Multiple sequence alignment - TraesCS7D01G207400

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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 TraesCS7D01G207400 chr7D 100.000 3769 0 0 1 3769 164753786 164750018 0.000000e+00 6961.0
1 TraesCS7D01G207400 chr7D 91.748 1842 86 22 1230 3031 165118317 165120132 0.000000e+00 2499.0
2 TraesCS7D01G207400 chr7D 85.312 1314 125 38 1810 3094 169421831 169420557 0.000000e+00 1295.0
3 TraesCS7D01G207400 chr7D 84.715 772 98 14 1014 1769 169024495 169025262 0.000000e+00 754.0
4 TraesCS7D01G207400 chr7D 83.636 825 111 16 967 1769 169422652 169421830 0.000000e+00 754.0
5 TraesCS7D01G207400 chr7A 91.047 2368 126 28 806 3119 166869088 166871423 0.000000e+00 3120.0
6 TraesCS7D01G207400 chr7A 92.049 1874 100 17 806 2652 166491752 166489901 0.000000e+00 2590.0
7 TraesCS7D01G207400 chr7A 85.266 1276 118 29 1850 3100 166595046 166593816 0.000000e+00 1251.0
8 TraesCS7D01G207400 chr7A 86.385 1065 80 21 1883 2903 172234328 172233285 0.000000e+00 1103.0
9 TraesCS7D01G207400 chr7A 87.349 664 56 19 2259 2902 171438297 171437642 0.000000e+00 736.0
10 TraesCS7D01G207400 chr7A 92.857 504 25 5 3269 3769 166488491 166487996 0.000000e+00 721.0
11 TraesCS7D01G207400 chr7A 89.677 465 33 4 204 661 166493128 166492672 2.520000e-161 579.0
12 TraesCS7D01G207400 chr7A 89.677 465 33 4 204 661 166867712 166868168 2.520000e-161 579.0
13 TraesCS7D01G207400 chr7A 86.207 551 52 17 2372 2905 171547286 171546743 3.260000e-160 575.0
14 TraesCS7D01G207400 chr7A 84.013 638 55 20 2489 3094 171556225 171555603 1.520000e-158 569.0
15 TraesCS7D01G207400 chr7A 89.443 341 19 9 2795 3119 166489312 166488973 7.530000e-112 414.0
16 TraesCS7D01G207400 chr7A 90.909 66 6 0 3011 3076 166872665 166872730 5.190000e-14 89.8
17 TraesCS7D01G207400 chr7B 90.588 2380 141 38 784 3119 128436432 128438772 0.000000e+00 3077.0
18 TraesCS7D01G207400 chr7B 91.276 2132 119 32 796 2906 127653517 127651432 0.000000e+00 2844.0
19 TraesCS7D01G207400 chr7B 90.956 1957 117 31 796 2731 127775040 127773123 0.000000e+00 2579.0
20 TraesCS7D01G207400 chr7B 90.189 1957 133 32 796 2731 128071281 128069363 0.000000e+00 2495.0
21 TraesCS7D01G207400 chr7B 94.322 634 30 4 3138 3768 127651098 127650468 0.000000e+00 966.0
22 TraesCS7D01G207400 chr7B 85.732 813 75 18 2276 3053 134493384 134494190 0.000000e+00 821.0
23 TraesCS7D01G207400 chr7B 85.714 595 39 17 204 764 128072660 128072078 1.510000e-163 586.0
24 TraesCS7D01G207400 chr7B 85.329 593 41 17 206 764 127654899 127654319 4.220000e-159 571.0
25 TraesCS7D01G207400 chr7B 84.823 593 44 17 206 764 127776420 127775840 4.250000e-154 555.0
26 TraesCS7D01G207400 chr7B 89.773 88 7 2 2974 3061 127651308 127651223 1.110000e-20 111.0
27 TraesCS7D01G207400 chr7B 100.000 35 0 0 2942 2976 127651432 127651398 8.740000e-07 65.8
28 TraesCS7D01G207400 chrUn 88.542 960 79 19 1964 2903 218480268 218481216 0.000000e+00 1134.0
29 TraesCS7D01G207400 chrUn 84.169 638 54 20 2489 3094 82714168 82713546 3.260000e-160 575.0
30 TraesCS7D01G207400 chrUn 85.688 552 51 19 2372 2903 374568661 374568118 1.180000e-154 556.0
31 TraesCS7D01G207400 chrUn 87.526 473 41 12 2445 2905 309086272 309085806 7.170000e-147 531.0
32 TraesCS7D01G207400 chrUn 89.474 114 9 3 77 189 42552599 42552710 1.410000e-29 141.0
33 TraesCS7D01G207400 chrUn 95.652 46 2 0 1810 1855 244607775 244607820 1.450000e-09 75.0
34 TraesCS7D01G207400 chr6A 83.867 812 100 19 979 1769 124422975 124423776 0.000000e+00 745.0
35 TraesCS7D01G207400 chr3B 79.348 552 59 26 2495 3022 576142297 576142817 1.680000e-88 337.0
36 TraesCS7D01G207400 chr2D 93.000 200 14 0 1 200 192308909 192309108 3.680000e-75 292.0
37 TraesCS7D01G207400 chr5D 91.500 200 17 0 1 200 435892348 435892547 3.710000e-70 276.0
38 TraesCS7D01G207400 chr5D 84.343 198 29 2 2 198 447422222 447422418 3.840000e-45 193.0
39 TraesCS7D01G207400 chr4A 87.179 195 25 0 4 198 731423263 731423457 4.900000e-54 222.0
40 TraesCS7D01G207400 chr4A 81.461 178 31 2 24 200 676215312 676215488 1.090000e-30 145.0
41 TraesCS7D01G207400 chr6D 87.402 127 14 2 75 200 86915171 86915046 1.090000e-30 145.0
42 TraesCS7D01G207400 chr6D 97.826 46 1 0 1810 1855 103052603 103052648 3.120000e-11 80.5
43 TraesCS7D01G207400 chr2A 83.200 125 19 2 77 200 631787192 631787315 3.080000e-21 113.0
44 TraesCS7D01G207400 chr2B 82.540 126 22 0 75 200 692868404 692868279 1.110000e-20 111.0


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 TraesCS7D01G207400 chr7D 164750018 164753786 3768 True 6961.000000 6961 100.000000 1 3769 1 chr7D.!!$R1 3768
1 TraesCS7D01G207400 chr7D 165118317 165120132 1815 False 2499.000000 2499 91.748000 1230 3031 1 chr7D.!!$F1 1801
2 TraesCS7D01G207400 chr7D 169420557 169422652 2095 True 1024.500000 1295 84.474000 967 3094 2 chr7D.!!$R2 2127
3 TraesCS7D01G207400 chr7D 169024495 169025262 767 False 754.000000 754 84.715000 1014 1769 1 chr7D.!!$F2 755
