Multiple sequence alignment - TraesCS6D01G116300

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 TraesCS6D01G116300 chr6D 100.000 4355 0 0 1 4355 82637617 82633263 0.000000e+00 8043.0
1 TraesCS6D01G116300 chr6D 88.525 61 7 0 2760 2820 332503487 332503547 1.680000e-09 75.0
2 TraesCS6D01G116300 chr6A 91.230 3512 149 56 608 4009 99423278 99426740 0.000000e+00 4632.0
3 TraesCS6D01G116300 chr6A 88.889 333 23 5 255 582 99422463 99422786 8.780000e-107 398.0
4 TraesCS6D01G116300 chr6A 87.500 304 24 7 4048 4338 99426809 99427111 5.390000e-89 339.0
5 TraesCS6D01G116300 chr6A 88.382 241 26 2 1560 1799 471800731 471800970 5.510000e-74 289.0
6 TraesCS6D01G116300 chr6B 91.764 3424 133 66 395 3751 157665225 157661884 0.000000e+00 4623.0
7 TraesCS6D01G116300 chr6B 88.671 459 38 11 3748 4202 157660534 157660086 8.230000e-152 547.0
8 TraesCS6D01G116300 chr6B 85.870 184 15 6 332 505 157665535 157665353 7.440000e-43 185.0
9 TraesCS6D01G116300 chr6B 85.507 69 10 0 2761 2829 487830725 487830657 6.040000e-09 73.1
10 TraesCS6D01G116300 chr3B 87.500 440 34 11 1354 1793 740545089 740544671 5.060000e-134 488.0
11 TraesCS6D01G116300 chr3B 90.854 164 15 0 1345 1508 222318448 222318611 2.040000e-53 220.0
12 TraesCS6D01G116300 chr3D 87.356 435 34 11 1355 1789 557925524 557925111 3.050000e-131 479.0
13 TraesCS6D01G116300 chrUn 86.591 440 38 11 1354 1793 295855478 295855060 2.370000e-127 466.0
14 TraesCS6D01G116300 chr2D 96.109 257 8 1 1 255 528094343 528094599 6.740000e-113 418.0
15 TraesCS6D01G116300 chr2D 95.257 253 12 0 1 253 607512451 607512703 6.780000e-108 401.0
16 TraesCS6D01G116300 chr2D 89.474 228 24 0 1560 1787 513764858 513764631 5.510000e-74 289.0
17 TraesCS6D01G116300 chr5D 94.922 256 10 2 1 256 361191849 361191597 8.780000e-107 398.0
18 TraesCS6D01G116300 chr5D 90.351 228 22 0 1560 1787 442331974 442332201 2.550000e-77 300.0
19 TraesCS6D01G116300 chr1B 94.186 258 15 0 1 258 62251171 62250914 1.140000e-105 394.0
20 TraesCS6D01G116300 chr1B 94.510 255 13 1 3 256 94551303 94551049 4.080000e-105 392.0
21 TraesCS6D01G116300 chr1B 93.870 261 12 3 1 259 583428350 583428608 1.470000e-104 390.0
22 TraesCS6D01G116300 chr7A 94.488 254 14 0 1 254 492243340 492243087 4.080000e-105 392.0
23 TraesCS6D01G116300 chr7B 94.141 256 12 3 1 255 634577400 634577147 1.900000e-103 387.0
24 TraesCS6D01G116300 chr5A 94.118 255 14 1 3 256 509637870 509637616 1.900000e-103 387.0
25 TraesCS6D01G116300 chr5A 90.625 64 6 0 3946 4009 700672885 700672822 7.760000e-13 86.1
26 TraesCS6D01G116300 chr2B 89.744 234 24 0 1554 1787 605381192 605380959 2.550000e-77 300.0
27 TraesCS6D01G116300 chr4D 92.121 165 12 1 1344 1508 433393662 433393499 9.420000e-57 231.0
28 TraesCS6D01G116300 chr4A 92.903 155 11 0 1354 1508 34787858 34787704 4.380000e-55 226.0
29 TraesCS6D01G116300 chr4B 92.258 155 12 0 1354 1508 531580985 531580831 2.040000e-53 220.0
30 TraesCS6D01G116300 chr2A 78.652 178 29 8 3942 4115 360867556 360867728 4.600000e-20 110.0


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 TraesCS6D01G116300 chr6D 82633263 82637617 4354 True 8043.000000 8043 100.000000 1 4355 1 chr6D.!!$R1 4354
1 TraesCS6D01G116300 chr6A 99422463 99427111 4648 False 1789.666667 4632 89.206333 255 4338 3 chr6A.!!$F2 4083
2 TraesCS6D01G116300 chr6B 157660086 157665535 5449 True 1785.000000 4623 88.768333 332 4202 3 chr6B.!!$R2 3870

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
64 65 0.029035 CGGAGCGTCGTATGTAGCTT 59.971 55.0 0.00 0.0 40.39 3.74 F
191 192 0.096281 GTGTGTGTTGGTGACGTGTG 59.904 55.0 0.00 0.0 0.00 3.82 F
192 193 0.320858 TGTGTGTTGGTGACGTGTGT 60.321 50.0 0.00 0.0 0.00 3.72 F
2051 2819 0.103755 ATCGATCGCTGCATGTCACT 59.896 50.0 11.09 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 2382 1.446907 AGAAGTGCTTCTTGATGCCG 58.553 50.000 8.51 0.0 46.95 5.69 R
1917 2679 3.351020 AATCACCGACTATCGTACTGC 57.649 47.619 0.00 0.0 38.40 4.40 R
2153 2938 3.559655 TGACCAGGAAATATTTGATCGCG 59.440 43.478 5.17 0.0 0.00 5.87 R
3630 4475 0.037303 CAGGCTGTGGAAGTGTGGAT 59.963 55.000 6.28 0.0 0.00 3.41 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 3.455685 CGCTTCGGTGTCGTAACC 58.544 61.111 0.00 0.00 37.69 2.85
18 19 1.080974 CGCTTCGGTGTCGTAACCT 60.081 57.895 7.51 0.00 38.14 3.50
19 20 0.665369 CGCTTCGGTGTCGTAACCTT 60.665 55.000 7.51 0.00 38.14 3.50
20 21 1.066136 GCTTCGGTGTCGTAACCTTC 58.934 55.000 7.51 0.00 38.14 3.46
21 22 1.706443 CTTCGGTGTCGTAACCTTCC 58.294 55.000 7.51 0.00 38.14 3.46
22 23 1.271656 CTTCGGTGTCGTAACCTTCCT 59.728 52.381 7.51 0.00 38.14 3.36
23 24 0.599558 TCGGTGTCGTAACCTTCCTG 59.400 55.000 7.51 0.00 38.14 3.86
24 25 0.389426 CGGTGTCGTAACCTTCCTGG 60.389 60.000 7.51 0.00 38.14 4.45
49 50 4.785453 GCCTTGGAGCCCACGGAG 62.785 72.222 17.45 3.50 44.56 4.63
50 51 4.785453 CCTTGGAGCCCACGGAGC 62.785 72.222 10.18 0.00 44.56 4.70
57 58 4.203076 GCCCACGGAGCGTCGTAT 62.203 66.667 7.03 0.00 41.86 3.06
58 59 2.278596 CCCACGGAGCGTCGTATG 60.279 66.667 7.03 2.77 41.86 2.39
59 60 2.488355 CCACGGAGCGTCGTATGT 59.512 61.111 7.03 0.00 41.86 2.29
60 61 1.717791 CCCACGGAGCGTCGTATGTA 61.718 60.000 7.03 0.00 41.86 2.29
61 62 0.316772 CCACGGAGCGTCGTATGTAG 60.317 60.000 7.03 0.00 41.86 2.74
