Multiple sequence alignment - TraesCS1D01G262000

Loading Multiple Alignment...

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 TraesCS1D01G262000 chr1D 100.000 2486 0 0 1 2486 355827013 355829498 0.000000e+00 4591
1 TraesCS1D01G262000 chr1D 91.972 710 50 6 682 1387 446475782 446476488 0.000000e+00 989
2 TraesCS1D01G262000 chr1D 94.664 581 31 0 810 1390 445367079 445366499 0.000000e+00 902
3 TraesCS1D01G262000 chr1D 88.929 560 48 12 1 557 446438825 446439373 0.000000e+00 678
4 TraesCS1D01G262000 chr1D 82.115 766 90 23 1634 2387 446476735 446477465 1.630000e-171 612
5 TraesCS1D01G262000 chr1A 86.125 1182 114 28 808 1959 541461051 541459890 0.000000e+00 1229
6 TraesCS1D01G262000 chr1A 96.902 581 11 2 814 1387 456653435 456654015 0.000000e+00 966
7 TraesCS1D01G262000 chr1A 94.042 621 20 8 1749 2357 456654271 456654886 0.000000e+00 926
8 TraesCS1D01G262000 chr1A 95.051 586 29 0 808 1393 541343556 541344141 0.000000e+00 922
9 TraesCS1D01G262000 chr1A 88.138 784 46 20 1 775 456652619 456653364 0.000000e+00 889
10 TraesCS1D01G262000 chr1A 89.379 499 42 7 1991 2486 541459887 541459397 3.510000e-173 617
11 TraesCS1D01G262000 chr1A 85.179 560 56 10 1 556 541461776 541461240 1.300000e-152 549
12 TraesCS1D01G262000 chr1A 88.278 273 22 7 285 556 541343194 541343457 3.990000e-83 318
13 TraesCS1D01G262000 chr1A 96.386 166 6 0 1478 1643 456654109 456654274 8.760000e-70 274
14 TraesCS1D01G262000 chr1A 74.813 401 65 22 2101 2484 487606767 487607148 5.540000e-32 148
15 TraesCS1D01G262000 chr1A 96.923 65 2 0 1388 1452 456654046 456654110 2.610000e-20 110
16 TraesCS1D01G262000 chr1A 92.754 69 5 0 489 557 487572596 487572664 1.570000e-17 100
17 TraesCS1D01G262000 chr1B 90.268 894 64 8 682 1555 608336022 608335132 0.000000e+00 1147
18 TraesCS1D01G262000 chr1B 94.085 710 41 1 682 1390 610892869 610893578 0.000000e+00 1077
19 TraesCS1D01G262000 chr1B 94.167 600 31 1 801 1396 608043033 608042434 0.000000e+00 911
20 TraesCS1D01G262000 chr1B 79.730 1036 134 38 1388 2387 610893606 610894601 0.000000e+00 680
21 TraesCS1D01G262000 chr1B 87.701 561 54 11 1 557 610562484 610563033 7.500000e-180 640
22 TraesCS1D01G262000 chr1B 87.591 274 29 3 286 557 607427465 607427195 1.860000e-81 313
23 TraesCS1D01G262000 chr1B 87.636 275 26 5 286 557 608353397 608353128 1.860000e-81 313
24 TraesCS1D01G262000 chr1B 90.351 114 11 0 2373 2486 607136746 607136633 1.540000e-32 150
25 TraesCS1D01G262000 chr1B 90.351 114 11 0 2373 2486 607315879 607315766 1.540000e-32 150
26 TraesCS1D01G262000 chr1B 93.182 88 5 1 2399 2486 610894643 610894729 7.220000e-26 128
