Multiple sequence alignment - TraesCS3A01G085800

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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 TraesCS3A01G085800 chr3A 100.000 2720 0 0 1 2720 55482923 55485642 0.000000e+00 5024.0
1 TraesCS3A01G085800 chr3A 86.299 489 49 12 1459 1940 55500690 55501167 1.440000e-142 516.0
2 TraesCS3A01G085800 chr3A 84.058 69 5 5 1269 1333 128222598 128222664 8.130000e-06 62.1
3 TraesCS3A01G085800 chr3B 97.962 1472 23 6 291 1760 68252766 68254232 0.000000e+00 2545.0
4 TraesCS3A01G085800 chr3B 97.612 963 19 3 1760 2720 68254476 68255436 0.000000e+00 1648.0
5 TraesCS3A01G085800 chr3B 85.481 489 53 14 1459 1940 68346269 68346746 6.770000e-136 494.0
6 TraesCS3A01G085800 chr3B 87.574 169 16 1 2552 2715 67942368 67942536 9.940000e-45 191.0
7 TraesCS3A01G085800 chr3B 83.529 85 13 1 2268 2352 641992244 641992327 8.070000e-11 78.7
8 TraesCS3A01G085800 chr3D 92.806 1390 72 9 738 2110 43512966 43514344 0.000000e+00 1988.0
9 TraesCS3A01G085800 chr3D 90.430 1233 77 22 1394 2600 43567891 43569108 0.000000e+00 1585.0
10 TraesCS3A01G085800 chr3D 96.695 938 22 8 291 1225 43508638 43509569 0.000000e+00 1552.0
11 TraesCS3A01G085800 chr3D 90.464 1185 80 18 1304 2466 43509629 43510802 0.000000e+00 1531.0
12 TraesCS3A01G085800 chr3D 91.853 626 34 12 2097 2715 43533694 43534309 0.000000e+00 857.0
13 TraesCS3A01G085800 chr3D 84.836 488 46 15 1460 1940 43726848 43727314 1.470000e-127 466.0
14 TraesCS3A01G085800 chr3D 89.320 309 31 2 1 307 22038168 22038476 1.180000e-103 387.0
15 TraesCS3A01G085800 chr3D 90.476 294 23 3 449 741 43512614 43512903 1.530000e-102 383.0
16 TraesCS3A01G085800 chr3D 94.400 125 1 5 291 413 43512497 43512617 1.290000e-43 187.0
17 TraesCS3A01G085800 chr3D 96.491 57 2 0 2601 2657 43576849 43576793 8.020000e-16 95.3
18 TraesCS3A01G085800 chr3D 96.970 33 1 0 1293 1325 121984566 121984598 3.780000e-04 56.5
19 TraesCS3A01G085800 chr6D 89.711 311 28 4 1 308 319459985 319460294 7.060000e-106 394.0
20 TraesCS3A01G085800 chr6D 80.620 129 18 6 1213 1336 276880329 276880203 2.880000e-15 93.5
21 TraesCS3A01G085800 chr1D 89.389 311 29 4 1 307 257845725 257845415 3.280000e-104 388.0
22 TraesCS3A01G085800 chr1D 88.673 309 33 2 1 307 353643614 353643922 2.560000e-100 375.0
23 TraesCS3A01G085800 chr1B 89.389 311 28 4 2 308 73287620 73287311 1.180000e-103 387.0
24 TraesCS3A01G085800 chr1B 89.068 311 29 4 2 308 73330538 73330229 5.500000e-102 381.0
25 TraesCS3A01G085800 chr1B 88.333 60 4 2 2268 2326 252901266 252901209 4.860000e-08 69.4
26 TraesCS3A01G085800 chr4D 88.608 316 33 3 1 313 479451762 479451447 5.500000e-102 381.0
27 TraesCS3A01G085800 chr7B 88.673 309 33 2 1 307 511238255 511238563 2.560000e-100 375.0
28 TraesCS3A01G085800 chr2D 88.673 309 33 2 1 307 605295023 605295331 2.560000e-100 375.0
29 TraesCS3A01G085800 chr5D 86.364 110 12 3 2254 2361 195652901 195652793 1.710000e-22 117.0
30 TraesCS3A01G085800 chr5A 86.239 109 13 2 2254 2361 232836552 232836445 1.710000e-22 117.0
31 TraesCS3A01G085800 chr6A 82.653 98 13 3 1236 1330 399216811 399216907 1.740000e-12 84.2
32 TraesCS3A01G085800 chr2A 82.979 94 15 1 2268 2361 775768475 775768383 1.740000e-12 84.2


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 TraesCS3A01G085800 chr3A 55482923 55485642 2719 False 5024.0 5024 100.0000 1 2720 1 chr3A.!!$F1 2719
1 TraesCS3A01G085800 chr3B 68252766 68255436 2670 False 2096.5 2545 97.7870 291 2720 2 chr3B.!!$F4 2429
2 TraesCS3A01G085800 chr3D 43567891 43569108 1217 False 1585.0 1585 90.4300 1394 2600 1 chr3D.!!$F3 1206
3 TraesCS3A01G085800 chr3D 43508638 43514344 5706 False 1128.2 1988 92.9682 291 2466 5 chr3D.!!$F6 2175
4 TraesCS3A01G085800 chr3D 43533694 43534309 615 False 857.0 857 91.8530 2097 2715 1 chr3D.!!$F2 618

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
164 165 0.034896 GGACCAAAAGTCTCAGGCGA 59.965 55.0 0.0 0.0 45.54 5.54 F
1041 1045 0.036732 TTGTCACCCTCATGTGCCTC 59.963 55.0 0.0 0.0 36.17 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1256 1285 1.376649 AGGGTGAGGGCAAGAATTCT 58.623 50.0 0.88 0.88 0.00 2.40 R
2677 6329 0.397941 ACACAAGCTAAGAGCCAGCA 59.602 50.0 0.00 0.00 43.77 4.41 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
26 27 7.957992 ATATATAGGGAACTCTTTAGTCCCG 57.042 40.000 2.37 0.00 42.95 5.14
27 28 1.569653 AGGGAACTCTTTAGTCCCGG 58.430 55.000 0.00 0.00 42.95 5.73
28 29 1.203275 AGGGAACTCTTTAGTCCCGGT 60.203 52.381 0.00 0.00 42.95 5.28
29 30 1.627329 GGGAACTCTTTAGTCCCGGTT 59.373 52.381 0.00 0.00 35.04 4.44
30 31 2.614734 GGGAACTCTTTAGTCCCGGTTG 60.615 54.545 0.00 0.00 35.04 3.77