62 63 0.928908 CACGGAGCGTCGTATGTAGC 60.929 60.000 7.03 0.00 41.86 3.58
63 64 1.094073 ACGGAGCGTCGTATGTAGCT 61.094 55.000 5.63 6.62 41.98 3.32
64 65 0.029035 CGGAGCGTCGTATGTAGCTT 59.971 55.000 0.00 0.00 40.39 3.74
65 66 1.756367 GGAGCGTCGTATGTAGCTTC 58.244 55.000 0.00 3.44 40.39 3.86
66 67 1.334243 GGAGCGTCGTATGTAGCTTCT 59.666 52.381 0.00 0.00 40.39 2.85
67 68 2.602694 GGAGCGTCGTATGTAGCTTCTC 60.603 54.545 0.00 0.00 40.39 2.87
68 69 1.334243 AGCGTCGTATGTAGCTTCTCC 59.666 52.381 0.00 0.00 36.41 3.71
69 70 1.334243 GCGTCGTATGTAGCTTCTCCT 59.666 52.381 0.00 0.00 0.00 3.69
70 71 2.602694 GCGTCGTATGTAGCTTCTCCTC 60.603 54.545 0.00 0.00 0.00 3.71
71 72 2.873472 CGTCGTATGTAGCTTCTCCTCT 59.127 50.000 0.00 0.00 0.00 3.69
72 73 3.312973 CGTCGTATGTAGCTTCTCCTCTT 59.687 47.826 0.00 0.00 0.00 2.85
73 74 4.553156 CGTCGTATGTAGCTTCTCCTCTTC 60.553 50.000 0.00 0.00 0.00 2.87
74 75 3.560481 TCGTATGTAGCTTCTCCTCTTCG 59.440 47.826 0.00 0.00 0.00 3.79
75 76 2.880963 ATGTAGCTTCTCCTCTTCGC 57.119 50.000 0.00 0.00 0.00 4.70
76 77 0.452184 TGTAGCTTCTCCTCTTCGCG 59.548 55.000 0.00 0.00 0.00 5.87
77 78 0.248702 GTAGCTTCTCCTCTTCGCGG 60.249 60.000 6.13 0.00 0.00 6.46
78 79 0.680280 TAGCTTCTCCTCTTCGCGGT 60.680 55.000 6.13 0.00 0.00 5.68
79 80 1.807573 GCTTCTCCTCTTCGCGGTG 60.808 63.158 6.13 0.00 0.00 4.94
80 81 1.153745 CTTCTCCTCTTCGCGGTGG 60.154 63.158 6.13 1.12 0.00 4.61
81 82 3.296709 TTCTCCTCTTCGCGGTGGC 62.297 63.158 6.13 0.00 0.00 5.01
82 83 4.069232 CTCCTCTTCGCGGTGGCA 62.069 66.667 6.13 0.00 39.92 4.92
83 84 3.376935 CTCCTCTTCGCGGTGGCAT 62.377 63.158 6.13 0.00 39.92 4.40
84 85 3.197790 CCTCTTCGCGGTGGCATG 61.198 66.667 6.13 0.00 39.92 4.06
85 86 2.434884 CTCTTCGCGGTGGCATGT 60.435 61.111 6.13 0.00 39.92 3.21
86 87 2.031919 TCTTCGCGGTGGCATGTT 59.968 55.556 6.13 0.00 39.92 2.71
87 88 1.970917 CTCTTCGCGGTGGCATGTTC 61.971 60.000 6.13 0.00 39.92 3.18
88 89 2.281139 TTCGCGGTGGCATGTTCA 60.281 55.556 6.13 0.00 39.92 3.18
89 90 2.513065 CTTCGCGGTGGCATGTTCAC 62.513 60.000 6.13 11.28 39.92 3.18
90 91 4.444024 CGCGGTGGCATGTTCACG 62.444 66.667 0.00 6.48 39.92 4.35
91 92 4.101790 GCGGTGGCATGTTCACGG 62.102 66.667 17.71 17.71 39.62 4.94
92 93 2.668212 CGGTGGCATGTTCACGGT 60.668 61.111 15.40 0.00 36.09 4.83
93 94 2.258013 CGGTGGCATGTTCACGGTT 61.258 57.895 15.40 0.00 36.09 4.44
94 95 1.285641 GGTGGCATGTTCACGGTTG 59.714 57.895 12.73 0.00 36.09 3.77
95 96 1.169661 GGTGGCATGTTCACGGTTGA 61.170 55.000 12.73 0.00 36.09 3.18
96 97 0.238289 GTGGCATGTTCACGGTTGAG 59.762 55.000 0.00 0.00 31.71 3.02
97 98 0.888736 TGGCATGTTCACGGTTGAGG 60.889 55.000 0.00 0.00 31.71 3.86
98 99 1.210155 GCATGTTCACGGTTGAGGC 59.790 57.895 0.00 0.00 31.71 4.70
99 100 1.875963 CATGTTCACGGTTGAGGCC 59.124 57.895 0.00 0.00 31.71 5.19
100 101 1.303317 ATGTTCACGGTTGAGGCCC 60.303 57.895 0.00 0.00 31.71 5.80
101 102 2.671963 GTTCACGGTTGAGGCCCC 60.672 66.667 0.00 0.00 31.71 5.80
116 117 2.212327 CCCCGATGGCTCTTGTAGT 58.788 57.895 0.00 0.00 0.00 2.73
117 118 0.179073 CCCCGATGGCTCTTGTAGTG 60.179 60.000 0.00 0.00 0.00 2.74
118 119 0.811616 CCCGATGGCTCTTGTAGTGC 60.812 60.000 0.00 0.00 34.23 4.40
119 120 0.176680 CCGATGGCTCTTGTAGTGCT 59.823 55.000 0.00 0.00 35.27 4.40
120 121 1.409064 CCGATGGCTCTTGTAGTGCTA 59.591 52.381 0.00 0.00 35.27 3.49
121 122 2.544694 CCGATGGCTCTTGTAGTGCTAG 60.545 54.545 0.00 0.00 35.27 3.42
122 123 2.544694 CGATGGCTCTTGTAGTGCTAGG 60.545 54.545 0.00 0.00 35.27 3.02
123 124 1.195115 TGGCTCTTGTAGTGCTAGGG 58.805 55.000 0.00 0.00 35.27 3.53
124 125 0.466124 GGCTCTTGTAGTGCTAGGGG 59.534 60.000 0.00 0.00 35.27 4.79
125 126 1.196012 GCTCTTGTAGTGCTAGGGGT 58.804 55.000 0.00 0.00 32.42 4.95
126 127 1.134670 GCTCTTGTAGTGCTAGGGGTG 60.135 57.143 0.00 0.00 32.42 4.61
127 128 1.482593 CTCTTGTAGTGCTAGGGGTGG 59.517 57.143 0.00 0.00 0.00 4.61
128 129 1.203262 TCTTGTAGTGCTAGGGGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
129 130 0.981183 TTGTAGTGCTAGGGGTGGTG 59.019 55.000 0.00 0.00 0.00 4.17
130 131 0.178915 TGTAGTGCTAGGGGTGGTGT 60.179 55.000 0.00 0.00 0.00 4.16
131 132 0.981943 GTAGTGCTAGGGGTGGTGTT 59.018 55.000 0.00 0.00 0.00 3.32
132 133 0.981183 TAGTGCTAGGGGTGGTGTTG 59.019 55.000 0.00 0.00 0.00 3.33
133 134 1.971695 GTGCTAGGGGTGGTGTTGC 60.972 63.158 0.00 0.00 0.00 4.17
134 135 2.153401 TGCTAGGGGTGGTGTTGCT 61.153 57.895 0.00 0.00 0.00 3.91
135 136 1.675641 GCTAGGGGTGGTGTTGCTG 60.676 63.158 0.00 0.00 0.00 4.41
136 137 1.675641 CTAGGGGTGGTGTTGCTGC 60.676 63.158 0.00 0.00 0.00 5.25
137 138 3.545124 TAGGGGTGGTGTTGCTGCG 62.545 63.158 0.00 0.00 0.00 5.18
140 141 4.030452 GGTGGTGTTGCTGCGCTC 62.030 66.667 9.73 0.28 0.00 5.03
141 142 3.279116 GTGGTGTTGCTGCGCTCA 61.279 61.111 9.73 3.52 0.00 4.26
142 143 2.974148 TGGTGTTGCTGCGCTCAG 60.974 61.111 9.73 0.00 43.16 3.35
158 159 2.221981 GCTCAGCGTTTATGTATCCTGC 59.778 50.000 0.00 0.00 0.00 4.85
159 160 2.802816 CTCAGCGTTTATGTATCCTGCC 59.197 50.000 0.00 0.00 0.00 4.85
160 161 2.434336 TCAGCGTTTATGTATCCTGCCT 59.566 45.455 0.00 0.00 0.00 4.75
161 162 3.118408 TCAGCGTTTATGTATCCTGCCTT 60.118 43.478 0.00 0.00 0.00 4.35
162 163 3.002656 CAGCGTTTATGTATCCTGCCTTG 59.997 47.826 0.00 0.00 0.00 3.61
163 164 2.290641 GCGTTTATGTATCCTGCCTTGG 59.709 50.000 0.00 0.00 0.00 3.61
