Multiple sequence alignment - TraesCS5A01G373700

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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 TraesCS5A01G373700 chr5A 100.000 1741 0 0 872 2612 571685586 571683846 0.000000e+00 3216.0
1 TraesCS5A01G373700 chr5A 100.000 635 0 0 1 635 571686457 571685823 0.000000e+00 1173.0
2 TraesCS5A01G373700 chr5D 93.670 1169 49 14 872 2037 452681904 452680758 0.000000e+00 1725.0
3 TraesCS5A01G373700 chr5D 84.950 505 25 11 2082 2548 452680769 452680278 5.090000e-127 464.0
4 TraesCS5A01G373700 chr5D 80.645 496 49 24 168 635 452682471 452681995 8.950000e-90 340.0
5 TraesCS5A01G373700 chr5D 91.667 48 3 1 2495 2542 238778091 238778045 6.030000e-07 65.8
6 TraesCS5A01G373700 chr5B 92.041 1181 52 21 872 2035 553185851 553184696 0.000000e+00 1622.0
7 TraesCS5A01G373700 chr5B 92.632 190 13 1 2082 2271 553184705 553184517 3.310000e-69 272.0
8 TraesCS5A01G373700 chr5B 89.691 97 9 1 218 314 665998612 665998517 3.530000e-24 122.0
9 TraesCS5A01G373700 chr5B 95.890 73 3 0 2364 2436 553182029 553181957 4.570000e-23 119.0
10 TraesCS5A01G373700 chr5B 86.792 53 5 2 2483 2534 17726209 17726158 1.010000e-04 58.4
11 TraesCS5A01G373700 chr1B 88.294 299 25 6 1460 1752 98440074 98440368 1.490000e-92 350.0
12 TraesCS5A01G373700 chr1B 87.748 302 24 7 1460 1752 98392719 98393016 8.950000e-90 340.0
13 TraesCS5A01G373700 chr1B 90.431 209 18 1 2137 2343 440500426 440500634 9.210000e-70 274.0
14 TraesCS5A01G373700 chr2A 85.514 214 27 3 228 440 17123767 17123557 1.220000e-53 220.0
15 TraesCS5A01G373700 chr7D 79.638 221 29 8 227 443 430111053 430111261 7.530000e-31 145.0
16 TraesCS5A01G373700 chr7A 82.143 168 25 5 259 424 84853763 84853599 3.510000e-29 139.0
17 TraesCS5A01G373700 chr3B 77.528 267 30 11 204 444 666473171 666473433 1.630000e-27 134.0
18 TraesCS5A01G373700 chr3B 93.182 44 3 0 2486 2529 716712534 716712577 6.030000e-07 65.8
19 TraesCS5A01G373700 chr7B 92.771 83 6 0 227 309 110693398 110693316 1.270000e-23 121.0
20 TraesCS5A01G373700 chr3A 90.217 92 9 0 218 309 620990128 620990037 1.270000e-23 121.0
21 TraesCS5A01G373700 chr3D 88.119 101 10 2 210 309 76875767 76875866 4.570000e-23 119.0
22 TraesCS5A01G373700 chr6B 88.298 94 10 1 216 309 286990705 286990797 7.640000e-21 111.0
23 TraesCS5A01G373700 chr6B 87.879 66 5 2 2483 2547 616309857 616309920 1.000000e-09 75.0
24 TraesCS5A01G373700 chr2D 91.667 48 2 2 2487 2532 198462321 198462274 6.030000e-07 65.8


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 TraesCS5A01G373700 chr5A 571683846 571686457 2611 True 2194.5 3216 100.000000 1 2612 2 chr5A.!!$R1 2611
1 TraesCS5A01G373700 chr5D 452680278 452682471 2193 True 843.0 1725 86.421667 168 2548 3 chr5D.!!$R2 2380
2 TraesCS5A01G373700 chr5B 553181957 553185851 3894 True 671.0 1622 93.521000 872 2436 3 chr5B.!!$R3 1564

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
110 111 0.034756 CAGTCGACATGAACCACCCA 59.965 55.0 19.5 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2091 0.402504 ACCAGCCAAATAACGGGTCA 59.597 50.0 0.0 0.0 27.07 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.789012 AATTGTAATTGTGGCTGGAGTG 57.211 40.909 0.00 0.00 0.00 3.51
24 25 2.198827 TGTAATTGTGGCTGGAGTGG 57.801 50.000 0.00 0.00 0.00 4.00
25 26 0.811281 GTAATTGTGGCTGGAGTGGC 59.189 55.000 0.00 0.00 0.00 5.01
26 27 0.676466 TAATTGTGGCTGGAGTGGCG 60.676 55.000 0.00 0.00 35.06 5.69
27 28 2.410322 AATTGTGGCTGGAGTGGCGA 62.410 55.000 0.00 0.00 35.06 5.54
28 29 3.825160 TTGTGGCTGGAGTGGCGAC 62.825 63.158 0.00 0.00 38.55 5.19
29 30 4.314440 GTGGCTGGAGTGGCGACA 62.314 66.667 0.45 0.00 38.10 4.35
30 31 3.321648 TGGCTGGAGTGGCGACAT 61.322 61.111 0.00 0.00 46.14 3.06
31 32 2.512515 GGCTGGAGTGGCGACATC 60.513 66.667 0.00 0.00 46.14 3.06
32 33 2.265739 GCTGGAGTGGCGACATCA 59.734 61.111 0.00 0.00 46.14 3.07
33 34 1.375908 GCTGGAGTGGCGACATCAA 60.376 57.895 0.00 0.00 46.14 2.57
34 35 1.639298 GCTGGAGTGGCGACATCAAC 61.639 60.000 0.00 0.00 46.14 3.18
35 36 0.320683 CTGGAGTGGCGACATCAACA 60.321 55.000 0.00 0.00 46.14 3.33
36 37 0.602638 TGGAGTGGCGACATCAACAC 60.603 55.000 0.00 0.00 46.14 3.32
37 38 0.320771 GGAGTGGCGACATCAACACT 60.321 55.000 0.00 5.44 45.99 3.55
38 39 1.512926 GAGTGGCGACATCAACACTT 58.487 50.000 0.00 0.00 43.61 3.16
39 40 2.611971 GGAGTGGCGACATCAACACTTA 60.612 50.000 0.00 0.00 43.61 2.24
40 41 2.668457 GAGTGGCGACATCAACACTTAG 59.332 50.000 0.00 0.00 43.61 2.18
