Multiple sequence alignment - TraesCS1D01G395500

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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 TraesCS1D01G395500 chr1D 100.000 2552 0 0 1 2552 464036994 464039545 0.000000e+00 4713.0
1 TraesCS1D01G395500 chr1D 93.496 1891 78 17 594 2447 347252970 347251088 0.000000e+00 2769.0
2 TraesCS1D01G395500 chr1D 94.619 223 12 0 377 599 202683487 202683265 1.880000e-91 346.0
3 TraesCS1D01G395500 chr1D 92.202 218 14 3 377 593 191302445 191302230 3.190000e-79 305.0
4 TraesCS1D01G395500 chr1D 91.441 222 19 0 377 598 403264616 403264837 3.190000e-79 305.0
5 TraesCS1D01G395500 chr1D 77.564 312 49 11 6 296 423783488 423783799 4.370000e-38 169.0
6 TraesCS1D01G395500 chr1A 93.607 2581 124 15 1 2552 556201170 556203738 0.000000e+00 3814.0
7 TraesCS1D01G395500 chr1A 90.306 1733 101 29 596 2295 38372360 38374058 0.000000e+00 2207.0
8 TraesCS1D01G395500 chr6D 93.467 1990 87 9 596 2552 312544305 312542326 0.000000e+00 2915.0
9 TraesCS1D01G395500 chr6D 93.458 214 14 0 386 599 460914108 460913895 4.100000e-83 318.0
10 TraesCS1D01G395500 chr6D 90.435 230 21 1 370 599 178904269 178904497 4.130000e-78 302.0
11 TraesCS1D01G395500 chr3D 93.380 1979 84 19 599 2552 447973574 447971618 0.000000e+00 2885.0
12 TraesCS1D01G395500 chr3D 91.089 2020 79 21 600 2552 573731195 573733180 0.000000e+00 2639.0
13 TraesCS1D01G395500 chr3D 93.371 1056 53 9 600 1639 519945751 519944697 0.000000e+00 1546.0
14 TraesCS1D01G395500 chr4D 93.253 1986 78 20 597 2549 50776931 50778893 0.000000e+00 2874.0
15 TraesCS1D01G395500 chr4D 92.369 249 15 4 351 599 122143283 122143527 4.040000e-93 351.0
16 TraesCS1D01G395500 chr4D 93.243 222 14 1 378 599 122140532 122140312 2.450000e-85 326.0
17 TraesCS1D01G395500 chr4D 92.056 214 17 0 386 599 161154639 161154426 4.130000e-78 302.0
18 TraesCS1D01G395500 chr4D 91.705 217 17 1 378 594 500807990 500807775 1.480000e-77 300.0
19 TraesCS1D01G395500 chr4D 91.589 214 18 0 386 599 91613402 91613189 1.920000e-76 296.0
20 TraesCS1D01G395500 chr4D 91.589 214 18 0 386 599 119942061 119941848 1.920000e-76 296.0
21 TraesCS1D01G395500 chr4D 91.589 214 18 0 386 599 433946704 433946917 1.920000e-76 296.0
22 TraesCS1D01G395500 chr4D 90.090 222 21 1 378 599 469286999 469286779 1.160000e-73 287.0
23 TraesCS1D01G395500 chr3A 92.973 1978 105 16 599 2552 235187478 235189445 0.000000e+00 2852.0
24 TraesCS1D01G395500 chr7D 93.860 1873 87 8 600 2447 623570819 623572688 0.000000e+00 2796.0
