Multiple sequence alignment - TraesCS5B01G168200

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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 TraesCS5B01G168200 chr5B 100.000 4080 0 0 1 4080 312131118 312127039 0 7535
1 TraesCS5B01G168200 chr2A 91.996 4098 307 12 1 4080 639405057 639409151 0 5731
2 TraesCS5B01G168200 chr2A 89.448 4094 410 13 1 4077 215767697 215763609 0 5147
3 TraesCS5B01G168200 chrUn 90.840 4105 343 17 1 4080 30508722 30504626 0 5467
4 TraesCS5B01G168200 chr4A 90.821 4107 336 23 1 4080 577421936 577426028 0 5457
5 TraesCS5B01G168200 chr1A 89.859 4102 378 26 1 4077 462461451 462457363 0 5236
6 TraesCS5B01G168200 chr1A 90.532 3665 326 12 3 3650 310628465 310624805 0 4826
7 TraesCS5B01G168200 chr5A 89.629 4098 402 14 1 4080 645835438 645831346 0 5192
8 TraesCS5B01G168200 chr5A 89.679 3827 365 20 271 4077 177676764 177680580 0 4852
9 TraesCS5B01G168200 chr5A 89.728 2424 229 12 1 2406 396921096 396923517 0 3079
10 TraesCS5B01G168200 chr6A 89.542 4102 396 24 1 4080 487176045 487171955 0 5168
11 TraesCS5B01G168200 chr6A 88.987 4095 426 14 3 4077 442710595 442714684 0 5040
12 TraesCS5B01G168200 chr6A 88.710 4110 422 28 1 4077 418204081 418208181 0 4981
13 TraesCS5B01G168200 chr6D 84.339 4125 581 52 1 4077 282379664 282383771 0 3978
14 TraesCS5B01G168200 chr1B 84.306 4097 600 36 1 4078 490524902 490520830 0 3964
15 TraesCS5B01G168200 chr3A 83.220 4118 627 54 1 4080 436770623 436774714 0 3718
16 TraesCS5B01G168200 chr2B 82.923 4105 626 56 1 4077 588532792 588528735 0 3627
17 TraesCS5B01G168200 chr1D 92.456 1034 76 2 3 1034 248871110 248870077 0 1476


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 TraesCS5B01G168200 chr5B 312127039 312131118 4079 True 7535 7535 100.000 1 4080 1 chr5B.!!$R1 4079
1 TraesCS5B01G168200 chr2A 639405057 639409151 4094 False 5731 5731 91.996 1 4080 1 chr2A.!!$F1 4079
2 TraesCS5B01G168200 chr2A 215763609 215767697 4088 True 5147 5147 89.448 1 4077 1 chr2A.!!$R1 4076
3 TraesCS5B01G168200 chrUn 30504626 30508722 4096 True 5467 5467 90.840 1 4080 1 chrUn.!!$R1 4079
4 TraesCS5B01G168200 chr4A 577421936 577426028 4092 False 5457 5457 90.821 1 4080 1 chr4A.!!$F1 4079
5 TraesCS5B01G168200 chr1A 462457363 462461451 4088 True 5236 5236 89.859 1 4077 1 chr1A.!!$R2 4076
6 TraesCS5B01G168200 chr1A 310624805 310628465 3660 True 4826 4826 90.532 3 3650 1 chr1A.!!$R1 3647
7 TraesCS5B01G168200 chr5A 645831346 645835438 4092 True 5192 5192 89.629 1 4080 1 chr5A.!!$R1 4079
8 TraesCS5B01G168200 chr5A 177676764 177680580 3816 False 4852 4852 89.679 271 4077 1 chr5A.!!$F1 3806
9 TraesCS5B01G168200 chr5A 396921096 396923517 2421 False 3079 3079 89.728 1 2406 1 chr5A.!!$F2 2405
