Multiple sequence alignment - TraesCS1D01G064300

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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 TraesCS1D01G064300 chr1D 100.000 3464 0 0 1 3464 45081090 45077627 0.000000e+00 6397
1 TraesCS1D01G064300 chr1D 96.566 3465 117 2 1 3464 45115027 45111564 0.000000e+00 5738
2 TraesCS1D01G064300 chr1D 96.837 2624 76 3 848 3464 44971199 44968576 0.000000e+00 4379
3 TraesCS1D01G064300 chr1D 95.626 823 28 5 1 816 44972022 44971201 0.000000e+00 1314
4 TraesCS1D01G064300 chr1D 84.509 794 111 10 578 1364 45078260 45079048 0.000000e+00 774
5 TraesCS1D01G064300 chr1D 84.509 794 111 10 2043 2831 45079727 45080513 0.000000e+00 774
6 TraesCS1D01G064300 chr1D 84.733 655 68 12 2820 3464 44973288 44973920 8.160000e-176 627
7 TraesCS1D01G064300 chr1D 82.353 391 62 4 1562 1945 74928562 74928172 1.990000e-87 333
8 TraesCS1D01G064300 chr1B 90.227 1412 125 12 2058 3464 64289248 64287845 0.000000e+00 1831
9 TraesCS1D01G064300 chr1B 89.796 1421 133 11 2048 3464 64018298 64016886 0.000000e+00 1810
10 TraesCS1D01G064300 chr1B 89.873 1412 133 8 2057 3464 64826087 64824682 0.000000e+00 1807
11 TraesCS1D01G064300 chr1B 89.023 1412 140 13 2056 3464 64902639 64901240 0.000000e+00 1735
12 TraesCS1D01G064300 chr1B 88.565 1408 137 13 2061 3464 64929444 64928057 0.000000e+00 1687
13 TraesCS1D01G064300 chr1B 90.777 965 77 9 403 1359 64019259 64018299 0.000000e+00 1279
14 TraesCS1D01G064300 chr1B 89.811 952 84 10 403 1345 64930409 64929462 0.000000e+00 1208
15 TraesCS1D01G064300 chr1B 89.119 965 95 7 403 1359 64290221 64289259 0.000000e+00 1192
16 TraesCS1D01G064300 chr1B 89.004 964 94 8 403 1357 64903600 64902640 0.000000e+00 1182
17 TraesCS1D01G064300 chr1B 88.935 958 93 9 403 1352 64153592 64152640 0.000000e+00 1170
18 TraesCS1D01G064300 chr1B 89.451 929 88 8 403 1323 64827041 64826115 0.000000e+00 1164
19 TraesCS1D01G064300 chr1B 91.816 782 57 7 2687 3464 64152058 64151280 0.000000e+00 1083
20 TraesCS1D01G064300 chr1B 85.115 786 110 6 2048 2831 64018299 64019079 0.000000e+00 797
21 TraesCS1D01G064300 chr1B 79.108 919 149 28 1060 1945 118488701 118487793 8.280000e-166 593
22 TraesCS1D01G064300 chr1B 91.605 405 23 3 1 405 64828795 64828402 1.820000e-152 549
23 TraesCS1D01G064300 chr1B 90.819 403 28 2 3 405 64932327 64931934 6.580000e-147 531
24 TraesCS1D01G064300 chr1B 89.901 406 31 3 1 405 64905317 64904921 6.630000e-142 514
25 TraesCS1D01G064300 chr1B 89.542 153 8 2 253 405 64155282 64155138 1.640000e-43 187
26 TraesCS1D01G064300 chr1B 89.542 153 8 2 253 405 64291901 64291757 1.640000e-43 187
27 TraesCS1D01G064300 chr1B 88.889 153 9 2 253 405 64020765 64020621 7.640000e-42 182
28 TraesCS1D01G064300 chr3D 80.705 1135 157 31 847 1945 93175981 93177089 0.000000e+00 826
29 TraesCS1D01G064300 chr3B 77.796 617 84 22 1360 1945 143175482 143174888 7.170000e-87 331


