Multiple sequence alignment - TraesCS3B01G082900

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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 TraesCS3B01G082900 chr3B 100.000 2825 0 0 1 2825 52435712 52438536 0.000000e+00 5217.0
1 TraesCS3B01G082900 chr3B 90.410 2023 129 27 1 1975 51227518 51229523 0.000000e+00 2601.0
2 TraesCS3B01G082900 chr3B 89.231 2015 79 40 33 1971 52778717 52776765 0.000000e+00 2392.0
3 TraesCS3B01G082900 chr3B 89.585 1757 132 26 254 1971 51770854 51772598 0.000000e+00 2183.0
4 TraesCS3B01G082900 chr3B 89.173 1524 116 18 484 1971 51947264 51948774 0.000000e+00 1855.0
5 TraesCS3B01G082900 chr3B 99.649 854 3 0 1972 2825 39305328 39306181 0.000000e+00 1561.0
6 TraesCS3B01G082900 chr3B 88.992 1081 94 9 912 1971 51789387 51790463 0.000000e+00 1314.0
7 TraesCS3B01G082900 chr3B 86.738 1033 118 6 958 1971 52839512 52838480 0.000000e+00 1131.0
8 TraesCS3B01G082900 chr3B 85.134 1083 136 9 912 1972 51249004 51250083 0.000000e+00 1085.0
9 TraesCS3B01G082900 chr3B 84.715 1086 136 14 914 1971 51243245 51244328 0.000000e+00 1059.0
10 TraesCS3B01G082900 chr3B 93.976 498 17 3 1 485 51946663 51947160 0.000000e+00 741.0
11 TraesCS3B01G082900 chr3B 85.235 149 14 5 616 756 52854139 52853991 2.270000e-31 147.0
12 TraesCS3B01G082900 chr3B 81.000 100 14 4 353 451 51788878 51788973 1.090000e-09 75.0
13 TraesCS3B01G082900 chr3A 88.310 1343 118 17 651 1971 40917744 40919069 0.000000e+00 1574.0
14 TraesCS3B01G082900 chr3A 87.917 1258 101 20 759 1967 41603908 41605163 0.000000e+00 1434.0
15 TraesCS3B01G082900 chr3A 87.599 1258 109 17 760 1971 41354817 41356073 0.000000e+00 1415.0
16 TraesCS3B01G082900 chr3A 89.259 1080 92 8 912 1971 41368743 41369818 0.000000e+00 1330.0
17 TraesCS3B01G082900 chr3A 87.672 1087 107 15 912 1977 41537140 41538220 0.000000e+00 1240.0
18 TraesCS3B01G082900 chr3A 85.926 1080 127 10 912 1971 41064147 41065221 0.000000e+00 1129.0
19 TraesCS3B01G082900 chr3A 89.922 129 3 1 1 119 40915957 40916085 1.050000e-34 158.0
20 TraesCS3B01G082900 chr3A 85.526 152 14 5 616 759 41354639 41354790 4.870000e-33 152.0
21 TraesCS3B01G082900 chr3A 97.561 41 1 0 612 652 40917690 40917730 1.400000e-08 71.3
22 TraesCS3B01G082900 chr7B 99.534 858 4 0 1968 2825 66209426 66208569 0.000000e+00 1563.0
23 TraesCS3B01G082900 chr7B 99.532 855 3 1 1972 2825 22952612 22953466 0.000000e+00 1555.0
24 TraesCS3B01G082900 chr1B 99.649 855 3 0 1971 2825 16744183 16745037 0.000000e+00 1563.0
25 TraesCS3B01G082900 chr1B 99.534 858 4 0 1968 2825 349819655 349820512 0.000000e+00 1563.0
26 TraesCS3B01G082900 chr5B 99.532 854 4 0 1972 2825 203371554 203370701 0.000000e+00 1555.0
27 TraesCS3B01G082900 chr5A 99.532 854 4 0 1972 2825 635448081 635447228 0.000000e+00 1555.0
28 TraesCS3B01G082900 chr2B 99.532 854 4 0 1972 2825 184650884 184650031 0.000000e+00 1555.0
29 TraesCS3B01G082900 chr4A 99.415 855 5 0 1971 2825 619519943 619519089 0.000000e+00 1552.0
30 TraesCS3B01G082900 chr3D 89.227 1086 87 10 912 1971 30006612 30007693 0.000000e+00 1330.0
31 TraesCS3B01G082900 chr3D 89.256 242 23 2 33 274 30063837 30064075 1.640000e-77 300.0
32 TraesCS3B01G082900 chr3D 83.838 99 11 1 648 746 29970494 29970587 3.880000e-14 89.8
33 TraesCS3B01G082900 chr7A 97.059 34 0 1 584 616 139671982 139671949 3.930000e-04 56.5


