Multiple sequence alignment - TraesCS2D01G547700

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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 TraesCS2D01G547700 chr2D 100.000 2154 0 0 1 2154 623959498 623957345 0.000000e+00 3978.0
1 TraesCS2D01G547700 chr2D 100.000 2148 0 0 2470 4617 623957029 623954882 0.000000e+00 3967.0
2 TraesCS2D01G547700 chr2D 88.704 903 97 5 1000 1901 623895270 623896168 0.000000e+00 1098.0
3 TraesCS2D01G547700 chr2D 83.577 889 117 16 2841 3717 623896426 623897297 0.000000e+00 806.0
4 TraesCS2D01G547700 chr2D 79.001 1181 200 36 2596 3750 617463562 617464720 0.000000e+00 763.0
5 TraesCS2D01G547700 chr2D 85.408 233 22 5 3 223 596192982 596192750 9.990000e-57 231.0
6 TraesCS2D01G547700 chr2D 85.065 154 21 2 48 200 252527972 252528124 6.190000e-34 156.0
7 TraesCS2D01G547700 chr2D 89.286 112 6 5 627 732 185383743 185383632 8.060000e-28 135.0
8 TraesCS2D01G547700 chr2B 89.357 2114 151 32 2471 4548 765592516 765590441 0.000000e+00 2590.0
9 TraesCS2D01G547700 chr2B 94.361 993 53 3 947 1937 765594867 765593876 0.000000e+00 1520.0
10 TraesCS2D01G547700 chr2B 90.466 902 83 3 1000 1901 753829991 753829093 0.000000e+00 1186.0
11 TraesCS2D01G547700 chr2B 89.381 904 89 6 1000 1901 753748002 753748900 0.000000e+00 1131.0
12 TraesCS2D01G547700 chr2B 88.634 915 96 6 988 1901 765572192 765573099 0.000000e+00 1107.0
13 TraesCS2D01G547700 chr2B 82.927 369 33 14 233 592 765595501 765595154 5.800000e-79 305.0
14 TraesCS2D01G547700 chr2B 87.143 210 25 2 1934 2143 765593790 765593583 2.150000e-58 237.0
15 TraesCS2D01G547700 chr2B 88.083 193 12 8 723 908 765595054 765594866 7.780000e-53 219.0
16 TraesCS2D01G547700 chr2B 89.565 115 7 4 2484 2596 765593171 765593060 1.730000e-29 141.0
17 TraesCS2D01G547700 chr2B 96.203 79 3 0 4539 4617 765590415 765590337 3.750000e-26 130.0
18 TraesCS2D01G547700 chr2A 93.745 1279 76 2 2625 3903 755175819 755174545 0.000000e+00 1916.0
19 TraesCS2D01G547700 chr2A 91.840 1299 60 19 756 2043 755177731 755176468 0.000000e+00 1770.0
20 TraesCS2D01G547700 chr2A 90.008 1271 97 12 2639 3900 755337149 755338398 0.000000e+00 1616.0
21 TraesCS2D01G547700 chr2A 93.983 1047 55 4 890 1934 755335597 755336637 0.000000e+00 1578.0
22 TraesCS2D01G547700 chr2A 90.733 928 81 5 989 1914 748078205 748079129 0.000000e+00 1232.0
23 TraesCS2D01G547700 chr2A 89.083 916 95 5 1000 1914 748088602 748089513 0.000000e+00 1133.0
24 TraesCS2D01G547700 chr2A 81.244 1093 176 20 2652 3721 755087282 755088368 0.000000e+00 856.0
25 TraesCS2D01G547700 chr2A 89.969 648 51 5 3902 4544 755174518 755173880 0.000000e+00 824.0
26 TraesCS2D01G547700 chr2A 78.795 1212 208 36 2596 3780 748079881 748081070 0.000000e+00 769.0
27 TraesCS2D01G547700 chr2A 81.101 963 150 23 2776 3720 755247682 755246734 0.000000e+00 741.0
28 TraesCS2D01G547700 chr2A 86.313 453 24 8 3902 4350 755338428 755338846 4.210000e-125 459.0
29 TraesCS2D01G547700 chr2A 93.000 200 10 3 219 417 755178271 755178075 5.840000e-74 289.0
30 TraesCS2D01G547700 chr2A 96.104 77 3 0 4376 4452 755338843 755338919 4.850000e-25 126.0
31 TraesCS2D01G547700 chr2A 98.039 51 1 0 534 584 755177956 755177906 6.360000e-14 89.8
32 TraesCS2D01G547700 chr7D 89.465 1196 82 23 3221 4383 534442981 534444165 0.000000e+00 1471.0
33 TraesCS2D01G547700 chr7D 90.406 271 14 8 316 586 534440242 534440500 3.420000e-91 346.0
34 TraesCS2D01G547700 chr7D 92.797 236 16 1 627 862 534440787 534441021 1.590000e-89 340.0
35 TraesCS2D01G547700 chr7D 92.771 166 12 0 4380 4545 534444279 534444444 1.660000e-59 241.0
36 TraesCS2D01G547700 chr7D 91.304 115 6 3 2476 2588 534442637 534442749 2.220000e-33 154.0
37 TraesCS2D01G547700 chr7D 97.468 79 2 0 4539 4617 534444473 534444551 8.060000e-28 135.0
38 TraesCS2D01G547700 chr7D 86.290 124 11 5 627 744 121926394 121926271 3.750000e-26 130.0
39 TraesCS2D01G547700 chr7D 86.066 122 12 4 626 743 49770829 49770709 4.850000e-25 126.0
40 TraesCS2D01G547700 chr7D 97.015 67 2 0 796 862 534441020 534441086 3.780000e-21 113.0
41 TraesCS2D01G547700 chr7D 88.043 92 7 3 2526 2615 534442754 534442843 6.320000e-19 106.0
42 TraesCS2D01G547700 chr3A 86.752 234 18 7 3 223 448476953 448476720 9.920000e-62 248.0
43 TraesCS2D01G547700 chr4D 87.678 211 22 3 1 208 345329206 345329415 4.620000e-60 243.0
44 TraesCS2D01G547700 chr4D 84.810 237 20 6 3 223 236933445 236933681 1.670000e-54 224.0
45 TraesCS2D01G547700 chr4D 84.615 234 22 8 3 223 78935134 78934902 2.160000e-53 220.0
46 TraesCS2D01G547700 chr3B 87.179 195 13 10 41 223 244231385 244231191 1.300000e-50 211.0
47 TraesCS2D01G547700 chr5A 83.691 233 26 6 3 223 278202907 278202675 4.680000e-50 209.0
48 TraesCS2D01G547700 chr5A 82.796 93 14 2 2001 2093 607718186 607718096 1.060000e-11 82.4
49 TraesCS2D01G547700 chr6D 83.544 237 22 15 3 223 29092340 29092105 6.060000e-49 206.0
50 TraesCS2D01G547700 chr7A 85.876 177 13 10 59 223 558085162 558085338 1.320000e-40 178.0
51 TraesCS2D01G547700 chr1D 91.262 103 5 3 626 724 474511944 474511842 2.240000e-28 137.0
52 TraesCS2D01G547700 chr5D 91.176 102 5 3 627 724 415988304 415988203 8.060000e-28 135.0
53 TraesCS2D01G547700 chr5D 88.393 112 9 3 626 733 64275003 64274892 1.040000e-26 132.0
54 TraesCS2D01G547700 chr4A 91.176 102 5 3 627 724 613173694 613173795 8.060000e-28 135.0
