Multiple sequence alignment - TraesCS5B01G503100

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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 TraesCS5B01G503100 chr5B 100.000 3536 0 0 1 3536 669737757 669741292 0.000000e+00 6530.0
1 TraesCS5B01G503100 chr5B 90.885 1909 159 11 961 2867 537974528 537972633 0.000000e+00 2547.0
2 TraesCS5B01G503100 chr5B 75.275 546 93 31 302 841 550147921 550148430 4.590000e-54 222.0
3 TraesCS5B01G503100 chr4A 97.196 2675 61 4 862 3536 624293343 624290683 0.000000e+00 4512.0
4 TraesCS5B01G503100 chr4A 92.922 551 21 5 309 841 624294079 624293529 0.000000e+00 785.0
5 TraesCS5B01G503100 chr1B 95.964 2676 106 2 862 3536 506333766 506336440 0.000000e+00 4342.0
6 TraesCS5B01G503100 chr1B 95.410 305 14 0 1 305 349174428 349174732 1.480000e-133 486.0
7 TraesCS5B01G503100 chr1B 95.395 304 14 0 2 305 95586336 95586033 5.310000e-133 484.0
8 TraesCS5B01G503100 chr1B 91.697 277 23 0 565 841 506333307 506333583 5.540000e-103 385.0
9 TraesCS5B01G503100 chr1B 91.386 267 17 4 308 574 506333004 506333264 9.330000e-96 361.0
10 TraesCS5B01G503100 chr5A 96.112 2675 72 6 862 3536 638407337 638404695 0.000000e+00 4335.0
11 TraesCS5B01G503100 chr5A 97.433 1714 42 2 1823 3536 631794045 631792334 0.000000e+00 2920.0
12 TraesCS5B01G503100 chr5A 91.877 554 28 8 305 841 638408075 638407522 0.000000e+00 758.0
13 TraesCS5B01G503100 chr5A 86.435 575 39 17 306 841 631794980 631794406 8.450000e-166 593.0
14 TraesCS5B01G503100 chr5A 89.375 160 5 3 862 1021 631794220 631794073 1.300000e-44 191.0
15 TraesCS5B01G503100 chr6B 94.026 2578 152 2 957 3534 294340989 294343564 0.000000e+00 3906.0
16 TraesCS5B01G503100 chr6B 86.982 169 18 4 305 472 90311923 90312088 1.680000e-43 187.0
17 TraesCS5B01G503100 chr7A 96.944 2160 53 3 863 3022 659714477 659716623 0.000000e+00 3611.0
18 TraesCS5B01G503100 chr7A 89.560 546 41 10 306 841 659713751 659714290 0.000000e+00 678.0
19 TraesCS5B01G503100 chr7A 97.368 38 1 0 495 532 659713886 659713923 8.190000e-07 65.8
20 TraesCS5B01G503100 chr7B 92.374 2308 167 7 1192 3499 712180109 712177811 0.000000e+00 3278.0
21 TraesCS5B01G503100 chr2B 93.251 1867 123 3 1671 3536 397051321 397053185 0.000000e+00 2747.0
22 TraesCS5B01G503100 chr2B 95.724 304 13 0 2 305 469757811 469758114 1.140000e-134 490.0
23 TraesCS5B01G503100 chr2B 94.386 285 14 2 301 585 581621486 581621768 1.510000e-118 436.0
24 TraesCS5B01G503100 chr2B 91.273 275 24 0 567 841 581621779 581622053 3.330000e-100 375.0
25 TraesCS5B01G503100 chr2B 94.964 139 7 0 862 1000 581622240 581622378 5.940000e-53 219.0
26 TraesCS5B01G503100 chr5D 91.147 1909 154 10 962 2867 441937339 441935443 0.000000e+00 2575.0
27 TraesCS5B01G503100 chr3B 90.680 794 69 3 2744 3536 758628855 758629644 0.000000e+00 1051.0
28 TraesCS5B01G503100 chr3B 88.291 316 33 1 3199 3510 55375054 55375369 3.330000e-100 375.0
29 TraesCS5B01G503100 chr3B 77.355 552 78 30 306 841 758627518 758628038 2.080000e-72 283.0
30 TraesCS5B01G503100 chr4D 95.738 305 13 0 1 305 196966434 196966130 3.170000e-135 492.0
31 TraesCS5B01G503100 chr6A 95.710 303 13 0 1 303 550891191 550891493 4.100000e-134 488.0
32 TraesCS5B01G503100 chr2D 95.410 305 14 0 1 305 58270295 58269991 1.480000e-133 486.0
33 TraesCS5B01G503100 chr2D 95.410 305 14 0 1 305 104557841 104557537 1.480000e-133 486.0
34 TraesCS5B01G503100 chr2D 95.410 305 14 0 1 305 510438023 510438327 1.480000e-133 486.0
35 TraesCS5B01G503100 chr2D 95.395 304 14 0 2 305 41831059 41831362 5.310000e-133 484.0


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 TraesCS5B01G503100 chr5B 669737757 669741292 3535 False 6530.000000 6530 100.000000 1 3536 1 chr5B.!!$F2 3535
1 TraesCS5B01G503100 chr5B 537972633 537974528 1895 True 2547.000000 2547 90.885000 961 2867 1 chr5B.!!$R1 1906
2 TraesCS5B01G503100 chr5B 550147921 550148430 509 False 222.000000 222 75.275000 302 841 1 chr5B.!!$F1 539
3 TraesCS5B01G503100 chr4A 624290683 624294079 3396 True 2648.500000 4512 95.059000 309 3536 2 chr4A.!!$R1 3227
4 TraesCS5B01G503100 chr1B 506333004 506336440 3436 False 1696.000000 4342 93.015667 308 3536 3 chr1B.!!$F2 3228
5 TraesCS5B01G503100 chr5A 638404695 638408075 3380 True 2546.500000 4335 93.994500 305 3536 2 chr5A.!!$R2 3231
6 TraesCS5B01G503100 chr5A 631792334 631794980 2646 True 1234.666667 2920 91.081000 306 3536 3 chr5A.!!$R1 3230
7 TraesCS5B01G503100 chr6B 294340989 294343564 2575 False 3906.000000 3906 94.026000 957 3534 1 chr6B.!!$F2 2577
8 TraesCS5B01G503100 chr7A 659713751 659716623 2872 False 1451.600000 3611 94.624000 306 3022 3 chr7A.!!$F1 2716
9 TraesCS5B01G503100 chr7B 712177811 712180109 2298 True 3278.000000 3278 92.374000 1192 3499 1 chr7B.!!$R1 2307
10 TraesCS5B01G503100 chr2B 397051321 397053185 1864 False 2747.000000 2747 93.251000 1671 3536 1 chr2B.!!$F1 1865
11 TraesCS5B01G503100 chr2B 581621486 581622378 892 False 343.333333 436 93.541000 301 1000 3 chr2B.!!$F3 699
12 TraesCS5B01G503100 chr5D 441935443 441937339 1896 True 2575.000000 2575 91.147000 962 2867 1 chr5D.!!$R1 1905
13 TraesCS5B01G503100 chr3B 758627518 758629644 2126 False 667.000000 1051 84.017500 306 3536 2 chr3B.!!$F2 3230

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
