Multiple sequence alignment - TraesCS5D01G108400

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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 TraesCS5D01G108400 chr5D 100.000 6621 0 0 1 6621 122202704 122196084 0.000000e+00 12227
1 TraesCS5D01G108400 chr5D 95.455 88 2 1 4190 4275 498655370 498655283 8.950000e-29 139
2 TraesCS5D01G108400 chr5A 96.386 6641 188 23 1 6621 134090227 134083619 0.000000e+00 10887
3 TraesCS5D01G108400 chr5B 93.658 2302 99 12 4143 6419 134917900 134915621 0.000000e+00 3398
4 TraesCS5D01G108400 chr5B 94.027 2210 100 16 716 2899 134921430 134919227 0.000000e+00 3321
5 TraesCS5D01G108400 chr5B 94.103 1204 60 7 2898 4098 134919103 134917908 0.000000e+00 1820
6 TraesCS5D01G108400 chr5B 94.897 725 32 2 1 720 134922201 134921477 0.000000e+00 1129
7 TraesCS5D01G108400 chr5B 93.388 121 7 1 6502 6621 134915619 134915499 1.900000e-40 178
8 TraesCS5D01G108400 chr4D 97.701 87 2 0 4191 4277 504090711 504090797 4.140000e-32 150
9 TraesCS5D01G108400 chr4D 92.708 96 6 1 4187 4281 497058800 497058705 3.220000e-28 137
10 TraesCS5D01G108400 chr7D 96.591 88 1 2 4189 4275 41146561 41146647 1.920000e-30 145
11 TraesCS5D01G108400 chr7A 96.591 88 2 1 4189 4275 40538157 40538244 1.920000e-30 145
12 TraesCS5D01G108400 chr4B 95.556 90 2 2 4187 4274 656162614 656162703 6.920000e-30 143
13 TraesCS5D01G108400 chr4A 94.505 91 4 1 4189 4278 647209391 647209301 8.950000e-29 139


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 TraesCS5D01G108400 chr5D 122196084 122202704 6620 True 12227.0 12227 100.0000 1 6621 1 chr5D.!!$R1 6620
1 TraesCS5D01G108400 chr5A 134083619 134090227 6608 True 10887.0 10887 96.3860 1 6621 1 chr5A.!!$R1 6620
2 TraesCS5D01G108400 chr5B 134915499 134922201 6702 True 1969.2 3398 94.0146 1 6621 5 chr5B.!!$R1 6620

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
343 344 1.821136 GTGAAAAGCTGGATGGGGAAG 59.179 52.381 0.00 0.0 0.00 3.46 F
1649 1717 0.868406 AGCAACTTCTTAGCGCACAC 59.132 50.000 11.47 0.0 0.00 3.82 F
2232 2305 2.757868 ACTCCAGACTAGTCAGTGCATC 59.242 50.000 24.44 0.0 34.21 3.91 F
3647 3862 1.276138 GACCATTTTTGGGAGCCAAGG 59.724 52.381 0.00 0.0 44.84 3.61 F
3648 3863 1.351076 CCATTTTTGGGAGCCAAGGT 58.649 50.000 0.00 0.0 44.84 3.50 F
4065 4281 2.574929 TGGTACACGGATGTCGGC 59.425 61.111 0.00 0.0 44.45 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2148 2.483013 GCATGTATCACAGCGGACCTTA 60.483 50.000 0.00 0.0 0.00 2.69 R
