Multiple sequence alignment - TraesCS5D01G116600

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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 TraesCS5D01G116600 chr5D 100.000 4822 0 0 1 4822 136942950 136947771 0.000000e+00 8905.0
1 TraesCS5D01G116600 chr5D 85.407 418 58 3 3166 3580 42011143 42011560 9.590000e-117 431.0
2 TraesCS5D01G116600 chr5D 88.412 233 18 3 3601 3824 42055990 42055758 6.150000e-69 272.0
3 TraesCS5D01G116600 chr5D 75.943 636 91 33 2419 3036 42010465 42011056 2.210000e-68 270.0
4 TraesCS5D01G116600 chr5D 90.955 199 13 2 3630 3824 42011778 42011975 3.700000e-66 263.0
5 TraesCS5D01G116600 chr5D 83.270 263 32 7 1735 1986 42009843 42010104 1.040000e-56 231.0
6 TraesCS5D01G116600 chr5D 82.873 181 22 7 2863 3036 42056867 42056689 2.320000e-33 154.0
7 TraesCS5D01G116600 chr5A 95.188 4385 157 24 1 4382 168239917 168235584 0.000000e+00 6879.0
8 TraesCS5D01G116600 chr5A 82.158 723 100 15 2863 3580 168130162 168129464 1.160000e-165 593.0
9 TraesCS5D01G116600 chr5A 86.905 420 50 5 3166 3580 30400927 30401346 2.630000e-127 466.0
10 TraesCS5D01G116600 chr5A 94.845 194 9 1 4376 4568 168208893 168208700 7.840000e-78 302.0
11 TraesCS5D01G116600 chr5A 84.190 253 38 2 2424 2675 168130586 168130335 1.340000e-60 244.0
12 TraesCS5D01G116600 chr5A 90.909 176 14 1 1735 1910 30400051 30400224 8.070000e-58 235.0
13 TraesCS5D01G116600 chr5A 85.321 218 20 3 2458 2675 30400356 30400561 1.050000e-51 215.0
14 TraesCS5D01G116600 chr5B 95.592 2904 105 15 229 3130 185506589 185509471 0.000000e+00 4632.0
15 TraesCS5D01G116600 chr5B 94.863 1129 36 11 3117 4238 185510761 185511874 0.000000e+00 1744.0
16 TraesCS5D01G116600 chr5B 86.747 415 54 1 3163 3577 185535144 185535557 1.220000e-125 460.0
17 TraesCS5D01G116600 chr5B 87.277 393 49 1 3188 3580 36695535 36695926 9.520000e-122 448.0
18 TraesCS5D01G116600 chr5B 87.147 389 50 0 3192 3580 36775292 36774904 4.430000e-120 442.0
19 TraesCS5D01G116600 chr5B 91.159 328 25 3 4239 4565 185511954 185512278 4.430000e-120 442.0
20 TraesCS5D01G116600 chr5B 82.184 522 70 15 1432 1938 36776547 36776034 1.240000e-115 427.0
21 TraesCS5D01G116600 chr5B 82.184 522 70 15 1432 1938 36817577 36817064 1.240000e-115 427.0
22 TraesCS5D01G116600 chr5B 79.173 677 93 33 1392 2033 185523948 185524611 4.460000e-115 425.0
23 TraesCS5D01G116600 chr5B 90.308 227 22 0 3598 3824 185535723 185535949 1.010000e-76 298.0
24 TraesCS5D01G116600 chr5B 88.608 237 23 3 2430 2666 36775989 36775757 7.900000e-73 285.0
25 TraesCS5D01G116600 chr5B 88.608 237 23 3 2430 2666 36817019 36816787 7.900000e-73 285.0
26 TraesCS5D01G116600 chr5B 88.584 219 21 2 2462 2680 36694902 36695116 3.700000e-66 263.0
27 TraesCS5D01G116600 chr5B 90.452 199 14 2 3630 3824 36696149 36696346 1.720000e-64 257.0
28 TraesCS5D01G116600 chr5B 90.452 199 14 2 3630 3824 36815896 36815699 1.720000e-64 257.0
29 TraesCS5D01G116600 chr5B 90.805 174 16 0 1737 1910 36694380 36694553 2.900000e-57 233.0
30 TraesCS5D01G116600 chr5B 95.413 109 3 2 65 172 185506182 185506289 6.420000e-39 172.0
31 TraesCS5D01G116600 chr5B 85.625 160 23 0 2516 2675 185534557 185534716 8.300000e-38 169.0
32 TraesCS5D01G116600 chr5B 86.275 102 12 2 2936 3036 36775510 36775410 5.100000e-20 110.0
33 TraesCS5D01G116600 chr5B 87.912 91 10 1 2439 2529 185524891 185524980 6.600000e-19 106.0
34 TraesCS5D01G116600 chr5B 100.000 32 0 0 1 32 185506137 185506168 5.210000e-05 60.2
35 TraesCS5D01G116600 chrUn 87.147 389 50 0 3192 3580 65844322 65844710 4.430000e-120 442.0
36 TraesCS5D01G116600 chrUn 82.184 522 70 15 1432 1938 65843175 65843688 1.240000e-115 427.0
37 TraesCS5D01G116600 chrUn 88.211 246 25 2 2430 2675 65843733 65843974 1.700000e-74 291.0
38 TraesCS5D01G116600 chrUn 90.452 199 14 2 3630 3824 340277500 340277697 1.720000e-64 257.0
39 TraesCS5D01G116600 chrUn 90.452 199 14 2 3630 3824 340336028 340336225 1.720000e-64 257.0
40 TraesCS5D01G116600 chrUn 86.275 102 12 2 2936 3036 65844104 65844204 5.100000e-20 110.0
41 TraesCS5D01G116600 chr7D 93.774 257 16 0 4566 4822 20572728 20572984 2.100000e-103 387.0
42 TraesCS5D01G116600 chr1B 92.996 257 18 0 4566 4822 268517048 268517304 4.560000e-100 375.0
43 TraesCS5D01G116600 chr1B 91.051 257 21 1 4566 4822 268539811 268540065 3.570000e-91 346.0
44 TraesCS5D01G116600 chr2D 92.218 257 19 1 4566 4822 174329541 174329796 3.550000e-96 363.0
45 TraesCS5D01G116600 chr2D 91.829 257 20 1 4566 4822 32144932 32144677 1.650000e-94 357.0
46 TraesCS5D01G116600 chr2D 79.902 204 30 6 4376 4568 98712926 98713129 6.510000e-29 139.0
47 TraesCS5D01G116600 chr6D 87.266 267 30 4 4560 4822 7249088 7249354 7.840000e-78 302.0
48 TraesCS5D01G116600 chr6B 85.874 269 34 4 4555 4820 130568272 130568005 2.840000e-72 283.0
49 TraesCS5D01G116600 chr1D 86.381 257 34 1 4565 4820 467631008 467630752 3.670000e-71 279.0
50 TraesCS5D01G116600 chr2B 85.714 259 36 1 4565 4822 790725853 790725595 6.150000e-69 272.0
51 TraesCS5D01G116600 chr7B 80.571 175 30 4 1464 1636 647752213 647752385 1.090000e-26 132.0
52 TraesCS5D01G116600 chr6A 95.714 70 3 0 1395 1464 111403088 111403019 3.940000e-21 113.0
53 TraesCS5D01G116600 chr6A 100.000 33 0 0 1024 1056 111403117 111403085 1.450000e-05 62.1


