Multiple sequence alignment - TraesCS1B01G087200

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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 TraesCS1B01G087200 chr1B 100.000 3283 0 0 1 3283 80847138 80843856 0 6063
1 TraesCS1B01G087200 chr1B 95.177 3297 141 3 1 3283 80814173 80810881 0 5192
2 TraesCS1B01G087200 chr1B 95.012 3308 136 4 1 3280 544609339 544612645 0 5168
3 TraesCS1B01G087200 chr1B 95.553 3238 114 4 1 3210 544593697 544596932 0 5155
4 TraesCS1B01G087200 chr1B 95.360 3233 122 3 1 3205 544623636 544626868 0 5114
5 TraesCS1B01G087200 chr1B 94.087 3298 179 5 1 3283 80779470 80776174 0 4996
6 TraesCS1B01G087200 chr1B 93.333 2415 128 15 851 3250 80750061 80747665 0 3537
7 TraesCS1B01G087200 chr1B 92.921 1907 105 10 1392 3283 80822449 80820558 0 2747
8 TraesCS1B01G087200 chr1B 93.571 700 43 2 2585 3283 80877095 80876397 0 1042
9 TraesCS1B01G087200 chrUn 95.017 3311 137 3 1 3283 3845814 3842504 0 5175
10 TraesCS1B01G087200 chrUn 95.577 2962 103 3 1 2934 199904744 199907705 0 4719
11 TraesCS1B01G087200 chrUn 94.415 3026 134 17 1 2993 274341282 274338259 0 4619
12 TraesCS1B01G087200 chrUn 94.347 3025 137 16 1 2993 229310227 229307205 0 4608
13 TraesCS1B01G087200 chrUn 94.347 3025 137 16 1 2993 291535440 291538462 0 4608
14 TraesCS1B01G087200 chrUn 95.440 2763 109 6 1 2747 245706068 245708829 0 4388
15 TraesCS1B01G087200 chrUn 94.675 2535 106 4 777 3283 260645621 260643088 0 3906
16 TraesCS1B01G087200 chrUn 94.322 1497 57 3 1454 2922 394611815 394613311 0 2268
17 TraesCS1B01G087200 chrUn 94.109 1358 52 3 1689 3018 408024409 408023052 0 2039
18 TraesCS1B01G087200 chrUn 93.639 1242 50 4 1799 3012 421394164 421395404 0 1829
19 TraesCS1B01G087200 chrUn 91.987 1223 69 4 2086 3280 416933289 416934510 0 1688
20 TraesCS1B01G087200 chr6B 94.567 3313 149 6 1 3283 123759693 123756382 0 5092
21 TraesCS1B01G087200 chr6B 94.231 3311 161 5 1 3283 111705419 111702111 0 5029


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 TraesCS1B01G087200 chr1B 80843856 80847138 3282 True 6063 6063 100.000 1 3283 1 chr1B.!!$R5 3282
1 TraesCS1B01G087200 chr1B 80810881 80814173 3292 True 5192 5192 95.177 1 3283 1 chr1B.!!$R3 3282
2 TraesCS1B01G087200 chr1B 544609339 544612645 3306 False 5168 5168 95.012 1 3280 1 chr1B.!!$F2 3279
3 TraesCS1B01G087200 chr1B 544593697 544596932 3235 False 5155 5155 95.553 1 3210 1 chr1B.!!$F1 3209
4 TraesCS1B01G087200 chr1B 544623636 544626868 3232 False 5114 5114 95.360 1 3205 1 chr1B.!!$F3 3204
5 TraesCS1B01G087200 chr1B 80776174 80779470 3296 True 4996 4996 94.087 1 3283 1 chr1B.!!$R2 3282
6 TraesCS1B01G087200 chr1B 80747665 80750061 2396 True 3537 3537 93.333 851 3250 1 chr1B.!!$R1 2399
7 TraesCS1B01G087200 chr1B 80820558 80822449 1891 True 2747 2747 92.921 1392 3283 1 chr1B.!!$R4 1891
