Multiple sequence alignment - TraesCS6A01G072800

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 TraesCS6A01G072800 chr6A 100.000 3257 0 0 1 3257 39671133 39667877 0.000000e+00 6015
1 TraesCS6A01G072800 chr6A 98.148 2915 50 2 346 3257 39628999 39626086 0.000000e+00 5081
2 TraesCS6A01G072800 chr6A 97.942 2916 56 2 346 3257 39581211 39578296 0.000000e+00 5049
3 TraesCS6A01G072800 chr6A 78.731 1434 218 61 361 1731 39878012 39876603 0.000000e+00 878
4 TraesCS6A01G072800 chr6A 87.184 632 74 5 2124 2754 39588760 39588135 0.000000e+00 712
5 TraesCS6A01G072800 chr6A 86.867 632 77 4 2124 2754 39546643 39546017 0.000000e+00 702
6 TraesCS6A01G072800 chr6A 83.671 741 93 15 1170 1896 39638031 39637305 0.000000e+00 673
7 TraesCS6A01G072800 chr6A 82.663 796 101 19 1083 1864 39548202 39547430 0.000000e+00 671
8 TraesCS6A01G072800 chr6A 82.139 823 110 19 1083 1891 39590315 39589516 0.000000e+00 671
9 TraesCS6A01G072800 chr6A 84.656 189 25 2 1911 2096 39588943 39588756 5.550000e-43 185
10 TraesCS6A01G072800 chr6A 84.737 190 24 3 1911 2096 39636736 39636548 5.550000e-43 185
11 TraesCS6A01G072800 chr6D 94.699 2396 85 11 749 3112 36084580 36082195 0.000000e+00 3683
12 TraesCS6A01G072800 chr6D 85.119 1391 176 23 399 1781 35717988 35716621 0.000000e+00 1393
13 TraesCS6A01G072800 chr6D 83.169 1218 150 35 1911 3114 35715937 35714761 0.000000e+00 1062
14 TraesCS6A01G072800 chr6D 79.690 1418 220 40 367 1746 35667513 35666126 0.000000e+00 961
15 TraesCS6A01G072800 chr6D 78.019 1565 259 45 328 1864 35642109 35640602 0.000000e+00 905
16 TraesCS6A01G072800 chr6D 93.927 494 29 1 262 754 36090567 36090074 0.000000e+00 745
17 TraesCS6A01G072800 chr6D 86.709 632 78 4 2124 2754 35639843 35639217 0.000000e+00 697
18 TraesCS6A01G072800 chr6D 81.260 619 99 13 376 981 36106098 36105484 4.890000e-133 484
19 TraesCS6A01G072800 chr6D 93.431 274 14 4 9 280 36090848 36090577 1.410000e-108 403
20 TraesCS6A01G072800 chr6D 94.326 141 5 1 3117 3257 36082158 36082021 2.550000e-51 213
21 TraesCS6A01G072800 chr6D 78.161 174 27 5 1581 1746 36073727 36073557 2.070000e-17 100
22 TraesCS6A01G072800 chr6B 93.489 1889 101 14 2 1886 75526670 75524800 0.000000e+00 2787
23 TraesCS6A01G072800 chr6B 96.240 1383 40 6 1878 3257 75524620 75523247 0.000000e+00 2255
24 TraesCS6A01G072800 chr6B 85.010 1541 194 25 368 1896 75423485 75421970 0.000000e+00 1531
25 TraesCS6A01G072800 chr6B 83.250 1397 164 43 1911 3257 75044692 75043316 0.000000e+00 1219
