Multiple sequence alignment - TraesCS1A01G414900

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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 TraesCS1A01G414900 chr1A 100.000 3236 0 0 1 3236 573951315 573954550 0.000000e+00 5976
1 TraesCS1A01G414900 chr1A 99.300 1715 8 2 1522 3236 21636084 21634374 0.000000e+00 3097
2 TraesCS1A01G414900 chr1A 99.097 997 8 1 493 1489 21637238 21636243 0.000000e+00 1790
3 TraesCS1A01G414900 chr1A 86.648 1438 163 24 1807 3235 95836775 95838192 0.000000e+00 1565
4 TraesCS1A01G414900 chr1A 78.873 639 124 9 879 1511 95835820 95836453 3.860000e-114 422
5 TraesCS1A01G414900 chr2D 95.438 2740 93 16 502 3236 471446804 471444092 0.000000e+00 4338
6 TraesCS1A01G414900 chr2D 85.136 1433 190 13 1820 3236 534514796 534513371 0.000000e+00 1445
7 TraesCS1A01G414900 chr2D 88.043 368 38 5 137 500 137169043 137169408 6.410000e-117 431
8 TraesCS1A01G414900 chr2D 76.560 593 102 30 499 1065 14262373 14262954 1.140000e-74 291
9 TraesCS1A01G414900 chr5B 99.271 1645 11 1 1592 3236 42178619 42180262 0.000000e+00 2970
10 TraesCS1A01G414900 chr5B 98.933 1031 11 0 501 1531 42177551 42178581 0.000000e+00 1844
11 TraesCS1A01G414900 chr5B 86.398 1441 162 29 1807 3235 79788388 79786970 0.000000e+00 1544
12 TraesCS1A01G414900 chr5B 78.151 595 120 8 922 1511 79789299 79788710 1.420000e-98 370
13 TraesCS1A01G414900 chr5B 83.901 323 45 7 501 820 79790572 79790254 5.250000e-78 302
14 TraesCS1A01G414900 chr4B 86.667 1440 159 28 1807 3235 633916831 633918248 0.000000e+00 1565
15 TraesCS1A01G414900 chr4B 78.717 639 125 9 879 1511 633915876 633916509 1.800000e-112 416
16 TraesCS1A01G414900 chr4B 85.093 322 43 5 501 820 633915555 633915873 1.120000e-84 324
17 TraesCS1A01G414900 chr1D 84.924 1446 193 16 1808 3236 78384339 78385776 0.000000e+00 1439
18 TraesCS1A01G414900 chr1D 92.032 502 37 2 1 500 393037006 393037506 0.000000e+00 702
19 TraesCS1A01G414900 chr1D 91.633 502 38 3 1 500 392970614 392971113 0.000000e+00 691
20 TraesCS1A01G414900 chr1D 89.474 361 35 3 137 495 290919336 290919695 1.370000e-123 453
21 TraesCS1A01G414900 chr1D 77.500 320 61 11 512 825 479709623 479709937 7.130000e-42 182
22 TraesCS1A01G414900 chr2A 83.544 1422 200 25 1837 3235 718367764 718366354 0.000000e+00 1299
23 TraesCS1A01G414900 chr2A 80.106 940 157 22 501 1419 718369070 718368140 0.000000e+00 673
24 TraesCS1A01G414900 chr3D 86.018 987 120 11 2264 3236 561029074 561028092 0.000000e+00 1042
25 TraesCS1A01G414900 chr3D 88.219 365 39 3 137 498 322845662 322845299 1.780000e-117 433
