Multiple sequence alignment - TraesCS1D01G042200

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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 TraesCS1D01G042200 chr1D 100.000 3441 0 0 1 3441 20702873 20699433 0.000000e+00 6355.0
1 TraesCS1D01G042200 chr1D 100.000 240 0 0 3801 4040 20699073 20698834 1.030000e-120 444.0
2 TraesCS1D01G042200 chr1D 96.491 114 4 0 3801 3914 20698994 20698881 5.330000e-44 189.0
3 TraesCS1D01G042200 chr1D 96.491 114 4 0 3880 3993 20699073 20698960 5.330000e-44 189.0
4 TraesCS1D01G042200 chr1A 97.308 3381 88 3 1 3379 22332110 22328731 0.000000e+00 5736.0
5 TraesCS1D01G042200 chr1A 85.714 63 9 0 3378 3440 559054254 559054316 2.610000e-07 67.6
6 TraesCS1D01G042200 chr2A 88.804 2617 259 15 467 3068 72941497 72938900 0.000000e+00 3179.0
7 TraesCS1D01G042200 chr2A 78.879 464 81 9 1 451 72942023 72941564 8.490000e-77 298.0
8 TraesCS1D01G042200 chr6A 85.579 3058 384 28 1 3026 4711653 4708621 0.000000e+00 3151.0
9 TraesCS1D01G042200 chr6A 94.737 76 4 0 3839 3914 562528477 562528402 7.090000e-23 119.0
10 TraesCS1D01G042200 chrUn 86.147 2476 282 29 583 3013 274770056 274772515 0.000000e+00 2615.0
11 TraesCS1D01G042200 chr3A 86.147 2476 282 29 583 3013 731762687 731765146 0.000000e+00 2615.0
12 TraesCS1D01G042200 chr3A 91.919 99 8 0 3918 4016 102625344 102625442 5.440000e-29 139.0
13 TraesCS1D01G042200 chr3A 87.069 116 13 2 3918 4033 744551617 744551730 3.280000e-26 130.0
14 TraesCS1D01G042200 chr3A 70.963 706 161 37 1540 2223 681663833 681664516 1.180000e-25 128.0
15 TraesCS1D01G042200 chr3A 89.899 99 10 0 3911 4009 730808203 730808301 1.180000e-25 128.0
16 TraesCS1D01G042200 chr3A 90.769 65 6 0 3377 3441 13912642 13912706 2.000000e-13 87.9
17 TraesCS1D01G042200 chr1B 96.272 1368 41 5 2020 3379 34137188 34135823 0.000000e+00 2235.0
18 TraesCS1D01G042200 chr1B 95.858 169 7 0 2079 2247 38165206 38165038 1.430000e-69 274.0
19 TraesCS1D01G042200 chr1B 93.750 64 4 0 3378 3441 443589153 443589216 3.320000e-16 97.1
20 TraesCS1D01G042200 chr2D 95.699 93 4 0 3918 4010 71386480 71386572 2.520000e-32 150.0
21 TraesCS1D01G042200 chr2D 96.053 76 3 0 3839 3914 71386480 71386555 1.520000e-24 124.0
22 TraesCS1D01G042200 chr2D 90.625 64 6 0 3378 3441 617130237 617130300 7.190000e-13 86.1
23 TraesCS1D01G042200 chr6D 95.652 92 4 0 3918 4009 418957078 418956987 9.050000e-32 148.0
24 TraesCS1D01G042200 chr6D 96.053 76 3 0 3839 3914 418957078 418957003 1.520000e-24 124.0
25 TraesCS1D01G042200 chr4D 93.069 101 6 1 3918 4017 465124141 465124241 3.250000e-31 147.0
26 TraesCS1D01G042200 chr3B 93.000 100 6 1 3911 4010 704132173 704132075 1.170000e-30 145.0
27 TraesCS1D01G042200 chr3B 92.000 100 8 0 3918 4017 707428689 707428590 1.510000e-29 141.0
28 TraesCS1D01G042200 chr3B 80.000 170 32 2 1540 1708 721047041 721047209 1.520000e-24 124.0
29 TraesCS1D01G042200 chr3B 91.566 83 6 1 3832 3914 704132173 704132092 3.300000e-21 113.0
30 TraesCS1D01G042200 chr3B 89.394 66 3 3 3378 3441 235854792 235854729 3.350000e-11 80.5
31 TraesCS1D01G042200 chr3D 94.565 92 5 0 3918 4009 108242207 108242116 4.210000e-30 143.0
32 TraesCS1D01G042200 chr3D 94.737 76 4 0 3839 3914 108242207 108242132 7.090000e-23 119.0
33 TraesCS1D01G042200 chr7D 96.053 76 3 0 3839 3914 593265086 593265161 1.520000e-24 124.0
34 TraesCS1D01G042200 chr7A 94.872 78 4 0 3837 3914 222942001 222941924 5.480000e-24 122.0
35 TraesCS1D01G042200 chr7A 89.062 64 7 0 3378 3441 115634931 115634994 3.350000e-11 80.5
36 TraesCS1D01G042200 chr5B 94.737 76 4 0 3839 3914 490224202 490224127 7.090000e-23 119.0
37 TraesCS1D01G042200 chr5D 84.848 99 15 0 3911 4009 47529635 47529537 2.570000e-17 100.0
38 TraesCS1D01G042200 chr5D 87.500 64 8 0 3378 3441 314738650 314738587 1.560000e-09 75.0
39 TraesCS1D01G042200 chr7B 85.897 78 9 2 3365 3441 431680233 431680309 9.310000e-12 82.4
40 TraesCS1D01G042200 chr2B 87.500 64 8 0 3378 3441 21905092 21905155 1.560000e-09 75.0
41 TraesCS1D01G042200 chr4A 94.286 35 1 1 3801 3834 580479925 580479959 7.000000e-03 52.8


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 TraesCS1D01G042200 chr1D 20698834 20702873 4039 True 1794.25 6355 98.2455 1 4040 4 chr1D.!!$R1 4039
1 TraesCS1D01G042200 chr1A 22328731 22332110 3379 True 5736.00 5736 97.3080 1 3379 1 chr1A.!!$R1 3378
2 TraesCS1D01G042200 chr2A 72938900 72942023 3123 True 1738.50 3179 83.8415 1 3068 2 chr2A.!!$R1 3067
3 TraesCS1D01G042200 chr6A 4708621 4711653 3032 True 3151.00 3151 85.5790 1 3026 1 chr6A.!!$R1 3025
4 TraesCS1D01G042200 chrUn 274770056 274772515 2459 False 2615.00 2615 86.1470 583 3013 1 chrUn.!!$F1 2430
5 TraesCS1D01G042200 chr3A 731762687 731765146 2459 False 2615.00 2615 86.1470 583 3013 1 chr3A.!!$F5 2430