10 TraesCS5B01G168200 chr6A 487171955 487176045 4090 True 5168 5168 89.542 1 4080 1 chr6A.!!$R1 4079
11 TraesCS5B01G168200 chr6A 442710595 442714684 4089 False 5040 5040 88.987 3 4077 1 chr6A.!!$F2 4074
12 TraesCS5B01G168200 chr6A 418204081 418208181 4100 False 4981 4981 88.710 1 4077 1 chr6A.!!$F1 4076
13 TraesCS5B01G168200 chr6D 282379664 282383771 4107 False 3978 3978 84.339 1 4077 1 chr6D.!!$F1 4076
14 TraesCS5B01G168200 chr1B 490520830 490524902 4072 True 3964 3964 84.306 1 4078 1 chr1B.!!$R1 4077
15 TraesCS5B01G168200 chr3A 436770623 436774714 4091 False 3718 3718 83.220 1 4080 1 chr3A.!!$F1 4079
16 TraesCS5B01G168200 chr2B 588528735 588532792 4057 True 3627 3627 82.923 1 4077 1 chr2B.!!$R1 4076
17 TraesCS5B01G168200 chr1D 248870077 248871110 1033 True 1476 1476 92.456 3 1034 1 chr1D.!!$R1 1031

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
94 97 0.034477 TTCTTCCCCAAATCCCGAGC 60.034 55.0 0.00 0.0 0.00 5.03 F
293 307 0.249657 CATCCTCCCTTAGCGAGCAC 60.250 60.0 0.00 0.0 0.00 4.40 F
1595 1647 0.310543 CTTGCGCACTTTGCTTACCA 59.689 50.0 11.12 0.0 42.25 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1774 0.181114 TGGCACATCATACCTCTGCC 59.819 55.0 0.00 0.0 46.49 4.85 R
1881 1946 0.527817 CGGTGTGAGCCTCGTATTCC 60.528 60.0 0.00 0.0 0.00 3.01 R
3489 3601 0.472734 ACCTCAGACTGGGTGAAGCT 60.473 55.0 13.07 0.0 34.16 3.74 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
94 97 0.034477 TTCTTCCCCAAATCCCGAGC 60.034 55.000 0.00 0.00 0.00 5.03
121 125 4.933400 TGTTAAATAGTGTCCGGCTTCTTC 59.067 41.667 0.00 0.00 0.00 2.87
293 307 0.249657 CATCCTCCCTTAGCGAGCAC 60.250 60.000 0.00 0.00 0.00 4.40
486 502 4.733542 GCCGGGCTTGCCACCTAA 62.734 66.667 12.87 0.00 0.00 2.69
838 855 2.636412 GGAACCCCAAAGAAGGCGC 61.636 63.158 0.00 0.00 0.00 6.53
925 942 4.392940 CGGCCTTCCTGAGATTGATAATT 58.607 43.478 0.00 0.00 0.00 1.40
1008 1025 2.416836 CGTTCTTTACCTGATGAGCCGA 60.417 50.000 0.00 0.00 0.00 5.54
1028 1045 5.221244 GCCGAATAAAGGTATTGGCTCAATT 60.221 40.000 5.85 0.00 38.96 2.32
1045 1084 4.009675 TCAATTAGGACAAGTCATGGCAC 58.990 43.478 0.00 0.00 39.66 5.01
1128 1168 2.746375 GGAGGATGACGCCACCCAT 61.746 63.158 0.00 0.00 39.13 4.00
1199 1240 3.055385 TCCGATTTGTACAAGGGAGAAGG 60.055 47.826 16.61 11.29 0.00 3.46
1257 1298 6.540438 TTTTCTATGTACAATCCTCCGAGT 57.460 37.500 0.00 0.00 0.00 4.18
1364 1409 4.745620 GCGTAAGGCTGTAAAGGAGATTAG 59.254 45.833 0.00 0.00 39.11 1.73
1561 1607 3.888930 TGAGACCAAAGTCCCAACATTTC 59.111 43.478 0.00 0.00 44.72 2.17
1562 1609 3.888930 GAGACCAAAGTCCCAACATTTCA 59.111 43.478 0.00 0.00 44.72 2.69
1595 1647 0.310543 CTTGCGCACTTTGCTTACCA 59.689 50.000 11.12 0.00 42.25 3.25
1712 1766 1.080569 GAACGCGGTCCGGACTAAA 60.081 57.895 32.52 0.00 42.52 1.85
