Multiple sequence alignment - TraesCS5A01G382500

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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 TraesCS5A01G382500 chr5A 100.000 3230 0 0 2634 5863 580461732 580464961 0.000000e+00 5965.0
1 TraesCS5A01G382500 chr5A 100.000 1957 0 0 1 1957 580459099 580461055 0.000000e+00 3615.0
2 TraesCS5A01G382500 chr5B 96.444 3093 78 11 2782 5863 565925824 565928895 0.000000e+00 5073.0
3 TraesCS5A01G382500 chr5B 93.761 1186 35 11 798 1954 565924402 565925577 0.000000e+00 1744.0
4 TraesCS5A01G382500 chr5B 95.518 357 16 0 177 533 565923614 565923970 6.590000e-159 571.0
5 TraesCS5A01G382500 chr5B 92.778 180 10 1 1 177 565903036 565903215 2.100000e-64 257.0
6 TraesCS5A01G382500 chr5B 97.297 148 4 0 2634 2781 565925600 565925747 9.750000e-63 252.0
7 TraesCS5A01G382500 chr5B 89.231 195 13 2 585 771 565924223 565924417 2.730000e-58 237.0
8 TraesCS5A01G382500 chr5B 93.694 111 7 0 5318 5428 166379183 166379073 3.630000e-37 167.0
9 TraesCS5A01G382500 chr5B 100.000 37 0 0 532 568 565924186 565924222 1.050000e-07 69.4
10 TraesCS5A01G382500 chr5D 98.391 2299 35 1 3017 5313 460390563 460392861 0.000000e+00 4039.0
11 TraesCS5A01G382500 chr5D 93.688 1204 25 16 798 1954 460388950 460390149 0.000000e+00 1755.0
12 TraesCS5A01G382500 chr5D 96.377 552 13 2 5312 5863 460393023 460393567 0.000000e+00 902.0
13 TraesCS5A01G382500 chr5D 90.422 616 36 7 177 771 460388352 460388965 0.000000e+00 789.0
14 TraesCS5A01G382500 chr5D 92.568 148 5 3 2634 2781 460390172 460390313 2.140000e-49 207.0
15 TraesCS5A01G382500 chr5D 95.918 98 4 0 5318 5415 139440915 139441012 6.080000e-35 159.0
16 TraesCS5A01G382500 chr5D 100.000 30 0 0 2782 2811 460390387 460390416 8.210000e-04 56.5
17 TraesCS5A01G382500 chr7B 94.845 97 5 0 5319 5415 162120812 162120908 1.020000e-32 152.0
18 TraesCS5A01G382500 chr7B 92.381 105 7 1 5312 5415 632337767 632337871 1.320000e-31 148.0
19 TraesCS5A01G382500 chr3A 93.269 104 5 2 5319 5420 470095778 470095675 1.020000e-32 152.0
20 TraesCS5A01G382500 chr4A 94.845 97 4 1 5319 5415 37060112 37060207 3.660000e-32 150.0
21 TraesCS5A01G382500 chr2B 93.204 103 6 1 5315 5417 480409476 480409375 3.660000e-32 150.0


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 TraesCS5A01G382500 chr5A 580459099 580464961 5862 False 4790.000000 5965 100.000000 1 5863 2 chr5A.!!$F1 5862
1 TraesCS5A01G382500 chr5B 565923614 565928895 5281 False 1324.400000 5073 95.375167 177 5863 6 chr5B.!!$F2 5686
2 TraesCS5A01G382500 chr5D 460388352 460393567 5215 False 1291.416667 4039 95.241000 177 5863 6 chr5D.!!$F2 5686

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
571 791 0.112412 AAGGGGCCACACAACCTAAG 59.888 55.000 8.31 0.0 31.88 2.18 F
577 797 0.395312 CCACACAACCTAAGACGGGT 59.605 55.000 0.00 0.0 38.94 5.28 F
906 1170 0.751643 ACGAAACAGCCAAGCAGGTT 60.752 50.000 0.00 0.0 40.61 3.50 F
1867 2172 1.060729 TCCCCGAATGTCCTGTTTCA 58.939 50.000 0.00 0.0 0.00 2.69 F
3262 3777 1.607148 GTTGGCTACACTGAAACCCAC 59.393 52.381 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 2228 2.884639 GCCTGGCTTGAAACTGTTCTAA 59.115 45.455 12.43 0.00 34.60 2.10 R
2637 2949 6.494835 ACTTGGAATTCAGAAACCAAAGCTAT 59.505 34.615 19.22 6.75 41.00 2.97 R
2932 3445 1.068352 AAAAGGGGCCAGACTCACCT 61.068 55.000 4.39 0.00 0.00 4.00 R
3432 3947 0.908910 ATGATTCGGCCACCAGTGTA 59.091 50.000 2.24 0.00 0.00 2.90 R
5204 5720 0.108472 CAGAGGCATCTCAACGCTCA 60.108 55.000 0.00 0.00 42.34 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.292784 GCAAGAGCTCCCAGTGAC 57.707 61.111 10.93 0.00 37.91 3.67
25 26 1.372683 GCAAGAGCTCCCAGTGACA 59.627 57.895 10.93 0.00 37.91 3.58
26 27 0.673022 GCAAGAGCTCCCAGTGACAG 60.673 60.000 10.93 0.00 37.91 3.51
27 28 0.972134 CAAGAGCTCCCAGTGACAGA 59.028 55.000 10.93 0.00 0.00 3.41
28 29 1.554160 CAAGAGCTCCCAGTGACAGAT 59.446 52.381 10.93 0.00 0.00 2.90
29 30 1.484038 AGAGCTCCCAGTGACAGATC 58.516 55.000 10.93 0.00 0.00 2.75
30 31 1.006998 AGAGCTCCCAGTGACAGATCT 59.993 52.381 10.93 3.86 0.00 2.75
31 32 1.830477 GAGCTCCCAGTGACAGATCTT 59.170 52.381 0.87 0.00 0.00 2.40
32 33 1.830477 AGCTCCCAGTGACAGATCTTC 59.170 52.381 0.00 0.00 0.00 2.87
33 34 1.470632 GCTCCCAGTGACAGATCTTCG 60.471 57.143 0.00 0.00 0.00 3.79
34 35 0.532573 TCCCAGTGACAGATCTTCGC 59.467 55.000 0.00 1.50 0.00 4.70
