Multiple sequence alignment - TraesCS3A01G008700

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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 TraesCS3A01G008700 chr3A 100.000 3133 0 0 1 3133 8213751 8210619 0.000000e+00 5786
1 TraesCS3A01G008700 chr3A 95.569 677 28 2 2457 3133 52989677 52990351 0.000000e+00 1083
2 TraesCS3A01G008700 chr3A 91.791 134 10 1 1 133 433993639 433993506 5.340000e-43 185
3 TraesCS3A01G008700 chr3D 90.963 2025 121 39 308 2314 1109024 1111004 0.000000e+00 2669
4 TraesCS3A01G008700 chr3D 96.455 677 24 0 2457 3133 166993938 166993262 0.000000e+00 1118
5 TraesCS3A01G008700 chr3D 95.716 677 29 0 2457 3133 94763669 94764345 0.000000e+00 1090
6 TraesCS3A01G008700 chr3D 96.386 166 3 2 128 291 1108339 1108503 1.430000e-68 270
7 TraesCS3A01G008700 chrUn 87.708 1806 134 42 559 2314 34136122 34134355 0.000000e+00 2025
8 TraesCS3A01G008700 chrUn 95.890 73 2 1 310 381 34137157 34137085 1.970000e-22 117
9 TraesCS3A01G008700 chr2A 97.046 677 20 0 2457 3133 95212375 95213051 0.000000e+00 1140
10 TraesCS3A01G008700 chr2A 94.978 677 34 0 2457 3133 100955191 100955867 0.000000e+00 1062
11 TraesCS3A01G008700 chr2A 91.852 135 10 1 1 134 34169839 34169973 1.480000e-43 187
12 TraesCS3A01G008700 chr2A 91.852 135 10 1 1 134 154412441 154412575 1.480000e-43 187
13 TraesCS3A01G008700 chr2A 97.674 86 2 0 2315 2400 78255295 78255210 7.000000e-32 148
14 TraesCS3A01G008700 chr7A 96.160 677 26 0 2457 3133 510753996 510753320 0.000000e+00 1107
15 TraesCS3A01G008700 chr7A 95.697 674 28 1 2457 3130 82129914 82130586 0.000000e+00 1083
16 TraesCS3A01G008700 chr7A 91.791 134 10 1 1 133 709991778 709991911 5.340000e-43 185
17 TraesCS3A01G008700 chr7A 97.701 87 2 0 2314 2400 79784534 79784620 1.950000e-32 150
18 TraesCS3A01G008700 chr5A 95.421 677 31 0 2457 3133 11169634 11170310 0.000000e+00 1079
19 TraesCS3A01G008700 chr5A 95.421 677 30 1 2457 3133 11150790 11151465 0.000000e+00 1077
20 TraesCS3A01G008700 chr5A 88.485 165 13 5 1 164 81350412 81350571 8.870000e-46 195
21 TraesCS3A01G008700 chr5A 95.506 89 3 1 2312 2400 11150717 11150804 1.170000e-29 141
22 TraesCS3A01G008700 chr5A 95.506 89 3 1 2312 2400 11169561 11169648 1.170000e-29 141
23 TraesCS3A01G008700 chr1B 92.593 135 9 1 1 134 240502123 240501989 3.190000e-45 193
24 TraesCS3A01G008700 chr5D 92.969 128 8 1 7 133 350229037 350228910 5.340000e-43 185
25 TraesCS3A01G008700 chr5D 91.729 133 11 0 1 133 478706997 478706865 5.340000e-43 185
26 TraesCS3A01G008700 chr6A 91.667 132 10 1 7 137 432233740 432233609 6.900000e-42 182
27 TraesCS3A01G008700 chr7D 96.591 88 3 0 2313 2400 598419855 598419768 2.520000e-31 147
28 TraesCS3A01G008700 chr4D 94.624 93 5 0 2308 2400 16788506 16788414 9.060000e-31 145
29 TraesCS3A01G008700 chr4D 96.512 86 3 0 2315 2400 440412969 440413054 3.260000e-30 143
30 TraesCS3A01G008700 chr1A 96.552 87 2 1 2314 2400 554602659 554602574 3.260000e-30 143
31 TraesCS3A01G008700 chr2D 93.548 93 6 0 2308 2400 628850045 628850137 4.210000e-29 139


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 TraesCS3A01G008700 chr3A 8210619 8213751 3132 True 5786.0 5786 100.0000 1 3133 1 chr3A.!!$R1 3132
1 TraesCS3A01G008700 chr3A 52989677 52990351 674 False 1083.0 1083 95.5690 2457 3133 1 chr3A.!!$F1 676
2 TraesCS3A01G008700 chr3D 1108339 1111004 2665 False 1469.5 2669 93.6745 128 2314 2 chr3D.!!$F2 2186