164 165 2.878406 CGTTTATGTATCCTGCCTTGGG 59.122 50.000 0.00 0.00 0.00 4.12
165 166 3.684413 CGTTTATGTATCCTGCCTTGGGT 60.684 47.826 0.00 0.00 0.00 4.51
166 167 3.576078 TTATGTATCCTGCCTTGGGTG 57.424 47.619 0.00 0.00 0.00 4.61
167 168 1.298953 ATGTATCCTGCCTTGGGTGT 58.701 50.000 0.00 0.00 0.00 4.16
168 169 0.327924 TGTATCCTGCCTTGGGTGTG 59.672 55.000 0.00 0.00 0.00 3.82
169 170 0.328258 GTATCCTGCCTTGGGTGTGT 59.672 55.000 0.00 0.00 0.00 3.72
170 171 0.327924 TATCCTGCCTTGGGTGTGTG 59.672 55.000 0.00 0.00 0.00 3.82
171 172 3.297620 CCTGCCTTGGGTGTGTGC 61.298 66.667 0.00 0.00 0.00 4.57
172 173 3.663176 CTGCCTTGGGTGTGTGCG 61.663 66.667 0.00 0.00 0.00 5.34
173 174 4.497984 TGCCTTGGGTGTGTGCGT 62.498 61.111 0.00 0.00 0.00 5.24
174 175 3.964875 GCCTTGGGTGTGTGCGTG 61.965 66.667 0.00 0.00 0.00 5.34
175 176 2.515991 CCTTGGGTGTGTGCGTGT 60.516 61.111 0.00 0.00 0.00 4.49
176 177 2.715005 CTTGGGTGTGTGCGTGTG 59.285 61.111 0.00 0.00 0.00 3.82
177 178 2.045829 TTGGGTGTGTGCGTGTGT 60.046 55.556 0.00 0.00 0.00 3.72
178 179 2.321668 CTTGGGTGTGTGCGTGTGTG 62.322 60.000 0.00 0.00 0.00 3.82
179 180 2.822255 GGGTGTGTGCGTGTGTGT 60.822 61.111 0.00 0.00 0.00 3.72
180 181 2.403378 GGGTGTGTGCGTGTGTGTT 61.403 57.895 0.00 0.00 0.00 3.32
181 182 1.226267 GGTGTGTGCGTGTGTGTTG 60.226 57.895 0.00 0.00 0.00 3.33
182 183 1.226267 GTGTGTGCGTGTGTGTTGG 60.226 57.895 0.00 0.00 0.00 3.77
183 184 1.672682 TGTGTGCGTGTGTGTTGGT 60.673 52.632 0.00 0.00 0.00 3.67
184 185 1.226267 GTGTGCGTGTGTGTTGGTG 60.226 57.895 0.00 0.00 0.00 4.17
185 186 1.376037 TGTGCGTGTGTGTTGGTGA 60.376 52.632 0.00 0.00 0.00 4.02
186 187 1.061887 GTGCGTGTGTGTTGGTGAC 59.938 57.895 0.00 0.00 0.00 3.67
187 188 2.323105 GCGTGTGTGTTGGTGACG 59.677 61.111 0.00 0.00 0.00 4.35
188 189 2.457778 GCGTGTGTGTTGGTGACGT 61.458 57.895 0.00 0.00 32.66 4.34
189 190 1.346879 CGTGTGTGTTGGTGACGTG 59.653 57.895 0.00 0.00 0.00 4.49
190 191 1.355796 CGTGTGTGTTGGTGACGTGT 61.356 55.000 0.00 0.00 0.00 4.49
191 192 0.096281 GTGTGTGTTGGTGACGTGTG 59.904 55.000 0.00 0.00 0.00 3.82
192 193 0.320858 TGTGTGTTGGTGACGTGTGT 60.321 50.000 0.00 0.00 0.00 3.72
193 194 0.800012 GTGTGTTGGTGACGTGTGTT 59.200 50.000 0.00 0.00 0.00 3.32
194 195 0.799393 TGTGTTGGTGACGTGTGTTG 59.201 50.000 0.00 0.00 0.00 3.33
195 196 0.800012 GTGTTGGTGACGTGTGTTGT 59.200 50.000 0.00 0.00 0.00 3.32
196 197 2.001159 GTGTTGGTGACGTGTGTTGTA 58.999 47.619 0.00 0.00 0.00 2.41
197 198 2.001159 TGTTGGTGACGTGTGTTGTAC 58.999 47.619 0.00 0.00 0.00 2.90
198 199 2.273557 GTTGGTGACGTGTGTTGTACT 58.726 47.619 0.00 0.00 0.00 2.73
199 200 1.929230 TGGTGACGTGTGTTGTACTG 58.071 50.000 0.00 0.00 0.00 2.74
200 201 1.477295 TGGTGACGTGTGTTGTACTGA 59.523 47.619 0.00 0.00 0.00 3.41
201 202 2.124903 GGTGACGTGTGTTGTACTGAG 58.875 52.381 0.00 0.00 0.00 3.35
202 203 2.480759 GGTGACGTGTGTTGTACTGAGT 60.481 50.000 0.00 0.00 0.00 3.41
203 204 3.184541 GTGACGTGTGTTGTACTGAGTT 58.815 45.455 0.00 0.00 0.00 3.01
204 205 3.000078 GTGACGTGTGTTGTACTGAGTTG 60.000 47.826 0.00 0.00 0.00 3.16
205 206 3.184541 GACGTGTGTTGTACTGAGTTGT 58.815 45.455 0.00 0.00 0.00 3.32
206 207 3.592059 ACGTGTGTTGTACTGAGTTGTT 58.408 40.909 0.00 0.00 0.00 2.83
207 208 3.369756 ACGTGTGTTGTACTGAGTTGTTG 59.630 43.478 0.00 0.00 0.00 3.33
208 209 3.242284 CGTGTGTTGTACTGAGTTGTTGG 60.242 47.826 0.00 0.00 0.00 3.77
209 210 3.687698 GTGTGTTGTACTGAGTTGTTGGT 59.312 43.478 0.00 0.00 0.00 3.67
210 211 3.687212 TGTGTTGTACTGAGTTGTTGGTG 59.313 43.478 0.00 0.00 0.00 4.17
211 212 3.936453 GTGTTGTACTGAGTTGTTGGTGA 59.064 43.478 0.00 0.00 0.00 4.02
212 213 4.574828 GTGTTGTACTGAGTTGTTGGTGAT 59.425 41.667 0.00 0.00 0.00 3.06
213 214 4.814234 TGTTGTACTGAGTTGTTGGTGATC 59.186 41.667 0.00 0.00 0.00 2.92
214 215 4.955811 TGTACTGAGTTGTTGGTGATCT 57.044 40.909 0.00 0.00 0.00 2.75
215 216 4.631131 TGTACTGAGTTGTTGGTGATCTG 58.369 43.478 0.00 0.00 0.00 2.90
216 217 3.845781 ACTGAGTTGTTGGTGATCTGT 57.154 42.857 0.00 0.00 0.00 3.41
217 218 3.470709 ACTGAGTTGTTGGTGATCTGTG 58.529 45.455 0.00 0.00 0.00 3.66
218 219 2.221169 TGAGTTGTTGGTGATCTGTGC 58.779 47.619 0.00 0.00 0.00 4.57
219 220 2.158769 TGAGTTGTTGGTGATCTGTGCT 60.159 45.455 0.00 0.00 0.00 4.40
220 221 2.880890 GAGTTGTTGGTGATCTGTGCTT 59.119 45.455 0.00 0.00 0.00 3.91
221 222 3.290710 AGTTGTTGGTGATCTGTGCTTT 58.709 40.909 0.00 0.00 0.00 3.51
222 223 4.460263 AGTTGTTGGTGATCTGTGCTTTA 58.540 39.130 0.00 0.00 0.00 1.85
223 224 5.072741 AGTTGTTGGTGATCTGTGCTTTAT 58.927 37.500 0.00 0.00 0.00 1.40
224 225 6.237901 AGTTGTTGGTGATCTGTGCTTTATA 58.762 36.000 0.00 0.00 0.00 0.98
225 226 6.886459 AGTTGTTGGTGATCTGTGCTTTATAT 59.114 34.615 0.00 0.00 0.00 0.86
226 227 8.046708 AGTTGTTGGTGATCTGTGCTTTATATA 58.953 33.333 0.00 0.00 0.00 0.86
227 228 8.840321 GTTGTTGGTGATCTGTGCTTTATATAT 58.160 33.333 0.00 0.00 0.00 0.86
241 242 6.730960 CTTTATATATAAAGCGGGGCGAAA 57.269 37.500 25.10 1.66 41.69 3.46
242 243 6.730960 TTTATATATAAAGCGGGGCGAAAG 57.269 37.500 12.90 0.00 0.00 2.62
259 260 5.789710 CGAAAGCCTTTTTCGGTAATAGA 57.210 39.130 12.72 0.00 45.17 1.98
260 261 5.796813 CGAAAGCCTTTTTCGGTAATAGAG 58.203 41.667 12.72 0.00 45.17 2.43
261 262 5.579511 CGAAAGCCTTTTTCGGTAATAGAGA 59.420 40.000 12.72 0.00 45.17 3.10
262 263 6.091713 CGAAAGCCTTTTTCGGTAATAGAGAA 59.908 38.462 12.72 0.00 45.17 2.87
