Multiple sequence alignment - TraesCS5A01G453000

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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 TraesCS5A01G453000 chr5A 100.000 3260 0 0 1 3260 634500250 634496991 0.000000e+00 6021.0
1 TraesCS5A01G453000 chr5A 78.190 1646 276 50 993 2597 634488325 634486722 0.000000e+00 974.0
2 TraesCS5A01G453000 chr5A 91.250 320 28 0 1043 1362 634491627 634491308 1.390000e-118 436.0
3 TraesCS5A01G453000 chr5A 92.135 89 6 1 3143 3230 634490776 634490688 1.230000e-24 124.0
4 TraesCS5A01G453000 chr5B 87.093 1937 167 33 361 2268 637447974 637446092 0.000000e+00 2115.0
5 TraesCS5A01G453000 chr5B 88.523 1002 71 9 2276 3242 637444084 637443092 0.000000e+00 1173.0
6 TraesCS5A01G453000 chr5D 81.497 1924 244 52 1407 3260 507197242 507195361 0.000000e+00 1478.0
7 TraesCS5A01G453000 chr5D 87.846 1193 109 10 1429 2597 507421627 507420447 0.000000e+00 1367.0
8 TraesCS5A01G453000 chr5D 91.982 661 32 7 2600 3242 507420411 507419754 0.000000e+00 907.0
9 TraesCS5A01G453000 chr5D 90.099 505 43 5 867 1364 507139620 507139116 0.000000e+00 649.0
10 TraesCS5A01G453000 chr5D 90.612 490 41 4 867 1352 507422168 507421680 0.000000e+00 645.0
11 TraesCS5A01G453000 chr5D 86.715 414 37 6 956 1360 507174331 507173927 8.300000e-121 444.0
12 TraesCS5A01G453000 chr5D 76.031 897 148 38 1407 2245 507166370 507165483 1.410000e-108 403.0
13 TraesCS5A01G453000 chr5D 89.068 311 34 0 1043 1353 507197540 507197230 1.420000e-103 387.0
14 TraesCS5A01G453000 chr5D 87.311 331 40 2 1023 1352 506943877 506943548 8.540000e-101 377.0
15 TraesCS5A01G453000 chr5D 78.268 589 79 22 2050 2607 506941352 506940782 1.870000e-87 333.0
16 TraesCS5A01G453000 chr5D 81.183 186 19 6 2419 2597 506948605 506948429 5.670000e-28 135.0
17 TraesCS5A01G453000 chr5D 91.011 89 7 1 3143 3230 507171477 507171389 5.710000e-23 119.0
18 TraesCS5A01G453000 chr6D 88.013 317 37 1 1037 1352 448872757 448872441 1.100000e-99 374.0
19 TraesCS5A01G453000 chr6D 81.685 273 39 8 78 348 448846179 448845916 1.970000e-52 217.0
20 TraesCS5A01G453000 chr4D 81.633 294 35 13 514 801 88148288 88148008 3.270000e-55 226.0
21 TraesCS5A01G453000 chr4D 80.000 100 11 7 438 529 51603847 51603945 7.550000e-07 65.8
22 TraesCS5A01G453000 chrUn 80.479 292 45 10 71 358 68242573 68242290 2.550000e-51 213.0
23 TraesCS5A01G453000 chr2A 80.068 296 46 12 71 363 14691950 14692235 1.190000e-49 207.0
24 TraesCS5A01G453000 chr2A 85.000 160 15 6 589 747 31388343 31388494 1.570000e-33 154.0
25 TraesCS5A01G453000 chr4A 81.600 250 38 7 501 747 4247883 4248127 1.980000e-47 200.0
26 TraesCS5A01G453000 chr4A 83.099 213 22 11 594 801 501128836 501128633 7.190000e-42 182.0
27 TraesCS5A01G453000 chr4A 88.636 44 3 2 4 45 449405751 449405708 6.000000e-03 52.8
28 TraesCS5A01G453000 chr4B 81.928 249 30 10 543 787 124922853 124922616 2.570000e-46 196.0
29 TraesCS5A01G453000 chr4B 84.874 119 14 3 398 512 414222172 414222290 2.060000e-22 117.0
30 TraesCS5A01G453000 chr2D 79.322 295 49 11 71 363 12627008 12627292 2.570000e-46 196.0
31 TraesCS5A01G453000 chr2B 81.034 232 34 8 526 755 105749827 105750050 3.340000e-40 176.0
32 TraesCS5A01G453000 chr2B 83.069 189 21 10 584 766 47370367 47370184 9.360000e-36 161.0
33 TraesCS5A01G453000 chr3D 85.366 164 19 3 558 720 96413806 96413647 7.240000e-37 165.0
34 TraesCS5A01G453000 chr3D 79.167 144 26 1 1217 1360 2677071 2676932 2.680000e-16 97.1
35 TraesCS5A01G453000 chr1A 80.447 179 29 5 350 527 58174712 58174539 7.340000e-27 132.0
36 TraesCS5A01G453000 chr1D 80.571 175 29 4 354 527 59526399 59526229 2.640000e-26 130.0
37 TraesCS5A01G453000 chr1B 94.872 39 2 0 1 39 505640743 505640781 9.770000e-06 62.1


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 TraesCS5A01G453000 chr5A 634496991 634500250 3259 True 6021.000000 6021 100.000000 1 3260 1 chr5A.!!$R1 3259
1 TraesCS5A01G453000 chr5A 634486722 634491627 4905 True 511.333333 974 87.191667 993 3230 3 chr5A.!!$R2 2237
2 TraesCS5A01G453000 chr5B 637443092 637447974 4882 True 1644.000000 2115 87.808000 361 3242 2 chr5B.!!$R1 2881
3 TraesCS5A01G453000 chr5D 507419754 507422168 2414 True 973.000000 1367 90.146667 867 3242 3 chr5D.!!$R7 2375
4 TraesCS5A01G453000 chr5D 507195361 507197540 2179 True 932.500000 1478 85.282500 1043 3260 2 chr5D.!!$R6 2217
5 TraesCS5A01G453000 chr5D 507139116 507139620 504 True 649.000000 649 90.099000 867 1364 1 chr5D.!!$R2 497
6 TraesCS5A01G453000 chr5D 507165483 507166370 887 True 403.000000 403 76.031000 1407 2245 1 chr5D.!!$R3 838
7 TraesCS5A01G453000 chr5D 506940782 506943877 3095 True 355.000000 377 82.789500 1023 2607 2 chr5D.!!$R4 1584
8 TraesCS5A01G453000 chr5D 507171389 507174331 2942 True 281.500000 444 88.863000 956 3230 2 chr5D.!!$R5 2274

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
819 825 0.029433 CATCGAGCGAGTCCGATTCA 59.971 55.0 0.0 0.0 42.79 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2560 11222 0.179029 TCGCCTGCCTATTTTAGGGC 60.179 55.0 2.9 0.0 46.32 5.19 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
24 25 7.283254 CAACTATGTCAACTCACTATGTCAC 57.717 40.000 0.00 0.00 0.00 3.67
25 26 6.842437 ACTATGTCAACTCACTATGTCACT 57.158 37.500 0.00 0.00 0.00 3.41
26 27 7.939784 ACTATGTCAACTCACTATGTCACTA 57.060 36.000 0.00 0.00 0.00 2.74
