Multiple sequence alignment - TraesCS1B01G081200

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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 TraesCS1B01G081200 chr1B 100.000 2488 0 0 1 2488 63808033 63810520 0.000000e+00 4595
1 TraesCS1B01G081200 chr1B 95.503 2446 96 5 55 2488 63479076 63481519 0.000000e+00 3895
2 TraesCS1B01G081200 chr1B 94.847 2445 105 7 55 2488 63467844 63470278 0.000000e+00 3797
3 TraesCS1B01G081200 chr1B 92.406 2502 158 14 1 2488 63758429 63760912 0.000000e+00 3539
4 TraesCS1B01G081200 chr1B 93.307 2002 131 3 1 2001 63613432 63615431 0.000000e+00 2952
5 TraesCS1B01G081200 chr1B 94.274 1764 97 3 1 1761 63888321 63890083 0.000000e+00 2695
6 TraesCS1B01G081200 chr1B 90.020 491 40 7 2003 2488 63624156 63624642 5.840000e-176 627
7 TraesCS1B01G081200 chr1A 90.876 2510 184 26 1 2488 43272404 43269918 0.000000e+00 3325
8 TraesCS1B01G081200 chr1A 89.746 2516 180 35 1 2488 43393021 43390556 0.000000e+00 3145
9 TraesCS1B01G081200 chr1A 79.111 225 30 15 118 329 590863741 590863521 3.340000e-29 139
10 TraesCS1B01G081200 chr1D 89.815 1895 141 22 615 2488 44275012 44276875 0.000000e+00 2383
11 TraesCS1B01G081200 chr1D 89.443 1904 151 25 615 2488 43823094 43824977 0.000000e+00 2357
12 TraesCS1B01G081200 chr1D 90.075 1592 121 23 494 2069 44628791 44630361 0.000000e+00 2030
13 TraesCS1B01G081200 chr1D 89.021 1093 91 15 1419 2488 44370322 44371408 0.000000e+00 1327
14 TraesCS1B01G081200 chr1D 90.780 282 23 3 328 607 43822414 43822694 8.400000e-100 374
15 TraesCS1B01G081200 chr7D 80.995 563 76 17 1948 2488 53257841 53258394 3.830000e-113 418
16 TraesCS1B01G081200 chr3A 82.963 135 19 4 194 324 724148073 724148207 4.350000e-23 119


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 TraesCS1B01G081200 chr1B 63808033 63810520 2487 False 4595.0 4595 100.0000 1 2488 1 chr1B.!!$F6 2487
1 TraesCS1B01G081200 chr1B 63479076 63481519 2443 False 3895.0 3895 95.5030 55 2488 1 chr1B.!!$F2 2433
2 TraesCS1B01G081200 chr1B 63467844 63470278 2434 False 3797.0 3797 94.8470 55 2488 1 chr1B.!!$F1 2433
3 TraesCS1B01G081200 chr1B 63758429 63760912 2483 False 3539.0 3539 92.4060 1 2488 1 chr1B.!!$F5 2487
4 TraesCS1B01G081200 chr1B 63613432 63615431 1999 False 2952.0 2952 93.3070 1 2001 1 chr1B.!!$F3 2000
5 TraesCS1B01G081200 chr1B 63888321 63890083 1762 False 2695.0 2695 94.2740 1 1761 1 chr1B.!!$F7 1760
6 TraesCS1B01G081200 chr1A 43269918 43272404 2486 True 3325.0 3325 90.8760 1 2488 1 chr1A.!!$R1 2487
7 TraesCS1B01G081200 chr1A 43390556 43393021 2465 True 3145.0 3145 89.7460 1 2488 1 chr1A.!!$R2 2487
8 TraesCS1B01G081200 chr1D 44275012 44276875 1863 False 2383.0 2383 89.8150 615 2488 1 chr1D.!!$F1 1873
9 TraesCS1B01G081200 chr1D 44628791 44630361 1570 False 2030.0 2030 90.0750 494 2069 1 chr1D.!!$F3 1575
10 TraesCS1B01G081200 chr1D 43822414 43824977 2563 False 1365.5 2357 90.1115 328 2488 2 chr1D.!!$F4 2160
11 TraesCS1B01G081200 chr1D 44370322 44371408 1086 False 1327.0 1327 89.0210 1419 2488 1 chr1D.!!$F2 1069
12 TraesCS1B01G081200 chr7D 53257841 53258394 553 False 418.0 418 80.9950 1948 2488 1 chr7D.!!$F1 540

