Multiple sequence alignment - TraesCS2A01G408600

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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 TraesCS2A01G408600 chr2A 100.000 4262 0 0 1 4262 666019886 666024147 0.000000e+00 7871.0
1 TraesCS2A01G408600 chr2A 78.483 2189 394 48 1069 3235 733348838 733346705 0.000000e+00 1362.0
2 TraesCS2A01G408600 chr2A 76.668 2233 449 52 1063 3271 733344393 733342209 0.000000e+00 1171.0
3 TraesCS2A01G408600 chr2A 76.843 2198 430 54 1097 3265 733289259 733287112 0.000000e+00 1166.0
4 TraesCS2A01G408600 chr2D 94.314 3183 126 25 120 3274 521569410 521566255 0.000000e+00 4824.0
5 TraesCS2A01G408600 chr2D 80.185 1948 319 44 1038 2971 599220313 599218419 0.000000e+00 1397.0
6 TraesCS2A01G408600 chr2D 77.075 2229 432 58 1063 3265 599111188 599109013 0.000000e+00 1212.0
7 TraesCS2A01G408600 chr2D 77.010 2201 425 62 1094 3264 599104731 599102582 0.000000e+00 1186.0
8 TraesCS2A01G408600 chr2D 76.182 2221 444 57 1080 3265 599154281 599152111 0.000000e+00 1092.0
9 TraesCS2A01G408600 chr2D 75.540 2224 460 67 1065 3252 521588068 521585893 0.000000e+00 1016.0
10 TraesCS2A01G408600 chr2D 91.690 722 40 8 3422 4140 521565748 521565044 0.000000e+00 983.0
11 TraesCS2A01G408600 chr2D 74.428 2229 468 77 1065 3252 521763258 521761091 0.000000e+00 865.0
12 TraesCS2A01G408600 chr2D 94.400 125 7 0 3658 3782 521563271 521563147 4.350000e-45 193.0
13 TraesCS2A01G408600 chr2B 93.951 3009 131 22 317 3302 614240799 614243779 0.000000e+00 4501.0
14 TraesCS2A01G408600 chr2B 78.909 2181 391 47 1073 3235 728611461 728609332 0.000000e+00 1415.0
15 TraesCS2A01G408600 chr2B 77.285 2232 433 51 1063 3265 728562170 728559984 0.000000e+00 1245.0
16 TraesCS2A01G408600 chr2B 77.102 2236 425 62 1063 3265 728586997 728584816 0.000000e+00 1212.0
17 TraesCS2A01G408600 chr2B 74.559 2213 473 69 1073 3249 613232752 613234910 0.000000e+00 885.0
18 TraesCS2A01G408600 chr2B 84.726 347 22 17 3326 3661 614243771 614244097 6.880000e-83 318.0
19 TraesCS2A01G408600 chr3B 77.220 2230 433 55 1063 3265 60155824 60158005 0.000000e+00 1234.0
20 TraesCS2A01G408600 chr4D 95.122 82 4 0 4181 4262 455295313 455295232 3.460000e-26 130.0
21 TraesCS2A01G408600 chr7B 95.000 80 4 0 4181 4260 672785113 672785034 4.470000e-25 126.0
22 TraesCS2A01G408600 chr1D 93.902 82 5 0 4181 4262 20787786 20787867 1.610000e-24 124.0
23 TraesCS2A01G408600 chr1D 93.902 82 5 0 4181 4262 490442679 490442760 1.610000e-24 124.0
24 TraesCS2A01G408600 chr1D 91.463 82 7 0 4181 4262 363731930 363732011 3.480000e-21 113.0
25 TraesCS2A01G408600 chr6A 92.683 82 6 0 4181 4262 604952959 604953040 7.490000e-23 119.0
26 TraesCS2A01G408600 chr4A 92.683 82 6 0 4181 4262 532206857 532206776 7.490000e-23 119.0
27 TraesCS2A01G408600 chr3D 92.683 82 6 0 4181 4262 483190221 483190140 7.490000e-23 119.0
28 TraesCS2A01G408600 chrUn 91.566 83 5 2 4181 4262 1696254 1696335 3.480000e-21 113.0
29 TraesCS2A01G408600 chr6B 100.000 28 0 0 4007 4034 716531920 716531947 8.000000e-03 52.8


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 TraesCS2A01G408600 chr2A 666019886 666024147 4261 False 7871.0 7871 100.0000 1 4262 1 chr2A.!!$F1 4261
1 TraesCS2A01G408600 chr2A 733342209 733348838 6629 True 1266.5 1362 77.5755 1063 3271 2 chr2A.!!$R2 2208
2 TraesCS2A01G408600 chr2A 733287112 733289259 2147 True 1166.0 1166 76.8430 1097 3265 1 chr2A.!!$R1 2168
3 TraesCS2A01G408600 chr2D 521563147 521569410 6263 True 2000.0 4824 93.4680 120 4140 3 chr2D.!!$R7 4020
4 TraesCS2A01G408600 chr2D 599218419 599220313 1894 True 1397.0 1397 80.1850 1038 2971 1 chr2D.!!$R6 1933
5 TraesCS2A01G408600 chr2D 599109013 599111188 2175 True 1212.0 1212 77.0750 1063 3265 1 chr2D.!!$R4 2202
6 TraesCS2A01G408600 chr2D 599102582 599104731 2149 True 1186.0 1186 77.0100 1094 3264 1 chr2D.!!$R3 2170
7 TraesCS2A01G408600 chr2D 599152111 599154281 2170 True 1092.0 1092 76.1820 1080 3265 1 chr2D.!!$R5 2185
8 TraesCS2A01G408600 chr2D 521585893 521588068 2175 True 1016.0 1016 75.5400 1065 3252 1 chr2D.!!$R1 2187
9 TraesCS2A01G408600 chr2D 521761091 521763258 2167 True 865.0 865 74.4280 1065 3252 1 chr2D.!!$R2 2187
