Multiple sequence alignment - TraesCS4D01G050500

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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 TraesCS4D01G050500 chr4D 100.000 3462 0 0 802 4263 26257605 26254144 0.000000e+00 6394.0
1 TraesCS4D01G050500 chr4D 100.000 394 0 0 1 394 26258406 26258013 0.000000e+00 728.0
2 TraesCS4D01G050500 chr4B 96.048 3365 107 9 802 4148 38797038 38793682 0.000000e+00 5454.0
3 TraesCS4D01G050500 chr4B 91.837 49 3 1 4208 4256 38793630 38793583 2.750000e-07 67.6
4 TraesCS4D01G050500 chr4A 95.240 3361 141 7 802 4148 577042680 577046035 0.000000e+00 5302.0
5 TraesCS4D01G050500 chr4A 90.196 306 22 2 3418 3716 624632164 624631860 4.000000e-105 392.0
6 TraesCS4D01G050500 chr6D 91.080 2556 193 23 878 3419 13071331 13068797 0.000000e+00 3424.0
7 TraesCS4D01G050500 chr6A 91.620 2482 187 15 951 3419 14355257 14352784 0.000000e+00 3411.0
8 TraesCS4D01G050500 chr6A 87.179 78 8 2 1245 1321 582492265 582492189 2.110000e-13 87.9
9 TraesCS4D01G050500 chr6B 92.170 2350 167 11 951 3295 23651270 23653607 0.000000e+00 3304.0
10 TraesCS4D01G050500 chr6B 91.784 1278 91 10 2023 3295 23673029 23674297 0.000000e+00 1766.0
11 TraesCS4D01G050500 chr2B 91.146 2451 190 18 978 3410 784618308 784620749 0.000000e+00 3299.0
12 TraesCS4D01G050500 chr5D 84.696 477 49 9 3773 4228 544700963 544700490 5.020000e-124 455.0
13 TraesCS4D01G050500 chr5D 85.342 307 22 10 3418 3716 544701406 544701115 3.220000e-76 296.0
14 TraesCS4D01G050500 chr5D 98.305 59 0 1 3717 3774 544701081 544701023 7.540000e-18 102.0
15 TraesCS4D01G050500 chr5B 83.537 492 55 10 3773 4243 687161646 687162132 1.820000e-118 436.0
16 TraesCS4D01G050500 chr5B 89.286 308 23 3 3418 3716 687161189 687161495 1.120000e-100 377.0
17 TraesCS4D01G050500 chr5B 98.333 60 0 1 3715 3774 687161528 687161586 2.100000e-18 104.0
18 TraesCS4D01G050500 chr7D 76.077 209 44 4 984 1187 9970232 9970025 2.100000e-18 104.0
19 TraesCS4D01G050500 chr1D 75.598 209 45 4 984 1187 441617848 441617641 9.760000e-17 99.0


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 TraesCS4D01G050500 chr4D 26254144 26258406 4262 True 3561.000000 6394 100.000000 1 4263 2 chr4D.!!$R1 4262
1 TraesCS4D01G050500 chr4B 38793583 38797038 3455 True 2760.800000 5454 93.942500 802 4256 2 chr4B.!!$R1 3454
2 TraesCS4D01G050500 chr4A 577042680 577046035 3355 False 5302.000000 5302 95.240000 802 4148 1 chr4A.!!$F1 3346
3 TraesCS4D01G050500 chr6D 13068797 13071331 2534 True 3424.000000 3424 91.080000 878 3419 1 chr6D.!!$R1 2541
4 TraesCS4D01G050500 chr6A 14352784 14355257 2473 True 3411.000000 3411 91.620000 951 3419 1 chr6A.!!$R1 2468
5 TraesCS4D01G050500 chr6B 23651270 23653607 2337 False 3304.000000 3304 92.170000 951 3295 1 chr6B.!!$F1 2344
6 TraesCS4D01G050500 chr6B 23673029 23674297 1268 False 1766.000000 1766 91.784000 2023 3295 1 chr6B.!!$F2 1272
7 TraesCS4D01G050500 chr2B 784618308 784620749 2441 False 3299.000000 3299 91.146000 978 3410 1 chr2B.!!$F1 2432
8 TraesCS4D01G050500 chr5D 544700490 544701406 916 True 284.333333 455 89.447667 3418 4228 3 chr5D.!!$R1 810
9 TraesCS4D01G050500 chr5B 687161189 687162132 943 False 305.666667 436 90.385333 3418 4243 3 chr5B.!!$F1 825

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
89 90 0.036388 TCAAACATGCTCGAGGGACC 60.036 55.0 15.58 0.0 0.00 4.46 F
114 115 0.104120 TCCCGTAATGCTGACATCCG 59.896 55.0 0.00 0.0 34.62 4.18 F
178 179 0.251916 TAACCACAATCTGGGCGAGG 59.748 55.0 0.00 0.0 45.78 4.63 F
389 390 0.394216 CCATCAGACAATTCCGGCCA 60.394 55.0 2.24 0.0 0.00 5.36 F
2266 2267 0.455005 GGCAGCTGATGAAGAAAGGC 59.545 55.0 20.43 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1588 1.553690 CCCGTGGTCCTTCATGTCCT 61.554 60.000 0.00 0.0 0.00 3.85 R
1677 1678 1.974265 TTCATCAAACACCTTCCGCA 58.026 45.000 0.00 0.0 0.00 5.69 R
2102 2103 2.740055 GAGCACCTCCACAGCACG 60.740 66.667 0.00 0.0 0.00 5.34 R
2348 2349 0.461163 CCACGGCGTGTCATAATGGA 60.461 55.000 34.74 0.0 0.00 3.41 R
4029 4174 0.457851 GCGAGCCAGTATGACAGACT 59.542 55.000 0.00 0.0 39.69 3.24 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
25 26 3.758931 GCCATTGGCGTTGTCCCC 61.759 66.667 12.82 0.00 39.62 4.81
26 27 2.035626 CCATTGGCGTTGTCCCCT 59.964 61.111 0.00 0.00 0.00 4.79
27 28 2.342650 CCATTGGCGTTGTCCCCTG 61.343 63.158 0.00 0.00 0.00 4.45
28 29 2.035626 ATTGGCGTTGTCCCCTGG 59.964 61.111 0.00 0.00 0.00 4.45
29 30 2.534396 ATTGGCGTTGTCCCCTGGA 61.534 57.895 0.00 0.00 0.00 3.86
30 31 2.075355 ATTGGCGTTGTCCCCTGGAA 62.075 55.000 0.00 0.00 31.38 3.53
31 32 2.671963 GGCGTTGTCCCCTGGAAC 60.672 66.667 0.00 0.00 31.38 3.62
32 33 2.671963 GCGTTGTCCCCTGGAACC 60.672 66.667 0.00 0.00 31.38 3.62
33 34 3.157680 CGTTGTCCCCTGGAACCT 58.842 61.111 0.00 0.00 31.38 3.50
34 35 1.454539 CGTTGTCCCCTGGAACCTT 59.545 57.895 0.00 0.00 31.38 3.50
35 36 0.889186 CGTTGTCCCCTGGAACCTTG 60.889 60.000 0.00 0.00 31.38 3.61
36 37 1.152830 TTGTCCCCTGGAACCTTGC 59.847 57.895 0.00 0.00 31.38 4.01
37 38 1.360393 TTGTCCCCTGGAACCTTGCT 61.360 55.000 0.00 0.00 31.38 3.91
38 39 1.002011 GTCCCCTGGAACCTTGCTC 60.002 63.158 0.00 0.00 31.38 4.26