41 42 2.037251 AGTGGCGACATCAACACTTAGT 59.963 45.455 0.00 0.00 46.14 2.24
42 43 2.806244 GTGGCGACATCAACACTTAGTT 59.194 45.455 0.00 0.00 46.14 2.24
44 45 3.742954 TGGCGACATCAACACTTAGTTGT 60.743 43.478 7.72 0.00 46.67 3.32
45 46 4.501743 TGGCGACATCAACACTTAGTTGTA 60.502 41.667 7.72 0.00 46.67 2.41
46 47 6.303711 TGGCGACATCAACACTTAGTTGTAG 61.304 44.000 7.72 4.87 46.67 2.74
55 56 6.796705 AACACTTAGTTGTAGCATTACCAC 57.203 37.500 0.00 0.00 39.49 4.16
56 57 5.860611 ACACTTAGTTGTAGCATTACCACA 58.139 37.500 0.00 0.00 30.02 4.17
57 58 6.292923 ACACTTAGTTGTAGCATTACCACAA 58.707 36.000 0.00 0.00 30.02 3.33
58 59 6.768861 ACACTTAGTTGTAGCATTACCACAAA 59.231 34.615 0.00 0.00 34.20 2.83
59 60 7.075741 CACTTAGTTGTAGCATTACCACAAAC 58.924 38.462 0.00 0.00 34.20 2.93
60 61 6.768861 ACTTAGTTGTAGCATTACCACAAACA 59.231 34.615 0.00 0.00 34.20 2.83
61 62 7.283580 ACTTAGTTGTAGCATTACCACAAACAA 59.716 33.333 0.00 0.00 34.20 2.83
62 63 6.458232 AGTTGTAGCATTACCACAAACAAA 57.542 33.333 0.00 0.00 34.20 2.83
63 64 6.868622 AGTTGTAGCATTACCACAAACAAAA 58.131 32.000 0.00 0.00 34.20 2.44
64 65 7.324178 AGTTGTAGCATTACCACAAACAAAAA 58.676 30.769 0.00 0.00 34.20 1.94
87 88 5.853572 AAAAACACCCAGGGAAGTATAGA 57.146 39.130 14.54 0.00 0.00 1.98
88 89 5.853572 AAAACACCCAGGGAAGTATAGAA 57.146 39.130 14.54 0.00 0.00 2.10
89 90 4.838904 AACACCCAGGGAAGTATAGAAC 57.161 45.455 14.54 0.00 0.00 3.01
90 91 3.798515 ACACCCAGGGAAGTATAGAACA 58.201 45.455 14.54 0.00 0.00 3.18
91 92 3.518303 ACACCCAGGGAAGTATAGAACAC 59.482 47.826 14.54 0.00 0.00 3.32
92 93 3.517901 CACCCAGGGAAGTATAGAACACA 59.482 47.826 14.54 0.00 0.00 3.72
93 94 3.775316 ACCCAGGGAAGTATAGAACACAG 59.225 47.826 14.54 0.00 0.00 3.66
94 95 3.775316 CCCAGGGAAGTATAGAACACAGT 59.225 47.826 0.00 0.00 0.00 3.55
95 96 4.141914 CCCAGGGAAGTATAGAACACAGTC 60.142 50.000 0.00 0.00 0.00 3.51
96 97 4.440250 CCAGGGAAGTATAGAACACAGTCG 60.440 50.000 0.00 0.00 0.00 4.18
97 98 4.398358 CAGGGAAGTATAGAACACAGTCGA 59.602 45.833 0.00 0.00 0.00 4.20
98 99 4.398673 AGGGAAGTATAGAACACAGTCGAC 59.601 45.833 7.70 7.70 0.00 4.20
99 100 4.157289 GGGAAGTATAGAACACAGTCGACA 59.843 45.833 19.50 0.00 0.00 4.35
100 101 5.163540 GGGAAGTATAGAACACAGTCGACAT 60.164 44.000 19.50 1.85 0.00 3.06
101 102 5.744345 GGAAGTATAGAACACAGTCGACATG 59.256 44.000 19.50 17.44 0.00 3.21
102 103 6.404403 GGAAGTATAGAACACAGTCGACATGA 60.404 42.308 22.36 4.57 0.00 3.07
103 104 6.510879 AGTATAGAACACAGTCGACATGAA 57.489 37.500 22.36 8.42 0.00 2.57
104 105 6.323266 AGTATAGAACACAGTCGACATGAAC 58.677 40.000 22.36 15.57 0.00 3.18
105 106 2.755650 AGAACACAGTCGACATGAACC 58.244 47.619 22.36 12.25 0.00 3.62
106 107 2.102420 AGAACACAGTCGACATGAACCA 59.898 45.455 22.36 0.00 0.00 3.67
107 108 1.865865 ACACAGTCGACATGAACCAC 58.134 50.000 22.36 0.00 0.00 4.16
108 109 1.148310 CACAGTCGACATGAACCACC 58.852 55.000 19.50 0.00 0.00 4.61
109 110 0.034896 ACAGTCGACATGAACCACCC 59.965 55.000 19.50 0.00 0.00 4.61
110 111 0.034756 CAGTCGACATGAACCACCCA 59.965 55.000 19.50 0.00 0.00 4.51
111 112 0.762418 AGTCGACATGAACCACCCAA 59.238 50.000 19.50 0.00 0.00 4.12
112 113 0.872388 GTCGACATGAACCACCCAAC 59.128 55.000 11.55 0.00 0.00 3.77
113 114 0.250553 TCGACATGAACCACCCAACC 60.251 55.000 0.00 0.00 0.00 3.77
114 115 0.536233 CGACATGAACCACCCAACCA 60.536 55.000 0.00 0.00 0.00 3.67
115 116 0.958822 GACATGAACCACCCAACCAC 59.041 55.000 0.00 0.00 0.00 4.16
116 117 0.260230 ACATGAACCACCCAACCACA 59.740 50.000 0.00 0.00 0.00 4.17
117 118 1.133199 ACATGAACCACCCAACCACAT 60.133 47.619 0.00 0.00 0.00 3.21
118 119 2.109128 ACATGAACCACCCAACCACATA 59.891 45.455 0.00 0.00 0.00 2.29
119 120 3.161067 CATGAACCACCCAACCACATAA 58.839 45.455 0.00 0.00 0.00 1.90
120 121 3.314307 TGAACCACCCAACCACATAAA 57.686 42.857 0.00 0.00 0.00 1.40
121 122 3.643237 TGAACCACCCAACCACATAAAA 58.357 40.909 0.00 0.00 0.00 1.52
122 123 4.030913 TGAACCACCCAACCACATAAAAA 58.969 39.130 0.00 0.00 0.00 1.94
142 143 4.600692 AAATACAAGAGCAAAACCACCC 57.399 40.909 0.00 0.00 0.00 4.61
143 144 2.738587 TACAAGAGCAAAACCACCCA 57.261 45.000 0.00 0.00 0.00 4.51
144 145 1.859302 ACAAGAGCAAAACCACCCAA 58.141 45.000 0.00 0.00 0.00 4.12
145 146 1.756538 ACAAGAGCAAAACCACCCAAG 59.243 47.619 0.00 0.00 0.00 3.61
146 147 1.069049 CAAGAGCAAAACCACCCAAGG 59.931 52.381 0.00 0.00 0.00 3.61
147 148 0.555769 AGAGCAAAACCACCCAAGGA 59.444 50.000 0.00 0.00 0.00 3.36
148 149 1.063266 AGAGCAAAACCACCCAAGGAA 60.063 47.619 0.00 0.00 0.00 3.36
149 150 1.341209 GAGCAAAACCACCCAAGGAAG 59.659 52.381 0.00 0.00 0.00 3.46
