Multiple sequence alignment - TraesCS1B01G222700

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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 TraesCS1B01G222700 chr1B 100.000 3634 0 0 1 3634 400315224 400311591 0.000000e+00 6711
1 TraesCS1B01G222700 chr1B 93.082 159 9 1 1 159 599228223 599228067 7.850000e-57 231
2 TraesCS1B01G222700 chr1B 91.304 115 10 0 1295 1409 505626346 505626460 1.350000e-34 158
3 TraesCS1B01G222700 chr1D 95.335 2358 65 22 162 2501 297539740 297537410 0.000000e+00 3703
4 TraesCS1B01G222700 chr1D 94.583 480 16 3 2519 2995 297537300 297536828 0.000000e+00 734
5 TraesCS1B01G222700 chr1D 94.885 391 18 2 3245 3634 297536641 297536252 8.630000e-171 610
6 TraesCS1B01G222700 chr1D 96.040 202 7 1 3026 3226 297536833 297536632 9.730000e-86 327
7 TraesCS1B01G222700 chr1D 91.304 115 10 0 1295 1409 377973957 377974071 1.350000e-34 158
8 TraesCS1B01G222700 chr1A 94.250 2348 87 28 162 2502 370111330 370109024 0.000000e+00 3544
9 TraesCS1B01G222700 chr1A 85.714 1148 89 41 2514 3634 370108944 370107845 0.000000e+00 1142
10 TraesCS1B01G222700 chr1A 92.174 115 9 0 1295 1409 478567443 478567557 2.900000e-36 163
11 TraesCS1B01G222700 chr7B 93.168 161 8 2 1 161 166478579 166478422 2.180000e-57 233
12 TraesCS1B01G222700 chr4B 91.176 170 9 4 1 170 106489655 106489492 3.650000e-55 226
13 TraesCS1B01G222700 chr2D 93.204 103 7 0 1310 1412 520526995 520526893 6.280000e-33 152
14 TraesCS1B01G222700 chr2D 84.167 120 18 1 2310 2428 520525767 520525648 8.250000e-22 115
15 TraesCS1B01G222700 chr6B 88.983 118 13 0 1295 1412 708668023 708667906 2.920000e-31 147
16 TraesCS1B01G222700 chr5A 85.507 138 19 1 1285 1421 547332381 547332244 3.780000e-30 143
17 TraesCS1B01G222700 chr5D 91.262 103 9 0 1310 1412 432514628 432514526 1.360000e-29 141
18 TraesCS1B01G222700 chr2A 74.545 330 68 14 2310 2630 665710108 665709786 2.940000e-26 130
19 TraesCS1B01G222700 chr2B 83.465 127 20 1 2310 2435 612688421 612688295 2.290000e-22 117


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 TraesCS1B01G222700 chr1B 400311591 400315224 3633 True 6711.0 6711 100.00000 1 3634 1 chr1B.!!$R1 3633
1 TraesCS1B01G222700 chr1D 297536252 297539740 3488 True 1343.5 3703 95.21075 162 3634 4 chr1D.!!$R1 3472
2 TraesCS1B01G222700 chr1A 370107845 370111330 3485 True 2343.0 3544 89.98200 162 3634 2 chr1A.!!$R1 3472

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
59 60 0.032912 AGGTTTGTCCGGTTTTGGGT 60.033 50.0 0.00 0.0 41.99 4.51 F
904 915 0.096281 TTTCGATGGATTTGTCGCGC 59.904 50.0 0.00 0.0 37.74 6.86 F
908 919 0.381801 GATGGATTTGTCGCGCCATT 59.618 50.0 13.73 0.0 41.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1763 0.179702 GCTGTCCATGATCTCCTGCA 59.820 55.0 0.00 0.0 0.0 4.41 R
2632 2759 0.179094 TGGTTCGTCGCTCACTGTTT 60.179 50.0 0.00 0.0 0.0 2.83 R
2873 3005 1.051812 AGGACTCACAGTTGGTCAGG 58.948 55.0 5.37 0.0 0.0 3.86 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
35 36 2.749621 CCCCCTTTTCAGTCTCATTTCG 59.250 50.000 0.00 0.00 0.00 3.46
36 37 2.162408 CCCCTTTTCAGTCTCATTTCGC 59.838 50.000 0.00 0.00 0.00 4.70
37 38 2.159653 CCCTTTTCAGTCTCATTTCGCG 60.160 50.000 0.00 0.00 0.00 5.87
38 39 2.499896 CTTTTCAGTCTCATTTCGCGC 58.500 47.619 0.00 0.00 0.00 6.86
39 40 1.507562 TTTCAGTCTCATTTCGCGCA 58.492 45.000 8.75 0.00 0.00 6.09
40 41 1.507562 TTCAGTCTCATTTCGCGCAA 58.492 45.000 8.75 0.00 0.00 4.85
41 42 1.070821 TCAGTCTCATTTCGCGCAAG 58.929 50.000 8.75 0.00 43.44 4.01
42 43 0.095935 CAGTCTCATTTCGCGCAAGG 59.904 55.000 8.75 0.00 38.28 3.61
43 44 0.320771 AGTCTCATTTCGCGCAAGGT 60.321 50.000 8.75 0.00 38.28 3.50
44 45 0.517316 GTCTCATTTCGCGCAAGGTT 59.483 50.000 8.75 0.00 38.28 3.50
45 46 1.069227 GTCTCATTTCGCGCAAGGTTT 60.069 47.619 8.75 0.00 38.28 3.27
46 47 1.069296 TCTCATTTCGCGCAAGGTTTG 60.069 47.619 8.75 0.00 38.28 2.93
47 48 0.665835 TCATTTCGCGCAAGGTTTGT 59.334 45.000 8.75 0.00 38.28 2.83
48 49 1.052287 CATTTCGCGCAAGGTTTGTC 58.948 50.000 8.75 0.00 38.28 3.18
49 50 0.039527 ATTTCGCGCAAGGTTTGTCC 60.040 50.000 8.75 0.00 38.28 4.02
50 51 2.381665 TTTCGCGCAAGGTTTGTCCG 62.382 55.000 8.75 0.00 41.99 4.79