3356 3569 0.108992 GTCGAACACATCCGCTACCA 60.109 55.000 0.00 0.0 0.00 3.25 R
3699 3914 0.393077 ATAAAGGGGATGCCGTCGAG 59.607 55.000 0.00 0.0 0.00 4.04 R
4818 5042 0.391661 GGAATGCTGCTGTTCCGAGA 60.392 55.000 17.25 0.0 35.03 4.04 R
5275 5503 4.122046 TGGATCGTGAATCATGTGATGAC 58.878 43.478 2.06 0.0 43.01 3.06 R
5723 5954 3.117888 ACCAATGAACAACCTGTGAGACT 60.118 43.478 0.00 0.0 0.00 3.24 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
310 311 7.327214 GGGCACACATTTTAGGATTTCATTAA 58.673 34.615 0.00 0.00 0.00 1.40
327 328 3.650070 TTAAATGTGCCGCAATGTGAA 57.350 38.095 0.00 0.00 0.00 3.18
343 344 1.821136 GTGAAAAGCTGGATGGGGAAG 59.179 52.381 0.00 0.00 0.00 3.46
486 496 3.132029 TTGGCCAGGTGACAGGGTG 62.132 63.158 5.11 0.00 37.51 4.61
522 532 9.546428 CAGTACTATATTCACAATGTTCATGGA 57.454 33.333 0.00 0.00 0.00 3.41
661 671 4.566545 TGTCATGTTGAATTGTGGACAC 57.433 40.909 0.00 0.00 0.00 3.67
676 686 3.006537 GTGGACACCAGCAACTTCTAGTA 59.993 47.826 0.00 0.00 32.34 1.82
683 693 6.170506 CACCAGCAACTTCTAGTACCAAATA 58.829 40.000 0.00 0.00 0.00 1.40
808 874 2.224137 CGGTGACATATCTGTGCATCCT 60.224 50.000 0.00 0.00 35.14 3.24
846 912 7.624549 AGAGACTAAATGCTGGAAAGACAATA 58.375 34.615 0.00 0.00 0.00 1.90
1145 1211 1.271926 CGGATCCCCAATTCCCCATAC 60.272 57.143 6.06 0.00 0.00 2.39
1161 1227 3.009695 CCCATACCCACCAGAGTAAAACA 59.990 47.826 0.00 0.00 0.00 2.83
1330 1396 8.573885 TGACTTGTATACTTATTATGTCTCCGG 58.426 37.037 4.17 0.00 0.00 5.14
1649 1717 0.868406 AGCAACTTCTTAGCGCACAC 59.132 50.000 11.47 0.00 0.00 3.82
1729 1798 6.811954 TCACAGACTCACACACTAACATTAA 58.188 36.000 0.00 0.00 0.00 1.40
1739 1808 7.066404 TCACACACTAACATTAAAACTTCTGCA 59.934 33.333 0.00 0.00 0.00 4.41
2041 2114 6.668133 AACCTAGATTCCCCCTTTTTCATA 57.332 37.500 0.00 0.00 0.00 2.15
2075 2148 9.412460 TCCAATTTGAGCTGACATCTTATATTT 57.588 29.630 0.00 0.00 0.00 1.40
2232 2305 2.757868 ACTCCAGACTAGTCAGTGCATC 59.242 50.000 24.44 0.00 34.21 3.91
2351 2424 9.906111 CTACATAATTTGCAGTATGTATATGCG 57.094 33.333 19.22 9.69 42.62 4.73
2520 2597 7.842525 TTCGTTCGATTACTATATTCCGTTC 57.157 36.000 0.00 0.00 0.00 3.95
2847 2935 7.316393 AGTATCCCTGTTAATAGCTTATGCA 57.684 36.000 0.00 0.00 42.74 3.96
3121 3334 7.168219 TCTATTGCTGATCAAAGTAAGTGGTT 58.832 34.615 0.00 0.00 38.34 3.67
3191 3404 7.962934 TGTTGTTGAATAGTTTCTTGAAACG 57.037 32.000 17.19 0.00 37.71 3.60
