Multiple sequence alignment - TraesCS3B01G429900

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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 TraesCS3B01G429900 chr3B 100.000 5189 0 0 1 5189 669424192 669429380 0.000000e+00 9583.0
1 TraesCS3B01G429900 chr3A 92.044 5015 216 76 215 5143 645129067 645133984 0.000000e+00 6881.0
2 TraesCS3B01G429900 chr3D 95.177 3048 112 16 2114 5143 507028107 507031137 0.000000e+00 4782.0
3 TraesCS3B01G429900 chr3D 90.816 1764 72 33 235 1950 507026067 507027788 0.000000e+00 2278.0
4 TraesCS3B01G429900 chr3D 90.476 63 6 0 235 297 507021610 507021672 3.330000e-12 84.2
5 TraesCS3B01G429900 chr3D 90.476 63 6 0 235 297 507022352 507022414 3.330000e-12 84.2
6 TraesCS3B01G429900 chr3D 90.476 63 6 0 235 297 507023851 507023913 3.330000e-12 84.2
7 TraesCS3B01G429900 chr3D 90.476 63 6 0 235 297 507024623 507024685 3.330000e-12 84.2
8 TraesCS3B01G429900 chr3D 88.889 63 7 0 235 297 507020114 507020176 1.550000e-10 78.7
9 TraesCS3B01G429900 chr3D 88.889 63 7 0 235 297 507020862 507020924 1.550000e-10 78.7
10 TraesCS3B01G429900 chr3D 88.889 63 7 0 235 297 507023097 507023159 1.550000e-10 78.7
11 TraesCS3B01G429900 chr4B 88.400 500 23 14 4601 5088 75832569 75832093 2.100000e-158 569.0
12 TraesCS3B01G429900 chr4B 88.438 493 23 14 4601 5082 6977494 6977963 9.750000e-157 564.0
13 TraesCS3B01G429900 chr7B 88.200 500 24 14 4601 5088 482346735 482347211 9.750000e-157 564.0
14 TraesCS3B01G429900 chr7B 89.759 166 11 3 4583 4743 121186502 121186338 1.890000e-49 207.0
15 TraesCS3B01G429900 chr5B 87.200 500 29 14 4601 5088 84142947 84143423 2.130000e-148 536.0
16 TraesCS3B01G429900 chr5B 93.671 158 9 1 4583 4740 566111606 566111762 8.690000e-58 235.0
17 TraesCS3B01G429900 chr5B 84.553 246 12 12 4847 5088 566111769 566111992 2.430000e-53 220.0
18 TraesCS3B01G429900 chr6D 88.942 208 20 3 8 212 2239711 2239918 2.400000e-63 254.0
19 TraesCS3B01G429900 chr6D 86.294 197 21 3 1 192 2198400 2198595 5.270000e-50 209.0
20 TraesCS3B01G429900 chr5A 94.937 158 7 1 4583 4740 589678102 589678258 4.010000e-61 246.0
21 TraesCS3B01G429900 chr6A 86.222 225 19 7 1 216 644738 644517 3.120000e-57 233.0
22 TraesCS3B01G429900 chr2A 84.146 246 13 12 4847 5088 357886240 357886017 1.130000e-51 215.0
23 TraesCS3B01G429900 chr7A 83.333 246 15 12 4847 5088 318138107 318137884 2.450000e-48 204.0
24 TraesCS3B01G429900 chr6B 83.645 214 29 3 1 209 3878749 3878961 4.100000e-46 196.0
25 TraesCS3B01G429900 chr6B 83.453 139 11 7 4948 5086 634999170 634999296 9.130000e-23 119.0


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 TraesCS3B01G429900 chr3B 669424192 669429380 5188 False 9583.0 9583 100.000000 1 5189 1 chr3B.!!$F1 5188
1 TraesCS3B01G429900 chr3A 645129067 645133984 4917 False 6881.0 6881 92.044000 215 5143 1 chr3A.!!$F1 4928
2 TraesCS3B01G429900 chr3D 507020114 507031137 11023 False 848.1 4782 90.507111 235 5143 9 chr3D.!!$F1 4908

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
688 6724 0.032130 CGGGATGCTTAGCTCGCTAA 59.968 55.000 5.6 10.61 37.06 3.09 F
832 6883 0.464452 AAAATACTCCTCCGCCTCCG 59.536 55.000 0.0 0.00 0.00 4.63 F
1371 7453 1.376037 CTCGGGAGGCAACAAGTCC 60.376 63.158 0.0 0.00 41.41 3.85 F
2605 8842 0.689055 ATTCCAGTGAGTGCTCTGCA 59.311 50.000 0.0 0.00 34.99 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 8065 1.077429 GGAAGGTGCAGGGGACATC 60.077 63.158 0.00 0.0 0.00 3.06 R
2547 8784 2.665000 CACACCATGGCTCGGTCT 59.335 61.111 13.04 0.0 33.25 3.85 R
3047 9286 2.501723 GGTCTCCAGTAAATCTGCTCCA 59.498 50.000 0.00 0.0 42.38 3.86 R
4567 10814 0.558220 TCCCTCCTCCGATGTCTGAT 59.442 55.000 0.00 0.0 0.00 2.90 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 2.280389 CACGATGATGCTCCCGGG 60.280 66.667 16.85 16.85 0.00 5.73
18 19 2.443952 ACGATGATGCTCCCGGGA 60.444 61.111 25.06 25.06 0.00 5.14
19 20 2.341543 CGATGATGCTCCCGGGAG 59.658 66.667 41.29 41.29 44.56 4.30
28 29 2.836944 CTCCCGGGAGAAAAACGAC 58.163 57.895 42.70 0.00 44.53 4.34
29 30 0.034337 CTCCCGGGAGAAAAACGACA 59.966 55.000 42.70 7.36 44.53 4.35
30 31 0.469070 TCCCGGGAGAAAAACGACAA 59.531 50.000 22.63 0.00 0.00 3.18
31 32 0.589708 CCCGGGAGAAAAACGACAAC 59.410 55.000 18.48 0.00 0.00 3.32
32 33 1.301423 CCGGGAGAAAAACGACAACA 58.699 50.000 0.00 0.00 0.00 3.33
33 34 1.671845 CCGGGAGAAAAACGACAACAA 59.328 47.619 0.00 0.00 0.00 2.83
34 35 2.292292 CCGGGAGAAAAACGACAACAAT 59.708 45.455 0.00 0.00 0.00 2.71
35 36 3.296628 CGGGAGAAAAACGACAACAATG 58.703 45.455 0.00 0.00 0.00 2.82
36 37 3.242936 CGGGAGAAAAACGACAACAATGT 60.243 43.478 0.00 0.00 44.25 2.71
37 38 4.041723 GGGAGAAAAACGACAACAATGTG 58.958 43.478 0.00 0.00 40.74 3.21
38 39 3.485743 GGAGAAAAACGACAACAATGTGC 59.514 43.478 0.00 0.00 40.74 4.57
39 40 3.443976 AGAAAAACGACAACAATGTGCC 58.556 40.909 0.00 0.00 40.74 5.01
40 41 2.217429 AAAACGACAACAATGTGCCC 57.783 45.000 0.00 0.00 40.74 5.36
41 42 0.387565 AAACGACAACAATGTGCCCC 59.612 50.000 0.00 0.00 40.74 5.80
42 43 1.460273 AACGACAACAATGTGCCCCC 61.460 55.000 0.00 0.00 40.74 5.40
43 44 1.900981 CGACAACAATGTGCCCCCA 60.901 57.895 0.00 0.00 40.74 4.96
44 45 1.250154 CGACAACAATGTGCCCCCAT 61.250 55.000 0.00 0.00 40.74 4.00