6 TraesCS1D01G042200 chr1B 34135823 34137188 1365 True 2235.00 2235 96.2720 2020 3379 1 chr1B.!!$R1 1359

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
860 933 3.297620 CCCAAGCAGCACACCACC 61.298 66.667 0.0 0.0 0.0 4.61 F
1719 1816 0.169009 GTCAGGCCGAGCATTGTTTC 59.831 55.000 0.0 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1843 0.598158 TACCAACGTCGCAAGGACAC 60.598 55.0 5.35 0.00 46.42 3.67 R
3407 3536 0.370273 CTTGAATCTCGGGAAACGCG 59.630 55.0 3.53 3.53 43.86 6.01 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
242 255 5.769162 AGAAGACTACTACCGGATGATAACC 59.231 44.000 9.46 0.00 0.00 2.85
311 324 4.703897 ACAAGTGCACTGAAAAGCTAGTA 58.296 39.130 22.49 0.00 0.00 1.82
314 327 4.899502 AGTGCACTGAAAAGCTAGTACAT 58.100 39.130 20.97 0.00 0.00 2.29
338 351 3.489229 GGCTTGAACAACAACAAGAGGAC 60.489 47.826 0.00 0.00 43.98 3.85
453 466 6.594159 GGAAAAATTCGACCACATCTTCTCTA 59.406 38.462 0.00 0.00 0.00 2.43
460 473 7.631717 TCGACCACATCTTCTCTATATATGG 57.368 40.000 0.00 0.00 0.00 2.74
462 475 6.552445 ACCACATCTTCTCTATATATGGCC 57.448 41.667 0.00 0.00 0.00 5.36
536 600 5.047802 GCTTGAAGAGGAATCCAACAAATCA 60.048 40.000 0.61 0.00 0.00 2.57
548 612 6.331369 TCCAACAAATCAGTGGAAGAATTC 57.669 37.500 0.00 0.00 46.67 2.17
615 679 4.399934 AGATCGAAGAGTACCTGGAGAAAC 59.600 45.833 0.00 0.00 43.63 2.78
860 933 3.297620 CCCAAGCAGCACACCACC 61.298 66.667 0.00 0.00 0.00 4.61
885 958 5.279056 CCGGGAAAAGTAGCCACAAATAAAA 60.279 40.000 0.00 0.00 0.00 1.52
886 959 6.217294 CGGGAAAAGTAGCCACAAATAAAAA 58.783 36.000 0.00 0.00 0.00 1.94
1029 1102 0.825010 CAGGCCAAGACCAGCTGTTT 60.825 55.000 13.81 0.00 0.00 2.83
1719 1816 0.169009 GTCAGGCCGAGCATTGTTTC 59.831 55.000 0.00 0.00 0.00 2.78
1887 1984 2.654079 CCTGGCTCGCCACTTCTCT 61.654 63.158 6.52 0.00 41.89 3.10
1927 2024 0.896019 CCGTCCCTCCGATAGCATCT 60.896 60.000 0.00 0.00 0.00 2.90
2310 2425 1.053835 TGGACCTGGAAGTGCTGTCA 61.054 55.000 0.00 0.00 0.00 3.58
2491 2606 1.524482 GAGATCAAGCCTCCGCCTT 59.476 57.895 0.00 0.00 34.57 4.35
2520 2641 0.453793 CTGCTACTCCTCCTGACGTG 59.546 60.000 0.00 0.00 0.00 4.49
2575 2696 2.949447 ACACACCCAAGCTTCTTGAAT 58.051 42.857 8.04 0.00 0.00 2.57
3094 3217 2.198827 TACAATGTGGTCAGCAAGGG 57.801 50.000 0.00 0.00 0.00 3.95
3232 3360 4.569564 GGGGTGTCTGAATGTAACGATAAC 59.430 45.833 0.00 0.00 0.00 1.89
3403 3532 6.992715 ACTCCCTTCATTATACAATGTAGTGC 59.007 38.462 0.00 0.00 41.96 4.40
3404 3533 5.989168 TCCCTTCATTATACAATGTAGTGCG 59.011 40.000 0.00 0.00 41.96 5.34
3405 3534 5.334105 CCCTTCATTATACAATGTAGTGCGC 60.334 44.000 0.00 0.00 41.96 6.09
3406 3535 5.334105 CCTTCATTATACAATGTAGTGCGCC 60.334 44.000 4.18 0.00 41.96 6.53
3407 3536 4.062293 TCATTATACAATGTAGTGCGCCC 58.938 43.478 4.18 0.00 41.96 6.13
3408 3537 2.143008 TATACAATGTAGTGCGCCCG 57.857 50.000 4.18 0.00 0.00 6.13
3409 3538 1.157870 ATACAATGTAGTGCGCCCGC 61.158 55.000 4.18 5.60 42.35 6.13
3410 3539 4.222589 CAATGTAGTGCGCCCGCG 62.223 66.667 4.18 4.36 45.51 6.46
3411 3540 4.752879 AATGTAGTGCGCCCGCGT 62.753 61.111 4.18 0.52 45.51 6.01
3412 3541 4.752879 ATGTAGTGCGCCCGCGTT 62.753 61.111 4.18 1.35 45.51 4.84
3413 3542 4.973055 TGTAGTGCGCCCGCGTTT 62.973 61.111 4.18 0.00 45.51 3.60
3414 3543 4.143363 GTAGTGCGCCCGCGTTTC 62.143 66.667 4.18 2.02 45.51 2.78
3421 3550 4.832608 GCCCGCGTTTCCCGAGAT 62.833 66.667 4.92 0.00 38.82 2.75
3422 3551 2.125269 CCCGCGTTTCCCGAGATT 60.125 61.111 4.92 0.00 38.82 2.40
3423 3552 2.171725 CCCGCGTTTCCCGAGATTC 61.172 63.158 4.92 0.00 38.82 2.52
3424 3553 1.447140 CCGCGTTTCCCGAGATTCA 60.447 57.895 4.92 0.00 38.82 2.57
3425 3554 1.017177 CCGCGTTTCCCGAGATTCAA 61.017 55.000 4.92 0.00 38.82 2.69
3426 3555 0.370273 CGCGTTTCCCGAGATTCAAG 59.630 55.000 0.00 0.00 38.82 3.02
3427 3556 1.439679 GCGTTTCCCGAGATTCAAGT 58.560 50.000 0.00 0.00 39.56 3.16
3428 3557 1.804748 GCGTTTCCCGAGATTCAAGTT 59.195 47.619 0.00 0.00 39.56 2.66
3429 3558 2.225727 GCGTTTCCCGAGATTCAAGTTT 59.774 45.455 0.00 0.00 39.56 2.66
3430 3559 3.810373 CGTTTCCCGAGATTCAAGTTTG 58.190 45.455 0.00 0.00 39.56 2.93
3431 3560 3.496884 CGTTTCCCGAGATTCAAGTTTGA 59.503 43.478 0.00 0.00 39.56 2.69
3432 3561 4.610680 CGTTTCCCGAGATTCAAGTTTGAC 60.611 45.833 0.00 0.00 39.56 3.18
3433 3562 3.053831 TCCCGAGATTCAAGTTTGACC 57.946 47.619 0.00 0.00 36.83 4.02
3434 3563 2.370519 TCCCGAGATTCAAGTTTGACCA 59.629 45.455 0.00 0.00 36.83 4.02
3435 3564 3.009033 TCCCGAGATTCAAGTTTGACCAT 59.991 43.478 0.00 0.00 36.83 3.55
3436 3565 4.224147 TCCCGAGATTCAAGTTTGACCATA 59.776 41.667 0.00 0.00 36.83 2.74
3437 3566 4.941263 CCCGAGATTCAAGTTTGACCATAA 59.059 41.667 0.00 0.00 36.83 1.90
3438 3567 5.414454 CCCGAGATTCAAGTTTGACCATAAA 59.586 40.000 0.00 0.00 36.83 1.40
3439 3568 6.095440 CCCGAGATTCAAGTTTGACCATAAAT 59.905 38.462 0.00 0.00 36.83 1.40
3440 3569 7.362920 CCCGAGATTCAAGTTTGACCATAAATT 60.363 37.037 0.00 0.00 36.83 1.82
