Multiple sequence alignment - TraesCS4A01G008900

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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 TraesCS4A01G008900 chr4A 100.000 4537 0 0 1 4537 5403668 5408204 0.000000e+00 8379
1 TraesCS4A01G008900 chr4D 91.770 3779 203 47 232 3966 465070876 465067162 0.000000e+00 5156
2 TraesCS4A01G008900 chr4B 93.150 2321 107 19 1592 3898 581537876 581535594 0.000000e+00 3358
3 TraesCS4A01G008900 chr4B 89.879 1492 80 33 149 1609 581539448 581537997 0.000000e+00 1853
4 TraesCS4A01G008900 chr2B 98.087 575 10 1 3963 4537 479849661 479850234 0.000000e+00 1000
5 TraesCS4A01G008900 chr2B 85.116 430 64 0 1760 2189 436992754 436993183 1.500000e-119 440
6 TraesCS4A01G008900 chr6B 97.902 572 12 0 3966 4537 626213382 626212811 0.000000e+00 990
7 TraesCS4A01G008900 chr7A 97.898 571 12 0 3967 4537 680916846 680916276 0.000000e+00 989
8 TraesCS4A01G008900 chr6A 97.739 575 11 1 3963 4537 67029444 67030016 0.000000e+00 989
9 TraesCS4A01G008900 chr6A 97.396 576 14 1 3963 4537 45758936 45759511 0.000000e+00 979
10 TraesCS4A01G008900 chr5A 97.260 584 14 2 3955 4537 668187170 668187752 0.000000e+00 989
11 TraesCS4A01G008900 chr1A 97.739 575 11 2 3963 4537 570224333 570224905 0.000000e+00 989
12 TraesCS4A01G008900 chr5B 97.731 573 13 0 3965 4537 308226905 308226333 0.000000e+00 987
13 TraesCS4A01G008900 chr5B 97.561 574 14 0 3963 4536 567582693 567583266 0.000000e+00 983
14 TraesCS4A01G008900 chr2D 85.349 430 63 0 1760 2189 367991306 367991735 3.220000e-121 446
15 TraesCS4A01G008900 chr2A 85.349 430 63 0 1760 2189 498086952 498087381 3.220000e-121 446


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 TraesCS4A01G008900 chr4A 5403668 5408204 4536 False 8379.0 8379 100.0000 1 4537 1 chr4A.!!$F1 4536
1 TraesCS4A01G008900 chr4D 465067162 465070876 3714 True 5156.0 5156 91.7700 232 3966 1 chr4D.!!$R1 3734
2 TraesCS4A01G008900 chr4B 581535594 581539448 3854 True 2605.5 3358 91.5145 149 3898 2 chr4B.!!$R1 3749
3 TraesCS4A01G008900 chr2B 479849661 479850234 573 False 1000.0 1000 98.0870 3963 4537 1 chr2B.!!$F2 574
4 TraesCS4A01G008900 chr6B 626212811 626213382 571 True 990.0 990 97.9020 3966 4537 1 chr6B.!!$R1 571
5 TraesCS4A01G008900 chr7A 680916276 680916846 570 True 989.0 989 97.8980 3967 4537 1 chr7A.!!$R1 570
6 TraesCS4A01G008900 chr6A 67029444 67030016 572 False 989.0 989 97.7390 3963 4537 1 chr6A.!!$F2 574
7 TraesCS4A01G008900 chr6A 45758936 45759511 575 False 979.0 979 97.3960 3963 4537 1 chr6A.!!$F1 574
8 TraesCS4A01G008900 chr5A 668187170 668187752 582 False 989.0 989 97.2600 3955 4537 1 chr5A.!!$F1 582
9 TraesCS4A01G008900 chr1A 570224333 570224905 572 False 989.0 989 97.7390 3963 4537 1 chr1A.!!$F1 574
10 TraesCS4A01G008900 chr5B 308226333 308226905 572 True 987.0 987 97.7310 3965 4537 1 chr5B.!!$R1 572
11 TraesCS4A01G008900 chr5B 567582693 567583266 573 False 983.0 983 97.5610 3963 4536 1 chr5B.!!$F1 573

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
40 41 0.036010 CAAAGACCGGGTCTGCTCAT 60.036 55.0 29.37 11.42 42.59 2.90 F
143 144 0.175989 TCTAACCACACACGCACACA 59.824 50.0 0.00 0.00 0.00 3.72 F
1511 1592 0.325296 TGAGTTCCGCCCATAGGAGT 60.325 55.0 0.00 0.00 39.22 3.85 F
2987 3239 0.255318 AGAAAGCTGCAGAGATGGGG 59.745 55.0 20.43 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1137 0.250081 GATTCCCTGGATGACCTCGC 60.250 60.000 0.00 0.0 37.04 5.03 R
1688 1912 3.007398 ACTTCAGTTTCTGACCTGGCTAG 59.993 47.826 0.00 0.0 40.46 3.42 R
3137 3389 0.249197 TCATGCTCTCATCTTCCGCG 60.249 55.000 0.00 0.0 0.00 6.46 R
4004 4262 1.069090 ACGAGGCGTGTGACACAAT 59.931 52.632 16.74 0.0 39.18 2.71 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
21 22 4.739046 GGTATGTGCATCTTAGTCATGC 57.261 45.455 0.00 0.00 45.92 4.06
28 29 4.284378 GCATCTTAGTCATGCAAAGACC 57.716 45.455 16.35 1.73 45.19 3.85
29 30 3.242543 GCATCTTAGTCATGCAAAGACCG 60.243 47.826 16.35 5.77 45.19 4.79
30 31 2.972625 TCTTAGTCATGCAAAGACCGG 58.027 47.619 16.35 0.00 36.68 5.28
31 32 2.009774 CTTAGTCATGCAAAGACCGGG 58.990 52.381 16.35 0.00 36.68 5.73
32 33 0.981183 TAGTCATGCAAAGACCGGGT 59.019 50.000 16.35 0.00 36.68 5.28
33 34 0.321653 AGTCATGCAAAGACCGGGTC 60.322 55.000 19.61 19.61 36.68 4.46
34 35 0.321653 GTCATGCAAAGACCGGGTCT 60.322 55.000 23.90 23.90 45.64 3.85
35 36 0.321564 TCATGCAAAGACCGGGTCTG 60.322 55.000 29.37 19.55 42.59 3.51
36 37 1.675641 ATGCAAAGACCGGGTCTGC 60.676 57.895 29.37 27.50 42.59 4.26
