TraesCS1B01G421000

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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 TraesCS1B01G421000 chr1B 100.000 3481 0 0 1 3481 645045378 645041898 0.000000e+00 6429
1 TraesCS1B01G421000 chr1B 96.508 1747 44 8 854 2583 93337076 93335330 0.000000e+00 2872
2 TraesCS1B01G421000 chr1B 96.770 743 22 2 854 1595 593169701 593168960 0.000000e+00 1238
3 TraesCS1B01G421000 chr1B 98.413 126 2 0 72 197 77641914 77642039 4.520000e-54 222
4 TraesCS1B01G421000 chr1B 98.780 82 0 1 1 81 128089567 128089486 1.010000e-30 145
5 TraesCS1B01G421000 chr4A 95.789 2422 54 15 854 3230 668048292 668050710 0.000000e+00 3864
6 TraesCS1B01G421000 chr4A 96.796 1748 38 9 854 2583 723905105 723906852 0.000000e+00 2902
7 TraesCS1B01G421000 chr4A 96.923 130 4 0 72 201 634023915 634024044 5.850000e-53 219
8 TraesCS1B01G421000 chr4B 96.424 2153 48 5 460 2583 619807783 619809935 0.000000e+00 3522
9 TraesCS1B01G421000 chr4B 96.504 1602 38 3 1000 2583 459583651 459582050 0.000000e+00 2632
10 TraesCS1B01G421000 chr4B 97.249 945 23 3 2538 3481 661863790 661864732 0.000000e+00 1598
11 TraesCS1B01G421000 chr4B 97.046 948 24 3 2538 3481 619809938 619810885 0.000000e+00 1592
12 TraesCS1B01G421000 chr4B 97.222 900 24 1 1 899 554166182 554165283 0.000000e+00 1522
13 TraesCS1B01G421000 chr4B 95.416 829 31 2 72 899 661861329 661862151 0.000000e+00 1314
14 TraesCS1B01G421000 chr4B 98.780 82 0 1 1 81 597285344 597285263 1.010000e-30 145
15 TraesCS1B01G421000 chr6B 96.855 1749 35 11 854 2583 683850209 683851956 0.000000e+00 2907
16 TraesCS1B01G421000 chr6B 97.117 763 21 1 138 899 20414265 20415027 0.000000e+00 1286
17 TraesCS1B01G421000 chr6B 96.723 763 24 1 138 899 683849451 683850213 0.000000e+00 1269
18 TraesCS1B01G421000 chr6B 97.039 743 21 1 854 1595 290995702 290996444 0.000000e+00 1249
19 TraesCS1B01G421000 chr2B 96.854 1748 36 10 854 2583 731753531 731751785 0.000000e+00 2905
20 TraesCS1B01G421000 chr2B 95.148 1752 51 18 1732 3481 762181084 762179365 0.000000e+00 2734
21 TraesCS1B01G421000 chr2B 97.669 944 22 0 2538 3481 178725099 178726042 0.000000e+00 1622
22 TraesCS1B01G421000 chr2B 97.354 945 23 2 2538 3481 731751782 731750839 0.000000e+00 1605
23 TraesCS1B01G421000 chr2B 97.257 948 21 2 2538 3481 316841278 316842224 0.000000e+00 1602
24 TraesCS1B01G421000 chr2B 97.132 767 21 1 141 906 371495954 371495188 0.000000e+00 1293
25 TraesCS1B01G421000 chr7B 96.672 1743 50 7 854 2592 604992083 604990345 0.000000e+00 2891
26 TraesCS1B01G421000 chr7B 98.411 944 15 0 2538 3481 611569108 611568165 0.000000e+00 1661
27 TraesCS1B01G421000 chr7B 97.672 945 20 2 2538 3481 179704956 179704013 0.000000e+00 1622
28 TraesCS1B01G421000 chr7B 97.161 951 17 5 2538 3481 505086066 505087013 0.000000e+00 1598