3 TraesCS3A01G008700 chr3D 166993262 166993938 676 True 1118.0 1118 96.4550 2457 3133 1 chr3D.!!$R1 676
4 TraesCS3A01G008700 chr3D 94763669 94764345 676 False 1090.0 1090 95.7160 2457 3133 1 chr3D.!!$F1 676
5 TraesCS3A01G008700 chrUn 34134355 34137157 2802 True 1071.0 2025 91.7990 310 2314 2 chrUn.!!$R1 2004
6 TraesCS3A01G008700 chr2A 95212375 95213051 676 False 1140.0 1140 97.0460 2457 3133 1 chr2A.!!$F2 676
7 TraesCS3A01G008700 chr2A 100955191 100955867 676 False 1062.0 1062 94.9780 2457 3133 1 chr2A.!!$F3 676
8 TraesCS3A01G008700 chr7A 510753320 510753996 676 True 1107.0 1107 96.1600 2457 3133 1 chr7A.!!$R1 676
9 TraesCS3A01G008700 chr7A 82129914 82130586 672 False 1083.0 1083 95.6970 2457 3130 1 chr7A.!!$F2 673
10 TraesCS3A01G008700 chr5A 11169561 11170310 749 False 610.0 1079 95.4635 2312 3133 2 chr5A.!!$F3 821
11 TraesCS3A01G008700 chr5A 11150717 11151465 748 False 609.0 1077 95.4635 2312 3133 2 chr5A.!!$F2 821

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
425 931 0.031857 CATGGCGGTTTCTGCAACAA 59.968 50.0 3.03 0.0 37.07 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 3773 0.193574 AGAGAACTCCCCCACCTGAA 59.806 55.0 0.0 0.0 0.0 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
40 41 9.625747 TCATACCAAATATTGCACTAATCAAGA 57.374 29.630 0.00 0.00 0.00 3.02
50 51 8.970691 ATTGCACTAATCAAGAATTAACACAC 57.029 30.769 0.00 0.00 29.44 3.82
51 52 7.503521 TGCACTAATCAAGAATTAACACACA 57.496 32.000 0.00 0.00 29.44 3.72
52 53 7.935520 TGCACTAATCAAGAATTAACACACAA 58.064 30.769 0.00 0.00 29.44 3.33
53 54 8.409371 TGCACTAATCAAGAATTAACACACAAA 58.591 29.630 0.00 0.00 29.44 2.83
54 55 9.410556 GCACTAATCAAGAATTAACACACAAAT 57.589 29.630 0.00 0.00 29.44 2.32
61 62 9.278978 TCAAGAATTAACACACAAATAGTAGCA 57.721 29.630 0.00 0.00 0.00 3.49
65 66 9.651718 GAATTAACACACAAATAGTAGCATAGC 57.348 33.333 0.00 0.00 0.00 2.97
66 67 8.964476 ATTAACACACAAATAGTAGCATAGCT 57.036 30.769 0.00 0.00 43.41 3.32
68 69 9.878667 TTAACACACAAATAGTAGCATAGCTAA 57.121 29.630 0.00 0.00 43.07 3.09
69 70 8.964476 AACACACAAATAGTAGCATAGCTAAT 57.036 30.769 0.00 4.37 43.07 1.73
73 74 9.877178 ACACAAATAGTAGCATAGCTAATATCC 57.123 33.333 16.32 0.00 46.82 2.59
74 75 9.025020 CACAAATAGTAGCATAGCTAATATCCG 57.975 37.037 16.32 13.20 46.82 4.18
75 76 7.707035 ACAAATAGTAGCATAGCTAATATCCGC 59.293 37.037 16.32 0.00 46.82 5.54
76 77 6.961360 ATAGTAGCATAGCTAATATCCGCA 57.039 37.500 11.80 0.00 45.24 5.69
77 78 5.860941 AGTAGCATAGCTAATATCCGCAT 57.139 39.130 0.00 0.00 43.07 4.73
78 79 5.595885 AGTAGCATAGCTAATATCCGCATG 58.404 41.667 0.00 0.00 43.07 4.06
79 80 3.201290 AGCATAGCTAATATCCGCATGC 58.799 45.455 7.91 7.91 36.99 4.06
80 81 2.938451 GCATAGCTAATATCCGCATGCA 59.062 45.455 19.57 0.00 38.88 3.96
81 82 3.374988 GCATAGCTAATATCCGCATGCAA 59.625 43.478 19.57 5.23 38.88 4.08
82 83 4.036027 GCATAGCTAATATCCGCATGCAAT 59.964 41.667 19.57 12.85 38.88 3.56
83 84 5.449588 GCATAGCTAATATCCGCATGCAATT 60.450 40.000 19.57 13.11 38.88 2.32
84 85 4.430137 AGCTAATATCCGCATGCAATTG 57.570 40.909 19.57 0.00 0.00 2.32
85 86 4.074259 AGCTAATATCCGCATGCAATTGA 58.926 39.130 19.57 8.54 0.00 2.57
86 87 4.083110 AGCTAATATCCGCATGCAATTGAC 60.083 41.667 19.57 1.02 0.00 3.18
87 88 4.320421 GCTAATATCCGCATGCAATTGACA 60.320 41.667 19.57 7.33 0.00 3.58
88 89 4.859304 AATATCCGCATGCAATTGACAT 57.141 36.364 19.57 9.43 0.00 3.06
89 90 5.963176 AATATCCGCATGCAATTGACATA 57.037 34.783 19.57 2.95 0.00 2.29