3199 3412 6.687081 ATAGTTTCTTGAAACGTTTCACCA 57.313 33.333 36.47 24.92 45.99 4.17
3356 3569 7.556996 AGAGAAATTGATAGTACGGACTACAGT 59.443 37.037 10.38 4.76 41.01 3.55
3602 3815 5.440234 TTTGTGCCGCTTATGTTTTCTAA 57.560 34.783 0.00 0.00 0.00 2.10
3603 3816 5.440234 TTGTGCCGCTTATGTTTTCTAAA 57.560 34.783 0.00 0.00 0.00 1.85
3604 3817 5.637006 TGTGCCGCTTATGTTTTCTAAAT 57.363 34.783 0.00 0.00 0.00 1.40
3647 3862 1.276138 GACCATTTTTGGGAGCCAAGG 59.724 52.381 0.00 0.00 44.84 3.61
3648 3863 1.351076 CCATTTTTGGGAGCCAAGGT 58.649 50.000 0.00 0.00 44.84 3.50
3699 3914 5.578336 GCCTTTGCAGAAATAATTTCCTGAC 59.422 40.000 0.00 0.00 40.54 3.51
3705 3920 5.500931 GCAGAAATAATTTCCTGACTCGACG 60.501 44.000 0.00 0.00 40.54 5.12
4065 4281 2.574929 TGGTACACGGATGTCGGC 59.425 61.111 0.00 0.00 44.45 5.54
4783 5007 3.634397 ACATGGTTCTGATGATTCGGT 57.366 42.857 0.00 0.00 0.00 4.69
5133 5361 3.945921 GGTTGGAGCTGGATTTTACTACC 59.054 47.826 0.00 0.00 0.00 3.18
5208 5436 8.063200 TCTGCTCATTACTAGTTGCTACTTTA 57.937 34.615 6.03 0.00 35.78 1.85
5275 5503 5.903810 AGCATTTAGTTAGGGAAGACGTAG 58.096 41.667 0.00 0.00 0.00 3.51
5329 5557 7.632721 CATGGCAAATAATTTCAGGCATTTAC 58.367 34.615 0.00 0.00 42.57 2.01
5342 5570 3.005791 AGGCATTTACTTTTGGTGCAGTC 59.994 43.478 0.00 0.00 37.53 3.51
5549 5780 4.450976 ACAAATGAGGCGTGCTTATATCA 58.549 39.130 0.00 0.00 0.00 2.15
5552 5783 6.881065 ACAAATGAGGCGTGCTTATATCATAT 59.119 34.615 0.00 0.00 0.00 1.78
5554 5785 8.882736 CAAATGAGGCGTGCTTATATCATATTA 58.117 33.333 0.00 0.00 0.00 0.98
5673 5904 5.606348 TTACCTTTTGACTTTGTTGCCAT 57.394 34.783 0.00 0.00 0.00 4.40
5723 5954 5.508567 TGAACAATGGCTAATCTTGGATCA 58.491 37.500 0.00 0.00 0.00 2.92
5847 6078 1.893801 GGGACCGGACGATCTGAATAT 59.106 52.381 9.46 0.00 0.00 1.28
6008 6239 4.253685 CCCTGGTGATGTAACTAAGTGTG 58.746 47.826 0.00 0.00 0.00 3.82
6044 6275 4.495844 GCGAAGTCCTTATGTTTATGTGCC 60.496 45.833 0.00 0.00 0.00 5.01
6095 6326 2.837591 TCTCCAAACCAGCAGTAGCATA 59.162 45.455 0.00 0.00 45.49 3.14
6098 6329 2.356125 CCAAACCAGCAGTAGCATAGGT 60.356 50.000 0.00 0.00 45.49 3.08
6196 6427 1.070134 TGTGGCAGGGTTATATCGAGC 59.930 52.381 0.00 0.00 0.00 5.03
6203 6434 4.547532 CAGGGTTATATCGAGCAGTACAC 58.452 47.826 0.00 0.00 0.00 2.90
6468 6713 7.097834 AGCCGACCTTATATAGTAATTTCAGC 58.902 38.462 0.00 0.00 0.00 4.26
6482 6727 2.125147 CAGCCCGCGAATTCCAGA 60.125 61.111 8.23 0.00 0.00 3.86
6485 6730 2.546494 GCCCGCGAATTCCAGATGG 61.546 63.158 8.23 0.00 0.00 3.51
