Multiple sequence alignment - TraesCS4A01G137600

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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 TraesCS4A01G137600 chr4A 100.000 2366 0 0 1 2366 197215288 197212923 0.000000e+00 4370
1 TraesCS4A01G137600 chr4A 86.553 1346 144 30 3 1328 205932280 205933608 0.000000e+00 1448
2 TraesCS4A01G137600 chr4A 86.533 1344 142 28 3 1328 205924354 205925676 0.000000e+00 1443
3 TraesCS4A01G137600 chr4A 93.611 767 34 5 1298 2062 205925761 205926514 0.000000e+00 1131
4 TraesCS4A01G137600 chr4A 92.857 742 39 4 1323 2062 205933716 205934445 0.000000e+00 1064
5 TraesCS4A01G137600 chr3A 94.304 2370 120 13 3 2366 347832932 347830572 0.000000e+00 3615
6 TraesCS4A01G137600 chr3A 87.830 682 77 6 1 680 293307468 293308145 0.000000e+00 795
7 TraesCS4A01G137600 chr6A 94.083 2366 129 8 1 2364 266018711 266021067 0.000000e+00 3583
8 TraesCS4A01G137600 chr6A 93.961 2368 133 9 1 2366 266026589 266028948 0.000000e+00 3572
9 TraesCS4A01G137600 chr6A 86.776 1346 147 23 1 1328 259362607 259361275 0.000000e+00 1471
10 TraesCS4A01G137600 chr6A 84.269 1265 164 30 1 1239 430717059 430715804 0.000000e+00 1201
11 TraesCS4A01G137600 chr6A 93.653 772 44 5 1294 2062 259361195 259360426 0.000000e+00 1149
12 TraesCS4A01G137600 chr6A 88.719 523 54 5 1845 2366 312689354 312689872 3.320000e-178 634
13 TraesCS4A01G137600 chr5A 93.966 2370 132 10 1 2366 176943789 176941427 0.000000e+00 3574
14 TraesCS4A01G137600 chr5A 89.177 693 68 7 1 690 131335351 131334663 0.000000e+00 857
15 TraesCS4A01G137600 chr5A 89.017 692 68 7 1 690 131342926 131342241 0.000000e+00 850
16 TraesCS4A01G137600 chr5A 88.905 685 71 5 1 683 131360473 131359792 0.000000e+00 839
17 TraesCS4A01G137600 chr7A 96.147 1739 60 5 629 2366 420702004 420703736 0.000000e+00 2833
18 TraesCS4A01G137600 chr7A 91.071 392 25 8 1498 1886 324976859 324977243 2.690000e-144 521
19 TraesCS4A01G137600 chr7A 91.336 277 18 6 1295 1570 324967844 324968115 7.980000e-100 374
20 TraesCS4A01G137600 chr7A 92.683 82 5 1 1248 1328 324967678 324967759 1.490000e-22 117
21 TraesCS4A01G137600 chr2A 86.831 691 79 11 3 690 305113653 305114334 0.000000e+00 761
22 TraesCS4A01G137600 chr1A 90.421 522 47 2 1845 2366 326543230 326542712 0.000000e+00 684
23 TraesCS4A01G137600 chr1A 90.038 522 49 2 1845 2366 385002421 385002939 0.000000e+00 673
24 TraesCS4A01G137600 chr1A 89.827 521 50 2 1846 2366 326535656 326535139 0.000000e+00 665