150 151 1.119684 GCAAAACCACCCAAGGAAGT 58.880 50.000 0.00 0.00 0.00 3.01
151 152 2.091555 AGCAAAACCACCCAAGGAAGTA 60.092 45.455 0.00 0.00 0.00 2.24
152 153 2.897326 GCAAAACCACCCAAGGAAGTAT 59.103 45.455 0.00 0.00 0.00 2.12
153 154 4.083565 GCAAAACCACCCAAGGAAGTATA 58.916 43.478 0.00 0.00 0.00 1.47
154 155 4.157840 GCAAAACCACCCAAGGAAGTATAG 59.842 45.833 0.00 0.00 0.00 1.31
155 156 5.566469 CAAAACCACCCAAGGAAGTATAGA 58.434 41.667 0.00 0.00 0.00 1.98
156 157 6.187682 CAAAACCACCCAAGGAAGTATAGAT 58.812 40.000 0.00 0.00 0.00 1.98
157 158 7.343357 CAAAACCACCCAAGGAAGTATAGATA 58.657 38.462 0.00 0.00 0.00 1.98
158 159 7.519347 AAACCACCCAAGGAAGTATAGATAA 57.481 36.000 0.00 0.00 0.00 1.75
159 160 7.519347 AACCACCCAAGGAAGTATAGATAAA 57.481 36.000 0.00 0.00 0.00 1.40
160 161 7.138054 ACCACCCAAGGAAGTATAGATAAAG 57.862 40.000 0.00 0.00 0.00 1.85
161 162 5.998363 CCACCCAAGGAAGTATAGATAAAGC 59.002 44.000 0.00 0.00 0.00 3.51
162 163 5.696724 CACCCAAGGAAGTATAGATAAAGCG 59.303 44.000 0.00 0.00 0.00 4.68
163 164 5.601313 ACCCAAGGAAGTATAGATAAAGCGA 59.399 40.000 0.00 0.00 0.00 4.93
164 165 6.159988 CCCAAGGAAGTATAGATAAAGCGAG 58.840 44.000 0.00 0.00 0.00 5.03
165 166 6.239345 CCCAAGGAAGTATAGATAAAGCGAGT 60.239 42.308 0.00 0.00 0.00 4.18
166 167 7.210873 CCAAGGAAGTATAGATAAAGCGAGTT 58.789 38.462 0.00 0.00 0.00 3.01
225 226 5.133660 TGCAGGTTTATATATTGGACCCTGT 59.866 40.000 0.00 0.00 40.24 4.00
297 298 7.905604 TTATGACAAGTTTAGTGACATGAGG 57.094 36.000 0.00 0.00 34.15 3.86
301 324 5.248640 ACAAGTTTAGTGACATGAGGATGG 58.751 41.667 0.00 0.00 33.39 3.51
310 333 3.084039 GACATGAGGATGGCAACTTTCA 58.916 45.455 0.00 0.00 37.57 2.69
330 353 7.645340 ACTTTCATTTCGAATGACAAGTTTCAG 59.355 33.333 18.41 4.61 31.70 3.02
332 355 7.026631 TCATTTCGAATGACAAGTTTCAGTT 57.973 32.000 0.00 0.00 0.00 3.16
399 422 1.972872 AAATAGGCAGGGCGAGATTG 58.027 50.000 0.00 0.00 0.00 2.67
402 425 0.618458 TAGGCAGGGCGAGATTGTTT 59.382 50.000 0.00 0.00 0.00 2.83
403 426 0.678048 AGGCAGGGCGAGATTGTTTC 60.678 55.000 0.00 0.00 0.00 2.78
405 428 1.098050 GCAGGGCGAGATTGTTTCAT 58.902 50.000 0.00 0.00 0.00 2.57
406 429 1.202222 GCAGGGCGAGATTGTTTCATG 60.202 52.381 0.00 0.00 0.00 3.07
407 430 1.098050 AGGGCGAGATTGTTTCATGC 58.902 50.000 0.00 0.00 0.00 4.06
408 431 0.101219 GGGCGAGATTGTTTCATGCC 59.899 55.000 0.00 0.00 42.88 4.40
409 432 0.810648 GGCGAGATTGTTTCATGCCA 59.189 50.000 0.00 0.00 43.03 4.92
414 437 3.119743 CGAGATTGTTTCATGCCACACAT 60.120 43.478 0.00 0.00 40.66 3.21
422 445 2.644887 ATGCCACACATGTGTCACC 58.355 52.632 28.38 18.44 42.83 4.02
432 455 5.412286 CACACATGTGTCACCTATCATTTGA 59.588 40.000 28.38 0.00 42.83 2.69
433 456 5.645067 ACACATGTGTCACCTATCATTTGAG 59.355 40.000 25.76 0.00 40.24 3.02
468 492 4.678509 TTTCGGATGTTCATTGTACTGC 57.321 40.909 0.00 0.00 0.00 4.40
478 502 6.851609 TGTTCATTGTACTGCCATGATAAAC 58.148 36.000 0.00 0.00 0.00 2.01
481 507 6.851609 TCATTGTACTGCCATGATAAACAAC 58.148 36.000 0.00 0.00 0.00 3.32
491 517 6.765512 TGCCATGATAAACAACGAATAGATCA 59.234 34.615 0.00 0.00 0.00 2.92
593 620 2.812499 CCACGGACGGGGATGTAG 59.188 66.667 7.32 0.00 42.48 2.74
955 982 2.436646 CCCGCAGCTTCCACGAAT 60.437 61.111 0.00 0.00 0.00 3.34
1233 1272 4.436998 GTGGTCCTGGACGCCTCG 62.437 72.222 19.98 0.00 32.65 4.63
1272 1311 2.683933 GAGGAAGGGGAGTGCGGA 60.684 66.667 0.00 0.00 0.00 5.54
1279 1318 2.710902 GGGGAGTGCGGATTTTGCC 61.711 63.158 0.00 0.00 0.00 4.52
1283 1322 0.598065 GAGTGCGGATTTTGCCTGTT 59.402 50.000 0.00 0.00 0.00 3.16
1555 1594 2.203788 AGGAGGAACAGGGCGACA 60.204 61.111 0.00 0.00 0.00 4.35
1638 1677 1.972660 GCCTAGGCGTGGGATCTTGT 61.973 60.000 20.16 0.00 0.00 3.16
1694 1733 9.705290 GATGTGAATTATTTTGTTTTACCTGGT 57.295 29.630 4.05 4.05 0.00 4.00
1776 1816 4.270325 GGGAATTATACACTGTTCACGAGC 59.730 45.833 0.00 0.00 0.00 5.03
1922 1964 2.787723 CGTAGCGAACAATTGACAGG 57.212 50.000 13.59 0.00 0.00 4.00
1944 1986 4.995487 GGAAGTTCGTCCAGTAATCAGTTT 59.005 41.667 0.00 0.00 37.65 2.66
1946 1988 4.957296 AGTTCGTCCAGTAATCAGTTTGT 58.043 39.130 0.00 0.00 0.00 2.83
2038 2083 2.514458 CCACTCTTATTTGGCTGGGT 57.486 50.000 0.00 0.00 0.00 4.51
2039 2084 2.807676 CCACTCTTATTTGGCTGGGTT 58.192 47.619 0.00 0.00 0.00 4.11
2040 2085 3.165071 CCACTCTTATTTGGCTGGGTTT 58.835 45.455 0.00 0.00 0.00 3.27
2041 2086 3.578282 CCACTCTTATTTGGCTGGGTTTT 59.422 43.478 0.00 0.00 0.00 2.43
2042 2087 4.040339 CCACTCTTATTTGGCTGGGTTTTT 59.960 41.667 0.00 0.00 0.00 1.94
2063 2108 3.651803 TTTTGACCCGTTATTTGGCTG 57.348 42.857 0.00 0.00 0.00 4.85
