Multiple sequence alignment - TraesCS5D01G021500

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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 TraesCS5D01G021500 chr5D 100.000 3283 0 0 1 3283 14029514 14032796 0.000000e+00 6063
1 TraesCS5D01G021500 chr5D 92.410 1199 70 9 1923 3105 127938812 127937619 0.000000e+00 1690
2 TraesCS5D01G021500 chr5D 92.447 331 24 1 943 1273 127939137 127938808 3.830000e-129 472
3 TraesCS5D01G021500 chr6D 97.541 3091 53 5 140 3213 13476080 13479164 0.000000e+00 5265
4 TraesCS5D01G021500 chr6D 92.327 1199 71 9 1923 3105 450188148 450186955 0.000000e+00 1685
5 TraesCS5D01G021500 chr6D 92.447 331 24 1 943 1273 450188473 450188144 3.830000e-129 472
6 TraesCS5D01G021500 chr6D 97.887 142 2 1 1 141 13475609 13475750 9.100000e-61 244
7 TraesCS5D01G021500 chr6D 91.489 141 10 2 3 141 450189767 450189627 3.340000e-45 193
8 TraesCS5D01G021500 chr1D 97.495 3074 69 4 140 3213 62894029 62897094 0.000000e+00 5243
9 TraesCS5D01G021500 chr1D 89.959 488 38 6 152 638 60174425 60173948 1.290000e-173 619
10 TraesCS5D01G021500 chr1D 83.485 660 62 26 1275 1922 37568514 37569138 3.680000e-159 571
11 TraesCS5D01G021500 chr1D 85.538 325 28 9 634 939 60173722 60173398 4.090000e-84 322
12 TraesCS5D01G021500 chr1D 94.309 123 7 0 3097 3219 415598994 415599116 4.320000e-44 189
13 TraesCS5D01G021500 chr1D 96.000 75 2 1 3209 3283 62899354 62899427 1.600000e-23 121
14 TraesCS5D01G021500 chr2D 92.876 1909 76 12 1207 3099 518814 520678 0.000000e+00 2717
15 TraesCS5D01G021500 chr2D 94.825 715 33 3 1207 1917 23116197 23115483 0.000000e+00 1112
16 TraesCS5D01G021500 chr2D 92.470 332 24 1 943 1273 29095570 29095239 1.070000e-129 473
17 TraesCS5D01G021500 chr2D 94.352 301 12 2 147 447 518523 518818 1.070000e-124 457
18 TraesCS5D01G021500 chr2D 93.464 306 15 2 143 447 23116494 23116193 1.800000e-122 449
19 TraesCS5D01G021500 chr2D 95.000 140 6 1 1 139 23116966 23116827 5.520000e-53 219
20 TraesCS5D01G021500 chr2D 94.366 142 7 1 1 141 518044 518185 1.980000e-52 217
21 TraesCS5D01G021500 chr2D 95.935 123 5 0 3097 3219 520736 520858 2.000000e-47 200
22 TraesCS5D01G021500 chr2D 95.935 123 5 0 3097 3219 23114321 23114199 2.000000e-47 200
23 TraesCS5D01G021500 chr5A 97.220 1187 31 2 1614 2800 689190312 689189128 0.000000e+00 2008
24 TraesCS5D01G021500 chr5A 97.051 1187 34 1 1614 2800 707255988 707257173 0.000000e+00 1997
25 TraesCS5D01G021500 chr5A 97.447 666 13 3 140 803 707255321 707255984 0.000000e+00 1133
26 TraesCS5D01G021500 chr5A 97.436 663 14 2 143 803 689190977 689190316 0.000000e+00 1127
27 TraesCS5D01G021500 chr5A 93.570 591 31 5 1207 1791 3948524 3947935 0.000000e+00 874
28 TraesCS5D01G021500 chr5A 96.479 142 4 1 1 141 689191646 689191505 1.970000e-57 233