35 36 0.460987 CCCAGTGACAGATCTTCGCC 60.461 60.000 12.11 2.53 0.00 5.54
36 37 0.247460 CCAGTGACAGATCTTCGCCA 59.753 55.000 12.11 0.00 0.00 5.69
37 38 1.354040 CAGTGACAGATCTTCGCCAC 58.646 55.000 12.11 9.05 0.00 5.01
38 39 1.067283 CAGTGACAGATCTTCGCCACT 60.067 52.381 12.11 10.66 35.51 4.00
39 40 1.067283 AGTGACAGATCTTCGCCACTG 60.067 52.381 12.53 0.00 34.08 3.66
40 41 1.067565 GTGACAGATCTTCGCCACTGA 60.068 52.381 0.00 0.00 34.88 3.41
41 42 1.067565 TGACAGATCTTCGCCACTGAC 60.068 52.381 0.00 0.00 34.88 3.51
42 43 0.969149 ACAGATCTTCGCCACTGACA 59.031 50.000 0.00 0.00 34.88 3.58
43 44 1.552337 ACAGATCTTCGCCACTGACAT 59.448 47.619 0.00 0.00 34.88 3.06
44 45 2.027745 ACAGATCTTCGCCACTGACATT 60.028 45.455 0.00 0.00 34.88 2.71
45 46 3.005554 CAGATCTTCGCCACTGACATTT 58.994 45.455 0.00 0.00 32.90 2.32
46 47 4.183865 CAGATCTTCGCCACTGACATTTA 58.816 43.478 0.00 0.00 32.90 1.40
47 48 4.813161 CAGATCTTCGCCACTGACATTTAT 59.187 41.667 0.00 0.00 32.90 1.40
48 49 5.985530 CAGATCTTCGCCACTGACATTTATA 59.014 40.000 0.00 0.00 32.90 0.98
49 50 6.648310 CAGATCTTCGCCACTGACATTTATAT 59.352 38.462 0.00 0.00 32.90 0.86
50 51 7.814587 CAGATCTTCGCCACTGACATTTATATA 59.185 37.037 0.00 0.00 32.90 0.86
51 52 7.815068 AGATCTTCGCCACTGACATTTATATAC 59.185 37.037 0.00 0.00 0.00 1.47
52 53 5.918576 TCTTCGCCACTGACATTTATATACG 59.081 40.000 0.00 0.00 0.00 3.06
53 54 5.441709 TCGCCACTGACATTTATATACGA 57.558 39.130 0.00 0.00 0.00 3.43
54 55 6.020971 TCGCCACTGACATTTATATACGAT 57.979 37.500 0.00 0.00 0.00 3.73
55 56 5.861787 TCGCCACTGACATTTATATACGATG 59.138 40.000 0.00 4.49 0.00 3.84
56 57 5.444613 CGCCACTGACATTTATATACGATGC 60.445 44.000 0.00 0.00 0.00 3.91
57 58 5.639506 GCCACTGACATTTATATACGATGCT 59.360 40.000 0.00 0.00 0.00 3.79
58 59 6.183360 GCCACTGACATTTATATACGATGCTC 60.183 42.308 0.00 4.38 0.00 4.26
59 60 6.311445 CCACTGACATTTATATACGATGCTCC 59.689 42.308 0.00 0.00 0.00 4.70
60 61 6.868339 CACTGACATTTATATACGATGCTCCA 59.132 38.462 0.00 2.57 0.00 3.86
61 62 7.384932 CACTGACATTTATATACGATGCTCCAA 59.615 37.037 0.00 0.00 0.00 3.53
62 63 7.931407 ACTGACATTTATATACGATGCTCCAAA 59.069 33.333 0.00 0.00 0.00 3.28
63 64 8.669946 TGACATTTATATACGATGCTCCAAAA 57.330 30.769 0.00 0.00 0.00 2.44
64 65 8.556194 TGACATTTATATACGATGCTCCAAAAC 58.444 33.333 0.00 0.00 0.00 2.43
65 66 8.445275 ACATTTATATACGATGCTCCAAAACA 57.555 30.769 0.00 0.00 0.00 2.83
66 67 9.066892 ACATTTATATACGATGCTCCAAAACAT 57.933 29.630 0.00 0.00 0.00 2.71
67 68 9.333497 CATTTATATACGATGCTCCAAAACATG 57.667 33.333 0.00 0.00 0.00 3.21
68 69 8.669946 TTTATATACGATGCTCCAAAACATGA 57.330 30.769 0.00 0.00 0.00 3.07
69 70 8.669946 TTATATACGATGCTCCAAAACATGAA 57.330 30.769 0.00 0.00 0.00 2.57
70 71 5.895636 ATACGATGCTCCAAAACATGAAA 57.104 34.783 0.00 0.00 0.00 2.69
71 72 4.164822 ACGATGCTCCAAAACATGAAAG 57.835 40.909 0.00 0.00 0.00 2.62
72 73 2.919229 CGATGCTCCAAAACATGAAAGC 59.081 45.455 0.00 0.00 37.83 3.51
73 74 3.612241 CGATGCTCCAAAACATGAAAGCA 60.612 43.478 0.00 5.38 45.48 3.91
74 75 3.096489 TGCTCCAAAACATGAAAGCAC 57.904 42.857 0.00 0.00 40.47 4.40
75 76 2.429971 TGCTCCAAAACATGAAAGCACA 59.570 40.909 0.00 0.00 40.47 4.57
76 77 3.069872 TGCTCCAAAACATGAAAGCACAT 59.930 39.130 0.00 0.00 40.47 3.21
77 78 6.309488 ATGCTCCAAAACATGAAAGCACATG 61.309 40.000 0.00 14.01 44.77 3.21
91 92 3.425577 GCACATGCTGCTAATTGCTAA 57.574 42.857 11.51 0.00 43.33 3.09
92 93 3.772932 GCACATGCTGCTAATTGCTAAA 58.227 40.909 11.51 0.00 43.33 1.85
93 94 4.175516 GCACATGCTGCTAATTGCTAAAA 58.824 39.130 11.51 0.00 43.33 1.52
94 95 4.032104 GCACATGCTGCTAATTGCTAAAAC 59.968 41.667 11.51 0.00 43.33 2.43
95 96 5.404946 CACATGCTGCTAATTGCTAAAACT 58.595 37.500 0.00 0.00 43.37 2.66
96 97 6.554419 CACATGCTGCTAATTGCTAAAACTA 58.446 36.000 0.00 0.00 43.37 2.24
97 98 6.470235 CACATGCTGCTAATTGCTAAAACTAC 59.530 38.462 0.00 0.00 43.37 2.73
98 99 5.216566 TGCTGCTAATTGCTAAAACTACG 57.783 39.130 0.00 0.00 43.37 3.51
99 100 4.094294 TGCTGCTAATTGCTAAAACTACGG 59.906 41.667 0.00 0.00 43.37 4.02
100 101 4.331717 GCTGCTAATTGCTAAAACTACGGA 59.668 41.667 0.00 0.00 43.37 4.69
101 102 5.726963 GCTGCTAATTGCTAAAACTACGGAC 60.727 44.000 0.00 0.00 43.37 4.79
102 103 5.239351 TGCTAATTGCTAAAACTACGGACA 58.761 37.500 0.00 0.00 43.37 4.02
103 104 5.701750 TGCTAATTGCTAAAACTACGGACAA 59.298 36.000 0.00 0.00 43.37 3.18
104 105 6.128391 TGCTAATTGCTAAAACTACGGACAAG 60.128 38.462 0.00 0.00 43.37 3.16
