Multiple sequence alignment - TraesCS5D01G028400

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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 TraesCS5D01G028400 chr5D 100.000 2132 0 0 640 2771 26959808 26957677 0.000000e+00 3938
1 TraesCS5D01G028400 chr5D 100.000 338 0 0 1 338 26960447 26960110 2.340000e-175 625
2 TraesCS5D01G028400 chr5D 96.992 266 6 1 1 264 501233680 501233415 1.960000e-121 446
3 TraesCS5D01G028400 chr2D 96.674 2135 68 2 640 2771 260867055 260864921 0.000000e+00 3546
4 TraesCS5D01G028400 chr2D 95.225 2136 63 13 640 2771 241270090 241272190 0.000000e+00 3343
5 TraesCS5D01G028400 chr2D 95.854 1785 54 3 640 2423 451468071 451469836 0.000000e+00 2868
6 TraesCS5D01G028400 chr2D 91.712 1834 93 6 640 2446 520043207 520045008 0.000000e+00 2490
7 TraesCS5D01G028400 chr2D 96.436 1375 49 0 640 2014 613419906 613421280 0.000000e+00 2268
8 TraesCS5D01G028400 chr2D 94.100 678 13 6 2097 2771 613421282 613421935 0.000000e+00 1005
9 TraesCS5D01G028400 chr2D 96.944 360 8 2 2415 2771 451487533 451487892 3.950000e-168 601
10 TraesCS5D01G028400 chr2D 94.026 385 11 2 2389 2771 520044984 520045358 8.610000e-160 573
11 TraesCS5D01G028400 chr2D 91.623 382 20 2 2392 2771 35330052 35329681 4.090000e-143 518
12 TraesCS5D01G028400 chr2D 96.241 266 8 1 1 264 54087253 54086988 4.240000e-118 435
13 TraesCS5D01G028400 chr2D 95.865 266 9 1 1 264 54092963 54092698 1.970000e-116 429
14 TraesCS5D01G028400 chr2D 94.681 94 2 3 246 338 241274318 241274227 2.880000e-30 143
15 TraesCS5D01G028400 chr2D 96.471 85 2 1 255 338 613419779 613419863 3.720000e-29 139
16 TraesCS5D01G028400 chr2D 96.386 83 2 1 257 338 451491043 451490961 4.810000e-28 135
17 TraesCS5D01G028400 chr7D 92.329 1812 112 9 640 2446 151512093 151513882 0.000000e+00 2551
18 TraesCS5D01G028400 chr7D 95.865 266 9 1 1 264 364477091 364477356 1.970000e-116 429
19 TraesCS5D01G028400 chr7D 98.734 79 1 0 260 338 564928014 564928092 1.030000e-29 141
20 TraesCS5D01G028400 chr7D 98.734 79 1 0 260 338 564929076 564928998 1.030000e-29 141
21 TraesCS5D01G028400 chr7A 89.807 1815 145 18 640 2446 471263768 471261986 0.000000e+00 2290
22 TraesCS5D01G028400 chr7A 91.837 98 6 2 242 338 471263906 471263810 4.810000e-28 135
23 TraesCS5D01G028400 chr6B 89.823 1808 142 16 640 2446 494076554 494078320 0.000000e+00 2281
24 TraesCS5D01G028400 chr6B 94.574 387 17 3 2389 2771 28119329 28119715 1.840000e-166 595
25 TraesCS5D01G028400 chr6B 92.987 385 15 2 2389 2771 494078296 494078670 4.030000e-153 551
26 TraesCS5D01G028400 chr6B 95.208 313 14 1 2135 2446 28119041 28119353 6.890000e-136 494
27 TraesCS5D01G028400 chr6D 95.754 1413 59 1 640 2052 114017437 114016026 0.000000e+00 2276
28 TraesCS5D01G028400 chr6D 96.241 266 8 1 1 264 115705136 115705401 4.240000e-118 435
29 TraesCS5D01G028400 chr6D 97.590 83 1 1 257 338 114015081 114015163 1.030000e-29 141
30 TraesCS5D01G028400 chr6D 97.531 81 2 0 258 338 16604208 16604288 3.720000e-29 139
31 TraesCS5D01G028400 chr6D 96.386 83 2 1 257 338 16605575 16605493 4.810000e-28 135
32 TraesCS5D01G028400 chr6A 89.653 1817 142 21 640 2446 144491595 144493375 0.000000e+00 2272
33 TraesCS5D01G028400 chr6A 93.384 393 14 5 2381 2771 596357344 596357726 3.100000e-159 571
34 TraesCS5D01G028400 chr6A 91.969 386 16 4 2389 2771 144493351 144493724 6.800000e-146 527
35 TraesCS5D01G028400 chr6A 91.633 251 17 2 1952 2201 596356913 596357160 7.350000e-91 344
36 TraesCS5D01G028400 chr5B 93.786 1400 84 2 640 2037 260235054 260236452 0.000000e+00 2100
37 TraesCS5D01G028400 chr5B 94.012 334 17 2 2389 2719 260236756 260237089 1.150000e-138 503
38 TraesCS5D01G028400 chr5B 95.865 266 9 1 1 264 274107845 274108110 1.970000e-116 429
39 TraesCS5D01G028400 chr5B 93.939 231 11 3 2218 2446 260236551 260236780 2.040000e-91 346
40 TraesCS5D01G028400 chr5A 86.719 512 46 11 1952 2446 407701248 407701754 1.450000e-152 549
41 TraesCS5D01G028400 chr5A 92.112 393 18 6 2381 2771 407701723 407702104 2.430000e-150 542
