Multiple sequence alignment - TraesCS1D01G204100

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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 TraesCS1D01G204100 chr1D 100.000 2720 0 0 1 2720 288937651 288940370 0.000000e+00 5024.0
1 TraesCS1D01G204100 chr1D 82.759 638 79 17 2009 2636 10376491 10377107 8.570000e-150 540.0
2 TraesCS1D01G204100 chr1D 82.540 126 20 2 1 125 462469688 462469812 2.860000e-20 110.0
3 TraesCS1D01G204100 chr1D 86.207 87 12 0 12 98 208754772 208754858 8.020000e-16 95.3
4 TraesCS1D01G204100 chr1B 92.177 1534 63 20 473 1965 390467112 390468629 0.000000e+00 2115.0
5 TraesCS1D01G204100 chr1B 90.735 993 80 6 1737 2720 390470948 390471937 0.000000e+00 1314.0
6 TraesCS1D01G204100 chr1B 84.066 364 48 6 123 476 390464300 390464663 2.590000e-90 342.0
7 TraesCS1D01G204100 chr1B 94.643 168 9 0 1571 1738 390470738 390470905 7.470000e-66 261.0
8 TraesCS1D01G204100 chr1B 95.968 124 5 0 1 124 390464108 390464231 4.590000e-48 202.0
9 TraesCS1D01G204100 chr1A 89.964 1664 100 27 127 1743 361234600 361236243 0.000000e+00 2085.0
10 TraesCS1D01G204100 chr1A 80.601 732 128 14 1993 2720 540185505 540186226 1.100000e-153 553.0
11 TraesCS1D01G204100 chr1A 91.200 125 11 0 1 125 361234404 361234528 1.300000e-38 171.0
12 TraesCS1D01G204100 chr1A 82.796 93 16 0 12 104 554277052 554276960 1.740000e-12 84.2
13 TraesCS1D01G204100 chr1A 82.292 96 17 0 3 98 554296316 554296411 1.740000e-12 84.2
14 TraesCS1D01G204100 chr3A 84.135 769 107 10 1963 2720 69265079 69264315 0.000000e+00 730.0
15 TraesCS1D01G204100 chr3A 82.921 404 65 4 2319 2720 68271470 68271069 7.160000e-96 361.0
16 TraesCS1D01G204100 chr7D 82.177 735 117 12 1994 2720 607028858 607028130 1.070000e-173 619.0
17 TraesCS1D01G204100 chr7D 86.066 122 16 1 3 124 470276022 470275902 2.200000e-26 130.0
18 TraesCS1D01G204100 chr6D 83.667 649 86 10 1962 2592 267726575 267727221 6.480000e-166 593.0
19 TraesCS1D01G204100 chr6D 81.667 120 22 0 1 120 333367435 333367316 1.720000e-17 100.0
20 TraesCS1D01G204100 chr2A 81.754 707 112 6 2019 2720 179349455 179350149 2.350000e-160 575.0
21 TraesCS1D01G204100 chr2A 79.630 216 31 10 2005 2214 468523252 468523044 2.820000e-30 143.0
22 TraesCS1D01G204100 chr2A 85.366 123 18 0 3 125 475866999 475866877 7.910000e-26 128.0
23 TraesCS1D01G204100 chr2A 78.571 182 32 4 2006 2181 84541661 84541481 2.210000e-21 113.0
24 TraesCS1D01G204100 chr7B 81.085 719 115 15 2008 2720 692622424 692623127 3.060000e-154 555.0
