Multiple sequence alignment - TraesCS5D01G483800

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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 TraesCS5D01G483800 chr5D 100.000 2527 0 0 707 3233 520302252 520299726 0.000000e+00 4667.0
1 TraesCS5D01G483800 chr5D 100.000 357 0 0 1 357 520302958 520302602 0.000000e+00 660.0
2 TraesCS5D01G483800 chrUn 92.744 2274 130 15 992 3233 294624926 294622656 0.000000e+00 3253.0
3 TraesCS5D01G483800 chr5B 95.109 1472 64 5 782 2250 655321968 655323434 0.000000e+00 2313.0
4 TraesCS5D01G483800 chr5B 94.208 1502 66 11 771 2257 655391360 655392855 0.000000e+00 2272.0
5 TraesCS5D01G483800 chr5B 92.832 1437 85 9 828 2252 655278731 655280161 0.000000e+00 2067.0
6 TraesCS5D01G483800 chr5B 86.183 1158 136 7 1107 2252 655283714 655284859 0.000000e+00 1230.0
7 TraesCS5D01G483800 chr5B 89.587 557 36 12 2470 3026 655323729 655324263 0.000000e+00 688.0
8 TraesCS5D01G483800 chr5B 80.462 476 71 18 2763 3231 655393105 655393565 8.590000e-91 344.0
9 TraesCS5D01G483800 chr5B 87.907 215 18 4 2252 2465 655323474 655323681 2.490000e-61 246.0
10 TraesCS5D01G483800 chr5B 77.327 419 58 18 2819 3231 655280199 655280586 2.530000e-51 213.0
11 TraesCS5D01G483800 chr5B 96.154 52 2 0 719 770 655278636 655278687 5.750000e-13 86.1
12 TraesCS5D01G483800 chr5B 97.368 38 1 0 733 770 655391304 655391341 7.490000e-07 65.8
13 TraesCS5D01G483800 chr5A 91.397 1639 117 10 990 2604 647967239 647965601 0.000000e+00 2224.0
14 TraesCS5D01G483800 chr5A 93.200 1500 79 10 772 2257 648361879 648360389 0.000000e+00 2183.0
15 TraesCS5D01G483800 chr5A 91.406 1280 94 6 995 2261 648228523 648227247 0.000000e+00 1740.0
16 TraesCS5D01G483800 chr5A 93.912 887 51 1 1374 2257 648175170 648174284 0.000000e+00 1336.0
17 TraesCS5D01G483800 chr5A 91.750 400 27 2 990 1383 648176047 648175648 4.710000e-153 551.0
18 TraesCS5D01G483800 chr5A 93.115 305 20 1 1953 2257 647976252 647975949 2.290000e-121 446.0
19 TraesCS5D01G483800 chr5A 83.511 376 46 14 2859 3231 647975606 647975244 1.440000e-88 337.0
20 TraesCS5D01G483800 chr5A 93.421 228 11 3 772 997 648238255 648238030 5.170000e-88 335.0
21 TraesCS5D01G483800 chr5A 96.296 189 5 2 2788 2975 647955865 647955678 3.130000e-80 309.0
22 TraesCS5D01G483800 chr5A 80.371 377 48 14 2244 2608 648174257 648173895 2.470000e-66 263.0
23 TraesCS5D01G483800 chr5A 88.000 225 10 2 3013 3233 647955677 647955466 1.930000e-62 250.0
24 TraesCS5D01G483800 chr5A 78.708 418 58 11 2818 3231 648360357 648359967 1.930000e-62 250.0
25 TraesCS5D01G483800 chr5A 78.095 420 60 12 2818 3231 648227220 648226827 1.500000e-58 237.0
26 TraesCS5D01G483800 chr5A 97.080 137 4 0 2599 2735 647957032 647956896 6.980000e-57 231.0
27 TraesCS5D01G483800 chr5A 96.774 62 2 0 2190 2251 648313988 648313927 1.590000e-18 104.0
28 TraesCS5D01G483800 chr5A 94.231 52 3 0 719 770 648361950 648361899 2.670000e-11 80.5
29 TraesCS5D01G483800 chr5A 97.674 43 1 0 728 770 648238317 648238275 1.240000e-09 75.0
30 TraesCS5D01G483800 chr6B 83.240 358 48 6 1 357 507375606 507375260 5.200000e-83 318.0
31 TraesCS5D01G483800 chr2B 78.571 350 65 9 14 357 249363547 249363202 4.200000e-54 222.0


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 TraesCS5D01G483800 chr5D 520299726 520302958 3232 True 2663.500000 4667 100.000000 1 3233 2 chr5D.!!$R1 3232
1 TraesCS5D01G483800 chrUn 294622656 294624926 2270 True 3253.000000 3253 92.744000 992 3233 1 chrUn.!!$R1 2241
2 TraesCS5D01G483800 chr5B 655321968 655324263 2295 False 1082.333333 2313 90.867667 782 3026 3 chr5B.!!$F2 2244
3 TraesCS5D01G483800 chr5B 655278636 655284859 6223 False 899.025000 2067 88.124000 719 3231 4 chr5B.!!$F1 2512
4 TraesCS5D01G483800 chr5B 655391304 655393565 2261 False 893.933333 2272 90.679333 733 3231 3 chr5B.!!$F3 2498
5 TraesCS5D01G483800 chr5A 647965601 647967239 1638 True 2224.000000 2224 91.397000 990 2604 1 chr5A.!!$R1 1614
6 TraesCS5D01G483800 chr5A 648226827 648228523 1696 True 988.500000 1740 84.750500 995 3231 2 chr5A.!!$R6 2236
7 TraesCS5D01G483800 chr5A 648359967 648361950 1983 True 837.833333 2183 88.713000 719 3231 3 chr5A.!!$R8 2512
8 TraesCS5D01G483800 chr5A 648173895 648176047 2152 True 716.666667 1336 88.677667 990 2608 3 chr5A.!!$R5 1618
9 TraesCS5D01G483800 chr5A 647975244 647976252 1008 True 391.500000 446 88.313000 1953 3231 2 chr5A.!!$R4 1278
