Multiple sequence alignment - TraesCS3D01G385400

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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 TraesCS3D01G385400 chr3D 100.000 3554 0 0 1 3554 501033291 501029738 0.000000e+00 6564.0
1 TraesCS3D01G385400 chr3D 90.549 1566 133 10 1034 2591 501062278 501060720 0.000000e+00 2058.0
2 TraesCS3D01G385400 chr3A 96.387 2934 86 9 1 2919 640390346 640393274 0.000000e+00 4813.0
3 TraesCS3D01G385400 chr3A 94.804 1655 68 8 960 2614 640497683 640499319 0.000000e+00 2564.0
4 TraesCS3D01G385400 chr3A 91.082 1581 123 12 1034 2605 640363379 640364950 0.000000e+00 2122.0
5 TraesCS3D01G385400 chr3A 93.579 950 46 4 2608 3554 640500662 640501599 0.000000e+00 1402.0
6 TraesCS3D01G385400 chr3A 95.861 749 27 4 221 966 640481721 640482468 0.000000e+00 1208.0
7 TraesCS3D01G385400 chr3B 94.473 2497 89 19 723 3214 662480110 662477658 0.000000e+00 3801.0
8 TraesCS3D01G385400 chr3B 90.949 1580 125 12 1034 2605 662527924 662526355 0.000000e+00 2109.0
9 TraesCS3D01G385400 chr3B 85.748 421 51 5 2212 2626 662508555 662508138 1.510000e-118 436.0
10 TraesCS3D01G385400 chr3B 89.968 309 28 3 1397 1705 461747723 461748028 2.570000e-106 396.0
11 TraesCS3D01G385400 chr3B 98.000 200 4 0 3202 3401 662476223 662476024 7.300000e-92 348.0
12 TraesCS3D01G385400 chr3B 89.130 276 26 3 1 275 662481160 662480888 1.220000e-89 340.0
13 TraesCS3D01G385400 chr3B 88.496 226 15 5 287 504 662480518 662480296 2.720000e-66 263.0
14 TraesCS3D01G385400 chr3B 92.593 162 8 3 3396 3554 662475904 662475744 2.760000e-56 230.0
15 TraesCS3D01G385400 chr3B 97.368 38 1 0 548 585 662480141 662480104 8.240000e-07 65.8
16 TraesCS3D01G385400 chr5D 90.378 291 27 1 1415 1705 47629231 47629520 7.200000e-102 381.0
17 TraesCS3D01G385400 chr1D 88.462 312 34 2 1395 1705 489787943 489788253 3.350000e-100 375.0
18 TraesCS3D01G385400 chr6B 100.000 34 0 0 584 617 612853496 612853463 2.960000e-06 63.9
19 TraesCS3D01G385400 chr2B 90.000 50 4 1 568 617 186376109 186376157 2.960000e-06 63.9
20 TraesCS3D01G385400 chr2B 94.872 39 2 0 579 617 59659699 59659737 1.070000e-05 62.1
21 TraesCS3D01G385400 chr2B 89.796 49 1 2 651 696 45609959 45610006 3.830000e-05 60.2
22 TraesCS3D01G385400 chr1A 90.385 52 0 3 571 617 311806734 311806683 2.960000e-06 63.9
23 TraesCS3D01G385400 chr5A 97.222 36 1 0 583 618 409331919 409331954 1.070000e-05 62.1
24 TraesCS3D01G385400 chr4B 95.000 40 1 1 578 617 316805767 316805729 1.070000e-05 62.1
