Multiple sequence alignment - TraesCS4B01G159100

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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 TraesCS4B01G159100 chr4B 100.000 3062 0 0 1 3062 308692882 308695943 0 5655
1 TraesCS4B01G159100 chr5D 96.455 3075 89 6 1 3062 6185345 6188412 0 5057
2 TraesCS4B01G159100 chr5D 96.483 2445 70 6 631 3062 503281195 503278754 0 4024
3 TraesCS4B01G159100 chr5D 97.588 1078 25 1 1 1078 503282895 503281819 0 1845
4 TraesCS4B01G159100 chr5D 95.455 924 25 5 2153 3062 503216770 503217690 0 1458
5 TraesCS4B01G159100 chr1D 96.424 3076 85 9 1 3062 254401702 254398638 0 5048
6 TraesCS4B01G159100 chr1D 96.135 1423 51 4 1 1422 51882464 51883883 0 2320
7 TraesCS4B01G159100 chr6D 96.244 3062 95 8 1 3046 45515973 45519030 0 5000
8 TraesCS4B01G159100 chr6D 95.243 925 26 6 2153 3062 168253213 168252292 0 1448
9 TraesCS4B01G159100 chr6D 95.243 925 26 6 2153 3062 168253477 168254398 0 1448
10 TraesCS4B01G159100 chr2A 95.873 3077 88 11 1 3062 335835048 335838100 0 4942
11 TraesCS4B01G159100 chr4A 94.718 3086 132 20 1 3062 309511525 309514603 0 4767
12 TraesCS4B01G159100 chr4A 94.125 3081 150 14 1 3062 310734983 310738051 0 4658
13 TraesCS4B01G159100 chr4A 96.172 653 21 3 2411 3062 73814113 73813464 0 1064
14 TraesCS4B01G159100 chr3D 96.440 2135 57 7 942 3062 589282199 589280070 0 3504
15 TraesCS4B01G159100 chr3D 94.796 807 28 3 2268 3062 571593332 571592528 0 1245
16 TraesCS4B01G159100 chr5A 94.995 1978 78 9 1101 3062 607271900 607273872 0 3085
17 TraesCS4B01G159100 chr5A 95.551 1034 46 0 71 1104 607216288 607217321 0 1655
18 TraesCS4B01G159100 chrUn 95.351 925 24 7 2153 3062 93411079 93410159 0 1452
19 TraesCS4B01G159100 chrUn 95.135 925 27 6 2153 3062 216520051 216519130 0 1443
20 TraesCS4B01G159100 chr3B 95.135 925 26 7 2153 3062 201525576 201526496 0 1441
21 TraesCS4B01G159100 chr2D 95.078 833 24 4 2245 3062 322927463 322926633 0 1295


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 TraesCS4B01G159100 chr4B 308692882 308695943 3061 False 5655.0 5655 100.0000 1 3062 1 chr4B.!!$F1 3061
1 TraesCS4B01G159100 chr5D 6185345 6188412 3067 False 5057.0 5057 96.4550 1 3062 1 chr5D.!!$F1 3061
2 TraesCS4B01G159100 chr5D 503278754 503282895 4141 True 2934.5 4024 97.0355 1 3062 2 chr5D.!!$R1 3061
3 TraesCS4B01G159100 chr5D 503216770 503217690 920 False 1458.0 1458 95.4550 2153 3062 1 chr5D.!!$F2 909
4 TraesCS4B01G159100 chr1D 254398638 254401702 3064 True 5048.0 5048 96.4240 1 3062 1 chr1D.!!$R1 3061
5 TraesCS4B01G159100 chr1D 51882464 51883883 1419 False 2320.0 2320 96.1350 1 1422 1 chr1D.!!$F1 1421