10 TraesCS2A01G408600 chr2B 614240799 614244097 3298 False 2409.5 4501 89.3385 317 3661 2 chr2B.!!$F2 3344
11 TraesCS2A01G408600 chr2B 728609332 728611461 2129 True 1415.0 1415 78.9090 1073 3235 1 chr2B.!!$R3 2162
12 TraesCS2A01G408600 chr2B 728559984 728562170 2186 True 1245.0 1245 77.2850 1063 3265 1 chr2B.!!$R1 2202
13 TraesCS2A01G408600 chr2B 728584816 728586997 2181 True 1212.0 1212 77.1020 1063 3265 1 chr2B.!!$R2 2202
14 TraesCS2A01G408600 chr2B 613232752 613234910 2158 False 885.0 885 74.5590 1073 3249 1 chr2B.!!$F1 2176
15 TraesCS2A01G408600 chr3B 60155824 60158005 2181 False 1234.0 1234 77.2200 1063 3265 1 chr3B.!!$F1 2202

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
456 464 0.035881 TTGAAGGAGTCAGCCTGCTG 59.964 55.000 12.91 12.91 41.66 4.41 F
552 560 1.072159 GTCAGTGCTGGTTCTGGCT 59.928 57.895 0.00 0.00 34.05 4.75 F
1401 1436 1.153369 CGTCATCATCGGGGTGCTT 60.153 57.895 0.00 0.00 0.00 3.91 F
2400 6945 0.457035 CGCAAATCATGTTCAGGGGG 59.543 55.000 0.00 0.00 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1436 2.265739 GGAGTGATGCCGCTGTCA 59.734 61.111 0.00 0.0 32.40 3.58 R
2068 6598 2.401766 GCGGGTAGAAGACGGTCGA 61.402 63.158 1.89 0.0 0.00 4.20 R
2571 7116 1.000496 GACTCGAAGTTGAAGGTCGGT 60.000 52.381 0.00 0.0 35.51 4.69 R
4047 8970 0.315251 GAAAACTGCCTCAAGTGCCC 59.685 55.000 0.00 0.0 0.00 5.36 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 7.662604 GCATGTTATACACATCATCTCATCA 57.337 36.000 0.00 0.00 43.17 3.07
25 26 8.091385 GCATGTTATACACATCATCTCATCAA 57.909 34.615 0.00 0.00 43.17 2.57
26 27 8.562052 GCATGTTATACACATCATCTCATCAAA 58.438 33.333 0.00 0.00 43.17 2.69
29 30 9.889128 TGTTATACACATCATCTCATCAAAAGA 57.111 29.630 0.00 0.00 0.00 2.52
34 35 8.807667 ACACATCATCTCATCAAAAGAAAAAC 57.192 30.769 0.00 0.00 0.00 2.43
35 36 8.415553 ACACATCATCTCATCAAAAGAAAAACA 58.584 29.630 0.00 0.00 0.00 2.83
36 37 9.251792 CACATCATCTCATCAAAAGAAAAACAA 57.748 29.630 0.00 0.00 0.00 2.83
37 38 9.820725 ACATCATCTCATCAAAAGAAAAACAAA 57.179 25.926 0.00 0.00 0.00 2.83
58 59 2.486951 AAAAGATCGATGCATGCAGC 57.513 45.000 25.69 25.69 45.96 5.25
72 73 4.949756 GCATGCAGCAAATTTGTTTCTAC 58.050 39.130 19.03 4.17 44.79 2.59
73 74 4.448395 GCATGCAGCAAATTTGTTTCTACA 59.552 37.500 19.03 9.34 44.79 2.74
74 75 5.050227 GCATGCAGCAAATTTGTTTCTACAA 60.050 36.000 19.03 0.00 44.79 2.41
85 86 6.509418 TTTGTTTCTACAAACTGCTGAGTT 57.491 33.333 0.00 0.00 46.46 3.01
97 98 6.588348 AACTGCTGAGTTTAACAAATTTGC 57.412 33.333 18.12 1.44 39.56 3.68
98 99 5.906073 ACTGCTGAGTTTAACAAATTTGCT 58.094 33.333 18.12 8.75 0.00 3.91
99 100 5.979517 ACTGCTGAGTTTAACAAATTTGCTC 59.020 36.000 18.12 15.09 0.00 4.26
100 101 5.288804 TGCTGAGTTTAACAAATTTGCTCC 58.711 37.500 18.12 5.40 0.00 4.70
101 102 4.382754 GCTGAGTTTAACAAATTTGCTCCG 59.617 41.667 18.12 12.40 0.00 4.63
102 103 4.295051 TGAGTTTAACAAATTTGCTCCGC 58.705 39.130 18.12 6.35 0.00 5.54
103 104 3.649073 AGTTTAACAAATTTGCTCCGCC 58.351 40.909 18.12 2.59 0.00 6.13
104 105 2.339728 TTAACAAATTTGCTCCGCCG 57.660 45.000 18.12 0.00 0.00 6.46
105 106 1.524848 TAACAAATTTGCTCCGCCGA 58.475 45.000 18.12 0.00 0.00 5.54
106 107 0.671251 AACAAATTTGCTCCGCCGAA 59.329 45.000 18.12 0.00 0.00 4.30
107 108 0.887933 ACAAATTTGCTCCGCCGAAT 59.112 45.000 18.12 0.00 0.00 3.34
108 109 1.135402 ACAAATTTGCTCCGCCGAATC 60.135 47.619 18.12 0.00 0.00 2.52
109 110 1.135431 CAAATTTGCTCCGCCGAATCA 60.135 47.619 5.01 0.00 0.00 2.57
110 111 1.173043 AATTTGCTCCGCCGAATCAA 58.827 45.000 0.00 0.00 0.00 2.57
111 112 1.173043 ATTTGCTCCGCCGAATCAAA 58.827 45.000 0.00 0.00 0.00 2.69
112 113 0.521291 TTTGCTCCGCCGAATCAAAG 59.479 50.000 0.00 0.00 0.00 2.77
113 114 1.305219 TTGCTCCGCCGAATCAAAGG 61.305 55.000 0.00 0.00 0.00 3.11
114 115 2.472909 GCTCCGCCGAATCAAAGGG 61.473 63.158 0.00 0.00 0.00 3.95
115 116 2.437716 TCCGCCGAATCAAAGGGC 60.438 61.111 0.00 0.00 43.42 5.19
116 117 3.518068 CCGCCGAATCAAAGGGCC 61.518 66.667 0.00 0.00 43.99 5.80
117 118 2.749839 CGCCGAATCAAAGGGCCA 60.750 61.111 6.18 0.00 43.99 5.36
118 119 2.120909 CGCCGAATCAAAGGGCCAT 61.121 57.895 6.18 0.00 43.99 4.40
132 133 3.414272 CCATAGGCAGCAACGAGC 58.586 61.111 0.00 0.00 46.19 5.03