105 106 6.091713 GCTAATTGCTAAAACTACGGACAAGA 59.908 38.462 0.00 0.00 38.95 3.02
106 107 6.481954 AATTGCTAAAACTACGGACAAGAG 57.518 37.500 0.00 0.00 0.00 2.85
107 108 4.595762 TGCTAAAACTACGGACAAGAGT 57.404 40.909 0.00 0.00 0.00 3.24
108 109 4.553323 TGCTAAAACTACGGACAAGAGTC 58.447 43.478 0.00 0.00 44.21 3.36
109 110 3.607209 GCTAAAACTACGGACAAGAGTCG 59.393 47.826 0.00 0.00 45.92 4.18
110 111 2.719426 AAACTACGGACAAGAGTCGG 57.281 50.000 0.00 0.00 45.92 4.79
111 112 0.886563 AACTACGGACAAGAGTCGGG 59.113 55.000 7.85 0.00 46.08 5.14
112 113 1.139095 CTACGGACAAGAGTCGGGC 59.861 63.158 7.85 0.00 46.08 6.13
113 114 1.592400 CTACGGACAAGAGTCGGGCA 61.592 60.000 7.85 0.00 46.08 5.36
114 115 1.180456 TACGGACAAGAGTCGGGCAA 61.180 55.000 7.85 0.00 46.08 4.52
115 116 2.027625 CGGACAAGAGTCGGGCAAC 61.028 63.158 0.00 0.00 45.92 4.17
116 117 1.371558 GGACAAGAGTCGGGCAACT 59.628 57.895 0.00 0.00 45.92 3.16
117 118 0.670854 GGACAAGAGTCGGGCAACTC 60.671 60.000 10.36 10.36 45.92 3.01
131 132 2.644078 GCAACTCTGCTTTTCTTGACG 58.356 47.619 0.00 0.00 45.74 4.35
132 133 2.287915 GCAACTCTGCTTTTCTTGACGA 59.712 45.455 0.00 0.00 45.74 4.20
133 134 3.058639 GCAACTCTGCTTTTCTTGACGAT 60.059 43.478 0.00 0.00 45.74 3.73
134 135 4.706527 CAACTCTGCTTTTCTTGACGATC 58.293 43.478 0.00 0.00 0.00 3.69
135 136 4.264460 ACTCTGCTTTTCTTGACGATCT 57.736 40.909 0.00 0.00 0.00 2.75
136 137 3.993081 ACTCTGCTTTTCTTGACGATCTG 59.007 43.478 0.00 0.00 0.00 2.90
137 138 3.993081 CTCTGCTTTTCTTGACGATCTGT 59.007 43.478 0.00 0.00 0.00 3.41
138 139 5.134202 TCTGCTTTTCTTGACGATCTGTA 57.866 39.130 0.00 0.00 0.00 2.74
139 140 4.923871 TCTGCTTTTCTTGACGATCTGTAC 59.076 41.667 0.00 0.00 0.00 2.90
140 141 4.627058 TGCTTTTCTTGACGATCTGTACA 58.373 39.130 0.00 0.00 0.00 2.90
141 142 4.686091 TGCTTTTCTTGACGATCTGTACAG 59.314 41.667 17.17 17.17 0.00 2.74
142 143 4.923871 GCTTTTCTTGACGATCTGTACAGA 59.076 41.667 27.07 27.07 42.37 3.41
154 155 5.814764 ATCTGTACAGATTCGAGTACGTT 57.185 39.130 28.95 6.94 45.31 3.99
155 156 4.966249 TCTGTACAGATTCGAGTACGTTG 58.034 43.478 21.74 0.00 42.62 4.10
156 157 4.453478 TCTGTACAGATTCGAGTACGTTGT 59.547 41.667 21.74 0.00 42.62 3.32
157 158 5.049198 TCTGTACAGATTCGAGTACGTTGTT 60.049 40.000 21.74 0.00 42.62 2.83
158 159 4.913345 TGTACAGATTCGAGTACGTTGTTG 59.087 41.667 0.00 0.00 42.62 3.33
159 160 3.973657 ACAGATTCGAGTACGTTGTTGT 58.026 40.909 0.00 0.00 40.69 3.32
160 161 3.979495 ACAGATTCGAGTACGTTGTTGTC 59.021 43.478 0.00 0.00 40.69 3.18
161 162 4.227538 CAGATTCGAGTACGTTGTTGTCT 58.772 43.478 0.00 0.00 40.69 3.41
162 163 5.049198 ACAGATTCGAGTACGTTGTTGTCTA 60.049 40.000 0.00 0.00 40.69 2.59
163 164 5.283247 CAGATTCGAGTACGTTGTTGTCTAC 59.717 44.000 0.00 0.00 40.69 2.59
164 165 4.550577 TTCGAGTACGTTGTTGTCTACA 57.449 40.909 0.00 0.00 40.69 2.74
165 166 4.550577 TCGAGTACGTTGTTGTCTACAA 57.449 40.909 0.00 0.00 40.15 2.41
172 173 2.858158 GTTGTCTACAACGCCGGC 59.142 61.111 19.07 19.07 45.44 6.13
173 174 1.666872 GTTGTCTACAACGCCGGCT 60.667 57.895 26.68 8.22 45.44 5.52
174 175 1.666553 TTGTCTACAACGCCGGCTG 60.667 57.895 26.68 19.76 0.00 4.85
175 176 2.089887 TTGTCTACAACGCCGGCTGA 62.090 55.000 26.68 9.74 0.00 4.26
197 198 2.781595 AAGTAGGCAACCGAGGTGCG 62.782 60.000 7.66 0.00 40.47 5.34
232 233 1.075601 TTGACCCCTTGGCAGATCTT 58.924 50.000 0.00 0.00 33.59 2.40
272 273 1.616865 GCTGGGCAATACATCATGCAT 59.383 47.619 0.00 0.00 44.32 3.96
335 338 1.199097 GACCCGCAACATCGTCAATTT 59.801 47.619 0.00 0.00 0.00 1.82
418 421 9.489084 TGTTAGTATCATTGCATTGGTAGATAC 57.511 33.333 8.64 8.76 38.56 2.24
484 487 9.231297 TCATGATATATATCGCTAATCATCCGA 57.769 33.333 16.21 0.10 35.61 4.55
508 511 9.803130 CGAAATAATGTGTGACTCATGATATTC 57.197 33.333 0.43 5.71 0.00 1.75
568 788 0.558712 TAAAAGGGGCCACACAACCT 59.441 50.000 8.31 0.00 34.04 3.50
569 789 0.558712 AAAAGGGGCCACACAACCTA 59.441 50.000 8.31 0.00 31.88 3.08
570 790 0.558712 AAAGGGGCCACACAACCTAA 59.441 50.000 8.31 0.00 31.88 2.69
571 791 0.112412 AAGGGGCCACACAACCTAAG 59.888 55.000 8.31 0.00 31.88 2.18
572 792 0.770557 AGGGGCCACACAACCTAAGA 60.771 55.000 8.31 0.00 0.00 2.10
573 793 0.608308 GGGGCCACACAACCTAAGAC 60.608 60.000 4.39 0.00 0.00 3.01
574 794 0.953960 GGGCCACACAACCTAAGACG 60.954 60.000 4.39 0.00 0.00 4.18
575 795 0.953960 GGCCACACAACCTAAGACGG 60.954 60.000 0.00 0.00 0.00 4.79
