Multiple sequence alignment - TraesCS5B01G068800

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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 TraesCS5B01G068800 chr5B 100.000 4501 0 0 1 4501 78442775 78447275 0.000000e+00 8312
1 TraesCS5B01G068800 chr5B 92.012 4519 309 28 1 4501 234171515 234167031 0.000000e+00 6298
2 TraesCS5B01G068800 chr5B 94.083 2569 149 2 564 3132 565691645 565694210 0.000000e+00 3899
3 TraesCS5B01G068800 chr6B 93.483 4511 271 19 2 4501 290892834 290888336 0.000000e+00 6680
4 TraesCS5B01G068800 chr4B 92.321 4519 299 24 1 4501 12256045 12260533 0.000000e+00 6379
5 TraesCS5B01G068800 chr4B 91.355 4523 327 27 1 4501 141544553 141549033 0.000000e+00 6128
6 TraesCS5B01G068800 chr4B 92.402 3606 246 20 898 4493 115046837 115050424 0.000000e+00 5116
7 TraesCS5B01G068800 chr4B 91.224 3236 252 23 1283 4501 362743697 362746917 0.000000e+00 4373
8 TraesCS5B01G068800 chr4B 93.103 261 17 1 1 260 114955015 114955275 9.140000e-102 381
9 TraesCS5B01G068800 chr4B 90.459 283 21 5 1 280 644774990 644775269 7.110000e-98 368
10 TraesCS5B01G068800 chr3B 91.294 4514 327 28 1 4501 467942775 467938315 0.000000e+00 6098
11 TraesCS5B01G068800 chr3B 92.802 4043 271 18 473 4501 276866015 276870051 0.000000e+00 5836
12 TraesCS5B01G068800 chr3B 90.974 2105 153 10 2432 4501 64847817 64845715 0.000000e+00 2800
13 TraesCS5B01G068800 chr3B 87.855 2182 215 22 2363 4499 383229853 383227677 0.000000e+00 2516
14 TraesCS5B01G068800 chr3B 87.992 1499 141 21 3022 4501 705856011 705854533 0.000000e+00 1735
15 TraesCS5B01G068800 chr3B 92.373 472 30 6 1 470 276854629 276855096 0.000000e+00 667
16 TraesCS5B01G068800 chr3B 90.268 411 35 5 1 408 383232218 383231810 2.380000e-147 532
17 TraesCS5B01G068800 chr7D 89.220 3358 332 23 282 3622 122694984 122698328 0.000000e+00 4169
18 TraesCS5B01G068800 chr3D 89.184 3356 338 20 282 3626 116345827 116349168 0.000000e+00 4163
19 TraesCS5B01G068800 chr4D 89.236 3298 312 25 342 3626 179922179 179918912 0.000000e+00 4084
20 TraesCS5B01G068800 chr4D 89.161 286 23 7 1 279 179922594 179922310 2.580000e-92 350
21 TraesCS5B01G068800 chr4D 89.123 285 20 7 1 275 170245653 170245370 1.200000e-90 344
22 TraesCS5B01G068800 chr2D 87.274 3481 392 34 283 3737 372622107 372625562 0.000000e+00 3927
23 TraesCS5B01G068800 chr2D 86.273 1559 168 29 2512 4046 543471676 543473212 0.000000e+00 1652
