Multiple sequence alignment - TraesCS4A01G170200

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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 TraesCS4A01G170200 chr4A 100.000 2985 0 0 1 2985 429487962 429490946 0.000000e+00 5513.0
1 TraesCS4A01G170200 chr4A 95.873 2956 70 13 41 2985 490340826 490343740 0.000000e+00 4735.0
2 TraesCS4A01G170200 chr4A 94.559 1305 53 9 929 2229 326303854 326302564 0.000000e+00 2001.0
3 TraesCS4A01G170200 chr4A 91.251 1383 87 11 1619 2985 29680458 29679094 0.000000e+00 1853.0
4 TraesCS4A01G170200 chr6A 95.030 2998 99 9 1 2985 401364269 401367229 0.000000e+00 4665.0
5 TraesCS4A01G170200 chr3A 94.194 2997 99 25 1 2985 513294790 513297723 0.000000e+00 4501.0
6 TraesCS4A01G170200 chr3A 95.962 1585 55 2 1 1584 733887576 733886000 0.000000e+00 2564.0
7 TraesCS4A01G170200 chr3A 91.689 758 35 11 1599 2350 157725101 157724366 0.000000e+00 1026.0
8 TraesCS4A01G170200 chr1A 95.286 2673 80 8 325 2985 575419163 575421801 0.000000e+00 4196.0
9 TraesCS4A01G170200 chr1A 93.309 1674 91 16 120 1786 443853300 443854959 0.000000e+00 2451.0
10 TraesCS4A01G170200 chr1A 96.708 638 20 1 2348 2985 539848643 539848007 0.000000e+00 1061.0
11 TraesCS4A01G170200 chr1A 98.294 586 9 1 122 707 497975155 497975739 0.000000e+00 1026.0
12 TraesCS4A01G170200 chr1A 97.864 515 10 1 1 515 580782941 580783454 0.000000e+00 889.0
13 TraesCS4A01G170200 chr5A 95.181 1826 75 9 1 1814 133817575 133819399 0.000000e+00 2872.0
14 TraesCS4A01G170200 chr5A 95.000 1780 64 15 41 1814 345672974 345671214 0.000000e+00 2771.0
15 TraesCS4A01G170200 chr5A 95.979 1492 53 6 120 1607 168400319 168398831 0.000000e+00 2416.0
16 TraesCS4A01G170200 chr5A 97.826 46 1 0 949 994 544898730 544898775 2.470000e-11 80.5
17 TraesCS4A01G170200 chr7A 93.879 1895 79 9 1094 2985 153039565 153037705 0.000000e+00 2822.0
18 TraesCS4A01G170200 chr7A 94.048 1697 68 14 120 1808 644066816 644065145 0.000000e+00 2543.0
19 TraesCS4A01G170200 chr7A 96.230 1512 46 7 120 1625 633712613 633711107 0.000000e+00 2466.0
20 TraesCS4A01G170200 chr7A 93.369 1659 88 17 109 1760 49623241 49621598 0.000000e+00 2435.0
21 TraesCS4A01G170200 chr7B 94.877 1425 38 10 1580 2985 471055180 471056588 0.000000e+00 2194.0
22 TraesCS4A01G170200 chr7B 90.304 1382 95 14 1619 2985 551209348 551210705 0.000000e+00 1773.0
23 TraesCS4A01G170200 chr5B 95.262 1393 47 5 1599 2985 703922864 703924243 0.000000e+00 2189.0
24 TraesCS4A01G170200 chr5B 94.310 1406 53 13 929 2322 133701796 133703186 0.000000e+00 2128.0
25 TraesCS4A01G170200 chr5B 93.826 1393 58 10 1599 2985 682901705 682903075 0.000000e+00 2071.0
26 TraesCS4A01G170200 chr5B 92.164 536 35 4 1619 2153 62386285 62385756 0.000000e+00 750.0
27 TraesCS4A01G170200 chr4B 94.526 1370 55 7 1619 2985 177765294 177766646 0.000000e+00 2097.0
28 TraesCS4A01G170200 chr3B 93.750 1424 41 11 1580 2985 317287617 317289010 0.000000e+00 2093.0
29 TraesCS4A01G170200 chr3B 93.596 1218 48 10 1619 2821 648362782 648361580 0.000000e+00 1790.0
