Multiple sequence alignment - TraesCS5D01G341500

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 TraesCS5D01G341500 chr5D 100.000 4219 0 0 1 4219 429717687 429713469 0.000000e+00 7792.0
1 TraesCS5D01G341500 chr5B 91.414 3331 117 57 134 3353 518963225 518959953 0.000000e+00 4410.0
2 TraesCS5D01G341500 chr5B 91.537 449 23 8 3778 4219 518959502 518959062 4.670000e-169 604.0
3 TraesCS5D01G341500 chr5B 80.098 407 36 23 3405 3777 518959953 518959558 1.160000e-65 261.0
4 TraesCS5D01G341500 chr5B 100.000 30 0 0 3706 3735 518959537 518959508 5.890000e-04 56.5
5 TraesCS5D01G341500 chr5A 89.181 2588 125 70 757 3299 545567415 545564938 0.000000e+00 3085.0
6 TraesCS5D01G341500 chr5A 87.405 921 57 32 3341 4219 545564946 545564043 0.000000e+00 1003.0
7 TraesCS5D01G341500 chr5A 85.942 313 18 10 354 651 545567825 545567524 1.140000e-80 311.0
8 TraesCS5D01G341500 chr5A 84.234 222 17 10 77 284 545587037 545586820 2.570000e-47 200.0
9 TraesCS5D01G341500 chr5A 91.228 57 0 1 670 721 545567474 545567418 5.850000e-09 73.1
10 TraesCS5D01G341500 chr6D 88.947 190 20 1 1055 1243 86025541 86025352 2.540000e-57 233.0
11 TraesCS5D01G341500 chr2D 88.421 190 21 1 1055 1243 190368425 190368236 1.180000e-55 228.0
12 TraesCS5D01G341500 chr2D 84.795 171 19 3 1073 1243 625162257 625162420 9.380000e-37 165.0
13 TraesCS5D01G341500 chr2B 87.766 188 22 1 1055 1241 158360082 158360269 7.100000e-53 219.0
14 TraesCS5D01G341500 chr1A 87.368 190 23 1 1055 1243 528933785 528933596 2.550000e-52 217.0


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 TraesCS5D01G341500 chr5D 429713469 429717687 4218 True 7792.000 7792 100.00000 1 4219 1 chr5D.!!$R1 4218
1 TraesCS5D01G341500 chr5B 518959062 518963225 4163 True 1332.875 4410 90.76225 134 4219 4 chr5B.!!$R1 4085
2 TraesCS5D01G341500 chr5A 545564043 545567825 3782 True 1118.025 3085 88.43900 354 4219 4 chr5A.!!$R2 3865

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
58 59 0.033504 GACTTGCTCCTCGTCCAACA 59.966 55.0 0.00 0.00 0.00 3.33 F
61 62 0.036388 TTGCTCCTCGTCCAACATCC 60.036 55.0 0.00 0.00 0.00 3.51 F
91 92 0.039437 AGTGGACACGTGTCATCGAC 60.039 55.0 40.51 30.33 46.47 4.20 F
2116 2233 0.108138 AATCACTCTACTGTGCCGCC 60.108 55.0 0.00 0.00 37.81 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1700 1.582968 GTGGTACGCGGTCTTGAGA 59.417 57.895 12.47 0.00 0.00 3.27 R
2108 2225 0.455410 GCAGAATTAATGGCGGCACA 59.545 50.000 16.34 1.46 0.00 4.57 R
2122 2239 0.602638 CCTGGTACGTGCTTGCAGAA 60.603 55.000 3.01 0.00 0.00 3.02 R
3900 4204 0.038744 CTTGGTGTCCATTGAGGCCT 59.961 55.000 3.86 3.86 37.29 5.19 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
17 18 4.390341 CCTCCTCCTCCTCCTTGG 57.610 66.667 0.00 0.00 37.10 3.61
18 19 2.069430 CCTCCTCCTCCTCCTTGGC 61.069 68.421 0.00 0.00 35.26 4.52
19 20 1.306482 CTCCTCCTCCTCCTTGGCA 60.306 63.158 0.00 0.00 35.26 4.92
20 21 1.613630 TCCTCCTCCTCCTTGGCAC 60.614 63.158 0.00 0.00 35.26 5.01
21 22 2.581354 CTCCTCCTCCTTGGCACG 59.419 66.667 0.00 0.00 35.26 5.34
22 23 1.984570 CTCCTCCTCCTTGGCACGA 60.985 63.158 0.00 0.00 35.26 4.35
23 24 1.954362 CTCCTCCTCCTTGGCACGAG 61.954 65.000 4.17 4.17 35.26 4.18
24 25 2.581354 CTCCTCCTTGGCACGAGG 59.419 66.667 19.43 19.43 46.07 4.63
25 26 3.003173 TCCTCCTTGGCACGAGGG 61.003 66.667 23.18 11.41 44.99 4.30
26 27 4.785453 CCTCCTTGGCACGAGGGC 62.785 72.222 18.23 0.00 41.79 5.19
41 42 3.519930 GGCGACCTCCTCCTCGAC 61.520 72.222 0.00 0.00 31.24 4.20
42 43 2.438795 GCGACCTCCTCCTCGACT 60.439 66.667 0.00 0.00 31.24 4.18
43 44 2.047443 GCGACCTCCTCCTCGACTT 61.047 63.158 0.00 0.00 31.24 3.01
44 45 1.803943 CGACCTCCTCCTCGACTTG 59.196 63.158 0.00 0.00 31.24 3.16
45 46 1.513622 GACCTCCTCCTCGACTTGC 59.486 63.158 0.00 0.00 0.00 4.01
46 47 0.968393 GACCTCCTCCTCGACTTGCT 60.968 60.000 0.00 0.00 0.00 3.91
47 48 0.968393 ACCTCCTCCTCGACTTGCTC 60.968 60.000 0.00 0.00 0.00 4.26
48 49 1.671901 CCTCCTCCTCGACTTGCTCC 61.672 65.000 0.00 0.00 0.00 4.70
49 50 0.682855 CTCCTCCTCGACTTGCTCCT 60.683 60.000 0.00 0.00 0.00 3.69
50 51 0.681564 TCCTCCTCGACTTGCTCCTC 60.682 60.000 0.00 0.00 0.00 3.71
51 52 1.431440 CTCCTCGACTTGCTCCTCG 59.569 63.158 0.00 0.00 0.00 4.63
52 53 1.303398 TCCTCGACTTGCTCCTCGT 60.303 57.895 0.00 0.00 0.00 4.18
53 54 1.137825 CCTCGACTTGCTCCTCGTC 59.862 63.158 0.00 0.00 0.00 4.20
54 55 1.137825 CTCGACTTGCTCCTCGTCC 59.862 63.158 0.00 0.00 0.00 4.79
55 56 1.587043 CTCGACTTGCTCCTCGTCCA 61.587 60.000 0.00 0.00 0.00 4.02
56 57 1.176619 TCGACTTGCTCCTCGTCCAA 61.177 55.000 0.00 0.00 0.00 3.53
57 58 1.009389 CGACTTGCTCCTCGTCCAAC 61.009 60.000 0.00 0.00 0.00 3.77
58 59 0.033504 GACTTGCTCCTCGTCCAACA 59.966 55.000 0.00 0.00 0.00 3.33
59 60 0.687354 ACTTGCTCCTCGTCCAACAT 59.313 50.000 0.00 0.00 0.00 2.71
60 61 1.338200 ACTTGCTCCTCGTCCAACATC 60.338 52.381 0.00 0.00 0.00 3.06
61 62 0.036388 TTGCTCCTCGTCCAACATCC 60.036 55.000 0.00 0.00 0.00 3.51
62 63 1.519455 GCTCCTCGTCCAACATCCG 60.519 63.158 0.00 0.00 0.00 4.18
63 64 1.519455 CTCCTCGTCCAACATCCGC 60.519 63.158 0.00 0.00 0.00 5.54
64 65 1.949847 CTCCTCGTCCAACATCCGCT 61.950 60.000 0.00 0.00 0.00 5.52