45 46 0.975887 GACAACAATGTGCCCCCATT 59.024 50.000 0.00 0.00 40.74 3.16
49 50 1.512230 CAATGTGCCCCCATTGTCG 59.488 57.895 10.90 0.00 44.24 4.35
50 51 0.964860 CAATGTGCCCCCATTGTCGA 60.965 55.000 10.90 0.00 44.24 4.20
51 52 0.680921 AATGTGCCCCCATTGTCGAG 60.681 55.000 0.00 0.00 33.86 4.04
52 53 1.561769 ATGTGCCCCCATTGTCGAGA 61.562 55.000 0.00 0.00 0.00 4.04
53 54 1.745489 GTGCCCCCATTGTCGAGAC 60.745 63.158 0.00 0.00 0.00 3.36
54 55 2.124695 GCCCCCATTGTCGAGACC 60.125 66.667 0.34 0.00 0.00 3.85
55 56 2.966732 GCCCCCATTGTCGAGACCA 61.967 63.158 0.34 0.00 0.00 4.02
56 57 1.682849 CCCCCATTGTCGAGACCAA 59.317 57.895 0.34 0.00 0.00 3.67
57 58 0.037590 CCCCCATTGTCGAGACCAAA 59.962 55.000 0.34 0.00 0.00 3.28
58 59 1.453155 CCCCATTGTCGAGACCAAAG 58.547 55.000 0.34 0.00 0.00 2.77
59 60 1.003118 CCCCATTGTCGAGACCAAAGA 59.997 52.381 0.34 0.00 0.00 2.52
60 61 2.552155 CCCCATTGTCGAGACCAAAGAA 60.552 50.000 0.34 0.00 0.00 2.52
61 62 3.146066 CCCATTGTCGAGACCAAAGAAA 58.854 45.455 0.34 0.00 0.00 2.52
62 63 3.058224 CCCATTGTCGAGACCAAAGAAAC 60.058 47.826 0.34 0.00 0.00 2.78
63 64 3.815401 CCATTGTCGAGACCAAAGAAACT 59.185 43.478 0.34 0.00 0.00 2.66
64 65 4.319766 CCATTGTCGAGACCAAAGAAACTG 60.320 45.833 0.34 0.00 0.00 3.16
65 66 3.536956 TGTCGAGACCAAAGAAACTGT 57.463 42.857 0.34 0.00 0.00 3.55
66 67 3.454375 TGTCGAGACCAAAGAAACTGTC 58.546 45.455 0.34 0.00 0.00 3.51
67 68 3.118920 TGTCGAGACCAAAGAAACTGTCA 60.119 43.478 0.34 0.00 0.00 3.58
68 69 3.491267 GTCGAGACCAAAGAAACTGTCAG 59.509 47.826 0.00 0.00 0.00 3.51
69 70 2.802816 CGAGACCAAAGAAACTGTCAGG 59.197 50.000 4.53 0.00 0.00 3.86
70 71 3.142174 GAGACCAAAGAAACTGTCAGGG 58.858 50.000 4.53 0.00 0.00 4.45
71 72 2.158608 AGACCAAAGAAACTGTCAGGGG 60.159 50.000 4.53 0.00 0.00 4.79
72 73 1.133482 ACCAAAGAAACTGTCAGGGGG 60.133 52.381 4.53 0.00 0.00 5.40
73 74 1.133482 CCAAAGAAACTGTCAGGGGGT 60.133 52.381 4.53 0.00 0.00 4.95
74 75 2.666317 CAAAGAAACTGTCAGGGGGTT 58.334 47.619 4.53 0.00 0.00 4.11
75 76 2.623416 CAAAGAAACTGTCAGGGGGTTC 59.377 50.000 4.53 2.75 0.00 3.62
76 77 0.396811 AGAAACTGTCAGGGGGTTCG 59.603 55.000 4.53 0.00 0.00 3.95
77 78 1.228154 AAACTGTCAGGGGGTTCGC 60.228 57.895 4.53 0.00 0.00 4.70
78 79 2.692273 AAACTGTCAGGGGGTTCGCC 62.692 60.000 4.53 0.00 36.67 5.54
88 89 4.785453 GGTTCGCCCAGAGCCCTG 62.785 72.222 0.00 0.00 43.57 4.45
96 97 3.548488 CAGAGCCCTGGCCTAGAG 58.452 66.667 3.32 0.00 43.17 2.43
97 98 1.075674 CAGAGCCCTGGCCTAGAGA 60.076 63.158 3.32 0.00 43.17 3.10
98 99 1.114722 CAGAGCCCTGGCCTAGAGAG 61.115 65.000 3.32 0.00 43.17 3.20
99 100 1.231641 GAGCCCTGGCCTAGAGAGA 59.768 63.158 3.32 0.00 43.17 3.10
100 101 0.178935 GAGCCCTGGCCTAGAGAGAT 60.179 60.000 3.32 0.00 43.17 2.75
101 102 0.471591 AGCCCTGGCCTAGAGAGATG 60.472 60.000 3.32 0.00 43.17 2.90
102 103 1.479368 GCCCTGGCCTAGAGAGATGG 61.479 65.000 3.32 0.00 34.56 3.51
103 104 0.189574 CCCTGGCCTAGAGAGATGGA 59.810 60.000 3.32 0.00 0.00 3.41
104 105 1.337118 CCTGGCCTAGAGAGATGGAC 58.663 60.000 3.32 0.00 0.00 4.02
105 106 1.337118 CTGGCCTAGAGAGATGGACC 58.663 60.000 3.32 0.00 0.00 4.46
106 107 0.468214 TGGCCTAGAGAGATGGACCG 60.468 60.000 3.32 0.00 0.00 4.79
107 108 1.663173 GCCTAGAGAGATGGACCGC 59.337 63.158 0.00 0.00 0.00 5.68
108 109 0.825840 GCCTAGAGAGATGGACCGCT 60.826 60.000 0.00 0.00 0.00 5.52
109 110 0.958091 CCTAGAGAGATGGACCGCTG 59.042 60.000 0.00 0.00 0.00 5.18
110 111 0.313672 CTAGAGAGATGGACCGCTGC 59.686 60.000 0.00 0.00 0.00 5.25
111 112 1.448119 TAGAGAGATGGACCGCTGCG 61.448 60.000 16.34 16.34 0.00 5.18
112 113 2.755876 AGAGATGGACCGCTGCGA 60.756 61.111 25.45 3.10 0.00 5.10
113 114 2.583593 GAGATGGACCGCTGCGAC 60.584 66.667 25.45 16.33 0.00 5.19
114 115 4.498520 AGATGGACCGCTGCGACG 62.499 66.667 25.45 10.38 0.00 5.12
136 137 3.733709 CCAAGAGGGATATGGCACC 57.266 57.895 0.00 0.00 40.01 5.01
137 138 0.111253 CCAAGAGGGATATGGCACCC 59.889 60.000 3.48 3.48 45.88 4.61
141 142 2.594592 GGGATATGGCACCCACGC 60.595 66.667 6.78 0.00 44.96 5.34
142 143 2.972505 GGATATGGCACCCACGCG 60.973 66.667 3.53 3.53 35.80 6.01
143 144 2.203015 GATATGGCACCCACGCGT 60.203 61.111 5.58 5.58 35.80 6.01
144 145 1.068417 GATATGGCACCCACGCGTA 59.932 57.895 13.44 0.00 35.80 4.42
145 146 0.320421 GATATGGCACCCACGCGTAT 60.320 55.000 13.44 1.83 35.80 3.06
146 147 0.320421 ATATGGCACCCACGCGTATC 60.320 55.000 13.44 0.00 35.80 2.24
147 148 2.686956 TATGGCACCCACGCGTATCG 62.687 60.000 13.44 4.40 45.38 2.92
164 165 2.826738 GCCGCCGCCCATCTTTAA 60.827 61.111 0.00 0.00 0.00 1.52
165 166 2.193536 GCCGCCGCCCATCTTTAAT 61.194 57.895 0.00 0.00 0.00 1.40
166 167 1.949257 CCGCCGCCCATCTTTAATC 59.051 57.895 0.00 0.00 0.00 1.75
167 168 0.817634 CCGCCGCCCATCTTTAATCA 60.818 55.000 0.00 0.00 0.00 2.57
168 169 1.238439 CGCCGCCCATCTTTAATCAT 58.762 50.000 0.00 0.00 0.00 2.45
169 170 1.197721 CGCCGCCCATCTTTAATCATC 59.802 52.381 0.00 0.00 0.00 2.92
170 171 2.508526 GCCGCCCATCTTTAATCATCT 58.491 47.619 0.00 0.00 0.00 2.90
171 172 2.887152 GCCGCCCATCTTTAATCATCTT 59.113 45.455 0.00 0.00 0.00 2.40
172 173 3.304928 GCCGCCCATCTTTAATCATCTTG 60.305 47.826 0.00 0.00 0.00 3.02
173 174 3.254166 CCGCCCATCTTTAATCATCTTGG 59.746 47.826 0.00 0.00 0.00 3.61
174 175 3.304928 CGCCCATCTTTAATCATCTTGGC 60.305 47.826 0.00 0.00 0.00 4.52