27 28 8.526667 ACTATGTCAACTCACTATGTCACTAT 57.473 34.615 0.00 0.00 0.00 2.12
28 29 8.409371 ACTATGTCAACTCACTATGTCACTATG 58.591 37.037 0.00 0.00 0.00 2.23
29 30 5.410924 TGTCAACTCACTATGTCACTATGC 58.589 41.667 0.00 0.00 0.00 3.14
30 31 5.047377 TGTCAACTCACTATGTCACTATGCA 60.047 40.000 0.00 0.00 0.00 3.96
31 32 6.045318 GTCAACTCACTATGTCACTATGCAT 58.955 40.000 3.79 3.79 0.00 3.96
32 33 6.019237 GTCAACTCACTATGTCACTATGCATG 60.019 42.308 10.16 1.82 0.00 4.06
33 34 5.859205 ACTCACTATGTCACTATGCATGA 57.141 39.130 10.16 0.00 0.00 3.07
34 35 6.225981 ACTCACTATGTCACTATGCATGAA 57.774 37.500 10.16 0.00 0.00 2.57
35 36 6.643388 ACTCACTATGTCACTATGCATGAAA 58.357 36.000 10.16 0.00 0.00 2.69
36 37 7.105588 ACTCACTATGTCACTATGCATGAAAA 58.894 34.615 10.16 0.00 0.00 2.29
37 38 7.607607 ACTCACTATGTCACTATGCATGAAAAA 59.392 33.333 10.16 0.00 0.00 1.94
56 57 5.638596 AAAAACCCACCAACTCGATTATC 57.361 39.130 0.00 0.00 0.00 1.75
57 58 4.569719 AAACCCACCAACTCGATTATCT 57.430 40.909 0.00 0.00 0.00 1.98
58 59 4.569719 AACCCACCAACTCGATTATCTT 57.430 40.909 0.00 0.00 0.00 2.40
59 60 3.873910 ACCCACCAACTCGATTATCTTG 58.126 45.455 0.00 0.00 0.00 3.02
60 61 3.517901 ACCCACCAACTCGATTATCTTGA 59.482 43.478 0.00 0.00 0.00 3.02
61 62 3.871594 CCCACCAACTCGATTATCTTGAC 59.128 47.826 0.00 0.00 0.00 3.18
62 63 4.503910 CCACCAACTCGATTATCTTGACA 58.496 43.478 0.00 0.00 0.00 3.58
63 64 5.118990 CCACCAACTCGATTATCTTGACAT 58.881 41.667 0.00 0.00 0.00 3.06
64 65 5.007039 CCACCAACTCGATTATCTTGACATG 59.993 44.000 0.00 0.00 0.00 3.21
65 66 4.572389 ACCAACTCGATTATCTTGACATGC 59.428 41.667 0.00 0.00 0.00 4.06
66 67 4.571984 CCAACTCGATTATCTTGACATGCA 59.428 41.667 0.00 0.00 0.00 3.96
67 68 5.065090 CCAACTCGATTATCTTGACATGCAA 59.935 40.000 0.00 0.00 34.73 4.08
68 69 5.725110 ACTCGATTATCTTGACATGCAAC 57.275 39.130 0.00 0.00 31.96 4.17
69 70 5.423015 ACTCGATTATCTTGACATGCAACT 58.577 37.500 0.00 0.00 31.96 3.16
70 71 6.573434 ACTCGATTATCTTGACATGCAACTA 58.427 36.000 0.00 0.00 31.96 2.24
71 72 7.212976 ACTCGATTATCTTGACATGCAACTAT 58.787 34.615 0.00 0.00 31.96 2.12
72 73 7.170489 ACTCGATTATCTTGACATGCAACTATG 59.830 37.037 0.00 0.00 31.96 2.23
88 89 4.385740 TGCCACCATGCATGCCCT 62.386 61.111 21.69 2.51 36.04 5.19
89 90 2.123769 GCCACCATGCATGCCCTA 60.124 61.111 21.69 0.00 0.00 3.53
90 91 1.532316 GCCACCATGCATGCCCTAT 60.532 57.895 21.69 0.00 0.00 2.57
91 92 0.251297 GCCACCATGCATGCCCTATA 60.251 55.000 21.69 0.00 0.00 1.31
92 93 1.822854 GCCACCATGCATGCCCTATAA 60.823 52.381 21.69 0.00 0.00 0.98
93 94 2.596346 CCACCATGCATGCCCTATAAA 58.404 47.619 21.69 0.00 0.00 1.40
94 95 2.964464 CCACCATGCATGCCCTATAAAA 59.036 45.455 21.69 0.00 0.00 1.52
95 96 3.579586 CCACCATGCATGCCCTATAAAAT 59.420 43.478 21.69 0.00 0.00 1.82
96 97 4.040706 CCACCATGCATGCCCTATAAAATT 59.959 41.667 21.69 0.00 0.00 1.82
97 98 5.455040 CCACCATGCATGCCCTATAAAATTT 60.455 40.000 21.69 0.00 0.00 1.82
98 99 6.239543 CCACCATGCATGCCCTATAAAATTTA 60.240 38.462 21.69 0.00 0.00 1.40
99 100 6.869913 CACCATGCATGCCCTATAAAATTTAG 59.130 38.462 21.69 4.16 0.00 1.85
100 101 6.554605 ACCATGCATGCCCTATAAAATTTAGT 59.445 34.615 21.69 4.80 0.00 2.24
101 102 7.071071 ACCATGCATGCCCTATAAAATTTAGTT 59.929 33.333 21.69 0.00 0.00 2.24
102 103 7.599998 CCATGCATGCCCTATAAAATTTAGTTC 59.400 37.037 21.69 0.00 0.00 3.01
103 104 7.896383 TGCATGCCCTATAAAATTTAGTTCT 57.104 32.000 16.68 0.00 0.00 3.01
104 105 7.940850 TGCATGCCCTATAAAATTTAGTTCTC 58.059 34.615 16.68 0.00 0.00 2.87
105 106 7.779798 TGCATGCCCTATAAAATTTAGTTCTCT 59.220 33.333 16.68 0.00 0.00 3.10
106 107 9.284968 GCATGCCCTATAAAATTTAGTTCTCTA 57.715 33.333 6.36 0.00 0.00 2.43
122 123 7.617041 AGTTCTCTAAACATTCAACTATGCC 57.383 36.000 0.00 0.00 0.00 4.40
123 124 7.168219 AGTTCTCTAAACATTCAACTATGCCA 58.832 34.615 0.00 0.00 0.00 4.92
124 125 7.665559 AGTTCTCTAAACATTCAACTATGCCAA 59.334 33.333 0.00 0.00 0.00 4.52
125 126 7.377766 TCTCTAAACATTCAACTATGCCAAC 57.622 36.000 0.00 0.00 0.00 3.77
126 127 7.168219 TCTCTAAACATTCAACTATGCCAACT 58.832 34.615 0.00 0.00 0.00 3.16
127 128 7.334421 TCTCTAAACATTCAACTATGCCAACTC 59.666 37.037 0.00 0.00 0.00 3.01
128 129 6.939730 TCTAAACATTCAACTATGCCAACTCA 59.060 34.615 0.00 0.00 0.00 3.41
129 130 5.376854 AACATTCAACTATGCCAACTCAC 57.623 39.130 0.00 0.00 0.00 3.51
130 131 4.655963 ACATTCAACTATGCCAACTCACT 58.344 39.130 0.00 0.00 0.00 3.41
131 132 5.804639 ACATTCAACTATGCCAACTCACTA 58.195 37.500 0.00 0.00 0.00 2.74
132 133 6.418101 ACATTCAACTATGCCAACTCACTAT 58.582 36.000 0.00 0.00 0.00 2.12
133 134 6.317140 ACATTCAACTATGCCAACTCACTATG 59.683 38.462 0.00 0.00 0.00 2.23
134 135 4.191544 TCAACTATGCCAACTCACTATGC 58.808 43.478 0.00 0.00 0.00 3.14
135 136 4.080919 TCAACTATGCCAACTCACTATGCT 60.081 41.667 0.00 0.00 0.00 3.79
136 137 5.128663 TCAACTATGCCAACTCACTATGCTA 59.871 40.000 0.00 0.00 0.00 3.49
137 138 4.950050 ACTATGCCAACTCACTATGCTAC 58.050 43.478 0.00 0.00 0.00 3.58
138 139 4.651503 ACTATGCCAACTCACTATGCTACT 59.348 41.667 0.00 0.00 0.00 2.57
139 140 5.833667 ACTATGCCAACTCACTATGCTACTA 59.166 40.000 0.00 0.00 0.00 1.82
140 141 5.815233 ATGCCAACTCACTATGCTACTAT 57.185 39.130 0.00 0.00 0.00 2.12
141 142 4.948847 TGCCAACTCACTATGCTACTATG 58.051 43.478 0.00 0.00 0.00 2.23
142 143 3.743396 GCCAACTCACTATGCTACTATGC 59.257 47.826 0.00 0.00 0.00 3.14
171 172 4.871933 AAAACCCACCTTCACATGAATC 57.128 40.909 0.00 0.00 33.01 2.52
