Multiple sequence alignment - TraesCS3A01G106000

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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 TraesCS3A01G106000 chr3A 100.000 2264 0 0 1 2264 69948381 69950644 0.000000e+00 4108.0
1 TraesCS3A01G106000 chr2A 99.408 1519 8 1 1 1518 148615285 148613767 0.000000e+00 2754.0
2 TraesCS3A01G106000 chr2A 99.408 1519 8 1 1 1518 728933671 728935189 0.000000e+00 2754.0
3 TraesCS3A01G106000 chr2A 97.791 498 11 0 1560 2057 728935738 728936235 0.000000e+00 859.0
4 TraesCS3A01G106000 chr7A 99.342 1520 8 2 1 1518 16005010 16006529 0.000000e+00 2750.0
5 TraesCS3A01G106000 chr7A 99.342 1519 9 1 1 1518 497719531 497718013 0.000000e+00 2748.0
6 TraesCS3A01G106000 chr7A 97.576 495 11 1 1564 2057 16006963 16007457 0.000000e+00 846.0
7 TraesCS3A01G106000 chr5B 99.342 1520 8 2 1 1518 351469617 351468098 0.000000e+00 2750.0
8 TraesCS3A01G106000 chr5B 99.342 1520 8 2 1 1518 433002514 433000995 0.000000e+00 2750.0
9 TraesCS3A01G106000 chr5B 99.342 1519 9 1 1 1518 471294934 471293416 0.000000e+00 2748.0
10 TraesCS3A01G106000 chr5B 97.791 498 11 0 1560 2057 433000564 433000067 0.000000e+00 859.0
11 TraesCS3A01G106000 chr5B 96.988 498 15 0 1560 2057 471292985 471292488 0.000000e+00 837.0
12 TraesCS3A01G106000 chr5B 96.761 494 16 0 1564 2057 281830783 281830290 0.000000e+00 824.0
13 TraesCS3A01G106000 chr5B 96.559 494 17 0 1564 2057 351467663 351467170 0.000000e+00 819.0
14 TraesCS3A01G106000 chr5B 100.000 197 0 0 2068 2264 281830048 281829852 4.600000e-97 364.0
15 TraesCS3A01G106000 chr5B 100.000 197 0 0 2068 2264 351466931 351466735 4.600000e-97 364.0
16 TraesCS3A01G106000 chr5B 100.000 197 0 0 2068 2264 432999865 432999669 4.600000e-97 364.0
17 TraesCS3A01G106000 chr5B 100.000 197 0 0 2068 2264 471292251 471292055 4.600000e-97 364.0
18 TraesCS3A01G106000 chr5B 98.387 62 1 0 1529 1590 281830500 281830439 2.380000e-20 110.0
19 TraesCS3A01G106000 chr5B 98.387 62 1 0 1529 1590 351467380 351467319 2.380000e-20 110.0
20 TraesCS3A01G106000 chr5B 96.875 64 2 0 1529 1592 281830736 281830673 8.550000e-20 108.0
21 TraesCS3A01G106000 chr1B 99.342 1519 9 1 1 1518 649301321 649299803 0.000000e+00 2748.0
22 TraesCS3A01G106000 chr1B 100.000 197 0 0 2068 2264 302769673 302769477 4.600000e-97 364.0
23 TraesCS3A01G106000 chr1B 100.000 197 0 0 2068 2264 649298574 649298378 4.600000e-97 364.0
24 TraesCS3A01G106000 chr1B 95.000 60 3 0 1529 1588 550438126 550438067 6.660000e-16 95.3
25 TraesCS3A01G106000 chr6B 99.210 1519 11 1 1 1518 381313995 381312477 0.000000e+00 2737.0
26 TraesCS3A01G106000 chr6B 100.000 197 0 0 2068 2264 381310935 381310739 4.600000e-97 364.0