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
73 74 1.004394 GAAGAGGAATGGGAAACGGGT 59.996 52.381 0.00 0.0 0.00 5.28 F
201 202 1.145759 CCGCGCGACACACAATAGAT 61.146 55.000 34.63 0.0 0.00 1.98 F
663 1060 1.552226 TGACACACTCGTTGTTCGAC 58.448 50.000 0.00 0.0 44.01 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1563 0.901124 TGTTTGCCTTTTGCCACACT 59.099 45.000 0.0 0.0 40.16 3.55 R
1251 1653 1.343506 GCTTCTTGCAGAAATTGGCG 58.656 50.000 0.0 0.0 42.31 5.69 R
1571 2001 2.093500 TGAGCACAGCCTCACGAATTAT 60.093 45.455 0.0 0.0 36.96 1.28 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
69 70 1.095600 GCCGAAGAGGAATGGGAAAC 58.904 55.000 0.00 0.00 45.00 2.78
73 74 1.004394 GAAGAGGAATGGGAAACGGGT 59.996 52.381 0.00 0.00 0.00 5.28
116 117 8.646900 AGAAAAACTACTCTGAGAGAGACAAAT 58.353 33.333 17.71 0.00 45.07 2.32
200 201 1.803922 CCGCGCGACACACAATAGA 60.804 57.895 34.63 0.00 0.00 1.98
201 202 1.145759 CCGCGCGACACACAATAGAT 61.146 55.000 34.63 0.00 0.00 1.98
240 241 2.226912 CGGGACAAAAATAGGTTTGCGA 59.773 45.455 0.00 0.00 41.33 5.10
295 296 5.048921 TCTGGACTTAGACGTGAAGTAGTTG 60.049 44.000 11.42 4.71 37.27 3.16
644 1041 3.921677 ACGTGTCGATGTGGAGTTAATT 58.078 40.909 0.00 0.00 0.00 1.40
645 1042 3.678072 ACGTGTCGATGTGGAGTTAATTG 59.322 43.478 0.00 0.00 0.00 2.32
654 1051 4.055360 TGTGGAGTTAATTGACACACTCG 58.945 43.478 20.67 0.00 37.16 4.18
663 1060 1.552226 TGACACACTCGTTGTTCGAC 58.448 50.000 0.00 0.00 44.01 4.20
872 1274 5.892686 TGCCCATATCATCATCTCAAACAAA 59.107 36.000 0.00 0.00 0.00 2.83
922 1324 3.797039 AGTCATGTATCCCACACATTCG 58.203 45.455 0.00 0.00 40.86 3.34
923 1325 2.872245 GTCATGTATCCCACACATTCGG 59.128 50.000 0.00 0.00 40.86 4.30
972 1374 3.724478 TCAAAGGGATAGAGAAGGCTCA 58.276 45.455 0.00 0.00 43.81 4.26
1041 1443 7.658982 TGCTTATGTTTCATCATCCTCACTATC 59.341 37.037 0.00 0.00 0.00 2.08
1106 1508 3.746751 GCCATGATCAAGGAGTGTGCTAT 60.747 47.826 21.00 0.00 0.00 2.97
1146 1548 4.796290 GCAAATCCGAAGATAGATCCGTCA 60.796 45.833 0.00 0.00 30.42 4.35
1206 1608 2.249309 CTTTGCGCTGGTGTCACG 59.751 61.111 9.73 0.00 0.00 4.35
1251 1653 0.606604 TGGAGAAGGTTGGCTACGTC 59.393 55.000 0.00 0.00 0.00 4.34
1293 1695 1.064003 TCCCACATGGCTACAAGTGT 58.936 50.000 0.00 0.00 42.97 3.55
1405 1832 9.221775 ACGATTTCGATTTTAGTTATGCATTTC 57.778 29.630 3.54 0.00 43.02 2.17
1406 1833 8.402275 CGATTTCGATTTTAGTTATGCATTTCG 58.598 33.333 3.54 2.02 43.02 3.46
1516 1943 4.706842 AGTTTAGCTGTGGAAGGAGAAA 57.293 40.909 0.00 0.00 0.00 2.52
