Multiple sequence alignment - TraesCS2D01G005200

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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 TraesCS2D01G005200 chr2D 100.000 3917 0 0 1 3917 2808600 2812516 0.000000e+00 7234.0
1 TraesCS2D01G005200 chr2D 91.176 1020 69 8 2541 3540 2846739 2847757 0.000000e+00 1365.0
2 TraesCS2D01G005200 chr2D 93.636 440 17 4 1 436 2872540 2872972 0.000000e+00 647.0
3 TraesCS2D01G005200 chr2D 86.504 452 35 5 3468 3917 2847777 2848204 1.270000e-129 473.0
4 TraesCS2D01G005200 chr2B 95.012 2867 118 11 747 3597 8309804 8306947 0.000000e+00 4479.0
5 TraesCS2D01G005200 chr2B 89.762 2520 195 18 1073 3565 7831808 7829325 0.000000e+00 3166.0
6 TraesCS2D01G005200 chr2B 88.266 2088 199 21 1856 3917 8271026 8268959 0.000000e+00 2457.0
7 TraesCS2D01G005200 chr2B 86.656 1289 126 16 2521 3789 39050482 39051744 0.000000e+00 1386.0
8 TraesCS2D01G005200 chr2B 90.000 930 82 7 1856 2784 8273008 8272089 0.000000e+00 1192.0
9 TraesCS2D01G005200 chr2B 91.896 728 55 1 1130 1857 8279704 8278981 0.000000e+00 1014.0
10 TraesCS2D01G005200 chr2B 87.361 451 51 5 631 1076 8280185 8279736 2.700000e-141 512.0
11 TraesCS2D01G005200 chr2B 92.049 327 20 4 3592 3917 8297988 8297667 4.610000e-124 455.0
12 TraesCS2D01G005200 chr2B 88.347 369 37 5 675 1039 7832166 7831800 4.650000e-119 438.0
13 TraesCS2D01G005200 chr2B 93.836 292 14 1 21 308 8280868 8280577 1.670000e-118 436.0
14 TraesCS2D01G005200 chr2B 94.946 277 14 0 357 633 7832522 7832246 6.010000e-118 435.0
15 TraesCS2D01G005200 chr2B 94.946 277 14 0 357 633 8280575 8280299 6.010000e-118 435.0
16 TraesCS2D01G005200 chr2B 91.026 312 18 2 1 308 7832829 7832524 2.820000e-111 412.0
17 TraesCS2D01G005200 chr2B 87.500 352 38 5 3568 3917 7829061 7828714 6.100000e-108 401.0
18 TraesCS2D01G005200 chr2B 81.466 232 31 10 404 629 6862489 6862714 3.110000e-41 180.0
19 TraesCS2D01G005200 chr2B 81.466 232 31 10 404 629 6950795 6951020 3.110000e-41 180.0
20 TraesCS2D01G005200 chr2A 94.378 1494 50 6 673 2159 2798945 2797479 0.000000e+00 2263.0
21 TraesCS2D01G005200 chr2A 96.369 661 19 1 2861 3521 2797127 2796472 0.000000e+00 1083.0
22 TraesCS2D01G005200 chr2A 96.067 356 14 0 3562 3917 2796472 2796117 7.300000e-162 580.0
23 TraesCS2D01G005200 chr2A 92.937 269 17 2 290 557 2799773 2799506 1.320000e-104 390.0
24 TraesCS2D01G005200 chr2A 97.452 157 4 0 2151 2307 2797268 2797112 6.450000e-68 268.0
25 TraesCS2D01G005200 chr5D 85.325 661 96 1 2273 2933 560791222 560791881 0.000000e+00 682.0
26 TraesCS2D01G005200 chr1A 80.738 244 40 6 390 629 503830611 503830371 2.400000e-42 183.0
27 TraesCS2D01G005200 chr4A 77.733 247 49 6 388 630 725584147 725583903 3.150000e-31 147.0
28 TraesCS2D01G005200 chr7A 81.111 180 28 6 403 577 74009000 74008822 5.280000e-29 139.0
29 TraesCS2D01G005200 chr5B 76.923 247 48 9 390 631 94260412 94260654 8.830000e-27 132.0
