Multiple sequence alignment - TraesCS5D01G042700

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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 TraesCS5D01G042700 chr5D 100.000 2222 0 0 1 2222 42204803 42207024 0.000000e+00 4104
1 TraesCS5D01G042700 chr5D 85.556 810 55 29 722 1507 42086627 42087398 0.000000e+00 791
2 TraesCS5D01G042700 chr5D 74.928 698 164 10 22 716 218680509 218679820 2.140000e-80 309
3 TraesCS5D01G042700 chr5D 90.135 223 20 2 1010 1231 41933942 41933721 2.790000e-74 289
4 TraesCS5D01G042700 chr5B 96.970 1386 28 6 1 1377 37045656 37047036 0.000000e+00 2314
5 TraesCS5D01G042700 chr5B 87.832 715 41 27 813 1507 36891175 36891863 0.000000e+00 797
6 TraesCS5D01G042700 chr5B 89.868 227 20 3 1005 1230 36602512 36602288 2.790000e-74 289
7 TraesCS5D01G042700 chr5A 92.424 726 36 10 939 1655 30679180 30679895 0.000000e+00 1018
8 TraesCS5D01G042700 chr5A 84.653 821 55 30 722 1507 30659618 30660402 0.000000e+00 752
9 TraesCS5D01G042700 chr5A 97.281 331 5 1 611 937 30673552 30673882 1.930000e-155 558
10 TraesCS5D01G042700 chr5A 77.459 732 160 5 1 730 653800524 653799796 1.220000e-117 433
11 TraesCS5D01G042700 chr5A 77.871 479 96 9 244 720 291899333 291898863 2.790000e-74 289
12 TraesCS5D01G042700 chr5A 90.367 218 19 2 1010 1226 30634388 30634604 3.610000e-73 285
13 TraesCS5D01G042700 chr5A 98.561 139 2 0 1 139 30673409 30673547 1.700000e-61 246
14 TraesCS5D01G042700 chr2D 98.343 543 9 0 1680 2222 639485012 639484470 0.000000e+00 953
15 TraesCS5D01G042700 chr2D 96.685 543 18 0 1680 2222 345251459 345252001 0.000000e+00 904
16 TraesCS5D01G042700 chr2D 79.137 278 48 3 1943 2220 116805990 116805723 1.360000e-42 183
17 TraesCS5D01G042700 chr1D 96.964 560 15 2 1664 2222 182580725 182581283 0.000000e+00 939
18 TraesCS5D01G042700 chr1D 97.243 544 15 0 1679 2222 71287177 71287720 0.000000e+00 922
19 TraesCS5D01G042700 chr7D 97.606 543 13 0 1680 2222 127375811 127376353 0.000000e+00 931
20 TraesCS5D01G042700 chr7D 96.869 543 13 1 1680 2222 58131751 58131213 0.000000e+00 905
21 TraesCS5D01G042700 chr7D 75.185 270 63 4 226 493 138796310 138796043 8.330000e-25 124
22 TraesCS5D01G042700 chr1A 92.066 542 30 2 1681 2222 546519079 546519607 0.000000e+00 750
23 TraesCS5D01G042700 chr2A 91.324 438 34 2 1676 2110 32113530 32113966 1.470000e-166 595
24 TraesCS5D01G042700 chr6A 78.112 731 156 4 2 730 593728001 593727273 5.590000e-126 460
25 TraesCS5D01G042700 chr3B 75.352 710 161 14 25 727 700346043 700345341 1.640000e-86 329
26 TraesCS5D01G042700 chr7B 74.714 700 161 16 25 716 196017231 196016540 4.640000e-77 298
27 TraesCS5D01G042700 chr3A 84.286 210 31 2 1016 1224 433427628 433427836 1.040000e-48 204