25 TraesCS1D01G204100 chr7B 95.074 203 10 0 1422 1624 481813695 481813897 1.220000e-83 320.0
26 TraesCS1D01G204100 chr6B 80.913 723 117 16 2015 2720 71303245 71303963 3.960000e-153 551.0
27 TraesCS1D01G204100 chr3D 90.400 125 12 0 1 125 348920158 348920034 6.030000e-37 165.0
28 TraesCS1D01G204100 chr6A 86.325 117 10 5 241 351 594822345 594822229 3.680000e-24 122.0
29 TraesCS1D01G204100 chr6A 79.775 89 14 3 7 93 530501747 530501833 8.130000e-06 62.1


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 TraesCS1D01G204100 chr1D 288937651 288940370 2719 False 5024.0 5024 100.0000 1 2720 1 chr1D.!!$F3 2719
1 TraesCS1D01G204100 chr1D 10376491 10377107 616 False 540.0 540 82.7590 2009 2636 1 chr1D.!!$F1 627
2 TraesCS1D01G204100 chr1B 390464108 390471937 7829 False 846.8 2115 91.5178 1 2720 5 chr1B.!!$F1 2719
3 TraesCS1D01G204100 chr1A 361234404 361236243 1839 False 1128.0 2085 90.5820 1 1743 2 chr1A.!!$F3 1742
4 TraesCS1D01G204100 chr1A 540185505 540186226 721 False 553.0 553 80.6010 1993 2720 1 chr1A.!!$F1 727
5 TraesCS1D01G204100 chr3A 69264315 69265079 764 True 730.0 730 84.1350 1963 2720 1 chr3A.!!$R2 757
6 TraesCS1D01G204100 chr7D 607028130 607028858 728 True 619.0 619 82.1770 1994 2720 1 chr7D.!!$R2 726
7 TraesCS1D01G204100 chr6D 267726575 267727221 646 False 593.0 593 83.6670 1962 2592 1 chr6D.!!$F1 630
8 TraesCS1D01G204100 chr2A 179349455 179350149 694 False 575.0 575 81.7540 2019 2720 1 chr2A.!!$F1 701
9 TraesCS1D01G204100 chr7B 692622424 692623127 703 False 555.0 555 81.0850 2008 2720 1 chr7B.!!$F2 712
10 TraesCS1D01G204100 chr6B 71303245 71303963 718 False 551.0 551 80.9130 2015 2720 1 chr6B.!!$F1 705

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
992 3560 0.248296 GATCTCTCACGAGTCACGCC 60.248 60.0 0.0 0.0 46.94 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2614 7813 0.536006 GTGGAGCACTGAGTTGCCTT 60.536 55.0 3.93 0.0 44.14 4.35 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
84 85 1.387539 GAAGAGAAGAAGGCCATGGC 58.612 55.000 29.47 29.47 41.06 4.40
104 105 1.384525 CGAGGAGAGGAAGACGATGT 58.615 55.000 0.00 0.00 0.00 3.06
125 126 4.644685 TGTTGGAAGAAAAGAAGGTGAAGG 59.355 41.667 0.00 0.00 0.00 3.46
183 254 1.821061 CGGAGAAGGAGGCCGCATAT 61.821 60.000 9.31 0.00 38.46 1.78
186 257 1.227943 GAAGGAGGCCGCATATGCA 60.228 57.895 26.52 0.00 42.21 3.96
200 271 1.587547 TATGCAGCAACGACAACACA 58.412 45.000 0.00 0.00 0.00 3.72
