Multiple sequence alignment - TraesCS2D01G580100

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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 TraesCS2D01G580100 chr2D 100.000 3662 0 0 1 3662 642208221 642211882 0.000000e+00 6763.0
1 TraesCS2D01G580100 chr2D 85.373 2092 264 17 846 2928 642216350 642218408 0.000000e+00 2130.0
2 TraesCS2D01G580100 chr2D 87.488 1079 121 9 761 1831 642124016 642122944 0.000000e+00 1232.0
3 TraesCS2D01G580100 chr2D 84.351 786 98 13 1830 2612 642121574 642120811 0.000000e+00 747.0
4 TraesCS2D01G580100 chr2D 91.453 117 8 2 3446 3561 642113575 642113460 3.790000e-35 159.0
5 TraesCS2D01G580100 chr2D 85.981 107 14 1 275 381 642348078 642347973 2.990000e-21 113.0
6 TraesCS2D01G580100 chr2D 92.063 63 4 1 211 272 642348387 642348325 1.810000e-13 87.9
7 TraesCS2D01G580100 chr2D 92.000 50 4 0 3511 3560 642338045 642337996 1.820000e-08 71.3
8 TraesCS2D01G580100 chr2D 95.455 44 1 1 464 506 642208645 642208688 6.560000e-08 69.4
9 TraesCS2D01G580100 chr2D 95.455 44 1 1 425 468 642208684 642208726 6.560000e-08 69.4
10 TraesCS2D01G580100 chr2D 100.000 33 0 0 3447 3479 642218459 642218491 1.100000e-05 62.1
11 TraesCS2D01G580100 chr2D 88.462 52 5 1 61 111 642348461 642348410 1.100000e-05 62.1
12 TraesCS2D01G580100 chr2D 100.000 31 0 0 3546 3576 642338031 642338001 1.420000e-04 58.4
13 TraesCS2D01G580100 chr2B 96.124 3122 67 14 585 3662 799609088 799605977 0.000000e+00 5046.0
14 TraesCS2D01G580100 chr2B 85.212 2191 267 29 546 2702 799548825 799546658 0.000000e+00 2198.0
15 TraesCS2D01G580100 chr2B 87.385 1950 198 26 781 2692 799568020 799566081 0.000000e+00 2194.0
16 TraesCS2D01G580100 chr2B 86.638 1886 226 18 846 2718 799537751 799535879 0.000000e+00 2063.0
17 TraesCS2D01G580100 chr2B 93.629 518 23 8 1 515 799609585 799609075 0.000000e+00 765.0
18 TraesCS2D01G580100 chr2B 74.571 700 126 25 3012 3661 799606996 799606299 3.630000e-65 259.0
19 TraesCS2D01G580100 chr2B 89.524 105 11 0 171 275 799549756 799549652 2.290000e-27 134.0
20 TraesCS2D01G580100 chr2B 88.350 103 11 1 171 272 799568567 799568465 4.970000e-24 122.0
21 TraesCS2D01G580100 chr2B 86.916 107 6 3 6 112 799568660 799568562 2.990000e-21 113.0
22 TraesCS2D01G580100 chr2B 95.122 41 0 2 427 467 799609123 799609085 3.050000e-06 63.9
23 TraesCS2D01G580100 chr2A 85.175 2091 264 27 846 2925 767024507 767026562 0.000000e+00 2102.0
24 TraesCS2D01G580100 chr2A 85.088 2099 252 38 515 2579 767032597 767034668 0.000000e+00 2085.0
25 TraesCS2D01G580100 chr2A 87.063 286 25 6 846 1126 767143717 767143439 2.750000e-81 313.0
26 TraesCS2D01G580100 chr2A 93.750 96 6 0 171 266 767032012 767032107 1.060000e-30 145.0
