Multiple sequence alignment - TraesCS4D01G038100

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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 TraesCS4D01G038100 chr4D 100.000 4145 0 0 1 4145 16450343 16446199 0.000000e+00 7655
1 TraesCS4D01G038100 chr4D 92.181 1522 106 5 1711 3230 16375605 16374095 0.000000e+00 2139
2 TraesCS4D01G038100 chr4D 93.254 504 28 3 896 1399 16403450 16402953 0.000000e+00 737
3 TraesCS4D01G038100 chr4D 89.522 544 33 11 368 894 16404072 16403536 0.000000e+00 667
4 TraesCS4D01G038100 chr4D 90.062 322 31 1 1395 1715 16387493 16387172 2.310000e-112 416
5 TraesCS4D01G038100 chr4D 93.846 65 4 0 282 346 16404135 16404071 9.480000e-17 99
6 TraesCS4D01G038100 chr4A 92.379 3215 185 31 283 3454 584039726 584042923 0.000000e+00 4525
7 TraesCS4D01G038100 chr4A 91.852 270 18 2 3876 4145 584043687 584043952 1.410000e-99 374
8 TraesCS4D01G038100 chr4A 93.151 146 7 3 140 283 352496726 352496870 1.170000e-50 211
9 TraesCS4D01G038100 chr4B 93.622 3026 161 19 282 3285 28320714 28317699 0.000000e+00 4490
10 TraesCS4D01G038100 chr4B 89.904 416 20 7 3321 3722 28317705 28317298 2.210000e-142 516
11 TraesCS4D01G038100 chr4B 88.000 375 21 11 3724 4077 28317167 28316796 4.950000e-114 422
12 TraesCS4D01G038100 chr4B 85.563 284 34 6 282 564 28325454 28325177 1.460000e-74 291
13 TraesCS4D01G038100 chr4B 92.361 144 9 2 140 283 450453457 450453598 1.950000e-48 204
14 TraesCS4D01G038100 chr4B 96.694 121 2 2 7 126 636171689 636171570 2.530000e-47 200
15 TraesCS4D01G038100 chr4B 98.230 113 2 0 5 117 242910415 242910303 9.090000e-47 198
16 TraesCS4D01G038100 chr6D 78.367 2131 421 29 1019 3120 84630958 84628839 0.000000e+00 1345
17 TraesCS4D01G038100 chr6D 78.364 2140 410 37 1019 3120 84231793 84229669 0.000000e+00 1338
18 TraesCS4D01G038100 chr6D 77.182 2108 437 34 1041 3116 84224354 84222259 0.000000e+00 1188
19 TraesCS4D01G038100 chr6D 76.428 2189 439 50 1015 3148 85581307 85583473 0.000000e+00 1112
20 TraesCS4D01G038100 chr6D 75.946 2166 455 45 1014 3148 84653843 84651713 0.000000e+00 1053
21 TraesCS4D01G038100 chr6D 75.819 2167 447 45 1042 3148 84661507 84659358 0.000000e+00 1027
22 TraesCS4D01G038100 chr6D 72.873 1187 287 25 1038 2205 81750103 81748933 3.910000e-100 375
23 TraesCS4D01G038100 chr6D 91.946 149 10 2 140 286 312104220 312104072 1.510000e-49 207
24 TraesCS4D01G038100 chr6B 78.320 2131 422 31 1019 3120 160716916 160714797 0.000000e+00 1339
25 TraesCS4D01G038100 chr6B 78.076 2162 431 30 1019 3148 160683084 160680934 0.000000e+00 1327
26 TraesCS4D01G038100 chr6B 78.121 2139 412 38 1014 3120 159989776 159987662 0.000000e+00 1306
27 TraesCS4D01G038100 chr6B 76.533 2152 456 34 1024 3139 160912092 160909954 0.000000e+00 1131
28 TraesCS4D01G038100 chr6B 78.600 1243 219 24 1302 2515 160708651 160707427 0.000000e+00 778
29 TraesCS4D01G038100 chr6B 71.604 2113 535 50 1035 3116 157900391 157902469 6.140000e-143 518
30 TraesCS4D01G038100 chr6A 78.208 2143 416 36 1014 3120 101562619 101560492 0.000000e+00 1323
31 TraesCS4D01G038100 chr6A 77.050 2183 452 40 1014 3169 101844944 101842784 0.000000e+00 1210
32 TraesCS4D01G038100 chr6A 77.155 2123 434 41 1030 3116 101554711 101552604 0.000000e+00 1186
33 TraesCS4D01G038100 chr6A 76.194 1382 291 27 1759 3120 101850947 101849584 0.000000e+00 695
34 TraesCS4D01G038100 chr6A 71.547 1202 308 26 1020 2204 98064877 98063693 1.130000e-75 294
35 TraesCS4D01G038100 chr2D 95.714 140 6 0 144 283 536091166 536091027 4.170000e-55 226
36 TraesCS4D01G038100 chr2D 99.138 116 1 0 3 118 111321517 111321402 4.200000e-50 209
37 TraesCS4D01G038100 chr2D 95.200 125 3 3 2 124 529636496 529636373 1.180000e-45 195
38 TraesCS4D01G038100 chr3A 94.326 141 6 2 145 283 126854226 126854086 9.020000e-52 215
39 TraesCS4D01G038100 chr3A 93.007 143 8 2 154 296 642715813 642715953 1.510000e-49 207
40 TraesCS4D01G038100 chr2B 94.928 138 6 1 157 293 548925010 548925147 9.020000e-52 215
41 TraesCS4D01G038100 chr7B 94.326 141 5 3 146 283 385066889 385066749 3.250000e-51 213
42 TraesCS4D01G038100 chr7B 97.414 116 3 0 5 120 730205112 730205227 9.090000e-47 198
43 TraesCS4D01G038100 chr7D 99.091 110 1 0 6 115 382742644 382742535 9.090000e-47 198
44 TraesCS4D01G038100 chr5D 95.200 125 5 1 7 130 408791894 408792018 3.270000e-46 196
45 TraesCS4D01G038100 chr3B 89.375 160 12 4 132 290 724754574 724754419 3.270000e-46 196
46 TraesCS4D01G038100 chr5B 95.798 119 5 0 6 124 622161362 622161244 4.230000e-45 193
47 TraesCS4D01G038100 chr5B 95.082 122 4 1 7 128 622630605 622630486 1.520000e-44 191


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 TraesCS4D01G038100 chr4D 16446199 16450343 4144 True 7655.000000 7655 100.000000 1 4145 1 chr4D.!!$R3 4144
1 TraesCS4D01G038100 chr4D 16374095 16375605 1510 True 2139.000000 2139 92.181000 1711 3230 1 chr4D.!!$R1 1519
2 TraesCS4D01G038100 chr4D 16402953 16404135 1182 True 501.000000 737 92.207333 282 1399 3 chr4D.!!$R4 1117
3 TraesCS4D01G038100 chr4A 584039726 584043952 4226 False 2449.500000 4525 92.115500 283 4145 2 chr4A.!!$F2 3862
