Multiple sequence alignment - TraesCS3D01G082700

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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 TraesCS3D01G082700 chr3D 100.000 5109 0 0 955 6063 42083998 42089106 0.000000e+00 9435
1 TraesCS3D01G082700 chr3D 100.000 631 0 0 1 631 42083044 42083674 0.000000e+00 1166
2 TraesCS3D01G082700 chr3D 76.242 463 86 15 2148 2603 42084422 42084867 2.200000e-54 224
3 TraesCS3D01G082700 chr3D 76.242 463 86 15 1379 1824 42085191 42085646 2.200000e-54 224
4 TraesCS3D01G082700 chr3D 98.261 115 2 0 1 115 477583815 477583701 1.030000e-47 202
5 TraesCS3D01G082700 chr3B 94.284 2869 137 13 955 3812 65564514 65561662 0.000000e+00 4364
6 TraesCS3D01G082700 chr3B 89.975 1975 124 39 4108 6034 65561315 65559367 0.000000e+00 2483
7 TraesCS3D01G082700 chr3B 92.644 503 20 8 132 631 65565240 65564752 0.000000e+00 708
8 TraesCS3D01G082700 chr3B 81.662 349 47 12 1306 1638 756077989 756078336 2.150000e-69 274
9 TraesCS3D01G082700 chr3B 84.053 301 22 6 3811 4111 65561617 65561343 3.600000e-67 267
10 TraesCS3D01G082700 chr3B 76.282 468 78 26 2148 2603 65564083 65563637 1.020000e-52 219
11 TraesCS3D01G082700 chr3B 73.669 338 58 21 2090 2410 756078013 756078336 1.080000e-17 102
12 TraesCS3D01G082700 chr3A 92.735 2051 128 9 955 2996 53573044 53571006 0.000000e+00 2942
13 TraesCS3D01G082700 chr3A 88.118 2003 135 53 4109 6063 53569924 53567977 0.000000e+00 2285
14 TraesCS3D01G082700 chr3A 97.103 725 21 0 3088 3812 53571010 53570286 0.000000e+00 1223
15 TraesCS3D01G082700 chr3A 87.547 530 25 11 132 631 53573808 53573290 5.270000e-160 575
16 TraesCS3D01G082700 chr3A 86.379 301 26 5 3812 4112 53570237 53569952 1.270000e-81 315
17 TraesCS3D01G082700 chr3A 77.124 459 81 16 1379 1824 53571843 53571396 1.690000e-60 244
18 TraesCS3D01G082700 chr4D 84.393 346 38 13 1306 1638 49848113 49847771 5.860000e-85 326
19 TraesCS3D01G082700 chr4D 90.123 81 8 0 2330 2410 49847851 49847771 8.310000e-19 106
20 TraesCS3D01G082700 chr6A 82.090 335 46 11 1316 1638 606415589 606415257 2.150000e-69 274
21 TraesCS3D01G082700 chr6A 86.224 196 26 1 1444 1638 60147241 60147436 1.710000e-50 211
22 TraesCS3D01G082700 chr7A 86.224 196 26 1 1444 1638 726115171 726114976 1.710000e-50 211
23 TraesCS3D01G082700 chr7D 100.000 112 0 0 2 113 399453695 399453806 2.210000e-49 207
24 TraesCS3D01G082700 chr7D 95.082 122 6 0 1 122 565527671 565527792 6.200000e-45 193
25 TraesCS3D01G082700 chr6D 98.246 114 2 0 1 114 404420517 404420630 3.710000e-47 200
26 TraesCS3D01G082700 chr6D 98.230 113 2 0 1 113 42849996 42850108 1.330000e-46 198
27 TraesCS3D01G082700 chr1D 95.902 122 4 1 1 122 305574299 305574419 4.790000e-46 196
28 TraesCS3D01G082700 chr1D 96.610 118 4 0 1 118 403988199 403988316 4.790000e-46 196
29 TraesCS3D01G082700 chr1D 96.610 118 4 0 1 118 404016145 404016262 4.790000e-46 196
30 TraesCS3D01G082700 chr1D 95.833 120 5 0 1 120 222262989 222263108 1.720000e-45 195


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 TraesCS3D01G082700 chr3D 42083044 42089106 6062 False 5300.5 9435 100.000000 1 6063 2 chr3D.!!$F1 6062
1 TraesCS3D01G082700 chr3D 42084422 42085646 1224 False 224.0 224 76.242000 1379 2603 2 chr3D.!!$F2 1224
2 TraesCS3D01G082700 chr3B 65559367 65565240 5873 True 1608.2 4364 87.447600 132 6034 5 chr3B.!!$R1 5902
3 TraesCS3D01G082700 chr3A 53567977 53573808 5831 True 1264.0 2942 88.167667 132 6063 6 chr3A.!!$R1 5931

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
79 80 0.099082 CCTCGCGACTAAGTCCTGAC 59.901 60.0 3.71 0.0 0.00 3.51 F
102 103 0.396435 AAGGACATCTGCCGTGACAA 59.604 50.0 0.00 0.0 0.00 3.18 F
123 124 0.611200 TCCACGACAACACCCATAGG 59.389 55.0 0.00 0.0 40.04 2.57 F
1282 1323 0.107459 GATCTGACTCTGGGTTGGCC 60.107 60.0 0.00 0.0 0.00 5.36 F
2738 2790 0.871057 GCTTCAGTCTGCTGTTCCAC 59.129 55.0 0.00 0.0 43.05 4.02 F
3550 3602 0.251209 AGAAACGGGGCTTTTCTCCC 60.251 55.0 4.22 0.0 38.67 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 1172 0.251297 CCCAAGGGCATGAACACAGA 60.251 55.000 0.00 0.00 0.00 3.41 R
1144 1184 0.257039 ATGAACTGCTAGCCCAAGGG 59.743 55.000 13.29 0.00 38.57 3.95 R
1302 1343 0.548682 AGCTCCACCTTGACTCCCAT 60.549 55.000 0.00 0.00 0.00 4.00 R
2798 2850 2.266055 GTCCCCGTCTGAAGCCAG 59.734 66.667 0.00 0.00 41.74 4.85 R
4545 4679 0.249120 AGCGAATCAATCACCGGTCA 59.751 50.000 2.59 0.00 0.00 4.02 R
5402 5609 0.099613 CTCGACTGATCTGGTCACGG 59.900 60.000 15.72 4.37 33.73 4.94 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
22 23 5.957910 CTTATGTTGTGTCTCTCGATTCC 57.042 43.478 0.00 0.00 0.00 3.01
23 24 3.961480 ATGTTGTGTCTCTCGATTCCA 57.039 42.857 0.00 0.00 0.00 3.53
24 25 3.026630 TGTTGTGTCTCTCGATTCCAC 57.973 47.619 0.00 0.00 0.00 4.02
25 26 2.288825 TGTTGTGTCTCTCGATTCCACC 60.289 50.000 0.00 0.00 0.00 4.61
26 27 0.895530 TGTGTCTCTCGATTCCACCC 59.104 55.000 0.00 0.00 0.00 4.61
27 28 0.895530 GTGTCTCTCGATTCCACCCA 59.104 55.000 0.00 0.00 0.00 4.51
28 29 1.275291 GTGTCTCTCGATTCCACCCAA 59.725 52.381 0.00 0.00 0.00 4.12
29 30 1.275291 TGTCTCTCGATTCCACCCAAC 59.725 52.381 0.00 0.00 0.00 3.77
30 31 0.902531 TCTCTCGATTCCACCCAACC 59.097 55.000 0.00 0.00 0.00 3.77
31 32 0.107654 CTCTCGATTCCACCCAACCC 60.108 60.000 0.00 0.00 0.00 4.11
32 33 1.077716 CTCGATTCCACCCAACCCC 60.078 63.158 0.00 0.00 0.00 4.95