25 TraesCS1D01G395500 chr7D 91.967 1718 83 23 596 2290 63995386 63997071 0.000000e+00 2357.0
26 TraesCS1D01G395500 chr7D 89.960 249 21 1 351 599 245561220 245561464 4.100000e-83 318.0
27 TraesCS1D01G395500 chr7A 90.986 2019 119 22 583 2552 30966331 30968335 0.000000e+00 2662.0
28 TraesCS1D01G395500 chr2A 90.868 1982 131 21 594 2552 742454762 742452808 0.000000e+00 2612.0
29 TraesCS1D01G395500 chr2A 90.862 1740 98 21 585 2295 677958483 677956776 0.000000e+00 2276.0
30 TraesCS1D01G395500 chr2A 82.682 179 26 2 181 354 334533844 334534022 1.220000e-33 154.0
31 TraesCS1D01G395500 chr6A 92.013 1878 115 9 600 2446 76046189 76048062 0.000000e+00 2604.0
32 TraesCS1D01G395500 chr5D 93.352 1399 56 14 580 1949 539819790 539818400 0.000000e+00 2034.0
33 TraesCS1D01G395500 chr5D 93.694 222 13 1 378 599 221737408 221737628 5.260000e-87 331.0
34 TraesCS1D01G395500 chr5D 92.857 224 16 0 376 599 339274940 339275163 2.450000e-85 326.0
35 TraesCS1D01G395500 chr5D 92.342 222 16 1 378 599 268688814 268688594 5.300000e-82 315.0
36 TraesCS1D01G395500 chr5D 92.593 216 15 1 378 593 197484351 197484565 2.470000e-80 309.0
37 TraesCS1D01G395500 chr2D 93.061 980 31 14 1491 2447 572813896 572814861 0.000000e+00 1399.0
38 TraesCS1D01G395500 chr2D 83.425 181 25 3 179 354 12466104 12465924 2.030000e-36 163.0
39 TraesCS1D01G395500 chr5B 93.519 216 14 0 378 593 153866273 153866058 3.170000e-84 322.0
40 TraesCS1D01G395500 chr5A 92.793 222 16 0 378 599 49243659 49243880 3.170000e-84 322.0
41 TraesCS1D01G395500 chr4A 90.361 249 18 6 351 599 473326168 473326410 3.170000e-84 322.0
42 TraesCS1D01G395500 chr7B 89.344 244 22 2 356 599 214932377 214932616 1.150000e-78 303.0
43 TraesCS1D01G395500 chr7B 98.256 172 2 1 2381 2552 663210112 663210282 1.480000e-77 300.0
44 TraesCS1D01G395500 chr7B 92.683 41 2 1 170 210 671423540 671423501 9.860000e-05 58.4
45 TraesCS1D01G395500 chr4B 90.991 222 20 0 378 599 491132068 491131847 1.480000e-77 300.0
46 TraesCS1D01G395500 chr4B 88.525 244 24 2 356 599 348255928 348255689 2.480000e-75 292.0
47 TraesCS1D01G395500 chr4B 87.395 119 13 2 180 297 4298660 4298777 4.430000e-28 135.0
48 TraesCS1D01G395500 chrUn 88.426 216 24 1 378 593 11254906 11255120 2.520000e-65 259.0
49 TraesCS1D01G395500 chrUn 88.318 214 25 0 386 599 233519082 233518869 9.060000e-65 257.0
50 TraesCS1D01G395500 chrUn 87.330 221 26 2 377 597 88191276 88191494 4.210000e-63 252.0
51 TraesCS1D01G395500 chrUn 87.500 216 26 1 378 593 218991731 218991945 5.450000e-62 248.0
52 TraesCS1D01G395500 chrUn 86.070 201 22 6 388 585 244763926 244764123 7.150000e-51 211.0
