Multiple sequence alignment - TraesCS5D01G023900

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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 TraesCS5D01G023900 chr5D 100.000 2568 0 0 1 2568 19748215 19745648 0.000000e+00 4743.0
1 TraesCS5D01G023900 chr5D 96.620 503 14 3 1 501 483580350 483580851 0.000000e+00 832.0
2 TraesCS5D01G023900 chr5D 90.566 159 14 1 548 706 59947680 59947837 2.590000e-50 209.0
3 TraesCS5D01G023900 chr7A 95.556 2025 83 4 544 2568 705968838 705966821 0.000000e+00 3234.0
4 TraesCS5D01G023900 chr7A 95.786 1495 56 3 544 2037 706003109 706001621 0.000000e+00 2405.0
5 TraesCS5D01G023900 chr7A 91.176 714 52 7 1309 2012 705938981 705938269 0.000000e+00 959.0
6 TraesCS5D01G023900 chr7A 96.462 537 19 0 2032 2568 706000847 706000311 0.000000e+00 887.0
7 TraesCS5D01G023900 chr7A 88.852 610 53 4 707 1316 705939614 705939020 0.000000e+00 736.0
8 TraesCS5D01G023900 chr7B 89.029 1504 121 17 544 2018 705465962 705464474 0.000000e+00 1823.0
9 TraesCS5D01G023900 chr7B 94.148 769 42 2 1275 2041 705518785 705518018 0.000000e+00 1168.0
10 TraesCS5D01G023900 chr7B 92.576 687 44 6 544 1228 705519465 705518784 0.000000e+00 979.0
11 TraesCS5D01G023900 chr7B 90.702 527 32 7 2044 2568 705517629 705517118 0.000000e+00 686.0
12 TraesCS5D01G023900 chr7B 80.612 98 10 3 2457 2545 705609319 705609222 1.650000e-07 67.6
13 TraesCS5D01G023900 chr7B 78.049 123 15 9 2457 2568 705665344 705665223 1.650000e-07 67.6
14 TraesCS5D01G023900 chr7B 85.714 63 8 1 2507 2568 705629414 705629352 5.930000e-07 65.8
15 TraesCS5D01G023900 chrUn 91.033 1316 91 10 707 2013 92847086 92848383 0.000000e+00 1751.0
16 TraesCS5D01G023900 chr1D 96.450 507 12 4 1 503 4166148 4166652 0.000000e+00 832.0
17 TraesCS5D01G023900 chr1D 96.086 511 10 4 1 501 420758790 420758280 0.000000e+00 824.0
18 TraesCS5D01G023900 chr2D 95.686 510 12 3 1 500 616012260 616012769 0.000000e+00 811.0
19 TraesCS5D01G023900 chr2D 95.276 508 16 4 1 500 96213135 96213642 0.000000e+00 798.0
20 TraesCS5D01G023900 chr7D 95.322 513 11 6 1 500 578479993 578480505 0.000000e+00 802.0
21 TraesCS5D01G023900 chr7D 94.716 511 14 6 1 501 636108219 636108726 0.000000e+00 782.0
22 TraesCS5D01G023900 chr7D 94.716 511 14 6 1 501 636150935 636151442 0.000000e+00 782.0
23 TraesCS5D01G023900 chr7D 79.389 131 23 4 2442 2568 613918036 613917906 3.520000e-14 89.8
24 TraesCS5D01G023900 chr3D 93.786 515 17 7 1 500 5200452 5199938 0.000000e+00 760.0
25 TraesCS5D01G023900 chr5B 92.517 147 10 1 560 706 70793532 70793387 2.590000e-50 209.0
26 TraesCS5D01G023900 chr4D 89.441 161 15 2 546 706 75266912 75266754 4.330000e-48 202.0