65 66 1.519455 CCTCGTCCAACATCCGCTC 60.519 63.158 0.00 0.00 0.00 5.03
66 67 1.513158 CTCGTCCAACATCCGCTCT 59.487 57.895 0.00 0.00 0.00 4.09
67 68 0.108615 CTCGTCCAACATCCGCTCTT 60.109 55.000 0.00 0.00 0.00 2.85
68 69 0.108804 TCGTCCAACATCCGCTCTTC 60.109 55.000 0.00 0.00 0.00 2.87
69 70 0.108615 CGTCCAACATCCGCTCTTCT 60.109 55.000 0.00 0.00 0.00 2.85
70 71 1.134367 CGTCCAACATCCGCTCTTCTA 59.866 52.381 0.00 0.00 0.00 2.10
71 72 2.796383 CGTCCAACATCCGCTCTTCTAG 60.796 54.545 0.00 0.00 0.00 2.43
72 73 2.427453 GTCCAACATCCGCTCTTCTAGA 59.573 50.000 0.00 0.00 0.00 2.43
73 74 2.690497 TCCAACATCCGCTCTTCTAGAG 59.310 50.000 0.00 0.00 45.04 2.43
74 75 2.428890 CCAACATCCGCTCTTCTAGAGT 59.571 50.000 5.67 0.00 44.12 3.24
80 81 2.553079 CGCTCTTCTAGAGTGGACAC 57.447 55.000 8.94 0.00 46.27 3.67
81 82 1.202087 CGCTCTTCTAGAGTGGACACG 60.202 57.143 8.94 0.00 46.27 4.49
82 83 1.813786 GCTCTTCTAGAGTGGACACGT 59.186 52.381 5.67 0.00 44.12 4.49
83 84 2.414824 GCTCTTCTAGAGTGGACACGTG 60.415 54.545 15.48 15.48 44.12 4.49
84 85 2.814919 CTCTTCTAGAGTGGACACGTGT 59.185 50.000 23.64 23.64 37.57 4.49
85 86 2.812591 TCTTCTAGAGTGGACACGTGTC 59.187 50.000 35.26 35.26 44.04 3.67
86 87 2.265589 TCTAGAGTGGACACGTGTCA 57.734 50.000 40.51 27.29 46.47 3.58
87 88 2.791655 TCTAGAGTGGACACGTGTCAT 58.208 47.619 40.51 28.89 46.47 3.06
88 89 2.747989 TCTAGAGTGGACACGTGTCATC 59.252 50.000 40.51 33.16 46.47 2.92
89 90 0.241213 AGAGTGGACACGTGTCATCG 59.759 55.000 40.51 8.91 46.47 3.84
90 91 0.240145 GAGTGGACACGTGTCATCGA 59.760 55.000 40.51 23.18 46.47 3.59
91 92 0.039437 AGTGGACACGTGTCATCGAC 60.039 55.000 40.51 30.33 46.47 4.20
92 93 0.318360 GTGGACACGTGTCATCGACA 60.318 55.000 40.51 28.83 46.47 4.35
93 94 0.386113 TGGACACGTGTCATCGACAA 59.614 50.000 40.51 19.20 44.49 3.18
94 95 0.782384 GGACACGTGTCATCGACAAC 59.218 55.000 40.51 22.35 44.49 3.32
95 96 1.602165 GGACACGTGTCATCGACAACT 60.602 52.381 40.51 8.79 44.49 3.16
96 97 2.351060 GGACACGTGTCATCGACAACTA 60.351 50.000 40.51 0.00 44.49 2.24
97 98 2.655474 GACACGTGTCATCGACAACTAC 59.345 50.000 37.16 11.22 44.49 2.73
98 99 2.033675 ACACGTGTCATCGACAACTACA 59.966 45.455 17.22 0.00 44.49 2.74
99 100 3.047093 CACGTGTCATCGACAACTACAA 58.953 45.455 7.58 0.00 44.49 2.41
100 101 3.487942 CACGTGTCATCGACAACTACAAA 59.512 43.478 7.58 0.00 44.49 2.83
101 102 3.734231 ACGTGTCATCGACAACTACAAAG 59.266 43.478 0.00 0.00 44.49 2.77
102 103 3.734231 CGTGTCATCGACAACTACAAAGT 59.266 43.478 0.00 0.00 44.49 2.66
103 104 4.143597 CGTGTCATCGACAACTACAAAGTC 60.144 45.833 0.00 0.00 44.49 3.01
104 105 4.982916 GTGTCATCGACAACTACAAAGTCT 59.017 41.667 0.00 0.00 44.49 3.24
105 106 6.147581 GTGTCATCGACAACTACAAAGTCTA 58.852 40.000 0.00 0.00 44.49 2.59
106 107 6.305877 GTGTCATCGACAACTACAAAGTCTAG 59.694 42.308 0.00 0.00 44.49 2.43
107 108 6.206048 TGTCATCGACAACTACAAAGTCTAGA 59.794 38.462 0.00 0.00 39.78 2.43
108 109 7.094334 TGTCATCGACAACTACAAAGTCTAGAT 60.094 37.037 0.00 0.00 39.78 1.98
109 110 7.755822 GTCATCGACAACTACAAAGTCTAGATT 59.244 37.037 0.00 0.00 33.75 2.40
110 111 8.304596 TCATCGACAACTACAAAGTCTAGATTT 58.695 33.333 0.00 0.00 33.75 2.17
111 112 9.569167 CATCGACAACTACAAAGTCTAGATTTA 57.431 33.333 0.32 0.00 33.75 1.40
112 113 9.790389 ATCGACAACTACAAAGTCTAGATTTAG 57.210 33.333 0.32 0.00 33.75 1.85
113 114 8.242053 TCGACAACTACAAAGTCTAGATTTAGG 58.758 37.037 0.32 0.11 33.75 2.69
114 115 8.027771 CGACAACTACAAAGTCTAGATTTAGGT 58.972 37.037 0.32 5.82 33.75 3.08
121 122 8.002984 ACAAAGTCTAGATTTAGGTAGAGAGC 57.997 38.462 0.32 0.00 0.00 4.09
122 123 7.837187 ACAAAGTCTAGATTTAGGTAGAGAGCT 59.163 37.037 0.32 0.00 37.19 4.09
123 124 7.817418 AAGTCTAGATTTAGGTAGAGAGCTG 57.183 40.000 0.00 0.00 34.50 4.24
124 125 5.768164 AGTCTAGATTTAGGTAGAGAGCTGC 59.232 44.000 0.00 0.00 34.50 5.25
125 126 5.768164 GTCTAGATTTAGGTAGAGAGCTGCT 59.232 44.000 0.00 0.00 34.50 4.24
126 127 6.938030 GTCTAGATTTAGGTAGAGAGCTGCTA 59.062 42.308 0.15 0.00 34.50 3.49
127 128 7.446013 GTCTAGATTTAGGTAGAGAGCTGCTAA 59.554 40.741 0.15 0.00 34.50 3.09
128 129 6.399639 AGATTTAGGTAGAGAGCTGCTAAC 57.600 41.667 0.15 0.00 34.50 2.34
129 130 5.894393 AGATTTAGGTAGAGAGCTGCTAACA 59.106 40.000 0.15 0.00 34.50 2.41
131 132 3.094484 AGGTAGAGAGCTGCTAACAGT 57.906 47.619 0.15 0.00 46.30 3.55
132 133 4.237976 AGGTAGAGAGCTGCTAACAGTA 57.762 45.455 0.15 0.00 46.30 2.74
145 146 6.483640 GCTGCTAACAGTAATTATTACAGGCT 59.516 38.462 16.23 4.35 46.30 4.58
146 147 7.656137 GCTGCTAACAGTAATTATTACAGGCTA 59.344 37.037 16.23 5.13 46.30 3.93
158 159 9.923143 AATTATTACAGGCTAAAAAGAAACACC 57.077 29.630 0.00 0.00 0.00 4.16
160 161 4.918810 ACAGGCTAAAAAGAAACACCAG 57.081 40.909 0.00 0.00 0.00 4.00
161 162 3.636764 ACAGGCTAAAAAGAAACACCAGG 59.363 43.478 0.00 0.00 0.00 4.45
162 163 3.888930 CAGGCTAAAAAGAAACACCAGGA 59.111 43.478 0.00 0.00 0.00 3.86
196 197 2.336088 CACGGCCACCAAAAGCAG 59.664 61.111 2.24 0.00 0.00 4.24
223 224 1.007271 CCTGCTCGTGTCAACTCGT 60.007 57.895 4.75 0.00 34.81 4.18
311 318 2.730928 GTCAACATTGGATTTGCCGTTG 59.269 45.455 0.00 0.00 40.66 4.10
339 354 0.391263 CTGCTGCATGCTCTGTCTCA 60.391 55.000 20.33 5.26 43.37 3.27
345 360 1.798446 GCATGCTCTGTCTCAGTCTCG 60.798 57.143 11.37 0.00 32.61 4.04
