Multiple sequence alignment - TraesCS1D01G160900

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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 TraesCS1D01G160900 chr1D 100.000 3122 0 0 1 3122 227729974 227733095 0.000000e+00 5766
1 TraesCS1D01G160900 chr1D 95.246 2482 81 6 646 3122 208398618 208396169 0.000000e+00 3895
2 TraesCS1D01G160900 chr1D 92.377 446 19 7 212 653 208399880 208399446 3.420000e-174 621
3 TraesCS1D01G160900 chr1D 95.706 163 7 0 51 213 22101348 22101186 2.390000e-66 263
4 TraesCS1D01G160900 chr1A 94.002 1684 71 17 604 2275 295225127 295223462 0.000000e+00 2523
5 TraesCS1D01G160900 chr1A 91.221 262 22 1 212 472 295228216 295227955 3.830000e-94 355
6 TraesCS1D01G160900 chr1A 94.545 165 9 0 49 213 549510374 549510210 4.000000e-64 255
7 TraesCS1D01G160900 chr1A 91.473 129 6 3 487 613 295227858 295227733 4.140000e-39 172
8 TraesCS1D01G160900 chr1B 93.365 1688 85 7 618 2287 327360263 327361941 0.000000e+00 2471
9 TraesCS1D01G160900 chr1B 87.470 423 27 16 212 623 327358766 327359173 6.100000e-127 464
10 TraesCS1D01G160900 chr1B 84.375 160 19 6 57 213 418815107 418815263 5.390000e-33 152
11 TraesCS1D01G160900 chr5D 89.774 665 60 5 2445 3107 242378165 242378823 0.000000e+00 845
12 TraesCS1D01G160900 chr5D 96.364 165 6 0 49 213 411823506 411823342 3.970000e-69 272
13 TraesCS1D01G160900 chr4B 88.955 670 64 7 2442 3107 358895589 358894926 0.000000e+00 819
14 TraesCS1D01G160900 chr2D 89.226 594 49 9 2442 3033 226527940 226528520 0.000000e+00 728
15 TraesCS1D01G160900 chr6B 86.478 673 71 14 2442 3106 330983198 330982538 0.000000e+00 721
16 TraesCS1D01G160900 chr6D 86.145 664 84 4 2445 3106 462399065 462398408 0.000000e+00 710
17 TraesCS1D01G160900 chr6D 85.822 663 87 3 2445 3106 452071366 452070710 0.000000e+00 697
18 TraesCS1D01G160900 chr6D 85.843 664 66 8 2445 3107 55435147 55434511 0.000000e+00 680
19 TraesCS1D01G160900 chr2A 87.669 592 63 6 2445 3033 271914331 271913747 0.000000e+00 680
20 TraesCS1D01G160900 chr5B 95.210 167 8 0 49 215 356254452 356254618 6.640000e-67 265
21 TraesCS1D01G160900 chr5B 83.256 215 19 10 1 213 529382916 529383115 6.880000e-42 182
22 TraesCS1D01G160900 chr7D 95.152 165 8 0 49 213 530744472 530744308 8.590000e-66 261
23 TraesCS1D01G160900 chr7B 94.545 165 9 0 49 213 498063940 498064104 4.000000e-64 255
24 TraesCS1D01G160900 chr7B 85.625 160 17 6 57 213 628754311 628754155 2.490000e-36 163


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 TraesCS1D01G160900 chr1D 227729974 227733095 3121 False 5766.000000 5766 100.0000 1 3122 1 chr1D.!!$F1 3121
1 TraesCS1D01G160900 chr1D 208396169 208399880 3711 True 2258.000000 3895 93.8115 212 3122 2 chr1D.!!$R2 2910
2 TraesCS1D01G160900 chr1A 295223462 295228216 4754 True 1016.666667 2523 92.2320 212 2275 3 chr1A.!!$R2 2063
3 TraesCS1D01G160900 chr1B 327358766 327361941 3175 False 1467.500000 2471 90.4175 212 2287 2 chr1B.!!$F2 2075
4 TraesCS1D01G160900 chr5D 242378165 242378823 658 False 845.000000 845 89.7740 2445 3107 1 chr5D.!!$F1 662
5 TraesCS1D01G160900 chr4B 358894926 358895589 663 True 819.000000 819 88.9550 2442 3107 1 chr4B.!!$R1 665
6 TraesCS1D01G160900 chr2D 226527940 226528520 580 False 728.000000 728 89.2260 2442 3033 1 chr2D.!!$F1 591
7 TraesCS1D01G160900 chr6B 330982538 330983198 660 True 721.000000 721 86.4780 2442 3106 1 chr6B.!!$R1 664
8 TraesCS1D01G160900 chr6D 462398408 462399065 657 True 710.000000 710 86.1450 2445 3106 1 chr6D.!!$R3 661
9 TraesCS1D01G160900 chr6D 452070710 452071366 656 True 697.000000 697 85.8220 2445 3106 1 chr6D.!!$R2 661
10 TraesCS1D01G160900 chr6D 55434511 55435147 636 True 680.000000 680 85.8430 2445 3107 1 chr6D.!!$R1 662
11 TraesCS1D01G160900 chr2A 271913747 271914331 584 True 680.000000 680 87.6690 2445 3033 1 chr2A.!!$R1 588

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
106 107 0.039527 GTCGCAACAACCACAATCCC 60.040 55.0 0.0 0.0 0.0 3.85 F
107 108 0.179004 TCGCAACAACCACAATCCCT 60.179 50.0 0.0 0.0 0.0 4.20 F
108 109 0.240945 CGCAACAACCACAATCCCTC 59.759 55.0 0.0 0.0 0.0 4.30 F
145 146 0.259356 AGAAACCCCCAACGAAACCA 59.741 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 5698 0.531532 GGAGGGACAGCATCGTCATG 60.532 60.000 3.75 0.00 37.66 3.07 R
1618 6275 2.361992 CTGCTGGGCCATCTTGCA 60.362 61.111 16.24 16.24 0.00 4.08 R
