Multiple sequence alignment - TraesCS3D01G351400

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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 TraesCS3D01G351400 chr3D 100.000 2411 0 0 1 2411 462456385 462453975 0.000000e+00 4453.0
1 TraesCS3D01G351400 chr3D 86.773 877 81 23 715 1569 462246913 462246050 0.000000e+00 944.0
2 TraesCS3D01G351400 chr3D 93.737 495 12 7 240 716 263006556 263007049 0.000000e+00 725.0
3 TraesCS3D01G351400 chr3D 78.214 840 114 38 730 1566 462791059 462790286 7.800000e-130 473.0
4 TraesCS3D01G351400 chr3D 79.744 469 80 11 1938 2397 462245554 462245092 2.310000e-85 326.0
5 TraesCS3D01G351400 chr3A 92.290 1712 89 24 715 2411 605241526 605239843 0.000000e+00 2390.0
6 TraesCS3D01G351400 chr3A 86.073 876 88 24 715 1569 605180471 605179609 0.000000e+00 911.0
7 TraesCS3D01G351400 chr3A 78.298 470 75 20 1938 2397 605176044 605175592 6.560000e-71 278.0
8 TraesCS3D01G351400 chr3A 82.906 234 30 8 2173 2402 605179032 605178805 4.060000e-48 202.0
9 TraesCS3D01G351400 chr3A 81.223 229 29 3 2182 2402 605176823 605176601 3.190000e-39 172.0
10 TraesCS3D01G351400 chr3B 92.579 1671 99 16 751 2411 614252141 614250486 0.000000e+00 2375.0
11 TraesCS3D01G351400 chr3B 87.400 873 83 24 715 1569 614266579 614265716 0.000000e+00 977.0
12 TraesCS3D01G351400 chr3B 86.567 871 85 20 715 1569 613812147 613811293 0.000000e+00 931.0
13 TraesCS3D01G351400 chr3B 86.667 675 59 14 1 653 306561894 306561229 0.000000e+00 719.0
14 TraesCS3D01G351400 chr3B 78.459 571 60 36 1717 2234 614265518 614264958 5.000000e-82 315.0
15 TraesCS3D01G351400 chr3B 79.070 430 57 15 1996 2402 613808620 613808201 5.110000e-67 265.0
16 TraesCS3D01G351400 chr3B 80.124 322 49 9 2082 2397 613810734 613810422 2.410000e-55 226.0
17 TraesCS3D01G351400 chr3B 91.935 62 5 0 2298 2359 614264959 614264898 1.190000e-13 87.9
18 TraesCS3D01G351400 chr6D 95.129 739 15 6 1 718 27531984 27531246 0.000000e+00 1146.0
19 TraesCS3D01G351400 chr6D 94.973 736 18 6 1 718 411198778 411198044 0.000000e+00 1136.0
20 TraesCS3D01G351400 chr6D 94.565 736 22 5 1 718 407225484 407226219 0.000000e+00 1122.0
21 TraesCS3D01G351400 chr6D 78.539 219 30 9 1355 1569 27757244 27757449 7.000000e-26 128.0
22 TraesCS3D01G351400 chrUn 95.082 732 26 5 1 722 27208860 27208129 0.000000e+00 1144.0
23 TraesCS3D01G351400 chr7D 95.115 737 17 6 1 718 15026144 15026880 0.000000e+00 1144.0
24 TraesCS3D01G351400 chr7D 90.845 426 29 7 996 1413 588409306 588409729 1.620000e-156 562.0
25 TraesCS3D01G351400 chr1D 94.830 735 19 8 1 716 303306452 303305718 0.000000e+00 1129.0
26 TraesCS3D01G351400 chr1D 94.181 739 21 7 1 718 32538907 32538170 0.000000e+00 1107.0
27 TraesCS3D01G351400 chr1D 95.683 278 11 1 442 718 481354050 481354327 1.700000e-121 446.0
28 TraesCS3D01G351400 chr2D 94.694 735 20 9 1 716 605462208 605462942 0.000000e+00 1123.0
29 TraesCS3D01G351400 chr2D 90.637 502 16 8 235 718 73115154 73114666 2.610000e-179 638.0
30 TraesCS3D01G351400 chr4D 94.158 736 18 10 1 718 9297533 9296805 0.000000e+00 1098.0
31 TraesCS3D01G351400 chr4D 81.667 240 37 5 1334 1569 6776545 6776309 2.450000e-45 193.0
32 TraesCS3D01G351400 chr4D 93.478 46 0 1 1001 1046 352755519 352755477 5.560000e-07 65.8
33 TraesCS3D01G351400 chr4D 87.500 56 4 2 996 1051 30195022 30195074 7.200000e-06 62.1
