Multiple sequence alignment - TraesCS7D01G301700

Loading Multiple Alignment...

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 TraesCS7D01G301700 chr7D 100.000 3354 0 0 1 3354 382102890 382099537 0.000000e+00 6194
1 TraesCS7D01G301700 chrUn 99.270 3015 18 1 344 3354 182448846 182445832 0.000000e+00 5443
2 TraesCS7D01G301700 chrUn 96.508 630 7 3 344 958 222879143 222878514 0.000000e+00 1027
3 TraesCS7D01G301700 chrUn 98.837 172 2 0 1 172 233529829 233529658 1.170000e-79 307
4 TraesCS7D01G301700 chrUn 98.837 172 2 0 1 172 257940069 257940240 1.170000e-79 307
5 TraesCS7D01G301700 chr4D 99.038 3016 23 2 344 3354 123639190 123642204 0.000000e+00 5404
6 TraesCS7D01G301700 chr4D 98.806 3015 32 1 344 3354 123469636 123466622 0.000000e+00 5365
7 TraesCS7D01G301700 chr5A 98.744 3026 23 2 344 3354 16538541 16535516 0.000000e+00 5363
8 TraesCS7D01G301700 chr5A 97.368 494 2 1 344 826 420179663 420179170 0.000000e+00 830
9 TraesCS7D01G301700 chr5A 98.837 172 2 0 1 172 112328782 112328953 1.170000e-79 307
10 TraesCS7D01G301700 chr5A 98.837 172 2 0 1 172 492877280 492877451 1.170000e-79 307
11 TraesCS7D01G301700 chr7B 98.711 3025 25 2 344 3354 742954779 742957803 0.000000e+00 5358
12 TraesCS7D01G301700 chr7B 98.579 3026 28 2 344 3354 716910384 716907359 0.000000e+00 5336
13 TraesCS7D01G301700 chr7B 98.546 3026 29 2 344 3354 716778568 716775543 0.000000e+00 5330
14 TraesCS7D01G301700 chr7B 99.419 172 1 0 1 172 531992304 531992475 2.510000e-81 313
15 TraesCS7D01G301700 chr7A 98.646 3027 25 2 344 3354 60349019 60345993 0.000000e+00 5349
16 TraesCS7D01G301700 chr1B 98.413 3025 34 2 344 3354 583567589 583570613 0.000000e+00 5308
17 TraesCS7D01G301700 chr1B 98.837 172 2 0 1 172 32984097 32983926 1.170000e-79 307
18 TraesCS7D01G301700 chr2B 98.381 3027 32 3 344 3354 391172403 391169378 0.000000e+00 5302
19 TraesCS7D01G301700 chr6B 98.837 172 2 0 1 172 388169620 388169449 1.170000e-79 307
20 TraesCS7D01G301700 chr6B 98.837 172 2 0 1 172 394462309 394462480 1.170000e-79 307
21 TraesCS7D01G301700 chr3D 98.837 172 2 0 1 172 145418813 145418984 1.170000e-79 307


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 TraesCS7D01G301700 chr7D 382099537 382102890 3353 True 6194 6194 100.000 1 3354 1 chr7D.!!$R1 3353
1 TraesCS7D01G301700 chrUn 182445832 182448846 3014 True 5443 5443 99.270 344 3354 1 chrUn.!!$R1 3010
2 TraesCS7D01G301700 chrUn 222878514 222879143 629 True 1027 1027 96.508 344 958 1 chrUn.!!$R2 614
3 TraesCS7D01G301700 chr4D 123639190 123642204 3014 False 5404 5404 99.038 344 3354 1 chr4D.!!$F1 3010
4 TraesCS7D01G301700 chr4D 123466622 123469636 3014 True 5365 5365 98.806 344 3354 1 chr4D.!!$R1 3010
5 TraesCS7D01G301700 chr5A 16535516 16538541 3025 True 5363 5363 98.744 344 3354 1 chr5A.!!$R1 3010
6 TraesCS7D01G301700 chr7B 742954779 742957803 3024 False 5358 5358 98.711 344 3354 1 chr7B.!!$F2 3010
7 TraesCS7D01G301700 chr7B 716907359 716910384 3025 True 5336 5336 98.579 344 3354 1 chr7B.!!$R2 3010
8 TraesCS7D01G301700 chr7B 716775543 716778568 3025 True 5330 5330 98.546 344 3354 1 chr7B.!!$R1 3010
9 TraesCS7D01G301700 chr7A 60345993 60349019 3026 True 5349 5349 98.646 344 3354 1 chr7A.!!$R1 3010
10 TraesCS7D01G301700 chr1B 583567589 583570613 3024 False 5308 5308 98.413 344 3354 1 chr1B.!!$F1 3010
11 TraesCS7D01G301700 chr2B 391169378 391172403 3025 True 5302 5302 98.381 344 3354 1 chr2B.!!$R1 3010

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
143 144 0.036732 TTCTCCTTGCCGAGTTGCAT 59.963 50.0 0.0 0.0 41.7 3.96 F
341 342 0.100503 GCTAAAATGCGGGCGATGTT 59.899 50.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 1908 0.527817 GGAGCGGTAGGTCGACATTG 60.528 60.000 18.91 5.19 45.26 2.82 R
2579 2597 4.357142 CTTTCTCTAACGCTAATACCGCA 58.643 43.478 0.00 0.00 0.00 5.69 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
23 24 6.086785 ACAAAGTCTTTCTACTTAGCTCGT 57.913 37.500 0.00 0.00 38.76 4.18
24 25 6.151004 ACAAAGTCTTTCTACTTAGCTCGTC 58.849 40.000 0.00 0.00 38.76 4.20
25 26 5.961396 AAGTCTTTCTACTTAGCTCGTCA 57.039 39.130 0.00 0.00 37.93 4.35
26 27 5.961396 AGTCTTTCTACTTAGCTCGTCAA 57.039 39.130 0.00 0.00 0.00 3.18
27 28 5.945155 AGTCTTTCTACTTAGCTCGTCAAG 58.055 41.667 0.00 0.00 0.00 3.02
28 29 7.062288 AAGTCTTTCTACTTAGCTCGTCAAGC 61.062 42.308 0.00 0.00 40.61 4.01
46 47 0.853419 GCGAAGTAGCTATCAACGGC 59.147 55.000 0.00 0.00 0.00 5.68
47 48 1.536284 GCGAAGTAGCTATCAACGGCT 60.536 52.381 0.00 0.00 41.92 5.52
48 49 2.810650 CGAAGTAGCTATCAACGGCTT 58.189 47.619 0.00 0.00 39.65 4.35
49 50 3.187700 CGAAGTAGCTATCAACGGCTTT 58.812 45.455 0.00 0.00 39.65 3.51
50 51 4.357142 CGAAGTAGCTATCAACGGCTTTA 58.643 43.478 0.00 0.00 39.65 1.85
51 52 4.441415 CGAAGTAGCTATCAACGGCTTTAG 59.559 45.833 0.00 0.00 39.65 1.85
52 53 3.718815 AGTAGCTATCAACGGCTTTAGC 58.281 45.455 0.00 0.00 39.65 3.09
53 54 2.691409 AGCTATCAACGGCTTTAGCA 57.309 45.000 3.88 0.00 44.36 3.49
54 55 3.199880 AGCTATCAACGGCTTTAGCAT 57.800 42.857 3.88 0.00 44.36 3.79
55 56 2.874701 AGCTATCAACGGCTTTAGCATG 59.125 45.455 3.88 0.00 44.36 4.06
56 57 2.872245 GCTATCAACGGCTTTAGCATGA 59.128 45.455 0.00 5.49 44.36 3.07
57 58 3.303395 GCTATCAACGGCTTTAGCATGAC 60.303 47.826 0.00 0.00 44.36 3.06
58 59 2.177394 TCAACGGCTTTAGCATGACA 57.823 45.000 0.00 0.00 44.36 3.58
59 60 2.499197 TCAACGGCTTTAGCATGACAA 58.501 42.857 0.00 0.00 44.36 3.18