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 TraesCS4A01G137600 chr4A 197212923 197215288 2365 True 4370 4370 100.0000 1 2366 1 chr4A.!!$R1 2365
1 TraesCS4A01G137600 chr4A 205924354 205926514 2160 False 1287 1443 90.0720 3 2062 2 chr4A.!!$F1 2059
2 TraesCS4A01G137600 chr4A 205932280 205934445 2165 False 1256 1448 89.7050 3 2062 2 chr4A.!!$F2 2059
3 TraesCS4A01G137600 chr3A 347830572 347832932 2360 True 3615 3615 94.3040 3 2366 1 chr3A.!!$R1 2363
4 TraesCS4A01G137600 chr3A 293307468 293308145 677 False 795 795 87.8300 1 680 1 chr3A.!!$F1 679
5 TraesCS4A01G137600 chr6A 266018711 266021067 2356 False 3583 3583 94.0830 1 2364 1 chr6A.!!$F1 2363
6 TraesCS4A01G137600 chr6A 266026589 266028948 2359 False 3572 3572 93.9610 1 2366 1 chr6A.!!$F2 2365
7 TraesCS4A01G137600 chr6A 259360426 259362607 2181 True 1310 1471 90.2145 1 2062 2 chr6A.!!$R2 2061
8 TraesCS4A01G137600 chr6A 430715804 430717059 1255 True 1201 1201 84.2690 1 1239 1 chr6A.!!$R1 1238
9 TraesCS4A01G137600 chr6A 312689354 312689872 518 False 634 634 88.7190 1845 2366 1 chr6A.!!$F3 521
10 TraesCS4A01G137600 chr5A 176941427 176943789 2362 True 3574 3574 93.9660 1 2366 1 chr5A.!!$R4 2365
11 TraesCS4A01G137600 chr5A 131334663 131335351 688 True 857 857 89.1770 1 690 1 chr5A.!!$R1 689
12 TraesCS4A01G137600 chr5A 131342241 131342926 685 True 850 850 89.0170 1 690 1 chr5A.!!$R2 689
13 TraesCS4A01G137600 chr5A 131359792 131360473 681 True 839 839 88.9050 1 683 1 chr5A.!!$R3 682
14 TraesCS4A01G137600 chr7A 420702004 420703736 1732 False 2833 2833 96.1470 629 2366 1 chr7A.!!$F2 1737
15 TraesCS4A01G137600 chr2A 305113653 305114334 681 False 761 761 86.8310 3 690 1 chr2A.!!$F1 687
16 TraesCS4A01G137600 chr1A 326542712 326543230 518 True 684 684 90.4210 1845 2366 1 chr1A.!!$R2 521
17 TraesCS4A01G137600 chr1A 385002421 385002939 518 False 673 673 90.0380 1845 2366 1 chr1A.!!$F1 521
18 TraesCS4A01G137600 chr1A 326535139 326535656 517 True 665 665 89.8270 1846 2366 1 chr1A.!!$R1 520