27 TraesCS5D01G023900 chr1A 89.157 166 12 5 544 706 181769420 181769582 4.330000e-48 202.0
28 TraesCS5D01G023900 chr2A 87.079 178 17 5 528 701 703708239 703708414 2.020000e-46 196.0
29 TraesCS5D01G023900 chr5A 91.489 47 3 1 497 543 545989266 545989221 2.130000e-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 TraesCS5D01G023900 chr5D 19745648 19748215 2567 True 4743.000000 4743 100.000000 1 2568 1 chr5D.!!$R1 2567
1 TraesCS5D01G023900 chr5D 483580350 483580851 501 False 832.000000 832 96.620000 1 501 1 chr5D.!!$F2 500
2 TraesCS5D01G023900 chr7A 705966821 705968838 2017 True 3234.000000 3234 95.556000 544 2568 1 chr7A.!!$R1 2024
3 TraesCS5D01G023900 chr7A 706000311 706003109 2798 True 1646.000000 2405 96.124000 544 2568 2 chr7A.!!$R3 2024
4 TraesCS5D01G023900 chr7A 705938269 705939614 1345 True 847.500000 959 90.014000 707 2012 2 chr7A.!!$R2 1305
5 TraesCS5D01G023900 chr7B 705464474 705465962 1488 True 1823.000000 1823 89.029000 544 2018 1 chr7B.!!$R1 1474
6 TraesCS5D01G023900 chr7B 705517118 705519465 2347 True 944.333333 1168 92.475333 544 2568 3 chr7B.!!$R5 2024
7 TraesCS5D01G023900 chrUn 92847086 92848383 1297 False 1751.000000 1751 91.033000 707 2013 1 chrUn.!!$F1 1306
8 TraesCS5D01G023900 chr1D 4166148 4166652 504 False 832.000000 832 96.450000 1 503 1 chr1D.!!$F1 502
9 TraesCS5D01G023900 chr1D 420758280 420758790 510 True 824.000000 824 96.086000 1 501 1 chr1D.!!$R1 500
10 TraesCS5D01G023900 chr2D 616012260 616012769 509 False 811.000000 811 95.686000 1 500 1 chr2D.!!$F2 499
11 TraesCS5D01G023900 chr2D 96213135 96213642 507 False 798.000000 798 95.276000 1 500 1 chr2D.!!$F1 499
12 TraesCS5D01G023900 chr7D 578479993 578480505 512 False 802.000000 802 95.322000 1 500 1 chr7D.!!$F1 499
13 TraesCS5D01G023900 chr7D 636108219 636108726 507 False 782.000000 782 94.716000 1 501 1 chr7D.!!$F2 500
14 TraesCS5D01G023900 chr7D 636150935 636151442 507 False 782.000000 782 94.716000 1 501 1 chr7D.!!$F3 500
15 TraesCS5D01G023900 chr3D 5199938 5200452 514 True 760.000000 760 93.786000 1 500 1 chr3D.!!$R1 499

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
516 547 0.179179 GTGAGCTCAAAATCCAGCGC 60.179 55.0 20.19 0.0 40.84 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 3624 0.180171 AGCACAGCACAACACCTGTA 59.82 50.0 0.0 0.0 40.12 2.74 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
72 79 4.990426 TCTGTATGCATATGTTCATGACGG 59.010 41.667 10.16 1.29 0.00 4.79
244 271 0.553113 CCCCCTAAACCACCCCCTTA 60.553 60.000 0.00 0.00 0.00 2.69
245 272 1.385014 CCCCTAAACCACCCCCTTAA 58.615 55.000 0.00 0.00 0.00 1.85
331 362 1.530655 CAACCGGGACAAAAGGCCT 60.531 57.895 6.32 0.00 0.00 5.19
332 363 1.530655 AACCGGGACAAAAGGCCTG 60.531 57.895 5.69 0.00 0.00 4.85