37 38 2.032681 GCAAAGACCGGGTCTGCT 59.967 61.111 29.37 17.13 42.59 4.24
38 39 2.035442 GCAAAGACCGGGTCTGCTC 61.035 63.158 29.37 16.76 42.59 4.26
39 40 1.371183 CAAAGACCGGGTCTGCTCA 59.629 57.895 29.37 0.00 42.59 4.26
40 41 0.036010 CAAAGACCGGGTCTGCTCAT 60.036 55.000 29.37 11.42 42.59 2.90
41 42 0.693049 AAAGACCGGGTCTGCTCATT 59.307 50.000 29.37 16.74 42.59 2.57
42 43 0.036010 AAGACCGGGTCTGCTCATTG 60.036 55.000 29.37 0.00 42.59 2.82
43 44 1.194781 AGACCGGGTCTGCTCATTGT 61.195 55.000 28.27 1.16 41.76 2.71
44 45 1.003355 ACCGGGTCTGCTCATTGTG 60.003 57.895 6.32 0.00 0.00 3.33
45 46 1.003355 CCGGGTCTGCTCATTGTGT 60.003 57.895 0.00 0.00 0.00 3.72
46 47 0.606401 CCGGGTCTGCTCATTGTGTT 60.606 55.000 0.00 0.00 0.00 3.32
47 48 1.238439 CGGGTCTGCTCATTGTGTTT 58.762 50.000 0.00 0.00 0.00 2.83
48 49 1.069022 CGGGTCTGCTCATTGTGTTTG 60.069 52.381 0.00 0.00 0.00 2.93
49 50 1.956477 GGGTCTGCTCATTGTGTTTGT 59.044 47.619 0.00 0.00 0.00 2.83
50 51 3.146066 GGGTCTGCTCATTGTGTTTGTA 58.854 45.455 0.00 0.00 0.00 2.41
51 52 3.758554 GGGTCTGCTCATTGTGTTTGTAT 59.241 43.478 0.00 0.00 0.00 2.29
52 53 4.142600 GGGTCTGCTCATTGTGTTTGTATC 60.143 45.833 0.00 0.00 0.00 2.24
53 54 4.142600 GGTCTGCTCATTGTGTTTGTATCC 60.143 45.833 0.00 0.00 0.00 2.59
54 55 4.009675 TCTGCTCATTGTGTTTGTATCCC 58.990 43.478 0.00 0.00 0.00 3.85
55 56 3.088532 TGCTCATTGTGTTTGTATCCCC 58.911 45.455 0.00 0.00 0.00 4.81
56 57 2.097466 GCTCATTGTGTTTGTATCCCCG 59.903 50.000 0.00 0.00 0.00 5.73
57 58 3.343617 CTCATTGTGTTTGTATCCCCGT 58.656 45.455 0.00 0.00 0.00 5.28
58 59 4.509616 CTCATTGTGTTTGTATCCCCGTA 58.490 43.478 0.00 0.00 0.00 4.02
59 60 4.907809 TCATTGTGTTTGTATCCCCGTAA 58.092 39.130 0.00 0.00 0.00 3.18
60 61 5.502079 TCATTGTGTTTGTATCCCCGTAAT 58.498 37.500 0.00 0.00 0.00 1.89
61 62 6.651086 TCATTGTGTTTGTATCCCCGTAATA 58.349 36.000 0.00 0.00 0.00 0.98
62 63 6.539464 TCATTGTGTTTGTATCCCCGTAATAC 59.461 38.462 0.00 0.00 0.00 1.89
63 64 5.680594 TGTGTTTGTATCCCCGTAATACT 57.319 39.130 0.00 0.00 32.05 2.12
64 65 6.052405 TGTGTTTGTATCCCCGTAATACTT 57.948 37.500 0.00 0.00 32.05 2.24
65 66 7.180322 TGTGTTTGTATCCCCGTAATACTTA 57.820 36.000 0.00 0.00 32.05 2.24
66 67 7.794041 TGTGTTTGTATCCCCGTAATACTTAT 58.206 34.615 0.00 0.00 32.05 1.73
67 68 8.266473 TGTGTTTGTATCCCCGTAATACTTATT 58.734 33.333 0.00 0.00 32.05 1.40
68 69 9.112725 GTGTTTGTATCCCCGTAATACTTATTT 57.887 33.333 0.00 0.00 32.05 1.40
72 73 8.954834 TGTATCCCCGTAATACTTATTTAGGA 57.045 34.615 4.77 0.00 32.05 2.94
73 74 9.028284 TGTATCCCCGTAATACTTATTTAGGAG 57.972 37.037 4.77 0.00 32.05 3.69
74 75 9.029368 GTATCCCCGTAATACTTATTTAGGAGT 57.971 37.037 4.77 0.00 0.00 3.85
75 76 7.530426 TCCCCGTAATACTTATTTAGGAGTC 57.470 40.000 4.77 0.00 0.00 3.36
76 77 7.068702 TCCCCGTAATACTTATTTAGGAGTCA 58.931 38.462 0.00 0.00 0.00 3.41
77 78 7.564660 TCCCCGTAATACTTATTTAGGAGTCAA 59.435 37.037 0.00 0.00 0.00 3.18
78 79 8.373220 CCCCGTAATACTTATTTAGGAGTCAAT 58.627 37.037 0.00 0.00 0.00 2.57
89 90 9.816787 TTATTTAGGAGTCAATAAAAACACCCT 57.183 29.630 4.46 0.00 0.00 4.34
90 91 8.721133 ATTTAGGAGTCAATAAAAACACCCTT 57.279 30.769 4.46 0.00 0.00 3.95
91 92 8.541899 TTTAGGAGTCAATAAAAACACCCTTT 57.458 30.769 0.00 0.00 0.00 3.11
92 93 9.643735 TTTAGGAGTCAATAAAAACACCCTTTA 57.356 29.630 0.00 0.00 0.00 1.85
93 94 9.816787 TTAGGAGTCAATAAAAACACCCTTTAT 57.183 29.630 0.00 0.00 31.71 1.40
94 95 8.721133 AGGAGTCAATAAAAACACCCTTTATT 57.279 30.769 0.00 0.00 38.76 1.40
101 102 8.596271 AATAAAAACACCCTTTATTGAAACCG 57.404 30.769 0.92 0.00 37.49 4.44
102 103 3.653539 AACACCCTTTATTGAAACCGC 57.346 42.857 0.00 0.00 0.00 5.68
103 104 1.538075 ACACCCTTTATTGAAACCGCG 59.462 47.619 0.00 0.00 0.00 6.46
104 105 1.135517 CACCCTTTATTGAAACCGCGG 60.136 52.381 26.86 26.86 0.00 6.46
105 106 1.271488 ACCCTTTATTGAAACCGCGGA 60.271 47.619 35.90 9.64 0.00 5.54
106 107 2.021457 CCCTTTATTGAAACCGCGGAT 58.979 47.619 35.90 19.90 0.00 4.18
107 108 2.223479 CCCTTTATTGAAACCGCGGATG 60.223 50.000 35.90 5.52 0.00 3.51
108 109 2.450160 CTTTATTGAAACCGCGGATGC 58.550 47.619 35.90 21.46 37.91 3.91
123 124 4.688966 TGCGCACGGGCACATACA 62.689 61.111 11.77 0.00 41.24 2.29
124 125 3.202001 GCGCACGGGCACATACAT 61.202 61.111 11.77 0.00 41.24 2.29
125 126 3.014036 CGCACGGGCACATACATC 58.986 61.111 11.77 0.00 41.24 3.06
126 127 1.521457 CGCACGGGCACATACATCT 60.521 57.895 11.77 0.00 41.24 2.90
127 128 0.249280 CGCACGGGCACATACATCTA 60.249 55.000 11.77 0.00 41.24 1.98