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 TraesCS5D01G116600 chr5D 136942950 136947771 4821 False 8905.000000 8905 100.000000 1 4822 1 chr5D.!!$F1 4821
1 TraesCS5D01G116600 chr5D 42009843 42011975 2132 False 298.750000 431 83.893750 1735 3824 4 chr5D.!!$F2 2089
2 TraesCS5D01G116600 chr5D 42055758 42056867 1109 True 213.000000 272 85.642500 2863 3824 2 chr5D.!!$R1 961
3 TraesCS5D01G116600 chr5A 168235584 168239917 4333 True 6879.000000 6879 95.188000 1 4382 1 chr5A.!!$R2 4381
4 TraesCS5D01G116600 chr5A 168129464 168130586 1122 True 418.500000 593 83.174000 2424 3580 2 chr5A.!!$R3 1156
5 TraesCS5D01G116600 chr5A 30400051 30401346 1295 False 305.333333 466 87.711667 1735 3580 3 chr5A.!!$F1 1845
6 TraesCS5D01G116600 chr5B 185506137 185512278 6141 False 1410.040000 4632 95.405400 1 4565 5 chr5B.!!$F2 4564
7 TraesCS5D01G116600 chr5B 36815699 36817577 1878 True 323.000000 427 87.081333 1432 3824 3 chr5B.!!$R2 2392
8 TraesCS5D01G116600 chr5B 36774904 36776547 1643 True 316.000000 442 86.053500 1432 3580 4 chr5B.!!$R1 2148
9 TraesCS5D01G116600 chr5B 185534557 185535949 1392 False 309.000000 460 87.560000 2516 3824 3 chr5B.!!$F4 1308
10 TraesCS5D01G116600 chr5B 36694380 36696346 1966 False 300.250000 448 89.279500 1737 3824 4 chr5B.!!$F1 2087
11 TraesCS5D01G116600 chr5B 185523948 185524980 1032 False 265.500000 425 83.542500 1392 2529 2 chr5B.!!$F3 1137
12 TraesCS5D01G116600 chrUn 65843175 65844710 1535 False 317.500000 442 85.954250 1432 3580 4 chrUn.!!$F3 2148

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
191 192 1.002430 ACCGCTGATCTGAACACACAT 59.998 47.619 3.42 0.00 0.00 3.21 F
449 693 1.063174 GATCCATGTGAGCTCAAACGC 59.937 52.381 20.19 6.54 0.00 4.84 F
1407 1651 0.550914 TCTTGCAGGTGGTTGAAGGT 59.449 50.000 0.00 0.00 0.00 3.50 F
1408 1652 1.064017 TCTTGCAGGTGGTTGAAGGTT 60.064 47.619 0.00 0.00 0.00 3.50 F
2423 2807 2.421314 GGCAAATTATGGGCCGCC 59.579 61.111 0.00 0.00 38.04 6.13 F
3513 5317 1.512156 GCTTCCTTTGCGGTTTCGGA 61.512 55.000 0.00 0.00 36.79 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1652 0.700564 AGCAAGGAATTCAGCAGGGA 59.299 50.000 15.96 0.0 0.00 4.20 R
1668 1915 2.042464 ACCTGACTGAGCTGAGTGAAA 58.958 47.619 11.70 0.0 0.00 2.69 R
2721 3117 0.184211 ACCCCAAAAGCACCTAACGT 59.816 50.000 0.00 0.0 0.00 3.99 R
2722 3118 0.879090 GACCCCAAAAGCACCTAACG 59.121 55.000 0.00 0.0 0.00 3.18 R
3773 5800 0.723414 CCATGAGTGTTGCTACAGCG 59.277 55.000 0.00 0.0 45.83 5.18 R
4653 6767 0.178068 GGACGTCACATAGTGGGCAT 59.822 55.000 18.91 0.0 33.87 4.40 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
69 70 1.436600 CACAGCTGTGCTCCTACTTG 58.563 55.000 32.39 6.58 36.40 3.16
140 141 7.053316 TCAGCTCAGGTAGTAGTAGTAGTAG 57.947 44.000 0.00 0.00 0.00 2.57
191 192 1.002430 ACCGCTGATCTGAACACACAT 59.998 47.619 3.42 0.00 0.00 3.21
192 193 2.233676 ACCGCTGATCTGAACACACATA 59.766 45.455 3.42 0.00 0.00 2.29
193 194 3.118629 ACCGCTGATCTGAACACACATAT 60.119 43.478 3.42 0.00 0.00 1.78
220 221 7.904558 ATATATCAAGACAGAGAGGACACAA 57.095 36.000 0.00 0.00 0.00 3.33
222 223 4.263018 TCAAGACAGAGAGGACACAATG 57.737 45.455 0.00 0.00 0.00 2.82
403 647 5.417266 TGTTGTGTGGTTCTCTTCATTTTGA 59.583 36.000 0.00 0.00 0.00 2.69
448 692 1.667724 GGATCCATGTGAGCTCAAACG 59.332 52.381 20.19 5.22 0.00 3.60
449 693 1.063174 GATCCATGTGAGCTCAAACGC 59.937 52.381 20.19 6.54 0.00 4.84
479 723 3.675698 GTCTCACTTTTCTCCATCGTGTC 59.324 47.826 0.00 0.00 0.00 3.67
496 740 7.011389 CCATCGTGTCTCTGAAGCAATAAATAA 59.989 37.037 0.00 0.00 0.00 1.40
497 741 7.525688 TCGTGTCTCTGAAGCAATAAATAAG 57.474 36.000 0.00 0.00 0.00 1.73
522 766 4.543590 ACAGAGTTCATACTTGTGGGAG 57.456 45.455 0.00 0.00 33.84 4.30
523 767 4.160329 ACAGAGTTCATACTTGTGGGAGA 58.840 43.478 0.00 0.00 33.84 3.71
524 768 4.593206 ACAGAGTTCATACTTGTGGGAGAA 59.407 41.667 0.00 0.00 33.84 2.87
525 769 5.071788 ACAGAGTTCATACTTGTGGGAGAAA 59.928 40.000 0.00 0.00 33.84 2.52
526 770 5.641209 CAGAGTTCATACTTGTGGGAGAAAG 59.359 44.000 0.00 0.00 33.84 2.62
530 774 6.486993 AGTTCATACTTGTGGGAGAAAGAAAC 59.513 38.462 0.00 0.00 0.00 2.78
645 889 8.167392 TGAAAGAGATGGTTTGGGTTCTTTATA 58.833 33.333 0.00 0.00 35.64 0.98
650 894 7.872138 AGATGGTTTGGGTTCTTTATATCTGA 58.128 34.615 0.00 0.00 0.00 3.27
701 945 4.848841 TGCTTACATTCAACATTTTACGCG 59.151 37.500 3.53 3.53 0.00 6.01
823 1067 2.043664 TCCATTTCTTGGCCCCATTACA 59.956 45.455 0.00 0.00 46.01 2.41
958 1202 7.016465 TGGACTTTGATTGAAAAGATCCCATTT 59.984 33.333 3.82 0.00 39.12 2.32
1123 1367 4.021104 CGGATTTGGGCTCATCTAGTCATA 60.021 45.833 0.00 0.00 0.00 2.15
1144 1388 8.912658 GTCATATTTTCTTTCCTTTTTCGTTCC 58.087 33.333 0.00 0.00 0.00 3.62
1181 1425 5.056480 TCTGTGGTAATTGGCATCTTATCG 58.944 41.667 0.00 0.00 0.00 2.92
1195 1439 3.096852 TCTTATCGACTTCCCTGCTCAA 58.903 45.455 0.00 0.00 0.00 3.02
1302 1546 5.352569 CGTAACAATCAAGAGCTCCAAATCT 59.647 40.000 10.93 0.00 0.00 2.40
1359 1603 6.147864 ACCATGGTTTCATTATCCAAATCG 57.852 37.500 13.00 0.00 34.80 3.34
1407 1651 0.550914 TCTTGCAGGTGGTTGAAGGT 59.449 50.000 0.00 0.00 0.00 3.50
1408 1652 1.064017 TCTTGCAGGTGGTTGAAGGTT 60.064 47.619 0.00 0.00 0.00 3.50
1958 2237 7.207383 AGTGCAATGAATACATTTGATGATGG 58.793 34.615 0.00 0.00 43.17 3.51
2234 2611 7.660617 TGATGGCAATAAAAGCATTCTTTGAAA 59.339 29.630 0.00 0.00 41.40 2.69
2269 2646 5.777850 TCATTCATTGAATTCCATCGCAT 57.222 34.783 9.19 0.00 28.87 4.73