25 TraesCS3D01G385400 chr4B 97.222 36 1 0 582 617 572045108 572045143 1.070000e-05 62.1


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 TraesCS3D01G385400 chr3D 501029738 501033291 3553 True 6564.0 6564 100.000000 1 3554 1 chr3D.!!$R1 3553
1 TraesCS3D01G385400 chr3D 501060720 501062278 1558 True 2058.0 2058 90.549000 1034 2591 1 chr3D.!!$R2 1557
2 TraesCS3D01G385400 chr3A 640390346 640393274 2928 False 4813.0 4813 96.387000 1 2919 1 chr3A.!!$F2 2918
3 TraesCS3D01G385400 chr3A 640363379 640364950 1571 False 2122.0 2122 91.082000 1034 2605 1 chr3A.!!$F1 1571
4 TraesCS3D01G385400 chr3A 640497683 640501599 3916 False 1983.0 2564 94.191500 960 3554 2 chr3A.!!$F4 2594
5 TraesCS3D01G385400 chr3A 640481721 640482468 747 False 1208.0 1208 95.861000 221 966 1 chr3A.!!$F3 745
6 TraesCS3D01G385400 chr3B 662526355 662527924 1569 True 2109.0 2109 90.949000 1034 2605 1 chr3B.!!$R2 1571
7 TraesCS3D01G385400 chr3B 662475744 662481160 5416 True 841.3 3801 93.343333 1 3554 6 chr3B.!!$R3 3553

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
704 1190 1.542108 GGGTGCTAGTGCTCATGATCC 60.542 57.143 0.00 0.0 40.48 3.36 F
999 1493 1.133407 TTCATCACACACACGCGTAC 58.867 50.000 13.44 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 2400 1.379044 CCCTCATGGTGTCCAAGCC 60.379 63.158 0.0 0.0 36.95 4.35 R
2645 4500 1.552337 GCTCTCACCTCATCACCTCAA 59.448 52.381 0.0 0.0 0.00 3.02 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
119 121 6.840780 TCATTGTCTGATGAGTGTCTTAGA 57.159 37.500 0.00 0.00 32.50 2.10
160 163 1.995376 ATGTTTGCCGAGTTCCCTTT 58.005 45.000 0.00 0.00 0.00 3.11
653 1139 3.359950 GAGCAAATTTCTGGTCCCTCAT 58.640 45.455 0.00 0.00 37.77 2.90
704 1190 1.542108 GGGTGCTAGTGCTCATGATCC 60.542 57.143 0.00 0.00 40.48 3.36
710 1196 3.887716 GCTAGTGCTCATGATCCCAAAAT 59.112 43.478 0.00 0.00 36.03 1.82
711 1197 4.340381 GCTAGTGCTCATGATCCCAAAATT 59.660 41.667 0.00 0.00 36.03 1.82
712 1198 4.730949 AGTGCTCATGATCCCAAAATTG 57.269 40.909 0.00 0.00 0.00 2.32
713 1199 4.091549 AGTGCTCATGATCCCAAAATTGT 58.908 39.130 0.00 0.00 0.00 2.71
871 1364 7.526518 CGCACATCGTATATATACTCGTATCAC 59.473 40.741 18.46 3.50 0.00 3.06
874 1367 7.170489 ACATCGTATATATACTCGTATCACCCG 59.830 40.741 18.46 3.65 0.00 5.28
999 1493 1.133407 TTCATCACACACACGCGTAC 58.867 50.000 13.44 0.00 0.00 3.67
1968 2468 2.586792 GAGCTCGGGATGTGCCTT 59.413 61.111 0.00 0.00 37.81 4.35
2124 2624 2.265739 GTGCTGCAGACCATCCGA 59.734 61.111 20.43 0.00 0.00 4.55
2645 4500 5.183530 TGAATGGACTGGATGTGAGATTT 57.816 39.130 0.00 0.00 0.00 2.17