27 TraesCS2D01G580100 chr2A 85.859 99 14 0 1230 1328 35489375 35489473 5.000000e-19 106.0
28 TraesCS2D01G580100 chr3B 85.329 2038 238 38 698 2686 829251350 829253375 0.000000e+00 2050.0
29 TraesCS2D01G580100 chr4D 80.943 530 92 7 2164 2686 504258153 504258680 9.460000e-111 411.0
30 TraesCS2D01G580100 chr4D 91.667 84 7 0 186 269 504243356 504243439 2.310000e-22 117.0
31 TraesCS2D01G580100 chr1A 91.667 48 3 1 109 156 517102821 517102775 8.490000e-07 65.8
32 TraesCS2D01G580100 chr7D 86.538 52 6 1 103 154 219387796 219387846 5.110000e-04 56.5


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 TraesCS2D01G580100 chr2D 642208221 642211882 3661 False 2300.600000 6763 96.970000 1 3662 3 chr2D.!!$F1 3661
1 TraesCS2D01G580100 chr2D 642216350 642218491 2141 False 1096.050000 2130 92.686500 846 3479 2 chr2D.!!$F2 2633
2 TraesCS2D01G580100 chr2D 642120811 642124016 3205 True 989.500000 1232 85.919500 761 2612 2 chr2D.!!$R2 1851
3 TraesCS2D01G580100 chr2B 799535879 799537751 1872 True 2063.000000 2063 86.638000 846 2718 1 chr2B.!!$R1 1872
4 TraesCS2D01G580100 chr2B 799605977 799609585 3608 True 1533.475000 5046 89.861500 1 3662 4 chr2B.!!$R4 3661
5 TraesCS2D01G580100 chr2B 799546658 799549756 3098 True 1166.000000 2198 87.368000 171 2702 2 chr2B.!!$R2 2531
6 TraesCS2D01G580100 chr2B 799566081 799568660 2579 True 809.666667 2194 87.550333 6 2692 3 chr2B.!!$R3 2686
7 TraesCS2D01G580100 chr2A 767024507 767026562 2055 False 2102.000000 2102 85.175000 846 2925 1 chr2A.!!$F2 2079
8 TraesCS2D01G580100 chr2A 767032012 767034668 2656 False 1115.000000 2085 89.419000 171 2579 2 chr2A.!!$F3 2408
9 TraesCS2D01G580100 chr3B 829251350 829253375 2025 False 2050.000000 2050 85.329000 698 2686 1 chr3B.!!$F1 1988
10 TraesCS2D01G580100 chr4D 504258153 504258680 527 False 411.000000 411 80.943000 2164 2686 1 chr4D.!!$F2 522

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
541 1187 1.129437 GTGCAAAGATGAGCTTCGTCC 59.871 52.381 0.0 0.0 35.24 4.79 F
1339 2029 1.815408 GCCACCTGCTCTCTTTTGTCA 60.815 52.381 0.0 0.0 36.87 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 4505 4.032960 TGATTGCCTCCACAACATAACT 57.967 40.909 0.0 0.0 31.03 2.24 R
2778 4897 0.252881 TCTGTCCAGCTCCTCCCAAT 60.253 55.000 0.0 0.0 0.00 3.16 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
136 137 6.044871 CCCCCTCCATCCCATAATATTAGATC 59.955 46.154 1.02 0.00 0.00 2.75
413 1050 3.835395 CCCTGATAGAACATACTCCCTCC 59.165 52.174 0.00 0.00 0.00 4.30
452 1089 9.744468 ATGTTTTAACTGTGGTTTACTCATTTC 57.256 29.630 0.00 0.00 36.92 2.17
