Multiple sequence alignment - TraesCS3D01G052000

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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 TraesCS3D01G052000 chr3D 100.000 1614 0 0 920 2533 21251981 21250368 0.000000e+00 2981.0
1 TraesCS3D01G052000 chr3D 96.748 1630 28 3 920 2533 537296727 537298347 0.000000e+00 2693.0
2 TraesCS3D01G052000 chr3D 100.000 615 0 0 1 615 21252900 21252286 0.000000e+00 1136.0
3 TraesCS3D01G052000 chr3D 95.255 274 8 4 65 338 554466418 554466150 1.800000e-116 429.0
4 TraesCS3D01G052000 chr3D 95.255 274 8 4 65 338 554476341 554476073 1.800000e-116 429.0
5 TraesCS3D01G052000 chr3D 95.802 262 7 3 65 326 264036208 264036465 1.080000e-113 420.0
6 TraesCS3D01G052000 chr3D 93.818 275 14 3 65 338 497171286 497171014 6.520000e-111 411.0
7 TraesCS3D01G052000 chr3D 95.556 45 2 0 1 45 55069773 55069817 3.500000e-09 73.1
8 TraesCS3D01G052000 chr5D 98.637 1614 22 0 920 2533 447966411 447968024 0.000000e+00 2859.0
9 TraesCS3D01G052000 chr5D 96.883 1604 24 4 946 2533 537773843 537772250 0.000000e+00 2662.0
10 TraesCS3D01G052000 chr5D 96.380 1630 31 4 920 2533 79126106 79124489 0.000000e+00 2658.0
11 TraesCS3D01G052000 chr5D 94.972 1631 30 13 920 2533 543865618 543867213 0.000000e+00 2510.0
12 TraesCS3D01G052000 chr5D 97.509 281 7 0 335 615 447965723 447966003 4.900000e-132 481.0
13 TraesCS3D01G052000 chr5D 97.834 277 6 0 339 615 543865238 543865514 1.760000e-131 479.0
14 TraesCS3D01G052000 chr5D 97.473 277 7 0 339 615 537774290 537774014 8.200000e-130 473.0
15 TraesCS3D01G052000 chr5D 95.273 275 10 3 65 338 555250499 555250227 1.390000e-117 433.0
16 TraesCS3D01G052000 chr5D 95.273 275 10 3 65 338 555259310 555259038 1.390000e-117 433.0
17 TraesCS3D01G052000 chr2D 98.451 1614 24 1 920 2533 634132403 634134015 0.000000e+00 2841.0
18 TraesCS3D01G052000 chr2D 96.752 1632 26 5 920 2533 645195032 645196654 0.000000e+00 2695.0
19 TraesCS3D01G052000 chr2D 98.195 277 5 0 339 615 634131593 634131869 3.790000e-133 484.0
20 TraesCS3D01G052000 chr2D 97.473 277 7 0 339 615 645194647 645194923 8.200000e-130 473.0
21 TraesCS3D01G052000 chr2D 95.255 274 9 3 65 338 457173964 457173695 5.010000e-117 431.0
22 TraesCS3D01G052000 chr2D 94.909 275 11 3 65 338 401219252 401218980 6.480000e-116 427.0
23 TraesCS3D01G052000 chr2D 94.526 274 11 3 65 338 426779650 426779381 1.080000e-113 420.0
24 TraesCS3D01G052000 chr2D 94.182 275 13 3 65 338 401229028 401228756 1.400000e-112 416.0
25 TraesCS3D01G052000 chr4D 98.656 1562 21 0 972 2533 398658408 398659969 0.000000e+00 2769.0
26 TraesCS3D01G052000 chr4D 97.411 1622 21 2 920 2533 36561238 36559630 0.000000e+00 2743.0
27 TraesCS3D01G052000 chr4D 98.195 277 5 0 339 615 36561616 36561340 3.790000e-133 484.0
28 TraesCS3D01G052000 chr4D 97.818 275 6 0 339 613 398657801 398658075 2.280000e-130 475.0
29 TraesCS3D01G052000 chr4D 95.420 262 8 3 65 326 478411479 478411736 5.040000e-112 414.0
30 TraesCS3D01G052000 chr4D 95.420 262 8 3 65 326 478421273 478421530 5.040000e-112 414.0
31 TraesCS3D01G052000 chr4D 98.690 229 3 0 333 561 1828230 1828458 8.440000e-110 407.0
32 TraesCS3D01G052000 chr4D 91.336 277 24 0 339 615 455275590 455275314 1.840000e-101 379.0
33 TraesCS3D01G052000 chr4D 90.681 279 18 6 65 338 438689957 438689682 5.150000e-97 364.0
34 TraesCS3D01G052000 chr4D 90.909 275 15 6 67 338 51261239 51261506 6.660000e-96 361.0
35 TraesCS3D01G052000 chr4D 90.909 275 15 5 67 338 51271155 51271422 6.660000e-96 361.0
36 TraesCS3D01G052000 chr4D 90.580 276 18 5 65 338 376250733 376251002 2.400000e-95 359.0
37 TraesCS3D01G052000 chr4D 90.545 275 18 6 64 338 160503131 160503397 8.620000e-95 357.0
38 TraesCS3D01G052000 chr4D 90.545 275 18 5 64 338 176210686 176210952 8.620000e-95 357.0
39 TraesCS3D01G052000 chr4D 90.288 278 17 7 65 338 109722566 109722295 3.100000e-94 355.0
40 TraesCS3D01G052000 chr4D 97.778 45 1 0 1 45 13427912 13427956 7.510000e-11 78.7
41 TraesCS3D01G052000 chr6D 96.803 1595 25 4 956 2533 436433018 436434603 0.000000e+00 2639.0
42 TraesCS3D01G052000 chr6D 95.084 651 7 3 1899 2533 463819967 463819326 0.000000e+00 1002.0
43 TraesCS3D01G052000 chr6D 97.834 277 6 0 339 615 17067058 17067334 1.760000e-131 479.0
44 TraesCS3D01G052000 chr6D 95.088 285 13 1 331 615 385525764 385526047 4.970000e-122 448.0