39 40 2.231380 TCCCCTGGAACCTTGCTCC 61.231 63.158 0.00 0.00 0.00 4.70
40 41 2.234296 CCCCTGGAACCTTGCTCCT 61.234 63.158 0.00 0.00 33.77 3.69
41 42 1.770324 CCCTGGAACCTTGCTCCTT 59.230 57.895 0.00 0.00 33.77 3.36
42 43 0.610232 CCCTGGAACCTTGCTCCTTG 60.610 60.000 0.00 0.00 33.77 3.61
43 44 0.610232 CCTGGAACCTTGCTCCTTGG 60.610 60.000 0.00 0.00 33.77 3.61
44 45 0.610232 CTGGAACCTTGCTCCTTGGG 60.610 60.000 0.00 0.00 33.77 4.12
45 46 1.979155 GGAACCTTGCTCCTTGGGC 60.979 63.158 0.00 0.00 0.00 5.36
46 47 1.979155 GAACCTTGCTCCTTGGGCC 60.979 63.158 0.00 0.00 0.00 5.80
47 48 3.529835 AACCTTGCTCCTTGGGCCC 62.530 63.158 17.59 17.59 0.00 5.80
48 49 4.766632 CCTTGCTCCTTGGGCCCC 62.767 72.222 22.27 2.17 0.00 5.80
49 50 3.983420 CTTGCTCCTTGGGCCCCA 61.983 66.667 22.27 7.58 0.00 4.96
50 51 3.275271 TTGCTCCTTGGGCCCCAT 61.275 61.111 22.27 0.00 31.53 4.00
51 52 3.605412 TTGCTCCTTGGGCCCCATG 62.605 63.158 22.27 5.85 31.53 3.66
52 53 4.847367 GCTCCTTGGGCCCCATGG 62.847 72.222 25.54 25.54 46.42 3.66
53 54 3.350163 CTCCTTGGGCCCCATGGT 61.350 66.667 28.82 0.00 45.58 3.55
54 55 3.667217 CTCCTTGGGCCCCATGGTG 62.667 68.421 28.82 23.92 45.58 4.17
61 62 3.070576 GCCCCATGGTGCCAAGTC 61.071 66.667 8.18 0.00 0.00 3.01
62 63 2.362889 CCCCATGGTGCCAAGTCC 60.363 66.667 11.73 0.00 0.00 3.85
63 64 2.751436 CCCATGGTGCCAAGTCCG 60.751 66.667 11.73 0.00 0.00 4.79
64 65 2.350895 CCATGGTGCCAAGTCCGA 59.649 61.111 2.57 0.00 0.00 4.55
65 66 2.040544 CCATGGTGCCAAGTCCGAC 61.041 63.158 2.57 0.00 0.00 4.79
66 67 2.040544 CATGGTGCCAAGTCCGACC 61.041 63.158 0.00 0.00 0.00 4.79
67 68 2.224159 ATGGTGCCAAGTCCGACCT 61.224 57.895 0.00 0.00 0.00 3.85
68 69 0.907704 ATGGTGCCAAGTCCGACCTA 60.908 55.000 0.00 0.00 0.00 3.08
69 70 0.907704 TGGTGCCAAGTCCGACCTAT 60.908 55.000 0.00 0.00 0.00 2.57
70 71 0.252197 GGTGCCAAGTCCGACCTATT 59.748 55.000 0.00 0.00 0.00 1.73
71 72 1.653151 GTGCCAAGTCCGACCTATTC 58.347 55.000 0.00 0.00 0.00 1.75
72 73 1.066430 GTGCCAAGTCCGACCTATTCA 60.066 52.381 0.00 0.00 0.00 2.57
73 74 1.626321 TGCCAAGTCCGACCTATTCAA 59.374 47.619 0.00 0.00 0.00 2.69
74 75 2.039216 TGCCAAGTCCGACCTATTCAAA 59.961 45.455 0.00 0.00 0.00 2.69
75 76 2.418976 GCCAAGTCCGACCTATTCAAAC 59.581 50.000 0.00 0.00 0.00 2.93
76 77 3.670625 CCAAGTCCGACCTATTCAAACA 58.329 45.455 0.00 0.00 0.00 2.83
77 78 4.261801 CCAAGTCCGACCTATTCAAACAT 58.738 43.478 0.00 0.00 0.00 2.71
78 79 4.094887 CCAAGTCCGACCTATTCAAACATG 59.905 45.833 0.00 0.00 0.00 3.21
79 80 3.270877 AGTCCGACCTATTCAAACATGC 58.729 45.455 0.00 0.00 0.00 4.06
80 81 3.055094 AGTCCGACCTATTCAAACATGCT 60.055 43.478 0.00 0.00 0.00 3.79
81 82 3.309954 GTCCGACCTATTCAAACATGCTC 59.690 47.826 0.00 0.00 0.00 4.26
82 83 2.285220 CCGACCTATTCAAACATGCTCG 59.715 50.000 0.00 0.00 0.00 5.03
83 84 3.186909 CGACCTATTCAAACATGCTCGA 58.813 45.455 0.00 0.00 0.00 4.04
84 85 3.243877 CGACCTATTCAAACATGCTCGAG 59.756 47.826 8.45 8.45 0.00 4.04
85 86 3.535561 ACCTATTCAAACATGCTCGAGG 58.464 45.455 15.58 0.00 0.00 4.63
86 87 2.874701 CCTATTCAAACATGCTCGAGGG 59.125 50.000 15.58 0.00 0.00 4.30
87 88 2.787473 ATTCAAACATGCTCGAGGGA 57.213 45.000 15.58 0.00 0.00 4.20
88 89 1.808411 TTCAAACATGCTCGAGGGAC 58.192 50.000 15.58 0.00 0.00 4.46
89 90 0.036388 TCAAACATGCTCGAGGGACC 60.036 55.000 15.58 0.00 0.00 4.46
90 91 1.026718 CAAACATGCTCGAGGGACCC 61.027 60.000 15.58 0.59 0.00 4.46
91 92 1.201429 AAACATGCTCGAGGGACCCT 61.201 55.000 14.79 14.79 36.03 4.34
92 93 1.903877 AACATGCTCGAGGGACCCTG 61.904 60.000 20.90 10.75 31.76 4.45
93 94 2.039624 ATGCTCGAGGGACCCTGT 59.960 61.111 20.90 0.00 31.76 4.00
94 95 1.613630 ATGCTCGAGGGACCCTGTT 60.614 57.895 20.90 0.00 31.76 3.16
95 96 1.201429 ATGCTCGAGGGACCCTGTTT 61.201 55.000 20.90 0.00 31.76 2.83
96 97 1.079057 GCTCGAGGGACCCTGTTTC 60.079 63.158 20.90 1.95 31.76 2.78
97 98 1.597461 CTCGAGGGACCCTGTTTCC 59.403 63.158 20.90 1.16 31.76 3.13
101 102 3.810255 GGGACCCTGTTTCCCGTA 58.190 61.111 2.09 0.00 43.62 4.02
102 103 2.068915 GGGACCCTGTTTCCCGTAA 58.931 57.895 2.09 0.00 43.62 3.18
103 104 0.622136 GGGACCCTGTTTCCCGTAAT 59.378 55.000 2.09 0.00 43.62 1.89
104 105 1.680860 GGGACCCTGTTTCCCGTAATG 60.681 57.143 2.09 0.00 43.62 1.90
105 106 1.092348 GACCCTGTTTCCCGTAATGC 58.908 55.000 0.00 0.00 0.00 3.56
106 107 0.696501 ACCCTGTTTCCCGTAATGCT 59.303 50.000 0.00 0.00 0.00 3.79
107 108 1.094785 CCCTGTTTCCCGTAATGCTG 58.905 55.000 0.00 0.00 0.00 4.41
108 109 1.339631 CCCTGTTTCCCGTAATGCTGA 60.340 52.381 0.00 0.00 0.00 4.26
109 110 1.737793 CCTGTTTCCCGTAATGCTGAC 59.262 52.381 0.00 0.00 0.00 3.51
110 111 2.422597 CTGTTTCCCGTAATGCTGACA 58.577 47.619 0.00 0.00 0.00 3.58
111 112 3.009723 CTGTTTCCCGTAATGCTGACAT 58.990 45.455 0.00 0.00 38.49 3.06
112 113 3.006940 TGTTTCCCGTAATGCTGACATC 58.993 45.455 0.00 0.00 34.62 3.06
113 114 2.325583 TTCCCGTAATGCTGACATCC 57.674 50.000 0.00 0.00 34.62 3.51
114 115 0.104120 TCCCGTAATGCTGACATCCG 59.896 55.000 0.00 0.00 34.62 4.18
115 116 1.498865 CCCGTAATGCTGACATCCGC 61.499 60.000 0.00 0.00 34.62 5.54
116 117 0.530650 CCGTAATGCTGACATCCGCT 60.531 55.000 0.00 0.00 34.62 5.52
117 118 0.578683 CGTAATGCTGACATCCGCTG 59.421 55.000 0.00 0.00 34.62 5.18
