Multiple sequence alignment - TraesCS1D01G318000

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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 TraesCS1D01G318000 chr1D 100.000 3155 0 0 1 3155 412683074 412686228 0.000000e+00 5827.0
1 TraesCS1D01G318000 chr1D 97.041 2670 57 8 495 3155 412897274 412899930 0.000000e+00 4473.0
2 TraesCS1D01G318000 chr1D 96.196 2103 34 7 611 2702 412814078 412816145 0.000000e+00 3398.0
3 TraesCS1D01G318000 chr1D 90.523 2026 122 29 684 2675 412641928 412643917 0.000000e+00 2614.0
4 TraesCS1D01G318000 chr1D 91.768 1895 88 27 684 2546 412745906 412747764 0.000000e+00 2573.0
5 TraesCS1D01G318000 chr1D 91.768 1895 88 27 684 2546 412763069 412764927 0.000000e+00 2573.0
6 TraesCS1D01G318000 chr1D 93.985 1596 56 14 684 2268 412660192 412661758 0.000000e+00 2379.0
7 TraesCS1D01G318000 chr1D 93.689 1537 50 14 754 2268 412786616 412788127 0.000000e+00 2257.0
8 TraesCS1D01G318000 chr1D 96.680 512 14 1 1 509 412896751 412897262 0.000000e+00 848.0
9 TraesCS1D01G318000 chr1D 92.235 528 16 5 754 1281 412854725 412855227 0.000000e+00 725.0
10 TraesCS1D01G318000 chr1D 84.242 660 75 16 2037 2675 412789310 412789961 1.610000e-172 616.0
11 TraesCS1D01G318000 chr1D 96.100 359 11 2 2800 3155 412816138 412816496 1.630000e-162 582.0
12 TraesCS1D01G318000 chr1D 91.061 358 28 3 539 896 413061282 413061635 6.120000e-132 481.0
13 TraesCS1D01G318000 chr1D 79.318 440 61 11 2256 2675 412662821 412663250 6.660000e-72 281.0
14 TraesCS1D01G318000 chr1D 81.429 210 28 9 2426 2629 412646518 412646722 9.060000e-36 161.0
15 TraesCS1D01G318000 chr1D 76.431 297 52 13 2674 2960 36486768 36486480 9.120000e-31 145.0
16 TraesCS1D01G318000 chr1D 85.821 134 18 1 2674 2807 14239766 14239898 1.180000e-29 141.0
17 TraesCS1D01G318000 chr1D 95.385 65 3 0 2426 2490 412749409 412749473 1.550000e-18 104.0
18 TraesCS1D01G318000 chr1B 92.589 2186 119 17 998 3148 556251420 556253597 0.000000e+00 3099.0
19 TraesCS1D01G318000 chr1B 92.203 1975 111 19 1199 3148 556834311 556836267 0.000000e+00 2754.0
20 TraesCS1D01G318000 chr1B 92.203 1975 111 19 1199 3148 556862732 556864688 0.000000e+00 2754.0
21 TraesCS1D01G318000 chr1B 92.992 1912 91 19 684 2579 556662844 556664728 0.000000e+00 2748.0
22 TraesCS1D01G318000 chr1B 91.575 1543 83 29 998 2520 556297340 556298855 0.000000e+00 2085.0
23 TraesCS1D01G318000 chr1B 87.588 1273 99 27 465 1723 556968902 556970129 0.000000e+00 1421.0
24 TraesCS1D01G318000 chr1B 87.801 582 39 7 2592 3155 556666532 556667099 0.000000e+00 652.0
25 TraesCS1D01G318000 chr1B 87.423 485 35 17 431 899 556833634 556834108 4.630000e-148 534.0