45 TraesCS3D01G052000 chr6D 97.338 263 7 0 335 597 446519597 446519859 4.970000e-122 448.0
46 TraesCS3D01G052000 chr6D 95.307 277 13 0 339 615 100358866 100359142 8.320000e-120 440.0
47 TraesCS3D01G052000 chr6D 93.929 280 17 0 336 615 82906267 82906546 8.380000e-115 424.0
48 TraesCS3D01G052000 chr6D 94.737 266 9 3 65 326 438159459 438159723 2.350000e-110 409.0
49 TraesCS3D01G052000 chr6D 95.726 234 10 0 360 593 464533527 464533294 6.610000e-101 377.0
50 TraesCS3D01G052000 chr6D 94.397 232 12 1 338 569 436432427 436432657 3.100000e-94 355.0
51 TraesCS3D01G052000 chr6D 90.943 265 16 6 65 326 313593286 313593545 1.440000e-92 350.0
52 TraesCS3D01G052000 chr6D 90.602 266 16 5 65 326 26930642 26930382 6.710000e-91 344.0
53 TraesCS3D01G052000 chr6D 90.494 263 15 6 65 326 313603057 313603310 3.120000e-89 339.0
54 TraesCS3D01G052000 chr6D 89.247 279 19 8 65 338 416045392 416045120 3.120000e-89 339.0
55 TraesCS3D01G052000 chr6D 89.247 279 19 8 65 338 416153838 416153566 3.120000e-89 339.0
56 TraesCS3D01G052000 chr6D 89.209 278 19 9 66 338 104157241 104157512 1.120000e-88 337.0
57 TraesCS3D01G052000 chr6D 89.209 278 19 9 66 338 104167054 104167325 1.120000e-88 337.0
58 TraesCS3D01G052000 chr6D 90.114 263 19 5 65 326 369514741 369514485 4.040000e-88 335.0
59 TraesCS3D01G052000 chr6D 88.889 279 20 8 65 338 416055187 416054915 1.450000e-87 333.0
60 TraesCS3D01G052000 chr6D 88.889 279 20 8 65 338 416162415 416162143 1.450000e-87 333.0
61 TraesCS3D01G052000 chr6D 95.238 84 3 1 335 418 17074981 17074899 5.690000e-27 132.0
62 TraesCS3D01G052000 chr6D 95.122 82 4 0 337 418 443299721 443299802 2.050000e-26 130.0
63 TraesCS3D01G052000 chr6D 95.000 80 4 0 339 418 82941031 82940952 2.650000e-25 126.0
64 TraesCS3D01G052000 chr6D 97.778 45 1 0 1 45 274908848 274908804 7.510000e-11 78.7
65 TraesCS3D01G052000 chr7D 95.703 1629 32 7 920 2532 3770405 3772011 0.000000e+00 2586.0
66 TraesCS3D01G052000 chr7D 94.526 274 10 3 65 338 27760128 27759860 3.900000e-113 418.0
67 TraesCS3D01G052000 chr1D 97.834 277 6 0 339 615 10554226 10554502 1.760000e-131 479.0
68 TraesCS3D01G052000 chr1D 95.307 277 13 0 339 615 490432738 490433014 8.320000e-120 440.0
69 TraesCS3D01G052000 chr1D 94.946 277 14 0 339 615 468090027 468089751 3.870000e-118 435.0
70 TraesCS3D01G052000 chr1D 94.465 271 11 3 68 338 67089139 67088873 5.040000e-112 414.0
71 TraesCS3D01G052000 chr1D 94.161 274 12 3 65 338 431280103 431279834 5.040000e-112 414.0
72 TraesCS3D01G052000 chr1D 94.182 275 11 4 65 338 431289905 431289635 5.040000e-112 414.0
73 TraesCS3D01G052000 chr1D 94.096 271 12 3 68 338 67066634 67066368 2.350000e-110 409.0
74 TraesCS3D01G052000 chr1D 94.096 271 12 3 68 338 67076316 67076050 2.350000e-110 409.0
75 TraesCS3D01G052000 chr1D 95.703 256 7 3 65 320 304686359 304686610 2.350000e-110 409.0
76 TraesCS3D01G052000 chr1D 93.796 274 12 4 65 338 243906402 243906670 8.440000e-110 407.0
77 TraesCS3D01G052000 chr1D 94.677 263 11 3 65 326 445853623 445853883 3.030000e-109 405.0
78 TraesCS3D01G052000 chr1D 81.860 215 29 8 115 327 385571069 385570863 3.350000e-39 172.0
79 TraesCS3D01G052000 chr1D 95.556 45 2 0 1 45 283684215 283684259 3.500000e-09 73.1
80 TraesCS3D01G052000 chr1A 95.699 279 12 0 337 615 567959236 567958958 1.380000e-122 449.0
81 TraesCS3D01G052000 chr3A 95.556 45 2 0 1 45 478945019 478945063 3.500000e-09 73.1
82 TraesCS3D01G052000 chr2A 95.556 45 2 0 1 45 98842734 98842778 3.500000e-09 73.1
83 TraesCS3D01G052000 chr7A 93.333 45 3 0 1 45 578773889 578773845 1.630000e-07 67.6
84 TraesCS3D01G052000 chr5B 93.333 45 3 0 1 45 268478788 268478744 1.630000e-07 67.6


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 TraesCS3D01G052000 chr3D 21250368 21252900 2532 True 2058.5 2981 100.0000 1 2533 2 chr3D.!!$R4 2532
1 TraesCS3D01G052000 chr3D 537296727 537298347 1620 False 2693.0 2693 96.7480 920 2533 1 chr3D.!!$F3 1613
2 TraesCS3D01G052000 chr5D 79124489 79126106 1617 True 2658.0 2658 96.3800 920 2533 1 chr5D.!!$R1 1613
3 TraesCS3D01G052000 chr5D 447965723 447968024 2301 False 1670.0 2859 98.0730 335 2533 2 chr5D.!!$F1 2198
4 TraesCS3D01G052000 chr5D 537772250 537774290 2040 True 1567.5 2662 97.1780 339 2533 2 chr5D.!!$R4 2194
5 TraesCS3D01G052000 chr5D 543865238 543867213 1975 False 1494.5 2510 96.4030 339 2533 2 chr5D.!!$F2 2194