27 TraesCS1D01G262000 chr1B 92.754 69 5 0 489 557 521768235 521768303 1.570000e-17 100
28 TraesCS1D01G262000 chr3D 93.220 590 35 3 808 1393 114880993 114880405 0.000000e+00 863
29 TraesCS1D01G262000 chr3D 85.346 737 87 9 1388 2112 114880376 114879649 0.000000e+00 743
30 TraesCS1D01G262000 chr3D 89.619 289 28 2 2198 2486 114879625 114879339 1.400000e-97 366
31 TraesCS1D01G262000 chr3B 82.532 395 39 12 2034 2427 168137273 168136908 1.110000e-83 320
32 TraesCS1D01G262000 chr3B 85.496 262 30 6 180 440 168138918 168138664 1.470000e-67 267
33 TraesCS1D01G262000 chr3A 86.692 263 27 5 180 441 111104737 111104482 4.050000e-73 285
34 TraesCS1D01G262000 chr3A 92.105 114 9 0 2373 2486 111102862 111102749 7.120000e-36 161
35 TraesCS1D01G262000 chr7A 80.460 174 26 4 1791 1958 678602815 678602986 2.600000e-25 126
36 TraesCS1D01G262000 chr6D 82.581 155 10 8 180 327 47813440 47813584 1.210000e-23 121
37 TraesCS1D01G262000 chr6D 86.408 103 6 5 232 327 47813589 47813690 3.380000e-19 106
38 TraesCS1D01G262000 chr6D 86.408 103 6 5 232 327 47813695 47813796 3.380000e-19 106


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 TraesCS1D01G262000 chr1D 355827013 355829498 2485 False 4591.000000 4591 100.000000 1 2486 1 chr1D.!!$F1 2485
1 TraesCS1D01G262000 chr1D 445366499 445367079 580 True 902.000000 902 94.664000 810 1390 1 chr1D.!!$R1 580
2 TraesCS1D01G262000 chr1D 446475782 446477465 1683 False 800.500000 989 87.043500 682 2387 2 chr1D.!!$F3 1705
3 TraesCS1D01G262000 chr1D 446438825 446439373 548 False 678.000000 678 88.929000 1 557 1 chr1D.!!$F2 556
4 TraesCS1D01G262000 chr1A 541459397 541461776 2379 True 798.333333 1229 86.894333 1 2486 3 chr1A.!!$R1 2485
5 TraesCS1D01G262000 chr1A 456652619 456654886 2267 False 633.000000 966 94.478200 1 2357 5 chr1A.!!$F3 2356
6 TraesCS1D01G262000 chr1A 541343194 541344141 947 False 620.000000 922 91.664500 285 1393 2 chr1A.!!$F4 1108
7 TraesCS1D01G262000 chr1B 608335132 608336022 890 True 1147.000000 1147 90.268000 682 1555 1 chr1B.!!$R5 873
8 TraesCS1D01G262000 chr1B 608042434 608043033 599 True 911.000000 911 94.167000 801 1396 1 chr1B.!!$R4 595
9 TraesCS1D01G262000 chr1B 610562484 610563033 549 False 640.000000 640 87.701000 1 557 1 chr1B.!!$F2 556
10 TraesCS1D01G262000 chr1B 610892869 610894729 1860 False 628.333333 1077 88.999000 682 2486 3 chr1B.!!$F3 1804
11 TraesCS1D01G262000 chr3D 114879339 114880993 1654 True 657.333333 863 89.395000 808 2486 3 chr3D.!!$R1 1678
12 TraesCS1D01G262000 chr3B 168136908 168138918 2010 True 293.500000 320 84.014000 180 2427 2 chr3B.!!$R1 2247
