Multiple sequence alignment - TraesCS7D01G316100

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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 TraesCS7D01G316100 chr7D 100.000 8665 0 0 1 8665 402141392 402150056 0.000000e+00 16002.0
1 TraesCS7D01G316100 chr7D 89.555 1034 89 11 4502 5518 383984142 383983111 0.000000e+00 1293.0
2 TraesCS7D01G316100 chr7D 80.786 229 33 6 20 237 219708547 219708319 1.500000e-37 169.0
3 TraesCS7D01G316100 chr7B 95.685 4195 112 27 4502 8665 411746166 411750322 0.000000e+00 6680.0
4 TraesCS7D01G316100 chr7B 94.424 3031 80 23 345 3325 411741721 411744712 0.000000e+00 4578.0
5 TraesCS7D01G316100 chr7B 97.001 667 12 3 3838 4501 411745435 411746096 0.000000e+00 1114.0
6 TraesCS7D01G316100 chr7B 96.075 535 10 2 3307 3841 411744754 411745277 0.000000e+00 861.0
7 TraesCS7D01G316100 chr7B 79.372 223 40 6 13 233 139096303 139096085 1.510000e-32 152.0
8 TraesCS7D01G316100 chr7B 77.889 199 41 3 40 237 643029862 643029666 4.250000e-23 121.0
9 TraesCS7D01G316100 chr7A 95.386 4205 110 25 4502 8665 460113641 460117802 0.000000e+00 6613.0
10 TraesCS7D01G316100 chr7A 96.305 3924 73 13 606 4501 460109687 460113566 0.000000e+00 6377.0
11 TraesCS7D01G316100 chr7A 90.929 452 30 5 163 610 460108971 460109415 1.610000e-166 597.0
12 TraesCS7D01G316100 chr2D 88.857 1032 96 10 4502 5516 317863371 317862342 0.000000e+00 1251.0
13 TraesCS7D01G316100 chr2D 80.645 217 39 3 20 235 619434311 619434097 1.940000e-36 165.0
14 TraesCS7D01G316100 chr2D 79.498 239 35 9 10 235 135197141 135196904 3.240000e-34 158.0
15 TraesCS7D01G316100 chr2D 88.679 53 4 2 10 61 627126373 627126322 7.260000e-06 63.9
16 TraesCS7D01G316100 chr3B 88.555 1031 95 13 4502 5511 78632284 78631256 0.000000e+00 1229.0
17 TraesCS7D01G316100 chr3B 88.332 1037 99 16 4502 5518 16695284 16694250 0.000000e+00 1225.0
18 TraesCS7D01G316100 chr3B 81.765 170 26 4 68 235 505834099 505833933 4.220000e-28 137.0
19 TraesCS7D01G316100 chr3B 81.481 162 28 2 20 180 552235732 552235892 1.960000e-26 132.0
20 TraesCS7D01G316100 chr1B 87.996 1033 92 20 4502 5512 50017417 50018439 0.000000e+00 1192.0
21 TraesCS7D01G316100 chr3D 87.788 1040 86 17 4502 5516 597283950 597284973 0.000000e+00 1179.0
22 TraesCS7D01G316100 chr2A 88.616 896 67 11 4637 5516 605245726 605244850 0.000000e+00 1057.0
23 TraesCS7D01G316100 chr2A 87.041 463 49 8 4502 4955 22445727 22445267 6.000000e-141 512.0
24 TraesCS7D01G316100 chr1D 87.988 691 62 5 4833 5515 470415556 470416233 0.000000e+00 797.0
25 TraesCS7D01G316100 chrUn 100.000 412 0 0 2582 2993 477531839 477532250 0.000000e+00 761.0
26 TraesCS7D01G316100 chr5A 84.299 656 68 15 4756 5392 534902778 534902139 7.440000e-170 608.0
27 TraesCS7D01G316100 chr6B 87.003 377 34 11 4514 4877 670031415 670031789 2.250000e-110 411.0
28 TraesCS7D01G316100 chr5B 83.938 193 27 3 47 237 489288795 489288605 1.920000e-41 182.0
29 TraesCS7D01G316100 chr2B 82.558 172 27 3 68 237 236888251 236888421 1.950000e-31 148.0
30 TraesCS7D01G316100 chr5D 79.397 199 32 9 10 203 487449172 487449366 1.960000e-26 132.0


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 TraesCS7D01G316100 chr7D 402141392 402150056 8664 False 16002.00 16002 100.000000 1 8665 1 chr7D.!!$F1 8664
1 TraesCS7D01G316100 chr7D 383983111 383984142 1031 True 1293.00 1293 89.555000 4502 5518 1 chr7D.!!$R2 1016
2 TraesCS7D01G316100 chr7B 411741721 411750322 8601 False 3308.25 6680 95.796250 345 8665 4 chr7B.!!$F1 8320
3 TraesCS7D01G316100 chr7A 460108971 460117802 8831 False 4529.00 6613 94.206667 163 8665 3 chr7A.!!$F1 8502
4 TraesCS7D01G316100 chr2D 317862342 317863371 1029 True 1251.00 1251 88.857000 4502 5516 1 chr2D.!!$R2 1014
5 TraesCS7D01G316100 chr3B 78631256 78632284 1028 True 1229.00 1229 88.555000 4502 5511 1 chr3B.!!$R2 1009
6 TraesCS7D01G316100 chr3B 16694250 16695284 1034 True 1225.00 1225 88.332000 4502 5518 1 chr3B.!!$R1 1016
7 TraesCS7D01G316100 chr1B 50017417 50018439 1022 False 1192.00 1192 87.996000 4502 5512 1 chr1B.!!$F1 1010
8 TraesCS7D01G316100 chr3D 597283950 597284973 1023 False 1179.00 1179 87.788000 4502 5516 1 chr3D.!!$F1 1014
9 TraesCS7D01G316100 chr2A 605244850 605245726 876 True 1057.00 1057 88.616000 4637 5516 1 chr2A.!!$R2 879
