Multiple sequence alignment - TraesCS7A01G324100

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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 TraesCS7A01G324100 chr7A 100.000 3020 0 0 1 3020 471269243 471272262 0.000000e+00 5578
1 TraesCS7A01G324100 chr7D 93.787 2221 45 37 404 2570 410907189 410905008 0.000000e+00 3251
2 TraesCS7A01G324100 chr7D 90.604 298 8 5 2554 2834 410902364 410902070 7.900000e-101 377
3 TraesCS7A01G324100 chr7D 92.929 198 4 2 2833 3020 410901866 410901669 2.290000e-71 279
4 TraesCS7A01G324100 chr7D 84.500 200 30 1 180 378 410907665 410907466 2.380000e-46 196
5 TraesCS7A01G324100 chr7B 95.849 1638 34 5 618 2236 424644551 424646173 0.000000e+00 2617
6 TraesCS7A01G324100 chr7B 90.588 340 9 9 2234 2561 424646296 424646624 2.150000e-116 429
7 TraesCS7A01G324100 chr7B 84.066 364 24 15 2582 2919 424647989 424648344 1.350000e-83 320
8 TraesCS7A01G324100 chr7B 83.172 309 45 6 1 308 424573051 424573353 2.970000e-70 276
9 TraesCS7A01G324100 chrUn 100.000 396 0 0 1628 2023 479209416 479209021 0.000000e+00 732


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 TraesCS7A01G324100 chr7A 471269243 471272262 3019 False 5578.00 5578 100.000000 1 3020 1 chr7A.!!$F1 3019
1 TraesCS7A01G324100 chr7D 410901669 410907665 5996 True 1025.75 3251 90.455000 180 3020 4 chr7D.!!$R1 2840
2 TraesCS7A01G324100 chr7B 424644551 424648344 3793 False 1122.00 2617 90.167667 618 2919 3 chr7B.!!$F2 2301

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
521 784 0.030908 GTACTGGTAGCAGGCTAGCG 59.969 60.0 24.84 18.11 46.51 4.26 F
546 820 0.764890 TGAGCCAGGCCCATATGTAC 59.235 55.0 8.22 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1920 0.179161 CCTTGTAGTCCTCGAGCACG 60.179 60.0 6.99 0.0 41.26 5.34 R
2350 2773 0.817654 CCGAGTGGTGCAGTGATCTA 59.182 55.0 0.00 0.0 0.00 1.98 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
19 20 1.389555 CTTCAATAAGGAACGGCCCC 58.610 55.000 0.00 0.00 37.37 5.80
20 21 0.393267 TTCAATAAGGAACGGCCCCG 60.393 55.000 4.96 4.96 46.03 5.73
21 22 1.822186 CAATAAGGAACGGCCCCGG 60.822 63.158 11.83 0.00 44.69 5.73
22 23 1.996748 AATAAGGAACGGCCCCGGA 60.997 57.895 0.73 0.00 44.69 5.14
23 24 1.564483 AATAAGGAACGGCCCCGGAA 61.564 55.000 0.73 0.00 44.69 4.30
24 25 1.979619 ATAAGGAACGGCCCCGGAAG 61.980 60.000 0.73 0.00 44.69 3.46
27 28 4.796495 GAACGGCCCCGGAAGCAT 62.796 66.667 16.89 3.19 44.69 3.79
33 34 2.825836 CCCCGGAAGCATGCTGTC 60.826 66.667 23.48 19.25 0.00 3.51
34 35 2.825836 CCCGGAAGCATGCTGTCC 60.826 66.667 23.48 25.37 0.00 4.02
35 36 2.825836 CCGGAAGCATGCTGTCCC 60.826 66.667 28.28 23.96 0.00 4.46
36 37 2.825836 CGGAAGCATGCTGTCCCC 60.826 66.667 28.28 22.15 0.00 4.81
37 38 2.356278 GGAAGCATGCTGTCCCCA 59.644 61.111 23.48 0.00 0.00 4.96
38 39 1.304381 GGAAGCATGCTGTCCCCAA 60.304 57.895 23.48 0.00 0.00 4.12
39 40 0.685458 GGAAGCATGCTGTCCCCAAT 60.685 55.000 23.48 1.63 0.00 3.16
40 41 0.743097 GAAGCATGCTGTCCCCAATC 59.257 55.000 23.48 8.59 0.00 2.67
41 42 0.685458 AAGCATGCTGTCCCCAATCC 60.685 55.000 23.48 0.00 0.00 3.01
42 43 1.076485 GCATGCTGTCCCCAATCCT 60.076 57.895 11.37 0.00 0.00 3.24
43 44 1.105759 GCATGCTGTCCCCAATCCTC 61.106 60.000 11.37 0.00 0.00 3.71
44 45 0.466922 CATGCTGTCCCCAATCCTCC 60.467 60.000 0.00 0.00 0.00 4.30
45 46 1.649271 ATGCTGTCCCCAATCCTCCC 61.649 60.000 0.00 0.00 0.00 4.30
46 47 2.308722 GCTGTCCCCAATCCTCCCA 61.309 63.158 0.00 0.00 0.00 4.37
47 48 1.863155 GCTGTCCCCAATCCTCCCAA 61.863 60.000 0.00 0.00 0.00 4.12
48 49 0.704076 CTGTCCCCAATCCTCCCAAA 59.296 55.000 0.00 0.00 0.00 3.28
49 50 1.077005 CTGTCCCCAATCCTCCCAAAA 59.923 52.381 0.00 0.00 0.00 2.44
50 51 1.721691 TGTCCCCAATCCTCCCAAAAT 59.278 47.619 0.00 0.00 0.00 1.82
51 52 2.113414 TGTCCCCAATCCTCCCAAAATT 59.887 45.455 0.00 0.00 0.00 1.82
52 53 3.181329 GTCCCCAATCCTCCCAAAATTT 58.819 45.455 0.00 0.00 0.00 1.82
53 54 3.197766 GTCCCCAATCCTCCCAAAATTTC 59.802 47.826 0.00 0.00 0.00 2.17
54 55 2.505407 CCCCAATCCTCCCAAAATTTCC 59.495 50.000 0.00 0.00 0.00 3.13
55 56 2.168313 CCCAATCCTCCCAAAATTTCCG 59.832 50.000 0.00 0.00 0.00 4.30
56 57 2.168313 CCAATCCTCCCAAAATTTCCGG 59.832 50.000 0.00 0.00 0.00 5.14
57 58 2.831526 CAATCCTCCCAAAATTTCCGGT 59.168 45.455 0.00 0.00 0.00 5.28
58 59 2.209690 TCCTCCCAAAATTTCCGGTC 57.790 50.000 0.00 0.00 0.00 4.79
59 60 1.182667 CCTCCCAAAATTTCCGGTCC 58.817 55.000 0.00 0.00 0.00 4.46
60 61 1.549037 CCTCCCAAAATTTCCGGTCCA 60.549 52.381 0.00 0.00 0.00 4.02
61 62 1.818674 CTCCCAAAATTTCCGGTCCAG 59.181 52.381 0.00 0.00 0.00 3.86
62 63 1.146152 TCCCAAAATTTCCGGTCCAGT 59.854 47.619 0.00 0.00 0.00 4.00
63 64 1.544246 CCCAAAATTTCCGGTCCAGTC 59.456 52.381 0.00 0.00 0.00 3.51
64 65 2.235016 CCAAAATTTCCGGTCCAGTCA 58.765 47.619 0.00 0.00 0.00 3.41
65 66 2.825532 CCAAAATTTCCGGTCCAGTCAT 59.174 45.455 0.00 0.00 0.00 3.06
66 67 3.367292 CCAAAATTTCCGGTCCAGTCATG 60.367 47.826 0.00 0.00 0.00 3.07
67 68 3.433306 AAATTTCCGGTCCAGTCATGA 57.567 42.857 0.00 0.00 0.00 3.07