60 61 2.225491 TCAACGGCTTTAGCATGACAAC 59.775 45.455 0.00 0.00 44.36 3.32
61 62 2.185004 ACGGCTTTAGCATGACAACT 57.815 45.000 0.00 0.00 44.36 3.16
62 63 3.328382 ACGGCTTTAGCATGACAACTA 57.672 42.857 0.00 0.00 44.36 2.24
63 64 3.262420 ACGGCTTTAGCATGACAACTAG 58.738 45.455 0.00 0.00 44.36 2.57
64 65 3.056107 ACGGCTTTAGCATGACAACTAGA 60.056 43.478 0.00 0.00 44.36 2.43
65 66 3.932710 CGGCTTTAGCATGACAACTAGAA 59.067 43.478 0.00 0.00 44.36 2.10
66 67 4.201724 CGGCTTTAGCATGACAACTAGAAC 60.202 45.833 0.00 0.00 44.36 3.01
67 68 4.695455 GGCTTTAGCATGACAACTAGAACA 59.305 41.667 0.00 0.00 44.36 3.18
68 69 5.355350 GGCTTTAGCATGACAACTAGAACAT 59.645 40.000 0.00 0.00 44.36 2.71
69 70 6.457528 GGCTTTAGCATGACAACTAGAACATC 60.458 42.308 0.00 0.00 44.36 3.06
70 71 6.092670 GCTTTAGCATGACAACTAGAACATCA 59.907 38.462 0.00 0.00 41.59 3.07
71 72 7.361201 GCTTTAGCATGACAACTAGAACATCAA 60.361 37.037 0.00 0.00 41.59 2.57
72 73 7.601073 TTAGCATGACAACTAGAACATCAAG 57.399 36.000 0.00 0.00 0.00 3.02
73 74 4.394300 AGCATGACAACTAGAACATCAAGC 59.606 41.667 0.00 3.69 34.96 4.01
74 75 4.437930 GCATGACAACTAGAACATCAAGCC 60.438 45.833 0.00 0.00 29.96 4.35
75 76 4.350368 TGACAACTAGAACATCAAGCCA 57.650 40.909 0.00 0.00 0.00 4.75
76 77 4.910195 TGACAACTAGAACATCAAGCCAT 58.090 39.130 0.00 0.00 0.00 4.40
77 78 4.696877 TGACAACTAGAACATCAAGCCATG 59.303 41.667 0.00 0.00 0.00 3.66
78 79 4.012374 ACAACTAGAACATCAAGCCATGG 58.988 43.478 7.63 7.63 0.00 3.66
79 80 4.012374 CAACTAGAACATCAAGCCATGGT 58.988 43.478 14.67 0.00 0.00 3.55
80 81 5.185454 CAACTAGAACATCAAGCCATGGTA 58.815 41.667 14.67 0.00 0.00 3.25
81 82 5.435686 ACTAGAACATCAAGCCATGGTAA 57.564 39.130 14.67 0.00 0.00 2.85
82 83 5.815581 ACTAGAACATCAAGCCATGGTAAA 58.184 37.500 14.67 0.00 0.00 2.01
83 84 5.648092 ACTAGAACATCAAGCCATGGTAAAC 59.352 40.000 14.67 0.00 0.00 2.01
84 85 4.666512 AGAACATCAAGCCATGGTAAACT 58.333 39.130 14.67 0.00 0.00 2.66
85 86 4.460382 AGAACATCAAGCCATGGTAAACTG 59.540 41.667 14.67 8.72 0.00 3.16
86 87 2.493278 ACATCAAGCCATGGTAAACTGC 59.507 45.455 14.67 0.00 0.00 4.40
87 88 1.544724 TCAAGCCATGGTAAACTGCC 58.455 50.000 14.67 0.00 0.00 4.85
88 89 1.202989 TCAAGCCATGGTAAACTGCCA 60.203 47.619 14.67 0.00 40.68 4.92
89 90 1.617850 CAAGCCATGGTAAACTGCCAA 59.382 47.619 14.67 0.00 39.72 4.52
90 91 2.008242 AGCCATGGTAAACTGCCAAA 57.992 45.000 14.67 0.00 39.72 3.28
91 92 1.895131 AGCCATGGTAAACTGCCAAAG 59.105 47.619 14.67 0.00 39.72 2.77
92 93 1.672737 GCCATGGTAAACTGCCAAAGC 60.673 52.381 14.67 0.00 39.72 3.51
93 94 1.895131 CCATGGTAAACTGCCAAAGCT 59.105 47.619 2.57 0.00 39.72 3.74
94 95 2.299867 CCATGGTAAACTGCCAAAGCTT 59.700 45.455 2.57 0.00 39.72 3.74
95 96 3.578688 CATGGTAAACTGCCAAAGCTTC 58.421 45.455 0.00 0.00 39.72 3.86
96 97 2.944129 TGGTAAACTGCCAAAGCTTCT 58.056 42.857 0.00 0.00 40.80 2.85
97 98 2.622942 TGGTAAACTGCCAAAGCTTCTG 59.377 45.455 0.00 0.32 40.80 3.02
98 99 2.608016 GGTAAACTGCCAAAGCTTCTGC 60.608 50.000 12.02 12.02 40.80 4.26
112 113 3.385577 GCTTCTGCTATAGTGTAGCACC 58.614 50.000 16.76 3.58 44.65 5.01
113 114 3.181475 GCTTCTGCTATAGTGTAGCACCA 60.181 47.826 16.76 4.83 44.65 4.17
114 115 4.615949 CTTCTGCTATAGTGTAGCACCAG 58.384 47.826 16.76 11.58 44.65 4.00
115 116 2.959030 TCTGCTATAGTGTAGCACCAGG 59.041 50.000 16.76 8.24 44.65 4.45
116 117 2.036475 CTGCTATAGTGTAGCACCAGGG 59.964 54.545 16.76 4.37 44.65 4.45
117 118 2.040178 GCTATAGTGTAGCACCAGGGT 58.960 52.381 13.52 0.00 40.14 4.34
118 119 2.434702 GCTATAGTGTAGCACCAGGGTT 59.565 50.000 13.52 0.00 40.14 4.11
119 120 3.492829 GCTATAGTGTAGCACCAGGGTTC 60.493 52.174 13.52 0.00 40.14 3.62
120 121 2.018355 TAGTGTAGCACCAGGGTTCA 57.982 50.000 0.00 0.00 34.49 3.18
121 122 0.687354 AGTGTAGCACCAGGGTTCAG 59.313 55.000 0.00 0.00 34.49 3.02
122 123 0.955919 GTGTAGCACCAGGGTTCAGC 60.956 60.000 0.00 0.00 0.00 4.26
123 124 1.377333 GTAGCACCAGGGTTCAGCC 60.377 63.158 0.00 0.00 0.00 4.85
124 125 1.538876 TAGCACCAGGGTTCAGCCT 60.539 57.895 0.00 0.00 37.43 4.58
125 126 1.133809 TAGCACCAGGGTTCAGCCTT 61.134 55.000 0.00 0.00 37.43 4.35
126 127 1.973812 GCACCAGGGTTCAGCCTTC 60.974 63.158 0.00 0.00 37.43 3.46
127 128 1.763770 CACCAGGGTTCAGCCTTCT 59.236 57.895 0.00 0.00 37.43 2.85
128 129 0.322008 CACCAGGGTTCAGCCTTCTC 60.322 60.000 0.00 0.00 37.43 2.87
129 130 1.301293 CCAGGGTTCAGCCTTCTCC 59.699 63.158 0.00 0.00 37.43 3.71
130 131 1.204113 CCAGGGTTCAGCCTTCTCCT 61.204 60.000 0.00 0.00 37.43 3.69
131 132 0.695347 CAGGGTTCAGCCTTCTCCTT 59.305 55.000 0.00 0.00 37.43 3.36
132 133 0.695347 AGGGTTCAGCCTTCTCCTTG 59.305 55.000 0.00 0.00 37.43 3.61
133 134 0.962855 GGGTTCAGCCTTCTCCTTGC 60.963 60.000 0.00 0.00 37.43 4.01
134 135 0.962855 GGTTCAGCCTTCTCCTTGCC 60.963 60.000 0.00 0.00 0.00 4.52
135 136 1.003355 TTCAGCCTTCTCCTTGCCG 60.003 57.895 0.00 0.00 0.00 5.69
136 137 1.480212 TTCAGCCTTCTCCTTGCCGA 61.480 55.000 0.00 0.00 0.00 5.54
137 138 1.449246 CAGCCTTCTCCTTGCCGAG 60.449 63.158 0.00 0.00 0.00 4.63
138 139 1.915769 AGCCTTCTCCTTGCCGAGT 60.916 57.895 0.00 0.00 0.00 4.18
139 140 1.003233 GCCTTCTCCTTGCCGAGTT 60.003 57.895 0.00 0.00 0.00 3.01
140 141 1.301677 GCCTTCTCCTTGCCGAGTTG 61.302 60.000 0.00 0.00 0.00 3.16
141 142 1.301677 CCTTCTCCTTGCCGAGTTGC 61.302 60.000 0.00 0.00 0.00 4.17
142 143 0.603707 CTTCTCCTTGCCGAGTTGCA 60.604 55.000 0.00 0.00 40.07 4.08
143 144 0.036732 TTCTCCTTGCCGAGTTGCAT 59.963 50.000 0.00 0.00 41.70 3.96