576 796 0.953960 GCCACACAACCTAAGACGGG 60.954 60.000 0.00 0.00 0.00 5.28
577 797 0.395312 CCACACAACCTAAGACGGGT 59.605 55.000 0.00 0.00 38.94 5.28
578 798 1.607251 CCACACAACCTAAGACGGGTC 60.607 57.143 0.00 0.00 35.83 4.46
579 799 1.343465 CACACAACCTAAGACGGGTCT 59.657 52.381 0.00 0.00 42.75 3.85
581 801 2.436911 ACACAACCTAAGACGGGTCTTT 59.563 45.455 18.23 0.00 46.95 2.52
582 802 3.118149 ACACAACCTAAGACGGGTCTTTT 60.118 43.478 18.23 5.44 46.95 2.27
583 803 3.881089 CACAACCTAAGACGGGTCTTTTT 59.119 43.478 18.23 7.84 46.95 1.94
711 961 9.081997 GTGAATTGAGTTACAGTAGAGATCAAG 57.918 37.037 0.00 0.00 0.00 3.02
741 1003 6.670077 TGTACATATGATTTGCAGCGTTTA 57.330 33.333 10.38 0.00 0.00 2.01
764 1026 9.981114 TTTATTTCAAAGCTCTTAGAAAAAGGG 57.019 29.630 6.84 0.00 34.13 3.95
765 1027 7.839680 ATTTCAAAGCTCTTAGAAAAAGGGA 57.160 32.000 6.84 0.00 34.13 4.20
766 1028 7.654022 TTTCAAAGCTCTTAGAAAAAGGGAA 57.346 32.000 0.00 0.00 0.00 3.97
767 1029 6.635030 TCAAAGCTCTTAGAAAAAGGGAAC 57.365 37.500 0.00 0.00 0.00 3.62
905 1169 1.152963 ACGAAACAGCCAAGCAGGT 60.153 52.632 0.00 0.00 40.61 4.00
906 1170 0.751643 ACGAAACAGCCAAGCAGGTT 60.752 50.000 0.00 0.00 40.61 3.50
920 1186 3.317406 AGCAGGTTGGGGAAAAAGAAAT 58.683 40.909 0.00 0.00 0.00 2.17
1262 1539 2.665000 CTCCTTCTGCGGCTCCAA 59.335 61.111 0.00 0.00 0.00 3.53
1263 1540 1.222936 CTCCTTCTGCGGCTCCAAT 59.777 57.895 0.00 0.00 0.00 3.16
1744 2031 2.143876 AGTCCACTGTTTTTGCCTGT 57.856 45.000 0.00 0.00 0.00 4.00
1746 2033 3.214328 AGTCCACTGTTTTTGCCTGTAG 58.786 45.455 0.00 0.00 0.00 2.74
1788 2093 5.429158 CAGTTTCTGATTCCAAGCATTGCG 61.429 45.833 2.38 0.00 38.10 4.85
1806 2111 5.637006 TTGCGCATATTGACTTAAACCTT 57.363 34.783 12.75 0.00 0.00 3.50
1867 2172 1.060729 TCCCCGAATGTCCTGTTTCA 58.939 50.000 0.00 0.00 0.00 2.69
1923 2228 9.850628 CATATTGAACAAAATCACAAGACAGAT 57.149 29.630 0.00 0.00 0.00 2.90
2705 3017 4.425577 AAATTAAGGCTCTCAGTTTGCG 57.574 40.909 0.00 0.00 0.00 4.85
2857 3362 8.731275 TTTGTCTTCTAAGATTGTTCTTGTCA 57.269 30.769 0.00 0.00 42.25 3.58
2872 3377 6.037500 TGTTCTTGTCAGATGTTTGACTCAAG 59.962 38.462 7.56 4.47 46.00 3.02
2932 3445 7.307930 CGCATATGCTCATGTCCATTAAACTAA 60.308 37.037 24.56 0.00 39.32 2.24
2956 3469 2.175931 TGAGTCTGGCCCCTTTTTGTAA 59.824 45.455 0.00 0.00 0.00 2.41
2965 3478 6.019748 TGGCCCCTTTTTGTAAATGAGAATA 58.980 36.000 0.00 0.00 0.00 1.75
2966 3479 6.498651 TGGCCCCTTTTTGTAAATGAGAATAA 59.501 34.615 0.00 0.00 0.00 1.40
3009 3522 5.663106 AGCAAGATGGGACTTTCAGTATCTA 59.337 40.000 0.00 0.00 0.00 1.98
3010 3523 6.156949 AGCAAGATGGGACTTTCAGTATCTAA 59.843 38.462 0.00 0.00 0.00 2.10
3011 3524 6.481644 GCAAGATGGGACTTTCAGTATCTAAG 59.518 42.308 0.00 0.00 0.00 2.18
3012 3525 6.168270 AGATGGGACTTTCAGTATCTAAGC 57.832 41.667 0.00 0.00 0.00 3.09
3013 3526 5.663106 AGATGGGACTTTCAGTATCTAAGCA 59.337 40.000 0.00 0.00 0.00 3.91
3014 3527 5.086104 TGGGACTTTCAGTATCTAAGCAC 57.914 43.478 0.00 0.00 0.00 4.40
3015 3528 4.777896 TGGGACTTTCAGTATCTAAGCACT 59.222 41.667 0.00 0.00 0.00 4.40
3016 3529 5.248477 TGGGACTTTCAGTATCTAAGCACTT 59.752 40.000 0.00 0.00 0.00 3.16
3019 3532 7.492994 GGGACTTTCAGTATCTAAGCACTTAAG 59.507 40.741 0.00 0.00 0.00 1.85
3080 3593 8.801715 ATGATTGTTTGTTTCACATCTGTTAC 57.198 30.769 0.00 0.00 0.00 2.50
3097 3610 4.641396 TGTTACTCAATTGGGTCAGTCAG 58.359 43.478 15.87 0.00 0.00 3.51
3117 3632 4.457949 TCAGACTCACTGCTAACGTCATTA 59.542 41.667 0.00 0.00 45.38 1.90
3262 3777 1.607148 GTTGGCTACACTGAAACCCAC 59.393 52.381 0.00 0.00 0.00 4.61
3432 3947 1.322442 GGAAAGTTGCTGCTCACCTT 58.678 50.000 0.00 0.00 0.00 3.50
3532 4047 1.130373 GAAGGCAATTCGTTCGCATCA 59.870 47.619 0.00 0.00 31.03 3.07
3590 4105 7.888250 AAAAGCCCAGGATTTCTATAAGAAG 57.112 36.000 0.00 0.00 35.37 2.85
3894 4409 3.184581 CAGACAAAACAGCTCGGTTAGTC 59.815 47.826 11.43 11.43 36.75 2.59
4616 5131 7.094463 GGCTATCATAAAGACCCAAATCATGAG 60.094 40.741 0.09 0.00 0.00 2.90
4933 5448 3.806521 CAGATCCTGAAGATACGGCTTTG 59.193 47.826 0.00 0.00 34.42 2.77
4989 5504 8.047859 GTGTTTACTTGCAAGTTTTATTGAACG 58.952 33.333 35.20 4.64 40.37 3.95
5282 5798 6.646267 TCTTGTTTTAGTTATGCGGTAGGAT 58.354 36.000 0.00 0.00 0.00 3.24
5289 5805 3.573110 AGTTATGCGGTAGGATAGTGACC 59.427 47.826 0.00 0.00 32.26 4.02
5290 5806 2.082140 ATGCGGTAGGATAGTGACCA 57.918 50.000 0.00 0.00 32.39 4.02
5341 6020 3.142174 CTCCCTCCGATCCAAAATAAGC 58.858 50.000 0.00 0.00 0.00 3.09