1693 6350 3.103911 CGGCCACGACTTGTCGAC 61.104 66.667 26.65 9.11 44.60 4.20 R
2173 6838 1.558294 TCTCATGCAGGATGAACAGCT 59.442 47.619 0.00 0.00 40.73 4.24 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 4.720127 TAGACCACGTGCGGACTA 57.280 55.556 10.91 5.01 33.04 2.59
18 19 2.174334 TAGACCACGTGCGGACTAC 58.826 57.895 10.91 0.00 33.04 2.73
19 20 0.321919 TAGACCACGTGCGGACTACT 60.322 55.000 10.91 3.65 33.04 2.57
20 21 1.177256 AGACCACGTGCGGACTACTT 61.177 55.000 10.91 0.00 28.76 2.24
21 22 1.006571 ACCACGTGCGGACTACTTG 60.007 57.895 10.91 0.00 0.00 3.16
22 23 2.380410 CCACGTGCGGACTACTTGC 61.380 63.158 10.91 0.00 0.00 4.01
23 24 1.372997 CACGTGCGGACTACTTGCT 60.373 57.895 0.82 0.00 0.00 3.91
24 25 0.109458 CACGTGCGGACTACTTGCTA 60.109 55.000 0.82 0.00 0.00 3.49
25 26 0.599558 ACGTGCGGACTACTTGCTAA 59.400 50.000 5.27 0.00 0.00 3.09
26 27 1.269166 CGTGCGGACTACTTGCTAAG 58.731 55.000 5.27 0.00 0.00 2.18
27 28 1.135489 CGTGCGGACTACTTGCTAAGA 60.135 52.381 5.27 0.00 0.00 2.10
28 29 2.531206 GTGCGGACTACTTGCTAAGAG 58.469 52.381 0.00 0.60 0.00 2.85
29 30 2.163815 GTGCGGACTACTTGCTAAGAGA 59.836 50.000 0.00 0.00 0.00 3.10
30 31 2.423892 TGCGGACTACTTGCTAAGAGAG 59.576 50.000 3.37 3.26 0.00 3.20
31 32 2.683867 GCGGACTACTTGCTAAGAGAGA 59.316 50.000 3.37 0.00 0.00 3.10
32 33 3.128938 GCGGACTACTTGCTAAGAGAGAA 59.871 47.826 3.37 0.00 0.00 2.87
33 34 4.380655 GCGGACTACTTGCTAAGAGAGAAA 60.381 45.833 3.37 0.00 0.00 2.52
34 35 5.096849 CGGACTACTTGCTAAGAGAGAAAC 58.903 45.833 3.37 0.00 0.00 2.78
35 36 5.106078 CGGACTACTTGCTAAGAGAGAAACT 60.106 44.000 3.37 0.00 0.00 2.66
36 37 6.327154 GGACTACTTGCTAAGAGAGAAACTC 58.673 44.000 3.37 0.00 45.22 3.01
37 38 6.275494 ACTACTTGCTAAGAGAGAAACTCC 57.725 41.667 3.37 0.00 45.96 3.85
38 39 5.775701 ACTACTTGCTAAGAGAGAAACTCCA 59.224 40.000 3.37 0.00 45.96 3.86
39 40 5.753721 ACTTGCTAAGAGAGAAACTCCAT 57.246 39.130 3.37 0.00 45.96 3.41
40 41 5.486526 ACTTGCTAAGAGAGAAACTCCATG 58.513 41.667 3.37 0.00 45.96 3.66
41 42 5.247110 ACTTGCTAAGAGAGAAACTCCATGA 59.753 40.000 0.00 0.00 45.96 3.07
42 43 5.078411 TGCTAAGAGAGAAACTCCATGAC 57.922 43.478 0.00 0.00 45.96 3.06
43 44 4.081420 TGCTAAGAGAGAAACTCCATGACC 60.081 45.833 0.00 0.00 45.96 4.02
44 45 3.990959 AAGAGAGAAACTCCATGACCC 57.009 47.619 0.00 0.00 45.96 4.46
45 46 2.907892 AGAGAGAAACTCCATGACCCA 58.092 47.619 0.00 0.00 45.96 4.51
46 47 3.251484 AGAGAGAAACTCCATGACCCAA 58.749 45.455 0.00 0.00 45.96 4.12
47 48 3.008485 AGAGAGAAACTCCATGACCCAAC 59.992 47.826 0.00 0.00 45.96 3.77
48 49 2.711009 AGAGAAACTCCATGACCCAACA 59.289 45.455 0.00 0.00 0.00 3.33
49 50 2.814336 GAGAAACTCCATGACCCAACAC 59.186 50.000 0.00 0.00 0.00 3.32
50 51 2.443255 AGAAACTCCATGACCCAACACT 59.557 45.455 0.00 0.00 0.00 3.55
51 52 2.568623 AACTCCATGACCCAACACTC 57.431 50.000 0.00 0.00 0.00 3.51
52 53 0.693049 ACTCCATGACCCAACACTCC 59.307 55.000 0.00 0.00 0.00 3.85
53 54 0.692476 CTCCATGACCCAACACTCCA 59.308 55.000 0.00 0.00 0.00 3.86
54 55 1.283029 CTCCATGACCCAACACTCCAT 59.717 52.381 0.00 0.00 0.00 3.41
55 56 1.004628 TCCATGACCCAACACTCCATG 59.995 52.381 0.00 0.00 35.61 3.66
56 57 1.004628 CCATGACCCAACACTCCATGA 59.995 52.381 0.00 0.00 37.41 3.07
57 58 2.086869 CATGACCCAACACTCCATGAC 58.913 52.381 0.00 0.00 37.41 3.06
58 59 0.400213 TGACCCAACACTCCATGACC 59.600 55.000 0.00 0.00 0.00 4.02
59 60 0.322546 GACCCAACACTCCATGACCC 60.323 60.000 0.00 0.00 0.00 4.46
60 61 1.065410 ACCCAACACTCCATGACCCA 61.065 55.000 0.00 0.00 0.00 4.51
61 62 0.112218 CCCAACACTCCATGACCCAA 59.888 55.000 0.00 0.00 0.00 4.12
62 63 1.247567 CCAACACTCCATGACCCAAC 58.752 55.000 0.00 0.00 0.00 3.77
63 64 0.874390 CAACACTCCATGACCCAACG 59.126 55.000 0.00 0.00 0.00 4.10
64 65 0.250727 AACACTCCATGACCCAACGG 60.251 55.000 0.00 0.00 0.00 4.44
82 83 3.909957 GTCAACCCGACAAACACAC 57.090 52.632 0.00 0.00 44.69 3.82
83 84 1.088306 GTCAACCCGACAAACACACA 58.912 50.000 0.00 0.00 44.69 3.72
84 85 1.673920 GTCAACCCGACAAACACACAT 59.326 47.619 0.00 0.00 44.69 3.21
85 86 2.873472 GTCAACCCGACAAACACACATA 59.127 45.455 0.00 0.00 44.69 2.29
86 87 3.312973 GTCAACCCGACAAACACACATAA 59.687 43.478 0.00 0.00 44.69 1.90
87 88 3.562141 TCAACCCGACAAACACACATAAG 59.438 43.478 0.00 0.00 0.00 1.73
88 89 3.202829 ACCCGACAAACACACATAAGT 57.797 42.857 0.00 0.00 0.00 2.24
89 90 3.135994 ACCCGACAAACACACATAAGTC 58.864 45.455 0.00 0.00 0.00 3.01
