Multiple sequence alignment - TraesCS5D01G527700

Loading Multiple Alignment...

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 TraesCS5D01G527700 chr5D 100.000 2464 0 0 1 2464 544798117 544800580 0.000000e+00 4551
1 TraesCS5D01G527700 chr5D 90.640 812 69 5 1200 2008 544817237 544818044 0.000000e+00 1072
2 TraesCS5D01G527700 chr5D 85.502 538 46 16 613 1144 544816470 544816981 1.520000e-147 532
3 TraesCS5D01G527700 chr5D 100.000 189 0 0 2692 2880 544800808 544800996 1.640000e-92 350
4 TraesCS5D01G527700 chr1A 90.304 2496 167 39 7 2455 569378320 569375853 0.000000e+00 3199
5 TraesCS5D01G527700 chr1A 91.067 806 65 5 1206 2008 569355605 569354804 0.000000e+00 1083
6 TraesCS5D01G527700 chr5B 92.831 2148 114 13 1 2143 687222758 687224870 0.000000e+00 3077
7 TraesCS5D01G527700 chr5B 92.774 1716 86 12 734 2448 687212504 687214182 0.000000e+00 2447
8 TraesCS5D01G527700 chr5B 90.259 811 67 8 1200 2008 687326382 687327182 0.000000e+00 1050
9 TraesCS5D01G527700 chr5B 93.701 508 25 2 1 508 687211882 687212382 0.000000e+00 754
10 TraesCS5D01G527700 chr5B 84.843 574 47 17 613 1173 687259261 687259807 2.520000e-150 542
11 TraesCS5D01G527700 chr5B 84.929 564 53 18 613 1165 687325610 687326152 2.520000e-150 542
12 TraesCS5D01G527700 chr5B 84.342 479 48 17 685 1155 687342066 687342525 7.320000e-121 444
13 TraesCS5D01G527700 chr5B 94.709 189 9 1 2692 2880 687214242 687214429 2.810000e-75 292
14 TraesCS5D01G527700 chr5B 91.765 170 12 2 2257 2426 687232767 687232934 4.800000e-58 235
15 TraesCS5D01G527700 chr5B 91.339 127 11 0 2133 2259 687231311 687231437 1.060000e-39 174
16 TraesCS5D01G527700 chr5B 88.652 141 16 0 2740 2880 687233034 687233174 3.820000e-39 172
17 TraesCS5D01G527700 chr4A 90.668 2261 147 31 218 2441 624732498 624734731 0.000000e+00 2948
18 TraesCS5D01G527700 chr4A 84.895 1483 135 43 612 2046 26324619 26323178 0.000000e+00 1415
19 TraesCS5D01G527700 chr4A 90.323 806 71 5 1206 2008 624747262 624748063 0.000000e+00 1050
20 TraesCS5D01G527700 chr4A 80.375 1279 177 38 635 1880 24919803 24918566 0.000000e+00 904
21 TraesCS5D01G527700 chr4A 84.317 542 44 18 613 1144 624746491 624747001 2.580000e-135 492
22 TraesCS5D01G527700 chr4B 86.612 1098 100 26 989 2046 547309456 547310546 0.000000e+00 1170
23 TraesCS5D01G527700 chr4B 81.784 1065 143 20 848 1880 550433244 550432199 0.000000e+00 845
24 TraesCS5D01G527700 chrUn 86.667 375 39 6 942 1306 480040797 480040424 3.460000e-109 405
25 TraesCS5D01G527700 chr4D 85.303 347 31 8 612 947 441255522 441255859 9.880000e-90 340


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 TraesCS5D01G527700 chr5D 544798117 544800996 2879 False 2450.500000 4551 100.000 1 2880 2 chr5D.!!$F1 2879
