Multiple sequence alignment - TraesCS2A01G530200

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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 TraesCS2A01G530200 chr2A 100.000 2555 0 0 1 2555 748189464 748192018 0.000000e+00 4719.0
1 TraesCS2A01G530200 chr2A 97.182 2555 69 2 1 2555 748165104 748167655 0.000000e+00 4316.0
2 TraesCS2A01G530200 chr2A 96.407 2171 73 4 388 2555 748124497 748126665 0.000000e+00 3572.0
3 TraesCS2A01G530200 chr2A 86.031 1310 157 16 728 2017 748080082 748081385 0.000000e+00 1382.0
4 TraesCS2A01G530200 chr2A 91.322 242 11 5 149 389 748089566 748089798 3.170000e-84 322.0
5 TraesCS2A01G530200 chr2A 94.545 110 6 0 1 110 544703853 544703962 1.220000e-38 171.0
6 TraesCS2A01G530200 chr2B 93.401 1091 68 3 728 1816 753765980 753767068 0.000000e+00 1613.0
7 TraesCS2A01G530200 chr2B 93.388 1089 69 2 731 1818 753828347 753827261 0.000000e+00 1609.0
8 TraesCS2A01G530200 chr2B 88.503 1296 107 17 732 2017 753749587 753750850 0.000000e+00 1530.0
9 TraesCS2A01G530200 chr2B 88.242 910 98 5 846 1749 753843317 753842411 0.000000e+00 1079.0
10 TraesCS2A01G530200 chr2B 90.136 588 50 6 149 729 753829027 753828441 0.000000e+00 758.0
11 TraesCS2A01G530200 chr2B 84.813 777 80 14 1812 2555 753767747 753768518 0.000000e+00 747.0
12 TraesCS2A01G530200 chr2B 91.589 535 42 3 197 729 753765356 753765889 0.000000e+00 736.0
13 TraesCS2A01G530200 chr2B 84.387 775 82 14 1812 2555 753826603 753825837 0.000000e+00 725.0
14 TraesCS2A01G530200 chr2B 83.390 295 35 6 424 716 753749197 753749479 7.010000e-66 261.0
15 TraesCS2A01G530200 chr2B 79.167 240 28 10 2309 2531 753750858 753751092 2.050000e-31 147.0
16 TraesCS2A01G530200 chr2D 89.564 1284 114 11 732 2006 617511513 617512785 0.000000e+00 1611.0
17 TraesCS2A01G530200 chr2D 85.659 1290 160 15 731 2002 617463765 617465047 0.000000e+00 1334.0
18 TraesCS2A01G530200 chr2D 93.694 111 7 0 1 111 144540109 144539999 1.570000e-37 167.0
19 TraesCS2A01G530200 chr7D 93.636 110 7 0 1 110 537414915 537415024 5.660000e-37 165.0
20 TraesCS2A01G530200 chr7D 92.857 112 8 0 1 112 566136764 566136653 2.030000e-36 163.0
21 TraesCS2A01G530200 chr6D 93.636 110 7 0 1 110 374335657 374335548 5.660000e-37 165.0
22 TraesCS2A01G530200 chr6D 92.727 110 8 0 1 110 106330784 106330893 2.630000e-35 159.0
23 TraesCS2A01G530200 chr4D 93.519 108 7 0 4 111 91308806 91308699 7.320000e-36 161.0
24 TraesCS2A01G530200 chr5D 92.727 110 8 0 1 110 30924571 30924462 2.630000e-35 159.0
25 TraesCS2A01G530200 chr5D 80.220 91 14 4 316 404 530875094 530875182 5.900000e-07 65.8
26 TraesCS2A01G530200 chr3D 85.417 96 14 0 316 411 43778223 43778318 1.620000e-17 100.0
27 TraesCS2A01G530200 chr5B 92.537 67 5 0 315 381 406576043 406575977 2.090000e-16 97.1
28 TraesCS2A01G530200 chrUn 80.808 99 15 4 315 411 92781400 92781304 9.800000e-10 75.0
29 TraesCS2A01G530200 chr1D 87.500 64 8 0 312 375 379503721 379503784 9.800000e-10 75.0


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 TraesCS2A01G530200 chr2A 748189464 748192018 2554 False 4719.000000 4719 100.000000 1 2555 1 chr2A.!!$F6 2554
1 TraesCS2A01G530200 chr2A 748165104 748167655 2551 False 4316.000000 4316 97.182000 1 2555 1 chr2A.!!$F5 2554
2 TraesCS2A01G530200 chr2A 748124497 748126665 2168 False 3572.000000 3572 96.407000 388 2555 1 chr2A.!!$F4 2167
3 TraesCS2A01G530200 chr2A 748080082 748081385 1303 False 1382.000000 1382 86.031000 728 2017 1 chr2A.!!$F2 1289
4 TraesCS2A01G530200 chr2B 753842411 753843317 906 True 1079.000000 1079 88.242000 846 1749 1 chr2B.!!$R1 903
5 TraesCS2A01G530200 chr2B 753765356 753768518 3162 False 1032.000000 1613 89.934333 197 2555 3 chr2B.!!$F2 2358
6 TraesCS2A01G530200 chr2B 753825837 753829027 3190 True 1030.666667 1609 89.303667 149 2555 3 chr2B.!!$R2 2406
7 TraesCS2A01G530200 chr2B 753749197 753751092 1895 False 646.000000 1530 83.686667 424 2531 3 chr2B.!!$F1 2107
8 TraesCS2A01G530200 chr2D 617511513 617512785 1272 False 1611.000000 1611 89.564000 732 2006 1 chr2D.!!$F2 1274
9 TraesCS2A01G530200 chr2D 617463765 617465047 1282 False 1334.000000 1334 85.659000 731 2002 1 chr2D.!!$F1 1271

