Multiple sequence alignment - TraesCS6B01G319600

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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 TraesCS6B01G319600 chr6B 100.000 2879 0 0 1 2879 567405489 567402611 0.000000e+00 5317
1 TraesCS6B01G319600 chr6B 86.667 285 35 3 266 549 204454308 204454590 2.150000e-81 313
2 TraesCS6B01G319600 chr6B 91.943 211 15 2 273 482 113323919 113324128 7.800000e-76 294
3 TraesCS6B01G319600 chr3A 90.583 1869 138 14 716 2583 698898413 698896582 0.000000e+00 2442
4 TraesCS6B01G319600 chr3A 94.465 271 15 0 271 541 698898826 698898556 4.440000e-113 418
5 TraesCS6B01G319600 chr3A 89.956 229 22 1 271 499 208733458 208733231 7.800000e-76 294
6 TraesCS6B01G319600 chr3A 88.325 197 22 1 270 466 102293427 102293622 4.800000e-58 235
7 TraesCS6B01G319600 chr1B 92.312 1652 116 11 948 2592 134628818 134627171 0.000000e+00 2337
8 TraesCS6B01G319600 chr1B 88.593 263 23 4 270 528 4837484 4837225 2.150000e-81 313
9 TraesCS6B01G319600 chr1B 89.130 230 21 4 272 499 453275662 453275435 1.690000e-72 283
10 TraesCS6B01G319600 chr1B 84.926 272 29 7 271 541 345318558 345318298 6.120000e-67 265
11 TraesCS6B01G319600 chr1D 93.060 1585 107 3 1000 2583 326162719 326164301 0.000000e+00 2314
12 TraesCS6B01G319600 chr1D 95.973 298 12 0 2582 2879 198892281 198892578 4.310000e-133 484
13 TraesCS6B01G319600 chr1D 95.638 298 13 0 2582 2879 326165812 326166109 2.010000e-131 479
14 TraesCS6B01G319600 chr1D 90.995 211 14 5 270 478 198883811 198884018 2.180000e-71 279
15 TraesCS6B01G319600 chr1D 88.038 209 17 4 271 478 391733844 391733643 1.030000e-59 241
16 TraesCS6B01G319600 chr4D 91.637 1674 132 6 912 2583 64354072 64352405 0.000000e+00 2309
17 TraesCS6B01G319600 chr4D 92.672 1583 116 0 1001 2583 504006752 504005170 0.000000e+00 2281
18 TraesCS6B01G319600 chr4D 95.987 299 11 1 2581 2879 504003662 504003365 4.310000e-133 484
19 TraesCS6B01G319600 chr4D 92.891 211 12 3 271 479 468306680 468306471 1.300000e-78 303
20 TraesCS6B01G319600 chr4D 88.785 214 17 7 269 478 422507822 422508032 3.680000e-64 255
21 TraesCS6B01G319600 chr4D 87.838 222 18 9 261 477 396423780 396423997 4.760000e-63 252
22 TraesCS6B01G319600 chr4D 91.525 177 12 2 271 447 504007405 504007232 1.030000e-59 241
23 TraesCS6B01G319600 chr4D 86.792 212 19 6 270 478 43147414 43147209 8.030000e-56 228
24 TraesCS6B01G319600 chr4D 88.701 177 16 4 273 448 85167010 85167183 2.250000e-51 213
25 TraesCS6B01G319600 chr4D 88.701 177 14 4 271 446 424057370 424057541 8.080000e-51 211
26 TraesCS6B01G319600 chr4D 88.268 179 15 4 271 448 424261434 424261607 2.910000e-50 209
27 TraesCS6B01G319600 chr4D 84.834 211 24 8 271 477 56740863 56740657 3.760000e-49 206
28 TraesCS6B01G319600 chr3D 92.817 1587 113 1 998 2583 556571184 556572770 0.000000e+00 2298
29 TraesCS6B01G319600 chr3D 91.814 1637 123 7 946 2577 92863893 92862263 0.000000e+00 2270
30 TraesCS6B01G319600 chr3D 95.973 298 12 0 2582 2879 556574279 556574576 4.310000e-133 484
31 TraesCS6B01G319600 chr3D 95.638 298 13 0 2582 2879 3342075 3341778 2.010000e-131 479
32 TraesCS6B01G319600 chr3D 91.739 230 16 3 271 499 92864557 92864330 1.660000e-82 316
33 TraesCS6B01G319600 chr3D 86.411 287 31 6 271 555 143638495 143638215 1.000000e-79 307
34 TraesCS6B01G319600 chr7D 92.370 1612 121 2 974 2583 58799440 58797829 0.000000e+00 2294
35 TraesCS6B01G319600 chr7D 90.838 1670 144 7 917 2583 292263520 292265183 0.000000e+00 2228
36 TraesCS6B01G319600 chr7D 81.944 720 65 32 271 964 126613344 126614024 1.510000e-152 549
37 TraesCS6B01G319600 chr7D 95.638 298 13 0 2582 2879 566456970 566456673 2.010000e-131 479
38 TraesCS6B01G319600 chr7D 95.623 297 13 0 2583 2879 58796320 58796024 7.220000e-131 477
39 TraesCS6B01G319600 chr7D 89.811 265 17 8 271 530 513136339 513136080 5.950000e-87 331
40 TraesCS6B01G319600 chr2D 87.053 1622 147 31 271 1874 159330575 159332151 0.000000e+00 1773
41 TraesCS6B01G319600 chr2D 95.973 298 12 0 2582 2879 28062278 28061981 4.310000e-133 484
42 TraesCS6B01G319600 chr2D 96.070 229 9 0 270 498 604244555 604244783 9.740000e-100 374
43 TraesCS6B01G319600 chr3B 94.136 972 47 2 267 1237 22444265 22445227 0.000000e+00 1471
44 TraesCS6B01G319600 chr6D 95.973 298 12 0 2582 2879 472882224 472881927 4.310000e-133 484
45 TraesCS6B01G319600 chr6D 96.296 270 8 2 3 270 379569776 379570045 2.630000e-120 442
46 TraesCS6B01G319600 chr6D 90.987 233 18 3 270 500 159857501 159857732 7.750000e-81 311
47 TraesCS6B01G319600 chr6D 91.266 229 19 1 271 499 472886194 472885967 7.750000e-81 311
48 TraesCS6B01G319600 chr6D 92.105 190 15 0 271 460 466524958 466524769 4.730000e-68 268
49 TraesCS6B01G319600 chr6A 93.407 273 10 5 5 270 521456292 521456021 5.780000e-107 398
50 TraesCS6B01G319600 chr7B 92.181 243 17 2 259 499 624712251 624712493 2.750000e-90 342
51 TraesCS6B01G319600 chr2B 88.112 286 29 4 270 553 106114138 106113856 4.600000e-88 335
52 TraesCS6B01G319600 chr2B 85.714 308 40 4 268 573 296011258 296010953 3.580000e-84 322
