Multiple sequence alignment - TraesCS7D01G454300

Loading Multiple Alignment...

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 TraesCS7D01G454300 chr7D 100.000 3131 0 0 1 3131 573698662 573695532 0.000000e+00 5782.0
1 TraesCS7D01G454300 chr7D 84.137 1494 177 34 883 2334 573827851 573826376 0.000000e+00 1391.0
2 TraesCS7D01G454300 chr7D 80.280 644 83 22 1727 2351 15322986 15323604 2.220000e-121 446.0
3 TraesCS7D01G454300 chr7D 76.680 253 42 14 995 1233 15322323 15322572 1.180000e-24 124.0
4 TraesCS7D01G454300 chr7D 94.595 37 2 0 33 69 573698603 573698567 1.210000e-04 58.4
5 TraesCS7D01G454300 chr7D 94.595 37 2 0 60 96 573698630 573698594 1.210000e-04 58.4
6 TraesCS7D01G454300 chr7B 92.174 2351 118 37 181 2479 632495593 632493257 0.000000e+00 3262.0
7 TraesCS7D01G454300 chr7B 86.107 691 80 9 1725 2408 632658223 632657542 0.000000e+00 730.0
8 TraesCS7D01G454300 chr7B 83.994 681 83 21 943 1605 632658987 632658315 5.700000e-177 630.0
9 TraesCS7D01G454300 chr7B 88.167 431 33 9 2641 3069 632493228 632492814 6.030000e-137 497.0
10 TraesCS7D01G454300 chr7A 85.917 2251 191 64 876 3059 663534498 663532307 0.000000e+00 2285.0
11 TraesCS7D01G454300 chr7A 81.293 588 79 20 1729 2302 14619309 14619879 6.160000e-122 448.0
12 TraesCS7D01G454300 chr7A 82.405 449 62 14 1983 2427 575286530 575286095 2.950000e-100 375.0
13 TraesCS7D01G454300 chr3B 94.571 350 17 2 1294 1641 14090480 14090131 9.880000e-150 540.0
14 TraesCS7D01G454300 chr2B 92.330 352 23 4 1292 1641 51284776 51284427 6.030000e-137 497.0
15 TraesCS7D01G454300 chr4A 81.154 589 82 19 1727 2302 720516287 720515715 2.220000e-121 446.0
16 TraesCS7D01G454300 chr4A 77.733 247 39 10 998 1233 720517090 720516849 1.510000e-28 137.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G454300 chr7D 573695532 573698662 3130 True 1966.266667 5782 96.396667 1 3131 3 chr7D.!!$R2 3130
1 TraesCS7D01G454300 chr7D 573826376 573827851 1475 True 1391.000000 1391 84.137000 883 2334 1 chr7D.!!$R1 1451
2 TraesCS7D01G454300 chr7D 15322323 15323604 1281 False 285.000000 446 78.480000 995 2351 2 chr7D.!!$F1 1356
3 TraesCS7D01G454300 chr7B 632492814 632495593 2779 True 1879.500000 3262 90.170500 181 3069 2 chr7B.!!$R1 2888
4 TraesCS7D01G454300 chr7B 632657542 632658987 1445 True 680.000000 730 85.050500 943 2408 2 chr7B.!!$R2 1465
5 TraesCS7D01G454300 chr7A 663532307 663534498 2191 True 2285.000000 2285 85.917000 876 3059 1 chr7A.!!$R2 2183
6 TraesCS7D01G454300 chr7A 14619309 14619879 570 False 448.000000 448 81.293000 1729 2302 1 chr7A.!!$F1 573
7 TraesCS7D01G454300 chr4A 720515715 720517090 1375 True 291.500000 446 79.443500 998 2302 2 chr4A.!!$R1 1304

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
30 31 0.109039 AACTTTCTCCGCGAGCTCTC 60.109 55.0 8.23 2.14 0.00 3.20 F
41 42 0.179140 CGAGCTCTCTCTTGGCTGTC 60.179 60.0 12.85 0.00 37.19 3.51 F
72 73 0.248843 CAGCCCCTTGACTCTCAGTC 59.751 60.0 0.00 0.00 45.26 3.51 F
104 105 0.250295 CCTTGACTCTCGCCCACAAA 60.250 55.0 0.00 0.00 0.00 2.83 F
106 107 0.250295 TTGACTCTCGCCCACAAAGG 60.250 55.0 0.00 0.00 37.03 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2267 1.599542 GGAGACACACTGCAAGAACAC 59.400 52.381 0.00 0.00 37.43 3.32 R
1901 2274 2.370281 ATACGGAGACACACTGCAAG 57.630 50.000 0.00 0.00 36.75 4.01 R
1912 2285 4.282449 TCCTTGTTGACTTGAATACGGAGA 59.718 41.667 0.00 0.00 0.00 3.71 R
1962 2335 5.643777 AGCAGATAAAACGCTAACAGTGAAT 59.356 36.000 0.00 0.00 33.25 2.57 R
2137 2510 4.373348 AAATCTCGGAAACTCGTAGGAG 57.627 45.455 10.86 10.86 46.13 3.69 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
18 19 3.520623 ACCTTGGCAGCAACTTTCT 57.479 47.368 0.00 0.00 0.00 2.52
19 20 1.322442 ACCTTGGCAGCAACTTTCTC 58.678 50.000 0.00 0.00 0.00 2.87
20 21 0.600057 CCTTGGCAGCAACTTTCTCC 59.400 55.000 0.00 0.00 0.00 3.71
21 22 0.239347 CTTGGCAGCAACTTTCTCCG 59.761 55.000 0.00 0.00 0.00 4.63
22 23 1.795170 TTGGCAGCAACTTTCTCCGC 61.795 55.000 0.00 0.00 0.00 5.54
23 24 2.174349 GCAGCAACTTTCTCCGCG 59.826 61.111 0.00 0.00 0.00 6.46
24 25 2.317609 GCAGCAACTTTCTCCGCGA 61.318 57.895 8.23 0.00 0.00 5.87
25 26 1.784062 CAGCAACTTTCTCCGCGAG 59.216 57.895 8.23 3.02 0.00 5.03
26 27 2.029844 AGCAACTTTCTCCGCGAGC 61.030 57.895 8.23 0.00 0.00 5.03
27 28 2.029844 GCAACTTTCTCCGCGAGCT 61.030 57.895 8.23 0.00 0.00 4.09
28 29 1.960994 GCAACTTTCTCCGCGAGCTC 61.961 60.000 8.23 2.73 0.00 4.09
29 30 0.389166 CAACTTTCTCCGCGAGCTCT 60.389 55.000 8.23 0.00 0.00 4.09
30 31 0.109039 AACTTTCTCCGCGAGCTCTC 60.109 55.000 8.23 2.14 0.00 3.20
31 32 0.963355 ACTTTCTCCGCGAGCTCTCT 60.963 55.000 8.23 0.00 0.00 3.10
32 33 0.248458 CTTTCTCCGCGAGCTCTCTC 60.248 60.000 8.23 0.00 35.99 3.20
33 34 0.678366 TTTCTCCGCGAGCTCTCTCT 60.678 55.000 8.23 0.00 37.19 3.10
34 35 0.678366 TTCTCCGCGAGCTCTCTCTT 60.678 55.000 8.23 0.00 37.19 2.85
35 36 1.063972 CTCCGCGAGCTCTCTCTTG 59.936 63.158 8.23 0.00 37.19 3.02
