Multiple sequence alignment - TraesCS5D01G166400

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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 TraesCS5D01G166400 chr5D 100.000 3672 0 0 888 4559 259236535 259232864 0.000000e+00 6782.0
1 TraesCS5D01G166400 chr5D 100.000 503 0 0 1 503 259237422 259236920 0.000000e+00 929.0
2 TraesCS5D01G166400 chr5A 96.223 3018 97 7 888 3890 343961310 343958295 0.000000e+00 4926.0
3 TraesCS5D01G166400 chr5A 93.614 689 27 11 3882 4559 343958119 343957437 0.000000e+00 1013.0
4 TraesCS5D01G166400 chr5A 87.452 518 19 9 1 503 343961847 343961361 5.150000e-154 555.0
5 TraesCS5D01G166400 chr5B 94.991 2935 105 12 888 3813 293210791 293207890 0.000000e+00 4567.0
6 TraesCS5D01G166400 chr5B 92.128 686 39 11 3882 4559 293207668 293206990 0.000000e+00 953.0
7 TraesCS5D01G166400 chr5B 88.780 508 34 11 1 503 293211328 293210839 6.530000e-168 601.0
8 TraesCS5D01G166400 chr4D 83.582 67 9 2 2913 2979 38304759 38304823 1.370000e-05 62.1
9 TraesCS5D01G166400 chr4B 83.582 67 9 2 2913 2979 55704977 55705041 1.370000e-05 62.1
10 TraesCS5D01G166400 chr4A 85.246 61 8 1 2919 2979 562483509 562483450 1.370000e-05 62.1


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 TraesCS5D01G166400 chr5D 259232864 259237422 4558 True 3855.500000 6782 100.000000 1 4559 2 chr5D.!!$R1 4558
1 TraesCS5D01G166400 chr5A 343957437 343961847 4410 True 2164.666667 4926 92.429667 1 4559 3 chr5A.!!$R1 4558
2 TraesCS5D01G166400 chr5B 293206990 293211328 4338 True 2040.333333 4567 91.966333 1 4559 3 chr5B.!!$R1 4558

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
117 120 0.458543 ACAATCACCTAGCGAGCACG 60.459 55.000 0.00 0.00 42.93 5.34 F
1432 1468 0.109689 CCGCTTCGAGAAGTCGTTCT 60.110 55.000 19.68 0.00 46.32 3.01 F
1548 1584 1.079405 CGACTACATGCCCAACCGT 60.079 57.895 0.00 0.00 0.00 4.83 F
2007 2043 1.204146 GGATTGTGCTCCTGGAGGTA 58.796 55.000 24.43 3.05 36.34 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2127 1.211190 GGCTTTGAGCAGCTTTCCG 59.789 57.895 0.0 0.0 44.75 4.30 R
2332 2368 1.081556 CCGGCGATTGTTGTCGATGA 61.082 55.000 9.3 0.0 44.06 2.92 R
3426 3462 1.796796 GTTGCCGTCCAGAATGCTC 59.203 57.895 0.0 0.0 31.97 4.26 R
3961 4212 0.589223 TCCAAAGTTAAAGCACGCCG 59.411 50.000 0.0 0.0 0.00 6.46 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
45 46 2.561478 AACACATTGCTAGAACCGGT 57.439 45.000 0.00 0.00 0.00 5.28
59 61 8.818860 TGCTAGAACCGGTTTATTATACCATAT 58.181 33.333 23.22 0.00 35.31 1.78
64 66 9.591792 GAACCGGTTTATTATACCATATACTCC 57.408 37.037 23.22 0.00 35.31 3.85
