Multiple sequence alignment - TraesCS5B01G021700

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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 TraesCS5B01G021700 chr5B 100.000 3771 0 0 1 3771 20670336 20666566 0.000000e+00 6964.0
1 TraesCS5B01G021700 chr5B 89.292 551 47 8 192 734 7205634 7205088 0.000000e+00 680.0
2 TraesCS5B01G021700 chr5B 88.561 542 53 7 192 731 607038051 607037517 0.000000e+00 649.0
3 TraesCS5B01G021700 chr5B 88.561 542 53 7 192 731 607094734 607094200 0.000000e+00 649.0
4 TraesCS5B01G021700 chr5B 98.462 325 5 0 1 325 20686546 20686222 1.170000e-159 573.0
5 TraesCS5B01G021700 chr5B 97.959 49 1 0 3723 3771 19630218 19630266 6.710000e-13 86.1
6 TraesCS5B01G021700 chr5B 96.000 50 1 1 3723 3771 20360093 20360142 3.120000e-11 80.5
7 TraesCS5B01G021700 chr5D 95.386 2601 77 11 733 3296 27616655 27614061 0.000000e+00 4098.0
8 TraesCS5B01G021700 chr5D 82.759 435 57 9 2430 2862 26923700 26923282 4.600000e-99 372.0
9 TraesCS5B01G021700 chr5D 94.220 173 9 1 3294 3466 27613990 27613819 2.890000e-66 263.0
10 TraesCS5B01G021700 chr5D 88.152 211 16 4 3458 3666 27613225 27613022 3.760000e-60 243.0
11 TraesCS5B01G021700 chr5D 88.298 94 3 5 3102 3195 27456022 27456107 5.150000e-19 106.0
12 TraesCS5B01G021700 chr5D 95.918 49 2 0 3723 3771 27437861 27437909 3.120000e-11 80.5
13 TraesCS5B01G021700 chr5D 95.745 47 1 1 3665 3711 27612983 27612938 1.450000e-09 75.0
14 TraesCS5B01G021700 chr5D 93.878 49 3 0 3723 3771 28481366 28481414 1.450000e-09 75.0
15 TraesCS5B01G021700 chr5D 95.556 45 2 0 2635 2679 27455957 27456001 5.220000e-09 73.1
16 TraesCS5B01G021700 chr6B 94.747 2532 84 16 733 3229 594856104 594853587 0.000000e+00 3893.0
17 TraesCS5B01G021700 chr6B 88.848 547 52 7 189 731 33327816 33328357 0.000000e+00 664.0
18 TraesCS5B01G021700 chr6B 78.571 238 33 15 3404 3630 594853427 594853197 1.410000e-29 141.0
19 TraesCS5B01G021700 chr4B 94.908 2239 80 9 817 3035 87009199 87011423 0.000000e+00 3472.0
20 TraesCS5B01G021700 chr4B 85.484 186 6 5 3049 3229 87011552 87011721 1.390000e-39 174.0
21 TraesCS5B01G021700 chr4B 96.491 57 2 0 733 789 87008840 87008896 1.120000e-15 95.3
22 TraesCS5B01G021700 chr5A 95.469 1589 58 5 732 2317 18908030 18906453 0.000000e+00 2523.0
23 TraesCS5B01G021700 chr5A 93.016 988 33 7 2315 3283 18906361 18905391 0.000000e+00 1410.0
24 TraesCS5B01G021700 chr5A 92.727 110 6 1 3559 3666 18904050 18903941 1.400000e-34 158.0
25 TraesCS5B01G021700 chr5A 92.857 56 4 0 3213 3268 18905354 18905299 8.680000e-12 82.4
26 TraesCS5B01G021700 chr5A 100.000 29 0 0 3102 3130 18787036 18787064 2.000000e-03 54.7
27 TraesCS5B01G021700 chr7B 90.959 542 41 7 193 731 14690499 14691035 0.000000e+00 723.0
28 TraesCS5B01G021700 chrUn 90.459 545 45 5 191 734 41985616 41985078 0.000000e+00 712.0
29 TraesCS5B01G021700 chr3B 90.459 545 45 5 191 734 800116799 800116261 0.000000e+00 712.0
30 TraesCS5B01G021700 chr4A 88.192 542 48 11 192 731 656914749 656915276 1.910000e-177 632.0
31 TraesCS5B01G021700 chr7D 87.868 544 56 7 192 734 19912971 19912437 6.870000e-177 630.0


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 TraesCS5B01G021700 chr5B 20666566 20670336 3770 True 6964.00 6964 100.000000 1 3771 1 chr5B.!!$R2 3770
1 TraesCS5B01G021700 chr5B 7205088 7205634 546 True 680.00 680 89.292000 192 734 1 chr5B.!!$R1 542
2 TraesCS5B01G021700 chr5B 607037517 607038051 534 True 649.00 649 88.561000 192 731 1 chr5B.!!$R4 539
3 TraesCS5B01G021700 chr5B 607094200 607094734 534 True 649.00 649 88.561000 192 731 1 chr5B.!!$R5 539
4 TraesCS5B01G021700 chr5D 27612938 27616655 3717 True 1169.75 4098 93.375750 733 3711 4 chr5D.!!$R2 2978
5 TraesCS5B01G021700 chr6B 594853197 594856104 2907 True 2017.00 3893 86.659000 733 3630 2 chr6B.!!$R1 2897
6 TraesCS5B01G021700 chr6B 33327816 33328357 541 False 664.00 664 88.848000 189 731 1 chr6B.!!$F1 542
7 TraesCS5B01G021700 chr4B 87008840 87011721 2881 False 1247.10 3472 92.294333 733 3229 3 chr4B.!!$F1 2496
8 TraesCS5B01G021700 chr5A 18903941 18908030 4089 True 1043.35 2523 93.517250 732 3666 4 chr5A.!!$R1 2934
9 TraesCS5B01G021700 chr7B 14690499 14691035 536 False 723.00 723 90.959000 193 731 1 chr7B.!!$F1 538
10 TraesCS5B01G021700 chrUn 41985078 41985616 538 True 712.00 712 90.459000 191 734 1 chrUn.!!$R1 543
11 TraesCS5B01G021700 chr3B 800116261 800116799 538 True 712.00 712 90.459000 191 734 1 chr3B.!!$R1 543
12 TraesCS5B01G021700 chr4A 656914749 656915276 527 False 632.00 632 88.192000 192 731 1 chr4A.!!$F1 539
13 TraesCS5B01G021700 chr7D 19912437 19912971 534 True 630.00 630 87.868000 192 734 1 chr7D.!!$R1 542

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
54 55 0.031585 GAACAAGTTTTCACCCCGGC 59.968 55.0 0.00 0.00 0.0 6.13 F
62 63 0.034863 TTTCACCCCGGCCATTACTC 60.035 55.0 2.24 0.00 0.0 2.59 F
160 161 0.094730 GAAATGGTCGTCCGAAAGCG 59.905 55.0 0.00 0.00 36.3 4.68 F