128 129 1.804746 CGCACGGGCACATACATCTAA 60.805 52.381 11.77 0.00 41.24 2.10
129 130 1.597663 GCACGGGCACATACATCTAAC 59.402 52.381 3.77 0.00 40.72 2.34
130 131 2.210116 CACGGGCACATACATCTAACC 58.790 52.381 0.00 0.00 0.00 2.85
131 132 1.834896 ACGGGCACATACATCTAACCA 59.165 47.619 0.00 0.00 0.00 3.67
132 133 2.210116 CGGGCACATACATCTAACCAC 58.790 52.381 0.00 0.00 0.00 4.16
133 134 2.419436 CGGGCACATACATCTAACCACA 60.419 50.000 0.00 0.00 0.00 4.17
134 135 2.943033 GGGCACATACATCTAACCACAC 59.057 50.000 0.00 0.00 0.00 3.82
135 136 3.605634 GGCACATACATCTAACCACACA 58.394 45.455 0.00 0.00 0.00 3.72
136 137 3.374058 GGCACATACATCTAACCACACAC 59.626 47.826 0.00 0.00 0.00 3.82
137 138 3.062099 GCACATACATCTAACCACACACG 59.938 47.826 0.00 0.00 0.00 4.49
138 139 3.062099 CACATACATCTAACCACACACGC 59.938 47.826 0.00 0.00 0.00 5.34
139 140 3.258228 CATACATCTAACCACACACGCA 58.742 45.455 0.00 0.00 0.00 5.24
140 141 1.508632 ACATCTAACCACACACGCAC 58.491 50.000 0.00 0.00 0.00 5.34
141 142 1.202592 ACATCTAACCACACACGCACA 60.203 47.619 0.00 0.00 0.00 4.57
142 143 1.194547 CATCTAACCACACACGCACAC 59.805 52.381 0.00 0.00 0.00 3.82
143 144 0.175989 TCTAACCACACACGCACACA 59.824 50.000 0.00 0.00 0.00 3.72
144 145 1.010580 CTAACCACACACGCACACAA 58.989 50.000 0.00 0.00 0.00 3.33
145 146 0.727970 TAACCACACACGCACACAAC 59.272 50.000 0.00 0.00 0.00 3.32
146 147 1.237954 AACCACACACGCACACAACA 61.238 50.000 0.00 0.00 0.00 3.33
147 148 1.237954 ACCACACACGCACACAACAA 61.238 50.000 0.00 0.00 0.00 2.83
153 154 0.455802 CACGCACACAACAAGCACAA 60.456 50.000 0.00 0.00 0.00 3.33
154 155 0.455972 ACGCACACAACAAGCACAAC 60.456 50.000 0.00 0.00 0.00 3.32
159 160 0.529833 CACAACAAGCACAACCCACA 59.470 50.000 0.00 0.00 0.00 4.17
163 164 1.063972 CAAGCACAACCCACACACG 59.936 57.895 0.00 0.00 0.00 4.49
164 165 2.118404 AAGCACAACCCACACACGG 61.118 57.895 0.00 0.00 0.00 4.94
180 181 2.343758 GGTCGGACAGCAAGCTCA 59.656 61.111 10.76 0.00 0.00 4.26
182 183 2.049156 TCGGACAGCAAGCTCACG 60.049 61.111 0.00 0.00 0.00 4.35
187 188 1.775039 GACAGCAAGCTCACGCACAA 61.775 55.000 5.63 0.00 39.10 3.33
190 191 1.063972 GCAAGCTCACGCACAAACA 59.936 52.632 0.00 0.00 39.10 2.83
194 195 3.014036 CTCACGCACAAACACGCT 58.986 55.556 0.00 0.00 0.00 5.07
195 196 1.368019 CTCACGCACAAACACGCTG 60.368 57.895 0.00 0.00 0.00 5.18
196 197 1.761244 CTCACGCACAAACACGCTGA 61.761 55.000 0.00 0.00 0.00 4.26
198 199 2.103647 ACGCACAAACACGCTGACA 61.104 52.632 0.00 0.00 0.00 3.58
199 200 1.651132 CGCACAAACACGCTGACAC 60.651 57.895 0.00 0.00 0.00 3.67
200 201 1.651132 GCACAAACACGCTGACACG 60.651 57.895 0.00 0.00 39.50 4.49
201 202 1.651132 CACAAACACGCTGACACGC 60.651 57.895 0.00 0.00 36.19 5.34
230 236 1.070105 ACACACACGCCCGTAATGT 59.930 52.632 4.61 4.61 0.00 2.71
258 265 1.010419 CCTGACAAAGCGCCAAATGC 61.010 55.000 2.29 0.00 0.00 3.56
289 296 1.664649 CAGACTCGAACGGCTGCAA 60.665 57.895 0.50 0.00 0.00 4.08
309 316 1.141053 ACAACGAAGAAGAAGCAGGGT 59.859 47.619 0.00 0.00 0.00 4.34
312 323 3.983044 ACGAAGAAGAAGCAGGGTTAT 57.017 42.857 0.00 0.00 0.00 1.89
317 328 5.520649 CGAAGAAGAAGCAGGGTTATTACTC 59.479 44.000 0.00 0.00 0.00 2.59
324 335 0.749049 AGGGTTATTACTCGCCGGTC 59.251 55.000 1.90 0.00 0.00 4.79
597 608 7.652105 TCGATAATTACAAGGTGCTAATCTCAC 59.348 37.037 0.00 0.00 0.00 3.51
602 613 4.353777 ACAAGGTGCTAATCTCACTAGGA 58.646 43.478 0.00 0.00 34.97 2.94
637 648 2.766263 TCAGTAATCCCAGTGGTAGCTG 59.234 50.000 8.74 8.91 36.31 4.24
686 697 3.304382 GCATGATGCACGTAACAGTAC 57.696 47.619 13.36 0.00 44.26 2.73
708 719 2.750948 GAACTGCGACAGTAGGAACAA 58.249 47.619 11.92 0.00 44.62 2.83
710 721 1.071605 CTGCGACAGTAGGAACAAGC 58.928 55.000 0.00 0.00 0.00 4.01
715 726 2.094700 CGACAGTAGGAACAAGCAGCTA 60.095 50.000 0.00 0.00 0.00 3.32
759 770 7.896383 TTTTTATTTATGTCTGATCTGGGGG 57.104 36.000 0.00 0.00 0.00 5.40
829 843 5.444176 GAGGAAACCAGATTCTGATTCCAT 58.556 41.667 31.31 23.10 43.30 3.41
878 893 1.004918 GTCCTTGACACGGACTGGG 60.005 63.158 20.90 0.00 45.87 4.45
1014 1032 0.384230 CAACAATGTCGCACACGTCC 60.384 55.000 0.00 0.00 41.18 4.79
1026 1044 1.242665 ACACGTCCGAGGAAGAGTCC 61.243 60.000 11.84 0.00 45.35 3.85
1029 1047 1.658686 CGTCCGAGGAAGAGTCCCTG 61.659 65.000 0.00 0.00 46.30 4.45
1119 1137 0.821711 TGCCCGTGGTGAAAAAGAGG 60.822 55.000 0.00 0.00 0.00 3.69
1146 1164 4.168101 GTCATCCAGGGAATCCAGGTATA 58.832 47.826 0.09 0.00 40.31 1.47
1147 1165 4.785376 GTCATCCAGGGAATCCAGGTATAT 59.215 45.833 0.09 0.00 40.31 0.86
