Multiple sequence alignment - TraesCS1D01G080500

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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 TraesCS1D01G080500 chr1D 100.000 3358 0 0 1 3358 62893659 62897016 0.000000e+00 6202.0
1 TraesCS1D01G080500 chr1D 88.855 664 59 9 203 863 60174599 60173948 0.000000e+00 802.0
2 TraesCS1D01G080500 chr1D 83.759 665 64 21 1499 2152 37568514 37569145 1.040000e-164 590.0
3 TraesCS1D01G080500 chr1D 84.308 325 32 9 859 1164 60173722 60173398 1.960000e-77 300.0
4 TraesCS1D01G080500 chr6D 97.516 3381 57 5 1 3358 13475710 13479086 0.000000e+00 5753.0
5 TraesCS1D01G080500 chr6D 93.656 331 19 2 1168 1497 450188473 450188144 8.370000e-136 494.0
6 TraesCS1D01G080500 chr5D 97.430 2996 69 4 371 3358 14029653 14032648 0.000000e+00 5099.0
7 TraesCS1D01G080500 chr5D 92.481 1197 72 7 2147 3328 127938812 127937619 0.000000e+00 1696.0
8 TraesCS1D01G080500 chr5D 93.656 331 19 2 1168 1497 127939137 127938808 8.370000e-136 494.0
9 TraesCS1D01G080500 chr2D 93.085 1909 70 20 1432 3322 518814 520678 0.000000e+00 2737.0
10 TraesCS1D01G080500 chr2D 95.385 715 28 4 1432 2141 23116197 23115483 0.000000e+00 1133.0
11 TraesCS1D01G080500 chr2D 94.387 677 30 5 1 672 518145 518818 0.000000e+00 1033.0
12 TraesCS1D01G080500 chr2D 94.083 676 33 5 1 672 23116865 23116193 0.000000e+00 1020.0
13 TraesCS1D01G080500 chr2D 94.277 332 17 2 1168 1497 29095570 29095239 1.080000e-139 507.0
14 TraesCS1D01G080500 chr5A 97.304 1187 30 2 1838 3024 689190312 689189128 0.000000e+00 2013.0
15 TraesCS1D01G080500 chr5A 97.136 1187 33 1 1838 3024 707255988 707257173 0.000000e+00 2002.0
16 TraesCS1D01G080500 chr5A 96.429 1036 28 4 1 1028 707254950 707255984 0.000000e+00 1700.0
17 TraesCS1D01G080500 chr5A 95.883 923 21 5 113 1028 689191228 689190316 0.000000e+00 1478.0
18 TraesCS1D01G080500 chr5A 92.889 675 37 8 6 672 3949191 3948520 0.000000e+00 970.0
19 TraesCS1D01G080500 chr5A 93.898 590 30 2 1432 2015 3948524 3947935 0.000000e+00 885.0
20 TraesCS1D01G080500 chr6A 97.136 1187 33 1 1838 3024 540806189 540805004 0.000000e+00 2002.0
21 TraesCS1D01G080500 chr6A 96.462 1187 41 1 1838 3024 589345936 589347121 0.000000e+00 1958.0
22 TraesCS1D01G080500 chr6A 95.176 995 38 6 1 986 540818317 540817324 0.000000e+00 1563.0
23 TraesCS1D01G080500 chr6A 96.344 848 19 4 191 1028 589345087 589345932 0.000000e+00 1384.0
24 TraesCS1D01G080500 chr6A 96.429 196 6 1 1 195 589344643 589344838 4.180000e-84 322.0
25 TraesCS1D01G080500 chr4A 96.630 1187 39 1 1838 3024 637544917 637546102 0.000000e+00 1969.0
26 TraesCS1D01G080500 chr4A 95.818 550 13 5 486 1028 637544367 637544913 0.000000e+00 880.0
27 TraesCS1D01G080500 chr4A 97.619 42 1 0 3317 3358 31395528 31395487 4.650000e-09 73.1
28 TraesCS1D01G080500 chr7D 92.275 1191 74 9 2147 3322 340174822 340176009 0.000000e+00 1674.0
29 TraesCS1D01G080500 chr7D 93.958 331 18 2 1168 1497 530740077 530739748 1.800000e-137 499.0
30 TraesCS1D01G080500 chr7D 97.436 39 1 0 3320 3358 449501613 449501575 2.160000e-07 67.6
31 TraesCS1D01G080500 chr7D 97.436 39 1 0 3320 3358 621799234 621799272 2.160000e-07 67.6
32 TraesCS1D01G080500 chr2A 87.707 968 80 19 219 1164 3758373 3759323 0.000000e+00 1092.0
33 TraesCS1D01G080500 chr3B 93.285 417 26 2 1168 1582 775658635 775658219 6.160000e-172 614.0
