Multiple sequence alignment - TraesCS2D01G118900

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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 TraesCS2D01G118900 chr2D 100.000 2267 0 0 1 2267 68565421 68567687 0.000000e+00 4187
1 TraesCS2D01G118900 chr2D 96.088 2275 69 7 3 2261 68589001 68591271 0.000000e+00 3690
2 TraesCS2D01G118900 chr2D 92.822 1825 95 14 3 1813 68626494 68628296 0.000000e+00 2612
3 TraesCS2D01G118900 chr2D 94.744 1465 56 11 637 2087 68658302 68659759 0.000000e+00 2259
4 TraesCS2D01G118900 chr2D 89.309 1534 113 24 657 2161 68672364 68673875 0.000000e+00 1877
5 TraesCS2D01G118900 chr2D 94.410 1145 44 9 637 1768 68692842 68693979 0.000000e+00 1742
6 TraesCS2D01G118900 chr2D 89.552 469 31 10 9 460 86472122 86471655 1.800000e-161 579
7 TraesCS2D01G118900 chr2D 100.000 210 0 0 2493 2702 68567913 68568122 3.260000e-104 388
8 TraesCS2D01G118900 chr2D 98.571 210 2 1 2493 2702 68591534 68591742 1.180000e-98 370
9 TraesCS2D01G118900 chr2A 89.593 1547 84 28 654 2161 66375666 66374158 0.000000e+00 1893
10 TraesCS2D01G118900 chr2A 88.781 1551 95 34 654 2161 66481373 66479859 0.000000e+00 1827
11 TraesCS2D01G118900 chr2A 88.638 1549 91 40 654 2161 66332129 66330625 0.000000e+00 1807
12 TraesCS2D01G118900 chr2A 87.969 1546 94 39 654 2161 66459763 66458272 0.000000e+00 1740
13 TraesCS2D01G118900 chr2A 86.672 1193 74 31 1115 2259 66522983 66521828 0.000000e+00 1243
14 TraesCS2D01G118900 chr2A 91.466 457 26 7 654 1102 66523676 66523225 1.370000e-172 616
15 TraesCS2D01G118900 chr2A 97.000 100 3 0 2160 2259 66330587 66330488 4.630000e-38 169
16 TraesCS2D01G118900 chr2A 96.939 98 3 0 2162 2259 66479819 66479722 5.980000e-37 165
17 TraesCS2D01G118900 chr2A 96.000 100 4 0 2160 2259 66458235 66458136 2.150000e-36 163
18 TraesCS2D01G118900 chr2A 94.000 100 5 1 2160 2259 66374121 66374023 1.680000e-32 150
19 TraesCS2D01G118900 chr7B 86.985 461 41 8 18 464 418330526 418330981 4.020000e-138 501
20 TraesCS2D01G118900 chr7B 89.091 165 14 3 2538 2699 726381261 726381424 4.560000e-48 202
21 TraesCS2D01G118900 chr7B 88.623 167 15 3 2538 2701 726376054 726376219 1.640000e-47 200
22 TraesCS2D01G118900 chr7B 88.485 165 15 3 2540 2701 726372559 726372722 2.120000e-46 196
23 TraesCS2D01G118900 chr5B 86.538 416 33 9 59 460 144798230 144798636 1.150000e-118 436
24 TraesCS2D01G118900 chr1A 84.722 432 52 6 42 463 62025981 62025554 1.160000e-113 420
25 TraesCS2D01G118900 chr1A 86.851 289 31 2 186 468 24366465 24366178 1.560000e-82 316
