Multiple sequence alignment - TraesCS3B01G511100

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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 TraesCS3B01G511100 chr3B 100.000 2429 0 0 1 2429 754986074 754983646 0.000000e+00 4486.0
1 TraesCS3B01G511100 chr3B 92.179 179 3 1 1389 1556 754990813 754990635 2.410000e-60 243.0
2 TraesCS3B01G511100 chr3B 81.181 271 44 6 1884 2149 756182387 756182655 6.800000e-51 211.0
3 TraesCS3B01G511100 chr3B 78.151 357 46 23 2086 2429 754971887 754971550 5.300000e-47 198.0
4 TraesCS3B01G511100 chr3B 83.117 231 22 12 2088 2314 755042084 755041867 6.850000e-46 195.0
5 TraesCS3B01G511100 chr5A 90.175 1486 79 21 2 1422 708544706 708546189 0.000000e+00 1873.0
6 TraesCS3B01G511100 chr6B 93.043 1078 36 18 336 1393 21424930 21423872 0.000000e+00 1539.0
7 TraesCS3B01G511100 chr6B 92.351 353 13 7 1 340 21425494 21425143 7.800000e-135 490.0
8 TraesCS3B01G511100 chr6B 83.103 290 36 3 966 1255 176753513 176753789 4.010000e-63 252.0
9 TraesCS3B01G511100 chr3D 96.045 885 22 7 1557 2429 567221253 567222136 0.000000e+00 1428.0
10 TraesCS3B01G511100 chr3D 89.706 340 16 11 2 326 136757139 136756804 1.340000e-112 416.0
11 TraesCS3B01G511100 chr3D 77.654 358 46 24 2086 2429 567226112 567226449 1.150000e-43 187.0
12 TraesCS3B01G511100 chr3D 94.318 88 5 0 2228 2315 567217081 567217168 4.210000e-28 135.0
13 TraesCS3B01G511100 chr3A 90.659 835 69 6 1598 2429 701859380 701858552 0.000000e+00 1101.0
14 TraesCS3B01G511100 chr3A 90.550 836 69 7 1598 2429 700570956 700570127 0.000000e+00 1098.0
15 TraesCS3B01G511100 chr3A 84.581 227 27 6 965 1183 107603502 107603276 4.070000e-53 219.0
16 TraesCS3B01G511100 chr3A 81.481 270 45 5 1884 2149 700575616 700575348 1.460000e-52 217.0
17 TraesCS3B01G511100 chr3A 77.586 232 29 19 2088 2315 700575345 700575133 4.240000e-23 119.0
18 TraesCS3B01G511100 chr3A 94.872 39 1 1 2112 2149 701862441 701862403 2.610000e-05 60.2
19 TraesCS3B01G511100 chr6A 92.857 770 28 8 2 746 552735411 552736178 0.000000e+00 1092.0
20 TraesCS3B01G511100 chr6A 89.252 735 54 9 715 1447 552736193 552736904 0.000000e+00 896.0
21 TraesCS3B01G511100 chr1B 93.402 682 30 7 714 1393 555056159 555056827 0.000000e+00 996.0
22 TraesCS3B01G511100 chr1B 94.500 400 15 3 336 728 555003384 555003783 5.740000e-171 610.0
23 TraesCS3B01G511100 chr1B 94.250 400 16 3 336 728 555055726 555056125 2.670000e-169 604.0
24 TraesCS3B01G511100 chr1B 93.162 351 10 7 1 337 555002818 555003168 1.000000e-138 503.0
25 TraesCS3B01G511100 chr1B 92.877 351 11 7 1 337 555055160 555055510 4.660000e-137 497.0
26 TraesCS3B01G511100 chr1B 97.004 267 7 1 714 980 555003817 555004082 4.760000e-122 448.0
27 TraesCS3B01G511100 chr1B 90.148 203 7 4 1367 1557 588432785 588432986 4.010000e-63 252.0
28 TraesCS3B01G511100 chr1B 90.761 184 4 3 1385 1556 588426833 588427015 1.450000e-57 233.0
29 TraesCS3B01G511100 chrUn 90.369 758 55 10 1676 2429 41108205 41108948 0.000000e+00 979.0
30 TraesCS3B01G511100 chrUn 91.176 340 11 10 2 326 91550976 91550641 6.160000e-121 444.0
31 TraesCS3B01G511100 chr5D 89.514 391 29 8 1097 1477 27263052 27262664 3.630000e-133 484.0
32 TraesCS3B01G511100 chr6D 88.858 359 21 10 2 345 98732608 98732254 8.030000e-115 424.0
33 TraesCS3B01G511100 chr7D 89.118 340 19 8 2 326 145897558 145897894 8.090000e-110 407.0
34 TraesCS3B01G511100 chr7D 81.941 443 52 6 824 1256 239771897 239772321 1.380000e-92 350.0
35 TraesCS3B01G511100 chr7D 81.716 443 53 6 824 1256 549828723 549829147 6.430000e-91 344.0
36 TraesCS3B01G511100 chr2A 86.545 275 25 9 1213 1477 44038662 44038390 2.360000e-75 292.0
37 TraesCS3B01G511100 chr2A 96.000 175 6 1 888 1062 44038835 44038662 1.420000e-72 283.0
38 TraesCS3B01G511100 chr5B 90.659 182 6 1 1386 1556 605520552 605520371 5.220000e-57 231.0
39 TraesCS3B01G511100 chr5B 90.055 181 6 2 1388 1556 283990514 283990694 8.740000e-55 224.0
40 TraesCS3B01G511100 chr5B 87.624 202 12 3 1367 1556 283996874 283997074 3.140000e-54 222.0
41 TraesCS3B01G511100 chr5B 88.333 180 6 3 1388 1556 605523996 605523821 4.100000e-48 202.0
42 TraesCS3B01G511100 chr4B 84.302 172 12 6 1399 1555 33055209 33055380 1.160000e-33 154.0
43 TraesCS3B01G511100 chr1A 94.231 52 2 1 1430 1480 555721535 555721586 7.200000e-11 78.7
44 TraesCS3B01G511100 chr2D 93.878 49 3 0 761 809 327747967 327747919 9.310000e-10 75.0
45 TraesCS3B01G511100 chr4D 90.385 52 5 0 758 809 67444491 67444542 4.330000e-08 69.4


