Multiple sequence alignment - TraesCS6A01G298200

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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 TraesCS6A01G298200 chr6A 100.000 3905 0 0 1 3905 531519488 531523392 0.000000e+00 7212.0
1 TraesCS6A01G298200 chr6D 92.612 3181 168 25 634 3770 386438275 386441432 0.000000e+00 4510.0
2 TraesCS6A01G298200 chr6D 89.109 303 26 4 319 621 386437996 386438291 1.710000e-98 370.0
3 TraesCS6A01G298200 chr6D 92.800 125 8 1 3782 3905 386441474 386441598 3.100000e-41 180.0
4 TraesCS6A01G298200 chr6D 89.362 94 10 0 154 247 386437907 386438000 6.850000e-23 119.0
5 TraesCS6A01G298200 chr6D 91.837 49 4 0 3857 3905 386441581 386441629 7.000000e-08 69.4
6 TraesCS6A01G298200 chr6B 93.790 2673 134 12 648 3304 577361951 577364607 0.000000e+00 3988.0
7 TraesCS6A01G298200 chr6B 84.414 648 35 26 3309 3905 577364671 577365303 9.410000e-161 577.0
8 TraesCS6A01G298200 chr6B 80.062 321 41 17 302 614 577361641 577361946 2.360000e-52 217.0
9 TraesCS6A01G298200 chr4D 92.308 52 4 0 642 693 53499953 53500004 1.500000e-09 75.0
10 TraesCS6A01G298200 chr5D 93.182 44 3 0 646 689 372332933 372332890 9.060000e-07 65.8
11 TraesCS6A01G298200 chr1B 96.875 32 1 0 732 763 563563487 563563518 2.000000e-03 54.7
12 TraesCS6A01G298200 chr7B 100.000 28 0 0 739 766 578300096 578300123 7.000000e-03 52.8
13 TraesCS6A01G298200 chr5B 100.000 28 0 0 739 766 281646236 281646263 7.000000e-03 52.8
14 TraesCS6A01G298200 chr3D 94.118 34 2 0 733 766 478537176 478537209 7.000000e-03 52.8
15 TraesCS6A01G298200 chr3B 96.774 31 1 0 739 769 492624279 492624249 7.000000e-03 52.8
16 TraesCS6A01G298200 chr1D 100.000 28 0 0 739 766 141544709 141544682 7.000000e-03 52.8
17 TraesCS6A01G298200 chr1D 100.000 28 0 0 739 766 199337798 199337771 7.000000e-03 52.8


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 TraesCS6A01G298200 chr6A 531519488 531523392 3904 False 7212.00 7212 100.000000 1 3905 1 chr6A.!!$F1 3904
1 TraesCS6A01G298200 chr6D 386437907 386441629 3722 False 1049.68 4510 91.144000 154 3905 5 chr6D.!!$F1 3751
2 TraesCS6A01G298200 chr6B 577361641 577365303 3662 False 1594.00 3988 86.088667 302 3905 3 chr6B.!!$F1 3603

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
281 282 0.034186 CCAGGGGCATGCTTCTTGTA 60.034 55.000 18.92 0.0 0.00 2.41 F
343 344 0.601558 AAGTCGGAGTCGCTTGCTAA 59.398 50.000 0.00 0.0 33.78 3.09 F
1188 1217 0.666374 CAACCAACCCAAGAACCGTC 59.334 55.000 0.00 0.0 0.00 4.79 F
2529 2558 1.002315 GTTGCCCGGTTACTGTTCCTA 59.998 52.381 0.00 0.0 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 1883 0.247460 CGATGAGGCAGTTCCAGACA 59.753 55.0 0.00 0.00 37.29 3.41 R
2196 2225 0.935898 GTCGAGCATGCTCCATCAAG 59.064 55.0 35.77 23.07 39.77 3.02 R
2855 2884 0.247419 CGAGAACGCATCATGCACAC 60.247 55.0 11.00 0.00 45.36 3.82 R
3622 3773 0.528684 GGTGAGTATCTGACGCTGCC 60.529 60.0 0.00 0.00 34.92 4.85 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
19 20 2.570442 GAGCTGTACTGTGGTCTAGC 57.430 55.000 0.00 0.00 35.87 3.42
20 21 0.811915 AGCTGTACTGTGGTCTAGCG 59.188 55.000 1.46 0.00 38.61 4.26
21 22 0.179134 GCTGTACTGTGGTCTAGCGG 60.179 60.000 1.46 0.00 0.00 5.52
22 23 1.174783 CTGTACTGTGGTCTAGCGGT 58.825 55.000 0.00 0.00 0.00 5.68
23 24 0.885879 TGTACTGTGGTCTAGCGGTG 59.114 55.000 0.00 0.00 0.00 4.94
24 25 0.458025 GTACTGTGGTCTAGCGGTGC 60.458 60.000 0.00 0.00 0.00 5.01
25 26 0.896479 TACTGTGGTCTAGCGGTGCA 60.896 55.000 0.00 0.00 0.00 4.57
26 27 1.446792 CTGTGGTCTAGCGGTGCAG 60.447 63.158 0.00 0.00 0.00 4.41
27 28 2.815647 GTGGTCTAGCGGTGCAGC 60.816 66.667 5.64 5.64 37.41 5.25
28 29 4.435436 TGGTCTAGCGGTGCAGCG 62.435 66.667 32.48 32.48 43.00 5.18
29 30 4.129737 GGTCTAGCGGTGCAGCGA 62.130 66.667 39.54 20.28 43.00 4.93
30 31 2.881352 GTCTAGCGGTGCAGCGAC 60.881 66.667 39.54 28.75 43.00 5.19
31 32 4.476410 TCTAGCGGTGCAGCGACG 62.476 66.667 39.54 25.09 43.00 5.12
37 38 2.356553 GGTGCAGCGACGGTGTTA 60.357 61.111 26.05 14.21 33.19 2.41
38 39 1.740296 GGTGCAGCGACGGTGTTAT 60.740 57.895 26.05 0.00 33.19 1.89
39 40 0.458889 GGTGCAGCGACGGTGTTATA 60.459 55.000 26.05 9.57 33.19 0.98
40 41 0.643820 GTGCAGCGACGGTGTTATAC 59.356 55.000 26.05 16.44 33.19 1.47
41 42 0.244178 TGCAGCGACGGTGTTATACA 59.756 50.000 26.05 13.52 33.19 2.29
56 57 6.435430 TGTTATACACATCTGTTGATTGCC 57.565 37.500 0.00 0.00 0.00 4.52
57 58 5.942826 TGTTATACACATCTGTTGATTGCCA 59.057 36.000 0.00 0.00 0.00 4.92
58 59 4.970662 ATACACATCTGTTGATTGCCAC 57.029 40.909 0.00 0.00 0.00 5.01
59 60 1.536766 ACACATCTGTTGATTGCCACG 59.463 47.619 0.00 0.00 0.00 4.94
60 61 0.523072 ACATCTGTTGATTGCCACGC 59.477 50.000 0.00 0.00 0.00 5.34
61 62 0.522626 CATCTGTTGATTGCCACGCA 59.477 50.000 0.00 0.00 36.47 5.24
76 77 3.924238 CGCAAGTGCTGAAACTGTT 57.076 47.368 1.21 0.00 39.32 3.16
77 78 1.469917 CGCAAGTGCTGAAACTGTTG 58.530 50.000 1.21 0.00 39.32 3.33
78 79 1.843992 GCAAGTGCTGAAACTGTTGG 58.156 50.000 0.00 0.00 38.21 3.77
79 80 1.405105 GCAAGTGCTGAAACTGTTGGA 59.595 47.619 0.00 0.00 38.21 3.53
80 81 2.035066 GCAAGTGCTGAAACTGTTGGAT 59.965 45.455 0.00 0.00 38.21 3.41
81 82 3.635331 CAAGTGCTGAAACTGTTGGATG 58.365 45.455 0.00 0.00 0.00 3.51
82 83 2.936202 AGTGCTGAAACTGTTGGATGT 58.064 42.857 0.00 0.00 0.00 3.06
