Multiple sequence alignment - TraesCS2D01G587500

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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 TraesCS2D01G587500 chr2D 100.000 2595 0 0 1 2595 645358949 645356355 0.000000e+00 4793
1 TraesCS2D01G587500 chr2D 86.747 166 20 1 1995 2158 525975148 525975313 1.590000e-42 183
2 TraesCS2D01G587500 chr2D 75.515 388 68 18 1282 1662 525972895 525973262 5.750000e-37 165
3 TraesCS2D01G587500 chr4A 92.527 1927 91 13 693 2592 642135925 642137825 0.000000e+00 2712
4 TraesCS2D01G587500 chr4A 74.780 567 89 34 1257 1790 196693498 196694043 3.380000e-49 206
5 TraesCS2D01G587500 chr4A 88.312 154 16 2 1845 1997 307221248 307221400 1.590000e-42 183
6 TraesCS2D01G587500 chr4A 88.312 154 17 1 1845 1997 355504869 355505022 1.590000e-42 183
7 TraesCS2D01G587500 chr3B 94.751 1486 63 9 1119 2595 87948221 87946742 0.000000e+00 2298
8 TraesCS2D01G587500 chr3B 97.414 580 11 1 1 576 766107322 766107901 0.000000e+00 985
9 TraesCS2D01G587500 chr3A 98.264 576 10 0 1 576 853590 854165 0.000000e+00 1009
10 TraesCS2D01G587500 chr3A 83.902 410 36 13 576 961 606012511 606012914 5.280000e-97 364
11 TraesCS2D01G587500 chr3A 90.756 238 18 3 2356 2590 606015500 606015736 5.390000e-82 315
12 TraesCS2D01G587500 chr3A 85.932 263 35 2 577 837 737013758 737014020 1.970000e-71 279
13 TraesCS2D01G587500 chr3A 88.312 154 17 1 1845 1997 737015410 737015563 1.590000e-42 183
14 TraesCS2D01G587500 chr3A 86.145 166 21 1 1995 2158 61925110 61924945 7.380000e-41 178
15 TraesCS2D01G587500 chr3A 74.662 517 71 33 1311 1791 737014409 737014901 9.550000e-40 174
16 TraesCS2D01G587500 chr3A 83.969 131 20 1 2197 2327 606013715 606013844 9.750000e-25 124
17 TraesCS2D01G587500 chr7A 98.090 576 11 0 1 576 724193650 724194225 0.000000e+00 1003
18 TraesCS2D01G587500 chr7A 88.554 166 17 1 1995 2158 248416761 248416926 1.570000e-47 200
19 TraesCS2D01G587500 chr7A 89.610 154 15 1 1845 1997 248416575 248416728 7.330000e-46 195
20 TraesCS2D01G587500 chr7A 79.000 300 31 19 1520 1791 248415772 248416067 2.650000e-40 176
21 TraesCS2D01G587500 chr6B 97.747 577 12 1 1 576 716407025 716407601 0.000000e+00 992
22 TraesCS2D01G587500 chr6B 97.400 577 14 1 1 576 689037289 689037865 0.000000e+00 981
23 TraesCS2D01G587500 chr5A 97.578 578 10 3 1 576 17670604 17670029 0.000000e+00 987
24 TraesCS2D01G587500 chr5A 97.400 577 14 1 1 576 1881215 1880639 0.000000e+00 981
25 TraesCS2D01G587500 chr5A 82.968 411 40 13 575 961 93196727 93197131 6.880000e-91 344
26 TraesCS2D01G587500 chr5A 89.179 268 25 4 576 840 268558905 268559171 5.350000e-87 331