90 91 6.519679 AATATCCGCATGCAATTGACATAT 57.480 33.333 19.57 5.07 0.00 1.78
91 92 4.859304 ATCCGCATGCAATTGACATATT 57.141 36.364 19.57 0.00 0.00 1.28
92 93 3.967401 TCCGCATGCAATTGACATATTG 58.033 40.909 19.57 3.97 38.31 1.90
110 111 9.329913 GACATATTGCCTAAATATTAAAGTGCG 57.670 33.333 0.00 0.00 39.07 5.34
111 112 8.846211 ACATATTGCCTAAATATTAAAGTGCGT 58.154 29.630 0.00 0.00 39.07 5.24
112 113 9.677567 CATATTGCCTAAATATTAAAGTGCGTT 57.322 29.630 0.00 0.00 39.07 4.84
113 114 7.985634 ATTGCCTAAATATTAAAGTGCGTTG 57.014 32.000 0.00 0.00 0.00 4.10
114 115 5.336744 TGCCTAAATATTAAAGTGCGTTGC 58.663 37.500 0.00 0.00 0.00 4.17
115 116 5.106118 TGCCTAAATATTAAAGTGCGTTGCA 60.106 36.000 0.00 0.00 35.60 4.08
161 162 4.408182 AGTTACCTATCGCTCTGCATTT 57.592 40.909 0.00 0.00 0.00 2.32
373 879 5.454613 CCTGTGGGGCCCATATTTTAATTTC 60.455 44.000 31.48 11.68 35.28 2.17
383 889 7.466320 GCCCATATTTTAATTTCTGCTGCTTTG 60.466 37.037 0.00 0.00 0.00 2.77
385 891 8.938906 CCATATTTTAATTTCTGCTGCTTTGTT 58.061 29.630 0.00 0.00 0.00 2.83
421 927 1.832883 AATACATGGCGGTTTCTGCA 58.167 45.000 0.00 0.00 0.00 4.41
422 928 1.832883 ATACATGGCGGTTTCTGCAA 58.167 45.000 0.00 0.00 0.00 4.08
423 929 0.878416 TACATGGCGGTTTCTGCAAC 59.122 50.000 0.00 0.00 34.18 4.17
424 930 1.106351 ACATGGCGGTTTCTGCAACA 61.106 50.000 0.00 0.00 37.07 3.33
425 931 0.031857 CATGGCGGTTTCTGCAACAA 59.968 50.000 3.03 0.00 37.07 2.83
426 932 0.031994 ATGGCGGTTTCTGCAACAAC 59.968 50.000 3.03 0.00 37.07 3.32
427 933 1.315981 TGGCGGTTTCTGCAACAACA 61.316 50.000 9.32 0.00 37.07 3.33
428 934 0.179124 GGCGGTTTCTGCAACAACAA 60.179 50.000 9.32 0.00 37.07 2.83
491 997 0.521291 CACTAACATGTGGGCCAACG 59.479 55.000 8.40 1.41 34.56 4.10
544 1050 2.333938 CGGGTACGTATGGAGGCG 59.666 66.667 0.00 0.00 34.81 5.52
553 1059 1.336148 CGTATGGAGGCGCCGTATTTA 60.336 52.381 23.20 7.93 40.22 1.40
557 1063 0.460635 GGAGGCGCCGTATTTACACA 60.461 55.000 23.20 0.00 0.00 3.72
573 1864 9.584839 GTATTTACACAGTAAAACAAGTTACGG 57.415 33.333 6.45 0.00 38.71 4.02
574 1865 7.608308 TTTACACAGTAAAACAAGTTACGGT 57.392 32.000 0.20 0.00 41.24 4.83
686 1983 5.742063 TCTCTTGTGAGACGATTAGGAGTA 58.258 41.667 0.00 0.00 43.73 2.59
688 1985 7.506971 TCTCTTGTGAGACGATTAGGAGTATA 58.493 38.462 0.00 0.00 43.73 1.47
697 1994 9.221933 GAGACGATTAGGAGTATATTCTGAGAA 57.778 37.037 0.00 0.00 0.00 2.87
698 1995 9.005777 AGACGATTAGGAGTATATTCTGAGAAC 57.994 37.037 0.00 0.00 0.00 3.01
699 1996 8.693120 ACGATTAGGAGTATATTCTGAGAACA 57.307 34.615 0.00 0.00 0.00 3.18
700 1997 9.132923 ACGATTAGGAGTATATTCTGAGAACAA 57.867 33.333 0.00 0.00 0.00 2.83
701 1998 9.619316 CGATTAGGAGTATATTCTGAGAACAAG 57.381 37.037 0.00 0.00 0.00 3.16
801 2105 0.532573 ACACTCCCGTAGCATCAGTG 59.467 55.000 0.00 0.00 40.33 3.66
927 2236 0.533755 GGATCAATGGCGTGAGGAGG 60.534 60.000 0.00 0.00 0.00 4.30
929 2238 0.467384 ATCAATGGCGTGAGGAGGAG 59.533 55.000 0.00 0.00 0.00 3.69
930 2239 1.817099 CAATGGCGTGAGGAGGAGC 60.817 63.158 0.00 0.00 0.00 4.70
938 2247 1.989508 TGAGGAGGAGCCATCGCAA 60.990 57.895 0.00 0.00 40.02 4.85
964 2273 5.335740 GGAACACTCGAGAGAATGAACAGTA 60.336 44.000 21.68 0.00 40.33 2.74
966 2275 4.762765 ACACTCGAGAGAATGAACAGTACT 59.237 41.667 21.68 0.00 40.33 2.73
967 2276 5.938710 ACACTCGAGAGAATGAACAGTACTA 59.061 40.000 21.68 0.00 40.33 1.82
968 2277 6.128227 ACACTCGAGAGAATGAACAGTACTAC 60.128 42.308 21.68 0.00 40.33 2.73
969 2278 6.092944 CACTCGAGAGAATGAACAGTACTACT 59.907 42.308 21.68 0.00 40.33 2.57