2726 4586 1.077005 AGAGAAGCTCACAGGAGGAGT 59.923 52.381 0.00 0.00 41.67 3.85
2727 4587 2.310349 AGAGAAGCTCACAGGAGGAGTA 59.690 50.000 0.00 0.00 41.67 2.59
2728 4588 3.052944 AGAGAAGCTCACAGGAGGAGTAT 60.053 47.826 0.00 0.00 41.67 2.12
2729 4589 3.030291 AGAAGCTCACAGGAGGAGTATG 58.970 50.000 0.00 0.00 41.67 2.39
2730 4590 1.118838 AGCTCACAGGAGGAGTATGC 58.881 55.000 0.00 0.00 41.67 3.14
2731 4591 0.249238 GCTCACAGGAGGAGTATGCG 60.249 60.000 0.00 0.00 41.67 4.73
2732 4592 1.107114 CTCACAGGAGGAGTATGCGT 58.893 55.000 0.00 0.00 37.51 5.24
2733 4593 2.298610 CTCACAGGAGGAGTATGCGTA 58.701 52.381 0.00 0.00 37.51 4.42
2734 4594 2.292016 CTCACAGGAGGAGTATGCGTAG 59.708 54.545 0.00 0.00 37.51 3.51
2735 4595 2.092592 TCACAGGAGGAGTATGCGTAGA 60.093 50.000 0.00 0.00 0.00 2.59
2736 4596 2.292016 CACAGGAGGAGTATGCGTAGAG 59.708 54.545 0.00 0.00 0.00 2.43
2737 4597 1.883275 CAGGAGGAGTATGCGTAGAGG 59.117 57.143 0.00 0.00 0.00 3.69
2738 4598 1.775459 AGGAGGAGTATGCGTAGAGGA 59.225 52.381 0.00 0.00 0.00 3.71
2822 4698 1.654105 GTGATCGTACCGCTTGACAAG 59.346 52.381 11.02 11.02 0.00 3.16
2843 4719 8.184304 ACAAGTTTTGTATAGGTATTTTGGCA 57.816 30.769 0.00 0.00 43.27 4.92
2939 4819 8.076178 ACTACTTTTTACACTGCAAATGTGATC 58.924 33.333 11.19 0.00 38.65 2.92
3105 4985 8.843262 GTTTGTTTAACCTATGTCCACTAAGTT 58.157 33.333 0.00 0.00 0.00 2.66
3152 5032 7.923344 GCTAACTGTTGAGCATTAATCTAGAGA 59.077 37.037 2.69 0.00 38.62 3.10
3153 5033 9.243637 CTAACTGTTGAGCATTAATCTAGAGAC 57.756 37.037 2.69 0.00 0.00 3.36
3154 5034 7.416964 ACTGTTGAGCATTAATCTAGAGACT 57.583 36.000 0.00 0.00 0.00 3.24
3155 5035 8.526667 ACTGTTGAGCATTAATCTAGAGACTA 57.473 34.615 0.00 0.00 0.00 2.59
3156 5036 8.629158 ACTGTTGAGCATTAATCTAGAGACTAG 58.371 37.037 0.00 0.00 0.00 2.57
3157 5037 8.753497 TGTTGAGCATTAATCTAGAGACTAGA 57.247 34.615 10.28 10.28 0.00 2.43
3158 5038 8.845227 TGTTGAGCATTAATCTAGAGACTAGAG 58.155 37.037 12.81 2.44 0.00 2.43
3177 5057 3.963676 GCATATTGCCCAATTCGCA 57.036 47.368 0.00 0.00 37.42 5.10
3218 6545 3.048337 TGGAAGGTAAAACTAGCGTGG 57.952 47.619 0.00 0.00 0.00 4.94
3400 6852 7.017319 AGCCATTACCCTAACCATATACTTC 57.983 40.000 0.00 0.00 0.00 3.01
3441 6894 1.529713 GGGAAAGGGTCGGTGCAAA 60.530 57.895 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 181 1.963515 GTTTGCCAAGTGTCCCAGATT 59.036 47.619 0.00 0.00 0.00 2.40
325 687 5.457140 TCATCACAAATGGTTTACGAAAGC 58.543 37.500 0.00 0.00 39.26 3.51
469 844 5.527214 CGTTGAGACAAAATCCATATAGGCA 59.473 40.000 0.00 0.00 37.29 4.75