31 32 2.614734 GGAACTCTTTAGTCCCGGTTGG 60.615 54.545 0.00 0.00 33.75 3.77
32 33 1.725803 ACTCTTTAGTCCCGGTTGGT 58.274 50.000 0.00 0.00 34.77 3.67
33 34 1.346722 ACTCTTTAGTCCCGGTTGGTG 59.653 52.381 0.00 0.00 34.77 4.17
34 35 0.688487 TCTTTAGTCCCGGTTGGTGG 59.312 55.000 0.00 0.00 34.77 4.61
35 36 0.958876 CTTTAGTCCCGGTTGGTGGC 60.959 60.000 0.00 0.00 34.77 5.01
36 37 1.420532 TTTAGTCCCGGTTGGTGGCT 61.421 55.000 0.00 0.00 34.77 4.75
37 38 0.544833 TTAGTCCCGGTTGGTGGCTA 60.545 55.000 0.00 0.00 34.77 3.93
38 39 0.544833 TAGTCCCGGTTGGTGGCTAA 60.545 55.000 0.00 0.00 34.77 3.09
39 40 1.073548 GTCCCGGTTGGTGGCTAAA 59.926 57.895 0.00 0.00 34.77 1.85
40 41 0.537828 GTCCCGGTTGGTGGCTAAAA 60.538 55.000 0.00 0.00 34.77 1.52
41 42 0.406361 TCCCGGTTGGTGGCTAAAAT 59.594 50.000 0.00 0.00 34.77 1.82
42 43 1.634459 TCCCGGTTGGTGGCTAAAATA 59.366 47.619 0.00 0.00 34.77 1.40
43 44 2.021457 CCCGGTTGGTGGCTAAAATAG 58.979 52.381 0.00 0.00 0.00 1.73
44 45 2.021457 CCGGTTGGTGGCTAAAATAGG 58.979 52.381 0.00 0.00 0.00 2.57
45 46 2.021457 CGGTTGGTGGCTAAAATAGGG 58.979 52.381 0.00 0.00 0.00 3.53
46 47 2.356330 CGGTTGGTGGCTAAAATAGGGA 60.356 50.000 0.00 0.00 0.00 4.20
47 48 3.021695 GGTTGGTGGCTAAAATAGGGAC 58.978 50.000 0.00 0.00 0.00 4.46
48 49 3.308904 GGTTGGTGGCTAAAATAGGGACT 60.309 47.826 0.00 0.00 46.37 3.85
64 65 5.138758 AGGGACTAAAGAAAAACCTTGGT 57.861 39.130 0.00 0.00 36.02 3.67
65 66 5.138276 AGGGACTAAAGAAAAACCTTGGTC 58.862 41.667 0.00 0.00 36.02 4.02
66 67 4.280174 GGGACTAAAGAAAAACCTTGGTCC 59.720 45.833 7.76 7.76 42.48 4.46
67 68 4.280174 GGACTAAAGAAAAACCTTGGTCCC 59.720 45.833 5.52 0.00 40.24 4.46
68 69 3.887110 ACTAAAGAAAAACCTTGGTCCCG 59.113 43.478 0.00 0.00 0.00 5.14
69 70 2.740506 AAGAAAAACCTTGGTCCCGA 57.259 45.000 0.00 0.00 0.00 5.14
70 71 2.971901 AGAAAAACCTTGGTCCCGAT 57.028 45.000 0.00 0.00 0.00 4.18
71 72 3.238788 AGAAAAACCTTGGTCCCGATT 57.761 42.857 0.00 0.00 0.00 3.34
72 73 3.154710 AGAAAAACCTTGGTCCCGATTC 58.845 45.455 0.00 0.00 0.00 2.52
73 74 2.971901 AAAACCTTGGTCCCGATTCT 57.028 45.000 0.00 0.00 0.00 2.40
74 75 4.042435 AGAAAAACCTTGGTCCCGATTCTA 59.958 41.667 0.00 0.00 0.00 2.10
75 76 3.629142 AAACCTTGGTCCCGATTCTAG 57.371 47.619 0.00 0.00 0.00 2.43
76 77 0.831307 ACCTTGGTCCCGATTCTAGC 59.169 55.000 0.00 0.00 0.00 3.42
77 78 0.106894 CCTTGGTCCCGATTCTAGCC 59.893 60.000 0.00 0.00 0.00 3.93
78 79 0.830648 CTTGGTCCCGATTCTAGCCA 59.169 55.000 0.00 0.00 0.00 4.75
79 80 1.417890 CTTGGTCCCGATTCTAGCCAT 59.582 52.381 0.00 0.00 0.00 4.40
80 81 1.048601 TGGTCCCGATTCTAGCCATC 58.951 55.000 0.00 0.00 0.00 3.51
81 82 1.048601 GGTCCCGATTCTAGCCATCA 58.951 55.000 0.00 0.00 0.00 3.07
82 83 1.416401 GGTCCCGATTCTAGCCATCAA 59.584 52.381 0.00 0.00 0.00 2.57
83 84 2.484889 GTCCCGATTCTAGCCATCAAC 58.515 52.381 0.00 0.00 0.00 3.18
84 85 1.416401 TCCCGATTCTAGCCATCAACC 59.584 52.381 0.00 0.00 0.00 3.77
85 86 1.502231 CCGATTCTAGCCATCAACCG 58.498 55.000 0.00 0.00 0.00 4.44
86 87 1.502231 CGATTCTAGCCATCAACCGG 58.498 55.000 0.00 0.00 0.00 5.28
87 88 1.873903 CGATTCTAGCCATCAACCGGG 60.874 57.143 6.32 0.00 0.00 5.73
88 89 1.416401 GATTCTAGCCATCAACCGGGA 59.584 52.381 6.32 0.00 0.00 5.14
89 90 0.539986 TTCTAGCCATCAACCGGGAC 59.460 55.000 6.32 0.00 0.00 4.46
90 91 0.325296 TCTAGCCATCAACCGGGACT 60.325 55.000 6.32 0.00 0.00 3.85
91 92 1.063492 TCTAGCCATCAACCGGGACTA 60.063 52.381 6.32 0.00 0.00 2.59
92 93 1.760613 CTAGCCATCAACCGGGACTAA 59.239 52.381 6.32 0.00 0.00 2.24
93 94 0.988832 AGCCATCAACCGGGACTAAA 59.011 50.000 6.32 0.00 0.00 1.85
94 95 1.065418 AGCCATCAACCGGGACTAAAG 60.065 52.381 6.32 0.00 0.00 1.85
95 96 2.017113 GCCATCAACCGGGACTAAAGG 61.017 57.143 6.32 0.00 0.00 3.11
96 97 1.280998 CCATCAACCGGGACTAAAGGT 59.719 52.381 6.32 0.00 40.50 3.50
97 98 2.356135 CATCAACCGGGACTAAAGGTG 58.644 52.381 6.32 0.00 38.44 4.00
98 99 1.426751 TCAACCGGGACTAAAGGTGT 58.573 50.000 6.32 0.00 38.44 4.16
99 100 1.770061 TCAACCGGGACTAAAGGTGTT 59.230 47.619 6.32 0.00 38.44 3.32
100 101 1.877443 CAACCGGGACTAAAGGTGTTG 59.123 52.381 6.32 0.00 38.44 3.33
101 102 0.399075 ACCGGGACTAAAGGTGTTGG 59.601 55.000 6.32 0.00 36.81 3.77
102 103 0.322187 CCGGGACTAAAGGTGTTGGG 60.322 60.000 0.00 0.00 0.00 4.12
103 104 0.958876 CGGGACTAAAGGTGTTGGGC 60.959 60.000 0.00 0.00 0.00 5.36
104 105 0.611062 GGGACTAAAGGTGTTGGGCC 60.611 60.000 0.00 0.00 0.00 5.80
105 106 0.111639 GGACTAAAGGTGTTGGGCCA 59.888 55.000 0.00 0.00 0.00 5.36
106 107 1.534729 GACTAAAGGTGTTGGGCCAG 58.465 55.000 6.23 0.00 0.00 4.85
107 108 0.112412 ACTAAAGGTGTTGGGCCAGG 59.888 55.000 6.23 0.00 0.00 4.45
108 109 0.404040 CTAAAGGTGTTGGGCCAGGA 59.596 55.000 6.23 0.00 0.00 3.86