4 TraesCS7D01G207400 chr7A 166867712 166872730 5018 False 1262.933333 3120 90.544333 204 3119 3 chr7A.!!$F1 2915
5 TraesCS7D01G207400 chr7A 166593816 166595046 1230 True 1251.000000 1251 85.266000 1850 3100 1 chr7A.!!$R1 1250
6 TraesCS7D01G207400 chr7A 172233285 172234328 1043 True 1103.000000 1103 86.385000 1883 2903 1 chr7A.!!$R5 1020
7 TraesCS7D01G207400 chr7A 166487996 166493128 5132 True 1076.000000 2590 91.006500 204 3769 4 chr7A.!!$R6 3565
8 TraesCS7D01G207400 chr7A 171437642 171438297 655 True 736.000000 736 87.349000 2259 2902 1 chr7A.!!$R2 643
9 TraesCS7D01G207400 chr7A 171546743 171547286 543 True 575.000000 575 86.207000 2372 2905 1 chr7A.!!$R3 533
10 TraesCS7D01G207400 chr7A 171555603 171556225 622 True 569.000000 569 84.013000 2489 3094 1 chr7A.!!$R4 605
11 TraesCS7D01G207400 chr7B 128436432 128438772 2340 False 3077.000000 3077 90.588000 784 3119 1 chr7B.!!$F1 2335
12 TraesCS7D01G207400 chr7B 127773123 127776420 3297 True 1567.000000 2579 87.889500 206 2731 2 chr7B.!!$R2 2525
13 TraesCS7D01G207400 chr7B 128069363 128072660 3297 True 1540.500000 2495 87.951500 204 2731 2 chr7B.!!$R3 2527
14 TraesCS7D01G207400 chr7B 127650468 127654899 4431 True 911.560000 2844 92.140000 206 3768 5 chr7B.!!$R1 3562
15 TraesCS7D01G207400 chr7B 134493384 134494190 806 False 821.000000 821 85.732000 2276 3053 1 chr7B.!!$F2 777
16 TraesCS7D01G207400 chrUn 218480268 218481216 948 False 1134.000000 1134 88.542000 1964 2903 1 chrUn.!!$F2 939
17 TraesCS7D01G207400 chrUn 82713546 82714168 622 True 575.000000 575 84.169000 2489 3094 1 chrUn.!!$R1 605
18 TraesCS7D01G207400 chrUn 374568118 374568661 543 True 556.000000 556 85.688000 2372 2903 1 chrUn.!!$R3 531
19 TraesCS7D01G207400 chr6A 124422975 124423776 801 False 745.000000 745 83.867000 979 1769 1 chr6A.!!$F1 790
20 TraesCS7D01G207400 chr3B 576142297 576142817 520 False 337.000000 337 79.348000 2495 3022 1 chr3B.!!$F1 527

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
949 1964 0.033503 TCACTACATCCTCGCCTCCA 60.034 55.0 0.00 0.0 0.0 3.86 F
2217 3343 0.036105 ACATGCTGCAGTCGGATGAA 60.036 50.0 16.64 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2307 3436 0.528466 GCGATGGAGCGTCAAGATCA 60.528 55.0 0.00 0.0 36.90 2.92 R
3076 4830 0.038599 ACTTCAGACATGGGCATGCA 59.961 50.0 21.36 0.0 42.39 3.96 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
30 31 3.118454 GCGCGAGTGGCTGCTTTA 61.118 61.111 12.10 0.00 40.44 1.85
31 32 2.677003 GCGCGAGTGGCTGCTTTAA 61.677 57.895 12.10 0.00 40.44 1.52
32 33 1.982073 GCGCGAGTGGCTGCTTTAAT 61.982 55.000 12.10 0.00 40.44 1.40
33 34 0.247814 CGCGAGTGGCTGCTTTAATG 60.248 55.000 0.00 0.00 40.44 1.90
34 35 0.099436 GCGAGTGGCTGCTTTAATGG 59.901 55.000 0.00 0.00 39.11 3.16
35 36 0.734889 CGAGTGGCTGCTTTAATGGG 59.265 55.000 0.00 0.00 0.00 4.00
36 37 0.457443 GAGTGGCTGCTTTAATGGGC 59.543 55.000 0.00 0.00 0.00 5.36
37 38 0.972471 AGTGGCTGCTTTAATGGGCC 60.972 55.000 0.00 0.00 42.73 5.80
38 39 2.051518 TGGCTGCTTTAATGGGCCG 61.052 57.895 0.00 0.00 45.06 6.13
39 40 2.785425 GGCTGCTTTAATGGGCCGG 61.785 63.158 0.00 0.00 33.30 6.13
40 41 2.807622 CTGCTTTAATGGGCCGGC 59.192 61.111 21.18 21.18 0.00 6.13
41 42 2.757917 TGCTTTAATGGGCCGGCC 60.758 61.111 38.57 38.57 0.00 6.13
51 52 2.833121 GGCCGGCCCGATTTGATT 60.833 61.111 36.64 0.00 0.00 2.57
52 53 2.423064 GGCCGGCCCGATTTGATTT 61.423 57.895 36.64 0.00 0.00 2.17
53 54 1.226945 GCCGGCCCGATTTGATTTG 60.227 57.895 18.11 0.00 0.00 2.32
54 55 1.226945 CCGGCCCGATTTGATTTGC 60.227 57.895 3.71 0.00 0.00 3.68
55 56 1.226945 CGGCCCGATTTGATTTGCC 60.227 57.895 0.00 0.00 35.55 4.52
56 57 1.896694 GGCCCGATTTGATTTGCCA 59.103 52.632 0.00 0.00 38.73 4.92
57 58 0.460109 GGCCCGATTTGATTTGCCAC 60.460 55.000 0.00 0.00 38.73 5.01
58 59 0.801836 GCCCGATTTGATTTGCCACG 60.802 55.000 0.00 0.00 0.00 4.94
59 60 0.525761 CCCGATTTGATTTGCCACGT 59.474 50.000 0.00 0.00 0.00 4.49
60 61 1.740585 CCCGATTTGATTTGCCACGTA 59.259 47.619 0.00 0.00 0.00 3.57
61 62 2.162608 CCCGATTTGATTTGCCACGTAA 59.837 45.455 0.00 0.00 0.00 3.18
63 64 2.845967 CGATTTGATTTGCCACGTAAGC 59.154 45.455 2.88 2.88 45.62 3.09
64 65 2.323939 TTTGATTTGCCACGTAAGCG 57.676 45.000 5.39 0.00 45.62 4.68
65 66 1.514003 TTGATTTGCCACGTAAGCGA 58.486 45.000 5.39 0.74 45.62 4.93
66 67 1.514003 TGATTTGCCACGTAAGCGAA 58.486 45.000 13.20 13.20 45.62 4.70
67 68 2.080693 TGATTTGCCACGTAAGCGAAT 58.919 42.857 19.86 19.86 45.10 3.34
68 69 3.263261 TGATTTGCCACGTAAGCGAATA 58.737 40.909 19.81 9.79 43.00 1.75
69 70 3.062909 TGATTTGCCACGTAAGCGAATAC 59.937 43.478 19.81 14.96 43.00 1.89
70 71 1.361793 TTGCCACGTAAGCGAATACC 58.638 50.000 5.39 0.00 45.62 2.73
71 72 0.246910 TGCCACGTAAGCGAATACCA 59.753 50.000 5.39 0.00 45.62 3.25
72 73 0.928229 GCCACGTAAGCGAATACCAG 59.072 55.000 0.00 0.00 45.62 4.00
73 74 1.738030 GCCACGTAAGCGAATACCAGT 60.738 52.381 0.00 0.00 45.62 4.00
74 75 1.924524 CCACGTAAGCGAATACCAGTG 59.075 52.381 0.00 0.00 45.62 3.66