261 264 7.495055 ACTTAATCATGATCATTGGCCTTTTC 58.505 34.615 9.06 0.00 0.00 2.29
262 265 4.579454 ATCATGATCATTGGCCTTTTCG 57.421 40.909 5.16 0.00 0.00 3.46
263 266 2.099592 TCATGATCATTGGCCTTTTCGC 59.900 45.455 5.16 0.00 0.00 4.70
264 267 1.543607 TGATCATTGGCCTTTTCGCA 58.456 45.000 3.32 0.00 0.00 5.10
265 268 1.202114 TGATCATTGGCCTTTTCGCAC 59.798 47.619 3.32 0.00 0.00 5.34
266 269 1.202114 GATCATTGGCCTTTTCGCACA 59.798 47.619 3.32 0.00 0.00 4.57
267 270 0.597568 TCATTGGCCTTTTCGCACAG 59.402 50.000 3.32 0.00 0.00 3.66
270 273 0.667993 TTGGCCTTTTCGCACAGAAG 59.332 50.000 3.32 0.00 40.40 2.85
273 276 1.877443 GGCCTTTTCGCACAGAAGTTA 59.123 47.619 0.00 0.00 40.40 2.24
275 278 3.057526 GGCCTTTTCGCACAGAAGTTAAT 60.058 43.478 0.00 0.00 40.40 1.40
276 279 4.546570 GCCTTTTCGCACAGAAGTTAATT 58.453 39.130 0.00 0.00 40.40 1.40
277 280 4.982295 GCCTTTTCGCACAGAAGTTAATTT 59.018 37.500 0.00 0.00 40.40 1.82
278 281 5.462068 GCCTTTTCGCACAGAAGTTAATTTT 59.538 36.000 0.00 0.00 40.40 1.82
300 304 2.405892 AAAACAATGTCAGTGCTCGC 57.594 45.000 0.00 0.00 0.00 5.03
311 315 2.287915 TCAGTGCTCGCAGTTCTTTTTC 59.712 45.455 0.00 0.00 0.00 2.29
312 316 1.604278 AGTGCTCGCAGTTCTTTTTCC 59.396 47.619 0.00 0.00 0.00 3.13
314 318 0.241213 GCTCGCAGTTCTTTTTCCCC 59.759 55.000 0.00 0.00 0.00 4.81
315 319 0.881796 CTCGCAGTTCTTTTTCCCCC 59.118 55.000 0.00 0.00 0.00 5.40
347 354 3.624861 CCCATAGTTCTCTGAACATGCAC 59.375 47.826 12.16 0.00 0.00 4.57
358 365 6.486320 TCTCTGAACATGCACTTATTTCACAA 59.514 34.615 0.00 0.00 0.00 3.33
366 373 3.429881 GCACTTATTTCACAAGCCAAAGC 59.570 43.478 0.00 0.00 40.32 3.51
381 388 2.755103 CCAAAGCTCACCCCATCTAAAC 59.245 50.000 0.00 0.00 0.00 2.01
382 389 2.403252 AAGCTCACCCCATCTAAACG 57.597 50.000 0.00 0.00 0.00 3.60
402 409 4.755411 ACGTGGTCTTGTACAATATCCAG 58.245 43.478 19.67 16.51 0.00 3.86
406 413 3.877508 GGTCTTGTACAATATCCAGCCAC 59.122 47.826 9.13 0.00 0.00 5.01
408 415 2.613026 TGTACAATATCCAGCCACGG 57.387 50.000 0.00 0.00 0.00 4.94
444 452 0.984230 CCACTAGGCCAGTTGAAGGA 59.016 55.000 5.01 0.00 34.26 3.36
450 458 0.957888 GGCCAGTTGAAGGAGTCAGC 60.958 60.000 0.00 0.00 37.61 4.26
451 459 0.957888 GCCAGTTGAAGGAGTCAGCC 60.958 60.000 0.00 0.00 38.18 4.85
452 460 0.689623 CCAGTTGAAGGAGTCAGCCT 59.310 55.000 0.00 0.00 38.18 4.58
453 461 1.610102 CCAGTTGAAGGAGTCAGCCTG 60.610 57.143 0.00 0.00 38.18 4.85
454 462 0.036022 AGTTGAAGGAGTCAGCCTGC 59.964 55.000 0.00 0.00 38.18 4.85
455 463 0.036022 GTTGAAGGAGTCAGCCTGCT 59.964 55.000 0.00 0.00 44.89 4.24
456 464 0.035881 TTGAAGGAGTCAGCCTGCTG 59.964 55.000 12.91 12.91 41.66 4.41
474 482 2.636830 CTGCCTGCACAAGTAGCTTAT 58.363 47.619 0.00 0.00 0.00 1.73
475 483 3.797039 CTGCCTGCACAAGTAGCTTATA 58.203 45.455 0.00 0.00 0.00 0.98
490 498 9.712305 AAGTAGCTTATATGCGAATTAATCAGT 57.288 29.630 4.95 0.00 38.13 3.41
499 507 4.091424 GCGAATTAATCAGTCAAGTGTGC 58.909 43.478 0.00 0.00 0.00 4.57
549 557 1.162698 CCATGTCAGTGCTGGTTCTG 58.837 55.000 0.00 0.00 0.00 3.02
552 560 1.072159 GTCAGTGCTGGTTCTGGCT 59.928 57.895 0.00 0.00 34.05 4.75
714 722 3.300388 TCCTACAGCTAACTCCCATCAG 58.700 50.000 0.00 0.00 0.00 2.90
719 727 3.055530 ACAGCTAACTCCCATCAGTTCTG 60.056 47.826 0.00 0.00 37.75 3.02
734 742 1.552799 TTCTGGATCGCCTTCTGCCA 61.553 55.000 0.00 0.00 36.24 4.92
777 785 1.176527 CAAGCGACCCAATCCATGTT 58.823 50.000 0.00 0.00 0.00 2.71
785 793 2.034124 CCCAATCCATGTTCATGACCC 58.966 52.381 13.51 0.00 0.00 4.46
904 921 2.742372 CTGCCCCAACGACGGAAG 60.742 66.667 0.00 0.00 0.00 3.46
905 922 4.323477 TGCCCCAACGACGGAAGG 62.323 66.667 0.00 0.00 0.00 3.46
907 924 3.315949 CCCCAACGACGGAAGGGA 61.316 66.667 19.31 0.00 44.30 4.20
974 991 3.004002 CGCACGTACCAGATAACCAGATA 59.996 47.826 0.00 0.00 0.00 1.98
975 992 4.498513 CGCACGTACCAGATAACCAGATAA 60.499 45.833 0.00 0.00 0.00 1.75
976 993 4.743644 GCACGTACCAGATAACCAGATAAC 59.256 45.833 0.00 0.00 0.00 1.89
977 994 5.287226 CACGTACCAGATAACCAGATAACC 58.713 45.833 0.00 0.00 0.00 2.85
978 995 4.957954 ACGTACCAGATAACCAGATAACCA 59.042 41.667 0.00 0.00 0.00 3.67
979 996 5.068723 ACGTACCAGATAACCAGATAACCAG 59.931 44.000 0.00 0.00 0.00 4.00