26 TraesCS6A01G072800 chr6B 81.965 1242 161 30 1911 3138 75421394 75420202 0.000000e+00 994
27 TraesCS6A01G072800 chr6B 78.618 1548 258 49 378 1894 75510362 75508857 0.000000e+00 957
28 TraesCS6A01G072800 chr1B 82.090 938 146 16 377 1311 57615192 57616110 0.000000e+00 782
29 TraesCS6A01G072800 chr1B 79.433 564 83 18 1350 1896 57616188 57616735 5.130000e-98 368
30 TraesCS6A01G072800 chr1D 79.751 563 83 17 1350 1896 37881018 37881565 2.370000e-101 379
31 TraesCS6A01G072800 chr1A 79.902 408 53 20 1507 1896 36790134 36790530 4.140000e-69 272


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 TraesCS6A01G072800 chr6A 39667877 39671133 3256 True 6015.000000 6015 100.000000 1 3257 1 chr6A.!!$R3 3256
1 TraesCS6A01G072800 chr6A 39626086 39628999 2913 True 5081.000000 5081 98.148000 346 3257 1 chr6A.!!$R2 2911
2 TraesCS6A01G072800 chr6A 39578296 39581211 2915 True 5049.000000 5049 97.942000 346 3257 1 chr6A.!!$R1 2911
3 TraesCS6A01G072800 chr6A 39876603 39878012 1409 True 878.000000 878 78.731000 361 1731 1 chr6A.!!$R4 1370
4 TraesCS6A01G072800 chr6A 39546017 39548202 2185 True 686.500000 702 84.765000 1083 2754 2 chr6A.!!$R5 1671
5 TraesCS6A01G072800 chr6A 39588135 39590315 2180 True 522.666667 712 84.659667 1083 2754 3 chr6A.!!$R6 1671
6 TraesCS6A01G072800 chr6A 39636548 39638031 1483 True 429.000000 673 84.204000 1170 2096 2 chr6A.!!$R7 926
7 TraesCS6A01G072800 chr6D 36082021 36084580 2559 True 1948.000000 3683 94.512500 749 3257 2 chr6D.!!$R6 2508
8 TraesCS6A01G072800 chr6D 35714761 35717988 3227 True 1227.500000 1393 84.144000 399 3114 2 chr6D.!!$R5 2715
9 TraesCS6A01G072800 chr6D 35666126 35667513 1387 True 961.000000 961 79.690000 367 1746 1 chr6D.!!$R1 1379
10 TraesCS6A01G072800 chr6D 35639217 35642109 2892 True 801.000000 905 82.364000 328 2754 2 chr6D.!!$R4 2426
11 TraesCS6A01G072800 chr6D 36090074 36090848 774 True 574.000000 745 93.679000 9 754 2 chr6D.!!$R7 745
12 TraesCS6A01G072800 chr6D 36105484 36106098 614 True 484.000000 484 81.260000 376 981 1 chr6D.!!$R3 605
13 TraesCS6A01G072800 chr6B 75523247 75526670 3423 True 2521.000000 2787 94.864500 2 3257 2 chr6B.!!$R4 3255
14 TraesCS6A01G072800 chr6B 75420202 75423485 3283 True 1262.500000 1531 83.487500 368 3138 2 chr6B.!!$R3 2770
15 TraesCS6A01G072800 chr6B 75043316 75044692 1376 True 1219.000000 1219 83.250000 1911 3257 1 chr6B.!!$R1 1346
16 TraesCS6A01G072800 chr6B 75508857 75510362 1505 True 957.000000 957 78.618000 378 1894 1 chr6B.!!$R2 1516