10 TraesCS7D01G316100 chr1D 470415556 470416233 677 False 797.00 797 87.988000 4833 5515 1 chr1D.!!$F1 682
11 TraesCS7D01G316100 chr5A 534902139 534902778 639 True 608.00 608 84.299000 4756 5392 1 chr5A.!!$R1 636

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
151 152 0.035820 ATTTAAGGCGCCCGTCTGAA 60.036 50.000 26.15 10.26 0.00 3.02 F
1072 1376 0.035458 GTGGAGTCCCAGTTCCAGTG 59.965 60.000 6.74 0.00 43.80 3.66 F
1295 1599 0.544697 GTTTCCTGCCGGGATCCTTA 59.455 55.000 12.58 0.00 44.66 2.69 F
1662 1966 2.480555 CGTGCTCCAAATGGCGTC 59.519 61.111 0.00 0.00 34.44 5.19 F
3211 3555 1.074405 TCAGCTTTGGCACTTCTGGAT 59.926 47.619 8.56 0.00 41.70 3.41 F
3253 3597 0.606604 ATAATAGGGGTACTGCGGCG 59.393 55.000 0.51 0.51 0.00 6.46 F
3726 4131 0.984995 AGTAGTGAACCTCCCTTGCC 59.015 55.000 0.00 0.00 0.00 4.52 F
5050 5715 0.320771 GACTGTGATGGCGAGTTGGT 60.321 55.000 0.00 0.00 0.00 3.67 F
5052 5717 0.603707 CTGTGATGGCGAGTTGGTGT 60.604 55.000 0.00 0.00 0.00 4.16 F
6617 7330 1.002257 ACAATGGTCATGCTCGCCA 60.002 52.632 0.00 0.00 36.64 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2461 0.179100 GCGCAGAATCAGCAGTCCTA 60.179 55.000 0.30 0.00 0.00 2.94 R
2119 2463 0.179100 TAGCGCAGAATCAGCAGTCC 60.179 55.000 11.47 0.00 0.00 3.85 R
2419 2763 0.322975 CAGGTGTAGCAGCAAGTCCT 59.677 55.000 0.00 0.00 33.95 3.85 R
3253 3597 2.576615 ACTTCACTTTCAAGGGCAGAC 58.423 47.619 0.00 0.00 0.00 3.51 R
4688 5344 0.530431 CATCACCGGCGATGATGTCA 60.530 55.000 31.35 0.00 45.59 3.58 R
4751 5407 1.371183 CTTCCTCGAGGCCACAACA 59.629 57.895 27.39 4.41 34.44 3.33 R
5060 5725 3.770040 CCTCATCCCGCGTCACCA 61.770 66.667 4.92 0.00 0.00 4.17 R
6906 7619 1.595382 CCGATGGGAAGATGACGGC 60.595 63.158 0.00 0.00 34.36 5.68 R
6957 7670 6.063496 AGAAGAATTAAGTAACTCACCCCC 57.937 41.667 0.00 0.00 0.00 5.40 R
7882 8604 0.934436 ACAGCACGCAAAATTGTCGC 60.934 50.000 8.97 3.68 33.29 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
20 21 1.887797 TCCGGACTGGGGATATTTGT 58.112 50.000 0.00 0.00 38.76 2.83
21 22 1.488812 TCCGGACTGGGGATATTTGTG 59.511 52.381 0.00 0.00 38.76 3.33
22 23 1.476833 CCGGACTGGGGATATTTGTGG 60.477 57.143 0.00 0.00 0.00 4.17
23 24 1.476833 CGGACTGGGGATATTTGTGGG 60.477 57.143 0.00 0.00 0.00 4.61
24 25 1.133482 GGACTGGGGATATTTGTGGGG 60.133 57.143 0.00 0.00 0.00 4.96
25 26 1.569072 GACTGGGGATATTTGTGGGGT 59.431 52.381 0.00 0.00 0.00 4.95
26 27 1.569072 ACTGGGGATATTTGTGGGGTC 59.431 52.381 0.00 0.00 0.00 4.46
27 28 0.548989 TGGGGATATTTGTGGGGTCG 59.451 55.000 0.00 0.00 0.00 4.79
28 29 0.179001 GGGGATATTTGTGGGGTCGG 60.179 60.000 0.00 0.00 0.00 4.79
29 30 0.179001 GGGATATTTGTGGGGTCGGG 60.179 60.000 0.00 0.00 0.00 5.14
30 31 0.179001 GGATATTTGTGGGGTCGGGG 60.179 60.000 0.00 0.00 0.00 5.73
31 32 0.549469 GATATTTGTGGGGTCGGGGT 59.451 55.000 0.00 0.00 0.00 4.95
32 33 0.257616 ATATTTGTGGGGTCGGGGTG 59.742 55.000 0.00 0.00 0.00 4.61
33 34 1.854345 TATTTGTGGGGTCGGGGTGG 61.854 60.000 0.00 0.00 0.00 4.61
46 47 4.530857 GGTGGGCCGAGTCCGATG 62.531 72.222 0.00 0.00 38.22 3.84
47 48 3.771160 GTGGGCCGAGTCCGATGT 61.771 66.667 0.00 0.00 38.22 3.06
48 49 3.770040 TGGGCCGAGTCCGATGTG 61.770 66.667 0.00 0.00 38.22 3.21
49 50 4.530857 GGGCCGAGTCCGATGTGG 62.531 72.222 0.00 0.00 38.22 4.17
81 82 4.275508 CAGCCCCATATGCGCCCT 62.276 66.667 4.18 0.00 0.00 5.19
82 83 2.529136 AGCCCCATATGCGCCCTA 60.529 61.111 4.18 0.00 0.00 3.53
83 84 1.925455 AGCCCCATATGCGCCCTAT 60.925 57.895 4.18 0.00 0.00 2.57
84 85 0.620410 AGCCCCATATGCGCCCTATA 60.620 55.000 4.18 0.00 0.00 1.31
85 86 0.474184 GCCCCATATGCGCCCTATAT 59.526 55.000 4.18 0.00 0.00 0.86
86 87 1.133792 GCCCCATATGCGCCCTATATT 60.134 52.381 4.18 0.00 0.00 1.28
87 88 2.686715 GCCCCATATGCGCCCTATATTT 60.687 50.000 4.18 0.00 0.00 1.40
88 89 2.951642 CCCCATATGCGCCCTATATTTG 59.048 50.000 4.18 0.00 0.00 2.32
89 90 2.951642 CCCATATGCGCCCTATATTTGG 59.048 50.000 4.18 6.05 0.00 3.28
100 101 5.715439 CCCTATATTTGGGCTGGATATGA 57.285 43.478 1.19 0.00 37.99 2.15
101 102 5.688807 CCCTATATTTGGGCTGGATATGAG 58.311 45.833 1.19 0.00 37.99 2.90
102 103 5.398353 CCCTATATTTGGGCTGGATATGAGG 60.398 48.000 1.19 0.00 37.99 3.86
103 104 2.986534 ATTTGGGCTGGATATGAGGG 57.013 50.000 0.00 0.00 0.00 4.30
104 105 0.852842 TTTGGGCTGGATATGAGGGG 59.147 55.000 0.00 0.00 0.00 4.79
105 106 1.719063 TTGGGCTGGATATGAGGGGC 61.719 60.000 0.00 0.00 0.00 5.80
