Multiple sequence alignment - TraesCS3A01G268400

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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 TraesCS3A01G268400 chr3A 100.000 2620 0 0 1 2620 494044495 494047114 0.000000e+00 4839.0
1 TraesCS3A01G268400 chr3A 85.912 362 28 8 1 341 49327027 49327386 5.330000e-97 364.0
2 TraesCS3A01G268400 chr3A 90.805 174 16 0 2146 2319 744921119 744920946 1.570000e-57 233.0
3 TraesCS3A01G268400 chr3B 91.966 2004 92 21 660 2618 486817594 486819573 0.000000e+00 2745.0
4 TraesCS3A01G268400 chr3B 87.963 216 9 8 338 538 486814753 486814966 3.370000e-59 239.0
5 TraesCS3A01G268400 chr3B 92.254 142 5 2 534 670 486815252 486815392 2.060000e-46 196.0
6 TraesCS3A01G268400 chr3D 90.031 1284 69 23 898 2155 372632531 372633781 0.000000e+00 1607.0
7 TraesCS3A01G268400 chr3D 94.043 554 22 9 338 885 372631936 372632484 0.000000e+00 830.0
8 TraesCS3A01G268400 chr3D 87.288 354 23 6 1 332 24569355 24569708 4.090000e-103 385.0
9 TraesCS3A01G268400 chr3D 85.515 359 29 2 1 337 452487427 452487070 1.150000e-93 353.0
10 TraesCS3A01G268400 chr3D 77.113 284 50 10 2324 2606 217654516 217654785 1.620000e-32 150.0
11 TraesCS3A01G268400 chr4A 88.563 341 30 4 1 332 137522881 137523221 3.140000e-109 405.0
12 TraesCS3A01G268400 chr4A 81.176 340 55 6 3 335 667262638 667262301 5.560000e-67 265.0
13 TraesCS3A01G268400 chr4A 92.121 165 13 0 2154 2318 195972593 195972429 1.570000e-57 233.0
14 TraesCS3A01G268400 chrUn 87.571 354 22 6 1 332 136394985 136395338 8.790000e-105 390.0
15 TraesCS3A01G268400 chrUn 92.169 166 13 0 2154 2319 280766298 280766133 4.360000e-58 235.0
16 TraesCS3A01G268400 chr5B 87.395 357 23 6 1 335 710235979 710235623 8.790000e-105 390.0
17 TraesCS3A01G268400 chr5B 92.216 167 13 0 2153 2319 680746848 680747014 1.210000e-58 237.0
18 TraesCS3A01G268400 chr5B 92.121 165 13 0 2154 2318 122835741 122835905 1.570000e-57 233.0
19 TraesCS3A01G268400 chr5B 82.828 198 25 5 2429 2617 136005996 136005799 4.480000e-38 169.0
20 TraesCS3A01G268400 chr6B 87.288 354 23 1 1 332 61211835 61212188 4.090000e-103 385.0
21 TraesCS3A01G268400 chr6B 85.552 353 29 1 12 342 688621168 688620816 1.490000e-92 350.0
22 TraesCS3A01G268400 chr6D 86.835 357 25 1 1 335 454064495 454064139 1.900000e-101 379.0
23 TraesCS3A01G268400 chr6D 86.076 79 7 4 2497 2573 472223810 472223734 6.010000e-12 82.4
24 TraesCS3A01G268400 chr7D 86.723 354 25 6 1 332 475155042 475155395 8.850000e-100 374.0
25 TraesCS3A01G268400 chr1B 86.351 359 24 4 1 337 192141805 192141450 4.120000e-98 368.0
26 TraesCS3A01G268400 chr5A 84.457 341 44 7 1 339 687226076 687226409 6.990000e-86 327.0
27 TraesCS3A01G268400 chr5A 81.272 283 38 13 2343 2618 338443118 338442844 5.680000e-52 215.0
28 TraesCS3A01G268400 chr1A 83.067 313 40 5 33 341 522959188 522959491 3.320000e-69 272.0
29 TraesCS3A01G268400 chr6A 92.771 166 12 0 2153 2318 598156400 598156565 9.370000e-60 241.0
30 TraesCS3A01G268400 chr5D 92.727 165 12 0 2154 2318 464930195 464930359 3.370000e-59 239.0
31 TraesCS3A01G268400 chr4D 83.094 278 31 13 2344 2618 470201547 470201283 3.370000e-59 239.0
32 TraesCS3A01G268400 chr4D 87.603 121 3 6 2498 2618 478233558 478233666 2.120000e-26 130.0
33 TraesCS3A01G268400 chr2B 92.121 165 13 0 2154 2318 181360040 181359876 1.570000e-57 233.0
34 TraesCS3A01G268400 chr2D 82.673 202 27 7 2419 2618 540828469 540828274 3.470000e-39 172.0
35 TraesCS3A01G268400 chr4B 90.083 121 5 4 2498 2618 80958023 80957910 1.620000e-32 150.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G268400 chr3A 494044495 494047114 2619 False 4839.0 4839 100.000000 1 2620 1 chr3A.!!$F2 2619
1 TraesCS3A01G268400 chr3B 486814753 486819573 4820 False 1060.0 2745 90.727667 338 2618 3 chr3B.!!$F1 2280
2 TraesCS3A01G268400 chr3D 372631936 372633781 1845 False 1218.5 1607 92.037000 338 2155 2 chr3D.!!$F3 1817

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
232 233 0.038159 GCTCCAGTGCTTGTAGTCGT 60.038 55.0 0.0 0.0 0.0 4.34 F
234 235 0.240145 TCCAGTGCTTGTAGTCGTCG 59.760 55.0 0.0 0.0 0.0 5.12 F
245 246 0.251354 TAGTCGTCGCTAGGTGGTCT 59.749 55.0 0.0 0.0 0.0 3.85 F
247 248 0.376502 GTCGTCGCTAGGTGGTCTAC 59.623 60.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 3796 0.596341 CATGGACACACACGACACGA 60.596 55.0 0.00 0.00 0.0 4.35 R
1250 3821 0.846401 CGTATGCCATCGACTTGACG 59.154 55.0 0.00 0.00 0.0 4.35 R
1388 3959 2.223803 TCTTCTTCTTCTCCTCCGCT 57.776 50.0 0.00 0.00 0.0 5.52 R
2009 4620 2.346741 GCATATGAAAGTTCGAGCGTCG 60.347 50.0 6.97 1.67 42.1 5.12 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 4.668118 TCCGGTCGGCGTTTGTCC 62.668 66.667 6.85 2.47 34.68 4.02
18 19 4.675029 CCGGTCGGCGTTTGTCCT 62.675 66.667 6.85 0.00 0.00 3.85
19 20 3.110178 CGGTCGGCGTTTGTCCTC 61.110 66.667 6.85 0.00 0.00 3.71
20 21 3.110178 GGTCGGCGTTTGTCCTCG 61.110 66.667 6.85 0.00 0.00 4.63
21 22 3.110178 GTCGGCGTTTGTCCTCGG 61.110 66.667 6.85 0.00 0.00 4.63
22 23 3.608662 TCGGCGTTTGTCCTCGGT 61.609 61.111 6.85 0.00 0.00 4.69
23 24 3.411351 CGGCGTTTGTCCTCGGTG 61.411 66.667 0.00 0.00 0.00 4.94
24 25 3.047877 GGCGTTTGTCCTCGGTGG 61.048 66.667 0.00 0.00 37.10 4.61
25 26 2.029964 GCGTTTGTCCTCGGTGGA 59.970 61.111 0.00 0.00 43.86 4.02