55 TraesCS2D01G547700 chr1A 88.596 114 8 4 627 735 14163547 14163660 2.900000e-27 134.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G547700 chr2D 623954882 623959498 4616 True 3972.500000 3978 100.000000 1 4617 2 chr2D.!!$R3 4616
1 TraesCS2D01G547700 chr2D 623895270 623897297 2027 False 952.000000 1098 86.140500 1000 3717 2 chr2D.!!$F3 2717
2 TraesCS2D01G547700 chr2D 617463562 617464720 1158 False 763.000000 763 79.001000 2596 3750 1 chr2D.!!$F2 1154
3 TraesCS2D01G547700 chr2B 753829093 753829991 898 True 1186.000000 1186 90.466000 1000 1901 1 chr2B.!!$R1 901
4 TraesCS2D01G547700 chr2B 753748002 753748900 898 False 1131.000000 1131 89.381000 1000 1901 1 chr2B.!!$F1 901
5 TraesCS2D01G547700 chr2B 765572192 765573099 907 False 1107.000000 1107 88.634000 988 1901 1 chr2B.!!$F2 913
6 TraesCS2D01G547700 chr2B 765590337 765595501 5164 True 734.571429 2590 89.662714 233 4617 7 chr2B.!!$R2 4384
7 TraesCS2D01G547700 chr2A 748088602 748089513 911 False 1133.000000 1133 89.083000 1000 1914 1 chr2A.!!$F1 914
8 TraesCS2D01G547700 chr2A 748078205 748081070 2865 False 1000.500000 1232 84.764000 989 3780 2 chr2A.!!$F3 2791
9 TraesCS2D01G547700 chr2A 755173880 755178271 4391 True 977.760000 1916 93.318600 219 4544 5 chr2A.!!$R2 4325
10 TraesCS2D01G547700 chr2A 755335597 755338919 3322 False 944.750000 1616 91.602000 890 4452 4 chr2A.!!$F4 3562
11 TraesCS2D01G547700 chr2A 755087282 755088368 1086 False 856.000000 856 81.244000 2652 3721 1 chr2A.!!$F2 1069
12 TraesCS2D01G547700 chr2A 755246734 755247682 948 True 741.000000 741 81.101000 2776 3720 1 chr2A.!!$R1 944
13 TraesCS2D01G547700 chr7D 534440242 534444551 4309 False 363.250000 1471 92.408625 316 4617 8 chr7D.!!$F1 4301

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
148 149 0.036875 AGCTTGTAGCCCGCTTTTCT 59.963 50.000 0.00 0.00 43.77 2.52 F
149 150 0.881796 GCTTGTAGCCCGCTTTTCTT 59.118 50.000 0.00 0.00 34.48 2.52 F
150 151 1.135660 GCTTGTAGCCCGCTTTTCTTC 60.136 52.381 0.00 0.00 34.48 2.87 F
157 158 1.200252 GCCCGCTTTTCTTCTCTTTCC 59.800 52.381 0.00 0.00 0.00 3.13 F
371 374 1.539065 GGCACGTGATATCCAGAGGTG 60.539 57.143 22.23 5.28 0.00 4.00 F
919 1365 2.035756 GCATAAATAGCGTTGCGTTTGC 60.036 45.455 5.77 0.00 43.20 3.68 F
2152 3522 0.318445 ATTCACGTATAGGGACGCGC 60.318 55.000 5.73 0.00 46.87 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 2539 1.673665 GAGCAGGTTCAGGCTGGTG 60.674 63.158 15.73 8.51 41.22 4.17 R
1656 2664 1.861971 GGAAGAAGTCCGACACGTTT 58.138 50.000 0.40 0.00 36.40 3.60 R
2054 3424 6.904626 ACGGGTAACTTCTAATCTCTACCTA 58.095 40.000 0.00 0.00 31.40 3.08 R
2105 3475 9.631257 TTAAAGTTACTTAAAAAGCCTACCACT 57.369 29.630 0.00 0.00 0.00 4.00 R
2106 3476 9.888878 CTTAAAGTTACTTAAAAAGCCTACCAC 57.111 33.333 0.00 0.00 0.00 4.16 R
2723 5297 0.035317 GCGGCATGTGAGGGATATGA 59.965 55.000 0.00 0.00 0.00 2.15 R
4079 6712 0.609131 ATTGTGTTGCCTTCCTCCGG 60.609 55.000 0.00 0.00 0.00 5.14 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
24 25 6.884280 ATCATTTGTAGCCAACCTAATAGC 57.116 37.500 0.00 0.00 0.00 2.97
25 26 5.130350 TCATTTGTAGCCAACCTAATAGCC 58.870 41.667 0.00 0.00 0.00 3.93
26 27 3.570912 TTGTAGCCAACCTAATAGCCC 57.429 47.619 0.00 0.00 0.00 5.19
27 28 2.483547 TGTAGCCAACCTAATAGCCCA 58.516 47.619 0.00 0.00 0.00 5.36
28 29 3.053077 TGTAGCCAACCTAATAGCCCAT 58.947 45.455 0.00 0.00 0.00 4.00
29 30 2.959465 AGCCAACCTAATAGCCCATC 57.041 50.000 0.00 0.00 0.00 3.51
30 31 1.425448 AGCCAACCTAATAGCCCATCC 59.575 52.381 0.00 0.00 0.00 3.51
31 32 1.144913 GCCAACCTAATAGCCCATCCA 59.855 52.381 0.00 0.00 0.00 3.41
32 33 2.225117 GCCAACCTAATAGCCCATCCAT 60.225 50.000 0.00 0.00 0.00 3.41
33 34 3.010138 GCCAACCTAATAGCCCATCCATA 59.990 47.826 0.00 0.00 0.00 2.74
34 35 4.325344 GCCAACCTAATAGCCCATCCATAT 60.325 45.833 0.00 0.00 0.00 1.78
35 36 5.104109 GCCAACCTAATAGCCCATCCATATA 60.104 44.000 0.00 0.00 0.00 0.86
36 37 6.580254 GCCAACCTAATAGCCCATCCATATAA 60.580 42.308 0.00 0.00 0.00 0.98
37 38 7.586349 CCAACCTAATAGCCCATCCATATAAT 58.414 38.462 0.00 0.00 0.00 1.28
38 39 8.723365 CCAACCTAATAGCCCATCCATATAATA 58.277 37.037 0.00 0.00 0.00 0.98
39 40 9.784531 CAACCTAATAGCCCATCCATATAATAG 57.215 37.037 0.00 0.00 0.00 1.73
40 41 9.520839 AACCTAATAGCCCATCCATATAATAGT 57.479 33.333 0.00 0.00 0.00 2.12
41 42 9.520839 ACCTAATAGCCCATCCATATAATAGTT 57.479 33.333 0.00 0.00 0.00 2.24
46 47 7.568128 AGCCCATCCATATAATAGTTACACA 57.432 36.000 0.00 0.00 0.00 3.72
47 48 8.162848 AGCCCATCCATATAATAGTTACACAT 57.837 34.615 0.00 0.00 0.00 3.21
48 49 9.279233 AGCCCATCCATATAATAGTTACACATA 57.721 33.333 0.00 0.00 0.00 2.29
49 50 9.326413 GCCCATCCATATAATAGTTACACATAC 57.674 37.037 0.00 0.00 0.00 2.39
87 88 9.574516 ACAATTAATATATGACCCACTCTTTCC 57.425 33.333 0.00 0.00 0.00 3.13
88 89 9.799106 CAATTAATATATGACCCACTCTTTCCT 57.201 33.333 0.00 0.00 0.00 3.36
90 91 8.798975 TTAATATATGACCCACTCTTTCCTCT 57.201 34.615 0.00 0.00 0.00 3.69
91 92 6.926630 ATATATGACCCACTCTTTCCTCTC 57.073 41.667 0.00 0.00 0.00 3.20
92 93 2.398754 TGACCCACTCTTTCCTCTCA 57.601 50.000 0.00 0.00 0.00 3.27
93 94 1.971357 TGACCCACTCTTTCCTCTCAC 59.029 52.381 0.00 0.00 0.00 3.51
94 95 1.971357 GACCCACTCTTTCCTCTCACA 59.029 52.381 0.00 0.00 0.00 3.58
95 96 2.368875 GACCCACTCTTTCCTCTCACAA 59.631 50.000 0.00 0.00 0.00 3.33