6 TraesCS4B01G159100 chr6D 45515973 45519030 3057 False 5000.0 5000 96.2440 1 3046 1 chr6D.!!$F1 3045
7 TraesCS4B01G159100 chr6D 168252292 168253213 921 True 1448.0 1448 95.2430 2153 3062 1 chr6D.!!$R1 909
8 TraesCS4B01G159100 chr6D 168253477 168254398 921 False 1448.0 1448 95.2430 2153 3062 1 chr6D.!!$F2 909
9 TraesCS4B01G159100 chr2A 335835048 335838100 3052 False 4942.0 4942 95.8730 1 3062 1 chr2A.!!$F1 3061
10 TraesCS4B01G159100 chr4A 309511525 309514603 3078 False 4767.0 4767 94.7180 1 3062 1 chr4A.!!$F1 3061
11 TraesCS4B01G159100 chr4A 310734983 310738051 3068 False 4658.0 4658 94.1250 1 3062 1 chr4A.!!$F2 3061
12 TraesCS4B01G159100 chr4A 73813464 73814113 649 True 1064.0 1064 96.1720 2411 3062 1 chr4A.!!$R1 651
13 TraesCS4B01G159100 chr3D 589280070 589282199 2129 True 3504.0 3504 96.4400 942 3062 1 chr3D.!!$R2 2120
14 TraesCS4B01G159100 chr3D 571592528 571593332 804 True 1245.0 1245 94.7960 2268 3062 1 chr3D.!!$R1 794
15 TraesCS4B01G159100 chr5A 607271900 607273872 1972 False 3085.0 3085 94.9950 1101 3062 1 chr5A.!!$F2 1961
16 TraesCS4B01G159100 chr5A 607216288 607217321 1033 False 1655.0 1655 95.5510 71 1104 1 chr5A.!!$F1 1033
17 TraesCS4B01G159100 chrUn 93410159 93411079 920 True 1452.0 1452 95.3510 2153 3062 1 chrUn.!!$R1 909
18 TraesCS4B01G159100 chrUn 216519130 216520051 921 True 1443.0 1443 95.1350 2153 3062 1 chrUn.!!$R2 909
19 TraesCS4B01G159100 chr3B 201525576 201526496 920 False 1441.0 1441 95.1350 2153 3062 1 chr3B.!!$F1 909
20 TraesCS4B01G159100 chr2D 322926633 322927463 830 True 1295.0 1295 95.0780 2245 3062 1 chr2D.!!$R1 817

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
659 1190 7.676683 AGCTATTTCTACATAGGGAAAGTCA 57.323 36.0 0.0 0.0 35.37 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2594 3704 0.685097 GCTACATCCGCCCCTTATCA 59.315 55.0 0.0 0.0 0.0 2.15 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
133 134 7.700846 TCCTATTAGTAAACCCATTTGGACAA 58.299 34.615 0.00 0.00 37.39 3.18
142 143 9.665719 GTAAACCCATTTGGACAAATTTATCAT 57.334 29.630 7.51 0.00 38.84 2.45
259 261 8.942338 AAAGTATATACTTCGACTTTCATGCA 57.058 30.769 24.80 0.00 45.17 3.96
659 1190 7.676683 AGCTATTTCTACATAGGGAAAGTCA 57.323 36.000 0.00 0.00 35.37 3.41
901 1977 8.983789 TGACTTGGTTGACATTGGTATATAGTA 58.016 33.333 0.00 0.00 0.00 1.82
1026 2102 2.923655 TGCAATTTTAGAGAGACGCGAG 59.076 45.455 15.93 0.00 0.00 5.03
1053 2129 2.069165 GCCTGTGGGGTTCCTTCTGT 62.069 60.000 0.00 0.00 37.43 3.41
1082 2158 6.374333 TGGATAACTAGCACTGAAAATTGTCC 59.626 38.462 0.00 0.00 0.00 4.02
1140 2216 4.250464 CCTTATTGACCGCAACTTCTGTA 58.750 43.478 0.00 0.00 36.72 2.74
