Multiple sequence alignment - TraesCS3D01G496100

Loading Multiple Alignment...

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 TraesCS3D01G496100 chr3D 100.000 5447 0 0 1 5447 587951356 587945910 0.000000e+00 10059.0
1 TraesCS3D01G496100 chr3D 96.842 190 5 1 4515 4704 428139679 428139867 3.170000e-82 316.0
2 TraesCS3D01G496100 chr3D 85.081 248 33 4 3650 3895 591709940 591710185 3.260000e-62 250.0
3 TraesCS3D01G496100 chr3B 95.127 3673 150 13 250 3896 785696355 785692686 0.000000e+00 5764.0
4 TraesCS3D01G496100 chr3B 83.842 2946 432 31 972 3896 786136800 786139722 0.000000e+00 2763.0
5 TraesCS3D01G496100 chr3B 95.509 757 28 4 4696 5447 785692152 785691397 0.000000e+00 1205.0
6 TraesCS3D01G496100 chr3B 94.891 548 28 0 3975 4522 785692691 785692144 0.000000e+00 857.0
7 TraesCS3D01G496100 chr3B 81.461 534 79 13 3975 4501 786139717 786140237 2.350000e-113 420.0
8 TraesCS3D01G496100 chr3B 87.739 261 26 5 1 259 785697022 785696766 3.190000e-77 300.0
9 TraesCS3D01G496100 chr3B 91.509 106 6 3 3881 3985 804117581 804117478 5.690000e-30 143.0
10 TraesCS3D01G496100 chr3A 97.024 2016 44 4 1897 3896 717853805 717851790 0.000000e+00 3376.0
11 TraesCS3D01G496100 chr3A 91.504 1848 128 19 1 1837 717855628 717853799 0.000000e+00 2516.0
12 TraesCS3D01G496100 chr3A 93.248 548 33 1 3975 4522 717851795 717851252 0.000000e+00 804.0
13 TraesCS3D01G496100 chr3A 84.414 802 122 2 1072 1873 717885016 717885814 0.000000e+00 785.0
14 TraesCS3D01G496100 chr3A 80.952 1029 161 20 2221 3233 717898942 717899951 0.000000e+00 782.0
15 TraesCS3D01G496100 chr3A 97.291 406 8 1 4696 5101 717851260 717850858 0.000000e+00 686.0
16 TraesCS3D01G496100 chr3A 85.404 644 94 0 3253 3896 717901164 717901807 0.000000e+00 669.0
17 TraesCS3D01G496100 chr3A 81.685 546 87 8 3977 4518 717901807 717902343 5.010000e-120 442.0
18 TraesCS3D01G496100 chr4D 98.413 189 3 0 4514 4702 401881601 401881413 3.140000e-87 333.0
19 TraesCS3D01G496100 chr4D 95.288 191 6 3 4517 4706 3846932 3846744 3.190000e-77 300.0
20 TraesCS3D01G496100 chr1D 95.745 188 8 0 4516 4703 297155797 297155984 2.470000e-78 303.0
21 TraesCS3D01G496100 chr1D 94.737 190 10 0 4513 4702 434389892 434389703 4.130000e-76 296.0
22 TraesCS3D01G496100 chr5D 97.126 174 5 0 4523 4696 539072648 539072821 1.480000e-75 294.0
23 TraesCS3D01G496100 chr5D 94.709 189 8 2 4511 4699 408742593 408742779 5.340000e-75 292.0
24 TraesCS3D01G496100 chr5D 81.188 101 12 6 4080 4178 555490270 555490365 2.100000e-09 75.0
25 TraesCS3D01G496100 chr2B 93.000 200 12 2 4506 4704 765569960 765570158 1.920000e-74 291.0
26 TraesCS3D01G496100 chr5B 93.367 196 9 4 4518 4713 346616341 346616150 2.480000e-73 287.0
27 TraesCS3D01G496100 chr5B 82.407 108 15 3 4080 4185 695874199 695874094 2.090000e-14 91.6
28 TraesCS3D01G496100 chr5B 77.143 140 32 0 4081 4220 695720398 695720259 1.260000e-11 82.4
29 TraesCS3D01G496100 chr6A 94.792 96 4 1 3886 3981 27342986 27342892 1.220000e-31 148.0
30 TraesCS3D01G496100 chr6A 100.000 30 0 0 878 907 181015649 181015678 7.620000e-04 56.5
31 TraesCS3D01G496100 chr4A 94.059 101 1 4 3886 3983 712733704 712733802 1.220000e-31 148.0
32 TraesCS3D01G496100 chr7D 94.737 95 3 2 3890 3983 49828773 49828866 4.400000e-31 147.0
33 TraesCS3D01G496100 chr1A 90.826 109 8 2 3889 3996 296213805 296213698 1.580000e-30 145.0
34 TraesCS3D01G496100 chr2A 90.265 113 6 4 3888 3996 15846402 15846291 5.690000e-30 143.0
35 TraesCS3D01G496100 chr6B 90.654 107 8 2 3893 3999 218219424 218219320 2.050000e-29 141.0
36 TraesCS3D01G496100 chr4B 90.741 108 6 4 3893 3997 107553538 107553644 2.050000e-29 141.0
37 TraesCS3D01G496100 chr7B 90.566 106 8 2 3889 3993 598012118 598012014 7.360000e-29 139.0
38 TraesCS3D01G496100 chr6D 81.731 104 19 0 4082 4185 436738003 436737900 2.700000e-13 87.9
39 TraesCS3D01G496100 chrUn 100.000 28 0 0 5005 5032 31808131 31808104 1.000000e-02 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 TraesCS3D01G496100 chr3D 587945910 587951356 5446 True 10059.0 10059 100.000000 1 5447 1 chr3D.!!$R1 5446
1 TraesCS3D01G496100 chr3B 785691397 785697022 5625 True 2031.5 5764 93.316500 1 5447 4 chr3B.!!$R2 5446
2 TraesCS3D01G496100 chr3B 786136800 786140237 3437 False 1591.5 2763 82.651500 972 4501 2 chr3B.!!$F1 3529
3 TraesCS3D01G496100 chr3A 717850858 717855628 4770 True 1845.5 3376 94.766750 1 5101 4 chr3A.!!$R1 5100
4 TraesCS3D01G496100 chr3A 717885016 717885814 798 False 785.0 785 84.414000 1072 1873 1 chr3A.!!$F1 801
5 TraesCS3D01G496100 chr3A 717898942 717902343 3401 False 631.0 782 82.680333 2221 4518 3 chr3A.!!$F2 2297

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
934 1385 0.036671 CACTCAGTGCAGCTCATCCA 60.037 55.0 0.0 0.0 0.00 3.41 F
1482 1951 0.321671 TGAGGGAGCTGAACCTTTCG 59.678 55.0 0.0 0.0 37.18 3.46 F
2040 2515 0.691078 TACCATCCTCACTCTGCCCC 60.691 60.0 0.0 0.0 0.00 5.80 F