33 34 1.540367 TCGATTCCACCCAACCCCT 60.540 57.895 0.00 0.00 0.00 4.79
34 35 1.077716 CGATTCCACCCAACCCCTC 60.078 63.158 0.00 0.00 0.00 4.30
35 36 1.562672 CGATTCCACCCAACCCCTCT 61.563 60.000 0.00 0.00 0.00 3.69
36 37 0.256177 GATTCCACCCAACCCCTCTC 59.744 60.000 0.00 0.00 0.00 3.20
37 38 0.477597 ATTCCACCCAACCCCTCTCA 60.478 55.000 0.00 0.00 0.00 3.27
38 39 0.699577 TTCCACCCAACCCCTCTCAA 60.700 55.000 0.00 0.00 0.00 3.02
39 40 1.133809 TCCACCCAACCCCTCTCAAG 61.134 60.000 0.00 0.00 0.00 3.02
40 41 1.303643 CACCCAACCCCTCTCAAGC 60.304 63.158 0.00 0.00 0.00 4.01
41 42 1.464198 ACCCAACCCCTCTCAAGCT 60.464 57.895 0.00 0.00 0.00 3.74
42 43 0.178873 ACCCAACCCCTCTCAAGCTA 60.179 55.000 0.00 0.00 0.00 3.32
43 44 0.253327 CCCAACCCCTCTCAAGCTAC 59.747 60.000 0.00 0.00 0.00 3.58
44 45 0.253327 CCAACCCCTCTCAAGCTACC 59.747 60.000 0.00 0.00 0.00 3.18
45 46 0.108138 CAACCCCTCTCAAGCTACCG 60.108 60.000 0.00 0.00 0.00 4.02
46 47 1.900545 AACCCCTCTCAAGCTACCGC 61.901 60.000 0.00 0.00 0.00 5.68
47 48 2.359169 CCCCTCTCAAGCTACCGCA 61.359 63.158 0.00 0.00 39.10 5.69
48 49 1.690219 CCCCTCTCAAGCTACCGCAT 61.690 60.000 0.00 0.00 39.10 4.73
49 50 1.040646 CCCTCTCAAGCTACCGCATA 58.959 55.000 0.00 0.00 39.10 3.14
50 51 1.000283 CCCTCTCAAGCTACCGCATAG 60.000 57.143 0.00 0.00 39.10 2.23
51 52 1.957177 CCTCTCAAGCTACCGCATAGA 59.043 52.381 0.00 0.00 39.10 1.98
52 53 2.560542 CCTCTCAAGCTACCGCATAGAT 59.439 50.000 0.00 0.00 39.10 1.98
53 54 3.573598 CTCTCAAGCTACCGCATAGATG 58.426 50.000 0.00 0.00 39.10 2.90
62 63 4.147701 GCATAGATGCGTTGGCCT 57.852 55.556 3.32 0.00 44.67 5.19
63 64 1.944778 GCATAGATGCGTTGGCCTC 59.055 57.895 3.32 0.00 44.67 4.70
64 65 1.835483 GCATAGATGCGTTGGCCTCG 61.835 60.000 3.32 10.54 44.67 4.63
70 71 4.789075 GCGTTGGCCTCGCGACTA 62.789 66.667 24.30 0.00 43.94 2.59
71 72 2.126228 CGTTGGCCTCGCGACTAA 60.126 61.111 3.71 0.00 0.00 2.24
72 73 2.158959 CGTTGGCCTCGCGACTAAG 61.159 63.158 3.71 0.00 0.00 2.18
73 74 1.080025 GTTGGCCTCGCGACTAAGT 60.080 57.895 3.71 0.00 0.00 2.24
74 75 1.077089 GTTGGCCTCGCGACTAAGTC 61.077 60.000 3.71 0.00 0.00 3.01
75 76 2.104530 GGCCTCGCGACTAAGTCC 59.895 66.667 3.71 0.00 0.00 3.85
76 77 2.416432 GGCCTCGCGACTAAGTCCT 61.416 63.158 3.71 0.00 0.00 3.85
77 78 1.226717 GCCTCGCGACTAAGTCCTG 60.227 63.158 3.71 0.00 0.00 3.86
78 79 1.654954 GCCTCGCGACTAAGTCCTGA 61.655 60.000 3.71 0.00 0.00 3.86
79 80 0.099082 CCTCGCGACTAAGTCCTGAC 59.901 60.000 3.71 0.00 0.00 3.51
80 81 0.803117 CTCGCGACTAAGTCCTGACA 59.197 55.000 3.71 0.00 0.00 3.58
81 82 0.520404 TCGCGACTAAGTCCTGACAC 59.480 55.000 3.71 0.00 0.00 3.67
82 83 0.522180 CGCGACTAAGTCCTGACACT 59.478 55.000 0.00 0.00 0.00 3.55
83 84 1.736126 CGCGACTAAGTCCTGACACTA 59.264 52.381 0.00 0.00 0.00 2.74
84 85 2.161012 CGCGACTAAGTCCTGACACTAA 59.839 50.000 0.00 0.00 0.00 2.24
85 86 3.728268 CGCGACTAAGTCCTGACACTAAG 60.728 52.174 0.00 0.00 0.00 2.18
86 87 3.427773 GCGACTAAGTCCTGACACTAAGG 60.428 52.174 0.00 0.00 36.02 2.69
87 88 4.008330 CGACTAAGTCCTGACACTAAGGA 58.992 47.826 0.00 0.00 41.66 3.36
94 95 2.497675 TCCTGACACTAAGGACATCTGC 59.502 50.000 0.00 0.00 38.96 4.26
95 96 2.419297 CCTGACACTAAGGACATCTGCC 60.419 54.545 0.00 0.00 36.91 4.85
96 97 1.204704 TGACACTAAGGACATCTGCCG 59.795 52.381 0.00 0.00 0.00 5.69
97 98 1.204941 GACACTAAGGACATCTGCCGT 59.795 52.381 0.00 0.00 0.00 5.68
98 99 1.066858 ACACTAAGGACATCTGCCGTG 60.067 52.381 0.00 0.00 0.00 4.94
99 100 1.204704 CACTAAGGACATCTGCCGTGA 59.795 52.381 0.00 0.00 0.00 4.35
100 101 1.204941 ACTAAGGACATCTGCCGTGAC 59.795 52.381 0.00 0.00 0.00 3.67
101 102 1.204704 CTAAGGACATCTGCCGTGACA 59.795 52.381 0.00 0.00 0.00 3.58
102 103 0.396435 AAGGACATCTGCCGTGACAA 59.604 50.000 0.00 0.00 0.00 3.18
103 104 0.615331 AGGACATCTGCCGTGACAAT 59.385 50.000 0.00 0.00 0.00 2.71
104 105 1.003580 AGGACATCTGCCGTGACAATT 59.996 47.619 0.00 0.00 0.00 2.32
105 106 1.398390 GGACATCTGCCGTGACAATTC 59.602 52.381 0.00 0.00 0.00 2.17
106 107 1.398390 GACATCTGCCGTGACAATTCC 59.602 52.381 0.00 0.00 0.00 3.01
107 108 1.271325 ACATCTGCCGTGACAATTCCA 60.271 47.619 0.00 0.00 0.00 3.53
108 109 1.131126 CATCTGCCGTGACAATTCCAC 59.869 52.381 0.00 0.00 0.00 4.02
116 117 2.981875 GTGACAATTCCACGACAACAC 58.018 47.619 0.00 0.00 0.00 3.32
117 118 1.944024 TGACAATTCCACGACAACACC 59.056 47.619 0.00 0.00 0.00 4.16
118 119 1.265905 GACAATTCCACGACAACACCC 59.734 52.381 0.00 0.00 0.00 4.61
119 120 1.313772 CAATTCCACGACAACACCCA 58.686 50.000 0.00 0.00 0.00 4.51
120 121 1.885887 CAATTCCACGACAACACCCAT 59.114 47.619 0.00 0.00 0.00 4.00
121 122 3.078097 CAATTCCACGACAACACCCATA 58.922 45.455 0.00 0.00 0.00 2.74
122 123 2.465860 TTCCACGACAACACCCATAG 57.534 50.000 0.00 0.00 0.00 2.23
123 124 0.611200 TCCACGACAACACCCATAGG 59.389 55.000 0.00 0.00 40.04 2.57
160 161 1.136169 ACGTTCGCTAAATTTCACCGC 60.136 47.619 0.00 0.00 0.00 5.68
165 166 3.560503 TCGCTAAATTTCACCGCTTTTG 58.439 40.909 0.00 0.00 0.00 2.44
166 167 3.003897 TCGCTAAATTTCACCGCTTTTGT 59.996 39.130 0.00 0.00 0.00 2.83
277 288 4.817517 AGAAAGAAATAAACTCTCGCGGA 58.182 39.130 6.13 1.01 0.00 5.54
314 325 4.461992 TTACCGTTCAAGCTTCGAAAAG 57.538 40.909 7.54 7.33 35.47 2.27
366 396 2.679996 AATTTCACCAGCCCGCCC 60.680 61.111 0.00 0.00 0.00 6.13
421 451 1.031571 CAGCTTTGCCGCCTAATCCA 61.032 55.000 0.00 0.00 0.00 3.41