27 TraesCS3A01G106000 chrUn 97.576 495 11 1 1564 2057 416567180 416566686 0.000000e+00 846.0
28 TraesCS3A01G106000 chrUn 100.000 197 0 0 2068 2264 361055105 361054909 4.600000e-97 364.0
29 TraesCS3A01G106000 chrUn 100.000 197 0 0 2068 2264 437368735 437368931 4.600000e-97 364.0
30 TraesCS3A01G106000 chr5A 96.761 494 16 0 1564 2057 300956993 300957486 0.000000e+00 824.0
31 TraesCS3A01G106000 chr5A 96.761 494 16 0 1564 2057 590567682 590568175 0.000000e+00 824.0
32 TraesCS3A01G106000 chr5A 96.393 499 16 2 1560 2057 591475638 591476135 0.000000e+00 821.0
33 TraesCS3A01G106000 chr5A 98.387 62 1 0 1529 1590 300957276 300957337 2.380000e-20 110.0
34 TraesCS3A01G106000 chr5A 98.387 62 1 0 1529 1590 591475925 591475986 2.380000e-20 110.0
35 TraesCS3A01G106000 chr6A 100.000 197 0 0 2068 2264 466681588 466681784 4.600000e-97 364.0
36 TraesCS3A01G106000 chr7B 98.387 62 1 0 1529 1590 133430418 133430357 2.380000e-20 110.0


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 TraesCS3A01G106000 chr3A 69948381 69950644 2263 False 4108.000000 4108 100.000000 1 2264 1 chr3A.!!$F1 2263
1 TraesCS3A01G106000 chr2A 148613767 148615285 1518 True 2754.000000 2754 99.408000 1 1518 1 chr2A.!!$R1 1517
2 TraesCS3A01G106000 chr2A 728933671 728936235 2564 False 1806.500000 2754 98.599500 1 2057 2 chr2A.!!$F1 2056
3 TraesCS3A01G106000 chr7A 497718013 497719531 1518 True 2748.000000 2748 99.342000 1 1518 1 chr7A.!!$R1 1517
4 TraesCS3A01G106000 chr7A 16005010 16007457 2447 False 1798.000000 2750 98.459000 1 2057 2 chr7A.!!$F1 2056
5 TraesCS3A01G106000 chr5B 432999669 433002514 2845 True 1324.333333 2750 99.044333 1 2264 3 chr5B.!!$R3 2263
6 TraesCS3A01G106000 chr5B 471292055 471294934 2879 True 1316.333333 2748 98.776667 1 2264 3 chr5B.!!$R4 2263
7 TraesCS3A01G106000 chr5B 351466735 351469617 2882 True 1010.750000 2750 98.572000 1 2264 4 chr5B.!!$R2 2263
8 TraesCS3A01G106000 chr5B 281829852 281830783 931 True 351.500000 824 98.005750 1529 2264 4 chr5B.!!$R1 735
9 TraesCS3A01G106000 chr1B 649298378 649301321 2943 True 1556.000000 2748 99.671000 1 2264 2 chr1B.!!$R3 2263
10 TraesCS3A01G106000 chr6B 381310739 381313995 3256 True 1550.500000 2737 99.605000 1 2264 2 chr6B.!!$R1 2263

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
814 818 0.830444 TGCTAGAGGTGGTCGTGGTT 60.83 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2452 1.219124 CCATCAGACACCCCAGACG 59.781 63.158 0.0 0.0 0.0 4.18 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
165 166 2.031069 CGAGGTGAAACTGAAGACTCGA 60.031 50.000 5.35 0.00 46.44 4.04
265 267 8.811017 ACATACATGTTAATGATGGAAAAACCA 58.189 29.630 14.22 0.00 45.56 3.67