2280 2657 4.439305 TTCCATCGCATTCTGGAAAAAG 57.561 40.909 1.65 0.00 46.01 2.27
2423 2807 2.421314 GGCAAATTATGGGCCGCC 59.579 61.111 0.00 0.00 38.04 6.13
2721 3117 8.573035 CATCTTAACCACTTTTTAACTTGCCTA 58.427 33.333 0.00 0.00 0.00 3.93
2722 3118 7.933396 TCTTAACCACTTTTTAACTTGCCTAC 58.067 34.615 0.00 0.00 0.00 3.18
3154 4934 6.657541 TGTCACCACTAAACTTTTTCTGAACT 59.342 34.615 0.00 0.00 0.00 3.01
3196 4998 9.847224 TGATCTGGTAAAACTTCTTACTTTTCT 57.153 29.630 0.00 0.00 33.17 2.52
3283 5085 1.961180 CTTCTCCCCGGCGATCAACT 61.961 60.000 9.30 0.00 0.00 3.16
3513 5317 1.512156 GCTTCCTTTGCGGTTTCGGA 61.512 55.000 0.00 0.00 36.79 4.55
3773 5800 1.016627 TGCTGCTCATGTTTATCGCC 58.983 50.000 0.00 0.00 0.00 5.54
3871 5898 4.955811 TCTAGTTTGCAACTCTTCCTGA 57.044 40.909 0.00 0.00 41.77 3.86
3906 5933 0.687354 TCCAGACAGGAAGACAAGGC 59.313 55.000 0.00 0.00 45.65 4.35
4025 6052 4.750952 TGGCAAATGTTGATGCATTTTG 57.249 36.364 13.92 13.92 43.97 2.44
4150 6177 7.981789 AGAATGCTACGAAAGATCACTATGAAA 59.018 33.333 0.00 0.00 0.00 2.69
4211 6244 5.147032 TCAAGAGTTTGAAATGGTGGGAAT 58.853 37.500 0.00 0.00 40.26 3.01
4317 6430 7.690256 TGATATATTTTCCTTTCCTCCTAGCC 58.310 38.462 0.00 0.00 0.00 3.93
4418 6531 5.869344 GTCATTTCATACCCTTTTCCTTTGC 59.131 40.000 0.00 0.00 0.00 3.68
4422 6535 0.111639 TACCCTTTTCCTTTGCGCCT 59.888 50.000 4.18 0.00 0.00 5.52
4424 6537 0.392706 CCCTTTTCCTTTGCGCCTTT 59.607 50.000 4.18 0.00 0.00 3.11
4433 6546 2.228822 CCTTTGCGCCTTTGTGTTAGAT 59.771 45.455 4.18 0.00 0.00 1.98
4462 6575 1.338294 TGTTCGCGCCCTTTTATCTGA 60.338 47.619 0.00 0.00 0.00 3.27
4478 6591 6.925610 TTATCTGATTTCACCAGGATTTCG 57.074 37.500 0.00 0.00 32.73 3.46
4480 6593 4.253685 TCTGATTTCACCAGGATTTCGTC 58.746 43.478 0.00 0.00 32.73 4.20
4488 6601 2.700897 ACCAGGATTTCGTCTATGGAGG 59.299 50.000 0.00 0.00 37.21 4.30
4493 6606 6.464465 CCAGGATTTCGTCTATGGAGGTATTT 60.464 42.308 0.00 0.00 36.40 1.40
4502 6615 2.507407 TGGAGGTATTTTGAGGCACC 57.493 50.000 0.00 0.00 0.00 5.01
4530 6644 7.559897 GGAAAGATCCAAAGGATATGGTGTAAA 59.440 37.037 0.00 0.00 43.27 2.01
4565 6679 8.995027 AATTGGCATGATAAAAGACTACCATA 57.005 30.769 0.00 0.00 0.00 2.74
4566 6680 8.995027 ATTGGCATGATAAAAGACTACCATAA 57.005 30.769 0.00 0.00 0.00 1.90
4567 6681 8.815565 TTGGCATGATAAAAGACTACCATAAA 57.184 30.769 0.00 0.00 0.00 1.40
4568 6682 8.995027 TGGCATGATAAAAGACTACCATAAAT 57.005 30.769 0.00 0.00 0.00 1.40
4573 6687 9.772973 ATGATAAAAGACTACCATAAATACGCA 57.227 29.630 0.00 0.00 0.00 5.24
4574 6688 9.772973 TGATAAAAGACTACCATAAATACGCAT 57.227 29.630 0.00 0.00 0.00 4.73
4576 6690 9.998106 ATAAAAGACTACCATAAATACGCATCT 57.002 29.630 0.00 0.00 0.00 2.90
4577 6691 8.732746 AAAAGACTACCATAAATACGCATCTT 57.267 30.769 0.00 0.00 0.00 2.40
4578 6692 7.948278 AAGACTACCATAAATACGCATCTTC 57.052 36.000 0.00 0.00 0.00 2.87
4579 6693 7.050970 AGACTACCATAAATACGCATCTTCA 57.949 36.000 0.00 0.00 0.00 3.02
4580 6694 7.671302 AGACTACCATAAATACGCATCTTCAT 58.329 34.615 0.00 0.00 0.00 2.57
4581 6695 7.600375 AGACTACCATAAATACGCATCTTCATG 59.400 37.037 0.00 0.00 0.00 3.07
4582 6696 7.217200 ACTACCATAAATACGCATCTTCATGT 58.783 34.615 0.00 0.00 31.86 3.21
4583 6697 6.304356 ACCATAAATACGCATCTTCATGTG 57.696 37.500 0.00 0.00 44.86 3.21
4584 6698 5.239306 ACCATAAATACGCATCTTCATGTGG 59.761 40.000 0.00 0.00 43.79 4.17
4585 6699 3.698029 AAATACGCATCTTCATGTGGC 57.302 42.857 0.00 0.00 43.79 5.01
4586 6700 2.330440 ATACGCATCTTCATGTGGCA 57.670 45.000 0.00 0.00 43.79 4.92
4587 6701 2.106477 TACGCATCTTCATGTGGCAA 57.894 45.000 0.00 0.00 43.79 4.52
4588 6702 1.466856 ACGCATCTTCATGTGGCAAT 58.533 45.000 0.00 0.00 43.79 3.56
4589 6703 1.133598 ACGCATCTTCATGTGGCAATG 59.866 47.619 0.00 0.00 43.79 2.82
4590 6704 1.535226 CGCATCTTCATGTGGCAATGG 60.535 52.381 0.00 0.00 36.94 3.16
4591 6705 1.752498 GCATCTTCATGTGGCAATGGA 59.248 47.619 0.00 0.00 31.86 3.41
4592 6706 2.364324 GCATCTTCATGTGGCAATGGAT 59.636 45.455 0.00 0.00 31.86 3.41
4593 6707 3.181469 GCATCTTCATGTGGCAATGGATT 60.181 43.478 0.00 0.00 31.86 3.01
4594 6708 4.617959 CATCTTCATGTGGCAATGGATTC 58.382 43.478 0.00 0.00 0.00 2.52
4595 6709 2.684374 TCTTCATGTGGCAATGGATTCG 59.316 45.455 0.00 0.00 0.00 3.34
4596 6710 2.127271 TCATGTGGCAATGGATTCGT 57.873 45.000 0.00 0.00 0.00 3.85
4597 6711 1.744522 TCATGTGGCAATGGATTCGTG 59.255 47.619 0.00 0.00 0.00 4.35
4598 6712 1.105457 ATGTGGCAATGGATTCGTGG 58.895 50.000 0.00 0.00 0.00 4.94
4599 6713 0.251121 TGTGGCAATGGATTCGTGGT 60.251 50.000 0.00 0.00 0.00 4.16
4600 6714 0.451783 GTGGCAATGGATTCGTGGTC 59.548 55.000 0.00 0.00 0.00 4.02
4601 6715 1.024046 TGGCAATGGATTCGTGGTCG 61.024 55.000 0.00 0.00 38.55 4.79
4602 6716 1.024579 GGCAATGGATTCGTGGTCGT 61.025 55.000 0.00 0.00 38.33 4.34
4603 6717 0.373716 GCAATGGATTCGTGGTCGTC 59.626 55.000 0.00 0.00 38.33 4.20
4604 6718 2.007049 GCAATGGATTCGTGGTCGTCT 61.007 52.381 0.00 0.00 38.33 4.18
4605 6719 1.660607 CAATGGATTCGTGGTCGTCTG 59.339 52.381 0.00 0.00 38.33 3.51
4606 6720 0.460284 ATGGATTCGTGGTCGTCTGC 60.460 55.000 0.00 0.00 38.33 4.26
4607 6721 1.810030 GGATTCGTGGTCGTCTGCC 60.810 63.158 0.00 0.00 38.33 4.85
4608 6722 1.810030 GATTCGTGGTCGTCTGCCC 60.810 63.158 0.00 0.00 38.33 5.36
4609 6723 2.227089 GATTCGTGGTCGTCTGCCCT 62.227 60.000 0.00 0.00 38.33 5.19
4610 6724 2.227089 ATTCGTGGTCGTCTGCCCTC 62.227 60.000 0.00 0.00 38.33 4.30