471 502 4.080299 CAGGACTAAAGGCCCTTATGAACT 60.080 45.833 0.00 0.00 0.00 3.01
501 532 3.108376 AGCCCCTTTTCCTACTAGTGAG 58.892 50.000 5.39 0.00 0.00 3.51
502 533 2.420269 GCCCCTTTTCCTACTAGTGAGC 60.420 54.545 5.39 0.00 0.00 4.26
503 534 3.108376 CCCCTTTTCCTACTAGTGAGCT 58.892 50.000 5.39 0.00 0.00 4.09
504 535 3.133183 CCCCTTTTCCTACTAGTGAGCTC 59.867 52.174 6.82 6.82 0.00 4.09
505 536 3.769844 CCCTTTTCCTACTAGTGAGCTCA 59.230 47.826 13.74 13.74 0.00 4.26
506 537 4.223032 CCCTTTTCCTACTAGTGAGCTCAA 59.777 45.833 20.19 2.35 0.00 3.02
507 538 5.280011 CCCTTTTCCTACTAGTGAGCTCAAA 60.280 44.000 20.19 8.99 0.00 2.69
508 539 6.231211 CCTTTTCCTACTAGTGAGCTCAAAA 58.769 40.000 20.19 9.88 0.00 2.44
509 540 6.881602 CCTTTTCCTACTAGTGAGCTCAAAAT 59.118 38.462 20.19 10.26 0.00 1.82
510 541 7.065204 CCTTTTCCTACTAGTGAGCTCAAAATC 59.935 40.741 20.19 5.90 0.00 2.17
511 542 5.599999 TCCTACTAGTGAGCTCAAAATCC 57.400 43.478 20.19 5.47 0.00 3.01
512 543 5.023452 TCCTACTAGTGAGCTCAAAATCCA 58.977 41.667 20.19 1.46 0.00 3.41
513 544 5.127845 TCCTACTAGTGAGCTCAAAATCCAG 59.872 44.000 20.19 11.23 0.00 3.86
514 545 3.604582 ACTAGTGAGCTCAAAATCCAGC 58.395 45.455 20.19 2.99 35.73 4.85
515 546 1.446907 AGTGAGCTCAAAATCCAGCG 58.553 50.000 20.19 0.00 40.84 5.18
516 547 0.179179 GTGAGCTCAAAATCCAGCGC 60.179 55.000 20.19 0.00 40.84 5.92
517 548 0.321919 TGAGCTCAAAATCCAGCGCT 60.322 50.000 15.67 2.64 40.84 5.92
518 549 1.066215 TGAGCTCAAAATCCAGCGCTA 60.066 47.619 15.67 0.00 40.84 4.26
519 550 1.328986 GAGCTCAAAATCCAGCGCTAC 59.671 52.381 10.99 0.00 40.84 3.58
520 551 1.065854 AGCTCAAAATCCAGCGCTACT 60.066 47.619 10.99 0.00 40.84 2.57
521 552 1.063174 GCTCAAAATCCAGCGCTACTG 59.937 52.381 10.99 1.22 46.77 2.74
529 560 3.760693 CAGCGCTACTGGTATGGTT 57.239 52.632 10.99 0.00 43.19 3.67
530 561 2.024176 CAGCGCTACTGGTATGGTTT 57.976 50.000 10.99 0.00 43.19 3.27
531 562 2.356135 CAGCGCTACTGGTATGGTTTT 58.644 47.619 10.99 0.00 43.19 2.43
532 563 2.747446 CAGCGCTACTGGTATGGTTTTT 59.253 45.455 10.99 0.00 43.19 1.94
754 797 5.777850 TGGGTAGTCTTTTAAACTTTGGC 57.222 39.130 0.00 0.00 0.00 4.52
779 822 1.134729 CAATGCGCCCCAAAATTAGCT 60.135 47.619 4.18 0.00 0.00 3.32
1228 1283 6.763303 AGTAAAAATGCCATTTGTTCGTTC 57.237 33.333 2.91 0.00 31.77 3.95
1517 1626 2.642139 ATGCCGCAAACATTCTTCAG 57.358 45.000 0.00 0.00 0.00 3.02
1691 1804 3.725634 AGTCATTACTCCTTAGGGCACT 58.274 45.455 0.00 0.00 0.00 4.40
1701 1814 2.224670 CCTTAGGGCACTGTTGTAACCA 60.225 50.000 0.00 0.00 0.00 3.67
1782 1895 6.252441 CACAACTTCAATCTCTCGTGTATCTC 59.748 42.308 0.00 0.00 0.00 2.75
1816 1929 9.408648 TCTCAAAACCCTCTTTCCATATTAATC 57.591 33.333 0.00 0.00 0.00 1.75