976 1010 1.228154 GACCTTTGTGCGGTTCCCT 60.228 57.895 0.00 0.00 34.19 4.20
985 1019 1.689273 GTGCGGTTCCCTATCTCATCT 59.311 52.381 0.00 0.00 0.00 2.90
995 1029 3.243569 CCCTATCTCATCTCGCTTCGTTT 60.244 47.826 0.00 0.00 0.00 3.60
1100 1134 2.158385 ACCAGATGGCCAACAAAGGTAA 60.158 45.455 10.96 0.00 39.32 2.85
1106 1143 1.339929 GGCCAACAAAGGTAACACCAG 59.660 52.381 0.00 0.00 41.95 4.00
1110 1147 2.428890 CAACAAAGGTAACACCAGCCAA 59.571 45.455 0.00 0.00 41.95 4.52
1118 1155 3.308188 GGTAACACCAGCCAACCTCTTAT 60.308 47.826 0.00 0.00 38.42 1.73
1132 1172 3.923425 ACCTCTTATTTGGTTTCCCTCCT 59.077 43.478 0.00 0.00 31.62 3.69
1134 1174 4.228438 CCTCTTATTTGGTTTCCCTCCTCT 59.772 45.833 0.00 0.00 0.00 3.69
1141 1181 1.420138 GGTTTCCCTCCTCTGTGTTCA 59.580 52.381 0.00 0.00 0.00 3.18
1144 1184 0.615331 TCCCTCCTCTGTGTTCATGC 59.385 55.000 0.00 0.00 0.00 4.06
1145 1185 0.393537 CCCTCCTCTGTGTTCATGCC 60.394 60.000 0.00 0.00 0.00 4.40
1154 1194 0.323360 GTGTTCATGCCCTTGGGCTA 60.323 55.000 28.37 16.63 35.66 3.93
1158 1198 1.826921 CATGCCCTTGGGCTAGCAG 60.827 63.158 28.37 5.24 38.89 4.24
1167 1207 1.289160 TGGGCTAGCAGTTCATTCCT 58.711 50.000 18.24 0.00 0.00 3.36
1175 1215 3.359950 AGCAGTTCATTCCTCATTTCCC 58.640 45.455 0.00 0.00 0.00 3.97
1177 1217 3.700538 CAGTTCATTCCTCATTTCCCCA 58.299 45.455 0.00 0.00 0.00 4.96
1179 1219 4.713321 CAGTTCATTCCTCATTTCCCCAAT 59.287 41.667 0.00 0.00 0.00 3.16
1183 1224 1.851304 TCCTCATTTCCCCAATGTGC 58.149 50.000 0.00 0.00 42.79 4.57
1184 1225 0.826062 CCTCATTTCCCCAATGTGCC 59.174 55.000 0.00 0.00 42.79 5.01
1187 1228 2.167075 CTCATTTCCCCAATGTGCCTTC 59.833 50.000 0.00 0.00 42.79 3.46
1282 1323 0.107459 GATCTGACTCTGGGTTGGCC 60.107 60.000 0.00 0.00 0.00 5.36
1302 1343 1.818131 CGATGAGATACCTCCCGTGGA 60.818 57.143 0.00 0.00 38.66 4.02
1315 1356 1.553690 CCGTGGATGGGAGTCAAGGT 61.554 60.000 0.00 0.00 0.00 3.50
2730 2782 1.433534 GGTGTACAGCTTCAGTCTGC 58.566 55.000 17.69 0.00 35.04 4.26
2738 2790 0.871057 GCTTCAGTCTGCTGTTCCAC 59.129 55.000 0.00 0.00 43.05 4.02
2809 2861 1.534595 CAAGAAGTGCTGGCTTCAGAC 59.465 52.381 15.00 0.00 45.28 3.51
2812 2864 2.738213 AAGTGCTGGCTTCAGACGGG 62.738 60.000 0.00 0.00 40.86 5.28
2859 2911 4.057432 GAGCTAACATCAGAGAGGAATGC 58.943 47.826 0.00 0.00 0.00 3.56
3024 3076 4.397730 GTCTGCTGTCTCTGAAGTATCTCA 59.602 45.833 0.00 0.00 0.00 3.27
3026 3078 5.299028 TCTGCTGTCTCTGAAGTATCTCATC 59.701 44.000 0.00 0.00 0.00 2.92
3034 3086 5.462240 TCTGAAGTATCTCATCAGGATGGT 58.538 41.667 9.25 0.01 40.82 3.55
3072 3124 5.130477 TGAAAGAGGTAACAGAGAAACCAGT 59.870 40.000 0.00 0.00 41.41 4.00
3107 3159 6.385176 AGATGGAGATGAGTCAAGTGGATTAA 59.615 38.462 0.00 0.00 0.00 1.40
3115 3167 6.950842 TGAGTCAAGTGGATTAACATCAGAT 58.049 36.000 0.00 0.00 0.00 2.90
3193 3245 1.201414 TGCAATGCTGATCTTGCTGTG 59.799 47.619 15.80 11.98 46.16 3.66
3221 3273 1.203441 ATGCCAGAGCCCAGAGTCAA 61.203 55.000 0.00 0.00 38.69 3.18
3235 3287 6.409704 CCCAGAGTCAAGATGTTCTATCAAA 58.590 40.000 0.00 0.00 0.00 2.69
3357 3409 3.006247 GCAAGCCTTCTGAACCTTCTAG 58.994 50.000 0.00 0.00 0.00 2.43
3550 3602 0.251209 AGAAACGGGGCTTTTCTCCC 60.251 55.000 4.22 0.00 38.67 4.30
3826 3927 7.035004 GTCCTTGTGATATATTTTGCTTTGCA 58.965 34.615 0.00 0.00 36.47 4.08
3842 3943 5.290643 TGCTTTGCAACTTGTTTTACATGAC 59.709 36.000 0.00 0.00 34.76 3.06
3847 3948 6.207928 TGCAACTTGTTTTACATGACTCATG 58.792 36.000 16.22 16.22 46.18 3.07
3884 3985 7.230747 TGAAAATTCATTGTCAGGACTAGGAA 58.769 34.615 11.89 11.89 39.97 3.36
3906 4007 0.478072 ATTTCAGGCTGTCACCCACA 59.522 50.000 15.27 0.00 0.00 4.17
3907 4008 0.478072 TTTCAGGCTGTCACCCACAT 59.522 50.000 15.27 0.00 33.23 3.21
3959 4060 6.017400 CCAAATCATGGTTATATCTGGCAC 57.983 41.667 0.00 0.00 44.85 5.01
3975 4076 3.005539 ACGAGCCCTCTGCATGGT 61.006 61.111 0.00 0.00 44.83 3.55
3976 4077 2.270205 CGAGCCCTCTGCATGGTT 59.730 61.111 0.00 0.00 44.83 3.67
3977 4078 2.110967 CGAGCCCTCTGCATGGTTG 61.111 63.158 0.00 0.00 44.83 3.77
3980 4081 1.303561 GCCCTCTGCATGGTTGTGA 60.304 57.895 0.00 0.00 40.77 3.58
3982 4083 1.100510 CCCTCTGCATGGTTGTGATG 58.899 55.000 0.00 0.00 0.00 3.07
3983 4084 1.615116 CCCTCTGCATGGTTGTGATGT 60.615 52.381 0.00 0.00 0.00 3.06
3984 4085 1.471287 CCTCTGCATGGTTGTGATGTG 59.529 52.381 0.00 0.00 0.00 3.21
3985 4086 2.156917 CTCTGCATGGTTGTGATGTGT 58.843 47.619 0.00 0.00 0.00 3.72
3986 4087 2.153645 TCTGCATGGTTGTGATGTGTC 58.846 47.619 0.00 0.00 0.00 3.67
3987 4088 2.156917 CTGCATGGTTGTGATGTGTCT 58.843 47.619 0.00 0.00 0.00 3.41
3988 4089 1.881324 TGCATGGTTGTGATGTGTCTG 59.119 47.619 0.00 0.00 0.00 3.51
3990 4091 2.294233 GCATGGTTGTGATGTGTCTGTT 59.706 45.455 0.00 0.00 0.00 3.16
3991 4092 3.610114 GCATGGTTGTGATGTGTCTGTTC 60.610 47.826 0.00 0.00 0.00 3.18
3992 4093 2.209273 TGGTTGTGATGTGTCTGTTCG 58.791 47.619 0.00 0.00 0.00 3.95
3993 4094 1.069906 GGTTGTGATGTGTCTGTTCGC 60.070 52.381 0.00 0.00 0.00 4.70
3994 4095 1.597195 GTTGTGATGTGTCTGTTCGCA 59.403 47.619 0.00 0.00 0.00 5.10
3995 4096 2.168326 TGTGATGTGTCTGTTCGCAT 57.832 45.000 0.00 0.00 40.57 4.73
3996 4097 1.799994 TGTGATGTGTCTGTTCGCATG 59.200 47.619 0.00 0.00 38.43 4.06
3997 4098 2.068519 GTGATGTGTCTGTTCGCATGA 58.931 47.619 0.00 0.00 38.43 3.07
3998 4099 2.093310 GTGATGTGTCTGTTCGCATGAG 59.907 50.000 0.00 0.00 38.43 2.90
3999 4100 2.029110 TGATGTGTCTGTTCGCATGAGA 60.029 45.455 0.00 0.00 38.43 3.27