4611 6725 4.778415 CGTGGTCGTCTGCCCTCG 62.778 72.222 0.00 0.00 0.00 4.63
4612 6726 4.436998 GTGGTCGTCTGCCCTCGG 62.437 72.222 0.00 0.00 0.00 4.63
4626 6740 2.439701 TCGGGCACGGAGGTCTAG 60.440 66.667 9.32 0.00 41.39 2.43
4627 6741 2.439701 CGGGCACGGAGGTCTAGA 60.440 66.667 0.00 0.00 36.18 2.43
4628 6742 2.050350 CGGGCACGGAGGTCTAGAA 61.050 63.158 0.00 0.00 36.18 2.10
4629 6743 1.817209 GGGCACGGAGGTCTAGAAG 59.183 63.158 0.00 0.00 0.00 2.85
4630 6744 1.142097 GGCACGGAGGTCTAGAAGC 59.858 63.158 0.00 0.00 0.00 3.86
4631 6745 1.226717 GCACGGAGGTCTAGAAGCG 60.227 63.158 0.00 0.00 0.00 4.68
4632 6746 1.433879 CACGGAGGTCTAGAAGCGG 59.566 63.158 0.00 0.00 0.00 5.52
4633 6747 2.413765 CGGAGGTCTAGAAGCGGC 59.586 66.667 0.00 0.00 0.00 6.53
4634 6748 2.415608 CGGAGGTCTAGAAGCGGCA 61.416 63.158 1.45 0.00 0.00 5.69
4635 6749 1.739338 CGGAGGTCTAGAAGCGGCAT 61.739 60.000 1.45 0.00 0.00 4.40
4636 6750 0.249657 GGAGGTCTAGAAGCGGCATG 60.250 60.000 1.45 0.00 0.00 4.06
4637 6751 0.249657 GAGGTCTAGAAGCGGCATGG 60.250 60.000 1.45 0.00 0.00 3.66
4638 6752 1.889573 GGTCTAGAAGCGGCATGGC 60.890 63.158 9.69 9.69 0.00 4.40
4639 6753 1.889573 GTCTAGAAGCGGCATGGCC 60.890 63.158 14.46 6.66 46.75 5.36
4648 6762 2.836360 GGCATGGCCCAGGTGATG 60.836 66.667 8.35 0.00 44.06 3.07
4656 6770 3.213264 CCAGGTGATGGCCAATGC 58.787 61.111 10.96 2.54 43.83 3.56
4667 6781 3.189568 GCCAATGCCCACTATGTGA 57.810 52.632 0.00 0.00 35.23 3.58
4668 6782 0.740737 GCCAATGCCCACTATGTGAC 59.259 55.000 0.00 0.00 35.23 3.67
4669 6783 1.016627 CCAATGCCCACTATGTGACG 58.983 55.000 0.00 0.00 35.23 4.35
4670 6784 1.678728 CCAATGCCCACTATGTGACGT 60.679 52.381 0.00 0.00 35.23 4.34
4671 6785 1.665679 CAATGCCCACTATGTGACGTC 59.334 52.381 9.11 9.11 35.23 4.34
4672 6786 0.178068 ATGCCCACTATGTGACGTCC 59.822 55.000 14.12 5.06 35.23 4.79
4673 6787 1.153429 GCCCACTATGTGACGTCCC 60.153 63.158 14.12 0.94 35.23 4.46
4674 6788 1.520666 CCCACTATGTGACGTCCCC 59.479 63.158 14.12 4.12 35.23 4.81
4675 6789 1.141019 CCACTATGTGACGTCCCCG 59.859 63.158 14.12 0.00 35.23 5.73
4676 6790 1.317431 CCACTATGTGACGTCCCCGA 61.317 60.000 14.12 0.00 35.23 5.14
4677 6791 0.528924 CACTATGTGACGTCCCCGAA 59.471 55.000 14.12 0.00 35.23 4.30
4678 6792 0.815734 ACTATGTGACGTCCCCGAAG 59.184 55.000 14.12 6.78 37.88 3.79
4679 6793 1.100510 CTATGTGACGTCCCCGAAGA 58.899 55.000 14.12 0.00 37.88 2.87
4680 6794 0.813184 TATGTGACGTCCCCGAAGAC 59.187 55.000 14.12 2.88 37.88 3.01
4681 6795 0.898789 ATGTGACGTCCCCGAAGACT 60.899 55.000 14.12 0.00 37.88 3.24
4682 6796 1.212229 GTGACGTCCCCGAAGACTC 59.788 63.158 14.12 1.98 37.88 3.36
4683 6797 1.074423 TGACGTCCCCGAAGACTCT 59.926 57.895 14.12 0.00 37.88 3.24
4684 6798 0.325933 TGACGTCCCCGAAGACTCTA 59.674 55.000 14.12 0.00 37.88 2.43
4685 6799 1.271543 TGACGTCCCCGAAGACTCTAA 60.272 52.381 14.12 0.00 37.88 2.10
4686 6800 1.132073 GACGTCCCCGAAGACTCTAAC 59.868 57.143 3.51 0.00 37.88 2.34
4687 6801 1.171308 CGTCCCCGAAGACTCTAACA 58.829 55.000 3.75 0.00 34.46 2.41
4688 6802 1.542915 CGTCCCCGAAGACTCTAACAA 59.457 52.381 3.75 0.00 34.46 2.83
4689 6803 2.165845 CGTCCCCGAAGACTCTAACAAT 59.834 50.000 3.75 0.00 34.46 2.71
4690 6804 3.379372 CGTCCCCGAAGACTCTAACAATA 59.621 47.826 3.75 0.00 34.46 1.90
4691 6805 4.037684 CGTCCCCGAAGACTCTAACAATAT 59.962 45.833 3.75 0.00 34.46 1.28
4692 6806 5.530712 GTCCCCGAAGACTCTAACAATATC 58.469 45.833 0.00 0.00 33.79 1.63
4693 6807 5.302313 GTCCCCGAAGACTCTAACAATATCT 59.698 44.000 0.00 0.00 33.79 1.98
4694 6808 5.897824 TCCCCGAAGACTCTAACAATATCTT 59.102 40.000 0.00 0.00 32.36 2.40
4695 6809 6.040616 TCCCCGAAGACTCTAACAATATCTTC 59.959 42.308 0.00 0.00 41.15 2.87
4696 6810 6.041069 CCCCGAAGACTCTAACAATATCTTCT 59.959 42.308 9.81 0.00 41.97 2.85
4697 6811 7.418025 CCCCGAAGACTCTAACAATATCTTCTT 60.418 40.741 9.81 0.00 41.97 2.52
4698 6812 7.982354 CCCGAAGACTCTAACAATATCTTCTTT 59.018 37.037 9.81 0.00 41.97 2.52
4699 6813 9.026074 CCGAAGACTCTAACAATATCTTCTTTC 57.974 37.037 9.81 0.00 41.97 2.62
4700 6814 8.738554 CGAAGACTCTAACAATATCTTCTTTCG 58.261 37.037 9.81 0.00 41.97 3.46
4701 6815 7.995463 AGACTCTAACAATATCTTCTTTCGC 57.005 36.000 0.00 0.00 0.00 4.70
4702 6816 7.777095 AGACTCTAACAATATCTTCTTTCGCT 58.223 34.615 0.00 0.00 0.00 4.93
4703 6817 7.704472 AGACTCTAACAATATCTTCTTTCGCTG 59.296 37.037 0.00 0.00 0.00 5.18
4704 6818 6.256757 ACTCTAACAATATCTTCTTTCGCTGC 59.743 38.462 0.00 0.00 0.00 5.25
4705 6819 4.622701 AACAATATCTTCTTTCGCTGCC 57.377 40.909 0.00 0.00 0.00 4.85
4706 6820 2.945668 ACAATATCTTCTTTCGCTGCCC 59.054 45.455 0.00 0.00 0.00 5.36
4707 6821 1.871080 ATATCTTCTTTCGCTGCCCG 58.129 50.000 0.00 0.00 38.61 6.13
4708 6822 0.179084 TATCTTCTTTCGCTGCCCGG 60.179 55.000 0.00 0.00 37.59 5.73
4709 6823 3.804193 CTTCTTTCGCTGCCCGGC 61.804 66.667 1.04 1.04 37.59 6.13
4724 6838 3.414700 GGCGGCGCGATTCCTATG 61.415 66.667 26.95 0.00 0.00 2.23
4725 6839 3.414700 GCGGCGCGATTCCTATGG 61.415 66.667 19.09 0.00 0.00 2.74
4726 6840 2.338620 CGGCGCGATTCCTATGGA 59.661 61.111 12.10 0.00 0.00 3.41
4727 6841 1.734477 CGGCGCGATTCCTATGGAG 60.734 63.158 12.10 0.00 31.21 3.86
4728 6842 1.367840 GGCGCGATTCCTATGGAGT 59.632 57.895 12.10 0.00 31.21 3.85
4729 6843 0.249911 GGCGCGATTCCTATGGAGTT 60.250 55.000 12.10 0.00 31.21 3.01
4730 6844 0.861837 GCGCGATTCCTATGGAGTTG 59.138 55.000 12.10 0.00 31.21 3.16
