Multiple sequence alignment - TraesCS2B01G629700

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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 TraesCS2B01G629700 chr2B 100.000 3518 0 0 1 3518 800708858 800705341 0 6497
1 TraesCS2B01G629700 chr2B 97.246 3522 85 10 1 3517 132063352 132066866 0 5956
2 TraesCS2B01G629700 chr2B 90.378 3544 273 43 1 3517 800754796 800751294 0 4593
3 TraesCS2B01G629700 chr2B 90.172 2493 177 36 1 2486 744286947 744289378 0 3184
4 TraesCS2B01G629700 chr2B 89.235 1765 134 27 1 1762 757133347 757131636 0 2156
5 TraesCS2B01G629700 chr5B 96.707 3523 100 11 1 3518 172605676 172609187 0 5849
6 TraesCS2B01G629700 chr5B 94.629 3519 167 15 1 3518 218929191 218932688 0 5432
7 TraesCS2B01G629700 chr5B 89.915 3540 282 47 1 3517 474303110 474306597 0 4490
8 TraesCS2B01G629700 chr5B 84.582 934 88 18 1 909 157575811 157576713 0 876
9 TraesCS2B01G629700 chr3B 91.629 3536 240 35 1 3518 555267945 555264448 0 4839
10 TraesCS2B01G629700 chr3B 89.770 3558 298 48 1 3518 236194120 236190589 0 4494
11 TraesCS2B01G629700 chr6B 91.280 3555 249 46 1 3518 239605237 239608767 0 4791
12 TraesCS2B01G629700 chr7B 91.137 3543 262 38 1 3518 734939954 734936439 0 4756
13 TraesCS2B01G629700 chr7B 89.515 3567 303 53 1 3518 746797769 746794225 0 4449
14 TraesCS2B01G629700 chr7B 89.185 1766 127 32 1 1762 697160218 697158513 0 2145
15 TraesCS2B01G629700 chr4A 84.793 822 105 16 2702 3518 647859264 647860070 0 808


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 TraesCS2B01G629700 chr2B 800705341 800708858 3517 True 6497 6497 100.000 1 3518 1 chr2B.!!$R2 3517
1 TraesCS2B01G629700 chr2B 132063352 132066866 3514 False 5956 5956 97.246 1 3517 1 chr2B.!!$F1 3516
2 TraesCS2B01G629700 chr2B 800751294 800754796 3502 True 4593 4593 90.378 1 3517 1 chr2B.!!$R3 3516
3 TraesCS2B01G629700 chr2B 744286947 744289378 2431 False 3184 3184 90.172 1 2486 1 chr2B.!!$F2 2485
4 TraesCS2B01G629700 chr2B 757131636 757133347 1711 True 2156 2156 89.235 1 1762 1 chr2B.!!$R1 1761
5 TraesCS2B01G629700 chr5B 172605676 172609187 3511 False 5849 5849 96.707 1 3518 1 chr5B.!!$F2 3517
6 TraesCS2B01G629700 chr5B 218929191 218932688 3497 False 5432 5432 94.629 1 3518 1 chr5B.!!$F3 3517
7 TraesCS2B01G629700 chr5B 474303110 474306597 3487 False 4490 4490 89.915 1 3517 1 chr5B.!!$F4 3516
8 TraesCS2B01G629700 chr5B 157575811 157576713 902 False 876 876 84.582 1 909 1 chr5B.!!$F1 908
9 TraesCS2B01G629700 chr3B 555264448 555267945 3497 True 4839 4839 91.629 1 3518 1 chr3B.!!$R2 3517
10 TraesCS2B01G629700 chr3B 236190589 236194120 3531 True 4494 4494 89.770 1 3518 1 chr3B.!!$R1 3517
11 TraesCS2B01G629700 chr6B 239605237 239608767 3530 False 4791 4791 91.280 1 3518 1 chr6B.!!$F1 3517
12 TraesCS2B01G629700 chr7B 734936439 734939954 3515 True 4756 4756 91.137 1 3518 1 chr7B.!!$R2 3517
13 TraesCS2B01G629700 chr7B 746794225 746797769 3544 True 4449 4449 89.515 1 3518 1 chr7B.!!$R3 3517
14 TraesCS2B01G629700 chr7B 697158513 697160218 1705 True 2145 2145 89.185 1 1762 1 chr7B.!!$R1 1761
15 TraesCS2B01G629700 chr4A 647859264 647860070 806 False 808 808 84.793 2702 3518 1 chr4A.!!$F1 816

