Multiple sequence alignment - TraesCS5D01G388000

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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 TraesCS5D01G388000 chr5D 100.000 3505 0 0 1 3505 457668630 457672134 0.000000e+00 6473.0
1 TraesCS5D01G388000 chr5B 92.130 1258 68 18 2254 3505 559769959 559771191 0.000000e+00 1746.0
2 TraesCS5D01G388000 chr5B 91.409 873 46 15 743 1595 559768272 559769135 0.000000e+00 1170.0
3 TraesCS5D01G388000 chr5B 96.338 628 23 0 104 731 711257489 711258116 0.000000e+00 1033.0
4 TraesCS5D01G388000 chr5B 82.209 489 64 16 1744 2215 559769225 559769707 1.960000e-107 399.0
5 TraesCS5D01G388000 chr5B 96.667 60 2 0 737 796 559768235 559768294 2.230000e-17 100.0
6 TraesCS5D01G388000 chr5A 90.857 1214 74 18 786 1974 575601245 575602446 0.000000e+00 1592.0
7 TraesCS5D01G388000 chr5A 92.169 830 57 4 2022 2843 575602675 575603504 0.000000e+00 1166.0
8 TraesCS5D01G388000 chr5A 94.946 653 33 0 84 736 470178584 470179236 0.000000e+00 1024.0
9 TraesCS5D01G388000 chr5A 94.648 654 34 1 84 737 467735698 467736350 0.000000e+00 1013.0
10 TraesCS5D01G388000 chr5A 93.304 687 21 8 2821 3505 575603517 575604180 0.000000e+00 990.0
11 TraesCS5D01G388000 chr5A 94.028 653 36 3 84 736 671975062 671974413 0.000000e+00 987.0
12 TraesCS5D01G388000 chr5A 97.872 47 1 0 1971 2017 575602602 575602648 8.060000e-12 82.4
13 TraesCS5D01G388000 chr5A 90.909 55 2 3 737 791 575599678 575599729 1.750000e-08 71.3
14 TraesCS5D01G388000 chr4A 95.865 653 26 1 84 736 733536759 733536108 0.000000e+00 1055.0
15 TraesCS5D01G388000 chr2B 95.122 656 30 2 84 739 796273598 796272945 0.000000e+00 1033.0
16 TraesCS5D01G388000 chr1A 94.479 652 34 2 84 735 13310866 13310217 0.000000e+00 1003.0
17 TraesCS5D01G388000 chrUn 94.696 641 32 2 95 735 51394173 51393535 0.000000e+00 994.0
18 TraesCS5D01G388000 chr3A 94.055 656 37 2 85 740 750494588 750493935 0.000000e+00 994.0


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 TraesCS5D01G388000 chr5D 457668630 457672134 3504 False 6473.00 6473 100.00000 1 3505 1 chr5D.!!$F1 3504
1 TraesCS5D01G388000 chr5B 711257489 711258116 627 False 1033.00 1033 96.33800 104 731 1 chr5B.!!$F1 627
2 TraesCS5D01G388000 chr5B 559768235 559771191 2956 False 853.75 1746 90.60375 737 3505 4 chr5B.!!$F2 2768
3 TraesCS5D01G388000 chr5A 470178584 470179236 652 False 1024.00 1024 94.94600 84 736 1 chr5A.!!$F2 652
4 TraesCS5D01G388000 chr5A 467735698 467736350 652 False 1013.00 1013 94.64800 84 737 1 chr5A.!!$F1 653
5 TraesCS5D01G388000 chr5A 671974413 671975062 649 True 987.00 987 94.02800 84 736 1 chr5A.!!$R1 652
6 TraesCS5D01G388000 chr5A 575599678 575604180 4502 False 780.34 1592 93.02220 737 3505 5 chr5A.!!$F3 2768
7 TraesCS5D01G388000 chr4A 733536108 733536759 651 True 1055.00 1055 95.86500 84 736 1 chr4A.!!$R1 652
8 TraesCS5D01G388000 chr2B 796272945 796273598 653 True 1033.00 1033 95.12200 84 739 1 chr2B.!!$R1 655
9 TraesCS5D01G388000 chr1A 13310217 13310866 649 True 1003.00 1003 94.47900 84 735 1 chr1A.!!$R1 651
10 TraesCS5D01G388000 chrUn 51393535 51394173 638 True 994.00 994 94.69600 95 735 1 chrUn.!!$R1 640
11 TraesCS5D01G388000 chr3A 750493935 750494588 653 True 994.00 994 94.05500 85 740 1 chr3A.!!$R1 655

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
73 74 0.249322 GTTAGCCGGCTATTGCGAGA 60.249 55.0 35.6 17.17 40.82 4.04 F
74 75 0.249322 TTAGCCGGCTATTGCGAGAC 60.249 55.0 35.6 0.00 40.82 3.36 F
1420 2955 0.038166 GGATGAAACCCTGGCACTGA 59.962 55.0 0.0 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 2928 0.038166 TCAGTGCCAGGGTTTCATCC 59.962 55.0 0.00 0.0 0.00 3.51 R
2010 3751 0.167908 AACCACGCATACGCATTGTG 59.832 50.0 0.00 0.0 45.53 3.33 R
2931 4976 0.968393 TATTGCCGGGGGAAAGTTGC 60.968 55.0 2.18 0.0 0.00 4.17 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