987 2304 0.526524 CTTAGCTCGCTCTTGGTCCG 60.527 60.000 0.00 0.00 0.00 4.79
1030 2347 3.096633 AAGACGAACACGGTGGGCA 62.097 57.895 13.48 0.00 0.00 5.36
1164 2486 2.186076 GTACTACACATGCTCTGCGTC 58.814 52.381 0.00 0.00 0.00 5.19
1165 2487 0.891373 ACTACACATGCTCTGCGTCT 59.109 50.000 0.00 0.00 0.00 4.18
1179 2501 1.153842 CGTCTACGCCATGCACAGA 60.154 57.895 0.00 0.00 0.00 3.41
1180 2502 1.142185 CGTCTACGCCATGCACAGAG 61.142 60.000 0.00 0.00 0.00 3.35
1181 2503 1.153568 TCTACGCCATGCACAGAGC 60.154 57.895 0.00 0.00 45.96 4.09
1182 2504 2.125147 TACGCCATGCACAGAGCC 60.125 61.111 0.00 0.00 44.83 4.70
1183 2505 2.857575 CTACGCCATGCACAGAGCCA 62.858 60.000 0.00 0.00 44.83 4.75
1184 2506 3.807538 CGCCATGCACAGAGCCAC 61.808 66.667 0.00 0.00 44.83 5.01
1185 2507 2.674033 GCCATGCACAGAGCCACA 60.674 61.111 0.00 0.00 44.83 4.17
1186 2508 2.697761 GCCATGCACAGAGCCACAG 61.698 63.158 0.00 0.00 44.83 3.66
1187 2509 1.002990 CCATGCACAGAGCCACAGA 60.003 57.895 0.00 0.00 44.83 3.41
1210 2532 2.959071 GCTGAGCATCGAGACCGC 60.959 66.667 0.00 0.00 38.61 5.68
1266 2591 7.763071 TCTGAGAGTGTCATCAGTTGATTAATG 59.237 37.037 0.00 0.00 42.86 1.90
1300 2632 8.843262 TGATGATCTTGTTAATTATGAAGCTGG 58.157 33.333 0.00 0.00 0.00 4.85
1500 2832 2.987125 GCCTTCCGCTACTTCCCA 59.013 61.111 0.00 0.00 0.00 4.37
1581 2913 1.349627 CGTCAACGCCATCATGAGC 59.650 57.895 0.09 0.00 0.00 4.26
1687 3019 2.580470 GCCGTGCTCATGATCGTCG 61.580 63.158 0.00 1.48 0.00 5.12
1703 3035 4.129737 CGTCTCCACCGTCGCCAT 62.130 66.667 0.00 0.00 0.00 4.40
1704 3036 2.509336 GTCTCCACCGTCGCCATG 60.509 66.667 0.00 0.00 0.00 3.66
1728 3060 0.597118 ACGCCGTAACTACACGCAAA 60.597 50.000 0.00 0.00 40.59 3.68
1729 3061 0.507785 CGCCGTAACTACACGCAAAA 59.492 50.000 0.00 0.00 40.59 2.44
1732 3064 3.158268 GCCGTAACTACACGCAAAAATC 58.842 45.455 0.00 0.00 40.59 2.17
1754 3092 5.747565 TCTATTTTACATACATGCAAGCGC 58.252 37.500 0.00 0.00 39.24 5.92
1810 3159 5.062683 CGATCGATCGCTTCCATTATTGATT 59.937 40.000 32.34 0.00 43.84 2.57
1977 3326 2.091830 ACCTCCATCTGGATCTACGTCA 60.092 50.000 0.00 0.00 44.46 4.35
1978 3327 2.294791 CCTCCATCTGGATCTACGTCAC 59.705 54.545 0.00 0.00 44.46 3.67
1979 3328 3.218453 CTCCATCTGGATCTACGTCACT 58.782 50.000 0.00 0.00 44.46 3.41
2023 3372 2.863153 CGCGCTCTTCAACAAGGG 59.137 61.111 5.56 0.00 32.48 3.95
2165 3517 1.671054 CGGAAGTGGCATCGGTTGT 60.671 57.895 0.00 0.00 0.00 3.32
2170 3522 2.264005 AGTGGCATCGGTTGTTGTAA 57.736 45.000 0.00 0.00 0.00 2.41
2223 3582 8.761575 AATCACCAAAAAGCACTAAATGTATG 57.238 30.769 0.00 0.00 0.00 2.39
2360 3725 1.674322 CTGAACGCGGGGTGGAAAT 60.674 57.895 12.47 0.00 0.00 2.17
2385 3750 2.668632 GACGGCCAGGATGAACCA 59.331 61.111 2.24 0.00 39.69 3.67
2386 3751 1.002624 GACGGCCAGGATGAACCAA 60.003 57.895 2.24 0.00 39.69 3.67
2387 3752 0.608035 GACGGCCAGGATGAACCAAA 60.608 55.000 2.24 0.00 39.69 3.28
2388 3753 0.178975 ACGGCCAGGATGAACCAAAA 60.179 50.000 2.24 0.00 39.69 2.44
2389 3754 0.965439 CGGCCAGGATGAACCAAAAA 59.035 50.000 2.24 0.00 39.69 1.94
2390 3755 1.336795 CGGCCAGGATGAACCAAAAAC 60.337 52.381 2.24 0.00 39.69 2.43
2391 3756 1.336795 GGCCAGGATGAACCAAAAACG 60.337 52.381 0.00 0.00 39.69 3.60
2392 3757 1.336795 GCCAGGATGAACCAAAAACGG 60.337 52.381 0.00 0.00 39.69 4.44
2393 3758 1.960689 CCAGGATGAACCAAAAACGGT 59.039 47.619 0.00 0.00 42.71 4.83
2419 3784 9.989296 TTCATAATATATATTTTCAGGTGGGGG 57.011 33.333 13.09 0.00 0.00 5.40
2420 3785 9.357921 TCATAATATATATTTTCAGGTGGGGGA 57.642 33.333 13.09 0.00 0.00 4.81
