Multiple sequence alignment - TraesCS2B01G160000

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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 TraesCS2B01G160000 chr2B 100.000 2378 0 0 1 2378 133620929 133618552 0 4392
1 TraesCS2B01G160000 chr2B 94.856 972 49 1 1 972 643823018 643822048 0 1517
2 TraesCS2B01G160000 chrUn 95.772 1419 53 4 967 2378 70523542 70524960 0 2281
3 TraesCS2B01G160000 chr5D 95.487 1418 58 4 967 2378 21195600 21197017 0 2259
4 TraesCS2B01G160000 chr6D 95.275 1418 61 3 967 2378 365463976 365462559 0 2242
5 TraesCS2B01G160000 chr1D 95.205 1418 62 3 967 2378 482445649 482444232 0 2237
6 TraesCS2B01G160000 chr1D 95.137 1419 61 4 967 2378 227095033 227096450 0 2231
7 TraesCS2B01G160000 chr3B 95.205 1418 61 4 967 2378 171036039 171037455 0 2235
8 TraesCS2B01G160000 chr7B 95.134 1418 63 3 967 2378 709310553 709311970 0 2231
9 TraesCS2B01G160000 chr7B 95.036 967 48 0 1 967 576079627 576080593 0 1520
10 TraesCS2B01G160000 chr4A 94.993 1418 65 3 967 2378 712104738 712106155 0 2220
11 TraesCS2B01G160000 chr1B 95.050 1414 64 3 967 2374 549681502 549680089 0 2218
12 TraesCS2B01G160000 chr1B 95.464 970 43 1 1 970 423233353 423234321 0 1546
13 TraesCS2B01G160000 chr1B 94.851 971 50 0 1 971 288857032 288856062 0 1517
14 TraesCS2B01G160000 chr1B 94.851 971 49 1 1 971 6083095 6082126 0 1515
15 TraesCS2B01G160000 chr6B 95.549 966 43 0 1 966 227692786 227693751 0 1546
16 TraesCS2B01G160000 chr5B 95.445 966 44 0 1 966 6951270 6952235 0 1541
17 TraesCS2B01G160000 chr5B 95.445 966 44 0 1 966 65338671 65339636 0 1541
18 TraesCS2B01G160000 chr5B 94.856 972 50 0 1 972 69019600 69018629 0 1519


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 TraesCS2B01G160000 chr2B 133618552 133620929 2377 True 4392 4392 100.000 1 2378 1 chr2B.!!$R1 2377
1 TraesCS2B01G160000 chr2B 643822048 643823018 970 True 1517 1517 94.856 1 972 1 chr2B.!!$R2 971
2 TraesCS2B01G160000 chrUn 70523542 70524960 1418 False 2281 2281 95.772 967 2378 1 chrUn.!!$F1 1411
3 TraesCS2B01G160000 chr5D 21195600 21197017 1417 False 2259 2259 95.487 967 2378 1 chr5D.!!$F1 1411
4 TraesCS2B01G160000 chr6D 365462559 365463976 1417 True 2242 2242 95.275 967 2378 1 chr6D.!!$R1 1411
5 TraesCS2B01G160000 chr1D 482444232 482445649 1417 True 2237 2237 95.205 967 2378 1 chr1D.!!$R1 1411
6 TraesCS2B01G160000 chr1D 227095033 227096450 1417 False 2231 2231 95.137 967 2378 1 chr1D.!!$F1 1411
7 TraesCS2B01G160000 chr3B 171036039 171037455 1416 False 2235 2235 95.205 967 2378 1 chr3B.!!$F1 1411
8 TraesCS2B01G160000 chr7B 709310553 709311970 1417 False 2231 2231 95.134 967 2378 1 chr7B.!!$F2 1411
9 TraesCS2B01G160000 chr7B 576079627 576080593 966 False 1520 1520 95.036 1 967 1 chr7B.!!$F1 966
10 TraesCS2B01G160000 chr4A 712104738 712106155 1417 False 2220 2220 94.993 967 2378 1 chr4A.!!$F1 1411
11 TraesCS2B01G160000 chr1B 549680089 549681502 1413 True 2218 2218 95.050 967 2374 1 chr1B.!!$R3 1407
12 TraesCS2B01G160000 chr1B 423233353 423234321 968 False 1546 1546 95.464 1 970 1 chr1B.!!$F1 969
13 TraesCS2B01G160000 chr1B 288856062 288857032 970 True 1517 1517 94.851 1 971 1 chr1B.!!$R2 970
14 TraesCS2B01G160000 chr1B 6082126 6083095 969 True 1515 1515 94.851 1 971 1 chr1B.!!$R1 970
15 TraesCS2B01G160000 chr6B 227692786 227693751 965 False 1546 1546 95.549 1 966 1 chr6B.!!$F1 965
16 TraesCS2B01G160000 chr5B 6951270 6952235 965 False 1541 1541 95.445 1 966 1 chr5B.!!$F1 965
17 TraesCS2B01G160000 chr5B 65338671 65339636 965 False 1541 1541 95.445 1 966 1 chr5B.!!$F2 965
18 TraesCS2B01G160000 chr5B 69018629 69019600 971 True 1519 1519 94.856 1 972 1 chr5B.!!$R1 971