10 TraesCS5D01G483800 chr5A 647955466 647957032 1566 True 263.333333 309 93.792000 2599 3233 3 chr5A.!!$R3 634

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
157 158 0.101219 CCATGATGTGCTCGACGAGA 59.899 55.0 28.43 8.17 0.0 4.04 F
324 325 0.177373 GTACGACCCCCAGACCAATC 59.823 60.0 0.00 0.00 0.0 2.67 F
325 326 0.979187 TACGACCCCCAGACCAATCC 60.979 60.0 0.00 0.00 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1964 0.108615 CGAAGTCCACGGATTCTGCT 60.109 55.000 0.00 0.00 0.0 4.24 R
1808 2338 1.604278 TGTCATACAGATCGGCGAGAG 59.396 52.381 17.22 10.08 0.0 3.20 R
2489 3136 2.475487 GTCCTTGTCGAGTTAACAGCAC 59.525 50.000 8.61 1.35 0.0 4.40 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
20 21 2.974698 GGAATGGCCGCCATCTCG 60.975 66.667 25.27 0.00 44.40 4.04
21 22 3.654020 GAATGGCCGCCATCTCGC 61.654 66.667 25.27 11.34 44.40 5.03
27 28 4.598894 CCGCCATCTCGCCCTCTG 62.599 72.222 0.00 0.00 0.00 3.35
28 29 3.531207 CGCCATCTCGCCCTCTGA 61.531 66.667 0.00 0.00 0.00 3.27
29 30 2.903357 GCCATCTCGCCCTCTGAA 59.097 61.111 0.00 0.00 0.00 3.02
30 31 1.522580 GCCATCTCGCCCTCTGAAC 60.523 63.158 0.00 0.00 0.00 3.18
31 32 1.965754 GCCATCTCGCCCTCTGAACT 61.966 60.000 0.00 0.00 0.00 3.01
32 33 0.103937 CCATCTCGCCCTCTGAACTC 59.896 60.000 0.00 0.00 0.00 3.01
33 34 1.110442 CATCTCGCCCTCTGAACTCT 58.890 55.000 0.00 0.00 0.00 3.24
34 35 1.480137 CATCTCGCCCTCTGAACTCTT 59.520 52.381 0.00 0.00 0.00 2.85
35 36 0.891373 TCTCGCCCTCTGAACTCTTG 59.109 55.000 0.00 0.00 0.00 3.02
36 37 0.891373 CTCGCCCTCTGAACTCTTGA 59.109 55.000 0.00 0.00 0.00 3.02
37 38 1.480137 CTCGCCCTCTGAACTCTTGAT 59.520 52.381 0.00 0.00 0.00 2.57
38 39 1.205655 TCGCCCTCTGAACTCTTGATG 59.794 52.381 0.00 0.00 0.00 3.07
39 40 1.066573 CGCCCTCTGAACTCTTGATGT 60.067 52.381 0.00 0.00 0.00 3.06
40 41 2.354259 GCCCTCTGAACTCTTGATGTG 58.646 52.381 0.00 0.00 0.00 3.21
41 42 2.938756 GCCCTCTGAACTCTTGATGTGG 60.939 54.545 0.00 0.00 0.00 4.17
42 43 2.568956 CCCTCTGAACTCTTGATGTGGA 59.431 50.000 0.00 0.00 0.00 4.02
43 44 3.199508 CCCTCTGAACTCTTGATGTGGAT 59.800 47.826 0.00 0.00 0.00 3.41
44 45 4.190001 CCTCTGAACTCTTGATGTGGATG 58.810 47.826 0.00 0.00 0.00 3.51
45 46 4.081254 CCTCTGAACTCTTGATGTGGATGA 60.081 45.833 0.00 0.00 0.00 2.92
46 47 4.825422 TCTGAACTCTTGATGTGGATGAC 58.175 43.478 0.00 0.00 0.00 3.06
47 48 3.588955 TGAACTCTTGATGTGGATGACG 58.411 45.455 0.00 0.00 0.00 4.35
48 49 2.015736 ACTCTTGATGTGGATGACGC 57.984 50.000 0.00 0.00 0.00 5.19
49 50 1.552337 ACTCTTGATGTGGATGACGCT 59.448 47.619 0.00 0.00 0.00 5.07
50 51 2.027745 ACTCTTGATGTGGATGACGCTT 60.028 45.455 0.00 0.00 0.00 4.68
51 52 2.606725 CTCTTGATGTGGATGACGCTTC 59.393 50.000 0.00 0.00 35.11 3.86
52 53 2.234661 TCTTGATGTGGATGACGCTTCT 59.765 45.455 0.00 0.00 35.46 2.85
53 54 2.768253 TGATGTGGATGACGCTTCTT 57.232 45.000 0.00 0.00 35.46 2.52
54 55 2.621338 TGATGTGGATGACGCTTCTTC 58.379 47.619 0.00 0.00 35.46 2.87
55 56 2.234661 TGATGTGGATGACGCTTCTTCT 59.765 45.455 6.13 0.00 35.46 2.85
56 57 2.084610 TGTGGATGACGCTTCTTCTG 57.915 50.000 6.13 0.00 0.00 3.02
57 58 0.723981 GTGGATGACGCTTCTTCTGC 59.276 55.000 6.13 0.00 0.00 4.26
58 59 0.391661 TGGATGACGCTTCTTCTGCC 60.392 55.000 6.13 0.00 0.00 4.85
59 60 1.424493 GGATGACGCTTCTTCTGCCG 61.424 60.000 6.13 0.00 0.00 5.69
60 61 2.029904 GATGACGCTTCTTCTGCCGC 62.030 60.000 0.00 0.00 0.00 6.53
61 62 3.491652 GACGCTTCTTCTGCCGCC 61.492 66.667 0.00 0.00 0.00 6.13
64 65 2.672996 GCTTCTTCTGCCGCCCAA 60.673 61.111 0.00 0.00 0.00 4.12
65 66 2.048603 GCTTCTTCTGCCGCCCAAT 61.049 57.895 0.00 0.00 0.00 3.16
66 67 1.997928 GCTTCTTCTGCCGCCCAATC 61.998 60.000 0.00 0.00 0.00 2.67
67 68 1.378514 TTCTTCTGCCGCCCAATCC 60.379 57.895 0.00 0.00 0.00 3.01
68 69 2.045045 CTTCTGCCGCCCAATCCA 60.045 61.111 0.00 0.00 0.00 3.41
69 70 2.045045 TTCTGCCGCCCAATCCAG 60.045 61.111 0.00 0.00 0.00 3.86
70 71 4.802051 TCTGCCGCCCAATCCAGC 62.802 66.667 0.00 0.00 0.00 4.85
74 75 4.431131 CCGCCCAATCCAGCACCT 62.431 66.667 0.00 0.00 0.00 4.00
75 76 3.136123 CGCCCAATCCAGCACCTG 61.136 66.667 0.00 0.00 0.00 4.00
76 77 3.455469 GCCCAATCCAGCACCTGC 61.455 66.667 0.00 0.00 42.49 4.85
87 88 4.504916 CACCTGCTCCGGCTCGAG 62.505 72.222 8.45 8.45 39.59 4.04
90 91 4.504916 CTGCTCCGGCTCGAGGTG 62.505 72.222 15.58 0.45 39.59 4.00
92 93 4.803426 GCTCCGGCTCGAGGTGTG 62.803 72.222 15.58 0.00 35.22 3.82