34 TraesCS3D01G351400 chr7A 94.609 371 16 3 1053 1419 680325382 680325752 2.690000e-159 571.0
35 TraesCS3D01G351400 chr7B 89.906 426 33 7 996 1413 661716680 661717103 7.580000e-150 540.0
36 TraesCS3D01G351400 chr1B 87.433 374 23 14 365 716 88000047 87999676 2.230000e-110 409.0
37 TraesCS3D01G351400 chr1A 85.475 179 22 4 2131 2306 242688846 242688669 1.470000e-42 183.0
38 TraesCS3D01G351400 chr4B 89.286 56 3 2 996 1051 43061217 43061269 1.550000e-07 67.6
39 TraesCS3D01G351400 chr4B 93.478 46 0 1 1001 1046 436312303 436312261 5.560000e-07 65.8


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 TraesCS3D01G351400 chr3D 462453975 462456385 2410 True 4453.000000 4453 100.000000 1 2411 1 chr3D.!!$R1 2410
1 TraesCS3D01G351400 chr3D 462245092 462246913 1821 True 635.000000 944 83.258500 715 2397 2 chr3D.!!$R3 1682
2 TraesCS3D01G351400 chr3D 462790286 462791059 773 True 473.000000 473 78.214000 730 1566 1 chr3D.!!$R2 836
3 TraesCS3D01G351400 chr3A 605239843 605241526 1683 True 2390.000000 2390 92.290000 715 2411 1 chr3A.!!$R1 1696
4 TraesCS3D01G351400 chr3A 605175592 605180471 4879 True 390.750000 911 82.125000 715 2402 4 chr3A.!!$R2 1687
5 TraesCS3D01G351400 chr3B 614250486 614252141 1655 True 2375.000000 2375 92.579000 751 2411 1 chr3B.!!$R2 1660
6 TraesCS3D01G351400 chr3B 306561229 306561894 665 True 719.000000 719 86.667000 1 653 1 chr3B.!!$R1 652
7 TraesCS3D01G351400 chr3B 613808201 613812147 3946 True 474.000000 931 81.920333 715 2402 3 chr3B.!!$R3 1687
8 TraesCS3D01G351400 chr3B 614264898 614266579 1681 True 459.966667 977 85.931333 715 2359 3 chr3B.!!$R4 1644
9 TraesCS3D01G351400 chr6D 27531246 27531984 738 True 1146.000000 1146 95.129000 1 718 1 chr6D.!!$R1 717
10 TraesCS3D01G351400 chr6D 411198044 411198778 734 True 1136.000000 1136 94.973000 1 718 1 chr6D.!!$R2 717
11 TraesCS3D01G351400 chr6D 407225484 407226219 735 False 1122.000000 1122 94.565000 1 718 1 chr6D.!!$F2 717
12 TraesCS3D01G351400 chrUn 27208129 27208860 731 True 1144.000000 1144 95.082000 1 722 1 chrUn.!!$R1 721
13 TraesCS3D01G351400 chr7D 15026144 15026880 736 False 1144.000000 1144 95.115000 1 718 1 chr7D.!!$F1 717
14 TraesCS3D01G351400 chr1D 303305718 303306452 734 True 1129.000000 1129 94.830000 1 716 1 chr1D.!!$R2 715
15 TraesCS3D01G351400 chr1D 32538170 32538907 737 True 1107.000000 1107 94.181000 1 718 1 chr1D.!!$R1 717
16 TraesCS3D01G351400 chr2D 605462208 605462942 734 False 1123.000000 1123 94.694000 1 716 1 chr2D.!!$F1 715
17 TraesCS3D01G351400 chr4D 9296805 9297533 728 True 1098.000000 1098 94.158000 1 718 1 chr4D.!!$R2 717

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
985 1062 0.476771 ATCTCTCGTCTCCTCCTCCC 59.523 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 4815 2.030893 TCAAAAGGCAGAAGCACATTCG 60.031 45.455 0.0 0.0 43.16 3.34 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
301 302 3.991536 GACCAGCTTCCCTCGACGC 62.992 68.421 0.00 0.0 33.54 5.19
516 550 2.756829 TGTACGCCGAACTTTTCATCA 58.243 42.857 0.00 0.0 0.00 3.07
783 834 2.746277 GTCACCGCGCCCAAATCT 60.746 61.111 0.00 0.0 0.00 2.40
809 860 0.969917 CCATCAAATCCAACGCCCCA 60.970 55.000 0.00 0.0 0.00 4.96
810 861 1.113788 CATCAAATCCAACGCCCCAT 58.886 50.000 0.00 0.0 0.00 4.00
811 862 1.481772 CATCAAATCCAACGCCCCATT 59.518 47.619 0.00 0.0 0.00 3.16
814 865 2.099405 CAAATCCAACGCCCCATTACT 58.901 47.619 0.00 0.0 0.00 2.24
