Multiple sequence alignment - TraesCS6D01G342700

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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 TraesCS6D01G342700 chr6D 100.000 2930 0 0 1 2930 441812477 441809548 0.000000e+00 5411.0
1 TraesCS6D01G342700 chr6B 94.319 2922 119 14 27 2930 667801110 667798218 0.000000e+00 4433.0
2 TraesCS6D01G342700 chr6B 100.000 29 0 0 1 29 690305067 690305095 1.000000e-03 54.7
3 TraesCS6D01G342700 chr6A 94.657 2695 120 8 250 2930 591091304 591088620 0.000000e+00 4157.0
4 TraesCS6D01G342700 chr6A 85.756 1720 209 17 1020 2715 591208345 591206638 0.000000e+00 1786.0
5 TraesCS6D01G342700 chr6A 86.645 307 29 6 688 985 591208644 591208341 2.180000e-86 329.0
6 TraesCS6D01G342700 chr6A 91.284 218 17 2 2713 2930 591206567 591206352 2.210000e-76 296.0
7 TraesCS6D01G342700 chr6A 88.750 80 9 0 69 148 591215094 591215015 6.680000e-17 99.0
8 TraesCS6D01G342700 chr1A 88.356 2439 219 23 507 2930 54362056 54359668 0.000000e+00 2870.0
9 TraesCS6D01G342700 chr1D 91.566 1162 75 13 1781 2930 56039261 56038111 0.000000e+00 1581.0
10 TraesCS6D01G342700 chr1D 86.874 1257 137 10 507 1760 56040465 56039234 0.000000e+00 1382.0
11 TraesCS6D01G342700 chr2B 100.000 31 0 0 1 31 772122595 772122565 1.130000e-04 58.4
12 TraesCS6D01G342700 chr7B 97.059 34 0 1 1 33 317579385 317579352 4.080000e-04 56.5
13 TraesCS6D01G342700 chr5D 100.000 30 0 0 1 30 189184418 189184447 4.080000e-04 56.5
14 TraesCS6D01G342700 chr5D 100.000 30 0 0 1 30 533633451 533633422 4.080000e-04 56.5
15 TraesCS6D01G342700 chr5D 100.000 29 0 0 1 29 490159263 490159291 1.000000e-03 54.7
16 TraesCS6D01G342700 chr5D 100.000 29 0 0 1 29 496744065 496744093 1.000000e-03 54.7
17 TraesCS6D01G342700 chr7D 100.000 29 0 0 1 29 590221401 590221429 1.000000e-03 54.7
18 TraesCS6D01G342700 chr3A 100.000 29 0 0 1 29 514515075 514515047 1.000000e-03 54.7


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 TraesCS6D01G342700 chr6D 441809548 441812477 2929 True 5411.000000 5411 100.000 1 2930 1 chr6D.!!$R1 2929
1 TraesCS6D01G342700 chr6B 667798218 667801110 2892 True 4433.000000 4433 94.319 27 2930 1 chr6B.!!$R1 2903
2 TraesCS6D01G342700 chr6A 591088620 591091304 2684 True 4157.000000 4157 94.657 250 2930 1 chr6A.!!$R1 2680
3 TraesCS6D01G342700 chr6A 591206352 591208644 2292 True 803.666667 1786 87.895 688 2930 3 chr6A.!!$R3 2242
4 TraesCS6D01G342700 chr1A 54359668 54362056 2388 True 2870.000000 2870 88.356 507 2930 1 chr1A.!!$R1 2423
5 TraesCS6D01G342700 chr1D 56038111 56040465 2354 True 1481.500000 1581 89.220 507 2930 2 chr1D.!!$R1 2423