144 145 0.391661 TCTCCTTGCCGAGTTGCATC 60.392 55.000 0.00 0.00 41.70 3.91
145 146 0.674581 CTCCTTGCCGAGTTGCATCA 60.675 55.000 0.00 0.00 41.70 3.07
146 147 0.955428 TCCTTGCCGAGTTGCATCAC 60.955 55.000 0.00 0.00 41.70 3.06
147 148 1.503542 CTTGCCGAGTTGCATCACC 59.496 57.895 0.00 0.00 41.70 4.02
148 149 1.926511 CTTGCCGAGTTGCATCACCC 61.927 60.000 0.00 0.00 41.70 4.61
149 150 3.499737 GCCGAGTTGCATCACCCG 61.500 66.667 0.00 0.00 0.00 5.28
150 151 3.499737 CCGAGTTGCATCACCCGC 61.500 66.667 0.00 0.00 0.00 6.13
151 152 2.741985 CGAGTTGCATCACCCGCA 60.742 61.111 0.00 0.00 37.68 5.69
152 153 2.108514 CGAGTTGCATCACCCGCAT 61.109 57.895 0.00 0.00 39.58 4.73
153 154 1.723870 GAGTTGCATCACCCGCATC 59.276 57.895 0.00 0.00 39.58 3.91
154 155 2.040213 GAGTTGCATCACCCGCATCG 62.040 60.000 0.00 0.00 39.58 3.84
155 156 2.046411 TTGCATCACCCGCATCGT 60.046 55.556 0.00 0.00 39.58 3.73
156 157 2.397754 TTGCATCACCCGCATCGTG 61.398 57.895 0.00 0.00 39.58 4.35
157 158 2.819595 GCATCACCCGCATCGTGT 60.820 61.111 0.00 0.00 32.86 4.49
158 159 2.398554 GCATCACCCGCATCGTGTT 61.399 57.895 0.00 0.00 32.86 3.32
159 160 1.715585 CATCACCCGCATCGTGTTC 59.284 57.895 0.00 0.00 32.86 3.18
160 161 1.018752 CATCACCCGCATCGTGTTCA 61.019 55.000 0.00 0.00 32.86 3.18
161 162 0.321210 ATCACCCGCATCGTGTTCAA 60.321 50.000 0.00 0.00 32.86 2.69
162 163 0.321210 TCACCCGCATCGTGTTCAAT 60.321 50.000 0.00 0.00 32.86 2.57
163 164 0.521291 CACCCGCATCGTGTTCAATT 59.479 50.000 0.00 0.00 0.00 2.32
164 165 0.521291 ACCCGCATCGTGTTCAATTG 59.479 50.000 0.00 0.00 0.00 2.32
165 166 0.179166 CCCGCATCGTGTTCAATTGG 60.179 55.000 5.42 0.00 0.00 3.16
166 167 0.801872 CCGCATCGTGTTCAATTGGA 59.198 50.000 5.42 0.00 0.00 3.53
167 168 1.198867 CCGCATCGTGTTCAATTGGAA 59.801 47.619 5.42 0.00 0.00 3.53
168 169 2.351253 CCGCATCGTGTTCAATTGGAAA 60.351 45.455 5.42 0.00 37.23 3.13
169 170 2.910482 CGCATCGTGTTCAATTGGAAAG 59.090 45.455 5.42 0.00 37.23 2.62
170 171 3.609175 CGCATCGTGTTCAATTGGAAAGT 60.609 43.478 5.42 0.00 37.23 2.66
171 172 3.914364 GCATCGTGTTCAATTGGAAAGTC 59.086 43.478 5.42 0.00 37.23 3.01
172 173 4.475944 CATCGTGTTCAATTGGAAAGTCC 58.524 43.478 5.42 0.00 37.23 3.85
173 174 3.546724 TCGTGTTCAATTGGAAAGTCCA 58.453 40.909 5.42 0.00 46.61 4.02
185 186 4.810345 TGGAAAGTCCAACCCTTATTTGT 58.190 39.130 0.00 0.00 45.00 2.83
186 187 5.212745 TGGAAAGTCCAACCCTTATTTGTT 58.787 37.500 0.00 0.00 45.00 2.83
187 188 6.374588 TGGAAAGTCCAACCCTTATTTGTTA 58.625 36.000 0.00 0.00 45.00 2.41
188 189 6.265876 TGGAAAGTCCAACCCTTATTTGTTAC 59.734 38.462 0.00 0.00 45.00 2.50
189 190 6.492429 GGAAAGTCCAACCCTTATTTGTTACT 59.508 38.462 0.00 0.00 36.28 2.24
190 191 7.309012 GGAAAGTCCAACCCTTATTTGTTACTC 60.309 40.741 0.00 0.00 36.28 2.59
191 192 5.567430 AGTCCAACCCTTATTTGTTACTCC 58.433 41.667 0.00 0.00 0.00 3.85
192 193 4.393990 GTCCAACCCTTATTTGTTACTCCG 59.606 45.833 0.00 0.00 0.00 4.63
193 194 4.041938 TCCAACCCTTATTTGTTACTCCGT 59.958 41.667 0.00 0.00 0.00 4.69
194 195 4.763279 CCAACCCTTATTTGTTACTCCGTT 59.237 41.667 0.00 0.00 0.00 4.44
195 196 5.242171 CCAACCCTTATTTGTTACTCCGTTT 59.758 40.000 0.00 0.00 0.00 3.60
196 197 5.952526 ACCCTTATTTGTTACTCCGTTTG 57.047 39.130 0.00 0.00 0.00 2.93
197 198 5.379187 ACCCTTATTTGTTACTCCGTTTGT 58.621 37.500 0.00 0.00 0.00 2.83
198 199 5.239963 ACCCTTATTTGTTACTCCGTTTGTG 59.760 40.000 0.00 0.00 0.00 3.33
199 200 5.470777 CCCTTATTTGTTACTCCGTTTGTGA 59.529 40.000 0.00 0.00 0.00 3.58
200 201 6.348213 CCCTTATTTGTTACTCCGTTTGTGAG 60.348 42.308 0.00 0.00 35.92 3.51
201 202 6.348213 CCTTATTTGTTACTCCGTTTGTGAGG 60.348 42.308 0.00 0.00 34.06 3.86
202 203 3.823281 TTGTTACTCCGTTTGTGAGGA 57.177 42.857 0.00 0.00 34.06 3.71
205 206 4.285851 CTCCGTTTGTGAGGAGCC 57.714 61.111 0.00 0.00 46.23 4.70
206 207 1.376037 CTCCGTTTGTGAGGAGCCC 60.376 63.158 0.00 0.00 46.23 5.19
207 208 2.111999 CTCCGTTTGTGAGGAGCCCA 62.112 60.000 0.00 0.00 46.23 5.36
208 209 1.228124 CCGTTTGTGAGGAGCCCAA 60.228 57.895 0.00 0.00 0.00 4.12
209 210 0.821711 CCGTTTGTGAGGAGCCCAAA 60.822 55.000 0.00 0.00 0.00 3.28
210 211 1.247567 CGTTTGTGAGGAGCCCAAAT 58.752 50.000 0.00 0.00 31.44 2.32
211 212 1.613437 CGTTTGTGAGGAGCCCAAATT 59.387 47.619 0.00 0.00 31.44 1.82
212 213 2.607771 CGTTTGTGAGGAGCCCAAATTG 60.608 50.000 0.00 0.00 31.44 2.32
213 214 2.627699 GTTTGTGAGGAGCCCAAATTGA 59.372 45.455 0.00 0.00 31.44 2.57
214 215 1.909700 TGTGAGGAGCCCAAATTGAC 58.090 50.000 0.00 0.00 0.00 3.18
215 216 1.177401 GTGAGGAGCCCAAATTGACC 58.823 55.000 0.00 0.00 0.00 4.02
216 217 0.776810 TGAGGAGCCCAAATTGACCA 59.223 50.000 0.00 0.00 0.00 4.02
217 218 1.146774 TGAGGAGCCCAAATTGACCAA 59.853 47.619 0.00 0.00 0.00 3.67
218 219 2.225343 TGAGGAGCCCAAATTGACCAAT 60.225 45.455 0.00 0.00 0.00 3.16
219 220 3.011144 TGAGGAGCCCAAATTGACCAATA 59.989 43.478 0.00 0.00 0.00 1.90
220 221 4.218312 GAGGAGCCCAAATTGACCAATAT 58.782 43.478 0.00 0.00 0.00 1.28
221 222 4.623863 AGGAGCCCAAATTGACCAATATT 58.376 39.130 0.00 0.00 0.00 1.28
222 223 4.651045 AGGAGCCCAAATTGACCAATATTC 59.349 41.667 0.00 0.00 0.00 1.75
223 224 4.405358 GGAGCCCAAATTGACCAATATTCA 59.595 41.667 0.00 0.00 0.00 2.57
224 225 5.070847 GGAGCCCAAATTGACCAATATTCAT 59.929 40.000 0.00 0.00 0.00 2.57
225 226 6.267471 GGAGCCCAAATTGACCAATATTCATA 59.733 38.462 0.00 0.00 0.00 2.15
226 227 7.201992 GGAGCCCAAATTGACCAATATTCATAA 60.202 37.037 0.00 0.00 0.00 1.90
227 228 8.088463 AGCCCAAATTGACCAATATTCATAAA 57.912 30.769 0.00 0.00 0.00 1.40