93 94 4.803426 CTCCGGCTCGAGGTGTGC 62.803 72.222 15.58 0.00 36.35 4.57
99 100 3.636231 CTCGAGGTGTGCCCCCAA 61.636 66.667 3.91 0.00 34.57 4.12
100 101 2.933287 TCGAGGTGTGCCCCCAAT 60.933 61.111 0.00 0.00 34.57 3.16
101 102 2.035626 CGAGGTGTGCCCCCAATT 59.964 61.111 0.00 0.00 34.57 2.32
102 103 2.342650 CGAGGTGTGCCCCCAATTG 61.343 63.158 0.00 0.00 34.57 2.32
103 104 1.984026 GAGGTGTGCCCCCAATTGG 60.984 63.158 18.21 18.21 34.57 3.16
104 105 2.119391 GGTGTGCCCCCAATTGGA 59.881 61.111 26.60 2.31 37.39 3.53
105 106 1.535202 GGTGTGCCCCCAATTGGAA 60.535 57.895 26.60 5.57 37.39 3.53
106 107 1.671166 GTGTGCCCCCAATTGGAAC 59.329 57.895 26.60 17.12 37.39 3.62
107 108 1.118356 GTGTGCCCCCAATTGGAACA 61.118 55.000 26.60 19.29 37.39 3.18
120 121 2.315925 TGGAACAATCGATCTGCCTC 57.684 50.000 0.00 0.95 31.92 4.70
121 122 1.134401 TGGAACAATCGATCTGCCTCC 60.134 52.381 0.00 9.60 31.92 4.30
122 123 1.139853 GGAACAATCGATCTGCCTCCT 59.860 52.381 0.00 0.00 0.00 3.69
123 124 2.478831 GAACAATCGATCTGCCTCCTC 58.521 52.381 0.00 0.00 0.00 3.71
124 125 0.755686 ACAATCGATCTGCCTCCTCC 59.244 55.000 0.00 0.00 0.00 4.30
125 126 1.047002 CAATCGATCTGCCTCCTCCT 58.953 55.000 0.00 0.00 0.00 3.69
126 127 1.000731 CAATCGATCTGCCTCCTCCTC 59.999 57.143 0.00 0.00 0.00 3.71
127 128 0.482446 ATCGATCTGCCTCCTCCTCT 59.518 55.000 0.00 0.00 0.00 3.69
128 129 0.467106 TCGATCTGCCTCCTCCTCTG 60.467 60.000 0.00 0.00 0.00 3.35
129 130 0.754957 CGATCTGCCTCCTCCTCTGT 60.755 60.000 0.00 0.00 0.00 3.41
130 131 1.039856 GATCTGCCTCCTCCTCTGTC 58.960 60.000 0.00 0.00 0.00 3.51
131 132 0.337773 ATCTGCCTCCTCCTCTGTCA 59.662 55.000 0.00 0.00 0.00 3.58
132 133 0.613292 TCTGCCTCCTCCTCTGTCAC 60.613 60.000 0.00 0.00 0.00 3.67
133 134 1.610673 TGCCTCCTCCTCTGTCACC 60.611 63.158 0.00 0.00 0.00 4.02
134 135 2.363172 GCCTCCTCCTCTGTCACCC 61.363 68.421 0.00 0.00 0.00 4.61
135 136 1.390125 CCTCCTCCTCTGTCACCCT 59.610 63.158 0.00 0.00 0.00 4.34
136 137 0.686112 CCTCCTCCTCTGTCACCCTC 60.686 65.000 0.00 0.00 0.00 4.30
137 138 1.000771 TCCTCCTCTGTCACCCTCG 60.001 63.158 0.00 0.00 0.00 4.63
138 139 2.716017 CCTCCTCTGTCACCCTCGC 61.716 68.421 0.00 0.00 0.00 5.03
139 140 2.680352 TCCTCTGTCACCCTCGCC 60.680 66.667 0.00 0.00 0.00 5.54
140 141 2.997315 CCTCTGTCACCCTCGCCA 60.997 66.667 0.00 0.00 0.00 5.69
141 142 2.362369 CCTCTGTCACCCTCGCCAT 61.362 63.158 0.00 0.00 0.00 4.40
142 143 1.153489 CTCTGTCACCCTCGCCATG 60.153 63.158 0.00 0.00 0.00 3.66
143 144 1.607801 CTCTGTCACCCTCGCCATGA 61.608 60.000 0.00 0.00 0.00 3.07
144 145 0.977627 TCTGTCACCCTCGCCATGAT 60.978 55.000 0.00 0.00 0.00 2.45
145 146 0.812811 CTGTCACCCTCGCCATGATG 60.813 60.000 0.00 0.00 0.00 3.07
146 147 1.221840 GTCACCCTCGCCATGATGT 59.778 57.895 0.00 0.00 0.00 3.06
147 148 1.091771 GTCACCCTCGCCATGATGTG 61.092 60.000 0.00 0.00 33.04 3.21
148 149 2.124570 ACCCTCGCCATGATGTGC 60.125 61.111 0.00 0.00 0.00 4.57
149 150 2.191375 CCCTCGCCATGATGTGCT 59.809 61.111 0.00 0.00 0.00 4.40
150 151 1.890979 CCCTCGCCATGATGTGCTC 60.891 63.158 0.00 0.00 0.00 4.26
151 152 2.242572 CCTCGCCATGATGTGCTCG 61.243 63.158 0.00 0.00 0.00 5.03
152 153 1.227060 CTCGCCATGATGTGCTCGA 60.227 57.895 0.00 0.00 32.87 4.04
153 154 1.485838 CTCGCCATGATGTGCTCGAC 61.486 60.000 0.00 0.00 31.37 4.20
154 155 2.863853 CGCCATGATGTGCTCGACG 61.864 63.158 0.00 0.00 0.00 5.12
155 156 1.519234 GCCATGATGTGCTCGACGA 60.519 57.895 0.00 0.00 0.00 4.20
156 157 1.485838 GCCATGATGTGCTCGACGAG 61.486 60.000 20.56 20.56 0.00 4.18
157 158 0.101219 CCATGATGTGCTCGACGAGA 59.899 55.000 28.43 8.17 0.00 4.04
165 166 2.881389 CTCGACGAGAGCCAGCTT 59.119 61.111 20.25 0.00 40.54 3.74
166 167 1.515952 CTCGACGAGAGCCAGCTTG 60.516 63.158 20.25 0.00 40.54 4.01
167 168 2.507992 CGACGAGAGCCAGCTTGG 60.508 66.667 0.00 0.00 41.55 3.61
176 177 2.437359 CCAGCTTGGCTTCCCTCG 60.437 66.667 0.00 0.00 36.40 4.63
177 178 3.130160 CAGCTTGGCTTCCCTCGC 61.130 66.667 0.00 0.00 36.40 5.03
183 184 2.188207 GGCTTCCCTCGCCTTCTC 59.812 66.667 0.00 0.00 44.17 2.87
184 185 2.188207 GCTTCCCTCGCCTTCTCC 59.812 66.667 0.00 0.00 0.00 3.71
185 186 2.496817 CTTCCCTCGCCTTCTCCG 59.503 66.667 0.00 0.00 0.00 4.63
186 187 3.724914 CTTCCCTCGCCTTCTCCGC 62.725 68.421 0.00 0.00 0.00 5.54
215 216 4.394712 CCGCCTTCTCCGCCTTGT 62.395 66.667 0.00 0.00 0.00 3.16
216 217 2.358737 CGCCTTCTCCGCCTTGTT 60.359 61.111 0.00 0.00 0.00 2.83
217 218 2.391389 CGCCTTCTCCGCCTTGTTC 61.391 63.158 0.00 0.00 0.00 3.18