493 528 2.568090 CTGTGGATTTGTGGGCGC 59.432 61.111 0.00 0.00 0.00 6.53
589 624 3.195698 GGTGGCGCATCGGTTCTC 61.196 66.667 10.83 0.00 0.00 2.87
663 703 1.153208 TCCCTCGCGACCTCTCTAC 60.153 63.158 3.71 0.00 0.00 2.59
724 798 2.420687 GGATTGGGGCTCAAGTAGACTG 60.421 54.545 5.79 0.00 38.95 3.51
725 799 0.324943 TTGGGGCTCAAGTAGACTGC 59.675 55.000 0.00 0.00 31.67 4.40
726 800 0.835971 TGGGGCTCAAGTAGACTGCA 60.836 55.000 0.00 0.00 31.67 4.41
871 945 5.372373 CTTCTTCCTTCCTTGAGTTGAGTT 58.628 41.667 0.00 0.00 0.00 3.01
894 968 1.196012 CCTCTTTAAGTCTCCCGCCT 58.804 55.000 0.00 0.00 0.00 5.52
944 1018 4.891727 CGCCCTTGATAGCGCGGT 62.892 66.667 17.70 17.70 46.50 5.68
946 1020 3.272334 CCCTTGATAGCGCGGTGC 61.272 66.667 23.02 13.48 46.98 5.01
997 1071 4.980592 TGCTCAGGGGGTGCTGGA 62.981 66.667 0.00 0.00 36.94 3.86
998 1072 3.650950 GCTCAGGGGGTGCTGGAA 61.651 66.667 0.00 0.00 33.29 3.53
1023 1097 4.436998 GCCGAGGTGGAGGTCGTG 62.437 72.222 0.00 0.00 42.00 4.35
1065 1139 2.269241 CCGGGCAAGAAGAGGACC 59.731 66.667 0.00 0.00 0.00 4.46
1089 1163 4.943252 ACGCTGCTGCACCTGCTT 62.943 61.111 16.29 0.00 42.66 3.91
1584 1682 3.082579 GCTGTTCGCCTCCGAGGAT 62.083 63.158 19.33 0.00 45.35 3.24
2083 2181 1.957113 GCTGCAGCTCCCAGGTAAAAT 60.957 52.381 31.33 0.00 38.21 1.82
2084 2182 2.450476 CTGCAGCTCCCAGGTAAAATT 58.550 47.619 0.00 0.00 0.00 1.82
2104 2221 2.288961 TCGTTTCCGCCTAATCACTC 57.711 50.000 0.00 0.00 0.00 3.51
2105 2222 1.822990 TCGTTTCCGCCTAATCACTCT 59.177 47.619 0.00 0.00 0.00 3.24
2106 2223 3.018856 TCGTTTCCGCCTAATCACTCTA 58.981 45.455 0.00 0.00 0.00 2.43
2107 2224 3.114065 CGTTTCCGCCTAATCACTCTAC 58.886 50.000 0.00 0.00 0.00 2.59
2108 2225 3.181489 CGTTTCCGCCTAATCACTCTACT 60.181 47.826 0.00 0.00 0.00 2.57
2109 2226 4.113354 GTTTCCGCCTAATCACTCTACTG 58.887 47.826 0.00 0.00 0.00 2.74
2110 2227 3.014304 TCCGCCTAATCACTCTACTGT 57.986 47.619 0.00 0.00 0.00 3.55
2111 2228 2.688446 TCCGCCTAATCACTCTACTGTG 59.312 50.000 0.00 0.00 39.15 3.66
2112 2229 2.464865 CGCCTAATCACTCTACTGTGC 58.535 52.381 0.00 0.00 37.81 4.57
2113 2230 2.799917 CGCCTAATCACTCTACTGTGCC 60.800 54.545 0.00 0.00 37.81 5.01
2114 2231 2.799917 GCCTAATCACTCTACTGTGCCG 60.800 54.545 0.00 0.00 37.81 5.69
2115 2232 2.464865 CTAATCACTCTACTGTGCCGC 58.535 52.381 0.00 0.00 37.81 6.53
2116 2233 0.108138 AATCACTCTACTGTGCCGCC 60.108 55.000 0.00 0.00 37.81 6.13
2117 2234 1.257750 ATCACTCTACTGTGCCGCCA 61.258 55.000 0.00 0.00 37.81 5.69
2118 2235 1.219124 CACTCTACTGTGCCGCCAT 59.781 57.895 0.00 0.00 0.00 4.40
2119 2236 0.391661 CACTCTACTGTGCCGCCATT 60.392 55.000 0.00 0.00 0.00 3.16
2120 2237 1.134818 CACTCTACTGTGCCGCCATTA 60.135 52.381 0.00 0.00 0.00 1.90
2121 2238 1.553248 ACTCTACTGTGCCGCCATTAA 59.447 47.619 0.00 0.00 0.00 1.40
2122 2239 2.170607 ACTCTACTGTGCCGCCATTAAT 59.829 45.455 0.00 0.00 0.00 1.40
2123 2240 3.206150 CTCTACTGTGCCGCCATTAATT 58.794 45.455 0.00 0.00 0.00 1.40
2129 2246 1.135141 GTGCCGCCATTAATTCTGCAA 60.135 47.619 5.52 0.00 0.00 4.08
2131 2248 1.843992 CCGCCATTAATTCTGCAAGC 58.156 50.000 0.00 0.00 0.00 4.01
2147 2264 2.151202 CAAGCACGTACCAGGTTCATT 58.849 47.619 0.00 0.00 0.00 2.57
2193 2312 7.285783 TCACGTGGTAATTTAGAATTTCGAG 57.714 36.000 17.00 0.00 0.00 4.04
2194 2313 6.869913 TCACGTGGTAATTTAGAATTTCGAGT 59.130 34.615 17.00 0.00 0.00 4.18
2195 2314 7.385752 TCACGTGGTAATTTAGAATTTCGAGTT 59.614 33.333 17.00 0.00 0.00 3.01
2196 2315 8.649841 CACGTGGTAATTTAGAATTTCGAGTTA 58.350 33.333 7.95 0.00 0.00 2.24
2198 2317 9.079833 CGTGGTAATTTAGAATTTCGAGTTAGA 57.920 33.333 0.00 0.00 0.00 2.10
2245 2382 6.147328 GGATTGCAGAATATACCGTTAGAACC 59.853 42.308 0.00 0.00 0.00 3.62
2246 2383 5.601583 TGCAGAATATACCGTTAGAACCA 57.398 39.130 0.00 0.00 0.00 3.67
2247 2384 5.353938 TGCAGAATATACCGTTAGAACCAC 58.646 41.667 0.00 0.00 0.00 4.16
2248 2385 5.128171 TGCAGAATATACCGTTAGAACCACT 59.872 40.000 0.00 0.00 0.00 4.00
2254 2391 2.229792 ACCGTTAGAACCACTACGTCA 58.770 47.619 0.00 0.00 0.00 4.35
2259 2396 4.147653 CGTTAGAACCACTACGTCACTTTG 59.852 45.833 0.00 0.00 0.00 2.77
2278 2419 6.756542 CACTTTGGTTTTAACTTTTGAGGAGG 59.243 38.462 0.00 0.00 0.00 4.30
2294 2435 1.688772 GAGGTCCATTCAGCATGCAT 58.311 50.000 21.98 1.08 34.76 3.96
2309 2450 2.599032 CATCAGCATCTGCCCCCA 59.401 61.111 0.00 0.00 43.38 4.96
2583 2729 0.539051 CTCCCGAAGAGAACATGGCT 59.461 55.000 0.00 0.00 46.50 4.75
2641 2787 0.962356 CACAGTGGAGGGAATGTGGC 60.962 60.000 0.00 0.00 39.45 5.01
2642 2788 1.379044 CAGTGGAGGGAATGTGGCC 60.379 63.158 0.00 0.00 0.00 5.36
2676 2842 2.434359 GCCACGTACACTCCAGCC 60.434 66.667 0.00 0.00 0.00 4.85
2690 2856 3.273434 CTCCAGCCGAATCATTCTGAAA 58.727 45.455 0.00 0.00 0.00 2.69
2750 2921 0.179084 GGCGATGATTTGACCGGAGA 60.179 55.000 9.46 0.00 0.00 3.71
2778 2949 1.066143 CCTTGTCGTGTAATCCAGCCT 60.066 52.381 0.00 0.00 0.00 4.58
2811 2987 5.046304 TGCCCTATCCTTAGCACTAATCATC 60.046 44.000 0.00 0.00 0.00 2.92
2815 2991 8.932610 CCCTATCCTTAGCACTAATCATCATAT 58.067 37.037 0.00 0.00 0.00 1.78
2833 3013 6.149129 TCATATACTACTTGACTGCTGTGG 57.851 41.667 0.00 0.00 0.00 4.17
2848 3028 1.059584 TGTGGTGATGAGTGGTGGGT 61.060 55.000 0.00 0.00 0.00 4.51