53 TraesCS1D01G395500 chrUn 93.939 132 8 0 377 508 110450583 110450452 1.550000e-47 200.0
54 TraesCS1D01G395500 chrUn 83.981 206 31 2 393 597 54337770 54337974 2.000000e-46 196.0
55 TraesCS1D01G395500 chrUn 93.182 132 9 0 377 508 110428224 110428093 7.200000e-46 195.0
56 TraesCS1D01G395500 chrUn 82.915 199 24 10 397 591 296904261 296904069 1.210000e-38 171.0
57 TraesCS1D01G395500 chrUn 81.106 217 33 7 388 599 128551367 128551154 1.570000e-37 167.0
58 TraesCS1D01G395500 chrUn 100.000 31 0 0 180 210 381317668 381317638 9.860000e-05 58.4
59 TraesCS1D01G395500 chr2B 83.060 183 25 4 177 353 748341869 748341687 7.310000e-36 161.0
60 TraesCS1D01G395500 chr1B 82.162 185 27 3 177 355 91297487 91297303 1.220000e-33 154.0
61 TraesCS1D01G395500 chr6B 87.288 118 15 0 179 296 632735417 632735534 4.430000e-28 135.0


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 TraesCS1D01G395500 chr1D 464036994 464039545 2551 False 4713 4713 100.000 1 2552 1 chr1D.!!$F3 2551
1 TraesCS1D01G395500 chr1D 347251088 347252970 1882 True 2769 2769 93.496 594 2447 1 chr1D.!!$R3 1853
2 TraesCS1D01G395500 chr1A 556201170 556203738 2568 False 3814 3814 93.607 1 2552 1 chr1A.!!$F2 2551
3 TraesCS1D01G395500 chr1A 38372360 38374058 1698 False 2207 2207 90.306 596 2295 1 chr1A.!!$F1 1699
4 TraesCS1D01G395500 chr6D 312542326 312544305 1979 True 2915 2915 93.467 596 2552 1 chr6D.!!$R1 1956
5 TraesCS1D01G395500 chr3D 447971618 447973574 1956 True 2885 2885 93.380 599 2552 1 chr3D.!!$R1 1953
6 TraesCS1D01G395500 chr3D 573731195 573733180 1985 False 2639 2639 91.089 600 2552 1 chr3D.!!$F1 1952
7 TraesCS1D01G395500 chr3D 519944697 519945751 1054 True 1546 1546 93.371 600 1639 1 chr3D.!!$R2 1039
8 TraesCS1D01G395500 chr4D 50776931 50778893 1962 False 2874 2874 93.253 597 2549 1 chr4D.!!$F1 1952
9 TraesCS1D01G395500 chr3A 235187478 235189445 1967 False 2852 2852 92.973 599 2552 1 chr3A.!!$F1 1953
10 TraesCS1D01G395500 chr7D 623570819 623572688 1869 False 2796 2796 93.860 600 2447 1 chr7D.!!$F3 1847
11 TraesCS1D01G395500 chr7D 63995386 63997071 1685 False 2357 2357 91.967 596 2290 1 chr7D.!!$F1 1694
12 TraesCS1D01G395500 chr7A 30966331 30968335 2004 False 2662 2662 90.986 583 2552 1 chr7A.!!$F1 1969
13 TraesCS1D01G395500 chr2A 742452808 742454762 1954 True 2612 2612 90.868 594 2552 1 chr2A.!!$R2 1958
14 TraesCS1D01G395500 chr2A 677956776 677958483 1707 True 2276 2276 90.862 585 2295 1 chr2A.!!$R1 1710
