Multiple sequence alignment - TraesCS1A01G156200

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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 TraesCS1A01G156200 chr1A 100.000 2634 0 0 853 3486 276864618 276861985 0.000000e+00 4865.0
1 TraesCS1A01G156200 chr1A 100.000 475 0 0 1 475 276865470 276864996 0.000000e+00 878.0
2 TraesCS1A01G156200 chr7D 96.600 2647 72 6 853 3486 283703946 283701305 0.000000e+00 4373.0
3 TraesCS1A01G156200 chr6D 96.626 2638 59 11 862 3486 273429625 273427005 0.000000e+00 4351.0
4 TraesCS1A01G156200 chr6D 93.103 464 22 2 11 474 273430638 273430185 0.000000e+00 671.0
5 TraesCS1A01G156200 chr6D 90.756 119 11 0 917 1035 273430164 273430046 3.600000e-35 159.0
6 TraesCS1A01G156200 chr7A 98.310 1834 14 5 1653 3486 401606928 401608744 0.000000e+00 3199.0
7 TraesCS1A01G156200 chr7A 97.525 808 20 0 853 1660 401605945 401606752 0.000000e+00 1382.0
8 TraesCS1A01G156200 chr7A 94.624 465 19 2 10 474 401605306 401605764 0.000000e+00 715.0
9 TraesCS1A01G156200 chr7A 93.421 76 5 0 11 86 408878081 408878006 2.840000e-21 113.0
10 TraesCS1A01G156200 chr4B 91.604 2001 133 17 1499 3486 294454869 294452891 0.000000e+00 2732.0
11 TraesCS1A01G156200 chr4B 88.430 726 65 9 1117 1836 242922202 242921490 0.000000e+00 857.0
12 TraesCS1A01G156200 chr4B 91.607 560 39 3 2299 2857 410074530 410075082 0.000000e+00 767.0
13 TraesCS1A01G156200 chr4B 86.024 737 68 10 853 1557 294459081 294458348 0.000000e+00 758.0
14 TraesCS1A01G156200 chr4B 88.248 451 49 2 4 452 126087085 126086637 1.420000e-148 536.0
15 TraesCS1A01G156200 chr4B 90.885 373 19 6 1091 1453 410074146 410074513 1.450000e-133 486.0
16 TraesCS1A01G156200 chr7B 91.934 1153 73 9 2299 3436 254251093 254249946 0.000000e+00 1596.0
17 TraesCS1A01G156200 chr7B 91.826 1150 79 4 2299 3436 256085916 256087062 0.000000e+00 1589.0
18 TraesCS1A01G156200 chr7B 90.933 375 19 4 1089 1453 254251479 254251110 1.120000e-134 490.0
19 TraesCS1A01G156200 chr7B 89.894 376 21 4 1089 1454 256085532 256085900 5.270000e-128 468.0
20 TraesCS1A01G156200 chr7B 91.176 204 9 4 3292 3486 264476326 264476529 5.740000e-68 268.0
21 TraesCS1A01G156200 chr1B 91.927 1152 74 10 2299 3436 380312068 380313214 0.000000e+00 1594.0
22 TraesCS1A01G156200 chr1B 91.840 1152 74 8 2299 3436 398649117 398650262 0.000000e+00 1589.0
23 TraesCS1A01G156200 chr1B 91.580 1152 79 10 2299 3436 116769823 116768676 0.000000e+00 1574.0
24 TraesCS1A01G156200 chr1B 89.594 394 34 3 53 446 157456562 157456176 8.690000e-136 494.0
25 TraesCS1A01G156200 chr1B 90.933 375 19 4 1089 1453 380311682 380312051 1.120000e-134 490.0
26 TraesCS1A01G156200 chr1B 89.867 375 23 4 1089 1453 116770209 116769840 5.270000e-128 468.0
27 TraesCS1A01G156200 chr3B 92.171 958 60 8 2299 3241 587004849 587005806 0.000000e+00 1339.0
28 TraesCS1A01G156200 chr3B 88.009 442 52 1 11 452 546151933 546151493 3.990000e-144 521.0