42 TraesCS5D01G028400 chr1D 95.273 275 10 2 1 273 100011090 100011363 1.520000e-117 433
43 TraesCS5D01G028400 chr1D 95.865 266 9 1 1 264 83767177 83766912 1.970000e-116 429
44 TraesCS5D01G028400 chr1D 95.865 266 9 1 1 264 194073264 194073529 1.970000e-116 429
45 TraesCS5D01G028400 chr3A 91.633 251 17 2 1952 2201 478914993 478915240 7.350000e-91 344
46 TraesCS5D01G028400 chr2A 90.438 251 20 2 1952 2201 673358973 673359220 7.400000e-86 327


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 TraesCS5D01G028400 chr5D 26957677 26960447 2770 True 2281.500000 3938 100.000000 1 2771 2 chr5D.!!$R2 2770
1 TraesCS5D01G028400 chr2D 260864921 260867055 2134 True 3546.000000 3546 96.674000 640 2771 1 chr2D.!!$R5 2131
2 TraesCS5D01G028400 chr2D 241270090 241272190 2100 False 3343.000000 3343 95.225000 640 2771 1 chr2D.!!$F1 2131
3 TraesCS5D01G028400 chr2D 451468071 451469836 1765 False 2868.000000 2868 95.854000 640 2423 1 chr2D.!!$F2 1783
4 TraesCS5D01G028400 chr2D 520043207 520045358 2151 False 1531.500000 2490 92.869000 640 2771 2 chr2D.!!$F4 2131
5 TraesCS5D01G028400 chr2D 613419779 613421935 2156 False 1137.333333 2268 95.669000 255 2771 3 chr2D.!!$F5 2516
6 TraesCS5D01G028400 chr7D 151512093 151513882 1789 False 2551.000000 2551 92.329000 640 2446 1 chr7D.!!$F1 1806
7 TraesCS5D01G028400 chr7A 471261986 471263906 1920 True 1212.500000 2290 90.822000 242 2446 2 chr7A.!!$R1 2204
8 TraesCS5D01G028400 chr6B 494076554 494078670 2116 False 1416.000000 2281 91.405000 640 2771 2 chr6B.!!$F2 2131
9 TraesCS5D01G028400 chr6B 28119041 28119715 674 False 544.500000 595 94.891000 2135 2771 2 chr6B.!!$F1 636
10 TraesCS5D01G028400 chr6D 114016026 114017437 1411 True 2276.000000 2276 95.754000 640 2052 1 chr6D.!!$R2 1412
11 TraesCS5D01G028400 chr6A 144491595 144493724 2129 False 1399.500000 2272 90.811000 640 2771 2 chr6A.!!$F1 2131
12 TraesCS5D01G028400 chr6A 596356913 596357726 813 False 457.500000 571 92.508500 1952 2771 2 chr6A.!!$F2 819
13 TraesCS5D01G028400 chr5B 260235054 260237089 2035 False 983.000000 2100 93.912333 640 2719 3 chr5B.!!$F2 2079
14 TraesCS5D01G028400 chr5A 407701248 407702104 856 False 545.500000 549 89.415500 1952 2771 2 chr5A.!!$F1 819

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
186 187 0.769247 ACGGACCCTAGGCTTTGTTT 59.231 50.000 2.05 0.0 0.0 2.83 F
217 218 1.001158 CAATACCGTTTTTGTGCCCGT 60.001 47.619 0.00 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1346 1348 0.389948 ATCTTTCACAGACGCCGTCC 60.390 55.0 14.6 0.0 32.83 4.79 R
2203 2352 0.179215 GTGATGTGCTACTTGCGTGC 60.179 55.0 0.0 0.0 46.63 5.34 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 4.657436 AGATCGAACGGAAAGAATAGCT 57.343 40.909 0.00 0.00 0.00 3.32
24 25 5.012328 AGATCGAACGGAAAGAATAGCTT 57.988 39.130 0.00 0.00 38.88 3.74
26 27 4.921470 TCGAACGGAAAGAATAGCTTTG 57.079 40.909 0.00 0.00 46.52 2.77
27 28 4.562082 TCGAACGGAAAGAATAGCTTTGA 58.438 39.130 0.00 0.00 46.52 2.69
28 29 4.625742 TCGAACGGAAAGAATAGCTTTGAG 59.374 41.667 0.00 0.00 46.52 3.02
29 30 4.201724 CGAACGGAAAGAATAGCTTTGAGG 60.202 45.833 0.00 0.00 46.52 3.86
30 31 4.287766 ACGGAAAGAATAGCTTTGAGGT 57.712 40.909 0.00 0.00 46.52 3.85
31 32 4.003648 ACGGAAAGAATAGCTTTGAGGTG 58.996 43.478 0.00 0.00 46.52 4.00
32 33 3.375299 CGGAAAGAATAGCTTTGAGGTGG 59.625 47.826 0.00 0.00 46.52 4.61
33 34 4.336280 GGAAAGAATAGCTTTGAGGTGGT 58.664 43.478 0.00 0.00 46.52 4.16
34 35 4.767409 GGAAAGAATAGCTTTGAGGTGGTT 59.233 41.667 0.00 0.00 46.52 3.67
35 36 5.243954 GGAAAGAATAGCTTTGAGGTGGTTT 59.756 40.000 0.00 0.00 46.52 3.27
36 37 5.966742 AAGAATAGCTTTGAGGTGGTTTC 57.033 39.130 0.00 0.00 31.11 2.78
37 38 4.003648 AGAATAGCTTTGAGGTGGTTTCG 58.996 43.478 0.00 0.00 0.00 3.46
38 39 2.922740 TAGCTTTGAGGTGGTTTCGT 57.077 45.000 0.00 0.00 0.00 3.85
39 40 2.922740 AGCTTTGAGGTGGTTTCGTA 57.077 45.000 0.00 0.00 0.00 3.43
40 41 2.490991 AGCTTTGAGGTGGTTTCGTAC 58.509 47.619 0.00 0.00 0.00 3.67
56 57 8.272545 GGTTTCGTACCCTACAAATAATTTCT 57.727 34.615 0.00 0.00 41.43 2.52