15 TraesCS1D01G395500 chr6A 76046189 76048062 1873 False 2604 2604 92.013 600 2446 1 chr6A.!!$F1 1846
16 TraesCS1D01G395500 chr5D 539818400 539819790 1390 True 2034 2034 93.352 580 1949 1 chr5D.!!$R2 1369
17 TraesCS1D01G395500 chr2D 572813896 572814861 965 False 1399 1399 93.061 1491 2447 1 chr2D.!!$F1 956


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
108 109 0.179086 AAAAAGCCCACTTTGCCGTG 60.179 50.0 0.0 0.00 45.48 4.94 F
530 531 0.889186 AGAATTTCTGGCGCCGTTGT 60.889 50.0 23.9 7.04 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1145 1244 0.676466 TACCCCATTCTTGCTGCACG 60.676 55.0 0.0 0.0 0.00 5.34 R
2284 2427 0.316937 CGCGTGTGCAAACATTCACT 60.317 50.0 8.0 0.0 42.97 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
24 25 6.879400 GTCTAAGATGTTACCAAGTCATCCT 58.121 40.000 0.00 0.00 38.79 3.24
38 39 1.134367 TCATCCTTCCGTGTGATCGAC 59.866 52.381 0.00 0.00 0.00 4.20
42 43 2.209064 CTTCCGTGTGATCGACCCGT 62.209 60.000 0.00 0.00 0.00 5.28
63 64 0.183492 TGGTGTGCTTCCTCTTTGCT 59.817 50.000 0.00 0.00 0.00 3.91
94 95 4.988708 AACAAACACACACAGCAAAAAG 57.011 36.364 0.00 0.00 0.00 2.27
108 109 0.179086 AAAAAGCCCACTTTGCCGTG 60.179 50.000 0.00 0.00 45.48 4.94
111 112 4.645921 GCCCACTTTGCCGTGTGC 62.646 66.667 0.00 0.00 41.77 4.57
113 114 3.276091 CCACTTTGCCGTGTGCGA 61.276 61.111 0.00 0.00 45.60 5.10
165 166 2.032178 GTCTGCCAGAACAAACACAGAC 59.968 50.000 0.00 5.32 44.86 3.51
175 176 2.159435 ACAAACACAGACGGCTTTGTTC 60.159 45.455 22.44 0.00 42.51 3.18
177 178 2.902705 ACACAGACGGCTTTGTTCTA 57.097 45.000 3.65 0.00 31.20 2.10
213 214 4.060900 TGAGCTCTTTGTCATCTGTGTTC 58.939 43.478 16.19 0.00 0.00 3.18
226 227 5.352846 TCATCTGTGTTCTTTTCACAAACGA 59.647 36.000 0.00 0.00 43.66 3.85
247 248 6.842163 ACGACAAAGTCTATTTTGCCATTAG 58.158 36.000 0.00 0.00 40.80 1.73
273 274 6.662414 TTTCTTTACCGTCTGCTGATTATG 57.338 37.500 0.00 0.00 0.00 1.90
279 280 2.223340 CCGTCTGCTGATTATGGCAAAC 60.223 50.000 0.00 0.00 38.02 2.93
289 290 6.432403 TGATTATGGCAAACCCTTTCTTTT 57.568 33.333 0.00 0.00 33.59 2.27
290 291 6.463360 TGATTATGGCAAACCCTTTCTTTTC 58.537 36.000 0.00 0.00 33.59 2.29
292 293 1.410882 TGGCAAACCCTTTCTTTTCCG 59.589 47.619 0.00 0.00 33.59 4.30
326 327 2.761213 GGCAAAGATGGCCCCTGG 60.761 66.667 0.00 0.00 45.87 4.45
362 363 4.273969 TGTTTCCCGTAGTGATTTTGTGTC 59.726 41.667 0.00 0.00 0.00 3.67
365 366 3.071892 TCCCGTAGTGATTTTGTGTCCTT 59.928 43.478 0.00 0.00 0.00 3.36
367 368 3.813166 CCGTAGTGATTTTGTGTCCTTGT 59.187 43.478 0.00 0.00 0.00 3.16
391 392 5.209240 GCTGTTAATTAACGAGTTGTTGCA 58.791 37.500 20.51 1.72 42.01 4.08
