Multiple sequence alignment - TraesCS6D01G178700

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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 TraesCS6D01G178700 chr6D 100.000 5673 0 0 1 5673 187501695 187496023 0.000000e+00 10477.0
1 TraesCS6D01G178700 chr6D 89.569 719 54 13 232 939 462610136 462610844 0.000000e+00 893.0
2 TraesCS6D01G178700 chr6D 99.163 239 2 0 2 240 76230857 76230619 1.130000e-116 431.0
3 TraesCS6D01G178700 chr6D 99.573 234 1 0 1 234 51771478 51771711 1.460000e-115 427.0
4 TraesCS6D01G178700 chr6D 98.354 243 2 2 1 242 113485333 113485574 5.250000e-115 425.0
5 TraesCS6D01G178700 chr6D 88.333 60 3 3 2135 2190 58002528 58002587 1.020000e-07 69.4
6 TraesCS6D01G178700 chr6D 93.478 46 3 0 2135 2180 325600825 325600870 1.020000e-07 69.4
7 TraesCS6D01G178700 chr6D 90.196 51 5 0 2138 2188 32861354 32861304 3.670000e-07 67.6
8 TraesCS6D01G178700 chr6D 91.667 48 4 0 2135 2182 87598666 87598713 3.670000e-07 67.6
9 TraesCS6D01G178700 chr6D 93.333 45 3 0 2135 2179 456557420 456557464 3.670000e-07 67.6
10 TraesCS6D01G178700 chr6D 87.500 56 7 0 2135 2190 47614719 47614664 1.320000e-06 65.8
11 TraesCS6D01G178700 chr6A 97.549 4244 83 10 966 5203 259771804 259767576 0.000000e+00 7241.0
12 TraesCS6D01G178700 chr6A 87.733 750 67 14 232 973 194802210 194801478 0.000000e+00 852.0
13 TraesCS6D01G178700 chr6A 95.730 281 9 1 5396 5673 259740037 259739757 3.120000e-122 449.0
14 TraesCS6D01G178700 chr6A 94.581 203 11 0 5195 5397 259740353 259740151 1.190000e-81 315.0
15 TraesCS6D01G178700 chr6A 90.385 52 5 0 2135 2186 360569369 360569318 1.020000e-07 69.4
16 TraesCS6D01G178700 chr6B 96.867 1979 32 10 2421 4391 389241180 389239224 0.000000e+00 3284.0
17 TraesCS6D01G178700 chr6B 98.118 1222 22 1 966 2186 389243113 389241892 0.000000e+00 2128.0
18 TraesCS6D01G178700 chr6B 94.487 653 33 1 5024 5673 389235655 389235003 0.000000e+00 1003.0
19 TraesCS6D01G178700 chr6B 94.255 644 35 1 4387 5028 389236985 389236342 0.000000e+00 983.0
20 TraesCS6D01G178700 chr6B 94.800 250 3 6 2184 2429 389241539 389241296 1.150000e-101 381.0
21 TraesCS6D01G178700 chr1D 90.413 751 53 14 232 972 190484496 190485237 0.000000e+00 970.0
22 TraesCS6D01G178700 chr1D 100.000 233 0 0 1 233 90405989 90405757 1.130000e-116 431.0
23 TraesCS6D01G178700 chr1D 98.755 241 3 0 1 241 110647028 110646788 4.060000e-116 429.0
24 TraesCS6D01G178700 chr1D 99.567 231 1 0 1 231 418540076 418540306 6.800000e-114 422.0
25 TraesCS6D01G178700 chr2D 90.201 745 57 10 232 970 48205621 48206355 0.000000e+00 957.0
26 TraesCS6D01G178700 chr2D 89.488 761 60 13 232 980 12764444 12763692 0.000000e+00 944.0
27 TraesCS6D01G178700 chr4D 89.037 748 64 10 232 972 243710153 243709417 0.000000e+00 911.0
28 TraesCS6D01G178700 chr4D 91.667 48 4 0 2135 2182 172109784 172109737 3.670000e-07 67.6
29 TraesCS6D01G178700 chr4D 93.333 45 3 0 2135 2179 441486770 441486814 3.670000e-07 67.6
30 TraesCS6D01G178700 chr5D 88.385 749 67 12 232 970 296882558 296881820 0.000000e+00 883.0
31 TraesCS6D01G178700 chr5D 87.899 752 69 13 232 974 420847211 420847949 0.000000e+00 865.0
32 TraesCS6D01G178700 chr5D 99.573 234 1 0 1 234 267711595 267711362 1.460000e-115 427.0
33 TraesCS6D01G178700 chr5D 98.739 238 3 0 1 238 384185688 384185925 1.890000e-114 424.0
34 TraesCS6D01G178700 chr5D 91.837 49 4 0 2135 2183 532242565 532242613 1.020000e-07 69.4
35 TraesCS6D01G178700 chr2A 87.567 748 74 12 232 970 19515754 19516491 0.000000e+00 848.0
36 TraesCS6D01G178700 chr2A 90.741 54 5 0 2135 2188 707748350 707748297 7.880000e-09 73.1
37 TraesCS6D01G178700 chr3D 98.739 238 3 0 1 238 173610397 173610634 1.890000e-114 424.0
38 TraesCS6D01G178700 chr3D 95.556 45 2 0 2135 2179 537914968 537915012 7.880000e-09 73.1
39 TraesCS6D01G178700 chr3D 89.474 57 5 1 2135 2191 96684562 96684507 2.840000e-08 71.3
40 TraesCS6D01G178700 chr7D 88.333 60 5 2 2137 2194 59413194 59413135 2.840000e-08 71.3
41 TraesCS6D01G178700 chr7B 92.000 50 4 0 2135 2184 463050409 463050360 2.840000e-08 71.3
42 TraesCS6D01G178700 chr7A 88.333 60 5 2 2137 2194 63776091 63776032 2.840000e-08 71.3
43 TraesCS6D01G178700 chr2B 92.000 50 4 0 2135 2184 734295966 734296015 2.840000e-08 71.3
44 TraesCS6D01G178700 chr1B 92.000 50 4 0 2135 2184 562928489 562928440 2.840000e-08 71.3
45 TraesCS6D01G178700 chr1B 92.000 50 4 0 2135 2184 572442109 572442060 2.840000e-08 71.3
46 TraesCS6D01G178700 chr1A 87.719 57 6 1 2135 2191 56105855 56105800 1.320000e-06 65.8
47 TraesCS6D01G178700 chr1A 88.679 53 6 0 2135 2187 485361317 485361369 1.320000e-06 65.8
48 TraesCS6D01G178700 chrUn 89.796 49 5 0 2135 2183 316165958 316166006 4.750000e-06 63.9
49 TraesCS6D01G178700 chrUn 89.583 48 5 0 2135 2182 150796013 150796060 1.710000e-05 62.1
50 TraesCS6D01G178700 chrUn 89.362 47 5 0 2135 2181 82594782 82594828 6.140000e-05 60.2
51 TraesCS6D01G178700 chrUn 89.130 46 5 0 2135 2180 111701429 111701384 2.210000e-04 58.4
52 TraesCS6D01G178700 chrUn 100.000 30 0 0 2135 2164 60521620 60521649 7.940000e-04 56.5
53 TraesCS6D01G178700 chrUn 100.000 30 0 0 2135 2164 81697188 81697217 7.940000e-04 56.5
54 TraesCS6D01G178700 chrUn 100.000 30 0 0 2135 2164 190888261 190888290 7.940000e-04 56.5
55 TraesCS6D01G178700 chrUn 88.889 45 5 0 2135 2179 283389541 283389497 7.940000e-04 56.5
56 TraesCS6D01G178700 chrUn 88.889 45 5 0 2135 2179 355880557 355880601 7.940000e-04 56.5