13 TraesCS1D01G262000 chr3A 111102749 111104737 1988 True 223.000000 285 89.398500 180 2486 2 chr3A.!!$R1 2306

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
640 789 1.202746 GCCCACAGCCCAAAAATTTCA 60.203 47.619 0.0 0.0 34.35 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1819 0.033504 CCACCTCAATATCGACCCGG 59.966 60.0 0.0 0.0 0.0 5.73 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
105 107 9.974980 TTATTACTGATGCACGATTATTACTGA 57.025 29.630 0.00 0.00 0.00 3.41
107 109 6.775939 ACTGATGCACGATTATTACTGATG 57.224 37.500 0.00 0.00 0.00 3.07
108 110 5.178252 ACTGATGCACGATTATTACTGATGC 59.822 40.000 0.00 0.00 0.00 3.91
109 111 5.055812 TGATGCACGATTATTACTGATGCA 58.944 37.500 0.00 0.00 44.87 3.96
110 112 4.794248 TGCACGATTATTACTGATGCAC 57.206 40.909 0.00 0.00 36.72 4.57
111 113 3.245048 TGCACGATTATTACTGATGCACG 59.755 43.478 0.00 0.00 36.72 5.34
112 114 3.489416 GCACGATTATTACTGATGCACGA 59.511 43.478 0.00 0.00 0.00 4.35
113 115 4.150627 GCACGATTATTACTGATGCACGAT 59.849 41.667 0.00 0.00 0.00 3.73
121 124 5.488645 TTACTGATGCACGATACGAGTTA 57.511 39.130 0.00 0.00 0.00 2.24
142 158 7.848128 AGTTATTTGACGGGAGAAGATTTCTA 58.152 34.615 0.00 0.00 40.87 2.10
144 160 6.986904 ATTTGACGGGAGAAGATTTCTAAC 57.013 37.500 0.00 0.00 40.87 2.34
196 213 3.378427 GGCCATTAAGTTTCTAGCACCAG 59.622 47.826 0.00 0.00 0.00 4.00
330 349 4.446857 TTACGTTCGAGCAAGTTTCTTG 57.553 40.909 0.00 5.28 0.00 3.02
331 350 2.277084 ACGTTCGAGCAAGTTTCTTGT 58.723 42.857 10.49 0.00 0.00 3.16
332 351 3.450578 ACGTTCGAGCAAGTTTCTTGTA 58.549 40.909 10.49 0.00 0.00 2.41
455 484 9.941664 GAATTGATATTCACAGTGAATTAGTGG 57.058 33.333 29.55 0.00 44.03 4.00
539 569 6.323203 ACTGAAGACAACCATTCTCATTTG 57.677 37.500 0.00 0.00 0.00 2.32
596 740 2.416372 GAACACGACACAGCACAGCG 62.416 60.000 0.00 0.00 0.00 5.18
640 789 1.202746 GCCCACAGCCCAAAAATTTCA 60.203 47.619 0.00 0.00 34.35 2.69
729 878 2.010145 TTGAGTGCCTGAATAGCGAC 57.990 50.000 0.00 0.00 0.00 5.19
968 1150 2.993853 GAGGCCTCCTCCAACCTG 59.006 66.667 23.19 0.00 44.36 4.00
1047 1244 0.036765 CCGTTCCTCCGATTCCACAA 60.037 55.000 0.00 0.00 0.00 3.33
1444 1688 2.626266 TGTCTAGTTCGCTGTTTCCTGA 59.374 45.455 0.00 0.00 0.00 3.86
1452 1696 1.737363 CGCTGTTTCCTGAGTAGCTCC 60.737 57.143 0.00 0.00 32.43 4.70
1455 1699 3.620966 GCTGTTTCCTGAGTAGCTCCAAT 60.621 47.826 0.00 0.00 0.00 3.16
1476 1720 6.920758 CCAATTGAATCGTGGAACAAAGTTAA 59.079 34.615 7.12 0.00 44.16 2.01
1554 1819 0.944386 TTTCGCTGTTTGGTCTCTGC 59.056 50.000 0.00 0.00 0.00 4.26
1555 1820 0.884704 TTCGCTGTTTGGTCTCTGCC 60.885 55.000 0.00 0.00 0.00 4.85
1600 1870 8.131100 CGATGAGTTGATTTGCCATAATTTACT 58.869 33.333 0.00 0.00 0.00 2.24