5345 6024 3.194861 CTCCGATCCAAAATAAGCGTCA 58.805 45.455 0.00 0.00 0.00 4.35
5427 6106 6.374417 TGGAGGGAGTATTTTATAGGCATC 57.626 41.667 0.00 0.00 0.00 3.91
5428 6107 5.250774 TGGAGGGAGTATTTTATAGGCATCC 59.749 44.000 0.00 0.00 0.00 3.51
5429 6108 5.420409 GAGGGAGTATTTTATAGGCATCCG 58.580 45.833 0.00 0.00 0.00 4.18
5430 6109 3.939592 GGGAGTATTTTATAGGCATCCGC 59.060 47.826 0.00 0.00 37.44 5.54
5431 6110 4.564821 GGGAGTATTTTATAGGCATCCGCA 60.565 45.833 0.00 0.00 41.24 5.69
5432 6111 5.186198 GGAGTATTTTATAGGCATCCGCAT 58.814 41.667 0.00 0.00 41.24 4.73
5445 6124 4.142600 GGCATCCGCATAATACATCCTTTC 60.143 45.833 0.00 0.00 41.24 2.62
5504 6183 1.067565 TGCCTCTGATCGTCTTCACAC 60.068 52.381 0.00 0.00 0.00 3.82
5561 6240 4.397420 ACAGCTGTGTGATTCCAATTGTA 58.603 39.130 20.97 0.00 34.75 2.41
5673 6352 4.137543 AGCTTATGCAATGTACTTAGCCC 58.862 43.478 3.16 0.00 42.74 5.19
5824 6503 2.973082 GCACATGGCTTGTTCCCC 59.027 61.111 2.88 0.00 36.00 4.81
5838 6517 1.764571 TTCCCCTCCACTTGACCACG 61.765 60.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.673022 CTGTCACTGGGAGCTCTTGC 60.673 60.000 14.64 0.00 40.05 4.01
8 9 0.972134 TCTGTCACTGGGAGCTCTTG 59.028 55.000 14.64 6.64 0.00 3.02
9 10 1.830477 GATCTGTCACTGGGAGCTCTT 59.170 52.381 14.64 0.00 0.00 2.85
10 11 1.006998 AGATCTGTCACTGGGAGCTCT 59.993 52.381 14.64 0.00 0.00 4.09
11 12 1.484038 AGATCTGTCACTGGGAGCTC 58.516 55.000 4.71 4.71 0.00 4.09
12 13 1.830477 GAAGATCTGTCACTGGGAGCT 59.170 52.381 0.00 0.00 0.00 4.09
13 14 1.470632 CGAAGATCTGTCACTGGGAGC 60.471 57.143 0.00 0.00 0.00 4.70
14 15 1.470632 GCGAAGATCTGTCACTGGGAG 60.471 57.143 0.00 0.00 0.00 4.30
15 16 0.532573 GCGAAGATCTGTCACTGGGA 59.467 55.000 0.00 0.00 0.00 4.37
16 17 0.460987 GGCGAAGATCTGTCACTGGG 60.461 60.000 0.00 0.00 0.00 4.45
17 18 0.247460 TGGCGAAGATCTGTCACTGG 59.753 55.000 0.00 0.00 0.00 4.00
18 19 1.067283 AGTGGCGAAGATCTGTCACTG 60.067 52.381 17.00 0.00 34.65 3.66
19 20 1.067283 CAGTGGCGAAGATCTGTCACT 60.067 52.381 13.12 13.12 36.09 3.41
20 21 1.067565 TCAGTGGCGAAGATCTGTCAC 60.068 52.381 9.24 9.24 0.00 3.67
21 22 1.067565 GTCAGTGGCGAAGATCTGTCA 60.068 52.381 0.00 0.00 0.00 3.58
22 23 1.067565 TGTCAGTGGCGAAGATCTGTC 60.068 52.381 0.00 0.00 0.00 3.51
23 24 0.969149 TGTCAGTGGCGAAGATCTGT 59.031 50.000 0.00 0.00 0.00 3.41
24 25 2.306341 ATGTCAGTGGCGAAGATCTG 57.694 50.000 0.00 0.00 0.00 2.90
25 26 3.340814 AAATGTCAGTGGCGAAGATCT 57.659 42.857 0.00 0.00 0.00 2.75
26 27 7.201359 CGTATATAAATGTCAGTGGCGAAGATC 60.201 40.741 0.00 0.00 0.00 2.75
27 28 6.586463 CGTATATAAATGTCAGTGGCGAAGAT 59.414 38.462 0.00 0.00 0.00 2.40
28 29 5.918576 CGTATATAAATGTCAGTGGCGAAGA 59.081 40.000 0.00 0.00 0.00 2.87
29 30 5.918576 TCGTATATAAATGTCAGTGGCGAAG 59.081 40.000 0.00 0.00 0.00 3.79
30 31 5.834169 TCGTATATAAATGTCAGTGGCGAA 58.166 37.500 0.00 0.00 0.00 4.70
31 32 5.441709 TCGTATATAAATGTCAGTGGCGA 57.558 39.130 0.00 0.00 0.00 5.54
32 33 5.444613 GCATCGTATATAAATGTCAGTGGCG 60.445 44.000 7.74 0.00 0.00 5.69
33 34 5.639506 AGCATCGTATATAAATGTCAGTGGC 59.360 40.000 7.74 0.00 0.00 5.01
34 35 6.311445 GGAGCATCGTATATAAATGTCAGTGG 59.689 42.308 7.74 0.00 34.37 4.00
35 36 6.868339 TGGAGCATCGTATATAAATGTCAGTG 59.132 38.462 7.74 0.00 34.37 3.66
36 37 6.993079 TGGAGCATCGTATATAAATGTCAGT 58.007 36.000 7.74 0.00 34.37 3.41
37 38 7.889589 TTGGAGCATCGTATATAAATGTCAG 57.110 36.000 7.74 0.00 34.37 3.51
38 39 8.556194 GTTTTGGAGCATCGTATATAAATGTCA 58.444 33.333 7.74 3.50 34.37 3.58
39 40 8.556194 TGTTTTGGAGCATCGTATATAAATGTC 58.444 33.333 7.74 5.19 34.37 3.06
40 41 8.445275 TGTTTTGGAGCATCGTATATAAATGT 57.555 30.769 7.74 0.00 34.37 2.71
41 42 9.333497 CATGTTTTGGAGCATCGTATATAAATG 57.667 33.333 0.00 3.14 34.37 2.32
42 43 9.283768 TCATGTTTTGGAGCATCGTATATAAAT 57.716 29.630 0.00 0.00 34.37 1.40
43 44 8.669946 TCATGTTTTGGAGCATCGTATATAAA 57.330 30.769 0.00 0.00 34.37 1.40
44 45 8.669946 TTCATGTTTTGGAGCATCGTATATAA 57.330 30.769 0.00 0.00 34.37 0.98
45 46 8.669946 TTTCATGTTTTGGAGCATCGTATATA 57.330 30.769 0.00 0.00 34.37 0.86
46 47 7.566760 TTTCATGTTTTGGAGCATCGTATAT 57.433 32.000 0.00 0.00 34.37 0.86
47 48 6.458206 GCTTTCATGTTTTGGAGCATCGTATA 60.458 38.462 0.00 0.00 35.95 1.47
48 49 5.677091 GCTTTCATGTTTTGGAGCATCGTAT 60.677 40.000 0.00 0.00 35.95 3.06
49 50 4.379394 GCTTTCATGTTTTGGAGCATCGTA 60.379 41.667 0.00 0.00 35.95 3.43