1 TraesCS5D01G527700 chr5D 544816470 544818044 1574 False 802.000000 1072 88.071 613 2008 2 chr5D.!!$F2 1395
2 TraesCS5D01G527700 chr1A 569375853 569378320 2467 True 3199.000000 3199 90.304 7 2455 1 chr1A.!!$R2 2448
3 TraesCS5D01G527700 chr1A 569354804 569355605 801 True 1083.000000 1083 91.067 1206 2008 1 chr1A.!!$R1 802
4 TraesCS5D01G527700 chr5B 687222758 687224870 2112 False 3077.000000 3077 92.831 1 2143 1 chr5B.!!$F1 2142
5 TraesCS5D01G527700 chr5B 687211882 687214429 2547 False 1164.333333 2447 93.728 1 2880 3 chr5B.!!$F4 2879
6 TraesCS5D01G527700 chr5B 687325610 687327182 1572 False 796.000000 1050 87.594 613 2008 2 chr5B.!!$F6 1395
7 TraesCS5D01G527700 chr5B 687259261 687259807 546 False 542.000000 542 84.843 613 1173 1 chr5B.!!$F2 560
8 TraesCS5D01G527700 chr4A 624732498 624734731 2233 False 2948.000000 2948 90.668 218 2441 1 chr4A.!!$F1 2223
9 TraesCS5D01G527700 chr4A 26323178 26324619 1441 True 1415.000000 1415 84.895 612 2046 1 chr4A.!!$R2 1434
10 TraesCS5D01G527700 chr4A 24918566 24919803 1237 True 904.000000 904 80.375 635 1880 1 chr4A.!!$R1 1245
11 TraesCS5D01G527700 chr4A 624746491 624748063 1572 False 771.000000 1050 87.320 613 2008 2 chr4A.!!$F2 1395
12 TraesCS5D01G527700 chr4B 547309456 547310546 1090 False 1170.000000 1170 86.612 989 2046 1 chr4B.!!$F1 1057
13 TraesCS5D01G527700 chr4B 550432199 550433244 1045 True 845.000000 845 81.784 848 1880 1 chr4B.!!$R1 1032

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
745 773 0.598065 GGCGCAAGTCAATCTTTGGT 59.402 50.000 10.83 0.0 45.31 3.67 F
1432 1746 1.071471 CTCCGCCACCAACTTCTGT 59.929 57.895 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 2142 0.762418 TCTGTCCGAACAACCACCAT 59.238 50.000 0.0 0.0 34.24 3.55 R
2823 3171 1.537202 GCATCGCCAACTTCTTCAACT 59.463 47.619 0.0 0.0 0.00 3.16 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
24 25 2.715046 ACCTACGAGTCGTATCCAACA 58.285 47.619 24.64 3.86 41.53 3.33
80 81 5.641155 TGCAGCTAGTTATACTCCCTGATA 58.359 41.667 0.00 0.00 31.86 2.15
92 93 4.337145 ACTCCCTGATATGATCCTACGAC 58.663 47.826 0.00 0.00 0.00 4.34
102 103 2.617308 TGATCCTACGACGTGAAGATCC 59.383 50.000 22.85 12.48 31.23 3.36
142 143 3.509442 AGAATCTTTCCATGGGTTTGCA 58.491 40.909 13.02 0.00 0.00 4.08
444 458 2.957402 TTTCAGGAGTGATTGGTGCT 57.043 45.000 0.00 0.00 30.85 4.40
484 508 7.925703 ACGTTGTAATCTAACTTATCGATGG 57.074 36.000 8.54 3.37 0.00 3.51
745 773 0.598065 GGCGCAAGTCAATCTTTGGT 59.402 50.000 10.83 0.00 45.31 3.67
910 974 1.850345 TCCTCACCTCCAAAACCACTT 59.150 47.619 0.00 0.00 0.00 3.16
960 1024 2.815647 GCGAGGGAAGCTCAACCG 60.816 66.667 0.00 0.00 0.00 4.44
1001 1069 2.244486 TCTGGGACTCTCAGCAGAAT 57.756 50.000 0.38 0.00 32.63 2.40
