Multiple sequence alignment - TraesCS6A01G043500

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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 TraesCS6A01G043500 chr6A 100.000 3205 0 0 1 3205 22756187 22752983 0 5919
1 TraesCS6A01G043500 chr6A 94.986 3211 142 14 1 3205 54974026 54970829 0 5020
2 TraesCS6A01G043500 chr3A 95.547 3211 130 12 1 3205 164756250 164753047 0 5125
3 TraesCS6A01G043500 chr3A 94.176 3211 152 22 1 3205 692601518 692598337 0 4861
4 TraesCS6A01G043500 chr2A 95.490 3215 131 10 1 3204 560675889 560672678 0 5121
5 TraesCS6A01G043500 chr2A 93.433 3213 187 23 1 3205 515499424 515496228 0 4743
6 TraesCS6A01G043500 chr7A 94.491 3213 152 21 9 3205 699089144 699085941 0 4929
7 TraesCS6A01G043500 chr7A 95.312 1749 67 14 1466 3205 595105853 595107595 0 2761
8 TraesCS6A01G043500 chr4A 94.183 3043 159 15 174 3205 516672483 516669448 0 4623
9 TraesCS6A01G043500 chrUn 92.181 3223 208 33 1 3203 76676720 76673522 0 4516
10 TraesCS6A01G043500 chr3B 90.847 3223 243 41 1 3205 725453316 725450128 0 4270
11 TraesCS6A01G043500 chr1A 95.191 2516 84 19 722 3205 399818381 399815871 0 3941


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 TraesCS6A01G043500 chr6A 22752983 22756187 3204 True 5919 5919 100.000 1 3205 1 chr6A.!!$R1 3204
1 TraesCS6A01G043500 chr6A 54970829 54974026 3197 True 5020 5020 94.986 1 3205 1 chr6A.!!$R2 3204
2 TraesCS6A01G043500 chr3A 164753047 164756250 3203 True 5125 5125 95.547 1 3205 1 chr3A.!!$R1 3204
3 TraesCS6A01G043500 chr3A 692598337 692601518 3181 True 4861 4861 94.176 1 3205 1 chr3A.!!$R2 3204
4 TraesCS6A01G043500 chr2A 560672678 560675889 3211 True 5121 5121 95.490 1 3204 1 chr2A.!!$R2 3203
5 TraesCS6A01G043500 chr2A 515496228 515499424 3196 True 4743 4743 93.433 1 3205 1 chr2A.!!$R1 3204
6 TraesCS6A01G043500 chr7A 699085941 699089144 3203 True 4929 4929 94.491 9 3205 1 chr7A.!!$R1 3196
7 TraesCS6A01G043500 chr7A 595105853 595107595 1742 False 2761 2761 95.312 1466 3205 1 chr7A.!!$F1 1739
8 TraesCS6A01G043500 chr4A 516669448 516672483 3035 True 4623 4623 94.183 174 3205 1 chr4A.!!$R1 3031
9 TraesCS6A01G043500 chrUn 76673522 76676720 3198 True 4516 4516 92.181 1 3203 1 chrUn.!!$R1 3202
10 TraesCS6A01G043500 chr3B 725450128 725453316 3188 True 4270 4270 90.847 1 3205 1 chr3B.!!$R1 3204
11 TraesCS6A01G043500 chr1A 399815871 399818381 2510 True 3941 3941 95.191 722 3205 1 chr1A.!!$R1 2483