552 554 1.779061 AAGGGGGACACAATGAGCGT 61.779 55.000 0.00 0.00 0.00 5.07
814 818 0.830444 TGCTAGAGGTGGTCGTGGTT 60.830 55.000 0.00 0.00 0.00 3.67
1074 1079 1.371558 GAAGACGTGGTTGGAGGCT 59.628 57.895 0.00 0.00 0.00 4.58
1552 1557 2.357517 CAGGCCGTCTGGTGTGTC 60.358 66.667 0.00 0.00 39.76 3.67
1553 1558 2.524394 AGGCCGTCTGGTGTGTCT 60.524 61.111 0.00 0.00 37.67 3.41
1554 1559 2.357517 GGCCGTCTGGTGTGTCTG 60.358 66.667 0.00 0.00 37.67 3.51
1556 1561 1.293498 GCCGTCTGGTGTGTCTGAT 59.707 57.895 0.00 0.00 37.67 2.90
1558 1563 0.390340 CCGTCTGGTGTGTCTGATGG 60.390 60.000 0.00 0.00 36.12 3.51
1560 1565 1.670087 CGTCTGGTGTGTCTGATGGAC 60.670 57.143 0.00 0.00 44.70 4.02
1622 2098 2.888447 GCAGGTGACCAGACAGGCT 61.888 63.158 3.63 0.00 43.14 4.58
1655 2249 3.625897 TGGACACCCAGACGCCAG 61.626 66.667 0.00 0.00 37.58 4.85
1744 2338 3.311110 TGACCAGACAGGCCGTCC 61.311 66.667 19.67 8.67 46.69 4.79
1804 2398 0.689080 TCTGCCTCCCAGATCCAGAC 60.689 60.000 0.00 0.00 45.44 3.51
1858 2452 2.348998 CAGGTGACCAGACAGGCC 59.651 66.667 3.63 0.00 43.14 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 166 2.267006 CTCTCGCACTGGCACCAT 59.733 61.111 0.00 0.00 41.24 3.55
265 267 3.053842 ACATGGAACTCTTGCATCCTCAT 60.054 43.478 4.96 0.00 39.89 2.90
814 818 1.141657 AGCACTTGTGCTTCCTCTTCA 59.858 47.619 20.95 0.00 43.52 3.02
1074 1079 6.464465 CCTTCTCCTTCTTCTTGTCCAAACTA 60.464 42.308 0.00 0.00 0.00 2.24
1534 1539 3.161450 ACACACCAGACGGCCTGT 61.161 61.111 0.00 0.00 41.33 4.00
1535 1540 2.357517 GACACACCAGACGGCCTG 60.358 66.667 0.00 0.00 42.55 4.85
1536 1541 2.524394 AGACACACCAGACGGCCT 60.524 61.111 0.00 0.00 34.57 5.19
1537 1542 2.172483 ATCAGACACACCAGACGGCC 62.172 60.000 0.00 0.00 34.57 6.13
1538 1543 1.016130 CATCAGACACACCAGACGGC 61.016 60.000 0.00 0.00 34.57 5.68
1539 1544 0.390340 CCATCAGACACACCAGACGG 60.390 60.000 0.00 0.00 38.77 4.79
1540 1545 0.603065 TCCATCAGACACACCAGACG 59.397 55.000 0.00 0.00 0.00 4.18
1541 1546 2.086054 GTCCATCAGACACACCAGAC 57.914 55.000 0.00 0.00 45.55 3.51
1550 1555 3.842869 GTCTGGGTGTCCATCAGAC 57.157 57.895 13.81 13.81 46.66 3.51
1551 1556 1.888436 GCGTCTGGGTGTCCATCAGA 61.888 60.000 0.00 0.00 43.11 3.27
1552 1557 1.448540 GCGTCTGGGTGTCCATCAG 60.449 63.158 0.00 0.00 43.11 2.90
1553 1558 2.662596 GCGTCTGGGTGTCCATCA 59.337 61.111 0.00 0.00 43.11 3.07
1554 1559 2.125106 GGCGTCTGGGTGTCCATC 60.125 66.667 0.00 0.00 43.11 3.51
1556 1561 3.625897 CTGGCGTCTGGGTGTCCA 61.626 66.667 0.00 0.00 41.58 4.02
1558 1563 4.394712 CCCTGGCGTCTGGGTGTC 62.395 72.222 22.99 0.00 44.42 3.67
1622 2098 1.344438 GTCCATCAGACACACCAGACA 59.656 52.381 0.00 0.00 45.55 3.41
1858 2452 1.219124 CCATCAGACACCCCAGACG 59.781 63.158 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.