Multiple sequence alignment - TraesCS5A01G115000

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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 TraesCS5A01G115000 chr5A 100.000 6931 0 0 1 6931 230066733 230073663 0.000000e+00 12800.0
1 TraesCS5A01G115000 chr5B 94.502 6129 159 45 477 6481 196465703 196471777 0.000000e+00 9287.0
2 TraesCS5A01G115000 chr5B 83.573 347 13 18 6614 6931 196471975 196472306 1.140000e-72 285.0
3 TraesCS5A01G115000 chr5B 91.964 112 9 0 6487 6598 449204294 449204183 2.590000e-34 158.0
4 TraesCS5A01G115000 chr5D 93.172 3017 123 34 219 3169 192264408 192267407 0.000000e+00 4353.0
5 TraesCS5A01G115000 chr5D 97.413 2281 51 4 4205 6481 192268314 192270590 0.000000e+00 3879.0
6 TraesCS5A01G115000 chr5D 83.208 399 39 16 1 385 40188730 40189114 2.390000e-89 340.0
7 TraesCS5A01G115000 chr5D 92.157 102 7 1 1670 1771 291244356 291244456 7.250000e-30 143.0
8 TraesCS5A01G115000 chr5D 97.059 34 1 0 4177 4210 192267399 192267432 2.700000e-04 58.4
9 TraesCS5A01G115000 chr6D 82.955 1056 121 35 3170 4173 153304159 153305207 0.000000e+00 898.0
10 TraesCS5A01G115000 chr6D 80.574 592 62 29 3615 4176 366542983 366543551 2.330000e-109 407.0
11 TraesCS5A01G115000 chr6D 91.197 284 24 1 3418 3700 366542720 366543003 1.090000e-102 385.0
12 TraesCS5A01G115000 chr6D 86.351 359 32 2 3172 3530 366542379 366542720 6.560000e-100 375.0
13 TraesCS5A01G115000 chr6D 83.117 308 28 8 3821 4127 894720 894436 6.900000e-65 259.0
14 TraesCS5A01G115000 chr6D 89.571 163 11 2 3172 3333 366542100 366542257 1.180000e-47 202.0
15 TraesCS5A01G115000 chr6D 91.429 105 8 1 1674 1778 437332694 437332591 7.250000e-30 143.0
16 TraesCS5A01G115000 chr6B 88.221 416 38 10 4178 4585 42814664 42814252 2.910000e-133 486.0
17 TraesCS5A01G115000 chr6B 90.722 97 8 1 6392 6488 583242094 583242189 2.030000e-25 128.0
18 TraesCS5A01G115000 chr6A 88.136 413 26 12 4178 4585 24424990 24424596 2.930000e-128 470.0
19 TraesCS5A01G115000 chrUn 87.681 414 27 11 4178 4585 93838859 93838464 1.760000e-125 460.0
20 TraesCS5A01G115000 chrUn 83.333 354 49 7 6 358 114242184 114242528 1.120000e-82 318.0
21 TraesCS5A01G115000 chr3D 82.881 479 73 6 1 477 416912985 416912514 8.310000e-114 422.0
22 TraesCS5A01G115000 chr3D 88.889 135 7 3 6750 6884 496954135 496954261 7.200000e-35 159.0
23 TraesCS5A01G115000 chr3D 91.071 112 10 0 6487 6598 110402772 110402661 1.200000e-32 152.0
24 TraesCS5A01G115000 chr3D 91.071 112 8 2 6487 6598 280046502 280046393 4.330000e-32 150.0
25 TraesCS5A01G115000 chr3D 93.814 97 6 0 1671 1767 445019035 445019131 5.600000e-31 147.0
26 TraesCS5A01G115000 chr3D 91.346 104 6 2 6651 6751 496954006 496954109 9.370000e-29 139.0
27 TraesCS5A01G115000 chr3D 93.182 44 2 1 957 999 417208947 417208904 5.800000e-06 63.9
28 TraesCS5A01G115000 chr4B 82.218 478 76 9 3 479 412180032 412180501 3.010000e-108 403.0
29 TraesCS5A01G115000 chr4B 84.270 356 41 9 7 358 409773279 409772935 4.010000e-87 333.0
30 TraesCS5A01G115000 chr2A 80.071 567 60 23 3643 4185 688590041 688589504 8.490000e-99 372.0
31 TraesCS5A01G115000 chr2A 87.719 285 23 5 3293 3567 688605278 688604996 8.670000e-84 322.0
32 TraesCS5A01G115000 chr2A 84.395 314 13 3 6647 6931 753538065 753538371 6.850000e-70 276.0
33 TraesCS5A01G115000 chr3B 82.045 440 73 5 40 477 543036106 543035671 3.050000e-98 370.0
34 TraesCS5A01G115000 chr3B 88.800 125 12 2 6476 6598 112514402 112514526 1.200000e-32 152.0
35 TraesCS5A01G115000 chr3B 88.000 125 13 2 6476 6598 112951682 112951806 5.600000e-31 147.0
36 TraesCS5A01G115000 chr3B 89.691 97 9 1 6392 6488 155888845 155888940 9.440000e-24 122.0
37 TraesCS5A01G115000 chr3B 89.691 97 9 1 6392 6488 451184488 451184583 9.440000e-24 122.0
38 TraesCS5A01G115000 chr3B 93.182 44 2 1 957 999 543540873 543540830 5.800000e-06 63.9
39 TraesCS5A01G115000 chr2B 82.506 423 64 5 63 477 415387796 415387376 5.110000e-96 363.0
40 TraesCS5A01G115000 chr2B 92.857 98 6 1 1677 1774 74002923 74002827 2.610000e-29 141.0
41 TraesCS5A01G115000 chr2B 90.816 98 8 1 6392 6489 718486448 718486352 5.640000e-26 130.0
42 TraesCS5A01G115000 chr4D 84.615 364 44 5 7 366 331626865 331627220 1.110000e-92 351.0
43 TraesCS5A01G115000 chr1D 78.348 448 80 15 46 487 476840651 476840215 2.460000e-69 274.0
44 TraesCS5A01G115000 chr1B 78.038 469 80 18 3587 4040 376612548 376612088 2.460000e-69 274.0
45 TraesCS5A01G115000 chr1B 86.792 159 20 1 3170 3327 376612996 376612838 7.140000e-40 176.0
46 TraesCS5A01G115000 chr1B 89.831 118 11 1 6481 6598 520092016 520091900 4.330000e-32 150.0
47 TraesCS5A01G115000 chr1B 82.051 156 26 2 2050 2204 595441810 595441656 1.570000e-26 132.0
48 TraesCS5A01G115000 chr1B 86.957 69 9 0 3632 3700 376612380 376612312 2.070000e-10 78.7
49 TraesCS5A01G115000 chr7D 87.264 212 27 0 3916 4127 572419373 572419162 6.950000e-60 243.0
50 TraesCS5A01G115000 chr7D 93.878 98 6 0 1675 1772 79301699 79301796 1.560000e-31 148.0
