Multiple sequence alignment - TraesCS4D01G009300

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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 TraesCS4D01G009300 chr4D 100.000 4544 0 0 1 4544 4416151 4420694 0.000000e+00 8392
1 TraesCS4D01G009300 chr4D 89.808 1040 86 9 516 1553 4458538 4459559 0.000000e+00 1315
2 TraesCS4D01G009300 chr4D 84.538 498 69 5 3749 4240 4461501 4461996 1.900000e-133 486
3 TraesCS4D01G009300 chr4B 91.703 3881 260 25 701 4538 7170329 7174190 0.000000e+00 5326
4 TraesCS4D01G009300 chr4B 91.138 3927 279 27 654 4538 7308357 7312256 0.000000e+00 5260
5 TraesCS4D01G009300 chr4B 91.321 3883 269 30 701 4538 7217288 7221147 0.000000e+00 5241
6 TraesCS4D01G009300 chr4B 91.111 3881 282 27 701 4538 7262904 7266764 0.000000e+00 5197
7 TraesCS4D01G009300 chr4B 91.291 3812 261 32 701 4476 7353326 7357102 0.000000e+00 5134
8 TraesCS4D01G009300 chr4B 84.950 897 71 18 233 1116 7374961 7375806 0.000000e+00 850
9 TraesCS4D01G009300 chr4B 85.540 491 64 4 3749 4234 7378645 7379133 1.460000e-139 507
10 TraesCS4D01G009300 chr4B 87.500 344 35 7 3405 3742 7378265 7378606 1.530000e-104 390
11 TraesCS4D01G009300 chr4B 88.732 142 11 2 516 657 7160286 7160422 7.820000e-38 169
12 TraesCS4D01G009300 chr4A 90.542 3172 236 30 1066 4196 598910263 598907115 0.000000e+00 4137
13 TraesCS4D01G009300 chr4A 91.261 2975 186 39 519 3452 599180155 599177214 0.000000e+00 3986
14 TraesCS4D01G009300 chr4A 91.221 2973 190 36 519 3452 599223582 599220642 0.000000e+00 3978
15 TraesCS4D01G009300 chr4A 91.053 2973 195 34 519 3452 599102776 599099836 0.000000e+00 3951
16 TraesCS4D01G009300 chr4A 90.474 1816 112 28 519 2301 599085053 599083266 0.000000e+00 2338
17 TraesCS4D01G009300 chr4A 90.084 1795 114 31 519 2279 599146995 599145231 0.000000e+00 2270
18 TraesCS4D01G009300 chr4A 94.805 77 4 0 4468 4544 598896402 598896326 2.220000e-23 121
19 TraesCS4D01G009300 chr4A 94.805 77 4 0 4468 4544 598946506 598946430 2.220000e-23 121
20 TraesCS4D01G009300 chr6A 91.517 2452 128 38 677 3097 593027288 593024886 0.000000e+00 3302
21 TraesCS4D01G009300 chr6A 89.163 729 58 4 3464 4188 593024590 593023879 0.000000e+00 889
22 TraesCS4D01G009300 chrUn 90.139 1795 113 33 519 2279 360633392 360631628 0.000000e+00 2276
23 TraesCS4D01G009300 chrUn 88.493 730 61 6 3464 4188 216673570 216672859 0.000000e+00 861
24 TraesCS4D01G009300 chrUn 88.842 708 37 20 519 1207 216652463 216651779 0.000000e+00 832
25 TraesCS4D01G009300 chrUn 91.962 423 17 8 519 930 385952830 385952414 1.100000e-160 577
26 TraesCS4D01G009300 chrUn 85.545 422 30 12 233 631 189399061 189399474 3.270000e-111 412
27 TraesCS4D01G009300 chrUn 85.545 422 30 12 233 631 264057918 264057505 3.270000e-111 412
28 TraesCS4D01G009300 chrUn 90.972 288 23 3 233 519 423536065 423536350 7.130000e-103 385
29 TraesCS4D01G009300 chrUn 90.972 288 23 3 233 519 440457871 440458156 7.130000e-103 385
30 TraesCS4D01G009300 chr7D 85.948 427 29 13 227 631 382056651 382057068 1.170000e-115 427
31 TraesCS4D01G009300 chr7D 85.343 423 30 7 233 631 626691255 626690841 4.230000e-110 409
32 TraesCS4D01G009300 chr7D 97.468 237 6 0 1 237 64293727 64293963 5.470000e-109 405
33 TraesCS4D01G009300 chr7D 97.479 238 5 1 1 237 155144612 155144375 5.470000e-109 405
34 TraesCS4D01G009300 chr7D 97.468 237 6 0 1 237 572591469 572591705 5.470000e-109 405
35 TraesCS4D01G009300 chr7D 97.479 238 3 3 1 237 142973051 142973286 1.970000e-108 403
36 TraesCS4D01G009300 chr7A 85.952 420 30 6 233 631 4966333 4966744 5.440000e-114 422
37 TraesCS4D01G009300 chr5B 85.343 423 30 7 233 631 567274845 567274431 4.230000e-110 409
38 TraesCS4D01G009300 chr1B 85.343 423 30 7 233 631 668817176 668816762 4.230000e-110 409
39 TraesCS4D01G009300 chr3D 97.490 239 5 1 1 238 61943028 61942790 1.520000e-109 407
40 TraesCS4D01G009300 chr3D 97.479 238 5 1 1 237 494618654 494618891 5.470000e-109 405
41 TraesCS4D01G009300 chr5D 97.872 235 4 1 4 237 511029761 511029527 5.470000e-109 405
42 TraesCS4D01G009300 chr6D 97.083 240 6 1 1 239 56624526 56624287 1.970000e-108 403
43 TraesCS4D01G009300 chr2D 96.327 245 6 2 1 242 57025997 57025753 2.550000e-107 399


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 TraesCS4D01G009300 chr4D 4416151 4420694 4543 False 8392.000000 8392 100.000000 1 4544 1 chr4D.!!$F1 4543
1 TraesCS4D01G009300 chr4D 4458538 4461996 3458 False 900.500000 1315 87.173000 516 4240 2 chr4D.!!$F2 3724
2 TraesCS4D01G009300 chr4B 7170329 7174190 3861 False 5326.000000 5326 91.703000 701 4538 1 chr4B.!!$F2 3837
3 TraesCS4D01G009300 chr4B 7308357 7312256 3899 False 5260.000000 5260 91.138000 654 4538 1 chr4B.!!$F5 3884
4 TraesCS4D01G009300 chr4B 7217288 7221147 3859 False 5241.000000 5241 91.321000 701 4538 1 chr4B.!!$F3 3837
5 TraesCS4D01G009300 chr4B 7262904 7266764 3860 False 5197.000000 5197 91.111000 701 4538 1 chr4B.!!$F4 3837
6 TraesCS4D01G009300 chr4B 7353326 7357102 3776 False 5134.000000 5134 91.291000 701 4476 1 chr4B.!!$F6 3775
7 TraesCS4D01G009300 chr4B 7374961 7379133 4172 False 582.333333 850 85.996667 233 4234 3 chr4B.!!$F7 4001
8 TraesCS4D01G009300 chr4A 598907115 598910263 3148 True 4137.000000 4137 90.542000 1066 4196 1 chr4A.!!$R2 3130
9 TraesCS4D01G009300 chr4A 599177214 599180155 2941 True 3986.000000 3986 91.261000 519 3452 1 chr4A.!!$R7 2933