497 500 0.177373 GCCCTTTAGTCCCGATTCGT 59.823 55.0 5.20 0.00 0.0 3.85 F
549 563 0.481128 AACACTAACCCCAACCCCTG 59.519 55.0 0.00 0.00 0.0 4.45 F
2085 2381 0.857287 GCTTTCACTTTTGCTGCTGC 59.143 50.0 8.89 8.89 40.2 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 1903 0.773644 ATGCCAAGGAACTGACCACT 59.226 50.000 0.00 0.0 40.86 4.00 R
1748 2044 5.965033 ATGACATCCCATAAGACAAGTCT 57.035 39.130 0.00 0.0 42.75 3.24 R
2085 2381 6.358030 GCGAAAATATGACATTCGATTCAAGG 59.642 38.462 11.96 0.0 46.50 3.61 R
2479 2875 2.575735 TGTGGGAACAATAGCAGGATCA 59.424 45.455 0.00 0.0 46.06 2.92 R
2760 3156 1.272769 CCACTAGCTTCTATACCGGGC 59.727 57.143 6.32 0.0 0.00 6.13 R
3161 3682 1.335182 CTCGATCTCTGCCGAAGCTAA 59.665 52.381 0.00 0.0 40.80 3.09 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
33 34 3.423154 CCGCCGGCTTGACAAGTC 61.423 66.667 26.68 13.30 0.00 3.01
34 35 2.664851 CGCCGGCTTGACAAGTCA 60.665 61.111 26.68 0.00 37.91 3.41
35 36 2.671177 CGCCGGCTTGACAAGTCAG 61.671 63.158 26.68 9.54 41.13 3.51
36 37 1.301716 GCCGGCTTGACAAGTCAGA 60.302 57.895 22.15 0.00 41.13 3.27
37 38 0.884704 GCCGGCTTGACAAGTCAGAA 60.885 55.000 22.15 0.00 41.13 3.02
38 39 0.868406 CCGGCTTGACAAGTCAGAAC 59.132 55.000 19.32 0.55 41.13 3.01
39 40 1.581934 CGGCTTGACAAGTCAGAACA 58.418 50.000 19.32 0.00 41.13 3.18
40 41 1.939934 CGGCTTGACAAGTCAGAACAA 59.060 47.619 19.32 0.00 41.13 2.83
41 42 2.032549 CGGCTTGACAAGTCAGAACAAG 60.033 50.000 19.32 0.00 41.13 3.16
42 43 2.945668 GGCTTGACAAGTCAGAACAAGT 59.054 45.455 14.92 0.00 41.13 3.16
43 44 3.378427 GGCTTGACAAGTCAGAACAAGTT 59.622 43.478 14.92 0.00 41.13 2.66
44 45 4.142381 GGCTTGACAAGTCAGAACAAGTTT 60.142 41.667 14.92 0.00 41.13 2.66
45 46 5.402398 GCTTGACAAGTCAGAACAAGTTTT 58.598 37.500 16.39 0.00 41.13 2.43
46 47 5.513141 GCTTGACAAGTCAGAACAAGTTTTC 59.487 40.000 16.39 0.00 41.13 2.29
47 48 6.567687 TTGACAAGTCAGAACAAGTTTTCA 57.432 33.333 2.87 0.00 41.13 2.69
48 49 5.938322 TGACAAGTCAGAACAAGTTTTCAC 58.062 37.500 0.00 0.00 34.14 3.18
49 50 5.106317 TGACAAGTCAGAACAAGTTTTCACC 60.106 40.000 0.00 0.00 34.14 4.02
50 51 4.157840 ACAAGTCAGAACAAGTTTTCACCC 59.842 41.667 0.00 0.00 0.00 4.61
51 52 3.288092 AGTCAGAACAAGTTTTCACCCC 58.712 45.455 0.00 0.00 0.00 4.95
52 53 2.032924 GTCAGAACAAGTTTTCACCCCG 59.967 50.000 0.00 0.00 0.00 5.73
53 54 1.336755 CAGAACAAGTTTTCACCCCGG 59.663 52.381 0.00 0.00 0.00 5.73
54 55 0.031585 GAACAAGTTTTCACCCCGGC 59.968 55.000 0.00 0.00 0.00 6.13
55 56 1.396607 AACAAGTTTTCACCCCGGCC 61.397 55.000 0.00 0.00 0.00 6.13
56 57 1.830408 CAAGTTTTCACCCCGGCCA 60.830 57.895 2.24 0.00 0.00 5.36
57 58 1.155155 AAGTTTTCACCCCGGCCAT 59.845 52.632 2.24 0.00 0.00 4.40
58 59 0.471022 AAGTTTTCACCCCGGCCATT 60.471 50.000 2.24 0.00 0.00 3.16
59 60 0.406361 AGTTTTCACCCCGGCCATTA 59.594 50.000 2.24 0.00 0.00 1.90
60 61 0.528924 GTTTTCACCCCGGCCATTAC 59.471 55.000 2.24 0.00 0.00 1.89
61 62 0.406361 TTTTCACCCCGGCCATTACT 59.594 50.000 2.24 0.00 0.00 2.24
62 63 0.034863 TTTCACCCCGGCCATTACTC 60.035 55.000 2.24 0.00 0.00 2.59
63 64 1.202099 TTCACCCCGGCCATTACTCA 61.202 55.000 2.24 0.00 0.00 3.41
64 65 0.986019 TCACCCCGGCCATTACTCAT 60.986 55.000 2.24 0.00 0.00 2.90
65 66 0.535102 CACCCCGGCCATTACTCATC 60.535 60.000 2.24 0.00 0.00 2.92
66 67 0.986019 ACCCCGGCCATTACTCATCA 60.986 55.000 2.24 0.00 0.00 3.07
67 68 0.250467 CCCCGGCCATTACTCATCAG 60.250 60.000 2.24 0.00 0.00 2.90
68 69 0.886490 CCCGGCCATTACTCATCAGC 60.886 60.000 2.24 0.00 0.00 4.26
69 70 0.179048 CCGGCCATTACTCATCAGCA 60.179 55.000 2.24 0.00 0.00 4.41
70 71 0.940126 CGGCCATTACTCATCAGCAC 59.060 55.000 2.24 0.00 0.00 4.40
71 72 1.312815 GGCCATTACTCATCAGCACC 58.687 55.000 0.00 0.00 0.00 5.01
72 73 1.408683 GGCCATTACTCATCAGCACCA 60.409 52.381 0.00 0.00 0.00 4.17
73 74 2.368439 GCCATTACTCATCAGCACCAA 58.632 47.619 0.00 0.00 0.00 3.67
74 75 2.357009 GCCATTACTCATCAGCACCAAG 59.643 50.000 0.00 0.00 0.00 3.61
75 76 3.877559 CCATTACTCATCAGCACCAAGA 58.122 45.455 0.00 0.00 0.00 3.02
76 77 3.624861 CCATTACTCATCAGCACCAAGAC 59.375 47.826 0.00 0.00 0.00 3.01
77 78 2.654749 TACTCATCAGCACCAAGACG 57.345 50.000 0.00 0.00 0.00 4.18
78 79 0.681733 ACTCATCAGCACCAAGACGT 59.318 50.000 0.00 0.00 0.00 4.34
79 80 1.073964 CTCATCAGCACCAAGACGTG 58.926 55.000 0.00 0.00 36.80 4.49
105 106 4.966787 AACCGCACCACCGCCATT 62.967 61.111 0.00 0.00 0.00 3.16
108 109 3.361158 CGCACCACCGCCATTGAA 61.361 61.111 0.00 0.00 0.00 2.69
109 110 2.913765 CGCACCACCGCCATTGAAA 61.914 57.895 0.00 0.00 0.00 2.69
110 111 1.080569 GCACCACCGCCATTGAAAG 60.081 57.895 0.00 0.00 0.00 2.62
111 112 1.080569 CACCACCGCCATTGAAAGC 60.081 57.895 0.00 0.00 0.00 3.51
112 113 2.275380 ACCACCGCCATTGAAAGCC 61.275 57.895 0.00 0.00 0.00 4.35
113 114 2.274645 CCACCGCCATTGAAAGCCA 61.275 57.895 0.00 0.00 0.00 4.75
114 115 1.606885 CCACCGCCATTGAAAGCCAT 61.607 55.000 0.00 0.00 0.00 4.40
115 116 1.102154 CACCGCCATTGAAAGCCATA 58.898 50.000 0.00 0.00 0.00 2.74