26 TraesCS2D01G118900 chr3D 84.977 426 48 9 45 463 148879555 148879139 4.160000e-113 418
27 TraesCS2D01G118900 chr6A 85.163 337 28 8 130 460 613284992 613285312 2.590000e-85 326
28 TraesCS2D01G118900 chr4A 91.667 168 12 2 2535 2701 603723147 603723313 5.820000e-57 231
29 TraesCS2D01G118900 chr4D 85.714 217 21 9 2493 2701 120834750 120834964 1.260000e-53 220
30 TraesCS2D01G118900 chrUn 88.623 167 15 3 2538 2701 461900758 461900593 1.640000e-47 200
31 TraesCS2D01G118900 chr3A 88.961 154 16 1 2548 2701 265171680 265171528 3.550000e-44 189
32 TraesCS2D01G118900 chr6B 86.550 171 18 5 2535 2701 171210219 171210050 1.650000e-42 183


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 TraesCS2D01G118900 chr2D 68565421 68568122 2701 False 2287.5 4187 100.0000 1 2702 2 chr2D.!!$F5 2701
1 TraesCS2D01G118900 chr2D 68626494 68628296 1802 False 2612.0 2612 92.8220 3 1813 1 chr2D.!!$F1 1810
2 TraesCS2D01G118900 chr2D 68658302 68659759 1457 False 2259.0 2259 94.7440 637 2087 1 chr2D.!!$F2 1450
3 TraesCS2D01G118900 chr2D 68589001 68591742 2741 False 2030.0 3690 97.3295 3 2702 2 chr2D.!!$F6 2699
4 TraesCS2D01G118900 chr2D 68672364 68673875 1511 False 1877.0 1877 89.3090 657 2161 1 chr2D.!!$F3 1504
5 TraesCS2D01G118900 chr2D 68692842 68693979 1137 False 1742.0 1742 94.4100 637 1768 1 chr2D.!!$F4 1131
6 TraesCS2D01G118900 chr2A 66374023 66375666 1643 True 1021.5 1893 91.7965 654 2259 2 chr2A.!!$R2 1605
7 TraesCS2D01G118900 chr2A 66479722 66481373 1651 True 996.0 1827 92.8600 654 2259 2 chr2A.!!$R4 1605
8 TraesCS2D01G118900 chr2A 66330488 66332129 1641 True 988.0 1807 92.8190 654 2259 2 chr2A.!!$R1 1605
9 TraesCS2D01G118900 chr2A 66458136 66459763 1627 True 951.5 1740 91.9845 654 2259 2 chr2A.!!$R3 1605
10 TraesCS2D01G118900 chr2A 66521828 66523676 1848 True 929.5 1243 89.0690 654 2259 2 chr2A.!!$R5 1605

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
289 298 0.176680 AAGCTAGCTGACCATGGACG 59.823 55.0 20.16 10.06 0.00 4.79 F
1483 1767 0.038526 GACGACAGCCGGAAAAGAGA 60.039 55.0 5.05 0.00 43.93 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1905 0.245813 GGGAACTGTCCGTGGTAGAC 59.754 60.000 1.09 0.0 46.04 2.59 R
2644 3038 4.777896 TGCAGGTAGAGATAAACCAAGAGT 59.222 41.667 0.00 0.0 0.00 3.24 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
122 123 1.615883 GCTCGCTCCTAGATGGATTCA 59.384 52.381 0.00 0.00 45.16 2.57
217 226 6.293004 GCTAGTTAGCTAATGGATGGATCT 57.707 41.667 9.88 1.26 45.62 2.75
225 234 0.250640 ATGGATGGATCTTGCGGCTC 60.251 55.000 0.00 0.00 0.00 4.70
