Multiple sequence alignment - TraesCS6A01G365900

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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 TraesCS6A01G365900 chr6A 100.000 2468 0 0 1 2468 593791311 593793778 0.000000e+00 4558.0
1 TraesCS6A01G365900 chr6A 81.031 543 61 27 987 1497 593777179 593777711 6.400000e-106 394.0
2 TraesCS6A01G365900 chr6A 81.690 497 51 23 995 1459 593785719 593786207 6.440000e-101 377.0
3 TraesCS6A01G365900 chr6A 79.835 486 45 27 995 1458 593732854 593733308 3.080000e-79 305.0
4 TraesCS6A01G365900 chr6A 78.080 552 52 32 986 1511 593562318 593561810 4.020000e-73 285.0
5 TraesCS6A01G365900 chr6A 81.362 279 33 11 422 692 593776400 593776667 2.490000e-50 209.0
6 TraesCS6A01G365900 chr6B 83.678 1887 152 68 140 1935 676135474 676137295 0.000000e+00 1635.0
7 TraesCS6A01G365900 chr6B 85.975 1590 112 48 365 1870 675569155 675567593 0.000000e+00 1598.0
8 TraesCS6A01G365900 chr6B 81.944 504 50 22 987 1462 675626747 675626257 2.980000e-104 388.0
9 TraesCS6A01G365900 chr6B 78.347 605 65 39 950 1523 676036392 676036961 5.090000e-87 331.0
10 TraesCS6A01G365900 chr6B 79.150 494 51 28 995 1459 676123577 676124047 6.670000e-76 294.0
11 TraesCS6A01G365900 chr6B 76.354 554 76 41 1049 1553 677045492 677044945 1.900000e-61 246.0
12 TraesCS6A01G365900 chr6B 90.278 144 11 1 2241 2384 676140106 676140246 4.190000e-43 185.0
13 TraesCS6A01G365900 chr6B 80.233 258 33 15 1307 1553 678357400 678357650 7.010000e-41 178.0
14 TraesCS6A01G365900 chr6B 85.714 168 15 3 422 580 676035630 676035797 4.220000e-38 169.0
15 TraesCS6A01G365900 chr6B 83.516 182 10 10 405 573 676498812 676498638 4.250000e-33 152.0
16 TraesCS6A01G365900 chr6B 91.919 99 8 0 995 1093 675614415 675614317 3.310000e-29 139.0
17 TraesCS6A01G365900 chr6B 81.868 182 9 2 2209 2384 675564462 675564299 5.540000e-27 132.0
18 TraesCS6A01G365900 chr6D 84.687 1613 131 50 365 1940 446947824 446949357 0.000000e+00 1504.0
19 TraesCS6A01G365900 chr6D 82.276 536 49 27 986 1493 446902014 446902531 2.930000e-114 422.0
20 TraesCS6A01G365900 chr6D 82.903 503 40 26 995 1459 446934808 446935302 6.350000e-111 411.0
21 TraesCS6A01G365900 chr6D 77.676 327 33 18 371 691 447214644 447214352 1.960000e-36 163.0
22 TraesCS6A01G365900 chr6D 90.654 107 7 2 2278 2384 446957050 446957153 3.310000e-29 139.0
23 TraesCS6A01G365900 chr6D 91.566 83 7 0 2386 2468 160040502 160040420 5.580000e-22 115.0
24 TraesCS6A01G365900 chr6D 89.130 92 10 0 2245 2336 446949540 446949631 5.580000e-22 115.0
25 TraesCS6A01G365900 chr6D 86.364 88 8 2 482 569 446728795 446728712 2.610000e-15 93.5
26 TraesCS6A01G365900 chr5A 93.023 86 6 0 2383 2468 437238751 437238836 2.580000e-25 126.0
27 TraesCS6A01G365900 chr4B 92.771 83 6 0 2386 2468 118741630 118741712 1.200000e-23 121.0
28 TraesCS6A01G365900 chr1B 92.771 83 6 0 2386 2468 313761715 313761633 1.200000e-23 121.0
29 TraesCS6A01G365900 chr1B 91.566 83 7 0 2386 2468 462607972 462608054 5.580000e-22 115.0
30 TraesCS6A01G365900 chr3B 92.500 80 6 0 2386 2465 602688000 602688079 5.580000e-22 115.0
31 TraesCS6A01G365900 chr3D 90.361 83 8 0 2386 2468 399419288 399419370 2.590000e-20 110.0
32 TraesCS6A01G365900 chr1D 90.361 83 8 0 2386 2468 323725970 323726052 2.590000e-20 110.0
33 TraesCS6A01G365900 chr1A 90.361 83 8 0 2386 2468 188495680 188495598 2.590000e-20 110.0


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 TraesCS6A01G365900 chr6A 593791311 593793778 2467 False 4558.0 4558 100.0000 1 2468 1 chr6A.!!$F3 2467
1 TraesCS6A01G365900 chr6A 593776400 593777711 1311 False 301.5 394 81.1965 422 1497 2 chr6A.!!$F4 1075
2 TraesCS6A01G365900 chr6A 593561810 593562318 508 True 285.0 285 78.0800 986 1511 1 chr6A.!!$R1 525
3 TraesCS6A01G365900 chr6B 676135474 676140246 4772 False 910.0 1635 86.9780 140 2384 2 chr6B.!!$F4 2244
4 TraesCS6A01G365900 chr6B 675564299 675569155 4856 True 865.0 1598 83.9215 365 2384 2 chr6B.!!$R5 2019
5 TraesCS6A01G365900 chr6B 676035630 676036961 1331 False 250.0 331 82.0305 422 1523 2 chr6B.!!$F3 1101
6 TraesCS6A01G365900 chr6B 677044945 677045492 547 True 246.0 246 76.3540 1049 1553 1 chr6B.!!$R4 504
7 TraesCS6A01G365900 chr6D 446947824 446949631 1807 False 809.5 1504 86.9085 365 2336 2 chr6D.!!$F4 1971
8 TraesCS6A01G365900 chr6D 446902014 446902531 517 False 422.0 422 82.2760 986 1493 1 chr6D.!!$F1 507

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
98 99 0.105964 TTACTGCGTTGTCAGTGGCT 59.894 50.0 6.67 0.0 45.95 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 7737 0.036388 AACATGCGAGTACCCAGGTG 60.036 55.0 0.0 0.0 0.0 4.0 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 4.379174 GGCCGTGACATGAACAGT 57.621 55.556 0.00 0.00 0.00 3.55
18 19 1.868997 GGCCGTGACATGAACAGTG 59.131 57.895 0.00 0.00 0.00 3.66
19 20 1.207593 GCCGTGACATGAACAGTGC 59.792 57.895 0.00 1.62 0.00 4.40
20 21 1.230635 GCCGTGACATGAACAGTGCT 61.231 55.000 0.00 0.00 0.00 4.40
21 22 0.514255 CCGTGACATGAACAGTGCTG 59.486 55.000 0.00 0.00 0.00 4.41
48 49 7.734924 TTTTTAGCACTAGATCTGCATATGG 57.265 36.000 5.18 0.00 37.08 2.74
49 50 3.977134 AGCACTAGATCTGCATATGGG 57.023 47.619 5.18 0.00 37.08 4.00