1187 1286 7.181143 GCACCATCAATTTGCCAAATAATAG 57.819 36.000 2.54 0.00 0.00 1.73
1188 1287 6.762661 GCACCATCAATTTGCCAAATAATAGT 59.237 34.615 2.54 0.00 0.00 2.12
1189 1288 7.925483 GCACCATCAATTTGCCAAATAATAGTA 59.075 33.333 2.54 0.00 0.00 1.82
1432 1746 1.071471 CTCCGCCACCAACTTCTGT 59.929 57.895 0.00 0.00 0.00 3.41
1435 1749 1.966451 CGCCACCAACTTCTGTCCC 60.966 63.158 0.00 0.00 0.00 4.46
1657 1971 3.256960 ACCAACATGGCCGGGAGT 61.257 61.111 2.18 0.00 42.67 3.85
2056 2393 1.333177 ATCCACGACTCCCTCTATGC 58.667 55.000 0.00 0.00 0.00 3.14
2097 2434 8.350722 ACAATATATACTAAGAGTGGACGTGTG 58.649 37.037 0.00 0.00 0.00 3.82
2098 2435 3.505464 ATACTAAGAGTGGACGTGTGC 57.495 47.619 0.00 0.00 0.00 4.57
2154 2492 6.815089 TCACATTTAAGTTTTGCTTCCATGT 58.185 32.000 0.00 0.00 39.04 3.21
2271 2610 7.490962 TTAGGAAGCAAAACATATACGATGG 57.509 36.000 0.00 0.00 0.00 3.51
2315 2661 4.023707 AGACTTCAATTTGGCTTGACGAAG 60.024 41.667 0.00 0.00 34.96 3.79
2437 2783 3.953542 ATTACAATTCCCTCCTCACCC 57.046 47.619 0.00 0.00 0.00 4.61
2456 2804 5.419788 TCACCCCTCAAAGATTTGATCAATG 59.580 40.000 9.40 4.28 45.26 2.82
2457 2805 5.419788 CACCCCTCAAAGATTTGATCAATGA 59.580 40.000 9.40 8.62 45.26 2.57
2458 2806 5.655532 ACCCCTCAAAGATTTGATCAATGAG 59.344 40.000 21.42 21.42 45.26 2.90
2459 2807 5.655532 CCCCTCAAAGATTTGATCAATGAGT 59.344 40.000 24.25 8.42 45.26 3.41
2460 2808 6.183360 CCCCTCAAAGATTTGATCAATGAGTC 60.183 42.308 24.25 14.72 45.26 3.36
2461 2809 6.602406 CCCTCAAAGATTTGATCAATGAGTCT 59.398 38.462 24.25 16.18 45.26 3.24
2720 3068 4.188462 TGTATTGACATAACCCTGAAGCG 58.812 43.478 0.00 0.00 0.00 4.68
2768 3116 1.352622 TGGAAGGTTGCTCTGGTGGT 61.353 55.000 0.00 0.00 0.00 4.16
2802 3150 1.953138 CCGAGAGCATCATGGCGAC 60.953 63.158 0.00 0.00 37.82 5.19
2813 3161 2.579657 ATGGCGACGGTGAAGGTGA 61.580 57.895 0.00 0.00 0.00 4.02
2823 3171 2.484065 CGGTGAAGGTGAAGTTGTACCA 60.484 50.000 8.24 0.00 39.46 3.25
2843 3191 1.537202 AGTTGAAGAAGTTGGCGATGC 59.463 47.619 0.00 0.00 0.00 3.91
2858 3206 4.829518 TGCCGCGACGATCGTCAG 62.830 66.667 38.62 31.45 44.77 3.51
2868 3216 2.433145 ATCGTCAGTGGTGCGCAG 60.433 61.111 12.22 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 5.163395 GGGAGTATAACTAGCTGCAAGAAGT 60.163 44.000 1.02 0.00 34.07 3.01
80 81 3.253677 GGATCTTCACGTCGTAGGATCAT 59.746 47.826 23.23 0.00 33.46 2.45
92 93 1.519455 GAGTGGCCGGATCTTCACG 60.519 63.158 5.05 0.00 35.50 4.35
102 103 1.734465 CTTTAAGCAAGAGAGTGGCCG 59.266 52.381 0.00 0.00 33.80 6.13
142 143 7.498239 ACTGAAATCATCGATGAAATCTGATGT 59.502 33.333 32.93 24.39 45.61 3.06
205 207 8.108999 TGATTGATTCAACCCTTTTGATCTCTA 58.891 33.333 0.15 0.00 0.00 2.43
213 215 6.729690 TTCACTGATTGATTCAACCCTTTT 57.270 33.333 0.15 0.00 32.84 2.27