980 997 5.301045 CGTACCAGATAACCAGATAACCAGA 59.699 44.000 0.00 0.00 0.00 3.86
981 998 5.878406 ACCAGATAACCAGATAACCAGAG 57.122 43.478 0.00 0.00 0.00 3.35
1023 1040 2.279784 GCCTTCAGGATCGCCTCG 60.280 66.667 0.00 0.00 44.80 4.63
1272 1307 2.676471 GCCATGCCTGGGTTCGTT 60.676 61.111 10.28 0.00 43.36 3.85
1401 1436 1.153369 CGTCATCATCGGGGTGCTT 60.153 57.895 0.00 0.00 0.00 3.91
2030 6557 1.376037 GCCTTGGGAACGGTCTCTG 60.376 63.158 0.03 0.00 0.00 3.35
2064 6594 3.050275 GTGAACCAGCCAGACGCC 61.050 66.667 0.00 0.00 38.78 5.68
2400 6945 0.457035 CGCAAATCATGTTCAGGGGG 59.543 55.000 0.00 0.00 0.00 5.40
2595 7140 0.389948 CCTTCAACTTCGAGTCCGGG 60.390 60.000 0.00 0.00 36.24 5.73
2817 7362 4.047125 ATGAACCCCGGCCTGGTG 62.047 66.667 12.79 6.31 35.88 4.17
2940 7485 3.782443 GTGATCCCGGACCGCCTT 61.782 66.667 8.86 0.00 0.00 4.35
2993 7538 1.080366 CGTCGTGGAACCCGATGAA 60.080 57.895 14.19 0.00 42.46 2.57
3271 7825 0.733150 CGGACACTAGAGCACGATCA 59.267 55.000 0.00 0.00 0.00 2.92
3291 7845 8.730680 ACGATCAGCTTGACAATTTATTTTACT 58.269 29.630 0.00 0.00 0.00 2.24
3297 7851 9.931210 AGCTTGACAATTTATTTTACTATACGC 57.069 29.630 0.00 0.00 0.00 4.42
3298 7852 9.166126 GCTTGACAATTTATTTTACTATACGCC 57.834 33.333 0.00 0.00 0.00 5.68
3301 7855 9.991388 TGACAATTTATTTTACTATACGCCAAC 57.009 29.630 0.00 0.00 0.00 3.77
3302 7856 9.442033 GACAATTTATTTTACTATACGCCAACC 57.558 33.333 0.00 0.00 0.00 3.77
3303 7857 9.181061 ACAATTTATTTTACTATACGCCAACCT 57.819 29.630 0.00 0.00 0.00 3.50
3354 7908 1.208706 TGATGCTACCATTTCCCCGA 58.791 50.000 0.00 0.00 0.00 5.14
3401 7955 6.274157 TGTTTGTCAGGTTTTTGCTTCTTA 57.726 33.333 0.00 0.00 0.00 2.10
3404 7958 5.452078 TGTCAGGTTTTTGCTTCTTATGG 57.548 39.130 0.00 0.00 0.00 2.74
3405 7959 4.280677 TGTCAGGTTTTTGCTTCTTATGGG 59.719 41.667 0.00 0.00 0.00 4.00
3407 7961 4.898861 TCAGGTTTTTGCTTCTTATGGGTT 59.101 37.500 0.00 0.00 0.00 4.11
3408 7962 6.015772 GTCAGGTTTTTGCTTCTTATGGGTTA 60.016 38.462 0.00 0.00 0.00 2.85
3409 7963 6.208599 TCAGGTTTTTGCTTCTTATGGGTTAG 59.791 38.462 0.00 0.00 0.00 2.34
3411 7965 6.553476 AGGTTTTTGCTTCTTATGGGTTAGTT 59.447 34.615 0.00 0.00 0.00 2.24
3412 7966 6.866770 GGTTTTTGCTTCTTATGGGTTAGTTC 59.133 38.462 0.00 0.00 0.00 3.01
3413 7967 5.873179 TTTGCTTCTTATGGGTTAGTTCG 57.127 39.130 0.00 0.00 0.00 3.95
3414 7968 4.811969 TGCTTCTTATGGGTTAGTTCGA 57.188 40.909 0.00 0.00 0.00 3.71
3416 7970 4.020928 TGCTTCTTATGGGTTAGTTCGACA 60.021 41.667 0.00 0.00 0.00 4.35
3417 7971 5.116882 GCTTCTTATGGGTTAGTTCGACAT 58.883 41.667 0.00 0.00 0.00 3.06
3418 7972 5.006746 GCTTCTTATGGGTTAGTTCGACATG 59.993 44.000 0.00 0.00 0.00 3.21
3419 7973 5.925506 TCTTATGGGTTAGTTCGACATGA 57.074 39.130 0.00 0.00 0.00 3.07
3420 7974 6.479972 TCTTATGGGTTAGTTCGACATGAT 57.520 37.500 0.00 0.00 0.00 2.45
3667 8588 8.782144 GGAGTGAGAGATTCAATTAAATCATCC 58.218 37.037 4.14 0.00 37.98 3.51
3727 8648 9.905713 TTAATATTCTGAGCTTTTCTACCACAT 57.094 29.630 0.00 0.00 0.00 3.21
3745 8666 4.442332 CCACATTGGTATGCATGCTCAAAT 60.442 41.667 20.33 11.32 35.03 2.32
3748 8669 5.583061 ACATTGGTATGCATGCTCAAATTTG 59.417 36.000 20.33 12.15 35.03 2.32
3789 8710 6.947733 TGTTCTTGGAATGGACATGACTAATT 59.052 34.615 0.00 0.00 0.00 1.40
3832 8753 8.908903 AGTGTCTTTAATCACACATGGTTAAAA 58.091 29.630 16.01 0.00 46.08 1.52
3886 8807 6.520792 AGATACTTGTTCGTGTGTTGTAAC 57.479 37.500 0.00 0.00 0.00 2.50
3888 8809 3.252400 ACTTGTTCGTGTGTTGTAACGA 58.748 40.909 0.00 0.00 46.33 3.85
3913 8834 9.291664 GAGCATAAATATTCTAGTAGGTTAGCG 57.708 37.037 0.00 0.00 0.00 4.26
3924 8845 8.004087 TCTAGTAGGTTAGCGTGTGATTTATT 57.996 34.615 0.00 0.00 0.00 1.40
3951 8873 9.814899 TGCCCATATTATTTGATTGTGTAAAAG 57.185 29.630 0.00 0.00 0.00 2.27
3952 8874 8.764287 GCCCATATTATTTGATTGTGTAAAAGC 58.236 33.333 0.00 0.00 0.00 3.51
3996 8919 4.370364 ACACTTGTTTGGTAAGCACTTG 57.630 40.909 0.00 0.00 0.00 3.16
3997 8920 3.761752 ACACTTGTTTGGTAAGCACTTGT 59.238 39.130 0.00 0.00 0.00 3.16
3998 8921 4.219725 ACACTTGTTTGGTAAGCACTTGTT 59.780 37.500 0.00 0.00 0.00 2.83
3999 8922 4.562394 CACTTGTTTGGTAAGCACTTGTTG 59.438 41.667 0.00 0.00 0.00 3.33
4000 8923 4.461081 ACTTGTTTGGTAAGCACTTGTTGA 59.539 37.500 0.00 0.00 0.00 3.18
4001 8924 5.127031 ACTTGTTTGGTAAGCACTTGTTGAT 59.873 36.000 0.00 0.00 0.00 2.57
