Multiple sequence alignment - TraesCS1A01G147800

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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 TraesCS1A01G147800 chr1A 100.000 3896 0 0 1 3896 255202431 255206326 0.000000e+00 7195
1 TraesCS1A01G147800 chr1A 95.214 2737 124 4 509 3241 423170699 423167966 0.000000e+00 4322
2 TraesCS1A01G147800 chr1A 95.214 2737 124 3 509 3241 423234394 423231661 0.000000e+00 4322
3 TraesCS1A01G147800 chr1A 94.775 2775 131 6 509 3272 423107280 423104509 0.000000e+00 4309
4 TraesCS1A01G147800 chr1A 94.642 2781 126 10 509 3272 423296283 423293509 0.000000e+00 4289
5 TraesCS1A01G147800 chr1A 96.492 2081 63 5 1820 3896 272648540 272650614 0.000000e+00 3430
6 TraesCS1A01G147800 chr1A 94.755 572 30 0 3325 3896 423293513 423292942 0.000000e+00 891
7 TraesCS1A01G147800 chr3A 96.523 3394 107 7 509 3896 382441264 382437876 0.000000e+00 5603
8 TraesCS1A01G147800 chr3A 91.589 107 7 1 1 105 110684704 110684598 3.140000e-31 147
9 TraesCS1A01G147800 chr4A 96.054 3269 111 9 630 3896 138467241 138463989 0.000000e+00 5306
10 TraesCS1A01G147800 chr4A 91.113 1114 88 7 229 1339 146401359 146402464 0.000000e+00 1498
11 TraesCS1A01G147800 chr4D 97.261 2592 57 9 1310 3896 349448342 349445760 0.000000e+00 4381
12 TraesCS1A01G147800 chr4D 97.129 1219 33 2 1 1218 349449557 349448340 0.000000e+00 2056
13 TraesCS1A01G147800 chr7A 96.156 2081 68 7 1820 3896 269297622 269299694 0.000000e+00 3389
14 TraesCS1A01G147800 chr3B 92.991 1441 92 7 229 1665 309750068 309751503 0.000000e+00 2093
15 TraesCS1A01G147800 chr1B 87.654 324 33 1 229 545 512150165 512149842 1.710000e-98 370
16 TraesCS1A01G147800 chr1B 96.610 59 2 0 172 230 398648204 398648262 8.910000e-17 99
17 TraesCS1A01G147800 chr2B 85.759 323 42 3 1313 1632 180610055 180609734 4.820000e-89 339
18 TraesCS1A01G147800 chr2A 90.055 181 17 1 1665 1845 305388487 305388666 2.340000e-57 233
19 TraesCS1A01G147800 chr5A 89.726 146 14 1 1661 1806 425253889 425254033 6.650000e-43 185
20 TraesCS1A01G147800 chr7B 88.785 107 10 1 1 105 392310750 392310856 3.160000e-26 130
21 TraesCS1A01G147800 chr7B 87.850 107 11 1 1 105 283700855 283700961 1.470000e-24 124
22 TraesCS1A01G147800 chr7B 96.610 59 2 0 172 230 283701103 283701161 8.910000e-17 99


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 TraesCS1A01G147800 chr1A 255202431 255206326 3895 False 7195.0 7195 100.0000 1 3896 1 chr1A.!!$F1 3895