172 173 3.524095 AACCCACCTTCACATGAATCA 57.476 42.857 0.00 0.00 33.01 2.57
173 174 3.744940 ACCCACCTTCACATGAATCAT 57.255 42.857 0.00 0.00 33.01 2.45
174 175 3.359033 ACCCACCTTCACATGAATCATG 58.641 45.455 20.58 20.58 46.18 3.07
175 176 2.100252 CCCACCTTCACATGAATCATGC 59.900 50.000 21.92 0.00 44.80 4.06
176 177 2.756207 CCACCTTCACATGAATCATGCA 59.244 45.455 21.92 7.22 44.80 3.96
177 178 3.383505 CCACCTTCACATGAATCATGCAT 59.616 43.478 21.92 1.79 44.80 3.96
178 179 4.359706 CACCTTCACATGAATCATGCATG 58.640 43.478 21.92 21.07 44.80 4.06
260 261 9.935241 AATTATATGTGCTCGAGTATCAATTCT 57.065 29.630 15.13 0.00 33.17 2.40
261 262 8.972262 TTATATGTGCTCGAGTATCAATTCTC 57.028 34.615 15.13 0.00 33.17 2.87
262 263 4.718940 TGTGCTCGAGTATCAATTCTCA 57.281 40.909 15.13 0.00 33.17 3.27
263 264 5.268118 TGTGCTCGAGTATCAATTCTCAT 57.732 39.130 15.13 0.00 33.17 2.90
264 265 6.391227 TGTGCTCGAGTATCAATTCTCATA 57.609 37.500 15.13 0.00 33.17 2.15
265 266 6.986250 TGTGCTCGAGTATCAATTCTCATAT 58.014 36.000 15.13 0.00 33.17 1.78
266 267 6.865205 TGTGCTCGAGTATCAATTCTCATATG 59.135 38.462 15.13 0.00 33.17 1.78
267 268 6.309980 GTGCTCGAGTATCAATTCTCATATGG 59.690 42.308 15.13 0.00 33.17 2.74
268 269 5.290643 GCTCGAGTATCAATTCTCATATGGC 59.709 44.000 15.13 0.00 33.17 4.40
269 270 6.596309 TCGAGTATCAATTCTCATATGGCT 57.404 37.500 2.13 0.00 33.17 4.75
270 271 7.629437 GCTCGAGTATCAATTCTCATATGGCTA 60.629 40.741 15.13 0.00 33.17 3.93
271 272 8.122472 TCGAGTATCAATTCTCATATGGCTAA 57.878 34.615 2.13 0.00 33.17 3.09
272 273 8.753133 TCGAGTATCAATTCTCATATGGCTAAT 58.247 33.333 2.13 0.00 33.17 1.73
273 274 9.029243 CGAGTATCAATTCTCATATGGCTAATC 57.971 37.037 2.13 0.00 33.17 1.75
274 275 9.881649 GAGTATCAATTCTCATATGGCTAATCA 57.118 33.333 2.13 0.00 33.17 2.57
279 280 9.187996 TCAATTCTCATATGGCTAATCAAAACA 57.812 29.630 2.13 0.00 0.00 2.83
280 281 9.241317 CAATTCTCATATGGCTAATCAAAACAC 57.759 33.333 2.13 0.00 0.00 3.32
281 282 8.757982 ATTCTCATATGGCTAATCAAAACACT 57.242 30.769 2.13 0.00 0.00 3.55
282 283 9.851686 ATTCTCATATGGCTAATCAAAACACTA 57.148 29.630 2.13 0.00 0.00 2.74
283 284 9.679661 TTCTCATATGGCTAATCAAAACACTAA 57.320 29.630 2.13 0.00 0.00 2.24
284 285 9.851686 TCTCATATGGCTAATCAAAACACTAAT 57.148 29.630 2.13 0.00 0.00 1.73
285 286 9.888878 CTCATATGGCTAATCAAAACACTAATG 57.111 33.333 2.13 0.00 0.00 1.90
286 287 9.407380 TCATATGGCTAATCAAAACACTAATGT 57.593 29.630 2.13 0.00 42.46 2.71
299 300 4.787551 ACACTAATGTTTCAACCCACTGA 58.212 39.130 0.00 0.00 34.46 3.41
300 301 5.197451 ACACTAATGTTTCAACCCACTGAA 58.803 37.500 0.00 0.00 34.46 3.02
301 302 5.833131 ACACTAATGTTTCAACCCACTGAAT 59.167 36.000 0.00 0.00 34.46 2.57
302 303 6.016276 ACACTAATGTTTCAACCCACTGAATC 60.016 38.462 0.00 0.00 34.46 2.52
303 304 6.207417 CACTAATGTTTCAACCCACTGAATCT 59.793 38.462 0.00 0.00 35.31 2.40
304 305 5.712152 AATGTTTCAACCCACTGAATCTC 57.288 39.130 0.00 0.00 35.31 2.75
305 306 4.163441 TGTTTCAACCCACTGAATCTCA 57.837 40.909 0.00 0.00 35.31 3.27
306 307 4.728772 TGTTTCAACCCACTGAATCTCAT 58.271 39.130 0.00 0.00 35.31 2.90
307 308 5.875224 TGTTTCAACCCACTGAATCTCATA 58.125 37.500 0.00 0.00 35.31 2.15
308 309 5.939883 TGTTTCAACCCACTGAATCTCATAG 59.060 40.000 0.00 0.00 35.31 2.23
309 310 6.173339 GTTTCAACCCACTGAATCTCATAGA 58.827 40.000 0.00 0.00 35.31 1.98
310 311 6.373005 TTCAACCCACTGAATCTCATAGAA 57.627 37.500 0.00 0.00 30.31 2.10
311 312 6.373005 TCAACCCACTGAATCTCATAGAAA 57.627 37.500 0.00 0.00 0.00 2.52
312 313 6.962182 TCAACCCACTGAATCTCATAGAAAT 58.038 36.000 0.00 0.00 0.00 2.17
313 314 7.405292 TCAACCCACTGAATCTCATAGAAATT 58.595 34.615 0.00 0.00 0.00 1.82
314 315 8.548025 TCAACCCACTGAATCTCATAGAAATTA 58.452 33.333 0.00 0.00 0.00 1.40
315 316 8.616076 CAACCCACTGAATCTCATAGAAATTAC 58.384 37.037 0.00 0.00 0.00 1.89
316 317 8.095452 ACCCACTGAATCTCATAGAAATTACT 57.905 34.615 0.00 0.00 0.00 2.24
317 318 7.989741 ACCCACTGAATCTCATAGAAATTACTG 59.010 37.037 0.00 0.00 0.00 2.74
318 319 7.041508 CCCACTGAATCTCATAGAAATTACTGC 60.042 40.741 0.00 0.00 0.00 4.40
319 320 7.496920 CCACTGAATCTCATAGAAATTACTGCA 59.503 37.037 0.00 0.00 0.00 4.41
320 321 9.053840 CACTGAATCTCATAGAAATTACTGCAT 57.946 33.333 0.00 0.00 0.00 3.96
321 322 9.270640 ACTGAATCTCATAGAAATTACTGCATC 57.729 33.333 0.00 0.00 0.00 3.91
322 323 8.613060 TGAATCTCATAGAAATTACTGCATCC 57.387 34.615 0.00 0.00 0.00 3.51
323 324 7.386025 TGAATCTCATAGAAATTACTGCATCCG 59.614 37.037 0.00 0.00 0.00 4.18
324 325 6.405278 TCTCATAGAAATTACTGCATCCGA 57.595 37.500 0.00 0.00 0.00 4.55
325 326 6.997655 TCTCATAGAAATTACTGCATCCGAT 58.002 36.000 0.00 0.00 0.00 4.18
326 327 7.445121 TCTCATAGAAATTACTGCATCCGATT 58.555 34.615 0.00 0.00 0.00 3.34
327 328 7.600375 TCTCATAGAAATTACTGCATCCGATTC 59.400 37.037 0.00 0.00 0.00 2.52
328 329 6.650807 TCATAGAAATTACTGCATCCGATTCC 59.349 38.462 0.00 0.00 0.00 3.01
329 330 4.137543 AGAAATTACTGCATCCGATTCCC 58.862 43.478 0.00 0.00 0.00 3.97
330 331 3.576078 AATTACTGCATCCGATTCCCA 57.424 42.857 0.00 0.00 0.00 4.37
331 332 2.325583 TTACTGCATCCGATTCCCAC 57.674 50.000 0.00 0.00 0.00 4.61
332 333 1.199615 TACTGCATCCGATTCCCACA 58.800 50.000 0.00 0.00 0.00 4.17
333 334 0.327924 ACTGCATCCGATTCCCACAA 59.672 50.000 0.00 0.00 0.00 3.33
334 335 0.734889 CTGCATCCGATTCCCACAAC 59.265 55.000 0.00 0.00 0.00 3.32
335 336 0.037447 TGCATCCGATTCCCACAACA 59.963 50.000 0.00 0.00 0.00 3.33
336 337 1.173043 GCATCCGATTCCCACAACAA 58.827 50.000 0.00 0.00 0.00 2.83