96 97 2.777692 ACCCACTCTTTCCTCTCACAAA 59.222 45.455 0.00 0.00 0.00 2.83
97 98 3.181450 ACCCACTCTTTCCTCTCACAAAG 60.181 47.826 0.00 0.00 0.00 2.77
98 99 3.406764 CCACTCTTTCCTCTCACAAAGG 58.593 50.000 0.00 0.00 35.05 3.11
99 100 3.406764 CACTCTTTCCTCTCACAAAGGG 58.593 50.000 0.00 0.00 36.34 3.95
100 101 3.049344 ACTCTTTCCTCTCACAAAGGGT 58.951 45.455 0.00 0.00 38.30 4.34
109 110 3.116091 CACAAAGGGTGTTGGAGCT 57.884 52.632 0.00 0.00 42.75 4.09
110 111 0.954452 CACAAAGGGTGTTGGAGCTC 59.046 55.000 4.71 4.71 42.75 4.09
111 112 0.535102 ACAAAGGGTGTTGGAGCTCG 60.535 55.000 7.83 0.00 37.01 5.03
112 113 0.535102 CAAAGGGTGTTGGAGCTCGT 60.535 55.000 7.83 0.00 0.00 4.18
113 114 0.535102 AAAGGGTGTTGGAGCTCGTG 60.535 55.000 7.83 0.00 0.00 4.35
114 115 3.050275 GGGTGTTGGAGCTCGTGC 61.050 66.667 7.83 0.07 40.05 5.34
127 128 2.575694 CTCGTGCTAGAGCTGATTGT 57.424 50.000 2.72 0.00 42.66 2.71
128 129 3.699779 CTCGTGCTAGAGCTGATTGTA 57.300 47.619 2.72 0.00 42.66 2.41
129 130 4.033990 CTCGTGCTAGAGCTGATTGTAA 57.966 45.455 2.72 0.00 42.66 2.41
130 131 4.033990 TCGTGCTAGAGCTGATTGTAAG 57.966 45.455 2.72 0.00 42.66 2.34
131 132 2.537625 CGTGCTAGAGCTGATTGTAAGC 59.462 50.000 2.72 0.00 42.66 3.09
139 140 3.682372 GCTGATTGTAAGCTTGTAGCC 57.318 47.619 9.86 0.00 43.77 3.93
140 141 2.356069 GCTGATTGTAAGCTTGTAGCCC 59.644 50.000 9.86 0.00 43.77 5.19
141 142 2.609459 CTGATTGTAAGCTTGTAGCCCG 59.391 50.000 9.86 0.00 43.77 6.13
142 143 1.330829 GATTGTAAGCTTGTAGCCCGC 59.669 52.381 9.86 0.00 43.77 6.13
143 144 0.323629 TTGTAAGCTTGTAGCCCGCT 59.676 50.000 9.86 0.00 43.77 5.52
144 145 0.323629 TGTAAGCTTGTAGCCCGCTT 59.676 50.000 9.86 0.00 43.77 4.68
145 146 1.271163 TGTAAGCTTGTAGCCCGCTTT 60.271 47.619 9.86 0.00 43.77 3.51
146 147 1.810755 GTAAGCTTGTAGCCCGCTTTT 59.189 47.619 9.86 0.00 43.77 2.27
147 148 0.881796 AAGCTTGTAGCCCGCTTTTC 59.118 50.000 0.00 0.00 43.77 2.29
148 149 0.036875 AGCTTGTAGCCCGCTTTTCT 59.963 50.000 0.00 0.00 43.77 2.52
149 150 0.881796 GCTTGTAGCCCGCTTTTCTT 59.118 50.000 0.00 0.00 34.48 2.52
150 151 1.135660 GCTTGTAGCCCGCTTTTCTTC 60.136 52.381 0.00 0.00 34.48 2.87
151 152 2.427506 CTTGTAGCCCGCTTTTCTTCT 58.572 47.619 0.00 0.00 0.00 2.85
152 153 2.094762 TGTAGCCCGCTTTTCTTCTC 57.905 50.000 0.00 0.00 0.00 2.87
153 154 1.623811 TGTAGCCCGCTTTTCTTCTCT 59.376 47.619 0.00 0.00 0.00 3.10
154 155 2.038557 TGTAGCCCGCTTTTCTTCTCTT 59.961 45.455 0.00 0.00 0.00 2.85
155 156 2.278332 AGCCCGCTTTTCTTCTCTTT 57.722 45.000 0.00 0.00 0.00 2.52
156 157 2.155279 AGCCCGCTTTTCTTCTCTTTC 58.845 47.619 0.00 0.00 0.00 2.62
157 158 1.200252 GCCCGCTTTTCTTCTCTTTCC 59.800 52.381 0.00 0.00 0.00 3.13
158 159 2.784347 CCCGCTTTTCTTCTCTTTCCT 58.216 47.619 0.00 0.00 0.00 3.36
159 160 3.149981 CCCGCTTTTCTTCTCTTTCCTT 58.850 45.455 0.00 0.00 0.00 3.36
160 161 3.189495 CCCGCTTTTCTTCTCTTTCCTTC 59.811 47.826 0.00 0.00 0.00 3.46
161 162 3.815401 CCGCTTTTCTTCTCTTTCCTTCA 59.185 43.478 0.00 0.00 0.00 3.02
162 163 4.319839 CCGCTTTTCTTCTCTTTCCTTCAC 60.320 45.833 0.00 0.00 0.00 3.18
163 164 4.319839 CGCTTTTCTTCTCTTTCCTTCACC 60.320 45.833 0.00 0.00 0.00 4.02
164 165 4.824537 GCTTTTCTTCTCTTTCCTTCACCT 59.175 41.667 0.00 0.00 0.00 4.00
165 166 5.998363 GCTTTTCTTCTCTTTCCTTCACCTA 59.002 40.000 0.00 0.00 0.00 3.08
166 167 6.148645 GCTTTTCTTCTCTTTCCTTCACCTAG 59.851 42.308 0.00 0.00 0.00 3.02
167 168 6.996180 TTTCTTCTCTTTCCTTCACCTAGA 57.004 37.500 0.00 0.00 0.00 2.43
168 169 5.986501 TCTTCTCTTTCCTTCACCTAGAC 57.013 43.478 0.00 0.00 0.00 2.59
169 170 5.394738 TCTTCTCTTTCCTTCACCTAGACA 58.605 41.667 0.00 0.00 0.00 3.41
170 171 6.019748 TCTTCTCTTTCCTTCACCTAGACAT 58.980 40.000 0.00 0.00 0.00 3.06
171 172 7.182760 TCTTCTCTTTCCTTCACCTAGACATA 58.817 38.462 0.00 0.00 0.00 2.29
172 173 7.674348 TCTTCTCTTTCCTTCACCTAGACATAA 59.326 37.037 0.00 0.00 0.00 1.90
173 174 7.792364 TCTCTTTCCTTCACCTAGACATAAA 57.208 36.000 0.00 0.00 0.00 1.40
174 175 8.380742 TCTCTTTCCTTCACCTAGACATAAAT 57.619 34.615 0.00 0.00 0.00 1.40
175 176 8.478877 TCTCTTTCCTTCACCTAGACATAAATC 58.521 37.037 0.00 0.00 0.00 2.17
176 177 8.380742 TCTTTCCTTCACCTAGACATAAATCT 57.619 34.615 0.00 0.00 0.00 2.40
177 178 8.260818 TCTTTCCTTCACCTAGACATAAATCTG 58.739 37.037 0.00 0.00 0.00 2.90
178 179 7.733773 TTCCTTCACCTAGACATAAATCTGA 57.266 36.000 0.00 0.00 0.00 3.27
179 180 7.113658 TCCTTCACCTAGACATAAATCTGAC 57.886 40.000 0.00 0.00 0.00 3.51
180 181 6.667848 TCCTTCACCTAGACATAAATCTGACA 59.332 38.462 0.00 0.00 0.00 3.58
181 182 7.345653 TCCTTCACCTAGACATAAATCTGACAT 59.654 37.037 0.00 0.00 0.00 3.06
182 183 7.440556 CCTTCACCTAGACATAAATCTGACATG 59.559 40.741 0.00 0.00 0.00 3.21
183 184 6.820335 TCACCTAGACATAAATCTGACATGG 58.180 40.000 0.00 0.00 0.00 3.66
184 185 5.468072 CACCTAGACATAAATCTGACATGGC 59.532 44.000 0.00 0.00 0.00 4.40
185 186 5.130975 ACCTAGACATAAATCTGACATGGCA 59.869 40.000 0.00 0.00 29.57 4.92
186 187 6.183361 ACCTAGACATAAATCTGACATGGCAT 60.183 38.462 0.00 0.00 29.57 4.40
187 188 6.370994 CCTAGACATAAATCTGACATGGCATC 59.629 42.308 0.00 0.00 29.57 3.91
188 189 5.938279 AGACATAAATCTGACATGGCATCT 58.062 37.500 0.00 0.00 29.57 2.90
189 190 5.996513 AGACATAAATCTGACATGGCATCTC 59.003 40.000 0.00 0.00 29.57 2.75
190 191 5.938279 ACATAAATCTGACATGGCATCTCT 58.062 37.500 0.00 0.00 0.00 3.10
191 192 6.363065 ACATAAATCTGACATGGCATCTCTT 58.637 36.000 0.00 0.00 0.00 2.85