51 52 4.383602 CGCGCAAGGTTTGTCCGG 62.384 66.667 8.75 0.00 41.99 5.14
52 53 3.284449 GCGCAAGGTTTGTCCGGT 61.284 61.111 0.30 0.00 41.99 5.28
53 54 2.841160 GCGCAAGGTTTGTCCGGTT 61.841 57.895 0.30 0.00 41.99 4.44
54 55 1.731093 CGCAAGGTTTGTCCGGTTT 59.269 52.632 0.00 0.00 41.99 3.27
55 56 0.101579 CGCAAGGTTTGTCCGGTTTT 59.898 50.000 0.00 0.00 41.99 2.43
56 57 1.566404 GCAAGGTTTGTCCGGTTTTG 58.434 50.000 0.00 0.00 41.99 2.44
57 58 1.804746 GCAAGGTTTGTCCGGTTTTGG 60.805 52.381 0.00 0.00 41.99 3.28
58 59 1.116308 AAGGTTTGTCCGGTTTTGGG 58.884 50.000 0.00 0.00 41.99 4.12
59 60 0.032912 AGGTTTGTCCGGTTTTGGGT 60.033 50.000 0.00 0.00 41.99 4.51
60 61 0.825410 GGTTTGTCCGGTTTTGGGTT 59.175 50.000 0.00 0.00 0.00 4.11
61 62 2.030371 GGTTTGTCCGGTTTTGGGTTA 58.970 47.619 0.00 0.00 0.00 2.85
62 63 2.034939 GGTTTGTCCGGTTTTGGGTTAG 59.965 50.000 0.00 0.00 0.00 2.34
63 64 2.689471 GTTTGTCCGGTTTTGGGTTAGT 59.311 45.455 0.00 0.00 0.00 2.24
64 65 2.732844 TGTCCGGTTTTGGGTTAGTT 57.267 45.000 0.00 0.00 0.00 2.24
65 66 2.299521 TGTCCGGTTTTGGGTTAGTTG 58.700 47.619 0.00 0.00 0.00 3.16
66 67 1.610038 GTCCGGTTTTGGGTTAGTTGG 59.390 52.381 0.00 0.00 0.00 3.77
67 68 1.214923 TCCGGTTTTGGGTTAGTTGGT 59.785 47.619 0.00 0.00 0.00 3.67
68 69 2.441001 TCCGGTTTTGGGTTAGTTGGTA 59.559 45.455 0.00 0.00 0.00 3.25
69 70 3.117738 TCCGGTTTTGGGTTAGTTGGTAA 60.118 43.478 0.00 0.00 0.00 2.85
70 71 3.827876 CCGGTTTTGGGTTAGTTGGTAAT 59.172 43.478 0.00 0.00 0.00 1.89
71 72 4.281435 CCGGTTTTGGGTTAGTTGGTAATT 59.719 41.667 0.00 0.00 0.00 1.40
72 73 5.463286 CGGTTTTGGGTTAGTTGGTAATTC 58.537 41.667 0.00 0.00 0.00 2.17
73 74 5.463286 GGTTTTGGGTTAGTTGGTAATTCG 58.537 41.667 0.00 0.00 0.00 3.34
74 75 5.463286 GTTTTGGGTTAGTTGGTAATTCGG 58.537 41.667 0.00 0.00 0.00 4.30
75 76 4.637387 TTGGGTTAGTTGGTAATTCGGA 57.363 40.909 0.00 0.00 0.00 4.55
76 77 4.847990 TGGGTTAGTTGGTAATTCGGAT 57.152 40.909 0.00 0.00 0.00 4.18
77 78 5.954153 TGGGTTAGTTGGTAATTCGGATA 57.046 39.130 0.00 0.00 0.00 2.59
78 79 5.673514 TGGGTTAGTTGGTAATTCGGATAC 58.326 41.667 0.00 0.00 0.00 2.24
79 80 5.426185 TGGGTTAGTTGGTAATTCGGATACT 59.574 40.000 0.00 0.00 0.00 2.12
80 81 6.610830 TGGGTTAGTTGGTAATTCGGATACTA 59.389 38.462 0.00 0.00 0.00 1.82
81 82 7.125507 TGGGTTAGTTGGTAATTCGGATACTAA 59.874 37.037 0.00 0.00 0.00 2.24
82 83 7.654923 GGGTTAGTTGGTAATTCGGATACTAAG 59.345 40.741 0.00 0.00 30.04 2.18
83 84 8.416329 GGTTAGTTGGTAATTCGGATACTAAGA 58.584 37.037 0.00 0.00 30.04 2.10
84 85 9.807649 GTTAGTTGGTAATTCGGATACTAAGAA 57.192 33.333 0.00 0.00 30.04 2.52
85 86 9.807649 TTAGTTGGTAATTCGGATACTAAGAAC 57.192 33.333 0.00 0.00 0.00 3.01
86 87 8.075761 AGTTGGTAATTCGGATACTAAGAACT 57.924 34.615 0.00 0.00 0.00 3.01
87 88 8.537858 AGTTGGTAATTCGGATACTAAGAACTT 58.462 33.333 0.00 0.00 0.00 2.66
88 89 8.601476 GTTGGTAATTCGGATACTAAGAACTTG 58.399 37.037 0.00 0.00 0.00 3.16
89 90 7.270047 TGGTAATTCGGATACTAAGAACTTGG 58.730 38.462 0.00 0.00 0.00 3.61
90 91 7.124599 TGGTAATTCGGATACTAAGAACTTGGA 59.875 37.037 5.02 0.00 0.00 3.53
91 92 8.148999 GGTAATTCGGATACTAAGAACTTGGAT 58.851 37.037 5.02 0.00 0.00 3.41
111 112 7.776618 TGGATACAGACTGATATATTTCCGT 57.223 36.000 10.08 0.00 46.17 4.69
112 113 8.190326 TGGATACAGACTGATATATTTCCGTT 57.810 34.615 10.08 0.00 46.17 4.44
113 114 8.088365 TGGATACAGACTGATATATTTCCGTTG 58.912 37.037 10.08 0.00 46.17 4.10
114 115 8.304596 GGATACAGACTGATATATTTCCGTTGA 58.695 37.037 10.08 0.00 0.00 3.18
115 116 9.862371 GATACAGACTGATATATTTCCGTTGAT 57.138 33.333 10.08 0.00 0.00 2.57
117 118 8.370493 ACAGACTGATATATTTCCGTTGATTG 57.630 34.615 10.08 0.00 0.00 2.67
118 119 7.987458 ACAGACTGATATATTTCCGTTGATTGT 59.013 33.333 10.08 0.00 0.00 2.71
119 120 9.476202 CAGACTGATATATTTCCGTTGATTGTA 57.524 33.333 0.00 0.00 0.00 2.41
131 132 9.982651 TTTCCGTTGATTGTAAAATTAATGGAA 57.017 25.926 23.55 23.55 44.81 3.53
132 133 9.982651 TTCCGTTGATTGTAAAATTAATGGAAA 57.017 25.926 24.49 13.89 44.16 3.13
133 134 9.632807 TCCGTTGATTGTAAAATTAATGGAAAG 57.367 29.630 17.67 0.00 39.43 2.62
134 135 8.868916 CCGTTGATTGTAAAATTAATGGAAAGG 58.131 33.333 13.78 0.00 37.12 3.11
135 136 8.868916 CGTTGATTGTAAAATTAATGGAAAGGG 58.131 33.333 0.00 0.00 0.00 3.95
