Multiple sequence alignment - TraesCS3D01G026600

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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 TraesCS3D01G026600 chr3D 100.000 3044 0 0 1 3044 9071272 9074315 0.000000e+00 5622
1 TraesCS3D01G026600 chr3D 97.754 846 19 0 1 846 602822285 602821440 0.000000e+00 1458
2 TraesCS3D01G026600 chr3D 97.633 845 14 2 1 845 143152590 143151752 0.000000e+00 1445
3 TraesCS3D01G026600 chr3D 92.697 534 24 4 12 545 321869880 321869362 0.000000e+00 756
4 TraesCS3D01G026600 chr3D 88.800 125 14 0 926 1050 9098475 9098351 1.460000e-33 154
5 TraesCS3D01G026600 chr3B 93.833 1800 80 6 852 2634 11128427 11130212 0.000000e+00 2680
6 TraesCS3D01G026600 chr3B 90.222 1350 87 16 1319 2646 11224923 11226249 0.000000e+00 1720
7 TraesCS3D01G026600 chr3B 90.456 482 44 2 2165 2646 809344721 809344242 4.280000e-178 634
8 TraesCS3D01G026600 chr3B 92.145 331 18 2 2715 3044 11227985 11228308 7.690000e-126 460
9 TraesCS3D01G026600 chr3B 94.068 236 7 1 2809 3044 11164016 11164244 4.830000e-93 351
10 TraesCS3D01G026600 chr3B 94.253 174 6 2 2642 2811 11130922 11131095 2.330000e-66 263
11 TraesCS3D01G026600 chr3A 90.814 1535 93 13 857 2359 11904684 11903166 0.000000e+00 2010
12 TraesCS3D01G026600 chr3A 90.891 505 43 3 2151 2655 730911707 730912208 0.000000e+00 675
13 TraesCS3D01G026600 chr3A 91.724 290 22 2 2357 2646 11902094 11901807 4.730000e-108 401
14 TraesCS3D01G026600 chr3A 90.164 305 15 2 2748 3044 11901648 11901351 1.710000e-102 383
15 TraesCS3D01G026600 chr7D 98.221 843 15 0 1 843 613373113 613372271 0.000000e+00 1474
16 TraesCS3D01G026600 chr7D 97.278 845 12 1 1 845 64068826 64069659 0.000000e+00 1423
17 TraesCS3D01G026600 chr2D 97.993 847 12 1 1 842 43781089 43781935 0.000000e+00 1465
18 TraesCS3D01G026600 chr2D 97.867 844 15 2 1 843 595505657 595506498 0.000000e+00 1456
19 TraesCS3D01G026600 chr6D 97.625 842 13 1 1 835 472321855 472321014 0.000000e+00 1437
20 TraesCS3D01G026600 chr5D 97.396 845 21 1 1 845 435681279 435682122 0.000000e+00 1437
21 TraesCS3D01G026600 chr5B 91.837 833 48 12 12 843 110044716 110043903 0.000000e+00 1144


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 TraesCS3D01G026600 chr3D 9071272 9074315 3043 False 5622.000000 5622 100.000000 1 3044 1 chr3D.!!$F1 3043
1 TraesCS3D01G026600 chr3D 602821440 602822285 845 True 1458.000000 1458 97.754000 1 846 1 chr3D.!!$R4 845
2 TraesCS3D01G026600 chr3D 143151752 143152590 838 True 1445.000000 1445 97.633000 1 845 1 chr3D.!!$R2 844
3 TraesCS3D01G026600 chr3D 321869362 321869880 518 True 756.000000 756 92.697000 12 545 1 chr3D.!!$R3 533
4 TraesCS3D01G026600 chr3B 11128427 11131095 2668 False 1471.500000 2680 94.043000 852 2811 2 chr3B.!!$F2 1959
5 TraesCS3D01G026600 chr3B 11224923 11228308 3385 False 1090.000000 1720 91.183500 1319 3044 2 chr3B.!!$F3 1725
