Multiple sequence alignment - TraesCS2B01G109600

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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 TraesCS2B01G109600 chr2B 100.000 2840 0 0 1 2840 71201997 71199158 0.000000e+00 5245
1 TraesCS2B01G109600 chr2B 93.091 1867 111 12 742 2598 173503419 173501561 0.000000e+00 2717
2 TraesCS2B01G109600 chr2B 90.899 1868 133 19 741 2588 19091946 19093796 0.000000e+00 2473
3 TraesCS2B01G109600 chr2B 95.570 745 31 2 1 744 520859561 520858818 0.000000e+00 1192
4 TraesCS2B01G109600 chr2B 94.228 745 40 3 1 744 121637278 121636536 0.000000e+00 1134
5 TraesCS2B01G109600 chr2B 93.827 243 14 1 2598 2840 485692715 485692956 5.780000e-97 364
6 TraesCS2B01G109600 chr2B 93.443 244 15 1 2598 2840 678813816 678814059 7.480000e-96 361
7 TraesCS2B01G109600 chr5B 92.966 2104 126 11 742 2840 548612963 548610877 0.000000e+00 3046
8 TraesCS2B01G109600 chr7B 92.102 2127 131 23 742 2840 486548590 486546473 0.000000e+00 2963
9 TraesCS2B01G109600 chr7B 92.219 1131 61 14 734 1841 723752401 723751275 0.000000e+00 1576
10 TraesCS2B01G109600 chr7B 95.115 737 35 1 1 736 287068463 287069199 0.000000e+00 1160
11 TraesCS2B01G109600 chr7B 94.239 243 14 0 2598 2840 58799259 58799501 3.460000e-99 372
12 TraesCS2B01G109600 chr7B 93.878 245 13 1 2598 2840 663210163 663210407 4.470000e-98 368
13 TraesCS2B01G109600 chr7D 93.543 1874 104 12 744 2604 90563634 90561765 0.000000e+00 2774
14 TraesCS2B01G109600 chr7A 90.009 2142 150 36 742 2840 12744485 12742365 0.000000e+00 2712
15 TraesCS2B01G109600 chr7A 90.458 2096 144 29 739 2803 30966343 30968413 0.000000e+00 2712
16 TraesCS2B01G109600 chr5D 93.056 1872 103 14 740 2598 45518957 45517100 0.000000e+00 2712
17 TraesCS2B01G109600 chr5D 91.636 1889 106 21 714 2598 84221182 84219342 0.000000e+00 2566
18 TraesCS2B01G109600 chr5D 94.228 745 41 2 1 744 247157865 247157122 0.000000e+00 1136
19 TraesCS2B01G109600 chr1D 93.029 1865 96 12 742 2598 25464319 25466157 0.000000e+00 2693
20 TraesCS2B01G109600 chr1D 93.053 950 53 9 739 1687 435252057 435251120 0.000000e+00 1376
21 TraesCS2B01G109600 chr5A 89.748 2146 153 27 735 2840 650703528 650701410 0.000000e+00 2682
22 TraesCS2B01G109600 chr5A 90.170 1882 148 15 732 2588 700182682 700184551 0.000000e+00 2416
23 TraesCS2B01G109600 chr4B 93.992 749 43 2 1 748 376328047 376328794 0.000000e+00 1133
24 TraesCS2B01G109600 chr4B 93.826 745 44 2 1 744 453395960 453395217 0.000000e+00 1120
25 TraesCS2B01G109600 chr3B 94.094 745 42 2 1 744 473578015 473577272 0.000000e+00 1131
26 TraesCS2B01G109600 chr3B 94.672 244 12 1 2598 2840 440313213 440313456 7.430000e-101 377