3820 3949 3.099267 AGTTAGATCTCGGGAAATGCG 57.901 47.619 0.00 0.00 0.00 4.73
3821 3950 2.135933 GTTAGATCTCGGGAAATGCGG 58.864 52.381 0.00 0.00 0.00 5.69
3822 3951 0.679505 TAGATCTCGGGAAATGCGGG 59.320 55.000 0.00 0.00 0.00 6.13
3823 3952 2.203209 ATCTCGGGAAATGCGGGC 60.203 61.111 0.00 0.00 0.00 6.13
3824 3953 4.830765 TCTCGGGAAATGCGGGCG 62.831 66.667 0.00 0.00 0.00 6.13
3835 3964 4.536687 GCGGGCGCACTACATTGC 62.537 66.667 8.62 0.00 41.49 3.56
3836 3965 2.819595 CGGGCGCACTACATTGCT 60.820 61.111 8.62 0.00 40.62 3.91
3837 3966 1.520564 CGGGCGCACTACATTGCTA 60.521 57.895 8.62 0.00 40.62 3.49
3838 3967 1.762222 CGGGCGCACTACATTGCTAC 61.762 60.000 8.62 0.00 40.62 3.58
3839 3968 0.462047 GGGCGCACTACATTGCTACT 60.462 55.000 10.83 0.00 40.62 2.57
3840 3969 0.931005 GGCGCACTACATTGCTACTC 59.069 55.000 10.83 0.00 40.62 2.59
3841 3970 0.931005 GCGCACTACATTGCTACTCC 59.069 55.000 0.30 0.00 40.62 3.85
3842 3971 1.571919 CGCACTACATTGCTACTCCC 58.428 55.000 0.00 0.00 40.62 4.30
3843 3972 1.571919 GCACTACATTGCTACTCCCG 58.428 55.000 0.00 0.00 39.59 5.14
3844 3973 1.571919 CACTACATTGCTACTCCCGC 58.428 55.000 0.00 0.00 0.00 6.13
3845 3974 0.464452 ACTACATTGCTACTCCCGCC 59.536 55.000 0.00 0.00 0.00 6.13
3846 3975 0.597637 CTACATTGCTACTCCCGCCG 60.598 60.000 0.00 0.00 0.00 6.46
3847 3976 2.638330 TACATTGCTACTCCCGCCGC 62.638 60.000 0.00 0.00 0.00 6.53
3848 3977 3.781307 ATTGCTACTCCCGCCGCA 61.781 61.111 0.00 0.00 0.00 5.69
3849 3978 3.740128 ATTGCTACTCCCGCCGCAG 62.740 63.158 0.00 0.00 33.48 5.18
3851 3980 4.874977 GCTACTCCCGCCGCAGTC 62.875 72.222 0.00 0.00 0.00 3.51
3852 3981 4.554363 CTACTCCCGCCGCAGTCG 62.554 72.222 0.00 0.00 0.00 4.18
3862 3991 2.805353 CGCAGTCGGTCTCGTTGG 60.805 66.667 0.00 0.00 37.69 3.77
3863 3992 2.338984 GCAGTCGGTCTCGTTGGT 59.661 61.111 0.00 0.00 37.69 3.67
3864 3993 1.300697 GCAGTCGGTCTCGTTGGTT 60.301 57.895 0.00 0.00 37.69 3.67
3865 3994 0.038892 GCAGTCGGTCTCGTTGGTTA 60.039 55.000 0.00 0.00 37.69 2.85
3866 3995 1.603678 GCAGTCGGTCTCGTTGGTTAA 60.604 52.381 0.00 0.00 37.69 2.01
3867 3996 2.746269 CAGTCGGTCTCGTTGGTTAAA 58.254 47.619 0.00 0.00 37.69 1.52
3868 3997 3.323243 CAGTCGGTCTCGTTGGTTAAAT 58.677 45.455 0.00 0.00 37.69 1.40
3869 3998 3.744426 CAGTCGGTCTCGTTGGTTAAATT 59.256 43.478 0.00 0.00 37.69 1.82
3870 3999 4.212636 CAGTCGGTCTCGTTGGTTAAATTT 59.787 41.667 0.00 0.00 37.69 1.82
3871 4000 5.406175 CAGTCGGTCTCGTTGGTTAAATTTA 59.594 40.000 0.00 0.00 37.69 1.40
3872 4001 6.091713 CAGTCGGTCTCGTTGGTTAAATTTAT 59.908 38.462 0.00 0.00 37.69 1.40
3873 4002 6.091713 AGTCGGTCTCGTTGGTTAAATTTATG 59.908 38.462 0.00 0.00 37.69 1.90
3874 4003 5.352016 TCGGTCTCGTTGGTTAAATTTATGG 59.648 40.000 0.00 0.00 37.69 2.74
3875 4004 5.122711 CGGTCTCGTTGGTTAAATTTATGGT 59.877 40.000 0.00 0.00 0.00 3.55
3876 4005 6.549061 GGTCTCGTTGGTTAAATTTATGGTC 58.451 40.000 0.00 0.00 0.00 4.02
3877 4006 6.149807 GGTCTCGTTGGTTAAATTTATGGTCA 59.850 38.462 0.00 0.00 0.00 4.02
3878 4007 7.308710 GGTCTCGTTGGTTAAATTTATGGTCAA 60.309 37.037 0.00 0.00 0.00 3.18
3879 4008 8.077386 GTCTCGTTGGTTAAATTTATGGTCAAA 58.923 33.333 0.00 0.00 0.00 2.69
3880 4009 8.293867 TCTCGTTGGTTAAATTTATGGTCAAAG 58.706 33.333 0.00 4.88 0.00 2.77
3881 4010 7.942990 TCGTTGGTTAAATTTATGGTCAAAGT 58.057 30.769 0.00 0.00 0.00 2.66
3882 4011 8.414778 TCGTTGGTTAAATTTATGGTCAAAGTT 58.585 29.630 0.00 0.00 31.36 2.66
3883 4012 9.680315 CGTTGGTTAAATTTATGGTCAAAGTTA 57.320 29.630 0.00 0.00 29.44 2.24
3891 4020 8.438676 AATTTATGGTCAAAGTTAGATCTCGG 57.561 34.615 0.00 0.00 0.00 4.63
3892 4021 3.887621 TGGTCAAAGTTAGATCTCGGG 57.112 47.619 0.00 0.00 0.00 5.14
3893 4022 3.437213 TGGTCAAAGTTAGATCTCGGGA 58.563 45.455 0.00 0.00 0.00 5.14
3894 4023 3.835978 TGGTCAAAGTTAGATCTCGGGAA 59.164 43.478 0.00 0.00 0.00 3.97
3895 4024 4.285003 TGGTCAAAGTTAGATCTCGGGAAA 59.715 41.667 0.00 0.00 0.00 3.13
3896 4025 4.630505 GGTCAAAGTTAGATCTCGGGAAAC 59.369 45.833 0.00 0.00 0.00 2.78
3897 4026 4.326548 GTCAAAGTTAGATCTCGGGAAACG 59.673 45.833 0.00 0.00 46.11 3.60
3898 4027 2.580966 AGTTAGATCTCGGGAAACGC 57.419 50.000 0.00 0.00 43.86 4.84
3899 4028 1.197910 GTTAGATCTCGGGAAACGCG 58.802 55.000 3.53 3.53 43.86 6.01
3900 4029 0.101759 TTAGATCTCGGGAAACGCGG 59.898 55.000 12.47 0.00 43.86 6.46
3901 4030 1.731433 TAGATCTCGGGAAACGCGGG 61.731 60.000 12.47 0.00 43.86 6.13
3902 4031 4.832608 ATCTCGGGAAACGCGGGC 62.833 66.667 12.47 0.00 40.12 6.13
3908 4037 2.357760 GGAAACGCGGGCACACTA 60.358 61.111 12.47 0.00 0.00 2.74
3909 4038 2.674084 GGAAACGCGGGCACACTAC 61.674 63.158 12.47 0.00 0.00 2.73
3910 4039 1.957186 GAAACGCGGGCACACTACA 60.957 57.895 12.47 0.00 0.00 2.74
3911 4040 1.296056 GAAACGCGGGCACACTACAT 61.296 55.000 12.47 0.00 0.00 2.29
3912 4041 0.887387 AAACGCGGGCACACTACATT 60.887 50.000 12.47 0.00 0.00 2.71
