Multiple sequence alignment - TraesCS7D01G253200

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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 TraesCS7D01G253200 chr7D 100.000 3143 0 0 1 3143 229768383 229771525 0.000000e+00 5805.0
1 TraesCS7D01G253200 chr7D 100.000 34 0 0 3059 3092 270772179 270772146 2.620000e-06 63.9
2 TraesCS7D01G253200 chr7B 94.432 3089 82 28 125 3143 200021268 200024336 0.000000e+00 4669.0
3 TraesCS7D01G253200 chr7B 82.278 316 26 9 2305 2597 742228452 742228760 2.420000e-61 246.0
4 TraesCS7D01G253200 chr7B 96.063 127 5 0 1 127 200021013 200021139 1.140000e-49 207.0
5 TraesCS7D01G253200 chr7A 94.436 2498 60 21 16 2449 241365952 241368434 0.000000e+00 3770.0
6 TraesCS7D01G253200 chr7A 93.906 640 27 5 2511 3143 241368433 241369067 0.000000e+00 955.0
7 TraesCS7D01G253200 chr2D 92.420 1781 92 18 551 2305 324016538 324014775 0.000000e+00 2501.0
8 TraesCS7D01G253200 chr2D 93.443 61 1 2 1165 1222 324036972 324037032 1.550000e-13 87.9
9 TraesCS7D01G253200 chr2B 95.245 1325 48 7 864 2188 392530682 392529373 0.000000e+00 2084.0
10 TraesCS7D01G253200 chr2B 88.889 279 27 3 551 828 392537434 392537159 1.080000e-89 340.0
11 TraesCS7D01G253200 chr2B 87.582 153 15 3 2163 2313 392524522 392524372 1.160000e-39 174.0
12 TraesCS7D01G253200 chr5A 91.667 540 36 6 2 537 106109253 106108719 0.000000e+00 739.0
13 TraesCS7D01G253200 chr5A 91.912 272 21 1 2595 2865 8649876 8649605 2.290000e-101 379.0
14 TraesCS7D01G253200 chr3D 87.956 274 30 3 2595 2867 546211351 546211622 1.410000e-83 320.0
15 TraesCS7D01G253200 chr6A 87.405 262 32 1 2595 2855 4807593 4807854 1.830000e-77 300.0
16 TraesCS7D01G253200 chr6B 84.672 274 33 6 2595 2867 1328441 1328176 6.680000e-67 265.0
17 TraesCS7D01G253200 chr5B 89.583 144 8 3 2309 2450 511783600 511783462 3.220000e-40 176.0
18 TraesCS7D01G253200 chr1B 77.561 205 43 3 1159 1360 389980342 389980546 1.530000e-23 121.0
19 TraesCS7D01G253200 chr1D 77.184 206 42 5 1159 1360 288546048 288546252 7.120000e-22 115.0
20 TraesCS7D01G253200 chr3B 98.039 51 1 0 2444 2494 584195527 584195577 4.320000e-14 89.8
21 TraesCS7D01G253200 chrUn 88.571 70 8 0 1165 1234 90726739 90726670 5.590000e-13 86.1
22 TraesCS7D01G253200 chr2A 85.542 83 10 2 1156 1237 711510066 711509985 5.590000e-13 86.1


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 TraesCS7D01G253200 chr7D 229768383 229771525 3142 False 5805.0 5805 100.0000 1 3143 1 chr7D.!!$F1 3142
1 TraesCS7D01G253200 chr7B 200021013 200024336 3323 False 2438.0 4669 95.2475 1 3143 2 chr7B.!!$F2 3142
2 TraesCS7D01G253200 chr7A 241365952 241369067 3115 False 2362.5 3770 94.1710 16 3143 2 chr7A.!!$F1 3127
3 TraesCS7D01G253200 chr2D 324014775 324016538 1763 True 2501.0 2501 92.4200 551 2305 1 chr2D.!!$R1 1754
4 TraesCS7D01G253200 chr2B 392529373 392530682 1309 True 2084.0 2084 95.2450 864 2188 1 chr2B.!!$R2 1324
5 TraesCS7D01G253200 chr5A 106108719 106109253 534 True 739.0 739 91.6670 2 537 1 chr5A.!!$R2 535

