Multiple sequence alignment - TraesCS3D01G205600

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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 TraesCS3D01G205600 chr3D 100.000 4613 0 0 1 4613 264139922 264144534 0.000000e+00 8519
1 TraesCS3D01G205600 chr3D 94.737 209 9 2 663 870 5645776 5645983 1.600000e-84 324
2 TraesCS3D01G205600 chr3D 83.196 363 47 9 4135 4489 113324876 113325232 2.070000e-83 320
3 TraesCS3D01G205600 chr3D 93.985 133 8 0 4481 4613 261137490 261137622 7.830000e-48 202
4 TraesCS3D01G205600 chr3A 97.808 2783 49 3 868 3638 322878584 322881366 0.000000e+00 4791
5 TraesCS3D01G205600 chr3A 94.673 413 13 4 3723 4135 322881368 322881771 2.340000e-177 632
6 TraesCS3D01G205600 chr3A 82.759 145 19 3 4308 4447 42449215 42449072 1.740000e-24 124
7 TraesCS3D01G205600 chr3B 98.340 2651 38 2 989 3638 353471728 353469083 0.000000e+00 4647
8 TraesCS3D01G205600 chr3B 95.075 670 26 5 1 670 602244097 602244759 0.000000e+00 1048
9 TraesCS3D01G205600 chr3B 85.153 815 44 26 3723 4489 353469081 353468296 0.000000e+00 763
10 TraesCS3D01G205600 chr3B 94.686 207 10 1 663 868 46587255 46587049 2.070000e-83 320
11 TraesCS3D01G205600 chr3B 94.258 209 12 0 663 871 602244798 602245006 2.070000e-83 320
12 TraesCS3D01G205600 chr2D 95.542 673 26 3 1 670 646026425 646025754 0.000000e+00 1074
13 TraesCS3D01G205600 chr2D 95.210 668 28 3 1 665 641012473 641013139 0.000000e+00 1053
14 TraesCS3D01G205600 chr2D 94.737 133 7 0 4481 4613 361186415 361186283 1.680000e-49 207
15 TraesCS3D01G205600 chr4D 95.428 678 21 5 1 670 72715652 72714977 0.000000e+00 1072
16 TraesCS3D01G205600 chr4D 83.844 359 41 12 4141 4489 396626395 396626044 4.450000e-85 326
17 TraesCS3D01G205600 chr4D 94.737 133 7 0 4481 4613 390380518 390380650 1.680000e-49 207
18 TraesCS3D01G205600 chr4D 93.985 133 8 0 4481 4613 290247025 290247157 7.830000e-48 202
19 TraesCS3D01G205600 chr1D 89.192 879 63 18 1 868 347254168 347255025 0.000000e+00 1068
20 TraesCS3D01G205600 chr1D 94.615 130 7 0 4481 4610 178610159 178610288 7.830000e-48 202
21 TraesCS3D01G205600 chr5D 95.414 676 20 5 1 666 546899002 546898328 0.000000e+00 1066
22 TraesCS3D01G205600 chr5D 94.675 676 29 3 1 670 10681436 10680762 0.000000e+00 1042
23 TraesCS3D01G205600 chr5D 94.214 674 35 2 1 670 296964115 296964788 0.000000e+00 1026
24 TraesCS3D01G205600 chr5D 96.651 209 6 1 663 870 428663266 428663058 3.420000e-91 346
25 TraesCS3D01G205600 chr5D 94.737 209 10 1 663 870 55620722 55620514 1.600000e-84 324
26 TraesCS3D01G205600 chr5D 82.521 349 40 16 4149 4489 270230803 270231138 2.100000e-73 287
27 TraesCS3D01G205600 chr5D 92.793 111 4 4 3628 3737 504792924 504793031 1.720000e-34 158
28 TraesCS3D01G205600 chr7D 94.179 670 33 4 1 666 521898574 521899241 0.000000e+00 1016
29 TraesCS3D01G205600 chr7D 85.981 321 30 10 4178 4489 30911523 30911209 3.440000e-86 329
30 TraesCS3D01G205600 chr7D 94.737 209 10 1 663 870 590076982 590077190 1.600000e-84 324
31 TraesCS3D01G205600 chr7D 94.737 133 7 0 4481 4613 447226515 447226383 1.680000e-49 207
32 TraesCS3D01G205600 chr7D 97.727 88 2 0 3636 3723 506141453 506141366 7.990000e-33 152
33 TraesCS3D01G205600 chr4A 94.162 668 35 4 1 666 113577287 113576622 0.000000e+00 1014
34 TraesCS3D01G205600 chr5B 85.950 363 37 8 4135 4489 73835376 73835732 4.360000e-100 375
35 TraesCS3D01G205600 chr5B 81.870 353 47 11 4135 4480 401142520 401142862 9.770000e-72 281
36 TraesCS3D01G205600 chr5A 86.916 321 28 7 4172 4483 10314102 10314417 9.500000e-92 348
37 TraesCS3D01G205600 chr6A 84.551 356 41 8 4141 4489 33289817 33290165 1.590000e-89 340
38 TraesCS3D01G205600 chr6A 96.739 92 2 1 3633 3723 27342983 27342892 7.990000e-33 152
39 TraesCS3D01G205600 chr6D 95.652 207 8 1 663 868 23079355 23079561 9.570000e-87 331
40 TraesCS3D01G205600 chr6D 94.737 133 7 0 4481 4613 169941088 169940956 1.680000e-49 207
41 TraesCS3D01G205600 chr6D 93.985 133 8 0 4481 4613 230610929 230611061 7.830000e-48 202
42 TraesCS3D01G205600 chr6D 93.985 133 8 0 4481 4613 306543641 306543509 7.830000e-48 202
43 TraesCS3D01G205600 chr2A 93.897 213 12 1 663 874 37043708 37043496 2.070000e-83 320
44 TraesCS3D01G205600 chr6B 98.864 88 1 0 3636 3723 96970760 96970847 1.720000e-34 158
45 TraesCS3D01G205600 chr6B 95.833 96 3 1 3629 3723 47140693 47140788 2.220000e-33 154
46 TraesCS3D01G205600 chr2B 98.864 88 1 0 3635 3722 41129492 41129579 1.720000e-34 158