116 117 1.102978 ACCGCCATTGAAAGCCATAC 58.897 50.000 0.00 0.00 0.00 2.39
117 118 0.385390 CCGCCATTGAAAGCCATACC 59.615 55.000 0.00 0.00 0.00 2.73
118 119 0.385390 CGCCATTGAAAGCCATACCC 59.615 55.000 0.00 0.00 0.00 3.69
119 120 0.752658 GCCATTGAAAGCCATACCCC 59.247 55.000 0.00 0.00 0.00 4.95
120 121 1.689258 GCCATTGAAAGCCATACCCCT 60.689 52.381 0.00 0.00 0.00 4.79
121 122 2.750814 CCATTGAAAGCCATACCCCTT 58.249 47.619 0.00 0.00 0.00 3.95
122 123 2.695147 CCATTGAAAGCCATACCCCTTC 59.305 50.000 0.00 0.00 0.00 3.46
123 124 2.525105 TTGAAAGCCATACCCCTTCC 57.475 50.000 0.00 0.00 0.00 3.46
124 125 1.377690 TGAAAGCCATACCCCTTCCA 58.622 50.000 0.00 0.00 0.00 3.53
125 126 1.005450 TGAAAGCCATACCCCTTCCAC 59.995 52.381 0.00 0.00 0.00 4.02
126 127 0.335019 AAAGCCATACCCCTTCCACC 59.665 55.000 0.00 0.00 0.00 4.61
127 128 0.849094 AAGCCATACCCCTTCCACCA 60.849 55.000 0.00 0.00 0.00 4.17
128 129 0.627469 AGCCATACCCCTTCCACCAT 60.627 55.000 0.00 0.00 0.00 3.55
129 130 0.468029 GCCATACCCCTTCCACCATG 60.468 60.000 0.00 0.00 0.00 3.66
130 131 0.468029 CCATACCCCTTCCACCATGC 60.468 60.000 0.00 0.00 0.00 4.06
131 132 0.552848 CATACCCCTTCCACCATGCT 59.447 55.000 0.00 0.00 0.00 3.79
132 133 0.552848 ATACCCCTTCCACCATGCTG 59.447 55.000 0.00 0.00 0.00 4.41
133 134 2.210144 TACCCCTTCCACCATGCTGC 62.210 60.000 0.00 0.00 0.00 5.25
134 135 2.757099 CCCTTCCACCATGCTGCC 60.757 66.667 0.00 0.00 0.00 4.85
135 136 2.757099 CCTTCCACCATGCTGCCC 60.757 66.667 0.00 0.00 0.00 5.36
136 137 2.036098 CTTCCACCATGCTGCCCA 59.964 61.111 0.00 0.00 0.00 5.36
137 138 2.283101 TTCCACCATGCTGCCCAC 60.283 61.111 0.00 0.00 0.00 4.61
138 139 3.144121 TTCCACCATGCTGCCCACA 62.144 57.895 0.00 0.00 0.00 4.17
139 140 2.363276 CCACCATGCTGCCCACAT 60.363 61.111 0.00 0.00 0.00 3.21
140 141 2.717044 CCACCATGCTGCCCACATG 61.717 63.158 0.00 0.00 43.67 3.21
143 144 4.021559 CATGCTGCCCACATGGAA 57.978 55.556 0.00 0.00 40.99 3.53
144 145 2.278849 CATGCTGCCCACATGGAAA 58.721 52.632 0.00 0.00 40.99 3.13
145 146 0.828022 CATGCTGCCCACATGGAAAT 59.172 50.000 0.00 0.00 40.99 2.17
146 147 0.828022 ATGCTGCCCACATGGAAATG 59.172 50.000 0.00 0.00 37.39 2.32
147 148 1.259142 TGCTGCCCACATGGAAATGG 61.259 55.000 0.00 0.00 37.39 3.16
148 149 1.259840 GCTGCCCACATGGAAATGGT 61.260 55.000 0.00 0.00 37.39 3.55
149 150 0.819582 CTGCCCACATGGAAATGGTC 59.180 55.000 0.00 0.00 37.39 4.02
150 151 0.964860 TGCCCACATGGAAATGGTCG 60.965 55.000 0.00 0.00 37.39 4.79
151 152 0.965363 GCCCACATGGAAATGGTCGT 60.965 55.000 0.00 0.00 37.39 4.34
152 153 1.094785 CCCACATGGAAATGGTCGTC 58.905 55.000 0.00 0.00 37.39 4.20
153 154 1.094785 CCACATGGAAATGGTCGTCC 58.905 55.000 0.00 0.00 37.39 4.79
154 155 0.726827 CACATGGAAATGGTCGTCCG 59.273 55.000 0.00 0.00 36.65 4.79
155 156 0.611200 ACATGGAAATGGTCGTCCGA 59.389 50.000 0.00 0.00 36.65 4.55
156 157 1.002659 ACATGGAAATGGTCGTCCGAA 59.997 47.619 0.00 0.00 36.65 4.30
157 158 2.080693 CATGGAAATGGTCGTCCGAAA 58.919 47.619 0.00 0.00 36.65 3.46
158 159 1.803334 TGGAAATGGTCGTCCGAAAG 58.197 50.000 0.00 0.00 36.65 2.62
159 160 0.446616 GGAAATGGTCGTCCGAAAGC 59.553 55.000 0.00 0.00 36.30 3.51
160 161 0.094730 GAAATGGTCGTCCGAAAGCG 59.905 55.000 0.00 0.00 36.30 4.68
161 162 1.908066 AAATGGTCGTCCGAAAGCGC 61.908 55.000 0.00 0.00 36.30 5.92
163 164 4.736896 GGTCGTCCGAAAGCGCCT 62.737 66.667 2.29 0.00 35.83 5.52
164 165 3.479269 GTCGTCCGAAAGCGCCTG 61.479 66.667 2.29 0.00 35.83 4.85
165 166 3.676605 TCGTCCGAAAGCGCCTGA 61.677 61.111 2.29 0.00 35.83 3.86
166 167 3.181967 CGTCCGAAAGCGCCTGAG 61.182 66.667 2.29 0.00 35.83 3.35
167 168 3.491652 GTCCGAAAGCGCCTGAGC 61.492 66.667 2.29 0.00 35.83 4.26
205 207 4.020485 ACGAGCACCCACTAGTAGAAAAAT 60.020 41.667 3.59 0.00 0.00 1.82
266 268 0.442310 CGGCACTAACGTGACCATTG 59.558 55.000 0.00 0.00 46.84 2.82
271 273 1.071699 ACTAACGTGACCATTGGTGCT 59.928 47.619 14.44 0.00 35.25 4.40
277 279 0.478072 TGACCATTGGTGCTGGTTCT 59.522 50.000 14.44 0.00 46.95 3.01
348 350 1.069823 TGGCACGAACCGGTACTAAAA 59.930 47.619 8.00 0.00 0.00 1.52
451 453 1.746470 AACCTATAGTGCCGGTTTGC 58.254 50.000 1.90 0.00 37.76 3.68
452 454 0.616371 ACCTATAGTGCCGGTTTGCA 59.384 50.000 1.90 0.00 39.37 4.08
478 481 2.292828 ACTGGGACAAAATGGGTCTG 57.707 50.000 0.00 0.00 38.70 3.51
479 482 0.890683 CTGGGACAAAATGGGTCTGC 59.109 55.000 0.00 0.00 38.70 4.26
492 495 1.262640 GGTCTGCCCTTTAGTCCCGA 61.263 60.000 0.00 0.00 0.00 5.14
495 498 1.485066 TCTGCCCTTTAGTCCCGATTC 59.515 52.381 0.00 0.00 0.00 2.52
497 500 0.177373 GCCCTTTAGTCCCGATTCGT 59.823 55.000 5.20 0.00 0.00 3.85
499 502 1.206371 CCCTTTAGTCCCGATTCGTGT 59.794 52.381 5.20 0.00 0.00 4.49
533 536 6.399639 GACTAAAGGTCCCATTTTCAAACA 57.600 37.500 0.00 0.00 38.93 2.83
537 540 6.800072 AAAGGTCCCATTTTCAAACACTAA 57.200 33.333 0.00 0.00 0.00 2.24
549 563 0.481128 AACACTAACCCCAACCCCTG 59.519 55.000 0.00 0.00 0.00 4.45
556 570 3.411517 CCCAACCCCTGATCGCCT 61.412 66.667 0.00 0.00 0.00 5.52
574 588 6.879188 TCGCCTTTTCAGTTTTGTAAAAAG 57.121 33.333 0.00 0.00 38.07 2.27