51 TraesCS5A01G115000 chr7D 92.727 55 4 0 4011 4065 55191830 55191884 5.760000e-11 80.5
52 TraesCS5A01G115000 chr7A 91.525 118 10 0 6481 6598 421831 421714 5.560000e-36 163.0
53 TraesCS5A01G115000 chr7A 93.750 96 6 0 1672 1767 250689109 250689014 2.010000e-30 145.0
54 TraesCS5A01G115000 chr7B 90.164 122 11 1 6481 6602 414077302 414077422 2.590000e-34 158.0
55 TraesCS5A01G115000 chr7B 94.792 96 5 0 1674 1769 709252646 709252551 4.330000e-32 150.0
56 TraesCS5A01G115000 chr7B 93.548 93 6 0 6389 6481 516266986 516266894 9.370000e-29 139.0
57 TraesCS5A01G115000 chr7B 90.722 97 8 1 6392 6488 33278112 33278207 2.030000e-25 128.0
58 TraesCS5A01G115000 chr7B 89.691 97 9 1 6392 6488 632557771 632557676 9.440000e-24 122.0
59 TraesCS5A01G115000 chr2D 88.430 121 13 1 6481 6601 106348226 106348107 2.010000e-30 145.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G115000 chr5A 230066733 230073663 6930 False 12800.000000 12800 100.000000 1 6931 1 chr5A.!!$F1 6930
1 TraesCS5A01G115000 chr5B 196465703 196472306 6603 False 4786.000000 9287 89.037500 477 6931 2 chr5B.!!$F1 6454
2 TraesCS5A01G115000 chr5D 192264408 192270590 6182 False 2763.466667 4353 95.881333 219 6481 3 chr5D.!!$F3 6262
3 TraesCS5A01G115000 chr6D 153304159 153305207 1048 False 898.000000 898 82.955000 3170 4173 1 chr6D.!!$F1 1003
4 TraesCS5A01G115000 chr6D 366542100 366543551 1451 False 342.250000 407 86.923250 3172 4176 4 chr6D.!!$F2 1004
5 TraesCS5A01G115000 chr2A 688589504 688590041 537 True 372.000000 372 80.071000 3643 4185 1 chr2A.!!$R1 542

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
130 131 0.035056 ATGGGGACGAGGAGCTTTTG 60.035 55.000 0.00 0.00 0.00 2.44 F
133 134 0.036306 GGGACGAGGAGCTTTTGGAA 59.964 55.000 0.00 0.00 0.00 3.53 F
154 155 0.105039 CAGATAAGGACGCACTCCCC 59.895 60.000 0.00 0.00 40.53 4.81 F
1964 2028 0.674895 GCCCAGCACGTCAAAGAGAT 60.675 55.000 0.00 0.00 0.00 2.75 F
2703 2775 0.395311 CCATGGAGCTGCAATGGAGT 60.395 55.000 23.13 1.33 43.00 3.85 F
2791 2874 1.033746 CGGTGCTTCCATGGAGCATT 61.034 55.000 29.44 0.00 40.84 3.56 F
2842 2925 1.067283 AGTGACAACTGATGCTCCGAG 60.067 52.381 0.00 0.00 34.48 4.63 F
3987 4560 0.454196 AAGGTTTGTCGTGGTTGCAC 59.546 50.000 0.00 0.00 0.00 4.57 F
4983 6485 0.035439 CATGGGCACGGGAGTAAGTT 60.035 55.000 0.00 0.00 44.67 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2028 1.067416 GTATGGATGGCTCGCGACA 59.933 57.895 3.71 2.46 0.00 4.35 R
2003 2067 1.077357 GAGGGAGGAGAGAGACGCA 60.077 63.158 0.00 0.00 0.00 5.24 R
2203 2267 2.661566 CGTGTCGGCTCTTGCAGTG 61.662 63.158 0.00 0.00 41.91 3.66 R
2944 3027 0.251653 ACGCCTCACTGGACTCCTAA 60.252 55.000 0.00 0.00 38.35 2.69 R
3702 4245 0.744414 AGACAGCAACAACAGCACGT 60.744 50.000 0.00 0.00 0.00 4.49 R
3911 4484 1.091771 CGATTCATTGCAGCTCCGGT 61.092 55.000 0.00 0.00 0.00 5.28 R
4849 6351 1.881973 GCTGGAAGAAATGTGCACTGA 59.118 47.619 19.41 0.00 34.07 3.41 R
5441 6943 2.439104 GCCCCCACAGGTTTTGCAA 61.439 57.895 0.00 0.00 0.00 4.08 R
6706 8286 0.320421 TCCTGTGTTCCTTGTAGCGC 60.320 55.000 0.00 0.00 0.00 5.92 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
42 43 2.924635 GGCCTTGCCCTTGCCTTT 60.925 61.111 0.00 0.00 44.06 3.11
43 44 2.344872 GCCTTGCCCTTGCCTTTG 59.655 61.111 0.00 0.00 36.33 2.77
44 45 2.510551 GCCTTGCCCTTGCCTTTGT 61.511 57.895 0.00 0.00 36.33 2.83
45 46 1.667722 CCTTGCCCTTGCCTTTGTC 59.332 57.895 0.00 0.00 36.33 3.18
46 47 1.286880 CTTGCCCTTGCCTTTGTCG 59.713 57.895 0.00 0.00 36.33 4.35
47 48 2.146073 CTTGCCCTTGCCTTTGTCGG 62.146 60.000 0.00 0.00 36.33 4.79
48 49 2.282180 GCCCTTGCCTTTGTCGGA 60.282 61.111 0.00 0.00 0.00 4.55
49 50 2.335712 GCCCTTGCCTTTGTCGGAG 61.336 63.158 0.00 0.00 0.00 4.63
50 51 1.374947 CCCTTGCCTTTGTCGGAGA 59.625 57.895 0.00 0.00 0.00 3.71
51 52 0.250727 CCCTTGCCTTTGTCGGAGAA 60.251 55.000 0.00 0.00 39.69 2.87
52 53 1.160137 CCTTGCCTTTGTCGGAGAAG 58.840 55.000 0.00 0.00 39.69 2.85
53 54 1.270839 CCTTGCCTTTGTCGGAGAAGA 60.271 52.381 3.35 0.00 39.69 2.87
54 55 2.494059 CTTGCCTTTGTCGGAGAAGAA 58.506 47.619 3.35 0.00 39.69 2.52
55 56 2.631160 TGCCTTTGTCGGAGAAGAAA 57.369 45.000 3.35 0.00 39.69 2.52
56 57 2.494059 TGCCTTTGTCGGAGAAGAAAG 58.506 47.619 3.35 0.00 39.69 2.62
57 58 1.197949 GCCTTTGTCGGAGAAGAAAGC 59.802 52.381 3.35 0.00 39.69 3.51
58 59 1.807142 CCTTTGTCGGAGAAGAAAGCC 59.193 52.381 3.35 0.00 39.69 4.35
59 60 1.807142 CTTTGTCGGAGAAGAAAGCCC 59.193 52.381 0.00 0.00 39.69 5.19
60 61 0.762418 TTGTCGGAGAAGAAAGCCCA 59.238 50.000 0.00 0.00 39.69 5.36
61 62 0.984230 TGTCGGAGAAGAAAGCCCAT 59.016 50.000 0.00 0.00 39.69 4.00
62 63 1.066143 TGTCGGAGAAGAAAGCCCATC 60.066 52.381 0.00 0.00 39.69 3.51
63 64 0.541863 TCGGAGAAGAAAGCCCATCC 59.458 55.000 0.00 0.00 0.00 3.51
64 65 0.543749 CGGAGAAGAAAGCCCATCCT 59.456 55.000 0.00 0.00 0.00 3.24
65 66 1.065126 CGGAGAAGAAAGCCCATCCTT 60.065 52.381 0.00 0.00 0.00 3.36
66 67 2.373224 GGAGAAGAAAGCCCATCCTTG 58.627 52.381 0.00 0.00 0.00 3.61