47 TraesCS3D01G205600 chr2B 91.589 107 4 4 3620 3723 782178858 782178754 4.810000e-30 143
48 TraesCS3D01G205600 chr7B 94.898 98 4 1 3626 3723 440325697 440325601 7.990000e-33 152
49 TraesCS3D01G205600 chrUn 94.845 97 3 2 3628 3723 17148591 17148686 2.880000e-32 150


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 TraesCS3D01G205600 chr3D 264139922 264144534 4612 False 8519.0 8519 100.0000 1 4613 1 chr3D.!!$F4 4612
1 TraesCS3D01G205600 chr3A 322878584 322881771 3187 False 2711.5 4791 96.2405 868 4135 2 chr3A.!!$F1 3267
2 TraesCS3D01G205600 chr3B 353468296 353471728 3432 True 2705.0 4647 91.7465 989 4489 2 chr3B.!!$R2 3500
3 TraesCS3D01G205600 chr3B 602244097 602245006 909 False 684.0 1048 94.6665 1 871 2 chr3B.!!$F1 870
4 TraesCS3D01G205600 chr2D 646025754 646026425 671 True 1074.0 1074 95.5420 1 670 1 chr2D.!!$R2 669
5 TraesCS3D01G205600 chr2D 641012473 641013139 666 False 1053.0 1053 95.2100 1 665 1 chr2D.!!$F1 664
6 TraesCS3D01G205600 chr4D 72714977 72715652 675 True 1072.0 1072 95.4280 1 670 1 chr4D.!!$R1 669
7 TraesCS3D01G205600 chr1D 347254168 347255025 857 False 1068.0 1068 89.1920 1 868 1 chr1D.!!$F2 867
8 TraesCS3D01G205600 chr5D 546898328 546899002 674 True 1066.0 1066 95.4140 1 666 1 chr5D.!!$R4 665
9 TraesCS3D01G205600 chr5D 10680762 10681436 674 True 1042.0 1042 94.6750 1 670 1 chr5D.!!$R1 669
10 TraesCS3D01G205600 chr5D 296964115 296964788 673 False 1026.0 1026 94.2140 1 670 1 chr5D.!!$F2 669
11 TraesCS3D01G205600 chr7D 521898574 521899241 667 False 1016.0 1016 94.1790 1 666 1 chr7D.!!$F1 665
12 TraesCS3D01G205600 chr4A 113576622 113577287 665 True 1014.0 1014 94.1620 1 666 1 chr4A.!!$R1 665

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
366 369 0.183014 ATCCGAACGGCTAGAGGAGA 59.817 55.000 8.48 0.0 34.14 3.71 F
641 677 2.192263 GAGTGGAGAAGAATGGAGGGT 58.808 52.381 0.00 0.0 0.00 4.34 F
1464 1564 2.400158 CGACGACCTCCGCTCTCTT 61.400 63.158 0.00 0.0 43.32 2.85 F
2745 2845 2.766239 TGGTGACACATATGCAGCG 58.234 52.632 8.08 0.0 34.87 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2056 0.249073 CGTCATCGTCCAGGGTGATC 60.249 60.0 0.00 0.0 0.0 2.92 R
2163 2263 0.794229 GTGTTGCCGCAATCACATCG 60.794 55.0 22.85 0.0 31.2 3.84 R
2826 2926 1.085091 GCATTGCCTGAGAGACACTG 58.915 55.0 0.00 0.0 0.0 3.66 R
4586 4734 0.036010 CAGGAAGGTGGTGCTCGATT 60.036 55.0 0.00 0.0 0.0 3.34 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
36 37 7.096023 CGAACATCTACTAAATTGCGCTCTATT 60.096 37.037 9.73 2.89 0.00 1.73
325 328 0.530650 CCGCCATTCGTGTATCTGCT 60.531 55.000 0.00 0.00 36.19 4.24
366 369 0.183014 ATCCGAACGGCTAGAGGAGA 59.817 55.000 8.48 0.00 34.14 3.71
472 475 4.537433 GCCGGGCGAGCTCAAGAT 62.537 66.667 15.40 0.00 0.00 2.40
641 677 2.192263 GAGTGGAGAAGAATGGAGGGT 58.808 52.381 0.00 0.00 0.00 4.34
880 967 6.811665 GTGGAGTTGGCCTAAATTTTTACATC 59.188 38.462 3.32 0.00 0.00 3.06
885 972 5.010933 TGGCCTAAATTTTTACATCACCGA 58.989 37.500 3.32 0.00 0.00 4.69
889 976 8.192110 GGCCTAAATTTTTACATCACCGATTTA 58.808 33.333 0.00 0.00 0.00 1.40
896 983 6.844696 TTTACATCACCGATTTAGAGCATC 57.155 37.500 0.00 0.00 0.00 3.91
908 995 9.979270 CCGATTTAGAGCATCAAAATATACATC 57.021 33.333 0.00 0.00 37.82 3.06
917 1004 8.139350 AGCATCAAAATATACATCATGTGTTGG 58.861 33.333 0.00 0.00 42.29 3.77
935 1022 6.209192 TGTGTTGGAAATGCTCTAATTGACAT 59.791 34.615 0.00 0.00 0.00 3.06
937 1024 7.912250 GTGTTGGAAATGCTCTAATTGACATAG 59.088 37.037 0.00 0.00 0.00 2.23
939 1026 6.662755 TGGAAATGCTCTAATTGACATAGGT 58.337 36.000 0.00 0.00 0.00 3.08
940 1027 6.767902 TGGAAATGCTCTAATTGACATAGGTC 59.232 38.462 0.00 0.00 44.57 3.85
941 1028 6.205658 GGAAATGCTCTAATTGACATAGGTCC 59.794 42.308 4.87 0.00 43.65 4.46
942 1029 4.322080 TGCTCTAATTGACATAGGTCCG 57.678 45.455 4.87 0.00 43.65 4.79
943 1030 3.704566 TGCTCTAATTGACATAGGTCCGT 59.295 43.478 4.87 0.00 43.65 4.69
944 1031 4.202121 TGCTCTAATTGACATAGGTCCGTC 60.202 45.833 4.87 0.00 43.65 4.79
945 1032 4.202121 GCTCTAATTGACATAGGTCCGTCA 60.202 45.833 4.87 0.00 43.65 4.35
947 1034 6.085555 TCTAATTGACATAGGTCCGTCATC 57.914 41.667 4.87 0.00 43.65 2.92
948 1035 2.863401 TTGACATAGGTCCGTCATCG 57.137 50.000 4.87 0.00 43.65 3.84
1464 1564 2.400158 CGACGACCTCCGCTCTCTT 61.400 63.158 0.00 0.00 43.32 2.85
1732 1832 3.340814 TTGATCTCAACCTTGCCTCTC 57.659 47.619 0.00 0.00 0.00 3.20
1878 1978 3.758973 TTCGCGGCACCTTGGACAA 62.759 57.895 6.13 0.00 0.00 3.18
2163 2263 2.815478 CTCCAGCTAACATCCGACTTC 58.185 52.381 0.00 0.00 0.00 3.01