228 229 8.206189 AGCCCAAATTGACCAATATTCATAAAG 58.794 33.333 0.00 0.00 0.00 1.85
229 230 8.203485 GCCCAAATTGACCAATATTCATAAAGA 58.797 33.333 0.00 0.00 0.00 2.52
230 231 9.533253 CCCAAATTGACCAATATTCATAAAGAC 57.467 33.333 0.00 0.00 0.00 3.01
231 232 9.236691 CCAAATTGACCAATATTCATAAAGACG 57.763 33.333 0.00 0.00 0.00 4.18
232 233 8.745837 CAAATTGACCAATATTCATAAAGACGC 58.254 33.333 0.00 0.00 0.00 5.19
233 234 6.371809 TTGACCAATATTCATAAAGACGCC 57.628 37.500 0.00 0.00 0.00 5.68
234 235 5.680619 TGACCAATATTCATAAAGACGCCT 58.319 37.500 0.00 0.00 0.00 5.52
235 236 6.119536 TGACCAATATTCATAAAGACGCCTT 58.880 36.000 0.00 0.00 0.00 4.35
236 237 6.601613 TGACCAATATTCATAAAGACGCCTTT 59.398 34.615 1.40 1.40 44.26 3.11
237 238 7.771361 TGACCAATATTCATAAAGACGCCTTTA 59.229 33.333 6.38 6.38 45.69 1.85
253 254 6.008364 CGCCTTTATTTTTGCGTCTTTATG 57.992 37.500 0.00 0.00 41.95 1.90
254 255 5.797934 CGCCTTTATTTTTGCGTCTTTATGA 59.202 36.000 0.00 0.00 41.95 2.15
255 256 6.306837 CGCCTTTATTTTTGCGTCTTTATGAA 59.693 34.615 0.00 0.00 41.95 2.57
256 257 7.009174 CGCCTTTATTTTTGCGTCTTTATGAAT 59.991 33.333 0.00 0.00 41.95 2.57
257 258 8.655970 GCCTTTATTTTTGCGTCTTTATGAATT 58.344 29.630 0.00 0.00 0.00 2.17
261 262 9.921637 TTATTTTTGCGTCTTTATGAATTTCCT 57.078 25.926 0.00 0.00 0.00 3.36
262 263 7.867445 TTTTTGCGTCTTTATGAATTTCCTC 57.133 32.000 0.00 0.00 0.00 3.71
263 264 4.857871 TGCGTCTTTATGAATTTCCTCG 57.142 40.909 0.00 0.00 0.00 4.63
264 265 3.063452 TGCGTCTTTATGAATTTCCTCGC 59.937 43.478 0.00 0.00 40.23 5.03
265 266 3.063452 GCGTCTTTATGAATTTCCTCGCA 59.937 43.478 0.00 0.00 39.72 5.10
266 267 4.260784 GCGTCTTTATGAATTTCCTCGCAT 60.261 41.667 0.00 0.00 39.72 4.73
267 268 5.435557 CGTCTTTATGAATTTCCTCGCATC 58.564 41.667 0.00 0.00 0.00 3.91
268 269 5.559035 CGTCTTTATGAATTTCCTCGCATCC 60.559 44.000 0.00 0.00 0.00 3.51
269 270 5.529060 GTCTTTATGAATTTCCTCGCATCCT 59.471 40.000 0.00 0.00 0.00 3.24
270 271 5.528690 TCTTTATGAATTTCCTCGCATCCTG 59.471 40.000 0.00 0.00 0.00 3.86
271 272 3.565764 ATGAATTTCCTCGCATCCTGA 57.434 42.857 0.00 0.00 0.00 3.86
272 273 3.348647 TGAATTTCCTCGCATCCTGAA 57.651 42.857 0.00 0.00 0.00 3.02
273 274 3.889815 TGAATTTCCTCGCATCCTGAAT 58.110 40.909 0.00 0.00 0.00 2.57
274 275 3.879295 TGAATTTCCTCGCATCCTGAATC 59.121 43.478 0.00 0.00 0.00 2.52
275 276 3.565764 ATTTCCTCGCATCCTGAATCA 57.434 42.857 0.00 0.00 0.00 2.57
276 277 3.565764 TTTCCTCGCATCCTGAATCAT 57.434 42.857 0.00 0.00 0.00 2.45
277 278 3.565764 TTCCTCGCATCCTGAATCATT 57.434 42.857 0.00 0.00 0.00 2.57
278 279 2.842457 TCCTCGCATCCTGAATCATTG 58.158 47.619 0.00 0.00 0.00 2.82
279 280 2.435437 TCCTCGCATCCTGAATCATTGA 59.565 45.455 0.00 0.00 0.00 2.57
280 281 3.072038 TCCTCGCATCCTGAATCATTGAT 59.928 43.478 0.00 0.00 0.00 2.57
281 282 4.284234 TCCTCGCATCCTGAATCATTGATA 59.716 41.667 0.00 0.00 0.00 2.15
282 283 4.630505 CCTCGCATCCTGAATCATTGATAG 59.369 45.833 0.00 0.00 0.00 2.08
283 284 4.572909 TCGCATCCTGAATCATTGATAGG 58.427 43.478 8.61 8.61 0.00 2.57
284 285 4.284234 TCGCATCCTGAATCATTGATAGGA 59.716 41.667 16.86 16.86 41.41 2.94
285 286 5.046087 TCGCATCCTGAATCATTGATAGGAT 60.046 40.000 19.12 19.12 46.38 3.24
286 287 6.155049 TCGCATCCTGAATCATTGATAGGATA 59.845 38.462 22.30 10.87 44.29 2.59
287 288 6.479331 CGCATCCTGAATCATTGATAGGATAG 59.521 42.308 22.30 18.32 44.29 2.08
288 289 6.766944 GCATCCTGAATCATTGATAGGATAGG 59.233 42.308 22.30 15.58 44.29 2.57
289 290 7.365384 GCATCCTGAATCATTGATAGGATAGGA 60.365 40.741 22.30 18.12 44.29 2.94
290 291 7.730672 TCCTGAATCATTGATAGGATAGGAG 57.269 40.000 12.33 0.00 28.98 3.69
291 292 6.155910 TCCTGAATCATTGATAGGATAGGAGC 59.844 42.308 12.33 0.00 28.98 4.70
292 293 6.070366 CCTGAATCATTGATAGGATAGGAGCA 60.070 42.308 9.12 0.00 26.70 4.26
293 294 7.365742 CCTGAATCATTGATAGGATAGGAGCAT 60.366 40.741 9.12 0.00 26.70 3.79
294 295 7.563020 TGAATCATTGATAGGATAGGAGCATC 58.437 38.462 0.00 0.00 0.00 3.91
308 309 3.584733 GAGCATCCTCCAACCCTTATT 57.415 47.619 0.00 0.00 31.68 1.40
309 310 3.903467 GAGCATCCTCCAACCCTTATTT 58.097 45.455 0.00 0.00 31.68 1.40
310 311 3.633986 GAGCATCCTCCAACCCTTATTTG 59.366 47.826 0.00 0.00 31.68 2.32
311 312 3.011708 AGCATCCTCCAACCCTTATTTGT 59.988 43.478 0.00 0.00 0.00 2.83
312 313 3.769300 GCATCCTCCAACCCTTATTTGTT 59.231 43.478 0.00 0.00 0.00 2.83
313 314 4.953579 GCATCCTCCAACCCTTATTTGTTA 59.046 41.667 0.00 0.00 0.00 2.41
314 315 5.163550 GCATCCTCCAACCCTTATTTGTTAC 60.164 44.000 0.00 0.00 0.00 2.50
315 316 5.853572 TCCTCCAACCCTTATTTGTTACT 57.146 39.130 0.00 0.00 0.00 2.24
316 317 5.812286 TCCTCCAACCCTTATTTGTTACTC 58.188 41.667 0.00 0.00 0.00 2.59
317 318 4.634443 CCTCCAACCCTTATTTGTTACTCG 59.366 45.833 0.00 0.00 0.00 4.18
318 319 5.484715 CTCCAACCCTTATTTGTTACTCGA 58.515 41.667 0.00 0.00 0.00 4.04
319 320 5.867330 TCCAACCCTTATTTGTTACTCGAA 58.133 37.500 0.00 0.00 0.00 3.71
320 321 6.478129 TCCAACCCTTATTTGTTACTCGAAT 58.522 36.000 0.00 0.00 34.77 3.34
321 322 6.373216 TCCAACCCTTATTTGTTACTCGAATG 59.627 38.462 0.00 0.00 32.85 2.67
322 323 6.404293 CCAACCCTTATTTGTTACTCGAATGG 60.404 42.308 0.00 0.00 32.85 3.16
323 324 4.638865 ACCCTTATTTGTTACTCGAATGGC 59.361 41.667 0.00 0.00 32.85 4.40
324 325 4.881850 CCCTTATTTGTTACTCGAATGGCT 59.118 41.667 0.00 0.00 32.85 4.75
325 326 6.053005 CCCTTATTTGTTACTCGAATGGCTA 58.947 40.000 0.00 0.00 32.85 3.93
326 327 6.540914 CCCTTATTTGTTACTCGAATGGCTAA 59.459 38.462 0.00 0.00 32.85 3.09
