Multiple sequence alignment - TraesCS6A01G324700

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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 TraesCS6A01G324700 chr6A 100.000 3248 0 0 1 3248 558919476 558922723 0.000000e+00 5999.0
1 TraesCS6A01G324700 chr6A 90.568 1919 108 26 1349 3248 558933763 558935627 0.000000e+00 2473.0
2 TraesCS6A01G324700 chr6A 89.137 1344 101 11 113 1429 558932608 558933933 0.000000e+00 1631.0
3 TraesCS6A01G324700 chr6A 87.634 558 43 13 1921 2462 558950866 558951413 2.750000e-175 625.0
4 TraesCS6A01G324700 chr6A 90.805 87 6 2 1523 1608 558933670 558933755 7.360000e-22 115.0
5 TraesCS6A01G324700 chr6D 95.696 1998 58 15 1261 3248 413383664 413385643 0.000000e+00 3188.0
6 TraesCS6A01G324700 chr6D 94.751 1524 68 7 1 1520 413382360 413383875 0.000000e+00 2361.0
7 TraesCS6A01G324700 chr6D 88.970 1233 97 23 2036 3248 413395887 413397100 0.000000e+00 1487.0
8 TraesCS6A01G324700 chr6D 79.897 582 73 27 400 959 413380677 413381236 1.410000e-103 387.0
9 TraesCS6A01G324700 chr6D 92.593 81 6 0 1519 1599 413383520 413383600 2.050000e-22 117.0
10 TraesCS6A01G324700 chr6B 90.701 1925 100 36 1349 3248 623445691 623447561 0.000000e+00 2490.0
11 TraesCS6A01G324700 chr6B 90.257 1437 108 12 3 1429 623444447 623445861 0.000000e+00 1849.0
12 TraesCS6A01G324700 chr6B 94.793 941 35 8 2309 3248 623388700 623389627 0.000000e+00 1454.0
13 TraesCS6A01G324700 chr6B 90.909 1001 73 6 441 1429 623368386 623369380 0.000000e+00 1328.0
14 TraesCS6A01G324700 chr6B 97.289 627 16 1 1349 1974 623369210 623369836 0.000000e+00 1062.0
15 TraesCS6A01G324700 chr6B 80.136 589 68 31 400 959 623358195 623358763 8.450000e-106 394.0
16 TraesCS6A01G324700 chr6B 93.358 271 10 3 1976 2239 623381735 623382004 8.450000e-106 394.0
17 TraesCS6A01G324700 chr6B 91.519 283 16 3 1 277 623367711 623367991 1.830000e-102 383.0
18 TraesCS6A01G324700 chr6B 90.476 168 16 0 276 443 623368096 623368263 4.220000e-54 222.0
19 TraesCS6A01G324700 chr6B 83.249 197 10 9 1861 2050 623443767 623443947 3.350000e-35 159.0
20 TraesCS6A01G324700 chr6B 95.181 83 3 1 2232 2313 623382214 623382296 2.630000e-26 130.0
21 TraesCS6A01G324700 chr6B 89.655 87 7 2 1523 1608 623369117 623369202 3.430000e-20 110.0
22 TraesCS6A01G324700 chr6B 89.655 87 7 2 1523 1608 623445598 623445683 3.430000e-20 110.0
23 TraesCS6A01G324700 chr6B 87.500 56 6 1 130 185 623358132 623358186 2.710000e-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 TraesCS6A01G324700 chr6A 558919476 558922723 3247 False 5999.000000 5999 100.00000 1 3248 1 chr6A.!!$F1 3247
1 TraesCS6A01G324700 chr6A 558932608 558935627 3019 False 1406.333333 2473 90.17000 113 3248 3 chr6A.!!$F3 3135
2 TraesCS6A01G324700 chr6A 558950866 558951413 547 False 625.000000 625 87.63400 1921 2462 1 chr6A.!!$F2 541
3 TraesCS6A01G324700 chr6D 413380677 413385643 4966 False 1513.250000 3188 90.73425 1 3248 4 chr6D.!!$F2 3247
4 TraesCS6A01G324700 chr6D 413395887 413397100 1213 False 1487.000000 1487 88.97000 2036 3248 1 chr6D.!!$F1 1212
5 TraesCS6A01G324700 chr6B 623388700 623389627 927 False 1454.000000 1454 94.79300 2309 3248 1 chr6B.!!$F1 939