29 TraesCS1A01G156200 chr3B 90.667 375 20 4 1089 1453 587004463 587004832 5.230000e-133 484.0
30 TraesCS1A01G156200 chr3B 88.764 89 10 0 938 1026 627896760 627896672 3.680000e-20 110.0
31 TraesCS1A01G156200 chr3B 90.000 70 7 0 853 922 330781111 330781042 1.330000e-14 91.6
32 TraesCS1A01G156200 chr1D 97.115 520 14 1 853 1371 72468796 72469315 0.000000e+00 876.0
33 TraesCS1A01G156200 chr1D 94.030 469 25 3 7 474 72468167 72468633 0.000000e+00 708.0
34 TraesCS1A01G156200 chrUn 100.000 437 0 0 2027 2463 476060741 476061177 0.000000e+00 808.0
35 TraesCS1A01G156200 chr5D 94.796 442 22 1 11 452 123559019 123559459 0.000000e+00 688.0
36 TraesCS1A01G156200 chr3A 93.228 443 28 2 11 452 330448097 330448538 0.000000e+00 651.0
37 TraesCS1A01G156200 chr3A 89.474 76 8 0 11 86 598354519 598354594 2.860000e-16 97.1
38 TraesCS1A01G156200 chr3D 90.860 372 33 1 75 446 95959945 95960315 6.720000e-137 497.0


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 TraesCS1A01G156200 chr1A 276861985 276865470 3485 True 2871.500000 4865 100.000000 1 3486 2 chr1A.!!$R1 3485
1 TraesCS1A01G156200 chr7D 283701305 283703946 2641 True 4373.000000 4373 96.600000 853 3486 1 chr7D.!!$R1 2633
2 TraesCS1A01G156200 chr6D 273427005 273430638 3633 True 1727.000000 4351 93.495000 11 3486 3 chr6D.!!$R1 3475
3 TraesCS1A01G156200 chr7A 401605306 401608744 3438 False 1765.333333 3199 96.819667 10 3486 3 chr7A.!!$F1 3476
4 TraesCS1A01G156200 chr4B 294452891 294459081 6190 True 1745.000000 2732 88.814000 853 3486 2 chr4B.!!$R3 2633
5 TraesCS1A01G156200 chr4B 242921490 242922202 712 True 857.000000 857 88.430000 1117 1836 1 chr4B.!!$R2 719
6 TraesCS1A01G156200 chr4B 410074146 410075082 936 False 626.500000 767 91.246000 1091 2857 2 chr4B.!!$F1 1766
7 TraesCS1A01G156200 chr7B 254249946 254251479 1533 True 1043.000000 1596 91.433500 1089 3436 2 chr7B.!!$R1 2347
8 TraesCS1A01G156200 chr7B 256085532 256087062 1530 False 1028.500000 1589 90.860000 1089 3436 2 chr7B.!!$F2 2347
9 TraesCS1A01G156200 chr1B 398649117 398650262 1145 False 1589.000000 1589 91.840000 2299 3436 1 chr1B.!!$F1 1137
10 TraesCS1A01G156200 chr1B 380311682 380313214 1532 False 1042.000000 1594 91.430000 1089 3436 2 chr1B.!!$F2 2347
11 TraesCS1A01G156200 chr1B 116768676 116770209 1533 True 1021.000000 1574 90.723500 1089 3436 2 chr1B.!!$R2 2347
12 TraesCS1A01G156200 chr3B 587004463 587005806 1343 False 911.500000 1339 91.419000 1089 3241 2 chr3B.!!$F1 2152
13 TraesCS1A01G156200 chr1D 72468167 72469315 1148 False 792.000000 876 95.572500 7 1371 2 chr1D.!!$F1 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
339 345 0.494095 ACACCTCTCCTTCCTCCCTT 59.506 55.0 0.00 0.0 0.00 3.95 F
1043 1225 0.250234 CTCATCTCCGTGGCTGGAAA 59.750 55.0 0.87 0.0 37.64 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 5690 0.867753 GATGCCGAGTCTGTACTGCG 60.868 60.000 0.0 0.0 35.56 5.18 R