2421 3786 9.632638 CATAATATATATTTTCAGGTGGGGGAG 57.367 37.037 13.09 0.00 0.00 4.30
2422 3787 7.663501 AATATATATTTTCAGGTGGGGGAGT 57.336 36.000 1.91 0.00 0.00 3.85
2423 3788 7.663501 ATATATATTTTCAGGTGGGGGAGTT 57.336 36.000 0.00 0.00 0.00 3.01
2424 3789 2.604912 ATTTTCAGGTGGGGGAGTTC 57.395 50.000 0.00 0.00 0.00 3.01
2425 3790 1.529744 TTTTCAGGTGGGGGAGTTCT 58.470 50.000 0.00 0.00 0.00 3.01
2426 3791 1.064825 TTTCAGGTGGGGGAGTTCTC 58.935 55.000 0.00 0.00 0.00 2.87
2427 3792 0.193574 TTCAGGTGGGGGAGTTCTCT 59.806 55.000 0.00 0.00 0.00 3.10
2428 3793 0.193574 TCAGGTGGGGGAGTTCTCTT 59.806 55.000 0.00 0.00 0.00 2.85
2429 3794 0.615850 CAGGTGGGGGAGTTCTCTTC 59.384 60.000 0.00 0.00 0.00 2.87
2430 3795 0.547954 AGGTGGGGGAGTTCTCTTCC 60.548 60.000 0.00 3.22 38.61 3.46
2452 3817 4.854587 CCCCCGGTTGAAAATCCA 57.145 55.556 0.00 0.00 0.00 3.41
2453 3818 3.059287 CCCCCGGTTGAAAATCCAA 57.941 52.632 0.00 0.00 0.00 3.53
2454 3819 1.343069 CCCCCGGTTGAAAATCCAAA 58.657 50.000 0.00 0.00 0.00 3.28
2455 3820 1.694696 CCCCCGGTTGAAAATCCAAAA 59.305 47.619 0.00 0.00 0.00 2.44
2484 3849 0.828022 TCATAACGAGGGGCACGATT 59.172 50.000 0.00 0.00 34.70 3.34
2516 3882 1.370172 CCGTGTATAGCCGTCGAGC 60.370 63.158 0.00 0.00 0.00 5.03
2577 3943 1.147376 GGCCGTATATGTGTGCCCA 59.853 57.895 0.00 0.00 36.07 5.36
2956 4322 0.468214 CTCCCTCCGCTGGTGATCTA 60.468 60.000 0.00 0.00 0.00 1.98
3005 4371 2.934932 TCCAGCCAGATGCACCCA 60.935 61.111 0.00 0.00 44.83 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.625747 TCTTGATTAGTGCAATATTTGGTATGA 57.374 29.630 0.00 0.00 0.00 2.15
25 26 8.575589 TGTGTGTTAATTCTTGATTAGTGCAAT 58.424 29.630 0.00 0.00 32.06 3.56
26 27 7.935520 TGTGTGTTAATTCTTGATTAGTGCAA 58.064 30.769 0.00 0.00 32.06 4.08
27 28 7.503521 TGTGTGTTAATTCTTGATTAGTGCA 57.496 32.000 0.00 0.00 32.06 4.57
28 29 8.795786 TTTGTGTGTTAATTCTTGATTAGTGC 57.204 30.769 0.00 0.00 32.06 4.40
35 36 9.278978 TGCTACTATTTGTGTGTTAATTCTTGA 57.721 29.630 0.00 0.00 0.00 3.02
39 40 9.651718 GCTATGCTACTATTTGTGTGTTAATTC 57.348 33.333 0.00 0.00 0.00 2.17
40 41 9.396022 AGCTATGCTACTATTTGTGTGTTAATT 57.604 29.630 0.00 0.00 36.99 1.40
41 42 8.964476 AGCTATGCTACTATTTGTGTGTTAAT 57.036 30.769 0.00 0.00 36.99 1.40
42 43 9.878667 TTAGCTATGCTACTATTTGTGTGTTAA 57.121 29.630 0.00 0.00 41.12 2.01
44 45 8.964476 ATTAGCTATGCTACTATTTGTGTGTT 57.036 30.769 0.00 0.00 41.12 3.32
47 48 9.877178 GGATATTAGCTATGCTACTATTTGTGT 57.123 33.333 9.65 0.00 41.12 3.72
48 49 9.025020 CGGATATTAGCTATGCTACTATTTGTG 57.975 37.037 9.65 0.79 41.12 3.33
49 50 7.707035 GCGGATATTAGCTATGCTACTATTTGT 59.293 37.037 9.65 0.00 41.12 2.83
50 51 7.706607 TGCGGATATTAGCTATGCTACTATTTG 59.293 37.037 9.65 7.45 41.12 2.32
51 52 7.782049 TGCGGATATTAGCTATGCTACTATTT 58.218 34.615 9.65 0.00 41.12 1.40
52 53 7.348080 TGCGGATATTAGCTATGCTACTATT 57.652 36.000 9.65 0.00 41.12 1.73
53 54 6.961360 TGCGGATATTAGCTATGCTACTAT 57.039 37.500 8.51 8.51 41.12 2.12
54 55 6.735968 GCATGCGGATATTAGCTATGCTACTA 60.736 42.308 20.04 0.00 41.12 1.82
55 56 5.595885 CATGCGGATATTAGCTATGCTACT 58.404 41.667 0.00 0.00 41.12 2.57
56 57 4.210120 GCATGCGGATATTAGCTATGCTAC 59.790 45.833 20.04 0.00 41.12 3.58
57 58 4.141959 TGCATGCGGATATTAGCTATGCTA 60.142 41.667 23.46 15.54 42.53 3.49
58 59 3.201290 GCATGCGGATATTAGCTATGCT 58.799 45.455 20.04 0.00 40.82 3.79
59 60 2.938451 TGCATGCGGATATTAGCTATGC 59.062 45.455 14.09 20.26 42.46 3.14