106 107 2.348998 GGCTGGATATGAGGGGCG 59.651 66.667 0.00 0.00 0.00 6.13
107 108 2.520536 GGCTGGATATGAGGGGCGT 61.521 63.158 0.00 0.00 0.00 5.68
108 109 1.004440 GCTGGATATGAGGGGCGTC 60.004 63.158 0.00 0.00 0.00 5.19
109 110 1.290324 CTGGATATGAGGGGCGTCG 59.710 63.158 0.00 0.00 0.00 5.12
110 111 2.159819 CTGGATATGAGGGGCGTCGG 62.160 65.000 0.00 0.00 0.00 4.79
111 112 1.906824 GGATATGAGGGGCGTCGGA 60.907 63.158 0.00 0.00 0.00 4.55
112 113 1.289380 GATATGAGGGGCGTCGGAC 59.711 63.158 0.00 0.00 0.00 4.79
113 114 1.456892 ATATGAGGGGCGTCGGACA 60.457 57.895 9.10 0.00 0.00 4.02
114 115 1.046472 ATATGAGGGGCGTCGGACAA 61.046 55.000 9.10 0.00 0.00 3.18
115 116 1.952102 TATGAGGGGCGTCGGACAAC 61.952 60.000 9.10 0.00 0.00 3.32
116 117 4.754667 GAGGGGCGTCGGACAACC 62.755 72.222 9.10 8.68 0.00 3.77
126 127 3.336566 GGACAACCCGGACGTTTG 58.663 61.111 0.73 3.07 0.00 2.93
127 128 1.227615 GGACAACCCGGACGTTTGA 60.228 57.895 0.73 0.00 0.00 2.69
128 129 1.226030 GGACAACCCGGACGTTTGAG 61.226 60.000 0.73 0.00 0.00 3.02
129 130 1.226030 GACAACCCGGACGTTTGAGG 61.226 60.000 0.73 0.00 0.00 3.86
130 131 2.281276 AACCCGGACGTTTGAGGC 60.281 61.111 0.73 0.00 0.00 4.70
131 132 3.837570 AACCCGGACGTTTGAGGCC 62.838 63.158 0.73 0.00 0.00 5.19
132 133 4.323477 CCCGGACGTTTGAGGCCA 62.323 66.667 5.01 0.00 0.00 5.36
133 134 2.046314 CCGGACGTTTGAGGCCAT 60.046 61.111 5.01 0.00 0.00 4.40
134 135 1.674322 CCGGACGTTTGAGGCCATT 60.674 57.895 5.01 0.00 0.00 3.16
135 136 1.241315 CCGGACGTTTGAGGCCATTT 61.241 55.000 5.01 0.00 0.00 2.32
136 137 1.444836 CGGACGTTTGAGGCCATTTA 58.555 50.000 5.01 0.00 0.00 1.40
137 138 1.807742 CGGACGTTTGAGGCCATTTAA 59.192 47.619 5.01 0.00 0.00 1.52
138 139 2.159572 CGGACGTTTGAGGCCATTTAAG 60.160 50.000 5.01 0.00 0.00 1.85
139 140 2.163613 GGACGTTTGAGGCCATTTAAGG 59.836 50.000 5.01 1.79 0.00 2.69
146 147 3.138128 GCCATTTAAGGCGCCCGT 61.138 61.111 26.15 14.92 46.12 5.28
147 148 3.107447 CCATTTAAGGCGCCCGTC 58.893 61.111 26.15 0.00 0.00 4.79
148 149 1.451387 CCATTTAAGGCGCCCGTCT 60.451 57.895 26.15 8.11 0.00 4.18
149 150 1.714899 CCATTTAAGGCGCCCGTCTG 61.715 60.000 26.15 14.46 0.00 3.51
150 151 0.742990 CATTTAAGGCGCCCGTCTGA 60.743 55.000 26.15 4.89 0.00 3.27
151 152 0.035820 ATTTAAGGCGCCCGTCTGAA 60.036 50.000 26.15 10.26 0.00 3.02
152 153 0.035820 TTTAAGGCGCCCGTCTGAAT 60.036 50.000 26.15 0.00 0.00 2.57
153 154 0.461339 TTAAGGCGCCCGTCTGAATC 60.461 55.000 26.15 0.00 0.00 2.52
154 155 1.609635 TAAGGCGCCCGTCTGAATCA 61.610 55.000 26.15 0.00 0.00 2.57
155 156 2.859273 AAGGCGCCCGTCTGAATCAG 62.859 60.000 26.15 3.38 0.00 2.90
156 157 2.184322 GCGCCCGTCTGAATCAGA 59.816 61.111 9.18 9.18 38.25 3.27
157 158 1.227380 GCGCCCGTCTGAATCAGAT 60.227 57.895 16.68 0.00 42.73 2.90
158 159 0.811616 GCGCCCGTCTGAATCAGATT 60.812 55.000 16.68 0.00 42.73 2.40
159 160 1.656652 CGCCCGTCTGAATCAGATTT 58.343 50.000 16.68 0.00 42.73 2.17
160 161 2.009774 CGCCCGTCTGAATCAGATTTT 58.990 47.619 16.68 0.00 42.73 1.82
161 162 2.223112 CGCCCGTCTGAATCAGATTTTG 60.223 50.000 16.68 6.96 42.73 2.44
162 163 2.098117 GCCCGTCTGAATCAGATTTTGG 59.902 50.000 16.68 14.65 42.73 3.28
163 164 3.347216 CCCGTCTGAATCAGATTTTGGT 58.653 45.455 16.68 0.00 42.73 3.67
164 165 3.127548 CCCGTCTGAATCAGATTTTGGTG 59.872 47.826 16.68 6.95 42.73 4.17
165 166 4.002982 CCGTCTGAATCAGATTTTGGTGA 58.997 43.478 16.68 0.00 42.73 4.02
166 167 4.142816 CCGTCTGAATCAGATTTTGGTGAC 60.143 45.833 16.68 0.03 42.73 3.67
167 168 4.142816 CGTCTGAATCAGATTTTGGTGACC 60.143 45.833 16.68 0.00 42.73 4.02
168 169 4.002982 TCTGAATCAGATTTTGGTGACCG 58.997 43.478 9.18 0.00 35.39 4.79
185 186 3.986006 GGTCAGTGACCGTGCGGA 61.986 66.667 26.12 0.00 43.14 5.54
206 207 4.697756 TCCGGGCGTTTGAGGCTG 62.698 66.667 0.00 0.00 42.05 4.85
211 212 2.256461 GCGTTTGAGGCTGGCTTG 59.744 61.111 4.82 0.00 0.00 4.01
212 213 2.956987 CGTTTGAGGCTGGCTTGG 59.043 61.111 4.82 0.00 0.00 3.61
213 214 1.600636 CGTTTGAGGCTGGCTTGGA 60.601 57.895 4.82 0.00 0.00 3.53
214 215 1.580845 CGTTTGAGGCTGGCTTGGAG 61.581 60.000 4.82 0.00 0.00 3.86
242 243 5.652891 CCGGGTGTAGATGCTCTTATACTAT 59.347 44.000 0.00 0.00 0.00 2.12
311 315 8.389603 TCGTACGTTATTGAGAAAAACAAAACT 58.610 29.630 16.05 0.00 0.00 2.66
398 403 7.497579 ACAAAATAATTGAACCTTGAACCAACC 59.502 33.333 0.00 0.00 0.00 3.77