3672 5364 0.667792 GGTTCCGTGAGAGACTGTGC 60.668 60.0 0.0 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 2752 1.377366 GATGAGGTGCTCGAGTCCGA 61.377 60.000 15.13 9.53 43.35 4.55 R
3028 3518 1.279271 GGATCCCATCTCCGGTATTGG 59.721 57.143 0.00 6.84 0.00 3.16 R
3723 5415 0.179215 CGCAGTGCAAGACGATTTCC 60.179 55.000 16.83 0.00 0.00 3.13 R
4605 6303 0.249155 AACCCACGTCAGTACACACG 60.249 55.000 13.39 13.39 41.90 4.49 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
37 38 4.973168 AGAAGTGTTGTTGCCTTCATAGA 58.027 39.130 0.00 0.00 37.62 1.98
38 39 5.564550 AGAAGTGTTGTTGCCTTCATAGAT 58.435 37.500 0.00 0.00 37.62 1.98
59 60 2.213499 GAATAGACGACAGGCAATGGG 58.787 52.381 0.00 0.00 0.00 4.00
82 83 2.151202 GAAAGCTCGAATGTGGGAACA 58.849 47.619 0.00 0.00 38.70 3.18
87 88 1.303236 CGAATGTGGGAACAGGGCA 60.303 57.895 0.00 0.00 44.46 5.36
123 126 3.591254 GAGGGAAACTCGCCTGCGT 62.591 63.158 11.68 0.00 40.74 5.24
173 176 2.290008 TGTTTGGTGTCAGCATACGGAT 60.290 45.455 17.15 0.00 31.68 4.18
177 180 1.227234 TGTCAGCATACGGATGGCG 60.227 57.895 10.28 0.00 41.37 5.69
204 207 2.305635 TGGCAGGAAGAGAATGCTACAA 59.694 45.455 0.00 0.00 39.88 2.41
206 209 3.604582 GCAGGAAGAGAATGCTACAACT 58.395 45.455 0.00 0.00 37.00 3.16
207 210 4.006319 GCAGGAAGAGAATGCTACAACTT 58.994 43.478 0.00 0.00 37.00 2.66
208 211 4.457257 GCAGGAAGAGAATGCTACAACTTT 59.543 41.667 0.00 0.00 37.00 2.66
236 239 4.846779 TTTTTGCGGAAAGAATGCTAGT 57.153 36.364 1.41 0.00 0.00 2.57
238 241 5.545658 TTTTGCGGAAAGAATGCTAGTAG 57.454 39.130 1.41 0.00 0.00 2.57
239 242 4.465632 TTGCGGAAAGAATGCTAGTAGA 57.534 40.909 0.00 0.00 0.00 2.59
241 244 4.827692 TGCGGAAAGAATGCTAGTAGAAA 58.172 39.130 0.00 0.00 0.00 2.52
242 245 5.428253 TGCGGAAAGAATGCTAGTAGAAAT 58.572 37.500 0.00 0.00 0.00 2.17
243 246 6.578944 TGCGGAAAGAATGCTAGTAGAAATA 58.421 36.000 0.00 0.00 0.00 1.40
244 247 7.217200 TGCGGAAAGAATGCTAGTAGAAATAT 58.783 34.615 0.00 0.00 0.00 1.28
282 705 9.362539 AGAAGCATAAAACATTTCAGCATAAAG 57.637 29.630 0.00 0.00 0.00 1.85
329 752 2.676342 AGCGTTCAAACCATATCGAACC 59.324 45.455 0.00 0.00 35.43 3.62
433 862 2.702592 AGTGACTTTTGGTCCAACGA 57.297 45.000 2.98 0.00 43.89 3.85
434 863 2.285977 AGTGACTTTTGGTCCAACGAC 58.714 47.619 2.98 0.00 43.89 4.34
435 864 1.004292 GTGACTTTTGGTCCAACGACG 60.004 52.381 2.98 0.00 43.89 5.12
546 975 6.820656 TGAGGAATCATCTTGTTTTAGAGAGC 59.179 38.462 0.00 0.00 0.00 4.09
609 1038 3.705043 ATCTCCCAACACGTCGTATAC 57.295 47.619 0.00 0.00 0.00 1.47
811 1254 6.457528 GGCAGGAAAAGATCGATTTTACAGAG 60.458 42.308 8.73 1.07 35.75 3.35
934 1385 0.036671 CACTCAGTGCAGCTCATCCA 60.037 55.000 0.00 0.00 0.00 3.41
952 1403 2.512056 TCCAGTCCAGAAACCCAAAAGA 59.488 45.455 0.00 0.00 0.00 2.52
953 1404 2.887152 CCAGTCCAGAAACCCAAAAGAG 59.113 50.000 0.00 0.00 0.00 2.85
956 1407 2.294512 GTCCAGAAACCCAAAAGAGCTG 59.705 50.000 0.00 0.00 0.00 4.24
959 1410 2.363359 CAGAAACCCAAAAGAGCTGCTT 59.637 45.455 2.53 0.00 38.88 3.91
1256 1713 1.606994 CCCACTTGACGTCGATTTCCA 60.607 52.381 11.62 0.00 0.00 3.53
1258 1715 3.517602 CCACTTGACGTCGATTTCCATA 58.482 45.455 11.62 0.00 0.00 2.74
1305 1762 0.322636 GTGGTCTCGAGGTCCTCAGA 60.323 60.000 19.15 16.08 0.00 3.27
1428 1897 4.530857 CTGGGTGGATCCGTCGCC 62.531 72.222 7.39 6.59 37.00 5.54
1482 1951 0.321671 TGAGGGAGCTGAACCTTTCG 59.678 55.000 0.00 0.00 37.18 3.46
1508 1983 4.555709 ACTCGTTGGCGGTGGCAA 62.556 61.111 1.29 1.29 45.54 4.52
1520 1995 4.697756 TGGCAACGCGAAGGGAGG 62.698 66.667 15.93 0.00 46.37 4.30
1551 2026 1.118356 TTTTTGCCCGCCTGGATGTT 61.118 50.000 0.00 0.00 37.49 2.71
1554 2029 1.558167 TTGCCCGCCTGGATGTTCTA 61.558 55.000 0.00 0.00 37.49 2.10
1626 2101 4.699522 GTCCGCCGGCTGAACCTT 62.700 66.667 26.68 0.00 35.61 3.50
2040 2515 0.691078 TACCATCCTCACTCTGCCCC 60.691 60.000 0.00 0.00 0.00 5.80
2092 2571 3.056465 GCTCTACCTGCAGAACAACTACT 60.056 47.826 17.39 0.00 0.00 2.57
2143 2622 1.689273 ACTGTGAAAGCCTCGAGTCTT 59.311 47.619 12.31 7.40 0.00 3.01
2273 2752 4.057428 GTCGCTCGGTGGTGCTCT 62.057 66.667 0.00 0.00 0.00 4.09
2345 2824 2.222886 CGTCGGAATTGATGAACTGCAG 60.223 50.000 13.48 13.48 0.00 4.41
2979 3469 3.444029 CCCAATCCCCAGTTCATTTTCT 58.556 45.455 0.00 0.00 0.00 2.52
3028 3518 7.615403 TCTATCATACAATAGGCTGAATGGAC 58.385 38.462 0.00 0.00 31.37 4.02
3672 5364 0.667792 GGTTCCGTGAGAGACTGTGC 60.668 60.000 0.00 0.00 0.00 4.57
3723 5415 6.183361 TGGAATATCTACACCATGGTTACCAG 60.183 42.308 16.84 9.89 36.75 4.00
3896 5588 5.418209 ACATGTCACCAGGTACTTAGTACTC 59.582 44.000 20.15 11.49 38.85 2.59
3897 5589 4.338879 TGTCACCAGGTACTTAGTACTCC 58.661 47.826 20.15 6.70 38.85 3.85
3898 5590 3.698539 GTCACCAGGTACTTAGTACTCCC 59.301 52.174 20.15 6.02 38.85 4.30
3899 5591 3.595138 TCACCAGGTACTTAGTACTCCCT 59.405 47.826 20.15 8.15 38.85 4.20
3900 5592 3.952967 CACCAGGTACTTAGTACTCCCTC 59.047 52.174 20.15 5.26 38.85 4.30
3901 5593 3.053019 ACCAGGTACTTAGTACTCCCTCC 60.053 52.174 20.15 4.65 38.85 4.30