36 37 2.103934 CCGCGAGCTCTCTCTTGG 59.896 66.667 8.23 0.00 37.19 3.61
37 38 2.581953 CGCGAGCTCTCTCTTGGC 60.582 66.667 12.85 4.77 37.19 4.52
38 39 2.891882 GCGAGCTCTCTCTTGGCT 59.108 61.111 12.85 0.00 37.19 4.75
39 40 1.519013 GCGAGCTCTCTCTTGGCTG 60.519 63.158 12.85 0.00 37.19 4.85
40 41 1.889454 CGAGCTCTCTCTTGGCTGT 59.111 57.895 12.85 0.00 37.19 4.40
41 42 0.179140 CGAGCTCTCTCTTGGCTGTC 60.179 60.000 12.85 0.00 37.19 3.51
42 43 0.894141 GAGCTCTCTCTTGGCTGTCA 59.106 55.000 6.43 0.00 36.37 3.58
43 44 0.896923 AGCTCTCTCTTGGCTGTCAG 59.103 55.000 0.00 0.00 34.82 3.51
44 45 0.607620 GCTCTCTCTTGGCTGTCAGT 59.392 55.000 0.93 0.00 0.00 3.41
45 46 1.404047 GCTCTCTCTTGGCTGTCAGTC 60.404 57.143 0.00 0.00 0.00 3.51
46 47 1.204467 CTCTCTCTTGGCTGTCAGTCC 59.796 57.143 1.07 4.27 0.00 3.85
47 48 0.972134 CTCTCTTGGCTGTCAGTCCA 59.028 55.000 10.78 10.78 0.00 4.02
48 49 1.554160 CTCTCTTGGCTGTCAGTCCAT 59.446 52.381 14.33 0.00 31.54 3.41
49 50 1.552337 TCTCTTGGCTGTCAGTCCATC 59.448 52.381 14.33 0.00 31.54 3.51
50 51 0.615331 TCTTGGCTGTCAGTCCATCC 59.385 55.000 14.33 2.39 31.54 3.51
51 52 0.742281 CTTGGCTGTCAGTCCATCCG 60.742 60.000 14.33 5.58 31.54 4.18
52 53 2.184020 TTGGCTGTCAGTCCATCCGG 62.184 60.000 14.33 0.00 31.54 5.14
53 54 2.512515 GCTGTCAGTCCATCCGGC 60.513 66.667 0.00 0.00 0.00 6.13
54 55 2.981302 CTGTCAGTCCATCCGGCA 59.019 61.111 0.00 0.00 0.00 5.69
55 56 1.153489 CTGTCAGTCCATCCGGCAG 60.153 63.158 0.00 0.00 0.00 4.85
56 57 2.512515 GTCAGTCCATCCGGCAGC 60.513 66.667 0.00 0.00 0.00 5.25
57 58 3.785859 TCAGTCCATCCGGCAGCC 61.786 66.667 0.00 0.00 0.00 4.85
58 59 4.864334 CAGTCCATCCGGCAGCCC 62.864 72.222 5.63 0.00 0.00 5.19
63 64 4.113815 CATCCGGCAGCCCCTTGA 62.114 66.667 5.63 0.00 0.00 3.02
64 65 4.115199 ATCCGGCAGCCCCTTGAC 62.115 66.667 5.63 0.00 0.00 3.18
66 67 4.785453 CCGGCAGCCCCTTGACTC 62.785 72.222 5.63 0.00 0.00 3.36
67 68 3.710722 CGGCAGCCCCTTGACTCT 61.711 66.667 5.63 0.00 0.00 3.24
68 69 2.270527 GGCAGCCCCTTGACTCTC 59.729 66.667 0.00 0.00 0.00 3.20
69 70 2.596851 GGCAGCCCCTTGACTCTCA 61.597 63.158 0.00 0.00 0.00 3.27
70 71 1.078567 GCAGCCCCTTGACTCTCAG 60.079 63.158 0.00 0.00 0.00 3.35
71 72 1.835927 GCAGCCCCTTGACTCTCAGT 61.836 60.000 0.00 0.00 0.00 3.41
72 73 0.248843 CAGCCCCTTGACTCTCAGTC 59.751 60.000 0.00 0.00 45.26 3.51
73 74 0.907230 AGCCCCTTGACTCTCAGTCC 60.907 60.000 1.23 0.00 44.44 3.85
74 75 1.194781 GCCCCTTGACTCTCAGTCCA 61.195 60.000 1.23 0.00 44.44 4.02
75 76 1.577736 CCCCTTGACTCTCAGTCCAT 58.422 55.000 1.23 0.00 44.44 3.41
76 77 1.484240 CCCCTTGACTCTCAGTCCATC 59.516 57.143 1.23 0.00 44.44 3.51
77 78 1.484240 CCCTTGACTCTCAGTCCATCC 59.516 57.143 1.23 0.00 44.44 3.51
78 79 1.135915 CCTTGACTCTCAGTCCATCCG 59.864 57.143 1.23 0.00 44.44 4.18
79 80 1.135915 CTTGACTCTCAGTCCATCCGG 59.864 57.143 0.00 0.00 44.44 5.14
80 81 1.323271 TGACTCTCAGTCCATCCGGC 61.323 60.000 0.00 0.00 44.44 6.13
81 82 1.305297 ACTCTCAGTCCATCCGGCA 60.305 57.895 0.00 0.00 0.00 5.69
82 83 1.326213 ACTCTCAGTCCATCCGGCAG 61.326 60.000 0.00 0.00 0.00 4.85
83 84 2.202987 CTCAGTCCATCCGGCAGC 60.203 66.667 0.00 0.00 0.00 5.25
84 85 3.746949 CTCAGTCCATCCGGCAGCC 62.747 68.421 0.00 0.00 0.00 4.85
85 86 4.864334 CAGTCCATCCGGCAGCCC 62.864 72.222 5.63 0.00 0.00 5.19
90 91 4.113815 CATCCGGCAGCCCCTTGA 62.114 66.667 5.63 0.00 0.00 3.02
91 92 4.115199 ATCCGGCAGCCCCTTGAC 62.115 66.667 5.63 0.00 0.00 3.18
93 94 4.785453 CCGGCAGCCCCTTGACTC 62.785 72.222 5.63 0.00 0.00 3.36
94 95 3.710722 CGGCAGCCCCTTGACTCT 61.711 66.667 5.63 0.00 0.00 3.24
95 96 2.270527 GGCAGCCCCTTGACTCTC 59.729 66.667 0.00 0.00 0.00 3.20
96 97 2.125350 GCAGCCCCTTGACTCTCG 60.125 66.667 0.00 0.00 0.00 4.04
97 98 2.125350 CAGCCCCTTGACTCTCGC 60.125 66.667 0.00 0.00 0.00 5.03
98 99 3.394836 AGCCCCTTGACTCTCGCC 61.395 66.667 0.00 0.00 0.00 5.54
99 100 4.475135 GCCCCTTGACTCTCGCCC 62.475 72.222 0.00 0.00 0.00 6.13
100 101 3.003173 CCCCTTGACTCTCGCCCA 61.003 66.667 0.00 0.00 0.00 5.36
101 102 2.266055 CCCTTGACTCTCGCCCAC 59.734 66.667 0.00 0.00 0.00 4.61
102 103 2.583441 CCCTTGACTCTCGCCCACA 61.583 63.158 0.00 0.00 0.00 4.17
103 104 1.371183 CCTTGACTCTCGCCCACAA 59.629 57.895 0.00 0.00 0.00 3.33
104 105 0.250295 CCTTGACTCTCGCCCACAAA 60.250 55.000 0.00 0.00 0.00 2.83
105 106 1.151668 CTTGACTCTCGCCCACAAAG 58.848 55.000 0.00 0.00 0.00 2.77
106 107 0.250295 TTGACTCTCGCCCACAAAGG 60.250 55.000 0.00 0.00 37.03 3.11
107 108 1.371558 GACTCTCGCCCACAAAGGT 59.628 57.895 0.00 0.00 34.66 3.50
108 109 0.606604 GACTCTCGCCCACAAAGGTA 59.393 55.000 0.00 0.00 34.66 3.08
109 110 0.320697 ACTCTCGCCCACAAAGGTAC 59.679 55.000 0.00 0.00 34.66 3.34
126 127 5.291905 AGGTACTTTGTTCAGCTTGTACT 57.708 39.130 0.00 0.00 27.25 2.73
127 128 5.298347 AGGTACTTTGTTCAGCTTGTACTC 58.702 41.667 0.00 0.00 27.25 2.59
128 129 4.451435 GGTACTTTGTTCAGCTTGTACTCC 59.549 45.833 0.00 0.00 33.15 3.85
129 130 3.131396 ACTTTGTTCAGCTTGTACTCCG 58.869 45.455 0.00 0.00 0.00 4.63
