Multiple sequence alignment - TraesCS2A01G087800

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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 TraesCS2A01G087800 chr2A 100.000 2982 0 0 1 2982 41216873 41219854 0.000000e+00 5507.0
1 TraesCS2A01G087800 chr2A 97.704 2047 32 9 943 2982 41207960 41209998 0.000000e+00 3506.0
2 TraesCS2A01G087800 chr2A 98.681 455 6 0 915 1369 41227462 41227916 0.000000e+00 808.0
3 TraesCS2A01G087800 chr2A 85.496 393 50 4 1449 1837 41227921 41228310 1.290000e-108 403.0
4 TraesCS2A01G087800 chr2A 78.660 403 61 13 1461 1847 41170527 41170920 8.260000e-61 244.0
5 TraesCS2A01G087800 chr2D 92.801 1139 56 10 1001 2120 36783349 36784480 0.000000e+00 1626.0
6 TraesCS2A01G087800 chr2D 93.381 559 28 2 2433 2982 20065760 20066318 0.000000e+00 819.0
7 TraesCS2A01G087800 chr2D 79.553 313 42 15 1474 1778 36751448 36751746 1.400000e-48 204.0
8 TraesCS2A01G087800 chr2D 78.358 134 29 0 142 275 153044496 153044363 1.470000e-13 87.9
9 TraesCS2A01G087800 chr2B 91.530 1157 52 16 979 2120 63255074 63256199 0.000000e+00 1552.0
10 TraesCS2A01G087800 chr2B 96.889 900 3 4 1 898 748524204 748525080 0.000000e+00 1483.0
11 TraesCS2A01G087800 chr2B 89.991 1169 80 18 979 2120 63249838 63250996 0.000000e+00 1476.0
12 TraesCS2A01G087800 chr2B 88.825 1208 91 17 943 2120 63220835 63222028 0.000000e+00 1443.0
13 TraesCS2A01G087800 chr2B 98.976 293 2 1 601 893 784691087 784690796 9.470000e-145 523.0
14 TraesCS2A01G087800 chr2B 87.028 424 48 4 1418 1837 63260976 63261396 3.480000e-129 472.0
15 TraesCS2A01G087800 chr2B 95.720 257 10 1 914 1170 63260067 63260322 2.140000e-111 412.0
16 TraesCS2A01G087800 chr2B 91.600 250 17 4 1161 1410 63260768 63261013 2.850000e-90 342.0
17 TraesCS2A01G087800 chr2B 78.780 377 61 14 1479 1847 63140940 63141305 4.970000e-58 235.0
18 TraesCS2A01G087800 chr2B 89.091 55 2 4 2119 2170 714493164 714493111 6.900000e-07 65.8
19 TraesCS2A01G087800 chr6A 99.180 610 3 2 291 898 606314081 606313472 0.000000e+00 1098.0
20 TraesCS2A01G087800 chr6A 93.571 560 27 2 2432 2982 106682846 106682287 0.000000e+00 826.0
21 TraesCS2A01G087800 chr6A 91.111 45 3 1 2121 2165 121626563 121626520 3.210000e-05 60.2
22 TraesCS2A01G087800 chr4A 99.016 610 3 3 291 898 104129082 104129690 0.000000e+00 1090.0
23 TraesCS2A01G087800 chr4A 97.667 300 5 2 601 898 13435816 13435517 5.700000e-142 514.0
24 TraesCS2A01G087800 chr7B 97.541 610 6 3 291 898 7016952 7016350 0.000000e+00 1035.0
25 TraesCS2A01G087800 chr7B 97.806 319 5 2 582 898 495192304 495192622 1.560000e-152 549.0
26 TraesCS2A01G087800 chr7B 85.714 182 16 8 291 470 220965409 220965582 1.830000e-42 183.0
27 TraesCS2A01G087800 chr7B 82.673 202 23 9 2241 2437 613232690 613232884 5.110000e-38 169.0