1148 1166 5.964477 GTCATCCAGGGAATCCAGGTATATA 59.036 44.000 0.09 0.00 40.31 0.86
1149 1167 6.617371 GTCATCCAGGGAATCCAGGTATATAT 59.383 42.308 0.09 0.00 40.31 0.86
1150 1168 6.616959 TCATCCAGGGAATCCAGGTATATATG 59.383 42.308 0.09 2.48 40.31 1.78
1151 1169 5.927465 TCCAGGGAATCCAGGTATATATGT 58.073 41.667 0.09 0.00 40.31 2.29
1152 1170 6.339220 TCCAGGGAATCCAGGTATATATGTT 58.661 40.000 0.09 0.00 40.31 2.71
1153 1171 6.215431 TCCAGGGAATCCAGGTATATATGTTG 59.785 42.308 0.09 0.00 40.31 3.33
1154 1172 5.882557 CAGGGAATCCAGGTATATATGTTGC 59.117 44.000 0.09 0.00 34.83 4.17
1155 1173 5.044846 AGGGAATCCAGGTATATATGTTGCC 60.045 44.000 0.09 0.00 34.83 4.52
1156 1174 5.044846 GGGAATCCAGGTATATATGTTGCCT 60.045 44.000 0.09 0.00 0.00 4.75
1157 1175 6.116126 GGAATCCAGGTATATATGTTGCCTC 58.884 44.000 0.00 0.00 0.00 4.70
1158 1176 6.296432 GGAATCCAGGTATATATGTTGCCTCA 60.296 42.308 0.00 0.00 0.00 3.86
1159 1177 6.702449 ATCCAGGTATATATGTTGCCTCAA 57.298 37.500 0.00 0.00 0.00 3.02
1160 1178 5.865085 TCCAGGTATATATGTTGCCTCAAC 58.135 41.667 2.96 2.96 43.78 3.18
1161 1179 5.606749 TCCAGGTATATATGTTGCCTCAACT 59.393 40.000 10.52 0.65 43.85 3.16
1162 1180 5.934625 CCAGGTATATATGTTGCCTCAACTC 59.065 44.000 10.52 0.00 43.85 3.01
1163 1181 6.464322 CCAGGTATATATGTTGCCTCAACTCA 60.464 42.308 10.52 0.15 43.85 3.41
1164 1182 6.992123 CAGGTATATATGTTGCCTCAACTCAA 59.008 38.462 10.52 0.00 43.85 3.02
1243 1276 7.844009 AGATGCACCAGATGAATGTTTAAAAT 58.156 30.769 0.00 0.00 0.00 1.82
1277 1348 5.915196 GCATGGTTTGTTAGAAAGTCTCAAC 59.085 40.000 0.00 0.00 0.00 3.18
1316 1390 7.159322 TCTTTCTTACTACCTAGCAACTGAG 57.841 40.000 0.00 0.00 0.00 3.35
1332 1406 7.288560 AGCAACTGAGATATGGAAGATCAAAT 58.711 34.615 0.00 0.00 0.00 2.32
1367 1441 6.367695 TCAGTGTTGTATAGATTTGACCAACG 59.632 38.462 0.00 0.00 36.00 4.10
1372 1446 7.117236 TGTTGTATAGATTTGACCAACGAACTC 59.883 37.037 0.00 0.00 36.00 3.01
1499 1580 2.767505 ACACGAACCTGAATGAGTTCC 58.232 47.619 0.00 0.00 39.36 3.62
1502 1583 1.087501 GAACCTGAATGAGTTCCGCC 58.912 55.000 0.00 0.00 37.08 6.13
1508 1589 1.140852 TGAATGAGTTCCGCCCATAGG 59.859 52.381 0.00 0.00 33.26 2.57
1509 1590 1.416401 GAATGAGTTCCGCCCATAGGA 59.584 52.381 0.00 0.00 35.69 2.94
1510 1591 1.051812 ATGAGTTCCGCCCATAGGAG 58.948 55.000 0.00 0.00 39.22 3.69
1511 1592 0.325296 TGAGTTCCGCCCATAGGAGT 60.325 55.000 0.00 0.00 39.22 3.85
1512 1593 1.063492 TGAGTTCCGCCCATAGGAGTA 60.063 52.381 0.00 0.00 39.22 2.59
1513 1594 2.249139 GAGTTCCGCCCATAGGAGTAT 58.751 52.381 0.00 0.00 39.22 2.12
1514 1595 1.971357 AGTTCCGCCCATAGGAGTATG 59.029 52.381 0.00 0.00 39.22 2.39
1518 1599 1.902508 CCGCCCATAGGAGTATGATGT 59.097 52.381 0.00 0.00 38.76 3.06
1533 1614 7.171678 GGAGTATGATGTAGTATTTGCCAACTC 59.828 40.741 0.00 0.00 0.00 3.01
1681 1905 5.391312 ACTGAATTGCTAAATGAACCCAC 57.609 39.130 0.00 0.00 0.00 4.61
1688 1912 5.637006 TGCTAAATGAACCCACAACATAC 57.363 39.130 0.00 0.00 0.00 2.39
1718 1945 4.816385 GGTCAGAAACTGAAGTGATGAACA 59.184 41.667 2.98 0.00 42.46 3.18
2227 2469 4.032445 CCAAGAATTCAAGCAAATGCATCG 59.968 41.667 8.44 0.00 45.16 3.84
2231 2473 6.389091 AGAATTCAAGCAAATGCATCGTTAA 58.611 32.000 8.44 0.00 45.16 2.01
2292 2539 6.592607 TGAACATTAAGGTCATTCGGTAAGAC 59.407 38.462 0.00 0.00 39.57 3.01
2300 2547 5.011329 AGGTCATTCGGTAAGACAACAGTAA 59.989 40.000 0.00 0.00 34.04 2.24
2301 2548 5.873164 GGTCATTCGGTAAGACAACAGTAAT 59.127 40.000 0.00 0.00 34.04 1.89
2313 2560 6.698380 AGACAACAGTAATTGTAGACCGAAT 58.302 36.000 0.00 0.00 42.89 3.34
2324 2571 5.907866 TGTAGACCGAATTACTGACATCA 57.092 39.130 0.00 0.00 0.00 3.07
2326 2573 6.873997 TGTAGACCGAATTACTGACATCATT 58.126 36.000 0.00 0.00 0.00 2.57
2483 2733 9.734620 TTTACATACTATTTGAAGCAATGCATC 57.265 29.630 8.35 5.61 0.00 3.91
2574 2826 3.271729 CCATGCCATTTAAAATGCAGCA 58.728 40.909 16.83 0.00 37.12 4.41
2596 2848 6.206634 AGCATTTCTTGGAACTCGACATTTAA 59.793 34.615 0.00 0.00 0.00 1.52
2618 2870 6.992063 AACTCTACTTTATGTCAATGCAGG 57.008 37.500 0.00 0.00 0.00 4.85
2642 2894 2.608016 GGATAGCTTCATCACGCATCGA 60.608 50.000 0.00 0.00 0.00 3.59
2693 2945 2.304761 CTCAAGGGTTAACCACAGCCTA 59.695 50.000 25.71 3.87 41.48 3.93
2792 3044 0.884704 ACATGTCCAGCAACGACCAC 60.885 55.000 0.00 0.00 0.00 4.16
2816 3068 5.866159 ACTCAGACATGCATCTAAGATCA 57.134 39.130 0.00 0.00 0.00 2.92
2943 3195 1.004745 ACATGTCCATGAACTCCCCAC 59.995 52.381 13.93 0.00 41.20 4.61
2987 3239 0.255318 AGAAAGCTGCAGAGATGGGG 59.745 55.000 20.43 0.00 0.00 4.96