206 277 0.383949 GCAACGACAACACATTGGGT 59.616 50.000 0.00 0.00 40.42 4.51
238 310 7.603784 GGTTCAGAATTATTTTTGCATGGACTT 59.396 33.333 0.00 0.00 0.00 3.01
252 324 4.708177 CATGGACTTCCGGACTGATATTT 58.292 43.478 1.83 0.00 39.43 1.40
319 393 3.316308 GGTTGTGATAAGGCATGTGATCC 59.684 47.826 0.00 0.00 0.00 3.36
336 410 1.299850 CCGACGCGCTATGGATCAA 60.300 57.895 5.73 0.00 0.00 2.57
398 478 7.394016 ACATAATATCATTGAATGACCGCCTA 58.606 34.615 10.45 0.00 43.01 3.93
427 513 1.752833 GGACTGGTCCCTTGTTCGT 59.247 57.895 8.48 0.00 43.94 3.85
439 525 3.369471 CCCTTGTTCGTGGATAGACACAT 60.369 47.826 0.00 0.00 41.38 3.21
445 531 5.163550 TGTTCGTGGATAGACACATAAGGAG 60.164 44.000 0.00 0.00 41.38 3.69
522 3065 7.229306 TCCTTCGTCGGTAAGTATATGTATGTT 59.771 37.037 0.00 0.00 0.00 2.71
526 3069 9.236691 TCGTCGGTAAGTATATGTATGTTTTTC 57.763 33.333 0.00 0.00 0.00 2.29
608 3163 7.663493 ACATAGTCTTTCTGAAGAGAAAAAGGG 59.337 37.037 0.00 0.00 45.57 3.95
909 3477 2.436469 CCAGTGCCACGCATAGCA 60.436 61.111 0.00 0.00 41.91 3.49
979 3547 5.435291 GTTGATCACTTGGATTGGATCTCT 58.565 41.667 0.00 0.00 37.60 3.10
985 3553 3.131933 ACTTGGATTGGATCTCTCACGAG 59.868 47.826 0.00 0.00 38.67 4.18
986 3554 2.739943 TGGATTGGATCTCTCACGAGT 58.260 47.619 0.00 0.00 38.45 4.18
992 3560 0.248296 GATCTCTCACGAGTCACGCC 60.248 60.000 0.00 0.00 46.94 5.68
998 3566 3.911698 ACGAGTCACGCCTGCACA 61.912 61.111 0.00 0.00 46.94 4.57
1180 3748 4.021925 GCAGACCGGCCCTGTCTT 62.022 66.667 17.69 3.73 41.02 3.01
1235 3811 3.575965 ACCCATTCGTTTCTTTGCATC 57.424 42.857 0.00 0.00 0.00 3.91
1306 3882 0.854062 CGGCACAAAACTTGCATGTG 59.146 50.000 12.08 12.08 45.54 3.21
1398 3979 1.304547 CCTCCGAGGAGTGGACAGT 60.305 63.158 17.04 0.00 37.67 3.55
1619 4206 3.695022 GACGCGGCTACGGTGATGT 62.695 63.158 12.47 0.00 41.36 3.06
1731 4318 0.666274 TCATGTGACGGCTTGACGAC 60.666 55.000 1.78 0.00 37.61 4.34
1759 6916 9.784531 ATATTCGTGGAACTATCATGAATCTTT 57.215 29.630 12.85 0.00 43.39 2.52
1794 6951 7.344093 TGAGATTGTAGTGAATCTGATCTCCTT 59.656 37.037 0.00 0.00 41.78 3.36
1799 6956 1.139654 TGAATCTGATCTCCTTGCCGG 59.860 52.381 0.00 0.00 0.00 6.13
1821 6978 5.625150 GGATGCAAATGTATTACTCCCTCT 58.375 41.667 0.00 0.00 0.00 3.69
1822 6979 5.471456 GGATGCAAATGTATTACTCCCTCTG 59.529 44.000 0.00 0.00 0.00 3.35
1852 7010 8.141909 TGTACTAAGCAGCTACAAGTAATATGG 58.858 37.037 11.79 0.00 0.00 2.74
1855 7013 8.432805 ACTAAGCAGCTACAAGTAATATGGATT 58.567 33.333 0.00 0.00 0.00 3.01
