Multiple sequence alignment - TraesCS7D01G346500

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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 TraesCS7D01G346500 chr7D 100.000 3701 0 0 1 3701 446211523 446207823 0.000000e+00 6835.0
1 TraesCS7D01G346500 chr7B 96.961 3718 81 8 1 3701 462534642 462538344 0.000000e+00 6211.0
2 TraesCS7D01G346500 chr7B 72.917 192 44 7 1397 1584 718823487 718823300 3.990000e-05 60.2
3 TraesCS7D01G346500 chr7A 92.907 3440 212 7 124 3548 496778739 496775317 0.000000e+00 4972.0
4 TraesCS7D01G346500 chr7A 77.500 120 21 5 886 1003 287905495 287905380 2.390000e-07 67.6
5 TraesCS7D01G346500 chr7A 83.333 60 10 0 1525 1584 73768648 73768589 5.160000e-04 56.5
6 TraesCS7D01G346500 chr1D 94.483 145 2 5 1 144 254396352 254396213 6.220000e-53 219.0
7 TraesCS7D01G346500 chrUn 96.899 129 3 1 1 129 216516845 216516718 8.050000e-52 215.0
8 TraesCS7D01G346500 chrUn 96.899 129 3 1 1 129 346594736 346594609 8.050000e-52 215.0
9 TraesCS7D01G346500 chrUn 96.899 129 3 1 1 129 436278398 436278271 8.050000e-52 215.0
10 TraesCS7D01G346500 chrUn 73.481 181 44 4 1391 1569 65763530 65763708 8.580000e-07 65.8
11 TraesCS7D01G346500 chr6D 96.899 129 3 1 1 129 14944717 14944590 8.050000e-52 215.0
12 TraesCS7D01G346500 chr6D 97.619 126 2 1 1 126 168256684 168256808 8.050000e-52 215.0
13 TraesCS7D01G346500 chr5D 97.619 126 2 1 1 126 6190698 6190822 8.050000e-52 215.0
14 TraesCS7D01G346500 chr4D 97.619 126 2 1 1 126 19930332 19930456 8.050000e-52 215.0
15 TraesCS7D01G346500 chr6A 73.822 191 44 5 1397 1584 598879054 598878867 1.840000e-08 71.3
16 TraesCS7D01G346500 chr6A 85.075 67 9 1 2162 2227 524804818 524804752 2.390000e-07 67.6
17 TraesCS7D01G346500 chr4B 74.033 181 43 4 1391 1569 520274188 520274366 1.840000e-08 71.3
18 TraesCS7D01G346500 chr1A 73.481 181 44 4 1391 1569 9151045 9151223 8.580000e-07 65.8
19 TraesCS7D01G346500 chr1A 73.481 181 44 4 1391 1569 50938531 50938709 8.580000e-07 65.8


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 TraesCS7D01G346500 chr7D 446207823 446211523 3700 True 6835 6835 100.000 1 3701 1 chr7D.!!$R1 3700
1 TraesCS7D01G346500 chr7B 462534642 462538344 3702 False 6211 6211 96.961 1 3701 1 chr7B.!!$F1 3700
2 TraesCS7D01G346500 chr7A 496775317 496778739 3422 True 4972 4972 92.907 124 3548 1 chr7A.!!$R3 3424