90 91 2.156891 CCCGACAAACACACATAAGTCG 59.843 50.000 0.00 0.00 45.82 4.18
91 92 2.411031 CCGACAAACACACATAAGTCGC 60.411 50.000 7.20 0.00 45.15 5.19
92 93 2.219903 CGACAAACACACATAAGTCGCA 59.780 45.455 0.00 0.00 41.59 5.10
93 94 3.302805 CGACAAACACACATAAGTCGCAA 60.303 43.478 0.00 0.00 41.59 4.85
94 95 3.947626 ACAAACACACATAAGTCGCAAC 58.052 40.909 0.00 0.00 0.00 4.17
95 96 3.375610 ACAAACACACATAAGTCGCAACA 59.624 39.130 0.00 0.00 0.00 3.33
96 97 4.142578 ACAAACACACATAAGTCGCAACAA 60.143 37.500 0.00 0.00 0.00 2.83
97 98 3.602390 ACACACATAAGTCGCAACAAC 57.398 42.857 0.00 0.00 0.00 3.32
98 99 2.289547 ACACACATAAGTCGCAACAACC 59.710 45.455 0.00 0.00 0.00 3.77
99 100 2.289274 CACACATAAGTCGCAACAACCA 59.711 45.455 0.00 0.00 0.00 3.67
100 101 2.289547 ACACATAAGTCGCAACAACCAC 59.710 45.455 0.00 0.00 0.00 4.16
101 102 2.289274 CACATAAGTCGCAACAACCACA 59.711 45.455 0.00 0.00 0.00 4.17
102 103 2.946329 ACATAAGTCGCAACAACCACAA 59.054 40.909 0.00 0.00 0.00 3.33
103 104 3.568007 ACATAAGTCGCAACAACCACAAT 59.432 39.130 0.00 0.00 0.00 2.71
104 105 2.774439 AAGTCGCAACAACCACAATC 57.226 45.000 0.00 0.00 0.00 2.67
105 106 0.951558 AGTCGCAACAACCACAATCC 59.048 50.000 0.00 0.00 0.00 3.01
106 107 0.039527 GTCGCAACAACCACAATCCC 60.040 55.000 0.00 0.00 0.00 3.85
107 108 0.179004 TCGCAACAACCACAATCCCT 60.179 50.000 0.00 0.00 0.00 4.20
108 109 0.240945 CGCAACAACCACAATCCCTC 59.759 55.000 0.00 0.00 0.00 4.30
109 110 1.327303 GCAACAACCACAATCCCTCA 58.673 50.000 0.00 0.00 0.00 3.86
110 111 1.000274 GCAACAACCACAATCCCTCAC 60.000 52.381 0.00 0.00 0.00 3.51
111 112 2.305928 CAACAACCACAATCCCTCACA 58.694 47.619 0.00 0.00 0.00 3.58
112 113 1.981256 ACAACCACAATCCCTCACAC 58.019 50.000 0.00 0.00 0.00 3.82
113 114 1.494721 ACAACCACAATCCCTCACACT 59.505 47.619 0.00 0.00 0.00 3.55
114 115 2.091885 ACAACCACAATCCCTCACACTT 60.092 45.455 0.00 0.00 0.00 3.16
115 116 2.554032 CAACCACAATCCCTCACACTTC 59.446 50.000 0.00 0.00 0.00 3.01
116 117 2.057922 ACCACAATCCCTCACACTTCT 58.942 47.619 0.00 0.00 0.00 2.85
117 118 3.248024 ACCACAATCCCTCACACTTCTA 58.752 45.455 0.00 0.00 0.00 2.10
118 119 3.846588 ACCACAATCCCTCACACTTCTAT 59.153 43.478 0.00 0.00 0.00 1.98
119 120 4.194640 CCACAATCCCTCACACTTCTATG 58.805 47.826 0.00 0.00 0.00 2.23
120 121 4.323792 CCACAATCCCTCACACTTCTATGT 60.324 45.833 0.00 0.00 0.00 2.29
121 122 5.248640 CACAATCCCTCACACTTCTATGTT 58.751 41.667 0.00 0.00 0.00 2.71
122 123 5.122869 CACAATCCCTCACACTTCTATGTTG 59.877 44.000 0.00 0.00 0.00 3.33
123 124 5.221925 ACAATCCCTCACACTTCTATGTTGT 60.222 40.000 0.00 0.00 0.00 3.32
124 125 6.013725 ACAATCCCTCACACTTCTATGTTGTA 60.014 38.462 0.00 0.00 0.00 2.41
125 126 6.620877 ATCCCTCACACTTCTATGTTGTAA 57.379 37.500 0.00 0.00 0.00 2.41
126 127 6.428083 TCCCTCACACTTCTATGTTGTAAA 57.572 37.500 0.00 0.00 0.00 2.01
127 128 6.464222 TCCCTCACACTTCTATGTTGTAAAG 58.536 40.000 0.00 0.00 0.00 1.85
128 129 6.269077 TCCCTCACACTTCTATGTTGTAAAGA 59.731 38.462 0.00 0.00 0.00 2.52
129 130 6.934645 CCCTCACACTTCTATGTTGTAAAGAA 59.065 38.462 0.00 0.00 0.00 2.52
130 131 7.444183 CCCTCACACTTCTATGTTGTAAAGAAA 59.556 37.037 0.00 0.00 0.00 2.52
131 132 8.283291 CCTCACACTTCTATGTTGTAAAGAAAC 58.717 37.037 0.00 0.00 0.00 2.78
132 133 8.149973 TCACACTTCTATGTTGTAAAGAAACC 57.850 34.615 0.00 0.00 0.00 3.27
133 134 7.227910 TCACACTTCTATGTTGTAAAGAAACCC 59.772 37.037 0.00 0.00 0.00 4.11
134 135 6.489022 ACACTTCTATGTTGTAAAGAAACCCC 59.511 38.462 0.00 0.00 0.00 4.95
135 136 6.008331 ACTTCTATGTTGTAAAGAAACCCCC 58.992 40.000 0.00 0.00 0.00 5.40
136 137 5.586155 TCTATGTTGTAAAGAAACCCCCA 57.414 39.130 0.00 0.00 0.00 4.96
137 138 5.954757 TCTATGTTGTAAAGAAACCCCCAA 58.045 37.500 0.00 0.00 0.00 4.12
138 139 4.948341 ATGTTGTAAAGAAACCCCCAAC 57.052 40.909 0.00 0.00 34.32 3.77
139 140 2.688958 TGTTGTAAAGAAACCCCCAACG 59.311 45.455 0.00 0.00 36.00 4.10
140 141 2.950975 GTTGTAAAGAAACCCCCAACGA 59.049 45.455 0.00 0.00 0.00 3.85
141 142 3.294038 TGTAAAGAAACCCCCAACGAA 57.706 42.857 0.00 0.00 0.00 3.85
142 143 3.629087 TGTAAAGAAACCCCCAACGAAA 58.371 40.909 0.00 0.00 0.00 3.46
143 144 3.380954 TGTAAAGAAACCCCCAACGAAAC 59.619 43.478 0.00 0.00 0.00 2.78
144 145 1.405872 AAGAAACCCCCAACGAAACC 58.594 50.000 0.00 0.00 0.00 3.27
145 146 0.259356 AGAAACCCCCAACGAAACCA 59.741 50.000 0.00 0.00 0.00 3.67
146 147 1.112950 GAAACCCCCAACGAAACCAA 58.887 50.000 0.00 0.00 0.00 3.67