4 TraesCS4D01G038100 chr4B 28316796 28320714 3918 True 1809.333333 4490 90.508667 282 4077 3 chr4B.!!$R4 3795
5 TraesCS4D01G038100 chr6D 84628839 84630958 2119 True 1345.000000 1345 78.367000 1019 3120 1 chr6D.!!$R4 2101
6 TraesCS4D01G038100 chr6D 84229669 84231793 2124 True 1338.000000 1338 78.364000 1019 3120 1 chr6D.!!$R3 2101
7 TraesCS4D01G038100 chr6D 84222259 84224354 2095 True 1188.000000 1188 77.182000 1041 3116 1 chr6D.!!$R2 2075
8 TraesCS4D01G038100 chr6D 85581307 85583473 2166 False 1112.000000 1112 76.428000 1015 3148 1 chr6D.!!$F1 2133
9 TraesCS4D01G038100 chr6D 84651713 84653843 2130 True 1053.000000 1053 75.946000 1014 3148 1 chr6D.!!$R5 2134
10 TraesCS4D01G038100 chr6D 84659358 84661507 2149 True 1027.000000 1027 75.819000 1042 3148 1 chr6D.!!$R6 2106
11 TraesCS4D01G038100 chr6D 81748933 81750103 1170 True 375.000000 375 72.873000 1038 2205 1 chr6D.!!$R1 1167
12 TraesCS4D01G038100 chr6B 160714797 160716916 2119 True 1339.000000 1339 78.320000 1019 3120 1 chr6B.!!$R4 2101
13 TraesCS4D01G038100 chr6B 160680934 160683084 2150 True 1327.000000 1327 78.076000 1019 3148 1 chr6B.!!$R2 2129
14 TraesCS4D01G038100 chr6B 159987662 159989776 2114 True 1306.000000 1306 78.121000 1014 3120 1 chr6B.!!$R1 2106
15 TraesCS4D01G038100 chr6B 160909954 160912092 2138 True 1131.000000 1131 76.533000 1024 3139 1 chr6B.!!$R5 2115
16 TraesCS4D01G038100 chr6B 160707427 160708651 1224 True 778.000000 778 78.600000 1302 2515 1 chr6B.!!$R3 1213
17 TraesCS4D01G038100 chr6B 157900391 157902469 2078 False 518.000000 518 71.604000 1035 3116 1 chr6B.!!$F1 2081
18 TraesCS4D01G038100 chr6A 101560492 101562619 2127 True 1323.000000 1323 78.208000 1014 3120 1 chr6A.!!$R3 2106
19 TraesCS4D01G038100 chr6A 101842784 101844944 2160 True 1210.000000 1210 77.050000 1014 3169 1 chr6A.!!$R4 2155
20 TraesCS4D01G038100 chr6A 101552604 101554711 2107 True 1186.000000 1186 77.155000 1030 3116 1 chr6A.!!$R2 2086
21 TraesCS4D01G038100 chr6A 101849584 101850947 1363 True 695.000000 695 76.194000 1759 3120 1 chr6A.!!$R5 1361
22 TraesCS4D01G038100 chr6A 98063693 98064877 1184 True 294.000000 294 71.547000 1020 2204 1 chr6A.!!$R1 1184

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
593 595 0.108329 ACGAATTACCTGTCGGGCAG 60.108 55.000 1.75 1.75 44.63 4.85 F
718 731 0.475475 CCCATTGCCATCTAGAGCCA 59.525 55.000 0.00 0.00 0.00 4.75 F
1113 1243 0.545309 CCCTCCTCCAGTTCCTCACA 60.545 60.000 0.00 0.00 0.00 3.58 F
1245 1383 1.813477 GCATCTAGAGGGCTTGAAGGC 60.813 57.143 10.64 10.64 40.51 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1843 1.270907 CAGGGAGAGTGCCACTTAGT 58.729 55.000 0.0 0.0 0.00 2.24 R
1738 1942 3.352648 CTTGTAATCCGTTGTTGGGGAT 58.647 45.455 0.0 0.0 44.83 3.85 R
2371 2586 3.633986 ACCTTCAAGTTTCTGAGCTTTGG 59.366 43.478 0.0 0.0 0.00 3.28 R
3212 3481 0.321653 GCAAGATCCAACTCGGGTGT 60.322 55.000 0.0 0.0 34.36 4.16 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 4.035843 CCTTGCTACTCCCTCCGT 57.964 61.111 0.00 0.00 0.00 4.69
18 19 2.287829 CCTTGCTACTCCCTCCGTT 58.712 57.895 0.00 0.00 0.00 4.44
19 20 0.175989 CCTTGCTACTCCCTCCGTTC 59.824 60.000 0.00 0.00 0.00 3.95
20 21 0.179134 CTTGCTACTCCCTCCGTTCG 60.179 60.000 0.00 0.00 0.00 3.95
21 22 1.601419 TTGCTACTCCCTCCGTTCGG 61.601 60.000 4.74 4.74 0.00 4.30
22 23 1.751927 GCTACTCCCTCCGTTCGGA 60.752 63.158 13.34 13.34 0.00 4.55
23 24 1.318158 GCTACTCCCTCCGTTCGGAA 61.318 60.000 14.79 0.04 33.41 4.30
24 25 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
25 26 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
26 27 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
27 28 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
28 29 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
29 30 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
30 31 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
31 32 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
32 33 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
33 34 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
34 35 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
35 36 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
36 37 3.495377 CCGTTCGGAATTACTTGTCACAA 59.505 43.478 5.19 0.00 0.00 3.33
37 38 4.024725 CCGTTCGGAATTACTTGTCACAAA 60.025 41.667 5.19 0.00 0.00 2.83
38 39 5.503498 CGTTCGGAATTACTTGTCACAAAA 58.497 37.500 0.00 0.00 0.00 2.44
39 40 5.966503 CGTTCGGAATTACTTGTCACAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
40 41 6.635239 CGTTCGGAATTACTTGTCACAAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
41 42 7.357206 CGTTCGGAATTACTTGTCACAAAAATG 60.357 37.037 0.00 0.00 0.00 2.32
42 43 6.442952 TCGGAATTACTTGTCACAAAAATGG 58.557 36.000 0.00 0.00 0.00 3.16
43 44 6.263392 TCGGAATTACTTGTCACAAAAATGGA 59.737 34.615 0.00 0.00 0.00 3.41
44 45 7.040062 TCGGAATTACTTGTCACAAAAATGGAT 60.040 33.333 0.00 0.00 0.00 3.41
45 46 7.062138 CGGAATTACTTGTCACAAAAATGGATG 59.938 37.037 0.00 0.00 0.00 3.51
46 47 7.872483 GGAATTACTTGTCACAAAAATGGATGT 59.128 33.333 0.00 0.00 0.00 3.06