427 428 6.153340 ACTGGATTGATAACCTTGGTTTCATG 59.847 38.462 10.52 0.00 0.00 3.07
441 442 6.817765 TGGTTTCATGACTGAGGAAAATAC 57.182 37.500 0.00 0.00 36.17 1.89
475 476 1.138568 CTGCATCATCCCCTCCTCTT 58.861 55.000 0.00 0.00 0.00 2.85
530 531 0.889186 AGAATTTCTGGCGCCGTTGT 60.889 50.000 23.90 7.04 0.00 3.32
561 562 6.983307 AGACATCATCAACATCTAGCAAGTAC 59.017 38.462 0.00 0.00 0.00 2.73
563 564 5.939764 TCATCAACATCTAGCAAGTACCT 57.060 39.130 0.00 0.00 0.00 3.08
564 565 7.069950 ACATCATCAACATCTAGCAAGTACCTA 59.930 37.037 0.00 0.00 0.00 3.08
565 566 6.806751 TCATCAACATCTAGCAAGTACCTAC 58.193 40.000 0.00 0.00 0.00 3.18
566 567 5.244785 TCAACATCTAGCAAGTACCTACG 57.755 43.478 0.00 0.00 0.00 3.51
675 676 4.868171 AGATGCGAATCGTGCTTAGTTTTA 59.132 37.500 4.07 0.00 0.00 1.52
702 703 4.059459 CGTGCGCACCAACTCGTC 62.059 66.667 33.23 6.88 0.00 4.20
805 807 3.636043 CAGACCGTTGCACGCGTT 61.636 61.111 10.22 0.00 40.91 4.84
1040 1138 2.125552 CACCTCGCGGATGCAGAA 60.126 61.111 6.13 0.00 42.97 3.02
1080 1178 1.583495 ATGTCTTCGTCTGTCCGCGA 61.583 55.000 8.23 0.00 35.17 5.87
1145 1244 2.128035 CCAGAATCGTCCGTTCTATGC 58.872 52.381 4.89 0.00 34.32 3.14
1414 1514 2.752354 GACAGAGAGCTAGCTGTTGAGA 59.248 50.000 24.99 0.00 44.77 3.27
1724 1857 2.495270 CTCTCTGCTCTGCCTTTCTGTA 59.505 50.000 0.00 0.00 0.00 2.74
1833 1967 1.550130 ATTCGGGGGTTCTCTTGCGA 61.550 55.000 0.00 0.00 0.00 5.10
1838 1972 1.157585 GGGGTTCTCTTGCGAGTTTC 58.842 55.000 0.00 0.00 38.45 2.78
1856 1992 7.505646 CGAGTTTCTATGTTTTCTGTTCTGAG 58.494 38.462 0.00 0.00 0.00 3.35
1928 2064 5.902613 TGAATTATTCCAGAGCCAAACAG 57.097 39.130 2.22 0.00 0.00 3.16
2080 2217 5.461032 TTACACCTGGTGCCAAAATTAAG 57.539 39.130 26.20 0.00 36.98 1.85
2284 2427 6.550108 GGAAGGAAGGTATACATAGTGAGACA 59.450 42.308 5.01 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.455674 TCACACGGAAGGATGACTTG 57.544 50.000 0.00 0.00 40.21 3.16
38 39 2.978010 GGAAGCACACCACACGGG 60.978 66.667 0.00 0.00 44.81 5.28
42 43 1.679139 CAAAGAGGAAGCACACCACA 58.321 50.000 0.00 0.00 0.00 4.17
63 64 2.226674 TGTGTGTTTGTTTTCGCAGACA 59.773 40.909 0.00 0.00 34.32 3.41
128 129 1.396301 CAGACGGCAGAGATTCTTTGC 59.604 52.381 18.36 18.36 40.26 3.68
165 166 0.716108 CGTCTGCTAGAACAAAGCCG 59.284 55.000 0.00 0.00 39.30 5.52
175 176 1.354040 CTCACTTTGCCGTCTGCTAG 58.646 55.000 0.00 0.00 42.00 3.42
177 178 1.963338 GCTCACTTTGCCGTCTGCT 60.963 57.895 0.00 0.00 42.00 4.24
204 205 5.123186 TGTCGTTTGTGAAAAGAACACAGAT 59.877 36.000 0.00 0.00 46.44 2.90
213 214 8.614994 AAATAGACTTTGTCGTTTGTGAAAAG 57.385 30.769 0.00 0.00 37.67 2.27
