Multiple sequence alignment - TraesCS5A01G319400

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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 TraesCS5A01G319400 chr5A 100.000 3393 0 0 1 3393 531084647 531081255 0.000000e+00 6266.0
1 TraesCS5A01G319400 chr5A 78.261 138 22 7 1751 1884 417255814 417255947 7.800000e-12 82.4
2 TraesCS5A01G319400 chr5D 94.511 3407 164 14 1 3393 417628577 417625180 0.000000e+00 5234.0
3 TraesCS5A01G319400 chr5D 78.261 138 22 7 1751 1884 322005206 322005339 7.800000e-12 82.4
4 TraesCS5A01G319400 chr5D 83.544 79 11 2 1800 1877 438370140 438370063 4.700000e-09 73.1
5 TraesCS5A01G319400 chr5B 91.728 3252 184 43 1 3225 504834739 504831546 0.000000e+00 4436.0
6 TraesCS5A01G319400 chr5B 85.882 85 10 2 1794 1877 532892176 532892093 4.660000e-14 89.8
7 TraesCS5A01G319400 chr5B 83.544 79 11 2 1800 1877 532878806 532878729 4.700000e-09 73.1
8 TraesCS5A01G319400 chr7B 79.261 487 76 22 1513 1991 672765218 672764749 1.970000e-82 316.0
9 TraesCS5A01G319400 chr7B 78.788 132 22 6 1704 1832 180040924 180040796 2.170000e-12 84.2
10 TraesCS5A01G319400 chr7B 83.529 85 11 3 1292 1375 672765331 672765249 3.630000e-10 76.8
11 TraesCS5A01G319400 chr7A 83.529 85 11 3 1292 1375 688314093 688314011 3.630000e-10 76.8
12 TraesCS5A01G319400 chr7A 84.211 57 9 0 1284 1340 200032961 200032905 4.730000e-04 56.5
13 TraesCS5A01G319400 chr7A 96.875 32 0 1 1304 1335 200065134 200065104 6.000000e-03 52.8
14 TraesCS5A01G319400 chr7D 77.344 128 25 4 1704 1829 219637163 219637288 4.700000e-09 73.1
15 TraesCS5A01G319400 chr7D 90.909 55 3 2 1293 1346 595328766 595328713 4.700000e-09 73.1
16 TraesCS5A01G319400 chr7D 84.211 57 9 0 1284 1340 191493551 191493495 4.730000e-04 56.5
17 TraesCS5A01G319400 chr7D 85.714 56 5 3 1281 1335 191558010 191557957 4.730000e-04 56.5
18 TraesCS5A01G319400 chrUn 83.562 73 10 2 1761 1832 270733643 270733572 2.190000e-07 67.6
19 TraesCS5A01G319400 chr3B 97.143 35 1 0 1972 2006 76433062 76433028 3.660000e-05 60.2
20 TraesCS5A01G319400 chr3A 100.000 28 0 0 1972 1999 50891166 50891193 6.000000e-03 52.8


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 TraesCS5A01G319400 chr5A 531081255 531084647 3392 True 6266 6266 100.000 1 3393 1 chr5A.!!$R1 3392
1 TraesCS5A01G319400 chr5D 417625180 417628577 3397 True 5234 5234 94.511 1 3393 1 chr5D.!!$R1 3392