109 110 0.404040 TAAAGGTGTTGGGCCAGGAG 59.596 55.000 6.23 0.00 0.00 3.69
110 111 3.513750 AAGGTGTTGGGCCAGGAGC 62.514 63.158 6.23 7.16 42.60 4.70
112 113 4.329545 GTGTTGGGCCAGGAGCGA 62.330 66.667 6.23 0.00 45.17 4.93
113 114 4.020617 TGTTGGGCCAGGAGCGAG 62.021 66.667 6.23 0.00 45.17 5.03
114 115 4.785453 GTTGGGCCAGGAGCGAGG 62.785 72.222 6.23 0.00 45.17 4.63
120 121 3.801997 CCAGGAGCGAGGCCCATT 61.802 66.667 0.00 0.00 0.00 3.16
121 122 2.515523 CAGGAGCGAGGCCCATTG 60.516 66.667 0.00 0.00 0.00 2.82
122 123 3.801997 AGGAGCGAGGCCCATTGG 61.802 66.667 0.00 0.00 0.00 3.16
123 124 4.115199 GGAGCGAGGCCCATTGGT 62.115 66.667 0.00 0.00 0.00 3.67
124 125 2.514824 GAGCGAGGCCCATTGGTC 60.515 66.667 0.00 0.00 36.05 4.02
125 126 4.115199 AGCGAGGCCCATTGGTCC 62.115 66.667 0.00 0.00 36.69 4.46
127 128 4.856801 CGAGGCCCATTGGTCCCG 62.857 72.222 0.00 0.00 36.69 5.14
128 129 4.506255 GAGGCCCATTGGTCCCGG 62.506 72.222 0.00 0.00 36.69 5.73
130 131 4.376170 GGCCCATTGGTCCCGGTT 62.376 66.667 0.00 0.00 0.00 4.44
131 132 2.754254 GCCCATTGGTCCCGGTTC 60.754 66.667 0.00 0.00 0.00 3.62
132 133 2.437716 CCCATTGGTCCCGGTTCG 60.438 66.667 0.00 0.00 0.00 3.95
133 134 2.349755 CCATTGGTCCCGGTTCGT 59.650 61.111 0.00 0.00 0.00 3.85
134 135 2.038269 CCATTGGTCCCGGTTCGTG 61.038 63.158 0.00 0.00 0.00 4.35
135 136 1.302192 CATTGGTCCCGGTTCGTGT 60.302 57.895 0.00 0.00 0.00 4.49
136 137 1.004200 ATTGGTCCCGGTTCGTGTC 60.004 57.895 0.00 0.00 0.00 3.67
137 138 2.459202 ATTGGTCCCGGTTCGTGTCC 62.459 60.000 0.00 0.00 0.00 4.02
138 139 4.729856 GGTCCCGGTTCGTGTCCG 62.730 72.222 0.00 8.23 46.49 4.79
147 148 2.911509 TCGTGTCCGAAACCGGGA 60.912 61.111 6.32 0.00 46.72 5.14
151 152 2.426887 GTCCGAAACCGGGACCAA 59.573 61.111 6.32 0.00 46.65 3.67
152 153 1.227913 GTCCGAAACCGGGACCAAA 60.228 57.895 6.32 0.00 46.65 3.28
153 154 0.818852 GTCCGAAACCGGGACCAAAA 60.819 55.000 6.32 0.00 46.65 2.44
154 155 0.535553 TCCGAAACCGGGACCAAAAG 60.536 55.000 6.32 0.00 46.72 2.27
155 156 0.820482 CCGAAACCGGGACCAAAAGT 60.820 55.000 6.32 0.00 43.22 2.66
156 157 0.589708 CGAAACCGGGACCAAAAGTC 59.410 55.000 6.32 0.00 45.51 3.01
157 158 1.812708 CGAAACCGGGACCAAAAGTCT 60.813 52.381 6.32 0.00 45.54 3.24
158 159 1.878088 GAAACCGGGACCAAAAGTCTC 59.122 52.381 6.32 0.00 45.54 3.36
162 163 2.948386 GGGACCAAAAGTCTCAGGC 58.052 57.895 0.00 0.00 46.23 4.85
163 164 0.955919 GGGACCAAAAGTCTCAGGCG 60.956 60.000 0.00 0.00 46.23 5.52
164 165 0.034896 GGACCAAAAGTCTCAGGCGA 59.965 55.000 0.00 0.00 45.54 5.54
165 166 1.542547 GGACCAAAAGTCTCAGGCGAA 60.543 52.381 0.00 0.00 45.54 4.70
166 167 1.531578 GACCAAAAGTCTCAGGCGAAC 59.468 52.381 0.00 0.00 42.69 3.95
167 168 1.141053 ACCAAAAGTCTCAGGCGAACT 59.859 47.619 0.00 0.00 0.00 3.01
168 169 4.894983 GACCAAAAGTCTCAGGCGAACTG 61.895 52.174 1.53 1.53 42.69 3.16
175 176 2.429930 CAGGCGAACTGGGACCAA 59.570 61.111 0.00 0.00 43.70 3.67
176 177 1.002134 CAGGCGAACTGGGACCAAT 60.002 57.895 0.00 0.00 43.70 3.16
177 178 1.002134 AGGCGAACTGGGACCAATG 60.002 57.895 0.00 0.00 0.00 2.82
178 179 2.046285 GGCGAACTGGGACCAATGG 61.046 63.158 0.00 0.00 0.00 3.16
179 180 2.700773 GCGAACTGGGACCAATGGC 61.701 63.158 0.00 0.00 0.00 4.40
180 181 2.046285 CGAACTGGGACCAATGGCC 61.046 63.158 0.00 0.00 0.00 5.36
181 182 1.682344 GAACTGGGACCAATGGCCC 60.682 63.158 20.36 20.36 38.78 5.80
182 183 3.238197 AACTGGGACCAATGGCCCC 62.238 63.158 17.58 17.58 37.95 5.80
183 184 4.463788 CTGGGACCAATGGCCCCC 62.464 72.222 21.44 20.46 37.95 5.40
185 186 4.004635 GGGACCAATGGCCCCCAA 62.005 66.667 13.28 0.00 38.33 4.12
186 187 2.364186 GGACCAATGGCCCCCAAG 60.364 66.667 0.00 0.00 36.95 3.61
187 188 2.364186 GACCAATGGCCCCCAAGG 60.364 66.667 0.00 0.00 36.95 3.61
216 217 4.760047 CCCTGGCCTCACGAACCG 62.760 72.222 3.32 0.00 0.00 4.44
217 218 4.760047 CCTGGCCTCACGAACCGG 62.760 72.222 3.32 0.00 0.00 5.28
218 219 4.760047 CTGGCCTCACGAACCGGG 62.760 72.222 6.32 0.00 0.00 5.73
220 221 4.754667 GGCCTCACGAACCGGGAC 62.755 72.222 6.32 0.00 32.99 4.46
221 222 3.692406 GCCTCACGAACCGGGACT 61.692 66.667 6.32 0.00 32.99 3.85
222 223 2.261671 CCTCACGAACCGGGACTG 59.738 66.667 6.32 0.00 32.99 3.51
223 224 2.273179 CCTCACGAACCGGGACTGA 61.273 63.158 6.32 0.00 32.99 3.41
224 225 1.605058 CCTCACGAACCGGGACTGAT 61.605 60.000 6.32 0.00 32.99 2.90
225 226 0.458543 CTCACGAACCGGGACTGATG 60.459 60.000 6.32 0.00 32.99 3.07
226 227 2.100631 CACGAACCGGGACTGATGC 61.101 63.158 6.32 0.00 28.17 3.91
227 228 2.511600 CGAACCGGGACTGATGCC 60.512 66.667 6.32 0.00 0.00 4.40
228 229 2.124695 GAACCGGGACTGATGCCC 60.125 66.667 6.32 0.00 42.41 5.36
229 230 3.699134 GAACCGGGACTGATGCCCC 62.699 68.421 6.32 0.00 42.92 5.80