53 TraesCS6B01G319600 chr4B 92.241 232 14 4 270 499 25281102 25280873 2.770000e-85 326
54 TraesCS6B01G319600 chr4B 90.000 210 18 3 271 478 119264921 119265129 4.730000e-68 268
55 TraesCS6B01G319600 chr5D 88.412 233 24 3 268 499 275606486 275606716 7.860000e-71 278
56 TraesCS6B01G319600 chr5D 86.939 245 29 3 261 503 23172158 23172401 3.660000e-69 272
57 TraesCS6B01G319600 chr5D 90.686 204 12 5 270 470 526278990 526278791 6.120000e-67 265
58 TraesCS6B01G319600 chr5D 84.727 275 28 10 269 540 539986116 539985853 2.200000e-66 263
59 TraesCS6B01G319600 chr1A 88.038 209 19 6 270 474 585000747 585000953 2.870000e-60 243
60 TraesCS6B01G319600 chrUn 89.888 178 14 3 271 447 95760494 95760320 2.890000e-55 226
61 TraesCS6B01G319600 chrUn 92.969 128 8 1 269 396 272008212 272008338 4.900000e-43 185
62 TraesCS6B01G319600 chrUn 92.126 127 10 0 269 395 96284789 96284915 2.280000e-41 180
63 TraesCS6B01G319600 chrUn 92.188 128 7 3 269 395 95737343 95737218 8.200000e-41 178
64 TraesCS6B01G319600 chrUn 90.400 125 12 0 271 395 284255552 284255428 6.380000e-37 165
65 TraesCS6B01G319600 chrUn 88.372 129 10 5 269 395 300552384 300552259 1.790000e-32 150


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 TraesCS6B01G319600 chr6B 567402611 567405489 2878 True 5317.0 5317 100.000000 1 2879 1 chr6B.!!$R1 2878
1 TraesCS6B01G319600 chr3A 698896582 698898826 2244 True 1430.0 2442 92.524000 271 2583 2 chr3A.!!$R2 2312
2 TraesCS6B01G319600 chr1B 134627171 134628818 1647 True 2337.0 2337 92.312000 948 2592 1 chr1B.!!$R2 1644
3 TraesCS6B01G319600 chr1D 326162719 326166109 3390 False 1396.5 2314 94.349000 1000 2879 2 chr1D.!!$F3 1879
4 TraesCS6B01G319600 chr4D 64352405 64354072 1667 True 2309.0 2309 91.637000 912 2583 1 chr4D.!!$R3 1671
5 TraesCS6B01G319600 chr4D 504003365 504007405 4040 True 1002.0 2281 93.394667 271 2879 3 chr4D.!!$R5 2608
6 TraesCS6B01G319600 chr3D 556571184 556574576 3392 False 1391.0 2298 94.395000 998 2879 2 chr3D.!!$F1 1881
7 TraesCS6B01G319600 chr3D 92862263 92864557 2294 True 1293.0 2270 91.776500 271 2577 2 chr3D.!!$R3 2306
8 TraesCS6B01G319600 chr7D 292263520 292265183 1663 False 2228.0 2228 90.838000 917 2583 1 chr7D.!!$F2 1666
9 TraesCS6B01G319600 chr7D 58796024 58799440 3416 True 1385.5 2294 93.996500 974 2879 2 chr7D.!!$R3 1905
10 TraesCS6B01G319600 chr7D 126613344 126614024 680 False 549.0 549 81.944000 271 964 1 chr7D.!!$F1 693
11 TraesCS6B01G319600 chr2D 159330575 159332151 1576 False 1773.0 1773 87.053000 271 1874 1 chr2D.!!$F1 1603
12 TraesCS6B01G319600 chr3B 22444265 22445227 962 False 1471.0 1471 94.136000 267 1237 1 chr3B.!!$F1 970
13 TraesCS6B01G319600 chr6D 472881927 472886194 4267 True 397.5 484 93.619500 271 2879 2 chr6D.!!$R2 2608

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
78 79 0.534203 GGTGGTTTTGAGCTCACCGA 60.534 55.0 18.03 0.0 39.97 4.69 F
154 155 0.983467 TTCCAGTGCTGCCTATGTCA 59.017 50.0 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 1907 0.390866 CTGAAGTGCGTGCTCCTGAT 60.391 55.000 0.0 0.00 0.00 2.90 R
2015 2619 1.134901 CGGAGTCGAGGAAGACACG 59.865 63.158 0.0 0.73 43.24 4.49 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 1.672881 GGCAAAGGGAGATGAATGACG 59.327 52.381 0.00 0.00 0.00 4.35
21 22 2.632377 GCAAAGGGAGATGAATGACGA 58.368 47.619 0.00 0.00 0.00 4.20
22 23 2.352960 GCAAAGGGAGATGAATGACGAC 59.647 50.000 0.00 0.00 0.00 4.34
23 24 3.599343 CAAAGGGAGATGAATGACGACA 58.401 45.455 0.00 0.00 0.00 4.35
24 25 4.194640 CAAAGGGAGATGAATGACGACAT 58.805 43.478 0.00 0.00 38.50 3.06
25 26 5.359756 CAAAGGGAGATGAATGACGACATA 58.640 41.667 0.00 0.00 35.50 2.29
26 27 4.592485 AGGGAGATGAATGACGACATAC 57.408 45.455 0.00 0.00 35.50 2.39
27 28 3.322254 AGGGAGATGAATGACGACATACC 59.678 47.826 0.00 0.00 35.50 2.73
28 29 3.069586 GGGAGATGAATGACGACATACCA 59.930 47.826 0.00 3.33 35.50 3.25
29 30 4.442893 GGGAGATGAATGACGACATACCAA 60.443 45.833 0.00 0.00 35.50 3.67
30 31 5.300752 GGAGATGAATGACGACATACCAAT 58.699 41.667 0.00 0.00 35.50 3.16
31 32 5.760253 GGAGATGAATGACGACATACCAATT 59.240 40.000 0.00 0.00 35.50 2.32
32 33 6.293081 GGAGATGAATGACGACATACCAATTG 60.293 42.308 0.00 0.00 35.50 2.32
33 34 5.528690 AGATGAATGACGACATACCAATTGG 59.471 40.000 23.31 23.31 37.17 3.16
47 48 4.510038 CCAATTGGTCAAAAGTCTCCTG 57.490 45.455 16.90 0.00 0.00 3.86
48 49 3.891366 CCAATTGGTCAAAAGTCTCCTGT 59.109 43.478 16.90 0.00 0.00 4.00
49 50 4.261741 CCAATTGGTCAAAAGTCTCCTGTG 60.262 45.833 16.90 0.00 0.00 3.66
50 51 3.644966 TTGGTCAAAAGTCTCCTGTGT 57.355 42.857 0.00 0.00 0.00 3.72
51 52 3.644966 TGGTCAAAAGTCTCCTGTGTT 57.355 42.857 0.00 0.00 0.00 3.32
52 53 3.278574 TGGTCAAAAGTCTCCTGTGTTG 58.721 45.455 0.00 0.00 0.00 3.33
53 54 3.279434 GGTCAAAAGTCTCCTGTGTTGT 58.721 45.455 0.00 0.00 0.00 3.32
54 55 3.694566 GGTCAAAAGTCTCCTGTGTTGTT 59.305 43.478 0.00 0.00 0.00 2.83
55 56 4.438744 GGTCAAAAGTCTCCTGTGTTGTTG 60.439 45.833 0.00 0.00 0.00 3.33
56 57 4.156008 GTCAAAAGTCTCCTGTGTTGTTGT 59.844 41.667 0.00 0.00 0.00 3.32
57 58 4.394920 TCAAAAGTCTCCTGTGTTGTTGTC 59.605 41.667 0.00 0.00 0.00 3.18