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 TraesCS1D01G064300 chr1D 45077627 45081090 3463 True 6397.000000 6397 100.000000 1 3464 1 chr1D.!!$R1 3463
1 TraesCS1D01G064300 chr1D 45111564 45115027 3463 True 5738.000000 5738 96.566000 1 3464 1 chr1D.!!$R2 3463
2 TraesCS1D01G064300 chr1D 44968576 44972022 3446 True 2846.500000 4379 96.231500 1 3464 2 chr1D.!!$R4 3463
3 TraesCS1D01G064300 chr1D 45078260 45080513 2253 False 774.000000 774 84.509000 578 2831 2 chr1D.!!$F2 2253
4 TraesCS1D01G064300 chr1D 44973288 44973920 632 False 627.000000 627 84.733000 2820 3464 1 chr1D.!!$F1 644
5 TraesCS1D01G064300 chr1B 64824682 64828795 4113 True 1173.333333 1807 90.309667 1 3464 3 chr1B.!!$R5 3463
6 TraesCS1D01G064300 chr1B 64901240 64905317 4077 True 1143.666667 1735 89.309333 1 3464 3 chr1B.!!$R6 3463
7 TraesCS1D01G064300 chr1B 64928057 64932327 4270 True 1142.000000 1687 89.731667 3 3464 3 chr1B.!!$R7 3461
8 TraesCS1D01G064300 chr1B 64016886 64020765 3879 True 1090.333333 1810 89.820667 253 3464 3 chr1B.!!$R2 3211
9 TraesCS1D01G064300 chr1B 64287845 64291901 4056 True 1070.000000 1831 89.629333 253 3464 3 chr1B.!!$R4 3211
10 TraesCS1D01G064300 chr1B 64151280 64155282 4002 True 813.333333 1170 90.097667 253 3464 3 chr1B.!!$R3 3211
11 TraesCS1D01G064300 chr1B 64018299 64019079 780 False 797.000000 797 85.115000 2048 2831 1 chr1B.!!$F1 783
12 TraesCS1D01G064300 chr1B 118487793 118488701 908 True 593.000000 593 79.108000 1060 1945 1 chr1B.!!$R1 885
13 TraesCS1D01G064300 chr3D 93175981 93177089 1108 False 826.000000 826 80.705000 847 1945 1 chr3D.!!$F1 1098
14 TraesCS1D01G064300 chr3B 143174888 143175482 594 True 331.000000 331 77.796000 1360 1945 1 chr3B.!!$R1 585