57 58 9.382275 GGTTTCGTACCCTACAAATAATTTCTA 57.618 33.333 0.00 0.00 41.43 2.10
79 80 9.823647 TTCTATCTTTTGTTCTCTGCTAATAGG 57.176 33.333 0.00 0.00 0.00 2.57
80 81 9.201989 TCTATCTTTTGTTCTCTGCTAATAGGA 57.798 33.333 0.00 0.00 0.00 2.94
81 82 9.823647 CTATCTTTTGTTCTCTGCTAATAGGAA 57.176 33.333 0.00 0.00 0.00 3.36
82 83 7.907214 TCTTTTGTTCTCTGCTAATAGGAAC 57.093 36.000 0.00 0.00 37.41 3.62
83 84 7.680730 TCTTTTGTTCTCTGCTAATAGGAACT 58.319 34.615 0.00 0.00 46.37 3.01
84 85 7.819900 TCTTTTGTTCTCTGCTAATAGGAACTC 59.180 37.037 0.00 0.00 41.75 3.01
85 86 5.250235 TGTTCTCTGCTAATAGGAACTCG 57.750 43.478 0.00 0.00 41.75 4.18
86 87 4.098044 TGTTCTCTGCTAATAGGAACTCGG 59.902 45.833 0.00 0.00 41.75 4.63
87 88 3.223435 TCTCTGCTAATAGGAACTCGGG 58.777 50.000 0.00 0.00 41.75 5.14
88 89 3.117625 TCTCTGCTAATAGGAACTCGGGA 60.118 47.826 0.00 0.00 41.75 5.14
89 90 3.223435 TCTGCTAATAGGAACTCGGGAG 58.777 50.000 0.00 0.00 41.75 4.30
90 91 2.959707 CTGCTAATAGGAACTCGGGAGT 59.040 50.000 0.00 0.00 44.94 3.85
91 92 2.693591 TGCTAATAGGAACTCGGGAGTG 59.306 50.000 1.44 0.00 41.58 3.51
92 93 2.957006 GCTAATAGGAACTCGGGAGTGA 59.043 50.000 1.44 0.00 41.58 3.41
93 94 3.574826 GCTAATAGGAACTCGGGAGTGAT 59.425 47.826 1.44 0.00 41.58 3.06
94 95 4.039366 GCTAATAGGAACTCGGGAGTGATT 59.961 45.833 1.44 3.63 41.58 2.57
95 96 4.674281 AATAGGAACTCGGGAGTGATTC 57.326 45.455 1.44 0.00 41.58 2.52
96 97 2.239681 AGGAACTCGGGAGTGATTCT 57.760 50.000 1.44 0.00 41.58 2.40
97 98 3.383698 AGGAACTCGGGAGTGATTCTA 57.616 47.619 1.44 0.00 41.58 2.10
98 99 3.917300 AGGAACTCGGGAGTGATTCTAT 58.083 45.455 1.44 0.00 41.58 1.98
99 100 4.290942 AGGAACTCGGGAGTGATTCTATT 58.709 43.478 1.44 0.00 41.58 1.73
100 101 4.100189 AGGAACTCGGGAGTGATTCTATTG 59.900 45.833 1.44 0.00 41.58 1.90
101 102 3.460857 ACTCGGGAGTGATTCTATTGC 57.539 47.619 0.00 0.00 40.75 3.56
102 103 2.766263 ACTCGGGAGTGATTCTATTGCA 59.234 45.455 0.00 0.00 40.75 4.08
103 104 3.126831 CTCGGGAGTGATTCTATTGCAC 58.873 50.000 0.00 0.00 0.00 4.57
104 105 2.766263 TCGGGAGTGATTCTATTGCACT 59.234 45.455 0.00 0.00 44.87 4.40
105 106 3.197766 TCGGGAGTGATTCTATTGCACTT 59.802 43.478 0.00 0.00 42.47 3.16
106 107 3.557595 CGGGAGTGATTCTATTGCACTTC 59.442 47.826 0.00 0.00 42.47 3.01
107 108 3.557595 GGGAGTGATTCTATTGCACTTCG 59.442 47.826 0.00 0.00 42.47 3.79
108 109 4.433615 GGAGTGATTCTATTGCACTTCGA 58.566 43.478 0.00 0.00 42.47 3.71
109 110 4.505922 GGAGTGATTCTATTGCACTTCGAG 59.494 45.833 0.00 0.00 42.47 4.04
110 111 4.437239 AGTGATTCTATTGCACTTCGAGG 58.563 43.478 0.00 0.00 39.69 4.63
111 112 3.557595 GTGATTCTATTGCACTTCGAGGG 59.442 47.826 0.00 0.00 0.00 4.30
112 113 3.450817 TGATTCTATTGCACTTCGAGGGA 59.549 43.478 0.00 0.00 0.00 4.20
113 114 4.101585 TGATTCTATTGCACTTCGAGGGAT 59.898 41.667 0.00 0.00 0.00 3.85
114 115 5.304357 TGATTCTATTGCACTTCGAGGGATA 59.696 40.000 0.00 0.00 0.00 2.59
115 116 5.607939 TTCTATTGCACTTCGAGGGATAA 57.392 39.130 0.00 0.00 0.00 1.75
116 117 5.808366 TCTATTGCACTTCGAGGGATAAT 57.192 39.130 0.00 0.00 0.00 1.28
117 118 5.784177 TCTATTGCACTTCGAGGGATAATC 58.216 41.667 0.00 0.00 0.00 1.75
118 119 3.904800 TTGCACTTCGAGGGATAATCA 57.095 42.857 0.00 0.00 0.00 2.57
119 120 4.422073 TTGCACTTCGAGGGATAATCAT 57.578 40.909 0.00 0.00 0.00 2.45
120 121 5.545063 TTGCACTTCGAGGGATAATCATA 57.455 39.130 0.00 0.00 0.00 2.15
121 122 5.745312 TGCACTTCGAGGGATAATCATAT 57.255 39.130 0.00 0.00 0.00 1.78
122 123 5.482006 TGCACTTCGAGGGATAATCATATG 58.518 41.667 0.00 0.00 0.00 1.78
123 124 5.245977 TGCACTTCGAGGGATAATCATATGA 59.754 40.000 8.10 8.10 0.00 2.15
124 125 6.070596 TGCACTTCGAGGGATAATCATATGAT 60.071 38.462 12.62 12.62 36.07 2.45
125 126 6.478344 GCACTTCGAGGGATAATCATATGATC 59.522 42.308 18.44 7.42 32.75 2.92
126 127 6.983307 CACTTCGAGGGATAATCATATGATCC 59.017 42.308 18.44 15.65 38.78 3.36
127 128 6.669591 ACTTCGAGGGATAATCATATGATCCA 59.330 38.462 18.44 10.10 40.90 3.41
128 129 7.180946 ACTTCGAGGGATAATCATATGATCCAA 59.819 37.037 18.44 8.04 40.90 3.53
129 130 6.878317 TCGAGGGATAATCATATGATCCAAC 58.122 40.000 18.44 12.17 40.90 3.77
