Multiple sequence alignment - TraesCS6B01G093200

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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 TraesCS6B01G093200 chr6B 100.000 5554 0 0 1 5554 69099549 69093996 0.000000e+00 10257
1 TraesCS6B01G093200 chr6B 94.370 5382 237 41 207 5554 542975678 542981027 0.000000e+00 8200
2 TraesCS6B01G093200 chr6B 89.401 434 36 8 5126 5554 423108798 423108370 6.330000e-149 538
3 TraesCS6B01G093200 chr3B 93.979 5132 247 32 207 5315 56576040 56570948 0.000000e+00 7709
4 TraesCS6B01G093200 chr3B 93.941 5133 245 36 207 5315 56693926 56688836 0.000000e+00 7696
5 TraesCS6B01G093200 chr3B 96.016 3062 99 15 207 3256 545631912 545634962 0.000000e+00 4957
6 TraesCS6B01G093200 chr3B 93.777 466 18 7 5098 5554 545636989 545637452 0.000000e+00 689
7 TraesCS6B01G093200 chr3B 84.953 638 55 28 4936 5554 56571224 56570609 4.760000e-170 608
8 TraesCS6B01G093200 chr3B 88.860 386 38 4 5169 5554 751579521 751579141 2.340000e-128 470
9 TraesCS6B01G093200 chr3B 86.429 420 32 12 5140 5554 79239768 79239369 2.380000e-118 436
10 TraesCS6B01G093200 chr3B 93.023 215 14 1 965 1178 281159668 281159882 4.180000e-81 313
11 TraesCS6B01G093200 chr1B 93.370 5038 259 49 207 5213 117794900 117799893 0.000000e+00 7384
12 TraesCS6B01G093200 chr1B 94.360 4450 199 29 781 5213 118420579 118416165 0.000000e+00 6780
13 TraesCS6B01G093200 chr1B 87.053 811 85 17 207 1005 117807210 117808012 0.000000e+00 898
14 TraesCS6B01G093200 chr2B 96.335 4447 137 13 774 5215 156050808 156046383 0.000000e+00 7286
15 TraesCS6B01G093200 chr2B 96.298 3431 106 10 1177 4604 793660223 793663635 0.000000e+00 5613
16 TraesCS6B01G093200 chr2B 90.600 1000 63 14 207 1178 793659198 793660194 0.000000e+00 1297
17 TraesCS6B01G093200 chr2D 90.374 4114 307 60 1177 5246 264004778 264000710 0.000000e+00 5321
18 TraesCS6B01G093200 chr6D 91.325 3827 265 41 1177 4977 157131081 157127296 0.000000e+00 5166
19 TraesCS6B01G093200 chr4D 90.377 3824 262 55 1177 4977 257564871 257561131 0.000000e+00 4926
20 TraesCS6B01G093200 chr4D 84.965 991 104 23 207 1178 257565864 257564900 0.000000e+00 963
21 TraesCS6B01G093200 chr4D 89.962 528 45 4 5035 5554 257560986 257560459 0.000000e+00 675
22 TraesCS6B01G093200 chr5B 96.970 2376 60 6 2799 5174 18178708 18181071 0.000000e+00 3978
23 TraesCS6B01G093200 chr5B 88.761 952 84 17 207 1143 18168985 18169928 0.000000e+00 1144
24 TraesCS6B01G093200 chr5B 86.948 996 98 22 207 1178 182667271 182668258 0.000000e+00 1090
25 TraesCS6B01G093200 chr5B 95.202 396 17 1 5159 5554 18191324 18191717 4.720000e-175 625
26 TraesCS6B01G093200 chr4A 87.159 989 83 25 209 1178 618798337 618797374 0.000000e+00 1083
27 TraesCS6B01G093200 chr2A 86.546 773 84 14 207 966 297564906 297564141 0.000000e+00 833
28 TraesCS6B01G093200 chr5D 87.200 375 45 2 5180 5554 166258786 166258415 1.850000e-114 424


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 TraesCS6B01G093200 chr6B 69093996 69099549 5553 True 10257.0 10257 100.000000 1 5554 1 chr6B.!!$R1 5553
1 TraesCS6B01G093200 chr6B 542975678 542981027 5349 False 8200.0 8200 94.370000 207 5554 1 chr6B.!!$F1 5347
2 TraesCS6B01G093200 chr3B 56688836 56693926 5090 True 7696.0 7696 93.941000 207 5315 1 chr3B.!!$R1 5108
3 TraesCS6B01G093200 chr3B 56570609 56576040 5431 True 4158.5 7709 89.466000 207 5554 2 chr3B.!!$R4 5347
4 TraesCS6B01G093200 chr3B 545631912 545637452 5540 False 2823.0 4957 94.896500 207 5554 2 chr3B.!!$F2 5347
5 TraesCS6B01G093200 chr1B 117794900 117799893 4993 False 7384.0 7384 93.370000 207 5213 1 chr1B.!!$F1 5006
6 TraesCS6B01G093200 chr1B 118416165 118420579 4414 True 6780.0 6780 94.360000 781 5213 1 chr1B.!!$R1 4432
7 TraesCS6B01G093200 chr1B 117807210 117808012 802 False 898.0 898 87.053000 207 1005 1 chr1B.!!$F2 798
8 TraesCS6B01G093200 chr2B 156046383 156050808 4425 True 7286.0 7286 96.335000 774 5215 1 chr2B.!!$R1 4441
9 TraesCS6B01G093200 chr2B 793659198 793663635 4437 False 3455.0 5613 93.449000 207 4604 2 chr2B.!!$F1 4397
10 TraesCS6B01G093200 chr2D 264000710 264004778 4068 True 5321.0 5321 90.374000 1177 5246 1 chr2D.!!$R1 4069
11 TraesCS6B01G093200 chr6D 157127296 157131081 3785 True 5166.0 5166 91.325000 1177 4977 1 chr6D.!!$R1 3800
12 TraesCS6B01G093200 chr4D 257560459 257565864 5405 True 2188.0 4926 88.434667 207 5554 3 chr4D.!!$R1 5347
13 TraesCS6B01G093200 chr5B 18178708 18181071 2363 False 3978.0 3978 96.970000 2799 5174 1 chr5B.!!$F2 2375
14 TraesCS6B01G093200 chr5B 18168985 18169928 943 False 1144.0 1144 88.761000 207 1143 1 chr5B.!!$F1 936
15 TraesCS6B01G093200 chr5B 182667271 182668258 987 False 1090.0 1090 86.948000 207 1178 1 chr5B.!!$F4 971
16 TraesCS6B01G093200 chr4A 618797374 618798337 963 True 1083.0 1083 87.159000 209 1178 1 chr4A.!!$R1 969
17 TraesCS6B01G093200 chr2A 297564141 297564906 765 True 833.0 833 86.546000 207 966 1 chr2A.!!$R1 759

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
23 24 0.037590 TTTACCTTGGGCACATCGCT 59.962 50.0 0.00 0.00 41.91 4.93 F
45 46 0.038166 TGCAACCAAGTCCAGATCCC 59.962 55.0 0.00 0.00 0.00 3.85 F
