Multiple sequence alignment - TraesCS3B01G606600

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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 TraesCS3B01G606600 chr3B 100.000 3405 0 0 1 3405 825643346 825646750 0.000000e+00 6288.0
1 TraesCS3B01G606600 chr3B 79.464 3433 591 73 1 3398 88989074 88992427 0.000000e+00 2329.0
2 TraesCS3B01G606600 chr3B 100.000 69 0 0 3700 3768 825647045 825647113 1.100000e-25 128.0
3 TraesCS3B01G606600 chr7B 96.128 3409 126 6 1 3405 724918574 724921980 0.000000e+00 5559.0
4 TraesCS3B01G606600 chr7B 95.805 3409 138 5 1 3405 724844896 724848303 0.000000e+00 5498.0
5 TraesCS3B01G606600 chr7B 94.927 3410 149 9 1 3405 719673559 719670169 0.000000e+00 5317.0
6 TraesCS3B01G606600 chr7B 96.577 2425 80 3 984 3405 724881619 724884043 0.000000e+00 4015.0
7 TraesCS3B01G606600 chr7B 94.686 2296 108 6 1113 3405 715908005 715905721 0.000000e+00 3552.0
8 TraesCS3B01G606600 chr7B 97.101 69 2 0 3700 3768 724848330 724848398 2.380000e-22 117.0
9 TraesCS3B01G606600 chr7B 97.101 69 2 0 3700 3768 724884070 724884138 2.380000e-22 117.0
10 TraesCS3B01G606600 chr7B 97.101 69 2 0 3700 3768 724922001 724922069 2.380000e-22 117.0
11 TraesCS3B01G606600 chr6A 95.279 3410 152 8 1 3405 1196915 1193510 0.000000e+00 5397.0
12 TraesCS3B01G606600 chr1B 94.339 3409 170 8 1 3405 636858080 636854691 0.000000e+00 5204.0
13 TraesCS3B01G606600 chr1B 98.485 66 1 0 3703 3768 677071443 677071508 2.380000e-22 117.0
14 TraesCS3B01G606600 chr1B 94.203 69 4 0 3700 3768 636854681 636854613 5.150000e-19 106.0
15 TraesCS3B01G606600 chr4A 93.827 3418 195 10 1 3405 716206928 716210342 0.000000e+00 5129.0
16 TraesCS3B01G606600 chr4A 93.739 3402 189 10 1 3379 717118465 717115065 0.000000e+00 5081.0
17 TraesCS3B01G606600 chr4A 97.101 69 2 0 3700 3768 716210353 716210421 2.380000e-22 117.0
18 TraesCS3B01G606600 chr4A 95.652 69 3 0 3700 3768 717115056 717114988 1.110000e-20 111.0
19 TraesCS3B01G606600 chr4B 91.208 3412 292 8 1 3405 663682264 663678854 0.000000e+00 4632.0
20 TraesCS3B01G606600 chrUn 97.101 69 2 0 3700 3768 223484112 223484180 2.380000e-22 117.0
21 TraesCS3B01G606600 chrUn 97.436 39 1 0 3730 3768 370491834 370491872 2.430000e-07 67.6


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 TraesCS3B01G606600 chr3B 825643346 825647113 3767 False 3208.0 6288 100.0000 1 3768 2 chr3B.!!$F2 3767
1 TraesCS3B01G606600 chr3B 88989074 88992427 3353 False 2329.0 2329 79.4640 1 3398 1 chr3B.!!$F1 3397
2 TraesCS3B01G606600 chr7B 719670169 719673559 3390 True 5317.0 5317 94.9270 1 3405 1 chr7B.!!$R2 3404
3 TraesCS3B01G606600 chr7B 715905721 715908005 2284 True 3552.0 3552 94.6860 1113 3405 1 chr7B.!!$R1 2292
4 TraesCS3B01G606600 chr7B 724918574 724922069 3495 False 2838.0 5559 96.6145 1 3768 2 chr7B.!!$F3 3767
5 TraesCS3B01G606600 chr7B 724844896 724848398 3502 False 2807.5 5498 96.4530 1 3768 2 chr7B.!!$F1 3767
6 TraesCS3B01G606600 chr7B 724881619 724884138 2519 False 2066.0 4015 96.8390 984 3768 2 chr7B.!!$F2 2784