30 TraesCS4A01G170200 chrUn 94.118 1394 49 13 1599 2985 39689343 39690710 0.000000e+00 2089.0
31 TraesCS4A01G170200 chr4D 90.169 1424 102 17 1580 2985 236680094 236678691 0.000000e+00 1820.0
32 TraesCS4A01G170200 chr4D 86.914 1536 133 45 322 1841 261239527 261238044 0.000000e+00 1661.0
33 TraesCS4A01G170200 chr4D 92.208 154 10 2 170 322 480889845 480889693 1.800000e-52 217.0
34 TraesCS4A01G170200 chr4D 86.932 176 8 12 1 175 480890044 480889883 1.830000e-42 183.0
35 TraesCS4A01G170200 chr2A 96.970 957 27 2 300 1256 605761987 605762941 0.000000e+00 1605.0
36 TraesCS4A01G170200 chr5D 98.416 505 8 0 319 823 140961168 140960664 0.000000e+00 889.0
37 TraesCS4A01G170200 chr6D 98.020 505 10 0 319 823 297179389 297178885 0.000000e+00 878.0


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 TraesCS4A01G170200 chr4A 429487962 429490946 2984 False 5513 5513 100.000 1 2985 1 chr4A.!!$F1 2984
1 TraesCS4A01G170200 chr4A 490340826 490343740 2914 False 4735 4735 95.873 41 2985 1 chr4A.!!$F2 2944
2 TraesCS4A01G170200 chr4A 326302564 326303854 1290 True 2001 2001 94.559 929 2229 1 chr4A.!!$R2 1300
3 TraesCS4A01G170200 chr4A 29679094 29680458 1364 True 1853 1853 91.251 1619 2985 1 chr4A.!!$R1 1366
4 TraesCS4A01G170200 chr6A 401364269 401367229 2960 False 4665 4665 95.030 1 2985 1 chr6A.!!$F1 2984
5 TraesCS4A01G170200 chr3A 513294790 513297723 2933 False 4501 4501 94.194 1 2985 1 chr3A.!!$F1 2984
6 TraesCS4A01G170200 chr3A 733886000 733887576 1576 True 2564 2564 95.962 1 1584 1 chr3A.!!$R2 1583
7 TraesCS4A01G170200 chr3A 157724366 157725101 735 True 1026 1026 91.689 1599 2350 1 chr3A.!!$R1 751
8 TraesCS4A01G170200 chr1A 575419163 575421801 2638 False 4196 4196 95.286 325 2985 1 chr1A.!!$F3 2660
9 TraesCS4A01G170200 chr1A 443853300 443854959 1659 False 2451 2451 93.309 120 1786 1 chr1A.!!$F1 1666
10 TraesCS4A01G170200 chr1A 539848007 539848643 636 True 1061 1061 96.708 2348 2985 1 chr1A.!!$R1 637
11 TraesCS4A01G170200 chr1A 497975155 497975739 584 False 1026 1026 98.294 122 707 1 chr1A.!!$F2 585
12 TraesCS4A01G170200 chr1A 580782941 580783454 513 False 889 889 97.864 1 515 1 chr1A.!!$F4 514
13 TraesCS4A01G170200 chr5A 133817575 133819399 1824 False 2872 2872 95.181 1 1814 1 chr5A.!!$F1 1813
14 TraesCS4A01G170200 chr5A 345671214 345672974 1760 True 2771 2771 95.000 41 1814 1 chr5A.!!$R2 1773
15 TraesCS4A01G170200 chr5A 168398831 168400319 1488 True 2416 2416 95.979 120 1607 1 chr5A.!!$R1 1487
16 TraesCS4A01G170200 chr7A 153037705 153039565 1860 True 2822 2822 93.879 1094 2985 1 chr7A.!!$R2 1891
17 TraesCS4A01G170200 chr7A 644065145 644066816 1671 True 2543 2543 94.048 120 1808 1 chr7A.!!$R4 1688
18 TraesCS4A01G170200 chr7A 633711107 633712613 1506 True 2466 2466 96.230 120 1625 1 chr7A.!!$R3 1505
19 TraesCS4A01G170200 chr7A 49621598 49623241 1643 True 2435 2435 93.369 109 1760 1 chr7A.!!$R1 1651
20 TraesCS4A01G170200 chr7B 471055180 471056588 1408 False 2194 2194 94.877 1580 2985 1 chr7B.!!$F1 1405
21 TraesCS4A01G170200 chr7B 551209348 551210705 1357 False 1773 1773 90.304 1619 2985 1 chr7B.!!$F2 1366