50 51 3.612479 GCTTTCATGTTTTGGAGCATCGT 60.612 43.478 0.00 0.00 35.95 3.73
51 52 2.919229 GCTTTCATGTTTTGGAGCATCG 59.081 45.455 0.00 0.00 35.95 3.84
52 53 3.676646 GTGCTTTCATGTTTTGGAGCATC 59.323 43.478 0.00 0.00 42.61 3.91
53 54 3.069872 TGTGCTTTCATGTTTTGGAGCAT 59.930 39.130 0.00 0.00 42.61 3.79
54 55 2.429971 TGTGCTTTCATGTTTTGGAGCA 59.570 40.909 0.00 0.00 40.33 4.26
55 56 3.096489 TGTGCTTTCATGTTTTGGAGC 57.904 42.857 0.00 0.00 36.24 4.70
56 57 3.430895 GCATGTGCTTTCATGTTTTGGAG 59.569 43.478 14.68 0.00 44.68 3.86
57 58 3.391965 GCATGTGCTTTCATGTTTTGGA 58.608 40.909 14.68 0.00 44.68 3.53
58 59 3.799137 GCATGTGCTTTCATGTTTTGG 57.201 42.857 14.68 0.00 44.68 3.28
80 81 5.789710 TGTCCGTAGTTTTAGCAATTAGC 57.210 39.130 0.00 0.00 46.19 3.09
81 82 7.331193 ACTCTTGTCCGTAGTTTTAGCAATTAG 59.669 37.037 0.00 0.00 0.00 1.73
82 83 7.156673 ACTCTTGTCCGTAGTTTTAGCAATTA 58.843 34.615 0.00 0.00 0.00 1.40
83 84 5.995897 ACTCTTGTCCGTAGTTTTAGCAATT 59.004 36.000 0.00 0.00 0.00 2.32
84 85 5.548406 ACTCTTGTCCGTAGTTTTAGCAAT 58.452 37.500 0.00 0.00 0.00 3.56
85 86 4.952460 ACTCTTGTCCGTAGTTTTAGCAA 58.048 39.130 0.00 0.00 0.00 3.91
86 87 4.553323 GACTCTTGTCCGTAGTTTTAGCA 58.447 43.478 0.00 0.00 37.24 3.49
87 88 3.607209 CGACTCTTGTCCGTAGTTTTAGC 59.393 47.826 0.00 0.00 39.94 3.09
88 89 4.164294 CCGACTCTTGTCCGTAGTTTTAG 58.836 47.826 0.00 0.00 39.94 1.85
89 90 3.057315 CCCGACTCTTGTCCGTAGTTTTA 60.057 47.826 0.00 0.00 39.94 1.52
90 91 2.288640 CCCGACTCTTGTCCGTAGTTTT 60.289 50.000 0.00 0.00 39.94 2.43
91 92 1.271656 CCCGACTCTTGTCCGTAGTTT 59.728 52.381 0.00 0.00 39.94 2.66
92 93 0.886563 CCCGACTCTTGTCCGTAGTT 59.113 55.000 0.00 0.00 39.94 2.24
93 94 1.593296 GCCCGACTCTTGTCCGTAGT 61.593 60.000 0.00 0.00 39.94 2.73
94 95 1.139095 GCCCGACTCTTGTCCGTAG 59.861 63.158 0.00 0.00 39.94 3.51
95 96 1.180456 TTGCCCGACTCTTGTCCGTA 61.180 55.000 0.00 0.00 39.94 4.02
96 97 2.504274 TTGCCCGACTCTTGTCCGT 61.504 57.895 0.00 0.00 39.94 4.69
97 98 2.027625 GTTGCCCGACTCTTGTCCG 61.028 63.158 0.00 0.00 39.94 4.79
98 99 0.670854 GAGTTGCCCGACTCTTGTCC 60.671 60.000 8.16 0.00 42.18 4.02
99 100 2.828933 GAGTTGCCCGACTCTTGTC 58.171 57.895 8.16 0.00 42.18 3.18
112 113 4.450419 AGATCGTCAAGAAAAGCAGAGTTG 59.550 41.667 0.00 0.00 0.00 3.16
113 114 4.450419 CAGATCGTCAAGAAAAGCAGAGTT 59.550 41.667 0.00 0.00 0.00 3.01
114 115 3.993081 CAGATCGTCAAGAAAAGCAGAGT 59.007 43.478 0.00 0.00 0.00 3.24
115 116 3.993081 ACAGATCGTCAAGAAAAGCAGAG 59.007 43.478 0.00 0.00 0.00 3.35
116 117 3.995199 ACAGATCGTCAAGAAAAGCAGA 58.005 40.909 0.00 0.00 0.00 4.26
117 118 4.686091 TGTACAGATCGTCAAGAAAAGCAG 59.314 41.667 0.00 0.00 0.00 4.24
118 119 4.627058 TGTACAGATCGTCAAGAAAAGCA 58.373 39.130 0.00 0.00 0.00 3.91
119 120 4.923871 TCTGTACAGATCGTCAAGAAAAGC 59.076 41.667 21.74 0.00 31.41 3.51
120 121 7.462069 CGAATCTGTACAGATCGTCAAGAAAAG 60.462 40.741 33.01 13.10 46.75 2.27
121 122 6.308041 CGAATCTGTACAGATCGTCAAGAAAA 59.692 38.462 33.01 6.67 46.75 2.29
122 123 5.800438 CGAATCTGTACAGATCGTCAAGAAA 59.200 40.000 33.01 6.87 46.75 2.52
123 124 5.123344 TCGAATCTGTACAGATCGTCAAGAA 59.877 40.000 33.01 18.77 46.75 2.52
124 125 4.634443 TCGAATCTGTACAGATCGTCAAGA 59.366 41.667 33.01 22.42 46.75 3.02
125 126 4.909894 TCGAATCTGTACAGATCGTCAAG 58.090 43.478 33.01 20.94 46.75 3.02
126 127 4.395231 ACTCGAATCTGTACAGATCGTCAA 59.605 41.667 33.01 20.66 46.75 3.18
127 128 3.939592 ACTCGAATCTGTACAGATCGTCA 59.060 43.478 33.01 21.18 46.75 4.35
128 129 4.539509 ACTCGAATCTGTACAGATCGTC 57.460 45.455 33.01 26.26 46.75 4.20
129 130 4.025896 CGTACTCGAATCTGTACAGATCGT 60.026 45.833 33.01 26.68 46.75 3.73
130 131 4.025896 ACGTACTCGAATCTGTACAGATCG 60.026 45.833 33.01 31.67 42.50 3.69
131 132 5.406767 ACGTACTCGAATCTGTACAGATC 57.593 43.478 33.01 24.49 42.50 2.75
132 133 5.123502 ACAACGTACTCGAATCTGTACAGAT 59.876 40.000 28.95 28.95 43.80 2.90
133 134 4.453478 ACAACGTACTCGAATCTGTACAGA 59.547 41.667 27.07 27.07 39.00 3.41
134 135 4.720090 ACAACGTACTCGAATCTGTACAG 58.280 43.478 17.17 17.17 39.00 2.74
135 136 4.754372 ACAACGTACTCGAATCTGTACA 57.246 40.909 11.75 0.00 39.00 2.90
136 137 4.913924 ACAACAACGTACTCGAATCTGTAC 59.086 41.667 0.00 3.29 40.62 2.90
137 138 5.049198 AGACAACAACGTACTCGAATCTGTA 60.049 40.000 0.00 0.00 40.62 2.74
138 139 3.973657 ACAACAACGTACTCGAATCTGT 58.026 40.909 0.00 0.00 40.62 3.41