23 24 6.543430 GGTATCTGATCAGAGATAGCCATT 57.457 41.667 28.26 12.38 43.29 3.16
24 25 6.339730 GGTATCTGATCAGAGATAGCCATTG 58.660 44.000 28.26 0.00 43.29 2.82
25 26 4.886496 TCTGATCAGAGATAGCCATTGG 57.114 45.455 21.67 0.00 32.82 3.16
26 27 4.486839 TCTGATCAGAGATAGCCATTGGA 58.513 43.478 21.67 0.00 32.82 3.53
27 28 4.282957 TCTGATCAGAGATAGCCATTGGAC 59.717 45.833 21.67 0.00 32.82 4.02
28 29 4.229639 TGATCAGAGATAGCCATTGGACT 58.770 43.478 6.95 5.90 0.00 3.85
29 30 4.040095 TGATCAGAGATAGCCATTGGACTG 59.960 45.833 6.95 5.67 0.00 3.51
30 31 3.646534 TCAGAGATAGCCATTGGACTGA 58.353 45.455 6.95 7.73 0.00 3.41
31 32 4.033009 TCAGAGATAGCCATTGGACTGAA 58.967 43.478 6.95 0.00 31.69 3.02
32 33 4.471025 TCAGAGATAGCCATTGGACTGAAA 59.529 41.667 6.95 0.00 31.69 2.69
33 34 4.574013 CAGAGATAGCCATTGGACTGAAAC 59.426 45.833 6.95 0.00 0.00 2.78
34 35 3.879892 GAGATAGCCATTGGACTGAAACC 59.120 47.826 6.95 0.00 0.00 3.27
35 36 2.507407 TAGCCATTGGACTGAAACCC 57.493 50.000 6.95 0.00 0.00 4.11
36 37 0.482446 AGCCATTGGACTGAAACCCA 59.518 50.000 6.95 0.00 0.00 4.51
38 39 1.547675 GCCATTGGACTGAAACCCAGA 60.548 52.381 6.95 0.00 45.78 3.86
39 40 2.875296 CCATTGGACTGAAACCCAGAA 58.125 47.619 0.00 0.00 45.78 3.02
40 41 2.821969 CCATTGGACTGAAACCCAGAAG 59.178 50.000 0.00 0.00 45.78 2.85
41 42 3.498481 CCATTGGACTGAAACCCAGAAGA 60.498 47.826 0.00 0.00 45.78 2.87
42 43 4.338879 CATTGGACTGAAACCCAGAAGAT 58.661 43.478 0.00 0.00 45.78 2.40
43 44 3.703001 TGGACTGAAACCCAGAAGATC 57.297 47.619 0.00 0.00 45.78 2.75
44 45 2.978978 TGGACTGAAACCCAGAAGATCA 59.021 45.455 0.00 0.00 45.78 2.92
45 46 3.394274 TGGACTGAAACCCAGAAGATCAA 59.606 43.478 0.00 0.00 45.78 2.57
46 47 4.043310 TGGACTGAAACCCAGAAGATCAAT 59.957 41.667 0.00 0.00 45.78 2.57
47 48 4.637977 GGACTGAAACCCAGAAGATCAATC 59.362 45.833 0.00 0.00 45.78 2.67
48 49 4.593956 ACTGAAACCCAGAAGATCAATCC 58.406 43.478 0.00 0.00 45.78 3.01
49 50 4.290722 ACTGAAACCCAGAAGATCAATCCT 59.709 41.667 0.00 0.00 45.78 3.24
50 51 5.488919 ACTGAAACCCAGAAGATCAATCCTA 59.511 40.000 0.00 0.00 45.78 2.94
51 52 6.012508 ACTGAAACCCAGAAGATCAATCCTAA 60.013 38.462 0.00 0.00 45.78 2.69
52 53 6.973642 TGAAACCCAGAAGATCAATCCTAAT 58.026 36.000 0.00 0.00 0.00 1.73
53 54 6.830324 TGAAACCCAGAAGATCAATCCTAATG 59.170 38.462 0.00 0.00 0.00 1.90
54 55 5.316158 ACCCAGAAGATCAATCCTAATGG 57.684 43.478 0.00 0.00 0.00 3.16
55 56 4.728860 ACCCAGAAGATCAATCCTAATGGT 59.271 41.667 0.00 0.00 34.23 3.55
56 57 5.194537 ACCCAGAAGATCAATCCTAATGGTT 59.805 40.000 0.00 0.00 34.23 3.67
57 58 6.389869 ACCCAGAAGATCAATCCTAATGGTTA 59.610 38.462 0.00 0.00 34.23 2.85
58 59 6.939163 CCCAGAAGATCAATCCTAATGGTTAG 59.061 42.308 0.00 0.00 34.23 2.34
59 60 6.429385 CCAGAAGATCAATCCTAATGGTTAGC 59.571 42.308 0.00 0.00 34.23 3.09
60 61 6.429385 CAGAAGATCAATCCTAATGGTTAGCC 59.571 42.308 0.00 0.00 34.23 3.93
61 62 4.899502 AGATCAATCCTAATGGTTAGCCG 58.100 43.478 0.00 0.00 37.67 5.52
62 63 3.485463 TCAATCCTAATGGTTAGCCGG 57.515 47.619 0.00 0.00 37.67 6.13
63 64 1.880027 CAATCCTAATGGTTAGCCGGC 59.120 52.381 21.89 21.89 37.67 6.13
64 65 1.435256 ATCCTAATGGTTAGCCGGCT 58.565 50.000 34.85 34.85 37.67 5.52
65 66 2.091098 TCCTAATGGTTAGCCGGCTA 57.909 50.000 32.24 32.24 37.67 3.93
66 67 2.616524 TCCTAATGGTTAGCCGGCTAT 58.383 47.619 35.60 22.84 37.67 2.97
67 68 2.976882 TCCTAATGGTTAGCCGGCTATT 59.023 45.455 35.60 28.18 37.67 1.73
68 69 3.074412 CCTAATGGTTAGCCGGCTATTG 58.926 50.000 35.60 20.41 37.67 1.90
69 70 1.318576 AATGGTTAGCCGGCTATTGC 58.681 50.000 35.60 25.95 37.67 3.56
70 71 0.884704 ATGGTTAGCCGGCTATTGCG 60.885 55.000 35.60 0.00 40.82 4.85
71 72 1.227438 GGTTAGCCGGCTATTGCGA 60.227 57.895 35.60 18.72 40.82 5.10
72 73 1.222115 GGTTAGCCGGCTATTGCGAG 61.222 60.000 35.60 0.00 40.82 5.03
73 74 0.249322 GTTAGCCGGCTATTGCGAGA 60.249 55.000 35.60 17.17 40.82 4.04
74 75 0.249322 TTAGCCGGCTATTGCGAGAC 60.249 55.000 35.60 0.00 40.82 3.36