2064 2109 1.540267 TTGACCCGTTATTTGGCTGG 58.460 50.000 0.00 0.00 0.00 4.85
2065 2110 0.402504 TGACCCGTTATTTGGCTGGT 59.597 50.000 0.00 0.00 0.00 4.00
2066 2111 1.202952 TGACCCGTTATTTGGCTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
2067 2112 1.890489 GACCCGTTATTTGGCTGGTTT 59.110 47.619 0.00 0.00 0.00 3.27
2068 2113 2.297880 GACCCGTTATTTGGCTGGTTTT 59.702 45.455 0.00 0.00 0.00 2.43
2069 2114 2.701423 ACCCGTTATTTGGCTGGTTTTT 59.299 40.909 0.00 0.00 0.00 1.94
2091 2136 3.651803 TTTTGACCCGTTATTTGGCTG 57.348 42.857 0.00 0.00 0.00 4.85
2092 2137 1.540267 TTGACCCGTTATTTGGCTGG 58.460 50.000 0.00 0.00 0.00 4.85
2093 2138 0.402504 TGACCCGTTATTTGGCTGGT 59.597 50.000 0.00 0.00 0.00 4.00
2094 2139 1.202952 TGACCCGTTATTTGGCTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
2097 2142 2.036604 ACCCGTTATTTGGCTGGTTTTG 59.963 45.455 0.00 0.00 0.00 2.44
2111 2156 3.030291 TGGTTTTGGACATTTGTCAGCT 58.970 40.909 12.43 0.00 46.47 4.24
2151 2196 5.718801 TGTAAAGATTATAGGGGTTGCCA 57.281 39.130 0.00 0.00 0.00 4.92
2212 2257 5.342433 CCGTGTTCTGTTCGGTATATGTTA 58.658 41.667 0.00 0.00 39.51 2.41
2261 2306 4.560108 GCAACAGCAAGAATTTCCTGACAT 60.560 41.667 7.79 0.00 31.44 3.06
2306 2351 9.859427 CTCAAAGAATGATTTGCTTGGTTATAA 57.141 29.630 0.00 0.00 39.51 0.98
2312 2357 6.449635 TGATTTGCTTGGTTATAATTCGCT 57.550 33.333 0.00 0.00 0.00 4.93
2321 2384 8.507249 GCTTGGTTATAATTCGCTATTTCATCT 58.493 33.333 0.00 0.00 0.00 2.90
2345 2408 1.073199 GCTGGTGTTACCCTGTGCT 59.927 57.895 0.00 0.00 37.50 4.40
2346 2409 0.323629 GCTGGTGTTACCCTGTGCTA 59.676 55.000 0.00 0.00 37.50 3.49
2347 2410 1.065418 GCTGGTGTTACCCTGTGCTAT 60.065 52.381 0.00 0.00 37.50 2.97
2348 2411 2.618045 GCTGGTGTTACCCTGTGCTATT 60.618 50.000 0.00 0.00 37.50 1.73
2396 4891 9.768662 AATTTACAGTTGAATTTGAGAATTGCT 57.231 25.926 0.00 0.00 35.65 3.91
2436 4931 4.652421 TGAATTGAAAGTTTCTGCTGCA 57.348 36.364 16.33 0.88 0.00 4.41
2454 4949 4.272489 CTGCATTTCTGTATTCTTGGGGA 58.728 43.478 0.00 0.00 0.00 4.81
2458 4953 5.500234 CATTTCTGTATTCTTGGGGACAGA 58.500 41.667 0.00 0.00 44.95 3.41
2493 4988 8.948631 TCATTCAGTAGTGGAATAAAGATGTC 57.051 34.615 0.00 0.00 33.40 3.06
2564 5059 4.004196 GGTACCAGTTCTGCTTACTTGT 57.996 45.455 7.15 0.00 0.00 3.16
2565 5060 4.386711 GGTACCAGTTCTGCTTACTTGTT 58.613 43.478 7.15 0.00 0.00 2.83
2566 5061 4.213482 GGTACCAGTTCTGCTTACTTGTTG 59.787 45.833 7.15 0.00 0.00 3.33
2567 5062 3.886123 ACCAGTTCTGCTTACTTGTTGT 58.114 40.909 0.00 0.00 0.00 3.32
2568 5063 3.627577 ACCAGTTCTGCTTACTTGTTGTG 59.372 43.478 0.00 0.00 0.00 3.33
2569 5064 3.876914 CCAGTTCTGCTTACTTGTTGTGA 59.123 43.478 0.00 0.00 0.00 3.58
2570 5065 4.260784 CCAGTTCTGCTTACTTGTTGTGAC 60.261 45.833 0.00 0.00 0.00 3.67
2571 5066 3.877508 AGTTCTGCTTACTTGTTGTGACC 59.122 43.478 0.00 0.00 0.00 4.02
2572 5067 3.838244 TCTGCTTACTTGTTGTGACCT 57.162 42.857 0.00 0.00 0.00 3.85
2573 5068 3.466836 TCTGCTTACTTGTTGTGACCTG 58.533 45.455 0.00 0.00 0.00 4.00
2574 5069 3.118408 TCTGCTTACTTGTTGTGACCTGT 60.118 43.478 0.00 0.00 0.00 4.00
2575 5070 3.616219 TGCTTACTTGTTGTGACCTGTT 58.384 40.909 0.00 0.00 0.00 3.16
2576 5071 4.013728 TGCTTACTTGTTGTGACCTGTTT 58.986 39.130 0.00 0.00 0.00 2.83
2577 5072 4.461081 TGCTTACTTGTTGTGACCTGTTTT 59.539 37.500 0.00 0.00 0.00 2.43
2578 5073 4.798387 GCTTACTTGTTGTGACCTGTTTTG 59.202 41.667 0.00 0.00 0.00 2.44
2579 5074 5.621329 GCTTACTTGTTGTGACCTGTTTTGT 60.621 40.000 0.00 0.00 0.00 2.83
2580 5075 4.864704 ACTTGTTGTGACCTGTTTTGTT 57.135 36.364 0.00 0.00 0.00 2.83
2581 5076 4.805219 ACTTGTTGTGACCTGTTTTGTTC 58.195 39.130 0.00 0.00 0.00 3.18
2582 5077 3.479505 TGTTGTGACCTGTTTTGTTCG 57.520 42.857 0.00 0.00 0.00 3.95
2583 5078 2.814919 TGTTGTGACCTGTTTTGTTCGT 59.185 40.909 0.00 0.00 0.00 3.85
2584 5079 3.120130 TGTTGTGACCTGTTTTGTTCGTC 60.120 43.478 0.00 0.00 0.00 4.20
2585 5080 1.661617 TGTGACCTGTTTTGTTCGTCG 59.338 47.619 0.00 0.00 0.00 5.12
2586 5081 1.928503 GTGACCTGTTTTGTTCGTCGA 59.071 47.619 0.00 0.00 0.00 4.20
2587 5082 1.928503 TGACCTGTTTTGTTCGTCGAC 59.071 47.619 5.18 5.18 0.00 4.20
2588 5083 1.928503 GACCTGTTTTGTTCGTCGACA 59.071 47.619 17.16 0.00 0.00 4.35
2589 5084 2.542595 GACCTGTTTTGTTCGTCGACAT 59.457 45.455 17.16 0.00 0.00 3.06
2590 5085 2.286833 ACCTGTTTTGTTCGTCGACATG 59.713 45.455 17.16 0.00 0.00 3.21
2591 5086 2.286833 CCTGTTTTGTTCGTCGACATGT 59.713 45.455 17.16 0.00 0.00 3.21
2592 5087 3.242608 CCTGTTTTGTTCGTCGACATGTT 60.243 43.478 17.16 0.00 0.00 2.71