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 TraesCS3B01G082900 chr3B 52435712 52438536 2824 False 5217.0 5217 100.0000 1 2825 1 chr3B.!!$F6 2824
1 TraesCS3B01G082900 chr3B 51227518 51229523 2005 False 2601.0 2601 90.4100 1 1975 1 chr3B.!!$F2 1974
2 TraesCS3B01G082900 chr3B 52776765 52778717 1952 True 2392.0 2392 89.2310 33 1971 1 chr3B.!!$R1 1938
3 TraesCS3B01G082900 chr3B 51770854 51772598 1744 False 2183.0 2183 89.5850 254 1971 1 chr3B.!!$F5 1717
4 TraesCS3B01G082900 chr3B 39305328 39306181 853 False 1561.0 1561 99.6490 1972 2825 1 chr3B.!!$F1 853
5 TraesCS3B01G082900 chr3B 51946663 51948774 2111 False 1298.0 1855 91.5745 1 1971 2 chr3B.!!$F8 1970
6 TraesCS3B01G082900 chr3B 52838480 52839512 1032 True 1131.0 1131 86.7380 958 1971 1 chr3B.!!$R2 1013
7 TraesCS3B01G082900 chr3B 51249004 51250083 1079 False 1085.0 1085 85.1340 912 1972 1 chr3B.!!$F4 1060
8 TraesCS3B01G082900 chr3B 51243245 51244328 1083 False 1059.0 1059 84.7150 914 1971 1 chr3B.!!$F3 1057
9 TraesCS3B01G082900 chr3B 51788878 51790463 1585 False 694.5 1314 84.9960 353 1971 2 chr3B.!!$F7 1618
10 TraesCS3B01G082900 chr3A 41603908 41605163 1255 False 1434.0 1434 87.9170 759 1967 1 chr3A.!!$F4 1208
11 TraesCS3B01G082900 chr3A 41368743 41369818 1075 False 1330.0 1330 89.2590 912 1971 1 chr3A.!!$F2 1059
12 TraesCS3B01G082900 chr3A 41537140 41538220 1080 False 1240.0 1240 87.6720 912 1977 1 chr3A.!!$F3 1065
13 TraesCS3B01G082900 chr3A 41064147 41065221 1074 False 1129.0 1129 85.9260 912 1971 1 chr3A.!!$F1 1059
14 TraesCS3B01G082900 chr3A 41354639 41356073 1434 False 783.5 1415 86.5625 616 1971 2 chr3A.!!$F6 1355
15 TraesCS3B01G082900 chr3A 40915957 40919069 3112 False 601.1 1574 91.9310 1 1971 3 chr3A.!!$F5 1970
16 TraesCS3B01G082900 chr7B 66208569 66209426 857 True 1563.0 1563 99.5340 1968 2825 1 chr7B.!!$R1 857
17 TraesCS3B01G082900 chr7B 22952612 22953466 854 False 1555.0 1555 99.5320 1972 2825 1 chr7B.!!$F1 853
18 TraesCS3B01G082900 chr1B 16744183 16745037 854 False 1563.0 1563 99.6490 1971 2825 1 chr1B.!!$F1 854
19 TraesCS3B01G082900 chr1B 349819655 349820512 857 False 1563.0 1563 99.5340 1968 2825 1 chr1B.!!$F2 857
20 TraesCS3B01G082900 chr5B 203370701 203371554 853 True 1555.0 1555 99.5320 1972 2825 1 chr5B.!!$R1 853
21 TraesCS3B01G082900 chr5A 635447228 635448081 853 True 1555.0 1555 99.5320 1972 2825 1 chr5A.!!$R1 853
22 TraesCS3B01G082900 chr2B 184650031 184650884 853 True 1555.0 1555 99.5320 1972 2825 1 chr2B.!!$R1 853
23 TraesCS3B01G082900 chr4A 619519089 619519943 854 True 1552.0 1552 99.4150 1971 2825 1 chr4A.!!$R1 854
24 TraesCS3B01G082900 chr3D 30006612 30007693 1081 False 1330.0 1330 89.2270 912 1971 1 chr3D.!!$F2 1059