83 84 2.620115 AGTGCTGAAACTGTTGGATGTG 59.380 45.455 0.00 0.00 0.00 3.21
84 85 2.358898 GTGCTGAAACTGTTGGATGTGT 59.641 45.455 0.00 0.00 0.00 3.72
85 86 2.358582 TGCTGAAACTGTTGGATGTGTG 59.641 45.455 0.00 0.00 0.00 3.82
86 87 2.859806 GCTGAAACTGTTGGATGTGTGC 60.860 50.000 0.00 0.00 0.00 4.57
87 88 2.620115 CTGAAACTGTTGGATGTGTGCT 59.380 45.455 0.00 0.00 0.00 4.40
88 89 3.023119 TGAAACTGTTGGATGTGTGCTT 58.977 40.909 0.00 0.00 0.00 3.91
89 90 3.066621 TGAAACTGTTGGATGTGTGCTTC 59.933 43.478 0.00 0.00 0.00 3.86
90 91 2.346766 ACTGTTGGATGTGTGCTTCA 57.653 45.000 0.00 0.00 0.00 3.02
91 92 2.867624 ACTGTTGGATGTGTGCTTCAT 58.132 42.857 0.00 0.00 0.00 2.57
92 93 3.225104 ACTGTTGGATGTGTGCTTCATT 58.775 40.909 0.00 0.00 0.00 2.57
93 94 3.005050 ACTGTTGGATGTGTGCTTCATTG 59.995 43.478 0.00 0.00 0.00 2.82
94 95 2.296752 TGTTGGATGTGTGCTTCATTGG 59.703 45.455 0.00 0.00 0.00 3.16
95 96 0.889994 TGGATGTGTGCTTCATTGGC 59.110 50.000 0.00 0.00 0.00 4.52
96 97 1.180029 GGATGTGTGCTTCATTGGCT 58.820 50.000 0.00 0.00 0.00 4.75
97 98 1.135199 GGATGTGTGCTTCATTGGCTG 60.135 52.381 0.00 0.00 0.00 4.85
98 99 1.542915 GATGTGTGCTTCATTGGCTGT 59.457 47.619 0.00 0.00 0.00 4.40
99 100 1.401761 TGTGTGCTTCATTGGCTGTT 58.598 45.000 0.00 0.00 0.00 3.16
100 101 1.337703 TGTGTGCTTCATTGGCTGTTC 59.662 47.619 0.00 0.00 0.00 3.18
101 102 1.610522 GTGTGCTTCATTGGCTGTTCT 59.389 47.619 0.00 0.00 0.00 3.01
102 103 1.881973 TGTGCTTCATTGGCTGTTCTC 59.118 47.619 0.00 0.00 0.00 2.87
103 104 2.157738 GTGCTTCATTGGCTGTTCTCT 58.842 47.619 0.00 0.00 0.00 3.10
104 105 3.244526 TGTGCTTCATTGGCTGTTCTCTA 60.245 43.478 0.00 0.00 0.00 2.43
105 106 3.373439 GTGCTTCATTGGCTGTTCTCTAG 59.627 47.826 0.00 0.00 0.00 2.43
106 107 3.008375 TGCTTCATTGGCTGTTCTCTAGT 59.992 43.478 0.00 0.00 0.00 2.57
107 108 4.006319 GCTTCATTGGCTGTTCTCTAGTT 58.994 43.478 0.00 0.00 0.00 2.24
108 109 4.094146 GCTTCATTGGCTGTTCTCTAGTTC 59.906 45.833 0.00 0.00 0.00 3.01
109 110 4.890158 TCATTGGCTGTTCTCTAGTTCA 57.110 40.909 0.00 0.00 0.00 3.18
110 111 5.426689 TCATTGGCTGTTCTCTAGTTCAT 57.573 39.130 0.00 0.00 0.00 2.57
111 112 5.809001 TCATTGGCTGTTCTCTAGTTCATT 58.191 37.500 0.00 0.00 0.00 2.57
112 113 5.877012 TCATTGGCTGTTCTCTAGTTCATTC 59.123 40.000 0.00 0.00 0.00 2.67
113 114 5.489792 TTGGCTGTTCTCTAGTTCATTCT 57.510 39.130 0.00 0.00 0.00 2.40
114 115 5.489792 TGGCTGTTCTCTAGTTCATTCTT 57.510 39.130 0.00 0.00 0.00 2.52
115 116 5.240891 TGGCTGTTCTCTAGTTCATTCTTG 58.759 41.667 0.00 0.00 0.00 3.02
116 117 4.094146 GGCTGTTCTCTAGTTCATTCTTGC 59.906 45.833 0.00 0.00 0.00 4.01
117 118 4.934602 GCTGTTCTCTAGTTCATTCTTGCT 59.065 41.667 0.00 0.00 0.00 3.91
118 119 5.163874 GCTGTTCTCTAGTTCATTCTTGCTG 60.164 44.000 0.00 0.00 0.00 4.41
119 120 4.692625 TGTTCTCTAGTTCATTCTTGCTGC 59.307 41.667 0.00 0.00 0.00 5.25
120 121 4.815533 TCTCTAGTTCATTCTTGCTGCT 57.184 40.909 0.00 0.00 0.00 4.24
121 122 5.921962 TCTCTAGTTCATTCTTGCTGCTA 57.078 39.130 0.00 0.00 0.00 3.49
122 123 5.655488 TCTCTAGTTCATTCTTGCTGCTAC 58.345 41.667 0.00 0.00 0.00 3.58
123 124 5.420421 TCTCTAGTTCATTCTTGCTGCTACT 59.580 40.000 0.00 0.00 0.00 2.57
124 125 5.414360 TCTAGTTCATTCTTGCTGCTACTG 58.586 41.667 0.00 0.00 0.00 2.74
125 126 4.013267 AGTTCATTCTTGCTGCTACTGT 57.987 40.909 0.00 0.00 0.00 3.55
126 127 5.152623 AGTTCATTCTTGCTGCTACTGTA 57.847 39.130 0.00 0.00 0.00 2.74
127 128 5.551233 AGTTCATTCTTGCTGCTACTGTAA 58.449 37.500 0.00 0.00 0.00 2.41
128 129 5.997746 AGTTCATTCTTGCTGCTACTGTAAA 59.002 36.000 0.00 0.00 0.00 2.01
129 130 6.486657 AGTTCATTCTTGCTGCTACTGTAAAA 59.513 34.615 0.00 0.00 0.00 1.52
130 131 6.875948 TCATTCTTGCTGCTACTGTAAAAA 57.124 33.333 0.00 0.00 0.00 1.94
131 132 6.902341 TCATTCTTGCTGCTACTGTAAAAAG 58.098 36.000 0.00 0.00 0.00 2.27
132 133 6.710295 TCATTCTTGCTGCTACTGTAAAAAGA 59.290 34.615 0.00 0.00 0.00 2.52
133 134 6.935741 TTCTTGCTGCTACTGTAAAAAGAA 57.064 33.333 0.00 1.71 31.79 2.52
134 135 7.510549 TTCTTGCTGCTACTGTAAAAAGAAT 57.489 32.000 0.00 0.00 29.87 2.40
135 136 7.510549 TCTTGCTGCTACTGTAAAAAGAATT 57.489 32.000 0.00 0.00 0.00 2.17
136 137 7.362662 TCTTGCTGCTACTGTAAAAAGAATTG 58.637 34.615 0.00 0.00 0.00 2.32
137 138 5.460646 TGCTGCTACTGTAAAAAGAATTGC 58.539 37.500 0.00 0.00 0.00 3.56
138 139 5.241506 TGCTGCTACTGTAAAAAGAATTGCT 59.758 36.000 0.00 0.00 0.00 3.91
139 140 6.152379 GCTGCTACTGTAAAAAGAATTGCTT 58.848 36.000 0.00 0.00 38.88 3.91
140 141 6.306596 GCTGCTACTGTAAAAAGAATTGCTTC 59.693 38.462 0.00 0.00 35.24 3.86
141 142 7.510549 TGCTACTGTAAAAAGAATTGCTTCT 57.489 32.000 0.00 0.00 43.71 2.85
142 143 7.362662 TGCTACTGTAAAAAGAATTGCTTCTG 58.637 34.615 0.00 0.00 40.93 3.02
143 144 7.228507 TGCTACTGTAAAAAGAATTGCTTCTGA 59.771 33.333 0.00 0.00 40.93 3.27
144 145 8.076178 GCTACTGTAAAAAGAATTGCTTCTGAA 58.924 33.333 0.00 0.00 40.93 3.02
145 146 9.950680 CTACTGTAAAAAGAATTGCTTCTGAAA 57.049 29.630 0.00 0.00 40.93 2.69
147 148 9.822185 ACTGTAAAAAGAATTGCTTCTGAAAAT 57.178 25.926 0.00 0.00 40.93 1.82
151 152 8.969260 AAAAAGAATTGCTTCTGAAAATTCCT 57.031 26.923 17.60 7.83 40.93 3.36
152 153 7.958053 AAAGAATTGCTTCTGAAAATTCCTG 57.042 32.000 17.60 0.00 40.93 3.86
159 160 6.684686 TGCTTCTGAAAATTCCTGAGATTTG 58.315 36.000 0.00 0.00 0.00 2.32
163 164 6.243900 TCTGAAAATTCCTGAGATTTGAGCT 58.756 36.000 0.00 0.00 0.00 4.09