118 119 1.656652 GTAATGCTGACATCCGCTGT 58.343 50.000 0.00 0.00 42.15 4.40
119 120 1.328680 GTAATGCTGACATCCGCTGTG 59.671 52.381 0.00 0.00 38.54 3.66
120 121 0.321919 AATGCTGACATCCGCTGTGT 60.322 50.000 0.00 0.00 38.54 3.72
121 122 1.022982 ATGCTGACATCCGCTGTGTG 61.023 55.000 0.00 0.00 38.54 3.82
122 123 3.031964 GCTGACATCCGCTGTGTGC 62.032 63.158 0.00 0.00 38.54 4.57
123 124 2.358615 TGACATCCGCTGTGTGCC 60.359 61.111 0.00 0.00 38.54 5.01
124 125 3.490759 GACATCCGCTGTGTGCCG 61.491 66.667 0.00 0.00 38.54 5.69
125 126 4.314440 ACATCCGCTGTGTGCCGT 62.314 61.111 0.00 0.00 36.48 5.68
126 127 3.792047 CATCCGCTGTGTGCCGTG 61.792 66.667 0.00 0.00 38.78 4.94
127 128 4.314440 ATCCGCTGTGTGCCGTGT 62.314 61.111 0.00 0.00 38.78 4.49
128 129 3.825160 ATCCGCTGTGTGCCGTGTT 62.825 57.895 0.00 0.00 38.78 3.32
129 130 2.443260 ATCCGCTGTGTGCCGTGTTA 62.443 55.000 0.00 0.00 38.78 2.41
130 131 2.667318 CCGCTGTGTGCCGTGTTAG 61.667 63.158 0.00 0.00 38.78 2.34
131 132 2.556287 GCTGTGTGCCGTGTTAGC 59.444 61.111 0.00 0.00 35.15 3.09
132 133 2.966309 GCTGTGTGCCGTGTTAGCC 61.966 63.158 0.00 0.00 35.15 3.93
133 134 1.596752 CTGTGTGCCGTGTTAGCCA 60.597 57.895 0.00 0.00 0.00 4.75
134 135 1.841663 CTGTGTGCCGTGTTAGCCAC 61.842 60.000 0.00 0.00 40.89 5.01
158 159 3.562250 CACACCAGAGTGGGGACA 58.438 61.111 1.15 0.00 46.22 4.02
159 160 2.069776 CACACCAGAGTGGGGACAT 58.930 57.895 1.15 0.00 46.22 3.06
160 161 1.275666 CACACCAGAGTGGGGACATA 58.724 55.000 1.15 0.00 46.22 2.29
161 162 1.628340 CACACCAGAGTGGGGACATAA 59.372 52.381 1.15 0.00 46.22 1.90
162 163 1.628846 ACACCAGAGTGGGGACATAAC 59.371 52.381 1.15 0.00 46.22 1.89
163 164 1.065418 CACCAGAGTGGGGACATAACC 60.065 57.143 0.00 0.00 46.22 2.85
164 165 1.285280 CCAGAGTGGGGACATAACCA 58.715 55.000 0.00 0.00 46.14 3.67
165 166 5.751824 CACCAGAGTGGGGACATAACCAC 62.752 56.522 5.74 5.74 46.22 4.16
171 172 3.364460 TGGGGACATAACCACAATCTG 57.636 47.619 0.00 0.00 40.68 2.90
172 173 2.025416 TGGGGACATAACCACAATCTGG 60.025 50.000 0.00 0.00 40.68 3.86
173 174 2.654863 GGGACATAACCACAATCTGGG 58.345 52.381 0.00 0.00 45.78 4.45
174 175 2.024414 GGACATAACCACAATCTGGGC 58.976 52.381 0.00 0.00 45.78 5.36
175 176 1.670811 GACATAACCACAATCTGGGCG 59.329 52.381 0.00 0.00 45.78 6.13
176 177 1.280710 ACATAACCACAATCTGGGCGA 59.719 47.619 0.00 0.00 45.78 5.54
177 178 1.942657 CATAACCACAATCTGGGCGAG 59.057 52.381 0.00 0.00 45.78 5.03
178 179 0.251916 TAACCACAATCTGGGCGAGG 59.748 55.000 0.00 0.00 45.78 4.63
179 180 1.779061 AACCACAATCTGGGCGAGGT 61.779 55.000 0.00 0.00 45.78 3.85
180 181 1.002134 CCACAATCTGGGCGAGGTT 60.002 57.895 0.00 0.00 36.18 3.50
181 182 1.308069 CCACAATCTGGGCGAGGTTG 61.308 60.000 19.35 19.35 46.89 3.77
182 183 1.675641 ACAATCTGGGCGAGGTTGC 60.676 57.895 20.63 0.00 45.60 4.17
183 184 1.377725 CAATCTGGGCGAGGTTGCT 60.378 57.895 9.63 0.00 35.98 3.91
184 185 1.078143 AATCTGGGCGAGGTTGCTC 60.078 57.895 0.00 0.00 35.30 4.26
185 186 2.543067 AATCTGGGCGAGGTTGCTCC 62.543 60.000 0.00 0.00 33.12 4.70
186 187 4.020617 CTGGGCGAGGTTGCTCCA 62.021 66.667 0.00 0.00 39.02 3.86
187 188 4.329545 TGGGCGAGGTTGCTCCAC 62.330 66.667 0.00 0.00 39.02 4.02
190 191 4.681978 GCGAGGTTGCTCCACCGT 62.682 66.667 0.00 0.00 42.33 4.83
191 192 2.432628 CGAGGTTGCTCCACCGTC 60.433 66.667 1.79 0.00 42.33 4.79
192 193 2.047179 GAGGTTGCTCCACCGTCC 60.047 66.667 1.79 0.00 42.33 4.79
193 194 2.847234 AGGTTGCTCCACCGTCCA 60.847 61.111 1.79 0.00 42.33 4.02
194 195 2.668550 GGTTGCTCCACCGTCCAC 60.669 66.667 0.00 0.00 35.97 4.02
195 196 2.110213 GTTGCTCCACCGTCCACA 59.890 61.111 0.00 0.00 0.00 4.17
196 197 2.110213 TTGCTCCACCGTCCACAC 59.890 61.111 0.00 0.00 0.00 3.82
197 198 3.800685 TTGCTCCACCGTCCACACG 62.801 63.158 0.00 0.00 46.29 4.49
202 203 4.602259 CACCGTCCACACGCCACT 62.602 66.667 0.00 0.00 45.29 4.00
203 204 2.913578 ACCGTCCACACGCCACTA 60.914 61.111 0.00 0.00 45.29 2.74
204 205 2.431942 CCGTCCACACGCCACTAC 60.432 66.667 0.00 0.00 45.29 2.73
205 206 2.649034 CGTCCACACGCCACTACT 59.351 61.111 0.00 0.00 39.69 2.57
206 207 1.588824 CCGTCCACACGCCACTACTA 61.589 60.000 0.00 0.00 45.29 1.82
207 208 0.454600 CGTCCACACGCCACTACTAT 59.545 55.000 0.00 0.00 39.69 2.12
208 209 1.672363 CGTCCACACGCCACTACTATA 59.328 52.381 0.00 0.00 39.69 1.31
209 210 2.292569 CGTCCACACGCCACTACTATAT 59.707 50.000 0.00 0.00 39.69 0.86
210 211 3.639538 GTCCACACGCCACTACTATATG 58.360 50.000 0.00 0.00 0.00 1.78
211 212 3.067742 GTCCACACGCCACTACTATATGT 59.932 47.826 0.00 0.00 0.00 2.29
212 213 4.276678 GTCCACACGCCACTACTATATGTA 59.723 45.833 0.00 0.00 0.00 2.29
213 214 4.276678 TCCACACGCCACTACTATATGTAC 59.723 45.833 0.00 0.00 0.00 2.90
214 215 4.037089 CCACACGCCACTACTATATGTACA 59.963 45.833 0.00 0.00 0.00 2.90
215 216 4.974275 CACACGCCACTACTATATGTACAC 59.026 45.833 0.00 0.00 0.00 2.90
216 217 4.641541 ACACGCCACTACTATATGTACACA 59.358 41.667 0.00 0.00 0.00 3.72
217 218 4.974275 CACGCCACTACTATATGTACACAC 59.026 45.833 0.00 0.00 0.00 3.82
218 219 4.641541 ACGCCACTACTATATGTACACACA 59.358 41.667 0.00 0.00 39.52 3.72
219 220 5.125900 ACGCCACTACTATATGTACACACAA 59.874 40.000 0.00 0.00 38.42 3.33