1141 2217 4.876107 CCTTATTGACCGCAACTTCTGTAT 59.124 41.667 0.00 0.00 36.72 2.29
1142 2218 5.354234 CCTTATTGACCGCAACTTCTGTATT 59.646 40.000 0.00 0.00 36.72 1.89
1143 2219 6.128007 CCTTATTGACCGCAACTTCTGTATTT 60.128 38.462 0.00 0.00 36.72 1.40
1291 2372 4.762289 TTGCACTTTTACCCAATTTGGT 57.238 36.364 14.26 6.44 42.62 3.67
1415 2496 4.492611 GAACTTAGTTTCCGTCTGGGTAG 58.507 47.826 0.00 0.00 37.00 3.18
1465 2546 0.036952 TCCTGTTGCAGCTGCTACTC 60.037 55.000 39.44 26.30 44.85 2.59
1544 2626 8.660295 TTAGGAATCTCTGGTACTTTCAACTA 57.340 34.615 0.00 0.00 0.00 2.24
1614 2696 3.072476 ACATGTTAGGTGTAGCTGGTGTT 59.928 43.478 0.00 0.00 0.00 3.32
1633 2715 0.460635 TTTCGGCGGTTCCCTATTCG 60.461 55.000 7.21 0.00 0.00 3.34
1654 2736 2.094675 GTGCTATGCATGGTTCCTTGT 58.905 47.619 10.16 0.00 41.91 3.16
1944 3032 5.745294 TGATAGTCAAGGTCGCGTTATTAAC 59.255 40.000 5.77 0.00 0.00 2.01
2033 3121 4.325084 ACTTCCCTCTAGACTTAGCTGT 57.675 45.455 0.00 0.00 0.00 4.40
2049 3137 3.554934 AGCTGTTGTTGAAGTTCCATCA 58.445 40.909 0.00 0.00 0.00 3.07
2134 3222 9.474313 AAATACCCAATATCTTGCTAGAACAAA 57.526 29.630 0.99 0.00 33.20 2.83
2387 3477 1.447643 GCTAGATGCACGGGACCAT 59.552 57.895 0.00 0.00 42.31 3.55
2549 3657 5.449314 CGATCGAAGTACAGAGGTCAGAATT 60.449 44.000 10.26 0.00 0.00 2.17
2623 3733 1.747206 GCGGATGTAGCCAAGTGGATT 60.747 52.381 0.18 0.00 37.39 3.01
2639 3749 4.227300 AGTGGATTAAGGCAGTGGATTGTA 59.773 41.667 0.00 0.00 0.00 2.41
2794 3906 7.492352 TTTTCCTTTTCCTAGTTCTTCTTCG 57.508 36.000 0.00 0.00 0.00 3.79
2802 3914 2.086054 AGTTCTTCTTCGAAGCGCAT 57.914 45.000 20.56 0.00 0.00 4.73
2983 4097 2.090999 ACCCCAACATTACCCACTTGTT 60.091 45.455 0.00 0.00 34.03 2.83
2992 4106 2.413310 ACCCACTTGTTCGACTGTTT 57.587 45.000 0.00 0.00 0.00 2.83
3034 4148 2.361085 ACTTACCTCCCCAGATGGTT 57.639 50.000 0.00 0.00 35.48 3.67
3038 4152 1.821088 ACCTCCCCAGATGGTTATCC 58.179 55.000 0.00 0.00 33.64 2.59
3046 4160 4.166144 CCCCAGATGGTTATCCTAAAGTGT 59.834 45.833 0.00 0.00 33.64 3.55
3047 4161 5.340027 CCCCAGATGGTTATCCTAAAGTGTT 60.340 44.000 0.00 0.00 33.64 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.549170 GCGGGGACTATGGTATCGAAT 59.451 52.381 0.00 0.00 0.00 3.34
142 143 8.163408 ACCAAATCGATCAAGAATATCCCAATA 58.837 33.333 0.00 0.00 0.00 1.90
259 261 9.918630 TTTATGTTTACGAGCTAAAGTTCTAGT 57.081 29.630 0.00 0.00 0.00 2.57
287 289 3.651206 TGCATAAAAGTTCGTACCGTGA 58.349 40.909 0.00 0.00 0.00 4.35
635 1166 7.676683 TGACTTTCCCTATGTAGAAATAGCT 57.323 36.000 0.00 0.00 31.89 3.32
849 1925 8.614814 AGCCCAAAGATTAGCTATCCATATAAA 58.385 33.333 0.00 0.00 32.73 1.40
1026 2102 0.400594 AACCCCACAGGCTTGTACTC 59.599 55.000 0.00 0.00 40.58 2.59