33 34 2.887790 TCCTCGGTGGATCTGACTG 58.112 57.895 0.00 0.00 40.56 3.51
34 35 0.684479 TCCTCGGTGGATCTGACTGG 60.684 60.000 0.00 0.00 40.56 4.00
35 36 0.684479 CCTCGGTGGATCTGACTGGA 60.684 60.000 0.00 0.00 38.35 3.86
36 37 1.407936 CTCGGTGGATCTGACTGGAT 58.592 55.000 0.00 0.00 0.00 3.41
37 38 1.339610 CTCGGTGGATCTGACTGGATC 59.660 57.143 0.00 0.00 40.78 3.36
50 51 1.914634 CTGGATCCAGTCTTCGTTCG 58.085 55.000 30.55 4.78 39.10 3.95
51 52 1.202582 CTGGATCCAGTCTTCGTTCGT 59.797 52.381 30.55 0.00 39.10 3.85
52 53 1.201647 TGGATCCAGTCTTCGTTCGTC 59.798 52.381 11.44 0.00 0.00 4.20
53 54 1.473278 GGATCCAGTCTTCGTTCGTCT 59.527 52.381 6.95 0.00 0.00 4.18
54 55 2.520979 GATCCAGTCTTCGTTCGTCTG 58.479 52.381 0.00 0.00 0.00 3.51
55 56 0.039437 TCCAGTCTTCGTTCGTCTGC 60.039 55.000 0.00 0.00 0.00 4.26
56 57 1.337817 CCAGTCTTCGTTCGTCTGCG 61.338 60.000 0.00 0.00 39.92 5.18
57 58 0.660595 CAGTCTTCGTTCGTCTGCGT 60.661 55.000 0.00 0.00 39.49 5.24
58 59 0.385723 AGTCTTCGTTCGTCTGCGTC 60.386 55.000 0.00 0.00 39.49 5.19
59 60 0.385723 GTCTTCGTTCGTCTGCGTCT 60.386 55.000 0.00 0.00 39.49 4.18
60 61 0.385598 TCTTCGTTCGTCTGCGTCTG 60.386 55.000 0.00 0.00 39.49 3.51
61 62 0.660595 CTTCGTTCGTCTGCGTCTGT 60.661 55.000 0.00 0.00 39.49 3.41
62 63 0.933047 TTCGTTCGTCTGCGTCTGTG 60.933 55.000 0.00 0.00 39.49 3.66
63 64 1.657487 CGTTCGTCTGCGTCTGTGT 60.657 57.895 0.00 0.00 39.49 3.72
64 65 1.846648 GTTCGTCTGCGTCTGTGTG 59.153 57.895 0.00 0.00 39.49 3.82
65 66 0.870307 GTTCGTCTGCGTCTGTGTGT 60.870 55.000 0.00 0.00 39.49 3.72
66 67 0.594028 TTCGTCTGCGTCTGTGTGTC 60.594 55.000 0.00 0.00 39.49 3.67
67 68 1.008424 CGTCTGCGTCTGTGTGTCT 60.008 57.895 0.00 0.00 0.00 3.41
68 69 1.271446 CGTCTGCGTCTGTGTGTCTG 61.271 60.000 0.00 0.00 0.00 3.51
69 70 1.300156 TCTGCGTCTGTGTGTCTGC 60.300 57.895 0.00 0.00 0.00 4.26
70 71 1.592400 CTGCGTCTGTGTGTCTGCA 60.592 57.895 0.00 0.00 0.00 4.41
71 72 1.554891 CTGCGTCTGTGTGTCTGCAG 61.555 60.000 7.63 7.63 43.08 4.41
72 73 2.947890 GCGTCTGTGTGTCTGCAGC 61.948 63.158 9.47 4.92 33.09 5.25
73 74 1.300465 CGTCTGTGTGTCTGCAGCT 60.300 57.895 9.47 0.00 33.09 4.24
74 75 1.280886 CGTCTGTGTGTCTGCAGCTC 61.281 60.000 9.47 5.29 33.09 4.09
75 76 1.006922 TCTGTGTGTCTGCAGCTCG 60.007 57.895 9.47 0.00 33.09 5.03
76 77 2.662857 TGTGTGTCTGCAGCTCGC 60.663 61.111 9.47 11.67 42.89 5.03
85 86 3.267860 GCAGCTCGCATCCTTCCG 61.268 66.667 3.64 0.00 41.79 4.30
86 87 2.587194 CAGCTCGCATCCTTCCGG 60.587 66.667 0.00 0.00 0.00 5.14
87 88 3.077556 AGCTCGCATCCTTCCGGT 61.078 61.111 0.00 0.00 0.00 5.28
88 89 2.586357 GCTCGCATCCTTCCGGTC 60.586 66.667 0.00 0.00 0.00 4.79
89 90 3.082579 GCTCGCATCCTTCCGGTCT 62.083 63.158 0.00 0.00 0.00 3.85
90 91 1.735376 GCTCGCATCCTTCCGGTCTA 61.735 60.000 0.00 0.00 0.00 2.59
91 92 0.962489 CTCGCATCCTTCCGGTCTAT 59.038 55.000 0.00 0.00 0.00 1.98
92 93 0.673985 TCGCATCCTTCCGGTCTATG 59.326 55.000 0.00 2.93 0.00 2.23
93 94 0.946221 CGCATCCTTCCGGTCTATGC 60.946 60.000 17.80 17.80 39.59 3.14
94 95 0.394565 GCATCCTTCCGGTCTATGCT 59.605 55.000 19.42 0.00 39.80 3.79
95 96 1.202698 GCATCCTTCCGGTCTATGCTT 60.203 52.381 19.42 0.00 39.80 3.91
96 97 2.760374 CATCCTTCCGGTCTATGCTTC 58.240 52.381 0.00 0.00 0.00 3.86
97 98 2.160721 TCCTTCCGGTCTATGCTTCT 57.839 50.000 0.00 0.00 0.00 2.85
98 99 2.032620 TCCTTCCGGTCTATGCTTCTC 58.967 52.381 0.00 0.00 0.00 2.87
99 100 2.035632 CCTTCCGGTCTATGCTTCTCT 58.964 52.381 0.00 0.00 0.00 3.10
100 101 2.432510 CCTTCCGGTCTATGCTTCTCTT 59.567 50.000 0.00 0.00 0.00 2.85
101 102 3.491792 CCTTCCGGTCTATGCTTCTCTTC 60.492 52.174 0.00 0.00 0.00 2.87
102 103 2.735151 TCCGGTCTATGCTTCTCTTCA 58.265 47.619 0.00 0.00 0.00 3.02
103 104 3.300388 TCCGGTCTATGCTTCTCTTCAT 58.700 45.455 0.00 0.00 0.00 2.57
104 105 3.319405 TCCGGTCTATGCTTCTCTTCATC 59.681 47.826 0.00 0.00 0.00 2.92
105 106 3.304257 CGGTCTATGCTTCTCTTCATCG 58.696 50.000 0.00 0.00 0.00 3.84
106 107 3.648009 GGTCTATGCTTCTCTTCATCGG 58.352 50.000 0.00 0.00 0.00 4.18
107 108 3.056304 GTCTATGCTTCTCTTCATCGGC 58.944 50.000 0.00 0.00 0.00 5.54
108 109 2.057316 CTATGCTTCTCTTCATCGGCG 58.943 52.381 0.00 0.00 0.00 6.46
109 110 0.531532 ATGCTTCTCTTCATCGGCGG 60.532 55.000 7.21 0.00 0.00 6.13
110 111 2.529619 GCTTCTCTTCATCGGCGGC 61.530 63.158 7.21 0.00 0.00 6.53
111 112 2.202743 TTCTCTTCATCGGCGGCG 60.203 61.111 27.15 27.15 0.00 6.46
112 113 3.716539 TTCTCTTCATCGGCGGCGG 62.717 63.158 31.73 16.54 0.00 6.13
113 114 4.514577 CTCTTCATCGGCGGCGGT 62.515 66.667 31.73 23.77 0.00 5.68
114 115 4.077184 TCTTCATCGGCGGCGGTT 62.077 61.111 31.73 16.58 0.00 4.44
115 116 3.864686 CTTCATCGGCGGCGGTTG 61.865 66.667 31.73 26.46 0.00 3.77
124 125 3.726517 CGGCGGTTGCTGTTCTGG 61.727 66.667 0.00 0.00 42.79 3.86
125 126 2.594592 GGCGGTTGCTGTTCTGGT 60.595 61.111 0.00 0.00 42.25 4.00
126 127 2.639286 GCGGTTGCTGTTCTGGTG 59.361 61.111 0.00 0.00 38.39 4.17
127 128 2.639286 CGGTTGCTGTTCTGGTGC 59.361 61.111 0.00 0.00 0.00 5.01
128 129 2.186160 CGGTTGCTGTTCTGGTGCA 61.186 57.895 0.00 0.00 34.69 4.57
129 130 1.360192 GGTTGCTGTTCTGGTGCAC 59.640 57.895 8.80 8.80 36.37 4.57
130 131 1.009675 GTTGCTGTTCTGGTGCACG 60.010 57.895 11.45 0.00 36.37 5.34
131 132 1.153269 TTGCTGTTCTGGTGCACGA 60.153 52.632 11.45 5.97 36.37 4.35
132 133 1.436195 TTGCTGTTCTGGTGCACGAC 61.436 55.000 11.45 7.48 36.37 4.34
