Multiple sequence alignment - TraesCS2D01G381500

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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 TraesCS2D01G381500 chr2D 100.000 2402 0 0 1 2402 485748637 485751038 0.000000e+00 4436
1 TraesCS2D01G381500 chr2B 92.632 2416 101 37 15 2402 570655218 570657584 0.000000e+00 3404
2 TraesCS2D01G381500 chr2A 89.451 1403 44 26 669 2034 631202663 631203998 0.000000e+00 1676
3 TraesCS2D01G381500 chr2A 92.480 492 22 2 152 641 631201955 631202433 0.000000e+00 689
4 TraesCS2D01G381500 chr2A 96.207 290 11 0 2113 2402 631204018 631204307 2.160000e-130 475


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 TraesCS2D01G381500 chr2D 485748637 485751038 2401 False 4436.000000 4436 100.000000 1 2402 1 chr2D.!!$F1 2401
1 TraesCS2D01G381500 chr2B 570655218 570657584 2366 False 3404.000000 3404 92.632000 15 2402 1 chr2B.!!$F1 2387
2 TraesCS2D01G381500 chr2A 631201955 631204307 2352 False 946.666667 1676 92.712667 152 2402 3 chr2A.!!$F1 2250

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
182 183 0.175073 GTGAGGACACACCGGATACC 59.825 60.0 9.46 4.02 45.32 2.73 F
815 1027 0.541863 CGAAGTTACCATCCTGCCCT 59.458 55.0 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1334 0.246635 TGGACAGCTCGGCTTTAGTC 59.753 55.0 0.0 1.95 36.40 2.59 R
2015 2275 0.606604 ATCGGCACCACGTTCTACTT 59.393 50.0 0.0 0.00 34.94 2.24 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
29 30 2.334838 CACGGGTTTTAGGTCTTCGAG 58.665 52.381 0.00 0.00 0.00 4.04
34 35 3.744942 GGGTTTTAGGTCTTCGAGTTGAC 59.255 47.826 6.71 6.71 0.00 3.18
37 38 6.218746 GGTTTTAGGTCTTCGAGTTGACTAA 58.781 40.000 12.63 5.37 34.01 2.24
125 126 7.540474 AAACTGACTATCTAAGTTCCTGTGA 57.460 36.000 0.00 0.00 39.07 3.58
182 183 0.175073 GTGAGGACACACCGGATACC 59.825 60.000 9.46 4.02 45.32 2.73
191 192 2.028476 CACACCGGATACCTGAGAAACA 60.028 50.000 9.46 0.00 0.00 2.83
202 203 9.841880 GGATACCTGAGAAACAAAAATAAGTTC 57.158 33.333 0.00 0.00 0.00 3.01
247 248 2.027192 TGGAAGCAACATAGGAGTGTCC 60.027 50.000 0.00 0.00 36.58 4.02
327 330 2.738213 AAACACCAGGCGCCAGAGAG 62.738 60.000 31.54 17.09 0.00 3.20
355 358 1.585297 AACGTACACCCCAAAACTCG 58.415 50.000 0.00 0.00 0.00 4.18
357 360 1.864176 GTACACCCCAAAACTCGCG 59.136 57.895 0.00 0.00 0.00 5.87