10 TraesCS4D01G009300 chr4A 599220642 599223582 2940 True 3978.000000 3978 91.221000 519 3452 1 chr4A.!!$R8 2933
11 TraesCS4D01G009300 chr4A 599099836 599102776 2940 True 3951.000000 3951 91.053000 519 3452 1 chr4A.!!$R5 2933
12 TraesCS4D01G009300 chr4A 599083266 599085053 1787 True 2338.000000 2338 90.474000 519 2301 1 chr4A.!!$R4 1782
13 TraesCS4D01G009300 chr4A 599145231 599146995 1764 True 2270.000000 2270 90.084000 519 2279 1 chr4A.!!$R6 1760
14 TraesCS4D01G009300 chr6A 593023879 593027288 3409 True 2095.500000 3302 90.340000 677 4188 2 chr6A.!!$R1 3511
15 TraesCS4D01G009300 chrUn 360631628 360633392 1764 True 2276.000000 2276 90.139000 519 2279 1 chrUn.!!$R4 1760
16 TraesCS4D01G009300 chrUn 216672859 216673570 711 True 861.000000 861 88.493000 3464 4188 1 chrUn.!!$R2 724
17 TraesCS4D01G009300 chrUn 216651779 216652463 684 True 832.000000 832 88.842000 519 1207 1 chrUn.!!$R1 688

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
493 494 0.034059 CCCGGCTAACTCCATGCTAG 59.966 60.000 0.00 0.00 0.00 3.42 F
500 501 0.105039 AACTCCATGCTAGTAGCCGC 59.895 55.000 19.41 0.00 41.51 6.53 F
507 508 0.462789 TGCTAGTAGCCGCCCTAAAC 59.537 55.000 19.41 0.00 41.51 2.01 F
508 509 0.462789 GCTAGTAGCCGCCCTAAACA 59.537 55.000 11.33 0.00 34.48 2.83 F
1133 1157 0.521735 GCCGACTAACTTGGCCTTTG 59.478 55.000 3.32 0.00 43.33 2.77 F
1306 1352 1.071385 GCCTCCACACCCTCTATCATG 59.929 57.143 0.00 0.00 0.00 3.07 F
1528 1591 1.202054 TGCGTCAATGTCATGCGATTG 60.202 47.619 9.22 9.22 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2572 0.320334 CATGACGTACACACCCTGCA 60.320 55.000 0.00 0.00 0.00 4.41 R
2427 2814 1.371467 TCCTCAAGGAGCCATTTCCA 58.629 50.000 0.00 0.00 39.78 3.53 R
2593 2985 4.777896 AGCTATTGAGTTCTGACCCTTGTA 59.222 41.667 0.00 0.00 0.00 2.41 R
2651 3044 7.115378 GGTTTGCATAGAGACATTGAAAAACAG 59.885 37.037 0.00 0.00 27.96 3.16 R
2672 3065 0.963962 AACATGAGCTGGCAGGTTTG 59.036 50.000 21.55 21.57 39.46 2.93 R
3046 3444 2.408271 TCATGACCTCCAACTCATGC 57.592 50.000 0.00 0.00 42.40 4.06 R
3650 4125 1.802365 CTAAGTTTTACGCGCACCCTT 59.198 47.619 5.73 4.90 0.00 3.95 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
41 42 2.371306 CCCCCAAACATTTAGTACCGG 58.629 52.381 0.00 0.00 0.00 5.28
42 43 2.291089 CCCCCAAACATTTAGTACCGGT 60.291 50.000 13.98 13.98 0.00 5.28
43 44 3.423749 CCCCAAACATTTAGTACCGGTT 58.576 45.455 15.04 0.00 0.00 4.44
44 45 3.191791 CCCCAAACATTTAGTACCGGTTG 59.808 47.826 15.04 6.22 0.00 3.77
45 46 3.191791 CCCAAACATTTAGTACCGGTTGG 59.808 47.826 15.04 10.33 42.84 3.77
61 62 4.604114 GGTGCTACCAACCGGTAC 57.396 61.111 8.00 0.00 46.71 3.34
62 63 1.977685 GGTGCTACCAACCGGTACT 59.022 57.895 8.00 0.00 46.71 2.73
63 64 1.185315 GGTGCTACCAACCGGTACTA 58.815 55.000 8.00 0.00 46.71 1.82
64 65 1.550072 GGTGCTACCAACCGGTACTAA 59.450 52.381 8.00 0.00 46.71 2.24
65 66 2.169144 GGTGCTACCAACCGGTACTAAT 59.831 50.000 8.00 0.00 46.71 1.73
66 67 3.192466 GTGCTACCAACCGGTACTAATG 58.808 50.000 8.00 0.73 46.71 1.90
67 68 2.168936 TGCTACCAACCGGTACTAATGG 59.831 50.000 18.75 18.75 46.71 3.16
68 69 2.169144 GCTACCAACCGGTACTAATGGT 59.831 50.000 26.66 26.66 46.71 3.55
69 70 3.739209 GCTACCAACCGGTACTAATGGTC 60.739 52.174 27.14 13.30 46.71 4.02
70 71 2.543635 ACCAACCGGTACTAATGGTCT 58.456 47.619 20.02 1.19 46.71 3.85
71 72 3.711863 ACCAACCGGTACTAATGGTCTA 58.288 45.455 20.02 0.00 46.71 2.59
72 73 3.448660 ACCAACCGGTACTAATGGTCTAC 59.551 47.826 20.02 0.00 46.71 2.59
73 74 3.181472 CCAACCGGTACTAATGGTCTACC 60.181 52.174 8.00 0.00 34.11 3.18
82 83 3.628989 TGGTCTACCAGCATCCGG 58.371 61.111 0.00 0.00 42.01 5.14
83 84 2.063979 TGGTCTACCAGCATCCGGG 61.064 63.158 0.00 0.00 42.01 5.73
84 85 2.109181 GTCTACCAGCATCCGGGC 59.891 66.667 0.00 0.00 0.00 6.13
85 86 3.161450 TCTACCAGCATCCGGGCC 61.161 66.667 0.00 0.00 0.00 5.80
86 87 3.164269 CTACCAGCATCCGGGCCT 61.164 66.667 0.84 0.00 0.00 5.19
87 88 3.466791 CTACCAGCATCCGGGCCTG 62.467 68.421 3.88 3.88 0.00 4.85
114 115 1.574428 CACGTGGTGGCACTTTAGC 59.426 57.895 18.45 0.25 0.00 3.09
115 116 1.959226 ACGTGGTGGCACTTTAGCG 60.959 57.895 18.45 15.80 34.64 4.26
116 117 2.561373 GTGGTGGCACTTTAGCGC 59.439 61.111 18.45 0.00 34.64 5.92
121 122 3.053896 GGCACTTTAGCGCCGGTT 61.054 61.111 2.29 0.00 38.82 4.44
122 123 2.479198 GCACTTTAGCGCCGGTTC 59.521 61.111 2.29 0.00 0.00 3.62
123 124 2.776072 CACTTTAGCGCCGGTTCG 59.224 61.111 2.29 0.00 0.00 3.95
124 125 2.025418 CACTTTAGCGCCGGTTCGT 61.025 57.895 2.29 0.00 0.00 3.85
125 126 2.025418 ACTTTAGCGCCGGTTCGTG 61.025 57.895 2.29 0.00 0.00 4.35
126 127 3.362851 CTTTAGCGCCGGTTCGTGC 62.363 63.158 2.29 0.00 0.00 5.34
144 145 3.746900 CCGAACCGGTAGTAAAGGG 57.253 57.895 8.00 0.00 42.73 3.95
145 146 0.176449 CCGAACCGGTAGTAAAGGGG 59.824 60.000 8.00 0.00 42.73 4.79
146 147 0.176449 CGAACCGGTAGTAAAGGGGG 59.824 60.000 8.00 0.00 0.00 5.40
161 162 4.164264 GGGGGCCTTTAGTCTCCA 57.836 61.111 0.84 0.00 0.00 3.86
162 163 1.608154 GGGGGCCTTTAGTCTCCAC 59.392 63.158 0.84 0.00 0.00 4.02
163 164 0.914902 GGGGGCCTTTAGTCTCCACT 60.915 60.000 0.84 0.00 36.55 4.00
164 165 0.542333 GGGGCCTTTAGTCTCCACTC 59.458 60.000 0.84 0.00 33.62 3.51
165 166 1.574263 GGGCCTTTAGTCTCCACTCT 58.426 55.000 0.84 0.00 33.62 3.24
166 167 1.909986 GGGCCTTTAGTCTCCACTCTT 59.090 52.381 0.84 0.00 33.62 2.85
167 168 2.306219 GGGCCTTTAGTCTCCACTCTTT 59.694 50.000 0.84 0.00 33.62 2.52
168 169 3.518303 GGGCCTTTAGTCTCCACTCTTTA 59.482 47.826 0.84 0.00 33.62 1.85
