Multiple sequence alignment - TraesCS7B01G086200

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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 TraesCS7B01G086200 chr7B 100.000 2974 0 0 1 2974 99490718 99493691 0.000000e+00 5493
1 TraesCS7B01G086200 chr7B 89.456 882 68 11 238 1115 586936111 586936971 0.000000e+00 1090
2 TraesCS7B01G086200 chr2A 95.166 2979 107 12 2 2972 736729486 736732435 0.000000e+00 4669
3 TraesCS7B01G086200 chr2A 93.618 2742 136 15 238 2974 569299923 569297216 0.000000e+00 4058
4 TraesCS7B01G086200 chr3A 94.825 2976 122 8 1 2972 710078396 710081343 0.000000e+00 4614
5 TraesCS7B01G086200 chr3A 93.066 2740 135 28 241 2974 55062381 55059691 0.000000e+00 3956
6 TraesCS7B01G086200 chr1A 93.290 2742 144 20 238 2974 302028050 302025344 0.000000e+00 4008
7 TraesCS7B01G086200 chr1A 91.962 2314 156 14 666 2974 58251746 58249458 0.000000e+00 3216
8 TraesCS7B01G086200 chr1A 91.862 2224 128 24 238 2455 555682741 555680565 0.000000e+00 3055
9 TraesCS7B01G086200 chr1A 85.510 559 49 7 238 781 58252226 58251685 3.350000e-154 555
10 TraesCS7B01G086200 chr1B 93.217 2757 133 20 238 2974 442214357 442211635 0.000000e+00 4006
11 TraesCS7B01G086200 chr1B 86.784 227 21 5 1 224 98745932 98746152 8.230000e-61 244
12 TraesCS7B01G086200 chr1B 85.965 228 21 6 1 224 98803932 98804152 1.780000e-57 233
13 TraesCS7B01G086200 chr6A 91.965 2315 155 15 666 2974 107622391 107620102 0.000000e+00 3216
14 TraesCS7B01G086200 chr6A 84.594 2207 307 29 779 2974 447685058 447682874 0.000000e+00 2161
15 TraesCS7B01G086200 chr6A 87.120 559 50 5 238 781 107622881 107622330 5.450000e-172 614
16 TraesCS7B01G086200 chr7A 85.365 2207 294 25 779 2974 25701338 25699150 0.000000e+00 2259
17 TraesCS7B01G086200 chr7A 85.034 2205 302 24 779 2974 545713401 545715586 0.000000e+00 2218
18 TraesCS7B01G086200 chr7A 90.832 709 52 6 54 762 59610097 59609402 0.000000e+00 937
19 TraesCS7B01G086200 chr5B 85.068 2210 300 23 779 2974 703940687 703938494 0.000000e+00 2226
20 TraesCS7B01G086200 chr3B 83.211 2037 312 24 934 2958 778284888 778286906 0.000000e+00 1840
21 TraesCS7B01G086200 chr4B 94.723 1156 53 2 1 1156 512704545 512703398 0.000000e+00 1790
22 TraesCS7B01G086200 chr5A 91.076 706 50 6 54 759 544167880 544168572 0.000000e+00 942
23 TraesCS7B01G086200 chr4D 85.750 793 54 25 1 789 11494770 11494033 0.000000e+00 784
24 TraesCS7B01G086200 chr1D 92.000 500 29 5 1 496 250206906 250207398 0.000000e+00 691


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 TraesCS7B01G086200 chr7B 99490718 99493691 2973 False 5493.0 5493 100.0000 1 2974 1 chr7B.!!$F1 2973