147 148 1.067974 GAAACCCCCAACGAAACCAAG 59.932 52.381 0.00 0.00 0.00 3.61
148 149 0.757561 AACCCCCAACGAAACCAAGG 60.758 55.000 0.00 0.00 0.00 3.61
149 150 1.152631 CCCCCAACGAAACCAAGGT 60.153 57.895 0.00 0.00 0.00 3.50
150 151 0.757561 CCCCCAACGAAACCAAGGTT 60.758 55.000 0.00 0.00 40.45 3.50
151 152 0.387565 CCCCAACGAAACCAAGGTTG 59.612 55.000 5.06 0.00 40.44 3.77
152 153 1.394618 CCCAACGAAACCAAGGTTGA 58.605 50.000 5.06 0.00 42.70 3.18
153 154 1.751924 CCCAACGAAACCAAGGTTGAA 59.248 47.619 5.06 0.00 42.70 2.69
154 155 2.223711 CCCAACGAAACCAAGGTTGAAG 60.224 50.000 5.06 3.02 42.70 3.02
155 156 2.223711 CCAACGAAACCAAGGTTGAAGG 60.224 50.000 5.06 0.69 42.70 3.46
156 157 1.029681 ACGAAACCAAGGTTGAAGGC 58.970 50.000 5.06 0.00 38.47 4.35
157 158 1.028905 CGAAACCAAGGTTGAAGGCA 58.971 50.000 5.06 0.00 38.47 4.75
158 159 1.407258 CGAAACCAAGGTTGAAGGCAA 59.593 47.619 5.06 0.00 38.47 4.52
169 170 1.904287 TGAAGGCAACACATACCACC 58.096 50.000 0.00 0.00 41.41 4.61
170 171 1.143889 TGAAGGCAACACATACCACCA 59.856 47.619 0.00 0.00 41.41 4.17
171 172 2.235016 GAAGGCAACACATACCACCAA 58.765 47.619 0.00 0.00 41.41 3.67
172 173 2.373335 AGGCAACACATACCACCAAA 57.627 45.000 0.00 0.00 41.41 3.28
173 174 2.888212 AGGCAACACATACCACCAAAT 58.112 42.857 0.00 0.00 41.41 2.32
174 175 2.825532 AGGCAACACATACCACCAAATC 59.174 45.455 0.00 0.00 41.41 2.17
175 176 2.094234 GGCAACACATACCACCAAATCC 60.094 50.000 0.00 0.00 0.00 3.01
176 177 2.560542 GCAACACATACCACCAAATCCA 59.439 45.455 0.00 0.00 0.00 3.41
177 178 3.613910 GCAACACATACCACCAAATCCAC 60.614 47.826 0.00 0.00 0.00 4.02
178 179 3.517296 ACACATACCACCAAATCCACA 57.483 42.857 0.00 0.00 0.00 4.17
179 180 3.838565 ACACATACCACCAAATCCACAA 58.161 40.909 0.00 0.00 0.00 3.33
180 181 4.219115 ACACATACCACCAAATCCACAAA 58.781 39.130 0.00 0.00 0.00 2.83
181 182 4.837860 ACACATACCACCAAATCCACAAAT 59.162 37.500 0.00 0.00 0.00 2.32
182 183 6.013379 ACACATACCACCAAATCCACAAATA 58.987 36.000 0.00 0.00 0.00 1.40
183 184 6.071616 ACACATACCACCAAATCCACAAATAC 60.072 38.462 0.00 0.00 0.00 1.89
184 185 5.124776 ACATACCACCAAATCCACAAATACG 59.875 40.000 0.00 0.00 0.00 3.06
185 186 3.757270 ACCACCAAATCCACAAATACGA 58.243 40.909 0.00 0.00 0.00 3.43
186 187 3.756434 ACCACCAAATCCACAAATACGAG 59.244 43.478 0.00 0.00 0.00 4.18
187 188 3.427503 CCACCAAATCCACAAATACGAGC 60.428 47.826 0.00 0.00 0.00 5.03
188 189 2.752903 ACCAAATCCACAAATACGAGCC 59.247 45.455 0.00 0.00 0.00 4.70
189 190 2.752354 CCAAATCCACAAATACGAGCCA 59.248 45.455 0.00 0.00 0.00 4.75
190 191 3.181497 CCAAATCCACAAATACGAGCCAG 60.181 47.826 0.00 0.00 0.00 4.85
191 192 3.350219 AATCCACAAATACGAGCCAGT 57.650 42.857 0.00 0.00 0.00 4.00
192 193 2.851263 TCCACAAATACGAGCCAGTT 57.149 45.000 0.00 0.00 0.00 3.16
193 194 2.422597 TCCACAAATACGAGCCAGTTG 58.577 47.619 0.00 0.00 0.00 3.16
194 195 1.468520 CCACAAATACGAGCCAGTTGG 59.531 52.381 0.00 0.00 38.53 3.77
195 196 2.422597 CACAAATACGAGCCAGTTGGA 58.577 47.619 1.45 0.00 37.39 3.53
196 197 2.416547 CACAAATACGAGCCAGTTGGAG 59.583 50.000 1.45 0.00 37.39 3.86
197 198 2.301870 ACAAATACGAGCCAGTTGGAGA 59.698 45.455 1.45 0.00 37.39 3.71
198 199 3.055094 ACAAATACGAGCCAGTTGGAGAT 60.055 43.478 1.45 0.00 37.39 2.75
199 200 2.898729 ATACGAGCCAGTTGGAGATG 57.101 50.000 1.45 0.00 37.39 2.90
200 201 1.847328 TACGAGCCAGTTGGAGATGA 58.153 50.000 1.45 0.00 37.39 2.92
201 202 1.198713 ACGAGCCAGTTGGAGATGAT 58.801 50.000 1.45 0.00 37.39 2.45
202 203 1.134580 ACGAGCCAGTTGGAGATGATG 60.135 52.381 1.45 0.00 37.39 3.07
203 204 1.809271 CGAGCCAGTTGGAGATGATGG 60.809 57.143 1.45 0.00 37.39 3.51
204 205 1.211457 GAGCCAGTTGGAGATGATGGT 59.789 52.381 1.45 0.00 37.39 3.55
205 206 1.211457 AGCCAGTTGGAGATGATGGTC 59.789 52.381 1.45 0.00 37.39 4.02
206 207 1.945387 CCAGTTGGAGATGATGGTCG 58.055 55.000 0.00 0.00 37.39 4.79
207 208 1.482182 CCAGTTGGAGATGATGGTCGA 59.518 52.381 0.00 0.00 37.39 4.20
208 209 2.093500 CCAGTTGGAGATGATGGTCGAA 60.093 50.000 0.00 0.00 37.39 3.71
209 210 3.193263 CAGTTGGAGATGATGGTCGAAG 58.807 50.000 0.00 0.00 0.00 3.79
210 211 3.099905 AGTTGGAGATGATGGTCGAAGA 58.900 45.455 0.00 0.00 0.00 2.87
228 229 7.065803 GGTCGAAGAGATTTCATTTCCATACAA 59.934 37.037 0.00 0.00 36.95 2.41
302 311 3.620488 TCTTCACCTGAAACTTTGCTGT 58.380 40.909 0.00 0.00 33.07 4.40