56 57 0.189574 CCAGATCCCTCCTCCAGCTA 59.810 60.0 0.00 0.00 0.00 3.32 F
328 333 0.462047 GTTGGGGTACGATCTGGCAG 60.462 60.0 8.58 8.58 0.00 4.85 F
2177 2395 0.952497 ACGCGTCTCTTCGTGAGGTA 60.952 55.0 5.58 0.00 42.86 3.08 F
2402 2628 0.178861 ATCGGATTAGGGGATGGCCT 60.179 55.0 3.32 0.00 0.00 5.19 F
2867 3094 0.739462 TGCGCTCGAATCCGAAACAT 60.739 50.0 9.73 0.00 45.04 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1005 1164 1.071471 ACGCCAACTGTGAGAAGGG 59.929 57.895 0.00 0.00 0.00 3.95 R
1029 1194 6.237755 CGTCGGACCAAGTTCATATAAACTTC 60.238 42.308 0.63 0.00 45.36 3.01 R
2051 2269 7.457218 AGATGATCATGTGTGGATAATAGGTCT 59.543 37.037 14.30 0.00 0.00 3.85 R
2254 2472 3.114616 CAAGGACACCAGCGCGAG 61.115 66.667 12.10 0.00 0.00 5.03 R
3706 3986 0.817634 TATAAGCATGCGTGGCCACC 60.818 55.000 29.95 21.83 0.00 4.61 R
4270 4556 1.675219 GGCCTCCACACGTTCCTTA 59.325 57.895 0.00 0.00 0.00 2.69 R
4639 4933 1.338769 ACGTGAATGGTTCTACTGGCC 60.339 52.381 0.00 0.00 0.00 5.36 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 3.541632 ACTATTTACCTTGGGCACATCG 58.458 45.455 0.00 0.00 0.00 3.84
22 23 1.102978 ATTTACCTTGGGCACATCGC 58.897 50.000 0.00 0.00 41.28 4.58
23 24 0.037590 TTTACCTTGGGCACATCGCT 59.962 50.000 0.00 0.00 41.91 4.93
24 25 0.037590 TTACCTTGGGCACATCGCTT 59.962 50.000 0.00 0.00 41.91 4.68
25 26 0.392461 TACCTTGGGCACATCGCTTC 60.392 55.000 0.00 0.00 41.91 3.86
26 27 1.377725 CCTTGGGCACATCGCTTCT 60.378 57.895 0.00 0.00 41.91 2.85
27 28 1.651240 CCTTGGGCACATCGCTTCTG 61.651 60.000 0.00 0.00 41.91 3.02
28 29 2.262471 CTTGGGCACATCGCTTCTGC 62.262 60.000 0.00 0.00 41.91 4.26
29 30 2.747460 GGGCACATCGCTTCTGCA 60.747 61.111 0.00 0.00 41.91 4.41
30 31 2.334946 GGGCACATCGCTTCTGCAA 61.335 57.895 0.00 0.00 41.91 4.08
31 32 1.154150 GGCACATCGCTTCTGCAAC 60.154 57.895 0.00 0.00 41.91 4.17
32 33 1.154150 GCACATCGCTTCTGCAACC 60.154 57.895 0.00 0.00 39.64 3.77
33 34 1.855213 GCACATCGCTTCTGCAACCA 61.855 55.000 0.00 0.00 39.64 3.67
34 35 0.592637 CACATCGCTTCTGCAACCAA 59.407 50.000 0.00 0.00 39.64 3.67
35 36 0.877071 ACATCGCTTCTGCAACCAAG 59.123 50.000 0.00 0.00 39.64 3.61
36 37 0.877071 CATCGCTTCTGCAACCAAGT 59.123 50.000 0.00 0.00 39.64 3.16
37 38 1.135859 CATCGCTTCTGCAACCAAGTC 60.136 52.381 0.00 0.00 39.64 3.01
38 39 0.884704 TCGCTTCTGCAACCAAGTCC 60.885 55.000 0.00 0.00 39.64 3.85
39 40 1.165907 CGCTTCTGCAACCAAGTCCA 61.166 55.000 0.00 0.00 39.64 4.02
40 41 0.595095 GCTTCTGCAACCAAGTCCAG 59.405 55.000 0.00 0.00 39.41 3.86
41 42 1.815408 GCTTCTGCAACCAAGTCCAGA 60.815 52.381 0.00 0.00 39.41 3.86
42 43 2.787994 CTTCTGCAACCAAGTCCAGAT 58.212 47.619 0.00 0.00 34.62 2.90
43 44 2.479566 TCTGCAACCAAGTCCAGATC 57.520 50.000 0.00 0.00 30.00 2.75
44 45 1.003580 TCTGCAACCAAGTCCAGATCC 59.996 52.381 0.00 0.00 30.00 3.36
45 46 0.038166 TGCAACCAAGTCCAGATCCC 59.962 55.000 0.00 0.00 0.00 3.85
46 47 0.329596 GCAACCAAGTCCAGATCCCT 59.670 55.000 0.00 0.00 0.00 4.20
47 48 1.680249 GCAACCAAGTCCAGATCCCTC 60.680 57.143 0.00 0.00 0.00 4.30
48 49 1.065126 CAACCAAGTCCAGATCCCTCC 60.065 57.143 0.00 0.00 0.00 4.30
49 50 0.419459 ACCAAGTCCAGATCCCTCCT 59.581 55.000 0.00 0.00 0.00 3.69
50 51 1.127343 CCAAGTCCAGATCCCTCCTC 58.873 60.000 0.00 0.00 0.00 3.71
51 52 1.127343 CAAGTCCAGATCCCTCCTCC 58.873 60.000 0.00 0.00 0.00 4.30
52 53 0.719015 AAGTCCAGATCCCTCCTCCA 59.281 55.000 0.00 0.00 0.00 3.86
53 54 0.264359 AGTCCAGATCCCTCCTCCAG 59.736 60.000 0.00 0.00 0.00 3.86
54 55 1.074926 TCCAGATCCCTCCTCCAGC 60.075 63.158 0.00 0.00 0.00 4.85
55 56 1.074623 CCAGATCCCTCCTCCAGCT 60.075 63.158 0.00 0.00 0.00 4.24
56 57 0.189574 CCAGATCCCTCCTCCAGCTA 59.810 60.000 0.00 0.00 0.00 3.32
57 58 1.413662 CCAGATCCCTCCTCCAGCTAA 60.414 57.143 0.00 0.00 0.00 3.09
58 59 2.618794 CAGATCCCTCCTCCAGCTAAT 58.381 52.381 0.00 0.00 0.00 1.73
59 60 2.978278 CAGATCCCTCCTCCAGCTAATT 59.022 50.000 0.00 0.00 0.00 1.40
60 61 3.393941 CAGATCCCTCCTCCAGCTAATTT 59.606 47.826 0.00 0.00 0.00 1.82
61 62 3.393941 AGATCCCTCCTCCAGCTAATTTG 59.606 47.826 0.00 0.00 0.00 2.32
62 63 2.562296 TCCCTCCTCCAGCTAATTTGT 58.438 47.619 0.00 0.00 0.00 2.83
63 64 2.505819 TCCCTCCTCCAGCTAATTTGTC 59.494 50.000 0.00 0.00 0.00 3.18
64 65 2.239654 CCCTCCTCCAGCTAATTTGTCA 59.760 50.000 0.00 0.00 0.00 3.58
65 66 3.117738 CCCTCCTCCAGCTAATTTGTCAT 60.118 47.826 0.00 0.00 0.00 3.06
66 67 4.530875 CCTCCTCCAGCTAATTTGTCATT 58.469 43.478 0.00 0.00 0.00 2.57
67 68 4.578105 CCTCCTCCAGCTAATTTGTCATTC 59.422 45.833 0.00 0.00 0.00 2.67
68 69 5.435291 CTCCTCCAGCTAATTTGTCATTCT 58.565 41.667 0.00 0.00 0.00 2.40
69 70 5.819991 TCCTCCAGCTAATTTGTCATTCTT 58.180 37.500 0.00 0.00 0.00 2.52
70 71 6.248433 TCCTCCAGCTAATTTGTCATTCTTT 58.752 36.000 0.00 0.00 0.00 2.52
71 72 6.151648 TCCTCCAGCTAATTTGTCATTCTTTG 59.848 38.462 0.00 0.00 0.00 2.77
72 73 6.271488 TCCAGCTAATTTGTCATTCTTTGG 57.729 37.500 0.00 0.00 0.00 3.28
73 74 4.866486 CCAGCTAATTTGTCATTCTTTGGC 59.134 41.667 0.00 0.00 0.00 4.52
74 75 5.337009 CCAGCTAATTTGTCATTCTTTGGCT 60.337 40.000 0.00 0.00 34.92 4.75
75 76 6.127647 CCAGCTAATTTGTCATTCTTTGGCTA 60.128 38.462 0.00 0.00 33.17 3.93
76 77 7.417116 CCAGCTAATTTGTCATTCTTTGGCTAT 60.417 37.037 0.00 0.00 33.17 2.97