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
287 289 1.203758 TGCTCGGCGAATTCTGAGTTA 59.796 47.619 12.13 7.27 40.67 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1884 0.380733 CAGCGTACCATCTCGTGCTA 59.619 55.0 0.0 0.0 0.0 3.49 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
45 46 2.211410 TCCGTCCCTCCGCAGAAAA 61.211 57.895 0.00 0.00 0.00 2.29
234 236 2.125552 CGATGCGGTCCAAGAGCA 60.126 61.111 0.00 0.00 45.46 4.26
287 289 1.203758 TGCTCGGCGAATTCTGAGTTA 59.796 47.619 12.13 7.27 40.67 2.24
298 300 6.687655 CGAATTCTGAGTTAACGTGAAGATC 58.312 40.000 3.52 12.49 0.00 2.75
356 358 2.432628 GAACAGGCGGTCACGAGG 60.433 66.667 0.00 0.00 44.60 4.63
447 449 1.773653 GGAGAGGCATCCTTCCTGATT 59.226 52.381 0.00 0.00 36.35 2.57
619 621 3.878086 TGGAGGTAAAACCCTACTCCTT 58.122 45.455 10.05 0.00 39.75 3.36
1205 1210 1.377202 GCCATGGGAAGAAGCACGA 60.377 57.895 15.13 0.00 0.00 4.35
1242 1247 9.123902 CTTGATGATAATATGGAGTTGTGGAAA 57.876 33.333 0.00 0.00 0.00 3.13
1375 1380 6.826893 GCAAATATGTATGCCGAACAAAAT 57.173 33.333 0.00 0.00 36.56 1.82
1424 1429 4.994852 TGGGATTGTTAGAAACGTTGAGAG 59.005 41.667 0.00 0.00 0.00 3.20
1509 1515 5.643379 TTGTAAATGGTGAGGCAATTCTC 57.357 39.130 0.00 0.00 0.00 2.87
1510 1516 4.661222 TGTAAATGGTGAGGCAATTCTCA 58.339 39.130 0.00 0.00 41.03 3.27
1540 1546 3.772572 TCTACCACTGCTGCAGGTAATTA 59.227 43.478 31.00 14.40 37.44 1.40
1622 1628 2.400399 CTGCTTTTGTTGTCATGCAGG 58.600 47.619 0.00 0.00 42.64 4.85
1668 1674 1.740025 GCACCAATTGGACTCTAGCAC 59.260 52.381 31.22 5.27 38.94 4.40
1690 1696 6.338146 CACCTCGTATGAATCAAGGTTAAGA 58.662 40.000 1.80 0.00 38.27 2.10
1723 1729 3.077556 TGGAGCGAGGAGAAGGCC 61.078 66.667 0.00 0.00 0.00 5.19
1729 1735 1.177401 GCGAGGAGAAGGCCAAAAAT 58.823 50.000 5.01 0.00 0.00 1.82
1768 1774 8.207350 TCCAGAATAATTATCTAGGAGTTGGG 57.793 38.462 0.00 0.00 0.00 4.12
1874 1880 0.915364 GGACCTGATGAGGCCTTTCT 59.085 55.000 6.77 0.00 44.33 2.52
1878 1884 2.646798 ACCTGATGAGGCCTTTCTTTCT 59.353 45.455 6.77 0.00 44.33 2.52
1952 1958 8.382030 TGAGTTACATCAGGCACAAATATATG 57.618 34.615 0.00 0.00 0.00 1.78
2022 2032 5.498393 AGTCTCAGATTAAGGTACTCGTCA 58.502 41.667 0.00 0.00 38.49 4.35
2023 2033 5.944599 AGTCTCAGATTAAGGTACTCGTCAA 59.055 40.000 0.00 0.00 38.49 3.18
2374 2385 0.251341 ACCTTCACACCCAATGGAGC 60.251 55.000 0.00 0.00 34.81 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.000896 CCCTCCATGCCGGTTTTCT 60.001 57.895 1.90 0.00 35.57 2.52