34 TraesCS1D01G080500 chr3B 94.792 96 5 0 1 96 775659866 775659771 2.090000e-32 150.0
35 TraesCS1D01G080500 chr1B 91.706 422 31 3 1165 1582 289694126 289694547 1.740000e-162 582.0
36 TraesCS1D01G080500 chr1B 82.515 652 47 25 1504 2146 57499162 57499755 8.310000e-141 510.0
37 TraesCS1D01G080500 chr1B 91.667 96 8 0 1 96 289692936 289693031 2.100000e-27 134.0
38 TraesCS1D01G080500 chr1B 90.000 80 7 1 1908 1986 57499714 57499793 5.930000e-18 102.0
39 TraesCS1D01G080500 chr2B 87.196 453 44 12 661 1111 62444613 62445053 1.390000e-138 503.0
40 TraesCS1D01G080500 chr4D 93.694 333 18 3 1168 1497 85851013 85850681 2.330000e-136 496.0
41 TraesCS1D01G080500 chr1A 91.176 170 14 1 1529 1697 36778741 36778910 2.610000e-56 230.0
42 TraesCS1D01G080500 chr1A 81.250 224 19 5 1682 1903 36779014 36779216 3.470000e-35 159.0
43 TraesCS1D01G080500 chrUn 97.297 37 1 0 3320 3356 284055832 284055796 2.800000e-06 63.9
44 TraesCS1D01G080500 chrUn 97.297 37 1 0 3320 3356 284069456 284069492 2.800000e-06 63.9
45 TraesCS1D01G080500 chrUn 97.297 37 1 0 3320 3356 289948950 289948914 2.800000e-06 63.9
46 TraesCS1D01G080500 chrUn 97.297 37 1 0 3320 3356 289969793 289969829 2.800000e-06 63.9


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 TraesCS1D01G080500 chr1D 62893659 62897016 3357 False 6202.000000 6202 100.000000 1 3358 1 chr1D.!!$F2 3357
1 TraesCS1D01G080500 chr1D 37568514 37569145 631 False 590.000000 590 83.759000 1499 2152 1 chr1D.!!$F1 653
2 TraesCS1D01G080500 chr1D 60173398 60174599 1201 True 551.000000 802 86.581500 203 1164 2 chr1D.!!$R1 961
3 TraesCS1D01G080500 chr6D 13475710 13479086 3376 False 5753.000000 5753 97.516000 1 3358 1 chr6D.!!$F1 3357
4 TraesCS1D01G080500 chr5D 14029653 14032648 2995 False 5099.000000 5099 97.430000 371 3358 1 chr5D.!!$F1 2987
5 TraesCS1D01G080500 chr5D 127937619 127939137 1518 True 1095.000000 1696 93.068500 1168 3328 2 chr5D.!!$R1 2160
6 TraesCS1D01G080500 chr2D 518145 520678 2533 False 1885.000000 2737 93.736000 1 3322 2 chr2D.!!$F1 3321
7 TraesCS1D01G080500 chr2D 23115483 23116865 1382 True 1076.500000 1133 94.734000 1 2141 2 chr2D.!!$R2 2140
8 TraesCS1D01G080500 chr5A 707254950 707257173 2223 False 1851.000000 2002 96.782500 1 3024 2 chr5A.!!$F1 3023
9 TraesCS1D01G080500 chr5A 689189128 689191228 2100 True 1745.500000 2013 96.593500 113 3024 2 chr5A.!!$R2 2911
10 TraesCS1D01G080500 chr5A 3947935 3949191 1256 True 927.500000 970 93.393500 6 2015 2 chr5A.!!$R1 2009
11 TraesCS1D01G080500 chr6A 540805004 540806189 1185 True 2002.000000 2002 97.136000 1838 3024 1 chr6A.!!$R1 1186
12 TraesCS1D01G080500 chr6A 540817324 540818317 993 True 1563.000000 1563 95.176000 1 986 1 chr6A.!!$R2 985
13 TraesCS1D01G080500 chr6A 589344643 589347121 2478 False 1221.333333 1958 96.411667 1 3024 3 chr6A.!!$F1 3023
14 TraesCS1D01G080500 chr4A 637544367 637546102 1735 False 1424.500000 1969 96.224000 486 3024 2 chr4A.!!$F1 2538
15 TraesCS1D01G080500 chr7D 340174822 340176009 1187 False 1674.000000 1674 92.275000 2147 3322 1 chr7D.!!$F1 1175
16 TraesCS1D01G080500 chr2A 3758373 3759323 950 False 1092.000000 1092 87.707000 219 1164 1 chr2A.!!$F1 945
17 TraesCS1D01G080500 chr3B 775658219 775659866 1647 True 382.000000 614 94.038500 1 1582 2 chr3B.!!$R1 1581