27 TraesCS2B01G109600 chr1B 94.094 745 42 2 1 744 372132921 372132178 0.000000e+00 1131
28 TraesCS2B01G109600 chr6B 93.960 745 43 2 1 744 228349009 228348266 0.000000e+00 1125
29 TraesCS2B01G109600 chr3D 90.148 406 33 4 733 1138 17578809 17578411 3.240000e-144 521


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 TraesCS2B01G109600 chr2B 71199158 71201997 2839 True 5245 5245 100.000 1 2840 1 chr2B.!!$R1 2839
1 TraesCS2B01G109600 chr2B 173501561 173503419 1858 True 2717 2717 93.091 742 2598 1 chr2B.!!$R3 1856
2 TraesCS2B01G109600 chr2B 19091946 19093796 1850 False 2473 2473 90.899 741 2588 1 chr2B.!!$F1 1847
3 TraesCS2B01G109600 chr2B 520858818 520859561 743 True 1192 1192 95.570 1 744 1 chr2B.!!$R4 743
4 TraesCS2B01G109600 chr2B 121636536 121637278 742 True 1134 1134 94.228 1 744 1 chr2B.!!$R2 743
5 TraesCS2B01G109600 chr5B 548610877 548612963 2086 True 3046 3046 92.966 742 2840 1 chr5B.!!$R1 2098
6 TraesCS2B01G109600 chr7B 486546473 486548590 2117 True 2963 2963 92.102 742 2840 1 chr7B.!!$R1 2098
7 TraesCS2B01G109600 chr7B 723751275 723752401 1126 True 1576 1576 92.219 734 1841 1 chr7B.!!$R2 1107
8 TraesCS2B01G109600 chr7B 287068463 287069199 736 False 1160 1160 95.115 1 736 1 chr7B.!!$F2 735
9 TraesCS2B01G109600 chr7D 90561765 90563634 1869 True 2774 2774 93.543 744 2604 1 chr7D.!!$R1 1860
10 TraesCS2B01G109600 chr7A 12742365 12744485 2120 True 2712 2712 90.009 742 2840 1 chr7A.!!$R1 2098
11 TraesCS2B01G109600 chr7A 30966343 30968413 2070 False 2712 2712 90.458 739 2803 1 chr7A.!!$F1 2064
12 TraesCS2B01G109600 chr5D 45517100 45518957 1857 True 2712 2712 93.056 740 2598 1 chr5D.!!$R1 1858
13 TraesCS2B01G109600 chr5D 84219342 84221182 1840 True 2566 2566 91.636 714 2598 1 chr5D.!!$R2 1884
14 TraesCS2B01G109600 chr5D 247157122 247157865 743 True 1136 1136 94.228 1 744 1 chr5D.!!$R3 743
15 TraesCS2B01G109600 chr1D 25464319 25466157 1838 False 2693 2693 93.029 742 2598 1 chr1D.!!$F1 1856
16 TraesCS2B01G109600 chr1D 435251120 435252057 937 True 1376 1376 93.053 739 1687 1 chr1D.!!$R1 948
17 TraesCS2B01G109600 chr5A 650701410 650703528 2118 True 2682 2682 89.748 735 2840 1 chr5A.!!$R1 2105
18 TraesCS2B01G109600 chr5A 700182682 700184551 1869 False 2416 2416 90.170 732 2588 1 chr5A.!!$F1 1856
19 TraesCS2B01G109600 chr4B 376328047 376328794 747 False 1133 1133 93.992 1 748 1 chr4B.!!$F1 747
20 TraesCS2B01G109600 chr4B 453395217 453395960 743 True 1120 1120 93.826 1 744 1 chr4B.!!$R1 743
21 TraesCS2B01G109600 chr3B 473577272 473578015 743 True 1131 1131 94.094 1 744 1 chr3B.!!$R1 743
22 TraesCS2B01G109600 chr1B 372132178 372132921 743 True 1131 1131 94.094 1 744 1 chr1B.!!$R1 743