220 221 5.457799 CGCCACTACTATATGTACACACAAC 59.542 44.000 0.00 0.00 38.42 3.32
221 222 5.751990 GCCACTACTATATGTACACACAACC 59.248 44.000 0.00 0.00 38.42 3.77
222 223 6.628621 GCCACTACTATATGTACACACAACCA 60.629 42.308 0.00 0.00 38.42 3.67
223 224 7.324935 CCACTACTATATGTACACACAACCAA 58.675 38.462 0.00 0.00 38.42 3.67
224 225 7.277098 CCACTACTATATGTACACACAACCAAC 59.723 40.741 0.00 0.00 38.42 3.77
225 226 7.815549 CACTACTATATGTACACACAACCAACA 59.184 37.037 0.00 0.00 38.42 3.33
226 227 8.537016 ACTACTATATGTACACACAACCAACAT 58.463 33.333 0.00 0.00 38.42 2.71
227 228 9.378551 CTACTATATGTACACACAACCAACATT 57.621 33.333 0.00 0.00 38.42 2.71
229 230 9.727859 ACTATATGTACACACAACCAACATTAA 57.272 29.630 0.00 0.00 38.42 1.40
254 255 6.575162 AAAAACTTACTATGCTCCAAGGTG 57.425 37.500 0.00 0.00 0.00 4.00
255 256 5.499004 AAACTTACTATGCTCCAAGGTGA 57.501 39.130 0.00 0.00 0.00 4.02
256 257 5.499004 AACTTACTATGCTCCAAGGTGAA 57.501 39.130 0.00 0.00 0.00 3.18
257 258 5.700402 ACTTACTATGCTCCAAGGTGAAT 57.300 39.130 0.00 0.00 0.00 2.57
258 259 5.675538 ACTTACTATGCTCCAAGGTGAATC 58.324 41.667 0.00 0.00 0.00 2.52
259 260 5.426833 ACTTACTATGCTCCAAGGTGAATCT 59.573 40.000 0.00 0.00 0.00 2.40
260 261 6.611642 ACTTACTATGCTCCAAGGTGAATCTA 59.388 38.462 0.00 0.00 0.00 1.98
261 262 7.291182 ACTTACTATGCTCCAAGGTGAATCTAT 59.709 37.037 0.00 0.00 0.00 1.98
262 263 6.506538 ACTATGCTCCAAGGTGAATCTATT 57.493 37.500 0.00 0.00 0.00 1.73
263 264 7.618019 ACTATGCTCCAAGGTGAATCTATTA 57.382 36.000 0.00 0.00 0.00 0.98
264 265 8.212259 ACTATGCTCCAAGGTGAATCTATTAT 57.788 34.615 0.00 0.00 0.00 1.28
265 266 8.664079 ACTATGCTCCAAGGTGAATCTATTATT 58.336 33.333 0.00 0.00 0.00 1.40
269 270 9.288576 TGCTCCAAGGTGAATCTATTATTATTG 57.711 33.333 0.00 0.00 0.00 1.90
270 271 9.507329 GCTCCAAGGTGAATCTATTATTATTGA 57.493 33.333 0.00 0.00 0.00 2.57
296 297 2.602257 AAAAGAGCAACAACAAGGCC 57.398 45.000 0.00 0.00 0.00 5.19
297 298 1.484038 AAAGAGCAACAACAAGGCCA 58.516 45.000 5.01 0.00 0.00 5.36
298 299 0.746659 AAGAGCAACAACAAGGCCAC 59.253 50.000 5.01 0.00 0.00 5.01
299 300 0.395586 AGAGCAACAACAAGGCCACA 60.396 50.000 5.01 0.00 0.00 4.17
300 301 0.675633 GAGCAACAACAAGGCCACAT 59.324 50.000 5.01 0.00 0.00 3.21
301 302 1.885887 GAGCAACAACAAGGCCACATA 59.114 47.619 5.01 0.00 0.00 2.29
302 303 2.493278 GAGCAACAACAAGGCCACATAT 59.507 45.455 5.01 0.00 0.00 1.78
303 304 3.694072 GAGCAACAACAAGGCCACATATA 59.306 43.478 5.01 0.00 0.00 0.86
304 305 3.696051 AGCAACAACAAGGCCACATATAG 59.304 43.478 5.01 0.00 0.00 1.31
305 306 3.734902 GCAACAACAAGGCCACATATAGC 60.735 47.826 5.01 0.00 0.00 2.97
311 312 3.834732 GGCCACATATAGCCTACGG 57.165 57.895 0.00 0.00 46.14 4.02
321 322 3.509659 GCCTACGGCCCATTTCAC 58.490 61.111 0.00 0.00 44.06 3.18
322 323 2.469516 GCCTACGGCCCATTTCACG 61.470 63.158 0.00 0.00 44.06 4.35
323 324 1.817941 CCTACGGCCCATTTCACGG 60.818 63.158 0.00 0.00 0.00 4.94
324 325 2.437002 TACGGCCCATTTCACGGC 60.437 61.111 0.00 0.00 44.92 5.68
328 329 3.451894 GCCCATTTCACGGCCCAG 61.452 66.667 0.00 0.00 39.39 4.45
329 330 3.451894 CCCATTTCACGGCCCAGC 61.452 66.667 0.00 0.00 0.00 4.85
330 331 2.361610 CCATTTCACGGCCCAGCT 60.362 61.111 0.00 0.00 0.00 4.24
331 332 1.077787 CCATTTCACGGCCCAGCTA 60.078 57.895 0.00 0.00 0.00 3.32
332 333 0.679640 CCATTTCACGGCCCAGCTAA 60.680 55.000 0.00 0.00 0.00 3.09
333 334 0.451783 CATTTCACGGCCCAGCTAAC 59.548 55.000 0.00 0.00 0.00 2.34
334 335 0.679960 ATTTCACGGCCCAGCTAACC 60.680 55.000 0.00 0.00 0.00 2.85
335 336 2.757980 TTTCACGGCCCAGCTAACCC 62.758 60.000 0.00 0.00 0.00 4.11
336 337 4.028490 CACGGCCCAGCTAACCCA 62.028 66.667 0.00 0.00 0.00 4.51
337 338 3.717294 ACGGCCCAGCTAACCCAG 61.717 66.667 0.00 0.00 0.00 4.45
346 347 3.111405 GCTAACCCAGCCCATTACC 57.889 57.895 0.00 0.00 45.23 2.85
347 348 0.467474 GCTAACCCAGCCCATTACCC 60.467 60.000 0.00 0.00 45.23 3.69
348 349 1.222567 CTAACCCAGCCCATTACCCT 58.777 55.000 0.00 0.00 0.00 4.34
349 350 2.414612 CTAACCCAGCCCATTACCCTA 58.585 52.381 0.00 0.00 0.00 3.53
350 351 1.688750 AACCCAGCCCATTACCCTAA 58.311 50.000 0.00 0.00 0.00 2.69
351 352 1.688750 ACCCAGCCCATTACCCTAAA 58.311 50.000 0.00 0.00 0.00 1.85
352 353 2.004589 ACCCAGCCCATTACCCTAAAA 58.995 47.619 0.00 0.00 0.00 1.52
353 354 2.384029 ACCCAGCCCATTACCCTAAAAA 59.616 45.455 0.00 0.00 0.00 1.94
372 373 3.673543 AAAAGTTAACCCAGTCCACCA 57.326 42.857 0.88 0.00 0.00 4.17
373 374 3.895704 AAAGTTAACCCAGTCCACCAT 57.104 42.857 0.88 0.00 0.00 3.55
374 375 3.434940 AAGTTAACCCAGTCCACCATC 57.565 47.619 0.88 0.00 0.00 3.51
375 376 2.344592 AGTTAACCCAGTCCACCATCA 58.655 47.619 0.88 0.00 0.00 3.07
376 377 2.305927 AGTTAACCCAGTCCACCATCAG 59.694 50.000 0.88 0.00 0.00 2.90
377 378 2.304761 GTTAACCCAGTCCACCATCAGA 59.695 50.000 0.00 0.00 0.00 3.27
378 379 0.693049 AACCCAGTCCACCATCAGAC 59.307 55.000 0.00 0.00 0.00 3.51
379 380 0.473694 ACCCAGTCCACCATCAGACA 60.474 55.000 0.00 0.00 35.38 3.41
380 381 0.692476 CCCAGTCCACCATCAGACAA 59.308 55.000 0.00 0.00 35.38 3.18
381 382 1.283029 CCCAGTCCACCATCAGACAAT 59.717 52.381 0.00 0.00 35.38 2.71
382 383 2.291153 CCCAGTCCACCATCAGACAATT 60.291 50.000 0.00 0.00 35.38 2.32