1781 1841 9.841295 TTGTCTTTAAAGATATATTAACGCCCT 57.159 29.630 20.41 0.00 37.39 5.19
1881 1946 2.434359 GGACACGGAAGCGGAAGG 60.434 66.667 0.00 0.00 0.00 3.46
1893 1958 2.029307 GCGGAAGGGAATACGAGGCT 62.029 60.000 0.00 0.00 0.00 4.58
1909 1974 2.187946 CTCACACCGGATGCTCCC 59.812 66.667 9.46 0.00 31.13 4.30
1940 2005 1.374560 TGCGGACAAAATATCCACCG 58.625 50.000 0.00 0.00 42.63 4.94
2077 2142 2.086869 GCTGCTCAAAATGGTCTAGCA 58.913 47.619 0.00 0.00 40.68 3.49
2087 2152 1.890894 GGTCTAGCAAGAGCCACGA 59.109 57.895 0.00 0.00 43.16 4.35
2116 2181 5.740290 ATGTAAAGGATATACGGGTGAGG 57.260 43.478 0.00 0.00 0.00 3.86
2123 2193 7.383156 AAGGATATACGGGTGAGGAAATTTA 57.617 36.000 0.00 0.00 0.00 1.40
2207 2278 6.509418 TCATTTGTTATGCAGGTTCTTACC 57.491 37.500 0.00 0.00 45.39 2.85
2227 2298 3.829601 ACCGAAAAGAATGCCCAATTGTA 59.170 39.130 4.43 0.00 0.00 2.41
2248 2319 1.738350 CCATGAGCTTGAAGAGTGCAG 59.262 52.381 0.00 0.00 0.00 4.41
2816 2918 0.671781 GCTTGCGGAGAAGCTGAAGA 60.672 55.000 0.00 0.00 44.26 2.87
3035 3137 3.448686 CAACAGGATTGTAGGCTAGACG 58.551 50.000 0.00 0.00 36.23 4.18
3037 3139 2.032620 CAGGATTGTAGGCTAGACGGT 58.967 52.381 0.00 0.00 0.00 4.83
3047 3149 2.029623 GGCTAGACGGTCTGTTGGATA 58.970 52.381 20.58 0.00 0.00 2.59
3214 3318 6.651975 ATACCCTCTCGGTTATGTAAGAAG 57.348 41.667 0.00 0.00 45.36 2.85
3215 3319 3.705072 ACCCTCTCGGTTATGTAAGAAGG 59.295 47.826 0.00 0.00 45.36 3.46
3433 3545 4.624913 TGGGGGCACATATGGAAAATAAA 58.375 39.130 7.80 0.00 0.00 1.40
3489 3601 3.259876 TCCCTTAAGAACGCTAGCTTTCA 59.740 43.478 29.18 12.16 0.00 2.69
3604 3717 3.201930 TGGGCATAAATACAAGAGCCAGA 59.798 43.478 0.00 0.00 43.72 3.86
3745 3861 1.141185 AAGAAGCCCCCAGGTATAGC 58.859 55.000 0.00 0.00 34.57 2.97
3746 3862 0.269173 AGAAGCCCCCAGGTATAGCT 59.731 55.000 0.00 0.00 34.57 3.32
3893 4035 0.536687 AGACGAACACAGAGTCCGGA 60.537 55.000 0.00 0.00 35.65 5.14
3910 4052 2.030981 CCGGAACTAGGCGTAGAATCTC 60.031 54.545 19.82 9.83 0.00 2.75
3938 4080 1.523154 GGCTGCGTTTCATGGGTTCA 61.523 55.000 0.00 0.00 0.00 3.18
3946 4088 1.538047 TTCATGGGTTCAGCTCAAGC 58.462 50.000 0.00 0.00 42.49 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 97 2.676342 GCCGGACACTATTTAACAGGTG 59.324 50.000 5.05 0.00 35.99 4.00
121 125 0.169672 CCAAGGAGCGCAACATTCAG 59.830 55.000 11.47 0.00 0.00 3.02
152 157 4.632153 ACACGTGGAAGATGGCTATTATC 58.368 43.478 21.57 0.00 0.00 1.75
220 227 2.751166 AGACAGCTCATTTGCGTAGT 57.249 45.000 0.00 0.00 38.13 2.73
346 361 1.541368 TGGGGGAACAAGAGGAGGG 60.541 63.158 0.00 0.00 0.00 4.30
446 462 0.391597 AACCGGGACCATATACGCTG 59.608 55.000 6.32 0.00 0.00 5.18
486 502 1.503542 CGCTTGCTCTTCGCCATTT 59.496 52.632 0.00 0.00 38.05 2.32
531 547 1.220749 GACAAGGCATACCCGCTCA 59.779 57.895 0.00 0.00 39.21 4.26