169 170 4.383226 GGGCCTTTAGTCTCCACTCTTTAG 60.383 50.000 0.84 0.00 33.62 1.85
170 171 4.223255 GGCCTTTAGTCTCCACTCTTTAGT 59.777 45.833 0.00 0.00 35.91 2.24
179 180 1.878953 CACTCTTTAGTGCCGGTTGT 58.121 50.000 1.90 0.00 46.28 3.32
180 181 3.034721 CACTCTTTAGTGCCGGTTGTA 57.965 47.619 1.90 0.00 46.28 2.41
181 182 2.993899 CACTCTTTAGTGCCGGTTGTAG 59.006 50.000 1.90 0.00 46.28 2.74
182 183 2.895404 ACTCTTTAGTGCCGGTTGTAGA 59.105 45.455 1.90 0.00 33.57 2.59
183 184 3.322828 ACTCTTTAGTGCCGGTTGTAGAA 59.677 43.478 1.90 0.00 33.57 2.10
184 185 3.656559 TCTTTAGTGCCGGTTGTAGAAC 58.343 45.455 1.90 0.00 0.00 3.01
185 186 7.752780 ACTCTTTAGTGCCGGTTGTAGAACC 62.753 48.000 11.77 11.77 40.61 3.62
193 194 2.460757 GGTTGTAGAACCGGCACTAA 57.539 50.000 5.96 0.00 42.47 2.24
194 195 2.769893 GGTTGTAGAACCGGCACTAAA 58.230 47.619 5.96 0.00 42.47 1.85
195 196 2.740447 GGTTGTAGAACCGGCACTAAAG 59.260 50.000 5.96 0.00 42.47 1.85
196 197 2.740447 GTTGTAGAACCGGCACTAAAGG 59.260 50.000 0.00 0.00 0.00 3.11
197 198 1.338389 TGTAGAACCGGCACTAAAGGC 60.338 52.381 0.00 0.00 0.00 4.35
204 205 2.776659 GGCACTAAAGGCCCTTACG 58.223 57.895 0.00 0.00 45.87 3.18
205 206 0.251073 GGCACTAAAGGCCCTTACGA 59.749 55.000 0.00 0.00 45.87 3.43
206 207 1.339342 GGCACTAAAGGCCCTTACGAA 60.339 52.381 0.00 0.00 45.87 3.85
207 208 1.736126 GCACTAAAGGCCCTTACGAAC 59.264 52.381 0.00 0.00 0.00 3.95
208 209 1.997606 CACTAAAGGCCCTTACGAACG 59.002 52.381 0.00 0.00 0.00 3.95
209 210 1.620323 ACTAAAGGCCCTTACGAACGT 59.380 47.619 0.00 5.03 0.00 3.99
210 211 1.997606 CTAAAGGCCCTTACGAACGTG 59.002 52.381 10.14 0.00 0.00 4.49
211 212 1.232621 AAAGGCCCTTACGAACGTGC 61.233 55.000 10.14 4.66 0.00 5.34
212 213 3.484547 GGCCCTTACGAACGTGCG 61.485 66.667 16.06 16.06 37.29 5.34
213 214 4.143363 GCCCTTACGAACGTGCGC 62.143 66.667 17.82 0.00 33.86 6.09
214 215 2.431942 CCCTTACGAACGTGCGCT 60.432 61.111 17.82 6.03 33.86 5.92
215 216 1.153978 CCCTTACGAACGTGCGCTA 60.154 57.895 17.82 4.94 33.86 4.26
216 217 0.733566 CCCTTACGAACGTGCGCTAA 60.734 55.000 17.82 12.61 33.86 3.09
217 218 1.062258 CCTTACGAACGTGCGCTAAA 58.938 50.000 17.82 7.33 33.86 1.85
218 219 1.058695 CCTTACGAACGTGCGCTAAAG 59.941 52.381 17.82 16.49 33.86 1.85
219 220 0.435769 TTACGAACGTGCGCTAAAGC 59.564 50.000 17.82 0.00 37.78 3.51
220 221 1.346378 TACGAACGTGCGCTAAAGCC 61.346 55.000 17.82 0.00 37.91 4.35
221 222 2.479198 GAACGTGCGCTAAAGCCC 59.521 61.111 9.73 0.00 37.91 5.19
222 223 3.362851 GAACGTGCGCTAAAGCCCG 62.363 63.158 9.73 1.96 37.91 6.13
225 226 3.053896 GTGCGCTAAAGCCCGGTT 61.054 61.111 9.73 0.00 37.91 4.44
226 227 2.744709 TGCGCTAAAGCCCGGTTC 60.745 61.111 9.73 0.00 37.91 3.62
227 228 2.436115 GCGCTAAAGCCCGGTTCT 60.436 61.111 0.00 0.00 37.91 3.01
228 229 2.750888 GCGCTAAAGCCCGGTTCTG 61.751 63.158 0.00 0.00 37.91 3.02
229 230 2.750888 CGCTAAAGCCCGGTTCTGC 61.751 63.158 0.00 0.00 37.91 4.26
230 231 1.674322 GCTAAAGCCCGGTTCTGCA 60.674 57.895 0.00 0.00 34.31 4.41
231 232 1.923227 GCTAAAGCCCGGTTCTGCAC 61.923 60.000 0.00 0.00 34.31 4.57
236 237 1.741770 GCCCGGTTCTGCACTAGTG 60.742 63.158 18.93 18.93 0.00 2.74
260 261 4.017177 AGTTAGTTGGTCAGGTAAAGGC 57.983 45.455 0.00 0.00 0.00 4.35
265 266 1.378646 GGTCAGGTAAAGGCTGGCC 60.379 63.158 3.00 3.00 35.62 5.36
288 289 1.336125 GCCAATGATGCTTAGCTGGTC 59.664 52.381 5.60 2.00 0.00 4.02
295 296 3.507233 TGATGCTTAGCTGGTCTTTTTGG 59.493 43.478 5.60 0.00 0.00 3.28
306 307 3.694072 TGGTCTTTTTGGATGATTAGCCG 59.306 43.478 0.00 0.00 34.20 5.52
310 311 1.388547 TTTGGATGATTAGCCGCACC 58.611 50.000 0.00 0.00 34.20 5.01
322 323 3.680786 CGCACCGGGACTGAGACA 61.681 66.667 6.32 0.00 0.00 3.41
323 324 2.048127 GCACCGGGACTGAGACAC 60.048 66.667 6.32 0.00 0.00 3.67
329 330 2.262915 GGACTGAGACACGGCCTG 59.737 66.667 0.00 0.21 0.00 4.85
342 343 2.692368 GCCTGGACTCCCATGGGA 60.692 66.667 31.83 31.83 42.59 4.37
351 352 3.736224 CCCATGGGAGGCAGCAGT 61.736 66.667 28.27 0.00 37.50 4.40
359 360 1.000396 GAGGCAGCAGTGGGGAATT 60.000 57.895 0.00 0.00 0.00 2.17
363 364 0.968405 GCAGCAGTGGGGAATTTTGA 59.032 50.000 0.00 0.00 0.00 2.69
375 376 3.556004 GGGAATTTTGAACAATGGGCGAA 60.556 43.478 0.00 0.00 0.00 4.70
395 396 1.356124 AGCCCGATCCAGCAATATCT 58.644 50.000 4.58 0.00 0.00 1.98
419 420 3.188048 GTGAGTGAAGAAGGTCAATGCTG 59.812 47.826 0.00 0.00 0.00 4.41
420 421 2.157738 AGTGAAGAAGGTCAATGCTGC 58.842 47.619 0.00 0.00 0.00 5.25
457 458 1.805261 CGAGTGCGCGATCATGACAG 61.805 60.000 12.10 0.00 0.00 3.51
459 460 0.108662 AGTGCGCGATCATGACAGAA 60.109 50.000 12.10 0.00 0.00 3.02
463 464 1.913317 CGCGATCATGACAGAACTCA 58.087 50.000 0.00 0.00 0.00 3.41
469 470 4.565962 CGATCATGACAGAACTCAAGGAAG 59.434 45.833 0.00 0.00 0.00 3.46
470 471 5.623141 CGATCATGACAGAACTCAAGGAAGA 60.623 44.000 0.00 0.00 0.00 2.87
471 472 5.551305 TCATGACAGAACTCAAGGAAGAA 57.449 39.130 0.00 0.00 0.00 2.52
473 474 3.733337 TGACAGAACTCAAGGAAGAAGC 58.267 45.455 0.00 0.00 0.00 3.86
474 475 3.070748 GACAGAACTCAAGGAAGAAGCC 58.929 50.000 0.00 0.00 0.00 4.35
475 476 2.224646 ACAGAACTCAAGGAAGAAGCCC 60.225 50.000 0.00 0.00 0.00 5.19
476 477 1.352687 AGAACTCAAGGAAGAAGCCCC 59.647 52.381 0.00 0.00 0.00 5.80
478 479 1.078143 CTCAAGGAAGAAGCCCCGG 60.078 63.158 0.00 0.00 0.00 5.73
479 480 2.751837 CAAGGAAGAAGCCCCGGC 60.752 66.667 0.00 0.00 42.33 6.13
489 490 2.203209 GCCCCGGCTAACTCCATG 60.203 66.667 0.00 0.00 38.26 3.66
490 491 2.203209 CCCCGGCTAACTCCATGC 60.203 66.667 0.00 0.00 0.00 4.06
