Multiple sequence alignment - TraesCS5D01G358200

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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 TraesCS5D01G358200 chr5D 100.000 4188 0 0 1 4188 438457577 438453390 0.000000e+00 7734
1 TraesCS5D01G358200 chr5D 89.481 1521 144 11 2319 3827 438559121 438557605 0.000000e+00 1908
2 TraesCS5D01G358200 chr5D 85.452 1581 197 23 2269 3827 438545270 438543701 0.000000e+00 1615
3 TraesCS5D01G358200 chr5D 82.038 1776 279 28 95 1853 438562572 438560820 0.000000e+00 1476
4 TraesCS5D01G358200 chr5D 80.448 1964 321 33 101 2028 438547562 438545626 0.000000e+00 1441
5 TraesCS5D01G358200 chr5D 83.544 1501 223 18 2344 3827 438605222 438603729 0.000000e+00 1382
6 TraesCS5D01G358200 chr5D 82.368 1554 243 21 2296 3827 438521635 438520091 0.000000e+00 1323
7 TraesCS5D01G358200 chr5D 78.271 1712 319 41 268 1952 438523718 438522033 0.000000e+00 1051
8 TraesCS5D01G358200 chr5D 77.419 279 55 6 1646 1919 438606025 438605750 4.330000e-35 159
9 TraesCS5D01G358200 chr5B 94.410 1592 72 9 110 1697 533093421 533091843 0.000000e+00 2431
10 TraesCS5D01G358200 chr5B 90.439 1663 137 13 2171 3827 533089352 533087706 0.000000e+00 2170
11 TraesCS5D01G358200 chr5B 82.388 1658 229 33 2195 3827 533383983 533382364 0.000000e+00 1386
12 TraesCS5D01G358200 chr5B 83.400 1500 226 18 2344 3827 533509302 533507810 0.000000e+00 1369
13 TraesCS5D01G358200 chr5B 81.356 1711 269 38 2147 3827 533389882 533388192 0.000000e+00 1347
14 TraesCS5D01G358200 chr5B 80.834 1487 231 35 2367 3827 533451375 533449917 0.000000e+00 1118
15 TraesCS5D01G358200 chr5B 82.462 1186 174 20 2655 3827 533565199 533564035 0.000000e+00 1007
16 TraesCS5D01G358200 chr5B 74.943 1317 300 24 307 1615 533381539 533380245 1.010000e-160 577
17 TraesCS5D01G358200 chr5B 89.007 282 26 2 1686 1963 533091821 533091541 1.110000e-90 344
18 TraesCS5D01G358200 chr5A 97.724 1362 29 2 2467 3827 553538907 553537547 0.000000e+00 2342
19 TraesCS5D01G358200 chr5A 84.468 1616 217 27 2233 3827 554060597 554058995 0.000000e+00 1563
20 TraesCS5D01G358200 chr5A 86.161 1438 175 15 3 1429 553562405 553560981 0.000000e+00 1531
21 TraesCS5D01G358200 chr5A 79.577 1890 313 46 99 1957 554063248 554061401 0.000000e+00 1284
22 TraesCS5D01G358200 chr5A 85.885 1169 145 13 2415 3568 554112644 554111481 0.000000e+00 1227
23 TraesCS5D01G358200 chr5A 94.991 559 25 1 1424 1979 553543168 553542610 0.000000e+00 874
24 TraesCS5D01G358200 chr5A 93.529 510 13 5 1980 2469 553541027 553540518 0.000000e+00 741