29 TraesCS5D01G021500 chr5A 96.479 142 4 1 1 141 707254849 707254990 1.970000e-57 233
30 TraesCS5D01G021500 chr5A 96.581 117 4 0 3103 3219 3942830 3942714 9.290000e-46 195
31 TraesCS5D01G021500 chr5A 95.833 72 3 0 3212 3283 707259253 707259324 2.070000e-22 117
32 TraesCS5D01G021500 chr6A 97.051 1187 34 1 1614 2800 540806189 540805004 0.000000e+00 1997
33 TraesCS5D01G021500 chr6A 96.546 1187 40 1 1614 2800 589345936 589347121 0.000000e+00 1964
34 TraesCS5D01G021500 chr6A 97.420 659 12 3 147 803 589345277 589345932 0.000000e+00 1118
35 TraesCS5D01G021500 chr6A 95.974 621 22 2 143 761 540817943 540817324 0.000000e+00 1005
36 TraesCS5D01G021500 chr6A 96.479 142 4 1 1 141 589344542 589344683 1.970000e-57 233
37 TraesCS5D01G021500 chr6A 95.775 142 5 1 1 141 540818418 540818277 9.160000e-56 228
38 TraesCS5D01G021500 chr6A 97.222 72 2 0 3212 3283 540802909 540802838 4.450000e-24 122
39 TraesCS5D01G021500 chr4A 96.462 1187 41 1 1614 2800 637544917 637546102 0.000000e+00 1958
40 TraesCS5D01G021500 chr4A 97.278 551 9 5 255 803 637544367 637544913 0.000000e+00 929
41 TraesCS5D01G021500 chr4A 94.667 75 3 1 3209 3283 637548194 637548267 7.440000e-22 115
42 TraesCS5D01G021500 chr2A 87.886 809 59 14 153 939 3758532 3759323 0.000000e+00 915
43 TraesCS5D01G021500 chr3B 92.086 417 32 1 943 1358 775658635 775658219 1.310000e-163 586
44 TraesCS5D01G021500 chr3B 95.070 142 6 1 1 141 775659967 775659826 4.260000e-54 222
45 TraesCS5D01G021500 chr1B 91.148 418 35 1 943 1358 289694130 289694547 1.710000e-157 566
46 TraesCS5D01G021500 chr1B 81.623 653 51 27 1280 1922 57499162 57499755 8.240000e-131 477
47 TraesCS5D01G021500 chr2B 87.225 454 44 12 435 886 62444612 62445053 3.780000e-139 505
48 TraesCS5D01G021500 chr7D 92.145 331 25 1 943 1273 530740077 530739748 1.780000e-127 466
49 TraesCS5D01G021500 chr7D 97.561 123 3 0 3097 3219 449501613 449501491 9.230000e-51 211
50 TraesCS5D01G021500 chr7D 95.935 123 4 1 3097 3219 621799234 621799355 7.190000e-47 198
51 TraesCS5D01G021500 chr4D 91.892 333 25 2 943 1273 85851013 85850681 6.420000e-127 464
52 TraesCS5D01G021500 chr1A 91.765 170 13 1 1305 1473 36778741 36778910 5.480000e-58 235
53 TraesCS5D01G021500 chr1A 81.696 224 18 5 1458 1679 36779014 36779216 7.290000e-37 165
54 TraesCS5D01G021500 chr3D 95.122 123 5 1 3097 3219 583598195 583598316 3.340000e-45 193


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 TraesCS5D01G021500 chr5D 14029514 14032796 3282 False 6063.000000 6063 100.000000 1 3283 1 chr5D.!!$F1 3282
1 TraesCS5D01G021500 chr5D 127937619 127939137 1518 True 1081.000000 1690 92.428500 943 3105 2 chr5D.!!$R1 2162
2 TraesCS5D01G021500 chr6D 13475609 13479164 3555 False 2754.500000 5265 97.714000 1 3213 2 chr6D.!!$F1 3212