45 46 4.096003 CGAACCCTCCATGCCGGT 62.096 66.667 1.90 0.00 35.57 5.28
234 236 2.152830 AGAGCTCTCGTCAGTAAACGT 58.847 47.619 11.45 0.00 43.08 3.99
287 289 3.745975 TCATCAAAAGCGATCTTCACGTT 59.254 39.130 0.00 0.00 0.00 3.99
298 300 1.002366 CTCTCGGGTCATCAAAAGCG 58.998 55.000 0.00 0.00 0.00 4.68
352 354 1.153628 CGGCTAGGTGGTTTCCTCG 60.154 63.158 0.00 0.00 38.86 4.63
356 358 1.761198 ACTATCCGGCTAGGTGGTTTC 59.239 52.381 16.39 0.00 41.99 2.78
392 394 2.805295 CGGTATAATCGCCAAAGGAGCA 60.805 50.000 0.00 0.00 0.00 4.26
428 430 2.172293 ACAATCAGGAAGGATGCCTCTC 59.828 50.000 0.00 0.00 46.61 3.20
642 644 6.075949 TGGTAGATCCACTCTTGTACTACT 57.924 41.667 0.00 0.00 41.93 2.57
824 826 1.168714 GTGGAAGGCAAGCTTGGTAG 58.831 55.000 27.10 2.64 0.00 3.18
826 828 1.898574 CGTGGAAGGCAAGCTTGGT 60.899 57.895 27.10 0.00 0.00 3.67
929 931 2.766651 GGGGTGTCCGGATAGCCA 60.767 66.667 39.33 18.76 41.15 4.75
1131 1136 2.023015 TGTGATCCTACATGGTCTCCCT 60.023 50.000 0.00 0.00 37.07 4.20
1205 1210 9.305555 CCATATTATCATCAAGATTTGAAGGGT 57.694 33.333 0.00 0.00 43.95 4.34
1242 1247 5.008316 GGTGTCATTACGGTCTTTCAGTTTT 59.992 40.000 0.00 0.00 0.00 2.43
1424 1429 4.023291 TCCAAGATTTGTGCCCTTTATCC 58.977 43.478 0.00 0.00 0.00 2.59
1479 1484 7.531857 TGCCTCACCATTTACAAAATTCTTA 57.468 32.000 0.00 0.00 0.00 2.10
1509 1515 1.561542 AGCAGTGGTAGATTCCCCTTG 59.438 52.381 0.00 0.00 0.00 3.61
1510 1516 1.561542 CAGCAGTGGTAGATTCCCCTT 59.438 52.381 0.00 0.00 0.00 3.95
1622 1628 4.106029 TGAACTTCTCGTAGTACCATGC 57.894 45.455 0.00 0.00 0.00 4.06
1668 1674 5.753921 GGTCTTAACCTTGATTCATACGAGG 59.246 44.000 0.00 0.00 42.80 4.63
1690 1696 0.904865 TCCAGTTCTGGATCAGCGGT 60.905 55.000 16.47 0.00 32.09 5.68
1874 1880 2.479049 GCGTACCATCTCGTGCTAGAAA 60.479 50.000 0.00 0.00 0.00 2.52
1878 1884 0.380733 CAGCGTACCATCTCGTGCTA 59.619 55.000 0.00 0.00 0.00 3.49
1909 1915 3.073062 ACTCATTTACCTGAGCACCAGTT 59.927 43.478 1.14 0.00 45.37 3.16
1997 2007 6.093771 TGACGAGTACCTTAATCTGAGACTTC 59.906 42.308 0.00 0.00 0.00 3.01
2022 2032 5.431420 TGCAAATCAGTCAATACACGTTT 57.569 34.783 0.00 0.00 0.00 3.60
2023 2033 5.238432 TCTTGCAAATCAGTCAATACACGTT 59.762 36.000 0.00 0.00 0.00 3.99


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

AutoCloner maintained by Alex Coulton.