50 51 3.246301 AGCACTAGATCTGCATATGGGT 58.754 45.455 5.18 0.00 37.08 4.51
51 52 3.649981 AGCACTAGATCTGCATATGGGTT 59.350 43.478 5.18 0.00 37.08 4.11
52 53 3.750130 GCACTAGATCTGCATATGGGTTG 59.250 47.826 5.18 0.00 34.56 3.77
53 54 4.503817 GCACTAGATCTGCATATGGGTTGA 60.504 45.833 5.18 0.00 34.56 3.18
54 55 5.614308 CACTAGATCTGCATATGGGTTGAA 58.386 41.667 5.18 0.00 0.00 2.69
55 56 6.057533 CACTAGATCTGCATATGGGTTGAAA 58.942 40.000 5.18 0.00 0.00 2.69
56 57 6.543465 CACTAGATCTGCATATGGGTTGAAAA 59.457 38.462 5.18 0.00 0.00 2.29
57 58 7.067372 CACTAGATCTGCATATGGGTTGAAAAA 59.933 37.037 5.18 0.00 0.00 1.94
74 75 3.775661 AAAAACGGAACACCAGAACTG 57.224 42.857 0.00 0.00 0.00 3.16
75 76 2.413310 AAACGGAACACCAGAACTGT 57.587 45.000 1.18 0.00 0.00 3.55
76 77 1.949465 AACGGAACACCAGAACTGTC 58.051 50.000 1.18 0.00 0.00 3.51
77 78 0.106149 ACGGAACACCAGAACTGTCC 59.894 55.000 1.18 1.00 0.00 4.02
78 79 0.393077 CGGAACACCAGAACTGTCCT 59.607 55.000 1.18 0.00 0.00 3.85
79 80 1.202651 CGGAACACCAGAACTGTCCTT 60.203 52.381 1.18 0.00 0.00 3.36
80 81 2.745152 CGGAACACCAGAACTGTCCTTT 60.745 50.000 1.18 0.00 0.00 3.11
81 82 3.493699 CGGAACACCAGAACTGTCCTTTA 60.494 47.826 1.18 0.00 0.00 1.85
82 83 3.813724 GGAACACCAGAACTGTCCTTTAC 59.186 47.826 1.18 0.00 0.00 2.01
83 84 4.444449 GGAACACCAGAACTGTCCTTTACT 60.444 45.833 1.18 0.00 0.00 2.24
84 85 4.073293 ACACCAGAACTGTCCTTTACTG 57.927 45.455 1.18 0.00 0.00 2.74
85 86 2.808543 CACCAGAACTGTCCTTTACTGC 59.191 50.000 1.18 0.00 0.00 4.40
86 87 2.069273 CCAGAACTGTCCTTTACTGCG 58.931 52.381 1.18 0.00 0.00 5.18
87 88 2.548067 CCAGAACTGTCCTTTACTGCGT 60.548 50.000 1.18 0.00 0.00 5.24
88 89 3.131396 CAGAACTGTCCTTTACTGCGTT 58.869 45.455 0.00 0.00 0.00 4.84
89 90 3.059597 CAGAACTGTCCTTTACTGCGTTG 60.060 47.826 0.00 0.00 0.00 4.10
90 91 2.614829 ACTGTCCTTTACTGCGTTGT 57.385 45.000 0.00 0.00 0.00 3.32
91 92 2.480845 ACTGTCCTTTACTGCGTTGTC 58.519 47.619 0.00 0.00 0.00 3.18
92 93 2.159014 ACTGTCCTTTACTGCGTTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
93 94 2.476619 CTGTCCTTTACTGCGTTGTCAG 59.523 50.000 0.00 0.00 39.86 3.51
95 96 2.221055 GTCCTTTACTGCGTTGTCAGTG 59.779 50.000 6.67 0.00 45.95 3.66
96 97 1.531149 CCTTTACTGCGTTGTCAGTGG 59.469 52.381 6.67 0.00 45.95 4.00
97 98 0.941542 TTTACTGCGTTGTCAGTGGC 59.058 50.000 6.67 0.00 45.95 5.01
98 99 0.105964 TTACTGCGTTGTCAGTGGCT 59.894 50.000 6.67 0.00 45.95 4.75
99 100 0.599991 TACTGCGTTGTCAGTGGCTG 60.600 55.000 6.67 0.00 45.95 4.85
100 101 2.591429 TGCGTTGTCAGTGGCTGG 60.591 61.111 0.00 0.00 31.51 4.85
101 102 2.280797 GCGTTGTCAGTGGCTGGA 60.281 61.111 0.00 0.00 31.51 3.86
102 103 1.672356 GCGTTGTCAGTGGCTGGAT 60.672 57.895 0.00 0.00 31.51 3.41
103 104 1.237285 GCGTTGTCAGTGGCTGGATT 61.237 55.000 0.00 0.00 31.51 3.01
104 105 0.518636 CGTTGTCAGTGGCTGGATTG 59.481 55.000 0.00 0.00 31.51 2.67
105 106 0.242017 GTTGTCAGTGGCTGGATTGC 59.758 55.000 0.00 0.00 31.51 3.56
106 107 0.111061 TTGTCAGTGGCTGGATTGCT 59.889 50.000 0.00 0.00 31.51 3.91
107 108 0.607217 TGTCAGTGGCTGGATTGCTG 60.607 55.000 0.00 0.00 31.51 4.41
108 109 0.321919 GTCAGTGGCTGGATTGCTGA 60.322 55.000 0.00 0.00 34.30 4.26
109 110 0.622136 TCAGTGGCTGGATTGCTGAT 59.378 50.000 0.00 0.00 32.09 2.90
110 111 1.005097 TCAGTGGCTGGATTGCTGATT 59.995 47.619 0.00 0.00 32.09 2.57
111 112 2.239402 TCAGTGGCTGGATTGCTGATTA 59.761 45.455 0.00 0.00 32.09 1.75
112 113 3.117776 TCAGTGGCTGGATTGCTGATTAT 60.118 43.478 0.00 0.00 32.09 1.28
113 114 3.004419 CAGTGGCTGGATTGCTGATTATG 59.996 47.826 0.00 0.00 0.00 1.90
114 115 1.958579 TGGCTGGATTGCTGATTATGC 59.041 47.619 0.00 0.00 0.00 3.14
115 116 1.271656 GGCTGGATTGCTGATTATGCC 59.728 52.381 0.00 0.00 0.00 4.40
116 117 1.271656 GCTGGATTGCTGATTATGCCC 59.728 52.381 0.00 0.00 0.00 5.36
117 118 2.589720 CTGGATTGCTGATTATGCCCA 58.410 47.619 0.00 0.00 0.00 5.36
118 119 2.295349 CTGGATTGCTGATTATGCCCAC 59.705 50.000 0.00 0.00 0.00 4.61
119 120 2.309613 GGATTGCTGATTATGCCCACA 58.690 47.619 0.00 0.00 0.00 4.17
120 121 2.295349 GGATTGCTGATTATGCCCACAG 59.705 50.000 0.00 0.00 0.00 3.66
121 122 2.804986 TTGCTGATTATGCCCACAGA 57.195 45.000 0.00 0.00 32.90 3.41
122 123 2.804986 TGCTGATTATGCCCACAGAA 57.195 45.000 0.00 0.00 32.90 3.02
123 124 3.301794 TGCTGATTATGCCCACAGAAT 57.698 42.857 0.00 0.00 40.35 2.40
129 130 3.998913 TTATGCCCACAGAATCACAGA 57.001 42.857 0.00 0.00 0.00 3.41
130 131 2.414994 ATGCCCACAGAATCACAGAG 57.585 50.000 0.00 0.00 0.00 3.35
131 132 0.325933 TGCCCACAGAATCACAGAGG 59.674 55.000 0.00 0.00 0.00 3.69
132 133 1.028868 GCCCACAGAATCACAGAGGC 61.029 60.000 0.00 0.00 0.00 4.70
133 134 0.325933 CCCACAGAATCACAGAGGCA 59.674 55.000 0.00 0.00 0.00 4.75
134 135 1.678123 CCCACAGAATCACAGAGGCAG 60.678 57.143 0.00 0.00 0.00 4.85
135 136 1.002888 CCACAGAATCACAGAGGCAGT 59.997 52.381 0.00 0.00 0.00 4.40
136 137 2.074576 CACAGAATCACAGAGGCAGTG 58.925 52.381 0.00 0.00 38.32 3.66
137 138 1.002888 ACAGAATCACAGAGGCAGTGG 59.997 52.381 5.19 0.00 37.58 4.00
138 139 0.617413 AGAATCACAGAGGCAGTGGG 59.383 55.000 5.19 0.00 37.58 4.61
158 159 1.263217 GCACGGTGTGTTAAACAGAGG 59.737 52.381 10.24 0.00 40.26 3.69
159 160 2.828877 CACGGTGTGTTAAACAGAGGA 58.171 47.619 0.00 0.00 40.26 3.71
160 161 2.800544 CACGGTGTGTTAAACAGAGGAG 59.199 50.000 0.00 0.00 40.26 3.69