6 TraesCS3D01G026600 chr3A 11901351 11904684 3333 True 931.333333 2010 90.900667 857 3044 3 chr3A.!!$R1 2187
7 TraesCS3D01G026600 chr3A 730911707 730912208 501 False 675.000000 675 90.891000 2151 2655 1 chr3A.!!$F1 504
8 TraesCS3D01G026600 chr7D 613372271 613373113 842 True 1474.000000 1474 98.221000 1 843 1 chr7D.!!$R1 842
9 TraesCS3D01G026600 chr7D 64068826 64069659 833 False 1423.000000 1423 97.278000 1 845 1 chr7D.!!$F1 844
10 TraesCS3D01G026600 chr2D 43781089 43781935 846 False 1465.000000 1465 97.993000 1 842 1 chr2D.!!$F1 841
11 TraesCS3D01G026600 chr2D 595505657 595506498 841 False 1456.000000 1456 97.867000 1 843 1 chr2D.!!$F2 842
12 TraesCS3D01G026600 chr6D 472321014 472321855 841 True 1437.000000 1437 97.625000 1 835 1 chr6D.!!$R1 834
13 TraesCS3D01G026600 chr5D 435681279 435682122 843 False 1437.000000 1437 97.396000 1 845 1 chr5D.!!$F1 844
14 TraesCS3D01G026600 chr5B 110043903 110044716 813 True 1144.000000 1144 91.837000 12 843 1 chr5B.!!$R1 831

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
912 930 0.463654 AAAATCGCTAGCCGCCATGA 60.464 50.0 9.66 0.0 36.73 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2296 0.179145 GATCATTGGCAGCACAGCAC 60.179 55.0 0.0 0.0 35.83 4.4 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
220 221 3.827898 CCGGCCTCGTCTGAGTCC 61.828 72.222 0.00 0.00 40.85 3.85
355 356 2.650116 GCTGCTTCCTCCTCCGTGA 61.650 63.158 0.00 0.00 0.00 4.35
390 391 2.441348 TATCCGTCAGCCTCGCCA 60.441 61.111 0.00 0.00 0.00 5.69
573 574 2.096248 GTGTGGAGAGTTCGAGAGGAT 58.904 52.381 0.00 0.00 0.00 3.24
727 735 7.972832 CCAGAAGAAAAGAAAATCAGATAAGCC 59.027 37.037 0.00 0.00 0.00 4.35
758 768 4.263209 CGTGCGTTGCAAGCCCAA 62.263 61.111 15.29 0.00 41.47 4.12
846 861 3.754965 GTGCATTGGAGATGCCCTAATA 58.245 45.455 8.36 0.00 43.94 0.98
847 862 4.144297 GTGCATTGGAGATGCCCTAATAA 58.856 43.478 8.36 0.00 43.94 1.40
848 863 4.584325 GTGCATTGGAGATGCCCTAATAAA 59.416 41.667 8.36 0.00 43.94 1.40
849 864 4.584325 TGCATTGGAGATGCCCTAATAAAC 59.416 41.667 8.36 0.00 43.94 2.01
850 865 4.829492 GCATTGGAGATGCCCTAATAAACT 59.171 41.667 0.00 0.00 39.01 2.66
865 880 9.135189 CCCTAATAAACTCATCAATCAATGGAA 57.865 33.333 0.00 0.00 0.00 3.53
878 893 3.866379 ATGGAAGCCAGGCACGCAA 62.866 57.895 15.80 0.00 36.75 4.85
912 930 0.463654 AAAATCGCTAGCCGCCATGA 60.464 50.000 9.66 0.00 36.73 3.07
941 959 2.284921 TCCAGCTCCTCCACCCTG 60.285 66.667 0.00 0.00 0.00 4.45
994 1018 2.262915 CGTCTCACCCAGGTCAGC 59.737 66.667 0.00 0.00 0.00 4.26
1050 1074 2.252072 GACATACCAAGGGCTCGGCA 62.252 60.000 0.00 0.00 0.00 5.69
1128 1152 3.384532 TTCTACCCCGACGGCCAC 61.385 66.667 8.86 0.00 33.26 5.01
1297 1321 1.372087 CTGCGCCTTCTCCACCAATC 61.372 60.000 4.18 0.00 0.00 2.67
1415 1439 2.969628 ATCATCGTGTCCAAGGAGAC 57.030 50.000 6.33 6.33 37.28 3.36