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 TraesCS6D01G178700 chr6D 187496023 187501695 5672 True 10477.0 10477 100.0000 1 5673 1 chr6D.!!$R4 5672
1 TraesCS6D01G178700 chr6D 462610136 462610844 708 False 893.0 893 89.5690 232 939 1 chr6D.!!$F7 707
2 TraesCS6D01G178700 chr6A 259767576 259771804 4228 True 7241.0 7241 97.5490 966 5203 1 chr6A.!!$R2 4237
3 TraesCS6D01G178700 chr6A 194801478 194802210 732 True 852.0 852 87.7330 232 973 1 chr6A.!!$R1 741
4 TraesCS6D01G178700 chr6A 259739757 259740353 596 True 382.0 449 95.1555 5195 5673 2 chr6A.!!$R4 478
5 TraesCS6D01G178700 chr6B 389235003 389243113 8110 True 1555.8 3284 95.7054 966 5673 5 chr6B.!!$R1 4707
6 TraesCS6D01G178700 chr1D 190484496 190485237 741 False 970.0 970 90.4130 232 972 1 chr1D.!!$F1 740
7 TraesCS6D01G178700 chr2D 48205621 48206355 734 False 957.0 957 90.2010 232 970 1 chr2D.!!$F1 738
8 TraesCS6D01G178700 chr2D 12763692 12764444 752 True 944.0 944 89.4880 232 980 1 chr2D.!!$R1 748
9 TraesCS6D01G178700 chr4D 243709417 243710153 736 True 911.0 911 89.0370 232 972 1 chr4D.!!$R2 740
10 TraesCS6D01G178700 chr5D 296881820 296882558 738 True 883.0 883 88.3850 232 970 1 chr5D.!!$R2 738
11 TraesCS6D01G178700 chr5D 420847211 420847949 738 False 865.0 865 87.8990 232 974 1 chr5D.!!$F2 742
12 TraesCS6D01G178700 chr2A 19515754 19516491 737 False 848.0 848 87.5670 232 970 1 chr2A.!!$F1 738

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
116 117 0.033504 TTCTCTTGAACGCTTCCGCT 59.966 50.000 0.00 0.0 38.22 5.52 F
128 129 0.248498 CTTCCGCTCGCGATCTACAA 60.248 55.000 10.36 0.0 42.83 2.41 F
156 157 0.423544 AGATTCACTCCCCTTCCCCT 59.576 55.000 0.00 0.0 0.00 4.79 F
276 277 0.613292 AGTGCAGGAGTCCATCGAGT 60.613 55.000 12.86 0.0 0.00 4.18 F
2133 2161 0.253160 ATGGTACTCCTTCTGCCCCA 60.253 55.000 0.00 0.0 34.23 4.96 F
2171 2199 1.674817 CGACAAGTAATTCGGGCCAGT 60.675 52.381 4.39 0.0 0.00 4.00 F
2836 3358 1.679032 GCACACCCTGAGTTGGATACC 60.679 57.143 0.00 0.0 0.00 2.73 F
2876 3398 2.159517 GCACTGGTATTTCAGCTTTCCG 60.160 50.000 0.00 0.0 38.26 4.30 F
3362 3884 2.508526 AGAACAAGATGGTGGACAAGC 58.491 47.619 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2109 4.665833 ATGGCTAGTATCAACGCTTACA 57.334 40.909 0.0 0.0 0.00 2.41 R
2124 2152 2.204463 TGGATGTATCTTGGGGCAGAA 58.796 47.619 0.0 0.0 0.00 3.02 R
2133 2161 4.769688 TGTCGCAGAAATGGATGTATCTT 58.230 39.130 0.0 0.0 39.69 2.40 R
2203 2586 1.123077 ATTCCAGCGAGGTATGCAGA 58.877 50.000 0.0 0.0 39.02 4.26 R
3440 3962 1.605710 CAGTTGTCCTTCTGTTGCCAG 59.394 52.381 0.0 0.0 40.25 4.85 R
3968 4490 2.842496 TGTGGGCTTCATCAAGATCTCT 59.158 45.455 0.0 0.0 0.00 3.10 R
4294 4816 0.301987 GAGCTGGCTTTCGTATTCGC 59.698 55.000 0.0 0.0 36.96 4.70 R
4659 7426 3.194116 TCGTGTTGGATACCCTGTAAGTC 59.806 47.826 0.0 0.0 0.00 3.01 R
4776 7543 5.826643 AGCATCCTTTAATCCAACAACCTA 58.173 37.500 0.0 0.0 0.00 3.08 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
17 18 2.049433 GCTGCTCCGTACGTGTGT 60.049 61.111 15.21 0.00 0.00 3.72
18 19 1.663702 GCTGCTCCGTACGTGTGTT 60.664 57.895 15.21 0.00 0.00 3.32
19 20 1.886861 GCTGCTCCGTACGTGTGTTG 61.887 60.000 15.21 0.00 0.00 3.33
20 21 0.318360 CTGCTCCGTACGTGTGTTGA 60.318 55.000 15.21 1.92 0.00 3.18
21 22 0.102663 TGCTCCGTACGTGTGTTGAA 59.897 50.000 15.21 0.00 0.00 2.69
22 23 0.505655 GCTCCGTACGTGTGTTGAAC 59.494 55.000 15.21 0.00 0.00 3.18
23 24 0.774098 CTCCGTACGTGTGTTGAACG 59.226 55.000 15.21 0.00 46.32 3.95
24 25 1.199859 CCGTACGTGTGTTGAACGC 59.800 57.895 15.21 1.20 44.80 4.84
29 30 2.935955 GTGTGTTGAACGCGGAGG 59.064 61.111 12.47 0.00 0.00 4.30
30 31 1.885850 GTGTGTTGAACGCGGAGGT 60.886 57.895 12.47 0.00 0.00 3.85
31 32 1.885388 TGTGTTGAACGCGGAGGTG 60.885 57.895 12.47 0.00 0.00 4.00
32 33 2.970324 TGTTGAACGCGGAGGTGC 60.970 61.111 12.47 0.00 0.00 5.01
33 34 3.723348 GTTGAACGCGGAGGTGCC 61.723 66.667 12.47 0.00 0.00 5.01
51 52 3.818787 GTCCGTTCGGCGCTAGGA 61.819 66.667 7.64 7.54 39.71 2.94
52 53 2.831742 TCCGTTCGGCGCTAGGAT 60.832 61.111 7.64 0.00 39.71 3.24
53 54 2.354773 CCGTTCGGCGCTAGGATC 60.355 66.667 7.64 1.16 39.71 3.36
54 55 2.411701 CGTTCGGCGCTAGGATCA 59.588 61.111 7.64 0.00 0.00 2.92
55 56 1.007271 CGTTCGGCGCTAGGATCAT 60.007 57.895 7.64 0.00 0.00 2.45
56 57 1.004277 CGTTCGGCGCTAGGATCATC 61.004 60.000 7.64 0.00 0.00 2.92
57 58 1.004277 GTTCGGCGCTAGGATCATCG 61.004 60.000 7.64 0.00 0.00 3.84
58 59 2.126307 CGGCGCTAGGATCATCGG 60.126 66.667 7.64 0.00 0.00 4.18
59 60 2.920645 CGGCGCTAGGATCATCGGT 61.921 63.158 7.64 0.00 0.00 4.69
60 61 1.373497 GGCGCTAGGATCATCGGTG 60.373 63.158 7.64 0.00 0.00 4.94
61 62 1.660355 GCGCTAGGATCATCGGTGA 59.340 57.895 0.00 0.00 39.04 4.02
63 64 1.337260 GCGCTAGGATCATCGGTGATT 60.337 52.381 13.46 0.00 44.96 2.57
64 65 2.868044 GCGCTAGGATCATCGGTGATTT 60.868 50.000 13.46 7.21 44.96 2.17
65 66 2.733552 CGCTAGGATCATCGGTGATTTG 59.266 50.000 13.46 4.89 44.96 2.32
66 67 3.070018 GCTAGGATCATCGGTGATTTGG 58.930 50.000 13.46 7.76 44.96 3.28
67 68 3.244215 GCTAGGATCATCGGTGATTTGGA 60.244 47.826 13.46 0.00 44.96 3.53
68 69 4.564406 GCTAGGATCATCGGTGATTTGGAT 60.564 45.833 13.46 0.35 44.96 3.41
69 70 4.013267 AGGATCATCGGTGATTTGGATC 57.987 45.455 13.46 0.00 44.96 3.36
70 71 3.392285 AGGATCATCGGTGATTTGGATCA 59.608 43.478 13.46 0.00 44.96 2.92
80 81 3.766151 TGATTTGGATCACGACGAGTAC 58.234 45.455 0.00 0.00 37.37 2.73
81 82 2.251869 TTTGGATCACGACGAGTACG 57.748 50.000 0.00 0.00 45.75 3.67
82 83 1.441738 TTGGATCACGACGAGTACGA 58.558 50.000 0.00 0.00 42.66 3.43