175 176 3.638160 GCCCATCTTTAATCATCTTGGCA 59.362 43.478 0.00 0.00 35.30 4.92
176 177 4.282703 GCCCATCTTTAATCATCTTGGCAT 59.717 41.667 0.00 0.00 35.30 4.40
177 178 5.221581 GCCCATCTTTAATCATCTTGGCATT 60.222 40.000 0.00 0.00 35.30 3.56
178 179 6.220930 CCCATCTTTAATCATCTTGGCATTG 58.779 40.000 0.00 0.00 0.00 2.82
179 180 5.694910 CCATCTTTAATCATCTTGGCATTGC 59.305 40.000 0.00 0.00 0.00 3.56
180 181 6.462487 CCATCTTTAATCATCTTGGCATTGCT 60.462 38.462 8.82 0.00 0.00 3.91
181 182 6.534475 TCTTTAATCATCTTGGCATTGCTT 57.466 33.333 8.82 0.00 0.00 3.91
182 183 6.334989 TCTTTAATCATCTTGGCATTGCTTG 58.665 36.000 8.82 0.00 0.00 4.01
183 184 3.536956 AATCATCTTGGCATTGCTTGG 57.463 42.857 8.82 0.00 0.00 3.61
184 185 1.187974 TCATCTTGGCATTGCTTGGG 58.812 50.000 8.82 0.00 0.00 4.12
185 186 0.461339 CATCTTGGCATTGCTTGGGC 60.461 55.000 8.82 0.00 39.26 5.36
203 204 4.479993 CCGGCCCAGCAGAAGGAG 62.480 72.222 0.00 0.00 0.00 3.69
204 205 3.710722 CGGCCCAGCAGAAGGAGT 61.711 66.667 0.00 0.00 0.00 3.85
205 206 2.759795 GGCCCAGCAGAAGGAGTT 59.240 61.111 0.00 0.00 0.00 3.01
206 207 1.676967 GGCCCAGCAGAAGGAGTTG 60.677 63.158 0.00 0.00 0.00 3.16
207 208 1.073897 GCCCAGCAGAAGGAGTTGT 59.926 57.895 0.00 0.00 0.00 3.32
208 209 0.538287 GCCCAGCAGAAGGAGTTGTT 60.538 55.000 0.00 0.00 0.00 2.83
209 210 1.242076 CCCAGCAGAAGGAGTTGTTG 58.758 55.000 0.00 0.00 0.00 3.33
210 211 1.242076 CCAGCAGAAGGAGTTGTTGG 58.758 55.000 0.00 0.00 38.93 3.77
211 212 1.242076 CAGCAGAAGGAGTTGTTGGG 58.758 55.000 0.00 0.00 0.00 4.12
212 213 0.111253 AGCAGAAGGAGTTGTTGGGG 59.889 55.000 0.00 0.00 0.00 4.96
213 214 1.527433 GCAGAAGGAGTTGTTGGGGC 61.527 60.000 0.00 0.00 0.00 5.80
217 218 1.628846 GAAGGAGTTGTTGGGGCTCTA 59.371 52.381 0.00 0.00 0.00 2.43
251 254 4.283467 TCTCCCATATAGTCCAACAATCCG 59.717 45.833 0.00 0.00 0.00 4.18
280 4792 1.581934 CAACTCGAACTCCAAGCACA 58.418 50.000 0.00 0.00 0.00 4.57
281 4793 1.261619 CAACTCGAACTCCAAGCACAC 59.738 52.381 0.00 0.00 0.00 3.82
282 4794 0.753262 ACTCGAACTCCAAGCACACT 59.247 50.000 0.00 0.00 0.00 3.55
283 4795 1.139058 ACTCGAACTCCAAGCACACTT 59.861 47.619 0.00 0.00 36.19 3.16
284 4796 1.795286 CTCGAACTCCAAGCACACTTC 59.205 52.381 0.00 0.00 32.29 3.01
285 4797 1.412710 TCGAACTCCAAGCACACTTCT 59.587 47.619 0.00 0.00 32.29 2.85
286 4798 2.626266 TCGAACTCCAAGCACACTTCTA 59.374 45.455 0.00 0.00 32.29 2.10
287 4799 3.069016 TCGAACTCCAAGCACACTTCTAA 59.931 43.478 0.00 0.00 32.29 2.10
288 4800 3.184581 CGAACTCCAAGCACACTTCTAAC 59.815 47.826 0.00 0.00 32.29 2.34
289 4801 3.127425 ACTCCAAGCACACTTCTAACC 57.873 47.619 0.00 0.00 32.29 2.85
290 4802 2.438021 ACTCCAAGCACACTTCTAACCA 59.562 45.455 0.00 0.00 32.29 3.67
291 4803 3.118038 ACTCCAAGCACACTTCTAACCAA 60.118 43.478 0.00 0.00 32.29 3.67
292 4804 3.211045 TCCAAGCACACTTCTAACCAAC 58.789 45.455 0.00 0.00 32.29 3.77
293 4805 2.293399 CCAAGCACACTTCTAACCAACC 59.707 50.000 0.00 0.00 32.29 3.77
294 4806 2.948979 CAAGCACACTTCTAACCAACCA 59.051 45.455 0.00 0.00 32.29 3.67
295 4807 2.572290 AGCACACTTCTAACCAACCAC 58.428 47.619 0.00 0.00 0.00 4.16
296 4808 2.092646 AGCACACTTCTAACCAACCACA 60.093 45.455 0.00 0.00 0.00 4.17
297 4809 2.290641 GCACACTTCTAACCAACCACAG 59.709 50.000 0.00 0.00 0.00 3.66
298 4810 3.541632 CACACTTCTAACCAACCACAGT 58.458 45.455 0.00 0.00 0.00 3.55
299 4811 3.945285 CACACTTCTAACCAACCACAGTT 59.055 43.478 0.00 0.00 36.33 3.16
342 4854 5.221244 ACCAACCATAGAAGAAAAACAGCAC 60.221 40.000 0.00 0.00 0.00 4.40
343 4855 5.221224 CCAACCATAGAAGAAAAACAGCACA 60.221 40.000 0.00 0.00 0.00 4.57
345 4857 6.463995 ACCATAGAAGAAAAACAGCACAAA 57.536 33.333 0.00 0.00 0.00 2.83
346 4858 7.054491 ACCATAGAAGAAAAACAGCACAAAT 57.946 32.000 0.00 0.00 0.00 2.32
347 4859 6.925165 ACCATAGAAGAAAAACAGCACAAATG 59.075 34.615 0.00 0.00 0.00 2.32
349 4861 5.343307 AGAAGAAAAACAGCACAAATGGT 57.657 34.783 0.00 0.00 36.87 3.55
355 6324 0.178981 ACAGCACAAATGGTCTGGCT 60.179 50.000 8.37 0.00 33.06 4.75
395 6364 0.311790 CAGCAACAAAGGCACACGAT 59.688 50.000 0.00 0.00 0.00 3.73
396 6365 0.593128 AGCAACAAAGGCACACGATC 59.407 50.000 0.00 0.00 0.00 3.69
410 6387 5.065988 GGCACACGATCCATATAAAACTTGT 59.934 40.000 0.00 0.00 0.00 3.16
432 6409 4.395583 GCTCGTGCCTGTTGCTGC 62.396 66.667 0.00 0.00 42.00 5.25
499 6476 1.650528 CCCTCTCCAACAACTCTCCT 58.349 55.000 0.00 0.00 0.00 3.69
505 6482 1.072331 TCCAACAACTCTCCTTCCAGC 59.928 52.381 0.00 0.00 0.00 4.85
513 6519 2.564947 ACTCTCCTTCCAGCAGTAGTTG 59.435 50.000 0.00 0.00 0.00 3.16
521 6527 4.901197 TCCAGCAGTAGTTGTTAATGGA 57.099 40.909 0.00 0.00 33.33 3.41
523 6529 4.286032 TCCAGCAGTAGTTGTTAATGGAGT 59.714 41.667 0.00 0.00 32.08 3.85
524 6530 5.482526 TCCAGCAGTAGTTGTTAATGGAGTA 59.517 40.000 0.00 0.00 32.08 2.59
560 6566 4.201881 GGTTATGCCCTGCTAAACTAAACG 60.202 45.833 0.00 0.00 0.00 3.60
561 6567 1.161843 TGCCCTGCTAAACTAAACGC 58.838 50.000 0.00 0.00 0.00 4.84
672 6708 4.483243 CGATGACCAACCCCCGGG 62.483 72.222 15.80 15.80 42.03 5.73
685 6721 2.663188 CCGGGATGCTTAGCTCGC 60.663 66.667 5.60 8.02 0.00 5.03
688 6724 0.032130 CGGGATGCTTAGCTCGCTAA 59.968 55.000 5.60 10.61 37.06 3.09
832 6883 0.464452 AAAATACTCCTCCGCCTCCG 59.536 55.000 0.00 0.00 0.00 4.63
925 6989 3.045634 TCTCCCCTCACTCTCTCTCTAG 58.954 54.545 0.00 0.00 0.00 2.43