58 59 3.914426 AAGTCTCCTGTGTTGTTGTCT 57.086 42.857 0.00 0.00 0.00 3.41
59 60 3.185246 AGTCTCCTGTGTTGTTGTCTG 57.815 47.619 0.00 0.00 0.00 3.51
60 61 2.158900 AGTCTCCTGTGTTGTTGTCTGG 60.159 50.000 0.00 0.00 0.00 3.86
61 62 1.837439 TCTCCTGTGTTGTTGTCTGGT 59.163 47.619 0.00 0.00 0.00 4.00
62 63 1.942657 CTCCTGTGTTGTTGTCTGGTG 59.057 52.381 0.00 0.00 0.00 4.17
63 64 1.024271 CCTGTGTTGTTGTCTGGTGG 58.976 55.000 0.00 0.00 0.00 4.61
64 65 1.681780 CCTGTGTTGTTGTCTGGTGGT 60.682 52.381 0.00 0.00 0.00 4.16
65 66 2.091541 CTGTGTTGTTGTCTGGTGGTT 58.908 47.619 0.00 0.00 0.00 3.67
66 67 2.491693 CTGTGTTGTTGTCTGGTGGTTT 59.508 45.455 0.00 0.00 0.00 3.27
67 68 2.894126 TGTGTTGTTGTCTGGTGGTTTT 59.106 40.909 0.00 0.00 0.00 2.43
68 69 3.249917 GTGTTGTTGTCTGGTGGTTTTG 58.750 45.455 0.00 0.00 0.00 2.44
69 70 3.057174 GTGTTGTTGTCTGGTGGTTTTGA 60.057 43.478 0.00 0.00 0.00 2.69
70 71 3.192422 TGTTGTTGTCTGGTGGTTTTGAG 59.808 43.478 0.00 0.00 0.00 3.02
71 72 1.748493 TGTTGTCTGGTGGTTTTGAGC 59.252 47.619 0.00 0.00 0.00 4.26
72 73 2.024414 GTTGTCTGGTGGTTTTGAGCT 58.976 47.619 0.00 0.00 0.00 4.09
73 74 1.967319 TGTCTGGTGGTTTTGAGCTC 58.033 50.000 6.82 6.82 0.00 4.09
74 75 1.211703 TGTCTGGTGGTTTTGAGCTCA 59.788 47.619 13.74 13.74 0.00 4.26
75 76 1.604278 GTCTGGTGGTTTTGAGCTCAC 59.396 52.381 18.03 5.40 0.00 3.51
77 78 1.949257 GGTGGTTTTGAGCTCACCG 59.051 57.895 18.03 0.00 39.97 4.94
78 79 0.534203 GGTGGTTTTGAGCTCACCGA 60.534 55.000 18.03 0.00 39.97 4.69
79 80 1.523758 GTGGTTTTGAGCTCACCGAT 58.476 50.000 18.03 0.00 32.71 4.18
80 81 1.464997 GTGGTTTTGAGCTCACCGATC 59.535 52.381 18.03 6.19 32.71 3.69
81 82 1.347707 TGGTTTTGAGCTCACCGATCT 59.652 47.619 18.03 0.00 32.71 2.75
82 83 2.224523 TGGTTTTGAGCTCACCGATCTT 60.225 45.455 18.03 0.00 32.71 2.40
83 84 2.814336 GGTTTTGAGCTCACCGATCTTT 59.186 45.455 18.03 0.00 0.00 2.52
84 85 3.365364 GGTTTTGAGCTCACCGATCTTTG 60.365 47.826 18.03 0.00 0.00 2.77
85 86 3.401033 TTTGAGCTCACCGATCTTTGA 57.599 42.857 18.03 0.00 0.00 2.69
86 87 3.401033 TTGAGCTCACCGATCTTTGAA 57.599 42.857 18.03 0.00 0.00 2.69
87 88 3.401033 TGAGCTCACCGATCTTTGAAA 57.599 42.857 13.74 0.00 0.00 2.69
88 89 3.738982 TGAGCTCACCGATCTTTGAAAA 58.261 40.909 13.74 0.00 0.00 2.29
89 90 4.326826 TGAGCTCACCGATCTTTGAAAAT 58.673 39.130 13.74 0.00 0.00 1.82
90 91 4.761739 TGAGCTCACCGATCTTTGAAAATT 59.238 37.500 13.74 0.00 0.00 1.82
91 92 5.937540 TGAGCTCACCGATCTTTGAAAATTA 59.062 36.000 13.74 0.00 0.00 1.40
92 93 6.599244 TGAGCTCACCGATCTTTGAAAATTAT 59.401 34.615 13.74 0.00 0.00 1.28
93 94 7.768582 TGAGCTCACCGATCTTTGAAAATTATA 59.231 33.333 13.74 0.00 0.00 0.98
94 95 8.147642 AGCTCACCGATCTTTGAAAATTATAG 57.852 34.615 0.00 0.00 0.00 1.31
95 96 7.227512 AGCTCACCGATCTTTGAAAATTATAGG 59.772 37.037 0.00 0.00 0.00 2.57
96 97 7.226720 GCTCACCGATCTTTGAAAATTATAGGA 59.773 37.037 0.00 0.00 0.00 2.94
97 98 8.662781 TCACCGATCTTTGAAAATTATAGGAG 57.337 34.615 0.00 0.00 0.00 3.69
98 99 8.482943 TCACCGATCTTTGAAAATTATAGGAGA 58.517 33.333 0.00 0.00 0.00 3.71
99 100 9.277783 CACCGATCTTTGAAAATTATAGGAGAT 57.722 33.333 0.00 0.00 0.00 2.75
100 101 9.277783 ACCGATCTTTGAAAATTATAGGAGATG 57.722 33.333 0.00 0.00 0.00 2.90
101 102 9.277783 CCGATCTTTGAAAATTATAGGAGATGT 57.722 33.333 0.00 0.00 0.00 3.06
120 121 5.550232 ATGTATGTTACATGCACACACAG 57.450 39.130 17.60 0.00 46.94 3.66
121 122 4.636249 TGTATGTTACATGCACACACAGA 58.364 39.130 11.88 0.00 32.89 3.41
122 123 5.059833 TGTATGTTACATGCACACACAGAA 58.940 37.500 11.88 0.00 32.89 3.02
123 124 5.529060 TGTATGTTACATGCACACACAGAAA 59.471 36.000 11.88 0.00 32.89 2.52
124 125 4.972514 TGTTACATGCACACACAGAAAA 57.027 36.364 0.00 0.00 0.00 2.29
125 126 5.316327 TGTTACATGCACACACAGAAAAA 57.684 34.783 0.00 0.00 0.00 1.94
126 127 5.339177 TGTTACATGCACACACAGAAAAAG 58.661 37.500 0.00 0.00 0.00 2.27
127 128 5.105957 TGTTACATGCACACACAGAAAAAGT 60.106 36.000 0.00 0.00 0.00 2.66
128 129 4.454728 ACATGCACACACAGAAAAAGTT 57.545 36.364 0.00 0.00 0.00 2.66
129 130 5.574891 ACATGCACACACAGAAAAAGTTA 57.425 34.783 0.00 0.00 0.00 2.24
130 131 5.581605 ACATGCACACACAGAAAAAGTTAG 58.418 37.500 0.00 0.00 0.00 2.34
131 132 4.630894 TGCACACACAGAAAAAGTTAGG 57.369 40.909 0.00 0.00 0.00 2.69
132 133 4.013728 TGCACACACAGAAAAAGTTAGGT 58.986 39.130 0.00 0.00 0.00 3.08
133 134 5.186942 TGCACACACAGAAAAAGTTAGGTA 58.813 37.500 0.00 0.00 0.00 3.08
134 135 5.825679 TGCACACACAGAAAAAGTTAGGTAT 59.174 36.000 0.00 0.00 0.00 2.73
135 136 6.320164 TGCACACACAGAAAAAGTTAGGTATT 59.680 34.615 0.00 0.00 0.00 1.89
136 137 7.147983 TGCACACACAGAAAAAGTTAGGTATTT 60.148 33.333 0.00 0.00 0.00 1.40
137 138 7.378728 GCACACACAGAAAAAGTTAGGTATTTC 59.621 37.037 0.00 0.00 33.13 2.17
138 139 7.860872 CACACACAGAAAAAGTTAGGTATTTCC 59.139 37.037 0.00 0.00 33.35 3.13
139 140 7.558444 ACACACAGAAAAAGTTAGGTATTTCCA 59.442 33.333 0.00 0.00 39.02 3.53
140 141 8.076178 CACACAGAAAAAGTTAGGTATTTCCAG 58.924 37.037 0.00 0.00 39.02 3.86
141 142 7.778382 ACACAGAAAAAGTTAGGTATTTCCAGT 59.222 33.333 0.00 0.00 39.02 4.00
142 143 8.076178 CACAGAAAAAGTTAGGTATTTCCAGTG 58.924 37.037 0.00 0.00 39.02 3.66