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
389 392 0.107508 CACACGATTGGCTCCTGGAT 60.108 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2330 0.439985 CTTGGATCGCTCACGTGTTG 59.56 55.0 16.51 10.93 41.18 3.33 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
23 24 4.662961 CGCGCGGGGCATCATCTA 62.663 66.667 24.84 0.00 43.84 1.98
24 25 2.740055 GCGCGGGGCATCATCTAG 60.740 66.667 8.83 0.00 42.87 2.43
25 26 2.737180 CGCGGGGCATCATCTAGT 59.263 61.111 0.00 0.00 0.00 2.57
35 36 7.499232 GCGGGGCATCATCTAGTTATTATATTT 59.501 37.037 0.00 0.00 0.00 1.40
56 57 1.208293 GAACACTCACCCTGATCCCTC 59.792 57.143 0.00 0.00 0.00 4.30
96 98 5.755409 ATCACCCTGACTACACATGTAAA 57.245 39.130 0.00 0.00 0.00 2.01
101 103 8.158132 TCACCCTGACTACACATGTAAATTTTA 58.842 33.333 0.00 0.00 0.00 1.52
242 244 4.017958 TGCTTTGGGGGTACATAAATCTGA 60.018 41.667 0.00 0.00 0.00 3.27
244 246 6.126332 TGCTTTGGGGGTACATAAATCTGATA 60.126 38.462 0.00 0.00 0.00 2.15
246 248 8.107095 GCTTTGGGGGTACATAAATCTGATATA 58.893 37.037 0.00 0.00 0.00 0.86
327 330 2.180946 AGTCAGCCCTGGATATGTGA 57.819 50.000 0.00 0.00 0.00 3.58
338 341 2.061773 GGATATGTGAGACCGCATTCG 58.938 52.381 0.00 0.00 42.85 3.34
389 392 0.107508 CACACGATTGGCTCCTGGAT 60.108 55.000 0.00 0.00 0.00 3.41
453 456 4.421131 ACCCAGCTAATCCTATGGTCTAG 58.579 47.826 0.00 0.00 0.00 2.43
476 479 3.275999 TGACTTGTCGTCTATGGATCGA 58.724 45.455 0.00 0.00 43.25 3.59
951 963 2.201210 CCCACCTGGCCAAAACCT 59.799 61.111 7.01 0.00 0.00 3.50
956 968 0.763986 ACCTGGCCAAAACCTGCAAT 60.764 50.000 7.01 0.00 0.00 3.56
987 999 6.973642 TCCATTTCTCATTTTATCCCTCTGT 58.026 36.000 0.00 0.00 0.00 3.41
988 1000 7.413446 TCCATTTCTCATTTTATCCCTCTGTT 58.587 34.615 0.00 0.00 0.00 3.16
989 1001 7.340232 TCCATTTCTCATTTTATCCCTCTGTTG 59.660 37.037 0.00 0.00 0.00 3.33
990 1002 7.417116 CCATTTCTCATTTTATCCCTCTGTTGG 60.417 40.741 0.00 0.00 0.00 3.77
991 1003 4.526970 TCTCATTTTATCCCTCTGTTGGC 58.473 43.478 0.00 0.00 0.00 4.52
992 1004 4.018506 TCTCATTTTATCCCTCTGTTGGCA 60.019 41.667 0.00 0.00 0.00 4.92
993 1005 4.016444 TCATTTTATCCCTCTGTTGGCAC 58.984 43.478 0.00 0.00 0.00 5.01
1404 1416 2.943690 GCTCACCATCGTCAGTAGTAGA 59.056 50.000 0.00 0.00 0.00 2.59
1533 1545 2.639065 GGGTCTTCGGCAATGTATCAA 58.361 47.619 0.00 0.00 0.00 2.57
1579 1591 0.247185 CAACAACATGGACATGGGGC 59.753 55.000 15.94 0.00 42.91 5.80
2247 2268 2.027073 CGTAAGTTGCGCCTGCTCA 61.027 57.895 4.18 0.00 43.34 4.26
2338 2359 3.056304 GAGCGATCCAAGTATGAAGAGC 58.944 50.000 0.00 0.00 0.00 4.09
2528 2555 4.687948 CGTCAGCTCCATCTTAATACATGG 59.312 45.833 0.00 2.96 41.04 3.66
2556 2583 6.471146 CATATATAAAGAGCTCCCAGTGCTT 58.529 40.000 10.93 0.00 41.30 3.91
2681 2720 3.350163 CAGACCAGGGCCCCCATT 61.350 66.667 21.43 0.00 38.92 3.16
2764 2877 2.680841 TGGAAATCTTTGGGCGAATACG 59.319 45.455 0.00 0.00 42.93 3.06