337 338 1.750778 GCATCCGATTCCCACAACAAT 59.249 47.619 0.00 0.00 0.00 2.71
338 339 2.480073 GCATCCGATTCCCACAACAATG 60.480 50.000 0.00 0.00 0.00 2.82
339 340 1.173043 TCCGATTCCCACAACAATGC 58.827 50.000 0.00 0.00 0.00 3.56
340 341 0.179166 CCGATTCCCACAACAATGCG 60.179 55.000 0.00 0.00 0.00 4.73
341 342 0.798009 CGATTCCCACAACAATGCGC 60.798 55.000 0.00 0.00 0.00 6.09
342 343 0.798009 GATTCCCACAACAATGCGCG 60.798 55.000 0.00 0.00 0.00 6.86
343 344 2.211619 ATTCCCACAACAATGCGCGG 62.212 55.000 8.83 0.00 0.00 6.46
344 345 4.418401 CCCACAACAATGCGCGGG 62.418 66.667 8.83 0.00 0.00 6.13
345 346 3.669344 CCACAACAATGCGCGGGT 61.669 61.111 8.83 0.00 0.00 5.28
346 347 2.328856 CCACAACAATGCGCGGGTA 61.329 57.895 8.83 0.00 0.00 3.69
347 348 1.653094 CCACAACAATGCGCGGGTAT 61.653 55.000 8.83 0.00 0.00 2.73
348 349 0.248054 CACAACAATGCGCGGGTATC 60.248 55.000 8.83 0.00 0.00 2.24
349 350 0.675208 ACAACAATGCGCGGGTATCA 60.675 50.000 8.83 0.00 0.00 2.15
350 351 0.662619 CAACAATGCGCGGGTATCAT 59.337 50.000 8.83 0.00 0.00 2.45
351 352 0.944386 AACAATGCGCGGGTATCATC 59.056 50.000 8.83 0.00 0.00 2.92
352 353 0.106708 ACAATGCGCGGGTATCATCT 59.893 50.000 8.83 0.00 0.00 2.90
353 354 0.792640 CAATGCGCGGGTATCATCTC 59.207 55.000 8.83 0.00 0.00 2.75
354 355 0.681733 AATGCGCGGGTATCATCTCT 59.318 50.000 8.83 0.00 0.00 3.10
355 356 1.545841 ATGCGCGGGTATCATCTCTA 58.454 50.000 8.83 0.00 0.00 2.43
356 357 0.881796 TGCGCGGGTATCATCTCTAG 59.118 55.000 8.83 0.00 0.00 2.43
357 358 0.882474 GCGCGGGTATCATCTCTAGT 59.118 55.000 8.83 0.00 0.00 2.57
358 359 2.082231 GCGCGGGTATCATCTCTAGTA 58.918 52.381 8.83 0.00 0.00 1.82
359 360 2.683867 GCGCGGGTATCATCTCTAGTAT 59.316 50.000 8.83 0.00 0.00 2.12
421 422 4.330894 ACATGCAACTATGACAACTCATCG 59.669 41.667 0.00 0.00 38.21 3.84
428 429 0.037326 TGACAACTCATCGAGCCACC 60.037 55.000 0.00 0.00 32.04 4.61
432 433 0.745845 AACTCATCGAGCCACCATGC 60.746 55.000 0.00 0.00 32.04 4.06
438 439 2.265739 GAGCCACCATGCACGAGA 59.734 61.111 0.00 0.00 0.00 4.04
442 443 0.527565 GCCACCATGCACGAGAAAAT 59.472 50.000 0.00 0.00 0.00 1.82
460 462 5.185056 AGAAAATACCCACCTTAACATGCAC 59.815 40.000 0.00 0.00 0.00 4.57
480 482 4.756642 GCACCATGCATGCTACTTATCTTA 59.243 41.667 21.69 0.00 44.26 2.10
481 483 5.334414 GCACCATGCATGCTACTTATCTTAC 60.334 44.000 21.69 0.00 44.26 2.34
486 488 8.499162 CCATGCATGCTACTTATCTTACTAAAC 58.501 37.037 21.69 0.00 0.00 2.01
488 490 9.784531 ATGCATGCTACTTATCTTACTAAACAT 57.215 29.630 20.33 0.00 0.00 2.71
541 543 0.254747 TGCAACTAGGTATGTGCCCC 59.745 55.000 0.00 0.00 0.00 5.80
594 596 7.852971 TTAAGAAAATACAAGGACCATACGG 57.147 36.000 0.00 0.00 38.77 4.02
714 720 9.601217 GGTATGTGTCTATGATTACTCTGTTTT 57.399 33.333 0.00 0.00 0.00 2.43
744 750 9.706691 GGTTACCGAATATAAGAGATTGATTGA 57.293 33.333 0.00 0.00 0.00 2.57
819 825 0.029433 CATCGAGCGAGTCCGATTCA 59.971 55.000 0.00 0.00 42.79 2.57
831 837 6.674519 GCGAGTCCGATTCAACAATGATTTTA 60.675 38.462 0.00 0.00 38.22 1.52
837 843 9.004717 TCCGATTCAACAATGATTTTAGTGTAA 57.995 29.630 0.00 0.00 34.96 2.41
838 844 9.277565 CCGATTCAACAATGATTTTAGTGTAAG 57.722 33.333 0.00 0.00 34.96 2.34
841 847 6.919721 TCAACAATGATTTTAGTGTAAGCCC 58.080 36.000 0.00 0.00 0.00 5.19
842 848 6.491745 TCAACAATGATTTTAGTGTAAGCCCA 59.508 34.615 0.00 0.00 0.00 5.36
843 849 6.909550 ACAATGATTTTAGTGTAAGCCCAA 57.090 33.333 0.00 0.00 0.00 4.12
871 877 0.036952 CAAGCTCGAGCCCTCTTTGA 60.037 55.000 32.94 0.00 43.38 2.69
899 905 1.202222 GCCGATTGCTCACATTCCTTG 60.202 52.381 0.00 0.00 36.87 3.61
945 951 2.436173 CCAGACTCTTCCATAACCCTCC 59.564 54.545 0.00 0.00 0.00 4.30
963 969 1.378119 CCCTAACCCTTTCCCGTGC 60.378 63.158 0.00 0.00 0.00 5.34
976 992 4.003788 CGTGCCCTCCCGTGAACT 62.004 66.667 0.00 0.00 0.00 3.01
1017 1036 3.474570 ATGGCCTCCGGTGAGCTC 61.475 66.667 6.82 6.82 37.29 4.09
1041 1069 0.727398 CGTCCAAGAAGAAATCCGGC 59.273 55.000 0.00 0.00 0.00 6.13
1203 4583 1.521681 CTTCCGCGATCTTCACCCC 60.522 63.158 8.23 0.00 0.00 4.95
1378 4842 1.895238 GATGAGGACGACGGGGAAA 59.105 57.895 0.00 0.00 0.00 3.13
1383 4847 2.808321 GACGACGGGGAAAGCGAC 60.808 66.667 0.00 0.00 0.00 5.19
1384 4848 3.562779 GACGACGGGGAAAGCGACA 62.563 63.158 0.00 0.00 0.00 4.35
1385 4849 2.809601 CGACGGGGAAAGCGACAG 60.810 66.667 0.00 0.00 0.00 3.51
1387 4851 4.699522 ACGGGGAAAGCGACAGCC 62.700 66.667 0.00 0.00 46.67 4.85
1388 4852 4.394712 CGGGGAAAGCGACAGCCT 62.395 66.667 0.00 0.00 46.67 4.58
1391 4855 2.815647 GGAAAGCGACAGCCTCGG 60.816 66.667 3.76 0.00 46.67 4.63
1392 4856 2.815647 GAAAGCGACAGCCTCGGG 60.816 66.667 3.76 0.00 46.67 5.14
1393 4857 3.591254 GAAAGCGACAGCCTCGGGT 62.591 63.158 3.76 0.00 46.67 5.28
1394 4858 3.883744 AAAGCGACAGCCTCGGGTG 62.884 63.158 13.23 13.23 46.67 4.61
1397 4861 4.436998 CGACAGCCTCGGGTGGTC 62.437 72.222 18.32 12.07 46.64 4.02
1398 4862 4.083862 GACAGCCTCGGGTGGTCC 62.084 72.222 18.32 4.76 46.64 4.46
1519 5006 3.208623 TACGACCCCCTCACACGGA 62.209 63.158 0.00 0.00 0.00 4.69
1575 5073 2.184579 GAAGACCCCGAAGAGGCG 59.815 66.667 0.00 0.00 39.21 5.52
1594 5104 0.313043 GGAAGTCGAGTTCCACGTGA 59.687 55.000 36.48 0.00 44.89 4.35
1602 5112 0.243907 AGTTCCACGTGATCACCTCG 59.756 55.000 19.30 11.26 37.73 4.63
1679 5897 4.117661 GGTCGCCGTCTTCTCGCT 62.118 66.667 0.00 0.00 0.00 4.93
1685 5903 1.444553 CCGTCTTCTCGCTGGACAC 60.445 63.158 0.00 0.00 0.00 3.67
