Multiple sequence alignment - TraesCS2A01G044600

Loading Multiple Alignment...

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 TraesCS2A01G044600 chr2A 100.000 2635 0 0 1 2635 17609428 17612062 0.000000e+00 4867
1 TraesCS2A01G044600 chr2A 95.731 609 24 2 2027 2635 24171440 24170834 0.000000e+00 979
2 TraesCS2A01G044600 chr2A 78.399 787 104 38 867 1630 17133285 17134028 4.000000e-123 451
3 TraesCS2A01G044600 chr2B 92.915 1722 106 11 5 1722 27635212 27636921 0.000000e+00 2490
4 TraesCS2A01G044600 chr2B 93.031 287 15 3 1742 2025 27636907 27637191 5.250000e-112 414
5 TraesCS2A01G044600 chr2B 86.066 244 32 2 1388 1630 27017786 27018028 7.230000e-66 261
6 TraesCS2A01G044600 chr2B 85.830 247 31 4 1386 1630 27030447 27030691 2.600000e-65 259
7 TraesCS2A01G044600 chr2D 94.345 1061 43 9 967 2025 15583148 15584193 0.000000e+00 1611
8 TraesCS2A01G044600 chr2D 95.329 578 26 1 1 577 15529252 15529829 0.000000e+00 917
9 TraesCS2A01G044600 chr2D 93.132 364 9 3 585 943 15582799 15583151 1.080000e-143 520
10 TraesCS2A01G044600 chr2D 77.534 819 118 34 834 1630 14976623 14977397 1.450000e-117 433
11 TraesCS2A01G044600 chr3A 87.118 621 62 12 2026 2635 11355553 11356166 0.000000e+00 688
12 TraesCS2A01G044600 chr3A 91.702 470 27 2 2026 2495 501927674 501927217 2.210000e-180 641
13 TraesCS2A01G044600 chr3A 89.933 298 30 0 2025 2322 743253731 743254028 4.110000e-103 385
14 TraesCS2A01G044600 chr3A 96.552 145 5 0 2491 2635 501901103 501900959 9.420000e-60 241
15 TraesCS2A01G044600 chr7B 86.753 619 53 18 2025 2635 592543145 592543742 0.000000e+00 662
16 TraesCS2A01G044600 chr7B 87.317 410 26 11 2026 2414 684440361 684439957 1.860000e-121 446
17 TraesCS2A01G044600 chr7B 85.106 188 7 7 2248 2414 158585581 158585768 3.490000e-39 172
18 TraesCS2A01G044600 chr5D 85.403 459 46 1 2026 2463 3589146 3589604 8.600000e-125 457
19 TraesCS2A01G044600 chr6B 89.694 359 33 2 2026 2384 577977911 577978265 3.090000e-124 455
20 TraesCS2A01G044600 chr5A 86.265 415 21 12 2026 2417 645286975 645287376 4.060000e-113 418
21 TraesCS2A01G044600 chr5B 85.203 419 34 7 2033 2432 662988596 662989005 3.160000e-109 405
22 TraesCS2A01G044600 chr3D 86.753 385 26 9 2025 2386 562434048 562434430 3.160000e-109 405
23 TraesCS2A01G044600 chr7A 89.527 296 30 1 2029 2323 114685623 114685328 8.910000e-100 374
24 TraesCS2A01G044600 chr6A 82.609 92 9 5 518 606 449690727 449690640 1.010000e-09 75


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 TraesCS2A01G044600 chr2A 17609428 17612062 2634 False 4867.0 4867 100.0000 1 2635 1 chr2A.!!$F2 2634
1 TraesCS2A01G044600 chr2A 24170834 24171440 606 True 979.0 979 95.7310 2027 2635 1 chr2A.!!$R1 608