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
462 463 1.203052 CATCATTTCCCAGTGGTGCAC 59.797 52.381 8.80 8.8 34.10 4.57 F
1148 1164 0.469917 GATTTGGATCCTCCTCCGCA 59.530 55.000 14.23 0.0 38.21 5.69 F
2264 2280 1.037579 GGTGCTTCTAATGGGGCCAC 61.038 60.000 4.39 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1713 0.961019 GATTTGCACAACCTGCCAGA 59.039 50.000 0.00 0.0 46.51 3.86 R
2595 2626 1.371467 TCCTCTTGCTGAATCCCCAA 58.629 50.000 0.00 0.0 0.00 4.12 R
3287 3320 8.937207 AAAGGTACCTCATCTAGATAATACGT 57.063 34.615 16.64 0.0 0.00 3.57 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
82 83 9.533831 AAGACAATGTTCCATACTAAAGGATTT 57.466 29.630 0.00 0.00 43.42 2.17
462 463 1.203052 CATCATTTCCCAGTGGTGCAC 59.797 52.381 8.80 8.80 34.10 4.57
465 466 1.619827 CATTTCCCAGTGGTGCACATT 59.380 47.619 20.43 0.00 36.74 2.71
778 779 1.948611 GCCGGACAGCTGAAATAACCA 60.949 52.381 23.35 0.00 0.00 3.67
867 868 6.909550 ATAAATTCCTGTGGCTGTGTAAAA 57.090 33.333 0.00 0.00 0.00 1.52
1055 1056 3.144120 CTCTGGACCCGCTGGATCG 62.144 68.421 0.00 0.00 34.81 3.69
1148 1164 0.469917 GATTTGGATCCTCCTCCGCA 59.530 55.000 14.23 0.00 38.21 5.69
1266 1282 1.090052 GGGTTGGAGATCCTTTCGCG 61.090 60.000 0.00 0.00 36.82 5.87
1697 1713 4.974438 TGTCGAGGGGGCTTGGGT 62.974 66.667 0.00 0.00 0.00 4.51
1747 1763 2.298163 GAGTTCACGGTAGTCTTCCCAA 59.702 50.000 0.00 0.00 0.00 4.12
2150 2166 1.425066 TCAGAACAATGGCAAGGGTCT 59.575 47.619 3.73 3.73 0.00 3.85
2264 2280 1.037579 GGTGCTTCTAATGGGGCCAC 61.038 60.000 4.39 0.00 0.00 5.01
2296 2312 2.493273 GAATTCGGTGCCTCCCCCAA 62.493 60.000 0.00 0.00 0.00 4.12
2595 2626 3.083349 TGGGCTAGCCATGCGTCT 61.083 61.111 34.09 0.00 37.98 4.18
2600 2631 1.524621 CTAGCCATGCGTCTTGGGG 60.525 63.158 11.69 0.00 34.66 4.96
2665 2696 2.347490 GCAAGAAGGCGTCCAGGA 59.653 61.111 0.00 0.00 0.00 3.86
2839 2870 2.648059 CACTTATCTCCAAGGCCAAGG 58.352 52.381 5.01 6.28 0.00 3.61
2929 2960 0.170116 CTCTCTCGAAAGCGCAGAGT 59.830 55.000 18.05 0.00 40.00 3.24
3051 3082 3.081061 TGATTGTGGGGTTGATTCTTCG 58.919 45.455 0.00 0.00 0.00 3.79
3104 3135 2.237143 TCATTCAATCGAAGGAGCTGGT 59.763 45.455 0.00 0.00 37.04 4.00
3287 3320 2.095466 CGCGTGGCCAAATCTTAGAAAA 60.095 45.455 7.24 0.00 0.00 2.29
3289 3322 3.488489 CGTGGCCAAATCTTAGAAAACG 58.512 45.455 7.24 0.00 0.00 3.60
3628 3661 2.513897 GTATGGGCCGGCAGACAC 60.514 66.667 30.85 16.45 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.324512 GTCTTTTCCAAGTAAAAACCCCCTAA 59.675 38.462 0.00 0.00 0.00 2.69
40 41 7.045416 ACATTGTCTTTTCCAAGTAAAAACCC 58.955 34.615 0.00 0.00 0.00 4.11
778 779 2.607750 ACTGGACCGGCACCATCT 60.608 61.111 19.07 7.01 36.79 2.90
867 868 3.036429 GCCAGGGATCCAGCGAACT 62.036 63.158 15.23 0.00 0.00 3.01
1067 1068 0.390866 CAGATCTTGCTCACTGCGGT 60.391 55.000 0.00 0.00 46.63 5.68
1148 1164 1.299541 CTGTTGCTTGTTCCACGACT 58.700 50.000 0.00 0.00 0.00 4.18
1266 1282 3.057526 ACGGCTTATGCTTTGGTTTCTTC 60.058 43.478 0.13 0.00 39.59 2.87
1697 1713 0.961019 GATTTGCACAACCTGCCAGA 59.039 50.000 0.00 0.00 46.51 3.86
1747 1763 2.175499 CCATCCATAACATGTCCAGGGT 59.825 50.000 0.00 0.00 0.00 4.34
1782 1798 3.460340 TGTTGAGGGGAAGGAACAACTTA 59.540 43.478 0.00 0.00 40.59 2.24
2150 2166 2.777094 TGTCTTTGTCATCGCCATCAA 58.223 42.857 0.00 0.00 0.00 2.57
2232 2248 3.508840 GCACCGCCATCCTTTCCG 61.509 66.667 0.00 0.00 0.00 4.30
2264 2280 1.434696 GAATTCACCGCCATGGCAG 59.565 57.895 34.93 27.28 43.94 4.85
2453 2469 2.182030 CGGACAGCGGAGAGAACC 59.818 66.667 0.00 0.00 0.00 3.62
2595 2626 1.371467 TCCTCTTGCTGAATCCCCAA 58.629 50.000 0.00 0.00 0.00 4.12
2600 2631 3.269178 CCAGAGTTCCTCTTGCTGAATC 58.731 50.000 0.00 0.00 38.99 2.52
2698 2729 2.285024 CCACCGGACGGGGAGTTTA 61.285 63.158 15.72 0.00 42.48 2.01
2839 2870 2.818274 CGTAGCCGCCTTGGAACC 60.818 66.667 0.00 0.00 42.00 3.62
3287 3320 8.937207 AAAGGTACCTCATCTAGATAATACGT 57.063 34.615 16.64 0.00 0.00 3.57
3628 3661 8.951722 TTCTCCCAAGAAATCCACAGAATGGG 62.952 46.154 0.00 0.00 42.71 4.00


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

AutoCloner maintained by Alex Coulton.