26 TraesCS1A01G414900 chr3D 84.559 408 61 2 1820 2227 561029478 561029073 1.400000e-108 403
27 TraesCS1A01G414900 chr3D 76.748 572 100 19 896 1460 422761104 422760559 4.080000e-74 289
28 TraesCS1A01G414900 chr3D 79.193 322 57 10 500 818 422761464 422761150 7.030000e-52 215
29 TraesCS1A01G414900 chr7D 90.782 358 29 3 141 495 374395792 374396148 2.920000e-130 475
30 TraesCS1A01G414900 chr5D 89.474 361 34 3 137 494 381400674 381401033 1.370000e-123 453
31 TraesCS1A01G414900 chr4D 88.950 362 36 3 137 495 45921088 45921448 8.240000e-121 444
32 TraesCS1A01G414900 chr4A 88.122 362 39 3 137 495 28241617 28241977 8.300000e-116 427
33 TraesCS1A01G414900 chr7B 78.769 325 61 8 506 826 676863535 676863855 9.100000e-51 211
34 TraesCS1A01G414900 chr7B 73.802 313 72 5 1116 1420 676864114 676864424 7.340000e-22 115


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 TraesCS1A01G414900 chr1A 573951315 573954550 3235 False 5976.000000 5976 100.000000 1 3236 1 chr1A.!!$F1 3235
1 TraesCS1A01G414900 chr1A 21634374 21637238 2864 True 2443.500000 3097 99.198500 493 3236 2 chr1A.!!$R1 2743
2 TraesCS1A01G414900 chr1A 95835820 95838192 2372 False 993.500000 1565 82.760500 879 3235 2 chr1A.!!$F2 2356
3 TraesCS1A01G414900 chr2D 471444092 471446804 2712 True 4338.000000 4338 95.438000 502 3236 1 chr2D.!!$R1 2734
4 TraesCS1A01G414900 chr2D 534513371 534514796 1425 True 1445.000000 1445 85.136000 1820 3236 1 chr2D.!!$R2 1416
5 TraesCS1A01G414900 chr2D 14262373 14262954 581 False 291.000000 291 76.560000 499 1065 1 chr2D.!!$F1 566
6 TraesCS1A01G414900 chr5B 42177551 42180262 2711 False 2407.000000 2970 99.102000 501 3236 2 chr5B.!!$F1 2735
7 TraesCS1A01G414900 chr5B 79786970 79790572 3602 True 738.666667 1544 82.816667 501 3235 3 chr5B.!!$R1 2734
8 TraesCS1A01G414900 chr4B 633915555 633918248 2693 False 768.333333 1565 83.492333 501 3235 3 chr4B.!!$F1 2734
9 TraesCS1A01G414900 chr1D 78384339 78385776 1437 False 1439.000000 1439 84.924000 1808 3236 1 chr1D.!!$F1 1428
10 TraesCS1A01G414900 chr1D 393037006 393037506 500 False 702.000000 702 92.032000 1 500 1 chr1D.!!$F4 499
11 TraesCS1A01G414900 chr2A 718366354 718369070 2716 True 986.000000 1299 81.825000 501 3235 2 chr2A.!!$R1 2734
12 TraesCS1A01G414900 chr3D 561028092 561029478 1386 True 722.500000 1042 85.288500 1820 3236 2 chr3D.!!$R3 1416
13 TraesCS1A01G414900 chr3D 422760559 422761464 905 True 252.000000 289 77.970500 500 1460 2 chr3D.!!$R2 960

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