18 TraesCS1D01G080500 chr1B 289692936 289694547 1611 False 358.000000 582 91.686500 1 1582 2 chr1B.!!$F2 1581
19 TraesCS1D01G080500 chr1B 57499162 57499793 631 False 306.000000 510 86.257500 1504 2146 2 chr1B.!!$F1 642

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
447 984 1.093159 GAGCTGATGGCAAGAACCTG 58.907 55.000 0.0 0.0 44.79 4.00 F
1066 2476 3.293337 CATCACACATGGACCCATTCAT 58.707 45.455 0.0 0.0 33.90 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 3326 1.117150 TTGTGAGCGGGGTATACCTC 58.883 55.000 21.25 17.05 40.03 3.85 R
3045 4755 1.271379 TGCCAGCCTTCCTACAGAAAC 60.271 52.381 0.00 0.00 32.88 2.78 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
89 91 1.772156 CCCCCTTCATCCCCCTCTC 60.772 68.421 0.00 0.00 0.00 3.20
447 984 1.093159 GAGCTGATGGCAAGAACCTG 58.907 55.000 0.00 0.00 44.79 4.00
580 1123 6.313164 GCCGCTTTTATCAGTTAGTTAGTTCT 59.687 38.462 0.00 0.00 0.00 3.01
581 1124 7.464311 GCCGCTTTTATCAGTTAGTTAGTTCTC 60.464 40.741 0.00 0.00 0.00 2.87
906 1809 6.978659 TGAACTTCTCTTGACGCGATAATAAT 59.021 34.615 15.93 0.00 0.00 1.28
1066 2476 3.293337 CATCACACATGGACCCATTCAT 58.707 45.455 0.00 0.00 33.90 2.57
1746 3403 5.689961 GCCAAACATTCGAATACAACTGTTT 59.310 36.000 10.97 14.01 37.31 2.83
2069 3734 5.426689 AGACATCTCTAATGGAAGTTGCA 57.573 39.130 0.00 0.00 0.00 4.08
2181 3859 1.117150 GGGACAATGCTGATGCCATT 58.883 50.000 0.00 0.00 38.71 3.16
2495 4193 1.647346 CCGCGCCTCAAACATAGTTA 58.353 50.000 0.00 0.00 0.00 2.24
2520 4218 8.621532 ATGATTATTTAGGCAATGTATGTCGT 57.378 30.769 0.00 0.00 39.19 4.34
3045 4755 7.011857 GGTGTTCCTGATGCTATTCTTTCTTAG 59.988 40.741 0.00 0.00 0.00 2.18
3211 4922 5.684030 GCGAGGTAATAATCTCCCACTCAAA 60.684 44.000 0.00 0.00 0.00 2.69
3279 4990 9.374838 CATTGCTCATGTGTTCTATATGCTATA 57.625 33.333 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.740822 GGCGGGGCTGGTGTCAAT 62.741 66.667 0.00 0.00 0.00 2.57
89 91 2.089201 TGCAGTGCCAATGAGATCAAG 58.911 47.619 13.72 0.00 0.00 3.02
447 984 3.204306 TGAGATCAGATGGTTCCATGC 57.796 47.619 9.21 1.82 0.00 4.06
580 1123 2.422591 GACCGACCAACCAACCGA 59.577 61.111 0.00 0.00 0.00 4.69
581 1124 2.775032 ATCGACCGACCAACCAACCG 62.775 60.000 0.00 0.00 0.00 4.44
891 1794 6.960468 TGCCAAATTATTATTATCGCGTCAA 58.040 32.000 5.77 1.19 0.00 3.18
906 1809 6.430864 TCCTCATCCTACAATTGCCAAATTA 58.569 36.000 5.05 0.00 34.14 1.40
1165 2743 3.365666 GCCACTGTGACATCTTTGATGTG 60.366 47.826 16.58 6.17 31.52 3.21
1670 3326 1.117150 TTGTGAGCGGGGTATACCTC 58.883 55.000 21.25 17.05 40.03 3.85
2069 3734 4.073293 ACCAAAGTGTCAGACTCGATTT 57.927 40.909 1.31 0.00 31.73 2.17
2181 3859 4.607955 CCTCGATGATGTACTTCGCTTTA 58.392 43.478 4.48 0.00 42.97 1.85
2375 4073 2.124983 CACCATCACTCCGCCAGG 60.125 66.667 0.00 0.00 39.46 4.45
2377 4075 2.981302 CTCACCATCACTCCGCCA 59.019 61.111 0.00 0.00 0.00 5.69
2495 4193 8.621532 ACGACATACATTGCCTAAATAATCAT 57.378 30.769 0.00 0.00 0.00 2.45
2567 4268 6.108015 GCATTCTTCCAAATTGAGCCAATTA 58.892 36.000 11.87 0.00 42.32 1.40
3045 4755 1.271379 TGCCAGCCTTCCTACAGAAAC 60.271 52.381 0.00 0.00 32.88 2.78
3211 4922 6.058833 ACACTACTATCTCTCACATCACGAT 58.941 40.000 0.00 0.00 0.00 3.73
3279 4990 7.457852 AGGCAGGGTAATTAAGGAAGAAAAATT 59.542 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.