218 219 2.391389 GCCTTCTCCGCCTTGTTCG 61.391 63.158 0.00 0.00 0.00 3.95
219 220 2.391389 CCTTCTCCGCCTTGTTCGC 61.391 63.158 0.00 0.00 0.00 4.70
220 221 2.358247 TTCTCCGCCTTGTTCGCC 60.358 61.111 0.00 0.00 0.00 5.54
221 222 4.735132 TCTCCGCCTTGTTCGCCG 62.735 66.667 0.00 0.00 0.00 6.46
226 227 2.668550 GCCTTGTTCGCCGTCCTT 60.669 61.111 0.00 0.00 0.00 3.36
227 228 1.375013 GCCTTGTTCGCCGTCCTTA 60.375 57.895 0.00 0.00 0.00 2.69
228 229 1.359459 GCCTTGTTCGCCGTCCTTAG 61.359 60.000 0.00 0.00 0.00 2.18
229 230 1.359459 CCTTGTTCGCCGTCCTTAGC 61.359 60.000 0.00 0.00 0.00 3.09
230 231 0.669318 CTTGTTCGCCGTCCTTAGCA 60.669 55.000 0.00 0.00 0.00 3.49
231 232 0.669318 TTGTTCGCCGTCCTTAGCAG 60.669 55.000 0.00 0.00 0.00 4.24
232 233 2.125673 TTCGCCGTCCTTAGCAGC 60.126 61.111 0.00 0.00 0.00 5.25
236 237 4.148825 CCGTCCTTAGCAGCGCCT 62.149 66.667 2.29 0.00 0.00 5.52
237 238 2.583593 CGTCCTTAGCAGCGCCTC 60.584 66.667 2.29 0.00 0.00 4.70
238 239 2.202946 GTCCTTAGCAGCGCCTCC 60.203 66.667 2.29 0.00 0.00 4.30
239 240 2.683572 TCCTTAGCAGCGCCTCCA 60.684 61.111 2.29 0.00 0.00 3.86
240 241 2.268920 CCTTAGCAGCGCCTCCAA 59.731 61.111 2.29 0.00 0.00 3.53
241 242 1.817099 CCTTAGCAGCGCCTCCAAG 60.817 63.158 2.29 2.90 0.00 3.61
242 243 1.078848 CTTAGCAGCGCCTCCAAGT 60.079 57.895 2.29 0.00 0.00 3.16
243 244 1.079127 TTAGCAGCGCCTCCAAGTC 60.079 57.895 2.29 0.00 0.00 3.01
244 245 1.544825 TTAGCAGCGCCTCCAAGTCT 61.545 55.000 2.29 0.00 0.00 3.24
245 246 1.544825 TAGCAGCGCCTCCAAGTCTT 61.545 55.000 2.29 0.00 0.00 3.01
246 247 1.968540 GCAGCGCCTCCAAGTCTTT 60.969 57.895 2.29 0.00 0.00 2.52
247 248 1.916697 GCAGCGCCTCCAAGTCTTTC 61.917 60.000 2.29 0.00 0.00 2.62
248 249 1.374758 AGCGCCTCCAAGTCTTTCG 60.375 57.895 2.29 0.00 0.00 3.46
249 250 1.374252 GCGCCTCCAAGTCTTTCGA 60.374 57.895 0.00 0.00 0.00 3.71
250 251 1.627550 GCGCCTCCAAGTCTTTCGAC 61.628 60.000 0.00 0.00 40.54 4.20
251 252 1.014564 CGCCTCCAAGTCTTTCGACC 61.015 60.000 0.00 0.00 41.16 4.79
252 253 0.321996 GCCTCCAAGTCTTTCGACCT 59.678 55.000 0.00 0.00 41.16 3.85
253 254 1.549170 GCCTCCAAGTCTTTCGACCTA 59.451 52.381 0.00 0.00 41.16 3.08
254 255 2.674462 GCCTCCAAGTCTTTCGACCTAC 60.674 54.545 0.00 0.00 41.16 3.18
255 256 2.415625 CCTCCAAGTCTTTCGACCTACG 60.416 54.545 0.00 0.00 41.16 3.51
256 257 1.542915 TCCAAGTCTTTCGACCTACGG 59.457 52.381 0.00 0.00 41.16 4.02
257 258 1.347320 CAAGTCTTTCGACCTACGGC 58.653 55.000 0.00 0.00 41.16 5.68
258 259 0.245813 AAGTCTTTCGACCTACGGCC 59.754 55.000 0.00 0.00 41.16 6.13
259 260 0.611340 AGTCTTTCGACCTACGGCCT 60.611 55.000 0.00 0.00 41.16 5.19
260 261 0.179142 GTCTTTCGACCTACGGCCTC 60.179 60.000 0.00 0.00 42.82 4.70
261 262 1.141234 CTTTCGACCTACGGCCTCC 59.859 63.158 0.00 0.00 42.82 4.30
262 263 1.304713 TTTCGACCTACGGCCTCCT 60.305 57.895 0.00 0.00 42.82 3.69
263 264 1.318158 TTTCGACCTACGGCCTCCTC 61.318 60.000 0.00 0.00 42.82 3.71
264 265 2.124236 CGACCTACGGCCTCCTCT 60.124 66.667 0.00 0.00 38.46 3.69
265 266 2.188161 CGACCTACGGCCTCCTCTC 61.188 68.421 0.00 0.00 38.46 3.20
266 267 2.124236 ACCTACGGCCTCCTCTCG 60.124 66.667 0.00 0.00 0.00 4.04
267 268 3.597728 CCTACGGCCTCCTCTCGC 61.598 72.222 0.00 0.00 0.00 5.03
268 269 2.517402 CTACGGCCTCCTCTCGCT 60.517 66.667 0.00 0.00 0.00 4.93
269 270 2.516460 TACGGCCTCCTCTCGCTC 60.516 66.667 0.00 0.00 0.00 5.03
272 273 2.909965 GGCCTCCTCTCGCTCGAT 60.910 66.667 0.00 0.00 0.00 3.59
273 274 2.642700 GCCTCCTCTCGCTCGATC 59.357 66.667 0.00 0.00 0.00 3.69
274 275 2.914908 GCCTCCTCTCGCTCGATCC 61.915 68.421 0.00 0.00 0.00 3.36
275 276 2.612567 CCTCCTCTCGCTCGATCCG 61.613 68.421 0.00 0.00 0.00 4.18
276 277 3.248630 CTCCTCTCGCTCGATCCGC 62.249 68.421 1.20 0.00 0.00 5.54
277 278 4.335584 CCTCTCGCTCGATCCGCC 62.336 72.222 1.20 0.00 0.00 6.13
278 279 4.674904 CTCTCGCTCGATCCGCCG 62.675 72.222 1.20 0.00 0.00 6.46
283 284 4.654412 GCTCGATCCGCCGCTCAT 62.654 66.667 0.00 0.00 0.00 2.90
284 285 2.429907 CTCGATCCGCCGCTCATC 60.430 66.667 0.00 0.00 0.00 2.92
285 286 3.905705 CTCGATCCGCCGCTCATCC 62.906 68.421 0.00 0.00 0.00 3.51
290 291 4.609018 CCGCCGCTCATCCCGAAT 62.609 66.667 0.00 0.00 0.00 3.34
291 292 3.038417 CGCCGCTCATCCCGAATC 61.038 66.667 0.00 0.00 0.00 2.52
292 293 3.038417 GCCGCTCATCCCGAATCG 61.038 66.667 0.00 0.00 0.00 3.34
303 304 3.923614 CGAATCGGATCTGGCGTC 58.076 61.111 0.62 0.00 0.00 5.19