1790 6023 1.143183 GGGCATCCGTAAGCGAAGA 59.857 57.895 0.00 0.00 41.33 2.87
1838 6083 0.107017 CTGCAATTCTCCCGGATGGT 60.107 55.000 0.73 0.00 34.77 3.55
1879 7723 0.613777 AATGGGTCTCAAGGTCGGTC 59.386 55.000 0.00 0.00 0.00 4.79
1939 7789 3.323115 TGAACTCACTCTTGATGTCTGCT 59.677 43.478 0.00 0.00 0.00 4.24
1981 7849 5.862678 TGGTGTCGATAAATGGATACTGA 57.137 39.130 0.00 0.00 37.61 3.41
1985 7853 6.201044 GGTGTCGATAAATGGATACTGAACAG 59.799 42.308 0.00 0.00 37.61 3.16
2007 7878 2.218603 ACATTTGAGTTGGTGGACGAC 58.781 47.619 0.00 0.00 0.00 4.34
2102 7985 5.084519 TGTGTATCTGTCTACTTTCCAGGT 58.915 41.667 0.00 0.00 0.00 4.00
2196 8797 5.104776 CCCTATCACCAACTCTGATTCTTCA 60.105 44.000 0.00 0.00 30.76 3.02
2206 8807 7.202038 CCAACTCTGATTCTTCATATCCCTACA 60.202 40.741 0.00 0.00 0.00 2.74
2246 8853 4.764823 TGTTTTGGTAGGCAATAAGGTGAG 59.235 41.667 0.00 0.00 0.00 3.51
2320 10939 6.777213 AGTCGGTCATTTTATCTGTACTCT 57.223 37.500 0.00 0.00 0.00 3.24
2388 11010 7.735917 TGGTTCTATATATCCAGTCTTGGTTG 58.264 38.462 0.00 0.00 45.26 3.77
2426 11068 7.461182 TTTTATAAATCAAGGTGTCCAGGTG 57.539 36.000 0.00 0.00 0.00 4.00
2434 11076 1.752198 GTGTCCAGGTGCAGGTGTA 59.248 57.895 0.00 0.00 0.00 2.90
2439 11086 0.396435 CCAGGTGCAGGTGTAGTTGA 59.604 55.000 0.00 0.00 0.00 3.18
2514 11166 7.934855 TGCCCGTGGTAAAATAAGTAAATAA 57.065 32.000 0.00 0.00 0.00 1.40
2557 11219 5.765677 TGTCAACTCCCAAAATTAACGATCA 59.234 36.000 0.00 0.00 0.00 2.92
2570 11232 7.556733 AATTAACGATCAACGCCCTAAAATA 57.443 32.000 0.00 0.00 46.94 1.40
2608 11270 0.613260 TGGTCCTACGCATTCTGCTT 59.387 50.000 0.00 0.00 42.25 3.91
2662 11361 5.635700 CCTCTGTGTCTGCTCTTAAGTTTAC 59.364 44.000 1.63 0.00 0.00 2.01
2771 11470 6.092396 TGCAATGAAATTTATGCCACATGTTC 59.908 34.615 16.14 0.00 38.00 3.18
2816 11516 5.409643 CGCAGGTGATTTTCATAGTTAGG 57.590 43.478 0.00 0.00 0.00 2.69
2906 11608 1.153524 AACCTGTTGAGCATGCCCA 59.846 52.632 15.66 5.73 0.00 5.36
2985 11687 4.415150 CCCAGCACAGGCACCGAT 62.415 66.667 0.00 0.00 44.61 4.18
3047 11749 6.072119 GGTCAGGGTTTAGATACTTTTTGTGG 60.072 42.308 0.00 0.00 0.00 4.17
3068 11770 0.615331 CATGGGTAGGGCATCGCTAT 59.385 55.000 0.00 0.00 31.86 2.97
3075 11777 4.184629 GGTAGGGCATCGCTATAATTCTG 58.815 47.826 0.00 0.00 31.86 3.02
3148 11868 1.072965 ACCAAGAGTGAAAGGCTCAGG 59.927 52.381 0.00 0.00 36.85 3.86
3157 11877 3.255397 AGGCTCAGGGCTGCTGTT 61.255 61.111 0.00 0.00 46.90 3.16
3242 11967 7.483059 GCACTTCTTAGTTGCAATAATGAGAAC 59.517 37.037 0.59 0.00 32.32 3.01
3245 11970 7.076842 TCTTAGTTGCAATAATGAGAACTGC 57.923 36.000 0.59 0.00 34.47 4.40
3246 11971 6.881065 TCTTAGTTGCAATAATGAGAACTGCT 59.119 34.615 0.59 0.00 34.47 4.24
3247 11972 5.972107 AGTTGCAATAATGAGAACTGCTT 57.028 34.783 0.59 0.00 32.54 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.233389 AGTGACATAGTGAGTTGACATAGTT 57.767 36.000 0.00 0.00 0.00 2.24
2 3 6.842437 AGTGACATAGTGAGTTGACATAGT 57.158 37.500 0.00 0.00 0.00 2.12
3 4 7.380870 GCATAGTGACATAGTGAGTTGACATAG 59.619 40.741 0.00 0.00 0.00 2.23
4 5 7.147915 TGCATAGTGACATAGTGAGTTGACATA 60.148 37.037 0.00 0.00 0.00 2.29
5 6 6.045318 GCATAGTGACATAGTGAGTTGACAT 58.955 40.000 0.00 0.00 0.00 3.06
6 7 5.047377 TGCATAGTGACATAGTGAGTTGACA 60.047 40.000 0.00 0.00 0.00 3.58
7 8 5.410924 TGCATAGTGACATAGTGAGTTGAC 58.589 41.667 0.00 0.00 0.00 3.18
8 9 5.659440 TGCATAGTGACATAGTGAGTTGA 57.341 39.130 0.00 0.00 0.00 3.18
9 10 6.044682 TCATGCATAGTGACATAGTGAGTTG 58.955 40.000 0.00 0.00 0.00 3.16
10 11 6.225981 TCATGCATAGTGACATAGTGAGTT 57.774 37.500 0.00 0.00 0.00 3.01
11 12 5.859205 TCATGCATAGTGACATAGTGAGT 57.141 39.130 0.00 0.00 0.00 3.41
12 13 7.543947 TTTTCATGCATAGTGACATAGTGAG 57.456 36.000 0.00 0.00 0.00 3.51
13 14 7.920160 TTTTTCATGCATAGTGACATAGTGA 57.080 32.000 0.00 0.00 0.00 3.41
34 35 5.321927 AGATAATCGAGTTGGTGGGTTTTT 58.678 37.500 0.00 0.00 0.00 1.94
35 36 4.918588 AGATAATCGAGTTGGTGGGTTTT 58.081 39.130 0.00 0.00 0.00 2.43
36 37 4.569719 AGATAATCGAGTTGGTGGGTTT 57.430 40.909 0.00 0.00 0.00 3.27
37 38 4.019681 TCAAGATAATCGAGTTGGTGGGTT 60.020 41.667 0.00 0.00 0.00 4.11
38 39 3.517901 TCAAGATAATCGAGTTGGTGGGT 59.482 43.478 0.00 0.00 0.00 4.51
39 40 3.871594 GTCAAGATAATCGAGTTGGTGGG 59.128 47.826 0.00 0.00 0.00 4.61
40 41 4.503910 TGTCAAGATAATCGAGTTGGTGG 58.496 43.478 0.00 0.00 0.00 4.61
41 42 5.503031 GCATGTCAAGATAATCGAGTTGGTG 60.503 44.000 0.00 0.00 0.00 4.17
42 43 4.572389 GCATGTCAAGATAATCGAGTTGGT 59.428 41.667 0.00 0.00 0.00 3.67
43 44 4.571984 TGCATGTCAAGATAATCGAGTTGG 59.428 41.667 0.00 0.00 0.00 3.77
44 45 5.723492 TGCATGTCAAGATAATCGAGTTG 57.277 39.130 0.00 0.00 0.00 3.16
45 46 5.877012 AGTTGCATGTCAAGATAATCGAGTT 59.123 36.000 0.00 0.00 34.91 3.01
46 47 5.423015 AGTTGCATGTCAAGATAATCGAGT 58.577 37.500 3.27 0.00 34.91 4.18
47 48 5.980698 AGTTGCATGTCAAGATAATCGAG 57.019 39.130 3.27 0.00 34.91 4.04
48 49 7.412137 CATAGTTGCATGTCAAGATAATCGA 57.588 36.000 3.27 0.00 34.91 3.59
72 73 0.251297 TATAGGGCATGCATGGTGGC 60.251 55.000 27.34 15.89 41.02 5.01
73 74 2.291209 TTATAGGGCATGCATGGTGG 57.709 50.000 27.34 2.89 0.00 4.61
74 75 4.877378 ATTTTATAGGGCATGCATGGTG 57.123 40.909 27.34 5.00 0.00 4.17
75 76 5.892524 AAATTTTATAGGGCATGCATGGT 57.107 34.783 27.34 5.07 0.00 3.55
76 77 6.996509 ACTAAATTTTATAGGGCATGCATGG 58.003 36.000 27.34 10.03 0.00 3.66
77 78 8.362639 AGAACTAAATTTTATAGGGCATGCATG 58.637 33.333 22.70 22.70 0.00 4.06