4002 8925 5.590530 TGTTTGGTAAGCACTTGTTGATT 57.409 34.783 0.00 0.00 37.64 2.57
4003 8926 5.971763 TGTTTGGTAAGCACTTGTTGATTT 58.028 33.333 0.00 0.00 34.90 2.17
4004 8927 7.101652 TGTTTGGTAAGCACTTGTTGATTTA 57.898 32.000 0.00 0.00 34.90 1.40
4005 8928 7.721402 TGTTTGGTAAGCACTTGTTGATTTAT 58.279 30.769 0.00 0.00 34.90 1.40
4068 8991 1.615392 GGCACTTGAGGCAGTTTTCAT 59.385 47.619 0.00 0.00 0.00 2.57
4124 9047 8.719596 AGTAGAGAGAGAGGATGAACTATGTAA 58.280 37.037 0.00 0.00 0.00 2.41
4147 9389 2.041755 GTTGGACAAAGGAGAAGGGGAT 59.958 50.000 0.00 0.00 0.00 3.85
4188 9430 9.840427 TTCTTTTTAAGTAAGATAAGTGCATGC 57.160 29.630 11.82 11.82 32.09 4.06
4189 9431 8.458843 TCTTTTTAAGTAAGATAAGTGCATGCC 58.541 33.333 16.68 6.65 0.00 4.40
4190 9432 5.984233 TTAAGTAAGATAAGTGCATGCCG 57.016 39.130 16.68 0.00 0.00 5.69
4191 9433 2.838736 AGTAAGATAAGTGCATGCCGG 58.161 47.619 16.68 0.00 0.00 6.13
4193 9435 1.668419 AAGATAAGTGCATGCCGGAC 58.332 50.000 16.68 6.91 35.88 4.79
4194 9436 0.179045 AGATAAGTGCATGCCGGACC 60.179 55.000 16.68 0.00 36.40 4.46
4195 9437 1.498865 GATAAGTGCATGCCGGACCG 61.499 60.000 16.68 6.99 36.40 4.79
4207 9449 1.755395 CGGACCGGTGAGACCCATA 60.755 63.158 14.63 0.00 33.75 2.74
4208 9450 1.821258 GGACCGGTGAGACCCATAC 59.179 63.158 14.63 0.00 33.75 2.39
4211 9453 2.792947 CCGGTGAGACCCATACCCG 61.793 68.421 0.00 0.00 33.75 5.28
4212 9454 2.792947 CGGTGAGACCCATACCCGG 61.793 68.421 0.00 0.00 33.75 5.73
4213 9455 2.504519 GTGAGACCCATACCCGGC 59.495 66.667 0.00 0.00 0.00 6.13
4214 9456 2.039787 TGAGACCCATACCCGGCA 59.960 61.111 0.00 0.00 0.00 5.69
4215 9457 2.063979 TGAGACCCATACCCGGCAG 61.064 63.158 0.00 0.00 0.00 4.85
4216 9458 2.768344 AGACCCATACCCGGCAGG 60.768 66.667 0.00 0.00 43.78 4.85
4217 9459 4.564110 GACCCATACCCGGCAGGC 62.564 72.222 0.00 0.00 40.58 4.85
4220 9462 4.910585 CCATACCCGGCAGGCGTC 62.911 72.222 16.17 0.00 40.58 5.19
4221 9463 4.910585 CATACCCGGCAGGCGTCC 62.911 72.222 16.17 0.00 40.58 4.79
4244 9486 5.886609 CTGGATAGGATCTCAGGTCTTAGA 58.113 45.833 0.00 0.00 0.00 2.10
4246 9488 6.252233 TGGATAGGATCTCAGGTCTTAGATG 58.748 44.000 0.00 0.00 32.60 2.90
4247 9489 6.183361 TGGATAGGATCTCAGGTCTTAGATGT 60.183 42.308 0.00 0.00 32.60 3.06
4248 9490 6.723977 GGATAGGATCTCAGGTCTTAGATGTT 59.276 42.308 0.00 0.00 32.60 2.71
4249 9491 7.891183 GGATAGGATCTCAGGTCTTAGATGTTA 59.109 40.741 0.00 0.00 32.60 2.41
4250 9492 8.877864 ATAGGATCTCAGGTCTTAGATGTTAG 57.122 38.462 0.00 0.00 32.60 2.34
4252 9494 7.129425 AGGATCTCAGGTCTTAGATGTTAGTT 58.871 38.462 0.00 0.00 32.60 2.24
4253 9495 7.621683 AGGATCTCAGGTCTTAGATGTTAGTTT 59.378 37.037 0.00 0.00 32.60 2.66
4255 9497 9.092876 GATCTCAGGTCTTAGATGTTAGTTTTG 57.907 37.037 0.00 0.00 32.60 2.44
4256 9498 7.963532 TCTCAGGTCTTAGATGTTAGTTTTGT 58.036 34.615 0.00 0.00 0.00 2.83
4257 9499 8.088981 TCTCAGGTCTTAGATGTTAGTTTTGTC 58.911 37.037 0.00 0.00 0.00 3.18
4259 9501 7.872993 TCAGGTCTTAGATGTTAGTTTTGTCTG 59.127 37.037 0.00 0.00 0.00 3.51
4260 9502 6.651225 AGGTCTTAGATGTTAGTTTTGTCTGC 59.349 38.462 0.00 0.00 0.00 4.26
4261 9503 6.401153 GGTCTTAGATGTTAGTTTTGTCTGCG 60.401 42.308 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.889128 TCTTTTGATGAGATGATGTGTATAACA 57.111 29.630 0.00 0.00 44.79 2.41
8 9 9.897744 GTTTTTCTTTTGATGAGATGATGTGTA 57.102 29.630 0.00 0.00 0.00 2.90
9 10 8.415553 TGTTTTTCTTTTGATGAGATGATGTGT 58.584 29.630 0.00 0.00 0.00 3.72
10 11 8.806177 TGTTTTTCTTTTGATGAGATGATGTG 57.194 30.769 0.00 0.00 0.00 3.21
11 12 9.820725 TTTGTTTTTCTTTTGATGAGATGATGT 57.179 25.926 0.00 0.00 0.00 3.06
38 39 2.805845 GCTGCATGCATCGATCTTTTT 58.194 42.857 22.97 0.00 42.31 1.94
39 40 2.486951 GCTGCATGCATCGATCTTTT 57.513 45.000 22.97 0.00 42.31 2.27
47 48 8.944303 TGTAGAAACAAATTTGCTGCATGCATC 61.944 37.037 22.97 18.46 41.47 3.91
48 49 7.236458 TGTAGAAACAAATTTGCTGCATGCAT 61.236 34.615 22.97 2.13 41.47 3.96
49 50 5.967770 TGTAGAAACAAATTTGCTGCATGCA 60.968 36.000 21.29 21.29 40.66 3.96
50 51 4.448395 TGTAGAAACAAATTTGCTGCATGC 59.552 37.500 18.12 11.82 35.80 4.06
51 52 6.528014 TTGTAGAAACAAATTTGCTGCATG 57.472 33.333 18.12 0.58 42.60 4.06
74 75 6.340522 AGCAAATTTGTTAAACTCAGCAGTT 58.659 32.000 19.03 0.00 45.43 3.16