28 TraesCS2A01G087800 chr7B 89.815 108 5 3 2172 2279 613233810 613233911 1.860000e-27 134.0
29 TraesCS2A01G087800 chr7B 89.815 108 5 3 2172 2279 613249751 613249852 1.860000e-27 134.0
30 TraesCS2A01G087800 chr7B 84.028 144 14 7 2259 2396 613244493 613244633 2.410000e-26 130.0
31 TraesCS2A01G087800 chr7B 84.028 144 14 7 2259 2396 613248647 613248787 2.410000e-26 130.0
32 TraesCS2A01G087800 chrUn 93.929 560 25 2 2432 2982 60979140 60978581 0.000000e+00 837.0
33 TraesCS2A01G087800 chrUn 94.131 443 2 5 458 898 462687800 462688220 0.000000e+00 652.0
34 TraesCS2A01G087800 chrUn 96.656 299 8 2 1 299 355376739 355377035 2.060000e-136 496.0
35 TraesCS2A01G087800 chrUn 84.774 243 33 2 1873 2111 326890008 326889766 1.070000e-59 241.0
36 TraesCS2A01G087800 chrUn 84.774 243 33 2 1873 2111 362953267 362953509 1.070000e-59 241.0
37 TraesCS2A01G087800 chrUn 88.095 84 8 2 2358 2440 243508558 243508476 6.800000e-17 99.0
38 TraesCS2A01G087800 chrUn 88.095 84 8 2 2358 2440 276475361 276475279 6.800000e-17 99.0
39 TraesCS2A01G087800 chrUn 88.095 84 8 2 2358 2440 422457276 422457194 6.800000e-17 99.0
40 TraesCS2A01G087800 chr6D 93.929 560 25 2 2432 2982 386160034 386159475 0.000000e+00 837.0
41 TraesCS2A01G087800 chr6D 93.571 560 27 2 2432 2982 30417390 30416831 0.000000e+00 826.0
42 TraesCS2A01G087800 chr6D 79.675 123 24 1 147 269 441893374 441893253 1.470000e-13 87.9
43 TraesCS2A01G087800 chr6B 93.571 560 27 2 2432 2982 219562530 219563089 0.000000e+00 826.0
44 TraesCS2A01G087800 chr6B 79.845 129 26 0 147 275 539620192 539620064 8.800000e-16 95.3
45 TraesCS2A01G087800 chr6B 89.130 46 3 2 2121 2165 42198069 42198025 4.150000e-04 56.5
46 TraesCS2A01G087800 chr3D 93.571 560 27 2 2432 2982 596701070 596701629 0.000000e+00 826.0
47 TraesCS2A01G087800 chr3D 93.571 560 27 2 2432 2982 606922184 606921625 0.000000e+00 826.0
48 TraesCS2A01G087800 chr3D 88.963 299 31 2 1 299 165505831 165506127 4.700000e-98 368.0
49 TraesCS2A01G087800 chr3D 92.308 91 6 1 2322 2412 611656328 611656417 8.680000e-26 128.0
50 TraesCS2A01G087800 chr3D 80.769 130 23 2 147 275 444068401 444068273 1.890000e-17 100.0
51 TraesCS2A01G087800 chr5B 95.652 299 12 1 1 299 253150437 253150734 2.080000e-131 479.0
52 TraesCS2A01G087800 chr4B 95.918 245 10 0 1 245 483852907 483852663 5.990000e-107 398.0
53 TraesCS2A01G087800 chr4B 90.769 130 11 1 291 419 168142690 168142561 3.950000e-39 172.0
54 TraesCS2A01G087800 chr4B 94.949 99 3 2 802 898 334214805 334214903 1.430000e-33 154.0
55 TraesCS2A01G087800 chr4B 95.122 41 0 1 259 299 483852672 483852634 2.480000e-06 63.9
56 TraesCS2A01G087800 chr3B 85.185 243 32 2 1873 2111 788978096 788977854 2.300000e-61 246.0