2311 2411 2.998279 GCATTGTGGGAGGCTGCAC 61.998 63.158 8.68 5.05 33.13 4.57
2349 2449 6.184266 TCCGTGCTGGAAGATAACTTCTCC 62.184 50.000 11.97 0.00 46.38 3.71
2745 2845 2.766239 TGGTGACACATATGCAGCG 58.234 52.632 8.08 0.00 34.87 5.18
2826 2926 0.615331 TGGATTCAGGCAGTGGTCTC 59.385 55.000 0.00 0.00 0.00 3.36
3153 3253 3.840831 TGCTCAACAGATCCTTCCG 57.159 52.632 0.00 0.00 0.00 4.30
3528 3628 5.772672 GGATACCTCAGAGAGCTATTTCTCA 59.227 44.000 0.00 0.00 44.85 3.27
3638 3738 6.722129 CCTCTACCCTGCAGTAAGATAATACT 59.278 42.308 13.81 0.00 36.57 2.12
3639 3739 7.094118 CCTCTACCCTGCAGTAAGATAATACTC 60.094 44.444 13.81 0.00 33.90 2.59
3640 3740 5.810080 ACCCTGCAGTAAGATAATACTCC 57.190 43.478 13.81 0.00 33.90 3.85
3641 3741 4.593634 ACCCTGCAGTAAGATAATACTCCC 59.406 45.833 13.81 0.00 33.90 4.30
3642 3742 4.841246 CCCTGCAGTAAGATAATACTCCCT 59.159 45.833 13.81 0.00 33.90 4.20
3643 3743 5.046950 CCCTGCAGTAAGATAATACTCCCTC 60.047 48.000 13.81 0.00 33.90 4.30
3644 3744 5.046950 CCTGCAGTAAGATAATACTCCCTCC 60.047 48.000 13.81 0.00 33.90 4.30
3645 3745 4.523173 TGCAGTAAGATAATACTCCCTCCG 59.477 45.833 0.00 0.00 33.90 4.63
3646 3746 4.523558 GCAGTAAGATAATACTCCCTCCGT 59.476 45.833 0.00 0.00 33.90 4.69
3647 3747 5.010820 GCAGTAAGATAATACTCCCTCCGTT 59.989 44.000 0.00 0.00 33.90 4.44
3648 3748 6.679843 CAGTAAGATAATACTCCCTCCGTTC 58.320 44.000 0.00 0.00 33.90 3.95
3649 3749 5.774184 AGTAAGATAATACTCCCTCCGTTCC 59.226 44.000 0.00 0.00 30.26 3.62
3650 3750 4.194678 AGATAATACTCCCTCCGTTCCA 57.805 45.455 0.00 0.00 0.00 3.53
3651 3751 4.753186 AGATAATACTCCCTCCGTTCCAT 58.247 43.478 0.00 0.00 0.00 3.41
3652 3752 5.900437 AGATAATACTCCCTCCGTTCCATA 58.100 41.667 0.00 0.00 0.00 2.74
3653 3753 6.320518 AGATAATACTCCCTCCGTTCCATAA 58.679 40.000 0.00 0.00 0.00 1.90
3654 3754 6.960542 AGATAATACTCCCTCCGTTCCATAAT 59.039 38.462 0.00 0.00 0.00 1.28
3655 3755 4.891992 ATACTCCCTCCGTTCCATAATG 57.108 45.455 0.00 0.00 0.00 1.90
3656 3756 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
3657 3757 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
3658 3758 4.035112 ACTCCCTCCGTTCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
3659 3759 4.101119 ACTCCCTCCGTTCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
3660 3760 4.291792 TCCCTCCGTTCCATAATGTAAGA 58.708 43.478 0.00 0.00 0.00 2.10
3661 3761 4.100498 TCCCTCCGTTCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
3662 3762 4.049186 CCTCCGTTCCATAATGTAAGACG 58.951 47.826 0.00 0.00 0.00 4.18
3663 3763 4.441079 CCTCCGTTCCATAATGTAAGACGT 60.441 45.833 0.00 0.00 0.00 4.34
3664 3764 5.075858 TCCGTTCCATAATGTAAGACGTT 57.924 39.130 0.00 0.00 0.00 3.99
3665 3765 5.481105 TCCGTTCCATAATGTAAGACGTTT 58.519 37.500 0.00 0.00 0.00 3.60
3666 3766 5.933463 TCCGTTCCATAATGTAAGACGTTTT 59.067 36.000 0.00 0.00 0.00 2.43
3667 3767 6.427547 TCCGTTCCATAATGTAAGACGTTTTT 59.572 34.615 0.00 0.00 0.00 1.94
3712 3812 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3713 3813 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3714 3814 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3715 3815 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3716 3816 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3717 3817 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3718 3818 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3719 3819 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3720 3820 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
3721 3821 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
3783 3883 9.103048 GTGTGTTAAAATCATTGTTCTTCTACG 57.897 33.333 0.00 0.00 0.00 3.51
3975 4075 0.179000 AGAACATCTCCACGGATGCC 59.821 55.000 4.63 0.00 44.81 4.40
4020 4120 2.300437 GGCTATAGGCGAGGTGAGAAAT 59.700 50.000 10.94 0.00 42.94 2.17
4081 4203 2.920724 TTTGAGAACCACATGTCCGA 57.079 45.000 0.00 0.00 0.00 4.55
4144 4280 1.378514 CCAACTCCAATGGTCCGGG 60.379 63.158 0.00 0.00 33.08 5.73
4148 4284 4.402528 TCCAATGGTCCGGGCGTG 62.403 66.667 0.00 0.00 0.00 5.34
4151 4287 4.404098 AATGGTCCGGGCGTGTCC 62.404 66.667 0.00 0.00 0.00 4.02
4207 4348 1.472662 CGCATCCCCGTCCTATCCTT 61.473 60.000 0.00 0.00 0.00 3.36
4208 4349 1.640917 GCATCCCCGTCCTATCCTTA 58.359 55.000 0.00 0.00 0.00 2.69
4209 4350 1.975680 GCATCCCCGTCCTATCCTTAA 59.024 52.381 0.00 0.00 0.00 1.85
4219 4360 4.506654 CGTCCTATCCTTAAATTGTGTCCG 59.493 45.833 0.00 0.00 0.00 4.79
4223 4364 6.943718 TCCTATCCTTAAATTGTGTCCGTTTT 59.056 34.615 0.00 0.00 0.00 2.43
4244 4390 4.803426 GCTCGACCACTCCAGGCG 62.803 72.222 0.00 0.00 0.00 5.52