481 856 6.497785 TTAGAAACAACCGTTGAGACAAAA 57.502 33.333 18.19 2.66 34.86 2.44
653 1139 0.030909 TTATAGAAGCCCACCCCGGA 60.031 55.000 0.73 0.00 36.56 5.14
710 1196 6.800072 AATAAACCACCTCCTCAAAAACAA 57.200 33.333 0.00 0.00 0.00 2.83
711 1197 6.460399 CGAAATAAACCACCTCCTCAAAAACA 60.460 38.462 0.00 0.00 0.00 2.83
712 1198 5.918576 CGAAATAAACCACCTCCTCAAAAAC 59.081 40.000 0.00 0.00 0.00 2.43
713 1199 5.595133 ACGAAATAAACCACCTCCTCAAAAA 59.405 36.000 0.00 0.00 0.00 1.94
720 1208 2.156098 TGCACGAAATAAACCACCTCC 58.844 47.619 0.00 0.00 0.00 4.30
871 1364 3.231889 ATATCTGCCTGCGCTCGGG 62.232 63.158 9.73 9.65 41.86 5.14
874 1367 1.839598 GCACATATCTGCCTGCGCTC 61.840 60.000 9.73 0.00 35.36 5.03
1329 1829 3.091190 AACCCACCACCGGACACA 61.091 61.111 9.46 0.00 0.00 3.72
1900 2400 1.379044 CCCTCATGGTGTCCAAGCC 60.379 63.158 0.00 0.00 36.95 4.35
1903 2403 2.763215 GGCCCTCATGGTGTCCAA 59.237 61.111 0.00 0.00 36.95 3.53
1968 2468 2.599281 TCGACGGCCCTGAACTCA 60.599 61.111 0.00 0.00 0.00 3.41
2645 4500 1.552337 GCTCTCACCTCATCACCTCAA 59.448 52.381 0.00 0.00 0.00 3.02
2726 4586 3.704566 ACCTTGAACATCCTCTACGCATA 59.295 43.478 0.00 0.00 0.00 3.14
2727 4587 2.501723 ACCTTGAACATCCTCTACGCAT 59.498 45.455 0.00 0.00 0.00 4.73
2728 4588 1.899814 ACCTTGAACATCCTCTACGCA 59.100 47.619 0.00 0.00 0.00 5.24
2729 4589 2.674796 ACCTTGAACATCCTCTACGC 57.325 50.000 0.00 0.00 0.00 4.42
2730 4590 5.913514 CGTAATACCTTGAACATCCTCTACG 59.086 44.000 0.00 0.00 0.00 3.51
2731 4591 6.696148 CACGTAATACCTTGAACATCCTCTAC 59.304 42.308 0.00 0.00 0.00 2.59
2732 4592 6.379133 ACACGTAATACCTTGAACATCCTCTA 59.621 38.462 0.00 0.00 0.00 2.43
2733 4593 5.187186 ACACGTAATACCTTGAACATCCTCT 59.813 40.000 0.00 0.00 0.00 3.69
2734 4594 5.291128 CACACGTAATACCTTGAACATCCTC 59.709 44.000 0.00 0.00 0.00 3.71
2735 4595 5.175859 CACACGTAATACCTTGAACATCCT 58.824 41.667 0.00 0.00 0.00 3.24
2736 4596 4.201783 GCACACGTAATACCTTGAACATCC 60.202 45.833 0.00 0.00 0.00 3.51
2737 4597 4.630069 AGCACACGTAATACCTTGAACATC 59.370 41.667 0.00 0.00 0.00 3.06
2738 4598 4.575885 AGCACACGTAATACCTTGAACAT 58.424 39.130 0.00 0.00 0.00 2.71
2822 4698 7.855904 CGATCTGCCAAAATACCTATACAAAAC 59.144 37.037 0.00 0.00 0.00 2.43
3011 4891 9.408648 CTGGATTTAGTTGGTATTCTAAACCAT 57.591 33.333 13.49 0.00 46.16 3.55
3200 5080 7.832503 TTATAACCACGCTAGTTTTACCTTC 57.167 36.000 0.00 0.00 0.00 3.46
3400 6852 9.142515 TCCCTTAAATATATACGCAACATAACG 57.857 33.333 0.00 0.00 0.00 3.18
3441 6894 3.970640 TGGCATTAACACTTTCCCCTTTT 59.029 39.130 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.