4731 6845 0.861837 CGCGATTCCTATGGAGTTGC 59.138 55.000 0.00 10.24 42.93 4.17
4732 6846 1.539065 CGCGATTCCTATGGAGTTGCT 60.539 52.381 15.94 0.00 43.80 3.91
4733 6847 2.565841 GCGATTCCTATGGAGTTGCTT 58.434 47.619 12.32 0.00 43.01 3.91
4734 6848 2.545946 GCGATTCCTATGGAGTTGCTTC 59.454 50.000 12.32 0.00 43.01 3.86
4735 6849 3.134458 CGATTCCTATGGAGTTGCTTCC 58.866 50.000 0.00 0.00 37.77 3.46
4736 6850 2.691409 TTCCTATGGAGTTGCTTCCG 57.309 50.000 0.00 0.00 40.27 4.30
4737 6851 0.830648 TCCTATGGAGTTGCTTCCGG 59.169 55.000 0.00 0.00 40.27 5.14
4738 6852 0.179045 CCTATGGAGTTGCTTCCGGG 60.179 60.000 0.00 0.00 40.27 5.73
4739 6853 0.830648 CTATGGAGTTGCTTCCGGGA 59.169 55.000 0.00 0.00 40.27 5.14
4740 6854 0.539986 TATGGAGTTGCTTCCGGGAC 59.460 55.000 0.00 0.00 40.27 4.46
4753 6867 4.309950 GGGACGTTGTCGGTGGCT 62.310 66.667 0.00 0.00 41.85 4.75
4754 6868 2.737376 GGACGTTGTCGGTGGCTC 60.737 66.667 0.00 0.00 41.85 4.70
4755 6869 2.338984 GACGTTGTCGGTGGCTCT 59.661 61.111 0.00 0.00 41.85 4.09
4756 6870 1.300697 GACGTTGTCGGTGGCTCTT 60.301 57.895 0.00 0.00 41.85 2.85
4757 6871 1.557443 GACGTTGTCGGTGGCTCTTG 61.557 60.000 0.00 0.00 41.85 3.02
4758 6872 2.317609 CGTTGTCGGTGGCTCTTGG 61.318 63.158 0.00 0.00 0.00 3.61
4759 6873 1.227853 GTTGTCGGTGGCTCTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
4760 6874 1.227823 TTGTCGGTGGCTCTTGGTG 60.228 57.895 0.00 0.00 0.00 4.17
4761 6875 3.050275 GTCGGTGGCTCTTGGTGC 61.050 66.667 0.00 0.00 0.00 5.01
4771 6885 1.678101 GCTCTTGGTGCCATGATAACC 59.322 52.381 7.18 0.00 31.27 2.85
4772 6886 2.684927 GCTCTTGGTGCCATGATAACCT 60.685 50.000 7.18 0.00 34.90 3.50
4773 6887 3.209410 CTCTTGGTGCCATGATAACCTC 58.791 50.000 7.18 0.00 34.90 3.85
4774 6888 2.092429 TCTTGGTGCCATGATAACCTCC 60.092 50.000 11.27 0.00 34.90 4.30
4775 6889 0.550914 TGGTGCCATGATAACCTCCC 59.449 55.000 11.27 0.00 34.90 4.30
4776 6890 0.846693 GGTGCCATGATAACCTCCCT 59.153 55.000 0.00 0.00 0.00 4.20
4777 6891 1.477558 GGTGCCATGATAACCTCCCTG 60.478 57.143 0.00 0.00 0.00 4.45
4778 6892 1.490490 GTGCCATGATAACCTCCCTGA 59.510 52.381 0.00 0.00 0.00 3.86
4779 6893 1.490490 TGCCATGATAACCTCCCTGAC 59.510 52.381 0.00 0.00 0.00 3.51
4780 6894 1.202818 GCCATGATAACCTCCCTGACC 60.203 57.143 0.00 0.00 0.00 4.02
4781 6895 2.412591 CCATGATAACCTCCCTGACCT 58.587 52.381 0.00 0.00 0.00 3.85
4782 6896 3.587498 CCATGATAACCTCCCTGACCTA 58.413 50.000 0.00 0.00 0.00 3.08
4783 6897 4.171234 CCATGATAACCTCCCTGACCTAT 58.829 47.826 0.00 0.00 0.00 2.57
4784 6898 4.599241 CCATGATAACCTCCCTGACCTATT 59.401 45.833 0.00 0.00 0.00 1.73
4785 6899 5.073691 CCATGATAACCTCCCTGACCTATTT 59.926 44.000 0.00 0.00 0.00 1.40
4786 6900 6.272324 CCATGATAACCTCCCTGACCTATTTA 59.728 42.308 0.00 0.00 0.00 1.40
4787 6901 6.996180 TGATAACCTCCCTGACCTATTTAG 57.004 41.667 0.00 0.00 0.00 1.85
4803 6917 7.247456 CCTATTTAGGGAGGTCTTAGATTCC 57.753 44.000 7.06 7.06 39.86 3.01
4807 6921 3.562343 GGGAGGTCTTAGATTCCCAAC 57.438 52.381 22.07 3.97 46.96 3.77
4808 6922 2.172930 GGGAGGTCTTAGATTCCCAACC 59.827 54.545 22.07 10.62 46.96 3.77
4809 6923 3.116174 GGAGGTCTTAGATTCCCAACCT 58.884 50.000 4.91 0.00 39.76 3.50
4810 6924 4.296056 GGAGGTCTTAGATTCCCAACCTA 58.704 47.826 4.91 0.00 37.26 3.08
4811 6925 4.908481 GGAGGTCTTAGATTCCCAACCTAT 59.092 45.833 4.91 0.00 37.26 2.57
4812 6926 5.012251 GGAGGTCTTAGATTCCCAACCTATC 59.988 48.000 4.91 0.00 37.26 2.08
4813 6927 4.908481 AGGTCTTAGATTCCCAACCTATCC 59.092 45.833 0.00 0.00 35.41 2.59
4814 6928 4.262506 GGTCTTAGATTCCCAACCTATCCG 60.263 50.000 0.00 0.00 0.00 4.18
4815 6929 4.344390 GTCTTAGATTCCCAACCTATCCGT 59.656 45.833 0.00 0.00 0.00 4.69
4816 6930 5.537674 GTCTTAGATTCCCAACCTATCCGTA 59.462 44.000 0.00 0.00 0.00 4.02
4817 6931 5.773680 TCTTAGATTCCCAACCTATCCGTAG 59.226 44.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 5.357878 TGATTAATCAGGCACTCCATTGTTC 59.642 40.000 14.23 0.00 34.60 3.18
140 141 5.072055 GTGGTTCTCCTCCTCCTATACTAC 58.928 50.000 0.00 0.00 34.23 2.73
146 147 2.158219 TGTTGTGGTTCTCCTCCTCCTA 60.158 50.000 0.00 0.00 34.23 2.94
147 148 1.353091 GTTGTGGTTCTCCTCCTCCT 58.647 55.000 0.00 0.00 34.23 3.69
148 149 1.056660 TGTTGTGGTTCTCCTCCTCC 58.943 55.000 0.00 0.00 34.23 4.30
205 206 2.462456 TGCATTGTGTCCTCTCTGTC 57.538 50.000 0.00 0.00 0.00 3.51
219 220 6.266103 TCTTCCTTGAAAGAACTCAATGCATT 59.734 34.615 5.99 5.99 34.86 3.56
220 221 5.771666 TCTTCCTTGAAAGAACTCAATGCAT 59.228 36.000 0.00 0.00 34.86 3.96
222 223 5.471456 TCTCTTCCTTGAAAGAACTCAATGC 59.529 40.000 0.00 0.00 34.95 3.56
403 647 0.036765 TTCGGCAGCGAATACCTTGT 60.037 50.000 0.00 0.00 0.00 3.16
448 692 0.391263 AAAAGTGAGACCCGATCGGC 60.391 55.000 29.12 16.06 33.26 5.54
449 693 1.204941 AGAAAAGTGAGACCCGATCGG 59.795 52.381 27.65 27.65 37.81 4.18
496 740 6.440647 TCCCACAAGTATGAACTCTGTATTCT 59.559 38.462 0.00 0.00 33.75 2.40
497 741 6.640518 TCCCACAAGTATGAACTCTGTATTC 58.359 40.000 0.00 0.00 33.75 1.75
515 759 2.507886 TGTCCTGTTTCTTTCTCCCACA 59.492 45.455 0.00 0.00 0.00 4.17
522 766 6.433766 CACTGAATCTTGTCCTGTTTCTTTC 58.566 40.000 0.00 0.00 0.00 2.62
523 767 5.221126 GCACTGAATCTTGTCCTGTTTCTTT 60.221 40.000 0.00 0.00 0.00 2.52
524 768 4.276926 GCACTGAATCTTGTCCTGTTTCTT 59.723 41.667 0.00 0.00 0.00 2.52
525 769 3.817647 GCACTGAATCTTGTCCTGTTTCT 59.182 43.478 0.00 0.00 0.00 2.52