2 TraesCS2A01G044600 chr2A 17133285 17134028 743 False 451.0 451 78.3990 867 1630 1 chr2A.!!$F1 763
3 TraesCS2A01G044600 chr2B 27635212 27637191 1979 False 1452.0 2490 92.9730 5 2025 2 chr2B.!!$F3 2020
4 TraesCS2A01G044600 chr2D 15582799 15584193 1394 False 1065.5 1611 93.7385 585 2025 2 chr2D.!!$F3 1440
5 TraesCS2A01G044600 chr2D 15529252 15529829 577 False 917.0 917 95.3290 1 577 1 chr2D.!!$F2 576
6 TraesCS2A01G044600 chr2D 14976623 14977397 774 False 433.0 433 77.5340 834 1630 1 chr2D.!!$F1 796
7 TraesCS2A01G044600 chr3A 11355553 11356166 613 False 688.0 688 87.1180 2026 2635 1 chr3A.!!$F1 609
8 TraesCS2A01G044600 chr7B 592543145 592543742 597 False 662.0 662 86.7530 2025 2635 1 chr7B.!!$F2 610

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
399 401 0.725117 GGTTCCGCGATAACTGGTTG 59.275 55.0 8.23 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2246 0.251916 TTCTTACATGCGGGTCCCAG 59.748 55.0 9.12 1.83 0.0 4.45 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 6.587226 CGTGAACAAATTTGAATCATGTCCAT 59.413 34.615 24.64 0.00 33.80 3.41
78 79 3.071874 TGTTGGAGATGCCCTAACTTG 57.928 47.619 0.00 0.00 34.97 3.16
107 108 6.803154 ACAAGTTGCTTCTGATAGTAAACC 57.197 37.500 1.81 0.00 0.00 3.27
340 342 4.082787 AGTCACTTATTTCAATTGGCCACG 60.083 41.667 3.88 0.00 0.00 4.94
360 362 2.152016 GCTCTTTTTGTAACCGGCTCT 58.848 47.619 0.00 0.00 0.00 4.09
399 401 0.725117 GGTTCCGCGATAACTGGTTG 59.275 55.000 8.23 0.00 0.00 3.77
480 483 1.115326 AAACCCACCTGGCTTCAAGC 61.115 55.000 0.00 0.00 41.46 4.01
518 522 6.135400 CGAATGCTCGCATATGTTGAATTTA 58.865 36.000 4.63 0.00 38.45 1.40
532 536 7.831691 TGTTGAATTTATTTCAGGTTCTCCA 57.168 32.000 0.00 0.00 44.90 3.86
562 566 3.007290 TCTTTCAGCGATATAGCATGCCT 59.993 43.478 15.66 4.66 40.15 4.75
578 582 3.788227 TGCCTGTCAACTATGAGGTTT 57.212 42.857 0.00 0.00 35.88 3.27
583 587 4.020218 CCTGTCAACTATGAGGTTTCTGGA 60.020 45.833 0.00 0.00 35.88 3.86
606 610 8.528643 TGGAAACTTCGTCAATCTTAAGATCTA 58.471 33.333 18.19 6.98 32.75 1.98
736 740 3.729966 ACGAACCTCTGAAAGAAGGAAC 58.270 45.455 0.00 0.00 46.34 3.62
898 908 2.824041 CGGCATCTTGGTTCCGGG 60.824 66.667 0.00 0.00 38.35 5.73
1179 1221 0.736053 TCGTGGACAGCAAAAACCAC 59.264 50.000 0.00 0.00 46.16 4.16
1257 1306 7.554959 ACTCCCTCCACGTCAAAATATATAT 57.445 36.000 0.00 0.00 0.00 0.86
1258 1307 8.660295 ACTCCCTCCACGTCAAAATATATATA 57.340 34.615 0.00 0.00 0.00 0.86
1259 1308 9.268282 ACTCCCTCCACGTCAAAATATATATAT 57.732 33.333 0.00 0.00 0.00 0.86
1295 1344 6.633500 TTAGCAGGTTGGATTATTACATGC 57.367 37.500 0.00 0.00 46.49 4.06
1318 1367 6.771267 TGCCTCTTCTCGATGATAACTTACTA 59.229 38.462 0.00 0.00 0.00 1.82