77 78 8.623903 CAGCTAATTTGTCATTCTTTGGCTATA 58.376 33.333 0.00 0.00 33.17 1.31
78 79 9.189156 AGCTAATTTGTCATTCTTTGGCTATAA 57.811 29.630 0.00 0.00 33.17 0.98
79 80 9.455847 GCTAATTTGTCATTCTTTGGCTATAAG 57.544 33.333 0.00 0.00 0.00 1.73
80 81 9.956720 CTAATTTGTCATTCTTTGGCTATAAGG 57.043 33.333 0.00 0.00 0.00 2.69
81 82 7.961326 ATTTGTCATTCTTTGGCTATAAGGT 57.039 32.000 0.00 0.00 0.00 3.50
82 83 9.474313 AATTTGTCATTCTTTGGCTATAAGGTA 57.526 29.630 0.00 0.00 0.00 3.08
83 84 9.646522 ATTTGTCATTCTTTGGCTATAAGGTAT 57.353 29.630 0.00 0.00 0.00 2.73
84 85 8.450578 TTGTCATTCTTTGGCTATAAGGTATG 57.549 34.615 0.00 0.00 0.00 2.39
85 86 7.573710 TGTCATTCTTTGGCTATAAGGTATGT 58.426 34.615 0.00 0.00 0.00 2.29
86 87 8.710239 TGTCATTCTTTGGCTATAAGGTATGTA 58.290 33.333 0.00 0.00 0.00 2.29
87 88 9.726438 GTCATTCTTTGGCTATAAGGTATGTAT 57.274 33.333 0.00 0.00 0.00 2.29
90 91 7.979444 TCTTTGGCTATAAGGTATGTATTGC 57.021 36.000 0.00 0.00 0.00 3.56
91 92 7.745717 TCTTTGGCTATAAGGTATGTATTGCT 58.254 34.615 0.00 0.00 32.47 3.91
92 93 7.661437 TCTTTGGCTATAAGGTATGTATTGCTG 59.339 37.037 0.00 0.00 32.47 4.41
93 94 6.433847 TGGCTATAAGGTATGTATTGCTGT 57.566 37.500 0.00 0.00 32.47 4.40
94 95 6.230472 TGGCTATAAGGTATGTATTGCTGTG 58.770 40.000 0.00 0.00 32.47 3.66
95 96 5.122396 GGCTATAAGGTATGTATTGCTGTGC 59.878 44.000 0.00 0.00 32.47 4.57
96 97 5.700832 GCTATAAGGTATGTATTGCTGTGCA 59.299 40.000 0.00 0.00 36.47 4.57
97 98 6.372659 GCTATAAGGTATGTATTGCTGTGCAT 59.627 38.462 0.00 0.00 38.76 3.96
98 99 7.094634 GCTATAAGGTATGTATTGCTGTGCATT 60.095 37.037 0.00 0.00 38.76 3.56
99 100 5.920193 AAGGTATGTATTGCTGTGCATTT 57.080 34.783 0.00 0.00 38.76 2.32
100 101 8.690203 ATAAGGTATGTATTGCTGTGCATTTA 57.310 30.769 0.00 0.00 38.76 1.40
101 102 7.587037 AAGGTATGTATTGCTGTGCATTTAT 57.413 32.000 0.00 0.00 38.76 1.40
102 103 7.587037 AGGTATGTATTGCTGTGCATTTATT 57.413 32.000 0.00 0.00 38.76 1.40
103 104 7.428020 AGGTATGTATTGCTGTGCATTTATTG 58.572 34.615 0.00 0.00 38.76 1.90
117 118 4.776743 CATTTATTGCTCCGTATCACAGC 58.223 43.478 0.00 0.00 0.00 4.40
118 119 3.819564 TTATTGCTCCGTATCACAGCT 57.180 42.857 0.00 0.00 34.03 4.24
119 120 1.945387 ATTGCTCCGTATCACAGCTG 58.055 50.000 13.48 13.48 34.03 4.24
120 121 0.894835 TTGCTCCGTATCACAGCTGA 59.105 50.000 23.35 0.00 34.03 4.26
121 122 1.114627 TGCTCCGTATCACAGCTGAT 58.885 50.000 23.35 7.26 40.47 2.90
122 123 1.067669 TGCTCCGTATCACAGCTGATC 59.932 52.381 23.35 4.64 38.21 2.92
123 124 1.604185 GCTCCGTATCACAGCTGATCC 60.604 57.143 23.35 2.18 38.21 3.36
124 125 1.959985 CTCCGTATCACAGCTGATCCT 59.040 52.381 23.35 4.40 38.21 3.24
125 126 1.957177 TCCGTATCACAGCTGATCCTC 59.043 52.381 23.35 6.80 38.21 3.71
126 127 1.000283 CCGTATCACAGCTGATCCTCC 60.000 57.143 23.35 2.38 38.21 4.30
127 128 1.959985 CGTATCACAGCTGATCCTCCT 59.040 52.381 23.35 0.00 38.21 3.69
128 129 2.363680 CGTATCACAGCTGATCCTCCTT 59.636 50.000 23.35 0.00 38.21 3.36
129 130 3.551863 CGTATCACAGCTGATCCTCCTTC 60.552 52.174 23.35 0.78 38.21 3.46
130 131 1.198713 TCACAGCTGATCCTCCTTCC 58.801 55.000 23.35 0.00 0.00 3.46
131 132 1.202330 CACAGCTGATCCTCCTTCCT 58.798 55.000 23.35 0.00 0.00 3.36
132 133 1.558756 CACAGCTGATCCTCCTTCCTT 59.441 52.381 23.35 0.00 0.00 3.36
133 134 2.768527 CACAGCTGATCCTCCTTCCTTA 59.231 50.000 23.35 0.00 0.00 2.69
134 135 2.769095 ACAGCTGATCCTCCTTCCTTAC 59.231 50.000 23.35 0.00 0.00 2.34
135 136 3.037549 CAGCTGATCCTCCTTCCTTACT 58.962 50.000 8.42 0.00 0.00 2.24
136 137 3.454082 CAGCTGATCCTCCTTCCTTACTT 59.546 47.826 8.42 0.00 0.00 2.24
137 138 3.709141 AGCTGATCCTCCTTCCTTACTTC 59.291 47.826 0.00 0.00 0.00 3.01
138 139 3.181459 GCTGATCCTCCTTCCTTACTTCC 60.181 52.174 0.00 0.00 0.00 3.46
139 140 3.385115 TGATCCTCCTTCCTTACTTCCC 58.615 50.000 0.00 0.00 0.00 3.97
140 141 3.014110 TGATCCTCCTTCCTTACTTCCCT 59.986 47.826 0.00 0.00 0.00 4.20
141 142 3.579742 TCCTCCTTCCTTACTTCCCTT 57.420 47.619 0.00 0.00 0.00 3.95
142 143 3.883135 TCCTCCTTCCTTACTTCCCTTT 58.117 45.455 0.00 0.00 0.00 3.11
143 144 3.844804 TCCTCCTTCCTTACTTCCCTTTC 59.155 47.826 0.00 0.00 0.00 2.62
144 145 3.847184 CCTCCTTCCTTACTTCCCTTTCT 59.153 47.826 0.00 0.00 0.00 2.52
145 146 4.323868 CCTCCTTCCTTACTTCCCTTTCTG 60.324 50.000 0.00 0.00 0.00 3.02
146 147 4.240323 TCCTTCCTTACTTCCCTTTCTGT 58.760 43.478 0.00 0.00 0.00 3.41
147 148 4.663592 TCCTTCCTTACTTCCCTTTCTGTT 59.336 41.667 0.00 0.00 0.00 3.16
148 149 4.762251 CCTTCCTTACTTCCCTTTCTGTTG 59.238 45.833 0.00 0.00 0.00 3.33
149 150 4.367039 TCCTTACTTCCCTTTCTGTTGG 57.633 45.455 0.00 0.00 0.00 3.77
150 151 3.720002 TCCTTACTTCCCTTTCTGTTGGT 59.280 43.478 0.00 0.00 0.00 3.67
151 152 4.909088 TCCTTACTTCCCTTTCTGTTGGTA 59.091 41.667 0.00 0.00 0.00 3.25
152 153 5.012768 TCCTTACTTCCCTTTCTGTTGGTAG 59.987 44.000 0.00 0.00 0.00 3.18
153 154 3.790089 ACTTCCCTTTCTGTTGGTAGG 57.210 47.619 0.00 0.00 0.00 3.18
155 156 1.368374 TCCCTTTCTGTTGGTAGGGG 58.632 55.000 6.21 0.00 46.10 4.79
156 157 1.132332 TCCCTTTCTGTTGGTAGGGGA 60.132 52.381 6.21 0.00 46.10 4.81
157 158 1.923148 CCCTTTCTGTTGGTAGGGGAT 59.077 52.381 0.00 0.00 43.04 3.85
158 159 2.311841 CCCTTTCTGTTGGTAGGGGATT 59.688 50.000 0.00 0.00 43.04 3.01
159 160 3.526019 CCCTTTCTGTTGGTAGGGGATTA 59.474 47.826 0.00 0.00 43.04 1.75