83 84 0.723414 TGGATCACGACGAGTACGAC 59.277 55.000 0.00 0.00 42.66 4.34
84 85 1.005340 GGATCACGACGAGTACGACT 58.995 55.000 0.00 0.00 42.66 4.18
85 86 1.005137 GGATCACGACGAGTACGACTC 60.005 57.143 0.00 0.00 41.71 3.36
86 87 1.005137 GATCACGACGAGTACGACTCC 60.005 57.143 0.00 0.00 42.12 3.85
87 88 0.319813 TCACGACGAGTACGACTCCA 60.320 55.000 0.00 0.00 42.12 3.86
88 89 0.725686 CACGACGAGTACGACTCCAT 59.274 55.000 0.00 0.00 42.12 3.41
89 90 1.005340 ACGACGAGTACGACTCCATC 58.995 55.000 0.00 6.63 42.12 3.51
90 91 1.004595 CGACGAGTACGACTCCATCA 58.995 55.000 8.73 0.00 42.12 3.07
91 92 1.395954 CGACGAGTACGACTCCATCAA 59.604 52.381 8.73 0.00 42.12 2.57
92 93 2.783333 GACGAGTACGACTCCATCAAC 58.217 52.381 8.73 0.00 42.12 3.18
93 94 1.471684 ACGAGTACGACTCCATCAACC 59.528 52.381 8.73 0.00 42.12 3.77
94 95 1.202268 CGAGTACGACTCCATCAACCC 60.202 57.143 8.73 0.00 42.12 4.11
95 96 1.136500 GAGTACGACTCCATCAACCCC 59.864 57.143 0.00 0.00 39.28 4.95
96 97 0.179119 GTACGACTCCATCAACCCCG 60.179 60.000 0.00 0.00 0.00 5.73
97 98 0.612732 TACGACTCCATCAACCCCGT 60.613 55.000 0.00 0.00 0.00 5.28
98 99 1.295423 CGACTCCATCAACCCCGTT 59.705 57.895 0.00 0.00 0.00 4.44
99 100 0.739813 CGACTCCATCAACCCCGTTC 60.740 60.000 0.00 0.00 0.00 3.95
100 101 0.613777 GACTCCATCAACCCCGTTCT 59.386 55.000 0.00 0.00 0.00 3.01
101 102 0.613777 ACTCCATCAACCCCGTTCTC 59.386 55.000 0.00 0.00 0.00 2.87
102 103 0.905357 CTCCATCAACCCCGTTCTCT 59.095 55.000 0.00 0.00 0.00 3.10
103 104 1.279271 CTCCATCAACCCCGTTCTCTT 59.721 52.381 0.00 0.00 0.00 2.85
104 105 1.003118 TCCATCAACCCCGTTCTCTTG 59.997 52.381 0.00 0.00 0.00 3.02
105 106 1.003118 CCATCAACCCCGTTCTCTTGA 59.997 52.381 0.00 0.00 0.00 3.02
106 107 2.552155 CCATCAACCCCGTTCTCTTGAA 60.552 50.000 0.00 0.00 0.00 2.69
107 108 2.249844 TCAACCCCGTTCTCTTGAAC 57.750 50.000 0.00 0.00 46.59 3.18
115 116 0.164002 GTTCTCTTGAACGCTTCCGC 59.836 55.000 0.00 0.00 42.39 5.54
116 117 0.033504 TTCTCTTGAACGCTTCCGCT 59.966 50.000 0.00 0.00 38.22 5.52
117 118 0.388649 TCTCTTGAACGCTTCCGCTC 60.389 55.000 0.00 0.00 38.22 5.03
118 119 1.678269 CTCTTGAACGCTTCCGCTCG 61.678 60.000 0.00 0.00 38.22 5.03
119 120 3.354499 CTTGAACGCTTCCGCTCGC 62.354 63.158 0.00 0.00 38.22 5.03
125 126 2.331805 GCTTCCGCTCGCGATCTA 59.668 61.111 10.36 0.00 42.83 1.98
126 127 2.011881 GCTTCCGCTCGCGATCTAC 61.012 63.158 10.36 0.00 42.83 2.59
127 128 1.355563 CTTCCGCTCGCGATCTACA 59.644 57.895 10.36 0.00 42.83 2.74
128 129 0.248498 CTTCCGCTCGCGATCTACAA 60.248 55.000 10.36 0.00 42.83 2.41
129 130 0.248498 TTCCGCTCGCGATCTACAAG 60.248 55.000 10.36 0.00 42.83 3.16
130 131 1.658717 CCGCTCGCGATCTACAAGG 60.659 63.158 10.36 0.00 42.83 3.61
131 132 1.658717 CGCTCGCGATCTACAAGGG 60.659 63.158 10.36 0.00 42.83 3.95
132 133 1.437986 GCTCGCGATCTACAAGGGT 59.562 57.895 10.36 0.00 0.00 4.34
133 134 0.666913 GCTCGCGATCTACAAGGGTA 59.333 55.000 10.36 0.00 0.00 3.69
134 135 1.269998 GCTCGCGATCTACAAGGGTAT 59.730 52.381 10.36 0.00 0.00 2.73
135 136 2.922758 GCTCGCGATCTACAAGGGTATG 60.923 54.545 10.36 0.00 0.00 2.39
136 137 2.293677 CTCGCGATCTACAAGGGTATGT 59.706 50.000 10.36 0.00 37.32 2.29
137 138 3.479489 TCGCGATCTACAAGGGTATGTA 58.521 45.455 3.71 0.00 34.75 2.29
147 148 5.615925 ACAAGGGTATGTAGATTCACTCC 57.384 43.478 0.00 0.00 0.00 3.85
148 149 4.409247 ACAAGGGTATGTAGATTCACTCCC 59.591 45.833 0.00 0.00 35.42 4.30
149 150 3.588569 AGGGTATGTAGATTCACTCCCC 58.411 50.000 0.00 0.00 35.62 4.81
150 151 3.210074 AGGGTATGTAGATTCACTCCCCT 59.790 47.826 0.00 0.00 35.62 4.79
151 152 3.974642 GGGTATGTAGATTCACTCCCCTT 59.025 47.826 0.00 0.00 31.91 3.95
152 153 4.040584 GGGTATGTAGATTCACTCCCCTTC 59.959 50.000 0.00 0.00 31.91 3.46
153 154 4.040584 GGTATGTAGATTCACTCCCCTTCC 59.959 50.000 0.00 0.00 0.00 3.46
154 155 2.478292 TGTAGATTCACTCCCCTTCCC 58.522 52.381 0.00 0.00 0.00 3.97
155 156 1.769465 GTAGATTCACTCCCCTTCCCC 59.231 57.143 0.00 0.00 0.00 4.81
156 157 0.423544 AGATTCACTCCCCTTCCCCT 59.576 55.000 0.00 0.00 0.00 4.79
157 158 0.840617 GATTCACTCCCCTTCCCCTC 59.159 60.000 0.00 0.00 0.00 4.30
158 159 0.983378 ATTCACTCCCCTTCCCCTCG 60.983 60.000 0.00 0.00 0.00 4.63
159 160 2.284699 CACTCCCCTTCCCCTCGT 60.285 66.667 0.00 0.00 0.00 4.18
160 161 1.918800 CACTCCCCTTCCCCTCGTT 60.919 63.158 0.00 0.00 0.00 3.85
161 162 1.918800 ACTCCCCTTCCCCTCGTTG 60.919 63.158 0.00 0.00 0.00 4.10
162 163 3.327404 TCCCCTTCCCCTCGTTGC 61.327 66.667 0.00 0.00 0.00 4.17
163 164 3.330720 CCCCTTCCCCTCGTTGCT 61.331 66.667 0.00 0.00 0.00 3.91
164 165 1.993391 CCCCTTCCCCTCGTTGCTA 60.993 63.158 0.00 0.00 0.00 3.49
165 166 1.522569 CCCTTCCCCTCGTTGCTAG 59.477 63.158 0.00 0.00 0.00 3.42
166 167 0.976073 CCCTTCCCCTCGTTGCTAGA 60.976 60.000 0.00 0.00 0.00 2.43
167 168 1.123928 CCTTCCCCTCGTTGCTAGAT 58.876 55.000 0.00 0.00 0.00 1.98
168 169 1.486726 CCTTCCCCTCGTTGCTAGATT 59.513 52.381 0.00 0.00 0.00 2.40
169 170 2.698797 CCTTCCCCTCGTTGCTAGATTA 59.301 50.000 0.00 0.00 0.00 1.75
170 171 3.492829 CCTTCCCCTCGTTGCTAGATTAC 60.493 52.174 0.00 0.00 0.00 1.89
171 172 3.028094 TCCCCTCGTTGCTAGATTACT 57.972 47.619 0.00 0.00 0.00 2.24
172 173 2.957006 TCCCCTCGTTGCTAGATTACTC 59.043 50.000 0.00 0.00 0.00 2.59
173 174 2.036089 CCCCTCGTTGCTAGATTACTCC 59.964 54.545 0.00 0.00 0.00 3.85
174 175 2.693591 CCCTCGTTGCTAGATTACTCCA 59.306 50.000 0.00 0.00 0.00 3.86
175 176 3.322254 CCCTCGTTGCTAGATTACTCCAT 59.678 47.826 0.00 0.00 0.00 3.41
176 177 4.523173 CCCTCGTTGCTAGATTACTCCATA 59.477 45.833 0.00 0.00 0.00 2.74