454 1091 9.233232 GTTTTAACTGTGGTTTACTCATTTCAG 57.767 33.333 0.00 0.00 36.92 3.02
456 1093 6.619801 AACTGTGGTTTACTCATTTCAGTC 57.380 37.500 0.00 0.00 34.50 3.51
457 1094 5.063880 ACTGTGGTTTACTCATTTCAGTCC 58.936 41.667 0.00 0.00 30.65 3.85
458 1095 4.062293 TGTGGTTTACTCATTTCAGTCCG 58.938 43.478 0.00 0.00 0.00 4.79
459 1096 4.062991 GTGGTTTACTCATTTCAGTCCGT 58.937 43.478 0.00 0.00 0.00 4.69
463 1100 7.546667 GTGGTTTACTCATTTCAGTCCGTATAA 59.453 37.037 0.00 0.00 0.00 0.98
464 1101 8.262227 TGGTTTACTCATTTCAGTCCGTATAAT 58.738 33.333 0.00 0.00 0.00 1.28
498 1135 5.221481 TGTGGTTTACTCATTTCAGTCCGTA 60.221 40.000 0.00 0.00 0.00 4.02
500 1137 7.037438 GTGGTTTACTCATTTCAGTCCGTATA 58.963 38.462 0.00 0.00 0.00 1.47
501 1138 7.546667 GTGGTTTACTCATTTCAGTCCGTATAA 59.453 37.037 0.00 0.00 0.00 0.98
502 1139 8.262227 TGGTTTACTCATTTCAGTCCGTATAAT 58.738 33.333 0.00 0.00 0.00 1.28
503 1140 9.754382 GGTTTACTCATTTCAGTCCGTATAATA 57.246 33.333 0.00 0.00 0.00 0.98
536 1182 2.649331 GCATGTGCAAAGATGAGCTT 57.351 45.000 0.00 0.00 41.59 3.74
538 1184 2.782163 CATGTGCAAAGATGAGCTTCG 58.218 47.619 0.00 0.00 35.24 3.79
541 1187 1.129437 GTGCAAAGATGAGCTTCGTCC 59.871 52.381 0.00 0.00 35.24 4.79
544 1190 2.485814 GCAAAGATGAGCTTCGTCCTTT 59.514 45.455 0.00 0.00 35.24 3.11
904 1589 7.008021 TGTCATGCTGGCTCTAATATTATCA 57.992 36.000 0.00 0.00 0.00 2.15
1339 2029 1.815408 GCCACCTGCTCTCTTTTGTCA 60.815 52.381 0.00 0.00 36.87 3.58
2398 4505 3.316588 GTCATCTCGTGAGGAAGAGCATA 59.683 47.826 3.12 0.00 37.56 3.14
2408 4518 6.109359 GTGAGGAAGAGCATAGTTATGTTGT 58.891 40.000 1.49 0.00 36.11 3.32
2409 4519 6.036517 GTGAGGAAGAGCATAGTTATGTTGTG 59.963 42.308 1.49 0.00 36.11 3.33
2410 4520 5.431765 AGGAAGAGCATAGTTATGTTGTGG 58.568 41.667 1.49 0.00 36.11 4.17
2582 4698 1.152830 GGGGGCTGGACAGAACAAA 59.847 57.895 3.00 0.00 0.00 2.83
2734 4853 2.753931 GAACAAGGCCGGCTTTGCAG 62.754 60.000 41.30 24.73 36.63 4.41
2751 4870 3.159984 GCGTGAAGCGGAACTGAG 58.840 61.111 0.00 0.00 41.69 3.35
2778 4897 2.106511 CAAGGGAGGAGTTGGACAGAAA 59.893 50.000 0.00 0.00 0.00 2.52
2794 4913 1.283321 AGAAATTGGGAGGAGCTGGAC 59.717 52.381 0.00 0.00 0.00 4.02
2810 4929 0.041982 GGACAGAAGGAGGGAGGAGT 59.958 60.000 0.00 0.00 0.00 3.85
2837 4956 2.702592 TATAAGGTTTGAGGTGGGCG 57.297 50.000 0.00 0.00 0.00 6.13
3096 5215 0.323629 CTGCCCGGTACAAAGGAGAA 59.676 55.000 0.00 0.00 0.00 2.87
3103 5222 3.064931 CGGTACAAAGGAGAAGTTGGAC 58.935 50.000 0.00 0.00 37.77 4.02
3135 5254 4.421131 GAGGAGCTGAATATAAGGAGGGA 58.579 47.826 0.00 0.00 0.00 4.20
3143 5262 4.140686 TGAATATAAGGAGGGAGGAGCTGA 60.141 45.833 0.00 0.00 0.00 4.26
3164 5304 2.704190 TATAAGGAGGGAGGAGCTGG 57.296 55.000 0.00 0.00 0.00 4.85