1 TraesCS7B01G086200 chr7B 586936111 586936971 860 False 1090.0 1090 89.4560 238 1115 1 chr7B.!!$F2 877
2 TraesCS7B01G086200 chr2A 736729486 736732435 2949 False 4669.0 4669 95.1660 2 2972 1 chr2A.!!$F1 2970
3 TraesCS7B01G086200 chr2A 569297216 569299923 2707 True 4058.0 4058 93.6180 238 2974 1 chr2A.!!$R1 2736
4 TraesCS7B01G086200 chr3A 710078396 710081343 2947 False 4614.0 4614 94.8250 1 2972 1 chr3A.!!$F1 2971
5 TraesCS7B01G086200 chr3A 55059691 55062381 2690 True 3956.0 3956 93.0660 241 2974 1 chr3A.!!$R1 2733
6 TraesCS7B01G086200 chr1A 302025344 302028050 2706 True 4008.0 4008 93.2900 238 2974 1 chr1A.!!$R1 2736
7 TraesCS7B01G086200 chr1A 555680565 555682741 2176 True 3055.0 3055 91.8620 238 2455 1 chr1A.!!$R2 2217
8 TraesCS7B01G086200 chr1A 58249458 58252226 2768 True 1885.5 3216 88.7360 238 2974 2 chr1A.!!$R3 2736
9 TraesCS7B01G086200 chr1B 442211635 442214357 2722 True 4006.0 4006 93.2170 238 2974 1 chr1B.!!$R1 2736
10 TraesCS7B01G086200 chr6A 447682874 447685058 2184 True 2161.0 2161 84.5940 779 2974 1 chr6A.!!$R1 2195
11 TraesCS7B01G086200 chr6A 107620102 107622881 2779 True 1915.0 3216 89.5425 238 2974 2 chr6A.!!$R2 2736
12 TraesCS7B01G086200 chr7A 25699150 25701338 2188 True 2259.0 2259 85.3650 779 2974 1 chr7A.!!$R1 2195
13 TraesCS7B01G086200 chr7A 545713401 545715586 2185 False 2218.0 2218 85.0340 779 2974 1 chr7A.!!$F1 2195
14 TraesCS7B01G086200 chr7A 59609402 59610097 695 True 937.0 937 90.8320 54 762 1 chr7A.!!$R2 708
15 TraesCS7B01G086200 chr5B 703938494 703940687 2193 True 2226.0 2226 85.0680 779 2974 1 chr5B.!!$R1 2195
16 TraesCS7B01G086200 chr3B 778284888 778286906 2018 False 1840.0 1840 83.2110 934 2958 1 chr3B.!!$F1 2024
17 TraesCS7B01G086200 chr4B 512703398 512704545 1147 True 1790.0 1790 94.7230 1 1156 1 chr4B.!!$R1 1155
18 TraesCS7B01G086200 chr5A 544167880 544168572 692 False 942.0 942 91.0760 54 759 1 chr5A.!!$F1 705
19 TraesCS7B01G086200 chr4D 11494033 11494770 737 True 784.0 784 85.7500 1 789 1 chr4D.!!$R1 788

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
274 277 1.601903 TGCTTACGTGGTTCTTGCTTG 59.398 47.619 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2373 0.245266 TATCTGCTGCAAACCGTCGA 59.755 50.0 3.02 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
48 51 7.632898 GCACATCTTATAAGTAGGTCACTTCCA 60.633 40.741 12.19 0.00 44.48 3.53
49 52 7.707035 CACATCTTATAAGTAGGTCACTTCCAC 59.293 40.741 12.19 0.00 44.48 4.02
50 53 7.620094 ACATCTTATAAGTAGGTCACTTCCACT 59.380 37.037 12.19 0.00 44.48 4.00
51 54 7.406031 TCTTATAAGTAGGTCACTTCCACTG 57.594 40.000 12.19 0.00 44.48 3.66