2962 6962 3.146066 ACCAAATACGTGATGCACTTGT 58.854 40.909 0.0 0.0 31.34 3.16 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
40 41 4.772624 ACAATACAGAGACTAGCCAACTCA 59.227 41.667 0.00 0.0 33.69 3.41
72 73 2.103373 CTCCCTCGATCAGTTCCTTCA 58.897 52.381 0.00 0.0 0.00 3.02
103 104 3.117131 TGGATCTGGCCATCTAGAGTGTA 60.117 47.826 5.51 0.0 31.66 2.90
113 114 3.277142 TCTAGAGTGTATGAGCCGTGA 57.723 47.619 0.00 0.0 0.00 4.35
134 135 6.313905 CGTGAGATCTTTACCTGCTGTTAAAT 59.686 38.462 0.00 0.0 0.00 1.40
339 345 0.494095 ACACCTCTCCTTCCTCCCTT 59.506 55.000 0.00 0.0 0.00 3.95
411 417 3.854669 CCGCCGCATCCCTTCTCT 61.855 66.667 0.00 0.0 0.00 3.10
1034 1215 2.556459 CGGATCGGCTCATCTCCGT 61.556 63.158 1.81 0.0 46.49 4.69
1043 1225 0.250234 CTCATCTCCGTGGCTGGAAA 59.750 55.000 0.87 0.0 37.64 3.13
1069 1251 4.643463 TCGATGGTAAGTTTGGCTTGTTA 58.357 39.130 0.00 0.0 38.05 2.41
1175 1379 2.061061 CAGAGGATAAGGCAGGGGAAT 58.939 52.381 0.00 0.0 0.00 3.01
1744 5690 0.525761 TGAGCGCTTATGGTTTTGCC 59.474 50.000 13.26 0.0 37.90 4.52
1854 5803 5.590530 TTAACACAATGTTTTCCTGCAGT 57.409 34.783 13.81 0.0 41.45 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.351017 TCGAGGGAGCATTTTCCAAGT 59.649 47.619 0.00 0.00 39.09 3.16
47 48 2.420687 GGAACTGATCGAGGGAGCATTT 60.421 50.000 0.00 0.00 38.03 2.32
72 73 2.671070 CCAGATCCAACGGCCAGT 59.329 61.111 2.24 0.00 0.00 4.00
103 104 3.034635 AGGTAAAGATCTCACGGCTCAT 58.965 45.455 0.00 0.00 0.00 2.90
113 114 5.817816 CGGATTTAACAGCAGGTAAAGATCT 59.182 40.000 5.54 0.00 0.00 2.75
188 189 3.772387 TCAACCCAGCCAATAAACATGA 58.228 40.909 0.00 0.00 0.00 3.07
190 191 3.381272 CGATCAACCCAGCCAATAAACAT 59.619 43.478 0.00 0.00 0.00 2.71
301 307 4.715523 GCGGCTAGGGTTGGTGCA 62.716 66.667 0.00 0.00 0.00 4.57
411 417 0.340208 GAGGAAGGAGGAGGAAGGGA 59.660 60.000 0.00 0.00 0.00 4.20
936 1114 1.298014 CTCCTTCTGCGGCTTCCTT 59.702 57.895 0.00 0.00 0.00 3.36
974 1152 0.325110 CTCTCCTCCTTCTCTGGCCA 60.325 60.000 4.71 4.71 0.00 5.36
1027 1208 1.604378 CCTTTCCAGCCACGGAGAT 59.396 57.895 0.00 0.00 36.12 2.75
1034 1215 1.078214 CATCGAGCCTTTCCAGCCA 60.078 57.895 0.00 0.00 0.00 4.75
1043 1225 1.679032 GCCAAACTTACCATCGAGCCT 60.679 52.381 0.00 0.00 0.00 4.58
1069 1251 1.549620 CAGGGCTCGCTGAGATATGAT 59.450 52.381 8.06 0.00 0.00 2.45
1175 1379 1.352083 AGAGCAAGCAGGTTCACCTA 58.648 50.000 0.00 0.00 46.65 3.08
1744 5690 0.867753 GATGCCGAGTCTGTACTGCG 60.868 60.000 0.00 0.00 35.56 5.18
2958 6958 5.334491 CCAAATACGTGATGCACTTGTTACA 60.334 40.000 0.00 0.00 31.34 2.41
2962 6962 3.146066 ACCAAATACGTGATGCACTTGT 58.854 40.909 0.00 0.00 31.34 3.16
3310 7314 7.971183 AGAGTTCAGATAGTTTCCTCAAAAC 57.029 36.000 0.00 0.00 46.36 2.43
3315 7319 7.033185 GTCAGAAGAGTTCAGATAGTTTCCTC 58.967 42.308 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.