3 TraesCS5D01G021500 chr6D 450186955 450189767 2812 True 783.333333 1685 92.087667 3 3105 3 chr6D.!!$R1 3102
4 TraesCS5D01G021500 chr1D 62894029 62899427 5398 False 2682.000000 5243 96.747500 140 3283 2 chr1D.!!$F3 3143
5 TraesCS5D01G021500 chr1D 37568514 37569138 624 False 571.000000 571 83.485000 1275 1922 1 chr1D.!!$F1 647
6 TraesCS5D01G021500 chr1D 60173398 60174425 1027 True 470.500000 619 87.748500 152 939 2 chr1D.!!$R1 787
7 TraesCS5D01G021500 chr2D 518044 520858 2814 False 897.750000 2717 94.382250 1 3219 4 chr2D.!!$F1 3218
8 TraesCS5D01G021500 chr2D 23114199 23116966 2767 True 495.000000 1112 94.806000 1 3219 4 chr2D.!!$R2 3218
9 TraesCS5D01G021500 chr5A 689189128 689191646 2518 True 1122.666667 2008 97.045000 1 2800 3 chr5A.!!$R3 2799
10 TraesCS5D01G021500 chr5A 3947935 3948524 589 True 874.000000 874 93.570000 1207 1791 1 chr5A.!!$R2 584
11 TraesCS5D01G021500 chr5A 707254849 707259324 4475 False 870.000000 1997 96.702500 1 3283 4 chr5A.!!$F1 3282
12 TraesCS5D01G021500 chr6A 589344542 589347121 2579 False 1105.000000 1964 96.815000 1 2800 3 chr6A.!!$F1 2799
13 TraesCS5D01G021500 chr6A 540802838 540806189 3351 True 1059.500000 1997 97.136500 1614 3283 2 chr6A.!!$R1 1669
14 TraesCS5D01G021500 chr6A 540817324 540818418 1094 True 616.500000 1005 95.874500 1 761 2 chr6A.!!$R2 760
15 TraesCS5D01G021500 chr4A 637544367 637548267 3900 False 1000.666667 1958 96.135667 255 3283 3 chr4A.!!$F1 3028
16 TraesCS5D01G021500 chr2A 3758532 3759323 791 False 915.000000 915 87.886000 153 939 1 chr2A.!!$F1 786
17 TraesCS5D01G021500 chr3B 775658219 775659967 1748 True 404.000000 586 93.578000 1 1358 2 chr3B.!!$R1 1357
18 TraesCS5D01G021500 chr1B 57499162 57499755 593 False 477.000000 477 81.623000 1280 1922 1 chr1B.!!$F1 642

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
501 2021 0.320073 TTCGGTCACGCTTACCTTGG 60.32 55.0 0.0 0.0 40.69 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 4946 2.024588 CAACGCGTGCAAAGCAGT 59.975 55.556 14.98 10.42 43.29 4.4 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
55 57 0.464036 CCCAACGCCTGCATCTAGTA 59.536 55.000 0.00 0.00 0.00 1.82
221 1019 3.349927 CTGATGGCAAGAACCTTCATGA 58.650 45.455 0.00 0.00 41.52 3.07
306 1106 5.475273 AACGCATGTTCTCATACATCAAG 57.525 39.130 0.00 0.00 36.64 3.02
501 2021 0.320073 TTCGGTCACGCTTACCTTGG 60.320 55.000 0.00 0.00 40.69 3.61
862 3089 8.939201 TTCACAGCATCATTTTTAGTCAAAAA 57.061 26.923 0.00 0.00 45.22 1.94
1051 3563 4.415332 GCTTCGACGGAGGCGACA 62.415 66.667 5.06 0.00 35.44 4.35
1103 3615 2.678580 TGACGTGCTCATCCCGGA 60.679 61.111 0.73 0.00 0.00 5.14
1384 3908 0.598065 ACCGCTGTTTGATTGGCTTC 59.402 50.000 0.00 0.00 0.00 3.86
1579 4105 3.063510 TCAGTAGCATGCAAAGCTTCT 57.936 42.857 21.98 17.35 43.25 2.85