22 TraesCS4A01G170200 chr5B 703922864 703924243 1379 False 2189 2189 95.262 1599 2985 1 chr5B.!!$F3 1386
23 TraesCS4A01G170200 chr5B 133701796 133703186 1390 False 2128 2128 94.310 929 2322 1 chr5B.!!$F1 1393
24 TraesCS4A01G170200 chr5B 682901705 682903075 1370 False 2071 2071 93.826 1599 2985 1 chr5B.!!$F2 1386
25 TraesCS4A01G170200 chr5B 62385756 62386285 529 True 750 750 92.164 1619 2153 1 chr5B.!!$R1 534
26 TraesCS4A01G170200 chr4B 177765294 177766646 1352 False 2097 2097 94.526 1619 2985 1 chr4B.!!$F1 1366
27 TraesCS4A01G170200 chr3B 317287617 317289010 1393 False 2093 2093 93.750 1580 2985 1 chr3B.!!$F1 1405
28 TraesCS4A01G170200 chr3B 648361580 648362782 1202 True 1790 1790 93.596 1619 2821 1 chr3B.!!$R1 1202
29 TraesCS4A01G170200 chrUn 39689343 39690710 1367 False 2089 2089 94.118 1599 2985 1 chrUn.!!$F1 1386
30 TraesCS4A01G170200 chr4D 236678691 236680094 1403 True 1820 1820 90.169 1580 2985 1 chr4D.!!$R1 1405
31 TraesCS4A01G170200 chr4D 261238044 261239527 1483 True 1661 1661 86.914 322 1841 1 chr4D.!!$R2 1519
32 TraesCS4A01G170200 chr2A 605761987 605762941 954 False 1605 1605 96.970 300 1256 1 chr2A.!!$F1 956
33 TraesCS4A01G170200 chr5D 140960664 140961168 504 True 889 889 98.416 319 823 1 chr5D.!!$R1 504
34 TraesCS4A01G170200 chr6D 297178885 297179389 504 True 878 878 98.020 319 823 1 chr6D.!!$R1 504

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
93 94 3.554752 CGTTTTGTTGATTCCAGCCCAAT 60.555 43.478 0.0 0.0 0.0 3.16 F
384 386 5.627499 ATTTGTCTAAAAAGATGCAGCGA 57.373 34.783 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 1064 0.472471 TCGAAACCTTCCAAGCCAGT 59.528 50.0 0.00 0.00 0.0 4.00 R
2176 2622 1.117994 TGAGCATGCACAAAAACCCA 58.882 45.0 21.98 0.46 0.0 4.51 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
45 46 4.760204 GGAATTGTGGTATACTACATGGCC 59.240 45.833 21.07 17.27 37.20 5.36
47 48 5.582950 ATTGTGGTATACTACATGGCCAT 57.417 39.130 21.07 14.09 37.20 4.40
93 94 3.554752 CGTTTTGTTGATTCCAGCCCAAT 60.555 43.478 0.00 0.00 0.00 3.16
384 386 5.627499 ATTTGTCTAAAAAGATGCAGCGA 57.373 34.783 0.00 0.00 0.00 4.93
1003 1064 5.219343 TGCTTTTCAGAGAAGTGAGATGA 57.781 39.130 2.79 0.00 0.00 2.92
1418 1479 0.321996 TGTGCCGCATGTACTACCAA 59.678 50.000 0.00 0.00 0.00 3.67
1598 1659 3.781770 GAGCAGAGCGGGGATGACG 62.782 68.421 0.00 0.00 0.00 4.35
1619 1680 2.835431 AGAGCGGGGATGACGAGG 60.835 66.667 0.00 0.00 0.00 4.63
1622 1683 4.593864 GCGGGGATGACGAGGAGC 62.594 72.222 0.00 0.00 0.00 4.70
1732 1901 2.676608 CCTGCTATGGTGGTGGCA 59.323 61.111 0.00 0.00 34.29 4.92
2098 2544 3.782656 TGCTCATGGATGCTGTATGAT 57.217 42.857 0.00 0.00 31.11 2.45
2166 2612 8.096414 AGTTTGGTAATTGATGGGAATTGAAAG 58.904 33.333 0.00 0.00 0.00 2.62
2167 2613 7.789202 TTGGTAATTGATGGGAATTGAAAGA 57.211 32.000 0.00 0.00 0.00 2.52
2168 2614 7.789202 TGGTAATTGATGGGAATTGAAAGAA 57.211 32.000 0.00 0.00 0.00 2.52
2169 2615 8.200024 TGGTAATTGATGGGAATTGAAAGAAA 57.800 30.769 0.00 0.00 0.00 2.52
