Multiple sequence alignment - TraesCS5B01G132900

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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 TraesCS5B01G132900 chr5B 100.000 3506 0 0 1 3506 247667857 247664352 0.000000e+00 6475.0
1 TraesCS5B01G132900 chr5D 96.260 3075 71 14 464 3506 223887188 223890250 0.000000e+00 5001.0
2 TraesCS5B01G132900 chr5D 89.394 396 30 6 82 467 223886773 223887166 4.070000e-134 488.0
3 TraesCS5B01G132900 chr5A 94.123 3080 93 32 464 3503 296467713 296470744 0.000000e+00 4604.0
4 TraesCS5B01G132900 chr5A 86.498 474 50 9 6 467 296467214 296467685 3.120000e-140 508.0
5 TraesCS5B01G132900 chr3D 83.333 108 16 2 1159 1265 95482324 95482430 8.010000e-17 99.0
6 TraesCS5B01G132900 chr3A 90.625 64 4 2 43 106 420735849 420735788 2.240000e-12 84.2


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 TraesCS5B01G132900 chr5B 247664352 247667857 3505 True 6475.0 6475 100.0000 1 3506 1 chr5B.!!$R1 3505
1 TraesCS5B01G132900 chr5D 223886773 223890250 3477 False 2744.5 5001 92.8270 82 3506 2 chr5D.!!$F1 3424
2 TraesCS5B01G132900 chr5A 296467214 296470744 3530 False 2556.0 4604 90.3105 6 3503 2 chr5A.!!$F1 3497

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
193 204 0.038166 AAACATCATCGCCCACACCT 59.962 50.000 0.0 0.00 0.00 4.00 F
333 344 0.593128 CCACGCCCTTTCAAGTGAAG 59.407 55.000 0.0 0.00 36.79 3.02 F
1530 1655 1.133976 AGAGCATGGTGGCTAATGGTC 60.134 52.381 0.0 14.66 45.99 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 1455 1.005924 CCTGCTTAGGACCAAACCCAT 59.994 52.381 0.00 0.00 0.00 4.00 R
1573 1698 1.275666 TGATCACAACCGGGATGTCT 58.724 50.000 6.32 0.04 0.00 3.41 R
3428 3568 0.109342 CCTTCACAGAACAGCCTGGT 59.891 55.000 0.00 0.00 38.44 4.00 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
53 54 8.477984 TTTTTAAGCTTGTCAAATATGATGCC 57.522 30.769 9.86 0.00 38.01 4.40
56 57 2.618241 GCTTGTCAAATATGATGCCCGA 59.382 45.455 0.00 0.00 38.01 5.14
70 71 5.590145 TGATGCCCGAAATGACAAATTATG 58.410 37.500 0.00 0.00 0.00 1.90
84 85 4.331443 ACAAATTATGTTGTCGCGAGCATA 59.669 37.500 10.24 15.71 40.06 3.14
86 87 4.715520 ATTATGTTGTCGCGAGCATAAG 57.284 40.909 28.23 0.00 37.27 1.73
113 114 5.556355 TTCTTCAGCAAGCATATCAAGTG 57.444 39.130 0.00 0.00 0.00 3.16
147 148 1.661341 ACTTGAGCATCGCAAGGATC 58.339 50.000 13.28 0.00 43.61 3.36
148 149 1.065926 ACTTGAGCATCGCAAGGATCA 60.066 47.619 13.28 0.00 43.61 2.92