75 76 1.388837 TAGCCGGCTATTGCGAGACA 61.389 55.000 32.24 8.26 40.82 3.41
76 77 2.240500 GCCGGCTATTGCGAGACAG 61.241 63.158 22.15 0.00 40.82 3.51
77 78 2.240500 CCGGCTATTGCGAGACAGC 61.241 63.158 0.00 0.00 40.82 4.40
78 79 2.580470 CGGCTATTGCGAGACAGCG 61.580 63.158 0.00 0.00 40.82 5.18
79 80 2.240500 GGCTATTGCGAGACAGCGG 61.241 63.158 0.00 0.00 40.82 5.52
80 81 2.875786 GCTATTGCGAGACAGCGGC 61.876 63.158 0.00 0.00 40.67 6.53
81 82 2.202878 TATTGCGAGACAGCGGCC 60.203 61.111 0.00 0.00 40.67 6.13
82 83 2.635229 CTATTGCGAGACAGCGGCCT 62.635 60.000 0.00 0.00 40.67 5.19
393 394 0.323816 TGTCTCCGGCTGATCTGTCT 60.324 55.000 0.00 0.00 0.00 3.41
535 536 0.526662 CCTTAGCACGACGACTTCCT 59.473 55.000 0.00 0.00 0.00 3.36
554 555 6.097839 ACTTCCTGACTGTCTACTACAACAAA 59.902 38.462 9.51 0.00 37.74 2.83
647 648 1.030457 CGCTAGGTGGTCTACGGATT 58.970 55.000 0.00 0.00 0.00 3.01
777 778 4.717233 TGTTCTTCTTTTTGCAGCAGAA 57.283 36.364 0.00 0.00 0.00 3.02
1401 2928 6.102006 TCCGTCTGTAAAATAGCGAAATTG 57.898 37.500 0.00 0.00 0.00 2.32
1402 2929 5.064198 TCCGTCTGTAAAATAGCGAAATTGG 59.936 40.000 0.00 0.00 0.00 3.16
1409 2944 8.682128 TGTAAAATAGCGAAATTGGATGAAAC 57.318 30.769 0.00 0.00 0.00 2.78
1417 2952 1.560505 ATTGGATGAAACCCTGGCAC 58.439 50.000 0.00 0.00 0.00 5.01
1419 2954 0.251297 TGGATGAAACCCTGGCACTG 60.251 55.000 0.00 0.00 0.00 3.66
1420 2955 0.038166 GGATGAAACCCTGGCACTGA 59.962 55.000 0.00 0.00 0.00 3.41
1421 2956 1.168714 GATGAAACCCTGGCACTGAC 58.831 55.000 0.00 0.00 0.00 3.51
1428 2963 2.111384 ACCCTGGCACTGACAGTATAG 58.889 52.381 8.02 6.84 36.87 1.31
1436 2971 3.304559 GCACTGACAGTATAGCAAAGTCG 59.695 47.826 8.02 0.00 32.08 4.18
1437 2972 4.486090 CACTGACAGTATAGCAAAGTCGT 58.514 43.478 8.02 0.00 32.08 4.34
1438 2973 4.324669 CACTGACAGTATAGCAAAGTCGTG 59.675 45.833 8.02 0.00 32.32 4.35
1439 2974 4.022242 ACTGACAGTATAGCAAAGTCGTGT 60.022 41.667 6.24 0.00 32.08 4.49
1441 2976 6.016213 TGACAGTATAGCAAAGTCGTGTAA 57.984 37.500 0.00 0.00 32.08 2.41
1442 2977 6.090783 TGACAGTATAGCAAAGTCGTGTAAG 58.909 40.000 0.00 0.00 32.08 2.34
1444 2979 5.184479 ACAGTATAGCAAAGTCGTGTAAGGA 59.816 40.000 0.00 0.00 0.00 3.36
1445 2980 6.097356 CAGTATAGCAAAGTCGTGTAAGGAA 58.903 40.000 0.00 0.00 29.57 3.36
1446 2981 6.588756 CAGTATAGCAAAGTCGTGTAAGGAAA 59.411 38.462 0.00 0.00 29.57 3.13
1447 2982 6.812160 AGTATAGCAAAGTCGTGTAAGGAAAG 59.188 38.462 0.00 0.00 29.57 2.62
1448 2983 3.139077 AGCAAAGTCGTGTAAGGAAAGG 58.861 45.455 0.00 0.00 29.57 3.11
1449 2984 2.350484 GCAAAGTCGTGTAAGGAAAGGC 60.350 50.000 0.00 0.00 29.57 4.35
1450 2985 2.875933 CAAAGTCGTGTAAGGAAAGGCA 59.124 45.455 0.00 0.00 29.57 4.75
1451 2986 2.922740 AGTCGTGTAAGGAAAGGCAA 57.077 45.000 0.00 0.00 29.57 4.52
1452 2987 2.490991 AGTCGTGTAAGGAAAGGCAAC 58.509 47.619 0.00 0.00 29.57 4.17
1471 3006 4.552184 GCAACTGAAAAACCAGTACTCGAC 60.552 45.833 0.00 0.00 45.82 4.20
1570 3114 1.340991 TGGCTGAGGTAGGATTTTGGC 60.341 52.381 0.00 0.00 0.00 4.52
1574 3118 3.370527 GCTGAGGTAGGATTTTGGCACTA 60.371 47.826 0.00 0.00 0.00 2.74
1598 3142 6.796705 TTCATGTGCTGCTATCTGATATTG 57.203 37.500 0.00 0.00 0.00 1.90
1604 3148 9.984190 ATGTGCTGCTATCTGATATTGATATAG 57.016 33.333 0.00 0.00 0.00 1.31
1605 3149 8.419442 TGTGCTGCTATCTGATATTGATATAGG 58.581 37.037 0.00 0.00 0.00 2.57
1606 3150 8.637099 GTGCTGCTATCTGATATTGATATAGGA 58.363 37.037 0.00 0.00 0.00 2.94
1607 3151 8.858094 TGCTGCTATCTGATATTGATATAGGAG 58.142 37.037 0.00 0.00 39.93 3.69
1653 3197 3.926058 AATGGGTATTCGTGGTAGCTT 57.074 42.857 0.00 0.00 0.00 3.74
1688 3232 5.418310 ACTTTCAAATGTAACCGTGAGTG 57.582 39.130 0.00 0.00 0.00 3.51
1696 3240 1.129917 TAACCGTGAGTGGGTTTCCA 58.870 50.000 1.09 0.00 45.25 3.53
1697 3241 0.476771 AACCGTGAGTGGGTTTCCAT 59.523 50.000 0.00 0.00 45.25 3.41
1698 3242 0.250727 ACCGTGAGTGGGTTTCCATG 60.251 55.000 0.00 0.00 46.09 3.66