304 305 2.011349 CGAATCGGATCTGGCGTCG 61.011 63.158 0.62 5.01 0.00 5.12
305 306 1.661821 GAATCGGATCTGGCGTCGG 60.662 63.158 0.62 0.00 0.00 4.79
306 307 2.351336 GAATCGGATCTGGCGTCGGT 62.351 60.000 0.62 0.00 0.00 4.69
307 308 1.105167 AATCGGATCTGGCGTCGGTA 61.105 55.000 0.62 0.00 0.00 4.02
308 309 1.793134 ATCGGATCTGGCGTCGGTAC 61.793 60.000 0.62 0.00 0.00 3.34
321 322 2.284112 GGTACGACCCCCAGACCA 60.284 66.667 0.00 0.00 30.04 4.02
322 323 1.914764 GGTACGACCCCCAGACCAA 60.915 63.158 0.00 0.00 30.04 3.67
323 324 1.269703 GGTACGACCCCCAGACCAAT 61.270 60.000 0.00 0.00 30.04 3.16
324 325 0.177373 GTACGACCCCCAGACCAATC 59.823 60.000 0.00 0.00 0.00 2.67
325 326 0.979187 TACGACCCCCAGACCAATCC 60.979 60.000 0.00 0.00 0.00 3.01
326 327 3.007542 GACCCCCAGACCAATCCC 58.992 66.667 0.00 0.00 0.00 3.85
327 328 1.619669 GACCCCCAGACCAATCCCT 60.620 63.158 0.00 0.00 0.00 4.20
328 329 1.926426 GACCCCCAGACCAATCCCTG 61.926 65.000 0.00 0.00 0.00 4.45
336 337 2.911143 CCAATCCCTGGGTCGGAG 59.089 66.667 13.56 0.00 42.17 4.63
337 338 2.190578 CAATCCCTGGGTCGGAGC 59.809 66.667 13.56 0.00 31.41 4.70
338 339 3.470888 AATCCCTGGGTCGGAGCG 61.471 66.667 13.56 0.00 31.41 5.03
779 798 4.334481 CCAACAGCCTATTAAACCCTAACG 59.666 45.833 0.00 0.00 0.00 3.18
802 821 1.284408 CGCGAGATAGGAGAGGTGC 59.716 63.158 0.00 0.00 0.00 5.01
814 833 3.901844 AGGAGAGGTGCTTAACTTGTACA 59.098 43.478 0.00 0.00 0.00 2.90
869 889 4.260170 TCTTCTACCGAGACCTTCTGTAC 58.740 47.826 0.00 0.00 0.00 2.90
875 895 2.164624 CCGAGACCTTCTGTACTTCCAG 59.835 54.545 0.00 0.00 0.00 3.86
929 951 4.335594 GCCACGGCTGTTCTCTTATTAATT 59.664 41.667 0.00 0.00 38.26 1.40
1036 1058 3.567478 AGTTCTTGTTCTGCTTGACCT 57.433 42.857 0.00 0.00 0.00 3.85
1047 1069 2.966309 CTTGACCTTGTTCGCCGCC 61.966 63.158 0.00 0.00 0.00 6.13
1188 1228 1.361668 CGGGGAGCAACTTCGTCATG 61.362 60.000 0.00 0.00 0.00 3.07
1463 1990 2.640989 CGTGGACTTCGTGTCGGA 59.359 61.111 5.54 0.00 46.24 4.55
2489 3136 2.102925 AGCCTTCAATGTGGTGGTTTTG 59.897 45.455 0.00 0.00 0.00 2.44
2505 3152 3.064271 GGTTTTGTGCTGTTAACTCGACA 59.936 43.478 7.22 3.87 0.00 4.35
3033 4669 1.202903 AGGACACGTGACTGTACTCCT 60.203 52.381 25.01 18.60 27.99 3.69
3096 4733 5.284582 AGGAAGAAGGGATGATCTTACTGT 58.715 41.667 0.00 0.00 32.61 3.55
3148 4795 9.653287 TGACAGAAATTTTCTATACGACAAGAT 57.347 29.630 11.21 0.00 38.11 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.974698 CGAGATGGCGGCCATTCC 60.975 66.667 33.35 24.96 45.26 3.01
4 5 3.654020 GCGAGATGGCGGCCATTC 61.654 66.667 33.35 27.15 45.26 2.67
10 11 4.598894 CAGAGGGCGAGATGGCGG 62.599 72.222 0.00 0.00 46.04 6.13
11 12 3.081311 TTCAGAGGGCGAGATGGCG 62.081 63.158 0.00 0.00 46.04 5.69
12 13 1.522580 GTTCAGAGGGCGAGATGGC 60.523 63.158 0.00 0.00 43.88 4.40
13 14 0.103937 GAGTTCAGAGGGCGAGATGG 59.896 60.000 0.00 0.00 0.00 3.51
14 15 1.110442 AGAGTTCAGAGGGCGAGATG 58.890 55.000 0.00 0.00 0.00 2.90
15 16 1.480137 CAAGAGTTCAGAGGGCGAGAT 59.520 52.381 0.00 0.00 0.00 2.75
16 17 0.891373 CAAGAGTTCAGAGGGCGAGA 59.109 55.000 0.00 0.00 0.00 4.04
17 18 0.891373 TCAAGAGTTCAGAGGGCGAG 59.109 55.000 0.00 0.00 0.00 5.03
18 19 1.205655 CATCAAGAGTTCAGAGGGCGA 59.794 52.381 0.00 0.00 0.00 5.54
19 20 1.066573 ACATCAAGAGTTCAGAGGGCG 60.067 52.381 0.00 0.00 0.00 6.13
20 21 2.354259 CACATCAAGAGTTCAGAGGGC 58.646 52.381 0.00 0.00 0.00 5.19
21 22 2.568956 TCCACATCAAGAGTTCAGAGGG 59.431 50.000 0.00 0.00 0.00 4.30
22 23 3.969287 TCCACATCAAGAGTTCAGAGG 57.031 47.619 0.00 0.00 0.00 3.69
23 24 4.869297 GTCATCCACATCAAGAGTTCAGAG 59.131 45.833 0.00 0.00 0.00 3.35
24 25 4.619160 CGTCATCCACATCAAGAGTTCAGA 60.619 45.833 0.00 0.00 0.00 3.27
25 26 3.615937 CGTCATCCACATCAAGAGTTCAG 59.384 47.826 0.00 0.00 0.00 3.02
26 27 3.588955 CGTCATCCACATCAAGAGTTCA 58.411 45.455 0.00 0.00 0.00 3.18
27 28 2.349886 GCGTCATCCACATCAAGAGTTC 59.650 50.000 0.00 0.00 0.00 3.01
28 29 2.027745 AGCGTCATCCACATCAAGAGTT 60.028 45.455 0.00 0.00 0.00 3.01
29 30 1.552337 AGCGTCATCCACATCAAGAGT 59.448 47.619 0.00 0.00 0.00 3.24
30 31 2.306341 AGCGTCATCCACATCAAGAG 57.694 50.000 0.00 0.00 0.00 2.85
31 32 2.234661 AGAAGCGTCATCCACATCAAGA 59.765 45.455 1.61 0.00 0.00 3.02
32 33 2.625737 AGAAGCGTCATCCACATCAAG 58.374 47.619 1.61 0.00 0.00 3.02
33 34 2.768253 AGAAGCGTCATCCACATCAA 57.232 45.000 1.61 0.00 0.00 2.57
34 35 2.234661 AGAAGAAGCGTCATCCACATCA 59.765 45.455 1.61 0.00 0.00 3.07
35 36 2.606725 CAGAAGAAGCGTCATCCACATC 59.393 50.000 1.61 0.00 0.00 3.06