23 TraesCS2B01G109600 chr6B 228348266 228349009 743 True 1125 1125 93.960 1 744 1 chr6B.!!$R1 743

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
865 867 0.315251 CGTGAACTCTGCAGTCTCCA 59.685 55.0 14.67 5.62 29.93 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2483 0.537188 ACCATCTGTCCTAGCGGTTG 59.463 55.0 0.0 0.0 30.39 3.77 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
178 179 7.031372 GTGATCAACAACATGTTTAGCATCAT 58.969 34.615 8.77 0.00 38.77 2.45
243 244 6.322969 TGCCCTTAAGATCGTCAAGAGTATAA 59.677 38.462 3.36 0.00 0.00 0.98
257 258 3.328050 AGAGTATAACCAATAGCAGCCCC 59.672 47.826 0.00 0.00 0.00 5.80
451 452 8.587952 AGTTTCAATAGGCAAATTGTGTTTAC 57.412 30.769 11.01 5.49 37.94 2.01
524 525 6.018588 CGCATATGCAAATCATTTTCATGGTT 60.019 34.615 26.52 0.00 42.21 3.67
689 690 6.694447 AGCTAACACCGATAGTTTGTTTCTA 58.306 36.000 0.00 0.00 39.97 2.10
783 785 1.522806 GTGGTGTCCGTGTGCTCAA 60.523 57.895 0.00 0.00 0.00 3.02
858 860 0.318699 CTCGTTCCGTGAACTCTGCA 60.319 55.000 12.80 0.00 40.05 4.41
865 867 0.315251 CGTGAACTCTGCAGTCTCCA 59.685 55.000 14.67 5.62 29.93 3.86
931 933 4.704965 GGTAGAGACGGCCAATTCTATTT 58.295 43.478 2.24 0.00 0.00 1.40
1064 1070 0.666274 GAGCACGACGATGACCACAA 60.666 55.000 0.00 0.00 0.00 3.33
1086 1096 4.023980 ACGAGAGAGAGAGAGAGAGAGAA 58.976 47.826 0.00 0.00 0.00 2.87
1181 1233 3.131933 CGAGATCCATGTCTTCCTCAAGT 59.868 47.826 0.00 0.00 0.00 3.16
1327 1380 4.186856 TCTATGTGTGCAACGAGAATGA 57.813 40.909 0.00 0.00 42.39 2.57
1496 1550 2.629137 TGAAGAATGGTTGTGCATGCTT 59.371 40.909 20.33 2.06 29.75 3.91
1547 1601 1.490574 CGGAAGAAGAGATGGAGGGT 58.509 55.000 0.00 0.00 0.00 4.34
1599 1653 5.489792 TGAGCTTAGGATGTTGAAGAAGT 57.510 39.130 0.00 0.00 0.00 3.01
1600 1654 5.240891 TGAGCTTAGGATGTTGAAGAAGTG 58.759 41.667 0.00 0.00 0.00 3.16
1676 1734 9.521841 TTTTGACATTTGTAGGTATGGTAATCA 57.478 29.630 0.00 0.00 0.00 2.57
1941 2019 1.017387 GGCCAAATTCAGAGCGTAGG 58.983 55.000 0.00 0.00 0.00 3.18
1942 2020 0.378610 GCCAAATTCAGAGCGTAGGC 59.621 55.000 0.00 0.00 40.37 3.93
1991 2069 1.891150 CTGCATCCAATTAGGCCCATC 59.109 52.381 0.00 0.00 37.29 3.51
2116 2196 7.504238 TCAGAGCCAAACAATTAAGGTTAGAAA 59.496 33.333 0.00 0.00 0.00 2.52
2264 2347 7.040548 CCTGGTGCCAAAATAAATGAACATTTT 60.041 33.333 16.12 4.33 40.99 1.82
2396 2483 4.056125 GTTTGGGGCTTCGCTGGC 62.056 66.667 0.00 0.00 0.00 4.85
2418 2505 2.679082 ACCGCTAGGACAGATGGTAAT 58.321 47.619 0.00 0.00 41.02 1.89
2436 2524 3.312736 AATACTTTGGCATGGGTAGGG 57.687 47.619 0.00 0.00 0.00 3.53
2483 2582 1.715519 GAATGTTTGCACATGCGTGAC 59.284 47.619 14.17 4.80 46.80 3.67