67 68 1.747924 GAGAAGAAAGCCCATCCTTGC 59.252 52.381 0.00 0.00 0.00 4.01
68 69 0.453390 GAAGAAAGCCCATCCTTGCG 59.547 55.000 0.00 0.00 0.00 4.85
69 70 0.038166 AAGAAAGCCCATCCTTGCGA 59.962 50.000 0.00 0.00 0.00 5.10
70 71 0.257039 AGAAAGCCCATCCTTGCGAT 59.743 50.000 0.00 0.00 0.00 4.58
71 72 0.383231 GAAAGCCCATCCTTGCGATG 59.617 55.000 0.00 0.00 46.95 3.84
80 81 4.963878 CTTGCGATGGCTAGGGTT 57.036 55.556 0.15 0.00 38.20 4.11
81 82 2.397751 CTTGCGATGGCTAGGGTTG 58.602 57.895 0.15 0.00 38.20 3.77
82 83 1.718757 CTTGCGATGGCTAGGGTTGC 61.719 60.000 0.15 0.00 38.20 4.17
110 111 4.154347 GGAGCAGAGGGTGGCGAG 62.154 72.222 0.00 0.00 34.54 5.03
111 112 3.071206 GAGCAGAGGGTGGCGAGA 61.071 66.667 0.00 0.00 34.54 4.04
112 113 2.364842 AGCAGAGGGTGGCGAGAT 60.365 61.111 0.00 0.00 34.54 2.75
113 114 2.202987 GCAGAGGGTGGCGAGATG 60.203 66.667 0.00 0.00 0.00 2.90
114 115 2.503061 CAGAGGGTGGCGAGATGG 59.497 66.667 0.00 0.00 0.00 3.51
115 116 2.765807 AGAGGGTGGCGAGATGGG 60.766 66.667 0.00 0.00 0.00 4.00
116 117 3.866582 GAGGGTGGCGAGATGGGG 61.867 72.222 0.00 0.00 0.00 4.96
117 118 4.414956 AGGGTGGCGAGATGGGGA 62.415 66.667 0.00 0.00 0.00 4.81
118 119 4.176752 GGGTGGCGAGATGGGGAC 62.177 72.222 0.00 0.00 0.00 4.46
119 120 4.530857 GGTGGCGAGATGGGGACG 62.531 72.222 0.00 0.00 0.00 4.79
120 121 3.458163 GTGGCGAGATGGGGACGA 61.458 66.667 0.00 0.00 0.00 4.20
121 122 3.147595 TGGCGAGATGGGGACGAG 61.148 66.667 0.00 0.00 0.00 4.18
122 123 3.917760 GGCGAGATGGGGACGAGG 61.918 72.222 0.00 0.00 0.00 4.63
123 124 2.833582 GCGAGATGGGGACGAGGA 60.834 66.667 0.00 0.00 0.00 3.71
124 125 2.851071 GCGAGATGGGGACGAGGAG 61.851 68.421 0.00 0.00 0.00 3.69
125 126 2.851071 CGAGATGGGGACGAGGAGC 61.851 68.421 0.00 0.00 0.00 4.70
126 127 1.456705 GAGATGGGGACGAGGAGCT 60.457 63.158 0.00 0.00 0.00 4.09
127 128 1.002274 AGATGGGGACGAGGAGCTT 59.998 57.895 0.00 0.00 0.00 3.74
128 129 0.618968 AGATGGGGACGAGGAGCTTT 60.619 55.000 0.00 0.00 0.00 3.51
129 130 0.253327 GATGGGGACGAGGAGCTTTT 59.747 55.000 0.00 0.00 0.00 2.27
130 131 0.035056 ATGGGGACGAGGAGCTTTTG 60.035 55.000 0.00 0.00 0.00 2.44
131 132 1.377333 GGGGACGAGGAGCTTTTGG 60.377 63.158 0.00 0.00 0.00 3.28
132 133 1.677552 GGGACGAGGAGCTTTTGGA 59.322 57.895 0.00 0.00 0.00 3.53
133 134 0.036306 GGGACGAGGAGCTTTTGGAA 59.964 55.000 0.00 0.00 0.00 3.53
134 135 1.443802 GGACGAGGAGCTTTTGGAAG 58.556 55.000 0.00 0.00 35.92 3.46
146 147 4.606457 CTTTTGGAAGCAGATAAGGACG 57.394 45.455 0.00 0.00 0.00 4.79
147 148 2.024176 TTGGAAGCAGATAAGGACGC 57.976 50.000 0.00 0.00 0.00 5.19
148 149 0.901827 TGGAAGCAGATAAGGACGCA 59.098 50.000 0.00 0.00 0.00 5.24
149 150 1.291132 GGAAGCAGATAAGGACGCAC 58.709 55.000 0.00 0.00 0.00 5.34
150 151 1.134670 GGAAGCAGATAAGGACGCACT 60.135 52.381 0.00 0.00 0.00 4.40
151 152 2.197577 GAAGCAGATAAGGACGCACTC 58.802 52.381 0.00 0.00 0.00 3.51
152 153 0.461961 AGCAGATAAGGACGCACTCC 59.538 55.000 0.00 0.00 39.81 3.85
153 154 0.530870 GCAGATAAGGACGCACTCCC 60.531 60.000 0.00 0.00 40.53 4.30
154 155 0.105039 CAGATAAGGACGCACTCCCC 59.895 60.000 0.00 0.00 40.53 4.81
155 156 1.049289 AGATAAGGACGCACTCCCCC 61.049 60.000 0.00 0.00 40.53 5.40
174 175 3.959520 CGCACGCTCGGATTAAAAA 57.040 47.368 0.00 0.00 0.00 1.94
188 189 4.813346 AAAAAGGCCGATCACCGT 57.187 50.000 0.00 0.00 36.31 4.83
189 190 2.551644 AAAAAGGCCGATCACCGTC 58.448 52.632 0.00 0.00 36.31 4.79
190 191 1.296056 AAAAAGGCCGATCACCGTCG 61.296 55.000 0.00 0.00 41.13 5.12
191 192 2.444700 AAAAGGCCGATCACCGTCGT 62.445 55.000 0.00 0.00 39.89 4.34
192 193 2.444700 AAAGGCCGATCACCGTCGTT 62.445 55.000 0.00 0.00 39.89 3.85
193 194 3.186047 GGCCGATCACCGTCGTTG 61.186 66.667 0.00 0.00 39.89 4.10
194 195 2.126228 GCCGATCACCGTCGTTGA 60.126 61.111 0.00 0.00 39.89 3.18
195 196 2.442188 GCCGATCACCGTCGTTGAC 61.442 63.158 0.00 0.00 39.89 3.18
204 205 3.698463 GTCGTTGACGCGTGTGGG 61.698 66.667 20.70 3.11 39.60 4.61
233 234 3.001939 GTGGGCGGTCGTCATAAATTAAG 59.998 47.826 0.00 0.00 0.00 1.85
240 241 4.025979 GGTCGTCATAAATTAAGCTGACCG 60.026 45.833 0.00 0.00 35.66 4.79
255 256 4.060038 CCGCGGTAGTTGGACGGT 62.060 66.667 19.50 0.00 39.05 4.83
265 266 2.279810 TTGGACGGTCGCCAGATGA 61.280 57.895 1.43 0.00 36.64 2.92
269 270 2.105128 CGGTCGCCAGATGAGGAC 59.895 66.667 0.00 0.00 0.00 3.85
270 271 2.105128 GGTCGCCAGATGAGGACG 59.895 66.667 0.00 0.00 0.00 4.79
271 272 2.583593 GTCGCCAGATGAGGACGC 60.584 66.667 0.00 0.00 0.00 5.19
273 274 4.193334 CGCCAGATGAGGACGCGA 62.193 66.667 15.93 0.00 45.41 5.87
280 281 2.337749 GATGAGGACGCGACGGACAT 62.338 60.000 15.93 12.93 0.00 3.06
282 283 4.175489 AGGACGCGACGGACATCG 62.175 66.667 15.93 0.00 45.09 3.84
287 288 1.513373 CGCGACGGACATCGAGAAA 60.513 57.895 0.00 0.00 45.13 2.52
288 289 1.730593 CGCGACGGACATCGAGAAAC 61.731 60.000 0.00 0.00 45.13 2.78
293 294 2.695646 GACATCGAGAAACCGCGC 59.304 61.111 0.00 0.00 0.00 6.86
296 297 2.126228 ATCGAGAAACCGCGCGAA 60.126 55.556 34.63 5.97 42.92 4.70
337 338 1.663445 CCGACGCATTTTTACCGCAAA 60.663 47.619 0.00 0.00 0.00 3.68