428 442 2.486472 AAGAGCACCAATCACTCCTG 57.514 50.000 0.00 0.00 0.00 3.86
443 457 6.893958 ACAACGTAAGAAGCATGATAAGAG 57.106 37.500 0.00 0.00 43.62 2.85
444 458 8.942338 ATTACAACGTAAGAAGCATGATAAGA 57.058 30.769 0.00 0.00 43.62 2.10
484 508 5.293079 GTGATTCACCTCTTTGATAGCTGAC 59.707 44.000 5.44 0.00 0.00 3.51
553 580 9.138596 AGCCACCAACTAGTTAAAATTTCTAAA 57.861 29.630 8.04 0.00 0.00 1.85
745 773 2.521224 TGCACATGGCTGCAACCA 60.521 55.556 12.07 12.07 44.28 3.67
910 974 1.206849 TGCTAGATGTTGTGGCGATCA 59.793 47.619 0.00 0.00 0.00 2.92
960 1024 3.971245 AGAAACAGGGAGTGATCAGAC 57.029 47.619 0.00 0.00 0.00 3.51
1001 1069 2.276409 GCATCCCAGCCACCATCA 59.724 61.111 0.00 0.00 0.00 3.07
1050 1130 2.815647 GCGGGCACGAAGGAGAAG 60.816 66.667 15.48 0.00 44.60 2.85
1184 1283 7.097192 CACACCCGCATGATAAGTAATACTAT 58.903 38.462 0.00 0.00 0.00 2.12
1185 1284 6.452242 CACACCCGCATGATAAGTAATACTA 58.548 40.000 0.00 0.00 0.00 1.82
1186 1285 5.297547 CACACCCGCATGATAAGTAATACT 58.702 41.667 0.00 0.00 0.00 2.12
1187 1286 4.084013 GCACACCCGCATGATAAGTAATAC 60.084 45.833 0.00 0.00 0.00 1.89
1188 1287 4.062293 GCACACCCGCATGATAAGTAATA 58.938 43.478 0.00 0.00 0.00 0.98
1189 1288 2.878406 GCACACCCGCATGATAAGTAAT 59.122 45.455 0.00 0.00 0.00 1.89
1204 1499 2.069273 GTACAGTCAGACATGCACACC 58.931 52.381 2.66 0.00 0.00 4.16
1519 1833 1.153429 GCGGTAGATGGCGAGGTTT 60.153 57.895 0.00 0.00 0.00 3.27
1603 1917 5.543714 TCAAAGTAGTTGAAGCCGTTGATA 58.456 37.500 0.00 0.00 43.43 2.15
1657 1971 1.002430 GACATGCTCTTGACTGACCCA 59.998 52.381 0.00 0.00 0.00 4.51
1663 1977 0.969149 TCACCGACATGCTCTTGACT 59.031 50.000 0.00 0.00 0.00 3.41
1828 2142 0.762418 TCTGTCCGAACAACCACCAT 59.238 50.000 0.00 0.00 34.24 3.55
2033 2370 1.777941 AGAGGGAGTCGTGGATTACC 58.222 55.000 0.00 0.00 0.00 2.85
2056 2393 9.707957 AGTATATATTGTTCCAGATAGAGGAGG 57.292 37.037 0.00 0.00 36.33 4.30
2209 2548 4.159244 TGTTTACCCTATTAGCGGCATT 57.841 40.909 1.45 0.00 0.00 3.56
2245 2584 8.567948 CCATCGTATATGTTTTGCTTCCTAAAT 58.432 33.333 0.00 0.00 0.00 1.40
2271 2610 5.001232 TCTGTTGGCAGTAGGTGTAATTTC 58.999 41.667 0.00 0.00 43.05 2.17
2415 2761 3.954258 GGGTGAGGAGGGAATTGTAATTG 59.046 47.826 0.00 0.00 0.00 2.32
2768 3116 2.900273 GGACGCCAGCATCACCTA 59.100 61.111 0.00 0.00 0.00 3.08
2802 3150 2.140717 GGTACAACTTCACCTTCACCG 58.859 52.381 0.00 0.00 0.00 4.94
2813 3161 5.357032 CCAACTTCTTCAACTGGTACAACTT 59.643 40.000 0.00 0.00 38.70 2.66
2823 3171 1.537202 GCATCGCCAACTTCTTCAACT 59.463 47.619 0.00 0.00 0.00 3.16
2855 3203 4.624364 CACCCTGCGCACCACTGA 62.624 66.667 5.66 0.00 0.00 3.41
2858 3206 3.660111 GTTCACCCTGCGCACCAC 61.660 66.667 5.66 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.