3137 3389 0.675633 ACAGTGTTTGCATGAAGGCC 59.324 50.000 0.00 0.00 0.00 5.19
3140 3392 2.504681 GTTTGCATGAAGGCCGCG 60.505 61.111 0.00 0.00 0.00 6.46
3197 3449 1.059098 TCAACTCAGCATGGACCAGT 58.941 50.000 0.00 0.00 36.16 4.00
3201 3453 3.129502 CAGCATGGACCAGTGGCG 61.130 66.667 9.78 0.00 0.00 5.69
3202 3454 4.415150 AGCATGGACCAGTGGCGG 62.415 66.667 9.78 0.00 0.00 6.13
3248 3500 5.170748 CCTTTAATTGGGCTCATGAACAAC 58.829 41.667 8.71 0.00 0.00 3.32
3302 3554 5.045359 CCCTCAGATTATGCCTGATATCCAA 60.045 44.000 0.00 0.00 39.62 3.53
3320 3572 0.808125 AAACGCAGCACAACAGACAA 59.192 45.000 0.00 0.00 0.00 3.18
3637 3893 9.588096 TTAAGAAGGTATAGCATGTATGAGAGA 57.412 33.333 4.48 0.00 0.00 3.10
3653 3909 1.970640 AGAGACAGTGCACCATGTGTA 59.029 47.619 15.71 0.00 35.75 2.90
3660 3916 4.455533 ACAGTGCACCATGTGTATTGTTAG 59.544 41.667 14.63 0.00 43.53 2.34
3732 3989 7.439655 CAGAAAGTAGCCAGGTAATCTTATCAC 59.560 40.741 0.00 0.00 0.00 3.06
3738 3995 6.534634 AGCCAGGTAATCTTATCACCATAAC 58.465 40.000 0.00 0.00 34.62 1.89
3739 3996 5.705905 GCCAGGTAATCTTATCACCATAACC 59.294 44.000 0.00 0.00 34.62 2.85
3740 3997 6.690460 GCCAGGTAATCTTATCACCATAACCA 60.690 42.308 0.00 0.00 34.62 3.67
3749 4006 1.638070 TCACCATAACCAGGCCATTCA 59.362 47.619 5.01 0.00 0.00 2.57
3943 4201 5.799827 ACAGAGTATTCCTTAGAGCATCC 57.200 43.478 0.00 0.00 33.66 3.51
3956 4214 2.517919 CATCCCTAGCCCTTGCCC 59.482 66.667 0.00 0.00 38.69 5.36
3960 4218 0.694444 TCCCTAGCCCTTGCCCTAAG 60.694 60.000 0.00 0.00 38.69 2.18
4004 4262 1.067706 CACGTGTGGTGTATCGGGTAA 60.068 52.381 7.58 0.00 41.89 2.85
4010 4268 3.008157 TGTGGTGTATCGGGTAATTGTGT 59.992 43.478 0.00 0.00 0.00 3.72
4155 4414 3.961838 GATAACGCCCACACGCCCA 62.962 63.158 0.00 0.00 36.19 5.36
4169 4428 1.839191 GCCCATATGTCAGGCCTCA 59.161 57.895 0.00 0.00 41.00 3.86
4529 4788 2.904866 GCACGTTGGGGCAGTTGA 60.905 61.111 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.739046 GCATGACTAAGATGCACATACC 57.261 45.455 0.00 0.00 44.74 2.73
8 9 3.310774 CCGGTCTTTGCATGACTAAGATG 59.689 47.826 16.48 6.76 41.24 2.90
9 10 3.535561 CCGGTCTTTGCATGACTAAGAT 58.464 45.455 16.48 0.00 41.24 2.40
10 11 2.354704 CCCGGTCTTTGCATGACTAAGA 60.355 50.000 16.48 6.94 37.72 2.10
11 12 2.009774 CCCGGTCTTTGCATGACTAAG 58.990 52.381 16.48 4.82 35.04 2.18
12 13 1.349688 ACCCGGTCTTTGCATGACTAA 59.650 47.619 16.48 0.00 35.04 2.24
13 14 0.981183 ACCCGGTCTTTGCATGACTA 59.019 50.000 16.48 0.00 35.04 2.59
14 15 0.321653 GACCCGGTCTTTGCATGACT 60.322 55.000 10.59 1.38 35.04 3.41
15 16 0.321653 AGACCCGGTCTTTGCATGAC 60.322 55.000 14.84 10.74 40.28 3.06
16 17 0.321564 CAGACCCGGTCTTTGCATGA 60.322 55.000 18.03 0.00 41.37 3.07
17 18 1.926511 GCAGACCCGGTCTTTGCATG 61.927 60.000 18.03 7.56 41.37 4.06
18 19 1.675641 GCAGACCCGGTCTTTGCAT 60.676 57.895 18.03 0.00 41.37 3.96
19 20 2.281484 GCAGACCCGGTCTTTGCA 60.281 61.111 18.03 0.00 41.37 4.08
20 21 2.032681 AGCAGACCCGGTCTTTGC 59.967 61.111 18.03 18.88 41.37 3.68
21 22 0.036010 ATGAGCAGACCCGGTCTTTG 60.036 55.000 18.03 9.76 41.37 2.77
22 23 0.693049 AATGAGCAGACCCGGTCTTT 59.307 50.000 18.03 9.12 41.37 2.52
23 24 0.036010 CAATGAGCAGACCCGGTCTT 60.036 55.000 18.03 4.24 41.37 3.01
24 25 1.194781 ACAATGAGCAGACCCGGTCT 61.195 55.000 14.84 14.84 44.44 3.85
25 26 1.021390 CACAATGAGCAGACCCGGTC 61.021 60.000 9.81 9.81 0.00 4.79
26 27 1.003355 CACAATGAGCAGACCCGGT 60.003 57.895 0.00 0.00 0.00 5.28
27 28 0.606401 AACACAATGAGCAGACCCGG 60.606 55.000 0.00 0.00 0.00 5.73
28 29 1.069022 CAAACACAATGAGCAGACCCG 60.069 52.381 0.00 0.00 0.00 5.28
29 30 1.956477 ACAAACACAATGAGCAGACCC 59.044 47.619 0.00 0.00 0.00 4.46
30 31 4.142600 GGATACAAACACAATGAGCAGACC 60.143 45.833 0.00 0.00 0.00 3.85
31 32 4.142600 GGGATACAAACACAATGAGCAGAC 60.143 45.833 0.00 0.00 39.74 3.51
32 33 4.009675 GGGATACAAACACAATGAGCAGA 58.990 43.478 0.00 0.00 39.74 4.26
33 34 3.129287 GGGGATACAAACACAATGAGCAG 59.871 47.826 0.00 0.00 39.74 4.24
34 35 3.088532 GGGGATACAAACACAATGAGCA 58.911 45.455 0.00 0.00 39.74 4.26
35 36 2.097466 CGGGGATACAAACACAATGAGC 59.903 50.000 0.00 0.00 39.74 4.26
36 37 3.343617 ACGGGGATACAAACACAATGAG 58.656 45.455 0.00 0.00 39.74 2.90
37 38 3.426787 ACGGGGATACAAACACAATGA 57.573 42.857 0.00 0.00 39.74 2.57
38 39 5.828299 ATTACGGGGATACAAACACAATG 57.172 39.130 0.00 0.00 39.74 2.82
39 40 6.655930 AGTATTACGGGGATACAAACACAAT 58.344 36.000 7.52 0.00 39.74 2.71
40 41 6.052405 AGTATTACGGGGATACAAACACAA 57.948 37.500 7.52 0.00 39.74 3.33
41 42 5.680594 AGTATTACGGGGATACAAACACA 57.319 39.130 7.52 0.00 39.74 3.72