935 6999 4.407621 CACTCTCTCTCTAGTCTCTACCCA 59.592 50.000 0.00 0.00 0.00 4.51
949 7013 6.159751 AGTCTCTACCCACTTTCTCTCTCTAT 59.840 42.308 0.00 0.00 0.00 1.98
1154 7224 4.452733 CTTCCTGCCGGACCCGTC 62.453 72.222 5.05 0.00 39.60 4.79
1165 7235 3.641925 GACCCGTCGTCCTCCTCCT 62.642 68.421 0.00 0.00 35.23 3.69
1371 7453 1.376037 CTCGGGAGGCAACAAGTCC 60.376 63.158 0.00 0.00 41.41 3.85
1680 7762 2.811317 GGGAAGAGCAGCGACACG 60.811 66.667 0.00 0.00 0.00 4.49
1842 7924 1.949631 GGAATTCTACTCGCCGCGG 60.950 63.158 24.05 24.05 0.00 6.46
2019 8101 3.965026 CTCCCCGCCTCTCCTGTCA 62.965 68.421 0.00 0.00 0.00 3.58
2605 8842 0.689055 ATTCCAGTGAGTGCTCTGCA 59.311 50.000 0.00 0.00 34.99 4.41
2612 8849 3.734231 CAGTGAGTGCTCTGCAAAATTTG 59.266 43.478 0.57 0.57 41.47 2.32
2645 8882 7.279615 TCTCAGTCCAAAGTTTGTTCTTCATA 58.720 34.615 14.36 0.00 0.00 2.15
2919 9158 7.816945 AATTCCTAAATTTGAGATGTTTGCG 57.183 32.000 0.00 0.00 30.79 4.85
2923 9162 6.150976 TCCTAAATTTGAGATGTTTGCGTCAT 59.849 34.615 0.00 0.00 33.18 3.06
2999 9238 5.543790 TCATCCAGCAGCCTTCACTAATATA 59.456 40.000 0.00 0.00 0.00 0.86
3022 9261 6.500684 ACTTACCAATTTGCTATGTGTCTG 57.499 37.500 0.00 0.00 0.00 3.51
3023 9262 6.003950 ACTTACCAATTTGCTATGTGTCTGT 58.996 36.000 0.00 0.00 0.00 3.41
3047 9286 2.914059 ACAGGTAACACGCAGAACTTT 58.086 42.857 0.00 0.00 41.41 2.66
3155 9394 3.123273 TCCTATTAAGCTTGGCCCTTCT 58.877 45.455 9.86 0.00 0.00 2.85
3212 9451 2.475111 TGCTTTCAAAAGAGTAGACGCG 59.525 45.455 3.53 3.53 38.28 6.01
3323 9563 1.702957 CCTCCACTTTTACTCCCACCA 59.297 52.381 0.00 0.00 0.00 4.17
3325 9565 1.422402 TCCACTTTTACTCCCACCACC 59.578 52.381 0.00 0.00 0.00 4.61
3335 9575 1.966451 CCCACCACCGCTCTGTTTC 60.966 63.158 0.00 0.00 0.00 2.78
3347 9587 5.648092 ACCGCTCTGTTTCATTAGCTAAATT 59.352 36.000 10.85 0.00 32.73 1.82
3489 9729 2.758423 TGCTCATGCATTCAAGCTTGAT 59.242 40.909 28.89 16.19 44.41 2.57
3606 9846 0.674581 TCTCTGCCAGCAACCAATCG 60.675 55.000 0.00 0.00 0.00 3.34
3609 9849 1.228094 TGCCAGCAACCAATCGACA 60.228 52.632 0.00 0.00 0.00 4.35
3639 9879 0.984230 TTGCAAACCCTCTCCGAGAT 59.016 50.000 0.00 0.00 0.00 2.75
3738 9978 1.079819 AATGGACTCCGACGTGCTG 60.080 57.895 0.00 0.00 0.00 4.41
3825 10065 1.215647 GCTGAACACGAGGGACGAT 59.784 57.895 0.00 0.00 45.77 3.73
3859 10099 2.820059 TGACACGATGCAGAAGTTCT 57.180 45.000 0.00 0.00 0.00 3.01
3948 10188 2.099427 GGAGATCACCGAGTACTTCCAC 59.901 54.545 0.00 0.00 0.00 4.02
4192 10432 4.351938 CGTCGTCGCCCTGACCAA 62.352 66.667 0.00 0.00 45.23 3.67
4205 10445 0.685097 TGACCAACACTAGTCTGCCC 59.315 55.000 0.00 0.00 34.02 5.36
4216 10456 6.116126 ACACTAGTCTGCCCATAGAATTTTC 58.884 40.000 0.00 0.00 0.00 2.29
4324 10567 0.893727 GCACGGGAACTCCAACCAAT 60.894 55.000 0.00 0.00 37.91 3.16
4454 10701 2.736995 CACGAACACCGATGGCGT 60.737 61.111 0.00 0.00 40.25 5.68
4469 10716 2.579201 CGTCGGGCCTGTTCATCT 59.421 61.111 12.43 0.00 0.00 2.90
4567 10814 4.724279 AGAAGGGACAAAAGGCTTTAGA 57.276 40.909 13.77 0.00 0.00 2.10
4577 10824 5.352569 ACAAAAGGCTTTAGATCAGACATCG 59.647 40.000 13.77 0.00 0.00 3.84
4585 10832 0.965439 GATCAGACATCGGAGGAGGG 59.035 60.000 0.00 0.00 0.00 4.30
4627 10878 5.121221 TGTATGTATGTATGCGGTCTCAG 57.879 43.478 0.00 0.00 0.00 3.35
4689 10940 1.002792 GAATTATTCGTTGGCCCGAGC 60.003 52.381 0.00 0.00 38.23 5.03
4690 10941 0.107410 ATTATTCGTTGGCCCGAGCA 60.107 50.000 0.00 0.00 42.56 4.26
4691 10942 0.107410 TTATTCGTTGGCCCGAGCAT 60.107 50.000 0.00 0.00 42.56 3.79
4692 10943 0.107410 TATTCGTTGGCCCGAGCATT 60.107 50.000 0.00 0.00 42.56 3.56
4747 11000 8.128582 TGTTGAGTAGTGAAAATGCTGTAAAAG 58.871 33.333 0.00 0.00 0.00 2.27
4750 11003 8.128582 TGAGTAGTGAAAATGCTGTAAAAGTTG 58.871 33.333 0.00 0.00 0.00 3.16
4751 11004 8.220755 AGTAGTGAAAATGCTGTAAAAGTTGA 57.779 30.769 0.00 0.00 0.00 3.18
4819 11072 0.617413 AACTGGGATGCAGGTGAGAG 59.383 55.000 0.00 0.00 0.00 3.20
4831 11084 4.889409 TGCAGGTGAGAGAGAAAACAAAAT 59.111 37.500 0.00 0.00 0.00 1.82
4878 11136 3.289797 TGGTGGTGCCAAGAAACAA 57.710 47.368 0.00 0.00 45.94 2.83
4879 11137 1.561643 TGGTGGTGCCAAGAAACAAA 58.438 45.000 0.00 0.00 45.94 2.83
4880 11138 1.902508 TGGTGGTGCCAAGAAACAAAA 59.097 42.857 0.00 0.00 45.94 2.44
4881 11139 2.503356 TGGTGGTGCCAAGAAACAAAAT 59.497 40.909 0.00 0.00 45.94 1.82
4882 11140 3.706594 TGGTGGTGCCAAGAAACAAAATA 59.293 39.130 0.00 0.00 45.94 1.40
4982 11246 3.156714 CTGTACCCACCAGCACCA 58.843 61.111 0.00 0.00 0.00 4.17
4983 11247 1.302511 CTGTACCCACCAGCACCAC 60.303 63.158 0.00 0.00 0.00 4.16
4984 11248 1.768482 TGTACCCACCAGCACCACT 60.768 57.895 0.00 0.00 0.00 4.00
5023 11287 4.394300 CCAGAGACTTTTTACCAGAGCATG 59.606 45.833 0.00 0.00 0.00 4.06
5143 11414 3.944015 GCAGAACCTGAGCAGTTCATTAT 59.056 43.478 6.44 0.00 34.68 1.28
5144 11415 4.201891 GCAGAACCTGAGCAGTTCATTATG 60.202 45.833 6.44 0.00 34.68 1.90
5145 11416 4.940046 CAGAACCTGAGCAGTTCATTATGT 59.060 41.667 6.44 0.00 34.68 2.29
5146 11417 4.940046 AGAACCTGAGCAGTTCATTATGTG 59.060 41.667 6.44 0.00 34.68 3.21
5147 11418 3.012518 ACCTGAGCAGTTCATTATGTGC 58.987 45.455 0.00 0.00 34.68 4.57
5148 11419 3.011818 CCTGAGCAGTTCATTATGTGCA 58.988 45.455 8.58 0.00 38.44 4.57
5149 11420 3.441222 CCTGAGCAGTTCATTATGTGCAA 59.559 43.478 8.58 0.00 38.44 4.08