1767 3344 6.395426 TCTAGCATTTTCATTGGGCATAAG 57.605 37.500 0.00 0.00 0.00 1.73
1821 3400 5.598769 AGAAACTTATCGATTAAGACGGGG 58.401 41.667 1.71 0.00 39.86 5.73
1872 3453 7.434307 GCTTGATCACTATGTCCATTTTGATTG 59.566 37.037 0.00 2.61 0.00 2.67
2010 3751 2.286950 TGTTCATGCTGTCGTTTGCTTC 60.287 45.455 0.00 0.00 0.00 3.86
2017 3758 2.046313 CTGTCGTTTGCTTCACAATGC 58.954 47.619 0.00 0.00 38.31 3.56
2018 3759 1.044725 GTCGTTTGCTTCACAATGCG 58.955 50.000 0.00 0.00 38.31 4.73
2019 3760 0.660488 TCGTTTGCTTCACAATGCGT 59.340 45.000 0.00 0.00 38.31 5.24
2020 3761 1.867865 TCGTTTGCTTCACAATGCGTA 59.132 42.857 0.00 0.00 38.31 4.42
2023 3786 2.261037 TTGCTTCACAATGCGTATGC 57.739 45.000 0.00 0.00 35.75 3.14
2054 3817 4.651503 TCCCATTCCTTTTAGTTTGTGCAA 59.348 37.500 0.00 0.00 0.00 4.08
2134 3902 0.680280 TCTGGGGTCGACTCTAGTGC 60.680 60.000 25.91 5.21 0.00 4.40
2141 3909 1.649662 GTCGACTCTAGTGCGCTTTTC 59.350 52.381 9.73 0.00 0.00 2.29
2174 3942 1.707427 AGCAATGGGGATATGGGAGAC 59.293 52.381 0.00 0.00 0.00 3.36
2175 3946 1.425066 GCAATGGGGATATGGGAGACA 59.575 52.381 0.00 0.00 0.00 3.41
2238 4009 0.533755 AGAAGGTCTGCACTGCACAC 60.534 55.000 0.00 0.00 33.79 3.82
2252 4023 4.275689 CACTGCACACACTTGATTTCCTTA 59.724 41.667 0.00 0.00 0.00 2.69
2256 4262 4.320494 GCACACACTTGATTTCCTTACCTG 60.320 45.833 0.00 0.00 0.00 4.00
2263 4269 6.246420 CTTGATTTCCTTACCTGTCAAGTG 57.754 41.667 0.00 0.00 38.33 3.16
2314 4320 5.402398 GCAGACCATTCAATTCCAGTTTAC 58.598 41.667 0.00 0.00 0.00 2.01
2372 4378 1.101331 CTCAGGCAGCCAAGGAATTC 58.899 55.000 15.80 0.00 0.00 2.17
2396 4402 5.294552 CGAAACAGAACTGAAGAAAGAACCT 59.705 40.000 8.87 0.00 0.00 3.50
2435 4441 4.614036 CCACCCACAACCCCCACC 62.614 72.222 0.00 0.00 0.00 4.61
2510 4516 1.649321 AAGAGAGCACATGAGGACCA 58.351 50.000 0.00 0.00 0.00 4.02
2518 4524 1.379044 CATGAGGACCAGGCCAACC 60.379 63.158 5.01 2.06 0.00 3.77
2594 4600 3.803778 CACATTGCTCCCTGTTTTTGTTC 59.196 43.478 0.00 0.00 0.00 3.18
2620 4626 2.148916 CAGGCCATGCAGCAATATTG 57.851 50.000 11.27 11.27 0.00 1.90
2647 4653 2.696759 CGGCGAAAATGTGTCCCCC 61.697 63.158 0.00 0.00 0.00 5.40
2676 4682 8.752005 AAATACCATGTTGCTAATGTATGAGT 57.248 30.769 0.00 0.00 0.00 3.41
2680 4686 8.574251 ACCATGTTGCTAATGTATGAGTTTAA 57.426 30.769 0.00 0.00 0.00 1.52
2740 4746 3.882888 TCTGCTGTTTTTCCTGTCGAAAT 59.117 39.130 0.00 0.00 40.18 2.17
2742 4748 5.529430 TCTGCTGTTTTTCCTGTCGAAATTA 59.471 36.000 0.00 0.00 40.18 1.40
2743 4749 6.206634 TCTGCTGTTTTTCCTGTCGAAATTAT 59.793 34.615 0.00 0.00 40.18 1.28
2744 4750 6.148948 TGCTGTTTTTCCTGTCGAAATTATG 58.851 36.000 0.00 0.00 40.18 1.90
2745 4751 5.572896 GCTGTTTTTCCTGTCGAAATTATGG 59.427 40.000 0.00 0.00 40.18 2.74
2746 4752 6.569610 GCTGTTTTTCCTGTCGAAATTATGGA 60.570 38.462 0.00 0.00 40.18 3.41
2747 4753 6.908825 TGTTTTTCCTGTCGAAATTATGGAG 58.091 36.000 0.00 0.00 40.18 3.86
2748 4754 6.488683 TGTTTTTCCTGTCGAAATTATGGAGT 59.511 34.615 0.00 0.00 40.18 3.85
2749 4755 7.662258 TGTTTTTCCTGTCGAAATTATGGAGTA 59.338 33.333 0.00 0.00 40.18 2.59
2751 4757 8.801882 TTTTCCTGTCGAAATTATGGAGTATT 57.198 30.769 0.00 0.00 40.18 1.89
2752 4758 7.786178 TTCCTGTCGAAATTATGGAGTATTG 57.214 36.000 0.00 0.00 0.00 1.90
2775 4785 5.189736 TGGTACATCAGTTTGGAATAGAGCT 59.810 40.000 0.00 0.00 0.00 4.09
2804 4814 0.677731 TGTGCCTGACATTGCTAGCC 60.678 55.000 13.29 0.00 0.00 3.93
2818 4828 1.474077 GCTAGCCCAGTTGGATTTGTG 59.526 52.381 2.29 0.00 37.39 3.33
2837 4847 1.195115 GGTAGTGAGGATGTGCCAGA 58.805 55.000 0.00 0.00 40.02 3.86
2843 4853 4.922206 AGTGAGGATGTGCCAGAATTTTA 58.078 39.130 0.00 0.00 40.02 1.52
2844 4854 4.946157 AGTGAGGATGTGCCAGAATTTTAG 59.054 41.667 0.00 0.00 40.02 1.85
2845 4855 4.702131 GTGAGGATGTGCCAGAATTTTAGT 59.298 41.667 0.00 0.00 40.02 2.24
2846 4856 4.943705 TGAGGATGTGCCAGAATTTTAGTC 59.056 41.667 0.00 0.00 40.02 2.59
2858 4903 7.577807 GCCAGAATTTTAGTCTGAGACACTAGA 60.578 40.741 15.86 0.00 44.44 2.43