164 165 6.718454 TCTGAAAATTCCTGAGATTTGAGCTT 59.282 34.615 0.00 0.00 0.00 3.74
171 172 4.214119 TCCTGAGATTTGAGCTTTTTCGTG 59.786 41.667 0.00 0.00 0.00 4.35
175 176 5.100751 AGATTTGAGCTTTTTCGTGTGAG 57.899 39.130 0.00 0.00 0.00 3.51
209 210 9.452287 AAAATTCCTATAAAATGCAGTGCAATT 57.548 25.926 23.90 18.01 43.62 2.32
229 230 6.238484 GCAATTAATTCGTTAGGAGCTGATGT 60.238 38.462 0.00 0.00 0.00 3.06
241 242 1.034292 GCTGATGTTCCTCCAAGGGC 61.034 60.000 0.00 0.00 35.59 5.19
242 243 0.745845 CTGATGTTCCTCCAAGGGCG 60.746 60.000 0.00 0.00 35.59 6.13
243 244 1.299976 GATGTTCCTCCAAGGGCGT 59.700 57.895 0.00 0.00 35.59 5.68
244 245 0.744771 GATGTTCCTCCAAGGGCGTC 60.745 60.000 0.00 0.00 35.59 5.19
245 246 2.434359 GTTCCTCCAAGGGCGTCG 60.434 66.667 0.00 0.00 35.59 5.12
246 247 2.920912 TTCCTCCAAGGGCGTCGT 60.921 61.111 0.00 0.00 35.59 4.34
247 248 2.939261 TTCCTCCAAGGGCGTCGTC 61.939 63.158 0.00 0.00 35.59 4.20
248 249 4.452733 CCTCCAAGGGCGTCGTCC 62.453 72.222 8.12 8.12 0.00 4.79
249 250 4.796231 CTCCAAGGGCGTCGTCCG 62.796 72.222 10.84 0.00 40.40 4.79
252 253 4.351938 CAAGGGCGTCGTCCGTCA 62.352 66.667 10.84 0.00 44.95 4.35
253 254 3.379445 AAGGGCGTCGTCCGTCAT 61.379 61.111 10.84 0.00 44.95 3.06
254 255 2.939261 AAGGGCGTCGTCCGTCATT 61.939 57.895 10.84 0.00 44.95 2.57
255 256 2.830704 AAGGGCGTCGTCCGTCATTC 62.831 60.000 10.84 0.00 42.05 2.67
256 257 2.884207 GGCGTCGTCCGTCATTCC 60.884 66.667 0.00 0.00 41.97 3.01
257 258 2.126228 GCGTCGTCCGTCATTCCA 60.126 61.111 0.00 0.00 39.32 3.53
258 259 1.735198 GCGTCGTCCGTCATTCCAA 60.735 57.895 0.00 0.00 39.32 3.53
259 260 1.683790 GCGTCGTCCGTCATTCCAAG 61.684 60.000 0.00 0.00 39.32 3.61
260 261 1.076533 CGTCGTCCGTCATTCCAAGG 61.077 60.000 0.00 0.00 0.00 3.61
261 262 0.739813 GTCGTCCGTCATTCCAAGGG 60.740 60.000 0.00 0.00 0.00 3.95
262 263 2.106683 CGTCCGTCATTCCAAGGGC 61.107 63.158 0.00 0.00 0.00 5.19
263 264 1.749258 GTCCGTCATTCCAAGGGCC 60.749 63.158 0.00 0.00 0.00 5.80
264 265 2.227757 TCCGTCATTCCAAGGGCCA 61.228 57.895 6.18 0.00 0.00 5.36
265 266 1.750399 CCGTCATTCCAAGGGCCAG 60.750 63.158 6.18 0.00 0.00 4.85
266 267 1.750399 CGTCATTCCAAGGGCCAGG 60.750 63.158 6.18 7.63 0.00 4.45
267 268 1.380380 GTCATTCCAAGGGCCAGGG 60.380 63.158 6.18 6.75 0.00 4.45
268 269 2.042639 CATTCCAAGGGCCAGGGG 60.043 66.667 6.18 3.71 0.00 4.79
279 280 3.612251 CCAGGGGCATGCTTCTTG 58.388 61.111 18.92 15.66 0.00 3.02
280 281 1.304713 CCAGGGGCATGCTTCTTGT 60.305 57.895 18.92 0.00 0.00 3.16
281 282 0.034186 CCAGGGGCATGCTTCTTGTA 60.034 55.000 18.92 0.00 0.00 2.41
282 283 1.410648 CCAGGGGCATGCTTCTTGTAT 60.411 52.381 18.92 0.00 0.00 2.29
283 284 1.679680 CAGGGGCATGCTTCTTGTATG 59.320 52.381 18.92 2.08 40.94 2.39
284 285 1.285962 AGGGGCATGCTTCTTGTATGT 59.714 47.619 18.92 0.00 40.27 2.29
285 286 2.102578 GGGGCATGCTTCTTGTATGTT 58.897 47.619 18.92 0.00 40.27 2.71
286 287 2.159198 GGGGCATGCTTCTTGTATGTTG 60.159 50.000 18.92 0.00 40.27 3.33
287 288 2.493278 GGGCATGCTTCTTGTATGTTGT 59.507 45.455 18.92 0.00 40.27 3.32
288 289 3.056607 GGGCATGCTTCTTGTATGTTGTT 60.057 43.478 18.92 0.00 40.27 2.83
289 290 4.168760 GGCATGCTTCTTGTATGTTGTTC 58.831 43.478 18.92 0.00 40.27 3.18
290 291 3.848019 GCATGCTTCTTGTATGTTGTTCG 59.152 43.478 11.37 0.00 40.27 3.95
291 292 4.613622 GCATGCTTCTTGTATGTTGTTCGT 60.614 41.667 11.37 0.00 40.27 3.85
292 293 5.451908 CATGCTTCTTGTATGTTGTTCGTT 58.548 37.500 0.00 0.00 34.66 3.85
293 294 5.090652 TGCTTCTTGTATGTTGTTCGTTC 57.909 39.130 0.00 0.00 0.00 3.95
294 295 4.141680 GCTTCTTGTATGTTGTTCGTTCG 58.858 43.478 0.00 0.00 0.00 3.95
295 296 4.698276 CTTCTTGTATGTTGTTCGTTCGG 58.302 43.478 0.00 0.00 0.00 4.30
296 297 3.061322 TCTTGTATGTTGTTCGTTCGGG 58.939 45.455 0.00 0.00 0.00 5.14
297 298 2.816204 TGTATGTTGTTCGTTCGGGA 57.184 45.000 0.00 0.00 0.00 5.14
298 299 2.679450 TGTATGTTGTTCGTTCGGGAG 58.321 47.619 0.00 0.00 0.00 4.30
299 300 2.296752 TGTATGTTGTTCGTTCGGGAGA 59.703 45.455 0.00 0.00 0.00 3.71
300 301 2.080286 ATGTTGTTCGTTCGGGAGAG 57.920 50.000 0.00 0.00 41.75 3.20
311 312 2.270527 GGGAGAGCTCTTGGTGGC 59.729 66.667 19.36 3.24 0.00 5.01
312 313 2.297129 GGGAGAGCTCTTGGTGGCT 61.297 63.158 19.36 0.00 41.88 4.75
316 317 1.220477 GAGCTCTTGGTGGCTCCTC 59.780 63.158 6.43 0.00 46.32 3.71
343 344 0.601558 AAGTCGGAGTCGCTTGCTAA 59.398 50.000 0.00 0.00 33.78 3.09
347 348 1.153349 GGAGTCGCTTGCTAAGGGG 60.153 63.158 11.18 0.00 41.38 4.79
419 420 4.564110 GGGTAGCCATGTCCGCCC 62.564 72.222 5.96 0.00 0.00 6.13
458 461 4.095782 TGGGCATGTTCTAATAGTTTTCGC 59.904 41.667 0.00 0.00 0.00 4.70
467 470 4.866486 TCTAATAGTTTTCGCCCGAGTTTC 59.134 41.667 0.00 0.00 0.00 2.78
469 472 1.205820 GTTTTCGCCCGAGTTTCCG 59.794 57.895 0.00 0.00 0.00 4.30
470 473 2.609759 TTTTCGCCCGAGTTTCCGC 61.610 57.895 0.00 0.00 0.00 5.54
487 491 2.000447 CCGCAAACTAGCTAGTCAACC 59.000 52.381 26.21 13.68 34.99 3.77
584 588 7.936584 AGAAAGTCTTATAAGATCGAGTCCTG 58.063 38.462 17.95 0.00 37.39 3.86
588 594 6.261381 AGTCTTATAAGATCGAGTCCTGTGAC 59.739 42.308 17.95 1.63 38.37 3.67
589 595 6.038382 GTCTTATAAGATCGAGTCCTGTGACA 59.962 42.308 17.95 0.00 39.54 3.58
718 724 7.147312 TCTAAGTTTTCATGTGCCTTGAAATG 58.853 34.615 13.26 0.00 41.36 2.32
720 726 5.916318 AGTTTTCATGTGCCTTGAAATGAA 58.084 33.333 13.26 1.58 41.36 2.57