3913 4042 1.573829 AACGCGGGCACACTACATTG 61.574 55.000 12.47 0.00 0.00 2.82
3914 4043 2.485122 GCGGGCACACTACATTGC 59.515 61.111 0.00 0.00 38.06 3.56
3915 4044 2.040544 GCGGGCACACTACATTGCT 61.041 57.895 0.00 0.00 38.85 3.91
3916 4045 0.742990 GCGGGCACACTACATTGCTA 60.743 55.000 0.00 0.00 38.85 3.49
3917 4046 1.006832 CGGGCACACTACATTGCTAC 58.993 55.000 0.00 0.00 38.85 3.58
3918 4047 1.405526 CGGGCACACTACATTGCTACT 60.406 52.381 0.00 0.00 38.85 2.57
3919 4048 2.280628 GGGCACACTACATTGCTACTC 58.719 52.381 0.00 0.00 38.85 2.59
3920 4049 2.280628 GGCACACTACATTGCTACTCC 58.719 52.381 0.00 0.00 38.85 3.85
3921 4050 2.280628 GCACACTACATTGCTACTCCC 58.719 52.381 0.00 0.00 35.74 4.30
3922 4051 2.540515 CACACTACATTGCTACTCCCG 58.459 52.381 0.00 0.00 0.00 5.14
3923 4052 1.134788 ACACTACATTGCTACTCCCGC 60.135 52.381 0.00 0.00 0.00 6.13
3924 4053 0.464452 ACTACATTGCTACTCCCGCC 59.536 55.000 0.00 0.00 0.00 6.13
3925 4054 0.597637 CTACATTGCTACTCCCGCCG 60.598 60.000 0.00 0.00 0.00 6.46
3926 4055 2.638330 TACATTGCTACTCCCGCCGC 62.638 60.000 0.00 0.00 0.00 6.53
3927 4056 3.781307 ATTGCTACTCCCGCCGCA 61.781 61.111 0.00 0.00 0.00 5.69
3928 4057 3.740128 ATTGCTACTCCCGCCGCAG 62.740 63.158 0.00 0.00 33.48 5.18
3930 4059 4.874977 GCTACTCCCGCCGCAGTC 62.875 72.222 0.00 0.00 0.00 3.51
3931 4060 4.554363 CTACTCCCGCCGCAGTCG 62.554 72.222 0.00 0.00 0.00 4.18
3941 4070 2.805353 CGCAGTCGGTCTCGTTGG 60.805 66.667 0.00 0.00 37.69 3.77
3942 4071 2.338984 GCAGTCGGTCTCGTTGGT 59.661 61.111 0.00 0.00 37.69 3.67
3943 4072 1.300697 GCAGTCGGTCTCGTTGGTT 60.301 57.895 0.00 0.00 37.69 3.67
3944 4073 0.038892 GCAGTCGGTCTCGTTGGTTA 60.039 55.000 0.00 0.00 37.69 2.85
3945 4074 1.603678 GCAGTCGGTCTCGTTGGTTAA 60.604 52.381 0.00 0.00 37.69 2.01
3946 4075 2.746269 CAGTCGGTCTCGTTGGTTAAA 58.254 47.619 0.00 0.00 37.69 1.52
3947 4076 3.323243 CAGTCGGTCTCGTTGGTTAAAT 58.677 45.455 0.00 0.00 37.69 1.40
3948 4077 3.744426 CAGTCGGTCTCGTTGGTTAAATT 59.256 43.478 0.00 0.00 37.69 1.82
3949 4078 4.212636 CAGTCGGTCTCGTTGGTTAAATTT 59.787 41.667 0.00 0.00 37.69 1.82
3950 4079 5.406175 CAGTCGGTCTCGTTGGTTAAATTTA 59.594 40.000 0.00 0.00 37.69 1.40
3951 4080 6.091713 CAGTCGGTCTCGTTGGTTAAATTTAT 59.908 38.462 0.00 0.00 37.69 1.40
3952 4081 6.091713 AGTCGGTCTCGTTGGTTAAATTTATG 59.908 38.462 0.00 0.00 37.69 1.90
3953 4082 5.352016 TCGGTCTCGTTGGTTAAATTTATGG 59.648 40.000 0.00 0.00 37.69 2.74
3954 4083 5.122711 CGGTCTCGTTGGTTAAATTTATGGT 59.877 40.000 0.00 0.00 0.00 3.55
3955 4084 6.549061 GGTCTCGTTGGTTAAATTTATGGTC 58.451 40.000 0.00 0.00 0.00 4.02
3956 4085 6.149807 GGTCTCGTTGGTTAAATTTATGGTCA 59.850 38.462 0.00 0.00 0.00 4.02
3957 4086 7.308710 GGTCTCGTTGGTTAAATTTATGGTCAA 60.309 37.037 0.00 0.00 0.00 3.18
3958 4087 8.077386 GTCTCGTTGGTTAAATTTATGGTCAAA 58.923 33.333 0.00 0.00 0.00 2.69
3959 4088 8.293867 TCTCGTTGGTTAAATTTATGGTCAAAG 58.706 33.333 0.00 4.88 0.00 2.77
3960 4089 7.942990 TCGTTGGTTAAATTTATGGTCAAAGT 58.057 30.769 0.00 0.00 0.00 2.66
3961 4090 8.414778 TCGTTGGTTAAATTTATGGTCAAAGTT 58.585 29.630 0.00 0.00 31.36 2.66
3962 4091 9.680315 CGTTGGTTAAATTTATGGTCAAAGTTA 57.320 29.630 0.00 0.00 29.44 2.24
3970 4099 8.438676 AATTTATGGTCAAAGTTAGATCTCGG 57.561 34.615 0.00 0.00 0.00 4.63
3971 4100 3.887621 TGGTCAAAGTTAGATCTCGGG 57.112 47.619 0.00 0.00 0.00 5.14
3972 4101 3.437213 TGGTCAAAGTTAGATCTCGGGA 58.563 45.455 0.00 0.00 0.00 5.14
3973 4102 3.835978 TGGTCAAAGTTAGATCTCGGGAA 59.164 43.478 0.00 0.00 0.00 3.97
3974 4103 4.285003 TGGTCAAAGTTAGATCTCGGGAAA 59.715 41.667 0.00 0.00 0.00 3.13
3975 4104 4.630505 GGTCAAAGTTAGATCTCGGGAAAC 59.369 45.833 0.00 0.00 0.00 2.78
3976 4105 4.326548 GTCAAAGTTAGATCTCGGGAAACG 59.673 45.833 0.00 0.00 46.11 3.60
3977 4106 2.580966 AGTTAGATCTCGGGAAACGC 57.419 50.000 0.00 0.00 43.86 4.84
3978 4107 1.197910 GTTAGATCTCGGGAAACGCG 58.802 55.000 3.53 3.53 43.86 6.01
3979 4108 0.101759 TTAGATCTCGGGAAACGCGG 59.898 55.000 12.47 0.00 43.86 6.46
3980 4109 1.731433 TAGATCTCGGGAAACGCGGG 61.731 60.000 12.47 0.00 43.86 6.13
3981 4110 4.832608 ATCTCGGGAAACGCGGGC 62.833 66.667 12.47 0.00 40.12 6.13
3988 4117 4.143363 GAAACGCGGGCGCACTAC 62.143 66.667 12.47 0.00 44.19 2.73
3994 4123 3.773630 CGGGCGCACTACGTTGTG 61.774 66.667 23.20 23.20 46.11 3.33
3995 4124 2.356553 GGGCGCACTACGTTGTGA 60.357 61.111 29.93 0.00 46.11 3.58
3996 4125 1.957186 GGGCGCACTACGTTGTGAA 60.957 57.895 29.93 0.00 46.11 3.18
3997 4126 1.500512 GGGCGCACTACGTTGTGAAA 61.501 55.000 29.93 0.00 46.11 2.69
3998 4127 0.515564 GGCGCACTACGTTGTGAAAT 59.484 50.000 29.93 0.00 46.11 2.17
3999 4128 1.591248 GCGCACTACGTTGTGAAATG 58.409 50.000 29.93 17.48 46.11 2.32
4000 4129 1.724654 GCGCACTACGTTGTGAAATGG 60.725 52.381 29.93 14.95 46.11 3.16
4001 4130 1.795872 CGCACTACGTTGTGAAATGGA 59.204 47.619 29.93 0.00 40.12 3.41
4002 4131 2.159841 CGCACTACGTTGTGAAATGGAG 60.160 50.000 29.93 3.73 40.12 3.86