338 339 2.246789 CGACGCATTTTTACCGCAAAT 58.753 42.857 0.00 0.00 0.00 2.32
339 340 2.659279 CGACGCATTTTTACCGCAAATT 59.341 40.909 0.00 0.00 0.00 1.82
340 341 3.120451 CGACGCATTTTTACCGCAAATTT 59.880 39.130 0.00 0.00 0.00 1.82
341 342 4.381983 GACGCATTTTTACCGCAAATTTG 58.618 39.130 14.03 14.03 0.00 2.32
342 343 3.185391 ACGCATTTTTACCGCAAATTTGG 59.815 39.130 19.47 6.66 0.00 3.28
343 344 3.424170 CGCATTTTTACCGCAAATTTGGG 60.424 43.478 24.24 24.24 40.42 4.12
344 345 3.500299 GCATTTTTACCGCAAATTTGGGT 59.500 39.130 27.43 26.18 39.24 4.51
345 346 4.377943 GCATTTTTACCGCAAATTTGGGTC 60.378 41.667 27.43 12.47 39.24 4.46
346 347 2.708386 TTTACCGCAAATTTGGGTCG 57.292 45.000 27.43 18.41 39.24 4.79
347 348 1.606903 TTACCGCAAATTTGGGTCGT 58.393 45.000 27.43 21.92 39.24 4.34
348 349 2.469274 TACCGCAAATTTGGGTCGTA 57.531 45.000 27.43 21.09 39.24 3.43
349 350 1.606903 ACCGCAAATTTGGGTCGTAA 58.393 45.000 27.43 0.00 39.24 3.18
356 357 4.490743 CAAATTTGGGTCGTAAATGGGTC 58.509 43.478 10.49 0.00 0.00 4.46
358 359 0.975135 TTGGGTCGTAAATGGGTCGA 59.025 50.000 0.00 0.00 0.00 4.20
362 363 1.514657 TCGTAAATGGGTCGACGCG 60.515 57.895 25.18 3.53 35.33 6.01
385 386 2.682856 ACACGAAGCAGACACATTTTGT 59.317 40.909 0.00 0.00 43.10 2.83
386 387 3.874543 ACACGAAGCAGACACATTTTGTA 59.125 39.130 0.00 0.00 39.17 2.41
390 391 7.075121 CACGAAGCAGACACATTTTGTAAATA 58.925 34.615 0.00 0.00 39.17 1.40
391 392 7.589587 CACGAAGCAGACACATTTTGTAAATAA 59.410 33.333 0.00 0.00 39.17 1.40
393 394 7.271223 CGAAGCAGACACATTTTGTAAATAAGG 59.729 37.037 0.00 0.00 39.17 2.69
400 401 1.166129 TTTGTAAATAAGGCGGCGCA 58.834 45.000 34.36 14.32 0.00 6.09
420 421 4.441792 GCATTGGGTCTTCACTTTTGTTT 58.558 39.130 0.00 0.00 0.00 2.83
424 425 3.829601 TGGGTCTTCACTTTTGTTTGTGT 59.170 39.130 0.00 0.00 35.82 3.72
435 436 3.428746 TTGTTTGTGTCGACCCAAATG 57.571 42.857 25.34 0.00 33.53 2.32
443 444 2.322081 CGACCCAAATGAACGGCGT 61.322 57.895 6.77 6.77 0.00 5.68
447 449 1.312371 CCCAAATGAACGGCGTGGAT 61.312 55.000 15.70 5.66 0.00 3.41
455 457 1.312371 AACGGCGTGGATGAAATGGG 61.312 55.000 15.70 0.00 0.00 4.00
482 484 2.607187 CGTCGGAGTTGCTCTTACATT 58.393 47.619 0.00 0.00 0.00 2.71
505 507 5.076182 TGTCAATGTGTATTTGTCCATGGT 58.924 37.500 12.58 0.00 0.00 3.55
563 568 4.306471 AGCGCGCGAGAGAGATCG 62.306 66.667 37.18 3.78 45.48 3.69
567 572 1.083015 GCGCGAGAGAGATCGAGAC 60.083 63.158 12.10 0.00 45.56 3.36
1095 1134 5.878406 ATAGTTCCATAGCTTGTAGTGCT 57.122 39.130 0.00 0.00 43.79 4.40
1104 1143 2.498078 AGCTTGTAGTGCTAGGGACTTC 59.502 50.000 0.00 0.00 41.75 3.01
1115 1154 3.879892 GCTAGGGACTTCCATGATGAAAC 59.120 47.826 0.00 0.00 41.75 2.78
1244 1284 3.005367 CCAGGTAGTTGCAATTTCGGTTT 59.995 43.478 0.59 0.00 0.00 3.27
1500 1540 2.421073 TCTTTTCATTCTGCATCGCTGG 59.579 45.455 0.00 0.00 0.00 4.85
1549 1589 7.829725 TGTCCTGATGGATTTTGATAAACTTG 58.170 34.615 0.00 0.00 45.29 3.16
1580 1620 5.189145 ACAGGATTTCTATTCCGTACTTGGT 59.811 40.000 0.00 0.00 38.36 3.67
1846 1893 5.941788 ACCTTCTTAGTCATCCTGTTGTTT 58.058 37.500 0.00 0.00 0.00 2.83
1928 1975 2.347114 CGTCCATCACCTGCCACA 59.653 61.111 0.00 0.00 0.00 4.17
1964 2028 0.674895 GCCCAGCACGTCAAAGAGAT 60.675 55.000 0.00 0.00 0.00 2.75
2082 2146 1.595929 AACCGCAACTGGTGTACCG 60.596 57.895 0.00 0.00 42.89 4.02
2122 2186 4.609018 ACCGTCGCTGCTGCAAGT 62.609 61.111 16.29 3.89 39.64 3.16
2203 2267 3.455469 GATGTGCAAGGCCAGCCC 61.455 66.667 16.44 6.72 36.58 5.19
2204 2268 4.304413 ATGTGCAAGGCCAGCCCA 62.304 61.111 16.44 12.17 36.58 5.36
2586 2655 4.388499 GGTGGTCATCGGTGCCGT 62.388 66.667 10.60 0.00 40.74 5.68
2637 2706 2.295885 GCTATTGAGCTGCAATGGAGT 58.704 47.619 19.16 0.00 45.33 3.85
2639 2708 1.471119 ATTGAGCTGCAATGGAGTGG 58.529 50.000 3.24 0.00 45.27 4.00
2703 2775 0.395311 CCATGGAGCTGCAATGGAGT 60.395 55.000 23.13 1.33 43.00 3.85
2791 2874 1.033746 CGGTGCTTCCATGGAGCATT 61.034 55.000 29.44 0.00 40.84 3.56
2831 2914 3.692257 AGCTGCTATGAAGTGACAACT 57.308 42.857 0.00 0.00 38.71 3.16
2842 2925 1.067283 AGTGACAACTGATGCTCCGAG 60.067 52.381 0.00 0.00 34.48 4.63
2944 3027 3.738982 TGCGGTACTGCATAGCATATTT 58.261 40.909 25.46 0.00 40.62 1.40
2954 3037 6.183361 ACTGCATAGCATATTTTAGGAGTCCA 60.183 38.462 12.86 0.00 38.13 4.02
3011 3094 1.674441 CTGTGAAGCATTGCATCGGAT 59.326 47.619 11.91 0.00 0.00 4.18
3053 3136 2.505982 CACGGGATCAGCCGGATT 59.494 61.111 5.05 0.00 40.07 3.01
3097 3180 6.856135 TCTTGTGATGATCAGATATGCAAC 57.144 37.500 0.09 0.00 0.00 4.17
3118 3201 6.546395 CAACCTTTTCATAGTCGATTTCCAG 58.454 40.000 0.00 0.00 0.00 3.86
3299 3657 1.680249 GGCAATCCTTCTTCTCCGCTT 60.680 52.381 0.00 0.00 0.00 4.68
3396 3754 1.645402 AACCACCACAGCTGGGAACT 61.645 55.000 20.22 0.00 42.74 3.01
3530 3888 1.674359 GTCAACACCCACACATGACA 58.326 50.000 0.00 0.00 40.02 3.58
3863 4436 2.882876 CCACTGGAGCTGCAATGC 59.117 61.111 11.54 0.00 0.00 3.56
3910 4483 1.075542 CCGAGTTGCAATGAAGCGTA 58.924 50.000 0.59 0.00 37.31 4.42
3911 4484 1.463056 CCGAGTTGCAATGAAGCGTAA 59.537 47.619 0.59 0.00 37.31 3.18