3902 5594 3.212685 CAGGTACTTAGTACTCCCTCCG 58.787 54.545 20.15 0.00 38.85 4.63
3903 5595 2.849318 AGGTACTTAGTACTCCCTCCGT 59.151 50.000 20.15 0.00 38.85 4.69
3904 5596 3.118075 AGGTACTTAGTACTCCCTCCGTC 60.118 52.174 20.15 2.66 38.85 4.79
3905 5597 2.433662 ACTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
3906 5598 1.064091 ACTTAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
3907 5599 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3908 5600 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
3909 5601 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3910 5602 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3911 5603 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3912 5604 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3913 5605 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3914 5606 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3915 5607 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3916 5608 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3917 5609 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3918 5610 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3920 5612 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3921 5613 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3922 5614 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3923 5615 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3924 5616 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
3970 5662 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3971 5663 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3972 5664 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3973 5665 3.640029 GTCTTACATTATGGGACGGAGGA 59.360 47.826 0.00 0.00 0.00 3.71
3974 5666 4.100498 GTCTTACATTATGGGACGGAGGAA 59.900 45.833 0.00 0.00 0.00 3.36
3975 5667 4.344102 TCTTACATTATGGGACGGAGGAAG 59.656 45.833 0.00 0.00 0.00 3.46
3976 5668 2.478292 ACATTATGGGACGGAGGAAGT 58.522 47.619 0.00 0.00 0.00 3.01
3977 5669 3.649843 ACATTATGGGACGGAGGAAGTA 58.350 45.455 0.00 0.00 0.00 2.24
3978 5670 3.387050 ACATTATGGGACGGAGGAAGTAC 59.613 47.826 0.00 0.00 0.00 2.73
3979 5671 3.393426 TTATGGGACGGAGGAAGTACT 57.607 47.619 0.00 0.00 0.00 2.73
4182 5877 1.717032 AGAGGCCAACGGATGCTATA 58.283 50.000 5.01 0.00 0.00 1.31
4236 5931 4.771590 TCATCAATTGTTTCAGGCAGAC 57.228 40.909 5.13 0.00 0.00 3.51
4254 5949 2.308570 AGACCAACTTGTCCATGCCATA 59.691 45.455 0.00 0.00 35.83 2.74
4264 5959 2.093973 GTCCATGCCATAGATAGACGGG 60.094 54.545 0.00 0.00 0.00 5.28
4276 5971 0.177141 TAGACGGGTACTGCAATGCC 59.823 55.000 1.53 0.00 39.14 4.40
4346 6041 0.469892 TGCTCCAGTGACTCACCTGA 60.470 55.000 5.51 2.30 34.49 3.86
4411 6106 4.093850 ACGTCAAAACAGAGTACACCAAAC 59.906 41.667 0.00 0.00 0.00 2.93
4476 6174 1.579964 TTGCTTCGTGGCTGCATGAG 61.580 55.000 0.50 0.00 36.55 2.90
4571 6269 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
4572 6270 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
4573 6271 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
4574 6272 9.927081 AGATATAATTTGGTCTCATTCACCTTT 57.073 29.630 0.00 0.00 34.66 3.11
4580 6278 7.391148 TTTGGTCTCATTCACCTTTTATAGC 57.609 36.000 0.00 0.00 34.66 2.97
4581 6279 5.437060 TGGTCTCATTCACCTTTTATAGCC 58.563 41.667 0.00 0.00 34.66 3.93
4582 6280 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
4583 6281 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
4584 6282 6.547510 GGTCTCATTCACCTTTTATAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
4585 6283 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
4586 6284 6.547141 TCTCATTCACCTTTTATAGCCATTGG 59.453 38.462 0.00 0.00 0.00 3.16
4587 6285 6.430864 TCATTCACCTTTTATAGCCATTGGA 58.569 36.000 6.95 0.00 0.00 3.53
4588 6286 7.068702 TCATTCACCTTTTATAGCCATTGGAT 58.931 34.615 6.95 1.78 0.00 3.41
4589 6287 6.713762 TTCACCTTTTATAGCCATTGGATG 57.286 37.500 6.95 0.00 0.00 3.51
4590 6288 5.765510 TCACCTTTTATAGCCATTGGATGT 58.234 37.500 6.95 0.10 0.00 3.06
4591 6289 5.593909 TCACCTTTTATAGCCATTGGATGTG 59.406 40.000 6.95 2.95 0.00 3.21
4592 6290 5.593909 CACCTTTTATAGCCATTGGATGTGA 59.406 40.000 6.95 0.00 0.00 3.58
4593 6291 6.266103 CACCTTTTATAGCCATTGGATGTGAT 59.734 38.462 6.95 0.00 0.00 3.06
4594 6292 6.266103 ACCTTTTATAGCCATTGGATGTGATG 59.734 38.462 6.95 0.00 0.00 3.07
4595 6293 5.710513 TTTATAGCCATTGGATGTGATGC 57.289 39.130 6.95 0.00 0.00 3.91
4596 6294 3.520691 ATAGCCATTGGATGTGATGCT 57.479 42.857 6.95 0.00 0.00 3.79
4597 6295 4.645863 ATAGCCATTGGATGTGATGCTA 57.354 40.909 6.95 0.00 0.00 3.49
4598 6296 3.520691 AGCCATTGGATGTGATGCTAT 57.479 42.857 6.95 0.00 0.00 2.97
4599 6297 4.645863 AGCCATTGGATGTGATGCTATA 57.354 40.909 6.95 0.00 0.00 1.31
4600 6298 4.989277 AGCCATTGGATGTGATGCTATAA 58.011 39.130 6.95 0.00 0.00 0.98
4601 6299 5.008331 AGCCATTGGATGTGATGCTATAAG 58.992 41.667 6.95 0.00 0.00 1.73
4602 6300 5.005740 GCCATTGGATGTGATGCTATAAGA 58.994 41.667 6.95 0.00 0.00 2.10