68 69 3.433306 AATTTCCGGTCCAGTCATGAA 57.567 42.857 0.00 0.00 0.00 2.57
69 70 3.652057 ATTTCCGGTCCAGTCATGAAT 57.348 42.857 0.00 0.00 0.00 2.57
70 71 3.433306 TTTCCGGTCCAGTCATGAATT 57.567 42.857 0.00 0.00 0.00 2.17
71 72 2.691409 TCCGGTCCAGTCATGAATTC 57.309 50.000 0.00 0.00 0.00 2.17
72 73 1.209504 TCCGGTCCAGTCATGAATTCC 59.790 52.381 0.00 0.00 0.00 3.01
73 74 1.668419 CGGTCCAGTCATGAATTCCC 58.332 55.000 2.27 0.00 0.00 3.97
74 75 1.065491 CGGTCCAGTCATGAATTCCCA 60.065 52.381 2.27 0.00 0.00 4.37
75 76 2.421952 CGGTCCAGTCATGAATTCCCAT 60.422 50.000 2.27 0.00 0.00 4.00
76 77 2.954318 GGTCCAGTCATGAATTCCCATG 59.046 50.000 2.27 1.86 43.88 3.66
77 78 2.360165 GTCCAGTCATGAATTCCCATGC 59.640 50.000 2.27 0.00 42.63 4.06
78 79 2.242965 TCCAGTCATGAATTCCCATGCT 59.757 45.455 2.27 1.49 42.63 3.79
79 80 3.459227 TCCAGTCATGAATTCCCATGCTA 59.541 43.478 2.27 0.00 42.63 3.49
80 81 3.567164 CCAGTCATGAATTCCCATGCTAC 59.433 47.826 2.27 0.00 42.63 3.58
81 82 3.567164 CAGTCATGAATTCCCATGCTACC 59.433 47.826 2.27 0.00 42.63 3.18
82 83 2.887152 GTCATGAATTCCCATGCTACCC 59.113 50.000 2.27 0.00 42.63 3.69
83 84 1.881973 CATGAATTCCCATGCTACCCG 59.118 52.381 2.27 0.00 37.68 5.28
84 85 1.208706 TGAATTCCCATGCTACCCGA 58.791 50.000 2.27 0.00 0.00 5.14
85 86 1.134220 TGAATTCCCATGCTACCCGAC 60.134 52.381 2.27 0.00 0.00 4.79
86 87 1.141053 GAATTCCCATGCTACCCGACT 59.859 52.381 0.00 0.00 0.00 4.18
87 88 2.097110 ATTCCCATGCTACCCGACTA 57.903 50.000 0.00 0.00 0.00 2.59
88 89 2.097110 TTCCCATGCTACCCGACTAT 57.903 50.000 0.00 0.00 0.00 2.12
89 90 1.338107 TCCCATGCTACCCGACTATG 58.662 55.000 0.00 0.00 0.00 2.23
90 91 0.321671 CCCATGCTACCCGACTATGG 59.678 60.000 0.00 0.00 38.37 2.74
91 92 0.320771 CCATGCTACCCGACTATGGC 60.321 60.000 0.00 0.00 32.72 4.40
92 93 0.681733 CATGCTACCCGACTATGGCT 59.318 55.000 0.00 0.00 0.00 4.75
93 94 1.070758 CATGCTACCCGACTATGGCTT 59.929 52.381 0.00 0.00 0.00 4.35
94 95 1.200519 TGCTACCCGACTATGGCTTT 58.799 50.000 0.00 0.00 0.00 3.51
95 96 1.138266 TGCTACCCGACTATGGCTTTC 59.862 52.381 0.00 0.00 0.00 2.62
96 97 1.413077 GCTACCCGACTATGGCTTTCT 59.587 52.381 0.00 0.00 0.00 2.52
97 98 2.158943 GCTACCCGACTATGGCTTTCTT 60.159 50.000 0.00 0.00 0.00 2.52
98 99 3.069158 GCTACCCGACTATGGCTTTCTTA 59.931 47.826 0.00 0.00 0.00 2.10
99 100 4.262506 GCTACCCGACTATGGCTTTCTTAT 60.263 45.833 0.00 0.00 0.00 1.73
100 101 4.338379 ACCCGACTATGGCTTTCTTATC 57.662 45.455 0.00 0.00 0.00 1.75
101 102 3.967987 ACCCGACTATGGCTTTCTTATCT 59.032 43.478 0.00 0.00 0.00 1.98
102 103 4.409247 ACCCGACTATGGCTTTCTTATCTT 59.591 41.667 0.00 0.00 0.00 2.40
103 104 5.104485 ACCCGACTATGGCTTTCTTATCTTT 60.104 40.000 0.00 0.00 0.00 2.52
104 105 5.237344 CCCGACTATGGCTTTCTTATCTTTG 59.763 44.000 0.00 0.00 0.00 2.77
105 106 5.277538 CCGACTATGGCTTTCTTATCTTTGC 60.278 44.000 0.00 0.00 0.00 3.68
106 107 5.525378 CGACTATGGCTTTCTTATCTTTGCT 59.475 40.000 0.00 0.00 0.00 3.91
107 108 6.037610 CGACTATGGCTTTCTTATCTTTGCTT 59.962 38.462 0.00 0.00 0.00 3.91
108 109 7.093322 ACTATGGCTTTCTTATCTTTGCTTG 57.907 36.000 0.00 0.00 0.00 4.01
109 110 4.178545 TGGCTTTCTTATCTTTGCTTGC 57.821 40.909 0.00 0.00 0.00 4.01
110 111 3.828451 TGGCTTTCTTATCTTTGCTTGCT 59.172 39.130 0.00 0.00 0.00 3.91
111 112 5.009631 TGGCTTTCTTATCTTTGCTTGCTA 58.990 37.500 0.00 0.00 0.00 3.49
112 113 5.106157 TGGCTTTCTTATCTTTGCTTGCTAC 60.106 40.000 0.00 0.00 0.00 3.58
113 114 5.335935 GCTTTCTTATCTTTGCTTGCTACC 58.664 41.667 0.00 0.00 0.00 3.18
114 115 5.677344 GCTTTCTTATCTTTGCTTGCTACCC 60.677 44.000 0.00 0.00 0.00 3.69
115 116 3.886123 TCTTATCTTTGCTTGCTACCCC 58.114 45.455 0.00 0.00 0.00 4.95
116 117 3.265737 TCTTATCTTTGCTTGCTACCCCA 59.734 43.478 0.00 0.00 0.00 4.96
117 118 2.834638 ATCTTTGCTTGCTACCCCAT 57.165 45.000 0.00 0.00 0.00 4.00
118 119 2.128771 TCTTTGCTTGCTACCCCATC 57.871 50.000 0.00 0.00 0.00 3.51
119 120 1.354031 TCTTTGCTTGCTACCCCATCA 59.646 47.619 0.00 0.00 0.00 3.07
120 121 1.747355 CTTTGCTTGCTACCCCATCAG 59.253 52.381 0.00 0.00 0.00 2.90
121 122 0.034186 TTGCTTGCTACCCCATCAGG 60.034 55.000 0.00 0.00 0.00 3.86
122 123 0.913934 TGCTTGCTACCCCATCAGGA 60.914 55.000 0.00 0.00 38.24 3.86
123 124 0.475906 GCTTGCTACCCCATCAGGAT 59.524 55.000 0.00 0.00 38.24 3.24
124 125 1.133668 GCTTGCTACCCCATCAGGATT 60.134 52.381 0.00 0.00 38.24 3.01
125 126 2.579873 CTTGCTACCCCATCAGGATTG 58.420 52.381 0.00 0.00 38.24 2.67
126 127 1.595311 TGCTACCCCATCAGGATTGT 58.405 50.000 0.00 0.00 38.24 2.71
127 128 1.490490 TGCTACCCCATCAGGATTGTC 59.510 52.381 0.00 0.00 38.24 3.18
128 129 1.541233 GCTACCCCATCAGGATTGTCG 60.541 57.143 0.00 0.00 38.24 4.35
129 130 2.039418 CTACCCCATCAGGATTGTCGA 58.961 52.381 0.00 0.00 38.24 4.20
130 131 1.285280 ACCCCATCAGGATTGTCGAA 58.715 50.000 0.00 0.00 38.24 3.71
131 132 1.846439 ACCCCATCAGGATTGTCGAAT 59.154 47.619 0.00 0.00 38.24 3.34
132 133 3.045634 ACCCCATCAGGATTGTCGAATA 58.954 45.455 0.00 0.00 38.24 1.75
133 134 3.458118 ACCCCATCAGGATTGTCGAATAA 59.542 43.478 0.00 0.00 38.24 1.40