206 207 0.032117 TCATCCACCATCGACCTCCT 60.032 55.0 0.0 0.0 0.0 3.69 F
290 291 0.034337 TCCACCGGCTACTGTTCAAC 59.966 55.0 0.0 0.0 0.0 3.18 F
301 302 0.036875 CTGTTCAACCACCCCTCTCC 59.963 60.0 0.0 0.0 0.0 3.71 F
303 304 0.250770 GTTCAACCACCCCTCTCCAC 60.251 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1811 0.040958 CTTGACGCAAGAGTTGTGCC 60.041 55.000 12.43 0.0 43.42 5.01 R
1733 2071 2.649531 TCTTCCACCACGGTCAAAAT 57.350 45.000 0.00 0.0 35.57 1.82 R
2143 2483 4.518211 CCTCTCATATTTGAAGCACCATCC 59.482 45.833 0.00 0.0 0.00 3.51 R
2758 3718 7.744276 TCTTGAACGTCACAAAATAAATCATCG 59.256 33.333 8.91 0.0 0.00 3.84 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 2.186903 CGGGGGTCCTGTTGATCG 59.813 66.667 0.00 0.00 0.00 3.69
18 19 2.590092 GGGGGTCCTGTTGATCGG 59.410 66.667 0.00 0.00 0.00 4.18
19 20 2.590092 GGGGTCCTGTTGATCGGG 59.410 66.667 0.00 0.00 43.70 5.14
23 24 4.050313 TCCTGTTGATCGGGAGGG 57.950 61.111 4.39 0.00 45.77 4.30
24 25 1.689233 TCCTGTTGATCGGGAGGGG 60.689 63.158 4.39 0.00 45.77 4.79
25 26 1.995626 CCTGTTGATCGGGAGGGGT 60.996 63.158 0.00 0.00 45.09 4.95
26 27 1.221840 CTGTTGATCGGGAGGGGTG 59.778 63.158 0.00 0.00 0.00 4.61
27 28 1.537889 TGTTGATCGGGAGGGGTGT 60.538 57.895 0.00 0.00 0.00 4.16
28 29 1.078426 GTTGATCGGGAGGGGTGTG 60.078 63.158 0.00 0.00 0.00 3.82
29 30 2.297895 TTGATCGGGAGGGGTGTGG 61.298 63.158 0.00 0.00 0.00 4.17
30 31 2.687566 GATCGGGAGGGGTGTGGT 60.688 66.667 0.00 0.00 0.00 4.16
31 32 3.009115 ATCGGGAGGGGTGTGGTG 61.009 66.667 0.00 0.00 0.00 4.17
32 33 3.864983 ATCGGGAGGGGTGTGGTGT 62.865 63.158 0.00 0.00 0.00 4.16
33 34 2.465010 ATCGGGAGGGGTGTGGTGTA 62.465 60.000 0.00 0.00 0.00 2.90
34 35 2.951101 CGGGAGGGGTGTGGTGTAC 61.951 68.421 0.00 0.00 0.00 2.90
35 36 2.599757 GGGAGGGGTGTGGTGTACC 61.600 68.421 0.00 0.00 37.48 3.34
36 37 2.660802 GAGGGGTGTGGTGTACCG 59.339 66.667 0.00 0.00 39.14 4.02
43 44 4.905836 GTGGTGTACCGCAAAACG 57.094 55.556 9.62 0.00 45.55 3.60
52 53 3.791446 CGCAAAACGGACGAAACG 58.209 55.556 0.00 0.00 38.44 3.60
53 54 1.719766 CGCAAAACGGACGAAACGG 60.720 57.895 0.00 0.00 38.44 4.44
54 55 1.642753 GCAAAACGGACGAAACGGA 59.357 52.632 0.00 0.00 35.23 4.69
55 56 0.655337 GCAAAACGGACGAAACGGAC 60.655 55.000 0.00 0.00 35.23 4.79
56 57 0.932399 CAAAACGGACGAAACGGACT 59.068 50.000 0.00 0.00 35.23 3.85
57 58 1.328374 CAAAACGGACGAAACGGACTT 59.672 47.619 0.00 0.00 35.23 3.01
58 59 0.932399 AAACGGACGAAACGGACTTG 59.068 50.000 0.00 0.00 35.23 3.16
59 60 0.179103 AACGGACGAAACGGACTTGT 60.179 50.000 0.00 0.00 35.23 3.16
60 61 0.872881 ACGGACGAAACGGACTTGTG 60.873 55.000 0.00 0.00 35.23 3.33
61 62 0.872881 CGGACGAAACGGACTTGTGT 60.873 55.000 0.00 0.00 0.00 3.72
62 63 1.292992 GGACGAAACGGACTTGTGTT 58.707 50.000 0.00 0.00 0.00 3.32
63 64 1.004292 GGACGAAACGGACTTGTGTTG 60.004 52.381 0.00 0.00 0.00 3.33
64 65 1.004292 GACGAAACGGACTTGTGTTGG 60.004 52.381 0.00 0.00 0.00 3.77
65 66 1.292061 CGAAACGGACTTGTGTTGGA 58.708 50.000 0.00 0.00 0.00 3.53
66 67 1.260561 CGAAACGGACTTGTGTTGGAG 59.739 52.381 0.00 0.00 0.00 3.86
67 68 1.002792 GAAACGGACTTGTGTTGGAGC 60.003 52.381 0.00 0.00 0.00 4.70
68 69 0.107410 AACGGACTTGTGTTGGAGCA 60.107 50.000 0.00 0.00 0.00 4.26
69 70 0.814010 ACGGACTTGTGTTGGAGCAC 60.814 55.000 0.00 0.00 39.65 4.40
70 71 0.532862 CGGACTTGTGTTGGAGCACT 60.533 55.000 0.00 0.00 39.89 4.40
71 72 1.230324 GGACTTGTGTTGGAGCACTC 58.770 55.000 0.00 0.00 39.89 3.51
80 81 2.654877 GGAGCACTCCGGTCGAAA 59.345 61.111 0.00 0.00 43.39 3.46
81 82 1.737008 GGAGCACTCCGGTCGAAAC 60.737 63.158 0.00 0.00 43.39 2.78
82 83 1.006571 GAGCACTCCGGTCGAAACA 60.007 57.895 0.00 0.00 31.26 2.83
83 84 1.006102 AGCACTCCGGTCGAAACAG 60.006 57.895 0.00 0.00 0.00 3.16
84 85 2.027625 GCACTCCGGTCGAAACAGG 61.028 63.158 0.00 0.00 41.65 4.00
85 86 1.374252 CACTCCGGTCGAAACAGGG 60.374 63.158 0.00 0.00 40.76 4.45
86 87 2.264794 CTCCGGTCGAAACAGGGG 59.735 66.667 0.00 0.00 40.76 4.79
87 88 2.524887 TCCGGTCGAAACAGGGGT 60.525 61.111 0.00 0.00 40.76 4.95
88 89 2.047560 CCGGTCGAAACAGGGGTC 60.048 66.667 0.00 0.00 37.12 4.46
89 90 2.047560 CGGTCGAAACAGGGGTCC 60.048 66.667 0.00 0.00 0.00 4.46
90 91 2.580601 CGGTCGAAACAGGGGTCCT 61.581 63.158 0.00 0.00 0.00 3.85
98 99 4.941609 CAGGGGTCCTGTTCATCG 57.058 61.111 5.82 0.00 45.82 3.84
99 100 1.221840 CAGGGGTCCTGTTCATCGG 59.778 63.158 5.82 0.00 45.82 4.18
100 101 1.995626 AGGGGTCCTGTTCATCGGG 60.996 63.158 0.00 0.00 43.70 5.14
104 105 4.050313 TCCTGTTCATCGGGAGGG 57.950 61.111 0.00 0.00 45.77 4.30
105 106 1.689233 TCCTGTTCATCGGGAGGGG 60.689 63.158 0.00 0.00 45.77 4.79
106 107 1.995626 CCTGTTCATCGGGAGGGGT 60.996 63.158 0.00 0.00 45.09 4.95
107 108 1.221840 CTGTTCATCGGGAGGGGTG 59.778 63.158 0.00 0.00 0.00 4.61
108 109 1.537889 TGTTCATCGGGAGGGGTGT 60.538 57.895 0.00 0.00 0.00 4.16
109 110 1.078426 GTTCATCGGGAGGGGTGTG 60.078 63.158 0.00 0.00 0.00 3.82
110 111 2.297895 TTCATCGGGAGGGGTGTGG 61.298 63.158 0.00 0.00 0.00 4.17
111 112 4.489771 CATCGGGAGGGGTGTGGC 62.490 72.222 0.00 0.00 0.00 5.01
115 116 4.091939 GGGAGGGGTGTGGCGTAC 62.092 72.222 0.00 0.00 0.00 3.67
116 117 4.091939 GGAGGGGTGTGGCGTACC 62.092 72.222 1.65 1.65 37.48 3.34
117 118 4.446413 GAGGGGTGTGGCGTACCG 62.446 72.222 4.21 0.00 39.14 4.02
135 136 1.860078 GCAAAACGAGACTCCACGG 59.140 57.895 0.00 0.00 0.00 4.94