192 193 7.512130 ACATAAATCTGACATGGCATCTCTTA 58.488 34.615 0.00 0.00 0.00 2.10
193 194 8.162085 ACATAAATCTGACATGGCATCTCTTAT 58.838 33.333 0.00 0.67 0.00 1.73
194 195 9.662947 CATAAATCTGACATGGCATCTCTTATA 57.337 33.333 0.00 0.00 0.00 0.98
195 196 9.887629 ATAAATCTGACATGGCATCTCTTATAG 57.112 33.333 0.00 0.00 0.00 1.31
196 197 5.144692 TCTGACATGGCATCTCTTATAGC 57.855 43.478 0.00 0.00 0.00 2.97
198 199 3.008375 TGACATGGCATCTCTTATAGCCC 59.992 47.826 0.00 0.00 46.45 5.19
199 200 2.027745 ACATGGCATCTCTTATAGCCCG 60.028 50.000 0.00 0.00 46.45 6.13
200 201 1.717032 TGGCATCTCTTATAGCCCGT 58.283 50.000 0.00 0.00 46.45 5.28
201 202 2.047061 TGGCATCTCTTATAGCCCGTT 58.953 47.619 0.00 0.00 46.45 4.44
202 203 2.438021 TGGCATCTCTTATAGCCCGTTT 59.562 45.455 0.00 0.00 46.45 3.60
203 204 3.644265 TGGCATCTCTTATAGCCCGTTTA 59.356 43.478 0.00 0.00 46.45 2.01
204 205 4.286032 TGGCATCTCTTATAGCCCGTTTAT 59.714 41.667 0.00 0.00 46.45 1.40
205 206 4.631813 GGCATCTCTTATAGCCCGTTTATG 59.368 45.833 0.00 0.00 41.25 1.90
206 207 5.238583 GCATCTCTTATAGCCCGTTTATGT 58.761 41.667 0.00 0.00 0.00 2.29
207 208 5.348997 GCATCTCTTATAGCCCGTTTATGTC 59.651 44.000 0.00 0.00 0.00 3.06
208 209 6.455647 CATCTCTTATAGCCCGTTTATGTCA 58.544 40.000 0.00 0.00 0.00 3.58
209 210 5.839621 TCTCTTATAGCCCGTTTATGTCAC 58.160 41.667 0.00 0.00 0.00 3.67
210 211 5.597182 TCTCTTATAGCCCGTTTATGTCACT 59.403 40.000 0.00 0.00 0.00 3.41
211 212 5.839621 TCTTATAGCCCGTTTATGTCACTC 58.160 41.667 0.00 0.00 0.00 3.51
212 213 5.597182 TCTTATAGCCCGTTTATGTCACTCT 59.403 40.000 0.00 0.00 0.00 3.24
213 214 6.774170 TCTTATAGCCCGTTTATGTCACTCTA 59.226 38.462 0.00 0.00 0.00 2.43
214 215 7.450634 TCTTATAGCCCGTTTATGTCACTCTAT 59.549 37.037 0.00 0.00 0.00 1.98
215 216 4.755266 AGCCCGTTTATGTCACTCTATT 57.245 40.909 0.00 0.00 0.00 1.73
216 217 4.442706 AGCCCGTTTATGTCACTCTATTG 58.557 43.478 0.00 0.00 0.00 1.90
217 218 4.081087 AGCCCGTTTATGTCACTCTATTGT 60.081 41.667 0.00 0.00 0.00 2.71
287 288 7.460296 TCGTTTTTATGTAGTATGTCGACGTA 58.540 34.615 13.48 13.48 0.00 3.57
371 374 1.539065 GGCACGTGATATCCAGAGGTG 60.539 57.143 22.23 5.28 0.00 4.00
387 391 5.393461 CCAGAGGTGCAAGGATAATGTTTTC 60.393 44.000 0.00 0.00 0.00 2.29
390 394 6.151817 AGAGGTGCAAGGATAATGTTTTCTTC 59.848 38.462 0.00 0.00 0.00 2.87
417 421 3.565482 TCTCCCGTACGTTATGGTCATAC 59.435 47.826 15.21 0.00 32.79 2.39
418 422 2.290367 TCCCGTACGTTATGGTCATACG 59.710 50.000 15.21 0.00 38.62 3.06
420 424 3.607422 CGTACGTTATGGTCATACGGA 57.393 47.619 7.22 0.00 36.00 4.69
421 425 3.548587 CGTACGTTATGGTCATACGGAG 58.451 50.000 7.22 0.00 36.00 4.63
590 639 3.342926 AGGAGGCATCAAGATACTCCT 57.657 47.619 20.87 20.87 43.64 3.69
591 640 3.238597 AGGAGGCATCAAGATACTCCTC 58.761 50.000 20.87 16.83 44.41 3.71
592 641 3.676291 GAGGCATCAAGATACTCCTCC 57.324 52.381 0.00 0.00 35.32 4.30
593 642 2.968574 GAGGCATCAAGATACTCCTCCA 59.031 50.000 0.00 0.00 35.32 3.86
594 643 3.582208 GAGGCATCAAGATACTCCTCCAT 59.418 47.826 0.00 0.00 35.32 3.41
595 644 4.756564 AGGCATCAAGATACTCCTCCATA 58.243 43.478 0.00 0.00 0.00 2.74
596 645 4.530161 AGGCATCAAGATACTCCTCCATAC 59.470 45.833 0.00 0.00 0.00 2.39
597 646 4.323104 GGCATCAAGATACTCCTCCATACC 60.323 50.000 0.00 0.00 0.00 2.73
598 647 4.284490 GCATCAAGATACTCCTCCATACCA 59.716 45.833 0.00 0.00 0.00 3.25
599 648 5.046014 GCATCAAGATACTCCTCCATACCAT 60.046 44.000 0.00 0.00 0.00 3.55
600 649 6.155221 GCATCAAGATACTCCTCCATACCATA 59.845 42.308 0.00 0.00 0.00 2.74
601 650 7.310671 GCATCAAGATACTCCTCCATACCATAA 60.311 40.741 0.00 0.00 0.00 1.90
603 652 8.138928 TCAAGATACTCCTCCATACCATAATG 57.861 38.462 0.00 0.00 0.00 1.90
604 653 7.955750 TCAAGATACTCCTCCATACCATAATGA 59.044 37.037 0.00 0.00 0.00 2.57
605 654 8.597167 CAAGATACTCCTCCATACCATAATGAA 58.403 37.037 0.00 0.00 0.00 2.57
606 655 8.742125 AGATACTCCTCCATACCATAATGAAA 57.258 34.615 0.00 0.00 0.00 2.69
607 656 8.820831 AGATACTCCTCCATACCATAATGAAAG 58.179 37.037 0.00 0.00 0.00 2.62
608 657 8.742125 ATACTCCTCCATACCATAATGAAAGA 57.258 34.615 0.00 0.00 0.00 2.52
610 659 7.456725 ACTCCTCCATACCATAATGAAAGATG 58.543 38.462 0.00 0.00 0.00 2.90
611 660 7.072961 ACTCCTCCATACCATAATGAAAGATGT 59.927 37.037 0.00 0.00 0.00 3.06
613 662 8.944138 TCCTCCATACCATAATGAAAGATGTTA 58.056 33.333 0.00 0.00 0.00 2.41
614 663 9.573166 CCTCCATACCATAATGAAAGATGTTAA 57.427 33.333 0.00 0.00 0.00 2.01
691 986 9.950680 ATCCGTATGTTATTCATTTGAAATGTC 57.049 29.630 16.62 5.65 37.61 3.06
692 987 9.173021 TCCGTATGTTATTCATTTGAAATGTCT 57.827 29.630 16.62 8.54 37.61 3.41
789 1090 2.559668 TCGTTCCATCCTACTTTGACGT 59.440 45.455 0.00 0.00 0.00 4.34
874 1314 2.225624 TGGTCTTCATTCCTCCCTCAGA 60.226 50.000 0.00 0.00 0.00 3.27
875 1315 2.169561 GGTCTTCATTCCTCCCTCAGAC 59.830 54.545 0.00 0.00 0.00 3.51
876 1316 3.103742 GTCTTCATTCCTCCCTCAGACT 58.896 50.000 0.00 0.00 0.00 3.24
878 1318 3.772025 TCTTCATTCCTCCCTCAGACTTC 59.228 47.826 0.00 0.00 0.00 3.01
916 1362 2.791158 GCAGCATAAATAGCGTTGCGTT 60.791 45.455 0.00 0.00 40.00 4.84
917 1363 3.425404 CAGCATAAATAGCGTTGCGTTT 58.575 40.909 0.00 2.00 40.00 3.60
918 1364 3.238114 CAGCATAAATAGCGTTGCGTTTG 59.762 43.478 0.00 0.00 40.00 2.93
919 1365 2.035756 GCATAAATAGCGTTGCGTTTGC 60.036 45.455 5.77 0.00 43.20 3.68
1989 3155 8.584157 TGCCTTCTCTTTTTAATTTTAGCATCA 58.416 29.630 0.00 0.00 0.00 3.07
2077 3447 7.999450 ATAGGTAGAGATTAGAAGTTACCCG 57.001 40.000 0.00 0.00 32.81 5.28