130 131 3.181469 ACTTTGTTCAGCTTGTACTCCGA 60.181 43.478 0.00 0.00 0.00 4.55
131 132 3.462483 TTGTTCAGCTTGTACTCCGAA 57.538 42.857 0.00 0.00 0.00 4.30
132 133 3.462483 TGTTCAGCTTGTACTCCGAAA 57.538 42.857 0.00 0.00 0.00 3.46
133 134 3.128349 TGTTCAGCTTGTACTCCGAAAC 58.872 45.455 0.00 0.00 0.00 2.78
134 135 3.128349 GTTCAGCTTGTACTCCGAAACA 58.872 45.455 0.00 0.00 0.00 2.83
135 136 3.678056 TCAGCTTGTACTCCGAAACAT 57.322 42.857 0.00 0.00 0.00 2.71
136 137 3.585862 TCAGCTTGTACTCCGAAACATC 58.414 45.455 0.00 0.00 0.00 3.06
137 138 2.345641 CAGCTTGTACTCCGAAACATCG 59.654 50.000 0.00 0.00 0.00 3.84
149 150 3.703420 CGAAACATCGGTACTTAGGAGG 58.297 50.000 0.00 0.00 0.00 4.30
150 151 3.490419 CGAAACATCGGTACTTAGGAGGG 60.490 52.174 0.00 0.00 0.00 4.30
151 152 2.083628 ACATCGGTACTTAGGAGGGG 57.916 55.000 0.00 0.00 0.00 4.79
152 153 1.572415 ACATCGGTACTTAGGAGGGGA 59.428 52.381 0.00 0.00 0.00 4.81
153 154 2.179424 ACATCGGTACTTAGGAGGGGAT 59.821 50.000 0.00 0.00 0.00 3.85
154 155 3.240302 CATCGGTACTTAGGAGGGGATT 58.760 50.000 0.00 0.00 0.00 3.01
155 156 4.140853 ACATCGGTACTTAGGAGGGGATTA 60.141 45.833 0.00 0.00 0.00 1.75
156 157 4.754411 TCGGTACTTAGGAGGGGATTAT 57.246 45.455 0.00 0.00 0.00 1.28
157 158 5.083953 TCGGTACTTAGGAGGGGATTATT 57.916 43.478 0.00 0.00 0.00 1.40
158 159 6.218195 TCGGTACTTAGGAGGGGATTATTA 57.782 41.667 0.00 0.00 0.00 0.98
159 160 6.808357 TCGGTACTTAGGAGGGGATTATTAT 58.192 40.000 0.00 0.00 0.00 1.28
160 161 7.251195 TCGGTACTTAGGAGGGGATTATTATT 58.749 38.462 0.00 0.00 0.00 1.40
161 162 7.736234 TCGGTACTTAGGAGGGGATTATTATTT 59.264 37.037 0.00 0.00 0.00 1.40
162 163 8.380867 CGGTACTTAGGAGGGGATTATTATTTT 58.619 37.037 0.00 0.00 0.00 1.82
166 167 9.475013 ACTTAGGAGGGGATTATTATTTTACCT 57.525 33.333 0.00 0.00 0.00 3.08
213 214 4.752879 GCCCGCTAACGCACTCCA 62.753 66.667 0.00 0.00 38.22 3.86
262 263 1.526917 CCCCACATCCTCCGCAATC 60.527 63.158 0.00 0.00 0.00 2.67
263 264 1.528824 CCCACATCCTCCGCAATCT 59.471 57.895 0.00 0.00 0.00 2.40
264 265 0.533755 CCCACATCCTCCGCAATCTC 60.534 60.000 0.00 0.00 0.00 2.75
267 268 1.134280 CACATCCTCCGCAATCTCCTT 60.134 52.381 0.00 0.00 0.00 3.36
278 279 2.952978 GCAATCTCCTTCTCCGTCTAGA 59.047 50.000 0.00 0.00 0.00 2.43
321 325 0.771127 CCCCCGATCTCTCTCTCTCT 59.229 60.000 0.00 0.00 0.00 3.10
322 326 1.271379 CCCCCGATCTCTCTCTCTCTC 60.271 61.905 0.00 0.00 0.00 3.20
323 327 1.699634 CCCCGATCTCTCTCTCTCTCT 59.300 57.143 0.00 0.00 0.00 3.10
324 328 2.289694 CCCCGATCTCTCTCTCTCTCTC 60.290 59.091 0.00 0.00 0.00 3.20
325 329 2.289694 CCCGATCTCTCTCTCTCTCTCC 60.290 59.091 0.00 0.00 0.00 3.71
343 347 4.367023 CCCTTCGGCGTCCACGAA 62.367 66.667 6.85 0.00 46.73 3.85
349 353 2.260434 GGCGTCCACGAACAGCTA 59.740 61.111 2.58 0.00 43.02 3.32
350 354 1.153628 GGCGTCCACGAACAGCTAT 60.154 57.895 2.58 0.00 43.02 2.97
415 425 4.069232 TGGGCGACGCTTCTCCTG 62.069 66.667 20.77 0.00 0.00 3.86
434 444 2.053618 CGGATCCATCCCTCCTGTC 58.946 63.158 13.41 0.00 44.24 3.51
487 497 2.807676 ACGAATGCCCTTTTGGATTCT 58.192 42.857 0.00 0.00 44.07 2.40
508 518 5.602628 TCTGAATGCTGATTGAGATCTCTG 58.397 41.667 22.95 9.41 27.95 3.35
521 531 1.607628 GATCTCTGGTTGATGCATGCC 59.392 52.381 16.68 4.11 0.00 4.40
566 576 8.809066 AGTAGAAATTTATTAACCAAACACCCC 58.191 33.333 0.00 0.00 0.00 4.95
579 589 4.589374 CCAAACACCCCCACAAAATAGTAA 59.411 41.667 0.00 0.00 0.00 2.24
580 590 5.070580 CCAAACACCCCCACAAAATAGTAAA 59.929 40.000 0.00 0.00 0.00 2.01
581 591 6.408206 CCAAACACCCCCACAAAATAGTAAAA 60.408 38.462 0.00 0.00 0.00 1.52
583 593 6.413783 ACACCCCCACAAAATAGTAAAAAG 57.586 37.500 0.00 0.00 0.00 2.27
622 636 2.882137 CCCTCGGTTTTTCTTGCTGTAA 59.118 45.455 0.00 0.00 0.00 2.41
650 664 9.436957 TGATTTTCTTCCTAGTTATTGTCAGTC 57.563 33.333 0.00 0.00 0.00 3.51
654 668 5.480422 TCTTCCTAGTTATTGTCAGTCTGCA 59.520 40.000 0.00 0.00 0.00 4.41
670 684 1.326328 TGCACATAAAACTGCAGCCA 58.674 45.000 15.27 0.00 38.49 4.75
700 714 7.051623 TGAATTATACGGATTGCCAGTTAACT 58.948 34.615 1.12 1.12 0.00 2.24
718 732 8.233190 CAGTTAACTCTTTGGTCATCTGAATTC 58.767 37.037 4.77 0.00 0.00 2.17
745 759 0.955178 CGATAGATGGCTCGGTGAGT 59.045 55.000 0.00 0.00 39.76 3.41
747 761 1.271102 GATAGATGGCTCGGTGAGTCC 59.729 57.143 0.00 0.00 32.68 3.85
772 786 2.512692 TTGGCATGCAAGTCCATAGT 57.487 45.000 21.36 0.00 0.00 2.12
777 791 2.287915 GCATGCAAGTCCATAGTAACCG 59.712 50.000 14.21 0.00 0.00 4.44
780 794 4.114058 TGCAAGTCCATAGTAACCGTAC 57.886 45.455 0.00 0.00 0.00 3.67
795 809 2.347452 ACCGTACGCATTTCGATTCTTG 59.653 45.455 10.49 0.00 41.67 3.02
848 862 3.424302 CGTAACGCTTACATGTGCATTGT 60.424 43.478 9.11 9.78 35.89 2.71
856 870 5.634439 GCTTACATGTGCATTGTCATTTTGA 59.366 36.000 9.11 0.00 0.00 2.69
860 874 5.693104 ACATGTGCATTGTCATTTTGAAGAC 59.307 36.000 0.00 0.00 35.37 3.01
914 928 4.467795 TCAGCTGCTAGGTTTTGATCTAGT 59.532 41.667 9.47 0.00 36.32 2.57
1089 1109 2.163010 CACGAATCTCAAGGCAATTGCT 59.837 45.455 28.42 12.86 41.70 3.91