575 589 6.391537 TCGCCTTTTCAGTTTTGTAAAAAGT 58.608 32.000 0.00 0.00 37.13 2.66
955 1248 7.994425 TCTTTTCTTGCACCTGAATTGTATA 57.006 32.000 0.00 0.00 0.00 1.47
1168 1461 1.266989 CCTTGTTGACCTTCGCCTTTC 59.733 52.381 0.00 0.00 0.00 2.62
1206 1499 9.582648 TGAGCTTGTATCATACTAACTGGTATA 57.417 33.333 0.00 0.00 31.96 1.47
1314 1607 7.122204 GGTATGCTGTAGGTTGTTCCTTAAATT 59.878 37.037 0.00 0.00 45.67 1.82
1338 1631 2.674852 ACATATGTTGCTCAACTGCGAG 59.325 45.455 1.41 3.69 41.67 5.03
1355 1648 2.032030 GCGAGTTTTGCACTTGAGCTTA 60.032 45.455 0.00 0.00 39.12 3.09
1481 1774 4.082841 GCTTAGTATAGGAAGTACCGGAGC 60.083 50.000 9.46 0.00 44.74 4.70
1492 1785 3.907221 AGTACCGGAGCCTTGTAATAGA 58.093 45.455 9.46 0.00 0.00 1.98
1493 1786 4.284178 AGTACCGGAGCCTTGTAATAGAA 58.716 43.478 9.46 0.00 0.00 2.10
1526 1819 8.886719 TCATGTATTGACTGCTTTGAGATAAAG 58.113 33.333 0.00 0.00 0.00 1.85
1607 1903 5.048083 GCAGTGGTTGAGTTCATTTGGATTA 60.048 40.000 0.00 0.00 0.00 1.75
1721 2017 3.243737 GGGTTCCAACATTCTTTGGTCAC 60.244 47.826 1.94 1.29 45.60 3.67
1858 2154 6.348868 GGGTCTCAGATTTGTTTTCAGATGAC 60.349 42.308 0.00 0.00 0.00 3.06
2085 2381 0.857287 GCTTTCACTTTTGCTGCTGC 59.143 50.000 8.89 8.89 40.20 5.25
2249 2545 2.674796 ACGTCTTGGAAGCAGGTATC 57.325 50.000 0.00 0.00 0.00 2.24
2258 2554 5.249780 TGGAAGCAGGTATCCAGTTTTTA 57.750 39.130 0.00 0.00 40.74 1.52
2479 2875 3.149196 CATAGCCTTGTGTGGAAGTGTT 58.851 45.455 0.00 0.00 0.00 3.32
2760 3156 0.172352 GAGTTCCTGCTCTCCGTCTG 59.828 60.000 0.00 0.00 32.99 3.51
2786 3182 4.341520 CGGTATAGAAGCTAGTGGGACTTT 59.658 45.833 0.00 0.00 0.00 2.66
2902 3299 5.794894 TCCTGTGTAAGTCCTGAATTTCTC 58.205 41.667 0.00 0.00 0.00 2.87
2950 3351 4.223144 AGCTCCAAACACCCTTTTAACAT 58.777 39.130 0.00 0.00 0.00 2.71
2951 3352 4.039124 AGCTCCAAACACCCTTTTAACATG 59.961 41.667 0.00 0.00 0.00 3.21
2958 3359 7.928706 CCAAACACCCTTTTAACATGTGATTAA 59.071 33.333 0.00 0.00 0.00 1.40
2999 3400 4.701651 TGACCAGGAACAATATGAGCTTTG 59.298 41.667 0.00 0.00 0.00 2.77
3024 3425 5.239963 TCTTCCATACAGCATGCACATTATG 59.760 40.000 21.98 17.88 42.53 1.90
3031 3432 4.034394 ACAGCATGCACATTATGTTACTCG 59.966 41.667 21.98 0.00 42.53 4.18
3063 3579 1.899142 GGCCTGGCTTTTGGTTGATTA 59.101 47.619 19.68 0.00 0.00 1.75
3171 3692 0.378610 GTGGCATCTTTAGCTTCGGC 59.621 55.000 0.00 0.00 42.17 5.54
3233 3754 4.574674 AATGGTTCAATAGGAGACAGCA 57.425 40.909 0.00 0.00 0.00 4.41
3278 3799 4.079253 GTTGGAACATGACCCATAGTTGT 58.921 43.478 0.00 0.00 39.30 3.32
3314 3996 3.015327 GGCTTCTAGGACTCGTAACTGA 58.985 50.000 0.00 0.00 0.00 3.41
3316 3998 4.098196 GGCTTCTAGGACTCGTAACTGATT 59.902 45.833 0.00 0.00 0.00 2.57
3369 4051 2.076100 CTTTACATTGCTGAGCCGTGA 58.924 47.619 12.20 0.00 0.00 4.35
3484 5056 3.055719 CTGCCGTTGCCCGTCAAT 61.056 61.111 0.00 0.00 36.99 2.57
3489 5061 1.414378 CCGTTGCCCGTCAATTTTTC 58.586 50.000 0.00 0.00 36.99 2.29
3499 5071 4.024977 CCCGTCAATTTTTCTTGGCAAAAG 60.025 41.667 0.00 0.00 30.02 2.27
3508 5165 8.816640 ATTTTTCTTGGCAAAAGTAGTATGTG 57.183 30.769 0.00 0.00 0.00 3.21
3509 5166 5.371115 TTCTTGGCAAAAGTAGTATGTGC 57.629 39.130 0.00 0.00 34.42 4.57
3517 5174 7.773224 TGGCAAAAGTAGTATGTGCTATAACAT 59.227 33.333 0.00 0.00 43.21 2.71
3518 5175 9.268268 GGCAAAAGTAGTATGTGCTATAACATA 57.732 33.333 0.00 0.00 41.09 2.29
3551 5208 3.640407 GTGAGGCTGGGGCTGTGA 61.640 66.667 0.00 0.00 38.98 3.58
3554 5211 2.856000 AGGCTGGGGCTGTGAAGT 60.856 61.111 0.00 0.00 36.97 3.01
3556 5213 0.916358 AGGCTGGGGCTGTGAAGTAT 60.916 55.000 0.00 0.00 36.97 2.12
3653 5312 2.103537 TTAAAGCCTGCTCCGGTAAC 57.896 50.000 0.00 0.00 0.00 2.50
3655 5314 1.272807 AAAGCCTGCTCCGGTAACTA 58.727 50.000 0.00 0.00 0.00 2.24
3663 5322 4.369182 CTGCTCCGGTAACTAAATAGTGG 58.631 47.826 0.00 0.00 36.50 4.00
3666 5325 4.369182 CTCCGGTAACTAAATAGTGGCTG 58.631 47.826 0.00 0.00 36.50 4.85
3667 5326 3.133362 TCCGGTAACTAAATAGTGGCTGG 59.867 47.826 0.00 12.63 38.02 4.85
3668 5327 3.118519 CCGGTAACTAAATAGTGGCTGGT 60.119 47.826 0.00 0.00 36.50 4.00
3669 5328 3.869246 CGGTAACTAAATAGTGGCTGGTG 59.131 47.826 0.00 0.00 36.50 4.17
3670 5329 4.382254 CGGTAACTAAATAGTGGCTGGTGA 60.382 45.833 0.00 0.00 36.50 4.02
3680 5378 1.279271 GTGGCTGGTGACTCCTAACAT 59.721 52.381 0.00 0.00 37.07 2.71
3711 5409 3.245229 TGGCCACTGAATTGTATGAACCT 60.245 43.478 0.00 0.00 0.00 3.50
3712 5410 3.129287 GGCCACTGAATTGTATGAACCTG 59.871 47.826 0.00 0.00 0.00 4.00
3713 5411 3.129287 GCCACTGAATTGTATGAACCTGG 59.871 47.826 0.00 0.00 0.00 4.45
3714 5412 4.588899 CCACTGAATTGTATGAACCTGGA 58.411 43.478 0.00 0.00 0.00 3.86
3715 5413 4.396166 CCACTGAATTGTATGAACCTGGAC 59.604 45.833 0.00 0.00 0.00 4.02
3716 5414 5.003160 CACTGAATTGTATGAACCTGGACA 58.997 41.667 0.00 0.25 0.00 4.02
3717 5415 5.122869 CACTGAATTGTATGAACCTGGACAG 59.877 44.000 0.00 0.00 0.00 3.51
3718 5416 5.221925 ACTGAATTGTATGAACCTGGACAGT 60.222 40.000 0.00 0.00 0.00 3.55