2085 3455 8.591940 AGAGATTAGAAGTTACCCGTTTTAGTT 58.408 33.333 0.00 0.00 0.00 2.24
2109 3479 4.989279 AAAAGGCATGCTAACATAGTGG 57.011 40.909 18.92 0.00 33.67 4.00
2146 3516 9.813446 AAGTAACTTTAAGATTCACGTATAGGG 57.187 33.333 0.00 0.00 0.00 3.53
2147 3517 9.193806 AGTAACTTTAAGATTCACGTATAGGGA 57.806 33.333 0.00 0.00 0.00 4.20
2148 3518 9.242477 GTAACTTTAAGATTCACGTATAGGGAC 57.758 37.037 0.00 0.00 0.00 4.46
2150 3520 3.366440 AAGATTCACGTATAGGGACGC 57.634 47.619 0.00 0.00 46.87 5.19
2151 3521 1.266175 AGATTCACGTATAGGGACGCG 59.734 52.381 3.53 3.53 46.87 6.01
2152 3522 0.318445 ATTCACGTATAGGGACGCGC 60.318 55.000 5.73 0.00 46.87 6.86
2153 3523 2.651367 TTCACGTATAGGGACGCGCG 62.651 60.000 30.96 30.96 46.87 6.86
2588 5122 8.278639 TGCTTAGGAATTTGTAGGAATTATGGA 58.721 33.333 0.00 0.00 29.75 3.41
2608 5143 7.997773 ATGGAATCCATTCATGAGATACAAG 57.002 36.000 9.36 0.00 42.23 3.16
2699 5271 1.828979 TTCAACCCGGCCTTATTGTC 58.171 50.000 0.00 0.00 0.00 3.18
2723 5297 1.554160 TGCCGCATTTCAAATTCCCAT 59.446 42.857 0.00 0.00 0.00 4.00
2728 5302 5.786311 CCGCATTTCAAATTCCCATCATAT 58.214 37.500 0.00 0.00 0.00 1.78
2750 5326 0.098200 CTCACATGCCGCACTTCATG 59.902 55.000 0.00 0.00 44.08 3.07
2799 5379 8.827677 ACGAACAATGGCTTCTTCTATTATAAC 58.172 33.333 0.00 0.00 0.00 1.89
2800 5380 8.826710 CGAACAATGGCTTCTTCTATTATAACA 58.173 33.333 0.00 0.00 0.00 2.41
2893 5478 9.546909 CAGTATCTATGTGCACTTTAAAACAAG 57.453 33.333 19.41 4.35 0.00 3.16
2982 5567 8.608844 AGTATCTAAATAGCTACATTTGCCAC 57.391 34.615 0.00 0.00 29.70 5.01
3132 5726 1.202031 GCTTGAACAAGTTATCGGCCG 60.202 52.381 22.12 22.12 40.45 6.13
3161 5755 6.675987 AGAAACATTGAAGAAGCTGACATTC 58.324 36.000 0.00 0.00 0.00 2.67
3181 5775 4.336889 TCTTCGGTTGCCCTATATTCAG 57.663 45.455 0.00 0.00 0.00 3.02
3305 5899 5.446143 AGGTTCACGCATTTTCATAAACA 57.554 34.783 0.00 0.00 0.00 2.83
3586 6180 3.672781 GCCTCACACTTACTAAGGTCGTC 60.673 52.174 0.88 0.00 0.00 4.20
3601 6195 2.081462 GTCGTCCCCCTTTGTATTGTG 58.919 52.381 0.00 0.00 0.00 3.33
3790 6392 7.222611 AGCTGAACAATGTTGTGTTATTGAAAC 59.777 33.333 2.20 0.00 41.78 2.78
3809 6411 7.181143 TGAAACGTTGTTCCTACAAAGATAC 57.819 36.000 0.00 3.09 45.33 2.24
3881 6483 2.590073 CGCGGTTGCATAAAATCAACA 58.410 42.857 0.00 0.00 43.06 3.33
3970 6603 5.633830 AACAAATACAACAGATCTGCCAG 57.366 39.130 22.83 14.40 0.00 4.85
3999 6632 4.466015 GTGGATGGTGGATGGTTTGTATTT 59.534 41.667 0.00 0.00 0.00 1.40
4000 6633 5.046663 GTGGATGGTGGATGGTTTGTATTTT 60.047 40.000 0.00 0.00 0.00 1.82
4059 6692 6.569780 ACTTTTACACCTTAAGCACCTTTTG 58.430 36.000 0.00 0.00 0.00 2.44
4065 6698 2.562738 CCTTAAGCACCTTTTGGGAAGG 59.437 50.000 0.00 3.35 46.08 3.46
4079 6712 7.013369 CCTTTTGGGAAGGATAATAACAGCTAC 59.987 40.741 0.00 0.00 39.81 3.58
4107 6741 7.284489 GGAGGAAGGCAACACAATTTGTATATA 59.716 37.037 0.86 0.00 37.51 0.86
4232 6888 6.907741 TGTTGTCTGAATATTTCGCATTCAA 58.092 32.000 0.00 0.00 40.81 2.69
4233 6889 7.366513 TGTTGTCTGAATATTTCGCATTCAAA 58.633 30.769 0.00 0.00 40.81 2.69
4234 6890 7.864882 TGTTGTCTGAATATTTCGCATTCAAAA 59.135 29.630 0.00 0.00 40.81 2.44
4235 6891 8.863049 GTTGTCTGAATATTTCGCATTCAAAAT 58.137 29.630 0.00 0.00 40.81 1.82
4236 6892 8.984891 TGTCTGAATATTTCGCATTCAAAATT 57.015 26.923 0.00 0.00 40.81 1.82
4237 6893 9.421806 TGTCTGAATATTTCGCATTCAAAATTT 57.578 25.926 0.00 0.00 40.81 1.82
4238 6894 9.891535 GTCTGAATATTTCGCATTCAAAATTTC 57.108 29.630 0.00 0.00 40.81 2.17
4239 6895 9.636879 TCTGAATATTTCGCATTCAAAATTTCA 57.363 25.926 0.00 0.00 40.81 2.69
4280 6936 8.316946 CCCAGAGTTCATAATCTAGCATAATCA 58.683 37.037 0.00 0.00 0.00 2.57
4464 7241 7.537991 CCATATGAACAAAATTTGCGCATTTTT 59.462 29.630 12.75 17.56 34.70 1.94
4518 7295 6.311935 CAGATTTAACATGGCTGGAACAAATG 59.688 38.462 0.00 0.00 38.70 2.32
4520 7297 3.389925 AACATGGCTGGAACAAATGTG 57.610 42.857 0.00 0.00 37.14 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.940298 GGCTATTAGGTTGGCTACAAATGATA 59.060 38.462 0.80 0.00 38.54 2.15
2 3 5.130350 GGCTATTAGGTTGGCTACAAATGA 58.870 41.667 0.80 0.00 38.54 2.57
5 6 3.267291 TGGGCTATTAGGTTGGCTACAAA 59.733 43.478 0.80 0.00 38.54 2.83
6 7 2.847449 TGGGCTATTAGGTTGGCTACAA 59.153 45.455 0.80 0.00 0.00 2.41
7 8 2.483547 TGGGCTATTAGGTTGGCTACA 58.516 47.619 0.80 0.00 0.00 2.74
8 9 3.559384 GGATGGGCTATTAGGTTGGCTAC 60.559 52.174 0.00 0.00 0.00 3.58
9 10 2.642807 GGATGGGCTATTAGGTTGGCTA 59.357 50.000 0.00 0.00 0.00 3.93
10 11 1.425448 GGATGGGCTATTAGGTTGGCT 59.575 52.381 0.00 0.00 0.00 4.75
11 12 1.144913 TGGATGGGCTATTAGGTTGGC 59.855 52.381 0.00 0.00 0.00 4.52
12 13 3.814504 ATGGATGGGCTATTAGGTTGG 57.185 47.619 0.00 0.00 0.00 3.77
13 14 9.784531 CTATTATATGGATGGGCTATTAGGTTG 57.215 37.037 0.00 0.00 0.00 3.77
14 15 9.520839 ACTATTATATGGATGGGCTATTAGGTT 57.479 33.333 0.00 0.00 0.00 3.50
15 16 9.520839 AACTATTATATGGATGGGCTATTAGGT 57.479 33.333 0.00 0.00 0.00 3.08
20 21 9.279233 TGTGTAACTATTATATGGATGGGCTAT 57.721 33.333 0.00 0.00 38.04 2.97
21 22 8.673456 TGTGTAACTATTATATGGATGGGCTA 57.327 34.615 0.00 0.00 38.04 3.93
22 23 7.568128 TGTGTAACTATTATATGGATGGGCT 57.432 36.000 0.00 0.00 38.04 5.19
23 24 9.326413 GTATGTGTAACTATTATATGGATGGGC 57.674 37.037 0.00 0.00 38.04 5.36
61 62 9.574516 GGAAAGAGTGGGTCATATATTAATTGT 57.425 33.333 0.00 0.00 0.00 2.71
62 63 9.799106 AGGAAAGAGTGGGTCATATATTAATTG 57.201 33.333 0.00 0.00 0.00 2.32