75 76 2.416296 CCACGTAAGCGAATACCAGTGA 60.416 50.000 0.00 0.00 45.62 3.41
76 77 3.247442 CACGTAAGCGAATACCAGTGAA 58.753 45.455 0.00 0.00 45.62 3.18
77 78 3.676172 CACGTAAGCGAATACCAGTGAAA 59.324 43.478 0.00 0.00 45.62 2.69
78 79 3.676646 ACGTAAGCGAATACCAGTGAAAC 59.323 43.478 0.00 0.00 45.62 2.78
79 80 3.241552 CGTAAGCGAATACCAGTGAAACG 60.242 47.826 0.00 0.00 41.18 3.60
80 81 1.076332 AGCGAATACCAGTGAAACGC 58.924 50.000 0.00 0.00 45.86 4.84
81 82 1.076332 GCGAATACCAGTGAAACGCT 58.924 50.000 0.00 0.00 45.86 5.07
82 83 1.060698 GCGAATACCAGTGAAACGCTC 59.939 52.381 0.00 0.00 45.86 5.03
83 84 2.607187 CGAATACCAGTGAAACGCTCT 58.393 47.619 0.00 0.00 45.86 4.09
84 85 2.993899 CGAATACCAGTGAAACGCTCTT 59.006 45.455 0.00 0.00 45.86 2.85
85 86 4.171005 CGAATACCAGTGAAACGCTCTTA 58.829 43.478 0.00 0.00 45.86 2.10
86 87 4.624024 CGAATACCAGTGAAACGCTCTTAA 59.376 41.667 0.00 0.00 45.86 1.85
87 88 5.220228 CGAATACCAGTGAAACGCTCTTAAG 60.220 44.000 0.00 0.00 45.86 1.85
88 89 2.767505 ACCAGTGAAACGCTCTTAAGG 58.232 47.619 1.85 0.00 45.86 2.69
89 90 2.104281 ACCAGTGAAACGCTCTTAAGGT 59.896 45.455 1.85 0.00 45.86 3.50
90 91 3.139077 CCAGTGAAACGCTCTTAAGGTT 58.861 45.455 1.85 0.00 45.86 3.50
91 92 3.186613 CCAGTGAAACGCTCTTAAGGTTC 59.813 47.826 1.85 0.00 45.86 3.62
92 93 3.807622 CAGTGAAACGCTCTTAAGGTTCA 59.192 43.478 1.85 0.00 45.86 3.18
93 94 4.272504 CAGTGAAACGCTCTTAAGGTTCAA 59.727 41.667 1.85 0.00 44.43 2.69
94 95 4.879545 AGTGAAACGCTCTTAAGGTTCAAA 59.120 37.500 1.85 0.00 44.43 2.69
95 96 5.355910 AGTGAAACGCTCTTAAGGTTCAAAA 59.644 36.000 1.85 0.00 44.43 2.44
96 97 6.039382 AGTGAAACGCTCTTAAGGTTCAAAAT 59.961 34.615 1.85 0.00 44.43 1.82
97 98 7.227910 AGTGAAACGCTCTTAAGGTTCAAAATA 59.772 33.333 1.85 0.00 44.43 1.40
98 99 7.534239 GTGAAACGCTCTTAAGGTTCAAAATAG 59.466 37.037 1.85 0.00 44.43 1.73
99 100 7.442969 TGAAACGCTCTTAAGGTTCAAAATAGA 59.557 33.333 1.85 0.00 40.63 1.98
100 101 7.923414 AACGCTCTTAAGGTTCAAAATAGAT 57.077 32.000 1.85 0.00 0.00 1.98
101 102 7.541122 ACGCTCTTAAGGTTCAAAATAGATC 57.459 36.000 1.85 0.00 0.00 2.75
102 103 6.255887 ACGCTCTTAAGGTTCAAAATAGATCG 59.744 38.462 1.85 0.00 0.00 3.69
103 104 6.475727 CGCTCTTAAGGTTCAAAATAGATCGA 59.524 38.462 1.85 0.00 0.00 3.59
104 105 7.306283 CGCTCTTAAGGTTCAAAATAGATCGAG 60.306 40.741 1.85 0.00 0.00 4.04
105 106 7.707035 GCTCTTAAGGTTCAAAATAGATCGAGA 59.293 37.037 1.85 0.00 0.00 4.04
106 107 9.757227 CTCTTAAGGTTCAAAATAGATCGAGAT 57.243 33.333 1.85 0.00 0.00 2.75
107 108 9.751542 TCTTAAGGTTCAAAATAGATCGAGATC 57.248 33.333 1.85 5.00 38.09 2.75
108 109 8.575565 TTAAGGTTCAAAATAGATCGAGATCG 57.424 34.615 7.37 0.00 42.48 3.69
120 121 3.217599 TCGAGATCGAAGAGTTTGGTG 57.782 47.619 1.76 0.00 46.30 4.17
121 122 2.557056 TCGAGATCGAAGAGTTTGGTGT 59.443 45.455 1.76 0.00 46.30 4.16
122 123 2.663602 CGAGATCGAAGAGTTTGGTGTG 59.336 50.000 0.00 0.00 43.63 3.82
123 124 2.413453 GAGATCGAAGAGTTTGGTGTGC 59.587 50.000 0.00 0.00 43.63 4.57
124 125 2.037772 AGATCGAAGAGTTTGGTGTGCT 59.962 45.455 0.00 0.00 43.63 4.40
125 126 1.581934 TCGAAGAGTTTGGTGTGCTG 58.418 50.000 0.00 0.00 0.00 4.41
126 127 1.138069 TCGAAGAGTTTGGTGTGCTGA 59.862 47.619 0.00 0.00 0.00 4.26
127 128 2.146342 CGAAGAGTTTGGTGTGCTGAT 58.854 47.619 0.00 0.00 0.00 2.90
128 129 2.549754 CGAAGAGTTTGGTGTGCTGATT 59.450 45.455 0.00 0.00 0.00 2.57
129 130 3.003689 CGAAGAGTTTGGTGTGCTGATTT 59.996 43.478 0.00 0.00 0.00 2.17
130 131 4.540824 GAAGAGTTTGGTGTGCTGATTTC 58.459 43.478 0.00 0.00 0.00 2.17
131 132 3.554934 AGAGTTTGGTGTGCTGATTTCA 58.445 40.909 0.00 0.00 0.00 2.69
132 133 3.953612 AGAGTTTGGTGTGCTGATTTCAA 59.046 39.130 0.00 0.00 0.00 2.69
133 134 4.037208 AGAGTTTGGTGTGCTGATTTCAAG 59.963 41.667 0.00 0.00 0.00 3.02
134 135 3.953612 AGTTTGGTGTGCTGATTTCAAGA 59.046 39.130 0.00 0.00 0.00 3.02
135 136 4.586001 AGTTTGGTGTGCTGATTTCAAGAT 59.414 37.500 0.00 0.00 0.00 2.40
136 137 5.069516 AGTTTGGTGTGCTGATTTCAAGATT 59.930 36.000 0.00 0.00 0.00 2.40
137 138 5.534207 TTGGTGTGCTGATTTCAAGATTT 57.466 34.783 0.00 0.00 0.00 2.17
138 139 6.647334 TTGGTGTGCTGATTTCAAGATTTA 57.353 33.333 0.00 0.00 0.00 1.40
139 140 6.647334 TGGTGTGCTGATTTCAAGATTTAA 57.353 33.333 0.00 0.00 0.00 1.52
140 141 7.048629 TGGTGTGCTGATTTCAAGATTTAAA 57.951 32.000 0.00 0.00 0.00 1.52
141 142 7.495901 TGGTGTGCTGATTTCAAGATTTAAAA 58.504 30.769 0.00 0.00 0.00 1.52
142 143 7.652909 TGGTGTGCTGATTTCAAGATTTAAAAG 59.347 33.333 0.00 0.00 0.00 2.27
143 144 7.653311 GGTGTGCTGATTTCAAGATTTAAAAGT 59.347 33.333 0.00 0.00 0.00 2.66
144 145 9.034544 GTGTGCTGATTTCAAGATTTAAAAGTT 57.965 29.630 0.00 0.00 0.00 2.66
145 146 9.248291 TGTGCTGATTTCAAGATTTAAAAGTTC 57.752 29.630 0.00 0.00 0.00 3.01
146 147 9.248291 GTGCTGATTTCAAGATTTAAAAGTTCA 57.752 29.630 0.00 0.00 0.00 3.18
147 148 9.467258 TGCTGATTTCAAGATTTAAAAGTTCAG 57.533 29.630 0.00 0.00 0.00 3.02
148 149 8.919661 GCTGATTTCAAGATTTAAAAGTTCAGG 58.080 33.333 0.00 0.00 0.00 3.86
164 165 9.481340 AAAAGTTCAGGATTCAATTTAGCTTTC 57.519 29.630 0.00 0.00 0.00 2.62