383 384 3.012518 CCAGTCCACCATCAGACAATTC 58.987 50.000 0.00 0.00 35.38 2.17
384 385 3.012518 CAGTCCACCATCAGACAATTCC 58.987 50.000 0.00 0.00 35.38 3.01
385 386 2.009774 GTCCACCATCAGACAATTCCG 58.990 52.381 0.00 0.00 33.08 4.30
386 387 1.065491 TCCACCATCAGACAATTCCGG 60.065 52.381 0.00 0.00 0.00 5.14
387 388 0.734889 CACCATCAGACAATTCCGGC 59.265 55.000 0.00 0.00 0.00 6.13
388 389 0.394352 ACCATCAGACAATTCCGGCC 60.394 55.000 0.00 0.00 0.00 6.13
389 390 0.394216 CCATCAGACAATTCCGGCCA 60.394 55.000 2.24 0.00 0.00 5.36
390 391 0.734889 CATCAGACAATTCCGGCCAC 59.265 55.000 2.24 0.00 0.00 5.01
391 392 0.620556 ATCAGACAATTCCGGCCACT 59.379 50.000 2.24 0.00 0.00 4.00
392 393 1.271856 TCAGACAATTCCGGCCACTA 58.728 50.000 2.24 0.00 0.00 2.74
393 394 1.626321 TCAGACAATTCCGGCCACTAA 59.374 47.619 2.24 0.00 0.00 2.24
878 879 2.107750 CCATCGACGCAGCATCCT 59.892 61.111 0.00 0.00 0.00 3.24
916 917 2.352032 CGAGACCCCGGAAGAAGCT 61.352 63.158 0.73 0.00 0.00 3.74
1008 1009 4.154347 GGAGCCCCTGCACGAGAG 62.154 72.222 0.00 0.00 41.13 3.20
1085 1086 1.379176 CTGCTCTCCCCGACTCTCA 60.379 63.158 0.00 0.00 0.00 3.27
1312 1313 4.748798 CCCCCTGAGGAGGCCACT 62.749 72.222 5.01 1.49 38.17 4.00
1677 1678 1.683917 GACAGGCGATATGGAGAGTGT 59.316 52.381 0.00 0.00 0.00 3.55
1678 1679 1.410517 ACAGGCGATATGGAGAGTGTG 59.589 52.381 0.00 0.00 0.00 3.82
1876 1877 1.648467 GGCTTTGTGATGACGAGGGC 61.648 60.000 0.00 0.00 31.92 5.19
2102 2103 2.076863 GTGCAGGTGGTAAGTGTGATC 58.923 52.381 0.00 0.00 0.00 2.92
2266 2267 0.455005 GGCAGCTGATGAAGAAAGGC 59.545 55.000 20.43 0.00 0.00 4.35
2348 2349 3.087781 GAGGCTGCAAAGGAGATTCTTT 58.912 45.455 0.50 0.00 37.44 2.52
2398 2399 1.152984 CCCCCATTCGCATGCACTA 60.153 57.895 19.57 1.81 0.00 2.74
2410 2411 5.842907 TCGCATGCACTACTTATTGATAGT 58.157 37.500 19.57 0.00 31.65 2.12
2542 2543 1.274703 ATGATGGCCGGGTTCAGACT 61.275 55.000 2.18 0.00 0.00 3.24
2687 2688 3.258872 TCTGATGGTGGAAAATGGCTTTG 59.741 43.478 0.00 0.00 0.00 2.77
2773 2774 1.203052 CTGGCTGATTTTGCGTTGGAT 59.797 47.619 0.00 0.00 0.00 3.41
2905 2906 1.003233 GGTGTTGTAGACCAGAAGGGG 59.997 57.143 0.00 0.00 42.91 4.79
3142 3146 1.017387 GTTGGGCCATCTGTCGAATC 58.983 55.000 7.26 0.00 0.00 2.52
3262 3271 9.888878 CATGTTTAATAATTGAGGCAGATGTAG 57.111 33.333 0.00 0.00 0.00 2.74
3367 3390 5.049336 CAGAATTTTGTTTTGCCATGATGCA 60.049 36.000 0.00 0.00 40.07 3.96
3574 3612 7.867909 TCAGCACATTATCTAACGATAGAAAGG 59.132 37.037 6.50 7.01 41.38 3.11
3696 3737 6.705381 TGTGTAGCCAAAGGAAAATTTGAATG 59.295 34.615 0.00 0.00 41.71 2.67
3822 3958 7.037873 TGGTTTTCTAGGAACAGCCTCTTAATA 60.038 37.037 10.65 0.00 46.97 0.98
3886 4024 7.925622 TGATATCATCAGAAGCCATATTCCTT 58.074 34.615 0.00 0.00 33.59 3.36
4016 4161 8.814038 AGGTTACAAAAGCATCTATTTCTCAT 57.186 30.769 0.00 0.00 35.49 2.90
4029 4174 8.583296 CATCTATTTCTCATCTCATAGTCACCA 58.417 37.037 0.00 0.00 0.00 4.17
4041 4186 5.510430 TCATAGTCACCAGTCTGTCATACT 58.490 41.667 0.00 0.11 0.00 2.12
4186 4358 7.620880 TCTGAAAGTTGTAACCATATAGCTGT 58.379 34.615 0.00 0.00 33.76 4.40
4194 4366 5.995282 TGTAACCATATAGCTGTATGTTGCC 59.005 40.000 23.89 12.59 31.55 4.52
4222 4394 6.515832 GGAAACATGCCATTATTCCCTTTAG 58.484 40.000 6.90 0.00 34.74 1.85
4257 4429 9.793252 AGTCAAATTTGTATGCTGTATTGATTC 57.207 29.630 17.47 0.00 0.00 2.52
4258 4430 9.571810 GTCAAATTTGTATGCTGTATTGATTCA 57.428 29.630 17.47 0.00 0.00 2.57
4259 4431 9.791820 TCAAATTTGTATGCTGTATTGATTCAG 57.208 29.630 17.47 0.00 35.12 3.02
4260 4432 9.791820 CAAATTTGTATGCTGTATTGATTCAGA 57.208 29.630 10.15 0.00 34.02 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.671963 GGTTCCAGGGGACAACGC 60.672 66.667 0.00 0.00 0.00 4.84
16 17 0.889186 CAAGGTTCCAGGGGACAACG 60.889 60.000 0.00 0.00 0.00 4.10
17 18 1.179174 GCAAGGTTCCAGGGGACAAC 61.179 60.000 0.00 0.00 0.00 3.32
18 19 1.152830 GCAAGGTTCCAGGGGACAA 59.847 57.895 0.00 0.00 0.00 3.18
19 20 1.774217 AGCAAGGTTCCAGGGGACA 60.774 57.895 0.00 0.00 0.00 4.02
20 21 1.002011 GAGCAAGGTTCCAGGGGAC 60.002 63.158 0.00 0.00 0.00 4.46
21 22 2.231380 GGAGCAAGGTTCCAGGGGA 61.231 63.158 0.00 0.00 34.74 4.81
22 23 1.793820 AAGGAGCAAGGTTCCAGGGG 61.794 60.000 1.96 0.00 37.18 4.79
23 24 0.610232 CAAGGAGCAAGGTTCCAGGG 60.610 60.000 1.96 0.00 37.18 4.45
24 25 0.610232 CCAAGGAGCAAGGTTCCAGG 60.610 60.000 1.96 0.00 37.18 4.45
25 26 0.610232 CCCAAGGAGCAAGGTTCCAG 60.610 60.000 1.96 0.00 37.18 3.86
26 27 1.460255 CCCAAGGAGCAAGGTTCCA 59.540 57.895 1.96 0.00 37.18 3.53
27 28 1.979155 GCCCAAGGAGCAAGGTTCC 60.979 63.158 0.00 0.00 34.83 3.62
28 29 1.979155 GGCCCAAGGAGCAAGGTTC 60.979 63.158 0.00 0.00 0.00 3.62
29 30 2.118294 GGCCCAAGGAGCAAGGTT 59.882 61.111 0.00 0.00 0.00 3.50
30 31 3.984732 GGGCCCAAGGAGCAAGGT 61.985 66.667 19.95 0.00 0.00 3.50
31 32 4.766632 GGGGCCCAAGGAGCAAGG 62.767 72.222 26.86 0.00 0.00 3.61
32 33 3.307089 ATGGGGCCCAAGGAGCAAG 62.307 63.158 32.57 0.00 36.95 4.01
33 34 3.275271 ATGGGGCCCAAGGAGCAA 61.275 61.111 32.57 2.58 36.95 3.91
34 35 4.064768 CATGGGGCCCAAGGAGCA 62.065 66.667 32.57 11.89 36.95 4.26
35 36 4.847367 CCATGGGGCCCAAGGAGC 62.847 72.222 38.01 5.10 44.32 4.70
36 37 3.350163 ACCATGGGGCCCAAGGAG 61.350 66.667 44.71 28.00 44.32 3.69