306 307 1.199852 GCGCAACGTTTGTTCACTGG 61.200 55.000 0.30 0.00 35.72 4.00
327 328 4.400884 TGGTAAACAGCAAAGAAAGCTTCA 59.599 37.500 0.00 0.00 41.14 3.02
336 337 5.180304 AGCAAAGAAAGCTTCAGTAAGTAGC 59.820 40.000 0.00 0.00 39.87 3.58
381 382 6.918569 CCATTTATATGTAGGGTCGATCGATC 59.081 42.308 22.50 21.33 0.00 3.69
387 397 1.374758 GGGTCGATCGATCATGGGC 60.375 63.158 28.32 10.62 0.00 5.36
405 415 1.623973 GCCGTGCCTACTTTGACGTC 61.624 60.000 9.11 9.11 0.00 4.34
413 423 4.336153 TGCCTACTTTGACGTCGTATCATA 59.664 41.667 11.62 0.00 0.00 2.15
455 465 7.810658 TCAGAAAATGAATCTGCTTCTTACAC 58.189 34.615 0.00 0.00 43.19 2.90
466 476 5.532406 TCTGCTTCTTACACAAAATCAAGCT 59.468 36.000 0.00 0.00 36.54 3.74
474 484 4.695396 ACACAAAATCAAGCTTGCATGAA 58.305 34.783 21.99 4.27 0.00 2.57
586 836 3.278574 GTGCATGCTTCCACTATGGTAA 58.721 45.455 20.33 0.00 39.03 2.85
600 1285 0.679640 TGGTAAAGCAAGGATGGGCG 60.680 55.000 0.00 0.00 34.54 6.13
603 1288 1.312371 TAAAGCAAGGATGGGCGTGC 61.312 55.000 0.00 0.00 34.54 5.34
623 1308 2.861335 GCCTAGCTTTTTAGTCGAGAGC 59.139 50.000 0.00 0.00 0.00 4.09
758 1476 0.396417 CCTCCTCCGTCACATCCTCT 60.396 60.000 0.00 0.00 0.00 3.69
894 1621 2.047465 AGTCTGCGCAGAAGCTGG 60.047 61.111 39.63 13.25 39.48 4.85
932 1659 2.760385 GGTAGCCTCGAGCCCACT 60.760 66.667 6.99 3.87 45.47 4.00
964 1696 1.287739 AGACAGAGAGAGAAGGGGAGG 59.712 57.143 0.00 0.00 0.00 4.30
985 1717 3.555168 GGCGAAAGAGAAAGAGACCAGAA 60.555 47.826 0.00 0.00 0.00 3.02
986 1718 3.677596 GCGAAAGAGAAAGAGACCAGAAG 59.322 47.826 0.00 0.00 0.00 2.85
1056 1790 4.554036 GGATCCAGCTCCCACGGC 62.554 72.222 6.95 0.00 0.00 5.68
1227 1970 3.658705 ACCCAGGTATGAAAAGTTACCCA 59.341 43.478 0.00 0.00 33.23 4.51
1243 1986 5.964477 AGTTACCCAAGACCTAGATCATCAA 59.036 40.000 0.00 0.00 0.00 2.57
1246 1989 4.785376 ACCCAAGACCTAGATCATCAACTT 59.215 41.667 0.00 0.00 0.00 2.66
1261 2008 4.559862 TCAACTTCTCCCTGAAATCCTC 57.440 45.455 0.00 0.00 33.79 3.71
1270 2017 2.376109 CCTGAAATCCTCAAGCTGCAT 58.624 47.619 1.02 0.00 32.17 3.96
1286 2033 3.727079 GCTGCATGTGTTGATTTCTCTCG 60.727 47.826 0.00 0.00 0.00 4.04
1294 2041 4.153117 GTGTTGATTTCTCTCGTCAAGCAT 59.847 41.667 0.00 0.00 32.98 3.79
1299 2046 0.890683 TCTCTCGTCAAGCATGCTGA 59.109 50.000 23.48 17.52 0.00 4.26
1337 2085 4.405680 TGTTCTTGTGGTTTCTCTCTCTGA 59.594 41.667 0.00 0.00 0.00 3.27
1897 2658 9.529325 CTTTTATCTGAATTCTCATGGTACGTA 57.471 33.333 7.05 0.00 0.00 3.57
1898 2659 9.878667 TTTTATCTGAATTCTCATGGTACGTAA 57.121 29.630 7.05 0.00 0.00 3.18
1899 2660 8.867112 TTATCTGAATTCTCATGGTACGTAAC 57.133 34.615 2.90 2.90 0.00 2.50
1994 2762 4.195225 TGCGGTAGACACATACATTTGA 57.805 40.909 0.00 0.00 0.00 2.69
2051 2819 0.103755 ATCGATCGCTGCATGTCACT 59.896 50.000 11.09 0.00 0.00 3.41
2153 2938 4.908601 ATTCCCATTTCCCTTGAAAACC 57.091 40.909 0.00 0.00 43.37 3.27
2154 2939 2.243810 TCCCATTTCCCTTGAAAACCG 58.756 47.619 0.00 0.00 43.37 4.44
2160 2945 0.035598 TCCCTTGAAAACCGCGATCA 59.964 50.000 8.23 3.46 0.00 2.92
2179 2964 6.811170 GCGATCAAATATTTCCTGGTCAAAAA 59.189 34.615 0.00 0.00 0.00 1.94
2180 2965 7.492344 GCGATCAAATATTTCCTGGTCAAAAAT 59.508 33.333 0.00 0.00 0.00 1.82
2237 3026 3.741476 CAAAGCACGAGGCCCTGC 61.741 66.667 0.00 3.99 46.50 4.85
2259 3048 4.666512 CCCAAAGCTTGCCTATATATGGT 58.333 43.478 0.00 0.00 0.00 3.55
2263 3052 6.183360 CCAAAGCTTGCCTATATATGGTATGC 60.183 42.308 0.00 15.36 39.41 3.14
2306 3105 3.243704 TGAAACACTTGGCATTTGTAGGC 60.244 43.478 2.25 0.00 0.00 3.93
2581 3391 3.546724 TCATAACTCTCCCTCTCTCACG 58.453 50.000 0.00 0.00 0.00 4.35
2659 3471 8.915871 ATCGAATACACCTTCAATTTTTCATG 57.084 30.769 0.00 0.00 0.00 3.07
2866 3689 0.740868 CAGCATCACCACTACCACCG 60.741 60.000 0.00 0.00 0.00 4.94
2906 3741 1.134075 GCAGCAGCAACGACATCAG 59.866 57.895 0.00 0.00 41.58 2.90
3012 3853 3.181454 TGTTTCTCTCCCAAGAACCTCAC 60.181 47.826 0.00 0.00 35.06 3.51
3072 3913 2.370189 CCTTGATGACCTCCCTATGACC 59.630 54.545 0.00 0.00 0.00 4.02
3132 3973 3.322466 CGGCTCACCCCAGAAGGT 61.322 66.667 0.00 0.00 42.40 3.50
3141 3982 1.003718 CCCAGAAGGTTCGGTGACC 60.004 63.158 0.00 0.00 40.11 4.02
3220 4061 1.882167 GTCGAGGAGCTGCAGATGC 60.882 63.158 20.43 18.34 42.50 3.91
3365 4206 3.071023 CACAACTTCTAGGGACTCACCAA 59.929 47.826 0.00 0.00 41.75 3.67
3492 4333 4.870363 AGTTATGTGCGTCTTTTGCATTT 58.130 34.783 0.00 0.00 45.34 2.32
3493 4334 5.288804 AGTTATGTGCGTCTTTTGCATTTT 58.711 33.333 0.00 0.00 45.34 1.82
3554 4395 1.745115 CACATGTGATCGCCCGGTT 60.745 57.895 21.64 0.00 0.00 4.44
3579 4424 1.676006 ACCGGCTTCTGACAACAAAAG 59.324 47.619 0.00 0.00 0.00 2.27
3586 4431 0.746063 CTGACAACAAAAGGCAGGCA 59.254 50.000 0.00 0.00 0.00 4.75
3630 4475 2.297315 CACCTCGCCAGCTTATCTATCA 59.703 50.000 0.00 0.00 0.00 2.15
3631 4476 3.056250 CACCTCGCCAGCTTATCTATCAT 60.056 47.826 0.00 0.00 0.00 2.45
3632 4477 3.194542 ACCTCGCCAGCTTATCTATCATC 59.805 47.826 0.00 0.00 0.00 2.92
3633 4478 3.430098 CCTCGCCAGCTTATCTATCATCC 60.430 52.174 0.00 0.00 0.00 3.51
3634 4479 3.165071 TCGCCAGCTTATCTATCATCCA 58.835 45.455 0.00 0.00 0.00 3.41
3635 4480 3.056536 TCGCCAGCTTATCTATCATCCAC 60.057 47.826 0.00 0.00 0.00 4.02
3636 4481 3.306294 CGCCAGCTTATCTATCATCCACA 60.306 47.826 0.00 0.00 0.00 4.17
3637 4482 3.999663 GCCAGCTTATCTATCATCCACAC 59.000 47.826 0.00 0.00 0.00 3.82