165 166 6.846350 AGTTCAGGATTCAATTTAGCTTTCG 58.154 36.000 0.00 0.00 0.00 3.46
166 167 6.431234 AGTTCAGGATTCAATTTAGCTTTCGT 59.569 34.615 0.00 0.00 0.00 3.85
167 168 6.422776 TCAGGATTCAATTTAGCTTTCGTC 57.577 37.500 0.00 0.00 0.00 4.20
168 169 6.173339 TCAGGATTCAATTTAGCTTTCGTCT 58.827 36.000 0.00 0.00 0.00 4.18
169 170 6.092670 TCAGGATTCAATTTAGCTTTCGTCTG 59.907 38.462 0.00 0.00 0.00 3.51
170 171 5.940470 AGGATTCAATTTAGCTTTCGTCTGT 59.060 36.000 0.00 0.00 0.00 3.41
171 172 6.024049 GGATTCAATTTAGCTTTCGTCTGTG 58.976 40.000 0.00 0.00 0.00 3.66
172 173 6.128282 GGATTCAATTTAGCTTTCGTCTGTGA 60.128 38.462 0.00 0.00 0.00 3.58
173 174 5.845985 TCAATTTAGCTTTCGTCTGTGAG 57.154 39.130 0.00 0.00 0.00 3.51
174 175 5.297547 TCAATTTAGCTTTCGTCTGTGAGT 58.702 37.500 0.00 0.00 0.00 3.41
175 176 5.758296 TCAATTTAGCTTTCGTCTGTGAGTT 59.242 36.000 0.00 0.00 0.00 3.01
176 177 5.847670 ATTTAGCTTTCGTCTGTGAGTTC 57.152 39.130 0.00 0.00 0.00 3.01
177 178 2.890808 AGCTTTCGTCTGTGAGTTCA 57.109 45.000 0.00 0.00 0.00 3.18
178 179 3.179443 AGCTTTCGTCTGTGAGTTCAA 57.821 42.857 0.00 0.00 0.00 2.69
179 180 3.126831 AGCTTTCGTCTGTGAGTTCAAG 58.873 45.455 0.00 0.00 0.00 3.02
180 181 2.221981 GCTTTCGTCTGTGAGTTCAAGG 59.778 50.000 0.00 0.00 0.00 3.61
181 182 3.458189 CTTTCGTCTGTGAGTTCAAGGT 58.542 45.455 0.00 0.00 0.00 3.50
182 183 3.536956 TTCGTCTGTGAGTTCAAGGTT 57.463 42.857 0.00 0.00 0.00 3.50
183 184 3.536956 TCGTCTGTGAGTTCAAGGTTT 57.463 42.857 0.00 0.00 0.00 3.27
184 185 4.659111 TCGTCTGTGAGTTCAAGGTTTA 57.341 40.909 0.00 0.00 0.00 2.01
185 186 5.209818 TCGTCTGTGAGTTCAAGGTTTAT 57.790 39.130 0.00 0.00 0.00 1.40
186 187 5.607477 TCGTCTGTGAGTTCAAGGTTTATT 58.393 37.500 0.00 0.00 0.00 1.40
187 188 6.053005 TCGTCTGTGAGTTCAAGGTTTATTT 58.947 36.000 0.00 0.00 0.00 1.40
188 189 6.540914 TCGTCTGTGAGTTCAAGGTTTATTTT 59.459 34.615 0.00 0.00 0.00 1.82
189 190 7.711772 TCGTCTGTGAGTTCAAGGTTTATTTTA 59.288 33.333 0.00 0.00 0.00 1.52
190 191 8.339714 CGTCTGTGAGTTCAAGGTTTATTTTAA 58.660 33.333 0.00 0.00 0.00 1.52
226 227 1.609783 CCGCCCCTTCATCTTTCCT 59.390 57.895 0.00 0.00 0.00 3.36
227 228 0.749454 CCGCCCCTTCATCTTTCCTG 60.749 60.000 0.00 0.00 0.00 3.86
265 266 2.045926 CCGCTAAACCAGGCTGCT 60.046 61.111 9.56 0.00 0.00 4.24
266 267 1.675641 CCGCTAAACCAGGCTGCTT 60.676 57.895 9.56 7.14 0.00 3.91
300 301 1.486726 GGATTGATTCGGACCAGACCT 59.513 52.381 0.00 0.00 0.00 3.85
301 302 2.092914 GGATTGATTCGGACCAGACCTT 60.093 50.000 0.00 0.00 0.00 3.50
337 338 2.432628 GCGGTCAACGTGAGGGAG 60.433 66.667 0.00 0.00 46.52 4.30
441 451 1.402896 GGCGAGGATGGTGGATCTCA 61.403 60.000 0.00 0.00 0.00 3.27
456 466 2.284625 TCAGCGGGGACAGTGGAT 60.285 61.111 0.00 0.00 0.00 3.41
458 468 4.101448 AGCGGGGACAGTGGATGC 62.101 66.667 0.00 0.00 0.00 3.91
500 510 4.243008 GGCTAAGAGGAGGCGGGC 62.243 72.222 0.00 0.00 31.65 6.13
598 634 2.895372 CGTATTCACGGCCCTGGC 60.895 66.667 0.00 0.00 44.59 4.85
652 694 0.179103 GGAAATGGGAATGGCTTGCG 60.179 55.000 0.00 0.00 0.00 4.85
669 711 1.001924 TGCGCAAAATTGATGTCGTGT 60.002 42.857 8.16 0.00 0.00 4.49
714 756 9.971922 ATTTTAATTAGAATTAGCTGATGGTGC 57.028 29.630 0.00 0.00 32.87 5.01
739 781 2.203470 TTTGCAGACATGATGAGGCA 57.797 45.000 0.00 2.84 0.00 4.75
764 806 4.264460 AGATATCGGCCTAAGCTCAAAG 57.736 45.455 0.00 0.00 39.73 2.77
765 807 2.240493 TATCGGCCTAAGCTCAAAGC 57.760 50.000 0.00 0.00 42.84 3.51
766 808 0.464554 ATCGGCCTAAGCTCAAAGCC 60.465 55.000 0.00 6.89 43.77 4.35
767 809 1.078143 CGGCCTAAGCTCAAAGCCT 60.078 57.895 0.00 0.00 43.77 4.58
769 811 1.034292 GGCCTAAGCTCAAAGCCTGG 61.034 60.000 0.00 0.00 43.77 4.45
770 812 1.034292 GCCTAAGCTCAAAGCCTGGG 61.034 60.000 0.00 0.00 43.77 4.45
771 813 0.620556 CCTAAGCTCAAAGCCTGGGA 59.379 55.000 0.00 0.00 43.77 4.37
772 814 1.407989 CCTAAGCTCAAAGCCTGGGAG 60.408 57.143 0.00 0.00 43.77 4.30
775 817 3.993535 CTCAAAGCCTGGGAGCAC 58.006 61.111 0.00 0.00 34.23 4.40
776 818 2.032528 TCAAAGCCTGGGAGCACG 59.967 61.111 0.00 0.00 34.23 5.34
777 819 3.058160 CAAAGCCTGGGAGCACGG 61.058 66.667 0.00 0.00 34.23 4.94
924 1939 1.927895 CCTGCAAGTCCATCGTCTAC 58.072 55.000 0.00 0.00 0.00 2.59
934 1949 6.716934 AGTCCATCGTCTACAAATATCACT 57.283 37.500 0.00 0.00 0.00 3.41
941 1956 7.818997 TCGTCTACAAATATCACTACATCCT 57.181 36.000 0.00 0.00 0.00 3.24
942 1957 7.872881 TCGTCTACAAATATCACTACATCCTC 58.127 38.462 0.00 0.00 0.00 3.71
943 1958 6.797513 CGTCTACAAATATCACTACATCCTCG 59.202 42.308 0.00 0.00 0.00 4.63
944 1959 6.583050 GTCTACAAATATCACTACATCCTCGC 59.417 42.308 0.00 0.00 0.00 5.03
945 1960 4.632153 ACAAATATCACTACATCCTCGCC 58.368 43.478 0.00 0.00 0.00 5.54
946 1961 4.345257 ACAAATATCACTACATCCTCGCCT 59.655 41.667 0.00 0.00 0.00 5.52
947 1962 4.792521 AATATCACTACATCCTCGCCTC 57.207 45.455 0.00 0.00 0.00 4.70
948 1963 1.333177 ATCACTACATCCTCGCCTCC 58.667 55.000 0.00 0.00 0.00 4.30
949 1964 0.033503 TCACTACATCCTCGCCTCCA 60.034 55.000 0.00 0.00 0.00 3.86