728 734 9.504708 TCATGTGCCTTGAAATGAAATATTTTT 57.495 25.926 1.43 0.00 0.00 1.94
779 785 8.642935 TGGTATTTTCATGTACCTTGAAATGA 57.357 30.769 17.05 4.96 41.36 2.57
801 811 9.468532 AATGATTCTTTTTGAAGCTTGTTCTAC 57.531 29.630 2.10 0.00 41.29 2.59
826 837 4.810491 GTGTTTTCATGTGCCTTGAAATGT 59.190 37.500 13.26 0.00 41.36 2.71
827 838 5.294060 GTGTTTTCATGTGCCTTGAAATGTT 59.706 36.000 13.26 0.00 41.36 2.71
1041 1058 1.971505 CTTATCCACAGCCGCTCCCA 61.972 60.000 0.00 0.00 0.00 4.37
1044 1061 4.767255 CCACAGCCGCTCCCACTC 62.767 72.222 0.00 0.00 0.00 3.51
1087 1104 2.973082 GTGCCCACCTCAAATGGC 59.027 61.111 0.00 0.00 44.27 4.40
1188 1217 0.666374 CAACCAACCCAAGAACCGTC 59.334 55.000 0.00 0.00 0.00 4.79
1276 1305 2.441378 TTCGACGAAATGCCTCGCG 61.441 57.895 8.05 0.00 42.69 5.87
1277 1306 3.179265 CGACGAAATGCCTCGCGT 61.179 61.111 5.77 0.00 42.69 6.01
1309 1338 3.792047 CGAGCGTACGTGACCCGA 61.792 66.667 17.90 0.00 40.70 5.14
1585 1614 2.022346 TCAGCGCGTACGTCGATC 59.978 61.111 27.63 15.29 42.83 3.69
1733 1762 4.445710 AATGCGGCATGCTGGGGA 62.446 61.111 27.34 13.85 46.63 4.81
1772 1801 1.278985 TCTTGTGATGGCGATTCAGGT 59.721 47.619 0.00 0.00 0.00 4.00
1793 1822 2.026014 CAGTGCGTTGTTGTGCCC 59.974 61.111 0.00 0.00 0.00 5.36
1800 1829 2.181521 GTTGTTGTGCCCGGTTCGA 61.182 57.895 0.00 0.00 0.00 3.71
1815 1844 2.124819 CGAGGGAAGCAGCTGCAT 60.125 61.111 38.24 29.24 45.16 3.96
1848 1877 2.497273 CGCCCTTGGATTTGAAAGGAAT 59.503 45.455 3.01 0.00 44.93 3.01
1854 1883 5.716703 CCTTGGATTTGAAAGGAATACCACT 59.283 40.000 0.00 0.00 44.93 4.00
1872 1901 1.277557 ACTGTCTGGAACTGCCTCATC 59.722 52.381 0.00 0.00 37.63 2.92
1893 1922 2.017049 GACATGTATGGGAAGTGTGGC 58.983 52.381 0.00 0.00 0.00 5.01
1950 1979 2.159028 GGTAGACAGGGATCAAGTGAGC 60.159 54.545 0.00 0.00 0.00 4.26
2038 2067 2.230508 CAGATGCAGCAATGTGGTTTCT 59.769 45.455 4.07 0.00 0.00 2.52
2043 2072 2.813754 GCAGCAATGTGGTTTCTCTGTA 59.186 45.455 0.00 0.00 0.00 2.74
2046 2075 4.153117 CAGCAATGTGGTTTCTCTGTAGAC 59.847 45.833 0.00 0.00 0.00 2.59
2137 2166 9.021807 CATTCCATGGCTATTTGATAAGAAGAT 57.978 33.333 6.96 0.00 0.00 2.40
2196 2225 1.400494 GACATGTACGGGAAATGTGGC 59.600 52.381 0.00 0.00 34.74 5.01
2253 2282 8.000709 AGAATGGATGAAAGGAATTATGTAGCA 58.999 33.333 0.00 0.00 0.00 3.49
2337 2366 2.489329 CCGACAAATGGAGTCTGCAAAT 59.511 45.455 0.00 0.00 33.89 2.32
2358 2387 8.630037 GCAAATATAAAGCCTAACCAACATACT 58.370 33.333 0.00 0.00 0.00 2.12
2403 2432 4.901197 TGGCAACAGAAGGTATACAGAA 57.099 40.909 5.01 0.00 46.17 3.02
2406 2435 6.346096 TGGCAACAGAAGGTATACAGAATAC 58.654 40.000 5.01 0.00 46.17 1.89
2409 2438 5.786264 ACAGAAGGTATACAGAATACGGG 57.214 43.478 5.01 0.00 41.32 5.28
2529 2558 1.002315 GTTGCCCGGTTACTGTTCCTA 59.998 52.381 0.00 0.00 0.00 2.94
2562 2591 4.837218 AGAGGAACCTGATATCCTGGAAT 58.163 43.478 15.98 0.00 46.04 3.01
2753 2782 6.244552 TGTCATTAAGATTGGCTCTGAGAT 57.755 37.500 9.28 0.00 33.29 2.75
2781 2810 3.194542 TGGTGCTGCAAACTTTACTTGTT 59.805 39.130 2.77 0.00 0.00 2.83
2841 2870 2.298629 CGTCTGCGCGATGATCCAG 61.299 63.158 12.10 6.55 0.00 3.86
2850 2879 1.622811 GCGATGATCCAGGAGAGGAAT 59.377 52.381 0.00 0.00 41.92 3.01
2855 2884 5.008415 CGATGATCCAGGAGAGGAATTTTTG 59.992 44.000 0.00 0.00 41.92 2.44
2950 2982 5.065731 GTCCAGTGGAGAAGATAAATGCTTG 59.934 44.000 13.61 0.00 29.39 4.01
2959 2991 6.131961 AGAAGATAAATGCTTGGGTGCTAAT 58.868 36.000 0.00 0.00 0.00 1.73
2960 2992 6.264067 AGAAGATAAATGCTTGGGTGCTAATC 59.736 38.462 0.00 0.00 0.00 1.75
3030 3063 1.205893 AGGCGTTCTCCAGATGTTCTC 59.794 52.381 0.00 0.00 0.00 2.87
3032 3065 1.740718 GCGTTCTCCAGATGTTCTCCC 60.741 57.143 0.00 0.00 0.00 4.30
3059 3092 0.108585 AAACAGGGCAGAGCTTCGAA 59.891 50.000 0.00 0.00 0.00 3.71
3065 3098 1.372087 GGCAGAGCTTCGAACCATGG 61.372 60.000 11.19 11.19 0.00 3.66
3216 3259 2.068519 GCAAATGGCTGGTAGTTTTGC 58.931 47.619 3.31 3.31 43.45 3.68
3242 3285 6.377146 AGTGTTGTTTACCACTGACTTTCATT 59.623 34.615 0.00 0.00 0.00 2.57
3268 3311 0.901124 GCTCACACAGGGTCTCTCAT 59.099 55.000 0.00 0.00 0.00 2.90
3319 3421 5.934625 CCTTGCACTTCTTGTAATAGTCAGT 59.065 40.000 0.00 0.00 0.00 3.41
3331 3433 1.595311 TAGTCAGTGGCAATGGGGAT 58.405 50.000 15.62 1.56 0.00 3.85
3333 3435 1.077663 AGTCAGTGGCAATGGGGATTT 59.922 47.619 15.62 0.00 0.00 2.17
3433 3562 4.084171 CCGATAGCAATCTTGTGTGCATAG 60.084 45.833 0.00 0.00 43.42 2.23
3488 3617 3.123050 TGTTGATCTGTCGTGTGTCTTG 58.877 45.455 0.00 0.00 0.00 3.02
3556 3696 2.436173 ACCTAGGAGTATCAGCAAAGGC 59.564 50.000 17.98 0.00 36.25 4.35
3591 3731 1.722011 ACCAGCCGTAGAAAATGACG 58.278 50.000 0.00 0.00 38.79 4.35
3592 3732 1.274167 ACCAGCCGTAGAAAATGACGA 59.726 47.619 0.00 0.00 41.60 4.20
3594 3734 1.927174 CAGCCGTAGAAAATGACGAGG 59.073 52.381 0.00 0.00 41.60 4.63
3595 3735 1.822990 AGCCGTAGAAAATGACGAGGA 59.177 47.619 0.00 0.00 41.60 3.71
3596 3736 2.232941 AGCCGTAGAAAATGACGAGGAA 59.767 45.455 0.00 0.00 41.60 3.36
3597 3737 2.997986 GCCGTAGAAAATGACGAGGAAA 59.002 45.455 0.00 0.00 41.60 3.13
3598 3738 3.621715 GCCGTAGAAAATGACGAGGAAAT 59.378 43.478 0.00 0.00 41.60 2.17
3599 3739 4.807304 GCCGTAGAAAATGACGAGGAAATA 59.193 41.667 0.00 0.00 41.60 1.40
3600 3740 5.050972 GCCGTAGAAAATGACGAGGAAATAG 60.051 44.000 0.00 0.00 41.60 1.73