136 137 1.566018 GCAAAACGAGACTCCACGGG 61.566 60.000 0.00 0.00 0.00 5.28
137 138 0.032952 CAAAACGAGACTCCACGGGA 59.967 55.000 0.00 0.00 0.00 5.14
138 139 0.974383 AAAACGAGACTCCACGGGAT 59.026 50.000 0.00 0.00 0.00 3.85
139 140 1.843368 AAACGAGACTCCACGGGATA 58.157 50.000 0.00 0.00 0.00 2.59
140 141 1.101331 AACGAGACTCCACGGGATAC 58.899 55.000 0.00 0.00 0.00 2.24
141 142 0.255318 ACGAGACTCCACGGGATACT 59.745 55.000 0.00 0.00 0.00 2.12
153 154 3.099267 CGGGATACTGTTCATCTCCAC 57.901 52.381 0.00 0.00 38.54 4.02
154 155 2.224066 CGGGATACTGTTCATCTCCACC 60.224 54.545 0.00 0.00 38.54 4.61
155 156 2.224066 GGGATACTGTTCATCTCCACCG 60.224 54.545 0.00 0.00 0.00 4.94
156 157 2.431057 GGATACTGTTCATCTCCACCGT 59.569 50.000 0.00 0.00 0.00 4.83
157 158 3.491104 GGATACTGTTCATCTCCACCGTC 60.491 52.174 0.00 0.00 0.00 4.79
158 159 0.243907 ACTGTTCATCTCCACCGTCG 59.756 55.000 0.00 0.00 0.00 5.12
159 160 0.526211 CTGTTCATCTCCACCGTCGA 59.474 55.000 0.00 0.00 0.00 4.20
160 161 0.242825 TGTTCATCTCCACCGTCGAC 59.757 55.000 5.18 5.18 0.00 4.20
161 162 0.458025 GTTCATCTCCACCGTCGACC 60.458 60.000 10.58 0.00 0.00 4.79
162 163 0.611062 TTCATCTCCACCGTCGACCT 60.611 55.000 10.58 0.00 0.00 3.85
163 164 1.030488 TCATCTCCACCGTCGACCTC 61.030 60.000 10.58 0.00 0.00 3.85
164 165 1.753463 ATCTCCACCGTCGACCTCC 60.753 63.158 10.58 0.00 0.00 4.30
165 166 2.212794 ATCTCCACCGTCGACCTCCT 62.213 60.000 10.58 0.00 0.00 3.69
166 167 2.360852 TCCACCGTCGACCTCCTC 60.361 66.667 10.58 0.00 0.00 3.71
167 168 3.450115 CCACCGTCGACCTCCTCC 61.450 72.222 10.58 0.00 0.00 4.30
168 169 2.675423 CACCGTCGACCTCCTCCA 60.675 66.667 10.58 0.00 0.00 3.86
169 170 2.116772 ACCGTCGACCTCCTCCAA 59.883 61.111 10.58 0.00 0.00 3.53
170 171 2.273912 ACCGTCGACCTCCTCCAAC 61.274 63.158 10.58 0.00 0.00 3.77
171 172 2.572284 CGTCGACCTCCTCCAACC 59.428 66.667 10.58 0.00 0.00 3.77
172 173 1.977544 CGTCGACCTCCTCCAACCT 60.978 63.158 10.58 0.00 0.00 3.50
173 174 1.891616 GTCGACCTCCTCCAACCTC 59.108 63.158 3.51 0.00 0.00 3.85
174 175 1.305046 TCGACCTCCTCCAACCTCC 60.305 63.158 0.00 0.00 0.00 4.30
175 176 1.609501 CGACCTCCTCCAACCTCCA 60.610 63.158 0.00 0.00 0.00 3.86
176 177 1.192146 CGACCTCCTCCAACCTCCAA 61.192 60.000 0.00 0.00 0.00 3.53
177 178 0.615850 GACCTCCTCCAACCTCCAAG 59.384 60.000 0.00 0.00 0.00 3.61
178 179 0.842467 ACCTCCTCCAACCTCCAAGG 60.842 60.000 0.00 0.00 42.49 3.61
179 180 1.566298 CCTCCTCCAACCTCCAAGGG 61.566 65.000 0.00 0.00 40.58 3.95
180 181 2.203549 CTCCTCCAACCTCCAAGGGC 62.204 65.000 0.00 0.00 40.58 5.19
181 182 2.234296 CCTCCAACCTCCAAGGGCT 61.234 63.158 0.00 0.00 40.58 5.19
182 183 0.914417 CCTCCAACCTCCAAGGGCTA 60.914 60.000 0.00 0.00 40.58 3.93
183 184 0.253327 CTCCAACCTCCAAGGGCTAC 59.747 60.000 0.00 0.00 40.58 3.58
184 185 0.178873 TCCAACCTCCAAGGGCTACT 60.179 55.000 0.00 0.00 40.58 2.57
185 186 0.035056 CCAACCTCCAAGGGCTACTG 60.035 60.000 0.00 0.00 40.58 2.74
186 187 0.693049 CAACCTCCAAGGGCTACTGT 59.307 55.000 0.00 0.00 40.58 3.55
187 188 1.073923 CAACCTCCAAGGGCTACTGTT 59.926 52.381 0.00 0.00 40.58 3.16
188 189 0.984995 ACCTCCAAGGGCTACTGTTC 59.015 55.000 0.00 0.00 40.58 3.18
189 190 0.984230 CCTCCAAGGGCTACTGTTCA 59.016 55.000 0.00 0.00 0.00 3.18
190 191 1.561542 CCTCCAAGGGCTACTGTTCAT 59.438 52.381 0.00 0.00 0.00 2.57
191 192 2.420687 CCTCCAAGGGCTACTGTTCATC 60.421 54.545 0.00 0.00 0.00 2.92
192 193 1.559682 TCCAAGGGCTACTGTTCATCC 59.440 52.381 0.00 0.00 0.00 3.51
193 194 1.281867 CCAAGGGCTACTGTTCATCCA 59.718 52.381 0.00 0.00 0.00 3.41
194 195 2.359900 CAAGGGCTACTGTTCATCCAC 58.640 52.381 0.00 0.00 0.00 4.02
195 196 0.912486 AGGGCTACTGTTCATCCACC 59.088 55.000 0.00 0.00 0.00 4.61
196 197 0.618458 GGGCTACTGTTCATCCACCA 59.382 55.000 0.00 0.00 0.00 4.17
197 198 1.212935 GGGCTACTGTTCATCCACCAT 59.787 52.381 0.00 0.00 0.00 3.55
198 199 2.565841 GGCTACTGTTCATCCACCATC 58.434 52.381 0.00 0.00 0.00 3.51
199 200 2.205074 GCTACTGTTCATCCACCATCG 58.795 52.381 0.00 0.00 0.00 3.84
200 201 2.159099 GCTACTGTTCATCCACCATCGA 60.159 50.000 0.00 0.00 0.00 3.59
201 202 2.386661 ACTGTTCATCCACCATCGAC 57.613 50.000 0.00 0.00 0.00 4.20
202 203 1.066143 ACTGTTCATCCACCATCGACC 60.066 52.381 0.00 0.00 0.00 4.79
203 204 1.208052 CTGTTCATCCACCATCGACCT 59.792 52.381 0.00 0.00 0.00 3.85
204 205 1.207089 TGTTCATCCACCATCGACCTC 59.793 52.381 0.00 0.00 0.00 3.85
205 206 0.830648 TTCATCCACCATCGACCTCC 59.169 55.000 0.00 0.00 0.00 4.30
206 207 0.032117 TCATCCACCATCGACCTCCT 60.032 55.000 0.00 0.00 0.00 3.69
207 208 0.390860 CATCCACCATCGACCTCCTC 59.609 60.000 0.00 0.00 0.00 3.71
208 209 0.760945 ATCCACCATCGACCTCCTCC 60.761 60.000 0.00 0.00 0.00 4.30
209 210 1.685765 CCACCATCGACCTCCTCCA 60.686 63.158 0.00 0.00 0.00 3.86
210 211 1.680522 CCACCATCGACCTCCTCCAG 61.681 65.000 0.00 0.00 0.00 3.86
211 212 2.060980 ACCATCGACCTCCTCCAGC 61.061 63.158 0.00 0.00 0.00 4.85
212 213 2.801631 CCATCGACCTCCTCCAGCC 61.802 68.421 0.00 0.00 0.00 4.85
213 214 1.760086 CATCGACCTCCTCCAGCCT 60.760 63.158 0.00 0.00 0.00 4.58
214 215 1.002274 ATCGACCTCCTCCAGCCTT 59.998 57.895 0.00 0.00 0.00 4.35
215 216 1.045911 ATCGACCTCCTCCAGCCTTC 61.046 60.000 0.00 0.00 0.00 3.46
216 217 1.984570 CGACCTCCTCCAGCCTTCA 60.985 63.158 0.00 0.00 0.00 3.02
217 218 1.599576 GACCTCCTCCAGCCTTCAC 59.400 63.158 0.00 0.00 0.00 3.18