4275 4423 0.038892 GAGCTTTACGGTCACGGACA 60.039 55.000 6.41 0.00 46.48 4.02
4278 4426 1.855513 CTTTACGGTCACGGACAACA 58.144 50.000 6.41 0.00 46.48 3.33
4282 4430 1.274476 CGGTCACGGACAACAAACG 59.726 57.895 6.41 0.00 33.68 3.60
4286 4434 1.662122 GTCACGGACAACAAACGAACT 59.338 47.619 0.00 0.00 32.09 3.01
4293 4441 0.098025 CAACAAACGAACTGGCACGT 59.902 50.000 0.00 0.00 44.57 4.49
4307 4455 3.908081 ACGTGGCGTCTCGGTGTT 61.908 61.111 16.40 0.00 33.69 3.32
4350 4498 3.246112 CCAACCACCTCCCACCGA 61.246 66.667 0.00 0.00 0.00 4.69
4377 4525 2.699768 AATGCGCACGGATGGTTGG 61.700 57.895 14.90 0.00 0.00 3.77
4381 4529 3.134127 GCACGGATGGTTGGGCTC 61.134 66.667 0.00 0.00 0.00 4.70
4382 4530 2.819595 CACGGATGGTTGGGCTCG 60.820 66.667 0.00 0.00 0.00 5.03
4385 4533 2.361104 GGATGGTTGGGCTCGCAA 60.361 61.111 0.00 0.00 0.00 4.85
4386 4534 2.409870 GGATGGTTGGGCTCGCAAG 61.410 63.158 0.00 0.00 0.00 4.01
4387 4535 1.675641 GATGGTTGGGCTCGCAAGT 60.676 57.895 0.00 0.00 39.48 3.16
4388 4536 1.648467 GATGGTTGGGCTCGCAAGTC 61.648 60.000 0.00 0.00 39.48 3.01
4389 4537 2.281484 GGTTGGGCTCGCAAGTCA 60.281 61.111 0.00 0.00 39.48 3.41
4390 4538 2.328099 GGTTGGGCTCGCAAGTCAG 61.328 63.158 0.00 0.00 39.48 3.51
4391 4539 2.669569 TTGGGCTCGCAAGTCAGC 60.670 61.111 0.00 0.00 39.48 4.26
4395 4543 3.426568 GCTCGCAAGTCAGCCACC 61.427 66.667 0.00 0.00 39.48 4.61
4396 4544 2.743928 CTCGCAAGTCAGCCACCC 60.744 66.667 0.00 0.00 39.48 4.61
4397 4545 3.535629 CTCGCAAGTCAGCCACCCA 62.536 63.158 0.00 0.00 39.48 4.51
4398 4546 3.052082 CGCAAGTCAGCCACCCAG 61.052 66.667 0.00 0.00 0.00 4.45
4399 4547 2.431683 GCAAGTCAGCCACCCAGA 59.568 61.111 0.00 0.00 0.00 3.86
4400 4548 1.968540 GCAAGTCAGCCACCCAGAC 60.969 63.158 0.00 0.00 0.00 3.51
4401 4549 1.669115 CAAGTCAGCCACCCAGACG 60.669 63.158 0.00 0.00 37.36 4.18
4402 4550 2.883828 AAGTCAGCCACCCAGACGG 61.884 63.158 0.00 0.00 37.36 4.79
4445 4593 1.671379 GGGAAGCCGTGGACTTCAC 60.671 63.158 18.32 13.92 44.35 3.18
4482 4630 1.086565 ATCCCCATCCACTTCCCCA 59.913 57.895 0.00 0.00 0.00 4.96
4485 4633 2.683475 CCATCCACTTCCCCACCC 59.317 66.667 0.00 0.00 0.00 4.61
4489 4637 0.477597 ATCCACTTCCCCACCCTTGA 60.478 55.000 0.00 0.00 0.00 3.02
4490 4638 1.074951 CCACTTCCCCACCCTTGAC 59.925 63.158 0.00 0.00 0.00 3.18
4491 4639 1.302511 CACTTCCCCACCCTTGACG 60.303 63.158 0.00 0.00 0.00 4.35
4492 4640 1.460689 ACTTCCCCACCCTTGACGA 60.461 57.895 0.00 0.00 0.00 4.20
4493 4641 1.003718 CTTCCCCACCCTTGACGAC 60.004 63.158 0.00 0.00 0.00 4.34
4494 4642 1.764571 CTTCCCCACCCTTGACGACA 61.765 60.000 0.00 0.00 0.00 4.35
4495 4643 1.346479 TTCCCCACCCTTGACGACAA 61.346 55.000 0.00 0.00 34.65 3.18
4496 4644 1.149627 CCCCACCCTTGACGACAAA 59.850 57.895 1.35 0.00 35.49 2.83
4497 4645 0.251165 CCCCACCCTTGACGACAAAT 60.251 55.000 1.35 0.00 35.49 2.32
4498 4646 1.003812 CCCCACCCTTGACGACAAATA 59.996 52.381 1.35 0.00 35.49 1.40
4499 4647 2.356135 CCCACCCTTGACGACAAATAG 58.644 52.381 1.35 0.00 35.49 1.73
4500 4648 2.356135 CCACCCTTGACGACAAATAGG 58.644 52.381 1.35 5.74 35.49 2.57
4501 4649 2.027561 CCACCCTTGACGACAAATAGGA 60.028 50.000 14.66 0.00 35.49 2.94
4502 4650 3.558321 CCACCCTTGACGACAAATAGGAA 60.558 47.826 14.66 0.00 35.49 3.36
4503 4651 4.069304 CACCCTTGACGACAAATAGGAAA 58.931 43.478 14.66 0.00 35.49 3.13
4504 4652 4.154195 CACCCTTGACGACAAATAGGAAAG 59.846 45.833 14.66 0.00 35.49 2.62
4505 4653 3.127030 CCCTTGACGACAAATAGGAAAGC 59.873 47.826 5.78 0.00 35.49 3.51
4506 4654 3.181520 CCTTGACGACAAATAGGAAAGCG 60.182 47.826 1.35 0.00 35.49 4.68
4507 4655 1.730064 TGACGACAAATAGGAAAGCGC 59.270 47.619 0.00 0.00 0.00 5.92
4508 4656 0.719465 ACGACAAATAGGAAAGCGCG 59.281 50.000 0.00 0.00 0.00 6.86
4509 4657 0.586502 CGACAAATAGGAAAGCGCGC 60.587 55.000 26.66 26.66 0.00 6.86
4510 4658 0.248094 GACAAATAGGAAAGCGCGCC 60.248 55.000 30.33 13.04 0.00 6.53
4511 4659 1.064134 CAAATAGGAAAGCGCGCCC 59.936 57.895 30.33 22.43 0.00 6.13
4512 4660 2.469516 AAATAGGAAAGCGCGCCCG 61.470 57.895 30.33 0.00 37.57 6.13
4513 4661 3.675619 AATAGGAAAGCGCGCCCGT 62.676 57.895 30.33 20.28 36.67 5.28
4514 4662 3.675619 ATAGGAAAGCGCGCCCGTT 62.676 57.895 30.33 19.93 36.67 4.44
4528 4676 4.697756 CGTTGCCTTCCTGCGGGA 62.698 66.667 11.27 11.27 40.36 5.14
4529 4677 2.747855 GTTGCCTTCCTGCGGGAG 60.748 66.667 15.42 5.32 43.29 4.30
4530 4678 2.927856 TTGCCTTCCTGCGGGAGA 60.928 61.111 15.42 5.36 43.29 3.71
4531 4679 2.525124 TTGCCTTCCTGCGGGAGAA 61.525 57.895 15.42 0.00 43.29 2.87