24 TraesCS5B01G068800 chr2D 91.304 276 21 3 1 274 324865036 324865310 1.530000e-99 374
25 TraesCS5B01G068800 chr5D 91.459 281 19 5 1 276 188383903 188383623 9.140000e-102 381
26 TraesCS5B01G068800 chr5D 90.175 285 23 4 1 280 464320931 464320647 2.560000e-97 366
27 TraesCS5B01G068800 chr1D 91.429 280 18 4 1 275 5544940 5544662 3.290000e-101 379
28 TraesCS5B01G068800 chr6D 90.175 285 21 6 1 280 72375774 72375492 9.200000e-97 364
29 TraesCS5B01G068800 chr6D 85.305 279 29 11 3 272 41380854 41381129 1.230000e-70 278
30 TraesCS5B01G068800 chr6D 83.755 277 35 10 3 272 347431011 347430738 2.080000e-63 254


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 TraesCS5B01G068800 chr5B 78442775 78447275 4500 False 8312 8312 100.0000 1 4501 1 chr5B.!!$F1 4500
1 TraesCS5B01G068800 chr5B 234167031 234171515 4484 True 6298 6298 92.0120 1 4501 1 chr5B.!!$R1 4500
2 TraesCS5B01G068800 chr5B 565691645 565694210 2565 False 3899 3899 94.0830 564 3132 1 chr5B.!!$F2 2568
3 TraesCS5B01G068800 chr6B 290888336 290892834 4498 True 6680 6680 93.4830 2 4501 1 chr6B.!!$R1 4499
4 TraesCS5B01G068800 chr4B 12256045 12260533 4488 False 6379 6379 92.3210 1 4501 1 chr4B.!!$F1 4500
5 TraesCS5B01G068800 chr4B 141544553 141549033 4480 False 6128 6128 91.3550 1 4501 1 chr4B.!!$F4 4500
6 TraesCS5B01G068800 chr4B 115046837 115050424 3587 False 5116 5116 92.4020 898 4493 1 chr4B.!!$F3 3595
7 TraesCS5B01G068800 chr4B 362743697 362746917 3220 False 4373 4373 91.2240 1283 4501 1 chr4B.!!$F5 3218
8 TraesCS5B01G068800 chr3B 467938315 467942775 4460 True 6098 6098 91.2940 1 4501 1 chr3B.!!$R2 4500
9 TraesCS5B01G068800 chr3B 276866015 276870051 4036 False 5836 5836 92.8020 473 4501 1 chr3B.!!$F2 4028
10 TraesCS5B01G068800 chr3B 64845715 64847817 2102 True 2800 2800 90.9740 2432 4501 1 chr3B.!!$R1 2069
11 TraesCS5B01G068800 chr3B 705854533 705856011 1478 True 1735 1735 87.9920 3022 4501 1 chr3B.!!$R3 1479
12 TraesCS5B01G068800 chr3B 383227677 383232218 4541 True 1524 2516 89.0615 1 4499 2 chr3B.!!$R4 4498
13 TraesCS5B01G068800 chr7D 122694984 122698328 3344 False 4169 4169 89.2200 282 3622 1 chr7D.!!$F1 3340
14 TraesCS5B01G068800 chr3D 116345827 116349168 3341 False 4163 4163 89.1840 282 3626 1 chr3D.!!$F1 3344
15 TraesCS5B01G068800 chr4D 179918912 179922594 3682 True 2217 4084 89.1985 1 3626 2 chr4D.!!$R2 3625
16 TraesCS5B01G068800 chr2D 372622107 372625562 3455 False 3927 3927 87.2740 283 3737 1 chr2D.!!$F2 3454