136 137 9.161629 GTTGATTGTAAAATTAATGGAAAGGGG 57.838 33.333 0.00 0.00 0.00 4.79
137 138 8.442660 TGATTGTAAAATTAATGGAAAGGGGT 57.557 30.769 0.00 0.00 0.00 4.95
138 139 8.885346 TGATTGTAAAATTAATGGAAAGGGGTT 58.115 29.630 0.00 0.00 0.00 4.11
139 140 9.161629 GATTGTAAAATTAATGGAAAGGGGTTG 57.838 33.333 0.00 0.00 0.00 3.77
140 141 7.619512 TGTAAAATTAATGGAAAGGGGTTGT 57.380 32.000 0.00 0.00 0.00 3.32
141 142 7.445945 TGTAAAATTAATGGAAAGGGGTTGTG 58.554 34.615 0.00 0.00 0.00 3.33
142 143 6.755542 AAAATTAATGGAAAGGGGTTGTGA 57.244 33.333 0.00 0.00 0.00 3.58
143 144 6.358974 AAATTAATGGAAAGGGGTTGTGAG 57.641 37.500 0.00 0.00 0.00 3.51
144 145 1.632589 AATGGAAAGGGGTTGTGAGC 58.367 50.000 0.00 0.00 0.00 4.26
145 146 0.251787 ATGGAAAGGGGTTGTGAGCC 60.252 55.000 0.00 0.00 42.86 4.70
146 147 1.360393 TGGAAAGGGGTTGTGAGCCT 61.360 55.000 0.00 0.00 43.15 4.58
147 148 0.895559 GGAAAGGGGTTGTGAGCCTG 60.896 60.000 0.00 0.00 43.15 4.85
148 149 0.895559 GAAAGGGGTTGTGAGCCTGG 60.896 60.000 0.00 0.00 43.15 4.45
149 150 1.655114 AAAGGGGTTGTGAGCCTGGT 61.655 55.000 0.00 0.00 43.15 4.00
150 151 1.655114 AAGGGGTTGTGAGCCTGGTT 61.655 55.000 0.00 0.00 43.15 3.67
151 152 1.903404 GGGGTTGTGAGCCTGGTTG 60.903 63.158 0.00 0.00 43.15 3.77
152 153 1.903404 GGGTTGTGAGCCTGGTTGG 60.903 63.158 0.00 0.00 40.37 3.77
153 154 1.150536 GGTTGTGAGCCTGGTTGGA 59.849 57.895 0.00 0.00 38.35 3.53
154 155 0.467290 GGTTGTGAGCCTGGTTGGAA 60.467 55.000 0.00 0.00 38.35 3.53
155 156 1.398692 GTTGTGAGCCTGGTTGGAAA 58.601 50.000 0.00 0.00 38.35 3.13
156 157 1.754226 GTTGTGAGCCTGGTTGGAAAA 59.246 47.619 0.00 0.00 38.35 2.29
157 158 2.151502 TGTGAGCCTGGTTGGAAAAA 57.848 45.000 0.00 0.00 38.35 1.94
224 225 7.013655 CCATGGTTGACTATCCCTTAATTTCAG 59.986 40.741 2.57 0.00 0.00 3.02
271 272 5.926542 CGATTTCTTTAGACAGACACTTCCA 59.073 40.000 0.00 0.00 0.00 3.53
291 292 5.947663 TCCATCCCACGACCAATAAAATAT 58.052 37.500 0.00 0.00 0.00 1.28
292 293 7.080653 TCCATCCCACGACCAATAAAATATA 57.919 36.000 0.00 0.00 0.00 0.86
293 294 7.165485 TCCATCCCACGACCAATAAAATATAG 58.835 38.462 0.00 0.00 0.00 1.31
294 295 7.016760 TCCATCCCACGACCAATAAAATATAGA 59.983 37.037 0.00 0.00 0.00 1.98
296 297 9.062524 CATCCCACGACCAATAAAATATAGAAA 57.937 33.333 0.00 0.00 0.00 2.52
298 299 8.487848 TCCCACGACCAATAAAATATAGAAAGA 58.512 33.333 0.00 0.00 0.00 2.52
320 321 5.888724 AGAAATCGAGTCACTAATCTCTCCA 59.111 40.000 0.00 0.00 0.00 3.86
413 415 1.881973 GTGCTCTGCCATTGTTGAGAA 59.118 47.619 0.00 0.00 0.00 2.87
422 424 6.096705 TCTGCCATTGTTGAGAAAGAGAAAAA 59.903 34.615 0.00 0.00 0.00 1.94
463 465 5.128499 CAGAGAGAAAGCTGATAGAGGGAAA 59.872 44.000 0.00 0.00 34.06 3.13
466 468 5.428131 AGAGAAAGCTGATAGAGGGAAACAT 59.572 40.000 0.00 0.00 0.00 2.71
500 502 5.418840 ACACAAGAGCTTTTCTTCTTCCAAA 59.581 36.000 0.00 0.00 44.34 3.28
586 588 0.486879 TGCTTCCCCTTCCCATTTGT 59.513 50.000 0.00 0.00 0.00 2.83
621 623 3.056322 GCATCCAACAGCCAAGAAGAATT 60.056 43.478 0.00 0.00 0.00 2.17
831 833 2.817258 TCGCTCAAATTTCGGGAAATGT 59.183 40.909 7.37 0.00 40.57 2.71
833 835 3.611530 CGCTCAAATTTCGGGAAATGTGT 60.612 43.478 18.88 2.99 43.29 3.72
875 877 4.290155 CACAGGAGTTCAAATTTTGTCCG 58.710 43.478 8.89 7.81 30.86 4.79
902 913 2.541588 CCCATTTCGATGGATTTGTCGC 60.542 50.000 6.63 0.00 44.39 5.19
903 914 2.365948 CATTTCGATGGATTTGTCGCG 58.634 47.619 0.00 0.00 37.74 5.87
904 915 0.096281 TTTCGATGGATTTGTCGCGC 59.904 50.000 0.00 0.00 37.74 6.86
905 916 1.701545 TTCGATGGATTTGTCGCGCC 61.702 55.000 0.00 0.00 37.74 6.53
906 917 2.460275 CGATGGATTTGTCGCGCCA 61.460 57.895 0.00 1.32 34.45 5.69
907 918 1.775039 CGATGGATTTGTCGCGCCAT 61.775 55.000 12.62 12.62 43.46 4.40
908 919 0.381801 GATGGATTTGTCGCGCCATT 59.618 50.000 13.73 0.00 41.00 3.16
909 920 0.381801 ATGGATTTGTCGCGCCATTC 59.618 50.000 0.00 0.00 37.88 2.67
910 921 1.297598 GGATTTGTCGCGCCATTCG 60.298 57.895 0.00 0.00 42.12 3.34
972 983 2.607187 CTAACTGTACTGCACGAAGGG 58.393 52.381 0.00 0.00 0.00 3.95
991 1002 2.619332 GGGAGGAAGAAAGGAAGGAAGC 60.619 54.545 0.00 0.00 0.00 3.86
992 1003 2.619332 GGAGGAAGAAAGGAAGGAAGCC 60.619 54.545 0.00 0.00 0.00 4.35