4532 4680 1.852157 TTGCCTTCCTGCGGGAGAAT 61.852 55.000 15.42 0.00 43.29 2.40
4533 4681 0.980754 TGCCTTCCTGCGGGAGAATA 60.981 55.000 15.42 0.00 43.29 1.75
4534 4682 0.398318 GCCTTCCTGCGGGAGAATAT 59.602 55.000 15.42 0.00 43.29 1.28
4535 4683 1.609320 GCCTTCCTGCGGGAGAATATC 60.609 57.143 15.42 0.00 43.29 1.63
4536 4684 1.337260 CCTTCCTGCGGGAGAATATCG 60.337 57.143 15.42 0.00 43.29 2.92
4537 4685 1.613925 CTTCCTGCGGGAGAATATCGA 59.386 52.381 15.42 0.00 43.29 3.59
4538 4686 1.924731 TCCTGCGGGAGAATATCGAT 58.075 50.000 11.27 2.16 36.57 3.59
4539 4687 1.546029 TCCTGCGGGAGAATATCGATG 59.454 52.381 11.27 0.00 36.57 3.84
4540 4688 1.273606 CCTGCGGGAGAATATCGATGT 59.726 52.381 5.28 0.00 33.58 3.06
4541 4689 2.332104 CTGCGGGAGAATATCGATGTG 58.668 52.381 8.54 0.00 0.00 3.21
4542 4690 1.686587 TGCGGGAGAATATCGATGTGT 59.313 47.619 8.54 0.00 0.00 3.72
4543 4691 2.102420 TGCGGGAGAATATCGATGTGTT 59.898 45.455 8.54 0.00 0.00 3.32
4544 4692 3.131396 GCGGGAGAATATCGATGTGTTT 58.869 45.455 8.54 0.00 0.00 2.83
4545 4693 3.059597 GCGGGAGAATATCGATGTGTTTG 60.060 47.826 8.54 0.00 0.00 2.93
4546 4694 3.059597 CGGGAGAATATCGATGTGTTTGC 60.060 47.826 8.54 0.00 0.00 3.68
4547 4695 3.251004 GGGAGAATATCGATGTGTTTGCC 59.749 47.826 8.54 2.10 0.00 4.52
4548 4696 4.130118 GGAGAATATCGATGTGTTTGCCT 58.870 43.478 8.54 0.00 0.00 4.75
4549 4697 5.297547 GGAGAATATCGATGTGTTTGCCTA 58.702 41.667 8.54 0.00 0.00 3.93
4550 4698 5.758296 GGAGAATATCGATGTGTTTGCCTAA 59.242 40.000 8.54 0.00 0.00 2.69
4551 4699 6.292919 GGAGAATATCGATGTGTTTGCCTAAC 60.293 42.308 8.54 0.00 37.26 2.34
4552 4700 6.112734 AGAATATCGATGTGTTTGCCTAACA 58.887 36.000 8.54 0.00 44.31 2.41
4565 4713 8.165239 TGTTTGCCTAACAACCATATGATATC 57.835 34.615 3.65 0.00 43.58 1.63
4566 4714 7.230510 TGTTTGCCTAACAACCATATGATATCC 59.769 37.037 3.65 0.00 43.58 2.59
4567 4715 5.815581 TGCCTAACAACCATATGATATCCC 58.184 41.667 3.65 0.00 0.00 3.85
4568 4716 5.551583 TGCCTAACAACCATATGATATCCCT 59.448 40.000 3.65 0.00 0.00 4.20
4569 4717 5.882557 GCCTAACAACCATATGATATCCCTG 59.117 44.000 3.65 0.00 0.00 4.45
4570 4718 6.418101 CCTAACAACCATATGATATCCCTGG 58.582 44.000 3.65 11.70 0.00 4.45
4571 4719 5.930209 AACAACCATATGATATCCCTGGT 57.070 39.130 3.65 12.71 41.89 4.00
4572 4720 5.246981 ACAACCATATGATATCCCTGGTG 57.753 43.478 17.06 14.02 40.04 4.17
4573 4721 4.665009 ACAACCATATGATATCCCTGGTGT 59.335 41.667 17.06 14.45 40.04 4.16
4574 4722 5.134339 ACAACCATATGATATCCCTGGTGTT 59.866 40.000 17.06 8.18 40.04 3.32
4575 4723 5.505181 ACCATATGATATCCCTGGTGTTC 57.495 43.478 16.10 0.00 38.74 3.18
4576 4724 4.289672 ACCATATGATATCCCTGGTGTTCC 59.710 45.833 16.10 0.00 38.74 3.62
4577 4725 4.324563 CCATATGATATCCCTGGTGTTCCC 60.325 50.000 3.65 0.00 0.00 3.97
4578 4726 2.278657 TGATATCCCTGGTGTTCCCA 57.721 50.000 0.00 0.00 42.51 4.37
4585 4733 2.292511 TGGTGTTCCCAGGGAGGT 59.707 61.111 8.67 0.00 38.72 3.85
4586 4734 1.554992 TGGTGTTCCCAGGGAGGTA 59.445 57.895 8.67 0.00 38.72 3.08
4587 4735 0.104356 TGGTGTTCCCAGGGAGGTAA 60.104 55.000 8.67 0.00 38.72 2.85
4588 4736 1.296002 GGTGTTCCCAGGGAGGTAAT 58.704 55.000 8.67 0.00 34.66 1.89
4589 4737 1.212195 GGTGTTCCCAGGGAGGTAATC 59.788 57.143 8.67 0.00 34.66 1.75
4590 4738 1.134491 GTGTTCCCAGGGAGGTAATCG 60.134 57.143 8.67 0.00 34.66 3.34
4591 4739 1.273381 TGTTCCCAGGGAGGTAATCGA 60.273 52.381 8.67 0.00 34.66 3.59
4592 4740 1.413077 GTTCCCAGGGAGGTAATCGAG 59.587 57.143 8.67 0.00 34.66 4.04
4593 4741 0.759436 TCCCAGGGAGGTAATCGAGC 60.759 60.000 3.01 0.00 34.66 5.03
4594 4742 1.048724 CCCAGGGAGGTAATCGAGCA 61.049 60.000 0.00 0.00 34.66 4.26
4595 4743 0.105039 CCAGGGAGGTAATCGAGCAC 59.895 60.000 0.00 0.00 0.00 4.40
4596 4744 0.105039 CAGGGAGGTAATCGAGCACC 59.895 60.000 9.66 9.66 35.71 5.01
4597 4745 0.325296 AGGGAGGTAATCGAGCACCA 60.325 55.000 17.78 0.00 37.98 4.17
4598 4746 0.179081 GGGAGGTAATCGAGCACCAC 60.179 60.000 17.78 12.41 37.98 4.16
4599 4747 0.179081 GGAGGTAATCGAGCACCACC 60.179 60.000 17.78 16.69 38.21 4.61
4600 4748 0.824759 GAGGTAATCGAGCACCACCT 59.175 55.000 17.78 11.99 42.29 4.00
4601 4749 1.207329 GAGGTAATCGAGCACCACCTT 59.793 52.381 17.78 0.27 39.71 3.50
4602 4750 1.207329 AGGTAATCGAGCACCACCTTC 59.793 52.381 17.78 0.00 36.16 3.46
4603 4751 1.653151 GTAATCGAGCACCACCTTCC 58.347 55.000 0.00 0.00 0.00 3.46
4604 4752 1.207329 GTAATCGAGCACCACCTTCCT 59.793 52.381 0.00 0.00 0.00 3.36
4605 4753 0.036010 AATCGAGCACCACCTTCCTG 60.036 55.000 0.00 0.00 0.00 3.86
4606 4754 1.194781 ATCGAGCACCACCTTCCTGT 61.195 55.000 0.00 0.00 0.00 4.00