57 TraesCS2A01G087800 chr3B 84.774 243 33 2 1873 2111 788921807 788921565 1.070000e-59 241.0
58 TraesCS2A01G087800 chr3B 93.333 45 2 1 2121 2165 16149141 16149184 6.900000e-07 65.8
59 TraesCS2A01G087800 chr3B 93.333 45 2 1 2121 2165 16172060 16172103 6.900000e-07 65.8
60 TraesCS2A01G087800 chr3B 89.362 47 3 2 2120 2165 28117922 28117877 1.150000e-04 58.4
61 TraesCS2A01G087800 chr1B 85.000 180 20 5 291 469 514088649 514088476 3.050000e-40 176.0
62 TraesCS2A01G087800 chr1B 90.769 130 11 1 291 419 403410091 403410220 3.950000e-39 172.0
63 TraesCS2A01G087800 chr1B 84.337 166 17 7 306 470 365780126 365779969 1.430000e-33 154.0
64 TraesCS2A01G087800 chr1B 87.156 109 11 3 804 910 623629248 623629355 1.450000e-23 121.0
65 TraesCS2A01G087800 chr1B 88.095 84 8 2 2358 2440 45467923 45467841 6.800000e-17 99.0
66 TraesCS2A01G087800 chr1A 95.050 101 4 1 2158 2258 586946181 586946082 1.110000e-34 158.0
67 TraesCS2A01G087800 chr1A 87.069 116 10 4 2264 2377 586945188 586945076 3.120000e-25 126.0
68 TraesCS2A01G087800 chr7A 89.899 99 10 0 480 578 310581704 310581606 8.680000e-26 128.0
69 TraesCS2A01G087800 chr7A 90.385 52 4 1 2114 2165 650590757 650590707 1.920000e-07 67.6
70 TraesCS2A01G087800 chr7A 89.583 48 3 2 2119 2165 14724603 14724649 3.210000e-05 60.2


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 TraesCS2A01G087800 chr2A 41216873 41219854 2981 False 5507.0 5507 100.0000 1 2982 1 chr2A.!!$F3 2981
1 TraesCS2A01G087800 chr2A 41207960 41209998 2038 False 3506.0 3506 97.7040 943 2982 1 chr2A.!!$F2 2039
2 TraesCS2A01G087800 chr2A 41227462 41228310 848 False 605.5 808 92.0885 915 1837 2 chr2A.!!$F4 922
3 TraesCS2A01G087800 chr2D 36783349 36784480 1131 False 1626.0 1626 92.8010 1001 2120 1 chr2D.!!$F3 1119
4 TraesCS2A01G087800 chr2D 20065760 20066318 558 False 819.0 819 93.3810 2433 2982 1 chr2D.!!$F1 549
5 TraesCS2A01G087800 chr2B 748524204 748525080 876 False 1483.0 1483 96.8890 1 898 1 chr2B.!!$F4 897
6 TraesCS2A01G087800 chr2B 63249838 63250996 1158 False 1476.0 1476 89.9910 979 2120 1 chr2B.!!$F3 1141
7 TraesCS2A01G087800 chr2B 63220835 63222028 1193 False 1443.0 1443 88.8250 943 2120 1 chr2B.!!$F2 1177
8 TraesCS2A01G087800 chr2B 63255074 63261396 6322 False 694.5 1552 91.4695 914 2120 4 chr2B.!!$F5 1206
9 TraesCS2A01G087800 chr6A 606313472 606314081 609 True 1098.0 1098 99.1800 291 898 1 chr6A.!!$R3 607
10 TraesCS2A01G087800 chr6A 106682287 106682846 559 True 826.0 826 93.5710 2432 2982 1 chr6A.!!$R1 550
11 TraesCS2A01G087800 chr4A 104129082 104129690 608 False 1090.0 1090 99.0160 291 898 1 chr4A.!!$F1 607
12 TraesCS2A01G087800 chr7B 7016350 7016952 602 True 1035.0 1035 97.5410 291 898 1 chr7B.!!$R1 607