130 131 6.669591 TCGAGGGATAATCATATGATCCAACT 59.330 38.462 18.44 12.67 40.90 3.16
131 132 7.839200 TCGAGGGATAATCATATGATCCAACTA 59.161 37.037 18.44 7.50 40.90 2.24
132 133 8.646004 CGAGGGATAATCATATGATCCAACTAT 58.354 37.037 18.44 11.75 40.90 2.12
133 134 9.775854 GAGGGATAATCATATGATCCAACTATG 57.224 37.037 18.44 0.00 40.90 2.23
134 135 9.289049 AGGGATAATCATATGATCCAACTATGT 57.711 33.333 18.44 2.63 40.90 2.29
135 136 9.911788 GGGATAATCATATGATCCAACTATGTT 57.088 33.333 18.44 2.72 40.90 2.71
140 141 9.970553 AATCATATGATCCAACTATGTTAGCAT 57.029 29.630 18.44 0.00 34.97 3.79
141 142 9.970553 ATCATATGATCCAACTATGTTAGCATT 57.029 29.630 12.62 0.00 36.58 3.56
142 143 9.223099 TCATATGATCCAACTATGTTAGCATTG 57.777 33.333 0.00 0.00 36.58 2.82
143 144 9.006839 CATATGATCCAACTATGTTAGCATTGT 57.993 33.333 0.00 0.00 41.48 2.71
144 145 7.886629 ATGATCCAACTATGTTAGCATTGTT 57.113 32.000 12.25 12.25 46.45 2.83
150 151 6.500684 AACTATGTTAGCATTGTTGACAGG 57.499 37.500 16.10 3.07 44.81 4.00
151 152 5.560724 ACTATGTTAGCATTGTTGACAGGT 58.439 37.500 0.00 3.58 37.71 4.00
152 153 6.003950 ACTATGTTAGCATTGTTGACAGGTT 58.996 36.000 0.00 0.00 37.71 3.50
153 154 4.566545 TGTTAGCATTGTTGACAGGTTG 57.433 40.909 0.00 0.00 0.00 3.77
154 155 3.243367 TGTTAGCATTGTTGACAGGTTGC 60.243 43.478 0.00 7.34 0.00 4.17
155 156 1.401761 AGCATTGTTGACAGGTTGCA 58.598 45.000 14.12 0.00 33.43 4.08
156 157 1.067516 AGCATTGTTGACAGGTTGCAC 59.932 47.619 14.12 0.00 33.43 4.57
157 158 1.067516 GCATTGTTGACAGGTTGCACT 59.932 47.619 0.00 0.00 32.20 4.40
158 159 2.293122 GCATTGTTGACAGGTTGCACTA 59.707 45.455 0.00 0.00 32.20 2.74
159 160 3.610114 GCATTGTTGACAGGTTGCACTAG 60.610 47.826 0.00 0.00 32.20 2.57
160 161 3.275617 TTGTTGACAGGTTGCACTAGT 57.724 42.857 0.00 0.00 0.00 2.57
161 162 2.560504 TGTTGACAGGTTGCACTAGTG 58.439 47.619 18.93 18.93 0.00 2.74
162 163 2.169561 TGTTGACAGGTTGCACTAGTGA 59.830 45.455 27.08 8.89 0.00 3.41
163 164 3.202906 GTTGACAGGTTGCACTAGTGAA 58.797 45.455 27.08 14.25 0.00 3.18
164 165 3.552132 TGACAGGTTGCACTAGTGAAA 57.448 42.857 27.08 20.07 0.00 2.69
165 166 3.466836 TGACAGGTTGCACTAGTGAAAG 58.533 45.455 27.08 12.89 0.00 2.62
166 167 3.118408 TGACAGGTTGCACTAGTGAAAGT 60.118 43.478 27.08 16.04 0.00 2.66
167 168 4.100344 TGACAGGTTGCACTAGTGAAAGTA 59.900 41.667 27.08 0.00 0.00 2.24
168 169 4.377897 ACAGGTTGCACTAGTGAAAGTAC 58.622 43.478 27.08 14.66 0.00 2.73
169 170 3.428870 CAGGTTGCACTAGTGAAAGTACG 59.571 47.826 27.08 7.37 0.00 3.67
170 171 2.735134 GGTTGCACTAGTGAAAGTACGG 59.265 50.000 27.08 0.00 0.00 4.02
171 172 3.553508 GGTTGCACTAGTGAAAGTACGGA 60.554 47.826 27.08 0.00 0.00 4.69
172 173 3.293311 TGCACTAGTGAAAGTACGGAC 57.707 47.619 27.08 5.03 0.00 4.79
173 174 2.029649 TGCACTAGTGAAAGTACGGACC 60.030 50.000 27.08 4.51 0.00 4.46
174 175 2.673326 GCACTAGTGAAAGTACGGACCC 60.673 54.545 27.08 0.00 0.00 4.46
175 176 2.824341 CACTAGTGAAAGTACGGACCCT 59.176 50.000 18.45 0.00 0.00 4.34
176 177 4.012374 CACTAGTGAAAGTACGGACCCTA 58.988 47.826 18.45 0.00 0.00 3.53
177 178 4.096081 CACTAGTGAAAGTACGGACCCTAG 59.904 50.000 18.45 0.00 0.00 3.02
178 179 2.454538 AGTGAAAGTACGGACCCTAGG 58.545 52.381 0.06 0.06 0.00 3.02
179 180 1.134877 GTGAAAGTACGGACCCTAGGC 60.135 57.143 2.05 0.00 0.00 3.93
180 181 1.272872 TGAAAGTACGGACCCTAGGCT 60.273 52.381 2.05 0.00 0.00 4.58
181 182 1.829849 GAAAGTACGGACCCTAGGCTT 59.170 52.381 2.05 0.00 0.00 4.35
182 183 1.948391 AAGTACGGACCCTAGGCTTT 58.052 50.000 2.05 0.00 0.00 3.51
183 184 1.192428 AGTACGGACCCTAGGCTTTG 58.808 55.000 2.05 0.00 0.00 2.77
184 185 0.900421 GTACGGACCCTAGGCTTTGT 59.100 55.000 2.05 1.66 0.00 2.83
185 186 1.277273 GTACGGACCCTAGGCTTTGTT 59.723 52.381 2.05 0.00 0.00 2.83
186 187 0.769247 ACGGACCCTAGGCTTTGTTT 59.231 50.000 2.05 0.00 0.00 2.83
187 188 1.144298 ACGGACCCTAGGCTTTGTTTT 59.856 47.619 2.05 0.00 0.00 2.43
188 189 1.810755 CGGACCCTAGGCTTTGTTTTC 59.189 52.381 2.05 0.00 0.00 2.29
189 190 2.812613 CGGACCCTAGGCTTTGTTTTCA 60.813 50.000 2.05 0.00 0.00 2.69
190 191 3.227614 GGACCCTAGGCTTTGTTTTCAA 58.772 45.455 2.05 0.00 38.10 2.69