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
67 68 1.673009 CCGCCGTTCCTGCCTTTAA 60.673 57.895 0.0 0.0 0.0 1.52 F
1162 1267 2.040442 TTCATCCTCCTGGCCCGA 59.960 61.111 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1398 0.107312 CCAGGAACCTCTCTGGCATG 60.107 60.000 0.00 0.0 43.22 4.06 R
2248 3083 4.797693 CATGTGATCTCAGATGAACAGC 57.202 45.455 10.88 0.0 46.80 4.40 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
66 67 2.046700 CCGCCGTTCCTGCCTTTA 60.047 61.111 0.00 0.00 0.00 1.85
67 68 1.673009 CCGCCGTTCCTGCCTTTAA 60.673 57.895 0.00 0.00 0.00 1.52
110 111 5.525378 GCAAAGTAGATGATTCCTGTAGTGG 59.475 44.000 0.00 0.00 0.00 4.00
144 145 3.053395 GGGTTTAGGGTTTAGGGTTAGGG 60.053 52.174 0.00 0.00 0.00 3.53
386 388 5.105513 TGCTAGATACATCTGTTTGGACGAA 60.106 40.000 1.88 0.00 37.76 3.85
518 526 8.268850 AGGAACACTAACAATGATAACATCAC 57.731 34.615 0.00 0.00 43.01 3.06
1069 1174 3.181516 CGAGCTTGCAGAAGTTATTGGAC 60.182 47.826 0.00 0.00 0.00 4.02
1087 1192 6.485830 TTGGACCCAAAATAAACATTGACA 57.514 33.333 0.00 0.00 32.44 3.58
1162 1267 2.040442 TTCATCCTCCTGGCCCGA 59.960 61.111 0.00 0.00 0.00 5.14
1252 1357 4.095782 GTGTGTTCATAAACATATGGGCGT 59.904 41.667 7.80 0.00 46.58 5.68
1293 1398 3.753294 TGGACTGAACCTGAGAAGTTC 57.247 47.619 0.00 0.00 43.20 3.01
1309 1414 1.280421 AGTTCATGCCAGAGAGGTTCC 59.720 52.381 0.00 0.00 40.61 3.62
1318 1423 1.002544 CAGAGAGGTTCCTGGGTTCAC 59.997 57.143 0.00 0.00 0.00 3.18
1339 1444 2.896685 CCAGTTGATTTTAAGGGTGCCA 59.103 45.455 0.00 0.00 0.00 4.92
1420 1525 3.737559 TTAGGATGGTGCATTTGGTCT 57.262 42.857 0.00 0.00 0.00 3.85
1423 1528 2.170166 GGATGGTGCATTTGGTCTTCA 58.830 47.619 0.00 0.00 0.00 3.02
1457 1562 4.591321 ATCAATTTAAGTGGAGCCTCCA 57.409 40.909 10.05 10.05 45.98 3.86
2461 3296 4.545610 TCTTTTGCGCATTCCAAAGTTAG 58.454 39.130 24.17 7.23 34.10 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 4.788617 ACCCTAAACCACTACAGGAATCAT 59.211 41.667 0.00 0.00 0.00 2.45
110 111 5.261040 ACCCTAAACCCTAAACCCTAAAC 57.739 43.478 0.00 0.00 0.00 2.01
144 145 1.079503 CTCAGTCGGCAAGGCTAAAC 58.920 55.000 0.00 0.00 30.67 2.01
360 362 5.419542 GTCCAAACAGATGTATCTAGCACA 58.580 41.667 0.00 0.22 34.85 4.57
518 526 8.731275 TTACATGAGTATCCAAATGGTACTTG 57.269 34.615 0.00 11.09 34.49 3.16
806 908 9.175312 CTCTTTGAACTACACATAGAGGTACTA 57.825 37.037 0.00 0.00 41.55 1.82
1069 1174 8.830201 TCATCTTTGTCAATGTTTATTTTGGG 57.170 30.769 0.00 0.00 0.00 4.12
1204 1309 8.092687 ACGTGAATCTTTAGGTATTGTGTAACT 58.907 33.333 0.00 0.00 38.04 2.24
1252 1357 7.670140 AGTCCATACATCATTATCTCGACCTAA 59.330 37.037 0.00 0.00 0.00 2.69
1293 1398 0.107312 CCAGGAACCTCTCTGGCATG 60.107 60.000 0.00 0.00 43.22 4.06
1318 1423 2.896685 TGGCACCCTTAAAATCAACTGG 59.103 45.455 0.00 0.00 0.00 4.00
1339 1444 4.594491 ACCAAATGGAAGGAGCTCAAAATT 59.406 37.500 17.19 4.21 38.94 1.82
1423 1528 9.458374 CCACTTAAATTGATTTAACAACGAAGT 57.542 29.630 5.11 0.00 38.77 3.01
1457 1562 3.094572 CCATCCCTTTCAAGCTCAACAT 58.905 45.455 0.00 0.00 0.00 2.71
1668 1781 3.013921 TGCGAGGAAGTCAAGTTTTGTT 58.986 40.909 0.00 0.00 0.00 2.83
1721 1841 8.879759 CAACTTTATAACACAACATATCTCCGT 58.120 33.333 0.00 0.00 0.00 4.69
2237 3072 9.842775 ATCTCAGATGAACAGCAAAATAATAGA 57.157 29.630 0.00 0.00 0.00 1.98
2248 3083 4.797693 CATGTGATCTCAGATGAACAGC 57.202 45.455 10.88 0.00 46.80 4.40
2350 3185 9.774742 GGTGACAAATTATGAGTAATGAAACTC 57.225 33.333 0.00 0.00 34.56 3.01


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

AutoCloner maintained by Alex Coulton.