177 178 5.336055 CCCTCGTTGCTAGATTACTCCATAG 60.336 48.000 0.00 0.00 0.00 2.23
178 179 5.473846 CCTCGTTGCTAGATTACTCCATAGA 59.526 44.000 0.00 0.00 0.00 1.98
179 180 6.151985 CCTCGTTGCTAGATTACTCCATAGAT 59.848 42.308 0.00 0.00 0.00 1.98
180 181 7.309499 CCTCGTTGCTAGATTACTCCATAGATT 60.309 40.741 0.00 0.00 0.00 2.40
181 182 7.371159 TCGTTGCTAGATTACTCCATAGATTG 58.629 38.462 0.00 0.00 0.00 2.67
182 183 7.230712 TCGTTGCTAGATTACTCCATAGATTGA 59.769 37.037 0.00 0.00 0.00 2.57
183 184 8.031864 CGTTGCTAGATTACTCCATAGATTGAT 58.968 37.037 0.00 0.00 0.00 2.57
184 185 9.364989 GTTGCTAGATTACTCCATAGATTGATC 57.635 37.037 0.00 0.00 0.00 2.92
185 186 8.891985 TGCTAGATTACTCCATAGATTGATCT 57.108 34.615 0.00 0.00 40.86 2.75
186 187 9.319060 TGCTAGATTACTCCATAGATTGATCTT 57.681 33.333 0.00 0.00 38.32 2.40
187 188 9.585099 GCTAGATTACTCCATAGATTGATCTTG 57.415 37.037 0.00 0.00 38.32 3.02
189 190 8.503428 AGATTACTCCATAGATTGATCTTGGT 57.497 34.615 15.48 6.45 38.32 3.67
190 191 8.373981 AGATTACTCCATAGATTGATCTTGGTG 58.626 37.037 15.48 15.28 38.32 4.17
191 192 7.675161 TTACTCCATAGATTGATCTTGGTGA 57.325 36.000 19.38 6.63 38.32 4.02
192 193 6.760440 ACTCCATAGATTGATCTTGGTGAT 57.240 37.500 19.38 0.00 38.32 3.06
193 194 6.531923 ACTCCATAGATTGATCTTGGTGATG 58.468 40.000 19.38 10.22 38.32 3.07
194 195 5.311265 TCCATAGATTGATCTTGGTGATGC 58.689 41.667 15.48 0.00 38.32 3.91
195 196 4.153655 CCATAGATTGATCTTGGTGATGCG 59.846 45.833 0.00 0.00 38.32 4.73
196 197 3.272574 AGATTGATCTTGGTGATGCGT 57.727 42.857 0.00 0.00 35.14 5.24
197 198 4.406648 AGATTGATCTTGGTGATGCGTA 57.593 40.909 0.00 0.00 35.14 4.42
198 199 4.375272 AGATTGATCTTGGTGATGCGTAG 58.625 43.478 0.00 0.00 35.14 3.51
199 200 3.885724 TTGATCTTGGTGATGCGTAGA 57.114 42.857 0.00 0.00 35.14 2.59
200 201 3.885724 TGATCTTGGTGATGCGTAGAA 57.114 42.857 0.00 0.00 35.14 2.10
201 202 4.200838 TGATCTTGGTGATGCGTAGAAA 57.799 40.909 0.00 0.00 35.14 2.52
202 203 4.574892 TGATCTTGGTGATGCGTAGAAAA 58.425 39.130 0.00 0.00 35.14 2.29
203 204 5.185454 TGATCTTGGTGATGCGTAGAAAAT 58.815 37.500 0.00 0.00 35.14 1.82
204 205 5.647658 TGATCTTGGTGATGCGTAGAAAATT 59.352 36.000 0.00 0.00 35.14 1.82
205 206 5.957842 TCTTGGTGATGCGTAGAAAATTT 57.042 34.783 0.00 0.00 0.00 1.82
206 207 6.325919 TCTTGGTGATGCGTAGAAAATTTT 57.674 33.333 2.28 2.28 0.00 1.82
207 208 6.148948 TCTTGGTGATGCGTAGAAAATTTTG 58.851 36.000 8.47 0.00 0.00 2.44
208 209 5.697473 TGGTGATGCGTAGAAAATTTTGA 57.303 34.783 8.47 0.00 0.00 2.69
209 210 6.078202 TGGTGATGCGTAGAAAATTTTGAA 57.922 33.333 8.47 0.00 0.00 2.69
210 211 6.686630 TGGTGATGCGTAGAAAATTTTGAAT 58.313 32.000 8.47 0.00 0.00 2.57
211 212 7.151308 TGGTGATGCGTAGAAAATTTTGAATT 58.849 30.769 8.47 0.00 0.00 2.17
212 213 7.655328 TGGTGATGCGTAGAAAATTTTGAATTT 59.345 29.630 8.47 0.00 0.00 1.82
213 214 8.162245 GGTGATGCGTAGAAAATTTTGAATTTC 58.838 33.333 8.47 0.00 36.11 2.17
214 215 8.915654 GTGATGCGTAGAAAATTTTGAATTTCT 58.084 29.630 8.47 0.48 45.29 2.52
215 216 8.914654 TGATGCGTAGAAAATTTTGAATTTCTG 58.085 29.630 8.47 0.00 43.67 3.02
216 217 7.104326 TGCGTAGAAAATTTTGAATTTCTGC 57.896 32.000 8.47 8.21 43.67 4.26
217 218 6.922957 TGCGTAGAAAATTTTGAATTTCTGCT 59.077 30.769 8.47 0.00 43.67 4.24
218 219 8.079203 TGCGTAGAAAATTTTGAATTTCTGCTA 58.921 29.630 8.47 0.00 43.67 3.49
219 220 8.365938 GCGTAGAAAATTTTGAATTTCTGCTAC 58.634 33.333 8.47 8.90 43.67 3.58
220 221 8.567221 CGTAGAAAATTTTGAATTTCTGCTACG 58.433 33.333 22.91 22.91 43.67 3.51
221 222 9.394477 GTAGAAAATTTTGAATTTCTGCTACGT 57.606 29.630 8.47 0.00 43.67 3.57
222 223 8.871686 AGAAAATTTTGAATTTCTGCTACGTT 57.128 26.923 8.47 0.00 42.62 3.99
223 224 8.968242 AGAAAATTTTGAATTTCTGCTACGTTC 58.032 29.630 8.47 0.00 42.62 3.95
224 225 7.637709 AAATTTTGAATTTCTGCTACGTTCC 57.362 32.000 0.00 0.00 0.00 3.62
225 226 4.759516 TTTGAATTTCTGCTACGTTCCC 57.240 40.909 0.00 0.00 0.00 3.97
226 227 2.706890 TGAATTTCTGCTACGTTCCCC 58.293 47.619 0.00 0.00 0.00 4.81
227 228 2.039216 TGAATTTCTGCTACGTTCCCCA 59.961 45.455 0.00 0.00 0.00 4.96
228 229 2.871096 ATTTCTGCTACGTTCCCCAA 57.129 45.000 0.00 0.00 0.00 4.12
229 230 1.886886 TTTCTGCTACGTTCCCCAAC 58.113 50.000 0.00 0.00 0.00 3.77
230 231 0.759959 TTCTGCTACGTTCCCCAACA 59.240 50.000 0.00 0.00 32.14 3.33
236 237 2.295070 GCTACGTTCCCCAACAAAACAT 59.705 45.455 0.00 0.00 32.14 2.71
276 277 0.613292 AGTGCAGGAGTCCATCGAGT 60.613 55.000 12.86 0.00 0.00 4.18
651 653 2.433838 CAGCTCTGACACCGCCAG 60.434 66.667 0.00 0.00 0.00 4.85
652 654 4.385405 AGCTCTGACACCGCCAGC 62.385 66.667 0.00 0.00 0.00 4.85
654 656 4.767255 CTCTGACACCGCCAGCCC 62.767 72.222 0.00 0.00 0.00 5.19
716 718 3.112075 CCGAGTGATGCGTTGCGT 61.112 61.111 0.00 0.00 0.00 5.24
719 721 1.341369 CGAGTGATGCGTTGCGTACA 61.341 55.000 0.00 0.00 0.00 2.90
776 786 3.928727 ATTTATCCGATCGCCGAACTA 57.071 42.857 10.32 0.00 41.76 2.24
788 804 1.586422 CCGAACTATGGCCTGTGATG 58.414 55.000 3.32 0.00 0.00 3.07
789 805 1.138859 CCGAACTATGGCCTGTGATGA 59.861 52.381 3.32 0.00 0.00 2.92
790 806 2.224378 CCGAACTATGGCCTGTGATGAT 60.224 50.000 3.32 0.00 0.00 2.45
798 814 1.368950 CCTGTGATGATCGCCGGAT 59.631 57.895 5.05 0.00 33.78 4.18
831 851 6.406692 TTTTTATGAATGGGAACGACCAAA 57.593 33.333 0.00 0.00 45.13 3.28
835 855 7.704578 TTATGAATGGGAACGACCAAATTTA 57.295 32.000 0.00 0.00 45.13 1.40
853 874 5.554822 ATTTAAAATTGCCGCGTCTTAGA 57.445 34.783 4.92 0.00 0.00 2.10
896 921 2.044252 AGCTAGGTCGCCCGAGAA 60.044 61.111 0.00 0.00 35.61 2.87
918 943 1.623542 AATCTAGGGCCGGTTCGCTT 61.624 55.000 1.90 0.00 0.00 4.68