437 442 7.926555 GCTATATACAGCTTGTCACTCCTTTTA 59.073 37.037 0.00 0.00 38.57 1.52
448 453 6.166279 TGTCACTCCTTTTATTCACAGCTAG 58.834 40.000 0.00 0.00 0.00 3.42
449 454 6.166982 GTCACTCCTTTTATTCACAGCTAGT 58.833 40.000 0.00 0.00 0.00 2.57
450 455 7.039293 TGTCACTCCTTTTATTCACAGCTAGTA 60.039 37.037 0.00 0.00 0.00 1.82
493 498 0.251916 CCACGCCCTCTTCACCATAA 59.748 55.000 0.00 0.00 0.00 1.90
494 499 1.134098 CCACGCCCTCTTCACCATAAT 60.134 52.381 0.00 0.00 0.00 1.28
545 550 6.916360 TCTTCTAATTTCCTGCCAATGTTT 57.084 33.333 0.00 0.00 0.00 2.83
720 1009 4.684484 AAAACAGGAACTAACGTCTCCT 57.316 40.909 0.00 0.00 40.33 3.69
723 1012 3.498334 ACAGGAACTAACGTCTCCTTCT 58.502 45.455 5.89 0.00 37.49 2.85
743 1032 1.902508 TCTCCCTCTCGCTGACAATTT 59.097 47.619 0.00 0.00 0.00 1.82
744 1033 2.093973 TCTCCCTCTCGCTGACAATTTC 60.094 50.000 0.00 0.00 0.00 2.17
745 1034 1.902508 TCCCTCTCGCTGACAATTTCT 59.097 47.619 0.00 0.00 0.00 2.52
746 1035 2.093973 TCCCTCTCGCTGACAATTTCTC 60.094 50.000 0.00 0.00 0.00 2.87
747 1036 2.093764 CCCTCTCGCTGACAATTTCTCT 60.094 50.000 0.00 0.00 0.00 3.10
748 1037 3.186119 CCTCTCGCTGACAATTTCTCTC 58.814 50.000 0.00 0.00 0.00 3.20
749 1038 3.119173 CCTCTCGCTGACAATTTCTCTCT 60.119 47.826 0.00 0.00 0.00 3.10
750 1039 4.103365 TCTCGCTGACAATTTCTCTCTC 57.897 45.455 0.00 0.00 0.00 3.20
751 1040 3.761218 TCTCGCTGACAATTTCTCTCTCT 59.239 43.478 0.00 0.00 0.00 3.10
752 1041 4.103365 TCGCTGACAATTTCTCTCTCTC 57.897 45.455 0.00 0.00 0.00 3.20
753 1042 3.761218 TCGCTGACAATTTCTCTCTCTCT 59.239 43.478 0.00 0.00 0.00 3.10
754 1043 4.104776 CGCTGACAATTTCTCTCTCTCTC 58.895 47.826 0.00 0.00 0.00 3.20
755 1044 4.142403 CGCTGACAATTTCTCTCTCTCTCT 60.142 45.833 0.00 0.00 0.00 3.10
756 1045 5.343249 GCTGACAATTTCTCTCTCTCTCTC 58.657 45.833 0.00 0.00 0.00 3.20
757 1046 5.126061 GCTGACAATTTCTCTCTCTCTCTCT 59.874 44.000 0.00 0.00 0.00 3.10
758 1047 6.678900 GCTGACAATTTCTCTCTCTCTCTCTC 60.679 46.154 0.00 0.00 0.00 3.20
759 1048 6.484288 TGACAATTTCTCTCTCTCTCTCTCT 58.516 40.000 0.00 0.00 0.00 3.10
760 1049 6.599244 TGACAATTTCTCTCTCTCTCTCTCTC 59.401 42.308 0.00 0.00 0.00 3.20
767 1056 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1072 1376 0.035458 GTGGAGTCCCAGTTCCAGTG 59.965 60.000 6.74 0.00 43.80 3.66
1080 1384 1.507141 CCAGTTCCAGTGGTCGTTGC 61.507 60.000 9.54 0.00 33.97 4.17
1240 1544 0.678048 GCCTGATGCGGGAGAAAGTT 60.678 55.000 0.00 0.00 29.82 2.66
1295 1599 0.544697 GTTTCCTGCCGGGATCCTTA 59.455 55.000 12.58 0.00 44.66 2.69
1590 1894 3.056328 GAGGAAGTGGCCGCAACC 61.056 66.667 20.59 20.02 0.00 3.77
1662 1966 2.480555 CGTGCTCCAAATGGCGTC 59.519 61.111 0.00 0.00 34.44 5.19
1927 2234 6.529125 GCCATCTATGTTCTGAATTGTGTTTG 59.471 38.462 0.00 0.00 0.00 2.93
1971 2278 3.380142 TCAAAGCGCTTGAACATTTTCC 58.620 40.909 25.80 0.00 41.21 3.13
2066 2390 5.940470 CAGTTAGAAAAATAGAGCCCACACT 59.060 40.000 0.00 0.00 0.00 3.55
2111 2455 9.798994 AGCAATCTGATTGATTAGAATTGAAAC 57.201 29.630 29.34 9.82 43.00 2.78
2112 2456 9.798994 GCAATCTGATTGATTAGAATTGAAACT 57.201 29.630 29.34 0.00 43.00 2.66
2134 2478 4.599047 ACTATAGGACTGCTGATTCTGC 57.401 45.455 4.43 8.46 0.00 4.26
2419 2763 2.430248 ACATGGAGCATGATCTTGCA 57.570 45.000 29.04 13.78 43.81 4.08
2553 2897 2.224523 TGCTGACTTCGGAAAATGACCT 60.225 45.455 0.00 0.00 0.00 3.85
2580 2924 2.621055 GGTCAAGTGTTACATGCACCAA 59.379 45.455 0.00 0.00 37.56 3.67
3211 3555 1.074405 TCAGCTTTGGCACTTCTGGAT 59.926 47.619 8.56 0.00 41.70 3.41
3253 3597 0.606604 ATAATAGGGGTACTGCGGCG 59.393 55.000 0.51 0.51 0.00 6.46
3298 3642 1.565759 TCTGGCTGCCCTTACATTCAT 59.434 47.619 17.53 0.00 0.00 2.57
3726 4131 0.984995 AGTAGTGAACCTCCCTTGCC 59.015 55.000 0.00 0.00 0.00 4.52
4015 4584 4.200283 CTCAGCCTCCTCCGCGTC 62.200 72.222 4.92 0.00 0.00 5.19
4196 4765 1.620259 CCAGTTGGCCCCATATGGT 59.380 57.895 20.46 0.00 31.33 3.55
4274 4843 2.429930 CAAGGTGGAGGTTGCGGA 59.570 61.111 0.00 0.00 0.00 5.54
4688 5344 2.914097 GCAGCTGCTGGGTTGGTT 60.914 61.111 31.33 0.00 38.21 3.67
4751 5407 1.215647 GGACCGACGAAGATGCACT 59.784 57.895 0.00 0.00 0.00 4.40
4805 5461 2.282555 CACGAGATCATGTTAACAGCCG 59.717 50.000 14.65 12.00 0.00 5.52
4818 5474 7.395190 TGTTAACAGCCGAATTACTACTAGA 57.605 36.000 3.59 0.00 0.00 2.43
4819 5475 7.829725 TGTTAACAGCCGAATTACTACTAGAA 58.170 34.615 3.59 0.00 0.00 2.10