134 135 4.104738 ACCCCATCAGGATTGTCGAATAAT 59.895 41.667 0.00 0.00 38.24 1.28
135 136 4.456911 CCCCATCAGGATTGTCGAATAATG 59.543 45.833 1.29 0.00 38.24 1.90
136 137 4.456911 CCCATCAGGATTGTCGAATAATGG 59.543 45.833 1.29 0.00 38.24 3.16
137 138 5.308014 CCATCAGGATTGTCGAATAATGGA 58.692 41.667 1.29 0.00 36.89 3.41
138 139 5.764686 CCATCAGGATTGTCGAATAATGGAA 59.235 40.000 1.29 0.00 36.89 3.53
139 140 6.262944 CCATCAGGATTGTCGAATAATGGAAA 59.737 38.462 1.29 0.00 36.89 3.13
140 141 7.040201 CCATCAGGATTGTCGAATAATGGAAAT 60.040 37.037 1.29 0.00 36.89 2.17
141 142 7.263100 TCAGGATTGTCGAATAATGGAAATG 57.737 36.000 1.29 0.00 0.00 2.32
142 143 7.053498 TCAGGATTGTCGAATAATGGAAATGA 58.947 34.615 1.29 0.00 0.00 2.57
143 144 7.012327 TCAGGATTGTCGAATAATGGAAATGAC 59.988 37.037 1.29 0.00 0.00 3.06
144 145 6.828273 AGGATTGTCGAATAATGGAAATGACA 59.172 34.615 1.29 0.00 33.47 3.58
145 146 7.503566 AGGATTGTCGAATAATGGAAATGACAT 59.496 33.333 1.29 0.00 35.12 3.06
146 147 8.137437 GGATTGTCGAATAATGGAAATGACATT 58.863 33.333 0.00 0.00 41.17 2.71
147 148 9.173939 GATTGTCGAATAATGGAAATGACATTC 57.826 33.333 0.05 0.00 39.18 2.67
148 149 7.864108 TGTCGAATAATGGAAATGACATTCT 57.136 32.000 0.05 0.00 39.18 2.40
149 150 7.919690 TGTCGAATAATGGAAATGACATTCTC 58.080 34.615 0.05 2.06 39.18 2.87
150 151 7.552330 TGTCGAATAATGGAAATGACATTCTCA 59.448 33.333 0.05 3.75 39.18 3.27
151 152 7.852945 GTCGAATAATGGAAATGACATTCTCAC 59.147 37.037 0.05 0.00 39.18 3.51
152 153 7.552330 TCGAATAATGGAAATGACATTCTCACA 59.448 33.333 0.05 0.00 39.18 3.58
153 154 7.641411 CGAATAATGGAAATGACATTCTCACAC 59.359 37.037 0.05 0.00 39.18 3.82
154 155 7.943079 ATAATGGAAATGACATTCTCACACA 57.057 32.000 0.05 0.00 39.18 3.72
155 156 5.892160 ATGGAAATGACATTCTCACACAG 57.108 39.130 0.05 0.00 0.00 3.66
156 157 4.971939 TGGAAATGACATTCTCACACAGA 58.028 39.130 0.05 0.00 0.00 3.41
157 158 4.756642 TGGAAATGACATTCTCACACAGAC 59.243 41.667 0.05 0.00 0.00 3.51
158 159 4.154918 GGAAATGACATTCTCACACAGACC 59.845 45.833 0.05 0.00 0.00 3.85
159 160 2.839486 TGACATTCTCACACAGACCC 57.161 50.000 0.00 0.00 0.00 4.46
160 161 1.347707 TGACATTCTCACACAGACCCC 59.652 52.381 0.00 0.00 0.00 4.95
161 162 1.625818 GACATTCTCACACAGACCCCT 59.374 52.381 0.00 0.00 0.00 4.79
162 163 2.039084 GACATTCTCACACAGACCCCTT 59.961 50.000 0.00 0.00 0.00 3.95
163 164 2.224621 ACATTCTCACACAGACCCCTTG 60.225 50.000 0.00 0.00 0.00 3.61
164 165 0.764890 TTCTCACACAGACCCCTTGG 59.235 55.000 0.00 0.00 37.80 3.61
173 174 4.681624 ACCCCTTGGTAGCCTGAA 57.318 55.556 0.00 0.00 45.45 3.02
174 175 2.877150 ACCCCTTGGTAGCCTGAAA 58.123 52.632 0.00 0.00 45.45 2.69
175 176 0.404426 ACCCCTTGGTAGCCTGAAAC 59.596 55.000 0.00 0.00 45.45 2.78
176 177 0.404040 CCCCTTGGTAGCCTGAAACA 59.596 55.000 0.00 0.00 0.00 2.83
177 178 1.534729 CCCTTGGTAGCCTGAAACAC 58.465 55.000 0.00 0.00 0.00 3.32
178 179 1.202879 CCCTTGGTAGCCTGAAACACA 60.203 52.381 0.00 0.00 0.00 3.72
184 185 3.146066 GGTAGCCTGAAACACAACATCA 58.854 45.455 0.00 0.00 0.00 3.07
186 187 3.996150 AGCCTGAAACACAACATCAAG 57.004 42.857 0.00 0.00 0.00 3.02
193 194 6.293081 CCTGAAACACAACATCAAGTAGACTG 60.293 42.308 0.00 0.00 0.00 3.51
195 196 4.955811 ACACAACATCAAGTAGACTGGA 57.044 40.909 0.00 0.00 0.00 3.86
202 203 4.080129 ACATCAAGTAGACTGGAATGGCAT 60.080 41.667 0.00 0.00 28.12 4.40
204 205 2.338577 AGTAGACTGGAATGGCATGC 57.661 50.000 9.90 9.90 0.00 4.06
206 207 0.815213 TAGACTGGAATGGCATGCGC 60.815 55.000 12.44 0.00 37.44 6.09
238 239 7.833285 TTTATCAAAACCTCTTTACCAGCTT 57.167 32.000 0.00 0.00 0.00 3.74
239 240 5.966742 ATCAAAACCTCTTTACCAGCTTC 57.033 39.130 0.00 0.00 0.00 3.86
241 242 5.063880 TCAAAACCTCTTTACCAGCTTCTC 58.936 41.667 0.00 0.00 0.00 2.87
249 250 4.100189 TCTTTACCAGCTTCTCATAGGAGC 59.900 45.833 0.00 0.00 41.13 4.70
265 266 2.345124 GAGCTTCTCCATGCATCCTT 57.655 50.000 0.00 0.00 0.00 3.36
270 271 5.206587 AGCTTCTCCATGCATCCTTTTATT 58.793 37.500 0.00 0.00 0.00 1.40
271 272 5.659971 AGCTTCTCCATGCATCCTTTTATTT 59.340 36.000 0.00 0.00 0.00 1.40
304 305 5.462530 TCGGTCTCTCAAATACTTGAACA 57.537 39.130 0.00 0.00 41.05 3.18
308 309 6.173339 GGTCTCTCAAATACTTGAACATCCA 58.827 40.000 0.00 0.00 41.05 3.41
321 322 2.751166 ACATCCAGTTCTTCGAGTGG 57.249 50.000 0.00 0.00 40.77 4.00
327 328 2.027625 GTTCTTCGAGTGGCCCACG 61.028 63.158 8.52 3.31 39.64 4.94
329 330 2.430382 TTCTTCGAGTGGCCCACGTC 62.430 60.000 8.52 5.79 39.64 4.34
367 369 1.382522 TGGCCGCTCAAAGATTCATC 58.617 50.000 0.00 0.00 0.00 2.92
375 377 5.297776 CCGCTCAAAGATTCATCATAAACCT 59.702 40.000 0.00 0.00 0.00 3.50
378 380 6.183360 GCTCAAAGATTCATCATAAACCTGCT 60.183 38.462 0.00 0.00 0.00 4.24
379 381 7.630082 GCTCAAAGATTCATCATAAACCTGCTT 60.630 37.037 0.00 0.00 0.00 3.91
380 382 8.806429 TCAAAGATTCATCATAAACCTGCTTA 57.194 30.769 0.00 0.00 0.00 3.09
381 383 9.412460 TCAAAGATTCATCATAAACCTGCTTAT 57.588 29.630 0.00 0.00 0.00 1.73
389 391 9.120538 TCATCATAAACCTGCTTATTTCTTACC 57.879 33.333 0.00 0.00 0.00 2.85