4000 4101 2.524569 TGTGTCTGTTCGCATGAGAA 57.475 45.000 7.89 7.89 0.00 2.87
4001 4102 2.832563 TGTGTCTGTTCGCATGAGAAA 58.167 42.857 13.76 4.04 0.00 2.52
4002 4103 2.802247 TGTGTCTGTTCGCATGAGAAAG 59.198 45.455 13.76 12.69 0.00 2.62
4041 4142 6.443934 ACTCTTGTGAGCACATACTAGTAG 57.556 41.667 8.85 3.62 43.85 2.57
4112 4213 4.012374 CAATGCCTGTAATCTGACCTGTT 58.988 43.478 0.00 0.00 0.00 3.16
4113 4214 5.185454 CAATGCCTGTAATCTGACCTGTTA 58.815 41.667 0.00 0.00 0.00 2.41
4121 4253 7.364232 CCTGTAATCTGACCTGTTAACTCATCT 60.364 40.741 7.22 0.00 0.00 2.90
4123 4255 8.035394 TGTAATCTGACCTGTTAACTCATCTTC 58.965 37.037 7.22 0.00 0.00 2.87
4124 4256 6.611613 ATCTGACCTGTTAACTCATCTTCA 57.388 37.500 7.22 0.89 0.00 3.02
4125 4257 6.611613 TCTGACCTGTTAACTCATCTTCAT 57.388 37.500 7.22 0.00 0.00 2.57
4183 4315 7.251704 AGCATTACTGTGACTTGCAATATAC 57.748 36.000 0.00 0.00 35.79 1.47
4193 4325 6.308766 GTGACTTGCAATATACTTGCCTTTTG 59.691 38.462 0.00 0.00 44.32 2.44
4195 4327 6.758254 ACTTGCAATATACTTGCCTTTTGTT 58.242 32.000 0.00 0.00 44.32 2.83
4264 4396 1.712977 GGAGCAGATGGAAGCTTGCG 61.713 60.000 13.65 0.00 42.04 4.85
4276 4408 2.357517 CTTGCGAGAGGGCGTTGT 60.358 61.111 0.00 0.00 35.06 3.32
4381 4515 1.001815 CTACCTTGTGCAACGGTTTGG 60.002 52.381 7.97 0.00 42.39 3.28
4392 4526 1.981256 ACGGTTTGGCATGAGAACTT 58.019 45.000 0.00 0.00 0.00 2.66
4428 4562 8.813282 GGTTTAACTAAACAATTGTGTCTTTGG 58.187 33.333 12.82 7.17 45.50 3.28
4484 4618 1.602237 GTCGAGGGAAAGATGGCCA 59.398 57.895 8.56 8.56 0.00 5.36
4529 4663 2.044353 AGGAGGCAATAACCCCATTTGT 59.956 45.455 0.00 0.00 0.00 2.83
4545 4679 2.023414 TTGTGAAGACGCCGGTGACT 62.023 55.000 24.59 19.14 0.00 3.41
4567 4701 1.011904 CGGTGATTGATTCGCTGCG 60.012 57.895 17.25 17.25 34.59 5.18
4574 4708 1.089481 TTGATTCGCTGCGGGATGTC 61.089 55.000 23.03 12.91 0.00 3.06
4584 4718 1.144057 CGGGATGTCTGTGGTAGCC 59.856 63.158 0.00 0.00 0.00 3.93
4605 4739 4.504689 GCCCTGAATTTTGTGGGAATTCAA 60.505 41.667 7.93 0.00 46.78 2.69
4776 4922 3.896888 TGAAACTGGAACATGCCAATCTT 59.103 39.130 0.00 0.00 38.20 2.40
4782 4928 3.084039 GGAACATGCCAATCTTGTCTCA 58.916 45.455 0.00 0.00 32.59 3.27
4843 5002 4.460731 ACTCAGCAATTTTAGCCCTCTTTC 59.539 41.667 0.00 0.00 0.00 2.62
4848 5007 4.218417 GCAATTTTAGCCCTCTTTCACTGA 59.782 41.667 0.00 0.00 0.00 3.41
4852 5011 4.908601 TTAGCCCTCTTTCACTGATGAA 57.091 40.909 0.00 0.00 43.28 2.57
4853 5012 5.441718 TTAGCCCTCTTTCACTGATGAAT 57.558 39.130 0.00 0.00 44.36 2.57
4854 5013 4.313020 AGCCCTCTTTCACTGATGAATT 57.687 40.909 0.00 0.00 44.36 2.17
4859 5026 6.618811 CCCTCTTTCACTGATGAATTTCTTG 58.381 40.000 0.00 0.00 44.36 3.02
4946 5113 5.104610 ACTGACAGACAATCCTGAGCATATT 60.105 40.000 10.08 0.00 37.59 1.28
4947 5114 6.098838 ACTGACAGACAATCCTGAGCATATTA 59.901 38.462 10.08 0.00 37.59 0.98
5011 5206 0.537188 TAGCTAGCTGGTGGTCTTGC 59.463 55.000 27.68 0.00 0.00 4.01
5012 5207 1.197430 AGCTAGCTGGTGGTCTTGCT 61.197 55.000 18.57 0.00 36.77 3.91
5017 5212 0.035458 GCTGGTGGTCTTGCTGTAGT 59.965 55.000 0.00 0.00 0.00 2.73
5293 5493 3.474570 CCGCCCCTCCCTCAAGAG 61.475 72.222 0.00 0.00 0.00 2.85
5294 5494 4.168291 CGCCCCTCCCTCAAGAGC 62.168 72.222 0.00 0.00 32.17 4.09
5295 5495 2.690510 GCCCCTCCCTCAAGAGCT 60.691 66.667 0.00 0.00 32.17 4.09
5296 5496 2.741055 GCCCCTCCCTCAAGAGCTC 61.741 68.421 5.27 5.27 32.17 4.09
5297 5497 1.002792 CCCCTCCCTCAAGAGCTCT 59.997 63.158 11.45 11.45 32.17 4.09
5299 5499 0.032217 CCCTCCCTCAAGAGCTCTCT 60.032 60.000 18.55 4.58 42.75 3.10
5301 5501 1.619432 CCTCCCTCAAGAGCTCTCTGT 60.619 57.143 18.55 0.00 40.36 3.41
5302 5502 1.750778 CTCCCTCAAGAGCTCTCTGTC 59.249 57.143 18.55 0.00 40.36 3.51
5304 5504 0.455410 CCTCAAGAGCTCTCTGTCCG 59.545 60.000 18.55 10.00 40.36 4.79
5331 5536 0.179936 AATGCTAGTGCTGCTCTCCC 59.820 55.000 7.59 1.52 40.48 4.30
5389 5596 0.738975 ATGACGACGACGGTGATGAT 59.261 50.000 12.58 0.00 44.46 2.45
5400 5607 1.290203 GGTGATGATAGTGTGGCGTG 58.710 55.000 0.00 0.00 0.00 5.34
5401 5608 1.134818 GGTGATGATAGTGTGGCGTGA 60.135 52.381 0.00 0.00 0.00 4.35
5402 5609 1.927174 GTGATGATAGTGTGGCGTGAC 59.073 52.381 0.00 0.00 0.00 3.67
5415 5623 1.584495 CGTGACCGTGACCAGATCA 59.416 57.895 0.00 0.00 33.79 2.92
5417 5625 0.603569 GTGACCGTGACCAGATCAGT 59.396 55.000 0.00 0.00 38.28 3.41
5499 5708 1.581934 CAGGCGAGTTCAAGTGTTGA 58.418 50.000 0.00 0.00 38.04 3.18
5508 5717 0.105964 TCAAGTGTTGAGTGGACCGG 59.894 55.000 0.00 0.00 34.08 5.28
5535 5744 4.630111 ACAAAACAAAACGCATCCATCAT 58.370 34.783 0.00 0.00 0.00 2.45
5558 5767 1.078848 CGGCTTCTGAGACCCCAAG 60.079 63.158 0.00 0.00 0.00 3.61
5560 5769 1.377856 GCTTCTGAGACCCCAAGGC 60.378 63.158 0.00 0.00 36.11 4.35
5561 5770 1.846712 GCTTCTGAGACCCCAAGGCT 61.847 60.000 0.00 0.00 36.11 4.58
5562 5771 0.035630 CTTCTGAGACCCCAAGGCTG 60.036 60.000 0.00 0.00 36.11 4.85
5563 5772 2.045536 CTGAGACCCCAAGGCTGC 60.046 66.667 0.00 0.00 36.11 5.25
5564 5773 2.853542 TGAGACCCCAAGGCTGCA 60.854 61.111 0.50 0.00 36.11 4.41
5590 5803 5.871396 TCTTGTGAGACCTAGACAACTTT 57.129 39.130 0.00 0.00 0.00 2.66
5614 5827 1.134551 GCAGTCTGGAGGAAGATCACC 60.135 57.143 1.14 0.00 0.00 4.02
5620 5833 2.304180 CTGGAGGAAGATCACCTGTGTT 59.696 50.000 14.70 0.00 37.93 3.32
5624 5837 4.505742 GGAGGAAGATCACCTGTGTTTCTT 60.506 45.833 14.70 13.91 37.93 2.52
5625 5838 4.646572 AGGAAGATCACCTGTGTTTCTTC 58.353 43.478 22.85 22.85 42.75 2.87