2 TraesCS5A01G319400 chr5B 504831546 504834739 3193 True 4436 4436 91.728 1 3225 1 chr5B.!!$R1 3224

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
819 830 0.033504 GCAAACACGAGGAGGACAGA 59.966 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 2453 0.670162 AGGCAGTGCAATGTTGTGAC 59.33 50.0 18.61 0.0 0.0 3.67 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
30 31 3.071206 AGATGCTCCACCGCTCGT 61.071 61.111 0.00 0.00 0.00 4.18
31 32 2.125512 GATGCTCCACCGCTCGTT 60.126 61.111 0.00 0.00 0.00 3.85
42 43 1.577328 CCGCTCGTTGTTGCAGGAAT 61.577 55.000 0.00 0.00 0.00 3.01
48 49 1.787012 GTTGTTGCAGGAATGCCTTG 58.213 50.000 0.00 0.00 43.90 3.61
51 52 0.033781 GTTGCAGGAATGCCTTGCAA 59.966 50.000 19.83 19.83 43.90 4.08
104 105 0.036765 CTGCCAAGCACCCGTAGTTA 60.037 55.000 0.00 0.00 33.79 2.24
184 185 2.994995 ACCGGATCTGGCACACGA 60.995 61.111 21.17 0.00 0.00 4.35
241 242 4.254709 TGGCCAACGTCTGCAGCT 62.255 61.111 9.47 0.00 0.00 4.24
246 247 1.889105 CAACGTCTGCAGCTGTGGT 60.889 57.895 16.64 3.61 0.00 4.16
247 248 0.599991 CAACGTCTGCAGCTGTGGTA 60.600 55.000 16.64 0.00 0.00 3.25
330 331 3.965539 GAGCGGTGGCACATGAGCT 62.966 63.158 20.82 21.75 44.70 4.09
338 339 3.181461 GGTGGCACATGAGCTAGTCTATT 60.181 47.826 20.82 0.00 44.52 1.73
342 343 3.805108 GCACATGAGCTAGTCTATTGGGG 60.805 52.174 7.97 0.00 0.00 4.96
344 345 4.040755 ACATGAGCTAGTCTATTGGGGTT 58.959 43.478 0.00 0.00 0.00 4.11
372 373 1.341976 TGATGGACTCGGGATGACTCA 60.342 52.381 0.00 0.00 0.00 3.41
410 413 7.639113 TCATGTCACCTTTGTAAGTCTTTTT 57.361 32.000 0.00 0.00 0.00 1.94
411 414 8.740123 TCATGTCACCTTTGTAAGTCTTTTTA 57.260 30.769 0.00 0.00 0.00 1.52
417 420 7.923878 TCACCTTTGTAAGTCTTTTTATTTGGC 59.076 33.333 0.00 0.00 0.00 4.52
419 422 7.926018 ACCTTTGTAAGTCTTTTTATTTGGCAG 59.074 33.333 0.00 0.00 0.00 4.85
462 466 5.306532 ACACAATACAGACGTAGACGATT 57.693 39.130 9.41 0.00 43.02 3.34
466 470 8.615211 ACACAATACAGACGTAGACGATTATAA 58.385 33.333 9.41 0.00 43.02 0.98
500 504 5.761234 TGAAACCGGACAATATAGTTATGGC 59.239 40.000 9.46 0.00 0.00 4.40
548 553 3.437049 GGGAGGTTTGTCATTCTTTCTCG 59.563 47.826 0.00 0.00 0.00 4.04
549 554 3.437049 GGAGGTTTGTCATTCTTTCTCGG 59.563 47.826 0.00 0.00 0.00 4.63
550 555 3.412386 AGGTTTGTCATTCTTTCTCGGG 58.588 45.455 0.00 0.00 0.00 5.14
648 659 6.595716 GCAACTACTATCATGACTTTGTTCCT 59.404 38.462 0.00 0.00 0.00 3.36
722 733 1.200020 CGCTTACAAAAGGCCCTTCTG 59.800 52.381 0.00 0.00 32.98 3.02