4607 4755 1.374758 CGAGCACCACCTTCCTGTC 60.375 63.158 0.00 0.00 0.00 3.51
4608 4756 1.821061 CGAGCACCACCTTCCTGTCT 61.821 60.000 0.00 0.00 0.00 3.41
4609 4757 0.321122 GAGCACCACCTTCCTGTCTG 60.321 60.000 0.00 0.00 0.00 3.51
4610 4758 1.968540 GCACCACCTTCCTGTCTGC 60.969 63.158 0.00 0.00 0.00 4.26
4611 4759 1.302832 CACCACCTTCCTGTCTGCC 60.303 63.158 0.00 0.00 0.00 4.85
4612 4760 2.352805 CCACCTTCCTGTCTGCCC 59.647 66.667 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.749340 TGGGAAGAAGAGTACATCGATATATTA 57.251 33.333 0.00 0.00 0.00 0.98
366 369 2.116772 ACATGCAGGCAGTGGCTT 59.883 55.556 17.98 0.00 40.87 4.35
608 619 2.182030 CACTCTTCCCTCGTCGCC 59.818 66.667 0.00 0.00 0.00 5.54
653 689 4.026357 GTCCACCCCCTCCCTCCT 62.026 72.222 0.00 0.00 0.00 3.69
826 913 4.373116 ATCCTGTCCGCACGCGTT 62.373 61.111 10.22 0.00 37.81 4.84
832 919 3.399181 GACCCCATCCTGTCCGCA 61.399 66.667 0.00 0.00 0.00 5.69
880 967 8.773645 TGTATATTTTGATGCTCTAAATCGGTG 58.226 33.333 8.13 0.00 34.58 4.94
889 976 8.687292 ACACATGATGTATATTTTGATGCTCT 57.313 30.769 0.00 0.00 40.88 4.09
908 995 6.529125 GTCAATTAGAGCATTTCCAACACATG 59.471 38.462 0.00 0.00 0.00 3.21
911 998 6.012658 TGTCAATTAGAGCATTTCCAACAC 57.987 37.500 0.00 0.00 0.00 3.32
913 1000 7.067494 ACCTATGTCAATTAGAGCATTTCCAAC 59.933 37.037 0.00 0.00 0.00 3.77
917 1004 6.073548 CGGACCTATGTCAATTAGAGCATTTC 60.074 42.308 0.41 0.00 43.65 2.17
919 1006 5.163301 ACGGACCTATGTCAATTAGAGCATT 60.163 40.000 0.41 0.00 43.65 3.56
941 1028 1.731709 TGATGCTTCAAACCGATGACG 59.268 47.619 0.00 0.00 39.43 4.35
942 1029 3.829886 TTGATGCTTCAAACCGATGAC 57.170 42.857 12.27 0.00 38.90 3.06
951 1038 8.437360 AGATGACGTATATTTTGATGCTTCAA 57.563 30.769 10.76 10.76 40.09 2.69
970 1059 8.093307 TCAATTAGAGCATCCTGAATAGATGAC 58.907 37.037 4.98 0.00 43.15 3.06
1087 1187 0.771755 ACCAGAAGAAACAGGGGGTC 59.228 55.000 0.00 0.00 0.00 4.46
1152 1252 1.248486 GTTGTGGGAGAAAGGGAAGC 58.752 55.000 0.00 0.00 0.00 3.86
1250 1350 4.452733 GGTCTGCTTCGGACGGGG 62.453 72.222 0.31 0.00 40.37 5.73
1956 2056 0.249073 CGTCATCGTCCAGGGTGATC 60.249 60.000 0.00 0.00 0.00 2.92
2163 2263 0.794229 GTGTTGCCGCAATCACATCG 60.794 55.000 22.85 0.00 31.20 3.84
2311 2411 3.320541 AGCACGGAGATCATCTTTCCTAG 59.679 47.826 0.00 0.00 0.00 3.02
2370 2470 6.704937 CAGCATAATCAGTTATGAGAAGCAGA 59.295 38.462 11.27 0.00 46.59 4.26
2826 2926 1.085091 GCATTGCCTGAGAGACACTG 58.915 55.000 0.00 0.00 0.00 3.66
3153 3253 2.811317 CGACGGAGCACTGGAAGC 60.811 66.667 0.00 0.00 37.60 3.86
3471 3571 5.502079 TCCGAGATAATTGCCACCTTTTTA 58.498 37.500 0.00 0.00 0.00 1.52
3528 3628 2.110011 AGCACCCCTAGTTCCAAATGTT 59.890 45.455 0.00 0.00 0.00 2.71
3613 3713 6.722129 AGTATTATCTTACTGCAGGGTAGAGG 59.278 42.308 19.93 0.96 31.25 3.69
3638 3738 4.100498 GTCTTACATTATGGAACGGAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
3639 3739 4.377897 GTCTTACATTATGGAACGGAGGG 58.622 47.826 0.00 0.00 0.00 4.30
3640 3740 4.049186 CGTCTTACATTATGGAACGGAGG 58.951 47.826 0.00 0.00 0.00 4.30
3641 3741 4.679662 ACGTCTTACATTATGGAACGGAG 58.320 43.478 6.60 0.00 0.00 4.63
3642 3742 4.724074 ACGTCTTACATTATGGAACGGA 57.276 40.909 6.60 0.00 0.00 4.69
3643 3743 5.789710 AAACGTCTTACATTATGGAACGG 57.210 39.130 6.60 0.00 0.00 4.44
3687 3787 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
3688 3788 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3689 3789 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3690 3790 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3691 3791 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3693 3793 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3694 3794 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3695 3795 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3696 3796 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3697 3797 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3698 3798 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3699 3799 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3700 3800 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3701 3801 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3702 3802 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3703 3803 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3704 3804 0.613853 CAACTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
3705 3805 1.957765 GCAACTACTCCCTCCGTCCC 61.958 65.000 0.00 0.00 0.00 4.46
3706 3806 1.255667 TGCAACTACTCCCTCCGTCC 61.256 60.000 0.00 0.00 0.00 4.79