26 TraesCS1D01G318000 chr1B 87.423 485 35 17 431 899 556862055 556862529 4.630000e-148 534.0
27 TraesCS1D01G318000 chr1B 86.450 369 37 7 567 935 556965928 556966283 2.950000e-105 392.0
28 TraesCS1D01G318000 chr1B 78.451 297 48 7 2674 2955 295427776 295427481 2.500000e-41 180.0
29 TraesCS1D01G318000 chr1A 91.709 1182 72 8 1758 2914 510111533 510112713 0.000000e+00 1616.0
30 TraesCS1D01G318000 chr1A 91.201 1182 68 12 1758 2914 509541974 509540804 0.000000e+00 1574.0
31 TraesCS1D01G318000 chr1A 87.469 407 38 7 541 947 509494029 509493636 1.030000e-124 457.0
32 TraesCS1D01G318000 chr1A 88.101 395 34 8 541 935 510184758 510185139 1.030000e-124 457.0
33 TraesCS1D01G318000 chr1A 85.774 239 29 3 1 234 554878458 554878696 6.760000e-62 248.0
34 TraesCS1D01G318000 chr1A 90.667 150 11 2 2976 3122 509540803 509540654 2.480000e-46 196.0
35 TraesCS1D01G318000 chr1A 89.796 147 12 2 2976 3119 510112714 510112860 5.370000e-43 185.0
36 TraesCS1D01G318000 chr1A 76.744 301 46 19 2674 2961 550895349 550895638 2.540000e-31 147.0
37 TraesCS1D01G318000 chr1A 83.571 140 16 5 505 637 509704021 509703882 1.190000e-24 124.0
38 TraesCS1D01G318000 chr1A 83.333 132 15 5 513 637 509777242 509777111 7.150000e-22 115.0
39 TraesCS1D01G318000 chr3B 85.022 227 26 7 1 221 365214381 365214605 1.140000e-54 224.0
40 TraesCS1D01G318000 chr5B 84.475 219 29 2 1 214 233920549 233920767 8.870000e-51 211.0
41 TraesCS1D01G318000 chr7D 80.201 298 42 4 2674 2955 21096411 21096707 1.150000e-49 207.0
42 TraesCS1D01G318000 chr2A 82.479 234 34 5 1 229 388461674 388461443 6.900000e-47 198.0
43 TraesCS1D01G318000 chr2A 78.378 148 22 10 98 237 423174917 423174772 1.560000e-13 87.9
44 TraesCS1D01G318000 chr2A 84.722 72 9 2 106 175 459527039 459527110 1.570000e-08 71.3
45 TraesCS1D01G318000 chr2B 79.195 298 45 8 2674 2955 19981534 19981830 1.160000e-44 191.0
46 TraesCS1D01G318000 chr4D 79.070 301 43 10 2674 2955 208646536 208646237 4.150000e-44 189.0
47 TraesCS1D01G318000 chr4D 77.241 290 52 8 2673 2953 398706038 398706322 1.170000e-34 158.0
48 TraesCS1D01G318000 chr4D 85.075 134 20 0 2674 2807 194855047 194854914 1.530000e-28 137.0
49 TraesCS1D01G318000 chr6D 88.235 153 16 2 1 151 272126914 272127066 6.950000e-42 182.0
50 TraesCS1D01G318000 chr6D 77.855 289 54 7 2674 2955 210072982 210072697 1.500000e-38 171.0
51 TraesCS1D01G318000 chr5A 86.486 74 8 1 2969 3040 342452334 342452407 2.610000e-11 80.5
52 TraesCS1D01G318000 chr7B 76.978 139 21 11 98 228 592001189 592001324 5.650000e-08 69.4