327 328 7.066525 CCCTTATTTGTTACTCGAATGGCTAAA 59.933 37.037 0.00 0.00 32.85 1.85
328 329 8.455682 CCTTATTTGTTACTCGAATGGCTAAAA 58.544 33.333 0.00 0.00 32.85 1.52
330 331 9.781834 TTATTTGTTACTCGAATGGCTAAAATG 57.218 29.630 0.00 0.00 32.85 2.32
331 332 5.229921 TGTTACTCGAATGGCTAAAATGC 57.770 39.130 0.00 0.00 0.00 3.56
332 333 4.201773 TGTTACTCGAATGGCTAAAATGCG 60.202 41.667 0.00 0.00 0.00 4.73
333 334 1.670811 ACTCGAATGGCTAAAATGCGG 59.329 47.619 0.00 0.00 0.00 5.69
334 335 1.002468 CTCGAATGGCTAAAATGCGGG 60.002 52.381 0.00 0.00 0.00 6.13
335 336 0.594796 CGAATGGCTAAAATGCGGGC 60.595 55.000 0.00 0.00 0.00 6.13
336 337 0.594796 GAATGGCTAAAATGCGGGCG 60.595 55.000 0.00 0.00 0.00 6.13
337 338 1.034838 AATGGCTAAAATGCGGGCGA 61.035 50.000 0.00 0.00 0.00 5.54
338 339 0.823356 ATGGCTAAAATGCGGGCGAT 60.823 50.000 0.00 0.00 0.00 4.58
339 340 1.008538 GGCTAAAATGCGGGCGATG 60.009 57.895 0.00 0.00 0.00 3.84
340 341 1.724582 GGCTAAAATGCGGGCGATGT 61.725 55.000 0.00 0.00 0.00 3.06
341 342 0.100503 GCTAAAATGCGGGCGATGTT 59.899 50.000 0.00 0.00 0.00 2.71
342 343 1.826327 CTAAAATGCGGGCGATGTTG 58.174 50.000 0.00 0.00 0.00 3.33
415 416 2.373169 TCAAGGAAGTGAGCCACTCAAT 59.627 45.455 8.09 0.00 44.62 2.57
786 798 3.447229 ACCCATGATTTCGTTTTCCCATC 59.553 43.478 0.00 0.00 0.00 3.51
2579 2597 1.003928 TGACAGCAATCATGACAGGCT 59.996 47.619 10.80 10.80 34.64 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.086785 ACGAGCTAAGTAGAAAGACTTTGT 57.913 37.500 4.85 3.74 40.22 2.83
1 2 6.150318 TGACGAGCTAAGTAGAAAGACTTTG 58.850 40.000 4.85 0.00 40.22 2.77
2 3 6.328641 TGACGAGCTAAGTAGAAAGACTTT 57.671 37.500 0.00 0.00 40.22 2.66
3 4 5.961396 TGACGAGCTAAGTAGAAAGACTT 57.039 39.130 0.00 0.00 42.35 3.01
4 5 5.945155 CTTGACGAGCTAAGTAGAAAGACT 58.055 41.667 0.00 0.00 0.00 3.24
21 22 3.066369 TGATAGCTACTTCGCTTGACG 57.934 47.619 0.00 0.00 41.30 4.35
22 23 3.240861 CGTTGATAGCTACTTCGCTTGAC 59.759 47.826 0.00 0.00 41.30 3.18
23 24 3.435566 CGTTGATAGCTACTTCGCTTGA 58.564 45.455 0.00 0.00 41.30 3.02
24 25 2.535984 CCGTTGATAGCTACTTCGCTTG 59.464 50.000 0.00 0.00 41.30 4.01
25 26 2.810650 CCGTTGATAGCTACTTCGCTT 58.189 47.619 0.00 0.00 41.30 4.68
26 27 1.536284 GCCGTTGATAGCTACTTCGCT 60.536 52.381 0.00 0.00 43.83 4.93
27 28 0.853419 GCCGTTGATAGCTACTTCGC 59.147 55.000 0.00 0.00 0.00 4.70
28 29 2.493713 AGCCGTTGATAGCTACTTCG 57.506 50.000 0.00 0.00 37.64 3.79
29 30 4.209495 GCTAAAGCCGTTGATAGCTACTTC 59.791 45.833 0.00 0.00 38.74 3.01
30 31 4.120589 GCTAAAGCCGTTGATAGCTACTT 58.879 43.478 0.00 0.00 38.74 2.24
31 32 3.132289 TGCTAAAGCCGTTGATAGCTACT 59.868 43.478 0.00 0.00 41.00 2.57
32 33 3.454375 TGCTAAAGCCGTTGATAGCTAC 58.546 45.455 0.00 0.00 41.00 3.58
33 34 3.812156 TGCTAAAGCCGTTGATAGCTA 57.188 42.857 0.00 0.00 41.00 3.32
34 35 2.691409 TGCTAAAGCCGTTGATAGCT 57.309 45.000 0.00 0.00 41.00 3.32
35 36 2.872245 TCATGCTAAAGCCGTTGATAGC 59.128 45.455 0.00 0.00 40.84 2.97
36 37 3.871006 TGTCATGCTAAAGCCGTTGATAG 59.129 43.478 0.00 0.00 41.18 2.08
37 38 3.867857 TGTCATGCTAAAGCCGTTGATA 58.132 40.909 0.00 0.00 41.18 2.15
38 39 2.710377 TGTCATGCTAAAGCCGTTGAT 58.290 42.857 0.00 0.00 41.18 2.57
39 40 2.177394 TGTCATGCTAAAGCCGTTGA 57.823 45.000 0.00 0.00 41.18 3.18
40 41 2.226437 AGTTGTCATGCTAAAGCCGTTG 59.774 45.455 0.00 0.00 41.18 4.10
41 42 2.504367 AGTTGTCATGCTAAAGCCGTT 58.496 42.857 0.00 0.00 41.18 4.44
42 43 2.185004 AGTTGTCATGCTAAAGCCGT 57.815 45.000 0.00 0.00 41.18 5.68
43 44 3.521560 TCTAGTTGTCATGCTAAAGCCG 58.478 45.455 0.00 0.00 41.18 5.52
44 45 4.695455 TGTTCTAGTTGTCATGCTAAAGCC 59.305 41.667 0.00 0.00 41.18 4.35
45 46 5.862924 TGTTCTAGTTGTCATGCTAAAGC 57.137 39.130 0.00 0.00 42.50 3.51
46 47 7.601073 TGATGTTCTAGTTGTCATGCTAAAG 57.399 36.000 0.00 0.00 0.00 1.85
47 48 7.361201 GCTTGATGTTCTAGTTGTCATGCTAAA 60.361 37.037 14.42 0.00 37.15 1.85
48 49 6.092670 GCTTGATGTTCTAGTTGTCATGCTAA 59.907 38.462 14.42 0.00 37.15 3.09
49 50 5.582269 GCTTGATGTTCTAGTTGTCATGCTA 59.418 40.000 14.42 0.00 37.15 3.49
50 51 4.394300 GCTTGATGTTCTAGTTGTCATGCT 59.606 41.667 14.42 0.00 37.15 3.79
51 52 4.437930 GGCTTGATGTTCTAGTTGTCATGC 60.438 45.833 13.85 13.85 38.49 4.06
52 53 4.696877 TGGCTTGATGTTCTAGTTGTCATG 59.303 41.667 0.00 0.00 0.00 3.07
53 54 4.910195 TGGCTTGATGTTCTAGTTGTCAT 58.090 39.130 0.00 0.00 0.00 3.06
54 55 4.350368 TGGCTTGATGTTCTAGTTGTCA 57.650 40.909 0.00 0.00 0.00 3.58
55 56 4.095483 CCATGGCTTGATGTTCTAGTTGTC 59.905 45.833 0.00 0.00 0.00 3.18
56 57 4.012374 CCATGGCTTGATGTTCTAGTTGT 58.988 43.478 0.00 0.00 0.00 3.32
57 58 4.012374 ACCATGGCTTGATGTTCTAGTTG 58.988 43.478 13.04 0.00 0.00 3.16
58 59 4.307032 ACCATGGCTTGATGTTCTAGTT 57.693 40.909 13.04 0.00 0.00 2.24
59 60 5.435686 TTACCATGGCTTGATGTTCTAGT 57.564 39.130 13.04 0.00 0.00 2.57
60 61 5.882557 AGTTTACCATGGCTTGATGTTCTAG 59.117 40.000 13.04 0.00 0.00 2.43
61 62 5.647658 CAGTTTACCATGGCTTGATGTTCTA 59.352 40.000 13.04 0.00 0.00 2.10
62 63 4.460382 CAGTTTACCATGGCTTGATGTTCT 59.540 41.667 13.04 0.00 0.00 3.01
63 64 4.737054 CAGTTTACCATGGCTTGATGTTC 58.263 43.478 13.04 0.00 0.00 3.18
64 65 3.056607 GCAGTTTACCATGGCTTGATGTT 60.057 43.478 13.04 0.00 0.00 2.71
65 66 2.493278 GCAGTTTACCATGGCTTGATGT 59.507 45.455 13.04 0.00 0.00 3.06
66 67 2.159198 GGCAGTTTACCATGGCTTGATG 60.159 50.000 13.04 7.07 38.83 3.07
67 68 2.102578 GGCAGTTTACCATGGCTTGAT 58.897 47.619 13.04 0.00 38.83 2.57
68 69 1.202989 TGGCAGTTTACCATGGCTTGA 60.203 47.619 13.04 0.00 42.16 3.02
