Multiple sequence alignment - TraesCS6A01G016600

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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 TraesCS6A01G016600 chr6A 100.000 1659 0 0 912 2570 8197969 8196311 0.000000e+00 3064
1 TraesCS6A01G016600 chr6A 89.706 1700 122 18 914 2570 7991797 7993486 0.000000e+00 2121
2 TraesCS6A01G016600 chr6A 100.000 532 0 0 1 532 8198880 8198349 0.000000e+00 983
3 TraesCS6A01G016600 chr6A 88.531 497 46 8 1088 1579 8395393 8394903 2.200000e-165 592
4 TraesCS6A01G016600 chr6A 86.101 554 44 13 1 532 7991244 7991786 1.330000e-157 566
5 TraesCS6A01G016600 chr6A 85.545 505 70 3 1077 1580 8211872 8211370 2.270000e-145 525
6 TraesCS6A01G016600 chr6A 84.135 416 50 10 112 525 7986867 7987268 3.100000e-104 388
7 TraesCS6A01G016600 chr6A 80.545 514 90 9 1434 1942 8130538 8131046 1.120000e-103 387
8 TraesCS6A01G016600 chr6A 80.872 413 59 15 113 521 9461534 9461930 8.930000e-80 307
9 TraesCS6A01G016600 chr6B 88.002 1717 135 24 914 2570 14544881 14543176 0.000000e+00 1964
10 TraesCS6A01G016600 chr6B 90.503 1074 77 9 914 1963 14333938 14335010 0.000000e+00 1395
11 TraesCS6A01G016600 chr6B 89.031 547 39 3 1992 2523 14335215 14335755 0.000000e+00 658
12 TraesCS6A01G016600 chr6B 85.688 545 46 14 1 525 14550257 14549725 1.740000e-151 545
13 TraesCS6A01G016600 chr6B 85.507 552 45 16 4 532 14545431 14544892 6.250000e-151 544
14 TraesCS6A01G016600 chr6B 85.018 554 50 11 1 532 14333385 14333927 1.350000e-147 532
15 TraesCS6A01G016600 chr6B 85.542 498 70 2 1077 1573 14629063 14628567 1.050000e-143 520
16 TraesCS6A01G016600 chr6B 79.189 370 62 10 162 525 16608092 16608452 2.550000e-60 243
17 TraesCS6A01G016600 chr6D 86.040 1712 142 48 914 2570 7989424 7987755 0.000000e+00 1748
18 TraesCS6A01G016600 chr6D 87.698 1512 120 18 922 2381 7719376 7720873 0.000000e+00 1701
19 TraesCS6A01G016600 chr6D 88.545 550 20 7 1 532 7989959 7989435 6.040000e-176 627
20 TraesCS6A01G016600 chr6D 85.844 551 48 12 1 532 7718821 7719360 2.230000e-155 558
21 TraesCS6A01G016600 chr6D 86.145 498 67 2 1077 1573 7998396 7997900 1.050000e-148 536
22 TraesCS6A01G016600 chr6D 81.102 508 86 9 1434 1936 7864562 7865064 5.150000e-107 398
23 TraesCS6A01G016600 chr6D 81.818 429 60 12 100 525 15358256 15357843 6.810000e-91 344
24 TraesCS6A01G016600 chr1B 87.949 473 41 9 65 532 27364557 27364096 6.250000e-151 544
25 TraesCS6A01G016600 chr1B 86.422 464 48 10 65 525 27752917 27752466 6.390000e-136 494
26 TraesCS6A01G016600 chr5D 80.822 365 53 13 162 521 42076178 42076530 1.170000e-68 270
27 TraesCS6A01G016600 chr2D 81.150 313 39 12 2215 2519 588164208 588164508 1.540000e-57 233


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 TraesCS6A01G016600 chr6A 8196311 8198880 2569 True 2023.500000 3064 100.000000 1 2570 2 chr6A.!!$R3 2569
1 TraesCS6A01G016600 chr6A 7986867 7993486 6619 False 1025.000000 2121 86.647333 1 2570 3 chr6A.!!$F3 2569
2 TraesCS6A01G016600 chr6A 8211370 8211872 502 True 525.000000 525 85.545000 1077 1580 1 chr6A.!!$R1 503
3 TraesCS6A01G016600 chr6A 8130538 8131046 508 False 387.000000 387 80.545000 1434 1942 1 chr6A.!!$F1 508
4 TraesCS6A01G016600 chr6B 14543176 14545431 2255 True 1254.000000 1964 86.754500 4 2570 2 chr6B.!!$R3 2566
5 TraesCS6A01G016600 chr6B 14333385 14335755 2370 False 861.666667 1395 88.184000 1 2523 3 chr6B.!!$F2 2522
6 TraesCS6A01G016600 chr6B 14549725 14550257 532 True 545.000000 545 85.688000 1 525 1 chr6B.!!$R1 524
7 TraesCS6A01G016600 chr6D 7987755 7989959 2204 True 1187.500000 1748 87.292500 1 2570 2 chr6D.!!$R3 2569
8 TraesCS6A01G016600 chr6D 7718821 7720873 2052 False 1129.500000 1701 86.771000 1 2381 2 chr6D.!!$F2 2380
9 TraesCS6A01G016600 chr6D 7864562 7865064 502 False 398.000000 398 81.102000 1434 1936 1 chr6D.!!$F1 502