4603 6301 5.651139 GCCATTGGATGTGATGCTATAAGAT 59.349 40.000 6.95 0.00 0.00 2.40
4604 6302 6.404403 GCCATTGGATGTGATGCTATAAGATG 60.404 42.308 6.95 0.00 0.00 2.90
4605 6303 6.404403 CCATTGGATGTGATGCTATAAGATGC 60.404 42.308 0.00 0.00 0.00 3.91
4606 6304 4.248058 TGGATGTGATGCTATAAGATGCG 58.752 43.478 0.00 0.00 0.00 4.73
4607 6305 4.248859 GGATGTGATGCTATAAGATGCGT 58.751 43.478 0.00 0.00 0.00 5.24
4608 6306 4.092529 GGATGTGATGCTATAAGATGCGTG 59.907 45.833 0.00 0.00 0.00 5.34
4609 6307 4.058721 TGTGATGCTATAAGATGCGTGT 57.941 40.909 0.00 0.00 0.00 4.49
4610 6308 3.803778 TGTGATGCTATAAGATGCGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
4611 6309 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
4612 6310 4.982295 GTGATGCTATAAGATGCGTGTGTA 59.018 41.667 0.00 0.00 0.00 2.90
4613 6311 4.982295 TGATGCTATAAGATGCGTGTGTAC 59.018 41.667 0.00 0.00 0.00 2.90
4614 6312 4.649088 TGCTATAAGATGCGTGTGTACT 57.351 40.909 0.00 0.00 0.00 2.73
4615 6313 4.359706 TGCTATAAGATGCGTGTGTACTG 58.640 43.478 0.00 0.00 0.00 2.74
4616 6314 4.097286 TGCTATAAGATGCGTGTGTACTGA 59.903 41.667 0.00 0.00 0.00 3.41
4617 6315 4.441415 GCTATAAGATGCGTGTGTACTGAC 59.559 45.833 0.00 0.00 0.00 3.51
4618 6316 1.698165 AAGATGCGTGTGTACTGACG 58.302 50.000 11.48 11.48 38.63 4.35
4619 6317 0.596577 AGATGCGTGTGTACTGACGT 59.403 50.000 15.55 0.00 37.89 4.34
4620 6318 0.708370 GATGCGTGTGTACTGACGTG 59.292 55.000 15.55 0.00 37.89 4.49
4621 6319 0.666274 ATGCGTGTGTACTGACGTGG 60.666 55.000 15.55 0.00 37.89 4.94
4622 6320 2.019951 GCGTGTGTACTGACGTGGG 61.020 63.158 15.55 0.00 37.89 4.61
4623 6321 1.361271 CGTGTGTACTGACGTGGGT 59.639 57.895 0.00 0.00 0.00 4.51
4624 6322 0.249155 CGTGTGTACTGACGTGGGTT 60.249 55.000 0.00 0.00 0.00 4.11
4625 6323 1.214367 GTGTGTACTGACGTGGGTTG 58.786 55.000 0.00 0.00 0.00 3.77
4626 6324 0.825410 TGTGTACTGACGTGGGTTGT 59.175 50.000 0.00 0.00 0.00 3.32
4627 6325 2.030371 TGTGTACTGACGTGGGTTGTA 58.970 47.619 0.00 0.00 0.00 2.41
4628 6326 2.629137 TGTGTACTGACGTGGGTTGTAT 59.371 45.455 0.00 0.00 0.00 2.29
4629 6327 3.248266 GTGTACTGACGTGGGTTGTATC 58.752 50.000 0.00 0.00 0.00 2.24
4630 6328 3.057033 GTGTACTGACGTGGGTTGTATCT 60.057 47.826 0.00 0.00 0.00 1.98
4631 6329 2.743636 ACTGACGTGGGTTGTATCTG 57.256 50.000 0.00 0.00 0.00 2.90
4632 6330 1.968493 ACTGACGTGGGTTGTATCTGT 59.032 47.619 0.00 0.00 0.00 3.41
4633 6331 2.367567 ACTGACGTGGGTTGTATCTGTT 59.632 45.455 0.00 0.00 0.00 3.16
4634 6332 3.181458 ACTGACGTGGGTTGTATCTGTTT 60.181 43.478 0.00 0.00 0.00 2.83
4635 6333 3.811083 TGACGTGGGTTGTATCTGTTTT 58.189 40.909 0.00 0.00 0.00 2.43
4636 6334 4.200874 TGACGTGGGTTGTATCTGTTTTT 58.799 39.130 0.00 0.00 0.00 1.94
4637 6335 4.035792 TGACGTGGGTTGTATCTGTTTTTG 59.964 41.667 0.00 0.00 0.00 2.44
4638 6336 3.949113 ACGTGGGTTGTATCTGTTTTTGT 59.051 39.130 0.00 0.00 0.00 2.83
4639 6337 4.399934 ACGTGGGTTGTATCTGTTTTTGTT 59.600 37.500 0.00 0.00 0.00 2.83
4640 6338 5.105675 ACGTGGGTTGTATCTGTTTTTGTTT 60.106 36.000 0.00 0.00 0.00 2.83
4641 6339 5.808030 CGTGGGTTGTATCTGTTTTTGTTTT 59.192 36.000 0.00 0.00 0.00 2.43
4642 6340 6.020201 CGTGGGTTGTATCTGTTTTTGTTTTC 60.020 38.462 0.00 0.00 0.00 2.29
4643 6341 6.814146 GTGGGTTGTATCTGTTTTTGTTTTCA 59.186 34.615 0.00 0.00 0.00 2.69
4644 6342 7.332182 GTGGGTTGTATCTGTTTTTGTTTTCAA 59.668 33.333 0.00 0.00 38.10 2.69
4645 6343 7.547370 TGGGTTGTATCTGTTTTTGTTTTCAAG 59.453 33.333 0.00 0.00 41.09 3.02
4646 6344 7.011016 GGGTTGTATCTGTTTTTGTTTTCAAGG 59.989 37.037 0.00 0.00 41.09 3.61
4647 6345 7.547722 GGTTGTATCTGTTTTTGTTTTCAAGGT 59.452 33.333 0.00 0.00 41.09 3.50
4648 6346 8.379902 GTTGTATCTGTTTTTGTTTTCAAGGTG 58.620 33.333 0.00 0.00 41.09 4.00
4649 6347 7.831753 TGTATCTGTTTTTGTTTTCAAGGTGA 58.168 30.769 0.00 0.00 41.09 4.02
4650 6348 8.307483 TGTATCTGTTTTTGTTTTCAAGGTGAA 58.693 29.630 0.00 0.00 41.09 3.18
4651 6349 9.313118 GTATCTGTTTTTGTTTTCAAGGTGAAT 57.687 29.630 0.00 0.00 41.09 2.57
4652 6350 7.593875 TCTGTTTTTGTTTTCAAGGTGAATG 57.406 32.000 0.00 0.00 41.09 2.67
4653 6351 7.382110 TCTGTTTTTGTTTTCAAGGTGAATGA 58.618 30.769 0.00 0.00 41.09 2.57
4654 6352 7.545265 TCTGTTTTTGTTTTCAAGGTGAATGAG 59.455 33.333 0.00 0.00 41.09 2.90
4655 6353 7.382110 TGTTTTTGTTTTCAAGGTGAATGAGA 58.618 30.769 0.00 0.00 41.09 3.27
4656 6354 7.330700 TGTTTTTGTTTTCAAGGTGAATGAGAC 59.669 33.333 0.00 0.00 41.09 3.36
4657 6355 5.514274 TTGTTTTCAAGGTGAATGAGACC 57.486 39.130 0.00 0.00 36.11 3.85
4658 6356 4.531854 TGTTTTCAAGGTGAATGAGACCA 58.468 39.130 0.00 0.00 36.11 4.02
4659 6357 4.952957 TGTTTTCAAGGTGAATGAGACCAA 59.047 37.500 0.00 0.00 36.11 3.67
4660 6358 5.420421 TGTTTTCAAGGTGAATGAGACCAAA 59.580 36.000 0.00 0.00 36.11 3.28
4661 6359 6.098124 TGTTTTCAAGGTGAATGAGACCAAAT 59.902 34.615 0.00 0.00 36.11 2.32
4662 6360 6.729690 TTTCAAGGTGAATGAGACCAAATT 57.270 33.333 0.00 0.00 36.11 1.82
4663 6361 7.831691 TTTCAAGGTGAATGAGACCAAATTA 57.168 32.000 0.00 0.00 36.11 1.40