1056 1081 3.134792 GACGAGAGCTCCGAGGCA 61.135 66.667 25.01 0.00 34.17 4.75
1413 1438 0.806102 CCATCACCAACCTCTACGCG 60.806 60.000 3.53 3.53 0.00 6.01
1691 1716 2.492088 ACGACGAGGTGATGATCTTTCA 59.508 45.455 0.00 0.00 36.00 2.69
1738 1763 4.630894 ACAAAATGTGTCGTTGACATGT 57.369 36.364 0.00 0.00 44.63 3.21
2364 2389 1.493861 CCTCCTCCTCTGCATCAAGA 58.506 55.000 0.00 0.00 0.00 3.02
2441 2471 4.151883 ACAAGGTAGCCAATCAACAACAT 58.848 39.130 0.00 0.00 0.00 2.71
2449 2479 3.676873 GCCAATCAACAACATCATCCCAC 60.677 47.826 0.00 0.00 0.00 4.61
2453 2483 3.355378 TCAACAACATCATCCCACATCC 58.645 45.455 0.00 0.00 0.00 3.51
2474 2504 3.348309 CGCATCATCTGAATTTGACACG 58.652 45.455 0.00 0.00 0.00 4.49
2502 2536 8.896744 ACATACATTTATCTGAACTTGACATGG 58.103 33.333 0.00 0.00 0.00 3.66
2503 2537 6.199937 ACATTTATCTGAACTTGACATGGC 57.800 37.500 0.00 0.00 0.00 4.40
2509 2543 3.896888 TCTGAACTTGACATGGCCATTTT 59.103 39.130 17.92 5.78 0.00 1.82
2632 2759 1.678728 CGACAAGGCTGCCAGGAAATA 60.679 52.381 22.65 0.00 0.00 1.40
2647 2774 2.991190 GGAAATAAACAGTGAGCGACGA 59.009 45.455 0.00 0.00 0.00 4.20
2684 2811 2.032302 CGGATTCGTCGAGAGAGTGAAT 59.968 50.000 0.00 0.00 44.41 2.57
2883 3015 1.972872 CAGAGTTTGCCTGACCAACT 58.027 50.000 0.00 0.00 33.65 3.16
2900 3034 4.348168 ACCAACTGTGAGTCCTGTAAGATT 59.652 41.667 0.00 0.00 34.07 2.40
2903 3037 6.263168 CCAACTGTGAGTCCTGTAAGATTTTT 59.737 38.462 0.00 0.00 34.07 1.94
2937 3072 6.017400 TGACTTTTTCATCTGATTTCAGGC 57.983 37.500 7.68 0.00 43.91 4.85
2938 3073 5.051891 ACTTTTTCATCTGATTTCAGGCG 57.948 39.130 7.68 0.20 43.91 5.52
2995 3135 2.897436 TCTTGCTCATCGATCTTGGTG 58.103 47.619 0.00 0.00 0.00 4.17
2999 3139 1.596727 GCTCATCGATCTTGGTGAAGC 59.403 52.381 0.00 0.00 0.00 3.86
3013 3153 2.038557 GGTGAAGCTAAGGACCAAGTGA 59.961 50.000 0.00 0.00 0.00 3.41
3016 3156 3.840666 TGAAGCTAAGGACCAAGTGAGAT 59.159 43.478 0.00 0.00 0.00 2.75
3017 3157 3.902881 AGCTAAGGACCAAGTGAGATG 57.097 47.619 0.00 0.00 0.00 2.90
3018 3158 2.093235 AGCTAAGGACCAAGTGAGATGC 60.093 50.000 0.00 0.00 0.00 3.91
3019 3159 2.093235 GCTAAGGACCAAGTGAGATGCT 60.093 50.000 0.00 0.00 0.00 3.79
3020 3160 3.620966 GCTAAGGACCAAGTGAGATGCTT 60.621 47.826 0.00 0.00 0.00 3.91
3021 3161 2.486472 AGGACCAAGTGAGATGCTTG 57.514 50.000 0.00 0.00 42.00 4.01
3022 3162 0.807496 GGACCAAGTGAGATGCTTGC 59.193 55.000 0.00 0.00 41.27 4.01
3026 3166 1.166129 CAAGTGAGATGCTTGCTGCT 58.834 50.000 0.00 0.00 43.37 4.24
3032 3172 2.295885 GAGATGCTTGCTGCTTGGTAT 58.704 47.619 0.00 0.00 43.37 2.73
3149 3291 2.158957 ACTTGACTCGCTGAAAACCTCA 60.159 45.455 0.00 0.00 0.00 3.86
3150 3292 2.613026 TGACTCGCTGAAAACCTCAA 57.387 45.000 0.00 0.00 32.17 3.02
3212 3356 2.780065 TCAAATGCACTGCACTTCAC 57.220 45.000 5.67 0.00 43.04 3.18
3227 3371 1.803555 CTTCACACACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
3228 3372 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
3230 3374 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3232 3376 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3233 3377 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3234 3378 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3235 3379 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3236 3380 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3238 3382 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3239 3383 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
3242 3386 1.225991 CACACACACACACACGCAC 60.226 57.895 0.00 0.00 0.00 5.34
3243 3387 2.021243 CACACACACACACGCACG 59.979 61.111 0.00 0.00 0.00 5.34
3244 3388 3.860125 ACACACACACACGCACGC 61.860 61.111 0.00 0.00 0.00 5.34
3245 3389 3.858989 CACACACACACGCACGCA 61.859 61.111 0.00 0.00 0.00 5.24
3246 3390 3.860125 ACACACACACGCACGCAC 61.860 61.111 0.00 0.00 0.00 5.34
3247 3391 4.918060 CACACACACGCACGCACG 62.918 66.667 0.00 0.00 39.50 5.34
3265 3409 1.200839 GCACGCACGTAGTTGACAC 59.799 57.895 0.00 0.00 41.61 3.67
3291 3435 6.204688 CCACTTTGAGTAACAGCAAATACAGA 59.795 38.462 0.00 0.00 33.94 3.41
3302 3446 3.879295 AGCAAATACAGATAGCGCACATT 59.121 39.130 11.47 0.00 0.00 2.71
3304 3448 4.672413 GCAAATACAGATAGCGCACATTTC 59.328 41.667 11.47 0.00 0.00 2.17