47 48 9.906660 GAATTACTTGTCACAAAAATGGATGTA 57.093 29.630 0.00 0.00 0.00 2.29
50 51 7.765695 ACTTGTCACAAAAATGGATGTATCT 57.234 32.000 0.00 0.00 0.00 1.98
51 52 8.862325 ACTTGTCACAAAAATGGATGTATCTA 57.138 30.769 0.00 0.00 0.00 1.98
52 53 8.730680 ACTTGTCACAAAAATGGATGTATCTAC 58.269 33.333 0.00 0.00 0.00 2.59
53 54 8.628630 TTGTCACAAAAATGGATGTATCTACA 57.371 30.769 0.00 0.00 40.98 2.74
54 55 8.628630 TGTCACAAAAATGGATGTATCTACAA 57.371 30.769 0.00 0.00 39.99 2.41
55 56 8.511321 TGTCACAAAAATGGATGTATCTACAAC 58.489 33.333 0.00 0.00 39.99 3.32
56 57 8.730680 GTCACAAAAATGGATGTATCTACAACT 58.269 33.333 0.00 0.00 39.99 3.16
57 58 9.952030 TCACAAAAATGGATGTATCTACAACTA 57.048 29.630 0.00 0.00 39.99 2.24
88 89 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
89 90 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
90 91 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
91 92 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
92 93 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
93 94 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
94 95 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
95 96 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
96 97 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
97 98 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
98 99 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
99 100 5.800296 TCATTTCTTGGACGAGTAATTCCA 58.200 37.500 0.00 0.00 0.00 3.53
100 101 6.234920 TCATTTCTTGGACGAGTAATTCCAA 58.765 36.000 3.17 3.17 39.62 3.53
101 102 6.712998 TCATTTCTTGGACGAGTAATTCCAAA 59.287 34.615 4.69 0.00 41.11 3.28
102 103 5.934935 TTCTTGGACGAGTAATTCCAAAC 57.065 39.130 4.69 0.00 41.11 2.93
103 104 3.991773 TCTTGGACGAGTAATTCCAAACG 59.008 43.478 4.69 0.00 41.11 3.60
104 105 2.690786 TGGACGAGTAATTCCAAACGG 58.309 47.619 0.00 0.00 0.00 4.44
105 106 2.299582 TGGACGAGTAATTCCAAACGGA 59.700 45.455 0.00 0.00 0.00 4.69
106 107 2.928116 GGACGAGTAATTCCAAACGGAG 59.072 50.000 0.00 0.00 32.88 4.63
107 108 2.928116 GACGAGTAATTCCAAACGGAGG 59.072 50.000 0.00 0.00 32.88 4.30
108 109 2.277084 CGAGTAATTCCAAACGGAGGG 58.723 52.381 0.00 0.00 32.88 4.30
109 110 2.093869 CGAGTAATTCCAAACGGAGGGA 60.094 50.000 0.00 0.00 32.88 4.20
110 111 3.532542 GAGTAATTCCAAACGGAGGGAG 58.467 50.000 0.00 0.00 34.02 4.30
111 112 2.910977 AGTAATTCCAAACGGAGGGAGT 59.089 45.455 0.00 0.00 34.02 3.85
112 113 4.098894 AGTAATTCCAAACGGAGGGAGTA 58.901 43.478 0.00 0.00 34.02 2.59
113 114 3.345508 AATTCCAAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 34.02 2.73
114 115 2.019807 TTCCAAACGGAGGGAGTACT 57.980 50.000 0.00 0.00 34.02 2.73
115 116 2.019807 TCCAAACGGAGGGAGTACTT 57.980 50.000 0.00 0.00 0.00 2.24
116 117 1.621814 TCCAAACGGAGGGAGTACTTG 59.378 52.381 0.00 0.00 0.00 3.16
117 118 1.346722 CCAAACGGAGGGAGTACTTGT 59.653 52.381 0.00 0.00 0.00 3.16
118 119 2.224450 CCAAACGGAGGGAGTACTTGTT 60.224 50.000 0.00 0.00 0.00 2.83
119 120 3.007182 CCAAACGGAGGGAGTACTTGTTA 59.993 47.826 0.00 0.00 0.00 2.41
120 121 4.323257 CCAAACGGAGGGAGTACTTGTTAT 60.323 45.833 0.00 0.00 0.00 1.89
121 122 4.467198 AACGGAGGGAGTACTTGTTATG 57.533 45.455 0.00 0.00 0.00 1.90
122 123 3.705051 ACGGAGGGAGTACTTGTTATGA 58.295 45.455 0.00 0.00 0.00 2.15
123 124 4.287552 ACGGAGGGAGTACTTGTTATGAT 58.712 43.478 0.00 0.00 0.00 2.45
124 125 5.452255 ACGGAGGGAGTACTTGTTATGATA 58.548 41.667 0.00 0.00 0.00 2.15
125 126 5.895534 ACGGAGGGAGTACTTGTTATGATAA 59.104 40.000 0.00 0.00 0.00 1.75
126 127 6.553852 ACGGAGGGAGTACTTGTTATGATAAT 59.446 38.462 0.00 0.00 0.00 1.28
127 128 6.868864 CGGAGGGAGTACTTGTTATGATAATG 59.131 42.308 0.00 0.00 0.00 1.90
128 129 7.255836 CGGAGGGAGTACTTGTTATGATAATGA 60.256 40.741 0.00 0.00 0.00 2.57
129 130 8.598041 GGAGGGAGTACTTGTTATGATAATGAT 58.402 37.037 0.00 0.00 0.00 2.45
130 131 9.429359 GAGGGAGTACTTGTTATGATAATGATG 57.571 37.037 0.00 0.00 0.00 3.07
131 132 7.880195 AGGGAGTACTTGTTATGATAATGATGC 59.120 37.037 0.00 0.00 0.00 3.91
132 133 7.148573 GGGAGTACTTGTTATGATAATGATGCG 60.149 40.741 0.00 0.00 0.00 4.73
133 134 7.598869 GGAGTACTTGTTATGATAATGATGCGA 59.401 37.037 0.00 0.00 0.00 5.10
134 135 9.144747 GAGTACTTGTTATGATAATGATGCGAT 57.855 33.333 0.00 0.00 0.00 4.58
135 136 8.929746 AGTACTTGTTATGATAATGATGCGATG 58.070 33.333 0.00 0.00 0.00 3.84
136 137 6.605849 ACTTGTTATGATAATGATGCGATGC 58.394 36.000 0.00 0.00 0.00 3.91
137 138 6.205270 ACTTGTTATGATAATGATGCGATGCA 59.795 34.615 0.00 0.00 44.86 3.96
165 166 6.912951 TTATGCTACTGTATTACTCCCTCC 57.087 41.667 0.00 0.00 0.00 4.30
166 167 3.220110 TGCTACTGTATTACTCCCTCCG 58.780 50.000 0.00 0.00 0.00 4.63
167 168 3.220940 GCTACTGTATTACTCCCTCCGT 58.779 50.000 0.00 0.00 0.00 4.69
168 169 3.252944 GCTACTGTATTACTCCCTCCGTC 59.747 52.174 0.00 0.00 0.00 4.79
169 170 3.377253 ACTGTATTACTCCCTCCGTCA 57.623 47.619 0.00 0.00 0.00 4.35
170 171 3.022406 ACTGTATTACTCCCTCCGTCAC 58.978 50.000 0.00 0.00 0.00 3.67
171 172 3.021695 CTGTATTACTCCCTCCGTCACA 58.978 50.000 0.00 0.00 0.00 3.58
172 173 3.433343 TGTATTACTCCCTCCGTCACAA 58.567 45.455 0.00 0.00 0.00 3.33
173 174 3.833650 TGTATTACTCCCTCCGTCACAAA 59.166 43.478 0.00 0.00 0.00 2.83