64 65 9.398921 AGAGGAAAGAGTGGGTCATATATTAAT 57.601 33.333 0.00 0.00 0.00 1.40
65 66 8.798975 AGAGGAAAGAGTGGGTCATATATTAA 57.201 34.615 0.00 0.00 0.00 1.40
66 67 8.010697 TGAGAGGAAAGAGTGGGTCATATATTA 58.989 37.037 0.00 0.00 0.00 0.98
67 68 6.846505 TGAGAGGAAAGAGTGGGTCATATATT 59.153 38.462 0.00 0.00 0.00 1.28
68 69 6.268847 GTGAGAGGAAAGAGTGGGTCATATAT 59.731 42.308 0.00 0.00 0.00 0.86
69 70 5.598830 GTGAGAGGAAAGAGTGGGTCATATA 59.401 44.000 0.00 0.00 0.00 0.86
70 71 4.407296 GTGAGAGGAAAGAGTGGGTCATAT 59.593 45.833 0.00 0.00 0.00 1.78
71 72 3.769844 GTGAGAGGAAAGAGTGGGTCATA 59.230 47.826 0.00 0.00 0.00 2.15
72 73 2.569404 GTGAGAGGAAAGAGTGGGTCAT 59.431 50.000 0.00 0.00 0.00 3.06
73 74 1.971357 GTGAGAGGAAAGAGTGGGTCA 59.029 52.381 0.00 0.00 0.00 4.02
74 75 1.971357 TGTGAGAGGAAAGAGTGGGTC 59.029 52.381 0.00 0.00 0.00 4.46
75 76 2.103153 TGTGAGAGGAAAGAGTGGGT 57.897 50.000 0.00 0.00 0.00 4.51
76 77 3.406764 CTTTGTGAGAGGAAAGAGTGGG 58.593 50.000 0.00 0.00 31.89 4.61
77 78 3.406764 CCTTTGTGAGAGGAAAGAGTGG 58.593 50.000 0.00 0.00 36.33 4.00
78 79 3.181450 ACCCTTTGTGAGAGGAAAGAGTG 60.181 47.826 0.00 0.00 36.33 3.51
79 80 3.049344 ACCCTTTGTGAGAGGAAAGAGT 58.951 45.455 0.00 0.00 36.33 3.24
80 81 3.778954 ACCCTTTGTGAGAGGAAAGAG 57.221 47.619 0.00 0.00 36.33 2.85
92 93 0.535102 CGAGCTCCAACACCCTTTGT 60.535 55.000 8.47 0.00 41.74 2.83
93 94 0.535102 ACGAGCTCCAACACCCTTTG 60.535 55.000 8.47 0.00 0.00 2.77
94 95 0.535102 CACGAGCTCCAACACCCTTT 60.535 55.000 8.47 0.00 0.00 3.11
95 96 1.071471 CACGAGCTCCAACACCCTT 59.929 57.895 8.47 0.00 0.00 3.95
96 97 2.743718 CACGAGCTCCAACACCCT 59.256 61.111 8.47 0.00 0.00 4.34
97 98 3.050275 GCACGAGCTCCAACACCC 61.050 66.667 8.47 0.00 37.91 4.61
108 109 2.575694 ACAATCAGCTCTAGCACGAG 57.424 50.000 4.54 0.00 45.16 4.18
109 110 3.735208 GCTTACAATCAGCTCTAGCACGA 60.735 47.826 4.54 0.72 45.16 4.35
110 111 2.537625 GCTTACAATCAGCTCTAGCACG 59.462 50.000 4.54 0.00 45.16 5.34
111 112 3.791245 AGCTTACAATCAGCTCTAGCAC 58.209 45.455 4.54 0.00 44.77 4.40
119 120 2.356069 GGGCTACAAGCTTACAATCAGC 59.644 50.000 0.00 1.78 41.99 4.26
120 121 2.609459 CGGGCTACAAGCTTACAATCAG 59.391 50.000 0.00 0.00 41.99 2.90
121 122 2.627945 CGGGCTACAAGCTTACAATCA 58.372 47.619 0.00 0.00 41.99 2.57
122 123 1.330829 GCGGGCTACAAGCTTACAATC 59.669 52.381 0.00 0.00 41.99 2.67
123 124 1.065418 AGCGGGCTACAAGCTTACAAT 60.065 47.619 0.00 0.00 41.99 2.71
124 125 0.323629 AGCGGGCTACAAGCTTACAA 59.676 50.000 0.00 0.00 41.99 2.41
125 126 1.980052 AGCGGGCTACAAGCTTACA 59.020 52.632 0.00 0.00 41.99 2.41
126 127 4.934989 AGCGGGCTACAAGCTTAC 57.065 55.556 0.00 0.00 41.99 2.34
129 130 0.036875 AGAAAAGCGGGCTACAAGCT 59.963 50.000 0.00 0.00 41.99 3.74
130 131 0.881796 AAGAAAAGCGGGCTACAAGC 59.118 50.000 0.00 0.00 41.46 4.01
131 132 2.416893 GAGAAGAAAAGCGGGCTACAAG 59.583 50.000 0.00 0.00 0.00 3.16
132 133 2.038557 AGAGAAGAAAAGCGGGCTACAA 59.961 45.455 0.00 0.00 0.00 2.41
133 134 1.623811 AGAGAAGAAAAGCGGGCTACA 59.376 47.619 0.00 0.00 0.00 2.74
134 135 2.388310 AGAGAAGAAAAGCGGGCTAC 57.612 50.000 0.00 0.00 0.00 3.58
135 136 3.335579 GAAAGAGAAGAAAAGCGGGCTA 58.664 45.455 0.00 0.00 0.00 3.93
136 137 2.155279 GAAAGAGAAGAAAAGCGGGCT 58.845 47.619 0.00 0.00 0.00 5.19
137 138 1.200252 GGAAAGAGAAGAAAAGCGGGC 59.800 52.381 0.00 0.00 0.00 6.13
138 139 2.784347 AGGAAAGAGAAGAAAAGCGGG 58.216 47.619 0.00 0.00 0.00 6.13
139 140 3.815401 TGAAGGAAAGAGAAGAAAAGCGG 59.185 43.478 0.00 0.00 0.00 5.52
140 141 4.319839 GGTGAAGGAAAGAGAAGAAAAGCG 60.320 45.833 0.00 0.00 0.00 4.68
141 142 4.824537 AGGTGAAGGAAAGAGAAGAAAAGC 59.175 41.667 0.00 0.00 0.00 3.51
142 143 7.386573 GTCTAGGTGAAGGAAAGAGAAGAAAAG 59.613 40.741 0.00 0.00 0.00 2.27
143 144 7.147549 TGTCTAGGTGAAGGAAAGAGAAGAAAA 60.148 37.037 0.00 0.00 0.00 2.29
144 145 6.326583 TGTCTAGGTGAAGGAAAGAGAAGAAA 59.673 38.462 0.00 0.00 0.00 2.52
145 146 5.839063 TGTCTAGGTGAAGGAAAGAGAAGAA 59.161 40.000 0.00 0.00 0.00 2.52
146 147 5.394738 TGTCTAGGTGAAGGAAAGAGAAGA 58.605 41.667 0.00 0.00 0.00 2.87
147 148 5.730296 TGTCTAGGTGAAGGAAAGAGAAG 57.270 43.478 0.00 0.00 0.00 2.85
148 149 7.792364 TTATGTCTAGGTGAAGGAAAGAGAA 57.208 36.000 0.00 0.00 0.00 2.87
149 150 7.792364 TTTATGTCTAGGTGAAGGAAAGAGA 57.208 36.000 0.00 0.00 0.00 3.10
150 151 8.482128 AGATTTATGTCTAGGTGAAGGAAAGAG 58.518 37.037 0.00 0.00 0.00 2.85
151 152 8.260818 CAGATTTATGTCTAGGTGAAGGAAAGA 58.739 37.037 0.00 0.00 0.00 2.52
152 153 8.260818 TCAGATTTATGTCTAGGTGAAGGAAAG 58.739 37.037 0.00 0.00 0.00 2.62
153 154 8.041323 GTCAGATTTATGTCTAGGTGAAGGAAA 58.959 37.037 0.00 0.00 0.00 3.13
154 155 7.180229 TGTCAGATTTATGTCTAGGTGAAGGAA 59.820 37.037 0.00 0.00 0.00 3.36
155 156 6.667848 TGTCAGATTTATGTCTAGGTGAAGGA 59.332 38.462 0.00 0.00 0.00 3.36
156 157 6.878317 TGTCAGATTTATGTCTAGGTGAAGG 58.122 40.000 0.00 0.00 0.00 3.46
157 158 7.440556 CCATGTCAGATTTATGTCTAGGTGAAG 59.559 40.741 0.00 0.00 0.00 3.02
158 159 7.275183 CCATGTCAGATTTATGTCTAGGTGAA 58.725 38.462 0.00 0.00 0.00 3.18
159 160 6.686378 GCCATGTCAGATTTATGTCTAGGTGA 60.686 42.308 0.00 0.00 0.00 4.02
160 161 5.468072 GCCATGTCAGATTTATGTCTAGGTG 59.532 44.000 0.00 0.00 0.00 4.00
161 162 5.130975 TGCCATGTCAGATTTATGTCTAGGT 59.869 40.000 0.00 0.00 0.00 3.08
162 163 5.614308 TGCCATGTCAGATTTATGTCTAGG 58.386 41.667 0.00 0.00 0.00 3.02
163 164 7.160049 AGATGCCATGTCAGATTTATGTCTAG 58.840 38.462 0.00 0.00 0.00 2.43