3313 3457 5.822519 AGATAGCGCACATTTCTTATCCAAA 59.177 36.000 11.47 0.00 0.00 3.28
3321 3465 7.329226 CGCACATTTCTTATCCAAAGAAACAAT 59.671 33.333 13.47 2.31 45.58 2.71
3349 3493 5.946972 TGGTCCAACTTAACTGAAAAGACAA 59.053 36.000 0.00 0.00 0.00 3.18
3352 3496 5.065474 TCCAACTTAACTGAAAAGACAACGG 59.935 40.000 0.00 0.00 0.00 4.44
3364 3508 4.759516 AAGACAACGGTATTTCGCAAAT 57.240 36.364 0.00 0.00 34.90 2.32
3371 3515 5.365403 ACGGTATTTCGCAAATTGAAGAA 57.635 34.783 0.00 0.00 32.38 2.52
3380 3524 3.120616 CGCAAATTGAAGAACATGCAGTG 59.879 43.478 0.00 0.00 33.55 3.66
3467 3611 4.728534 ACACATGTACACACAAACACAAC 58.271 39.130 0.00 0.00 38.42 3.32
3470 3614 4.201773 ACATGTACACACAAACACAACGAG 60.202 41.667 0.00 0.00 38.42 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.749621 CGAAATGAGACTGAAAAGGGGG 59.250 50.000 0.00 0.00 0.00 5.40
15 16 2.162408 GCGAAATGAGACTGAAAAGGGG 59.838 50.000 0.00 0.00 0.00 4.79
16 17 2.159653 CGCGAAATGAGACTGAAAAGGG 60.160 50.000 0.00 0.00 0.00 3.95
17 18 2.726066 GCGCGAAATGAGACTGAAAAGG 60.726 50.000 12.10 0.00 0.00 3.11
18 19 2.096268 TGCGCGAAATGAGACTGAAAAG 60.096 45.455 12.10 0.00 0.00 2.27
19 20 1.870402 TGCGCGAAATGAGACTGAAAA 59.130 42.857 12.10 0.00 0.00 2.29
20 21 1.507562 TGCGCGAAATGAGACTGAAA 58.492 45.000 12.10 0.00 0.00 2.69
21 22 1.460743 CTTGCGCGAAATGAGACTGAA 59.539 47.619 12.10 0.00 0.00 3.02
22 23 1.070821 CTTGCGCGAAATGAGACTGA 58.929 50.000 12.10 0.00 0.00 3.41
23 24 0.095935 CCTTGCGCGAAATGAGACTG 59.904 55.000 12.10 0.00 0.00 3.51
24 25 0.320771 ACCTTGCGCGAAATGAGACT 60.321 50.000 12.10 0.00 0.00 3.24
25 26 0.517316 AACCTTGCGCGAAATGAGAC 59.483 50.000 12.10 0.00 0.00 3.36
26 27 1.069296 CAAACCTTGCGCGAAATGAGA 60.069 47.619 12.10 0.00 0.00 3.27
27 28 1.330306 CAAACCTTGCGCGAAATGAG 58.670 50.000 12.10 0.00 0.00 2.90
28 29 0.665835 ACAAACCTTGCGCGAAATGA 59.334 45.000 12.10 0.00 0.00 2.57
29 30 1.052287 GACAAACCTTGCGCGAAATG 58.948 50.000 12.10 5.11 0.00 2.32
30 31 0.039527 GGACAAACCTTGCGCGAAAT 60.040 50.000 12.10 0.00 35.41 2.17
31 32 1.357334 GGACAAACCTTGCGCGAAA 59.643 52.632 12.10 4.03 35.41 3.46
32 33 2.887889 CGGACAAACCTTGCGCGAA 61.888 57.895 12.10 0.00 36.31 4.70
33 34 3.342627 CGGACAAACCTTGCGCGA 61.343 61.111 12.10 0.00 36.31 5.87
34 35 4.383602 CCGGACAAACCTTGCGCG 62.384 66.667 0.00 0.00 36.31 6.86
35 36 2.344521 AAACCGGACAAACCTTGCGC 62.345 55.000 9.46 0.00 36.31 6.09
36 37 0.101579 AAAACCGGACAAACCTTGCG 59.898 50.000 9.46 0.00 36.31 4.85
37 38 1.566404 CAAAACCGGACAAACCTTGC 58.434 50.000 9.46 0.00 36.31 4.01
38 39 1.202475 CCCAAAACCGGACAAACCTTG 60.202 52.381 9.46 0.25 36.31 3.61
39 40 1.116308 CCCAAAACCGGACAAACCTT 58.884 50.000 9.46 0.00 36.31 3.50
40 41 0.032912 ACCCAAAACCGGACAAACCT 60.033 50.000 9.46 0.00 36.31 3.50
41 42 0.825410 AACCCAAAACCGGACAAACC 59.175 50.000 9.46 0.00 0.00 3.27
42 43 2.689471 ACTAACCCAAAACCGGACAAAC 59.311 45.455 9.46 0.00 0.00 2.93
43 44 3.015675 ACTAACCCAAAACCGGACAAA 57.984 42.857 9.46 0.00 0.00 2.83
44 45 2.688958 CAACTAACCCAAAACCGGACAA 59.311 45.455 9.46 0.00 0.00 3.18
45 46 2.299521 CAACTAACCCAAAACCGGACA 58.700 47.619 9.46 0.00 0.00 4.02
46 47 1.610038 CCAACTAACCCAAAACCGGAC 59.390 52.381 9.46 0.00 0.00 4.79
47 48 1.214923 ACCAACTAACCCAAAACCGGA 59.785 47.619 9.46 0.00 0.00 5.14
48 49 1.694844 ACCAACTAACCCAAAACCGG 58.305 50.000 0.00 0.00 0.00 5.28
49 50 5.456548 AATTACCAACTAACCCAAAACCG 57.543 39.130 0.00 0.00 0.00 4.44
50 51 5.463286 CGAATTACCAACTAACCCAAAACC 58.537 41.667 0.00 0.00 0.00 3.27
51 52 5.241285 TCCGAATTACCAACTAACCCAAAAC 59.759 40.000 0.00 0.00 0.00 2.43
52 53 5.383476 TCCGAATTACCAACTAACCCAAAA 58.617 37.500 0.00 0.00 0.00 2.44
53 54 4.983053 TCCGAATTACCAACTAACCCAAA 58.017 39.130 0.00 0.00 0.00 3.28
54 55 4.637387 TCCGAATTACCAACTAACCCAA 57.363 40.909 0.00 0.00 0.00 4.12
55 56 4.847990 ATCCGAATTACCAACTAACCCA 57.152 40.909 0.00 0.00 0.00 4.51
56 57 5.922053 AGTATCCGAATTACCAACTAACCC 58.078 41.667 0.00 0.00 0.00 4.11
57 58 8.416329 TCTTAGTATCCGAATTACCAACTAACC 58.584 37.037 0.00 0.00 0.00 2.85
58 59 9.807649 TTCTTAGTATCCGAATTACCAACTAAC 57.192 33.333 0.00 0.00 0.00 2.34