3719 5417 5.003160 TGAATTGTATGAACCTGGACAGTG 58.997 41.667 0.00 0.00 0.00 3.66
3720 5418 3.417069 TTGTATGAACCTGGACAGTGG 57.583 47.619 0.00 0.00 0.00 4.00
3721 5419 2.615391 TGTATGAACCTGGACAGTGGA 58.385 47.619 0.00 0.00 0.00 4.02
3722 5420 2.301870 TGTATGAACCTGGACAGTGGAC 59.698 50.000 0.00 0.00 0.00 4.02
3723 5421 1.434188 ATGAACCTGGACAGTGGACA 58.566 50.000 0.00 0.00 0.00 4.02
3724 5422 0.468226 TGAACCTGGACAGTGGACAC 59.532 55.000 0.00 0.00 0.00 3.67
3725 5423 0.759346 GAACCTGGACAGTGGACACT 59.241 55.000 0.00 0.00 43.61 3.55
3726 5424 1.968493 GAACCTGGACAGTGGACACTA 59.032 52.381 4.41 0.00 40.20 2.74
3727 5425 1.633774 ACCTGGACAGTGGACACTAG 58.366 55.000 4.41 0.00 40.20 2.57
3728 5426 0.898320 CCTGGACAGTGGACACTAGG 59.102 60.000 4.41 4.75 40.20 3.02
3729 5427 1.550179 CCTGGACAGTGGACACTAGGA 60.550 57.143 11.77 0.00 40.20 2.94
3730 5428 2.248248 CTGGACAGTGGACACTAGGAA 58.752 52.381 4.41 0.00 40.20 3.36
3731 5429 2.632996 CTGGACAGTGGACACTAGGAAA 59.367 50.000 4.41 0.00 40.20 3.13
3732 5430 2.367567 TGGACAGTGGACACTAGGAAAC 59.632 50.000 4.41 0.00 40.20 2.78
3733 5431 2.367567 GGACAGTGGACACTAGGAAACA 59.632 50.000 4.41 0.00 40.20 2.83
3734 5432 3.008049 GGACAGTGGACACTAGGAAACAT 59.992 47.826 4.41 0.00 40.20 2.71
3735 5433 3.997021 GACAGTGGACACTAGGAAACATG 59.003 47.826 4.41 0.00 40.20 3.21
3736 5434 3.646162 ACAGTGGACACTAGGAAACATGA 59.354 43.478 4.41 0.00 40.20 3.07
3737 5435 3.997021 CAGTGGACACTAGGAAACATGAC 59.003 47.826 4.41 0.00 40.20 3.06
3738 5436 2.993899 GTGGACACTAGGAAACATGACG 59.006 50.000 0.00 0.00 0.00 4.35
3739 5437 2.631062 TGGACACTAGGAAACATGACGT 59.369 45.455 0.00 0.00 0.00 4.34
3740 5438 3.251571 GGACACTAGGAAACATGACGTC 58.748 50.000 9.11 9.11 0.00 4.34
3741 5439 3.305813 GGACACTAGGAAACATGACGTCA 60.306 47.826 22.48 22.48 0.00 4.35
3742 5440 3.650139 ACACTAGGAAACATGACGTCAC 58.350 45.455 22.71 7.54 0.00 3.67
3743 5441 3.321111 ACACTAGGAAACATGACGTCACT 59.679 43.478 22.71 14.57 0.00 3.41
3744 5442 3.921021 CACTAGGAAACATGACGTCACTC 59.079 47.826 22.71 14.41 0.00 3.51
3745 5443 3.572682 ACTAGGAAACATGACGTCACTCA 59.427 43.478 22.71 0.00 0.00 3.41
3746 5444 3.469008 AGGAAACATGACGTCACTCAA 57.531 42.857 22.71 0.00 0.00 3.02
3747 5445 3.393800 AGGAAACATGACGTCACTCAAG 58.606 45.455 22.71 10.96 0.00 3.02
3748 5446 2.480419 GGAAACATGACGTCACTCAAGG 59.520 50.000 22.71 8.82 0.00 3.61
3749 5447 2.910688 AACATGACGTCACTCAAGGT 57.089 45.000 22.71 9.46 0.00 3.50
3750 5448 4.304110 GAAACATGACGTCACTCAAGGTA 58.696 43.478 22.71 0.00 0.00 3.08
3751 5449 3.299340 ACATGACGTCACTCAAGGTAC 57.701 47.619 22.71 0.00 0.00 3.34
3769 5467 6.767524 AGGTACTTGATTTGTCAAACAACA 57.232 33.333 0.00 0.00 33.50 3.33
3770 5468 7.164230 AGGTACTTGATTTGTCAAACAACAA 57.836 32.000 0.00 7.09 33.50 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.423154 GACTTGTCAAGCCGGCGG 61.423 66.667 24.35 24.35 0.00 6.13
17 18 2.664851 TGACTTGTCAAGCCGGCG 60.665 61.111 23.20 8.11 0.00 6.46
18 19 0.884704 TTCTGACTTGTCAAGCCGGC 60.885 55.000 21.89 21.89 0.00 6.13
19 20 0.868406 GTTCTGACTTGTCAAGCCGG 59.132 55.000 12.66 6.94 0.00 6.13
20 21 1.581934 TGTTCTGACTTGTCAAGCCG 58.418 50.000 12.66 1.66 0.00 5.52
21 22 2.945668 ACTTGTTCTGACTTGTCAAGCC 59.054 45.455 12.66 1.82 38.99 4.35
22 23 4.622701 AACTTGTTCTGACTTGTCAAGC 57.377 40.909 12.66 6.31 38.99 4.01
23 24 6.524586 GTGAAAACTTGTTCTGACTTGTCAAG 59.475 38.462 11.17 11.17 40.54 3.02
24 25 6.378582 GTGAAAACTTGTTCTGACTTGTCAA 58.621 36.000 4.95 0.00 0.00 3.18
25 26 5.106317 GGTGAAAACTTGTTCTGACTTGTCA 60.106 40.000 3.32 3.32 0.00 3.58
26 27 5.332707 GGTGAAAACTTGTTCTGACTTGTC 58.667 41.667 0.00 0.00 0.00 3.18
27 28 4.157840 GGGTGAAAACTTGTTCTGACTTGT 59.842 41.667 0.00 0.00 0.00 3.16
28 29 4.440112 GGGGTGAAAACTTGTTCTGACTTG 60.440 45.833 0.00 0.00 0.00 3.16
29 30 3.699538 GGGGTGAAAACTTGTTCTGACTT 59.300 43.478 0.00 0.00 0.00 3.01
30 31 3.288092 GGGGTGAAAACTTGTTCTGACT 58.712 45.455 0.00 0.00 0.00 3.41
31 32 2.032924 CGGGGTGAAAACTTGTTCTGAC 59.967 50.000 0.00 0.00 0.00 3.51
32 33 2.294074 CGGGGTGAAAACTTGTTCTGA 58.706 47.619 0.00 0.00 0.00 3.27
33 34 1.336755 CCGGGGTGAAAACTTGTTCTG 59.663 52.381 0.00 0.00 0.00 3.02
34 35 1.687563 CCGGGGTGAAAACTTGTTCT 58.312 50.000 0.00 0.00 0.00 3.01
35 36 0.031585 GCCGGGGTGAAAACTTGTTC 59.968 55.000 2.18 0.00 0.00 3.18
36 37 1.396607 GGCCGGGGTGAAAACTTGTT 61.397 55.000 2.18 0.00 0.00 2.83
37 38 1.830847 GGCCGGGGTGAAAACTTGT 60.831 57.895 2.18 0.00 0.00 3.16
38 39 1.184970 ATGGCCGGGGTGAAAACTTG 61.185 55.000 2.18 0.00 0.00 3.16
39 40 0.471022 AATGGCCGGGGTGAAAACTT 60.471 50.000 2.18 0.00 0.00 2.66
40 41 0.406361 TAATGGCCGGGGTGAAAACT 59.594 50.000 2.18 0.00 0.00 2.66
41 42 0.528924 GTAATGGCCGGGGTGAAAAC 59.471 55.000 2.18 0.00 0.00 2.43
42 43 0.406361 AGTAATGGCCGGGGTGAAAA 59.594 50.000 2.18 0.00 0.00 2.29
43 44 0.034863 GAGTAATGGCCGGGGTGAAA 60.035 55.000 2.18 0.00 0.00 2.69
44 45 1.202099 TGAGTAATGGCCGGGGTGAA 61.202 55.000 2.18 0.00 0.00 3.18