6 TraesCS6A01G324700 chr6B 623443767 623447561 3794 False 1152.000000 2490 88.46550 3 3248 4 chr6B.!!$F5 3245
7 TraesCS6A01G324700 chr6B 623367711 623369836 2125 False 621.000000 1328 91.96960 1 1974 5 chr6B.!!$F3 1973
8 TraesCS6A01G324700 chr6B 623381735 623382296 561 False 262.000000 394 94.26950 1976 2313 2 chr6B.!!$F4 337
9 TraesCS6A01G324700 chr6B 623358132 623358763 631 False 228.950000 394 83.81800 130 959 2 chr6B.!!$F2 829

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
221 1913 1.227764 CGACATGCCAGCCTGCTAT 60.228 57.895 0.00 0.0 0.00 2.97 F
1275 3262 0.108424 CTCCAAGAGCAAGGTCTCCG 60.108 60.000 1.86 0.0 33.66 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1346 3375 1.002868 GGAGAGCTTGCTCTTGCCA 60.003 57.895 23.68 0.0 38.71 4.92 R
3056 5342 0.245539 CTTGCAGAGCCAAATGTGGG 59.754 55.000 3.47 0.0 46.09 4.61 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
220 1912 2.187685 CGACATGCCAGCCTGCTA 59.812 61.111 0.00 0.00 0.00 3.49
221 1913 1.227764 CGACATGCCAGCCTGCTAT 60.228 57.895 0.00 0.00 0.00 2.97
263 1956 3.995199 ACATATCAGATAACCACAGCCG 58.005 45.455 0.00 0.00 0.00 5.52
278 2077 6.285990 ACCACAGCCGTTAATTATTACTAGG 58.714 40.000 0.00 0.00 0.00 3.02
292 2091 9.614792 AATTATTACTAGGAAAAAGATCGCTGT 57.385 29.630 0.00 0.00 0.00 4.40
294 2093 4.537135 ACTAGGAAAAAGATCGCTGTGA 57.463 40.909 0.00 0.00 0.00 3.58
309 2108 2.028112 GCTGTGATGGTCCTCAACAGTA 60.028 50.000 15.42 0.00 32.07 2.74
576 2530 4.523083 AGCTCTGTGTTGTAAAACCTGAA 58.477 39.130 0.00 0.00 0.00 3.02
621 2575 9.839817 ATTCCCTTTTCTATCTAGCTTTAAGAC 57.160 33.333 0.00 0.00 0.00 3.01
694 2648 1.728971 GAGAGACGAAATGCACCACAG 59.271 52.381 0.00 0.00 0.00 3.66
840 2819 1.775039 GCTTGCACAAGACACTCGCA 61.775 55.000 14.44 0.00 40.79 5.10
1097 3084 2.750166 GAGTGAGAGGATGTCGACAAGA 59.250 50.000 24.13 0.00 0.00 3.02
1127 3114 2.470362 GCTCCTCGTCGTGATCCGA 61.470 63.158 2.65 2.65 45.00 4.55
1189 3176 0.403271 ACAGAGTTCAAGCAGGCCAT 59.597 50.000 5.01 0.00 0.00 4.40
1275 3262 0.108424 CTCCAAGAGCAAGGTCTCCG 60.108 60.000 1.86 0.00 33.66 4.63
1335 3364 1.393746 TCCACAGGAGATGAGGGCT 59.606 57.895 0.00 0.00 39.91 5.19
1336 3365 0.689080 TCCACAGGAGATGAGGGCTC 60.689 60.000 0.00 0.00 39.91 4.70
1337 3366 1.440893 CACAGGAGATGAGGGCTCG 59.559 63.158 0.00 0.00 33.19 5.03
1340 3369 2.107953 GGAGATGAGGGCTCGCAC 59.892 66.667 0.00 0.00 33.19 5.34
1346 3375 1.406065 ATGAGGGCTCGCACATAGCT 61.406 55.000 0.00 0.00 42.61 3.32
1347 3376 1.593750 GAGGGCTCGCACATAGCTG 60.594 63.158 0.00 0.00 42.61 4.24
1830 3862 0.401738 CACCAAGGGAAAGAGAGCCA 59.598 55.000 0.00 0.00 0.00 4.75
1858 3890 0.689745 AAGCCCTAGGATGCACCGTA 60.690 55.000 11.48 0.00 44.74 4.02
1915 3949 5.658468 TGTGAATCTCTTCAGCTATGTGAG 58.342 41.667 0.00 0.00 41.96 3.51
1956 3994 7.599998 GGTCCGATGTACACTTCTTTAACTTTA 59.400 37.037 0.00 0.00 0.00 1.85
2041 4079 7.133891 AGTGTATCAGCAACAATAGTTTCAC 57.866 36.000 0.00 0.00 35.28 3.18
2165 4224 5.412286 GCAAATATGGTCAAAGTTGCCAATT 59.588 36.000 10.03 8.75 37.70 2.32
2168 4227 3.731652 TGGTCAAAGTTGCCAATTGAG 57.268 42.857 7.12 0.00 34.02 3.02
2326 4603 2.928116 GGTAGAACCACAGTCGTATTGC 59.072 50.000 0.00 0.00 38.42 3.56