42 43 8.667076 AATAAGTATTACGGGGATACAAACAC 57.333 34.615 7.52 0.00 33.43 3.32
46 47 9.378504 TCCTAAATAAGTATTACGGGGATACAA 57.621 33.333 7.52 0.00 33.43 2.41
47 48 8.954834 TCCTAAATAAGTATTACGGGGATACA 57.045 34.615 7.52 0.00 33.43 2.29
48 49 9.029368 ACTCCTAAATAAGTATTACGGGGATAC 57.971 37.037 5.77 0.00 30.46 2.24
49 50 9.247861 GACTCCTAAATAAGTATTACGGGGATA 57.752 37.037 5.77 0.00 30.46 2.59
50 51 7.731688 TGACTCCTAAATAAGTATTACGGGGAT 59.268 37.037 5.77 0.00 30.46 3.85
51 52 7.068702 TGACTCCTAAATAAGTATTACGGGGA 58.931 38.462 5.77 0.00 30.46 4.81
52 53 7.294017 TGACTCCTAAATAAGTATTACGGGG 57.706 40.000 0.00 0.00 30.46 5.73
63 64 9.816787 AGGGTGTTTTTATTGACTCCTAAATAA 57.183 29.630 0.00 0.00 31.75 1.40
64 65 9.816787 AAGGGTGTTTTTATTGACTCCTAAATA 57.183 29.630 0.00 0.00 31.75 1.40
65 66 8.721133 AAGGGTGTTTTTATTGACTCCTAAAT 57.279 30.769 0.00 0.00 31.75 1.40
66 67 8.541899 AAAGGGTGTTTTTATTGACTCCTAAA 57.458 30.769 0.00 0.00 31.75 1.85
67 68 9.816787 ATAAAGGGTGTTTTTATTGACTCCTAA 57.183 29.630 0.00 0.00 28.87 2.69
68 69 9.816787 AATAAAGGGTGTTTTTATTGACTCCTA 57.183 29.630 3.05 0.00 38.56 2.94
69 70 8.721133 AATAAAGGGTGTTTTTATTGACTCCT 57.279 30.769 3.05 0.00 38.56 3.69
76 77 7.171848 GCGGTTTCAATAAAGGGTGTTTTTATT 59.828 33.333 0.00 0.00 39.85 1.40
77 78 6.647481 GCGGTTTCAATAAAGGGTGTTTTTAT 59.353 34.615 0.00 0.00 33.37 1.40
78 79 5.984323 GCGGTTTCAATAAAGGGTGTTTTTA 59.016 36.000 0.00 0.00 0.00 1.52
79 80 4.812091 GCGGTTTCAATAAAGGGTGTTTTT 59.188 37.500 0.00 0.00 0.00 1.94
80 81 4.373527 GCGGTTTCAATAAAGGGTGTTTT 58.626 39.130 0.00 0.00 0.00 2.43
81 82 3.551250 CGCGGTTTCAATAAAGGGTGTTT 60.551 43.478 0.00 0.00 0.00 2.83
82 83 2.030628 CGCGGTTTCAATAAAGGGTGTT 60.031 45.455 0.00 0.00 0.00 3.32
83 84 1.538075 CGCGGTTTCAATAAAGGGTGT 59.462 47.619 0.00 0.00 0.00 4.16
84 85 1.135517 CCGCGGTTTCAATAAAGGGTG 60.136 52.381 19.50 0.00 0.00 4.61
85 86 1.170442 CCGCGGTTTCAATAAAGGGT 58.830 50.000 19.50 0.00 0.00 4.34
86 87 1.455248 TCCGCGGTTTCAATAAAGGG 58.545 50.000 27.15 0.00 0.00 3.95
87 88 2.794631 GCATCCGCGGTTTCAATAAAGG 60.795 50.000 27.15 4.85 0.00 3.11
88 89 2.450160 GCATCCGCGGTTTCAATAAAG 58.550 47.619 27.15 3.18 0.00 1.85
89 90 2.553079 GCATCCGCGGTTTCAATAAA 57.447 45.000 27.15 1.58 0.00 1.40
108 109 0.249280 TAGATGTATGTGCCCGTGCG 60.249 55.000 0.00 0.00 41.78 5.34
109 110 1.597663 GTTAGATGTATGTGCCCGTGC 59.402 52.381 0.00 0.00 38.26 5.34
110 111 2.210116 GGTTAGATGTATGTGCCCGTG 58.790 52.381 0.00 0.00 0.00 4.94
111 112 1.834896 TGGTTAGATGTATGTGCCCGT 59.165 47.619 0.00 0.00 0.00 5.28
112 113 2.210116 GTGGTTAGATGTATGTGCCCG 58.790 52.381 0.00 0.00 0.00 6.13
113 114 2.943033 GTGTGGTTAGATGTATGTGCCC 59.057 50.000 0.00 0.00 0.00 5.36
114 115 3.374058 GTGTGTGGTTAGATGTATGTGCC 59.626 47.826 0.00 0.00 0.00 5.01
115 116 3.062099 CGTGTGTGGTTAGATGTATGTGC 59.938 47.826 0.00 0.00 0.00 4.57
116 117 3.062099 GCGTGTGTGGTTAGATGTATGTG 59.938 47.826 0.00 0.00 0.00 3.21
117 118 3.259064 GCGTGTGTGGTTAGATGTATGT 58.741 45.455 0.00 0.00 0.00 2.29
118 119 3.062099 GTGCGTGTGTGGTTAGATGTATG 59.938 47.826 0.00 0.00 0.00 2.39
119 120 3.259064 GTGCGTGTGTGGTTAGATGTAT 58.741 45.455 0.00 0.00 0.00 2.29
120 121 2.036089 TGTGCGTGTGTGGTTAGATGTA 59.964 45.455 0.00 0.00 0.00 2.29
121 122 1.202592 TGTGCGTGTGTGGTTAGATGT 60.203 47.619 0.00 0.00 0.00 3.06
122 123 1.194547 GTGTGCGTGTGTGGTTAGATG 59.805 52.381 0.00 0.00 0.00 2.90
123 124 1.202592 TGTGTGCGTGTGTGGTTAGAT 60.203 47.619 0.00 0.00 0.00 1.98
124 125 0.175989 TGTGTGCGTGTGTGGTTAGA 59.824 50.000 0.00 0.00 0.00 2.10
125 126 1.010580 TTGTGTGCGTGTGTGGTTAG 58.989 50.000 0.00 0.00 0.00 2.34
126 127 0.727970 GTTGTGTGCGTGTGTGGTTA 59.272 50.000 0.00 0.00 0.00 2.85
127 128 1.237954 TGTTGTGTGCGTGTGTGGTT 61.238 50.000 0.00 0.00 0.00 3.67
128 129 1.237954 TTGTTGTGTGCGTGTGTGGT 61.238 50.000 0.00 0.00 0.00 4.16
129 130 0.523125 CTTGTTGTGTGCGTGTGTGG 60.523 55.000 0.00 0.00 0.00 4.17
130 131 1.133363 GCTTGTTGTGTGCGTGTGTG 61.133 55.000 0.00 0.00 0.00 3.82
131 132 1.136565 GCTTGTTGTGTGCGTGTGT 59.863 52.632 0.00 0.00 0.00 3.72
132 133 1.133363 GTGCTTGTTGTGTGCGTGTG 61.133 55.000 0.00 0.00 0.00 3.82
133 134 1.136565 GTGCTTGTTGTGTGCGTGT 59.863 52.632 0.00 0.00 0.00 4.49
134 135 0.455802 TTGTGCTTGTTGTGTGCGTG 60.456 50.000 0.00 0.00 0.00 5.34
135 136 0.455972 GTTGTGCTTGTTGTGTGCGT 60.456 50.000 0.00 0.00 0.00 5.24
136 137 1.139226 GGTTGTGCTTGTTGTGTGCG 61.139 55.000 0.00 0.00 0.00 5.34