941 966 2.686816 GCCGCTCTTTTTAGGCGCA 61.687 57.895 10.83 0.00 46.29 6.09
942 967 1.425428 CCGCTCTTTTTAGGCGCAG 59.575 57.895 10.83 0.00 46.29 5.18
943 968 1.019278 CCGCTCTTTTTAGGCGCAGA 61.019 55.000 10.83 0.34 46.29 4.26
944 969 0.796312 CGCTCTTTTTAGGCGCAGAA 59.204 50.000 10.83 0.00 42.28 3.02
977 1004 2.370349 CTCGAGAAGCTCTTAGACCCA 58.630 52.381 6.58 0.00 0.00 4.51
1125 1153 2.117156 CGTCACCGTATCCCCGACT 61.117 63.158 0.00 0.00 0.00 4.18
1752 1780 1.608590 GGAATGGTATGACAATGGGCG 59.391 52.381 0.00 0.00 0.00 6.13
1963 1991 2.649331 TTAACTAGACTGTGAGCGGC 57.351 50.000 0.00 0.00 0.00 6.53
2007 2035 3.074538 ACCAGAGGGATTTTGTTAGTGCT 59.925 43.478 0.00 0.00 38.05 4.40
2009 2037 4.074970 CAGAGGGATTTTGTTAGTGCTGT 58.925 43.478 0.00 0.00 0.00 4.40
2047 2075 3.466836 TCAAGACGTCAGTTGAGCATTT 58.533 40.909 19.50 0.00 0.00 2.32
2081 2109 7.328277 TGTGATAACCGCAAAAGCTTATTAT 57.672 32.000 0.00 0.00 31.33 1.28
2133 2161 0.253160 ATGGTACTCCTTCTGCCCCA 60.253 55.000 0.00 0.00 34.23 4.96
2171 2199 1.674817 CGACAAGTAATTCGGGCCAGT 60.675 52.381 4.39 0.00 0.00 4.00
2203 2586 3.326880 AGTTAATGTTGGACTTCCGGAGT 59.673 43.478 3.34 5.13 42.70 3.85
2244 2627 6.642733 ATAATTGGAACCTCTTCTGGAGAA 57.357 37.500 0.00 0.00 44.45 2.87
2337 2720 4.279169 ACATACACAAGCAAAGCTGTCATT 59.721 37.500 0.00 0.00 39.62 2.57
2348 2734 8.202745 AGCAAAGCTGTCATTAATACTAGAAC 57.797 34.615 0.00 0.00 37.57 3.01
2349 2735 7.824289 AGCAAAGCTGTCATTAATACTAGAACA 59.176 33.333 0.00 0.00 37.57 3.18
2350 2736 8.119226 GCAAAGCTGTCATTAATACTAGAACAG 58.881 37.037 0.00 0.00 0.00 3.16
2351 2737 9.155975 CAAAGCTGTCATTAATACTAGAACAGT 57.844 33.333 0.00 0.00 41.62 3.55
2352 2738 8.709386 AAGCTGTCATTAATACTAGAACAGTG 57.291 34.615 0.00 0.00 38.24 3.66
2353 2739 7.841956 AGCTGTCATTAATACTAGAACAGTGT 58.158 34.615 0.00 0.00 38.24 3.55
2390 2776 5.278169 GCAATGATGTCATGTCCCTGATTAC 60.278 44.000 0.00 0.00 36.56 1.89
2392 2778 5.434182 TGATGTCATGTCCCTGATTACAA 57.566 39.130 0.00 0.00 0.00 2.41
2394 2780 6.425735 TGATGTCATGTCCCTGATTACAAAT 58.574 36.000 0.00 0.00 0.00 2.32
2548 3062 5.800296 TCTGCTGTAGTAAATTAGCCACAA 58.200 37.500 0.00 0.00 35.36 3.33
2551 3065 6.674066 TGCTGTAGTAAATTAGCCACAAAAC 58.326 36.000 0.00 0.00 35.36 2.43
2599 3113 6.040391 ACACTAAAATAGGCAAAAGCTGTTGA 59.960 34.615 21.21 0.00 0.00 3.18
2714 3228 3.386768 TGTTGTAGCCTGACTCAGTTC 57.613 47.619 5.32 0.00 0.00 3.01
2754 3268 4.957954 AGATGCAATAAATCTTTGGCCTCA 59.042 37.500 3.32 0.00 29.94 3.86
2800 3314 5.220265 GCTTCCATTGTTGAACAATAATGCG 60.220 40.000 21.71 10.16 46.22 4.73
2836 3358 1.679032 GCACACCCTGAGTTGGATACC 60.679 57.143 0.00 0.00 0.00 2.73
2876 3398 2.159517 GCACTGGTATTTCAGCTTTCCG 60.160 50.000 0.00 0.00 38.26 4.30
2943 3465 6.276832 AGCTTGCATATCTGTGAAATGTTT 57.723 33.333 0.00 0.00 0.00 2.83
3109 3631 6.489361 ACATCTCATTAGGATTGCCATTTCTC 59.511 38.462 0.00 0.00 36.29 2.87
3362 3884 2.508526 AGAACAAGATGGTGGACAAGC 58.491 47.619 0.00 0.00 0.00 4.01
3392 3914 7.659799 TCTTTGTACTTTCCAAAATGATCGAGA 59.340 33.333 0.00 0.00 31.86 4.04
3968 4490 7.411486 TTGATAAACTGTCTTGGGAAAAACA 57.589 32.000 0.00 0.00 0.00 2.83
4275 4797 3.500680 TCAATACTTGAGCGGTTGGAAAC 59.499 43.478 0.00 0.00 39.64 2.78
4294 4816 3.773860 ACTAGATCTCAGCGAACAGTG 57.226 47.619 0.00 0.00 0.00 3.66
4659 7426 7.198390 CAGATATGTGGGTTCTTGCAATTAAG 58.802 38.462 0.00 0.00 0.00 1.85
4737 7504 3.386768 TGCAACTGAGACAGGTTAGAC 57.613 47.619 0.00 0.00 35.51 2.59
5074 8532 3.631250 TCCTTCCCTATGTTTTGATGGC 58.369 45.455 0.00 0.00 0.00 4.40
5146 8604 6.461370 CCATCTGATTGTTTTTGTGGAAGTCA 60.461 38.462 0.00 0.00 0.00 3.41
5231 8689 5.757320 AGCGATTCATCTCAGATTTAACCAG 59.243 40.000 0.00 0.00 0.00 4.00
5309 8767 3.498774 ACTGAGGACATGAGCTTTTGT 57.501 42.857 0.00 2.43 0.00 2.83
5628 9204 8.856153 TTAACTTCCTGCACACATCTTTATTA 57.144 30.769 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.663702 AACACACGTACGGAGCAGC 60.664 57.895 21.06 0.00 0.00 5.25
1 2 0.318360 TCAACACACGTACGGAGCAG 60.318 55.000 21.06 10.25 0.00 4.24
2 3 0.102663 TTCAACACACGTACGGAGCA 59.897 50.000 21.06 0.00 0.00 4.26
3 4 0.505655 GTTCAACACACGTACGGAGC 59.494 55.000 21.06 4.18 0.00 4.70
4 5 0.774098 CGTTCAACACACGTACGGAG 59.226 55.000 21.06 14.04 32.80 4.63
5 6 1.208009 GCGTTCAACACACGTACGGA 61.208 55.000 21.06 2.65 39.92 4.69
6 7 1.199859 GCGTTCAACACACGTACGG 59.800 57.895 21.06 11.05 39.92 4.02
7 8 1.155158 CGCGTTCAACACACGTACG 60.155 57.895 15.01 15.01 39.92 3.67
8 9 1.199859 CCGCGTTCAACACACGTAC 59.800 57.895 4.92 0.00 39.92 3.67
9 10 0.935831 CTCCGCGTTCAACACACGTA 60.936 55.000 4.92 0.00 39.92 3.57
10 11 2.202770 TCCGCGTTCAACACACGT 60.203 55.556 4.92 0.00 39.92 4.49
11 12 2.544359 CTCCGCGTTCAACACACG 59.456 61.111 4.92 0.00 40.75 4.49
12 13 1.885850 ACCTCCGCGTTCAACACAC 60.886 57.895 4.92 0.00 0.00 3.82
13 14 1.885388 CACCTCCGCGTTCAACACA 60.885 57.895 4.92 0.00 0.00 3.72
14 15 2.935955 CACCTCCGCGTTCAACAC 59.064 61.111 4.92 0.00 0.00 3.32
15 16 2.970324 GCACCTCCGCGTTCAACA 60.970 61.111 4.92 0.00 0.00 3.33
16 17 3.723348 GGCACCTCCGCGTTCAAC 61.723 66.667 4.92 0.00 0.00 3.18
34 35 3.135056 ATCCTAGCGCCGAACGGAC 62.135 63.158 17.63 7.92 43.93 4.79
35 36 2.831742 ATCCTAGCGCCGAACGGA 60.832 61.111 17.63 3.21 43.93 4.69
36 37 2.354773 GATCCTAGCGCCGAACGG 60.355 66.667 2.29 9.00 43.93 4.44
38 39 1.004277 CGATGATCCTAGCGCCGAAC 61.004 60.000 2.29 0.00 0.00 3.95
39 40 1.285950 CGATGATCCTAGCGCCGAA 59.714 57.895 2.29 0.00 0.00 4.30