143 144 7.084486 CAGAAAAAGTTAGGTATTTCCAGTGC 58.916 38.462 0.00 0.00 39.02 4.40
144 145 7.004691 AGAAAAAGTTAGGTATTTCCAGTGCT 58.995 34.615 0.00 0.00 39.02 4.40
145 146 6.575162 AAAAGTTAGGTATTTCCAGTGCTG 57.425 37.500 0.00 0.00 39.02 4.41
146 147 3.610911 AGTTAGGTATTTCCAGTGCTGC 58.389 45.455 0.00 0.00 39.02 5.25
147 148 2.683362 GTTAGGTATTTCCAGTGCTGCC 59.317 50.000 0.00 0.00 39.02 4.85
148 149 0.995024 AGGTATTTCCAGTGCTGCCT 59.005 50.000 0.00 0.00 39.02 4.75
149 150 2.196595 AGGTATTTCCAGTGCTGCCTA 58.803 47.619 0.00 0.00 39.02 3.93
150 151 2.780010 AGGTATTTCCAGTGCTGCCTAT 59.220 45.455 0.00 0.00 39.02 2.57
151 152 2.880890 GGTATTTCCAGTGCTGCCTATG 59.119 50.000 0.00 0.00 35.97 2.23
152 153 2.814805 ATTTCCAGTGCTGCCTATGT 57.185 45.000 0.00 0.00 0.00 2.29
153 154 2.113860 TTTCCAGTGCTGCCTATGTC 57.886 50.000 0.00 0.00 0.00 3.06
154 155 0.983467 TTCCAGTGCTGCCTATGTCA 59.017 50.000 0.00 0.00 0.00 3.58
155 156 0.983467 TCCAGTGCTGCCTATGTCAA 59.017 50.000 0.00 0.00 0.00 3.18
156 157 1.065926 TCCAGTGCTGCCTATGTCAAG 60.066 52.381 0.00 0.00 0.00 3.02
157 158 1.065926 CCAGTGCTGCCTATGTCAAGA 60.066 52.381 0.00 0.00 0.00 3.02
158 159 2.277969 CAGTGCTGCCTATGTCAAGAG 58.722 52.381 0.00 0.00 0.00 2.85
159 160 1.905215 AGTGCTGCCTATGTCAAGAGT 59.095 47.619 0.00 0.00 0.00 3.24
160 161 3.099905 AGTGCTGCCTATGTCAAGAGTA 58.900 45.455 0.00 0.00 0.00 2.59
161 162 3.515502 AGTGCTGCCTATGTCAAGAGTAA 59.484 43.478 0.00 0.00 0.00 2.24
162 163 3.868077 GTGCTGCCTATGTCAAGAGTAAG 59.132 47.826 0.00 0.00 0.00 2.34
163 164 3.118629 TGCTGCCTATGTCAAGAGTAAGG 60.119 47.826 0.00 0.00 0.00 2.69
164 165 3.133003 GCTGCCTATGTCAAGAGTAAGGA 59.867 47.826 0.00 0.00 0.00 3.36
165 166 4.383118 GCTGCCTATGTCAAGAGTAAGGAA 60.383 45.833 0.00 0.00 0.00 3.36
166 167 5.734720 CTGCCTATGTCAAGAGTAAGGAAA 58.265 41.667 0.00 0.00 0.00 3.13
167 168 5.488341 TGCCTATGTCAAGAGTAAGGAAAC 58.512 41.667 0.00 0.00 0.00 2.78
168 169 5.012664 TGCCTATGTCAAGAGTAAGGAAACA 59.987 40.000 0.00 0.00 0.00 2.83
169 170 5.938125 GCCTATGTCAAGAGTAAGGAAACAA 59.062 40.000 0.00 0.00 0.00 2.83
170 171 6.430000 GCCTATGTCAAGAGTAAGGAAACAAA 59.570 38.462 0.00 0.00 0.00 2.83
171 172 7.121315 GCCTATGTCAAGAGTAAGGAAACAAAT 59.879 37.037 0.00 0.00 0.00 2.32
172 173 8.454106 CCTATGTCAAGAGTAAGGAAACAAATG 58.546 37.037 0.00 0.00 0.00 2.32
173 174 7.823745 ATGTCAAGAGTAAGGAAACAAATGT 57.176 32.000 0.00 0.00 0.00 2.71
174 175 7.026631 TGTCAAGAGTAAGGAAACAAATGTG 57.973 36.000 0.00 0.00 0.00 3.21
175 176 5.915196 GTCAAGAGTAAGGAAACAAATGTGC 59.085 40.000 0.00 0.00 0.00 4.57
176 177 5.827797 TCAAGAGTAAGGAAACAAATGTGCT 59.172 36.000 0.00 0.00 0.00 4.40
177 178 5.948992 AGAGTAAGGAAACAAATGTGCTC 57.051 39.130 0.00 0.00 0.00 4.26
178 179 5.376625 AGAGTAAGGAAACAAATGTGCTCA 58.623 37.500 0.00 0.00 0.00 4.26
179 180 5.827797 AGAGTAAGGAAACAAATGTGCTCAA 59.172 36.000 0.00 0.00 0.00 3.02
180 181 6.321181 AGAGTAAGGAAACAAATGTGCTCAAA 59.679 34.615 0.00 0.00 0.00 2.69
181 182 6.507023 AGTAAGGAAACAAATGTGCTCAAAG 58.493 36.000 0.00 0.00 0.00 2.77
182 183 3.721035 AGGAAACAAATGTGCTCAAAGC 58.279 40.909 0.00 0.00 42.82 3.51
183 184 2.802247 GGAAACAAATGTGCTCAAAGCC 59.198 45.455 0.00 0.00 41.51 4.35
184 185 3.456280 GAAACAAATGTGCTCAAAGCCA 58.544 40.909 0.00 0.00 41.51 4.75
185 186 2.806608 ACAAATGTGCTCAAAGCCAG 57.193 45.000 0.00 0.00 41.51 4.85
186 187 1.269936 ACAAATGTGCTCAAAGCCAGC 60.270 47.619 0.00 0.00 41.51 4.85
187 188 1.042229 AAATGTGCTCAAAGCCAGCA 58.958 45.000 0.00 0.00 44.80 4.41
232 233 8.911918 TTAAGGATGACTAAAACTTGCTAACA 57.088 30.769 0.00 0.00 0.00 2.41
233 234 6.803154 AGGATGACTAAAACTTGCTAACAC 57.197 37.500 0.00 0.00 0.00 3.32
234 235 5.705905 AGGATGACTAAAACTTGCTAACACC 59.294 40.000 0.00 0.00 0.00 4.16
235 236 5.106277 GGATGACTAAAACTTGCTAACACCC 60.106 44.000 0.00 0.00 0.00 4.61
236 237 5.043737 TGACTAAAACTTGCTAACACCCT 57.956 39.130 0.00 0.00 0.00 4.34
237 238 6.177310 TGACTAAAACTTGCTAACACCCTA 57.823 37.500 0.00 0.00 0.00 3.53
238 239 6.775708 TGACTAAAACTTGCTAACACCCTAT 58.224 36.000 0.00 0.00 0.00 2.57
239 240 7.909518 TGACTAAAACTTGCTAACACCCTATA 58.090 34.615 0.00 0.00 0.00 1.31
240 241 7.820872 TGACTAAAACTTGCTAACACCCTATAC 59.179 37.037 0.00 0.00 0.00 1.47
241 242 7.914859 ACTAAAACTTGCTAACACCCTATACT 58.085 34.615 0.00 0.00 0.00 2.12
242 243 9.039165 ACTAAAACTTGCTAACACCCTATACTA 57.961 33.333 0.00 0.00 0.00 1.82
246 247 8.779096 AACTTGCTAACACCCTATACTATAGT 57.221 34.615 10.87 10.87 0.00 2.12
247 248 8.779096 ACTTGCTAACACCCTATACTATAGTT 57.221 34.615 11.40 1.99 0.00 2.24
248 249 8.858094 ACTTGCTAACACCCTATACTATAGTTC 58.142 37.037 11.40 0.00 0.00 3.01
249 250 8.771521 TTGCTAACACCCTATACTATAGTTCA 57.228 34.615 11.40 0.00 0.00 3.18
250 251 8.951614 TGCTAACACCCTATACTATAGTTCAT 57.048 34.615 11.40 1.91 0.00 2.57
258 259 9.702253 ACCCTATACTATAGTTCATAGTCATGG 57.298 37.037 11.40 11.06 45.63 3.66
259 260 9.702253 CCCTATACTATAGTTCATAGTCATGGT 57.298 37.037 11.40 0.00 45.63 3.55
263 264 7.914427 ACTATAGTTCATAGTCATGGTTGGA 57.086 36.000 0.00 0.00 45.63 3.53
264 265 8.319057 ACTATAGTTCATAGTCATGGTTGGAA 57.681 34.615 0.00 0.00 45.63 3.53