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
683 708 0.249826 AAACGAACGGGCCGAAACTA 60.25 50.0 35.78 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 2376 0.039437 CTGTCGCTACCGTTGTGTCT 60.039 55.0 0.0 0.0 35.54 3.41 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
27 28 3.129113 GCACAACCAAGTATGATGCATGA 59.871 43.478 2.46 0.00 0.00 3.07
36 37 4.380531 AGTATGATGCATGACCGGTTTAG 58.619 43.478 9.42 2.14 0.00 1.85
88 91 6.245408 ACAATCCTACAAATTAAGTGGAGCA 58.755 36.000 0.00 0.00 0.00 4.26
154 159 8.291032 TGACTTCTTTAGTTCTCTCTCGTTTAG 58.709 37.037 0.00 0.00 37.17 1.85
158 163 8.627208 TCTTTAGTTCTCTCTCGTTTAGGTAA 57.373 34.615 0.00 0.00 0.00 2.85
263 269 3.548014 CGGAAGCAACGAACAACAATTCT 60.548 43.478 0.00 0.00 0.00 2.40
278 284 6.607198 ACAACAATTCTGGTAAATCCCCATAG 59.393 38.462 0.00 0.00 34.77 2.23
287 295 8.010105 TCTGGTAAATCCCCATAGCATATTTTT 58.990 33.333 0.00 0.00 34.77 1.94
298 306 6.762187 CCATAGCATATTTTTGATTTGGTGCA 59.238 34.615 0.00 0.00 31.86 4.57
313 321 0.517316 GTGCAGTTCTGCCCTAAACG 59.483 55.000 19.91 0.00 0.00 3.60
328 336 6.207025 TGCCCTAAACGCAATTTTAGAGTTAA 59.793 34.615 9.86 0.00 40.24 2.01
386 395 4.252878 GCAAAATTCCACCCCATTTACAG 58.747 43.478 0.00 0.00 0.00 2.74
683 708 0.249826 AAACGAACGGGCCGAAACTA 60.250 50.000 35.78 0.00 0.00 2.24
863 899 1.084370 CCCGGTTCGATGCAGAGAAC 61.084 60.000 21.81 21.81 44.22 3.01
938 974 1.225855 CAGCGACAGGTAAAACAGCA 58.774 50.000 0.00 0.00 0.00 4.41
941 977 1.225855 CGACAGGTAAAACAGCAGCA 58.774 50.000 0.00 0.00 0.00 4.41
1159 1195 4.424711 GGATGGGCCAACGCAGGA 62.425 66.667 11.89 0.00 42.66 3.86
1951 2329 2.333688 AGAAAAATAGGCGAGGGAGC 57.666 50.000 0.00 0.00 0.00 4.70
1998 2376 9.342308 GTTTTATAGATGTTTGAGGATGATCCA 57.658 33.333 14.90 0.00 39.61 3.41
2021 2399 2.995574 AACGGTAGCGACAGCCCT 60.996 61.111 22.88 0.00 46.67 5.19
2064 2443 4.980805 GCGCACGTGAGGGGTTCA 62.981 66.667 22.23 0.00 32.68 3.18
2154 2533 0.941963 AGGATGGACTAGGTGGGCTA 59.058 55.000 0.00 0.00 0.00 3.93
2156 2535 2.728013 AGGATGGACTAGGTGGGCTATA 59.272 50.000 0.00 0.00 0.00 1.31
2185 2567 1.106944 CGAGGGGGAGAAGAGAGAGC 61.107 65.000 0.00 0.00 0.00 4.09
2208 2590 1.201429 AGGGCCCGACATCTGTTTCT 61.201 55.000 18.44 0.00 0.00 2.52
2229 2611 1.005804 GAGACCGAAAACGTCCGACC 61.006 60.000 6.54 0.00 0.00 4.79
2240 2622 1.732308 GTCCGACCTATGACCGACC 59.268 63.158 0.00 0.00 0.00 4.79
2262 2644 8.583810 GACCATAATGTCGCTATAGTTTAACA 57.416 34.615 0.84 1.91 0.00 2.41
2273 2655 6.482308 CGCTATAGTTTAACAGTTGGGCTATT 59.518 38.462 0.84 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.875514 CCGGTCATGCATCATACTTGG 59.124 52.381 0.00 0.00 0.00 3.61
27 28 1.679032 GCCATGCTTCTCTAAACCGGT 60.679 52.381 0.00 0.00 0.00 5.28
36 37 0.533491 TTTGCCATGCCATGCTTCTC 59.467 50.000 0.00 0.00 0.00 2.87
263 269 7.786943 TCAAAAATATGCTATGGGGATTTACCA 59.213 33.333 0.00 0.00 43.22 3.25
278 284 6.369615 AGAACTGCACCAAATCAAAAATATGC 59.630 34.615 0.00 0.00 0.00 3.14
298 306 2.200373 ATTGCGTTTAGGGCAGAACT 57.800 45.000 0.00 0.00 42.12 3.01
328 336 5.476599 TGGTCTACTTGCTTTGCATGTTTAT 59.523 36.000 14.48 0.00 42.78 1.40
668 692 1.359459 CTGCTAGTTTCGGCCCGTTC 61.359 60.000 1.63 0.00 0.00 3.95
669 693 1.375523 CTGCTAGTTTCGGCCCGTT 60.376 57.895 1.63 0.00 0.00 4.44
683 708 3.988678 ATGTTGGGCCAGCCTGCT 61.989 61.111 18.29 0.00 36.10 4.24
938 974 1.980772 GCCAAGTCCCTGCATTGCT 60.981 57.895 10.49 0.00 0.00 3.91
941 977 2.361610 CCGCCAAGTCCCTGCATT 60.362 61.111 0.00 0.00 0.00 3.56
1047 1083 3.394836 GAGCTCCTCCTTGCCCGT 61.395 66.667 0.87 0.00 0.00 5.28
1742 2117 4.035102 GCCGCCAGGTCCCTTCTT 62.035 66.667 0.00 0.00 40.50 2.52
1988 2366 1.208052 CCGTTGTGTCTGGATCATCCT 59.792 52.381 4.96 0.00 37.46 3.24
1998 2376 0.039437 CTGTCGCTACCGTTGTGTCT 60.039 55.000 0.00 0.00 35.54 3.41
2021 2399 4.938074 TTGTCCCGGACCCGACCA 62.938 66.667 15.24 0.59 42.83 4.02
2154 2533 2.196925 CCCCTCGCAGTCTCGCTAT 61.197 63.158 0.00 0.00 0.00 2.97
2185 2567 2.835431 AGATGTCGGGCCCTCTCG 60.835 66.667 22.43 6.49 0.00 4.04
2240 2622 9.849607 CAACTGTTAAACTATAGCGACATTATG 57.150 33.333 0.00 0.00 0.00 1.90
2262 2644 4.457949 CGGAGTTTGTTTAATAGCCCAACT 59.542 41.667 0.00 0.00 0.00 3.16
2273 2655 3.997681 TCATCGCATTCGGAGTTTGTTTA 59.002 39.130 0.00 0.00 36.13 2.01


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

AutoCloner maintained by Alex Coulton.