5626 5839 4.349342 AGGAAGATCACCTGTGTTTCTTCT 59.651 41.667 26.05 17.60 42.88 2.85
5627 5840 4.453819 GGAAGATCACCTGTGTTTCTTCTG 59.546 45.833 26.05 0.00 42.88 3.02
5630 5843 6.611613 AGATCACCTGTGTTTCTTCTGATA 57.388 37.500 0.00 0.00 0.00 2.15
5633 5846 8.105829 AGATCACCTGTGTTTCTTCTGATAATT 58.894 33.333 0.00 0.00 0.00 1.40
5651 5868 0.037326 TTCTGCCTTAGCCTCGTGTG 60.037 55.000 0.00 0.00 38.69 3.82
5670 5887 1.291877 GCTACACCACCAGCTGAACG 61.292 60.000 17.39 0.15 34.86 3.95
5683 5900 4.214437 CAGCTGAACGTGTCATCTTTTTC 58.786 43.478 8.42 0.00 35.07 2.29
5690 5907 5.924475 ACGTGTCATCTTTTTCCTGTTAG 57.076 39.130 0.00 0.00 0.00 2.34
5734 5954 2.800544 GACTGGTGTATGTGTGTGTGTC 59.199 50.000 0.00 0.00 0.00 3.67
5735 5955 2.143122 CTGGTGTATGTGTGTGTGTCC 58.857 52.381 0.00 0.00 0.00 4.02
5802 6024 1.810755 CATGCATGCTCACTTGTCAGT 59.189 47.619 20.33 0.00 0.00 3.41
5875 6097 2.366916 GTCCACCATATCCTCACTCTGG 59.633 54.545 0.00 0.00 0.00 3.86
5900 6122 2.025416 TCTCAAGACTAGGCTCAGCTCT 60.025 50.000 0.00 0.00 0.00 4.09
5906 6128 1.552792 ACTAGGCTCAGCTCTTTCACC 59.447 52.381 0.00 0.00 0.00 4.02
5934 6168 5.298347 CAGCTCTGCATCATTCTCTGAATA 58.702 41.667 0.00 0.00 37.44 1.75
5935 6169 5.758784 CAGCTCTGCATCATTCTCTGAATAA 59.241 40.000 0.00 0.00 37.44 1.40
5936 6170 5.759273 AGCTCTGCATCATTCTCTGAATAAC 59.241 40.000 0.00 0.00 37.44 1.89
5937 6171 5.759273 GCTCTGCATCATTCTCTGAATAACT 59.241 40.000 0.00 0.00 37.44 2.24
5938 6172 6.073657 GCTCTGCATCATTCTCTGAATAACTC 60.074 42.308 0.00 0.00 37.44 3.01
5939 6173 7.122138 TCTGCATCATTCTCTGAATAACTCT 57.878 36.000 0.00 0.00 37.44 3.24
5940 6174 7.208777 TCTGCATCATTCTCTGAATAACTCTC 58.791 38.462 0.00 0.00 37.44 3.20
5941 6175 7.069702 TCTGCATCATTCTCTGAATAACTCTCT 59.930 37.037 0.00 0.00 37.44 3.10
5942 6176 6.985059 TGCATCATTCTCTGAATAACTCTCTG 59.015 38.462 0.00 0.00 37.44 3.35
5943 6177 7.147776 TGCATCATTCTCTGAATAACTCTCTGA 60.148 37.037 0.00 0.00 37.44 3.27
5944 6178 7.710044 GCATCATTCTCTGAATAACTCTCTGAA 59.290 37.037 0.00 0.00 37.44 3.02
5945 6179 9.767228 CATCATTCTCTGAATAACTCTCTGAAT 57.233 33.333 0.00 0.00 37.44 2.57
6037 6275 9.773328 AATCACTTTCATATCAATTTACACACG 57.227 29.630 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.289675 GTGGAATCGAGAGACACAACATAAG 59.710 44.000 7.25 0.00 46.97 1.73
1 2 5.168569 GTGGAATCGAGAGACACAACATAA 58.831 41.667 7.25 0.00 46.97 1.90
2 3 4.381612 GGTGGAATCGAGAGACACAACATA 60.382 45.833 12.35 0.00 46.97 2.29
3 4 3.589988 GTGGAATCGAGAGACACAACAT 58.410 45.455 7.25 0.00 46.97 2.71
4 5 2.288825 GGTGGAATCGAGAGACACAACA 60.289 50.000 12.35 0.00 46.97 3.33
5 6 2.338500 GGTGGAATCGAGAGACACAAC 58.662 52.381 12.35 0.00 46.97 3.32
6 7 1.275291 GGGTGGAATCGAGAGACACAA 59.725 52.381 12.35 0.00 46.97 3.33
7 8 0.895530 GGGTGGAATCGAGAGACACA 59.104 55.000 12.35 0.00 46.97 3.72
8 9 0.895530 TGGGTGGAATCGAGAGACAC 59.104 55.000 0.00 0.00 46.97 3.67
9 10 1.275291 GTTGGGTGGAATCGAGAGACA 59.725 52.381 0.00 0.00 46.97 3.41
10 11 1.405661 GGTTGGGTGGAATCGAGAGAC 60.406 57.143 0.00 0.00 46.97 3.36
12 13 0.107654 GGGTTGGGTGGAATCGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
13 14 1.559065 GGGGTTGGGTGGAATCGAGA 61.559 60.000 0.00 0.00 0.00 4.04
14 15 1.077716 GGGGTTGGGTGGAATCGAG 60.078 63.158 0.00 0.00 0.00 4.04
15 16 1.540367 AGGGGTTGGGTGGAATCGA 60.540 57.895 0.00 0.00 0.00 3.59
16 17 1.077716 GAGGGGTTGGGTGGAATCG 60.078 63.158 0.00 0.00 0.00 3.34
17 18 0.256177 GAGAGGGGTTGGGTGGAATC 59.744 60.000 0.00 0.00 0.00 2.52
18 19 0.477597 TGAGAGGGGTTGGGTGGAAT 60.478 55.000 0.00 0.00 0.00 3.01
19 20 0.699577 TTGAGAGGGGTTGGGTGGAA 60.700 55.000 0.00 0.00 0.00 3.53
20 21 1.073319 TTGAGAGGGGTTGGGTGGA 60.073 57.895 0.00 0.00 0.00 4.02
21 22 1.380302 CTTGAGAGGGGTTGGGTGG 59.620 63.158 0.00 0.00 0.00 4.61
22 23 1.303643 GCTTGAGAGGGGTTGGGTG 60.304 63.158 0.00 0.00 0.00 4.61
23 24 0.178873 TAGCTTGAGAGGGGTTGGGT 60.179 55.000 0.00 0.00 0.00 4.51
24 25 0.253327 GTAGCTTGAGAGGGGTTGGG 59.747 60.000 0.00 0.00 0.00 4.12
25 26 0.253327 GGTAGCTTGAGAGGGGTTGG 59.747 60.000 0.00 0.00 0.00 3.77
26 27 0.108138 CGGTAGCTTGAGAGGGGTTG 60.108 60.000 0.00 0.00 0.00 3.77
27 28 1.900545 GCGGTAGCTTGAGAGGGGTT 61.901 60.000 0.00 0.00 41.01 4.11
28 29 2.359967 GCGGTAGCTTGAGAGGGGT 61.360 63.158 0.00 0.00 41.01 4.95
29 30 1.690219 ATGCGGTAGCTTGAGAGGGG 61.690 60.000 0.00 0.00 45.42 4.79
30 31 1.000283 CTATGCGGTAGCTTGAGAGGG 60.000 57.143 0.00 0.00 45.42 4.30
31 32 1.957177 TCTATGCGGTAGCTTGAGAGG 59.043 52.381 0.00 0.00 45.42 3.69
32 33 3.573598 CATCTATGCGGTAGCTTGAGAG 58.426 50.000 0.00 0.00 45.42 3.20
33 34 2.288457 GCATCTATGCGGTAGCTTGAGA 60.288 50.000 0.00 0.00 44.67 3.27
34 35 2.064762 GCATCTATGCGGTAGCTTGAG 58.935 52.381 0.00 0.00 44.67 3.02
35 36 2.154854 GCATCTATGCGGTAGCTTGA 57.845 50.000 0.00 0.00 44.67 3.02
46 47 2.229039 CGAGGCCAACGCATCTATG 58.771 57.895 5.01 0.00 43.65 2.23
47 48 4.758692 CGAGGCCAACGCATCTAT 57.241 55.556 5.01 0.00 43.65 1.98
54 55 2.126228 TTAGTCGCGAGGCCAACG 60.126 61.111 10.24 16.13 35.23 4.10
55 56 1.077089 GACTTAGTCGCGAGGCCAAC 61.077 60.000 10.24 0.00 35.23 3.77
56 57 1.214589 GACTTAGTCGCGAGGCCAA 59.785 57.895 10.24 0.00 35.23 4.52
57 58 2.707849 GGACTTAGTCGCGAGGCCA 61.708 63.158 10.24 0.00 40.98 5.36
58 59 2.104530 GGACTTAGTCGCGAGGCC 59.895 66.667 10.24 5.38 35.23 5.19
59 60 1.226717 CAGGACTTAGTCGCGAGGC 60.227 63.158 10.24 0.00 32.65 4.70