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
52 53 1.364626 CTCAGTGTGAATGGAGCGCC 61.365 60.000 2.29 0.0 0.00 6.53 F
1398 1631 1.192980 GACGCCGTCAATTTTGTACGT 59.807 47.619 13.23 0.0 33.23 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2301 0.245266 TCATAGCGACGGCAAAGTCA 59.755 50.0 0.0 0.0 43.41 3.41 R
2221 2502 0.948678 GCACCCTGCGTGTAGAAAAA 59.051 50.0 0.0 0.0 44.97 1.94 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
40 41 5.171339 AGAAGAATATGCCAACTCAGTGT 57.829 39.130 0.00 0.00 0.00 3.55
41 42 4.940046 AGAAGAATATGCCAACTCAGTGTG 59.060 41.667 0.00 0.00 0.00 3.82
46 47 1.608055 TGCCAACTCAGTGTGAATGG 58.392 50.000 13.73 13.73 36.83 3.16
52 53 1.364626 CTCAGTGTGAATGGAGCGCC 61.365 60.000 2.29 0.00 0.00 6.53
492 647 2.666994 GTGTTAGCCGACTGAAAGCTAC 59.333 50.000 0.00 0.00 38.77 3.58
513 669 1.370064 GCCTGGTATTATCGGGCGT 59.630 57.895 11.02 0.00 45.38 5.68
642 817 4.839796 ACATACAAGAACAAACGAAACGG 58.160 39.130 0.00 0.00 0.00 4.44
668 843 4.409218 CAGCGCCGCAAAGCACAT 62.409 61.111 13.36 0.00 35.48 3.21
847 1051 1.738099 ATGGCGAGCACGAACTGTC 60.738 57.895 8.01 0.00 42.66 3.51
958 1191 1.371467 TCCATTCCCTCTTCCTTGCA 58.629 50.000 0.00 0.00 0.00 4.08
1077 1310 1.439353 CGCAGGCCGATTTGCAGTAT 61.439 55.000 14.39 0.00 40.28 2.12
1397 1630 1.780636 CGACGCCGTCAATTTTGTACG 60.781 52.381 18.40 0.00 34.14 3.67
1398 1631 1.192980 GACGCCGTCAATTTTGTACGT 59.807 47.619 13.23 0.00 33.23 3.57
1399 1632 2.402305 ACGCCGTCAATTTTGTACGTA 58.598 42.857 0.00 0.00 33.23 3.57
1400 1633 2.409378 ACGCCGTCAATTTTGTACGTAG 59.591 45.455 0.00 8.62 33.23 3.51
1714 1969 6.946340 ACCTGACTGAACATGTCATACAATA 58.054 36.000 0.00 0.00 42.57 1.90
2036 2291 1.587933 AACGCCTCCTCTCTCGACAC 61.588 60.000 0.00 0.00 0.00 3.67
2046 2301 0.523966 CTCTCGACACCTTCTTCGCT 59.476 55.000 0.00 0.00 35.15 4.93
2061 2316 3.044305 GCTGACTTTGCCGTCGCT 61.044 61.111 0.00 0.00 36.71 4.93
2094 2349 2.925170 AGGGCTGGCGTTCTCACT 60.925 61.111 0.00 0.00 0.00 3.41
2221 2502 5.584649 TGATTTGCTACTCGATCGGAATTTT 59.415 36.000 16.41 0.00 0.00 1.82
2222 2503 5.873179 TTTGCTACTCGATCGGAATTTTT 57.127 34.783 16.41 0.00 0.00 1.94
2463 2747 1.821136 GCCCTTGATCAAAAGTGAGGG 59.179 52.381 19.70 19.70 38.18 4.30
2493 2777 4.502604 GGCTATTGACCGGTCATTTAGCTA 60.503 45.833 42.08 29.72 43.60 3.32
2515 2801 3.005367 AGCCCAACCATTTAACTTTCACG 59.995 43.478 0.00 0.00 0.00 4.35
2562 2848 2.172505 AGTACATGGGCCGATTGATTCA 59.827 45.455 0.00 0.00 0.00 2.57
2784 3071 1.144936 GCTAGCACGCCCTCATCTT 59.855 57.895 10.63 0.00 0.00 2.40