2850 3030 0.850100 TGGTGATGAGTGGTGGGTTT 59.150 50.000 0.00 0.00 0.00 3.27
2858 3038 2.036733 TGAGTGGTGGGTTTAACGAGAG 59.963 50.000 0.00 0.00 0.00 3.20
2860 3040 2.701951 AGTGGTGGGTTTAACGAGAGAA 59.298 45.455 0.00 0.00 0.00 2.87
2861 3041 3.135167 AGTGGTGGGTTTAACGAGAGAAA 59.865 43.478 0.00 0.00 0.00 2.52
2862 3042 3.878699 GTGGTGGGTTTAACGAGAGAAAA 59.121 43.478 0.00 0.00 0.00 2.29
2864 3044 4.132336 GGTGGGTTTAACGAGAGAAAACT 58.868 43.478 0.00 0.00 39.07 2.66
2865 3045 4.577693 GGTGGGTTTAACGAGAGAAAACTT 59.422 41.667 0.00 0.00 39.07 2.66
2867 3047 6.429078 GGTGGGTTTAACGAGAGAAAACTTAT 59.571 38.462 0.00 0.00 39.07 1.73
2868 3048 7.040892 GGTGGGTTTAACGAGAGAAAACTTATT 60.041 37.037 0.00 0.00 39.07 1.40
2869 3049 7.801783 GTGGGTTTAACGAGAGAAAACTTATTG 59.198 37.037 0.00 0.00 39.07 1.90
2870 3050 7.499895 TGGGTTTAACGAGAGAAAACTTATTGT 59.500 33.333 0.00 0.00 39.07 2.71
2871 3051 7.801783 GGGTTTAACGAGAGAAAACTTATTGTG 59.198 37.037 0.00 0.00 39.07 3.33
2875 3055 6.920569 ACGAGAGAAAACTTATTGTGTGTT 57.079 33.333 0.00 0.00 0.00 3.32
2876 3056 6.715464 ACGAGAGAAAACTTATTGTGTGTTG 58.285 36.000 0.00 0.00 0.00 3.33
2877 3057 6.315393 ACGAGAGAAAACTTATTGTGTGTTGT 59.685 34.615 0.00 0.00 0.00 3.32
2879 3059 7.164171 CGAGAGAAAACTTATTGTGTGTTGTTG 59.836 37.037 0.00 0.00 0.00 3.33
2880 3060 6.751888 AGAGAAAACTTATTGTGTGTTGTTGC 59.248 34.615 0.00 0.00 0.00 4.17
2885 3067 6.826893 ACTTATTGTGTGTTGTTGCATTTC 57.173 33.333 0.00 0.00 0.00 2.17
2984 3166 4.162690 ATCCTGCCGCCCTTCGTC 62.163 66.667 0.00 0.00 36.19 4.20
3210 3392 4.056125 CCGACGCTGACCTGAGCA 62.056 66.667 0.00 0.00 39.07 4.26
3259 3442 2.518949 GCTTTGTACATTGCGTGATGG 58.481 47.619 0.00 0.00 0.00 3.51
3338 3540 1.278637 GTTGGTTTCAGCCACGACG 59.721 57.895 0.00 0.00 38.42 5.12
3341 3543 4.072088 GTTTCAGCCACGACGCGG 62.072 66.667 12.47 0.00 0.00 6.46
3392 3597 0.994995 CGCATGCGCCTACTGATATC 59.005 55.000 29.09 0.00 33.11 1.63
3397 3602 0.109226 GCGCCTACTGATATCGGACC 60.109 60.000 18.63 2.65 0.00 4.46
3420 3625 5.635280 CCGAGATAACTGCATATTCGTTGAT 59.365 40.000 0.00 0.00 0.00 2.57
3421 3626 6.806739 CCGAGATAACTGCATATTCGTTGATA 59.193 38.462 0.00 0.00 0.00 2.15
3422 3627 7.201359 CCGAGATAACTGCATATTCGTTGATAC 60.201 40.741 0.00 0.00 0.00 2.24
3453 3661 2.730382 AGTTTGTCACGTTTTCCCCTT 58.270 42.857 0.00 0.00 0.00 3.95
3484 3692 7.074507 GCACAAAATTGCATCAAAATATCCA 57.925 32.000 0.00 0.00 42.49 3.41
3486 3694 8.021973 GCACAAAATTGCATCAAAATATCCAAA 58.978 29.630 0.00 0.00 42.49 3.28
3507 3716 1.963515 AGGCATCAAGTTGAAACCCAC 59.036 47.619 18.99 5.08 0.00 4.61
3515 3724 1.040339 GTTGAAACCCACCACTGGCA 61.040 55.000 0.00 0.00 36.00 4.92
3516 3725 0.754957 TTGAAACCCACCACTGGCAG 60.755 55.000 14.16 14.16 36.00 4.85
3535 3744 3.060895 GCAGTCACGTGCATAGAAACTAC 59.939 47.826 11.67 0.00 43.41 2.73
3536 3745 4.486090 CAGTCACGTGCATAGAAACTACT 58.514 43.478 11.67 1.73 0.00 2.57
3537 3746 4.559251 CAGTCACGTGCATAGAAACTACTC 59.441 45.833 11.67 0.00 0.00 2.59
3538 3747 3.858238 GTCACGTGCATAGAAACTACTCC 59.142 47.826 11.67 0.00 0.00 3.85
3540 3749 2.490903 ACGTGCATAGAAACTACTCCGT 59.509 45.455 0.00 0.00 0.00 4.69
3542 3751 4.156556 ACGTGCATAGAAACTACTCCGTAA 59.843 41.667 0.00 0.00 0.00 3.18
3543 3752 5.097529 CGTGCATAGAAACTACTCCGTAAA 58.902 41.667 0.00 0.00 0.00 2.01
3544 3753 5.747197 CGTGCATAGAAACTACTCCGTAAAT 59.253 40.000 0.00 0.00 0.00 1.40
3545 3754 6.291637 CGTGCATAGAAACTACTCCGTAAATG 60.292 42.308 0.00 0.00 0.00 2.32
3546 3755 6.755141 GTGCATAGAAACTACTCCGTAAATGA 59.245 38.462 0.00 0.00 0.00 2.57
3554 3788 8.561738 AAACTACTCCGTAAATGACATGATTT 57.438 30.769 0.00 0.00 0.00 2.17
3558 3792 7.915293 ACTCCGTAAATGACATGATTTACAA 57.085 32.000 21.04 12.39 44.14 2.41
3572 3806 4.022416 TGATTTACAATGTGACAGGCCAAC 60.022 41.667 5.01 0.00 0.00 3.77
3573 3807 1.904287 TACAATGTGACAGGCCAACC 58.096 50.000 5.01 0.00 0.00 3.77
3574 3808 0.106268 ACAATGTGACAGGCCAACCA 60.106 50.000 5.01 0.00 39.06 3.67
3575 3809 1.039068 CAATGTGACAGGCCAACCAA 58.961 50.000 5.01 0.00 39.06 3.67
3576 3810 1.619827 CAATGTGACAGGCCAACCAAT 59.380 47.619 5.01 0.00 39.06 3.16
3581 3815 0.603065 GACAGGCCAACCAATCCAAC 59.397 55.000 5.01 0.00 39.06 3.77
3582 3816 1.178534 ACAGGCCAACCAATCCAACG 61.179 55.000 5.01 0.00 39.06 4.10
3585 3819 1.584495 GCCAACCAATCCAACGTCC 59.416 57.895 0.00 0.00 0.00 4.79
3587 3821 0.881118 CCAACCAATCCAACGTCCTG 59.119 55.000 0.00 0.00 0.00 3.86
3597 3831 1.675552 CAACGTCCTGGTTCCTTGTT 58.324 50.000 0.00 0.00 0.00 2.83
3605 3839 1.484240 CTGGTTCCTTGTTGGGCAAAA 59.516 47.619 0.00 0.00 36.53 2.44
3633 3867 4.041567 ACACATGAGATGAACCAACAGGTA 59.958 41.667 0.00 0.00 33.53 3.08
3676 3921 1.854743 CGACAACAGATAGTGCATCCG 59.145 52.381 0.00 0.00 33.75 4.18
3696 3941 7.481798 GCATCCGTACTACAAAAGAAAAATGAG 59.518 37.037 0.00 0.00 0.00 2.90
3765 4011 3.308866 GTGTATCATACGTGAAAGCACCC 59.691 47.826 0.00 0.00 42.09 4.61
3809 4110 2.224257 GGTCAGGCTCATCTTCAGATCC 60.224 54.545 0.00 0.00 31.21 3.36
3821 4122 1.256812 TCAGATCCAGCGTTCTGACA 58.743 50.000 6.79 0.00 42.52 3.58
3867 4171 2.027192 ACTTATCGTCAACAGCCACCAT 60.027 45.455 0.00 0.00 0.00 3.55