65 67 7.775120 ACCGGTTTATTATACCATATACTCCG 58.225 38.462 0.00 0.00 35.31 4.63
66 68 7.397192 ACCGGTTTATTATACCATATACTCCGT 59.603 37.037 0.00 0.00 35.31 4.69
67 69 8.902806 CCGGTTTATTATACCATATACTCCGTA 58.097 37.037 0.00 0.00 35.31 4.02
117 120 0.458543 ACAATCACCTAGCGAGCACG 60.459 55.000 0.00 0.00 42.93 5.34
162 165 2.161030 AGACGGTAGGAGAAGTGTGTC 58.839 52.381 0.00 0.00 0.00 3.67
168 171 2.510768 AGGAGAAGTGTGTCGTGTTC 57.489 50.000 0.00 0.00 0.00 3.18
194 197 4.386951 CGGCCCGTGACATCACCA 62.387 66.667 6.44 0.00 43.66 4.17
264 267 3.007940 TCCGATCTGGACAAGACAATTGT 59.992 43.478 11.78 11.78 43.74 2.71
420 434 1.525995 CACACCCCACACTCACACC 60.526 63.158 0.00 0.00 0.00 4.16
457 485 2.027192 GGCATCTTGTGTCACCTTCCTA 60.027 50.000 0.00 0.00 30.99 2.94
458 486 3.370953 GGCATCTTGTGTCACCTTCCTAT 60.371 47.826 0.00 0.00 30.99 2.57
460 488 4.446371 CATCTTGTGTCACCTTCCTATCC 58.554 47.826 0.00 0.00 0.00 2.59
461 489 3.791320 TCTTGTGTCACCTTCCTATCCT 58.209 45.455 0.00 0.00 0.00 3.24
1086 1122 2.498466 GACGACCACGACGACGAC 60.498 66.667 15.32 0.00 42.66 4.34
1308 1344 4.749310 ACCAGCGGCTTCAGCGAG 62.749 66.667 0.00 0.00 43.26 5.03
1395 1431 3.712881 GTGGCCGTCAAGTGCGTC 61.713 66.667 0.00 0.00 0.00 5.19
1432 1468 0.109689 CCGCTTCGAGAAGTCGTTCT 60.110 55.000 19.68 0.00 46.32 3.01
1548 1584 1.079405 CGACTACATGCCCAACCGT 60.079 57.895 0.00 0.00 0.00 4.83
1563 1599 4.253257 CGTAGCCTCGACCGCCTC 62.253 72.222 0.00 0.00 0.00 4.70
1728 1764 1.527696 GCAACGTCATGCTTGATTCG 58.472 50.000 5.49 8.13 43.06 3.34
2007 2043 1.204146 GGATTGTGCTCCTGGAGGTA 58.796 55.000 24.43 3.05 36.34 3.08
2310 2346 4.678256 TCCCAAAGTACATCTCTCTCACT 58.322 43.478 0.00 0.00 0.00 3.41
2332 2368 2.833604 ATCCTCCGACGACTCCGGTT 62.834 60.000 0.00 0.00 46.53 4.44
2334 2370 2.281692 TCCGACGACTCCGGTTCA 60.282 61.111 0.00 0.00 46.53 3.18
2430 2466 2.027929 TGGTACCACCATTTACCTCACG 60.028 50.000 11.60 0.00 44.79 4.35
2601 2637 2.034532 TCCGAGTCGCAGGTGGTA 59.965 61.111 7.12 0.00 0.00 3.25
2751 2787 1.303561 CTGCAACCTGGCCAAGCTA 60.304 57.895 7.01 0.00 0.00 3.32
3426 3462 0.994995 CGAGCATGAGGAAAGTCGTG 59.005 55.000 0.00 0.00 36.65 4.35
3507 3543 2.628290 GGAGGAGTGGGAGAGGAAGAAT 60.628 54.545 0.00 0.00 0.00 2.40
3509 3545 2.192263 GGAGTGGGAGAGGAAGAATGT 58.808 52.381 0.00 0.00 0.00 2.71
3517 3553 0.678048 GAGGAAGAATGTGGCGGCTT 60.678 55.000 11.43 0.00 0.00 4.35
3629 3665 5.016051 TGAGAAGAGGCTGTCATATGTTC 57.984 43.478 1.90 0.00 0.00 3.18
3637 3673 5.815581 AGGCTGTCATATGTTCCTTTGTTA 58.184 37.500 1.90 0.00 0.00 2.41
3640 3676 6.974622 GGCTGTCATATGTTCCTTTGTTAATG 59.025 38.462 1.90 0.00 0.00 1.90