37 38 3.671410 CACCATGGGGCCCAAGGA 61.671 66.667 44.71 18.65 44.32 3.36
44 45 3.070576 GACTTGGCACCATGGGGC 61.071 66.667 31.91 31.91 37.90 5.80
45 46 2.362889 GGACTTGGCACCATGGGG 60.363 66.667 18.09 14.63 41.29 4.96
46 47 2.751436 CGGACTTGGCACCATGGG 60.751 66.667 18.09 6.26 0.00 4.00
47 48 2.040544 GTCGGACTTGGCACCATGG 61.041 63.158 11.19 11.19 0.00 3.66
48 49 2.040544 GGTCGGACTTGGCACCATG 61.041 63.158 8.23 1.22 0.00 3.66
49 50 0.907704 TAGGTCGGACTTGGCACCAT 60.908 55.000 8.23 0.00 0.00 3.55
50 51 0.907704 ATAGGTCGGACTTGGCACCA 60.908 55.000 8.23 0.00 0.00 4.17
51 52 0.252197 AATAGGTCGGACTTGGCACC 59.748 55.000 8.23 0.00 0.00 5.01
52 53 1.066430 TGAATAGGTCGGACTTGGCAC 60.066 52.381 8.23 0.00 0.00 5.01
53 54 1.271856 TGAATAGGTCGGACTTGGCA 58.728 50.000 8.23 0.00 0.00 4.92
54 55 2.396590 TTGAATAGGTCGGACTTGGC 57.603 50.000 8.23 0.00 0.00 4.52
55 56 3.670625 TGTTTGAATAGGTCGGACTTGG 58.329 45.455 8.23 0.00 0.00 3.61
56 57 4.437390 GCATGTTTGAATAGGTCGGACTTG 60.437 45.833 8.23 0.00 0.00 3.16
57 58 3.689649 GCATGTTTGAATAGGTCGGACTT 59.310 43.478 8.23 2.64 0.00 3.01
58 59 3.055094 AGCATGTTTGAATAGGTCGGACT 60.055 43.478 8.23 0.00 0.00 3.85
59 60 3.270877 AGCATGTTTGAATAGGTCGGAC 58.729 45.455 0.00 0.00 0.00 4.79
60 61 3.531538 GAGCATGTTTGAATAGGTCGGA 58.468 45.455 0.00 0.00 0.00 4.55
61 62 2.285220 CGAGCATGTTTGAATAGGTCGG 59.715 50.000 0.00 0.00 43.83 4.79
62 63 3.575858 CGAGCATGTTTGAATAGGTCG 57.424 47.619 0.00 0.00 42.47 4.79
63 64 3.557595 CCTCGAGCATGTTTGAATAGGTC 59.442 47.826 6.99 0.00 0.00 3.85
64 65 3.535561 CCTCGAGCATGTTTGAATAGGT 58.464 45.455 6.99 0.00 0.00 3.08
65 66 2.874701 CCCTCGAGCATGTTTGAATAGG 59.125 50.000 6.99 0.00 0.00 2.57
66 67 3.557595 GTCCCTCGAGCATGTTTGAATAG 59.442 47.826 6.99 0.00 0.00 1.73
67 68 3.531538 GTCCCTCGAGCATGTTTGAATA 58.468 45.455 6.99 0.00 0.00 1.75
68 69 2.359900 GTCCCTCGAGCATGTTTGAAT 58.640 47.619 6.99 0.00 0.00 2.57
69 70 1.610624 GGTCCCTCGAGCATGTTTGAA 60.611 52.381 6.99 0.00 36.48 2.69
70 71 0.036388 GGTCCCTCGAGCATGTTTGA 60.036 55.000 6.99 0.00 36.48 2.69
71 72 1.026718 GGGTCCCTCGAGCATGTTTG 61.027 60.000 6.99 0.00 38.30 2.93
72 73 1.201429 AGGGTCCCTCGAGCATGTTT 61.201 55.000 3.85 0.00 38.30 2.83
73 74 1.613630 AGGGTCCCTCGAGCATGTT 60.614 57.895 3.85 0.00 38.30 2.71
74 75 2.039624 AGGGTCCCTCGAGCATGT 59.960 61.111 3.85 0.00 38.30 3.21
75 76 2.503061 CAGGGTCCCTCGAGCATG 59.497 66.667 7.76 0.00 41.31 4.06
76 77 1.201429 AAACAGGGTCCCTCGAGCAT 61.201 55.000 7.76 0.00 38.30 3.79
77 78 1.827399 GAAACAGGGTCCCTCGAGCA 61.827 60.000 7.76 0.00 38.30 4.26
78 79 1.079057 GAAACAGGGTCCCTCGAGC 60.079 63.158 7.76 0.00 35.68 5.03
79 80 1.597461 GGAAACAGGGTCCCTCGAG 59.403 63.158 7.76 5.13 0.00 4.04
80 81 3.801620 GGAAACAGGGTCCCTCGA 58.198 61.111 7.76 0.00 0.00 4.04
85 86 1.746470 CATTACGGGAAACAGGGTCC 58.254 55.000 0.00 0.00 0.00 4.46
86 87 1.092348 GCATTACGGGAAACAGGGTC 58.908 55.000 0.00 0.00 0.00 4.46
87 88 0.696501 AGCATTACGGGAAACAGGGT 59.303 50.000 0.00 0.00 0.00 4.34
88 89 1.094785 CAGCATTACGGGAAACAGGG 58.905 55.000 0.00 0.00 0.00 4.45
89 90 1.737793 GTCAGCATTACGGGAAACAGG 59.262 52.381 0.00 0.00 0.00 4.00
90 91 2.422597 TGTCAGCATTACGGGAAACAG 58.577 47.619 0.00 0.00 0.00 3.16
91 92 2.552599 TGTCAGCATTACGGGAAACA 57.447 45.000 0.00 0.00 0.00 2.83
92 93 2.354821 GGATGTCAGCATTACGGGAAAC 59.645 50.000 0.00 0.00 35.07 2.78
93 94 2.639065 GGATGTCAGCATTACGGGAAA 58.361 47.619 0.00 0.00 35.07 3.13
94 95 1.472552 CGGATGTCAGCATTACGGGAA 60.473 52.381 0.00 0.00 35.07 3.97
95 96 0.104120 CGGATGTCAGCATTACGGGA 59.896 55.000 0.00 0.00 35.07 5.14
96 97 1.498865 GCGGATGTCAGCATTACGGG 61.499 60.000 0.21 0.00 36.75 5.28
97 98 0.530650 AGCGGATGTCAGCATTACGG 60.531 55.000 7.82 0.00 39.54 4.02
98 99 0.578683 CAGCGGATGTCAGCATTACG 59.421 55.000 7.82 0.00 39.54 3.18
99 100 1.328680 CACAGCGGATGTCAGCATTAC 59.671 52.381 7.82 0.00 41.41 1.89
100 101 1.066215 ACACAGCGGATGTCAGCATTA 60.066 47.619 7.82 0.00 41.41 1.90
101 102 0.321919 ACACAGCGGATGTCAGCATT 60.322 50.000 7.82 0.00 41.41 3.56
102 103 1.022982 CACACAGCGGATGTCAGCAT 61.023 55.000 7.82 0.00 41.41 3.79
103 104 1.668793 CACACAGCGGATGTCAGCA 60.669 57.895 7.82 0.00 41.41 4.41
104 105 3.031964 GCACACAGCGGATGTCAGC 62.032 63.158 0.00 0.00 41.41 4.26
105 106 3.171987 GCACACAGCGGATGTCAG 58.828 61.111 0.00 0.00 41.41 3.51
114 115 2.556287 GCTAACACGGCACACAGC 59.444 61.111 0.00 0.00 44.65 4.40
115 116 1.596752 TGGCTAACACGGCACACAG 60.597 57.895 0.00 0.00 34.24 3.66
116 117 2.506472 TGGCTAACACGGCACACA 59.494 55.556 0.00 0.00 34.24 3.72
141 142 1.275666 TATGTCCCCACTCTGGTGTG 58.724 55.000 0.00 0.00 41.53 3.82
142 143 1.628846 GTTATGTCCCCACTCTGGTGT 59.371 52.381 0.00 0.00 41.53 4.16
143 144 1.065418 GGTTATGTCCCCACTCTGGTG 60.065 57.143 0.00 0.00 42.65 4.17
144 145 1.286248 GGTTATGTCCCCACTCTGGT 58.714 55.000 0.00 0.00 35.17 4.00
145 146 1.065418 GTGGTTATGTCCCCACTCTGG 60.065 57.143 1.65 0.00 46.17 3.86
146 147 2.403252 GTGGTTATGTCCCCACTCTG 57.597 55.000 1.65 0.00 46.17 3.35
151 152 2.025416 CCAGATTGTGGTTATGTCCCCA 60.025 50.000 0.00 0.00 42.17 4.96
152 153 2.654863 CCAGATTGTGGTTATGTCCCC 58.345 52.381 0.00 0.00 42.17 4.81