4003 4132 2.159627 GCACTACGTTGTGAAATGGAGG 59.840 50.000 29.93 4.37 40.12 4.30
4004 4133 2.742053 CACTACGTTGTGAAATGGAGGG 59.258 50.000 23.14 0.00 40.12 4.30
4005 4134 2.635915 ACTACGTTGTGAAATGGAGGGA 59.364 45.455 0.73 0.00 0.00 4.20
4006 4135 2.185004 ACGTTGTGAAATGGAGGGAG 57.815 50.000 0.00 0.00 0.00 4.30
4007 4136 1.420138 ACGTTGTGAAATGGAGGGAGT 59.580 47.619 0.00 0.00 0.00 3.85
4008 4137 2.635915 ACGTTGTGAAATGGAGGGAGTA 59.364 45.455 0.00 0.00 0.00 2.59
4009 4138 3.263425 ACGTTGTGAAATGGAGGGAGTAT 59.737 43.478 0.00 0.00 0.00 2.12
4010 4139 4.261801 CGTTGTGAAATGGAGGGAGTATT 58.738 43.478 0.00 0.00 0.00 1.89
4011 4140 4.700213 CGTTGTGAAATGGAGGGAGTATTT 59.300 41.667 0.00 0.00 0.00 1.40
4012 4141 5.391950 CGTTGTGAAATGGAGGGAGTATTTG 60.392 44.000 0.00 0.00 0.00 2.32
4013 4142 5.255397 TGTGAAATGGAGGGAGTATTTGT 57.745 39.130 0.00 0.00 0.00 2.83
4014 4143 5.640147 TGTGAAATGGAGGGAGTATTTGTT 58.360 37.500 0.00 0.00 0.00 2.83
4015 4144 6.074648 TGTGAAATGGAGGGAGTATTTGTTT 58.925 36.000 0.00 0.00 0.00 2.83
4016 4145 6.553100 TGTGAAATGGAGGGAGTATTTGTTTT 59.447 34.615 0.00 0.00 0.00 2.43
4017 4146 6.868339 GTGAAATGGAGGGAGTATTTGTTTTG 59.132 38.462 0.00 0.00 0.00 2.44
4018 4147 6.553100 TGAAATGGAGGGAGTATTTGTTTTGT 59.447 34.615 0.00 0.00 0.00 2.83
4019 4148 6.994421 AATGGAGGGAGTATTTGTTTTGTT 57.006 33.333 0.00 0.00 0.00 2.83
4020 4149 5.782893 TGGAGGGAGTATTTGTTTTGTTG 57.217 39.130 0.00 0.00 0.00 3.33
4021 4150 5.205056 TGGAGGGAGTATTTGTTTTGTTGT 58.795 37.500 0.00 0.00 0.00 3.32
4022 4151 5.659079 TGGAGGGAGTATTTGTTTTGTTGTT 59.341 36.000 0.00 0.00 0.00 2.83
4023 4152 6.183360 TGGAGGGAGTATTTGTTTTGTTGTTC 60.183 38.462 0.00 0.00 0.00 3.18
4024 4153 5.827666 AGGGAGTATTTGTTTTGTTGTTCG 58.172 37.500 0.00 0.00 0.00 3.95
4025 4154 5.591067 AGGGAGTATTTGTTTTGTTGTTCGA 59.409 36.000 0.00 0.00 0.00 3.71
4026 4155 5.912955 GGGAGTATTTGTTTTGTTGTTCGAG 59.087 40.000 0.00 0.00 0.00 4.04
4027 4156 6.238538 GGGAGTATTTGTTTTGTTGTTCGAGA 60.239 38.462 0.00 0.00 0.00 4.04
4028 4157 6.631636 GGAGTATTTGTTTTGTTGTTCGAGAC 59.368 38.462 0.00 0.00 0.00 3.36
4029 4158 7.316544 AGTATTTGTTTTGTTGTTCGAGACT 57.683 32.000 0.00 0.00 0.00 3.24
4030 4159 7.758495 AGTATTTGTTTTGTTGTTCGAGACTT 58.242 30.769 0.00 0.00 0.00 3.01
4031 4160 8.241367 AGTATTTGTTTTGTTGTTCGAGACTTT 58.759 29.630 0.00 0.00 0.00 2.66
4032 4161 6.921332 TTTGTTTTGTTGTTCGAGACTTTC 57.079 33.333 0.00 0.00 0.00 2.62
4033 4162 5.873179 TGTTTTGTTGTTCGAGACTTTCT 57.127 34.783 0.00 0.00 0.00 2.52
4034 4163 6.971527 TGTTTTGTTGTTCGAGACTTTCTA 57.028 33.333 0.00 0.00 0.00 2.10
4035 4164 7.548196 TGTTTTGTTGTTCGAGACTTTCTAT 57.452 32.000 0.00 0.00 0.00 1.98
4036 4165 7.981142 TGTTTTGTTGTTCGAGACTTTCTATT 58.019 30.769 0.00 0.00 0.00 1.73
4037 4166 7.908082 TGTTTTGTTGTTCGAGACTTTCTATTG 59.092 33.333 0.00 0.00 0.00 1.90
4038 4167 5.591643 TGTTGTTCGAGACTTTCTATTGC 57.408 39.130 0.00 0.00 0.00 3.56
4039 4168 4.451096 TGTTGTTCGAGACTTTCTATTGCC 59.549 41.667 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 0.391661 TCCATCAGCTTCTTGTCGGC 60.392 55.000 0.00 0.00 0.00 5.54
242 255 0.598680 GCTCCCTTCGTGGATCATCG 60.599 60.000 0.00 0.00 38.35 3.84
311 324 3.883830 TGTTGTTGTTCAAGCCAATGT 57.116 38.095 0.00 0.00 36.66 2.71
314 327 3.119173 CCTCTTGTTGTTGTTCAAGCCAA 60.119 43.478 0.00 0.00 40.27 4.52
338 351 0.457035 CAATGGCTTGGAATGGACCG 59.543 55.000 0.00 0.00 0.00 4.79
536 600 0.108138 CCTCGCCGAATTCTTCCACT 60.108 55.000 3.52 0.00 0.00 4.00
548 612 1.370657 GTCGATAGCTTCCTCGCCG 60.371 63.158 0.00 0.00 34.94 6.46
860 933 0.250989 TTGTGGCTACTTTTCCCGGG 60.251 55.000 16.85 16.85 0.00 5.73
885 958 0.468226 TATGATCCTCGCCGGCTTTT 59.532 50.000 26.68 4.22 0.00 2.27
886 959 0.687354 ATATGATCCTCGCCGGCTTT 59.313 50.000 26.68 3.80 0.00 3.51
1029 1102 2.363018 CAGTCCTCCTCGCCTGGA 60.363 66.667 0.00 0.00 34.52 3.86
1719 1816 1.030457 ATAGGTCGGCAAGTACCTCG 58.970 55.000 0.00 0.00 42.60 4.63
1746 1843 0.598158 TACCAACGTCGCAAGGACAC 60.598 55.000 5.35 0.00 46.42 3.67
1887 1984 0.955428 GCCGGATGTTGCTGAGAACA 60.955 55.000 5.05 0.00 40.08 3.18
1917 2014 6.653273 TTCAAGAAGTTGAAGATGCTATCG 57.347 37.500 0.00 0.00 45.82 2.92
2310 2425 3.120321 TGTTTCGAAGCCTGTACATGT 57.880 42.857 9.65 2.69 0.00 3.21
2491 2606 2.284921 AGTAGCAGCCTGCCTGGA 60.285 61.111 14.25 0.00 46.52 3.86
2606 2727 2.636830 CGAACAATGGGAGAAGATGCT 58.363 47.619 0.00 0.00 0.00 3.79
2712 2833 2.264794 CTGAGGCCGCGTAGGTTT 59.735 61.111 4.92 0.00 43.70 3.27
3094 3217 4.565564 GCTTGAATGAATGGATGAAGCAAC 59.434 41.667 0.00 0.00 35.50 4.17
3188 3316 6.275618 ACCCCTATTGGCTGTATAGAAATGAT 59.724 38.462 0.00 0.00 0.00 2.45
3232 3360 3.177487 CTCACTCATGAGTCATGACACG 58.823 50.000 28.18 21.36 44.60 4.49
3379 3508 6.146184 CGCACTACATTGTATAATGAAGGGAG 59.854 42.308 17.96 9.24 45.21 4.30