17 TraesCS5B01G068800 chr2D 543471676 543473212 1536 False 1652 1652 86.2730 2512 4046 1 chr2D.!!$F3 1534

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
379 526 0.033781 GCTGCCATGGCTCAAAAACA 59.966 50.0 35.53 13.44 42.51 2.83 F
1311 1483 0.583438 CAGCAGACGTCACAAACCTG 59.417 55.0 19.50 6.33 0.00 4.00 F
2001 2175 0.453390 CAGCGCTTCTTCCCATTTCC 59.547 55.0 7.50 0.00 0.00 3.13 F
2071 2245 0.991146 TGAGCCCTGGCAACTCATTA 59.009 50.0 11.38 0.00 44.88 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1985 0.038251 TTGTGCAGCTCTAGACGGTG 60.038 55.0 13.66 13.66 0.00 4.94 R
3212 3565 2.136298 TCCTGTGTTTTTCTGCCACA 57.864 45.0 0.00 0.00 37.52 4.17 R
3353 3706 0.467290 TGCTTGTTGTTCCAGACCCC 60.467 55.0 0.00 0.00 0.00 4.95 R
3659 4031 0.815213 CACATGGCGGATTCGATGGT 60.815 55.0 0.00 0.00 39.00 3.55 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
196 198 7.925483 TGAACTAGCAAAACAATAGTGCATTTT 59.075 29.630 0.00 0.00 40.83 1.82
206 208 5.990996 ACAATAGTGCATTTTCTTTTGTGGG 59.009 36.000 9.14 0.00 35.65 4.61
253 261 1.817209 GGTGGTGGCGGAAAACAAA 59.183 52.632 0.00 0.00 0.00 2.83
280 378 1.695893 CTACCAAGTGGACGCATGCG 61.696 60.000 36.79 36.79 41.24 4.73
379 526 0.033781 GCTGCCATGGCTCAAAAACA 59.966 50.000 35.53 13.44 42.51 2.83
539 703 3.071479 GGCCTTCGACTACAATCAACAA 58.929 45.455 0.00 0.00 0.00 2.83
689 854 0.756442 AGCACACCTTTGCACACCAT 60.756 50.000 0.00 0.00 45.62 3.55
747 912 8.668353 GCTAATACTGAAGTGAATGATGAAACA 58.332 33.333 0.00 0.00 0.00 2.83
916 1082 7.394923 TGAACACCGAATACCATAGGAAAATTT 59.605 33.333 0.00 0.00 0.00 1.82
917 1083 7.712204 ACACCGAATACCATAGGAAAATTTT 57.288 32.000 2.28 2.28 0.00 1.82
984 1153 2.152016 CGAAGGAACAAGAAGGGGAAC 58.848 52.381 0.00 0.00 0.00 3.62
1029 1198 5.292101 GGAACGAAAGAGAGGTATCATTGTG 59.708 44.000 0.00 0.00 0.00 3.33
1050 1220 3.805928 ACAGAATGCCCTGTCCGA 58.194 55.556 0.00 0.00 43.34 4.55
1199 1371 4.776532 CGAGAAGAAATTCGTAAAGTTGCG 59.223 41.667 0.00 0.00 37.63 4.85
1230 1402 2.762535 ATGTCGGTCCGTCAAGAATT 57.237 45.000 15.10 0.00 0.00 2.17
1257 1429 5.195940 CAAATACTGTCCCTGATCCACAAT 58.804 41.667 0.00 0.00 0.00 2.71
1311 1483 0.583438 CAGCAGACGTCACAAACCTG 59.417 55.000 19.50 6.33 0.00 4.00
1319 1491 1.002468 CGTCACAAACCTGAAGGCAAG 60.002 52.381 0.00 0.00 39.32 4.01
1334 1506 2.091775 AGGCAAGGTACCGTAGAGAGAT 60.092 50.000 6.18 0.00 0.00 2.75
1593 1765 3.187227 ACAATCAGTCATTGCAGTTCGAC 59.813 43.478 0.00 0.00 45.37 4.20