391 393 8.506168 TCATAAACCTGCTTATTTCTTACCAG 57.494 34.615 0.00 0.00 0.00 4.00
394 396 4.844884 ACCTGCTTATTTCTTACCAGACC 58.155 43.478 0.00 0.00 0.00 3.85
395 397 4.200092 CCTGCTTATTTCTTACCAGACCC 58.800 47.826 0.00 0.00 0.00 4.46
396 398 3.869065 TGCTTATTTCTTACCAGACCCG 58.131 45.455 0.00 0.00 0.00 5.28
397 399 3.203716 GCTTATTTCTTACCAGACCCGG 58.796 50.000 0.00 0.00 0.00 5.73
398 400 3.118519 GCTTATTTCTTACCAGACCCGGA 60.119 47.826 0.73 0.00 0.00 5.14
401 656 0.971386 TTCTTACCAGACCCGGACAC 59.029 55.000 0.73 0.00 0.00 3.67
403 658 1.530013 CTTACCAGACCCGGACACGT 61.530 60.000 0.73 0.00 38.78 4.49
474 729 6.403866 AGTGGAATTTTCATTGCTTGTACA 57.596 33.333 0.00 0.00 32.04 2.90
476 731 6.925165 AGTGGAATTTTCATTGCTTGTACAAG 59.075 34.615 27.85 27.85 41.24 3.16
479 734 6.088085 GGAATTTTCATTGCTTGTACAAGTCG 59.912 38.462 30.90 18.91 40.45 4.18
485 740 0.234884 GCTTGTACAAGTCGTGTGCC 59.765 55.000 30.90 12.43 41.81 5.01
508 771 1.739338 CTCGCCTGGCCTAGTACTGG 61.739 65.000 14.12 1.52 0.00 4.00
510 773 0.754217 CGCCTGGCCTAGTACTGGTA 60.754 60.000 14.12 0.00 0.00 3.25
511 774 1.041437 GCCTGGCCTAGTACTGGTAG 58.959 60.000 7.66 7.87 0.00 3.18
512 775 1.041437 CCTGGCCTAGTACTGGTAGC 58.959 60.000 5.39 2.10 0.00 3.58
513 776 1.688311 CCTGGCCTAGTACTGGTAGCA 60.688 57.143 5.39 0.00 0.00 3.49
514 777 1.683917 CTGGCCTAGTACTGGTAGCAG 59.316 57.143 20.16 20.16 0.00 4.24
515 778 1.041437 GGCCTAGTACTGGTAGCAGG 58.959 60.000 24.84 8.92 0.00 4.85
516 779 0.389757 GCCTAGTACTGGTAGCAGGC 59.610 60.000 24.84 14.70 41.57 4.85
517 780 2.030045 GCCTAGTACTGGTAGCAGGCT 61.030 57.143 24.84 21.99 44.15 4.58
518 781 2.752154 GCCTAGTACTGGTAGCAGGCTA 60.752 54.545 24.84 21.94 44.15 3.93
520 783 1.404843 AGTACTGGTAGCAGGCTAGC 58.595 55.000 24.84 20.39 44.56 3.42
521 784 0.030908 GTACTGGTAGCAGGCTAGCG 59.969 60.000 24.84 18.11 46.51 4.26
522 785 2.419198 CTGGTAGCAGGCTAGCGG 59.581 66.667 20.87 20.87 46.51 5.52
542 816 1.697394 TGGTGAGCCAGGCCCATAT 60.697 57.895 8.22 0.00 40.46 1.78
543 817 1.228367 GGTGAGCCAGGCCCATATG 60.228 63.158 8.22 0.00 34.09 1.78
544 818 1.533711 GTGAGCCAGGCCCATATGT 59.466 57.895 8.22 0.00 0.00 2.29
546 820 0.764890 TGAGCCAGGCCCATATGTAC 59.235 55.000 8.22 0.00 0.00 2.90
547 821 0.764890 GAGCCAGGCCCATATGTACA 59.235 55.000 8.22 0.00 0.00 2.90
548 822 1.142870 GAGCCAGGCCCATATGTACAA 59.857 52.381 8.22 0.00 0.00 2.41
549 823 1.133792 AGCCAGGCCCATATGTACAAC 60.134 52.381 8.22 0.00 0.00 3.32
550 824 1.593196 CCAGGCCCATATGTACAACG 58.407 55.000 0.00 0.00 0.00 4.10
551 825 1.593196 CAGGCCCATATGTACAACGG 58.407 55.000 0.00 0.18 0.00 4.44
552 826 1.134220 CAGGCCCATATGTACAACGGT 60.134 52.381 0.00 0.00 0.00 4.83
553 827 2.103432 CAGGCCCATATGTACAACGGTA 59.897 50.000 0.00 0.00 0.00 4.02
554 828 2.773087 AGGCCCATATGTACAACGGTAA 59.227 45.455 0.00 0.00 0.00 2.85
555 829 2.874086 GGCCCATATGTACAACGGTAAC 59.126 50.000 0.00 0.00 0.00 2.50
687 963 3.864686 CGCCCCGCTTCATTCGTG 61.865 66.667 0.00 0.00 0.00 4.35
702 978 4.065281 GTGGGTCTGTCGGTCGGG 62.065 72.222 0.00 0.00 0.00 5.14
706 982 2.675772 GTCTGTCGGTCGGGGTCT 60.676 66.667 0.00 0.00 0.00 3.85
711 987 3.000819 TCGGTCGGGGTCTGCAAT 61.001 61.111 0.00 0.00 0.00 3.56
883 1177 1.265635 CACGCGAACAAAAGAATCCCA 59.734 47.619 15.93 0.00 0.00 4.37
892 1186 4.238669 ACAAAAGAATCCCAAAATCCCCA 58.761 39.130 0.00 0.00 0.00 4.96
906 1200 4.856801 CCCATCCCCTTCCACGCG 62.857 72.222 3.53 3.53 0.00 6.01
907 1201 4.096003 CCATCCCCTTCCACGCGT 62.096 66.667 5.58 5.58 0.00 6.01
911 1205 4.077184 CCCCTTCCACGCGTGCTA 62.077 66.667 33.17 20.26 0.00 3.49
1128 1422 3.114647 CTTCGTCCTCCCGCTCTCG 62.115 68.421 0.00 0.00 0.00 4.04
1180 1474 1.617018 CGCCCTCTTCTCCACCATCA 61.617 60.000 0.00 0.00 0.00 3.07
1290 1584 2.347490 GTCCTCTTCAAGGCCGCA 59.653 61.111 0.00 0.00 45.78 5.69
1332 1626 4.742649 TCGCTCCTCTCCACCGCT 62.743 66.667 0.00 0.00 0.00 5.52
1575 1869 1.298413 CGTCATCGTCGCCTACCTG 60.298 63.158 0.00 0.00 0.00 4.00
1593 1887 2.050934 GGTCGGGCTCGTCTACCTT 61.051 63.158 5.57 0.00 37.69 3.50
1626 1920 4.838486 CTCGCCAGCGTCGTCTCC 62.838 72.222 12.32 0.00 40.74 3.71
2144 2439 6.424812 CCAAAACAAAATGAGATGGAAGGAAC 59.575 38.462 0.00 0.00 0.00 3.62
2253 2673 6.094881 TGCTTGTAGTAATTTGTAATGGAGGC 59.905 38.462 0.00 0.00 0.00 4.70
2368 2791 1.474478 ACTAGATCACTGCACCACTCG 59.526 52.381 0.00 0.00 0.00 4.18
2369 2792 0.817654 TAGATCACTGCACCACTCGG 59.182 55.000 0.00 0.00 38.77 4.63
2463 2903 7.658982 GGCTATGAGATGAATTGAGATTACACA 59.341 37.037 0.00 0.00 0.00 3.72
2526 2966 5.163447 TGAGTAATTAAGCATGCCGTAGAGT 60.163 40.000 15.66 0.00 0.00 3.24
2557 2997 1.673626 GCCATGCAAATGACAGTTGGG 60.674 52.381 16.65 10.62 0.00 4.12
2561 3001 2.382882 TGCAAATGACAGTTGGGTTGA 58.617 42.857 16.65 0.00 0.00 3.18
2674 6856 1.857965 TGAGTGATCCACAGAGGGAG 58.142 55.000 0.00 0.00 41.08 4.30
2722 6904 3.243877 CGATGTTGAATCAGTAGCCTTCG 59.756 47.826 0.00 0.00 0.00 3.79
2765 6950 0.983467 TGCATCCAACCAGACTGCTA 59.017 50.000 0.00 0.00 34.02 3.49
