Multiple sequence alignment - TraesCS4D01G070000

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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 TraesCS4D01G070000 chr4D 100.000 2213 0 0 1 2213 45248030 45250242 0.000000e+00 4087.0
1 TraesCS4D01G070000 chr4D 93.474 521 30 4 1694 2210 79144420 79144940 0.000000e+00 771.0
2 TraesCS4D01G070000 chr4D 77.030 505 93 17 1207 1693 244318535 244318036 3.620000e-68 268.0
3 TraesCS4D01G070000 chr4D 96.226 53 2 0 1 53 356762614 356762666 1.090000e-13 87.9
4 TraesCS4D01G070000 chr4D 97.959 49 1 0 1 49 457151093 457151045 3.920000e-13 86.1
5 TraesCS4D01G070000 chr4A 96.535 1645 54 3 51 1695 552223023 552221382 0.000000e+00 2719.0
6 TraesCS4D01G070000 chr4A 94.888 1467 70 5 51 1515 465122000 465123463 0.000000e+00 2289.0
7 TraesCS4D01G070000 chr4A 93.484 798 37 5 903 1699 653011942 653011159 0.000000e+00 1171.0
8 TraesCS4D01G070000 chr6B 95.496 1643 66 3 51 1693 483464178 483465812 0.000000e+00 2617.0
9 TraesCS4D01G070000 chr6B 96.177 1465 54 2 51 1515 177081498 177080036 0.000000e+00 2394.0
10 TraesCS4D01G070000 chr2A 95.846 1613 63 4 51 1663 591092120 591093728 0.000000e+00 2604.0
11 TraesCS4D01G070000 chr3A 95.775 1491 60 2 51 1541 664911370 664912857 0.000000e+00 2401.0
12 TraesCS4D01G070000 chr1B 96.180 1466 54 2 51 1515 27643421 27644885 0.000000e+00 2396.0
13 TraesCS4D01G070000 chr1B 94.946 277 13 1 1421 1697 87146722 87146997 1.210000e-117 433.0
14 TraesCS4D01G070000 chr4B 95.839 1466 59 2 51 1516 569527642 569529105 0.000000e+00 2368.0
15 TraesCS4D01G070000 chr4B 98.113 53 1 0 1 53 248643760 248643812 2.340000e-15 93.5
16 TraesCS4D01G070000 chr4B 98.113 53 1 0 1 53 272448361 272448309 2.340000e-15 93.5
17 TraesCS4D01G070000 chr4B 94.737 57 2 1 1 57 526872049 526872104 1.090000e-13 87.9
18 TraesCS4D01G070000 chr2B 94.114 1529 85 4 51 1578 686782524 686784048 0.000000e+00 2320.0
19 TraesCS4D01G070000 chr2B 94.737 57 2 1 1 57 647286635 647286690 1.090000e-13 87.9
20 TraesCS4D01G070000 chr2D 92.963 540 33 5 1679 2213 368057878 368057339 0.000000e+00 782.0
21 TraesCS4D01G070000 chr2D 92.557 524 31 7 1694 2210 612427752 612428274 0.000000e+00 745.0
22 TraesCS4D01G070000 chr7D 93.064 519 32 4 1694 2208 480014087 480014605 0.000000e+00 756.0
23 TraesCS4D01G070000 chr7D 92.706 521 34 4 1694 2210 181223034 181223554 0.000000e+00 749.0
24 TraesCS4D01G070000 chr7D 85.173 607 63 7 1566 2164 114425283 114425870 4.070000e-167 597.0
25 TraesCS4D01G070000 chr7D 91.051 257 21 2 1437 1693 561631869 561631615 1.630000e-91 346.0
26 TraesCS4D01G070000 chr7D 94.737 57 2 1 1 57 213944199 213944254 1.090000e-13 87.9
27 TraesCS4D01G070000 chr5D 92.748 524 33 4 1694 2213 238487039 238486517 0.000000e+00 752.0
28 TraesCS4D01G070000 chr5D 96.226 53 2 0 1 53 226532782 226532730 1.090000e-13 87.9
29 TraesCS4D01G070000 chr1D 92.706 521 34 4 1694 2210 494436509 494437029 0.000000e+00 749.0
30 TraesCS4D01G070000 chr1D 76.750 757 137 30 968 1696 170227401 170228146 9.580000e-104 387.0
31 TraesCS4D01G070000 chr1D 76.923 325 58 12 1206 1517 21731291 21730971 3.780000e-38 169.0
32 TraesCS4D01G070000 chr1D 97.959 49 1 0 1 49 172795493 172795445 3.920000e-13 86.1