232 233 3.411517 CGGGACTGATGCCCCCTT 61.412 66.667 0.00 0.00 42.92 3.95
233 234 2.983879 CGGGACTGATGCCCCCTTT 61.984 63.158 0.00 0.00 42.92 3.11
234 235 1.380380 GGGACTGATGCCCCCTTTG 60.380 63.158 0.00 0.00 39.81 2.77
235 236 1.691219 GGACTGATGCCCCCTTTGA 59.309 57.895 0.00 0.00 0.00 2.69
236 237 0.259938 GGACTGATGCCCCCTTTGAT 59.740 55.000 0.00 0.00 0.00 2.57
237 238 1.685148 GACTGATGCCCCCTTTGATC 58.315 55.000 0.00 0.00 0.00 2.92
238 239 0.259938 ACTGATGCCCCCTTTGATCC 59.740 55.000 0.00 0.00 0.00 3.36
239 240 0.468771 CTGATGCCCCCTTTGATCCC 60.469 60.000 0.00 0.00 0.00 3.85
240 241 1.529244 GATGCCCCCTTTGATCCCG 60.529 63.158 0.00 0.00 0.00 5.14
241 242 2.983725 GATGCCCCCTTTGATCCCGG 62.984 65.000 0.00 0.00 0.00 5.73
242 243 3.739613 GCCCCCTTTGATCCCGGT 61.740 66.667 0.00 0.00 0.00 5.28
243 244 3.096357 CCCCCTTTGATCCCGGTT 58.904 61.111 0.00 0.00 0.00 4.44
244 245 1.076995 CCCCCTTTGATCCCGGTTC 60.077 63.158 0.00 0.00 0.00 3.62
245 246 1.451387 CCCCTTTGATCCCGGTTCG 60.451 63.158 0.00 0.00 0.00 3.95
258 259 4.695560 GTTCGGGAGTGAACAGGG 57.304 61.111 1.98 0.00 45.92 4.45
259 260 2.055299 GTTCGGGAGTGAACAGGGA 58.945 57.895 1.98 0.00 45.92 4.20
260 261 0.613777 GTTCGGGAGTGAACAGGGAT 59.386 55.000 1.98 0.00 45.92 3.85
261 262 1.003233 GTTCGGGAGTGAACAGGGATT 59.997 52.381 1.98 0.00 45.92 3.01
262 263 2.235402 GTTCGGGAGTGAACAGGGATTA 59.765 50.000 1.98 0.00 45.92 1.75
263 264 2.542550 TCGGGAGTGAACAGGGATTAA 58.457 47.619 0.00 0.00 0.00 1.40
264 265 3.112263 TCGGGAGTGAACAGGGATTAAT 58.888 45.455 0.00 0.00 0.00 1.40
265 266 3.118408 TCGGGAGTGAACAGGGATTAATG 60.118 47.826 0.00 0.00 0.00 1.90
266 267 2.952310 GGGAGTGAACAGGGATTAATGC 59.048 50.000 0.00 0.00 0.00 3.56
267 268 3.372025 GGGAGTGAACAGGGATTAATGCT 60.372 47.826 6.93 0.00 0.00 3.79
268 269 3.879892 GGAGTGAACAGGGATTAATGCTC 59.120 47.826 6.93 0.00 0.00 4.26
269 270 4.384647 GGAGTGAACAGGGATTAATGCTCT 60.385 45.833 6.93 0.00 0.00 4.09
270 271 5.184892 AGTGAACAGGGATTAATGCTCTT 57.815 39.130 6.93 0.00 0.00 2.85
271 272 6.313519 AGTGAACAGGGATTAATGCTCTTA 57.686 37.500 6.93 0.00 0.00 2.10
272 273 6.116126 AGTGAACAGGGATTAATGCTCTTAC 58.884 40.000 6.93 0.46 0.00 2.34
273 274 5.297029 GTGAACAGGGATTAATGCTCTTACC 59.703 44.000 6.93 0.00 0.00 2.85
274 275 5.045213 TGAACAGGGATTAATGCTCTTACCA 60.045 40.000 6.93 0.00 0.00 3.25
275 276 5.041191 ACAGGGATTAATGCTCTTACCAG 57.959 43.478 6.93 0.00 0.00 4.00
276 277 4.141390 ACAGGGATTAATGCTCTTACCAGG 60.141 45.833 6.93 0.00 0.00 4.45
277 278 3.149981 GGGATTAATGCTCTTACCAGGC 58.850 50.000 6.93 0.00 0.00 4.85
278 279 3.149981 GGATTAATGCTCTTACCAGGCC 58.850 50.000 0.00 0.00 0.00 5.19
279 280 3.181439 GGATTAATGCTCTTACCAGGCCT 60.181 47.826 0.00 0.00 0.00 5.19
280 281 3.560636 TTAATGCTCTTACCAGGCCTC 57.439 47.619 0.00 0.00 0.00 4.70
281 282 1.289160 AATGCTCTTACCAGGCCTCA 58.711 50.000 0.00 0.00 0.00 3.86
282 283 1.289160 ATGCTCTTACCAGGCCTCAA 58.711 50.000 0.00 0.00 0.00 3.02
283 284 0.324943 TGCTCTTACCAGGCCTCAAC 59.675 55.000 0.00 0.00 0.00 3.18
284 285 0.393132 GCTCTTACCAGGCCTCAACC 60.393 60.000 0.00 0.00 0.00 3.77
285 286 0.984230 CTCTTACCAGGCCTCAACCA 59.016 55.000 0.00 0.00 0.00 3.67
286 287 1.351017 CTCTTACCAGGCCTCAACCAA 59.649 52.381 0.00 0.00 0.00 3.67
287 288 1.777878 TCTTACCAGGCCTCAACCAAA 59.222 47.619 0.00 0.00 0.00 3.28
288 289 2.162681 CTTACCAGGCCTCAACCAAAG 58.837 52.381 0.00 0.00 0.00 2.77
289 290 0.251165 TACCAGGCCTCAACCAAAGC 60.251 55.000 0.00 0.00 0.00 3.51
290 291 2.278330 CCAGGCCTCAACCAAAGCC 61.278 63.158 0.00 0.00 46.13 4.35
292 293 2.118294 GGCCTCAACCAAAGCCCT 59.882 61.111 0.00 0.00 39.60 5.19
293 294 2.278330 GGCCTCAACCAAAGCCCTG 61.278 63.158 0.00 0.00 39.60 4.45
294 295 1.531602 GCCTCAACCAAAGCCCTGT 60.532 57.895 0.00 0.00 0.00 4.00
295 296 1.115326 GCCTCAACCAAAGCCCTGTT 61.115 55.000 0.00 0.00 0.00 3.16
296 297 1.413118 CCTCAACCAAAGCCCTGTTT 58.587 50.000 0.00 0.00 0.00 2.83
297 298 1.762370 CCTCAACCAAAGCCCTGTTTT 59.238 47.619 0.00 0.00 0.00 2.43
298 299 2.224042 CCTCAACCAAAGCCCTGTTTTC 60.224 50.000 0.00 0.00 0.00 2.29
299 300 2.695147 CTCAACCAAAGCCCTGTTTTCT 59.305 45.455 0.00 0.00 0.00 2.52
300 301 3.888930 CTCAACCAAAGCCCTGTTTTCTA 59.111 43.478 0.00 0.00 0.00 2.10
301 302 3.634910 TCAACCAAAGCCCTGTTTTCTAC 59.365 43.478 0.00 0.00 0.00 2.59
302 303 3.595190 ACCAAAGCCCTGTTTTCTACT 57.405 42.857 0.00 0.00 0.00 2.57
303 304 4.717279 ACCAAAGCCCTGTTTTCTACTA 57.283 40.909 0.00 0.00 0.00 1.82
304 305 4.652822 ACCAAAGCCCTGTTTTCTACTAG 58.347 43.478 0.00 0.00 0.00 2.57
305 306 4.104261 ACCAAAGCCCTGTTTTCTACTAGT 59.896 41.667 0.00 0.00 0.00 2.57