60 61 5.746307 ATTGCATGCGGATATTAGCTATG 57.254 39.130 14.09 7.64 0.00 2.23
61 62 5.882000 TCAATTGCATGCGGATATTAGCTAT 59.118 36.000 14.09 0.00 0.00 2.97
62 63 5.122239 GTCAATTGCATGCGGATATTAGCTA 59.878 40.000 14.09 0.00 0.00 3.32
63 64 4.074259 TCAATTGCATGCGGATATTAGCT 58.926 39.130 14.09 0.00 0.00 3.32
64 65 4.161333 GTCAATTGCATGCGGATATTAGC 58.839 43.478 14.09 0.00 0.00 3.09
65 66 5.361135 TGTCAATTGCATGCGGATATTAG 57.639 39.130 14.09 5.75 0.00 1.73
66 67 5.963176 ATGTCAATTGCATGCGGATATTA 57.037 34.783 14.09 0.00 0.00 0.98
67 68 4.859304 ATGTCAATTGCATGCGGATATT 57.141 36.364 14.09 7.22 0.00 1.28
68 69 6.327154 CAATATGTCAATTGCATGCGGATAT 58.673 36.000 14.09 13.17 30.59 1.63
69 70 5.701855 CAATATGTCAATTGCATGCGGATA 58.298 37.500 14.09 6.78 30.59 2.59
70 71 4.552355 CAATATGTCAATTGCATGCGGAT 58.448 39.130 14.09 6.89 30.59 4.18
71 72 3.967401 CAATATGTCAATTGCATGCGGA 58.033 40.909 14.09 4.43 30.59 5.54
84 85 9.329913 CGCACTTTAATATTTAGGCAATATGTC 57.670 33.333 0.00 0.00 38.00 3.06
85 86 8.846211 ACGCACTTTAATATTTAGGCAATATGT 58.154 29.630 0.00 0.00 38.00 2.29
86 87 9.677567 AACGCACTTTAATATTTAGGCAATATG 57.322 29.630 0.00 0.00 38.00 1.78
87 88 9.677567 CAACGCACTTTAATATTTAGGCAATAT 57.322 29.630 0.00 0.00 39.43 1.28
88 89 7.646130 GCAACGCACTTTAATATTTAGGCAATA 59.354 33.333 0.00 0.00 0.00 1.90
89 90 6.475402 GCAACGCACTTTAATATTTAGGCAAT 59.525 34.615 0.00 0.00 0.00 3.56
90 91 5.802956 GCAACGCACTTTAATATTTAGGCAA 59.197 36.000 0.00 0.00 0.00 4.52
91 92 5.106118 TGCAACGCACTTTAATATTTAGGCA 60.106 36.000 0.00 0.00 31.71 4.75
92 93 5.336744 TGCAACGCACTTTAATATTTAGGC 58.663 37.500 0.00 0.00 31.71 3.93
113 114 4.171005 TCTACTAGTAAATGTGCACGTGC 58.829 43.478 33.11 33.11 42.50 5.34
114 115 6.033966 TGATCTACTAGTAAATGTGCACGTG 58.966 40.000 13.39 12.28 0.00 4.49
115 116 6.203808 TGATCTACTAGTAAATGTGCACGT 57.796 37.500 13.13 9.52 0.00 4.49
116 117 7.275779 ACTTTGATCTACTAGTAAATGTGCACG 59.724 37.037 13.13 0.00 0.00 5.34
117 118 8.480643 ACTTTGATCTACTAGTAAATGTGCAC 57.519 34.615 10.75 10.75 0.00 4.57
303 694 7.068470 AGAGTAAAATAAAACACCGGGACAAAA 59.932 33.333 6.32 0.00 0.00 2.44
304 695 6.546772 AGAGTAAAATAAAACACCGGGACAAA 59.453 34.615 6.32 0.00 0.00 2.83
305 696 6.063404 AGAGTAAAATAAAACACCGGGACAA 58.937 36.000 6.32 0.00 0.00 3.18
306 697 5.623169 AGAGTAAAATAAAACACCGGGACA 58.377 37.500 6.32 0.00 0.00 4.02
373 879 9.740239 ATTTGATTATGTATAACAAAGCAGCAG 57.260 29.630 0.00 0.00 32.44 4.24
404 910 0.878416 GTTGCAGAAACCGCCATGTA 59.122 50.000 0.00 0.00 32.13 2.29
405 911 1.106351 TGTTGCAGAAACCGCCATGT 61.106 50.000 0.00 0.00 38.06 3.21
406 912 0.031857 TTGTTGCAGAAACCGCCATG 59.968 50.000 0.00 0.00 38.06 3.66
407 913 0.031994 GTTGTTGCAGAAACCGCCAT 59.968 50.000 2.91 0.00 38.06 4.40
408 914 1.315981 TGTTGTTGCAGAAACCGCCA 61.316 50.000 10.14 0.00 38.06 5.69
464 970 2.503331 CCACATGTTAGTGTCTGGCAA 58.497 47.619 0.00 0.00 37.82 4.52
512 1018 4.108299 CCGGGTGTATGGCCTGCA 62.108 66.667 3.32 0.00 0.00 4.41
544 1050 6.661669 ACTTGTTTTACTGTGTAAATACGGC 58.338 36.000 4.10 0.00 0.00 5.68
553 1059 6.985645 TGATACCGTAACTTGTTTTACTGTGT 59.014 34.615 0.00 0.00 33.20 3.72
686 1983 6.652481 CCACTTGTGACTTGTTCTCAGAATAT 59.348 38.462 1.89 0.00 0.00 1.28
688 1985 4.818546 CCACTTGTGACTTGTTCTCAGAAT 59.181 41.667 1.89 0.00 0.00 2.40
697 1994 3.199946 TCCTTCTTCCACTTGTGACTTGT 59.800 43.478 1.89 0.00 0.00 3.16
698 1995 3.808728 TCCTTCTTCCACTTGTGACTTG 58.191 45.455 1.89 0.00 0.00 3.16