3707 3807 0.824759 ATGCAACTACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
3708 3808 0.537188 CATGCAACTACTCCCTCCGT 59.463 55.000 0.00 0.00 0.00 4.69
3709 3809 0.537188 ACATGCAACTACTCCCTCCG 59.463 55.000 0.00 0.00 0.00 4.63
3710 3810 3.906720 TTACATGCAACTACTCCCTCC 57.093 47.619 0.00 0.00 0.00 4.30
3711 3811 6.017852 GCTAAATTACATGCAACTACTCCCTC 60.018 42.308 0.00 0.00 0.00 4.30
3712 3812 5.823045 GCTAAATTACATGCAACTACTCCCT 59.177 40.000 0.00 0.00 0.00 4.20
3713 3813 5.823045 AGCTAAATTACATGCAACTACTCCC 59.177 40.000 0.00 0.00 0.00 4.30
3714 3814 6.927294 AGCTAAATTACATGCAACTACTCC 57.073 37.500 0.00 0.00 0.00 3.85
3715 3815 7.752695 ACAAGCTAAATTACATGCAACTACTC 58.247 34.615 0.00 0.00 0.00 2.59
3716 3816 7.687941 ACAAGCTAAATTACATGCAACTACT 57.312 32.000 0.00 0.00 0.00 2.57
3717 3817 9.438291 CATACAAGCTAAATTACATGCAACTAC 57.562 33.333 0.00 0.00 0.00 2.73
3718 3818 9.173021 ACATACAAGCTAAATTACATGCAACTA 57.827 29.630 0.00 0.00 0.00 2.24
3719 3819 7.970061 CACATACAAGCTAAATTACATGCAACT 59.030 33.333 0.00 0.00 0.00 3.16
3720 3820 7.220683 CCACATACAAGCTAAATTACATGCAAC 59.779 37.037 0.00 0.00 0.00 4.17
3721 3821 7.093988 ACCACATACAAGCTAAATTACATGCAA 60.094 33.333 0.00 0.00 0.00 4.08
3783 3883 9.708092 ACTCTACCTTCAAGAAAATTGTAGTAC 57.292 33.333 0.00 0.00 0.00 2.73
3975 4075 7.369607 CCATTTTTAGGGCTTCAAATTTTTGG 58.630 34.615 3.38 0.00 38.66 3.28
4008 4108 4.228912 AGCAAAAACATTTCTCACCTCG 57.771 40.909 0.00 0.00 0.00 4.63
4094 4216 2.084546 CAGTTTTTGGATCCGTCTCCC 58.915 52.381 7.39 0.00 34.12 4.30
4144 4280 3.351416 GGACCCAAACGGACACGC 61.351 66.667 0.00 0.00 46.04 5.34
4188 4329 1.472662 AAGGATAGGACGGGGATGCG 61.473 60.000 0.00 0.00 0.00 4.73
4198 4339 5.687166 ACGGACACAATTTAAGGATAGGA 57.313 39.130 0.00 0.00 0.00 2.94
4226 4367 4.459089 GCCTGGAGTGGTCGAGCC 62.459 72.222 12.85 4.60 37.90 4.70
4227 4368 4.803426 CGCCTGGAGTGGTCGAGC 62.803 72.222 7.89 7.89 0.00 5.03
4230 4371 2.960957 CTATGCGCCTGGAGTGGTCG 62.961 65.000 4.18 0.00 0.00 4.79
4232 4373 1.553690 AACTATGCGCCTGGAGTGGT 61.554 55.000 4.18 0.00 0.00 4.16
4244 4390 2.034507 CGTAAAGCTCGCTCAACTATGC 60.035 50.000 0.00 0.00 0.00 3.14
4263 4409 1.422950 CGTTTGTTGTCCGTGACCGT 61.423 55.000 2.23 0.00 0.00 4.83
4275 4423 0.098025 CACGTGCCAGTTCGTTTGTT 59.902 50.000 0.82 0.00 38.23 2.83
4278 4426 2.830285 GCCACGTGCCAGTTCGTTT 61.830 57.895 10.91 0.00 38.23 3.60
4282 4430 3.712881 GACGCCACGTGCCAGTTC 61.713 66.667 10.91 0.00 41.37 3.01
4350 4498 1.447838 CGTGCGCATTGACTAGGGT 60.448 57.895 15.91 0.00 0.00 4.34
4378 4526 3.426568 GGTGGCTGACTTGCGAGC 61.427 66.667 0.00 0.00 32.73 5.03
4380 4528 3.535629 CTGGGTGGCTGACTTGCGA 62.536 63.158 0.00 0.00 0.00 5.10
4381 4529 3.052082 CTGGGTGGCTGACTTGCG 61.052 66.667 0.00 0.00 0.00 4.85
4382 4530 1.968540 GTCTGGGTGGCTGACTTGC 60.969 63.158 0.00 0.00 0.00 4.01
4385 4533 3.314331 CCGTCTGGGTGGCTGACT 61.314 66.667 0.00 0.00 0.00 3.41
4403 4551 2.685804 AAAAAGGACGTGGTCGGGGG 62.686 60.000 0.00 0.00 41.85 5.40
4445 4593 1.631405 TGGGGAAGTGGAAATTGCAG 58.369 50.000 0.00 0.00 32.43 4.41
4448 4596 2.110578 GGGATGGGGAAGTGGAAATTG 58.889 52.381 0.00 0.00 0.00 2.32
4449 4597 1.008327 GGGGATGGGGAAGTGGAAATT 59.992 52.381 0.00 0.00 0.00 1.82
4482 4630 4.324267 CTTTCCTATTTGTCGTCAAGGGT 58.676 43.478 0.00 0.00 34.88 4.34
4485 4633 3.725010 GCGCTTTCCTATTTGTCGTCAAG 60.725 47.826 0.00 0.00 34.88 3.02
4489 4637 0.719465 CGCGCTTTCCTATTTGTCGT 59.281 50.000 5.56 0.00 0.00 4.34
4490 4638 0.586502 GCGCGCTTTCCTATTTGTCG 60.587 55.000 26.67 0.00 0.00 4.35
4491 4639 0.248094 GGCGCGCTTTCCTATTTGTC 60.248 55.000 32.29 5.07 0.00 3.18
4492 4640 1.654023 GGGCGCGCTTTCCTATTTGT 61.654 55.000 32.29 0.00 0.00 2.83
4493 4641 1.064134 GGGCGCGCTTTCCTATTTG 59.936 57.895 32.29 0.00 0.00 2.32
4494 4642 2.469516 CGGGCGCGCTTTCCTATTT 61.470 57.895 32.29 0.00 0.00 1.40
4495 4643 2.895372 CGGGCGCGCTTTCCTATT 60.895 61.111 32.29 0.00 0.00 1.73
4496 4644 3.675619 AACGGGCGCGCTTTCCTAT 62.676 57.895 32.29 11.58 0.00 2.57
4497 4645 4.382320 AACGGGCGCGCTTTCCTA 62.382 61.111 32.29 0.00 0.00 2.94
4521 4669 2.288457 ACACATCGATATTCTCCCGCAG 60.288 50.000 0.00 0.00 0.00 5.18
4522 4670 1.686587 ACACATCGATATTCTCCCGCA 59.313 47.619 0.00 0.00 0.00 5.69
4523 4671 2.440539 ACACATCGATATTCTCCCGC 57.559 50.000 0.00 0.00 0.00 6.13
4524 4672 3.059597 GCAAACACATCGATATTCTCCCG 60.060 47.826 0.00 0.00 0.00 5.14
4525 4673 3.251004 GGCAAACACATCGATATTCTCCC 59.749 47.826 0.00 0.00 0.00 4.30