343 353 9.910511 CTTTCAATATAAACATGAAGCAAATGC 57.089 29.630 0.00 0.00 42.49 3.56
367 377 2.738846 CAGTTTCTGACCATTCCTGTCG 59.261 50.000 0.00 0.00 35.46 4.35
391 401 6.379386 GTTTTCAGTAGGGAATGTAAGCAAC 58.621 40.000 0.00 0.00 0.00 4.17
402 412 0.794473 GTAAGCAACCGTGTACAGGC 59.206 55.000 10.09 3.03 0.00 4.85
421 431 1.740025 GCTATGAAGCTTCGTTTGCCT 59.260 47.619 25.50 4.96 45.85 4.75
579 674 2.048597 TGTACAGCACCGCGGAAG 60.049 61.111 35.90 24.47 0.00 3.46
897 5551 1.077787 CATAAACCCTCCCGCAGCA 60.078 57.895 0.00 0.00 0.00 4.41
1063 5720 3.147595 CGATGCTGTCCCTCCCGA 61.148 66.667 0.00 0.00 0.00 5.14
2173 6838 2.956132 TGATGTTTTTGGCTTGGGAGA 58.044 42.857 0.00 0.00 0.00 3.71
2179 6844 0.185901 TTTGGCTTGGGAGAGCTGTT 59.814 50.000 0.00 0.00 42.32 3.16
2267 6934 1.014564 GTGAGGCTCCGTTCCGAAAG 61.015 60.000 12.86 0.00 0.00 2.62
2388 7055 9.799106 AAAACATCTTCCCATATAGGAGTATTG 57.201 33.333 0.00 0.00 41.22 1.90
2434 7101 2.811431 TGGTTCATTAGAGCAAACCACG 59.189 45.455 1.83 0.00 44.62 4.94
2435 7102 2.812011 GGTTCATTAGAGCAAACCACGT 59.188 45.455 0.00 0.00 40.70 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.321919 AGTAGTCCGCACGTGGTCTA 60.322 55.000 18.88 6.25 0.00 2.59
1 2 1.177256 AAGTAGTCCGCACGTGGTCT 61.177 55.000 18.88 7.29 0.00 3.85
2 3 1.007336 CAAGTAGTCCGCACGTGGTC 61.007 60.000 18.88 0.00 0.00 4.02
3 4 1.006571 CAAGTAGTCCGCACGTGGT 60.007 57.895 18.88 0.00 0.00 4.16
4 5 2.380410 GCAAGTAGTCCGCACGTGG 61.380 63.158 18.88 7.38 0.00 4.94
5 6 0.109458 TAGCAAGTAGTCCGCACGTG 60.109 55.000 12.28 12.28 0.00 4.49
6 7 0.599558 TTAGCAAGTAGTCCGCACGT 59.400 50.000 0.00 0.00 0.00 4.49
7 8 1.135489 TCTTAGCAAGTAGTCCGCACG 60.135 52.381 0.00 0.00 0.00 5.34
8 9 2.163815 TCTCTTAGCAAGTAGTCCGCAC 59.836 50.000 0.00 0.00 0.00 5.34
9 10 2.423892 CTCTCTTAGCAAGTAGTCCGCA 59.576 50.000 0.00 0.00 0.00 5.69
10 11 2.683867 TCTCTCTTAGCAAGTAGTCCGC 59.316 50.000 0.00 0.00 0.00 5.54
11 12 4.966965 TTCTCTCTTAGCAAGTAGTCCG 57.033 45.455 0.00 0.00 0.00 4.79
12 13 6.275494 AGTTTCTCTCTTAGCAAGTAGTCC 57.725 41.667 0.00 0.00 0.00 3.85
13 14 6.071840 TGGAGTTTCTCTCTTAGCAAGTAGTC 60.072 42.308 0.00 0.00 42.40 2.59
14 15 5.775701 TGGAGTTTCTCTCTTAGCAAGTAGT 59.224 40.000 0.00 0.00 42.40 2.73
15 16 6.274157 TGGAGTTTCTCTCTTAGCAAGTAG 57.726 41.667 0.00 0.00 42.40 2.57
16 17 6.437477 TCATGGAGTTTCTCTCTTAGCAAGTA 59.563 38.462 0.00 0.00 42.40 2.24
17 18 5.247110 TCATGGAGTTTCTCTCTTAGCAAGT 59.753 40.000 0.00 0.00 42.40 3.16
18 19 5.580297 GTCATGGAGTTTCTCTCTTAGCAAG 59.420 44.000 0.00 0.00 42.40 4.01
19 20 5.482908 GTCATGGAGTTTCTCTCTTAGCAA 58.517 41.667 0.00 0.00 42.40 3.91
20 21 4.081420 GGTCATGGAGTTTCTCTCTTAGCA 60.081 45.833 0.00 0.00 42.40 3.49
21 22 4.438148 GGTCATGGAGTTTCTCTCTTAGC 58.562 47.826 0.00 0.00 42.40 3.09
22 23 4.467795 TGGGTCATGGAGTTTCTCTCTTAG 59.532 45.833 0.00 0.00 42.40 2.18
23 24 4.425772 TGGGTCATGGAGTTTCTCTCTTA 58.574 43.478 0.00 0.00 42.40 2.10
24 25 3.251484 TGGGTCATGGAGTTTCTCTCTT 58.749 45.455 0.00 0.00 42.40 2.85
25 26 2.907892 TGGGTCATGGAGTTTCTCTCT 58.092 47.619 0.00 0.00 42.40 3.10
26 27 3.244561 TGTTGGGTCATGGAGTTTCTCTC 60.245 47.826 0.00 0.00 42.07 3.20
27 28 2.711009 TGTTGGGTCATGGAGTTTCTCT 59.289 45.455 0.00 0.00 0.00 3.10
28 29 2.814336 GTGTTGGGTCATGGAGTTTCTC 59.186 50.000 0.00 0.00 0.00 2.87
29 30 2.443255 AGTGTTGGGTCATGGAGTTTCT 59.557 45.455 0.00 0.00 0.00 2.52
30 31 2.814336 GAGTGTTGGGTCATGGAGTTTC 59.186 50.000 0.00 0.00 0.00 2.78
31 32 2.489073 GGAGTGTTGGGTCATGGAGTTT 60.489 50.000 0.00 0.00 0.00 2.66
32 33 1.073923 GGAGTGTTGGGTCATGGAGTT 59.926 52.381 0.00 0.00 0.00 3.01
33 34 0.693049 GGAGTGTTGGGTCATGGAGT 59.307 55.000 0.00 0.00 0.00 3.85
34 35 0.692476 TGGAGTGTTGGGTCATGGAG 59.308 55.000 0.00 0.00 0.00 3.86
35 36 1.004628 CATGGAGTGTTGGGTCATGGA 59.995 52.381 0.00 0.00 33.60 3.41
36 37 1.004628 TCATGGAGTGTTGGGTCATGG 59.995 52.381 0.00 0.00 36.72 3.66
37 38 2.086869 GTCATGGAGTGTTGGGTCATG 58.913 52.381 0.00 0.00 37.23 3.07
38 39 1.004745 GGTCATGGAGTGTTGGGTCAT 59.995 52.381 0.00 0.00 0.00 3.06
39 40 0.400213 GGTCATGGAGTGTTGGGTCA 59.600 55.000 0.00 0.00 0.00 4.02
40 41 0.322546 GGGTCATGGAGTGTTGGGTC 60.323 60.000 0.00 0.00 0.00 4.46
41 42 1.065410 TGGGTCATGGAGTGTTGGGT 61.065 55.000 0.00 0.00 0.00 4.51
42 43 0.112218 TTGGGTCATGGAGTGTTGGG 59.888 55.000 0.00 0.00 0.00 4.12
43 44 1.247567 GTTGGGTCATGGAGTGTTGG 58.752 55.000 0.00 0.00 0.00 3.77