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 TraesCS3B01G511100 chr3B 754983646 754986074 2428 True 4486.000000 4486 100.000000 1 2429 1 chr3B.!!$R2 2428
1 TraesCS3B01G511100 chr5A 708544706 708546189 1483 False 1873.000000 1873 90.175000 2 1422 1 chr5A.!!$F1 1420
2 TraesCS3B01G511100 chr6B 21423872 21425494 1622 True 1014.500000 1539 92.697000 1 1393 2 chr6B.!!$R1 1392
3 TraesCS3B01G511100 chr3D 567221253 567226449 5196 False 807.500000 1428 86.849500 1557 2429 2 chr3D.!!$F2 872
4 TraesCS3B01G511100 chr3A 700570127 700570956 829 True 1098.000000 1098 90.550000 1598 2429 1 chr3A.!!$R2 831
5 TraesCS3B01G511100 chr3A 701858552 701862441 3889 True 580.600000 1101 92.765500 1598 2429 2 chr3A.!!$R4 831
6 TraesCS3B01G511100 chr6A 552735411 552736904 1493 False 994.000000 1092 91.054500 2 1447 2 chr6A.!!$F1 1445
7 TraesCS3B01G511100 chr1B 555055160 555056827 1667 False 699.000000 996 93.509667 1 1393 3 chr1B.!!$F4 1392
8 TraesCS3B01G511100 chr1B 555002818 555004082 1264 False 520.333333 610 94.888667 1 980 3 chr1B.!!$F3 979
9 TraesCS3B01G511100 chrUn 41108205 41108948 743 False 979.000000 979 90.369000 1676 2429 1 chrUn.!!$F1 753
10 TraesCS3B01G511100 chr5B 605520371 605523996 3625 True 216.500000 231 89.496000 1386 1556 2 chr5B.!!$R1 170