25 TraesCS5D01G358200 chr5A 78.534 1132 195 24 932 2028 554140989 554139871 0.000000e+00 701
26 TraesCS5D01G358200 chr5A 95.095 367 15 2 3824 4188 553537519 553537154 3.630000e-160 575
27 TraesCS5D01G358200 chrUn 86.161 1438 175 15 3 1429 63333170 63331746 0.000000e+00 1531
28 TraesCS5D01G358200 chrUn 77.548 2080 353 62 1 2029 63296599 63294583 0.000000e+00 1149
29 TraesCS5D01G358200 chrUn 77.511 2081 353 63 1 2029 319150806 319148789 0.000000e+00 1144
30 TraesCS5D01G358200 chrUn 76.590 393 70 17 1639 2023 63397232 63397610 3.300000e-46 196
31 TraesCS5D01G358200 chr2A 74.196 1306 287 39 332 1614 14723334 14722056 2.250000e-137 499


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 TraesCS5D01G358200 chr5D 438453390 438457577 4187 True 7734.000000 7734 100.000000 1 4188 1 chr5D.!!$R1 4187
1 TraesCS5D01G358200 chr5D 438557605 438562572 4967 True 1692.000000 1908 85.759500 95 3827 2 chr5D.!!$R4 3732
2 TraesCS5D01G358200 chr5D 438543701 438547562 3861 True 1528.000000 1615 82.950000 101 3827 2 chr5D.!!$R3 3726
3 TraesCS5D01G358200 chr5D 438520091 438523718 3627 True 1187.000000 1323 80.319500 268 3827 2 chr5D.!!$R2 3559
4 TraesCS5D01G358200 chr5D 438603729 438606025 2296 True 770.500000 1382 80.481500 1646 3827 2 chr5D.!!$R5 2181
5 TraesCS5D01G358200 chr5B 533087706 533093421 5715 True 1648.333333 2431 91.285333 110 3827 3 chr5B.!!$R5 3717
6 TraesCS5D01G358200 chr5B 533507810 533509302 1492 True 1369.000000 1369 83.400000 2344 3827 1 chr5B.!!$R3 1483
7 TraesCS5D01G358200 chr5B 533388192 533389882 1690 True 1347.000000 1347 81.356000 2147 3827 1 chr5B.!!$R1 1680
8 TraesCS5D01G358200 chr5B 533449917 533451375 1458 True 1118.000000 1118 80.834000 2367 3827 1 chr5B.!!$R2 1460
9 TraesCS5D01G358200 chr5B 533564035 533565199 1164 True 1007.000000 1007 82.462000 2655 3827 1 chr5B.!!$R4 1172
10 TraesCS5D01G358200 chr5B 533380245 533383983 3738 True 981.500000 1386 78.665500 307 3827 2 chr5B.!!$R6 3520
11 TraesCS5D01G358200 chr5A 553560981 553562405 1424 True 1531.000000 1531 86.161000 3 1429 1 chr5A.!!$R1 1426
12 TraesCS5D01G358200 chr5A 554058995 554063248 4253 True 1423.500000 1563 82.022500 99 3827 2 chr5A.!!$R5 3728
13 TraesCS5D01G358200 chr5A 554111481 554112644 1163 True 1227.000000 1227 85.885000 2415 3568 1 chr5A.!!$R2 1153
14 TraesCS5D01G358200 chr5A 553537154 553543168 6014 True 1133.000000 2342 95.334750 1424 4188 4 chr5A.!!$R4 2764
15 TraesCS5D01G358200 chr5A 554139871 554140989 1118 True 701.000000 701 78.534000 932 2028 1 chr5A.!!$R3 1096