1642 1923 7.523219 CCGTACTTGTTTGCAGTATAATTTGA 58.477 34.615 0.00 0.00 0.00 2.69
1659 1941 5.568747 ATTTGAAATGTTAAACAACGCCG 57.431 34.783 0.00 0.00 0.00 6.46
1669 1951 2.967076 CAACGCCGCAGTGACTGT 60.967 61.111 14.82 0.00 33.43 3.55
1682 1964 5.621422 GCAGTGACTGTACAATTGTGTATG 58.379 41.667 21.42 10.53 42.18 2.39
1719 2001 5.808042 TCATTTGCTCTGCTTCTGTTATC 57.192 39.130 0.00 0.00 0.00 1.75
1728 2010 3.801698 TGCTTCTGTTATCTGATCTGGC 58.198 45.455 0.00 0.00 0.00 4.85
1747 2029 1.260561 GCGCATTTATACTGGACACCG 59.739 52.381 0.30 0.00 0.00 4.94
1780 2062 2.098934 TCTGTGGTGCAATGTGTGAAAC 59.901 45.455 0.00 0.00 37.35 2.78
1828 2135 0.247814 CATCGCGTTGTGGATTGAGC 60.248 55.000 5.77 0.00 0.00 4.26
2073 2555 1.056700 ACCCTCTTGGCAGTGACAGT 61.057 55.000 0.00 0.00 37.83 3.55
2086 2568 5.479306 GCAGTGACAGTAACTTCATCCTTA 58.521 41.667 0.00 0.00 0.00 2.69
2324 2823 7.117379 GTCGTTTGGCTTTGAAGTATACTTACT 59.883 37.037 18.03 0.00 40.48 2.24
2414 2943 8.659925 ACATATTGCAGTCTTCTCTATTTGAG 57.340 34.615 0.00 0.00 43.96 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 9.905713 TTCATAAACATAATACTGCCTCTCTTT 57.094 29.630 0.00 0.00 0.00 2.52
97 99 5.684550 ACTCGTATCGTGCATCAGTAATA 57.315 39.130 0.00 0.00 0.00 0.98
98 100 4.569761 ACTCGTATCGTGCATCAGTAAT 57.430 40.909 0.00 0.00 0.00 1.89
99 101 4.365899 AACTCGTATCGTGCATCAGTAA 57.634 40.909 0.00 0.00 0.00 2.24
100 102 5.684550 ATAACTCGTATCGTGCATCAGTA 57.315 39.130 0.00 0.00 0.00 2.74
101 103 2.941453 AACTCGTATCGTGCATCAGT 57.059 45.000 0.00 0.00 0.00 3.41
102 104 5.458779 TCAAATAACTCGTATCGTGCATCAG 59.541 40.000 0.00 0.00 0.00 2.90
103 105 5.231357 GTCAAATAACTCGTATCGTGCATCA 59.769 40.000 0.00 0.00 0.00 3.07
104 106 5.607570 CGTCAAATAACTCGTATCGTGCATC 60.608 44.000 0.00 0.00 0.00 3.91
105 107 4.206404 CGTCAAATAACTCGTATCGTGCAT 59.794 41.667 0.00 0.00 0.00 3.96
106 108 3.544682 CGTCAAATAACTCGTATCGTGCA 59.455 43.478 0.00 0.00 0.00 4.57
107 109 3.061403 CCGTCAAATAACTCGTATCGTGC 60.061 47.826 0.00 0.00 0.00 5.34
108 110 3.484649 CCCGTCAAATAACTCGTATCGTG 59.515 47.826 0.00 0.00 0.00 4.35
109 111 3.378112 TCCCGTCAAATAACTCGTATCGT 59.622 43.478 0.00 0.00 0.00 3.73
110 112 3.956233 TCCCGTCAAATAACTCGTATCG 58.044 45.455 0.00 0.00 0.00 2.92
111 113 5.179045 TCTCCCGTCAAATAACTCGTATC 57.821 43.478 0.00 0.00 0.00 2.24
112 114 5.359009 TCTTCTCCCGTCAAATAACTCGTAT 59.641 40.000 0.00 0.00 0.00 3.06
113 115 4.701651 TCTTCTCCCGTCAAATAACTCGTA 59.298 41.667 0.00 0.00 0.00 3.43
121 124 5.581085 CGTTAGAAATCTTCTCCCGTCAAAT 59.419 40.000 0.00 0.00 41.14 2.32
142 158 1.880027 GCATCCCTTTTGAGTCACGTT 59.120 47.619 0.00 0.00 0.00 3.99
144 160 1.466167 CTGCATCCCTTTTGAGTCACG 59.534 52.381 0.00 0.00 0.00 4.35