139 140 4.227538 AGACAACAACGTACTCGAATCTG 58.772 43.478 0.00 0.00 40.62 2.90
140 141 4.500603 AGACAACAACGTACTCGAATCT 57.499 40.909 0.00 0.00 40.62 2.40
141 142 5.149273 TGTAGACAACAACGTACTCGAATC 58.851 41.667 0.00 0.00 35.47 2.52
142 143 5.112220 TGTAGACAACAACGTACTCGAAT 57.888 39.130 0.00 0.00 35.47 3.34
143 144 4.550577 TGTAGACAACAACGTACTCGAA 57.449 40.909 0.00 0.00 35.47 3.71
144 145 4.550577 TTGTAGACAACAACGTACTCGA 57.449 40.909 0.00 0.00 43.22 4.04
156 157 1.666553 CAGCCGGCGTTGTAGACAA 60.667 57.895 23.20 0.00 0.00 3.18
157 158 2.048597 CAGCCGGCGTTGTAGACA 60.049 61.111 23.20 0.00 0.00 3.41
158 159 1.373748 TTCAGCCGGCGTTGTAGAC 60.374 57.895 23.20 0.00 0.00 2.59
159 160 1.373748 GTTCAGCCGGCGTTGTAGA 60.374 57.895 23.20 10.59 0.00 2.59
160 161 1.225376 TTGTTCAGCCGGCGTTGTAG 61.225 55.000 23.20 8.23 0.00 2.74
161 162 1.225376 CTTGTTCAGCCGGCGTTGTA 61.225 55.000 23.20 5.76 0.00 2.41
162 163 2.515057 TTGTTCAGCCGGCGTTGT 60.515 55.556 23.20 0.00 0.00 3.32
163 164 1.225376 TACTTGTTCAGCCGGCGTTG 61.225 55.000 23.20 15.74 0.00 4.10
164 165 0.949105 CTACTTGTTCAGCCGGCGTT 60.949 55.000 23.20 0.00 0.00 4.84
165 166 1.374252 CTACTTGTTCAGCCGGCGT 60.374 57.895 23.20 13.63 0.00 5.68
166 167 2.100631 CCTACTTGTTCAGCCGGCG 61.101 63.158 23.20 16.49 0.00 6.46
167 168 2.399356 GCCTACTTGTTCAGCCGGC 61.399 63.158 21.89 21.89 34.86 6.13
168 169 0.605319 TTGCCTACTTGTTCAGCCGG 60.605 55.000 0.00 0.00 0.00 6.13
169 170 0.517316 GTTGCCTACTTGTTCAGCCG 59.483 55.000 0.00 0.00 0.00 5.52
170 171 0.881796 GGTTGCCTACTTGTTCAGCC 59.118 55.000 0.00 0.00 0.00 4.85
171 172 0.517316 CGGTTGCCTACTTGTTCAGC 59.483 55.000 0.00 0.00 0.00 4.26
172 173 2.069273 CTCGGTTGCCTACTTGTTCAG 58.931 52.381 0.00 0.00 0.00 3.02
173 174 1.270625 CCTCGGTTGCCTACTTGTTCA 60.271 52.381 0.00 0.00 0.00 3.18
174 175 1.270678 ACCTCGGTTGCCTACTTGTTC 60.271 52.381 0.00 0.00 0.00 3.18
175 176 0.763035 ACCTCGGTTGCCTACTTGTT 59.237 50.000 0.00 0.00 0.00 2.83
232 233 2.481276 GCGTATGTGCCAGTGATACTCA 60.481 50.000 0.00 0.00 0.00 3.41
272 273 4.920999 TCATCTTGATGTCCATGAAACCA 58.079 39.130 10.01 0.00 33.42 3.67
335 338 2.115052 AAACTGGGCACGATGGCA 59.885 55.556 12.19 0.00 45.76 4.92
418 421 1.250154 ACGCCATGGTGGGAACAATG 61.250 55.000 28.34 1.90 46.06 2.82
508 511 6.949578 AACAAAAATGGATGTTTAGCGATG 57.050 33.333 0.00 0.00 36.39 3.84
570 790 4.884668 TGTATGAGAAAAAGACCCGTCT 57.115 40.909 0.00 0.00 42.75 4.18
571 791 5.175859 TGATGTATGAGAAAAAGACCCGTC 58.824 41.667 0.00 0.00 0.00 4.79
572 792 5.160607 TGATGTATGAGAAAAAGACCCGT 57.839 39.130 0.00 0.00 0.00 5.28
573 793 5.008019 CCATGATGTATGAGAAAAAGACCCG 59.992 44.000 0.00 0.00 39.21 5.28
574 794 5.221126 GCCATGATGTATGAGAAAAAGACCC 60.221 44.000 0.00 0.00 39.21 4.46
575 795 5.357878 TGCCATGATGTATGAGAAAAAGACC 59.642 40.000 0.00 0.00 39.21 3.85
576 796 6.441093 TGCCATGATGTATGAGAAAAAGAC 57.559 37.500 0.00 0.00 39.21 3.01
577 797 6.829811 TCATGCCATGATGTATGAGAAAAAGA 59.170 34.615 2.53 0.00 39.21 2.52
578 798 7.034685 TCATGCCATGATGTATGAGAAAAAG 57.965 36.000 2.53 0.00 39.21 2.27
654 903 7.307493 TGCAATTACTGACTCATAATGTCAC 57.693 36.000 0.00 0.00 39.23 3.67
711 961 9.265938 CGCTGCAAATCATATGTACATAAATAC 57.734 33.333 19.11 9.69 0.00 1.89
741 1003 7.839680 TCCCTTTTTCTAAGAGCTTTGAAAT 57.160 32.000 16.44 0.00 41.35 2.17
785 1047 9.403583 GGGTTCCCTTTTTCTTTTTCTTTTTAT 57.596 29.630 0.00 0.00 0.00 1.40
786 1048 8.383947 TGGGTTCCCTTTTTCTTTTTCTTTTTA 58.616 29.630 9.43 0.00 0.00 1.52
787 1049 7.175990 GTGGGTTCCCTTTTTCTTTTTCTTTTT 59.824 33.333 9.43 0.00 0.00 1.94
788 1050 6.657541 GTGGGTTCCCTTTTTCTTTTTCTTTT 59.342 34.615 9.43 0.00 0.00 2.27
789 1051 6.177610 GTGGGTTCCCTTTTTCTTTTTCTTT 58.822 36.000 9.43 0.00 0.00 2.52
790 1052 5.338871 GGTGGGTTCCCTTTTTCTTTTTCTT 60.339 40.000 9.43 0.00 0.00 2.52
791 1053 4.163458 GGTGGGTTCCCTTTTTCTTTTTCT 59.837 41.667 9.43 0.00 0.00 2.52
792 1054 4.448210 GGTGGGTTCCCTTTTTCTTTTTC 58.552 43.478 9.43 0.00 0.00 2.29
793 1055 3.118555 CGGTGGGTTCCCTTTTTCTTTTT 60.119 43.478 9.43 0.00 0.00 1.94
794 1056 2.432874 CGGTGGGTTCCCTTTTTCTTTT 59.567 45.455 9.43 0.00 0.00 2.27
795 1057 2.036387 CGGTGGGTTCCCTTTTTCTTT 58.964 47.619 9.43 0.00 0.00 2.52
796 1058 1.699730 CGGTGGGTTCCCTTTTTCTT 58.300 50.000 9.43 0.00 0.00 2.52
797 1059 0.178973 CCGGTGGGTTCCCTTTTTCT 60.179 55.000 9.43 0.00 0.00 2.52
798 1060 0.178984 TCCGGTGGGTTCCCTTTTTC 60.179 55.000 0.00 0.00 33.83 2.29