137 138 0.805711 GGGTTGTGCTTGTTGTGTGC 60.806 55.000 0.00 0.00 0.00 4.57
138 139 0.529833 TGGGTTGTGCTTGTTGTGTG 59.470 50.000 0.00 0.00 0.00 3.82
139 140 0.530288 GTGGGTTGTGCTTGTTGTGT 59.470 50.000 0.00 0.00 0.00 3.72
140 141 0.529833 TGTGGGTTGTGCTTGTTGTG 59.470 50.000 0.00 0.00 0.00 3.33
141 142 0.530288 GTGTGGGTTGTGCTTGTTGT 59.470 50.000 0.00 0.00 0.00 3.32
142 143 0.529833 TGTGTGGGTTGTGCTTGTTG 59.470 50.000 0.00 0.00 0.00 3.33
143 144 0.530288 GTGTGTGGGTTGTGCTTGTT 59.470 50.000 0.00 0.00 0.00 2.83
144 145 1.653094 CGTGTGTGGGTTGTGCTTGT 61.653 55.000 0.00 0.00 0.00 3.16
145 146 1.063972 CGTGTGTGGGTTGTGCTTG 59.936 57.895 0.00 0.00 0.00 4.01
146 147 2.118404 CCGTGTGTGGGTTGTGCTT 61.118 57.895 0.00 0.00 0.00 3.91
147 148 2.515991 CCGTGTGTGGGTTGTGCT 60.516 61.111 0.00 0.00 0.00 4.40
153 154 3.920196 GTCCGACCGTGTGTGGGT 61.920 66.667 0.00 0.00 43.01 4.51
154 155 3.858868 CTGTCCGACCGTGTGTGGG 62.859 68.421 0.00 0.00 43.80 4.61
159 160 2.029073 CTTGCTGTCCGACCGTGT 59.971 61.111 0.00 0.00 0.00 4.49
163 164 2.029844 GTGAGCTTGCTGTCCGACC 61.030 63.158 0.00 0.00 0.00 4.79
164 165 2.375766 CGTGAGCTTGCTGTCCGAC 61.376 63.158 0.00 0.00 0.00 4.79
180 181 2.103647 TGTCAGCGTGTTTGTGCGT 61.104 52.632 0.00 0.00 35.87 5.24
182 183 1.651132 CGTGTCAGCGTGTTTGTGC 60.651 57.895 0.00 0.00 0.00 4.57
210 211 2.322081 ATTACGGGCGTGTGTGTGC 61.322 57.895 0.00 0.00 0.00 4.57
211 212 1.225376 ACATTACGGGCGTGTGTGTG 61.225 55.000 0.00 0.00 30.85 3.82
213 214 1.495509 CACATTACGGGCGTGTGTG 59.504 57.895 2.76 2.76 38.66 3.82
237 243 1.181098 ATTTGGCGCTTTGTCAGGCT 61.181 50.000 7.64 0.00 30.83 4.58
258 265 3.305964 TCGAGTCTGTTCGTTGCTTTAG 58.694 45.455 4.78 0.00 41.22 1.85
268 275 1.618640 GCAGCCGTTCGAGTCTGTTC 61.619 60.000 0.00 0.00 0.00 3.18
270 277 2.049063 GCAGCCGTTCGAGTCTGT 60.049 61.111 0.00 0.00 0.00 3.41
273 280 1.495584 TTGTTGCAGCCGTTCGAGTC 61.496 55.000 0.00 0.00 0.00 3.36
289 296 1.141053 ACCCTGCTTCTTCTTCGTTGT 59.859 47.619 0.00 0.00 0.00 3.32
309 316 2.492881 TGTTCTGACCGGCGAGTAATAA 59.507 45.455 9.30 0.00 0.00 1.40
312 323 0.675083 TTGTTCTGACCGGCGAGTAA 59.325 50.000 9.30 0.00 0.00 2.24
317 328 2.549282 CGTTTGTTCTGACCGGCG 59.451 61.111 0.00 0.00 0.00 6.46
324 335 1.657181 GTTGGCCGCGTTTGTTCTG 60.657 57.895 4.92 0.00 0.00 3.02
456 467 8.669658 ACTGATAATGCAGTTTTCTGGGGACA 62.670 42.308 0.00 0.00 46.42 4.02
597 608 3.861840 TGAGATCGCTGGTTTTTCCTAG 58.138 45.455 0.00 0.00 37.07 3.02
602 613 4.636206 GGATTACTGAGATCGCTGGTTTTT 59.364 41.667 8.14 0.00 0.00 1.94
637 648 2.633481 ACGTAGATAGGCCCCTGATTTC 59.367 50.000 0.00 0.00 0.00 2.17
686 697 0.242825 TTCCTACTGTCGCAGTTCGG 59.757 55.000 15.81 15.53 42.59 4.30
708 719 6.353404 AGAGAAAAGTAGTCTTTAGCTGCT 57.647 37.500 7.57 7.57 42.26 4.24
710 721 8.770438 ATGAAGAGAAAAGTAGTCTTTAGCTG 57.230 34.615 0.00 0.00 42.26 4.24
829 843 5.389098 GCTCGCGTTCAGTATTAGAAAACAA 60.389 40.000 5.77 0.00 0.00 2.83
844 859 3.702334 GACGGCAATGCTCGCGTTC 62.702 63.158 5.77 0.00 0.00 3.95
878 893 1.399440 GTAAACGGCGAAAATCCCCTC 59.601 52.381 16.62 0.00 0.00 4.30
1014 1032 0.967887 TGCTCAGGGACTCTTCCTCG 60.968 60.000 0.00 0.00 42.38 4.63
1119 1137 0.250081 GATTCCCTGGATGACCTCGC 60.250 60.000 0.00 0.00 37.04 5.03
1146 1164 5.769662 TGAAACTTGAGTTGAGGCAACATAT 59.230 36.000 12.25 0.00 45.66 1.78
1147 1165 5.129634 TGAAACTTGAGTTGAGGCAACATA 58.870 37.500 12.25 0.00 45.66 2.29
1148 1166 3.953612 TGAAACTTGAGTTGAGGCAACAT 59.046 39.130 12.25 0.00 45.66 2.71
1149 1167 3.351740 TGAAACTTGAGTTGAGGCAACA 58.648 40.909 12.25 0.00 45.66 3.33
1150 1168 4.105486 GTTGAAACTTGAGTTGAGGCAAC 58.895 43.478 2.22 2.22 43.83 4.17
1151 1169 4.016444 AGTTGAAACTTGAGTTGAGGCAA 58.984 39.130 0.00 0.00 38.44 4.52
1152 1170 3.620488 AGTTGAAACTTGAGTTGAGGCA 58.380 40.909 0.00 0.00 38.44 4.75
1153 1171 5.948992 ATAGTTGAAACTTGAGTTGAGGC 57.051 39.130 0.21 0.00 40.37 4.70
1154 1172 7.264373 ACAATAGTTGAAACTTGAGTTGAGG 57.736 36.000 0.21 0.00 40.37 3.86
1243 1276 4.634703 AACCATGCACGGTCGCCA 62.635 61.111 4.20 0.00 38.76 5.69
1287 1358 8.688151 AGTTGCTAGGTAGTAAGAAAGATACAG 58.312 37.037 0.00 0.00 0.00 2.74
1293 1364 7.159322 TCTCAGTTGCTAGGTAGTAAGAAAG 57.841 40.000 0.00 0.00 0.00 2.62
1301 1372 6.491745 TCTTCCATATCTCAGTTGCTAGGTAG 59.508 42.308 0.00 0.00 0.00 3.18
1307 1381 5.883685 TGATCTTCCATATCTCAGTTGCT 57.116 39.130 0.00 0.00 0.00 3.91
1316 1390 8.230472 ACAAGGACAATTTGATCTTCCATATC 57.770 34.615 2.79 0.00 0.00 1.63
1332 1406 6.822442 TCTATACAACACTGAACAAGGACAA 58.178 36.000 0.00 0.00 0.00 3.18