3675 3720 4.340666 TGGCGCATTTTGTGTGGATATTAT 59.659 37.500 10.83 0.00 38.77 1.28
3676 3721 4.681025 GGCGCATTTTGTGTGGATATTATG 59.319 41.667 10.83 0.00 38.77 1.90
3683 3729 8.623903 CATTTTGTGTGGATATTATGCTGTACT 58.376 33.333 0.00 0.00 0.00 2.73
3847 3901 1.312815 AAAGTGCTTGTGTGCTCTCC 58.687 50.000 0.00 0.00 36.00 3.71
3850 3904 2.343758 GCTTGTGTGCTCTCCGGA 59.656 61.111 2.93 2.93 0.00 5.14
3952 4203 0.928229 CGCGGCACATTAGTTCCTAC 59.072 55.000 0.00 0.00 0.00 3.18
3961 4212 7.248437 GGCACATTAGTTCCTACAAAATGTAC 58.752 38.462 0.00 0.00 39.29 2.90
3984 4235 2.604614 GCGTGCTTTAACTTTGGACAGG 60.605 50.000 0.00 0.00 0.00 4.00
3995 4246 5.319043 ACTTTGGACAGGACTAATTTCCA 57.681 39.130 0.00 0.00 38.25 3.53
4005 4256 6.183360 ACAGGACTAATTTCCAAATGCTATGC 60.183 38.462 0.00 0.00 38.25 3.14
4284 4543 6.170506 AGCGTGAAATTGGATAGTCAAACTA 58.829 36.000 0.00 0.00 34.82 2.24
4294 4553 5.410439 TGGATAGTCAAACTACGCCTTTTTC 59.590 40.000 8.46 0.00 32.84 2.29
4297 4556 1.874872 TCAAACTACGCCTTTTTCCCG 59.125 47.619 0.00 0.00 0.00 5.14
4299 4558 0.535553 AACTACGCCTTTTTCCCGCA 60.536 50.000 0.00 0.00 0.00 5.69
4365 4624 2.027192 GGTCCAAACTCACTATGGCAGA 60.027 50.000 0.00 0.00 34.13 4.26
4405 4664 0.443478 CGATCGTGATGCTTGCAACA 59.557 50.000 7.03 0.00 0.00 3.33
4472 4731 2.289631 ACGAAGTTGATGTGCATCCTCA 60.290 45.455 9.39 0.00 37.78 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.090652 TCTAGCAATGTGTTTCAACGTTC 57.909 39.130 0.00 0.00 0.00 3.95
64 66 8.858003 AGCCGTTATTTATGATATCTCATACG 57.142 34.615 3.98 3.92 42.66 3.06
67 69 9.302345 CGTTAGCCGTTATTTATGATATCTCAT 57.698 33.333 3.98 0.00 44.39 2.90
68 70 8.683550 CGTTAGCCGTTATTTATGATATCTCA 57.316 34.615 3.98 0.00 35.41 3.27
102 105 3.449227 CCCGTGCTCGCTAGGTGA 61.449 66.667 1.89 0.00 35.54 4.02
117 120 5.413833 CCTATGATATGATTGTGTCAAGCCC 59.586 44.000 0.00 0.00 40.97 5.19
457 485 1.464198 GGGGCAGGTGGGATAGGAT 60.464 63.158 0.00 0.00 0.00 3.24
458 486 2.039831 GGGGCAGGTGGGATAGGA 60.040 66.667 0.00 0.00 0.00 2.94
896 928 1.582461 CGTTTAAAGTTGGGGCCGG 59.418 57.895 0.00 0.00 0.00 6.13
898 934 1.290955 GGCGTTTAAAGTTGGGGCC 59.709 57.895 0.00 0.00 0.00 5.80
899 935 1.081041 CGGCGTTTAAAGTTGGGGC 60.081 57.895 0.00 0.00 0.00 5.80
902 938 0.994737 CGTGCGGCGTTTAAAGTTGG 60.995 55.000 9.37 0.00 35.54 3.77
1109 1145 3.450115 GGACGTACGAGCCCAGCT 61.450 66.667 24.41 0.00 43.88 4.24
1193 1229 1.890894 CCGTCCATGTCCTCGAAGT 59.109 57.895 0.00 0.00 0.00 3.01
1728 1764 4.078516 AGGCGGGCGTTGTACTCC 62.079 66.667 0.00 0.00 0.00 3.85
2091 2127 1.211190 GGCTTTGAGCAGCTTTCCG 59.789 57.895 0.00 0.00 44.75 4.30