164 165 3.189287 GGTGTGTTAAACAGAGGAGCATG 59.811 47.826 0.00 0.00 40.26 4.06
191 192 1.268625 TGCACAAGAGTACACGACGAT 59.731 47.619 0.00 0.00 0.00 3.73
192 193 2.485038 TGCACAAGAGTACACGACGATA 59.515 45.455 0.00 0.00 0.00 2.92
195 196 5.163733 TGCACAAGAGTACACGACGATAATA 60.164 40.000 0.00 0.00 0.00 0.98
196 197 5.913514 GCACAAGAGTACACGACGATAATAT 59.086 40.000 0.00 0.00 0.00 1.28
197 198 6.086502 GCACAAGAGTACACGACGATAATATC 59.913 42.308 0.00 0.00 0.00 1.63
199 200 6.261603 ACAAGAGTACACGACGATAATATCCA 59.738 38.462 0.00 0.00 0.00 3.41
201 202 5.180868 AGAGTACACGACGATAATATCCACC 59.819 44.000 0.00 0.00 0.00 4.61
202 203 3.278367 ACACGACGATAATATCCACCG 57.722 47.619 0.00 0.00 0.00 4.94
213 214 0.106769 TATCCACCGGCATGCATGTT 60.107 50.000 26.79 7.42 0.00 2.71
227 228 2.224159 ATGTTGCCAGGGACGGACT 61.224 57.895 0.00 0.00 0.00 3.85
238 239 1.202604 GGGACGGACTTTCACAGTGAA 60.203 52.381 12.24 12.24 35.01 3.18
244 245 3.486875 CGGACTTTCACAGTGAAACAACC 60.487 47.826 22.53 21.26 41.02 3.77
247 248 5.059404 ACTTTCACAGTGAAACAACCAAG 57.941 39.130 22.53 14.28 41.02 3.61
254 255 6.071672 TCACAGTGAAACAACCAAGATCAAAA 60.072 34.615 0.00 0.00 41.43 2.44
272 273 2.606751 AAGACGGGAAGAGGAAGAGA 57.393 50.000 0.00 0.00 0.00 3.10
284 285 2.099098 GAGGAAGAGAGAGCGAAAGAGG 59.901 54.545 0.00 0.00 0.00 3.69
300 317 0.108567 GAGGGAGTGAAAGAGACGGC 60.109 60.000 0.00 0.00 0.00 5.68
305 322 1.006571 GTGAAAGAGACGGCCACGA 60.007 57.895 2.24 0.00 44.60 4.35
325 342 2.408022 GATCGTCCGGTCGACCAG 59.592 66.667 32.80 23.19 42.56 4.00
330 347 1.888018 GTCCGGTCGACCAGAATCA 59.112 57.895 32.80 4.01 35.23 2.57
333 350 1.067142 TCCGGTCGACCAGAATCAAAG 60.067 52.381 32.80 13.73 35.14 2.77
400 426 1.876416 CGGACTCCACGGACAAACATT 60.876 52.381 0.00 0.00 0.00 2.71
409 435 2.909965 ACAAACATTGGCGGGCGT 60.910 55.556 0.00 0.00 34.12 5.68
491 527 2.089349 GTGTCGAGCGTTCAGAGGC 61.089 63.158 0.00 0.00 36.93 4.70
513 549 1.299014 CCGCGTTTCAAGCAAAGCA 60.299 52.632 4.92 0.00 34.19 3.91
692 756 1.403679 CCGGTTTTCTGACAGCAACAA 59.596 47.619 15.37 0.00 0.00 2.83
774 1129 6.258068 CACGAGTCCTAAAATATTCTGAACCC 59.742 42.308 0.00 0.00 0.00 4.11
780 1135 7.780271 GTCCTAAAATATTCTGAACCCATTCCT 59.220 37.037 0.00 0.00 33.49 3.36
809 1164 4.660938 GTCCGGGCCCACTGCTTT 62.661 66.667 24.92 0.00 40.92 3.51
810 1165 2.931105 TCCGGGCCCACTGCTTTA 60.931 61.111 24.92 0.00 40.92 1.85
812 1167 3.124921 CGGGCCCACTGCTTTACG 61.125 66.667 24.92 0.00 40.92 3.18
813 1168 3.440415 GGGCCCACTGCTTTACGC 61.440 66.667 19.95 0.00 40.92 4.42
816 1171 3.124921 CCCACTGCTTTACGCCCG 61.125 66.667 0.00 0.00 38.05 6.13
817 1172 2.358247 CCACTGCTTTACGCCCGT 60.358 61.111 0.00 0.00 38.05 5.28
818 1173 1.964373 CCACTGCTTTACGCCCGTT 60.964 57.895 0.00 0.00 38.05 4.44
898 1274 0.471401 AGAATACCCCTCCCGGCTAC 60.471 60.000 0.00 0.00 0.00 3.58
905 1281 1.003233 CCCCTCCCGGCTACATAAATC 59.997 57.143 0.00 0.00 0.00 2.17
944 1337 4.202409 CCTTCTCTCAAGTCTCCAAAACCT 60.202 45.833 0.00 0.00 0.00 3.50
954 1352 0.112995 TCCAAAACCTGCAGCCATCT 59.887 50.000 8.66 0.00 0.00 2.90
991 1396 6.036577 GATTCCATCCACTCTAATCTCTCC 57.963 45.833 0.00 0.00 0.00 3.71
1149 1601 4.671590 TCCACCAGGAGCCGTCGA 62.672 66.667 0.00 0.00 39.61 4.20
1522 2054 9.979578 GCAAGATAGTAGAGTACTAGTACTACA 57.020 37.037 30.80 20.08 45.63 2.74
1544 2076 6.245408 ACAGTACATAGGAAAGAAATTGCCA 58.755 36.000 0.00 0.00 0.00 4.92
1655 2202 7.274250 GCGTTAATTGAGATTCAAGAAGCAAAT 59.726 33.333 0.63 0.00 40.05 2.32
1674 2221 5.798934 GCAAATCAATCACTGTTTGAGCTAG 59.201 40.000 8.22 0.00 37.77 3.42
1709 2256 6.075310 CGAATCACTCTGATTTACTTACTCGC 60.075 42.308 0.00 0.00 46.20 5.03
1724 2271 5.640357 ACTTACTCGCGATTTGGTGAATTTA 59.360 36.000 10.36 0.00 0.00 1.40
1731 2278 3.437395 CGATTTGGTGAATTTACGGGTCA 59.563 43.478 0.00 0.00 0.00 4.02
1783 2334 4.580868 TCTGCGTGTGGGTTTATTAATCA 58.419 39.130 0.00 0.00 0.00 2.57
1839 2390 1.578583 ACAAACAGTACAGCCACGAC 58.421 50.000 0.00 0.00 0.00 4.34
1870 2421 3.808728 TCAGGTTCAGAAGAAGTGGTTG 58.191 45.455 0.00 0.00 33.63 3.77
1894 5069 0.606401 CTGAGACGGTGTTGGCCAAT 60.606 55.000 23.66 4.47 0.00 3.16
1895 5070 0.179004 TGAGACGGTGTTGGCCAATT 60.179 50.000 23.66 3.73 0.00 2.32
1931 5106 1.105457 GGGCATTGCAGAGCACATAA 58.895 50.000 11.39 0.00 38.71 1.90
1948 7707 5.562696 GCACATAAGCTTGTTAGACTGCAAA 60.563 40.000 9.86 0.00 0.00 3.68
1952 7711 5.835113 AAGCTTGTTAGACTGCAAAGAAA 57.165 34.783 0.00 0.00 0.00 2.52
2008 7773 7.796838 TCGCATGTTAACTTTGCAGATATATC 58.203 34.615 24.19 4.42 36.15 1.63
2049 7815 4.729227 ATGATGCAACATTGATGCTTGA 57.271 36.364 18.17 8.17 44.14 3.02
2050 7816 4.522722 TGATGCAACATTGATGCTTGAA 57.477 36.364 18.17 0.39 44.14 2.69
2051 7817 4.884247 TGATGCAACATTGATGCTTGAAA 58.116 34.783 18.17 0.04 44.14 2.69
2053 7819 4.056092 TGCAACATTGATGCTTGAAACA 57.944 36.364 18.17 0.00 44.14 2.83
2054 7820 4.439968 TGCAACATTGATGCTTGAAACAA 58.560 34.783 18.17 0.00 44.14 2.83
2055 7821 4.874396 TGCAACATTGATGCTTGAAACAAA 59.126 33.333 18.17 0.00 44.14 2.83
2056 7822 5.353400 TGCAACATTGATGCTTGAAACAAAA 59.647 32.000 18.17 0.00 44.14 2.44
2057 7823 6.128090 TGCAACATTGATGCTTGAAACAAAAA 60.128 30.769 18.17 0.00 44.14 1.94