1 TraesCS1A01G147800 chr1A 423167966 423170699 2733 True 4322.0 4322 95.2140 509 3241 1 chr1A.!!$R2 2732
2 TraesCS1A01G147800 chr1A 423231661 423234394 2733 True 4322.0 4322 95.2140 509 3241 1 chr1A.!!$R3 2732
3 TraesCS1A01G147800 chr1A 423104509 423107280 2771 True 4309.0 4309 94.7750 509 3272 1 chr1A.!!$R1 2763
4 TraesCS1A01G147800 chr1A 272648540 272650614 2074 False 3430.0 3430 96.4920 1820 3896 1 chr1A.!!$F2 2076
5 TraesCS1A01G147800 chr1A 423292942 423296283 3341 True 2590.0 4289 94.6985 509 3896 2 chr1A.!!$R4 3387
6 TraesCS1A01G147800 chr3A 382437876 382441264 3388 True 5603.0 5603 96.5230 509 3896 1 chr3A.!!$R2 3387
7 TraesCS1A01G147800 chr4A 138463989 138467241 3252 True 5306.0 5306 96.0540 630 3896 1 chr4A.!!$R1 3266
8 TraesCS1A01G147800 chr4A 146401359 146402464 1105 False 1498.0 1498 91.1130 229 1339 1 chr4A.!!$F1 1110
9 TraesCS1A01G147800 chr4D 349445760 349449557 3797 True 3218.5 4381 97.1950 1 3896 2 chr4D.!!$R1 3895
10 TraesCS1A01G147800 chr7A 269297622 269299694 2072 False 3389.0 3389 96.1560 1820 3896 1 chr7A.!!$F1 2076
11 TraesCS1A01G147800 chr3B 309750068 309751503 1435 False 2093.0 2093 92.9910 229 1665 1 chr3B.!!$F1 1436

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
40 41 0.177836 ACGGTGGATGAATCGATGCA 59.822 50.0 8.96 8.96 0.00 3.96 F
122 124 0.179000 CCATTAGGGTCGAAGCTGCT 59.821 55.0 0.00 0.00 0.00 4.24 F
819 826 0.546747 AGTACCCTGGGTAGCTGCAA 60.547 55.0 25.77 1.46 39.02 4.08 F
1413 1422 0.733150 GCTCTACGCAACCATTTCCC 59.267 55.0 0.00 0.00 38.92 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1036 1044 1.282248 CGTTGGATGCACTCGTCGTT 61.282 55.000 0.00 0.0 0.00 3.85 R
1075 1083 3.473113 AATGCCAATACCTTGTTCCCT 57.527 42.857 0.00 0.0 0.00 4.20 R
2800 2832 0.108585 ATGGGGCGCATAGTACCTTG 59.891 55.000 16.13 0.0 0.00 3.61 R
3298 3339 4.156739 GCCAAACAAAGGAGAGATTGGTAG 59.843 45.833 0.00 0.0 39.53 3.18 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 0.177836 ACGGTGGATGAATCGATGCA 59.822 50.000 8.96 8.96 0.00 3.96
91 93 3.849951 GCGAGGCCGGAGATCCAA 61.850 66.667 5.05 0.00 36.06 3.53
122 124 0.179000 CCATTAGGGTCGAAGCTGCT 59.821 55.000 0.00 0.00 0.00 4.24
129 131 4.061346 TCGAAGCTGCTGCGCTCT 62.061 61.111 24.94 0.00 45.42 4.09
149 151 2.858476 TCCCCAAGCTGCCTCCAA 60.858 61.111 0.00 0.00 0.00 3.53
193 195 1.674057 CACGGAGGCAAGGTTCTCT 59.326 57.895 0.00 0.00 0.00 3.10
469 471 4.298332 CAAACCGAGCTTTGCTTTACAAT 58.702 39.130 0.00 0.00 39.88 2.71