3601 3741 6.040878 CCGTAGAAAATGACGAGGAAATAGT 58.959 40.000 0.00 0.00 41.60 2.12
3602 3742 6.198591 CCGTAGAAAATGACGAGGAAATAGTC 59.801 42.308 0.00 0.00 41.60 2.59
3608 3748 4.920640 TGACGAGGAAATAGTCATCTCC 57.079 45.455 0.00 0.00 38.46 3.71
3609 3749 4.278310 TGACGAGGAAATAGTCATCTCCA 58.722 43.478 0.00 0.00 38.46 3.86
3610 3750 4.339530 TGACGAGGAAATAGTCATCTCCAG 59.660 45.833 0.00 0.00 38.46 3.86
3611 3751 4.282496 ACGAGGAAATAGTCATCTCCAGT 58.718 43.478 0.00 0.00 34.80 4.00
3612 3752 4.339814 ACGAGGAAATAGTCATCTCCAGTC 59.660 45.833 0.00 0.00 34.80 3.51
3613 3753 4.339530 CGAGGAAATAGTCATCTCCAGTCA 59.660 45.833 0.00 0.00 34.80 3.41
3615 3755 6.207614 CGAGGAAATAGTCATCTCCAGTCATA 59.792 42.308 0.00 0.00 34.80 2.15
3616 3756 7.255625 CGAGGAAATAGTCATCTCCAGTCATAA 60.256 40.741 0.00 0.00 34.80 1.90
3618 3758 8.772250 AGGAAATAGTCATCTCCAGTCATAAAA 58.228 33.333 0.00 0.00 0.00 1.52
3665 3816 2.349886 GCTGCTTCTACGATTTCTGTGG 59.650 50.000 0.00 0.00 0.00 4.17
3712 3866 9.492730 TCCATAGCAATATACAGATATTCAGGA 57.507 33.333 0.00 0.00 36.31 3.86
3747 3901 5.414454 TGCATAAAGTGAGTCCATAACCAAC 59.586 40.000 0.00 0.00 0.00 3.77
3749 3903 4.447138 AAAGTGAGTCCATAACCAACCA 57.553 40.909 0.00 0.00 0.00 3.67
3798 3982 4.795278 GCAGAGCACACTTTATGTTAATGC 59.205 41.667 0.00 0.00 40.64 3.56
3827 4011 0.387622 TACACTTGTACACGCTCGCC 60.388 55.000 0.00 0.00 0.00 5.54
3847 4031 3.807209 GCCTCCTAAACAGAAAGCACAGA 60.807 47.826 0.00 0.00 0.00 3.41
3868 4084 4.101585 AGACAATCCTCACAAACTCTCACA 59.898 41.667 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.202200 CGCTAGACCACAGTACAGCTC 60.202 57.143 0.00 0.00 32.97 4.09
1 2 0.811915 CGCTAGACCACAGTACAGCT 59.188 55.000 0.00 0.00 32.97 4.24
2 3 0.179134 CCGCTAGACCACAGTACAGC 60.179 60.000 0.00 0.00 32.19 4.40
3 4 1.135373 CACCGCTAGACCACAGTACAG 60.135 57.143 0.00 0.00 0.00 2.74
4 5 0.885879 CACCGCTAGACCACAGTACA 59.114 55.000 0.00 0.00 0.00 2.90
5 6 0.458025 GCACCGCTAGACCACAGTAC 60.458 60.000 0.00 0.00 0.00 2.73
6 7 0.896479 TGCACCGCTAGACCACAGTA 60.896 55.000 0.00 0.00 0.00 2.74
7 8 2.159819 CTGCACCGCTAGACCACAGT 62.160 60.000 0.00 0.00 0.00 3.55
8 9 1.446792 CTGCACCGCTAGACCACAG 60.447 63.158 0.00 0.00 0.00 3.66
9 10 2.656646 CTGCACCGCTAGACCACA 59.343 61.111 0.00 0.00 0.00 4.17
10 11 2.815647 GCTGCACCGCTAGACCAC 60.816 66.667 0.00 0.00 0.00 4.16
11 12 4.435436 CGCTGCACCGCTAGACCA 62.435 66.667 0.00 0.00 0.00 4.02
12 13 4.129737 TCGCTGCACCGCTAGACC 62.130 66.667 0.00 0.00 0.00 3.85
13 14 2.881352 GTCGCTGCACCGCTAGAC 60.881 66.667 0.00 0.00 0.00 2.59
14 15 4.476410 CGTCGCTGCACCGCTAGA 62.476 66.667 0.00 0.00 0.00 2.43
20 21 0.458889 TATAACACCGTCGCTGCACC 60.459 55.000 0.00 0.00 0.00 5.01
21 22 0.643820 GTATAACACCGTCGCTGCAC 59.356 55.000 0.00 0.00 0.00 4.57
22 23 0.244178 TGTATAACACCGTCGCTGCA 59.756 50.000 0.00 0.00 0.00 4.41
23 24 0.643820 GTGTATAACACCGTCGCTGC 59.356 55.000 0.00 0.00 43.05 5.25
33 34 5.942826 TGGCAATCAACAGATGTGTATAACA 59.057 36.000 0.00 0.00 44.79 2.41
34 35 6.258160 GTGGCAATCAACAGATGTGTATAAC 58.742 40.000 0.00 0.00 35.08 1.89
35 36 5.064579 CGTGGCAATCAACAGATGTGTATAA 59.935 40.000 0.00 0.00 35.08 0.98
36 37 4.570369 CGTGGCAATCAACAGATGTGTATA 59.430 41.667 0.00 0.00 35.08 1.47
37 38 3.374988 CGTGGCAATCAACAGATGTGTAT 59.625 43.478 0.00 0.00 35.08 2.29
38 39 2.741517 CGTGGCAATCAACAGATGTGTA 59.258 45.455 0.00 0.00 35.08 2.90
39 40 1.536766 CGTGGCAATCAACAGATGTGT 59.463 47.619 0.00 0.00 39.19 3.72
40 41 1.730121 GCGTGGCAATCAACAGATGTG 60.730 52.381 0.00 0.00 0.00 3.21
41 42 0.523072 GCGTGGCAATCAACAGATGT 59.477 50.000 0.00 0.00 0.00 3.06
42 43 0.522626 TGCGTGGCAATCAACAGATG 59.477 50.000 0.00 0.00 34.76 2.90
43 44 1.246649 TTGCGTGGCAATCAACAGAT 58.753 45.000 0.00 0.00 43.99 2.90
44 45 2.712984 TTGCGTGGCAATCAACAGA 58.287 47.368 0.00 0.00 43.99 3.41
52 53 1.661498 TTTCAGCACTTGCGTGGCAA 61.661 50.000 2.77 2.77 46.80 4.52
59 60 1.405105 TCCAACAGTTTCAGCACTTGC 59.595 47.619 0.00 0.00 42.49 4.01
60 61 3.067180 ACATCCAACAGTTTCAGCACTTG 59.933 43.478 0.00 0.00 0.00 3.16
61 62 3.067180 CACATCCAACAGTTTCAGCACTT 59.933 43.478 0.00 0.00 0.00 3.16
62 63 2.620115 CACATCCAACAGTTTCAGCACT 59.380 45.455 0.00 0.00 0.00 4.40
63 64 2.358898 ACACATCCAACAGTTTCAGCAC 59.641 45.455 0.00 0.00 0.00 4.40
64 65 2.358582 CACACATCCAACAGTTTCAGCA 59.641 45.455 0.00 0.00 0.00 4.41
65 66 2.859806 GCACACATCCAACAGTTTCAGC 60.860 50.000 0.00 0.00 0.00 4.26
66 67 2.620115 AGCACACATCCAACAGTTTCAG 59.380 45.455 0.00 0.00 0.00 3.02
67 68 2.653726 AGCACACATCCAACAGTTTCA 58.346 42.857 0.00 0.00 0.00 2.69
68 69 3.066621 TGAAGCACACATCCAACAGTTTC 59.933 43.478 0.00 0.00 0.00 2.78
69 70 3.023119 TGAAGCACACATCCAACAGTTT 58.977 40.909 0.00 0.00 0.00 2.66
70 71 2.653726 TGAAGCACACATCCAACAGTT 58.346 42.857 0.00 0.00 0.00 3.16
71 72 2.346766 TGAAGCACACATCCAACAGT 57.653 45.000 0.00 0.00 0.00 3.55
72 73 3.571571 CAATGAAGCACACATCCAACAG 58.428 45.455 0.00 0.00 0.00 3.16
73 74 2.296752 CCAATGAAGCACACATCCAACA 59.703 45.455 0.00 0.00 0.00 3.33
74 75 2.927871 GCCAATGAAGCACACATCCAAC 60.928 50.000 0.00 0.00 0.00 3.77
75 76 1.273048 GCCAATGAAGCACACATCCAA 59.727 47.619 0.00 0.00 0.00 3.53
76 77 0.889994 GCCAATGAAGCACACATCCA 59.110 50.000 0.00 0.00 0.00 3.41
77 78 1.135199 CAGCCAATGAAGCACACATCC 60.135 52.381 0.00 0.00 0.00 3.51