174 175 4.283978 TGTATTACTCCCTCCGTCACAAAA 59.716 41.667 0.00 0.00 0.00 2.44
175 176 4.569719 ATTACTCCCTCCGTCACAAAAT 57.430 40.909 0.00 0.00 0.00 1.82
176 177 2.951229 ACTCCCTCCGTCACAAAATT 57.049 45.000 0.00 0.00 0.00 1.82
177 178 2.779506 ACTCCCTCCGTCACAAAATTC 58.220 47.619 0.00 0.00 0.00 2.17
178 179 2.372172 ACTCCCTCCGTCACAAAATTCT 59.628 45.455 0.00 0.00 0.00 2.40
179 180 3.181443 ACTCCCTCCGTCACAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
180 181 3.408634 TCCCTCCGTCACAAAATTCTTC 58.591 45.455 0.00 0.00 0.00 2.87
181 182 3.072476 TCCCTCCGTCACAAAATTCTTCT 59.928 43.478 0.00 0.00 0.00 2.85
182 183 3.437049 CCCTCCGTCACAAAATTCTTCTC 59.563 47.826 0.00 0.00 0.00 2.87
183 184 4.319177 CCTCCGTCACAAAATTCTTCTCT 58.681 43.478 0.00 0.00 0.00 3.10
184 185 4.757149 CCTCCGTCACAAAATTCTTCTCTT 59.243 41.667 0.00 0.00 0.00 2.85
185 186 5.932303 CCTCCGTCACAAAATTCTTCTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
186 187 6.091441 CCTCCGTCACAAAATTCTTCTCTTAG 59.909 42.308 0.00 0.00 0.00 2.18
187 188 6.755206 TCCGTCACAAAATTCTTCTCTTAGA 58.245 36.000 0.00 0.00 0.00 2.10
188 189 7.386851 TCCGTCACAAAATTCTTCTCTTAGAT 58.613 34.615 0.00 0.00 0.00 1.98
189 190 7.878127 TCCGTCACAAAATTCTTCTCTTAGATT 59.122 33.333 0.00 0.00 0.00 2.40
190 191 9.151471 CCGTCACAAAATTCTTCTCTTAGATTA 57.849 33.333 0.00 0.00 0.00 1.75
202 203 9.932207 TCTTCTCTTAGATTAGTCTAGATACGG 57.068 37.037 0.00 0.00 38.17 4.02
203 204 9.932207 CTTCTCTTAGATTAGTCTAGATACGGA 57.068 37.037 0.00 0.00 38.17 4.69
205 206 9.878667 TCTCTTAGATTAGTCTAGATACGGATG 57.121 37.037 0.00 0.00 38.17 3.51
206 207 9.661563 CTCTTAGATTAGTCTAGATACGGATGT 57.338 37.037 0.00 0.00 38.17 3.06
224 225 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
225 226 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
226 227 9.622004 CGGATGTATCTAATACTAAAACGTGAT 57.378 33.333 0.00 0.00 36.70 3.06
238 239 7.000575 ACTAAAACGTGATTTGATACATCCG 57.999 36.000 0.00 0.00 0.00 4.18
239 240 5.873179 AAAACGTGATTTGATACATCCGT 57.127 34.783 0.00 0.00 32.42 4.69
240 241 6.971527 AAAACGTGATTTGATACATCCGTA 57.028 33.333 0.00 0.00 31.50 4.02
241 242 7.548196 AAAACGTGATTTGATACATCCGTAT 57.452 32.000 0.00 0.00 41.16 3.06
242 243 7.548196 AAACGTGATTTGATACATCCGTATT 57.452 32.000 0.00 0.00 38.48 1.89
243 244 7.548196 AACGTGATTTGATACATCCGTATTT 57.452 32.000 0.00 0.00 38.48 1.40
244 245 8.651391 AACGTGATTTGATACATCCGTATTTA 57.349 30.769 0.00 0.00 38.48 1.40
245 246 8.294341 ACGTGATTTGATACATCCGTATTTAG 57.706 34.615 0.00 0.00 38.48 1.85
246 247 8.139350 ACGTGATTTGATACATCCGTATTTAGA 58.861 33.333 0.00 0.00 38.48 2.10
247 248 9.140286 CGTGATTTGATACATCCGTATTTAGAT 57.860 33.333 0.00 0.00 38.48 1.98
273 274 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
274 275 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
275 276 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
276 277 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
277 278 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
278 279 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
279 280 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
280 281 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
313 314 8.806429 ATGGATGTTTAGTGTTATGATGTGAA 57.194 30.769 0.00 0.00 0.00 3.18
314 315 8.806429 TGGATGTTTAGTGTTATGATGTGAAT 57.194 30.769 0.00 0.00 0.00 2.57
481 482 6.183360 GCAACTACTATGCTATTGAACTGCAA 60.183 38.462 0.00 0.00 40.64 4.08
484 485 6.983307 ACTACTATGCTATTGAACTGCAAGAG 59.017 38.462 0.00 0.00 46.13 2.85
485 486 5.738909 ACTATGCTATTGAACTGCAAGAGT 58.261 37.500 0.00 0.00 45.36 3.24
487 488 7.331026 ACTATGCTATTGAACTGCAAGAGTTA 58.669 34.615 0.00 0.00 45.48 2.24
488 489 7.989741 ACTATGCTATTGAACTGCAAGAGTTAT 59.010 33.333 0.00 0.00 45.48 1.89
489 490 6.426980 TGCTATTGAACTGCAAGAGTTATG 57.573 37.500 0.00 0.00 45.48 1.90
490 491 6.172630 TGCTATTGAACTGCAAGAGTTATGA 58.827 36.000 0.00 0.00 45.48 2.15
491 492 6.825213 TGCTATTGAACTGCAAGAGTTATGAT 59.175 34.615 0.00 0.00 45.48 2.45
532 533 5.712004 CTGGTTTGATATGTGTGAATTGCA 58.288 37.500 0.00 0.00 0.00 4.08
575 576 2.864471 CGGGTATACCTGCGGGGAC 61.864 68.421 21.25 10.66 38.76 4.46
592 594 0.108520 GACGAATTACCTGTCGGGCA 60.109 55.000 0.00 0.00 41.56 5.36
593 595 0.108329 ACGAATTACCTGTCGGGCAG 60.108 55.000 1.75 1.75 44.63 4.85
608 610 1.595382 GCAGCGAGTATGGGCGAAT 60.595 57.895 0.00 0.00 0.00 3.34
660 662 3.291611 GCATGTGCTTTCAGGGGG 58.708 61.111 0.00 0.00 38.21 5.40
661 663 3.010413 GCATGTGCTTTCAGGGGGC 62.010 63.158 0.00 0.00 38.21 5.80
662 664 1.607178 CATGTGCTTTCAGGGGGCA 60.607 57.895 0.00 0.00 0.00 5.36
663 665 0.974010 CATGTGCTTTCAGGGGGCAT 60.974 55.000 0.00 0.00 38.27 4.40
664 666 0.974010 ATGTGCTTTCAGGGGGCATG 60.974 55.000 0.00 0.00 38.27 4.06
665 667 1.304381 GTGCTTTCAGGGGGCATGA 60.304 57.895 0.00 0.00 38.27 3.07
666 668 0.899717 GTGCTTTCAGGGGGCATGAA 60.900 55.000 0.00 0.00 38.27 2.57
718 731 0.475475 CCCATTGCCATCTAGAGCCA 59.525 55.000 0.00 0.00 0.00 4.75
750 763 2.670414 GCTCAGAAAGAACCAGATGACG 59.330 50.000 0.00 0.00 0.00 4.35
820 850 0.989602 AGCCTAAGGTTGGTACCCAC 59.010 55.000 10.07 8.74 46.28 4.61