60 61 0.099082 GTCAGGACTTAGTCGCGAGG 59.901 60.000 10.24 2.60 32.65 4.63
61 62 0.803117 TGTCAGGACTTAGTCGCGAG 59.197 55.000 10.24 0.00 32.65 5.03
62 63 0.520404 GTGTCAGGACTTAGTCGCGA 59.480 55.000 3.71 3.71 32.65 5.87
63 64 0.522180 AGTGTCAGGACTTAGTCGCG 59.478 55.000 0.00 0.00 32.65 5.87
64 65 3.427773 CCTTAGTGTCAGGACTTAGTCGC 60.428 52.174 6.27 0.00 32.41 5.19
65 66 4.008330 TCCTTAGTGTCAGGACTTAGTCG 58.992 47.826 6.27 0.00 35.34 4.18
73 74 2.497675 GCAGATGTCCTTAGTGTCAGGA 59.502 50.000 0.00 0.00 38.18 3.86
74 75 2.419297 GGCAGATGTCCTTAGTGTCAGG 60.419 54.545 0.00 0.00 0.00 3.86
75 76 2.736719 CGGCAGATGTCCTTAGTGTCAG 60.737 54.545 0.00 0.00 0.00 3.51
76 77 1.204704 CGGCAGATGTCCTTAGTGTCA 59.795 52.381 0.00 0.00 0.00 3.58
77 78 1.204941 ACGGCAGATGTCCTTAGTGTC 59.795 52.381 0.00 0.00 0.00 3.67
78 79 1.066858 CACGGCAGATGTCCTTAGTGT 60.067 52.381 0.00 0.00 0.00 3.55
79 80 1.204704 TCACGGCAGATGTCCTTAGTG 59.795 52.381 0.00 0.00 0.00 2.74
80 81 1.204941 GTCACGGCAGATGTCCTTAGT 59.795 52.381 0.00 0.00 0.00 2.24
81 82 1.204704 TGTCACGGCAGATGTCCTTAG 59.795 52.381 0.00 0.00 0.00 2.18
82 83 1.262417 TGTCACGGCAGATGTCCTTA 58.738 50.000 0.00 0.00 0.00 2.69
83 84 0.396435 TTGTCACGGCAGATGTCCTT 59.604 50.000 0.00 0.00 0.00 3.36
84 85 0.615331 ATTGTCACGGCAGATGTCCT 59.385 50.000 0.00 0.00 0.00 3.85
85 86 1.398390 GAATTGTCACGGCAGATGTCC 59.602 52.381 0.00 0.00 0.00 4.02
86 87 1.398390 GGAATTGTCACGGCAGATGTC 59.602 52.381 0.00 0.00 0.00 3.06
87 88 1.271325 TGGAATTGTCACGGCAGATGT 60.271 47.619 0.00 0.00 0.00 3.06
88 89 1.131126 GTGGAATTGTCACGGCAGATG 59.869 52.381 0.00 0.00 0.00 2.90
89 90 1.453155 GTGGAATTGTCACGGCAGAT 58.547 50.000 0.00 0.00 0.00 2.90
90 91 2.927004 GTGGAATTGTCACGGCAGA 58.073 52.632 0.00 0.00 0.00 4.26
96 97 2.286772 GGTGTTGTCGTGGAATTGTCAC 60.287 50.000 0.00 0.00 0.00 3.67
97 98 1.944024 GGTGTTGTCGTGGAATTGTCA 59.056 47.619 0.00 0.00 0.00 3.58
98 99 1.265905 GGGTGTTGTCGTGGAATTGTC 59.734 52.381 0.00 0.00 0.00 3.18
99 100 1.314730 GGGTGTTGTCGTGGAATTGT 58.685 50.000 0.00 0.00 0.00 2.71
100 101 1.313772 TGGGTGTTGTCGTGGAATTG 58.686 50.000 0.00 0.00 0.00 2.32
101 102 2.286365 ATGGGTGTTGTCGTGGAATT 57.714 45.000 0.00 0.00 0.00 2.17
102 103 2.355716 CCTATGGGTGTTGTCGTGGAAT 60.356 50.000 0.00 0.00 0.00 3.01
103 104 1.002659 CCTATGGGTGTTGTCGTGGAA 59.997 52.381 0.00 0.00 0.00 3.53
104 105 0.611200 CCTATGGGTGTTGTCGTGGA 59.389 55.000 0.00 0.00 0.00 4.02
105 106 0.392461 CCCTATGGGTGTTGTCGTGG 60.392 60.000 0.00 0.00 38.25 4.94
106 107 3.153024 CCCTATGGGTGTTGTCGTG 57.847 57.895 0.00 0.00 38.25 4.35
117 118 4.344968 TGCGATGATATGATACCCCTATGG 59.655 45.833 0.00 0.00 41.37 2.74
118 119 5.292765 GTGCGATGATATGATACCCCTATG 58.707 45.833 0.00 0.00 0.00 2.23
119 120 4.038042 CGTGCGATGATATGATACCCCTAT 59.962 45.833 0.00 0.00 0.00 2.57
120 121 3.380320 CGTGCGATGATATGATACCCCTA 59.620 47.826 0.00 0.00 0.00 3.53
121 122 2.166459 CGTGCGATGATATGATACCCCT 59.834 50.000 0.00 0.00 0.00 4.79
122 123 2.094182 ACGTGCGATGATATGATACCCC 60.094 50.000 0.00 0.00 0.00 4.95
123 124 3.232213 ACGTGCGATGATATGATACCC 57.768 47.619 0.00 0.00 0.00 3.69
124 125 3.300853 CGAACGTGCGATGATATGATACC 59.699 47.826 11.51 0.00 0.00 2.73
125 126 3.241364 GCGAACGTGCGATGATATGATAC 60.241 47.826 22.89 0.00 0.00 2.24
126 127 2.914838 GCGAACGTGCGATGATATGATA 59.085 45.455 22.89 0.00 0.00 2.15
127 128 1.721389 GCGAACGTGCGATGATATGAT 59.279 47.619 22.89 0.00 0.00 2.45
128 129 1.128513 GCGAACGTGCGATGATATGA 58.871 50.000 22.89 0.00 0.00 2.15
129 130 1.131771 AGCGAACGTGCGATGATATG 58.868 50.000 22.89 0.00 40.67 1.78
130 131 2.699251 TAGCGAACGTGCGATGATAT 57.301 45.000 22.89 0.00 40.67 1.63
160 161 4.935702 TCCTGCATGAAAACTGACAAAAG 58.064 39.130 0.00 0.00 0.00 2.27
165 166 3.988379 TGTTCCTGCATGAAAACTGAC 57.012 42.857 5.96 0.00 0.00 3.51
166 167 4.206375 TCTTGTTCCTGCATGAAAACTGA 58.794 39.130 5.96 0.20 0.00 3.41
415 445 2.360423 GGGGGAGAAGAGGACTGGATTA 60.360 54.545 0.00 0.00 0.00 1.75
447 479 1.123928 GGATTGGACGATGGGAGAGT 58.876 55.000 0.00 0.00 0.00 3.24
976 1010 4.105486 CACAAACGAAGCGAGATGAGATA 58.895 43.478 0.00 0.00 0.00 1.98
985 1019 1.872388 TCCATTCACAAACGAAGCGA 58.128 45.000 0.00 0.00 0.00 4.93
1100 1134 3.157087 CAAATAAGAGGTTGGCTGGTGT 58.843 45.455 0.00 0.00 0.00 4.16
1106 1143 4.188247 GGAAACCAAATAAGAGGTTGGC 57.812 45.455 2.37 0.00 46.92 4.52
1132 1172 0.251297 CCCAAGGGCATGAACACAGA 60.251 55.000 0.00 0.00 0.00 3.41
1134 1174 4.517663 CCCAAGGGCATGAACACA 57.482 55.556 0.00 0.00 0.00 3.72
1144 1184 0.257039 ATGAACTGCTAGCCCAAGGG 59.743 55.000 13.29 0.00 38.57 3.95
1145 1185 2.019984 GAATGAACTGCTAGCCCAAGG 58.980 52.381 13.29 0.00 0.00 3.61
1154 1194 3.359950 GGGAAATGAGGAATGAACTGCT 58.640 45.455 0.00 0.00 0.00 4.24
1184 1225 3.969287 TGAGATGTCTGAACCTGGAAG 57.031 47.619 0.00 0.00 0.00 3.46
1187 1228 2.354259 GCTTGAGATGTCTGAACCTGG 58.646 52.381 0.00 0.00 0.00 4.45
1282 1323 0.598562 CCACGGGAGGTATCTCATCG 59.401 60.000 13.98 13.98 41.69 3.84
1302 1343 0.548682 AGCTCCACCTTGACTCCCAT 60.549 55.000 0.00 0.00 0.00 4.00
1330 1371 4.467084 GGCGGCTCCACGGAATCA 62.467 66.667 0.00 0.00 34.01 2.57
2685 2737 7.279758 CCTTCAAAAGATAGTTCTCATCTGGTC 59.720 40.741 0.00 0.00 33.03 4.02
2730 2782 2.805099 GAGACTTCTGCAAGTGGAACAG 59.195 50.000 0.00 0.00 43.37 3.16