699 1996 4.505742 GGATCCTTCTTCCACTTGTGACTT 60.506 45.833 3.84 0.00 33.21 3.01
700 1997 3.008485 GGATCCTTCTTCCACTTGTGACT 59.992 47.826 3.84 0.00 33.21 3.41
701 1998 3.244561 TGGATCCTTCTTCCACTTGTGAC 60.245 47.826 14.23 0.00 38.35 3.67
702 1999 2.978978 TGGATCCTTCTTCCACTTGTGA 59.021 45.455 14.23 0.00 38.35 3.58
703 2000 3.423539 TGGATCCTTCTTCCACTTGTG 57.576 47.619 14.23 0.00 38.35 3.33
743 2047 2.690786 TCAACTGAATTAACCGACCCG 58.309 47.619 0.00 0.00 0.00 5.28
801 2105 2.841988 ATGCGGAGGAGGAGAGGC 60.842 66.667 0.00 0.00 0.00 4.70
802 2106 3.136750 CATGCGGAGGAGGAGAGG 58.863 66.667 0.00 0.00 0.00 3.69
803 2107 2.420890 GCATGCGGAGGAGGAGAG 59.579 66.667 0.00 0.00 0.00 3.20
804 2108 3.157252 GGCATGCGGAGGAGGAGA 61.157 66.667 12.44 0.00 0.00 3.71
805 2109 2.937379 CTTGGCATGCGGAGGAGGAG 62.937 65.000 12.44 0.00 0.00 3.69
833 2137 1.228245 GTTGGAACAGAGCAGCCCA 60.228 57.895 0.00 0.00 42.39 5.36
892 2197 2.230508 TGATCCGCCAATATAGTCGTCC 59.769 50.000 0.00 0.00 0.00 4.79
927 2236 0.169009 GTGTTCCTTTGCGATGGCTC 59.831 55.000 0.15 0.00 40.82 4.70
929 2238 0.169009 GAGTGTTCCTTTGCGATGGC 59.831 55.000 0.72 0.00 40.52 4.40
930 2239 0.443869 CGAGTGTTCCTTTGCGATGG 59.556 55.000 0.00 0.00 0.00 3.51
931 2240 1.391485 CTCGAGTGTTCCTTTGCGATG 59.609 52.381 3.62 0.00 0.00 3.84
938 2247 4.039245 TGTTCATTCTCTCGAGTGTTCCTT 59.961 41.667 13.13 0.00 0.00 3.36
964 2273 2.424246 GACCAAGAGCGAGCTAAGTAGT 59.576 50.000 0.00 0.00 0.00 2.73
966 2275 1.749634 GGACCAAGAGCGAGCTAAGTA 59.250 52.381 0.00 0.00 0.00 2.24
967 2276 0.533032 GGACCAAGAGCGAGCTAAGT 59.467 55.000 0.00 0.00 0.00 2.24
968 2277 0.526524 CGGACCAAGAGCGAGCTAAG 60.527 60.000 0.00 0.00 0.00 2.18
969 2278 1.511305 CGGACCAAGAGCGAGCTAA 59.489 57.895 0.00 0.00 0.00 3.09
987 2304 2.440409 AGATCCATTGTGTGTTCCAGC 58.560 47.619 0.00 0.00 0.00 4.85
995 2312 3.748048 CGTCTTGTCAAGATCCATTGTGT 59.252 43.478 18.08 0.00 40.18 3.72
1047 2364 2.365635 TGCTCTAGGTCCTGCCCC 60.366 66.667 0.00 0.00 38.26 5.80
1164 2486 2.176273 GGCTCTGTGCATGGCGTAG 61.176 63.158 3.96 0.00 45.15 3.51
1165 2487 2.125147 GGCTCTGTGCATGGCGTA 60.125 61.111 3.96 0.00 45.15 4.42
1176 2498 1.153862 GCTCGTCTCTGTGGCTCTG 60.154 63.158 0.00 0.00 0.00 3.35
1179 2501 1.594194 CTCAGCTCGTCTCTGTGGCT 61.594 60.000 0.00 0.00 33.48 4.75
1180 2502 1.153862 CTCAGCTCGTCTCTGTGGC 60.154 63.158 0.00 0.00 33.48 5.01
1181 2503 1.153862 GCTCAGCTCGTCTCTGTGG 60.154 63.158 0.00 0.00 33.48 4.17
1182 2504 0.173029 ATGCTCAGCTCGTCTCTGTG 59.827 55.000 0.00 0.00 33.48 3.66
1183 2505 0.455410 GATGCTCAGCTCGTCTCTGT 59.545 55.000 0.00 0.00 33.48 3.41
1184 2506 0.591994 CGATGCTCAGCTCGTCTCTG 60.592 60.000 0.00 0.00 0.00 3.35
1185 2507 0.746204 TCGATGCTCAGCTCGTCTCT 60.746 55.000 15.26 0.00 36.33 3.10
1186 2508 0.316937 CTCGATGCTCAGCTCGTCTC 60.317 60.000 15.26 0.00 36.33 3.36
1187 2509 0.746204 TCTCGATGCTCAGCTCGTCT 60.746 55.000 15.26 0.00 36.33 4.18
1210 2532 6.456449 GCTCAGAAATGCTGCAAATTAATTGG 60.456 38.462 6.36 0.00 44.52 3.16
1375 2707 3.322466 CGTGGGGAAGGTCAGGCT 61.322 66.667 0.00 0.00 0.00 4.58
1581 2913 2.654912 GAAGTTGTCGTCGTGCGGG 61.655 63.158 0.00 0.00 41.72 6.13
1641 2973 3.418744 GAGCTCGAGGAGGAACGGC 62.419 68.421 15.58 0.00 0.00 5.68
1687 3019 2.509336 CATGGCGACGGTGGAGAC 60.509 66.667 0.00 0.00 0.00 3.36
1703 3035 0.314618 TGTAGTTACGGCGTTGCTCA 59.685 50.000 21.24 13.21 0.00 4.26
1704 3036 0.712222 GTGTAGTTACGGCGTTGCTC 59.288 55.000 21.24 10.99 0.00 4.26