876 906 5.358442 AGAAGACGTACTCTGATGCAACTAT 59.642 40.000 0.00 0.00 0.00 2.12
952 1070 3.576982 CCTATCGGCTACCAGATAACCAA 59.423 47.826 0.00 0.00 0.00 3.67
953 1071 2.973694 TCGGCTACCAGATAACCAAC 57.026 50.000 0.00 0.00 0.00 3.77
954 1072 1.483415 TCGGCTACCAGATAACCAACC 59.517 52.381 0.00 0.00 0.00 3.77
955 1073 1.208535 CGGCTACCAGATAACCAACCA 59.791 52.381 0.00 0.00 0.00 3.67
962 1080 2.159393 CCAGATAACCAACCATTGCACG 60.159 50.000 0.00 0.00 0.00 5.34
969 1087 0.664166 CAACCATTGCACGAACAGGC 60.664 55.000 0.00 0.00 0.00 4.85
1113 1243 0.545309 CCCTCCTCCAGTTCCTCACA 60.545 60.000 0.00 0.00 0.00 3.58
1205 1343 3.636231 CTGCAACAGGGACGGGGA 61.636 66.667 0.00 0.00 0.00 4.81
1245 1383 1.813477 GCATCTAGAGGGCTTGAAGGC 60.813 57.143 10.64 10.64 40.51 4.35
2295 2510 3.455177 AGATGATGCCACAAGATGAGACT 59.545 43.478 0.00 0.00 0.00 3.24
2371 2586 2.034179 GGACACTTGCCAGTTTGGTTAC 59.966 50.000 0.00 0.00 40.46 2.50
2491 2719 7.424803 TCTGGATGTATCAAACAACAGTTTTG 58.575 34.615 10.82 0.00 42.88 2.44
2979 3235 5.235186 CACTATGCTTATTCACCAGTGTAGC 59.765 44.000 0.00 4.36 32.23 3.58
3079 3335 1.689813 TGTTCTTTGGAGTAGGCGTGA 59.310 47.619 0.00 0.00 0.00 4.35
3231 3501 0.321653 ACACCCGAGTTGGATCTTGC 60.322 55.000 0.00 0.00 42.00 4.01
3248 3518 9.905713 TGGATCTTGCTTTATATTAGTTGAGTT 57.094 29.630 0.00 0.00 0.00 3.01
3269 3539 7.066404 TGAGTTTGCTACAGTTTATGTTGTTCA 59.934 33.333 0.00 0.00 39.96 3.18
3270 3540 7.940850 AGTTTGCTACAGTTTATGTTGTTCAT 58.059 30.769 0.00 0.00 39.96 2.57
3329 3600 0.543277 TGGCAGCCTTATGAGAGGTG 59.457 55.000 14.15 0.00 39.11 4.00
3365 3637 3.762407 TTTCAGATTGGAAGTCGTGGA 57.238 42.857 0.00 0.00 0.00 4.02
3366 3638 2.743636 TCAGATTGGAAGTCGTGGAC 57.256 50.000 0.00 0.00 0.00 4.02
3367 3639 2.248248 TCAGATTGGAAGTCGTGGACT 58.752 47.619 0.00 0.00 45.64 3.85
3368 3640 2.231478 TCAGATTGGAAGTCGTGGACTC 59.769 50.000 0.00 0.00 42.59 3.36
3370 3642 0.966920 ATTGGAAGTCGTGGACTCGT 59.033 50.000 0.00 0.00 42.59 4.18
3371 3643 0.031585 TTGGAAGTCGTGGACTCGTG 59.968 55.000 0.00 0.00 42.59 4.35
3416 3688 6.127730 GGAAGTGTCCAGGGTAATGTAATTTG 60.128 42.308 0.00 0.00 44.26 2.32
3448 3721 4.411212 AGGGTTGGACCTAGCGTAAATATT 59.589 41.667 0.00 0.00 39.65 1.28
3461 3837 9.864034 CTAGCGTAAATATTAAACTGGTCATTG 57.136 33.333 0.00 0.00 0.00 2.82
3466 3842 9.581099 GTAAATATTAAACTGGTCATTGGTTGG 57.419 33.333 0.00 0.00 0.00 3.77
3569 3953 8.128582 TCTTTTTGCAACACTACTTCATGTAAG 58.871 33.333 0.00 0.00 41.33 2.34
3635 4063 2.715046 CCAGCCAAGTTCATGCTAGAA 58.285 47.619 0.00 0.00 33.16 2.10
3711 4140 5.273674 TCATTCAGAGCTCAATCTACAGG 57.726 43.478 17.77 0.00 0.00 4.00
3825 4561 2.506472 GATTCCACCGAGGGCCTC 59.494 66.667 24.06 24.06 38.24 4.70
3909 4683 1.803555 GCTCTCTCTTTTGTGTGCTCC 59.196 52.381 0.00 0.00 0.00 4.70
3919 4693 4.002506 TGTGCTCCGGATGTGCGT 62.003 61.111 3.57 0.00 36.24 5.24
4041 4815 3.515286 CATGGGCCGAAGCTGCTG 61.515 66.667 1.35 0.00 39.73 4.41
4053 4827 2.046507 CTGCTGAAAGGGAGCGCT 60.047 61.111 11.27 11.27 39.47 5.92
4059 4833 1.734465 CTGAAAGGGAGCGCTTACAAG 59.266 52.381 13.26 0.00 0.00 3.16
4073 4847 3.642705 CTTACAAGTTGGGCTTTGCTTC 58.357 45.455 7.96 0.00 34.69 3.86
4077 4851 1.999648 AGTTGGGCTTTGCTTCATCA 58.000 45.000 0.00 0.00 0.00 3.07
4082 4856 3.666274 TGGGCTTTGCTTCATCAAAATG 58.334 40.909 0.00 0.00 35.75 2.32
4084 4858 3.306919 GGGCTTTGCTTCATCAAAATGGA 60.307 43.478 0.00 0.00 35.75 3.41
4119 4893 5.885912 GCCCATACAGATTGAGGTAGAAAAA 59.114 40.000 0.00 0.00 0.00 1.94
4120 4894 6.547510 GCCCATACAGATTGAGGTAGAAAAAT 59.452 38.462 0.00 0.00 0.00 1.82
4121 4895 7.469181 GCCCATACAGATTGAGGTAGAAAAATG 60.469 40.741 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.175989 GAACGGAGGGAGTAGCAAGG 59.824 60.000 0.00 0.00 0.00 3.61
1 2 0.179134 CGAACGGAGGGAGTAGCAAG 60.179 60.000 0.00 0.00 0.00 4.01
2 3 1.601419 CCGAACGGAGGGAGTAGCAA 61.601 60.000 7.53 0.00 37.50 3.91
3 4 2.050350 CCGAACGGAGGGAGTAGCA 61.050 63.158 7.53 0.00 37.50 3.49
4 5 1.318158 TTCCGAACGGAGGGAGTAGC 61.318 60.000 15.34 0.00 46.06 3.58
5 6 1.400737 ATTCCGAACGGAGGGAGTAG 58.599 55.000 15.34 0.00 46.06 2.57
6 7 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
7 8 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
8 9 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
9 10 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
10 11 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
11 12 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
12 13 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
13 14 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
14 15 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
15 16 4.718858 TTGTGACAAGTAATTCCGAACG 57.281 40.909 0.00 0.00 0.00 3.95
16 17 7.096230 CCATTTTTGTGACAAGTAATTCCGAAC 60.096 37.037 0.00 0.00 0.00 3.95
17 18 6.920758 CCATTTTTGTGACAAGTAATTCCGAA 59.079 34.615 0.00 0.00 0.00 4.30
18 19 6.263392 TCCATTTTTGTGACAAGTAATTCCGA 59.737 34.615 0.00 0.00 0.00 4.55
19 20 6.442952 TCCATTTTTGTGACAAGTAATTCCG 58.557 36.000 0.00 0.00 0.00 4.30
20 21 7.872483 ACATCCATTTTTGTGACAAGTAATTCC 59.128 33.333 0.00 0.00 0.00 3.01