265 266 8.424918 ACTATAGTTCATAGTCATGGTTGGAAG 58.575 37.037 0.00 0.00 45.63 3.46
582 719 1.811266 CATCTCGTCCGGTTGCTGG 60.811 63.158 0.00 0.00 0.00 4.85
635 785 4.756458 GCTCGGCAGCTGCTCAGT 62.756 66.667 35.82 0.00 43.09 3.41
636 786 2.508887 CTCGGCAGCTGCTCAGTC 60.509 66.667 35.82 19.17 41.70 3.51
637 787 4.074526 TCGGCAGCTGCTCAGTCC 62.075 66.667 35.82 18.44 41.70 3.85
675 825 4.514577 CCCCGTCTGGCAGCTACG 62.515 72.222 18.63 18.63 36.42 3.51
926 1285 1.473610 CCCTACTCGCTCTCTCTCGAA 60.474 57.143 0.00 0.00 34.07 3.71
1259 1673 3.337358 TCGATGATGTTGCAGTTGATGT 58.663 40.909 0.00 0.00 0.00 3.06
1292 1706 5.071519 AGCAGGTATCAGCTTATTCAGATGT 59.928 40.000 0.00 0.00 40.12 3.06
1328 1742 3.715495 GTGATGATCTGTCTGCCTACAG 58.285 50.000 8.81 8.81 46.78 2.74
1359 1773 1.496403 ATGATGATGCTCGTGCTGCG 61.496 55.000 11.19 0.00 40.48 5.18
1372 1786 2.386660 GCTGCGGCTGTTCTCACTC 61.387 63.158 11.21 0.00 35.22 3.51
1493 1907 1.064240 TCTCTACCTATCCGTGGTGCA 60.064 52.381 0.00 0.00 38.42 4.57
1646 2060 2.559698 TCCGATTTGGAGTTTCAGCA 57.440 45.000 0.00 0.00 43.74 4.41
1721 2140 3.414700 GCTTGCTCGTGGTCGTGG 61.415 66.667 0.00 0.00 38.33 4.94
1828 2247 4.087892 CCCGGGCTCCTGTGTCAG 62.088 72.222 8.08 0.00 0.00 3.51
1856 2275 1.459348 TCACTGCTCCACCACTCCA 60.459 57.895 0.00 0.00 0.00 3.86
1916 2520 3.372676 GAAGAGTACGTCGCGCCGA 62.373 63.158 19.37 5.45 0.00 5.54
1919 2523 3.165670 GAGTACGTCGCGCCGAGAT 62.166 63.158 19.37 0.00 36.23 2.75
2015 2619 2.610859 TCTTCCAGTGGCCCTCCC 60.611 66.667 3.51 0.00 0.00 4.30
2321 2925 2.978978 TGGTCTTCTTTCCACTCCATCA 59.021 45.455 0.00 0.00 0.00 3.07
2432 3036 3.357203 TCTTGATACCGACTCTTGCTCT 58.643 45.455 0.00 0.00 0.00 4.09
2442 3046 4.202202 CCGACTCTTGCTCTATTCAGGATT 60.202 45.833 0.00 0.00 0.00 3.01
2601 4719 1.115930 ACTGTCCGCACTCTCCTTGT 61.116 55.000 0.00 0.00 0.00 3.16
2608 4726 1.518903 GCACTCTCCTTGTTGTGGCC 61.519 60.000 0.00 0.00 0.00 5.36
2617 4735 0.817634 TTGTTGTGGCCTCTGTTCGG 60.818 55.000 3.32 0.00 0.00 4.30
2651 4769 4.344968 TCTCTCAACTTGATGTCCAGAACA 59.655 41.667 0.00 0.00 43.51 3.18
2746 4864 1.373497 CTGTCAACTTCGCCGCTCT 60.373 57.895 0.00 0.00 0.00 4.09
2759 4877 1.000717 GCCGCTCTCTCTATGGTCTTC 60.001 57.143 0.00 0.00 0.00 2.87
2850 4968 0.179166 CATGATCCCGCGTTGTTTGG 60.179 55.000 4.92 0.00 0.00 3.28
2865 4983 1.116308 TTTGGTCACACGTCTCCTCA 58.884 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.672881 CGTCATTCATCTCCCTTTGCC 59.327 52.381 0.00 0.00 0.00 4.52
1 2 2.352960 GTCGTCATTCATCTCCCTTTGC 59.647 50.000 0.00 0.00 0.00 3.68
2 3 3.599343 TGTCGTCATTCATCTCCCTTTG 58.401 45.455 0.00 0.00 0.00 2.77
3 4 3.981071 TGTCGTCATTCATCTCCCTTT 57.019 42.857 0.00 0.00 0.00 3.11
4 5 4.202264 GGTATGTCGTCATTCATCTCCCTT 60.202 45.833 0.00 0.00 35.70 3.95
5 6 3.322254 GGTATGTCGTCATTCATCTCCCT 59.678 47.826 0.00 0.00 35.70 4.20
6 7 3.069586 TGGTATGTCGTCATTCATCTCCC 59.930 47.826 0.00 0.00 35.70 4.30
7 8 4.322080 TGGTATGTCGTCATTCATCTCC 57.678 45.455 0.00 0.00 35.70 3.71
8 9 6.293081 CCAATTGGTATGTCGTCATTCATCTC 60.293 42.308 16.90 0.00 35.70 2.75
9 10 5.528690 CCAATTGGTATGTCGTCATTCATCT 59.471 40.000 16.90 0.00 35.70 2.90
10 11 5.751680 CCAATTGGTATGTCGTCATTCATC 58.248 41.667 16.90 0.00 35.70 2.92
11 12 5.756195 CCAATTGGTATGTCGTCATTCAT 57.244 39.130 16.90 0.00 35.70 2.57
20 21 8.444146 AGGAGACTTTTGACCAATTGGTATGTC 61.444 40.741 29.89 26.38 44.76 3.06
21 22 6.694086 AGGAGACTTTTGACCAATTGGTATGT 60.694 38.462 29.89 20.82 44.76 2.29
22 23 5.711976 AGGAGACTTTTGACCAATTGGTATG 59.288 40.000 29.89 17.97 44.76 2.39
23 24 5.711976 CAGGAGACTTTTGACCAATTGGTAT 59.288 40.000 29.89 8.91 45.19 2.73
24 25 5.070001 CAGGAGACTTTTGACCAATTGGTA 58.930 41.667 29.89 13.22 45.19 3.25
26 27 3.891366 ACAGGAGACTTTTGACCAATTGG 59.109 43.478 23.31 23.31 40.21 3.16
27 28 4.339247 ACACAGGAGACTTTTGACCAATTG 59.661 41.667 0.00 0.00 40.21 2.32
28 29 4.536765 ACACAGGAGACTTTTGACCAATT 58.463 39.130 0.00 0.00 40.21 2.32
29 30 4.170468 ACACAGGAGACTTTTGACCAAT 57.830 40.909 0.00 0.00 40.21 3.16
30 31 3.644966 ACACAGGAGACTTTTGACCAA 57.355 42.857 0.00 0.00 40.21 3.67
31 32 3.278574 CAACACAGGAGACTTTTGACCA 58.721 45.455 0.00 0.00 40.21 4.02
32 33 3.279434 ACAACACAGGAGACTTTTGACC 58.721 45.455 0.00 0.00 40.21 4.02
33 34 4.156008 ACAACAACACAGGAGACTTTTGAC 59.844 41.667 0.00 0.00 40.21 3.18
34 35 4.331968 ACAACAACACAGGAGACTTTTGA 58.668 39.130 0.00 0.00 40.21 2.69
35 36 4.396166 AGACAACAACACAGGAGACTTTTG 59.604 41.667 0.00 0.00 40.21 2.44
36 37 4.396166 CAGACAACAACACAGGAGACTTTT 59.604 41.667 0.00 0.00 40.21 2.27
37 38 3.941483 CAGACAACAACACAGGAGACTTT 59.059 43.478 0.00 0.00 40.21 2.66
38 39 3.535561 CAGACAACAACACAGGAGACTT 58.464 45.455 0.00 0.00 40.21 3.01
39 40 2.158900 CCAGACAACAACACAGGAGACT 60.159 50.000 0.00 0.00 46.44 3.24
40 41 2.213499 CCAGACAACAACACAGGAGAC 58.787 52.381 0.00 0.00 0.00 3.36
41 42 1.837439 ACCAGACAACAACACAGGAGA 59.163 47.619 0.00 0.00 0.00 3.71
42 43 1.942657 CACCAGACAACAACACAGGAG 59.057 52.381 0.00 0.00 0.00 3.69
43 44 1.408127 CCACCAGACAACAACACAGGA 60.408 52.381 0.00 0.00 0.00 3.86