5150 11421 4.438336 CCTGAGCAGTTCATTATGTGCAAG 60.438 45.833 8.58 5.84 38.44 4.01
5151 11422 4.325972 TGAGCAGTTCATTATGTGCAAGA 58.674 39.130 8.58 0.00 38.44 3.02
5152 11423 4.393990 TGAGCAGTTCATTATGTGCAAGAG 59.606 41.667 8.58 0.00 38.44 2.85
5153 11424 3.693085 AGCAGTTCATTATGTGCAAGAGG 59.307 43.478 8.58 0.00 38.44 3.69
5154 11425 3.441572 GCAGTTCATTATGTGCAAGAGGT 59.558 43.478 0.00 0.00 35.91 3.85
5155 11426 4.673580 GCAGTTCATTATGTGCAAGAGGTG 60.674 45.833 0.00 0.00 35.91 4.00
5167 11438 3.632855 CAAGAGGTGCAAGAAACTTCC 57.367 47.619 0.00 0.00 0.00 3.46
5168 11439 2.951642 CAAGAGGTGCAAGAAACTTCCA 59.048 45.455 0.00 0.00 0.00 3.53
5169 11440 2.856222 AGAGGTGCAAGAAACTTCCAG 58.144 47.619 0.00 0.00 0.00 3.86
5170 11441 2.173569 AGAGGTGCAAGAAACTTCCAGT 59.826 45.455 0.00 0.00 0.00 4.00
5171 11442 2.952310 GAGGTGCAAGAAACTTCCAGTT 59.048 45.455 0.00 0.00 40.80 3.16
5181 11452 4.843220 AAACTTCCAGTTTGAGCATCTG 57.157 40.909 1.02 0.00 45.83 2.90
5182 11453 2.157738 ACTTCCAGTTTGAGCATCTGC 58.842 47.619 0.00 0.00 42.49 4.26
5183 11454 2.156917 CTTCCAGTTTGAGCATCTGCA 58.843 47.619 4.79 0.00 45.16 4.41
5184 11455 1.817357 TCCAGTTTGAGCATCTGCAG 58.183 50.000 7.63 7.63 45.16 4.41
5185 11456 0.170561 CCAGTTTGAGCATCTGCAGC 59.829 55.000 9.47 0.00 45.16 5.25
5186 11457 0.879090 CAGTTTGAGCATCTGCAGCA 59.121 50.000 9.47 0.00 45.16 4.41
5187 11458 0.879765 AGTTTGAGCATCTGCAGCAC 59.120 50.000 9.47 0.02 45.16 4.40
5188 11459 0.879765 GTTTGAGCATCTGCAGCACT 59.120 50.000 9.47 5.71 45.16 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.280389 CCCGGGAGCATCATCGTG 60.280 66.667 18.48 0.00 36.25 4.35
1 2 2.443952 TCCCGGGAGCATCATCGT 60.444 61.111 22.63 0.00 36.25 3.73
2 3 1.748329 TTCTCCCGGGAGCATCATCG 61.748 60.000 40.97 19.91 41.71 3.84
3 4 0.469917 TTTCTCCCGGGAGCATCATC 59.530 55.000 40.97 0.00 41.71 2.92
4 5 0.918983 TTTTCTCCCGGGAGCATCAT 59.081 50.000 40.97 0.00 41.71 2.45
5 6 0.695924 TTTTTCTCCCGGGAGCATCA 59.304 50.000 40.97 24.39 41.71 3.07
6 7 1.095600 GTTTTTCTCCCGGGAGCATC 58.904 55.000 40.97 24.91 41.71 3.91
7 8 0.676782 CGTTTTTCTCCCGGGAGCAT 60.677 55.000 40.97 0.00 41.71 3.79
8 9 1.302192 CGTTTTTCTCCCGGGAGCA 60.302 57.895 40.97 31.53 41.71 4.26
9 10 1.004200 TCGTTTTTCTCCCGGGAGC 60.004 57.895 40.97 26.75 41.71 4.70
10 11 0.034337 TGTCGTTTTTCTCCCGGGAG 59.966 55.000 40.33 40.33 43.21 4.30
11 12 0.469070 TTGTCGTTTTTCTCCCGGGA 59.531 50.000 25.06 25.06 0.00 5.14
12 13 0.589708 GTTGTCGTTTTTCTCCCGGG 59.410 55.000 16.85 16.85 0.00 5.73
13 14 1.301423 TGTTGTCGTTTTTCTCCCGG 58.699 50.000 0.00 0.00 0.00 5.73
14 15 3.242936 ACATTGTTGTCGTTTTTCTCCCG 60.243 43.478 0.00 0.00 0.00 5.14
15 16 4.041723 CACATTGTTGTCGTTTTTCTCCC 58.958 43.478 0.00 0.00 32.34 4.30
16 17 3.485743 GCACATTGTTGTCGTTTTTCTCC 59.514 43.478 0.00 0.00 32.34 3.71
17 18 3.485743 GGCACATTGTTGTCGTTTTTCTC 59.514 43.478 0.00 0.00 32.34 2.87
18 19 3.443976 GGCACATTGTTGTCGTTTTTCT 58.556 40.909 0.00 0.00 32.34 2.52
19 20 2.538037 GGGCACATTGTTGTCGTTTTTC 59.462 45.455 0.00 0.00 32.34 2.29
20 21 2.545731 GGGCACATTGTTGTCGTTTTT 58.454 42.857 0.00 0.00 32.34 1.94
21 22 1.202475 GGGGCACATTGTTGTCGTTTT 60.202 47.619 0.00 0.00 32.34 2.43
22 23 0.387565 GGGGCACATTGTTGTCGTTT 59.612 50.000 0.00 0.00 32.34 3.60
23 24 1.460273 GGGGGCACATTGTTGTCGTT 61.460 55.000 0.00 0.00 32.34 3.85
24 25 1.901464 GGGGGCACATTGTTGTCGT 60.901 57.895 0.00 0.00 32.34 4.34
25 26 1.250154 ATGGGGGCACATTGTTGTCG 61.250 55.000 0.00 0.00 32.34 4.35
26 27 0.975887 AATGGGGGCACATTGTTGTC 59.024 50.000 5.95 0.00 39.47 3.18
27 28 3.162394 AATGGGGGCACATTGTTGT 57.838 47.368 5.95 0.00 39.47 3.32
32 33 0.680921 CTCGACAATGGGGGCACATT 60.681 55.000 0.00 0.00 41.51 2.71
33 34 1.077501 CTCGACAATGGGGGCACAT 60.078 57.895 0.00 0.00 0.00 3.21
34 35 2.220586 TCTCGACAATGGGGGCACA 61.221 57.895 0.00 0.00 0.00 4.57
35 36 1.745489 GTCTCGACAATGGGGGCAC 60.745 63.158 0.00 0.00 0.00 5.01
36 37 2.668632 GTCTCGACAATGGGGGCA 59.331 61.111 0.00 0.00 0.00 5.36
37 38 2.124695 GGTCTCGACAATGGGGGC 60.125 66.667 0.00 0.00 0.00 5.80
38 39 0.037590 TTTGGTCTCGACAATGGGGG 59.962 55.000 0.00 0.00 0.00 5.40
39 40 1.003118 TCTTTGGTCTCGACAATGGGG 59.997 52.381 0.00 0.00 0.00 4.96
40 41 2.472695 TCTTTGGTCTCGACAATGGG 57.527 50.000 0.00 0.00 0.00 4.00
41 42 3.815401 AGTTTCTTTGGTCTCGACAATGG 59.185 43.478 0.00 0.00 0.00 3.16
42 43 4.273480 ACAGTTTCTTTGGTCTCGACAATG 59.727 41.667 0.00 0.00 0.00 2.82
43 44 4.451900 ACAGTTTCTTTGGTCTCGACAAT 58.548 39.130 0.00 0.00 0.00 2.71
44 45 3.869065 ACAGTTTCTTTGGTCTCGACAA 58.131 40.909 0.00 0.00 0.00 3.18
45 46 3.118920 TGACAGTTTCTTTGGTCTCGACA 60.119 43.478 0.00 0.00 0.00 4.35
46 47 3.454375 TGACAGTTTCTTTGGTCTCGAC 58.546 45.455 0.00 0.00 0.00 4.20
47 48 3.492656 CCTGACAGTTTCTTTGGTCTCGA 60.493 47.826 0.93 0.00 0.00 4.04
48 49 2.802816 CCTGACAGTTTCTTTGGTCTCG 59.197 50.000 0.93 0.00 0.00 4.04
49 50 3.142174 CCCTGACAGTTTCTTTGGTCTC 58.858 50.000 0.93 0.00 0.00 3.36
50 51 2.158608 CCCCTGACAGTTTCTTTGGTCT 60.159 50.000 0.93 0.00 0.00 3.85
51 52 2.230660 CCCCTGACAGTTTCTTTGGTC 58.769 52.381 0.93 0.00 0.00 4.02
52 53 1.133482 CCCCCTGACAGTTTCTTTGGT 60.133 52.381 0.93 0.00 0.00 3.67
53 54 1.133482 ACCCCCTGACAGTTTCTTTGG 60.133 52.381 0.93 0.00 0.00 3.28