1002 2023 1.443407 CCCTCGATCGGCATCAACT 59.557 57.895 16.41 0.00 0.00 3.16
1006 2027 1.609072 CTCGATCGGCATCAACTCCTA 59.391 52.381 16.41 0.00 0.00 2.94
1007 2028 1.609072 TCGATCGGCATCAACTCCTAG 59.391 52.381 16.41 0.00 0.00 3.02
1011 2032 1.681793 TCGGCATCAACTCCTAGCTAC 59.318 52.381 0.00 0.00 0.00 3.58
1566 2638 2.048127 GAACCGCAACGAGAGCCT 60.048 61.111 0.00 0.00 0.00 4.58
1694 2772 2.279851 TGCCACACCGTCGTTCTG 60.280 61.111 0.00 0.00 0.00 3.02
1750 2828 1.604604 GCTGGCTTGTACCAACTTCA 58.395 50.000 0.00 0.00 39.86 3.02
2108 3234 1.468914 GGAAGACGACCCAATTGAAGC 59.531 52.381 7.12 0.00 0.00 3.86
2196 3322 2.048603 GGACCAAGGCATGCTGGAC 61.049 63.158 27.64 21.90 36.49 4.02
2217 3343 0.036105 ACATGCTGCAGTCGGATGAA 60.036 50.000 16.64 0.00 0.00 2.57
2224 3350 1.899814 TGCAGTCGGATGAACCTTACT 59.100 47.619 0.00 0.00 34.37 2.24
2234 3363 5.440610 GGATGAACCTTACTCAATGTGGAT 58.559 41.667 0.00 0.00 35.41 3.41
2263 3392 4.740822 GGGCCATGCACGACCCTT 62.741 66.667 4.39 0.00 39.42 3.95
2307 3436 1.153628 GAGGTACAATGCCGCGTCT 60.154 57.895 4.92 0.00 0.00 4.18
2554 3699 5.243954 ACTCGCTGGCTGATATATTAGTTCA 59.756 40.000 6.40 4.95 0.00 3.18
2557 3702 6.071391 TCGCTGGCTGATATATTAGTTCATCA 60.071 38.462 6.40 0.00 0.00 3.07
2561 3706 8.272545 TGGCTGATATATTAGTTCATCATTGC 57.727 34.615 6.40 0.00 0.00 3.56
2611 3756 1.985473 TTGCTCCACTTGTTCATGCT 58.015 45.000 0.00 0.00 0.00 3.79
2615 3760 1.662629 CTCCACTTGTTCATGCTAGCG 59.337 52.381 10.77 0.00 0.00 4.26
2751 4255 2.515926 TAGGCTCAGATAAGCAAGCG 57.484 50.000 0.00 0.00 44.35 4.68
2791 4295 3.991367 GGCAACCGCAGATAAGTATAGT 58.009 45.455 0.00 0.00 41.24 2.12
2792 4296 5.130292 GGCAACCGCAGATAAGTATAGTA 57.870 43.478 0.00 0.00 41.24 1.82
2793 4297 4.922103 GGCAACCGCAGATAAGTATAGTAC 59.078 45.833 0.00 0.00 41.24 2.73
2794 4298 5.508489 GGCAACCGCAGATAAGTATAGTACA 60.508 44.000 0.00 0.00 41.24 2.90
3076 4830 1.302285 CCTCAGGGCAGCAACTGAT 59.698 57.895 16.70 0.00 42.33 2.90
3115 4869 1.668751 TCTGAACCGTGTTGCTTTCAC 59.331 47.619 0.00 0.00 0.00 3.18
3167 6199 0.617413 AGATCTGTGCAAGGTCCAGG 59.383 55.000 0.00 0.00 36.60 4.45
3168 6200 0.615331 GATCTGTGCAAGGTCCAGGA 59.385 55.000 0.00 0.00 28.63 3.86
3203 6235 3.760673 GCGAGAAGCGAGTGACAG 58.239 61.111 0.00 0.00 44.57 3.51
3236 6268 0.319083 AACGGTAGCACGATTCCACA 59.681 50.000 2.50 0.00 37.61 4.17
3254 6286 6.573664 TCCACAATCTTAAAGTCCAACATG 57.426 37.500 0.00 0.00 0.00 3.21
3287 6320 3.072184 AGGCATCATCCCATGTTCTCTAC 59.928 47.826 0.00 0.00 0.00 2.59
3365 6400 2.916716 GGCAACGCACACAAATCTAATG 59.083 45.455 0.00 0.00 0.00 1.90
3438 6473 5.867174 CCAACGTACATGACATTTCAGACTA 59.133 40.000 0.00 0.00 34.35 2.59
3454 6489 5.592054 TCAGACTAAAGAATACGCAGATGG 58.408 41.667 0.00 0.00 0.00 3.51
3491 6526 1.823899 CGCTAGGGCATTTGGGACC 60.824 63.158 0.00 0.00 38.60 4.46
3565 6604 7.987458 ACATGATTTACCACTATACACTCTTGG 59.013 37.037 0.00 0.00 0.00 3.61
3566 6605 7.727578 TGATTTACCACTATACACTCTTGGA 57.272 36.000 0.00 0.00 0.00 3.53
3567 6606 8.319057 TGATTTACCACTATACACTCTTGGAT 57.681 34.615 0.00 0.00 0.00 3.41
3568 6607 9.429109 TGATTTACCACTATACACTCTTGGATA 57.571 33.333 0.00 0.00 0.00 2.59
3605 6644 1.490490 GAATGAGTAGCCATGGGACCA 59.510 52.381 15.13 0.00 0.00 4.02
3607 6646 1.147153 GAGTAGCCATGGGACCAGC 59.853 63.158 15.13 0.00 0.00 4.85
3619 6658 0.103208 GGACCAGCCACTACTCGATG 59.897 60.000 0.00 0.00 36.34 3.84
3620 6659 0.103208 GACCAGCCACTACTCGATGG 59.897 60.000 0.00 0.00 39.16 3.51
3667 6706 3.689161 TGTTCACAATAAGCTTCCCATCG 59.311 43.478 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.982073 ATTAAAGCAGCCACTCGCGC 61.982 55.000 0.00 0.00 44.76 6.86
14 15 0.247814 CATTAAAGCAGCCACTCGCG 60.248 55.000 0.00 0.00 44.76 5.87
15 16 0.099436 CCATTAAAGCAGCCACTCGC 59.901 55.000 0.00 0.00 37.98 5.03
16 17 0.734889 CCCATTAAAGCAGCCACTCG 59.265 55.000 0.00 0.00 0.00 4.18
17 18 0.457443 GCCCATTAAAGCAGCCACTC 59.543 55.000 0.00 0.00 0.00 3.51
18 19 0.972471 GGCCCATTAAAGCAGCCACT 60.972 55.000 0.00 0.00 43.32 4.00
19 20 1.517361 GGCCCATTAAAGCAGCCAC 59.483 57.895 0.00 0.00 43.32 5.01
20 21 2.051518 CGGCCCATTAAAGCAGCCA 61.052 57.895 0.00 0.00 44.06 4.75
21 22 2.785425 CCGGCCCATTAAAGCAGCC 61.785 63.158 0.00 0.00 40.33 4.85
22 23 2.807622 CCGGCCCATTAAAGCAGC 59.192 61.111 0.00 0.00 0.00 5.25
23 24 2.785425 GGCCGGCCCATTAAAGCAG 61.785 63.158 36.64 0.00 0.00 4.24
24 25 2.757917 GGCCGGCCCATTAAAGCA 60.758 61.111 36.64 0.00 0.00 3.91
34 35 2.423064 AAATCAAATCGGGCCGGCC 61.423 57.895 38.57 38.57 0.00 6.13
35 36 1.226945 CAAATCAAATCGGGCCGGC 60.227 57.895 27.98 21.18 0.00 6.13
36 37 1.226945 GCAAATCAAATCGGGCCGG 60.227 57.895 27.98 10.15 0.00 6.13
37 38 1.226945 GGCAAATCAAATCGGGCCG 60.227 57.895 22.51 22.51 0.00 6.13
38 39 0.460109 GTGGCAAATCAAATCGGGCC 60.460 55.000 0.00 0.00 41.70 5.80
39 40 0.801836 CGTGGCAAATCAAATCGGGC 60.802 55.000 0.00 0.00 0.00 6.13
40 41 0.525761 ACGTGGCAAATCAAATCGGG 59.474 50.000 0.00 0.00 0.00 5.14
41 42 3.425404 CTTACGTGGCAAATCAAATCGG 58.575 45.455 0.00 0.00 0.00 4.18