44 45 1.024271 CCACCAGACAACAACACAGG 58.976 55.000 0.00 0.00 0.00 4.00
45 46 1.750193 ACCACCAGACAACAACACAG 58.250 50.000 0.00 0.00 0.00 3.66
46 47 2.208132 AACCACCAGACAACAACACA 57.792 45.000 0.00 0.00 0.00 3.72
47 48 3.057174 TCAAAACCACCAGACAACAACAC 60.057 43.478 0.00 0.00 0.00 3.32
48 49 3.157881 TCAAAACCACCAGACAACAACA 58.842 40.909 0.00 0.00 0.00 3.33
49 50 3.769536 CTCAAAACCACCAGACAACAAC 58.230 45.455 0.00 0.00 0.00 3.32
50 51 2.165437 GCTCAAAACCACCAGACAACAA 59.835 45.455 0.00 0.00 0.00 2.83
51 52 1.748493 GCTCAAAACCACCAGACAACA 59.252 47.619 0.00 0.00 0.00 3.33
52 53 2.024414 AGCTCAAAACCACCAGACAAC 58.976 47.619 0.00 0.00 0.00 3.32
53 54 2.297701 GAGCTCAAAACCACCAGACAA 58.702 47.619 9.40 0.00 0.00 3.18
54 55 1.211703 TGAGCTCAAAACCACCAGACA 59.788 47.619 15.67 0.00 0.00 3.41
55 56 1.604278 GTGAGCTCAAAACCACCAGAC 59.396 52.381 20.19 0.00 0.00 3.51
56 57 1.476833 GGTGAGCTCAAAACCACCAGA 60.477 52.381 20.19 0.00 46.13 3.86
57 58 0.954452 GGTGAGCTCAAAACCACCAG 59.046 55.000 20.19 0.00 46.13 4.00
58 59 0.817634 CGGTGAGCTCAAAACCACCA 60.818 55.000 20.19 0.00 46.96 4.17
59 60 0.534203 TCGGTGAGCTCAAAACCACC 60.534 55.000 20.19 13.91 44.08 4.61
60 61 1.464997 GATCGGTGAGCTCAAAACCAC 59.535 52.381 20.19 5.08 33.30 4.16
61 62 1.347707 AGATCGGTGAGCTCAAAACCA 59.652 47.619 20.19 7.16 33.30 3.67
62 63 2.100605 AGATCGGTGAGCTCAAAACC 57.899 50.000 20.19 14.87 0.00 3.27
63 64 3.498397 TCAAAGATCGGTGAGCTCAAAAC 59.502 43.478 20.19 11.00 0.00 2.43
64 65 3.738982 TCAAAGATCGGTGAGCTCAAAA 58.261 40.909 20.19 7.22 0.00 2.44
65 66 3.401033 TCAAAGATCGGTGAGCTCAAA 57.599 42.857 20.19 7.62 0.00 2.69
66 67 3.401033 TTCAAAGATCGGTGAGCTCAA 57.599 42.857 20.19 2.92 0.00 3.02
67 68 3.401033 TTTCAAAGATCGGTGAGCTCA 57.599 42.857 13.74 13.74 0.00 4.26
68 69 4.954092 ATTTTCAAAGATCGGTGAGCTC 57.046 40.909 6.82 6.82 0.00 4.09
69 70 7.227512 CCTATAATTTTCAAAGATCGGTGAGCT 59.772 37.037 0.00 0.00 0.00 4.09
70 71 7.226720 TCCTATAATTTTCAAAGATCGGTGAGC 59.773 37.037 2.26 0.00 0.00 4.26
71 72 8.662781 TCCTATAATTTTCAAAGATCGGTGAG 57.337 34.615 2.26 0.00 0.00 3.51
72 73 8.482943 TCTCCTATAATTTTCAAAGATCGGTGA 58.517 33.333 0.00 0.00 0.00 4.02
73 74 8.662781 TCTCCTATAATTTTCAAAGATCGGTG 57.337 34.615 0.00 0.00 0.00 4.94
74 75 9.277783 CATCTCCTATAATTTTCAAAGATCGGT 57.722 33.333 0.00 0.00 0.00 4.69
75 76 9.277783 ACATCTCCTATAATTTTCAAAGATCGG 57.722 33.333 0.00 0.00 0.00 4.18
88 89 9.658799 GTGCATGTAACATACATCTCCTATAAT 57.341 33.333 0.00 0.00 45.83 1.28
89 90 8.646900 TGTGCATGTAACATACATCTCCTATAA 58.353 33.333 0.00 0.00 45.83 0.98
90 91 8.088365 GTGTGCATGTAACATACATCTCCTATA 58.912 37.037 6.64 0.00 45.83 1.31
91 92 6.931281 GTGTGCATGTAACATACATCTCCTAT 59.069 38.462 6.64 0.00 45.83 2.57
92 93 6.127196 TGTGTGCATGTAACATACATCTCCTA 60.127 38.462 6.64 0.00 45.83 2.94
93 94 5.118990 GTGTGCATGTAACATACATCTCCT 58.881 41.667 6.64 0.00 45.83 3.69
94 95 4.875536 TGTGTGCATGTAACATACATCTCC 59.124 41.667 6.64 0.00 45.83 3.71
95 96 5.351189 TGTGTGTGCATGTAACATACATCTC 59.649 40.000 20.97 5.52 45.83 2.75
96 97 5.244755 TGTGTGTGCATGTAACATACATCT 58.755 37.500 20.97 0.00 45.83 2.90
97 98 5.351189 TCTGTGTGTGCATGTAACATACATC 59.649 40.000 23.30 11.12 45.83 3.06
99 100 4.636249 TCTGTGTGTGCATGTAACATACA 58.364 39.130 22.36 22.36 44.28 2.29
100 101 5.605564 TTCTGTGTGTGCATGTAACATAC 57.394 39.130 17.59 17.59 39.36 2.39
101 102 6.625873 TTTTCTGTGTGTGCATGTAACATA 57.374 33.333 6.64 2.10 0.00 2.29
102 103 5.512753 TTTTCTGTGTGTGCATGTAACAT 57.487 34.783 6.64 0.00 0.00 2.71
103 104 4.972514 TTTTCTGTGTGTGCATGTAACA 57.027 36.364 0.00 0.00 0.00 2.41
104 105 5.339990 ACTTTTTCTGTGTGTGCATGTAAC 58.660 37.500 0.00 0.00 0.00 2.50
105 106 5.574891 ACTTTTTCTGTGTGTGCATGTAA 57.425 34.783 0.00 0.00 0.00 2.41
106 107 5.574891 AACTTTTTCTGTGTGTGCATGTA 57.425 34.783 0.00 0.00 0.00 2.29
107 108 4.454728 AACTTTTTCTGTGTGTGCATGT 57.545 36.364 0.00 0.00 0.00 3.21
108 109 4.977963 CCTAACTTTTTCTGTGTGTGCATG 59.022 41.667 0.00 0.00 0.00 4.06
109 110 4.644685 ACCTAACTTTTTCTGTGTGTGCAT 59.355 37.500 0.00 0.00 0.00 3.96
110 111 4.013728 ACCTAACTTTTTCTGTGTGTGCA 58.986 39.130 0.00 0.00 0.00 4.57
111 112 4.632538 ACCTAACTTTTTCTGTGTGTGC 57.367 40.909 0.00 0.00 0.00 4.57
112 113 7.860872 GGAAATACCTAACTTTTTCTGTGTGTG 59.139 37.037 0.00 0.00 35.41 3.82
113 114 7.558444 TGGAAATACCTAACTTTTTCTGTGTGT 59.442 33.333 0.00 0.00 39.86 3.72
114 115 7.936584 TGGAAATACCTAACTTTTTCTGTGTG 58.063 34.615 0.00 0.00 39.86 3.82
115 116 7.778382 ACTGGAAATACCTAACTTTTTCTGTGT 59.222 33.333 0.00 0.00 39.86 3.72
116 117 8.076178 CACTGGAAATACCTAACTTTTTCTGTG 58.924 37.037 0.00 0.00 39.86 3.66
117 118 7.255486 GCACTGGAAATACCTAACTTTTTCTGT 60.255 37.037 0.00 0.00 39.86 3.41
118 119 7.040409 AGCACTGGAAATACCTAACTTTTTCTG 60.040 37.037 0.00 0.00 39.86 3.02
119 120 7.004691 AGCACTGGAAATACCTAACTTTTTCT 58.995 34.615 0.00 0.00 39.86 2.52
120 121 7.084486 CAGCACTGGAAATACCTAACTTTTTC 58.916 38.462 0.00 0.00 39.86 2.29
121 122 6.516693 GCAGCACTGGAAATACCTAACTTTTT 60.517 38.462 0.00 0.00 39.86 1.94