54 55 2.364972 ACCCCCTGACAGTTTCTTTG 57.635 50.000 0.93 0.00 0.00 2.77
55 56 2.748465 CGAACCCCCTGACAGTTTCTTT 60.748 50.000 0.93 0.00 0.00 2.52
56 57 1.202770 CGAACCCCCTGACAGTTTCTT 60.203 52.381 0.93 0.00 0.00 2.52
57 58 0.396811 CGAACCCCCTGACAGTTTCT 59.603 55.000 0.93 0.00 0.00 2.52
58 59 1.235281 GCGAACCCCCTGACAGTTTC 61.235 60.000 0.93 0.00 0.00 2.78
59 60 1.228154 GCGAACCCCCTGACAGTTT 60.228 57.895 0.93 0.00 0.00 2.66
60 61 2.430367 GCGAACCCCCTGACAGTT 59.570 61.111 0.93 0.00 0.00 3.16
61 62 3.637273 GGCGAACCCCCTGACAGT 61.637 66.667 0.93 0.00 0.00 3.55
71 72 4.785453 CAGGGCTCTGGGCGAACC 62.785 72.222 5.38 0.00 42.94 3.62
79 80 1.075674 TCTCTAGGCCAGGGCTCTG 60.076 63.158 21.26 13.95 39.70 3.35
80 81 1.232792 CTCTCTAGGCCAGGGCTCT 59.767 63.158 21.26 12.29 39.70 4.09
81 82 0.178935 ATCTCTCTAGGCCAGGGCTC 60.179 60.000 21.26 4.95 39.70 4.70
82 83 0.471591 CATCTCTCTAGGCCAGGGCT 60.472 60.000 21.38 21.38 42.39 5.19
83 84 1.479368 CCATCTCTCTAGGCCAGGGC 61.479 65.000 5.01 4.33 41.06 5.19
84 85 0.189574 TCCATCTCTCTAGGCCAGGG 59.810 60.000 5.01 0.00 0.00 4.45
85 86 1.337118 GTCCATCTCTCTAGGCCAGG 58.663 60.000 5.01 0.00 0.00 4.45
86 87 1.337118 GGTCCATCTCTCTAGGCCAG 58.663 60.000 5.01 0.00 0.00 4.85
87 88 0.468214 CGGTCCATCTCTCTAGGCCA 60.468 60.000 5.01 0.00 0.00 5.36
88 89 1.811645 GCGGTCCATCTCTCTAGGCC 61.812 65.000 0.00 0.00 0.00 5.19
89 90 0.825840 AGCGGTCCATCTCTCTAGGC 60.826 60.000 0.00 0.00 0.00 3.93
90 91 0.958091 CAGCGGTCCATCTCTCTAGG 59.042 60.000 0.00 0.00 0.00 3.02
91 92 0.313672 GCAGCGGTCCATCTCTCTAG 59.686 60.000 0.00 0.00 0.00 2.43
92 93 1.448119 CGCAGCGGTCCATCTCTCTA 61.448 60.000 7.00 0.00 0.00 2.43
93 94 2.780094 CGCAGCGGTCCATCTCTCT 61.780 63.158 7.00 0.00 0.00 3.10
94 95 2.279120 CGCAGCGGTCCATCTCTC 60.279 66.667 7.00 0.00 0.00 3.20
95 96 2.755876 TCGCAGCGGTCCATCTCT 60.756 61.111 16.42 0.00 0.00 3.10
96 97 2.583593 GTCGCAGCGGTCCATCTC 60.584 66.667 16.42 0.00 0.00 2.75
97 98 4.498520 CGTCGCAGCGGTCCATCT 62.499 66.667 16.42 0.00 0.00 2.90
118 119 0.111253 GGGTGCCATATCCCTCTTGG 59.889 60.000 0.00 0.00 40.48 3.61
119 120 0.846015 TGGGTGCCATATCCCTCTTG 59.154 55.000 0.00 0.00 43.74 3.02
120 121 0.846693 GTGGGTGCCATATCCCTCTT 59.153 55.000 0.00 0.00 43.74 2.85
121 122 1.410850 CGTGGGTGCCATATCCCTCT 61.411 60.000 0.00 0.00 43.74 3.69
122 123 1.071471 CGTGGGTGCCATATCCCTC 59.929 63.158 0.00 0.00 43.74 4.30
123 124 3.120086 GCGTGGGTGCCATATCCCT 62.120 63.158 0.00 0.00 43.74 4.20
124 125 2.594592 GCGTGGGTGCCATATCCC 60.595 66.667 0.00 0.00 43.67 3.85
125 126 2.372040 TACGCGTGGGTGCCATATCC 62.372 60.000 24.59 0.00 35.28 2.59
126 127 0.320421 ATACGCGTGGGTGCCATATC 60.320 55.000 24.59 0.00 35.28 1.63
127 128 0.320421 GATACGCGTGGGTGCCATAT 60.320 55.000 24.59 3.01 35.28 1.78
128 129 1.068417 GATACGCGTGGGTGCCATA 59.932 57.895 24.59 0.00 35.28 2.74
129 130 2.203015 GATACGCGTGGGTGCCAT 60.203 61.111 24.59 4.79 35.28 4.40
130 131 4.805231 CGATACGCGTGGGTGCCA 62.805 66.667 24.59 0.00 34.64 4.92
147 148 2.130073 GATTAAAGATGGGCGGCGGC 62.130 60.000 26.59 26.59 38.90 6.53
148 149 0.817634 TGATTAAAGATGGGCGGCGG 60.818 55.000 9.78 0.00 0.00 6.13
149 150 1.197721 GATGATTAAAGATGGGCGGCG 59.802 52.381 0.51 0.51 0.00 6.46
150 151 2.508526 AGATGATTAAAGATGGGCGGC 58.491 47.619 0.00 0.00 0.00 6.53
151 152 3.254166 CCAAGATGATTAAAGATGGGCGG 59.746 47.826 0.00 0.00 0.00 6.13
152 153 3.304928 GCCAAGATGATTAAAGATGGGCG 60.305 47.826 0.00 0.00 0.00 6.13
153 154 3.638160 TGCCAAGATGATTAAAGATGGGC 59.362 43.478 0.00 0.00 38.16 5.36
154 155 6.220930 CAATGCCAAGATGATTAAAGATGGG 58.779 40.000 0.00 0.00 0.00 4.00
155 156 5.694910 GCAATGCCAAGATGATTAAAGATGG 59.305 40.000 0.00 0.00 0.00 3.51
156 157 6.513180 AGCAATGCCAAGATGATTAAAGATG 58.487 36.000 0.00 0.00 0.00 2.90
157 158 6.726490 AGCAATGCCAAGATGATTAAAGAT 57.274 33.333 0.00 0.00 0.00 2.40
158 159 6.334989 CAAGCAATGCCAAGATGATTAAAGA 58.665 36.000 0.00 0.00 0.00 2.52
159 160 5.522460 CCAAGCAATGCCAAGATGATTAAAG 59.478 40.000 0.00 0.00 0.00 1.85
160 161 5.421277 CCAAGCAATGCCAAGATGATTAAA 58.579 37.500 0.00 0.00 0.00 1.52
161 162 4.141892 CCCAAGCAATGCCAAGATGATTAA 60.142 41.667 0.00 0.00 0.00 1.40
162 163 3.385433 CCCAAGCAATGCCAAGATGATTA 59.615 43.478 0.00 0.00 0.00 1.75
163 164 2.169769 CCCAAGCAATGCCAAGATGATT 59.830 45.455 0.00 0.00 0.00 2.57
164 165 1.760613 CCCAAGCAATGCCAAGATGAT 59.239 47.619 0.00 0.00 0.00 2.45
165 166 1.187974 CCCAAGCAATGCCAAGATGA 58.812 50.000 0.00 0.00 0.00 2.92
166 167 0.461339 GCCCAAGCAATGCCAAGATG 60.461 55.000 0.00 0.00 39.53 2.90
167 168 1.619807 GGCCCAAGCAATGCCAAGAT 61.620 55.000 0.00 0.00 44.70 2.40
168 169 2.285024 GGCCCAAGCAATGCCAAGA 61.285 57.895 0.00 0.00 44.70 3.02
169 170 2.266689 GGCCCAAGCAATGCCAAG 59.733 61.111 0.00 0.00 44.70 3.61
186 187 4.479993 CTCCTTCTGCTGGGCCGG 62.480 72.222 8.39 8.39 0.00 6.13
187 188 3.259633 AACTCCTTCTGCTGGGCCG 62.260 63.158 0.00 0.00 0.00 6.13
188 189 1.676967 CAACTCCTTCTGCTGGGCC 60.677 63.158 0.00 0.00 0.00 5.80
189 190 0.538287 AACAACTCCTTCTGCTGGGC 60.538 55.000 0.00 0.00 0.00 5.36
190 191 1.242076 CAACAACTCCTTCTGCTGGG 58.758 55.000 0.00 0.00 0.00 4.45
191 192 1.242076 CCAACAACTCCTTCTGCTGG 58.758 55.000 0.00 0.00 0.00 4.85