27 TraesCS2D01G587500 chr5A 90.756 238 18 3 2356 2590 93199716 93199952 5.390000e-82 315
28 TraesCS2D01G587500 chr5A 88.312 154 16 2 1845 1997 435635855 435636007 1.590000e-42 183
29 TraesCS2D01G587500 chr5A 86.585 164 20 1 1995 2156 435636039 435636202 2.050000e-41 180
30 TraesCS2D01G587500 chr5A 83.969 131 20 1 2197 2327 93197932 93198061 9.750000e-25 124
31 TraesCS2D01G587500 chr2B 97.405 578 13 1 1 576 778424216 778424793 0.000000e+00 983
32 TraesCS2D01G587500 chr2B 85.338 266 34 4 577 840 732210912 732211174 1.180000e-68 270
33 TraesCS2D01G587500 chr2B 87.952 166 17 2 1995 2158 732212290 732212454 2.640000e-45 193
34 TraesCS2D01G587500 chr2B 77.815 302 33 20 1521 1791 732211761 732212059 3.460000e-34 156
35 TraesCS2D01G587500 chr1D 97.561 574 10 2 1 574 107479837 107479268 0.000000e+00 979
36 TraesCS2D01G587500 chr5D 86.486 259 30 5 576 831 124722644 124722900 1.970000e-71 279
37 TraesCS2D01G587500 chr5D 86.047 258 33 3 576 831 133540783 133541039 9.150000e-70 274
38 TraesCS2D01G587500 chr5D 85.328 259 36 2 575 831 542170402 542170660 1.530000e-67 267
39 TraesCS2D01G587500 chr5D 79.167 336 50 14 1361 1689 542184111 542184433 5.620000e-52 215
40 TraesCS2D01G587500 chr3D 85.448 268 33 6 577 840 38455489 38455224 9.150000e-70 274
41 TraesCS2D01G587500 chr3D 87.952 166 18 1 1995 2158 38453630 38453465 7.330000e-46 195
42 TraesCS2D01G587500 chr3D 89.172 157 16 1 1845 2000 38453815 38453659 7.330000e-46 195
43 TraesCS2D01G587500 chr2A 88.554 166 17 1 1995 2158 464445917 464445752 1.570000e-47 200
44 TraesCS2D01G587500 chr1A 88.889 162 12 4 1845 2000 509943206 509943045 7.330000e-46 195
45 TraesCS2D01G587500 chr1A 74.755 511 79 25 1311 1791 509944220 509943730 1.590000e-42 183


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 TraesCS2D01G587500 chr2D 645356355 645358949 2594 True 4793.000000 4793 100.000000 1 2595 1 chr2D.!!$R1 2594
1 TraesCS2D01G587500 chr4A 642135925 642137825 1900 False 2712.000000 2712 92.527000 693 2592 1 chr4A.!!$F4 1899
2 TraesCS2D01G587500 chr4A 196693498 196694043 545 False 206.000000 206 74.780000 1257 1790 1 chr4A.!!$F1 533
3 TraesCS2D01G587500 chr3B 87946742 87948221 1479 True 2298.000000 2298 94.751000 1119 2595 1 chr3B.!!$R1 1476
4 TraesCS2D01G587500 chr3B 766107322 766107901 579 False 985.000000 985 97.414000 1 576 1 chr3B.!!$F1 575
5 TraesCS2D01G587500 chr3A 853590 854165 575 False 1009.000000 1009 98.264000 1 576 1 chr3A.!!$F1 575
6 TraesCS2D01G587500 chr3A 606012511 606015736 3225 False 267.666667 364 86.209000 576 2590 3 chr3A.!!$F2 2014
7 TraesCS2D01G587500 chr3A 737013758 737015563 1805 False 212.000000 279 82.968667 577 1997 3 chr3A.!!$F3 1420