508 511 1.270785 TGACATCCATGTGAGTGCGTT 60.271 47.619 0.0 0.0 41.95 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 3569 2.691409 TTCTCTCCCATTGTAAGCGG 57.309 50.0 0.0 0.0 0.0 5.52 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
26 27 7.518731 TTTCAGGATTCACGTTTTCTTTTTG 57.481 32.000 0.00 0.00 0.00 2.44
34 35 4.991687 TCACGTTTTCTTTTTGTTTTGGCT 59.008 33.333 0.00 0.00 0.00 4.75
40 41 7.201478 CGTTTTCTTTTTGTTTTGGCTATGTCA 60.201 33.333 0.00 0.00 0.00 3.58
100 101 5.104109 TGGGGAAAGATAGAATACCCAACTG 60.104 44.000 0.00 0.00 43.26 3.16
103 104 7.017254 GGGGAAAGATAGAATACCCAACTGATA 59.983 40.741 0.00 0.00 39.10 2.15
136 137 7.250569 TCTCGCCATCTTTATTCATTCAAAAC 58.749 34.615 0.00 0.00 0.00 2.43
152 153 5.295431 TCAAAACATAGGTCGAGCAAATG 57.705 39.130 18.15 20.14 0.00 2.32
169 170 5.769662 AGCAAATGTTGTTCTAGTGGATCAA 59.230 36.000 0.00 0.00 32.98 2.57
175 176 6.992063 GTTGTTCTAGTGGATCAACATGAT 57.008 37.500 19.79 0.00 46.10 2.45
182 183 5.282055 AGTGGATCAACATGATGTACGAT 57.718 39.130 2.34 9.41 37.20 3.73
245 246 7.730364 ATTCTTTATTATGAGGTTGCCTACG 57.270 36.000 0.00 0.00 31.76 3.51
252 253 4.546829 ATGAGGTTGCCTACGAAACTTA 57.453 40.909 0.00 0.00 31.76 2.24
292 293 6.734137 TGAGACACATCACCAAAATTAACAC 58.266 36.000 0.00 0.00 0.00 3.32
295 296 6.545666 AGACACATCACCAAAATTAACACTGA 59.454 34.615 0.00 0.00 0.00 3.41
296 297 7.231317 AGACACATCACCAAAATTAACACTGAT 59.769 33.333 0.00 0.00 0.00 2.90
314 315 5.404366 CACTGATGGTTTCTTTCTTGCAATG 59.596 40.000 0.00 0.00 0.00 2.82
322 323 8.514594 TGGTTTCTTTCTTGCAATGTATCTTAG 58.485 33.333 0.00 0.00 0.00 2.18
329 330 9.787532 TTTCTTGCAATGTATCTTAGCATTAAC 57.212 29.630 0.00 0.00 34.01 2.01
343 344 8.559536 TCTTAGCATTAACAGTGTTCAAGAAAG 58.440 33.333 12.82 10.41 0.00 2.62
360 361 8.792830 TCAAGAAAGGTCTACCAAAGATAATG 57.207 34.615 1.26 0.00 36.36 1.90
418 419 7.740805 AGGAAATCAGTTGGGTATTCTATCTC 58.259 38.462 0.00 0.00 0.00 2.75
419 420 6.937465 GGAAATCAGTTGGGTATTCTATCTCC 59.063 42.308 0.00 0.00 0.00 3.71
420 421 7.420214 GGAAATCAGTTGGGTATTCTATCTCCA 60.420 40.741 0.00 0.00 0.00 3.86
421 422 7.639062 AATCAGTTGGGTATTCTATCTCCAT 57.361 36.000 0.00 0.00 0.00 3.41
452 455 7.004086 ACTTCAACATCTCTAACAATCCCAAA 58.996 34.615 0.00 0.00 0.00 3.28
455 458 7.174413 TCAACATCTCTAACAATCCCAAATGA 58.826 34.615 0.00 0.00 0.00 2.57
508 511 1.270785 TGACATCCATGTGAGTGCGTT 60.271 47.619 0.00 0.00 41.95 4.84
1041 1979 0.467474 TCCTACTGGATGCGGTCGAT 60.467 55.000 0.23 0.00 37.46 3.59
2345 3569 1.333524 CGAGCCACAATCATTCGATGC 60.334 52.381 0.00 0.00 33.38 3.91
2910 4134 6.041523 ACCTGCACCAAAAACAATACTAACAT 59.958 34.615 0.00 0.00 0.00 2.71