160 161 4.017867 CCCTTTCTGTTGGTAGGGGATTAA 60.018 45.833 0.00 0.00 43.04 1.40
161 162 5.517655 CCCTTTCTGTTGGTAGGGGATTAAA 60.518 44.000 0.00 0.00 43.04 1.52
162 163 6.014012 CCTTTCTGTTGGTAGGGGATTAAAA 58.986 40.000 0.00 0.00 0.00 1.52
163 164 6.667848 CCTTTCTGTTGGTAGGGGATTAAAAT 59.332 38.462 0.00 0.00 0.00 1.82
164 165 7.147897 CCTTTCTGTTGGTAGGGGATTAAAATC 60.148 40.741 0.00 0.00 34.66 2.17
165 166 6.395780 TCTGTTGGTAGGGGATTAAAATCA 57.604 37.500 5.15 0.00 37.15 2.57
166 167 6.980577 TCTGTTGGTAGGGGATTAAAATCAT 58.019 36.000 5.15 0.00 37.15 2.45
167 168 8.108378 TCTGTTGGTAGGGGATTAAAATCATA 57.892 34.615 5.15 0.00 37.15 2.15
168 169 8.732854 TCTGTTGGTAGGGGATTAAAATCATAT 58.267 33.333 5.15 0.00 37.15 1.78
169 170 8.934023 TGTTGGTAGGGGATTAAAATCATATC 57.066 34.615 5.15 0.00 37.15 1.63
170 171 7.947890 TGTTGGTAGGGGATTAAAATCATATCC 59.052 37.037 5.15 0.00 37.15 2.59
171 172 7.905144 TGGTAGGGGATTAAAATCATATCCT 57.095 36.000 5.15 7.76 38.30 3.24
172 173 8.300752 TGGTAGGGGATTAAAATCATATCCTT 57.699 34.615 5.15 0.00 38.30 3.36
173 174 8.742437 TGGTAGGGGATTAAAATCATATCCTTT 58.258 33.333 5.15 0.00 38.30 3.11
174 175 9.025041 GGTAGGGGATTAAAATCATATCCTTTG 57.975 37.037 5.15 0.00 38.30 2.77
175 176 7.544804 AGGGGATTAAAATCATATCCTTTGC 57.455 36.000 5.15 0.00 38.30 3.68
176 177 7.308320 AGGGGATTAAAATCATATCCTTTGCT 58.692 34.615 5.15 0.00 38.30 3.91
177 178 7.234166 AGGGGATTAAAATCATATCCTTTGCTG 59.766 37.037 5.15 0.00 38.30 4.41
178 179 7.233348 GGGGATTAAAATCATATCCTTTGCTGA 59.767 37.037 5.15 0.00 38.30 4.26
179 180 8.641541 GGGATTAAAATCATATCCTTTGCTGAA 58.358 33.333 5.15 0.00 38.30 3.02
180 181 9.688592 GGATTAAAATCATATCCTTTGCTGAAG 57.311 33.333 5.15 0.00 37.15 3.02
184 185 6.851222 AATCATATCCTTTGCTGAAGTACG 57.149 37.500 0.00 0.00 33.29 3.67
185 186 4.693283 TCATATCCTTTGCTGAAGTACGG 58.307 43.478 0.00 0.00 33.29 4.02
186 187 4.404394 TCATATCCTTTGCTGAAGTACGGA 59.596 41.667 0.00 0.00 33.29 4.69
187 188 3.914426 ATCCTTTGCTGAAGTACGGAT 57.086 42.857 0.00 0.00 33.29 4.18
188 189 3.247006 TCCTTTGCTGAAGTACGGATC 57.753 47.619 0.00 0.00 33.29 3.36
189 190 2.832129 TCCTTTGCTGAAGTACGGATCT 59.168 45.455 0.00 0.00 33.29 2.75
190 191 2.932614 CCTTTGCTGAAGTACGGATCTG 59.067 50.000 0.00 0.00 33.29 2.90
191 192 3.368427 CCTTTGCTGAAGTACGGATCTGA 60.368 47.826 9.00 0.00 33.29 3.27
192 193 3.510388 TTGCTGAAGTACGGATCTGAG 57.490 47.619 9.00 0.00 0.00 3.35
193 194 1.135139 TGCTGAAGTACGGATCTGAGC 59.865 52.381 9.00 6.13 0.00 4.26
194 195 1.407258 GCTGAAGTACGGATCTGAGCT 59.593 52.381 9.00 2.67 0.00 4.09
195 196 2.159170 GCTGAAGTACGGATCTGAGCTT 60.159 50.000 9.00 11.32 0.00 3.74
196 197 3.677424 GCTGAAGTACGGATCTGAGCTTT 60.677 47.826 9.00 0.00 0.00 3.51
197 198 4.499183 CTGAAGTACGGATCTGAGCTTTT 58.501 43.478 9.00 0.00 0.00 2.27
198 199 5.651530 CTGAAGTACGGATCTGAGCTTTTA 58.348 41.667 9.00 5.02 0.00 1.52
199 200 6.032956 TGAAGTACGGATCTGAGCTTTTAA 57.967 37.500 9.00 0.50 0.00 1.52
200 201 6.460781 TGAAGTACGGATCTGAGCTTTTAAA 58.539 36.000 9.00 0.00 0.00 1.52
201 202 6.367969 TGAAGTACGGATCTGAGCTTTTAAAC 59.632 38.462 9.00 1.15 0.00 2.01
202 203 5.176592 AGTACGGATCTGAGCTTTTAAACC 58.823 41.667 9.00 0.00 0.00 3.27
203 204 3.344515 ACGGATCTGAGCTTTTAAACCC 58.655 45.455 9.00 0.00 0.00 4.11
204 205 3.244770 ACGGATCTGAGCTTTTAAACCCA 60.245 43.478 9.00 0.00 0.00 4.51
205 206 3.375299 CGGATCTGAGCTTTTAAACCCAG 59.625 47.826 0.00 0.00 0.00 4.45
218 219 6.887626 TTTAAACCCAGATGTTGGTAAGTC 57.112 37.500 0.00 0.00 46.25 3.01
223 224 4.595781 ACCCAGATGTTGGTAAGTCTGTAA 59.404 41.667 0.00 0.00 46.25 2.41
233 234 9.431887 TGTTGGTAAGTCTGTAATTAGTTCATC 57.568 33.333 0.00 0.00 0.00 2.92
259 261 9.181805 CCAGATATACAAGTACGTACTGATTTG 57.818 37.037 28.00 22.87 36.50 2.32
263 265 4.797471 ACAAGTACGTACTGATTTGCGTA 58.203 39.130 28.00 0.00 38.56 4.42
270 272 2.094762 ACTGATTTGCGTACCCTGAC 57.905 50.000 0.00 0.00 0.00 3.51
273 275 1.346395 TGATTTGCGTACCCTGACTGT 59.654 47.619 0.00 0.00 0.00 3.55
279 281 0.974383 CGTACCCTGACTGTCCCTTT 59.026 55.000 5.17 0.00 0.00 3.11
312 316 5.684704 TCCTCTAATATTGCAGGAAGGTTG 58.315 41.667 12.64 0.00 31.78 3.77
313 317 4.823989 CCTCTAATATTGCAGGAAGGTTGG 59.176 45.833 8.28 0.00 0.00 3.77
319 323 1.376812 GCAGGAAGGTTGGGGTACG 60.377 63.158 0.00 0.00 0.00 3.67
322 327 1.134491 CAGGAAGGTTGGGGTACGATC 60.134 57.143 0.00 0.00 0.00 3.69
323 328 1.201424 GGAAGGTTGGGGTACGATCT 58.799 55.000 0.00 0.00 0.00 2.75
328 333 0.462047 GTTGGGGTACGATCTGGCAG 60.462 60.000 8.58 8.58 0.00 4.85
334 339 2.420129 GGGTACGATCTGGCAGAACAAT 60.420 50.000 22.84 12.08 0.00 2.71
336 341 3.430929 GGTACGATCTGGCAGAACAATCT 60.431 47.826 22.84 3.04 35.88 2.40
338 343 3.005554 ACGATCTGGCAGAACAATCTTG 58.994 45.455 22.84 10.13 32.03 3.02
365 371 2.048444 TCGGACGTATACCTGCTCTT 57.952 50.000 0.00 0.00 0.00 2.85
367 373 2.098607 TCGGACGTATACCTGCTCTTTG 59.901 50.000 0.00 0.00 0.00 2.77
368 374 2.202566 GGACGTATACCTGCTCTTTGC 58.797 52.381 0.00 0.00 43.25 3.68
377 383 2.027100 ACCTGCTCTTTGCTTAGGTACC 60.027 50.000 2.73 2.73 43.60 3.34
382 388 4.469945 TGCTCTTTGCTTAGGTACCATACT 59.530 41.667 15.94 0.00 43.37 2.12
384 390 5.524281 GCTCTTTGCTTAGGTACCATACTTC 59.476 44.000 15.94 0.00 38.95 3.01