218 219 1.904990 GACCTCCTCCAGCCTTCACC 61.905 65.000 0.00 0.00 0.00 4.02
219 220 2.674220 CCTCCTCCAGCCTTCACCC 61.674 68.421 0.00 0.00 0.00 4.61
220 221 3.003173 TCCTCCAGCCTTCACCCG 61.003 66.667 0.00 0.00 0.00 5.28
221 222 4.785453 CCTCCAGCCTTCACCCGC 62.785 72.222 0.00 0.00 0.00 6.13
225 226 4.379243 CAGCCTTCACCCGCGACT 62.379 66.667 8.23 0.00 0.00 4.18
226 227 4.379243 AGCCTTCACCCGCGACTG 62.379 66.667 8.23 1.36 0.00 3.51
227 228 4.681978 GCCTTCACCCGCGACTGT 62.682 66.667 8.23 0.00 0.00 3.55
228 229 2.030562 CCTTCACCCGCGACTGTT 59.969 61.111 8.23 0.00 0.00 3.16
229 230 2.027625 CCTTCACCCGCGACTGTTC 61.028 63.158 8.23 0.00 0.00 3.18
230 231 1.300620 CTTCACCCGCGACTGTTCA 60.301 57.895 8.23 0.00 0.00 3.18
231 232 0.670546 CTTCACCCGCGACTGTTCAT 60.671 55.000 8.23 0.00 0.00 2.57
232 233 0.669318 TTCACCCGCGACTGTTCATC 60.669 55.000 8.23 0.00 0.00 2.92
233 234 2.100631 CACCCGCGACTGTTCATCC 61.101 63.158 8.23 0.00 0.00 3.51
234 235 2.264480 CCCGCGACTGTTCATCCA 59.736 61.111 8.23 0.00 0.00 3.41
235 236 2.100631 CCCGCGACTGTTCATCCAC 61.101 63.158 8.23 0.00 0.00 4.02
236 237 2.444624 CCGCGACTGTTCATCCACG 61.445 63.158 8.23 0.00 0.00 4.94
237 238 2.444624 CGCGACTGTTCATCCACGG 61.445 63.158 0.00 0.00 0.00 4.94
238 239 1.374252 GCGACTGTTCATCCACGGT 60.374 57.895 0.00 0.00 39.09 4.83
239 240 1.352156 GCGACTGTTCATCCACGGTC 61.352 60.000 3.14 3.14 45.98 4.79
240 241 0.243907 CGACTGTTCATCCACGGTCT 59.756 55.000 10.32 0.00 46.88 3.85
241 242 1.732732 CGACTGTTCATCCACGGTCTC 60.733 57.143 10.32 0.00 46.88 3.36
242 243 0.608640 ACTGTTCATCCACGGTCTCC 59.391 55.000 0.00 0.00 29.64 3.71
243 244 0.898320 CTGTTCATCCACGGTCTCCT 59.102 55.000 0.00 0.00 0.00 3.69
244 245 2.100197 CTGTTCATCCACGGTCTCCTA 58.900 52.381 0.00 0.00 0.00 2.94
245 246 2.695666 CTGTTCATCCACGGTCTCCTAT 59.304 50.000 0.00 0.00 0.00 2.57
246 247 3.104512 TGTTCATCCACGGTCTCCTATT 58.895 45.455 0.00 0.00 0.00 1.73
247 248 3.132289 TGTTCATCCACGGTCTCCTATTC 59.868 47.826 0.00 0.00 0.00 1.75
248 249 3.026707 TCATCCACGGTCTCCTATTCA 57.973 47.619 0.00 0.00 0.00 2.57
249 250 3.576861 TCATCCACGGTCTCCTATTCAT 58.423 45.455 0.00 0.00 0.00 2.57
250 251 3.574396 TCATCCACGGTCTCCTATTCATC 59.426 47.826 0.00 0.00 0.00 2.92
251 252 2.317040 TCCACGGTCTCCTATTCATCC 58.683 52.381 0.00 0.00 0.00 3.51
252 253 2.039418 CCACGGTCTCCTATTCATCCA 58.961 52.381 0.00 0.00 0.00 3.41
253 254 2.036475 CCACGGTCTCCTATTCATCCAG 59.964 54.545 0.00 0.00 0.00 3.86
254 255 1.689273 ACGGTCTCCTATTCATCCAGC 59.311 52.381 0.00 0.00 0.00 4.85
255 256 1.001406 CGGTCTCCTATTCATCCAGCC 59.999 57.143 0.00 0.00 0.00 4.85
256 257 2.334023 GGTCTCCTATTCATCCAGCCT 58.666 52.381 0.00 0.00 0.00 4.58
257 258 2.301583 GGTCTCCTATTCATCCAGCCTC 59.698 54.545 0.00 0.00 0.00 4.70
258 259 2.301583 GTCTCCTATTCATCCAGCCTCC 59.698 54.545 0.00 0.00 0.00 4.30
259 260 2.090550 TCTCCTATTCATCCAGCCTCCA 60.091 50.000 0.00 0.00 0.00 3.86
260 261 2.038295 CTCCTATTCATCCAGCCTCCAC 59.962 54.545 0.00 0.00 0.00 4.02
261 262 1.072965 CCTATTCATCCAGCCTCCACC 59.927 57.143 0.00 0.00 0.00 4.61
262 263 0.758734 TATTCATCCAGCCTCCACCG 59.241 55.000 0.00 0.00 0.00 4.94
263 264 2.615227 ATTCATCCAGCCTCCACCGC 62.615 60.000 0.00 0.00 0.00 5.68
281 282 3.524606 GCGCTACTCCACCGGCTA 61.525 66.667 0.00 0.00 0.00 3.93
282 283 2.412112 CGCTACTCCACCGGCTAC 59.588 66.667 0.00 0.00 0.00 3.58
283 284 2.119655 CGCTACTCCACCGGCTACT 61.120 63.158 0.00 0.00 0.00 2.57
284 285 1.437986 GCTACTCCACCGGCTACTG 59.562 63.158 0.00 0.00 0.00 2.74
285 286 1.321074 GCTACTCCACCGGCTACTGT 61.321 60.000 0.00 0.00 0.00 3.55
286 287 1.183549 CTACTCCACCGGCTACTGTT 58.816 55.000 0.00 0.00 0.00 3.16
287 288 1.134560 CTACTCCACCGGCTACTGTTC 59.865 57.143 0.00 0.00 0.00 3.18
288 289 0.830444 ACTCCACCGGCTACTGTTCA 60.830 55.000 0.00 0.00 0.00 3.18
289 290 0.320374 CTCCACCGGCTACTGTTCAA 59.680 55.000 0.00 0.00 0.00 2.69
290 291 0.034337 TCCACCGGCTACTGTTCAAC 59.966 55.000 0.00 0.00 0.00 3.18
291 292 0.953960 CCACCGGCTACTGTTCAACC 60.954 60.000 0.00 0.00 0.00 3.77
292 293 0.250124 CACCGGCTACTGTTCAACCA 60.250 55.000 0.00 0.00 0.00 3.67
293 294 0.250166 ACCGGCTACTGTTCAACCAC 60.250 55.000 0.00 0.00 0.00 4.16
294 295 0.953960 CCGGCTACTGTTCAACCACC 60.954 60.000 0.00 0.00 0.00 4.61
295 296 0.953960 CGGCTACTGTTCAACCACCC 60.954 60.000 0.00 0.00 0.00 4.61
296 297 0.608308 GGCTACTGTTCAACCACCCC 60.608 60.000 0.00 0.00 0.00 4.95
297 298 0.400594 GCTACTGTTCAACCACCCCT 59.599 55.000 0.00 0.00 0.00 4.79
298 299 1.610886 GCTACTGTTCAACCACCCCTC 60.611 57.143 0.00 0.00 0.00 4.30
299 300 1.978580 CTACTGTTCAACCACCCCTCT 59.021 52.381 0.00 0.00 0.00 3.69
300 301 0.765510 ACTGTTCAACCACCCCTCTC 59.234 55.000 0.00 0.00 0.00 3.20
301 302 0.036875 CTGTTCAACCACCCCTCTCC 59.963 60.000 0.00 0.00 0.00 3.71
302 303 0.696143 TGTTCAACCACCCCTCTCCA 60.696 55.000 0.00 0.00 0.00 3.86
303 304 0.250770 GTTCAACCACCCCTCTCCAC 60.251 60.000 0.00 0.00 0.00 4.02
405 408 8.974060 ATTAAATAAAGGGCTAAACTGATCGA 57.026 30.769 0.00 0.00 0.00 3.59
427 430 5.277634 CGATAACTTAATTTACCCGGGCAAG 60.278 44.000 24.08 16.08 0.00 4.01
446 449 2.477972 GAAAGCAACTGGGCCTTCGC 62.478 60.000 4.53 2.05 0.00 4.70
489 501 7.535139 CCCAACAATCAACAAACGATTAGTAT 58.465 34.615 0.00 0.00 31.88 2.12
590 676 2.737783 TCTCTCTCGTGTCTCTTCGTTC 59.262 50.000 0.00 0.00 0.00 3.95