3638 4483 4.262808 GCCAGCTTATCTATCATCCACACT 60.263 45.833 0.00 0.00 0.00 3.55
3657 4502 2.972713 ACTTCCACAGCCTGTTCTTCTA 59.027 45.455 0.00 0.00 0.00 2.10
3688 4533 3.692101 ACACGAACACCTTTTTGATGTCA 59.308 39.130 0.00 0.00 0.00 3.58
3695 4540 6.723298 ACACCTTTTTGATGTCAATGGTTA 57.277 33.333 10.68 0.00 34.50 2.85
3712 4559 8.192774 TCAATGGTTATCTTCATGCTTGAATTC 58.807 33.333 14.72 0.00 40.95 2.17
3739 4586 9.841295 ATGTTAATTAGACGCTTAATTTCCCTA 57.159 29.630 9.25 0.00 35.47 3.53
3763 5969 3.018856 ACACATTAGGGTACGTCGATCA 58.981 45.455 0.00 0.00 0.00 2.92
3767 5973 6.656270 ACACATTAGGGTACGTCGATCATATA 59.344 38.462 0.00 0.00 0.00 0.86
3772 5978 5.446860 AGGGTACGTCGATCATATATGGAT 58.553 41.667 12.78 5.31 0.00 3.41
3780 5986 6.129352 CGTCGATCATATATGGATTATGCGTG 60.129 42.308 12.78 2.05 0.00 5.34
3802 6008 3.193479 GGATCGATCCAACCTTTGCTTTT 59.807 43.478 34.65 0.00 46.38 2.27
3803 6009 3.915437 TCGATCCAACCTTTGCTTTTC 57.085 42.857 0.00 0.00 0.00 2.29
3805 6011 3.253188 TCGATCCAACCTTTGCTTTTCTG 59.747 43.478 0.00 0.00 0.00 3.02
3806 6012 3.004734 CGATCCAACCTTTGCTTTTCTGT 59.995 43.478 0.00 0.00 0.00 3.41
3807 6013 4.499696 CGATCCAACCTTTGCTTTTCTGTT 60.500 41.667 0.00 0.00 0.00 3.16
3940 6146 1.387420 CGTTTAGCACGCGTATGTTGA 59.613 47.619 13.44 0.00 43.37 3.18
3975 6221 6.543465 TCCAACATGGATGACAACATAATCTC 59.457 38.462 0.00 0.00 42.67 2.75
3994 6240 0.248289 CCGAATCGGTACACCACCTT 59.752 55.000 14.46 0.00 46.19 3.50
4009 6255 3.322254 ACCACCTTCTTCGATATAGGCAG 59.678 47.826 7.03 2.72 0.00 4.85
4013 6259 4.279671 ACCTTCTTCGATATAGGCAGAGTG 59.720 45.833 7.03 0.00 0.00 3.51
4069 6315 8.807667 ATGTCAGTTTTTCATCATTTCTGTTC 57.192 30.769 0.00 0.00 0.00 3.18
4116 6365 5.777223 TGTGTATCTTATCTATGCAGAGGCT 59.223 40.000 8.78 0.00 41.91 4.58
4118 6367 6.589523 GTGTATCTTATCTATGCAGAGGCTTG 59.410 42.308 8.78 0.00 41.91 4.01
4152 6401 5.185454 TCATTCTTTGTATCCGCTTGATGT 58.815 37.500 0.00 0.00 34.76 3.06
4273 6535 4.139786 GGTATCCAACATGCATGAGACAT 58.860 43.478 32.75 19.17 0.00 3.06
4276 6538 3.275999 TCCAACATGCATGAGACATCAG 58.724 45.455 32.75 11.73 39.29 2.90
4282 6544 6.615264 ACATGCATGAGACATCAGTAATTC 57.385 37.500 32.75 0.00 39.29 2.17
4290 6552 5.979517 TGAGACATCAGTAATTCAGTATGCG 59.020 40.000 0.00 0.00 34.76 4.73
4306 6568 4.949856 AGTATGCGGTTTGATGGAAGATTT 59.050 37.500 0.00 0.00 0.00 2.17
4312 6574 5.639082 GCGGTTTGATGGAAGATTTCATTTT 59.361 36.000 0.00 0.00 0.00 1.82
4314 6576 6.401367 CGGTTTGATGGAAGATTTCATTTTGC 60.401 38.462 0.00 0.00 0.00 3.68
4337 6599 9.976255 TTGCGTATTTATTACAACATAGTGTTC 57.024 29.630 0.00 0.00 38.77 3.18
4338 6600 9.373603 TGCGTATTTATTACAACATAGTGTTCT 57.626 29.630 0.00 0.00 38.77 3.01
4349 6611 8.635765 ACAACATAGTGTTCTTGGAATTATGT 57.364 30.769 0.00 0.00 38.77 2.29
4350 6612 8.730680 ACAACATAGTGTTCTTGGAATTATGTC 58.269 33.333 11.50 0.00 38.77 3.06
4351 6613 8.729756 CAACATAGTGTTCTTGGAATTATGTCA 58.270 33.333 11.50 0.00 38.77 3.58
4352 6614 8.862325 ACATAGTGTTCTTGGAATTATGTCAA 57.138 30.769 0.00 0.00 0.00 3.18
4353 6615 9.295825 ACATAGTGTTCTTGGAATTATGTCAAA 57.704 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.665369 AAGGTTACGACACCGAAGCG 60.665 55.000 0.00 0.00 42.33 4.68
2 3 1.271656 AGGAAGGTTACGACACCGAAG 59.728 52.381 0.00 0.00 42.33 3.79
3 4 1.000060 CAGGAAGGTTACGACACCGAA 60.000 52.381 0.00 0.00 42.33 4.30
4 5 0.599558 CAGGAAGGTTACGACACCGA 59.400 55.000 0.00 0.00 42.33 4.69
40 41 4.203076 ATACGACGCTCCGTGGGC 62.203 66.667 9.95 0.00 41.37 5.36
41 42 1.717791 TACATACGACGCTCCGTGGG 61.718 60.000 9.95 5.16 41.37 4.61
42 43 0.316772 CTACATACGACGCTCCGTGG 60.317 60.000 9.95 0.00 41.37 4.94
43 44 0.928908 GCTACATACGACGCTCCGTG 60.929 60.000 9.95 0.00 41.37 4.94
44 45 1.094073 AGCTACATACGACGCTCCGT 61.094 55.000 0.00 5.62 45.10 4.69
45 46 0.029035 AAGCTACATACGACGCTCCG 59.971 55.000 0.00 0.00 31.30 4.63
46 47 1.334243 AGAAGCTACATACGACGCTCC 59.666 52.381 0.00 0.00 31.30 4.70
47 48 2.602694 GGAGAAGCTACATACGACGCTC 60.603 54.545 0.00 0.00 31.30 5.03
48 49 1.334243 GGAGAAGCTACATACGACGCT 59.666 52.381 0.00 0.00 0.00 5.07
49 50 1.334243 AGGAGAAGCTACATACGACGC 59.666 52.381 0.00 0.00 0.00 5.19
50 51 2.873472 AGAGGAGAAGCTACATACGACG 59.127 50.000 0.00 0.00 0.00 5.12
51 52 4.553156 CGAAGAGGAGAAGCTACATACGAC 60.553 50.000 0.00 0.00 0.00 4.34
52 53 3.560481 CGAAGAGGAGAAGCTACATACGA 59.440 47.826 0.00 0.00 0.00 3.43
53 54 3.850374 GCGAAGAGGAGAAGCTACATACG 60.850 52.174 0.00 0.00 0.00 3.06
54 55 3.634283 GCGAAGAGGAGAAGCTACATAC 58.366 50.000 0.00 0.00 0.00 2.39
55 56 2.290916 CGCGAAGAGGAGAAGCTACATA 59.709 50.000 0.00 0.00 0.00 2.29
56 57 1.066303 CGCGAAGAGGAGAAGCTACAT 59.934 52.381 0.00 0.00 0.00 2.29
57 58 0.452184 CGCGAAGAGGAGAAGCTACA 59.548 55.000 0.00 0.00 0.00 2.74
58 59 3.243855 CGCGAAGAGGAGAAGCTAC 57.756 57.895 0.00 0.00 0.00 3.58
68 69 1.970917 GAACATGCCACCGCGAAGAG 61.971 60.000 8.23 0.00 38.08 2.85
69 70 2.031919 AACATGCCACCGCGAAGA 59.968 55.556 8.23 0.00 38.08 2.87
70 71 2.324330 TGAACATGCCACCGCGAAG 61.324 57.895 8.23 0.00 38.08 3.79
71 72 2.281139 TGAACATGCCACCGCGAA 60.281 55.556 8.23 0.00 38.08 4.70
72 73 3.047280 GTGAACATGCCACCGCGA 61.047 61.111 8.23 0.00 38.08 5.87
73 74 4.444024 CGTGAACATGCCACCGCG 62.444 66.667 0.00 0.00 38.08 6.46