191 192 3.255888 GGACCCTAGGCTTTGTTTTCAAG 59.744 47.826 2.05 0.00 41.09 3.02
192 193 2.628178 ACCCTAGGCTTTGTTTTCAAGC 59.372 45.455 2.05 0.00 41.09 4.01
193 194 2.627699 CCCTAGGCTTTGTTTTCAAGCA 59.372 45.455 2.05 0.00 41.09 3.91
194 195 3.259123 CCCTAGGCTTTGTTTTCAAGCAT 59.741 43.478 2.05 2.23 41.09 3.79
195 196 4.262592 CCCTAGGCTTTGTTTTCAAGCATT 60.263 41.667 2.05 0.00 41.09 3.56
209 210 4.988708 CAAGCATTGCAATACCGTTTTT 57.011 36.364 12.53 0.00 40.39 1.94
210 211 4.700332 CAAGCATTGCAATACCGTTTTTG 58.300 39.130 12.53 3.07 40.39 2.44
211 212 3.988819 AGCATTGCAATACCGTTTTTGT 58.011 36.364 12.53 0.00 0.00 2.83
212 213 3.740321 AGCATTGCAATACCGTTTTTGTG 59.260 39.130 12.53 0.00 0.00 3.33
213 214 3.664014 GCATTGCAATACCGTTTTTGTGC 60.664 43.478 12.53 4.49 0.00 4.57
214 215 2.141535 TGCAATACCGTTTTTGTGCC 57.858 45.000 0.00 0.00 0.00 5.01
215 216 1.269831 TGCAATACCGTTTTTGTGCCC 60.270 47.619 0.00 0.00 0.00 5.36
216 217 1.692296 CAATACCGTTTTTGTGCCCG 58.308 50.000 0.00 0.00 0.00 6.13
217 218 1.001158 CAATACCGTTTTTGTGCCCGT 60.001 47.619 0.00 0.00 0.00 5.28
218 219 1.320507 ATACCGTTTTTGTGCCCGTT 58.679 45.000 0.00 0.00 0.00 4.44
219 220 1.101331 TACCGTTTTTGTGCCCGTTT 58.899 45.000 0.00 0.00 0.00 3.60
220 221 1.101331 ACCGTTTTTGTGCCCGTTTA 58.899 45.000 0.00 0.00 0.00 2.01
221 222 1.202279 ACCGTTTTTGTGCCCGTTTAC 60.202 47.619 0.00 0.00 0.00 2.01
222 223 1.065851 CCGTTTTTGTGCCCGTTTACT 59.934 47.619 0.00 0.00 0.00 2.24
223 224 2.290093 CCGTTTTTGTGCCCGTTTACTA 59.710 45.455 0.00 0.00 0.00 1.82
224 225 3.058085 CCGTTTTTGTGCCCGTTTACTAT 60.058 43.478 0.00 0.00 0.00 2.12
225 226 4.538917 CGTTTTTGTGCCCGTTTACTATT 58.461 39.130 0.00 0.00 0.00 1.73
226 227 4.977347 CGTTTTTGTGCCCGTTTACTATTT 59.023 37.500 0.00 0.00 0.00 1.40
227 228 5.108179 CGTTTTTGTGCCCGTTTACTATTTG 60.108 40.000 0.00 0.00 0.00 2.32
228 229 3.562567 TTGTGCCCGTTTACTATTTGC 57.437 42.857 0.00 0.00 0.00 3.68
229 230 2.785562 TGTGCCCGTTTACTATTTGCT 58.214 42.857 0.00 0.00 0.00 3.91
230 231 3.940319 TGTGCCCGTTTACTATTTGCTA 58.060 40.909 0.00 0.00 0.00 3.49
231 232 3.685756 TGTGCCCGTTTACTATTTGCTAC 59.314 43.478 0.00 0.00 0.00 3.58
232 233 3.064408 GTGCCCGTTTACTATTTGCTACC 59.936 47.826 0.00 0.00 0.00 3.18
233 234 3.054948 TGCCCGTTTACTATTTGCTACCT 60.055 43.478 0.00 0.00 0.00 3.08
234 235 3.943381 GCCCGTTTACTATTTGCTACCTT 59.057 43.478 0.00 0.00 0.00 3.50
235 236 4.201881 GCCCGTTTACTATTTGCTACCTTG 60.202 45.833 0.00 0.00 0.00 3.61
236 237 4.201881 CCCGTTTACTATTTGCTACCTTGC 60.202 45.833 0.00 0.00 0.00 4.01
237 238 4.634443 CCGTTTACTATTTGCTACCTTGCT 59.366 41.667 0.00 0.00 0.00 3.91
238 239 5.447279 CCGTTTACTATTTGCTACCTTGCTG 60.447 44.000 0.00 0.00 0.00 4.41
239 240 5.121768 CGTTTACTATTTGCTACCTTGCTGT 59.878 40.000 0.00 0.00 0.00 4.40
240 241 6.348213 CGTTTACTATTTGCTACCTTGCTGTT 60.348 38.462 0.00 0.00 0.00 3.16
241 242 7.368059 GTTTACTATTTGCTACCTTGCTGTTT 58.632 34.615 0.00 0.00 0.00 2.83
242 243 7.519032 TTACTATTTGCTACCTTGCTGTTTT 57.481 32.000 0.00 0.00 0.00 2.43
243 244 6.405278 ACTATTTGCTACCTTGCTGTTTTT 57.595 33.333 0.00 0.00 0.00 1.94
244 245 7.519032 ACTATTTGCTACCTTGCTGTTTTTA 57.481 32.000 0.00 0.00 0.00 1.52
245 246 8.122472 ACTATTTGCTACCTTGCTGTTTTTAT 57.878 30.769 0.00 0.00 0.00 1.40
246 247 8.585018 ACTATTTGCTACCTTGCTGTTTTTATT 58.415 29.630 0.00 0.00 0.00 1.40
247 248 9.423061 CTATTTGCTACCTTGCTGTTTTTATTT 57.577 29.630 0.00 0.00 0.00 1.40
249 250 9.942850 ATTTGCTACCTTGCTGTTTTTATTTAT 57.057 25.926 0.00 0.00 0.00 1.40
250 251 9.771534 TTTGCTACCTTGCTGTTTTTATTTATT 57.228 25.926 0.00 0.00 0.00 1.40
251 252 8.980143 TGCTACCTTGCTGTTTTTATTTATTC 57.020 30.769 0.00 0.00 0.00 1.75
252 253 8.580720 TGCTACCTTGCTGTTTTTATTTATTCA 58.419 29.630 0.00 0.00 0.00 2.57
253 254 9.076596 GCTACCTTGCTGTTTTTATTTATTCAG 57.923 33.333 0.00 0.00 0.00 3.02
309 310 2.036571 GGTGGTTCGCTTTACCCCG 61.037 63.158 0.00 0.00 34.66 5.73
694 695 1.175983 GCGGTTTTGACCATGGTGGA 61.176 55.000 25.52 7.49 40.96 4.02
859 861 3.071837 TGAGCACCGCCGATGGTA 61.072 61.111 0.00 0.00 41.38 3.25