6 TraesCS3D01G052000 chr2D 634131593 634134015 2422 False 1662.5 2841 98.3230 339 2533 2 chr2D.!!$F1 2194
7 TraesCS3D01G052000 chr2D 645194647 645196654 2007 False 1584.0 2695 97.1125 339 2533 2 chr2D.!!$F2 2194
8 TraesCS3D01G052000 chr4D 398657801 398659969 2168 False 1622.0 2769 98.2370 339 2533 2 chr4D.!!$F10 2194
9 TraesCS3D01G052000 chr4D 36559630 36561616 1986 True 1613.5 2743 97.8030 339 2533 2 chr4D.!!$R4 2194
10 TraesCS3D01G052000 chr6D 436432427 436434603 2176 False 1497.0 2639 95.6000 338 2533 2 chr6D.!!$F12 2195
11 TraesCS3D01G052000 chr6D 463819326 463819967 641 True 1002.0 1002 95.0840 1899 2533 1 chr6D.!!$R10 634
12 TraesCS3D01G052000 chr7D 3770405 3772011 1606 False 2586.0 2586 95.7030 920 2532 1 chr7D.!!$F1 1612

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
331 332 0.038744 CCTCTTGCCATGACCCAAGT 59.961 55.0 15.53 0.0 39.47 3.16 F
987 1217 0.981183 TACCGTTGACAAGATGCCCT 59.019 50.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1297 1528 0.984230 ATTGAGCTCTTGGGTTCCGA 59.016 50.000 16.19 0.0 0.00 4.55 R
2472 2734 1.235696 GCCTGGAGGAGGAGGAGAT 59.764 63.158 0.00 0.0 46.33 2.75 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
27 28 9.319143 ACTCACTGCTTGTCATTATACTAATTC 57.681 33.333 0.00 0.00 0.00 2.17
28 29 9.539825 CTCACTGCTTGTCATTATACTAATTCT 57.460 33.333 0.00 0.00 0.00 2.40
29 30 9.890629 TCACTGCTTGTCATTATACTAATTCTT 57.109 29.630 0.00 0.00 0.00 2.52
46 47 9.256228 ACTAATTCTTCTTACTCCATACTGACA 57.744 33.333 0.00 0.00 0.00 3.58
49 50 9.793259 AATTCTTCTTACTCCATACTGACAAAA 57.207 29.630 0.00 0.00 0.00 2.44
50 51 9.793259 ATTCTTCTTACTCCATACTGACAAAAA 57.207 29.630 0.00 0.00 0.00 1.94
51 52 9.793259 TTCTTCTTACTCCATACTGACAAAAAT 57.207 29.630 0.00 0.00 0.00 1.82
59 60 9.295825 ACTCCATACTGACAAAAATAATTGTGA 57.704 29.630 0.00 0.00 43.31 3.58
60 61 9.559958 CTCCATACTGACAAAAATAATTGTGAC 57.440 33.333 0.00 0.00 43.31 3.67
61 62 9.072375 TCCATACTGACAAAAATAATTGTGACA 57.928 29.630 0.00 0.00 43.31 3.58
62 63 9.128107 CCATACTGACAAAAATAATTGTGACAC 57.872 33.333 0.00 0.00 43.31 3.67
63 64 9.128107 CATACTGACAAAAATAATTGTGACACC 57.872 33.333 2.45 0.00 43.31 4.16
64 65 6.512297 ACTGACAAAAATAATTGTGACACCC 58.488 36.000 2.45 0.00 43.31 4.61
65 66 6.097554 ACTGACAAAAATAATTGTGACACCCA 59.902 34.615 2.45 0.00 43.31 4.51
66 67 6.878317 TGACAAAAATAATTGTGACACCCAA 58.122 32.000 2.45 0.00 43.31 4.12
67 68 7.331026 TGACAAAAATAATTGTGACACCCAAA 58.669 30.769 2.45 0.00 43.31 3.28
68 69 7.824289 TGACAAAAATAATTGTGACACCCAAAA 59.176 29.630 2.45 0.00 43.31 2.44
69 70 8.744568 ACAAAAATAATTGTGACACCCAAAAT 57.255 26.923 2.45 0.00 41.78 1.82
70 71 9.183368 ACAAAAATAATTGTGACACCCAAAATT 57.817 25.926 2.45 5.14 43.32 1.82
78 79 8.970859 ATTGTGACACCCAAAATTTTATTTGA 57.029 26.923 2.44 0.00 41.73 2.69
79 80 8.970859 TTGTGACACCCAAAATTTTATTTGAT 57.029 26.923 2.44 0.00 41.73 2.57
80 81 8.970859 TGTGACACCCAAAATTTTATTTGATT 57.029 26.923 2.44 0.00 41.73 2.57
81 82 9.401058 TGTGACACCCAAAATTTTATTTGATTT 57.599 25.926 2.44 0.00 41.73 2.17
132 133 8.800370 GAGAACTCTCCCTCTCAAAATATTTT 57.200 34.615 7.64 7.64 38.38 1.82
133 134 9.237187 GAGAACTCTCCCTCTCAAAATATTTTT 57.763 33.333 10.77 0.00 38.38 1.94
134 135 9.237187 AGAACTCTCCCTCTCAAAATATTTTTC 57.763 33.333 10.77 2.17 0.00 2.29
135 136 9.237187 GAACTCTCCCTCTCAAAATATTTTTCT 57.763 33.333 10.77 0.00 0.00 2.52
136 137 9.593565 AACTCTCCCTCTCAAAATATTTTTCTT 57.406 29.630 10.77 0.00 0.00 2.52
137 138 9.593565 ACTCTCCCTCTCAAAATATTTTTCTTT 57.406 29.630 10.77 0.00 0.00 2.52
159 160 8.930760 TCTTTTATGACAAGTGTTTTGTTTTGG 58.069 29.630 0.00 0.00 31.96 3.28
160 161 8.833231 TTTTATGACAAGTGTTTTGTTTTGGA 57.167 26.923 0.00 0.00 31.96 3.53
161 162 9.442047 TTTTATGACAAGTGTTTTGTTTTGGAT 57.558 25.926 0.00 0.00 31.96 3.41
162 163 9.442047 TTTATGACAAGTGTTTTGTTTTGGATT 57.558 25.926 0.00 0.00 31.96 3.01
163 164 6.959671 TGACAAGTGTTTTGTTTTGGATTC 57.040 33.333 0.00 0.00 31.96 2.52
164 165 6.459066 TGACAAGTGTTTTGTTTTGGATTCA 58.541 32.000 0.00 0.00 31.96 2.57
165 166 6.367422 TGACAAGTGTTTTGTTTTGGATTCAC 59.633 34.615 0.00 0.00 31.96 3.18
166 167 5.641636 ACAAGTGTTTTGTTTTGGATTCACC 59.358 36.000 0.00 0.00 39.54 4.02
167 168 4.765273 AGTGTTTTGTTTTGGATTCACCC 58.235 39.130 0.00 0.00 38.00 4.61
168 169 4.223923 AGTGTTTTGTTTTGGATTCACCCA 59.776 37.500 0.00 0.00 38.00 4.51
169 170 4.938226 GTGTTTTGTTTTGGATTCACCCAA 59.062 37.500 0.00 0.00 43.90 4.12