8 TraesCS1B01G087200 chr1B 80876397 80877095 698 True 1042 1042 93.571 2585 3283 1 chr1B.!!$R6 698
9 TraesCS1B01G087200 chrUn 3842504 3845814 3310 True 5175 5175 95.017 1 3283 1 chrUn.!!$R1 3282
10 TraesCS1B01G087200 chrUn 199904744 199907705 2961 False 4719 4719 95.577 1 2934 1 chrUn.!!$F1 2933
11 TraesCS1B01G087200 chrUn 274338259 274341282 3023 True 4619 4619 94.415 1 2993 1 chrUn.!!$R4 2992
12 TraesCS1B01G087200 chrUn 229307205 229310227 3022 True 4608 4608 94.347 1 2993 1 chrUn.!!$R2 2992
13 TraesCS1B01G087200 chrUn 291535440 291538462 3022 False 4608 4608 94.347 1 2993 1 chrUn.!!$F3 2992
14 TraesCS1B01G087200 chrUn 245706068 245708829 2761 False 4388 4388 95.440 1 2747 1 chrUn.!!$F2 2746
15 TraesCS1B01G087200 chrUn 260643088 260645621 2533 True 3906 3906 94.675 777 3283 1 chrUn.!!$R3 2506
16 TraesCS1B01G087200 chrUn 394611815 394613311 1496 False 2268 2268 94.322 1454 2922 1 chrUn.!!$F4 1468
17 TraesCS1B01G087200 chrUn 408023052 408024409 1357 True 2039 2039 94.109 1689 3018 1 chrUn.!!$R5 1329
18 TraesCS1B01G087200 chrUn 421394164 421395404 1240 False 1829 1829 93.639 1799 3012 1 chrUn.!!$F6 1213
19 TraesCS1B01G087200 chrUn 416933289 416934510 1221 False 1688 1688 91.987 2086 3280 1 chrUn.!!$F5 1194
20 TraesCS1B01G087200 chr6B 123756382 123759693 3311 True 5092 5092 94.567 1 3283 1 chr6B.!!$R2 3282
21 TraesCS1B01G087200 chr6B 111702111 111705419 3308 True 5029 5029 94.231 1 3283 1 chr6B.!!$R1 3282

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
780 781 0.032515 TAGGAAGTCCGGAGATGCCA 60.033 55.0 14.88 0.26 42.08 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2689 2709 0.956633 AGTTTAGCCTGTGACGACGA 59.043 50.0 0.0 0.0 0.0 4.2 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
50 51 1.409427 AGGGGCGAAAGACTAATCGAG 59.591 52.381 13.14 0.00 41.43 4.04
84 85 0.399075 GTTCCCTCCGAAGTTTCCCA 59.601 55.000 0.00 0.00 0.00 4.37
119 120 3.961408 AGCCCATTACGAGTTCTATCAGT 59.039 43.478 0.00 0.00 0.00 3.41
160 161 1.773856 TTGGGGATGCAACGTCCTCA 61.774 55.000 3.12 3.12 44.38 3.86
271 272 0.036483 TAAGCAGAACTGGCGATGCA 60.036 50.000 3.99 0.00 41.14 3.96
288 289 1.299648 CAGGATGAACCGGAAGCCA 59.700 57.895 9.46 0.00 44.74 4.75
421 422 1.899814 TCACCTGCCGAATCAACTAGT 59.100 47.619 0.00 0.00 0.00 2.57
435 436 5.943349 TCAACTAGTCCCGAAAATGGATA 57.057 39.130 0.00 0.00 33.65 2.59
522 523 4.279043 GCGGCCGTTGCAAAACCT 62.279 61.111 28.70 0.00 40.13 3.50
567 568 0.670546 CGTCGGTGCAGATCTTGGTT 60.671 55.000 0.00 0.00 0.00 3.67
752 753 4.552365 CGGGATGTGGCGGCTGAT 62.552 66.667 11.43 1.19 0.00 2.90
776 777 2.623889 CGACATTAGGAAGTCCGGAGAT 59.376 50.000 3.06 0.00 42.08 2.75
780 781 0.032515 TAGGAAGTCCGGAGATGCCA 60.033 55.000 14.88 0.26 42.08 4.92