133 134 2.943345 GCTGTTCTGGTGCACGACG 61.943 63.158 11.45 1.33 0.00 5.12
134 135 1.299850 CTGTTCTGGTGCACGACGA 60.300 57.895 11.45 3.96 0.00 4.20
135 136 1.548973 CTGTTCTGGTGCACGACGAC 61.549 60.000 11.45 7.84 0.00 4.34
136 137 1.299926 GTTCTGGTGCACGACGACT 60.300 57.895 11.45 0.00 0.00 4.18
137 138 0.874607 GTTCTGGTGCACGACGACTT 60.875 55.000 11.45 0.00 0.00 3.01
138 139 0.179094 TTCTGGTGCACGACGACTTT 60.179 50.000 11.45 0.00 0.00 2.66
139 140 0.596600 TCTGGTGCACGACGACTTTC 60.597 55.000 11.45 0.00 0.00 2.62
140 141 1.557443 CTGGTGCACGACGACTTTCC 61.557 60.000 11.45 0.00 0.00 3.13
141 142 2.654912 GGTGCACGACGACTTTCCG 61.655 63.158 11.45 0.00 0.00 4.30
142 143 1.659335 GTGCACGACGACTTTCCGA 60.659 57.895 0.00 0.00 0.00 4.55
143 144 1.659335 TGCACGACGACTTTCCGAC 60.659 57.895 0.00 0.00 0.00 4.79
144 145 1.371389 GCACGACGACTTTCCGACT 60.371 57.895 0.00 0.00 0.00 4.18
145 146 1.606350 GCACGACGACTTTCCGACTG 61.606 60.000 0.00 0.00 0.00 3.51
146 147 0.317603 CACGACGACTTTCCGACTGT 60.318 55.000 0.00 0.00 0.00 3.55
147 148 0.040603 ACGACGACTTTCCGACTGTC 60.041 55.000 0.00 0.00 0.00 3.51
148 149 0.237761 CGACGACTTTCCGACTGTCT 59.762 55.000 6.21 0.00 0.00 3.41
149 150 1.462283 CGACGACTTTCCGACTGTCTA 59.538 52.381 6.21 0.00 0.00 2.59
150 151 2.724228 CGACGACTTTCCGACTGTCTAC 60.724 54.545 6.21 0.00 0.00 2.59
151 152 2.483491 GACGACTTTCCGACTGTCTACT 59.517 50.000 6.21 0.00 0.00 2.57
152 153 3.668447 ACGACTTTCCGACTGTCTACTA 58.332 45.455 6.21 0.00 0.00 1.82
153 154 3.434984 ACGACTTTCCGACTGTCTACTAC 59.565 47.826 6.21 0.00 0.00 2.73
154 155 3.434641 CGACTTTCCGACTGTCTACTACA 59.565 47.826 6.21 0.00 36.42 2.74
155 156 4.083643 CGACTTTCCGACTGTCTACTACAA 60.084 45.833 6.21 0.00 37.74 2.41
156 157 5.118642 ACTTTCCGACTGTCTACTACAAC 57.881 43.478 6.21 0.00 37.74 3.32
157 158 4.581824 ACTTTCCGACTGTCTACTACAACA 59.418 41.667 6.21 0.00 37.74 3.33
158 159 5.068198 ACTTTCCGACTGTCTACTACAACAA 59.932 40.000 6.21 0.00 37.74 2.83
159 160 5.717078 TTCCGACTGTCTACTACAACAAT 57.283 39.130 6.21 0.00 37.74 2.71
160 161 5.055642 TCCGACTGTCTACTACAACAATG 57.944 43.478 6.21 0.00 37.74 2.82
161 162 4.521639 TCCGACTGTCTACTACAACAATGT 59.478 41.667 6.21 0.00 43.74 2.71
162 163 5.010314 TCCGACTGTCTACTACAACAATGTT 59.990 40.000 6.21 0.00 41.05 2.71
163 164 5.345202 CCGACTGTCTACTACAACAATGTTC 59.655 44.000 6.21 0.00 41.05 3.18
164 165 5.059343 CGACTGTCTACTACAACAATGTTCG 59.941 44.000 6.21 0.00 41.05 3.95
165 166 4.684703 ACTGTCTACTACAACAATGTTCGC 59.315 41.667 0.00 0.00 41.05 4.70
166 167 3.991773 TGTCTACTACAACAATGTTCGCC 59.008 43.478 0.00 0.00 41.05 5.54
167 168 3.370061 GTCTACTACAACAATGTTCGCCC 59.630 47.826 0.00 0.00 41.05 6.13
168 169 1.153353 ACTACAACAATGTTCGCCCG 58.847 50.000 0.00 0.00 41.05 6.13
169 170 1.270412 ACTACAACAATGTTCGCCCGA 60.270 47.619 0.00 0.00 41.05 5.14
170 171 1.127951 CTACAACAATGTTCGCCCGAC 59.872 52.381 0.00 0.00 41.05 4.79
171 172 0.534203 ACAACAATGTTCGCCCGACT 60.534 50.000 0.00 0.00 35.91 4.18
172 173 0.165944 CAACAATGTTCGCCCGACTC 59.834 55.000 0.00 0.00 0.00 3.36
173 174 0.953960 AACAATGTTCGCCCGACTCC 60.954 55.000 0.00 0.00 0.00 3.85
174 175 2.125673 AATGTTCGCCCGACTCCG 60.126 61.111 0.00 0.00 0.00 4.63
175 176 2.642254 AATGTTCGCCCGACTCCGA 61.642 57.895 0.00 0.00 38.22 4.55
176 177 2.830704 AATGTTCGCCCGACTCCGAC 62.831 60.000 0.00 0.00 38.22 4.79
182 183 4.790962 CCCGACTCCGACGAGGGA 62.791 72.222 0.00 0.00 44.70 4.20
190 191 3.470888 CGACGAGGGAGGGGCAAT 61.471 66.667 0.00 0.00 0.00 3.56
191 192 2.190578 GACGAGGGAGGGGCAATG 59.809 66.667 0.00 0.00 0.00 2.82
192 193 2.285368 ACGAGGGAGGGGCAATGA 60.285 61.111 0.00 0.00 0.00 2.57
193 194 2.190578 CGAGGGAGGGGCAATGAC 59.809 66.667 0.00 0.00 0.00 3.06
194 195 2.190578 GAGGGAGGGGCAATGACG 59.809 66.667 0.00 0.00 0.00 4.35
195 196 3.406595 GAGGGAGGGGCAATGACGG 62.407 68.421 0.00 0.00 0.00 4.79
220 221 3.764466 CCTTCGGCTCGCTCCAGT 61.764 66.667 0.00 0.00 0.00 4.00
221 222 2.507992 CTTCGGCTCGCTCCAGTG 60.508 66.667 0.00 0.00 0.00 3.66
222 223 4.742201 TTCGGCTCGCTCCAGTGC 62.742 66.667 0.00 0.00 0.00 4.40
224 225 4.749310 CGGCTCGCTCCAGTGCTT 62.749 66.667 0.00 0.00 0.00 3.91
225 226 3.123620 GGCTCGCTCCAGTGCTTG 61.124 66.667 0.00 0.00 0.00 4.01
226 227 2.358003 GCTCGCTCCAGTGCTTGT 60.358 61.111 0.00 0.00 0.00 3.16
227 228 1.079819 GCTCGCTCCAGTGCTTGTA 60.080 57.895 0.00 0.00 0.00 2.41
228 229 1.080995 GCTCGCTCCAGTGCTTGTAG 61.081 60.000 0.00 0.00 0.00 2.74
229 230 0.244994 CTCGCTCCAGTGCTTGTAGT 59.755 55.000 0.00 0.00 0.00 2.73
230 231 0.243907 TCGCTCCAGTGCTTGTAGTC 59.756 55.000 0.00 0.00 0.00 2.59
231 232 1.073216 CGCTCCAGTGCTTGTAGTCG 61.073 60.000 0.00 0.00 0.00 4.18
232 233 0.038159 GCTCCAGTGCTTGTAGTCGT 60.038 55.000 0.00 0.00 0.00 4.34
233 234 1.983972 CTCCAGTGCTTGTAGTCGTC 58.016 55.000 0.00 0.00 0.00 4.20
234 235 0.240145 TCCAGTGCTTGTAGTCGTCG 59.760 55.000 0.00 0.00 0.00 5.12
235 236 1.344942 CCAGTGCTTGTAGTCGTCGC 61.345 60.000 0.00 0.00 0.00 5.19
236 237 0.387367 CAGTGCTTGTAGTCGTCGCT 60.387 55.000 0.00 0.00 0.00 4.93
237 238 1.135774 CAGTGCTTGTAGTCGTCGCTA 60.136 52.381 0.00 0.00 0.00 4.26
238 239 1.130749 AGTGCTTGTAGTCGTCGCTAG 59.869 52.381 0.00 0.00 0.00 3.42
239 240 0.450583 TGCTTGTAGTCGTCGCTAGG 59.549 55.000 0.00 0.00 0.00 3.02
240 241 0.450983 GCTTGTAGTCGTCGCTAGGT 59.549 55.000 0.00 0.00 0.00 3.08