3380 3509 5.989168 CGCACTACATTGTATAATGAAGGGA 59.011 40.000 17.96 0.00 45.21 4.20
3381 3510 5.334105 GCGCACTACATTGTATAATGAAGGG 60.334 44.000 17.96 12.44 45.21 3.95
3382 3511 5.334105 GGCGCACTACATTGTATAATGAAGG 60.334 44.000 17.96 9.72 45.21 3.46
3383 3512 5.334105 GGGCGCACTACATTGTATAATGAAG 60.334 44.000 17.96 6.44 45.21 3.02
3384 3513 4.513692 GGGCGCACTACATTGTATAATGAA 59.486 41.667 17.96 0.00 45.21 2.57
3385 3514 4.062293 GGGCGCACTACATTGTATAATGA 58.938 43.478 17.96 2.50 45.21 2.57
3386 3515 6.644994 GCGGGCGCACTACATTGTATAATG 62.645 50.000 8.62 10.37 43.69 1.90
3387 3516 3.064207 CGGGCGCACTACATTGTATAAT 58.936 45.455 8.62 0.00 0.00 1.28
3388 3517 2.475818 CGGGCGCACTACATTGTATAA 58.524 47.619 8.62 0.00 0.00 0.98
3389 3518 1.870580 GCGGGCGCACTACATTGTATA 60.871 52.381 8.62 0.00 41.49 1.47
3390 3519 1.157870 GCGGGCGCACTACATTGTAT 61.158 55.000 8.62 0.00 41.49 2.29
3391 3520 1.812093 GCGGGCGCACTACATTGTA 60.812 57.895 8.62 0.00 41.49 2.41
3392 3521 3.124921 GCGGGCGCACTACATTGT 61.125 61.111 8.62 0.00 41.49 2.71
3393 3522 4.222589 CGCGGGCGCACTACATTG 62.223 66.667 8.62 0.00 42.06 2.82
3394 3523 4.752879 ACGCGGGCGCACTACATT 62.753 61.111 12.47 0.00 44.19 2.71
3395 3524 4.752879 AACGCGGGCGCACTACAT 62.753 61.111 12.47 0.00 44.19 2.29
3396 3525 4.973055 AAACGCGGGCGCACTACA 62.973 61.111 12.47 0.00 44.19 2.74
3397 3526 4.143363 GAAACGCGGGCGCACTAC 62.143 66.667 12.47 0.00 44.19 2.73
3404 3533 4.832608 ATCTCGGGAAACGCGGGC 62.833 66.667 12.47 0.00 40.12 6.13
3405 3534 2.125269 AATCTCGGGAAACGCGGG 60.125 61.111 12.47 0.00 43.86 6.13
3406 3535 1.017177 TTGAATCTCGGGAAACGCGG 61.017 55.000 12.47 0.00 43.86 6.46
3407 3536 0.370273 CTTGAATCTCGGGAAACGCG 59.630 55.000 3.53 3.53 43.86 6.01
3408 3537 1.439679 ACTTGAATCTCGGGAAACGC 58.560 50.000 0.00 0.00 43.86 4.84
3409 3538 3.496884 TCAAACTTGAATCTCGGGAAACG 59.503 43.478 0.00 0.00 37.92 3.60
3410 3539 4.320275 GGTCAAACTTGAATCTCGGGAAAC 60.320 45.833 0.00 0.00 39.21 2.78
3411 3540 3.818773 GGTCAAACTTGAATCTCGGGAAA 59.181 43.478 0.00 0.00 39.21 3.13
3412 3541 3.181449 TGGTCAAACTTGAATCTCGGGAA 60.181 43.478 0.00 0.00 39.21 3.97
3413 3542 2.370519 TGGTCAAACTTGAATCTCGGGA 59.629 45.455 0.00 0.00 39.21 5.14
3414 3543 2.778299 TGGTCAAACTTGAATCTCGGG 58.222 47.619 0.00 0.00 39.21 5.14
3415 3544 6.494893 TTTATGGTCAAACTTGAATCTCGG 57.505 37.500 0.00 0.00 39.21 4.63
3800 3929 2.224066 CCGCATTTCCCGAGATCTAACT 60.224 50.000 0.00 0.00 0.00 2.24
3801 3930 2.135933 CCGCATTTCCCGAGATCTAAC 58.864 52.381 0.00 0.00 0.00 2.34
3802 3931 1.070134 CCCGCATTTCCCGAGATCTAA 59.930 52.381 0.00 0.00 0.00 2.10
3803 3932 0.679505 CCCGCATTTCCCGAGATCTA 59.320 55.000 0.00 0.00 0.00 1.98
3804 3933 1.447643 CCCGCATTTCCCGAGATCT 59.552 57.895 0.00 0.00 0.00 2.75
3805 3934 2.254464 GCCCGCATTTCCCGAGATC 61.254 63.158 0.00 0.00 0.00 2.75
3806 3935 2.203209 GCCCGCATTTCCCGAGAT 60.203 61.111 0.00 0.00 0.00 2.75
3807 3936 4.830765 CGCCCGCATTTCCCGAGA 62.831 66.667 0.00 0.00 0.00 4.04
3818 3947 4.536687 GCAATGTAGTGCGCCCGC 62.537 66.667 4.18 5.60 42.35 6.13
3824 3953 1.571919 CGGGAGTAGCAATGTAGTGC 58.428 55.000 0.00 0.00 45.28 4.40
3825 3954 1.571919 GCGGGAGTAGCAATGTAGTG 58.428 55.000 0.00 0.00 34.19 2.74
3826 3955 0.464452 GGCGGGAGTAGCAATGTAGT 59.536 55.000 0.00 0.00 36.08 2.73
3827 3956 0.597637 CGGCGGGAGTAGCAATGTAG 60.598 60.000 0.00 0.00 36.08 2.74
3828 3957 1.440060 CGGCGGGAGTAGCAATGTA 59.560 57.895 0.00 0.00 36.08 2.29
3829 3958 2.186903 CGGCGGGAGTAGCAATGT 59.813 61.111 0.00 0.00 36.08 2.71
3830 3959 3.272334 GCGGCGGGAGTAGCAATG 61.272 66.667 9.78 0.00 36.08 2.82
3831 3960 3.740128 CTGCGGCGGGAGTAGCAAT 62.740 63.158 9.78 0.00 41.89 3.56
3832 3961 4.451150 CTGCGGCGGGAGTAGCAA 62.451 66.667 9.78 0.00 41.89 3.91
3834 3963 4.874977 GACTGCGGCGGGAGTAGC 62.875 72.222 18.21 3.76 45.69 3.58
3835 3964 4.554363 CGACTGCGGCGGGAGTAG 62.554 72.222 18.21 14.39 45.69 2.57
3845 3974 2.805353 CCAACGAGACCGACTGCG 60.805 66.667 0.00 0.00 39.50 5.18
3846 3975 0.038892 TAACCAACGAGACCGACTGC 60.039 55.000 0.00 0.00 39.50 4.40
3847 3976 2.427232 TTAACCAACGAGACCGACTG 57.573 50.000 0.00 0.00 39.50 3.51
3848 3977 3.672767 ATTTAACCAACGAGACCGACT 57.327 42.857 0.00 0.00 39.50 4.18
3849 3978 4.737353 AAATTTAACCAACGAGACCGAC 57.263 40.909 0.00 0.00 39.50 4.79
3850 3979 5.352016 CCATAAATTTAACCAACGAGACCGA 59.648 40.000 1.21 0.00 39.50 4.69
3851 3980 5.122711 ACCATAAATTTAACCAACGAGACCG 59.877 40.000 1.21 0.00 42.50 4.79
3852 3981 6.149807 TGACCATAAATTTAACCAACGAGACC 59.850 38.462 1.21 0.00 0.00 3.85
3853 3982 7.136289 TGACCATAAATTTAACCAACGAGAC 57.864 36.000 1.21 0.00 0.00 3.36
3854 3983 7.747155 TTGACCATAAATTTAACCAACGAGA 57.253 32.000 1.21 0.00 0.00 4.04
3855 3984 8.079809 ACTTTGACCATAAATTTAACCAACGAG 58.920 33.333 1.21 3.35 0.00 4.18
3856 3985 7.942990 ACTTTGACCATAAATTTAACCAACGA 58.057 30.769 1.21 0.00 0.00 3.85