69 70 1.255882 TGGCAGTTTACCATGGCTTG 58.744 50.000 13.04 4.45 42.16 4.01
70 71 2.008242 TTGGCAGTTTACCATGGCTT 57.992 45.000 13.04 0.00 42.16 4.35
71 72 1.895131 CTTTGGCAGTTTACCATGGCT 59.105 47.619 13.04 1.45 42.16 4.75
72 73 1.672737 GCTTTGGCAGTTTACCATGGC 60.673 52.381 13.04 0.00 42.01 4.40
73 74 1.895131 AGCTTTGGCAGTTTACCATGG 59.105 47.619 11.19 11.19 41.70 3.66
74 75 3.256631 AGAAGCTTTGGCAGTTTACCATG 59.743 43.478 0.00 0.00 41.70 3.66
75 76 3.256631 CAGAAGCTTTGGCAGTTTACCAT 59.743 43.478 0.00 0.00 41.70 3.55
76 77 2.622942 CAGAAGCTTTGGCAGTTTACCA 59.377 45.455 0.00 0.00 41.70 3.25
77 78 2.608016 GCAGAAGCTTTGGCAGTTTACC 60.608 50.000 15.82 0.00 41.70 2.85
78 79 2.666026 GCAGAAGCTTTGGCAGTTTAC 58.334 47.619 15.82 0.00 41.70 2.01
80 81 3.974222 GCAGAAGCTTTGGCAGTTT 57.026 47.368 15.82 0.00 41.70 2.66
96 97 2.039418 CCCTGGTGCTACACTATAGCA 58.961 52.381 4.53 4.53 47.00 3.49
97 98 2.040178 ACCCTGGTGCTACACTATAGC 58.960 52.381 0.00 0.00 40.76 2.97
98 99 3.704566 TGAACCCTGGTGCTACACTATAG 59.295 47.826 0.00 0.00 34.40 1.31
99 100 3.704566 CTGAACCCTGGTGCTACACTATA 59.295 47.826 0.00 0.00 34.40 1.31
100 101 2.501723 CTGAACCCTGGTGCTACACTAT 59.498 50.000 0.00 0.00 34.40 2.12
101 102 1.899814 CTGAACCCTGGTGCTACACTA 59.100 52.381 0.00 0.00 34.40 2.74
102 103 0.687354 CTGAACCCTGGTGCTACACT 59.313 55.000 0.00 0.00 34.40 3.55
103 104 0.955919 GCTGAACCCTGGTGCTACAC 60.956 60.000 0.00 0.00 0.00 2.90
104 105 1.374947 GCTGAACCCTGGTGCTACA 59.625 57.895 0.00 0.00 0.00 2.74
105 106 1.377333 GGCTGAACCCTGGTGCTAC 60.377 63.158 0.00 0.00 0.00 3.58
106 107 1.133809 AAGGCTGAACCCTGGTGCTA 61.134 55.000 0.00 0.00 40.58 3.49
107 108 2.417558 GAAGGCTGAACCCTGGTGCT 62.418 60.000 0.00 0.00 40.58 4.40
108 109 1.973812 GAAGGCTGAACCCTGGTGC 60.974 63.158 0.00 0.00 40.58 5.01
109 110 0.322008 GAGAAGGCTGAACCCTGGTG 60.322 60.000 0.00 0.00 40.58 4.17
110 111 1.492993 GGAGAAGGCTGAACCCTGGT 61.493 60.000 0.00 0.00 40.58 4.00
111 112 1.204113 AGGAGAAGGCTGAACCCTGG 61.204 60.000 0.00 0.00 40.58 4.45
112 113 0.695347 AAGGAGAAGGCTGAACCCTG 59.305 55.000 0.00 0.00 40.58 4.45
113 114 0.695347 CAAGGAGAAGGCTGAACCCT 59.305 55.000 0.00 0.00 40.58 4.34
114 115 0.962855 GCAAGGAGAAGGCTGAACCC 60.963 60.000 0.00 0.00 40.58 4.11
115 116 0.962855 GGCAAGGAGAAGGCTGAACC 60.963 60.000 0.00 0.00 39.61 3.62
116 117 1.301677 CGGCAAGGAGAAGGCTGAAC 61.302 60.000 0.00 0.00 35.98 3.18
117 118 1.003355 CGGCAAGGAGAAGGCTGAA 60.003 57.895 0.00 0.00 35.98 3.02
118 119 1.892819 CTCGGCAAGGAGAAGGCTGA 61.893 60.000 0.00 0.00 40.41 4.26
119 120 1.449246 CTCGGCAAGGAGAAGGCTG 60.449 63.158 0.00 0.00 36.08 4.85
120 121 1.484444 AACTCGGCAAGGAGAAGGCT 61.484 55.000 5.77 0.00 37.49 4.58
121 122 1.003233 AACTCGGCAAGGAGAAGGC 60.003 57.895 5.77 0.00 37.49 4.35
122 123 1.301677 GCAACTCGGCAAGGAGAAGG 61.302 60.000 5.77 0.00 37.49 3.46
123 124 0.603707 TGCAACTCGGCAAGGAGAAG 60.604 55.000 5.77 0.07 41.65 2.85
124 125 1.449782 TGCAACTCGGCAAGGAGAA 59.550 52.632 5.77 0.00 41.65 2.87
125 126 3.147132 TGCAACTCGGCAAGGAGA 58.853 55.556 5.77 0.00 41.65 3.71
132 133 3.499737 CGGGTGATGCAACTCGGC 61.500 66.667 2.76 0.00 40.43 5.54
133 134 3.499737 GCGGGTGATGCAACTCGG 61.500 66.667 12.47 2.78 44.36 4.63
134 135 2.040213 GATGCGGGTGATGCAACTCG 62.040 60.000 6.44 6.44 46.87 4.18
135 136 1.723870 GATGCGGGTGATGCAACTC 59.276 57.895 0.00 0.00 46.87 3.01
136 137 2.108514 CGATGCGGGTGATGCAACT 61.109 57.895 0.00 0.00 46.87 3.16
137 138 2.398554 ACGATGCGGGTGATGCAAC 61.399 57.895 0.00 0.00 46.87 4.17
138 139 2.046411 ACGATGCGGGTGATGCAA 60.046 55.556 0.00 0.00 46.87 4.08
139 140 3.604129 ACACGATGCGGGTGATGCA 62.604 57.895 8.37 0.00 43.84 3.96
140 141 2.309764 GAACACGATGCGGGTGATGC 62.310 60.000 8.37 0.00 45.17 3.91
141 142 1.018752 TGAACACGATGCGGGTGATG 61.019 55.000 8.37 0.00 45.17 3.07
142 143 0.321210 TTGAACACGATGCGGGTGAT 60.321 50.000 8.37 0.00 45.17 3.06
143 144 0.321210 ATTGAACACGATGCGGGTGA 60.321 50.000 8.37 0.00 45.17 4.02
144 145 0.521291 AATTGAACACGATGCGGGTG 59.479 50.000 0.00 0.66 45.17 4.61
146 147 0.179166 CCAATTGAACACGATGCGGG 60.179 55.000 7.12 0.00 35.82 6.13
147 148 0.801872 TCCAATTGAACACGATGCGG 59.198 50.000 7.12 0.00 0.00 5.69
148 149 2.610219 TTCCAATTGAACACGATGCG 57.390 45.000 7.12 0.00 0.00 4.73
149 150 3.900941 ACTTTCCAATTGAACACGATGC 58.099 40.909 7.12 0.00 31.05 3.91
150 151 4.023279 TGGACTTTCCAATTGAACACGATG 60.023 41.667 7.12 0.00 45.00 3.84
151 152 4.141287 TGGACTTTCCAATTGAACACGAT 58.859 39.130 7.12 0.00 45.00 3.73
152 153 3.546724 TGGACTTTCCAATTGAACACGA 58.453 40.909 7.12 0.00 45.00 4.35
153 154 3.980646 TGGACTTTCCAATTGAACACG 57.019 42.857 7.12 0.00 45.00 4.49
163 164 4.810345 ACAAATAAGGGTTGGACTTTCCA 58.190 39.130 0.00 0.00 46.61 3.53
164 165 5.801531 AACAAATAAGGGTTGGACTTTCC 57.198 39.130 0.00 0.00 36.96 3.13
165 166 7.309012 GGAGTAACAAATAAGGGTTGGACTTTC 60.309 40.741 0.00 0.00 30.70 2.62
166 167 6.492429 GGAGTAACAAATAAGGGTTGGACTTT 59.508 38.462 0.00 0.00 30.70 2.66
167 168 6.008331 GGAGTAACAAATAAGGGTTGGACTT 58.992 40.000 0.00 0.00 30.70 3.01
168 169 5.567430 GGAGTAACAAATAAGGGTTGGACT 58.433 41.667 0.00 0.00 32.24 3.85
169 170 4.393990 CGGAGTAACAAATAAGGGTTGGAC 59.606 45.833 0.00 0.00 0.00 4.02
170 171 4.041938 ACGGAGTAACAAATAAGGGTTGGA 59.958 41.667 0.00 0.00 41.94 3.53
171 172 4.329392 ACGGAGTAACAAATAAGGGTTGG 58.671 43.478 0.00 0.00 41.94 3.77
172 173 5.952526 AACGGAGTAACAAATAAGGGTTG 57.047 39.130 0.00 0.00 45.00 3.77