3888 4192 7.886970 CACCATGATTCAAAGGATATACTGGAT 59.113 37.037 13.60 0.00 0.00 3.41
3900 4204 0.044092 TACTGGATGCTCCCCCTCAA 59.956 55.000 0.50 0.00 35.03 3.02
3901 4205 1.277580 ACTGGATGCTCCCCCTCAAG 61.278 60.000 0.50 0.00 35.03 3.02
3902 4206 1.992519 CTGGATGCTCCCCCTCAAGG 61.993 65.000 0.50 0.00 35.03 3.61
3903 4207 2.194326 GATGCTCCCCCTCAAGGC 59.806 66.667 0.00 0.00 0.00 4.35
3904 4208 3.424105 ATGCTCCCCCTCAAGGCC 61.424 66.667 0.00 0.00 0.00 5.19
3905 4209 3.978241 ATGCTCCCCCTCAAGGCCT 62.978 63.158 0.00 0.00 0.00 5.19
3906 4210 3.803162 GCTCCCCCTCAAGGCCTC 61.803 72.222 5.23 0.00 0.00 4.70
3907 4211 2.285668 CTCCCCCTCAAGGCCTCA 60.286 66.667 5.23 0.00 0.00 3.86
3923 4227 1.171308 CTCAATGGACACCAAGCCAG 58.829 55.000 0.00 0.00 36.95 4.85
3937 4241 3.448686 CAAGCCAGGTTCGTCTGTATAG 58.551 50.000 0.00 0.00 33.14 1.31
4149 4457 0.179020 CACAAGGTCTGAGGGTGCAA 60.179 55.000 0.00 0.00 0.00 4.08
4150 4458 0.109342 ACAAGGTCTGAGGGTGCAAG 59.891 55.000 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.069430 GCCAAGGAGGAGGAGGAGG 61.069 68.421 0.00 0.00 41.22 4.30
1 2 1.306482 TGCCAAGGAGGAGGAGGAG 60.306 63.158 0.00 0.00 41.22 3.69
2 3 1.613630 GTGCCAAGGAGGAGGAGGA 60.614 63.158 0.00 0.00 41.22 3.71
3 4 2.993853 GTGCCAAGGAGGAGGAGG 59.006 66.667 0.00 0.00 41.22 4.30
4 5 1.954362 CTCGTGCCAAGGAGGAGGAG 61.954 65.000 0.00 0.00 41.22 3.69
5 6 1.984570 CTCGTGCCAAGGAGGAGGA 60.985 63.158 0.00 0.00 41.22 3.71
6 7 2.581354 CTCGTGCCAAGGAGGAGG 59.419 66.667 0.00 0.00 41.22 4.30
22 23 4.824515 CGAGGAGGAGGTCGCCCT 62.825 72.222 0.00 0.00 46.66 5.19
23 24 4.816984 TCGAGGAGGAGGTCGCCC 62.817 72.222 0.00 0.00 35.80 6.13
24 25 3.519930 GTCGAGGAGGAGGTCGCC 61.520 72.222 0.00 0.00 36.11 5.54
25 26 2.047443 AAGTCGAGGAGGAGGTCGC 61.047 63.158 0.00 0.00 36.11 5.19
26 27 1.803943 CAAGTCGAGGAGGAGGTCG 59.196 63.158 0.00 0.00 37.54 4.79
27 28 0.968393 AGCAAGTCGAGGAGGAGGTC 60.968 60.000 0.00 0.00 0.00 3.85
28 29 0.968393 GAGCAAGTCGAGGAGGAGGT 60.968 60.000 0.00 0.00 0.00 3.85
29 30 1.671901 GGAGCAAGTCGAGGAGGAGG 61.672 65.000 0.00 0.00 0.00 4.30
30 31 0.682855 AGGAGCAAGTCGAGGAGGAG 60.683 60.000 0.00 0.00 0.00 3.69
31 32 0.681564 GAGGAGCAAGTCGAGGAGGA 60.682 60.000 0.00 0.00 0.00 3.71
32 33 1.813192 GAGGAGCAAGTCGAGGAGG 59.187 63.158 0.00 0.00 0.00 4.30
33 34 1.309499 ACGAGGAGCAAGTCGAGGAG 61.309 60.000 8.39 0.00 39.53 3.69
34 35 1.303398 ACGAGGAGCAAGTCGAGGA 60.303 57.895 8.39 0.00 39.53 3.71
35 36 1.137825 GACGAGGAGCAAGTCGAGG 59.862 63.158 8.39 0.00 39.53 4.63
36 37 1.137825 GGACGAGGAGCAAGTCGAG 59.862 63.158 8.39 0.00 39.53 4.04
37 38 1.176619 TTGGACGAGGAGCAAGTCGA 61.177 55.000 8.39 0.00 39.53 4.20
38 39 1.009389 GTTGGACGAGGAGCAAGTCG 61.009 60.000 0.00 0.62 42.04 4.18
39 40 0.033504 TGTTGGACGAGGAGCAAGTC 59.966 55.000 0.00 0.00 0.00 3.01
40 41 0.687354 ATGTTGGACGAGGAGCAAGT 59.313 50.000 0.00 0.00 0.00 3.16
41 42 1.363744 GATGTTGGACGAGGAGCAAG 58.636 55.000 0.00 0.00 0.00 4.01
42 43 0.036388 GGATGTTGGACGAGGAGCAA 60.036 55.000 0.00 0.00 0.00 3.91
43 44 1.596934 GGATGTTGGACGAGGAGCA 59.403 57.895 0.00 0.00 0.00 4.26
44 45 1.519455 CGGATGTTGGACGAGGAGC 60.519 63.158 0.00 0.00 0.00 4.70
45 46 1.519455 GCGGATGTTGGACGAGGAG 60.519 63.158 0.00 0.00 0.00 3.69
46 47 1.945354 GAGCGGATGTTGGACGAGGA 61.945 60.000 0.00 0.00 0.00 3.71
47 48 1.519455 GAGCGGATGTTGGACGAGG 60.519 63.158 0.00 0.00 0.00 4.63
48 49 0.108615 AAGAGCGGATGTTGGACGAG 60.109 55.000 0.00 0.00 0.00 4.18
49 50 0.108804 GAAGAGCGGATGTTGGACGA 60.109 55.000 0.00 0.00 0.00 4.20
50 51 0.108615 AGAAGAGCGGATGTTGGACG 60.109 55.000 0.00 0.00 0.00 4.79
51 52 2.427453 TCTAGAAGAGCGGATGTTGGAC 59.573 50.000 0.00 0.00 0.00 4.02
52 53 2.690497 CTCTAGAAGAGCGGATGTTGGA 59.310 50.000 0.00 0.00 35.30 3.53
53 54 2.428890 ACTCTAGAAGAGCGGATGTTGG 59.571 50.000 3.85 0.00 46.12 3.77
54 55 3.443037 CACTCTAGAAGAGCGGATGTTG 58.557 50.000 3.85 0.00 46.12 3.33
55 56 2.428890 CCACTCTAGAAGAGCGGATGTT 59.571 50.000 5.24 0.00 45.19 2.71
56 57 2.028130 CCACTCTAGAAGAGCGGATGT 58.972 52.381 5.24 0.00 45.19 3.06
57 58 2.302260 TCCACTCTAGAAGAGCGGATG 58.698 52.381 9.16 0.00 45.74 3.51
58 59 2.738587 TCCACTCTAGAAGAGCGGAT 57.261 50.000 9.16 0.00 45.74 4.18
60 61 1.133407 GTGTCCACTCTAGAAGAGCGG 59.867 57.143 4.87 4.87 46.12 5.52
61 62 1.202087 CGTGTCCACTCTAGAAGAGCG 60.202 57.143 3.85 0.00 46.12 5.03
62 63 1.813786 ACGTGTCCACTCTAGAAGAGC 59.186 52.381 3.85 0.00 46.12 4.09
63 64 3.120130 GACACGTGTCCACTCTAGAAGAG 60.120 52.174 33.62 2.39 42.19 2.85
64 65 2.812591 GACACGTGTCCACTCTAGAAGA 59.187 50.000 33.62 0.00 39.07 2.87
65 66 2.552743 TGACACGTGTCCACTCTAGAAG 59.447 50.000 38.12 2.15 44.15 2.85
66 67 2.578786 TGACACGTGTCCACTCTAGAA 58.421 47.619 38.12 18.80 44.15 2.10
67 68 2.265589 TGACACGTGTCCACTCTAGA 57.734 50.000 38.12 19.48 44.15 2.43
68 69 2.476352 CGATGACACGTGTCCACTCTAG 60.476 54.545 38.12 21.39 44.15 2.43
69 70 1.467342 CGATGACACGTGTCCACTCTA 59.533 52.381 38.12 23.23 44.15 2.43
70 71 0.241213 CGATGACACGTGTCCACTCT 59.759 55.000 38.12 21.21 44.15 3.24
71 72 0.240145 TCGATGACACGTGTCCACTC 59.760 55.000 38.12 29.58 44.15 3.51
72 73 0.039437 GTCGATGACACGTGTCCACT 60.039 55.000 38.12 25.66 44.15 4.00