2738 2790 3.055963 ACATCCAGAGAGACTTCTGCAAG 60.056 47.826 8.37 0.00 42.58 4.01
2798 2850 2.266055 GTCCCCGTCTGAAGCCAG 59.734 66.667 0.00 0.00 41.74 4.85
2812 2864 3.328050 CCTTGTCTGGGGATAATAGGTCC 59.672 52.174 0.00 0.00 34.92 4.46
3024 3076 6.505048 TTTCATCTGTATCACCATCCTGAT 57.495 37.500 0.00 0.00 35.05 2.90
3026 3078 6.293698 TCATTTCATCTGTATCACCATCCTG 58.706 40.000 0.00 0.00 0.00 3.86
3034 3086 9.383519 GTTACCTCTTTCATTTCATCTGTATCA 57.616 33.333 0.00 0.00 0.00 2.15
3072 3124 4.652881 ACTCATCTCCATCTGCAGTCAATA 59.347 41.667 14.67 0.00 0.00 1.90
3107 3159 5.485353 TCAGAAACTCACCCTTATCTGATGT 59.515 40.000 0.00 0.00 38.59 3.06
3115 3167 6.433847 TCTTTCATCAGAAACTCACCCTTA 57.566 37.500 0.00 0.00 38.76 2.69
3221 3273 8.950210 CACCATTACTGTTTTGATAGAACATCT 58.050 33.333 0.00 0.00 36.51 2.90
3235 3287 2.647299 TCCACCATCCACCATTACTGTT 59.353 45.455 0.00 0.00 0.00 3.16
3281 3333 2.941720 GAGAAGCCACAGAATCATGTCC 59.058 50.000 0.00 0.00 0.00 4.02
3357 3409 0.253044 TGCTGATAAGGGTGAGCCAC 59.747 55.000 2.50 0.00 36.17 5.01
3550 3602 5.594317 TCCCTTCTTTGGAGAAAGTTTCTTG 59.406 40.000 18.96 8.00 41.19 3.02
3694 3746 9.011095 TCCTCCAGTAAGTTCACTATTATATCG 57.989 37.037 0.00 0.00 0.00 2.92
3826 3927 8.509690 CAGATCATGAGTCATGTAAAACAAGTT 58.490 33.333 28.03 6.00 41.98 2.66
3837 3938 5.995897 TCATTTAGGCAGATCATGAGTCATG 59.004 40.000 24.60 24.60 42.60 3.07
3842 3943 8.410912 TGAATTTTCATTTAGGCAGATCATGAG 58.589 33.333 0.09 0.00 31.01 2.90
3879 3980 5.437060 GGTGACAGCCTGAAATAATTCCTA 58.563 41.667 0.00 0.00 34.49 2.94
3881 3982 3.381590 GGGTGACAGCCTGAAATAATTCC 59.618 47.826 16.60 0.00 34.49 3.01
3884 3985 3.245229 TGTGGGTGACAGCCTGAAATAAT 60.245 43.478 23.55 0.00 36.53 1.28
3888 3989 0.478072 ATGTGGGTGACAGCCTGAAA 59.522 50.000 23.55 7.76 38.23 2.69
3956 4057 3.200593 CATGCAGAGGGCTCGTGC 61.201 66.667 7.00 7.00 45.15 5.34
3959 4060 2.110967 CAACCATGCAGAGGGCTCG 61.111 63.158 12.16 0.00 45.15 5.03
3975 4076 1.946745 TGCGAACAGACACATCACAA 58.053 45.000 0.00 0.00 0.00 3.33
3976 4077 1.799994 CATGCGAACAGACACATCACA 59.200 47.619 0.00 0.00 0.00 3.58
3977 4078 2.068519 TCATGCGAACAGACACATCAC 58.931 47.619 0.00 0.00 0.00 3.06
3980 4081 2.749280 TCTCATGCGAACAGACACAT 57.251 45.000 0.00 0.00 0.00 3.21
3982 4083 2.412065 GCTTTCTCATGCGAACAGACAC 60.412 50.000 0.00 0.00 0.00 3.67
3983 4084 1.800586 GCTTTCTCATGCGAACAGACA 59.199 47.619 0.00 0.00 0.00 3.41
3984 4085 2.072298 AGCTTTCTCATGCGAACAGAC 58.928 47.619 0.00 0.00 0.00 3.51
3985 4086 2.462456 AGCTTTCTCATGCGAACAGA 57.538 45.000 0.00 0.00 0.00 3.41
3986 4087 4.871993 AATAGCTTTCTCATGCGAACAG 57.128 40.909 0.00 1.22 0.00 3.16
3987 4088 6.316140 ACATAAATAGCTTTCTCATGCGAACA 59.684 34.615 0.00 0.00 0.00 3.18
3988 4089 6.630443 CACATAAATAGCTTTCTCATGCGAAC 59.370 38.462 0.00 0.00 0.00 3.95
3990 4091 5.817296 ACACATAAATAGCTTTCTCATGCGA 59.183 36.000 0.00 0.00 0.00 5.10
3991 4092 5.905733 CACACATAAATAGCTTTCTCATGCG 59.094 40.000 0.00 0.00 0.00 4.73
3992 4093 5.684626 GCACACATAAATAGCTTTCTCATGC 59.315 40.000 0.00 0.00 0.00 4.06
3993 4094 6.788243 TGCACACATAAATAGCTTTCTCATG 58.212 36.000 0.00 0.00 0.00 3.07
3994 4095 7.121759 AGTTGCACACATAAATAGCTTTCTCAT 59.878 33.333 0.00 0.00 0.00 2.90
3995 4096 6.430925 AGTTGCACACATAAATAGCTTTCTCA 59.569 34.615 0.00 0.00 0.00 3.27
3996 4097 6.846350 AGTTGCACACATAAATAGCTTTCTC 58.154 36.000 0.00 0.00 0.00 2.87
3997 4098 6.656693 AGAGTTGCACACATAAATAGCTTTCT 59.343 34.615 0.00 0.00 0.00 2.52
3998 4099 6.846350 AGAGTTGCACACATAAATAGCTTTC 58.154 36.000 0.00 0.00 0.00 2.62
3999 4100 6.824305 AGAGTTGCACACATAAATAGCTTT 57.176 33.333 0.00 0.00 0.00 3.51
4000 4101 6.207417 ACAAGAGTTGCACACATAAATAGCTT 59.793 34.615 0.00 0.00 0.00 3.74
4001 4102 5.707298 ACAAGAGTTGCACACATAAATAGCT 59.293 36.000 0.00 0.00 0.00 3.32
4002 4103 5.796935 CACAAGAGTTGCACACATAAATAGC 59.203 40.000 0.00 0.00 0.00 2.97
4041 4142 5.590259 TGAAAGCCAGCTTCCTAATATGTTC 59.410 40.000 5.17 0.00 34.84 3.18
4055 4156 7.307160 GGTTTTAATTTAGTGTTGAAAGCCAGC 60.307 37.037 0.00 0.00 30.84 4.85
4112 4213 7.855375 ACAGGATTCTCAATGAAGATGAGTTA 58.145 34.615 3.72 0.00 43.77 2.24
4113 4214 6.719301 ACAGGATTCTCAATGAAGATGAGTT 58.281 36.000 3.72 0.00 43.77 3.01
4121 4253 8.413309 AATCTTCAAACAGGATTCTCAATGAA 57.587 30.769 0.00 0.00 39.24 2.57
4125 4257 8.299570 GCTAAAATCTTCAAACAGGATTCTCAA 58.700 33.333 0.00 0.00 0.00 3.02
4183 4315 9.920826 GAGATTTTCTTTTAAACAAAAGGCAAG 57.079 29.630 9.34 0.00 39.56 4.01
4264 4396 1.218316 CTACCCACAACGCCCTCTC 59.782 63.158 0.00 0.00 0.00 3.20
4276 4408 2.040606 GGCCACCTCCTCTACCCA 59.959 66.667 0.00 0.00 0.00 4.51
4381 4515 0.674895 ACTCCGGCAAGTTCTCATGC 60.675 55.000 0.00 0.00 41.82 4.06
4428 4562 1.406903 CCTTGGGCCCTGAATTCATC 58.593 55.000 25.70 1.48 0.00 2.92
4529 4663 2.197605 TCAGTCACCGGCGTCTTCA 61.198 57.895 6.01 0.00 0.00 3.02
4545 4679 0.249120 AGCGAATCAATCACCGGTCA 59.751 50.000 2.59 0.00 0.00 4.02
4567 4701 0.983378 AGGGCTACCACAGACATCCC 60.983 60.000 0.00 0.00 40.13 3.85
4574 4708 3.057315 CACAAAATTCAGGGCTACCACAG 60.057 47.826 0.00 0.00 40.13 3.66
4605 4739 2.796031 CAACAATTGCATTGAACTGCGT 59.204 40.909 5.05 0.00 45.30 5.24
4652 4797 0.846693 AACCAACAGAGCTTCCACCT 59.153 50.000 0.00 0.00 0.00 4.00
4653 4798 1.239347 GAACCAACAGAGCTTCCACC 58.761 55.000 0.00 0.00 0.00 4.61
4739 4884 5.241506 TCCAGTTTCACAGCTTTGATTTAGG 59.758 40.000 2.84 4.74 0.00 2.69