8 TraesCS2D01G587500 chr7A 724193650 724194225 575 False 1003.000000 1003 98.090000 1 576 1 chr7A.!!$F1 575
9 TraesCS2D01G587500 chr6B 716407025 716407601 576 False 992.000000 992 97.747000 1 576 1 chr6B.!!$F2 575
10 TraesCS2D01G587500 chr6B 689037289 689037865 576 False 981.000000 981 97.400000 1 576 1 chr6B.!!$F1 575
11 TraesCS2D01G587500 chr5A 17670029 17670604 575 True 987.000000 987 97.578000 1 576 1 chr5A.!!$R2 575
12 TraesCS2D01G587500 chr5A 1880639 1881215 576 True 981.000000 981 97.400000 1 576 1 chr5A.!!$R1 575
13 TraesCS2D01G587500 chr5A 93196727 93199952 3225 False 261.000000 344 85.897667 575 2590 3 chr5A.!!$F2 2015
14 TraesCS2D01G587500 chr2B 778424216 778424793 577 False 983.000000 983 97.405000 1 576 1 chr2B.!!$F1 575
15 TraesCS2D01G587500 chr2B 732210912 732212454 1542 False 206.333333 270 83.701667 577 2158 3 chr2B.!!$F2 1581
16 TraesCS2D01G587500 chr1D 107479268 107479837 569 True 979.000000 979 97.561000 1 574 1 chr1D.!!$R1 573
17 TraesCS2D01G587500 chr3D 38453465 38455489 2024 True 221.333333 274 87.524000 577 2158 3 chr3D.!!$R1 1581

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
449 450 0.318699 CAAGAGCGTCGAAGGTCACA 60.319 55.0 27.73 0.0 40.77 3.58 F
1278 1465 0.248825 CGCTCCTCCTCTTCACGATG 60.249 60.0 0.00 0.0 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1689 1.084018 TCAAGGAGGGAGGGCAAATT 58.916 50.000 0.0 0.0 0.0 1.82 R
2479 4876 2.639839 ACTGCACTGTATGTTCCTTCCT 59.360 45.455 0.0 0.0 0.0 3.36 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
449 450 0.318699 CAAGAGCGTCGAAGGTCACA 60.319 55.000 27.73 0.00 40.77 3.58
521 522 9.825972 ACGATCTGTGTAAGATAAAAACAAATG 57.174 29.630 0.00 0.00 46.12 2.32
635 640 5.071788 TGCCGGGAGAAATATGAGAATAAGT 59.928 40.000 2.18 0.00 0.00 2.24
727 732 2.058125 TAAGCAACAAGGGCGGGTGA 62.058 55.000 0.00 0.00 36.08 4.02
811 817 2.364973 TGTCTGCCGGCCTATCCA 60.365 61.111 26.77 10.69 34.01 3.41
848 872 3.916438 TAGTTGGGCCGGGAGAGCA 62.916 63.158 2.18 0.00 0.00 4.26
978 1164 2.359967 GCAGCCCCCTTAGTCGACT 61.360 63.158 23.66 23.66 0.00 4.18
1023 1210 4.227134 CCGGGGCATCGAGGTCAG 62.227 72.222 3.31 0.00 0.00 3.51
1063 1250 3.683587 CTGATGCGCGAGGTCGACA 62.684 63.158 18.91 0.00 43.02 4.35
1066 1253 2.936829 GATGCGCGAGGTCGACATCA 62.937 60.000 27.59 11.11 45.44 3.07
1076 1263 0.970937 GTCGACATCACCTCCCTCCA 60.971 60.000 11.55 0.00 0.00 3.86
1102 1289 1.282248 ACAAACATCGACGACGCCTG 61.282 55.000 0.00 5.36 39.58 4.85
1203 1390 1.167851 CCTTGTCCATTGTGATGCGT 58.832 50.000 0.00 0.00 31.67 5.24
1228 1415 1.672356 GGCAAGCGCAAGAGGAAGA 60.672 57.895 11.47 0.00 41.24 2.87