1154 1184 7.675195 AGACTATCTGATTGCTGATCCTATTCT 59.325 37.037 0.00 0.00 34.88 2.40
1233 1271 7.361713 CCTTGTTCAGGTAATTTTTCGATGCTA 60.362 37.037 0.00 0.00 37.99 3.49
1234 1272 7.441890 TGTTCAGGTAATTTTTCGATGCTAA 57.558 32.000 0.00 0.00 0.00 3.09
1239 1277 8.234546 TCAGGTAATTTTTCGATGCTAAACTTC 58.765 33.333 0.00 0.00 0.00 3.01
1324 1370 5.532779 TCGATAATACATGAGTGCAGAGAGT 59.467 40.000 0.00 0.00 0.00 3.24
1367 1413 6.656632 TCTTGTTCTAGTATAGCATGAGGG 57.343 41.667 0.00 0.00 38.99 4.30
1383 1494 0.686789 AGGGTTTGGAAAGGCAATGC 59.313 50.000 0.00 0.00 0.00 3.56
1465 1696 7.241042 TCAAAAATCTGCTGTACCTAGTACT 57.759 36.000 0.00 0.00 39.49 2.73
1477 1710 2.761208 ACCTAGTACTGTCATCTGGCAC 59.239 50.000 5.39 0.00 0.00 5.01
1586 1828 3.958018 TGTTTTCTAGGTGGTGTGTGTT 58.042 40.909 0.00 0.00 0.00 3.32
1604 1846 4.468153 TGTGTTATATAGTGTGTCCTGGCA 59.532 41.667 0.00 0.00 0.00 4.92
1638 1921 4.164843 TCAGTGCAAGTTCCCTTTAAGT 57.835 40.909 0.00 0.00 0.00 2.24
1640 1923 5.876357 TCAGTGCAAGTTCCCTTTAAGTAT 58.124 37.500 0.00 0.00 0.00 2.12
1702 2012 5.046520 AGTCTTCTGTTCACCCATAGTTACC 60.047 44.000 0.00 0.00 0.00 2.85
1887 2251 3.483421 CTTCCTTGGCTGCATGATATGA 58.517 45.455 0.50 0.00 0.00 2.15
1895 2266 3.881688 GGCTGCATGATATGAAACTGTCT 59.118 43.478 0.50 0.00 0.00 3.41
1896 2267 4.261072 GGCTGCATGATATGAAACTGTCTG 60.261 45.833 0.50 0.00 0.00 3.51
1901 2274 6.128200 TGCATGATATGAAACTGTCTGTGTTC 60.128 38.462 0.00 0.00 0.00 3.18
1912 2285 2.009774 GTCTGTGTTCTTGCAGTGTGT 58.990 47.619 0.00 0.00 34.57 3.72
2137 2510 1.757699 ACTTCCTCGGATAAGCCACTC 59.242 52.381 1.38 0.00 35.94 3.51
2166 2539 4.434330 CGAGTTTCCGAGATTTTGTAGTGC 60.434 45.833 0.00 0.00 0.00 4.40
2174 2551 4.260784 CGAGATTTTGTAGTGCCCTAATGC 60.261 45.833 0.00 0.00 0.00 3.56
2239 2616 0.524392 GTCTGCGTGATCCGAGAGTG 60.524 60.000 7.64 0.00 39.56 3.51
2383 2768 7.062957 ACTATGCAAGCTGTTAAGGGAAATAT 58.937 34.615 0.00 0.00 0.00 1.28
2471 2860 7.362662 TGATTTCTGTACTGAGTTTCATTTGC 58.637 34.615 2.51 0.00 0.00 3.68
2510 2900 4.481368 TGTGTGGTACTGGATATCCAAC 57.519 45.455 24.54 19.70 46.97 3.77
2515 2905 5.128827 TGTGGTACTGGATATCCAACTTCTC 59.871 44.000 24.54 14.92 46.97 2.87
2592 2982 2.575532 CCTGTGTTGGATCAGTGTGTT 58.424 47.619 0.00 0.00 0.00 3.32
2593 2983 2.951642 CCTGTGTTGGATCAGTGTGTTT 59.048 45.455 0.00 0.00 0.00 2.83
2599 2989 2.653726 TGGATCAGTGTGTTTTGCTGT 58.346 42.857 0.00 0.00 0.00 4.40
2608 2998 1.933181 GTGTTTTGCTGTTTTCCTGGC 59.067 47.619 0.00 0.00 0.00 4.85
2617 3007 1.133513 TGTTTTCCTGGCACCATGAGT 60.134 47.619 0.00 0.00 0.00 3.41
2645 3035 5.269505 TGGTTGTGGTACAAAATTTCCTG 57.730 39.130 0.00 0.00 44.16 3.86
2765 3155 7.911130 TCATTCTCTCCTGTAATCTGATCTT 57.089 36.000 0.00 0.00 0.00 2.40
2788 3178 5.978934 AGTTGTGTTAGTACCAAAGTTCG 57.021 39.130 0.00 0.00 0.00 3.95
2799 3189 2.422127 ACCAAAGTTCGACCAAACACAG 59.578 45.455 0.00 0.00 0.00 3.66
2803 3199 0.730265 GTTCGACCAAACACAGCACA 59.270 50.000 0.00 0.00 0.00 4.57
2815 3211 5.567138 AACACAGCACATTATAAGAAGGC 57.433 39.130 0.00 0.00 0.00 4.35
2829 3225 8.723942 TTATAAGAAGGCTCTGTTTGATCTTC 57.276 34.615 0.00 0.00 36.25 2.87
2849 3245 0.673333 TATGCCACGCACCAGTTCTG 60.673 55.000 0.00 0.00 43.04 3.02
2882 3281 4.218417 TGCCCTTGCAGTTTAGAGATTTTC 59.782 41.667 0.00 0.00 44.23 2.29
2918 3317 4.616835 GCAAAACAGATGCCACTTTCCTAG 60.617 45.833 0.00 0.00 37.85 3.02
2974 3374 5.335127 CAATCCAAAATAGCAGGAACTTCG 58.665 41.667 0.00 0.00 34.60 3.79
2975 3375 4.015872 TCCAAAATAGCAGGAACTTCGT 57.984 40.909 0.00 0.00 34.60 3.85
2976 3376 5.155278 TCCAAAATAGCAGGAACTTCGTA 57.845 39.130 0.00 0.00 34.60 3.43
2989 3389 7.009357 GCAGGAACTTCGTAGTATAAGAAACAG 59.991 40.741 0.00 0.00 38.53 3.16
3066 3470 7.784470 ATAACAGAATCTATGTACTCCCTCC 57.216 40.000 0.00 0.00 0.00 4.30
3067 3471 4.145807 ACAGAATCTATGTACTCCCTCCG 58.854 47.826 0.00 0.00 0.00 4.63
3068 3472 4.145807 CAGAATCTATGTACTCCCTCCGT 58.854 47.826 0.00 0.00 0.00 4.69
3069 3473 4.585162 CAGAATCTATGTACTCCCTCCGTT 59.415 45.833 0.00 0.00 0.00 4.44
3070 3474 5.768662 CAGAATCTATGTACTCCCTCCGTTA 59.231 44.000 0.00 0.00 0.00 3.18
3071 3475 5.769162 AGAATCTATGTACTCCCTCCGTTAC 59.231 44.000 0.00 0.00 0.00 2.50
3072 3476 4.785346 TCTATGTACTCCCTCCGTTACT 57.215 45.455 0.00 0.00 0.00 2.24
3073 3477 4.458397 TCTATGTACTCCCTCCGTTACTG 58.542 47.826 0.00 0.00 0.00 2.74
3074 3478 2.885135 TGTACTCCCTCCGTTACTGA 57.115 50.000 0.00 0.00 0.00 3.41
3075 3479 3.159213 TGTACTCCCTCCGTTACTGAA 57.841 47.619 0.00 0.00 0.00 3.02
3076 3480 3.705051 TGTACTCCCTCCGTTACTGAAT 58.295 45.455 0.00 0.00 0.00 2.57
3077 3481 4.858850 TGTACTCCCTCCGTTACTGAATA 58.141 43.478 0.00 0.00 0.00 1.75
3078 3482 5.452255 TGTACTCCCTCCGTTACTGAATAT 58.548 41.667 0.00 0.00 0.00 1.28
3079 3483 6.604171 TGTACTCCCTCCGTTACTGAATATA 58.396 40.000 0.00 0.00 0.00 0.86
3080 3484 6.713903 TGTACTCCCTCCGTTACTGAATATAG 59.286 42.308 0.00 0.00 0.00 1.31
3081 3485 5.078256 ACTCCCTCCGTTACTGAATATAGG 58.922 45.833 0.00 0.00 0.00 2.57