78 79 1.542915 ACAGCCAATGAAGCACACATC 59.457 47.619 0.00 0.00 0.00 3.06
79 80 1.624336 ACAGCCAATGAAGCACACAT 58.376 45.000 0.00 0.00 0.00 3.21
80 81 1.337703 GAACAGCCAATGAAGCACACA 59.662 47.619 0.00 0.00 0.00 3.72
81 82 1.610522 AGAACAGCCAATGAAGCACAC 59.389 47.619 0.00 0.00 0.00 3.82
82 83 1.881973 GAGAACAGCCAATGAAGCACA 59.118 47.619 0.00 0.00 0.00 4.57
83 84 2.157738 AGAGAACAGCCAATGAAGCAC 58.842 47.619 0.00 0.00 0.00 4.40
84 85 2.574006 AGAGAACAGCCAATGAAGCA 57.426 45.000 0.00 0.00 0.00 3.91
85 86 3.604582 ACTAGAGAACAGCCAATGAAGC 58.395 45.455 0.00 0.00 0.00 3.86
86 87 5.240891 TGAACTAGAGAACAGCCAATGAAG 58.759 41.667 0.00 0.00 0.00 3.02
87 88 5.227569 TGAACTAGAGAACAGCCAATGAA 57.772 39.130 0.00 0.00 0.00 2.57
88 89 4.890158 TGAACTAGAGAACAGCCAATGA 57.110 40.909 0.00 0.00 0.00 2.57
89 90 5.879223 AGAATGAACTAGAGAACAGCCAATG 59.121 40.000 0.00 0.00 0.00 2.82
90 91 6.059787 AGAATGAACTAGAGAACAGCCAAT 57.940 37.500 0.00 0.00 0.00 3.16
91 92 5.489792 AGAATGAACTAGAGAACAGCCAA 57.510 39.130 0.00 0.00 0.00 4.52
92 93 5.240891 CAAGAATGAACTAGAGAACAGCCA 58.759 41.667 0.00 0.00 0.00 4.75
93 94 4.094146 GCAAGAATGAACTAGAGAACAGCC 59.906 45.833 0.00 0.00 0.00 4.85
94 95 4.934602 AGCAAGAATGAACTAGAGAACAGC 59.065 41.667 0.00 0.00 0.00 4.40
95 96 5.163874 GCAGCAAGAATGAACTAGAGAACAG 60.164 44.000 0.00 0.00 0.00 3.16
96 97 4.692625 GCAGCAAGAATGAACTAGAGAACA 59.307 41.667 0.00 0.00 0.00 3.18
97 98 4.934602 AGCAGCAAGAATGAACTAGAGAAC 59.065 41.667 0.00 0.00 0.00 3.01
98 99 5.157940 AGCAGCAAGAATGAACTAGAGAA 57.842 39.130 0.00 0.00 0.00 2.87
99 100 4.815533 AGCAGCAAGAATGAACTAGAGA 57.184 40.909 0.00 0.00 0.00 3.10
100 101 5.519566 CAGTAGCAGCAAGAATGAACTAGAG 59.480 44.000 0.00 0.00 0.00 2.43
101 102 5.047021 ACAGTAGCAGCAAGAATGAACTAGA 60.047 40.000 0.00 0.00 0.00 2.43
102 103 5.174395 ACAGTAGCAGCAAGAATGAACTAG 58.826 41.667 0.00 0.00 0.00 2.57
103 104 5.152623 ACAGTAGCAGCAAGAATGAACTA 57.847 39.130 0.00 0.00 0.00 2.24
104 105 4.013267 ACAGTAGCAGCAAGAATGAACT 57.987 40.909 0.00 0.00 0.00 3.01
105 106 5.862924 TTACAGTAGCAGCAAGAATGAAC 57.137 39.130 0.00 0.00 0.00 3.18
106 107 6.875948 TTTTACAGTAGCAGCAAGAATGAA 57.124 33.333 0.00 0.00 0.00 2.57
107 108 6.710295 TCTTTTTACAGTAGCAGCAAGAATGA 59.290 34.615 0.00 0.00 0.00 2.57
108 109 6.902341 TCTTTTTACAGTAGCAGCAAGAATG 58.098 36.000 0.00 0.00 0.00 2.67
109 110 7.510549 TTCTTTTTACAGTAGCAGCAAGAAT 57.489 32.000 0.00 0.00 0.00 2.40
110 111 6.935741 TTCTTTTTACAGTAGCAGCAAGAA 57.064 33.333 0.00 0.00 0.00 2.52
111 112 7.362662 CAATTCTTTTTACAGTAGCAGCAAGA 58.637 34.615 0.00 0.00 0.00 3.02
112 113 6.088616 GCAATTCTTTTTACAGTAGCAGCAAG 59.911 38.462 0.00 0.00 0.00 4.01
113 114 5.920273 GCAATTCTTTTTACAGTAGCAGCAA 59.080 36.000 0.00 0.00 0.00 3.91
114 115 5.241506 AGCAATTCTTTTTACAGTAGCAGCA 59.758 36.000 0.00 0.00 0.00 4.41
115 116 5.703876 AGCAATTCTTTTTACAGTAGCAGC 58.296 37.500 0.00 0.00 0.00 5.25
116 117 7.536622 CAGAAGCAATTCTTTTTACAGTAGCAG 59.463 37.037 0.00 0.00 34.56 4.24
117 118 7.228507 TCAGAAGCAATTCTTTTTACAGTAGCA 59.771 33.333 0.00 0.00 34.56 3.49
118 119 7.584987 TCAGAAGCAATTCTTTTTACAGTAGC 58.415 34.615 0.00 0.00 34.56 3.58
119 120 9.950680 TTTCAGAAGCAATTCTTTTTACAGTAG 57.049 29.630 0.00 0.00 34.56 2.57
121 122 9.822185 ATTTTCAGAAGCAATTCTTTTTACAGT 57.178 25.926 0.00 0.00 34.56 3.55
126 127 8.833493 CAGGAATTTTCAGAAGCAATTCTTTTT 58.167 29.630 15.42 2.97 37.18 1.94
127 128 8.206189 TCAGGAATTTTCAGAAGCAATTCTTTT 58.794 29.630 15.42 4.64 37.18 2.27
128 129 7.729116 TCAGGAATTTTCAGAAGCAATTCTTT 58.271 30.769 15.42 6.32 37.18 2.52
129 130 7.232127 TCTCAGGAATTTTCAGAAGCAATTCTT 59.768 33.333 15.42 8.74 37.18 2.52
130 131 6.718454 TCTCAGGAATTTTCAGAAGCAATTCT 59.282 34.615 15.42 4.52 37.18 2.40
131 132 6.917533 TCTCAGGAATTTTCAGAAGCAATTC 58.082 36.000 10.23 10.23 36.55 2.17
132 133 6.906157 TCTCAGGAATTTTCAGAAGCAATT 57.094 33.333 0.00 0.00 0.00 2.32
133 134 7.477945 AATCTCAGGAATTTTCAGAAGCAAT 57.522 32.000 0.00 0.00 0.00 3.56
134 135 6.906157 AATCTCAGGAATTTTCAGAAGCAA 57.094 33.333 0.00 0.00 0.00 3.91
135 136 6.491062 TCAAATCTCAGGAATTTTCAGAAGCA 59.509 34.615 0.00 0.00 0.00 3.91
136 137 6.917533 TCAAATCTCAGGAATTTTCAGAAGC 58.082 36.000 0.00 0.00 0.00 3.86
137 138 7.028361 GCTCAAATCTCAGGAATTTTCAGAAG 58.972 38.462 0.00 0.00 0.00 2.85
138 139 6.718454 AGCTCAAATCTCAGGAATTTTCAGAA 59.282 34.615 0.00 0.00 0.00 3.02
139 140 6.243900 AGCTCAAATCTCAGGAATTTTCAGA 58.756 36.000 0.00 0.00 0.00 3.27
140 141 6.512342 AGCTCAAATCTCAGGAATTTTCAG 57.488 37.500 0.00 0.00 0.00 3.02
141 142 6.906157 AAGCTCAAATCTCAGGAATTTTCA 57.094 33.333 0.00 0.00 0.00 2.69
142 143 8.599055 AAAAAGCTCAAATCTCAGGAATTTTC 57.401 30.769 0.00 0.00 0.00 2.29
143 144 7.383300 CGAAAAAGCTCAAATCTCAGGAATTTT 59.617 33.333 0.00 0.00 0.00 1.82
144 145 6.865205 CGAAAAAGCTCAAATCTCAGGAATTT 59.135 34.615 0.00 0.00 0.00 1.82
145 146 6.015940 ACGAAAAAGCTCAAATCTCAGGAATT 60.016 34.615 0.00 0.00 0.00 2.17
146 147 5.474876 ACGAAAAAGCTCAAATCTCAGGAAT 59.525 36.000 0.00 0.00 0.00 3.01
147 148 4.821805 ACGAAAAAGCTCAAATCTCAGGAA 59.178 37.500 0.00 0.00 0.00 3.36
148 149 4.214119 CACGAAAAAGCTCAAATCTCAGGA 59.786 41.667 0.00 0.00 0.00 3.86
149 150 4.023707 ACACGAAAAAGCTCAAATCTCAGG 60.024 41.667 0.00 0.00 0.00 3.86