4664 6362 8.421249 TTTCAAGGTGAATGAGACCAAATTAT 57.579 30.769 0.00 0.00 36.11 1.28
4665 6363 9.527157 TTTCAAGGTGAATGAGACCAAATTATA 57.473 29.630 0.00 0.00 36.11 0.98
4666 6364 9.699410 TTCAAGGTGAATGAGACCAAATTATAT 57.301 29.630 0.00 0.00 35.76 0.86
4667 6365 9.342308 TCAAGGTGAATGAGACCAAATTATATC 57.658 33.333 0.00 0.00 35.76 1.63
4668 6366 9.347240 CAAGGTGAATGAGACCAAATTATATCT 57.653 33.333 0.00 0.00 35.76 1.98
4669 6367 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
4691 6389 6.798427 TCATCTAAATGAGTTCTAGGCACT 57.202 37.500 0.00 0.00 38.74 4.40
4692 6390 6.810911 TCATCTAAATGAGTTCTAGGCACTC 58.189 40.000 13.40 13.40 37.09 3.51
4693 6391 5.599999 TCTAAATGAGTTCTAGGCACTCC 57.400 43.478 16.20 4.17 40.12 3.85
4694 6392 3.636153 AAATGAGTTCTAGGCACTCCC 57.364 47.619 16.20 0.00 40.12 4.30
4695 6393 9.047928 CATCTAAATGAGTTCTAGGCACTCCCT 62.048 44.444 16.20 5.46 40.12 4.20
4696 6394 3.689872 ATGAGTTCTAGGCACTCCCTA 57.310 47.619 16.20 3.46 44.08 3.53
4697 6395 3.689872 TGAGTTCTAGGCACTCCCTAT 57.310 47.619 16.20 0.00 45.11 2.57
4698 6396 4.808767 TGAGTTCTAGGCACTCCCTATA 57.191 45.455 16.20 0.39 45.11 1.31
4699 6397 5.340891 TGAGTTCTAGGCACTCCCTATAT 57.659 43.478 16.20 0.00 45.11 0.86
4700 6398 5.716979 TGAGTTCTAGGCACTCCCTATATT 58.283 41.667 16.20 0.00 45.11 1.28
4701 6399 6.860034 TGAGTTCTAGGCACTCCCTATATTA 58.140 40.000 16.20 0.00 45.11 0.98
4702 6400 7.479579 TGAGTTCTAGGCACTCCCTATATTAT 58.520 38.462 16.20 0.00 45.11 1.28
4703 6401 7.956315 TGAGTTCTAGGCACTCCCTATATTATT 59.044 37.037 16.20 0.00 45.11 1.40
5101 6799 8.514594 CAAATGAAATAGTGGCTGACTCTTTTA 58.485 33.333 0.00 0.00 32.58 1.52
5152 6850 5.687285 CAGGAGAAAACTTTGGTGATTTTCG 59.313 40.000 0.00 0.00 43.78 3.46
5171 6869 1.225936 CAAGCAACATGAGCGAGCG 60.226 57.895 0.00 0.00 37.01 5.03
5193 6891 2.047274 GCAAGCGCTCCCACTACA 60.047 61.111 12.06 0.00 34.30 2.74
5210 6908 5.809051 CCACTACAGGTTTTACGGACTATTC 59.191 44.000 0.00 0.00 0.00 1.75
5300 7000 2.359900 CACAAACACCTCTATGGGAGC 58.640 52.381 0.00 0.00 40.57 4.70
5316 7016 1.970640 GGAGCCAGTCCAACCATTTTT 59.029 47.619 0.00 0.00 46.10 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.927142 GCAACAACACTTCTACTAGCGAT 59.073 43.478 0.00 0.00 0.00 4.58
37 38 3.470709 CCATTGCCTGTCGTCTATTCAT 58.529 45.455 0.00 0.00 0.00 2.57
38 39 2.419990 CCCATTGCCTGTCGTCTATTCA 60.420 50.000 0.00 0.00 0.00 2.57
59 60 1.425428 CCACATTCGAGCTTTCGCC 59.575 57.895 0.00 0.00 36.60 5.54
62 63 2.151202 TGTTCCCACATTCGAGCTTTC 58.849 47.619 0.00 0.00 0.00 2.62
82 83 4.699522 GAGTTTCCCGCGTGCCCT 62.700 66.667 4.92 0.00 0.00 5.19
87 88 1.674322 CCATTGGAGTTTCCCGCGT 60.674 57.895 4.92 0.00 35.03 6.01
177 180 0.889186 TTCTCTTCCTGCCAAACGCC 60.889 55.000 0.00 0.00 36.24 5.68
243 246 9.905713 TGTTTTATGCTTCTCTTATAGACCAAT 57.094 29.630 0.00 0.00 32.51 3.16
244 247 9.905713 ATGTTTTATGCTTCTCTTATAGACCAA 57.094 29.630 0.00 0.00 32.51 3.67
299 722 2.423892 TGGTTTGAACGCTAAGTTGCAA 59.576 40.909 0.00 0.00 44.35 4.08
300 723 2.017782 TGGTTTGAACGCTAAGTTGCA 58.982 42.857 0.00 0.00 44.35 4.08
433 862 2.485426 CAGCAGAATTGTTCATGGTCGT 59.515 45.455 0.00 0.00 0.00 4.34
434 863 2.485426 ACAGCAGAATTGTTCATGGTCG 59.515 45.455 0.00 0.00 0.00 4.79
435 864 4.697352 ACTACAGCAGAATTGTTCATGGTC 59.303 41.667 0.00 0.00 0.00 4.02
546 975 6.890558 TGATATGCACGTGAAACATATGATG 58.109 36.000 23.39 0.00 37.17 3.07
609 1038 1.951602 TCTATACGTGTGTGGATCCGG 59.048 52.381 7.39 0.00 0.00 5.14
661 1091 6.405538 ACAAATTGAGTTGCTTCCTTGAAAA 58.594 32.000 0.00 0.00 31.29 2.29
811 1254 2.215587 CGTACGTATATATGCGCCATGC 59.784 50.000 21.13 6.71 46.70 4.06
873 1316 6.771749 AGTGCTAGTAGGTATGATCGTTAGTT 59.228 38.462 0.00 0.00 0.00 2.24
934 1385 2.175715 AGCTCTTTTGGGTTTCTGGACT 59.824 45.455 0.00 0.00 0.00 3.85
952 1403 5.884792 AGCTATGAGAATGTTTAAAGCAGCT 59.115 36.000 0.00 0.00 0.00 4.24
953 1404 5.970023 CAGCTATGAGAATGTTTAAAGCAGC 59.030 40.000 0.00 0.00 0.00 5.25
996 1453 0.615331 ACAGAGCAGTACCCATGGTG 59.385 55.000 11.73 3.08 36.19 4.17
999 1456 2.772739 GCACAGAGCAGTACCCATG 58.227 57.895 0.00 0.00 44.79 3.66
1233 1690 0.677288 AATCGACGTCAAGTGGGACA 59.323 50.000 17.16 0.00 37.66 4.02
1291 1748 0.248825 CGCAATCTGAGGACCTCGAG 60.249 60.000 16.81 14.22 32.35 4.04
1405 1874 2.520260 GGATCCACCCAGCATGCC 60.520 66.667 15.66 0.00 31.97 4.40
1507 1982 4.699522 GCCACCTCCCTTCGCGTT 62.700 66.667 5.77 0.00 0.00 4.84
1520 1995 1.374125 GCAAAAATGTCCCCGCCAC 60.374 57.895 0.00 0.00 0.00 5.01
1551 2026 2.281539 TGTTGTCCGACAGGTCTAGA 57.718 50.000 0.64 0.00 39.05 2.43
1554 2029 0.828022 TGTTGTTGTCCGACAGGTCT 59.172 50.000 0.64 0.00 39.05 3.85
1626 2101 1.667154 CGGAGATCGAGTTCCAGGCA 61.667 60.000 15.80 0.00 42.43 4.75
1665 2140 0.108585 TCCTGGAGCAGTTGGTGAAC 59.891 55.000 0.00 0.00 0.00 3.18
2040 2515 1.966451 GGACTTGGAGCCGGTGTTG 60.966 63.158 1.90 0.00 0.00 3.33
2092 2571 4.841861 CGGGATGCCGCCGGTAAA 62.842 66.667 14.38 0.00 0.00 2.01