45 46 0.986019 ATGAGTAATGGCCGGGGTGA 60.986 55.000 2.18 0.00 0.00 4.02
46 47 0.535102 GATGAGTAATGGCCGGGGTG 60.535 60.000 2.18 0.00 0.00 4.61
47 48 0.986019 TGATGAGTAATGGCCGGGGT 60.986 55.000 2.18 0.00 0.00 4.95
48 49 0.250467 CTGATGAGTAATGGCCGGGG 60.250 60.000 2.18 0.00 0.00 5.73
49 50 0.886490 GCTGATGAGTAATGGCCGGG 60.886 60.000 2.18 0.00 0.00 5.73
50 51 0.179048 TGCTGATGAGTAATGGCCGG 60.179 55.000 0.00 0.00 0.00 6.13
51 52 0.940126 GTGCTGATGAGTAATGGCCG 59.060 55.000 0.00 0.00 0.00 6.13
52 53 1.312815 GGTGCTGATGAGTAATGGCC 58.687 55.000 0.00 0.00 0.00 5.36
53 54 2.042686 TGGTGCTGATGAGTAATGGC 57.957 50.000 0.00 0.00 0.00 4.40
54 55 3.624861 GTCTTGGTGCTGATGAGTAATGG 59.375 47.826 0.00 0.00 0.00 3.16
55 56 3.308053 CGTCTTGGTGCTGATGAGTAATG 59.692 47.826 0.00 0.00 0.00 1.90
56 57 3.055819 ACGTCTTGGTGCTGATGAGTAAT 60.056 43.478 0.00 0.00 0.00 1.89
57 58 2.299013 ACGTCTTGGTGCTGATGAGTAA 59.701 45.455 0.00 0.00 0.00 2.24
58 59 1.893137 ACGTCTTGGTGCTGATGAGTA 59.107 47.619 0.00 0.00 0.00 2.59
59 60 0.681733 ACGTCTTGGTGCTGATGAGT 59.318 50.000 0.00 0.00 0.00 3.41
60 61 1.073964 CACGTCTTGGTGCTGATGAG 58.926 55.000 0.00 0.00 0.00 2.90
61 62 0.320683 CCACGTCTTGGTGCTGATGA 60.321 55.000 0.00 0.00 41.10 2.92
62 63 2.165380 CCACGTCTTGGTGCTGATG 58.835 57.895 0.00 0.00 41.10 3.07
63 64 4.701663 CCACGTCTTGGTGCTGAT 57.298 55.556 0.00 0.00 41.10 2.90
71 72 1.134226 GTTGACCGTACCACGTCTTG 58.866 55.000 0.00 0.00 40.58 3.02
72 73 0.032540 GGTTGACCGTACCACGTCTT 59.967 55.000 0.00 0.00 40.58 3.01
73 74 1.662044 GGTTGACCGTACCACGTCT 59.338 57.895 0.00 0.00 40.58 4.18
74 75 4.250080 GGTTGACCGTACCACGTC 57.750 61.111 0.00 0.00 40.58 4.34
88 89 4.966787 AATGGCGGTGGTGCGGTT 62.967 61.111 0.00 0.00 35.06 4.44
91 92 2.801113 CTTTCAATGGCGGTGGTGCG 62.801 60.000 0.00 0.00 35.06 5.34
92 93 1.080569 CTTTCAATGGCGGTGGTGC 60.081 57.895 0.00 0.00 0.00 5.01
93 94 1.080569 GCTTTCAATGGCGGTGGTG 60.081 57.895 0.00 0.00 0.00 4.17
94 95 2.275380 GGCTTTCAATGGCGGTGGT 61.275 57.895 0.00 0.00 0.00 4.16
95 96 1.606885 ATGGCTTTCAATGGCGGTGG 61.607 55.000 0.00 0.00 0.00 4.61
96 97 1.102154 TATGGCTTTCAATGGCGGTG 58.898 50.000 0.00 0.00 0.00 4.94
97 98 1.102978 GTATGGCTTTCAATGGCGGT 58.897 50.000 0.00 0.00 0.00 5.68
98 99 0.385390 GGTATGGCTTTCAATGGCGG 59.615 55.000 0.00 0.00 0.00 6.13
99 100 0.385390 GGGTATGGCTTTCAATGGCG 59.615 55.000 0.00 0.00 0.00 5.69
100 101 0.752658 GGGGTATGGCTTTCAATGGC 59.247 55.000 0.00 0.00 0.00 4.40
101 102 2.459555 AGGGGTATGGCTTTCAATGG 57.540 50.000 0.00 0.00 0.00 3.16
102 103 2.695147 GGAAGGGGTATGGCTTTCAATG 59.305 50.000 0.00 0.00 0.00 2.82
103 104 2.314549 TGGAAGGGGTATGGCTTTCAAT 59.685 45.455 0.00 0.00 0.00 2.57
104 105 1.713647 TGGAAGGGGTATGGCTTTCAA 59.286 47.619 0.00 0.00 0.00 2.69
105 106 1.005450 GTGGAAGGGGTATGGCTTTCA 59.995 52.381 0.00 0.00 0.00 2.69
106 107 1.685180 GGTGGAAGGGGTATGGCTTTC 60.685 57.143 0.00 0.00 0.00 2.62
107 108 0.335019 GGTGGAAGGGGTATGGCTTT 59.665 55.000 0.00 0.00 0.00 3.51
108 109 0.849094 TGGTGGAAGGGGTATGGCTT 60.849 55.000 0.00 0.00 0.00 4.35
109 110 0.627469 ATGGTGGAAGGGGTATGGCT 60.627 55.000 0.00 0.00 0.00 4.75
110 111 0.468029 CATGGTGGAAGGGGTATGGC 60.468 60.000 0.00 0.00 0.00 4.40
111 112 0.468029 GCATGGTGGAAGGGGTATGG 60.468 60.000 0.00 0.00 0.00 2.74
112 113 0.552848 AGCATGGTGGAAGGGGTATG 59.447 55.000 0.00 0.00 0.00 2.39
113 114 0.552848 CAGCATGGTGGAAGGGGTAT 59.447 55.000 17.24 0.00 0.00 2.73
114 115 1.998530 CAGCATGGTGGAAGGGGTA 59.001 57.895 17.24 0.00 0.00 3.69
115 116 2.765969 CAGCATGGTGGAAGGGGT 59.234 61.111 17.24 0.00 0.00 4.95
116 117 2.757099 GCAGCATGGTGGAAGGGG 60.757 66.667 25.24 0.00 35.86 4.79
117 118 2.757099 GGCAGCATGGTGGAAGGG 60.757 66.667 25.24 0.00 35.86 3.95
118 119 2.757099 GGGCAGCATGGTGGAAGG 60.757 66.667 25.24 0.74 35.86 3.46
119 120 2.036098 TGGGCAGCATGGTGGAAG 59.964 61.111 25.24 1.13 35.86 3.46
120 121 2.283101 GTGGGCAGCATGGTGGAA 60.283 61.111 25.24 0.00 35.86 3.53
121 122 2.921500 ATGTGGGCAGCATGGTGGA 61.921 57.895 25.24 0.00 35.86 4.02
122 123 2.363276 ATGTGGGCAGCATGGTGG 60.363 61.111 25.24 8.33 35.86 4.61
123 124 2.889617 CATGTGGGCAGCATGGTG 59.110 61.111 20.52 20.52 39.82 4.17
126 127 0.828022 ATTTCCATGTGGGCAGCATG 59.172 50.000 11.87 11.87 42.29 4.06
127 128 0.828022 CATTTCCATGTGGGCAGCAT 59.172 50.000 0.00 0.00 36.21 3.79
128 129 1.259142 CCATTTCCATGTGGGCAGCA 61.259 55.000 0.00 0.00 36.21 4.41
129 130 1.259840 ACCATTTCCATGTGGGCAGC 61.260 55.000 5.19 0.00 39.86 5.25
130 131 0.819582 GACCATTTCCATGTGGGCAG 59.180 55.000 1.04 0.00 43.32 4.85
131 132 0.964860 CGACCATTTCCATGTGGGCA 60.965 55.000 6.72 0.00 44.08 5.36
132 133 0.965363 ACGACCATTTCCATGTGGGC 60.965 55.000 5.19 0.65 40.28 5.36
133 134 1.094785 GACGACCATTTCCATGTGGG 58.905 55.000 5.19 0.00 39.86 4.61
134 135 1.094785 GGACGACCATTTCCATGTGG 58.905 55.000 0.00 0.00 41.35 4.17
135 136 0.726827 CGGACGACCATTTCCATGTG 59.273 55.000 4.48 0.00 35.59 3.21
136 137 0.611200 TCGGACGACCATTTCCATGT 59.389 50.000 4.48 0.00 35.59 3.21