385 391 6.614694 TCTTTGCTTAGGTACCATACTTCA 57.385 37.500 15.94 1.10 0.00 3.02
395 401 7.923414 AGGTACCATACTTCATGTCTTTTTC 57.077 36.000 15.94 0.00 32.21 2.29
397 405 6.884836 GGTACCATACTTCATGTCTTTTTCCT 59.115 38.462 7.15 0.00 32.21 3.36
403 417 9.626045 CATACTTCATGTCTTTTTCCTTTTACC 57.374 33.333 0.00 0.00 0.00 2.85
407 421 8.990163 TTCATGTCTTTTTCCTTTTACCTACT 57.010 30.769 0.00 0.00 0.00 2.57
411 425 7.226441 TGTCTTTTTCCTTTTACCTACTACCC 58.774 38.462 0.00 0.00 0.00 3.69
423 437 2.700897 CCTACTACCCTCACAGATTGGG 59.299 54.545 0.00 0.00 46.07 4.12
430 444 3.813443 CCCTCACAGATTGGGTGAATAG 58.187 50.000 0.00 0.00 44.04 1.73
432 446 4.446371 CCTCACAGATTGGGTGAATAGTC 58.554 47.826 0.00 0.00 44.04 2.59
559 575 4.724074 AATATACGAACTTGGTCCGACA 57.276 40.909 0.00 0.00 0.00 4.35
947 1095 2.642139 TATGAACTTGGTCCGACGTC 57.358 50.000 5.18 5.18 0.00 4.34
1005 1164 8.283291 GCTCATTTTAAGGCTACACACATATAC 58.717 37.037 0.00 0.00 0.00 1.47
2051 2269 2.517959 CAATTCCCTGACTTCTTGGCA 58.482 47.619 0.00 0.00 0.00 4.92
2064 2282 4.721776 ACTTCTTGGCAGACCTATTATCCA 59.278 41.667 0.00 0.00 36.63 3.41
2158 2376 1.544691 GCGAGACCACTCTGTTCCTTA 59.455 52.381 0.00 0.00 40.65 2.69
2177 2395 0.952497 ACGCGTCTCTTCGTGAGGTA 60.952 55.000 5.58 0.00 42.86 3.08
2250 2468 2.111251 GCGGGGGAGCCTATGTTC 59.889 66.667 0.00 0.00 0.00 3.18
2251 2469 2.421739 CGGGGGAGCCTATGTTCG 59.578 66.667 0.00 0.00 0.00 3.95
2252 2470 2.111251 GGGGGAGCCTATGTTCGC 59.889 66.667 0.00 0.00 34.51 4.70
2253 2471 2.280186 GGGGAGCCTATGTTCGCG 60.280 66.667 0.00 0.00 35.83 5.87
2254 2472 2.967615 GGGAGCCTATGTTCGCGC 60.968 66.667 0.00 0.00 0.00 6.86
2402 2628 0.178861 ATCGGATTAGGGGATGGCCT 60.179 55.000 3.32 0.00 0.00 5.19
2637 2864 3.389983 TGACTTGGCTAGTACTTGTTGGT 59.610 43.478 0.00 0.00 37.17 3.67
2867 3094 0.739462 TGCGCTCGAATCCGAAACAT 60.739 50.000 9.73 0.00 45.04 2.71
2968 3195 1.848652 TTCACTAGCGTTCTAGGCCT 58.151 50.000 11.78 11.78 45.15 5.19
2969 3196 2.723322 TCACTAGCGTTCTAGGCCTA 57.277 50.000 13.09 13.09 45.15 3.93
2998 3225 2.125310 TAACATGCACGGGCGAGG 60.125 61.111 4.58 0.00 45.35 4.63
3058 3285 8.434589 AATGGGAAGAAACATATTTTTCCTCA 57.565 30.769 12.69 5.76 36.31 3.86
3189 3416 4.715297 GGAGGGACATCTTAAGAGGTTACA 59.285 45.833 22.54 0.00 39.36 2.41
3190 3417 5.395435 GGAGGGACATCTTAAGAGGTTACAC 60.395 48.000 22.54 12.76 39.36 2.90
3381 3660 2.498078 GTTCCTCTTCCAATCCTCGACT 59.502 50.000 0.00 0.00 0.00 4.18
3492 3771 5.796424 AGTCCAAATGCAACAATCTCTTT 57.204 34.783 0.00 0.00 0.00 2.52
3706 3986 3.090037 CCCCACGTATCTATACTCAGGG 58.910 54.545 11.48 11.48 36.67 4.45
3739 4019 6.746822 CGCATGCTTATATTTCAAACACTTCA 59.253 34.615 17.13 0.00 0.00 3.02
4001 4286 5.592688 GCTTTAGATGCCCCTACATTAACAA 59.407 40.000 0.00 0.00 0.00 2.83
4007 4292 6.897413 AGATGCCCCTACATTAACAAATTCTT 59.103 34.615 0.00 0.00 0.00 2.52
4270 4556 4.363991 ACTGGAGAAACAAGCTGAGAAT 57.636 40.909 0.00 0.00 0.00 2.40
4528 4814 1.522355 CTGGCGCTCCATGTCGAAT 60.522 57.895 7.64 0.00 42.51 3.34
4639 4933 5.180868 CCCATTTTCTCTTGTCTTCTCACAG 59.819 44.000 0.00 0.00 0.00 3.66
5197 5766 4.567747 CCTTATGTGCCCCAGTTTAGACTT 60.568 45.833 0.00 0.00 32.54 3.01
5271 5840 4.836125 ACTCGTAAGTCGTTGGAGTAAA 57.164 40.909 0.00 0.00 36.28 2.01
5272 5841 5.186996 ACTCGTAAGTCGTTGGAGTAAAA 57.813 39.130 0.00 0.00 36.28 1.52
5414 6085 1.154263 CCTATACGCGCCGCTAGAC 60.154 63.158 5.73 0.00 0.00 2.59
5427 6098 3.617706 GCCGCTAGACTAAACCTCTTTTC 59.382 47.826 0.00 0.00 0.00 2.29
5431 6102 6.157211 CGCTAGACTAAACCTCTTTTCTGAA 58.843 40.000 0.00 0.00 0.00 3.02
5459 6130 3.138304 GCCTTCCCATTTTGGTTCAAAC 58.862 45.455 0.00 0.00 35.17 2.93
5475 6146 2.225491 TCAAACTTTCCTTTCATCCGCG 59.775 45.455 0.00 0.00 0.00 6.46
5499 6170 3.433274 CGTGATATTCATGGGACGAATGG 59.567 47.826 0.00 0.00 34.89 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.541632 CGATGTGCCCAAGGTAAATAGT 58.458 45.455 0.00 0.00 0.00 2.12
1 2 2.290641 GCGATGTGCCCAAGGTAAATAG 59.709 50.000 0.00 0.00 37.76 1.73
2 3 2.294074 GCGATGTGCCCAAGGTAAATA 58.706 47.619 0.00 0.00 37.76 1.40
3 4 1.102978 GCGATGTGCCCAAGGTAAAT 58.897 50.000 0.00 0.00 37.76 1.40
4 5 2.562125 GCGATGTGCCCAAGGTAAA 58.438 52.632 0.00 0.00 37.76 2.01
5 6 4.312052 GCGATGTGCCCAAGGTAA 57.688 55.556 0.00 0.00 37.76 2.85
15 16 0.592637 TTGGTTGCAGAAGCGATGTG 59.407 50.000 0.00 0.00 46.23 3.21
16 17 0.877071 CTTGGTTGCAGAAGCGATGT 59.123 50.000 0.00 0.00 46.23 3.06
17 18 0.877071 ACTTGGTTGCAGAAGCGATG 59.123 50.000 0.00 0.00 46.23 3.84
18 19 1.160137 GACTTGGTTGCAGAAGCGAT 58.840 50.000 0.00 0.00 46.23 4.58
19 20 0.884704 GGACTTGGTTGCAGAAGCGA 60.885 55.000 0.00 0.00 46.23 4.93
20 21 1.165907 TGGACTTGGTTGCAGAAGCG 61.166 55.000 2.93 0.00 46.23 4.68
21 22 0.595095 CTGGACTTGGTTGCAGAAGC 59.405 55.000 2.93 0.00 37.11 3.86
22 23 2.260844 TCTGGACTTGGTTGCAGAAG 57.739 50.000 0.00 0.00 40.63 2.85
23 24 2.553028 GGATCTGGACTTGGTTGCAGAA 60.553 50.000 0.00 0.00 45.80 3.02
24 25 1.003580 GGATCTGGACTTGGTTGCAGA 59.996 52.381 0.00 0.00 46.60 4.26
25 26 1.457346 GGATCTGGACTTGGTTGCAG 58.543 55.000 0.00 0.00 36.32 4.41
26 27 0.038166 GGGATCTGGACTTGGTTGCA 59.962 55.000 0.00 0.00 0.00 4.08
