Multiple sequence alignment - TraesCS4D01G149900

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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 TraesCS4D01G149900 chr4D 100.000 2889 0 0 1 2889 163413957 163411069 0 5336
1 TraesCS4D01G149900 chr2A 93.588 2308 136 10 58 2360 140707514 140709814 0 3432
2 TraesCS4D01G149900 chr2A 84.547 2925 383 48 10 2889 266908599 266905699 0 2833
3 TraesCS4D01G149900 chr6A 88.107 2926 278 48 6 2889 462850469 462853366 0 3411
4 TraesCS4D01G149900 chr6A 89.314 2302 199 32 6 2290 462855017 462857288 0 2844
5 TraesCS4D01G149900 chr2B 87.096 2844 311 39 78 2889 405161443 405164262 0 3168
6 TraesCS4D01G149900 chr6B 85.029 2899 374 42 3 2860 272298739 272295860 0 2894
7 TraesCS4D01G149900 chr4B 84.952 2924 364 54 17 2889 376027702 376030600 0 2892
8 TraesCS4D01G149900 chr4B 84.282 2933 384 58 7 2889 230486543 230483638 0 2791
9 TraesCS4D01G149900 chr2D 89.058 2303 218 29 1 2281 323249152 323246862 0 2826
10 TraesCS4D01G149900 chr7A 91.892 1258 94 7 1634 2889 494456157 494457408 0 1751


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 TraesCS4D01G149900 chr4D 163411069 163413957 2888 True 5336.0 5336 100.0000 1 2889 1 chr4D.!!$R1 2888
1 TraesCS4D01G149900 chr2A 140707514 140709814 2300 False 3432.0 3432 93.5880 58 2360 1 chr2A.!!$F1 2302
2 TraesCS4D01G149900 chr2A 266905699 266908599 2900 True 2833.0 2833 84.5470 10 2889 1 chr2A.!!$R1 2879
3 TraesCS4D01G149900 chr6A 462850469 462857288 6819 False 3127.5 3411 88.7105 6 2889 2 chr6A.!!$F1 2883
4 TraesCS4D01G149900 chr2B 405161443 405164262 2819 False 3168.0 3168 87.0960 78 2889 1 chr2B.!!$F1 2811
5 TraesCS4D01G149900 chr6B 272295860 272298739 2879 True 2894.0 2894 85.0290 3 2860 1 chr6B.!!$R1 2857
6 TraesCS4D01G149900 chr4B 376027702 376030600 2898 False 2892.0 2892 84.9520 17 2889 1 chr4B.!!$F1 2872
7 TraesCS4D01G149900 chr4B 230483638 230486543 2905 True 2791.0 2791 84.2820 7 2889 1 chr4B.!!$R1 2882
8 TraesCS4D01G149900 chr2D 323246862 323249152 2290 True 2826.0 2826 89.0580 1 2281 1 chr2D.!!$R1 2280
9 TraesCS4D01G149900 chr7A 494456157 494457408 1251 False 1751.0 1751 91.8920 1634 2889 1 chr7A.!!$F1 1255