73 74 0.318360 TGTCGATGACACGTGTCCAC 60.318 55.000 38.12 29.89 44.15 4.02
74 75 0.386113 TTGTCGATGACACGTGTCCA 59.614 50.000 38.12 27.42 42.60 4.02
75 76 0.782384 GTTGTCGATGACACGTGTCC 59.218 55.000 38.12 25.60 42.60 4.02
76 77 1.767289 AGTTGTCGATGACACGTGTC 58.233 50.000 36.01 36.01 42.60 3.67
77 78 2.033675 TGTAGTTGTCGATGACACGTGT 59.966 45.455 23.64 23.64 42.60 4.49
78 79 2.657184 TGTAGTTGTCGATGACACGTG 58.343 47.619 15.48 15.48 42.60 4.49
79 80 3.358707 TTGTAGTTGTCGATGACACGT 57.641 42.857 0.00 0.00 42.60 4.49
80 81 3.734231 ACTTTGTAGTTGTCGATGACACG 59.266 43.478 0.00 0.00 42.60 4.49
81 82 4.982916 AGACTTTGTAGTTGTCGATGACAC 59.017 41.667 0.00 0.00 42.60 3.67
82 83 5.196341 AGACTTTGTAGTTGTCGATGACA 57.804 39.130 0.00 0.00 41.09 3.58
83 84 6.609533 TCTAGACTTTGTAGTTGTCGATGAC 58.390 40.000 0.00 0.00 33.84 3.06
84 85 6.812879 TCTAGACTTTGTAGTTGTCGATGA 57.187 37.500 0.00 0.00 33.84 2.92
85 86 8.467402 AAATCTAGACTTTGTAGTTGTCGATG 57.533 34.615 0.00 0.00 33.84 3.84
86 87 9.790389 CTAAATCTAGACTTTGTAGTTGTCGAT 57.210 33.333 0.00 0.00 33.84 3.59
87 88 8.242053 CCTAAATCTAGACTTTGTAGTTGTCGA 58.758 37.037 0.00 0.00 33.84 4.20
88 89 8.027771 ACCTAAATCTAGACTTTGTAGTTGTCG 58.972 37.037 0.00 0.00 33.84 4.35
95 96 9.122779 GCTCTCTACCTAAATCTAGACTTTGTA 57.877 37.037 0.00 0.00 0.00 2.41
96 97 7.837187 AGCTCTCTACCTAAATCTAGACTTTGT 59.163 37.037 0.00 0.00 0.00 2.83
97 98 8.134895 CAGCTCTCTACCTAAATCTAGACTTTG 58.865 40.741 0.00 0.00 0.00 2.77
98 99 7.201875 GCAGCTCTCTACCTAAATCTAGACTTT 60.202 40.741 0.00 0.16 0.00 2.66
99 100 6.264518 GCAGCTCTCTACCTAAATCTAGACTT 59.735 42.308 0.00 0.00 0.00 3.01
100 101 5.768164 GCAGCTCTCTACCTAAATCTAGACT 59.232 44.000 0.00 0.00 0.00 3.24
101 102 5.768164 AGCAGCTCTCTACCTAAATCTAGAC 59.232 44.000 0.00 0.00 0.00 2.59
102 103 5.947663 AGCAGCTCTCTACCTAAATCTAGA 58.052 41.667 0.00 0.00 0.00 2.43
103 104 7.229707 TGTTAGCAGCTCTCTACCTAAATCTAG 59.770 40.741 0.00 0.00 0.00 2.43
104 105 7.061054 TGTTAGCAGCTCTCTACCTAAATCTA 58.939 38.462 0.00 0.00 0.00 1.98
105 106 5.894393 TGTTAGCAGCTCTCTACCTAAATCT 59.106 40.000 0.00 0.00 0.00 2.40
106 107 6.150396 TGTTAGCAGCTCTCTACCTAAATC 57.850 41.667 0.00 0.00 0.00 2.17
107 108 5.659079 ACTGTTAGCAGCTCTCTACCTAAAT 59.341 40.000 6.48 0.00 46.30 1.40
108 109 5.017490 ACTGTTAGCAGCTCTCTACCTAAA 58.983 41.667 6.48 0.00 46.30 1.85
109 110 4.601084 ACTGTTAGCAGCTCTCTACCTAA 58.399 43.478 6.48 0.00 46.30 2.69
110 111 4.237976 ACTGTTAGCAGCTCTCTACCTA 57.762 45.455 6.48 0.00 46.30 3.08
111 112 3.094484 ACTGTTAGCAGCTCTCTACCT 57.906 47.619 6.48 0.00 46.30 3.08
112 113 4.985538 TTACTGTTAGCAGCTCTCTACC 57.014 45.455 6.48 0.00 46.30 3.18
115 116 8.696374 TGTAATAATTACTGTTAGCAGCTCTCT 58.304 33.333 6.48 0.00 46.30 3.10
116 117 8.873215 TGTAATAATTACTGTTAGCAGCTCTC 57.127 34.615 6.48 0.00 46.30 3.20
117 118 7.928706 CCTGTAATAATTACTGTTAGCAGCTCT 59.071 37.037 6.48 0.00 46.30 4.09
118 119 7.307455 GCCTGTAATAATTACTGTTAGCAGCTC 60.307 40.741 6.48 0.00 46.30 4.09
119 120 6.483640 GCCTGTAATAATTACTGTTAGCAGCT 59.516 38.462 6.48 0.00 46.30 4.24
120 121 6.483640 AGCCTGTAATAATTACTGTTAGCAGC 59.516 38.462 6.48 0.00 46.30 5.25
122 123 9.893634 TTTAGCCTGTAATAATTACTGTTAGCA 57.106 29.630 0.00 0.00 37.06 3.49
132 133 9.923143 GGTGTTTCTTTTTAGCCTGTAATAATT 57.077 29.630 0.00 0.00 0.00 1.40
145 146 2.882137 CGGCTCCTGGTGTTTCTTTTTA 59.118 45.455 0.00 0.00 0.00 1.52
146 147 1.681264 CGGCTCCTGGTGTTTCTTTTT 59.319 47.619 0.00 0.00 0.00 1.94
152 153 2.032681 GCTCGGCTCCTGGTGTTT 59.967 61.111 0.00 0.00 0.00 2.83
154 155 3.699894 CTGCTCGGCTCCTGGTGT 61.700 66.667 0.00 0.00 0.00 4.16
157 158 4.154347 GACCTGCTCGGCTCCTGG 62.154 72.222 0.00 0.00 35.61 4.45
158 159 4.504916 CGACCTGCTCGGCTCCTG 62.505 72.222 0.00 0.00 38.87 3.86
160 161 4.500116 GTCGACCTGCTCGGCTCC 62.500 72.222 3.51 0.00 44.08 4.70
161 162 4.838486 CGTCGACCTGCTCGGCTC 62.838 72.222 10.58 0.00 45.36 4.70
322 329 0.391395 ACTGAGACAGAGCATGCAGC 60.391 55.000 21.98 11.59 38.06 5.25
323 330 1.205179 AGACTGAGACAGAGCATGCAG 59.795 52.381 21.98 11.80 35.18 4.41
339 354 1.979693 GTGAGGGGTGAGCGAGACT 60.980 63.158 0.00 0.00 0.00 3.24
345 360 2.985456 CTGAGGTGAGGGGTGAGC 59.015 66.667 0.00 0.00 0.00 4.26
449 480 0.818040 GCGGTGGATTTAGCCGGATT 60.818 55.000 5.05 0.00 45.02 3.01
482 517 2.699768 CCGTGATGCGCCCACAAAT 61.700 57.895 23.58 3.29 39.71 2.32
589 624 1.663702 CGCTTTATACGCGGGAGGG 60.664 63.158 12.47 5.14 46.32 4.30
663 703 0.736325 CGTCGCCACCTTTGTAGAGG 60.736 60.000 0.00 0.00 42.75 3.69
871 945 1.286248 GGGAGACTTAAAGAGGCCCA 58.714 55.000 0.00 0.00 36.15 5.36
997 1071 4.473520 CACCTCGGCGCCCATCTT 62.474 66.667 23.46 0.00 0.00 2.40
1065 1139 4.994471 TGCAGCAGCGTGGTGGAG 62.994 66.667 15.50 0.00 45.26 3.86
1089 1163 2.599281 TCGGGGTTGTCGAGCTGA 60.599 61.111 0.00 0.00 32.51 4.26
1602 1700 1.582968 GTGGTACGCGGTCTTGAGA 59.417 57.895 12.47 0.00 0.00 3.27
2104 2221 3.002656 CAGAATTAATGGCGGCACAGTAG 59.997 47.826 16.34 0.00 0.00 2.57
2105 2222 2.942376 CAGAATTAATGGCGGCACAGTA 59.058 45.455 16.34 4.07 0.00 2.74
2106 2223 1.745087 CAGAATTAATGGCGGCACAGT 59.255 47.619 16.34 5.21 0.00 3.55