7 TraesCS3B01G606600 chr6A 1193510 1196915 3405 True 5397.0 5397 95.2790 1 3405 1 chr6A.!!$R1 3404
8 TraesCS3B01G606600 chr1B 636854613 636858080 3467 True 2655.0 5204 94.2710 1 3768 2 chr1B.!!$R1 3767
9 TraesCS3B01G606600 chr4A 716206928 716210421 3493 False 2623.0 5129 95.4640 1 3768 2 chr4A.!!$F1 3767
10 TraesCS3B01G606600 chr4A 717114988 717118465 3477 True 2596.0 5081 94.6955 1 3768 2 chr4A.!!$R1 3767
11 TraesCS3B01G606600 chr4B 663678854 663682264 3410 True 4632.0 4632 91.2080 1 3405 1 chr4B.!!$R1 3404

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
975 1001 0.032678 CATCTATCCAGCGCCGAAGT 59.967 55.0 2.29 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2911 2992 1.208052 AGATGGTGGATCAACAGTCGG 59.792 52.381 1.86 0.0 33.31 4.79 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
86 87 2.609491 GCGGTCGACTGGATTATATGCA 60.609 50.000 25.20 0.00 0.00 3.96
228 231 3.937079 ACTGGTAACGCCTTACATAAAGC 59.063 43.478 7.72 0.00 42.51 3.51
295 299 0.178921 AGTGGCTCTTGGACTCCTGA 60.179 55.000 0.00 0.00 0.00 3.86
464 488 1.780309 TCATTAGCCCCCGAATGGATT 59.220 47.619 0.00 0.00 35.54 3.01
622 646 1.026584 TCGAGTGAACTCCGTGAACA 58.973 50.000 4.90 0.00 39.79 3.18
662 686 4.101119 ACGGATCGGAGGAAATCTGTTATT 59.899 41.667 7.35 0.00 38.10 1.40
677 701 5.297547 TCTGTTATTTGACGAGTTGCTCTT 58.702 37.500 0.00 0.00 0.00 2.85
678 702 5.758296 TCTGTTATTTGACGAGTTGCTCTTT 59.242 36.000 0.00 0.00 0.00 2.52
715 739 2.735151 GGGATCCGAATTTTGGGAAGT 58.265 47.619 5.45 0.00 38.59 3.01
744 768 1.959226 GAGAAAACCGCGGCACTCA 60.959 57.895 28.58 0.00 0.00 3.41
910 935 1.930371 GCATTTTGAACAGTGCGACCC 60.930 52.381 0.00 0.00 0.00 4.46
961 987 0.382158 CTCGCCACGCTCTTCATCTA 59.618 55.000 0.00 0.00 0.00 1.98
975 1001 0.032678 CATCTATCCAGCGCCGAAGT 59.967 55.000 2.29 0.00 0.00 3.01
995 1021 4.699522 GGAACTTGCCTCGCCGGT 62.700 66.667 1.90 0.00 34.25 5.28
1303 1329 0.392998 TTCTCTGCCGCCAAATCCTC 60.393 55.000 0.00 0.00 0.00 3.71
1415 1441 2.478894 GCGAGAATTTCTTCGGTTGTCA 59.521 45.455 15.25 0.00 36.45 3.58
1453 1479 7.497249 GTCTCTTCAAGCACATATTCACCTATT 59.503 37.037 0.00 0.00 0.00 1.73
1488 1514 2.403252 AGAAAACGAGCCCGAATGAT 57.597 45.000 0.00 0.00 39.50 2.45
1509 1535 3.736094 TGAGAGGACCCAAGTAATCCAT 58.264 45.455 0.00 0.00 34.73 3.41
1619 1660 2.582052 CTGGTTTTACTGCCAAGACCA 58.418 47.619 5.46 5.46 39.61 4.02
1620 1661 2.582052 TGGTTTTACTGCCAAGACCAG 58.418 47.619 2.27 0.00 37.66 4.00
1621 1662 1.269723 GGTTTTACTGCCAAGACCAGC 59.730 52.381 0.00 0.00 33.81 4.85
1622 1663 1.269723 GTTTTACTGCCAAGACCAGCC 59.730 52.381 0.00 0.00 33.65 4.85
1623 1664 0.605319 TTTACTGCCAAGACCAGCCG 60.605 55.000 0.00 0.00 33.65 5.52
1624 1665 1.476845 TTACTGCCAAGACCAGCCGA 61.477 55.000 0.00 0.00 33.65 5.54
1625 1666 1.264749 TACTGCCAAGACCAGCCGAT 61.265 55.000 0.00 0.00 33.65 4.18
1626 1667 2.046023 TGCCAAGACCAGCCGATG 60.046 61.111 0.00 0.00 0.00 3.84
1627 1668 3.512516 GCCAAGACCAGCCGATGC 61.513 66.667 0.00 0.00 37.95 3.91
1628 1669 2.825836 CCAAGACCAGCCGATGCC 60.826 66.667 0.00 0.00 38.69 4.40
1629 1670 3.197790 CAAGACCAGCCGATGCCG 61.198 66.667 0.00 0.00 38.69 5.69