241 242 1.794437 GCTTGTAGTCGTCGCTAGGTG 60.794 57.143 0.00 0.00 0.00 4.00
242 243 0.806868 TTGTAGTCGTCGCTAGGTGG 59.193 55.000 0.00 0.00 0.00 4.61
243 244 0.321919 TGTAGTCGTCGCTAGGTGGT 60.322 55.000 0.00 0.00 0.00 4.16
244 245 0.376502 GTAGTCGTCGCTAGGTGGTC 59.623 60.000 0.00 0.00 0.00 4.02
245 246 0.251354 TAGTCGTCGCTAGGTGGTCT 59.749 55.000 0.00 0.00 0.00 3.85
246 247 0.251354 AGTCGTCGCTAGGTGGTCTA 59.749 55.000 0.00 0.00 0.00 2.59
247 248 0.376502 GTCGTCGCTAGGTGGTCTAC 59.623 60.000 0.00 0.00 0.00 2.59
248 249 1.086067 TCGTCGCTAGGTGGTCTACG 61.086 60.000 0.00 0.00 0.00 3.51
249 250 1.726265 GTCGCTAGGTGGTCTACGG 59.274 63.158 0.00 0.00 0.00 4.02
250 251 0.745845 GTCGCTAGGTGGTCTACGGA 60.746 60.000 0.00 0.00 0.00 4.69
251 252 0.745845 TCGCTAGGTGGTCTACGGAC 60.746 60.000 0.00 0.00 41.43 4.79
263 264 4.667519 GTCTACGGACCTGGATGTAAAT 57.332 45.455 0.00 0.00 36.53 1.40
264 265 5.019785 GTCTACGGACCTGGATGTAAATT 57.980 43.478 0.00 0.00 36.53 1.82
265 266 5.425630 GTCTACGGACCTGGATGTAAATTT 58.574 41.667 0.00 0.00 36.53 1.82
266 267 5.878669 GTCTACGGACCTGGATGTAAATTTT 59.121 40.000 0.00 0.00 36.53 1.82
267 268 7.043565 GTCTACGGACCTGGATGTAAATTTTA 58.956 38.462 0.00 0.00 36.53 1.52
268 269 7.713942 GTCTACGGACCTGGATGTAAATTTTAT 59.286 37.037 0.00 0.00 36.53 1.40
269 270 8.269317 TCTACGGACCTGGATGTAAATTTTATT 58.731 33.333 0.00 0.00 0.00 1.40
270 271 7.712204 ACGGACCTGGATGTAAATTTTATTT 57.288 32.000 0.00 0.00 0.00 1.40
271 272 7.768240 ACGGACCTGGATGTAAATTTTATTTC 58.232 34.615 0.00 0.00 0.00 2.17
272 273 7.614192 ACGGACCTGGATGTAAATTTTATTTCT 59.386 33.333 0.00 0.00 0.00 2.52
273 274 9.116067 CGGACCTGGATGTAAATTTTATTTCTA 57.884 33.333 0.00 0.00 0.00 2.10
308 309 5.481200 CTGCCTTGACAGTTGATGAATAG 57.519 43.478 0.00 0.00 32.78 1.73
309 310 5.164620 TGCCTTGACAGTTGATGAATAGA 57.835 39.130 0.00 0.00 0.00 1.98
310 311 5.748402 TGCCTTGACAGTTGATGAATAGAT 58.252 37.500 0.00 0.00 0.00 1.98
311 312 5.819379 TGCCTTGACAGTTGATGAATAGATC 59.181 40.000 0.00 0.00 0.00 2.75
312 313 5.050499 GCCTTGACAGTTGATGAATAGATCG 60.050 44.000 0.00 0.00 0.00 3.69
313 314 6.276091 CCTTGACAGTTGATGAATAGATCGA 58.724 40.000 0.00 0.00 0.00 3.59
314 315 6.758416 CCTTGACAGTTGATGAATAGATCGAA 59.242 38.462 0.00 0.00 0.00 3.71
315 316 7.278646 CCTTGACAGTTGATGAATAGATCGAAA 59.721 37.037 0.00 0.00 0.00 3.46
316 317 7.761651 TGACAGTTGATGAATAGATCGAAAG 57.238 36.000 0.00 0.00 0.00 2.62
317 318 7.323420 TGACAGTTGATGAATAGATCGAAAGT 58.677 34.615 0.00 0.00 0.00 2.66
318 319 7.819415 TGACAGTTGATGAATAGATCGAAAGTT 59.181 33.333 0.00 0.00 0.00 2.66
319 320 8.553459 ACAGTTGATGAATAGATCGAAAGTTT 57.447 30.769 0.00 0.00 0.00 2.66
320 321 9.003658 ACAGTTGATGAATAGATCGAAAGTTTT 57.996 29.630 0.00 0.00 0.00 2.43
321 322 9.483062 CAGTTGATGAATAGATCGAAAGTTTTC 57.517 33.333 0.00 0.00 0.00 2.29
322 323 9.442047 AGTTGATGAATAGATCGAAAGTTTTCT 57.558 29.630 0.00 0.00 35.07 2.52
323 324 9.695884 GTTGATGAATAGATCGAAAGTTTTCTC 57.304 33.333 0.00 0.00 35.07 2.87
324 325 8.120030 TGATGAATAGATCGAAAGTTTTCTCG 57.880 34.615 0.00 0.00 35.07 4.04
325 326 7.759886 TGATGAATAGATCGAAAGTTTTCTCGT 59.240 33.333 0.00 0.00 36.46 4.18
326 327 9.234384 GATGAATAGATCGAAAGTTTTCTCGTA 57.766 33.333 0.00 0.00 36.46 3.43
327 328 8.975410 TGAATAGATCGAAAGTTTTCTCGTAA 57.025 30.769 0.00 0.00 36.46 3.18
328 329 9.414295 TGAATAGATCGAAAGTTTTCTCGTAAA 57.586 29.630 0.00 0.00 36.46 2.01
466 482 1.142870 AGGTTGCTGGTTAGTCAAGCA 59.857 47.619 6.24 0.00 39.09 3.91
503 519 2.168521 TGACTATGCTAACCAGACAGCC 59.831 50.000 0.00 0.00 36.95 4.85
704 3229 1.338020 TCTCATCATGTCGACATCCGG 59.662 52.381 27.79 17.01 39.14 5.14
721 3246 1.079750 GGTGGAGAGTCGGCTGAAC 60.080 63.158 0.00 0.00 0.00 3.18
726 3251 1.634702 GAGAGTCGGCTGAACACATC 58.365 55.000 0.00 0.00 0.00 3.06
859 3385 4.571375 CAATGATTGTTGCAATTGACCG 57.429 40.909 10.34 0.00 0.00 4.79
977 3537 5.940470 AGCAACCTTCAAGTATCCTAGTTTG 59.060 40.000 0.00 0.00 0.00 2.93
1028 3588 4.400567 GGTTCTGCATGCTCTTAATTTCCT 59.599 41.667 20.33 0.00 0.00 3.36
1036 3596 3.591527 TGCTCTTAATTTCCTTCCTCCCA 59.408 43.478 0.00 0.00 0.00 4.37
1037 3597 4.044065 TGCTCTTAATTTCCTTCCTCCCAA 59.956 41.667 0.00 0.00 0.00 4.12
1058 3618 7.233348 TCCCAAGCTTGTTTCTGAGATTTTATT 59.767 33.333 24.35 0.00 0.00 1.40
1062 3622 7.955918 AGCTTGTTTCTGAGATTTTATTGGTT 58.044 30.769 0.00 0.00 0.00 3.67
1179 3746 7.354751 AGGTCAAAGGTCTGTATATTCTCTC 57.645 40.000 0.00 0.00 0.00 3.20
1180 3747 6.039941 AGGTCAAAGGTCTGTATATTCTCTCG 59.960 42.308 0.00 0.00 0.00 4.04
1181 3748 5.688176 GTCAAAGGTCTGTATATTCTCTCGC 59.312 44.000 0.00 0.00 0.00 5.03
1182 3749 5.594725 TCAAAGGTCTGTATATTCTCTCGCT 59.405 40.000 0.00 0.00 0.00 4.93
1208 3779 1.065701 GCCTTGATTCGCTCGTCTCTA 59.934 52.381 0.00 0.00 0.00 2.43
1223 3794 6.908284 GCTCGTCTCTATAACTTACTTGACAG 59.092 42.308 0.00 0.00 0.00 3.51
1224 3795 7.317842 TCGTCTCTATAACTTACTTGACAGG 57.682 40.000 0.00 0.00 0.00 4.00
1225 3796 6.883217 TCGTCTCTATAACTTACTTGACAGGT 59.117 38.462 0.00 0.00 0.00 4.00
1226 3797 7.065563 TCGTCTCTATAACTTACTTGACAGGTC 59.934 40.741 0.00 0.00 0.00 3.85
1227 3798 7.188157 GTCTCTATAACTTACTTGACAGGTCG 58.812 42.308 0.00 0.00 0.00 4.79
1228 3799 6.883217 TCTCTATAACTTACTTGACAGGTCGT 59.117 38.462 0.00 0.00 0.00 4.34
1250 3821 2.282391 TGTGTGTCCATGGCAGGC 60.282 61.111 6.96 5.12 0.00 4.85