3127 4368 6.976934 AAATTTATCCAAACACTGTCCACT 57.023 33.333 0.00 0.00 0.00 4.00
3172 4413 1.141053 AGAAGGCGAAGGAAACACTGT 59.859 47.619 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.999456 ACATAGCCAAAACAAAAAGAAAACG 58.001 32.000 0.00 0.0 0.00 3.60
21 22 5.921004 GCATGACATAGCCAAAACAAAAA 57.079 34.783 0.00 0.0 0.00 1.94
46 47 0.835941 AAAAACAAGTGGCCCATGCA 59.164 45.000 0.00 0.0 40.13 3.96
103 104 8.908786 TGAATAAAGATGGCGAGAATTAGAAT 57.091 30.769 0.00 0.0 0.00 2.40
109 110 7.572523 TTGAATGAATAAAGATGGCGAGAAT 57.427 32.000 0.00 0.0 0.00 2.40
136 137 4.393062 AGAACAACATTTGCTCGACCTATG 59.607 41.667 0.00 0.0 31.27 2.23
232 233 2.922740 AAGTTTCGTAGGCAACCTCA 57.077 45.000 0.00 0.0 34.61 3.86
233 234 4.082354 TCTCTAAGTTTCGTAGGCAACCTC 60.082 45.833 0.00 0.0 34.61 3.85
252 253 9.160496 GATGTGTCTCATGAGTTTAATTTCTCT 57.840 33.333 21.92 0.0 36.83 3.10
266 267 7.326789 GTGTTAATTTTGGTGATGTGTCTCATG 59.673 37.037 0.00 0.0 36.83 3.07
292 293 5.535333 ACATTGCAAGAAAGAAACCATCAG 58.465 37.500 4.94 0.0 0.00 2.90
295 296 7.472334 AGATACATTGCAAGAAAGAAACCAT 57.528 32.000 4.94 0.0 0.00 3.55
296 297 6.899393 AGATACATTGCAAGAAAGAAACCA 57.101 33.333 4.94 0.0 0.00 3.67
314 315 9.151471 TCTTGAACACTGTTAATGCTAAGATAC 57.849 33.333 0.00 0.0 0.00 2.24
322 323 5.831997 ACCTTTCTTGAACACTGTTAATGC 58.168 37.500 0.00 0.0 0.00 3.56
329 330 4.703897 TGGTAGACCTTTCTTGAACACTG 58.296 43.478 0.00 0.0 36.82 3.66
343 344 8.561738 TTTTGTCTCATTATCTTTGGTAGACC 57.438 34.615 0.00 0.0 35.19 3.85
360 361 4.253685 TCCCACGAGATGATTTTTGTCTC 58.746 43.478 0.00 0.0 36.02 3.36
376 377 2.853705 TCCTAGTTTTGGTTTCCCACG 58.146 47.619 0.00 0.0 41.67 4.94
377 378 5.303333 TGATTTCCTAGTTTTGGTTTCCCAC 59.697 40.000 0.00 0.0 41.67 4.61
402 403 7.873505 GTCTTGTATGGAGATAGAATACCCAAC 59.126 40.741 0.00 0.0 0.00 3.77
418 419 7.819415 TGTTAGAGATGTTGAAGTCTTGTATGG 59.181 37.037 0.00 0.0 0.00 2.74
419 420 8.763049 TGTTAGAGATGTTGAAGTCTTGTATG 57.237 34.615 0.00 0.0 0.00 2.39
420 421 9.950496 ATTGTTAGAGATGTTGAAGTCTTGTAT 57.050 29.630 0.00 0.0 0.00 2.29
421 422 9.424319 GATTGTTAGAGATGTTGAAGTCTTGTA 57.576 33.333 0.00 0.0 0.00 2.41
1697 2763 3.023832 AGTTTTTCAACCTCCCTGTGTG 58.976 45.455 0.00 0.0 32.70 3.82
2345 3569 2.691409 TTCTCTCCCATTGTAAGCGG 57.309 50.000 0.00 0.0 0.00 5.52
2910 4134 9.814899 ACATTTTTAGTGTTCAAATCAATCACA 57.185 25.926 0.00 0.0 0.00 3.58
3172 4413 4.082679 ACACTTTTTCGTGTAAAACAGCCA 60.083 37.500 0.00 0.0 45.65 4.75


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

AutoCloner maintained by Alex Coulton.