2013 2054 5.535406 AGACCAGGTATAACCACTTATCTCG 59.465 44.000 0.00 0.00 41.95 4.04
2030 2071 0.969149 TCGGACTGTGATTCTGCTGT 59.031 50.000 0.00 0.00 0.00 4.40
2140 2182 2.281484 GGGCGCAGGAAACAGTCA 60.281 61.111 10.83 0.00 0.00 3.41
2421 2464 1.439858 CGAGCGACGTCGTCAAAGA 60.440 57.895 35.48 0.00 42.22 2.52
2815 2896 4.069869 GCAAGGCTGCTCAAGTCA 57.930 55.556 0.00 0.00 45.74 3.41
2911 2992 2.125793 GTACCCGACCCACTTCGC 60.126 66.667 0.00 0.00 37.70 4.70
2954 3035 0.466543 TTTGCTACACACCACGTCCT 59.533 50.000 0.00 0.00 0.00 3.85
3015 3096 1.271982 GCAGGGATCATGATGGAGCAT 60.272 52.381 14.30 0.00 0.00 3.79
3728 3834 2.257353 GGCTGACCGCTGACAATTT 58.743 52.632 0.00 0.00 39.13 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 1.834896 TCGCACCCCTGTAACACATAT 59.165 47.619 0.00 0.00 0.00 1.78
295 299 1.208052 CATGAAGACCCACTCGACCAT 59.792 52.381 0.00 0.00 0.00 3.55
464 488 2.634940 CTCCTTCCTCACTCAAACCTCA 59.365 50.000 0.00 0.00 0.00 3.86
622 646 0.249073 CGTCGCTCGGAAATCCTCAT 60.249 55.000 0.00 0.00 35.71 2.90
662 686 2.325583 ACCAAAGAGCAACTCGTCAA 57.674 45.000 0.00 0.00 35.36 3.18
744 768 2.029828 GCGTCATCGTCTTATCCCATCT 60.030 50.000 0.00 0.00 39.49 2.90
910 935 1.388547 CGGAGAGAGGAGAAGTCTGG 58.611 60.000 0.00 0.00 0.00 3.86
961 987 2.509336 CGAACTTCGGCGCTGGAT 60.509 61.111 17.88 0.00 36.00 3.41
975 1001 2.358247 GGCGAGGCAAGTTCCGAA 60.358 61.111 0.00 0.00 0.00 4.30
995 1021 3.198635 GGTCTTCTCCTTCACCATGATCA 59.801 47.826 0.00 0.00 0.00 2.92
1237 1263 1.694696 GAGGACACACTCACCCTCTTT 59.305 52.381 0.00 0.00 41.40 2.52
1303 1329 4.753516 AGTTCAAAAACCCCCAGAAAAG 57.246 40.909 0.00 0.00 35.92 2.27
1415 1441 2.113243 GAAGAGACCCCAGTGCGGTT 62.113 60.000 0.00 0.00 32.27 4.44
1453 1479 1.328279 TTCTTCACCGTCTGAGAGCA 58.672 50.000 0.00 0.00 0.00 4.26
1488 1514 3.199442 TGGATTACTTGGGTCCTCTCA 57.801 47.619 0.00 0.00 33.15 3.27
1509 1535 1.687840 CCCGAGTCCCCCACACATA 60.688 63.158 0.00 0.00 0.00 2.29
1630 1671 4.459089 GAGCCCAGTCGACTGCCC 62.459 72.222 35.09 26.70 42.47 5.36
1631 1672 4.459089 GGAGCCCAGTCGACTGCC 62.459 72.222 35.09 26.96 42.47 4.85
1632 1673 4.459089 GGGAGCCCAGTCGACTGC 62.459 72.222 35.09 26.31 42.47 4.40
1633 1674 2.681778 AGGGAGCCCAGTCGACTG 60.682 66.667 33.87 33.87 43.40 3.51
2013 2054 4.507710 TGAATACAGCAGAATCACAGTCC 58.492 43.478 0.00 0.00 0.00 3.85
2030 2071 8.312564 TGAATTGGCATCAAAACAGAATGAATA 58.687 29.630 0.00 0.00 36.47 1.75
2140 2182 4.413851 ACCTCCACTTCCTTCTTCTTCTTT 59.586 41.667 0.00 0.00 0.00 2.52
2441 2484 2.624029 GGTGGGGATGACCATTCACATT 60.624 50.000 0.00 0.00 43.59 2.71
2815 2896 2.490217 CGTCTCAGGAATCGCCGT 59.510 61.111 0.00 0.00 43.43 5.68
2911 2992 1.208052 AGATGGTGGATCAACAGTCGG 59.792 52.381 1.86 0.00 33.31 4.79
2954 3035 2.810400 GCAGCACTTACTTGGTCTTCCA 60.810 50.000 0.00 0.00 42.66 3.53
3015 3096 1.289066 CTCTCGGACCGCTTTCACA 59.711 57.895 9.66 0.00 0.00 3.58
3257 3348 7.537596 AGATCACAGCATAAAGACTATAGCT 57.462 36.000 0.00 0.00 0.00 3.32
3728 3834 7.716799 AAGTTATGATTCTAAAACCATGGCA 57.283 32.000 13.04 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.