1630 1802 3.344904 ACGAAGATACGGATGGTTACG 57.655 47.619 0.00 0.00 37.61 3.18
1653 1826 4.758688 CTTGGCTGTTCAAAACCTTCTTT 58.241 39.130 0.00 0.00 0.00 2.52
1692 1865 7.994911 TGGACTTGCTCTGATGAACATAATAAT 59.005 33.333 0.00 0.00 0.00 1.28
1699 1872 9.494271 GCTCTGATGAACATAATAATAGACCAA 57.506 33.333 0.00 0.00 0.00 3.67
1852 2026 1.867233 GCATTCGAGTTATGCGTGGAT 59.133 47.619 4.89 0.00 39.02 3.41
1859 2033 1.066215 AGTTATGCGTGGATCACAGCA 60.066 47.619 15.38 15.38 43.32 4.41
1873 2047 1.126488 ACAGCATGACGATGGAGGAT 58.874 50.000 0.00 0.00 39.69 3.24
1902 2076 2.866762 GGAGTTGGACGACTATGATTGC 59.133 50.000 0.00 0.00 0.00 3.56
1921 2095 3.156293 TGCAACATACCAAGTGCAAGAT 58.844 40.909 0.00 0.00 0.00 2.40
1940 2114 5.339008 AGATAACGAGACACTTATTGGCA 57.661 39.130 0.00 0.00 34.40 4.92
1985 2159 2.182842 CCGGCCTACTTCATGCAGC 61.183 63.158 0.00 0.00 0.00 5.25
2001 2175 0.453390 CAGCGCTTCTTCCCATTTCC 59.547 55.000 7.50 0.00 0.00 3.13
2071 2245 0.991146 TGAGCCCTGGCAACTCATTA 59.009 50.000 11.38 0.00 44.88 1.90
2212 2386 6.666980 AGAGGCAGATGAGCAAGATATATACA 59.333 38.462 0.00 0.00 35.83 2.29
2418 2593 3.265737 TGCCATGTGGGTTGAACTATAGT 59.734 43.478 0.00 0.00 39.65 2.12
2427 2602 5.045505 TGGGTTGAACTATAGTTGCCATGTA 60.046 40.000 22.68 7.15 38.56 2.29
2463 2684 1.539827 GCCATGTGGGTTGAACTGTAC 59.460 52.381 0.54 0.00 39.65 2.90
2473 2694 3.317993 GGTTGAACTGTACTTGCCATGTT 59.682 43.478 0.00 0.00 0.00 2.71
2621 2934 3.568443 TCATGCAGTTGCCATATGGAAT 58.432 40.909 26.47 1.24 41.18 3.01
2672 2994 1.176527 ACAAGATTTCCATGCCACCG 58.823 50.000 0.00 0.00 0.00 4.94
2933 3260 5.334879 GGCAACGATAAATGAAGGCGAATAT 60.335 40.000 0.00 0.00 0.00 1.28
3170 3523 5.458015 GTTGTGTTAACCAAGAACTATGCC 58.542 41.667 2.48 0.00 0.00 4.40
3180 3533 6.047231 ACCAAGAACTATGCCGAACTAATAC 58.953 40.000 0.00 0.00 0.00 1.89
3212 3565 3.305950 GCAAGAGTGATGAGACAGTGAGT 60.306 47.826 0.00 0.00 0.00 3.41
3345 3698 1.418264 TGGGTCCGTCATCTGAAAACA 59.582 47.619 0.00 0.00 0.00 2.83
3379 3733 1.067565 TGGAACAACAAGCACGCAAAA 60.068 42.857 0.00 0.00 31.92 2.44
3467 3821 4.821260 GGGTTGGAAATTCAAGCAAAACAT 59.179 37.500 10.21 0.00 44.25 2.71
3509 3865 5.452636 GGCGGGAAATCCATAAAAGCAATTA 60.453 40.000 1.22 0.00 37.91 1.40
3784 4161 4.972751 AAAATGGCAACTGGGTACATTT 57.027 36.364 0.00 0.00 41.84 2.32
3833 4220 4.188462 TGTGAAATCACCTATAGTTGCCG 58.812 43.478 10.83 0.00 45.88 5.69
3834 4221 3.002348 GTGAAATCACCTATAGTTGCCGC 59.998 47.826 2.04 0.00 40.85 6.53