16 TraesCS5D01G358200 chrUn 63331746 63333170 1424 True 1531.000000 1531 86.161000 3 1429 1 chrUn.!!$R2 1426
17 TraesCS5D01G358200 chrUn 63294583 63296599 2016 True 1149.000000 1149 77.548000 1 2029 1 chrUn.!!$R1 2028
18 TraesCS5D01G358200 chrUn 319148789 319150806 2017 True 1144.000000 1144 77.511000 1 2029 1 chrUn.!!$R3 2028
19 TraesCS5D01G358200 chr2A 14722056 14723334 1278 True 499.000000 499 74.196000 332 1614 1 chr2A.!!$R1 1282

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
354 371 0.538057 CCTGCCTTTGAGTGCTTCCA 60.538 55.000 0.0 0.0 0.00 3.53 F
755 778 1.078848 GTGGCAGAGCTTCGACCAT 60.079 57.895 0.0 0.0 30.88 3.55 F
1784 1882 0.957395 AGGATTGTGCTGCCAGTTCG 60.957 55.000 0.0 0.0 0.00 3.95 F
2530 10123 2.079170 TGCAACCCACAATTTCTCCA 57.921 45.000 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1203 0.957395 ATTCAGCAGACGGCCACTTG 60.957 55.0 2.24 0.0 46.50 3.16 R
2365 8344 1.855213 TTGCCTGCTCGCACAATGTC 61.855 55.0 0.00 0.0 38.83 3.06 R
3004 10624 0.394352 ATAGAAGCCCCCTTGCAACG 60.394 55.0 0.00 0.0 0.00 4.10 R
4070 12609 1.009829 GCAGCCCTATTCAACACTCG 58.990 55.0 0.00 0.0 0.00 4.18 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
40 41 0.974010 ATTCCAATGTGGGCAGCTGG 60.974 55.000 17.12 0.00 38.32 4.85
57 58 5.068987 GCAGCTGGATTATAAATCCCAACAA 59.931 40.000 17.12 0.00 37.40 2.83
59 60 6.980397 CAGCTGGATTATAAATCCCAACAAAC 59.020 38.462 14.53 0.00 37.40 2.93
61 62 6.405397 GCTGGATTATAAATCCCAACAAACGT 60.405 38.462 14.53 0.00 37.40 3.99
75 76 2.743126 ACAAACGTCGACTTGGAAAACA 59.257 40.909 18.44 0.00 0.00 2.83
167 171 1.067199 GCGTTCCTGCGAGCATTTTG 61.067 55.000 0.00 0.00 0.00 2.44
169 173 1.725931 CGTTCCTGCGAGCATTTTGTC 60.726 52.381 0.00 0.00 0.00 3.18
174 180 2.487762 CCTGCGAGCATTTTGTCCTTTA 59.512 45.455 0.00 0.00 0.00 1.85
175 181 3.492313 CTGCGAGCATTTTGTCCTTTAC 58.508 45.455 0.00 0.00 0.00 2.01
176 182 2.881513 TGCGAGCATTTTGTCCTTTACA 59.118 40.909 0.00 0.00 35.88 2.41
354 371 0.538057 CCTGCCTTTGAGTGCTTCCA 60.538 55.000 0.00 0.00 0.00 3.53
389 406 4.189580 GGCAAGCCGCTATCCCCA 62.190 66.667 0.00 0.00 41.91 4.96
392 409 2.366972 AAGCCGCTATCCCCAGGT 60.367 61.111 0.00 0.00 0.00 4.00
755 778 1.078848 GTGGCAGAGCTTCGACCAT 60.079 57.895 0.00 0.00 30.88 3.55
826 849 3.061260 GAGGCACTACCGACCGTCC 62.061 68.421 0.00 0.00 46.52 4.79
1173 1203 3.315191 CGTTGGTGTGGGATATCATTTCC 59.685 47.826 4.83 0.00 0.00 3.13
1304 1337 1.692411 GCAAACAAGGAGGAGTGGTT 58.308 50.000 0.00 0.00 0.00 3.67
1784 1882 0.957395 AGGATTGTGCTGCCAGTTCG 60.957 55.000 0.00 0.00 0.00 3.95