170 171 5.064579 GTGTTTTGTTTTGGATTCACCCAAG 59.935 40.000 0.00 0.00 45.89 3.61
171 172 5.046304 TGTTTTGTTTTGGATTCACCCAAGA 60.046 36.000 0.00 0.00 45.89 3.02
172 173 4.664150 TTGTTTTGGATTCACCCAAGAC 57.336 40.909 8.77 8.77 45.89 3.01
173 174 3.909732 TGTTTTGGATTCACCCAAGACT 58.090 40.909 14.58 0.00 45.94 3.24
174 175 4.285863 TGTTTTGGATTCACCCAAGACTT 58.714 39.130 14.58 0.00 45.94 3.01
175 176 4.099266 TGTTTTGGATTCACCCAAGACTTG 59.901 41.667 8.31 8.31 45.94 3.16
176 177 3.874383 TTGGATTCACCCAAGACTTGA 57.126 42.857 16.99 0.00 40.99 3.02
177 178 4.387026 TTGGATTCACCCAAGACTTGAT 57.613 40.909 16.99 1.37 40.99 2.57
178 179 4.387026 TGGATTCACCCAAGACTTGATT 57.613 40.909 16.99 0.00 38.00 2.57
179 180 4.739793 TGGATTCACCCAAGACTTGATTT 58.260 39.130 16.99 0.00 38.00 2.17
180 181 5.147032 TGGATTCACCCAAGACTTGATTTT 58.853 37.500 16.99 0.00 38.00 1.82
181 182 5.010922 TGGATTCACCCAAGACTTGATTTTG 59.989 40.000 16.99 7.67 38.00 2.44
182 183 4.935352 TTCACCCAAGACTTGATTTTGG 57.065 40.909 16.99 10.84 40.79 3.28
183 184 3.909732 TCACCCAAGACTTGATTTTGGT 58.090 40.909 16.99 11.47 39.74 3.67
184 185 4.285863 TCACCCAAGACTTGATTTTGGTT 58.714 39.130 16.99 0.00 39.74 3.67
185 186 4.714308 TCACCCAAGACTTGATTTTGGTTT 59.286 37.500 16.99 0.00 39.74 3.27
186 187 5.188751 TCACCCAAGACTTGATTTTGGTTTT 59.811 36.000 16.99 0.00 39.74 2.43
187 188 5.294060 CACCCAAGACTTGATTTTGGTTTTG 59.706 40.000 16.99 0.43 39.74 2.44
188 189 4.815846 CCCAAGACTTGATTTTGGTTTTGG 59.184 41.667 16.99 0.00 41.71 3.28
189 190 5.396213 CCCAAGACTTGATTTTGGTTTTGGA 60.396 40.000 16.99 0.00 43.45 3.53
190 191 5.754890 CCAAGACTTGATTTTGGTTTTGGAG 59.245 40.000 16.99 0.00 43.45 3.86
191 192 5.535753 AGACTTGATTTTGGTTTTGGAGG 57.464 39.130 0.00 0.00 0.00 4.30
192 193 4.962362 AGACTTGATTTTGGTTTTGGAGGT 59.038 37.500 0.00 0.00 0.00 3.85
193 194 5.425217 AGACTTGATTTTGGTTTTGGAGGTT 59.575 36.000 0.00 0.00 0.00 3.50
194 195 6.061022 ACTTGATTTTGGTTTTGGAGGTTT 57.939 33.333 0.00 0.00 0.00 3.27
195 196 6.480763 ACTTGATTTTGGTTTTGGAGGTTTT 58.519 32.000 0.00 0.00 0.00 2.43
196 197 6.945435 ACTTGATTTTGGTTTTGGAGGTTTTT 59.055 30.769 0.00 0.00 0.00 1.94
197 198 6.993786 TGATTTTGGTTTTGGAGGTTTTTC 57.006 33.333 0.00 0.00 0.00 2.29
198 199 5.883115 TGATTTTGGTTTTGGAGGTTTTTCC 59.117 36.000 0.00 0.00 37.77 3.13
212 213 5.953571 AGGTTTTTCCTTCTTATGTGGACT 58.046 37.500 0.00 0.00 45.67 3.85
213 214 6.004574 AGGTTTTTCCTTCTTATGTGGACTC 58.995 40.000 0.00 0.00 45.67 3.36
214 215 5.768164 GGTTTTTCCTTCTTATGTGGACTCA 59.232 40.000 0.00 0.00 0.00 3.41
215 216 6.264518 GGTTTTTCCTTCTTATGTGGACTCAA 59.735 38.462 0.00 0.00 0.00 3.02
216 217 7.201875 GGTTTTTCCTTCTTATGTGGACTCAAA 60.202 37.037 0.00 0.00 0.00 2.69
217 218 7.889873 TTTTCCTTCTTATGTGGACTCAAAA 57.110 32.000 0.00 0.00 0.00 2.44
218 219 6.877611 TTCCTTCTTATGTGGACTCAAAAC 57.122 37.500 0.00 0.00 0.00 2.43
219 220 5.313712 TCCTTCTTATGTGGACTCAAAACC 58.686 41.667 0.00 0.00 0.00 3.27
220 221 5.070001 CCTTCTTATGTGGACTCAAAACCA 58.930 41.667 0.00 0.00 0.00 3.67
221 222 5.534654 CCTTCTTATGTGGACTCAAAACCAA 59.465 40.000 0.00 0.00 37.94 3.67
222 223 6.040391 CCTTCTTATGTGGACTCAAAACCAAA 59.960 38.462 0.00 0.00 37.94 3.28
223 224 7.255942 CCTTCTTATGTGGACTCAAAACCAAAT 60.256 37.037 0.00 0.00 37.76 2.32
224 225 6.980593 TCTTATGTGGACTCAAAACCAAATG 58.019 36.000 0.00 0.00 35.24 2.32
225 226 3.451141 TGTGGACTCAAAACCAAATGC 57.549 42.857 0.00 0.00 37.94 3.56
226 227 3.030291 TGTGGACTCAAAACCAAATGCT 58.970 40.909 0.00 0.00 37.94 3.79
227 228 3.450457 TGTGGACTCAAAACCAAATGCTT 59.550 39.130 0.00 0.00 37.94 3.91
228 229 4.081198 TGTGGACTCAAAACCAAATGCTTT 60.081 37.500 0.00 0.00 37.94 3.51
229 230 4.875536 GTGGACTCAAAACCAAATGCTTTT 59.124 37.500 0.00 0.00 37.94 2.27
230 231 5.006649 GTGGACTCAAAACCAAATGCTTTTC 59.993 40.000 0.00 0.00 37.94 2.29
231 232 5.115480 GGACTCAAAACCAAATGCTTTTCA 58.885 37.500 0.00 0.00 0.00 2.69
232 233 5.006649 GGACTCAAAACCAAATGCTTTTCAC 59.993 40.000 0.00 0.00 0.00 3.18
233 234 5.733676 ACTCAAAACCAAATGCTTTTCACT 58.266 33.333 0.00 0.00 0.00 3.41
234 235 6.172630 ACTCAAAACCAAATGCTTTTCACTT 58.827 32.000 0.00 0.00 0.00 3.16
235 236 6.092533 ACTCAAAACCAAATGCTTTTCACTTG 59.907 34.615 0.00 0.00 32.12 3.16
238 239 3.749665 CCAAATGCTTTTCACTTGGGA 57.250 42.857 0.00 0.00 45.64 4.37
239 240 3.656559 CCAAATGCTTTTCACTTGGGAG 58.343 45.455 0.00 0.00 45.64 4.30