4005 4423 6.566141 CAGTTGCCATGTCAAAATATCATGA 58.434 36.000 0.00 0.00 40.64 3.07
4097 4526 5.069318 TGTTTTCAGGCATCATAGACACAA 58.931 37.500 0.00 0.00 0.00 3.33
4246 4677 4.760715 ACACGCCACCACTATATACTAGAG 59.239 45.833 0.00 0.00 0.00 2.43
4260 4691 3.166560 ACTAGAGTACGGAAGGGTTGT 57.833 47.619 0.00 0.00 0.00 3.32
4278 4709 8.370266 AGGGTTGTAGTCATAACATAGTACAA 57.630 34.615 0.00 0.00 38.53 2.41
4425 4860 2.254546 ATGAACTCTTGTGCGTTGGA 57.745 45.000 0.00 0.00 0.00 3.53
4454 4889 6.293081 CGTGTTGAAATCTTCAGTCATCAACT 60.293 38.462 15.02 0.00 44.18 3.16
4463 4898 6.634805 TCTTCAGTCATCAACTAGTTCCATC 58.365 40.000 4.77 0.00 36.07 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 198 1.969923 CCCATGCTTTCCCACAAAAGA 59.030 47.619 0.75 0.00 38.30 2.52
206 208 2.187100 TCCATTTTCCCCCATGCTTTC 58.813 47.619 0.00 0.00 0.00 2.62
340 486 4.943705 CAGCTATAGTTCAACAACCATGGT 59.056 41.667 13.00 13.00 32.22 3.55
689 854 1.672363 CTGCTTGAGTGTTGCTTGTGA 59.328 47.619 0.00 0.00 0.00 3.58
747 912 0.036010 CCCCTTGTGCTTCGTCATCT 60.036 55.000 0.00 0.00 0.00 2.90
916 1082 7.981225 ACCTCTGTTGTACTCGTTAGTTTTTAA 59.019 33.333 0.00 0.00 37.15 1.52
917 1083 7.436080 CACCTCTGTTGTACTCGTTAGTTTTTA 59.564 37.037 0.00 0.00 37.15 1.52
984 1153 1.447317 GCATGATAGGGGCAACACCG 61.447 60.000 0.00 0.00 46.76 4.94
1050 1220 5.163447 TGCTCCATCTACGTTTAGCTTACAT 60.163 40.000 0.00 0.00 0.00 2.29
1134 1304 2.519963 GCGCTCAGAAATTTTACCAGC 58.480 47.619 0.00 0.00 0.00 4.85
1199 1371 3.245284 CGGACCGACATTACAATCATGTC 59.755 47.826 8.64 3.40 44.89 3.06
1230 1402 3.199946 GGATCAGGGACAGTATTTGGACA 59.800 47.826 0.00 0.00 0.00 4.02
1257 1429 3.053619 TGCTACTCAGTCTACCATCTCCA 60.054 47.826 0.00 0.00 0.00 3.86
1311 1483 2.097825 TCTCTACGGTACCTTGCCTTC 58.902 52.381 10.90 0.00 0.00 3.46
1319 1491 3.211718 ACCTGATCTCTCTACGGTACC 57.788 52.381 0.16 0.16 0.00 3.34
1398 1570 6.920758 CGTCCAATCTTATCCTGTAGAAGAAG 59.079 42.308 0.00 0.00 38.84 2.85
1593 1765 2.087009 GTTCCGAACGAGTCCGCAG 61.087 63.158 0.00 0.00 39.95 5.18
1630 1802 2.101415 AGAAGGTTTTGAACAGCCAAGC 59.899 45.455 0.00 0.00 0.00 4.01
1653 1826 0.994247 AAGTCCATCCATGCACTCCA 59.006 50.000 0.00 0.00 0.00 3.86
1692 1865 4.332543 CACGCATGCTAAAATCTTGGTCTA 59.667 41.667 17.13 0.00 0.00 2.59
1699 1872 2.614057 GCCTACACGCATGCTAAAATCT 59.386 45.455 17.13 0.00 0.00 2.40
1808 1981 0.609406 TGCAGCTCTAGACGGTGAGT 60.609 55.000 19.17 0.00 33.22 3.41
1811 1985 0.038251 TTGTGCAGCTCTAGACGGTG 60.038 55.000 13.66 13.66 0.00 4.94