40 41 2.626780 CCGATGATCCTAGCGCCGA 61.627 63.158 2.29 0.00 0.00 5.54
41 42 2.126307 CCGATGATCCTAGCGCCG 60.126 66.667 2.29 0.00 0.00 6.46
42 43 1.373497 CACCGATGATCCTAGCGCC 60.373 63.158 2.29 0.00 0.00 6.53
43 44 0.244994 ATCACCGATGATCCTAGCGC 59.755 55.000 0.00 0.00 42.15 5.92
44 45 2.732412 AATCACCGATGATCCTAGCG 57.268 50.000 0.00 0.00 45.26 4.26
45 46 3.070018 CCAAATCACCGATGATCCTAGC 58.930 50.000 0.00 0.00 45.26 3.42
46 47 4.607293 TCCAAATCACCGATGATCCTAG 57.393 45.455 0.00 0.00 45.26 3.02
47 48 4.592778 TGATCCAAATCACCGATGATCCTA 59.407 41.667 0.00 0.00 45.26 2.94
48 49 3.392285 TGATCCAAATCACCGATGATCCT 59.608 43.478 0.00 0.00 45.26 3.24
49 50 3.743521 TGATCCAAATCACCGATGATCC 58.256 45.455 0.00 0.00 45.26 3.36
58 59 7.861595 TCGTACTCGTCGTGATCCAAATCAC 62.862 48.000 8.20 8.20 45.52 3.06
59 60 3.729762 CGTACTCGTCGTGATCCAAATCA 60.730 47.826 0.56 0.00 39.63 2.57
60 61 2.782192 CGTACTCGTCGTGATCCAAATC 59.218 50.000 0.56 0.00 0.00 2.17
61 62 2.421073 TCGTACTCGTCGTGATCCAAAT 59.579 45.455 0.56 0.00 38.33 2.32
62 63 1.805943 TCGTACTCGTCGTGATCCAAA 59.194 47.619 0.56 0.00 38.33 3.28
63 64 1.129251 GTCGTACTCGTCGTGATCCAA 59.871 52.381 0.56 0.00 38.33 3.53
64 65 0.723414 GTCGTACTCGTCGTGATCCA 59.277 55.000 0.56 0.00 38.33 3.41
65 66 1.005137 GAGTCGTACTCGTCGTGATCC 60.005 57.143 0.56 0.00 35.28 3.36
66 67 1.005137 GGAGTCGTACTCGTCGTGATC 60.005 57.143 0.56 0.00 45.96 2.92
67 68 1.005340 GGAGTCGTACTCGTCGTGAT 58.995 55.000 0.56 0.00 45.96 3.06
68 69 0.319813 TGGAGTCGTACTCGTCGTGA 60.320 55.000 0.56 0.00 45.96 4.35
69 70 0.725686 ATGGAGTCGTACTCGTCGTG 59.274 55.000 8.33 0.00 45.96 4.35
70 71 1.005340 GATGGAGTCGTACTCGTCGT 58.995 55.000 8.33 0.00 45.96 4.34
71 72 1.004595 TGATGGAGTCGTACTCGTCG 58.995 55.000 8.33 0.00 45.96 5.12
72 73 2.477525 GGTTGATGGAGTCGTACTCGTC 60.478 54.545 8.33 9.13 45.96 4.20
73 74 1.471684 GGTTGATGGAGTCGTACTCGT 59.528 52.381 8.33 1.85 45.96 4.18
74 75 1.202268 GGGTTGATGGAGTCGTACTCG 60.202 57.143 8.33 0.00 45.96 4.18
75 76 1.136500 GGGGTTGATGGAGTCGTACTC 59.864 57.143 6.50 6.50 44.32 2.59
76 77 1.192428 GGGGTTGATGGAGTCGTACT 58.808 55.000 0.00 0.00 0.00 2.73
77 78 0.179119 CGGGGTTGATGGAGTCGTAC 60.179 60.000 0.00 0.00 0.00 3.67
78 79 0.612732 ACGGGGTTGATGGAGTCGTA 60.613 55.000 0.00 0.00 0.00 3.43
79 80 1.477685 AACGGGGTTGATGGAGTCGT 61.478 55.000 0.00 0.00 0.00 4.34
80 81 0.739813 GAACGGGGTTGATGGAGTCG 60.740 60.000 0.00 0.00 0.00 4.18
81 82 0.613777 AGAACGGGGTTGATGGAGTC 59.386 55.000 0.00 0.00 0.00 3.36
82 83 0.613777 GAGAACGGGGTTGATGGAGT 59.386 55.000 0.00 0.00 0.00 3.85
83 84 0.905357 AGAGAACGGGGTTGATGGAG 59.095 55.000 0.00 0.00 0.00 3.86
84 85 1.003118 CAAGAGAACGGGGTTGATGGA 59.997 52.381 0.00 0.00 0.00 3.41
85 86 1.003118 TCAAGAGAACGGGGTTGATGG 59.997 52.381 0.00 0.00 0.00 3.51
86 87 2.472695 TCAAGAGAACGGGGTTGATG 57.527 50.000 0.00 0.00 0.00 3.07
87 88 2.779506 GTTCAAGAGAACGGGGTTGAT 58.220 47.619 0.00 0.00 44.11 2.57
88 89 2.249844 GTTCAAGAGAACGGGGTTGA 57.750 50.000 0.00 0.00 44.11 3.18
109 110 0.248498 TTGTAGATCGCGAGCGGAAG 60.248 55.000 19.77 0.00 40.25 3.46
110 111 0.248498 CTTGTAGATCGCGAGCGGAA 60.248 55.000 19.77 11.67 40.25 4.30
111 112 1.355563 CTTGTAGATCGCGAGCGGA 59.644 57.895 19.77 8.43 40.25 5.54
112 113 1.658717 CCTTGTAGATCGCGAGCGG 60.659 63.158 19.77 9.89 40.25 5.52
113 114 1.658717 CCCTTGTAGATCGCGAGCG 60.659 63.158 19.77 11.64 41.35 5.03
114 115 0.666913 TACCCTTGTAGATCGCGAGC 59.333 55.000 18.21 18.21 0.00 5.03
115 116 2.293677 ACATACCCTTGTAGATCGCGAG 59.706 50.000 16.66 0.00 0.00 5.03
116 117 2.304092 ACATACCCTTGTAGATCGCGA 58.696 47.619 13.09 13.09 0.00 5.87
117 118 2.795175 ACATACCCTTGTAGATCGCG 57.205 50.000 0.00 0.00 0.00 5.87
123 124 6.239345 GGGAGTGAATCTACATACCCTTGTAG 60.239 46.154 5.47 5.47 46.85 2.74
124 125 5.601313 GGGAGTGAATCTACATACCCTTGTA 59.399 44.000 0.00 0.00 36.18 2.41
125 126 4.409247 GGGAGTGAATCTACATACCCTTGT 59.591 45.833 0.00 0.00 36.18 3.16
126 127 4.202367 GGGGAGTGAATCTACATACCCTTG 60.202 50.000 0.00 0.00 37.75 3.61
127 128 3.974642 GGGGAGTGAATCTACATACCCTT 59.025 47.826 0.00 0.00 37.75 3.95
128 129 3.210074 AGGGGAGTGAATCTACATACCCT 59.790 47.826 0.00 0.00 37.75 4.34
129 130 3.588569 AGGGGAGTGAATCTACATACCC 58.411 50.000 0.00 0.00 37.31 3.69
130 131 4.040584 GGAAGGGGAGTGAATCTACATACC 59.959 50.000 0.00 0.00 0.00 2.73
131 132 4.040584 GGGAAGGGGAGTGAATCTACATAC 59.959 50.000 0.00 0.00 0.00 2.39
132 133 4.232091 GGGAAGGGGAGTGAATCTACATA 58.768 47.826 0.00 0.00 0.00 2.29
133 134 3.049344 GGGAAGGGGAGTGAATCTACAT 58.951 50.000 0.00 0.00 0.00 2.29
134 135 2.478292 GGGAAGGGGAGTGAATCTACA 58.522 52.381 0.00 0.00 0.00 2.74
135 136 1.769465 GGGGAAGGGGAGTGAATCTAC 59.231 57.143 0.00 0.00 0.00 2.59
136 137 1.657162 AGGGGAAGGGGAGTGAATCTA 59.343 52.381 0.00 0.00 0.00 1.98
137 138 0.423544 AGGGGAAGGGGAGTGAATCT 59.576 55.000 0.00 0.00 0.00 2.40
138 139 0.840617 GAGGGGAAGGGGAGTGAATC 59.159 60.000 0.00 0.00 0.00 2.52
139 140 0.983378 CGAGGGGAAGGGGAGTGAAT 60.983 60.000 0.00 0.00 0.00 2.57
140 141 1.612442 CGAGGGGAAGGGGAGTGAA 60.612 63.158 0.00 0.00 0.00 3.18
141 142 2.038975 CGAGGGGAAGGGGAGTGA 59.961 66.667 0.00 0.00 0.00 3.41
142 143 1.918800 AACGAGGGGAAGGGGAGTG 60.919 63.158 0.00 0.00 0.00 3.51
143 144 1.918800 CAACGAGGGGAAGGGGAGT 60.919 63.158 0.00 0.00 0.00 3.85
144 145 2.990479 CAACGAGGGGAAGGGGAG 59.010 66.667 0.00 0.00 0.00 4.30
145 146 2.465010 TAGCAACGAGGGGAAGGGGA 62.465 60.000 0.00 0.00 0.00 4.81
146 147 1.972660 CTAGCAACGAGGGGAAGGGG 61.973 65.000 0.00 0.00 0.00 4.79