173 174 5.829391 ACAAACGGAGTAACAAATAAGGGTT 59.171 36.000 0.00 0.00 45.00 4.11
174 175 5.239963 CACAAACGGAGTAACAAATAAGGGT 59.760 40.000 0.00 0.00 45.00 4.34
175 176 5.470777 TCACAAACGGAGTAACAAATAAGGG 59.529 40.000 0.00 0.00 45.00 3.95
176 177 6.348213 CCTCACAAACGGAGTAACAAATAAGG 60.348 42.308 0.00 0.00 45.00 2.69
177 178 6.425721 TCCTCACAAACGGAGTAACAAATAAG 59.574 38.462 0.00 0.00 45.00 1.73
178 179 6.289834 TCCTCACAAACGGAGTAACAAATAA 58.710 36.000 0.00 0.00 45.00 1.40
179 180 5.856156 TCCTCACAAACGGAGTAACAAATA 58.144 37.500 0.00 0.00 45.00 1.40
180 181 4.710324 TCCTCACAAACGGAGTAACAAAT 58.290 39.130 0.00 0.00 45.00 2.32
181 182 4.124238 CTCCTCACAAACGGAGTAACAAA 58.876 43.478 0.00 0.00 45.00 2.83
182 183 3.724374 CTCCTCACAAACGGAGTAACAA 58.276 45.455 0.00 0.00 45.00 2.83
183 184 2.547218 GCTCCTCACAAACGGAGTAACA 60.547 50.000 7.12 0.00 45.00 2.41
184 185 2.067013 GCTCCTCACAAACGGAGTAAC 58.933 52.381 7.12 0.00 45.00 2.50
185 186 1.001633 GGCTCCTCACAAACGGAGTAA 59.998 52.381 7.12 0.00 45.00 2.24
186 187 0.606604 GGCTCCTCACAAACGGAGTA 59.393 55.000 7.12 0.00 45.00 2.59
189 190 1.701031 TTGGGCTCCTCACAAACGGA 61.701 55.000 0.00 0.00 0.00 4.69
190 191 0.821711 TTTGGGCTCCTCACAAACGG 60.822 55.000 0.00 0.00 0.00 4.44
191 192 1.247567 ATTTGGGCTCCTCACAAACG 58.752 50.000 0.00 0.00 36.98 3.60
192 193 2.627699 TCAATTTGGGCTCCTCACAAAC 59.372 45.455 0.00 0.00 36.98 2.93
193 194 2.627699 GTCAATTTGGGCTCCTCACAAA 59.372 45.455 0.00 0.00 38.33 2.83
194 195 2.238521 GTCAATTTGGGCTCCTCACAA 58.761 47.619 0.00 0.00 0.00 3.33
195 196 1.547675 GGTCAATTTGGGCTCCTCACA 60.548 52.381 0.00 0.00 0.00 3.58
196 197 1.177401 GGTCAATTTGGGCTCCTCAC 58.823 55.000 0.00 0.00 0.00 3.51
197 198 0.776810 TGGTCAATTTGGGCTCCTCA 59.223 50.000 0.00 0.00 0.00 3.86
198 199 1.923356 TTGGTCAATTTGGGCTCCTC 58.077 50.000 0.00 0.00 0.00 3.71
199 200 2.629017 ATTGGTCAATTTGGGCTCCT 57.371 45.000 0.00 0.00 0.00 3.69
200 201 4.405358 TGAATATTGGTCAATTTGGGCTCC 59.595 41.667 1.28 0.00 32.50 4.70
201 202 5.596836 TGAATATTGGTCAATTTGGGCTC 57.403 39.130 1.28 0.00 32.50 4.70
202 203 7.673641 TTATGAATATTGGTCAATTTGGGCT 57.326 32.000 1.28 0.00 32.50 5.19
203 204 8.203485 TCTTTATGAATATTGGTCAATTTGGGC 58.797 33.333 1.28 0.00 32.50 5.36
204 205 9.533253 GTCTTTATGAATATTGGTCAATTTGGG 57.467 33.333 1.28 0.00 32.50 4.12
205 206 9.236691 CGTCTTTATGAATATTGGTCAATTTGG 57.763 33.333 1.28 0.00 32.50 3.28
206 207 8.745837 GCGTCTTTATGAATATTGGTCAATTTG 58.254 33.333 1.28 0.00 32.50 2.32
207 208 7.920682 GGCGTCTTTATGAATATTGGTCAATTT 59.079 33.333 1.28 0.00 32.50 1.82
208 209 7.285401 AGGCGTCTTTATGAATATTGGTCAATT 59.715 33.333 1.28 0.00 32.50 2.32
209 210 6.772716 AGGCGTCTTTATGAATATTGGTCAAT 59.227 34.615 0.00 1.65 34.93 2.57
210 211 6.119536 AGGCGTCTTTATGAATATTGGTCAA 58.880 36.000 0.00 0.00 0.00 3.18
211 212 5.680619 AGGCGTCTTTATGAATATTGGTCA 58.319 37.500 0.00 0.00 0.00 4.02
212 213 6.619801 AAGGCGTCTTTATGAATATTGGTC 57.380 37.500 0.00 0.00 0.00 4.02
231 232 7.575332 TTCATAAAGACGCAAAAATAAAGGC 57.425 32.000 0.00 0.00 0.00 4.35
235 236 9.921637 AGGAAATTCATAAAGACGCAAAAATAA 57.078 25.926 0.00 0.00 0.00 1.40
236 237 9.567848 GAGGAAATTCATAAAGACGCAAAAATA 57.432 29.630 0.00 0.00 0.00 1.40
237 238 7.273381 CGAGGAAATTCATAAAGACGCAAAAAT 59.727 33.333 0.00 0.00 0.00 1.82
238 239 6.580791 CGAGGAAATTCATAAAGACGCAAAAA 59.419 34.615 0.00 0.00 0.00 1.94
239 240 6.083630 CGAGGAAATTCATAAAGACGCAAAA 58.916 36.000 0.00 0.00 0.00 2.44
240 241 5.627172 CGAGGAAATTCATAAAGACGCAAA 58.373 37.500 0.00 0.00 0.00 3.68
241 242 4.436852 GCGAGGAAATTCATAAAGACGCAA 60.437 41.667 0.00 0.00 41.50 4.85
242 243 3.063452 GCGAGGAAATTCATAAAGACGCA 59.937 43.478 0.00 0.00 41.50 5.24
243 244 3.063452 TGCGAGGAAATTCATAAAGACGC 59.937 43.478 0.00 0.00 42.05 5.19
244 245 4.857871 TGCGAGGAAATTCATAAAGACG 57.142 40.909 0.00 0.00 0.00 4.18
245 246 5.529060 AGGATGCGAGGAAATTCATAAAGAC 59.471 40.000 0.00 0.00 0.00 3.01
246 247 5.528690 CAGGATGCGAGGAAATTCATAAAGA 59.471 40.000 0.00 0.00 0.00 2.52
247 248 5.528690 TCAGGATGCGAGGAAATTCATAAAG 59.471 40.000 0.00 0.00 34.76 1.85
248 249 5.436175 TCAGGATGCGAGGAAATTCATAAA 58.564 37.500 0.00 0.00 34.76 1.40
249 250 5.034852 TCAGGATGCGAGGAAATTCATAA 57.965 39.130 0.00 0.00 34.76 1.90
250 251 4.687901 TCAGGATGCGAGGAAATTCATA 57.312 40.909 0.00 0.00 34.76 2.15
251 252 3.565764 TCAGGATGCGAGGAAATTCAT 57.434 42.857 0.00 0.00 34.76 2.57
252 253 3.348647 TTCAGGATGCGAGGAAATTCA 57.651 42.857 0.00 0.00 34.76 2.57
253 254 3.879295 TGATTCAGGATGCGAGGAAATTC 59.121 43.478 0.00 0.00 34.76 2.17
254 255 3.889815 TGATTCAGGATGCGAGGAAATT 58.110 40.909 0.00 0.00 34.76 1.82
255 256 3.565764 TGATTCAGGATGCGAGGAAAT 57.434 42.857 0.00 0.00 34.76 2.17
256 257 3.565764 ATGATTCAGGATGCGAGGAAA 57.434 42.857 0.00 0.00 34.76 3.13
257 258 3.118298 TCAATGATTCAGGATGCGAGGAA 60.118 43.478 0.00 0.00 34.76 3.36
258 259 2.435437 TCAATGATTCAGGATGCGAGGA 59.565 45.455 0.00 0.00 34.76 3.71
259 260 2.842457 TCAATGATTCAGGATGCGAGG 58.158 47.619 0.00 0.00 34.76 4.63
260 261 4.630505 CCTATCAATGATTCAGGATGCGAG 59.369 45.833 6.24 4.24 34.76 5.03
261 262 4.284234 TCCTATCAATGATTCAGGATGCGA 59.716 41.667 9.99 6.12 34.76 5.10
262 263 4.572909 TCCTATCAATGATTCAGGATGCG 58.427 43.478 9.99 5.27 34.76 4.73
263 264 6.766944 CCTATCCTATCAATGATTCAGGATGC 59.233 42.308 26.41 0.00 44.10 3.91