360 363 4.612412 ACCCCAAAACTCGCGCGA 62.612 61.111 32.60 32.60 0.00 5.87
448 452 1.233080 GAATTCCCCATCCACCCCC 59.767 63.158 0.00 0.00 0.00 5.40
646 650 5.241662 GCTCCAGTATAAATAGGAGGCAAG 58.758 45.833 9.16 0.00 46.08 4.01
699 908 2.679349 GCCAGAATTTTCTCTCGCCTCT 60.679 50.000 0.00 0.00 34.74 3.69
700 909 3.194062 CCAGAATTTTCTCTCGCCTCTC 58.806 50.000 0.00 0.00 34.74 3.20
702 911 2.834549 AGAATTTTCTCTCGCCTCTCCA 59.165 45.455 0.00 0.00 29.94 3.86
703 912 3.454082 AGAATTTTCTCTCGCCTCTCCAT 59.546 43.478 0.00 0.00 29.94 3.41
706 915 0.757188 TTCTCTCGCCTCTCCATCCC 60.757 60.000 0.00 0.00 0.00 3.85
707 916 1.152567 CTCTCGCCTCTCCATCCCT 60.153 63.158 0.00 0.00 0.00 4.20
709 918 2.123251 TCGCCTCTCCATCCCTCC 60.123 66.667 0.00 0.00 0.00 4.30
710 919 2.444706 CGCCTCTCCATCCCTCCA 60.445 66.667 0.00 0.00 0.00 3.86
712 921 1.383803 GCCTCTCCATCCCTCCACT 60.384 63.158 0.00 0.00 0.00 4.00
714 923 1.053264 CCTCTCCATCCCTCCACTGG 61.053 65.000 0.00 0.00 0.00 4.00
717 929 2.693864 CCATCCCTCCACTGGCCT 60.694 66.667 3.32 0.00 0.00 5.19
739 951 2.393646 CCCTCTCTCCTCCGATCTTTT 58.606 52.381 0.00 0.00 0.00 2.27
743 955 4.202111 CCTCTCTCCTCCGATCTTTTTCTC 60.202 50.000 0.00 0.00 0.00 2.87
744 956 4.605183 TCTCTCCTCCGATCTTTTTCTCT 58.395 43.478 0.00 0.00 0.00 3.10
749 961 3.440228 CTCCGATCTTTTTCTCTCGTCC 58.560 50.000 0.00 0.00 0.00 4.79
752 964 2.541556 GATCTTTTTCTCTCGTCCCGG 58.458 52.381 0.00 0.00 0.00 5.73
786 998 2.776913 CCTCCTCTCGTTCGGCCTC 61.777 68.421 0.00 0.00 0.00 4.70
787 999 1.751162 CTCCTCTCGTTCGGCCTCT 60.751 63.158 0.00 0.00 0.00 3.69
806 1018 1.003839 CTGCCCTGCGAAGTTACCA 60.004 57.895 0.00 0.00 0.00 3.25
815 1027 0.541863 CGAAGTTACCATCCTGCCCT 59.458 55.000 0.00 0.00 0.00 5.19
816 1028 1.065418 CGAAGTTACCATCCTGCCCTT 60.065 52.381 0.00 0.00 0.00 3.95
881 1093 7.003402 TCCTCCTCCCAATTGTTTTTATTTG 57.997 36.000 4.43 0.00 0.00 2.32
924 1139 6.946340 TCCACATACATACATATCCCATCAC 58.054 40.000 0.00 0.00 0.00 3.06
925 1140 6.070251 TCCACATACATACATATCCCATCACC 60.070 42.308 0.00 0.00 0.00 4.02
926 1141 6.296374 CCACATACATACATATCCCATCACCA 60.296 42.308 0.00 0.00 0.00 4.17
1448 1676 0.537371 CCCAGAAGAACCACCACCAC 60.537 60.000 0.00 0.00 0.00 4.16
1449 1677 0.537371 CCAGAAGAACCACCACCACC 60.537 60.000 0.00 0.00 0.00 4.61
1450 1678 0.182537 CAGAAGAACCACCACCACCA 59.817 55.000 0.00 0.00 0.00 4.17