78 79 8.482852 AGAACTAAATTTTATAGGGCATGCAT 57.517 30.769 21.36 10.08 0.00 3.96
79 80 7.779798 AGAGAACTAAATTTTATAGGGCATGCA 59.220 33.333 21.36 0.00 0.00 3.96
80 81 8.171164 AGAGAACTAAATTTTATAGGGCATGC 57.829 34.615 9.90 9.90 0.00 4.06
96 97 9.162764 GGCATAGTTGAATGTTTAGAGAACTAA 57.837 33.333 0.00 0.00 36.90 2.24
97 98 8.318412 TGGCATAGTTGAATGTTTAGAGAACTA 58.682 33.333 0.00 0.00 32.15 2.24
98 99 7.168219 TGGCATAGTTGAATGTTTAGAGAACT 58.832 34.615 0.00 0.00 0.00 3.01
99 100 7.377766 TGGCATAGTTGAATGTTTAGAGAAC 57.622 36.000 0.00 0.00 0.00 3.01
100 101 7.665559 AGTTGGCATAGTTGAATGTTTAGAGAA 59.334 33.333 0.00 0.00 0.00 2.87
101 102 7.168219 AGTTGGCATAGTTGAATGTTTAGAGA 58.832 34.615 0.00 0.00 0.00 3.10
102 103 7.119699 TGAGTTGGCATAGTTGAATGTTTAGAG 59.880 37.037 0.00 0.00 0.00 2.43
103 104 6.939730 TGAGTTGGCATAGTTGAATGTTTAGA 59.060 34.615 0.00 0.00 0.00 2.10
104 105 7.023575 GTGAGTTGGCATAGTTGAATGTTTAG 58.976 38.462 0.00 0.00 0.00 1.85
105 106 6.714810 AGTGAGTTGGCATAGTTGAATGTTTA 59.285 34.615 0.00 0.00 0.00 2.01
106 107 5.536161 AGTGAGTTGGCATAGTTGAATGTTT 59.464 36.000 0.00 0.00 0.00 2.83
107 108 5.072741 AGTGAGTTGGCATAGTTGAATGTT 58.927 37.500 0.00 0.00 0.00 2.71
108 109 4.655963 AGTGAGTTGGCATAGTTGAATGT 58.344 39.130 0.00 0.00 0.00 2.71
109 110 6.722301 CATAGTGAGTTGGCATAGTTGAATG 58.278 40.000 0.00 0.00 0.00 2.67
110 111 5.297776 GCATAGTGAGTTGGCATAGTTGAAT 59.702 40.000 0.00 0.00 0.00 2.57
111 112 4.635765 GCATAGTGAGTTGGCATAGTTGAA 59.364 41.667 0.00 0.00 0.00 2.69
112 113 4.080919 AGCATAGTGAGTTGGCATAGTTGA 60.081 41.667 0.00 0.00 0.00 3.18
113 114 4.194640 AGCATAGTGAGTTGGCATAGTTG 58.805 43.478 0.00 0.00 0.00 3.16
114 115 4.494091 AGCATAGTGAGTTGGCATAGTT 57.506 40.909 0.00 0.00 0.00 2.24
115 116 4.651503 AGTAGCATAGTGAGTTGGCATAGT 59.348 41.667 0.00 0.00 0.00 2.12
116 117 5.207110 AGTAGCATAGTGAGTTGGCATAG 57.793 43.478 0.00 0.00 0.00 2.23
117 118 6.691508 CATAGTAGCATAGTGAGTTGGCATA 58.308 40.000 0.00 0.00 0.00 3.14
118 119 5.545588 CATAGTAGCATAGTGAGTTGGCAT 58.454 41.667 0.00 0.00 0.00 4.40
119 120 4.740634 GCATAGTAGCATAGTGAGTTGGCA 60.741 45.833 0.00 0.00 0.00 4.92
120 121 3.743396 GCATAGTAGCATAGTGAGTTGGC 59.257 47.826 0.00 0.00 0.00 4.52
121 122 4.948847 TGCATAGTAGCATAGTGAGTTGG 58.051 43.478 0.00 0.00 40.11 3.77
149 150 4.653341 TGATTCATGTGAAGGTGGGTTTTT 59.347 37.500 1.65 0.00 37.48 1.94
150 151 4.222336 TGATTCATGTGAAGGTGGGTTTT 58.778 39.130 1.65 0.00 37.48 2.43
151 152 3.843422 TGATTCATGTGAAGGTGGGTTT 58.157 40.909 1.65 0.00 37.48 3.27
152 153 3.524095 TGATTCATGTGAAGGTGGGTT 57.476 42.857 1.65 0.00 37.48 4.11
153 154 3.359033 CATGATTCATGTGAAGGTGGGT 58.641 45.455 16.93 0.00 37.12 4.51
154 155 2.100252 GCATGATTCATGTGAAGGTGGG 59.900 50.000 23.86 0.00 43.10 4.61
155 156 2.756207 TGCATGATTCATGTGAAGGTGG 59.244 45.455 23.86 0.39 43.10 4.61
156 157 4.359706 CATGCATGATTCATGTGAAGGTG 58.640 43.478 22.59 12.13 43.10 4.00
157 158 4.649088 CATGCATGATTCATGTGAAGGT 57.351 40.909 22.59 5.49 43.10 3.50
234 235 9.935241 AGAATTGATACTCGAGCACATATAATT 57.065 29.630 13.61 12.57 0.00 1.40
235 236 9.579768 GAGAATTGATACTCGAGCACATATAAT 57.420 33.333 13.61 5.60 0.00 1.28
236 237 8.576442 TGAGAATTGATACTCGAGCACATATAA 58.424 33.333 13.61 3.61 36.11 0.98
237 238 8.110860 TGAGAATTGATACTCGAGCACATATA 57.889 34.615 13.61 0.00 36.11 0.86
238 239 6.986250 TGAGAATTGATACTCGAGCACATAT 58.014 36.000 13.61 2.34 36.11 1.78
239 240 6.391227 TGAGAATTGATACTCGAGCACATA 57.609 37.500 13.61 0.00 36.11 2.29
240 241 5.268118 TGAGAATTGATACTCGAGCACAT 57.732 39.130 13.61 3.16 36.11 3.21
241 242 4.718940 TGAGAATTGATACTCGAGCACA 57.281 40.909 13.61 7.52 36.11 4.57
242 243 6.309980 CCATATGAGAATTGATACTCGAGCAC 59.690 42.308 13.61 4.73 36.11 4.40
243 244 6.393171 CCATATGAGAATTGATACTCGAGCA 58.607 40.000 13.61 0.00 36.11 4.26
244 245 5.290643 GCCATATGAGAATTGATACTCGAGC 59.709 44.000 13.61 0.00 36.11 5.03
245 246 6.629128 AGCCATATGAGAATTGATACTCGAG 58.371 40.000 11.84 11.84 36.11 4.04
246 247 6.596309 AGCCATATGAGAATTGATACTCGA 57.404 37.500 3.65 0.00 36.11 4.04
247 248 8.939201 ATTAGCCATATGAGAATTGATACTCG 57.061 34.615 3.65 0.00 36.11 4.18
248 249 9.881649 TGATTAGCCATATGAGAATTGATACTC 57.118 33.333 3.65 0.00 0.00 2.59
253 254 9.187996 TGTTTTGATTAGCCATATGAGAATTGA 57.812 29.630 3.65 0.00 0.00 2.57
254 255 9.241317 GTGTTTTGATTAGCCATATGAGAATTG 57.759 33.333 3.65 0.00 0.00 2.32
255 256 9.193806 AGTGTTTTGATTAGCCATATGAGAATT 57.806 29.630 3.65 0.00 0.00 2.17
256 257 8.757982 AGTGTTTTGATTAGCCATATGAGAAT 57.242 30.769 3.65 0.47 0.00 2.40
257 258 9.679661 TTAGTGTTTTGATTAGCCATATGAGAA 57.320 29.630 3.65 0.00 0.00 2.87
258 259 9.851686 ATTAGTGTTTTGATTAGCCATATGAGA 57.148 29.630 3.65 0.00 0.00 3.27
259 260 9.888878 CATTAGTGTTTTGATTAGCCATATGAG 57.111 33.333 3.65 0.00 0.00 2.90
260 261 9.407380 ACATTAGTGTTTTGATTAGCCATATGA 57.593 29.630 3.65 0.00 34.01 2.15
277 278 4.787551 TCAGTGGGTTGAAACATTAGTGT 58.212 39.130 0.00 0.00 41.28 3.55
278 279 5.766150 TTCAGTGGGTTGAAACATTAGTG 57.234 39.130 0.00 0.00 34.32 2.74
279 280 6.306987 AGATTCAGTGGGTTGAAACATTAGT 58.693 36.000 0.00 0.00 40.21 2.24
280 281 6.430925 TGAGATTCAGTGGGTTGAAACATTAG 59.569 38.462 0.00 0.00 40.21 1.73
281 282 6.303054 TGAGATTCAGTGGGTTGAAACATTA 58.697 36.000 0.00 0.00 40.21 1.90
282 283 5.139727 TGAGATTCAGTGGGTTGAAACATT 58.860 37.500 0.00 0.00 40.21 2.71