491 492 2.746375 CCCCGGCTAACTCCATGCT 61.746 63.158 0.00 0.00 0.00 3.79
493 494 0.034059 CCCGGCTAACTCCATGCTAG 59.966 60.000 0.00 0.00 0.00 3.42
494 495 0.753262 CCGGCTAACTCCATGCTAGT 59.247 55.000 0.00 0.00 0.00 2.57
495 496 1.961394 CCGGCTAACTCCATGCTAGTA 59.039 52.381 0.00 0.00 0.00 1.82
496 497 2.029828 CCGGCTAACTCCATGCTAGTAG 60.030 54.545 0.00 0.00 0.00 2.57
497 498 2.608261 CGGCTAACTCCATGCTAGTAGC 60.608 54.545 15.56 15.56 42.82 3.58
498 499 2.289133 GGCTAACTCCATGCTAGTAGCC 60.289 54.545 19.41 19.19 41.51 3.93
499 500 2.608261 GCTAACTCCATGCTAGTAGCCG 60.608 54.545 19.41 10.34 41.51 5.52
500 501 0.105039 AACTCCATGCTAGTAGCCGC 59.895 55.000 19.41 0.00 41.51 6.53
501 502 1.005630 CTCCATGCTAGTAGCCGCC 60.006 63.158 19.41 0.00 41.51 6.13
502 503 2.031163 CCATGCTAGTAGCCGCCC 59.969 66.667 19.41 0.00 41.51 6.13
503 504 2.511452 CCATGCTAGTAGCCGCCCT 61.511 63.158 19.41 0.00 41.51 5.19
504 505 1.185618 CCATGCTAGTAGCCGCCCTA 61.186 60.000 19.41 0.00 41.51 3.53
505 506 0.679505 CATGCTAGTAGCCGCCCTAA 59.320 55.000 19.41 0.00 41.51 2.69
506 507 1.070134 CATGCTAGTAGCCGCCCTAAA 59.930 52.381 19.41 0.00 41.51 1.85
507 508 0.462789 TGCTAGTAGCCGCCCTAAAC 59.537 55.000 19.41 0.00 41.51 2.01
508 509 0.462789 GCTAGTAGCCGCCCTAAACA 59.537 55.000 11.33 0.00 34.48 2.83
509 510 1.538419 GCTAGTAGCCGCCCTAAACAG 60.538 57.143 11.33 0.00 34.48 3.16
510 511 1.068741 CTAGTAGCCGCCCTAAACAGG 59.931 57.143 0.00 0.00 0.00 4.00
539 540 1.139455 GTAAAGGGCATGTAGGCGGTA 59.861 52.381 0.00 0.00 45.36 4.02
646 647 4.712337 AGAGTGGATGGTCTTCTATTCGTT 59.288 41.667 0.00 0.00 0.00 3.85
910 918 2.307768 CTATACAACCTCCGCTCCTCA 58.692 52.381 0.00 0.00 0.00 3.86
942 961 1.741401 CACTCCGCAGCCGAATTCA 60.741 57.895 6.22 0.00 36.29 2.57
1078 1102 3.953652 TGAGGCCCTTCCCCTCCA 61.954 66.667 0.00 0.00 46.69 3.86
1100 1124 1.338973 TCTAGTCGTGTGGTTGTGGAC 59.661 52.381 0.00 0.00 0.00 4.02
1123 1147 2.125106 CCTGGCTGGCCGACTAAC 60.125 66.667 7.14 0.00 39.42 2.34
1124 1148 2.660064 CCTGGCTGGCCGACTAACT 61.660 63.158 7.14 0.00 39.42 2.24
1125 1149 1.296715 CTGGCTGGCCGACTAACTT 59.703 57.895 7.14 0.00 39.42 2.66
1126 1150 1.003839 TGGCTGGCCGACTAACTTG 60.004 57.895 7.14 0.00 39.42 3.16
1127 1151 1.745489 GGCTGGCCGACTAACTTGG 60.745 63.158 0.00 0.00 0.00 3.61
1131 1155 4.716003 GCCGACTAACTTGGCCTT 57.284 55.556 3.32 0.00 43.33 4.35
1132 1156 2.942641 GCCGACTAACTTGGCCTTT 58.057 52.632 3.32 0.00 43.33 3.11
1133 1157 0.521735 GCCGACTAACTTGGCCTTTG 59.478 55.000 3.32 0.00 43.33 2.77
1134 1158 0.521735 CCGACTAACTTGGCCTTTGC 59.478 55.000 3.32 0.00 0.00 3.68
1289 1334 2.607750 ACACCCTGATGTCCGCCT 60.608 61.111 0.00 0.00 0.00 5.52
1306 1352 1.071385 GCCTCCACACCCTCTATCATG 59.929 57.143 0.00 0.00 0.00 3.07
1496 1556 9.391006 CCACCTGCTTATTTTTAACTCTATGTA 57.609 33.333 0.00 0.00 0.00 2.29
1528 1591 1.202054 TGCGTCAATGTCATGCGATTG 60.202 47.619 9.22 9.22 0.00 2.67
1534 1597 4.271776 GTCAATGTCATGCGATTGAGATCA 59.728 41.667 15.60 0.00 38.85 2.92
1555 1624 6.693315 TCAGTTTATTATACTGGGCAAAGC 57.307 37.500 12.49 0.00 42.53 3.51
1887 2253 1.593933 GTTCGTGTCGTTTTACAGGCA 59.406 47.619 0.00 0.00 35.68 4.75
1912 2281 4.096682 CGTATAGCCATAGGTAGAAGAGCC 59.903 50.000 0.00 0.00 0.00 4.70
1975 2347 7.083875 TCTTCCCAATGTTAATCAAATCGTC 57.916 36.000 0.00 0.00 0.00 4.20
1977 2349 6.677781 TCCCAATGTTAATCAAATCGTCTC 57.322 37.500 0.00 0.00 0.00 3.36
2031 2403 6.642917 CAAACGTTTGTTCTACTATCGTGTT 58.357 36.000 28.72 0.00 37.31 3.32
2067 2439 3.618690 GCCATTATTCTAGGCCGAGAT 57.381 47.619 16.99 9.33 42.58 2.75
2068 2440 3.265791 GCCATTATTCTAGGCCGAGATG 58.734 50.000 16.99 11.40 42.58 2.90
2096 2470 5.376854 AATATCGTTTCATAAGCATGGCC 57.623 39.130 0.00 0.00 32.61 5.36
2189 2572 7.502226 TGTTGTTTCTATTCAGATTTGTCAGGT 59.498 33.333 0.00 0.00 0.00 4.00
2325 2708 4.421058 GTTCGGCAAGAAAAACTTTGTCT 58.579 39.130 0.00 0.00 41.10 3.41
2326 2709 4.287238 TCGGCAAGAAAAACTTTGTCTC 57.713 40.909 0.00 0.00 36.61 3.36
2347 2730 9.146984 TGTCTCTTTGTAAATATTTCTGGTACG 57.853 33.333 3.39 0.00 0.00 3.67
2379 2762 4.759096 GCACGTGACGGCAATGGC 62.759 66.667 22.23 0.00 40.13 4.40
2427 2814 9.811995 CAATTTATGGAGTTGACAATCATGATT 57.188 29.630 15.36 15.36 0.00 2.57
2562 2954 1.375908 GTGAACCTCGCCTGCATGA 60.376 57.895 0.00 0.00 0.00 3.07
2651 3044 8.662369 TGTTACACAATAATTATTCGCAACAC 57.338 30.769 7.76 2.77 0.00 3.32
2672 3065 6.672147 ACACTGTTTTTCAATGTCTCTATGC 58.328 36.000 0.00 0.00 30.26 3.14
2707 3100 5.403897 TCATGTTGTCTTTTCTGTCGTTC 57.596 39.130 0.00 0.00 0.00 3.95
2746 3141 9.498176 ACCAATCTAACGTTGTTAAGAAGTAAT 57.502 29.630 11.99 0.00 0.00 1.89
2827 3223 5.065914 TCTGAATATGCTACCCTTTGATGC 58.934 41.667 0.00 0.00 0.00 3.91
2838 3234 5.184892 ACCCTTTGATGCTTCTCTTGTAT 57.815 39.130 0.88 0.00 0.00 2.29
2839 3235 6.313519 ACCCTTTGATGCTTCTCTTGTATA 57.686 37.500 0.88 0.00 0.00 1.47
3015 3413 5.560722 TTTAGGTGTCTCTTGTCATTGGA 57.439 39.130 0.00 0.00 0.00 3.53
3046 3444 5.300752 AGGAATGAGTTCTATATTGTGCGG 58.699 41.667 0.00 0.00 34.68 5.69
3074 3472 2.195727 TGGAGGTCATGATGCAGGTAA 58.804 47.619 0.00 0.00 0.00 2.85
3130 3528 6.001460 CCAACTTCCCACTAGTTTCATAACA 58.999 40.000 0.00 0.00 36.70 2.41
3248 3648 2.747446 GCCGAAAAGTCTCATTTAGCCA 59.253 45.455 0.00 0.00 0.00 4.75
3250 3650 4.496507 GCCGAAAAGTCTCATTTAGCCATC 60.497 45.833 0.00 0.00 0.00 3.51
3264 3664 8.916062 TCATTTAGCCATCAAATGATTATGTGT 58.084 29.630 6.43 0.00 43.81 3.72
3377 3779 6.456795 AATGCCCAAATAAGAAACTAGCTC 57.543 37.500 0.00 0.00 0.00 4.09