74 75 4.101790 CCGTGAACATGCCACCGC 62.102 66.667 11.72 0.00 0.00 5.68
75 76 2.258013 AACCGTGAACATGCCACCG 61.258 57.895 11.72 8.70 0.00 4.94
76 77 1.169661 TCAACCGTGAACATGCCACC 61.170 55.000 11.72 0.00 0.00 4.61
77 78 0.238289 CTCAACCGTGAACATGCCAC 59.762 55.000 8.35 8.35 31.88 5.01
78 79 0.888736 CCTCAACCGTGAACATGCCA 60.889 55.000 0.00 0.00 31.88 4.92
79 80 1.875963 CCTCAACCGTGAACATGCC 59.124 57.895 0.00 0.00 31.88 4.40
80 81 1.210155 GCCTCAACCGTGAACATGC 59.790 57.895 0.00 0.00 31.88 4.06
81 82 1.586154 GGGCCTCAACCGTGAACATG 61.586 60.000 0.84 0.00 31.88 3.21
82 83 1.303317 GGGCCTCAACCGTGAACAT 60.303 57.895 0.84 0.00 31.88 2.71
83 84 2.112297 GGGCCTCAACCGTGAACA 59.888 61.111 0.84 0.00 31.88 3.18
84 85 2.671963 GGGGCCTCAACCGTGAAC 60.672 66.667 0.84 0.00 31.88 3.18
85 86 4.323477 CGGGGCCTCAACCGTGAA 62.323 66.667 1.96 0.00 44.85 3.18
98 99 0.179073 CACTACAAGAGCCATCGGGG 60.179 60.000 0.00 0.00 40.85 5.73
99 100 0.811616 GCACTACAAGAGCCATCGGG 60.812 60.000 0.00 0.00 37.18 5.14
100 101 0.176680 AGCACTACAAGAGCCATCGG 59.823 55.000 0.00 0.00 31.96 4.18
101 102 2.544694 CCTAGCACTACAAGAGCCATCG 60.545 54.545 0.00 0.00 31.96 3.84
102 103 2.224161 CCCTAGCACTACAAGAGCCATC 60.224 54.545 0.00 0.00 31.96 3.51
103 104 1.765314 CCCTAGCACTACAAGAGCCAT 59.235 52.381 0.00 0.00 31.96 4.40
104 105 1.195115 CCCTAGCACTACAAGAGCCA 58.805 55.000 0.00 0.00 31.96 4.75
105 106 0.466124 CCCCTAGCACTACAAGAGCC 59.534 60.000 0.00 0.00 31.96 4.70
106 107 1.134670 CACCCCTAGCACTACAAGAGC 60.135 57.143 0.00 0.00 31.73 4.09
107 108 1.482593 CCACCCCTAGCACTACAAGAG 59.517 57.143 0.00 0.00 0.00 2.85
108 109 1.203262 ACCACCCCTAGCACTACAAGA 60.203 52.381 0.00 0.00 0.00 3.02
109 110 1.066143 CACCACCCCTAGCACTACAAG 60.066 57.143 0.00 0.00 0.00 3.16
110 111 0.981183 CACCACCCCTAGCACTACAA 59.019 55.000 0.00 0.00 0.00 2.41
111 112 0.178915 ACACCACCCCTAGCACTACA 60.179 55.000 0.00 0.00 0.00 2.74
112 113 0.981943 AACACCACCCCTAGCACTAC 59.018 55.000 0.00 0.00 0.00 2.73
113 114 0.981183 CAACACCACCCCTAGCACTA 59.019 55.000 0.00 0.00 0.00 2.74
114 115 1.761174 CAACACCACCCCTAGCACT 59.239 57.895 0.00 0.00 0.00 4.40
115 116 1.971695 GCAACACCACCCCTAGCAC 60.972 63.158 0.00 0.00 0.00 4.40
116 117 2.153401 AGCAACACCACCCCTAGCA 61.153 57.895 0.00 0.00 0.00 3.49
117 118 1.675641 CAGCAACACCACCCCTAGC 60.676 63.158 0.00 0.00 0.00 3.42
118 119 1.675641 GCAGCAACACCACCCCTAG 60.676 63.158 0.00 0.00 0.00 3.02
119 120 2.434331 GCAGCAACACCACCCCTA 59.566 61.111 0.00 0.00 0.00 3.53
120 121 4.954970 CGCAGCAACACCACCCCT 62.955 66.667 0.00 0.00 0.00 4.79
137 138 2.221981 GCAGGATACATAAACGCTGAGC 59.778 50.000 0.00 0.00 41.41 4.26
138 139 2.802816 GGCAGGATACATAAACGCTGAG 59.197 50.000 0.00 0.00 41.41 3.35
139 140 2.434336 AGGCAGGATACATAAACGCTGA 59.566 45.455 0.00 0.00 41.41 4.26
140 141 2.838736 AGGCAGGATACATAAACGCTG 58.161 47.619 0.00 0.00 41.41 5.18
141 142 3.206150 CAAGGCAGGATACATAAACGCT 58.794 45.455 0.00 0.00 41.41 5.07
142 143 2.290641 CCAAGGCAGGATACATAAACGC 59.709 50.000 0.00 0.00 41.41 4.84
143 144 2.878406 CCCAAGGCAGGATACATAAACG 59.122 50.000 0.00 0.00 41.41 3.60
144 145 3.632145 CACCCAAGGCAGGATACATAAAC 59.368 47.826 0.00 0.00 41.41 2.01
145 146 3.268334 ACACCCAAGGCAGGATACATAAA 59.732 43.478 0.00 0.00 41.41 1.40
146 147 2.849943 ACACCCAAGGCAGGATACATAA 59.150 45.455 0.00 0.00 41.41 1.90
147 148 2.172505 CACACCCAAGGCAGGATACATA 59.827 50.000 0.00 0.00 41.41 2.29
148 149 1.064463 CACACCCAAGGCAGGATACAT 60.064 52.381 0.00 0.00 41.41 2.29
149 150 0.327924 CACACCCAAGGCAGGATACA 59.672 55.000 0.00 0.00 41.41 2.29
150 151 0.328258 ACACACCCAAGGCAGGATAC 59.672 55.000 0.00 0.00 0.00 2.24
151 152 0.327924 CACACACCCAAGGCAGGATA 59.672 55.000 0.00 0.00 0.00 2.59
152 153 1.075482 CACACACCCAAGGCAGGAT 59.925 57.895 0.00 0.00 0.00 3.24
153 154 2.515398 CACACACCCAAGGCAGGA 59.485 61.111 0.00 0.00 0.00 3.86
154 155 3.297620 GCACACACCCAAGGCAGG 61.298 66.667 0.00 0.00 0.00 4.85
155 156 3.663176 CGCACACACCCAAGGCAG 61.663 66.667 0.00 0.00 0.00 4.85
156 157 4.497984 ACGCACACACCCAAGGCA 62.498 61.111 0.00 0.00 0.00 4.75
157 158 3.964875 CACGCACACACCCAAGGC 61.965 66.667 0.00 0.00 0.00 4.35
158 159 2.515991 ACACGCACACACCCAAGG 60.516 61.111 0.00 0.00 0.00 3.61
159 160 2.112198 ACACACGCACACACCCAAG 61.112 57.895 0.00 0.00 0.00 3.61
160 161 2.045829 ACACACGCACACACCCAA 60.046 55.556 0.00 0.00 0.00 4.12
161 162 2.821810 CACACACGCACACACCCA 60.822 61.111 0.00 0.00 0.00 4.51
162 163 2.403378 AACACACACGCACACACCC 61.403 57.895 0.00 0.00 0.00 4.61
163 164 1.226267 CAACACACACGCACACACC 60.226 57.895 0.00 0.00 0.00 4.16
164 165 1.226267 CCAACACACACGCACACAC 60.226 57.895 0.00 0.00 0.00 3.82
165 166 1.672682 ACCAACACACACGCACACA 60.673 52.632 0.00 0.00 0.00 3.72
166 167 1.226267 CACCAACACACACGCACAC 60.226 57.895 0.00 0.00 0.00 3.82
167 168 1.376037 TCACCAACACACACGCACA 60.376 52.632 0.00 0.00 0.00 4.57
168 169 1.061887 GTCACCAACACACACGCAC 59.938 57.895 0.00 0.00 0.00 5.34
169 170 2.456948 CGTCACCAACACACACGCA 61.457 57.895 0.00 0.00 0.00 5.24
170 171 2.323105 CGTCACCAACACACACGC 59.677 61.111 0.00 0.00 0.00 5.34
171 172 1.346879 CACGTCACCAACACACACG 59.653 57.895 0.00 0.00 36.54 4.49
172 173 0.096281 CACACGTCACCAACACACAC 59.904 55.000 0.00 0.00 0.00 3.82
173 174 0.320858 ACACACGTCACCAACACACA 60.321 50.000 0.00 0.00 0.00 3.72