33 TraesCS4D01G070000 chr1D 97.959 49 1 0 1 49 372897456 372897408 3.920000e-13 86.1
34 TraesCS4D01G070000 chr3D 92.586 526 30 8 1694 2213 488123972 488123450 0.000000e+00 747.0
35 TraesCS4D01G070000 chr3D 98.113 53 1 0 1 53 417916743 417916691 2.340000e-15 93.5
36 TraesCS4D01G070000 chr3D 96.226 53 2 0 1 53 450048499 450048551 1.090000e-13 87.9
37 TraesCS4D01G070000 chr3B 92.706 521 32 6 1694 2210 423785423 423785941 0.000000e+00 747.0
38 TraesCS4D01G070000 chr3B 98.039 51 1 0 1 51 68865420 68865470 3.030000e-14 89.8
39 TraesCS4D01G070000 chr3B 98.039 51 1 0 1 51 696405380 696405330 3.030000e-14 89.8
40 TraesCS4D01G070000 chr1A 88.296 581 57 11 1636 2210 104604429 104605004 0.000000e+00 686.0
41 TraesCS4D01G070000 chr1A 81.643 414 61 8 898 1297 585729465 585729053 1.640000e-86 329.0
42 TraesCS4D01G070000 chr1A 76.201 458 67 21 1206 1623 80618793 80618338 1.040000e-48 204.0
43 TraesCS4D01G070000 chr1A 96.226 53 2 0 1 53 179957297 179957349 1.090000e-13 87.9
44 TraesCS4D01G070000 chr1A 96.226 53 2 0 1 53 348193357 348193409 1.090000e-13 87.9
45 TraesCS4D01G070000 chr7B 88.593 263 26 4 1432 1693 537021182 537021441 1.280000e-82 316.0
46 TraesCS4D01G070000 chr7B 98.113 53 1 0 1 53 488842038 488841986 2.340000e-15 93.5
47 TraesCS4D01G070000 chr6D 75.337 742 137 33 976 1694 281543395 281542677 4.590000e-82 315.0
48 TraesCS4D01G070000 chr6D 81.791 335 47 7 976 1297 395212885 395212552 3.620000e-68 268.0
49 TraesCS4D01G070000 chr6D 78.151 357 57 9 898 1238 46495557 46495206 8.010000e-50 207.0
50 TraesCS4D01G070000 chr6D 97.959 49 1 0 1 49 150859802 150859754 3.920000e-13 86.1
51 TraesCS4D01G070000 chr6D 97.959 49 1 0 1 49 399688017 399687969 3.920000e-13 86.1
52 TraesCS4D01G070000 chr6D 94.340 53 3 0 1 53 218817263 218817211 5.060000e-12 82.4
53 TraesCS4D01G070000 chr6D 94.340 53 3 0 1 53 463356149 463356201 5.060000e-12 82.4
54 TraesCS4D01G070000 chr6D 94.340 53 2 1 1 53 184670710 184670761 1.820000e-11 80.5
55 TraesCS4D01G070000 chr6D 95.918 49 2 0 1 49 349895714 349895762 1.820000e-11 80.5
56 TraesCS4D01G070000 chr6D 93.878 49 3 0 1 49 155016935 155016983 8.470000e-10 75.0
57 TraesCS4D01G070000 chrUn 83.186 339 41 9 909 1234 56309131 56308796 1.660000e-76 296.0
58 TraesCS4D01G070000 chrUn 80.712 337 50 8 974 1297 304777415 304777081 4.720000e-62 248.0
59 TraesCS4D01G070000 chrUn 75.719 556 96 28 976 1514 11557940 11558473 2.200000e-60 243.0
60 TraesCS4D01G070000 chrUn 78.191 188 29 10 1062 1237 61793015 61793202 2.320000e-20 110.0
61 TraesCS4D01G070000 chrUn 97.959 49 1 0 1 49 63850183 63850135 3.920000e-13 86.1
62 TraesCS4D01G070000 chrUn 95.918 49 2 0 5 53 73778387 73778435 1.820000e-11 80.5
63 TraesCS4D01G070000 chrUn 90.566 53 3 2 1187 1237 38730294 38730242 3.940000e-08 69.4
64 TraesCS4D01G070000 chrUn 100.000 33 0 0 4 36 56872507 56872475 6.600000e-06 62.1
65 TraesCS4D01G070000 chrUn 100.000 33 0 0 4 36 325600725 325600693 6.600000e-06 62.1
66 TraesCS4D01G070000 chrUn 88.000 50 5 1 1 50 55361271 55361319 8.530000e-05 58.4
67 TraesCS4D01G070000 chrUn 88.000 50 5 1 1 50 280277650 280277602 8.530000e-05 58.4