59 60 9.807649 GTTCTTAGTATCCGAATTACCAACTAA 57.192 33.333 0.00 0.00 0.00 2.24
60 61 9.193806 AGTTCTTAGTATCCGAATTACCAACTA 57.806 33.333 0.00 0.00 0.00 2.24
61 62 8.075761 AGTTCTTAGTATCCGAATTACCAACT 57.924 34.615 0.00 0.00 0.00 3.16
62 63 8.601476 CAAGTTCTTAGTATCCGAATTACCAAC 58.399 37.037 0.00 0.00 0.00 3.77
63 64 7.767198 CCAAGTTCTTAGTATCCGAATTACCAA 59.233 37.037 0.00 0.00 0.00 3.67
64 65 7.124599 TCCAAGTTCTTAGTATCCGAATTACCA 59.875 37.037 0.00 0.00 0.00 3.25
65 66 7.495055 TCCAAGTTCTTAGTATCCGAATTACC 58.505 38.462 0.00 0.00 0.00 2.85
68 69 8.701895 TGTATCCAAGTTCTTAGTATCCGAATT 58.298 33.333 0.00 0.00 0.00 2.17
69 70 8.246430 TGTATCCAAGTTCTTAGTATCCGAAT 57.754 34.615 0.00 0.00 0.00 3.34
70 71 7.558807 TCTGTATCCAAGTTCTTAGTATCCGAA 59.441 37.037 0.00 0.00 0.00 4.30
71 72 7.013083 GTCTGTATCCAAGTTCTTAGTATCCGA 59.987 40.741 0.00 0.00 0.00 4.55
72 73 7.013464 AGTCTGTATCCAAGTTCTTAGTATCCG 59.987 40.741 0.00 0.00 0.00 4.18
73 74 8.138712 CAGTCTGTATCCAAGTTCTTAGTATCC 58.861 40.741 0.00 0.00 0.00 2.59
74 75 8.904834 TCAGTCTGTATCCAAGTTCTTAGTATC 58.095 37.037 0.00 0.00 0.00 2.24
75 76 8.824756 TCAGTCTGTATCCAAGTTCTTAGTAT 57.175 34.615 0.00 0.00 0.00 2.12
76 77 8.824756 ATCAGTCTGTATCCAAGTTCTTAGTA 57.175 34.615 0.00 0.00 0.00 1.82
77 78 7.726033 ATCAGTCTGTATCCAAGTTCTTAGT 57.274 36.000 0.00 0.00 0.00 2.24
84 85 8.307483 CGGAAATATATCAGTCTGTATCCAAGT 58.693 37.037 0.00 0.00 0.00 3.16
85 86 8.307483 ACGGAAATATATCAGTCTGTATCCAAG 58.693 37.037 0.00 0.00 0.00 3.61
86 87 8.190326 ACGGAAATATATCAGTCTGTATCCAA 57.810 34.615 0.00 0.00 0.00 3.53
87 88 7.776618 ACGGAAATATATCAGTCTGTATCCA 57.223 36.000 0.00 0.00 0.00 3.41
88 89 8.304596 TCAACGGAAATATATCAGTCTGTATCC 58.695 37.037 0.00 0.00 0.00 2.59
89 90 9.862371 ATCAACGGAAATATATCAGTCTGTATC 57.138 33.333 0.00 0.00 0.00 2.24
91 92 9.476202 CAATCAACGGAAATATATCAGTCTGTA 57.524 33.333 0.00 0.00 0.00 2.74
92 93 7.987458 ACAATCAACGGAAATATATCAGTCTGT 59.013 33.333 0.00 0.00 0.00 3.41
93 94 8.370493 ACAATCAACGGAAATATATCAGTCTG 57.630 34.615 0.00 0.00 0.00 3.51
105 106 9.982651 TTCCATTAATTTTACAATCAACGGAAA 57.017 25.926 0.00 0.00 0.00 3.13
106 107 9.982651 TTTCCATTAATTTTACAATCAACGGAA 57.017 25.926 0.00 0.00 0.00 4.30
107 108 9.632807 CTTTCCATTAATTTTACAATCAACGGA 57.367 29.630 0.00 0.00 0.00 4.69
108 109 8.868916 CCTTTCCATTAATTTTACAATCAACGG 58.131 33.333 0.00 0.00 0.00 4.44
109 110 8.868916 CCCTTTCCATTAATTTTACAATCAACG 58.131 33.333 0.00 0.00 0.00 4.10
110 111 9.161629 CCCCTTTCCATTAATTTTACAATCAAC 57.838 33.333 0.00 0.00 0.00 3.18
111 112 8.885346 ACCCCTTTCCATTAATTTTACAATCAA 58.115 29.630 0.00 0.00 0.00 2.57
112 113 8.442660 ACCCCTTTCCATTAATTTTACAATCA 57.557 30.769 0.00 0.00 0.00 2.57
113 114 9.161629 CAACCCCTTTCCATTAATTTTACAATC 57.838 33.333 0.00 0.00 0.00 2.67
114 115 8.664992 ACAACCCCTTTCCATTAATTTTACAAT 58.335 29.630 0.00 0.00 0.00 2.71
115 116 7.934120 CACAACCCCTTTCCATTAATTTTACAA 59.066 33.333 0.00 0.00 0.00 2.41
116 117 7.290248 TCACAACCCCTTTCCATTAATTTTACA 59.710 33.333 0.00 0.00 0.00 2.41
117 118 7.672240 TCACAACCCCTTTCCATTAATTTTAC 58.328 34.615 0.00 0.00 0.00 2.01
118 119 7.526359 GCTCACAACCCCTTTCCATTAATTTTA 60.526 37.037 0.00 0.00 0.00 1.52
119 120 6.744056 GCTCACAACCCCTTTCCATTAATTTT 60.744 38.462 0.00 0.00 0.00 1.82
120 121 5.279960 GCTCACAACCCCTTTCCATTAATTT 60.280 40.000 0.00 0.00 0.00 1.82
121 122 4.222810 GCTCACAACCCCTTTCCATTAATT 59.777 41.667 0.00 0.00 0.00 1.40
122 123 3.769300 GCTCACAACCCCTTTCCATTAAT 59.231 43.478 0.00 0.00 0.00 1.40
123 124 3.161866 GCTCACAACCCCTTTCCATTAA 58.838 45.455 0.00 0.00 0.00 1.40
124 125 2.556559 GGCTCACAACCCCTTTCCATTA 60.557 50.000 0.00 0.00 0.00 1.90
125 126 1.632589 GCTCACAACCCCTTTCCATT 58.367 50.000 0.00 0.00 0.00 3.16
126 127 0.251787 GGCTCACAACCCCTTTCCAT 60.252 55.000 0.00 0.00 0.00 3.41
127 128 1.152830 GGCTCACAACCCCTTTCCA 59.847 57.895 0.00 0.00 0.00 3.53
128 129 0.895559 CAGGCTCACAACCCCTTTCC 60.896 60.000 0.00 0.00 0.00 3.13
129 130 0.895559 CCAGGCTCACAACCCCTTTC 60.896 60.000 0.00 0.00 0.00 2.62
130 131 1.153756 CCAGGCTCACAACCCCTTT 59.846 57.895 0.00 0.00 0.00 3.11
131 132 1.655114 AACCAGGCTCACAACCCCTT 61.655 55.000 0.00 0.00 0.00 3.95