2310 2346 1.374343 CGGAGTCGTCGGAGGATGAA 61.374 60.000 3.47 0.00 39.80 2.57
2332 2368 1.081556 CCGGCGATTGTTGTCGATGA 61.082 55.000 9.30 0.00 44.06 2.92
2334 2370 2.461110 GCCGGCGATTGTTGTCGAT 61.461 57.895 12.58 0.00 44.06 3.59
2430 2466 2.435059 GACCTGCCGTCTTCTGCC 60.435 66.667 0.00 0.00 38.57 4.85
2601 2637 3.764466 CCGAAGTCCAGCTCCGCT 61.764 66.667 0.00 0.00 40.77 5.52
3163 3199 3.252484 GTACACGTCGGCCATCGC 61.252 66.667 15.02 0.00 39.05 4.58
3278 3314 3.680786 CACGGACGTCCTGCTCCA 61.681 66.667 30.92 0.00 0.00 3.86
3426 3462 1.796796 GTTGCCGTCCAGAATGCTC 59.203 57.895 0.00 0.00 31.97 4.26
3507 3543 2.192861 CAAGGACAAAGCCGCCACA 61.193 57.895 0.00 0.00 0.00 4.17
3509 3545 2.597217 CCAAGGACAAAGCCGCCA 60.597 61.111 0.00 0.00 0.00 5.69
3629 3665 8.069574 GCCAGAAAATTTTCACATTAACAAAGG 58.930 33.333 28.00 14.12 39.61 3.11
3637 3673 3.726607 TGCGCCAGAAAATTTTCACATT 58.273 36.364 28.00 8.82 39.61 2.71
3640 3676 4.730600 AAATGCGCCAGAAAATTTTCAC 57.269 36.364 28.00 17.44 39.61 3.18
3675 3720 6.052360 TCACTACAAAATCACAAGTACAGCA 58.948 36.000 0.00 0.00 0.00 4.41
3676 3721 6.423905 TCTCACTACAAAATCACAAGTACAGC 59.576 38.462 0.00 0.00 0.00 4.40
3683 3729 6.582636 AGTCACTCTCACTACAAAATCACAA 58.417 36.000 0.00 0.00 0.00 3.33
3758 3812 8.143193 TGAACAATGTGATAGTGCAAGAAAAAT 58.857 29.630 0.00 0.00 0.00 1.82
3827 3881 1.678101 GGAGAGCACACAAGCACTTTT 59.322 47.619 0.00 0.00 35.56 2.27
3828 3882 1.312815 GGAGAGCACACAAGCACTTT 58.687 50.000 0.00 0.00 35.56 2.66
3833 3887 0.884704 TTTCCGGAGAGCACACAAGC 60.885 55.000 3.34 0.00 0.00 4.01
3902 4153 4.105697 TGTCCCCTTTAAAGAATGGACTGT 59.894 41.667 30.40 0.00 38.59 3.55
3906 4157 6.519891 GCAAATTGTCCCCTTTAAAGAATGGA 60.520 38.462 16.98 15.04 32.67 3.41
3909 4160 6.572314 CGAGCAAATTGTCCCCTTTAAAGAAT 60.572 38.462 16.98 5.15 0.00 2.40
3911 4162 4.217550 CGAGCAAATTGTCCCCTTTAAAGA 59.782 41.667 16.98 0.00 0.00 2.52
3952 4203 2.044888 AAAGCACGCCGTACATTTTG 57.955 45.000 0.00 0.00 0.00 2.44
3961 4212 0.589223 TCCAAAGTTAAAGCACGCCG 59.411 50.000 0.00 0.00 0.00 6.46
3984 4235 5.008613 TCCGCATAGCATTTGGAAATTAGTC 59.991 40.000 0.00 0.00 0.00 2.59
3995 4246 3.125829 CGCAATAGATCCGCATAGCATTT 59.874 43.478 0.00 0.00 0.00 2.32
4005 4256 2.033407 CAGCAGTTTCGCAATAGATCCG 60.033 50.000 0.00 0.00 0.00 4.18
4284 4543 0.175989 TTTTTGCGGGAAAAAGGCGT 59.824 45.000 14.93 0.00 38.38 5.68
4365 4624 7.384115 CGATCGATATACTTTGTTGGTAATGGT 59.616 37.037 10.26 0.00 0.00 3.55
4405 4664 0.620556 AGAAGGACGATGGTGGCATT 59.379 50.000 0.00 0.00 0.00 3.56
4472 4731 2.371179 CACATGAGGCATCTGGATAGGT 59.629 50.000 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.