1304 3875 3.246112 CTGACGGTGGTGGGGGAA 61.246 66.667 0.00 0.00 0.00 3.97
1388 3959 1.183030 TGGGCGACGAGAAGAAGGAA 61.183 55.000 0.00 0.00 0.00 3.36
1454 4031 1.136110 GAGGCCGAGGAGAAGAAGAAG 59.864 57.143 0.00 0.00 0.00 2.85
1470 4047 2.555664 AGAAGAAGGAATGCCTGGAGA 58.444 47.619 0.00 0.00 46.28 3.71
1471 4048 2.915604 AGAAGAAGGAATGCCTGGAGAA 59.084 45.455 0.00 0.00 46.28 2.87
1757 4360 0.594602 TTCAGAGCTTGCATGCACAC 59.405 50.000 22.58 15.59 34.99 3.82
1919 4530 4.141018 GGATATAAGATTGGTGGTGGGGTT 60.141 45.833 0.00 0.00 0.00 4.11
2009 4620 8.034804 AGTTTATTGCAACAATTTGTCCCTATC 58.965 33.333 0.00 0.00 34.90 2.08
2016 4627 2.510768 ATTTGTCCCTATCGACGCTC 57.489 50.000 0.00 0.00 35.40 5.03
2047 4658 2.757056 GCCGTTGCCGATTGGTACC 61.757 63.158 4.43 4.43 37.67 3.34
2159 4770 4.875561 AACACTCTTGAGACTTACTCCC 57.124 45.455 4.49 0.00 44.34 4.30
2179 4790 8.185506 ACTCCCTCCGTTTTTAAATATTTGTT 57.814 30.769 11.05 0.00 0.00 2.83
2212 4823 9.350357 GAGATTTCAACAAGTAACTACATACGA 57.650 33.333 0.00 0.00 0.00 3.43
2232 4843 9.478019 CATACGAAACAAAATGAGTGAATCTAC 57.522 33.333 0.00 0.00 0.00 2.59
2233 4844 6.590357 ACGAAACAAAATGAGTGAATCTACG 58.410 36.000 0.00 0.00 0.00 3.51
2236 4847 5.786401 ACAAAATGAGTGAATCTACGCTC 57.214 39.130 0.00 0.00 44.55 5.03
2327 4938 1.889829 CGGATGGAGTAGGAGCTAAGG 59.110 57.143 0.00 0.00 0.00 2.69
2346 4957 1.153086 GCATCTCCAGCCATTCGGT 60.153 57.895 0.00 0.00 33.28 4.69
2351 4962 4.431131 CCAGCCATTCGGTGCCCT 62.431 66.667 0.00 0.00 38.73 5.19
2388 4999 2.844839 GTCTGGGGGCTAGCCGAT 60.845 66.667 27.24 0.00 36.85 4.18
2409 5020 3.332445 TATTTCCACCGTGGGGGCG 62.332 63.158 17.76 0.00 40.62 6.13
2435 5046 4.958897 CCCAACCGCCGTCCCAAA 62.959 66.667 0.00 0.00 0.00 3.28
2439 5050 1.228306 AACCGCCGTCCCAAATTGA 60.228 52.632 0.00 0.00 0.00 2.57
2440 5051 0.610785 AACCGCCGTCCCAAATTGAT 60.611 50.000 0.00 0.00 0.00 2.57
2447 5058 2.017049 CGTCCCAAATTGATCCCAGAC 58.983 52.381 0.00 0.00 0.00 3.51
2449 5060 0.740737 CCCAAATTGATCCCAGACGC 59.259 55.000 0.00 0.00 0.00 5.19
2451 5062 1.462616 CAAATTGATCCCAGACGCCA 58.537 50.000 0.00 0.00 0.00 5.69
2480 5091 6.377327 TGAAATCCAAATTCGGCTAGATTC 57.623 37.500 0.00 0.00 0.00 2.52
2481 5092 5.885352 TGAAATCCAAATTCGGCTAGATTCA 59.115 36.000 0.00 0.00 0.00 2.57
2503 5115 9.775854 ATTCATACAAAATGACACAAATTTGGA 57.224 25.926 21.74 3.82 37.15 3.53
2511 5123 7.406799 AATGACACAAATTTGGACGAAATTC 57.593 32.000 21.74 6.83 42.41 2.17
2516 5128 2.919666 ATTTGGACGAAATTCAGGCG 57.080 45.000 0.00 0.00 29.22 5.52
2613 5225 2.187685 CGAGCCTACTGCATGCCA 59.812 61.111 16.68 2.21 44.83 4.92
2618 5230 1.379642 GCCTACTGCATGCCAAGGAC 61.380 60.000 25.93 16.43 40.77 3.85
2619 5231 0.749454 CCTACTGCATGCCAAGGACC 60.749 60.000 20.04 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.668118 GGACAAACGCCGACCGGA 62.668 66.667 9.46 0.00 42.52 5.14
1 2 4.675029 AGGACAAACGCCGACCGG 62.675 66.667 0.00 0.00 42.52 5.28
2 3 3.110178 GAGGACAAACGCCGACCG 61.110 66.667 0.00 0.00 44.21 4.79
3 4 3.110178 CGAGGACAAACGCCGACC 61.110 66.667 0.00 0.00 0.00 4.79
4 5 3.110178 CCGAGGACAAACGCCGAC 61.110 66.667 0.00 0.00 0.00 4.79
5 6 3.608662 ACCGAGGACAAACGCCGA 61.609 61.111 0.00 0.00 0.00 5.54
6 7 3.411351 CACCGAGGACAAACGCCG 61.411 66.667 0.00 0.00 0.00 6.46
7 8 3.047877 CCACCGAGGACAAACGCC 61.048 66.667 0.00 0.00 41.22 5.68
8 9 2.029964 TCCACCGAGGACAAACGC 59.970 61.111 0.00 0.00 43.07 4.84
16 17 0.684479 TCCAGTCAGATCCACCGAGG 60.684 60.000 0.00 0.00 39.47 4.63
17 18 1.339610 GATCCAGTCAGATCCACCGAG 59.660 57.143 0.00 0.00 37.31 4.63
18 19 1.403814 GATCCAGTCAGATCCACCGA 58.596 55.000 0.00 0.00 37.31 4.69
19 20 3.976339 GATCCAGTCAGATCCACCG 57.024 57.895 0.00 0.00 37.31 4.94
32 33 1.201647 GACGAACGAAGACTGGATCCA 59.798 52.381 15.27 15.27 0.00 3.41
33 34 1.473278 AGACGAACGAAGACTGGATCC 59.527 52.381 4.20 4.20 0.00 3.36
34 35 2.520979 CAGACGAACGAAGACTGGATC 58.479 52.381 0.14 0.00 0.00 3.36
35 36 1.402984 GCAGACGAACGAAGACTGGAT 60.403 52.381 0.14 0.00 0.00 3.41
36 37 0.039437 GCAGACGAACGAAGACTGGA 60.039 55.000 0.14 0.00 0.00 3.86
37 38 1.337817 CGCAGACGAACGAAGACTGG 61.338 60.000 0.14 0.00 43.93 4.00
38 39 0.660595 ACGCAGACGAACGAAGACTG 60.661 55.000 0.14 0.00 43.93 3.51
39 40 0.385723 GACGCAGACGAACGAAGACT 60.386 55.000 0.14 0.00 43.93 3.24
40 41 0.385723 AGACGCAGACGAACGAAGAC 60.386 55.000 0.14 0.00 43.93 3.01
41 42 0.385598 CAGACGCAGACGAACGAAGA 60.386 55.000 0.14 0.00 43.93 2.87
42 43 0.660595 ACAGACGCAGACGAACGAAG 60.661 55.000 0.14 0.00 43.93 3.79
43 44 0.933047 CACAGACGCAGACGAACGAA 60.933 55.000 0.14 0.00 43.93 3.85
44 45 1.370051 CACAGACGCAGACGAACGA 60.370 57.895 0.14 0.00 43.93 3.85
45 46 1.657487 ACACAGACGCAGACGAACG 60.657 57.895 0.00 0.00 43.93 3.95
46 47 0.870307 ACACACAGACGCAGACGAAC 60.870 55.000 0.00 0.00 43.93 3.95
47 48 0.594028 GACACACAGACGCAGACGAA 60.594 55.000 0.00 0.00 43.93 3.85
48 49 1.008881 GACACACAGACGCAGACGA 60.009 57.895 0.00 0.00 43.93 4.20
50 51 1.552348 GCAGACACACAGACGCAGAC 61.552 60.000 0.00 0.00 0.00 3.51
51 52 1.300156 GCAGACACACAGACGCAGA 60.300 57.895 0.00 0.00 0.00 4.26
52 53 1.554891 CTGCAGACACACAGACGCAG 61.555 60.000 8.42 0.00 40.68 5.18
53 54 1.592400 CTGCAGACACACAGACGCA 60.592 57.895 8.42 0.00 35.90 5.24
54 55 2.947890 GCTGCAGACACACAGACGC 61.948 63.158 20.43 0.00 35.90 5.19