3082 3486 5.070823 TCCCTCCGTTACTGAATATAGGT 57.929 43.478 0.00 0.00 0.00 3.08
3083 3487 5.075493 TCCCTCCGTTACTGAATATAGGTC 58.925 45.833 0.00 0.00 0.00 3.85
3084 3488 5.078256 CCCTCCGTTACTGAATATAGGTCT 58.922 45.833 0.00 0.00 0.00 3.85
3085 3489 5.539193 CCCTCCGTTACTGAATATAGGTCTT 59.461 44.000 0.00 0.00 0.00 3.01
3086 3490 6.041751 CCCTCCGTTACTGAATATAGGTCTTT 59.958 42.308 0.00 0.00 0.00 2.52
3087 3491 7.418712 CCCTCCGTTACTGAATATAGGTCTTTT 60.419 40.741 0.00 0.00 0.00 2.27
3088 3492 7.652507 CCTCCGTTACTGAATATAGGTCTTTTC 59.347 40.741 0.00 0.00 0.00 2.29
3089 3493 8.070034 TCCGTTACTGAATATAGGTCTTTTCA 57.930 34.615 0.00 0.00 0.00 2.69
3090 3494 8.195436 TCCGTTACTGAATATAGGTCTTTTCAG 58.805 37.037 9.34 9.34 46.63 3.02
3091 3495 8.195436 CCGTTACTGAATATAGGTCTTTTCAGA 58.805 37.037 16.04 0.77 44.97 3.27
3092 3496 9.239002 CGTTACTGAATATAGGTCTTTTCAGAG 57.761 37.037 16.04 3.75 44.97 3.35
3103 3507 7.684937 AGGTCTTTTCAGAGATTTCAATGAG 57.315 36.000 0.00 0.00 0.00 2.90
3104 3508 6.658391 AGGTCTTTTCAGAGATTTCAATGAGG 59.342 38.462 0.00 0.00 0.00 3.86
3105 3509 6.656693 GGTCTTTTCAGAGATTTCAATGAGGA 59.343 38.462 0.00 0.00 0.00 3.71
3106 3510 7.361628 GGTCTTTTCAGAGATTTCAATGAGGAC 60.362 40.741 0.00 0.00 0.00 3.85
3107 3511 7.390162 GTCTTTTCAGAGATTTCAATGAGGACT 59.610 37.037 0.00 0.00 0.00 3.85
3108 3512 7.389884 TCTTTTCAGAGATTTCAATGAGGACTG 59.610 37.037 0.00 0.00 0.00 3.51
3109 3513 4.511527 TCAGAGATTTCAATGAGGACTGC 58.488 43.478 0.00 0.00 0.00 4.40
3110 3514 4.019950 TCAGAGATTTCAATGAGGACTGCA 60.020 41.667 0.00 0.00 0.00 4.41
3111 3515 4.094590 CAGAGATTTCAATGAGGACTGCAC 59.905 45.833 0.00 0.00 0.00 4.57
3112 3516 4.005650 GAGATTTCAATGAGGACTGCACA 58.994 43.478 0.00 0.00 0.00 4.57
3113 3517 3.755378 AGATTTCAATGAGGACTGCACAC 59.245 43.478 0.00 0.00 0.00 3.82
3114 3518 2.636647 TTCAATGAGGACTGCACACA 57.363 45.000 0.00 0.00 0.00 3.72
3115 3519 2.865119 TCAATGAGGACTGCACACAT 57.135 45.000 0.00 0.00 0.00 3.21
3116 3520 3.979101 TCAATGAGGACTGCACACATA 57.021 42.857 0.00 0.00 0.00 2.29
3117 3521 4.492494 TCAATGAGGACTGCACACATAT 57.508 40.909 0.00 0.00 0.00 1.78
3118 3522 4.193865 TCAATGAGGACTGCACACATATG 58.806 43.478 0.00 0.00 0.00 1.78
3119 3523 3.920231 ATGAGGACTGCACACATATGT 57.080 42.857 1.41 1.41 40.80 2.29
3120 3524 5.104982 TCAATGAGGACTGCACACATATGTA 60.105 40.000 8.32 0.00 36.72 2.29
3121 3525 5.557576 ATGAGGACTGCACACATATGTAT 57.442 39.130 8.32 0.00 36.72 2.29
3122 3526 6.670695 ATGAGGACTGCACACATATGTATA 57.329 37.500 8.32 0.00 36.72 1.47
3123 3527 6.670695 TGAGGACTGCACACATATGTATAT 57.329 37.500 8.32 0.00 36.72 0.86
3124 3528 7.775053 TGAGGACTGCACACATATGTATATA 57.225 36.000 8.32 0.00 36.72 0.86
3125 3529 7.830739 TGAGGACTGCACACATATGTATATAG 58.169 38.462 8.32 7.76 36.72 1.31
3126 3530 7.669722 TGAGGACTGCACACATATGTATATAGA 59.330 37.037 8.32 0.00 36.72 1.98
3127 3531 7.831753 AGGACTGCACACATATGTATATAGAC 58.168 38.462 8.32 5.82 36.72 2.59
3128 3532 7.451566 AGGACTGCACACATATGTATATAGACA 59.548 37.037 8.32 2.07 36.72 3.41
3129 3533 8.253810 GGACTGCACACATATGTATATAGACAT 58.746 37.037 16.67 16.67 42.68 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.322442 GAGAAAGTTGCTGCCAAGGT 58.678 50.000 0.00 0.00 0.00 3.50
1 2 0.600057 GGAGAAAGTTGCTGCCAAGG 59.400 55.000 0.00 0.00 0.00 3.61
3 4 1.795170 GCGGAGAAAGTTGCTGCCAA 61.795 55.000 0.00 0.00 0.00 4.52
4 5 2.260869 GCGGAGAAAGTTGCTGCCA 61.261 57.895 0.00 0.00 0.00 4.92
6 7 2.174349 CGCGGAGAAAGTTGCTGC 59.826 61.111 0.00 0.00 0.00 5.25
7 8 1.784062 CTCGCGGAGAAAGTTGCTG 59.216 57.895 6.13 0.00 0.00 4.41
8 9 2.029844 GCTCGCGGAGAAAGTTGCT 61.030 57.895 6.13 0.00 0.00 3.91
9 10 1.960994 GAGCTCGCGGAGAAAGTTGC 61.961 60.000 6.13 0.00 0.00 4.17
10 11 0.389166 AGAGCTCGCGGAGAAAGTTG 60.389 55.000 6.13 0.00 0.00 3.16
11 12 0.109039 GAGAGCTCGCGGAGAAAGTT 60.109 55.000 6.13 0.00 0.00 2.66
12 13 0.963355 AGAGAGCTCGCGGAGAAAGT 60.963 55.000 12.03 0.00 34.09 2.66
14 15 0.678366 AGAGAGAGCTCGCGGAGAAA 60.678 55.000 12.03 0.00 45.98 2.52
15 16 0.678366 AAGAGAGAGCTCGCGGAGAA 60.678 55.000 12.03 0.00 45.98 2.87
16 17 1.078072 AAGAGAGAGCTCGCGGAGA 60.078 57.895 12.03 0.00 45.98 3.71
17 18 1.063972 CAAGAGAGAGCTCGCGGAG 59.936 63.158 12.03 3.47 45.98 4.63
18 19 2.410687 CCAAGAGAGAGCTCGCGGA 61.411 63.158 12.03 0.00 45.98 5.54
19 20 2.103934 CCAAGAGAGAGCTCGCGG 59.896 66.667 12.03 3.29 45.98 6.46
20 21 2.581953 GCCAAGAGAGAGCTCGCG 60.582 66.667 12.03 0.00 45.98 5.87
21 22 1.519013 CAGCCAAGAGAGAGCTCGC 60.519 63.158 9.76 9.76 45.98 5.03
22 23 0.179140 GACAGCCAAGAGAGAGCTCG 60.179 60.000 8.37 0.00 45.98 5.03
23 24 0.894141 TGACAGCCAAGAGAGAGCTC 59.106 55.000 5.27 5.27 41.62 4.09
24 25 0.896923 CTGACAGCCAAGAGAGAGCT 59.103 55.000 0.00 0.00 37.32 4.09
25 26 0.607620 ACTGACAGCCAAGAGAGAGC 59.392 55.000 1.25 0.00 0.00 4.09
26 27 1.204467 GGACTGACAGCCAAGAGAGAG 59.796 57.143 1.25 0.00 0.00 3.20