1820 1933 9.768215 AAAACCCTCTTTCCATATTAATCAAGA 57.232 29.630 0.00 0.00 0.00 3.02
1883 1996 0.735632 GCACTCTTCCTCTCACGCTG 60.736 60.000 0.00 0.00 0.00 5.18
1890 2003 1.181741 TCCTCTCACGCTGAAGCTGT 61.182 55.000 0.10 0.00 39.32 4.40
1991 2116 0.343372 TTGGTCCATCCTCTAGGGCT 59.657 55.000 0.00 0.00 37.07 5.19
2050 3340 1.697432 CCCCATGAGCCGGAACTATTA 59.303 52.381 5.05 0.00 0.00 0.98
2089 3379 2.609350 GGCGACCGTGAACTTAATACA 58.391 47.619 0.00 0.00 0.00 2.29
2227 3517 4.036734 GTGATGCATGATAAAACGACCCAT 59.963 41.667 2.46 0.00 0.00 4.00
2552 3844 1.355563 GCGAGACCGATCGATCACA 59.644 57.895 24.40 0.00 45.56 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 79 8.787852 AGTAATCAAATGAAGGAAACAGAAGAC 58.212 33.333 0.00 0.00 0.00 3.01
251 278 1.268899 CTGGCAGGAGCTGAGTTTTTG 59.731 52.381 6.61 0.00 41.70 2.44
449 480 4.080299 CAGTTCATAAGGGCCTTTAGTCCT 60.080 45.833 26.29 12.40 0.00 3.85
501 532 1.063174 CAGTAGCGCTGGATTTTGAGC 59.937 52.381 22.90 0.00 41.42 4.26
511 542 2.024176 AAACCATACCAGTAGCGCTG 57.976 50.000 22.90 5.37 44.63 5.18
512 543 2.781681 AAAACCATACCAGTAGCGCT 57.218 45.000 17.26 17.26 0.00 5.92
754 797 1.897225 TTTTGGGGCGCATTGATGGG 61.897 55.000 10.83 3.88 42.88 4.00
779 822 4.458989 GTGGTGAACATTAAATCTCAGGCA 59.541 41.667 0.00 0.00 0.00 4.75
899 951 2.030717 AGACTGCTAGCCATATCGTTCG 60.031 50.000 13.29 0.00 0.00 3.95
992 1044 1.702401 TGTACTTCTCCATGCCCACAA 59.298 47.619 0.00 0.00 0.00 3.33
1022 1074 2.277858 AGCGGCACTAGTAACTGCT 58.722 52.632 20.45 20.45 41.16 4.24
1038 1090 3.518634 ACGAGAAGAAGAATCCAGAGC 57.481 47.619 0.00 0.00 0.00 4.09
1100 1152 9.567848 GTATACGGAAACAATTTTTCATCATGT 57.432 29.630 12.21 0.00 0.00 3.21
1101 1153 9.787532 AGTATACGGAAACAATTTTTCATCATG 57.212 29.630 12.21 0.00 0.00 3.07
1296 1353 8.762481 AGCAACATATATATCATGGATGCAAT 57.238 30.769 20.31 8.28 40.19 3.56
1517 1626 1.933853 CGCTGCCTCCACTATGTTAAC 59.066 52.381 0.00 0.00 0.00 2.01
1681 1794 3.134574 TGGTTACAACAGTGCCCTAAG 57.865 47.619 0.00 0.00 0.00 2.18
1782 1895 3.445987 AGAGGGTTTTGAGAGGGACTAG 58.554 50.000 0.00 0.00 41.55 2.57
1816 1929 6.100004 AGAACATGGTAGTAACACGATCTTG 58.900 40.000 0.00 0.00 0.00 3.02
1820 1933 7.874016 TGTTAAAGAACATGGTAGTAACACGAT 59.126 33.333 8.56 0.00 40.72 3.73
1883 1996 3.443329 TCTCATGAGAGTCTCACAGCTTC 59.557 47.826 24.93 0.00 43.63 3.86
1890 2003 3.500343 TGTTGGTCTCATGAGAGTCTCA 58.500 45.455 25.76 24.66 44.99 3.27
2227 3517 7.221259 CGTGAATACGTTGTTTCTGACCATATA 59.779 37.037 0.00 0.00 44.99 0.86
2334 3624 0.180171 AGCACAGCACAACACCTGTA 59.820 50.000 0.00 0.00 40.12 2.74
2534 3826 0.248498 TTGTGATCGATCGGTCTCGC 60.248 55.000 27.39 20.43 38.52 5.03


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

AutoCloner maintained by Alex Coulton.