1816 1914 8.090831 GTGGTCTTCTCATACTCATATGCATAA 58.909 37.037 11.13 0.00 38.50 1.90
1887 2023 7.216973 ACAATAATGTTTTAGTTTACGGCCA 57.783 32.000 2.24 0.00 35.91 5.36
2142 4794 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2167 4953 9.168451 TCTCTAAGTGTGTTTTTCAAACATACA 57.832 29.630 23.09 9.30 42.36 2.29
2168 4954 9.950680 CTCTAAGTGTGTTTTTCAAACATACAT 57.049 29.630 23.09 16.96 42.36 2.29
2530 10123 2.079170 TGCAACCCACAATTTCTCCA 57.921 45.000 0.00 0.00 0.00 3.86
2700 10311 2.808543 GGTCAAGAAGTCGCAGTCAAAT 59.191 45.455 0.00 0.00 0.00 2.32
2748 10359 7.543756 AGGAACAAAAGAATTCAAGAACGAAA 58.456 30.769 8.44 0.00 0.00 3.46
2916 10528 9.131791 ACAAACATATTTTCCTAACACAACTCT 57.868 29.630 0.00 0.00 0.00 3.24
3004 10624 7.971722 ACAACACGGTTTAATATAATCAAAGGC 59.028 33.333 0.00 0.00 0.00 4.35
3265 10907 4.422073 TTCTTTGGGTATGATCGAGCAT 57.578 40.909 21.25 21.25 0.00 3.79
3839 11523 2.038557 GGGACGATGTACCTAATGCCAT 59.961 50.000 0.00 0.00 32.80 4.40
3929 11736 3.722147 ACAGTTGAAGCAGAGTACACAG 58.278 45.455 0.00 0.00 0.00 3.66
4070 12609 6.261826 TCCACTACTCGACTTAACTATAAGCC 59.738 42.308 0.00 0.00 41.92 4.35
4081 12620 7.328737 ACTTAACTATAAGCCGAGTGTTGAAT 58.671 34.615 0.00 0.00 41.92 2.57
4097 12636 0.536006 GAATAGGGCTGCTCGGCATT 60.536 55.000 0.00 0.00 38.13 3.56
4105 12644 1.603802 GCTGCTCGGCATTATAAAGCA 59.396 47.619 14.13 10.97 40.45 3.91
4128 12667 4.219944 ACTTTGACTATAAGCCGAGTGTCA 59.780 41.667 0.00 0.00 33.41 3.58
4154 12693 8.728833 ACAAAACAATGTGTTGAAACATTTCAT 58.271 25.926 21.90 0.00 46.19 2.57
4159 12698 7.551974 ACAATGTGTTGAAACATTTCATTTGGA 59.448 29.630 7.83 0.00 46.19 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.903479 GTCGACGTTTGTTGGGATTTATAATC 59.097 38.462 0.00 0.00 0.00 1.75
57 58 2.348660 TGTGTTTTCCAAGTCGACGTT 58.651 42.857 10.46 2.10 0.00 3.99
59 60 2.350498 AGTTGTGTTTTCCAAGTCGACG 59.650 45.455 10.46 0.00 0.00 5.12
61 62 3.869065 AGAGTTGTGTTTTCCAAGTCGA 58.131 40.909 0.00 0.00 43.72 4.20
167 171 5.181433 GTGGAACCTTGATCTTGTAAAGGAC 59.819 44.000 14.08 8.27 46.24 3.85
169 173 4.154195 CGTGGAACCTTGATCTTGTAAAGG 59.846 45.833 7.13 7.13 46.24 3.11
174 180 1.523758 GCGTGGAACCTTGATCTTGT 58.476 50.000 0.00 0.00 0.00 3.16
175 181 0.804989 GGCGTGGAACCTTGATCTTG 59.195 55.000 0.00 0.00 0.00 3.02
176 182 0.400213 TGGCGTGGAACCTTGATCTT 59.600 50.000 0.00 0.00 0.00 2.40
180 186 1.227823 CACTGGCGTGGAACCTTGA 60.228 57.895 2.23 0.00 37.50 3.02
249 262 6.749118 GCCAAAATCTTAATCACTAAGCTGTG 59.251 38.462 0.00 0.00 37.51 3.66