240 241 3.321682 CCAAATGCTTTTCACTTGGGAGA 59.678 43.478 0.00 0.00 45.64 3.71
241 242 4.020839 CCAAATGCTTTTCACTTGGGAGAT 60.021 41.667 0.00 0.00 45.64 2.75
242 243 5.511888 CCAAATGCTTTTCACTTGGGAGATT 60.512 40.000 0.00 0.00 45.64 2.40
243 244 5.813513 AATGCTTTTCACTTGGGAGATTT 57.186 34.783 0.00 0.00 0.00 2.17
244 245 4.853924 TGCTTTTCACTTGGGAGATTTC 57.146 40.909 0.00 0.00 0.00 2.17
245 246 3.573967 TGCTTTTCACTTGGGAGATTTCC 59.426 43.478 0.00 0.00 43.23 3.13
246 247 3.829026 GCTTTTCACTTGGGAGATTTCCT 59.171 43.478 1.74 0.00 43.49 3.36
247 248 4.281941 GCTTTTCACTTGGGAGATTTCCTT 59.718 41.667 1.74 0.00 43.49 3.36
248 249 5.221521 GCTTTTCACTTGGGAGATTTCCTTT 60.222 40.000 1.74 0.00 43.49 3.11
249 250 5.789643 TTTCACTTGGGAGATTTCCTTTG 57.210 39.130 1.74 0.00 43.49 2.77
250 251 4.722526 TCACTTGGGAGATTTCCTTTGA 57.277 40.909 1.74 0.00 43.49 2.69
251 252 5.060427 TCACTTGGGAGATTTCCTTTGAA 57.940 39.130 1.74 0.00 43.49 2.69
252 253 5.454062 TCACTTGGGAGATTTCCTTTGAAA 58.546 37.500 1.74 0.00 44.22 2.69
253 254 5.896678 TCACTTGGGAGATTTCCTTTGAAAA 59.103 36.000 1.74 0.00 43.37 2.29
254 255 6.382570 TCACTTGGGAGATTTCCTTTGAAAAA 59.617 34.615 1.74 0.00 43.37 1.94
288 289 2.734755 CCCTATGGCATTTGGAGTGA 57.265 50.000 17.31 0.00 0.00 3.41
289 290 3.234234 CCCTATGGCATTTGGAGTGAT 57.766 47.619 17.31 0.00 0.00 3.06
290 291 4.371624 CCCTATGGCATTTGGAGTGATA 57.628 45.455 17.31 0.00 0.00 2.15
291 292 4.927049 CCCTATGGCATTTGGAGTGATAT 58.073 43.478 17.31 0.00 0.00 1.63
292 293 5.327732 CCCTATGGCATTTGGAGTGATATT 58.672 41.667 17.31 0.00 0.00 1.28
293 294 5.416952 CCCTATGGCATTTGGAGTGATATTC 59.583 44.000 17.31 0.00 0.00 1.75
294 295 6.243900 CCTATGGCATTTGGAGTGATATTCT 58.756 40.000 4.78 0.00 0.00 2.40
295 296 6.373774 CCTATGGCATTTGGAGTGATATTCTC 59.626 42.308 4.78 1.70 0.00 2.87
304 305 5.373812 GGAGTGATATTCTCCCCTTTTCA 57.626 43.478 13.63 0.00 43.90 2.69
305 306 5.755849 GGAGTGATATTCTCCCCTTTTCAA 58.244 41.667 13.63 0.00 43.90 2.69
306 307 6.187682 GGAGTGATATTCTCCCCTTTTCAAA 58.812 40.000 13.63 0.00 43.90 2.69
307 308 6.663523 GGAGTGATATTCTCCCCTTTTCAAAA 59.336 38.462 13.63 0.00 43.90 2.44
308 309 7.178451 GGAGTGATATTCTCCCCTTTTCAAAAA 59.822 37.037 13.63 0.00 43.90 1.94
309 310 8.670521 AGTGATATTCTCCCCTTTTCAAAAAT 57.329 30.769 0.00 0.00 0.00 1.82
310 311 9.104713 AGTGATATTCTCCCCTTTTCAAAAATT 57.895 29.630 0.00 0.00 0.00 1.82
311 312 9.725019 GTGATATTCTCCCCTTTTCAAAAATTT 57.275 29.630 0.00 0.00 0.00 1.82
312 313 9.942850 TGATATTCTCCCCTTTTCAAAAATTTC 57.057 29.630 0.00 0.00 0.00 2.17
313 314 9.383519 GATATTCTCCCCTTTTCAAAAATTTCC 57.616 33.333 0.00 0.00 0.00 3.13
314 315 6.823286 TTCTCCCCTTTTCAAAAATTTCCT 57.177 33.333 0.00 0.00 0.00 3.36
315 316 6.419484 TCTCCCCTTTTCAAAAATTTCCTC 57.581 37.500 0.00 0.00 0.00 3.71
316 317 6.143206 TCTCCCCTTTTCAAAAATTTCCTCT 58.857 36.000 0.00 0.00 0.00 3.69
317 318 6.615316 TCTCCCCTTTTCAAAAATTTCCTCTT 59.385 34.615 0.00 0.00 0.00 2.85
318 319 6.591001 TCCCCTTTTCAAAAATTTCCTCTTG 58.409 36.000 0.00 0.00 0.00 3.02
319 320 5.239306 CCCCTTTTCAAAAATTTCCTCTTGC 59.761 40.000 0.00 0.00 0.00 4.01
320 321 5.239306 CCCTTTTCAAAAATTTCCTCTTGCC 59.761 40.000 0.00 0.00 0.00 4.52
321 322 5.821995 CCTTTTCAAAAATTTCCTCTTGCCA 59.178 36.000 0.00 0.00 0.00 4.92
322 323 6.487668 CCTTTTCAAAAATTTCCTCTTGCCAT 59.512 34.615 0.00 0.00 0.00 4.40
323 324 6.864360 TTTCAAAAATTTCCTCTTGCCATG 57.136 33.333 0.00 0.00 0.00 3.66
324 325 5.804944 TCAAAAATTTCCTCTTGCCATGA 57.195 34.783 0.00 0.00 0.00 3.07
325 326 5.540911 TCAAAAATTTCCTCTTGCCATGAC 58.459 37.500 0.00 0.00 0.00 3.06
326 327 4.541973 AAAATTTCCTCTTGCCATGACC 57.458 40.909 0.00 0.00 0.00 4.02
327 328 2.149973 ATTTCCTCTTGCCATGACCC 57.850 50.000 0.00 0.00 0.00 4.46
328 329 0.776810 TTTCCTCTTGCCATGACCCA 59.223 50.000 0.00 0.00 0.00 4.51
329 330 0.776810 TTCCTCTTGCCATGACCCAA 59.223 50.000 0.00 0.00 0.00 4.12
330 331 0.329261 TCCTCTTGCCATGACCCAAG 59.671 55.000 11.94 11.94 39.74 3.61
331 332 0.038744 CCTCTTGCCATGACCCAAGT 59.961 55.000 15.53 0.00 39.47 3.16
332 333 1.281867 CCTCTTGCCATGACCCAAGTA 59.718 52.381 15.53 6.64 39.47 2.24
333 334 2.636830 CTCTTGCCATGACCCAAGTAG 58.363 52.381 15.53 10.46 39.47 2.57
432 433 4.554973 GTGATGCGATGTTTTAGAAGCAAC 59.445 41.667 0.00 0.00 38.15 4.17
528 529 2.829592 GCGGGCCCTAGCAGTTAT 59.170 61.111 22.43 0.00 42.56 1.89
569 570 2.420022 ACAACTTATCCACGCAAGCATC 59.580 45.455 0.00 0.00 45.62 3.91