227 236 1.599240 GATGGATCTTGCGGCTCCC 60.599 63.158 0.00 0.00 0.00 4.30
289 298 0.176680 AAGCTAGCTGACCATGGACG 59.823 55.000 20.16 10.06 0.00 4.79
306 316 0.381089 ACGCGGACGAGAGGAATAAG 59.619 55.000 12.47 0.00 43.93 1.73
312 322 3.878103 CGGACGAGAGGAATAAGAAGAGA 59.122 47.826 0.00 0.00 0.00 3.10
317 327 4.021544 CGAGAGGAATAAGAAGAGATGGGG 60.022 50.000 0.00 0.00 0.00 4.96
381 397 1.335496 GTTCTGCCGCAGTAAAAACCA 59.665 47.619 19.77 0.00 32.61 3.67
393 409 6.107343 GCAGTAAAAACCAACCCTTAAAACA 58.893 36.000 0.00 0.00 0.00 2.83
414 430 2.726633 CGTTTTCCGTGAACTGCAAAT 58.273 42.857 0.00 0.00 0.00 2.32
432 448 2.278792 GCATTTTGCGGATCGGCC 60.279 61.111 21.10 0.00 31.71 6.13
473 489 3.896888 AGATGCTCTAAGCTAGCTCACAT 59.103 43.478 19.65 16.18 42.97 3.21
474 490 3.724508 TGCTCTAAGCTAGCTCACATC 57.275 47.619 19.65 8.39 42.97 3.06
475 491 3.026694 TGCTCTAAGCTAGCTCACATCA 58.973 45.455 19.65 10.94 42.97 3.07
488 504 1.887242 ACATCACGCACGCACTTGT 60.887 52.632 0.00 0.00 0.00 3.16
491 507 0.950555 ATCACGCACGCACTTGTCAT 60.951 50.000 0.00 0.00 0.00 3.06
510 526 1.827789 GCCACACCACACCACATGT 60.828 57.895 0.00 0.00 44.81 3.21
520 536 0.599060 CACCACATGTTGCATGCAGA 59.401 50.000 21.50 12.19 0.00 4.26
525 541 3.185594 CCACATGTTGCATGCAGAAAAAG 59.814 43.478 21.50 12.18 0.00 2.27
631 651 3.929610 GTCAGAAAGATGCAGGTAGTCAC 59.070 47.826 0.00 0.00 0.00 3.67
664 684 0.326927 CCACCTATTGTCCCGTTGGT 59.673 55.000 0.00 0.00 0.00 3.67
1037 1092 1.531739 GGCCTCAACAAAATCCGCCA 61.532 55.000 0.00 0.00 34.98 5.69
1328 1612 4.388499 GAGCGCCGGAACTCCCAA 62.388 66.667 5.05 0.00 34.14 4.12
1359 1643 4.343323 CCGTCACCACCATGCCCA 62.343 66.667 0.00 0.00 0.00 5.36
1477 1761 2.342279 CCAAGACGACAGCCGGAA 59.658 61.111 5.05 0.00 43.93 4.30
1483 1767 0.038526 GACGACAGCCGGAAAAGAGA 60.039 55.000 5.05 0.00 43.93 3.10
1621 1905 2.119801 AGCTGGCTACATTGAAGTGG 57.880 50.000 0.00 0.00 0.00 4.00
1652 1936 4.771127 GTTCCCTCGAACTGTGCA 57.229 55.556 0.00 0.00 44.29 4.57
2048 2368 0.811281 AAGCCGCAAATAGTTCAGGC 59.189 50.000 9.42 9.42 44.45 4.85
2063 2383 4.514066 AGTTCAGGCCGTAACTTAGTTTTG 59.486 41.667 17.19 0.00 32.00 2.44
2261 2624 9.298774 CTCCATAAGATTTCTTGATCAAAAAGC 57.701 33.333 9.88 14.23 37.40 3.51
2263 2626 7.253883 CCATAAGATTTCTTGATCAAAAAGCGC 60.254 37.037 9.88 0.00 37.40 5.92
2264 2627 5.382618 AGATTTCTTGATCAAAAAGCGCT 57.617 34.783 2.64 2.64 0.00 5.92
2265 2628 5.776744 AGATTTCTTGATCAAAAAGCGCTT 58.223 33.333 18.98 18.98 0.00 4.68
2266 2629 5.860716 AGATTTCTTGATCAAAAAGCGCTTC 59.139 36.000 25.24 10.60 0.00 3.86