264 265 8.087303 TCCTATCCTATCAATGATTCAGGATG 57.913 38.462 26.41 18.90 44.10 3.51
265 266 7.147514 GCTCCTATCCTATCAATGATTCAGGAT 60.148 40.741 23.55 23.55 45.75 3.24
266 267 6.155910 GCTCCTATCCTATCAATGATTCAGGA 59.844 42.308 15.01 15.01 39.63 3.86
267 268 6.070366 TGCTCCTATCCTATCAATGATTCAGG 60.070 42.308 0.00 3.24 0.00 3.86
268 269 6.944096 TGCTCCTATCCTATCAATGATTCAG 58.056 40.000 0.00 0.00 0.00 3.02
269 270 6.940430 TGCTCCTATCCTATCAATGATTCA 57.060 37.500 0.00 0.00 0.00 2.57
270 271 6.991531 GGATGCTCCTATCCTATCAATGATTC 59.008 42.308 0.00 0.00 42.73 2.52
271 272 6.897986 GGATGCTCCTATCCTATCAATGATT 58.102 40.000 0.00 0.00 42.73 2.57
272 273 6.497624 GGATGCTCCTATCCTATCAATGAT 57.502 41.667 0.00 0.00 42.73 2.45
273 274 5.946942 GGATGCTCCTATCCTATCAATGA 57.053 43.478 0.00 0.00 42.73 2.57
287 288 1.213296 TAAGGGTTGGAGGATGCTCC 58.787 55.000 25.49 25.49 43.60 4.70
288 289 3.584733 AATAAGGGTTGGAGGATGCTC 57.415 47.619 5.52 5.52 0.00 4.26
289 290 3.011708 ACAAATAAGGGTTGGAGGATGCT 59.988 43.478 0.00 0.00 0.00 3.79
290 291 3.365472 ACAAATAAGGGTTGGAGGATGC 58.635 45.455 0.00 0.00 0.00 3.91
291 292 6.187682 AGTAACAAATAAGGGTTGGAGGATG 58.812 40.000 0.00 0.00 0.00 3.51
292 293 6.402981 AGTAACAAATAAGGGTTGGAGGAT 57.597 37.500 0.00 0.00 0.00 3.24
293 294 5.570034 CGAGTAACAAATAAGGGTTGGAGGA 60.570 44.000 0.00 0.00 0.00 3.71
294 295 4.634443 CGAGTAACAAATAAGGGTTGGAGG 59.366 45.833 0.00 0.00 0.00 4.30
295 296 5.484715 TCGAGTAACAAATAAGGGTTGGAG 58.515 41.667 0.00 0.00 0.00 3.86
296 297 5.486735 TCGAGTAACAAATAAGGGTTGGA 57.513 39.130 0.00 0.00 0.00 3.53
297 298 6.404293 CCATTCGAGTAACAAATAAGGGTTGG 60.404 42.308 0.00 0.00 0.00 3.77
298 299 6.551736 CCATTCGAGTAACAAATAAGGGTTG 58.448 40.000 0.00 0.00 0.00 3.77
299 300 5.124936 GCCATTCGAGTAACAAATAAGGGTT 59.875 40.000 0.00 0.00 0.00 4.11
300 301 4.638865 GCCATTCGAGTAACAAATAAGGGT 59.361 41.667 0.00 0.00 0.00 4.34
301 302 4.881850 AGCCATTCGAGTAACAAATAAGGG 59.118 41.667 0.00 0.00 0.00 3.95
302 303 7.548196 TTAGCCATTCGAGTAACAAATAAGG 57.452 36.000 0.00 0.00 0.00 2.69
304 305 9.781834 CATTTTAGCCATTCGAGTAACAAATAA 57.218 29.630 0.00 0.00 0.00 1.40
305 306 7.913297 GCATTTTAGCCATTCGAGTAACAAATA 59.087 33.333 0.00 0.00 0.00 1.40
306 307 6.751888 GCATTTTAGCCATTCGAGTAACAAAT 59.248 34.615 0.00 0.00 0.00 2.32
307 308 6.090129 GCATTTTAGCCATTCGAGTAACAAA 58.910 36.000 0.00 0.00 0.00 2.83
308 309 5.636837 GCATTTTAGCCATTCGAGTAACAA 58.363 37.500 0.00 0.00 0.00 2.83
309 310 4.201773 CGCATTTTAGCCATTCGAGTAACA 60.202 41.667 0.00 0.00 0.00 2.41
310 311 4.271687 CGCATTTTAGCCATTCGAGTAAC 58.728 43.478 0.00 0.00 0.00 2.50
311 312 3.311322 CCGCATTTTAGCCATTCGAGTAA 59.689 43.478 0.00 0.00 0.00 2.24
312 313 2.869801 CCGCATTTTAGCCATTCGAGTA 59.130 45.455 0.00 0.00 0.00 2.59
313 314 1.670811 CCGCATTTTAGCCATTCGAGT 59.329 47.619 0.00 0.00 0.00 4.18
314 315 1.002468 CCCGCATTTTAGCCATTCGAG 60.002 52.381 0.00 0.00 0.00 4.04
315 316 1.021202 CCCGCATTTTAGCCATTCGA 58.979 50.000 0.00 0.00 0.00 3.71
316 317 0.594796 GCCCGCATTTTAGCCATTCG 60.595 55.000 0.00 0.00 0.00 3.34
317 318 0.594796 CGCCCGCATTTTAGCCATTC 60.595 55.000 0.00 0.00 0.00 2.67
318 319 1.034838 TCGCCCGCATTTTAGCCATT 61.035 50.000 0.00 0.00 0.00 3.16
319 320 0.823356 ATCGCCCGCATTTTAGCCAT 60.823 50.000 0.00 0.00 0.00 4.40
320 321 1.453015 ATCGCCCGCATTTTAGCCA 60.453 52.632 0.00 0.00 0.00 4.75
321 322 1.008538 CATCGCCCGCATTTTAGCC 60.009 57.895 0.00 0.00 0.00 3.93
322 323 0.100503 AACATCGCCCGCATTTTAGC 59.899 50.000 0.00 0.00 0.00 3.09
323 324 1.533756 CCAACATCGCCCGCATTTTAG 60.534 52.381 0.00 0.00 0.00 1.85
324 325 0.453793 CCAACATCGCCCGCATTTTA 59.546 50.000 0.00 0.00 0.00 1.52
325 326 1.215117 CCAACATCGCCCGCATTTT 59.785 52.632 0.00 0.00 0.00 1.82
326 327 1.656818 CTCCAACATCGCCCGCATTT 61.657 55.000 0.00 0.00 0.00 2.32
327 328 2.045438 TCCAACATCGCCCGCATT 60.045 55.556 0.00 0.00 0.00 3.56
328 329 2.329539 ATCTCCAACATCGCCCGCAT 62.330 55.000 0.00 0.00 0.00 4.73
329 330 2.923426 GATCTCCAACATCGCCCGCA 62.923 60.000 0.00 0.00 0.00 5.69
330 331 2.203070 ATCTCCAACATCGCCCGC 60.203 61.111 0.00 0.00 0.00 6.13
331 332 0.250038 ATGATCTCCAACATCGCCCG 60.250 55.000 0.00 0.00 0.00 6.13
332 333 2.839486 TATGATCTCCAACATCGCCC 57.161 50.000 0.00 0.00 0.00 6.13
333 334 3.005554 CCATATGATCTCCAACATCGCC 58.994 50.000 3.65 0.00 0.00 5.54
334 335 3.005554 CCCATATGATCTCCAACATCGC 58.994 50.000 3.65 0.00 0.00 4.58
335 336 4.248859 GACCCATATGATCTCCAACATCG 58.751 47.826 3.65 0.00 0.00 3.84
336 337 5.233083 TGACCCATATGATCTCCAACATC 57.767 43.478 3.65 0.00 0.00 3.06
337 338 5.103982 TGTTGACCCATATGATCTCCAACAT 60.104 40.000 3.65 0.00 38.05 2.71
338 339 4.227073 TGTTGACCCATATGATCTCCAACA 59.773 41.667 3.65 12.92 39.85 3.33
339 340 4.780815 TGTTGACCCATATGATCTCCAAC 58.219 43.478 3.65 10.78 34.83 3.77
340 341 5.449297 TTGTTGACCCATATGATCTCCAA 57.551 39.130 3.65 6.14 0.00 3.53
341 342 5.651612 ATTGTTGACCCATATGATCTCCA 57.348 39.130 3.65 0.64 0.00 3.86
342 343 6.302269 AGAATTGTTGACCCATATGATCTCC 58.698 40.000 3.65 0.00 0.00 3.71
415 416 1.323412 GAGAATCCGCTAGGCTGAGA 58.677 55.000 0.00 0.00 37.47 3.27
786 798 2.581637 TCGTCTTCGTCTGATTTGTCG 58.418 47.619 0.00 0.00 38.33 4.35
1092 1110 1.741145 ACGAATAACCAACCCGCAATC 59.259 47.619 0.00 0.00 0.00 2.67
1890 1908 0.527817 GGAGCGGTAGGTCGACATTG 60.528 60.000 18.91 5.19 45.26 2.82
2579 2597 4.357142 CTTTCTCTAACGCTAATACCGCA 58.643 43.478 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.