17 TraesCS6A01G072800 chr1B 57615192 57616735 1543 False 575.000000 782 80.761500 377 1896 2 chr1B.!!$F1 1519
18 TraesCS6A01G072800 chr1D 37881018 37881565 547 False 379.000000 379 79.751000 1350 1896 1 chr1D.!!$F1 546

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
886 968 1.270839 TGGTCTTGGTAAGCACAGAGC 60.271 52.381 0.0 0.0 46.19 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2619 3636 7.922811 GCTGATAAAATATTTAGGCAAACTGCT 59.077 33.333 0.01 0.0 44.28 4.24 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
29 30 4.830600 TCTATTATGGCGTGTGGTCTATGA 59.169 41.667 0.00 0.0 0.00 2.15
53 54 2.441001 CCAGGGATCTAACTTGGCTCAT 59.559 50.000 0.00 0.0 0.00 2.90
70 71 6.061441 TGGCTCATCACTGAAACTTCTTTTA 58.939 36.000 0.00 0.0 0.00 1.52
71 72 6.716628 TGGCTCATCACTGAAACTTCTTTTAT 59.283 34.615 0.00 0.0 0.00 1.40
208 222 2.095314 TCTGCGCATTGTGTTTATGTGG 60.095 45.455 12.24 0.0 34.80 4.17
219 233 3.034635 TGTTTATGTGGTGTGGGCTTTT 58.965 40.909 0.00 0.0 0.00 2.27
251 265 2.733956 CTGTAGTGGGCTCTCTCTCTT 58.266 52.381 0.00 0.0 0.00 2.85
252 266 2.687935 CTGTAGTGGGCTCTCTCTCTTC 59.312 54.545 0.00 0.0 0.00 2.87
253 267 2.310349 TGTAGTGGGCTCTCTCTCTTCT 59.690 50.000 0.00 0.0 0.00 2.85
254 268 2.143876 AGTGGGCTCTCTCTCTTCTC 57.856 55.000 0.00 0.0 0.00 2.87
269 283 8.356000 TCTCTCTTCTCCTACCTAAAAGAAAG 57.644 38.462 0.00 0.0 0.00 2.62
292 334 4.565652 GGAGTTTTGGGCTTCTATCTCACA 60.566 45.833 0.00 0.0 0.00 3.58
299 341 2.167281 GGCTTCTATCTCACAGACAGCA 59.833 50.000 0.00 0.0 32.51 4.41
304 346 2.687700 ATCTCACAGACAGCATGACC 57.312 50.000 0.00 0.0 39.69 4.02
374 416 2.829003 CGAGAGGAGTAGCCGCCA 60.829 66.667 0.00 0.0 43.43 5.69
886 968 1.270839 TGGTCTTGGTAAGCACAGAGC 60.271 52.381 0.00 0.0 46.19 4.09
1112 1221 4.279420 ACTTGAGTTTGATTTGGAGAAGCC 59.721 41.667 0.00 0.0 37.10 4.35
2247 3260 5.010922 ACATGATGGAGCTAAACTTTTGCAA 59.989 36.000 0.00 0.0 0.00 4.08
2329 3343 9.733219 AGTAAGCTTATCTTTTTAGTAGTAGCG 57.267 33.333 9.88 0.0 36.25 4.26
2694 3711 8.824756 TCACTTATGTAATCTCCTTCTAGTGT 57.175 34.615 0.00 0.0 33.07 3.55
3148 4216 8.161699 TCCAAAATGAGAACTGTTTACCTTAC 57.838 34.615 0.00 0.0 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.547855 GCATCATAGACCACACGCCATA 60.548 50.000 0.00 0.00 0.00 2.74
29 30 1.133668 GCCAAGTTAGATCCCTGGCAT 60.134 52.381 13.37 0.00 40.37 4.40
75 76 9.184523 TCCCCTAAAAATGTACACATAATCAAG 57.815 33.333 0.00 0.00 35.10 3.02
76 77 9.184523 CTCCCCTAAAAATGTACACATAATCAA 57.815 33.333 0.00 0.00 35.10 2.57