2879 4924 3.645660 TGGGCCCGCATTGTCAGA 61.646 61.111 19.37 0.00 0.00 3.27
2927 4972 1.128321 GCAGCAGAGAAAGAAGAAGCG 59.872 52.381 0.00 0.00 0.00 4.68
2928 4973 1.731160 CAGCAGAGAAAGAAGAAGCGG 59.269 52.381 0.00 0.00 0.00 5.52
2929 4974 1.082690 GCAGAGAAAGAAGAAGCGGG 58.917 55.000 0.00 0.00 0.00 6.13
2930 4975 1.731720 CAGAGAAAGAAGAAGCGGGG 58.268 55.000 0.00 0.00 0.00 5.73
2931 4976 0.615850 AGAGAAAGAAGAAGCGGGGG 59.384 55.000 0.00 0.00 0.00 5.40
2932 4977 1.002011 AGAAAGAAGAAGCGGGGGC 60.002 57.895 0.00 0.00 0.00 5.80
2933 4978 1.303317 GAAAGAAGAAGCGGGGGCA 60.303 57.895 0.00 0.00 0.00 5.36
2934 4979 0.893727 GAAAGAAGAAGCGGGGGCAA 60.894 55.000 0.00 0.00 0.00 4.52
2936 4981 2.034221 GAAGAAGCGGGGGCAACT 59.966 61.111 0.00 0.00 0.00 3.16
2938 4983 1.152546 AAGAAGCGGGGGCAACTTT 60.153 52.632 0.00 0.00 0.00 2.66
3063 5109 1.212195 CCCTAAACCCTACCTTGAGCC 59.788 57.143 0.00 0.00 0.00 4.70
3064 5110 1.212195 CCTAAACCCTACCTTGAGCCC 59.788 57.143 0.00 0.00 0.00 5.19
3065 5111 1.212195 CTAAACCCTACCTTGAGCCCC 59.788 57.143 0.00 0.00 0.00 5.80
3066 5112 0.774491 AAACCCTACCTTGAGCCCCA 60.774 55.000 0.00 0.00 0.00 4.96
3067 5113 1.208165 AACCCTACCTTGAGCCCCAG 61.208 60.000 0.00 0.00 0.00 4.45
3068 5114 2.592308 CCTACCTTGAGCCCCAGC 59.408 66.667 0.00 0.00 40.32 4.85
3071 5117 3.881926 TACCTTGAGCCCCAGCCCA 62.882 63.158 0.00 0.00 41.25 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.339730 CAATGGCTATCTCTGATCAGATACC 58.660 44.000 25.30 20.06 36.76 2.73
1 2 6.154192 TCCAATGGCTATCTCTGATCAGATAC 59.846 42.308 25.30 12.66 36.76 2.24
2 3 6.154192 GTCCAATGGCTATCTCTGATCAGATA 59.846 42.308 25.30 18.81 36.76 1.98
3 4 5.046448 GTCCAATGGCTATCTCTGATCAGAT 60.046 44.000 25.30 14.41 36.76 2.90
4 5 4.282957 GTCCAATGGCTATCTCTGATCAGA 59.717 45.833 23.75 23.75 35.85 3.27
5 6 4.283978 AGTCCAATGGCTATCTCTGATCAG 59.716 45.833 17.07 17.07 0.00 2.90
6 7 4.040095 CAGTCCAATGGCTATCTCTGATCA 59.960 45.833 0.00 0.00 0.00 2.92
7 8 4.282957 TCAGTCCAATGGCTATCTCTGATC 59.717 45.833 0.00 0.00 0.00 2.92
8 9 4.229639 TCAGTCCAATGGCTATCTCTGAT 58.770 43.478 0.00 0.00 0.00 2.90
9 10 3.646534 TCAGTCCAATGGCTATCTCTGA 58.353 45.455 0.00 0.00 0.00 3.27
10 11 4.412796 TTCAGTCCAATGGCTATCTCTG 57.587 45.455 0.00 0.00 0.00 3.35
11 12 4.384647 GGTTTCAGTCCAATGGCTATCTCT 60.385 45.833 0.00 0.00 0.00 3.10
12 13 3.879892 GGTTTCAGTCCAATGGCTATCTC 59.120 47.826 0.00 0.00 0.00 2.75
13 14 3.372025 GGGTTTCAGTCCAATGGCTATCT 60.372 47.826 0.00 0.00 0.00 1.98
14 15 2.952310 GGGTTTCAGTCCAATGGCTATC 59.048 50.000 0.00 0.00 0.00 2.08
15 16 2.311542 TGGGTTTCAGTCCAATGGCTAT 59.688 45.455 0.00 0.00 0.00 2.97
16 17 1.707989 TGGGTTTCAGTCCAATGGCTA 59.292 47.619 0.00 0.00 0.00 3.93
17 18 0.482446 TGGGTTTCAGTCCAATGGCT 59.518 50.000 0.00 0.00 0.00 4.75
18 19 0.890683 CTGGGTTTCAGTCCAATGGC 59.109 55.000 0.00 0.00 38.64 4.40
19 20 2.584835 TCTGGGTTTCAGTCCAATGG 57.415 50.000 0.00 0.00 43.76 3.16
20 21 3.754965 TCTTCTGGGTTTCAGTCCAATG 58.245 45.455 0.00 0.00 43.76 2.82
21 22 4.043310 TGATCTTCTGGGTTTCAGTCCAAT 59.957 41.667 0.00 0.00 43.76 3.16
22 23 3.394274 TGATCTTCTGGGTTTCAGTCCAA 59.606 43.478 0.00 0.00 43.76 3.53
23 24 2.978978 TGATCTTCTGGGTTTCAGTCCA 59.021 45.455 0.00 0.00 43.76 4.02
24 25 3.703001 TGATCTTCTGGGTTTCAGTCC 57.297 47.619 0.00 0.00 43.76 3.85
25 26 4.637977 GGATTGATCTTCTGGGTTTCAGTC 59.362 45.833 0.00 0.00 43.76 3.51
26 27 4.290722 AGGATTGATCTTCTGGGTTTCAGT 59.709 41.667 0.00 0.00 43.76 3.41
27 28 4.853007 AGGATTGATCTTCTGGGTTTCAG 58.147 43.478 0.00 0.00 44.68 3.02
28 29 4.934797 AGGATTGATCTTCTGGGTTTCA 57.065 40.909 0.00 0.00 0.00 2.69
29 30 6.264067 CCATTAGGATTGATCTTCTGGGTTTC 59.736 42.308 0.00 0.00 36.89 2.78
30 31 6.131961 CCATTAGGATTGATCTTCTGGGTTT 58.868 40.000 0.00 0.00 36.89 3.27
31 32 5.194537 ACCATTAGGATTGATCTTCTGGGTT 59.805 40.000 0.00 0.00 38.69 4.11