226 227 9.830975 AAAAACTAATGGCAAAATAGACTTTGT 57.169 25.926 10.98 0.00 38.35 2.83
247 248 4.806342 TCAGCAGACGGTAAAGAAAAAC 57.194 40.909 0.00 0.00 0.00 2.43
273 274 1.411246 ACGGAAAAGAAAGGGTTTGCC 59.589 47.619 0.00 0.00 29.93 4.52
279 280 1.604604 TGCAGACGGAAAAGAAAGGG 58.395 50.000 0.00 0.00 0.00 3.95
289 290 1.879380 CATGAGGTTTTTGCAGACGGA 59.121 47.619 0.00 0.00 0.00 4.69
290 291 1.068333 CCATGAGGTTTTTGCAGACGG 60.068 52.381 0.00 0.00 0.00 4.79
292 293 1.340889 TGCCATGAGGTTTTTGCAGAC 59.659 47.619 0.00 0.00 37.19 3.51
341 342 3.816523 GGACACAAAATCACTACGGGAAA 59.183 43.478 0.00 0.00 0.00 3.13
345 346 3.813166 ACAAGGACACAAAATCACTACGG 59.187 43.478 0.00 0.00 0.00 4.02
362 363 5.607119 ACTCGTTAATTAACAGCACAAGG 57.393 39.130 24.27 8.68 35.99 3.61
365 366 5.994887 ACAACTCGTTAATTAACAGCACA 57.005 34.783 24.27 5.33 35.99 4.57
367 368 5.209240 GCAACAACTCGTTAATTAACAGCA 58.791 37.500 24.27 9.52 35.52 4.41
441 442 7.763528 GGGATGATGCAGTACAATAGAGATAAG 59.236 40.741 0.00 0.00 0.00 1.73
530 531 1.567357 TGTTGATGATGTCTCCCCGA 58.433 50.000 0.00 0.00 0.00 5.14
561 562 4.626042 AGAGATGAAAGCTTATGCGTAGG 58.374 43.478 0.00 0.00 45.42 3.18
563 564 5.220662 GCAAAGAGATGAAAGCTTATGCGTA 60.221 40.000 0.00 0.00 45.42 4.42
564 565 4.437930 GCAAAGAGATGAAAGCTTATGCGT 60.438 41.667 0.00 0.00 45.42 5.24
565 566 4.033684 GCAAAGAGATGAAAGCTTATGCG 58.966 43.478 0.00 0.00 45.42 4.73
566 567 4.990257 TGCAAAGAGATGAAAGCTTATGC 58.010 39.130 0.00 0.77 40.05 3.14
702 703 2.432628 GACGGCAGAGTTCACGGG 60.433 66.667 0.00 0.00 0.00 5.28
805 807 3.496309 CTGCTGGGTCCCACAAGCA 62.496 63.158 19.41 19.41 0.00 3.91
922 991 2.881266 CGCCGCTCTCTCTCTCTCG 61.881 68.421 0.00 0.00 0.00 4.04
1145 1244 0.676466 TACCCCATTCTTGCTGCACG 60.676 55.000 0.00 0.00 0.00 5.34
1197 1297 3.094572 CAACCCATTGCTCAAAGATCCT 58.905 45.455 0.00 0.00 0.00 3.24
1414 1514 8.049721 CCTAACCTTCTTCTTCAACATCCTAAT 58.950 37.037 0.00 0.00 0.00 1.73
1689 1822 3.422417 CAGAGAGCTGCATTTCATTGG 57.578 47.619 1.02 0.00 34.95 3.16
1731 1864 0.696501 GGCCCACAGAGGAACCTTTA 59.303 55.000 0.00 0.00 41.22 1.85
1833 1967 8.738645 AACTCAGAACAGAAAACATAGAAACT 57.261 30.769 0.00 0.00 0.00 2.66
1856 1992 9.124807 GCATTATGATTTACCGCCTAAATTAAC 57.875 33.333 0.00 0.00 35.51 2.01
1928 2064 9.529325 AGCTCCAAAACAATTTCTAAACTTAAC 57.471 29.630 0.00 0.00 0.00 2.01
2284 2427 0.316937 CGCGTGTGCAAACATTCACT 60.317 50.000 8.00 0.00 42.97 3.41



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

AutoCloner maintained by Alex Coulton.