52 55 6.380274 TCTTATAAGTAGGTCACTTCCACTGG 59.620 42.308 12.19 0.00 44.48 4.00
274 277 1.601903 TGCTTACGTGGTTCTTGCTTG 59.398 47.619 0.00 0.00 0.00 4.01
824 921 4.722700 CAGCCTGTTGGGGGTCCG 62.723 72.222 0.00 0.00 34.56 4.79
1068 1175 7.438564 AGTTCTTAGTTTGTTGTTGGTTGTTT 58.561 30.769 0.00 0.00 0.00 2.83
1083 1192 3.321497 GTTGTTTTTGTTGGCTGTGTGA 58.679 40.909 0.00 0.00 0.00 3.58
1382 1494 2.229784 GGATTGGCAAGGTTTCTCAGTG 59.770 50.000 5.96 0.00 0.00 3.66
1445 1557 6.073819 GCCTTTGTTGTTTTGGTTATGTGATC 60.074 38.462 0.00 0.00 0.00 2.92
1695 1808 2.748641 GATCCCCCGGCCTATCTCCA 62.749 65.000 0.00 0.00 0.00 3.86
1711 1824 1.484240 CTCCAGGAGCTCCTTCGATTT 59.516 52.381 33.33 7.68 46.09 2.17
1849 1963 7.283354 GGACCTAAGATTTTTAAGATCAGTGGG 59.717 40.741 0.00 0.55 0.00 4.61
1941 2055 3.834489 ACATGACCCAGCTAATGAGAG 57.166 47.619 0.00 0.00 0.00 3.20
2059 2180 3.895704 ACCCATTGGTACAGACCTTTT 57.104 42.857 1.20 0.00 45.45 2.27
2129 2250 8.276060 GAGGATATCTCGATTCGTATTATTGC 57.724 38.462 5.89 0.00 32.18 3.56
2252 2373 6.347888 CGGGATATTGTTGTTTGTAGTCGTTT 60.348 38.462 0.00 0.00 0.00 3.60
2379 2502 6.356556 TCACTTGATTGTTCCTGAAGAAGAA 58.643 36.000 0.00 0.00 41.54 2.52
2958 3086 1.743958 CTCACCGAGTACTTGGACGAT 59.256 52.381 32.27 10.00 37.57 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 51 7.016153 TGTTAACATAAAGATCCAGTCCAGT 57.984 36.000 3.59 0.00 0.00 4.00
49 52 7.414540 GCTTGTTAACATAAAGATCCAGTCCAG 60.415 40.741 9.56 0.00 0.00 3.86
50 53 6.374333 GCTTGTTAACATAAAGATCCAGTCCA 59.626 38.462 9.56 0.00 0.00 4.02
51 54 6.374333 TGCTTGTTAACATAAAGATCCAGTCC 59.626 38.462 9.56 0.00 0.00 3.85
52 55 7.377766 TGCTTGTTAACATAAAGATCCAGTC 57.622 36.000 9.56 0.00 0.00 3.51
274 277 2.289547 ACACACACGCTGGACAAATAAC 59.710 45.455 0.00 0.00 0.00 1.89
824 921 0.171903 TACTTGTACGGCTTCGAGGC 59.828 55.000 11.69 11.69 37.44 4.70
1068 1175 2.653726 AGACATCACACAGCCAACAAA 58.346 42.857 0.00 0.00 0.00 2.83
1083 1192 4.655963 ACATGCAGAACCAAGTAAGACAT 58.344 39.130 0.00 0.00 0.00 3.06
1382 1494 2.467566 TAAGGGACTCGGCAAACTTC 57.532 50.000 0.00 0.00 38.49 3.01
1445 1557 4.832823 ACCAAGGGTAAAAGGAAGACAATG 59.167 41.667 0.00 0.00 32.11 2.82
1711 1824 4.794278 TTTAGCACGAGAAGTACCATCA 57.206 40.909 0.00 0.00 0.00 3.07
1849 1963 3.262420 ACCAATACGATGAGACACTTGC 58.738 45.455 0.00 0.00 0.00 4.01
1941 2055 7.120432 GGATTTAAGGCATTCATCCTATGTCTC 59.880 40.741 12.77 0.00 36.97 3.36
2059 2180 2.088104 ATCATCTTACTCGCCTCCCA 57.912 50.000 0.00 0.00 0.00 4.37
2252 2373 0.245266 TATCTGCTGCAAACCGTCGA 59.755 50.000 3.02 0.00 0.00 4.20
2379 2502 4.221703 GGATCAATAGGTCCGTCATCATCT 59.778 45.833 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.