2593 5088 3.675481 TGTTTTGTTCGTCGACATGTTG 58.325 40.909 17.16 6.77 0.00 3.33
2594 5089 3.033185 GTTTTGTTCGTCGACATGTTGG 58.967 45.455 17.16 2.41 0.00 3.77
2595 5090 2.226602 TTGTTCGTCGACATGTTGGA 57.773 45.000 17.16 4.90 0.00 3.53
2596 5091 1.493772 TGTTCGTCGACATGTTGGAC 58.506 50.000 17.16 15.29 0.00 4.02
2598 5093 2.769617 CGTCGACATGTTGGACGC 59.230 61.111 28.43 12.21 45.55 5.19
2599 5094 2.019408 CGTCGACATGTTGGACGCA 61.019 57.895 28.43 4.28 45.55 5.24
2600 5095 1.781555 GTCGACATGTTGGACGCAG 59.218 57.895 11.55 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.184864 CCACTCCAGCCACAATTACAATTAA 59.815 40.000 0.00 0.00 0.00 1.40
1 2 4.704540 CCACTCCAGCCACAATTACAATTA 59.295 41.667 0.00 0.00 0.00 1.40
2 3 3.511146 CCACTCCAGCCACAATTACAATT 59.489 43.478 0.00 0.00 0.00 2.32
3 4 3.091545 CCACTCCAGCCACAATTACAAT 58.908 45.455 0.00 0.00 0.00 2.71
4 5 2.513753 CCACTCCAGCCACAATTACAA 58.486 47.619 0.00 0.00 0.00 2.41
5 6 1.886222 GCCACTCCAGCCACAATTACA 60.886 52.381 0.00 0.00 0.00 2.41
6 7 0.811281 GCCACTCCAGCCACAATTAC 59.189 55.000 0.00 0.00 0.00 1.89
7 8 0.676466 CGCCACTCCAGCCACAATTA 60.676 55.000 0.00 0.00 0.00 1.40
8 9 1.973281 CGCCACTCCAGCCACAATT 60.973 57.895 0.00 0.00 0.00 2.32
9 10 2.360350 CGCCACTCCAGCCACAAT 60.360 61.111 0.00 0.00 0.00 2.71
10 11 3.555324 TCGCCACTCCAGCCACAA 61.555 61.111 0.00 0.00 0.00 3.33
11 12 4.314440 GTCGCCACTCCAGCCACA 62.314 66.667 0.00 0.00 0.00 4.17
12 13 3.612247 ATGTCGCCACTCCAGCCAC 62.612 63.158 0.00 0.00 0.00 5.01
13 14 3.315142 GATGTCGCCACTCCAGCCA 62.315 63.158 0.00 0.00 0.00 4.75
14 15 2.512515 GATGTCGCCACTCCAGCC 60.513 66.667 0.00 0.00 0.00 4.85
15 16 1.375908 TTGATGTCGCCACTCCAGC 60.376 57.895 0.00 0.00 0.00 4.85
16 17 0.320683 TGTTGATGTCGCCACTCCAG 60.321 55.000 0.00 0.00 0.00 3.86
17 18 0.602638 GTGTTGATGTCGCCACTCCA 60.603 55.000 0.00 0.00 0.00 3.86
18 19 0.320771 AGTGTTGATGTCGCCACTCC 60.321 55.000 0.00 0.00 32.97 3.85
19 20 1.512926 AAGTGTTGATGTCGCCACTC 58.487 50.000 5.28 0.00 37.18 3.51
20 21 2.037251 ACTAAGTGTTGATGTCGCCACT 59.963 45.455 0.00 0.00 39.73 4.00
21 22 2.413837 ACTAAGTGTTGATGTCGCCAC 58.586 47.619 0.00 0.00 0.00 5.01
22 23 2.831685 ACTAAGTGTTGATGTCGCCA 57.168 45.000 0.00 0.00 0.00 5.69
32 33 6.292923 TGTGGTAATGCTACAACTAAGTGTT 58.707 36.000 0.00 0.00 35.58 3.32
33 34 5.860611 TGTGGTAATGCTACAACTAAGTGT 58.139 37.500 0.00 0.00 35.58 3.55
34 35 6.795098 TTGTGGTAATGCTACAACTAAGTG 57.205 37.500 0.00 0.00 42.42 3.16
35 36 6.768861 TGTTTGTGGTAATGCTACAACTAAGT 59.231 34.615 0.00 0.00 46.01 2.24
36 37 7.197071 TGTTTGTGGTAATGCTACAACTAAG 57.803 36.000 0.00 0.00 46.01 2.18
37 38 7.569639 TTGTTTGTGGTAATGCTACAACTAA 57.430 32.000 0.00 0.00 46.01 2.24
38 39 7.569639 TTTGTTTGTGGTAATGCTACAACTA 57.430 32.000 0.00 0.00 46.01 2.24
39 40 6.458232 TTTGTTTGTGGTAATGCTACAACT 57.542 33.333 0.00 0.00 46.01 3.16
40 41 7.527084 TTTTTGTTTGTGGTAATGCTACAAC 57.473 32.000 0.00 0.00 46.01 3.32
65 66 5.853572 TCTATACTTCCCTGGGTGTTTTT 57.146 39.130 13.56 5.04 0.00 1.94
66 67 5.073965 TGTTCTATACTTCCCTGGGTGTTTT 59.926 40.000 13.56 7.18 0.00 2.43
67 68 4.600111 TGTTCTATACTTCCCTGGGTGTTT 59.400 41.667 13.56 10.51 0.00 2.83
68 69 4.019591 GTGTTCTATACTTCCCTGGGTGTT 60.020 45.833 13.56 0.16 0.00 3.32
69 70 3.518303 GTGTTCTATACTTCCCTGGGTGT 59.482 47.826 13.56 14.92 0.00 4.16
70 71 3.517901 TGTGTTCTATACTTCCCTGGGTG 59.482 47.826 13.56 9.64 0.00 4.61
71 72 3.775316 CTGTGTTCTATACTTCCCTGGGT 59.225 47.826 13.56 0.00 0.00 4.51
72 73 3.775316 ACTGTGTTCTATACTTCCCTGGG 59.225 47.826 6.33 6.33 0.00 4.45
73 74 4.440250 CGACTGTGTTCTATACTTCCCTGG 60.440 50.000 0.00 0.00 0.00 4.45
74 75 4.398358 TCGACTGTGTTCTATACTTCCCTG 59.602 45.833 0.00 0.00 0.00 4.45
75 76 4.398673 GTCGACTGTGTTCTATACTTCCCT 59.601 45.833 8.70 0.00 0.00 4.20
76 77 4.157289 TGTCGACTGTGTTCTATACTTCCC 59.843 45.833 17.92 0.00 0.00 3.97
77 78 5.306532 TGTCGACTGTGTTCTATACTTCC 57.693 43.478 17.92 0.00 0.00 3.46
78 79 6.552629 TCATGTCGACTGTGTTCTATACTTC 58.447 40.000 17.92 0.00 0.00 3.01
79 80 6.510879 TCATGTCGACTGTGTTCTATACTT 57.489 37.500 17.92 0.00 0.00 2.24
80 81 6.323266 GTTCATGTCGACTGTGTTCTATACT 58.677 40.000 17.92 0.00 0.00 2.12
81 82 5.515626 GGTTCATGTCGACTGTGTTCTATAC 59.484 44.000 17.92 8.36 0.00 1.47
82 83 5.184287 TGGTTCATGTCGACTGTGTTCTATA 59.816 40.000 17.92 0.00 0.00 1.31
83 84 4.021456 TGGTTCATGTCGACTGTGTTCTAT 60.021 41.667 17.92 0.00 0.00 1.98
84 85 3.319689 TGGTTCATGTCGACTGTGTTCTA 59.680 43.478 17.92 8.34 0.00 2.10