3987 4560 0.454196 AAGGTTTGTCGTGGTTGCAC 59.546 50.000 0.00 0.00 0.00 4.57
3997 4570 3.286751 GGTTGCACTGAAGCGGCA 61.287 61.111 1.45 0.00 37.31 5.69
4102 4712 2.665000 CAGATCGTGTGGCTGGGT 59.335 61.111 0.00 0.00 0.00 4.51
4113 4723 1.067295 TGGCTGGGTGAGTCTGAATT 58.933 50.000 0.00 0.00 0.00 2.17
4145 4755 1.079503 GAGCGGTTTAAGTCTGCCTG 58.920 55.000 9.06 0.00 37.86 4.85
4322 5822 7.441760 CCATTTTGTTTGGACTCAAATGAATGA 59.558 33.333 16.68 0.00 43.73 2.57
4460 5960 7.990886 AGACCTGTAGTTTATTTTCTGTGTTGA 59.009 33.333 0.00 0.00 0.00 3.18
4587 6087 7.981789 TCAGCTCCTTATAACACTTCTTGTATG 59.018 37.037 0.00 0.00 37.51 2.39
4622 6122 8.532186 TTCTCTTAGCTCTCTTACTGATTGAT 57.468 34.615 0.00 0.00 0.00 2.57
4685 6185 1.533625 TGTTTGTGCACTAGCCATCC 58.466 50.000 19.41 0.00 41.13 3.51
4970 6472 2.037847 AAGGGTTCTGGCATGGGC 59.962 61.111 0.00 0.00 40.13 5.36
4983 6485 0.035439 CATGGGCACGGGAGTAAGTT 60.035 55.000 0.00 0.00 44.67 2.66
4986 6488 1.698532 TGGGCACGGGAGTAAGTTTTA 59.301 47.619 0.00 0.00 44.67 1.52
5625 7127 6.208797 TGTTCTCTCGGATTCAGTTCTTAAGA 59.791 38.462 0.00 0.00 0.00 2.10
5666 7168 6.711277 TCTCTACACATGCAAGGTTTCTTAT 58.289 36.000 0.00 0.00 0.00 1.73
5911 7413 2.348998 CCTCAACAAGGCCGAGCT 59.651 61.111 0.00 0.00 38.67 4.09
6002 7504 0.162294 GCAAATTGCAGCGACAAAGC 59.838 50.000 13.73 1.19 44.26 3.51
6385 7888 6.985188 TTAAGTAGTCCTTTGCAGCTATTG 57.015 37.500 0.00 0.00 34.46 1.90
6400 7903 3.390639 AGCTATTGCAATCTACTGCCTCT 59.609 43.478 16.86 0.00 41.90 3.69
6510 8045 9.619316 CAAATCCAACGATATAACTTTTGTTGA 57.381 29.630 4.60 0.00 43.41 3.18
6588 8168 1.648504 GGAACCGATAAACCAGGACG 58.351 55.000 0.00 0.00 0.00 4.79
6591 8171 1.492764 ACCGATAAACCAGGACGGAT 58.507 50.000 0.00 0.00 45.31 4.18
6592 8172 1.138266 ACCGATAAACCAGGACGGATG 59.862 52.381 0.00 0.00 45.31 3.51
6603 8183 7.642082 AACCAGGACGGATGTAGTATATATC 57.358 40.000 0.00 0.00 38.33 1.63
6604 8184 6.971340 ACCAGGACGGATGTAGTATATATCT 58.029 40.000 0.00 0.00 38.97 1.98
6605 8185 8.098963 ACCAGGACGGATGTAGTATATATCTA 57.901 38.462 0.00 0.00 38.97 1.98
6606 8186 8.212312 ACCAGGACGGATGTAGTATATATCTAG 58.788 40.741 0.00 0.00 38.97 2.43
6607 8187 7.173562 CCAGGACGGATGTAGTATATATCTAGC 59.826 44.444 0.00 0.00 38.97 3.42
6608 8188 7.934665 CAGGACGGATGTAGTATATATCTAGCT 59.065 40.741 0.00 0.00 38.97 3.32
6609 8189 8.496088 AGGACGGATGTAGTATATATCTAGCTT 58.504 37.037 0.00 0.00 38.97 3.74
6610 8190 8.776470 GGACGGATGTAGTATATATCTAGCTTC 58.224 40.741 0.00 0.00 38.97 3.86
6611 8191 9.550406 GACGGATGTAGTATATATCTAGCTTCT 57.450 37.037 0.00 0.00 38.97 2.85
6612 8192 9.550406 ACGGATGTAGTATATATCTAGCTTCTC 57.450 37.037 0.00 0.00 38.97 2.87
6613 8193 9.772973 CGGATGTAGTATATATCTAGCTTCTCT 57.227 37.037 0.00 0.00 38.97 3.10
6632 8212 4.287067 TCTCTTGCCATCTAGGTGAACTTT 59.713 41.667 3.99 0.00 40.61 2.66
6643 8223 5.964477 TCTAGGTGAACTTTGGGACATATCT 59.036 40.000 0.00 0.00 39.30 1.98
6645 8225 6.240549 AGGTGAACTTTGGGACATATCTAG 57.759 41.667 0.00 0.00 39.30 2.43
6646 8226 4.816925 GGTGAACTTTGGGACATATCTAGC 59.183 45.833 0.00 0.00 39.30 3.42
6697 8277 8.178964 TGTATAAATTAAACACGAGCATTGTCC 58.821 33.333 0.00 0.00 0.00 4.02
6706 8286 1.938577 CGAGCATTGTCCTTCCTGATG 59.061 52.381 0.00 0.00 0.00 3.07
6774 8383 1.252904 ATGTGCGGGCTCATTTGCTT 61.253 50.000 2.60 0.00 0.00 3.91
6775 8384 1.153958 GTGCGGGCTCATTTGCTTC 60.154 57.895 0.00 0.00 0.00 3.86
6800 8409 5.820947 TCTCTTGGTAAACTGAAGTTGGAAC 59.179 40.000 0.00 0.00 38.44 3.62
6801 8410 5.751586 TCTTGGTAAACTGAAGTTGGAACT 58.248 37.500 0.00 0.00 42.04 3.01
6843 8452 3.373439 CAGTAAGCTCCAGAACTTCATGC 59.627 47.826 0.00 0.00 0.00 4.06
6865 8474 1.592081 GTGTCGCTGCAATCTCTGATC 59.408 52.381 0.00 0.00 0.00 2.92
6866 8475 1.205417 TGTCGCTGCAATCTCTGATCA 59.795 47.619 0.00 0.00 0.00 2.92
6876 8485 7.624554 GCTGCAATCTCTGATCAATCATATGAC 60.625 40.741 7.78 0.00 36.02 3.06
6922 8531 6.762702 TCTGCAAAGCATCAGATTCAATAA 57.237 33.333 0.00 0.00 38.13 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.344872 CAAAGGCAAGGGCAAGGC 59.655 61.111 0.00 0.00 43.71 4.35
27 28 1.667722 GACAAAGGCAAGGGCAAGG 59.332 57.895 0.00 0.00 43.71 3.61
28 29 1.286880 CGACAAAGGCAAGGGCAAG 59.713 57.895 0.00 0.00 43.71 4.01
29 30 2.199652 CCGACAAAGGCAAGGGCAA 61.200 57.895 0.00 0.00 43.71 4.52
30 31 2.597217 CCGACAAAGGCAAGGGCA 60.597 61.111 0.00 0.00 43.71 5.36
31 32 2.282180 TCCGACAAAGGCAAGGGC 60.282 61.111 0.00 0.00 40.13 5.19
32 33 0.250727 TTCTCCGACAAAGGCAAGGG 60.251 55.000 0.00 0.00 0.00 3.95
33 34 1.160137 CTTCTCCGACAAAGGCAAGG 58.840 55.000 0.00 0.00 0.00 3.61
34 35 2.169832 TCTTCTCCGACAAAGGCAAG 57.830 50.000 0.00 0.00 0.00 4.01
35 36 2.631160 TTCTTCTCCGACAAAGGCAA 57.369 45.000 0.00 0.00 0.00 4.52
36 37 2.494059 CTTTCTTCTCCGACAAAGGCA 58.506 47.619 0.00 0.00 0.00 4.75
37 38 1.197949 GCTTTCTTCTCCGACAAAGGC 59.802 52.381 0.00 0.00 0.00 4.35
38 39 1.807142 GGCTTTCTTCTCCGACAAAGG 59.193 52.381 0.00 0.00 0.00 3.11