27 28 0.329596 AGGGATCTGGACTTGGTTGC 59.670 55.000 0.00 0.00 0.00 4.17
28 29 1.065126 GGAGGGATCTGGACTTGGTTG 60.065 57.143 0.00 0.00 0.00 3.77
29 30 1.203492 AGGAGGGATCTGGACTTGGTT 60.203 52.381 0.00 0.00 0.00 3.67
30 31 0.419459 AGGAGGGATCTGGACTTGGT 59.581 55.000 0.00 0.00 0.00 3.67
31 32 1.127343 GAGGAGGGATCTGGACTTGG 58.873 60.000 0.00 0.00 0.00 3.61
32 33 1.127343 GGAGGAGGGATCTGGACTTG 58.873 60.000 0.00 0.00 0.00 3.16
33 34 0.719015 TGGAGGAGGGATCTGGACTT 59.281 55.000 0.00 0.00 0.00 3.01
34 35 0.264359 CTGGAGGAGGGATCTGGACT 59.736 60.000 0.00 0.00 0.00 3.85
35 36 1.406860 GCTGGAGGAGGGATCTGGAC 61.407 65.000 0.00 0.00 0.00 4.02
36 37 1.074926 GCTGGAGGAGGGATCTGGA 60.075 63.158 0.00 0.00 0.00 3.86
37 38 0.189574 TAGCTGGAGGAGGGATCTGG 59.810 60.000 0.00 0.00 0.00 3.86
38 39 2.094100 TTAGCTGGAGGAGGGATCTG 57.906 55.000 0.00 0.00 0.00 2.90
39 40 3.359110 AATTAGCTGGAGGAGGGATCT 57.641 47.619 0.00 0.00 0.00 2.75
40 41 3.137360 ACAAATTAGCTGGAGGAGGGATC 59.863 47.826 0.00 0.00 0.00 3.36
41 42 3.126453 ACAAATTAGCTGGAGGAGGGAT 58.874 45.455 0.00 0.00 0.00 3.85
42 43 2.505819 GACAAATTAGCTGGAGGAGGGA 59.494 50.000 0.00 0.00 0.00 4.20
43 44 2.239654 TGACAAATTAGCTGGAGGAGGG 59.760 50.000 0.00 0.00 0.00 4.30
44 45 3.634397 TGACAAATTAGCTGGAGGAGG 57.366 47.619 0.00 0.00 0.00 4.30
45 46 5.435291 AGAATGACAAATTAGCTGGAGGAG 58.565 41.667 0.00 0.00 0.00 3.69
46 47 5.441718 AGAATGACAAATTAGCTGGAGGA 57.558 39.130 0.00 0.00 0.00 3.71
47 48 6.327934 CAAAGAATGACAAATTAGCTGGAGG 58.672 40.000 0.00 0.00 0.00 4.30
48 49 6.327934 CCAAAGAATGACAAATTAGCTGGAG 58.672 40.000 0.00 0.00 0.00 3.86
49 50 5.336690 GCCAAAGAATGACAAATTAGCTGGA 60.337 40.000 0.00 0.00 0.00 3.86
50 51 4.866486 GCCAAAGAATGACAAATTAGCTGG 59.134 41.667 0.00 0.00 0.00 4.85
51 52 5.717119 AGCCAAAGAATGACAAATTAGCTG 58.283 37.500 0.00 0.00 0.00 4.24
52 53 5.990120 AGCCAAAGAATGACAAATTAGCT 57.010 34.783 0.00 0.00 0.00 3.32
53 54 9.455847 CTTATAGCCAAAGAATGACAAATTAGC 57.544 33.333 0.00 0.00 0.00 3.09
54 55 9.956720 CCTTATAGCCAAAGAATGACAAATTAG 57.043 33.333 0.00 0.00 0.00 1.73
55 56 9.474313 ACCTTATAGCCAAAGAATGACAAATTA 57.526 29.630 0.00 0.00 0.00 1.40
56 57 8.366359 ACCTTATAGCCAAAGAATGACAAATT 57.634 30.769 0.00 0.00 0.00 1.82
57 58 7.961326 ACCTTATAGCCAAAGAATGACAAAT 57.039 32.000 0.00 0.00 0.00 2.32
58 59 8.902806 CATACCTTATAGCCAAAGAATGACAAA 58.097 33.333 0.00 0.00 0.00 2.83
59 60 8.052748 ACATACCTTATAGCCAAAGAATGACAA 58.947 33.333 10.10 0.00 0.00 3.18
60 61 7.573710 ACATACCTTATAGCCAAAGAATGACA 58.426 34.615 10.10 0.00 0.00 3.58
61 62 9.726438 ATACATACCTTATAGCCAAAGAATGAC 57.274 33.333 10.10 0.00 0.00 3.06
64 65 9.014297 GCAATACATACCTTATAGCCAAAGAAT 57.986 33.333 0.00 0.00 0.00 2.40
65 66 8.217799 AGCAATACATACCTTATAGCCAAAGAA 58.782 33.333 0.00 0.00 0.00 2.52
66 67 7.661437 CAGCAATACATACCTTATAGCCAAAGA 59.339 37.037 0.00 0.00 0.00 2.52
67 68 7.445402 ACAGCAATACATACCTTATAGCCAAAG 59.555 37.037 0.00 0.00 0.00 2.77
68 69 7.228507 CACAGCAATACATACCTTATAGCCAAA 59.771 37.037 0.00 0.00 0.00 3.28
69 70 6.710295 CACAGCAATACATACCTTATAGCCAA 59.290 38.462 0.00 0.00 0.00 4.52
70 71 6.230472 CACAGCAATACATACCTTATAGCCA 58.770 40.000 0.00 0.00 0.00 4.75
71 72 5.122396 GCACAGCAATACATACCTTATAGCC 59.878 44.000 0.00 0.00 0.00 3.93
72 73 5.700832 TGCACAGCAATACATACCTTATAGC 59.299 40.000 0.00 0.00 34.76 2.97
73 74 7.912056 ATGCACAGCAATACATACCTTATAG 57.088 36.000 0.00 0.00 43.62 1.31
74 75 8.690203 AAATGCACAGCAATACATACCTTATA 57.310 30.769 0.00 0.00 43.62 0.98
75 76 7.587037 AAATGCACAGCAATACATACCTTAT 57.413 32.000 0.00 0.00 43.62 1.73
76 77 8.690203 ATAAATGCACAGCAATACATACCTTA 57.310 30.769 0.00 0.00 43.62 2.69
77 78 5.920193 AAATGCACAGCAATACATACCTT 57.080 34.783 0.00 0.00 43.62 3.50
78 79 7.428020 CAATAAATGCACAGCAATACATACCT 58.572 34.615 0.00 0.00 43.62 3.08
79 80 7.627585 CAATAAATGCACAGCAATACATACC 57.372 36.000 0.00 0.00 43.62 2.73
95 96 4.512944 AGCTGTGATACGGAGCAATAAATG 59.487 41.667 0.00 0.00 35.03 2.32
96 97 4.512944 CAGCTGTGATACGGAGCAATAAAT 59.487 41.667 5.25 0.00 35.03 1.40
97 98 3.871006 CAGCTGTGATACGGAGCAATAAA 59.129 43.478 5.25 0.00 35.03 1.40
98 99 3.132111 TCAGCTGTGATACGGAGCAATAA 59.868 43.478 14.67 0.00 35.03 1.40
99 100 2.693074 TCAGCTGTGATACGGAGCAATA 59.307 45.455 14.67 0.00 35.03 1.90
100 101 1.482182 TCAGCTGTGATACGGAGCAAT 59.518 47.619 14.67 0.00 35.03 3.56
101 102 0.894835 TCAGCTGTGATACGGAGCAA 59.105 50.000 14.67 0.00 35.03 3.91
102 103 1.067669 GATCAGCTGTGATACGGAGCA 59.932 52.381 14.67 0.00 43.92 4.26
103 104 1.604185 GGATCAGCTGTGATACGGAGC 60.604 57.143 14.67 0.00 43.92 4.70
104 105 2.430546 GGATCAGCTGTGATACGGAG 57.569 55.000 14.67 0.00 43.92 4.63
108 109 3.244044 GGAAGGAGGATCAGCTGTGATAC 60.244 52.174 14.67 1.32 43.92 2.24
109 110 2.968574 GGAAGGAGGATCAGCTGTGATA 59.031 50.000 14.67 0.00 43.92 2.15
110 111 1.767681 GGAAGGAGGATCAGCTGTGAT 59.232 52.381 14.67 0.00 46.75 3.06
111 112 1.198713 GGAAGGAGGATCAGCTGTGA 58.801 55.000 14.67 0.00 36.25 3.58
112 113 1.202330 AGGAAGGAGGATCAGCTGTG 58.798 55.000 14.67 0.00 36.25 3.66
113 114 1.963985 AAGGAAGGAGGATCAGCTGT 58.036 50.000 14.67 0.42 36.25 4.40
114 115 3.037549 AGTAAGGAAGGAGGATCAGCTG 58.962 50.000 7.63 7.63 36.25 4.24