122 123 5.048013 GCAGCACTGGAAATACCTAACTTTT 60.048 40.000 0.00 0.00 39.86 2.27
123 124 4.459337 GCAGCACTGGAAATACCTAACTTT 59.541 41.667 0.00 0.00 39.86 2.66
124 125 4.010349 GCAGCACTGGAAATACCTAACTT 58.990 43.478 0.00 0.00 39.86 2.66
125 126 3.610911 GCAGCACTGGAAATACCTAACT 58.389 45.455 0.00 0.00 39.86 2.24
126 127 2.683362 GGCAGCACTGGAAATACCTAAC 59.317 50.000 0.00 0.00 39.86 2.34
127 128 2.576191 AGGCAGCACTGGAAATACCTAA 59.424 45.455 0.00 0.00 39.86 2.69
128 129 2.196595 AGGCAGCACTGGAAATACCTA 58.803 47.619 0.00 0.00 39.86 3.08
129 130 0.995024 AGGCAGCACTGGAAATACCT 59.005 50.000 0.00 0.00 39.86 3.08
130 131 2.710096 TAGGCAGCACTGGAAATACC 57.290 50.000 0.00 0.00 39.54 2.73
131 132 3.545703 ACATAGGCAGCACTGGAAATAC 58.454 45.455 0.00 0.00 0.00 1.89
132 133 3.199727 TGACATAGGCAGCACTGGAAATA 59.800 43.478 0.00 0.00 0.00 1.40
133 134 2.025981 TGACATAGGCAGCACTGGAAAT 60.026 45.455 0.00 0.00 0.00 2.17
134 135 1.350684 TGACATAGGCAGCACTGGAAA 59.649 47.619 0.00 0.00 0.00 3.13
135 136 0.983467 TGACATAGGCAGCACTGGAA 59.017 50.000 0.00 0.00 0.00 3.53
136 137 0.983467 TTGACATAGGCAGCACTGGA 59.017 50.000 0.00 0.00 0.00 3.86
137 138 1.065926 TCTTGACATAGGCAGCACTGG 60.066 52.381 0.00 0.00 0.00 4.00
138 139 2.277969 CTCTTGACATAGGCAGCACTG 58.722 52.381 0.00 0.00 0.00 3.66
139 140 1.905215 ACTCTTGACATAGGCAGCACT 59.095 47.619 0.00 0.00 0.00 4.40
140 141 2.393271 ACTCTTGACATAGGCAGCAC 57.607 50.000 0.00 0.00 0.00 4.40
141 142 3.118629 CCTTACTCTTGACATAGGCAGCA 60.119 47.826 0.00 0.00 0.00 4.41
142 143 3.133003 TCCTTACTCTTGACATAGGCAGC 59.867 47.826 0.00 0.00 0.00 5.25
143 144 5.344743 TTCCTTACTCTTGACATAGGCAG 57.655 43.478 0.00 0.00 0.00 4.85
144 145 5.012664 TGTTTCCTTACTCTTGACATAGGCA 59.987 40.000 0.00 0.00 0.00 4.75
145 146 5.488341 TGTTTCCTTACTCTTGACATAGGC 58.512 41.667 0.00 0.00 0.00 3.93
146 147 7.979444 TTTGTTTCCTTACTCTTGACATAGG 57.021 36.000 0.00 0.00 0.00 2.57
147 148 9.003658 ACATTTGTTTCCTTACTCTTGACATAG 57.996 33.333 0.00 0.00 0.00 2.23
148 149 8.783093 CACATTTGTTTCCTTACTCTTGACATA 58.217 33.333 0.00 0.00 0.00 2.29
149 150 7.651808 CACATTTGTTTCCTTACTCTTGACAT 58.348 34.615 0.00 0.00 0.00 3.06
150 151 6.459573 GCACATTTGTTTCCTTACTCTTGACA 60.460 38.462 0.00 0.00 0.00 3.58
151 152 5.915196 GCACATTTGTTTCCTTACTCTTGAC 59.085 40.000 0.00 0.00 0.00 3.18
152 153 5.827797 AGCACATTTGTTTCCTTACTCTTGA 59.172 36.000 0.00 0.00 0.00 3.02
153 154 6.076981 AGCACATTTGTTTCCTTACTCTTG 57.923 37.500 0.00 0.00 0.00 3.02
154 155 5.827797 TGAGCACATTTGTTTCCTTACTCTT 59.172 36.000 0.00 0.00 0.00 2.85
155 156 5.376625 TGAGCACATTTGTTTCCTTACTCT 58.623 37.500 0.00 0.00 0.00 3.24
156 157 5.689383 TGAGCACATTTGTTTCCTTACTC 57.311 39.130 0.00 0.00 0.00 2.59
157 158 6.463995 TTTGAGCACATTTGTTTCCTTACT 57.536 33.333 0.00 0.00 0.00 2.24
158 159 5.175673 GCTTTGAGCACATTTGTTTCCTTAC 59.824 40.000 0.00 0.00 41.89 2.34
159 160 5.288804 GCTTTGAGCACATTTGTTTCCTTA 58.711 37.500 0.00 0.00 41.89 2.69
160 161 4.122046 GCTTTGAGCACATTTGTTTCCTT 58.878 39.130 0.00 0.00 41.89 3.36
161 162 3.493176 GGCTTTGAGCACATTTGTTTCCT 60.493 43.478 2.04 0.00 44.75 3.36
162 163 2.802247 GGCTTTGAGCACATTTGTTTCC 59.198 45.455 2.04 0.00 44.75 3.13
163 164 3.456280 TGGCTTTGAGCACATTTGTTTC 58.544 40.909 2.04 0.00 44.75 2.78
164 165 3.460103 CTGGCTTTGAGCACATTTGTTT 58.540 40.909 2.04 0.00 44.75 2.83
165 166 2.804212 GCTGGCTTTGAGCACATTTGTT 60.804 45.455 2.04 0.00 44.75 2.83
166 167 1.269936 GCTGGCTTTGAGCACATTTGT 60.270 47.619 2.04 0.00 44.75 2.83
167 168 1.269883 TGCTGGCTTTGAGCACATTTG 60.270 47.619 2.04 0.00 44.75 2.32
168 169 1.042229 TGCTGGCTTTGAGCACATTT 58.958 45.000 2.04 0.00 44.75 2.32
169 170 2.736197 TGCTGGCTTTGAGCACATT 58.264 47.368 2.04 0.00 44.75 2.71
170 171 4.506039 TGCTGGCTTTGAGCACAT 57.494 50.000 2.04 0.00 44.75 3.21
174 175 0.453390 GTACCATGCTGGCTTTGAGC 59.547 55.000 2.50 0.00 42.67 4.26
175 176 1.470098 GTGTACCATGCTGGCTTTGAG 59.530 52.381 2.50 0.00 42.67 3.02
176 177 1.073763 AGTGTACCATGCTGGCTTTGA 59.926 47.619 2.50 0.00 42.67 2.69
177 178 1.200716 CAGTGTACCATGCTGGCTTTG 59.799 52.381 2.50 0.00 42.67 2.77
178 179 1.073763 TCAGTGTACCATGCTGGCTTT 59.926 47.619 2.50 0.00 42.67 3.51
179 180 0.692476 TCAGTGTACCATGCTGGCTT 59.308 50.000 2.50 0.00 42.67 4.35
180 181 0.692476 TTCAGTGTACCATGCTGGCT 59.308 50.000 2.50 0.00 42.67 4.75
181 182 1.755179 ATTCAGTGTACCATGCTGGC 58.245 50.000 2.50 0.00 42.67 4.85
182 183 6.455360 AATAAATTCAGTGTACCATGCTGG 57.545 37.500 1.16 1.16 45.02 4.85
183 184 8.761575 AAAAATAAATTCAGTGTACCATGCTG 57.238 30.769 0.00 0.00 0.00 4.41
206 207 9.344772 TGTTAGCAAGTTTTAGTCATCCTTAAA 57.655 29.630 0.00 0.00 0.00 1.52
207 208 8.780249 GTGTTAGCAAGTTTTAGTCATCCTTAA 58.220 33.333 0.00 0.00 0.00 1.85
208 209 7.389607 GGTGTTAGCAAGTTTTAGTCATCCTTA 59.610 37.037 0.00 0.00 0.00 2.69
209 210 6.206829 GGTGTTAGCAAGTTTTAGTCATCCTT 59.793 38.462 0.00 0.00 0.00 3.36
210 211 5.705905 GGTGTTAGCAAGTTTTAGTCATCCT 59.294 40.000 0.00 0.00 0.00 3.24
211 212 5.106277 GGGTGTTAGCAAGTTTTAGTCATCC 60.106 44.000 0.00 0.00 0.00 3.51
212 213 5.705905 AGGGTGTTAGCAAGTTTTAGTCATC 59.294 40.000 0.00 0.00 0.00 2.92