526 770 3.057946 GGCACTGAATCTTGTCCTGTTTC 60.058 47.826 0.00 0.00 0.00 2.78
530 774 1.271543 TGGGCACTGAATCTTGTCCTG 60.272 52.381 7.42 0.00 38.41 3.86
645 889 5.946942 AGTATCACACTCATTGGTCAGAT 57.053 39.130 0.00 0.00 28.33 2.90
672 916 6.506500 AAATGTTGAATGTAAGCAGGAGAG 57.493 37.500 0.00 0.00 0.00 3.20
701 945 9.906660 TGAAAATTAAACCTATGTGTGTGATTC 57.093 29.630 0.00 0.00 0.00 2.52
958 1202 2.430465 GCTCACAAAAGCTGGAGATCA 58.570 47.619 0.00 0.00 39.27 2.92
1066 1310 4.712337 CCAACAGGAGTAAGAGTAGGATGT 59.288 45.833 0.00 0.00 0.00 3.06
1123 1367 6.280643 CAGGGAACGAAAAAGGAAAGAAAAT 58.719 36.000 0.00 0.00 0.00 1.82
1144 1388 4.970860 ACCACAGATGAGATTATCCAGG 57.029 45.455 0.00 0.00 0.00 4.45
1181 1425 2.303311 ACCTAACTTGAGCAGGGAAGTC 59.697 50.000 0.00 0.00 31.02 3.01
1195 1439 5.591877 GCATCCAATCATTGAGAACCTAACT 59.408 40.000 0.00 0.00 0.00 2.24
1359 1603 6.309737 ACGTTCGTCAGATATTTCAAGTTACC 59.690 38.462 0.00 0.00 0.00 2.85
1407 1651 1.076024 AGCAAGGAATTCAGCAGGGAA 59.924 47.619 15.96 0.00 0.00 3.97
1408 1652 0.700564 AGCAAGGAATTCAGCAGGGA 59.299 50.000 15.96 0.00 0.00 4.20
1668 1915 2.042464 ACCTGACTGAGCTGAGTGAAA 58.958 47.619 11.70 0.00 0.00 2.69
1958 2237 8.804743 CACATGCATCATCAGAAGAAAAATAAC 58.195 33.333 0.00 0.00 0.00 1.89
1966 2253 4.081309 TGACTCACATGCATCATCAGAAGA 60.081 41.667 0.00 0.00 0.00 2.87
2269 2646 6.915843 GTGAACGCTAATTTCTTTTTCCAGAA 59.084 34.615 0.00 0.00 0.00 3.02
2280 2657 7.148474 TGTCCTCTTATTGTGAACGCTAATTTC 60.148 37.037 0.00 0.00 0.00 2.17
2363 2741 3.704566 ACAGGATAATAGTGGAGCAACGA 59.295 43.478 0.00 0.00 0.00 3.85
2721 3117 0.184211 ACCCCAAAAGCACCTAACGT 59.816 50.000 0.00 0.00 0.00 3.99
2722 3118 0.879090 GACCCCAAAAGCACCTAACG 59.121 55.000 0.00 0.00 0.00 3.18
2768 3210 8.559536 CCTGTAAAAGTACGCATTATGATGATT 58.440 33.333 0.85 0.00 34.90 2.57
3154 4934 4.021104 CCAGATCAGTTCAGTGGTCTTACA 60.021 45.833 0.00 0.00 35.61 2.41
3196 4998 5.450818 AAGGTGCTTGATCCAAATACCTA 57.549 39.130 12.09 0.00 38.16 3.08
3318 5120 1.900981 CACCAAATGCGGGACACCA 60.901 57.895 0.00 0.00 36.13 4.17
3773 5800 0.723414 CCATGAGTGTTGCTACAGCG 59.277 55.000 0.00 0.00 45.83 5.18
3871 5898 2.154462 CTGGATTTCTTCGCCTTGTGT 58.846 47.619 0.00 0.00 0.00 3.72
3906 5933 1.242076 CTTGGTCAAGGGCTCAAGTG 58.758 55.000 2.94 0.00 34.87 3.16
3964 5991 5.043248 CAGCTCCATTCAAACGAAAACTTT 58.957 37.500 0.00 0.00 0.00 2.66
4057 6084 9.661563 AGAACGAACAACACATCCTTTTATATA 57.338 29.630 0.00 0.00 0.00 0.86
4058 6085 8.561738 AGAACGAACAACACATCCTTTTATAT 57.438 30.769 0.00 0.00 0.00 0.86
4059 6086 7.972832 AGAACGAACAACACATCCTTTTATA 57.027 32.000 0.00 0.00 0.00 0.98
4060 6087 6.877611 AGAACGAACAACACATCCTTTTAT 57.122 33.333 0.00 0.00 0.00 1.40
4061 6088 7.789273 TTAGAACGAACAACACATCCTTTTA 57.211 32.000 0.00 0.00 0.00 1.52
4211 6244 3.953612 AGCAACAGAGTCAAACCAATCAA 59.046 39.130 0.00 0.00 0.00 2.57
4317 6430 3.459063 GGAGGGAGTTCGACGGGG 61.459 72.222 0.00 0.00 0.00 5.73
4393 6506 6.398095 CAAAGGAAAAGGGTATGAAATGACC 58.602 40.000 0.00 0.00 34.75 4.02
4400 6513 1.816224 GCGCAAAGGAAAAGGGTATGA 59.184 47.619 0.30 0.00 0.00 2.15
4412 6525 1.606668 TCTAACACAAAGGCGCAAAGG 59.393 47.619 10.83 0.00 0.00 3.11
4418 6531 6.009115 AGGTAAAAATCTAACACAAAGGCG 57.991 37.500 0.00 0.00 0.00 5.52
4422 6535 7.432838 GCGAACAAGGTAAAAATCTAACACAAA 59.567 33.333 0.00 0.00 0.00 2.83
4424 6537 6.432107 GCGAACAAGGTAAAAATCTAACACA 58.568 36.000 0.00 0.00 0.00 3.72
4433 6546 0.311477 GGGCGCGAACAAGGTAAAAA 59.689 50.000 12.10 0.00 0.00 1.94
4462 6575 5.104527 TCCATAGACGAAATCCTGGTGAAAT 60.105 40.000 0.00 0.00 33.92 2.17
4478 6591 4.816925 GTGCCTCAAAATACCTCCATAGAC 59.183 45.833 0.00 0.00 0.00 2.59
4480 6593 4.137543 GGTGCCTCAAAATACCTCCATAG 58.862 47.826 0.00 0.00 0.00 2.23
4488 6601 4.079253 TCTTTCCTGGTGCCTCAAAATAC 58.921 43.478 0.00 0.00 0.00 1.89
4493 6606 1.004745 GGATCTTTCCTGGTGCCTCAA 59.995 52.381 0.00 0.00 39.14 3.02
4502 6615 5.533903 CACCATATCCTTTGGATCTTTCCTG 59.466 44.000 1.98 0.00 42.11 3.86
4556 6670 7.385205 ACATGAAGATGCGTATTTATGGTAGTC 59.615 37.037 18.72 0.00 29.66 2.59
4558 6672 7.360353 CCACATGAAGATGCGTATTTATGGTAG 60.360 40.741 18.72 10.16 29.66 3.18
4565 6679 3.016031 TGCCACATGAAGATGCGTATTT 58.984 40.909 0.00 0.00 32.14 1.40
4566 6680 2.642427 TGCCACATGAAGATGCGTATT 58.358 42.857 0.00 0.00 32.14 1.89
4567 6681 2.330440 TGCCACATGAAGATGCGTAT 57.670 45.000 0.00 0.00 32.14 3.06
4568 6682 2.106477 TTGCCACATGAAGATGCGTA 57.894 45.000 0.00 0.00 32.14 4.42
4569 6683 1.133598 CATTGCCACATGAAGATGCGT 59.866 47.619 0.00 0.00 32.14 5.24
4570 6684 1.535226 CCATTGCCACATGAAGATGCG 60.535 52.381 0.00 0.00 32.14 4.73
4571 6685 1.752498 TCCATTGCCACATGAAGATGC 59.248 47.619 0.00 0.00 32.14 3.91
4572 6686 4.617959 GAATCCATTGCCACATGAAGATG 58.382 43.478 0.00 0.00 35.49 2.90
4573 6687 3.317149 CGAATCCATTGCCACATGAAGAT 59.683 43.478 0.00 0.00 0.00 2.40
4574 6688 2.684374 CGAATCCATTGCCACATGAAGA 59.316 45.455 0.00 0.00 0.00 2.87
4575 6689 2.424601 ACGAATCCATTGCCACATGAAG 59.575 45.455 0.00 0.00 0.00 3.02
4576 6690 2.164017 CACGAATCCATTGCCACATGAA 59.836 45.455 0.00 0.00 0.00 2.57
4577 6691 1.744522 CACGAATCCATTGCCACATGA 59.255 47.619 0.00 0.00 0.00 3.07
4578 6692 1.202325 CCACGAATCCATTGCCACATG 60.202 52.381 0.00 0.00 0.00 3.21
4579 6693 1.105457 CCACGAATCCATTGCCACAT 58.895 50.000 0.00 0.00 0.00 3.21