3379 3781 4.943705 TGCCCAAATAAGAAACTAGCTCAG 59.056 41.667 0.00 0.00 0.00 3.35
3392 3794 3.455910 ACTAGCTCAGTTGGAATATGGCA 59.544 43.478 0.00 0.00 31.59 4.92
3562 4019 1.192146 AGTAGCGGCAAGTGAAGGGA 61.192 55.000 1.45 0.00 0.00 4.20
3650 4125 4.967084 TTCAAAGGGTGTCTAGCACTAA 57.033 40.909 14.28 1.96 46.86 2.24
3707 4186 0.794473 GGAACTTTGGGCTCGTAACG 59.206 55.000 0.00 0.00 0.00 3.18
3718 4197 1.342082 CTCGTAACGCTGTGAACGGG 61.342 60.000 16.30 11.71 36.08 5.28
3805 4320 2.706890 CCTACGGGCTGTGTGTAAAAT 58.293 47.619 9.79 0.00 0.00 1.82
3815 4330 5.007724 GGCTGTGTGTAAAATCTATACCTGC 59.992 44.000 0.00 0.00 0.00 4.85
3819 4334 7.165485 TGTGTGTAAAATCTATACCTGCTTGT 58.835 34.615 0.00 0.00 0.00 3.16
3826 4341 5.700402 ATCTATACCTGCTTGTTTGGTCT 57.300 39.130 0.00 0.00 35.48 3.85
3861 4376 5.347342 TGTTTTGCTGTATGTTCTGTTTGG 58.653 37.500 0.00 0.00 0.00 3.28
3894 4409 1.926510 GCAAGTCTTGTTGTTGGTTGC 59.073 47.619 14.03 0.00 32.80 4.17
3916 4431 2.910319 TGTACCCAGAGTGTAGCCAATT 59.090 45.455 0.00 0.00 0.00 2.32
3918 4433 4.532916 TGTACCCAGAGTGTAGCCAATTAA 59.467 41.667 0.00 0.00 0.00 1.40
3961 4477 6.805713 ACATGACTTTTCGGTCTGAAATTTT 58.194 32.000 7.67 0.00 45.62 1.82
3966 4482 5.237779 ACTTTTCGGTCTGAAATTTTAGCGA 59.762 36.000 7.67 15.07 45.62 4.93
4017 4536 1.381872 GCAGTAGCTGGAGGAGGGA 60.382 63.158 0.00 0.00 37.91 4.20
4093 4612 2.202492 CGAGACGGCGTGAAGAGG 60.202 66.667 21.19 0.00 0.00 3.69
4149 4668 6.539173 TGAAAAGTCTGGGCTAATTAAGTCA 58.461 36.000 0.00 0.00 0.00 3.41
4150 4669 7.175104 TGAAAAGTCTGGGCTAATTAAGTCAT 58.825 34.615 0.00 0.00 0.00 3.06
4176 4696 0.807275 CAGCTCCAACGATGATCGCA 60.807 55.000 15.62 0.00 45.12 5.10
4188 4708 3.611549 CGATGATCGCAGGAACATCATAG 59.388 47.826 0.41 0.00 46.89 2.23
4191 4711 5.529581 TGATCGCAGGAACATCATAGTAA 57.470 39.130 0.00 0.00 0.00 2.24
4201 4721 6.726764 AGGAACATCATAGTAATCCTAGTCCC 59.273 42.308 0.00 0.00 35.59 4.46
4248 4768 1.064017 ACCAACTGGGCAAGAGAACAA 60.064 47.619 0.00 0.00 42.05 2.83
4264 4784 0.670546 ACAAGTGGCCATCTTCGTCG 60.671 55.000 9.72 5.28 0.00 5.12
4272 4792 1.404391 GCCATCTTCGTCGTTCTCCTA 59.596 52.381 0.00 0.00 0.00 2.94
4289 4809 4.141158 TCTCCTATAGTGGCTGATCTCACA 60.141 45.833 13.78 0.00 36.43 3.58
4311 4831 0.874390 TTGCGAACCATGTTCTGCTC 59.126 50.000 17.68 3.51 0.00 4.26
4317 4837 3.438087 CGAACCATGTTCTGCTCTGAAAT 59.562 43.478 5.53 0.00 0.00 2.17
4328 4848 2.813754 TGCTCTGAAATTTCGGGTCTTG 59.186 45.455 23.64 11.81 34.32 3.02
4334 4854 1.474330 AATTTCGGGTCTTGGATGGC 58.526 50.000 0.00 0.00 0.00 4.40
4343 4863 3.274288 GGTCTTGGATGGCAGTAGAAAG 58.726 50.000 0.00 0.00 0.00 2.62
4358 4878 6.955963 GCAGTAGAAAGTGTTGTTATTCATCG 59.044 38.462 0.00 0.00 0.00 3.84
4387 4907 0.179045 GCCGATGCTCATACACCCTT 60.179 55.000 0.00 0.00 33.53 3.95
4417 4937 1.146637 CTGCTATCGCTTCTCATGCC 58.853 55.000 0.00 0.00 36.97 4.40
4442 4964 0.532196 GCCGACTAGGGTATGGTTGC 60.532 60.000 0.00 0.00 41.48 4.17
4477 5000 2.552315 ACTCTACCACGCACCAAATTTG 59.448 45.455 11.40 11.40 0.00 2.32
4502 5025 4.575885 TCCCGCTTTCTTATATATGTGCC 58.424 43.478 0.00 0.00 0.00 5.01
4505 5028 5.240623 CCCGCTTTCTTATATATGTGCCAAA 59.759 40.000 0.00 0.00 0.00 3.28
4506 5029 6.238897 CCCGCTTTCTTATATATGTGCCAAAA 60.239 38.462 0.00 0.00 0.00 2.44
4521 5044 3.054166 GCCAAAATTTCGGTACAACCAC 58.946 45.455 0.00 0.00 38.47 4.16
4531 5054 1.066716 GGTACAACCACGCTCCACATA 60.067 52.381 0.00 0.00 38.42 2.29
4538 5061 1.337728 CCACGCTCCACATACAACTCA 60.338 52.381 0.00 0.00 0.00 3.41
4539 5062 2.412870 CACGCTCCACATACAACTCAA 58.587 47.619 0.00 0.00 0.00 3.02
4540 5063 3.002791 CACGCTCCACATACAACTCAAT 58.997 45.455 0.00 0.00 0.00 2.57
4541 5064 3.436704 CACGCTCCACATACAACTCAATT 59.563 43.478 0.00 0.00 0.00 2.32
4542 5065 4.072131 ACGCTCCACATACAACTCAATTT 58.928 39.130 0.00 0.00 0.00 1.82
4543 5066 4.518970 ACGCTCCACATACAACTCAATTTT 59.481 37.500 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.291089 ACCGGTACTAAATGTTTGGGGG 60.291 50.000 4.49 0.00 0.00 5.40
22 23 3.076079 ACCGGTACTAAATGTTTGGGG 57.924 47.619 4.49 0.00 0.00 4.96
23 24 3.191791 CCAACCGGTACTAAATGTTTGGG 59.808 47.826 8.00 0.00 31.35 4.12
24 25 3.822167 ACCAACCGGTACTAAATGTTTGG 59.178 43.478 8.00 10.60 46.71 3.28
25 26 4.789784 CACCAACCGGTACTAAATGTTTG 58.210 43.478 8.00 0.00 46.94 2.93
26 27 3.253921 GCACCAACCGGTACTAAATGTTT 59.746 43.478 8.00 0.00 46.94 2.83
27 28 2.815503 GCACCAACCGGTACTAAATGTT 59.184 45.455 8.00 0.00 46.94 2.71
28 29 2.039348 AGCACCAACCGGTACTAAATGT 59.961 45.455 8.00 0.00 46.94 2.71
29 30 2.706890 AGCACCAACCGGTACTAAATG 58.293 47.619 8.00 0.00 46.94 2.32
30 31 3.369787 GGTAGCACCAACCGGTACTAAAT 60.370 47.826 8.00 0.00 46.94 1.40
31 32 2.028203 GGTAGCACCAACCGGTACTAAA 60.028 50.000 8.00 0.00 46.94 1.85
32 33 1.550072 GGTAGCACCAACCGGTACTAA 59.450 52.381 8.00 0.00 46.94 2.24
33 34 1.185315 GGTAGCACCAACCGGTACTA 58.815 55.000 8.00 2.12 46.94 1.82
34 35 1.977685 GGTAGCACCAACCGGTACT 59.022 57.895 8.00 3.20 46.94 2.73
35 36 4.604114 GGTAGCACCAACCGGTAC 57.396 61.111 8.00 0.00 46.94 3.34
48 49 8.127481 GGTAGACCATTAGTACCGGTTGGTAG 62.127 50.000 24.44 6.75 42.88 3.18
49 50 6.388106 GGTAGACCATTAGTACCGGTTGGTA 61.388 48.000 24.44 10.25 40.67 3.25
50 51 5.658044 GGTAGACCATTAGTACCGGTTGGT 61.658 50.000 24.60 24.60 43.19 3.67
51 52 3.181472 GGTAGACCATTAGTACCGGTTGG 60.181 52.174 15.04 17.37 37.33 3.77
52 53 3.448301 TGGTAGACCATTAGTACCGGTTG 59.552 47.826 15.04 3.82 42.01 3.77
