Multiple sequence alignment - TraesCS6A01G204200

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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 TraesCS6A01G204200 chr6A 100.000 2802 0 0 1 2802 353341473 353338672 0.000000e+00 5175
1 TraesCS6A01G204200 chr6A 97.653 2088 48 1 4 2090 353349378 353347291 0.000000e+00 3583
2 TraesCS6A01G204200 chr6A 96.779 714 23 0 2089 2802 295436875 295436162 0.000000e+00 1192
3 TraesCS6A01G204200 chr6A 96.774 713 19 2 2090 2802 20939958 20940666 0.000000e+00 1186
4 TraesCS6A01G204200 chr6A 89.879 247 22 3 1 244 414896291 414896537 5.830000e-82 315
5 TraesCS6A01G204200 chr6A 89.069 247 23 4 1 244 414888391 414888636 1.260000e-78 303
6 TraesCS6A01G204200 chr6A 88.571 245 24 4 1 243 398692585 398692827 7.590000e-76 294
7 TraesCS6A01G204200 chr1A 95.514 2051 74 14 4 2049 469357776 469355739 0.000000e+00 3262
8 TraesCS6A01G204200 chr1A 95.974 1838 64 4 260 2090 168235210 168237044 0.000000e+00 2976
9 TraesCS6A01G204200 chr1A 97.199 714 20 0 2089 2802 136909503 136908790 0.000000e+00 1208
10 TraesCS6A01G204200 chr1A 87.747 253 21 8 5 247 86896813 86896561 1.270000e-73 287
11 TraesCS6A01G204200 chr1A 86.800 250 30 3 1 247 183776845 183776596 2.750000e-70 276
12 TraesCS6A01G204200 chr1A 86.561 253 23 9 5 247 184256750 184256499 4.600000e-68 268
13 TraesCS6A01G204200 chr3A 95.024 2050 86 12 4 2049 279045792 279043755 0.000000e+00 3206
14 TraesCS6A01G204200 chr3A 95.466 2007 75 13 4 2008 279037894 279035902 0.000000e+00 3188
15 TraesCS6A01G204200 chr3A 94.295 2051 88 14 4 2049 271848241 271846215 0.000000e+00 3112
16 TraesCS6A01G204200 chr3A 93.772 1975 107 9 4 1967 254286775 254284806 0.000000e+00 2952
17 TraesCS6A01G204200 chr3A 92.333 2100 113 20 4 2086 254257408 254255340 0.000000e+00 2942
18 TraesCS6A01G204200 chr3A 91.847 2122 114 20 1 2086 254265497 254263399 0.000000e+00 2905
19 TraesCS6A01G204200 chr3A 96.639 714 24 0 2089 2802 327926426 327925713 0.000000e+00 1186
20 TraesCS6A01G204200 chr3A 96.861 223 7 0 4 226 334149167 334148945 9.480000e-100 374
21 TraesCS6A01G204200 chr3A 77.715 534 80 28 1572 2090 433915926 433916435 9.820000e-75 291
22 TraesCS6A01G204200 chr3A 83.045 289 36 10 1813 2090 279569092 279568806 1.670000e-62 250
23 TraesCS6A01G204200 chr3A 75.734 511 84 29 1590 2084 374202695 374203181 1.310000e-53 220
24 TraesCS6A01G204200 chr2A 90.395 2124 152 32 1 2090 321742249 321744354 0.000000e+00 2745
25 TraesCS6A01G204200 chr2A 89.835 2125 163 32 1 2091 321750222 321752327 0.000000e+00 2678
26 TraesCS6A01G204200 chr2A 97.059 714 18 1 2089 2802 226199216 226199926 0.000000e+00 1199
27 TraesCS6A01G204200 chr5A 96.919 714 19 1 2089 2802 562374517 562375227 0.000000e+00 1194
28 TraesCS6A01G204200 chr5A 96.779 714 20 1 2089 2802 68585661 68584951 0.000000e+00 1188
29 TraesCS6A01G204200 chr5A 90.283 247 21 3 1 244 606324911 606325157 1.250000e-83 320
30 TraesCS6A01G204200 chr5A 77.400 500 76 27 1627 2108 223041722 223041242 2.140000e-66 263
31 TraesCS6A01G204200 chr4A 96.542 723 22 3 2081 2802 201509532 201510252 0.000000e+00 1194
32 TraesCS6A01G204200 chr4A 96.779 714 23 0 2089 2802 523968575 523967862 0.000000e+00 1192