21 22 8.816640 ACATCCATTTTTGTGACAAGTAATTC 57.183 30.769 0.00 0.00 0.00 2.17
24 25 9.295825 AGATACATCCATTTTTGTGACAAGTAA 57.704 29.630 0.00 0.00 0.00 2.24
25 26 8.862325 AGATACATCCATTTTTGTGACAAGTA 57.138 30.769 0.00 0.00 0.00 2.24
26 27 7.765695 AGATACATCCATTTTTGTGACAAGT 57.234 32.000 0.00 0.00 0.00 3.16
27 28 8.729756 TGTAGATACATCCATTTTTGTGACAAG 58.270 33.333 0.00 0.00 0.00 3.16
28 29 8.628630 TGTAGATACATCCATTTTTGTGACAA 57.371 30.769 0.00 0.00 0.00 3.18
29 30 8.511321 GTTGTAGATACATCCATTTTTGTGACA 58.489 33.333 0.00 0.00 35.89 3.58
30 31 8.730680 AGTTGTAGATACATCCATTTTTGTGAC 58.269 33.333 0.00 0.00 35.89 3.67
31 32 8.862325 AGTTGTAGATACATCCATTTTTGTGA 57.138 30.769 0.00 0.00 35.89 3.58
62 63 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
63 64 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
64 65 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
65 66 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
66 67 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
67 68 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
68 69 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
69 70 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
70 71 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
71 72 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
72 73 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
73 74 7.148255 TGGAATTACTCGTCCAAGAAATGAATG 60.148 37.037 0.00 0.00 41.02 2.67
74 75 6.884295 TGGAATTACTCGTCCAAGAAATGAAT 59.116 34.615 0.00 0.00 41.02 2.57
75 76 6.234920 TGGAATTACTCGTCCAAGAAATGAA 58.765 36.000 0.00 0.00 41.02 2.57
76 77 5.800296 TGGAATTACTCGTCCAAGAAATGA 58.200 37.500 0.00 0.00 41.02 2.57
77 78 6.494893 TTGGAATTACTCGTCCAAGAAATG 57.505 37.500 1.01 0.00 46.58 2.32
84 85 2.299582 TCCGTTTGGAATTACTCGTCCA 59.700 45.455 0.00 0.00 42.85 4.02
85 86 2.928116 CTCCGTTTGGAATTACTCGTCC 59.072 50.000 0.00 0.00 45.87 4.79
86 87 2.928116 CCTCCGTTTGGAATTACTCGTC 59.072 50.000 0.00 0.00 45.87 4.20
87 88 2.354403 CCCTCCGTTTGGAATTACTCGT 60.354 50.000 0.00 0.00 45.87 4.18
88 89 2.093869 TCCCTCCGTTTGGAATTACTCG 60.094 50.000 0.00 0.00 45.87 4.18
89 90 3.055312 ACTCCCTCCGTTTGGAATTACTC 60.055 47.826 0.00 0.00 45.87 2.59
90 91 2.910977 ACTCCCTCCGTTTGGAATTACT 59.089 45.455 0.00 0.00 45.87 2.24
91 92 3.345508 ACTCCCTCCGTTTGGAATTAC 57.654 47.619 0.00 0.00 45.87 1.89
92 93 4.098894 AGTACTCCCTCCGTTTGGAATTA 58.901 43.478 0.00 0.00 45.87 1.40
93 94 2.910977 AGTACTCCCTCCGTTTGGAATT 59.089 45.455 0.00 0.00 45.87 2.17
94 95 2.547990 AGTACTCCCTCCGTTTGGAAT 58.452 47.619 0.00 0.00 45.87 3.01
95 96 2.019807 AGTACTCCCTCCGTTTGGAA 57.980 50.000 0.00 0.00 45.87 3.53
96 97 1.621814 CAAGTACTCCCTCCGTTTGGA 59.378 52.381 0.00 0.00 43.88 3.53
97 98 1.346722 ACAAGTACTCCCTCCGTTTGG 59.653 52.381 0.00 0.00 0.00 3.28
98 99 2.833631 ACAAGTACTCCCTCCGTTTG 57.166 50.000 0.00 0.00 0.00 2.93
99 100 4.529377 TCATAACAAGTACTCCCTCCGTTT 59.471 41.667 0.00 0.00 0.00 3.60
100 101 4.091549 TCATAACAAGTACTCCCTCCGTT 58.908 43.478 0.00 0.00 0.00 4.44
101 102 3.705051 TCATAACAAGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
102 103 4.939052 ATCATAACAAGTACTCCCTCCG 57.061 45.455 0.00 0.00 0.00 4.63
103 104 7.963532 TCATTATCATAACAAGTACTCCCTCC 58.036 38.462 0.00 0.00 0.00 4.30
104 105 9.429359 CATCATTATCATAACAAGTACTCCCTC 57.571 37.037 0.00 0.00 0.00 4.30
105 106 7.880195 GCATCATTATCATAACAAGTACTCCCT 59.120 37.037 0.00 0.00 0.00 4.20
106 107 7.148573 CGCATCATTATCATAACAAGTACTCCC 60.149 40.741 0.00 0.00 0.00 4.30
107 108 7.598869 TCGCATCATTATCATAACAAGTACTCC 59.401 37.037 0.00 0.00 0.00 3.85
108 109 8.520835 TCGCATCATTATCATAACAAGTACTC 57.479 34.615 0.00 0.00 0.00 2.59
109 110 8.929746 CATCGCATCATTATCATAACAAGTACT 58.070 33.333 0.00 0.00 0.00 2.73
110 111 7.689812 GCATCGCATCATTATCATAACAAGTAC 59.310 37.037 0.00 0.00 0.00 2.73
111 112 7.387397 TGCATCGCATCATTATCATAACAAGTA 59.613 33.333 0.00 0.00 31.71 2.24
112 113 6.205270 TGCATCGCATCATTATCATAACAAGT 59.795 34.615 0.00 0.00 31.71 3.16
113 114 6.604930 TGCATCGCATCATTATCATAACAAG 58.395 36.000 0.00 0.00 31.71 3.16
114 115 6.557291 TGCATCGCATCATTATCATAACAA 57.443 33.333 0.00 0.00 31.71 2.83
139 140 8.376270 GGAGGGAGTAATACAGTAGCATAATTT 58.624 37.037 0.00 0.00 0.00 1.82
140 141 7.309867 CGGAGGGAGTAATACAGTAGCATAATT 60.310 40.741 0.00 0.00 0.00 1.40
141 142 6.153000 CGGAGGGAGTAATACAGTAGCATAAT 59.847 42.308 0.00 0.00 0.00 1.28
142 143 5.475909 CGGAGGGAGTAATACAGTAGCATAA 59.524 44.000 0.00 0.00 0.00 1.90
143 144 5.008331 CGGAGGGAGTAATACAGTAGCATA 58.992 45.833 0.00 0.00 0.00 3.14
144 145 3.827302 CGGAGGGAGTAATACAGTAGCAT 59.173 47.826 0.00 0.00 0.00 3.79
145 146 3.220110 CGGAGGGAGTAATACAGTAGCA 58.780 50.000 0.00 0.00 0.00 3.49
146 147 3.220940 ACGGAGGGAGTAATACAGTAGC 58.779 50.000 0.00 0.00 0.00 3.58
147 148 4.275443 GTGACGGAGGGAGTAATACAGTAG 59.725 50.000 0.00 0.00 0.00 2.57
148 149 4.202441 GTGACGGAGGGAGTAATACAGTA 58.798 47.826 0.00 0.00 0.00 2.74
149 150 3.022406 GTGACGGAGGGAGTAATACAGT 58.978 50.000 0.00 0.00 0.00 3.55
150 151 3.021695 TGTGACGGAGGGAGTAATACAG 58.978 50.000 0.00 0.00 0.00 2.74