2059 7825 8.068977 GCAACATTGATGCTTGAAACAAAAATA 58.931 29.630 11.27 0.00 40.64 1.40
2064 7830 9.941325 ATTGATGCTTGAAACAAAAATATACCA 57.059 25.926 0.00 0.00 0.00 3.25
2069 7835 7.014711 TGCTTGAAACAAAAATATACCAGGTCA 59.985 33.333 0.00 0.00 0.00 4.02
2079 7845 2.945447 TACCAGGTCATCGGTTAACG 57.055 50.000 0.00 0.00 46.11 3.18
2093 7865 4.739716 TCGGTTAACGTACAAGAAGTTCAC 59.260 41.667 5.50 0.00 44.69 3.18
2109 7893 5.091261 AGTTCACCTGCTAAATAGACCAG 57.909 43.478 0.00 0.00 0.00 4.00
2111 7895 2.170607 TCACCTGCTAAATAGACCAGGC 59.829 50.000 11.72 0.00 33.41 4.85
2122 7906 0.106819 AGACCAGGCCAATGCATCTC 60.107 55.000 5.01 0.00 40.13 2.75
2130 7914 3.019564 GGCCAATGCATCTCTACAAGTT 58.980 45.455 0.00 0.00 40.13 2.66
2132 7916 3.691118 GCCAATGCATCTCTACAAGTTCA 59.309 43.478 0.00 0.00 37.47 3.18
2138 7922 6.732531 TGCATCTCTACAAGTTCAGAAATG 57.267 37.500 0.00 0.00 0.00 2.32
2159 7943 3.004524 TGAAACGGTCAAATTAAACCCCG 59.995 43.478 0.00 0.00 41.09 5.73
2168 7952 6.238703 GGTCAAATTAAACCCCGCGATATTTA 60.239 38.462 8.23 6.11 0.00 1.40
2169 7953 6.854381 GTCAAATTAAACCCCGCGATATTTAG 59.146 38.462 8.23 0.00 0.00 1.85
2174 7958 2.968675 ACCCCGCGATATTTAGTATGC 58.031 47.619 8.23 0.00 0.00 3.14
2192 7976 4.751767 ATGCCAAGTTGGTTCTTGAAAA 57.248 36.364 22.85 0.00 45.11 2.29
2259 8205 1.746615 CGAGTTGGGTGGCTCATGG 60.747 63.158 0.00 0.00 0.00 3.66
2346 8292 6.589907 GCAAAATCATCTTTTAACACGGGATT 59.410 34.615 0.00 0.00 0.00 3.01
2357 8312 2.795329 ACACGGGATTGAGATGCTTTT 58.205 42.857 0.00 0.00 0.00 2.27
2358 8313 3.157087 ACACGGGATTGAGATGCTTTTT 58.843 40.909 0.00 0.00 0.00 1.94
2359 8314 3.191371 ACACGGGATTGAGATGCTTTTTC 59.809 43.478 0.00 0.00 0.00 2.29
2384 8339 0.318441 TTCCAGTGAGCTTCTCGGTG 59.682 55.000 0.00 0.00 32.35 4.94
2385 8340 0.539669 TCCAGTGAGCTTCTCGGTGA 60.540 55.000 0.00 0.00 32.35 4.02
2386 8341 0.108898 CCAGTGAGCTTCTCGGTGAG 60.109 60.000 0.00 0.00 32.35 3.51
2387 8342 0.108898 CAGTGAGCTTCTCGGTGAGG 60.109 60.000 0.00 0.00 32.35 3.86
2388 8343 1.216710 GTGAGCTTCTCGGTGAGGG 59.783 63.158 0.00 0.00 32.35 4.30
2389 8344 2.185608 GAGCTTCTCGGTGAGGGC 59.814 66.667 0.00 0.14 32.51 5.19
2390 8345 3.378399 GAGCTTCTCGGTGAGGGCC 62.378 68.421 0.00 0.00 32.65 5.80
2391 8346 3.394836 GCTTCTCGGTGAGGGCCT 61.395 66.667 5.25 5.25 0.00 5.19
2392 8347 2.896443 CTTCTCGGTGAGGGCCTC 59.104 66.667 26.95 26.95 0.00 4.70
2393 8348 1.684049 CTTCTCGGTGAGGGCCTCT 60.684 63.158 32.28 0.00 0.00 3.69
2394 8349 1.229209 TTCTCGGTGAGGGCCTCTT 60.229 57.895 32.28 0.00 0.00 2.85
2395 8350 0.836400 TTCTCGGTGAGGGCCTCTTT 60.836 55.000 32.28 0.00 0.00 2.52
2396 8351 1.078848 CTCGGTGAGGGCCTCTTTG 60.079 63.158 32.28 21.13 0.00 2.77
2397 8352 1.535444 TCGGTGAGGGCCTCTTTGA 60.535 57.895 32.28 22.88 0.00 2.69
2398 8353 0.909610 TCGGTGAGGGCCTCTTTGAT 60.910 55.000 32.28 0.00 0.00 2.57
2399 8354 0.035056 CGGTGAGGGCCTCTTTGATT 60.035 55.000 32.28 0.00 0.00 2.57
2400 8355 1.756430 GGTGAGGGCCTCTTTGATTC 58.244 55.000 32.28 13.96 0.00 2.52
2401 8356 1.373570 GTGAGGGCCTCTTTGATTCG 58.626 55.000 32.28 0.00 0.00 3.34
2402 8357 0.984230 TGAGGGCCTCTTTGATTCGT 59.016 50.000 32.28 0.00 0.00 3.85
2403 8358 2.093658 GTGAGGGCCTCTTTGATTCGTA 60.094 50.000 32.28 6.95 0.00 3.43
2404 8359 2.569853 TGAGGGCCTCTTTGATTCGTAA 59.430 45.455 32.28 6.40 0.00 3.18
2405 8360 3.198872 GAGGGCCTCTTTGATTCGTAAG 58.801 50.000 26.44 0.00 0.00 2.34
2421 8376 5.309323 TCGTAAGATTTCCAAAATGCAGG 57.691 39.130 0.00 0.00 45.01 4.85
2422 8377 5.007034 TCGTAAGATTTCCAAAATGCAGGA 58.993 37.500 0.00 0.00 45.01 3.86
2423 8378 5.475220 TCGTAAGATTTCCAAAATGCAGGAA 59.525 36.000 1.16 1.16 45.01 3.36
2424 8379 6.152661 TCGTAAGATTTCCAAAATGCAGGAAT 59.847 34.615 6.02 0.00 42.09 3.01
2425 8380 7.338196 TCGTAAGATTTCCAAAATGCAGGAATA 59.662 33.333 6.02 0.00 42.09 1.75
2426 8381 7.645340 CGTAAGATTTCCAAAATGCAGGAATAG 59.355 37.037 6.02 0.00 41.29 1.73
2427 8382 6.475596 AGATTTCCAAAATGCAGGAATAGG 57.524 37.500 6.02 0.00 43.02 2.57
2428 8383 6.197168 AGATTTCCAAAATGCAGGAATAGGA 58.803 36.000 6.02 0.00 43.02 2.94
2429 8384 6.669154 AGATTTCCAAAATGCAGGAATAGGAA 59.331 34.615 6.02 5.25 43.02 3.36
2430 8385 6.678568 TTTCCAAAATGCAGGAATAGGAAA 57.321 33.333 13.50 13.50 43.02 3.13
2431 8386 6.678568 TTCCAAAATGCAGGAATAGGAAAA 57.321 33.333 1.16 0.00 38.91 2.29
2432 8387 6.678568 TCCAAAATGCAGGAATAGGAAAAA 57.321 33.333 0.00 0.00 0.00 1.94
2433 8388 7.256494 TCCAAAATGCAGGAATAGGAAAAAT 57.744 32.000 0.00 0.00 0.00 1.82
2434 8389 7.104939 TCCAAAATGCAGGAATAGGAAAAATG 58.895 34.615 0.00 0.00 0.00 2.32
2435 8390 6.880529 CCAAAATGCAGGAATAGGAAAAATGT 59.119 34.615 0.00 0.00 0.00 2.71
2436 8391 7.148373 CCAAAATGCAGGAATAGGAAAAATGTG 60.148 37.037 0.00 0.00 0.00 3.21
2437 8392 6.855763 AATGCAGGAATAGGAAAAATGTGA 57.144 33.333 0.00 0.00 0.00 3.58
2438 8393 6.855763 ATGCAGGAATAGGAAAAATGTGAA 57.144 33.333 0.00 0.00 0.00 3.18
2439 8394 6.662865 TGCAGGAATAGGAAAAATGTGAAA 57.337 33.333 0.00 0.00 0.00 2.69
2440 8395 7.243604 TGCAGGAATAGGAAAAATGTGAAAT 57.756 32.000 0.00 0.00 0.00 2.17
2441 8396 7.678837 TGCAGGAATAGGAAAAATGTGAAATT 58.321 30.769 0.00 0.00 0.00 1.82
2442 8397 8.811017 TGCAGGAATAGGAAAAATGTGAAATTA 58.189 29.630 0.00 0.00 0.00 1.40
2443 8398 9.305925 GCAGGAATAGGAAAAATGTGAAATTAG 57.694 33.333 0.00 0.00 0.00 1.73