115 116 3.413105 AGTAAGGAAGGAGGATCAGCT 57.587 47.619 0.00 0.00 36.25 4.24
116 117 3.181459 GGAAGTAAGGAAGGAGGATCAGC 60.181 52.174 0.00 0.00 36.25 4.26
117 118 3.389656 GGGAAGTAAGGAAGGAGGATCAG 59.610 52.174 0.00 0.00 36.25 2.90
118 119 3.014110 AGGGAAGTAAGGAAGGAGGATCA 59.986 47.826 0.00 0.00 36.25 2.92
119 120 3.659841 AGGGAAGTAAGGAAGGAGGATC 58.340 50.000 0.00 0.00 0.00 3.36
120 121 3.805360 AGGGAAGTAAGGAAGGAGGAT 57.195 47.619 0.00 0.00 0.00 3.24
121 122 3.579742 AAGGGAAGTAAGGAAGGAGGA 57.420 47.619 0.00 0.00 0.00 3.71
122 123 3.847184 AGAAAGGGAAGTAAGGAAGGAGG 59.153 47.826 0.00 0.00 0.00 4.30
123 124 4.287326 ACAGAAAGGGAAGTAAGGAAGGAG 59.713 45.833 0.00 0.00 0.00 3.69
124 125 4.240323 ACAGAAAGGGAAGTAAGGAAGGA 58.760 43.478 0.00 0.00 0.00 3.36
125 126 4.642466 ACAGAAAGGGAAGTAAGGAAGG 57.358 45.455 0.00 0.00 0.00 3.46
126 127 4.762251 CCAACAGAAAGGGAAGTAAGGAAG 59.238 45.833 0.00 0.00 0.00 3.46
127 128 4.167307 ACCAACAGAAAGGGAAGTAAGGAA 59.833 41.667 0.00 0.00 0.00 3.36
128 129 3.720002 ACCAACAGAAAGGGAAGTAAGGA 59.280 43.478 0.00 0.00 0.00 3.36
129 130 4.100279 ACCAACAGAAAGGGAAGTAAGG 57.900 45.455 0.00 0.00 0.00 2.69
130 131 5.246307 CCTACCAACAGAAAGGGAAGTAAG 58.754 45.833 0.00 0.00 0.00 2.34
131 132 5.237236 CCTACCAACAGAAAGGGAAGTAA 57.763 43.478 0.00 0.00 0.00 2.24
132 133 4.903045 CCTACCAACAGAAAGGGAAGTA 57.097 45.455 0.00 0.00 0.00 2.24
133 134 3.790089 CCTACCAACAGAAAGGGAAGT 57.210 47.619 0.00 0.00 0.00 3.01
138 139 3.739401 AATCCCCTACCAACAGAAAGG 57.261 47.619 0.00 0.00 0.00 3.11
139 140 7.396055 TGATTTTAATCCCCTACCAACAGAAAG 59.604 37.037 0.32 0.00 34.50 2.62
140 141 7.242359 TGATTTTAATCCCCTACCAACAGAAA 58.758 34.615 0.32 0.00 34.50 2.52
141 142 6.795590 TGATTTTAATCCCCTACCAACAGAA 58.204 36.000 0.32 0.00 34.50 3.02
142 143 6.395780 TGATTTTAATCCCCTACCAACAGA 57.604 37.500 0.32 0.00 34.50 3.41
143 144 8.940397 ATATGATTTTAATCCCCTACCAACAG 57.060 34.615 0.32 0.00 34.50 3.16
144 145 7.947890 GGATATGATTTTAATCCCCTACCAACA 59.052 37.037 0.32 0.00 34.30 3.33
145 146 8.170730 AGGATATGATTTTAATCCCCTACCAAC 58.829 37.037 0.32 0.00 40.11 3.77
146 147 8.300752 AGGATATGATTTTAATCCCCTACCAA 57.699 34.615 0.32 0.00 40.11 3.67
147 148 7.905144 AGGATATGATTTTAATCCCCTACCA 57.095 36.000 0.32 0.00 40.11 3.25
148 149 9.025041 CAAAGGATATGATTTTAATCCCCTACC 57.975 37.037 0.32 0.00 40.11 3.18
149 150 8.523658 GCAAAGGATATGATTTTAATCCCCTAC 58.476 37.037 0.32 0.00 40.11 3.18
150 151 8.456124 AGCAAAGGATATGATTTTAATCCCCTA 58.544 33.333 0.32 0.00 40.11 3.53
151 152 7.234166 CAGCAAAGGATATGATTTTAATCCCCT 59.766 37.037 0.32 0.00 40.11 4.79
152 153 7.233348 TCAGCAAAGGATATGATTTTAATCCCC 59.767 37.037 0.32 0.00 40.11 4.81
153 154 8.181904 TCAGCAAAGGATATGATTTTAATCCC 57.818 34.615 0.32 0.00 40.11 3.85
154 155 9.688592 CTTCAGCAAAGGATATGATTTTAATCC 57.311 33.333 0.32 0.00 39.64 3.01
158 159 8.826710 CGTACTTCAGCAAAGGATATGATTTTA 58.173 33.333 4.18 0.00 39.47 1.52
159 160 7.201732 CCGTACTTCAGCAAAGGATATGATTTT 60.202 37.037 4.18 0.00 39.47 1.82
160 161 6.260936 CCGTACTTCAGCAAAGGATATGATTT 59.739 38.462 4.18 0.00 39.47 2.17
161 162 5.760253 CCGTACTTCAGCAAAGGATATGATT 59.240 40.000 4.18 0.00 39.47 2.57
162 163 5.070446 TCCGTACTTCAGCAAAGGATATGAT 59.930 40.000 4.18 0.00 39.47 2.45
163 164 4.404394 TCCGTACTTCAGCAAAGGATATGA 59.596 41.667 4.18 0.00 39.47 2.15
164 165 4.693283 TCCGTACTTCAGCAAAGGATATG 58.307 43.478 4.18 0.00 39.47 1.78
165 166 5.305644 AGATCCGTACTTCAGCAAAGGATAT 59.694 40.000 4.18 0.00 39.47 1.63
166 167 4.649674 AGATCCGTACTTCAGCAAAGGATA 59.350 41.667 4.18 0.00 39.47 2.59
167 168 3.452627 AGATCCGTACTTCAGCAAAGGAT 59.547 43.478 4.18 0.00 39.47 3.24
168 169 2.832129 AGATCCGTACTTCAGCAAAGGA 59.168 45.455 4.18 0.00 39.47 3.36
169 170 2.932614 CAGATCCGTACTTCAGCAAAGG 59.067 50.000 4.18 0.00 39.47 3.11
170 171 3.849911 TCAGATCCGTACTTCAGCAAAG 58.150 45.455 0.00 0.00 41.08 2.77
171 172 3.849911 CTCAGATCCGTACTTCAGCAAA 58.150 45.455 0.00 0.00 0.00 3.68
172 173 2.417379 GCTCAGATCCGTACTTCAGCAA 60.417 50.000 0.00 0.00 0.00 3.91
173 174 1.135139 GCTCAGATCCGTACTTCAGCA 59.865 52.381 0.00 0.00 0.00 4.41
174 175 1.407258 AGCTCAGATCCGTACTTCAGC 59.593 52.381 0.00 0.00 0.00 4.26
175 176 3.791973 AAGCTCAGATCCGTACTTCAG 57.208 47.619 0.00 0.00 0.00 3.02
176 177 4.537135 AAAAGCTCAGATCCGTACTTCA 57.463 40.909 0.00 0.00 0.00 3.02
177 178 6.183360 GGTTTAAAAGCTCAGATCCGTACTTC 60.183 42.308 0.00 0.00 0.00 3.01
178 179 5.642491 GGTTTAAAAGCTCAGATCCGTACTT 59.358 40.000 0.00 0.00 0.00 2.24
179 180 5.176592 GGTTTAAAAGCTCAGATCCGTACT 58.823 41.667 0.00 0.00 0.00 2.73
180 181 4.331992 GGGTTTAAAAGCTCAGATCCGTAC 59.668 45.833 0.00 0.00 0.00 3.67
181 182 4.020039 TGGGTTTAAAAGCTCAGATCCGTA 60.020 41.667 0.00 0.00 0.00 4.02
182 183 3.244770 TGGGTTTAAAAGCTCAGATCCGT 60.245 43.478 0.00 0.00 0.00 4.69
183 184 3.343617 TGGGTTTAAAAGCTCAGATCCG 58.656 45.455 0.00 0.00 0.00 4.18
184 185 4.589908 TCTGGGTTTAAAAGCTCAGATCC 58.410 43.478 11.78 0.00 33.99 3.36
185 186 5.649831 ACATCTGGGTTTAAAAGCTCAGATC 59.350 40.000 20.00 0.00 41.04 2.75
186 187 5.574188 ACATCTGGGTTTAAAAGCTCAGAT 58.426 37.500 18.27 18.27 42.33 2.90