995 997 1.040339 GTCCTGATCTCCCGCACTCT 61.040 60.000 0.00 0.00 0.00 3.24
1077 1079 2.595463 GGCAAGCAGGCAGTGACA 60.595 61.111 0.00 0.00 43.51 3.58
1318 1320 1.446099 TACAAGAGCAAGCTCGGCG 60.446 57.895 15.67 0.00 46.90 6.46
1466 1468 1.134759 TCGTGACCCTTCGTTTGTTGA 60.135 47.619 0.00 0.00 0.00 3.18
1568 1570 4.083003 GCAATTTGAATTGGGTGACTACGA 60.083 41.667 15.89 0.00 44.54 3.43
1733 1736 4.763073 CATATCTTCAAGACTGTGCTGGA 58.237 43.478 0.00 0.00 0.00 3.86
1754 1757 0.817654 AAGATCGATGGCACTGACGA 59.182 50.000 0.54 9.48 39.01 4.20
1774 1777 3.124297 CGATGCTGAAGGAGTTTGAGTTC 59.876 47.826 0.00 0.00 0.00 3.01
1852 1865 7.859325 ATTTGTAGTGTTGTACTGTGTCTTT 57.141 32.000 0.00 0.00 40.65 2.52
1893 1906 3.550820 TGTTGTGGTGAAGCAACTGTAT 58.449 40.909 8.54 0.00 43.66 2.29
2089 2169 9.607988 TCTTTCAACAGAGAACATAGTAAACAA 57.392 29.630 0.00 0.00 0.00 2.83
2198 2347 6.704512 AACAAACACAAGTTCATCAAACAC 57.295 33.333 0.00 0.00 40.56 3.32
2203 2352 5.401550 ACACAAGTTCATCAAACACAAGTG 58.598 37.500 0.00 0.00 40.56 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.291128 TCAAAGCTATTCTTTCCGTTCGATC 59.709 40.000 0.00 0.00 42.82 3.69
6 7 4.201724 CCTCAAAGCTATTCTTTCCGTTCG 60.202 45.833 0.00 0.00 42.82 3.95
7 8 4.695928 ACCTCAAAGCTATTCTTTCCGTTC 59.304 41.667 0.00 0.00 42.82 3.95
8 9 4.455877 CACCTCAAAGCTATTCTTTCCGTT 59.544 41.667 0.00 0.00 42.82 4.44
9 10 4.003648 CACCTCAAAGCTATTCTTTCCGT 58.996 43.478 0.00 0.00 42.82 4.69
10 11 3.375299 CCACCTCAAAGCTATTCTTTCCG 59.625 47.826 0.00 0.00 42.82 4.30
11 12 4.336280 ACCACCTCAAAGCTATTCTTTCC 58.664 43.478 0.00 0.00 42.82 3.13
13 14 5.048713 CGAAACCACCTCAAAGCTATTCTTT 60.049 40.000 0.00 0.00 45.43 2.52
14 15 4.455877 CGAAACCACCTCAAAGCTATTCTT 59.544 41.667 0.00 0.00 36.34 2.52
18 19 3.418684 ACGAAACCACCTCAAAGCTAT 57.581 42.857 0.00 0.00 0.00 2.97
19 20 2.922740 ACGAAACCACCTCAAAGCTA 57.077 45.000 0.00 0.00 0.00 3.32
20 21 2.490991 GTACGAAACCACCTCAAAGCT 58.509 47.619 0.00 0.00 0.00 3.74
21 22 2.963498 GTACGAAACCACCTCAAAGC 57.037 50.000 0.00 0.00 0.00 3.51
53 54 9.823647 CCTATTAGCAGAGAACAAAAGATAGAA 57.176 33.333 0.00 0.00 0.00 2.10
54 55 9.201989 TCCTATTAGCAGAGAACAAAAGATAGA 57.798 33.333 0.00 0.00 0.00 1.98
55 56 9.823647 TTCCTATTAGCAGAGAACAAAAGATAG 57.176 33.333 0.00 0.00 0.00 2.08
56 57 9.601217 GTTCCTATTAGCAGAGAACAAAAGATA 57.399 33.333 0.00 0.00 37.39 1.98
57 58 8.325046 AGTTCCTATTAGCAGAGAACAAAAGAT 58.675 33.333 10.97 0.00 39.39 2.40
58 59 7.680730 AGTTCCTATTAGCAGAGAACAAAAGA 58.319 34.615 10.97 0.00 39.39 2.52
59 60 7.201478 CGAGTTCCTATTAGCAGAGAACAAAAG 60.201 40.741 10.97 0.00 39.39 2.27
60 61 6.590292 CGAGTTCCTATTAGCAGAGAACAAAA 59.410 38.462 10.97 0.00 39.39 2.44
61 62 6.100004 CGAGTTCCTATTAGCAGAGAACAAA 58.900 40.000 10.97 0.00 39.39 2.83
62 63 5.394224 CCGAGTTCCTATTAGCAGAGAACAA 60.394 44.000 10.97 0.00 39.39 2.83
63 64 4.098044 CCGAGTTCCTATTAGCAGAGAACA 59.902 45.833 10.97 0.00 39.39 3.18
64 65 4.500035 CCCGAGTTCCTATTAGCAGAGAAC 60.500 50.000 0.00 0.00 37.65 3.01
65 66 3.637229 CCCGAGTTCCTATTAGCAGAGAA 59.363 47.826 0.00 0.00 0.00 2.87
66 67 3.117625 TCCCGAGTTCCTATTAGCAGAGA 60.118 47.826 0.00 0.00 0.00 3.10
67 68 3.223435 TCCCGAGTTCCTATTAGCAGAG 58.777 50.000 0.00 0.00 0.00 3.35
68 69 3.223435 CTCCCGAGTTCCTATTAGCAGA 58.777 50.000 0.00 0.00 0.00 4.26
69 70 2.959707 ACTCCCGAGTTCCTATTAGCAG 59.040 50.000 0.00 0.00 38.83 4.24
70 71 2.693591 CACTCCCGAGTTCCTATTAGCA 59.306 50.000 0.00 0.00 40.20 3.49
71 72 2.957006 TCACTCCCGAGTTCCTATTAGC 59.043 50.000 0.00 0.00 40.20 3.09
72 73 5.536916 AGAATCACTCCCGAGTTCCTATTAG 59.463 44.000 0.00 0.00 40.20 1.73
73 74 5.455872 AGAATCACTCCCGAGTTCCTATTA 58.544 41.667 0.00 0.00 40.20 0.98
74 75 4.290942 AGAATCACTCCCGAGTTCCTATT 58.709 43.478 0.00 0.00 40.20 1.73
75 76 3.917300 AGAATCACTCCCGAGTTCCTAT 58.083 45.455 0.00 0.00 40.20 2.57
76 77 3.383698 AGAATCACTCCCGAGTTCCTA 57.616 47.619 0.00 0.00 40.20 2.94
77 78 2.239681 AGAATCACTCCCGAGTTCCT 57.760 50.000 0.00 0.00 40.20 3.36
78 79 4.372656 CAATAGAATCACTCCCGAGTTCC 58.627 47.826 0.00 0.00 40.20 3.62