137 138 1.732941 TTCGGACGACCATTTCCATG 58.267 50.000 4.48 0.00 35.59 3.66
138 139 2.356135 CTTTCGGACGACCATTTCCAT 58.644 47.619 4.48 0.00 35.59 3.41
139 140 1.803334 CTTTCGGACGACCATTTCCA 58.197 50.000 4.48 0.00 35.59 3.53
140 141 0.446616 GCTTTCGGACGACCATTTCC 59.553 55.000 4.48 0.00 35.59 3.13
141 142 0.094730 CGCTTTCGGACGACCATTTC 59.905 55.000 4.48 0.00 35.59 2.17
142 143 1.908066 GCGCTTTCGGACGACCATTT 61.908 55.000 0.00 0.00 35.95 2.32
143 144 2.388232 GCGCTTTCGGACGACCATT 61.388 57.895 0.00 0.00 35.95 3.16
144 145 2.813908 GCGCTTTCGGACGACCAT 60.814 61.111 0.00 0.00 35.95 3.55
146 147 4.736896 AGGCGCTTTCGGACGACC 62.737 66.667 7.64 0.00 38.35 4.79
147 148 3.479269 CAGGCGCTTTCGGACGAC 61.479 66.667 7.64 0.00 37.66 4.34
148 149 3.626680 CTCAGGCGCTTTCGGACGA 62.627 63.158 7.64 0.00 35.95 4.20
149 150 3.181967 CTCAGGCGCTTTCGGACG 61.182 66.667 7.64 0.00 35.95 4.79
150 151 3.491652 GCTCAGGCGCTTTCGGAC 61.492 66.667 7.64 0.00 35.95 4.79
151 152 3.695606 AGCTCAGGCGCTTTCGGA 61.696 61.111 7.64 0.00 44.37 4.55
152 153 3.494336 CAGCTCAGGCGCTTTCGG 61.494 66.667 7.64 0.00 44.37 4.30
153 154 3.494336 CCAGCTCAGGCGCTTTCG 61.494 66.667 7.64 0.00 44.37 3.46
154 155 3.130160 CCCAGCTCAGGCGCTTTC 61.130 66.667 7.64 0.00 44.37 2.62
155 156 3.958860 ACCCAGCTCAGGCGCTTT 61.959 61.111 7.64 0.00 44.37 3.51
156 157 4.711949 CACCCAGCTCAGGCGCTT 62.712 66.667 7.64 0.00 44.37 4.68
178 179 3.665675 CTAGTGGGTGCTCGTGGGC 62.666 68.421 0.00 0.00 0.00 5.36
179 180 0.968901 TACTAGTGGGTGCTCGTGGG 60.969 60.000 5.39 0.00 0.00 4.61
180 181 0.456221 CTACTAGTGGGTGCTCGTGG 59.544 60.000 5.39 0.00 0.00 4.94
181 182 1.460504 TCTACTAGTGGGTGCTCGTG 58.539 55.000 5.39 0.00 0.00 4.35
182 183 2.211250 TTCTACTAGTGGGTGCTCGT 57.789 50.000 5.39 0.00 0.00 4.18
183 184 3.587797 TTTTCTACTAGTGGGTGCTCG 57.412 47.619 5.39 0.00 0.00 5.03
184 185 5.351740 GTCATTTTTCTACTAGTGGGTGCTC 59.648 44.000 5.39 0.00 0.00 4.26
185 186 5.246307 GTCATTTTTCTACTAGTGGGTGCT 58.754 41.667 5.39 0.00 0.00 4.40
186 187 4.395231 GGTCATTTTTCTACTAGTGGGTGC 59.605 45.833 5.39 0.00 0.00 5.01
187 188 5.805728 AGGTCATTTTTCTACTAGTGGGTG 58.194 41.667 5.39 0.00 0.00 4.61
188 189 7.563724 TTAGGTCATTTTTCTACTAGTGGGT 57.436 36.000 5.39 0.00 0.00 4.51
189 190 8.047310 ACATTAGGTCATTTTTCTACTAGTGGG 58.953 37.037 5.39 0.00 0.00 4.61
205 207 2.642311 TGAAGGGCTGAACATTAGGTCA 59.358 45.455 0.00 0.00 0.00 4.02
266 268 2.710096 TAGCCATTAGAACCAGCACC 57.290 50.000 0.00 0.00 0.00 5.01
277 279 3.307410 CCGGGACTAATGCATAGCCATTA 60.307 47.826 0.00 0.00 36.80 1.90
451 453 4.309099 CCATTTTGTCCCAGTTTGTGATG 58.691 43.478 0.00 0.00 0.00 3.07
452 454 3.324556 CCCATTTTGTCCCAGTTTGTGAT 59.675 43.478 0.00 0.00 0.00 3.06
478 481 0.177373 ACGAATCGGGACTAAAGGGC 59.823 55.000 7.80 0.00 0.00 5.19
479 482 1.206371 ACACGAATCGGGACTAAAGGG 59.794 52.381 13.47 0.00 32.98 3.95
492 495 0.682852 TCCCGGTTTGAGACACGAAT 59.317 50.000 0.00 0.00 0.00 3.34
495 498 0.599558 TAGTCCCGGTTTGAGACACG 59.400 55.000 9.96 0.00 32.82 4.49
497 500 2.038033 CCTTTAGTCCCGGTTTGAGACA 59.962 50.000 9.96 0.00 32.82 3.41
499 502 2.301009 GACCTTTAGTCCCGGTTTGAGA 59.699 50.000 0.00 0.00 39.84 3.27
521 524 4.946478 TGGGGTTAGTGTTTGAAAATGG 57.054 40.909 0.00 0.00 0.00 3.16
522 525 5.053811 GGTTGGGGTTAGTGTTTGAAAATG 58.946 41.667 0.00 0.00 0.00 2.32
533 536 1.296002 GATCAGGGGTTGGGGTTAGT 58.704 55.000 0.00 0.00 0.00 2.24
537 540 3.728373 GCGATCAGGGGTTGGGGT 61.728 66.667 0.00 0.00 0.00 4.95
549 563 7.222031 ACTTTTTACAAAACTGAAAAGGCGATC 59.778 33.333 10.88 0.00 41.20 3.69
1075 1368 1.148273 TGTGCACGGGAGCTTCTTT 59.852 52.632 13.13 0.00 34.99 2.52
1082 1375 1.335872 GGAAATTTGTGTGCACGGGAG 60.336 52.381 13.13 0.00 0.00 4.30
1135 1428 2.035961 TCAACAAGGAGTCAAGGAGTCG 59.964 50.000 0.00 0.00 33.20 4.18
1168 1461 2.775890 ACAAGCTCACACATTCAGGAG 58.224 47.619 0.00 0.00 0.00 3.69
1206 1499 4.014406 TGAGAGCTGCATGAACATTTGAT 58.986 39.130 1.02 0.00 0.00 2.57
1314 1607 3.120234 CGCAGTTGAGCAACATATGTCAA 60.120 43.478 9.23 6.22 43.47 3.18
1338 1631 5.757886 TGTACATAAGCTCAAGTGCAAAAC 58.242 37.500 0.00 0.00 34.99 2.43
1355 1648 7.229306 CCATCAATTGGTGTAGCTTATGTACAT 59.771 37.037 17.29 13.93 40.99 2.29
1476 1769 6.927294 AGATTTTTCTATTACAAGGCTCCG 57.073 37.500 0.00 0.00 0.00 4.63
1492 1785 9.199982 CAAAGCAGTCAATACATGAAGATTTTT 57.800 29.630 0.00 0.00 40.50 1.94
1493 1786 8.579006 TCAAAGCAGTCAATACATGAAGATTTT 58.421 29.630 0.00 0.00 40.50 1.82
1526 1819 7.099266 TGTTACCATGATGAATTGATGAACC 57.901 36.000 0.00 0.00 0.00 3.62
1607 1903 0.773644 ATGCCAAGGAACTGACCACT 59.226 50.000 0.00 0.00 40.86 4.00
1748 2044 5.965033 ATGACATCCCATAAGACAAGTCT 57.035 39.130 0.00 0.00 42.75 3.24
2085 2381 6.358030 GCGAAAATATGACATTCGATTCAAGG 59.642 38.462 11.96 0.00 46.50 3.61
2479 2875 2.575735 TGTGGGAACAATAGCAGGATCA 59.424 45.455 0.00 0.00 46.06 2.92
2760 3156 1.272769 CCACTAGCTTCTATACCGGGC 59.727 57.143 6.32 0.00 0.00 6.13