30 TraesCS2D01G005200 chrUn 72.683 205 52 4 2596 2798 24905886 24906088 9.080000e-07 65.8


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 TraesCS2D01G005200 chr2D 2808600 2812516 3916 False 7234.00 7234 100.00000 1 3917 1 chr2D.!!$F1 3916
1 TraesCS2D01G005200 chr2D 2846739 2848204 1465 False 919.00 1365 88.84000 2541 3917 2 chr2D.!!$F3 1376
2 TraesCS2D01G005200 chr2B 8306947 8309804 2857 True 4479.00 4479 95.01200 747 3597 1 chr2B.!!$R2 2850
3 TraesCS2D01G005200 chr2B 8268959 8273008 4049 True 1824.50 2457 89.13300 1856 3917 2 chr2B.!!$R4 2061
4 TraesCS2D01G005200 chr2B 39050482 39051744 1262 False 1386.00 1386 86.65600 2521 3789 1 chr2B.!!$F3 1268
5 TraesCS2D01G005200 chr2B 7828714 7832829 4115 True 970.40 3166 90.31620 1 3917 5 chr2B.!!$R3 3916
6 TraesCS2D01G005200 chr2B 8278981 8280868 1887 True 599.25 1014 92.00975 21 1857 4 chr2B.!!$R5 1836
7 TraesCS2D01G005200 chr2A 2796117 2799773 3656 True 916.80 2263 95.44060 290 3917 5 chr2A.!!$R1 3627
8 TraesCS2D01G005200 chr5D 560791222 560791881 659 False 682.00 682 85.32500 2273 2933 1 chr5D.!!$F1 660

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
399 405 0.031449 GAGCAGACATACTCCCGCTC 59.969 60.000 0.00 0.0 37.62 5.03 F
823 1323 1.067354 CCCTTGCAATCTTCTTGTGGC 60.067 52.381 0.00 0.0 0.00 5.01 F
1022 1532 1.576356 GAGATGGAGCGCTGGTTAAG 58.424 55.000 18.48 0.0 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 2159 0.107654 GCCCATAAGCTCGTTCACCT 60.108 55.000 0.0 0.0 0.0 4.00 R
2301 5042 1.254026 CAGTTCCGGTGGTCTCAGTA 58.746 55.000 0.0 0.0 0.0 2.74 R
2945 5690 1.745653 GCATCCTGGTTCAGTAAAGGC 59.254 52.381 0.0 0.0 0.0 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
29 30 5.881447 TGTTGTTGCGTTACAGTTACAATT 58.119 33.333 0.00 0.00 0.00 2.32
33 34 5.049954 TGTTGCGTTACAGTTACAATTCCTC 60.050 40.000 0.00 0.00 0.00 3.71
52 53 3.433314 CCTCGTACTAGCTCAACCTCCTA 60.433 52.174 0.00 0.00 0.00 2.94
58 59 1.783071 AGCTCAACCTCCTAGTAGGC 58.217 55.000 11.75 0.00 40.62 3.93
147 148 3.431673 TCATTGTTGGCCACTCATACA 57.568 42.857 3.88 3.34 0.00 2.29
182 183 2.755655 GGACGATGATGTATCTCCGGAT 59.244 50.000 3.57 0.00 33.44 4.18
222 223 1.820877 GCATCCCTGTCCCCATTGATC 60.821 57.143 0.00 0.00 0.00 2.92
243 244 0.040958 GACAAACGAGCTGCACCAAG 60.041 55.000 1.02 0.00 0.00 3.61
259 260 1.065102 CCAAGAATCATTGCGGCTCTG 59.935 52.381 0.00 0.00 0.00 3.35
262 263 0.659957 GAATCATTGCGGCTCTGTCC 59.340 55.000 0.00 0.00 0.00 4.02
263 264 0.035152 AATCATTGCGGCTCTGTCCA 60.035 50.000 0.00 0.00 0.00 4.02
264 265 0.745845 ATCATTGCGGCTCTGTCCAC 60.746 55.000 0.00 0.00 0.00 4.02
265 266 2.434884 ATTGCGGCTCTGTCCACG 60.435 61.111 0.00 0.00 0.00 4.94
266 267 2.942796 ATTGCGGCTCTGTCCACGA 61.943 57.895 0.00 0.00 0.00 4.35
267 268 2.244117 ATTGCGGCTCTGTCCACGAT 62.244 55.000 0.00 0.00 0.00 3.73
268 269 2.125512 GCGGCTCTGTCCACGATT 60.126 61.111 0.00 0.00 0.00 3.34