29 TraesCS1B01G421000 chr7B 96.864 829 25 1 72 899 64911785 64910957 0.000000e+00 1386
30 TraesCS1B01G421000 chr7B 96.974 760 21 2 141 899 29889862 29889104 0.000000e+00 1275
31 TraesCS1B01G421000 chr7B 95.984 747 20 3 854 1599 505084410 505085147 0.000000e+00 1205
32 TraesCS1B01G421000 chr7B 93.778 225 6 2 72 296 107414074 107413858 7.200000e-87 331
33 TraesCS1B01G421000 chr5B 96.597 1734 55 3 854 2583 39639428 39641161 0.000000e+00 2872
34 TraesCS1B01G421000 chr5B 96.480 1733 47 9 854 2583 462701160 462702881 0.000000e+00 2850
35 TraesCS1B01G421000 chr5B 96.723 763 24 1 138 899 682754868 682755630 0.000000e+00 1269
36 TraesCS1B01G421000 chr5B 97.308 743 19 1 854 1595 36685759 36686501 0.000000e+00 1260
37 TraesCS1B01G421000 chr5B 97.039 743 21 1 854 1595 36652328 36653070 0.000000e+00 1249
38 TraesCS1B01G421000 chr3B 96.501 743 15 3 854 1595 326635706 326634974 0.000000e+00 1218
39 TraesCS1B01G421000 chr3B 98.780 82 0 1 1 81 45251983 45251902 1.010000e-30 145
40 TraesCS1B01G421000 chr3B 98.780 82 0 1 1 81 460764093 460764012 1.010000e-30 145
41 TraesCS1B01G421000 chr3B 98.780 82 0 1 1 81 783839124 783839205 1.010000e-30 145
42 TraesCS1B01G421000 chr3A 99.206 126 1 0 72 197 15928020 15928145 9.720000e-56 228
43 TraesCS1B01G421000 chr3A 97.619 126 3 0 72 197 40402443 40402318 2.100000e-52 217
44 TraesCS1B01G421000 chr5A 98.387 124 2 0 72 195 546753205 546753082 5.850000e-53 219
45 TraesCS1B01G421000 chr5A 98.780 82 0 1 1 81 5492870 5492789 1.010000e-30 145
46 TraesCS1B01G421000 chrUn 98.750 80 1 0 1 80 101281284 101281363 3.620000e-30 143
47 TraesCS1B01G421000 chr7D 98.750 80 1 0 1 80 283785761 283785840 3.620000e-30 143


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 TraesCS1B01G421000 chr1B 645041898 645045378 3480 True 6429.0 6429 100.0000 1 3481 1 chr1B.!!$R4 3480
1 TraesCS1B01G421000 chr1B 93335330 93337076 1746 True 2872.0 2872 96.5080 854 2583 1 chr1B.!!$R1 1729
2 TraesCS1B01G421000 chr1B 593168960 593169701 741 True 1238.0 1238 96.7700 854 1595 1 chr1B.!!$R3 741
3 TraesCS1B01G421000 chr4A 668048292 668050710 2418 False 3864.0 3864 95.7890 854 3230 1 chr4A.!!$F2 2376
4 TraesCS1B01G421000 chr4A 723905105 723906852 1747 False 2902.0 2902 96.7960 854 2583 1 chr4A.!!$F3 1729
5 TraesCS1B01G421000 chr4B 459582050 459583651 1601 True 2632.0 2632 96.5040 1000 2583 1 chr4B.!!$R1 1583
6 TraesCS1B01G421000 chr4B 619807783 619810885 3102 False 2557.0 3522 96.7350 460 3481 2 chr4B.!!$F1 3021
7 TraesCS1B01G421000 chr4B 554165283 554166182 899 True 1522.0 1522 97.2220 1 899 1 chr4B.!!$R2 898
8 TraesCS1B01G421000 chr4B 661861329 661864732 3403 False 1456.0 1598 96.3325 72 3481 2 chr4B.!!$F2 3409
9 TraesCS1B01G421000 chr6B 683849451 683851956 2505 False 2088.0 2907 96.7890 138 2583 2 chr6B.!!$F3 2445