2107 2224 1.534595 GCAGAATTAATGGCGGCACAG 60.535 52.381 16.34 0.00 0.00 3.66
2108 2225 0.455410 GCAGAATTAATGGCGGCACA 59.545 50.000 16.34 1.46 0.00 4.57
2109 2226 0.455410 TGCAGAATTAATGGCGGCAC 59.545 50.000 16.34 0.00 0.00 5.01
2110 2227 1.134753 CTTGCAGAATTAATGGCGGCA 59.865 47.619 16.34 16.34 0.00 5.69
2111 2228 1.843992 CTTGCAGAATTAATGGCGGC 58.156 50.000 0.00 0.00 0.00 6.53
2112 2229 1.134753 TGCTTGCAGAATTAATGGCGG 59.865 47.619 0.00 0.00 0.00 6.13
2113 2230 2.187707 GTGCTTGCAGAATTAATGGCG 58.812 47.619 0.00 0.00 0.00 5.69
2114 2231 2.187707 CGTGCTTGCAGAATTAATGGC 58.812 47.619 0.00 0.00 0.00 4.40
2115 2232 3.492421 ACGTGCTTGCAGAATTAATGG 57.508 42.857 0.00 0.00 0.00 3.16
2116 2233 4.142708 TGGTACGTGCTTGCAGAATTAATG 60.143 41.667 3.01 0.00 0.00 1.90
2117 2234 4.006989 TGGTACGTGCTTGCAGAATTAAT 58.993 39.130 3.01 0.00 0.00 1.40
2118 2235 3.403968 TGGTACGTGCTTGCAGAATTAA 58.596 40.909 3.01 0.00 0.00 1.40
2119 2236 3.000041 CTGGTACGTGCTTGCAGAATTA 59.000 45.455 3.01 0.00 0.00 1.40
2120 2237 1.806542 CTGGTACGTGCTTGCAGAATT 59.193 47.619 3.01 0.00 0.00 2.17
2121 2238 1.442769 CTGGTACGTGCTTGCAGAAT 58.557 50.000 3.01 0.00 0.00 2.40
2122 2239 0.602638 CCTGGTACGTGCTTGCAGAA 60.603 55.000 3.01 0.00 0.00 3.02
2123 2240 1.005037 CCTGGTACGTGCTTGCAGA 60.005 57.895 3.01 0.00 0.00 4.26
2129 2246 2.151202 CAAATGAACCTGGTACGTGCT 58.849 47.619 0.00 0.00 0.00 4.40
2131 2248 3.062099 CGATCAAATGAACCTGGTACGTG 59.938 47.826 0.00 0.00 0.00 4.49
2147 2264 9.489393 CGTGATTAAGATTTCAATTTCGATCAA 57.511 29.630 0.00 0.00 0.00 2.57
2172 2291 9.079833 TCTAACTCGAAATTCTAAATTACCACG 57.920 33.333 0.00 0.00 0.00 4.94
2193 2312 5.047943 TGTCAGTCTGAAGCCTTACTCTAAC 60.048 44.000 3.51 0.00 0.00 2.34
2194 2313 5.077564 TGTCAGTCTGAAGCCTTACTCTAA 58.922 41.667 3.51 0.00 0.00 2.10
2195 2314 4.663334 TGTCAGTCTGAAGCCTTACTCTA 58.337 43.478 3.51 0.00 0.00 2.43
2196 2315 3.501349 TGTCAGTCTGAAGCCTTACTCT 58.499 45.455 3.51 0.00 0.00 3.24
2198 2317 4.564406 CCAATGTCAGTCTGAAGCCTTACT 60.564 45.833 3.51 0.00 0.00 2.24
2199 2318 3.686726 CCAATGTCAGTCTGAAGCCTTAC 59.313 47.826 3.51 0.00 0.00 2.34
2200 2319 3.582647 TCCAATGTCAGTCTGAAGCCTTA 59.417 43.478 3.51 0.00 0.00 2.69
2247 2384 7.964011 TCAAAAGTTAAAACCAAAGTGACGTAG 59.036 33.333 0.00 0.00 0.00 3.51
2248 2385 7.814642 TCAAAAGTTAAAACCAAAGTGACGTA 58.185 30.769 0.00 0.00 0.00 3.57
2254 2391 6.439375 ACCTCCTCAAAAGTTAAAACCAAAGT 59.561 34.615 0.00 0.00 0.00 2.66
2259 2396 4.891168 TGGACCTCCTCAAAAGTTAAAACC 59.109 41.667 0.00 0.00 36.82 3.27
2278 2419 1.269102 GCTGATGCATGCTGAATGGAC 60.269 52.381 20.33 2.18 39.72 4.02
2294 2435 0.987613 TGTATGGGGGCAGATGCTGA 60.988 55.000 4.59 0.00 41.70 4.26
2309 2450 5.097742 TGCAGCCAACTAACTGTATGTAT 57.902 39.130 0.00 0.00 36.26 2.29
2572 2718 1.131883 GCATGTGACAGCCATGTTCTC 59.868 52.381 7.61 0.00 40.68 2.87
2573 2719 1.171308 GCATGTGACAGCCATGTTCT 58.829 50.000 7.61 0.00 40.68 3.01
2583 2729 1.303155 TTGGCATCGGCATGTGACA 60.303 52.632 0.00 0.00 43.71 3.58
2690 2856 6.432783 TGCAAAGTTAGTTGGTACTAATGCAT 59.567 34.615 15.41 0.00 45.81 3.96
2750 2921 4.024641 GGATTACACGACAAGGAACGTTTT 60.025 41.667 0.46 0.00 40.76 2.43
2778 2949 5.074377 TGCTAAGGATAGGGCAATTATCCAA 59.926 40.000 18.31 9.24 45.94 3.53
2811 2987 5.750547 CACCACAGCAGTCAAGTAGTATATG 59.249 44.000 0.00 0.00 0.00 1.78
2815 2991 3.227614 TCACCACAGCAGTCAAGTAGTA 58.772 45.455 0.00 0.00 0.00 1.82
2816 2992 2.039418 TCACCACAGCAGTCAAGTAGT 58.961 47.619 0.00 0.00 0.00 2.73
2817 2993 2.820059 TCACCACAGCAGTCAAGTAG 57.180 50.000 0.00 0.00 0.00 2.57
2818 2994 2.632512 TCATCACCACAGCAGTCAAGTA 59.367 45.455 0.00 0.00 0.00 2.24
2830 3010 0.110486 AACCCACCACTCATCACCAC 59.890 55.000 0.00 0.00 0.00 4.16
2833 3013 2.482721 CGTTAAACCCACCACTCATCAC 59.517 50.000 0.00 0.00 0.00 3.06
2848 3028 8.885722 ACACACAATAAGTTTTCTCTCGTTAAA 58.114 29.630 0.00 0.00 0.00 1.52
2850 3030 8.332464 CAACACACAATAAGTTTTCTCTCGTTA 58.668 33.333 0.00 0.00 0.00 3.18
2858 3038 6.639671 TGCAACAACACACAATAAGTTTTC 57.360 33.333 0.00 0.00 0.00 2.29
2860 3040 7.201600 GGAAATGCAACAACACACAATAAGTTT 60.202 33.333 0.00 0.00 0.00 2.66
2861 3041 6.257630 GGAAATGCAACAACACACAATAAGTT 59.742 34.615 0.00 0.00 0.00 2.66
2862 3042 5.752955 GGAAATGCAACAACACACAATAAGT 59.247 36.000 0.00 0.00 0.00 2.24
2864 3044 5.664457 TGGAAATGCAACAACACACAATAA 58.336 33.333 0.00 0.00 0.00 1.40
2865 3045 5.268118 TGGAAATGCAACAACACACAATA 57.732 34.783 0.00 0.00 0.00 1.90
2867 3047 3.519579 CTGGAAATGCAACAACACACAA 58.480 40.909 0.00 0.00 0.00 3.33
2868 3048 2.159128 CCTGGAAATGCAACAACACACA 60.159 45.455 0.00 0.00 0.00 3.72
2869 3049 2.159114 ACCTGGAAATGCAACAACACAC 60.159 45.455 0.00 0.00 0.00 3.82
2870 3050 2.106566 ACCTGGAAATGCAACAACACA 58.893 42.857 0.00 0.00 0.00 3.72
2871 3051 2.472816 CACCTGGAAATGCAACAACAC 58.527 47.619 0.00 0.00 0.00 3.32
2875 3055 1.804396 CGCCACCTGGAAATGCAACA 61.804 55.000 0.00 0.00 37.39 3.33
2876 3056 1.080569 CGCCACCTGGAAATGCAAC 60.081 57.895 0.00 0.00 37.39 4.17
2877 3057 2.274645 CCGCCACCTGGAAATGCAA 61.275 57.895 0.00 0.00 37.39 4.08
2879 3059 2.361104 TCCGCCACCTGGAAATGC 60.361 61.111 0.00 0.00 37.39 3.56