27 28 1.261480 GGACTGACAGCCAAGAGAGA 58.739 55.000 1.25 0.00 0.00 3.10
28 29 0.972134 TGGACTGACAGCCAAGAGAG 59.028 55.000 14.01 0.00 0.00 3.20
29 30 1.552337 GATGGACTGACAGCCAAGAGA 59.448 52.381 18.50 0.64 37.78 3.10
30 31 1.406614 GGATGGACTGACAGCCAAGAG 60.407 57.143 18.50 0.00 45.95 2.85
31 32 0.615331 GGATGGACTGACAGCCAAGA 59.385 55.000 18.50 1.23 45.95 3.02
32 33 3.165606 GGATGGACTGACAGCCAAG 57.834 57.895 18.50 0.00 45.95 3.61
35 36 2.187946 CCGGATGGACTGACAGCC 59.812 66.667 0.00 5.69 43.32 4.85
36 37 2.512515 GCCGGATGGACTGACAGC 60.513 66.667 5.05 0.00 37.49 4.40
37 38 1.153489 CTGCCGGATGGACTGACAG 60.153 63.158 5.05 0.00 37.49 3.51
38 39 2.981302 CTGCCGGATGGACTGACA 59.019 61.111 5.05 0.00 37.49 3.58
39 40 2.512515 GCTGCCGGATGGACTGAC 60.513 66.667 5.05 0.00 37.49 3.51
40 41 3.785859 GGCTGCCGGATGGACTGA 61.786 66.667 5.05 0.00 37.49 3.41
41 42 4.864334 GGGCTGCCGGATGGACTG 62.864 72.222 13.40 0.00 37.49 3.51
46 47 4.113815 TCAAGGGGCTGCCGGATG 62.114 66.667 13.40 10.93 0.00 3.51
47 48 4.115199 GTCAAGGGGCTGCCGGAT 62.115 66.667 13.40 0.00 0.00 4.18
49 50 4.785453 GAGTCAAGGGGCTGCCGG 62.785 72.222 13.40 0.00 0.00 6.13
50 51 3.672295 GAGAGTCAAGGGGCTGCCG 62.672 68.421 13.40 0.00 0.00 5.69
51 52 2.270527 GAGAGTCAAGGGGCTGCC 59.729 66.667 11.05 11.05 0.00 4.85
52 53 1.078567 CTGAGAGTCAAGGGGCTGC 60.079 63.158 0.00 0.00 0.00 5.25
53 54 0.248843 GACTGAGAGTCAAGGGGCTG 59.751 60.000 0.00 0.00 44.45 4.85
54 55 0.907230 GGACTGAGAGTCAAGGGGCT 60.907 60.000 6.10 0.00 46.79 5.19
55 56 1.194781 TGGACTGAGAGTCAAGGGGC 61.195 60.000 6.10 0.00 46.79 5.80
56 57 1.484240 GATGGACTGAGAGTCAAGGGG 59.516 57.143 6.10 0.00 46.79 4.79
57 58 1.484240 GGATGGACTGAGAGTCAAGGG 59.516 57.143 6.10 0.00 46.79 3.95
58 59 1.135915 CGGATGGACTGAGAGTCAAGG 59.864 57.143 6.10 0.00 46.79 3.61
59 60 1.135915 CCGGATGGACTGAGAGTCAAG 59.864 57.143 0.00 0.00 46.79 3.02
60 61 1.186200 CCGGATGGACTGAGAGTCAA 58.814 55.000 0.00 0.00 46.79 3.18
61 62 1.323271 GCCGGATGGACTGAGAGTCA 61.323 60.000 5.05 0.00 46.79 3.41
62 63 1.323271 TGCCGGATGGACTGAGAGTC 61.323 60.000 5.05 0.00 44.32 3.36
63 64 1.305297 TGCCGGATGGACTGAGAGT 60.305 57.895 5.05 0.00 37.49 3.24
64 65 1.440893 CTGCCGGATGGACTGAGAG 59.559 63.158 5.05 0.00 37.49 3.20
65 66 2.725312 GCTGCCGGATGGACTGAGA 61.725 63.158 5.05 0.00 37.49 3.27
66 67 2.202987 GCTGCCGGATGGACTGAG 60.203 66.667 5.05 0.00 37.49 3.35
67 68 3.785859 GGCTGCCGGATGGACTGA 61.786 66.667 5.05 0.00 37.49 3.41
68 69 4.864334 GGGCTGCCGGATGGACTG 62.864 72.222 13.40 0.00 37.49 3.51
73 74 4.113815 TCAAGGGGCTGCCGGATG 62.114 66.667 13.40 10.93 0.00 3.51
74 75 4.115199 GTCAAGGGGCTGCCGGAT 62.115 66.667 13.40 0.00 0.00 4.18
76 77 4.785453 GAGTCAAGGGGCTGCCGG 62.785 72.222 13.40 0.00 0.00 6.13
77 78 3.672295 GAGAGTCAAGGGGCTGCCG 62.672 68.421 13.40 0.00 0.00 5.69
78 79 2.270527 GAGAGTCAAGGGGCTGCC 59.729 66.667 11.05 11.05 0.00 4.85
79 80 2.125350 CGAGAGTCAAGGGGCTGC 60.125 66.667 0.00 0.00 0.00 5.25
80 81 2.125350 GCGAGAGTCAAGGGGCTG 60.125 66.667 0.00 0.00 0.00 4.85
81 82 3.394836 GGCGAGAGTCAAGGGGCT 61.395 66.667 0.00 0.00 34.40 5.19
82 83 4.475135 GGGCGAGAGTCAAGGGGC 62.475 72.222 0.00 0.00 37.54 5.80
83 84 3.003173 TGGGCGAGAGTCAAGGGG 61.003 66.667 0.00 0.00 37.54 4.79
84 85 2.111999 TTGTGGGCGAGAGTCAAGGG 62.112 60.000 0.00 0.00 37.54 3.95
85 86 0.250295 TTTGTGGGCGAGAGTCAAGG 60.250 55.000 0.00 0.00 37.54 3.61
86 87 1.151668 CTTTGTGGGCGAGAGTCAAG 58.848 55.000 0.00 0.00 37.54 3.02
87 88 0.250295 CCTTTGTGGGCGAGAGTCAA 60.250 55.000 0.00 0.00 37.54 3.18
88 89 1.371183 CCTTTGTGGGCGAGAGTCA 59.629 57.895 0.00 0.00 37.54 3.41
89 90 0.606604 TACCTTTGTGGGCGAGAGTC 59.393 55.000 0.00 0.00 41.11 3.36
90 91 0.320697 GTACCTTTGTGGGCGAGAGT 59.679 55.000 0.00 0.00 41.11 3.24
91 92 0.608640 AGTACCTTTGTGGGCGAGAG 59.391 55.000 0.00 0.00 41.11 3.20
92 93 1.053424 AAGTACCTTTGTGGGCGAGA 58.947 50.000 0.00 0.00 41.11 4.04
93 94 1.535462 CAAAGTACCTTTGTGGGCGAG 59.465 52.381 8.25 0.00 43.85 5.03
94 95 1.600023 CAAAGTACCTTTGTGGGCGA 58.400 50.000 8.25 0.00 43.85 5.54
102 103 6.120220 AGTACAAGCTGAACAAAGTACCTTT 58.880 36.000 0.00 0.00 34.03 3.11
103 104 5.681639 AGTACAAGCTGAACAAAGTACCTT 58.318 37.500 0.00 0.00 34.03 3.50
104 105 5.291905 AGTACAAGCTGAACAAAGTACCT 57.708 39.130 0.00 0.00 34.03 3.08
105 106 4.451435 GGAGTACAAGCTGAACAAAGTACC 59.549 45.833 0.00 0.00 34.03 3.34
106 107 4.150098 CGGAGTACAAGCTGAACAAAGTAC 59.850 45.833 0.00 0.00 33.80 2.73
107 108 4.038282 TCGGAGTACAAGCTGAACAAAGTA 59.962 41.667 0.00 0.00 0.00 2.24
108 109 3.131396 CGGAGTACAAGCTGAACAAAGT 58.869 45.455 0.00 0.00 0.00 2.66
109 110 3.390135 TCGGAGTACAAGCTGAACAAAG 58.610 45.455 0.00 0.00 0.00 2.77
110 111 3.462483 TCGGAGTACAAGCTGAACAAA 57.538 42.857 0.00 0.00 0.00 2.83
111 112 3.462483 TTCGGAGTACAAGCTGAACAA 57.538 42.857 0.00 0.00 0.00 2.83
112 113 3.128349 GTTTCGGAGTACAAGCTGAACA 58.872 45.455 0.00 0.00 0.00 3.18
113 114 3.128349 TGTTTCGGAGTACAAGCTGAAC 58.872 45.455 0.00 0.00 0.00 3.18