32 33 4.728860 ACCATTAGGATTGATCTTCTGGGT 59.271 41.667 0.00 0.00 38.69 4.51
33 34 5.316158 ACCATTAGGATTGATCTTCTGGG 57.684 43.478 0.00 0.00 38.69 4.45
34 35 6.429385 GCTAACCATTAGGATTGATCTTCTGG 59.571 42.308 0.00 0.00 38.69 3.86
35 36 6.429385 GGCTAACCATTAGGATTGATCTTCTG 59.571 42.308 0.00 0.00 38.69 3.02
36 37 6.538263 GGCTAACCATTAGGATTGATCTTCT 58.462 40.000 0.00 0.00 38.69 2.85
37 38 5.409826 CGGCTAACCATTAGGATTGATCTTC 59.590 44.000 0.00 0.00 38.69 2.87
38 39 5.308825 CGGCTAACCATTAGGATTGATCTT 58.691 41.667 0.00 0.00 38.69 2.40
39 40 4.263068 CCGGCTAACCATTAGGATTGATCT 60.263 45.833 0.00 0.00 38.69 2.75
40 41 4.003648 CCGGCTAACCATTAGGATTGATC 58.996 47.826 0.00 0.00 38.69 2.92
41 42 3.810743 GCCGGCTAACCATTAGGATTGAT 60.811 47.826 22.15 0.00 38.69 2.57
42 43 2.486548 GCCGGCTAACCATTAGGATTGA 60.487 50.000 22.15 0.00 38.69 2.57
43 44 1.880027 GCCGGCTAACCATTAGGATTG 59.120 52.381 22.15 0.00 38.69 2.67
44 45 1.774856 AGCCGGCTAACCATTAGGATT 59.225 47.619 31.86 0.00 38.69 3.01
45 46 1.435256 AGCCGGCTAACCATTAGGAT 58.565 50.000 31.86 0.00 38.69 3.24
46 47 2.091098 TAGCCGGCTAACCATTAGGA 57.909 50.000 33.63 9.15 38.69 2.94
47 48 3.074412 CAATAGCCGGCTAACCATTAGG 58.926 50.000 38.14 15.12 42.21 2.69
48 49 2.484264 GCAATAGCCGGCTAACCATTAG 59.516 50.000 38.14 22.04 34.57 1.73
49 50 2.500229 GCAATAGCCGGCTAACCATTA 58.500 47.619 38.14 18.19 34.57 1.90
50 51 1.318576 GCAATAGCCGGCTAACCATT 58.681 50.000 38.14 26.13 34.57 3.16
51 52 0.884704 CGCAATAGCCGGCTAACCAT 60.885 55.000 38.14 21.72 37.52 3.55
52 53 1.522806 CGCAATAGCCGGCTAACCA 60.523 57.895 38.14 20.26 37.52 3.67
53 54 1.222115 CTCGCAATAGCCGGCTAACC 61.222 60.000 38.14 25.96 37.52 2.85
54 55 0.249322 TCTCGCAATAGCCGGCTAAC 60.249 55.000 38.14 27.48 37.52 2.34
55 56 0.249322 GTCTCGCAATAGCCGGCTAA 60.249 55.000 38.14 21.34 37.52 3.09
56 57 1.362717 GTCTCGCAATAGCCGGCTA 59.637 57.895 36.88 36.88 37.52 3.93
57 58 2.107141 GTCTCGCAATAGCCGGCT 59.893 61.111 34.85 34.85 37.52 5.52
58 59 2.202878 TGTCTCGCAATAGCCGGC 60.203 61.111 21.89 21.89 37.52 6.13
59 60 2.240500 GCTGTCTCGCAATAGCCGG 61.241 63.158 0.00 0.00 37.52 6.13
60 61 2.580470 CGCTGTCTCGCAATAGCCG 61.580 63.158 0.00 0.00 37.52 5.52
61 62 2.240500 CCGCTGTCTCGCAATAGCC 61.241 63.158 0.00 0.00 37.52 3.93
62 63 2.875786 GCCGCTGTCTCGCAATAGC 61.876 63.158 0.00 0.00 37.42 2.97
63 64 2.240500 GGCCGCTGTCTCGCAATAG 61.241 63.158 0.00 0.00 0.00 1.73
64 65 2.202878 GGCCGCTGTCTCGCAATA 60.203 61.111 0.00 0.00 0.00 1.90
65 66 4.087892 AGGCCGCTGTCTCGCAAT 62.088 61.111 0.00 0.00 0.00 3.56
66 67 4.742201 GAGGCCGCTGTCTCGCAA 62.742 66.667 0.00 0.00 32.68 4.85
70 71 1.016653 GTCAAAGAGGCCGCTGTCTC 61.017 60.000 10.77 0.85 43.84 3.36
71 72 1.004440 GTCAAAGAGGCCGCTGTCT 60.004 57.895 10.77 0.00 0.00 3.41
72 73 2.035442 GGTCAAAGAGGCCGCTGTC 61.035 63.158 10.77 0.00 28.17 3.51
73 74 2.032681 GGTCAAAGAGGCCGCTGT 59.967 61.111 10.77 0.00 28.17 4.40
78 79 0.107459 CTGGCTAGGTCAAAGAGGCC 60.107 60.000 0.00 0.00 44.66 5.19
79 80 0.746204 GCTGGCTAGGTCAAAGAGGC 60.746 60.000 0.00 0.00 36.36 4.70
80 81 0.107459 GGCTGGCTAGGTCAAAGAGG 60.107 60.000 0.00 0.00 0.00 3.69
81 82 0.460987 CGGCTGGCTAGGTCAAAGAG 60.461 60.000 0.00 0.00 0.00 2.85
82 83 1.596934 CGGCTGGCTAGGTCAAAGA 59.403 57.895 0.00 0.00 0.00 2.52
191 192 4.918201 GGCAAGGGGCGAGATCCG 62.918 72.222 0.00 0.00 46.16 4.18
243 244 4.678622 CAGGACACAAACCCTAACAAAAC 58.321 43.478 0.00 0.00 0.00 2.43
355 356 3.484806 AACTCCACACGCCCACCA 61.485 61.111 0.00 0.00 0.00 4.17
393 394 2.091541 GATCCGAGCAAATCCACCAAA 58.908 47.619 0.00 0.00 0.00 3.28
479 480 2.972505 CTGAACAGCAACCGCCGT 60.973 61.111 0.00 0.00 39.83 5.68
495 496 0.035439 CCCATAGAACCAACGCACCT 60.035 55.000 0.00 0.00 0.00 4.00
535 536 6.036735 GCAAACTTTGTTGTAGTAGACAGTCA 59.963 38.462 2.66 0.00 39.88 3.41
554 555 1.978617 CATTGGAGCCGGGCAAACT 60.979 57.895 23.09 0.00 0.00 2.66