39 40 1.807142 GGGCTTTCTTCTCCGACAAAG 59.193 52.381 0.00 0.00 0.00 2.77
40 41 1.142060 TGGGCTTTCTTCTCCGACAAA 59.858 47.619 0.00 0.00 0.00 2.83
41 42 0.762418 TGGGCTTTCTTCTCCGACAA 59.238 50.000 0.00 0.00 0.00 3.18
42 43 0.984230 ATGGGCTTTCTTCTCCGACA 59.016 50.000 0.00 0.00 0.00 4.35
43 44 1.657822 GATGGGCTTTCTTCTCCGAC 58.342 55.000 0.00 0.00 0.00 4.79
44 45 0.541863 GGATGGGCTTTCTTCTCCGA 59.458 55.000 0.00 0.00 0.00 4.55
45 46 0.543749 AGGATGGGCTTTCTTCTCCG 59.456 55.000 0.00 0.00 0.00 4.63
46 47 2.373224 CAAGGATGGGCTTTCTTCTCC 58.627 52.381 0.00 0.00 0.00 3.71
47 48 1.747924 GCAAGGATGGGCTTTCTTCTC 59.252 52.381 0.00 0.00 0.00 2.87
48 49 1.844687 GCAAGGATGGGCTTTCTTCT 58.155 50.000 0.00 0.00 0.00 2.85
49 50 0.453390 CGCAAGGATGGGCTTTCTTC 59.547 55.000 0.00 0.00 32.32 2.87
50 51 0.038166 TCGCAAGGATGGGCTTTCTT 59.962 50.000 0.00 0.00 39.24 2.52
51 52 0.257039 ATCGCAAGGATGGGCTTTCT 59.743 50.000 0.00 0.00 39.24 2.52
52 53 2.799176 ATCGCAAGGATGGGCTTTC 58.201 52.632 0.00 0.00 39.24 2.62
60 61 1.056700 ACCCTAGCCATCGCAAGGAT 61.057 55.000 0.00 0.00 37.52 3.24
61 62 1.271840 AACCCTAGCCATCGCAAGGA 61.272 55.000 0.00 0.00 37.52 3.36
62 63 1.097547 CAACCCTAGCCATCGCAAGG 61.098 60.000 0.00 0.00 37.52 3.61
63 64 1.718757 GCAACCCTAGCCATCGCAAG 61.719 60.000 0.00 0.00 37.52 4.01
64 65 1.748879 GCAACCCTAGCCATCGCAA 60.749 57.895 0.00 0.00 37.52 4.85
65 66 2.124736 GCAACCCTAGCCATCGCA 60.125 61.111 0.00 0.00 37.52 5.10
93 94 4.154347 CTCGCCACCCTCTGCTCC 62.154 72.222 0.00 0.00 0.00 4.70
94 95 2.430610 ATCTCGCCACCCTCTGCTC 61.431 63.158 0.00 0.00 0.00 4.26
95 96 2.364842 ATCTCGCCACCCTCTGCT 60.365 61.111 0.00 0.00 0.00 4.24
96 97 2.202987 CATCTCGCCACCCTCTGC 60.203 66.667 0.00 0.00 0.00 4.26
97 98 2.503061 CCATCTCGCCACCCTCTG 59.497 66.667 0.00 0.00 0.00 3.35
98 99 2.765807 CCCATCTCGCCACCCTCT 60.766 66.667 0.00 0.00 0.00 3.69
99 100 3.866582 CCCCATCTCGCCACCCTC 61.867 72.222 0.00 0.00 0.00 4.30
100 101 4.414956 TCCCCATCTCGCCACCCT 62.415 66.667 0.00 0.00 0.00 4.34
101 102 4.176752 GTCCCCATCTCGCCACCC 62.177 72.222 0.00 0.00 0.00 4.61
102 103 4.530857 CGTCCCCATCTCGCCACC 62.531 72.222 0.00 0.00 0.00 4.61
103 104 3.432051 CTCGTCCCCATCTCGCCAC 62.432 68.421 0.00 0.00 0.00 5.01
104 105 3.147595 CTCGTCCCCATCTCGCCA 61.148 66.667 0.00 0.00 0.00 5.69
105 106 3.917760 CCTCGTCCCCATCTCGCC 61.918 72.222 0.00 0.00 0.00 5.54
106 107 2.833582 TCCTCGTCCCCATCTCGC 60.834 66.667 0.00 0.00 0.00 5.03
107 108 2.851071 GCTCCTCGTCCCCATCTCG 61.851 68.421 0.00 0.00 0.00 4.04
108 109 1.045911 AAGCTCCTCGTCCCCATCTC 61.046 60.000 0.00 0.00 0.00 2.75
109 110 0.618968 AAAGCTCCTCGTCCCCATCT 60.619 55.000 0.00 0.00 0.00 2.90
110 111 0.253327 AAAAGCTCCTCGTCCCCATC 59.747 55.000 0.00 0.00 0.00 3.51
111 112 0.035056 CAAAAGCTCCTCGTCCCCAT 60.035 55.000 0.00 0.00 0.00 4.00
112 113 1.374947 CAAAAGCTCCTCGTCCCCA 59.625 57.895 0.00 0.00 0.00 4.96
113 114 1.377333 CCAAAAGCTCCTCGTCCCC 60.377 63.158 0.00 0.00 0.00 4.81
114 115 0.036306 TTCCAAAAGCTCCTCGTCCC 59.964 55.000 0.00 0.00 0.00 4.46
115 116 1.443802 CTTCCAAAAGCTCCTCGTCC 58.556 55.000 0.00 0.00 0.00 4.79
125 126 3.181506 GCGTCCTTATCTGCTTCCAAAAG 60.182 47.826 0.00 0.00 35.47 2.27
126 127 2.747446 GCGTCCTTATCTGCTTCCAAAA 59.253 45.455 0.00 0.00 0.00 2.44
127 128 2.290008 TGCGTCCTTATCTGCTTCCAAA 60.290 45.455 0.00 0.00 0.00 3.28
128 129 1.277842 TGCGTCCTTATCTGCTTCCAA 59.722 47.619 0.00 0.00 0.00 3.53
129 130 0.901827 TGCGTCCTTATCTGCTTCCA 59.098 50.000 0.00 0.00 0.00 3.53
130 131 1.134670 AGTGCGTCCTTATCTGCTTCC 60.135 52.381 0.00 0.00 0.00 3.46
131 132 2.197577 GAGTGCGTCCTTATCTGCTTC 58.802 52.381 0.00 0.00 0.00 3.86
132 133 1.134670 GGAGTGCGTCCTTATCTGCTT 60.135 52.381 0.00 0.00 42.99 3.91
133 134 0.461961 GGAGTGCGTCCTTATCTGCT 59.538 55.000 0.00 0.00 42.99 4.24
134 135 0.530870 GGGAGTGCGTCCTTATCTGC 60.531 60.000 4.99 0.00 46.06 4.26
135 136 0.105039 GGGGAGTGCGTCCTTATCTG 59.895 60.000 4.99 0.00 46.06 2.90
136 137 1.049289 GGGGGAGTGCGTCCTTATCT 61.049 60.000 4.99 0.00 46.06 1.98
137 138 1.446366 GGGGGAGTGCGTCCTTATC 59.554 63.158 4.99 0.00 46.06 1.75
138 139 3.643398 GGGGGAGTGCGTCCTTAT 58.357 61.111 4.99 0.00 46.06 1.73
156 157 3.959520 TTTTTAATCCGAGCGTGCG 57.040 47.368 0.00 0.00 0.00 5.34
171 172 1.296056 CGACGGTGATCGGCCTTTTT 61.296 55.000 0.00 0.00 45.97 1.94
172 173 1.740296 CGACGGTGATCGGCCTTTT 60.740 57.895 0.00 0.00 45.97 2.27
173 174 2.125673 CGACGGTGATCGGCCTTT 60.126 61.111 0.00 0.00 45.97 3.11
174 175 2.939261 AACGACGGTGATCGGCCTT 61.939 57.895 0.00 0.00 45.97 4.35
175 176 3.379445 AACGACGGTGATCGGCCT 61.379 61.111 0.00 0.00 45.97 5.19
176 177 3.186047 CAACGACGGTGATCGGCC 61.186 66.667 7.21 0.00 45.97 6.13
177 178 2.126228 TCAACGACGGTGATCGGC 60.126 61.111 12.49 0.00 46.56 5.54
178 179 3.763319 GTCAACGACGGTGATCGG 58.237 61.111 20.07 0.00 46.56 4.18
187 188 3.698463 CCCACACGCGTCAACGAC 61.698 66.667 9.86 0.00 43.02 4.34
208 209 1.952102 TTATGACGACCGCCCACCTC 61.952 60.000 0.00 0.00 0.00 3.85