1045 2121 5.955959 TGCTAGTTATCCAGTTACAGAAGGA 59.044 40.000 0.00 0.00 34.12 3.36
1046 2122 6.043411 GTGCTAGTTATCCAGTTACAGAAGG 58.957 44.000 0.00 0.00 0.00 3.46
1053 2129 8.946085 CAATTTTCAGTGCTAGTTATCCAGTTA 58.054 33.333 0.00 0.00 0.00 2.24
1082 2158 3.861840 ACACTGAACCATCCGATGTAAG 58.138 45.455 7.60 2.37 0.00 2.34
1140 2216 5.182001 GGCAGCGATGAAGGTGATAATAAAT 59.818 40.000 4.02 0.00 41.72 1.40
1141 2217 4.515191 GGCAGCGATGAAGGTGATAATAAA 59.485 41.667 4.02 0.00 41.72 1.40
1142 2218 4.065088 GGCAGCGATGAAGGTGATAATAA 58.935 43.478 4.02 0.00 41.72 1.40
1143 2219 3.557054 GGGCAGCGATGAAGGTGATAATA 60.557 47.826 4.02 0.00 41.72 0.98
1291 2372 3.937079 CACTCATCAACAGATGCAGCTTA 59.063 43.478 0.00 0.00 39.18 3.09
1415 2496 0.958822 AACAACAATCCAAGGACGCC 59.041 50.000 0.00 0.00 0.00 5.68
1465 2546 8.986477 CCAATAGGGTAAATCAAGAAAACAAG 57.014 34.615 0.00 0.00 0.00 3.16
1544 2626 5.221986 TGCTCTGCCTGGAATACAATCATAT 60.222 40.000 0.00 0.00 0.00 1.78
1633 2715 1.406539 CAAGGAACCATGCATAGCACC 59.593 52.381 0.00 0.00 43.04 5.01
1654 2736 6.945636 TTCCCTGATCAAACTAGAGGTTAA 57.054 37.500 0.00 0.00 37.12 2.01
1748 2830 2.094286 CGGCCAAAATAACCATGAGCAA 60.094 45.455 2.24 0.00 0.00 3.91
1837 2919 8.611051 AAAGTAGTGAACCAGATTCCTACTAT 57.389 34.615 13.48 6.39 43.42 2.12
1944 3032 4.825546 GTTGATGATATCAGCCCAAGTG 57.174 45.455 17.90 0.00 40.94 3.16
2378 3468 4.563140 AACAATAGTAACATGGTCCCGT 57.437 40.909 0.00 0.00 0.00 5.28
2387 3477 7.974504 AGGAGGAGAAAGAAACAATAGTAACA 58.025 34.615 0.00 0.00 0.00 2.41
2489 3597 7.669722 ACATAGAATGGCACTCTTTAAAAAGGA 59.330 33.333 2.86 0.00 34.00 3.36
2505 3613 6.694844 CGATCGAGATATTGGACATAGAATGG 59.305 42.308 10.26 0.00 33.60 3.16
2594 3704 0.685097 GCTACATCCGCCCCTTATCA 59.315 55.000 0.00 0.00 0.00 2.15
2623 3733 5.186256 TGGATTTACAATCCACTGCCTTA 57.814 39.130 13.25 0.00 42.81 2.69
2794 3906 1.334869 CTTGGGGTTATCATGCGCTTC 59.665 52.381 9.73 0.00 0.00 3.86
2802 3914 1.076350 CACAACCCCTTGGGGTTATCA 59.924 52.381 34.97 0.00 42.24 2.15
2830 3943 4.086457 GGAAAGCTCCCATTGGTAGAAAA 58.914 43.478 0.00 0.00 35.42 2.29
2911 4025 6.351966 GGATCTAAGTGTTGGCTAGGTAAACT 60.352 42.308 0.00 0.00 0.00 2.66
2983 4097 4.272504 CCAAAACTGCTTAGAAACAGTCGA 59.727 41.667 0.00 0.00 46.17 4.20
2992 4106 7.686434 AGTTTAGTATCCCAAAACTGCTTAGA 58.314 34.615 0.00 0.00 40.85 2.10
3017 4131 3.050564 AGGATAACCATCTGGGGAGGTAA 60.051 47.826 0.54 0.00 42.91 2.85
3018 4132 2.527057 AGGATAACCATCTGGGGAGGTA 59.473 50.000 0.54 0.00 42.91 3.08
3034 4148 7.343833 AGAGGGTAAATCGAACACTTTAGGATA 59.656 37.037 0.00 0.00 28.36 2.59


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

AutoCloner maintained by Alex Coulton.