85 86 2.102420 TGGTTCATGTCGACTGTGTTCT 59.898 45.455 17.92 0.00 0.00 3.01
86 87 2.221055 GTGGTTCATGTCGACTGTGTTC 59.779 50.000 17.92 11.83 0.00 3.18
87 88 2.210116 GTGGTTCATGTCGACTGTGTT 58.790 47.619 17.92 0.00 0.00 3.32
88 89 1.540363 GGTGGTTCATGTCGACTGTGT 60.540 52.381 17.92 0.00 0.00 3.72
89 90 1.148310 GGTGGTTCATGTCGACTGTG 58.852 55.000 17.92 15.17 0.00 3.66
90 91 0.034896 GGGTGGTTCATGTCGACTGT 59.965 55.000 17.92 2.41 0.00 3.55
91 92 0.034756 TGGGTGGTTCATGTCGACTG 59.965 55.000 17.92 12.33 0.00 3.51
92 93 0.762418 TTGGGTGGTTCATGTCGACT 59.238 50.000 17.92 0.00 0.00 4.18
93 94 0.872388 GTTGGGTGGTTCATGTCGAC 59.128 55.000 9.11 9.11 0.00 4.20
94 95 0.250553 GGTTGGGTGGTTCATGTCGA 60.251 55.000 0.00 0.00 0.00 4.20
95 96 0.536233 TGGTTGGGTGGTTCATGTCG 60.536 55.000 0.00 0.00 0.00 4.35
96 97 0.958822 GTGGTTGGGTGGTTCATGTC 59.041 55.000 0.00 0.00 0.00 3.06
97 98 0.260230 TGTGGTTGGGTGGTTCATGT 59.740 50.000 0.00 0.00 0.00 3.21
98 99 1.631405 ATGTGGTTGGGTGGTTCATG 58.369 50.000 0.00 0.00 0.00 3.07
99 100 3.534357 TTATGTGGTTGGGTGGTTCAT 57.466 42.857 0.00 0.00 0.00 2.57
100 101 3.314307 TTTATGTGGTTGGGTGGTTCA 57.686 42.857 0.00 0.00 0.00 3.18
101 102 4.674281 TTTTTATGTGGTTGGGTGGTTC 57.326 40.909 0.00 0.00 0.00 3.62
119 120 5.104735 TGGGTGGTTTTGCTCTTGTATTTTT 60.105 36.000 0.00 0.00 0.00 1.94
120 121 4.407296 TGGGTGGTTTTGCTCTTGTATTTT 59.593 37.500 0.00 0.00 0.00 1.82
121 122 3.964031 TGGGTGGTTTTGCTCTTGTATTT 59.036 39.130 0.00 0.00 0.00 1.40
122 123 3.571590 TGGGTGGTTTTGCTCTTGTATT 58.428 40.909 0.00 0.00 0.00 1.89
123 124 3.237268 TGGGTGGTTTTGCTCTTGTAT 57.763 42.857 0.00 0.00 0.00 2.29
124 125 2.738587 TGGGTGGTTTTGCTCTTGTA 57.261 45.000 0.00 0.00 0.00 2.41
125 126 1.756538 CTTGGGTGGTTTTGCTCTTGT 59.243 47.619 0.00 0.00 0.00 3.16
126 127 1.069049 CCTTGGGTGGTTTTGCTCTTG 59.931 52.381 0.00 0.00 0.00 3.02
127 128 1.063266 TCCTTGGGTGGTTTTGCTCTT 60.063 47.619 0.00 0.00 0.00 2.85
128 129 0.555769 TCCTTGGGTGGTTTTGCTCT 59.444 50.000 0.00 0.00 0.00 4.09
129 130 1.341209 CTTCCTTGGGTGGTTTTGCTC 59.659 52.381 0.00 0.00 0.00 4.26
130 131 1.342975 ACTTCCTTGGGTGGTTTTGCT 60.343 47.619 0.00 0.00 0.00 3.91
131 132 1.119684 ACTTCCTTGGGTGGTTTTGC 58.880 50.000 0.00 0.00 0.00 3.68
132 133 5.566469 TCTATACTTCCTTGGGTGGTTTTG 58.434 41.667 0.00 0.00 0.00 2.44
133 134 5.853572 TCTATACTTCCTTGGGTGGTTTT 57.146 39.130 0.00 0.00 0.00 2.43
134 135 7.519347 TTATCTATACTTCCTTGGGTGGTTT 57.481 36.000 0.00 0.00 0.00 3.27
135 136 7.519347 TTTATCTATACTTCCTTGGGTGGTT 57.481 36.000 0.00 0.00 0.00 3.67
136 137 6.409349 GCTTTATCTATACTTCCTTGGGTGGT 60.409 42.308 0.00 0.00 0.00 4.16
137 138 5.998363 GCTTTATCTATACTTCCTTGGGTGG 59.002 44.000 0.00 0.00 0.00 4.61
138 139 5.696724 CGCTTTATCTATACTTCCTTGGGTG 59.303 44.000 0.00 0.00 0.00 4.61
139 140 5.601313 TCGCTTTATCTATACTTCCTTGGGT 59.399 40.000 0.00 0.00 0.00 4.51
140 141 6.097915 TCGCTTTATCTATACTTCCTTGGG 57.902 41.667 0.00 0.00 0.00 4.12
141 142 6.750148 ACTCGCTTTATCTATACTTCCTTGG 58.250 40.000 0.00 0.00 0.00 3.61
142 143 8.649973 AAACTCGCTTTATCTATACTTCCTTG 57.350 34.615 0.00 0.00 0.00 3.61
143 144 9.668497 AAAAACTCGCTTTATCTATACTTCCTT 57.332 29.630 0.00 0.00 0.00 3.36
199 200 6.721208 CAGGGTCCAATATATAAACCTGCAAT 59.279 38.462 11.70 0.00 37.96 3.56
200 201 6.068010 CAGGGTCCAATATATAAACCTGCAA 58.932 40.000 11.70 0.00 37.96 4.08
205 206 9.063615 CACTTAACAGGGTCCAATATATAAACC 57.936 37.037 0.00 3.55 0.00 3.27
208 209 7.147284 TGGCACTTAACAGGGTCCAATATATAA 60.147 37.037 0.00 0.00 29.58 0.98
210 211 5.133660 TGGCACTTAACAGGGTCCAATATAT 59.866 40.000 0.00 0.00 29.58 0.86
211 212 4.475381 TGGCACTTAACAGGGTCCAATATA 59.525 41.667 0.00 0.00 29.58 0.86
212 213 3.268334 TGGCACTTAACAGGGTCCAATAT 59.732 43.478 0.00 0.00 29.58 1.28
246 247 3.817187 TGGAGTTGCCATGTGTTCA 57.183 47.368 0.00 0.00 43.33 3.18
278 279 5.248640 CCATCCTCATGTCACTAAACTTGT 58.751 41.667 0.00 0.00 0.00 3.16
291 292 4.730949 AATGAAAGTTGCCATCCTCATG 57.269 40.909 0.00 0.00 0.00 3.07
292 293 4.142315 CGAAATGAAAGTTGCCATCCTCAT 60.142 41.667 0.00 0.00 0.00 2.90
295 296 3.420893 TCGAAATGAAAGTTGCCATCCT 58.579 40.909 0.00 0.00 0.00 3.24
297 298 5.287035 GTCATTCGAAATGAAAGTTGCCATC 59.713 40.000 0.00 0.00 40.71 3.51
301 324 5.687285 ACTTGTCATTCGAAATGAAAGTTGC 59.313 36.000 0.00 0.00 40.71 4.17
310 333 8.702163 AAAAACTGAAACTTGTCATTCGAAAT 57.298 26.923 0.00 0.00 0.00 2.17
383 406 0.618458 AAACAATCTCGCCCTGCCTA 59.382 50.000 0.00 0.00 0.00 3.93
384 407 0.678048 GAAACAATCTCGCCCTGCCT 60.678 55.000 0.00 0.00 0.00 4.75