943 944 3.175133 GGAGGACCGAGTACCGTTA 57.825 57.895 0.00 0.00 36.31 3.18
964 965 0.313043 CGCCCGGTCGTACTCATAAT 59.687 55.000 0.00 0.00 0.00 1.28
968 969 1.315497 CGGTCGTACTCATAATCGCG 58.685 55.000 0.00 0.00 0.00 5.87
976 977 1.067212 ACTCATAATCGCGTCAGGTCC 59.933 52.381 5.77 0.00 0.00 4.46
988 989 1.074951 CAGGTCCCCAAGGTGAACC 59.925 63.158 0.00 0.00 0.00 3.62
1023 1024 3.245586 TGGAACAATGTAGGCAAGGGAAT 60.246 43.478 0.00 0.00 31.92 3.01
1058 1059 1.356938 CGTAGCTTCGGGAAAAGGAC 58.643 55.000 4.63 0.00 0.00 3.85
1073 1074 2.632763 AGGACTGGCTCTAAGGACTT 57.367 50.000 0.00 0.00 0.00 3.01
1260 1261 5.045432 ACAAGGGGAATCCGACTGTTTAATA 60.045 40.000 0.00 0.00 41.52 0.98
1457 1458 1.645710 AACGAGATTCCCACTGTCCT 58.354 50.000 0.00 0.00 0.00 3.85
1472 1473 4.707448 CACTGTCCTTGTCTACTATCCAGT 59.293 45.833 0.00 0.00 38.91 4.00
1480 1481 6.352222 CCTTGTCTACTATCCAGTGAAACCAT 60.352 42.308 0.00 0.00 37.80 3.55
1495 1496 1.205460 ACCATAGCCAAGGGAACGGT 61.205 55.000 0.00 0.00 0.00 4.83
1800 1803 3.667497 AGATGAGCTCAACGAGAACAA 57.333 42.857 22.50 0.00 0.00 2.83
1974 1977 1.815421 AGCCAAGCGTTCATAGCGG 60.815 57.895 0.00 0.00 40.04 5.52
2029 2032 8.267183 TCTTCCTATCATTGTGAAGCAGAATTA 58.733 33.333 0.00 0.00 35.35 1.40
2145 2148 4.382160 GTCGCGATAGTAATTCAACCTAGC 59.618 45.833 14.06 0.00 39.35 3.42
2224 2227 2.048503 GAAGCTACCGTGTGCCGT 60.049 61.111 0.00 0.00 33.66 5.68
2244 2247 3.975670 CGTATTATGACTGAACGCCTCTC 59.024 47.826 0.00 0.00 0.00 3.20
2257 2260 1.202394 CGCCTCTCAGTCAGAATCCAG 60.202 57.143 0.00 0.00 0.00 3.86
2304 2307 4.376176 CGCCCCGACCCACGTTAA 62.376 66.667 0.00 0.00 40.78 2.01
2422 2426 1.538047 GGCTGAATCCTTTGCAGACA 58.462 50.000 0.00 0.00 37.61 3.41
2705 2725 0.039798 GTGTCGTCGTCACAGGCTAA 60.040 55.000 16.13 0.00 36.05 3.09
2856 2891 2.352715 CGGATGCCTTCGCTATGTCATA 60.353 50.000 0.00 0.00 35.36 2.15
3002 3038 4.102524 ACTCATCACAAAGACCCTTACACA 59.897 41.667 0.00 0.00 0.00 3.72
3024 3060 0.107214 CCCATGAACGGGCTGTACAT 60.107 55.000 0.00 0.00 40.07 2.29
3026 3062 0.378257 CATGAACGGGCTGTACATGC 59.622 55.000 0.00 2.21 33.42 4.06
3031 3067 1.670730 CGGGCTGTACATGCACACA 60.671 57.895 16.38 0.00 32.55 3.72
3212 3248 1.693627 TGGGCAAAACCACGTACAAT 58.306 45.000 0.00 0.00 42.05 2.71
3271 3307 2.738480 GGGCTGTACGTGGACACA 59.262 61.111 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 0.401105 ATGGGCTCCAGCTATCCTGT 60.401 55.000 0.00 0.00 40.06 4.00
119 120 6.808829 CAATGCCTCTAATCATTGGCTTTAA 58.191 36.000 0.00 0.00 43.36 1.52
225 226 4.284550 GCCCACTTGGAGCACCCA 62.285 66.667 0.00 0.00 44.93 4.51
271 272 1.604378 CTGGCTTCCGGTTCATCCT 59.396 57.895 0.00 0.00 0.00 3.24
421 422 0.468226 AGCGCTATCCATTTTCGGGA 59.532 50.000 8.99 0.00 39.14 5.14
512 513 3.922640 GCGCCCCAGGTTTTGCAA 61.923 61.111 0.00 0.00 0.00 4.08