306 307 4.455877 CCAAAGCCCTGTTTTCTACTAGTG 59.544 45.833 5.39 0.00 0.00 2.74
370 371 3.440173 TCTTTTGCCGATTGAAGGATGAC 59.560 43.478 0.00 0.00 0.00 3.06
484 487 9.865321 TTTAGTACAAATCGCAAGTATAGAACT 57.135 29.630 0.00 0.00 41.49 3.01
520 523 5.547465 TGGATGAACACAAGATCGTAGTTT 58.453 37.500 1.42 0.00 0.00 2.66
633 637 0.950836 TTCAACATGCAGTGGGAACG 59.049 50.000 0.00 0.00 0.00 3.95
1041 1045 0.036732 TTGTCACCCTCATGTGCCTC 59.963 55.000 0.00 0.00 36.17 4.70
1256 1285 0.745128 GTGGTGTGTTTGGGTCGACA 60.745 55.000 18.91 0.00 0.00 4.35
1291 1320 6.663523 CCCTCACCCTTGTACATATTTCTTTT 59.336 38.462 0.00 0.00 0.00 2.27
1332 1361 2.872245 CTCTCCTGCGTGTTTGAGAAAA 59.128 45.455 0.00 0.00 33.74 2.29
1844 2130 6.183360 TGTGTGCAATCTGAATCTTCTGTTTT 60.183 34.615 0.00 0.00 0.00 2.43
1845 2131 6.143438 GTGTGCAATCTGAATCTTCTGTTTTG 59.857 38.462 0.00 2.60 0.00 2.44
1865 2153 3.955471 TGTTTTTGGGTGAAATTTGCCA 58.045 36.364 0.00 0.00 0.00 4.92
2005 2310 4.480115 ACGACTCCATCCAATATACTCCA 58.520 43.478 0.00 0.00 0.00 3.86
2348 2658 2.550180 TGTTCATTTTCGCGTGGAATGA 59.450 40.909 21.41 21.41 37.85 2.57
2469 2780 4.366684 CAGCCCTTCCCCACCCAC 62.367 72.222 0.00 0.00 0.00 4.61
2677 6329 5.043248 GCTTGCTTTGTATTCACAAGTGTT 58.957 37.500 0.00 0.00 45.17 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.052468 ACCAACCGGGACTAAAGAGTT 58.948 47.619 6.32 0.00 41.15 3.01
13 14 1.346722 CACCAACCGGGACTAAAGAGT 59.653 52.381 6.32 0.00 41.15 3.24
14 15 1.338769 CCACCAACCGGGACTAAAGAG 60.339 57.143 6.32 0.00 41.15 2.85
15 16 0.688487 CCACCAACCGGGACTAAAGA 59.312 55.000 6.32 0.00 41.15 2.52
16 17 0.958876 GCCACCAACCGGGACTAAAG 60.959 60.000 6.32 0.00 41.15 1.85
17 18 1.073548 GCCACCAACCGGGACTAAA 59.926 57.895 6.32 0.00 41.15 1.85
18 19 0.544833 TAGCCACCAACCGGGACTAA 60.545 55.000 6.32 0.00 41.15 2.24
19 20 0.544833 TTAGCCACCAACCGGGACTA 60.545 55.000 6.32 0.00 41.15 2.59
20 21 1.420532 TTTAGCCACCAACCGGGACT 61.421 55.000 6.32 0.00 41.15 3.85
21 22 0.537828 TTTTAGCCACCAACCGGGAC 60.538 55.000 6.32 0.00 41.15 4.46
22 23 0.406361 ATTTTAGCCACCAACCGGGA 59.594 50.000 6.32 0.00 41.15 5.14
23 24 2.021457 CTATTTTAGCCACCAACCGGG 58.979 52.381 6.32 0.00 44.81 5.73
24 25 2.021457 CCTATTTTAGCCACCAACCGG 58.979 52.381 0.00 0.00 38.77 5.28
25 26 2.021457 CCCTATTTTAGCCACCAACCG 58.979 52.381 0.00 0.00 0.00 4.44
26 27 3.021695 GTCCCTATTTTAGCCACCAACC 58.978 50.000 0.00 0.00 0.00 3.77
27 28 3.964411 AGTCCCTATTTTAGCCACCAAC 58.036 45.455 0.00 0.00 0.00 3.77
28 29 5.782677 TTAGTCCCTATTTTAGCCACCAA 57.217 39.130 0.00 0.00 0.00 3.67
29 30 5.489637 TCTTTAGTCCCTATTTTAGCCACCA 59.510 40.000 0.00 0.00 0.00 4.17
30 31 5.997843 TCTTTAGTCCCTATTTTAGCCACC 58.002 41.667 0.00 0.00 0.00 4.61
31 32 7.933215 TTTCTTTAGTCCCTATTTTAGCCAC 57.067 36.000 0.00 0.00 0.00 5.01
32 33 8.799367 GTTTTTCTTTAGTCCCTATTTTAGCCA 58.201 33.333 0.00 0.00 0.00 4.75
33 34 8.248945 GGTTTTTCTTTAGTCCCTATTTTAGCC 58.751 37.037 0.00 0.00 0.00 3.93
34 35 9.021807 AGGTTTTTCTTTAGTCCCTATTTTAGC 57.978 33.333 0.00 0.00 0.00 3.09
37 38 8.647796 CCAAGGTTTTTCTTTAGTCCCTATTTT 58.352 33.333 0.00 0.00 0.00 1.82
38 39 7.787904 ACCAAGGTTTTTCTTTAGTCCCTATTT 59.212 33.333 0.00 0.00 0.00 1.40
39 40 7.302948 ACCAAGGTTTTTCTTTAGTCCCTATT 58.697 34.615 0.00 0.00 0.00 1.73
40 41 6.860034 ACCAAGGTTTTTCTTTAGTCCCTAT 58.140 36.000 0.00 0.00 0.00 2.57
41 42 6.270219 ACCAAGGTTTTTCTTTAGTCCCTA 57.730 37.500 0.00 0.00 0.00 3.53
42 43 5.138276 GACCAAGGTTTTTCTTTAGTCCCT 58.862 41.667 0.00 0.00 0.00 4.20
43 44 4.280174 GGACCAAGGTTTTTCTTTAGTCCC 59.720 45.833 10.28 0.00 39.42 4.46
44 45 4.280174 GGGACCAAGGTTTTTCTTTAGTCC 59.720 45.833 11.93 11.93 41.87 3.85
45 46 4.023450 CGGGACCAAGGTTTTTCTTTAGTC 60.023 45.833 0.00 0.00 31.63 2.59
46 47 3.887110 CGGGACCAAGGTTTTTCTTTAGT 59.113 43.478 0.00 0.00 0.00 2.24
47 48 4.139038 TCGGGACCAAGGTTTTTCTTTAG 58.861 43.478 0.00 0.00 0.00 1.85
48 49 4.167652 TCGGGACCAAGGTTTTTCTTTA 57.832 40.909 0.00 0.00 0.00 1.85
49 50 3.021177 TCGGGACCAAGGTTTTTCTTT 57.979 42.857 0.00 0.00 0.00 2.52
50 51 2.740506 TCGGGACCAAGGTTTTTCTT 57.259 45.000 0.00 0.00 0.00 2.52
51 52 2.971901 ATCGGGACCAAGGTTTTTCT 57.028 45.000 0.00 0.00 0.00 2.52
52 53 3.154710 AGAATCGGGACCAAGGTTTTTC 58.845 45.455 0.00 0.00 0.00 2.29
53 54 3.238788 AGAATCGGGACCAAGGTTTTT 57.761 42.857 0.00 0.00 0.00 1.94
54 55 2.971901 AGAATCGGGACCAAGGTTTT 57.028 45.000 0.00 0.00 0.00 2.43
55 56 2.355818 GCTAGAATCGGGACCAAGGTTT 60.356 50.000 0.00 0.00 0.00 3.27
56 57 1.209747 GCTAGAATCGGGACCAAGGTT 59.790 52.381 0.00 0.00 0.00 3.50
57 58 0.831307 GCTAGAATCGGGACCAAGGT 59.169 55.000 0.00 0.00 0.00 3.50
58 59 0.106894 GGCTAGAATCGGGACCAAGG 59.893 60.000 0.00 0.00 0.00 3.61