75 76 5.906073 AGCAAATTTGTTAAACTCAGCAGT 58.094 33.333 19.03 0.00 0.00 4.40
76 77 5.403466 GGAGCAAATTTGTTAAACTCAGCAG 59.597 40.000 19.03 0.00 0.00 4.24
77 78 5.288804 GGAGCAAATTTGTTAAACTCAGCA 58.711 37.500 19.03 0.00 0.00 4.41
78 79 4.382754 CGGAGCAAATTTGTTAAACTCAGC 59.617 41.667 19.03 1.14 0.00 4.26
97 98 2.472909 GCCCTTTGATTCGGCGGAG 61.473 63.158 7.21 0.00 31.92 4.63
98 99 2.437716 GCCCTTTGATTCGGCGGA 60.438 61.111 7.21 0.00 31.92 5.54
99 100 3.518068 GGCCCTTTGATTCGGCGG 61.518 66.667 7.21 0.00 43.99 6.13
100 101 0.817634 TATGGCCCTTTGATTCGGCG 60.818 55.000 0.00 0.00 43.99 6.46
101 102 0.954452 CTATGGCCCTTTGATTCGGC 59.046 55.000 0.00 0.00 42.23 5.54
102 103 1.609208 CCTATGGCCCTTTGATTCGG 58.391 55.000 0.00 0.00 0.00 4.30
103 104 0.954452 GCCTATGGCCCTTTGATTCG 59.046 55.000 0.00 0.00 44.06 3.34
115 116 3.414272 GCTCGTTGCTGCCTATGG 58.586 61.111 0.00 0.00 38.95 2.74
136 137 3.117372 GCATCCACTGCCATGAGC 58.883 61.111 0.00 0.00 45.66 4.26
145 146 2.303022 TCTTCTTCTTTCCGCATCCACT 59.697 45.455 0.00 0.00 0.00 4.00
178 179 4.460263 TGCATAATACAACCATGTCCTCC 58.540 43.478 0.00 0.00 41.05 4.30
230 233 8.177663 GGCCAATGATCATGATTAAGTATTACG 58.822 37.037 9.46 2.52 0.00 3.18
276 279 5.231147 GCGAGCACTGACATTGTTTTAAAAA 59.769 36.000 1.31 0.00 0.00 1.94
277 280 4.737765 GCGAGCACTGACATTGTTTTAAAA 59.262 37.500 0.00 0.00 0.00 1.52
278 281 4.201960 TGCGAGCACTGACATTGTTTTAAA 60.202 37.500 0.00 0.00 0.00 1.52
280 283 2.875317 TGCGAGCACTGACATTGTTTTA 59.125 40.909 0.00 0.00 0.00 1.52
284 288 0.250038 ACTGCGAGCACTGACATTGT 60.250 50.000 0.00 0.00 0.00 2.71
291 295 2.603173 GGAAAAAGAACTGCGAGCACTG 60.603 50.000 0.00 0.00 0.00 3.66
300 304 0.111639 TCCCGGGGGAAAAAGAACTG 59.888 55.000 23.50 0.00 42.05 3.16
326 333 4.511527 AGTGCATGTTCAGAGAACTATGG 58.488 43.478 10.79 0.56 0.00 2.74
333 340 5.997129 TGTGAAATAAGTGCATGTTCAGAGA 59.003 36.000 0.00 0.00 0.00 3.10
366 373 1.278127 ACCACGTTTAGATGGGGTGAG 59.722 52.381 0.00 0.00 46.98 3.51
372 379 4.562082 TGTACAAGACCACGTTTAGATGG 58.438 43.478 0.00 0.00 42.13 3.51
381 388 3.555956 GCTGGATATTGTACAAGACCACG 59.444 47.826 19.95 17.19 0.00 4.94
382 389 3.877508 GGCTGGATATTGTACAAGACCAC 59.122 47.826 19.95 16.93 0.00 4.16
402 409 3.937079 AGTAGTAGTATTTTTGCCGTGGC 59.063 43.478 3.30 3.30 42.35 5.01
406 413 5.416947 AGTGGAGTAGTAGTATTTTTGCCG 58.583 41.667 0.00 0.00 0.00 5.69
408 415 6.479331 GCCTAGTGGAGTAGTAGTATTTTTGC 59.521 42.308 0.00 0.00 34.57 3.68
453 461 1.239968 AAGCTACTTGTGCAGGCAGC 61.240 55.000 0.00 0.00 45.96 5.25
454 462 2.099141 TAAGCTACTTGTGCAGGCAG 57.901 50.000 0.00 0.00 0.00 4.85
455 463 2.787473 ATAAGCTACTTGTGCAGGCA 57.213 45.000 0.00 0.00 0.00 4.75
456 464 3.058639 GCATATAAGCTACTTGTGCAGGC 60.059 47.826 7.14 0.00 32.32 4.85
474 482 6.456853 GCACACTTGACTGATTAATTCGCATA 60.457 38.462 0.00 0.00 0.00 3.14
475 483 5.674569 GCACACTTGACTGATTAATTCGCAT 60.675 40.000 0.00 0.00 0.00 4.73
516 524 2.100087 TGACATGGCGATGTACGTATGT 59.900 45.455 14.81 0.00 43.22 2.29
517 525 2.726241 CTGACATGGCGATGTACGTATG 59.274 50.000 14.81 0.00 43.22 2.39
549 557 0.456312 CCACTTAGACGTCGACAGCC 60.456 60.000 17.16 3.52 0.00 4.85
552 560 1.162698 CCTCCACTTAGACGTCGACA 58.837 55.000 17.16 0.00 0.00 4.35
619 627 1.604604 CAACAGGAAACATCCACCGT 58.395 50.000 0.00 0.00 0.00 4.83
664 672 1.521681 AGCCGCCTGTTTCGCTATC 60.522 57.895 0.00 0.00 0.00 2.08
714 722 1.092345 GGCAGAAGGCGATCCAGAAC 61.092 60.000 0.00 0.00 46.16 3.01
719 727 2.514824 GGTGGCAGAAGGCGATCC 60.515 66.667 0.00 0.00 46.16 3.36
777 785 1.183030 ACGACAAGACCGGGTCATGA 61.183 55.000 32.31 0.00 35.25 3.07
785 793 4.554163 GTGAGGACGACAAGACCG 57.446 61.111 0.00 0.00 39.69 4.79
842 859 0.178068 TATCCGAGGCAGTTTGGAGC 59.822 55.000 0.00 0.00 34.12 4.70
892 909 1.375523 CCTTCCCTTCCGTCGTTGG 60.376 63.158 0.00 0.00 0.00 3.77
903 920 4.209154 TCCCGTTAGATTATCCTTCCCT 57.791 45.455 0.00 0.00 0.00 4.20
904 921 4.504514 GGTTCCCGTTAGATTATCCTTCCC 60.505 50.000 0.00 0.00 0.00 3.97
905 922 4.639334 GGTTCCCGTTAGATTATCCTTCC 58.361 47.826 0.00 0.00 0.00 3.46
906 923 4.304939 CGGTTCCCGTTAGATTATCCTTC 58.695 47.826 0.00 0.00 42.73 3.46