78 79 8.747538 ACTCCCCTAAAAATGTACACATAATC 57.252 34.615 0.00 0.00 35.10 1.75
79 80 8.966868 CAACTCCCCTAAAAATGTACACATAAT 58.033 33.333 0.00 0.00 35.10 1.28
80 81 7.945664 ACAACTCCCCTAAAAATGTACACATAA 59.054 33.333 0.00 0.00 35.10 1.90
81 82 7.463431 ACAACTCCCCTAAAAATGTACACATA 58.537 34.615 0.00 0.00 35.10 2.29
82 83 6.311735 ACAACTCCCCTAAAAATGTACACAT 58.688 36.000 0.00 0.00 38.41 3.21
83 84 5.697067 ACAACTCCCCTAAAAATGTACACA 58.303 37.500 0.00 0.00 0.00 3.72
84 85 7.446319 AGTTACAACTCCCCTAAAAATGTACAC 59.554 37.037 0.00 0.00 32.86 2.90
85 86 7.519927 AGTTACAACTCCCCTAAAAATGTACA 58.480 34.615 0.00 0.00 32.86 2.90
86 87 7.991084 AGTTACAACTCCCCTAAAAATGTAC 57.009 36.000 0.00 0.00 32.86 2.90
87 88 8.852135 CAAAGTTACAACTCCCCTAAAAATGTA 58.148 33.333 0.00 0.00 38.57 2.29
88 89 7.343574 ACAAAGTTACAACTCCCCTAAAAATGT 59.656 33.333 0.00 0.00 38.57 2.71
89 90 7.722363 ACAAAGTTACAACTCCCCTAAAAATG 58.278 34.615 0.00 0.00 38.57 2.32
90 91 7.907841 ACAAAGTTACAACTCCCCTAAAAAT 57.092 32.000 0.00 0.00 38.57 1.82
91 92 7.833183 TGTACAAAGTTACAACTCCCCTAAAAA 59.167 33.333 0.00 0.00 38.57 1.94
219 233 5.627135 AGCCCACTACAGCTAAAGTAAAAA 58.373 37.500 0.11 0.00 37.64 1.94
253 267 7.002276 CCAAAACTCCTTTCTTTTAGGTAGGA 58.998 38.462 0.00 0.00 34.29 2.94
254 268 6.208797 CCCAAAACTCCTTTCTTTTAGGTAGG 59.791 42.308 0.00 0.00 34.29 3.18
269 283 3.942115 GTGAGATAGAAGCCCAAAACTCC 59.058 47.826 0.00 0.00 0.00 3.85
292 334 1.326213 CGAGAGGGGTCATGCTGTCT 61.326 60.000 0.00 0.00 0.00 3.41
299 341 0.923358 AGAGAGACGAGAGGGGTCAT 59.077 55.000 0.00 0.00 36.87 3.06
304 346 0.034960 TGACCAGAGAGACGAGAGGG 60.035 60.000 0.00 0.00 0.00 4.30
846 928 3.057104 CCACCCGGAAGTGTTAAATTTCC 60.057 47.826 0.73 4.56 37.58 3.13
849 931 3.151554 GACCACCCGGAAGTGTTAAATT 58.848 45.455 0.73 0.00 35.93 1.82
853 935 1.071071 CAAGACCACCCGGAAGTGTTA 59.929 52.381 0.73 0.00 35.93 2.41
886 968 1.002366 GTATGTTGCTGCTCGTCTGG 58.998 55.000 0.00 0.00 0.00 3.86
948 1030 2.170397 TGGTGTTGATATGCGATCACCT 59.830 45.455 12.25 0.00 43.64 4.00
1112 1221 2.093973 ACTGGTTTCACAGCTAGGATCG 60.094 50.000 0.00 0.00 42.21 3.69
2619 3636 7.922811 GCTGATAAAATATTTAGGCAAACTGCT 59.077 33.333 0.01 0.00 44.28 4.24
2663 3680 8.919145 AGAAGGAGATTACATAAGTGAGTTAGG 58.081 37.037 0.00 0.00 0.00 2.69
3148 4216 6.377327 AAAACATAGAACCTTCACACAGTG 57.623 37.500 0.00 0.00 34.45 3.66


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

AutoCloner maintained by Alex Coulton.