322 327 0.040781 AAAATTGTTCGTGGTCGCCG 60.041 50.000 0.00 0.00 36.96 6.46
347 352 2.358898 TGGAAAACAGAGAGCAGCAAAC 59.641 45.455 0.00 0.00 0.00 2.93
399 405 0.031449 GAGCAGACATACTCCCGCTC 59.969 60.000 0.00 0.00 37.62 5.03
421 427 7.770897 CGCTCTTCAAATATATAGGGCCTAATT 59.229 37.037 18.91 10.21 30.26 1.40
467 473 5.418840 ACCACTGGTTAGAGCAAAAATATGG 59.581 40.000 0.00 0.00 27.29 2.74
491 497 5.902613 ATGCATGTTACACAAAGCATACT 57.097 34.783 14.79 0.00 45.55 2.12
727 1227 1.510480 GGTGAGTGAGCACTTGCACC 61.510 60.000 19.41 19.41 44.03 5.01
736 1236 1.806568 CACTTGCACCCGTTGTTGT 59.193 52.632 0.00 0.00 0.00 3.32
785 1285 5.773680 TGTTAGAGAGAACCCCTTATATCGG 59.226 44.000 0.00 0.00 0.00 4.18
808 1308 4.010349 GGTACCAAGTCTCAATTCCCTTG 58.990 47.826 7.15 0.00 35.26 3.61
823 1323 1.067354 CCCTTGCAATCTTCTTGTGGC 60.067 52.381 0.00 0.00 0.00 5.01
870 1370 3.437741 ACCGTAAATAGGCCGTTGAAAAG 59.562 43.478 0.00 0.00 0.00 2.27
930 1433 9.573166 TTTGAGGGTGAATTGGTCTATATATTG 57.427 33.333 0.00 0.00 0.00 1.90
1022 1532 1.576356 GAGATGGAGCGCTGGTTAAG 58.424 55.000 18.48 0.00 0.00 1.85
1110 1625 2.278332 ACCCCAAGAAGAAGCAACTC 57.722 50.000 0.00 0.00 0.00 3.01
1619 2159 3.107601 AGTACCTCCATGAGCTAAGCAA 58.892 45.455 0.00 0.00 0.00 3.91
1620 2160 2.706339 ACCTCCATGAGCTAAGCAAG 57.294 50.000 0.00 0.00 0.00 4.01
1759 2299 4.826183 ACATCATCACTGAGATCATCGAGA 59.174 41.667 0.00 0.00 33.72 4.04
1760 2300 4.827304 TCATCACTGAGATCATCGAGAC 57.173 45.455 0.00 0.00 33.72 3.36
2137 4659 7.012421 GCAGAGTCAAAATAAATCCCGAATAGT 59.988 37.037 0.00 0.00 0.00 2.12
2233 4974 9.357652 CCATAGGACATATTTTGTTTCAACTTG 57.642 33.333 0.00 0.00 39.18 3.16
2301 5042 2.240667 ACAGGACATATTTGGAGCTGCT 59.759 45.455 6.82 0.00 0.00 4.24
2423 5164 2.002586 CCAAGGTCGACATGTCATCAC 58.997 52.381 24.93 16.73 0.00 3.06
3689 6835 5.536161 ACTGCACATGGTTCAAACTTATTCT 59.464 36.000 0.00 0.00 0.00 2.40
3699 6845 8.092687 TGGTTCAAACTTATTCTACACCTCTAC 58.907 37.037 0.00 0.00 0.00 2.59
3755 6902 1.321474 CACTTTCTTTCAGCTGGGCA 58.679 50.000 15.13 0.00 0.00 5.36
3789 6936 6.525629 AGTAACATATTGGCTAGCAGTTAGG 58.474 40.000 18.24 8.42 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.219726 GCTAGTACGAGGAATTGTAACTGTAAC 59.780 40.741 5.08 0.00 0.00 2.50
16 17 7.121759 AGCTAGTACGAGGAATTGTAACTGTAA 59.878 37.037 5.08 0.00 0.00 2.41
17 18 6.600822 AGCTAGTACGAGGAATTGTAACTGTA 59.399 38.462 5.08 0.00 0.00 2.74
18 19 5.418209 AGCTAGTACGAGGAATTGTAACTGT 59.582 40.000 5.08 0.00 0.00 3.55
19 20 5.892568 AGCTAGTACGAGGAATTGTAACTG 58.107 41.667 5.08 0.00 0.00 3.16
29 30 2.641305 GAGGTTGAGCTAGTACGAGGA 58.359 52.381 5.08 0.00 0.00 3.71
33 34 3.543665 ACTAGGAGGTTGAGCTAGTACG 58.456 50.000 0.00 0.00 0.00 3.67
52 53 0.533032 GAGCTTGTTCTCCGCCTACT 59.467 55.000 0.00 0.00 0.00 2.57
147 148 2.631160 TCGTCCTTGGTGTCACATTT 57.369 45.000 5.12 0.00 0.00 2.32
182 183 2.122769 TCAAGGACGGGGACACCA 60.123 61.111 0.00 0.00 40.22 4.17