354 371 4.324991 GGGGACAAGGCGGTCGTT 62.325 66.667 6.32 0.00 38.70 3.85
389 406 2.492484 GTCAGAGACGATGGTTGTACCT 59.508 50.000 0.00 0.00 39.58 3.08
755 778 3.047718 GAGGATCGTGTCGGTGCGA 62.048 63.158 0.00 0.00 41.50 5.10
891 914 4.754667 GGTTCGAGGGGCGTGTCC 62.755 72.222 0.00 0.00 41.80 4.02
892 915 2.798148 AATGGTTCGAGGGGCGTGTC 62.798 60.000 0.00 0.00 41.80 3.67
1173 1203 0.957395 ATTCAGCAGACGGCCACTTG 60.957 55.000 2.24 0.00 46.50 3.16
1304 1337 1.228245 GCCAAGAACCTGCCACTGA 60.228 57.895 0.00 0.00 0.00 3.41
1663 1725 6.614162 GCACATTAGCAAAGACAAAATCAACG 60.614 38.462 0.00 0.00 0.00 4.10
1784 1882 2.166664 AGTATGAGAAGACCACCGCTTC 59.833 50.000 0.00 0.00 41.53 3.86
2098 4730 6.897966 AGAGAGAGAGAGAGAGAGAGAGTAAA 59.102 42.308 0.00 0.00 0.00 2.01
2142 4794 9.950680 ATGTATGTTTGAAAAACACACTTAGAG 57.049 29.630 13.57 0.00 29.57 2.43
2167 4953 7.754851 ATGACTTAACAAAGAAAACGGGTAT 57.245 32.000 0.00 0.00 0.00 2.73
2168 4954 7.173047 GGTATGACTTAACAAAGAAAACGGGTA 59.827 37.037 0.00 0.00 0.00 3.69
2365 8344 1.855213 TTGCCTGCTCGCACAATGTC 61.855 55.000 0.00 0.00 38.83 3.06
2530 10123 7.037297 TCCTCCTTGTCCAATCTTAGATTCTTT 60.037 37.037 4.24 0.00 0.00 2.52
2700 10311 6.351371 CCTTGTTGAGAATCTCTACTTAGCCA 60.351 42.308 21.51 2.24 37.20 4.75
2916 10528 7.978975 AGAAACAAATGTAAGCAGCAAAAAGTA 59.021 29.630 0.00 0.00 0.00 2.24
3004 10624 0.394352 ATAGAAGCCCCCTTGCAACG 60.394 55.000 0.00 0.00 0.00 4.10
3265 10907 0.543277 CTCAGGAGCCATGTAGCCAA 59.457 55.000 0.00 0.00 0.00 4.52
3389 11031 1.476833 GCGAGGCTGGAAAATCCCATA 60.477 52.381 0.00 0.00 35.03 2.74
3503 11156 9.846248 GACTAAAACAAGCAAGAACATCATATT 57.154 29.630 0.00 0.00 0.00 1.28
3839 11523 4.597404 TTGTGAGCCATACAATTTGCAA 57.403 36.364 0.00 0.00 33.43 4.08
3848 11532 6.311935 TCACGTTACTATTTTGTGAGCCATAC 59.688 38.462 0.00 0.00 34.85 2.39
3894 11701 6.710295 TGCTTCAACTGTTATTCATGTAGTGT 59.290 34.615 0.00 0.00 0.00 3.55
3968 12505 2.154462 GCCAAGTGTTACACTCAGCAT 58.846 47.619 25.04 7.62 44.62 3.79
4027 12566 4.586001 AGTGGACGAAAAGTACTTGACCTA 59.414 41.667 9.34 0.00 33.83 3.08
4070 12609 1.009829 GCAGCCCTATTCAACACTCG 58.990 55.000 0.00 0.00 0.00 4.18
4081 12620 1.639722 TATAATGCCGAGCAGCCCTA 58.360 50.000 4.90 0.00 43.65 3.53
4097 12636 7.494211 TCGGCTTATAGTCAAAGTGCTTTATA 58.506 34.615 0.00 0.00 0.00 0.98
4105 12644 4.219944 TGACACTCGGCTTATAGTCAAAGT 59.780 41.667 0.00 0.00 33.55 2.66
4128 12667 8.092521 TGAAATGTTTCAACACATTGTTTTGT 57.907 26.923 13.73 0.00 44.95 2.83


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

AutoCloner maintained by Alex Coulton.