4821 5477 4.918037 ACAGCCGAATTACTACTAGAACG 58.082 43.478 0.00 0.00 0.00 3.95
4823 5479 4.733887 CAGCCGAATTACTACTAGAACGTG 59.266 45.833 0.00 0.00 0.00 4.49
4824 5480 4.637534 AGCCGAATTACTACTAGAACGTGA 59.362 41.667 0.00 0.00 0.00 4.35
4825 5481 5.124457 AGCCGAATTACTACTAGAACGTGAA 59.876 40.000 0.00 0.00 0.00 3.18
4826 5482 5.975939 GCCGAATTACTACTAGAACGTGAAT 59.024 40.000 0.00 0.00 0.00 2.57
4827 5483 6.474751 GCCGAATTACTACTAGAACGTGAATT 59.525 38.462 0.00 0.00 0.00 2.17
4868 5531 1.535028 TGAATGCTCGCACGTGAATTT 59.465 42.857 22.23 3.00 0.00 1.82
4983 5648 2.877043 TTTATAAGAGACCGCCGTCC 57.123 50.000 1.30 0.00 40.12 4.79
5050 5715 0.320771 GACTGTGATGGCGAGTTGGT 60.321 55.000 0.00 0.00 0.00 3.67
5052 5717 0.603707 CTGTGATGGCGAGTTGGTGT 60.604 55.000 0.00 0.00 0.00 4.16
5060 5725 4.681978 GAGTTGGTGTCGGCCGCT 62.682 66.667 23.51 10.01 0.00 5.52
5334 6030 2.746277 GCGGCGGGTGATGAACTT 60.746 61.111 9.78 0.00 0.00 2.66
5872 6582 7.603024 CCGAAATATCCTCCAAGTAAGGAATAC 59.397 40.741 0.00 0.00 45.79 1.89
5875 6585 8.437274 AATATCCTCCAAGTAAGGAATACGAT 57.563 34.615 0.00 0.00 45.79 3.73
6617 7330 1.002257 ACAATGGTCATGCTCGCCA 60.002 52.632 0.00 0.00 36.64 5.69
6906 7619 4.644103 ATCGCATCAATTCCAAGAAAGG 57.356 40.909 0.00 0.00 0.00 3.11
6957 7670 3.896317 GGCAGATAAGGAGCCTACG 57.104 57.895 0.00 0.00 44.92 3.51
7059 7772 1.473434 CCTAGCCTTTAAGAGCCGTGG 60.473 57.143 0.00 0.00 0.00 4.94
7406 8119 0.988832 AGAGAGACCAGTCGGAGTCT 59.011 55.000 0.00 0.00 45.90 3.24
7415 8128 2.571212 CAGTCGGAGTCTCTGCTCTAT 58.429 52.381 3.55 0.00 35.89 1.98
8044 8766 1.699257 CCTCCCCCTACCATTAGCCTT 60.699 57.143 0.00 0.00 0.00 4.35
8060 8791 3.249189 TTTCGCTCCCCACCAGCT 61.249 61.111 0.00 0.00 34.45 4.24
8061 8792 2.754664 CTTTCGCTCCCCACCAGCTT 62.755 60.000 0.00 0.00 34.45 3.74
8062 8793 2.748058 TTTCGCTCCCCACCAGCTTC 62.748 60.000 0.00 0.00 34.45 3.86
8065 8796 4.785453 CTCCCCACCAGCTTCGCC 62.785 72.222 0.00 0.00 0.00 5.54
8134 8865 3.256960 GCCCTTCTCCCACCACCA 61.257 66.667 0.00 0.00 0.00 4.17
8268 9005 3.430497 TCCCCCTCCTCCCTCTCG 61.430 72.222 0.00 0.00 0.00 4.04
8278 9015 1.036707 CTCCCTCTCGTCCATTCTCC 58.963 60.000 0.00 0.00 0.00 3.71
8286 9023 1.006043 TCGTCCATTCTCCTCTCCTGT 59.994 52.381 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.092646 CACAAATATCCCCAGTCCGGAA 60.093 50.000 5.23 0.00 36.56 4.30
2 3 1.476833 CCACAAATATCCCCAGTCCGG 60.477 57.143 0.00 0.00 0.00 5.14
3 4 1.476833 CCCACAAATATCCCCAGTCCG 60.477 57.143 0.00 0.00 0.00 4.79
4 5 1.133482 CCCCACAAATATCCCCAGTCC 60.133 57.143 0.00 0.00 0.00 3.85
5 6 1.569072 ACCCCACAAATATCCCCAGTC 59.431 52.381 0.00 0.00 0.00 3.51
7 8 1.476833 CGACCCCACAAATATCCCCAG 60.477 57.143 0.00 0.00 0.00 4.45
8 9 0.548989 CGACCCCACAAATATCCCCA 59.451 55.000 0.00 0.00 0.00 4.96
9 10 0.179001 CCGACCCCACAAATATCCCC 60.179 60.000 0.00 0.00 0.00 4.81
10 11 0.179001 CCCGACCCCACAAATATCCC 60.179 60.000 0.00 0.00 0.00 3.85
11 12 0.179001 CCCCGACCCCACAAATATCC 60.179 60.000 0.00 0.00 0.00 2.59
12 13 0.549469 ACCCCGACCCCACAAATATC 59.451 55.000 0.00 0.00 0.00 1.63
13 14 0.257616 CACCCCGACCCCACAAATAT 59.742 55.000 0.00 0.00 0.00 1.28
14 15 1.686416 CACCCCGACCCCACAAATA 59.314 57.895 0.00 0.00 0.00 1.40
15 16 2.438795 CACCCCGACCCCACAAAT 59.561 61.111 0.00 0.00 0.00 2.32
16 17 3.892162 CCACCCCGACCCCACAAA 61.892 66.667 0.00 0.00 0.00 2.83
29 30 4.530857 CATCGGACTCGGCCCACC 62.531 72.222 0.00 0.00 36.95 4.61
30 31 3.771160 ACATCGGACTCGGCCCAC 61.771 66.667 0.00 0.00 36.95 4.61
31 32 3.770040 CACATCGGACTCGGCCCA 61.770 66.667 0.00 0.00 36.95 5.36
32 33 4.530857 CCACATCGGACTCGGCCC 62.531 72.222 0.00 0.00 36.56 5.80
58 59 4.666253 CATATGGGGCTGCCCGGG 62.666 72.222 30.32 19.09 46.66 5.73
67 68 2.951642 CAAATATAGGGCGCATATGGGG 59.048 50.000 20.15 3.77 0.00 4.96
68 69 2.951642 CCAAATATAGGGCGCATATGGG 59.048 50.000 15.11 15.11 0.00 4.00
69 70 2.951642 CCCAAATATAGGGCGCATATGG 59.048 50.000 10.83 6.03 39.96 2.74
79 80 5.398353 CCCTCATATCCAGCCCAAATATAGG 60.398 48.000 0.00 0.00 0.00 2.57
80 81 5.398353 CCCCTCATATCCAGCCCAAATATAG 60.398 48.000 0.00 0.00 0.00 1.31
81 82 4.478317 CCCCTCATATCCAGCCCAAATATA 59.522 45.833 0.00 0.00 0.00 0.86
82 83 3.270433 CCCCTCATATCCAGCCCAAATAT 59.730 47.826 0.00 0.00 0.00 1.28
83 84 2.649312 CCCCTCATATCCAGCCCAAATA 59.351 50.000 0.00 0.00 0.00 1.40