1370 1430 7.146648 TCCATGTTTAACCGTTTGTTATTTCC 58.853 34.615 0.00 0.00 39.14 3.13
1376 1438 4.823790 ACCGTTTGTTATTTCCTGTGAC 57.176 40.909 0.00 0.00 0.00 3.67
1383 1445 6.494893 TTGTTATTTCCTGTGACTATGTGC 57.505 37.500 0.00 0.00 0.00 4.57
1610 1672 2.751913 CGACGACTACCTCAGCGCT 61.752 63.158 2.64 2.64 0.00 5.92
1631 1693 5.468072 CGCTATTGGTGCTTATCTCAAGATT 59.532 40.000 0.00 0.00 36.05 2.40
1637 1699 7.325660 TGGTGCTTATCTCAAGATTTGATTC 57.674 36.000 0.00 0.00 39.30 2.52
1639 1701 7.558807 TGGTGCTTATCTCAAGATTTGATTCAT 59.441 33.333 0.00 0.00 39.30 2.57
1682 1744 3.728076 ATGATTCCGTTCGCTAGCTAA 57.272 42.857 13.93 5.19 0.00 3.09
1684 1746 2.125685 GATTCCGTTCGCTAGCTAACC 58.874 52.381 22.30 7.78 0.00 2.85
1714 1776 4.319549 GCTAGAAGGTTACTTTGTGTGTGC 60.320 45.833 0.00 0.00 36.97 4.57
1716 1778 0.661020 AGGTTACTTTGTGTGTGCGC 59.339 50.000 0.00 0.00 0.00 6.09
1783 1851 2.485903 ACGTCGTTGTTCAATAAGGCA 58.514 42.857 0.00 0.00 0.00 4.75
1821 1889 0.835543 AGACTGGCAGGTTGCTCTCT 60.836 55.000 20.34 7.59 44.28 3.10
1822 1890 0.390998 GACTGGCAGGTTGCTCTCTC 60.391 60.000 20.34 0.00 44.28 3.20
1884 1952 3.129871 TGCTGTTTAATGTTTTGCTGGC 58.870 40.909 0.00 0.00 0.00 4.85
2010 2078 6.292919 GGACGCGCATATTTATTCTCTTTCTT 60.293 38.462 5.73 0.00 0.00 2.52
2022 2090 9.653287 TTTATTCTCTTTCTTCTCTGCGATTTA 57.347 29.630 0.00 0.00 0.00 1.40
2159 2229 7.078228 CCAAAACATCTAGTGCTTTACAGTTC 58.922 38.462 0.00 0.00 32.79 3.01
2176 2246 6.992063 ACAGTTCATCCTGATTATGACAAC 57.008 37.500 0.00 0.00 36.30 3.32
2188 2258 1.852157 ATGACAACTGGGACCCGCAT 61.852 55.000 5.91 0.00 0.00 4.73
2446 2558 1.597854 CAACTTGACGCCAGCCTCA 60.598 57.895 0.00 0.00 0.00 3.86
2624 2736 3.855503 CTCCTGCACAAGCTGCCCA 62.856 63.158 0.00 0.00 46.51 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.874664 CCATGGACATGATTCAAATTTGTTCA 59.125 34.615 20.76 20.76 41.20 3.18
19 20 4.202461 ACGCTATCAAATACCCATGGACAT 60.202 41.667 15.22 2.36 0.00 3.06
26 27 1.758280 ACGGACGCTATCAAATACCCA 59.242 47.619 0.00 0.00 0.00 4.51
78 79 4.756084 ATCAGAAGCAACTTGTTACAGC 57.244 40.909 0.00 0.00 0.00 4.40
281 283 6.695713 GTCAGTTGAAAATTCCAACCAACTAC 59.304 38.462 15.74 0.00 43.64 2.73
330 332 1.412343 ACAAAAAGAGCGTGGCCAATT 59.588 42.857 7.24 0.00 0.00 2.32
331 333 1.039856 ACAAAAAGAGCGTGGCCAAT 58.960 45.000 7.24 0.00 0.00 3.16
340 342 2.095718 CAGAGCCGGTTACAAAAAGAGC 60.096 50.000 1.90 0.00 0.00 4.09
384 386 0.179200 GTTGCAACCAGTTATCGCGG 60.179 55.000 19.15 0.00 0.00 6.46
399 401 0.391228 ATTTTTGGACCACCCGTTGC 59.609 50.000 0.00 0.00 37.93 4.17
480 483 5.251081 CGAGCATTCGTGTCAAATCTAAAG 58.749 41.667 0.00 0.00 41.84 1.85
518 522 2.568623 AGCGTTGGAGAACCTGAAAT 57.431 45.000 0.00 0.00 37.04 2.17