59 60 0.830648 TGGCTAGAATCGGGACCAAG 59.169 55.000 0.00 0.00 0.00 3.61
60 61 1.416401 GATGGCTAGAATCGGGACCAA 59.584 52.381 0.00 0.00 0.00 3.67
61 62 1.048601 GATGGCTAGAATCGGGACCA 58.951 55.000 0.00 0.00 0.00 4.02
62 63 1.048601 TGATGGCTAGAATCGGGACC 58.951 55.000 0.00 0.00 0.00 4.46
63 64 2.484889 GTTGATGGCTAGAATCGGGAC 58.515 52.381 0.00 0.00 0.00 4.46
64 65 1.416401 GGTTGATGGCTAGAATCGGGA 59.584 52.381 0.00 0.00 0.00 5.14
65 66 1.873903 CGGTTGATGGCTAGAATCGGG 60.874 57.143 0.00 0.00 0.00 5.14
66 67 1.502231 CGGTTGATGGCTAGAATCGG 58.498 55.000 0.00 0.00 0.00 4.18
67 68 1.502231 CCGGTTGATGGCTAGAATCG 58.498 55.000 0.00 0.00 0.00 3.34
68 69 1.416401 TCCCGGTTGATGGCTAGAATC 59.584 52.381 0.00 0.00 0.00 2.52
69 70 1.141053 GTCCCGGTTGATGGCTAGAAT 59.859 52.381 0.00 0.00 0.00 2.40
70 71 0.539986 GTCCCGGTTGATGGCTAGAA 59.460 55.000 0.00 0.00 0.00 2.10
71 72 0.325296 AGTCCCGGTTGATGGCTAGA 60.325 55.000 0.00 0.00 0.00 2.43
72 73 1.410004 TAGTCCCGGTTGATGGCTAG 58.590 55.000 0.00 0.00 0.00 3.42
73 74 1.868713 TTAGTCCCGGTTGATGGCTA 58.131 50.000 0.00 0.00 0.00 3.93
74 75 0.988832 TTTAGTCCCGGTTGATGGCT 59.011 50.000 0.00 0.00 0.00 4.75
75 76 1.379527 CTTTAGTCCCGGTTGATGGC 58.620 55.000 0.00 0.00 0.00 4.40
76 77 1.280998 ACCTTTAGTCCCGGTTGATGG 59.719 52.381 0.00 0.00 0.00 3.51
77 78 2.290071 ACACCTTTAGTCCCGGTTGATG 60.290 50.000 0.00 0.00 0.00 3.07
78 79 1.982958 ACACCTTTAGTCCCGGTTGAT 59.017 47.619 0.00 0.00 0.00 2.57
79 80 1.426751 ACACCTTTAGTCCCGGTTGA 58.573 50.000 0.00 0.00 0.00 3.18
80 81 1.877443 CAACACCTTTAGTCCCGGTTG 59.123 52.381 0.00 0.00 0.00 3.77
81 82 1.202842 CCAACACCTTTAGTCCCGGTT 60.203 52.381 0.00 0.00 0.00 4.44
82 83 0.399075 CCAACACCTTTAGTCCCGGT 59.601 55.000 0.00 0.00 0.00 5.28
83 84 0.322187 CCCAACACCTTTAGTCCCGG 60.322 60.000 0.00 0.00 0.00 5.73
84 85 0.958876 GCCCAACACCTTTAGTCCCG 60.959 60.000 0.00 0.00 0.00 5.14
85 86 0.611062 GGCCCAACACCTTTAGTCCC 60.611 60.000 0.00 0.00 0.00 4.46
86 87 0.111639 TGGCCCAACACCTTTAGTCC 59.888 55.000 0.00 0.00 0.00 3.85
87 88 1.534729 CTGGCCCAACACCTTTAGTC 58.465 55.000 0.00 0.00 0.00 2.59
88 89 0.112412 CCTGGCCCAACACCTTTAGT 59.888 55.000 0.00 0.00 0.00 2.24
89 90 0.404040 TCCTGGCCCAACACCTTTAG 59.596 55.000 0.00 0.00 0.00 1.85
90 91 0.404040 CTCCTGGCCCAACACCTTTA 59.596 55.000 0.00 0.00 0.00 1.85
91 92 1.153756 CTCCTGGCCCAACACCTTT 59.846 57.895 0.00 0.00 0.00 3.11
92 93 2.846532 CTCCTGGCCCAACACCTT 59.153 61.111 0.00 0.00 0.00 3.50
93 94 3.971702 GCTCCTGGCCCAACACCT 61.972 66.667 0.00 0.00 34.27 4.00
95 96 4.329545 TCGCTCCTGGCCCAACAC 62.330 66.667 0.00 0.00 37.74 3.32
96 97 4.020617 CTCGCTCCTGGCCCAACA 62.021 66.667 0.00 0.00 37.74 3.33
97 98 4.785453 CCTCGCTCCTGGCCCAAC 62.785 72.222 0.00 0.00 37.74 3.77
103 104 3.801997 AATGGGCCTCGCTCCTGG 61.802 66.667 4.53 0.00 0.00 4.45
104 105 2.515523 CAATGGGCCTCGCTCCTG 60.516 66.667 4.53 0.00 0.00 3.86
105 106 3.801997 CCAATGGGCCTCGCTCCT 61.802 66.667 4.53 0.00 0.00 3.69
106 107 4.115199 ACCAATGGGCCTCGCTCC 62.115 66.667 4.53 0.00 37.90 4.70
107 108 2.514824 GACCAATGGGCCTCGCTC 60.515 66.667 4.53 0.00 37.90 5.03
114 115 2.754254 GAACCGGGACCAATGGGC 60.754 66.667 6.32 0.00 37.90 5.36
115 116 2.437716 CGAACCGGGACCAATGGG 60.438 66.667 6.32 0.00 41.29 4.00
116 117 2.038269 CACGAACCGGGACCAATGG 61.038 63.158 6.32 0.00 28.17 3.16
117 118 1.296056 GACACGAACCGGGACCAATG 61.296 60.000 6.32 0.00 32.98 2.82
118 119 1.004200 GACACGAACCGGGACCAAT 60.004 57.895 6.32 0.00 32.98 3.16
119 120 2.422591 GACACGAACCGGGACCAA 59.577 61.111 6.32 0.00 32.98 3.67
120 121 3.618750 GGACACGAACCGGGACCA 61.619 66.667 6.32 0.00 43.76 4.02
121 122 4.729856 CGGACACGAACCGGGACC 62.730 72.222 6.32 0.00 45.65 4.46
137 138 0.589708 GACTTTTGGTCCCGGTTTCG 59.410 55.000 0.00 0.00 38.93 3.46
138 139 1.878088 GAGACTTTTGGTCCCGGTTTC 59.122 52.381 0.00 0.00 45.54 2.78
139 140 1.213430 TGAGACTTTTGGTCCCGGTTT 59.787 47.619 0.00 0.00 45.54 3.27
140 141 0.841289 TGAGACTTTTGGTCCCGGTT 59.159 50.000 0.00 0.00 45.54 4.44
141 142 0.396811 CTGAGACTTTTGGTCCCGGT 59.603 55.000 0.00 0.00 45.54 5.28
142 143 0.321653 CCTGAGACTTTTGGTCCCGG 60.322 60.000 0.00 0.00 45.54 5.73
143 144 0.955919 GCCTGAGACTTTTGGTCCCG 60.956 60.000 0.00 0.00 45.54 5.14
144 145 0.955919 CGCCTGAGACTTTTGGTCCC 60.956 60.000 0.00 0.00 45.54 4.46
145 146 0.034896 TCGCCTGAGACTTTTGGTCC 59.965 55.000 0.00 0.00 45.54 4.46
146 147 1.531578 GTTCGCCTGAGACTTTTGGTC 59.468 52.381 0.00 0.00 44.80 4.02
147 148 1.141053 AGTTCGCCTGAGACTTTTGGT 59.859 47.619 0.00 0.00 0.00 3.67
148 149 1.532868 CAGTTCGCCTGAGACTTTTGG 59.467 52.381 0.00 0.00 44.49 3.28