1436 1460 1.991121 TCCACTGAGTACGTTCCTGT 58.009 50.000 0.00 0.00 0.00 4.00
1492 1528 1.379176 CTCGGTCAGCTCCTCTCCA 60.379 63.158 0.00 0.00 0.00 3.86
1541 1577 2.044555 TCGGCGGTGAGATCTTCGT 61.045 57.895 7.21 0.00 0.00 3.85
1587 1623 1.535444 TTCCTCCGTCTTCAGGGCA 60.535 57.895 0.00 0.00 0.00 5.36
1653 1689 4.403432 CACATAAAGGACATGGAGCCAAAT 59.597 41.667 0.00 0.00 0.00 2.32
1660 1696 3.953612 GGACATGGAGCCAAATGTATTCA 59.046 43.478 0.00 0.00 37.15 2.57
1692 1728 6.260050 TGCTTCATTTTATCTACACCGATTCC 59.740 38.462 0.00 0.00 0.00 3.01
1805 1841 2.349886 CCTGCGAAGAGAAACTATGCAC 59.650 50.000 0.00 0.00 35.83 4.57
1902 1938 2.171003 TGCTTCAGATTCCTCGAGTCA 58.829 47.619 12.31 0.00 0.00 3.41
1956 1992 3.932089 GGAGTTCTGACTTTGAGCATCTC 59.068 47.826 0.00 0.00 35.88 2.75
1980 2016 5.659048 CAAGAAGTTGCCCGTCTATTATC 57.341 43.478 0.00 0.00 31.17 1.75
2002 2038 5.010282 TCAAGGAGCTTATTCCCAAACTTC 58.990 41.667 0.00 0.00 38.02 3.01
2052 2088 4.819105 TGGCAACATGTAACTAGCTACT 57.181 40.909 0.00 0.00 46.17 2.57
2053 2089 4.755411 TGGCAACATGTAACTAGCTACTC 58.245 43.478 0.00 0.00 46.17 2.59
2054 2090 4.120589 GGCAACATGTAACTAGCTACTCC 58.879 47.826 0.00 0.00 0.00 3.85
2055 2091 4.120589 GCAACATGTAACTAGCTACTCCC 58.879 47.826 0.00 0.00 0.00 4.30
2056 2092 4.694339 CAACATGTAACTAGCTACTCCCC 58.306 47.826 0.00 0.00 0.00 4.81
2057 2093 4.267341 ACATGTAACTAGCTACTCCCCT 57.733 45.455 0.00 0.00 0.00 4.79
2058 2094 4.621769 ACATGTAACTAGCTACTCCCCTT 58.378 43.478 0.00 0.00 0.00 3.95
2059 2095 4.406003 ACATGTAACTAGCTACTCCCCTTG 59.594 45.833 0.00 0.00 0.00 3.61
2060 2096 4.326600 TGTAACTAGCTACTCCCCTTGA 57.673 45.455 4.98 0.00 0.00 3.02
2140 2179 1.969208 TGCACATGATGGCCAAAGAAA 59.031 42.857 10.96 0.00 0.00 2.52
2542 3664 5.856126 TGTTGTACTAATTCCTCTTTGCG 57.144 39.130 0.00 0.00 0.00 4.85
2831 6260 6.640137 CATCGATGATGTGTTGTATGTGTAC 58.360 40.000 21.02 0.00 35.54 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
355 356 4.699522 GGAAGAGGGCGCCGTGTT 62.700 66.667 28.94 28.94 0.00 3.32
390 391 3.171388 GAGGCCGGATGGGATGGT 61.171 66.667 5.05 0.00 38.47 3.55
573 574 3.888323 CAGTCCTCATTCAGCTAGCTCTA 59.112 47.826 16.15 5.97 0.00 2.43
727 735 1.638467 GCACGAGCGCTATTTGAGG 59.362 57.895 11.50 0.00 0.00 3.86
846 861 4.773674 TGGCTTCCATTGATTGATGAGTTT 59.226 37.500 0.00 0.00 0.00 2.66
847 862 4.346730 TGGCTTCCATTGATTGATGAGTT 58.653 39.130 0.00 0.00 0.00 3.01
848 863 3.952323 CTGGCTTCCATTGATTGATGAGT 59.048 43.478 0.00 0.00 30.82 3.41
849 864 3.318275 CCTGGCTTCCATTGATTGATGAG 59.682 47.826 0.00 0.00 30.82 2.90
850 865 3.293337 CCTGGCTTCCATTGATTGATGA 58.707 45.455 0.00 0.00 30.82 2.92
865 880 2.437359 GATCTTGCGTGCCTGGCT 60.437 61.111 21.03 0.00 0.00 4.75
878 893 3.119708 GCGATTTTCCTTGCACAAGATCT 60.120 43.478 11.94 0.00 40.79 2.75
994 1018 3.238108 ACAGAAGTAGAACATGCGAGG 57.762 47.619 0.00 0.00 0.00 4.63