55 56 1.280886 GAGCTGCAGACACACAGACG 61.281 60.000 20.43 0.00 35.90 4.18
56 57 1.280886 CGAGCTGCAGACACACAGAC 61.281 60.000 20.43 0.00 35.90 3.51
57 58 1.006922 CGAGCTGCAGACACACAGA 60.007 57.895 20.43 0.00 35.90 3.41
58 59 2.665395 GCGAGCTGCAGACACACAG 61.665 63.158 20.43 1.64 45.45 3.66
59 60 2.662857 GCGAGCTGCAGACACACA 60.663 61.111 20.43 0.00 45.45 3.72
68 69 3.267860 CGGAAGGATGCGAGCTGC 61.268 66.667 0.00 0.00 43.91 5.25
80 81 3.131223 TGAAGAGAAGCATAGACCGGAAG 59.869 47.826 9.46 0.00 0.00 3.46
81 82 3.096852 TGAAGAGAAGCATAGACCGGAA 58.903 45.455 9.46 0.00 0.00 4.30
82 83 2.735151 TGAAGAGAAGCATAGACCGGA 58.265 47.619 9.46 0.00 0.00 5.14
83 84 3.648009 GATGAAGAGAAGCATAGACCGG 58.352 50.000 0.00 0.00 0.00 5.28
84 85 3.304257 CGATGAAGAGAAGCATAGACCG 58.696 50.000 0.00 0.00 0.00 4.79
85 86 3.648009 CCGATGAAGAGAAGCATAGACC 58.352 50.000 0.00 0.00 0.00 3.85
86 87 3.056304 GCCGATGAAGAGAAGCATAGAC 58.944 50.000 0.00 0.00 0.00 2.59
87 88 2.287849 CGCCGATGAAGAGAAGCATAGA 60.288 50.000 0.00 0.00 0.00 1.98
88 89 2.057316 CGCCGATGAAGAGAAGCATAG 58.943 52.381 0.00 0.00 0.00 2.23
89 90 1.269778 CCGCCGATGAAGAGAAGCATA 60.270 52.381 0.00 0.00 0.00 3.14
90 91 0.531532 CCGCCGATGAAGAGAAGCAT 60.532 55.000 0.00 0.00 0.00 3.79
91 92 1.153568 CCGCCGATGAAGAGAAGCA 60.154 57.895 0.00 0.00 0.00 3.91
92 93 2.529619 GCCGCCGATGAAGAGAAGC 61.530 63.158 0.00 0.00 0.00 3.86
93 94 2.233654 CGCCGCCGATGAAGAGAAG 61.234 63.158 0.00 0.00 36.29 2.85
94 95 2.202743 CGCCGCCGATGAAGAGAA 60.203 61.111 0.00 0.00 36.29 2.87
95 96 4.207281 CCGCCGCCGATGAAGAGA 62.207 66.667 0.00 0.00 36.29 3.10
96 97 4.514577 ACCGCCGCCGATGAAGAG 62.515 66.667 0.00 0.00 36.29 2.85
97 98 4.077184 AACCGCCGCCGATGAAGA 62.077 61.111 0.00 0.00 36.29 2.87
98 99 3.864686 CAACCGCCGCCGATGAAG 61.865 66.667 0.00 0.00 36.29 3.02
106 107 4.389576 CAGAACAGCAACCGCCGC 62.390 66.667 0.00 0.00 39.83 6.53
107 108 3.726517 CCAGAACAGCAACCGCCG 61.727 66.667 0.00 0.00 39.83 6.46
108 109 2.594592 ACCAGAACAGCAACCGCC 60.595 61.111 0.00 0.00 39.83 6.13
109 110 2.639286 CACCAGAACAGCAACCGC 59.361 61.111 0.00 0.00 38.99 5.68
110 111 2.186160 TGCACCAGAACAGCAACCG 61.186 57.895 0.00 0.00 34.97 4.44
111 112 1.360192 GTGCACCAGAACAGCAACC 59.640 57.895 5.22 0.00 40.35 3.77
112 113 1.009675 CGTGCACCAGAACAGCAAC 60.010 57.895 12.15 0.00 40.35 4.17
113 114 1.153269 TCGTGCACCAGAACAGCAA 60.153 52.632 12.15 0.00 40.35 3.91
114 115 1.887242 GTCGTGCACCAGAACAGCA 60.887 57.895 12.15 0.00 35.63 4.41
115 116 2.939022 GTCGTGCACCAGAACAGC 59.061 61.111 12.15 0.00 0.00 4.40
116 117 1.299850 TCGTCGTGCACCAGAACAG 60.300 57.895 12.15 0.00 0.00 3.16
117 118 1.590525 GTCGTCGTGCACCAGAACA 60.591 57.895 12.15 0.00 0.00 3.18
118 119 0.874607 AAGTCGTCGTGCACCAGAAC 60.875 55.000 12.15 5.15 0.00 3.01
119 120 0.179094 AAAGTCGTCGTGCACCAGAA 60.179 50.000 12.15 0.00 0.00 3.02
120 121 0.596600 GAAAGTCGTCGTGCACCAGA 60.597 55.000 12.15 5.33 0.00 3.86
121 122 1.557443 GGAAAGTCGTCGTGCACCAG 61.557 60.000 12.15 2.71 0.00 4.00
122 123 1.593209 GGAAAGTCGTCGTGCACCA 60.593 57.895 12.15 0.00 0.00 4.17
123 124 2.654912 CGGAAAGTCGTCGTGCACC 61.655 63.158 12.15 0.00 0.00 5.01
124 125 1.659335 TCGGAAAGTCGTCGTGCAC 60.659 57.895 6.82 6.82 0.00 4.57
125 126 1.659335 GTCGGAAAGTCGTCGTGCA 60.659 57.895 0.00 0.00 0.00 4.57
126 127 1.371389 AGTCGGAAAGTCGTCGTGC 60.371 57.895 0.00 0.00 0.00 5.34
127 128 0.317603 ACAGTCGGAAAGTCGTCGTG 60.318 55.000 0.00 0.00 0.00 4.35
128 129 0.040603 GACAGTCGGAAAGTCGTCGT 60.041 55.000 0.00 0.00 0.00 4.34
129 130 0.237761 AGACAGTCGGAAAGTCGTCG 59.762 55.000 0.00 0.00 37.36 5.12
130 131 2.483491 AGTAGACAGTCGGAAAGTCGTC 59.517 50.000 0.00 0.00 37.36 4.20
131 132 2.502295 AGTAGACAGTCGGAAAGTCGT 58.498 47.619 0.00 0.00 37.36 4.34
132 133 3.434641 TGTAGTAGACAGTCGGAAAGTCG 59.565 47.826 0.00 0.00 37.36 4.18
133 134 5.152804 GTTGTAGTAGACAGTCGGAAAGTC 58.847 45.833 0.00 3.60 39.88 3.01
134 135 4.581824 TGTTGTAGTAGACAGTCGGAAAGT 59.418 41.667 0.00 0.00 39.88 2.66
135 136 5.117355 TGTTGTAGTAGACAGTCGGAAAG 57.883 43.478 0.00 0.00 39.88 2.62
136 137 5.518848 TTGTTGTAGTAGACAGTCGGAAA 57.481 39.130 0.00 0.00 39.88 3.13
137 138 5.010314 ACATTGTTGTAGTAGACAGTCGGAA 59.990 40.000 0.00 0.00 39.88 4.30
138 139 4.521639 ACATTGTTGTAGTAGACAGTCGGA 59.478 41.667 0.00 0.00 39.88 4.55
139 140 4.806330 ACATTGTTGTAGTAGACAGTCGG 58.194 43.478 0.00 0.00 39.88 4.79
140 141 5.059343 CGAACATTGTTGTAGTAGACAGTCG 59.941 44.000 6.80 0.00 39.88 4.18
141 142 5.164080 GCGAACATTGTTGTAGTAGACAGTC 60.164 44.000 6.80 0.00 39.88 3.51
142 143 4.684703 GCGAACATTGTTGTAGTAGACAGT 59.315 41.667 6.80 0.00 39.88 3.55
143 144 4.091509 GGCGAACATTGTTGTAGTAGACAG 59.908 45.833 6.80 0.00 39.88 3.51
144 145 3.991773 GGCGAACATTGTTGTAGTAGACA 59.008 43.478 6.80 0.00 34.06 3.41
145 146 3.370061 GGGCGAACATTGTTGTAGTAGAC 59.630 47.826 6.80 0.00 34.06 2.59
146 147 3.592059 GGGCGAACATTGTTGTAGTAGA 58.408 45.455 6.80 0.00 34.06 2.59
147 148 2.347452 CGGGCGAACATTGTTGTAGTAG 59.653 50.000 6.80 0.00 34.06 2.57
148 149 2.029200 TCGGGCGAACATTGTTGTAGTA 60.029 45.455 6.80 0.00 34.06 1.82
149 150 1.153353 CGGGCGAACATTGTTGTAGT 58.847 50.000 6.80 0.00 34.06 2.73
150 151 1.127951 GTCGGGCGAACATTGTTGTAG 59.872 52.381 6.80 0.00 34.06 2.74