132 133 2.084930 AACCAGGCTCACAACCCCT 61.085 57.895 0.00 0.00 0.00 4.79
133 134 1.903404 CAACCAGGCTCACAACCCC 60.903 63.158 0.00 0.00 0.00 4.95
134 135 1.903404 CCAACCAGGCTCACAACCC 60.903 63.158 0.00 0.00 0.00 4.11
135 136 0.467290 TTCCAACCAGGCTCACAACC 60.467 55.000 0.00 0.00 37.29 3.77
136 137 1.398692 TTTCCAACCAGGCTCACAAC 58.601 50.000 0.00 0.00 37.29 3.32
137 138 2.151502 TTTTCCAACCAGGCTCACAA 57.848 45.000 0.00 0.00 37.29 3.33
138 139 2.151502 TTTTTCCAACCAGGCTCACA 57.848 45.000 0.00 0.00 37.29 3.58
157 158 9.715121 ATCATTGCTAATCTTTGTGATGTTTTT 57.285 25.926 0.00 0.00 35.21 1.94
158 159 9.362539 GATCATTGCTAATCTTTGTGATGTTTT 57.637 29.630 0.00 0.00 35.21 2.43
159 160 7.977853 GGATCATTGCTAATCTTTGTGATGTTT 59.022 33.333 0.00 0.00 35.21 2.83
160 161 7.123098 TGGATCATTGCTAATCTTTGTGATGTT 59.877 33.333 0.00 0.00 35.21 2.71
224 225 2.477863 GGCAGGATTATGTTTGCGTGTC 60.478 50.000 0.00 0.00 37.43 3.67
271 272 9.284968 CTTTCTATATTTTATTGGTCGTGGGAT 57.715 33.333 0.00 0.00 0.00 3.85
291 292 9.179909 AGAGATTAGTGACTCGATTTCTTTCTA 57.820 33.333 0.00 0.00 38.08 2.10
292 293 8.062065 AGAGATTAGTGACTCGATTTCTTTCT 57.938 34.615 0.00 0.00 38.08 2.52
293 294 7.434013 GGAGAGATTAGTGACTCGATTTCTTTC 59.566 40.741 0.00 0.00 38.08 2.62
294 295 7.093727 TGGAGAGATTAGTGACTCGATTTCTTT 60.094 37.037 0.00 0.00 38.08 2.52
296 297 5.888724 TGGAGAGATTAGTGACTCGATTTCT 59.111 40.000 0.00 0.00 38.08 2.52
298 299 6.531503 TTGGAGAGATTAGTGACTCGATTT 57.468 37.500 0.00 0.00 38.08 2.17
301 302 4.339530 CCATTGGAGAGATTAGTGACTCGA 59.660 45.833 0.00 0.00 38.08 4.04
303 304 4.141846 TGCCATTGGAGAGATTAGTGACTC 60.142 45.833 6.95 0.00 0.00 3.36
305 306 4.142609 TGCCATTGGAGAGATTAGTGAC 57.857 45.455 6.95 0.00 0.00 3.67
353 355 2.290008 TGTGAGCAACGGATGGTATGTT 60.290 45.455 0.00 0.00 40.59 2.71
413 415 2.965831 GGCAGGTTTCCCTTTTTCTCTT 59.034 45.455 0.00 0.00 39.89 2.85
422 424 2.156098 TGCTCTGGCAGGTTTCCCT 61.156 57.895 15.73 0.00 44.28 4.20
463 465 3.817647 GCTCTTGTGTTCTCTCCAAATGT 59.182 43.478 0.00 0.00 0.00 2.71
466 468 3.845781 AGCTCTTGTGTTCTCTCCAAA 57.154 42.857 0.00 0.00 0.00 3.28
500 502 0.971386 CCTTGTCCTTGCCAAATGCT 59.029 50.000 0.00 0.00 42.00 3.79
505 507 1.704628 TGATCTCCTTGTCCTTGCCAA 59.295 47.619 0.00 0.00 0.00 4.52
586 588 5.287674 TGTTGGATGCAAATCAAAGGAAA 57.712 34.783 0.00 0.00 0.00 3.13
621 623 3.539604 CCTTTTTGCAATTCCACCACAA 58.460 40.909 0.00 0.00 0.00 3.33
739 741 3.397527 AGGTGACTCCATACCAATCCAT 58.602 45.455 0.00 0.00 39.46 3.41
831 833 8.575565 TGTGCGCTTAATACAAAATTTAAACA 57.424 26.923 9.73 0.00 0.00 2.83
833 835 8.082852 TCCTGTGCGCTTAATACAAAATTTAAA 58.917 29.630 9.73 0.00 0.00 1.52
849 851 1.609208 AATTTGAACTCCTGTGCGCT 58.391 45.000 9.73 0.00 0.00 5.92
850 852 2.422276 AAATTTGAACTCCTGTGCGC 57.578 45.000 0.00 0.00 0.00 6.09
903 914 0.028110 GGTGAATTCTCGCGAATGGC 59.972 55.000 11.33 0.00 39.72 4.40
904 915 0.301687 CGGTGAATTCTCGCGAATGG 59.698 55.000 11.33 0.00 39.72 3.16
905 916 0.301687 CCGGTGAATTCTCGCGAATG 59.698 55.000 11.33 0.00 39.72 2.67
906 917 0.810031 CCCGGTGAATTCTCGCGAAT 60.810 55.000 11.33 0.00 41.53 3.34
907 918 1.447140 CCCGGTGAATTCTCGCGAA 60.447 57.895 11.33 0.00 32.47 4.70
908 919 2.183300 CCCGGTGAATTCTCGCGA 59.817 61.111 9.26 9.26 32.47 5.87
909 920 2.165301 GTCCCGGTGAATTCTCGCG 61.165 63.158 7.05 0.00 32.47 5.87
910 921 1.814169 GGTCCCGGTGAATTCTCGC 60.814 63.158 7.05 0.00 0.00 5.03
972 983 2.040412 TGGCTTCCTTCCTTTCTTCCTC 59.960 50.000 0.00 0.00 0.00 3.71
991 1002 1.406539 GCTGTCAGCCATGGTTATTGG 59.593 52.381 14.27 1.72 34.48 3.16
992 1003 2.093890 TGCTGTCAGCCATGGTTATTG 58.906 47.619 21.99 7.42 41.51 1.90
1032 1057 1.810532 GGAGCTCTCGTCGGACAAT 59.189 57.895 14.64 0.00 0.00 2.71
1315 1340 1.303155 GCAGCAGCTTGGAGAACCT 60.303 57.895 0.00 0.00 37.91 3.50
1413 1438 1.737008 GCAGTTCCCGAAGACCGTC 60.737 63.158 0.00 0.00 36.31 4.79
1465 1490 0.344790 ATCTCCCTCCTCCACATGGT 59.655 55.000 0.00 0.00 36.34 3.55
1691 1716 4.095483 GCACTGATCAGAATTCGGAACAAT 59.905 41.667 29.27 6.94 0.00 2.71
1738 1763 0.179702 GCTGTCCATGATCTCCTGCA 59.820 55.000 0.00 0.00 0.00 4.41
1853 1878 1.728426 CTGGGTCGTCGTTGTCGTC 60.728 63.158 0.00 0.00 38.33 4.20