44 45 0.874390 CGTTGGGTCATGGAGTGTTG 59.126 55.000 0.00 0.00 0.00 3.33
45 46 0.250727 CCGTTGGGTCATGGAGTGTT 60.251 55.000 0.00 0.00 0.00 3.32
46 47 1.374947 CCGTTGGGTCATGGAGTGT 59.625 57.895 0.00 0.00 0.00 3.55
47 48 1.374947 ACCGTTGGGTCATGGAGTG 59.625 57.895 0.00 0.00 46.01 3.51
48 49 3.900888 ACCGTTGGGTCATGGAGT 58.099 55.556 0.00 0.00 46.01 3.85
65 66 2.045561 ATGTGTGTTTGTCGGGTTGA 57.954 45.000 0.00 0.00 0.00 3.18
66 67 3.314080 ACTTATGTGTGTTTGTCGGGTTG 59.686 43.478 0.00 0.00 0.00 3.77
67 68 3.547746 ACTTATGTGTGTTTGTCGGGTT 58.452 40.909 0.00 0.00 0.00 4.11
68 69 3.135994 GACTTATGTGTGTTTGTCGGGT 58.864 45.455 0.00 0.00 0.00 5.28
69 70 2.156891 CGACTTATGTGTGTTTGTCGGG 59.843 50.000 0.00 0.00 42.06 5.14
70 71 2.411031 GCGACTTATGTGTGTTTGTCGG 60.411 50.000 13.71 0.00 44.69 4.79
71 72 2.219903 TGCGACTTATGTGTGTTTGTCG 59.780 45.455 8.65 8.65 46.45 4.35
72 73 3.870723 TGCGACTTATGTGTGTTTGTC 57.129 42.857 0.00 0.00 0.00 3.18
73 74 3.375610 TGTTGCGACTTATGTGTGTTTGT 59.624 39.130 5.50 0.00 0.00 2.83
74 75 3.946402 TGTTGCGACTTATGTGTGTTTG 58.054 40.909 5.50 0.00 0.00 2.93
75 76 4.347813 GTTGTTGCGACTTATGTGTGTTT 58.652 39.130 5.50 0.00 0.00 2.83
76 77 3.242936 GGTTGTTGCGACTTATGTGTGTT 60.243 43.478 5.50 0.00 0.00 3.32
77 78 2.289547 GGTTGTTGCGACTTATGTGTGT 59.710 45.455 5.50 0.00 0.00 3.72
78 79 2.289274 TGGTTGTTGCGACTTATGTGTG 59.711 45.455 5.50 0.00 0.00 3.82
79 80 2.289547 GTGGTTGTTGCGACTTATGTGT 59.710 45.455 5.50 0.00 0.00 3.72
80 81 2.289274 TGTGGTTGTTGCGACTTATGTG 59.711 45.455 5.50 0.00 0.00 3.21
81 82 2.566913 TGTGGTTGTTGCGACTTATGT 58.433 42.857 5.50 0.00 0.00 2.29
82 83 3.617540 TTGTGGTTGTTGCGACTTATG 57.382 42.857 5.50 0.00 0.00 1.90
83 84 3.190535 GGATTGTGGTTGTTGCGACTTAT 59.809 43.478 5.50 0.00 0.00 1.73
84 85 2.550606 GGATTGTGGTTGTTGCGACTTA 59.449 45.455 5.50 0.00 0.00 2.24
85 86 1.336755 GGATTGTGGTTGTTGCGACTT 59.663 47.619 5.50 0.00 0.00 3.01
86 87 0.951558 GGATTGTGGTTGTTGCGACT 59.048 50.000 5.50 0.00 0.00 4.18
87 88 0.039527 GGGATTGTGGTTGTTGCGAC 60.040 55.000 0.00 0.00 0.00 5.19
88 89 0.179004 AGGGATTGTGGTTGTTGCGA 60.179 50.000 0.00 0.00 0.00 5.10
89 90 0.240945 GAGGGATTGTGGTTGTTGCG 59.759 55.000 0.00 0.00 0.00 4.85
90 91 1.000274 GTGAGGGATTGTGGTTGTTGC 60.000 52.381 0.00 0.00 0.00 4.17
91 92 2.034558 GTGTGAGGGATTGTGGTTGTTG 59.965 50.000 0.00 0.00 0.00 3.33
92 93 2.091885 AGTGTGAGGGATTGTGGTTGTT 60.092 45.455 0.00 0.00 0.00 2.83
93 94 1.494721 AGTGTGAGGGATTGTGGTTGT 59.505 47.619 0.00 0.00 0.00 3.32
94 95 2.276732 AGTGTGAGGGATTGTGGTTG 57.723 50.000 0.00 0.00 0.00 3.77
95 96 2.443255 AGAAGTGTGAGGGATTGTGGTT 59.557 45.455 0.00 0.00 0.00 3.67
96 97 2.057922 AGAAGTGTGAGGGATTGTGGT 58.942 47.619 0.00 0.00 0.00 4.16
97 98 2.867109 AGAAGTGTGAGGGATTGTGG 57.133 50.000 0.00 0.00 0.00 4.17
98 99 4.836825 ACATAGAAGTGTGAGGGATTGTG 58.163 43.478 0.00 0.00 0.00 3.33
99 100 5.221925 ACAACATAGAAGTGTGAGGGATTGT 60.222 40.000 0.00 0.00 31.49 2.71
100 101 5.248640 ACAACATAGAAGTGTGAGGGATTG 58.751 41.667 0.00 0.00 31.49 2.67
101 102 5.505181 ACAACATAGAAGTGTGAGGGATT 57.495 39.130 0.00 0.00 31.49 3.01
102 103 6.620877 TTACAACATAGAAGTGTGAGGGAT 57.379 37.500 0.00 0.00 31.49 3.85
103 104 6.269077 TCTTTACAACATAGAAGTGTGAGGGA 59.731 38.462 0.00 0.00 31.49 4.20
104 105 6.464222 TCTTTACAACATAGAAGTGTGAGGG 58.536 40.000 0.00 0.00 31.49 4.30
105 106 7.962964 TTCTTTACAACATAGAAGTGTGAGG 57.037 36.000 0.00 0.00 31.49 3.86
106 107 8.283291 GGTTTCTTTACAACATAGAAGTGTGAG 58.717 37.037 0.00 0.00 31.49 3.51
107 108 7.227910 GGGTTTCTTTACAACATAGAAGTGTGA 59.772 37.037 0.00 0.00 31.49 3.58
108 109 7.360361 GGGTTTCTTTACAACATAGAAGTGTG 58.640 38.462 0.00 0.00 31.49 3.82
109 110 6.489022 GGGGTTTCTTTACAACATAGAAGTGT 59.511 38.462 0.00 0.00 30.32 3.55
110 111 6.072119 GGGGGTTTCTTTACAACATAGAAGTG 60.072 42.308 0.00 0.00 30.32 3.16
111 112 6.008331 GGGGGTTTCTTTACAACATAGAAGT 58.992 40.000 0.00 0.00 30.32 3.01
112 113 6.007703 TGGGGGTTTCTTTACAACATAGAAG 58.992 40.000 0.00 0.00 30.32 2.85
113 114 5.954757 TGGGGGTTTCTTTACAACATAGAA 58.045 37.500 0.00 0.00 0.00 2.10
114 115 5.586155 TGGGGGTTTCTTTACAACATAGA 57.414 39.130 0.00 0.00 0.00 1.98
115 116 5.335348 CGTTGGGGGTTTCTTTACAACATAG 60.335 44.000 0.00 0.00 38.39 2.23
116 117 4.519730 CGTTGGGGGTTTCTTTACAACATA 59.480 41.667 0.00 0.00 38.39 2.29
117 118 3.319689 CGTTGGGGGTTTCTTTACAACAT 59.680 43.478 0.00 0.00 38.39 2.71