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
446 2373 0.472734 AGAAGGCAGGTGGACAGTCT 60.473 55.000 0.00 0.0 0.0 3.24 F
1295 3236 1.078426 GTCATACAAGTGGGCGGCT 60.078 57.895 9.56 0.0 0.0 5.52 F
1783 4298 1.341209 AGCGCGATAAGGACATCATCA 59.659 47.619 12.10 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1463 3524 0.318441 CCGTGGCATCCGAGTCATAT 59.682 55.000 0.00 0.00 0.00 1.78 R
2283 4811 0.872388 CAAGTACCACAACGGCTTCC 59.128 55.000 0.00 0.00 39.03 3.46 R
3282 5826 2.485426 CCGAGTTGAGCAACATGATGTT 59.515 45.455 14.99 4.72 42.08 2.71 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
141 142 2.949451 AGCCTGAATAGAGACACACG 57.051 50.000 0.00 0.00 0.00 4.49
300 302 2.930019 TCCCACCTGCAGACCTGG 60.930 66.667 17.39 15.80 38.43 4.45
353 355 0.698818 TTTTTCTGGGGGAGAGAGGC 59.301 55.000 0.00 0.00 30.18 4.70
396 398 1.074926 GGGAGGGAGAGAGGCATCA 60.075 63.158 0.00 0.00 0.00 3.07
446 2373 0.472734 AGAAGGCAGGTGGACAGTCT 60.473 55.000 0.00 0.00 0.00 3.24
573 2501 7.570982 TCAAGATAAATAGATTAGTGGGGGTGA 59.429 37.037 0.00 0.00 0.00 4.02
691 2625 2.036475 GCGTCCTGTCCATCTATGTGAT 59.964 50.000 0.00 0.00 35.40 3.06
1295 3236 1.078426 GTCATACAAGTGGGCGGCT 60.078 57.895 9.56 0.00 0.00 5.52
1463 3524 2.577059 GACTCGGATGGCACGGAA 59.423 61.111 0.00 0.00 0.00 4.30
1499 4014 1.792941 GGAGTACGACGACGAGCTT 59.207 57.895 15.32 0.00 42.66 3.74
1543 4058 1.757118 CACCTGTGTATCCTCCGACAT 59.243 52.381 0.00 0.00 0.00 3.06
1783 4298 1.341209 AGCGCGATAAGGACATCATCA 59.659 47.619 12.10 0.00 0.00 3.07
1824 4339 2.301870 TGGCATCAGTAAGGACGTCTTT 59.698 45.455 17.55 17.55 36.93 2.52
2283 4811 0.689623 ACCTGCCTCACCTTCTTGAG 59.310 55.000 0.00 0.00 42.46 3.02
2331 4859 1.228033 TCTCCGTGGTGTCACTCGA 60.228 57.895 17.62 0.00 41.53 4.04
2418 4946 7.521871 GAGGAAAACTCGTAAGGATAGGATA 57.478 40.000 0.00 0.00 36.29 2.59
2759 5289 2.353406 GCGTGTAGACCACCATTGTACT 60.353 50.000 0.00 0.00 41.26 2.73
3069 5612 1.103803 AGCTATTCTCGACGAGGCAA 58.896 50.000 23.92 12.73 0.00 4.52
3282 5826 1.200519 ATAGCTAAGCCAACCACCGA 58.799 50.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 2.522193 CTAGTCCTCCCCTCCCGC 60.522 72.222 0.00 0.00 0.00 6.13
198 199 9.765795 CGGTTCTCTAAAATTCTCTATGGTATT 57.234 33.333 0.00 0.00 0.00 1.89
300 302 0.674895 CTCCTTGGCTACAGGTGCAC 60.675 60.000 8.80 8.80 0.00 4.57
353 355 4.408694 GGAAATAAACACAAACCGATCGG 58.591 43.478 32.20 32.20 42.03 4.18
396 398 3.443681 CCACTTTCCAGCCATAAATCGTT 59.556 43.478 0.00 0.00 0.00 3.85
446 2373 3.814625 TCAGTTACCAATGTGCAGAACA 58.185 40.909 0.00 0.00 44.79 3.18
691 2625 1.039856 GCTTTTTGCAGGGGTCTTCA 58.960 50.000 0.00 0.00 42.31 3.02
932 2873 4.489810 AGAGCAACAATGACTCTAACGAG 58.510 43.478 0.00 0.00 43.10 4.18
1302 3243 0.821711 TGGTGCAAGTTGTAGTGGCC 60.822 55.000 4.48 0.00 0.00 5.36
1463 3524 0.318441 CCGTGGCATCCGAGTCATAT 59.682 55.000 0.00 0.00 0.00 1.78
1499 4014 1.229051 TGATGTGGTGGGGAGACGA 60.229 57.895 0.00 0.00 0.00 4.20
1543 4058 1.596203 GCAGCTGCTATGCCATCGA 60.596 57.895 31.33 0.00 37.73 3.59
1690 4205 4.418359 TGGTAGGTAGTGAACATGGTGTA 58.582 43.478 0.00 0.00 0.00 2.90
1691 4206 3.244582 TGGTAGGTAGTGAACATGGTGT 58.755 45.455 0.00 0.00 0.00 4.16
1783 4298 0.322816 ATGTCATGGCACCTCGCTTT 60.323 50.000 0.00 0.00 41.91 3.51
1824 4339 1.429930 TGTTGTGCCTCCAGTTCCTA 58.570 50.000 0.00 0.00 0.00 2.94
2283 4811 0.872388 CAAGTACCACAACGGCTTCC 59.128 55.000 0.00 0.00 39.03 3.46
2331 4859 6.775629 ACACAAGTGGGTAATATTTGTCAAGT 59.224 34.615 5.08 0.00 30.15 3.16
2418 4946 6.464222 TCTAACCTCACAGATTTCGTTTCAT 58.536 36.000 0.00 0.00 0.00 2.57
3069 5612 3.823873 TGTTGCGTTAGTGGGATTTGATT 59.176 39.130 0.00 0.00 0.00 2.57
3282 5826 2.485426 CCGAGTTGAGCAACATGATGTT 59.515 45.455 14.99 4.72 42.08 2.71


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

AutoCloner maintained by Alex Coulton.