36 37 2.625737 CAGAAGAAGCGTCATCCACAT 58.374 47.619 1.61 0.00 0.00 3.21
37 38 1.941209 GCAGAAGAAGCGTCATCCACA 60.941 52.381 1.61 0.00 0.00 4.17
38 39 0.723981 GCAGAAGAAGCGTCATCCAC 59.276 55.000 1.61 0.00 0.00 4.02
39 40 0.391661 GGCAGAAGAAGCGTCATCCA 60.392 55.000 1.61 0.00 0.00 3.41
40 41 1.424493 CGGCAGAAGAAGCGTCATCC 61.424 60.000 1.61 0.00 0.00 3.51
41 42 2.002127 CGGCAGAAGAAGCGTCATC 58.998 57.895 1.61 0.00 0.00 2.92
42 43 2.103042 GCGGCAGAAGAAGCGTCAT 61.103 57.895 1.61 0.00 0.00 3.06
43 44 2.738521 GCGGCAGAAGAAGCGTCA 60.739 61.111 1.61 0.00 0.00 4.35
44 45 3.491652 GGCGGCAGAAGAAGCGTC 61.492 66.667 3.07 0.00 0.00 5.19
47 48 1.997928 GATTGGGCGGCAGAAGAAGC 61.998 60.000 12.47 0.00 0.00 3.86
48 49 1.379642 GGATTGGGCGGCAGAAGAAG 61.380 60.000 12.47 0.00 0.00 2.85
49 50 1.378514 GGATTGGGCGGCAGAAGAA 60.379 57.895 12.47 0.00 0.00 2.52
50 51 2.272146 GGATTGGGCGGCAGAAGA 59.728 61.111 12.47 0.00 0.00 2.87
51 52 2.045045 TGGATTGGGCGGCAGAAG 60.045 61.111 12.47 0.00 0.00 2.85
52 53 2.045045 CTGGATTGGGCGGCAGAA 60.045 61.111 12.47 2.79 0.00 3.02
53 54 4.802051 GCTGGATTGGGCGGCAGA 62.802 66.667 12.47 0.00 0.00 4.26
57 58 4.431131 AGGTGCTGGATTGGGCGG 62.431 66.667 0.00 0.00 0.00 6.13
58 59 3.136123 CAGGTGCTGGATTGGGCG 61.136 66.667 0.00 0.00 0.00 6.13
59 60 3.455469 GCAGGTGCTGGATTGGGC 61.455 66.667 0.00 0.00 38.21 5.36
70 71 4.504916 CTCGAGCCGGAGCAGGTG 62.505 72.222 5.05 0.00 43.56 4.00
73 74 4.504916 CACCTCGAGCCGGAGCAG 62.505 72.222 5.05 0.00 43.56 4.24
75 76 4.803426 CACACCTCGAGCCGGAGC 62.803 72.222 5.05 0.00 40.32 4.70
76 77 4.803426 GCACACCTCGAGCCGGAG 62.803 72.222 5.05 0.00 0.00 4.63
82 83 2.484287 AATTGGGGGCACACCTCGAG 62.484 60.000 5.13 5.13 45.67 4.04
83 84 2.534396 AATTGGGGGCACACCTCGA 61.534 57.895 0.00 0.00 45.67 4.04
84 85 2.035626 AATTGGGGGCACACCTCG 59.964 61.111 0.00 0.00 45.67 4.63
85 86 1.984026 CCAATTGGGGGCACACCTC 60.984 63.158 17.36 0.00 41.63 3.85
86 87 2.029892 TTCCAATTGGGGGCACACCT 62.030 55.000 24.29 0.00 40.03 4.00
87 88 1.535202 TTCCAATTGGGGGCACACC 60.535 57.895 24.29 0.00 37.22 4.16
88 89 1.118356 TGTTCCAATTGGGGGCACAC 61.118 55.000 24.29 11.57 37.22 3.82
89 90 0.399091 TTGTTCCAATTGGGGGCACA 60.399 50.000 24.29 17.55 37.22 4.57
90 91 0.983467 ATTGTTCCAATTGGGGGCAC 59.017 50.000 24.29 15.39 37.22 5.01
91 92 1.274712 GATTGTTCCAATTGGGGGCA 58.725 50.000 24.29 16.61 37.22 5.36
92 93 0.175531 CGATTGTTCCAATTGGGGGC 59.824 55.000 24.29 14.36 37.22 5.80
93 94 1.846007 TCGATTGTTCCAATTGGGGG 58.154 50.000 24.29 0.00 37.22 5.40
94 95 3.067180 CAGATCGATTGTTCCAATTGGGG 59.933 47.826 24.29 0.00 37.22 4.96
95 96 3.489738 GCAGATCGATTGTTCCAATTGGG 60.490 47.826 24.29 6.48 35.41 4.12
96 97 3.489738 GGCAGATCGATTGTTCCAATTGG 60.490 47.826 19.08 19.08 0.00 3.16
97 98 3.379372 AGGCAGATCGATTGTTCCAATTG 59.621 43.478 0.00 0.00 0.00 2.32
98 99 3.624777 AGGCAGATCGATTGTTCCAATT 58.375 40.909 0.00 0.00 0.00 2.32
99 100 3.209410 GAGGCAGATCGATTGTTCCAAT 58.791 45.455 0.00 0.00 0.00 3.16
100 101 2.632377 GAGGCAGATCGATTGTTCCAA 58.368 47.619 0.00 0.00 0.00 3.53
101 102 1.134401 GGAGGCAGATCGATTGTTCCA 60.134 52.381 0.00 0.00 0.00 3.53
102 103 1.139853 AGGAGGCAGATCGATTGTTCC 59.860 52.381 0.00 10.92 0.00 3.62
103 104 2.478831 GAGGAGGCAGATCGATTGTTC 58.521 52.381 0.00 3.29 0.00 3.18
104 105 1.139853 GGAGGAGGCAGATCGATTGTT 59.860 52.381 0.00 0.00 0.00 2.83
105 106 0.755686 GGAGGAGGCAGATCGATTGT 59.244 55.000 0.00 0.00 0.00 2.71
106 107 1.000731 GAGGAGGAGGCAGATCGATTG 59.999 57.143 0.00 1.24 0.00 2.67
107 108 1.133199 AGAGGAGGAGGCAGATCGATT 60.133 52.381 0.00 0.00 0.00 3.34
108 109 0.482446 AGAGGAGGAGGCAGATCGAT 59.518 55.000 0.00 0.00 0.00 3.59
109 110 0.467106 CAGAGGAGGAGGCAGATCGA 60.467 60.000 0.00 0.00 0.00 3.59
110 111 0.754957 ACAGAGGAGGAGGCAGATCG 60.755 60.000 0.00 0.00 0.00 3.69
111 112 1.039856 GACAGAGGAGGAGGCAGATC 58.960 60.000 0.00 0.00 0.00 2.75
112 113 0.337773 TGACAGAGGAGGAGGCAGAT 59.662 55.000 0.00 0.00 0.00 2.90
113 114 0.613292 GTGACAGAGGAGGAGGCAGA 60.613 60.000 0.00 0.00 0.00 4.26
114 115 1.612395 GGTGACAGAGGAGGAGGCAG 61.612 65.000 0.00 0.00 0.00 4.85
115 116 1.610673 GGTGACAGAGGAGGAGGCA 60.611 63.158 0.00 0.00 0.00 4.75
116 117 2.363172 GGGTGACAGAGGAGGAGGC 61.363 68.421 0.00 0.00 0.00 4.70
117 118 0.686112 GAGGGTGACAGAGGAGGAGG 60.686 65.000 0.00 0.00 0.00 4.30
118 119 1.034838 CGAGGGTGACAGAGGAGGAG 61.035 65.000 0.00 0.00 0.00 3.69