2449 8404 6.691508 AGGAAAAATGTGAAATTAGAGTGGC 58.308 36.000 0.00 0.00 0.00 5.01
2450 8405 6.267471 AGGAAAAATGTGAAATTAGAGTGGCA 59.733 34.615 0.00 0.00 0.00 4.92
2451 8406 7.038799 AGGAAAAATGTGAAATTAGAGTGGCAT 60.039 33.333 0.00 0.00 0.00 4.40
2452 8407 7.063780 GGAAAAATGTGAAATTAGAGTGGCATG 59.936 37.037 0.00 0.00 0.00 4.06
2453 8408 6.594788 AAATGTGAAATTAGAGTGGCATGT 57.405 33.333 0.00 0.00 0.00 3.21
2454 8409 5.824904 ATGTGAAATTAGAGTGGCATGTC 57.175 39.130 0.00 0.00 0.00 3.06
2455 8410 3.684305 TGTGAAATTAGAGTGGCATGTCG 59.316 43.478 0.00 0.00 0.00 4.35
2456 8411 3.684788 GTGAAATTAGAGTGGCATGTCGT 59.315 43.478 0.00 0.00 0.00 4.34
2457 8412 3.932710 TGAAATTAGAGTGGCATGTCGTC 59.067 43.478 0.00 0.00 0.00 4.20
2458 8413 3.895232 AATTAGAGTGGCATGTCGTCT 57.105 42.857 7.14 7.14 0.00 4.18
2459 8414 3.895232 ATTAGAGTGGCATGTCGTCTT 57.105 42.857 7.26 0.00 0.00 3.01
2460 8415 2.654749 TAGAGTGGCATGTCGTCTTG 57.345 50.000 7.26 0.00 0.00 3.02
2461 8416 0.969149 AGAGTGGCATGTCGTCTTGA 59.031 50.000 0.00 0.00 0.00 3.02
2462 8417 1.344438 AGAGTGGCATGTCGTCTTGAA 59.656 47.619 0.00 0.00 0.00 2.69
2463 8418 2.027745 AGAGTGGCATGTCGTCTTGAAT 60.028 45.455 0.00 0.00 0.00 2.57
2464 8419 2.349886 GAGTGGCATGTCGTCTTGAATC 59.650 50.000 0.00 0.00 0.00 2.52
2465 8420 1.398390 GTGGCATGTCGTCTTGAATCC 59.602 52.381 0.00 0.00 0.00 3.01
2466 8421 1.278985 TGGCATGTCGTCTTGAATCCT 59.721 47.619 0.00 0.00 0.00 3.24
2467 8422 2.499693 TGGCATGTCGTCTTGAATCCTA 59.500 45.455 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.868997 CACTGTTCATGTCACGGCC 59.131 57.895 0.00 0.00 0.00 6.13
1 2 1.207593 GCACTGTTCATGTCACGGC 59.792 57.895 6.55 2.80 0.00 5.68
2 3 0.514255 CAGCACTGTTCATGTCACGG 59.486 55.000 0.00 0.00 0.00 4.94
3 4 1.220529 ACAGCACTGTTCATGTCACG 58.779 50.000 0.00 0.00 41.83 4.35
24 25 6.712095 CCCATATGCAGATCTAGTGCTAAAAA 59.288 38.462 6.93 0.00 41.78 1.94
25 26 6.183361 ACCCATATGCAGATCTAGTGCTAAAA 60.183 38.462 6.93 0.00 41.78 1.52
26 27 5.307976 ACCCATATGCAGATCTAGTGCTAAA 59.692 40.000 6.93 0.00 41.78 1.85
27 28 4.840680 ACCCATATGCAGATCTAGTGCTAA 59.159 41.667 6.93 0.00 41.78 3.09
28 29 4.420206 ACCCATATGCAGATCTAGTGCTA 58.580 43.478 6.93 0.00 41.78 3.49
29 30 3.246301 ACCCATATGCAGATCTAGTGCT 58.754 45.455 6.93 0.00 41.78 4.40
30 31 3.692257 ACCCATATGCAGATCTAGTGC 57.308 47.619 0.00 0.00 41.59 4.40
31 32 5.219343 TCAACCCATATGCAGATCTAGTG 57.781 43.478 0.00 0.00 0.00 2.74
32 33 5.894298 TTCAACCCATATGCAGATCTAGT 57.106 39.130 0.00 0.00 0.00 2.57
33 34 7.572523 TTTTTCAACCCATATGCAGATCTAG 57.427 36.000 0.00 0.00 0.00 2.43
54 55 3.086282 ACAGTTCTGGTGTTCCGTTTTT 58.914 40.909 4.82 0.00 36.30 1.94
55 56 2.681344 GACAGTTCTGGTGTTCCGTTTT 59.319 45.455 4.82 0.00 36.30 2.43
56 57 2.285977 GACAGTTCTGGTGTTCCGTTT 58.714 47.619 4.82 0.00 36.30 3.60
57 58 1.474498 GGACAGTTCTGGTGTTCCGTT 60.474 52.381 4.82 0.00 36.30 4.44
58 59 0.106149 GGACAGTTCTGGTGTTCCGT 59.894 55.000 4.82 0.00 36.30 4.69
59 60 0.393077 AGGACAGTTCTGGTGTTCCG 59.607 55.000 4.82 0.00 36.30 4.30
60 61 2.640316 AAGGACAGTTCTGGTGTTCC 57.360 50.000 4.82 2.55 0.00 3.62
61 62 4.511826 CAGTAAAGGACAGTTCTGGTGTTC 59.488 45.833 4.82 0.00 0.00 3.18
62 63 4.451900 CAGTAAAGGACAGTTCTGGTGTT 58.548 43.478 4.82 0.00 0.00 3.32
63 64 3.744530 GCAGTAAAGGACAGTTCTGGTGT 60.745 47.826 4.82 0.00 0.00 4.16
64 65 2.808543 GCAGTAAAGGACAGTTCTGGTG 59.191 50.000 4.82 0.00 0.00 4.17
65 66 2.548067 CGCAGTAAAGGACAGTTCTGGT 60.548 50.000 4.82 0.00 0.00 4.00
66 67 2.069273 CGCAGTAAAGGACAGTTCTGG 58.931 52.381 4.82 0.00 0.00 3.86
67 68 2.755650 ACGCAGTAAAGGACAGTTCTG 58.244 47.619 0.00 0.00 41.94 3.02
68 69 3.131396 CAACGCAGTAAAGGACAGTTCT 58.869 45.455 0.00 0.00 45.00 3.01
69 70 2.870411 ACAACGCAGTAAAGGACAGTTC 59.130 45.455 0.00 0.00 45.00 3.01
70 71 2.870411 GACAACGCAGTAAAGGACAGTT 59.130 45.455 0.00 0.00 45.00 3.16
71 72 2.159014 TGACAACGCAGTAAAGGACAGT 60.159 45.455 0.00 0.00 45.00 3.55
72 73 2.476619 CTGACAACGCAGTAAAGGACAG 59.523 50.000 0.00 0.00 45.00 3.51
73 74 2.159014 ACTGACAACGCAGTAAAGGACA 60.159 45.455 0.00 0.00 46.67 4.02
74 75 2.221055 CACTGACAACGCAGTAAAGGAC 59.779 50.000 0.00 0.00 46.80 3.85
75 76 2.479837 CACTGACAACGCAGTAAAGGA 58.520 47.619 0.00 0.00 46.80 3.36
76 77 1.531149 CCACTGACAACGCAGTAAAGG 59.469 52.381 0.00 0.00 46.80 3.11
77 78 1.069906 GCCACTGACAACGCAGTAAAG 60.070 52.381 0.00 0.00 46.80 1.85
78 79 0.941542 GCCACTGACAACGCAGTAAA 59.058 50.000 0.00 0.00 46.80 2.01
79 80 0.105964 AGCCACTGACAACGCAGTAA 59.894 50.000 0.00 0.00 46.80 2.24
80 81 0.599991 CAGCCACTGACAACGCAGTA 60.600 55.000 0.00 0.00 46.80 2.74
82 83 2.610694 CCAGCCACTGACAACGCAG 61.611 63.158 0.00 0.00 41.63 5.18
83 84 2.395988 ATCCAGCCACTGACAACGCA 62.396 55.000 0.00 0.00 32.44 5.24
84 85 1.237285 AATCCAGCCACTGACAACGC 61.237 55.000 0.00 0.00 32.44 4.84
85 86 0.518636 CAATCCAGCCACTGACAACG 59.481 55.000 0.00 0.00 32.44 4.10
86 87 0.242017 GCAATCCAGCCACTGACAAC 59.758 55.000 0.00 0.00 32.44 3.32
87 88 0.111061 AGCAATCCAGCCACTGACAA 59.889 50.000 0.00 0.00 32.44 3.18
88 89 0.607217 CAGCAATCCAGCCACTGACA 60.607 55.000 0.00 0.00 32.44 3.58
89 90 0.321919 TCAGCAATCCAGCCACTGAC 60.322 55.000 0.00 0.00 32.65 3.51
90 91 0.622136 ATCAGCAATCCAGCCACTGA 59.378 50.000 0.00 0.00 41.28 3.41