4740 4885 6.317789 TCCAGTTTCACAGCTTTGATTTAG 57.682 37.500 2.84 0.00 0.00 1.85
4878 5045 2.364632 TGGTTGATTTGAGCCATACCG 58.635 47.619 0.00 0.00 0.00 4.02
5011 5206 1.668919 CCGGCGCCATACATACTACAG 60.669 57.143 28.98 4.53 0.00 2.74
5012 5207 0.315886 CCGGCGCCATACATACTACA 59.684 55.000 28.98 0.00 0.00 2.74
5017 5212 2.579657 CCCTCCGGCGCCATACATA 61.580 63.158 28.98 3.10 0.00 2.29
5289 5489 1.917872 AAGACGGACAGAGAGCTCTT 58.082 50.000 19.36 0.88 37.98 2.85
5290 5490 2.026636 AGTAAGACGGACAGAGAGCTCT 60.027 50.000 18.28 18.28 41.37 4.09
5291 5491 2.361789 AGTAAGACGGACAGAGAGCTC 58.638 52.381 5.27 5.27 0.00 4.09
5293 5493 4.602995 CATTAGTAAGACGGACAGAGAGC 58.397 47.826 0.00 0.00 0.00 4.09
5294 5494 4.336993 AGCATTAGTAAGACGGACAGAGAG 59.663 45.833 0.00 0.00 0.00 3.20
5295 5495 4.270834 AGCATTAGTAAGACGGACAGAGA 58.729 43.478 0.00 0.00 0.00 3.10
5296 5496 4.640789 AGCATTAGTAAGACGGACAGAG 57.359 45.455 0.00 0.00 0.00 3.35
5297 5497 5.066117 CACTAGCATTAGTAAGACGGACAGA 59.934 44.000 0.00 0.00 38.05 3.41
5299 5499 4.439700 GCACTAGCATTAGTAAGACGGACA 60.440 45.833 0.00 0.00 38.05 4.02
5301 5501 3.952323 AGCACTAGCATTAGTAAGACGGA 59.048 43.478 0.00 0.00 45.49 4.69
5302 5502 4.045104 CAGCACTAGCATTAGTAAGACGG 58.955 47.826 0.00 0.00 45.49 4.79
5304 5504 4.688021 AGCAGCACTAGCATTAGTAAGAC 58.312 43.478 0.00 0.00 45.49 3.01
5365 5572 2.031516 ACCGTCGTCGTCATCGTCT 61.032 57.895 0.71 0.00 38.33 4.18
5389 5596 2.194889 TCACGGTCACGCCACACTA 61.195 57.895 0.00 0.00 46.04 2.74
5400 5607 0.179161 CGACTGATCTGGTCACGGTC 60.179 60.000 15.72 0.00 33.73 4.79
5401 5608 0.608308 TCGACTGATCTGGTCACGGT 60.608 55.000 15.72 0.00 33.73 4.83
5402 5609 0.099613 CTCGACTGATCTGGTCACGG 59.900 60.000 15.72 4.37 33.73 4.94
5499 5708 2.575455 TTTTGTTGCCCCGGTCCACT 62.575 55.000 0.00 0.00 0.00 4.00
5508 5717 1.079503 TGCGTTTTGTTTTGTTGCCC 58.920 45.000 0.00 0.00 0.00 5.36
5535 5744 1.112113 GGGTCTCAGAAGCCGTGATA 58.888 55.000 0.00 0.00 0.00 2.15
5558 5767 1.198637 GTCTCACAAGATGTTGCAGCC 59.801 52.381 1.83 0.00 37.14 4.85
5560 5769 2.775890 AGGTCTCACAAGATGTTGCAG 58.224 47.619 1.83 0.00 37.14 4.41
5561 5770 2.936919 AGGTCTCACAAGATGTTGCA 57.063 45.000 1.83 0.00 37.14 4.08
5562 5771 3.929610 GTCTAGGTCTCACAAGATGTTGC 59.070 47.826 1.83 0.00 37.14 4.17
5563 5772 5.139435 TGTCTAGGTCTCACAAGATGTTG 57.861 43.478 0.13 0.13 39.82 3.33
5564 5773 5.305644 AGTTGTCTAGGTCTCACAAGATGTT 59.694 40.000 0.00 0.00 33.08 2.71
5590 5803 3.072915 TGATCTTCCTCCAGACTGCAAAA 59.927 43.478 0.00 0.00 0.00 2.44
5604 5817 4.453819 CAGAAGAAACACAGGTGATCTTCC 59.546 45.833 28.14 19.11 46.00 3.46
5614 5827 6.373774 AGGCAGAATTATCAGAAGAAACACAG 59.626 38.462 0.00 0.00 0.00 3.66
5620 5833 6.058183 GGCTAAGGCAGAATTATCAGAAGAA 58.942 40.000 0.00 0.00 40.87 2.52
5624 5837 4.262207 CGAGGCTAAGGCAGAATTATCAGA 60.262 45.833 0.00 0.00 40.87 3.27
5625 5838 3.993081 CGAGGCTAAGGCAGAATTATCAG 59.007 47.826 0.00 0.00 40.87 2.90
5626 5839 3.388024 ACGAGGCTAAGGCAGAATTATCA 59.612 43.478 0.00 0.00 40.87 2.15
5627 5840 3.743396 CACGAGGCTAAGGCAGAATTATC 59.257 47.826 0.00 0.00 40.87 1.75
5630 5843 1.279271 ACACGAGGCTAAGGCAGAATT 59.721 47.619 0.00 0.00 40.87 2.17
5633 5846 1.591703 CACACGAGGCTAAGGCAGA 59.408 57.895 0.00 0.00 40.87 4.26
5651 5868 1.291877 CGTTCAGCTGGTGGTGTAGC 61.292 60.000 15.13 0.00 41.91 3.58
5670 5887 6.708949 TGGTACTAACAGGAAAAAGATGACAC 59.291 38.462 0.00 0.00 0.00 3.67
5683 5900 4.282703 ACAGTAGTGGTTGGTACTAACAGG 59.717 45.833 21.78 6.81 32.84 4.00
5690 5907 8.255905 AGTCAAATATACAGTAGTGGTTGGTAC 58.744 37.037 1.92 0.00 0.00 3.34
5734 5954 2.094258 GTGACACATTATCTGCACACGG 59.906 50.000 0.00 0.00 0.00 4.94
5735 5955 2.995939 AGTGACACATTATCTGCACACG 59.004 45.455 8.59 0.00 33.63 4.49
5786 6008 1.995484 CCGTACTGACAAGTGAGCATG 59.005 52.381 0.00 0.00 37.19 4.06
5802 6024 0.320073 GTGCCTGTTGTGTAGCCGTA 60.320 55.000 0.00 0.00 0.00 4.02
5875 6097 2.358898 CTGAGCCTAGTCTTGAGAGAGC 59.641 54.545 0.00 0.00 31.07 4.09
5900 6122 2.918571 CAGAGCTGCTTCGGTGAAA 58.081 52.632 2.53 0.00 0.00 2.69
5934 6168 3.072944 GCTGCAAGTGATTCAGAGAGTT 58.927 45.455 0.00 0.00 35.30 3.01
5935 6169 2.614987 GGCTGCAAGTGATTCAGAGAGT 60.615 50.000 0.50 0.00 35.30 3.24
5936 6170 2.008329 GGCTGCAAGTGATTCAGAGAG 58.992 52.381 0.50 0.00 35.30 3.20
5937 6171 1.627329 AGGCTGCAAGTGATTCAGAGA 59.373 47.619 0.50 0.00 35.30 3.10
5938 6172 1.738350 CAGGCTGCAAGTGATTCAGAG 59.262 52.381 0.00 0.00 35.30 3.35
5939 6173 1.348696 TCAGGCTGCAAGTGATTCAGA 59.651 47.619 10.34 0.00 35.30 3.27
5940 6174 1.817357 TCAGGCTGCAAGTGATTCAG 58.183 50.000 10.34 0.00 35.30 3.02
5941 6175 2.275134 TTCAGGCTGCAAGTGATTCA 57.725 45.000 10.34 0.00 35.30 2.57
5942 6176 2.734492 GCATTCAGGCTGCAAGTGATTC 60.734 50.000 10.34 0.00 39.46 2.52
5943 6177 1.203994 GCATTCAGGCTGCAAGTGATT 59.796 47.619 10.34 0.00 39.46 2.57
5944 6178 0.815734 GCATTCAGGCTGCAAGTGAT 59.184 50.000 10.34 0.00 39.46 3.06
5945 6179 0.537828 TGCATTCAGGCTGCAAGTGA 60.538 50.000 10.34 0.00 46.06 3.41
5968 6202 1.077123 CTGCTGCTGCTTCAGTGTAG 58.923 55.000 17.00 0.00 40.48 2.74
5992 6226 7.451732 AGTGATTCAGATAATAATGCAGAGCT 58.548 34.615 0.00 0.00 0.00 4.09
6022 6256 4.393680 GGAACTGGCGTGTGTAAATTGATA 59.606 41.667 0.00 0.00 0.00 2.15
6024 6258 2.550606 GGAACTGGCGTGTGTAAATTGA 59.449 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.