2794 5079 7.923344 CGAATATCTTGTTCTTGTGGAGACTAT 59.077 37.037 0.00 0.00 33.02 2.12
2795 5080 9.606631 GAATATCTTGTTCTTGTGGAGACTATT 57.393 33.333 0.00 0.00 33.02 1.73
3056 5342 0.950555 TGAACTGTCAGCATCACGGC 60.951 55.000 0.00 0.00 0.00 5.68
3059 5346 3.610619 CTGTCAGCATCACGGCCCA 62.611 63.158 0.00 0.00 0.00 5.36
3124 5413 4.406649 TGATCATCATTCCAGCTGAGTGTA 59.593 41.667 17.39 0.00 32.79 2.90
3141 5430 9.595823 GCTGAGTGTAACCAGAATAGTAATTAA 57.404 33.333 0.00 0.00 37.32 1.40
3175 5476 6.446781 AATGCATAAATCAGAAGACACAGG 57.553 37.500 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.058328 GCGTTTCCCGTTATTTAAGTAGATTAC 58.942 37.037 0.00 0.00 39.32 1.89
220 1912 5.159209 GTTGTAACGCGAGCCTGTATATAT 58.841 41.667 15.93 0.00 0.00 0.86
221 1913 4.036616 TGTTGTAACGCGAGCCTGTATATA 59.963 41.667 15.93 0.00 0.00 0.86
233 1925 5.460748 TGGTTATCTGATATGTTGTAACGCG 59.539 40.000 3.53 3.53 0.00 6.01
278 2077 3.181506 GGACCATCACAGCGATCTTTTTC 60.182 47.826 0.00 0.00 29.21 2.29
292 2091 7.437713 AAGATTATACTGTTGAGGACCATCA 57.562 36.000 0.00 0.00 0.00 3.07
294 2093 7.287005 TCGTAAGATTATACTGTTGAGGACCAT 59.713 37.037 0.00 0.00 45.01 3.55
358 2157 8.197439 GGCAAACATTTAGAGTATGCCTAAAAT 58.803 33.333 6.63 0.00 46.34 1.82
576 2530 5.071115 GGGAATGAGTCTATTTACCTCTGCT 59.929 44.000 0.00 0.00 0.00 4.24
621 2575 3.190874 GAGTCGGAGAAGTGCCTTTATG 58.809 50.000 0.00 0.00 39.69 1.90
694 2648 4.418401 TTTTGCGATGCTGGCGGC 62.418 61.111 12.43 12.43 42.22 6.53
857 2837 1.672356 GCACGGTGCCATGAGAACT 60.672 57.895 22.19 0.00 37.42 3.01
1189 3176 2.409064 TCTCCACTTGAAGGGGTACA 57.591 50.000 14.10 0.00 40.57 2.90
1275 3262 2.447714 GGTCCCCCTCATCTCCTGC 61.448 68.421 0.00 0.00 0.00 4.85
1299 3286 1.650825 GAGAGCTTGCTCTTACCTGC 58.349 55.000 23.68 8.46 33.21 4.85
1300 3287 1.552337 TGGAGAGCTTGCTCTTACCTG 59.448 52.381 23.68 0.00 35.26 4.00
1318 3305 1.828768 GAGCCCTCATCTCCTGTGG 59.171 63.158 0.00 0.00 38.10 4.17
1320 3307 2.430610 GCGAGCCCTCATCTCCTGT 61.431 63.158 0.00 0.00 0.00 4.00
1337 3366 1.028330 TGCTCTTGCCAGCTATGTGC 61.028 55.000 0.00 0.00 40.39 4.57
1346 3375 1.002868 GGAGAGCTTGCTCTTGCCA 60.003 57.895 23.68 0.00 38.71 4.92
1347 3376 2.105466 CGGAGAGCTTGCTCTTGCC 61.105 63.158 23.68 19.47 38.71 4.52
1635 3664 4.215613 CCTGATATTCTCCATGTCGTCGTA 59.784 45.833 0.00 0.00 0.00 3.43
1830 3862 2.344093 TCCTAGGGCTTTCTCCTTGT 57.656 50.000 9.46 0.00 35.92 3.16
1915 3949 2.132762 CGGACCAGTACACAAGTTGTC 58.867 52.381 5.27 0.00 39.91 3.18
1999 4037 3.942748 ACACTTTAGGAAACAAGCACGAA 59.057 39.130 0.00 0.00 0.00 3.85
2041 4079 8.864069 TTGGTTAGTGTGTTAATGAATTTGTG 57.136 30.769 0.00 0.00 0.00 3.33
2165 4224 6.403866 ACCAAACTTGTGAATATTTGCTCA 57.596 33.333 0.00 0.00 31.95 4.26
2168 4227 5.571357 CCGTACCAAACTTGTGAATATTTGC 59.429 40.000 0.00 0.00 31.95 3.68
2326 4603 0.675522 AACTAATGCACGGGGGAACG 60.676 55.000 0.00 0.00 40.31 3.95
2744 5029 6.536582 CGTATGTTGACTCCTTCATTTCTCAT 59.463 38.462 0.00 0.00 32.84 2.90
3056 5342 0.245539 CTTGCAGAGCCAAATGTGGG 59.754 55.000 3.47 0.00 46.09 4.61
3175 5476 2.283298 CATAGAGTGTCATGGTGTGGC 58.717 52.381 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.