1252 1439 2.114411 GTCCAAGGGACCGCCAAA 59.886 61.111 4.00 0.00 46.19 3.28
1278 1465 0.248825 CGCTCCTCCTCTTCACGATG 60.249 60.000 0.00 0.00 0.00 3.84
1292 1479 3.869272 GATGCTTCACGCTGGCGG 61.869 66.667 18.99 8.28 44.69 6.13
1627 1828 3.430098 GGAGACTGATTCTAGCAGTGGTG 60.430 52.174 4.76 0.00 45.94 4.17
1671 1878 2.412847 GCTCGTGATTTGCGTTTAAGCT 60.413 45.455 0.00 0.00 38.13 3.74
1806 2034 6.058183 ACTGAAGACAATTGTTAGACAGCTT 58.942 36.000 22.95 16.14 0.00 3.74
1829 2057 5.488341 TGAGAAAGTTTACTCACTATGGCC 58.512 41.667 0.00 0.00 38.08 5.36
2033 2799 6.426937 GCTCTTCACAACTCTAATTGTTGGTA 59.573 38.462 10.76 0.00 46.28 3.25
2094 2862 9.787532 GCTCTCTGCTAATTCTAGATGTTATAG 57.212 37.037 0.00 0.00 38.95 1.31
2167 2935 4.129380 TGATTAGCTCCATCAATCAACCG 58.871 43.478 6.42 0.00 36.12 4.44
2194 2963 9.899226 GGCTAAATACTGATGTATGAAATTTCC 57.101 33.333 15.48 1.08 39.16 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
521 522 7.667043 TTTCCACTAATGTATTGTGTCTGTC 57.333 36.000 0.00 0.00 0.00 3.51
635 640 0.332293 TCCCTGGCAGATGATTTGCA 59.668 50.000 17.94 0.00 43.28 4.08
675 680 4.093850 GGCAGTTTAACCACCGTTATGTAG 59.906 45.833 0.00 0.00 34.44 2.74
727 732 1.180029 GGACATCATTGCTGGCAGTT 58.820 50.000 17.16 0.00 0.00 3.16
848 872 3.930634 AAAGTCTTTAGTCTACCGCGT 57.069 42.857 4.92 0.00 0.00 6.01
962 1098 1.900545 GCAAGTCGACTAAGGGGGCT 61.901 60.000 20.39 0.00 0.00 5.19
1013 1199 2.043852 AGGCGACCTGACCTCGAT 60.044 61.111 0.00 0.00 32.65 3.59
1023 1210 4.459089 GTCTGGAGGCAGGCGACC 62.459 72.222 6.35 6.35 0.00 4.79
1063 1250 1.700042 GCCGAATGGAGGGAGGTGAT 61.700 60.000 0.00 0.00 37.49 3.06
1066 1253 2.285368 TGCCGAATGGAGGGAGGT 60.285 61.111 0.00 0.00 37.49 3.85
1076 1263 0.442310 CGTCGATGTTTGTGCCGAAT 59.558 50.000 0.00 0.00 32.60 3.34
1495 1689 1.084018 TCAAGGAGGGAGGGCAAATT 58.916 50.000 0.00 0.00 0.00 1.82
1500 1694 2.456443 GGGATCAAGGAGGGAGGGC 61.456 68.421 0.00 0.00 0.00 5.19
1527 1721 7.122353 AGCAATAAGGAAGACTAAGTAACTCGA 59.878 37.037 0.00 0.00 0.00 4.04
1671 1878 6.418101 AGGAGAGTACACGTACAATAACCTA 58.582 40.000 9.85 0.00 38.48 3.08
1806 2034 5.488341 GGCCATAGTGAGTAAACTTTCTCA 58.512 41.667 0.00 0.00 38.20 3.27
1829 2057 7.082602 ACTTTGTAGAGTTGTATACACAGTCG 58.917 38.462 4.68 0.16 36.95 4.18
1945 2677 8.664079 ACAATTAGCTAGATGATAAATCAGGGT 58.336 33.333 13.08 0.00 40.64 4.34
2094 2862 9.774742 GTGTTCATTATTCAAAGTTCATACTCC 57.225 33.333 0.00 0.00 31.99 3.85
2167 2935 9.899226 GAAATTTCATACATCAGTATTTAGCCC 57.101 33.333 13.40 0.00 38.88 5.19
2479 4876 2.639839 ACTGCACTGTATGTTCCTTCCT 59.360 45.455 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.