2958 3359 6.407074 CCTGGTCATATTCCGTAGAAACTTCT 60.407 42.308 0.00 0.00 41.24 2.85
2999 3400 2.358957 TGTGCATGCTGTATGGAAGAC 58.641 47.619 20.33 4.86 38.95 3.01
3024 3425 6.036844 CCAGGCCTATTAAAAAGTCGAGTAAC 59.963 42.308 3.98 0.00 0.00 2.50
3031 3432 5.661056 AAAGCCAGGCCTATTAAAAAGTC 57.339 39.130 3.98 0.00 0.00 3.01
3063 3579 6.426587 ACCATTATAAGAAACTCAGTGGCAT 58.573 36.000 0.00 0.00 0.00 4.40
3161 3682 1.335182 CTCGATCTCTGCCGAAGCTAA 59.665 52.381 0.00 0.00 40.80 3.09
3171 3692 1.337703 CTGGCTCTTCCTCGATCTCTG 59.662 57.143 0.00 0.00 35.26 3.35
3233 3754 2.224843 TGGGACATGAAGATTGTGCACT 60.225 45.455 19.41 0.00 37.18 4.40
3278 3799 2.891580 AGAAGCCTCTTGTCTAACACGA 59.108 45.455 0.00 0.00 0.00 4.35
3316 3998 9.225436 TGTGAACATCATATGCTAAAACACTTA 57.775 29.630 0.00 0.00 0.00 2.24
3369 4051 7.672983 AAATCGACACATGAACTCTTATGTT 57.327 32.000 0.00 0.00 35.46 2.71
3484 5056 6.699642 GCACATACTACTTTTGCCAAGAAAAA 59.300 34.615 0.00 0.00 0.00 1.94
3489 5061 6.683974 ATAGCACATACTACTTTTGCCAAG 57.316 37.500 0.00 0.00 33.48 3.61
3517 5174 7.395617 CAGCCTCACCTCTGTATATACTACTA 58.604 42.308 13.89 0.00 0.00 1.82
3518 5175 6.242396 CAGCCTCACCTCTGTATATACTACT 58.758 44.000 13.89 0.00 0.00 2.57
3519 5176 5.416326 CCAGCCTCACCTCTGTATATACTAC 59.584 48.000 13.89 0.00 0.00 2.73
3520 5177 5.516768 CCCAGCCTCACCTCTGTATATACTA 60.517 48.000 13.89 1.97 0.00 1.82
3521 5178 4.411927 CCAGCCTCACCTCTGTATATACT 58.588 47.826 13.89 0.00 0.00 2.12
3522 5179 3.511934 CCCAGCCTCACCTCTGTATATAC 59.488 52.174 5.89 5.89 0.00 1.47
3551 5208 8.801882 TCCTCCAAAATCGAACAAATATACTT 57.198 30.769 0.00 0.00 0.00 2.24
3554 5211 8.972458 TGATCCTCCAAAATCGAACAAATATA 57.028 30.769 0.00 0.00 0.00 0.86
3556 5213 7.880160 ATGATCCTCCAAAATCGAACAAATA 57.120 32.000 0.00 0.00 0.00 1.40
3653 5312 3.452627 AGGAGTCACCAGCCACTATTTAG 59.547 47.826 0.00 0.00 42.04 1.85
3655 5314 2.269940 AGGAGTCACCAGCCACTATTT 58.730 47.619 0.00 0.00 42.04 1.40
3663 5322 3.702045 ACTAGATGTTAGGAGTCACCAGC 59.298 47.826 0.00 0.00 42.04 4.85
3666 5325 4.951094 AGACACTAGATGTTAGGAGTCACC 59.049 45.833 0.00 0.00 43.56 4.02
3667 5326 5.163602 CCAGACACTAGATGTTAGGAGTCAC 60.164 48.000 0.00 0.00 43.56 3.67
3668 5327 4.950475 CCAGACACTAGATGTTAGGAGTCA 59.050 45.833 0.00 0.00 43.56 3.41
3669 5328 4.202070 GCCAGACACTAGATGTTAGGAGTC 60.202 50.000 0.00 0.00 43.56 3.36
3670 5329 3.702045 GCCAGACACTAGATGTTAGGAGT 59.298 47.826 0.00 0.00 43.56 3.85
3711 5409 2.367567 GTTTCCTAGTGTCCACTGTCCA 59.632 50.000 10.15 0.00 42.52 4.02
3712 5410 2.367567 TGTTTCCTAGTGTCCACTGTCC 59.632 50.000 10.15 0.00 42.52 4.02
3713 5411 3.746045 TGTTTCCTAGTGTCCACTGTC 57.254 47.619 10.15 0.00 42.52 3.51
3714 5412 3.646162 TCATGTTTCCTAGTGTCCACTGT 59.354 43.478 10.15 0.00 42.52 3.55
3715 5413 3.997021 GTCATGTTTCCTAGTGTCCACTG 59.003 47.826 10.15 0.91 42.52 3.66
3716 5414 3.306088 CGTCATGTTTCCTAGTGTCCACT 60.306 47.826 5.15 5.15 45.02 4.00
3717 5415 2.993899 CGTCATGTTTCCTAGTGTCCAC 59.006 50.000 0.00 0.00 0.00 4.02
3718 5416 2.631062 ACGTCATGTTTCCTAGTGTCCA 59.369 45.455 0.00 0.00 0.00 4.02
3719 5417 3.251571 GACGTCATGTTTCCTAGTGTCC 58.748 50.000 11.55 0.00 0.00 4.02
3720 5418 3.673809 GTGACGTCATGTTTCCTAGTGTC 59.326 47.826 23.12 0.00 0.00 3.67
3721 5419 3.321111 AGTGACGTCATGTTTCCTAGTGT 59.679 43.478 23.12 0.00 0.00 3.55
3722 5420 3.914312 AGTGACGTCATGTTTCCTAGTG 58.086 45.455 23.12 0.00 0.00 2.74
3723 5421 3.572682 TGAGTGACGTCATGTTTCCTAGT 59.427 43.478 23.12 0.00 0.00 2.57
3724 5422 4.174411 TGAGTGACGTCATGTTTCCTAG 57.826 45.455 23.12 0.00 0.00 3.02
3725 5423 4.556233 CTTGAGTGACGTCATGTTTCCTA 58.444 43.478 23.12 7.53 0.00 2.94
3726 5424 3.393800 CTTGAGTGACGTCATGTTTCCT 58.606 45.455 23.12 12.77 0.00 3.36
3727 5425 2.480419 CCTTGAGTGACGTCATGTTTCC 59.520 50.000 23.12 7.55 0.00 3.13
3728 5426 3.131396 ACCTTGAGTGACGTCATGTTTC 58.869 45.455 23.12 16.52 0.00 2.78
3729 5427 3.194005 ACCTTGAGTGACGTCATGTTT 57.806 42.857 23.12 8.01 0.00 2.83
3730 5428 2.910688 ACCTTGAGTGACGTCATGTT 57.089 45.000 23.12 10.68 0.00 2.71
3731 5429 2.891580 AGTACCTTGAGTGACGTCATGT 59.108 45.455 23.12 12.48 0.00 3.21
3732 5430 3.577649 AGTACCTTGAGTGACGTCATG 57.422 47.619 23.12 9.60 0.00 3.07
3733 5431 3.572682 TCAAGTACCTTGAGTGACGTCAT 59.427 43.478 23.12 10.80 44.27 3.06
3734 5432 2.953648 TCAAGTACCTTGAGTGACGTCA 59.046 45.455 15.76 15.76 44.27 4.35
3735 5433 3.637998 TCAAGTACCTTGAGTGACGTC 57.362 47.619 9.11 9.11 44.27 4.34
3742 5440 7.432252 GTTGTTTGACAAATCAAGTACCTTGAG 59.568 37.037 11.82 2.42 45.54 3.02
3743 5441 7.094162 TGTTGTTTGACAAATCAAGTACCTTGA 60.094 33.333 8.95 8.95 45.54 3.02
3744 5442 7.032580 TGTTGTTTGACAAATCAAGTACCTTG 58.967 34.615 3.49 0.00 45.54 3.61
3745 5443 7.164230 TGTTGTTTGACAAATCAAGTACCTT 57.836 32.000 3.49 0.00 45.54 3.50
3746 5444 6.767524 TGTTGTTTGACAAATCAAGTACCT 57.232 33.333 3.49 0.00 45.54 3.08


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

AutoCloner maintained by Alex Coulton.