595 681 2.160205 TCGTGTCTCTTCGTTCCTCAT 58.840 47.619 0.00 0.00 0.00 2.90
841 950 4.081087 TGAATAGTTGGTCTGGGAAGTAGC 60.081 45.833 0.00 0.00 0.00 3.58
842 951 0.984995 AGTTGGTCTGGGAAGTAGCC 59.015 55.000 0.00 0.00 0.00 3.93
843 952 0.690762 GTTGGTCTGGGAAGTAGCCA 59.309 55.000 0.00 0.00 0.00 4.75
844 953 1.073284 GTTGGTCTGGGAAGTAGCCAA 59.927 52.381 0.00 0.00 32.67 4.52
845 954 0.984230 TGGTCTGGGAAGTAGCCAAG 59.016 55.000 0.00 0.00 0.00 3.61
846 955 0.984995 GGTCTGGGAAGTAGCCAAGT 59.015 55.000 0.00 0.00 30.51 3.16
847 956 2.185387 GGTCTGGGAAGTAGCCAAGTA 58.815 52.381 0.00 0.00 30.51 2.24
848 957 2.168728 GGTCTGGGAAGTAGCCAAGTAG 59.831 54.545 0.00 0.00 30.51 2.57
860 969 2.105477 AGCCAAGTAGGATTGATGCGAT 59.895 45.455 0.00 0.00 41.22 4.58
882 1208 3.052036 GCAACTTGCAAACTGTGGTATG 58.948 45.455 8.97 0.00 44.26 2.39
943 1279 8.553459 AGAATTCTGTACTATGAACTTGTTGG 57.447 34.615 7.30 0.00 0.00 3.77
984 1320 8.940924 CGTTTAGCAACTAACTTCAAACTTTAC 58.059 33.333 0.00 0.00 0.00 2.01
1200 1536 9.920133 GATCAAGTGAGAAGAGCATATGTATTA 57.080 33.333 4.29 0.00 0.00 0.98
1469 1805 5.044919 TCAAAGATCATATTGGTGGTCCTGT 60.045 40.000 0.00 0.00 29.23 4.00
1475 1811 6.479972 TCATATTGGTGGTCCTGTTAGTAG 57.520 41.667 0.00 0.00 34.23 2.57
1733 2071 8.908786 ACTAAAAATGAACAAGTGAGAGATGA 57.091 30.769 0.00 0.00 0.00 2.92
1855 2194 5.327091 CAGAGCTTGGTGATAAACAATTCG 58.673 41.667 0.00 0.00 0.00 3.34
1856 2195 5.003804 AGAGCTTGGTGATAAACAATTCGT 58.996 37.500 0.00 0.00 0.00 3.85
1980 2319 9.672673 ATTTATTCTCTATGTTGTGCACTAACT 57.327 29.630 19.41 12.00 0.00 2.24
2143 2483 2.530701 AGGATACGAGGGCAAGGATAG 58.469 52.381 0.00 0.00 46.39 2.08
2758 3718 5.288543 CAACATTAAGAGAGAGTGGTTGC 57.711 43.478 0.00 0.00 0.00 4.17
2776 3736 5.861251 TGGTTGCGATGATTTATTTTGTGAC 59.139 36.000 0.00 0.00 0.00 3.67
2809 3769 6.693315 TTTTGTGCTGCTAATAGTATTCCC 57.307 37.500 0.00 0.00 0.00 3.97
3098 4059 3.576982 TGACCGTGGAACAATAAGAGAGT 59.423 43.478 0.00 0.00 44.16 3.24
3379 4340 1.276989 ACCGAGCGGGAGTTATTCAAA 59.723 47.619 14.07 0.00 39.97 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.590092 CCGATCAACAGGACCCCC 59.410 66.667 0.00 0.00 0.00 5.40
3 4 1.522569 CTCCCGATCAACAGGACCC 59.477 63.158 0.00 0.00 0.00 4.46
4 5 1.522569 CCTCCCGATCAACAGGACC 59.477 63.158 0.00 0.00 0.00 4.46
6 7 1.689233 CCCCTCCCGATCAACAGGA 60.689 63.158 2.93 0.00 0.00 3.86
7 8 1.995626 ACCCCTCCCGATCAACAGG 60.996 63.158 0.00 0.00 0.00 4.00
8 9 1.221840 CACCCCTCCCGATCAACAG 59.778 63.158 0.00 0.00 0.00 3.16
9 10 1.537889 ACACCCCTCCCGATCAACA 60.538 57.895 0.00 0.00 0.00 3.33
10 11 1.078426 CACACCCCTCCCGATCAAC 60.078 63.158 0.00 0.00 0.00 3.18
11 12 2.297895 CCACACCCCTCCCGATCAA 61.298 63.158 0.00 0.00 0.00 2.57
12 13 2.687200 CCACACCCCTCCCGATCA 60.687 66.667 0.00 0.00 0.00 2.92
13 14 2.687566 ACCACACCCCTCCCGATC 60.688 66.667 0.00 0.00 0.00 3.69
14 15 2.465010 TACACCACACCCCTCCCGAT 62.465 60.000 0.00 0.00 0.00 4.18
15 16 3.163231 TACACCACACCCCTCCCGA 62.163 63.158 0.00 0.00 0.00 5.14
16 17 2.605295 TACACCACACCCCTCCCG 60.605 66.667 0.00 0.00 0.00 5.14
17 18 2.599757 GGTACACCACACCCCTCCC 61.600 68.421 0.00 0.00 35.64 4.30
18 19 2.951101 CGGTACACCACACCCCTCC 61.951 68.421 0.00 0.00 35.14 4.30
19 20 2.660802 CGGTACACCACACCCCTC 59.339 66.667 0.00 0.00 35.14 4.30
20 21 3.633116 GCGGTACACCACACCCCT 61.633 66.667 0.00 0.00 35.14 4.79
21 22 2.962142 TTTGCGGTACACCACACCCC 62.962 60.000 0.00 0.00 35.14 4.95
22 23 1.102222 TTTTGCGGTACACCACACCC 61.102 55.000 0.00 0.00 35.14 4.61
23 24 0.029700 GTTTTGCGGTACACCACACC 59.970 55.000 0.00 0.00 35.14 4.16
24 25 0.316360 CGTTTTGCGGTACACCACAC 60.316 55.000 0.00 0.00 36.85 3.82
25 26 2.015382 CGTTTTGCGGTACACCACA 58.985 52.632 0.00 0.00 36.85 4.17
26 27 4.905836 CGTTTTGCGGTACACCAC 57.094 55.556 0.00 0.00 36.85 4.16
35 36 1.719766 CCGTTTCGTCCGTTTTGCG 60.720 57.895 0.00 0.00 40.95 4.85
36 37 0.655337 GTCCGTTTCGTCCGTTTTGC 60.655 55.000 0.00 0.00 0.00 3.68
37 38 0.932399 AGTCCGTTTCGTCCGTTTTG 59.068 50.000 0.00 0.00 0.00 2.44
38 39 1.328374 CAAGTCCGTTTCGTCCGTTTT 59.672 47.619 0.00 0.00 0.00 2.43
39 40 0.932399 CAAGTCCGTTTCGTCCGTTT 59.068 50.000 0.00 0.00 0.00 3.60
40 41 0.179103 ACAAGTCCGTTTCGTCCGTT 60.179 50.000 0.00 0.00 0.00 4.44
41 42 0.872881 CACAAGTCCGTTTCGTCCGT 60.873 55.000 0.00 0.00 0.00 4.69
42 43 0.872881 ACACAAGTCCGTTTCGTCCG 60.873 55.000 0.00 0.00 0.00 4.79
43 44 1.004292 CAACACAAGTCCGTTTCGTCC 60.004 52.381 0.00 0.00 0.00 4.79
44 45 1.004292 CCAACACAAGTCCGTTTCGTC 60.004 52.381 0.00 0.00 0.00 4.20
45 46 1.011333 CCAACACAAGTCCGTTTCGT 58.989 50.000 0.00 0.00 0.00 3.85
46 47 1.260561 CTCCAACACAAGTCCGTTTCG 59.739 52.381 0.00 0.00 0.00 3.46
47 48 1.002792 GCTCCAACACAAGTCCGTTTC 60.003 52.381 0.00 0.00 0.00 2.78
48 49 1.021968 GCTCCAACACAAGTCCGTTT 58.978 50.000 0.00 0.00 0.00 3.60
49 50 0.107410 TGCTCCAACACAAGTCCGTT 60.107 50.000 0.00 0.00 0.00 4.44
50 51 0.814010 GTGCTCCAACACAAGTCCGT 60.814 55.000 0.00 0.00 40.40 4.69
51 52 0.532862 AGTGCTCCAACACAAGTCCG 60.533 55.000 0.00 0.00 43.23 4.79
52 53 1.230324 GAGTGCTCCAACACAAGTCC 58.770 55.000 0.00 0.00 43.23 3.85
63 64 1.737008 GTTTCGACCGGAGTGCTCC 60.737 63.158 9.46 8.14 46.18 4.70
64 65 1.006571 TGTTTCGACCGGAGTGCTC 60.007 57.895 9.46 0.00 0.00 4.26