164 165 7.015974 AGAGATGCCATGTCAGATTTATGTCTA 59.984 37.037 4.51 0.00 0.00 2.59
165 166 5.938279 AGATGCCATGTCAGATTTATGTCT 58.062 37.500 0.00 0.00 0.00 3.41
166 167 5.996513 AGAGATGCCATGTCAGATTTATGTC 59.003 40.000 4.51 0.00 0.00 3.06
167 168 5.938279 AGAGATGCCATGTCAGATTTATGT 58.062 37.500 4.51 0.00 0.00 2.29
168 169 6.879276 AAGAGATGCCATGTCAGATTTATG 57.121 37.500 4.51 0.00 0.00 1.90
169 170 9.887629 CTATAAGAGATGCCATGTCAGATTTAT 57.112 33.333 4.51 2.71 0.00 1.40
170 171 7.821359 GCTATAAGAGATGCCATGTCAGATTTA 59.179 37.037 4.51 0.00 0.00 1.40
171 172 6.654161 GCTATAAGAGATGCCATGTCAGATTT 59.346 38.462 4.51 0.00 0.00 2.17
172 173 6.171921 GCTATAAGAGATGCCATGTCAGATT 58.828 40.000 4.51 0.00 0.00 2.40
173 174 5.338219 GGCTATAAGAGATGCCATGTCAGAT 60.338 44.000 4.51 0.00 44.34 2.90
174 175 4.020751 GGCTATAAGAGATGCCATGTCAGA 60.021 45.833 4.51 0.00 44.34 3.27
175 176 4.252073 GGCTATAAGAGATGCCATGTCAG 58.748 47.826 4.51 0.00 44.34 3.51
176 177 3.008375 GGGCTATAAGAGATGCCATGTCA 59.992 47.826 4.51 0.00 46.53 3.58
177 178 3.604582 GGGCTATAAGAGATGCCATGTC 58.395 50.000 5.21 0.00 46.53 3.06
178 179 2.027745 CGGGCTATAAGAGATGCCATGT 60.028 50.000 5.21 0.00 46.53 3.21
179 180 2.027745 ACGGGCTATAAGAGATGCCATG 60.028 50.000 5.21 0.00 46.53 3.66
180 181 2.260822 ACGGGCTATAAGAGATGCCAT 58.739 47.619 5.21 0.00 46.53 4.40
181 182 1.717032 ACGGGCTATAAGAGATGCCA 58.283 50.000 5.21 0.00 46.53 4.92
182 183 2.841442 AACGGGCTATAAGAGATGCC 57.159 50.000 0.00 0.00 44.22 4.40
183 184 5.238583 ACATAAACGGGCTATAAGAGATGC 58.761 41.667 0.00 0.00 0.00 3.91
184 185 6.366332 GTGACATAAACGGGCTATAAGAGATG 59.634 42.308 0.00 0.00 0.00 2.90
185 186 6.267928 AGTGACATAAACGGGCTATAAGAGAT 59.732 38.462 0.00 0.00 0.00 2.75
186 187 5.597182 AGTGACATAAACGGGCTATAAGAGA 59.403 40.000 0.00 0.00 0.00 3.10
187 188 5.844004 AGTGACATAAACGGGCTATAAGAG 58.156 41.667 0.00 0.00 0.00 2.85
188 189 5.597182 AGAGTGACATAAACGGGCTATAAGA 59.403 40.000 0.00 0.00 0.00 2.10
189 190 5.844004 AGAGTGACATAAACGGGCTATAAG 58.156 41.667 0.00 0.00 0.00 1.73
190 191 5.864418 AGAGTGACATAAACGGGCTATAA 57.136 39.130 0.00 0.00 0.00 0.98
191 192 7.014905 ACAATAGAGTGACATAAACGGGCTATA 59.985 37.037 0.00 0.00 0.00 1.31
192 193 6.183360 ACAATAGAGTGACATAAACGGGCTAT 60.183 38.462 0.00 0.00 0.00 2.97
193 194 5.128171 ACAATAGAGTGACATAAACGGGCTA 59.872 40.000 0.00 0.00 0.00 3.93
194 195 4.081087 ACAATAGAGTGACATAAACGGGCT 60.081 41.667 0.00 0.00 0.00 5.19
195 196 4.189231 ACAATAGAGTGACATAAACGGGC 58.811 43.478 0.00 0.00 0.00 6.13
196 197 8.335356 CAAATACAATAGAGTGACATAAACGGG 58.665 37.037 0.00 0.00 0.00 5.28
197 198 8.335356 CCAAATACAATAGAGTGACATAAACGG 58.665 37.037 0.00 0.00 0.00 4.44
198 199 7.850982 GCCAAATACAATAGAGTGACATAAACG 59.149 37.037 0.00 0.00 0.00 3.60
199 200 8.129211 GGCCAAATACAATAGAGTGACATAAAC 58.871 37.037 0.00 0.00 0.00 2.01
200 201 7.831690 TGGCCAAATACAATAGAGTGACATAAA 59.168 33.333 0.61 0.00 0.00 1.40
201 202 7.282224 GTGGCCAAATACAATAGAGTGACATAA 59.718 37.037 7.24 0.00 0.00 1.90
202 203 6.765989 GTGGCCAAATACAATAGAGTGACATA 59.234 38.462 7.24 0.00 0.00 2.29
203 204 5.590259 GTGGCCAAATACAATAGAGTGACAT 59.410 40.000 7.24 0.00 0.00 3.06
204 205 4.941263 GTGGCCAAATACAATAGAGTGACA 59.059 41.667 7.24 0.00 0.00 3.58
205 206 4.034048 CGTGGCCAAATACAATAGAGTGAC 59.966 45.833 7.24 0.00 0.00 3.67
206 207 4.188462 CGTGGCCAAATACAATAGAGTGA 58.812 43.478 7.24 0.00 0.00 3.41
207 208 3.312421 CCGTGGCCAAATACAATAGAGTG 59.688 47.826 7.24 0.00 0.00 3.51
208 209 3.541632 CCGTGGCCAAATACAATAGAGT 58.458 45.455 7.24 0.00 0.00 3.24
209 210 2.290641 GCCGTGGCCAAATACAATAGAG 59.709 50.000 7.24 0.00 34.56 2.43
210 211 2.294074 GCCGTGGCCAAATACAATAGA 58.706 47.619 7.24 0.00 34.56 1.98
211 212 2.020720 TGCCGTGGCCAAATACAATAG 58.979 47.619 7.24 0.00 41.09 1.73
212 213 2.020720 CTGCCGTGGCCAAATACAATA 58.979 47.619 7.24 0.00 41.09 1.90
213 214 0.817013 CTGCCGTGGCCAAATACAAT 59.183 50.000 7.24 0.00 41.09 2.71
214 215 1.247419 CCTGCCGTGGCCAAATACAA 61.247 55.000 7.24 0.00 41.09 2.41
215 216 1.677300 CCTGCCGTGGCCAAATACA 60.677 57.895 7.24 2.46 41.09 2.29
216 217 3.063743 GCCTGCCGTGGCCAAATAC 62.064 63.158 7.24 0.00 46.82 1.89
217 218 2.753849 GCCTGCCGTGGCCAAATA 60.754 61.111 7.24 0.00 46.82 1.40
273 274 5.295045 TCTGCTCAAATACGTCGACATACTA 59.705 40.000 17.16 0.00 0.00 1.82
274 275 4.095932 TCTGCTCAAATACGTCGACATACT 59.904 41.667 17.16 0.00 0.00 2.12
275 276 4.348656 TCTGCTCAAATACGTCGACATAC 58.651 43.478 17.16 0.00 0.00 2.39
276 277 4.625972 TCTGCTCAAATACGTCGACATA 57.374 40.909 17.16 4.77 0.00 2.29
280 281 3.630769 AGGTATCTGCTCAAATACGTCGA 59.369 43.478 0.00 0.00 30.61 4.20
371 374 7.552330 AGAGAGAGAAGAAAACATTATCCTTGC 59.448 37.037 0.00 0.00 0.00 4.01
387 391 2.027003 ACGTACGGGAGAGAGAGAAG 57.973 55.000 21.06 0.00 0.00 2.85
390 394 2.548904 CCATAACGTACGGGAGAGAGAG 59.451 54.545 21.06 0.00 0.00 3.20
417 421 6.428465 TGCTTCAGAATCTATCTAGTACTCCG 59.572 42.308 0.00 0.00 36.32 4.63
418 422 7.753309 TGCTTCAGAATCTATCTAGTACTCC 57.247 40.000 0.00 0.00 36.32 3.85
419 423 8.175069 CGATGCTTCAGAATCTATCTAGTACTC 58.825 40.741 0.00 0.00 36.32 2.59
420 424 7.880713 TCGATGCTTCAGAATCTATCTAGTACT 59.119 37.037 0.00 0.00 36.32 2.73
421 425 8.035165 TCGATGCTTCAGAATCTATCTAGTAC 57.965 38.462 0.08 0.00 36.32 2.73