562 566 5.560722 TTCCAGAAACCTCATAGTTGACA 57.439 39.130 0.00 0.00 0.00 3.58
578 582 7.545965 GATCTTAAGATTGACGAAGTTTCCAGA 59.454 37.037 18.88 0.00 36.08 3.86
583 587 9.360093 CAGTAGATCTTAAGATTGACGAAGTTT 57.640 33.333 18.88 1.86 36.08 2.66
606 610 1.341531 CTTCCGAGACACTGAACCAGT 59.658 52.381 0.00 0.00 46.51 4.00
736 740 6.338146 TCATACACGAAATTTCCTACTCCAG 58.662 40.000 12.54 0.00 0.00 3.86
898 908 1.494824 CTGCTTGCTTGTTTTCTGCC 58.505 50.000 0.00 0.00 0.00 4.85
1179 1221 2.094390 CCATGGACCTGCTTTGTTCATG 60.094 50.000 5.56 12.46 45.44 3.07
1258 1307 9.321532 TCCAACCTGCTAATATACACTGTATAT 57.678 33.333 13.84 13.84 0.00 0.86
1259 1308 8.715190 TCCAACCTGCTAATATACACTGTATA 57.285 34.615 10.68 10.68 0.00 1.47
1260 1309 7.612065 TCCAACCTGCTAATATACACTGTAT 57.388 36.000 6.90 6.90 0.00 2.29
1261 1310 7.612065 ATCCAACCTGCTAATATACACTGTA 57.388 36.000 0.00 0.00 0.00 2.74
1262 1311 5.950544 TCCAACCTGCTAATATACACTGT 57.049 39.130 0.00 0.00 0.00 3.55
1294 1343 6.079424 AGTAAGTTATCATCGAGAAGAGGC 57.921 41.667 0.00 0.00 0.00 4.70
1295 1344 9.619316 CAATAGTAAGTTATCATCGAGAAGAGG 57.381 37.037 0.00 0.00 0.00 3.69
1370 1430 0.439985 GCACGTGCACATAGTCACAG 59.560 55.000 34.52 0.00 41.59 3.66
1383 1445 3.121944 GTCAAGTGAATAGTCTGCACGTG 59.878 47.826 12.28 12.28 41.31 4.49
1529 1591 1.669760 GCGGAAATGGGTGTCGACA 60.670 57.895 15.76 15.76 0.00 4.35
1610 1672 8.985315 ATCAAATCTTGAGATAAGCACCAATA 57.015 30.769 0.00 0.00 43.98 1.90
1669 1731 1.132643 AGTCTGGTTAGCTAGCGAACG 59.867 52.381 27.40 18.01 33.37 3.95
1682 1744 5.195848 AGTAACCTTCTAGCTAGTCTGGT 57.804 43.478 20.10 20.54 0.00 4.00
1684 1746 6.809196 CACAAAGTAACCTTCTAGCTAGTCTG 59.191 42.308 20.10 11.64 0.00 3.51
1736 1798 4.918060 CACACGCACACACGCACG 62.918 66.667 0.00 0.00 36.19 5.34
1758 1826 4.445052 CCTTATTGAACAACGACGTACACA 59.555 41.667 0.00 0.00 0.00 3.72
1821 1889 4.378563 CCAACATTAACATTAACGCACGGA 60.379 41.667 0.00 0.00 0.00 4.69
1822 1890 3.849145 CCAACATTAACATTAACGCACGG 59.151 43.478 0.00 0.00 0.00 4.94
1884 1952 4.616802 GCTTGACCAACACAATAAACATCG 59.383 41.667 0.00 0.00 0.00 3.84
2010 2078 6.924060 GCTATTTACTCCTTAAATCGCAGAGA 59.076 38.462 7.86 0.00 43.52 3.10
2159 2229 4.818546 GTCCCAGTTGTCATAATCAGGATG 59.181 45.833 0.00 0.00 37.54 3.51
2176 2246 0.251916 TTCTTACATGCGGGTCCCAG 59.748 55.000 9.12 1.83 0.00 4.45
2360 2472 1.380112 GTAGTGGAGGCGGAGGAGT 60.380 63.158 0.00 0.00 0.00 3.85
2463 2575 2.029073 CGGCCTTGTGAGACGTGT 59.971 61.111 0.00 0.00 0.00 4.49
2519 2631 4.819761 GATGGCTCGAGCGTGGCA 62.820 66.667 29.81 22.03 45.45 4.92


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

AutoCloner maintained by Alex Coulton.