860 911 2.681778 CCTCTCCGCCAGTCAGGT 60.682 66.667 0.00 0.0 40.61 4.00
979 1056 2.621055 CAAATCCGATCTCTCGTCTCCT 59.379 50.000 0.00 0.0 43.49 3.69
985 1062 0.476771 ATCTCTCGTCTCCTCCTCCC 59.523 60.000 0.00 0.0 0.00 4.30
987 1064 2.517402 CTCGTCTCCTCCTCCCCG 60.517 72.222 0.00 0.0 0.00 5.73
988 1065 4.816984 TCGTCTCCTCCTCCCCGC 62.817 72.222 0.00 0.0 0.00 6.13
989 1066 4.824515 CGTCTCCTCCTCCCCGCT 62.825 72.222 0.00 0.0 0.00 5.52
996 1073 2.602267 TCCTCCCCGCTCGAAACA 60.602 61.111 0.00 0.0 0.00 2.83
1436 1527 3.053455 CCGTCGCCTGAATCTCTTATTC 58.947 50.000 0.00 0.0 0.00 1.75
1684 3381 3.688272 CCATGTTTGATTAAGCTGCTCG 58.312 45.455 1.00 0.0 0.00 5.03
1705 3402 3.457234 GGGAAAGTTGACCTTTTGCTTG 58.543 45.455 0.00 0.0 43.47 4.01
1710 3407 0.102120 TTGACCTTTTGCTTGTGCCG 59.898 50.000 0.00 0.0 38.71 5.69
1715 3431 2.147958 CCTTTTGCTTGTGCCGTACTA 58.852 47.619 0.00 0.0 38.71 1.82
1808 3710 6.243216 TCTACAGGTGGAAAGTTTGTAACT 57.757 37.500 0.00 0.0 45.46 2.24
1936 4105 5.394333 GCCGTACTCTAGGAAGTTTCAGAAT 60.394 44.000 0.00 0.0 0.00 2.40
2084 5558 8.552083 TGATATGCTATACTATGCTTGGTTTG 57.448 34.615 0.00 0.0 0.00 2.93
2148 5650 7.734865 TGAGGTTGGGAGATGTACAGATTATAT 59.265 37.037 0.33 0.0 0.00 0.86
2319 6199 4.999950 CCAGTGCTGAAATGTCTACTTCTT 59.000 41.667 0.02 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.068472 TCTTCTCTTCACGAAGGACGC 60.068 52.381 6.94 0.00 46.94 5.19
237 238 4.680237 CACGCCTTGACCGCCTCA 62.680 66.667 0.00 0.00 0.00 3.86
372 379 4.155733 TCGGCGGCATCATCGGTT 62.156 61.111 10.53 0.00 0.00 4.44
416 430 2.883828 CGGGGTCTCTGTGCTTGGT 61.884 63.158 0.00 0.00 0.00 3.67
516 550 2.173669 CAAGCGGTGATCGGCGATT 61.174 57.895 24.81 7.73 43.21 3.34
745 796 4.832608 GTGGATCCGCGTGGGGAC 62.833 72.222 16.49 5.98 39.34 4.46
783 834 2.432444 GTTGGATTTGATGGACGGACA 58.568 47.619 0.00 0.00 0.00 4.02
809 860 1.217244 GGTGACGTGGCGGAGTAAT 59.783 57.895 0.00 0.00 0.00 1.89
810 861 2.652530 GGTGACGTGGCGGAGTAA 59.347 61.111 0.00 0.00 0.00 2.24
838 889 3.959991 GACTGGCGGAGAGGGTTGC 62.960 68.421 0.00 0.00 0.00 4.17
979 1056 2.602267 TGTTTCGAGCGGGGAGGA 60.602 61.111 0.00 0.00 0.00 3.71
985 1062 2.753966 CCATGGCTGTTTCGAGCGG 61.754 63.158 0.00 0.00 40.13 5.52
987 1064 2.486966 GCCATGGCTGTTTCGAGC 59.513 61.111 29.98 0.00 38.26 5.03
988 1065 2.787249 CGCCATGGCTGTTTCGAG 59.213 61.111 33.07 12.26 39.32 4.04
989 1066 3.430862 GCGCCATGGCTGTTTCGA 61.431 61.111 33.07 0.00 39.32 3.71
1436 1527 1.591248 CGAACATTCGGAACAAAGCG 58.409 50.000 6.11 0.00 46.30 4.68
1456 1547 2.104792 ACCCCCTATGATTGACGACATG 59.895 50.000 0.00 0.00 0.00 3.21
1705 3402 2.268298 CTCAACCATGTAGTACGGCAC 58.732 52.381 0.00 0.00 0.00 5.01
1710 3407 7.331193 CCAAGAGTTTACTCAACCATGTAGTAC 59.669 40.741 12.10 0.00 45.21 2.73
1715 3431 3.821033 GCCAAGAGTTTACTCAACCATGT 59.179 43.478 12.10 0.00 45.21 3.21
1847 3749 7.464977 GCGTTAAAAGCTCGGAATGAAATACTA 60.465 37.037 0.00 0.00 0.00 1.82
1901 4046 4.273969 CCTAGAGTACGGCTTGACTTCTAG 59.726 50.000 0.00 4.02 0.00 2.43
1991 4815 2.030893 TCAAAAGGCAGAAGCACATTCG 60.031 45.455 0.00 0.00 43.16 3.34
2084 5558 8.151141 TCATCTCATCAAATGAATTCTACAGC 57.849 34.615 7.05 0.00 39.11 4.40
2148 5650 9.707957 AATATGACCAAATAACAACTTCCCATA 57.292 29.630 0.00 0.00 0.00 2.74
2319 6199 8.493607 TGACCAAAATATCATCTGTATTCCTCA 58.506 33.333 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.