65 66 1.006102 CTGTTTCGACCGGAGTGCT 60.006 57.895 9.46 0.00 0.00 4.40
66 67 2.027625 CCTGTTTCGACCGGAGTGC 61.028 63.158 9.46 0.00 0.00 4.40
67 68 1.374252 CCCTGTTTCGACCGGAGTG 60.374 63.158 9.46 0.00 0.00 3.51
68 69 2.580601 CCCCTGTTTCGACCGGAGT 61.581 63.158 9.46 0.00 0.00 3.85
69 70 2.264794 CCCCTGTTTCGACCGGAG 59.735 66.667 9.46 0.85 0.00 4.63
70 71 2.524887 ACCCCTGTTTCGACCGGA 60.525 61.111 9.46 0.00 0.00 5.14
71 72 2.047560 GACCCCTGTTTCGACCGG 60.048 66.667 0.00 0.00 0.00 5.28
72 73 2.047560 GGACCCCTGTTTCGACCG 60.048 66.667 0.00 0.00 0.00 4.79
73 74 1.003718 CAGGACCCCTGTTTCGACC 60.004 63.158 4.88 0.00 45.82 4.79
74 75 4.695560 CAGGACCCCTGTTTCGAC 57.304 61.111 4.88 0.00 45.82 4.20
82 83 1.995626 CCCGATGAACAGGACCCCT 60.996 63.158 0.00 0.00 0.00 4.79
83 84 1.972660 CTCCCGATGAACAGGACCCC 61.973 65.000 0.00 0.00 0.00 4.95
84 85 1.522569 CTCCCGATGAACAGGACCC 59.477 63.158 0.00 0.00 0.00 4.46
85 86 1.522569 CCTCCCGATGAACAGGACC 59.477 63.158 0.00 0.00 0.00 4.46
86 87 1.522569 CCCTCCCGATGAACAGGAC 59.477 63.158 0.00 0.00 0.00 3.85
87 88 1.689233 CCCCTCCCGATGAACAGGA 60.689 63.158 0.00 0.00 0.00 3.86
88 89 1.995626 ACCCCTCCCGATGAACAGG 60.996 63.158 0.00 0.00 0.00 4.00
89 90 1.221840 CACCCCTCCCGATGAACAG 59.778 63.158 0.00 0.00 0.00 3.16
90 91 1.537889 ACACCCCTCCCGATGAACA 60.538 57.895 0.00 0.00 0.00 3.18
91 92 1.078426 CACACCCCTCCCGATGAAC 60.078 63.158 0.00 0.00 0.00 3.18
92 93 2.297895 CCACACCCCTCCCGATGAA 61.298 63.158 0.00 0.00 0.00 2.57
93 94 2.687200 CCACACCCCTCCCGATGA 60.687 66.667 0.00 0.00 0.00 2.92
94 95 4.489771 GCCACACCCCTCCCGATG 62.490 72.222 0.00 0.00 0.00 3.84
98 99 4.091939 GTACGCCACACCCCTCCC 62.092 72.222 0.00 0.00 0.00 4.30
99 100 4.091939 GGTACGCCACACCCCTCC 62.092 72.222 0.00 0.00 34.09 4.30
112 113 1.066136 GGAGTCTCGTTTTGCGGTAC 58.934 55.000 0.00 0.00 41.72 3.34
113 114 0.675083 TGGAGTCTCGTTTTGCGGTA 59.325 50.000 0.00 0.00 41.72 4.02
114 115 0.878961 GTGGAGTCTCGTTTTGCGGT 60.879 55.000 0.00 0.00 41.72 5.68
115 116 1.860078 GTGGAGTCTCGTTTTGCGG 59.140 57.895 0.00 0.00 41.72 5.69
116 117 1.487231 CGTGGAGTCTCGTTTTGCG 59.513 57.895 0.00 0.00 43.01 4.85
117 118 1.566018 CCCGTGGAGTCTCGTTTTGC 61.566 60.000 0.00 0.00 0.00 3.68
118 119 0.032952 TCCCGTGGAGTCTCGTTTTG 59.967 55.000 0.00 0.00 0.00 2.44
119 120 0.974383 ATCCCGTGGAGTCTCGTTTT 59.026 50.000 0.00 0.00 34.05 2.43
120 121 1.475682 GTATCCCGTGGAGTCTCGTTT 59.524 52.381 0.00 0.00 34.05 3.60
121 122 1.101331 GTATCCCGTGGAGTCTCGTT 58.899 55.000 0.00 0.00 34.05 3.85
122 123 0.255318 AGTATCCCGTGGAGTCTCGT 59.745 55.000 0.00 0.00 34.05 4.18
123 124 0.663688 CAGTATCCCGTGGAGTCTCG 59.336 60.000 0.00 0.00 34.05 4.04
124 125 1.765230 ACAGTATCCCGTGGAGTCTC 58.235 55.000 0.00 0.00 34.05 3.36
125 126 2.100989 GAACAGTATCCCGTGGAGTCT 58.899 52.381 0.00 0.00 34.05 3.24
126 127 1.822990 TGAACAGTATCCCGTGGAGTC 59.177 52.381 0.00 0.00 34.05 3.36
127 128 1.933021 TGAACAGTATCCCGTGGAGT 58.067 50.000 0.00 0.00 34.05 3.85
128 129 2.695666 AGATGAACAGTATCCCGTGGAG 59.304 50.000 0.00 0.00 34.05 3.86
129 130 2.693591 GAGATGAACAGTATCCCGTGGA 59.306 50.000 0.00 0.00 35.55 4.02
130 131 2.224066 GGAGATGAACAGTATCCCGTGG 60.224 54.545 0.00 0.00 0.00 4.94
131 132 2.430694 TGGAGATGAACAGTATCCCGTG 59.569 50.000 0.00 0.00 0.00 4.94
132 133 2.431057 GTGGAGATGAACAGTATCCCGT 59.569 50.000 0.00 0.00 0.00 5.28
133 134 2.224066 GGTGGAGATGAACAGTATCCCG 60.224 54.545 0.00 0.00 0.00 5.14
134 135 2.224066 CGGTGGAGATGAACAGTATCCC 60.224 54.545 0.00 0.00 0.00 3.85
135 136 2.431057 ACGGTGGAGATGAACAGTATCC 59.569 50.000 0.00 0.00 0.00 2.59
136 137 3.707793 GACGGTGGAGATGAACAGTATC 58.292 50.000 0.00 0.00 0.00 2.24
137 138 2.099263 CGACGGTGGAGATGAACAGTAT 59.901 50.000 0.00 0.00 0.00 2.12
138 139 1.471287 CGACGGTGGAGATGAACAGTA 59.529 52.381 0.00 0.00 0.00 2.74
139 140 0.243907 CGACGGTGGAGATGAACAGT 59.756 55.000 0.00 0.00 0.00 3.55
140 141 0.526211 TCGACGGTGGAGATGAACAG 59.474 55.000 0.00 0.00 0.00 3.16
141 142 0.242825 GTCGACGGTGGAGATGAACA 59.757 55.000 0.00 0.00 0.00 3.18
142 143 0.458025 GGTCGACGGTGGAGATGAAC 60.458 60.000 9.92 0.00 0.00 3.18
143 144 0.611062 AGGTCGACGGTGGAGATGAA 60.611 55.000 9.92 0.00 0.00 2.57
144 145 1.001269 AGGTCGACGGTGGAGATGA 60.001 57.895 9.92 0.00 0.00 2.92
145 146 1.433879 GAGGTCGACGGTGGAGATG 59.566 63.158 9.92 0.00 0.00 2.90
146 147 1.753463 GGAGGTCGACGGTGGAGAT 60.753 63.158 9.92 0.00 0.00 2.75
147 148 2.360852 GGAGGTCGACGGTGGAGA 60.361 66.667 9.92 0.00 0.00 3.71
148 149 2.361357 AGGAGGTCGACGGTGGAG 60.361 66.667 9.92 0.00 0.00 3.86
149 150 2.360852 GAGGAGGTCGACGGTGGA 60.361 66.667 9.92 0.00 0.00 4.02
150 151 3.450115 GGAGGAGGTCGACGGTGG 61.450 72.222 9.92 0.00 0.00 4.61
151 152 2.273179 TTGGAGGAGGTCGACGGTG 61.273 63.158 9.92 0.00 0.00 4.94
152 153 2.116772 TTGGAGGAGGTCGACGGT 59.883 61.111 9.92 0.00 0.00 4.83
153 154 2.572284 GTTGGAGGAGGTCGACGG 59.428 66.667 9.92 0.00 0.00 4.79
154 155 1.935327 GAGGTTGGAGGAGGTCGACG 61.935 65.000 9.92 0.00 0.00 5.12
155 156 1.605971 GGAGGTTGGAGGAGGTCGAC 61.606 65.000 7.13 7.13 0.00 4.20
156 157 1.305046 GGAGGTTGGAGGAGGTCGA 60.305 63.158 0.00 0.00 0.00 4.20
157 158 1.192146 TTGGAGGTTGGAGGAGGTCG 61.192 60.000 0.00 0.00 0.00 4.79
158 159 0.615850 CTTGGAGGTTGGAGGAGGTC 59.384 60.000 0.00 0.00 0.00 3.85
159 160 0.842467 CCTTGGAGGTTGGAGGAGGT 60.842 60.000 0.00 0.00 0.00 3.85