1050 1074 1.452145 ATTTGACGCACCTGCCGTTT 61.452 50.000 0.00 0.00 37.91 3.60
1136 1160 1.004440 GATATCCAGCCAGCGTCCC 60.004 63.158 0.00 0.00 0.00 4.46
1143 1167 1.048601 GGAAGACGGATATCCAGCCA 58.951 55.000 21.70 0.00 35.14 4.75
1197 1221 0.456824 TGATCTTGAGCTGCGTCGTC 60.457 55.000 0.00 0.00 0.00 4.20
1282 1306 1.467920 CCTTGATTGGTGGAGAAGGC 58.532 55.000 0.00 0.00 0.00 4.35
1297 1321 0.036671 GAGTAACCCCACGACCCTTG 60.037 60.000 0.00 0.00 0.00 3.61
1415 1439 2.296471 ACAGGAACGTACTCAGTGGAAG 59.704 50.000 0.00 0.00 0.00 3.46
1506 1542 1.126421 CGACCTCGAACGTGACATCG 61.126 60.000 0.97 0.97 43.02 3.84
1587 1623 1.661463 TCATTGGACCCAGAAGCTCT 58.339 50.000 0.00 0.00 0.00 4.09
1632 1668 4.403432 ACATTTGGCTCCATGTCCTTTATG 59.597 41.667 0.00 0.00 0.00 1.90
1636 1672 2.610438 ACATTTGGCTCCATGTCCTT 57.390 45.000 0.00 0.00 0.00 3.36
1653 1689 5.664294 AATGAAGCAATGCCTTGAATACA 57.336 34.783 0.00 0.79 34.04 2.29
1660 1696 7.260603 GTGTAGATAAAATGAAGCAATGCCTT 58.739 34.615 0.00 0.00 0.00 4.35
1692 1728 0.932123 CATCGTCGATCTCAGGCACG 60.932 60.000 4.34 0.00 0.00 5.34
1864 1900 3.177228 AGCATTCCTCCTTGAGTGTAGT 58.823 45.455 0.00 0.00 0.00 2.73
1867 1903 2.373169 TGAAGCATTCCTCCTTGAGTGT 59.627 45.455 0.00 0.00 46.93 3.55
1902 1938 5.472478 CAGATCCAGCATGCTATTGTTACAT 59.528 40.000 22.19 3.38 31.97 2.29
1980 2016 4.158579 GGAAGTTTGGGAATAAGCTCCTTG 59.841 45.833 0.00 0.00 35.63 3.61
2002 2038 2.115266 ACAAGGGGGTTTGCGAGG 59.885 61.111 0.00 0.00 0.00 4.63
2032 2068 4.120589 GGAGTAGCTAGTTACATGTTGCC 58.879 47.826 17.72 6.35 0.00 4.52
2052 2088 8.757307 ATTTCCTCAATATATACTCAAGGGGA 57.243 34.615 0.00 0.00 0.00 4.81
2053 2089 9.236006 CAATTTCCTCAATATATACTCAAGGGG 57.764 37.037 0.00 0.00 0.00 4.79
2054 2090 8.734386 GCAATTTCCTCAATATATACTCAAGGG 58.266 37.037 0.00 0.00 0.00 3.95
2055 2091 8.734386 GGCAATTTCCTCAATATATACTCAAGG 58.266 37.037 0.00 0.00 0.00 3.61
2056 2092 9.288576 TGGCAATTTCCTCAATATATACTCAAG 57.711 33.333 0.00 0.00 0.00 3.02
2057 2093 9.639563 TTGGCAATTTCCTCAATATATACTCAA 57.360 29.630 0.00 0.00 0.00 3.02
2058 2094 9.639563 TTTGGCAATTTCCTCAATATATACTCA 57.360 29.630 0.00 0.00 0.00 3.41
2060 2096 9.646522 ACTTTGGCAATTTCCTCAATATATACT 57.353 29.630 0.00 0.00 0.00 2.12
2061 2097 9.899226 GACTTTGGCAATTTCCTCAATATATAC 57.101 33.333 0.00 0.00 0.00 1.47
2062 2098 9.077885 GGACTTTGGCAATTTCCTCAATATATA 57.922 33.333 16.63 0.00 0.00 0.86
2063 2099 7.255590 CGGACTTTGGCAATTTCCTCAATATAT 60.256 37.037 19.80 0.00 0.00 0.86
2140 2179 4.938226 GCAAAAAGATAGCAGTCCAGTACT 59.062 41.667 0.00 0.00 39.81 2.73
2248 2296 0.179145 GATCATTGGCAGCACAGCAC 60.179 55.000 0.00 0.00 35.83 4.40
2569 3693 8.310382 ACATCATAGTACCTTCTTCATATCAGC 58.690 37.037 0.00 0.00 0.00 4.26
2744 6173 7.701539 TTGTGCACCAATTATCAGAGTTAAT 57.298 32.000 15.69 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.