2273 2752 1.377366 GATGAGGTGCTCGAGTCCGA 61.377 60.000 15.13 9.53 43.35 4.55
2345 2824 3.406764 AGCGCTATCCATTTCAGATTCC 58.593 45.455 8.99 0.00 0.00 3.01
2979 3469 5.427378 TCAATCTCCGACAATGATAGCAAA 58.573 37.500 0.00 0.00 0.00 3.68
3028 3518 1.279271 GGATCCCATCTCCGGTATTGG 59.721 57.143 0.00 6.84 0.00 3.16
3532 5224 5.924356 ACATGTGGTGATTATCCGTATCAA 58.076 37.500 0.00 0.00 34.06 2.57
3672 5364 3.181507 CCATTGACACCTCAAGCATAACG 60.182 47.826 0.00 0.00 39.83 3.18
3723 5415 0.179215 CGCAGTGCAAGACGATTTCC 60.179 55.000 16.83 0.00 0.00 3.13
3896 5588 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3897 5589 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3898 5590 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3899 5591 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3945 5637 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
3946 5638 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3947 5639 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3948 5640 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3949 5641 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3951 5643 3.640029 TCCTCCGTCCCATAATGTAAGAC 59.360 47.826 0.00 0.00 0.00 3.01
3952 5644 3.918566 TCCTCCGTCCCATAATGTAAGA 58.081 45.455 0.00 0.00 0.00 2.10
3953 5645 4.101119 ACTTCCTCCGTCCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
3954 5646 4.035112 ACTTCCTCCGTCCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
3955 5647 3.649843 ACTTCCTCCGTCCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
3956 5648 2.478292 ACTTCCTCCGTCCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
3957 5649 3.641906 AGTACTTCCTCCGTCCCATAATG 59.358 47.826 0.00 0.00 0.00 1.90
3958 5650 3.924922 AGTACTTCCTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
3959 5651 3.393426 AGTACTTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
3960 5652 3.393426 AAGTACTTCCTCCGTCCCATA 57.607 47.619 1.12 0.00 0.00 2.74
3961 5653 2.249309 AAGTACTTCCTCCGTCCCAT 57.751 50.000 1.12 0.00 0.00 4.00
3962 5654 2.905415 TAAGTACTTCCTCCGTCCCA 57.095 50.000 12.39 0.00 0.00 4.37
3963 5655 5.774184 AGATAATAAGTACTTCCTCCGTCCC 59.226 44.000 12.39 0.00 0.00 4.46
3964 5656 6.897706 AGATAATAAGTACTTCCTCCGTCC 57.102 41.667 12.39 0.00 0.00 4.79
3965 5657 6.641723 GCAAGATAATAAGTACTTCCTCCGTC 59.358 42.308 12.39 4.69 0.00 4.79
3966 5658 6.324254 AGCAAGATAATAAGTACTTCCTCCGT 59.676 38.462 12.39 0.00 0.00 4.69
3967 5659 6.750148 AGCAAGATAATAAGTACTTCCTCCG 58.250 40.000 12.39 1.47 0.00 4.63
3968 5660 7.727181 TGAGCAAGATAATAAGTACTTCCTCC 58.273 38.462 12.39 0.00 29.33 4.30
3969 5661 9.771534 ATTGAGCAAGATAATAAGTACTTCCTC 57.228 33.333 12.39 5.11 30.61 3.71
3970 5662 9.553064 CATTGAGCAAGATAATAAGTACTTCCT 57.447 33.333 12.39 2.95 0.00 3.36
3971 5663 9.331282 ACATTGAGCAAGATAATAAGTACTTCC 57.669 33.333 12.39 0.00 0.00 3.46
4037 5732 7.981225 GGATAAATGCACATTCCAACATAAGTT 59.019 33.333 0.00 0.00 38.88 2.66
4098 5793 2.210116 TCGCTCTTTCGTGAAGCTTTT 58.790 42.857 0.00 0.00 35.24 2.27
4182 5877 3.515602 AGGCTCAGTTCTCCAACAAAT 57.484 42.857 0.00 0.00 34.60 2.32
4236 5931 3.003394 TCTATGGCATGGACAAGTTGG 57.997 47.619 9.71 0.00 0.00 3.77
4254 5949 2.224066 GCATTGCAGTACCCGTCTATCT 60.224 50.000 3.15 0.00 0.00 1.98
4264 5959 2.159338 CCATGTCAAGGCATTGCAGTAC 60.159 50.000 11.39 0.00 36.30 2.73
4276 5971 6.072286 ACAAGAAAGCTAATGTCCATGTCAAG 60.072 38.462 0.00 0.00 0.00 3.02
4346 6041 7.710676 ACATCGCTCATAGTTATCCTATCTT 57.289 36.000 0.00 0.00 33.96 2.40
4411 6106 9.561270 CACACTTCCTAATGTAGACGATATATG 57.439 37.037 0.00 0.00 0.00 1.78
4476 6174 5.494632 TTTTCTTTCTCCGAAACAGTTCC 57.505 39.130 0.00 0.00 30.72 3.62
4547 6245 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
4548 6246 9.927081 AAAGGTGAATGAGACCAAATTATATCT 57.073 29.630 0.00 0.00 35.76 1.98
4554 6252 8.470002 GCTATAAAAGGTGAATGAGACCAAATT 58.530 33.333 0.00 0.00 35.76 1.82
4555 6253 7.068716 GGCTATAAAAGGTGAATGAGACCAAAT 59.931 37.037 0.00 0.00 35.76 2.32
4556 6254 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
4557 6255 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
4558 6256 5.045213 TGGCTATAAAAGGTGAATGAGACCA 60.045 40.000 0.00 0.00 35.76 4.02
4559 6257 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
4560 6258 7.420800 CAATGGCTATAAAAGGTGAATGAGAC 58.579 38.462 0.00 0.00 0.00 3.36
4561 6259 6.547141 CCAATGGCTATAAAAGGTGAATGAGA 59.453 38.462 0.00 0.00 0.00 3.27
4562 6260 6.547141 TCCAATGGCTATAAAAGGTGAATGAG 59.453 38.462 0.00 0.00 0.00 2.90
4563 6261 6.430864 TCCAATGGCTATAAAAGGTGAATGA 58.569 36.000 0.00 0.00 0.00 2.57
4564 6262 6.713762 TCCAATGGCTATAAAAGGTGAATG 57.286 37.500 0.00 0.00 0.00 2.67
4565 6263 6.840705 ACATCCAATGGCTATAAAAGGTGAAT 59.159 34.615 0.00 0.00 33.60 2.57
4566 6264 6.096705 CACATCCAATGGCTATAAAAGGTGAA 59.903 38.462 0.00 0.00 33.60 3.18
4567 6265 5.593909 CACATCCAATGGCTATAAAAGGTGA 59.406 40.000 0.00 0.00 33.60 4.02