1542 1972 3.625764 GGCTTTTACATTCGATGTGCCTA 59.374 43.478 14.29 0.00 44.60 3.93
1571 2001 7.851228 TCACAATAGCTTTCCTTTCAGATCTA 58.149 34.615 0.00 0.00 0.00 1.98
1604 2034 4.829492 AGGCTGTGCTCAGAAAAGTTTATT 59.171 37.500 19.61 0.00 43.76 1.40
1718 2152 7.071950 TGGTTCTACTAGTAAATATGCCCATGT 59.928 37.037 3.76 0.00 0.00 3.21
1930 2371 4.396166 CGACTTGATTTTCTAAGGCACCAT 59.604 41.667 0.00 0.00 31.26 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.103934 CTCTTCGGCAGGAGCTCG 59.896 66.667 7.83 0.00 41.70 5.03
69 70 0.378257 CCTCGCATTCATTTCACCCG 59.622 55.000 0.00 0.00 0.00 5.28
73 74 3.348647 TTCTCCCTCGCATTCATTTCA 57.651 42.857 0.00 0.00 0.00 2.69
200 201 2.436469 TGGTGCATTCGCTCGCAT 60.436 55.556 0.00 0.00 40.89 4.73
201 202 3.120385 CTGGTGCATTCGCTCGCA 61.120 61.111 0.00 0.00 39.64 5.10
240 241 6.378564 TGGATCTCGTCTGTCTTTAAGATTCT 59.621 38.462 0.00 0.00 0.00 2.40
654 1051 2.503943 ATGAAATCGCGTCGAACAAC 57.496 45.000 5.77 0.87 39.99 3.32
663 1060 6.712241 ATACCTTGAAGATATGAAATCGCG 57.288 37.500 0.00 0.00 0.00 5.87
815 1217 8.874156 TCAGTTGTATATCTTGAAGATATGGCT 58.126 33.333 28.92 19.75 45.01 4.75
899 1301 4.635765 CGAATGTGTGGGATACATGACTTT 59.364 41.667 0.00 0.00 42.24 2.66
922 1324 1.967319 TGTTTGTGTGGCTTCTCTCC 58.033 50.000 0.00 0.00 0.00 3.71
923 1325 4.574599 AATTGTTTGTGTGGCTTCTCTC 57.425 40.909 0.00 0.00 0.00 3.20
972 1374 4.651778 TGGCTTTTGTATCTGCTACACTT 58.348 39.130 0.00 0.00 40.06 3.16
1106 1508 2.284754 TGCTGGCCACTTTTGATACA 57.715 45.000 0.00 0.00 0.00 2.29
1161 1563 0.901124 TGTTTGCCTTTTGCCACACT 59.099 45.000 0.00 0.00 40.16 3.55
1251 1653 1.343506 GCTTCTTGCAGAAATTGGCG 58.656 50.000 0.00 0.00 42.31 5.69
1323 1725 5.379827 CATGTATGCAATGTCGATCATCAC 58.620 41.667 0.00 0.00 35.48 3.06
1405 1832 4.805719 TCAGAATAGCACAAGAAGCATACG 59.194 41.667 0.00 0.00 0.00 3.06
1406 1833 6.481313 TGATCAGAATAGCACAAGAAGCATAC 59.519 38.462 0.00 0.00 0.00 2.39
1516 1943 4.615912 GCACATCGAATGTAAAAGCCAAGT 60.616 41.667 0.00 0.00 42.70 3.16
1542 1972 3.728385 AAGGAAAGCTATTGTGAGGCT 57.272 42.857 0.00 0.00 37.99 4.58
1571 2001 2.093500 TGAGCACAGCCTCACGAATTAT 60.093 45.455 0.00 0.00 36.96 1.28
1604 2034 9.176181 GAAACGTTCTCATACAAAATGCTTAAA 57.824 29.630 0.00 0.00 0.00 1.52
1718 2152 2.366533 TGTTTTACTCCCGTTGCAACA 58.633 42.857 28.01 9.07 0.00 3.33
2393 2868 6.478016 TGTTTGCATTCATGAAAAATCACGAA 59.522 30.769 13.09 2.40 37.08 3.85


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

AutoCloner maintained by Alex Coulton.