612 613 1.162698 AGCGACGACTACAAGCACTA 58.837 50.000 0.00 0.00 0.00 2.74
674 675 6.588756 TCTTCAATCATGGTAGTACAACGAAC 59.411 38.462 2.06 0.00 0.00 3.95
731 732 5.765182 TCACTGATCTTCTGGGTTTCTTTTC 59.235 40.000 0.00 0.00 0.00 2.29
777 778 6.375455 AGGCGAGAAATAAACATCACTGATTT 59.625 34.615 0.00 0.00 0.00 2.17
1281 2808 1.068921 GATCTCGGGGAGCTGCTTC 59.931 63.158 2.53 0.00 0.00 3.86
1401 2928 0.038166 TCAGTGCCAGGGTTTCATCC 59.962 55.000 0.00 0.00 0.00 3.51
1402 2929 1.168714 GTCAGTGCCAGGGTTTCATC 58.831 55.000 0.00 0.00 0.00 2.92
1409 2944 1.202580 GCTATACTGTCAGTGCCAGGG 60.203 57.143 16.03 1.62 34.16 4.45
1417 2952 4.486090 ACACGACTTTGCTATACTGTCAG 58.514 43.478 0.00 0.00 0.00 3.51
1419 2954 5.515626 CCTTACACGACTTTGCTATACTGTC 59.484 44.000 0.00 0.00 0.00 3.51
1420 2955 5.184479 TCCTTACACGACTTTGCTATACTGT 59.816 40.000 0.00 0.00 0.00 3.55
1421 2956 5.647589 TCCTTACACGACTTTGCTATACTG 58.352 41.667 0.00 0.00 0.00 2.74
1428 2963 2.350484 GCCTTTCCTTACACGACTTTGC 60.350 50.000 0.00 0.00 0.00 3.68
1436 2971 4.911514 TTTCAGTTGCCTTTCCTTACAC 57.088 40.909 0.00 0.00 0.00 2.90
1437 2972 5.394773 GGTTTTTCAGTTGCCTTTCCTTACA 60.395 40.000 0.00 0.00 0.00 2.41
1438 2973 5.047847 GGTTTTTCAGTTGCCTTTCCTTAC 58.952 41.667 0.00 0.00 0.00 2.34
1439 2974 4.712337 TGGTTTTTCAGTTGCCTTTCCTTA 59.288 37.500 0.00 0.00 0.00 2.69
1441 2976 3.103742 TGGTTTTTCAGTTGCCTTTCCT 58.896 40.909 0.00 0.00 0.00 3.36
1442 2977 3.118775 ACTGGTTTTTCAGTTGCCTTTCC 60.119 43.478 0.00 0.00 44.74 3.13
1444 2979 4.709886 AGTACTGGTTTTTCAGTTGCCTTT 59.290 37.500 0.00 0.00 44.74 3.11
1445 2980 4.278310 AGTACTGGTTTTTCAGTTGCCTT 58.722 39.130 0.00 0.00 44.74 4.35
1446 2981 3.883489 GAGTACTGGTTTTTCAGTTGCCT 59.117 43.478 0.00 0.00 44.74 4.75
1447 2982 3.303791 CGAGTACTGGTTTTTCAGTTGCC 60.304 47.826 0.00 0.00 44.74 4.52
1448 2983 3.558418 TCGAGTACTGGTTTTTCAGTTGC 59.442 43.478 0.00 0.00 44.74 4.17
1449 2984 4.809426 AGTCGAGTACTGGTTTTTCAGTTG 59.191 41.667 0.00 0.00 44.74 3.16
1450 2985 5.019785 AGTCGAGTACTGGTTTTTCAGTT 57.980 39.130 0.00 0.00 44.74 3.16
1452 2987 5.290386 AGAAGTCGAGTACTGGTTTTTCAG 58.710 41.667 0.00 0.00 38.88 3.02
1453 2988 5.272283 AGAAGTCGAGTACTGGTTTTTCA 57.728 39.130 0.00 0.00 38.88 2.69
1454 2989 6.675987 TCTAGAAGTCGAGTACTGGTTTTTC 58.324 40.000 0.00 5.52 38.88 2.29
1455 2990 6.645790 TCTAGAAGTCGAGTACTGGTTTTT 57.354 37.500 0.00 0.00 38.88 1.94
1460 2995 3.003897 GGCATCTAGAAGTCGAGTACTGG 59.996 52.174 0.00 0.00 38.88 4.00
1502 3037 8.773033 ATTCCCATAAGCTCAAATATTTCAGT 57.227 30.769 0.82 0.00 0.00 3.41
1509 3044 7.175104 GTCCCATATTCCCATAAGCTCAAATA 58.825 38.462 0.00 0.00 0.00 1.40
1557 3099 5.594317 ACATGAATAGTGCCAAAATCCTACC 59.406 40.000 0.00 0.00 0.00 3.18
1570 3114 5.295152 TCAGATAGCAGCACATGAATAGTG 58.705 41.667 0.00 0.00 39.92 2.74
1574 3118 7.166167 TCAATATCAGATAGCAGCACATGAAT 58.834 34.615 0.00 0.00 0.00 2.57
1624 3168 6.474630 ACCACGAATACCCATTTACAGTTTA 58.525 36.000 0.00 0.00 0.00 2.01
1625 3169 5.318630 ACCACGAATACCCATTTACAGTTT 58.681 37.500 0.00 0.00 0.00 2.66
1636 3180 1.537562 CGGAAGCTACCACGAATACCC 60.538 57.143 0.00 0.00 0.00 3.69
1653 3197 9.602568 TTACATTTGAAAGTAATATAGCACGGA 57.397 29.630 0.00 0.00 0.00 4.69
1688 3232 4.079253 ACAGAACACATACATGGAAACCC 58.921 43.478 0.00 0.00 0.00 4.11
1696 3240 6.942005 TGATTGAAAGGACAGAACACATACAT 59.058 34.615 0.00 0.00 0.00 2.29
1697 3241 6.295249 TGATTGAAAGGACAGAACACATACA 58.705 36.000 0.00 0.00 0.00 2.29
1698 3242 6.801539 TGATTGAAAGGACAGAACACATAC 57.198 37.500 0.00 0.00 0.00 2.39
1767 3344 3.508793 CCCATATTCCCTGATTGACATGC 59.491 47.826 0.00 0.00 0.00 4.06
1821 3400 7.915923 GCTAAGCTTCAAATATTCCCAAACTAC 59.084 37.037 0.00 0.00 0.00 2.73
1941 3522 7.643528 CATATATGCATATGTATCCACCGAC 57.356 40.000 26.21 0.00 39.40 4.79
2010 3751 0.167908 AACCACGCATACGCATTGTG 59.832 50.000 0.00 0.00 45.53 3.33
2017 3758 1.374885 TGGGACAACCACGCATACG 60.375 57.895 0.00 0.00 46.80 3.06
