Multiple sequence alignment - TraesCS1B01G154900

Loading Multiple Alignment...

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 TraesCS1B01G154900 chr1B 100.000 2762 0 0 1 2762 260842691 260839930 0.000000e+00 5101.0
1 TraesCS1B01G154900 chr1B 95.544 763 30 4 1 761 473835295 473836055 0.000000e+00 1218.0
2 TraesCS1B01G154900 chr7B 88.933 2024 188 31 757 2761 518289545 518287539 0.000000e+00 2464.0
3 TraesCS1B01G154900 chr7B 88.933 2024 188 31 757 2761 518305554 518303548 0.000000e+00 2464.0
4 TraesCS1B01G154900 chr7B 88.425 838 67 14 754 1585 456122483 456123296 0.000000e+00 983.0
5 TraesCS1B01G154900 chr4B 88.422 2021 203 26 757 2762 165971187 165969183 0.000000e+00 2407.0
6 TraesCS1B01G154900 chr4B 85.017 2029 245 41 763 2762 376028449 376030447 0.000000e+00 2008.0
7 TraesCS1B01G154900 chr4B 96.073 764 26 4 1 761 386695415 386696177 0.000000e+00 1242.0
8 TraesCS1B01G154900 chr2A 87.618 2019 205 26 757 2762 82414052 82412066 0.000000e+00 2302.0
9 TraesCS1B01G154900 chr3A 87.469 2019 209 25 757 2762 167682981 167680994 0.000000e+00 2287.0
10 TraesCS1B01G154900 chr3B 86.496 2029 237 24 754 2762 40495601 40497612 0.000000e+00 2194.0
11 TraesCS1B01G154900 chr3B 95.425 765 30 4 1 761 17555819 17555056 0.000000e+00 1214.0
12 TraesCS1B01G154900 chr3B 95.431 766 26 6 1 761 380034984 380035745 0.000000e+00 1212.0
13 TraesCS1B01G154900 chr3B 95.300 766 29 6 1 761 61054404 61053641 0.000000e+00 1208.0
14 TraesCS1B01G154900 chr3B 91.549 71 5 1 2693 2762 291336921 291336991 2.260000e-16 97.1
15 TraesCS1B01G154900 chr1A 87.363 1915 221 14 757 2664 313569071 313567171 0.000000e+00 2176.0
16 TraesCS1B01G154900 chr6B 86.224 2018 246 22 757 2762 272297982 272295985 0.000000e+00 2158.0
17 TraesCS1B01G154900 chr5B 95.675 763 28 5 1 761 321434550 321435309 0.000000e+00 1221.0
18 TraesCS1B01G154900 chr5B 95.325 770 27 5 1 761 123352953 123353722 0.000000e+00 1214.0
19 TraesCS1B01G154900 chr5B 95.306 767 29 6 1 761 344181267 344182032 0.000000e+00 1210.0
20 TraesCS1B01G154900 chr5B 95.176 767 31 5 1 764 598140073 598139310 0.000000e+00 1206.0


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 TraesCS1B01G154900 chr1B 260839930 260842691 2761 True 5101 5101 100.000 1 2762 1 chr1B.!!$R1 2761
1 TraesCS1B01G154900 chr1B 473835295 473836055 760 False 1218 1218 95.544 1 761 1 chr1B.!!$F1 760
2 TraesCS1B01G154900 chr7B 518287539 518289545 2006 True 2464 2464 88.933 757 2761 1 chr7B.!!$R1 2004
3 TraesCS1B01G154900 chr7B 518303548 518305554 2006 True 2464 2464 88.933 757 2761 1 chr7B.!!$R2 2004
4 TraesCS1B01G154900 chr7B 456122483 456123296 813 False 983 983 88.425 754 1585 1 chr7B.!!$F1 831
5 TraesCS1B01G154900 chr4B 165969183 165971187 2004 True 2407 2407 88.422 757 2762 1 chr4B.!!$R1 2005
6 TraesCS1B01G154900 chr4B 376028449 376030447 1998 False 2008 2008 85.017 763 2762 1 chr4B.!!$F1 1999
7 TraesCS1B01G154900 chr4B 386695415 386696177 762 False 1242 1242 96.073 1 761 1 chr4B.!!$F2 760
8 TraesCS1B01G154900 chr2A 82412066 82414052 1986 True 2302 2302 87.618 757 2762 1 chr2A.!!$R1 2005