1719 4251 3.877559 TCTGTCTGGCCACATTTATCTG 58.122 45.455 0.00 0.00 0.00 2.90
1752 4284 2.507484 TGCACCATCTTCTGAACTTGG 58.493 47.619 10.74 10.74 0.00 3.61
2262 4819 3.076258 TACATGACCCGCGCCTCAG 62.076 63.158 0.00 0.42 0.00 3.35
2391 4948 9.905713 TGCCTACTTTATATGAATTTCTTGACT 57.094 29.630 0.00 0.00 0.00 3.41
2639 5202 4.962995 TGTTAGAGTAAAGCTAGCTGGGAT 59.037 41.667 20.16 7.88 0.00 3.85
2724 5287 3.308866 GCTCCATGTATCGCGTTAGTTTT 59.691 43.478 5.77 0.00 0.00 2.43
3077 6767 9.131791 GCTATGATTTTTCTTCCCTAATTACCA 57.868 33.333 0.00 0.00 0.00 3.25
3253 9268 4.103357 AGATACGCGTGTGATAAGTGTTC 58.897 43.478 24.59 0.00 33.56 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 2.889045 TGCAGTGTAGTTAAGGTCGACT 59.111 45.455 16.46 0.00 0.00 4.18
166 961 0.534427 CATCATCATCAGCCGCCACT 60.534 55.000 0.00 0.00 0.00 4.00
221 1019 5.996513 GCAGACATATGAGATCAGATGGTTT 59.003 40.000 18.69 1.50 46.58 3.27
306 1106 7.674471 AAGCGGCTTCCTATATTTATTCTTC 57.326 36.000 9.94 0.00 0.00 2.87
457 1977 7.972301 AGATTCAGAAAGAAAAGAGAGAAGGA 58.028 34.615 0.00 0.00 40.22 3.36
501 2021 1.202604 TCAGTTTGTCTGACGGTTCCC 60.203 52.381 2.98 0.00 46.77 3.97
862 3089 9.842775 ACTATTGTGATGATGTCAGACATTATT 57.157 29.630 19.14 8.06 39.27 1.40
1021 3533 1.153568 CGAAGCCCTTGATCTCGCA 60.154 57.895 0.00 0.00 0.00 5.10
1025 3537 0.970937 TCCGTCGAAGCCCTTGATCT 60.971 55.000 0.00 0.00 0.00 2.75
1051 3563 1.215647 GCAAGATCAGGTCGACGGT 59.784 57.895 9.92 0.00 0.00 4.83
1103 3615 2.856760 TATGACTCCTCCCAGAGCTT 57.143 50.000 0.00 0.00 37.39 3.74
1243 3759 9.902196 AATCGAACGGACTTTTTATTAACAAAT 57.098 25.926 0.00 0.00 0.00 2.32
1384 3908 2.031516 CCTGCCTTCTCACACTGCG 61.032 63.158 0.00 0.00 0.00 5.18
1719 4251 3.881688 AGATGGTGCATTCTGAATACTGC 59.118 43.478 1.98 5.10 35.21 4.40
1776 4309 6.350027 CCATGTTAATTAATGTGTGGACTGCA 60.350 38.462 0.31 0.00 0.00 4.41
1899 4434 9.458374 AAAAACTGAAGATAAACGGTACAATTG 57.542 29.630 3.24 3.24 0.00 2.32
2294 4851 8.779303 CATAATTACTGTCCATTTTATACGGCA 58.221 33.333 0.00 0.00 0.00 5.69
2389 4946 2.024588 CAACGCGTGCAAAGCAGT 59.975 55.556 14.98 10.42 43.29 4.40
2415 4972 3.520691 ATGGCTGAGGCATGATAATGT 57.479 42.857 21.37 0.00 46.89 2.71
2639 5202 5.931294 TGGGTAACAATACTGAAACAGACA 58.069 37.500 5.76 0.00 34.66 3.41
2724 5287 1.136500 TGCAGCTTGTGTTTTGCATCA 59.864 42.857 0.00 0.00 41.23 3.07
2878 5873 1.335145 AAAATTCAGGCTGCAGCACT 58.665 45.000 37.63 28.18 44.36 4.40
3034 6724 9.445878 AAATCATAGCATATAGAACACATGAGG 57.554 33.333 0.00 0.00 0.00 3.86
3068 6758 3.213206 TGGCTGAGGCATGGTAATTAG 57.787 47.619 3.93 0.00 40.87 1.73
3253 9268 5.276270 CAATTTTTGGCTCGTAGATGGATG 58.724 41.667 0.00 0.00 33.89 3.51


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

AutoCloner maintained by Alex Coulton.