485 487 6.554334 TTTACAATAACTTGACTGCCTGTC 57.446 37.500 0.00 0.00 45.54 3.51
560 562 7.896811 TCCTTGATAAATACATCGCTCTACAT 58.103 34.615 0.00 0.00 0.00 2.29
715 717 6.655425 GTCCTAACTGCTGTTCTAAATCCTTT 59.345 38.462 12.67 0.00 37.59 3.11
819 826 0.546747 AGTACCCTGGGTAGCTGCAA 60.547 55.000 25.77 1.46 39.02 4.08
899 907 2.514458 AAGGAGACCCATGCGAAATT 57.486 45.000 0.00 0.00 33.88 1.82
1075 1083 1.603842 CACCATGCTGCTGGTCCTA 59.396 57.895 17.21 0.00 46.79 2.94
1345 1353 4.100189 GCATCCTCTCCTAACTGCTTCTAA 59.900 45.833 0.00 0.00 0.00 2.10
1413 1422 0.733150 GCTCTACGCAACCATTTCCC 59.267 55.000 0.00 0.00 38.92 3.97
2125 2156 3.485463 ACATCTCGGAACAACCTTTCA 57.515 42.857 0.00 0.00 36.31 2.69
2143 2174 6.044404 ACCTTTCATGTCCCCGATATTATCTT 59.956 38.462 2.36 0.00 0.00 2.40
2320 2352 1.071471 AGTTGTTGCTGAGGGTCCG 59.929 57.895 0.00 0.00 0.00 4.79
2395 2427 3.958147 CTGAACTGGTGTTTAGGGGTTTT 59.042 43.478 0.00 0.00 36.51 2.43
2419 2451 2.028112 TGCAGGACTACTACTTGCTTGG 60.028 50.000 0.00 0.00 0.00 3.61
2423 2455 5.627040 GCAGGACTACTACTTGCTTGGTTAT 60.627 44.000 0.00 0.00 0.00 1.89
2800 2832 6.799512 ACATCTTGATGTTAATAGGCTTTGC 58.200 36.000 10.15 0.00 0.00 3.68
2818 2851 1.524961 CAAGGTACTATGCGCCCCA 59.475 57.895 4.18 0.00 38.49 4.96
2997 3030 9.884636 CATATAATTCCCACGATCCTATTACAA 57.115 33.333 0.00 0.00 0.00 2.41
3102 3135 6.125029 ACTAAGCCTTTGTGCATTCTGATAT 58.875 36.000 0.00 0.00 0.00 1.63
3151 3184 2.797786 CCCATTTTAAACCGAGACCCA 58.202 47.619 0.00 0.00 0.00 4.51
3197 3230 7.865820 TCATCCATTCTCCTGAATTTTAGTCT 58.134 34.615 0.00 0.00 40.61 3.24
3287 3328 2.039746 TGTGATTTGGTCAATCCTCGGT 59.960 45.455 0.00 0.00 40.80 4.69
3298 3339 2.311124 ATCCTCGGTGTTTCGATTCC 57.689 50.000 0.00 0.00 38.55 3.01
3361 3459 1.405105 GCTGCAAGTCCAAGACAACAA 59.595 47.619 0.00 0.00 34.60 2.83
3509 3607 7.398332 AGACTTCCATTTTCATTGGCTTAGAAT 59.602 33.333 0.00 0.00 34.06 2.40
3529 3627 6.294473 AGAATATAGTGAGAATTGCCTGGTG 58.706 40.000 0.00 0.00 0.00 4.17
3573 3671 4.112634 ACCAATACAACTCAACCCACAT 57.887 40.909 0.00 0.00 0.00 3.21
3626 3724 2.301583 TGCTAACAGATGGCTACACACA 59.698 45.455 0.00 0.00 36.30 3.72
3656 3754 6.824305 ATTGACAAATCCGACTTTGAAGAT 57.176 33.333 14.15 4.62 38.17 2.40
3859 3957 3.704061 TCTGGATGTGATGTCCGTCATTA 59.296 43.478 0.00 0.00 38.64 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.359848 GTCGTCACCTTGCATCGATT 58.640 50.000 0.00 0.00 33.35 3.34