2018 3759 4.705746 TGGGACAACCACGCATAC 57.294 55.556 0.00 0.00 46.80 2.39
2054 3817 1.337447 GCAAGCACAAATCAGCATGGT 60.337 47.619 0.00 0.00 36.16 3.55
2134 3902 0.039617 TCACGGGCAAATGAAAAGCG 60.040 50.000 0.00 0.00 0.00 4.68
2238 4009 6.246420 CTTGACAGGTAAGGAAATCAAGTG 57.754 41.667 0.00 0.00 38.69 3.16
2314 4320 3.741344 CAGACAGGTAAGGAAACAAGTCG 59.259 47.826 0.00 0.00 32.90 4.18
2372 4378 5.294552 AGGTTCTTTCTTCAGTTCTGTTTCG 59.705 40.000 0.00 0.00 0.00 3.46
2453 4459 6.351711 CCTCTAGCTCCTTTTTCTCTTCATCA 60.352 42.308 0.00 0.00 0.00 3.07
2510 4516 1.895020 TAGTTCGCGATGGTTGGCCT 61.895 55.000 10.88 0.00 35.27 5.19
2518 4524 5.333513 ACTTTACTCTTCTAGTTCGCGATG 58.666 41.667 10.88 0.68 39.80 3.84
2620 4626 2.722116 CACATTTTCGCCGGTTACAAAC 59.278 45.455 1.90 0.00 0.00 2.93
2647 4653 6.455360 ACATTAGCAACATGGTATTTCAGG 57.545 37.500 0.00 0.00 29.73 3.86
2680 4686 9.109393 GTAACCTCATACATTGATGTACACAAT 57.891 33.333 14.20 14.20 45.11 2.71
2709 4715 5.239306 CAGGAAAAACAGCAGAGATGTACAA 59.761 40.000 0.00 0.00 29.75 2.41
2740 4746 7.773224 CCAAACTGATGTACCAATACTCCATAA 59.227 37.037 0.00 0.00 32.00 1.90
2742 4748 6.069673 TCCAAACTGATGTACCAATACTCCAT 60.070 38.462 0.00 0.00 32.00 3.41
2743 4749 5.249622 TCCAAACTGATGTACCAATACTCCA 59.750 40.000 0.00 0.00 32.00 3.86
2744 4750 5.741011 TCCAAACTGATGTACCAATACTCC 58.259 41.667 0.00 0.00 32.00 3.85
2745 4751 7.865706 ATTCCAAACTGATGTACCAATACTC 57.134 36.000 0.00 0.00 32.00 2.59
2746 4752 8.768397 TCTATTCCAAACTGATGTACCAATACT 58.232 33.333 0.00 0.00 32.00 2.12
2747 4753 8.958119 TCTATTCCAAACTGATGTACCAATAC 57.042 34.615 0.00 0.00 0.00 1.89
2748 4754 7.715249 GCTCTATTCCAAACTGATGTACCAATA 59.285 37.037 0.00 0.00 0.00 1.90
2749 4755 6.543831 GCTCTATTCCAAACTGATGTACCAAT 59.456 38.462 0.00 0.00 0.00 3.16
2751 4757 5.189736 AGCTCTATTCCAAACTGATGTACCA 59.810 40.000 0.00 0.00 0.00 3.25
2752 4758 5.525378 CAGCTCTATTCCAAACTGATGTACC 59.475 44.000 0.00 0.00 0.00 3.34
2775 4785 2.929641 TGTCAGGCACAATTCTTCACA 58.070 42.857 0.00 0.00 29.30 3.58
2804 4814 3.750371 TCACTACCACAAATCCAACTGG 58.250 45.455 0.00 0.00 0.00 4.00
2818 4828 1.195115 TCTGGCACATCCTCACTACC 58.805 55.000 0.00 0.00 38.20 3.18
2837 4847 6.726764 ACCCTCTAGTGTCTCAGACTAAAATT 59.273 38.462 6.33 0.00 33.15 1.82
2843 4853 2.291282 CCACCCTCTAGTGTCTCAGACT 60.291 54.545 6.33 0.00 35.93 3.24
2844 4854 2.096248 CCACCCTCTAGTGTCTCAGAC 58.904 57.143 0.00 0.00 35.93 3.51
2845 4855 1.006043 CCCACCCTCTAGTGTCTCAGA 59.994 57.143 0.00 0.00 35.93 3.27
2846 4856 1.479709 CCCACCCTCTAGTGTCTCAG 58.520 60.000 0.00 0.00 35.93 3.35
2879 4924 2.997986 CCAAAACGTTCGGCTATAGTGT 59.002 45.455 0.00 0.00 0.00 3.55
2930 4975 4.986708 TGCCGGGGGAAAGTTGCC 62.987 66.667 2.18 0.00 38.05 4.52
2931 4976 0.968393 TATTGCCGGGGGAAAGTTGC 60.968 55.000 2.18 0.00 0.00 4.17
2932 4977 1.551452 TTATTGCCGGGGGAAAGTTG 58.449 50.000 2.18 0.00 0.00 3.16
2933 4978 1.897133 GTTTATTGCCGGGGGAAAGTT 59.103 47.619 2.18 0.00 0.00 2.66
2934 4979 1.076513 AGTTTATTGCCGGGGGAAAGT 59.923 47.619 2.18 0.00 0.00 2.66
2936 4981 1.842052 GAGTTTATTGCCGGGGGAAA 58.158 50.000 2.18 0.00 0.00 3.13
2938 4983 1.222387 CGAGTTTATTGCCGGGGGA 59.778 57.895 2.18 0.00 0.00 4.81
2943 4988 1.636340 CCTCGCGAGTTTATTGCCG 59.364 57.895 32.41 11.77 34.44 5.69
2979 5024 5.728637 ATTTCGGATTTTGCTTTCCTTCT 57.271 34.783 0.00 0.00 0.00 2.85
2980 5025 7.044052 CGATAATTTCGGATTTTGCTTTCCTTC 60.044 37.037 0.00 0.00 44.28 3.46
3090 5136 2.835895 GGAGCCGAGGAGGAGACC 60.836 72.222 0.00 0.00 45.00 3.85
3102 5148 3.934962 GCGGAGATGGGAGGAGCC 61.935 72.222 0.00 0.00 0.00 4.70
3372 5418 2.035066 GCTCAGCCAATGCCGAAATTAT 59.965 45.455 0.00 0.00 38.69 1.28
3477 5523 0.897401 TTTGGCGGCATCCATGAACA 60.897 50.000 14.32 0.00 35.77 3.18


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

AutoCloner maintained by Alex Coulton.