1435 1516 5.948992 AGAGCTACATGTTTTGAGAAACC 57.051 39.130 2.30 0.00 43.57 3.27
1499 1580 3.764434 ACTACATCATACTCCTATGGGCG 59.236 47.826 0.00 0.00 31.92 6.13
1502 1583 7.766278 GGCAAATACTACATCATACTCCTATGG 59.234 40.741 0.00 0.00 31.92 2.74
1508 1589 7.710907 TGAGTTGGCAAATACTACATCATACTC 59.289 37.037 0.00 0.05 0.00 2.59
1509 1590 7.564793 TGAGTTGGCAAATACTACATCATACT 58.435 34.615 0.00 0.00 0.00 2.12
1510 1591 7.519008 GCTGAGTTGGCAAATACTACATCATAC 60.519 40.741 0.00 0.00 0.00 2.39
1511 1592 6.483307 GCTGAGTTGGCAAATACTACATCATA 59.517 38.462 0.00 0.00 0.00 2.15
1512 1593 5.297776 GCTGAGTTGGCAAATACTACATCAT 59.702 40.000 0.00 0.00 0.00 2.45
1513 1594 4.635765 GCTGAGTTGGCAAATACTACATCA 59.364 41.667 0.00 0.00 0.00 3.07
1514 1595 4.635765 TGCTGAGTTGGCAAATACTACATC 59.364 41.667 0.00 0.00 36.71 3.06
1518 1599 4.635765 GTGATGCTGAGTTGGCAAATACTA 59.364 41.667 0.00 0.00 43.14 1.82
1533 1614 7.577979 ACAATTTGCTTTATTTTGTGATGCTG 58.422 30.769 0.00 0.00 0.00 4.41
1618 1840 8.677300 TCTGTTCTTTAGTATCCATTTGCAATC 58.323 33.333 0.00 0.00 0.00 2.67
1658 1881 6.007076 TGTGGGTTCATTTAGCAATTCAGTA 58.993 36.000 0.00 0.00 0.00 2.74
1674 1898 3.270877 CTGGCTAGTATGTTGTGGGTTC 58.729 50.000 0.00 0.00 0.00 3.62
1681 1905 4.471904 TTCTGACCTGGCTAGTATGTTG 57.528 45.455 0.00 0.00 0.00 3.33
1688 1912 3.007398 ACTTCAGTTTCTGACCTGGCTAG 59.993 47.826 0.00 0.00 40.46 3.42
2260 2502 9.219603 CCGAATGACCTTAATGTTCATATGTAT 57.780 33.333 1.90 0.00 0.00 2.29
2262 2504 7.054124 ACCGAATGACCTTAATGTTCATATGT 58.946 34.615 1.90 0.00 0.00 2.29
2263 2505 7.496529 ACCGAATGACCTTAATGTTCATATG 57.503 36.000 0.00 0.00 0.00 1.78
2265 2507 8.479689 TCTTACCGAATGACCTTAATGTTCATA 58.520 33.333 0.00 0.00 0.00 2.15
2285 2532 6.309737 CGGTCTACAATTACTGTTGTCTTACC 59.690 42.308 0.00 2.78 41.18 2.85
2292 2539 8.475331 AGTAATTCGGTCTACAATTACTGTTG 57.525 34.615 13.73 0.00 46.76 3.33
2300 2547 6.873997 TGATGTCAGTAATTCGGTCTACAAT 58.126 36.000 0.00 0.00 0.00 2.71
2301 2548 6.275494 TGATGTCAGTAATTCGGTCTACAA 57.725 37.500 0.00 0.00 0.00 2.41
2483 2733 3.976942 GCCACAGATGCTAAAATATTGCG 59.023 43.478 0.00 0.00 0.00 4.85
2574 2826 7.661847 AGAGTTAAATGTCGAGTTCCAAGAAAT 59.338 33.333 0.00 0.00 0.00 2.17
2596 2848 6.299805 TCCTGCATTGACATAAAGTAGAGT 57.700 37.500 0.00 0.00 0.00 3.24
2642 2894 2.548920 GGCTAATACATCGCAGAAGGCT 60.549 50.000 0.00 0.00 43.58 4.58
2693 2945 2.026822 CAGACTTCCCACCATTGTAGCT 60.027 50.000 0.00 0.00 0.00 3.32
2792 3044 6.047231 TGATCTTAGATGCATGTCTGAGTTG 58.953 40.000 2.46 0.00 34.47 3.16
2816 3068 7.550597 TGTGATGAGAGCATAAGGAGATAAT 57.449 36.000 0.00 0.00 34.11 1.28
2943 3195 3.490759 GGCTGTCGCGGACATGTG 61.491 66.667 1.15 0.00 41.94 3.21
3080 3332 3.397482 CATAGAATCTCCTTGGCTTCCG 58.603 50.000 0.00 0.00 0.00 4.30
3137 3389 0.249197 TCATGCTCTCATCTTCCGCG 60.249 55.000 0.00 0.00 0.00 6.46
3140 3392 3.814283 GACCATTCATGCTCTCATCTTCC 59.186 47.826 0.00 0.00 0.00 3.46
3197 3449 2.438254 GGTGTCATCATGCCGCCA 60.438 61.111 0.00 0.00 0.00 5.69
3201 3453 1.571919 GTAGTCGGTGTCATCATGCC 58.428 55.000 0.00 0.00 0.00 4.40
3202 3454 1.571919 GGTAGTCGGTGTCATCATGC 58.428 55.000 0.00 0.00 0.00 4.06
3203 3455 1.134367 ACGGTAGTCGGTGTCATCATG 59.866 52.381 0.00 0.00 44.45 3.07
3248 3500 4.592942 TCTCTTGTCTCATGGAAAATGGG 58.407 43.478 0.00 0.00 0.00 4.00
3302 3554 0.378257 CTTGTCTGTTGTGCTGCGTT 59.622 50.000 0.00 0.00 0.00 4.84
3320 3572 4.601857 TCTCCTACCCCTGAAATGTTTTCT 59.398 41.667 2.08 0.00 0.00 2.52
3636 3892 2.813754 ACAATACACATGGTGCACTGTC 59.186 45.455 17.98 0.00 36.98 3.51
3637 3893 2.862541 ACAATACACATGGTGCACTGT 58.137 42.857 17.98 15.26 36.98 3.55
3732 3989 1.696063 CCTGAATGGCCTGGTTATGG 58.304 55.000 3.32 0.00 0.00 2.74
3749 4006 9.700831 AATACAATAGTTTCTTAAATCTGCCCT 57.299 29.630 0.00 0.00 0.00 5.19
3832 4089 5.596772 TGATCTACAATCTACATCCACCGAA 59.403 40.000 0.00 0.00 0.00 4.30
3915 4173 7.903145 TGCTCTAAGGAATACTCTGTTGTTTA 58.097 34.615 0.00 0.00 0.00 2.01
3943 4201 1.149401 GCTTAGGGCAAGGGCTAGG 59.851 63.158 0.00 0.00 41.35 3.02
3956 4214 4.344390 AGTTATCGGGACCCTAAAGCTTAG 59.656 45.833 9.41 0.00 0.00 2.18
3960 4218 2.835027 CAGTTATCGGGACCCTAAAGC 58.165 52.381 9.41 0.00 0.00 3.51
4004 4262 1.069090 ACGAGGCGTGTGACACAAT 59.931 52.632 16.74 0.00 39.18 2.71
4155 4414 3.282135 AGGGTATGAGGCCTGACATAT 57.718 47.619 12.00 0.00 32.77 1.78


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

AutoCloner maintained by Alex Coulton.