151 152 1.149987 GTCGGGCGAACATTGTTGTA 58.850 50.000 6.80 0.00 34.06 2.41
152 153 0.534203 AGTCGGGCGAACATTGTTGT 60.534 50.000 6.80 0.00 37.82 3.32
153 154 0.165944 GAGTCGGGCGAACATTGTTG 59.834 55.000 6.80 1.05 0.00 3.33
154 155 0.953960 GGAGTCGGGCGAACATTGTT 60.954 55.000 0.63 0.63 0.00 2.83
155 156 1.375523 GGAGTCGGGCGAACATTGT 60.376 57.895 0.00 0.00 0.00 2.71
156 157 2.452813 CGGAGTCGGGCGAACATTG 61.453 63.158 0.00 0.00 0.00 2.82
157 158 2.125673 CGGAGTCGGGCGAACATT 60.126 61.111 0.00 0.00 0.00 2.71
158 159 3.066190 TCGGAGTCGGGCGAACAT 61.066 61.111 0.00 0.00 36.95 2.71
159 160 4.047059 GTCGGAGTCGGGCGAACA 62.047 66.667 0.00 0.00 36.95 3.18
165 166 4.790962 TCCCTCGTCGGAGTCGGG 62.791 72.222 0.00 0.00 39.67 5.14
166 167 3.203412 CTCCCTCGTCGGAGTCGG 61.203 72.222 11.10 0.00 43.94 4.79
173 174 3.470888 ATTGCCCCTCCCTCGTCG 61.471 66.667 0.00 0.00 0.00 5.12
174 175 2.190578 CATTGCCCCTCCCTCGTC 59.809 66.667 0.00 0.00 0.00 4.20
175 176 2.285368 TCATTGCCCCTCCCTCGT 60.285 61.111 0.00 0.00 0.00 4.18
176 177 2.190578 GTCATTGCCCCTCCCTCG 59.809 66.667 0.00 0.00 0.00 4.63
177 178 2.190578 CGTCATTGCCCCTCCCTC 59.809 66.667 0.00 0.00 0.00 4.30
178 179 3.411517 CCGTCATTGCCCCTCCCT 61.412 66.667 0.00 0.00 0.00 4.20
204 205 2.507992 CACTGGAGCGAGCCGAAG 60.508 66.667 0.00 0.00 0.00 3.79
205 206 4.742201 GCACTGGAGCGAGCCGAA 62.742 66.667 0.00 0.00 0.00 4.30
207 208 4.749310 AAGCACTGGAGCGAGCCG 62.749 66.667 0.00 0.00 40.15 5.52
208 209 2.507110 TACAAGCACTGGAGCGAGCC 62.507 60.000 0.00 0.00 40.15 4.70
209 210 1.079819 TACAAGCACTGGAGCGAGC 60.080 57.895 0.00 0.00 40.15 5.03
210 211 0.244994 ACTACAAGCACTGGAGCGAG 59.755 55.000 0.00 0.00 40.05 5.03
211 212 0.243907 GACTACAAGCACTGGAGCGA 59.756 55.000 0.00 0.00 40.05 4.93
212 213 1.073216 CGACTACAAGCACTGGAGCG 61.073 60.000 0.00 0.53 40.05 5.03
213 214 0.038159 ACGACTACAAGCACTGGAGC 60.038 55.000 0.00 0.00 40.05 4.70
214 215 1.729472 CGACGACTACAAGCACTGGAG 60.729 57.143 0.00 0.00 42.47 3.86
215 216 0.240145 CGACGACTACAAGCACTGGA 59.760 55.000 0.00 0.00 0.00 3.86
216 217 1.344942 GCGACGACTACAAGCACTGG 61.345 60.000 0.00 0.00 0.00 4.00
217 218 0.387367 AGCGACGACTACAAGCACTG 60.387 55.000 0.00 0.00 0.00 3.66
218 219 1.130749 CTAGCGACGACTACAAGCACT 59.869 52.381 0.00 0.00 0.00 4.40
219 220 1.536149 CTAGCGACGACTACAAGCAC 58.464 55.000 0.00 0.00 0.00 4.40
220 221 0.450583 CCTAGCGACGACTACAAGCA 59.549 55.000 0.00 0.00 0.00 3.91
221 222 0.450983 ACCTAGCGACGACTACAAGC 59.549 55.000 0.00 0.00 0.00 4.01
222 223 1.202154 CCACCTAGCGACGACTACAAG 60.202 57.143 0.00 0.00 0.00 3.16
223 224 0.806868 CCACCTAGCGACGACTACAA 59.193 55.000 0.00 0.00 0.00 2.41
224 225 0.321919 ACCACCTAGCGACGACTACA 60.322 55.000 0.00 0.00 0.00 2.74
225 226 0.376502 GACCACCTAGCGACGACTAC 59.623 60.000 0.00 0.00 0.00 2.73
226 227 0.251354 AGACCACCTAGCGACGACTA 59.749 55.000 0.00 0.00 0.00 2.59
227 228 0.251354 TAGACCACCTAGCGACGACT 59.749 55.000 0.00 0.00 0.00 4.18
228 229 0.376502 GTAGACCACCTAGCGACGAC 59.623 60.000 0.00 0.00 0.00 4.34
229 230 1.086067 CGTAGACCACCTAGCGACGA 61.086 60.000 0.00 0.00 0.00 4.20
230 231 1.351012 CGTAGACCACCTAGCGACG 59.649 63.158 0.00 0.00 0.00 5.12
231 232 0.745845 TCCGTAGACCACCTAGCGAC 60.746 60.000 0.00 0.00 0.00 5.19
232 233 0.745845 GTCCGTAGACCACCTAGCGA 60.746 60.000 0.00 0.00 37.00 4.93
233 234 1.726265 GTCCGTAGACCACCTAGCG 59.274 63.158 0.00 0.00 37.00 4.26
242 243 4.667519 ATTTACATCCAGGTCCGTAGAC 57.332 45.455 0.00 0.00 42.73 2.59
243 244 5.687166 AAATTTACATCCAGGTCCGTAGA 57.313 39.130 0.00 0.00 0.00 2.59
244 245 8.446599 AATAAAATTTACATCCAGGTCCGTAG 57.553 34.615 0.00 0.00 0.00 3.51
245 246 8.810990 AAATAAAATTTACATCCAGGTCCGTA 57.189 30.769 0.00 0.00 0.00 4.02
246 247 7.614192 AGAAATAAAATTTACATCCAGGTCCGT 59.386 33.333 0.00 0.00 0.00 4.69
247 248 7.996385 AGAAATAAAATTTACATCCAGGTCCG 58.004 34.615 0.00 0.00 0.00 4.79
286 287 5.181009 TCTATTCATCAACTGTCAAGGCAG 58.819 41.667 0.00 0.00 41.92 4.85
287 288 5.164620 TCTATTCATCAACTGTCAAGGCA 57.835 39.130 0.00 0.00 0.00 4.75
288 289 5.050499 CGATCTATTCATCAACTGTCAAGGC 60.050 44.000 0.00 0.00 0.00 4.35
289 290 6.276091 TCGATCTATTCATCAACTGTCAAGG 58.724 40.000 0.00 0.00 0.00 3.61
290 291 7.761651 TTCGATCTATTCATCAACTGTCAAG 57.238 36.000 0.00 0.00 0.00 3.02
291 292 7.819415 ACTTTCGATCTATTCATCAACTGTCAA 59.181 33.333 0.00 0.00 0.00 3.18
292 293 7.323420 ACTTTCGATCTATTCATCAACTGTCA 58.677 34.615 0.00 0.00 0.00 3.58
293 294 7.763172 ACTTTCGATCTATTCATCAACTGTC 57.237 36.000 0.00 0.00 0.00 3.51
294 295 8.553459 AAACTTTCGATCTATTCATCAACTGT 57.447 30.769 0.00 0.00 0.00 3.55
295 296 9.483062 GAAAACTTTCGATCTATTCATCAACTG 57.517 33.333 0.00 0.00 0.00 3.16
296 297 9.442047 AGAAAACTTTCGATCTATTCATCAACT 57.558 29.630 0.00 0.00 41.92 3.16
297 298 9.695884 GAGAAAACTTTCGATCTATTCATCAAC 57.304 33.333 0.00 0.00 41.92 3.18
298 299 8.595533 CGAGAAAACTTTCGATCTATTCATCAA 58.404 33.333 0.00 0.00 41.92 2.57
299 300 7.759886 ACGAGAAAACTTTCGATCTATTCATCA 59.240 33.333 0.51 0.00 41.92 3.07
300 301 8.121167 ACGAGAAAACTTTCGATCTATTCATC 57.879 34.615 0.51 0.00 41.92 2.92
301 302 9.582431 TTACGAGAAAACTTTCGATCTATTCAT 57.418 29.630 0.51 0.00 41.92 2.57
302 303 8.975410 TTACGAGAAAACTTTCGATCTATTCA 57.025 30.769 0.51 0.00 41.92 2.57
329 330 8.876790 GCAGTAGTTGGTTCGTATTAGTTATTT 58.123 33.333 0.00 0.00 0.00 1.40