151 152 3.090210 TGTGACGGAGGGAGTAATACA 57.910 47.619 0.00 0.00 0.00 2.29
152 153 4.460948 TTTGTGACGGAGGGAGTAATAC 57.539 45.455 0.00 0.00 0.00 1.89
153 154 5.687166 ATTTTGTGACGGAGGGAGTAATA 57.313 39.130 0.00 0.00 0.00 0.98
154 155 4.569719 ATTTTGTGACGGAGGGAGTAAT 57.430 40.909 0.00 0.00 0.00 1.89
155 156 4.041198 AGAATTTTGTGACGGAGGGAGTAA 59.959 41.667 0.00 0.00 0.00 2.24
156 157 3.581332 AGAATTTTGTGACGGAGGGAGTA 59.419 43.478 0.00 0.00 0.00 2.59
157 158 2.372172 AGAATTTTGTGACGGAGGGAGT 59.628 45.455 0.00 0.00 0.00 3.85
158 159 3.059352 AGAATTTTGTGACGGAGGGAG 57.941 47.619 0.00 0.00 0.00 4.30
159 160 3.072476 AGAAGAATTTTGTGACGGAGGGA 59.928 43.478 0.00 0.00 0.00 4.20
160 161 3.412386 AGAAGAATTTTGTGACGGAGGG 58.588 45.455 0.00 0.00 0.00 4.30
161 162 4.319177 AGAGAAGAATTTTGTGACGGAGG 58.681 43.478 0.00 0.00 0.00 4.30
162 163 5.931441 AAGAGAAGAATTTTGTGACGGAG 57.069 39.130 0.00 0.00 0.00 4.63
163 164 6.755206 TCTAAGAGAAGAATTTTGTGACGGA 58.245 36.000 0.00 0.00 0.00 4.69
164 165 7.602517 ATCTAAGAGAAGAATTTTGTGACGG 57.397 36.000 0.00 0.00 0.00 4.79
176 177 9.932207 CCGTATCTAGACTAATCTAAGAGAAGA 57.068 37.037 0.00 0.00 36.98 2.87
177 178 9.932207 TCCGTATCTAGACTAATCTAAGAGAAG 57.068 37.037 0.00 0.00 36.98 2.85
179 180 9.878667 CATCCGTATCTAGACTAATCTAAGAGA 57.121 37.037 0.00 0.00 36.98 3.10
180 181 9.661563 ACATCCGTATCTAGACTAATCTAAGAG 57.338 37.037 0.00 0.00 36.98 2.85
198 199 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
199 200 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
200 201 9.622004 ATCACGTTTTAGTATTAGATACATCCG 57.378 33.333 0.00 0.00 38.21 4.18
212 213 8.761497 CGGATGTATCAAATCACGTTTTAGTAT 58.239 33.333 0.00 0.00 0.00 2.12
213 214 7.760794 ACGGATGTATCAAATCACGTTTTAGTA 59.239 33.333 0.00 0.00 31.40 1.82
214 215 6.592607 ACGGATGTATCAAATCACGTTTTAGT 59.407 34.615 0.00 0.00 31.40 2.24
215 216 7.000575 ACGGATGTATCAAATCACGTTTTAG 57.999 36.000 0.00 0.00 31.40 1.85
216 217 6.971527 ACGGATGTATCAAATCACGTTTTA 57.028 33.333 0.00 0.00 31.40 1.52
217 218 5.873179 ACGGATGTATCAAATCACGTTTT 57.127 34.783 0.00 0.00 31.40 2.43
218 219 7.548196 AATACGGATGTATCAAATCACGTTT 57.452 32.000 0.00 0.00 40.42 3.60
219 220 7.548196 AAATACGGATGTATCAAATCACGTT 57.452 32.000 0.00 0.00 40.42 3.99
220 221 8.139350 TCTAAATACGGATGTATCAAATCACGT 58.861 33.333 0.00 0.00 40.42 4.49
221 222 8.515473 TCTAAATACGGATGTATCAAATCACG 57.485 34.615 0.00 0.00 40.42 4.35
247 248 8.726988 CGTCCCAAAATTCTTGTCTTAGATTTA 58.273 33.333 0.00 0.00 0.00 1.40
248 249 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
249 250 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
250 251 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
251 252 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
252 253 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
253 254 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
254 255 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
255 256 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
256 257 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
257 258 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
258 259 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
259 260 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
260 261 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
261 262 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
262 263 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
263 264 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
264 265 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
265 266 1.732117 TTTACTCCCTCCGTCCCAAA 58.268 50.000 0.00 0.00 0.00 3.28
266 267 1.961133 ATTTACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
267 268 1.557832 CAATTTACTCCCTCCGTCCCA 59.442 52.381 0.00 0.00 0.00 4.37
268 269 1.835531 TCAATTTACTCCCTCCGTCCC 59.164 52.381 0.00 0.00 0.00 4.46
269 270 3.467803 CATCAATTTACTCCCTCCGTCC 58.532 50.000 0.00 0.00 0.00 4.79
270 271 3.134081 TCCATCAATTTACTCCCTCCGTC 59.866 47.826 0.00 0.00 0.00 4.79
271 272 3.112263 TCCATCAATTTACTCCCTCCGT 58.888 45.455 0.00 0.00 0.00 4.69
272 273 3.838244 TCCATCAATTTACTCCCTCCG 57.162 47.619 0.00 0.00 0.00 4.63
273 274 5.053978 ACATCCATCAATTTACTCCCTCC 57.946 43.478 0.00 0.00 0.00 4.30
274 275 7.775561 ACTAAACATCCATCAATTTACTCCCTC 59.224 37.037 0.00 0.00 0.00 4.30
275 276 7.557719 CACTAAACATCCATCAATTTACTCCCT 59.442 37.037 0.00 0.00 0.00 4.20
276 277 7.339466 ACACTAAACATCCATCAATTTACTCCC 59.661 37.037 0.00 0.00 0.00 4.30
277 278 8.281212 ACACTAAACATCCATCAATTTACTCC 57.719 34.615 0.00 0.00 0.00 3.85
359 360 3.247648 GCATACCATCACATCGTAACACC 59.752 47.826 0.00 0.00 0.00 4.16
454 455 6.183360 GCAGTTCAATAGCATAGTAGTTGCAA 60.183 38.462 0.00 0.00 42.62 4.08
462 463 5.738909 ACTCTTGCAGTTCAATAGCATAGT 58.261 37.500 0.00 0.00 38.19 2.12
463 464 6.674694 AACTCTTGCAGTTCAATAGCATAG 57.325 37.500 0.00 0.00 42.07 2.23
464 465 7.986889 TCATAACTCTTGCAGTTCAATAGCATA 59.013 33.333 0.00 0.00 42.07 3.14
487 488 8.761689 ACCAGCAACTTATTATCCAAAAATCAT 58.238 29.630 0.00 0.00 0.00 2.45