799 1061 0.468585 GTCCGGTGGGTTCCCTTTTT 60.469 55.000 0.00 0.00 33.83 1.94
800 1062 1.152138 GTCCGGTGGGTTCCCTTTT 59.848 57.895 0.00 0.00 33.83 2.27
801 1063 2.064242 CTGTCCGGTGGGTTCCCTTT 62.064 60.000 0.00 0.00 33.83 3.11
802 1064 2.448931 TGTCCGGTGGGTTCCCTT 60.449 61.111 0.00 0.00 33.83 3.95
803 1065 2.928396 CTGTCCGGTGGGTTCCCT 60.928 66.667 0.00 0.00 33.83 4.20
905 1169 5.130145 TCTGCTTTCATTTCTTTTTCCCCAA 59.870 36.000 0.00 0.00 0.00 4.12
906 1170 4.653341 TCTGCTTTCATTTCTTTTTCCCCA 59.347 37.500 0.00 0.00 0.00 4.96
910 1174 8.645487 CATTAGCTCTGCTTTCATTTCTTTTTC 58.355 33.333 0.00 0.00 40.44 2.29
920 1186 2.026915 TCTGCCATTAGCTCTGCTTTCA 60.027 45.455 0.00 0.00 44.23 2.69
1262 1539 4.123545 GCGGGTAGGGGTTGGCAT 62.124 66.667 0.00 0.00 0.00 4.40
1746 2033 9.220767 AGAAACTGTTCTTTTCTCACCATATAC 57.779 33.333 0.00 0.00 41.55 1.47
1788 2093 6.509418 TGTGGAAGGTTTAAGTCAATATGC 57.491 37.500 0.00 0.00 0.00 3.14
1806 2111 3.138283 GGTAAGATCCCCATTGATGTGGA 59.862 47.826 0.00 0.00 42.02 4.02
1896 2201 7.809331 TCTGTCTTGTGATTTTGTTCAATATGC 59.191 33.333 0.00 0.00 0.00 3.14
1923 2228 2.884639 GCCTGGCTTGAAACTGTTCTAA 59.115 45.455 12.43 0.00 34.60 2.10
2637 2949 6.494835 ACTTGGAATTCAGAAACCAAAGCTAT 59.505 34.615 19.22 6.75 41.00 2.97
2741 3053 6.146021 CCAACTTTTTGTGATTTCATGGCTAC 59.854 38.462 0.00 0.00 0.00 3.58
2851 3356 5.757320 ACTCTTGAGTCAAACATCTGACAAG 59.243 40.000 7.06 0.00 46.81 3.16
2857 3362 5.238214 GCAGAAACTCTTGAGTCAAACATCT 59.762 40.000 7.06 4.16 0.00 2.90
2872 3377 1.203287 GAGGCCCAAATGCAGAAACTC 59.797 52.381 0.00 0.00 0.00 3.01
2932 3445 1.068352 AAAAGGGGCCAGACTCACCT 61.068 55.000 4.39 0.00 0.00 4.00
2971 3484 5.047092 CCCATCTTGCTGTTCAGGTTTAAAT 60.047 40.000 1.97 0.00 0.00 1.40
2979 3492 2.486472 AGTCCCATCTTGCTGTTCAG 57.514 50.000 0.00 0.00 0.00 3.02
3039 3552 2.734755 TCATTCGCCATCCAGGAAAT 57.265 45.000 0.00 0.00 41.22 2.17
3080 3593 3.007290 TGAGTCTGACTGACCCAATTGAG 59.993 47.826 16.28 0.00 46.46 3.02
3097 3610 5.061064 CAGTTAATGACGTTAGCAGTGAGTC 59.939 44.000 0.00 0.00 0.00 3.36
3162 3677 5.346181 AGCCTCTTAGATACACAGAAACC 57.654 43.478 0.00 0.00 0.00 3.27
3189 3704 7.161404 AGAAGTTGCTGTATCTGAAACATACA 58.839 34.615 0.00 0.00 35.77 2.29
3262 3777 3.549299 ACAAAAATCTCTGCGCTTCAG 57.451 42.857 9.73 1.22 44.21 3.02
3432 3947 0.908910 ATGATTCGGCCACCAGTGTA 59.091 50.000 2.24 0.00 0.00 2.90
3532 4047 4.393680 GCACATTGCCATTGAAAATGTCAT 59.606 37.500 11.64 0.00 41.39 3.06
3590 4105 2.485814 GTCTGTCAATCTCTTGGCAACC 59.514 50.000 0.00 0.00 45.82 3.77
3894 4409 4.160252 CCCACCCTCACCAATTTCTTTATG 59.840 45.833 0.00 0.00 0.00 1.90
4616 5131 2.413837 TCAAGCAGCTTCCGTAAGTTC 58.586 47.619 4.07 0.00 34.99 3.01
4933 5448 7.063898 CCGTGAATATGACATTCCATCTATCAC 59.936 40.741 0.00 0.00 34.16 3.06
4989 5504 1.464997 GTACAGCCAGTTACTGCAAGC 59.535 52.381 6.88 5.43 38.79 4.01
5041 5556 7.224297 AGATAACATACGGCCAGAAATAACAT 58.776 34.615 2.24 0.00 0.00 2.71
5204 5720 0.108472 CAGAGGCATCTCAACGCTCA 60.108 55.000 0.00 0.00 42.34 4.26
5302 5818 6.439058 GGAGGGAGTAGCATCTAGACATTAAT 59.561 42.308 0.00 0.00 0.00 1.40
5341 6020 5.479716 AACCTTAGTTCAAAACTGTGACG 57.520 39.130 2.65 0.00 42.84 4.35
5375 6054 2.844122 AAGTGTCGCAGTTTTGAACC 57.156 45.000 0.00 0.00 0.00 3.62
5427 6106 3.814842 TGCTGAAAGGATGTATTATGCGG 59.185 43.478 0.00 0.00 0.00 5.69
5428 6107 4.512944 ACTGCTGAAAGGATGTATTATGCG 59.487 41.667 0.00 0.00 29.63 4.73
5429 6108 6.038603 TGAACTGCTGAAAGGATGTATTATGC 59.961 38.462 0.00 0.00 29.63 3.14
5430 6109 7.558161 TGAACTGCTGAAAGGATGTATTATG 57.442 36.000 0.00 0.00 29.63 1.90
5431 6110 8.757982 AATGAACTGCTGAAAGGATGTATTAT 57.242 30.769 0.00 0.00 29.63 1.28
5432 6111 8.579850 AAATGAACTGCTGAAAGGATGTATTA 57.420 30.769 0.00 0.00 29.63 0.98
5445 6124 5.469373 TGCGTAATAGAAATGAACTGCTG 57.531 39.130 0.00 0.00 0.00 4.41
5504 6183 6.270815 CCTCAAAAGGAATATGCAGATGTTG 58.729 40.000 0.00 0.00 46.67 3.33
5673 6352 2.436417 CCAGGGTTGTGGTGATAACAG 58.564 52.381 0.00 0.00 32.32 3.16
5816 6495 0.476771 GGTCAAGTGGAGGGGAACAA 59.523 55.000 0.00 0.00 0.00 2.83
5824 6503 1.224069 CTGTGCGTGGTCAAGTGGAG 61.224 60.000 0.00 0.00 0.00 3.86
5838 6517 6.381801 AGCACACTATTTTTGTAATCTGTGC 58.618 36.000 17.23 17.23 46.12 4.57


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

AutoCloner maintained by Alex Coulton.