91 92 1.471119 AATCAGCAATCCAGCCACTG 58.529 50.000 0.00 0.00 34.23 3.66
92 93 3.220110 CATAATCAGCAATCCAGCCACT 58.780 45.455 0.00 0.00 34.23 4.00
93 94 2.288030 GCATAATCAGCAATCCAGCCAC 60.288 50.000 0.00 0.00 34.23 5.01
94 95 1.958579 GCATAATCAGCAATCCAGCCA 59.041 47.619 0.00 0.00 34.23 4.75
95 96 1.271656 GGCATAATCAGCAATCCAGCC 59.728 52.381 0.00 0.00 34.23 4.85
96 97 1.271656 GGGCATAATCAGCAATCCAGC 59.728 52.381 0.00 0.00 0.00 4.85
97 98 2.295349 GTGGGCATAATCAGCAATCCAG 59.705 50.000 0.00 0.00 0.00 3.86
98 99 2.309613 GTGGGCATAATCAGCAATCCA 58.690 47.619 0.00 0.00 0.00 3.41
99 100 2.295349 CTGTGGGCATAATCAGCAATCC 59.705 50.000 0.00 0.00 0.00 3.01
100 101 3.216800 TCTGTGGGCATAATCAGCAATC 58.783 45.455 0.00 0.00 0.00 2.67
101 102 3.301794 TCTGTGGGCATAATCAGCAAT 57.698 42.857 0.00 0.00 0.00 3.56
102 103 2.804986 TCTGTGGGCATAATCAGCAA 57.195 45.000 0.00 0.00 0.00 3.91
103 104 2.804986 TTCTGTGGGCATAATCAGCA 57.195 45.000 0.00 0.00 0.00 4.41
104 105 3.004106 GTGATTCTGTGGGCATAATCAGC 59.996 47.826 8.11 0.00 43.84 4.26
105 106 4.201657 TGTGATTCTGTGGGCATAATCAG 58.798 43.478 8.11 0.00 43.84 2.90
106 107 4.080413 TCTGTGATTCTGTGGGCATAATCA 60.080 41.667 4.89 4.89 42.24 2.57
107 108 4.454678 TCTGTGATTCTGTGGGCATAATC 58.545 43.478 0.00 0.00 38.16 1.75
108 109 4.458397 CTCTGTGATTCTGTGGGCATAAT 58.542 43.478 0.00 0.00 0.00 1.28
109 110 3.370846 CCTCTGTGATTCTGTGGGCATAA 60.371 47.826 0.00 0.00 0.00 1.90
110 111 2.171237 CCTCTGTGATTCTGTGGGCATA 59.829 50.000 0.00 0.00 0.00 3.14
111 112 1.064906 CCTCTGTGATTCTGTGGGCAT 60.065 52.381 0.00 0.00 0.00 4.40
112 113 0.325933 CCTCTGTGATTCTGTGGGCA 59.674 55.000 0.00 0.00 0.00 5.36
113 114 1.028868 GCCTCTGTGATTCTGTGGGC 61.029 60.000 0.00 0.00 32.02 5.36
114 115 0.325933 TGCCTCTGTGATTCTGTGGG 59.674 55.000 0.00 0.00 32.02 4.61
115 116 1.002888 ACTGCCTCTGTGATTCTGTGG 59.997 52.381 0.00 0.00 33.68 4.17
116 117 2.074576 CACTGCCTCTGTGATTCTGTG 58.925 52.381 0.00 0.00 35.76 3.66
117 118 1.002888 CCACTGCCTCTGTGATTCTGT 59.997 52.381 5.58 0.00 35.76 3.41
118 119 1.678123 CCCACTGCCTCTGTGATTCTG 60.678 57.143 5.58 0.00 35.76 3.02
119 120 0.617413 CCCACTGCCTCTGTGATTCT 59.383 55.000 5.58 0.00 35.76 2.40
120 121 1.028868 GCCCACTGCCTCTGTGATTC 61.029 60.000 5.58 0.00 35.76 2.52
121 122 1.001641 GCCCACTGCCTCTGTGATT 60.002 57.895 5.58 0.00 35.76 2.57
122 123 2.226315 TGCCCACTGCCTCTGTGAT 61.226 57.895 5.58 0.00 40.16 3.06
123 124 2.848679 TGCCCACTGCCTCTGTGA 60.849 61.111 5.58 0.00 40.16 3.58
124 125 2.670934 GTGCCCACTGCCTCTGTG 60.671 66.667 0.00 0.00 40.16 3.66
125 126 4.320456 CGTGCCCACTGCCTCTGT 62.320 66.667 0.00 0.00 40.16 3.41
132 133 0.816018 TTAACACACCGTGCCCACTG 60.816 55.000 0.00 0.00 36.98 3.66
133 134 0.107116 TTTAACACACCGTGCCCACT 60.107 50.000 0.00 0.00 36.98 4.00
134 135 0.029700 GTTTAACACACCGTGCCCAC 59.970 55.000 0.00 0.00 36.98 4.61
135 136 0.393944 TGTTTAACACACCGTGCCCA 60.394 50.000 0.00 0.00 36.98 5.36
136 137 0.309612 CTGTTTAACACACCGTGCCC 59.690 55.000 0.00 0.00 36.98 5.36
137 138 1.263217 CTCTGTTTAACACACCGTGCC 59.737 52.381 0.00 0.00 36.98 5.01
138 139 1.263217 CCTCTGTTTAACACACCGTGC 59.737 52.381 0.00 0.00 36.98 5.34
178 179 5.388944 GGTGGATATTATCGTCGTGTACTC 58.611 45.833 0.00 0.00 0.00 2.59
191 192 2.224744 ACATGCATGCCGGTGGATATTA 60.225 45.455 26.53 0.00 0.00 0.98
192 193 1.250328 CATGCATGCCGGTGGATATT 58.750 50.000 14.93 0.00 0.00 1.28
195 196 1.380246 AACATGCATGCCGGTGGAT 60.380 52.632 26.53 1.08 0.00 3.41
196 197 2.035469 AACATGCATGCCGGTGGA 59.965 55.556 26.53 0.00 0.00 4.02
197 198 2.182284 CAACATGCATGCCGGTGG 59.818 61.111 26.53 7.04 0.00 4.61
213 214 2.144078 TGAAAGTCCGTCCCTGGCA 61.144 57.895 0.00 0.00 0.00 4.92
227 228 5.417266 TGATCTTGGTTGTTTCACTGTGAAA 59.583 36.000 27.14 27.14 43.37 2.69
238 239 3.317993 CCCGTCTTTTGATCTTGGTTGTT 59.682 43.478 0.00 0.00 0.00 2.83
244 245 3.686726 CCTCTTCCCGTCTTTTGATCTTG 59.313 47.826 0.00 0.00 0.00 3.02
247 248 3.611766 TCCTCTTCCCGTCTTTTGATC 57.388 47.619 0.00 0.00 0.00 2.92
254 255 1.636519 TCTCTCTTCCTCTTCCCGTCT 59.363 52.381 0.00 0.00 0.00 4.18
272 273 1.633774 TTCACTCCCTCTTTCGCTCT 58.366 50.000 0.00 0.00 0.00 4.09
284 285 0.670854 GTGGCCGTCTCTTTCACTCC 60.671 60.000 0.00 0.00 0.00 3.85
391 413 2.126502 CGCCCGCCAATGTTTGTC 60.127 61.111 0.00 0.00 0.00 3.18
394 416 2.596046 TCACGCCCGCCAATGTTT 60.596 55.556 0.00 0.00 0.00 2.83
400 426 4.980805 GTTCACTCACGCCCGCCA 62.981 66.667 0.00 0.00 0.00 5.69
409 435 1.014044 GCGCCGAATCTGTTCACTCA 61.014 55.000 0.00 0.00 33.86 3.41
463 493 2.880879 CTCGACACACCGGCATCG 60.881 66.667 0.00 6.10 35.91 3.84
464 494 3.188786 GCTCGACACACCGGCATC 61.189 66.667 0.00 0.00 0.00 3.91
471 507 1.004277 CCTCTGAACGCTCGACACAC 61.004 60.000 0.00 0.00 0.00 3.82
576 628 4.410400 AGGTTGGCACGGCTAGGC 62.410 66.667 6.15 6.15 0.00 3.93
582 638 4.619227 ACGGTCAGGTTGGCACGG 62.619 66.667 0.00 0.00 0.00 4.94
598 654 4.803426 CGGAGCGAGGCAGGTGAC 62.803 72.222 0.00 0.00 0.00 3.67
692 756 4.457496 CTGTGCCCATCCGACGCT 62.457 66.667 0.00 0.00 0.00 5.07
724 840 9.118300 TGCCAACTTGTTTTGAATATTTTGATT 57.882 25.926 0.00 0.00 0.00 2.57
740 1059 1.045407 TAGGACTCGTGCCAACTTGT 58.955 50.000 0.00 0.00 0.00 3.16