987 1217 0.981183 TACCGTTGACAAGATGCCCT 59.019 50.000 0.00 0.00 0.00 5.19
1297 1528 4.951603 AGGTTGAAATTGGAGGGATCAAT 58.048 39.130 0.00 0.00 36.50 2.57
1525 1756 9.573133 GGGTTTATTTTACTTGATGTTCATCAG 57.427 33.333 13.89 11.20 31.46 2.90
1642 1873 6.804534 TTTGAATTAGTGTGAAGCAAAACG 57.195 33.333 0.00 0.00 0.00 3.60
1734 1967 8.420374 TTTGTTCTTCAGTTAACAGAGTACAG 57.580 34.615 8.61 0.00 36.96 2.74
1753 1986 7.690256 AGTACAGACCCAAATTCAGTTTCTAT 58.310 34.615 0.00 0.00 0.00 1.98
2472 2734 2.224450 GGGTTCTTCTTCGGGTTCTTCA 60.224 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.319143 GAATTAGTATAATGACAAGCAGTGAGT 57.681 33.333 0.00 0.00 0.00 3.41
2 3 9.539825 AGAATTAGTATAATGACAAGCAGTGAG 57.460 33.333 0.00 0.00 0.00 3.51
3 4 9.890629 AAGAATTAGTATAATGACAAGCAGTGA 57.109 29.630 0.00 0.00 0.00 3.41
20 21 9.256228 TGTCAGTATGGAGTAAGAAGAATTAGT 57.744 33.333 0.00 0.00 36.16 2.24
23 24 9.793259 TTTTGTCAGTATGGAGTAAGAAGAATT 57.207 29.630 0.00 0.00 36.16 2.17
24 25 9.793259 TTTTTGTCAGTATGGAGTAAGAAGAAT 57.207 29.630 0.00 0.00 36.16 2.40
25 26 9.793259 ATTTTTGTCAGTATGGAGTAAGAAGAA 57.207 29.630 0.00 0.00 36.16 2.52
33 34 9.295825 TCACAATTATTTTTGTCAGTATGGAGT 57.704 29.630 0.00 0.00 37.73 3.85
34 35 9.559958 GTCACAATTATTTTTGTCAGTATGGAG 57.440 33.333 0.00 0.00 37.73 3.86
35 36 9.072375 TGTCACAATTATTTTTGTCAGTATGGA 57.928 29.630 0.00 0.00 37.73 3.41
36 37 9.128107 GTGTCACAATTATTTTTGTCAGTATGG 57.872 33.333 0.00 0.00 37.73 2.74
37 38 9.128107 GGTGTCACAATTATTTTTGTCAGTATG 57.872 33.333 5.12 0.00 37.73 2.39
38 39 8.303876 GGGTGTCACAATTATTTTTGTCAGTAT 58.696 33.333 5.12 0.00 37.73 2.12
39 40 7.285629 TGGGTGTCACAATTATTTTTGTCAGTA 59.714 33.333 5.12 0.00 37.73 2.74
40 41 6.097554 TGGGTGTCACAATTATTTTTGTCAGT 59.902 34.615 5.12 0.00 37.73 3.41
41 42 6.511416 TGGGTGTCACAATTATTTTTGTCAG 58.489 36.000 5.12 0.00 37.73 3.51
42 43 6.471233 TGGGTGTCACAATTATTTTTGTCA 57.529 33.333 5.12 0.00 37.73 3.58
43 44 7.778470 TTTGGGTGTCACAATTATTTTTGTC 57.222 32.000 5.12 0.00 37.73 3.18
44 45 8.744568 ATTTTGGGTGTCACAATTATTTTTGT 57.255 26.923 5.12 0.00 40.39 2.83
52 53 9.401058 TCAAATAAAATTTTGGGTGTCACAATT 57.599 25.926 13.76 0.00 37.35 2.32
53 54 8.970859 TCAAATAAAATTTTGGGTGTCACAAT 57.029 26.923 13.76 0.00 37.23 2.71
54 55 8.970859 ATCAAATAAAATTTTGGGTGTCACAA 57.029 26.923 13.76 0.00 37.23 3.33
55 56 8.970859 AATCAAATAAAATTTTGGGTGTCACA 57.029 26.923 13.76 0.00 37.23 3.58
107 108 8.800370 AAAATATTTTGAGAGGGAGAGTTCTC 57.200 34.615 12.62 0.39 42.14 2.87
108 109 9.237187 GAAAAATATTTTGAGAGGGAGAGTTCT 57.763 33.333 14.04 0.00 0.00 3.01
109 110 9.237187 AGAAAAATATTTTGAGAGGGAGAGTTC 57.763 33.333 14.04 3.74 0.00 3.01
110 111 9.593565 AAGAAAAATATTTTGAGAGGGAGAGTT 57.406 29.630 14.04 0.00 0.00 3.01
111 112 9.593565 AAAGAAAAATATTTTGAGAGGGAGAGT 57.406 29.630 14.04 0.00 0.00 3.24
133 134 8.930760 CCAAAACAAAACACTTGTCATAAAAGA 58.069 29.630 0.00 0.00 0.00 2.52
134 135 8.930760 TCCAAAACAAAACACTTGTCATAAAAG 58.069 29.630 0.00 0.00 0.00 2.27
135 136 8.833231 TCCAAAACAAAACACTTGTCATAAAA 57.167 26.923 0.00 0.00 0.00 1.52
136 137 9.442047 AATCCAAAACAAAACACTTGTCATAAA 57.558 25.926 0.00 0.00 0.00 1.40
137 138 9.092876 GAATCCAAAACAAAACACTTGTCATAA 57.907 29.630 0.00 0.00 0.00 1.90
138 139 8.253810 TGAATCCAAAACAAAACACTTGTCATA 58.746 29.630 0.00 0.00 0.00 2.15
139 140 7.064490 GTGAATCCAAAACAAAACACTTGTCAT 59.936 33.333 0.00 0.00 0.00 3.06
140 141 6.367422 GTGAATCCAAAACAAAACACTTGTCA 59.633 34.615 0.00 0.00 0.00 3.58
141 142 6.183360 GGTGAATCCAAAACAAAACACTTGTC 60.183 38.462 0.00 0.00 35.97 3.18
142 143 5.641636 GGTGAATCCAAAACAAAACACTTGT 59.358 36.000 0.00 0.00 35.97 3.16
143 144 5.064579 GGGTGAATCCAAAACAAAACACTTG 59.935 40.000 0.00 0.00 38.11 3.16
144 145 5.182487 GGGTGAATCCAAAACAAAACACTT 58.818 37.500 0.00 0.00 38.11 3.16
145 146 4.223923 TGGGTGAATCCAAAACAAAACACT 59.776 37.500 0.00 0.00 38.11 3.55
146 147 4.508662 TGGGTGAATCCAAAACAAAACAC 58.491 39.130 0.00 0.00 38.11 3.32
147 148 4.826274 TGGGTGAATCCAAAACAAAACA 57.174 36.364 0.00 0.00 38.11 2.83
148 149 5.293324 GTCTTGGGTGAATCCAAAACAAAAC 59.707 40.000 0.00 0.00 45.13 2.43
149 150 5.188751 AGTCTTGGGTGAATCCAAAACAAAA 59.811 36.000 1.80 0.00 45.13 2.44
150 151 4.714308 AGTCTTGGGTGAATCCAAAACAAA 59.286 37.500 1.80 0.00 45.13 2.83
151 152 4.285863 AGTCTTGGGTGAATCCAAAACAA 58.714 39.130 1.80 0.00 45.13 2.83
152 153 3.909732 AGTCTTGGGTGAATCCAAAACA 58.090 40.909 1.80 0.00 45.13 2.83