2867 3159 1.591863 GGTACGCATCGAGGGAAGC 60.592 63.158 0.00 0.00 33.67 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.747460 GCACAGGCGCTCCATTCA 60.747 61.111 7.64 0.00 33.74 2.57
41 42 0.815213 TATGCACAGGCGCTCCATTC 60.815 55.000 7.64 0.00 45.35 2.67
46 47 0.249615 TCAGATATGCACAGGCGCTC 60.250 55.000 7.64 0.00 45.35 5.03
52 53 9.880064 CTCATAAATTTCTTCAGATATGCACAG 57.120 33.333 0.00 0.00 0.00 3.66
168 300 3.885484 AACTTGAAATCAGACACAGCG 57.115 42.857 0.00 0.00 0.00 5.18
338 478 1.271856 TCCTGAACCATAACCGCTCA 58.728 50.000 0.00 0.00 0.00 4.26
392 536 6.183360 CCGCTGATACAATGGTAAAGCTTAAA 60.183 38.462 13.59 0.00 39.38 1.52
393 537 5.295787 CCGCTGATACAATGGTAAAGCTTAA 59.704 40.000 13.59 0.00 39.38 1.85
492 647 1.135083 CGCCCGATAATACCAGGCTAG 60.135 57.143 0.00 0.00 41.60 3.42
556 731 2.750237 GCCCGGCGAATTCCTTGT 60.750 61.111 9.30 0.00 0.00 3.16
642 817 2.962253 GCGGCGCTGGATACTGTC 60.962 66.667 26.86 0.00 37.92 3.51
958 1191 1.136147 GTACGCACGGTCTGATCGT 59.864 57.895 10.68 10.68 41.93 3.73
974 1207 4.023980 AGAGGACTCGATGAACCAATGTA 58.976 43.478 0.00 0.00 34.09 2.29
1077 1310 2.730069 CACGTCGTGTTGTAGTAACCA 58.270 47.619 17.30 0.00 0.00 3.67
1397 1630 2.365408 AACAGCAAGGAGTACGCTAC 57.635 50.000 0.00 0.00 33.82 3.58
1398 1631 3.087031 AGTAACAGCAAGGAGTACGCTA 58.913 45.455 0.00 0.00 33.82 4.26
1399 1632 1.893801 AGTAACAGCAAGGAGTACGCT 59.106 47.619 0.00 0.00 36.10 5.07
1400 1633 2.365408 AGTAACAGCAAGGAGTACGC 57.635 50.000 0.00 0.00 0.00 4.42
1648 1893 4.622199 CGCGATCGAGTTATGAATGATTG 58.378 43.478 21.57 0.00 38.10 2.67
1714 1969 1.527611 CCGCTGCATCCATCCATGT 60.528 57.895 0.00 0.00 0.00 3.21
2036 2291 0.519077 GGCAAAGTCAGCGAAGAAGG 59.481 55.000 0.00 0.00 0.00 3.46
2046 2301 0.245266 TCATAGCGACGGCAAAGTCA 59.755 50.000 0.00 0.00 43.41 3.41
2061 2316 1.479205 GCCCTGCCCATGTTGATCATA 60.479 52.381 0.00 0.00 34.67 2.15
2094 2349 3.329542 GATCTCGCCTTGGGTGCCA 62.330 63.158 0.00 0.00 32.51 4.92
2177 2434 1.972223 AGTCGACCGGTCAGACCAG 60.972 63.158 34.96 21.40 38.47 4.00
2221 2502 0.948678 GCACCCTGCGTGTAGAAAAA 59.051 50.000 0.00 0.00 44.97 1.94
2222 2503 2.624169 GCACCCTGCGTGTAGAAAA 58.376 52.632 0.00 0.00 44.97 2.29
2463 2747 2.876550 GACCGGTCAATAGCCCATTAAC 59.123 50.000 29.75 0.00 0.00 2.01
2493 2777 3.005367 CGTGAAAGTTAAATGGTTGGGCT 59.995 43.478 0.00 0.00 0.00 5.19
2721 3008 2.729479 CGCCTCCTCATGTCTGGCT 61.729 63.158 15.43 0.00 41.25 4.75
2784 3071 1.621814 CGTACCCTGGGAACAAGAGAA 59.378 52.381 22.23 0.00 42.06 2.87


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

AutoCloner maintained by Alex Coulton.