209 210 1.546589 TTTATGACGACCGCCCACCT 61.547 55.000 0.00 0.00 0.00 4.00
210 211 0.463116 ATTTATGACGACCGCCCACC 60.463 55.000 0.00 0.00 0.00 4.61
211 212 1.375551 AATTTATGACGACCGCCCAC 58.624 50.000 0.00 0.00 0.00 4.61
212 213 2.983907 TAATTTATGACGACCGCCCA 57.016 45.000 0.00 0.00 0.00 5.36
213 214 2.032290 GCTTAATTTATGACGACCGCCC 60.032 50.000 0.00 0.00 0.00 6.13
214 215 2.870411 AGCTTAATTTATGACGACCGCC 59.130 45.455 0.00 0.00 0.00 6.13
215 216 3.554324 TCAGCTTAATTTATGACGACCGC 59.446 43.478 0.00 0.00 0.00 5.68
216 217 4.025979 GGTCAGCTTAATTTATGACGACCG 60.026 45.833 11.46 0.00 42.34 4.79
217 218 4.025979 CGGTCAGCTTAATTTATGACGACC 60.026 45.833 14.35 14.35 42.34 4.79
233 234 2.813908 CCAACTACCGCGGTCAGC 60.814 66.667 38.01 0.00 43.95 4.26
240 241 2.505557 CGACCGTCCAACTACCGC 60.506 66.667 0.00 0.00 0.00 5.68
265 266 4.175489 CGATGTCCGTCGCGTCCT 62.175 66.667 5.77 0.00 34.56 3.85
269 270 1.513373 TTTCTCGATGTCCGTCGCG 60.513 57.895 0.00 0.00 41.22 5.87
270 271 1.411493 GGTTTCTCGATGTCCGTCGC 61.411 60.000 4.07 0.00 41.22 5.19
271 272 1.132199 CGGTTTCTCGATGTCCGTCG 61.132 60.000 2.54 2.54 42.74 5.12
273 274 1.445582 GCGGTTTCTCGATGTCCGT 60.446 57.895 15.75 0.00 42.62 4.69
280 281 2.803670 CTTCGCGCGGTTTCTCGA 60.804 61.111 31.69 4.34 0.00 4.04
328 329 1.606903 ACGACCCAAATTTGCGGTAA 58.393 45.000 23.23 0.00 33.69 2.85
330 331 1.606903 TTACGACCCAAATTTGCGGT 58.393 45.000 23.34 23.34 35.40 5.68
337 338 2.027007 TCGACCCATTTACGACCCAAAT 60.027 45.455 0.00 0.00 0.00 2.32
338 339 1.347050 TCGACCCATTTACGACCCAAA 59.653 47.619 0.00 0.00 0.00 3.28
339 340 0.975135 TCGACCCATTTACGACCCAA 59.025 50.000 0.00 0.00 0.00 4.12
340 341 0.247185 GTCGACCCATTTACGACCCA 59.753 55.000 3.51 0.00 46.66 4.51
341 342 3.055144 GTCGACCCATTTACGACCC 57.945 57.895 3.51 0.00 46.66 4.46
344 345 1.514657 CGCGTCGACCCATTTACGA 60.515 57.895 10.58 0.00 37.53 3.43
345 346 2.510594 CCGCGTCGACCCATTTACG 61.511 63.158 10.58 0.00 38.34 3.18
346 347 1.153784 TCCGCGTCGACCCATTTAC 60.154 57.895 10.58 0.00 0.00 2.01
347 348 1.153784 GTCCGCGTCGACCCATTTA 60.154 57.895 10.58 0.00 0.00 1.40
348 349 2.433664 GTCCGCGTCGACCCATTT 60.434 61.111 10.58 0.00 0.00 2.32
349 350 3.687102 TGTCCGCGTCGACCCATT 61.687 61.111 10.58 0.00 31.35 3.16
358 359 3.973516 TCTGCTTCGTGTCCGCGT 61.974 61.111 4.92 0.00 0.00 6.01
362 363 1.512926 AATGTGTCTGCTTCGTGTCC 58.487 50.000 0.00 0.00 0.00 4.02
368 369 7.062255 GCCTTATTTACAAAATGTGTCTGCTTC 59.938 37.037 0.00 0.00 41.98 3.86
385 386 0.665835 CCAATGCGCCGCCTTATTTA 59.334 50.000 6.63 0.00 0.00 1.40
386 387 1.437160 CCAATGCGCCGCCTTATTT 59.563 52.632 6.63 0.00 0.00 1.40
393 394 4.179579 GAAGACCCAATGCGCCGC 62.180 66.667 4.18 0.00 0.00 6.53
400 401 5.046663 ACACAAACAAAAGTGAAGACCCAAT 60.047 36.000 0.00 0.00 39.03 3.16
420 421 1.222300 CGTTCATTTGGGTCGACACA 58.778 50.000 18.52 18.52 0.00 3.72
424 425 2.030401 CGCCGTTCATTTGGGTCGA 61.030 57.895 0.00 0.00 0.00 4.20
435 436 0.098728 CCATTTCATCCACGCCGTTC 59.901 55.000 0.00 0.00 0.00 3.95
443 444 0.971959 GCAGGTGCCCATTTCATCCA 60.972 55.000 0.00 0.00 34.31 3.41
447 449 1.971167 GACGCAGGTGCCCATTTCA 60.971 57.895 0.00 0.00 37.91 2.69
455 457 3.414700 CAACTCCGACGCAGGTGC 61.415 66.667 0.00 0.00 37.78 5.01
461 463 0.388134 TGTAAGAGCAACTCCGACGC 60.388 55.000 0.00 0.00 0.00 5.19
482 484 5.076182 ACCATGGACAAATACACATTGACA 58.924 37.500 21.47 0.00 0.00 3.58
563 568 2.579249 CAGCTCGCGCTCTGTCTC 60.579 66.667 16.03 0.00 45.15 3.36
916 955 1.078497 CCGGAGCAGCATACCACAA 60.078 57.895 0.00 0.00 0.00 3.33
1095 1134 5.044919 ACATGTTTCATCATGGAAGTCCCTA 60.045 40.000 10.64 0.00 46.39 3.53
1104 1143 4.787260 TTGACCACATGTTTCATCATGG 57.213 40.909 7.58 1.04 46.39 3.66
1244 1284 6.671190 CACATCTTTAATTGTTCAGCTGACA 58.329 36.000 18.03 14.92 0.00 3.58
1500 1540 9.204570 ACATCAAGTACTTACAGACAATAACAC 57.795 33.333 8.04 0.00 0.00 3.32
1549 1589 5.066505 ACGGAATAGAAATCCTGTCAATTGC 59.933 40.000 0.00 0.00 34.66 3.56
1580 1620 6.531594 CAGATTTACTAGCATTTCTCGACACA 59.468 38.462 0.00 0.00 0.00 3.72
1928 1975 1.759299 GCCACATCCACATGGGCAT 60.759 57.895 0.00 0.00 42.06 4.40
1964 2028 1.067416 GTATGGATGGCTCGCGACA 59.933 57.895 3.71 2.46 0.00 4.35
2003 2067 1.077357 GAGGGAGGAGAGAGACGCA 60.077 63.158 0.00 0.00 0.00 5.24
2203 2267 2.661566 CGTGTCGGCTCTTGCAGTG 61.662 63.158 0.00 0.00 41.91 3.66
2204 2268 2.356313 CGTGTCGGCTCTTGCAGT 60.356 61.111 0.00 0.00 41.91 4.40
2586 2655 3.770040 CCCGGTGATGCTCCGTCA 61.770 66.667 0.00 0.00 45.63 4.35
2720 2792 3.470433 TGCTCTGTGGCAGCACTA 58.530 55.556 0.00 0.00 42.09 2.74
2762 2845 1.440145 GGAAGCACCGATAGCCAAGC 61.440 60.000 0.00 0.00 0.00 4.01
2791 2874 2.730524 TGCCATAGCAGCAGCGGTA 61.731 57.895 0.00 0.00 46.52 4.02
2831 2914 1.617018 CCCTGTTCCTCGGAGCATCA 61.617 60.000 2.89 0.00 34.97 3.07
2944 3027 0.251653 ACGCCTCACTGGACTCCTAA 60.252 55.000 0.00 0.00 38.35 2.69
2954 3037 2.591715 GGCAACACACGCCTCACT 60.592 61.111 0.00 0.00 46.56 3.41
3053 3136 4.229582 AGAATTTGGTGGGTGCTAGGAATA 59.770 41.667 0.00 0.00 0.00 1.75