13 TraesCS2A01G087800 chrUn 60978581 60979140 559 True 837.0 837 93.9290 2432 2982 1 chrUn.!!$R1 550
14 TraesCS2A01G087800 chr6D 386159475 386160034 559 True 837.0 837 93.9290 2432 2982 1 chr6D.!!$R2 550
15 TraesCS2A01G087800 chr6D 30416831 30417390 559 True 826.0 826 93.5710 2432 2982 1 chr6D.!!$R1 550
16 TraesCS2A01G087800 chr6B 219562530 219563089 559 False 826.0 826 93.5710 2432 2982 1 chr6B.!!$F1 550
17 TraesCS2A01G087800 chr3D 596701070 596701629 559 False 826.0 826 93.5710 2432 2982 1 chr3D.!!$F2 550
18 TraesCS2A01G087800 chr3D 606921625 606922184 559 True 826.0 826 93.5710 2432 2982 1 chr3D.!!$R2 550

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
47 48 3.398920 CGCCTCACACCATTAGCG 58.601 61.111 0.0 0.0 37.39 4.26 F
895 896 4.866508 CACTCCGTGCTTTATATAGGGA 57.133 45.455 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2028 6.884096 TCGTGTTTTACTCGTTGTTTTAGA 57.116 33.333 0.0 0.0 36.59 2.10 R
2065 2116 2.040278 ACCTGCTTAGGTCTGATTGCAA 59.960 45.455 0.0 0.0 37.74 4.08 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
47 48 3.398920 CGCCTCACACCATTAGCG 58.601 61.111 0.00 0.0 37.39 4.26
834 835 7.208080 GCGGGTTGAATACTAAGAAATAGAGA 58.792 38.462 0.00 0.0 35.47 3.10
895 896 4.866508 CACTCCGTGCTTTATATAGGGA 57.133 45.455 0.00 0.0 0.00 4.20
896 897 5.209818 CACTCCGTGCTTTATATAGGGAA 57.790 43.478 0.00 0.0 0.00 3.97
897 898 5.607477 CACTCCGTGCTTTATATAGGGAAA 58.393 41.667 0.00 0.0 0.00 3.13
898 899 6.053005 CACTCCGTGCTTTATATAGGGAAAA 58.947 40.000 0.00 0.0 0.00 2.29
899 900 6.202954 CACTCCGTGCTTTATATAGGGAAAAG 59.797 42.308 0.00 0.0 34.14 2.27
900 901 6.099269 ACTCCGTGCTTTATATAGGGAAAAGA 59.901 38.462 0.00 0.0 33.05 2.52
901 902 6.522054 TCCGTGCTTTATATAGGGAAAAGAG 58.478 40.000 0.00 0.0 33.05 2.85
902 903 5.701290 CCGTGCTTTATATAGGGAAAAGAGG 59.299 44.000 0.00 0.0 33.05 3.69
903 904 5.701290 CGTGCTTTATATAGGGAAAAGAGGG 59.299 44.000 0.00 0.0 33.05 4.30
904 905 6.463897 CGTGCTTTATATAGGGAAAAGAGGGA 60.464 42.308 0.00 0.0 33.05 4.20
905 906 7.287810 GTGCTTTATATAGGGAAAAGAGGGAA 58.712 38.462 0.00 0.0 33.05 3.97
906 907 7.778382 GTGCTTTATATAGGGAAAAGAGGGAAA 59.222 37.037 0.00 0.0 33.05 3.13
907 908 7.998964 TGCTTTATATAGGGAAAAGAGGGAAAG 59.001 37.037 0.00 0.0 33.05 2.62
908 909 8.218488 GCTTTATATAGGGAAAAGAGGGAAAGA 58.782 37.037 0.00 0.0 33.05 2.52
915 916 7.336475 AGGGAAAAGAGGGAAAGATATATCC 57.664 40.000 9.18 0.0 34.85 2.59
916 917 6.857222 AGGGAAAAGAGGGAAAGATATATCCA 59.143 38.462 9.18 0.0 37.46 3.41
1977 2028 7.448748 AAATAACCGAATAACAAAGAGCACT 57.551 32.000 0.00 0.0 0.00 4.40
2065 2116 1.610522 GACTCCTGCAACACAAGCATT 59.389 47.619 0.00 0.0 41.82 3.56
2404 2761 4.884164 CCCCCTAATCTTGACTTTGTCATC 59.116 45.833 1.05 0.0 42.40 2.92