2766 6951 1.065926 TGCATCCAACCAGACTGCTAG 60.066 52.381 0.00 0.00 34.02 3.42
2767 6952 1.745141 GCATCCAACCAGACTGCTAGG 60.745 57.143 0.00 0.00 0.00 3.02
2878 7303 1.178276 GAGTGGAGAAGGAAGCGAGA 58.822 55.000 0.00 0.00 0.00 4.04
2879 7304 1.546476 GAGTGGAGAAGGAAGCGAGAA 59.454 52.381 0.00 0.00 0.00 2.87
2901 7326 3.277142 AAAGTGGGTTTCAGAGACGTT 57.723 42.857 0.00 0.00 0.00 3.99
2951 7376 2.341257 CTATGAATCCCGAGATTGCCG 58.659 52.381 0.00 0.00 42.93 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.389555 GGGGCCGTTCCTTATTGAAG 58.610 55.000 0.00 0.00 34.39 3.02
1 2 0.393267 CGGGGCCGTTCCTTATTGAA 60.393 55.000 0.00 0.00 34.39 2.69
2 3 1.222387 CGGGGCCGTTCCTTATTGA 59.778 57.895 0.00 0.00 34.39 2.57
3 4 1.822186 CCGGGGCCGTTCCTTATTG 60.822 63.158 0.00 0.00 37.81 1.90
4 5 1.564483 TTCCGGGGCCGTTCCTTATT 61.564 55.000 0.00 0.00 37.81 1.40
5 6 1.979619 CTTCCGGGGCCGTTCCTTAT 61.980 60.000 0.00 0.00 37.81 1.73
6 7 2.607134 TTCCGGGGCCGTTCCTTA 60.607 61.111 0.00 0.00 37.81 2.69
7 8 4.029809 CTTCCGGGGCCGTTCCTT 62.030 66.667 0.00 0.00 37.81 3.36
10 11 4.796495 ATGCTTCCGGGGCCGTTC 62.796 66.667 15.57 0.00 37.81 3.95
16 17 2.825836 GACAGCATGCTTCCGGGG 60.826 66.667 19.98 8.31 42.53 5.73
17 18 2.825836 GGACAGCATGCTTCCGGG 60.826 66.667 19.98 9.14 42.53 5.73
18 19 2.825836 GGGACAGCATGCTTCCGG 60.826 66.667 27.77 17.81 42.53 5.14
19 20 2.825836 GGGGACAGCATGCTTCCG 60.826 66.667 27.77 18.10 42.53 4.30
20 21 0.685458 ATTGGGGACAGCATGCTTCC 60.685 55.000 27.40 27.40 44.54 3.46
21 22 0.743097 GATTGGGGACAGCATGCTTC 59.257 55.000 19.98 17.92 44.54 3.86
22 23 0.685458 GGATTGGGGACAGCATGCTT 60.685 55.000 19.98 9.90 44.54 3.91
23 24 1.076485 GGATTGGGGACAGCATGCT 60.076 57.895 16.30 16.30 44.54 3.79
24 25 1.076485 AGGATTGGGGACAGCATGC 60.076 57.895 10.51 10.51 44.54 4.06
25 26 0.466922 GGAGGATTGGGGACAGCATG 60.467 60.000 0.00 0.00 44.54 4.06
26 27 1.649271 GGGAGGATTGGGGACAGCAT 61.649 60.000 0.00 0.00 44.54 3.79
27 28 2.308722 GGGAGGATTGGGGACAGCA 61.309 63.158 0.00 0.00 44.54 4.41
28 29 1.863155 TTGGGAGGATTGGGGACAGC 61.863 60.000 0.00 0.00 44.54 4.40
29 30 0.704076 TTTGGGAGGATTGGGGACAG 59.296 55.000 0.00 0.00 44.54 3.51
30 31 1.162505 TTTTGGGAGGATTGGGGACA 58.837 50.000 0.00 0.00 39.83 4.02
31 32 2.550277 ATTTTGGGAGGATTGGGGAC 57.450 50.000 0.00 0.00 0.00 4.46
32 33 3.449918 GAAATTTTGGGAGGATTGGGGA 58.550 45.455 0.00 0.00 0.00 4.81
33 34 2.505407 GGAAATTTTGGGAGGATTGGGG 59.495 50.000 0.00 0.00 0.00 4.96
34 35 2.168313 CGGAAATTTTGGGAGGATTGGG 59.832 50.000 0.00 0.00 0.00 4.12
35 36 2.168313 CCGGAAATTTTGGGAGGATTGG 59.832 50.000 0.00 0.00 0.00 3.16
36 37 2.831526 ACCGGAAATTTTGGGAGGATTG 59.168 45.455 9.46 0.00 0.00 2.67
37 38 3.096852 GACCGGAAATTTTGGGAGGATT 58.903 45.455 9.46 0.00 0.00 3.01
38 39 2.623239 GGACCGGAAATTTTGGGAGGAT 60.623 50.000 9.46 0.00 0.00 3.24
39 40 1.272258 GGACCGGAAATTTTGGGAGGA 60.272 52.381 9.46 0.00 0.00 3.71
40 41 1.182667 GGACCGGAAATTTTGGGAGG 58.817 55.000 9.46 6.24 0.00 4.30
41 42 1.818674 CTGGACCGGAAATTTTGGGAG 59.181 52.381 9.46 4.53 0.00 4.30
42 43 1.146152 ACTGGACCGGAAATTTTGGGA 59.854 47.619 9.46 0.00 0.00 4.37
43 44 1.544246 GACTGGACCGGAAATTTTGGG 59.456 52.381 9.46 10.13 0.00 4.12
44 45 2.235016 TGACTGGACCGGAAATTTTGG 58.765 47.619 9.46 8.44 0.00 3.28
45 46 3.505680 TCATGACTGGACCGGAAATTTTG 59.494 43.478 9.46 0.00 0.00 2.44
46 47 3.761897 TCATGACTGGACCGGAAATTTT 58.238 40.909 9.46 0.00 0.00 1.82
47 48 3.433306 TCATGACTGGACCGGAAATTT 57.567 42.857 9.46 0.00 0.00 1.82
48 49 3.433306 TTCATGACTGGACCGGAAATT 57.567 42.857 9.46 0.00 0.00 1.82
49 50 3.652057 ATTCATGACTGGACCGGAAAT 57.348 42.857 9.46 0.00 0.00 2.17
50 51 3.343617 GAATTCATGACTGGACCGGAAA 58.656 45.455 9.46 0.00 0.00 3.13
51 52 2.355716 GGAATTCATGACTGGACCGGAA 60.356 50.000 9.46 0.00 0.00 4.30
52 53 1.209504 GGAATTCATGACTGGACCGGA 59.790 52.381 9.46 0.00 0.00 5.14
53 54 1.668419 GGAATTCATGACTGGACCGG 58.332 55.000 7.93 0.00 0.00 5.28
54 55 1.065491 TGGGAATTCATGACTGGACCG 60.065 52.381 7.93 0.00 0.00 4.79
55 56 2.806945 TGGGAATTCATGACTGGACC 57.193 50.000 7.93 0.00 0.00 4.46
56 57 2.360165 GCATGGGAATTCATGACTGGAC 59.640 50.000 7.93 0.00 45.30 4.02
57 58 2.242965 AGCATGGGAATTCATGACTGGA 59.757 45.455 7.93 0.00 45.30 3.86
58 59 2.662866 AGCATGGGAATTCATGACTGG 58.337 47.619 7.93 0.00 45.30 4.00
59 60 3.567164 GGTAGCATGGGAATTCATGACTG 59.433 47.826 7.93 0.00 45.30 3.51
60 61 3.435601 GGGTAGCATGGGAATTCATGACT 60.436 47.826 7.93 8.12 45.30 3.41
61 62 2.887152 GGGTAGCATGGGAATTCATGAC 59.113 50.000 7.93 0.00 45.30 3.06
62 63 2.487086 CGGGTAGCATGGGAATTCATGA 60.487 50.000 7.93 0.00 45.30 3.07
63 64 1.881973 CGGGTAGCATGGGAATTCATG 59.118 52.381 7.93 5.31 45.26 3.07
64 65 1.774254 TCGGGTAGCATGGGAATTCAT 59.226 47.619 7.93 0.00 0.00 2.57
65 66 1.134220 GTCGGGTAGCATGGGAATTCA 60.134 52.381 7.93 0.00 0.00 2.57
66 67 1.141053 AGTCGGGTAGCATGGGAATTC 59.859 52.381 0.00 0.00 0.00 2.17
67 68 1.213296 AGTCGGGTAGCATGGGAATT 58.787 50.000 0.00 0.00 0.00 2.17