3097 3180 4.035675 GGCTGGAAATCGACTATGAAAAGG 59.964 45.833 0.00 0.00 0.00 3.11
3118 3201 9.574458 GACTAAAAGAGAATTAAAATTGGAGGC 57.426 33.333 0.00 0.00 0.00 4.70
3189 3272 6.887002 GGTTTAAGTGAGGAAGAAATCATCCT 59.113 38.462 6.90 6.90 45.77 3.24
3299 3657 3.884037 AAGGGGAAAAGAGAGAAAGCA 57.116 42.857 0.00 0.00 0.00 3.91
3591 4061 1.208052 AGCTCATAGCAACGACACCAT 59.792 47.619 1.22 0.00 45.56 3.55
3702 4245 0.744414 AGACAGCAACAACAGCACGT 60.744 50.000 0.00 0.00 0.00 4.49
3822 4367 2.437180 CGAGCTCCATGGCAGCAA 60.437 61.111 27.31 4.71 39.56 3.91
3910 4483 1.098050 GATTCATTGCAGCTCCGGTT 58.902 50.000 0.00 0.00 0.00 4.44
3911 4484 1.091771 CGATTCATTGCAGCTCCGGT 61.092 55.000 0.00 0.00 0.00 5.28
3945 4518 2.270205 CCCTCTGCGGTGCTTCAT 59.730 61.111 0.00 0.00 0.00 2.57
3997 4570 2.117156 GCTCCATTGCAGCGTCCAT 61.117 57.895 0.00 0.00 0.00 3.41
4043 4653 2.829003 CAGCTCCCATGGCAGCAG 60.829 66.667 29.29 18.33 38.18 4.24
4061 4671 4.034258 CAAGCCAGCACCACGCAG 62.034 66.667 0.00 0.00 46.13 5.18
4102 4712 2.632996 AGAACCGTCCAATTCAGACTCA 59.367 45.455 4.17 0.00 31.83 3.41
4113 4723 2.050350 CCGCTCCTAGAACCGTCCA 61.050 63.158 0.00 0.00 0.00 4.02
4293 5793 3.451141 TGAGTCCAAACAAAATGGCAC 57.549 42.857 0.00 0.00 37.88 5.01
4322 5822 9.230122 TGACATAACAACATCATAAACTCATGT 57.770 29.630 0.00 0.00 31.90 3.21
4587 6087 8.716646 AAGAGAGCTAAGAGAAAATAAGAAGC 57.283 34.615 0.00 0.00 0.00 3.86
4617 6117 5.991861 AGATGAGAAGAGCACAAGATCAAT 58.008 37.500 0.00 0.00 30.99 2.57
4622 6122 4.965814 ACAAAGATGAGAAGAGCACAAGA 58.034 39.130 0.00 0.00 0.00 3.02
4685 6185 5.504337 GCTCTTTGATCAAGCTAGATGCAAG 60.504 44.000 8.41 0.00 45.94 4.01
4849 6351 1.881973 GCTGGAAGAAATGTGCACTGA 59.118 47.619 19.41 0.00 34.07 3.41
4970 6472 8.866956 CACTATTAAGTAAAACTTACTCCCGTG 58.133 37.037 0.00 1.41 40.12 4.94
4983 6485 9.485206 GTGAACTGGAGAACACTATTAAGTAAA 57.515 33.333 0.00 0.00 33.48 2.01
4986 6488 7.062749 TGTGAACTGGAGAACACTATTAAGT 57.937 36.000 0.00 0.00 35.91 2.24
5441 6943 2.439104 GCCCCCACAGGTTTTGCAA 61.439 57.895 0.00 0.00 0.00 4.08
5625 7127 5.485353 TGTAGAGAATGTTTGTCCCATCTCT 59.515 40.000 8.06 8.06 34.36 3.10
5911 7413 5.189736 AGTTATCATCTCCTACTGTTTGCCA 59.810 40.000 0.00 0.00 0.00 4.92
6385 7888 1.484240 AGGACAGAGGCAGTAGATTGC 59.516 52.381 0.00 0.00 43.34 3.56
6395 7898 2.290960 ACCAATAAACCAGGACAGAGGC 60.291 50.000 0.00 0.00 0.00 4.70
6490 8025 9.715123 TGCATATCAACAAAAGTTATATCGTTG 57.285 29.630 0.00 0.00 36.05 4.10
6566 8101 2.026542 GTCCTGGTTTATCGGTTCCCTT 60.027 50.000 0.00 0.00 0.00 3.95
6571 8106 1.269012 TCCGTCCTGGTTTATCGGTT 58.731 50.000 0.00 0.00 41.58 4.44
6591 8171 9.179909 GGCAAGAGAAGCTAGATATATACTACA 57.820 37.037 0.00 0.00 0.00 2.74
6592 8172 9.179909 TGGCAAGAGAAGCTAGATATATACTAC 57.820 37.037 0.00 0.00 0.00 2.73
6603 8183 3.640967 ACCTAGATGGCAAGAGAAGCTAG 59.359 47.826 0.00 0.00 40.22 3.42
6604 8184 3.386078 CACCTAGATGGCAAGAGAAGCTA 59.614 47.826 0.00 0.00 40.22 3.32
6605 8185 2.170187 CACCTAGATGGCAAGAGAAGCT 59.830 50.000 0.00 0.00 40.22 3.74
6606 8186 2.169352 TCACCTAGATGGCAAGAGAAGC 59.831 50.000 0.00 0.00 40.22 3.86
6607 8187 4.081198 AGTTCACCTAGATGGCAAGAGAAG 60.081 45.833 0.00 0.00 40.22 2.85
6608 8188 3.840666 AGTTCACCTAGATGGCAAGAGAA 59.159 43.478 0.00 0.00 40.22 2.87
6609 8189 3.445008 AGTTCACCTAGATGGCAAGAGA 58.555 45.455 0.00 0.00 40.22 3.10
6610 8190 3.902881 AGTTCACCTAGATGGCAAGAG 57.097 47.619 0.00 0.00 40.22 2.85
6611 8191 4.326826 CAAAGTTCACCTAGATGGCAAGA 58.673 43.478 0.00 0.00 40.22 3.02
6612 8192 3.441572 CCAAAGTTCACCTAGATGGCAAG 59.558 47.826 0.00 0.00 40.22 4.01
6613 8193 3.420893 CCAAAGTTCACCTAGATGGCAA 58.579 45.455 0.00 0.00 40.22 4.52
6697 8277 1.134699 TCCTTGTAGCGCATCAGGAAG 60.135 52.381 11.47 2.41 0.00 3.46
6706 8286 0.320421 TCCTGTGTTCCTTGTAGCGC 60.320 55.000 0.00 0.00 0.00 5.92
6758 8367 1.303561 AGAAGCAAATGAGCCCGCA 60.304 52.632 0.00 0.00 34.23 5.69
6762 8371 2.422832 CCAAGAGAGAAGCAAATGAGCC 59.577 50.000 0.00 0.00 34.23 4.70
6774 8383 5.365605 TCCAACTTCAGTTTACCAAGAGAGA 59.634 40.000 0.00 0.00 35.83 3.10
6775 8384 5.611374 TCCAACTTCAGTTTACCAAGAGAG 58.389 41.667 0.00 0.00 35.83 3.20
6803 8412 8.268065 GCTTACTGCTAACATGGAACACTTCC 62.268 46.154 0.00 0.00 43.68 3.46
6804 8413 5.390991 GCTTACTGCTAACATGGAACACTTC 60.391 44.000 0.00 0.00 39.42 3.01
6805 8414 4.455877 GCTTACTGCTAACATGGAACACTT 59.544 41.667 0.00 0.00 39.42 3.16
6806 8415 4.003648 GCTTACTGCTAACATGGAACACT 58.996 43.478 0.00 0.00 39.42 3.55
6830 8439 1.462283 CGACACTGCATGAAGTTCTGG 59.538 52.381 2.59 0.00 0.00 3.86
6832 8441 1.151668 GCGACACTGCATGAAGTTCT 58.848 50.000 2.59 0.00 34.15 3.01
6865 8474 8.991243 ATGTGGAAAACAAAGTCATATGATTG 57.009 30.769 9.02 12.49 43.61 2.67
6876 8485 9.778993 CAGATAGTGAATATGTGGAAAACAAAG 57.221 33.333 0.00 0.00 43.61 2.77
6884 8493 5.528690 GCTTTGCAGATAGTGAATATGTGGA 59.471 40.000 0.00 0.00 36.02 4.02


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

AutoCloner maintained by Alex Coulton.