774 1129 0.391661 ACGGCTAGCACACAGGAATG 60.392 55.000 18.24 0.00 0.00 2.67
780 1135 4.063967 CCGGACGGCTAGCACACA 62.064 66.667 18.24 0.00 0.00 3.72
807 1162 2.637947 GGGGTTAATAACGGGCGTAAA 58.362 47.619 0.00 0.00 0.00 2.01
808 1163 1.472376 CGGGGTTAATAACGGGCGTAA 60.472 52.381 0.00 0.00 0.00 3.18
809 1164 0.103937 CGGGGTTAATAACGGGCGTA 59.896 55.000 0.00 0.00 0.00 4.42
810 1165 1.153389 CGGGGTTAATAACGGGCGT 60.153 57.895 0.00 0.00 0.00 5.68
812 1167 4.146058 CCGGGGTTAATAACGGGC 57.854 61.111 0.00 0.00 42.48 6.13
816 1171 8.879759 GTTAACTAACTAACCGGGGTTAATAAC 58.120 37.037 6.32 16.94 39.69 1.89
817 1172 8.044309 GGTTAACTAACTAACCGGGGTTAATAA 58.956 37.037 6.32 10.85 41.03 1.40
818 1173 7.561251 GGTTAACTAACTAACCGGGGTTAATA 58.439 38.462 6.32 7.05 41.03 0.98
898 1274 1.452145 CGGGTTGGGCGGGATTTATG 61.452 60.000 0.00 0.00 0.00 1.90
944 1337 4.166888 GCGGAGGAGATGGCTGCA 62.167 66.667 0.50 0.00 34.49 4.41
982 1380 4.021632 CGCCATGAGAGATTGGAGAGATTA 60.022 45.833 0.00 0.00 35.07 1.75
983 1381 3.244146 CGCCATGAGAGATTGGAGAGATT 60.244 47.826 0.00 0.00 35.07 2.40
984 1382 2.299582 CGCCATGAGAGATTGGAGAGAT 59.700 50.000 0.00 0.00 35.07 2.75
991 1396 1.493950 GCCGTCGCCATGAGAGATTG 61.494 60.000 0.00 0.00 0.00 2.67
1149 1601 1.530771 GGAGCACATGCAGGAGGAT 59.469 57.895 4.84 0.00 45.16 3.24
1305 1793 3.785859 GGGATGAGCCACGCCAGA 61.786 66.667 0.00 0.00 38.95 3.86
1522 2054 6.721318 TCTGGCAATTTCTTTCCTATGTACT 58.279 36.000 0.00 0.00 0.00 2.73
1523 2055 7.336931 TCTTCTGGCAATTTCTTTCCTATGTAC 59.663 37.037 0.00 0.00 0.00 2.90
1524 2056 7.402054 TCTTCTGGCAATTTCTTTCCTATGTA 58.598 34.615 0.00 0.00 0.00 2.29
1525 2057 6.248433 TCTTCTGGCAATTTCTTTCCTATGT 58.752 36.000 0.00 0.00 0.00 2.29
1526 2058 6.764308 TCTTCTGGCAATTTCTTTCCTATG 57.236 37.500 0.00 0.00 0.00 2.23
1544 2076 8.533569 TTGGTTCTAAAAACTCCAATTCTTCT 57.466 30.769 0.00 0.00 33.95 2.85
1619 2166 3.693578 TCTCAATTAACGCCATTCATGCA 59.306 39.130 0.00 0.00 0.00 3.96
1655 2202 2.995939 CGCTAGCTCAAACAGTGATTGA 59.004 45.455 13.93 14.34 35.07 2.57
1674 2221 3.046390 CAGAGTGATTCGAAGTATCCGC 58.954 50.000 3.35 0.00 0.00 5.54
1709 2256 3.437395 TGACCCGTAAATTCACCAAATCG 59.563 43.478 0.00 0.00 0.00 3.34
1758 2305 2.851263 ATAAACCCACACGCAGAGAA 57.149 45.000 0.00 0.00 0.00 2.87
1783 2334 6.473758 GTCAGTTTTACCTCCTCCAAATACT 58.526 40.000 0.00 0.00 0.00 2.12
1839 2390 1.572085 CTGAACCTGAACTGCCTGCG 61.572 60.000 0.00 0.00 0.00 5.18
1870 2421 1.374758 CAACACCGTCTCAGGAGGC 60.375 63.158 0.00 0.00 34.73 4.70
1894 5069 2.289569 GCCCCAGCATCAACATTTTCAA 60.290 45.455 0.00 0.00 39.53 2.69
1895 5070 1.275856 GCCCCAGCATCAACATTTTCA 59.724 47.619 0.00 0.00 39.53 2.69
1931 5106 5.835113 TTTTCTTTGCAGTCTAACAAGCT 57.165 34.783 0.00 0.00 0.00 3.74
1948 7707 1.076024 TGGGCAAGCAGGAGATTTTCT 59.924 47.619 0.00 0.00 0.00 2.52
1952 7711 0.324091 CCTTGGGCAAGCAGGAGATT 60.324 55.000 0.00 0.00 37.11 2.40
1972 7737 0.036388 AACATGCGAGTACCCAGGTG 60.036 55.000 0.00 0.00 0.00 4.00
1980 7745 4.311606 TCTGCAAAGTTAACATGCGAGTA 58.688 39.130 23.11 10.91 42.91 2.59
2008 7773 8.385111 GCATCATTGGTTCATTAACAATTGAAG 58.615 33.333 13.59 0.00 34.31 3.02
2016 7781 7.457868 CAATGTTGCATCATTGGTTCATTAAC 58.542 34.615 30.39 5.08 46.08 2.01
2044 7810 7.375053 TGACCTGGTATATTTTTGTTTCAAGC 58.625 34.615 0.00 0.00 0.00 4.01
2049 7815 6.661805 ACCGATGACCTGGTATATTTTTGTTT 59.338 34.615 0.00 0.00 36.50 2.83
2050 7816 6.184789 ACCGATGACCTGGTATATTTTTGTT 58.815 36.000 0.00 0.00 36.50 2.83
2051 7817 5.751586 ACCGATGACCTGGTATATTTTTGT 58.248 37.500 0.00 0.00 36.50 2.83
2053 7819 7.011669 CGTTAACCGATGACCTGGTATATTTTT 59.988 37.037 0.00 0.00 37.54 1.94
2054 7820 6.480981 CGTTAACCGATGACCTGGTATATTTT 59.519 38.462 0.00 0.00 37.54 1.82
2055 7821 5.987347 CGTTAACCGATGACCTGGTATATTT 59.013 40.000 0.00 0.00 37.54 1.40
2056 7822 5.069516 ACGTTAACCGATGACCTGGTATATT 59.930 40.000 0.00 0.00 37.54 1.28
2057 7823 4.586001 ACGTTAACCGATGACCTGGTATAT 59.414 41.667 0.00 0.00 37.54 0.86
2059 7825 2.762327 ACGTTAACCGATGACCTGGTAT 59.238 45.455 0.00 0.00 37.54 2.73
2060 7826 2.170166 ACGTTAACCGATGACCTGGTA 58.830 47.619 0.00 0.00 37.54 3.25
2061 7827 0.971386 ACGTTAACCGATGACCTGGT 59.029 50.000 0.00 0.00 41.20 4.00
2062 7828 2.094597 TGTACGTTAACCGATGACCTGG 60.095 50.000 0.00 0.00 40.70 4.45
2064 7830 3.507233 TCTTGTACGTTAACCGATGACCT 59.493 43.478 0.00 0.00 40.70 3.85
2069 7835 5.403466 GTGAACTTCTTGTACGTTAACCGAT 59.597 40.000 0.00 0.00 40.70 4.18
2079 7845 6.803154 ATTTAGCAGGTGAACTTCTTGTAC 57.197 37.500 0.00 0.00 0.00 2.90
2109 7893 2.648059 ACTTGTAGAGATGCATTGGCC 58.352 47.619 0.00 0.00 40.13 5.36
2111 7895 5.181009 TCTGAACTTGTAGAGATGCATTGG 58.819 41.667 0.00 0.00 0.00 3.16
2122 7906 6.018262 TGACCGTTTCATTTCTGAACTTGTAG 60.018 38.462 0.00 0.00 41.05 2.74
2130 7914 7.650104 GGTTTAATTTGACCGTTTCATTTCTGA 59.350 33.333 0.00 0.00 32.84 3.27
2132 7916 6.926826 GGGTTTAATTTGACCGTTTCATTTCT 59.073 34.615 4.43 0.00 36.78 2.52
2138 7922 3.567530 CGGGGTTTAATTTGACCGTTTC 58.432 45.455 0.00 0.00 36.78 2.78
2159 7943 5.238650 ACCAACTTGGCATACTAAATATCGC 59.761 40.000 7.81 0.00 42.67 4.58
2168 7952 4.098914 TCAAGAACCAACTTGGCATACT 57.901 40.909 7.81 0.03 42.67 2.12
2169 7953 4.846779 TTCAAGAACCAACTTGGCATAC 57.153 40.909 7.81 0.00 42.67 2.39