3188 5328 0.821711 TTCAAGGTTTGAGGTGGCCG 60.822 55.000 0.00 0.00 41.38 6.13
3199 5339 2.266055 GTGGCCGGGACAAGAGAG 59.734 66.667 2.81 0.00 0.00 3.20
3212 5352 2.235898 ACAAGAGAGAAGATGGAGGTGC 59.764 50.000 0.00 0.00 0.00 5.01
3249 5389 4.279922 GGAGGAGCTAGATAGAACAAGGAC 59.720 50.000 0.00 0.00 0.00 3.85
3269 5409 0.106967 GGGGCTGGAGAGAATGGTTC 60.107 60.000 0.00 0.00 0.00 3.62
3278 5418 3.381949 GAGAGAATGGTTCGGGATTACG 58.618 50.000 0.00 0.00 34.02 3.18
3301 5441 4.798682 GGGAGGGAGCGAGGGGAA 62.799 72.222 0.00 0.00 0.00 3.97
3356 5496 1.202330 CAGGAGAATGGAGGAGCTGT 58.798 55.000 0.00 0.00 0.00 4.40
3369 5509 1.552792 GGAGCTGTACAGAAGAAGGCT 59.447 52.381 27.08 14.89 0.00 4.58
3397 5537 2.600792 GCAACGTGAAGCAGAACTGAAG 60.601 50.000 5.97 0.00 0.00 3.02
3407 5547 5.104259 AGCAGAACTGAAGGGTATAAAGG 57.896 43.478 5.97 0.00 0.00 3.11
3463 5603 1.270907 GGGAGGAGCTGAACAGAAGA 58.729 55.000 5.97 0.00 0.00 2.87
3464 5604 1.625818 GGGAGGAGCTGAACAGAAGAA 59.374 52.381 5.97 0.00 0.00 2.52
3564 5725 1.650528 CTGGACAGAAGAAGGGAGGT 58.349 55.000 0.00 0.00 0.00 3.85
3584 5745 3.198872 GTGCTGGACAGAATAGTTAGGC 58.801 50.000 3.00 0.00 0.00 3.93
3585 5746 3.107601 TGCTGGACAGAATAGTTAGGCT 58.892 45.455 3.00 0.00 0.00 4.58
3590 5751 5.657474 TGGACAGAATAGTTAGGCTTTACG 58.343 41.667 0.00 0.00 0.00 3.18
3604 5765 0.616679 TTTACGGAGGAGGGTGGGAG 60.617 60.000 0.00 0.00 0.00 4.30
3624 5785 4.479619 GAGCTGGACATGACAATGAAAAC 58.520 43.478 0.00 0.00 37.24 2.43
3633 5794 6.176183 ACATGACAATGAAAACTCTAGAGGG 58.824 40.000 23.50 0.75 37.24 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 5.296966 TCTAATATTATGGGATGGAGGGGG 58.703 45.833 0.00 0.0 0.00 5.40
136 137 7.253618 CGTCCCATAAAATAAGATTGCAAAACG 60.254 37.037 1.71 0.0 0.00 3.60
152 153 2.112998 CTACCCACTCCGTCCCATAAA 58.887 52.381 0.00 0.0 0.00 1.40
437 1074 4.062991 ACGGACTGAAATGAGTAAACCAC 58.937 43.478 0.00 0.0 0.00 4.16
439 1076 8.658499 ATTATACGGACTGAAATGAGTAAACC 57.342 34.615 0.00 0.0 0.00 3.27
467 1104 9.131791 ACTGAAATGAGTAAACCACAGTAAAAT 57.868 29.630 0.00 0.0 35.95 1.82
517 1163 2.527100 GAAGCTCATCTTTGCACATGC 58.473 47.619 0.00 0.0 36.99 4.06
904 1589 2.888414 CAAAAGAAATACACCCCACGGT 59.112 45.455 0.00 0.0 46.31 4.83
975 1665 0.106708 ACCACTGAATGCACACGAGT 59.893 50.000 0.00 0.0 0.00 4.18
1339 2029 2.665000 CACTCCCACCGTCTGCAT 59.335 61.111 0.00 0.0 0.00 3.96
2398 4505 4.032960 TGATTGCCTCCACAACATAACT 57.967 40.909 0.00 0.0 31.03 2.24
2408 4518 4.410099 AGACAATTTCTTGATTGCCTCCA 58.590 39.130 0.00 0.0 39.97 3.86
2409 4519 6.151817 AGTTAGACAATTTCTTGATTGCCTCC 59.848 38.462 0.00 0.0 39.97 4.30
2410 4520 7.150783 AGTTAGACAATTTCTTGATTGCCTC 57.849 36.000 0.00 0.0 39.97 4.70