4568 6266 5.593909 TCACATCCAATGGCTATAAAAGGTG 59.406 40.000 0.00 0.00 33.60 4.00
4569 6267 5.765510 TCACATCCAATGGCTATAAAAGGT 58.234 37.500 0.00 0.00 33.60 3.50
4570 6268 6.684686 CATCACATCCAATGGCTATAAAAGG 58.315 40.000 0.00 0.00 33.60 3.11
4571 6269 6.015688 AGCATCACATCCAATGGCTATAAAAG 60.016 38.462 0.00 0.00 33.60 2.27
4572 6270 5.834742 AGCATCACATCCAATGGCTATAAAA 59.165 36.000 0.00 0.00 33.60 1.52
4573 6271 5.387788 AGCATCACATCCAATGGCTATAAA 58.612 37.500 0.00 0.00 33.60 1.40
4574 6272 4.989277 AGCATCACATCCAATGGCTATAA 58.011 39.130 0.00 0.00 33.60 0.98
4575 6273 4.645863 AGCATCACATCCAATGGCTATA 57.354 40.909 0.00 0.00 33.60 1.31
4576 6274 3.520691 AGCATCACATCCAATGGCTAT 57.479 42.857 0.00 0.00 33.60 2.97
4577 6275 4.645863 ATAGCATCACATCCAATGGCTA 57.354 40.909 0.00 0.00 33.60 3.93
4578 6276 3.520691 ATAGCATCACATCCAATGGCT 57.479 42.857 0.00 0.00 33.60 4.75
4579 6277 5.005740 TCTTATAGCATCACATCCAATGGC 58.994 41.667 0.00 0.00 33.60 4.40
4580 6278 6.404403 GCATCTTATAGCATCACATCCAATGG 60.404 42.308 0.00 0.00 33.60 3.16
4581 6279 6.552629 GCATCTTATAGCATCACATCCAATG 58.447 40.000 0.00 0.00 0.00 2.82
4582 6280 5.353400 CGCATCTTATAGCATCACATCCAAT 59.647 40.000 0.00 0.00 0.00 3.16
4583 6281 4.692155 CGCATCTTATAGCATCACATCCAA 59.308 41.667 0.00 0.00 0.00 3.53
4584 6282 4.248058 CGCATCTTATAGCATCACATCCA 58.752 43.478 0.00 0.00 0.00 3.41
4585 6283 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
4586 6284 4.687948 ACACGCATCTTATAGCATCACATC 59.312 41.667 0.00 0.00 0.00 3.06
4587 6285 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
4588 6286 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
4589 6287 3.804325 ACACACGCATCTTATAGCATCAC 59.196 43.478 0.00 0.00 0.00 3.06
4590 6288 4.058721 ACACACGCATCTTATAGCATCA 57.941 40.909 0.00 0.00 0.00 3.07
4591 6289 5.117745 CAGTACACACGCATCTTATAGCATC 59.882 44.000 0.00 0.00 0.00 3.91
4592 6290 4.984785 CAGTACACACGCATCTTATAGCAT 59.015 41.667 0.00 0.00 0.00 3.79
4593 6291 4.097286 TCAGTACACACGCATCTTATAGCA 59.903 41.667 0.00 0.00 0.00 3.49
4594 6292 4.441415 GTCAGTACACACGCATCTTATAGC 59.559 45.833 0.00 0.00 0.00 2.97
4595 6293 4.671068 CGTCAGTACACACGCATCTTATAG 59.329 45.833 3.95 0.00 0.00 1.31
4596 6294 4.095334 ACGTCAGTACACACGCATCTTATA 59.905 41.667 14.55 0.00 39.73 0.98
4597 6295 3.119602 ACGTCAGTACACACGCATCTTAT 60.120 43.478 14.55 0.00 39.73 1.73
4598 6296 2.227149 ACGTCAGTACACACGCATCTTA 59.773 45.455 14.55 0.00 39.73 2.10
4599 6297 1.000607 ACGTCAGTACACACGCATCTT 60.001 47.619 14.55 0.00 39.73 2.40
4600 6298 0.596577 ACGTCAGTACACACGCATCT 59.403 50.000 14.55 0.00 39.73 2.90
4601 6299 0.708370 CACGTCAGTACACACGCATC 59.292 55.000 14.55 0.00 39.73 3.91
4602 6300 0.666274 CCACGTCAGTACACACGCAT 60.666 55.000 14.55 0.00 39.73 4.73
4603 6301 1.299544 CCACGTCAGTACACACGCA 60.300 57.895 14.55 0.00 39.73 5.24
4604 6302 2.019951 CCCACGTCAGTACACACGC 61.020 63.158 14.55 0.00 39.73 5.34
4605 6303 0.249155 AACCCACGTCAGTACACACG 60.249 55.000 13.39 13.39 41.90 4.49
4606 6304 1.214367 CAACCCACGTCAGTACACAC 58.786 55.000 0.00 0.00 0.00 3.82
4607 6305 0.825410 ACAACCCACGTCAGTACACA 59.175 50.000 0.00 0.00 0.00 3.72
4608 6306 2.798976 TACAACCCACGTCAGTACAC 57.201 50.000 0.00 0.00 0.00 2.90
4609 6307 3.057104 CAGATACAACCCACGTCAGTACA 60.057 47.826 0.00 0.00 0.00 2.90
4610 6308 3.057033 ACAGATACAACCCACGTCAGTAC 60.057 47.826 0.00 0.00 0.00 2.73
4611 6309 3.159472 ACAGATACAACCCACGTCAGTA 58.841 45.455 0.00 0.00 0.00 2.74
4612 6310 1.968493 ACAGATACAACCCACGTCAGT 59.032 47.619 0.00 0.00 0.00 3.41
4613 6311 2.743636 ACAGATACAACCCACGTCAG 57.256 50.000 0.00 0.00 0.00 3.51
4614 6312 3.478857 AAACAGATACAACCCACGTCA 57.521 42.857 0.00 0.00 0.00 4.35
4615 6313 4.035909 ACAAAAACAGATACAACCCACGTC 59.964 41.667 0.00 0.00 0.00 4.34
4616 6314 3.949113 ACAAAAACAGATACAACCCACGT 59.051 39.130 0.00 0.00 0.00 4.49
4617 6315 4.561735 ACAAAAACAGATACAACCCACG 57.438 40.909 0.00 0.00 0.00 4.94
4618 6316 6.814146 TGAAAACAAAAACAGATACAACCCAC 59.186 34.615 0.00 0.00 0.00 4.61
4619 6317 6.936279 TGAAAACAAAAACAGATACAACCCA 58.064 32.000 0.00 0.00 0.00 4.51
4620 6318 7.011016 CCTTGAAAACAAAAACAGATACAACCC 59.989 37.037 0.00 0.00 0.00 4.11
4621 6319 7.547722 ACCTTGAAAACAAAAACAGATACAACC 59.452 33.333 0.00 0.00 0.00 3.77
4622 6320 8.379902 CACCTTGAAAACAAAAACAGATACAAC 58.620 33.333 0.00 0.00 0.00 3.32
4623 6321 8.307483 TCACCTTGAAAACAAAAACAGATACAA 58.693 29.630 0.00 0.00 0.00 2.41
4624 6322 7.831753 TCACCTTGAAAACAAAAACAGATACA 58.168 30.769 0.00 0.00 0.00 2.29
4625 6323 8.696410 TTCACCTTGAAAACAAAAACAGATAC 57.304 30.769 0.00 0.00 32.71 2.24
4626 6324 9.311916 CATTCACCTTGAAAACAAAAACAGATA 57.688 29.630 0.00 0.00 40.12 1.98
4627 6325 8.040132 TCATTCACCTTGAAAACAAAAACAGAT 58.960 29.630 0.00 0.00 40.12 2.90
4628 6326 7.382110 TCATTCACCTTGAAAACAAAAACAGA 58.618 30.769 0.00 0.00 40.12 3.41
4629 6327 7.545265 TCTCATTCACCTTGAAAACAAAAACAG 59.455 33.333 0.00 0.00 40.12 3.16