149 150 1.532868 CCAGTTCGCCTGAGACTTTTG 59.467 52.381 3.77 0.00 44.49 2.44
150 151 1.543429 CCCAGTTCGCCTGAGACTTTT 60.543 52.381 3.77 0.00 44.49 2.27
151 152 0.035458 CCCAGTTCGCCTGAGACTTT 59.965 55.000 3.77 0.00 44.49 2.66
152 153 0.832135 TCCCAGTTCGCCTGAGACTT 60.832 55.000 3.77 0.00 44.49 3.01
153 154 1.228894 TCCCAGTTCGCCTGAGACT 60.229 57.895 3.77 0.00 44.49 3.24
154 155 1.079750 GTCCCAGTTCGCCTGAGAC 60.080 63.158 3.77 2.80 44.49 3.36
155 156 2.283529 GGTCCCAGTTCGCCTGAGA 61.284 63.158 3.77 0.00 44.49 3.27
156 157 2.111999 TTGGTCCCAGTTCGCCTGAG 62.112 60.000 3.77 0.00 44.49 3.35
157 158 1.488705 ATTGGTCCCAGTTCGCCTGA 61.489 55.000 3.77 0.00 44.49 3.86
158 159 1.002134 ATTGGTCCCAGTTCGCCTG 60.002 57.895 0.00 0.00 41.15 4.85
159 160 1.002134 CATTGGTCCCAGTTCGCCT 60.002 57.895 0.00 0.00 0.00 5.52
160 161 2.046285 CCATTGGTCCCAGTTCGCC 61.046 63.158 0.00 0.00 0.00 5.54
161 162 2.700773 GCCATTGGTCCCAGTTCGC 61.701 63.158 4.26 0.00 0.00 4.70
162 163 2.046285 GGCCATTGGTCCCAGTTCG 61.046 63.158 4.26 0.00 0.00 3.95
163 164 1.682344 GGGCCATTGGTCCCAGTTC 60.682 63.158 22.92 0.00 42.67 3.01
164 165 2.445155 GGGCCATTGGTCCCAGTT 59.555 61.111 22.92 0.00 42.67 3.16
170 171 2.364186 CCTTGGGGGCCATTGGTC 60.364 66.667 4.39 0.54 31.53 4.02
199 200 4.760047 CGGTTCGTGAGGCCAGGG 62.760 72.222 5.01 0.00 0.00 4.45
200 201 4.760047 CCGGTTCGTGAGGCCAGG 62.760 72.222 5.01 0.00 0.00 4.45
201 202 4.760047 CCCGGTTCGTGAGGCCAG 62.760 72.222 5.01 0.00 0.00 4.85
203 204 4.754667 GTCCCGGTTCGTGAGGCC 62.755 72.222 0.00 0.00 0.00 5.19
204 205 3.692406 AGTCCCGGTTCGTGAGGC 61.692 66.667 0.00 0.00 0.00 4.70
205 206 1.605058 ATCAGTCCCGGTTCGTGAGG 61.605 60.000 0.00 0.00 0.00 3.86
206 207 0.458543 CATCAGTCCCGGTTCGTGAG 60.459 60.000 0.00 0.00 0.00 3.51
207 208 1.589630 CATCAGTCCCGGTTCGTGA 59.410 57.895 0.00 0.00 0.00 4.35
208 209 2.100631 GCATCAGTCCCGGTTCGTG 61.101 63.158 0.00 0.00 0.00 4.35
209 210 2.264794 GCATCAGTCCCGGTTCGT 59.735 61.111 0.00 0.00 0.00 3.85
210 211 2.511600 GGCATCAGTCCCGGTTCG 60.512 66.667 0.00 0.00 0.00 3.95
211 212 2.124695 GGGCATCAGTCCCGGTTC 60.125 66.667 0.00 0.00 33.43 3.62
217 218 0.259938 ATCAAAGGGGGCATCAGTCC 59.740 55.000 0.00 0.00 39.43 3.85
218 219 1.685148 GATCAAAGGGGGCATCAGTC 58.315 55.000 0.00 0.00 0.00 3.51
219 220 0.259938 GGATCAAAGGGGGCATCAGT 59.740 55.000 0.00 0.00 0.00 3.41
220 221 0.468771 GGGATCAAAGGGGGCATCAG 60.469 60.000 0.00 0.00 0.00 2.90
221 222 1.620259 GGGATCAAAGGGGGCATCA 59.380 57.895 0.00 0.00 0.00 3.07
222 223 1.529244 CGGGATCAAAGGGGGCATC 60.529 63.158 0.00 0.00 0.00 3.91
223 224 2.603008 CGGGATCAAAGGGGGCAT 59.397 61.111 0.00 0.00 0.00 4.40
224 225 3.738481 CCGGGATCAAAGGGGGCA 61.738 66.667 0.00 0.00 0.00 5.36
225 226 3.296842 AACCGGGATCAAAGGGGGC 62.297 63.158 6.32 0.00 0.00 5.80
226 227 1.076995 GAACCGGGATCAAAGGGGG 60.077 63.158 6.32 0.00 0.00 5.40
227 228 1.451387 CGAACCGGGATCAAAGGGG 60.451 63.158 6.32 0.00 0.00 4.79
228 229 1.451387 CCGAACCGGGATCAAAGGG 60.451 63.158 6.32 0.00 44.15 3.95
229 230 4.218722 CCGAACCGGGATCAAAGG 57.781 61.111 6.32 0.00 44.15 3.11
239 240 1.374252 CCTGTTCACTCCCGAACCG 60.374 63.158 0.00 0.00 43.84 4.44
240 241 1.003718 CCCTGTTCACTCCCGAACC 60.004 63.158 0.00 0.00 43.84 3.62
241 242 0.613777 ATCCCTGTTCACTCCCGAAC 59.386 55.000 0.00 0.00 44.56 3.95
242 243 1.358152 AATCCCTGTTCACTCCCGAA 58.642 50.000 0.00 0.00 0.00 4.30
243 244 2.241281 TAATCCCTGTTCACTCCCGA 57.759 50.000 0.00 0.00 0.00 5.14
244 245 3.206150 CATTAATCCCTGTTCACTCCCG 58.794 50.000 0.00 0.00 0.00 5.14
245 246 2.952310 GCATTAATCCCTGTTCACTCCC 59.048 50.000 0.00 0.00 0.00 4.30
246 247 3.879892 GAGCATTAATCCCTGTTCACTCC 59.120 47.826 0.00 0.00 0.00 3.85
247 248 4.775236 AGAGCATTAATCCCTGTTCACTC 58.225 43.478 0.00 0.00 0.00 3.51
248 249 4.851639 AGAGCATTAATCCCTGTTCACT 57.148 40.909 0.00 0.00 0.00 3.41
249 250 5.297029 GGTAAGAGCATTAATCCCTGTTCAC 59.703 44.000 0.00 0.00 0.00 3.18
250 251 5.045213 TGGTAAGAGCATTAATCCCTGTTCA 60.045 40.000 0.00 0.00 0.00 3.18
251 252 5.437060 TGGTAAGAGCATTAATCCCTGTTC 58.563 41.667 0.00 0.00 0.00 3.18
252 253 5.440610 CTGGTAAGAGCATTAATCCCTGTT 58.559 41.667 0.00 0.00 0.00 3.16
253 254 4.141390 CCTGGTAAGAGCATTAATCCCTGT 60.141 45.833 0.00 0.00 0.00 4.00
254 255 4.392940 CCTGGTAAGAGCATTAATCCCTG 58.607 47.826 0.00 0.00 0.00 4.45
255 256 3.181439 GCCTGGTAAGAGCATTAATCCCT 60.181 47.826 0.00 0.00 0.00 4.20
256 257 3.149981 GCCTGGTAAGAGCATTAATCCC 58.850 50.000 0.00 0.00 0.00 3.85
257 258 3.149981 GGCCTGGTAAGAGCATTAATCC 58.850 50.000 0.00 0.00 0.00 3.01
258 259 4.068599 GAGGCCTGGTAAGAGCATTAATC 58.931 47.826 12.00 0.00 0.00 1.75