149 150 1.329906 CTTGAGCATCGCAAGGATCAC 59.670 52.381 0.00 0.00 37.56 3.06
193 204 0.038166 AAACATCATCGCCCACACCT 59.962 50.000 0.00 0.00 0.00 4.00
197 208 1.545582 CATCATCGCCCACACCTTTTT 59.454 47.619 0.00 0.00 0.00 1.94
199 210 2.156098 TCATCGCCCACACCTTTTTAC 58.844 47.619 0.00 0.00 0.00 2.01
213 224 7.064134 CACACCTTTTTACGATACAATCTGCTA 59.936 37.037 0.00 0.00 0.00 3.49
242 253 2.158559 TGCCATACTCGCAACAACATT 58.841 42.857 0.00 0.00 32.05 2.71
248 259 5.229887 CCATACTCGCAACAACATTAATTGC 59.770 40.000 1.42 1.42 44.21 3.56
260 271 0.626382 TTAATTGCCATCCCGGACCA 59.374 50.000 0.73 0.00 36.56 4.02
283 294 7.093640 ACCATCAGATTTGCTATGTTTGTTCAT 60.094 33.333 0.00 0.00 0.00 2.57
318 329 1.086696 AAGAAACATCATCGCCCACG 58.913 50.000 0.00 0.00 42.01 4.94
333 344 0.593128 CCACGCCCTTTCAAGTGAAG 59.407 55.000 0.00 0.00 36.79 3.02
407 421 2.224079 GGTCGTAACACGTCTGTACTGA 59.776 50.000 0.00 0.00 43.14 3.41
417 431 3.314635 ACGTCTGTACTGAAAACTCGACT 59.685 43.478 13.91 0.00 0.00 4.18
934 1029 2.507471 CTCCTGCCTTTCCTCTACCATT 59.493 50.000 0.00 0.00 0.00 3.16
943 1038 5.478332 CCTTTCCTCTACCATTCTTGCTTTT 59.522 40.000 0.00 0.00 0.00 2.27
948 1043 6.012858 TCCTCTACCATTCTTGCTTTTTCCTA 60.013 38.462 0.00 0.00 0.00 2.94
991 1086 3.689649 ACAAAACACACGCTCTCTCTTTT 59.310 39.130 0.00 0.00 0.00 2.27
992 1087 4.156008 ACAAAACACACGCTCTCTCTTTTT 59.844 37.500 0.00 0.00 0.00 1.94
1109 1204 6.467677 TCAAGACATCTTCTTTCCAAGGTAG 58.532 40.000 0.00 0.00 42.37 3.18
1110 1205 6.043243 TCAAGACATCTTCTTTCCAAGGTAGT 59.957 38.462 0.00 0.00 42.37 2.73
1111 1206 7.234782 TCAAGACATCTTCTTTCCAAGGTAGTA 59.765 37.037 0.00 0.00 42.37 1.82
1157 1252 1.334869 GAAGTTGTGTTCCTGCTGTGG 59.665 52.381 0.00 0.00 0.00 4.17
1210 1305 1.734163 CAGTTACCACCGTGGATTCC 58.266 55.000 24.80 8.59 40.96 3.01
1345 1440 7.054855 CACTACTAGTGCTCTGAAATTGTTC 57.945 40.000 5.39 0.00 39.62 3.18
1356 1451 6.530534 GCTCTGAAATTGTTCCTGATTGATTG 59.469 38.462 0.00 0.00 32.28 2.67
1530 1655 1.133976 AGAGCATGGTGGCTAATGGTC 60.134 52.381 0.00 14.66 45.99 4.02
1572 1697 1.951602 TCAGGAGTCGTCGTCTTTCAA 59.048 47.619 0.00 0.00 0.00 2.69
1573 1698 2.359848 TCAGGAGTCGTCGTCTTTCAAA 59.640 45.455 0.00 0.00 0.00 2.69
1776 1901 8.830580 CATTACTACATGTTTGATAGACCTTGG 58.169 37.037 2.30 0.00 0.00 3.61
2042 2167 4.142491 TGCGCATATGAAGTAAAAACCCAG 60.142 41.667 5.66 0.00 0.00 4.45