1468 1702 2.770475 GGAGGAGGAGGAAGGGCC 60.770 72.222 0.00 0.00 0.00 5.80
1539 1773 1.988846 CCCTCCCCTTGTCTTCTTTCT 59.011 52.381 0.00 0.00 0.00 2.52
1793 2048 1.327690 TGGTGGAGATGGCTCGGTAC 61.328 60.000 0.00 0.00 42.25 3.34
1794 2049 1.043673 GGTGGAGATGGCTCGGTACT 61.044 60.000 0.00 0.00 42.25 2.73
1795 2050 0.386113 GTGGAGATGGCTCGGTACTC 59.614 60.000 0.00 0.00 42.25 2.59
1796 2051 1.101635 TGGAGATGGCTCGGTACTCG 61.102 60.000 0.00 0.00 42.25 4.18
1797 2052 1.655329 GAGATGGCTCGGTACTCGG 59.345 63.158 0.00 0.00 39.77 4.63
1798 2053 1.076923 AGATGGCTCGGTACTCGGT 60.077 57.895 0.00 0.00 39.77 4.69
1799 2054 0.182061 AGATGGCTCGGTACTCGGTA 59.818 55.000 0.00 0.00 39.77 4.02
2005 2265 8.496707 TCATCTGTGTATGTTTCGTAGTAGTA 57.503 34.615 0.00 0.00 0.00 1.82
2042 2315 3.462483 ACGTGGTGCCGATTGATTATA 57.538 42.857 0.00 0.00 0.00 0.98
2052 2325 4.322349 GCCGATTGATTATACAGAGAGGCT 60.322 45.833 0.00 0.00 36.97 4.58
2074 2347 5.451242 GCTTTGGTTGTGACCTTTACATGAA 60.451 40.000 0.00 0.00 46.66 2.57
2096 2369 5.728637 AGATGATGCGTATATCCTTGTGA 57.271 39.130 0.00 0.00 0.00 3.58
2103 2376 6.603237 TGCGTATATCCTTGTGATTTTGAG 57.397 37.500 0.00 0.00 34.76 3.02
2140 2413 5.317808 TGTTTATTGGATCAAGGGACGAAA 58.682 37.500 0.00 0.00 0.00 3.46
2142 2415 1.821216 TTGGATCAAGGGACGAAAGC 58.179 50.000 0.00 0.00 0.00 3.51
2237 2510 2.229792 TGATGAGTTGGTCCTTGTTGC 58.770 47.619 0.00 0.00 0.00 4.17
2254 2527 4.201657 TGTTGCTTCCATTGATCGATGAT 58.798 39.130 22.50 0.00 0.00 2.45
2348 2621 0.659957 GCTGCTGATTTGGTCGATCC 59.340 55.000 0.00 0.00 0.00 3.36
2351 2624 0.659957 GCTGATTTGGTCGATCCTGC 59.340 55.000 0.00 0.00 37.07 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.181452 ACCTAAAACCCGTGCTTGACTTA 60.181 43.478 0.00 0.00 0.00 2.24
1 2 2.227194 CCTAAAACCCGTGCTTGACTT 58.773 47.619 0.00 0.00 0.00 3.01
2 3 1.142262 ACCTAAAACCCGTGCTTGACT 59.858 47.619 0.00 0.00 0.00 3.41
3 4 1.534163 GACCTAAAACCCGTGCTTGAC 59.466 52.381 0.00 0.00 0.00 3.18
4 5 1.418637 AGACCTAAAACCCGTGCTTGA 59.581 47.619 0.00 0.00 0.00 3.02
5 6 1.892209 AGACCTAAAACCCGTGCTTG 58.108 50.000 0.00 0.00 0.00 4.01
6 7 2.501261 GAAGACCTAAAACCCGTGCTT 58.499 47.619 0.00 0.00 0.00 3.91
7 8 1.607251 CGAAGACCTAAAACCCGTGCT 60.607 52.381 0.00 0.00 0.00 4.40
8 9 0.794473 CGAAGACCTAAAACCCGTGC 59.206 55.000 0.00 0.00 0.00 5.34