53 54 3.703052 CTGGTAGACCATTAGTACCGGTT 59.297 47.826 15.04 0.00 46.46 4.44
54 55 3.294214 CTGGTAGACCATTAGTACCGGT 58.706 50.000 13.98 13.98 46.46 5.28
55 56 2.035576 GCTGGTAGACCATTAGTACCGG 59.964 54.545 0.00 0.00 46.46 5.28
56 57 2.691526 TGCTGGTAGACCATTAGTACCG 59.308 50.000 0.89 0.00 46.46 4.02
57 58 4.262506 GGATGCTGGTAGACCATTAGTACC 60.263 50.000 0.89 0.00 46.46 3.34
58 59 4.558898 CGGATGCTGGTAGACCATTAGTAC 60.559 50.000 0.89 0.00 46.46 2.73
59 60 3.572682 CGGATGCTGGTAGACCATTAGTA 59.427 47.826 0.89 0.00 46.46 1.82
60 61 2.365617 CGGATGCTGGTAGACCATTAGT 59.634 50.000 0.89 0.00 46.46 2.24
61 62 2.289072 CCGGATGCTGGTAGACCATTAG 60.289 54.545 0.00 0.00 46.46 1.73
62 63 1.691976 CCGGATGCTGGTAGACCATTA 59.308 52.381 0.00 0.00 46.46 1.90
63 64 0.469917 CCGGATGCTGGTAGACCATT 59.530 55.000 0.00 0.00 46.46 3.16
64 65 1.410850 CCCGGATGCTGGTAGACCAT 61.411 60.000 0.73 0.00 46.46 3.55
65 66 2.063979 CCCGGATGCTGGTAGACCA 61.064 63.158 0.73 0.55 45.30 4.02
66 67 2.822399 CCCGGATGCTGGTAGACC 59.178 66.667 0.73 0.00 0.00 3.85
67 68 2.109181 GCCCGGATGCTGGTAGAC 59.891 66.667 0.73 0.00 0.00 2.59
68 69 3.161450 GGCCCGGATGCTGGTAGA 61.161 66.667 0.73 0.00 0.00 2.59
69 70 3.164269 AGGCCCGGATGCTGGTAG 61.164 66.667 0.73 0.00 0.00 3.18
70 71 3.479203 CAGGCCCGGATGCTGGTA 61.479 66.667 0.73 0.00 0.00 3.25
96 97 1.574428 GCTAAAGTGCCACCACGTG 59.426 57.895 9.08 9.08 46.62 4.49
97 98 1.959226 CGCTAAAGTGCCACCACGT 60.959 57.895 0.00 0.00 46.62 4.49
98 99 2.860293 CGCTAAAGTGCCACCACG 59.140 61.111 0.00 0.00 46.62 4.94
99 100 2.561373 GCGCTAAAGTGCCACCAC 59.439 61.111 0.00 0.00 45.15 4.16
106 107 2.025418 ACGAACCGGCGCTAAAGTG 61.025 57.895 7.64 0.00 33.86 3.16
107 108 2.025418 CACGAACCGGCGCTAAAGT 61.025 57.895 7.64 0.00 33.86 2.66
108 109 2.776072 CACGAACCGGCGCTAAAG 59.224 61.111 7.64 0.00 33.86 1.85
109 110 3.416382 GCACGAACCGGCGCTAAA 61.416 61.111 7.64 0.00 33.86 1.85
127 128 0.176449 CCCCCTTTACTACCGGTTCG 59.824 60.000 15.04 7.30 0.00 3.95
144 145 0.914902 AGTGGAGACTAAAGGCCCCC 60.915 60.000 0.00 0.00 0.00 5.40
145 146 0.542333 GAGTGGAGACTAAAGGCCCC 59.458 60.000 0.00 0.00 30.16 5.80
146 147 1.574263 AGAGTGGAGACTAAAGGCCC 58.426 55.000 0.00 0.00 30.16 5.80
147 148 3.704800 AAAGAGTGGAGACTAAAGGCC 57.295 47.619 0.00 0.00 30.16 5.19
148 149 5.408880 ACTAAAGAGTGGAGACTAAAGGC 57.591 43.478 0.00 0.00 33.41 4.35
161 162 2.895404 TCTACAACCGGCACTAAAGAGT 59.105 45.455 0.00 0.00 35.80 3.24
162 163 3.587797 TCTACAACCGGCACTAAAGAG 57.412 47.619 0.00 0.00 0.00 2.85
163 164 3.555586 GGTTCTACAACCGGCACTAAAGA 60.556 47.826 0.00 0.00 43.00 2.52
164 165 2.740447 GGTTCTACAACCGGCACTAAAG 59.260 50.000 0.00 0.00 43.00 1.85
165 166 2.769893 GGTTCTACAACCGGCACTAAA 58.230 47.619 0.00 0.00 43.00 1.85
166 167 2.460757 GGTTCTACAACCGGCACTAA 57.539 50.000 0.00 0.00 43.00 2.24
175 176 2.740447 CCTTTAGTGCCGGTTCTACAAC 59.260 50.000 1.90 0.00 0.00 3.32
176 177 2.872842 GCCTTTAGTGCCGGTTCTACAA 60.873 50.000 1.90 3.65 0.00 2.41
177 178 1.338389 GCCTTTAGTGCCGGTTCTACA 60.338 52.381 1.90 0.00 0.00 2.74
178 179 1.366679 GCCTTTAGTGCCGGTTCTAC 58.633 55.000 1.90 0.00 0.00 2.59
179 180 0.251073 GGCCTTTAGTGCCGGTTCTA 59.749 55.000 1.90 3.32 39.48 2.10
180 181 1.002502 GGCCTTTAGTGCCGGTTCT 60.003 57.895 1.90 4.41 39.48 3.01
181 182 3.587095 GGCCTTTAGTGCCGGTTC 58.413 61.111 1.90 0.00 39.48 3.62
187 188 1.736126 GTTCGTAAGGGCCTTTAGTGC 59.264 52.381 26.29 8.97 38.47 4.40
188 189 1.997606 CGTTCGTAAGGGCCTTTAGTG 59.002 52.381 26.29 11.88 38.47 2.74
189 190 1.620323 ACGTTCGTAAGGGCCTTTAGT 59.380 47.619 26.29 12.36 38.47 2.24
190 191 1.997606 CACGTTCGTAAGGGCCTTTAG 59.002 52.381 26.29 18.30 38.47 1.85
191 192 1.940752 GCACGTTCGTAAGGGCCTTTA 60.941 52.381 26.29 2.60 38.47 1.85
192 193 1.232621 GCACGTTCGTAAGGGCCTTT 61.233 55.000 26.29 5.08 38.47 3.11
193 194 1.670083 GCACGTTCGTAAGGGCCTT 60.670 57.895 24.44 24.44 38.47 4.35
194 195 2.047560 GCACGTTCGTAAGGGCCT 60.048 61.111 0.00 0.00 38.47 5.19
195 196 3.484547 CGCACGTTCGTAAGGGCC 61.485 66.667 0.00 0.00 38.47 5.80
196 197 4.143363 GCGCACGTTCGTAAGGGC 62.143 66.667 9.74 1.86 38.47 5.19
197 198 0.733566 TTAGCGCACGTTCGTAAGGG 60.734 55.000 11.47 0.00 38.47 3.95
198 199 1.058695 CTTTAGCGCACGTTCGTAAGG 59.941 52.381 11.47 4.01 38.47 2.69
199 200 1.524391 GCTTTAGCGCACGTTCGTAAG 60.524 52.381 11.47 11.21 0.00 2.34
200 201 0.435769 GCTTTAGCGCACGTTCGTAA 59.564 50.000 11.47 4.26 0.00 3.18
201 202 1.346378 GGCTTTAGCGCACGTTCGTA 61.346 55.000 11.47 0.00 43.26 3.43
202 203 2.664436 GGCTTTAGCGCACGTTCGT 61.664 57.895 11.47 0.00 43.26 3.85
203 204 2.095843 GGCTTTAGCGCACGTTCG 59.904 61.111 11.47 2.39 43.26 3.95
211 212 2.750888 GCAGAACCGGGCTTTAGCG 61.751 63.158 6.32 0.00 43.26 4.26
212 213 1.674322 TGCAGAACCGGGCTTTAGC 60.674 57.895 6.32 3.45 41.14 3.09
213 214 0.321653 AGTGCAGAACCGGGCTTTAG 60.322 55.000 6.32 0.00 0.00 1.85
214 215 0.978151 TAGTGCAGAACCGGGCTTTA 59.022 50.000 6.32 0.00 0.00 1.85
215 216 0.321653 CTAGTGCAGAACCGGGCTTT 60.322 55.000 6.32 0.00 0.00 3.51
216 217 1.296715 CTAGTGCAGAACCGGGCTT 59.703 57.895 6.32 0.00 0.00 4.35
217 218 1.913762 ACTAGTGCAGAACCGGGCT 60.914 57.895 6.32 0.00 0.00 5.19
218 219 1.741770 CACTAGTGCAGAACCGGGC 60.742 63.158 10.54 0.00 0.00 6.13
219 220 0.034896 AACACTAGTGCAGAACCGGG 59.965 55.000 22.90 0.00 0.00 5.73
220 221 2.029290 ACTAACACTAGTGCAGAACCGG 60.029 50.000 22.90 0.00 36.98 5.28