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 TraesCS5D01G042700 chr5D 42204803 42207024 2221 False 4104 4104 100.000 1 2222 1 chr5D.!!$F2 2221
1 TraesCS5D01G042700 chr5D 42086627 42087398 771 False 791 791 85.556 722 1507 1 chr5D.!!$F1 785
2 TraesCS5D01G042700 chr5D 218679820 218680509 689 True 309 309 74.928 22 716 1 chr5D.!!$R2 694
3 TraesCS5D01G042700 chr5B 37045656 37047036 1380 False 2314 2314 96.970 1 1377 1 chr5B.!!$F2 1376
4 TraesCS5D01G042700 chr5B 36891175 36891863 688 False 797 797 87.832 813 1507 1 chr5B.!!$F1 694
5 TraesCS5D01G042700 chr5A 30679180 30679895 715 False 1018 1018 92.424 939 1655 1 chr5A.!!$F3 716
6 TraesCS5D01G042700 chr5A 30659618 30660402 784 False 752 752 84.653 722 1507 1 chr5A.!!$F2 785
7 TraesCS5D01G042700 chr5A 653799796 653800524 728 True 433 433 77.459 1 730 1 chr5A.!!$R2 729
8 TraesCS5D01G042700 chr2D 639484470 639485012 542 True 953 953 98.343 1680 2222 1 chr2D.!!$R2 542
9 TraesCS5D01G042700 chr2D 345251459 345252001 542 False 904 904 96.685 1680 2222 1 chr2D.!!$F1 542
10 TraesCS5D01G042700 chr1D 182580725 182581283 558 False 939 939 96.964 1664 2222 1 chr1D.!!$F2 558
11 TraesCS5D01G042700 chr1D 71287177 71287720 543 False 922 922 97.243 1679 2222 1 chr1D.!!$F1 543
12 TraesCS5D01G042700 chr7D 127375811 127376353 542 False 931 931 97.606 1680 2222 1 chr7D.!!$F1 542
13 TraesCS5D01G042700 chr7D 58131213 58131751 538 True 905 905 96.869 1680 2222 1 chr7D.!!$R1 542
14 TraesCS5D01G042700 chr1A 546519079 546519607 528 False 750 750 92.066 1681 2222 1 chr1A.!!$F1 541
15 TraesCS5D01G042700 chr6A 593727273 593728001 728 True 460 460 78.112 2 730 1 chr6A.!!$R1 728
16 TraesCS5D01G042700 chr3B 700345341 700346043 702 True 329 329 75.352 25 727 1 chr3B.!!$R1 702
17 TraesCS5D01G042700 chr7B 196016540 196017231 691 True 298 298 74.714 25 716 1 chr7B.!!$R1 691