42 43 2.845967 GCTTACGTGGCAAATCAAATCG 59.154 45.455 0.00 0.00 0.00 3.34
43 44 2.845967 CGCTTACGTGGCAAATCAAATC 59.154 45.455 13.99 0.00 33.53 2.17
44 45 2.486203 TCGCTTACGTGGCAAATCAAAT 59.514 40.909 13.99 0.00 41.18 2.32
45 46 1.874231 TCGCTTACGTGGCAAATCAAA 59.126 42.857 13.99 0.00 41.18 2.69
46 47 1.514003 TCGCTTACGTGGCAAATCAA 58.486 45.000 13.99 0.00 41.18 2.57
47 48 1.514003 TTCGCTTACGTGGCAAATCA 58.486 45.000 13.99 0.00 41.18 2.57
48 49 2.825086 ATTCGCTTACGTGGCAAATC 57.175 45.000 13.99 0.00 41.18 2.17
49 50 2.353579 GGTATTCGCTTACGTGGCAAAT 59.646 45.455 13.99 10.29 41.18 2.32
50 51 1.733360 GGTATTCGCTTACGTGGCAAA 59.267 47.619 13.99 4.10 41.18 3.68
51 52 1.337917 TGGTATTCGCTTACGTGGCAA 60.338 47.619 13.99 8.58 41.18 4.52
52 53 0.246910 TGGTATTCGCTTACGTGGCA 59.753 50.000 13.99 0.00 41.18 4.92
53 54 0.928229 CTGGTATTCGCTTACGTGGC 59.072 55.000 0.00 1.22 41.18 5.01
54 55 1.924524 CACTGGTATTCGCTTACGTGG 59.075 52.381 0.00 0.00 41.18 4.94
55 56 2.871133 TCACTGGTATTCGCTTACGTG 58.129 47.619 0.00 0.00 41.18 4.49
56 57 3.581024 TTCACTGGTATTCGCTTACGT 57.419 42.857 0.00 0.00 41.18 3.57
57 58 3.241552 CGTTTCACTGGTATTCGCTTACG 60.242 47.826 0.00 0.00 42.01 3.18
58 59 3.483085 GCGTTTCACTGGTATTCGCTTAC 60.483 47.826 0.00 0.00 39.26 2.34
59 60 2.669434 GCGTTTCACTGGTATTCGCTTA 59.331 45.455 0.00 0.00 39.26 3.09
60 61 1.463444 GCGTTTCACTGGTATTCGCTT 59.537 47.619 0.00 0.00 39.26 4.68
61 62 1.076332 GCGTTTCACTGGTATTCGCT 58.924 50.000 0.00 0.00 39.26 4.93
62 63 1.060698 GAGCGTTTCACTGGTATTCGC 59.939 52.381 0.00 0.00 41.96 4.70
63 64 2.607187 AGAGCGTTTCACTGGTATTCG 58.393 47.619 0.00 0.00 0.00 3.34
64 65 5.063564 CCTTAAGAGCGTTTCACTGGTATTC 59.936 44.000 3.36 0.00 0.00 1.75
65 66 4.935808 CCTTAAGAGCGTTTCACTGGTATT 59.064 41.667 3.36 0.00 0.00 1.89
66 67 4.020485 ACCTTAAGAGCGTTTCACTGGTAT 60.020 41.667 3.36 0.00 0.00 2.73
67 68 3.322828 ACCTTAAGAGCGTTTCACTGGTA 59.677 43.478 3.36 0.00 0.00 3.25
68 69 2.104281 ACCTTAAGAGCGTTTCACTGGT 59.896 45.455 3.36 0.00 0.00 4.00
69 70 2.767505 ACCTTAAGAGCGTTTCACTGG 58.232 47.619 3.36 0.00 0.00 4.00
70 71 3.807622 TGAACCTTAAGAGCGTTTCACTG 59.192 43.478 3.36 0.00 0.00 3.66
71 72 4.067972 TGAACCTTAAGAGCGTTTCACT 57.932 40.909 3.36 0.00 0.00 3.41
72 73 4.806342 TTGAACCTTAAGAGCGTTTCAC 57.194 40.909 3.36 0.00 0.00 3.18
73 74 5.821516 TTTTGAACCTTAAGAGCGTTTCA 57.178 34.783 3.36 2.24 0.00 2.69
74 75 7.803724 TCTATTTTGAACCTTAAGAGCGTTTC 58.196 34.615 3.36 0.00 0.00 2.78
75 76 7.739498 TCTATTTTGAACCTTAAGAGCGTTT 57.261 32.000 3.36 0.00 0.00 3.60
76 77 7.201530 CGATCTATTTTGAACCTTAAGAGCGTT 60.202 37.037 3.36 0.00 36.84 4.84
77 78 6.255887 CGATCTATTTTGAACCTTAAGAGCGT 59.744 38.462 3.36 0.00 36.84 5.07
78 79 6.475727 TCGATCTATTTTGAACCTTAAGAGCG 59.524 38.462 3.36 0.00 41.30 5.03
79 80 7.707035 TCTCGATCTATTTTGAACCTTAAGAGC 59.293 37.037 3.36 0.00 0.00 4.09
80 81 9.757227 ATCTCGATCTATTTTGAACCTTAAGAG 57.243 33.333 3.36 0.00 0.00 2.85
81 82 9.751542 GATCTCGATCTATTTTGAACCTTAAGA 57.248 33.333 3.36 0.00 35.04 2.10
82 83 8.695284 CGATCTCGATCTATTTTGAACCTTAAG 58.305 37.037 5.47 0.00 43.02 1.85
83 84 8.410912 TCGATCTCGATCTATTTTGAACCTTAA 58.589 33.333 0.00 0.00 44.22 1.85
84 85 7.937649 TCGATCTCGATCTATTTTGAACCTTA 58.062 34.615 0.00 0.00 44.22 2.69
85 86 6.806751 TCGATCTCGATCTATTTTGAACCTT 58.193 36.000 0.00 0.00 44.22 3.50
86 87 6.392625 TCGATCTCGATCTATTTTGAACCT 57.607 37.500 0.00 0.00 44.22 3.50
101 102 2.663602 CACACCAAACTCTTCGATCTCG 59.336 50.000 0.00 0.00 41.45 4.04
102 103 2.413453 GCACACCAAACTCTTCGATCTC 59.587 50.000 0.00 0.00 0.00 2.75
103 104 2.037772 AGCACACCAAACTCTTCGATCT 59.962 45.455 0.00 0.00 0.00 2.75
104 105 2.158449 CAGCACACCAAACTCTTCGATC 59.842 50.000 0.00 0.00 0.00 3.69
105 106 2.146342 CAGCACACCAAACTCTTCGAT 58.854 47.619 0.00 0.00 0.00 3.59
106 107 1.138069 TCAGCACACCAAACTCTTCGA 59.862 47.619 0.00 0.00 0.00 3.71
107 108 1.581934 TCAGCACACCAAACTCTTCG 58.418 50.000 0.00 0.00 0.00 3.79
108 109 4.036734 TGAAATCAGCACACCAAACTCTTC 59.963 41.667 0.00 0.00 0.00 2.87
109 110 3.953612 TGAAATCAGCACACCAAACTCTT 59.046 39.130 0.00 0.00 0.00 2.85
110 111 3.554934 TGAAATCAGCACACCAAACTCT 58.445 40.909 0.00 0.00 0.00 3.24
111 112 3.988379 TGAAATCAGCACACCAAACTC 57.012 42.857 0.00 0.00 0.00 3.01
112 113 3.953612 TCTTGAAATCAGCACACCAAACT 59.046 39.130 0.00 0.00 0.00 2.66
113 114 4.305989 TCTTGAAATCAGCACACCAAAC 57.694 40.909 0.00 0.00 0.00 2.93
114 115 5.534207 AATCTTGAAATCAGCACACCAAA 57.466 34.783 0.00 0.00 0.00 3.28
115 116 5.534207 AAATCTTGAAATCAGCACACCAA 57.466 34.783 0.00 0.00 0.00 3.67
116 117 6.647334 TTAAATCTTGAAATCAGCACACCA 57.353 33.333 0.00 0.00 0.00 4.17
117 118 7.653311 ACTTTTAAATCTTGAAATCAGCACACC 59.347 33.333 0.00 0.00 0.00 4.16
118 119 8.579682 ACTTTTAAATCTTGAAATCAGCACAC 57.420 30.769 0.00 0.00 0.00 3.82
119 120 9.248291 GAACTTTTAAATCTTGAAATCAGCACA 57.752 29.630 0.00 0.00 0.00 4.57
120 121 9.248291 TGAACTTTTAAATCTTGAAATCAGCAC 57.752 29.630 0.00 0.00 0.00 4.40