68 TraesCS4D01G070000 chr7A 85.664 286 30 11 1420 1699 581048706 581048426 7.730000e-75 291.0
69 TraesCS4D01G070000 chr6A 75.429 525 84 25 1206 1693 31920255 31920771 1.720000e-51 213.0


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 TraesCS4D01G070000 chr4D 45248030 45250242 2212 False 4087 4087 100.000 1 2213 1 chr4D.!!$F1 2212
1 TraesCS4D01G070000 chr4D 79144420 79144940 520 False 771 771 93.474 1694 2210 1 chr4D.!!$F2 516
2 TraesCS4D01G070000 chr4A 552221382 552223023 1641 True 2719 2719 96.535 51 1695 1 chr4A.!!$R1 1644
3 TraesCS4D01G070000 chr4A 465122000 465123463 1463 False 2289 2289 94.888 51 1515 1 chr4A.!!$F1 1464
4 TraesCS4D01G070000 chr4A 653011159 653011942 783 True 1171 1171 93.484 903 1699 1 chr4A.!!$R2 796
5 TraesCS4D01G070000 chr6B 483464178 483465812 1634 False 2617 2617 95.496 51 1693 1 chr6B.!!$F1 1642
6 TraesCS4D01G070000 chr6B 177080036 177081498 1462 True 2394 2394 96.177 51 1515 1 chr6B.!!$R1 1464
7 TraesCS4D01G070000 chr2A 591092120 591093728 1608 False 2604 2604 95.846 51 1663 1 chr2A.!!$F1 1612
8 TraesCS4D01G070000 chr3A 664911370 664912857 1487 False 2401 2401 95.775 51 1541 1 chr3A.!!$F1 1490
9 TraesCS4D01G070000 chr1B 27643421 27644885 1464 False 2396 2396 96.180 51 1515 1 chr1B.!!$F1 1464
10 TraesCS4D01G070000 chr4B 569527642 569529105 1463 False 2368 2368 95.839 51 1516 1 chr4B.!!$F3 1465
11 TraesCS4D01G070000 chr2B 686782524 686784048 1524 False 2320 2320 94.114 51 1578 1 chr2B.!!$F2 1527
12 TraesCS4D01G070000 chr2D 368057339 368057878 539 True 782 782 92.963 1679 2213 1 chr2D.!!$R1 534
13 TraesCS4D01G070000 chr2D 612427752 612428274 522 False 745 745 92.557 1694 2210 1 chr2D.!!$F1 516
14 TraesCS4D01G070000 chr7D 480014087 480014605 518 False 756 756 93.064 1694 2208 1 chr7D.!!$F4 514
15 TraesCS4D01G070000 chr7D 181223034 181223554 520 False 749 749 92.706 1694 2210 1 chr7D.!!$F2 516
16 TraesCS4D01G070000 chr7D 114425283 114425870 587 False 597 597 85.173 1566 2164 1 chr7D.!!$F1 598
17 TraesCS4D01G070000 chr5D 238486517 238487039 522 True 752 752 92.748 1694 2213 1 chr5D.!!$R2 519
18 TraesCS4D01G070000 chr1D 494436509 494437029 520 False 749 749 92.706 1694 2210 1 chr1D.!!$F2 516
19 TraesCS4D01G070000 chr1D 170227401 170228146 745 False 387 387 76.750 968 1696 1 chr1D.!!$F1 728
20 TraesCS4D01G070000 chr3D 488123450 488123972 522 True 747 747 92.586 1694 2213 1 chr3D.!!$R2 519
21 TraesCS4D01G070000 chr3B 423785423 423785941 518 False 747 747 92.706 1694 2210 1 chr3B.!!$F2 516
22 TraesCS4D01G070000 chr1A 104604429 104605004 575 False 686 686 88.296 1636 2210 1 chr1A.!!$F1 574
23 TraesCS4D01G070000 chr6D 281542677 281543395 718 True 315 315 75.337 976 1694 1 chr6D.!!$R4 718
24 TraesCS4D01G070000 chrUn 11557940 11558473 533 False 243 243 75.719 976 1514 1 chrUn.!!$F1 538
25 TraesCS4D01G070000 chr6A 31920255 31920771 516 False 213 213 75.429 1206 1693 1 chr6A.!!$F1 487

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
464 465 1.302511 GCGTCATCCACCCTGTTGT 60.303 57.895 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1888 1.856265 GACTTTTCTGGCACCCTGCG 61.856 60.0 0.0 0.0 46.21 5.18 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