2170 2616 8.654997 TGGTAATTGATGGGAATTGAAAGAAAA 58.345 29.630 0.00 0.00 0.00 2.29
2171 2617 9.500785 GGTAATTGATGGGAATTGAAAGAAAAA 57.499 29.630 0.00 0.00 0.00 1.94
2322 2770 1.140161 CGGTGACTAAATCCGCCGA 59.860 57.895 8.47 0.00 43.53 5.54
2612 3076 9.579610 CCGTTATTTTCACTAAAAATGCTTTTG 57.420 29.630 0.00 0.00 45.15 2.44
2661 3125 3.814842 AGAATCGACAACAGATTTGCACA 59.185 39.130 0.00 0.00 38.32 4.57
2684 3148 1.909781 AAACCCTAGCCACGGACGA 60.910 57.895 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.202177 GCAGGCACAATACGACCAATG 60.202 52.381 0.00 0.00 0.00 2.82
47 48 1.295357 CGCAGGCACAATACGACCAA 61.295 55.000 0.00 0.00 0.00 3.67
75 76 2.971330 ACAATTGGGCTGGAATCAACAA 59.029 40.909 10.83 0.00 0.00 2.83
93 94 0.669318 GTGGTCCAATCGCTCGACAA 60.669 55.000 0.00 0.00 0.00 3.18
384 386 4.644685 ACAAGTTTAACTGCTCCAATGTGT 59.355 37.500 0.00 0.00 0.00 3.72
875 919 4.859304 AAAATGAGAAGAGCAATGCACA 57.141 36.364 8.35 0.00 0.00 4.57
1003 1064 0.472471 TCGAAACCTTCCAAGCCAGT 59.528 50.000 0.00 0.00 0.00 4.00
1375 1436 2.792674 GTGTTGTCGAACATCTTCACGA 59.207 45.455 0.00 0.00 43.95 4.35
1418 1479 1.579964 TACTGGCATCGTCGTCGTGT 61.580 55.000 1.33 0.00 38.33 4.49
1548 1609 2.568612 CGCTCTGCTCCTCGTCAA 59.431 61.111 0.00 0.00 0.00 3.18
1598 1659 2.107953 GTCATCCCCGCTCTGCTC 59.892 66.667 0.00 0.00 0.00 4.26
1619 1680 2.107953 GTCATCCCCGCTCTGCTC 59.892 66.667 0.00 0.00 0.00 4.26
1622 1683 2.415010 CTCGTCATCCCCGCTCTG 59.585 66.667 0.00 0.00 0.00 3.35
1732 1901 2.111384 ACCATAGCAAGGTCGTCATCT 58.889 47.619 0.00 0.00 32.90 2.90
2040 2486 9.733556 AAACCTGACATACTTAACATTGACATA 57.266 29.630 0.00 0.00 0.00 2.29
2168 2614 6.264970 AGCATGCACAAAAACCCATAATTTTT 59.735 30.769 21.98 0.00 39.30 1.94
2169 2615 5.769162 AGCATGCACAAAAACCCATAATTTT 59.231 32.000 21.98 0.00 0.00 1.82
2170 2616 5.315348 AGCATGCACAAAAACCCATAATTT 58.685 33.333 21.98 0.00 0.00 1.82
2171 2617 4.909001 AGCATGCACAAAAACCCATAATT 58.091 34.783 21.98 0.00 0.00 1.40
2172 2618 4.020396 TGAGCATGCACAAAAACCCATAAT 60.020 37.500 21.98 0.00 0.00 1.28
2173 2619 3.323115 TGAGCATGCACAAAAACCCATAA 59.677 39.130 21.98 0.00 0.00 1.90
2174 2620 2.896044 TGAGCATGCACAAAAACCCATA 59.104 40.909 21.98 0.00 0.00 2.74
2175 2621 1.693062 TGAGCATGCACAAAAACCCAT 59.307 42.857 21.98 0.00 0.00 4.00
2176 2622 1.117994 TGAGCATGCACAAAAACCCA 58.882 45.000 21.98 0.46 0.00 4.51
2177 2623 2.070783 CATGAGCATGCACAAAAACCC 58.929 47.619 21.69 0.00 31.39 4.11
2178 2624 2.070783 CCATGAGCATGCACAAAAACC 58.929 47.619 21.69 0.00 37.49 3.27
2179 2625 3.029320 TCCATGAGCATGCACAAAAAC 57.971 42.857 21.69 3.51 37.49 2.43
2185 2631 2.686405 TCTTTCATCCATGAGCATGCAC 59.314 45.455 21.98 15.08 38.19 4.57
2305 2753 1.949465 AATCGGCGGATTTAGTCACC 58.051 50.000 13.31 0.00 39.90 4.02
2612 3076 2.409948 AATGCCTACCTGTGAAGCTC 57.590 50.000 0.00 0.00 0.00 4.09
2661 3125 1.296715 CGTGGCTAGGGTTTGAGCT 59.703 57.895 0.00 0.00 38.79 4.09
2684 3148 3.320078 CGATTTCGTCGCGGCGAT 61.320 61.111 37.64 23.98 44.33 4.58


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

AutoCloner maintained by Alex Coulton.