9 TraesCS1B01G154900 chr3A 167680994 167682981 1987 True 2287 2287 87.469 757 2762 1 chr3A.!!$R1 2005
10 TraesCS1B01G154900 chr3B 40495601 40497612 2011 False 2194 2194 86.496 754 2762 1 chr3B.!!$F1 2008
11 TraesCS1B01G154900 chr3B 17555056 17555819 763 True 1214 1214 95.425 1 761 1 chr3B.!!$R1 760
12 TraesCS1B01G154900 chr3B 380034984 380035745 761 False 1212 1212 95.431 1 761 1 chr3B.!!$F3 760
13 TraesCS1B01G154900 chr3B 61053641 61054404 763 True 1208 1208 95.300 1 761 1 chr3B.!!$R2 760
14 TraesCS1B01G154900 chr1A 313567171 313569071 1900 True 2176 2176 87.363 757 2664 1 chr1A.!!$R1 1907
15 TraesCS1B01G154900 chr6B 272295985 272297982 1997 True 2158 2158 86.224 757 2762 1 chr6B.!!$R1 2005
16 TraesCS1B01G154900 chr5B 321434550 321435309 759 False 1221 1221 95.675 1 761 1 chr5B.!!$F2 760
17 TraesCS1B01G154900 chr5B 123352953 123353722 769 False 1214 1214 95.325 1 761 1 chr5B.!!$F1 760
18 TraesCS1B01G154900 chr5B 344181267 344182032 765 False 1210 1210 95.306 1 761 1 chr5B.!!$F3 760
19 TraesCS1B01G154900 chr5B 598139310 598140073 763 True 1206 1206 95.176 1 764 1 chr5B.!!$R1 763

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
399 419 0.323908 CCTCTCCTCCTCCGTTGAGT 60.324 60.0 0.0 0.0 36.86 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1862 1.374758 CTCCCTTCCTCGTGTGTGC 60.375 63.158 0.0 0.0 0.0 4.57 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
200 206 2.589540 CCATGCGCCTAGGGTTGA 59.410 61.111 11.72 0.00 0.00 3.18
399 419 0.323908 CCTCTCCTCCTCCGTTGAGT 60.324 60.000 0.00 0.00 36.86 3.41
444 464 1.211212 CTGCCTCTCCACCATCATCAA 59.789 52.381 0.00 0.00 0.00 2.57
489 509 3.551635 TCTTCCTCAACCTCTCCTTCT 57.448 47.619 0.00 0.00 0.00 2.85
523 543 2.296073 AGAAGGAGGAGACGTTGTCT 57.704 50.000 0.00 0.00 46.42 3.41
901 932 1.152589 TCATGTGCAAGTGCCCCAA 60.153 52.632 0.00 0.00 41.18 4.12
1066 1097 6.537355 AGGAAGATTGAGAAGAACATCAACA 58.463 36.000 0.00 0.00 38.19 3.33
1301 1342 7.005296 ACTACTCCTGAAGAAGTACAAGAAGA 58.995 38.462 0.00 0.00 0.00 2.87
1533 1574 6.577103 TCTCATTCCTGATGATGACACTTAC 58.423 40.000 0.00 0.00 43.59 2.34
1535 1576 7.561356 TCTCATTCCTGATGATGACACTTACTA 59.439 37.037 0.00 0.00 43.59 1.82
1537 1578 8.708378 TCATTCCTGATGATGACACTTACTATT 58.292 33.333 0.00 0.00 39.83 1.73
1568 1609 9.618890 TGCTAGTCTTGAGCTTAATGATAAATT 57.381 29.630 0.00 0.00 40.76 1.82
1590 1631 4.371855 TCATCCTCATGTTAGTGTCGAC 57.628 45.455 9.11 9.11 0.00 4.20
1708 1749 5.357878 ACTTGCATTGTCTCTTTTGTTGAGA 59.642 36.000 0.00 0.00 38.13 3.27
1711 1752 5.210715 GCATTGTCTCTTTTGTTGAGAGTG 58.789 41.667 0.00 0.00 40.70 3.51
1716 1757 5.415701 TGTCTCTTTTGTTGAGAGTGCTTTT 59.584 36.000 0.00 0.00 40.70 2.27
1741 1782 4.720127 TGCTTGTGCACGATCCAT 57.280 50.000 13.13 0.00 45.31 3.41
1821 1862 0.182299 GATGAGGAGAAGCAAGGGGG 59.818 60.000 0.00 0.00 0.00 5.40
1881 1924 2.488204 AGAGAAGCAAAAGGAGAGGC 57.512 50.000 0.00 0.00 0.00 4.70
1906 1959 1.546029 CAGTTGGTGAGGTGATCGAGA 59.454 52.381 0.00 0.00 0.00 4.04
1950 2003 1.537202 GTGAGCTGTTTCATGACCCAC 59.463 52.381 0.00 0.00 0.00 4.61
1988 2042 7.407393 TCCATTGATACATGCTGAAATCAAA 57.593 32.000 15.13 5.08 37.10 2.69