2259 2385 5.870433 CCACATAATGAAAAGCAGATGCAAA 59.130 36.000 7.68 0.00 45.16 3.68
2427 2553 1.148157 CGGATAACAGCAGCGGTGAG 61.148 60.000 20.69 12.34 34.87 3.51
2441 2567 0.321919 GGTGAGAGCAGCAACATCCA 60.322 55.000 0.00 0.00 42.00 3.41
2636 2762 2.868583 CGGATACTGCTTGAATCCAGTG 59.131 50.000 8.36 0.00 41.96 3.66
2918 3044 2.531522 AGCACCATTTTCAGCAAACC 57.468 45.000 0.00 0.00 0.00 3.27
3295 3432 2.084546 GCAAGTGGTCAGGATGGTAAC 58.915 52.381 0.00 0.00 36.16 2.50
3424 3564 0.453390 GCAGACCAATAGGCAACAGC 59.547 55.000 0.00 0.00 39.06 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.948853 TTGACAAGCTTAAAAATTCATAGTCG 57.051 30.769 0.00 0.00 0.00 4.18
28 29 7.548780 GGGCATCATATTTGACAAGCTTAAAAA 59.451 33.333 0.00 0.52 33.85 1.94
37 38 5.359292 TCATTTCGGGCATCATATTTGACAA 59.641 36.000 0.00 0.00 33.85 3.18
70 71 3.658351 AATTCTTATGCTCGCGACAAC 57.342 42.857 3.71 0.00 0.00 3.32
77 78 5.872635 TGCTGAAGAAAATTCTTATGCTCG 58.127 37.500 21.88 7.26 46.84 5.03
86 87 7.758528 ACTTGATATGCTTGCTGAAGAAAATTC 59.241 33.333 0.00 0.00 0.00 2.17
128 129 1.065926 TGATCCTTGCGATGCTCAAGT 60.066 47.619 0.00 0.00 39.30 3.16
129 130 1.329906 GTGATCCTTGCGATGCTCAAG 59.670 52.381 0.00 0.00 40.31 3.02
130 131 1.338960 TGTGATCCTTGCGATGCTCAA 60.339 47.619 0.00 0.00 0.00 3.02
134 135 2.542411 GGATTTGTGATCCTTGCGATGC 60.542 50.000 0.00 0.00 35.36 3.91
137 138 1.066502 TCGGATTTGTGATCCTTGCGA 60.067 47.619 3.78 0.00 36.07 5.10
138 139 1.062587 GTCGGATTTGTGATCCTTGCG 59.937 52.381 3.78 0.00 36.07 4.85
193 204 8.780846 TCCTTTAGCAGATTGTATCGTAAAAA 57.219 30.769 0.00 0.00 0.00 1.94
197 208 8.826710 CAATTTCCTTTAGCAGATTGTATCGTA 58.173 33.333 0.00 0.00 0.00 3.43
199 210 6.634436 GCAATTTCCTTTAGCAGATTGTATCG 59.366 38.462 0.00 0.00 0.00 2.92
213 224 3.782889 GCGAGTATGGCAATTTCCTTT 57.217 42.857 0.00 0.00 40.68 3.11
242 253 0.850100 ATGGTCCGGGATGGCAATTA 59.150 50.000 0.00 0.00 37.80 1.40
248 259 0.767375 AATCTGATGGTCCGGGATGG 59.233 55.000 0.00 0.00 40.09 3.51
260 271 9.793252 GTAATGAACAAACATAGCAAATCTGAT 57.207 29.630 0.00 0.00 0.00 2.90
295 306 4.378978 CGTGGGCGATGATGTTTCTTTTTA 60.379 41.667 0.00 0.00 41.33 1.52
318 329 0.315251 GGCACTTCACTTGAAAGGGC 59.685 55.000 1.52 1.52 33.72 5.19
333 344 0.168128 GTGTTGCTAATCGGTGGCAC 59.832 55.000 9.70 9.70 35.62 5.01
407 421 1.274447 CTACCCGGGAAGTCGAGTTTT 59.726 52.381 32.02 1.34 0.00 2.43
417 431 0.474273 AGTTGGTTCCTACCCGGGAA 60.474 55.000 32.02 8.15 44.35 3.97