147 148 0.976073 TCTAGCAACGAGGGGAAGGG 60.976 60.000 0.00 0.00 0.00 3.95
148 149 1.123928 ATCTAGCAACGAGGGGAAGG 58.876 55.000 0.00 0.00 0.00 3.46
149 150 2.990066 AATCTAGCAACGAGGGGAAG 57.010 50.000 0.00 0.00 0.00 3.46
150 151 3.371965 AGTAATCTAGCAACGAGGGGAA 58.628 45.455 0.00 0.00 0.00 3.97
151 152 2.957006 GAGTAATCTAGCAACGAGGGGA 59.043 50.000 0.00 0.00 0.00 4.81
152 153 2.036089 GGAGTAATCTAGCAACGAGGGG 59.964 54.545 0.00 0.00 0.00 4.79
153 154 2.693591 TGGAGTAATCTAGCAACGAGGG 59.306 50.000 0.00 0.00 0.00 4.30
154 155 4.592485 ATGGAGTAATCTAGCAACGAGG 57.408 45.455 0.00 0.00 0.00 4.63
155 156 6.561737 TCTATGGAGTAATCTAGCAACGAG 57.438 41.667 0.00 0.00 0.00 4.18
156 157 7.230712 TCAATCTATGGAGTAATCTAGCAACGA 59.769 37.037 0.00 0.00 0.00 3.85
157 158 7.371159 TCAATCTATGGAGTAATCTAGCAACG 58.629 38.462 0.00 0.00 0.00 4.10
158 159 9.364989 GATCAATCTATGGAGTAATCTAGCAAC 57.635 37.037 0.00 0.00 0.00 4.17
159 160 9.319060 AGATCAATCTATGGAGTAATCTAGCAA 57.681 33.333 0.00 0.00 34.85 3.91
160 161 8.891985 AGATCAATCTATGGAGTAATCTAGCA 57.108 34.615 0.00 0.00 34.85 3.49
161 162 9.585099 CAAGATCAATCTATGGAGTAATCTAGC 57.415 37.037 0.00 0.00 35.76 3.42
163 164 9.607333 ACCAAGATCAATCTATGGAGTAATCTA 57.393 33.333 19.34 0.00 37.92 1.98
164 165 8.373981 CACCAAGATCAATCTATGGAGTAATCT 58.626 37.037 19.34 0.00 37.92 2.40
165 166 8.370940 TCACCAAGATCAATCTATGGAGTAATC 58.629 37.037 19.34 0.00 37.92 1.75
166 167 8.267620 TCACCAAGATCAATCTATGGAGTAAT 57.732 34.615 19.34 3.63 37.92 1.89
167 168 7.675161 TCACCAAGATCAATCTATGGAGTAA 57.325 36.000 19.34 6.75 37.92 2.24
168 169 7.674120 CATCACCAAGATCAATCTATGGAGTA 58.326 38.462 19.34 10.06 37.92 2.59
169 170 6.531923 CATCACCAAGATCAATCTATGGAGT 58.468 40.000 19.34 8.56 37.92 3.85
170 171 5.411977 GCATCACCAAGATCAATCTATGGAG 59.588 44.000 19.34 14.57 37.92 3.86
171 172 5.311265 GCATCACCAAGATCAATCTATGGA 58.689 41.667 19.34 6.96 37.92 3.41
172 173 4.153655 CGCATCACCAAGATCAATCTATGG 59.846 45.833 14.46 14.46 39.18 2.74
173 174 4.753610 ACGCATCACCAAGATCAATCTATG 59.246 41.667 0.00 0.00 35.76 2.23
174 175 4.965814 ACGCATCACCAAGATCAATCTAT 58.034 39.130 0.00 0.00 35.76 1.98
175 176 4.406648 ACGCATCACCAAGATCAATCTA 57.593 40.909 0.00 0.00 35.76 1.98
176 177 3.272574 ACGCATCACCAAGATCAATCT 57.727 42.857 0.00 0.00 39.22 2.40
177 178 4.371786 TCTACGCATCACCAAGATCAATC 58.628 43.478 0.00 0.00 33.72 2.67
178 179 4.406648 TCTACGCATCACCAAGATCAAT 57.593 40.909 0.00 0.00 33.72 2.57
179 180 3.885724 TCTACGCATCACCAAGATCAA 57.114 42.857 0.00 0.00 33.72 2.57
180 181 3.885724 TTCTACGCATCACCAAGATCA 57.114 42.857 0.00 0.00 33.72 2.92
181 182 5.741388 ATTTTCTACGCATCACCAAGATC 57.259 39.130 0.00 0.00 33.72 2.75
182 183 6.515272 AAATTTTCTACGCATCACCAAGAT 57.485 33.333 0.00 0.00 37.48 2.40
183 184 5.957842 AAATTTTCTACGCATCACCAAGA 57.042 34.783 0.00 0.00 0.00 3.02
184 185 6.148948 TCAAAATTTTCTACGCATCACCAAG 58.851 36.000 0.00 0.00 0.00 3.61
185 186 6.078202 TCAAAATTTTCTACGCATCACCAA 57.922 33.333 0.00 0.00 0.00 3.67
186 187 5.697473 TCAAAATTTTCTACGCATCACCA 57.303 34.783 0.00 0.00 0.00 4.17
187 188 7.581011 AATTCAAAATTTTCTACGCATCACC 57.419 32.000 0.00 0.00 0.00 4.02
188 189 8.915654 AGAAATTCAAAATTTTCTACGCATCAC 58.084 29.630 0.00 0.00 39.70 3.06
189 190 8.914654 CAGAAATTCAAAATTTTCTACGCATCA 58.085 29.630 0.00 0.00 39.53 3.07
190 191 7.894753 GCAGAAATTCAAAATTTTCTACGCATC 59.105 33.333 0.00 0.00 39.53 3.91
191 192 7.599998 AGCAGAAATTCAAAATTTTCTACGCAT 59.400 29.630 0.00 0.00 39.53 4.73
192 193 6.922957 AGCAGAAATTCAAAATTTTCTACGCA 59.077 30.769 0.00 0.00 39.53 5.24
193 194 7.338440 AGCAGAAATTCAAAATTTTCTACGC 57.662 32.000 0.00 0.00 39.53 4.42
194 195 8.567221 CGTAGCAGAAATTCAAAATTTTCTACG 58.433 33.333 19.51 19.51 39.53 3.51
195 196 9.394477 ACGTAGCAGAAATTCAAAATTTTCTAC 57.606 29.630 0.00 5.68 39.53 2.59
196 197 9.959749 AACGTAGCAGAAATTCAAAATTTTCTA 57.040 25.926 0.00 0.00 39.53 2.10
197 198 8.871686 AACGTAGCAGAAATTCAAAATTTTCT 57.128 26.923 0.00 0.00 41.61 2.52
198 199 8.214472 GGAACGTAGCAGAAATTCAAAATTTTC 58.786 33.333 0.00 0.00 33.08 2.29
199 200 7.170828 GGGAACGTAGCAGAAATTCAAAATTTT 59.829 33.333 0.00 0.00 0.00 1.82
200 201 6.645003 GGGAACGTAGCAGAAATTCAAAATTT 59.355 34.615 0.00 0.00 0.00 1.82
201 202 6.156519 GGGAACGTAGCAGAAATTCAAAATT 58.843 36.000 0.00 0.00 0.00 1.82
202 203 5.336451 GGGGAACGTAGCAGAAATTCAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
203 204 4.022676 GGGGAACGTAGCAGAAATTCAAAA 60.023 41.667 0.00 0.00 0.00 2.44
204 205 3.504520 GGGGAACGTAGCAGAAATTCAAA 59.495 43.478 0.00 0.00 0.00 2.69
205 206 3.078837 GGGGAACGTAGCAGAAATTCAA 58.921 45.455 0.00 0.00 0.00 2.69
206 207 2.039216 TGGGGAACGTAGCAGAAATTCA 59.961 45.455 0.00 0.00 0.00 2.57
207 208 2.706890 TGGGGAACGTAGCAGAAATTC 58.293 47.619 0.00 0.00 0.00 2.17
208 209 2.817844 GTTGGGGAACGTAGCAGAAATT 59.182 45.455 0.00 0.00 0.00 1.82
209 210 2.224670 TGTTGGGGAACGTAGCAGAAAT 60.225 45.455 0.00 0.00 0.00 2.17
210 211 1.141254 TGTTGGGGAACGTAGCAGAAA 59.859 47.619 0.00 0.00 0.00 2.52
211 212 0.759959 TGTTGGGGAACGTAGCAGAA 59.240 50.000 0.00 0.00 0.00 3.02
212 213 0.759959 TTGTTGGGGAACGTAGCAGA 59.240 50.000 0.00 0.00 0.00 4.26
213 214 1.600023 TTTGTTGGGGAACGTAGCAG 58.400 50.000 0.00 0.00 0.00 4.24
214 215 1.677052 GTTTTGTTGGGGAACGTAGCA 59.323 47.619 0.00 0.00 0.00 3.49
215 216 1.677052 TGTTTTGTTGGGGAACGTAGC 59.323 47.619 0.00 0.00 0.00 3.58
216 217 3.855524 GCATGTTTTGTTGGGGAACGTAG 60.856 47.826 0.00 0.00 0.00 3.51