1852 2026 0.176449 CCTCCATCGTCATGCTGTGA 59.824 55.000 0.00 0.00 0.00 3.58
1859 2033 4.581824 CCATTCAAAATCCTCCATCGTCAT 59.418 41.667 0.00 0.00 0.00 3.06
1873 2047 3.815809 AGTCGTCCAACTCCATTCAAAA 58.184 40.909 0.00 0.00 0.00 2.44
1902 2076 5.121611 TCGTTATCTTGCACTTGGTATGTTG 59.878 40.000 0.00 0.00 0.00 3.33
1921 2095 4.629634 CACATGCCAATAAGTGTCTCGTTA 59.370 41.667 0.00 0.00 0.00 3.18
1940 2114 2.501723 AGTACATTCGCTTCTCCCACAT 59.498 45.455 0.00 0.00 0.00 3.21
1985 2159 1.305219 TGCGGAAATGGGAAGAAGCG 61.305 55.000 0.00 0.00 0.00 4.68
2071 2245 2.200989 TTGCTTGGCAAACTGCAGT 58.799 47.368 15.25 15.25 45.96 4.40
2212 2386 8.885722 TCGACTTACTTGTTACAAATCTTGTTT 58.114 29.630 0.00 0.00 42.22 2.83
2418 2593 3.222173 ACAGTTCAACCTACATGGCAA 57.778 42.857 0.00 0.00 40.22 4.52
2427 2602 3.149196 CATGGCAACTACAGTTCAACCT 58.851 45.455 0.00 0.00 35.83 3.50
2670 2992 6.471839 CAACACGTATATCTAAAACCAACGG 58.528 40.000 0.00 0.00 33.44 4.44
2672 2994 7.068692 AGCAACACGTATATCTAAAACCAAC 57.931 36.000 0.00 0.00 0.00 3.77
2933 3260 3.587923 GAATTTGCAGCATTGGCAGTAA 58.412 40.909 0.00 0.00 43.05 2.24
3170 3523 5.408204 TGCATGCTTCATGTATTAGTTCG 57.592 39.130 20.33 0.00 43.10 3.95
3180 3533 3.377172 TCATCACTCTTGCATGCTTCATG 59.623 43.478 20.33 10.78 43.91 3.07
3212 3565 2.136298 TCCTGTGTTTTTCTGCCACA 57.864 45.000 0.00 0.00 37.52 4.17
3345 3698 3.477956 TTCCAGACCCCACCTCCGT 62.478 63.158 0.00 0.00 0.00 4.69
3353 3706 0.467290 TGCTTGTTGTTCCAGACCCC 60.467 55.000 0.00 0.00 0.00 4.95
3467 3821 2.556622 CGCCCCTTTCTTTGCTTTCTTA 59.443 45.455 0.00 0.00 0.00 2.10
3509 3865 5.824624 CAGCACATAAGTTACAATCCTCCAT 59.175 40.000 0.00 0.00 0.00 3.41
3659 4031 0.815213 CACATGGCGGATTCGATGGT 60.815 55.000 0.00 0.00 39.00 3.55
3833 4220 3.181541 GCAACTGCATTTTCATTACACGC 60.182 43.478 0.00 0.00 41.59 5.34
3834 4221 3.364621 GGCAACTGCATTTTCATTACACG 59.635 43.478 3.76 0.00 44.36 4.49
4155 4584 5.810080 ACTTAGGTTTGACAGAAGCTACT 57.190 39.130 0.00 0.00 38.80 2.57
4246 4677 3.881937 ATGACTACAACCCTTCCGTAC 57.118 47.619 0.00 0.00 0.00 3.67
4402 4837 3.935203 CCAACGCACAAGAGTTCATAGAT 59.065 43.478 0.00 0.00 35.49 1.98
4425 4860 1.531149 CTGAAGATTTCAACACGCGGT 59.469 47.619 12.47 2.05 39.58 5.68
4454 4889 7.042051 GCTTCGCAAAATATACAGATGGAACTA 60.042 37.037 0.00 0.00 0.00 2.24
4463 4898 7.587757 GGTAATTGAGCTTCGCAAAATATACAG 59.412 37.037 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.