187 188 4.985538 ACATCTGGGTTTAAAAGCTCAGA 58.014 39.130 16.07 16.07 39.08 3.27
188 189 5.464168 CAACATCTGGGTTTAAAAGCTCAG 58.536 41.667 8.26 8.26 0.00 3.35
189 190 4.280677 CCAACATCTGGGTTTAAAAGCTCA 59.719 41.667 0.00 0.00 42.17 4.26
190 191 4.809673 CCAACATCTGGGTTTAAAAGCTC 58.190 43.478 0.00 0.00 42.17 4.09
191 192 4.871933 CCAACATCTGGGTTTAAAAGCT 57.128 40.909 0.00 0.00 42.17 3.74
203 204 9.436957 AACTAATTACAGACTTACCAACATCTG 57.563 33.333 0.00 0.00 43.47 2.90
204 205 9.654663 GAACTAATTACAGACTTACCAACATCT 57.345 33.333 0.00 0.00 0.00 2.90
205 206 9.431887 TGAACTAATTACAGACTTACCAACATC 57.568 33.333 0.00 0.00 0.00 3.06
233 234 9.181805 CAAATCAGTACGTACTTGTATATCTGG 57.818 37.037 25.35 10.35 33.46 3.86
240 241 4.797471 ACGCAAATCAGTACGTACTTGTA 58.203 39.130 25.35 14.12 36.91 2.41
259 261 1.542187 AAGGGACAGTCAGGGTACGC 61.542 60.000 2.17 0.77 0.00 4.42
263 265 4.741928 AAAATAAAGGGACAGTCAGGGT 57.258 40.909 2.17 0.00 0.00 4.34
293 296 3.891366 CCCCAACCTTCCTGCAATATTAG 59.109 47.826 0.00 0.00 0.00 1.73
294 297 3.270960 ACCCCAACCTTCCTGCAATATTA 59.729 43.478 0.00 0.00 0.00 0.98
312 316 0.179081 GTTCTGCCAGATCGTACCCC 60.179 60.000 0.00 0.00 0.00 4.95
313 317 0.535335 TGTTCTGCCAGATCGTACCC 59.465 55.000 0.00 0.00 0.00 3.69
334 339 5.577945 GGTATACGTCCGAAATCAAACAAGA 59.422 40.000 0.00 0.00 0.00 3.02
336 341 5.349270 CAGGTATACGTCCGAAATCAAACAA 59.651 40.000 0.00 0.00 0.00 2.83
338 343 4.260091 GCAGGTATACGTCCGAAATCAAAC 60.260 45.833 0.00 0.00 0.00 2.93
342 347 3.004524 AGAGCAGGTATACGTCCGAAATC 59.995 47.826 0.00 0.00 0.00 2.17
365 371 6.156256 AGACATGAAGTATGGTACCTAAGCAA 59.844 38.462 14.36 0.00 41.25 3.91
367 373 6.163135 AGACATGAAGTATGGTACCTAAGC 57.837 41.667 14.36 0.92 41.25 3.09
368 374 9.449719 AAAAAGACATGAAGTATGGTACCTAAG 57.550 33.333 14.36 0.00 41.25 2.18
377 383 9.626045 GGTAAAAGGAAAAAGACATGAAGTATG 57.374 33.333 0.00 0.00 42.68 2.39
382 388 8.990163 AGTAGGTAAAAGGAAAAAGACATGAA 57.010 30.769 0.00 0.00 0.00 2.57
384 390 8.727910 GGTAGTAGGTAAAAGGAAAAAGACATG 58.272 37.037 0.00 0.00 0.00 3.21
385 391 7.886970 GGGTAGTAGGTAAAAGGAAAAAGACAT 59.113 37.037 0.00 0.00 0.00 3.06
395 401 5.021458 TCTGTGAGGGTAGTAGGTAAAAGG 58.979 45.833 0.00 0.00 0.00 3.11
397 405 6.070424 CCAATCTGTGAGGGTAGTAGGTAAAA 60.070 42.308 0.00 0.00 0.00 1.52
411 425 5.350504 AGACTATTCACCCAATCTGTGAG 57.649 43.478 0.00 0.00 43.14 3.51
423 437 9.311916 GCATGGATTCATCTATAGACTATTCAC 57.688 37.037 4.10 0.00 0.00 3.18
430 444 5.473931 ACGTGCATGGATTCATCTATAGAC 58.526 41.667 11.36 0.00 0.00 2.59
432 446 6.311445 GGTTACGTGCATGGATTCATCTATAG 59.689 42.308 11.36 0.00 0.00 1.31
538 554 4.724074 TGTCGGACCAAGTTCGTATATT 57.276 40.909 5.55 0.00 35.80 1.28
1005 1164 1.071471 ACGCCAACTGTGAGAAGGG 59.929 57.895 0.00 0.00 0.00 3.95
1029 1194 6.237755 CGTCGGACCAAGTTCATATAAACTTC 60.238 42.308 0.63 0.00 45.36 3.01
2051 2269 7.457218 AGATGATCATGTGTGGATAATAGGTCT 59.543 37.037 14.30 0.00 0.00 3.85
2064 2282 3.959293 TCTTGGCAAGATGATCATGTGT 58.041 40.909 25.38 0.00 31.20 3.72
2254 2472 3.114616 CAAGGACACCAGCGCGAG 61.115 66.667 12.10 0.00 0.00 5.03
2402 2628 3.118075 TCCAGCCGATAATGAAATGGACA 60.118 43.478 0.00 0.00 30.63 4.02
2998 3225 3.129462 GGCAAGCCTTTCTTCATAGGAAC 59.871 47.826 3.29 0.00 33.13 3.62
3058 3285 6.314917 ACAAGATCCCCTTCTAAAATGTTGT 58.685 36.000 0.00 0.00 31.37 3.32
3068 3295 3.103080 ACTACGACAAGATCCCCTTCT 57.897 47.619 0.00 0.00 31.42 2.85
3189 3416 1.360852 TGGGGCATTGTTATCCAAGGT 59.639 47.619 0.00 0.00 37.18 3.50
3190 3417 1.756538 GTGGGGCATTGTTATCCAAGG 59.243 52.381 0.00 0.00 37.88 3.61
3254 3481 9.462174 GCACATAATAATAGCAGCAAAAATGTA 57.538 29.630 0.00 0.00 0.00 2.29
3255 3482 7.439056 GGCACATAATAATAGCAGCAAAAATGT 59.561 33.333 0.00 0.00 0.00 2.71
3381 3660 5.049198 CCTGATACGGTCACGCTTATAAGTA 60.049 44.000 13.91 0.00 46.04 2.24
3492 3771 1.230497 GGTCTCTCCTCCCCATCGA 59.770 63.158 0.00 0.00 0.00 3.59
3664 3943 4.413851 GGGGGAGTTGGAAGATTAAGAGAT 59.586 45.833 0.00 0.00 0.00 2.75
3688 3968 3.506455 CCACCCCTGAGTATAGATACGTG 59.494 52.174 0.00 0.00 38.28 4.49
3706 3986 0.817634 TATAAGCATGCGTGGCCACC 60.818 55.000 29.95 21.83 0.00 4.61
3739 4019 2.492012 CTACCGTGCGTAGAGATAGGT 58.508 52.381 0.00 0.00 46.53 3.08
4001 4286 8.125978 TGAAAAATCTCATGGTGCTAAGAATT 57.874 30.769 0.00 0.00 0.00 2.17
4007 4292 3.696051 GCCTGAAAAATCTCATGGTGCTA 59.304 43.478 0.00 0.00 0.00 3.49
4270 4556 1.675219 GGCCTCCACACGTTCCTTA 59.325 57.895 0.00 0.00 0.00 2.69
4639 4933 1.338769 ACGTGAATGGTTCTACTGGCC 60.339 52.381 0.00 0.00 0.00 5.36
5197 5766 3.116096 AGCTTACTCCATACCCTCACA 57.884 47.619 0.00 0.00 0.00 3.58
5274 5843 6.513393 CGAGTCTAAACTGAGGCACAAATTTT 60.513 38.462 0.00 0.00 35.28 1.82
5275 5844 5.049405 CGAGTCTAAACTGAGGCACAAATTT 60.049 40.000 0.00 0.00 35.28 1.82
5277 5846 3.997021 CGAGTCTAAACTGAGGCACAAAT 59.003 43.478 0.00 0.00 35.28 2.32
5459 6130 1.429423 GCCGCGGATGAAAGGAAAG 59.571 57.895 33.48 0.00 0.00 2.62
5475 6146 1.148310 CGTCCCATGAATATCACGCC 58.852 55.000 0.00 0.00 0.00 5.68
5499 6170 0.518195 GGAGATCTAGTACTCGCGGC 59.482 60.000 6.13 0.00 34.40 6.53


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

AutoCloner maintained by Alex Coulton.