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
51 55 1.066858 GCGAGAATTGTGAGGGTGAGA 60.067 52.381 0.0 0.0 0.00 3.27 F
626 656 2.046314 CCACGAGGCAAACGGGAT 60.046 61.111 0.0 0.0 36.15 3.85 F
1390 1478 1.541670 GCACGAACCTTGTCAACCCTA 60.542 52.381 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1289 0.242017 GTTGAGCCTGTTGCCATGTC 59.758 55.0 0.0 0.0 42.71 3.06 R
1682 1770 0.533308 AGTGGTAGGCGCGAAAACAA 60.533 50.0 12.1 0.0 0.00 2.83 R
2655 2769 0.321671 CTCAGAAGGGCAAGACGGAA 59.678 55.0 0.0 0.0 0.00 4.30 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
50 54 1.338105 TGCGAGAATTGTGAGGGTGAG 60.338 52.381 0.00 0.00 0.00 3.51
51 55 1.066858 GCGAGAATTGTGAGGGTGAGA 60.067 52.381 0.00 0.00 0.00 3.27
55 59 4.697352 CGAGAATTGTGAGGGTGAGATTTT 59.303 41.667 0.00 0.00 0.00 1.82
330 350 2.908015 GCATGCTCTTCCCGGGTA 59.092 61.111 22.86 10.78 0.00 3.69
391 415 5.051774 CCGCAAAAATATGCTTTACGAATGG 60.052 40.000 0.00 0.00 44.21 3.16
442 467 4.053469 ACAAATGTGTGGCAACTAAACC 57.947 40.909 0.00 0.00 36.31 3.27
508 534 3.601360 GCGGCAACAAATTTTCTGAAACG 60.601 43.478 1.58 1.40 0.00 3.60
522 548 2.485426 CTGAAACGGACTGTCGTAGGTA 59.515 50.000 1.07 0.00 43.07 3.08
625 655 2.725203 CTTCCACGAGGCAAACGGGA 62.725 60.000 0.00 0.00 36.15 5.14
626 656 2.046314 CCACGAGGCAAACGGGAT 60.046 61.111 0.00 0.00 36.15 3.85
814 887 4.206375 TGGGTTGTATAATCATGTGGCAG 58.794 43.478 0.00 0.00 0.00 4.85
965 1045 3.509575 ACCCATTGCATTTACATGTTCGT 59.490 39.130 2.30 0.00 32.28 3.85
1203 1289 9.801714 GAACTAAATTTTCATGACATTGCAAAG 57.198 29.630 1.71 0.19 0.00 2.77
1390 1478 1.541670 GCACGAACCTTGTCAACCCTA 60.542 52.381 0.00 0.00 0.00 3.53
1438 1526 2.998097 CCGCCTCCAGGGAATTCA 59.002 61.111 7.93 0.00 37.23 2.57
1628 1716 4.385405 AGACTCGCTGCAGGCCAC 62.385 66.667 17.12 0.00 37.74 5.01
1682 1770 6.310941 AGCTACTCATGTACCTCATATCAGT 58.689 40.000 0.00 0.00 34.67 3.41
1774 1863 3.630312 TGTACTCTTTGCCAGTGTTTTCC 59.370 43.478 0.00 0.00 31.49 3.13
1889 1983 8.807948 ATATGAACTGGTGTAAGTTTATTGCT 57.192 30.769 0.51 0.00 40.48 3.91
2063 2162 2.040278 ACTGCCATAGTGACAATGTGGT 59.960 45.455 18.24 0.00 38.49 4.16
2099 2198 0.394938 ACGTGGCAACTGTCATACCA 59.605 50.000 0.00 0.00 37.61 3.25
2160 2259 3.550437 ATCACAGTAGGATGGCAACTC 57.450 47.619 0.00 0.00 37.61 3.01
2161 2260 2.540383 TCACAGTAGGATGGCAACTCT 58.460 47.619 0.00 0.00 37.61 3.24
2316 2423 7.841915 TTTAAATCAGCTCATGTATGTCGAA 57.158 32.000 0.00 0.00 0.00 3.71
2458 2565 3.620488 ACTGATGGCACGTATGGAAAAT 58.380 40.909 0.00 0.00 0.00 1.82
2520 2632 5.681337 TGCTTACAAATTTGACATGACGA 57.319 34.783 24.64 0.00 0.00 4.20
2655 2769 1.293498 GGATGGACGTGCACTCAGT 59.707 57.895 13.47 5.31 0.00 3.41
2679 2793 2.701107 GTCTTGCCCTTCTGAGGTAAC 58.299 52.381 0.00 0.00 41.85 2.50
2760 2884 4.390264 TCAATACGGGTTGTTGTTGATGA 58.610 39.130 2.62 0.00 32.45 2.92
2787 2912 4.671590 TCGTGGACAGGCGAGGGA 62.672 66.667 0.00 0.00 32.98 4.20