902 919 0.471617 ATCAATCTCAGGAAGGCCGG 59.528 55.000 0.00 0.00 39.96 6.13
925 942 0.687354 AGGCGCTTCTTCAAAGGAGA 59.313 50.000 7.64 0.00 33.17 3.71
1008 1025 8.058847 TGTCCTAATTGAGCCAATACCTTTATT 58.941 33.333 1.52 0.00 32.43 1.40
1028 1045 3.432186 GCATAGTGCCATGACTTGTCCTA 60.432 47.826 0.00 0.00 37.42 2.94
1045 1084 2.079158 CACCCCTCGCATAATGCATAG 58.921 52.381 0.00 0.00 45.36 2.23
1059 1099 2.085343 ATTGAAGTGGCTGCACCCCT 62.085 55.000 0.50 0.00 37.83 4.79
1257 1298 6.461788 GGCATAAAAAGTGTTGACTTACCCAA 60.462 38.462 0.00 0.00 41.87 4.12
1595 1647 6.489603 TCCCTGTGAAACACCATTTGTATAT 58.510 36.000 0.00 0.00 45.67 0.86
1712 1766 1.615424 ATACCTCTGCCCCGGTGTT 60.615 57.895 0.00 0.00 34.76 3.32
1720 1774 0.181114 TGGCACATCATACCTCTGCC 59.819 55.000 0.00 0.00 46.49 4.85
1881 1946 0.527817 CGGTGTGAGCCTCGTATTCC 60.528 60.000 0.00 0.00 0.00 3.01
1909 1974 0.758734 TGTCCGCATCCTCTATTGGG 59.241 55.000 0.00 0.00 0.00 4.12
2077 2142 1.623811 ACATACTGGTTCGTGGCTCTT 59.376 47.619 0.00 0.00 0.00 2.85
2087 2152 6.556116 ACCCGTATATCCTTTACATACTGGTT 59.444 38.462 0.00 0.00 38.71 3.67
2207 2278 4.173256 GGTACAATTGGGCATTCTTTTCG 58.827 43.478 10.83 0.00 0.00 3.46
2217 2288 1.767759 AGCTCATGGTACAATTGGGC 58.232 50.000 10.83 5.84 44.48 5.36
2227 2298 1.072806 TGCACTCTTCAAGCTCATGGT 59.927 47.619 0.00 0.00 0.00 3.55
2248 2319 2.180159 TACGGCCTGAAGTTGGGCTC 62.180 60.000 13.91 5.93 46.80 4.70
2850 2952 4.641645 CACCTTGACGGCAGGCCA 62.642 66.667 5.01 0.00 35.61 5.36
3035 3137 7.005296 TCCTCTTCTATACTATCCAACAGACC 58.995 42.308 0.00 0.00 0.00 3.85
3037 3139 9.661954 AATTCCTCTTCTATACTATCCAACAGA 57.338 33.333 0.00 0.00 0.00 3.41
3047 3149 7.565398 TGACTGGCTAAATTCCTCTTCTATACT 59.435 37.037 0.00 0.00 0.00 2.12
3115 3219 6.429078 CCATGACAAATGATCTACAATCCGAT 59.571 38.462 0.00 0.00 0.00 4.18
3215 3319 2.440980 GTCTCCAAGCATGCCCCC 60.441 66.667 15.66 0.00 0.00 5.40
3407 3514 2.431687 TCCATATGTGCCCCCAGATA 57.568 50.000 1.24 0.00 32.51 1.98
3433 3545 7.382218 GTCGGTGAACAAAAGATGATTTTTCAT 59.618 33.333 0.00 0.00 30.12 2.57
3489 3601 0.472734 ACCTCAGACTGGGTGAAGCT 60.473 55.000 13.07 0.00 34.16 3.74
3604 3717 0.980231 TTTTGGCCAAGCTGGGTTGT 60.980 50.000 19.48 0.00 38.19 3.32
3650 3763 3.482436 TCCGCATGTACCTTTTCTTTGT 58.518 40.909 0.00 0.00 0.00 2.83
3861 4002 1.887198 GTTCGTCTCCTTCCTCTGTCA 59.113 52.381 0.00 0.00 0.00 3.58
3893 4035 1.955080 CCGGAGATTCTACGCCTAGTT 59.045 52.381 13.00 0.00 36.34 2.24
3928 4070 0.322816 GGCTTGAGCTGAACCCATGA 60.323 55.000 0.00 0.00 41.70 3.07
3938 4080 1.040646 TCGGATAATCGGCTTGAGCT 58.959 50.000 2.66 0.00 41.70 4.09
3946 4088 0.736325 GGGACGCATCGGATAATCGG 60.736 60.000 9.94 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.