84 85 1.430464 CCCCTCATATCCAGCCCAAAT 59.570 52.381 0.00 0.00 0.00 2.32
85 86 0.852842 CCCCTCATATCCAGCCCAAA 59.147 55.000 0.00 0.00 0.00 3.28
86 87 1.719063 GCCCCTCATATCCAGCCCAA 61.719 60.000 0.00 0.00 0.00 4.12
87 88 2.156098 GCCCCTCATATCCAGCCCA 61.156 63.158 0.00 0.00 0.00 5.36
88 89 2.759795 GCCCCTCATATCCAGCCC 59.240 66.667 0.00 0.00 0.00 5.19
89 90 2.348998 CGCCCCTCATATCCAGCC 59.651 66.667 0.00 0.00 0.00 4.85
90 91 1.004440 GACGCCCCTCATATCCAGC 60.004 63.158 0.00 0.00 0.00 4.85
91 92 1.290324 CGACGCCCCTCATATCCAG 59.710 63.158 0.00 0.00 0.00 3.86
92 93 2.207229 CCGACGCCCCTCATATCCA 61.207 63.158 0.00 0.00 0.00 3.41
93 94 1.906824 TCCGACGCCCCTCATATCC 60.907 63.158 0.00 0.00 0.00 2.59
94 95 1.289380 GTCCGACGCCCCTCATATC 59.711 63.158 0.00 0.00 0.00 1.63
95 96 1.046472 TTGTCCGACGCCCCTCATAT 61.046 55.000 0.00 0.00 0.00 1.78
96 97 1.683025 TTGTCCGACGCCCCTCATA 60.683 57.895 0.00 0.00 0.00 2.15
97 98 3.000819 TTGTCCGACGCCCCTCAT 61.001 61.111 0.00 0.00 0.00 2.90
98 99 3.998672 GTTGTCCGACGCCCCTCA 61.999 66.667 0.00 0.00 0.00 3.86
99 100 4.754667 GGTTGTCCGACGCCCCTC 62.755 72.222 0.00 0.00 0.00 4.30
109 110 1.226030 CTCAAACGTCCGGGTTGTCC 61.226 60.000 0.00 0.00 0.00 4.02
110 111 1.226030 CCTCAAACGTCCGGGTTGTC 61.226 60.000 0.00 0.00 0.00 3.18
111 112 1.227734 CCTCAAACGTCCGGGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
112 113 2.613506 GCCTCAAACGTCCGGGTTG 61.614 63.158 0.00 1.48 0.00 3.77
113 114 2.281276 GCCTCAAACGTCCGGGTT 60.281 61.111 0.00 0.00 0.00 4.11
114 115 4.324991 GGCCTCAAACGTCCGGGT 62.325 66.667 0.00 0.00 0.00 5.28
115 116 3.622060 ATGGCCTCAAACGTCCGGG 62.622 63.158 3.32 0.00 0.00 5.73
116 117 1.241315 AAATGGCCTCAAACGTCCGG 61.241 55.000 3.32 0.00 0.00 5.14
117 118 1.444836 TAAATGGCCTCAAACGTCCG 58.555 50.000 3.32 0.00 0.00 4.79
118 119 2.163613 CCTTAAATGGCCTCAAACGTCC 59.836 50.000 3.32 0.00 0.00 4.79
119 120 2.415491 GCCTTAAATGGCCTCAAACGTC 60.415 50.000 3.32 0.00 46.82 4.34
120 121 1.544246 GCCTTAAATGGCCTCAAACGT 59.456 47.619 3.32 0.00 46.82 3.99
121 122 2.278026 GCCTTAAATGGCCTCAAACG 57.722 50.000 3.32 0.00 46.82 3.60
130 131 1.451387 AGACGGGCGCCTTAAATGG 60.451 57.895 28.56 9.38 0.00 3.16
131 132 0.742990 TCAGACGGGCGCCTTAAATG 60.743 55.000 28.56 18.29 0.00 2.32
132 133 0.035820 TTCAGACGGGCGCCTTAAAT 60.036 50.000 28.56 7.31 0.00 1.40
133 134 0.035820 ATTCAGACGGGCGCCTTAAA 60.036 50.000 28.56 12.55 0.00 1.52
134 135 0.461339 GATTCAGACGGGCGCCTTAA 60.461 55.000 28.56 11.83 0.00 1.85
135 136 1.143183 GATTCAGACGGGCGCCTTA 59.857 57.895 28.56 4.25 0.00 2.69
136 137 2.125106 GATTCAGACGGGCGCCTT 60.125 61.111 28.56 14.32 0.00 4.35
137 138 3.376935 CTGATTCAGACGGGCGCCT 62.377 63.158 28.56 7.30 32.44 5.52
138 139 2.650813 ATCTGATTCAGACGGGCGCC 62.651 60.000 21.18 21.18 43.63 6.53
139 140 0.811616 AATCTGATTCAGACGGGCGC 60.812 55.000 18.35 0.00 43.63 6.53
140 141 1.656652 AAATCTGATTCAGACGGGCG 58.343 50.000 18.35 0.00 43.63 6.13
141 142 2.098117 CCAAAATCTGATTCAGACGGGC 59.902 50.000 18.35 0.00 43.63 6.13
142 143 3.127548 CACCAAAATCTGATTCAGACGGG 59.872 47.826 18.35 17.44 43.63 5.28
143 144 4.002982 TCACCAAAATCTGATTCAGACGG 58.997 43.478 18.35 17.02 43.63 4.79
144 145 4.142816 GGTCACCAAAATCTGATTCAGACG 60.143 45.833 18.35 7.68 43.63 4.18
145 146 4.142816 CGGTCACCAAAATCTGATTCAGAC 60.143 45.833 18.35 3.75 43.63 3.51
146 147 4.002982 CGGTCACCAAAATCTGATTCAGA 58.997 43.478 18.29 18.29 44.99 3.27
147 148 3.127548 CCGGTCACCAAAATCTGATTCAG 59.872 47.826 7.38 7.38 0.00 3.02
148 149 3.081061 CCGGTCACCAAAATCTGATTCA 58.919 45.455 2.92 0.00 0.00 2.57
149 150 3.081804 ACCGGTCACCAAAATCTGATTC 58.918 45.455 0.00 0.00 0.00 2.52
150 151 3.081804 GACCGGTCACCAAAATCTGATT 58.918 45.455 29.75 0.00 0.00 2.57
151 152 2.039746 TGACCGGTCACCAAAATCTGAT 59.960 45.455 33.23 0.00 34.14 2.90
152 153 1.418264 TGACCGGTCACCAAAATCTGA 59.582 47.619 33.23 5.92 34.14 3.27
153 154 1.806542 CTGACCGGTCACCAAAATCTG 59.193 52.381 33.23 16.20 35.46 2.90
154 155 1.420138 ACTGACCGGTCACCAAAATCT 59.580 47.619 33.23 5.44 35.46 2.40
155 156 1.535462 CACTGACCGGTCACCAAAATC 59.465 52.381 33.23 5.07 35.46 2.17
156 157 1.142060 TCACTGACCGGTCACCAAAAT 59.858 47.619 33.23 11.54 35.46 1.82
157 158 0.542333 TCACTGACCGGTCACCAAAA 59.458 50.000 33.23 13.96 35.46 2.44