544 545 4.148825 GATCTGCACCGACGGCCT 62.149 66.667 15.39 0.00 0.00 5.19
597 598 1.677217 CCTTTCTCCTCTTCGGCCTTG 60.677 57.143 0.00 0.00 0.00 3.61
748 749 3.126831 GACTTCCTAATGTCGCCATCAG 58.873 50.000 0.00 0.00 0.00 2.90
752 753 0.174845 CGGACTTCCTAATGTCGCCA 59.825 55.000 0.00 0.00 34.31 5.69
759 760 1.694696 GGCATCTCCGGACTTCCTAAT 59.305 52.381 0.00 0.00 0.00 1.73
909 910 0.395586 CTCCGGATTTTCATGGGCCA 60.396 55.000 9.61 9.61 0.00 5.36
943 944 1.031571 TATGAGTACGACCGGGCGTT 61.032 55.000 43.98 26.45 42.71 4.84
988 989 2.787473 TGTTCCATTGGCTAGAGGTG 57.213 50.000 0.00 0.00 0.00 4.00
1023 1024 3.568686 CGGATCCGTTTTGCCGAA 58.431 55.556 26.35 0.00 46.29 4.30
1043 1044 1.587043 GCCAGTCCTTTTCCCGAAGC 61.587 60.000 0.00 0.00 0.00 3.86
1058 1059 0.908198 AGCCAAGTCCTTAGAGCCAG 59.092 55.000 0.00 0.00 0.00 4.85
1194 1195 0.811281 GTTTCATGCTCGGGGAAAGG 59.189 55.000 0.00 0.00 31.75 3.11
1260 1261 3.465871 ACCATCGCAATGCTTTGTTTTT 58.534 36.364 13.29 0.00 35.17 1.94
1424 1425 5.239306 GGAATCTCGTTAATCCATTCATGCA 59.761 40.000 0.00 0.00 32.08 3.96
1457 1458 6.620877 ATGGTTTCACTGGATAGTAGACAA 57.379 37.500 0.00 0.00 34.74 3.18
1472 1473 2.802719 GTTCCCTTGGCTATGGTTTCA 58.197 47.619 1.22 0.00 0.00 2.69
1480 1481 0.323629 CAAGACCGTTCCCTTGGCTA 59.676 55.000 0.00 0.00 36.90 3.93
1495 1496 2.125147 CCGCTGATTCCGCCAAGA 60.125 61.111 0.00 0.00 0.00 3.02
1598 1599 6.952773 AAAAGTAGTGGTATTTCACTTGCA 57.047 33.333 2.76 0.00 44.74 4.08
1800 1803 4.202111 CCCTTTTGTTCCACACGAGATTTT 60.202 41.667 0.00 0.00 0.00 1.82
1906 1909 3.963428 TTTCTGACACCTCTAGCTTCC 57.037 47.619 0.00 0.00 0.00 3.46
1974 1977 1.978782 CGAAGGATCAAAAAGCAACGC 59.021 47.619 0.00 0.00 0.00 4.84
2044 2047 3.756434 CGTTCAATATTGGTGGGTGAACT 59.244 43.478 15.36 0.00 43.71 3.01
2084 2087 6.155737 AGGGTAAAACTAACCTATCACACGAT 59.844 38.462 0.00 0.00 37.18 3.73
2090 2093 8.701895 CATCAGTAGGGTAAAACTAACCTATCA 58.298 37.037 0.00 0.00 37.85 2.15
2093 2096 7.675195 TGTCATCAGTAGGGTAAAACTAACCTA 59.325 37.037 0.00 0.00 37.18 3.08
2145 2148 1.993370 GAATCAACGGTTCCTCTCGTG 59.007 52.381 0.00 0.00 39.70 4.35
2224 2227 5.188327 CTGAGAGGCGTTCAGTCATAATA 57.812 43.478 11.59 0.00 37.79 0.98
2244 2247 1.483827 TGCTAGCCTGGATTCTGACTG 59.516 52.381 13.29 0.00 0.00 3.51
2367 2370 4.821589 GAGCTTCGAGGTGGCCGG 62.822 72.222 0.00 0.00 0.00 6.13
2400 2404 1.006281 TCTGCAAAGGATTCAGCCCAT 59.994 47.619 0.00 0.00 0.00 4.00
2422 2426 1.643880 CCCCGTCGCGTATTAAAGTT 58.356 50.000 5.77 0.00 0.00 2.66
2689 2709 0.956633 AGTTTAGCCTGTGACGACGA 59.043 50.000 0.00 0.00 0.00 4.20
2705 2725 3.008375 TCCTTGAGCATGACTTAGCAGTT 59.992 43.478 0.00 0.00 31.22 3.16
2856 2891 5.535030 GGGACTTTACCATTTTGTCTTGTCT 59.465 40.000 0.00 0.00 0.00 3.41
3212 3248 0.882484 CCGTGTATGTGGTGTGTGCA 60.882 55.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.