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
686 1967 0.670162 CATTGGATGGCGCCCTTAAG 59.330 55.0 26.77 3.81 0.0 1.85 F
687 1968 1.109323 ATTGGATGGCGCCCTTAAGC 61.109 55.0 26.77 7.76 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 2884 3.913855 TTGGGCTCAACAAGGTTGA 57.086 47.368 10.96 10.96 0.00 3.18 R
2683 4100 4.276058 TGCATGTGAACATCTCTTGAGA 57.724 40.909 2.59 2.59 33.61 3.27 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
19 20 4.803426 CGCCTCCTCGAGTGTGCC 62.803 72.222 12.31 0.00 0.00 5.01
42 53 5.432885 TTTCACCGATTTTTGTTCTCTCC 57.567 39.130 0.00 0.00 0.00 3.71
295 314 3.923354 CTGCAGGTGTAGAAGCAGT 57.077 52.632 5.57 0.00 46.92 4.40
297 316 3.533606 CTGCAGGTGTAGAAGCAGTAT 57.466 47.619 5.57 0.00 46.92 2.12
319 461 4.222336 TGGTTTTCTGGTGGTGATTGAAT 58.778 39.130 0.00 0.00 0.00 2.57
403 1057 9.262358 GATCACTATTGGTTCTTACTATTGACC 57.738 37.037 0.00 0.00 0.00 4.02
686 1967 0.670162 CATTGGATGGCGCCCTTAAG 59.330 55.000 26.77 3.81 0.00 1.85
687 1968 1.109323 ATTGGATGGCGCCCTTAAGC 61.109 55.000 26.77 7.76 0.00 3.09
751 2034 4.439305 ACACATGTAAATTTGCGAGCAT 57.561 36.364 0.00 0.00 0.00 3.79
918 2295 8.490355 CCTTGTCTAATTTTTGAAAGCATTCAC 58.510 33.333 3.39 0.00 45.01 3.18
1071 2460 6.082338 GCAAAATATCATTACAGATGAGGCG 58.918 40.000 0.00 0.00 0.00 5.52
1490 2884 8.816894 TCCAACATCTAGACTGATAAGAAGTTT 58.183 33.333 0.00 0.00 30.99 2.66
1725 3119 5.740099 GCGAGACTACAATGAAGTTACTCTC 59.260 44.000 0.00 0.00 0.00 3.20
1842 3252 2.251409 AGATGATGTCTGGCATTCCG 57.749 50.000 0.00 0.00 38.06 4.30
2683 4100 9.495572 CTGTAAGAATCAGAAAGGTTACTCTTT 57.504 33.333 0.00 0.00 36.37 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.452777 GGAGAGAACAAAAATCGGTGAAAG 58.547 41.667 0.00 0.00 0.00 2.62
42 53 2.678324 GTGTGGAGAAGAGGAAGAACG 58.322 52.381 0.00 0.00 0.00 3.95
208 224 2.897207 CCTCCCACCGCGATACAA 59.103 61.111 8.23 0.00 0.00 2.41
295 314 4.991776 TCAATCACCACCAGAAAACCATA 58.008 39.130 0.00 0.00 0.00 2.74
296 315 3.843422 TCAATCACCACCAGAAAACCAT 58.157 40.909 0.00 0.00 0.00 3.55
297 316 3.304911 TCAATCACCACCAGAAAACCA 57.695 42.857 0.00 0.00 0.00 3.67
319 461 6.998673 TCAGTCGATCTCATAGAAGATTACCA 59.001 38.462 0.00 0.00 36.13 3.25
403 1057 1.798813 CTCTCCGGTCAAGGAAAAACG 59.201 52.381 0.00 0.00 40.25 3.60
686 1967 9.586435 AAATATTTATTAGTTTGTCTTGCCTGC 57.414 29.630 0.00 0.00 0.00 4.85
918 2295 4.516365 AGCAGAAATTGGAAGCTGAAAG 57.484 40.909 0.00 0.00 33.67 2.62
1071 2460 4.658901 TCTTCCACCCCAAGGATTAGTATC 59.341 45.833 0.00 0.00 34.56 2.24
1295 2687 2.164219 CCTTTACATGCAGCCGATTTGT 59.836 45.455 0.00 0.00 0.00 2.83
1473 2866 8.429641 ACAAGGTTGAAACTTCTTATCAGTCTA 58.570 33.333 0.00 0.00 0.00 2.59
1490 2884 3.913855 TTGGGCTCAACAAGGTTGA 57.086 47.368 10.96 10.96 0.00 3.18
1842 3252 8.709308 AGGCCTTAATAGATACATCCATACATC 58.291 37.037 0.00 0.00 0.00 3.06
2683 4100 4.276058 TGCATGTGAACATCTCTTGAGA 57.724 40.909 2.59 2.59 33.61 3.27


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

AutoCloner maintained by Alex Coulton.