907 924 3.070590 CCGGTTCCCGTTAGATTATCCTT 59.929 47.826 0.00 0.00 46.80 3.36
974 991 0.179009 TTTGCTGCTCTGCTCTGGTT 60.179 50.000 0.00 0.00 0.00 3.67
975 992 0.888285 GTTTGCTGCTCTGCTCTGGT 60.888 55.000 0.00 0.00 0.00 4.00
976 993 1.584380 GGTTTGCTGCTCTGCTCTGG 61.584 60.000 0.00 0.00 0.00 3.86
977 994 0.887836 TGGTTTGCTGCTCTGCTCTG 60.888 55.000 0.00 0.00 0.00 3.35
978 995 0.605860 CTGGTTTGCTGCTCTGCTCT 60.606 55.000 0.00 0.00 0.00 4.09
979 996 1.874562 CTGGTTTGCTGCTCTGCTC 59.125 57.895 0.00 0.00 0.00 4.26
980 997 2.266627 GCTGGTTTGCTGCTCTGCT 61.267 57.895 0.00 0.00 0.00 4.24
981 998 2.257676 GCTGGTTTGCTGCTCTGC 59.742 61.111 0.00 0.68 0.00 4.26
1023 1040 3.223589 GCGAGGAGGAGGGAGAGC 61.224 72.222 0.00 0.00 0.00 4.09
1401 1436 2.265739 GGAGTGATGCCGCTGTCA 59.734 61.111 0.00 0.00 32.40 3.58
1552 1590 3.948719 GGTGGTGCGGTTCCCAGA 61.949 66.667 0.00 0.00 0.00 3.86
2068 6598 2.401766 GCGGGTAGAAGACGGTCGA 61.402 63.158 1.89 0.00 0.00 4.20
2400 6945 4.773117 GACGTGCCGAGGACCGTC 62.773 72.222 14.79 14.79 42.22 4.79
2571 7116 1.000496 GACTCGAAGTTGAAGGTCGGT 60.000 52.381 0.00 0.00 35.51 4.69
2595 7140 3.188786 GGCGCTGACATGGACGTC 61.189 66.667 7.64 7.13 36.40 4.34
2817 7362 2.202837 GCCGGGGTGATGTCGTAC 60.203 66.667 2.18 0.00 0.00 3.67
2940 7485 2.286872 GAGATCGACGGGTAGTTCAGA 58.713 52.381 0.00 0.00 0.00 3.27
2993 7538 1.218047 CGTGTCACCACCATCGGAT 59.782 57.895 0.00 0.00 38.41 4.18
3054 7605 2.035237 TTTCCGGCAGGTCGAACTGT 62.035 55.000 30.03 0.00 40.59 3.55
3271 7825 9.931210 GCGTATAGTAAAATAAATTGTCAAGCT 57.069 29.630 0.00 0.00 0.00 3.74
3308 7862 4.107622 GGCGTATAGTACTCTCGCAAAAA 58.892 43.478 27.35 1.07 46.98 1.94
3309 7863 3.129113 TGGCGTATAGTACTCTCGCAAAA 59.871 43.478 27.35 16.45 46.98 2.44
3310 7864 2.684374 TGGCGTATAGTACTCTCGCAAA 59.316 45.455 27.35 18.12 46.98 3.68
3311 7865 2.291365 TGGCGTATAGTACTCTCGCAA 58.709 47.619 27.35 19.95 46.98 4.85
3312 7866 1.957668 TGGCGTATAGTACTCTCGCA 58.042 50.000 27.35 17.13 46.98 5.10
3313 7867 2.290093 AGTTGGCGTATAGTACTCTCGC 59.710 50.000 22.19 22.19 44.95 5.03
3314 7868 4.034858 TCAAGTTGGCGTATAGTACTCTCG 59.965 45.833 0.00 4.27 0.00 4.04
3315 7869 5.496133 TCAAGTTGGCGTATAGTACTCTC 57.504 43.478 0.00 0.00 0.00 3.20
3316 7870 5.736492 GCATCAAGTTGGCGTATAGTACTCT 60.736 44.000 0.00 0.00 0.00 3.24
3317 7871 4.444720 GCATCAAGTTGGCGTATAGTACTC 59.555 45.833 0.00 0.00 0.00 2.59
3318 7872 4.099573 AGCATCAAGTTGGCGTATAGTACT 59.900 41.667 2.34 0.00 0.00 2.73
3319 7873 4.369182 AGCATCAAGTTGGCGTATAGTAC 58.631 43.478 2.34 0.00 0.00 2.73
3320 7874 4.665833 AGCATCAAGTTGGCGTATAGTA 57.334 40.909 2.34 0.00 0.00 1.82
3321 7875 3.543680 AGCATCAAGTTGGCGTATAGT 57.456 42.857 2.34 0.00 0.00 2.12
3322 7876 3.741344 GGTAGCATCAAGTTGGCGTATAG 59.259 47.826 2.34 0.00 0.00 1.31
3323 7877 3.133183 TGGTAGCATCAAGTTGGCGTATA 59.867 43.478 2.34 0.00 0.00 1.47
3324 7878 2.093181 TGGTAGCATCAAGTTGGCGTAT 60.093 45.455 2.34 0.00 0.00 3.06
3363 7917 3.821033 GACAAACAAAGGTAGCATCAGGT 59.179 43.478 0.00 0.00 0.00 4.00
3365 7919 4.083110 CCTGACAAACAAAGGTAGCATCAG 60.083 45.833 0.00 0.00 0.00 2.90
3375 7929 5.639082 AGAAGCAAAAACCTGACAAACAAAG 59.361 36.000 0.00 0.00 0.00 2.77
3401 7955 4.199310 CCAATCATGTCGAACTAACCCAT 58.801 43.478 0.00 0.00 0.00 4.00
3404 7958 3.606687 ACCCAATCATGTCGAACTAACC 58.393 45.455 0.00 0.00 0.00 2.85
3405 7959 4.693566 TCAACCCAATCATGTCGAACTAAC 59.306 41.667 0.00 0.00 0.00 2.34
3407 7961 4.250464 GTCAACCCAATCATGTCGAACTA 58.750 43.478 0.00 0.00 0.00 2.24
3408 7962 3.074412 GTCAACCCAATCATGTCGAACT 58.926 45.455 0.00 0.00 0.00 3.01
3409 7963 2.811431 TGTCAACCCAATCATGTCGAAC 59.189 45.455 0.00 0.00 0.00 3.95
3411 7965 2.849294 TGTCAACCCAATCATGTCGA 57.151 45.000 0.00 0.00 0.00 4.20
3412 7966 3.009026 TCATGTCAACCCAATCATGTCG 58.991 45.455 0.00 0.00 38.78 4.35
3413 7967 6.698008 TTATCATGTCAACCCAATCATGTC 57.302 37.500 0.00 0.00 38.78 3.06
3414 7968 6.608405 ACATTATCATGTCAACCCAATCATGT 59.392 34.615 0.00 0.00 39.69 3.21
3416 7970 8.765488 TTACATTATCATGTCAACCCAATCAT 57.235 30.769 0.00 0.00 43.06 2.45
3417 7971 8.631797 CATTACATTATCATGTCAACCCAATCA 58.368 33.333 0.00 0.00 43.06 2.57
3418 7972 8.084073 CCATTACATTATCATGTCAACCCAATC 58.916 37.037 0.00 0.00 43.06 2.67