153 154 4.340950 TCAAGTCTTGGGTGAATCCAAAAC 59.659 41.667 12.66 0.00 45.13 2.43
154 155 4.541705 TCAAGTCTTGGGTGAATCCAAAA 58.458 39.130 12.66 0.00 45.13 2.44
155 156 4.177537 TCAAGTCTTGGGTGAATCCAAA 57.822 40.909 12.66 0.00 45.13 3.28
156 157 3.874383 TCAAGTCTTGGGTGAATCCAA 57.126 42.857 12.66 0.00 43.82 3.53
157 158 4.387026 AATCAAGTCTTGGGTGAATCCA 57.613 40.909 12.66 0.00 38.11 3.41
158 159 5.473039 CAAAATCAAGTCTTGGGTGAATCC 58.527 41.667 12.66 0.00 0.00 3.01
159 160 5.011023 ACCAAAATCAAGTCTTGGGTGAATC 59.989 40.000 12.66 0.00 43.30 2.52
160 161 4.901250 ACCAAAATCAAGTCTTGGGTGAAT 59.099 37.500 12.66 0.00 43.30 2.57
161 162 4.285863 ACCAAAATCAAGTCTTGGGTGAA 58.714 39.130 12.66 0.00 43.30 3.18
162 163 3.909732 ACCAAAATCAAGTCTTGGGTGA 58.090 40.909 12.66 0.00 43.30 4.02
163 164 4.670896 AACCAAAATCAAGTCTTGGGTG 57.329 40.909 12.66 5.90 43.30 4.61
164 165 5.427378 CAAAACCAAAATCAAGTCTTGGGT 58.573 37.500 12.66 8.46 42.02 4.51
165 166 4.815846 CCAAAACCAAAATCAAGTCTTGGG 59.184 41.667 12.66 7.85 43.30 4.12
166 167 5.669477 TCCAAAACCAAAATCAAGTCTTGG 58.331 37.500 12.66 0.00 44.35 3.61
167 168 5.754890 CCTCCAAAACCAAAATCAAGTCTTG 59.245 40.000 6.21 6.21 0.00 3.02
168 169 5.425217 ACCTCCAAAACCAAAATCAAGTCTT 59.575 36.000 0.00 0.00 0.00 3.01
169 170 4.962362 ACCTCCAAAACCAAAATCAAGTCT 59.038 37.500 0.00 0.00 0.00 3.24
170 171 5.276461 ACCTCCAAAACCAAAATCAAGTC 57.724 39.130 0.00 0.00 0.00 3.01
171 172 5.692115 AACCTCCAAAACCAAAATCAAGT 57.308 34.783 0.00 0.00 0.00 3.16
172 173 7.389803 AAAAACCTCCAAAACCAAAATCAAG 57.610 32.000 0.00 0.00 0.00 3.02
173 174 6.375736 GGAAAAACCTCCAAAACCAAAATCAA 59.624 34.615 0.00 0.00 35.36 2.57
174 175 5.883115 GGAAAAACCTCCAAAACCAAAATCA 59.117 36.000 0.00 0.00 35.36 2.57
175 176 6.371809 GGAAAAACCTCCAAAACCAAAATC 57.628 37.500 0.00 0.00 35.36 2.17
190 191 5.768164 TGAGTCCACATAAGAAGGAAAAACC 59.232 40.000 0.00 0.00 39.35 3.27
191 192 6.877611 TGAGTCCACATAAGAAGGAAAAAC 57.122 37.500 0.00 0.00 32.30 2.43
192 193 7.889873 TTTGAGTCCACATAAGAAGGAAAAA 57.110 32.000 0.00 0.00 32.30 1.94
193 194 7.201875 GGTTTTGAGTCCACATAAGAAGGAAAA 60.202 37.037 0.00 0.00 32.30 2.29
194 195 6.264518 GGTTTTGAGTCCACATAAGAAGGAAA 59.735 38.462 0.00 0.00 32.30 3.13
195 196 5.768164 GGTTTTGAGTCCACATAAGAAGGAA 59.232 40.000 0.00 0.00 32.30 3.36
196 197 5.163141 TGGTTTTGAGTCCACATAAGAAGGA 60.163 40.000 0.00 0.00 0.00 3.36
197 198 5.070001 TGGTTTTGAGTCCACATAAGAAGG 58.930 41.667 0.00 0.00 0.00 3.46
198 199 6.633500 TTGGTTTTGAGTCCACATAAGAAG 57.367 37.500 0.00 0.00 33.12 2.85
199 200 7.432869 CATTTGGTTTTGAGTCCACATAAGAA 58.567 34.615 0.00 0.00 33.12 2.52
200 201 6.516527 GCATTTGGTTTTGAGTCCACATAAGA 60.517 38.462 0.00 0.00 33.12 2.10
201 202 5.634859 GCATTTGGTTTTGAGTCCACATAAG 59.365 40.000 0.00 0.00 33.12 1.73
202 203 5.304101 AGCATTTGGTTTTGAGTCCACATAA 59.696 36.000 0.00 0.00 33.12 1.90
203 204 4.832266 AGCATTTGGTTTTGAGTCCACATA 59.168 37.500 0.00 0.00 33.12 2.29
204 205 3.642848 AGCATTTGGTTTTGAGTCCACAT 59.357 39.130 0.00 0.00 33.12 3.21
205 206 3.030291 AGCATTTGGTTTTGAGTCCACA 58.970 40.909 0.00 0.00 33.12 4.17
206 207 3.733443 AGCATTTGGTTTTGAGTCCAC 57.267 42.857 0.00 0.00 33.12 4.02
207 208 4.751767 AAAGCATTTGGTTTTGAGTCCA 57.248 36.364 2.06 0.00 42.34 4.02
219 220 4.589216 TCTCCCAAGTGAAAAGCATTTG 57.411 40.909 0.00 0.00 42.11 2.32
220 221 5.813513 AATCTCCCAAGTGAAAAGCATTT 57.186 34.783 0.00 0.00 42.41 2.32
221 222 5.279657 GGAAATCTCCCAAGTGAAAAGCATT 60.280 40.000 0.00 0.00 35.42 3.56
222 223 4.221482 GGAAATCTCCCAAGTGAAAAGCAT 59.779 41.667 0.00 0.00 35.42 3.79
223 224 3.573967 GGAAATCTCCCAAGTGAAAAGCA 59.426 43.478 0.00 0.00 35.42 3.91
224 225 3.829026 AGGAAATCTCCCAAGTGAAAAGC 59.171 43.478 0.00 0.00 43.64 3.51
225 226 6.040842 TCAAAGGAAATCTCCCAAGTGAAAAG 59.959 38.462 0.00 0.00 43.64 2.27
226 227 5.896678 TCAAAGGAAATCTCCCAAGTGAAAA 59.103 36.000 0.00 0.00 43.64 2.29
227 228 5.454062 TCAAAGGAAATCTCCCAAGTGAAA 58.546 37.500 0.00 0.00 43.64 2.69
228 229 5.060427 TCAAAGGAAATCTCCCAAGTGAA 57.940 39.130 0.00 0.00 43.64 3.18
229 230 4.722526 TCAAAGGAAATCTCCCAAGTGA 57.277 40.909 0.00 0.00 43.64 3.41
230 231 5.789643 TTTCAAAGGAAATCTCCCAAGTG 57.210 39.130 0.00 0.00 43.64 3.16
231 232 6.806668 TTTTTCAAAGGAAATCTCCCAAGT 57.193 33.333 0.00 0.00 43.64 3.16
269 270 2.734755 TCACTCCAAATGCCATAGGG 57.265 50.000 0.00 0.00 37.18 3.53