1857 7015 6.000219 AGCAGCTACAAGTAATATGGATTGG 59.000 40.000 0.00 0.00 0.00 3.16
1865 7023 7.006509 ACAAGTAATATGGATTGGAGGGATTG 58.993 38.462 0.00 0.00 0.00 2.67
1869 7027 3.763557 ATGGATTGGAGGGATTGTGTT 57.236 42.857 0.00 0.00 0.00 3.32
1870 7028 4.879295 ATGGATTGGAGGGATTGTGTTA 57.121 40.909 0.00 0.00 0.00 2.41
1945 7103 3.712091 AGTATAGTACAGTTGCTCCGC 57.288 47.619 0.00 0.00 0.00 5.54
1958 7116 4.973055 TCCGCGGGTGTTGGAACG 62.973 66.667 27.83 0.00 0.00 3.95
2151 7318 2.345244 CTGCTTCTGACGCCCTGT 59.655 61.111 3.54 0.00 0.00 4.00
2371 7565 4.805768 CGCCCCATTAACCCCGCA 62.806 66.667 0.00 0.00 0.00 5.69
2378 7574 1.684869 CCATTAACCCCGCATGGAAGT 60.685 52.381 0.00 0.00 40.10 3.01
2411 7607 2.586635 TGCCACACGTCCGTTCAC 60.587 61.111 0.00 0.00 0.00 3.18
2461 7658 1.755008 GAGCTCCTACTGTCCGCCT 60.755 63.158 0.87 0.00 0.00 5.52
2548 7745 0.325933 CCACCACTCTTCTGATGGCA 59.674 55.000 0.00 0.00 36.96 4.92
2577 7774 1.405526 GCAGTTCTCCGGCATACAAGA 60.406 52.381 0.00 0.00 0.00 3.02
2650 7849 3.636231 CCTTCCGTGCCTCACCCA 61.636 66.667 0.00 0.00 0.00 4.51
2664 7863 0.738389 CACCCAACGAAGCAAGTTGT 59.262 50.000 14.70 0.00 45.31 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 0.665835 CATCGTCTTCCTCTCCTCGG 59.334 60.000 0.00 0.00 0.00 4.63
104 105 4.644685 CACCTTCACCTTCTTTTCTTCCAA 59.355 41.667 0.00 0.00 0.00 3.53
125 126 3.423154 CCGCCGCCTTCAACTCAC 61.423 66.667 0.00 0.00 0.00 3.51
177 248 0.096802 TTGTCGTTGCTGCATATGCG 59.903 50.000 22.21 17.15 45.83 4.73
183 254 0.737804 AATGTGTTGTCGTTGCTGCA 59.262 45.000 0.00 0.00 0.00 4.41
186 257 0.667993 CCCAATGTGTTGTCGTTGCT 59.332 50.000 0.00 0.00 34.23 3.91
200 271 1.444933 TCTGAACCTCCACACCCAAT 58.555 50.000 0.00 0.00 0.00 3.16
206 277 6.041409 TGCAAAAATAATTCTGAACCTCCACA 59.959 34.615 0.00 0.00 0.00 4.17
256 328 9.539825 TGTTTAAGTTTTTACATGCATGTTCAT 57.460 25.926 35.45 14.88 41.97 2.57
292 365 5.069648 TCACATGCCTTATCACAACCAAAAA 59.930 36.000 0.00 0.00 0.00 1.94
298 372 3.002656 CGGATCACATGCCTTATCACAAC 59.997 47.826 0.00 0.00 0.00 3.32
306 380 1.815421 GCGTCGGATCACATGCCTT 60.815 57.895 0.00 0.00 0.00 4.35
319 393 1.139989 ATTTGATCCATAGCGCGTCG 58.860 50.000 8.43 0.00 0.00 5.12
376 456 6.170506 GGTAGGCGGTCATTCAATGATATTA 58.829 40.000 2.67 0.00 42.04 0.98
427 513 7.255836 CCGTAAATCTCCTTATGTGTCTATCCA 60.256 40.741 0.00 0.00 0.00 3.41
439 525 1.766496 CCCTGCCCGTAAATCTCCTTA 59.234 52.381 0.00 0.00 0.00 2.69