2880 3060 2.409870 GCTCCGCCACCTGGAAATG 61.410 63.158 0.00 0.00 37.39 2.32
2984 3166 4.680237 TTGTCCTCCACGCTGGCG 62.680 66.667 13.56 13.56 46.03 5.69
3077 3259 2.799371 CAGCGGTCGTAGAGGTCC 59.201 66.667 0.00 0.00 36.95 4.46
3193 3375 3.978723 CTGCTCAGGTCAGCGTCGG 62.979 68.421 0.00 0.00 42.92 4.79
3194 3376 1.923227 TACTGCTCAGGTCAGCGTCG 61.923 60.000 1.66 0.00 42.92 5.12
3195 3377 0.179150 CTACTGCTCAGGTCAGCGTC 60.179 60.000 1.66 0.00 42.92 5.19
3196 3378 1.886585 CTACTGCTCAGGTCAGCGT 59.113 57.895 1.66 0.00 42.92 5.07
3197 3379 1.518133 GCTACTGCTCAGGTCAGCG 60.518 63.158 1.66 0.00 42.92 5.18
3198 3380 4.511636 GCTACTGCTCAGGTCAGC 57.488 61.111 1.66 3.75 40.13 4.26
3338 3540 4.307908 AAATATTCGCCGCGCCGC 62.308 61.111 3.85 10.88 0.00 6.53
3341 3543 1.061887 ACACAAATATTCGCCGCGC 59.938 52.632 8.21 0.00 0.00 6.86
3392 3597 3.577649 ATATGCAGTTATCTCGGTCCG 57.422 47.619 4.39 4.39 0.00 4.79
3397 3602 6.696825 ATCAACGAATATGCAGTTATCTCG 57.303 37.500 0.00 2.11 0.00 4.04
3420 3625 7.542534 ACGTGACAAACTTTTCATTGTAGTA 57.457 32.000 0.00 0.00 39.73 1.82
3421 3626 6.431198 ACGTGACAAACTTTTCATTGTAGT 57.569 33.333 0.00 0.00 39.73 2.73
3422 3627 7.734538 AAACGTGACAAACTTTTCATTGTAG 57.265 32.000 0.00 0.00 39.73 2.74
3481 3689 4.442753 GGTTTCAACTTGATGCCTTTTGGA 60.443 41.667 0.00 0.00 44.07 3.53
3482 3690 3.809279 GGTTTCAACTTGATGCCTTTTGG 59.191 43.478 0.00 0.00 44.18 3.28
3483 3691 3.809279 GGGTTTCAACTTGATGCCTTTTG 59.191 43.478 10.28 0.00 0.00 2.44
3484 3692 3.454082 TGGGTTTCAACTTGATGCCTTTT 59.546 39.130 10.28 0.00 0.00 2.27
3486 3694 2.365293 GTGGGTTTCAACTTGATGCCTT 59.635 45.455 10.28 0.00 0.00 4.35
3507 3716 3.349006 GCACGTGACTGCCAGTGG 61.349 66.667 22.23 4.20 35.35 4.00
3515 3724 4.380655 GGAGTAGTTTCTATGCACGTGACT 60.381 45.833 22.23 14.14 0.00 3.41
3516 3725 3.858238 GGAGTAGTTTCTATGCACGTGAC 59.142 47.826 22.23 11.46 0.00 3.67
3535 3744 8.397906 ACATTGTAAATCATGTCATTTACGGAG 58.602 33.333 18.13 14.05 46.07 4.63
3536 3745 8.180920 CACATTGTAAATCATGTCATTTACGGA 58.819 33.333 18.13 12.79 46.07 4.69
3537 3746 8.180920 TCACATTGTAAATCATGTCATTTACGG 58.819 33.333 18.13 14.29 46.07 4.02
3538 3747 8.998989 GTCACATTGTAAATCATGTCATTTACG 58.001 33.333 18.13 10.88 46.07 3.18
3542 3751 7.541162 CCTGTCACATTGTAAATCATGTCATT 58.459 34.615 0.00 0.00 0.00 2.57
3543 3752 6.405065 GCCTGTCACATTGTAAATCATGTCAT 60.405 38.462 0.00 0.00 0.00 3.06
3544 3753 5.106197 GCCTGTCACATTGTAAATCATGTCA 60.106 40.000 0.00 0.00 0.00 3.58
3545 3754 5.335127 GCCTGTCACATTGTAAATCATGTC 58.665 41.667 0.00 0.00 0.00 3.06
3546 3755 4.158394 GGCCTGTCACATTGTAAATCATGT 59.842 41.667 0.00 0.00 0.00 3.21
3554 3788 1.143889 TGGTTGGCCTGTCACATTGTA 59.856 47.619 3.32 0.00 35.27 2.41
3558 3792 1.549203 GATTGGTTGGCCTGTCACAT 58.451 50.000 3.32 0.00 35.27 3.21
3572 3806 1.165270 GAACCAGGACGTTGGATTGG 58.835 55.000 13.22 8.01 40.87 3.16
3573 3807 1.165270 GGAACCAGGACGTTGGATTG 58.835 55.000 13.22 0.00 40.87 2.67
3574 3808 1.064825 AGGAACCAGGACGTTGGATT 58.935 50.000 13.22 3.94 40.87 3.01
3575 3809 1.064825 AAGGAACCAGGACGTTGGAT 58.935 50.000 13.22 0.63 40.87 3.41
3576 3810 0.107831 CAAGGAACCAGGACGTTGGA 59.892 55.000 13.22 0.00 40.87 3.53
3581 3815 0.889186 CCCAACAAGGAACCAGGACG 60.889 60.000 0.00 0.00 41.22 4.79
3582 3816 1.179174 GCCCAACAAGGAACCAGGAC 61.179 60.000 0.00 0.00 41.22 3.85
3585 3819 1.118838 TTTGCCCAACAAGGAACCAG 58.881 50.000 0.00 0.00 40.06 4.00
3587 3821 2.700722 TTTTTGCCCAACAAGGAACC 57.299 45.000 0.00 0.00 40.06 3.62
3610 3844 3.181440 ACCTGTTGGTTCATCTCATGTGT 60.181 43.478 0.00 0.00 46.05 3.72
3611 3845 3.415212 ACCTGTTGGTTCATCTCATGTG 58.585 45.455 0.00 0.00 46.05 3.21
3612 3846 3.795688 ACCTGTTGGTTCATCTCATGT 57.204 42.857 0.00 0.00 46.05 3.21
3622 3856 2.290960 GGCAGATCCTTACCTGTTGGTT 60.291 50.000 0.00 0.00 46.05 3.67
3633 3867 5.450965 CGAATTGCTTTTATGGCAGATCCTT 60.451 40.000 0.00 0.00 40.90 3.36
3676 3921 8.221766 CGACTCCTCATTTTTCTTTTGTAGTAC 58.778 37.037 0.00 0.00 0.00 2.73
3765 4011 5.122396 CCGTTCTTGGACTTTATTCTCCTTG 59.878 44.000 0.00 0.00 0.00 3.61
3809 4110 0.788995 CTCTTGCTGTCAGAACGCTG 59.211 55.000 3.32 0.00 43.67 5.18
3836 4137 6.846283 GCTGTTGACGATAAGTTATGTAATGC 59.154 38.462 0.00 0.00 0.00 3.56
3853 4154 2.161855 TGAATCATGGTGGCTGTTGAC 58.838 47.619 0.00 0.00 0.00 3.18
3867 4171 7.083062 AGCATCCAGTATATCCTTTGAATCA 57.917 36.000 0.00 0.00 0.00 2.57
3888 4192 4.682714 AGGCCTTGAGGGGGAGCA 62.683 66.667 0.00 0.00 35.18 4.26
3900 4204 0.038744 CTTGGTGTCCATTGAGGCCT 59.961 55.000 3.86 3.86 37.29 5.19
3901 4205 1.598701 GCTTGGTGTCCATTGAGGCC 61.599 60.000 0.00 0.00 37.29 5.19
3902 4206 1.598701 GGCTTGGTGTCCATTGAGGC 61.599 60.000 0.00 0.00 37.29 4.70
3903 4207 0.251297 TGGCTTGGTGTCCATTGAGG 60.251 55.000 0.00 0.00 39.47 3.86
3904 4208 1.171308 CTGGCTTGGTGTCCATTGAG 58.829 55.000 0.00 0.00 31.53 3.02
3905 4209 0.251297 CCTGGCTTGGTGTCCATTGA 60.251 55.000 0.00 0.00 31.53 2.57
3906 4210 0.540365 ACCTGGCTTGGTGTCCATTG 60.540 55.000 0.00 0.00 39.17 2.82
3907 4211 0.188342 AACCTGGCTTGGTGTCCATT 59.812 50.000 3.70 0.00 40.73 3.16
3923 4227 6.924060 AGCATAATGAACTATACAGACGAACC 59.076 38.462 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.