4580 6694 0.251121 ACCACGAATCCATTGCCACA 60.251 50.000 0.00 0.00 0.00 4.17
4581 6695 0.451783 GACCACGAATCCATTGCCAC 59.548 55.000 0.00 0.00 0.00 5.01
4582 6696 1.024046 CGACCACGAATCCATTGCCA 61.024 55.000 0.00 0.00 42.66 4.92
4583 6697 1.024579 ACGACCACGAATCCATTGCC 61.025 55.000 0.00 0.00 42.66 4.52
4584 6698 0.373716 GACGACCACGAATCCATTGC 59.626 55.000 0.00 0.00 42.66 3.56
4585 6699 1.660607 CAGACGACCACGAATCCATTG 59.339 52.381 0.00 0.00 42.66 2.82
4586 6700 2.007049 GCAGACGACCACGAATCCATT 61.007 52.381 0.00 0.00 42.66 3.16
4587 6701 0.460284 GCAGACGACCACGAATCCAT 60.460 55.000 0.00 0.00 42.66 3.41
4588 6702 1.080093 GCAGACGACCACGAATCCA 60.080 57.895 0.00 0.00 42.66 3.41
4589 6703 1.810030 GGCAGACGACCACGAATCC 60.810 63.158 0.00 0.00 42.66 3.01
4590 6704 1.810030 GGGCAGACGACCACGAATC 60.810 63.158 0.00 0.00 41.77 2.52
4591 6705 2.227089 GAGGGCAGACGACCACGAAT 62.227 60.000 0.00 0.00 46.60 3.34
4592 6706 2.915659 AGGGCAGACGACCACGAA 60.916 61.111 0.00 0.00 46.60 3.85
4593 6707 3.371063 GAGGGCAGACGACCACGA 61.371 66.667 0.00 0.00 46.60 4.35
4595 6709 4.436998 CCGAGGGCAGACGACCAC 62.437 72.222 0.00 0.00 46.60 4.16
4608 6722 2.439701 TAGACCTCCGTGCCCGAG 60.440 66.667 0.00 0.00 35.63 4.63
4609 6723 2.439701 CTAGACCTCCGTGCCCGA 60.440 66.667 0.00 0.00 35.63 5.14
4610 6724 2.005960 CTTCTAGACCTCCGTGCCCG 62.006 65.000 0.00 0.00 0.00 6.13
4611 6725 1.817209 CTTCTAGACCTCCGTGCCC 59.183 63.158 0.00 0.00 0.00 5.36
4612 6726 1.142097 GCTTCTAGACCTCCGTGCC 59.858 63.158 0.00 0.00 0.00 5.01
4613 6727 1.226717 CGCTTCTAGACCTCCGTGC 60.227 63.158 0.00 0.00 0.00 5.34
4614 6728 1.433879 CCGCTTCTAGACCTCCGTG 59.566 63.158 0.00 0.00 0.00 4.94
4615 6729 2.416432 GCCGCTTCTAGACCTCCGT 61.416 63.158 0.00 0.00 0.00 4.69
4616 6730 1.739338 ATGCCGCTTCTAGACCTCCG 61.739 60.000 0.00 0.00 0.00 4.63
4617 6731 0.249657 CATGCCGCTTCTAGACCTCC 60.250 60.000 0.00 0.00 0.00 4.30
4618 6732 0.249657 CCATGCCGCTTCTAGACCTC 60.250 60.000 0.00 0.00 0.00 3.85
4619 6733 1.826024 CCATGCCGCTTCTAGACCT 59.174 57.895 0.00 0.00 0.00 3.85
4620 6734 1.889573 GCCATGCCGCTTCTAGACC 60.890 63.158 0.00 0.00 0.00 3.85
4621 6735 1.889573 GGCCATGCCGCTTCTAGAC 60.890 63.158 0.00 0.00 39.62 2.59
4622 6736 2.505982 GGCCATGCCGCTTCTAGA 59.494 61.111 0.00 0.00 39.62 2.43
4632 6746 2.836360 CCATCACCTGGGCCATGC 60.836 66.667 6.72 0.00 41.82 4.06
4633 6747 2.836360 GCCATCACCTGGGCCATG 60.836 66.667 6.72 7.06 46.06 3.66
4638 6752 2.428925 GCATTGGCCATCACCTGGG 61.429 63.158 6.09 0.00 46.06 4.45
4649 6763 0.740737 GTCACATAGTGGGCATTGGC 59.259 55.000 0.70 0.70 33.87 4.52
4650 6764 1.016627 CGTCACATAGTGGGCATTGG 58.983 55.000 0.00 0.00 33.87 3.16
4651 6765 1.665679 GACGTCACATAGTGGGCATTG 59.334 52.381 11.55 0.00 33.87 2.82
4652 6766 1.406887 GGACGTCACATAGTGGGCATT 60.407 52.381 18.91 0.00 33.87 3.56
4653 6767 0.178068 GGACGTCACATAGTGGGCAT 59.822 55.000 18.91 0.00 33.87 4.40
4654 6768 1.594833 GGACGTCACATAGTGGGCA 59.405 57.895 18.91 0.00 33.87 5.36
4655 6769 1.153429 GGGACGTCACATAGTGGGC 60.153 63.158 18.91 0.00 33.87 5.36
4656 6770 1.520666 GGGGACGTCACATAGTGGG 59.479 63.158 21.40 0.00 33.87 4.61
4669 6783 3.889520 ATTGTTAGAGTCTTCGGGGAC 57.110 47.619 0.00 1.44 36.56 4.46
4670 6784 5.455872 AGATATTGTTAGAGTCTTCGGGGA 58.544 41.667 0.00 0.00 0.00 4.81
4671 6785 5.793030 AGATATTGTTAGAGTCTTCGGGG 57.207 43.478 0.00 0.00 0.00 5.73
4672 6786 7.045126 AGAAGATATTGTTAGAGTCTTCGGG 57.955 40.000 0.00 0.00 45.74 5.14
4673 6787 8.934507 AAAGAAGATATTGTTAGAGTCTTCGG 57.065 34.615 0.00 0.00 45.74 4.30
4674 6788 8.738554 CGAAAGAAGATATTGTTAGAGTCTTCG 58.261 37.037 0.00 0.00 45.74 3.79
4675 6789 8.536407 GCGAAAGAAGATATTGTTAGAGTCTTC 58.464 37.037 0.00 5.52 43.05 2.87
4676 6790 8.254508 AGCGAAAGAAGATATTGTTAGAGTCTT 58.745 33.333 0.00 0.00 32.23 3.01
4677 6791 7.704472 CAGCGAAAGAAGATATTGTTAGAGTCT 59.296 37.037 0.00 0.00 0.00 3.24
4678 6792 7.515998 GCAGCGAAAGAAGATATTGTTAGAGTC 60.516 40.741 0.00 0.00 0.00 3.36
4679 6793 6.256757 GCAGCGAAAGAAGATATTGTTAGAGT 59.743 38.462 0.00 0.00 0.00 3.24
4680 6794 6.292596 GGCAGCGAAAGAAGATATTGTTAGAG 60.293 42.308 0.00 0.00 0.00 2.43
4681 6795 5.523916 GGCAGCGAAAGAAGATATTGTTAGA 59.476 40.000 0.00 0.00 0.00 2.10
4682 6796 5.277538 GGGCAGCGAAAGAAGATATTGTTAG 60.278 44.000 0.00 0.00 0.00 2.34
4683 6797 4.574828 GGGCAGCGAAAGAAGATATTGTTA 59.425 41.667 0.00 0.00 0.00 2.41
4684 6798 3.378427 GGGCAGCGAAAGAAGATATTGTT 59.622 43.478 0.00 0.00 0.00 2.83
4685 6799 2.945668 GGGCAGCGAAAGAAGATATTGT 59.054 45.455 0.00 0.00 0.00 2.71
4686 6800 2.032549 CGGGCAGCGAAAGAAGATATTG 60.033 50.000 0.00 0.00 0.00 1.90
4687 6801 2.213499 CGGGCAGCGAAAGAAGATATT 58.787 47.619 0.00 0.00 0.00 1.28
4688 6802 1.541233 CCGGGCAGCGAAAGAAGATAT 60.541 52.381 0.00 0.00 0.00 1.63
4689 6803 0.179084 CCGGGCAGCGAAAGAAGATA 60.179 55.000 0.00 0.00 0.00 1.98
4690 6804 1.450312 CCGGGCAGCGAAAGAAGAT 60.450 57.895 0.00 0.00 0.00 2.40
4691 6805 2.047274 CCGGGCAGCGAAAGAAGA 60.047 61.111 0.00 0.00 0.00 2.87
4692 6806 3.804193 GCCGGGCAGCGAAAGAAG 61.804 66.667 15.62 0.00 0.00 2.85
4707 6821 3.414700 CATAGGAATCGCGCCGCC 61.415 66.667 2.28 1.38 0.00 6.13
4708 6822 3.414700 CCATAGGAATCGCGCCGC 61.415 66.667 0.00 0.00 0.00 6.53
4709 6823 1.734477 CTCCATAGGAATCGCGCCG 60.734 63.158 0.00 0.00 0.00 6.46
4710 6824 0.249911 AACTCCATAGGAATCGCGCC 60.250 55.000 0.00 0.00 0.00 6.53