37 38 4.106925 CCTGCTCCTGCCTCCCAC 62.107 72.222 0.00 0.00 38.71 4.61
38 39 4.463879 CTGCTCCTGCCTCCCACG 62.464 72.222 0.00 0.00 38.71 4.94
171 172 3.749665 AGGAGATGATGCTAGCAAGTC 57.250 47.619 23.54 16.33 0.00 3.01
464 465 1.302511 GCGTCATCCACCCTGTTGT 60.303 57.895 0.00 0.00 0.00 3.32
503 504 4.193334 CGATCGGCAGTCTCGGCA 62.193 66.667 7.38 0.00 0.00 5.69
521 522 2.358247 GACCGGACGCCAACATGT 60.358 61.111 9.46 0.00 0.00 3.21
730 731 2.899900 TGGCTGTGAGTAGAGTGTGAAT 59.100 45.455 0.00 0.00 0.00 2.57
880 881 6.128445 CCAACTCTGAACTGTATGCTAGTTTG 60.128 42.308 0.00 0.00 38.42 2.93
905 906 6.791867 AATGATGTACTGTTACTCTGGCTA 57.208 37.500 0.00 0.00 0.00 3.93
1079 1080 1.152312 ACTCGGAGGTGGACTTGGT 60.152 57.895 10.23 0.00 0.00 3.67
1156 1159 4.043100 TCGCCGAGGAGGAGGACA 62.043 66.667 0.00 0.00 45.00 4.02
1172 1175 1.626654 GACATTGACGCCACAGTCCG 61.627 60.000 0.00 0.00 40.26 4.79
1785 1888 1.755384 GTGATCGAATCCCCCTCCC 59.245 63.158 0.00 0.00 0.00 4.30
1803 1906 1.898574 CGCAGGGTGCCAGAAAAGT 60.899 57.895 0.00 0.00 41.12 2.66
1881 1984 1.620822 GATGCTTCTGGTGGTTTGGT 58.379 50.000 0.00 0.00 0.00 3.67
1942 2047 3.953775 CACGAGGGGCCCACAAGT 61.954 66.667 27.72 15.65 0.00 3.16
2097 2209 7.243604 TGGACTCCGTTTAGTATTCCTTTTA 57.756 36.000 0.00 0.00 0.00 1.52
2151 2264 2.166664 CTGACACTGGGCTCTAGGTTAC 59.833 54.545 0.00 0.00 0.00 2.50
2155 2268 3.011482 ACACTGGGCTCTAGGTTACTAGT 59.989 47.826 0.00 0.00 45.60 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.106925 GTGGGAGGCAGGAGCAGG 62.107 72.222 0.00 0.0 44.61 4.85
21 22 4.463879 CGTGGGAGGCAGGAGCAG 62.464 72.222 0.00 0.0 44.61 4.24
38 39 4.129737 CATGCAGCACAGCCAGCC 62.130 66.667 0.00 0.0 30.76 4.85
39 40 4.796231 GCATGCAGCACAGCCAGC 62.796 66.667 14.21 0.0 44.79 4.85
48 49 2.098607 ACATACAACATCAGCATGCAGC 59.901 45.455 21.98 0.0 46.19 5.25
49 50 3.691498 CACATACAACATCAGCATGCAG 58.309 45.455 21.98 12.9 34.76 4.41
171 172 7.278135 TGATCTATCCATTCAAGAGAGTTTGG 58.722 38.462 0.00 0.0 0.00 3.28
464 465 1.676635 CCTCGTACGTCCTGGTGGA 60.677 63.158 16.05 0.0 40.69 4.02
503 504 2.047274 CATGTTGGCGTCCGGTCT 60.047 61.111 0.00 0.0 0.00 3.85
730 731 9.913310 AGAGATATGATTCGTATCCTCTATGAA 57.087 33.333 18.24 0.0 34.05 2.57
880 881 6.574350 AGCCAGAGTAACAGTACATCATTAC 58.426 40.000 0.00 0.0 32.12 1.89
905 906 6.734871 GCACATGCACATGAATCAATAGTGAT 60.735 38.462 17.19 0.0 42.79 3.06
1039 1040 0.111061 TTGAAGAGCACACTGCCCAT 59.889 50.000 0.00 0.0 46.52 4.00
1079 1080 4.047059 GGTCGCCGGTCTTCACGA 62.047 66.667 1.90 0.0 0.00 4.35
1156 1159 2.047274 CCGGACTGTGGCGTCAAT 60.047 61.111 0.00 0.0 35.63 2.57
1457 1532 2.756760 TGTTTCCCCACGCTACTACTAG 59.243 50.000 0.00 0.0 0.00 2.57
1785 1888 1.856265 GACTTTTCTGGCACCCTGCG 61.856 60.000 0.00 0.0 46.21 5.18
1823 1926 2.251642 GCCGCAACCTTCTGTTCGT 61.252 57.895 0.00 0.0 34.00 3.85
1824 1927 2.556287 GCCGCAACCTTCTGTTCG 59.444 61.111 0.00 0.0 34.00 3.95
1859 1962 2.173519 CAAACCACCAGAAGCATCCAT 58.826 47.619 0.00 0.0 0.00 3.41
2097 2209 5.596836 TTCCTTGTTTTTGAGCTTCACAT 57.403 34.783 0.00 0.0 0.00 3.21


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

AutoCloner maintained by Alex Coulton.