422 426 8.097662 TCTCGATGCTTCAGAATCTATCTAGTA 58.902 37.037 0.08 0.00 36.32 1.82
423 427 6.939730 TCTCGATGCTTCAGAATCTATCTAGT 59.060 38.462 0.08 0.00 36.32 2.57
424 428 7.376435 TCTCGATGCTTCAGAATCTATCTAG 57.624 40.000 0.08 0.00 36.32 2.43
425 429 6.374053 CCTCTCGATGCTTCAGAATCTATCTA 59.626 42.308 0.08 0.00 36.32 1.98
426 430 5.183713 CCTCTCGATGCTTCAGAATCTATCT 59.816 44.000 0.08 0.00 39.68 1.98
427 431 5.182950 TCCTCTCGATGCTTCAGAATCTATC 59.817 44.000 0.08 0.00 0.00 2.08
428 432 5.076182 TCCTCTCGATGCTTCAGAATCTAT 58.924 41.667 0.08 0.00 0.00 1.98
429 433 4.464947 TCCTCTCGATGCTTCAGAATCTA 58.535 43.478 0.08 0.00 0.00 1.98
430 434 3.295093 TCCTCTCGATGCTTCAGAATCT 58.705 45.455 0.08 0.00 0.00 2.40
431 435 3.068024 ACTCCTCTCGATGCTTCAGAATC 59.932 47.826 0.08 0.00 0.00 2.52
465 473 6.198966 CACATTTGAAGCTTTGAACAAGTACC 59.801 38.462 0.00 0.00 0.00 3.34
663 958 9.734620 CATTTCAAATGAATAACATACGGATGT 57.265 29.630 7.68 7.68 39.80 3.06
732 1027 3.501950 GGCGAGCCAATTTAAGAACAAG 58.498 45.455 9.58 0.00 35.81 3.16
789 1090 1.342076 TGTTGGTTGGTGGTGCCTAAA 60.342 47.619 0.00 0.00 38.35 1.85
874 1314 4.716784 TGCTCCATCTTGGTATAGTGAAGT 59.283 41.667 0.00 0.00 39.03 3.01
875 1315 5.282055 TGCTCCATCTTGGTATAGTGAAG 57.718 43.478 0.00 0.00 39.03 3.02
876 1316 4.443457 GCTGCTCCATCTTGGTATAGTGAA 60.443 45.833 0.00 0.00 39.03 3.18
878 1318 3.181462 TGCTGCTCCATCTTGGTATAGTG 60.181 47.826 0.00 0.00 39.03 2.74
916 1362 1.135373 GCTAGCTAGTCAGTCACGCAA 60.135 52.381 21.62 0.00 0.00 4.85
917 1363 0.452184 GCTAGCTAGTCAGTCACGCA 59.548 55.000 21.62 0.00 0.00 5.24
918 1364 0.452184 TGCTAGCTAGTCAGTCACGC 59.548 55.000 21.62 5.79 0.00 5.34
919 1365 1.740585 ACTGCTAGCTAGTCAGTCACG 59.259 52.381 29.51 16.44 36.60 4.35
920 1366 3.859411 AACTGCTAGCTAGTCAGTCAC 57.141 47.619 32.34 14.98 38.66 3.67
921 1367 4.873746 AAAACTGCTAGCTAGTCAGTCA 57.126 40.909 32.34 18.91 38.66 3.41
968 1414 4.020617 CCTTCTGCACCTCGGCCA 62.021 66.667 2.24 0.00 0.00 5.36
1533 2539 1.673665 GAGCAGGTTCAGGCTGGTG 60.674 63.158 15.73 8.51 41.22 4.17
1656 2664 1.861971 GGAAGAAGTCCGACACGTTT 58.138 50.000 0.40 0.00 36.40 3.60
1964 3129 8.986477 TGATGCTAAAATTAAAAAGAGAAGGC 57.014 30.769 0.00 0.00 0.00 4.35
2008 3174 8.561738 AAACTTTTCTATGTGATGTACGGAAT 57.438 30.769 0.00 0.00 0.00 3.01
2012 3178 9.135843 TCTGTAAACTTTTCTATGTGATGTACG 57.864 33.333 0.00 0.00 0.00 3.67
2054 3424 6.904626 ACGGGTAACTTCTAATCTCTACCTA 58.095 40.000 0.00 0.00 31.40 3.08
2105 3475 9.631257 TTAAAGTTACTTAAAAAGCCTACCACT 57.369 29.630 0.00 0.00 0.00 4.00
2106 3476 9.888878 CTTAAAGTTACTTAAAAAGCCTACCAC 57.111 33.333 0.00 0.00 0.00 4.16
2490 4354 9.868277 TGAATTTAACAGTGTTCATGTTTTCTT 57.132 25.926 12.82 0.00 41.08 2.52
2588 5122 6.520021 TCCCTTGTATCTCATGAATGGATT 57.480 37.500 0.00 0.00 0.00 3.01
2608 5143 2.288579 GGAAAATTCCAACGGTGTTCCC 60.289 50.000 8.27 0.00 46.76 3.97
2699 5271 3.120234 GGGAATTTGAAATGCGGCAAAAG 60.120 43.478 6.82 0.00 37.52 2.27
2723 5297 0.035317 GCGGCATGTGAGGGATATGA 59.965 55.000 0.00 0.00 0.00 2.15
2728 5302 2.803155 GAAGTGCGGCATGTGAGGGA 62.803 60.000 5.72 0.00 0.00 4.20
2750 5326 4.394920 TGGACTTATTTTCTTCCACGATGC 59.605 41.667 0.00 0.00 33.02 3.91
2982 5567 7.700505 ACATGCAAAGTCACATCAATATAGTG 58.299 34.615 0.00 0.00 34.67 2.74
3031 5625 1.336332 ACTGTGCTAGAGCTTGTGTCG 60.336 52.381 2.72 0.00 42.66 4.35
3132 5726 6.855403 GTCAGCTTCTTCAATGTTTCTTCTTC 59.145 38.462 0.00 0.00 0.00 2.87
3181 5775 8.831550 AGTCGAAAAATCTCTTTTATGATAGCC 58.168 33.333 0.00 0.00 33.44 3.93
3198 5792 1.066430 CGGGAGGATGGAGTCGAAAAA 60.066 52.381 0.00 0.00 0.00 1.94
3586 6180 1.275010 GTTGCCACAATACAAAGGGGG 59.725 52.381 0.00 0.00 0.00 5.40
3601 6195 1.067821 TCAATTCAAACCGGTGTTGCC 59.932 47.619 8.52 0.00 34.13 4.52
3790 6392 7.758076 TGTATGAGTATCTTTGTAGGAACAACG 59.242 37.037 0.00 0.00 45.18 4.10
3809 6411 4.037208 GGTGGAAAGAATGGCATGTATGAG 59.963 45.833 0.00 0.00 0.00 2.90
3900 6504 5.062934 GGTTTTGCACAAACCTCAAGTTAAC 59.937 40.000 24.39 0.00 44.71 2.01
3961 6594 1.448540 CCACCGTGTCTGGCAGATC 60.449 63.158 21.84 15.39 0.00 2.75
3970 6603 0.744414 CATCCACCATCCACCGTGTC 60.744 60.000 0.00 0.00 0.00 3.67
4059 6692 4.562963 CCGGTAGCTGTTATTATCCTTCCC 60.563 50.000 0.00 0.00 0.00 3.97
4065 6698 5.464030 TTCCTCCGGTAGCTGTTATTATC 57.536 43.478 0.00 0.00 0.00 1.75
4079 6712 0.609131 ATTGTGTTGCCTTCCTCCGG 60.609 55.000 0.00 0.00 0.00 5.14
4107 6741 7.867403 GCGATATAAACATCCCAAATGTGAAAT 59.133 33.333 0.00 0.00 31.80 2.17
4232 6888 6.168389 GGGATGTGCAAGAGATTTGAAATTT 58.832 36.000 0.00 0.00 0.00 1.82
4233 6889 5.246656 TGGGATGTGCAAGAGATTTGAAATT 59.753 36.000 0.00 0.00 0.00 1.82
4234 6890 4.773674 TGGGATGTGCAAGAGATTTGAAAT 59.226 37.500 0.00 0.00 0.00 2.17
4235 6891 4.151121 TGGGATGTGCAAGAGATTTGAAA 58.849 39.130 0.00 0.00 0.00 2.69
4236 6892 3.760151 CTGGGATGTGCAAGAGATTTGAA 59.240 43.478 0.00 0.00 0.00 2.69
4237 6893 3.009363 TCTGGGATGTGCAAGAGATTTGA 59.991 43.478 0.00 0.00 0.00 2.69
4238 6894 3.349927 TCTGGGATGTGCAAGAGATTTG 58.650 45.455 0.00 0.00 0.00 2.32
4239 6895 3.009916 ACTCTGGGATGTGCAAGAGATTT 59.990 43.478 15.94 0.00 38.77 2.17
4464 7241 1.172175 TTGCTTGTTCTGTGCACACA 58.828 45.000 17.42 10.23 39.32 3.72
4493 7270 5.389859 TTGTTCCAGCCATGTTAAATCTG 57.610 39.130 0.00 0.00 0.00 2.90
4498 7275 4.586421 TCACATTTGTTCCAGCCATGTTAA 59.414 37.500 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.