158 159 0.179067 GTCACTGACCGGTCACCAAA 60.179 55.000 33.23 15.74 35.46 3.28
159 160 1.444250 GTCACTGACCGGTCACCAA 59.556 57.895 33.23 17.55 35.46 3.67
160 161 2.504274 GGTCACTGACCGGTCACCA 61.504 63.158 33.23 16.56 43.14 4.17
161 162 2.342648 GGTCACTGACCGGTCACC 59.657 66.667 33.23 27.01 43.14 4.02
185 186 4.675029 CTCAAACGCCCGGACGGT 62.675 66.667 16.46 4.35 37.37 4.83
188 189 4.699522 AGCCTCAAACGCCCGGAC 62.700 66.667 0.73 0.00 0.00 4.79
193 194 2.985847 AAGCCAGCCTCAAACGCC 60.986 61.111 0.00 0.00 0.00 5.68
195 196 1.580845 CTCCAAGCCAGCCTCAAACG 61.581 60.000 0.00 0.00 0.00 3.60
212 213 3.537874 ATCTACACCCGGGCGCTC 61.538 66.667 24.08 0.06 0.00 5.03
213 214 3.849951 CATCTACACCCGGGCGCT 61.850 66.667 24.08 5.21 0.00 5.92
257 258 8.003044 ACAGCTAGACCCAAGTATATTGTACTA 58.997 37.037 0.00 0.00 0.00 1.82
258 259 6.839657 ACAGCTAGACCCAAGTATATTGTACT 59.160 38.462 0.00 0.00 0.00 2.73
259 260 7.014422 AGACAGCTAGACCCAAGTATATTGTAC 59.986 40.741 0.00 0.00 0.00 2.90
398 403 7.504922 GCTGTATATAGCGAGAGAAATCAAG 57.495 40.000 5.66 0.00 33.46 3.02
437 442 9.765795 GATAAATTAGTGGTACTAGCTGTGAAT 57.234 33.333 0.00 0.00 31.47 2.57
493 498 5.419542 ACAGATGAATAGCACACGTACAAT 58.580 37.500 0.00 0.00 0.00 2.71
494 499 4.816392 ACAGATGAATAGCACACGTACAA 58.184 39.130 0.00 0.00 0.00 2.41
545 550 1.269517 GCCGTGTCAAAAGCATCCAAA 60.270 47.619 0.00 0.00 0.00 3.28
697 986 5.536260 AGGAGACGTTAGTTCCTGTTTTAC 58.464 41.667 10.01 0.00 36.89 2.01
720 1009 0.038310 TGTCAGCGAGAGGGAGAGAA 59.962 55.000 0.00 0.00 0.00 2.87
723 1012 1.561643 AATTGTCAGCGAGAGGGAGA 58.438 50.000 0.00 0.00 0.00 3.71
743 1032 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
744 1033 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
745 1034 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
746 1035 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
747 1036 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
748 1037 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
749 1038 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
750 1039 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
751 1040 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
752 1041 3.494048 GGCAGAGAGAGAGAGAGAGAGAG 60.494 56.522 0.00 0.00 0.00 3.20
753 1042 2.435805 GGCAGAGAGAGAGAGAGAGAGA 59.564 54.545 0.00 0.00 0.00 3.10
754 1043 2.486191 GGGCAGAGAGAGAGAGAGAGAG 60.486 59.091 0.00 0.00 0.00 3.20
755 1044 1.490490 GGGCAGAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
756 1045 1.492176 AGGGCAGAGAGAGAGAGAGAG 59.508 57.143 0.00 0.00 0.00 3.20
757 1046 1.490490 GAGGGCAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
758 1047 1.492176 AGAGGGCAGAGAGAGAGAGAG 59.508 57.143 0.00 0.00 0.00 3.20
759 1048 1.490490 GAGAGGGCAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
760 1049 1.477558 GGAGAGGGCAGAGAGAGAGAG 60.478 61.905 0.00 0.00 0.00 3.20
767 1056 1.747444 AAAAAGGGAGAGGGCAGAGA 58.253 50.000 0.00 0.00 0.00 3.10
788 1077 3.295973 CCTTCTCCTTTTTGGTTGGTGA 58.704 45.455 0.00 0.00 37.07 4.02
802 1096 0.254462 CTGCTTCCCTTCCCTTCTCC 59.746 60.000 0.00 0.00 0.00 3.71
1017 1321 1.065854 CGGGATCTTCTTGGAGCACTT 60.066 52.381 0.00 0.00 0.00 3.16
1096 1400 4.514577 CCGAATCAGGGAGCGCGT 62.515 66.667 8.43 0.00 0.00 6.01
1204 1508 1.755783 GCCCTCATTGCTCCCCAAG 60.756 63.158 0.00 0.00 36.76 3.61
1206 1510 3.743017 GGCCCTCATTGCTCCCCA 61.743 66.667 0.00 0.00 0.00 4.96
1240 1544 3.703286 TCAAGACGACGACTTGAAGAA 57.297 42.857 30.83 15.09 46.68 2.52
1602 1906 2.710902 CGCCCTCTCCACATCGACA 61.711 63.158 0.00 0.00 0.00 4.35
1653 1957 1.915614 CTTGCTCTGCGACGCCATTT 61.916 55.000 18.69 0.00 0.00 2.32
1662 1966 0.603707 TCCTTGGTTCTTGCTCTGCG 60.604 55.000 0.00 0.00 0.00 5.18
1776 2080 1.541310 CCTCTGTTGCCACCTCCGTA 61.541 60.000 0.00 0.00 0.00 4.02
1927 2234 5.705609 AACATTCACACTAAATCACACCC 57.294 39.130 0.00 0.00 0.00 4.61
2066 2390 3.838317 TGCTTTAAAGGACTAGGAGCTGA 59.162 43.478 16.78 0.00 0.00 4.26
2105 2449 7.661536 ATCAGCAGTCCTATAGTAGTTTCAA 57.338 36.000 0.00 0.00 0.00 2.69
2106 2450 7.561722 AGAATCAGCAGTCCTATAGTAGTTTCA 59.438 37.037 0.00 0.00 0.00 2.69
2107 2451 7.865385 CAGAATCAGCAGTCCTATAGTAGTTTC 59.135 40.741 0.00 0.00 0.00 2.78
2108 2452 7.685641 GCAGAATCAGCAGTCCTATAGTAGTTT 60.686 40.741 0.00 0.00 0.00 2.66