1991 2045 7.709182 CCATTGATACATGCTGAAATCAAATGT 59.291 33.333 13.05 13.05 37.10 2.71
2009 2063 5.806654 AATGTTATTTGGGTTGCTTGAGT 57.193 34.783 0.00 0.00 0.00 3.41
2023 2077 7.755373 GGGTTGCTTGAGTCATTTCTTAAATAC 59.245 37.037 0.00 0.00 0.00 1.89
2037 2092 5.667466 TCTTAAATACCGTCCCACTGAATC 58.333 41.667 0.00 0.00 0.00 2.52
2134 2190 4.024387 ACAATGCTTGCTTTGCTGAAATTG 60.024 37.500 17.35 7.67 0.00 2.32
2256 2313 2.223782 GCTGAATTTGTGCCAAGTGTCA 60.224 45.455 0.00 0.00 0.00 3.58
2566 2634 3.028130 TCCTTTGGGGAGACAAACAAAC 58.972 45.455 0.00 0.00 39.58 2.93
2567 2635 3.031013 CCTTTGGGGAGACAAACAAACT 58.969 45.455 0.00 0.00 35.57 2.66
2568 2636 3.450817 CCTTTGGGGAGACAAACAAACTT 59.549 43.478 0.00 0.00 35.57 2.66
2571 2639 6.351456 CCTTTGGGGAGACAAACAAACTTAAA 60.351 38.462 0.00 0.00 35.57 1.52
2572 2640 6.607004 TTGGGGAGACAAACAAACTTAAAA 57.393 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
330 350 2.121963 AGGTGTTCAGCCCTCCCA 60.122 61.111 0.00 0.00 0.00 4.37
489 509 1.283029 CCTTCTTGATCCAGCAAGGGA 59.717 52.381 4.79 0.00 44.14 4.20
523 543 2.458951 GTTCAACACACGTACGGTACA 58.541 47.619 21.06 0.00 0.00 2.90
669 690 6.535963 TCTAAGCAATGAGTCATGAGAGAA 57.464 37.500 6.34 0.00 0.00 2.87
746 767 3.537580 GAGCATATGTTGGGGAACGTTA 58.462 45.455 0.00 0.00 0.00 3.18
1066 1097 6.561070 AGGAGAGATGAGATAGTACTACCAGT 59.439 42.308 4.31 0.00 0.00 4.00
1301 1342 7.932491 CAGGTTCTTCATCTTCATCTACATCAT 59.068 37.037 0.00 0.00 0.00 2.45
1464 1505 7.878547 TGTATGATCATGTCCAAGCAAATAA 57.121 32.000 18.72 0.00 0.00 1.40
1533 1574 4.040217 AGCTCAAGACTAGCATGGGAATAG 59.960 45.833 0.00 0.00 42.62 1.73
1535 1576 2.776536 AGCTCAAGACTAGCATGGGAAT 59.223 45.455 0.00 0.00 42.62 3.01
1537 1578 1.871418 AGCTCAAGACTAGCATGGGA 58.129 50.000 0.00 0.00 42.62 4.37
1568 1609 4.381612 GGTCGACACTAACATGAGGATGAA 60.382 45.833 18.91 0.00 33.36 2.57
1585 1626 4.433615 TGATAGAAATCAGCAAGGTCGAC 58.566 43.478 7.13 7.13 37.20 4.20
1587 1628 5.588568 GATGATAGAAATCAGCAAGGTCG 57.411 43.478 0.00 0.00 45.81 4.79
1708 1749 4.869861 CACAAGCAAAAACCTAAAAGCACT 59.130 37.500 0.00 0.00 0.00 4.40
1711 1752 4.195744 GCACAAGCAAAAACCTAAAAGC 57.804 40.909 0.00 0.00 41.58 3.51
1741 1782 3.411446 CTCAAACCTGGTCAGCATGTAA 58.589 45.455 0.00 0.00 37.40 2.41
1821 1862 1.374758 CTCCCTTCCTCGTGTGTGC 60.375 63.158 0.00 0.00 0.00 4.57
1881 1924 2.281070 ACCTCACCAACTGCAGCG 60.281 61.111 15.27 5.03 0.00 5.18
1906 1959 3.539604 GGCTTTGATGATGTAGCACTCT 58.460 45.455 0.00 0.00 35.36 3.24
1988 2042 4.832266 TGACTCAAGCAACCCAAATAACAT 59.168 37.500 0.00 0.00 0.00 2.71
1991 2045 6.267471 AGAAATGACTCAAGCAACCCAAATAA 59.733 34.615 0.00 0.00 0.00 1.40
2009 2063 5.878116 CAGTGGGACGGTATTTAAGAAATGA 59.122 40.000 0.00 0.00 32.38 2.57
2023 2077 1.831736 AGGTAAGATTCAGTGGGACGG 59.168 52.381 0.00 0.00 0.00 4.79
2037 2092 4.939052 ATCACCCTATGTCGAAGGTAAG 57.061 45.455 1.10 0.00 31.70 2.34
2134 2190 6.072452 AGCACTCAAAACTAATAGCTTTCACC 60.072 38.462 0.00 0.00 0.00 4.02
2256 2313 4.803329 AGGTAATTGCTCTCAATGGGAT 57.197 40.909 0.00 0.00 41.77 3.85
2733 2809 4.942483 AGAGCATGATCCTGAGAACAAAAG 59.058 41.667 7.49 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.