68 69 2.097110 TAGTCGGGTAGCATGGGAAT 57.903 50.000 0.00 0.00 0.00 3.01
69 70 1.691976 CATAGTCGGGTAGCATGGGAA 59.308 52.381 0.00 0.00 0.00 3.97
70 71 1.338107 CATAGTCGGGTAGCATGGGA 58.662 55.000 0.00 0.00 0.00 4.37
71 72 0.321671 CCATAGTCGGGTAGCATGGG 59.678 60.000 0.00 0.00 33.87 4.00
72 73 0.320771 GCCATAGTCGGGTAGCATGG 60.321 60.000 4.31 4.31 39.35 3.66
73 74 0.681733 AGCCATAGTCGGGTAGCATG 59.318 55.000 0.00 0.00 34.17 4.06
74 75 1.424638 AAGCCATAGTCGGGTAGCAT 58.575 50.000 0.00 0.00 35.11 3.79
75 76 1.138266 GAAAGCCATAGTCGGGTAGCA 59.862 52.381 0.00 0.00 35.11 3.49
76 77 1.413077 AGAAAGCCATAGTCGGGTAGC 59.587 52.381 0.00 0.00 35.11 3.58
77 78 3.821421 AAGAAAGCCATAGTCGGGTAG 57.179 47.619 0.00 0.00 35.11 3.18
78 79 5.145564 AGATAAGAAAGCCATAGTCGGGTA 58.854 41.667 0.00 0.00 35.11 3.69
79 80 3.967987 AGATAAGAAAGCCATAGTCGGGT 59.032 43.478 0.00 0.00 38.81 5.28
80 81 4.608948 AGATAAGAAAGCCATAGTCGGG 57.391 45.455 0.00 0.00 0.00 5.14
81 82 5.277538 GCAAAGATAAGAAAGCCATAGTCGG 60.278 44.000 0.00 0.00 0.00 4.79
82 83 5.525378 AGCAAAGATAAGAAAGCCATAGTCG 59.475 40.000 0.00 0.00 0.00 4.18
83 84 6.934048 AGCAAAGATAAGAAAGCCATAGTC 57.066 37.500 0.00 0.00 0.00 2.59
84 85 6.405176 GCAAGCAAAGATAAGAAAGCCATAGT 60.405 38.462 0.00 0.00 0.00 2.12
85 86 5.975939 GCAAGCAAAGATAAGAAAGCCATAG 59.024 40.000 0.00 0.00 0.00 2.23
86 87 5.653769 AGCAAGCAAAGATAAGAAAGCCATA 59.346 36.000 0.00 0.00 0.00 2.74
87 88 4.465305 AGCAAGCAAAGATAAGAAAGCCAT 59.535 37.500 0.00 0.00 0.00 4.40
88 89 3.828451 AGCAAGCAAAGATAAGAAAGCCA 59.172 39.130 0.00 0.00 0.00 4.75
89 90 4.446994 AGCAAGCAAAGATAAGAAAGCC 57.553 40.909 0.00 0.00 0.00 4.35
90 91 5.335935 GGTAGCAAGCAAAGATAAGAAAGC 58.664 41.667 0.00 0.00 0.00 3.51
91 92 5.163612 GGGGTAGCAAGCAAAGATAAGAAAG 60.164 44.000 0.00 0.00 0.00 2.62
92 93 4.705023 GGGGTAGCAAGCAAAGATAAGAAA 59.295 41.667 0.00 0.00 0.00 2.52
93 94 4.263727 TGGGGTAGCAAGCAAAGATAAGAA 60.264 41.667 0.00 0.00 0.00 2.52
94 95 3.265737 TGGGGTAGCAAGCAAAGATAAGA 59.734 43.478 0.00 0.00 0.00 2.10
95 96 3.620488 TGGGGTAGCAAGCAAAGATAAG 58.380 45.455 0.00 0.00 0.00 1.73
96 97 3.730215 TGGGGTAGCAAGCAAAGATAA 57.270 42.857 0.00 0.00 0.00 1.75
97 98 3.201930 TGATGGGGTAGCAAGCAAAGATA 59.798 43.478 0.00 0.00 0.00 1.98
98 99 2.025037 TGATGGGGTAGCAAGCAAAGAT 60.025 45.455 0.00 0.00 0.00 2.40
99 100 1.354031 TGATGGGGTAGCAAGCAAAGA 59.646 47.619 0.00 0.00 0.00 2.52
100 101 1.747355 CTGATGGGGTAGCAAGCAAAG 59.253 52.381 0.00 0.00 0.00 2.77
101 102 1.616725 CCTGATGGGGTAGCAAGCAAA 60.617 52.381 0.00 0.00 0.00 3.68
102 103 0.034186 CCTGATGGGGTAGCAAGCAA 60.034 55.000 0.00 0.00 0.00 3.91
103 104 0.913934 TCCTGATGGGGTAGCAAGCA 60.914 55.000 0.00 0.00 35.33 3.91
104 105 0.475906 ATCCTGATGGGGTAGCAAGC 59.524 55.000 0.00 0.00 35.33 4.01
105 106 2.092212 ACAATCCTGATGGGGTAGCAAG 60.092 50.000 0.00 0.00 35.33 4.01
106 107 1.922447 ACAATCCTGATGGGGTAGCAA 59.078 47.619 0.00 0.00 35.33 3.91
107 108 1.490490 GACAATCCTGATGGGGTAGCA 59.510 52.381 0.00 0.00 35.33 3.49
108 109 1.541233 CGACAATCCTGATGGGGTAGC 60.541 57.143 0.00 0.00 35.33 3.58
109 110 2.039418 TCGACAATCCTGATGGGGTAG 58.961 52.381 0.00 0.00 35.33 3.18
110 111 2.168458 TCGACAATCCTGATGGGGTA 57.832 50.000 0.00 0.00 35.33 3.69
111 112 1.285280 TTCGACAATCCTGATGGGGT 58.715 50.000 0.00 0.00 35.33 4.95
112 113 2.645838 ATTCGACAATCCTGATGGGG 57.354 50.000 0.00 0.00 35.33 4.96
113 114 4.456911 CCATTATTCGACAATCCTGATGGG 59.543 45.833 0.00 0.00 0.00 4.00
114 115 5.308014 TCCATTATTCGACAATCCTGATGG 58.692 41.667 0.00 0.00 34.31 3.51
115 116 6.866010 TTCCATTATTCGACAATCCTGATG 57.134 37.500 0.00 0.00 0.00 3.07
116 117 7.720957 TCATTTCCATTATTCGACAATCCTGAT 59.279 33.333 0.00 0.00 0.00 2.90
117 118 7.012327 GTCATTTCCATTATTCGACAATCCTGA 59.988 37.037 0.00 0.00 0.00 3.86
118 119 7.134815 GTCATTTCCATTATTCGACAATCCTG 58.865 38.462 0.00 0.00 0.00 3.86
119 120 6.828273 TGTCATTTCCATTATTCGACAATCCT 59.172 34.615 0.00 0.00 0.00 3.24
120 121 7.026631 TGTCATTTCCATTATTCGACAATCC 57.973 36.000 0.00 0.00 0.00 3.01
121 122 9.173939 GAATGTCATTTCCATTATTCGACAATC 57.826 33.333 0.00 0.00 35.72 2.67
122 123 8.906867 AGAATGTCATTTCCATTATTCGACAAT 58.093 29.630 0.00 0.00 35.72 2.71
123 124 8.279970 AGAATGTCATTTCCATTATTCGACAA 57.720 30.769 0.00 0.00 35.72 3.18
124 125 7.552330 TGAGAATGTCATTTCCATTATTCGACA 59.448 33.333 0.00 0.00 36.45 4.35
125 126 7.852945 GTGAGAATGTCATTTCCATTATTCGAC 59.147 37.037 0.00 0.00 37.56 4.20
126 127 7.552330 TGTGAGAATGTCATTTCCATTATTCGA 59.448 33.333 0.00 0.00 37.56 3.71
127 128 7.641411 GTGTGAGAATGTCATTTCCATTATTCG 59.359 37.037 0.00 0.00 37.56 3.34
128 129 8.461222 TGTGTGAGAATGTCATTTCCATTATTC 58.539 33.333 0.00 0.00 37.56 1.75
129 130 8.352137 TGTGTGAGAATGTCATTTCCATTATT 57.648 30.769 0.00 0.00 37.56 1.40
130 131 7.830697 TCTGTGTGAGAATGTCATTTCCATTAT 59.169 33.333 0.00 0.00 37.56 1.28
131 132 7.119699 GTCTGTGTGAGAATGTCATTTCCATTA 59.880 37.037 0.00 0.00 37.56 1.90
132 133 6.005823 TCTGTGTGAGAATGTCATTTCCATT 58.994 36.000 0.00 0.00 37.56 3.16