819 830 0.033504 GCAAACACGAGGAGGACAGA 59.966 55.000 0.00 0.00 0.00 3.41
988 1000 0.806884 TTGTTCCACACGTCGTCCAC 60.807 55.000 0.00 0.00 0.00 4.02
1092 1106 2.201732 CGGAGGTACACATACACATGC 58.798 52.381 0.00 0.00 35.39 4.06
1093 1107 2.159099 CGGAGGTACACATACACATGCT 60.159 50.000 0.00 0.00 35.39 3.79
1098 1112 3.378112 GGTACACATACACATGCTTGCAT 59.622 43.478 1.81 1.81 35.39 3.96
1101 1115 1.135527 ACATACACATGCTTGCATGCC 59.864 47.619 28.75 0.00 35.39 4.40
1138 1152 6.566197 AGTTCTTGATTCATTTGGTGAGAC 57.434 37.500 0.00 0.00 38.29 3.36
1180 1194 1.107114 TTTTGGTGTGCGGTGTTGAT 58.893 45.000 0.00 0.00 0.00 2.57
1181 1195 0.383590 TTTGGTGTGCGGTGTTGATG 59.616 50.000 0.00 0.00 0.00 3.07
1381 1395 0.817013 TCGAGGTACGCCGGTAAATT 59.183 50.000 1.90 0.00 42.26 1.82
1382 1396 0.925466 CGAGGTACGCCGGTAAATTG 59.075 55.000 1.90 0.00 40.50 2.32
1468 1487 1.338337 GGTCTCATGGATCGACATCGT 59.662 52.381 0.54 0.00 40.80 3.73
1469 1488 2.552743 GGTCTCATGGATCGACATCGTA 59.447 50.000 0.54 0.00 40.80 3.43
1470 1489 3.556513 GTCTCATGGATCGACATCGTAC 58.443 50.000 0.54 0.00 40.80 3.67
1475 1494 1.267682 TGGATCGACATCGTACGTTCG 60.268 52.381 22.04 22.04 40.80 3.95
1660 1679 1.298993 CCACAGCCTGCTCACTCAT 59.701 57.895 0.00 0.00 0.00 2.90
1702 1721 4.891037 GCCTCCCAGCAGCATCCC 62.891 72.222 0.00 0.00 0.00 3.85
2238 2257 0.452184 GAGGTCGTCGAGATGCTCAA 59.548 55.000 0.00 0.00 0.00 3.02
2398 2417 0.589229 CGACGCTGAGGTGATACGAC 60.589 60.000 0.00 0.00 0.00 4.34
2434 2453 1.598676 CCATTTCGATCCATGCTTGCG 60.599 52.381 0.00 0.00 0.00 4.85
2500 2519 7.761409 TGCAAATTCATGATTAGTGGTTCTAC 58.239 34.615 0.00 0.00 0.00 2.59
2518 2537 7.174253 TGGTTCTACTTAGATCGCATTTTGTTT 59.826 33.333 0.00 0.00 31.40 2.83
2615 2634 3.335579 ACCAAGAGTTGTTAATCCTCGC 58.664 45.455 0.00 0.00 0.00 5.03
2732 2757 5.277345 CGTAGCTTGAAAGGTATACATTGGC 60.277 44.000 3.11 6.61 40.65 4.52
2924 2955 6.894103 AGTCAATGAAAGCTTCCATTTCCTAT 59.106 34.615 8.36 0.00 36.11 2.57
3029 3060 6.601332 TGGTTTGACTTAAGAAGAATGGAGT 58.399 36.000 10.09 0.00 0.00 3.85
3039 3070 2.706339 AGAATGGAGTGAGCATGGTC 57.294 50.000 18.01 18.01 0.00 4.02
3043 3074 3.834489 ATGGAGTGAGCATGGTCTTAG 57.166 47.619 24.30 0.00 0.00 2.18
3151 3186 7.742151 TGACGAACAGATGACATTTAATTCAG 58.258 34.615 0.00 0.00 0.00 3.02
3174 3211 6.980397 CAGTAGAGGAAACAATTTTTGCTTGT 59.020 34.615 7.95 0.00 38.44 3.16
3308 3345 1.271856 TCAAACCGGTGAGCCTATCA 58.728 50.000 8.52 0.00 34.79 2.15