119 120 1.000771 CGAGGGTGACAGAGGAGGA 60.001 63.158 0.00 0.00 0.00 3.71
120 121 2.716017 GCGAGGGTGACAGAGGAGG 61.716 68.421 0.00 0.00 0.00 4.30
121 122 2.716017 GGCGAGGGTGACAGAGGAG 61.716 68.421 0.00 0.00 0.00 3.69
122 123 2.680352 GGCGAGGGTGACAGAGGA 60.680 66.667 0.00 0.00 0.00 3.71
123 124 2.362369 ATGGCGAGGGTGACAGAGG 61.362 63.158 0.00 0.00 0.00 3.69
124 125 1.153489 CATGGCGAGGGTGACAGAG 60.153 63.158 0.00 0.00 0.00 3.35
125 126 0.977627 ATCATGGCGAGGGTGACAGA 60.978 55.000 0.00 0.00 0.00 3.41
126 127 0.812811 CATCATGGCGAGGGTGACAG 60.813 60.000 0.00 0.00 0.00 3.51
127 128 1.221566 CATCATGGCGAGGGTGACA 59.778 57.895 0.00 0.00 0.00 3.58
128 129 1.091771 CACATCATGGCGAGGGTGAC 61.092 60.000 0.00 0.00 35.78 3.67
129 130 1.221566 CACATCATGGCGAGGGTGA 59.778 57.895 0.00 0.00 35.78 4.02
130 131 2.475466 GCACATCATGGCGAGGGTG 61.475 63.158 0.00 0.00 36.45 4.61
131 132 2.124570 GCACATCATGGCGAGGGT 60.125 61.111 0.00 0.00 0.00 4.34
132 133 1.890979 GAGCACATCATGGCGAGGG 60.891 63.158 0.00 0.00 34.54 4.30
133 134 2.242572 CGAGCACATCATGGCGAGG 61.243 63.158 0.00 0.00 34.54 4.63
134 135 1.227060 TCGAGCACATCATGGCGAG 60.227 57.895 0.00 0.00 34.54 5.03
135 136 1.519234 GTCGAGCACATCATGGCGA 60.519 57.895 0.00 0.00 34.54 5.54
136 137 2.863853 CGTCGAGCACATCATGGCG 61.864 63.158 0.00 0.00 34.54 5.69
137 138 1.485838 CTCGTCGAGCACATCATGGC 61.486 60.000 9.74 0.00 0.00 4.40
138 139 0.101219 TCTCGTCGAGCACATCATGG 59.899 55.000 17.61 0.00 0.00 3.66
139 140 1.475045 CTCTCGTCGAGCACATCATG 58.525 55.000 17.61 0.00 31.99 3.07
140 141 3.934521 CTCTCGTCGAGCACATCAT 57.065 52.632 17.61 0.00 31.99 2.45
148 149 1.515952 CAAGCTGGCTCTCGTCGAG 60.516 63.158 16.33 16.33 42.88 4.04
149 150 2.568612 CAAGCTGGCTCTCGTCGA 59.431 61.111 0.00 0.00 0.00 4.20
150 151 2.507992 CCAAGCTGGCTCTCGTCG 60.508 66.667 0.00 0.00 0.00 5.12
159 160 2.437359 CGAGGGAAGCCAAGCTGG 60.437 66.667 0.00 0.00 39.62 4.85
160 161 3.130160 GCGAGGGAAGCCAAGCTG 61.130 66.667 0.00 0.00 39.62 4.24
167 168 2.188207 GGAGAAGGCGAGGGAAGC 59.812 66.667 0.00 0.00 0.00 3.86
168 169 2.496817 CGGAGAAGGCGAGGGAAG 59.503 66.667 0.00 0.00 0.00 3.46
169 170 3.771160 GCGGAGAAGGCGAGGGAA 61.771 66.667 0.00 0.00 0.00 3.97
198 199 3.901797 AACAAGGCGGAGAAGGCGG 62.902 63.158 0.00 0.00 41.99 6.13
199 200 2.358737 AACAAGGCGGAGAAGGCG 60.359 61.111 0.00 0.00 41.99 5.52
200 201 2.391389 CGAACAAGGCGGAGAAGGC 61.391 63.158 0.00 0.00 0.00 4.35
201 202 2.391389 GCGAACAAGGCGGAGAAGG 61.391 63.158 0.00 0.00 0.00 3.46
202 203 2.391389 GGCGAACAAGGCGGAGAAG 61.391 63.158 0.00 0.00 0.00 2.85
203 204 2.358247 GGCGAACAAGGCGGAGAA 60.358 61.111 0.00 0.00 0.00 2.87
209 210 1.359459 CTAAGGACGGCGAACAAGGC 61.359 60.000 16.62 0.00 0.00 4.35
210 211 1.359459 GCTAAGGACGGCGAACAAGG 61.359 60.000 16.62 0.25 0.00 3.61
211 212 0.669318 TGCTAAGGACGGCGAACAAG 60.669 55.000 16.62 8.54 0.00 3.16
212 213 0.669318 CTGCTAAGGACGGCGAACAA 60.669 55.000 16.62 0.00 0.00 2.83
213 214 1.080093 CTGCTAAGGACGGCGAACA 60.080 57.895 16.62 0.00 0.00 3.18
214 215 2.453638 GCTGCTAAGGACGGCGAAC 61.454 63.158 16.62 5.56 0.00 3.95
215 216 2.125673 GCTGCTAAGGACGGCGAA 60.126 61.111 16.62 0.00 0.00 4.70
219 220 4.148825 AGGCGCTGCTAAGGACGG 62.149 66.667 7.64 0.00 0.00 4.79
220 221 2.583593 GAGGCGCTGCTAAGGACG 60.584 66.667 7.64 0.00 0.00 4.79
221 222 2.202946 GGAGGCGCTGCTAAGGAC 60.203 66.667 7.64 0.00 0.00 3.85
222 223 2.244117 CTTGGAGGCGCTGCTAAGGA 62.244 60.000 7.64 0.00 0.00 3.36
223 224 1.817099 CTTGGAGGCGCTGCTAAGG 60.817 63.158 7.64 0.00 0.00 2.69
224 225 1.078848 ACTTGGAGGCGCTGCTAAG 60.079 57.895 18.82 18.82 0.00 2.18
225 226 1.079127 GACTTGGAGGCGCTGCTAA 60.079 57.895 7.64 2.87 0.00 3.09
226 227 1.544825 AAGACTTGGAGGCGCTGCTA 61.545 55.000 7.64 0.00 0.00 3.49
227 228 2.403132 AAAGACTTGGAGGCGCTGCT 62.403 55.000 7.64 0.00 0.00 4.24
228 229 1.916697 GAAAGACTTGGAGGCGCTGC 61.917 60.000 7.64 0.00 0.00 5.25
229 230 1.630244 CGAAAGACTTGGAGGCGCTG 61.630 60.000 7.64 0.00 0.00 5.18
230 231 1.374758 CGAAAGACTTGGAGGCGCT 60.375 57.895 7.64 0.00 0.00 5.92
231 232 1.374252 TCGAAAGACTTGGAGGCGC 60.374 57.895 0.00 0.00 33.31 6.53
232 233 4.988065 TCGAAAGACTTGGAGGCG 57.012 55.556 0.00 0.00 33.31 5.52
251 252 2.517402 AGCGAGAGGAGGCCGTAG 60.517 66.667 0.00 0.00 0.00 3.51
252 253 2.516460 GAGCGAGAGGAGGCCGTA 60.516 66.667 0.00 0.00 0.00 4.02