3857 3986 8.582433 AACTTTGACCATAAATTTAACCAACG 57.418 30.769 1.21 5.06 0.00 4.10
3865 3994 8.893727 CCGAGATCTAACTTTGACCATAAATTT 58.106 33.333 0.00 0.00 0.00 1.82
3866 3995 7.499232 CCCGAGATCTAACTTTGACCATAAATT 59.501 37.037 0.00 0.00 0.00 1.82
3867 3996 6.992715 CCCGAGATCTAACTTTGACCATAAAT 59.007 38.462 0.00 0.00 0.00 1.40
3868 3997 6.155565 TCCCGAGATCTAACTTTGACCATAAA 59.844 38.462 0.00 0.00 0.00 1.40
3869 3998 5.659525 TCCCGAGATCTAACTTTGACCATAA 59.340 40.000 0.00 0.00 0.00 1.90
3870 3999 5.205821 TCCCGAGATCTAACTTTGACCATA 58.794 41.667 0.00 0.00 0.00 2.74
3871 4000 4.030913 TCCCGAGATCTAACTTTGACCAT 58.969 43.478 0.00 0.00 0.00 3.55
3872 4001 3.437213 TCCCGAGATCTAACTTTGACCA 58.563 45.455 0.00 0.00 0.00 4.02
3873 4002 4.467198 TTCCCGAGATCTAACTTTGACC 57.533 45.455 0.00 0.00 0.00 4.02
3874 4003 4.326548 CGTTTCCCGAGATCTAACTTTGAC 59.673 45.833 0.00 0.00 39.56 3.18
3875 4004 4.491676 CGTTTCCCGAGATCTAACTTTGA 58.508 43.478 0.00 0.00 39.56 2.69
3876 4005 3.062234 GCGTTTCCCGAGATCTAACTTTG 59.938 47.826 0.00 0.00 39.56 2.77
3877 4006 3.259902 GCGTTTCCCGAGATCTAACTTT 58.740 45.455 0.00 0.00 39.56 2.66
3878 4007 2.734492 CGCGTTTCCCGAGATCTAACTT 60.734 50.000 0.00 0.00 38.82 2.66
3879 4008 1.202268 CGCGTTTCCCGAGATCTAACT 60.202 52.381 0.00 0.00 38.82 2.24
3880 4009 1.197910 CGCGTTTCCCGAGATCTAAC 58.802 55.000 0.00 0.00 38.82 2.34
3881 4010 0.101759 CCGCGTTTCCCGAGATCTAA 59.898 55.000 4.92 0.00 38.82 2.10
3882 4011 1.731433 CCCGCGTTTCCCGAGATCTA 61.731 60.000 4.92 0.00 38.82 1.98
3883 4012 2.494918 CCGCGTTTCCCGAGATCT 59.505 61.111 4.92 0.00 38.82 2.75
3884 4013 2.585247 CCCGCGTTTCCCGAGATC 60.585 66.667 4.92 0.00 38.82 2.75
3885 4014 4.832608 GCCCGCGTTTCCCGAGAT 62.833 66.667 4.92 0.00 38.82 2.75
3890 4019 3.887335 TAGTGTGCCCGCGTTTCCC 62.887 63.158 4.92 0.00 0.00 3.97
3891 4020 2.357760 TAGTGTGCCCGCGTTTCC 60.358 61.111 4.92 0.00 0.00 3.13
3892 4021 1.296056 ATGTAGTGTGCCCGCGTTTC 61.296 55.000 4.92 0.00 0.00 2.78
3893 4022 0.887387 AATGTAGTGTGCCCGCGTTT 60.887 50.000 4.92 0.00 0.00 3.60
3894 4023 1.302192 AATGTAGTGTGCCCGCGTT 60.302 52.632 4.92 0.00 0.00 4.84
3895 4024 2.032634 CAATGTAGTGTGCCCGCGT 61.033 57.895 4.92 0.00 0.00 6.01
3896 4025 2.784596 CAATGTAGTGTGCCCGCG 59.215 61.111 0.00 0.00 0.00 6.46
3897 4026 0.742990 TAGCAATGTAGTGTGCCCGC 60.743 55.000 0.00 0.00 41.88 6.13
3898 4027 1.006832 GTAGCAATGTAGTGTGCCCG 58.993 55.000 0.00 0.00 41.88 6.13
3899 4028 2.280628 GAGTAGCAATGTAGTGTGCCC 58.719 52.381 0.00 0.00 41.88 5.36
3900 4029 2.280628 GGAGTAGCAATGTAGTGTGCC 58.719 52.381 0.00 0.00 41.88 5.01
3901 4030 2.280628 GGGAGTAGCAATGTAGTGTGC 58.719 52.381 0.00 0.00 41.22 4.57
3902 4031 2.540515 CGGGAGTAGCAATGTAGTGTG 58.459 52.381 0.00 0.00 0.00 3.82
3903 4032 1.134788 GCGGGAGTAGCAATGTAGTGT 60.135 52.381 0.00 0.00 34.19 3.55
3904 4033 1.571919 GCGGGAGTAGCAATGTAGTG 58.428 55.000 0.00 0.00 34.19 2.74
3905 4034 0.464452 GGCGGGAGTAGCAATGTAGT 59.536 55.000 0.00 0.00 36.08 2.73
3906 4035 0.597637 CGGCGGGAGTAGCAATGTAG 60.598 60.000 0.00 0.00 36.08 2.74
3907 4036 1.440060 CGGCGGGAGTAGCAATGTA 59.560 57.895 0.00 0.00 36.08 2.29
3908 4037 2.186903 CGGCGGGAGTAGCAATGT 59.813 61.111 0.00 0.00 36.08 2.71
3909 4038 3.272334 GCGGCGGGAGTAGCAATG 61.272 66.667 9.78 0.00 36.08 2.82
3910 4039 3.740128 CTGCGGCGGGAGTAGCAAT 62.740 63.158 9.78 0.00 41.89 3.56
3911 4040 4.451150 CTGCGGCGGGAGTAGCAA 62.451 66.667 9.78 0.00 41.89 3.91
3913 4042 4.874977 GACTGCGGCGGGAGTAGC 62.875 72.222 18.21 3.76 45.69 3.58
3914 4043 4.554363 CGACTGCGGCGGGAGTAG 62.554 72.222 18.21 14.39 45.69 2.57
3924 4053 2.805353 CCAACGAGACCGACTGCG 60.805 66.667 0.00 0.00 39.50 5.18
3925 4054 0.038892 TAACCAACGAGACCGACTGC 60.039 55.000 0.00 0.00 39.50 4.40
3926 4055 2.427232 TTAACCAACGAGACCGACTG 57.573 50.000 0.00 0.00 39.50 3.51
3927 4056 3.672767 ATTTAACCAACGAGACCGACT 57.327 42.857 0.00 0.00 39.50 4.18
3928 4057 4.737353 AAATTTAACCAACGAGACCGAC 57.263 40.909 0.00 0.00 39.50 4.79
3929 4058 5.352016 CCATAAATTTAACCAACGAGACCGA 59.648 40.000 1.21 0.00 39.50 4.69
3930 4059 5.122711 ACCATAAATTTAACCAACGAGACCG 59.877 40.000 1.21 0.00 42.50 4.79
3931 4060 6.149807 TGACCATAAATTTAACCAACGAGACC 59.850 38.462 1.21 0.00 0.00 3.85
3932 4061 7.136289 TGACCATAAATTTAACCAACGAGAC 57.864 36.000 1.21 0.00 0.00 3.36
3933 4062 7.747155 TTGACCATAAATTTAACCAACGAGA 57.253 32.000 1.21 0.00 0.00 4.04
3934 4063 8.079809 ACTTTGACCATAAATTTAACCAACGAG 58.920 33.333 1.21 3.35 0.00 4.18
3935 4064 7.942990 ACTTTGACCATAAATTTAACCAACGA 58.057 30.769 1.21 0.00 0.00 3.85
3936 4065 8.582433 AACTTTGACCATAAATTTAACCAACG 57.418 30.769 1.21 5.06 0.00 4.10
3944 4073 8.893727 CCGAGATCTAACTTTGACCATAAATTT 58.106 33.333 0.00 0.00 0.00 1.82
3945 4074 7.499232 CCCGAGATCTAACTTTGACCATAAATT 59.501 37.037 0.00 0.00 0.00 1.82