488 489 8.133024 ACCAGCAACTTATTATCCAAAAATCA 57.867 30.769 0.00 0.00 0.00 2.57
489 490 9.435688 AAACCAGCAACTTATTATCCAAAAATC 57.564 29.630 0.00 0.00 0.00 2.17
490 491 9.218440 CAAACCAGCAACTTATTATCCAAAAAT 57.782 29.630 0.00 0.00 0.00 1.82
491 492 8.424918 TCAAACCAGCAACTTATTATCCAAAAA 58.575 29.630 0.00 0.00 0.00 1.94
532 533 1.067295 TCTGATGCCAACCTCCAAGT 58.933 50.000 0.00 0.00 0.00 3.16
534 535 1.272092 CCTTCTGATGCCAACCTCCAA 60.272 52.381 0.00 0.00 0.00 3.53
575 576 2.677971 CTGCCCGACAGGTAATTCG 58.322 57.895 0.00 0.00 43.19 3.34
592 594 1.139058 AGAAATTCGCCCATACTCGCT 59.861 47.619 0.00 0.00 0.00 4.93
593 595 1.583054 AGAAATTCGCCCATACTCGC 58.417 50.000 0.00 0.00 0.00 5.03
604 606 1.743995 ACCGCGGGGAAGAAATTCG 60.744 57.895 31.76 0.00 36.97 3.34
718 731 4.174704 TCTTTCTGAGCATGCCCATTAT 57.825 40.909 15.66 0.00 0.00 1.28
750 763 8.665685 CACCTTTTAGTCCTACATTTACACATC 58.334 37.037 0.00 0.00 0.00 3.06
952 1070 0.036164 TAGCCTGTTCGTGCAATGGT 59.964 50.000 0.00 0.00 0.00 3.55
953 1071 1.131126 CTTAGCCTGTTCGTGCAATGG 59.869 52.381 0.00 0.00 0.00 3.16
954 1072 2.076100 TCTTAGCCTGTTCGTGCAATG 58.924 47.619 0.00 0.00 0.00 2.82
955 1073 2.472695 TCTTAGCCTGTTCGTGCAAT 57.527 45.000 0.00 0.00 0.00 3.56
962 1080 3.118445 AGCCTTCTCATCTTAGCCTGTTC 60.118 47.826 0.00 0.00 0.00 3.18
969 1087 7.225734 GGTAAGCTTAAAGCCTTCTCATCTTAG 59.774 40.741 7.99 0.00 43.77 2.18
1113 1243 0.683973 CGGCATCTTGAGATAGCCCT 59.316 55.000 19.51 0.00 41.45 5.19
1205 1343 1.601197 AGCGAGACCTCAGTGACGT 60.601 57.895 0.00 0.00 0.00 4.34
1680 1843 1.270907 CAGGGAGAGTGCCACTTAGT 58.729 55.000 0.00 0.00 0.00 2.24
1689 1852 3.556004 GGAAGAGTTCAACAGGGAGAGTG 60.556 52.174 0.00 0.00 0.00 3.51
1738 1942 3.352648 CTTGTAATCCGTTGTTGGGGAT 58.647 45.455 0.00 0.00 44.83 3.85
2295 2510 6.294361 TGAAGATTCCGAAAACCATCTAGA 57.706 37.500 0.00 0.00 0.00 2.43
2371 2586 3.633986 ACCTTCAAGTTTCTGAGCTTTGG 59.366 43.478 0.00 0.00 0.00 3.28
2979 3235 5.981088 ATATAGGATGTGCTCTGACTGAG 57.019 43.478 5.04 5.04 45.33 3.35
3152 3411 7.962964 TTATTGCTTGATTTACCTCTATCCG 57.037 36.000 0.00 0.00 0.00 4.18
3212 3481 0.321653 GCAAGATCCAACTCGGGTGT 60.322 55.000 0.00 0.00 34.36 4.16
3248 3518 7.865385 GGAAATGAACAACATAAACTGTAGCAA 59.135 33.333 0.00 0.00 36.98 3.91
3292 3562 5.817816 GCTGCCAGCTAGAAAAAGAATACTA 59.182 40.000 10.04 0.00 38.45 1.82
3293 3563 4.637977 GCTGCCAGCTAGAAAAAGAATACT 59.362 41.667 10.04 0.00 38.45 2.12
3295 3565 3.947834 GGCTGCCAGCTAGAAAAAGAATA 59.052 43.478 17.55 0.00 41.99 1.75
3311 3581 0.179034 CCACCTCTCATAAGGCTGCC 60.179 60.000 11.65 11.65 40.34 4.85
3329 3600 8.616076 CCAATCTGAAATCACTGAATTACTACC 58.384 37.037 0.00 0.00 0.00 3.18
3365 3637 1.873591 GAATTGCTCACAACCACGAGT 59.126 47.619 0.00 0.00 38.99 4.18
3366 3638 1.872952 TGAATTGCTCACAACCACGAG 59.127 47.619 0.00 0.00 38.99 4.18
3367 3639 1.960417 TGAATTGCTCACAACCACGA 58.040 45.000 0.00 0.00 38.99 4.35
3368 3640 2.033299 ACTTGAATTGCTCACAACCACG 59.967 45.455 0.00 0.00 38.99 4.94
3370 3642 2.361757 CCACTTGAATTGCTCACAACCA 59.638 45.455 0.00 0.00 38.99 3.67
3371 3643 2.288395 CCCACTTGAATTGCTCACAACC 60.288 50.000 0.00 0.00 38.99 3.77
3416 3688 4.398358 GCTAGGTCCAACCCTGATTAAAAC 59.602 45.833 0.00 0.00 39.75 2.43
3448 3721 2.243810 GGCCAACCAATGACCAGTTTA 58.756 47.619 0.00 0.00 30.59 2.01
3461 3837 1.269723 GTTTTAGCTGTCTGGCCAACC 59.730 52.381 7.01 0.00 0.00 3.77
3466 3842 6.113411 TCCTATAAAGTTTTAGCTGTCTGGC 58.887 40.000 0.00 0.00 0.00 4.85
3647 4075 7.093377 ACCCCGTCATTAACAGTTACTGTATTA 60.093 37.037 18.93 5.64 44.62 0.98
3666 4094 2.050350 TCGGTGATCTGACCCCGTC 61.050 63.158 10.16 0.00 41.17 4.79
3683 4111 6.680874 AGATTGAGCTCTGAATGAAATGTC 57.319 37.500 16.19 0.00 0.00 3.06
3711 4140 5.491982 AGGTATTTTGTCAGTGATCTGGAC 58.508 41.667 0.00 0.00 41.59 4.02
3746 4482 0.745845 AGCGTGAATGATCTGGTGGC 60.746 55.000 0.00 0.00 0.00 5.01
3784 4520 2.923634 ATCAAGCTGGGGATGCTGGC 62.924 60.000 0.00 0.00 41.03 4.85
3795 4531 3.728864 CGGTGGAATCGAAAATCAAGCTG 60.729 47.826 0.00 0.00 0.00 4.24
3825 4561 1.218230 GCGAGCCCTAGCGAATCTTG 61.218 60.000 0.00 0.00 46.67 3.02
3884 4658 1.374758 ACAAAAGAGAGAGCGCCCG 60.375 57.895 2.29 0.00 0.00 6.13
3909 4683 0.595053 AGCTATCGAACGCACATCCG 60.595 55.000 11.22 0.00 0.00 4.18
3919 4693 0.171679 TCGCCGTTCAAGCTATCGAA 59.828 50.000 0.00 0.00 0.00 3.71
4039 4813 1.734465 CTTGTAAGCGCTCCCTTTCAG 59.266 52.381 12.06 0.00 0.00 3.02
4040 4814 1.071699 ACTTGTAAGCGCTCCCTTTCA 59.928 47.619 12.06 0.00 0.00 2.69
4041 4815 1.809684 ACTTGTAAGCGCTCCCTTTC 58.190 50.000 12.06 0.00 0.00 2.62
4053 4827 3.027412 TGAAGCAAAGCCCAACTTGTAA 58.973 40.909 0.00 0.00 39.09 2.41
4059 4833 2.818130 TTGATGAAGCAAAGCCCAAC 57.182 45.000 0.00 0.00 0.00 3.77
4073 4847 5.166398 GCCAAGAAGACTTCCATTTTGATG 58.834 41.667 11.67 0.54 33.70 3.07
4077 4851 2.899900 GGGCCAAGAAGACTTCCATTTT 59.100 45.455 11.67 0.00 33.70 1.82
4082 4856 2.026262 TGTATGGGCCAAGAAGACTTCC 60.026 50.000 11.89 0.00 33.70 3.46
4084 4858 2.912956 TCTGTATGGGCCAAGAAGACTT 59.087 45.455 11.89 0.00 36.73 3.01


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

AutoCloner maintained by Alex Coulton.