2219 8165 5.753713 GACGGATCGACAAATCTCATATG 57.246 43.478 0.00 0.00 0.00 1.78
2346 8292 6.322201 ACTGGAAAAGAAGAAAAAGCATCTCA 59.678 34.615 0.00 0.00 0.00 3.27
2357 8312 5.041191 AGAAGCTCACTGGAAAAGAAGAA 57.959 39.130 0.00 0.00 0.00 2.52
2358 8313 4.636249 GAGAAGCTCACTGGAAAAGAAGA 58.364 43.478 0.00 0.00 0.00 2.87
2359 8314 3.431572 CGAGAAGCTCACTGGAAAAGAAG 59.568 47.826 0.00 0.00 0.00 2.85
2384 8339 2.981859 TACGAATCAAAGAGGCCCTC 57.018 50.000 1.26 1.26 0.00 4.30
2385 8340 2.838202 TCTTACGAATCAAAGAGGCCCT 59.162 45.455 0.00 0.00 0.00 5.19
2386 8341 3.261981 TCTTACGAATCAAAGAGGCCC 57.738 47.619 0.00 0.00 0.00 5.80
2387 8342 5.220873 GGAAATCTTACGAATCAAAGAGGCC 60.221 44.000 0.00 0.00 35.32 5.19
2388 8343 5.354234 TGGAAATCTTACGAATCAAAGAGGC 59.646 40.000 0.00 0.00 35.32 4.70
2389 8344 6.985188 TGGAAATCTTACGAATCAAAGAGG 57.015 37.500 0.00 0.00 35.32 3.69
2390 8345 9.846248 ATTTTGGAAATCTTACGAATCAAAGAG 57.154 29.630 0.00 0.00 35.32 2.85
2391 8346 9.624697 CATTTTGGAAATCTTACGAATCAAAGA 57.375 29.630 0.00 0.00 36.24 2.52
2392 8347 8.375465 GCATTTTGGAAATCTTACGAATCAAAG 58.625 33.333 0.00 0.00 0.00 2.77
2393 8348 7.869937 TGCATTTTGGAAATCTTACGAATCAAA 59.130 29.630 0.00 0.00 0.00 2.69
2394 8349 7.374272 TGCATTTTGGAAATCTTACGAATCAA 58.626 30.769 0.00 0.00 0.00 2.57
2395 8350 6.918626 TGCATTTTGGAAATCTTACGAATCA 58.081 32.000 0.00 0.00 0.00 2.57
2396 8351 6.473455 CCTGCATTTTGGAAATCTTACGAATC 59.527 38.462 0.00 0.00 0.00 2.52
2397 8352 6.152661 TCCTGCATTTTGGAAATCTTACGAAT 59.847 34.615 0.00 0.00 0.00 3.34
2398 8353 5.475220 TCCTGCATTTTGGAAATCTTACGAA 59.525 36.000 0.00 0.00 0.00 3.85
2399 8354 5.007034 TCCTGCATTTTGGAAATCTTACGA 58.993 37.500 0.00 0.00 0.00 3.43
2400 8355 5.309323 TCCTGCATTTTGGAAATCTTACG 57.691 39.130 0.00 0.00 0.00 3.18
2401 8356 7.922811 CCTATTCCTGCATTTTGGAAATCTTAC 59.077 37.037 9.02 0.00 44.34 2.34
2402 8357 7.838696 TCCTATTCCTGCATTTTGGAAATCTTA 59.161 33.333 9.02 0.00 44.34 2.10
2403 8358 6.669154 TCCTATTCCTGCATTTTGGAAATCTT 59.331 34.615 9.02 0.00 44.34 2.40
2404 8359 6.197168 TCCTATTCCTGCATTTTGGAAATCT 58.803 36.000 9.02 0.00 44.34 2.40
2405 8360 6.469782 TCCTATTCCTGCATTTTGGAAATC 57.530 37.500 9.02 0.00 44.34 2.17
2406 8361 6.872585 TTCCTATTCCTGCATTTTGGAAAT 57.127 33.333 9.02 2.19 44.34 2.17
2407 8362 6.678568 TTTCCTATTCCTGCATTTTGGAAA 57.321 33.333 9.02 10.69 44.34 3.13
2408 8363 6.678568 TTTTCCTATTCCTGCATTTTGGAA 57.321 33.333 7.53 7.53 45.11 3.53
2409 8364 6.678568 TTTTTCCTATTCCTGCATTTTGGA 57.321 33.333 0.00 0.00 0.00 3.53
2410 8365 6.880529 ACATTTTTCCTATTCCTGCATTTTGG 59.119 34.615 0.00 0.00 0.00 3.28
2411 8366 7.603404 TCACATTTTTCCTATTCCTGCATTTTG 59.397 33.333 0.00 0.00 0.00 2.44
2412 8367 7.678837 TCACATTTTTCCTATTCCTGCATTTT 58.321 30.769 0.00 0.00 0.00 1.82
2413 8368 7.243604 TCACATTTTTCCTATTCCTGCATTT 57.756 32.000 0.00 0.00 0.00 2.32
2414 8369 6.855763 TCACATTTTTCCTATTCCTGCATT 57.144 33.333 0.00 0.00 0.00 3.56
2415 8370 6.855763 TTCACATTTTTCCTATTCCTGCAT 57.144 33.333 0.00 0.00 0.00 3.96
2416 8371 6.662865 TTTCACATTTTTCCTATTCCTGCA 57.337 33.333 0.00 0.00 0.00 4.41
2417 8372 9.305925 CTAATTTCACATTTTTCCTATTCCTGC 57.694 33.333 0.00 0.00 0.00 4.85
2423 8378 8.470002 GCCACTCTAATTTCACATTTTTCCTAT 58.530 33.333 0.00 0.00 0.00 2.57
2424 8379 7.450014 TGCCACTCTAATTTCACATTTTTCCTA 59.550 33.333 0.00 0.00 0.00 2.94
2425 8380 6.267471 TGCCACTCTAATTTCACATTTTTCCT 59.733 34.615 0.00 0.00 0.00 3.36
2426 8381 6.454795 TGCCACTCTAATTTCACATTTTTCC 58.545 36.000 0.00 0.00 0.00 3.13
2427 8382 7.599998 ACATGCCACTCTAATTTCACATTTTTC 59.400 33.333 0.00 0.00 0.00 2.29
2428 8383 7.444299 ACATGCCACTCTAATTTCACATTTTT 58.556 30.769 0.00 0.00 0.00 1.94
2429 8384 6.996509 ACATGCCACTCTAATTTCACATTTT 58.003 32.000 0.00 0.00 0.00 1.82
2430 8385 6.594788 ACATGCCACTCTAATTTCACATTT 57.405 33.333 0.00 0.00 0.00 2.32
2431 8386 5.163723 CGACATGCCACTCTAATTTCACATT 60.164 40.000 0.00 0.00 0.00 2.71
2432 8387 4.333649 CGACATGCCACTCTAATTTCACAT 59.666 41.667 0.00 0.00 0.00 3.21
2433 8388 3.684305 CGACATGCCACTCTAATTTCACA 59.316 43.478 0.00 0.00 0.00 3.58
2434 8389 3.684788 ACGACATGCCACTCTAATTTCAC 59.315 43.478 0.00 0.00 0.00 3.18
2435 8390 3.932710 GACGACATGCCACTCTAATTTCA 59.067 43.478 0.00 0.00 0.00 2.69
2436 8391 4.184629 AGACGACATGCCACTCTAATTTC 58.815 43.478 0.00 0.00 0.00 2.17
2437 8392 4.207891 AGACGACATGCCACTCTAATTT 57.792 40.909 0.00 0.00 0.00 1.82
2438 8393 3.895232 AGACGACATGCCACTCTAATT 57.105 42.857 0.00 0.00 0.00 1.40
2439 8394 3.195610 TCAAGACGACATGCCACTCTAAT 59.804 43.478 0.00 0.00 0.00 1.73
2440 8395 2.560981 TCAAGACGACATGCCACTCTAA 59.439 45.455 0.00 0.00 0.00 2.10
2441 8396 2.167662 TCAAGACGACATGCCACTCTA 58.832 47.619 0.00 0.00 0.00 2.43
2442 8397 0.969149 TCAAGACGACATGCCACTCT 59.031 50.000 0.00 0.00 0.00 3.24
2443 8398 1.795768 TTCAAGACGACATGCCACTC 58.204 50.000 0.00 0.00 0.00 3.51
2444 8399 2.350522 GATTCAAGACGACATGCCACT 58.649 47.619 0.00 0.00 0.00 4.00
2445 8400 1.398390 GGATTCAAGACGACATGCCAC 59.602 52.381 0.00 0.00 0.00 5.01
2446 8401 1.278985 AGGATTCAAGACGACATGCCA 59.721 47.619 0.00 0.00 0.00 4.92
2447 8402 2.029838 AGGATTCAAGACGACATGCC 57.970 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.