259 260 3.459598 TGAGGCCTGGTAAGAGCATTAAT 59.540 43.478 12.00 0.00 0.00 1.40
260 261 2.843730 TGAGGCCTGGTAAGAGCATTAA 59.156 45.455 12.00 0.00 0.00 1.40
261 262 2.477245 TGAGGCCTGGTAAGAGCATTA 58.523 47.619 12.00 0.00 0.00 1.90
262 263 1.289160 TGAGGCCTGGTAAGAGCATT 58.711 50.000 12.00 0.00 0.00 3.56
263 264 1.065126 GTTGAGGCCTGGTAAGAGCAT 60.065 52.381 12.00 0.00 0.00 3.79
264 265 0.324943 GTTGAGGCCTGGTAAGAGCA 59.675 55.000 12.00 0.00 0.00 4.26
265 266 0.393132 GGTTGAGGCCTGGTAAGAGC 60.393 60.000 12.00 0.00 0.00 4.09
266 267 0.984230 TGGTTGAGGCCTGGTAAGAG 59.016 55.000 12.00 0.00 0.00 2.85
267 268 1.440618 TTGGTTGAGGCCTGGTAAGA 58.559 50.000 12.00 0.00 0.00 2.10
268 269 2.162681 CTTTGGTTGAGGCCTGGTAAG 58.837 52.381 12.00 0.85 0.00 2.34
269 270 1.821666 GCTTTGGTTGAGGCCTGGTAA 60.822 52.381 12.00 0.00 0.00 2.85
270 271 0.251165 GCTTTGGTTGAGGCCTGGTA 60.251 55.000 12.00 0.00 0.00 3.25
271 272 1.531602 GCTTTGGTTGAGGCCTGGT 60.532 57.895 12.00 0.00 0.00 4.00
272 273 2.278330 GGCTTTGGTTGAGGCCTGG 61.278 63.158 12.00 0.00 41.20 4.45
273 274 3.369921 GGCTTTGGTTGAGGCCTG 58.630 61.111 12.00 0.00 41.20 4.85
276 277 1.115326 AACAGGGCTTTGGTTGAGGC 61.115 55.000 0.00 0.00 38.83 4.70
277 278 1.413118 AAACAGGGCTTTGGTTGAGG 58.587 50.000 0.00 0.00 0.00 3.86
278 279 2.695147 AGAAAACAGGGCTTTGGTTGAG 59.305 45.455 0.00 0.00 0.00 3.02
279 280 2.745968 AGAAAACAGGGCTTTGGTTGA 58.254 42.857 0.00 0.00 0.00 3.18
280 281 3.636764 AGTAGAAAACAGGGCTTTGGTTG 59.363 43.478 0.00 0.00 0.00 3.77
281 282 3.910989 AGTAGAAAACAGGGCTTTGGTT 58.089 40.909 0.00 0.00 0.00 3.67
282 283 3.595190 AGTAGAAAACAGGGCTTTGGT 57.405 42.857 0.00 0.00 0.00 3.67
283 284 4.455877 CACTAGTAGAAAACAGGGCTTTGG 59.544 45.833 3.59 0.00 0.00 3.28
284 285 4.455877 CCACTAGTAGAAAACAGGGCTTTG 59.544 45.833 3.59 0.00 0.00 2.77
285 286 4.104261 ACCACTAGTAGAAAACAGGGCTTT 59.896 41.667 3.59 0.00 0.00 3.51
286 287 3.651423 ACCACTAGTAGAAAACAGGGCTT 59.349 43.478 3.59 0.00 0.00 4.35
287 288 3.008049 CACCACTAGTAGAAAACAGGGCT 59.992 47.826 3.59 0.00 0.00 5.19
288 289 3.335579 CACCACTAGTAGAAAACAGGGC 58.664 50.000 3.59 0.00 0.00 5.19
289 290 3.008049 AGCACCACTAGTAGAAAACAGGG 59.992 47.826 3.59 0.00 0.00 4.45
290 291 4.273148 AGCACCACTAGTAGAAAACAGG 57.727 45.455 3.59 0.00 0.00 4.00
291 292 5.297547 TCAAGCACCACTAGTAGAAAACAG 58.702 41.667 3.59 0.00 0.00 3.16
292 293 5.284861 TCAAGCACCACTAGTAGAAAACA 57.715 39.130 3.59 0.00 0.00 2.83
293 294 6.803154 AATCAAGCACCACTAGTAGAAAAC 57.197 37.500 3.59 0.00 0.00 2.43
294 295 8.911918 TTTAATCAAGCACCACTAGTAGAAAA 57.088 30.769 3.59 0.00 0.00 2.29
295 296 8.946085 CATTTAATCAAGCACCACTAGTAGAAA 58.054 33.333 3.59 0.00 0.00 2.52
296 297 7.552687 CCATTTAATCAAGCACCACTAGTAGAA 59.447 37.037 3.59 0.00 0.00 2.10
297 298 7.047891 CCATTTAATCAAGCACCACTAGTAGA 58.952 38.462 3.59 0.00 0.00 2.59
298 299 6.823689 ACCATTTAATCAAGCACCACTAGTAG 59.176 38.462 0.00 0.00 0.00 2.57
299 300 6.597672 CACCATTTAATCAAGCACCACTAGTA 59.402 38.462 0.00 0.00 0.00 1.82
300 301 5.415701 CACCATTTAATCAAGCACCACTAGT 59.584 40.000 0.00 0.00 0.00 2.57
301 302 5.415701 ACACCATTTAATCAAGCACCACTAG 59.584 40.000 0.00 0.00 0.00 2.57
302 303 5.321102 ACACCATTTAATCAAGCACCACTA 58.679 37.500 0.00 0.00 0.00 2.74
303 304 4.151883 ACACCATTTAATCAAGCACCACT 58.848 39.130 0.00 0.00 0.00 4.00
304 305 4.519540 ACACCATTTAATCAAGCACCAC 57.480 40.909 0.00 0.00 0.00 4.16
305 306 6.656632 TTAACACCATTTAATCAAGCACCA 57.343 33.333 0.00 0.00 0.00 4.17
306 307 7.096551 ACATTAACACCATTTAATCAAGCACC 58.903 34.615 0.00 0.00 30.65 5.01
449 452 9.777843 CTTGCGATTTGTACTAAAAATGTTTTC 57.222 29.630 0.00 0.00 0.00 2.29
484 487 1.578897 TCATCCAATTCCGTCCTCCA 58.421 50.000 0.00 0.00 0.00 3.86
633 637 6.420604 TGATCGAAAACTTTCCAATTGCTTTC 59.579 34.615 0.00 1.61 33.68 2.62
1256 1285 1.376649 AGGGTGAGGGCAAGAATTCT 58.623 50.000 0.88 0.88 0.00 2.40
1291 1320 7.722728 AGGAGAGCTGCATATCATTTCAATAAA 59.277 33.333 1.02 0.00 0.00 1.40
1332 1361 8.913487 AGCAGGAGAAATCAAAATTCATTTTT 57.087 26.923 0.00 0.00 37.86 1.94
1844 2130 3.944015 CTGGCAAATTTCACCCAAAAACA 59.056 39.130 4.66 0.00 0.00 2.83
1845 2131 4.195416 TCTGGCAAATTTCACCCAAAAAC 58.805 39.130 4.66 0.00 0.00 2.43
1865 2153 4.452455 CAGCTGGTAATCGTTTTCAGTTCT 59.548 41.667 5.57 0.72 0.00 3.01
2005 2310 4.861102 AAAGCAAGCACATAGAAAAGCT 57.139 36.364 0.00 0.00 39.37 3.74
2348 2658 1.596934 CACGGATACCACAGGCACT 59.403 57.895 0.00 0.00 43.88 4.40
2469 2780 2.400399 TCTCTGCCGTGTTTAGTTTCG 58.600 47.619 0.00 0.00 0.00 3.46
2677 6329 0.397941 ACACAAGCTAAGAGCCAGCA 59.602 50.000 0.00 0.00 43.77 4.41


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

AutoCloner maintained by Alex Coulton.