150 151 4.908156 CACACGAAAAAGCTCAAATCTCAG 59.092 41.667 0.00 0.00 0.00 3.35
151 152 4.574421 TCACACGAAAAAGCTCAAATCTCA 59.426 37.500 0.00 0.00 0.00 3.27
152 153 5.095691 TCACACGAAAAAGCTCAAATCTC 57.904 39.130 0.00 0.00 0.00 2.75
159 160 2.210116 TCCACTCACACGAAAAAGCTC 58.790 47.619 0.00 0.00 0.00 4.09
163 164 2.293170 TGCATCCACTCACACGAAAAA 58.707 42.857 0.00 0.00 0.00 1.94
164 165 1.960417 TGCATCCACTCACACGAAAA 58.040 45.000 0.00 0.00 0.00 2.29
171 172 5.841957 ATAGGAATTTTGCATCCACTCAC 57.158 39.130 6.83 0.00 38.23 3.51
175 176 7.495279 TGCATTTTATAGGAATTTTGCATCCAC 59.505 33.333 6.83 0.00 38.23 4.02
209 210 5.128827 AGGAACATCAGCTCCTAACGAATTA 59.871 40.000 0.00 0.00 38.57 1.40
229 230 2.920912 ACGACGCCCTTGGAGGAA 60.921 61.111 0.00 0.00 37.67 3.36
242 243 0.739813 CCCTTGGAATGACGGACGAC 60.740 60.000 0.00 0.00 0.00 4.34
243 244 1.594833 CCCTTGGAATGACGGACGA 59.405 57.895 0.00 0.00 0.00 4.20
244 245 2.106683 GCCCTTGGAATGACGGACG 61.107 63.158 0.00 0.00 0.00 4.79
245 246 1.749258 GGCCCTTGGAATGACGGAC 60.749 63.158 0.00 0.00 0.00 4.79
246 247 2.196997 CTGGCCCTTGGAATGACGGA 62.197 60.000 0.00 0.00 0.00 4.69
247 248 1.750399 CTGGCCCTTGGAATGACGG 60.750 63.158 0.00 0.00 0.00 4.79
248 249 1.750399 CCTGGCCCTTGGAATGACG 60.750 63.158 0.00 0.00 0.00 4.35
249 250 1.380380 CCCTGGCCCTTGGAATGAC 60.380 63.158 0.00 0.00 0.00 3.06
250 251 2.625460 CCCCTGGCCCTTGGAATGA 61.625 63.158 0.00 0.00 0.00 2.57
251 252 2.042639 CCCCTGGCCCTTGGAATG 60.043 66.667 0.00 0.00 0.00 2.67
252 253 4.079961 GCCCCTGGCCCTTGGAAT 62.080 66.667 0.00 0.00 44.06 3.01
262 263 0.034186 TACAAGAAGCATGCCCCTGG 60.034 55.000 15.66 11.76 0.00 4.45
263 264 1.679680 CATACAAGAAGCATGCCCCTG 59.320 52.381 15.66 9.30 0.00 4.45
264 265 1.285962 ACATACAAGAAGCATGCCCCT 59.714 47.619 15.66 8.97 0.00 4.79
265 266 1.767759 ACATACAAGAAGCATGCCCC 58.232 50.000 15.66 6.43 0.00 5.80
266 267 2.493278 ACAACATACAAGAAGCATGCCC 59.507 45.455 15.66 6.84 0.00 5.36
267 268 3.855689 ACAACATACAAGAAGCATGCC 57.144 42.857 15.66 0.00 0.00 4.40
268 269 3.848019 CGAACAACATACAAGAAGCATGC 59.152 43.478 10.51 10.51 0.00 4.06
269 270 5.034554 ACGAACAACATACAAGAAGCATG 57.965 39.130 0.00 0.00 0.00 4.06
270 271 5.614668 CGAACGAACAACATACAAGAAGCAT 60.615 40.000 0.00 0.00 0.00 3.79
271 272 4.318475 CGAACGAACAACATACAAGAAGCA 60.318 41.667 0.00 0.00 0.00 3.91
272 273 4.141680 CGAACGAACAACATACAAGAAGC 58.858 43.478 0.00 0.00 0.00 3.86
273 274 4.377022 CCCGAACGAACAACATACAAGAAG 60.377 45.833 0.00 0.00 0.00 2.85
274 275 3.495377 CCCGAACGAACAACATACAAGAA 59.505 43.478 0.00 0.00 0.00 2.52
275 276 3.061322 CCCGAACGAACAACATACAAGA 58.939 45.455 0.00 0.00 0.00 3.02
276 277 3.061322 TCCCGAACGAACAACATACAAG 58.939 45.455 0.00 0.00 0.00 3.16
277 278 3.061322 CTCCCGAACGAACAACATACAA 58.939 45.455 0.00 0.00 0.00 2.41
278 279 2.296752 TCTCCCGAACGAACAACATACA 59.703 45.455 0.00 0.00 0.00 2.29
279 280 2.921754 CTCTCCCGAACGAACAACATAC 59.078 50.000 0.00 0.00 0.00 2.39
280 281 2.673043 GCTCTCCCGAACGAACAACATA 60.673 50.000 0.00 0.00 0.00 2.29
281 282 1.939838 GCTCTCCCGAACGAACAACAT 60.940 52.381 0.00 0.00 0.00 2.71
282 283 0.599204 GCTCTCCCGAACGAACAACA 60.599 55.000 0.00 0.00 0.00 3.33
283 284 0.319641 AGCTCTCCCGAACGAACAAC 60.320 55.000 0.00 0.00 0.00 3.32
284 285 0.038526 GAGCTCTCCCGAACGAACAA 60.039 55.000 6.43 0.00 0.00 2.83
285 286 0.894184 AGAGCTCTCCCGAACGAACA 60.894 55.000 11.45 0.00 0.00 3.18
286 287 0.244178 AAGAGCTCTCCCGAACGAAC 59.756 55.000 18.55 0.00 0.00 3.95
287 288 0.243907 CAAGAGCTCTCCCGAACGAA 59.756 55.000 18.55 0.00 0.00 3.85
288 289 1.595993 CCAAGAGCTCTCCCGAACGA 61.596 60.000 18.55 0.00 0.00 3.85
289 290 1.153745 CCAAGAGCTCTCCCGAACG 60.154 63.158 18.55 0.00 0.00 3.95
290 291 0.390472 CACCAAGAGCTCTCCCGAAC 60.390 60.000 18.55 0.00 0.00 3.95
291 292 1.544825 CCACCAAGAGCTCTCCCGAA 61.545 60.000 18.55 0.00 0.00 4.30
292 293 1.984570 CCACCAAGAGCTCTCCCGA 60.985 63.158 18.55 0.00 0.00 5.14
293 294 2.581354 CCACCAAGAGCTCTCCCG 59.419 66.667 18.55 9.81 0.00 5.14
294 295 2.270527 GCCACCAAGAGCTCTCCC 59.729 66.667 18.55 0.00 0.00 4.30
295 296 3.397906 AGCCACCAAGAGCTCTCC 58.602 61.111 18.55 1.76 32.71 3.71
299 300 1.537397 TGAGGAGCCACCAAGAGCT 60.537 57.895 0.00 0.00 43.55 4.09
300 301 1.078567 CTGAGGAGCCACCAAGAGC 60.079 63.158 0.47 0.00 42.04 4.09
311 312 0.244994 CCGACTTCACCACTGAGGAG 59.755 60.000 0.00 0.00 41.22 3.69
312 313 0.178973 TCCGACTTCACCACTGAGGA 60.179 55.000 0.00 0.00 41.22 3.71
313 314 0.244994 CTCCGACTTCACCACTGAGG 59.755 60.000 0.00 0.00 45.67 3.86
314 315 0.962489 ACTCCGACTTCACCACTGAG 59.038 55.000 0.00 0.00 0.00 3.35
316 317 0.387367 CGACTCCGACTTCACCACTG 60.387 60.000 0.00 0.00 38.22 3.66
343 344 2.709934 CCATCATCATCACTTCTCCCCT 59.290 50.000 0.00 0.00 0.00 4.79
347 348 2.799412 GACGCCATCATCATCACTTCTC 59.201 50.000 0.00 0.00 0.00 2.87
419 420 2.751166 CCCATAAGATAGGGCACTCG 57.249 55.000 0.00 0.00 38.44 4.18
467 470 2.000447 GGTTGACTAGCTAGTTTGCGG 59.000 52.381 26.71 0.00 36.50 5.69
469 472 3.055747 AGAGGGTTGACTAGCTAGTTTGC 60.056 47.826 26.71 17.93 36.50 3.68
470 473 4.810191 AGAGGGTTGACTAGCTAGTTTG 57.190 45.455 26.71 1.74 36.50 2.93
477 481 5.862678 AAGATAGAAGAGGGTTGACTAGC 57.137 43.478 0.00 0.00 0.00 3.42