174 175 0.800012 AACACACGTCACCAACACAC 59.200 50.000 0.00 0.00 0.00 3.82
175 176 0.799393 CAACACACGTCACCAACACA 59.201 50.000 0.00 0.00 0.00 3.72
176 177 0.800012 ACAACACACGTCACCAACAC 59.200 50.000 0.00 0.00 0.00 3.32
177 178 2.001159 GTACAACACACGTCACCAACA 58.999 47.619 0.00 0.00 0.00 3.33
178 179 2.029970 CAGTACAACACACGTCACCAAC 59.970 50.000 0.00 0.00 0.00 3.77
179 180 2.094130 TCAGTACAACACACGTCACCAA 60.094 45.455 0.00 0.00 0.00 3.67
180 181 1.477295 TCAGTACAACACACGTCACCA 59.523 47.619 0.00 0.00 0.00 4.17
181 182 2.124903 CTCAGTACAACACACGTCACC 58.875 52.381 0.00 0.00 0.00 4.02
182 183 2.805845 ACTCAGTACAACACACGTCAC 58.194 47.619 0.00 0.00 0.00 3.67
183 184 3.183754 CAACTCAGTACAACACACGTCA 58.816 45.455 0.00 0.00 0.00 4.35
184 185 3.184541 ACAACTCAGTACAACACACGTC 58.815 45.455 0.00 0.00 0.00 4.34
185 186 3.241067 ACAACTCAGTACAACACACGT 57.759 42.857 0.00 0.00 0.00 4.49
186 187 3.242284 CCAACAACTCAGTACAACACACG 60.242 47.826 0.00 0.00 0.00 4.49
187 188 3.687698 ACCAACAACTCAGTACAACACAC 59.312 43.478 0.00 0.00 0.00 3.82
188 189 3.687212 CACCAACAACTCAGTACAACACA 59.313 43.478 0.00 0.00 0.00 3.72
189 190 3.936453 TCACCAACAACTCAGTACAACAC 59.064 43.478 0.00 0.00 0.00 3.32
190 191 4.209307 TCACCAACAACTCAGTACAACA 57.791 40.909 0.00 0.00 0.00 3.33
191 192 5.050091 CAGATCACCAACAACTCAGTACAAC 60.050 44.000 0.00 0.00 0.00 3.32
192 193 5.056480 CAGATCACCAACAACTCAGTACAA 58.944 41.667 0.00 0.00 0.00 2.41
193 194 4.100963 ACAGATCACCAACAACTCAGTACA 59.899 41.667 0.00 0.00 0.00 2.90
194 195 4.449068 CACAGATCACCAACAACTCAGTAC 59.551 45.833 0.00 0.00 0.00 2.73
195 196 4.631131 CACAGATCACCAACAACTCAGTA 58.369 43.478 0.00 0.00 0.00 2.74
196 197 3.470709 CACAGATCACCAACAACTCAGT 58.529 45.455 0.00 0.00 0.00 3.41
197 198 2.225019 GCACAGATCACCAACAACTCAG 59.775 50.000 0.00 0.00 0.00 3.35
198 199 2.158769 AGCACAGATCACCAACAACTCA 60.159 45.455 0.00 0.00 0.00 3.41
199 200 2.498167 AGCACAGATCACCAACAACTC 58.502 47.619 0.00 0.00 0.00 3.01
200 201 2.645838 AGCACAGATCACCAACAACT 57.354 45.000 0.00 0.00 0.00 3.16
201 202 3.715628 AAAGCACAGATCACCAACAAC 57.284 42.857 0.00 0.00 0.00 3.32
202 203 8.978874 ATATATAAAGCACAGATCACCAACAA 57.021 30.769 0.00 0.00 0.00 2.83
219 220 5.122711 GCTTTCGCCCCGCTTTATATATAAA 59.877 40.000 15.47 15.47 0.00 1.40
220 221 4.632688 GCTTTCGCCCCGCTTTATATATAA 59.367 41.667 0.81 0.81 0.00 0.98
221 222 4.186159 GCTTTCGCCCCGCTTTATATATA 58.814 43.478 0.00 0.00 0.00 0.86
222 223 3.007635 GCTTTCGCCCCGCTTTATATAT 58.992 45.455 0.00 0.00 0.00 0.86
223 224 2.419667 GCTTTCGCCCCGCTTTATATA 58.580 47.619 0.00 0.00 0.00 0.86
224 225 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
225 226 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
226 227 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
236 237 2.691984 TTACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
238 239 6.980051 TCTCTATTACCGAAAAAGGCTTTC 57.020 37.500 13.76 0.41 33.69 2.62
239 240 7.754851 TTTCTCTATTACCGAAAAAGGCTTT 57.245 32.000 6.68 6.68 33.69 3.51
240 241 7.754851 TTTTCTCTATTACCGAAAAAGGCTT 57.245 32.000 0.00 0.00 34.72 4.35
241 242 7.754851 TTTTTCTCTATTACCGAAAAAGGCT 57.245 32.000 0.00 0.00 39.99 4.58
267 268 4.023878 GCGCTTCTACAGTACTGCTAGTAT 60.024 45.833 22.90 4.71 32.65 2.12
274 275 1.649171 CGTTGCGCTTCTACAGTACTG 59.351 52.381 21.44 21.44 0.00 2.74
282 283 1.934525 TGAACAAACGTTGCGCTTCTA 59.065 42.857 9.73 0.00 0.00 2.10
306 307 5.582550 ACTGAAGCTTTCTTTGCTGTTTAC 58.417 37.500 0.00 0.00 41.03 2.01
360 361 6.039382 CCATGATCGATCGACCCTACATATAA 59.961 42.308 22.06 0.00 0.00 0.98
361 362 5.531287 CCATGATCGATCGACCCTACATATA 59.469 44.000 22.06 0.00 0.00 0.86
362 363 4.339530 CCATGATCGATCGACCCTACATAT 59.660 45.833 22.06 0.00 0.00 1.78
363 364 3.694566 CCATGATCGATCGACCCTACATA 59.305 47.826 22.06 0.00 0.00 2.29
387 397 1.342082 CGACGTCAAAGTAGGCACGG 61.342 60.000 17.16 0.00 36.56 4.94
455 465 5.345202 GTCTCTTCATGCAAGCTTGATTTTG 59.655 40.000 30.39 18.62 31.64 2.44
466 476 6.182627 ACCAGATATTTGTCTCTTCATGCAA 58.817 36.000 0.00 0.00 0.00 4.08
474 484 7.989741 CCACTTATCAACCAGATATTTGTCTCT 59.010 37.037 0.00 0.00 38.93 3.10
513 525 9.743057 CATGTGGTGAAAACAAGAGTAAAATAA 57.257 29.630 0.00 0.00 0.00 1.40
514 526 8.908903 ACATGTGGTGAAAACAAGAGTAAAATA 58.091 29.630 0.00 0.00 0.00 1.40
515 527 7.781056 ACATGTGGTGAAAACAAGAGTAAAAT 58.219 30.769 0.00 0.00 0.00 1.82
586 836 3.064324 GCACGCCCATCCTTGCTT 61.064 61.111 0.00 0.00 32.00 3.91
600 1285 3.846360 TCTCGACTAAAAAGCTAGGCAC 58.154 45.455 0.00 0.00 0.00 5.01
603 1288 3.109619 CGCTCTCGACTAAAAAGCTAGG 58.890 50.000 0.00 0.00 38.10 3.02
758 1476 1.878102 GCAGGAAAAGGCGTCAGAGAA 60.878 52.381 0.00 0.00 0.00 2.87
894 1621 3.305950 CCACTGATGAGATACTGCTAGCC 60.306 52.174 13.29 0.00 0.00 3.93
932 1659 3.200165 TCTCTCTGTCTCGAGGTGGATAA 59.800 47.826 13.56 0.00 0.00 1.75
964 1696 3.305398 TCTGGTCTCTTTCTCTTTCGC 57.695 47.619 0.00 0.00 0.00 4.70
985 1717 3.106054 AGAGCATCATGTTCACTCTCCT 58.894 45.455 4.11 0.00 37.82 3.69
986 1718 3.196463 CAGAGCATCATGTTCACTCTCC 58.804 50.000 4.11 0.00 35.57 3.71
1056 1790 2.492090 CTGAAGCCGAGGTCTCCG 59.508 66.667 0.00 0.00 0.00 4.63
1227 1970 5.365314 GGGAGAAGTTGATGATCTAGGTCTT 59.635 44.000 4.28 0.00 0.00 3.01