2852 2977 2.617021 GGATTGCTCGGGAAGTTGGTTA 60.617 50.000 0.00 0.00 0.00 2.85
2978 3103 6.342906 CGGTATGACTATAACAGTTCCCAAA 58.657 40.000 0.00 0.00 37.72 3.28
3074 3202 0.037697 GCACCAGGACACGTATGACA 60.038 55.000 0.00 0.00 0.00 3.58
3101 3229 0.533032 AGCTGAAGTTCGTAGAGGCC 59.467 55.000 0.00 0.00 38.43 5.19
3463 3606 3.650139 ACGAGCAGTTACGAAGAAACAT 58.350 40.909 0.00 0.00 0.00 2.71
3485 3628 2.677003 CCAACGCTAACCCGTGCTG 61.677 63.158 0.00 0.00 41.90 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 54 4.933400 TGGCAACTACTTCGACCTAAAATC 59.067 41.667 0.00 0.00 37.61 2.17
51 55 4.901868 TGGCAACTACTTCGACCTAAAAT 58.098 39.130 0.00 0.00 37.61 1.82
55 59 3.512329 TCAATGGCAACTACTTCGACCTA 59.488 43.478 0.00 0.00 37.61 3.08
391 415 2.222027 GTCATACTGCCATAGTTGCCC 58.778 52.381 0.00 0.00 40.89 5.36
412 436 2.223479 GCCACACATTTGTTCACGTTCT 60.223 45.455 0.00 0.00 31.66 3.01
442 467 1.682854 ACTGCCACATTTGTTCAGGTG 59.317 47.619 11.90 0.00 33.17 4.00
508 534 1.538047 TGTGGTACCTACGACAGTCC 58.462 55.000 14.36 0.00 39.47 3.85
634 664 8.731275 TGTGGTTACTATCATGTAAATTCAGG 57.269 34.615 0.00 0.00 34.67 3.86
814 887 5.032863 AGACATTGTGTTCGCGTACTATAC 58.967 41.667 16.93 7.56 0.00 1.47
965 1045 3.888930 GGAACAGACCAAATTGTCAAGGA 59.111 43.478 0.00 0.00 37.73 3.36
1074 1154 1.065854 ACCTGATCGCCCTCTTTTCTG 60.066 52.381 0.00 0.00 0.00 3.02
1090 1170 2.048597 TGCGCGGACAGTTACCTG 60.049 61.111 8.83 0.00 44.68 4.00
1115 1196 1.435256 ACATAAATCGGGAGGAGGGG 58.565 55.000 0.00 0.00 0.00 4.79
1203 1289 0.242017 GTTGAGCCTGTTGCCATGTC 59.758 55.000 0.00 0.00 42.71 3.06
1390 1478 0.541392 TCACCAAGCCAGTCGCATAT 59.459 50.000 0.00 0.00 41.38 1.78
1523 1611 5.529800 TCGATCTCATTATTGACCTCGTACA 59.470 40.000 11.08 0.00 34.58 2.90
1628 1716 0.732880 AACTTCTCCGTGCGTCATCG 60.733 55.000 0.00 0.00 40.37 3.84
1682 1770 0.533308 AGTGGTAGGCGCGAAAACAA 60.533 50.000 12.10 0.00 0.00 2.83
1889 1983 2.839486 AAGCATCGTGGAGAAAGTCA 57.161 45.000 0.00 0.00 0.00 3.41
2316 2423 1.902508 ACGGTGGACAGATCAAGACAT 59.097 47.619 0.00 0.00 0.00 3.06
2430 2537 1.078497 CGTGCCATCAGTTGCCCTA 60.078 57.895 0.00 0.00 0.00 3.53
2458 2565 8.685838 AGACATAAGCAAAAACTAACCTGTAA 57.314 30.769 0.00 0.00 0.00 2.41
2520 2632 4.320421 GCCTTATAAAACCACGGACGTTTT 60.320 41.667 12.23 12.23 43.79 2.43
2655 2769 0.321671 CTCAGAAGGGCAAGACGGAA 59.678 55.000 0.00 0.00 0.00 4.30
2679 2793 6.091169 GCAAAACATGGATGTAGACATTTTGG 59.909 38.462 14.18 4.08 40.80 3.28
2760 2884 2.293399 GCCTGTCCACGAAAACAAGAAT 59.707 45.455 0.00 0.00 0.00 2.40
2787 2912 4.563374 GCCCAATTAAATGCTCAACTGGTT 60.563 41.667 0.00 0.00 0.00 3.67
2978 3103 1.525995 CTTGTGTGTCACCGGGCTT 60.526 57.895 6.32 0.00 32.73 4.35
3101 3229 1.880819 GCATCCTTGCCCCTGTTGTG 61.881 60.000 0.00 0.00 43.38 3.33
3474 3617 2.047274 GAGCAGCAGCACGGGTTA 60.047 61.111 3.17 0.00 45.49 2.85


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

AutoCloner maintained by Alex Coulton.