192 193 1.242076 CCCAACAACTCCTTCTGCTG 58.758 55.000 0.00 0.00 0.00 4.41
193 194 0.111253 CCCCAACAACTCCTTCTGCT 59.889 55.000 0.00 0.00 0.00 4.24
194 195 1.527433 GCCCCAACAACTCCTTCTGC 61.527 60.000 0.00 0.00 0.00 4.26
195 196 0.111253 AGCCCCAACAACTCCTTCTG 59.889 55.000 0.00 0.00 0.00 3.02
196 197 0.402121 GAGCCCCAACAACTCCTTCT 59.598 55.000 0.00 0.00 0.00 2.85
197 198 0.402121 AGAGCCCCAACAACTCCTTC 59.598 55.000 0.00 0.00 0.00 3.46
198 199 1.742308 TAGAGCCCCAACAACTCCTT 58.258 50.000 0.00 0.00 0.00 3.36
199 200 1.742308 TTAGAGCCCCAACAACTCCT 58.258 50.000 0.00 0.00 0.00 3.69
200 201 2.160205 GTTTAGAGCCCCAACAACTCC 58.840 52.381 0.00 0.00 0.00 3.85
201 202 1.804748 CGTTTAGAGCCCCAACAACTC 59.195 52.381 0.00 0.00 0.00 3.01
202 203 1.142262 ACGTTTAGAGCCCCAACAACT 59.858 47.619 0.00 0.00 0.00 3.16
203 204 1.601166 ACGTTTAGAGCCCCAACAAC 58.399 50.000 0.00 0.00 0.00 3.32
204 205 3.181452 ACTTACGTTTAGAGCCCCAACAA 60.181 43.478 0.00 0.00 0.00 2.83
205 206 2.369532 ACTTACGTTTAGAGCCCCAACA 59.630 45.455 0.00 0.00 0.00 3.33
206 207 2.740447 CACTTACGTTTAGAGCCCCAAC 59.260 50.000 0.00 0.00 0.00 3.77
207 208 2.369532 ACACTTACGTTTAGAGCCCCAA 59.630 45.455 0.00 0.00 0.00 4.12
208 209 1.972795 ACACTTACGTTTAGAGCCCCA 59.027 47.619 0.00 0.00 0.00 4.96
209 210 2.233186 AGACACTTACGTTTAGAGCCCC 59.767 50.000 0.00 0.00 0.00 5.80
210 211 3.509740 GAGACACTTACGTTTAGAGCCC 58.490 50.000 0.00 0.00 0.00 5.19
211 212 3.509740 GGAGACACTTACGTTTAGAGCC 58.490 50.000 0.00 0.00 0.00 4.70
212 213 3.057033 TGGGAGACACTTACGTTTAGAGC 60.057 47.826 0.00 0.00 0.00 4.09
213 214 4.778534 TGGGAGACACTTACGTTTAGAG 57.221 45.455 0.00 0.00 0.00 2.43
217 218 6.183360 GGACTATATGGGAGACACTTACGTTT 60.183 42.308 0.00 0.00 0.00 3.60
229 230 4.283467 TCGGATTGTTGGACTATATGGGAG 59.717 45.833 0.00 0.00 0.00 4.30
231 232 4.617253 TCGGATTGTTGGACTATATGGG 57.383 45.455 0.00 0.00 0.00 4.00
232 233 5.643777 GGAATCGGATTGTTGGACTATATGG 59.356 44.000 8.18 0.00 0.00 2.74
251 254 0.442699 GTTCGAGTTGGCGTGGAATC 59.557 55.000 0.00 0.00 0.00 2.52
307 4819 8.990163 TCTTCTATGGTTGGTTAGAAGTTTTT 57.010 30.769 15.53 0.00 46.01 1.94
308 4820 8.990163 TTCTTCTATGGTTGGTTAGAAGTTTT 57.010 30.769 15.53 0.00 46.01 2.43
309 4821 8.990163 TTTCTTCTATGGTTGGTTAGAAGTTT 57.010 30.769 15.53 0.00 46.01 2.66
310 4822 8.990163 TTTTCTTCTATGGTTGGTTAGAAGTT 57.010 30.769 15.53 0.00 46.01 2.66
326 4838 6.321181 AGACCATTTGTGCTGTTTTTCTTCTA 59.679 34.615 0.00 0.00 0.00 2.10
328 4840 5.232838 CAGACCATTTGTGCTGTTTTTCTTC 59.767 40.000 0.00 0.00 0.00 2.87
342 4854 1.002134 ACCCGAGCCAGACCATTTG 60.002 57.895 0.00 0.00 0.00 2.32
343 4855 1.299976 GACCCGAGCCAGACCATTT 59.700 57.895 0.00 0.00 0.00 2.32
345 4857 2.284625 TGACCCGAGCCAGACCAT 60.285 61.111 0.00 0.00 0.00 3.55
346 4858 3.311110 GTGACCCGAGCCAGACCA 61.311 66.667 0.00 0.00 0.00 4.02
347 4859 2.997897 AGTGACCCGAGCCAGACC 60.998 66.667 0.00 0.00 0.00 3.85
349 4861 2.997315 CCAGTGACCCGAGCCAGA 60.997 66.667 0.00 0.00 0.00 3.86
355 6324 1.147376 CACCAAACCAGTGACCCGA 59.853 57.895 0.00 0.00 37.42 5.14
395 6364 2.685897 GCGGGCACAAGTTTTATATGGA 59.314 45.455 0.00 0.00 0.00 3.41
396 6365 2.687935 AGCGGGCACAAGTTTTATATGG 59.312 45.455 0.00 0.00 0.00 2.74
432 6409 2.462456 ATGTGCAGTGTAGTGTGGAG 57.538 50.000 0.00 0.00 0.00 3.86
474 6451 2.106684 GAGTTGTTGGAGAGGGGAAAGT 59.893 50.000 0.00 0.00 0.00 2.66
475 6452 2.373502 AGAGTTGTTGGAGAGGGGAAAG 59.626 50.000 0.00 0.00 0.00 2.62
478 6455 1.645710 GAGAGTTGTTGGAGAGGGGA 58.354 55.000 0.00 0.00 0.00 4.81
499 6476 5.221843 ACTCCATTAACAACTACTGCTGGAA 60.222 40.000 0.00 0.00 31.57 3.53
513 6519 9.676861 ACCCTTGTTTATTACTACTCCATTAAC 57.323 33.333 0.00 0.00 0.00 2.01
560 6566 0.109132 CTCATTCCTTGGCCGTTTGC 60.109 55.000 0.00 0.00 40.16 3.68
561 6567 1.533625 TCTCATTCCTTGGCCGTTTG 58.466 50.000 0.00 0.00 0.00 2.93
628 6644 1.951602 GCGCCGGTTTTAATTAGGGAT 59.048 47.619 1.90 0.00 0.00 3.85
685 6721 2.888414 TCCCTTTCCGGTTTTTGCTTAG 59.112 45.455 0.00 0.00 0.00 2.18
688 6724 1.686587 CTTCCCTTTCCGGTTTTTGCT 59.313 47.619 0.00 0.00 0.00 3.91
690 6726 4.394439 TTTCTTCCCTTTCCGGTTTTTG 57.606 40.909 0.00 0.00 0.00 2.44
781 6818 0.109272 CTTTCTCCTCTACGCGCACA 60.109 55.000 5.73 0.00 0.00 4.57
838 6889 0.175989 AGCTAGCTTTACGTGGAGGC 59.824 55.000 12.68 0.00 0.00 4.70
925 6989 4.595986 AGAGAGAGAAAGTGGGTAGAGAC 58.404 47.826 0.00 0.00 0.00 3.36
935 6999 8.497745 AGATCTTGAGAGATAGAGAGAGAAAGT 58.502 37.037 0.00 0.00 42.66 2.66
949 7013 0.735471 CCGCGACAGATCTTGAGAGA 59.265 55.000 8.23 0.00 36.09 3.10
1281 7351 4.410400 GGGTTGGGGAGCACGAGG 62.410 72.222 0.00 0.00 0.00 4.63
1350 7432 4.697756 TTGTTGCCTCCCGAGCCG 62.698 66.667 0.00 0.00 0.00 5.52
1351 7433 2.747855 CTTGTTGCCTCCCGAGCC 60.748 66.667 0.00 0.00 0.00 4.70
1352 7434 2.032681 ACTTGTTGCCTCCCGAGC 59.967 61.111 0.00 0.00 0.00 5.03
1353 7435 1.376037 GGACTTGTTGCCTCCCGAG 60.376 63.158 0.00 0.00 0.00 4.63
1354 7436 1.827399 GAGGACTTGTTGCCTCCCGA 61.827 60.000 0.00 0.00 43.91 5.14
1355 7437 1.376037 GAGGACTTGTTGCCTCCCG 60.376 63.158 0.00 0.00 43.91 5.14
1356 7438 4.724262 GAGGACTTGTTGCCTCCC 57.276 61.111 0.00 0.00 43.91 4.30
1359 7441 1.072965 CTCTTGGAGGACTTGTTGCCT 59.927 52.381 0.00 0.00 37.18 4.75