6489 6734 0.652592 CGCGAATTCCAGATGGTGTC 59.347 55.000 0.00 0.00 36.34 3.67
6517 6762 0.035056 AAGGATTCTGCAGTTCGGGG 60.035 55.000 14.67 0.00 0.00 5.73
6593 6838 5.840243 TTCCGAAGAATTGCAATGATCAT 57.160 34.783 13.82 1.18 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.239306 TCACAAGACATGGCTTCACTAAAAG 59.761 40.000 12.02 0.00 0.00 2.27
310 311 2.406130 CTTTTCACATTGCGGCACATT 58.594 42.857 0.05 0.00 0.00 2.71
313 314 0.318955 AGCTTTTCACATTGCGGCAC 60.319 50.000 0.05 0.00 0.00 5.01
327 328 0.332972 GACCTTCCCCATCCAGCTTT 59.667 55.000 0.00 0.00 0.00 3.51
343 344 7.820648 AGAATTGAACTGATGTTACATTGACC 58.179 34.615 0.00 0.00 36.39 4.02
381 391 9.849166 CTGAGAGTTAAACCAAAACTGTAAAAA 57.151 29.630 0.00 0.00 37.31 1.94
522 532 6.665680 TCAAACTCCAAGCTCTCTAAGTATCT 59.334 38.462 0.00 0.00 0.00 1.98
642 652 3.560105 TGGTGTCCACAATTCAACATGA 58.440 40.909 0.00 0.00 0.00 3.07
661 671 7.865706 AATATTTGGTACTAGAAGTTGCTGG 57.134 36.000 0.00 0.00 0.00 4.85
846 912 9.959721 ACTTGTAGTTTGATTATATGTCTGGTT 57.040 29.630 0.00 0.00 0.00 3.67
961 1027 4.309099 ACATTGAACCAAATGCACATGAC 58.691 39.130 0.00 0.00 40.54 3.06
1145 1211 4.969484 ACTACTTGTTTTACTCTGGTGGG 58.031 43.478 0.00 0.00 0.00 4.61
1330 1396 8.258708 ACTACCTCCAAACAGAGATAATGTAAC 58.741 37.037 0.00 0.00 35.82 2.50
1408 1474 9.056005 CCGAAATTCAGTTCTCCAAATATGATA 57.944 33.333 0.00 0.00 0.00 2.15
1580 1648 4.883585 TCATTAATCACCTCATCTGCCAAC 59.116 41.667 0.00 0.00 0.00 3.77
1649 1717 5.221880 TCTTCATCAAGCAAATTTGGTTCG 58.778 37.500 27.98 22.44 46.06 3.95
1729 1798 4.768968 ACTGATAAAGGCATGCAGAAGTTT 59.231 37.500 21.36 12.27 0.00 2.66
1918 1991 6.912082 TCATAAATTGTGGTGTCAACTGATG 58.088 36.000 0.00 0.00 0.00 3.07
1929 2002 9.801873 GCACATAACTAAATCATAAATTGTGGT 57.198 29.630 0.00 0.00 33.25 4.16
2041 2114 4.082354 GTCAGCTCAAATTGGAAGCAGAAT 60.082 41.667 8.96 0.00 0.00 2.40
2075 2148 2.483013 GCATGTATCACAGCGGACCTTA 60.483 50.000 0.00 0.00 0.00 2.69
2232 2305 4.156922 TCCAACCAAAACAGTGTGTAGTTG 59.843 41.667 16.95 16.95 32.20 3.16
2351 2424 0.591170 CAACACAACGACATGGGGTC 59.409 55.000 0.00 0.00 43.36 4.46
3121 3334 9.573166 TTCACCAGATTGAATTAGAAAGAAAGA 57.427 29.630 0.00 0.00 30.29 2.52
3356 3569 0.108992 GTCGAACACATCCGCTACCA 60.109 55.000 0.00 0.00 0.00 3.25
3399 3612 6.904626 AGCTACCAATTGAAACATCTATCCT 58.095 36.000 7.12 0.00 0.00 3.24
3647 3862 5.174943 CCAATTCCGTGTTTAAGAGCAAAAC 59.825 40.000 0.00 0.00 37.35 2.43