4630 6328 7.330700 GTCTCATTCACCTTGAAAACAAAAACA 59.669 33.333 0.00 0.00 40.12 2.83
4631 6329 7.201522 GGTCTCATTCACCTTGAAAACAAAAAC 60.202 37.037 0.00 0.00 40.12 2.43
4632 6330 6.816140 GGTCTCATTCACCTTGAAAACAAAAA 59.184 34.615 0.00 0.00 40.12 1.94
4633 6331 6.071108 TGGTCTCATTCACCTTGAAAACAAAA 60.071 34.615 0.00 0.00 40.12 2.44
4634 6332 5.420421 TGGTCTCATTCACCTTGAAAACAAA 59.580 36.000 0.00 0.00 40.12 2.83
4635 6333 4.952957 TGGTCTCATTCACCTTGAAAACAA 59.047 37.500 0.00 0.00 40.12 2.83
4636 6334 4.531854 TGGTCTCATTCACCTTGAAAACA 58.468 39.130 0.00 0.00 40.12 2.83
4637 6335 5.514274 TTGGTCTCATTCACCTTGAAAAC 57.486 39.130 0.00 0.00 40.12 2.43
4638 6336 6.729690 ATTTGGTCTCATTCACCTTGAAAA 57.270 33.333 0.00 0.00 40.12 2.29
4639 6337 6.729690 AATTTGGTCTCATTCACCTTGAAA 57.270 33.333 0.00 0.00 40.12 2.69
4640 6338 9.699410 ATATAATTTGGTCTCATTCACCTTGAA 57.301 29.630 0.00 0.00 41.09 2.69
4641 6339 9.342308 GATATAATTTGGTCTCATTCACCTTGA 57.658 33.333 0.00 0.00 34.66 3.02
4642 6340 9.347240 AGATATAATTTGGTCTCATTCACCTTG 57.653 33.333 0.00 0.00 34.66 3.61
4643 6341 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
4644 6342 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
4645 6343 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
4668 6366 6.183360 GGAGTGCCTAGAACTCATTTAGATGA 60.183 42.308 20.54 0.00 44.86 2.92
4669 6367 5.988561 GGAGTGCCTAGAACTCATTTAGATG 59.011 44.000 20.54 0.00 44.86 2.90
4670 6368 5.071115 GGGAGTGCCTAGAACTCATTTAGAT 59.929 44.000 20.54 0.00 44.86 1.98
4671 6369 4.406003 GGGAGTGCCTAGAACTCATTTAGA 59.594 45.833 20.54 0.00 44.86 2.10
4672 6370 4.407296 AGGGAGTGCCTAGAACTCATTTAG 59.593 45.833 20.54 0.00 44.86 1.85
4673 6371 4.362677 AGGGAGTGCCTAGAACTCATTTA 58.637 43.478 20.54 0.00 44.86 1.40
4674 6372 3.185455 AGGGAGTGCCTAGAACTCATTT 58.815 45.455 20.54 8.10 44.86 2.32
4675 6373 2.839228 AGGGAGTGCCTAGAACTCATT 58.161 47.619 20.54 9.88 44.86 2.57
4676 6374 2.559381 AGGGAGTGCCTAGAACTCAT 57.441 50.000 20.54 10.40 44.86 2.90
4677 6375 3.689872 ATAGGGAGTGCCTAGAACTCA 57.310 47.619 16.26 7.02 44.86 3.41
4678 6376 7.964666 ATAATATAGGGAGTGCCTAGAACTC 57.035 40.000 16.26 14.10 42.79 3.01
4679 6377 8.598041 CAAATAATATAGGGAGTGCCTAGAACT 58.402 37.037 16.26 6.12 0.00 3.01
4680 6378 7.824779 CCAAATAATATAGGGAGTGCCTAGAAC 59.175 40.741 16.26 0.00 0.00 3.01
4681 6379 7.737607 TCCAAATAATATAGGGAGTGCCTAGAA 59.262 37.037 16.26 7.23 0.00 2.10
4682 6380 7.253421 TCCAAATAATATAGGGAGTGCCTAGA 58.747 38.462 16.26 12.11 0.00 2.43
4683 6381 7.400339 TCTCCAAATAATATAGGGAGTGCCTAG 59.600 40.741 16.26 0.00 44.33 3.02
4684 6382 7.253421 TCTCCAAATAATATAGGGAGTGCCTA 58.747 38.462 13.42 13.42 44.33 3.93
4685 6383 6.091555 TCTCCAAATAATATAGGGAGTGCCT 58.908 40.000 8.78 8.78 44.33 4.75
4686 6384 6.374417 TCTCCAAATAATATAGGGAGTGCC 57.626 41.667 15.41 0.00 44.33 5.01
4687 6385 7.454225 AGTTCTCCAAATAATATAGGGAGTGC 58.546 38.462 15.41 11.20 44.33 4.40
4689 6387 9.900112 ACTAGTTCTCCAAATAATATAGGGAGT 57.100 33.333 15.41 4.52 44.33 3.85
4692 6390 9.726438 CCAACTAGTTCTCCAAATAATATAGGG 57.274 37.037 4.77 0.00 0.00 3.53
4693 6391 9.220767 GCCAACTAGTTCTCCAAATAATATAGG 57.779 37.037 4.77 0.00 0.00 2.57
4694 6392 8.926710 CGCCAACTAGTTCTCCAAATAATATAG 58.073 37.037 4.77 0.00 0.00 1.31
4695 6393 8.426489 ACGCCAACTAGTTCTCCAAATAATATA 58.574 33.333 4.77 0.00 0.00 0.86
4696 6394 7.280356 ACGCCAACTAGTTCTCCAAATAATAT 58.720 34.615 4.77 0.00 0.00 1.28
4697 6395 6.646267 ACGCCAACTAGTTCTCCAAATAATA 58.354 36.000 4.77 0.00 0.00 0.98
4698 6396 5.497474 ACGCCAACTAGTTCTCCAAATAAT 58.503 37.500 4.77 0.00 0.00 1.28
4699 6397 4.901868 ACGCCAACTAGTTCTCCAAATAA 58.098 39.130 4.77 0.00 0.00 1.40
4700 6398 4.546829 ACGCCAACTAGTTCTCCAAATA 57.453 40.909 4.77 0.00 0.00 1.40
4701 6399 3.418684 ACGCCAACTAGTTCTCCAAAT 57.581 42.857 4.77 0.00 0.00 2.32
4702 6400 2.922740 ACGCCAACTAGTTCTCCAAA 57.077 45.000 4.77 0.00 0.00 3.28
4703 6401 2.922740 AACGCCAACTAGTTCTCCAA 57.077 45.000 4.77 0.00 0.00 3.53
5125 6823 3.202906 TCACCAAAGTTTTCTCCTGACG 58.797 45.455 0.00 0.00 0.00 4.35
5152 6850 1.513586 GCTCGCTCATGTTGCTTGC 60.514 57.895 10.58 10.12 0.00 4.01
5193 6891 3.428045 CCGACGAATAGTCCGTAAAACCT 60.428 47.826 0.00 0.00 46.92 3.50
5210 6908 2.065993 ATTCATCGCCTTATCCGACG 57.934 50.000 0.00 0.00 37.56 5.12
5254 6952 1.131883 GCACTCAGCATTTCTCGCAAT 59.868 47.619 0.00 0.00 44.79 3.56
5256 6954 2.165380 GCACTCAGCATTTCTCGCA 58.835 52.632 0.00 0.00 44.79 5.10
5276 6976 1.086696 CATAGAGGTGTTTGTGGGCG 58.913 55.000 0.00 0.00 0.00 6.13
5298 6998 1.970640 GGAAAAATGGTTGGACTGGCT 59.029 47.619 0.00 0.00 0.00 4.75
5300 7000 2.965147 ACTGGAAAAATGGTTGGACTGG 59.035 45.455 0.00 0.00 0.00 4.00
5310 7010 9.981114 AGAACCATTAGTAAAACTGGAAAAATG 57.019 29.630 7.82 0.00 32.92 2.32
5316 7016 7.801893 TCCTAGAACCATTAGTAAAACTGGA 57.198 36.000 7.82 0.00 32.92 3.86


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

AutoCloner maintained by Alex Coulton.