153 154 2.654863 CCCAGATTGTGGTTATGTCCC 58.345 52.381 0.00 0.00 46.37 4.46
154 155 2.024414 GCCCAGATTGTGGTTATGTCC 58.976 52.381 0.00 0.00 46.37 4.02
155 156 1.670811 CGCCCAGATTGTGGTTATGTC 59.329 52.381 0.00 0.00 46.37 3.06
156 157 1.280710 TCGCCCAGATTGTGGTTATGT 59.719 47.619 0.00 0.00 46.37 2.29
157 158 1.942657 CTCGCCCAGATTGTGGTTATG 59.057 52.381 0.00 0.00 46.37 1.90
158 159 1.134098 CCTCGCCCAGATTGTGGTTAT 60.134 52.381 0.00 0.00 46.37 1.89
159 160 0.251916 CCTCGCCCAGATTGTGGTTA 59.748 55.000 0.00 0.00 46.37 2.85
160 161 1.002134 CCTCGCCCAGATTGTGGTT 60.002 57.895 0.00 0.00 46.37 3.67
161 162 1.779061 AACCTCGCCCAGATTGTGGT 61.779 55.000 0.00 0.00 46.37 4.16
163 164 1.926511 GCAACCTCGCCCAGATTGTG 61.927 60.000 0.00 0.00 0.00 3.33
164 165 1.675641 GCAACCTCGCCCAGATTGT 60.676 57.895 0.00 0.00 0.00 2.71
165 166 1.372087 GAGCAACCTCGCCCAGATTG 61.372 60.000 0.00 0.00 0.00 2.67
166 167 1.078143 GAGCAACCTCGCCCAGATT 60.078 57.895 0.00 0.00 0.00 2.40
167 168 2.586792 GAGCAACCTCGCCCAGAT 59.413 61.111 0.00 0.00 0.00 2.90
168 169 3.706373 GGAGCAACCTCGCCCAGA 61.706 66.667 0.00 0.00 39.06 3.86
169 170 4.020617 TGGAGCAACCTCGCCCAG 62.021 66.667 1.91 0.00 39.06 4.45
170 171 4.329545 GTGGAGCAACCTCGCCCA 62.330 66.667 1.91 0.00 39.06 5.36
173 174 4.681978 ACGGTGGAGCAACCTCGC 62.682 66.667 12.59 0.00 39.06 5.03
174 175 2.432628 GACGGTGGAGCAACCTCG 60.433 66.667 11.69 11.69 39.06 4.63
175 176 2.047179 GGACGGTGGAGCAACCTC 60.047 66.667 2.29 0.00 38.14 3.85
176 177 2.847234 TGGACGGTGGAGCAACCT 60.847 61.111 2.29 0.00 38.14 3.50
177 178 2.668550 GTGGACGGTGGAGCAACC 60.669 66.667 0.00 0.00 36.82 3.77
178 179 2.110213 TGTGGACGGTGGAGCAAC 59.890 61.111 0.00 0.00 0.00 4.17
179 180 2.110213 GTGTGGACGGTGGAGCAA 59.890 61.111 0.00 0.00 0.00 3.91
180 181 4.293648 CGTGTGGACGGTGGAGCA 62.294 66.667 0.00 0.00 42.18 4.26
185 186 3.215597 TAGTGGCGTGTGGACGGTG 62.216 63.158 0.00 0.00 46.20 4.94
186 187 2.913578 TAGTGGCGTGTGGACGGT 60.914 61.111 0.00 0.00 46.20 4.83
187 188 1.588824 TAGTAGTGGCGTGTGGACGG 61.589 60.000 0.00 0.00 46.20 4.79
188 189 8.894268 GTACATATAGTAGTGGCGTGTGGACG 62.894 50.000 0.00 0.00 40.06 4.79
189 190 3.067742 ACATATAGTAGTGGCGTGTGGAC 59.932 47.826 0.00 0.00 0.00 4.02
190 191 3.293337 ACATATAGTAGTGGCGTGTGGA 58.707 45.455 0.00 0.00 0.00 4.02
191 192 3.728076 ACATATAGTAGTGGCGTGTGG 57.272 47.619 0.00 0.00 0.00 4.17
192 193 4.974275 GTGTACATATAGTAGTGGCGTGTG 59.026 45.833 0.00 0.00 32.19 3.82
193 194 4.641541 TGTGTACATATAGTAGTGGCGTGT 59.358 41.667 0.00 0.00 32.19 4.49
194 195 4.974275 GTGTGTACATATAGTAGTGGCGTG 59.026 45.833 0.00 0.00 32.19 5.34
195 196 4.641541 TGTGTGTACATATAGTAGTGGCGT 59.358 41.667 0.00 0.00 32.19 5.68
196 197 5.177725 TGTGTGTACATATAGTAGTGGCG 57.822 43.478 0.00 0.00 32.19 5.69
197 198 5.751990 GGTTGTGTGTACATATAGTAGTGGC 59.248 44.000 0.00 0.00 36.53 5.01
198 199 6.869695 TGGTTGTGTGTACATATAGTAGTGG 58.130 40.000 0.00 0.00 36.53 4.00
199 200 7.815549 TGTTGGTTGTGTGTACATATAGTAGTG 59.184 37.037 0.00 0.00 36.53 2.74
200 201 7.898918 TGTTGGTTGTGTGTACATATAGTAGT 58.101 34.615 0.00 0.00 36.53 2.73
201 202 8.942338 ATGTTGGTTGTGTGTACATATAGTAG 57.058 34.615 0.00 0.00 36.53 2.57
203 204 9.727859 TTAATGTTGGTTGTGTGTACATATAGT 57.272 29.630 0.00 0.00 36.53 2.12
231 232 6.303839 TCACCTTGGAGCATAGTAAGTTTTT 58.696 36.000 0.00 0.00 0.00 1.94
232 233 5.876357 TCACCTTGGAGCATAGTAAGTTTT 58.124 37.500 0.00 0.00 0.00 2.43
233 234 5.499004 TCACCTTGGAGCATAGTAAGTTT 57.501 39.130 0.00 0.00 0.00 2.66
234 235 5.499004 TTCACCTTGGAGCATAGTAAGTT 57.501 39.130 0.00 0.00 0.00 2.66
235 236 5.426833 AGATTCACCTTGGAGCATAGTAAGT 59.573 40.000 0.00 0.00 0.00 2.24
236 237 5.923204 AGATTCACCTTGGAGCATAGTAAG 58.077 41.667 0.00 0.00 0.00 2.34
237 238 5.957771 AGATTCACCTTGGAGCATAGTAA 57.042 39.130 0.00 0.00 0.00 2.24
238 239 7.618019 AATAGATTCACCTTGGAGCATAGTA 57.382 36.000 0.00 0.00 0.00 1.82
239 240 6.506538 AATAGATTCACCTTGGAGCATAGT 57.493 37.500 0.00 0.00 0.00 2.12
243 244 9.288576 CAATAATAATAGATTCACCTTGGAGCA 57.711 33.333 0.00 0.00 0.00 4.26
244 245 9.507329 TCAATAATAATAGATTCACCTTGGAGC 57.493 33.333 0.00 0.00 0.00 4.70
276 277 2.235898 TGGCCTTGTTGTTGCTCTTTTT 59.764 40.909 3.32 0.00 0.00 1.94
277 278 1.830477 TGGCCTTGTTGTTGCTCTTTT 59.170 42.857 3.32 0.00 0.00 2.27
278 279 1.136891 GTGGCCTTGTTGTTGCTCTTT 59.863 47.619 3.32 0.00 0.00 2.52
279 280 0.746659 GTGGCCTTGTTGTTGCTCTT 59.253 50.000 3.32 0.00 0.00 2.85
280 281 0.395586 TGTGGCCTTGTTGTTGCTCT 60.396 50.000 3.32 0.00 0.00 4.09
281 282 0.675633 ATGTGGCCTTGTTGTTGCTC 59.324 50.000 3.32 0.00 0.00 4.26
282 283 1.993956 TATGTGGCCTTGTTGTTGCT 58.006 45.000 3.32 0.00 0.00 3.91
283 284 3.734902 GCTATATGTGGCCTTGTTGTTGC 60.735 47.826 3.32 0.00 0.00 4.17
284 285 4.032703 GCTATATGTGGCCTTGTTGTTG 57.967 45.455 3.32 0.00 0.00 3.33
305 306 1.817941 CCGTGAAATGGGCCGTAGG 60.818 63.158 0.00 0.00 43.94 3.18
306 307 2.469516 GCCGTGAAATGGGCCGTAG 61.470 63.158 0.00 0.00 45.58 3.51
307 308 2.437002 GCCGTGAAATGGGCCGTA 60.437 61.111 0.00 0.00 45.58 4.02
312 313 2.550699 TAGCTGGGCCGTGAAATGGG 62.551 60.000 0.00 0.00 45.58 4.00