160 161 1.566298 CCCTTGGAGGTTGGAGGAGG 61.566 65.000 0.00 0.00 31.93 4.30
161 162 1.994463 CCCTTGGAGGTTGGAGGAG 59.006 63.158 0.00 0.00 31.93 3.69
162 163 2.231380 GCCCTTGGAGGTTGGAGGA 61.231 63.158 0.00 0.00 31.93 3.71
163 164 0.914417 TAGCCCTTGGAGGTTGGAGG 60.914 60.000 0.00 0.00 31.93 4.30
164 165 0.253327 GTAGCCCTTGGAGGTTGGAG 59.747 60.000 0.00 0.00 31.93 3.86
165 166 0.178873 AGTAGCCCTTGGAGGTTGGA 60.179 55.000 0.00 0.00 31.93 3.53
166 167 0.035056 CAGTAGCCCTTGGAGGTTGG 60.035 60.000 0.00 0.00 31.93 3.77
167 168 0.693049 ACAGTAGCCCTTGGAGGTTG 59.307 55.000 0.00 0.00 31.93 3.77
168 169 1.351350 GAACAGTAGCCCTTGGAGGTT 59.649 52.381 0.00 0.00 31.93 3.50
169 170 0.984995 GAACAGTAGCCCTTGGAGGT 59.015 55.000 0.00 0.00 31.93 3.85
170 171 0.984230 TGAACAGTAGCCCTTGGAGG 59.016 55.000 0.00 0.00 34.30 4.30
171 172 2.420687 GGATGAACAGTAGCCCTTGGAG 60.421 54.545 0.00 0.00 0.00 3.86
172 173 1.559682 GGATGAACAGTAGCCCTTGGA 59.440 52.381 0.00 0.00 0.00 3.53
173 174 1.281867 TGGATGAACAGTAGCCCTTGG 59.718 52.381 0.00 0.00 0.00 3.61
174 175 2.359900 GTGGATGAACAGTAGCCCTTG 58.640 52.381 0.00 0.00 0.00 3.61
175 176 1.282157 GGTGGATGAACAGTAGCCCTT 59.718 52.381 0.00 0.00 0.00 3.95
176 177 0.912486 GGTGGATGAACAGTAGCCCT 59.088 55.000 0.00 0.00 0.00 5.19
177 178 0.618458 TGGTGGATGAACAGTAGCCC 59.382 55.000 0.00 0.00 0.00 5.19
178 179 2.565841 GATGGTGGATGAACAGTAGCC 58.434 52.381 0.00 0.00 0.00 3.93
179 180 2.159099 TCGATGGTGGATGAACAGTAGC 60.159 50.000 0.00 0.00 0.00 3.58
180 181 3.448686 GTCGATGGTGGATGAACAGTAG 58.551 50.000 0.00 0.00 0.00 2.57
181 182 2.167693 GGTCGATGGTGGATGAACAGTA 59.832 50.000 0.00 0.00 0.00 2.74
182 183 1.066143 GGTCGATGGTGGATGAACAGT 60.066 52.381 0.00 0.00 0.00 3.55
183 184 1.208052 AGGTCGATGGTGGATGAACAG 59.792 52.381 0.00 0.00 0.00 3.16
184 185 1.207089 GAGGTCGATGGTGGATGAACA 59.793 52.381 0.00 0.00 0.00 3.18
185 186 1.473434 GGAGGTCGATGGTGGATGAAC 60.473 57.143 0.00 0.00 0.00 3.18
186 187 0.830648 GGAGGTCGATGGTGGATGAA 59.169 55.000 0.00 0.00 0.00 2.57
187 188 0.032117 AGGAGGTCGATGGTGGATGA 60.032 55.000 0.00 0.00 0.00 2.92
188 189 0.390860 GAGGAGGTCGATGGTGGATG 59.609 60.000 0.00 0.00 0.00 3.51
189 190 0.760945 GGAGGAGGTCGATGGTGGAT 60.761 60.000 0.00 0.00 0.00 3.41
190 191 1.381327 GGAGGAGGTCGATGGTGGA 60.381 63.158 0.00 0.00 0.00 4.02
191 192 1.680522 CTGGAGGAGGTCGATGGTGG 61.681 65.000 0.00 0.00 0.00 4.61
192 193 1.819229 CTGGAGGAGGTCGATGGTG 59.181 63.158 0.00 0.00 0.00 4.17
193 194 2.060980 GCTGGAGGAGGTCGATGGT 61.061 63.158 0.00 0.00 0.00 3.55
194 195 2.801631 GGCTGGAGGAGGTCGATGG 61.802 68.421 0.00 0.00 0.00 3.51
195 196 1.333636 AAGGCTGGAGGAGGTCGATG 61.334 60.000 0.00 0.00 0.00 3.84
196 197 1.002274 AAGGCTGGAGGAGGTCGAT 59.998 57.895 0.00 0.00 0.00 3.59
197 198 1.682684 GAAGGCTGGAGGAGGTCGA 60.683 63.158 0.00 0.00 0.00 4.20
198 199 1.984570 TGAAGGCTGGAGGAGGTCG 60.985 63.158 0.00 0.00 0.00 4.79
199 200 1.599576 GTGAAGGCTGGAGGAGGTC 59.400 63.158 0.00 0.00 0.00 3.85
200 201 1.920835 GGTGAAGGCTGGAGGAGGT 60.921 63.158 0.00 0.00 0.00 3.85
201 202 2.674220 GGGTGAAGGCTGGAGGAGG 61.674 68.421 0.00 0.00 0.00 4.30
202 203 2.993853 GGGTGAAGGCTGGAGGAG 59.006 66.667 0.00 0.00 0.00 3.69
203 204 3.003173 CGGGTGAAGGCTGGAGGA 61.003 66.667 0.00 0.00 0.00 3.71
204 205 4.785453 GCGGGTGAAGGCTGGAGG 62.785 72.222 0.00 0.00 0.00 4.30
208 209 4.379243 AGTCGCGGGTGAAGGCTG 62.379 66.667 6.13 0.00 0.00 4.85
209 210 4.379243 CAGTCGCGGGTGAAGGCT 62.379 66.667 6.13 0.00 0.00 4.58
210 211 4.681978 ACAGTCGCGGGTGAAGGC 62.682 66.667 6.13 0.00 0.00 4.35
211 212 2.027625 GAACAGTCGCGGGTGAAGG 61.028 63.158 6.13 0.00 0.00 3.46
212 213 0.670546 ATGAACAGTCGCGGGTGAAG 60.671 55.000 6.13 0.00 0.00 3.02
213 214 0.669318 GATGAACAGTCGCGGGTGAA 60.669 55.000 6.13 0.00 0.00 3.18
214 215 1.080093 GATGAACAGTCGCGGGTGA 60.080 57.895 6.13 0.00 0.00 4.02
215 216 2.100631 GGATGAACAGTCGCGGGTG 61.101 63.158 6.13 6.68 0.00 4.61
216 217 2.264794 GGATGAACAGTCGCGGGT 59.735 61.111 6.13 0.00 0.00 5.28
217 218 2.100631 GTGGATGAACAGTCGCGGG 61.101 63.158 6.13 0.00 0.00 6.13
218 219 2.444624 CGTGGATGAACAGTCGCGG 61.445 63.158 6.13 0.00 0.00 6.46
219 220 2.444624 CCGTGGATGAACAGTCGCG 61.445 63.158 0.00 0.00 0.00 5.87
220 221 1.352156 GACCGTGGATGAACAGTCGC 61.352 60.000 0.00 0.00 0.00 5.19
221 222 0.243907 AGACCGTGGATGAACAGTCG 59.756 55.000 0.00 0.00 0.00 4.18
222 223 1.404315 GGAGACCGTGGATGAACAGTC 60.404 57.143 0.00 0.00 0.00 3.51
223 224 0.608640 GGAGACCGTGGATGAACAGT 59.391 55.000 0.00 0.00 0.00 3.55
224 225 0.898320 AGGAGACCGTGGATGAACAG 59.102 55.000 0.00 0.00 0.00 3.16
225 226 2.225382 TAGGAGACCGTGGATGAACA 57.775 50.000 0.00 0.00 0.00 3.18
226 227 3.132289 TGAATAGGAGACCGTGGATGAAC 59.868 47.826 0.00 0.00 0.00 3.18
227 228 3.371034 TGAATAGGAGACCGTGGATGAA 58.629 45.455 0.00 0.00 0.00 2.57
228 229 3.026707 TGAATAGGAGACCGTGGATGA 57.973 47.619 0.00 0.00 0.00 2.92
229 230 3.306364 GGATGAATAGGAGACCGTGGATG 60.306 52.174 0.00 0.00 0.00 3.51
230 231 2.900546 GGATGAATAGGAGACCGTGGAT 59.099 50.000 0.00 0.00 0.00 3.41
231 232 2.317040 GGATGAATAGGAGACCGTGGA 58.683 52.381 0.00 0.00 0.00 4.02
232 233 2.036475 CTGGATGAATAGGAGACCGTGG 59.964 54.545 0.00 0.00 0.00 4.94
233 234 2.546795 GCTGGATGAATAGGAGACCGTG 60.547 54.545 0.00 0.00 0.00 4.94