385 408 0.960364 TGAAACAATCTCGCCCTGCC 60.960 55.000 0.00 0.00 0.00 4.85
386 409 1.098050 ATGAAACAATCTCGCCCTGC 58.902 50.000 0.00 0.00 0.00 4.85
387 410 1.202222 GCATGAAACAATCTCGCCCTG 60.202 52.381 0.00 0.00 0.00 4.45
390 413 0.810648 TGGCATGAAACAATCTCGCC 59.189 50.000 0.00 0.00 42.83 5.54
391 414 1.199789 TGTGGCATGAAACAATCTCGC 59.800 47.619 0.00 0.00 0.00 5.03
392 415 2.226200 TGTGTGGCATGAAACAATCTCG 59.774 45.455 0.00 0.00 0.00 4.04
414 437 8.862325 AAAATACTCAAATGATAGGTGACACA 57.138 30.769 8.08 0.00 0.00 3.72
451 475 3.947196 TCATGGCAGTACAATGAACATCC 59.053 43.478 0.00 0.00 0.00 3.51
459 483 5.645929 TCGTTGTTTATCATGGCAGTACAAT 59.354 36.000 0.00 0.00 0.00 2.71
462 486 5.539582 TTCGTTGTTTATCATGGCAGTAC 57.460 39.130 0.00 0.00 0.00 2.73
468 492 8.593492 TCTGATCTATTCGTTGTTTATCATGG 57.407 34.615 0.00 0.00 0.00 3.66
586 613 2.731341 CGTTGACGACAGGACTACATCC 60.731 54.545 0.00 0.00 44.92 3.51
955 982 1.895020 CTGTTGAATCGGACGGGGGA 61.895 60.000 0.00 0.00 0.00 4.81
1272 1311 2.027837 GCCCTTCATGAACAGGCAAAAT 60.028 45.455 28.28 0.00 43.32 1.82
1279 1318 2.753966 CGCCGCCCTTCATGAACAG 61.754 63.158 3.38 0.00 0.00 3.16
1315 1354 2.352805 GCACTTCTCCCACCCCAG 59.647 66.667 0.00 0.00 0.00 4.45
1536 1575 2.683933 TCGCCCTGTTCCTCCTCC 60.684 66.667 0.00 0.00 0.00 4.30
1555 1594 0.464554 GGCTCCGCCTGCTTCTTATT 60.465 55.000 0.00 0.00 46.69 1.40
1573 1612 1.764571 TTCTCCTTCACCACCACCGG 61.765 60.000 0.00 0.00 0.00 5.28
1583 1622 2.503356 GCAAGATCCTCCTTCTCCTTCA 59.497 50.000 0.00 0.00 0.00 3.02
1694 1733 0.745486 CCCATCTTGCAGATCACGCA 60.745 55.000 5.78 5.78 31.32 5.24
1737 1776 7.660030 ATAATTCCCACCAAAAGAATCGAAT 57.340 32.000 0.00 0.00 30.06 3.34
1776 1816 6.428465 TCTCCATATTAGTTCACGAGCTAGAG 59.572 42.308 0.00 0.00 0.00 2.43
1909 1950 4.319549 GGACGAACTTCCTGTCAATTGTTC 60.320 45.833 5.13 1.16 34.32 3.18
1922 1964 5.465724 ACAAACTGATTACTGGACGAACTTC 59.534 40.000 0.00 0.00 0.00 3.01
1944 1986 4.039124 TGCTCACTCAGTTACTGATTGACA 59.961 41.667 24.86 22.81 42.41 3.58
1946 1988 4.281941 AGTGCTCACTCAGTTACTGATTGA 59.718 41.667 26.17 26.17 44.10 2.57
2042 2087 3.243907 CCAGCCAAATAACGGGTCAAAAA 60.244 43.478 0.00 0.00 29.87 1.94
2043 2088 2.297597 CCAGCCAAATAACGGGTCAAAA 59.702 45.455 0.00 0.00 29.87 2.44
2044 2089 1.889829 CCAGCCAAATAACGGGTCAAA 59.110 47.619 0.00 0.00 29.87 2.69
2045 2090 1.202952 ACCAGCCAAATAACGGGTCAA 60.203 47.619 0.00 0.00 27.07 3.18
2046 2091 0.402504 ACCAGCCAAATAACGGGTCA 59.597 50.000 0.00 0.00 27.07 4.02
2047 2092 1.541379 AACCAGCCAAATAACGGGTC 58.459 50.000 0.00 0.00 32.90 4.46
2048 2093 2.003937 AAACCAGCCAAATAACGGGT 57.996 45.000 0.00 0.00 35.77 5.28
2049 2094 3.394674 AAAAACCAGCCAAATAACGGG 57.605 42.857 0.00 0.00 0.00 5.28
2070 2115 3.243907 CCAGCCAAATAACGGGTCAAAAA 60.244 43.478 0.00 0.00 29.87 1.94
2071 2116 2.297597 CCAGCCAAATAACGGGTCAAAA 59.702 45.455 0.00 0.00 29.87 2.44
2072 2117 1.889829 CCAGCCAAATAACGGGTCAAA 59.110 47.619 0.00 0.00 29.87 2.69
2073 2118 1.202952 ACCAGCCAAATAACGGGTCAA 60.203 47.619 0.00 0.00 27.07 3.18
2074 2119 0.402504 ACCAGCCAAATAACGGGTCA 59.597 50.000 0.00 0.00 27.07 4.02
2075 2120 1.541379 AACCAGCCAAATAACGGGTC 58.459 50.000 0.00 0.00 32.90 4.46
2076 2121 2.003937 AAACCAGCCAAATAACGGGT 57.996 45.000 0.00 0.00 35.77 5.28
2077 2122 2.611722 CCAAAACCAGCCAAATAACGGG 60.612 50.000 0.00 0.00 0.00 5.28
2078 2123 2.297597 TCCAAAACCAGCCAAATAACGG 59.702 45.455 0.00 0.00 0.00 4.44
2079 2124 3.243569 TGTCCAAAACCAGCCAAATAACG 60.244 43.478 0.00 0.00 0.00 3.18
2080 2125 4.329462 TGTCCAAAACCAGCCAAATAAC 57.671 40.909 0.00 0.00 0.00 1.89
2081 2126 5.559148 AATGTCCAAAACCAGCCAAATAA 57.441 34.783 0.00 0.00 0.00 1.40
2082 2127 5.163258 ACAAATGTCCAAAACCAGCCAAATA 60.163 36.000 0.00 0.00 0.00 1.40
2083 2128 4.136051 CAAATGTCCAAAACCAGCCAAAT 58.864 39.130 0.00 0.00 0.00 2.32
2084 2129 3.054802 ACAAATGTCCAAAACCAGCCAAA 60.055 39.130 0.00 0.00 0.00 3.28
2085 2130 2.503356 ACAAATGTCCAAAACCAGCCAA 59.497 40.909 0.00 0.00 0.00 4.52
2086 2131 2.102252 GACAAATGTCCAAAACCAGCCA 59.898 45.455 2.04 0.00 39.07 4.75
2087 2132 2.102252 TGACAAATGTCCAAAACCAGCC 59.898 45.455 10.83 0.00 44.15 4.85
2088 2133 3.383761 CTGACAAATGTCCAAAACCAGC 58.616 45.455 10.83 0.00 44.15 4.85
2089 2134 3.068590 AGCTGACAAATGTCCAAAACCAG 59.931 43.478 10.83 2.12 44.15 4.00
2090 2135 3.030291 AGCTGACAAATGTCCAAAACCA 58.970 40.909 10.83 0.00 44.15 3.67
2091 2136 3.733443 AGCTGACAAATGTCCAAAACC 57.267 42.857 10.83 0.00 44.15 3.27