330 331 8.036575 TGCAGTAGTTGGTTCGTATTAGTTATT 58.963 33.333 0.00 0.00 0.00 1.40
331 332 7.549839 TGCAGTAGTTGGTTCGTATTAGTTAT 58.450 34.615 0.00 0.00 0.00 1.89
332 333 6.923012 TGCAGTAGTTGGTTCGTATTAGTTA 58.077 36.000 0.00 0.00 0.00 2.24
333 334 5.786311 TGCAGTAGTTGGTTCGTATTAGTT 58.214 37.500 0.00 0.00 0.00 2.24
334 335 5.395682 TGCAGTAGTTGGTTCGTATTAGT 57.604 39.130 0.00 0.00 0.00 2.24
335 336 9.856488 ATATATGCAGTAGTTGGTTCGTATTAG 57.144 33.333 0.00 0.00 0.00 1.73
433 449 1.592223 CAACCTGGGGAGACGACTC 59.408 63.158 6.33 6.33 41.94 3.36
479 495 5.279708 GGCTGTCTGGTTAGCATAGTCATAT 60.280 44.000 0.00 0.00 41.63 1.78
480 496 4.039245 GGCTGTCTGGTTAGCATAGTCATA 59.961 45.833 0.00 0.00 41.63 2.15
482 498 2.168521 GGCTGTCTGGTTAGCATAGTCA 59.831 50.000 0.00 0.00 41.63 3.41
489 505 0.955919 GTGGTGGCTGTCTGGTTAGC 60.956 60.000 0.00 0.00 39.17 3.09
503 519 2.831685 TAATAGCTATGGCCGTGGTG 57.168 50.000 8.05 0.00 39.73 4.17
627 940 9.620259 GGATTTTCAGTACCTTCTCATCTATTT 57.380 33.333 0.00 0.00 0.00 1.40
637 950 2.237893 TCCCGGGATTTTCAGTACCTTC 59.762 50.000 22.63 0.00 0.00 3.46
704 3229 0.667792 GTGTTCAGCCGACTCTCCAC 60.668 60.000 0.00 0.00 0.00 4.02
721 3246 3.434319 GTGTGCAGCCCGGATGTG 61.434 66.667 0.73 0.00 0.00 3.21
726 3251 2.355986 TAGTAGGTGTGCAGCCCGG 61.356 63.158 0.00 0.00 0.00 5.73
818 3344 1.802508 GCCACAGTGCAAAACCAACTC 60.803 52.381 0.00 0.00 0.00 3.01
859 3385 1.270893 GGTGGTTTGGACTCTGGACTC 60.271 57.143 0.00 0.00 0.00 3.36
995 3555 2.751259 GCATGCAGAACCTTCATCTTCA 59.249 45.455 14.21 0.00 0.00 3.02
1028 3588 2.174639 TCAGAAACAAGCTTGGGAGGAA 59.825 45.455 29.18 8.83 0.00 3.36
1036 3596 7.955918 ACCAATAAAATCTCAGAAACAAGCTT 58.044 30.769 0.00 0.00 0.00 3.74
1037 3597 7.530426 ACCAATAAAATCTCAGAAACAAGCT 57.470 32.000 0.00 0.00 0.00 3.74
1062 3622 6.335471 TCAGAATAACAGAAACGGTGAGTA 57.665 37.500 0.00 0.00 0.00 2.59
1179 3746 1.143305 CGAATCAAGGCCATAGAGCG 58.857 55.000 5.01 4.28 0.00 5.03
1180 3747 0.871057 GCGAATCAAGGCCATAGAGC 59.129 55.000 5.01 0.00 0.00 4.09
1181 3748 2.411904 GAGCGAATCAAGGCCATAGAG 58.588 52.381 5.01 0.00 0.00 2.43
1182 3749 1.269778 CGAGCGAATCAAGGCCATAGA 60.270 52.381 5.01 0.00 0.00 1.98
1208 3779 5.464030 ACACGACCTGTCAAGTAAGTTAT 57.536 39.130 0.00 0.00 0.00 1.89
1223 3794 1.947642 GGACACACACGACACGACC 60.948 63.158 0.00 0.00 0.00 4.79
1224 3795 0.596600 ATGGACACACACGACACGAC 60.597 55.000 0.00 0.00 0.00 4.34
1225 3796 0.596341 CATGGACACACACGACACGA 60.596 55.000 0.00 0.00 0.00 4.35
1226 3797 1.556591 CCATGGACACACACGACACG 61.557 60.000 5.56 0.00 0.00 4.49
1227 3798 1.841663 GCCATGGACACACACGACAC 61.842 60.000 18.40 0.00 0.00 3.67
1228 3799 1.596752 GCCATGGACACACACGACA 60.597 57.895 18.40 0.00 0.00 4.35
1250 3821 0.846401 CGTATGCCATCGACTTGACG 59.154 55.000 0.00 0.00 0.00 4.35
1304 3875 2.766651 ACCACCACCACGTCCACT 60.767 61.111 0.00 0.00 0.00 4.00
1388 3959 2.223803 TCTTCTTCTTCTCCTCCGCT 57.776 50.000 0.00 0.00 0.00 5.52
1454 4031 3.212685 CATCTTCTCCAGGCATTCCTTC 58.787 50.000 0.00 0.00 41.93 3.46
1757 4360 9.774742 CGGAAAAGATACAGGAAAAGAAAATAG 57.225 33.333 0.00 0.00 0.00 1.73
1812 4416 5.048224 TGAGTAGTAAAAGAAGGTCTCCGTG 60.048 44.000 0.00 0.00 0.00 4.94
1883 4494 4.546570 TCTTATATCCAAGTCGTCGCATG 58.453 43.478 0.00 0.00 0.00 4.06
1919 4530 7.847096 TGTCACATTATTAGGTGAAGCTAAGA 58.153 34.615 0.19 0.89 45.57 2.10
2009 4620 2.346741 GCATATGAAAGTTCGAGCGTCG 60.347 50.000 6.97 1.67 42.10 5.12
2016 4627 2.440501 GCAACGGCATATGAAAGTTCG 58.559 47.619 6.97 2.63 40.72 3.95
2063 4674 4.190772 TCATTGCGTGATCTGCAGAAATA 58.809 39.130 22.50 7.18 44.28 1.40
2201 4812 8.373048 TCACTCATTTTGTTTCGTATGTAGTT 57.627 30.769 0.00 0.00 0.00 2.24
2210 4821 5.504755 GCGTAGATTCACTCATTTTGTTTCG 59.495 40.000 0.00 0.00 0.00 3.46
2212 4823 6.428159 AGAGCGTAGATTCACTCATTTTGTTT 59.572 34.615 0.00 0.00 0.00 2.83
2214 4825 5.482908 AGAGCGTAGATTCACTCATTTTGT 58.517 37.500 0.00 0.00 0.00 2.83
2293 4904 8.311836 CCTACTCCATCCGCTTCTAAATATTTA 58.688 37.037 7.66 7.66 0.00 1.40
2304 4915 0.397816 AGCTCCTACTCCATCCGCTT 60.398 55.000 0.00 0.00 0.00 4.68
2311 4922 0.338467 TGCCCTTAGCTCCTACTCCA 59.662 55.000 0.00 0.00 44.23 3.86
2346 4957 1.965414 TATTTCAGTCCCTGAGGGCA 58.035 50.000 14.20 0.00 43.94 5.36
2351 4962 2.238646 ACGGCAATATTTCAGTCCCTGA 59.761 45.455 0.00 0.00 38.87 3.86
2372 4983 2.844362 CATCGGCTAGCCCCCAGA 60.844 66.667 28.09 19.01 0.00 3.86
2387 4998 0.106719 CCCCACGGTGGAAATAGCAT 60.107 55.000 28.36 0.00 40.96 3.79
2388 4999 1.301623 CCCCACGGTGGAAATAGCA 59.698 57.895 28.36 0.00 40.96 3.49
2429 5040 1.681780 GCGTCTGGGATCAATTTGGGA 60.682 52.381 0.00 0.00 0.00 4.37
2432 5043 1.462616 TGGCGTCTGGGATCAATTTG 58.537 50.000 0.00 0.00 0.00 2.32
2435 5046 2.442236 AAATGGCGTCTGGGATCAAT 57.558 45.000 0.00 0.00 0.00 2.57
2480 5091 7.380870 TCGTCCAAATTTGTGTCATTTTGTATG 59.619 33.333 16.73 0.00 0.00 2.39
2481 5092 7.429633 TCGTCCAAATTTGTGTCATTTTGTAT 58.570 30.769 16.73 0.00 0.00 2.29
2503 5115 1.950909 TGAAAACCGCCTGAATTTCGT 59.049 42.857 0.00 0.00 35.15 3.85
2511 5123 5.410067 ACAAATATCAATGAAAACCGCCTG 58.590 37.500 0.00 0.00 0.00 4.85
2595 5207 2.590007 GGCATGCAGTAGGCTCGG 60.590 66.667 21.36 0.00 45.15 4.63


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

AutoCloner maintained by Alex Coulton.