3946 4075 6.992715 CCCGAGATCTAACTTTGACCATAAAT 59.007 38.462 0.00 0.00 0.00 1.40
3947 4076 6.155565 TCCCGAGATCTAACTTTGACCATAAA 59.844 38.462 0.00 0.00 0.00 1.40
3948 4077 5.659525 TCCCGAGATCTAACTTTGACCATAA 59.340 40.000 0.00 0.00 0.00 1.90
3949 4078 5.205821 TCCCGAGATCTAACTTTGACCATA 58.794 41.667 0.00 0.00 0.00 2.74
3950 4079 4.030913 TCCCGAGATCTAACTTTGACCAT 58.969 43.478 0.00 0.00 0.00 3.55
3951 4080 3.437213 TCCCGAGATCTAACTTTGACCA 58.563 45.455 0.00 0.00 0.00 4.02
3952 4081 4.467198 TTCCCGAGATCTAACTTTGACC 57.533 45.455 0.00 0.00 0.00 4.02
3953 4082 4.326548 CGTTTCCCGAGATCTAACTTTGAC 59.673 45.833 0.00 0.00 39.56 3.18
3954 4083 4.491676 CGTTTCCCGAGATCTAACTTTGA 58.508 43.478 0.00 0.00 39.56 2.69
3955 4084 3.062234 GCGTTTCCCGAGATCTAACTTTG 59.938 47.826 0.00 0.00 39.56 2.77
3956 4085 3.259902 GCGTTTCCCGAGATCTAACTTT 58.740 45.455 0.00 0.00 39.56 2.66
3957 4086 2.734492 CGCGTTTCCCGAGATCTAACTT 60.734 50.000 0.00 0.00 38.82 2.66
3958 4087 1.202268 CGCGTTTCCCGAGATCTAACT 60.202 52.381 0.00 0.00 38.82 2.24
3959 4088 1.197910 CGCGTTTCCCGAGATCTAAC 58.802 55.000 0.00 0.00 38.82 2.34
3960 4089 0.101759 CCGCGTTTCCCGAGATCTAA 59.898 55.000 4.92 0.00 38.82 2.10
3961 4090 1.731433 CCCGCGTTTCCCGAGATCTA 61.731 60.000 4.92 0.00 38.82 1.98
3962 4091 2.494918 CCGCGTTTCCCGAGATCT 59.505 61.111 4.92 0.00 38.82 2.75
3963 4092 2.585247 CCCGCGTTTCCCGAGATC 60.585 66.667 4.92 0.00 38.82 2.75
3964 4093 4.832608 GCCCGCGTTTCCCGAGAT 62.833 66.667 4.92 0.00 38.82 2.75
3971 4100 4.143363 GTAGTGCGCCCGCGTTTC 62.143 66.667 4.18 2.02 45.51 2.78
3977 4106 3.773630 CACAACGTAGTGCGCCCG 61.774 66.667 4.18 4.47 45.00 6.13
3978 4107 1.500512 TTTCACAACGTAGTGCGCCC 61.501 55.000 4.18 0.00 45.00 6.13
3979 4108 0.515564 ATTTCACAACGTAGTGCGCC 59.484 50.000 4.18 0.00 45.00 6.53
3980 4109 1.591248 CATTTCACAACGTAGTGCGC 58.409 50.000 0.00 0.00 45.00 6.09
3981 4110 1.795872 TCCATTTCACAACGTAGTGCG 59.204 47.619 0.00 0.00 45.00 5.34
3982 4111 2.159627 CCTCCATTTCACAACGTAGTGC 59.840 50.000 0.00 0.00 45.00 4.40
3983 4112 2.742053 CCCTCCATTTCACAACGTAGTG 59.258 50.000 0.00 0.00 45.00 2.74
3985 4114 3.262420 CTCCCTCCATTTCACAACGTAG 58.738 50.000 0.00 0.00 0.00 3.51
3986 4115 2.635915 ACTCCCTCCATTTCACAACGTA 59.364 45.455 0.00 0.00 0.00 3.57
3987 4116 1.420138 ACTCCCTCCATTTCACAACGT 59.580 47.619 0.00 0.00 0.00 3.99
3988 4117 2.185004 ACTCCCTCCATTTCACAACG 57.815 50.000 0.00 0.00 0.00 4.10
3989 4118 5.476945 ACAAATACTCCCTCCATTTCACAAC 59.523 40.000 0.00 0.00 0.00 3.32
3990 4119 5.640147 ACAAATACTCCCTCCATTTCACAA 58.360 37.500 0.00 0.00 0.00 3.33
3991 4120 5.255397 ACAAATACTCCCTCCATTTCACA 57.745 39.130 0.00 0.00 0.00 3.58
3992 4121 6.590234 AAACAAATACTCCCTCCATTTCAC 57.410 37.500 0.00 0.00 0.00 3.18
3993 4122 6.553100 ACAAAACAAATACTCCCTCCATTTCA 59.447 34.615 0.00 0.00 0.00 2.69
3994 4123 6.993079 ACAAAACAAATACTCCCTCCATTTC 58.007 36.000 0.00 0.00 0.00 2.17
3995 4124 6.994421 ACAAAACAAATACTCCCTCCATTT 57.006 33.333 0.00 0.00 0.00 2.32
3996 4125 6.326323 ACAACAAAACAAATACTCCCTCCATT 59.674 34.615 0.00 0.00 0.00 3.16
3997 4126 5.838521 ACAACAAAACAAATACTCCCTCCAT 59.161 36.000 0.00 0.00 0.00 3.41
3998 4127 5.205056 ACAACAAAACAAATACTCCCTCCA 58.795 37.500 0.00 0.00 0.00 3.86
3999 4128 5.784578 ACAACAAAACAAATACTCCCTCC 57.215 39.130 0.00 0.00 0.00 4.30
4000 4129 5.912955 CGAACAACAAAACAAATACTCCCTC 59.087 40.000 0.00 0.00 0.00 4.30
4001 4130 5.591067 TCGAACAACAAAACAAATACTCCCT 59.409 36.000 0.00 0.00 0.00 4.20
4002 4131 5.823353 TCGAACAACAAAACAAATACTCCC 58.177 37.500 0.00 0.00 0.00 4.30
4003 4132 6.631636 GTCTCGAACAACAAAACAAATACTCC 59.368 38.462 0.00 0.00 0.00 3.85
4004 4133 7.407337 AGTCTCGAACAACAAAACAAATACTC 58.593 34.615 0.00 0.00 0.00 2.59
4005 4134 7.316544 AGTCTCGAACAACAAAACAAATACT 57.683 32.000 0.00 0.00 0.00 2.12
4006 4135 7.964545 AAGTCTCGAACAACAAAACAAATAC 57.035 32.000 0.00 0.00 0.00 1.89
4007 4136 8.455682 AGAAAGTCTCGAACAACAAAACAAATA 58.544 29.630 0.00 0.00 0.00 1.40
4008 4137 7.312899 AGAAAGTCTCGAACAACAAAACAAAT 58.687 30.769 0.00 0.00 0.00 2.32
4009 4138 6.674066 AGAAAGTCTCGAACAACAAAACAAA 58.326 32.000 0.00 0.00 0.00 2.83
4010 4139 6.249035 AGAAAGTCTCGAACAACAAAACAA 57.751 33.333 0.00 0.00 0.00 2.83
4011 4140 5.873179 AGAAAGTCTCGAACAACAAAACA 57.127 34.783 0.00 0.00 0.00 2.83
4012 4141 7.097006 GCAATAGAAAGTCTCGAACAACAAAAC 60.097 37.037 0.00 0.00 0.00 2.43
4013 4142 6.910433 GCAATAGAAAGTCTCGAACAACAAAA 59.090 34.615 0.00 0.00 0.00 2.44
4014 4143 6.427150 GCAATAGAAAGTCTCGAACAACAAA 58.573 36.000 0.00 0.00 0.00 2.83
4015 4144 5.049680 GGCAATAGAAAGTCTCGAACAACAA 60.050 40.000 0.00 0.00 0.00 2.83
4016 4145 4.451096 GGCAATAGAAAGTCTCGAACAACA 59.549 41.667 0.00 0.00 0.00 3.33
4017 4146 4.959149 GGCAATAGAAAGTCTCGAACAAC 58.041 43.478 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.