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
909 932 0.10741 TCCGTGTTCTGCACTTTGGT 60.107 50.0 0.0 0.0 45.57 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2459 2582 1.14287 CACCCCTCAACCAACTTCTCA 59.857 52.381 0.0 0.0 0.0 3.27 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
41 42 7.521910 GCATTTTAACATGGCAATTTCAACCTT 60.522 33.333 3.87 0.00 0.00 3.50
120 123 1.745653 GCTGCCACATCTTAGGTTTCC 59.254 52.381 0.00 0.00 0.00 3.13
150 154 6.379703 TGGAGGATTTTGTGACTTTCTTTTCA 59.620 34.615 0.00 0.00 0.00 2.69
172 176 7.360113 TCATACTATCTTGTGCTAACATGGA 57.640 36.000 0.00 0.00 35.83 3.41
343 361 0.250684 TTTTCACTCGAGCCCATGCA 60.251 50.000 13.61 0.00 41.13 3.96
455 473 0.170116 TCGCGGCAATCATCAAAACC 59.830 50.000 6.13 0.00 0.00 3.27
491 509 3.524095 TGGATCCACCACAACAGAATT 57.476 42.857 11.44 0.00 44.64 2.17
546 564 1.213296 ACTGTCCACACACCCTCTTT 58.787 50.000 0.00 0.00 0.00 2.52
555 573 2.633481 ACACACCCTCTTTCTCCTACAC 59.367 50.000 0.00 0.00 0.00 2.90
592 612 1.067565 CCTTGAGCTTGCAGTCGTCTA 60.068 52.381 0.00 0.00 0.00 2.59
715 737 3.906998 ACGACTGACTTCATTGACTGAG 58.093 45.455 0.00 0.00 34.68 3.35
801 823 2.611971 GGTGCACGAATCTAGTCAACCA 60.612 50.000 11.45 0.00 0.00 3.67
909 932 0.107410 TCCGTGTTCTGCACTTTGGT 60.107 50.000 0.00 0.00 45.57 3.67
1071 1096 4.759516 TGGCGAGGTTTTTAAGATGAAC 57.240 40.909 0.00 0.00 0.00 3.18
1219 1244 1.004185 CGATGTCATGTGCAAGCTAGC 60.004 52.381 6.62 6.62 0.00 3.42
1439 1468 3.864789 ACCAGTCCTTTCTGTGAACAT 57.135 42.857 0.00 0.00 34.02 2.71
1452 1482 9.352784 CTTTCTGTGAACATTCTTTTTAACACA 57.647 29.630 0.00 0.00 36.03 3.72
1478 1509 1.855295 TCATGCATGGCAACCTGATT 58.145 45.000 25.97 0.00 43.62 2.57
1494 1525 6.949352 ACCTGATTATAACAAGATGGCAAG 57.051 37.500 0.00 0.00 0.00 4.01
1806 1913 0.324943 CCGTGGATTTCACTGGGACT 59.675 55.000 0.00 0.00 43.94 3.85
2430 2553 3.010584 ACCTGTTCAGCATCTAATTGGGT 59.989 43.478 0.00 0.00 0.00 4.51
2459 2582 4.002797 GGAATGACCGGCTTGCTT 57.997 55.556 0.00 0.00 0.00 3.91
2633 2757 6.155910 ACACACAAGATGAACTAGATGGAGAT 59.844 38.462 0.00 0.00 0.00 2.75
2840 2966 1.566298 GGCTCCAGAGGATGTTGGGT 61.566 60.000 0.00 0.00 35.13 4.51
2968 3094 6.376581 TGATCCCTTTTTGCATTTGTTTTTGT 59.623 30.769 0.00 0.00 0.00 2.83
2969 3095 5.947443 TCCCTTTTTGCATTTGTTTTTGTG 58.053 33.333 0.00 0.00 0.00 3.33
3035 3163 5.527214 TGTTTTCCTCCATCTTATATGTGCG 59.473 40.000 0.00 0.00 0.00 5.34
3099 3227 1.445716 CCAACGCCAACCCGTGTTTA 61.446 55.000 0.00 0.00 41.90 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.943381 TGTTTCAATGGCAAAAATGTGCA 59.057 34.783 0.00 0.00 46.81 4.57
120 123 1.197721 GTCACAAAATCCTCCACTGCG 59.802 52.381 0.00 0.00 0.00 5.18
150 154 8.267894 AGTTTCCATGTTAGCACAAGATAGTAT 58.732 33.333 0.00 0.00 36.16 2.12
172 176 9.605955 GCACTTAAAAACAAAATGTTGAAGTTT 57.394 25.926 1.62 2.45 40.14 2.66
222 227 6.128849 GCAATTAAGCACATTGGTTACACTTG 60.129 38.462 0.00 4.44 39.68 3.16
225 232 4.625311 GGCAATTAAGCACATTGGTTACAC 59.375 41.667 0.00 0.00 39.68 2.90
455 473 6.350194 GGTGGATCCATGAAATCATCATCATG 60.350 42.308 19.62 8.42 45.91 3.07
491 509 1.701031 TTTCTCCGTCCAGTTGCCCA 61.701 55.000 0.00 0.00 0.00 5.36
546 564 4.941263 GCAACCAATAACATGTGTAGGAGA 59.059 41.667 0.00 0.00 0.00 3.71
669 691 1.522569 GAGGCCCTGTTGCGAGTAT 59.477 57.895 0.00 0.00 0.00 2.12
715 737 5.067936 TCCCTTCTGATCGTCAGTAAATCTC 59.932 44.000 12.62 0.00 44.58 2.75
801 823 0.253044 ACCAAGCCAGTCGCATACAT 59.747 50.000 0.00 0.00 41.38 2.29
909 932 1.152652 ATTTGTCCACGGGGCACAA 60.153 52.632 15.08 15.08 0.00 3.33
1071 1096 5.596361 AGTTGAGATGAGGTACATGAGTAGG 59.404 44.000 0.00 0.00 39.56 3.18
1248 1276 6.455513 CGAGTTGTCGCATCAGAAATCAAATA 60.456 38.462 0.00 0.00 39.88 1.40
1452 1482 5.104859 TCAGGTTGCCATGCATGAATAAAAT 60.105 36.000 28.31 5.38 38.76 1.82
2197 2317 2.423898 ATGCTTGGCCATCAGCTGC 61.424 57.895 25.89 15.07 43.05 5.25
2415 2538 4.398988 TGCAAACTACCCAATTAGATGCTG 59.601 41.667 0.00 0.00 36.87 4.41
2430 2553 2.639065 GGTCATTCCGGATGCAAACTA 58.361 47.619 4.15 0.00 35.64 2.24
2459 2582 1.142870 CACCCCTCAACCAACTTCTCA 59.857 52.381 0.00 0.00 0.00 3.27
2762 2887 4.153475 GCAGCCGTATGTTCTTTGACTTTA 59.847 41.667 0.00 0.00 0.00 1.85
2840 2966 1.573108 CTCTTGCCAGGAGAACCCTA 58.427 55.000 0.00 0.00 45.60 3.53
2968 3094 1.514678 AAACTCATTGCCGCGCTTCA 61.515 50.000 5.56 0.00 0.00 3.02
2969 3095 1.067199 CAAACTCATTGCCGCGCTTC 61.067 55.000 5.56 0.00 31.00 3.86
3035 3163 4.008933 ACCAGCTGTCGCCTCACC 62.009 66.667 13.81 0.00 36.60 4.02
3099 3227 1.608590 CACCTTTGTTCAACCGAGCAT 59.391 47.619 0.00 0.00 31.87 3.79


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

AutoCloner maintained by Alex Coulton.