283 284 4.728772 TGAGATTCAGTGGGTTGAAACAT 58.271 39.130 0.00 0.00 40.21 2.71
284 285 4.163441 TGAGATTCAGTGGGTTGAAACA 57.837 40.909 0.00 0.00 40.21 2.83
285 286 6.173339 TCTATGAGATTCAGTGGGTTGAAAC 58.827 40.000 0.00 0.00 40.21 2.78
286 287 6.373005 TCTATGAGATTCAGTGGGTTGAAA 57.627 37.500 0.00 0.00 40.21 2.69
287 288 6.373005 TTCTATGAGATTCAGTGGGTTGAA 57.627 37.500 0.00 0.00 41.00 2.69
288 289 6.373005 TTTCTATGAGATTCAGTGGGTTGA 57.627 37.500 0.00 0.00 0.00 3.18
289 290 7.636150 AATTTCTATGAGATTCAGTGGGTTG 57.364 36.000 0.00 0.00 0.00 3.77
290 291 8.552296 AGTAATTTCTATGAGATTCAGTGGGTT 58.448 33.333 0.00 0.00 0.00 4.11
291 292 7.989741 CAGTAATTTCTATGAGATTCAGTGGGT 59.010 37.037 0.00 0.00 0.00 4.51
292 293 7.041508 GCAGTAATTTCTATGAGATTCAGTGGG 60.042 40.741 0.00 0.00 0.00 4.61
293 294 7.496920 TGCAGTAATTTCTATGAGATTCAGTGG 59.503 37.037 0.00 0.00 0.00 4.00
294 295 8.429493 TGCAGTAATTTCTATGAGATTCAGTG 57.571 34.615 0.00 0.00 0.00 3.66
295 296 9.270640 GATGCAGTAATTTCTATGAGATTCAGT 57.729 33.333 0.00 0.00 0.00 3.41
296 297 8.719648 GGATGCAGTAATTTCTATGAGATTCAG 58.280 37.037 0.00 0.00 0.00 3.02
297 298 7.386025 CGGATGCAGTAATTTCTATGAGATTCA 59.614 37.037 0.00 0.00 0.00 2.57
298 299 7.600375 TCGGATGCAGTAATTTCTATGAGATTC 59.400 37.037 0.00 0.00 0.00 2.52
299 300 7.445121 TCGGATGCAGTAATTTCTATGAGATT 58.555 34.615 0.00 0.00 0.00 2.40
300 301 6.997655 TCGGATGCAGTAATTTCTATGAGAT 58.002 36.000 0.00 0.00 0.00 2.75
301 302 6.405278 TCGGATGCAGTAATTTCTATGAGA 57.595 37.500 0.00 0.00 0.00 3.27
302 303 7.148507 GGAATCGGATGCAGTAATTTCTATGAG 60.149 40.741 0.00 0.00 0.00 2.90
303 304 6.650807 GGAATCGGATGCAGTAATTTCTATGA 59.349 38.462 0.00 0.00 0.00 2.15
304 305 6.128172 GGGAATCGGATGCAGTAATTTCTATG 60.128 42.308 0.00 0.00 0.00 2.23
305 306 5.940470 GGGAATCGGATGCAGTAATTTCTAT 59.060 40.000 0.00 0.00 0.00 1.98
306 307 5.163248 TGGGAATCGGATGCAGTAATTTCTA 60.163 40.000 0.00 0.00 0.00 2.10
307 308 4.137543 GGGAATCGGATGCAGTAATTTCT 58.862 43.478 0.00 0.00 0.00 2.52
308 309 3.882888 TGGGAATCGGATGCAGTAATTTC 59.117 43.478 0.00 0.00 0.00 2.17
309 310 3.632145 GTGGGAATCGGATGCAGTAATTT 59.368 43.478 0.00 0.00 0.00 1.82
310 311 3.214328 GTGGGAATCGGATGCAGTAATT 58.786 45.455 0.00 0.00 0.00 1.40
311 312 2.172505 TGTGGGAATCGGATGCAGTAAT 59.827 45.455 0.00 0.00 0.00 1.89
312 313 1.557371 TGTGGGAATCGGATGCAGTAA 59.443 47.619 0.00 0.00 0.00 2.24
313 314 1.199615 TGTGGGAATCGGATGCAGTA 58.800 50.000 0.00 0.00 0.00 2.74
314 315 0.327924 TTGTGGGAATCGGATGCAGT 59.672 50.000 0.00 0.00 0.00 4.40
315 316 0.734889 GTTGTGGGAATCGGATGCAG 59.265 55.000 0.00 0.00 0.00 4.41
316 317 0.037447 TGTTGTGGGAATCGGATGCA 59.963 50.000 0.00 0.00 0.00 3.96
317 318 1.173043 TTGTTGTGGGAATCGGATGC 58.827 50.000 0.00 0.00 0.00 3.91
318 319 2.480073 GCATTGTTGTGGGAATCGGATG 60.480 50.000 0.00 0.00 0.00 3.51
319 320 1.750778 GCATTGTTGTGGGAATCGGAT 59.249 47.619 0.00 0.00 0.00 4.18
320 321 1.173043 GCATTGTTGTGGGAATCGGA 58.827 50.000 0.00 0.00 0.00 4.55
321 322 0.179166 CGCATTGTTGTGGGAATCGG 60.179 55.000 0.00 0.00 34.27 4.18
322 323 0.798009 GCGCATTGTTGTGGGAATCG 60.798 55.000 0.30 0.00 34.27 3.34
323 324 0.798009 CGCGCATTGTTGTGGGAATC 60.798 55.000 8.75 0.00 46.13 2.52
324 325 1.212490 CGCGCATTGTTGTGGGAAT 59.788 52.632 8.75 0.00 46.13 3.01
325 326 2.642129 CGCGCATTGTTGTGGGAA 59.358 55.556 8.75 0.00 46.13 3.97
326 327 3.361158 CCGCGCATTGTTGTGGGA 61.361 61.111 8.75 0.00 46.13 4.37
328 329 1.653094 ATACCCGCGCATTGTTGTGG 61.653 55.000 8.75 0.00 33.82 4.17
329 330 0.248054 GATACCCGCGCATTGTTGTG 60.248 55.000 8.75 0.00 36.41 3.33
330 331 0.675208 TGATACCCGCGCATTGTTGT 60.675 50.000 8.75 0.00 0.00 3.32
331 332 0.662619 ATGATACCCGCGCATTGTTG 59.337 50.000 8.75 0.00 0.00 3.33
332 333 0.944386 GATGATACCCGCGCATTGTT 59.056 50.000 8.75 0.00 0.00 2.83
333 334 0.106708 AGATGATACCCGCGCATTGT 59.893 50.000 8.75 3.10 0.00 2.71
334 335 0.792640 GAGATGATACCCGCGCATTG 59.207 55.000 8.75 0.00 0.00 2.82
335 336 0.681733 AGAGATGATACCCGCGCATT 59.318 50.000 8.75 0.00 0.00 3.56
336 337 1.474478 CTAGAGATGATACCCGCGCAT 59.526 52.381 8.75 0.00 0.00 4.73
337 338 0.881796 CTAGAGATGATACCCGCGCA 59.118 55.000 8.75 0.00 0.00 6.09
338 339 0.882474 ACTAGAGATGATACCCGCGC 59.118 55.000 0.00 0.00 0.00 6.86
339 340 5.585445 AGTTATACTAGAGATGATACCCGCG 59.415 44.000 0.00 0.00 0.00 6.46
340 341 8.503458 TTAGTTATACTAGAGATGATACCCGC 57.497 38.462 0.00 0.00 31.47 6.13
341 342 9.669887 ACTTAGTTATACTAGAGATGATACCCG 57.330 37.037 0.00 0.00 31.47 5.28
411 412 0.615331 ATGGTGGCTCGATGAGTTGT 59.385 50.000 0.00 0.00 31.39 3.32
415 416 1.153309 TGCATGGTGGCTCGATGAG 60.153 57.895 14.50 0.00 34.84 2.90
421 422 0.955428 TTTCTCGTGCATGGTGGCTC 60.955 55.000 5.98 0.00 34.04 4.70
428 429 2.097466 GGTGGGTATTTTCTCGTGCATG 59.903 50.000 0.00 0.00 0.00 4.06
432 433 4.998672 TGTTAAGGTGGGTATTTTCTCGTG 59.001 41.667 0.00 0.00 0.00 4.35
436 437 5.185056 GTGCATGTTAAGGTGGGTATTTTCT 59.815 40.000 0.00 0.00 0.00 2.52
438 439 4.221924 GGTGCATGTTAAGGTGGGTATTTT 59.778 41.667 0.00 0.00 0.00 1.82
442 443 1.705745 TGGTGCATGTTAAGGTGGGTA 59.294 47.619 0.00 0.00 0.00 3.69
460 462 8.499162 GTTTAGTAAGATAAGTAGCATGCATGG 58.501 37.037 27.34 10.03 0.00 3.66
510 512 9.681062 ACATACCTAGTTGCAACTAAAATACAT 57.319 29.630 32.86 19.51 40.70 2.29
511 513 8.941977 CACATACCTAGTTGCAACTAAAATACA 58.058 33.333 32.86 16.35 40.70 2.29
573 575 4.472108 TCCCGTATGGTCCTTGTATTTTCT 59.528 41.667 0.00 0.00 34.77 2.52