40 41 1.587933 GAGGAGCTCGTCGTCACCTT 61.588 60.000 19.74 0.00 39.48 3.50
107 109 2.579201 GCAGCAGCTTCGACCCTA 59.421 61.111 0.00 0.00 37.91 3.53
149 151 1.382420 ATGGAGGAGGAAGCGAGCT 60.382 57.895 0.00 0.00 0.00 4.09
245 247 3.252974 AGAAGCTACAGGACAAATCGG 57.747 47.619 0.00 0.00 0.00 4.18
258 260 6.449956 TCCTTTATAGAGGGGAAAGAAGCTA 58.550 40.000 9.36 0.00 37.41 3.32
678 680 4.777896 AGCAGTTAGGACCAATAGAACTCA 59.222 41.667 0.00 0.00 0.00 3.41
819 826 5.483583 AGAGAGAAAGAAAGAGCACCACTAT 59.516 40.000 0.00 0.00 0.00 2.12
899 907 4.314440 GCACCACCAGGACGCTCA 62.314 66.667 0.00 0.00 38.69 4.26
1020 1028 3.736100 TTGCTTGATGCGTGCGGG 61.736 61.111 0.00 0.00 46.63 6.13
1036 1044 1.282248 CGTTGGATGCACTCGTCGTT 61.282 55.000 0.00 0.00 0.00 3.85
1075 1083 3.473113 AATGCCAATACCTTGTTCCCT 57.527 42.857 0.00 0.00 0.00 4.20
1345 1353 5.927281 AAAGCTATTTCCATGAAGTGCAT 57.073 34.783 0.00 0.00 37.85 3.96
1413 1422 4.259970 CGCCATCTTCTGAAGTTAATCACG 60.260 45.833 16.43 9.13 0.00 4.35
1861 1873 7.227512 GCTTATGGCAGAATTAACACTGATAGT 59.772 37.037 12.88 0.00 41.35 2.12
2073 2098 4.617959 TCTAACAGTTAGACAGCACACAC 58.382 43.478 17.71 0.00 37.35 3.82
2125 2156 6.044404 AGGAAACAAGATAATATCGGGGACAT 59.956 38.462 0.00 0.00 0.00 3.06
2347 2379 5.084818 TCCATATTATACACATCCCTGCG 57.915 43.478 0.00 0.00 0.00 5.18
2395 2427 3.698289 AGCAAGTAGTAGTCCTGCACTA 58.302 45.455 4.82 0.00 36.43 2.74
2423 2455 9.793259 AAATCTCTAAACACCAGTTGATCTAAA 57.207 29.630 0.00 0.00 38.17 1.85
2800 2832 0.108585 ATGGGGCGCATAGTACCTTG 59.891 55.000 16.13 0.00 0.00 3.61
2818 2851 6.183360 TGGTGCAAATTCTGTAAACCTTGAAT 60.183 34.615 0.00 0.00 0.00 2.57
2997 3030 6.149308 TGCTCAATATTGTCGTCAGAACAAAT 59.851 34.615 14.97 0.00 0.00 2.32
3287 3328 5.395324 GGAGAGATTGGTAGGAATCGAAACA 60.395 44.000 0.00 0.00 37.41 2.83
3298 3339 4.156739 GCCAAACAAAGGAGAGATTGGTAG 59.843 45.833 0.00 0.00 39.53 3.18
3349 3447 5.046159 AGGATATTACCGTTGTTGTCTTGGA 60.046 40.000 0.00 0.00 34.73 3.53
3509 3607 5.692115 TTCACCAGGCAATTCTCACTATA 57.308 39.130 0.00 0.00 0.00 1.31
3529 3627 1.545841 AGCCCGGTTTTCCTCAATTC 58.454 50.000 0.00 0.00 37.95 2.17
3573 3671 1.603306 GCCGGTGGTACCCATGTTA 59.397 57.895 10.07 0.00 35.28 2.41
3626 3724 3.813166 AGTCGGATTTGTCAATTGTTCGT 59.187 39.130 5.13 0.00 0.00 3.85
3707 3805 4.913335 TGATAGACACTCGGTGGTTATC 57.087 45.455 8.57 12.63 37.94 1.75


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

AutoCloner maintained by Alex Coulton.