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 TraesCS1D01G318000 chr1D 412683074 412686228 3154 False 5827.0 5827 100.0000 1 3155 1 chr1D.!!$F2 3154
1 TraesCS1D01G318000 chr1D 412896751 412899930 3179 False 2660.5 4473 96.8605 1 3155 2 chr1D.!!$F11 3154
2 TraesCS1D01G318000 chr1D 412763069 412764927 1858 False 2573.0 2573 91.7680 684 2546 1 chr1D.!!$F3 1862
3 TraesCS1D01G318000 chr1D 412814078 412816496 2418 False 1990.0 3398 96.1480 611 3155 2 chr1D.!!$F10 2544
4 TraesCS1D01G318000 chr1D 412786616 412789961 3345 False 1436.5 2257 88.9655 754 2675 2 chr1D.!!$F9 1921
5 TraesCS1D01G318000 chr1D 412641928 412646722 4794 False 1387.5 2614 85.9760 684 2675 2 chr1D.!!$F6 1991
6 TraesCS1D01G318000 chr1D 412745906 412749473 3567 False 1338.5 2573 93.5765 684 2546 2 chr1D.!!$F8 1862
7 TraesCS1D01G318000 chr1D 412660192 412663250 3058 False 1330.0 2379 86.6515 684 2675 2 chr1D.!!$F7 1991
8 TraesCS1D01G318000 chr1D 412854725 412855227 502 False 725.0 725 92.2350 754 1281 1 chr1D.!!$F4 527
9 TraesCS1D01G318000 chr1B 556251420 556253597 2177 False 3099.0 3099 92.5890 998 3148 1 chr1B.!!$F1 2150
10 TraesCS1D01G318000 chr1B 556297340 556298855 1515 False 2085.0 2085 91.5750 998 2520 1 chr1B.!!$F2 1522
11 TraesCS1D01G318000 chr1B 556662844 556667099 4255 False 1700.0 2748 90.3965 684 3155 2 chr1B.!!$F3 2471
12 TraesCS1D01G318000 chr1B 556833634 556836267 2633 False 1644.0 2754 89.8130 431 3148 2 chr1B.!!$F4 2717
13 TraesCS1D01G318000 chr1B 556862055 556864688 2633 False 1644.0 2754 89.8130 431 3148 2 chr1B.!!$F5 2717
14 TraesCS1D01G318000 chr1B 556965928 556970129 4201 False 906.5 1421 87.0190 465 1723 2 chr1B.!!$F6 1258
15 TraesCS1D01G318000 chr1A 510111533 510112860 1327 False 900.5 1616 90.7525 1758 3119 2 chr1A.!!$F4 1361
16 TraesCS1D01G318000 chr1A 509540654 509541974 1320 True 885.0 1574 90.9340 1758 3122 2 chr1A.!!$R4 1364

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
601 639 1.615384 GGCATTCACTCTGGCCTTCTT 60.615 52.381 3.32 0.0 43.09 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 4789 1.337074 CCAACAGTCAATGCCGCAAAT 60.337 47.619 0.0 0.0 0.0 2.32 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
96 97 4.286297 TGTTCCTCTCATAAAGGGTGTG 57.714 45.455 0.00 0.0 34.46 3.82
136 137 2.349722 GGTTGTAAGTTTGTAACCCGCG 60.350 50.000 0.00 0.0 37.25 6.46
207 211 7.742556 ATAAGTCTTACTACCCGTCTACATC 57.257 40.000 0.00 0.0 0.00 3.06
210 214 4.880696 GTCTTACTACCCGTCTACATCACT 59.119 45.833 0.00 0.0 0.00 3.41
601 639 1.615384 GGCATTCACTCTGGCCTTCTT 60.615 52.381 3.32 0.0 43.09 2.52
1013 1066 0.179045 GAGAATATGGCGTGCAGGGT 60.179 55.000 8.72 0.0 0.00 4.34