213 214 5.631119 AGGGTGTTAGCAAGTTTTAGTCAT 58.369 37.500 0.00 0.00 0.00 3.06
214 215 5.043737 AGGGTGTTAGCAAGTTTTAGTCA 57.956 39.130 0.00 0.00 0.00 3.41
215 216 8.039538 AGTATAGGGTGTTAGCAAGTTTTAGTC 58.960 37.037 0.00 0.00 0.00 2.59
216 217 7.914859 AGTATAGGGTGTTAGCAAGTTTTAGT 58.085 34.615 0.00 0.00 0.00 2.24
220 221 9.210228 ACTATAGTATAGGGTGTTAGCAAGTTT 57.790 33.333 19.18 0.00 0.00 2.66
221 222 8.779096 ACTATAGTATAGGGTGTTAGCAAGTT 57.221 34.615 19.18 0.00 0.00 2.66
222 223 8.779096 AACTATAGTATAGGGTGTTAGCAAGT 57.221 34.615 19.18 0.00 0.00 3.16
223 224 8.857098 TGAACTATAGTATAGGGTGTTAGCAAG 58.143 37.037 19.18 0.00 0.00 4.01
224 225 8.771521 TGAACTATAGTATAGGGTGTTAGCAA 57.228 34.615 19.18 0.00 0.00 3.91
225 226 8.951614 ATGAACTATAGTATAGGGTGTTAGCA 57.048 34.615 19.18 7.29 0.00 3.49
240 241 8.424918 ACTTCCAACCATGACTATGAACTATAG 58.575 37.037 0.00 0.00 43.65 1.31
241 242 8.319057 ACTTCCAACCATGACTATGAACTATA 57.681 34.615 0.00 0.00 36.36 1.31
242 243 7.200434 ACTTCCAACCATGACTATGAACTAT 57.800 36.000 0.00 0.00 36.36 2.12
243 244 6.620877 ACTTCCAACCATGACTATGAACTA 57.379 37.500 0.00 0.00 36.36 2.24
244 245 5.505181 ACTTCCAACCATGACTATGAACT 57.495 39.130 0.00 0.00 36.36 3.01
245 246 5.106157 CCAACTTCCAACCATGACTATGAAC 60.106 44.000 0.00 0.00 36.36 3.18
246 247 5.009631 CCAACTTCCAACCATGACTATGAA 58.990 41.667 0.00 0.00 36.36 2.57
247 248 4.042809 ACCAACTTCCAACCATGACTATGA 59.957 41.667 0.00 0.00 36.36 2.15
248 249 4.156556 CACCAACTTCCAACCATGACTATG 59.843 45.833 0.00 0.00 0.00 2.23
249 250 4.202567 ACACCAACTTCCAACCATGACTAT 60.203 41.667 0.00 0.00 0.00 2.12
250 251 3.137544 ACACCAACTTCCAACCATGACTA 59.862 43.478 0.00 0.00 0.00 2.59
251 252 2.091885 ACACCAACTTCCAACCATGACT 60.092 45.455 0.00 0.00 0.00 3.41
252 253 2.306847 ACACCAACTTCCAACCATGAC 58.693 47.619 0.00 0.00 0.00 3.06
253 254 2.746279 ACACCAACTTCCAACCATGA 57.254 45.000 0.00 0.00 0.00 3.07
254 255 4.141287 TCTAACACCAACTTCCAACCATG 58.859 43.478 0.00 0.00 0.00 3.66
255 256 4.447138 TCTAACACCAACTTCCAACCAT 57.553 40.909 0.00 0.00 0.00 3.55
256 257 3.935818 TCTAACACCAACTTCCAACCA 57.064 42.857 0.00 0.00 0.00 3.67
257 258 4.023193 CACATCTAACACCAACTTCCAACC 60.023 45.833 0.00 0.00 0.00 3.77
258 259 4.578928 ACACATCTAACACCAACTTCCAAC 59.421 41.667 0.00 0.00 0.00 3.77
259 260 4.787551 ACACATCTAACACCAACTTCCAA 58.212 39.130 0.00 0.00 0.00 3.53
260 261 4.431416 ACACATCTAACACCAACTTCCA 57.569 40.909 0.00 0.00 0.00 3.53
261 262 7.328737 ACTATACACATCTAACACCAACTTCC 58.671 38.462 0.00 0.00 0.00 3.46
262 263 8.251721 AGACTATACACATCTAACACCAACTTC 58.748 37.037 0.00 0.00 0.00 3.01
263 264 8.135382 AGACTATACACATCTAACACCAACTT 57.865 34.615 0.00 0.00 0.00 2.66
264 265 7.616150 AGAGACTATACACATCTAACACCAACT 59.384 37.037 0.00 0.00 0.00 3.16
265 266 7.773149 AGAGACTATACACATCTAACACCAAC 58.227 38.462 0.00 0.00 0.00 3.77
551 688 2.284625 AGATGGCGGGGTGAGACA 60.285 61.111 0.00 0.00 0.00 3.41
658 808 4.514577 CGTAGCTGCCAGACGGGG 62.515 72.222 10.44 0.00 37.04 5.73
661 811 2.202623 GTCCGTAGCTGCCAGACG 60.203 66.667 11.12 11.12 36.36 4.18
662 812 2.202623 CGTCCGTAGCTGCCAGAC 60.203 66.667 0.00 2.81 0.00 3.51
663 813 4.129737 GCGTCCGTAGCTGCCAGA 62.130 66.667 0.00 0.00 0.00 3.86
910 1269 0.321741 TGGTTCGAGAGAGAGCGAGT 60.322 55.000 0.00 0.00 43.69 4.18
977 1377 7.935210 ACATAACGAGGTCTTCCTTTTCTTTTA 59.065 33.333 0.00 0.00 45.24 1.52
1259 1673 3.455910 AGCTGATACCTGCTGGTCATAAA 59.544 43.478 19.71 1.11 44.78 1.40
1292 1706 4.594123 TCATCACGGTACACAGAAAGAA 57.406 40.909 0.00 0.00 0.00 2.52
1328 1742 2.479049 GCATCATCATTGCACCACTGAC 60.479 50.000 0.00 0.00 39.90 3.51
1437 1851 1.676529 TGATAGCGCTGACAGAGGTAC 59.323 52.381 22.90 13.19 31.25 3.34
1493 1907 0.390866 CTGAAGTGCGTGCTCCTGAT 60.391 55.000 0.00 0.00 0.00 2.90
1646 2060 5.654650 AGACGAGATAAGAACTCATGAACCT 59.345 40.000 0.00 0.00 34.47 3.50
1721 2140 2.293955 GCAAGTACCTCCGAGATAGGAC 59.706 54.545 0.00 0.00 37.57 3.85
1856 2275 2.612115 CCCCTGAAGGAGTGGGCT 60.612 66.667 0.00 0.00 39.61 5.19
1879 2301 2.457598 TCTCAGCATAAAGAGGACGGT 58.542 47.619 0.00 0.00 32.76 4.83
1916 2520 5.337652 GGAGCAGTAACCACAGAAAGTATCT 60.338 44.000 0.00 0.00 39.68 1.98
1919 2523 3.007614 GGGAGCAGTAACCACAGAAAGTA 59.992 47.826 0.00 0.00 0.00 2.24
2015 2619 1.134901 CGGAGTCGAGGAAGACACG 59.865 63.158 0.00 0.73 43.24 4.49
2321 2925 7.287696 ACATGGGAAACACTAGAAACAGAAAAT 59.712 33.333 0.00 0.00 0.00 1.82
2432 3036 3.270027 CTTGGTGCGACAATCCTGAATA 58.730 45.455 0.00 0.00 0.00 1.75
2442 3046 2.192861 CCAAAGCCTTGGTGCGACA 61.193 57.895 5.87 0.00 46.25 4.35
2617 4735 4.081972 TCAAGTTGAGAGATAGACCACTGC 60.082 45.833 0.08 0.00 0.00 4.40
2651 4769 2.030805 GCAACTCGCCATTGAGAAAAGT 60.031 45.455 0.00 0.00 39.35 2.66
2733 4851 1.066303 CATAGAGAGAGCGGCGAAGTT 59.934 52.381 12.98 0.00 0.00 2.66
2746 4864 2.501723 GGCCTGTTGAAGACCATAGAGA 59.498 50.000 0.00 0.00 0.00 3.10
2850 4968 0.603569 ACCATGAGGAGACGTGTGAC 59.396 55.000 0.00 0.00 38.69 3.67


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

AutoCloner maintained by Alex Coulton.