121 122 9.467258 CTGAACTTTTAAATCTTGAAATCAGCA 57.533 29.630 0.00 0.00 0.00 4.41
122 123 8.919661 CCTGAACTTTTAAATCTTGAAATCAGC 58.080 33.333 0.00 0.00 0.00 4.26
138 139 9.481340 GAAAGCTAAATTGAATCCTGAACTTTT 57.519 29.630 0.00 0.00 0.00 2.27
139 140 7.809806 CGAAAGCTAAATTGAATCCTGAACTTT 59.190 33.333 0.00 0.00 0.00 2.66
140 141 7.040409 ACGAAAGCTAAATTGAATCCTGAACTT 60.040 33.333 0.00 0.00 0.00 2.66
141 142 6.431234 ACGAAAGCTAAATTGAATCCTGAACT 59.569 34.615 0.00 0.00 0.00 3.01
142 143 6.612306 ACGAAAGCTAAATTGAATCCTGAAC 58.388 36.000 0.00 0.00 0.00 3.18
143 144 6.655003 AGACGAAAGCTAAATTGAATCCTGAA 59.345 34.615 0.00 0.00 0.00 3.02
144 145 6.092670 CAGACGAAAGCTAAATTGAATCCTGA 59.907 38.462 0.00 0.00 0.00 3.86
145 146 6.128172 ACAGACGAAAGCTAAATTGAATCCTG 60.128 38.462 0.00 0.00 0.00 3.86
146 147 5.940470 ACAGACGAAAGCTAAATTGAATCCT 59.060 36.000 0.00 0.00 0.00 3.24
147 148 6.024049 CACAGACGAAAGCTAAATTGAATCC 58.976 40.000 0.00 0.00 0.00 3.01
148 149 6.831769 TCACAGACGAAAGCTAAATTGAATC 58.168 36.000 0.00 0.00 0.00 2.52
149 150 6.428159 ACTCACAGACGAAAGCTAAATTGAAT 59.572 34.615 0.00 0.00 0.00 2.57
150 151 5.758296 ACTCACAGACGAAAGCTAAATTGAA 59.242 36.000 0.00 0.00 0.00 2.69
151 152 5.297547 ACTCACAGACGAAAGCTAAATTGA 58.702 37.500 0.00 0.00 0.00 2.57
152 153 5.597813 ACTCACAGACGAAAGCTAAATTG 57.402 39.130 0.00 0.00 0.00 2.32
153 154 5.758296 TGAACTCACAGACGAAAGCTAAATT 59.242 36.000 0.00 0.00 0.00 1.82
154 155 5.297547 TGAACTCACAGACGAAAGCTAAAT 58.702 37.500 0.00 0.00 0.00 1.40
155 156 4.689071 TGAACTCACAGACGAAAGCTAAA 58.311 39.130 0.00 0.00 0.00 1.85
156 157 4.316205 TGAACTCACAGACGAAAGCTAA 57.684 40.909 0.00 0.00 0.00 3.09
157 158 4.299155 CTTGAACTCACAGACGAAAGCTA 58.701 43.478 0.00 0.00 0.00 3.32
158 159 2.890808 TGAACTCACAGACGAAAGCT 57.109 45.000 0.00 0.00 0.00 3.74
159 160 2.221981 CCTTGAACTCACAGACGAAAGC 59.778 50.000 0.00 0.00 0.00 3.51
160 161 3.458189 ACCTTGAACTCACAGACGAAAG 58.542 45.455 0.00 0.00 0.00 2.62
161 162 3.536956 ACCTTGAACTCACAGACGAAA 57.463 42.857 0.00 0.00 0.00 3.46
162 163 3.536956 AACCTTGAACTCACAGACGAA 57.463 42.857 0.00 0.00 0.00 3.85
163 164 3.536956 AAACCTTGAACTCACAGACGA 57.463 42.857 0.00 0.00 0.00 4.20
164 165 5.924475 AATAAACCTTGAACTCACAGACG 57.076 39.130 0.00 0.00 0.00 4.18
182 183 9.116054 GCGACGTATGGAAAAAGTTTAAAATAA 57.884 29.630 0.00 0.00 0.00 1.40
183 184 7.750014 GGCGACGTATGGAAAAAGTTTAAAATA 59.250 33.333 0.00 0.00 0.00 1.40
184 185 6.583427 GGCGACGTATGGAAAAAGTTTAAAAT 59.417 34.615 0.00 0.00 0.00 1.82
185 186 5.914074 GGCGACGTATGGAAAAAGTTTAAAA 59.086 36.000 0.00 0.00 0.00 1.52
186 187 5.451039 GGCGACGTATGGAAAAAGTTTAAA 58.549 37.500 0.00 0.00 0.00 1.52
187 188 5.033326 GGCGACGTATGGAAAAAGTTTAA 57.967 39.130 0.00 0.00 0.00 1.52
188 189 4.666928 GGCGACGTATGGAAAAAGTTTA 57.333 40.909 0.00 0.00 0.00 2.01
189 190 3.547649 GGCGACGTATGGAAAAAGTTT 57.452 42.857 0.00 0.00 0.00 2.66
226 227 2.343758 GAGAAGTGGCTGGCGACA 59.656 61.111 10.07 0.00 39.59 4.35
227 228 2.435059 GGAGAAGTGGCTGGCGAC 60.435 66.667 0.00 0.00 0.00 5.19
287 288 2.890766 GGCCAAGGTCTGGTCCGAA 61.891 63.158 0.00 0.00 44.93 4.30
321 322 2.214181 CTCCTCCCTCACGTTGACCG 62.214 65.000 0.00 0.00 44.03 4.79
326 327 3.382832 CGGCTCCTCCCTCACGTT 61.383 66.667 0.00 0.00 0.00 3.99
392 402 3.637273 AACTCCAGGACCCGGCAC 61.637 66.667 0.00 0.00 0.00 5.01
441 451 4.101448 GCATCCACTGTCCCCGCT 62.101 66.667 0.00 0.00 0.00 5.52
486 496 4.772231 ACCGCCCGCCTCCTCTTA 62.772 66.667 0.00 0.00 0.00 2.10
598 634 4.155733 TACCGAGCATGGCGTGGG 62.156 66.667 9.08 3.88 33.29 4.61
652 694 5.160641 ACCAATACACGACATCAATTTTGC 58.839 37.500 0.00 0.00 0.00 3.68
693 735 6.359804 TCAGCACCATCAGCTAATTCTAATT 58.640 36.000 0.00 0.00 41.14 1.40
694 736 5.933617 TCAGCACCATCAGCTAATTCTAAT 58.066 37.500 0.00 0.00 41.14 1.73
695 737 5.357742 TCAGCACCATCAGCTAATTCTAA 57.642 39.130 0.00 0.00 41.14 2.10
696 738 5.557576 ATCAGCACCATCAGCTAATTCTA 57.442 39.130 0.00 0.00 41.14 2.10
697 739 3.920231 TCAGCACCATCAGCTAATTCT 57.080 42.857 0.00 0.00 41.14 2.40
698 740 5.511234 AAATCAGCACCATCAGCTAATTC 57.489 39.130 0.00 0.00 41.14 2.17
714 756 5.340803 CCTCATCATGTCTGCAAAAATCAG 58.659 41.667 0.00 0.00 0.00 2.90
739 781 3.898123 TGAGCTTAGGCCGATATCTTCTT 59.102 43.478 0.00 0.00 39.73 2.52
769 811 3.540367 TTTTCCCGTCCCGTGCTCC 62.540 63.158 0.00 0.00 0.00 4.70
770 812 2.031465 TTTTCCCGTCCCGTGCTC 59.969 61.111 0.00 0.00 0.00 4.26
771 813 1.474332 TAGTTTTCCCGTCCCGTGCT 61.474 55.000 0.00 0.00 0.00 4.40
772 814 0.603439 TTAGTTTTCCCGTCCCGTGC 60.603 55.000 0.00 0.00 0.00 5.34
774 816 1.879372 GCTTTAGTTTTCCCGTCCCGT 60.879 52.381 0.00 0.00 0.00 5.28
775 817 0.800631 GCTTTAGTTTTCCCGTCCCG 59.199 55.000 0.00 0.00 0.00 5.14
776 818 1.900245 TGCTTTAGTTTTCCCGTCCC 58.100 50.000 0.00 0.00 0.00 4.46
777 819 2.350102 CGTTGCTTTAGTTTTCCCGTCC 60.350 50.000 0.00 0.00 0.00 4.79
779 821 1.605232 CCGTTGCTTTAGTTTTCCCGT 59.395 47.619 0.00 0.00 0.00 5.28