1316 1377 2.332362 GATGCGACGGCTCGGTTCTA 62.332 60.000 0.00 0.0 40.53 2.10
2204 2548 9.541143 TTTTGATTTGTAACATCCTTTTTCCTC 57.459 29.630 0.00 0.0 0.00 3.71
2205 2549 7.831691 TGATTTGTAACATCCTTTTTCCTCA 57.168 32.000 0.00 0.0 0.00 3.86
2234 2590 9.780186 AATTACTGTAAGATTGTTATAGCTCCC 57.220 33.333 6.40 0.0 37.43 4.30
2248 2604 3.136641 AGCTCCCTTCTCTCCCAAATA 57.863 47.619 0.00 0.0 0.00 1.40
2365 4155 6.426328 GTCATCTGGAGATTATTCATGTCACC 59.574 42.308 0.00 0.0 31.21 4.02
2396 4191 9.704098 CTAGTTTTGTCTAAGTTTGTCTTTGTC 57.296 33.333 0.00 0.0 37.56 3.18
2708 6817 8.500238 TGTCTAGGTGTATAAGTCATCTAAGGA 58.500 37.037 0.00 0.0 29.72 3.36
2898 9588 2.746904 CGATGTGGAAGTTAATGCACCA 59.253 45.455 0.00 0.0 40.53 4.17
2902 9592 2.493278 GTGGAAGTTAATGCACCATGCT 59.507 45.455 2.02 0.0 45.31 3.79
2949 9639 7.498239 GGTTTTCCTAAGATGACTTATACACCC 59.502 40.741 0.00 0.0 37.85 4.61
3039 9986 3.018856 TCATTAGGGTGCATTTGAGCTG 58.981 45.455 0.00 0.0 34.99 4.24
3095 10042 7.176340 AGGCGTTTATAGACCTAAGAATACGAT 59.824 37.037 0.00 0.0 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.900437 ACTAGCTATTGTATGGGTAGGCTA 58.100 41.667 11.99 0.0 43.45 3.93
72 73 5.817816 CACACCCTTTATGAGAGGAACATAC 59.182 44.000 0.00 0.0 36.33 2.39
77 78 2.576191 CCCACACCCTTTATGAGAGGAA 59.424 50.000 0.00 0.0 36.33 3.36
136 137 7.156876 TGAGAGAGAAGATGAAAGAAGAGAC 57.843 40.000 0.00 0.0 0.00 3.36
601 639 3.407698 TCGCTGCCAAGTTCTAATCAAA 58.592 40.909 0.00 0.0 0.00 2.69
901 954 7.577361 TGATTAATCAGGGAAAGCTTGAGCTG 61.577 42.308 14.23 0.0 40.38 4.24
902 955 5.574326 TGATTAATCAGGGAAAGCTTGAGCT 60.574 40.000 14.23 0.0 41.85 4.09
903 956 4.641989 TGATTAATCAGGGAAAGCTTGAGC 59.358 41.667 14.23 0.0 35.24 4.26
1316 1377 1.071471 CTTGTTGGCCGAGTCCAGT 59.929 57.895 0.00 0.0 37.44 4.00
1445 1506 1.895798 CTAGCAATGAGGGCGAGGATA 59.104 52.381 0.00 0.0 36.08 2.59
1614 1954 2.489971 GTCTCGTTGGAAATGGACACA 58.510 47.619 0.00 0.0 34.92 3.72
2365 4155 9.028185 AGACAAACTTAGACAAAACTAGTAACG 57.972 33.333 0.00 0.0 0.00 3.18
2547 4789 1.337074 CCAACAGTCAATGCCGCAAAT 60.337 47.619 0.00 0.0 0.00 2.32
2631 6675 0.592247 GCTTGTGCACTTGGTGTTCG 60.592 55.000 19.41 0.0 39.41 3.95
2708 6817 2.108514 CCTTGGTCGCGATGCACAT 61.109 57.895 14.06 0.0 0.00 3.21
2898 9588 9.218440 CCAAATAATCCAAAAACACTTAAGCAT 57.782 29.630 1.29 0.0 0.00 3.79
2949 9639 6.539649 TTTTTCTTAATGACTCCACGTCTG 57.460 37.500 0.00 0.0 43.25 3.51
3039 9986 5.761234 AGAGGACACGAAGTATCTAGACATC 59.239 44.000 0.00 0.0 41.61 3.06
3095 10042 3.053619 GGAGGAGGAAAATTAAGGAGGCA 60.054 47.826 0.00 0.0 0.00 4.75


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

AutoCloner maintained by Alex Coulton.