513 583 3.372440 AAGCGGGAAAAAGATGAGGAT 57.628 42.857 0.00 0.00 0.00 3.24
943 1038 4.213531 TGGAGGAGGATGCTATTAGGAA 57.786 45.455 0.00 0.00 36.27 3.36
948 1043 3.072184 GTGTGATGGAGGAGGATGCTATT 59.928 47.826 0.00 0.00 36.27 1.73
1059 1154 2.235650 CCTCTCAATGAGCTTCCTGTCA 59.764 50.000 5.18 0.00 41.35 3.58
1109 1204 7.528481 TGCTGCAAATGAAATTGATTGATAC 57.472 32.000 0.00 0.00 36.10 2.24
1110 1205 9.471084 CTATGCTGCAAATGAAATTGATTGATA 57.529 29.630 6.36 0.00 36.10 2.15
1111 1206 7.441157 CCTATGCTGCAAATGAAATTGATTGAT 59.559 33.333 6.36 0.00 36.10 2.57
1154 1249 2.487532 GCCTCAGATGCCATGCCAC 61.488 63.158 0.00 0.00 0.00 5.01
1157 1252 1.153025 TCTGCCTCAGATGCCATGC 60.153 57.895 0.00 0.00 35.39 4.06
1210 1305 3.068691 TCGAGAGCCTTGGTCCCG 61.069 66.667 0.00 0.00 32.91 5.14
1296 1391 1.675483 TGCGCACATGATAAACCATCC 59.325 47.619 5.66 0.00 32.09 3.51
1323 1418 6.312426 CAGGAACAATTTCAGAGCACTAGTAG 59.688 42.308 0.00 0.00 32.80 2.57
1345 1440 6.098695 ACCAAACCCATAATCAATCAATCAGG 59.901 38.462 0.00 0.00 0.00 3.86
1356 1451 4.532834 TGCTTAGGACCAAACCCATAATC 58.467 43.478 0.00 0.00 0.00 1.75
1360 1455 1.005924 CCTGCTTAGGACCAAACCCAT 59.994 52.381 0.00 0.00 0.00 4.00
1439 1534 5.781210 TGATCTTCTTGAGCAGATCGTAT 57.219 39.130 13.41 0.00 44.25 3.06
1479 1574 7.201767 GCTTGAGCAGACCAAATCAAACTATAT 60.202 37.037 0.00 0.00 41.59 0.86
1530 1655 2.517959 TCAACAAAAGCCAGATGGAGG 58.482 47.619 2.18 0.00 37.39 4.30
1572 1697 1.628340 TGATCACAACCGGGATGTCTT 59.372 47.619 6.32 0.00 0.00 3.01
1573 1698 1.275666 TGATCACAACCGGGATGTCT 58.724 50.000 6.32 0.04 0.00 3.41
1750 1875 8.830580 CCAAGGTCTATCAAACATGTAGTAATG 58.169 37.037 0.00 0.00 0.00 1.90
1776 1901 9.660180 AAGAGATCTTGGTGTCTAAATTTAGAC 57.340 33.333 35.89 35.89 45.01 2.59
2259 2385 2.527624 TCCTGGTGGCAGTGCTCT 60.528 61.111 16.11 0.00 0.00 4.09
2427 2553 2.294233 TCTTTTGTGGATGTTGCTGCTC 59.706 45.455 0.00 0.00 0.00 4.26
2441 2567 1.270550 CATCTGCCGCCTTTCTTTTGT 59.729 47.619 0.00 0.00 0.00 2.83
2636 2762 1.067142 TGTTACACCGAGCATGGTCTC 60.067 52.381 21.73 6.79 41.38 3.36
3295 3432 6.148976 GTGATGATGGAGACCATTGATACATG 59.851 42.308 4.74 0.00 45.26 3.21
3427 3567 1.517242 CTTCACAGAACAGCCTGGTC 58.483 55.000 0.10 0.10 38.44 4.02
3428 3568 0.109342 CCTTCACAGAACAGCCTGGT 59.891 55.000 0.00 0.00 38.44 4.00


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

AutoCloner maintained by Alex Coulton.