79 80 3.804873 GCAATAGAATCACTCCCGAGTTC 59.195 47.826 0.00 0.00 40.20 3.01
80 81 3.197766 TGCAATAGAATCACTCCCGAGTT 59.802 43.478 0.00 0.00 40.20 3.01
81 82 2.766263 TGCAATAGAATCACTCCCGAGT 59.234 45.455 0.00 0.00 43.61 4.18
82 83 3.126831 GTGCAATAGAATCACTCCCGAG 58.873 50.000 0.00 0.00 0.00 4.63
83 84 2.766263 AGTGCAATAGAATCACTCCCGA 59.234 45.455 0.00 0.00 36.42 5.14
84 85 3.185246 AGTGCAATAGAATCACTCCCG 57.815 47.619 0.00 0.00 36.42 5.14
85 86 3.557595 CGAAGTGCAATAGAATCACTCCC 59.442 47.826 0.00 0.00 39.86 4.30
86 87 4.433615 TCGAAGTGCAATAGAATCACTCC 58.566 43.478 0.00 0.00 39.86 3.85
87 88 4.505922 CCTCGAAGTGCAATAGAATCACTC 59.494 45.833 0.00 0.00 39.86 3.51
88 89 4.437239 CCTCGAAGTGCAATAGAATCACT 58.563 43.478 0.00 0.00 42.28 3.41
89 90 3.557595 CCCTCGAAGTGCAATAGAATCAC 59.442 47.826 0.00 0.00 0.00 3.06
90 91 3.450817 TCCCTCGAAGTGCAATAGAATCA 59.549 43.478 0.00 0.00 0.00 2.57
91 92 4.060038 TCCCTCGAAGTGCAATAGAATC 57.940 45.455 0.00 0.00 0.00 2.52
92 93 4.696479 ATCCCTCGAAGTGCAATAGAAT 57.304 40.909 0.00 0.00 0.00 2.40
93 94 5.607939 TTATCCCTCGAAGTGCAATAGAA 57.392 39.130 0.00 0.00 0.00 2.10
94 95 5.304357 TGATTATCCCTCGAAGTGCAATAGA 59.696 40.000 0.00 0.00 0.00 1.98
95 96 5.541845 TGATTATCCCTCGAAGTGCAATAG 58.458 41.667 0.00 0.00 0.00 1.73
96 97 5.545063 TGATTATCCCTCGAAGTGCAATA 57.455 39.130 0.00 0.00 0.00 1.90
97 98 4.422073 TGATTATCCCTCGAAGTGCAAT 57.578 40.909 0.00 0.00 0.00 3.56
98 99 3.904800 TGATTATCCCTCGAAGTGCAA 57.095 42.857 0.00 0.00 0.00 4.08
99 100 5.245977 TCATATGATTATCCCTCGAAGTGCA 59.754 40.000 0.00 0.00 0.00 4.57
100 101 5.724328 TCATATGATTATCCCTCGAAGTGC 58.276 41.667 0.00 0.00 0.00 4.40
101 102 6.983307 GGATCATATGATTATCCCTCGAAGTG 59.017 42.308 19.11 0.00 34.30 3.16
102 103 6.669591 TGGATCATATGATTATCCCTCGAAGT 59.330 38.462 19.11 0.00 38.76 3.01
103 104 7.117285 TGGATCATATGATTATCCCTCGAAG 57.883 40.000 19.11 0.00 38.76 3.79
104 105 7.180946 AGTTGGATCATATGATTATCCCTCGAA 59.819 37.037 19.11 6.62 38.76 3.71
105 106 6.669591 AGTTGGATCATATGATTATCCCTCGA 59.330 38.462 19.11 0.59 38.76 4.04
106 107 6.882656 AGTTGGATCATATGATTATCCCTCG 58.117 40.000 19.11 0.00 38.76 4.63
107 108 9.775854 CATAGTTGGATCATATGATTATCCCTC 57.224 37.037 19.11 11.75 38.76 4.30
108 109 9.289049 ACATAGTTGGATCATATGATTATCCCT 57.711 33.333 19.11 12.09 38.76 4.20
109 110 9.911788 AACATAGTTGGATCATATGATTATCCC 57.088 33.333 19.11 15.26 38.76 3.85
114 115 9.970553 ATGCTAACATAGTTGGATCATATGATT 57.029 29.630 19.11 5.92 33.67 2.57
115 116 9.970553 AATGCTAACATAGTTGGATCATATGAT 57.029 29.630 18.21 18.21 34.62 2.45
116 117 9.223099 CAATGCTAACATAGTTGGATCATATGA 57.777 33.333 8.10 8.10 34.62 2.15
117 118 9.006839 ACAATGCTAACATAGTTGGATCATATG 57.993 33.333 0.00 0.00 34.62 1.78
118 119 9.578576 AACAATGCTAACATAGTTGGATCATAT 57.421 29.630 0.00 0.00 34.62 1.78
119 120 8.839343 CAACAATGCTAACATAGTTGGATCATA 58.161 33.333 0.00 0.00 34.62 2.15
120 121 7.557358 TCAACAATGCTAACATAGTTGGATCAT 59.443 33.333 0.00 0.00 37.52 2.45
121 122 6.883756 TCAACAATGCTAACATAGTTGGATCA 59.116 34.615 0.00 0.00 37.52 2.92
122 123 7.148255 TGTCAACAATGCTAACATAGTTGGATC 60.148 37.037 0.00 0.00 37.52 3.36
123 124 6.658816 TGTCAACAATGCTAACATAGTTGGAT 59.341 34.615 0.00 0.00 37.52 3.41
124 125 6.000840 TGTCAACAATGCTAACATAGTTGGA 58.999 36.000 0.00 0.00 37.52 3.53
125 126 6.252967 TGTCAACAATGCTAACATAGTTGG 57.747 37.500 0.00 0.00 37.52 3.77
126 127 6.072508 ACCTGTCAACAATGCTAACATAGTTG 60.073 38.462 0.00 0.00 34.62 3.16
127 128 6.003950 ACCTGTCAACAATGCTAACATAGTT 58.996 36.000 0.00 0.00 34.62 2.24
128 129 5.560724 ACCTGTCAACAATGCTAACATAGT 58.439 37.500 0.00 0.00 34.62 2.12
129 130 6.317088 CAACCTGTCAACAATGCTAACATAG 58.683 40.000 0.00 0.00 34.62 2.23
130 131 5.335583 GCAACCTGTCAACAATGCTAACATA 60.336 40.000 7.56 0.00 34.62 2.29
131 132 4.559300 GCAACCTGTCAACAATGCTAACAT 60.559 41.667 7.56 0.00 38.49 2.71
132 133 3.243367 GCAACCTGTCAACAATGCTAACA 60.243 43.478 7.56 0.00 31.46 2.41
133 134 3.243367 TGCAACCTGTCAACAATGCTAAC 60.243 43.478 13.14 0.00 33.73 2.34