221 222 3.299340 ACTAACACTAGTGCAGAACCG 57.701 47.619 22.90 7.01 36.98 4.44
222 223 5.780984 ACTAACTAACACTAGTGCAGAACC 58.219 41.667 22.90 0.00 38.43 3.62
223 224 6.145696 CCAACTAACTAACACTAGTGCAGAAC 59.854 42.308 22.90 0.00 38.43 3.01
224 225 6.183360 ACCAACTAACTAACACTAGTGCAGAA 60.183 38.462 22.90 12.04 38.43 3.02
225 226 5.303589 ACCAACTAACTAACACTAGTGCAGA 59.696 40.000 22.90 7.25 38.43 4.26
226 227 5.539048 ACCAACTAACTAACACTAGTGCAG 58.461 41.667 22.90 20.52 38.43 4.41
227 228 5.069383 TGACCAACTAACTAACACTAGTGCA 59.931 40.000 22.90 10.02 38.43 4.57
228 229 5.535333 TGACCAACTAACTAACACTAGTGC 58.465 41.667 22.90 1.81 38.43 4.40
229 230 6.157211 CCTGACCAACTAACTAACACTAGTG 58.843 44.000 21.44 21.44 38.43 2.74
230 231 5.837438 ACCTGACCAACTAACTAACACTAGT 59.163 40.000 0.00 0.00 40.25 2.57
231 232 6.342338 ACCTGACCAACTAACTAACACTAG 57.658 41.667 0.00 0.00 0.00 2.57
236 237 5.410746 GCCTTTACCTGACCAACTAACTAAC 59.589 44.000 0.00 0.00 0.00 2.34
288 289 3.438360 GTGCGGCTAATCATCCAAAAAG 58.562 45.455 0.00 0.00 0.00 2.27
295 296 1.961277 CCCGGTGCGGCTAATCATC 60.961 63.158 0.00 0.00 46.86 2.92
306 307 2.048127 GTGTCTCAGTCCCGGTGC 60.048 66.667 0.00 0.00 0.00 5.01
310 311 4.436998 GGCCGTGTCTCAGTCCCG 62.437 72.222 0.00 0.00 0.00 5.14
342 343 0.178924 AAAATTCCCCACTGCTGCCT 60.179 50.000 0.00 0.00 0.00 4.75
351 352 2.039613 GCCCATTGTTCAAAATTCCCCA 59.960 45.455 0.00 0.00 0.00 4.96
359 360 2.147436 GCTTTCGCCCATTGTTCAAA 57.853 45.000 0.00 0.00 0.00 2.69
375 376 1.701847 AGATATTGCTGGATCGGGCTT 59.298 47.619 9.37 1.64 0.00 4.35
395 396 3.653344 CATTGACCTTCTTCACTCACGA 58.347 45.455 0.00 0.00 0.00 4.35
420 421 4.321217 CACTCGACGTAAGAGCTTTACAAG 59.679 45.833 17.36 10.12 39.23 3.16
437 438 1.586303 GTCATGATCGCGCACTCGA 60.586 57.895 8.75 0.00 43.09 4.04
438 439 1.805261 CTGTCATGATCGCGCACTCG 61.805 60.000 8.75 0.00 39.07 4.18
457 458 1.827681 GGGGCTTCTTCCTTGAGTTC 58.172 55.000 0.00 0.00 0.00 3.01
459 460 1.679898 CGGGGCTTCTTCCTTGAGT 59.320 57.895 0.00 0.00 0.00 3.41
473 474 1.407656 TAGCATGGAGTTAGCCGGGG 61.408 60.000 2.18 0.00 0.00 5.73
474 475 0.034059 CTAGCATGGAGTTAGCCGGG 59.966 60.000 2.18 0.00 0.00 5.73
475 476 0.753262 ACTAGCATGGAGTTAGCCGG 59.247 55.000 0.00 0.00 34.68 6.13
476 477 2.608261 GCTACTAGCATGGAGTTAGCCG 60.608 54.545 2.96 0.00 41.89 5.52
478 479 2.608261 CGGCTACTAGCATGGAGTTAGC 60.608 54.545 10.27 0.00 44.75 3.09
479 480 2.608261 GCGGCTACTAGCATGGAGTTAG 60.608 54.545 10.27 0.00 44.75 2.34
480 481 1.340248 GCGGCTACTAGCATGGAGTTA 59.660 52.381 10.27 0.00 44.75 2.24
481 482 0.105039 GCGGCTACTAGCATGGAGTT 59.895 55.000 10.27 0.00 44.75 3.01
482 483 1.742768 GCGGCTACTAGCATGGAGT 59.257 57.895 10.27 0.00 44.75 3.85
483 484 1.005630 GGCGGCTACTAGCATGGAG 60.006 63.158 10.27 0.00 44.75 3.86
485 486 1.185618 TAGGGCGGCTACTAGCATGG 61.186 60.000 9.56 0.25 44.75 3.66
486 487 0.679505 TTAGGGCGGCTACTAGCATG 59.320 55.000 9.56 3.14 44.75 4.06
487 488 1.070289 GTTTAGGGCGGCTACTAGCAT 59.930 52.381 9.56 0.00 44.75 3.79
488 489 0.462789 GTTTAGGGCGGCTACTAGCA 59.537 55.000 9.56 0.00 44.75 3.49
489 490 0.462789 TGTTTAGGGCGGCTACTAGC 59.537 55.000 9.56 0.00 41.46 3.42
490 491 1.068741 CCTGTTTAGGGCGGCTACTAG 59.931 57.143 9.56 0.39 40.63 2.57
491 492 1.117150 CCTGTTTAGGGCGGCTACTA 58.883 55.000 9.56 0.00 40.63 1.82
493 494 4.534401 CCTGTTTAGGGCGGCTAC 57.466 61.111 9.56 3.10 40.63 3.58
501 502 4.815108 GCCCGCCCCCTGTTTAGG 62.815 72.222 0.00 0.00 44.18 2.69
513 514 3.887868 CATGCCCTTTACGCCCGC 61.888 66.667 0.00 0.00 0.00 6.13
539 540 4.401202 ACAGTTTCACTTTCAACCCGATTT 59.599 37.500 0.00 0.00 0.00 2.17
577 578 0.107703 TTCGAGAGCATTCCGCCATT 60.108 50.000 0.00 0.00 44.04 3.16
578 579 0.107703 TTTCGAGAGCATTCCGCCAT 60.108 50.000 0.00 0.00 44.04 4.40
617 618 2.452600 AGACCATCCACTCTCCTCTC 57.547 55.000 0.00 0.00 0.00 3.20
646 647 7.743116 TTAGTCCCTCACAATGTTTATAGGA 57.257 36.000 3.28 0.00 0.00 2.94
710 711 2.560981 TGTTCATGGAAGTGAGCGTCTA 59.439 45.455 0.00 0.00 32.70 2.59
885 893 0.880718 GCGGAGGTTGTATAGCTGGC 60.881 60.000 0.00 0.00 33.94 4.85
910 918 1.321074 GGAGTGAACGAGGACGGGAT 61.321 60.000 0.00 0.00 44.46 3.85
942 961 4.988716 TGAGCGGTGGAGACGGGT 62.989 66.667 0.00 0.00 35.98 5.28
1034 1053 3.329386 GTGTACATGCTGGCGATATGAT 58.671 45.455 0.00 0.00 0.00 2.45
1045 1064 1.134699 CCTCACATCGGTGTACATGCT 60.135 52.381 0.00 0.00 45.45 3.79
1078 1102 1.340248 CCACAACCACACGACTAGAGT 59.660 52.381 0.00 0.00 0.00 3.24
1127 1151 1.301953 CCAAGGCAAAGGCAAAGGC 60.302 57.895 0.00 0.00 43.71 4.35
1139 1163 1.766143 GACGTCGATCATGCCAAGGC 61.766 60.000 3.61 3.61 42.35 4.35
1140 1164 1.482621 CGACGTCGATCATGCCAAGG 61.483 60.000 33.35 0.00 43.02 3.61
1174 1216 1.509370 CTCGAACGTGTCCTCGTCG 60.509 63.158 7.20 2.45 43.38 5.12
1289 1334 3.300388 GAGACATGATAGAGGGTGTGGA 58.700 50.000 0.00 0.00 0.00 4.02
1306 1352 1.102978 GACAGAGAGCAGAGGGAGAC 58.897 60.000 0.00 0.00 0.00 3.36
1496 1556 3.737172 GACGCAGCGGGCAAACAT 61.737 61.111 21.15 0.00 45.17 2.71
1528 1591 8.677148 TTTGCCCAGTATAATAAACTGATCTC 57.323 34.615 4.84 0.00 45.89 2.75
1534 1597 8.996651 AATAGCTTTGCCCAGTATAATAAACT 57.003 30.769 0.00 0.00 0.00 2.66
1555 1624 1.135689 GGCAGTGCAACCGACAAATAG 60.136 52.381 18.61 0.00 37.80 1.73
1782 1884 2.198827 TCGATGCCATGGACAAACTT 57.801 45.000 18.40 0.00 0.00 2.66
1887 2253 5.591067 GCTCTTCTACCTATGGCTATACGAT 59.409 44.000 0.00 0.00 0.00 3.73
1912 2281 9.797473 TCGTTACACGATATATAACTAAACTCG 57.203 33.333 0.00 0.00 46.73 4.18