133 134 5.413833 GTCTGTGTGAGAATGTCATTTCCAT 59.586 40.000 0.00 0.00 37.56 3.41
134 135 4.756642 GTCTGTGTGAGAATGTCATTTCCA 59.243 41.667 0.00 0.00 37.56 3.53
135 136 4.154918 GGTCTGTGTGAGAATGTCATTTCC 59.845 45.833 0.00 0.00 37.56 3.13
136 137 4.154918 GGGTCTGTGTGAGAATGTCATTTC 59.845 45.833 0.00 0.95 37.56 2.17
137 138 4.074970 GGGTCTGTGTGAGAATGTCATTT 58.925 43.478 0.00 0.00 37.56 2.32
138 139 3.560025 GGGGTCTGTGTGAGAATGTCATT 60.560 47.826 0.00 0.00 37.56 2.57
139 140 2.026822 GGGGTCTGTGTGAGAATGTCAT 60.027 50.000 0.00 0.00 37.56 3.06
140 141 1.347707 GGGGTCTGTGTGAGAATGTCA 59.652 52.381 0.00 0.00 30.26 3.58
141 142 1.625818 AGGGGTCTGTGTGAGAATGTC 59.374 52.381 0.00 0.00 30.26 3.06
142 143 1.734655 AGGGGTCTGTGTGAGAATGT 58.265 50.000 0.00 0.00 30.26 2.71
143 144 2.430465 CAAGGGGTCTGTGTGAGAATG 58.570 52.381 0.00 0.00 30.26 2.67
144 145 1.352352 CCAAGGGGTCTGTGTGAGAAT 59.648 52.381 0.00 0.00 30.26 2.40
145 146 0.764890 CCAAGGGGTCTGTGTGAGAA 59.235 55.000 0.00 0.00 30.26 2.87
146 147 2.452116 CCAAGGGGTCTGTGTGAGA 58.548 57.895 0.00 0.00 0.00 3.27
157 158 0.404040 TGTTTCAGGCTACCAAGGGG 59.596 55.000 0.00 0.00 41.29 4.79
158 159 1.202879 TGTGTTTCAGGCTACCAAGGG 60.203 52.381 0.00 0.00 0.00 3.95
159 160 2.270352 TGTGTTTCAGGCTACCAAGG 57.730 50.000 0.00 0.00 0.00 3.61
160 161 2.948979 TGTTGTGTTTCAGGCTACCAAG 59.051 45.455 0.00 0.00 0.00 3.61
161 162 3.006112 TGTTGTGTTTCAGGCTACCAA 57.994 42.857 0.00 0.00 0.00 3.67
162 163 2.719531 TGTTGTGTTTCAGGCTACCA 57.280 45.000 0.00 0.00 0.00 3.25
163 164 3.146066 TGATGTTGTGTTTCAGGCTACC 58.854 45.455 0.00 0.00 0.00 3.18
164 165 4.275936 ACTTGATGTTGTGTTTCAGGCTAC 59.724 41.667 0.00 0.00 0.00 3.58
165 166 4.460263 ACTTGATGTTGTGTTTCAGGCTA 58.540 39.130 0.00 0.00 0.00 3.93
166 167 3.290710 ACTTGATGTTGTGTTTCAGGCT 58.709 40.909 0.00 0.00 0.00 4.58
167 168 3.715628 ACTTGATGTTGTGTTTCAGGC 57.284 42.857 0.00 0.00 0.00 4.85
168 169 5.760253 AGTCTACTTGATGTTGTGTTTCAGG 59.240 40.000 0.00 0.00 0.00 3.86
169 170 6.293081 CCAGTCTACTTGATGTTGTGTTTCAG 60.293 42.308 0.00 0.00 0.00 3.02
170 171 5.527214 CCAGTCTACTTGATGTTGTGTTTCA 59.473 40.000 0.00 0.00 0.00 2.69
171 172 5.758296 TCCAGTCTACTTGATGTTGTGTTTC 59.242 40.000 0.00 0.00 0.00 2.78
172 173 5.680619 TCCAGTCTACTTGATGTTGTGTTT 58.319 37.500 0.00 0.00 0.00 2.83
173 174 5.290493 TCCAGTCTACTTGATGTTGTGTT 57.710 39.130 0.00 0.00 0.00 3.32
174 175 4.955811 TCCAGTCTACTTGATGTTGTGT 57.044 40.909 0.00 0.00 0.00 3.72
175 176 5.122869 CCATTCCAGTCTACTTGATGTTGTG 59.877 44.000 0.00 0.00 0.00 3.33
176 177 5.248640 CCATTCCAGTCTACTTGATGTTGT 58.751 41.667 0.00 0.00 0.00 3.32
177 178 4.095483 GCCATTCCAGTCTACTTGATGTTG 59.905 45.833 0.00 0.00 0.00 3.33
178 179 4.263462 TGCCATTCCAGTCTACTTGATGTT 60.263 41.667 0.00 0.00 0.00 2.71
184 185 2.648059 GCATGCCATTCCAGTCTACTT 58.352 47.619 6.36 0.00 0.00 2.24
186 187 0.940126 CGCATGCCATTCCAGTCTAC 59.060 55.000 13.15 0.00 0.00 2.59
202 203 5.046950 AGGTTTTGATAAAATAAAGGGCGCA 60.047 36.000 10.83 0.00 32.22 6.09
204 205 6.863275 AGAGGTTTTGATAAAATAAAGGGCG 58.137 36.000 0.00 0.00 32.22 6.13
235 236 3.385193 GGAGAAGCTCCTATGAGAAGC 57.615 52.381 6.23 0.00 46.41 3.86
270 271 1.139455 AGAGACCGAACGTGGGAAAAA 59.861 47.619 12.48 0.00 0.00 1.94
271 272 0.754472 AGAGACCGAACGTGGGAAAA 59.246 50.000 12.48 0.00 0.00 2.29
279 280 4.482386 TCAAGTATTTGAGAGACCGAACG 58.518 43.478 0.00 0.00 38.37 3.95
280 281 5.694910 TGTTCAAGTATTTGAGAGACCGAAC 59.305 40.000 0.65 0.00 43.76 3.95
281 282 5.849510 TGTTCAAGTATTTGAGAGACCGAA 58.150 37.500 0.65 0.00 43.76 4.30
282 283 5.462530 TGTTCAAGTATTTGAGAGACCGA 57.537 39.130 0.65 0.00 43.76 4.69
286 287 7.009179 ACTGGATGTTCAAGTATTTGAGAGA 57.991 36.000 0.65 0.00 43.76 3.10
304 305 0.250513 GGCCACTCGAAGAACTGGAT 59.749 55.000 0.00 0.00 36.75 3.41
308 309 1.371558 GTGGGCCACTCGAAGAACT 59.628 57.895 29.22 0.00 34.09 3.01
327 328 4.685924 CAATATTTGGGATGCCAACTGAC 58.314 43.478 19.51 0.00 0.00 3.51
347 349 1.745087 GATGAATCTTTGAGCGGCCAA 59.255 47.619 2.24 0.00 0.00 4.52
367 369 8.398665 GTCTGGTAAGAAATAAGCAGGTTTATG 58.601 37.037 0.00 0.00 40.70 1.90
375 377 3.370103 CCGGGTCTGGTAAGAAATAAGCA 60.370 47.826 0.00 0.00 33.05 3.91
378 380 3.839490 TGTCCGGGTCTGGTAAGAAATAA 59.161 43.478 0.00 0.00 33.05 1.40
379 381 3.196254 GTGTCCGGGTCTGGTAAGAAATA 59.804 47.826 0.00 0.00 33.05 1.40
380 382 2.027469 GTGTCCGGGTCTGGTAAGAAAT 60.027 50.000 0.00 0.00 33.05 2.17
381 383 1.345415 GTGTCCGGGTCTGGTAAGAAA 59.655 52.381 0.00 0.00 33.05 2.52
382 384 0.971386 GTGTCCGGGTCTGGTAAGAA 59.029 55.000 0.00 0.00 33.05 2.52
383 385 1.246056 CGTGTCCGGGTCTGGTAAGA 61.246 60.000 0.00 0.00 0.00 2.10
384 386 1.214589 CGTGTCCGGGTCTGGTAAG 59.785 63.158 0.00 0.00 0.00 2.34
386 388 2.115910 ACGTGTCCGGGTCTGGTA 59.884 61.111 0.00 0.00 38.78 3.25
387 389 3.612681 CACGTGTCCGGGTCTGGT 61.613 66.667 7.58 0.00 38.78 4.00
394 396 3.175976 AAAAAGCGCACGTGTCCGG 62.176 57.895 18.38 0.00 38.78 5.14