114 115 3.462483 TGTTTCGGAGTACAAGCTGAA 57.538 42.857 0.00 0.00 0.00 3.02
115 116 3.585862 GATGTTTCGGAGTACAAGCTGA 58.414 45.455 0.00 0.00 0.00 4.26
116 117 2.345641 CGATGTTTCGGAGTACAAGCTG 59.654 50.000 0.00 0.00 41.74 4.24
117 118 2.607187 CGATGTTTCGGAGTACAAGCT 58.393 47.619 0.00 0.00 41.74 3.74
128 129 3.490419 CCCTCCTAAGTACCGATGTTTCG 60.490 52.174 0.00 0.00 45.08 3.46
129 130 3.181468 CCCCTCCTAAGTACCGATGTTTC 60.181 52.174 0.00 0.00 0.00 2.78
130 131 2.770232 CCCCTCCTAAGTACCGATGTTT 59.230 50.000 0.00 0.00 0.00 2.83
131 132 2.023695 TCCCCTCCTAAGTACCGATGTT 60.024 50.000 0.00 0.00 0.00 2.71
132 133 1.572415 TCCCCTCCTAAGTACCGATGT 59.428 52.381 0.00 0.00 0.00 3.06
133 134 2.376695 TCCCCTCCTAAGTACCGATG 57.623 55.000 0.00 0.00 0.00 3.84
134 135 3.632420 AATCCCCTCCTAAGTACCGAT 57.368 47.619 0.00 0.00 0.00 4.18
135 136 4.754411 ATAATCCCCTCCTAAGTACCGA 57.246 45.455 0.00 0.00 0.00 4.69
136 137 7.492077 AATAATAATCCCCTCCTAAGTACCG 57.508 40.000 0.00 0.00 0.00 4.02
140 141 9.475013 AGGTAAAATAATAATCCCCTCCTAAGT 57.525 33.333 0.00 0.00 0.00 2.24
176 177 2.485302 GCTGAGCCCACCAAACATTTTT 60.485 45.455 0.00 0.00 0.00 1.94
177 178 1.070601 GCTGAGCCCACCAAACATTTT 59.929 47.619 0.00 0.00 0.00 1.82
178 179 0.681175 GCTGAGCCCACCAAACATTT 59.319 50.000 0.00 0.00 0.00 2.32
179 180 1.187567 GGCTGAGCCCACCAAACATT 61.188 55.000 13.77 0.00 44.06 2.71
213 214 3.121030 GCAATCCGTCTGCGCAGT 61.121 61.111 34.70 14.63 36.67 4.40
219 220 2.046023 TGGGCTGCAATCCGTCTG 60.046 61.111 0.50 0.00 0.00 3.51
241 242 4.554036 GCGGAGGATGTGGGGCTC 62.554 72.222 0.00 0.00 0.00 4.70
376 380 4.489771 AATCAGCGAAGGGGCCGG 62.490 66.667 0.00 0.00 0.00 6.13
378 382 1.821332 CTCAATCAGCGAAGGGGCC 60.821 63.158 0.00 0.00 0.00 5.80
385 389 2.268920 GCCCACCTCAATCAGCGA 59.731 61.111 0.00 0.00 0.00 4.93
391 395 3.254024 AAGCGTCGCCCACCTCAAT 62.254 57.895 14.86 0.00 0.00 2.57
458 468 0.390735 AGGGCATTCGTTACACGGAC 60.391 55.000 0.00 0.00 42.81 4.79
487 497 4.163649 ACCAGAGATCTCAATCAGCATTCA 59.836 41.667 24.39 0.00 34.07 2.57
508 518 0.171903 GACAGTGGCATGCATCAACC 59.828 55.000 21.36 0.64 0.00 3.77
521 531 4.013267 ACTTGGGATTCTGAAGACAGTG 57.987 45.455 0.00 0.00 43.81 3.66
563 573 5.476091 TGCTTTTTACTATTTTGTGGGGG 57.524 39.130 0.00 0.00 0.00 5.40
565 575 6.426328 TGCAATGCTTTTTACTATTTTGTGGG 59.574 34.615 6.82 0.00 0.00 4.61
566 576 7.418840 TGCAATGCTTTTTACTATTTTGTGG 57.581 32.000 6.82 0.00 0.00 4.17
579 589 3.727376 GCGTGTTTGTTTGCAATGCTTTT 60.727 39.130 6.82 0.00 34.18 2.27
580 590 2.222999 GCGTGTTTGTTTGCAATGCTTT 60.223 40.909 6.82 0.00 34.18 3.51
581 591 1.327156 GCGTGTTTGTTTGCAATGCTT 59.673 42.857 6.82 0.00 34.18 3.91
583 593 0.042274 GGCGTGTTTGTTTGCAATGC 60.042 50.000 0.00 0.00 34.18 3.56
654 668 3.192001 CAGATGTGGCTGCAGTTTTATGT 59.808 43.478 16.64 1.53 0.00 2.29
668 682 5.106555 GGCAATCCGTATAATTCAGATGTGG 60.107 44.000 0.00 0.00 0.00 4.17
670 684 5.620206 TGGCAATCCGTATAATTCAGATGT 58.380 37.500 0.00 0.00 34.14 3.06
700 714 6.437928 CAAAACGAATTCAGATGACCAAAGA 58.562 36.000 6.22 0.00 0.00 2.52
747 761 2.093921 TGGACTTGCATGCCAATTCATG 60.094 45.455 16.68 3.35 44.93 3.07
772 786 3.772932 AGAATCGAAATGCGTACGGTTA 58.227 40.909 18.39 0.00 41.80 2.85
777 791 2.538939 GGGCAAGAATCGAAATGCGTAC 60.539 50.000 0.00 0.00 39.66 3.67
780 794 0.451383 TGGGCAAGAATCGAAATGCG 59.549 50.000 0.00 0.00 39.66 4.73
795 809 1.175983 TTGTTGTGAACCGGATGGGC 61.176 55.000 9.46 0.00 40.62 5.36
831 845 2.898181 TGACAATGCACATGTAAGCG 57.102 45.000 6.94 0.00 0.00 4.68
863 877 5.164002 GCACGCATCGGAAATTTTGTATTTT 60.164 36.000 0.00 0.00 0.00 1.82
866 880 3.119673 TGCACGCATCGGAAATTTTGTAT 60.120 39.130 0.00 0.00 0.00 2.29
868 882 1.000827 TGCACGCATCGGAAATTTTGT 60.001 42.857 0.00 0.00 0.00 2.83
870 884 2.261345 CATGCACGCATCGGAAATTTT 58.739 42.857 0.44 0.00 33.90 1.82
914 928 3.113514 TTCCAGCACCGTGGCAAGA 62.114 57.895 0.76 0.00 37.53 3.02
1089 1109 3.506067 TGACAGCAACACGAGAGAGAATA 59.494 43.478 0.00 0.00 0.00 1.75
1154 1184 6.660521 AGGTCAATGATCTGCAGAAATGTTAA 59.339 34.615 22.50 0.00 0.00 2.01
1233 1271 9.965902 AAATCACATATCCTCAGTAAGAAGTTT 57.034 29.630 0.00 0.00 0.00 2.66
1239 1277 9.650539 CATCCTAAATCACATATCCTCAGTAAG 57.349 37.037 0.00 0.00 0.00 2.34
1324 1370 8.510243 ACAAGATATTTCATAATGTGACAGCA 57.490 30.769 0.00 0.00 36.32 4.41
1383 1494 5.833406 TGTGGCATAATAGACAAACATGG 57.167 39.130 0.00 0.00 0.00 3.66
1465 1696 2.299582 CAAATTTGGGTGCCAGATGACA 59.700 45.455 10.49 0.00 33.81 3.58
1477 1710 3.742433 TTACACCTGCACAAATTTGGG 57.258 42.857 21.74 19.22 33.81 4.12
1586 1828 6.747414 AATCTTGCCAGGACACACTATATA 57.253 37.500 0.00 0.00 0.00 0.86
1604 1846 7.500559 GGAACTTGCACTGATCCTAATAATCTT 59.499 37.037 7.63 0.00 0.00 2.40
1887 2251 3.127548 CACTGCAAGAACACAGACAGTTT 59.872 43.478 0.00 0.00 36.28 2.66
1895 2266 2.279741 GAGACACACTGCAAGAACACA 58.720 47.619 0.00 0.00 37.43 3.72