2532 2632 3.975479 TTTTGGAGGGTTGGAAGGTTA 57.025 42.857 0.00 0.00 0.00 2.85
2722 2866 5.878332 AGAAATGATATGTTTGTGCACGA 57.122 34.783 13.13 7.71 0.00 4.35
2778 2922 4.824537 ACTTACATAACATGCAACACACCA 59.175 37.500 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 179 7.557358 ATGTCAGCACAAGATTAATATGGAACA 59.443 33.333 0.00 0.0 38.64 3.18
243 244 0.981277 AGTACGGGGCTGCTATTGGT 60.981 55.000 0.00 0.0 0.00 3.67
451 452 1.021202 TTCAAACAACCACCTCTGCG 58.979 50.000 0.00 0.0 0.00 5.18
689 690 8.736244 ACACCGTAAATGCTAAAATAGATTGTT 58.264 29.630 0.00 0.0 0.00 2.83
783 785 1.838112 TTCGCATCTGAGGGCAAAAT 58.162 45.000 5.18 0.0 0.00 1.82
858 860 1.633774 ACGTTGACCTGATGGAGACT 58.366 50.000 0.00 0.0 37.04 3.24
1026 1032 4.293648 CTGTCGCCGTGGTCACCA 62.294 66.667 0.00 0.0 0.00 4.17
1064 1070 3.632333 TCTCTCTCTCTCTCTCTCTCGT 58.368 50.000 0.00 0.0 0.00 4.18
1086 1096 2.648059 GCTGCTCTCTCTCTCTCTCTT 58.352 52.381 0.00 0.0 0.00 2.85
1163 1214 3.054065 GGGAACTTGAGGAAGACATGGAT 60.054 47.826 0.00 0.0 32.98 3.41
1267 1319 0.944311 CGGTGTGTGAGAAACCCTCG 60.944 60.000 0.00 0.0 44.92 4.63
1327 1380 2.501316 GCAATTGCCCCAATTCTTACCT 59.499 45.455 20.06 0.0 41.40 3.08
1515 1569 1.006102 CTTCCGGAGCTCGTGTTGT 60.006 57.895 3.34 0.0 37.11 3.32
1547 1601 0.598419 CTCTGTCAGTGCGTGCTTCA 60.598 55.000 0.00 0.0 0.00 3.02
1599 1653 3.587061 TGATCTTCAAGCTTCCTAACCCA 59.413 43.478 0.00 0.0 0.00 4.51
1600 1654 4.222124 TGATCTTCAAGCTTCCTAACCC 57.778 45.455 0.00 0.0 0.00 4.11
1676 1734 6.872920 ACATTTTCAACATTACAACCAGTGT 58.127 32.000 0.00 0.0 44.82 3.55
1916 1993 2.105766 GCTCTGAATTTGGCCCAAGAT 58.894 47.619 0.00 0.0 0.00 2.40
1942 2020 1.195115 TAGTCTAGCCTGCACTTGGG 58.805 55.000 0.00 0.0 0.00 4.12
1991 2069 3.470888 ACGCAAGAGATCCCCCGG 61.471 66.667 0.00 0.0 43.62 5.73
1998 2077 4.900635 AACAGAAAAACACGCAAGAGAT 57.099 36.364 0.00 0.0 43.62 2.75
2186 2268 8.428063 ACATTTTCCATGACATTTTGGTCTTTA 58.572 29.630 0.00 0.0 38.61 1.85
2305 2391 4.230455 TGTCCATTTTCCACCCTTCATTT 58.770 39.130 0.00 0.0 0.00 2.32
2396 2483 0.537188 ACCATCTGTCCTAGCGGTTG 59.463 55.000 0.00 0.0 30.39 3.77
2418 2505 1.974028 TCCCTACCCATGCCAAAGTA 58.026 50.000 0.00 0.0 0.00 2.24
2483 2582 3.999663 TGCAAAACAAAGGAAAACCACTG 59.000 39.130 0.00 0.0 0.00 3.66
2532 2632 4.025313 GTGGCATTGCAAACATACGTTTTT 60.025 37.500 11.39 0.0 42.82 1.94
2632 2776 3.192944 TGAAAATCAGAGGGGGTGAGAT 58.807 45.455 0.00 0.0 0.00 2.75
2760 2904 4.439974 GGGTATGGTGTGTTGCATGTTATG 60.440 45.833 0.00 0.0 0.00 1.90
2812 2956 4.152938 CGTGTCATGTTTCATCATGTGTCT 59.847 41.667 6.57 0.0 43.70 3.41


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

AutoCloner maintained by Alex Coulton.