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
73 78 0.872021 CACCTAGCTTTAGCCGAGCG 60.872 60.0 0.0 0.0 44.71 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 1936 1.22184 CAGCTCACCGGGCACTATT 59.778 57.895 6.32 0.0 0.0 1.73 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
48 52 7.967890 ATTTTCAGTTTTCATCACCCAATTC 57.032 32.000 0.00 0.00 0.00 2.17
73 78 0.872021 CACCTAGCTTTAGCCGAGCG 60.872 60.000 0.00 0.00 44.71 5.03
76 81 1.201343 CTAGCTTTAGCCGAGCGTTC 58.799 55.000 0.00 0.00 44.71 3.95
149 160 7.801783 GCGTAAAAACCCTGCTATATTACAATC 59.198 37.037 0.00 0.00 0.00 2.67
222 233 5.755861 GGCTATAGACTAGGTTTTGCTTCTG 59.244 44.000 3.21 0.00 0.00 3.02
360 374 4.392445 GCATTCTACTCAGATCATCATGCC 59.608 45.833 0.00 0.00 35.41 4.40
526 540 3.455910 TCCTTATGTTGCTCCTACATGCT 59.544 43.478 0.00 0.00 36.89 3.79
772 786 1.339610 GCCACAACTATGCACCACAAA 59.660 47.619 0.00 0.00 0.00 2.83
823 837 2.167281 CAGTACCAGGAGATGTGTCCAG 59.833 54.545 0.00 0.00 39.34 3.86
856 870 5.656206 TGGTCCTCCATTTGGTCAACCAG 62.656 52.174 12.50 0.00 42.30 4.00
864 878 1.227823 TGGTCAACCAGCAACTCCG 60.228 57.895 0.00 0.00 42.01 4.63
1044 1058 4.936802 AGGAGCTAGTGGAAGAAGTAAGA 58.063 43.478 0.00 0.00 0.00 2.10
1106 1120 2.158755 CCCTCCTTGAGTTGAGTGTTGT 60.159 50.000 0.00 0.00 0.00 3.32
1260 1274 3.941483 AGCTCGAATACCCAAATGAACAG 59.059 43.478 0.00 0.00 0.00 3.16
1288 1302 2.335681 TCCAATGTCTACCACTCCCA 57.664 50.000 0.00 0.00 0.00 4.37
1337 1351 6.486253 TGAAGATGAAGAACCAGAAATTCG 57.514 37.500 0.00 0.00 0.00 3.34
1341 1355 7.277174 AGATGAAGAACCAGAAATTCGTTTT 57.723 32.000 0.00 0.00 0.00 2.43
1913 1936 5.183331 AGAGTGATCAAGCGAGTGTTACTTA 59.817 40.000 0.00 0.00 0.00 2.24
1935 1961 2.193536 GTGCCCGGTGAGCTGTTTT 61.194 57.895 0.00 0.00 0.00 2.43
2301 2337 2.487805 GCATGCTATGTTCCCTGGATCA 60.488 50.000 11.37 0.00 0.00 2.92
2430 2470 3.774766 ACAGTAGCATGTCATGTTCCCTA 59.225 43.478 14.26 4.54 0.00 3.53
2434 2474 4.785346 AGCATGTCATGTTCCCTAGATT 57.215 40.909 14.26 0.00 0.00 2.40
2552 2595 2.629051 GTATGTTCCTTTGGGGAGACG 58.371 52.381 0.00 0.00 46.01 4.18
2700 2745 7.107542 GGTTCTACCACAATGTTATGTTCCTA 58.892 38.462 0.00 0.00 38.42 2.94
2707 2752 9.832445 ACCACAATGTTATGTTCCTAGTAATAG 57.168 33.333 0.00 0.00 0.00 1.73
2879 2952 1.531423 ACCAAGTCTGAAGCATGCAG 58.469 50.000 21.98 8.96 45.89 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 4.895297 ACACAGAATTGGGTGATGAAAACT 59.105 37.500 11.83 0.00 40.16 2.66
48 52 2.622436 GGCTAAAGCTAGGTGACACAG 58.378 52.381 8.08 0.00 41.70 3.66
73 78 1.077089 GACTAGGCGACGGCAAGAAC 61.077 60.000 24.23 6.99 42.47 3.01
76 81 2.202756 GGACTAGGCGACGGCAAG 60.203 66.667 24.23 6.73 42.47 4.01
111 118 2.540265 TTTTACGCCCAAACTACGGA 57.460 45.000 0.00 0.00 0.00 4.69
135 145 8.236586 GCCAAAATGATCGATTGTAATATAGCA 58.763 33.333 0.00 0.00 0.00 3.49
149 160 1.133363 CAACGGCGCCAAAATGATCG 61.133 55.000 28.98 11.48 0.00 3.69
191 202 6.388435 AAACCTAGTCTATAGCCTAACACG 57.612 41.667 0.00 0.00 0.00 4.49
360 374 3.431912 TGTTTGTAGTGTTGCTCGCATAG 59.568 43.478 0.00 0.00 0.00 2.23
526 540 5.136068 TGGCCCTGAAATCCACAAATATA 57.864 39.130 0.00 0.00 0.00 0.86
557 571 3.064207 GAGTAACCACGCTGACATTCAA 58.936 45.455 0.00 0.00 0.00 2.69
623 637 8.729756 CATGTGAGTAATTGTTTTGGTATGAGA 58.270 33.333 0.00 0.00 0.00 3.27
856 870 2.594592 AACAGGTGCCGGAGTTGC 60.595 61.111 5.05 0.00 0.00 4.17
1044 1058 5.471456 AGCGTTGATGTTCTTCTCAATCTTT 59.529 36.000 0.00 0.00 34.18 2.52
1260 1274 4.636206 GTGGTAGACATTGGATCTTCAACC 59.364 45.833 0.00 0.00 0.00 3.77
1288 1302 7.501844 ACTACAACAGCTTCTTCTACTTCTTT 58.498 34.615 0.00 0.00 0.00 2.52
1337 1351 8.230486 CACACTCTTGTATGACAATAGGAAAAC 58.770 37.037 8.90 0.00 36.84 2.43
1341 1355 6.850752 TCACACTCTTGTATGACAATAGGA 57.149 37.500 8.90 0.00 36.84 2.94
1913 1936 1.221840 CAGCTCACCGGGCACTATT 59.778 57.895 6.32 0.00 0.00 1.73
2208 2243 6.869913 CACAAATTCAGCATCTAAACATGGTT 59.130 34.615 0.00 0.00 32.01 3.67
2301 2337 3.603532 CATGTCTGGTTCACATGCTACT 58.396 45.455 0.00 0.00 43.48 2.57
2430 2470 3.508793 CAGATTTCACAAGCCACCAATCT 59.491 43.478 0.00 0.00 32.38 2.40
2434 2474 1.133513 ACCAGATTTCACAAGCCACCA 60.134 47.619 0.00 0.00 0.00 4.17
2522 2565 2.176247 AGGAACATACCACCGATCCT 57.824 50.000 0.00 0.00 32.55 3.24
2700 2745 5.529289 TGATCCCAAGAGACACCTATTACT 58.471 41.667 0.00 0.00 0.00 2.24
2707 2752 1.211457 AGCATGATCCCAAGAGACACC 59.789 52.381 0.00 0.00 0.00 4.16
2712 2784 3.842007 AAGAGAGCATGATCCCAAGAG 57.158 47.619 7.49 0.00 0.00 2.85
2806 2879 8.591072 ACAAAGCAATAGGACACTAGTAAACTA 58.409 33.333 0.00 0.00 31.54 2.24
2860 2933 1.202855 ACTGCATGCTTCAGACTTGGT 60.203 47.619 20.33 0.00 35.61 3.67
2862 2935 1.878088 ACACTGCATGCTTCAGACTTG 59.122 47.619 20.33 5.28 35.61 3.16


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

AutoCloner maintained by Alex Coulton.