9 10 2.288640 ACTCGAAGACCTAAAACCCGTG 60.289 50.000 0.00 0.00 0.00 4.94
10 11 1.966354 ACTCGAAGACCTAAAACCCGT 59.034 47.619 0.00 0.00 0.00 5.28
11 12 2.735134 CAACTCGAAGACCTAAAACCCG 59.265 50.000 0.00 0.00 0.00 5.28
12 13 3.744942 GTCAACTCGAAGACCTAAAACCC 59.255 47.826 1.93 0.00 0.00 4.11
13 14 4.629092 AGTCAACTCGAAGACCTAAAACC 58.371 43.478 8.26 0.00 35.38 3.27
20 21 5.978934 TTTTGTTAGTCAACTCGAAGACC 57.021 39.130 8.26 0.00 35.61 3.85
97 98 9.091220 ACAGGAACTTAGATAGTCAGTTTAACT 57.909 33.333 0.00 0.00 34.60 2.24
125 126 6.261435 TCTCCGGATGGGAATATAAGTATGT 58.739 40.000 3.57 0.00 46.61 2.29
202 203 7.645340 CCATTTTCCTTTGCTGATAAATCTACG 59.355 37.037 0.00 0.00 0.00 3.51
496 500 2.310538 GGAAGGGCAGATGGGTAATTG 58.689 52.381 0.00 0.00 0.00 2.32
620 624 3.258372 CCTCCTATTTATACTGGAGCGCA 59.742 47.826 11.47 0.00 43.34 6.09
699 908 2.692368 GGCCAGTGGAGGGATGGA 60.692 66.667 15.20 0.00 36.09 3.41
700 909 2.693864 AGGCCAGTGGAGGGATGG 60.694 66.667 15.20 0.00 37.15 3.51
702 911 2.367512 GGAGGCCAGTGGAGGGAT 60.368 66.667 15.20 0.00 0.00 3.85
703 912 4.741239 GGGAGGCCAGTGGAGGGA 62.741 72.222 15.20 0.00 0.00 4.20
706 915 3.086600 GAGGGGAGGCCAGTGGAG 61.087 72.222 15.20 0.00 0.00 3.86
707 916 3.615811 AGAGGGGAGGCCAGTGGA 61.616 66.667 15.20 0.00 0.00 4.02
709 918 2.040278 AGAGAGGGGAGGCCAGTG 59.960 66.667 5.01 0.00 0.00 3.66
710 919 2.366570 GAGAGAGGGGAGGCCAGT 59.633 66.667 5.01 0.00 0.00 4.00
712 921 2.955246 AGGAGAGAGGGGAGGCCA 60.955 66.667 5.01 0.00 0.00 5.36
714 923 2.123033 GGAGGAGAGAGGGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
717 929 0.699577 AGATCGGAGGAGAGAGGGGA 60.700 60.000 0.00 0.00 0.00 4.81
721 933 4.644685 AGAGAAAAAGATCGGAGGAGAGAG 59.355 45.833 0.00 0.00 0.00 3.20
752 964 4.735358 GGGGAGGGAACAACGGGC 62.735 72.222 0.00 0.00 0.00 6.13
786 998 0.741221 GGTAACTTCGCAGGGCAGAG 60.741 60.000 0.00 0.00 0.00 3.35
787 999 1.295423 GGTAACTTCGCAGGGCAGA 59.705 57.895 0.00 0.00 0.00 4.26
796 1008 0.541863 AGGGCAGGATGGTAACTTCG 59.458 55.000 0.00 0.00 41.51 3.79
857 1069 6.556874 ACAAATAAAAACAATTGGGAGGAGGA 59.443 34.615 10.83 0.00 0.00 3.71
881 1093 3.636764 TGGAGGAGGCAAAGAAAAGAAAC 59.363 43.478 0.00 0.00 0.00 2.78
924 1139 1.443802 GAGAGGAAAGCGGTTTCTGG 58.556 55.000 32.01 0.00 41.72 3.86
925 1140 1.270839 TGGAGAGGAAAGCGGTTTCTG 60.271 52.381 32.01 0.00 41.72 3.02