3353 3390 0.796312 CCGGTTCACTGGTTCAATCG 59.204 55.000 0.00 0.00 37.62 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.895100 GATGGGACTGTTGCAAGGCA 60.895 55.000 0.00 0.00 36.47 4.75
48 49 1.589716 GGCAGTGATGGGACTGTTGC 61.590 60.000 0.00 0.00 44.53 4.17
51 52 1.539869 AGGGCAGTGATGGGACTGT 60.540 57.895 0.00 0.00 44.53 3.55
76 77 3.286751 GCTTGGCAGCAACCGTCA 61.287 61.111 0.00 0.00 46.49 4.35
160 161 3.077907 CCAGATCCGGTGGTGGTT 58.922 61.111 0.00 0.00 0.00 3.67
164 165 2.927856 TGTGCCAGATCCGGTGGT 60.928 61.111 10.99 0.00 37.40 4.16
192 193 1.328430 GCCCCTGCTACGAAGGTAGT 61.328 60.000 0.00 0.00 46.42 2.73
241 242 3.449227 CCTCGCCTCGCTACCACA 61.449 66.667 0.00 0.00 0.00 4.17
246 247 4.143333 GCCAACCTCGCCTCGCTA 62.143 66.667 0.00 0.00 0.00 4.26
330 331 4.764823 CAGCAAAACAACCCCAATAGACTA 59.235 41.667 0.00 0.00 0.00 2.59
338 339 1.047002 CCATCAGCAAAACAACCCCA 58.953 50.000 0.00 0.00 0.00 4.96
342 343 2.350772 CCGAGTCCATCAGCAAAACAAC 60.351 50.000 0.00 0.00 0.00 3.32
344 345 1.522668 CCGAGTCCATCAGCAAAACA 58.477 50.000 0.00 0.00 0.00 2.83
372 373 7.765695 AGGTGACATGAAAATGATAAACACT 57.234 32.000 0.00 0.00 0.00 3.55
410 413 4.728772 ACTATATTGCCTGCTGCCAAATA 58.271 39.130 0.00 0.00 40.16 1.40
411 414 3.569491 ACTATATTGCCTGCTGCCAAAT 58.431 40.909 0.00 0.00 40.16 2.32
445 449 9.964253 CGTATTTATAATCGTCTACGTCTGTAT 57.036 33.333 0.00 0.29 40.80 2.29
446 450 9.191995 TCGTATTTATAATCGTCTACGTCTGTA 57.808 33.333 0.00 0.00 40.80 2.74
448 452 8.006027 TGTCGTATTTATAATCGTCTACGTCTG 58.994 37.037 0.00 0.00 40.80 3.51
462 466 7.040494 TGTCCGGTTTCAATGTCGTATTTATA 58.960 34.615 0.00 0.00 0.00 0.98
466 470 3.666274 TGTCCGGTTTCAATGTCGTATT 58.334 40.909 0.00 0.00 0.00 1.89
479 483 4.312443 CGCCATAACTATATTGTCCGGTT 58.688 43.478 0.00 0.00 0.00 4.44
500 504 0.041047 CGCACCATGAATGCATACCG 60.041 55.000 18.41 2.30 43.57 4.02
532 537 5.845391 AAAACCCGAGAAAGAATGACAAA 57.155 34.783 0.00 0.00 0.00 2.83
648 659 3.072330 TGTGTAGCTTCCAGATGGTCAAA 59.928 43.478 0.00 0.00 36.34 2.69
722 733 0.179062 CCTGCTGTACATCTGCCTCC 60.179 60.000 0.00 0.00 39.70 4.30
819 830 3.208594 GTTTGTTTCTCCGGGTACAAGT 58.791 45.455 0.00 0.00 32.67 3.16
988 1000 2.939103 GGTTGATCATTTCCTCAGACGG 59.061 50.000 0.00 0.00 0.00 4.79
1090 1102 3.124270 CGTACGGGCATGCAAGCA 61.124 61.111 21.36 0.00 35.83 3.91
1091 1105 3.876198 CCGTACGGGCATGCAAGC 61.876 66.667 27.00 5.09 0.00 4.01