1728 3060 7.379529 GCGCTTGCATGTATGTAAAATAGATTT 59.620 33.333 0.00 0.00 38.92 2.17
1729 3061 6.857964 GCGCTTGCATGTATGTAAAATAGATT 59.142 34.615 0.00 0.00 38.92 2.40
1732 3064 4.608470 CGCGCTTGCATGTATGTAAAATAG 59.392 41.667 5.56 0.00 39.07 1.73
1740 3078 2.719677 CGCGCGCTTGCATGTATG 60.720 61.111 30.48 5.07 39.07 2.39
1741 3079 3.940640 CCGCGCGCTTGCATGTAT 61.941 61.111 30.48 0.00 39.07 2.29
1754 3092 1.491563 CAAAGTTTCGTCTCCCGCG 59.508 57.895 0.00 0.00 36.19 6.46
1810 3159 1.592400 GCTCTGCATGCAAGCCAAGA 61.592 55.000 29.21 19.21 0.00 3.02
2165 3517 5.647658 CCATGCTCTTACAAGTGGATTACAA 59.352 40.000 0.00 0.00 29.87 2.41
2170 3522 4.164796 TCATCCATGCTCTTACAAGTGGAT 59.835 41.667 6.18 6.18 44.85 3.41
2246 3607 6.893583 ACATTATCTATTGGAGTTGCAGAGT 58.106 36.000 0.00 0.00 0.00 3.24
2296 3661 4.419522 AACGTTTTACATCATCTGGTGC 57.580 40.909 0.00 0.00 0.00 5.01
2337 3702 4.003788 ACCCCGCGTTCAGACCAG 62.004 66.667 4.92 0.00 0.00 4.00
2338 3703 4.308458 CACCCCGCGTTCAGACCA 62.308 66.667 4.92 0.00 0.00 4.02
2341 3706 2.119484 ATTTCCACCCCGCGTTCAGA 62.119 55.000 4.92 0.00 0.00 3.27
2360 3725 1.040893 ATCCTGGCCGTCGATGTGTA 61.041 55.000 3.52 0.00 0.00 2.90
2393 3758 9.989296 CCCCCACCTGAAAATATATATTATGAA 57.011 33.333 8.39 0.00 0.00 2.57
2394 3759 9.357921 TCCCCCACCTGAAAATATATATTATGA 57.642 33.333 8.39 0.00 0.00 2.15
2395 3760 9.632638 CTCCCCCACCTGAAAATATATATTATG 57.367 37.037 8.39 1.93 0.00 1.90
2396 3761 9.364302 ACTCCCCCACCTGAAAATATATATTAT 57.636 33.333 8.39 0.00 0.00 1.28
2397 3762 8.766492 ACTCCCCCACCTGAAAATATATATTA 57.234 34.615 8.39 0.00 0.00 0.98
2398 3763 7.663501 ACTCCCCCACCTGAAAATATATATT 57.336 36.000 1.91 1.91 0.00 1.28
2399 3764 7.521115 AGAACTCCCCCACCTGAAAATATATAT 59.479 37.037 0.00 0.00 0.00 0.86
2400 3765 6.855061 AGAACTCCCCCACCTGAAAATATATA 59.145 38.462 0.00 0.00 0.00 0.86
2401 3766 5.676811 AGAACTCCCCCACCTGAAAATATAT 59.323 40.000 0.00 0.00 0.00 0.86
2402 3767 5.043762 AGAACTCCCCCACCTGAAAATATA 58.956 41.667 0.00 0.00 0.00 0.86
2403 3768 3.858638 AGAACTCCCCCACCTGAAAATAT 59.141 43.478 0.00 0.00 0.00 1.28
2404 3769 3.265489 AGAACTCCCCCACCTGAAAATA 58.735 45.455 0.00 0.00 0.00 1.40
2405 3770 2.041755 GAGAACTCCCCCACCTGAAAAT 59.958 50.000 0.00 0.00 0.00 1.82
2406 3771 1.423921 GAGAACTCCCCCACCTGAAAA 59.576 52.381 0.00 0.00 0.00 2.29
2407 3772 1.064825 GAGAACTCCCCCACCTGAAA 58.935 55.000 0.00 0.00 0.00 2.69
2408 3773 0.193574 AGAGAACTCCCCCACCTGAA 59.806 55.000 0.00 0.00 0.00 3.02
2409 3774 0.193574 AAGAGAACTCCCCCACCTGA 59.806 55.000 0.00 0.00 0.00 3.86
2410 3775 0.615850 GAAGAGAACTCCCCCACCTG 59.384 60.000 0.00 0.00 0.00 4.00
2411 3776 0.547954 GGAAGAGAACTCCCCCACCT 60.548 60.000 0.00 0.00 0.00 4.00
2412 3777 1.563577 GGGAAGAGAACTCCCCCACC 61.564 65.000 18.45 7.81 40.56 4.61
2413 3778 1.992037 GGGAAGAGAACTCCCCCAC 59.008 63.158 18.45 0.55 40.56 4.61
2414 3779 4.581391 GGGAAGAGAACTCCCCCA 57.419 61.111 18.45 0.00 40.56 4.96
2435 3800 1.343069 TTTGGATTTTCAACCGGGGG 58.657 50.000 6.32 0.00 0.00 5.40
2436 3801 3.477210 TTTTTGGATTTTCAACCGGGG 57.523 42.857 6.32 0.00 0.00 5.73
2484 3849 1.826054 CACGGGGGCAACAAAGACA 60.826 57.895 0.00 0.00 39.74 3.41
2857 4223 3.002583 TCCACCAGATCTGCGCCA 61.003 61.111 17.76 0.00 0.00 5.69
2950 4316 1.692762 GCCCCCACCTTCTCTAGATCA 60.693 57.143 0.00 0.00 0.00 2.92
3005 4371 4.070552 GCCGGAGTTCGCCAGAGT 62.071 66.667 5.05 0.00 37.59 3.24


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

AutoCloner maintained by Alex Coulton.