33 TraesCS6A01G204200 chrUn 93.431 137 7 1 1 135 74799453 74799589 4.730000e-48 202


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 TraesCS6A01G204200 chr6A 353338672 353341473 2801 True 5175 5175 100.000 1 2802 1 chr6A.!!$R2 2801
1 TraesCS6A01G204200 chr6A 353347291 353349378 2087 True 3583 3583 97.653 4 2090 1 chr6A.!!$R3 2086
2 TraesCS6A01G204200 chr6A 295436162 295436875 713 True 1192 1192 96.779 2089 2802 1 chr6A.!!$R1 713
3 TraesCS6A01G204200 chr6A 20939958 20940666 708 False 1186 1186 96.774 2090 2802 1 chr6A.!!$F1 712
4 TraesCS6A01G204200 chr1A 469355739 469357776 2037 True 3262 3262 95.514 4 2049 1 chr1A.!!$R5 2045
5 TraesCS6A01G204200 chr1A 168235210 168237044 1834 False 2976 2976 95.974 260 2090 1 chr1A.!!$F1 1830
6 TraesCS6A01G204200 chr1A 136908790 136909503 713 True 1208 1208 97.199 2089 2802 1 chr1A.!!$R2 713
7 TraesCS6A01G204200 chr3A 279043755 279045792 2037 True 3206 3206 95.024 4 2049 1 chr3A.!!$R6 2045
8 TraesCS6A01G204200 chr3A 279035902 279037894 1992 True 3188 3188 95.466 4 2008 1 chr3A.!!$R5 2004
9 TraesCS6A01G204200 chr3A 271846215 271848241 2026 True 3112 3112 94.295 4 2049 1 chr3A.!!$R4 2045
10 TraesCS6A01G204200 chr3A 254284806 254286775 1969 True 2952 2952 93.772 4 1967 1 chr3A.!!$R3 1963
11 TraesCS6A01G204200 chr3A 254255340 254257408 2068 True 2942 2942 92.333 4 2086 1 chr3A.!!$R1 2082
12 TraesCS6A01G204200 chr3A 254263399 254265497 2098 True 2905 2905 91.847 1 2086 1 chr3A.!!$R2 2085
13 TraesCS6A01G204200 chr3A 327925713 327926426 713 True 1186 1186 96.639 2089 2802 1 chr3A.!!$R8 713
14 TraesCS6A01G204200 chr3A 433915926 433916435 509 False 291 291 77.715 1572 2090 1 chr3A.!!$F2 518
15 TraesCS6A01G204200 chr2A 321742249 321744354 2105 False 2745 2745 90.395 1 2090 1 chr2A.!!$F2 2089
16 TraesCS6A01G204200 chr2A 321750222 321752327 2105 False 2678 2678 89.835 1 2091 1 chr2A.!!$F3 2090
17 TraesCS6A01G204200 chr2A 226199216 226199926 710 False 1199 1199 97.059 2089 2802 1 chr2A.!!$F1 713
18 TraesCS6A01G204200 chr5A 562374517 562375227 710 False 1194 1194 96.919 2089 2802 1 chr5A.!!$F1 713
19 TraesCS6A01G204200 chr5A 68584951 68585661 710 True 1188 1188 96.779 2089 2802 1 chr5A.!!$R1 713
20 TraesCS6A01G204200 chr4A 201509532 201510252 720 False 1194 1194 96.542 2081 2802 1 chr4A.!!$F1 721
21 TraesCS6A01G204200 chr4A 523967862 523968575 713 True 1192 1192 96.779 2089 2802 1 chr4A.!!$R1 713

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
225 235 1.067974 TCTCAAAGCGGTTCGAGTTCA 59.932 47.619 14.46 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2166 1.41271 TGAAGACTTTCTGTGACGCCT 59.587 47.619 0.0 0.0 34.31 5.52 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
76 82 1.761174 GGGTGTCCCATGTGTCAGT 59.239 57.895 0.00 0.00 44.65 3.41
161 171 4.153296 TCGTATCACAAAACATGCATTCGT 59.847 37.500 0.00 0.00 0.00 3.85
210 220 3.955471 CCTTACAAGGGAGCATTCTCAA 58.045 45.455 0.00 0.00 42.66 3.02
225 235 1.067974 TCTCAAAGCGGTTCGAGTTCA 59.932 47.619 14.46 0.00 0.00 3.18
236 246 4.380655 CGGTTCGAGTTCATAGAGGAAGTT 60.381 45.833 0.00 0.00 30.77 2.66
404 442 4.630111 CGGTAGAAGTAGTCGTCCTATCT 58.370 47.826 0.00 0.00 0.00 1.98