1243 1986 3.308046 GCTTGAGGATTTCAGGGAGAAGT 60.308 47.826 0.00 0.00 37.57 3.01
1246 1989 2.238144 CAGCTTGAGGATTTCAGGGAGA 59.762 50.000 0.00 0.00 37.07 3.71
1261 2008 3.909430 AGAAATCAACACATGCAGCTTG 58.091 40.909 6.74 6.74 0.00 4.01
1270 2017 3.494626 GCTTGACGAGAGAAATCAACACA 59.505 43.478 0.00 0.00 0.00 3.72
1286 2033 2.923121 TCCCTAATCAGCATGCTTGAC 58.077 47.619 19.98 0.00 34.76 3.18
1294 2041 8.593945 AGAACAAATTAATTCCCTAATCAGCA 57.406 30.769 0.10 0.00 0.00 4.41
1299 2046 9.100197 ACCACAAGAACAAATTAATTCCCTAAT 57.900 29.630 0.10 0.00 0.00 1.73
1337 2085 2.812178 GCCGTACGTGCGTTCCAT 60.812 61.111 24.09 0.00 0.00 3.41
1628 2382 1.446907 AGAAGTGCTTCTTGATGCCG 58.553 50.000 8.51 0.00 46.95 5.69
1897 2658 4.692475 GTGCCGGCCAGGTACGTT 62.692 66.667 26.77 0.00 45.43 3.99
1917 2679 3.351020 AATCACCGACTATCGTACTGC 57.649 47.619 0.00 0.00 38.40 4.40
2068 2836 3.832490 ACATTAAGTGAAAAGGGAAGCCC 59.168 43.478 0.00 0.00 45.90 5.19
2153 2938 3.559655 TGACCAGGAAATATTTGATCGCG 59.440 43.478 5.17 0.00 0.00 5.87
2154 2939 5.499139 TTGACCAGGAAATATTTGATCGC 57.501 39.130 5.17 0.00 0.00 4.58
2179 2964 4.586884 CTTGCTGCAGGATGGTGATATAT 58.413 43.478 17.12 0.00 35.86 0.86
2180 2965 3.808265 GCTTGCTGCAGGATGGTGATATA 60.808 47.826 20.26 0.00 42.31 0.86
2237 3026 4.666512 ACCATATATAGGCAAGCTTTGGG 58.333 43.478 11.61 0.00 0.00 4.12
2259 3048 3.643199 TGCCTCTTGGTTACATGCATA 57.357 42.857 0.00 0.00 35.27 3.14
2263 3052 4.641541 TCATCAATGCCTCTTGGTTACATG 59.358 41.667 0.00 0.00 35.27 3.21
2306 3105 1.220206 CTACTGCAGGGACAGGCTG 59.780 63.158 19.93 14.16 42.21 4.85
2505 3309 5.048224 GCTGGAGATGTAAATTCCATGATGG 60.048 44.000 4.74 4.74 40.06 3.51
2581 3391 3.130340 TGTTGAAGAAAAGTTCCTGCCAC 59.870 43.478 0.00 0.00 0.00 5.01
2620 3430 9.449719 AGGTGTATTCGATTATTTCTTTGAACT 57.550 29.630 0.00 0.00 0.00 3.01
2636 3448 6.585702 TGCATGAAAAATTGAAGGTGTATTCG 59.414 34.615 0.00 0.00 31.52 3.34
2680 3492 5.590530 AGTTCAATTTGTTGGCTAACACA 57.409 34.783 15.94 9.90 45.91 3.72
2681 3493 6.735130 AGTAGTTCAATTTGTTGGCTAACAC 58.265 36.000 15.94 2.26 45.91 3.32
2849 3672 2.106683 GCGGTGGTAGTGGTGATGC 61.107 63.158 0.00 0.00 0.00 3.91
2854 3677 4.016706 GCAGGCGGTGGTAGTGGT 62.017 66.667 0.00 0.00 0.00 4.16
2866 3689 1.945662 CGCTGTTGTTGTTGCAGGC 60.946 57.895 0.00 0.00 0.00 4.85
2906 3741 1.067974 TGCTTGGCATGAGCATATTGC 59.932 47.619 9.72 0.00 44.63 3.56
3123 3964 1.003718 GGTCACCGAACCTTCTGGG 60.004 63.158 0.00 0.00 41.89 4.45
3132 3973 3.047280 GCGTGCATGGTCACCGAA 61.047 61.111 8.27 0.00 33.57 4.30
3492 4333 5.477637 TGCATGTTCCATTTCTCATTCTCAA 59.522 36.000 0.00 0.00 0.00 3.02
3493 4334 5.011586 TGCATGTTCCATTTCTCATTCTCA 58.988 37.500 0.00 0.00 0.00 3.27
3554 4395 0.181587 TTGTCAGAAGCCGGTGGAAA 59.818 50.000 1.90 0.00 0.00 3.13
3579 4424 1.678970 ACCCTTCGATTTGCCTGCC 60.679 57.895 0.00 0.00 0.00 4.85
3586 4431 4.457949 GTCAATTACCACACCCTTCGATTT 59.542 41.667 0.00 0.00 0.00 2.17
3630 4475 0.037303 CAGGCTGTGGAAGTGTGGAT 59.963 55.000 6.28 0.00 0.00 3.41
3631 4476 1.344953 ACAGGCTGTGGAAGTGTGGA 61.345 55.000 21.37 0.00 0.00 4.02
3632 4477 0.466189 AACAGGCTGTGGAAGTGTGG 60.466 55.000 22.83 0.00 0.00 4.17
3633 4478 0.947244 GAACAGGCTGTGGAAGTGTG 59.053 55.000 22.83 0.00 0.00 3.82
3634 4479 0.839946 AGAACAGGCTGTGGAAGTGT 59.160 50.000 22.83 2.62 0.00 3.55
3635 4480 1.876156 GAAGAACAGGCTGTGGAAGTG 59.124 52.381 22.83 0.00 0.00 3.16
3636 4481 1.771255 AGAAGAACAGGCTGTGGAAGT 59.229 47.619 22.83 4.37 0.00 3.01
3637 4482 2.557920 AGAAGAACAGGCTGTGGAAG 57.442 50.000 22.83 0.00 0.00 3.46
3638 4483 2.303022 CCTAGAAGAACAGGCTGTGGAA 59.697 50.000 22.83 3.21 0.00 3.53
3657 4502 1.004918 GTGTTCGTGTGGCTAGCCT 60.005 57.895 33.07 0.00 36.94 4.58
3712 4559 8.621286 AGGGAAATTAAGCGTCTAATTAACATG 58.379 33.333 0.00 0.00 32.41 3.21
3725 4572 6.377327 AATGTGTGATAGGGAAATTAAGCG 57.623 37.500 0.00 0.00 0.00 4.68
3739 4586 3.018856 TCGACGTACCCTAATGTGTGAT 58.981 45.455 0.00 0.00 0.00 3.06
3763 5969 6.405278 TCGATCCACGCATAATCCATATAT 57.595 37.500 0.00 0.00 42.26 0.86
3767 5973 3.525537 GATCGATCCACGCATAATCCAT 58.474 45.455 14.76 0.00 42.26 3.41
3820 6026 1.491274 TTGGCCAGGCATCTCTCACA 61.491 55.000 15.19 0.00 0.00 3.58
3994 6240 4.038042 CCAACACTCTGCCTATATCGAAGA 59.962 45.833 0.00 0.00 45.75 2.87
4034 6280 6.852858 TGAAAAACTGACATATCGACAACA 57.147 33.333 0.00 0.00 0.00 3.33
4069 6315 7.588854 CACACAATGAAATAACAACAGTCTGAG 59.411 37.037 6.91 1.10 0.00 3.35
4116 6365 4.768448 ACAAAGAATGATGATCAGCACCAA 59.232 37.500 17.26 0.00 0.00 3.67
4118 6367 4.978083 ACAAAGAATGATGATCAGCACC 57.022 40.909 17.26 11.24 0.00 5.01
4173 6425 7.810766 TTGTCATTTTTCGATAAAAGGATGC 57.189 32.000 16.92 9.96 36.02 3.91
4262 6524 5.737860 ACTGAATTACTGATGTCTCATGCA 58.262 37.500 0.00 0.00 0.00 3.96
4273 6535 5.483811 TCAAACCGCATACTGAATTACTGA 58.516 37.500 0.00 0.00 0.00 3.41
4276 6538 5.295787 TCCATCAAACCGCATACTGAATTAC 59.704 40.000 0.00 0.00 0.00 1.89
4282 6544 3.270027 TCTTCCATCAAACCGCATACTG 58.730 45.455 0.00 0.00 0.00 2.74
4290 6552 6.401367 CGCAAAATGAAATCTTCCATCAAACC 60.401 38.462 0.00 0.00 0.00 3.27
4312 6574 9.373603 AGAACACTATGTTGTAATAAATACGCA 57.626 29.630 0.00 0.00 41.28 5.24


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

AutoCloner maintained by Alex Coulton.