395 397 2.326550 AAAAAGCGCACGTGTCCG 59.673 55.556 18.38 14.14 40.83 4.79
441 696 8.397148 GCAATGAAAATTCCACTTTCTCAAAAA 58.603 29.630 0.00 0.00 34.51 1.94
442 697 7.769970 AGCAATGAAAATTCCACTTTCTCAAAA 59.230 29.630 0.00 0.00 34.51 2.44
443 698 7.274447 AGCAATGAAAATTCCACTTTCTCAAA 58.726 30.769 0.00 0.00 34.51 2.69
444 699 6.819284 AGCAATGAAAATTCCACTTTCTCAA 58.181 32.000 0.00 0.00 34.51 3.02
445 700 6.409524 AGCAATGAAAATTCCACTTTCTCA 57.590 33.333 0.00 0.00 34.51 3.27
446 701 6.703165 ACAAGCAATGAAAATTCCACTTTCTC 59.297 34.615 0.00 0.00 34.51 2.87
447 702 6.585416 ACAAGCAATGAAAATTCCACTTTCT 58.415 32.000 0.00 0.00 34.51 2.52
448 703 6.849588 ACAAGCAATGAAAATTCCACTTTC 57.150 33.333 0.00 0.00 34.09 2.62
449 704 7.271511 TGTACAAGCAATGAAAATTCCACTTT 58.728 30.769 0.00 0.00 0.00 2.66
450 705 6.815089 TGTACAAGCAATGAAAATTCCACTT 58.185 32.000 0.00 0.00 0.00 3.16
451 706 6.403866 TGTACAAGCAATGAAAATTCCACT 57.596 33.333 0.00 0.00 0.00 4.00
452 707 6.701400 ACTTGTACAAGCAATGAAAATTCCAC 59.299 34.615 30.97 0.00 41.99 4.02
453 708 6.815089 ACTTGTACAAGCAATGAAAATTCCA 58.185 32.000 30.97 0.00 41.99 3.53
493 748 1.041437 GCTACCAGTACTAGGCCAGG 58.959 60.000 5.01 0.00 0.00 4.45
508 771 2.279784 CAGCCGCTAGCCTGCTAC 60.280 66.667 21.99 1.39 45.47 3.58
512 775 3.729965 CTCACCAGCCGCTAGCCTG 62.730 68.421 9.66 11.41 45.47 4.85
513 776 3.465403 CTCACCAGCCGCTAGCCT 61.465 66.667 9.66 0.00 45.47 4.58
542 816 1.417145 AGGGCAAGTTACCGTTGTACA 59.583 47.619 0.00 0.00 0.00 2.90
543 817 2.174363 AGGGCAAGTTACCGTTGTAC 57.826 50.000 0.00 0.00 0.00 2.90
544 818 2.354003 GCTAGGGCAAGTTACCGTTGTA 60.354 50.000 0.00 0.00 38.54 2.41
546 820 1.084289 GCTAGGGCAAGTTACCGTTG 58.916 55.000 0.00 0.00 38.54 4.10
547 821 0.035725 GGCTAGGGCAAGTTACCGTT 60.036 55.000 0.00 0.00 40.87 4.44
548 822 1.600638 GGCTAGGGCAAGTTACCGT 59.399 57.895 0.00 0.00 40.87 4.83
549 823 1.153229 GGGCTAGGGCAAGTTACCG 60.153 63.158 0.00 0.00 40.87 4.02
550 824 0.393944 GTGGGCTAGGGCAAGTTACC 60.394 60.000 0.00 0.00 40.87 2.85
551 825 0.743345 CGTGGGCTAGGGCAAGTTAC 60.743 60.000 0.00 0.00 40.87 2.50
552 826 1.600107 CGTGGGCTAGGGCAAGTTA 59.400 57.895 0.00 0.00 40.87 2.24
553 827 2.351276 CGTGGGCTAGGGCAAGTT 59.649 61.111 0.00 0.00 40.87 2.66
554 828 3.717294 CCGTGGGCTAGGGCAAGT 61.717 66.667 0.00 0.00 40.87 3.16
581 855 1.337167 TGTGATCGTTGACTGCTCCAG 60.337 52.381 0.00 0.00 37.52 3.86
585 859 4.611355 CGAAAAATGTGATCGTTGACTGCT 60.611 41.667 0.00 0.00 0.00 4.24
709 985 1.282570 CCGTCACACGCTTGCAATT 59.717 52.632 0.00 0.00 40.91 2.32
711 987 3.276091 CCCGTCACACGCTTGCAA 61.276 61.111 0.00 0.00 40.91 4.08
883 1177 1.008327 GTGGAAGGGGATGGGGATTTT 59.992 52.381 0.00 0.00 0.00 1.82
892 1186 4.778143 GCACGCGTGGAAGGGGAT 62.778 66.667 37.47 0.00 38.11 3.85
911 1205 0.395724 GAATTGGGGATTGAGGGCGT 60.396 55.000 0.00 0.00 0.00 5.68
1131 1425 1.144936 GATGTGGGCGAGGAAGAGG 59.855 63.158 0.00 0.00 0.00 3.69
1180 1474 3.745803 GGCGGAGTCGTCGGAGTT 61.746 66.667 0.00 0.00 38.89 3.01
1290 1584 1.899534 GAGGAGCGCGAGGAGGTAT 60.900 63.158 12.10 0.00 0.00 2.73
1575 1869 0.749454 TAAGGTAGACGAGCCCGACC 60.749 60.000 0.00 0.00 39.50 4.79
1593 1887 2.675423 AGGTGCCAGACGACGCTA 60.675 61.111 0.00 0.00 0.00 4.26
1626 1920 0.179161 CCTTGTAGTCCTCGAGCACG 60.179 60.000 6.99 0.00 41.26 5.34
2144 2439 6.882656 TCAAATGATCCTACTTCTCTTCAGG 58.117 40.000 0.00 0.00 0.00 3.86
2253 2673 5.871396 AGTAGTGTAGTACCAATCCCATG 57.129 43.478 0.00 0.00 0.00 3.66
2349 2772 1.202348 CCGAGTGGTGCAGTGATCTAG 60.202 57.143 0.00 0.00 0.00 2.43
2350 2773 0.817654 CCGAGTGGTGCAGTGATCTA 59.182 55.000 0.00 0.00 0.00 1.98
2351 2774 0.900182 TCCGAGTGGTGCAGTGATCT 60.900 55.000 0.00 0.00 36.30 2.75
2368 2791 4.333649 TGCAGAATCTTCAAACGATGATCC 59.666 41.667 0.00 0.00 38.03 3.36
2369 2792 5.475273 TGCAGAATCTTCAAACGATGATC 57.525 39.130 0.00 0.00 38.03 2.92
2463 2903 5.584551 AAACCCAGTAAACTCTCCAGATT 57.415 39.130 0.00 0.00 0.00 2.40
2561 3001 9.372369 CAGCTTATAAAGTTGCTACTCTTTAGT 57.628 33.333 0.07 0.00 38.79 2.24
2588 6767 0.174162 GCAGCAAAAGGGGCACATAG 59.826 55.000 0.00 0.00 0.00 2.23
2631 6813 8.526978 TCATCTCATATCTTGTAGAGTTATGGC 58.473 37.037 0.00 0.00 38.08 4.40
2674 6856 3.044059 GAGCAGCGAACATGTGGCC 62.044 63.158 16.14 0.00 0.00 5.36
2722 6904 1.393883 GTGCTAAGTGTTTCGCTAGCC 59.606 52.381 9.66 0.00 0.00 3.93
2758 6943 6.037610 CCATGTCAACTTTTATCCTAGCAGTC 59.962 42.308 0.00 0.00 0.00 3.51
2765 6950 4.922206 TGCTCCATGTCAACTTTTATCCT 58.078 39.130 0.00 0.00 0.00 3.24
2766 6951 5.643379 TTGCTCCATGTCAACTTTTATCC 57.357 39.130 0.00 0.00 0.00 2.59
2767 6952 6.446318 TGTTTGCTCCATGTCAACTTTTATC 58.554 36.000 0.00 0.00 0.00 1.75
2879 7304 3.617284 ACGTCTCTGAAACCCACTTTTT 58.383 40.909 0.00 0.00 0.00 1.94
2901 7326 1.134401 CAAGCGAGGAATAAGCTCCCA 60.134 52.381 0.00 0.00 40.78 4.37
2951 7376 2.359975 CCCTCCAAGACGGGCAAC 60.360 66.667 0.00 0.00 32.83 4.17


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

AutoCloner maintained by Alex Coulton.