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
464 4877 2.008242 CAGTCCCCCAACAATTTCCA 57.992 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 7003 0.099436 GAATTCCAGTGATGCGTGCC 59.901 55.0 0.0 0.0 0.0 5.01 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
391 4804 4.176752 GCCTGTCCCCCATCGTCC 62.177 72.222 0.00 0.00 0.00 4.79
392 4805 3.849951 CCTGTCCCCCATCGTCCG 61.850 72.222 0.00 0.00 0.00 4.79
423 4836 2.615493 CGGCCTAGGTTTGTCACATTCT 60.615 50.000 11.31 0.00 0.00 2.40
464 4877 2.008242 CAGTCCCCCAACAATTTCCA 57.992 50.000 0.00 0.00 0.00 3.53
1051 5470 2.200370 TCACCACCGACCTGGAGT 59.800 61.111 0.00 0.00 42.00 3.85
1081 5500 1.750778 GAATGGTGGCATTGACCGAAT 59.249 47.619 0.00 0.00 36.12 3.34
1217 5636 2.512515 GGATGCCGAGGTGAGCAC 60.513 66.667 0.00 0.00 42.84 4.40
1332 5751 0.809636 CGTACATTGCTCATCGGCCA 60.810 55.000 2.24 0.00 0.00 5.36
1527 5946 2.686405 CCTTGCTGAAGATTATGCTGCA 59.314 45.455 4.13 4.13 35.22 4.41
1608 6039 5.178252 AGCAATATGTGTAGAATCACGATGC 59.822 40.000 0.00 0.00 40.74 3.91
1917 6381 0.806868 CACAAGCTGTAGGTGCATGG 59.193 55.000 0.00 0.00 34.01 3.66
1988 6464 2.435059 GGGCAGCTGGAAGACGTC 60.435 66.667 17.12 7.70 34.07 4.34
2076 6727 1.186200 TCTGTCTATGAAGCAGGCGT 58.814 50.000 0.00 0.00 31.63 5.68
2096 6747 4.569943 CGTCTTGGGATGATTATCGGATT 58.430 43.478 0.00 0.00 33.98 3.01
2097 6748 4.627467 CGTCTTGGGATGATTATCGGATTC 59.373 45.833 0.00 0.00 33.98 2.52
2266 6934 7.730364 TCTCCTTCTTTTTCATCACTAACAC 57.270 36.000 0.00 0.00 0.00 3.32
2273 6941 7.648142 TCTTTTTCATCACTAACACATGTTCC 58.352 34.615 0.00 0.00 39.31 3.62
2274 6942 7.502226 TCTTTTTCATCACTAACACATGTTCCT 59.498 33.333 0.00 0.00 39.31 3.36
2275 6943 6.801539 TTTCATCACTAACACATGTTCCTC 57.198 37.500 0.00 0.00 39.31 3.71
2276 6944 5.745312 TCATCACTAACACATGTTCCTCT 57.255 39.130 0.00 0.00 39.31 3.69
2277 6945 5.724328 TCATCACTAACACATGTTCCTCTC 58.276 41.667 0.00 0.00 39.31 3.20
2335 7003 0.170561 GAGCTGCATTGGCTTCAGTG 59.829 55.000 1.02 0.00 40.40 3.66
2360 7028 2.797087 CGCATCACTGGAATTCATTGGC 60.797 50.000 7.93 0.72 0.00 4.52
2385 7053 3.123621 CCTCACTTCCTTTCGTGAATTCG 59.876 47.826 0.04 0.00 39.43 3.34
2430 7098 8.723942 ATTAGTTCACTTGGTCTAATCATGTC 57.276 34.615 0.00 0.00 30.41 3.06
2496 7164 6.386927 TGATAGAACTCCCTCCAATGTTATGT 59.613 38.462 0.00 0.00 0.00 2.29
2499 7167 5.964477 AGAACTCCCTCCAATGTTATGTAGA 59.036 40.000 0.00 0.00 0.00 2.59
2548 7216 1.421268 AGAAACTGAGGTGGCATGTCA 59.579 47.619 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 4627 3.651980 CTTGGGGGAGGCCTTGAGC 62.652 68.421 6.77 0.00 42.60 4.26