2109 2453 6.239176 GCAGAATCAGCAGTCCTATAGTAGTT 60.239 42.308 0.00 0.00 0.00 2.24
2110 2454 5.242838 GCAGAATCAGCAGTCCTATAGTAGT 59.757 44.000 0.00 0.00 0.00 2.73
2111 2455 5.618863 CGCAGAATCAGCAGTCCTATAGTAG 60.619 48.000 0.00 0.00 0.00 2.57
2112 2456 4.216472 CGCAGAATCAGCAGTCCTATAGTA 59.784 45.833 0.00 0.00 0.00 1.82
2113 2457 3.005261 CGCAGAATCAGCAGTCCTATAGT 59.995 47.826 0.00 0.00 0.00 2.12
2114 2458 3.573598 CGCAGAATCAGCAGTCCTATAG 58.426 50.000 0.00 0.00 0.00 1.31
2115 2459 2.288457 GCGCAGAATCAGCAGTCCTATA 60.288 50.000 0.30 0.00 0.00 1.31
2116 2460 1.539929 GCGCAGAATCAGCAGTCCTAT 60.540 52.381 0.30 0.00 0.00 2.57
2117 2461 0.179100 GCGCAGAATCAGCAGTCCTA 60.179 55.000 0.30 0.00 0.00 2.94
2118 2462 1.449246 GCGCAGAATCAGCAGTCCT 60.449 57.895 0.30 0.00 0.00 3.85
2119 2463 0.179100 TAGCGCAGAATCAGCAGTCC 60.179 55.000 11.47 0.00 0.00 3.85
2120 2464 0.926846 GTAGCGCAGAATCAGCAGTC 59.073 55.000 11.47 0.00 0.00 3.51
2121 2465 0.534412 AGTAGCGCAGAATCAGCAGT 59.466 50.000 11.47 0.00 0.00 4.40
2134 2478 2.344741 GGTGAGAAAAAGCGTAGTAGCG 59.655 50.000 0.00 0.00 43.00 4.26
2419 2763 0.322975 CAGGTGTAGCAGCAAGTCCT 59.677 55.000 0.00 0.00 33.95 3.85
2553 2897 5.411361 GTGCATGTAACACTTGACCTGAATA 59.589 40.000 0.00 0.00 35.12 1.75
2580 2924 2.628657 GTGACCAAGTCCAGACAGTAGT 59.371 50.000 0.00 0.00 0.00 2.73
3211 3555 4.038282 TCAGGTTCTACAGCAAGTAAACGA 59.962 41.667 0.00 0.00 30.92 3.85
3253 3597 2.576615 ACTTCACTTTCAAGGGCAGAC 58.423 47.619 0.00 0.00 0.00 3.51
3355 3759 8.290325 AGCACTTTTAGCTAACATTTTAGACAC 58.710 33.333 5.45 0.00 41.32 3.67
3726 4131 2.289631 TGGTGTCATCCTGTAGCAACTG 60.290 50.000 0.00 0.00 0.00 3.16
3757 4162 0.174845 CATTCCAAGGTGCTGCATGG 59.825 55.000 13.33 13.33 0.00 3.66
3799 4204 2.451273 TGGTCCTTTTCCAAATGGGGTA 59.549 45.455 0.00 0.00 37.22 3.69
4015 4584 0.951040 GAACTTGGAGGCCACGTCTG 60.951 60.000 5.01 0.00 34.88 3.51
4196 4765 1.039068 CCCACCAAAGCACACAATCA 58.961 50.000 0.00 0.00 0.00 2.57
4274 4843 2.848694 TCTGGCATTTCATCCCTCTCTT 59.151 45.455 0.00 0.00 0.00 2.85
4688 5344 0.530431 CATCACCGGCGATGATGTCA 60.530 55.000 31.35 0.00 45.59 3.58
4751 5407 1.371183 CTTCCTCGAGGCCACAACA 59.629 57.895 27.39 4.41 34.44 3.33
4818 5474 6.529125 GCTTTTGATGATGATGAATTCACGTT 59.471 34.615 11.07 0.00 37.11 3.99
4819 5475 6.032094 GCTTTTGATGATGATGAATTCACGT 58.968 36.000 11.07 6.38 37.11 4.49
4821 5477 7.821595 TTGCTTTTGATGATGATGAATTCAC 57.178 32.000 11.07 5.73 37.11 3.18
4823 5479 8.755941 CAGATTGCTTTTGATGATGATGAATTC 58.244 33.333 0.00 0.00 0.00 2.17
4824 5480 8.474831 TCAGATTGCTTTTGATGATGATGAATT 58.525 29.630 0.00 0.00 0.00 2.17
4825 5481 8.007405 TCAGATTGCTTTTGATGATGATGAAT 57.993 30.769 0.00 0.00 0.00 2.57
4826 5482 7.399245 TCAGATTGCTTTTGATGATGATGAA 57.601 32.000 0.00 0.00 0.00 2.57
4827 5483 7.399245 TTCAGATTGCTTTTGATGATGATGA 57.601 32.000 0.00 0.00 0.00 2.92
4868 5531 5.997129 TCTCATTACTGTCACTCATGCAAAA 59.003 36.000 0.00 0.00 0.00 2.44
5060 5725 3.770040 CCTCATCCCGCGTCACCA 61.770 66.667 4.92 0.00 0.00 4.17
5324 6020 9.659830 ACGTTTTTCTATAAACAAGTTCATCAC 57.340 29.630 0.00 0.00 37.77 3.06
5942 6652 2.880268 CCATCTGGCGAAATTGCAGATA 59.120 45.455 0.00 0.00 33.77 1.98
5956 6666 2.099098 GCCAACGATAAAACCCATCTGG 59.901 50.000 0.00 0.00 41.37 3.86
6275 6987 4.025360 AGAAGCAATTGCATTACATCCCA 58.975 39.130 30.89 0.00 45.16 4.37
6282 6994 8.186163 CAGACAAATAGAGAAGCAATTGCATTA 58.814 33.333 30.89 15.41 45.16 1.90
6617 7330 4.091549 ACCAGCATTCATCAAAGGAACAT 58.908 39.130 0.00 0.00 0.00 2.71
6906 7619 1.595382 CCGATGGGAAGATGACGGC 60.595 63.158 0.00 0.00 34.36 5.68
6957 7670 6.063496 AGAAGAATTAAGTAACTCACCCCC 57.937 41.667 0.00 0.00 0.00 5.40
7247 7960 3.838903 AGTACTGGATTCGGTTCTTCCTT 59.161 43.478 0.00 0.00 33.86 3.36
7406 8119 6.622289 CCATTATGGGCAGCATAGAGCAGA 62.622 50.000 2.72 0.00 38.92 4.26
7882 8604 0.934436 ACAGCACGCAAAATTGTCGC 60.934 50.000 8.97 3.68 33.29 5.19
7883 8605 1.044725 GACAGCACGCAAAATTGTCG 58.955 50.000 7.92 7.92 35.13 4.35
7884 8606 2.046313 CAGACAGCACGCAAAATTGTC 58.954 47.619 1.31 1.31 38.68 3.18
8029 8751 1.594331 GCGAAAGGCTAATGGTAGGG 58.406 55.000 0.00 0.00 39.11 3.53
8044 8766 3.249189 AAGCTGGTGGGGAGCGAA 61.249 61.111 0.00 0.00 41.61 4.70
8268 9005 1.134551 GCACAGGAGAGGAGAATGGAC 60.135 57.143 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.