314 315 0.451783 GTTAGCTGGGCCGTGAAATG 59.548 55.000 0.00 0.00 0.00 2.32
315 316 0.679960 GGTTAGCTGGGCCGTGAAAT 60.680 55.000 0.00 0.00 0.00 2.17
316 317 1.302993 GGTTAGCTGGGCCGTGAAA 60.303 57.895 0.00 0.00 0.00 2.69
317 318 2.349755 GGTTAGCTGGGCCGTGAA 59.650 61.111 0.00 0.00 0.00 3.18
318 319 3.712907 GGGTTAGCTGGGCCGTGA 61.713 66.667 0.00 0.00 0.00 4.35
319 320 3.976701 CTGGGTTAGCTGGGCCGTG 62.977 68.421 0.00 0.00 0.00 4.94
320 321 3.717294 CTGGGTTAGCTGGGCCGT 61.717 66.667 0.00 0.00 0.00 5.68
329 330 1.222567 AGGGTAATGGGCTGGGTTAG 58.777 55.000 0.00 0.00 0.00 2.34
330 331 2.590793 TAGGGTAATGGGCTGGGTTA 57.409 50.000 0.00 0.00 0.00 2.85
331 332 1.688750 TTAGGGTAATGGGCTGGGTT 58.311 50.000 0.00 0.00 0.00 4.11
332 333 1.688750 TTTAGGGTAATGGGCTGGGT 58.311 50.000 0.00 0.00 0.00 4.51
333 334 2.838637 TTTTAGGGTAATGGGCTGGG 57.161 50.000 0.00 0.00 0.00 4.45
351 352 3.983821 TGGTGGACTGGGTTAACTTTTT 58.016 40.909 5.42 0.00 0.00 1.94
352 353 3.673543 TGGTGGACTGGGTTAACTTTT 57.326 42.857 5.42 0.00 0.00 2.27
353 354 3.139397 TGATGGTGGACTGGGTTAACTTT 59.861 43.478 5.42 0.00 0.00 2.66
354 355 2.714250 TGATGGTGGACTGGGTTAACTT 59.286 45.455 5.42 0.00 0.00 2.66
355 356 2.305927 CTGATGGTGGACTGGGTTAACT 59.694 50.000 5.42 0.00 0.00 2.24
356 357 2.304761 TCTGATGGTGGACTGGGTTAAC 59.695 50.000 0.00 0.00 0.00 2.01
357 358 2.304761 GTCTGATGGTGGACTGGGTTAA 59.695 50.000 0.00 0.00 0.00 2.01
358 359 1.906574 GTCTGATGGTGGACTGGGTTA 59.093 52.381 0.00 0.00 0.00 2.85
359 360 0.693049 GTCTGATGGTGGACTGGGTT 59.307 55.000 0.00 0.00 0.00 4.11
360 361 0.473694 TGTCTGATGGTGGACTGGGT 60.474 55.000 0.00 0.00 34.01 4.51
361 362 0.692476 TTGTCTGATGGTGGACTGGG 59.308 55.000 0.00 0.00 34.01 4.45
362 363 2.795231 ATTGTCTGATGGTGGACTGG 57.205 50.000 0.00 0.00 34.01 4.00
363 364 3.012518 GGAATTGTCTGATGGTGGACTG 58.987 50.000 0.00 0.00 34.01 3.51
364 365 2.355108 CGGAATTGTCTGATGGTGGACT 60.355 50.000 0.00 0.00 34.01 3.85
365 366 2.009774 CGGAATTGTCTGATGGTGGAC 58.990 52.381 0.00 0.00 30.94 4.02
366 367 1.065491 CCGGAATTGTCTGATGGTGGA 60.065 52.381 0.00 0.00 30.94 4.02
367 368 1.382522 CCGGAATTGTCTGATGGTGG 58.617 55.000 0.00 0.00 30.94 4.61
368 369 0.734889 GCCGGAATTGTCTGATGGTG 59.265 55.000 5.05 0.00 30.94 4.17
369 370 0.394352 GGCCGGAATTGTCTGATGGT 60.394 55.000 5.05 0.00 30.94 3.55
370 371 0.394216 TGGCCGGAATTGTCTGATGG 60.394 55.000 5.05 0.00 30.94 3.51
371 372 0.734889 GTGGCCGGAATTGTCTGATG 59.265 55.000 5.05 0.00 30.94 3.07
372 373 0.620556 AGTGGCCGGAATTGTCTGAT 59.379 50.000 5.05 0.00 30.94 2.90
373 374 1.271856 TAGTGGCCGGAATTGTCTGA 58.728 50.000 5.05 0.00 30.94 3.27
374 375 2.107950 TTAGTGGCCGGAATTGTCTG 57.892 50.000 5.05 0.00 0.00 3.51
808 809 2.038762 AGGTTGAGGGTGGTGGGT 60.039 61.111 0.00 0.00 0.00 4.51
815 816 2.610859 ATGGCGGAGGTTGAGGGT 60.611 61.111 0.00 0.00 0.00 4.34
821 822 2.044946 GAAGGCATGGCGGAGGTT 60.045 61.111 14.30 1.60 0.00 3.50
898 899 2.184579 GCTTCTTCCGGGGTCTCG 59.815 66.667 0.00 0.00 0.00 4.04
1587 1588 1.553690 CCCGTGGTCCTTCATGTCCT 61.554 60.000 0.00 0.00 0.00 3.85
1677 1678 1.974265 TTCATCAAACACCTTCCGCA 58.026 45.000 0.00 0.00 0.00 5.69
1678 1679 3.244976 CATTTCATCAAACACCTTCCGC 58.755 45.455 0.00 0.00 0.00 5.54
2102 2103 2.740055 GAGCACCTCCACAGCACG 60.740 66.667 0.00 0.00 0.00 5.34
2224 2225 2.622064 AGAACGTCTCAGCCTTGTTT 57.378 45.000 0.00 0.00 0.00 2.83
2266 2267 1.730501 ATGCAGACTTGTCATCCACG 58.269 50.000 3.49 0.00 0.00 4.94
2348 2349 0.461163 CCACGGCGTGTCATAATGGA 60.461 55.000 34.74 0.00 0.00 3.41
2410 2411 4.262164 GCTGGCTCATTTTTCTTCAGGAAA 60.262 41.667 0.00 0.00 41.58 3.13
2542 2543 2.906389 ACTCTTCATGACCCTACTTGCA 59.094 45.455 0.00 0.00 0.00 4.08
2687 2688 4.954875 AGCAACTTATCTAGATCAGGCAC 58.045 43.478 16.47 6.56 0.00 5.01
2773 2774 3.764237 AAGCTAACTTCAAAGTCCCGA 57.236 42.857 0.00 0.00 38.57 5.14
2905 2906 3.881688 AGCTATCCATCAAAGCATCACAC 59.118 43.478 0.00 0.00 38.75 3.82
3090 3093 8.770438 AACAAAACAAACAAAGAGCTGATTTA 57.230 26.923 0.00 0.00 0.00 1.40
3299 3309 8.116753 CCACTTATAAAGAATGAAGTAACAGCG 58.883 37.037 0.00 0.00 31.05 5.18
3367 3390 2.376518 TGTGGATCAAAGCCTTCCTCTT 59.623 45.455 0.00 0.00 0.00 2.85
3369 3392 2.496899 TGTGGATCAAAGCCTTCCTC 57.503 50.000 0.00 0.00 0.00 3.71
3457 3482 6.407525 GGTGGCTACTATCTTTCACTGAAGAT 60.408 42.308 0.00 5.56 45.65 2.40
3574 3612 4.521943 CTCATTAAATCTGTAAGCTGCGC 58.478 43.478 0.00 0.00 0.00 6.09
3696 3737 2.488153 GTTCATTGCAGGTACCACTTCC 59.512 50.000 15.94 0.00 0.00 3.46
3927 4066 2.043227 CCTTTAGTCCCCAGAGCTAGG 58.957 57.143 0.00 0.00 0.00 3.02
4016 4161 4.034285 TGACAGACTGGTGACTATGAGA 57.966 45.455 7.51 0.00 0.00 3.27
4029 4174 0.457851 GCGAGCCAGTATGACAGACT 59.542 55.000 0.00 0.00 39.69 3.24
4041 4186 1.153309 CATCAGGTGATGCGAGCCA 60.153 57.895 7.02 0.00 44.44 4.75
4153 4325 5.126222 TGGTTACAACTTTCAGAATTGTGCA 59.874 36.000 11.06 0.00 37.17 4.57
4194 4366 3.070015 GGAATAATGGCATGTTTCCCCTG 59.930 47.826 22.25 0.00 31.60 4.45
4222 4394 8.391106 CAGCATACAAATTTGACTAACTACCTC 58.609 37.037 24.64 1.66 0.00 3.85


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

AutoCloner maintained by Alex Coulton.