405 443 5.777802 CGGTAGAAGTAGTCGTCCTATCTA 58.222 45.833 0.00 0.00 0.00 1.98
445 483 1.270550 CGGTAGTGGTACAAGGTCGTT 59.729 52.381 0.00 0.00 44.16 3.85
1342 1392 1.957177 GGTATCGAGCAGTGAGATGGA 59.043 52.381 0.00 0.00 0.00 3.41
1398 1455 1.227176 CTCGCTAGGTTTACGGGGC 60.227 63.158 0.00 0.00 0.00 5.80
1625 1692 5.812642 TGAGCTCGATCTAGGAAAATGAAAC 59.187 40.000 9.64 0.00 0.00 2.78
1739 1811 3.045634 TGGGAAAACAGGAAGAGTCTCA 58.954 45.455 1.94 0.00 0.00 3.27
1932 2005 2.502538 TCCCTCGGTTTAAATGGATCGT 59.497 45.455 0.00 0.00 0.00 3.73
2080 2166 1.205655 CATCTGAAGCTCCGGACTTGA 59.794 52.381 19.69 12.81 0.00 3.02
2258 2347 2.480416 GCAAGGAGTATGACTCTGACGG 60.480 54.545 6.58 0.00 44.46 4.79
2264 2353 2.425312 AGTATGACTCTGACGGCAAGAG 59.575 50.000 14.00 14.00 35.92 2.85
2319 2408 5.936956 GTCTTCCTCAAAGTCTTCATCACAT 59.063 40.000 0.00 0.00 36.31 3.21
2343 2432 1.224039 GAGCTCATCTGGCAAGGCT 59.776 57.895 9.40 0.00 0.00 4.58
2461 2550 4.243270 GAGTCTGGCTACAACATACGTTT 58.757 43.478 0.00 0.00 31.13 3.60
2509 2598 1.338107 TGACTTCATCACCGACACCT 58.662 50.000 0.00 0.00 29.99 4.00
2523 2612 3.378112 CCGACACCTATGCAAATGACAAT 59.622 43.478 0.00 0.00 0.00 2.71
2721 2810 5.142061 TGTTAGACAAAAGCGATGACCTA 57.858 39.130 0.00 0.00 0.00 3.08
2753 2842 4.097135 TGAAATGACTCGATCTCAGTCCTC 59.903 45.833 15.53 11.19 39.78 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 82 4.738998 CCCTCGGTTGCCATGCCA 62.739 66.667 0.00 0.00 0.00 4.92
161 171 1.290955 GACACGACCGTCCATGGAA 59.709 57.895 18.20 0.00 0.00 3.53
210 220 2.159226 CCTCTATGAACTCGAACCGCTT 60.159 50.000 0.00 0.00 0.00 4.68
225 235 3.367087 CCGTGAACGACAACTTCCTCTAT 60.367 47.826 4.03 0.00 43.02 1.98
236 246 4.986587 CGACGGCCGTGAACGACA 62.987 66.667 39.65 0.00 43.02 4.35
404 442 0.455815 CCCGATGATCGCCGATGATA 59.544 55.000 3.34 0.00 38.82 2.15
405 443 1.216444 CCCGATGATCGCCGATGAT 59.784 57.895 3.34 0.00 38.82 2.45
445 483 2.079158 CGAGTACGACTACTTCCCACA 58.921 52.381 0.00 0.00 42.66 4.17
915 959 2.743928 CCGCTCTTTTGCTCGCCT 60.744 61.111 0.00 0.00 0.00 5.52
1398 1455 4.722700 CCCAAGGCCCAGTCACGG 62.723 72.222 0.00 0.00 0.00 4.94
1625 1692 9.373603 TGAATTTAAATCTTTCAATCATGCCAG 57.626 29.630 0.10 0.00 0.00 4.85
1739 1811 7.286313 TGCCAACAATTCTTTTCCCTTTTATT 58.714 30.769 0.00 0.00 0.00 1.40
1932 2005 9.976511 CTCAACTAAATAAACCGTATGGATCTA 57.023 33.333 8.33 0.00 39.21 1.98
2080 2166 1.412710 TGAAGACTTTCTGTGACGCCT 59.587 47.619 0.00 0.00 34.31 5.52
2258 2347 7.174080 ACTTTGAGTATTTCTTCTTCCTCTTGC 59.826 37.037 0.00 0.00 0.00 4.01
2264 2353 8.840833 AGAAGACTTTGAGTATTTCTTCTTCC 57.159 34.615 6.38 0.00 46.69 3.46
2319 2408 3.118482 CCTTGCCAGATGAGCTCTTCTTA 60.118 47.826 25.27 14.18 29.16 2.10
2343 2432 1.063327 CTTGCCAACAAACGCACGA 59.937 52.632 0.00 0.00 34.74 4.35
2392 2481 2.279073 CTCCACCTCCGCCTCCTA 59.721 66.667 0.00 0.00 0.00 2.94
2461 2550 3.390967 TCAGTGTTGAAGATGGACTTGGA 59.609 43.478 0.00 0.00 39.13 3.53
2509 2598 5.523552 CGGAGTAGTCATTGTCATTTGCATA 59.476 40.000 0.00 0.00 0.00 3.14
2523 2612 0.917533 AGGTAGGAGCGGAGTAGTCA 59.082 55.000 0.00 0.00 0.00 3.41
2721 2810 4.371855 TCGAGTCATTTCAGCGTCTAAT 57.628 40.909 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.