118 119 2.688958 CGTTGGGGGTTTCTTTACAACA 59.311 45.455 0.00 0.00 38.39 3.33
119 120 2.950975 TCGTTGGGGGTTTCTTTACAAC 59.049 45.455 0.00 0.00 35.96 3.32
120 121 3.294038 TCGTTGGGGGTTTCTTTACAA 57.706 42.857 0.00 0.00 0.00 2.41
121 122 3.294038 TTCGTTGGGGGTTTCTTTACA 57.706 42.857 0.00 0.00 0.00 2.41
122 123 3.243501 GGTTTCGTTGGGGGTTTCTTTAC 60.244 47.826 0.00 0.00 0.00 2.01
123 124 2.957680 GGTTTCGTTGGGGGTTTCTTTA 59.042 45.455 0.00 0.00 0.00 1.85
124 125 1.758280 GGTTTCGTTGGGGGTTTCTTT 59.242 47.619 0.00 0.00 0.00 2.52
125 126 1.342175 TGGTTTCGTTGGGGGTTTCTT 60.342 47.619 0.00 0.00 0.00 2.52
126 127 0.259356 TGGTTTCGTTGGGGGTTTCT 59.741 50.000 0.00 0.00 0.00 2.52
127 128 1.067974 CTTGGTTTCGTTGGGGGTTTC 59.932 52.381 0.00 0.00 0.00 2.78
128 129 1.116308 CTTGGTTTCGTTGGGGGTTT 58.884 50.000 0.00 0.00 0.00 3.27
129 130 0.757561 CCTTGGTTTCGTTGGGGGTT 60.758 55.000 0.00 0.00 0.00 4.11
130 131 1.152631 CCTTGGTTTCGTTGGGGGT 60.153 57.895 0.00 0.00 0.00 4.95
131 132 0.757561 AACCTTGGTTTCGTTGGGGG 60.758 55.000 0.00 0.00 0.00 5.40
132 133 0.387565 CAACCTTGGTTTCGTTGGGG 59.612 55.000 1.76 0.00 34.55 4.96
133 134 1.394618 TCAACCTTGGTTTCGTTGGG 58.605 50.000 1.76 0.00 37.93 4.12
134 135 2.223711 CCTTCAACCTTGGTTTCGTTGG 60.224 50.000 1.76 0.00 37.93 3.77
135 136 2.798145 GCCTTCAACCTTGGTTTCGTTG 60.798 50.000 1.76 0.00 38.56 4.10
136 137 1.407618 GCCTTCAACCTTGGTTTCGTT 59.592 47.619 1.76 0.00 0.00 3.85
137 138 1.029681 GCCTTCAACCTTGGTTTCGT 58.970 50.000 1.76 0.00 0.00 3.85
138 139 1.028905 TGCCTTCAACCTTGGTTTCG 58.971 50.000 1.76 0.00 0.00 3.46
139 140 2.821546 GTTGCCTTCAACCTTGGTTTC 58.178 47.619 1.76 0.00 45.15 2.78
140 141 2.979814 GTTGCCTTCAACCTTGGTTT 57.020 45.000 1.76 0.00 45.15 3.27
149 150 2.235016 GGTGGTATGTGTTGCCTTCAA 58.765 47.619 0.00 0.00 0.00 2.69
150 151 1.143889 TGGTGGTATGTGTTGCCTTCA 59.856 47.619 0.00 0.00 0.00 3.02
151 152 1.904287 TGGTGGTATGTGTTGCCTTC 58.096 50.000 0.00 0.00 0.00 3.46
152 153 2.373335 TTGGTGGTATGTGTTGCCTT 57.627 45.000 0.00 0.00 0.00 4.35
153 154 2.373335 TTTGGTGGTATGTGTTGCCT 57.627 45.000 0.00 0.00 0.00 4.75
154 155 2.094234 GGATTTGGTGGTATGTGTTGCC 60.094 50.000 0.00 0.00 0.00 4.52
155 156 2.560542 TGGATTTGGTGGTATGTGTTGC 59.439 45.455 0.00 0.00 0.00 4.17
156 157 3.571828 TGTGGATTTGGTGGTATGTGTTG 59.428 43.478 0.00 0.00 0.00 3.33
157 158 3.838565 TGTGGATTTGGTGGTATGTGTT 58.161 40.909 0.00 0.00 0.00 3.32
158 159 3.517296 TGTGGATTTGGTGGTATGTGT 57.483 42.857 0.00 0.00 0.00 3.72
159 160 4.862902 TTTGTGGATTTGGTGGTATGTG 57.137 40.909 0.00 0.00 0.00 3.21
160 161 5.124776 CGTATTTGTGGATTTGGTGGTATGT 59.875 40.000 0.00 0.00 0.00 2.29
161 162 5.355630 TCGTATTTGTGGATTTGGTGGTATG 59.644 40.000 0.00 0.00 0.00 2.39
162 163 5.502079 TCGTATTTGTGGATTTGGTGGTAT 58.498 37.500 0.00 0.00 0.00 2.73
163 164 4.907809 TCGTATTTGTGGATTTGGTGGTA 58.092 39.130 0.00 0.00 0.00 3.25
164 165 3.756434 CTCGTATTTGTGGATTTGGTGGT 59.244 43.478 0.00 0.00 0.00 4.16
165 166 3.427503 GCTCGTATTTGTGGATTTGGTGG 60.428 47.826 0.00 0.00 0.00 4.61
166 167 3.427503 GGCTCGTATTTGTGGATTTGGTG 60.428 47.826 0.00 0.00 0.00 4.17
167 168 2.752903 GGCTCGTATTTGTGGATTTGGT 59.247 45.455 0.00 0.00 0.00 3.67
168 169 2.752354 TGGCTCGTATTTGTGGATTTGG 59.248 45.455 0.00 0.00 0.00 3.28
169 170 3.440173 ACTGGCTCGTATTTGTGGATTTG 59.560 43.478 0.00 0.00 0.00 2.32
170 171 3.686016 ACTGGCTCGTATTTGTGGATTT 58.314 40.909 0.00 0.00 0.00 2.17
171 172 3.350219 ACTGGCTCGTATTTGTGGATT 57.650 42.857 0.00 0.00 0.00 3.01
172 173 3.009723 CAACTGGCTCGTATTTGTGGAT 58.990 45.455 0.00 0.00 0.00 3.41
173 174 2.422597 CAACTGGCTCGTATTTGTGGA 58.577 47.619 0.00 0.00 0.00 4.02
174 175 1.468520 CCAACTGGCTCGTATTTGTGG 59.531 52.381 0.00 0.00 0.00 4.17
175 176 2.416547 CTCCAACTGGCTCGTATTTGTG 59.583 50.000 0.00 0.00 34.44 3.33
176 177 2.301870 TCTCCAACTGGCTCGTATTTGT 59.698 45.455 0.00 0.00 34.44 2.83
177 178 2.972625 TCTCCAACTGGCTCGTATTTG 58.027 47.619 0.00 0.00 34.44 2.32
178 179 3.197766 TCATCTCCAACTGGCTCGTATTT 59.802 43.478 0.00 0.00 34.44 1.40
179 180 2.766263 TCATCTCCAACTGGCTCGTATT 59.234 45.455 0.00 0.00 34.44 1.89
180 181 2.388735 TCATCTCCAACTGGCTCGTAT 58.611 47.619 0.00 0.00 34.44 3.06
181 182 1.847328 TCATCTCCAACTGGCTCGTA 58.153 50.000 0.00 0.00 34.44 3.43
182 183 1.134580 CATCATCTCCAACTGGCTCGT 60.135 52.381 0.00 0.00 34.44 4.18