222 223 1.159713 TGGTGCAGCTCGTTTGTCTG 61.160 55.000 18.08 0.00 0.00 3.51
243 244 0.659957 GGACAGAGCCGCAATGATTC 59.340 55.000 2.17 0.00 0.00 2.52
259 260 1.871080 CAGGCATCCTAATCGTGGAC 58.129 55.000 0.00 0.00 36.30 4.02
262 263 1.224075 CAGCAGGCATCCTAATCGTG 58.776 55.000 0.00 0.00 29.64 4.35
263 264 0.533755 GCAGCAGGCATCCTAATCGT 60.534 55.000 0.00 0.00 43.97 3.73
264 265 1.563435 CGCAGCAGGCATCCTAATCG 61.563 60.000 0.00 0.00 45.17 3.34
265 266 1.233285 CCGCAGCAGGCATCCTAATC 61.233 60.000 0.00 0.00 45.17 1.75
266 267 1.228063 CCGCAGCAGGCATCCTAAT 60.228 57.895 0.00 0.00 45.17 1.73
267 268 1.334384 TACCGCAGCAGGCATCCTAA 61.334 55.000 3.49 0.00 45.17 2.69
268 269 1.334384 TTACCGCAGCAGGCATCCTA 61.334 55.000 3.49 0.00 45.17 2.94
322 327 2.363683 CTGCTCTCTGTTTTCCATCCC 58.636 52.381 0.00 0.00 0.00 3.85
421 427 6.381420 TGGTCAAAGGTAACCTTGAAAAATGA 59.619 34.615 0.00 0.00 43.92 2.57
491 497 8.862325 ACCTACTTTCACATATGAATTTGACA 57.138 30.769 10.38 0.00 44.36 3.58
658 784 3.823281 TTAGTTCACCGTGTGGAAAGA 57.177 42.857 0.00 0.00 39.21 2.52
669 795 1.154469 GCGTGCGCTTTAGTTCACC 60.154 57.895 9.73 0.00 38.26 4.02
727 1227 5.116180 ACATATGAGACCATACAACAACGG 58.884 41.667 10.38 0.00 38.02 4.44
736 1236 5.307976 CCTCCTTGGAACATATGAGACCATA 59.692 44.000 10.38 6.16 39.30 2.74
785 1285 2.576648 AGGGAATTGAGACTTGGTACCC 59.423 50.000 10.07 0.00 35.53 3.69
808 1308 3.338249 TCTAGTGCCACAAGAAGATTGC 58.662 45.455 0.00 0.00 0.00 3.56
823 1323 7.912250 GTGGCATTTCATCTGTAAAATCTAGTG 59.088 37.037 0.00 0.00 0.00 2.74
908 1409 8.311836 CGTACAATATATAGACCAATTCACCCT 58.688 37.037 0.00 0.00 0.00 4.34
930 1433 0.243907 TGCTGCTTGGAGAGACGTAC 59.756 55.000 0.00 0.00 0.00 3.67
1022 1532 6.402550 CGTGGATATGCCTATGAAATACAAGC 60.403 42.308 0.00 0.00 37.63 4.01
1619 2159 0.107654 GCCCATAAGCTCGTTCACCT 60.108 55.000 0.00 0.00 0.00 4.00
1620 2160 0.392461 TGCCCATAAGCTCGTTCACC 60.392 55.000 0.00 0.00 0.00 4.02
1954 4476 9.820725 TGATTGAAGTCAACATCAAAATTTTCT 57.179 25.926 0.00 0.00 37.17 2.52
2075 4597 9.905171 ATCTGATGATGCATATGACGTATATAC 57.095 33.333 6.97 2.53 30.75 1.47
2077 4599 9.473640 GAATCTGATGATGCATATGACGTATAT 57.526 33.333 6.97 0.00 32.44 0.86
2301 5042 1.254026 CAGTTCCGGTGGTCTCAGTA 58.746 55.000 0.00 0.00 0.00 2.74
2423 5164 2.093973 AGCTCATTGAGGTCGGTACTTG 60.094 50.000 12.50 0.00 35.30 3.16
2945 5690 1.745653 GCATCCTGGTTCAGTAAAGGC 59.254 52.381 0.00 0.00 0.00 4.35
3050 5797 7.985184 ACATAGCTAATGTCACTCGGAATAAAA 59.015 33.333 0.00 0.00 46.15 1.52
3140 5887 6.842437 AGTATGTGGTCTGCTATATAGTGG 57.158 41.667 11.38 4.98 0.00 4.00
3436 6191 7.238723 ACCAAAAACTACCAATAAAATCCCCAT 59.761 33.333 0.00 0.00 0.00 4.00
3585 6731 3.402628 AGAGACCACGTATTTTGTGCT 57.597 42.857 0.00 0.00 36.01 4.40
3755 6902 3.434167 CCAATATGTTACTCAGCCAGGCT 60.434 47.826 8.70 8.70 40.77 4.58


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

AutoCloner maintained by Alex Coulton.