4711 6825 0.861837 CAACTCCATAGGAATCGCGC 59.138 55.000 0.00 0.00 0.00 6.86
4712 6826 0.861837 GCAACTCCATAGGAATCGCG 59.138 55.000 0.00 0.00 0.00 5.87
4713 6827 2.246719 AGCAACTCCATAGGAATCGC 57.753 50.000 0.00 0.00 0.00 4.58
4714 6828 3.134458 GGAAGCAACTCCATAGGAATCG 58.866 50.000 0.00 0.00 35.36 3.34
4715 6829 3.134458 CGGAAGCAACTCCATAGGAATC 58.866 50.000 0.00 0.00 34.91 2.52
4716 6830 2.158755 CCGGAAGCAACTCCATAGGAAT 60.159 50.000 0.00 0.00 34.91 3.01
4717 6831 1.209504 CCGGAAGCAACTCCATAGGAA 59.790 52.381 0.00 0.00 34.91 3.36
4718 6832 0.830648 CCGGAAGCAACTCCATAGGA 59.169 55.000 0.00 0.00 34.91 2.94
4719 6833 0.179045 CCCGGAAGCAACTCCATAGG 60.179 60.000 0.73 0.00 34.91 2.57
4720 6834 0.830648 TCCCGGAAGCAACTCCATAG 59.169 55.000 0.73 0.00 34.91 2.23
4721 6835 0.539986 GTCCCGGAAGCAACTCCATA 59.460 55.000 0.73 0.00 34.91 2.74
4722 6836 1.299976 GTCCCGGAAGCAACTCCAT 59.700 57.895 0.73 0.00 34.91 3.41
4723 6837 2.747686 GTCCCGGAAGCAACTCCA 59.252 61.111 0.73 0.00 34.91 3.86
4724 6838 2.434359 CGTCCCGGAAGCAACTCC 60.434 66.667 0.73 0.00 0.00 3.85
4725 6839 1.301479 AACGTCCCGGAAGCAACTC 60.301 57.895 0.73 0.00 0.00 3.01
4726 6840 1.597027 CAACGTCCCGGAAGCAACT 60.597 57.895 0.73 0.00 0.00 3.16
4727 6841 1.838568 GACAACGTCCCGGAAGCAAC 61.839 60.000 0.73 0.00 0.00 4.17
4728 6842 1.595929 GACAACGTCCCGGAAGCAA 60.596 57.895 0.73 0.00 0.00 3.91
4729 6843 2.029964 GACAACGTCCCGGAAGCA 59.970 61.111 0.73 0.00 0.00 3.91
4730 6844 3.110178 CGACAACGTCCCGGAAGC 61.110 66.667 0.73 0.00 34.56 3.86
4731 6845 2.431942 CCGACAACGTCCCGGAAG 60.432 66.667 15.34 0.00 45.58 3.46
4732 6846 3.225798 ACCGACAACGTCCCGGAA 61.226 61.111 23.74 0.00 45.58 4.30
4733 6847 3.980989 CACCGACAACGTCCCGGA 61.981 66.667 23.74 0.00 45.58 5.14
4736 6850 4.309950 AGCCACCGACAACGTCCC 62.310 66.667 0.00 0.00 37.88 4.46
4737 6851 2.710724 AAGAGCCACCGACAACGTCC 62.711 60.000 0.00 0.00 37.88 4.79
4738 6852 1.300697 AAGAGCCACCGACAACGTC 60.301 57.895 0.00 0.00 37.88 4.34
4739 6853 1.594293 CAAGAGCCACCGACAACGT 60.594 57.895 0.00 0.00 37.88 3.99
4740 6854 2.317609 CCAAGAGCCACCGACAACG 61.318 63.158 0.00 0.00 39.43 4.10
4741 6855 1.227853 ACCAAGAGCCACCGACAAC 60.228 57.895 0.00 0.00 0.00 3.32
4742 6856 1.227823 CACCAAGAGCCACCGACAA 60.228 57.895 0.00 0.00 0.00 3.18
4743 6857 2.425592 CACCAAGAGCCACCGACA 59.574 61.111 0.00 0.00 0.00 4.35
4744 6858 3.050275 GCACCAAGAGCCACCGAC 61.050 66.667 0.00 0.00 0.00 4.79
4751 6865 1.678101 GGTTATCATGGCACCAAGAGC 59.322 52.381 0.75 0.00 0.00 4.09
4752 6866 3.209410 GAGGTTATCATGGCACCAAGAG 58.791 50.000 10.40 0.00 32.43 2.85
4753 6867 2.092429 GGAGGTTATCATGGCACCAAGA 60.092 50.000 10.40 0.00 32.43 3.02
4754 6868 2.301346 GGAGGTTATCATGGCACCAAG 58.699 52.381 10.40 0.00 32.43 3.61
4755 6869 1.064017 GGGAGGTTATCATGGCACCAA 60.064 52.381 10.40 0.00 32.43 3.67
4756 6870 0.550914 GGGAGGTTATCATGGCACCA 59.449 55.000 10.40 0.00 32.43 4.17
4757 6871 0.846693 AGGGAGGTTATCATGGCACC 59.153 55.000 0.00 0.00 0.00 5.01
4758 6872 1.490490 TCAGGGAGGTTATCATGGCAC 59.510 52.381 0.00 0.00 0.00 5.01
4759 6873 1.490490 GTCAGGGAGGTTATCATGGCA 59.510 52.381 0.00 0.00 0.00 4.92
4760 6874 1.202818 GGTCAGGGAGGTTATCATGGC 60.203 57.143 0.00 0.00 0.00 4.40
4761 6875 2.412591 AGGTCAGGGAGGTTATCATGG 58.587 52.381 0.00 0.00 0.00 3.66
4762 6876 5.832539 AATAGGTCAGGGAGGTTATCATG 57.167 43.478 0.00 0.00 0.00 3.07
4763 6877 6.502158 CCTAAATAGGTCAGGGAGGTTATCAT 59.498 42.308 0.00 0.00 38.69 2.45
4764 6878 5.844516 CCTAAATAGGTCAGGGAGGTTATCA 59.155 44.000 0.00 0.00 38.69 2.15
4765 6879 6.361768 CCTAAATAGGTCAGGGAGGTTATC 57.638 45.833 0.00 0.00 38.69 1.75
4779 6893 6.213802 GGGAATCTAAGACCTCCCTAAATAGG 59.786 46.154 7.70 0.00 43.74 2.57
4780 6894 6.787957 TGGGAATCTAAGACCTCCCTAAATAG 59.212 42.308 14.11 0.00 46.72 1.73
4781 6895 6.699688 TGGGAATCTAAGACCTCCCTAAATA 58.300 40.000 14.11 0.00 46.72 1.40
4782 6896 5.548573 TGGGAATCTAAGACCTCCCTAAAT 58.451 41.667 14.11 0.00 46.72 1.40
4783 6897 4.967871 TGGGAATCTAAGACCTCCCTAAA 58.032 43.478 14.11 0.00 46.72 1.85
4784 6898 4.637288 TGGGAATCTAAGACCTCCCTAA 57.363 45.455 14.11 0.00 46.72 2.69
4785 6899 4.296056 GTTGGGAATCTAAGACCTCCCTA 58.704 47.826 14.11 6.15 46.72 3.53
4786 6900 3.116174 GTTGGGAATCTAAGACCTCCCT 58.884 50.000 14.11 0.00 46.72 4.20
4787 6901 2.172930 GGTTGGGAATCTAAGACCTCCC 59.827 54.545 7.96 7.96 46.77 4.30
4788 6902 3.116174 AGGTTGGGAATCTAAGACCTCC 58.884 50.000 0.00 0.00 32.25 4.30
4789 6903 5.012251 GGATAGGTTGGGAATCTAAGACCTC 59.988 48.000 0.00 0.00 38.40 3.85
4790 6904 4.908481 GGATAGGTTGGGAATCTAAGACCT 59.092 45.833 0.00 0.00 40.40 3.85
4791 6905 4.262506 CGGATAGGTTGGGAATCTAAGACC 60.263 50.000 0.00 0.00 0.00 3.85
4792 6906 4.344390 ACGGATAGGTTGGGAATCTAAGAC 59.656 45.833 0.00 0.00 0.00 3.01
4793 6907 4.553678 ACGGATAGGTTGGGAATCTAAGA 58.446 43.478 0.00 0.00 0.00 2.10
4794 6908 4.957684 ACGGATAGGTTGGGAATCTAAG 57.042 45.455 0.00 0.00 0.00 2.18
4795 6909 4.836736 CCTACGGATAGGTTGGGAATCTAA 59.163 45.833 0.00 0.00 42.95 2.10
4796 6910 4.413760 CCTACGGATAGGTTGGGAATCTA 58.586 47.826 0.00 0.00 42.95 1.98
4797 6911 3.240302 CCTACGGATAGGTTGGGAATCT 58.760 50.000 0.00 0.00 42.95 2.40
4798 6912 3.679824 CCTACGGATAGGTTGGGAATC 57.320 52.381 0.00 0.00 42.95 2.52


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

AutoCloner maintained by Alex Coulton.