311 329 2.277084 ACAAGAAACTTGCTCGAACGT 58.723 42.857 10.78 0.00 0.00 3.99
330 349 9.798994 TTTTGAGTTCCGAAGATAATCTACTAC 57.201 33.333 0.00 0.00 0.00 2.73
332 351 9.152595 GTTTTTGAGTTCCGAAGATAATCTACT 57.847 33.333 0.00 0.00 0.00 2.57
455 484 5.010617 TCCAAACCCAGAAAACAAGATAAGC 59.989 40.000 0.00 0.00 0.00 3.09
539 569 7.281040 TGAATGCATGGAATTTTCTCTATCC 57.719 36.000 0.00 0.00 0.00 2.59
596 740 1.067060 GCCAGGTGTTTGTTCAGAACC 59.933 52.381 10.93 0.00 0.00 3.62
968 1150 1.210931 GCGTTTTAAAGGGGGCGAC 59.789 57.895 0.00 0.00 0.00 5.19
1217 1418 0.847373 TCTCCTCGTAGATGAGCCCT 59.153 55.000 0.00 0.00 46.53 5.19
1444 1688 3.197766 TCCACGATTCAATTGGAGCTACT 59.802 43.478 5.42 0.00 34.35 2.57
1452 1696 7.922505 TTAACTTTGTTCCACGATTCAATTG 57.077 32.000 0.00 0.00 0.00 2.32
1455 1699 6.367421 CGATTAACTTTGTTCCACGATTCAA 58.633 36.000 0.00 0.00 0.00 2.69
1476 1720 3.724508 TTTCCAACAAACACATGCGAT 57.275 38.095 0.00 0.00 0.00 4.58
1554 1819 0.033504 CCACCTCAATATCGACCCGG 59.966 60.000 0.00 0.00 0.00 5.73
1555 1820 0.600255 GCCACCTCAATATCGACCCG 60.600 60.000 0.00 0.00 0.00 5.28
1600 1870 1.535687 GGCTAATCCGGGGCTCCTA 60.536 63.158 0.00 0.00 0.00 2.94
1642 1923 2.223618 ACTGCGGCGTTGTTTAACATTT 60.224 40.909 9.37 0.00 36.58 2.32
1648 1929 0.531090 AGTCACTGCGGCGTTGTTTA 60.531 50.000 9.37 0.00 0.00 2.01
1652 1933 1.663388 TACAGTCACTGCGGCGTTG 60.663 57.895 9.37 4.06 34.37 4.10
1659 1941 5.179368 ACATACACAATTGTACAGTCACTGC 59.821 40.000 11.53 0.00 41.12 4.40
1669 1951 5.872070 TGCTGAATCGACATACACAATTGTA 59.128 36.000 11.53 0.00 42.53 2.41
1709 1991 2.799412 GCGCCAGATCAGATAACAGAAG 59.201 50.000 0.00 0.00 0.00 2.85
1719 2001 3.434641 CCAGTATAAATGCGCCAGATCAG 59.565 47.826 4.18 0.00 0.00 2.90
1728 2010 2.546778 ACGGTGTCCAGTATAAATGCG 58.453 47.619 0.00 0.00 0.00 4.73
1747 2029 3.563808 TGCACCACAGAAGTAACATCAAC 59.436 43.478 0.00 0.00 0.00 3.18
1780 2062 1.667724 GCAGACAAATCACCATCTCCG 59.332 52.381 0.00 0.00 0.00 4.63
1828 2135 5.930837 AGAACTCTGGTCAAGGATAGAAG 57.069 43.478 0.00 0.00 0.00 2.85
1976 2292 8.782339 AAAAGGTTATTGCAGTAACTACGTAT 57.218 30.769 25.54 9.72 35.43 3.06
1989 2465 6.873605 AGTTCAGGCAATTAAAAGGTTATTGC 59.126 34.615 9.81 9.81 44.72 3.56
2086 2568 3.119708 GCGCCTCTTGATCAATTCAACTT 60.120 43.478 8.96 0.00 39.44 2.66
2247 2738 5.601313 TCCCAGTATCCATCTAACTTGGTAC 59.399 44.000 0.00 0.00 35.64 3.34
2414 2943 0.459489 TTGTGACAAAGCTGTTGGCC 59.541 50.000 10.68 0.00 43.05 5.36
2457 2986 2.227865 GGCGTTCAGTTTCATAAAGGCA 59.772 45.455 0.00 0.00 34.98 4.75


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

AutoCloner maintained by Alex Coulton.