1896 2267 1.599542 GGAGACACACTGCAAGAACAC 59.400 52.381 0.00 0.00 37.43 3.32
1901 2274 2.370281 ATACGGAGACACACTGCAAG 57.630 50.000 0.00 0.00 36.75 4.01
1912 2285 4.282449 TCCTTGTTGACTTGAATACGGAGA 59.718 41.667 0.00 0.00 0.00 3.71
1962 2335 5.643777 AGCAGATAAAACGCTAACAGTGAAT 59.356 36.000 0.00 0.00 33.25 2.57
2137 2510 4.373348 AAATCTCGGAAACTCGTAGGAG 57.627 45.455 10.86 10.86 46.13 3.69
2166 2539 3.616956 TGACAGTCTCAAGCATTAGGG 57.383 47.619 1.31 0.00 0.00 3.53
2174 2551 9.761504 AATATCTAACATGATGACAGTCTCAAG 57.238 33.333 0.00 3.40 30.60 3.02
2363 2745 6.207691 TCAATATTTCCCTTAACAGCTTGC 57.792 37.500 0.00 0.00 0.00 4.01
2441 2826 5.552870 AACTCAGTACAGAAATCAGGTGT 57.447 39.130 0.00 0.00 0.00 4.16
2471 2860 5.444613 CCACACAATATTTCACTCTTCGACG 60.445 44.000 0.00 0.00 0.00 5.12
2510 2900 8.517062 AAGTAATCTTGGATTGAATGGAGAAG 57.483 34.615 3.37 0.00 32.09 2.85
2515 2905 7.636150 ACTGAAGTAATCTTGGATTGAATGG 57.364 36.000 3.37 0.00 33.64 3.16
2552 2942 5.170748 CAGGCAAAACTGGATACCAAAATC 58.829 41.667 0.00 0.00 34.84 2.17
2592 2982 0.463620 GGTGCCAGGAAAACAGCAAA 59.536 50.000 0.00 0.00 36.91 3.68
2593 2983 0.685785 TGGTGCCAGGAAAACAGCAA 60.686 50.000 0.00 0.00 38.73 3.91
2599 2989 1.144708 TGACTCATGGTGCCAGGAAAA 59.855 47.619 7.02 0.00 36.28 2.29
2645 3035 5.915196 GGAAGTTGCATAACTGTTCAAGAAC 59.085 40.000 6.01 6.01 46.14 3.01
2739 3129 8.316497 AGATCAGATTACAGGAGAGAATGAAA 57.684 34.615 0.00 0.00 0.00 2.69
2740 3130 7.911130 AGATCAGATTACAGGAGAGAATGAA 57.089 36.000 0.00 0.00 0.00 2.57
2747 3137 7.397476 ACACAACTAAGATCAGATTACAGGAGA 59.603 37.037 0.00 0.00 0.00 3.71
2765 3155 6.697019 GTCGAACTTTGGTACTAACACAACTA 59.303 38.462 0.00 0.00 0.00 2.24
2788 3178 6.494893 TCTTATAATGTGCTGTGTTTGGTC 57.505 37.500 0.00 0.00 0.00 4.02
2799 3189 6.094048 TCAAACAGAGCCTTCTTATAATGTGC 59.906 38.462 0.00 0.00 0.00 4.57
2803 3199 9.336171 GAAGATCAAACAGAGCCTTCTTATAAT 57.664 33.333 0.00 0.00 37.13 1.28
2815 3211 4.269603 CGTGGCATAGAAGATCAAACAGAG 59.730 45.833 0.00 0.00 0.00 3.35
2829 3225 0.391661 AGAACTGGTGCGTGGCATAG 60.392 55.000 0.00 0.00 41.91 2.23
2918 3317 7.648142 TGATTCACAATGTAGTTTTGGTCTTC 58.352 34.615 0.00 0.00 0.00 2.87
2989 3389 8.784994 GGCTTTCTTAAGGTTATTAATAGGCTC 58.215 37.037 1.85 0.00 31.76 4.70
3059 3463 5.078256 ACCTATATTCAGTAACGGAGGGAG 58.922 45.833 0.00 0.00 0.00 4.30
3061 3465 5.078256 AGACCTATATTCAGTAACGGAGGG 58.922 45.833 0.00 0.00 0.00 4.30
3063 3467 8.195436 TGAAAAGACCTATATTCAGTAACGGAG 58.805 37.037 0.00 0.00 0.00 4.63
3064 3468 8.070034 TGAAAAGACCTATATTCAGTAACGGA 57.930 34.615 0.00 0.00 0.00 4.69
3066 3470 9.239002 CTCTGAAAAGACCTATATTCAGTAACG 57.761 37.037 12.50 0.00 45.59 3.18
3077 3481 9.393512 CTCATTGAAATCTCTGAAAAGACCTAT 57.606 33.333 0.00 0.00 0.00 2.57
3078 3482 7.826252 CCTCATTGAAATCTCTGAAAAGACCTA 59.174 37.037 0.00 0.00 0.00 3.08
3079 3483 6.658391 CCTCATTGAAATCTCTGAAAAGACCT 59.342 38.462 0.00 0.00 0.00 3.85
3080 3484 6.656693 TCCTCATTGAAATCTCTGAAAAGACC 59.343 38.462 0.00 0.00 0.00 3.85
3081 3485 7.390162 AGTCCTCATTGAAATCTCTGAAAAGAC 59.610 37.037 0.00 0.00 0.00 3.01
3082 3486 7.389884 CAGTCCTCATTGAAATCTCTGAAAAGA 59.610 37.037 0.00 0.00 0.00 2.52
3083 3487 7.528307 CAGTCCTCATTGAAATCTCTGAAAAG 58.472 38.462 0.00 0.00 0.00 2.27
3084 3488 6.072286 GCAGTCCTCATTGAAATCTCTGAAAA 60.072 38.462 0.00 0.00 0.00 2.29
3085 3489 5.413833 GCAGTCCTCATTGAAATCTCTGAAA 59.586 40.000 0.00 0.00 0.00 2.69
3086 3490 4.940046 GCAGTCCTCATTGAAATCTCTGAA 59.060 41.667 0.00 0.00 0.00 3.02
3087 3491 4.019950 TGCAGTCCTCATTGAAATCTCTGA 60.020 41.667 0.00 0.00 0.00 3.27
3088 3492 4.094590 GTGCAGTCCTCATTGAAATCTCTG 59.905 45.833 0.00 0.00 0.00 3.35
3089 3493 4.260170 GTGCAGTCCTCATTGAAATCTCT 58.740 43.478 0.00 0.00 0.00 3.10
3090 3494 4.005650 TGTGCAGTCCTCATTGAAATCTC 58.994 43.478 0.00 0.00 0.00 2.75
3091 3495 3.755378 GTGTGCAGTCCTCATTGAAATCT 59.245 43.478 0.00 0.00 0.00 2.40
3092 3496 3.503363 TGTGTGCAGTCCTCATTGAAATC 59.497 43.478 0.00 0.00 0.00 2.17
3093 3497 3.489355 TGTGTGCAGTCCTCATTGAAAT 58.511 40.909 0.00 0.00 0.00 2.17
3094 3498 2.929641 TGTGTGCAGTCCTCATTGAAA 58.070 42.857 0.00 0.00 0.00 2.69
3095 3499 2.636647 TGTGTGCAGTCCTCATTGAA 57.363 45.000 0.00 0.00 0.00 2.69
3096 3500 2.865119 ATGTGTGCAGTCCTCATTGA 57.135 45.000 0.00 0.00 0.00 2.57
3097 3501 3.943381 ACATATGTGTGCAGTCCTCATTG 59.057 43.478 7.78 0.00 37.14 2.82
3098 3502 4.226427 ACATATGTGTGCAGTCCTCATT 57.774 40.909 7.78 0.00 37.14 2.57
3099 3503 3.920231 ACATATGTGTGCAGTCCTCAT 57.080 42.857 7.78 0.00 37.14 2.90
3100 3504 6.670695 ATATACATATGTGTGCAGTCCTCA 57.329 37.500 18.81 0.00 39.39 3.86
3101 3505 7.971168 GTCTATATACATATGTGTGCAGTCCTC 59.029 40.741 18.81 3.85 39.39 3.71
3102 3506 7.451566 TGTCTATATACATATGTGTGCAGTCCT 59.548 37.037 18.81 0.00 39.39 3.85
3103 3507 7.602753 TGTCTATATACATATGTGTGCAGTCC 58.397 38.462 18.81 8.80 39.39 3.85


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

AutoCloner maintained by Alex Coulton.