10 TraesCS1B01G421000 chr6B 20414265 20415027 762 False 1286.0 1286 97.1170 138 899 1 chr6B.!!$F1 761
11 TraesCS1B01G421000 chr6B 290995702 290996444 742 False 1249.0 1249 97.0390 854 1595 1 chr6B.!!$F2 741
12 TraesCS1B01G421000 chr2B 762179365 762181084 1719 True 2734.0 2734 95.1480 1732 3481 1 chr2B.!!$R2 1749
13 TraesCS1B01G421000 chr2B 731750839 731753531 2692 True 2255.0 2905 97.1040 854 3481 2 chr2B.!!$R3 2627
14 TraesCS1B01G421000 chr2B 178725099 178726042 943 False 1622.0 1622 97.6690 2538 3481 1 chr2B.!!$F1 943
15 TraesCS1B01G421000 chr2B 316841278 316842224 946 False 1602.0 1602 97.2570 2538 3481 1 chr2B.!!$F2 943
16 TraesCS1B01G421000 chr2B 371495188 371495954 766 True 1293.0 1293 97.1320 141 906 1 chr2B.!!$R1 765
17 TraesCS1B01G421000 chr7B 604990345 604992083 1738 True 2891.0 2891 96.6720 854 2592 1 chr7B.!!$R5 1738
18 TraesCS1B01G421000 chr7B 611568165 611569108 943 True 1661.0 1661 98.4110 2538 3481 1 chr7B.!!$R6 943
19 TraesCS1B01G421000 chr7B 179704013 179704956 943 True 1622.0 1622 97.6720 2538 3481 1 chr7B.!!$R4 943
20 TraesCS1B01G421000 chr7B 505084410 505087013 2603 False 1401.5 1598 96.5725 854 3481 2 chr7B.!!$F1 2627
21 TraesCS1B01G421000 chr7B 64910957 64911785 828 True 1386.0 1386 96.8640 72 899 1 chr7B.!!$R2 827
22 TraesCS1B01G421000 chr7B 29889104 29889862 758 True 1275.0 1275 96.9740 141 899 1 chr7B.!!$R1 758
23 TraesCS1B01G421000 chr5B 39639428 39641161 1733 False 2872.0 2872 96.5970 854 2583 1 chr5B.!!$F3 1729
24 TraesCS1B01G421000 chr5B 462701160 462702881 1721 False 2850.0 2850 96.4800 854 2583 1 chr5B.!!$F4 1729
25 TraesCS1B01G421000 chr5B 682754868 682755630 762 False 1269.0 1269 96.7230 138 899 1 chr5B.!!$F5 761
26 TraesCS1B01G421000 chr5B 36685759 36686501 742 False 1260.0 1260 97.3080 854 1595 1 chr5B.!!$F2 741
27 TraesCS1B01G421000 chr5B 36652328 36653070 742 False 1249.0 1249 97.0390 854 1595 1 chr5B.!!$F1 741
28 TraesCS1B01G421000 chr3B 326634974 326635706 732 True 1218.0 1218 96.5010 854 1595 1 chr3B.!!$R2 741

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
773 775 1.673920 GGCAGGACGTTTGAGTTTTCA 59.326 47.619 5.32 0.0 0.00 2.69 F
1162 1207 1.568504 TATCCACTTGAAGGAGCCGT 58.431 50.000 0.00 0.0 38.83 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2470 2982 4.735369 ACCACAAACAACTCAATATCCCA 58.265 39.130 0.00 0.00 0.00 4.37 R
3100 3739 2.919856 AGCTCCACTGTGCGAGGT 60.920 61.111 18.74 18.74 36.14 3.85 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
21 22 2.263021 GCTGCCATCTGTGTGTGCA 61.263 57.895 0.00 0.0 0.00 4.57
59 60 4.241555 ATCCTCGGCGGCACCATC 62.242 66.667 10.53 0.0 39.03 3.51
303 304 2.302260 TGACCTTTGCAAAATGGTCGA 58.698 42.857 30.35 21.9 45.08 4.20
455 456 5.401033 GCAAGTAACTGCATCAGTATGAG 57.599 43.478 0.00 0.0 44.62 2.90