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
104 106 0.321298 GACCACCCTTAAGCGCTTCA 60.321 55.0 28.82 15.81 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1587 0.179124 ATCTTGAACGCGAGAGGAGC 60.179 55.0 15.93 0.0 37.94 4.7 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
104 106 0.321298 GACCACCCTTAAGCGCTTCA 60.321 55.000 28.82 15.81 0.00 3.02
836 841 0.814010 AGTGTGCCGTCAACCACTTC 60.814 55.000 0.00 0.00 34.64 3.01
852 872 1.202222 ACTTCGATAACCACCGCTACG 60.202 52.381 0.00 0.00 0.00 3.51
1255 1311 6.270927 TCATCCTAATCTAATCCCTTCCTGTG 59.729 42.308 0.00 0.00 0.00 3.66
1259 1315 6.326583 CCTAATCTAATCCCTTCCTGTGTGTA 59.673 42.308 0.00 0.00 0.00 2.90
1260 1316 6.831664 AATCTAATCCCTTCCTGTGTGTAT 57.168 37.500 0.00 0.00 0.00 2.29
1261 1317 5.614324 TCTAATCCCTTCCTGTGTGTATG 57.386 43.478 0.00 0.00 0.00 2.39
1262 1318 5.030147 TCTAATCCCTTCCTGTGTGTATGT 58.970 41.667 0.00 0.00 0.00 2.29
1385 1454 2.878406 TGCTTTGTGAGGAGTTTGCTAC 59.122 45.455 0.00 0.00 0.00 3.58
1430 1499 3.074412 CGCTGGGTTAACTTGACTGATT 58.926 45.455 5.42 0.00 0.00 2.57
1518 1587 6.745907 TCTCGTCAATATTACTGTTCTCGTTG 59.254 38.462 0.00 0.00 0.00 4.10
1528 1597 1.073768 GTTCTCGTTGCTCCTCTCGC 61.074 60.000 0.00 0.00 0.00 5.03
1539 1608 2.189342 CTCCTCTCGCGTTCAAGATTC 58.811 52.381 5.77 0.00 0.00 2.52
1541 1610 2.231478 TCCTCTCGCGTTCAAGATTCTT 59.769 45.455 5.77 0.00 0.00 2.52
1589 1658 1.544246 CGGCGGTAGTCATCCATATGA 59.456 52.381 3.65 0.00 39.87 2.15
1602 1671 2.104792 TCCATATGAGCCTACCTTGTGC 59.895 50.000 3.65 0.00 0.00 4.57
1620 1689 4.728110 AGATGCAGCAGCCCGCAA 62.728 61.111 7.13 0.00 46.13 4.85
1655 1724 9.553064 CCTTCATAATAACTAGTTTCTCTGCAT 57.447 33.333 14.49 0.00 0.00 3.96
1671 1740 6.721318 TCTCTGCATAATTTTGTAGGGAAGT 58.279 36.000 12.82 0.00 36.11 3.01
1672 1741 7.857456 TCTCTGCATAATTTTGTAGGGAAGTA 58.143 34.615 12.82 0.00 36.11 2.24
1673 1742 8.325787 TCTCTGCATAATTTTGTAGGGAAGTAA 58.674 33.333 12.82 0.00 36.11 2.24
1676 1745 6.605594 TGCATAATTTTGTAGGGAAGTAAGGG 59.394 38.462 0.00 0.00 0.00 3.95
1677 1746 6.831868 GCATAATTTTGTAGGGAAGTAAGGGA 59.168 38.462 0.00 0.00 0.00 4.20
1930 1999 1.375523 GGCCTGTAACGGTGAGGTG 60.376 63.158 0.00 0.00 0.00 4.00
2052 2121 0.182775 ACTCGCCCCACAGTTTCTTT 59.817 50.000 0.00 0.00 0.00 2.52
2083 2152 4.962995 TCCCAAATCGGAGAAGATAGAAGT 59.037 41.667 0.00 0.00 43.58 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 106 1.745087 CAAGCAATCATTACGGGCAGT 59.255 47.619 0.00 0.0 0.00 4.40
301 304 1.830477 AGATGGCTGTCTCCAAGTCTC 59.170 52.381 0.00 0.0 39.96 3.36
1255 1311 2.159707 CGCAGCAGGTTACAACATACAC 60.160 50.000 0.00 0.0 0.00 2.90
1259 1315 1.604604 AACGCAGCAGGTTACAACAT 58.395 45.000 0.00 0.0 0.00 2.71
1260 1316 1.064803 CAAACGCAGCAGGTTACAACA 59.935 47.619 0.00 0.0 0.00 3.33
1261 1317 1.064952 ACAAACGCAGCAGGTTACAAC 59.935 47.619 0.00 0.0 0.00 3.32
1262 1318 1.064803 CACAAACGCAGCAGGTTACAA 59.935 47.619 0.00 0.0 0.00 2.41
1401 1470 4.951715 TCAAGTTAACCCAGCGATCTACTA 59.048 41.667 0.88 0.0 0.00 1.82
1430 1499 0.609151 TCGAACTCGTATTTGGCCCA 59.391 50.000 0.00 0.0 40.80 5.36
1518 1587 0.179124 ATCTTGAACGCGAGAGGAGC 60.179 55.000 15.93 0.0 37.94 4.70
1541 1610 5.757808 GCCAACAAAAATCTCCTGCTAAAAA 59.242 36.000 0.00 0.0 0.00 1.94
1555 1624 1.586564 CGCCGTTCGCCAACAAAAA 60.587 52.632 0.00 0.0 32.14 1.94
1589 1658 0.393537 GCATCTGCACAAGGTAGGCT 60.394 55.000 0.00 0.0 41.59 4.58
1617 1686 7.428826 AGTTATTATGAAGGCTTATTGCTTGC 58.571 34.615 0.00 0.0 42.39 4.01
1619 1688 9.853177 ACTAGTTATTATGAAGGCTTATTGCTT 57.147 29.630 0.00 0.0 42.39 3.91
1620 1689 9.853177 AACTAGTTATTATGAAGGCTTATTGCT 57.147 29.630 6.26 0.0 42.39 3.91
1655 1724 6.420638 GCTCCCTTACTTCCCTACAAAATTA 58.579 40.000 0.00 0.0 0.00 1.40
1656 1725 5.262009 GCTCCCTTACTTCCCTACAAAATT 58.738 41.667 0.00 0.0 0.00 1.82
1657 1726 4.625564 CGCTCCCTTACTTCCCTACAAAAT 60.626 45.833 0.00 0.0 0.00 1.82
1658 1727 3.307199 CGCTCCCTTACTTCCCTACAAAA 60.307 47.826 0.00 0.0 0.00 2.44
1659 1728 2.235402 CGCTCCCTTACTTCCCTACAAA 59.765 50.000 0.00 0.0 0.00 2.83
1660 1729 1.829222 CGCTCCCTTACTTCCCTACAA 59.171 52.381 0.00 0.0 0.00 2.41
1661 1730 1.006281 TCGCTCCCTTACTTCCCTACA 59.994 52.381 0.00 0.0 0.00 2.74
1662 1731 1.772836 TCGCTCCCTTACTTCCCTAC 58.227 55.000 0.00 0.0 0.00 3.18
1671 1740 3.306780 GCCTAGCAATTATCGCTCCCTTA 60.307 47.826 0.00 0.0 40.96 2.69
1672 1741 2.551071 GCCTAGCAATTATCGCTCCCTT 60.551 50.000 0.00 0.0 40.96 3.95
1673 1742 1.002544 GCCTAGCAATTATCGCTCCCT 59.997 52.381 0.00 0.0 40.96 4.20
1707 1776 1.971505 ATGAAGATTCCGGGAGCGCA 61.972 55.000 11.47 0.0 0.00 6.09
1930 1999 1.366854 GCCGGCCAACTACTTACTGC 61.367 60.000 18.11 0.0 0.00 4.40
2052 2121 1.479323 CTCCGATTTGGGACGACCTAA 59.521 52.381 3.44 0.4 41.11 2.69
2083 2152 4.100279 TCTGCCATCTTCGATACCTAGA 57.900 45.455 0.00 0.0 0.00 2.43


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

AutoCloner maintained by Alex Coulton.