255 256 2.909965 ATCGAGCGAGAGGAGGCC 60.910 66.667 0.00 0.00 0.00 5.19
256 257 2.642700 GATCGAGCGAGAGGAGGC 59.357 66.667 0.00 0.00 0.00 4.70
257 258 2.612567 CGGATCGAGCGAGAGGAGG 61.613 68.421 0.00 0.00 0.00 4.30
258 259 2.942879 CGGATCGAGCGAGAGGAG 59.057 66.667 0.00 0.00 0.00 3.69
259 260 3.280634 GCGGATCGAGCGAGAGGA 61.281 66.667 0.00 0.00 0.00 3.71
260 261 4.335584 GGCGGATCGAGCGAGAGG 62.336 72.222 0.00 0.00 35.00 3.69
261 262 4.674904 CGGCGGATCGAGCGAGAG 62.675 72.222 0.00 0.00 35.00 3.20
266 267 4.654412 ATGAGCGGCGGATCGAGC 62.654 66.667 9.78 0.00 33.75 5.03
267 268 2.429907 GATGAGCGGCGGATCGAG 60.430 66.667 9.78 0.00 0.00 4.04
268 269 3.978491 GGATGAGCGGCGGATCGA 61.978 66.667 9.78 0.00 0.00 3.59
273 274 4.609018 ATTCGGGATGAGCGGCGG 62.609 66.667 9.78 0.00 0.00 6.13
274 275 3.038417 GATTCGGGATGAGCGGCG 61.038 66.667 0.51 0.51 0.00 6.46
275 276 3.038417 CGATTCGGGATGAGCGGC 61.038 66.667 0.00 0.00 0.00 6.53
276 277 2.356313 CCGATTCGGGATGAGCGG 60.356 66.667 17.53 0.00 44.15 5.52
277 278 0.734253 GATCCGATTCGGGATGAGCG 60.734 60.000 24.15 0.00 46.75 5.03
278 279 0.605589 AGATCCGATTCGGGATGAGC 59.394 55.000 24.15 8.38 46.75 4.26
279 280 1.067283 CCAGATCCGATTCGGGATGAG 60.067 57.143 24.15 10.97 46.75 2.90
280 281 0.969149 CCAGATCCGATTCGGGATGA 59.031 55.000 24.15 5.96 46.75 2.92
281 282 0.671781 GCCAGATCCGATTCGGGATG 60.672 60.000 24.15 18.44 46.75 3.51
286 287 2.011349 CGACGCCAGATCCGATTCG 61.011 63.158 0.00 0.00 0.00 3.34
287 288 1.661821 CCGACGCCAGATCCGATTC 60.662 63.158 0.00 0.00 0.00 2.52
288 289 1.105167 TACCGACGCCAGATCCGATT 61.105 55.000 0.00 0.00 0.00 3.34
289 290 1.527611 TACCGACGCCAGATCCGAT 60.528 57.895 0.00 0.00 0.00 4.18
290 291 2.124612 TACCGACGCCAGATCCGA 60.125 61.111 0.00 0.00 0.00 4.55
291 292 2.025727 GTACCGACGCCAGATCCG 59.974 66.667 0.00 0.00 0.00 4.18
292 293 2.025727 CGTACCGACGCCAGATCC 59.974 66.667 0.00 0.00 43.21 3.36
302 303 2.361610 GTCTGGGGGTCGTACCGA 60.362 66.667 0.00 0.00 39.83 4.69
303 304 3.455469 GGTCTGGGGGTCGTACCG 61.455 72.222 0.00 0.00 39.83 4.02
304 305 1.269703 ATTGGTCTGGGGGTCGTACC 61.270 60.000 0.00 0.00 37.60 3.34
305 306 0.177373 GATTGGTCTGGGGGTCGTAC 59.823 60.000 0.00 0.00 0.00 3.67
306 307 0.979187 GGATTGGTCTGGGGGTCGTA 60.979 60.000 0.00 0.00 0.00 3.43
307 308 2.298661 GGATTGGTCTGGGGGTCGT 61.299 63.158 0.00 0.00 0.00 4.34
308 309 2.590092 GGATTGGTCTGGGGGTCG 59.410 66.667 0.00 0.00 0.00 4.79
309 310 1.619669 AGGGATTGGTCTGGGGGTC 60.620 63.158 0.00 0.00 0.00 4.46
310 311 1.930656 CAGGGATTGGTCTGGGGGT 60.931 63.158 0.00 0.00 0.00 4.95
311 312 2.693871 CCAGGGATTGGTCTGGGGG 61.694 68.421 0.00 0.00 44.99 5.40
312 313 3.010144 CCAGGGATTGGTCTGGGG 58.990 66.667 0.00 0.00 44.99 4.96
314 315 1.609783 GACCCAGGGATTGGTCTGG 59.390 63.158 14.54 0.00 46.13 3.86
317 318 1.972660 CTCCGACCCAGGGATTGGTC 61.973 65.000 14.54 0.00 46.25 4.02
318 319 1.995626 CTCCGACCCAGGGATTGGT 60.996 63.158 14.54 0.00 46.25 3.67
320 321 2.190578 GCTCCGACCCAGGGATTG 59.809 66.667 14.54 0.33 31.99 2.67
321 322 3.470888 CGCTCCGACCCAGGGATT 61.471 66.667 14.54 0.00 31.99 3.01
709 710 9.148879 TGGAAACATTAATTAACCTTGAAAGGA 57.851 29.630 16.02 0.00 42.05 3.36
779 798 0.237235 CTCTCCTATCTCGCGTCTGC 59.763 60.000 5.77 0.00 37.91 4.26
837 857 5.391843 GGTCTCGGTAGAAGAGTTAGAACAC 60.392 48.000 0.00 0.00 37.07 3.32
875 895 8.978953 CGAAAGGAGATCGCTAGGATTCATCC 62.979 50.000 0.00 0.00 39.18 3.51
949 971 0.746923 GATGGAAGCGTGTAACCCCC 60.747 60.000 0.00 0.00 0.00 5.40
1188 1228 4.451150 TGGATGGACAGCGGCGAC 62.451 66.667 12.98 1.23 0.00 5.19
1437 1964 0.108615 CGAAGTCCACGGATTCTGCT 60.109 55.000 0.00 0.00 0.00 4.24
1808 2338 1.604278 TGTCATACAGATCGGCGAGAG 59.396 52.381 17.22 10.08 0.00 3.20
2489 3136 2.475487 GTCCTTGTCGAGTTAACAGCAC 59.525 50.000 8.61 1.35 0.00 4.40
2585 3232 5.451908 CGAGAAACAACACATAACATTGCT 58.548 37.500 0.00 0.00 0.00 3.91
3005 4638 3.825014 ACAGTCACGTGTCCTACTTGTAT 59.175 43.478 16.51 0.00 31.03 2.29
3006 4639 3.216800 ACAGTCACGTGTCCTACTTGTA 58.783 45.455 16.51 0.00 31.03 2.41
3007 4640 2.029623 ACAGTCACGTGTCCTACTTGT 58.970 47.619 16.51 7.10 31.03 3.16
3008 4641 2.795175 ACAGTCACGTGTCCTACTTG 57.205 50.000 16.51 6.45 0.00 3.16
3096 4733 6.183361 TGTTTGGTTCTCCTGTTTATCTCTGA 60.183 38.462 0.00 0.00 34.23 3.27
3190 4841 4.635699 AATCCAGGACTTTTCGTAACCT 57.364 40.909 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.