2811 2924 5.585820 TCCATACAACATGAGCGTACTTA 57.414 39.130 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.662961 TAGATGATGCCCCGCGCG 62.663 66.667 25.67 25.67 42.08 6.86
7 8 2.740055 CTAGATGATGCCCCGCGC 60.740 66.667 0.00 0.00 38.31 6.86
8 9 0.317160 TAACTAGATGATGCCCCGCG 59.683 55.000 0.00 0.00 0.00 6.46
9 10 2.770164 ATAACTAGATGATGCCCCGC 57.230 50.000 0.00 0.00 0.00 6.13
10 11 8.830580 CAAATATAATAACTAGATGATGCCCCG 58.169 37.037 0.00 0.00 0.00 5.73
11 12 9.905713 TCAAATATAATAACTAGATGATGCCCC 57.094 33.333 0.00 0.00 0.00 5.80
23 24 9.396022 CAGGGTGAGTGTTCAAATATAATAACT 57.604 33.333 0.00 0.00 34.49 2.24
24 25 9.391006 TCAGGGTGAGTGTTCAAATATAATAAC 57.609 33.333 0.00 0.00 34.49 1.89
35 36 0.984230 GGGATCAGGGTGAGTGTTCA 59.016 55.000 0.00 0.00 0.00 3.18
65 67 6.183361 TGTGTAGTCAGGGTGATTGTTCTTTA 60.183 38.462 0.00 0.00 0.00 1.85
128 130 2.497675 AGCTAAGCTAACTAGTGCTGCA 59.502 45.455 15.52 0.00 39.71 4.41
338 341 8.696175 CACTTTCATTTTTCCAATACGTTAACC 58.304 33.333 0.00 0.00 0.00 2.85
476 479 0.736325 GCACACGACTTATGGACGCT 60.736 55.000 0.00 0.00 0.00 5.07
486 489 1.016130 GCACTGCTATGCACACGACT 61.016 55.000 7.76 0.00 45.39 4.18
487 490 1.421485 GCACTGCTATGCACACGAC 59.579 57.895 7.76 0.00 45.39 4.34
616 619 6.861065 ATTGTACATCATCCGATTAACCAC 57.139 37.500 0.00 0.00 0.00 4.16
951 963 9.947433 AAAATGAGAAATGGAAATTAGATTGCA 57.053 25.926 0.00 0.00 35.04 4.08
987 999 1.818959 GAGCCATTGCCAAGTGCCAA 61.819 55.000 0.00 0.00 40.16 4.52
988 1000 2.203669 AGCCATTGCCAAGTGCCA 60.204 55.556 0.00 0.00 40.16 4.92
989 1001 2.575461 GAGCCATTGCCAAGTGCC 59.425 61.111 0.00 0.00 40.16 5.01
990 1002 2.180017 CGAGCCATTGCCAAGTGC 59.820 61.111 0.00 0.00 38.69 4.40
991 1003 2.144833 TTGCGAGCCATTGCCAAGTG 62.145 55.000 0.00 0.00 38.69 3.16
992 1004 1.870055 CTTGCGAGCCATTGCCAAGT 61.870 55.000 0.00 0.00 38.69 3.16
993 1005 1.153901 CTTGCGAGCCATTGCCAAG 60.154 57.895 0.00 0.00 38.69 3.61
1193 1205 4.399219 TCTGTACCTATTCAGGAGATCCG 58.601 47.826 0.00 0.00 45.91 4.18
1551 1563 2.222445 GTCCATGTTGTTGGTGACGTAC 59.778 50.000 0.00 0.00 38.01 3.67
1579 1591 1.065102 CTGCTGATTCATGGCGAAAGG 59.935 52.381 0.00 0.00 37.12 3.11
2309 2330 0.439985 CTTGGATCGCTCACGTGTTG 59.560 55.000 16.51 10.93 41.18 3.33
2338 2359 4.261801 AGATACGTCAAAATTGGAGTGGG 58.738 43.478 0.00 0.00 0.00 4.61
2418 2445 9.598517 TCAATTGTTCTTCTTTTTGTGCTAAAT 57.401 25.926 5.13 0.00 0.00 1.40
2422 2449 7.413328 GCTTTCAATTGTTCTTCTTTTTGTGCT 60.413 33.333 5.13 0.00 0.00 4.40
2423 2450 6.684131 GCTTTCAATTGTTCTTCTTTTTGTGC 59.316 34.615 5.13 0.00 0.00 4.57
2528 2555 5.165961 TGGGAGCTCTTTATATATGGTGC 57.834 43.478 14.64 0.00 0.00 5.01
2556 2583 2.816087 GGCTCCGTACTACAATATCCGA 59.184 50.000 0.00 0.00 0.00 4.55
2618 2657 6.713450 ACGGTATGGTTTTGACAAATAGAAGT 59.287 34.615 0.50 0.00 0.00 3.01
2749 2862 2.754946 AACTCGTATTCGCCCAAAGA 57.245 45.000 0.00 0.00 36.96 2.52


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

AutoCloner maintained by Alex Coulton.