335 4748 4.735358 GGAACTTGGGTCCCGGGC 62.735 72.222 18.49 11.44 0.00 6.13
336 4749 2.933834 AGGAACTTGGGTCCCGGG 60.934 66.667 16.85 16.85 27.25 5.73
337 4750 1.918800 AGAGGAACTTGGGTCCCGG 60.919 63.158 2.65 0.00 41.55 5.73
338 4751 1.296715 CAGAGGAACTTGGGTCCCG 59.703 63.158 2.65 0.00 41.55 5.14
339 4752 1.002011 GCAGAGGAACTTGGGTCCC 60.002 63.158 0.00 0.00 41.55 4.46
340 4753 0.606673 GTGCAGAGGAACTTGGGTCC 60.607 60.000 0.00 0.00 41.55 4.46
341 4754 0.606673 GGTGCAGAGGAACTTGGGTC 60.607 60.000 0.00 0.00 41.55 4.46
342 4755 1.456287 GGTGCAGAGGAACTTGGGT 59.544 57.895 0.00 0.00 41.55 4.51
408 4821 4.248859 CGATCTCAGAATGTGACAAACCT 58.751 43.478 0.00 0.00 41.87 3.50
464 4877 1.123928 GGGACGATGGATCTGGAACT 58.876 55.000 0.00 0.00 0.00 3.01
911 5327 1.029681 GAGGGCGGTGTTGAAGTTTT 58.970 50.000 0.00 0.00 0.00 2.43
912 5328 0.822121 GGAGGGCGGTGTTGAAGTTT 60.822 55.000 0.00 0.00 0.00 2.66
936 5355 1.912043 AGCTCCACCTTGCTCTTGTAT 59.088 47.619 0.00 0.00 33.90 2.29
1051 5470 1.142667 TGCCACCATTCTCTGAACACA 59.857 47.619 0.00 0.00 0.00 3.72
1147 5566 0.321919 TTGGCTGCGATCTGCTTCTT 60.322 50.000 10.16 0.00 46.63 2.52
1235 5654 0.028770 CGACTTGGCGAGCAAAAACA 59.971 50.000 0.37 0.00 0.00 2.83
1302 5721 1.091537 CAATGTACGCCGGTTCCAAT 58.908 50.000 1.90 0.00 0.00 3.16
1332 5751 6.322712 CCTCTAGGCTGTAACAGAGAATTACT 59.677 42.308 11.88 0.00 37.33 2.24
1527 5946 2.930562 ACTTCCCCTCCGCAAGCT 60.931 61.111 0.00 0.00 0.00 3.74
1608 6039 5.695851 AAACATAGTTGGCTTCAGAACTG 57.304 39.130 0.00 0.00 34.28 3.16
1988 6464 6.630444 ATCTCATACCAAAGCTTAAGCATG 57.370 37.500 28.39 23.88 45.16 4.06
2076 6727 4.597075 TGGAATCCGATAATCATCCCAAGA 59.403 41.667 0.00 0.00 0.00 3.02
2096 6747 8.632679 GGCATCATCTAAAAGTAATTGAATGGA 58.367 33.333 0.00 0.00 0.00 3.41
2097 6748 7.869429 GGGCATCATCTAAAAGTAATTGAATGG 59.131 37.037 0.00 0.00 0.00 3.16
2169 6835 4.060900 AGCTTATATCATTGCACGGACAG 58.939 43.478 0.00 0.00 0.00 3.51
2245 6913 7.651808 ACATGTGTTAGTGATGAAAAAGAAGG 58.348 34.615 0.00 0.00 0.00 3.46
2293 6961 4.800993 CACAGTTTGTTTTGGTAAATGCGA 59.199 37.500 0.00 0.00 0.00 5.10
2335 7003 0.099436 GAATTCCAGTGATGCGTGCC 59.901 55.000 0.00 0.00 0.00 5.01
2348 7016 1.037030 TGAGGGCGCCAATGAATTCC 61.037 55.000 30.85 7.16 0.00 3.01
2360 7028 1.004918 ACGAAAGGAAGTGAGGGCG 60.005 57.895 0.00 0.00 0.00 6.13
2385 7053 1.227853 ACCAACTCAACAGACCGCC 60.228 57.895 0.00 0.00 0.00 6.13
2452 7120 2.083774 CAGATAGCGGGCAAGTTTTCA 58.916 47.619 0.00 0.00 0.00 2.69
2465 7133 4.411927 TGGAGGGAGTTCTATCAGATAGC 58.588 47.826 12.17 0.38 32.85 2.97


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

AutoCloner maintained by Alex Coulton.