445 531 1.807226 GCAACCCTGCCCGTAAATC 59.193 57.895 0.00 0.00 43.26 2.17
522 3065 5.642063 ACTCGAGATTAGCCGAAATTGAAAA 59.358 36.000 21.68 0.00 34.17 2.29
526 3069 6.771188 ATAACTCGAGATTAGCCGAAATTG 57.229 37.500 21.68 0.00 34.17 2.32
909 3477 1.874872 GATCGACCGAGTAGCTAGCTT 59.125 52.381 24.88 5.38 0.00 3.74
923 3491 1.719600 ACAAGCTCTTGCAGATCGAC 58.280 50.000 9.36 0.00 44.03 4.20
979 3547 3.601685 TGCAGGCGTGACTCGTGA 61.602 61.111 11.29 0.00 42.13 4.35
985 3553 2.557805 CATGTGTGCAGGCGTGAC 59.442 61.111 11.29 6.34 0.00 3.67
986 3554 2.669229 CCATGTGTGCAGGCGTGA 60.669 61.111 11.29 0.00 0.00 4.35
992 3560 3.434319 GGTCCGCCATGTGTGCAG 61.434 66.667 0.00 0.00 34.09 4.41
998 3566 2.607750 AGACCAGGTCCGCCATGT 60.608 61.111 16.72 0.00 37.19 3.21
1109 3677 4.796231 GGTGACGATGCGCGGAGT 62.796 66.667 8.83 0.00 46.49 3.85
1180 3748 3.552384 ACGCGGGTGAACCTGGAA 61.552 61.111 12.47 0.00 42.72 3.53
1277 3853 1.677052 GTTTTGTGCCGGTCAGGTAAA 59.323 47.619 1.90 1.66 43.70 2.01
1278 3854 1.134037 AGTTTTGTGCCGGTCAGGTAA 60.134 47.619 1.90 0.00 43.70 2.85
1306 3882 2.433318 GAGCTCCACCGTCTGCAC 60.433 66.667 0.87 0.00 0.00 4.57
1425 4006 2.677524 TACCCCGTCACCCTCACG 60.678 66.667 0.00 0.00 36.99 4.35
1619 4206 2.047655 GGCCGTGACGATCACCAA 60.048 61.111 6.54 0.00 44.20 3.67
1731 4318 7.757173 AGATTCATGATAGTTCCACGAATATCG 59.243 37.037 0.00 0.00 46.93 2.92
1759 6916 8.251026 AGATTCACTACAATCTCATCGTACAAA 58.749 33.333 0.00 0.00 38.53 2.83
1799 6956 6.291377 TCAGAGGGAGTAATACATTTGCATC 58.709 40.000 0.00 0.00 0.00 3.91
1821 6978 6.464222 ACTTGTAGCTGCTTAGTACAAATCA 58.536 36.000 7.79 0.00 36.48 2.57
1822 6979 6.969828 ACTTGTAGCTGCTTAGTACAAATC 57.030 37.500 7.79 0.00 36.48 2.17
1945 7103 1.503818 CCTTCACGTTCCAACACCCG 61.504 60.000 0.00 0.00 0.00 5.28
1958 7116 1.614413 CCGCCTAGAGATACCCTTCAC 59.386 57.143 0.00 0.00 0.00 3.18
2151 7318 1.432023 GGAGGGGTTCTTTGGTGGGA 61.432 60.000 0.00 0.00 0.00 4.37
2371 7565 3.447944 GGAGTAGGTTTCTCGACTTCCAT 59.552 47.826 0.00 0.00 33.26 3.41
2378 7574 1.183549 GGCAGGAGTAGGTTTCTCGA 58.816 55.000 0.00 0.00 33.26 4.04
2411 7607 1.812093 TTTAATGTCGGCCCGCTCG 60.812 57.895 0.00 0.00 0.00 5.03
2461 7658 4.866486 GCGTCTTCCCTCGTTTAAATAGAA 59.134 41.667 0.00 0.00 0.00 2.10
2614 7813 0.536006 GTGGAGCACTGAGTTGCCTT 60.536 55.000 3.93 0.00 44.14 4.35
2650 7849 1.647084 GGCGACAACTTGCTTCGTT 59.353 52.632 4.33 0.00 35.17 3.85


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

AutoCloner maintained by Alex Coulton.