524 526 5.738619 TCAGTTAATGCAAGTACTCCTCA 57.261 39.130 0.00 0.0 0.00 3.86
606 608 9.979578 ATGTTGTTAACTGAATTTTAATCAGCA 57.020 25.926 7.22 0.0 46.56 4.41
773 775 1.673920 GGCAGGACGTTTGAGTTTTCA 59.326 47.619 5.32 0.0 0.00 2.69
802 804 1.913762 CCACGTCTCCCCTCCACTT 60.914 63.158 0.00 0.0 0.00 3.16
1162 1207 1.568504 TATCCACTTGAAGGAGCCGT 58.431 50.000 0.00 0.0 38.83 5.68
1472 1682 8.972127 AGATGCAATACTAGTTCTGAAGTTCTA 58.028 33.333 0.00 0.0 0.00 2.10
1870 2381 5.865013 TGTTATGCTTGCTGTTTTGATCATG 59.135 36.000 0.00 0.0 0.00 3.07
1898 2409 5.539582 TGTTGTCTTGTAGTTGTTGTGAC 57.460 39.130 0.00 0.0 0.00 3.67
2075 2587 2.529389 AGGCCCAAGGAACTCCGT 60.529 61.111 0.00 0.0 38.49 4.69
2579 3162 7.288317 TGTTATGTTGAACAAGTTTGCTTTG 57.712 32.000 0.62 0.0 36.39 2.77
3109 3748 2.994387 CTTGCCTGTCACCTCGCACA 62.994 60.000 0.00 0.0 0.00 4.57
3174 3814 3.787001 GTGAAGGCGAGGGAGGGG 61.787 72.222 0.00 0.0 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.078214 CACCACTGATGATGGCGGT 60.078 57.895 0.00 0.00 41.31 5.68
59 60 1.079127 GTCGGGGATGACACCACTG 60.079 63.158 0.00 0.00 40.12 3.66
422 423 0.611896 GTTACTTGCATGGGCCTGGT 60.612 55.000 4.53 0.00 40.13 4.00
499 501 7.168219 TGAGGAGTACTTGCATTAACTGAAAT 58.832 34.615 0.00 0.00 0.00 2.17
524 526 6.426587 AGAGAAGAGAGAAAGTAGAGAGCAT 58.573 40.000 0.00 0.00 0.00 3.79
580 582 9.979578 TGCTGATTAAAATTCAGTTAACAACAT 57.020 25.926 8.61 0.00 34.27 2.71
679 681 3.202906 CTCCTGTTTCTGAAACGTCCAA 58.797 45.455 23.72 8.89 44.28 3.53
773 775 2.113243 GAGACGTGGGGAGTTGCCTT 62.113 60.000 0.00 0.00 36.66 4.35
802 804 0.681887 CTGCATCATGGGGAGTTGCA 60.682 55.000 0.00 0.00 38.84 4.08
915 959 1.151810 TGGAGGCAGAGGGGAGTTT 60.152 57.895 0.00 0.00 0.00 2.66
945 989 2.366301 TCCGCCATTGCCCTCCTA 60.366 61.111 0.00 0.00 0.00 2.94
1162 1207 2.011548 GCTGGTGCATACGACATCCAA 61.012 52.381 0.00 0.00 39.41 3.53
1645 2150 6.889301 ATTGCATCTCTTCAGAAACTTCAA 57.111 33.333 0.00 0.00 30.24 2.69
1740 2246 6.475504 AGACAACATTCTGTATGATCACCAA 58.524 36.000 0.00 0.00 37.69 3.67
1789 2296 8.236586 GCATTACAAGACAACATTCATAACAGA 58.763 33.333 0.00 0.00 0.00 3.41
1870 2381 5.424121 ACAACTACAAGACAACATTCTGC 57.576 39.130 0.00 0.00 0.00 4.26
1898 2409 9.383519 AGTATGATCACAACAACTACTAAATGG 57.616 33.333 0.00 0.00 0.00 3.16
1983 2494 9.974980 GAAACTACAGAATTAAAATGGGTTCAA 57.025 29.630 0.00 0.00 0.00 2.69
2470 2982 4.735369 ACCACAAACAACTCAATATCCCA 58.265 39.130 0.00 0.00 0.00 4.37
2701 3332 9.914131 GTCATTAGAAACTTGGAAGCTAAAAAT 57.086 29.630 0.00 0.00 0.00 1.82
3100 3739 2.919856 AGCTCCACTGTGCGAGGT 60.920 61.111 18.74 18.74 36.14 3.85
3109 3748 3.073735 CAGCCCTCGAGCTCCACT 61.074 66.667 6.99 0.00 42.61 4.00
3174 3814 2.124695 GTCCGCTCCCAATCCACC 60.125 66.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.