2644 3038 4.322198 GGTGAGTAGTATCGAACACCCAAA 60.322 45.833 0.00 0.00 40.96 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.718107 GCCAGGCGAGCTTTATGC 59.282 61.111 0.00 0.00 43.29 3.14
217 226 1.460273 GGTCAAAAAGGGAGCCGCAA 61.460 55.000 0.00 0.00 0.00 4.85
225 234 0.040425 CACGAAGCGGTCAAAAAGGG 60.040 55.000 0.00 0.00 0.00 3.95
227 236 1.063469 ACACACGAAGCGGTCAAAAAG 59.937 47.619 0.00 0.00 0.00 2.27
289 298 2.358267 TCTTCTTATTCCTCTCGTCCGC 59.642 50.000 0.00 0.00 0.00 5.54
306 316 9.278978 GAACTTATATTCTTTCCCCATCTCTTC 57.721 37.037 0.00 0.00 0.00 2.87
312 322 6.262056 ACGGAACTTATATTCTTTCCCCAT 57.738 37.500 0.00 0.00 35.06 4.00
381 397 4.031418 CGGAAAACGTGTTTTAAGGGTT 57.969 40.909 10.46 0.00 42.26 4.11
414 430 2.489285 GCCGATCCGCAAAATGCA 59.511 55.556 0.82 0.00 45.36 3.96
432 448 3.506059 CTAGCAGACCCCGCATCCG 62.506 68.421 0.00 0.00 0.00 4.18
473 489 1.594021 ATGACAAGTGCGTGCGTGA 60.594 52.632 2.12 0.00 0.00 4.35
474 490 1.439201 CATGACAAGTGCGTGCGTG 60.439 57.895 0.00 0.00 0.00 5.34
475 491 2.938253 CATGACAAGTGCGTGCGT 59.062 55.556 0.00 0.00 0.00 5.24
488 504 1.528076 GTGGTGTGGTGTGGCATGA 60.528 57.895 0.00 0.00 0.00 3.07
491 507 1.827354 CATGTGGTGTGGTGTGGCA 60.827 57.895 0.00 0.00 0.00 4.92
510 526 5.464057 CAGTCATTTCTTTTTCTGCATGCAA 59.536 36.000 22.88 10.06 0.00 4.08
520 536 6.986231 GTGAATTGGGTCAGTCATTTCTTTTT 59.014 34.615 0.00 0.00 0.00 1.94
525 541 5.452078 TTGTGAATTGGGTCAGTCATTTC 57.548 39.130 0.00 0.00 0.00 2.17
596 616 4.504916 CTGACGCAGAGGCCGAGG 62.505 72.222 0.00 0.00 36.38 4.63
598 618 2.492449 CTTTCTGACGCAGAGGCCGA 62.492 60.000 0.00 0.00 41.75 5.54
606 626 0.035317 ACCTGCATCTTTCTGACGCA 59.965 50.000 0.00 0.00 41.91 5.24
609 629 3.929610 GTGACTACCTGCATCTTTCTGAC 59.070 47.826 0.00 0.00 0.00 3.51
631 651 4.162690 GTGGCGTGGGCTAGGGAG 62.163 72.222 0.00 0.00 39.81 4.30
1037 1092 3.713205 CTGCGTCGCTGGAGCTCAT 62.713 63.158 19.50 0.00 39.32 2.90
1328 1612 3.325201 GACGGGGCGGTGGATTTCT 62.325 63.158 0.00 0.00 0.00 2.52
1477 1761 3.431486 GGGATCGTCTTGATGCTCTCTTT 60.431 47.826 0.00 0.00 44.29 2.52
1483 1767 1.443407 CCGGGATCGTCTTGATGCT 59.557 57.895 0.00 0.00 44.29 3.79
1621 1905 0.245813 GGGAACTGTCCGTGGTAGAC 59.754 60.000 1.09 0.00 46.04 2.59
2048 2368 7.918643 TGAACTAAACCAAAACTAAGTTACGG 58.081 34.615 0.00 0.00 0.00 4.02
2063 2383 6.705825 AGAACAATGCCATTTTGAACTAAACC 59.294 34.615 0.00 0.00 0.00 3.27
2644 3038 4.777896 TGCAGGTAGAGATAAACCAAGAGT 59.222 41.667 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.