234 235 1.689273 GCTGGATGAATAGGAGACCGT 59.311 52.381 0.00 0.00 0.00 4.83
235 236 1.001406 GGCTGGATGAATAGGAGACCG 59.999 57.143 0.00 0.00 0.00 4.79
236 237 2.301583 GAGGCTGGATGAATAGGAGACC 59.698 54.545 0.00 0.00 0.00 3.85
237 238 2.301583 GGAGGCTGGATGAATAGGAGAC 59.698 54.545 0.00 0.00 0.00 3.36
238 239 2.090550 TGGAGGCTGGATGAATAGGAGA 60.091 50.000 0.00 0.00 0.00 3.71
239 240 2.038295 GTGGAGGCTGGATGAATAGGAG 59.962 54.545 0.00 0.00 0.00 3.69
240 241 2.050144 GTGGAGGCTGGATGAATAGGA 58.950 52.381 0.00 0.00 0.00 2.94
241 242 1.072965 GGTGGAGGCTGGATGAATAGG 59.927 57.143 0.00 0.00 0.00 2.57
242 243 1.270518 CGGTGGAGGCTGGATGAATAG 60.271 57.143 0.00 0.00 0.00 1.73
243 244 0.758734 CGGTGGAGGCTGGATGAATA 59.241 55.000 0.00 0.00 0.00 1.75
244 245 1.528824 CGGTGGAGGCTGGATGAAT 59.471 57.895 0.00 0.00 0.00 2.57
245 246 2.989639 CGGTGGAGGCTGGATGAA 59.010 61.111 0.00 0.00 0.00 2.57
246 247 3.785859 GCGGTGGAGGCTGGATGA 61.786 66.667 0.00 0.00 0.00 2.92
266 267 1.321074 ACAGTAGCCGGTGGAGTAGC 61.321 60.000 1.90 0.00 0.00 3.58
267 268 1.134560 GAACAGTAGCCGGTGGAGTAG 59.865 57.143 1.90 0.00 0.00 2.57
268 269 1.180029 GAACAGTAGCCGGTGGAGTA 58.820 55.000 1.90 0.00 0.00 2.59
269 270 0.830444 TGAACAGTAGCCGGTGGAGT 60.830 55.000 1.90 0.00 0.00 3.85
270 271 0.320374 TTGAACAGTAGCCGGTGGAG 59.680 55.000 1.90 0.00 0.00 3.86
271 272 0.034337 GTTGAACAGTAGCCGGTGGA 59.966 55.000 1.90 0.00 0.00 4.02
272 273 0.953960 GGTTGAACAGTAGCCGGTGG 60.954 60.000 1.90 0.00 0.00 4.61
273 274 0.250124 TGGTTGAACAGTAGCCGGTG 60.250 55.000 1.90 0.00 0.00 4.94
274 275 0.250166 GTGGTTGAACAGTAGCCGGT 60.250 55.000 1.90 0.00 0.00 5.28
275 276 0.953960 GGTGGTTGAACAGTAGCCGG 60.954 60.000 0.00 0.00 0.00 6.13
276 277 0.953960 GGGTGGTTGAACAGTAGCCG 60.954 60.000 0.00 0.00 0.00 5.52
277 278 0.608308 GGGGTGGTTGAACAGTAGCC 60.608 60.000 0.00 2.10 0.00 3.93
278 279 0.400594 AGGGGTGGTTGAACAGTAGC 59.599 55.000 0.00 0.00 0.00 3.58
279 280 1.978580 AGAGGGGTGGTTGAACAGTAG 59.021 52.381 0.00 0.00 0.00 2.57
280 281 1.975680 GAGAGGGGTGGTTGAACAGTA 59.024 52.381 0.00 0.00 0.00 2.74
281 282 0.765510 GAGAGGGGTGGTTGAACAGT 59.234 55.000 0.00 0.00 0.00 3.55
282 283 0.036875 GGAGAGGGGTGGTTGAACAG 59.963 60.000 0.00 0.00 0.00 3.16
283 284 0.696143 TGGAGAGGGGTGGTTGAACA 60.696 55.000 0.00 0.00 0.00 3.18
284 285 0.250770 GTGGAGAGGGGTGGTTGAAC 60.251 60.000 0.00 0.00 0.00 3.18
285 286 1.764571 CGTGGAGAGGGGTGGTTGAA 61.765 60.000 0.00 0.00 0.00 2.69
286 287 2.214216 CGTGGAGAGGGGTGGTTGA 61.214 63.158 0.00 0.00 0.00 3.18
287 288 2.347490 CGTGGAGAGGGGTGGTTG 59.653 66.667 0.00 0.00 0.00 3.77
288 289 3.637273 GCGTGGAGAGGGGTGGTT 61.637 66.667 0.00 0.00 0.00 3.67
289 290 4.954118 TGCGTGGAGAGGGGTGGT 62.954 66.667 0.00 0.00 0.00 4.16
290 291 4.087892 CTGCGTGGAGAGGGGTGG 62.088 72.222 0.00 0.00 0.00 4.61
291 292 3.314331 ACTGCGTGGAGAGGGGTG 61.314 66.667 0.00 0.00 0.00 4.61
292 293 3.314331 CACTGCGTGGAGAGGGGT 61.314 66.667 0.00 0.00 0.00 4.95
405 408 5.757988 TCTTGCCCGGGTAAATTAAGTTAT 58.242 37.500 25.04 0.00 0.00 1.89
427 430 1.581447 CGAAGGCCCAGTTGCTTTC 59.419 57.895 0.00 0.00 42.15 2.62
446 449 1.423395 GGCTGTGAACGTGAGAGAAG 58.577 55.000 0.00 0.00 0.00 2.85
489 501 1.097232 GCTGATTGCATGTAGCCACA 58.903 50.000 5.55 0.00 44.83 4.17
590 676 0.531311 TGCGCTAGTCATGCATGAGG 60.531 55.000 29.38 21.26 37.51 3.86
595 681 2.187685 CCCTGCGCTAGTCATGCA 59.812 61.111 9.73 0.00 37.07 3.96
841 950 2.225019 GCATCGCATCAATCCTACTTGG 59.775 50.000 0.00 0.00 37.10 3.61
842 951 2.874086 TGCATCGCATCAATCCTACTTG 59.126 45.455 0.00 0.00 31.71 3.16
843 952 3.198409 TGCATCGCATCAATCCTACTT 57.802 42.857 0.00 0.00 31.71 2.24
844 953 2.874701 GTTGCATCGCATCAATCCTACT 59.125 45.455 0.00 0.00 38.76 2.57
845 954 2.874701 AGTTGCATCGCATCAATCCTAC 59.125 45.455 0.00 0.00 38.76 3.18
846 955 3.198409 AGTTGCATCGCATCAATCCTA 57.802 42.857 0.00 0.00 38.76 2.94
847 956 2.048444 AGTTGCATCGCATCAATCCT 57.952 45.000 0.00 0.00 38.76 3.24
848 957 2.456989 CAAGTTGCATCGCATCAATCC 58.543 47.619 0.00 0.00 38.76 3.01
871 1197 4.540359 AATTTGCATGCATACCACAGTT 57.460 36.364 23.37 5.43 0.00 3.16
882 1208 6.783892 TGAAGGTAAGAAAAATTTGCATGC 57.216 33.333 11.82 11.82 0.00 4.06
984 1320 8.921353 ATCTCCTCATCTCTGAAATTTAATGG 57.079 34.615 0.00 0.00 0.00 3.16
1200 1536 0.393820 CTGGTTGCATTGCACCCTTT 59.606 50.000 23.59 0.00 41.79 3.11
1469 1805 2.036733 ACGCAAGAGTTGTGCCTACTAA 59.963 45.455 0.15 0.00 44.75 2.24
1475 1811 0.040958 CTTGACGCAAGAGTTGTGCC 60.041 55.000 12.43 0.00 43.42 5.01
1733 2071 2.649531 TCTTCCACCACGGTCAAAAT 57.350 45.000 0.00 0.00 35.57 1.82
1855 2194 5.509272 CACGTGATTCATCAATAAGCACAAC 59.491 40.000 10.90 0.00 41.99 3.32
1856 2195 5.411053 TCACGTGATTCATCAATAAGCACAA 59.589 36.000 15.76 0.00 41.99 3.33
1951 2290 8.743085 AGTGCACAACATAGAGAATAAATGAT 57.257 30.769 21.04 0.00 0.00 2.45
2143 2483 4.518211 CCTCTCATATTTGAAGCACCATCC 59.482 45.833 0.00 0.00 0.00 3.51
2758 3718 7.744276 TCTTGAACGTCACAAAATAAATCATCG 59.256 33.333 8.91 0.00 0.00 3.84
2776 3736 3.374745 AGCAGCACAAAATTCTTGAACG 58.625 40.909 0.00 0.00 0.00 3.95
2809 3769 1.733389 GCTTCATCCATGTTTGGCACG 60.733 52.381 0.00 0.00 43.29 5.34
3409 4370 2.432444 CGAGACCCCATTGCAGTAAAA 58.568 47.619 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.