1857 1882 4.657824 CCGCTGGGTCGTCGTTGT 62.658 66.667 0.00 0.00 0.00 3.32
1858 1883 3.851845 TTCCGCTGGGTCGTCGTTG 62.852 63.158 0.00 0.00 33.83 4.10
1859 1884 3.608662 TTCCGCTGGGTCGTCGTT 61.609 61.111 0.00 0.00 33.83 3.85
1883 1908 4.265056 ACCGGCACCCACCACTTC 62.265 66.667 0.00 0.00 0.00 3.01
2265 2290 3.394836 GGCGAGCTCCTTGACCCT 61.395 66.667 8.47 0.00 0.00 4.34
2441 2471 0.766752 ATGATGCGGATGTGGGATGA 59.233 50.000 0.00 0.00 0.00 2.92
2449 2479 4.035909 TGTCAAATTCAGATGATGCGGATG 59.964 41.667 0.00 0.00 0.00 3.51
2453 2483 3.062504 TCGTGTCAAATTCAGATGATGCG 59.937 43.478 0.00 0.00 0.00 4.73
2509 2543 2.235016 GCCCAACATCCTACACACAAA 58.765 47.619 0.00 0.00 0.00 2.83
2511 2545 0.767998 TGCCCAACATCCTACACACA 59.232 50.000 0.00 0.00 0.00 3.72
2512 2546 1.453155 CTGCCCAACATCCTACACAC 58.547 55.000 0.00 0.00 0.00 3.82
2632 2759 0.179094 TGGTTCGTCGCTCACTGTTT 60.179 50.000 0.00 0.00 0.00 2.83
2647 2774 1.227734 CCGTCCGTCAGGTTTGGTT 60.228 57.895 0.00 0.00 39.05 3.67
2873 3005 1.051812 AGGACTCACAGTTGGTCAGG 58.948 55.000 5.37 0.00 0.00 3.86
2916 3050 4.082571 CCGCCTGAAATCAGATGAAAAAGT 60.083 41.667 11.94 0.00 46.59 2.66
2938 3073 1.299541 CACACTGTTGGTCAGACACC 58.700 55.000 2.17 0.00 46.27 4.16
2995 3135 3.963428 TCTCACTTGGTCCTTAGCTTC 57.037 47.619 0.00 0.00 0.00 3.86
2999 3139 3.902881 AGCATCTCACTTGGTCCTTAG 57.097 47.619 0.00 0.00 0.00 2.18
3017 3157 3.249559 GTCATAGATACCAAGCAGCAAGC 59.750 47.826 0.00 0.00 46.19 4.01
3018 3158 4.510711 CAGTCATAGATACCAAGCAGCAAG 59.489 45.833 0.00 0.00 0.00 4.01
3019 3159 4.080919 ACAGTCATAGATACCAAGCAGCAA 60.081 41.667 0.00 0.00 0.00 3.91
3020 3160 3.452264 ACAGTCATAGATACCAAGCAGCA 59.548 43.478 0.00 0.00 0.00 4.41
3021 3161 4.054671 GACAGTCATAGATACCAAGCAGC 58.945 47.826 0.00 0.00 0.00 5.25
3022 3162 5.268118 TGACAGTCATAGATACCAAGCAG 57.732 43.478 0.00 0.00 0.00 4.24
3026 3166 7.168219 AGCTTTTTGACAGTCATAGATACCAA 58.832 34.615 3.45 0.00 0.00 3.67
3032 3172 6.942532 AACAAGCTTTTTGACAGTCATAGA 57.057 33.333 3.45 0.00 0.00 1.98
3149 3291 9.821662 GTTATCGCAGTAAATTCAACTAAACTT 57.178 29.630 0.00 0.00 0.00 2.66
3150 3292 8.995220 TGTTATCGCAGTAAATTCAACTAAACT 58.005 29.630 0.00 0.00 0.00 2.66
3212 3356 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3227 3371 3.860125 GCGTGCGTGTGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
3228 3372 3.858989 TGCGTGCGTGTGTGTGTG 61.859 61.111 0.00 0.00 0.00 3.82
3230 3374 4.918060 CGTGCGTGCGTGTGTGTG 62.918 66.667 0.00 0.00 0.00 3.82
3243 3387 3.698463 AACTACGTGCGTGCGTGC 61.698 61.111 14.68 0.00 45.33 5.34
3244 3388 2.167684 CAACTACGTGCGTGCGTG 59.832 61.111 14.68 8.48 45.33 5.34
3246 3390 2.297195 TGTCAACTACGTGCGTGCG 61.297 57.895 7.55 1.32 37.94 5.34
3247 3391 1.200839 GTGTCAACTACGTGCGTGC 59.799 57.895 7.55 0.00 0.00 5.34
3248 3392 1.554042 GGGTGTCAACTACGTGCGTG 61.554 60.000 7.55 0.00 0.00 5.34
3249 3393 1.300388 GGGTGTCAACTACGTGCGT 60.300 57.895 0.00 2.05 0.00 5.24
3250 3394 1.300311 TGGGTGTCAACTACGTGCG 60.300 57.895 0.00 0.00 0.00 5.34
3251 3395 0.249741 AGTGGGTGTCAACTACGTGC 60.250 55.000 0.00 0.00 0.00 5.34
3252 3396 2.234300 AAGTGGGTGTCAACTACGTG 57.766 50.000 0.00 0.00 0.00 4.49
3253 3397 2.168936 TCAAAGTGGGTGTCAACTACGT 59.831 45.455 0.00 0.00 0.00 3.57
3254 3398 2.800544 CTCAAAGTGGGTGTCAACTACG 59.199 50.000 0.00 0.00 0.00 3.51
3265 3409 4.853924 ATTTGCTGTTACTCAAAGTGGG 57.146 40.909 8.61 0.00 35.89 4.61
3291 3435 5.822519 TCTTTGGATAAGAAATGTGCGCTAT 59.177 36.000 9.73 0.00 0.00 2.97
3302 3446 6.148948 CACGCATTGTTTCTTTGGATAAGAA 58.851 36.000 0.00 0.00 34.73 2.52
3304 3448 4.858692 CCACGCATTGTTTCTTTGGATAAG 59.141 41.667 0.00 0.00 0.00 1.73
3313 3457 1.336755 GTTGGACCACGCATTGTTTCT 59.663 47.619 0.00 0.00 0.00 2.52
3321 3465 1.139256 TCAGTTAAGTTGGACCACGCA 59.861 47.619 0.00 0.00 0.00 5.24
3349 3493 5.151389 GTTCTTCAATTTGCGAAATACCGT 58.849 37.500 0.00 0.00 0.00 4.83
3352 3496 6.089283 TGCATGTTCTTCAATTTGCGAAATAC 59.911 34.615 0.00 0.00 32.90 1.89
3364 3508 1.689984 TGCCACTGCATGTTCTTCAA 58.310 45.000 0.00 0.00 44.23 2.69


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

AutoCloner maintained by Alex Coulton.