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
961 1311 3.46997 AGCGGCGGATCCATGACA 61.47 61.111 13.41 0.0 34.01 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 4147 0.038166 TTCCTCTGTTGCCATCACCC 59.962 55.0 0.0 0.0 0.0 4.61 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
171 187 9.745880 TCTAGAGGTACTAAATTTATCTTTGCG 57.254 33.333 0.00 0.00 41.55 4.85
448 681 8.759782 AGCCTCTTTTGCTAATTCTAGTAACTA 58.240 33.333 0.00 0.00 37.28 2.24
961 1311 3.469970 AGCGGCGGATCCATGACA 61.470 61.111 13.41 0.00 34.01 3.58
1075 1425 3.760035 TCGGACTCGAGCCTTGGC 61.760 66.667 13.61 2.97 40.88 4.52
1121 1489 3.200593 GCACATCGGGCTGCAGAG 61.201 66.667 20.43 7.97 33.31 3.35
1344 1718 3.248024 TCAGCTTTTCCCTGTTCTCCTA 58.752 45.455 0.00 0.00 0.00 2.94
1364 1738 1.272490 AGTCTTCTCGTCGGAATTGCA 59.728 47.619 0.00 0.00 0.00 4.08
1589 3669 4.642542 GGCGGGGCGTCGACTATC 62.643 72.222 14.70 2.42 34.89 2.08
1591 3671 3.117372 CGGGGCGTCGACTATCTT 58.883 61.111 14.70 0.00 0.00 2.40
1602 3689 4.608951 GTCGACTATCTTGCCGTAAATCT 58.391 43.478 8.70 0.00 0.00 2.40
1640 3727 1.244697 GCAGTGGACAGACCGAGAGA 61.245 60.000 0.00 0.00 42.61 3.10
1767 3857 1.346479 TTGGGGGTTCTGAACGTCCA 61.346 55.000 23.45 22.50 34.07 4.02
1775 3865 3.816523 GGTTCTGAACGTCCAAATTGGTA 59.183 43.478 12.28 0.00 39.03 3.25
1777 3867 4.074627 TCTGAACGTCCAAATTGGTACA 57.925 40.909 12.28 5.74 39.03 2.90
1924 4014 6.020678 CAGACGAACACCAAAAATTGAAACTC 60.021 38.462 0.00 0.00 0.00 3.01
1968 4058 0.671796 TTCGTGTGACCATCGACAGT 59.328 50.000 0.00 0.00 33.38 3.55
2087 4181 1.207329 GAGGAAACCAGGTGAGCGTAT 59.793 52.381 0.00 0.00 0.00 3.06
2169 4264 7.253422 CAGTTTCAGTGTTCTTTTGTCAGATT 58.747 34.615 0.00 0.00 0.00 2.40
2196 4292 7.833682 ACATTTGGTATCATGGACAGAAACATA 59.166 33.333 0.00 0.00 0.00 2.29
2244 4341 2.485903 ACATGAACGGTTAAAGCACGA 58.514 42.857 0.00 0.00 0.00 4.35
2317 4414 7.218228 TCATCACAAGTTAATGTTGCAAGAT 57.782 32.000 2.67 2.67 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 9.801714 CATTTTGTTGAATTATCTTGCAACTTC 57.198 29.630 0.00 0.0 40.78 3.01
121 136 7.981789 AGAGTACTGATTTGCGATTGAGAATTA 59.018 33.333 0.00 0.0 0.00 1.40
171 187 9.630098 TGCAATTGAGATTTGTTTTTATCTCTC 57.370 29.630 10.34 0.0 44.51 3.20
448 681 4.527427 GTCTCTTTACACTAAGGTCCCTGT 59.473 45.833 0.00 0.0 0.00 4.00
961 1311 1.000955 CTGCACCAGTACGACTTTCCT 59.999 52.381 0.00 0.0 0.00 3.36
991 1341 4.408821 TCGGTGCATGGCTGGGTC 62.409 66.667 0.00 0.0 0.00 4.46
1062 1412 4.749310 CTGCGCCAAGGCTCGAGT 62.749 66.667 15.13 0.0 39.32 4.18
1125 1493 4.790962 AGCCCGTGCAGCCATCTG 62.791 66.667 0.00 0.0 43.16 2.90
1133 1501 4.980805 GTCGAACCAGCCCGTGCA 62.981 66.667 0.00 0.0 41.13 4.57
1344 1718 1.272490 TGCAATTCCGACGAGAAGACT 59.728 47.619 0.00 0.0 0.00 3.24
1364 1738 4.749310 CAGCACGCTCTCCGGCTT 62.749 66.667 0.00 0.0 40.05 4.35
1472 3541 2.504244 CAGTCGCGTCTCCGTTCC 60.504 66.667 5.77 0.0 36.15 3.62
1504 3584 0.754472 GAATAATCCCCGTCCCGTCA 59.246 55.000 0.00 0.0 0.00 4.35
1544 3624 9.582431 GCTGTATGTAGACACTGTTAAGATTAA 57.418 33.333 0.00 0.0 0.00 1.40
1589 3669 2.416547 CACTGTCCAGATTTACGGCAAG 59.583 50.000 0.40 0.0 0.00 4.01
1591 3671 1.338674 CCACTGTCCAGATTTACGGCA 60.339 52.381 0.40 0.0 0.00 5.69
1602 3689 1.275666 CCAGTCATACCCACTGTCCA 58.724 55.000 0.00 0.0 39.84 4.02
1767 3857 9.466497 AGTCATGATATTTGTCTGTACCAATTT 57.534 29.630 0.00 0.0 0.00 1.82
1775 3865 7.414873 GCAATGTGAGTCATGATATTTGTCTGT 60.415 37.037 0.00 0.0 36.81 3.41
1777 3867 6.600427 TGCAATGTGAGTCATGATATTTGTCT 59.400 34.615 0.00 0.0 36.81 3.41
1924 4014 1.311859 TGCCTCAGCTTGTCAGTTTG 58.688 50.000 0.00 0.0 40.80 2.93
2053 4147 0.038166 TTCCTCTGTTGCCATCACCC 59.962 55.000 0.00 0.0 0.00 4.61
2087 4181 3.118629 TGCAAACCAGCACATAACCAAAA 60.119 39.130 0.00 0.0 40.11 2.44
2169 4264 7.171653 TGTTTCTGTCCATGATACCAAATGTA 58.828 34.615 0.00 0.0 0.00 2.29
2196 4292 1.474478 CGTGCAGGTCTGATAGTCTGT 59.526 52.381 1.65 0.0 0.00 3.41
2244 4341 0.327924 TCCGGACATTGCTGGATGTT 59.672 50.000 0.00 0.0 40.21 2.71
2317 4414 2.036098 CCATTGCCTGTCCCAGCA 59.964 61.111 0.00 0.0 0.00 4.41
2331 4428 2.158943 GCGGCTAGGTTAGAAAGACCAT 60.159 50.000 0.00 0.0 39.71 3.55
2332 4429 1.206371 GCGGCTAGGTTAGAAAGACCA 59.794 52.381 0.00 0.0 39.71 4.02


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

AutoCloner maintained by Alex Coulton.