572 576 2.628178 TGTTTGTCACAGGACTCGATCT 59.372 45.455 0.00 0.00 44.61 2.75
576 580 2.276201 TGTTGTTTGTCACAGGACTCG 58.724 47.619 0.00 0.00 44.61 4.18
579 583 4.167554 TGTTTGTTGTTTGTCACAGGAC 57.832 40.909 0.00 0.00 44.57 3.85
779 785 6.039382 ACCGTAGAACAAGCTTCAAAAAGAAT 59.961 34.615 0.00 0.00 35.25 2.40
801 811 1.336440 TCAAGGCACATGAAAACACCG 59.664 47.619 0.00 0.00 31.17 4.94
946 959 4.979197 CGGAGTACTACTACTAACGACGAT 59.021 45.833 0.00 0.00 36.35 3.73
995 1012 1.202330 CAGGCAGGAGTCCATCTTCT 58.798 55.000 12.86 0.00 30.84 2.85
1047 1064 2.386935 GGAGGTGGGATTGGAGGGG 61.387 68.421 0.00 0.00 0.00 4.79
1234 1263 3.723348 GTCCGCCGTGTTGGAAGC 61.723 66.667 0.00 0.00 42.00 3.86
1250 1279 1.263217 GCATTTCGTCGAACAGGTTGT 59.737 47.619 7.29 0.00 0.00 3.32
1399 1428 0.743701 CGCATCCTGCAGAAGAGCTT 60.744 55.000 17.39 0.00 45.36 3.74
1507 1536 2.819595 GATGACCACGGCATGCGT 60.820 61.111 12.44 10.45 0.00 5.24
1585 1614 0.954449 GCATCATCCATCAGCCCGAG 60.954 60.000 0.00 0.00 0.00 4.63
1772 1801 1.136356 CACAACAACGCACTGCACA 59.864 52.632 1.11 0.00 0.00 4.57
1793 1822 2.815647 GCTGCTTCCCTCGAACCG 60.816 66.667 0.00 0.00 0.00 4.44
1800 1829 2.754658 GCATGCAGCTGCTTCCCT 60.755 61.111 36.61 15.11 42.66 4.20
1833 1862 5.640147 ACAGTGGTATTCCTTTCAAATCCA 58.360 37.500 0.00 0.00 34.23 3.41
1854 1883 0.247460 CGATGAGGCAGTTCCAGACA 59.753 55.000 0.00 0.00 37.29 3.41
1872 1901 2.279741 CCACACTTCCCATACATGTCG 58.720 52.381 0.00 0.00 0.00 4.35
1893 1922 1.586422 CCCTGCAACTATCCATGTCG 58.414 55.000 0.00 0.00 0.00 4.35
2038 2067 2.496070 CAAGGGTGAATCGGTCTACAGA 59.504 50.000 0.00 0.00 0.00 3.41
2043 2072 1.299976 GCCAAGGGTGAATCGGTCT 59.700 57.895 0.00 0.00 0.00 3.85
2046 2075 1.002134 ACTGCCAAGGGTGAATCGG 60.002 57.895 0.00 0.00 0.00 4.18
2137 2166 4.021981 CCGGATAGCATCAGTGTCTAATGA 60.022 45.833 0.00 0.00 35.12 2.57
2196 2225 0.935898 GTCGAGCATGCTCCATCAAG 59.064 55.000 35.77 23.07 39.77 3.02
2253 2282 1.064906 CCAGACAAGAGTGCATCCCAT 60.065 52.381 0.00 0.00 0.00 4.00
2337 2366 9.523168 ACAAAAGTATGTTGGTTAGGCTTTATA 57.477 29.630 0.00 0.00 37.74 0.98
2403 2432 1.956477 GCATGAATTTGCCTCCCGTAT 59.044 47.619 0.00 0.00 36.60 3.06
2529 2558 2.234908 CAGGTTCCTCTCGTTCATCCTT 59.765 50.000 0.00 0.00 0.00 3.36
2753 2782 1.401761 AGTTTGCAGCACCACATTCA 58.598 45.000 0.00 0.00 0.00 2.57
2781 2810 3.317149 GCCTACACCTGACGTACATATGA 59.683 47.826 10.38 0.00 0.00 2.15
2823 2852 2.278792 TGGATCATCGCGCAGACG 60.279 61.111 8.75 0.00 44.07 4.18
2829 2858 1.175347 TCCTCTCCTGGATCATCGCG 61.175 60.000 0.00 0.00 0.00 5.87
2841 2870 4.022068 TCATGCACACAAAAATTCCTCTCC 60.022 41.667 0.00 0.00 0.00 3.71
2850 2879 2.505628 ACGCATCATGCACACAAAAA 57.494 40.000 11.00 0.00 45.36 1.94
2855 2884 0.247419 CGAGAACGCATCATGCACAC 60.247 55.000 11.00 0.00 45.36 3.82
2950 2982 0.824759 ACTCCACTCGATTAGCACCC 59.175 55.000 0.00 0.00 0.00 4.61
2959 2991 2.430694 CACATATCCCAACTCCACTCGA 59.569 50.000 0.00 0.00 0.00 4.04
2960 2992 2.430694 TCACATATCCCAACTCCACTCG 59.569 50.000 0.00 0.00 0.00 4.18
3006 3039 1.338200 ACATCTGGAGAACGCCTTGTC 60.338 52.381 0.00 0.00 0.00 3.18
3030 3063 2.561037 GCCCTGTTTGGACGTTGGG 61.561 63.158 0.00 0.00 38.35 4.12
3032 3065 0.817634 TCTGCCCTGTTTGGACGTTG 60.818 55.000 0.00 0.00 38.35 4.10
3059 3092 1.715931 TCCTCCATTGGTTTCCATGGT 59.284 47.619 12.58 0.00 35.34 3.55
3065 3098 3.721087 TCCTTCTCCTCCATTGGTTTC 57.279 47.619 1.86 0.00 0.00 2.78
3242 3285 1.550524 GACCCTGTGTGAGCTGACATA 59.449 52.381 9.85 5.85 0.00 2.29
3268 3311 1.907807 GGCTGCACCCAATGACCAA 60.908 57.895 0.50 0.00 0.00 3.67
3319 3421 1.313889 TCCCTAAATCCCCATTGCCA 58.686 50.000 0.00 0.00 0.00 4.92
3331 3433 1.908619 TGTGAGCTGAGCATCCCTAAA 59.091 47.619 7.39 0.00 0.00 1.85
3333 3435 1.571955 TTGTGAGCTGAGCATCCCTA 58.428 50.000 7.39 0.00 0.00 3.53
3488 3617 7.595130 GTGAACCAAGATCAAATTACTTGTTCC 59.405 37.037 0.00 0.00 39.19 3.62
3556 3696 2.906354 CTGGTAGAAACCTTCATCGGG 58.094 52.381 0.00 0.00 46.91 5.14
3578 3718 6.750501 TGACTATTTCCTCGTCATTTTCTACG 59.249 38.462 0.00 0.00 40.40 3.51
3591 3731 5.860941 TGACTGGAGATGACTATTTCCTC 57.139 43.478 0.00 0.00 38.19 3.71
3592 3732 7.921041 TTATGACTGGAGATGACTATTTCCT 57.079 36.000 0.00 0.00 38.19 3.36
3618 3758 2.028112 TGAGTATCTGACGCTGCCTTTT 60.028 45.455 0.00 0.00 34.92 2.27
3622 3773 0.528684 GGTGAGTATCTGACGCTGCC 60.529 60.000 0.00 0.00 34.92 4.85
3665 3816 6.640518 TGGATGTAACAAGAATAGGAGTGAC 58.359 40.000 0.00 0.00 0.00 3.67
3711 3865 9.118236 GACTCACTTTATGCAAAATTGTTACTC 57.882 33.333 0.00 0.00 0.00 2.59
3712 3866 8.082242 GGACTCACTTTATGCAAAATTGTTACT 58.918 33.333 0.00 0.00 0.00 2.24
3716 3870 6.403866 TGGACTCACTTTATGCAAAATTGT 57.596 33.333 0.00 0.00 0.00 2.71
3747 3901 6.352516 AGAAGGTCACAGAATAGCTTAATGG 58.647 40.000 0.00 0.00 33.80 3.16
3749 3903 9.553064 CATAAGAAGGTCACAGAATAGCTTAAT 57.447 33.333 0.00 0.00 33.80 1.40
3825 4009 2.485814 CTGTGCTTTCTGTTTAGGAGGC 59.514 50.000 0.00 0.00 0.00 4.70
3827 4011 4.380531 TGTCTGTGCTTTCTGTTTAGGAG 58.619 43.478 0.00 0.00 0.00 3.69
3847 4031 4.101585 TCTGTGAGAGTTTGTGAGGATTGT 59.898 41.667 0.00 0.00 0.00 2.71
3868 4084 7.680730 AGTCTGTTTGTAAACTGGTGATATCT 58.319 34.615 3.98 0.00 39.59 1.98


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

AutoCloner maintained by Alex Coulton.