4526 4674 4.130118 AGGCAAACACATCGATATTCTCC 58.870 43.478 0.00 0.00 0.00 3.71
4527 4675 6.257849 TGTTAGGCAAACACATCGATATTCTC 59.742 38.462 0.00 0.00 43.22 2.87
4528 4676 6.112734 TGTTAGGCAAACACATCGATATTCT 58.887 36.000 0.00 0.00 43.22 2.40
4529 4677 6.358118 TGTTAGGCAAACACATCGATATTC 57.642 37.500 0.00 0.00 43.22 1.75
4530 4678 8.707284 TGGTTGTTAGGCAAACACATCGATATT 61.707 37.037 0.00 0.00 46.84 1.28
4531 4679 7.299868 TGGTTGTTAGGCAAACACATCGATAT 61.300 38.462 0.00 0.00 46.84 1.63
4532 4680 6.031492 TGGTTGTTAGGCAAACACATCGATA 61.031 40.000 0.00 0.00 46.84 2.92
4533 4681 5.285100 TGGTTGTTAGGCAAACACATCGAT 61.285 41.667 3.56 0.00 46.84 3.59
4534 4682 3.994474 TGGTTGTTAGGCAAACACATCGA 60.994 43.478 3.56 0.00 46.84 3.59
4535 4683 2.292016 TGGTTGTTAGGCAAACACATCG 59.708 45.455 3.56 0.00 46.84 3.84
4541 4689 7.309194 GGGATATCATATGGTTGTTAGGCAAAC 60.309 40.741 4.83 0.00 44.77 2.93
4542 4690 6.719370 GGGATATCATATGGTTGTTAGGCAAA 59.281 38.462 4.83 0.00 39.03 3.68
4543 4691 6.045459 AGGGATATCATATGGTTGTTAGGCAA 59.955 38.462 4.83 0.00 34.16 4.52
4544 4692 5.551583 AGGGATATCATATGGTTGTTAGGCA 59.448 40.000 4.83 0.00 0.00 4.75
4545 4693 5.882557 CAGGGATATCATATGGTTGTTAGGC 59.117 44.000 4.83 0.00 0.00 3.93
4546 4694 6.012508 ACCAGGGATATCATATGGTTGTTAGG 60.013 42.308 16.07 0.04 41.44 2.69
4547 4695 6.881065 CACCAGGGATATCATATGGTTGTTAG 59.119 42.308 18.18 7.60 42.29 2.34
4548 4696 6.331572 ACACCAGGGATATCATATGGTTGTTA 59.668 38.462 18.18 0.00 42.29 2.41
4549 4697 5.134339 ACACCAGGGATATCATATGGTTGTT 59.866 40.000 18.18 7.52 42.29 2.83
4550 4698 4.665009 ACACCAGGGATATCATATGGTTGT 59.335 41.667 18.18 16.31 42.29 3.32
4551 4699 5.246981 ACACCAGGGATATCATATGGTTG 57.753 43.478 18.18 15.88 42.29 3.77
4552 4700 5.222130 GGAACACCAGGGATATCATATGGTT 60.222 44.000 18.18 9.07 42.29 3.67
4553 4701 4.289672 GGAACACCAGGGATATCATATGGT 59.710 45.833 16.07 16.07 45.00 3.55
4554 4702 4.324563 GGGAACACCAGGGATATCATATGG 60.325 50.000 15.05 15.05 39.85 2.74
4555 4703 4.289410 TGGGAACACCAGGGATATCATATG 59.711 45.833 4.83 0.00 46.80 1.78
4556 4704 4.512298 TGGGAACACCAGGGATATCATAT 58.488 43.478 4.83 0.00 46.80 1.78
4557 4705 3.948126 TGGGAACACCAGGGATATCATA 58.052 45.455 4.83 0.00 46.80 2.15
4558 4706 2.787956 TGGGAACACCAGGGATATCAT 58.212 47.619 4.83 0.00 46.80 2.45
4559 4707 2.278657 TGGGAACACCAGGGATATCA 57.721 50.000 4.83 0.00 46.80 2.15
4569 4717 1.212195 GATTACCTCCCTGGGAACACC 59.788 57.143 17.81 0.56 42.46 4.16
4570 4718 1.134491 CGATTACCTCCCTGGGAACAC 60.134 57.143 17.81 4.67 42.46 3.32
4571 4719 1.200519 CGATTACCTCCCTGGGAACA 58.799 55.000 17.81 1.49 42.46 3.18
4572 4720 1.413077 CTCGATTACCTCCCTGGGAAC 59.587 57.143 17.81 3.66 42.46 3.62
4573 4721 1.789523 CTCGATTACCTCCCTGGGAA 58.210 55.000 17.81 1.47 44.09 3.97
4574 4722 0.759436 GCTCGATTACCTCCCTGGGA 60.759 60.000 16.13 16.13 41.11 4.37
4575 4723 1.048724 TGCTCGATTACCTCCCTGGG 61.049 60.000 6.33 6.33 41.11 4.45
4576 4724 0.105039 GTGCTCGATTACCTCCCTGG 59.895 60.000 0.00 0.00 42.93 4.45
4577 4725 0.105039 GGTGCTCGATTACCTCCCTG 59.895 60.000 10.15 0.00 34.11 4.45
4578 4726 0.325296 TGGTGCTCGATTACCTCCCT 60.325 55.000 16.37 0.00 37.84 4.20
4579 4727 0.179081 GTGGTGCTCGATTACCTCCC 60.179 60.000 16.37 4.43 37.84 4.30
4580 4728 0.179081 GGTGGTGCTCGATTACCTCC 60.179 60.000 17.99 17.99 41.69 4.30
4581 4729 0.824759 AGGTGGTGCTCGATTACCTC 59.175 55.000 16.37 13.25 37.15 3.85
4582 4730 1.207329 GAAGGTGGTGCTCGATTACCT 59.793 52.381 16.37 9.25 43.27 3.08
4583 4731 1.653151 GAAGGTGGTGCTCGATTACC 58.347 55.000 10.43 10.43 37.48 2.85
4584 4732 1.207329 AGGAAGGTGGTGCTCGATTAC 59.793 52.381 0.00 0.00 0.00 1.89
4585 4733 1.207089 CAGGAAGGTGGTGCTCGATTA 59.793 52.381 0.00 0.00 0.00 1.75
4586 4734 0.036010 CAGGAAGGTGGTGCTCGATT 60.036 55.000 0.00 0.00 0.00 3.34
4587 4735 1.194781 ACAGGAAGGTGGTGCTCGAT 61.195 55.000 0.00 0.00 0.00 3.59
4588 4736 1.816863 GACAGGAAGGTGGTGCTCGA 61.817 60.000 0.00 0.00 0.00 4.04
4589 4737 1.374758 GACAGGAAGGTGGTGCTCG 60.375 63.158 0.00 0.00 0.00 5.03
4590 4738 0.321122 CAGACAGGAAGGTGGTGCTC 60.321 60.000 0.00 0.00 0.00 4.26
4591 4739 1.757306 CAGACAGGAAGGTGGTGCT 59.243 57.895 0.00 0.00 0.00 4.40
4592 4740 1.968540 GCAGACAGGAAGGTGGTGC 60.969 63.158 0.00 0.00 0.00 5.01
4593 4741 1.302832 GGCAGACAGGAAGGTGGTG 60.303 63.158 0.00 0.00 0.00 4.17
4594 4742 2.529744 GGGCAGACAGGAAGGTGGT 61.530 63.158 0.00 0.00 0.00 4.16
4595 4743 2.352805 GGGCAGACAGGAAGGTGG 59.647 66.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.