3648 3863 5.163499 ACCAATTCCGTGTTTAAGAGCAAAA 60.163 36.000 0.00 0.00 0.00 2.44
3699 3914 0.393077 ATAAAGGGGATGCCGTCGAG 59.607 55.000 0.00 0.00 0.00 4.04
3705 3920 5.717119 ATAGGACATATAAAGGGGATGCC 57.283 43.478 0.00 0.00 0.00 4.40
3850 4066 4.219115 TCACTCCTAGACATCATTCTCCC 58.781 47.826 0.00 0.00 0.00 4.30
3998 4214 1.075482 CTGTTGGGTGGGCATCAGT 59.925 57.895 0.00 0.00 0.00 3.41
4065 4281 6.980593 TCAACCAGAATTGATACCAAACAAG 58.019 36.000 0.00 0.00 33.62 3.16
4384 4601 2.545537 AGGACCCGAACAAGAAACTC 57.454 50.000 0.00 0.00 0.00 3.01
4818 5042 0.391661 GGAATGCTGCTGTTCCGAGA 60.392 55.000 17.25 0.00 35.03 4.04
5275 5503 4.122046 TGGATCGTGAATCATGTGATGAC 58.878 43.478 2.06 0.00 43.01 3.06
5329 5557 5.452078 TTATTGAAGGACTGCACCAAAAG 57.548 39.130 0.00 0.00 0.00 2.27
5503 5731 4.265904 TCTGCAGGTTTCGAGACATAAA 57.734 40.909 15.13 0.00 0.00 1.40
5552 5783 7.482169 TGCCTAGAGAAGAGAAATCAAGTAA 57.518 36.000 0.00 0.00 0.00 2.24
5554 5785 6.365970 TTGCCTAGAGAAGAGAAATCAAGT 57.634 37.500 0.00 0.00 0.00 3.16
5673 5904 7.041235 GCACCAAATTCCAAGATTTGAAATTCA 60.041 33.333 10.89 0.00 45.47 2.57
5723 5954 3.117888 ACCAATGAACAACCTGTGAGACT 60.118 43.478 0.00 0.00 0.00 3.24
5798 6029 8.876248 GTCATTCCGACTAGAACAAATTTTAC 57.124 34.615 0.00 0.00 41.81 2.01
5847 6078 9.268282 AGATAGAGACTTACCAAAATGACCTTA 57.732 33.333 0.00 0.00 0.00 2.69
6044 6275 6.777091 TCATCATGTCATTTATAACAAGGGGG 59.223 38.462 0.00 0.00 0.00 5.40
6171 6402 4.836175 TCGATATAACCCTGCCACAGATTA 59.164 41.667 0.00 0.00 32.44 1.75
6196 6427 4.451096 AGTTTCTTGTTATGGCGTGTACTG 59.549 41.667 0.00 0.00 0.00 2.74
6203 6434 2.420022 CTCCCAGTTTCTTGTTATGGCG 59.580 50.000 0.00 0.00 0.00 5.69
6266 6497 1.565759 AGCACATTATCTTGCCAGGGA 59.434 47.619 0.00 0.00 39.75 4.20
6271 6502 4.981806 TGGTTTAGCACATTATCTTGCC 57.018 40.909 0.00 0.00 39.75 4.52
6442 6685 7.603024 GCTGAAATTACTATATAAGGTCGGCTT 59.397 37.037 0.00 0.00 33.17 4.35
6468 6713 1.153168 ACCATCTGGAATTCGCGGG 60.153 57.895 6.13 0.00 38.94 6.13
6482 6727 0.537188 CCTTGGCTCTACGACACCAT 59.463 55.000 0.00 0.00 30.85 3.55
6485 6730 2.166664 AGAATCCTTGGCTCTACGACAC 59.833 50.000 0.00 0.00 0.00 3.67
6489 6734 1.134699 TGCAGAATCCTTGGCTCTACG 60.135 52.381 0.00 0.00 0.00 3.51
6517 6762 6.640499 CAGAATCTCGATCATACTCTCAAACC 59.360 42.308 0.00 0.00 0.00 3.27
6593 6838 1.371467 TTCTTTGATGGAGGAGGGCA 58.629 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.