270 271 6.243900 AGAATATCACTCCAAATGCCATAGG 58.756 40.000 0.00 0.00 0.00 2.57
271 272 7.375106 GAGAATATCACTCCAAATGCCATAG 57.625 40.000 0.00 0.00 0.00 2.23
283 284 7.703058 TTTTGAAAAGGGGAGAATATCACTC 57.297 36.000 0.00 0.00 0.00 3.51
284 285 8.670521 ATTTTTGAAAAGGGGAGAATATCACT 57.329 30.769 0.00 0.00 0.00 3.41
285 286 9.725019 AAATTTTTGAAAAGGGGAGAATATCAC 57.275 29.630 0.00 0.00 0.00 3.06
286 287 9.942850 GAAATTTTTGAAAAGGGGAGAATATCA 57.057 29.630 0.00 0.00 0.00 2.15
287 288 9.383519 GGAAATTTTTGAAAAGGGGAGAATATC 57.616 33.333 0.00 0.00 0.00 1.63
288 289 9.116080 AGGAAATTTTTGAAAAGGGGAGAATAT 57.884 29.630 0.00 0.00 0.00 1.28
289 290 8.504811 AGGAAATTTTTGAAAAGGGGAGAATA 57.495 30.769 0.00 0.00 0.00 1.75
290 291 7.293299 AGAGGAAATTTTTGAAAAGGGGAGAAT 59.707 33.333 0.00 0.00 0.00 2.40
291 292 6.615316 AGAGGAAATTTTTGAAAAGGGGAGAA 59.385 34.615 0.00 0.00 0.00 2.87
292 293 6.143206 AGAGGAAATTTTTGAAAAGGGGAGA 58.857 36.000 0.00 0.00 0.00 3.71
293 294 6.425210 AGAGGAAATTTTTGAAAAGGGGAG 57.575 37.500 0.00 0.00 0.00 4.30
294 295 6.591001 CAAGAGGAAATTTTTGAAAAGGGGA 58.409 36.000 0.00 0.00 0.00 4.81
295 296 5.239306 GCAAGAGGAAATTTTTGAAAAGGGG 59.761 40.000 4.82 0.00 0.00 4.79
296 297 5.239306 GGCAAGAGGAAATTTTTGAAAAGGG 59.761 40.000 4.82 0.00 0.00 3.95
297 298 5.821995 TGGCAAGAGGAAATTTTTGAAAAGG 59.178 36.000 4.82 0.00 0.00 3.11
298 299 6.923928 TGGCAAGAGGAAATTTTTGAAAAG 57.076 33.333 4.82 0.00 0.00 2.27
299 300 7.012232 GTCATGGCAAGAGGAAATTTTTGAAAA 59.988 33.333 4.82 0.00 0.00 2.29
300 301 6.482973 GTCATGGCAAGAGGAAATTTTTGAAA 59.517 34.615 4.82 0.00 0.00 2.69
301 302 5.990996 GTCATGGCAAGAGGAAATTTTTGAA 59.009 36.000 4.82 0.00 0.00 2.69
302 303 5.511202 GGTCATGGCAAGAGGAAATTTTTGA 60.511 40.000 0.00 0.00 0.00 2.69
303 304 4.692155 GGTCATGGCAAGAGGAAATTTTTG 59.308 41.667 0.00 0.00 0.00 2.44
304 305 4.263025 GGGTCATGGCAAGAGGAAATTTTT 60.263 41.667 0.00 0.00 0.00 1.94
305 306 3.261643 GGGTCATGGCAAGAGGAAATTTT 59.738 43.478 0.00 0.00 0.00 1.82
306 307 2.833943 GGGTCATGGCAAGAGGAAATTT 59.166 45.455 0.00 0.00 0.00 1.82
307 308 2.225343 TGGGTCATGGCAAGAGGAAATT 60.225 45.455 0.00 0.00 0.00 1.82
308 309 1.358787 TGGGTCATGGCAAGAGGAAAT 59.641 47.619 0.00 0.00 0.00 2.17
309 310 0.776810 TGGGTCATGGCAAGAGGAAA 59.223 50.000 0.00 0.00 0.00 3.13
310 311 0.776810 TTGGGTCATGGCAAGAGGAA 59.223 50.000 0.00 0.00 0.00 3.36
311 312 0.329261 CTTGGGTCATGGCAAGAGGA 59.671 55.000 0.00 0.00 0.00 3.71
312 313 0.038744 ACTTGGGTCATGGCAAGAGG 59.961 55.000 0.00 0.00 0.00 3.69
313 314 2.237143 TCTACTTGGGTCATGGCAAGAG 59.763 50.000 0.00 0.00 0.00 2.85
314 315 2.265367 TCTACTTGGGTCATGGCAAGA 58.735 47.619 0.00 0.00 0.00 3.02
315 316 2.787473 TCTACTTGGGTCATGGCAAG 57.213 50.000 0.00 0.00 0.00 4.01
316 317 3.517296 TTTCTACTTGGGTCATGGCAA 57.483 42.857 0.00 0.00 0.00 4.52
317 318 3.355378 CATTTCTACTTGGGTCATGGCA 58.645 45.455 0.00 0.00 0.00 4.92
318 319 2.689983 CCATTTCTACTTGGGTCATGGC 59.310 50.000 0.00 0.00 0.00 4.40
319 320 3.290710 CCCATTTCTACTTGGGTCATGG 58.709 50.000 0.00 0.00 46.38 3.66
326 327 3.319122 GCTATTGGCCCATTTCTACTTGG 59.681 47.826 0.00 0.00 34.27 3.61
327 328 4.210331 AGCTATTGGCCCATTTCTACTTG 58.790 43.478 0.00 0.00 43.05 3.16
328 329 4.464947 GAGCTATTGGCCCATTTCTACTT 58.535 43.478 0.00 0.00 43.05 2.24
329 330 3.181439 GGAGCTATTGGCCCATTTCTACT 60.181 47.826 0.00 0.00 43.05 2.57
330 331 3.149981 GGAGCTATTGGCCCATTTCTAC 58.850 50.000 0.00 0.00 43.05 2.59
331 332 3.056080 AGGAGCTATTGGCCCATTTCTA 58.944 45.455 0.00 0.00 43.05 2.10
332 333 1.855599 AGGAGCTATTGGCCCATTTCT 59.144 47.619 0.00 0.00 43.05 2.52
333 334 1.959282 CAGGAGCTATTGGCCCATTTC 59.041 52.381 0.00 0.00 43.05 2.17
432 433 1.667236 TGTCGCATTGGAGCTATTGG 58.333 50.000 0.00 0.00 0.00 3.16
569 570 4.457496 ACGCTGATGAGCACGGGG 62.457 66.667 4.68 0.00 46.62 5.73
969 1199 0.606401 CAGGGCATCTTGTCAACGGT 60.606 55.000 0.00 0.00 0.00 4.83
1251 1482 2.862536 CAACATAGTCATCGAGCCACTG 59.137 50.000 4.38 0.00 0.00 3.66
1297 1528 0.984230 ATTGAGCTCTTGGGTTCCGA 59.016 50.000 16.19 0.00 0.00 4.55
1525 1756 8.870879 ACTGAAACTATAACAAATTCTAGCGAC 58.129 33.333 0.00 0.00 0.00 5.19
2472 2734 1.235696 GCCTGGAGGAGGAGGAGAT 59.764 63.158 0.00 0.00 46.33 2.75
2505 2768 1.920835 GGAGTGAAGGGAGGCACCT 60.921 63.158 0.00 0.00 44.56 4.00


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

AutoCloner maintained by Alex Coulton.