3419 7973 7.564660 ACCATTACATTATCATGTCAACCCAAT 59.435 33.333 0.00 0.00 43.06 3.16
3420 7974 6.894654 ACCATTACATTATCATGTCAACCCAA 59.105 34.615 0.00 0.00 43.06 4.12
3645 8566 7.282585 ACCGGATGATTTAATTGAATCTCTCA 58.717 34.615 20.01 5.67 37.04 3.27
3647 8568 9.627123 TTTACCGGATGATTTAATTGAATCTCT 57.373 29.630 20.01 10.19 37.04 3.10
3667 8588 3.606687 AGCATGGGTACTTTCTTTACCG 58.393 45.455 0.00 0.00 40.12 4.02
3727 8648 5.149973 ACAAATTTGAGCATGCATACCAA 57.850 34.783 24.64 14.57 0.00 3.67
3745 8666 3.468770 ACACACACTACGCCATAACAAA 58.531 40.909 0.00 0.00 0.00 2.83
3748 8669 3.323243 AGAACACACACTACGCCATAAC 58.677 45.455 0.00 0.00 0.00 1.89
3789 8710 6.585695 AGACACTATTGACTTCTAAACGGA 57.414 37.500 0.00 0.00 0.00 4.69
3868 8789 3.839954 GCTCGTTACAACACACGAACAAG 60.840 47.826 0.00 0.00 44.45 3.16
3886 8807 9.291664 GCTAACCTACTAGAATATTTATGCTCG 57.708 37.037 0.00 0.00 0.00 5.03
3888 8809 8.804204 ACGCTAACCTACTAGAATATTTATGCT 58.196 33.333 0.00 0.00 0.00 3.79
3906 8827 4.102649 GGCAAATAAATCACACGCTAACC 58.897 43.478 0.00 0.00 0.00 2.85
4024 8947 7.885399 GCCCCATCTCTTATGTACTTATCAAAT 59.115 37.037 0.00 0.00 0.00 2.32
4040 8963 1.919600 GCCTCAAGTGCCCCATCTCT 61.920 60.000 0.00 0.00 0.00 3.10
4041 8964 1.452833 GCCTCAAGTGCCCCATCTC 60.453 63.158 0.00 0.00 0.00 2.75
4042 8965 2.207501 CTGCCTCAAGTGCCCCATCT 62.208 60.000 0.00 0.00 0.00 2.90
4044 8967 2.085343 AACTGCCTCAAGTGCCCCAT 62.085 55.000 0.00 0.00 0.00 4.00
4045 8968 2.296945 AAACTGCCTCAAGTGCCCCA 62.297 55.000 0.00 0.00 0.00 4.96
4046 8969 1.115326 AAAACTGCCTCAAGTGCCCC 61.115 55.000 0.00 0.00 0.00 5.80
4047 8970 0.315251 GAAAACTGCCTCAAGTGCCC 59.685 55.000 0.00 0.00 0.00 5.36
4107 9030 5.964477 TCCAACCTTACATAGTTCATCCTCT 59.036 40.000 0.00 0.00 0.00 3.69
4124 9047 1.425448 CCCTTCTCCTTTGTCCAACCT 59.575 52.381 0.00 0.00 0.00 3.50
4173 9415 2.484770 GGTCCGGCATGCACTTATCTTA 60.485 50.000 21.36 0.00 0.00 2.10
4174 9416 1.668419 GTCCGGCATGCACTTATCTT 58.332 50.000 21.36 0.00 0.00 2.40
4176 9418 1.498865 CGGTCCGGCATGCACTTATC 61.499 60.000 21.36 0.00 0.00 1.75
4177 9419 1.523711 CGGTCCGGCATGCACTTAT 60.524 57.895 21.36 0.00 0.00 1.73
4178 9420 2.125310 CGGTCCGGCATGCACTTA 60.125 61.111 21.36 0.00 0.00 2.24
4189 9431 1.755395 TATGGGTCTCACCGGTCCG 60.755 63.158 2.59 3.60 39.83 4.79
4190 9432 1.683418 GGTATGGGTCTCACCGGTCC 61.683 65.000 2.59 1.82 39.83 4.46
4191 9433 1.683418 GGGTATGGGTCTCACCGGTC 61.683 65.000 2.59 0.00 39.83 4.79
4193 9435 2.792947 CGGGTATGGGTCTCACCGG 61.793 68.421 0.00 0.00 39.83 5.28
4194 9436 2.792947 CCGGGTATGGGTCTCACCG 61.793 68.421 0.00 0.00 39.83 4.94
4195 9437 3.103091 GCCGGGTATGGGTCTCACC 62.103 68.421 2.18 0.00 37.60 4.02
4196 9438 2.311688 CTGCCGGGTATGGGTCTCAC 62.312 65.000 2.18 0.00 0.00 3.51
4197 9439 2.039787 TGCCGGGTATGGGTCTCA 59.960 61.111 2.18 0.00 0.00 3.27
4198 9440 2.808206 CCTGCCGGGTATGGGTCTC 61.808 68.421 2.18 0.00 0.00 3.36
4200 9442 4.564110 GCCTGCCGGGTATGGGTC 62.564 72.222 2.18 0.00 37.43 4.46
4203 9445 4.910585 GACGCCTGCCGGGTATGG 62.911 72.222 2.18 0.00 42.52 2.74
4213 9455 4.277552 TCCTATCCAGGACGCCTG 57.722 61.111 16.22 16.22 46.58 4.85
4220 9462 3.541242 AGACCTGAGATCCTATCCAGG 57.459 52.381 16.47 16.47 45.44 4.45
4221 9463 5.886609 TCTAAGACCTGAGATCCTATCCAG 58.113 45.833 0.00 0.00 0.00 3.86
4222 9464 5.932027 TCTAAGACCTGAGATCCTATCCA 57.068 43.478 0.00 0.00 0.00 3.41
4223 9465 6.252995 ACATCTAAGACCTGAGATCCTATCC 58.747 44.000 0.00 0.00 29.73 2.59
4224 9466 7.775053 AACATCTAAGACCTGAGATCCTATC 57.225 40.000 0.00 0.00 29.73 2.08
4226 9468 7.817440 ACTAACATCTAAGACCTGAGATCCTA 58.183 38.462 0.00 0.00 29.73 2.94
4228 9470 6.969993 ACTAACATCTAAGACCTGAGATCC 57.030 41.667 0.00 0.00 29.73 3.36
4231 9473 7.963532 ACAAAACTAACATCTAAGACCTGAGA 58.036 34.615 0.00 0.00 0.00 3.27
4232 9474 8.091449 AGACAAAACTAACATCTAAGACCTGAG 58.909 37.037 0.00 0.00 0.00 3.35
4233 9475 7.872993 CAGACAAAACTAACATCTAAGACCTGA 59.127 37.037 0.00 0.00 0.00 3.86
4237 9479 6.526222 CGCAGACAAAACTAACATCTAAGAC 58.474 40.000 0.00 0.00 0.00 3.01
4238 9480 6.706055 CGCAGACAAAACTAACATCTAAGA 57.294 37.500 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.