183 184 1.579698 CATCATCTCCAACTGGCTCG 58.420 55.000 0.00 0.00 34.44 5.03
184 185 1.211457 ACCATCATCTCCAACTGGCTC 59.789 52.381 0.00 0.00 34.44 4.70
185 186 1.211457 GACCATCATCTCCAACTGGCT 59.789 52.381 0.00 0.00 34.44 4.75
186 187 1.673168 GACCATCATCTCCAACTGGC 58.327 55.000 0.00 0.00 34.44 4.85
187 188 1.482182 TCGACCATCATCTCCAACTGG 59.518 52.381 0.00 0.00 0.00 4.00
188 189 2.967599 TCGACCATCATCTCCAACTG 57.032 50.000 0.00 0.00 0.00 3.16
189 190 3.099905 TCTTCGACCATCATCTCCAACT 58.900 45.455 0.00 0.00 0.00 3.16
190 191 3.131223 TCTCTTCGACCATCATCTCCAAC 59.869 47.826 0.00 0.00 0.00 3.77
191 192 3.365472 TCTCTTCGACCATCATCTCCAA 58.635 45.455 0.00 0.00 0.00 3.53
192 193 3.018423 TCTCTTCGACCATCATCTCCA 57.982 47.619 0.00 0.00 0.00 3.86
193 194 4.599047 AATCTCTTCGACCATCATCTCC 57.401 45.455 0.00 0.00 0.00 3.71
194 195 5.595885 TGAAATCTCTTCGACCATCATCTC 58.404 41.667 0.00 0.00 0.00 2.75
195 196 5.604758 TGAAATCTCTTCGACCATCATCT 57.395 39.130 0.00 0.00 0.00 2.90
196 197 6.857777 AATGAAATCTCTTCGACCATCATC 57.142 37.500 0.00 0.00 0.00 2.92
197 198 6.261826 GGAAATGAAATCTCTTCGACCATCAT 59.738 38.462 0.00 0.00 0.00 2.45
198 199 5.586243 GGAAATGAAATCTCTTCGACCATCA 59.414 40.000 0.00 0.00 0.00 3.07
199 200 5.586243 TGGAAATGAAATCTCTTCGACCATC 59.414 40.000 0.00 0.00 0.00 3.51
200 201 5.500234 TGGAAATGAAATCTCTTCGACCAT 58.500 37.500 0.00 0.00 0.00 3.55
201 202 4.905429 TGGAAATGAAATCTCTTCGACCA 58.095 39.130 0.00 0.00 0.00 4.02
202 203 6.538742 TGTATGGAAATGAAATCTCTTCGACC 59.461 38.462 0.00 0.00 0.00 4.79
203 204 7.539712 TGTATGGAAATGAAATCTCTTCGAC 57.460 36.000 0.00 0.00 0.00 4.20
204 205 8.615211 CATTGTATGGAAATGAAATCTCTTCGA 58.385 33.333 0.00 0.00 37.22 3.71
205 206 8.400947 ACATTGTATGGAAATGAAATCTCTTCG 58.599 33.333 3.32 0.00 38.21 3.79
208 209 9.471702 AGAACATTGTATGGAAATGAAATCTCT 57.528 29.630 3.32 0.00 38.21 3.10
209 210 9.727627 GAGAACATTGTATGGAAATGAAATCTC 57.272 33.333 3.32 8.54 38.21 2.75
210 211 9.471702 AGAGAACATTGTATGGAAATGAAATCT 57.528 29.630 3.32 4.14 38.21 2.40
320 329 6.985645 GGGCATTTGCTTCATGTTTATATTGA 59.014 34.615 2.12 0.00 41.70 2.57
327 336 1.698532 TGGGGCATTTGCTTCATGTTT 59.301 42.857 2.12 0.00 41.70 2.83
332 342 1.344114 GAAACTGGGGCATTTGCTTCA 59.656 47.619 2.12 1.06 41.70 3.02
343 353 1.355720 AGGAATGGTCAGAAACTGGGG 59.644 52.381 0.00 0.00 31.51 4.96
367 377 6.379386 GTTGCTTACATTCCCTACTGAAAAC 58.621 40.000 0.00 0.00 0.00 2.43
391 401 1.571919 GCTTCATAGCCTGTACACGG 58.428 55.000 0.00 0.00 41.74 4.94
402 412 2.352960 GGAGGCAAACGAAGCTTCATAG 59.647 50.000 25.47 12.26 39.57 2.23
421 431 2.551270 ACTTCCTAAGCATGTCAGGGA 58.449 47.619 8.83 3.38 0.00 4.20
475 487 9.823647 CATCTCTTACACAATACTCCATAAACT 57.176 33.333 0.00 0.00 0.00 2.66
476 488 9.817809 TCATCTCTTACACAATACTCCATAAAC 57.182 33.333 0.00 0.00 0.00 2.01
484 496 9.836864 TGCATTAATCATCTCTTACACAATACT 57.163 29.630 0.00 0.00 0.00 2.12
579 674 1.535226 GCAAACTGGTTCCCGTGAAAC 60.535 52.381 0.00 0.00 38.74 2.78
674 5315 1.283321 GAGTTTTCCTCCAGATGGGCT 59.717 52.381 0.00 0.00 36.21 5.19
678 5319 2.751806 GGCTTGAGTTTTCCTCCAGATG 59.248 50.000 0.00 0.00 39.65 2.90
897 5551 2.673368 GTGATCGCAACGAAGAAGGAAT 59.327 45.455 0.16 0.00 39.99 3.01
1041 5698 0.531532 GGAGGGACAGCATCGTCATG 60.532 60.000 3.75 0.00 37.66 3.07
1557 6214 3.826754 TAGCACTCGAGCGCCTGG 61.827 66.667 21.24 1.50 40.15 4.45
1608 6265 3.437795 ATCTTGCAGCACAGCGCC 61.438 61.111 2.29 0.00 44.04 6.53
1618 6275 2.361992 CTGCTGGGCCATCTTGCA 60.362 61.111 16.24 16.24 0.00 4.08
1619 6276 3.145551 CCTGCTGGGCCATCTTGC 61.146 66.667 6.72 7.77 0.00 4.01
1624 6281 4.437587 GCTCACCTGCTGGGCCAT 62.438 66.667 6.72 0.00 41.09 4.40
1693 6350 3.103911 CGGCCACGACTTGTCGAC 61.104 66.667 26.65 9.11 44.60 4.20
2173 6838 1.558294 TCTCATGCAGGATGAACAGCT 59.442 47.619 0.00 0.00 40.73 4.24
2179 6844 2.121129 TCCACATCTCATGCAGGATGA 58.879 47.619 24.25 15.22 41.05 2.92
2267 6934 5.163632 GGTTCTCTGGTCTAACTACTACAGC 60.164 48.000 0.00 0.00 0.00 4.40
2434 7101 5.865552 AGACAACAATCATTTTGCTATGCAC 59.134 36.000 0.00 0.00 38.71 4.57
2435 7102 6.028146 AGACAACAATCATTTTGCTATGCA 57.972 33.333 0.00 0.00 36.47 3.96
2539 7208 3.117888 TGATGTAAGGGCAAGAATCCTCC 60.118 47.826 0.00 0.00 32.02 4.30
2818 7491 7.596248 TCCGAGTTAATAATAAGGCGATTACAC 59.404 37.037 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.