926 1141 1.056660 TGGAGAGGAAAGCGGTTTCT 58.943 50.000 32.01 21.11 41.72 2.52
1110 1325 3.118454 GCTTTAGTCGCAGCGGCA 61.118 61.111 23.70 4.66 41.24 5.69
1114 1329 2.803713 GCTCGGCTTTAGTCGCAGC 61.804 63.158 10.64 10.64 43.77 5.25
1115 1330 1.153745 AGCTCGGCTTTAGTCGCAG 60.154 57.895 0.00 0.00 43.77 5.18
1116 1331 1.446099 CAGCTCGGCTTTAGTCGCA 60.446 57.895 0.00 0.00 43.77 5.10
1119 1334 0.246635 TGGACAGCTCGGCTTTAGTC 59.753 55.000 0.00 1.95 36.40 2.59
1120 1335 0.685097 TTGGACAGCTCGGCTTTAGT 59.315 50.000 0.00 0.00 36.40 2.24
1448 1676 1.383803 CCCTTCCTCCTCCTCCTGG 60.384 68.421 0.00 0.00 0.00 4.45
1449 1677 2.069430 GCCCTTCCTCCTCCTCCTG 61.069 68.421 0.00 0.00 0.00 3.86
1450 1678 2.370633 GCCCTTCCTCCTCCTCCT 59.629 66.667 0.00 0.00 0.00 3.69
1468 1702 1.959747 CTTTGTCTTGATGTGCTGCG 58.040 50.000 0.00 0.00 0.00 5.18
1539 1773 6.090898 GCAACAAGTTTTCTCGCTAGATCTAA 59.909 38.462 3.57 0.00 0.00 2.10
2005 2265 6.404074 GCACCACGTTCTACTTACTGTATACT 60.404 42.308 4.17 0.00 0.00 2.12
2012 2272 1.068055 CGGCACCACGTTCTACTTACT 60.068 52.381 0.00 0.00 0.00 2.24
2013 2273 1.068333 TCGGCACCACGTTCTACTTAC 60.068 52.381 0.00 0.00 34.94 2.34
2014 2274 1.246649 TCGGCACCACGTTCTACTTA 58.753 50.000 0.00 0.00 34.94 2.24
2015 2275 0.606604 ATCGGCACCACGTTCTACTT 59.393 50.000 0.00 0.00 34.94 2.24
2021 2288 2.102070 TAATCAATCGGCACCACGTT 57.898 45.000 0.00 0.00 34.94 3.99
2042 2315 1.490490 TCACAACCAAAGCCTCTCTGT 59.510 47.619 0.00 0.00 0.00 3.41
2074 2347 5.728637 TCACAAGGATATACGCATCATCT 57.271 39.130 0.00 0.00 0.00 2.90
2096 2369 8.922931 AAACAAAATCTAAATGGCCTCAAAAT 57.077 26.923 3.32 0.00 0.00 1.82
2103 2376 8.962884 ATCCAATAAACAAAATCTAAATGGCC 57.037 30.769 0.00 0.00 0.00 5.36
2140 2413 2.118513 AGACCAGACCAGACCGCT 59.881 61.111 0.00 0.00 0.00 5.52
2142 2415 1.878656 GACCAGACCAGACCAGACCG 61.879 65.000 0.00 0.00 0.00 4.79
2169 2442 1.798813 GCTTTCGTCTGGAAACACGAT 59.201 47.619 0.00 0.00 39.67 3.73
2237 2510 8.783833 AAATACCTATCATCGATCAATGGAAG 57.216 34.615 0.00 0.00 0.00 3.46
2254 2527 2.014128 GCGCAAGAGCCAAAATACCTA 58.986 47.619 0.30 0.00 43.02 3.08
2348 2621 1.303309 GGACGATGGATGGAAAGCAG 58.697 55.000 0.00 0.00 0.00 4.24
2351 2624 1.668419 GGTGGACGATGGATGGAAAG 58.332 55.000 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.