2092 2137 7.713764 AAATTAGCTGACAAATGTCCAAAAC 57.286 32.000 10.83 0.00 44.15 2.43
2093 2138 7.984050 TCAAAATTAGCTGACAAATGTCCAAAA 59.016 29.630 10.83 1.64 44.15 2.44
2094 2139 7.495901 TCAAAATTAGCTGACAAATGTCCAAA 58.504 30.769 10.83 1.34 44.15 3.28
2097 2142 5.574443 GCTCAAAATTAGCTGACAAATGTCC 59.426 40.000 10.83 0.00 44.15 4.02
2134 2179 6.126185 ACACTAAATGGCAACCCCTATAATCT 60.126 38.462 0.00 0.00 0.00 2.40
2135 2180 6.068670 ACACTAAATGGCAACCCCTATAATC 58.931 40.000 0.00 0.00 0.00 1.75
2151 2196 3.935203 CACCGCTGATTCAGACACTAAAT 59.065 43.478 17.87 0.00 32.44 1.40
2212 2257 2.142292 AAATGAGGCCGGCTGGAACT 62.142 55.000 28.56 14.88 37.49 3.01
2284 2329 9.520204 CGAATTATAACCAAGCAAATCATTCTT 57.480 29.630 0.00 0.00 0.00 2.52
2306 2351 5.464722 CAGCAGTGTAGATGAAATAGCGAAT 59.535 40.000 0.00 0.00 0.00 3.34
2307 2352 4.805719 CAGCAGTGTAGATGAAATAGCGAA 59.194 41.667 0.00 0.00 0.00 4.70
2345 2408 7.225784 TGCAAAAGTAGCCAAAGATGAAATA 57.774 32.000 0.00 0.00 0.00 1.40
2346 2409 6.100404 TGCAAAAGTAGCCAAAGATGAAAT 57.900 33.333 0.00 0.00 0.00 2.17
2347 2410 5.528043 TGCAAAAGTAGCCAAAGATGAAA 57.472 34.783 0.00 0.00 0.00 2.69
2348 2411 5.528043 TTGCAAAAGTAGCCAAAGATGAA 57.472 34.783 0.00 0.00 0.00 2.57
2396 4891 8.417106 TCAATTCAAATGTACTTTAAACAGGCA 58.583 29.630 0.00 0.00 0.00 4.75
2436 4931 5.779241 TCTGTCCCCAAGAATACAGAAAT 57.221 39.130 0.00 0.00 43.90 2.17
2454 4949 7.604164 CACTACTGAATGAACCTTACAATCTGT 59.396 37.037 0.00 0.00 35.06 3.41
2458 4953 7.016153 TCCACTACTGAATGAACCTTACAAT 57.984 36.000 0.00 0.00 0.00 2.71
2528 5023 6.707273 ACTGGTACCCCTGTTTCTAAATAA 57.293 37.500 10.07 0.00 39.68 1.40
2542 5037 3.244457 ACAAGTAAGCAGAACTGGTACCC 60.244 47.826 10.07 0.00 40.87 3.69
2548 5043 4.260784 GGTCACAACAAGTAAGCAGAACTG 60.261 45.833 0.00 0.00 0.00 3.16
2549 5044 3.877508 GGTCACAACAAGTAAGCAGAACT 59.122 43.478 0.00 0.00 0.00 3.01
2550 5045 3.877508 AGGTCACAACAAGTAAGCAGAAC 59.122 43.478 0.00 0.00 0.00 3.01
2551 5046 3.876914 CAGGTCACAACAAGTAAGCAGAA 59.123 43.478 0.00 0.00 0.00 3.02
2552 5047 3.118408 ACAGGTCACAACAAGTAAGCAGA 60.118 43.478 0.00 0.00 0.00 4.26
2553 5048 3.206150 ACAGGTCACAACAAGTAAGCAG 58.794 45.455 0.00 0.00 0.00 4.24
2554 5049 3.275617 ACAGGTCACAACAAGTAAGCA 57.724 42.857 0.00 0.00 0.00 3.91
2555 5050 4.632538 AAACAGGTCACAACAAGTAAGC 57.367 40.909 0.00 0.00 0.00 3.09
2556 5051 5.949735 ACAAAACAGGTCACAACAAGTAAG 58.050 37.500 0.00 0.00 0.00 2.34
2557 5052 5.968528 ACAAAACAGGTCACAACAAGTAA 57.031 34.783 0.00 0.00 0.00 2.24
2558 5053 5.391097 CGAACAAAACAGGTCACAACAAGTA 60.391 40.000 0.00 0.00 0.00 2.24
2559 5054 4.614993 CGAACAAAACAGGTCACAACAAGT 60.615 41.667 0.00 0.00 0.00 3.16
2560 5055 3.851403 CGAACAAAACAGGTCACAACAAG 59.149 43.478 0.00 0.00 0.00 3.16
2561 5056 3.253677 ACGAACAAAACAGGTCACAACAA 59.746 39.130 0.00 0.00 0.00 2.83
2562 5057 2.814919 ACGAACAAAACAGGTCACAACA 59.185 40.909 0.00 0.00 0.00 3.33
2563 5058 3.422655 GACGAACAAAACAGGTCACAAC 58.577 45.455 0.00 0.00 0.00 3.32
2564 5059 2.094575 CGACGAACAAAACAGGTCACAA 59.905 45.455 0.00 0.00 0.00 3.33
2565 5060 1.661617 CGACGAACAAAACAGGTCACA 59.338 47.619 0.00 0.00 0.00 3.58
2566 5061 1.928503 TCGACGAACAAAACAGGTCAC 59.071 47.619 0.00 0.00 0.00 3.67
2567 5062 1.928503 GTCGACGAACAAAACAGGTCA 59.071 47.619 0.00 0.00 0.00 4.02
2568 5063 1.928503 TGTCGACGAACAAAACAGGTC 59.071 47.619 11.62 0.00 0.00 3.85
2569 5064 2.012937 TGTCGACGAACAAAACAGGT 57.987 45.000 11.62 0.00 0.00 4.00
2570 5065 2.286833 ACATGTCGACGAACAAAACAGG 59.713 45.455 11.62 0.00 31.81 4.00
2571 5066 3.585748 ACATGTCGACGAACAAAACAG 57.414 42.857 11.62 0.00 31.81 3.16
2572 5067 3.486043 CCAACATGTCGACGAACAAAACA 60.486 43.478 11.62 0.00 31.81 2.83
2573 5068 3.033185 CCAACATGTCGACGAACAAAAC 58.967 45.455 11.62 0.00 31.81 2.43
2574 5069 2.937149 TCCAACATGTCGACGAACAAAA 59.063 40.909 11.62 0.00 31.81 2.44
2575 5070 2.285756 GTCCAACATGTCGACGAACAAA 59.714 45.455 11.62 0.00 31.81 2.83
2576 5071 1.862201 GTCCAACATGTCGACGAACAA 59.138 47.619 11.62 0.00 31.81 2.83
2577 5072 1.493772 GTCCAACATGTCGACGAACA 58.506 50.000 11.62 0.47 0.00 3.18
2582 5077 0.944311 ACTGCGTCCAACATGTCGAC 60.944 55.000 9.11 9.11 0.00 4.20
2583 5078 0.666274 GACTGCGTCCAACATGTCGA 60.666 55.000 8.68 0.42 0.00 4.20
2584 5079 1.781555 GACTGCGTCCAACATGTCG 59.218 57.895 0.00 0.00 0.00 4.35
2594 5089 4.164252 CTGTAACGGGACTGCGTC 57.836 61.111 0.00 0.79 0.00 5.19


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

AutoCloner maintained by Alex Coulton.