2734 4853 3.016474 GCTCAGTTCCGCTTCACGC 62.016 63.158 0.00 0.0 41.76 5.34
2751 4870 0.391263 CAACTCCTCCCTTGTACCGC 60.391 60.000 0.00 0.0 0.00 5.68
2778 4897 0.252881 TCTGTCCAGCTCCTCCCAAT 60.253 55.000 0.00 0.0 0.00 3.16
2794 4913 0.908198 CCAACTCCTCCCTCCTTCTG 59.092 60.000 0.00 0.0 0.00 3.02
2810 4929 5.949354 CCACCTCAAACCTTATATTGTCCAA 59.051 40.000 0.00 0.0 0.00 3.53
2837 4956 3.412237 TGTAGTGCCCACCTCTAAAAC 57.588 47.619 0.00 0.0 0.00 2.43
3043 5162 2.941480 AGCAAATCCAGCCCTATTCTG 58.059 47.619 0.00 0.0 0.00 3.02
3073 5192 1.296715 CTTTGTACCGGGCAGCTCT 59.703 57.895 6.32 0.0 0.00 4.09
3081 5200 2.038033 TCCAACTTCTCCTTTGTACCGG 59.962 50.000 0.00 0.0 0.00 5.28
3096 5215 1.421646 CCTCCCAACTTCTGTCCAACT 59.578 52.381 0.00 0.0 0.00 3.16
3103 5222 0.979665 TCAGCTCCTCCCAACTTCTG 59.020 55.000 0.00 0.0 0.00 3.02
3135 5254 4.424842 CTCCCTCCTTATATTCAGCTCCT 58.575 47.826 0.00 0.0 0.00 3.69
3143 5262 3.116159 ACCAGCTCCTCCCTCCTTATATT 60.116 47.826 0.00 0.0 0.00 1.28
3164 5304 3.552890 GCCACCTCAAACCTTGAATTGAC 60.553 47.826 0.00 0.0 39.58 3.18
3188 5328 2.433970 CCTCCATCTTCTCTCTTGTCCC 59.566 54.545 0.00 0.0 0.00 4.46
3199 5339 2.027745 TCTGTTCAGCACCTCCATCTTC 60.028 50.000 0.00 0.0 0.00 2.87
3212 5352 2.354604 GCTCCTCCCTTCTTCTGTTCAG 60.355 54.545 0.00 0.0 0.00 3.02
3249 5389 1.915078 AACCATTCTCTCCAGCCCCG 61.915 60.000 0.00 0.0 0.00 5.73
3269 5409 1.745320 CTCCCTCCACCGTAATCCCG 61.745 65.000 0.00 0.0 0.00 5.14
3278 5418 4.779733 TCGCTCCCTCCCTCCACC 62.780 72.222 0.00 0.0 0.00 4.61
3301 5441 4.646492 AGCTTTTCCATTGTTCTGTTCAGT 59.354 37.500 0.00 0.0 0.00 3.41
3356 5496 3.181455 TGCAAAGTCAGCCTTCTTCTGTA 60.181 43.478 0.00 0.0 33.48 2.74
3369 5509 1.063912 CTGCTTCACGTTGCAAAGTCA 59.936 47.619 15.40 9.4 38.81 3.41
3397 5537 5.071923 ACTTATGTCCAGCTCCTTTATACCC 59.928 44.000 0.00 0.0 0.00 3.69
3407 5547 2.420687 CCTCCCAACTTATGTCCAGCTC 60.421 54.545 0.00 0.0 0.00 4.09
3463 5603 0.618968 AATCGTCCAGCTCCTCCCTT 60.619 55.000 0.00 0.0 0.00 3.95
3464 5604 0.618968 AAATCGTCCAGCTCCTCCCT 60.619 55.000 0.00 0.0 0.00 4.20
3564 5725 3.107601 AGCCTAACTATTCTGTCCAGCA 58.892 45.455 0.00 0.0 0.00 4.41
3584 5745 0.616679 TCCCACCCTCCTCCGTAAAG 60.617 60.000 0.00 0.0 0.00 1.85
3585 5746 0.616679 CTCCCACCCTCCTCCGTAAA 60.617 60.000 0.00 0.0 0.00 2.01
3590 5751 3.086600 CAGCTCCCACCCTCCTCC 61.087 72.222 0.00 0.0 0.00 4.30
3604 5765 4.217118 AGAGTTTTCATTGTCATGTCCAGC 59.783 41.667 0.00 0.0 0.00 4.85
3633 5794 2.572104 TCCTCCCTTCTTTTGTCTAGCC 59.428 50.000 0.00 0.0 0.00 3.93


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

AutoCloner maintained by Alex Coulton.