1987 2359 2.428890 TGCAAAACGACAACAATTCCCT 59.571 40.909 0.00 0.00 0.00 4.20
1995 2367 3.121295 ACAAACGTTTGCAAAACGACAAC 60.121 39.130 34.70 11.73 45.64 3.32
2031 2403 1.963679 GGCATTGCCCGAAGAACAA 59.036 52.632 17.28 0.00 44.06 2.83
2077 2451 1.603802 CGGCCATGCTTATGAAACGAT 59.396 47.619 2.24 0.00 0.00 3.73
2084 2458 4.699735 TCATTAATACCGGCCATGCTTATG 59.300 41.667 0.00 0.00 0.00 1.90
2096 2470 8.310406 TGTAGAATTGCAGATCATTAATACCG 57.690 34.615 0.00 0.00 0.00 4.02
2189 2572 0.320334 CATGACGTACACACCCTGCA 60.320 55.000 0.00 0.00 0.00 4.41
2325 2708 9.146984 CAGTCGTACCAGAAATATTTACAAAGA 57.853 33.333 0.00 0.00 0.00 2.52
2326 2709 9.146984 TCAGTCGTACCAGAAATATTTACAAAG 57.853 33.333 0.00 0.00 0.00 2.77
2386 2773 8.187913 TCCATAAATTGTTTGATGAACCAGAA 57.812 30.769 0.00 0.00 37.45 3.02
2427 2814 1.371467 TCCTCAAGGAGCCATTTCCA 58.629 50.000 0.00 0.00 39.78 3.53
2593 2985 4.777896 AGCTATTGAGTTCTGACCCTTGTA 59.222 41.667 0.00 0.00 0.00 2.41
2651 3044 7.115378 GGTTTGCATAGAGACATTGAAAAACAG 59.885 37.037 0.00 0.00 27.96 3.16
2672 3065 0.963962 AACATGAGCTGGCAGGTTTG 59.036 50.000 21.55 21.57 39.46 2.93
2707 3100 6.313905 ACGTTAGATTGGTATGAGCTGAAAAG 59.686 38.462 0.00 0.00 0.00 2.27
2746 3141 7.143340 CAGATGAAGTGAAAAAGCAAATCAGA 58.857 34.615 0.00 0.00 0.00 3.27
2943 3340 7.971183 AATTCTGAAGAGGTTAACAGAACTC 57.029 36.000 8.10 4.81 46.87 3.01
3005 3403 7.174413 TCATTCCTAACAAGATCCAATGACAA 58.826 34.615 0.00 0.00 0.00 3.18
3046 3444 2.408271 TCATGACCTCCAACTCATGC 57.592 50.000 0.00 0.00 42.40 4.06
3377 3779 6.057533 TCACTAATCTGCCATATTCCAACTG 58.942 40.000 0.00 0.00 0.00 3.16
3379 3781 6.942532 TTCACTAATCTGCCATATTCCAAC 57.057 37.500 0.00 0.00 0.00 3.77
3383 3785 6.942532 TGGTTTCACTAATCTGCCATATTC 57.057 37.500 0.00 0.00 0.00 1.75
3386 3788 5.589855 CACATGGTTTCACTAATCTGCCATA 59.410 40.000 0.00 0.00 33.96 2.74
3392 3794 6.533730 TCAAGTCACATGGTTTCACTAATCT 58.466 36.000 0.00 0.00 0.00 2.40
3492 3949 2.079158 TCTTCGAGCTGCATCAAAAGG 58.921 47.619 1.02 0.00 0.00 3.11
3562 4019 1.978617 CATGGGGCCACGCTCTTTT 60.979 57.895 4.39 0.00 0.00 2.27
3584 4041 2.455557 TGGAACACATAATGCAAGGGG 58.544 47.619 0.00 0.00 0.00 4.79
3650 4125 1.802365 CTAAGTTTTACGCGCACCCTT 59.198 47.619 5.73 4.90 0.00 3.95
3707 4186 0.307760 CAACAGTTCCCGTTCACAGC 59.692 55.000 0.00 0.00 0.00 4.40
3718 4197 3.063452 ACATCAACACACGACAACAGTTC 59.937 43.478 0.00 0.00 0.00 3.01
3805 4320 5.248477 AGAAGACCAAACAAGCAGGTATAGA 59.752 40.000 0.00 0.00 35.36 1.98
3815 4330 6.316390 ACAAAGTCACTAGAAGACCAAACAAG 59.684 38.462 13.79 3.99 36.68 3.16
3819 4334 7.535139 CAAAACAAAGTCACTAGAAGACCAAA 58.465 34.615 13.79 0.00 36.68 3.28
3826 4341 7.282224 ACATACAGCAAAACAAAGTCACTAGAA 59.718 33.333 0.00 0.00 0.00 2.10
3861 4376 8.560374 ACAACAAGACTTGCTTATAGAGAAAAC 58.440 33.333 15.24 0.00 34.31 2.43
3894 4409 1.557099 TGGCTACACTCTGGGTACAG 58.443 55.000 0.00 0.00 46.30 2.74
3942 4457 5.237779 TCGCTAAAATTTCAGACCGAAAAGT 59.762 36.000 0.00 0.00 46.48 2.66
3961 4477 4.471548 ACTCTTATAAGAAGGCCTCGCTA 58.528 43.478 15.85 0.00 34.03 4.26
3966 4482 4.275443 CGTCGTACTCTTATAAGAAGGCCT 59.725 45.833 15.85 0.00 34.03 5.19
3998 4517 1.687146 CCCTCCTCCAGCTACTGCA 60.687 63.158 0.00 0.00 42.74 4.41
4093 4612 7.671302 TGCAAACATACCTAATCCTAGAGATC 58.329 38.462 0.00 0.00 32.47 2.75
4103 4622 8.532186 TTCATACCAATGCAAACATACCTAAT 57.468 30.769 0.00 0.00 34.62 1.73
4149 4668 4.769688 TCATCGTTGGAGCTGTAATTGAT 58.230 39.130 0.00 0.00 0.00 2.57
4150 4669 4.200838 TCATCGTTGGAGCTGTAATTGA 57.799 40.909 0.00 0.00 0.00 2.57
4176 4696 6.726764 GGGACTAGGATTACTATGATGTTCCT 59.273 42.308 0.00 0.00 37.38 3.36
4188 4708 9.557061 CTAAATAACTTTGGGGACTAGGATTAC 57.443 37.037 0.00 0.00 0.00 1.89
4191 4711 7.628101 AGTCTAAATAACTTTGGGGACTAGGAT 59.372 37.037 0.00 0.00 33.02 3.24
4201 4721 9.110502 GATTCAGGGTAGTCTAAATAACTTTGG 57.889 37.037 0.00 0.00 0.00 3.28
4248 4768 0.389948 GAACGACGAAGATGGCCACT 60.390 55.000 8.16 4.50 0.00 4.00
4264 4784 4.830046 TGAGATCAGCCACTATAGGAGAAC 59.170 45.833 4.43 0.00 0.00 3.01
4272 4792 4.449131 CAACATGTGAGATCAGCCACTAT 58.551 43.478 0.00 4.39 34.57 2.12
4289 4809 1.068333 GCAGAACATGGTTCGCAACAT 60.068 47.619 15.63 0.00 0.00 2.71
4311 4831 3.129287 CCATCCAAGACCCGAAATTTCAG 59.871 47.826 17.99 10.75 0.00 3.02
4317 4837 0.322456 CTGCCATCCAAGACCCGAAA 60.322 55.000 0.00 0.00 0.00 3.46
4328 4848 3.412386 ACAACACTTTCTACTGCCATCC 58.588 45.455 0.00 0.00 0.00 3.51
4334 4854 6.955963 GCGATGAATAACAACACTTTCTACTG 59.044 38.462 0.00 0.00 0.00 2.74
4343 4863 3.694734 CCATGGCGATGAATAACAACAC 58.305 45.455 10.66 0.00 0.00 3.32
4358 4878 3.360340 GCATCGGCTAGCCATGGC 61.360 66.667 32.47 30.12 38.09 4.40
4378 4898 3.200825 CAGTCATGGAAGGAAGGGTGTAT 59.799 47.826 0.00 0.00 0.00 2.29
4382 4902 0.329596 GCAGTCATGGAAGGAAGGGT 59.670 55.000 0.00 0.00 0.00 4.34
4383 4903 0.622665 AGCAGTCATGGAAGGAAGGG 59.377 55.000 0.00 0.00 0.00 3.95
4477 5000 5.294552 GCACATATATAAGAAAGCGGGATCC 59.705 44.000 1.92 1.92 0.00 3.36
4502 5025 2.722116 GCGTGGTTGTACCGAAATTTTG 59.278 45.455 0.00 0.00 42.58 2.44
4505 5028 1.802365 GAGCGTGGTTGTACCGAAATT 59.198 47.619 0.00 0.00 42.58 1.82
4506 5029 1.435577 GAGCGTGGTTGTACCGAAAT 58.564 50.000 0.00 0.00 42.58 2.17
4510 5033 2.025418 GTGGAGCGTGGTTGTACCG 61.025 63.158 0.00 0.00 42.58 4.02
4521 5044 4.685169 AAATTGAGTTGTATGTGGAGCG 57.315 40.909 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.