1515 7597 2.620112 CGGGTGCAGGAACTTGCTG 61.620 63.158 5.94 5.94 38.97 4.41
1842 7924 2.202892 GACGCCTTGGACGATCCC 60.203 66.667 9.64 0.00 35.03 3.85
1983 8065 1.077429 GGAAGGTGCAGGGGACATC 60.077 63.158 0.00 0.00 0.00 3.06
2547 8784 2.665000 CACACCATGGCTCGGTCT 59.335 61.111 13.04 0.00 33.25 3.85
2605 8842 6.819284 TGGACTGAGAAAAGATGCAAATTTT 58.181 32.000 10.92 10.92 0.00 1.82
2612 8849 5.444663 AACTTTGGACTGAGAAAAGATGC 57.555 39.130 11.76 0.00 35.39 3.91
2645 8882 5.994250 TCAGCTAAATAGATCAGCAAACCT 58.006 37.500 4.95 0.00 37.78 3.50
2919 9158 8.763356 CAGTATAGAGCTCATCAAGAAAATGAC 58.237 37.037 17.77 0.00 30.82 3.06
2923 9162 6.643388 TGCAGTATAGAGCTCATCAAGAAAA 58.357 36.000 17.77 0.00 0.00 2.29
2999 9238 6.003950 ACAGACACATAGCAAATTGGTAAGT 58.996 36.000 9.04 8.04 33.30 2.24
3022 9261 3.293311 TCTGCGTGTTACCTGTAGAAC 57.707 47.619 0.00 0.00 0.00 3.01
3023 9262 3.319972 AGTTCTGCGTGTTACCTGTAGAA 59.680 43.478 1.71 1.71 32.98 2.10
3047 9286 2.501723 GGTCTCCAGTAAATCTGCTCCA 59.498 50.000 0.00 0.00 42.38 3.86
3323 9563 2.770164 AGCTAATGAAACAGAGCGGT 57.230 45.000 0.00 0.00 39.96 5.68
3325 9565 8.551205 TGATAATTTAGCTAATGAAACAGAGCG 58.449 33.333 7.08 0.00 39.96 5.03
3347 9587 4.631377 CAGCCTGTCAAACGAAGAATGATA 59.369 41.667 0.00 0.00 0.00 2.15
3489 9729 1.970640 TCAGCCAGTTTGAGCAGAGTA 59.029 47.619 0.00 0.00 0.00 2.59
3639 9879 2.497107 GCTTTTTGCACTCAAGCTCA 57.503 45.000 13.91 0.00 39.92 4.26
3859 10099 1.372499 CGTCGTCGGCCTTCTTCAA 60.372 57.895 0.00 0.00 0.00 2.69
3948 10188 4.771356 TCTTTCGCCGAGTCGCCG 62.771 66.667 10.00 10.00 0.00 6.46
4192 10432 5.700402 AAATTCTATGGGCAGACTAGTGT 57.300 39.130 0.00 0.00 0.00 3.55
4205 10445 9.639601 CATTGATGATCCATGGAAAATTCTATG 57.360 33.333 20.67 18.88 43.35 2.23
4216 10456 4.280174 GGTTTCCTCATTGATGATCCATGG 59.720 45.833 4.97 4.97 36.02 3.66
4257 10500 1.876156 CCTGTTGAGTTGTCCTTCTGC 59.124 52.381 0.00 0.00 0.00 4.26
4309 10552 2.492088 GTGCTAATTGGTTGGAGTTCCC 59.508 50.000 0.00 0.00 34.29 3.97
4316 10559 1.247419 TGCCGGTGCTAATTGGTTGG 61.247 55.000 1.90 0.00 38.71 3.77
4324 10567 1.419381 TGGATAGATGCCGGTGCTAA 58.581 50.000 1.90 0.00 38.71 3.09
4364 10607 1.261480 ACTCACCTGAGCTTGACGAT 58.739 50.000 2.01 0.00 45.79 3.73
4454 10701 0.984230 AAAGAGATGAACAGGCCCGA 59.016 50.000 0.00 0.00 0.00 5.14
4469 10716 7.067008 CAGGTACAAAAAGTCAGGAAAGAAAGA 59.933 37.037 0.00 0.00 0.00 2.52
4567 10814 0.558220 TCCCTCCTCCGATGTCTGAT 59.442 55.000 0.00 0.00 0.00 2.90
4577 10824 3.653835 ACTGCTTATTTTCCCTCCTCC 57.346 47.619 0.00 0.00 0.00 4.30
4627 10878 6.540189 ACTGCTCCATGTTAATGTACAGAATC 59.460 38.462 0.33 0.00 33.54 2.52
4680 10931 2.362760 ATTGCAATGCTCGGGCCA 60.363 55.556 12.09 0.00 37.74 5.36
4689 10940 7.353497 TGAAATTTGTTTACAGCATTGCAATG 58.647 30.769 30.92 30.92 39.40 2.82
4690 10941 7.493743 TGAAATTTGTTTACAGCATTGCAAT 57.506 28.000 11.91 5.99 0.00 3.56
4691 10942 6.915544 TGAAATTTGTTTACAGCATTGCAA 57.084 29.167 11.91 0.00 0.00 4.08
4692 10943 6.915544 TTGAAATTTGTTTACAGCATTGCA 57.084 29.167 11.91 0.00 0.00 4.08
4747 11000 5.291614 TGCAGATTCAGCAAAGTTTTTCAAC 59.708 36.000 0.70 0.00 39.39 3.18
4750 11003 4.805192 TGTGCAGATTCAGCAAAGTTTTTC 59.195 37.500 5.22 0.00 44.64 2.29
4751 11004 4.757594 TGTGCAGATTCAGCAAAGTTTTT 58.242 34.783 5.22 0.00 44.64 1.94
4819 11072 9.286946 CATCTCATGCTCTTATTTTGTTTTCTC 57.713 33.333 0.00 0.00 0.00 2.87
4831 11084 4.583907 CCAGAGTCTCATCTCATGCTCTTA 59.416 45.833 1.94 0.00 36.97 2.10
4878 11136 5.095145 TGATGAGTGCTCTGCTCTTATTT 57.905 39.130 0.00 0.00 30.68 1.40
4879 11137 4.750021 TGATGAGTGCTCTGCTCTTATT 57.250 40.909 0.00 0.00 30.68 1.40
4880 11138 4.503469 CCATGATGAGTGCTCTGCTCTTAT 60.503 45.833 0.00 0.00 32.60 1.73
4881 11139 3.181468 CCATGATGAGTGCTCTGCTCTTA 60.181 47.826 0.00 0.00 32.35 2.10
4882 11140 2.420269 CCATGATGAGTGCTCTGCTCTT 60.420 50.000 0.00 0.00 32.35 2.85
4982 11246 4.537751 TCTGGCTGCATCTTAGTAGTAGT 58.462 43.478 0.50 0.00 0.00 2.73
4983 11247 4.824537 TCTCTGGCTGCATCTTAGTAGTAG 59.175 45.833 0.50 0.00 0.00 2.57
4984 11248 4.580995 GTCTCTGGCTGCATCTTAGTAGTA 59.419 45.833 0.50 0.00 0.00 1.82
5023 11287 6.201806 GCAGATGAAAGTATGTATGTCAGGAC 59.798 42.308 0.00 0.00 0.00 3.85
5147 11418 2.951642 TGGAAGTTTCTTGCACCTCTTG 59.048 45.455 0.00 0.00 0.00 3.02
5148 11419 3.217626 CTGGAAGTTTCTTGCACCTCTT 58.782 45.455 0.00 0.00 0.00 2.85
5149 11420 2.856222 CTGGAAGTTTCTTGCACCTCT 58.144 47.619 0.00 0.00 0.00 3.69
5162 11433 2.157738 GCAGATGCTCAAACTGGAAGT 58.842 47.619 0.00 0.00 44.48 3.01
5163 11434 2.156917 TGCAGATGCTCAAACTGGAAG 58.843 47.619 6.35 0.00 42.66 3.46
5164 11435 2.156917 CTGCAGATGCTCAAACTGGAA 58.843 47.619 8.42 0.00 42.66 3.53
5165 11436 1.817357 CTGCAGATGCTCAAACTGGA 58.183 50.000 8.42 0.00 42.66 3.86
5166 11437 0.170561 GCTGCAGATGCTCAAACTGG 59.829 55.000 20.43 0.00 42.66 4.00
5167 11438 0.879090 TGCTGCAGATGCTCAAACTG 59.121 50.000 20.43 0.00 42.66 3.16
5168 11439 0.879765 GTGCTGCAGATGCTCAAACT 59.120 50.000 20.43 0.00 42.66 2.66
5169 11440 0.879765 AGTGCTGCAGATGCTCAAAC 59.120 50.000 20.43 0.00 42.66 2.93
5170 11441 3.334413 AGTGCTGCAGATGCTCAAA 57.666 47.368 20.43 0.00 42.66 2.69


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

AutoCloner maintained by Alex Coulton.