2474 3067 3.510360 GCTAAGATGGAGGCGGATAACTA 59.490 47.826 0.00 0.0 0.00 2.24
2611 4202 2.076863 AGTTTATGTCCAAGACTGCGC 58.923 47.619 0.00 0.0 33.15 6.09
2658 4284 3.396946 AGTTGTATGGGATGAGGATGCAT 59.603 43.478 0.00 0.0 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 2.897350 GATGCTGGCGGTGGCTAC 60.897 66.667 0.00 0.00 39.81 3.58
889 890 9.063484 GGATATATCTTTCCCTCTTTTCCCTAT 57.937 37.037 12.42 0.00 0.00 2.57
890 891 8.022666 TGGATATATCTTTCCCTCTTTTCCCTA 58.977 37.037 12.42 0.00 0.00 3.53
891 892 6.857222 TGGATATATCTTTCCCTCTTTTCCCT 59.143 38.462 12.42 0.00 0.00 4.20
892 893 7.091533 TGGATATATCTTTCCCTCTTTTCCC 57.908 40.000 12.42 0.00 0.00 3.97
893 894 9.593565 AATTGGATATATCTTTCCCTCTTTTCC 57.406 33.333 12.42 0.00 0.00 3.13
898 899 9.052365 GGTAGAATTGGATATATCTTTCCCTCT 57.948 37.037 12.42 9.30 0.00 3.69
899 900 8.268605 GGGTAGAATTGGATATATCTTTCCCTC 58.731 40.741 12.42 3.18 34.71 4.30
900 901 7.744068 TGGGTAGAATTGGATATATCTTTCCCT 59.256 37.037 12.42 7.45 36.59 4.20
901 902 7.928873 TGGGTAGAATTGGATATATCTTTCCC 58.071 38.462 12.42 12.13 36.39 3.97
902 903 8.826765 TCTGGGTAGAATTGGATATATCTTTCC 58.173 37.037 12.42 0.00 0.00 3.13
903 904 9.883142 CTCTGGGTAGAATTGGATATATCTTTC 57.117 37.037 12.42 12.20 31.21 2.62
904 905 8.830741 CCTCTGGGTAGAATTGGATATATCTTT 58.169 37.037 12.42 4.60 31.21 2.52
905 906 7.092668 GCCTCTGGGTAGAATTGGATATATCTT 60.093 40.741 12.42 0.00 31.21 2.40
906 907 6.385467 GCCTCTGGGTAGAATTGGATATATCT 59.615 42.308 12.42 0.00 31.21 1.98
907 908 6.587273 GCCTCTGGGTAGAATTGGATATATC 58.413 44.000 3.96 3.96 31.21 1.63
908 909 5.129485 CGCCTCTGGGTAGAATTGGATATAT 59.871 44.000 0.00 0.00 31.21 0.86
909 910 4.466370 CGCCTCTGGGTAGAATTGGATATA 59.534 45.833 0.00 0.00 31.21 0.86
910 911 3.261897 CGCCTCTGGGTAGAATTGGATAT 59.738 47.826 0.00 0.00 31.21 1.63
911 912 2.632996 CGCCTCTGGGTAGAATTGGATA 59.367 50.000 0.00 0.00 31.21 2.59
912 913 1.417890 CGCCTCTGGGTAGAATTGGAT 59.582 52.381 0.00 0.00 31.21 3.41
913 914 0.830648 CGCCTCTGGGTAGAATTGGA 59.169 55.000 0.00 0.00 31.21 3.53
914 915 0.179045 CCGCCTCTGGGTAGAATTGG 60.179 60.000 0.00 0.00 31.21 3.16
915 916 0.830648 TCCGCCTCTGGGTAGAATTG 59.169 55.000 0.00 0.00 31.21 2.32
916 917 1.123928 CTCCGCCTCTGGGTAGAATT 58.876 55.000 0.00 0.00 31.21 2.17
1977 2028 6.884096 TCGTGTTTTACTCGTTGTTTTAGA 57.116 33.333 0.00 0.00 36.59 2.10
2065 2116 2.040278 ACCTGCTTAGGTCTGATTGCAA 59.960 45.455 0.00 0.00 37.74 4.08
2404 2761 3.999663 AGATGAGAAAAAGCACGAGGAAG 59.000 43.478 0.00 0.00 0.00 3.46
2474 3067 5.279556 GCTACTTTCAACTGTAACTCCTCCT 60.280 44.000 0.00 0.00 0.00 3.69
2611 4202 2.893637 CTTCAGATACACCTTGGTCGG 58.106 52.381 0.00 0.00 0.00 4.79
2658 4284 3.107601 CTCCACAAGATCTAACCCCTCA 58.892 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.