1092 1106 2.038269 AACCGTACGGGCATGCAAG 61.038 57.895 35.86 14.86 40.62 4.01
1093 1107 2.032834 AACCGTACGGGCATGCAA 59.967 55.556 35.86 0.00 40.62 4.08
1098 1112 0.392336 ACTAAACAACCGTACGGGCA 59.608 50.000 35.86 14.08 40.62 5.36
1101 1115 4.050553 TCAAGAACTAAACAACCGTACGG 58.949 43.478 32.22 32.22 42.03 4.02
1138 1152 0.813184 ATGCAACTCAGCCAAATCCG 59.187 50.000 0.00 0.00 0.00 4.18
1180 1194 0.038166 GATCCCTGCTCCCAAACACA 59.962 55.000 0.00 0.00 0.00 3.72
1181 1195 0.681243 GGATCCCTGCTCCCAAACAC 60.681 60.000 0.00 0.00 0.00 3.32
1336 1350 3.712907 GAGGTGCGGCCCCAGTAA 61.713 66.667 3.85 0.00 38.26 2.24
1439 1458 0.042581 TCCATGAGACCTGTAGGCCA 59.957 55.000 5.01 0.00 39.32 5.36
1441 1460 1.000283 CGATCCATGAGACCTGTAGGC 60.000 57.143 0.00 0.00 39.32 3.93
1468 1487 1.336148 ACCGCAATCTGAACGAACGTA 60.336 47.619 0.00 0.00 0.00 3.57
1469 1488 0.599204 ACCGCAATCTGAACGAACGT 60.599 50.000 0.00 0.00 0.00 3.99
1470 1489 0.179250 CACCGCAATCTGAACGAACG 60.179 55.000 0.00 0.00 0.00 3.95
1475 1494 0.179215 CGCTTCACCGCAATCTGAAC 60.179 55.000 0.00 0.00 0.00 3.18
1999 2018 4.427661 GCGCTGACGAGCTCCAGT 62.428 66.667 17.84 7.76 43.77 4.00
2398 2417 3.492102 AATGGTGGGAGATGGTAATCG 57.508 47.619 0.00 0.00 37.92 3.34
2434 2453 0.670162 AGGCAGTGCAATGTTGTGAC 59.330 50.000 18.61 0.00 0.00 3.67
2474 2493 7.230849 AGAACCACTAATCATGAATTTGCAA 57.769 32.000 0.00 0.00 0.00 4.08
2493 2512 6.663944 ACAAAATGCGATCTAAGTAGAACC 57.336 37.500 0.00 0.00 35.69 3.62
2615 2634 2.563702 ACAAAACTTTGCAGGCCAATG 58.436 42.857 5.01 0.00 41.79 2.82
2874 2905 9.553418 CTCTGATGATAACTACTCGAATATGTG 57.447 37.037 0.00 0.00 0.00 3.21
2951 2982 4.950475 TCCATATTTTTGGACATTACCGCA 59.050 37.500 0.00 0.00 40.90 5.69
3021 3052 2.706339 AGACCATGCTCACTCCATTC 57.294 50.000 0.00 0.00 0.00 2.67
3029 3060 5.957771 AACCTATTCTAAGACCATGCTCA 57.042 39.130 0.00 0.00 0.00 4.26
3039 3070 6.828785 ACCACCAAAGCATAACCTATTCTAAG 59.171 38.462 0.00 0.00 0.00 2.18
3043 3074 7.582667 AATACCACCAAAGCATAACCTATTC 57.417 36.000 0.00 0.00 0.00 1.75
3151 3186 6.292328 GCACAAGCAAAAATTGTTTCCTCTAC 60.292 38.462 0.00 0.00 38.80 2.59
3174 3211 4.385825 AGTTGACAATCTTCCTTAACGCA 58.614 39.130 0.00 0.00 0.00 5.24
3308 3345 6.146673 CAGTTCGACGGGTAAAAATTAGAACT 59.853 38.462 0.00 1.73 44.19 3.01
3343 3380 6.428465 TGTCTAATAAAACAGCGATTGAACCA 59.572 34.615 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.