217 218 2.034812 GCATGTTTTGTTGGGGAACGTA 59.965 45.455 0.00 0.00 0.00 3.57
218 219 1.202475 GCATGTTTTGTTGGGGAACGT 60.202 47.619 0.00 0.00 0.00 3.99
219 220 1.496934 GCATGTTTTGTTGGGGAACG 58.503 50.000 0.00 0.00 0.00 3.95
220 221 1.871822 CGGCATGTTTTGTTGGGGAAC 60.872 52.381 0.00 0.00 0.00 3.62
221 222 0.390860 CGGCATGTTTTGTTGGGGAA 59.609 50.000 0.00 0.00 0.00 3.97
222 223 0.468214 TCGGCATGTTTTGTTGGGGA 60.468 50.000 0.00 0.00 0.00 4.81
223 224 0.319469 GTCGGCATGTTTTGTTGGGG 60.319 55.000 0.00 0.00 0.00 4.96
224 225 0.662970 CGTCGGCATGTTTTGTTGGG 60.663 55.000 0.00 0.00 0.00 4.12
225 226 1.274798 GCGTCGGCATGTTTTGTTGG 61.275 55.000 0.00 0.00 39.62 3.77
226 227 1.595982 CGCGTCGGCATGTTTTGTTG 61.596 55.000 0.00 0.00 39.92 3.33
227 228 1.369930 CGCGTCGGCATGTTTTGTT 60.370 52.632 0.00 0.00 39.92 2.83
228 229 2.251075 CGCGTCGGCATGTTTTGT 59.749 55.556 0.00 0.00 39.92 2.83
229 230 2.501650 CCGCGTCGGCATGTTTTG 60.502 61.111 4.92 0.00 41.17 2.44
307 308 0.603569 GGTCTTCTCTTCACGCAGGA 59.396 55.000 0.00 0.00 0.00 3.86
398 399 2.047830 AGGTCGGTGTTCCTCTTCTTT 58.952 47.619 0.00 0.00 0.00 2.52
560 561 2.735772 ATCATCGCTCGGGCTTGGT 61.736 57.895 5.36 0.00 36.09 3.67
664 666 4.773117 GTCGGTGGAGTCGGCGTC 62.773 72.222 6.85 0.00 0.00 5.19
719 721 2.029073 CGCCACAAGTCTGGACGT 59.971 61.111 0.00 0.00 36.20 4.34
776 786 1.228063 GGCGATCATCACAGGCCAT 60.228 57.895 5.01 0.00 43.23 4.40
788 804 2.715624 GCCACAAATCCGGCGATC 59.284 61.111 9.30 0.00 38.82 3.69
808 824 6.406692 TTTGGTCGTTCCCATTCATAAAAA 57.593 33.333 0.00 0.00 33.60 1.94
817 836 6.148645 GCAATTTTAAATTTGGTCGTTCCCAT 59.851 34.615 19.25 0.00 33.60 4.00
831 851 5.448632 CCTCTAAGACGCGGCAATTTTAAAT 60.449 40.000 17.71 0.00 0.00 1.40
835 855 1.737793 CCTCTAAGACGCGGCAATTTT 59.262 47.619 17.71 0.85 0.00 1.82
866 887 2.037367 TAGCTCCCAGTCACGCCT 59.963 61.111 0.00 0.00 0.00 5.52
892 914 0.106894 CCGGCCCTAGATTGGTTCTC 59.893 60.000 0.00 0.00 35.79 2.87
893 915 0.620700 ACCGGCCCTAGATTGGTTCT 60.621 55.000 0.00 0.00 38.57 3.01
896 921 1.912971 GAACCGGCCCTAGATTGGT 59.087 57.895 0.00 0.00 33.45 3.67
918 943 0.035439 CCTAAAAAGAGCGGCCTGGA 60.035 55.000 0.00 0.00 0.00 3.86
964 991 1.324005 GGCGTCTGGGTCTAAGAGCT 61.324 60.000 0.00 0.00 0.00 4.09
1752 1780 8.893727 AGTACCATCTAAAAATATGTCAAGTGC 58.106 33.333 0.00 0.00 0.00 4.40
1963 1991 9.941664 CTGGTATTGCAAAATCATCTTTACTAG 57.058 33.333 1.71 1.68 0.00 2.57
2007 2035 8.337532 CGTCTTGATCAAATAGCATCAATTACA 58.662 33.333 9.88 0.00 38.15 2.41
2009 2037 8.437360 ACGTCTTGATCAAATAGCATCAATTA 57.563 30.769 9.88 0.00 38.15 1.40
2047 2075 9.781834 CTTTTGCGGTTATCACAATCTAATAAA 57.218 29.630 0.00 0.00 0.00 1.40
2081 2109 4.665833 ATGGCTAGTATCAACGCTTACA 57.334 40.909 0.00 0.00 0.00 2.41
2124 2152 2.204463 TGGATGTATCTTGGGGCAGAA 58.796 47.619 0.00 0.00 0.00 3.02
2133 2161 4.769688 TGTCGCAGAAATGGATGTATCTT 58.230 39.130 0.00 0.00 39.69 2.40
2171 2199 6.021030 AGTCCAACATTAACTAGTACTCCCA 58.979 40.000 0.00 0.00 0.00 4.37
2203 2586 1.123077 ATTCCAGCGAGGTATGCAGA 58.877 50.000 0.00 0.00 39.02 4.26
2244 2627 3.181445 TGGTTGCAATGAGAACTACAGGT 60.181 43.478 0.59 0.00 0.00 4.00
2337 2720 7.229907 TGACACACTGACACTGTTCTAGTATTA 59.770 37.037 0.00 0.00 37.60 0.98
2348 2734 0.786581 GCGATGACACACTGACACTG 59.213 55.000 0.00 0.00 0.00 3.66
2349 2735 0.389025 TGCGATGACACACTGACACT 59.611 50.000 0.00 0.00 0.00 3.55
2350 2736 1.217001 TTGCGATGACACACTGACAC 58.783 50.000 0.00 0.00 0.00 3.67
2351 2737 1.799994 CATTGCGATGACACACTGACA 59.200 47.619 8.37 0.00 35.16 3.58
2352 2738 2.068519 TCATTGCGATGACACACTGAC 58.931 47.619 12.88 0.00 37.37 3.51
2353 2739 2.453983 TCATTGCGATGACACACTGA 57.546 45.000 12.88 0.00 37.37 3.41
2548 3062 4.935352 TTGATGTGCTTTTGCCTAGTTT 57.065 36.364 0.00 0.00 46.87 2.66
2551 3065 4.510038 AGTTTGATGTGCTTTTGCCTAG 57.490 40.909 0.00 0.00 46.87 3.02
2599 3113 1.691976 TCACGGTGATCCTGTTTGTCT 59.308 47.619 6.76 0.00 0.00 3.41
2714 3228 3.459145 CATCTGGCAATCTCAGACTCTG 58.541 50.000 0.00 0.00 43.07 3.35
2754 3268 6.125029 AGCCATTCTCAACAGCATATTAAGT 58.875 36.000 0.00 0.00 0.00 2.24
2800 3314 4.334481 GGGTGTGCATAGTGTAACCATTAC 59.666 45.833 0.00 0.00 37.80 1.89
2836 3358 6.592994 CCAGTGCTACATGAGGTGATATTATG 59.407 42.308 0.00 0.00 0.00 1.90
2954 3476 8.342634 ACACAACTTCATGTTTACATTCACTAC 58.657 33.333 0.00 0.00 36.63 2.73
3109 3631 6.636666 AACAAATATCAGCTGCGAAAATTG 57.363 33.333 9.47 11.30 0.00 2.32
3392 3914 3.984193 GATTGGGCTGGCAGTCGCT 62.984 63.158 17.16 0.97 38.60 4.93
3440 3962 1.605710 CAGTTGTCCTTCTGTTGCCAG 59.394 52.381 0.00 0.00 40.25 4.85
3968 4490 2.842496 TGTGGGCTTCATCAAGATCTCT 59.158 45.455 0.00 0.00 0.00 3.10
4275 4797 2.458951 GCACTGTTCGCTGAGATCTAG 58.541 52.381 0.00 0.00 0.00 2.43
4294 4816 0.301987 GAGCTGGCTTTCGTATTCGC 59.698 55.000 0.00 0.00 36.96 4.70
4659 7426 3.194116 TCGTGTTGGATACCCTGTAAGTC 59.806 47.826 0.00 0.00 0.00 3.01
4737 7504 5.866092 TCTCTCTTTTTGATGTCATGACTCG 59.134 40.000 25.55 8.51 0.00 4.18
4776 7543 5.826643 AGCATCCTTTAATCCAACAACCTA 58.173 37.500 0.00 0.00 0.00 3.08
5074 8532 7.063308 GGATGCATTACAAAGTTACCACAAATG 59.937 37.037 0.00 0.00 0.00 2.32
5146 8604 6.639632 ATCTTGATAACAGCAACAAAGTGT 57.360 33.333 0.00 0.00 0.00 3.55
5309 8767 6.665992 ATGAGTAATTATCTAGTTCGGCCA 57.334 37.500 2.24 0.00 0.00 5.36
5377 8835 6.834107 TGTATTAGGTATCAAGGGCCTAAAC 58.166 40.000 6.41 2.45 44.83 2.01


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

AutoCloner maintained by Alex Coulton.