574 576 4.573607 GTCCCGTATGGTCCTTGTATTTTC 59.426 45.833 0.00 0.00 34.77 2.29
583 585 2.478292 AGATTTGTCCCGTATGGTCCT 58.522 47.619 0.00 0.00 34.77 3.85
593 595 3.256558 GCTTTGCATCAAGATTTGTCCC 58.743 45.455 2.23 0.00 0.00 4.46
594 596 3.916761 TGCTTTGCATCAAGATTTGTCC 58.083 40.909 2.23 0.00 31.71 4.02
685 691 9.815306 ACAGAGTAATCATAGACACATACCTAT 57.185 33.333 0.00 0.00 0.00 2.57
702 708 8.851541 TTCGGTAACCAATAAAACAGAGTAAT 57.148 30.769 0.00 0.00 0.00 1.89
717 723 9.489084 CAATCAATCTCTTATATTCGGTAACCA 57.511 33.333 0.00 0.00 0.00 3.67
755 761 1.040339 ACACGGCCCAGAAGCAAAAA 61.040 50.000 0.00 0.00 0.00 1.94
798 804 1.263484 GAATCGGACTCGCTCGATGTA 59.737 52.381 0.00 0.00 44.10 2.29
801 807 0.738975 TTGAATCGGACTCGCTCGAT 59.261 50.000 0.00 0.00 46.40 3.59
819 825 6.909550 TGGGCTTACACTAAAATCATTGTT 57.090 33.333 0.00 0.00 0.00 2.83
831 837 5.606348 TGTTGAAAATTTGGGCTTACACT 57.394 34.783 0.00 0.00 0.00 3.55
837 843 3.732212 GAGCTTGTTGAAAATTTGGGCT 58.268 40.909 0.00 0.00 0.00 5.19
838 844 2.476241 CGAGCTTGTTGAAAATTTGGGC 59.524 45.455 0.00 0.00 0.00 5.36
841 847 3.426525 GGCTCGAGCTTGTTGAAAATTTG 59.573 43.478 34.46 0.00 41.70 2.32
842 848 3.552890 GGGCTCGAGCTTGTTGAAAATTT 60.553 43.478 34.46 0.00 41.70 1.82
843 849 2.029918 GGGCTCGAGCTTGTTGAAAATT 60.030 45.455 34.46 0.00 41.70 1.82
871 877 0.611618 TGAGCAATCGGCCCAACATT 60.612 50.000 0.00 0.00 46.50 2.71
899 905 1.518572 CCGCCGTCACTATGTCCAC 60.519 63.158 0.00 0.00 0.00 4.02
932 938 2.495227 GGTTAGGGGAGGGTTATGGAA 58.505 52.381 0.00 0.00 0.00 3.53
945 951 1.378119 GCACGGGAAAGGGTTAGGG 60.378 63.158 0.00 0.00 0.00 3.53
963 969 4.760047 CGGCAGTTCACGGGAGGG 62.760 72.222 0.00 0.00 0.00 4.30
1017 1036 2.084546 GATTTCTTCTTGGACGGTGGG 58.915 52.381 0.00 0.00 0.00 4.61
1020 1039 1.338769 CCGGATTTCTTCTTGGACGGT 60.339 52.381 0.00 0.00 35.67 4.83
1041 1069 1.151450 GGAGCATATGGTGGTGGGG 59.849 63.158 13.10 0.00 39.00 4.96
1397 4861 1.737355 TTCGCCTCCGTAATACCCGG 61.737 60.000 0.00 0.00 46.83 5.73
1398 4862 0.318445 CTTCGCCTCCGTAATACCCG 60.318 60.000 0.00 0.00 35.54 5.28
1399 4863 0.033090 CCTTCGCCTCCGTAATACCC 59.967 60.000 0.00 0.00 35.54 3.69
1400 4864 0.599466 GCCTTCGCCTCCGTAATACC 60.599 60.000 0.00 0.00 35.54 2.73
1402 4866 1.102809 TCGCCTTCGCCTCCGTAATA 61.103 55.000 0.00 0.00 35.54 0.98
1404 4868 3.063704 TCGCCTTCGCCTCCGTAA 61.064 61.111 0.00 0.00 35.54 3.18
1405 4869 3.818787 GTCGCCTTCGCCTCCGTA 61.819 66.667 0.00 0.00 35.54 4.02
1423 4887 3.461773 CATCGACCACCCGGCTCT 61.462 66.667 0.00 0.00 34.57 4.09
1425 4889 3.771160 GTCATCGACCACCCGGCT 61.771 66.667 0.00 0.00 34.57 5.52
1519 5006 2.771762 GGGGAGGAGATGCAGGCT 60.772 66.667 0.00 0.00 0.00 4.58
1602 5112 4.144703 GACCGGCGGTCCTCTTCC 62.145 72.222 41.63 20.84 46.19 3.46
1620 5130 3.306134 GACGAAGACGACGCGGAGT 62.306 63.158 12.47 10.17 42.66 3.85
1679 5897 3.249189 GCCACTCCCTGGTGTCCA 61.249 66.667 0.00 0.00 42.99 4.02
1685 5903 1.694133 GGAGATCTGCCACTCCCTGG 61.694 65.000 0.00 0.00 44.70 4.45
1856 6101 0.744771 GACCTTGAGACCCATTCGCC 60.745 60.000 0.00 0.00 0.00 5.54
1861 7702 0.544357 TGACCGACCTTGAGACCCAT 60.544 55.000 0.00 0.00 0.00 4.00
1879 7723 0.617413 AGCTTCCCATCACTGGTCTG 59.383 55.000 0.00 0.00 41.37 3.51
1939 7789 1.266178 TTGTCATCTGCTCTCCGGAA 58.734 50.000 5.23 0.00 31.26 4.30
1977 7845 3.885297 CCAACTCAAATGTCCTGTTCAGT 59.115 43.478 0.00 0.00 0.00 3.41
1981 7849 2.958355 CCACCAACTCAAATGTCCTGTT 59.042 45.455 0.00 0.00 0.00 3.16
1985 7853 1.535462 CGTCCACCAACTCAAATGTCC 59.465 52.381 0.00 0.00 0.00 4.02
2102 7985 3.639094 GCCAGAAGAACTAGGATGCTCTA 59.361 47.826 0.00 0.00 0.00 2.43
2196 8797 2.237143 CCACGCCATGATGTAGGGATAT 59.763 50.000 0.00 0.00 29.57 1.63
2246 8853 1.460273 CCCCTTCTAGCCGAGAGAGC 61.460 65.000 0.00 0.00 34.93 4.09
2294 10911 6.931838 AGTACAGATAAAATGACCGACTTCA 58.068 36.000 0.00 0.00 0.00 3.02
2416 11050 0.320771 CTACACCTGCACCTGGACAC 60.321 60.000 0.00 0.00 0.00 3.67
2426 11068 2.813754 TGCAATTCTCAACTACACCTGC 59.186 45.455 0.00 0.00 0.00 4.85
2458 11105 7.607607 TGCTCATAATGATAACAAGTCAACAGT 59.392 33.333 0.00 0.00 0.00 3.55
2465 11112 9.961265 CATCATTTGCTCATAATGATAACAAGT 57.039 29.630 9.89 0.00 45.96 3.16
2514 11166 2.170607 ACACTACTGTTGTCAGCCAAGT 59.829 45.455 0.00 0.00 44.77 3.16
2527 11179 7.360361 GTTAATTTTGGGAGTTGACACTACTG 58.640 38.462 0.00 0.00 33.69 2.74
2560 11222 0.179029 TCGCCTGCCTATTTTAGGGC 60.179 55.000 2.90 0.00 46.32 5.19
2570 11232 2.166829 CATAGATACTCTCGCCTGCCT 58.833 52.381 0.00 0.00 0.00 4.75
2753 11452 6.112927 ACAAGGAACATGTGGCATAAATTT 57.887 33.333 0.00 0.00 39.47 1.82
2771 11470 1.429463 GACGTGCTAACTCCACAAGG 58.571 55.000 0.00 0.00 32.85 3.61
2816 11516 8.621532 TCCAGCATATACATTTGGATAACTTC 57.378 34.615 0.00 0.00 33.21 3.01
2835 11535 2.027561 AGGCAACGTTATAACTCCAGCA 60.028 45.455 13.56 0.00 46.39 4.41
2900 11602 1.447643 GAGTAGCGGACATGGGCAT 59.552 57.895 0.00 0.00 0.00 4.40
2906 11608 0.818296 GTCACAGGAGTAGCGGACAT 59.182 55.000 0.00 0.00 0.00 3.06
2969 11671 3.129502 CATCGGTGCCTGTGCTGG 61.130 66.667 0.00 0.00 38.71 4.85
2985 11687 5.551233 CAAGAAAAGTGAGGACCTATGTCA 58.449 41.667 0.00 0.00 43.65 3.58
3148 11868 2.355481 GCAGCAACAACAGCAGCC 60.355 61.111 0.00 0.00 38.40 4.85
3192 11912 1.001860 GAACAGCAGCTCCAAGTCTCT 59.998 52.381 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.