780 822 1.068816 CCCGTTGCTTTAGTTTTCCCG 60.069 52.381 0.00 0.00 0.00 5.14
781 823 2.228103 CTCCCGTTGCTTTAGTTTTCCC 59.772 50.000 0.00 0.00 0.00 3.97
782 824 2.351447 GCTCCCGTTGCTTTAGTTTTCC 60.351 50.000 0.00 0.00 0.00 3.13
788 830 2.750888 GCCGCTCCCGTTGCTTTAG 61.751 63.158 0.00 0.00 0.00 1.85
825 1839 1.406887 CGATTCGGTCCCCAATTCACT 60.407 52.381 0.00 0.00 0.00 3.41
827 1841 0.107410 CCGATTCGGTCCCCAATTCA 60.107 55.000 17.08 0.00 42.73 2.57
851 1865 1.002142 CACGGACGGTTTCCTTTTTCC 60.002 52.381 0.00 0.00 43.25 3.13
924 1939 4.887748 AGGCGAGGATGTAGTGATATTTG 58.112 43.478 0.00 0.00 0.00 2.32
934 1949 0.613572 TGTGTGGAGGCGAGGATGTA 60.614 55.000 0.00 0.00 0.00 2.29
941 1956 3.936203 GGTGGTGTGTGGAGGCGA 61.936 66.667 0.00 0.00 0.00 5.54
942 1957 2.958578 AAAGGTGGTGTGTGGAGGCG 62.959 60.000 0.00 0.00 0.00 5.52
943 1958 1.152756 AAAGGTGGTGTGTGGAGGC 60.153 57.895 0.00 0.00 0.00 4.70
944 1959 0.474184 AGAAAGGTGGTGTGTGGAGG 59.526 55.000 0.00 0.00 0.00 4.30
945 1960 3.600388 GATAGAAAGGTGGTGTGTGGAG 58.400 50.000 0.00 0.00 0.00 3.86
946 1961 2.304761 GGATAGAAAGGTGGTGTGTGGA 59.695 50.000 0.00 0.00 0.00 4.02
947 1962 2.039746 TGGATAGAAAGGTGGTGTGTGG 59.960 50.000 0.00 0.00 0.00 4.17
948 1963 3.007940 TCTGGATAGAAAGGTGGTGTGTG 59.992 47.826 0.00 0.00 0.00 3.82
949 1964 3.248024 TCTGGATAGAAAGGTGGTGTGT 58.752 45.455 0.00 0.00 0.00 3.72
1002 2023 1.852633 TCTGCTGCTTGTAGCTAGGA 58.147 50.000 11.58 5.28 42.97 2.94
1006 2027 0.179089 CCGATCTGCTGCTTGTAGCT 60.179 55.000 11.58 0.00 42.97 3.32
1007 2028 1.156645 CCCGATCTGCTGCTTGTAGC 61.157 60.000 0.00 3.79 43.95 3.58
1011 2032 2.437180 TGCCCGATCTGCTGCTTG 60.437 61.111 0.00 0.00 0.00 4.01
1252 2301 3.782244 GCTCTTGCGCGTGGTGAG 61.782 66.667 8.43 11.62 0.00 3.51
1694 2772 2.821366 CTGCCTCACCATGCGTCC 60.821 66.667 0.00 0.00 0.00 4.79
1703 2781 1.378250 ATTGCTCTGGCTGCCTCAC 60.378 57.895 21.03 7.39 39.59 3.51
1750 2828 2.645838 ACTTGTGCATCCTGAACAGT 57.354 45.000 0.00 0.00 37.20 3.55
2108 3234 2.575993 CTCCAGTGACCGGCTCAG 59.424 66.667 0.00 0.00 0.00 3.35
2211 3337 4.843728 TCCACATTGAGTAAGGTTCATCC 58.156 43.478 0.00 0.00 0.00 3.51
2217 3343 6.042552 CCTCTGATATCCACATTGAGTAAGGT 59.957 42.308 0.00 0.00 0.00 3.50
2224 3350 4.221482 CCGATCCTCTGATATCCACATTGA 59.779 45.833 0.00 0.00 0.00 2.57
2234 3363 1.269958 CATGGCCCGATCCTCTGATA 58.730 55.000 0.00 0.00 0.00 2.15
2257 3386 1.213926 AGCATCATGGAAGGAAGGGTC 59.786 52.381 0.00 0.00 0.00 4.46
2263 3392 2.942752 GCTTGTCAGCATCATGGAAGGA 60.943 50.000 0.00 0.00 46.49 3.36
2284 3413 1.009829 GCGGCATTGTACCTCTTCTG 58.990 55.000 0.00 0.00 0.00 3.02
2307 3436 0.528466 GCGATGGAGCGTCAAGATCA 60.528 55.000 0.00 0.00 36.90 2.92
2364 3493 3.684908 TGCTTCAAATGGATCGGAGAAA 58.315 40.909 0.00 0.00 43.58 2.52
2557 3702 1.026182 ATGTGTGGCGATCGTGCAAT 61.026 50.000 17.81 0.89 36.28 3.56
2561 3706 0.645355 GTACATGTGTGGCGATCGTG 59.355 55.000 17.81 7.52 0.00 4.35
2611 3756 5.729454 GCAAGAAGAACAACAGTTTTCGCTA 60.729 40.000 0.00 0.00 0.00 4.26
2615 3760 4.112634 GGGCAAGAAGAACAACAGTTTTC 58.887 43.478 0.00 0.00 0.00 2.29
2751 4255 2.551459 GCCCAGATCATAACTGCATCAC 59.449 50.000 0.00 0.00 34.47 3.06
2918 4562 9.624373 AGTTGATAATAGAAGACATTCAGCAAT 57.376 29.630 0.00 0.00 37.94 3.56
3076 4830 0.038599 ACTTCAGACATGGGCATGCA 59.961 50.000 21.36 0.00 42.39 3.96
3115 4869 6.183360 GGTCTGTATATGTTTCAACTGGTTCG 60.183 42.308 0.00 0.00 0.00 3.95
3116 4870 6.093633 GGGTCTGTATATGTTTCAACTGGTTC 59.906 42.308 0.00 0.00 0.00 3.62
3167 6199 1.457346 CTTGGCCTCAACCTCATGTC 58.543 55.000 3.32 0.00 0.00 3.06
3168 6200 0.610232 GCTTGGCCTCAACCTCATGT 60.610 55.000 3.32 0.00 0.00 3.21
3203 6235 4.879545 TGCTACCGTTAGGATTCAAAATCC 59.120 41.667 10.16 10.16 41.02 3.01
3236 6268 6.479884 AGAGAGCATGTTGGACTTTAAGATT 58.520 36.000 0.00 0.00 0.00 2.40
3254 6286 2.029110 GGATGATGCCTACAGAGAGAGC 60.029 54.545 0.00 0.00 0.00 4.09
3287 6320 9.270576 CATTTGTCGATTAAAGATGTTCTCTTG 57.729 33.333 0.00 0.00 43.60 3.02
3302 6335 3.804036 TCCGGCTATTCATTTGTCGATT 58.196 40.909 0.00 0.00 0.00 3.34
3365 6400 5.644206 GTCTCTGGGTTAAGAGTTGGATTTC 59.356 44.000 1.44 0.00 43.57 2.17
3438 6473 6.582636 TGTAGATTCCATCTGCGTATTCTTT 58.417 36.000 0.00 0.00 43.82 2.52
3454 6489 3.496130 AGCGCTTGTGCATATGTAGATTC 59.504 43.478 2.64 0.00 39.64 2.52
3491 6526 2.066262 TGGCGACTTAAGAGAAAAGCG 58.934 47.619 10.09 2.56 0.00 4.68
3565 6604 5.751243 TTCTTTTCGCCAGCCTTATTATC 57.249 39.130 0.00 0.00 0.00 1.75
3566 6605 5.827797 TCATTCTTTTCGCCAGCCTTATTAT 59.172 36.000 0.00 0.00 0.00 1.28
3567 6606 5.189928 TCATTCTTTTCGCCAGCCTTATTA 58.810 37.500 0.00 0.00 0.00 0.98
3568 6607 4.016444 TCATTCTTTTCGCCAGCCTTATT 58.984 39.130 0.00 0.00 0.00 1.40
3607 6646 0.108804 ACGTTGCCATCGAGTAGTGG 60.109 55.000 1.59 0.00 38.55 4.00
3633 6672 1.135960 TGTGAACAGGGACATGGTGA 58.864 50.000 0.00 0.00 0.00 4.02
3667 6706 2.206576 AGCTTTTCACCAGGGATGAC 57.793 50.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.