134 135 2.954989 TGCAACCTGTCAACAATGCTAA 59.045 40.909 13.14 0.00 33.73 3.09
135 136 2.293122 GTGCAACCTGTCAACAATGCTA 59.707 45.455 13.14 2.39 33.73 3.49
136 137 1.067516 GTGCAACCTGTCAACAATGCT 59.932 47.619 13.14 0.00 33.73 3.79
137 138 1.067516 AGTGCAACCTGTCAACAATGC 59.932 47.619 0.00 7.78 37.80 3.56
138 139 3.565482 ACTAGTGCAACCTGTCAACAATG 59.435 43.478 0.00 0.00 37.80 2.82
139 140 3.565482 CACTAGTGCAACCTGTCAACAAT 59.435 43.478 10.54 0.00 37.80 2.71
140 141 2.942376 CACTAGTGCAACCTGTCAACAA 59.058 45.455 10.54 0.00 37.80 2.83
141 142 2.169561 TCACTAGTGCAACCTGTCAACA 59.830 45.455 18.45 0.00 37.80 3.33
142 143 2.833794 TCACTAGTGCAACCTGTCAAC 58.166 47.619 18.45 0.00 37.80 3.18
143 144 3.552132 TTCACTAGTGCAACCTGTCAA 57.448 42.857 18.45 0.89 37.80 3.18
144 145 3.118408 ACTTTCACTAGTGCAACCTGTCA 60.118 43.478 18.45 0.00 37.80 3.58
145 146 3.467803 ACTTTCACTAGTGCAACCTGTC 58.532 45.455 18.45 0.00 37.80 3.51
146 147 3.560636 ACTTTCACTAGTGCAACCTGT 57.439 42.857 18.45 5.48 37.80 4.00
147 148 3.428870 CGTACTTTCACTAGTGCAACCTG 59.571 47.826 18.45 4.84 37.80 4.00
148 149 3.554337 CCGTACTTTCACTAGTGCAACCT 60.554 47.826 18.45 2.34 37.80 3.50
149 150 2.735134 CCGTACTTTCACTAGTGCAACC 59.265 50.000 18.45 1.95 37.80 3.77
150 151 3.427863 GTCCGTACTTTCACTAGTGCAAC 59.572 47.826 18.45 9.74 31.14 4.17
151 152 3.553508 GGTCCGTACTTTCACTAGTGCAA 60.554 47.826 18.45 12.86 31.14 4.08
152 153 2.029649 GGTCCGTACTTTCACTAGTGCA 60.030 50.000 18.45 4.20 31.14 4.57
153 154 2.603953 GGTCCGTACTTTCACTAGTGC 58.396 52.381 18.45 1.95 0.00 4.40
154 155 2.824341 AGGGTCCGTACTTTCACTAGTG 59.176 50.000 17.17 17.17 0.00 2.74
155 156 3.166560 AGGGTCCGTACTTTCACTAGT 57.833 47.619 0.00 0.00 0.00 2.57
156 157 3.631227 CCTAGGGTCCGTACTTTCACTAG 59.369 52.174 0.00 9.08 0.00 2.57
157 158 3.624777 CCTAGGGTCCGTACTTTCACTA 58.375 50.000 0.00 0.00 0.00 2.74
158 159 2.454538 CCTAGGGTCCGTACTTTCACT 58.545 52.381 0.00 0.00 0.00 3.41
159 160 1.134877 GCCTAGGGTCCGTACTTTCAC 60.135 57.143 11.72 0.00 0.00 3.18
160 161 1.188863 GCCTAGGGTCCGTACTTTCA 58.811 55.000 11.72 0.00 0.00 2.69
161 162 1.482954 AGCCTAGGGTCCGTACTTTC 58.517 55.000 7.93 0.00 0.00 2.62
162 163 1.948391 AAGCCTAGGGTCCGTACTTT 58.052 50.000 15.24 0.00 0.00 2.66
163 164 1.553704 CAAAGCCTAGGGTCCGTACTT 59.446 52.381 15.24 0.13 0.00 2.24
164 165 1.192428 CAAAGCCTAGGGTCCGTACT 58.808 55.000 15.24 0.00 0.00 2.73
165 166 0.900421 ACAAAGCCTAGGGTCCGTAC 59.100 55.000 15.24 0.00 0.00 3.67
166 167 1.648116 AACAAAGCCTAGGGTCCGTA 58.352 50.000 15.24 0.00 0.00 4.02
167 168 0.769247 AAACAAAGCCTAGGGTCCGT 59.231 50.000 15.24 11.56 0.00 4.69
168 169 1.810755 GAAAACAAAGCCTAGGGTCCG 59.189 52.381 15.24 10.87 0.00 4.79
169 170 2.871453 TGAAAACAAAGCCTAGGGTCC 58.129 47.619 15.24 0.00 0.00 4.46
170 171 3.305403 GCTTGAAAACAAAGCCTAGGGTC 60.305 47.826 15.24 0.00 43.45 4.46
171 172 2.628178 GCTTGAAAACAAAGCCTAGGGT 59.372 45.455 7.93 7.93 43.45 4.34
172 173 3.303881 GCTTGAAAACAAAGCCTAGGG 57.696 47.619 11.72 0.00 43.45 3.53
179 180 6.365050 GGTATTGCAATGCTTGAAAACAAAG 58.635 36.000 24.03 0.00 30.50 2.77
180 181 5.050499 CGGTATTGCAATGCTTGAAAACAAA 60.050 36.000 24.03 0.00 30.50 2.83
181 182 4.447054 CGGTATTGCAATGCTTGAAAACAA 59.553 37.500 24.03 0.00 30.50 2.83
182 183 3.986572 CGGTATTGCAATGCTTGAAAACA 59.013 39.130 24.03 0.00 30.50 2.83
183 184 3.987220 ACGGTATTGCAATGCTTGAAAAC 59.013 39.130 24.03 11.07 30.50 2.43
184 185 4.250116 ACGGTATTGCAATGCTTGAAAA 57.750 36.364 24.03 0.00 30.50 2.29
185 186 3.932545 ACGGTATTGCAATGCTTGAAA 57.067 38.095 24.03 0.00 31.47 2.69
186 187 3.932545 AACGGTATTGCAATGCTTGAA 57.067 38.095 24.03 0.28 0.00 2.69
187 188 3.932545 AAACGGTATTGCAATGCTTGA 57.067 38.095 24.03 1.03 0.00 3.02
188 189 4.210955 ACAAAAACGGTATTGCAATGCTTG 59.789 37.500 24.03 20.85 0.00 4.01
189 190 4.210955 CACAAAAACGGTATTGCAATGCTT 59.789 37.500 24.03 11.08 0.00 3.91
190 191 3.740321 CACAAAAACGGTATTGCAATGCT 59.260 39.130 24.03 5.54 0.00 3.79
191 192 3.664014 GCACAAAAACGGTATTGCAATGC 60.664 43.478 22.27 20.14 0.00 3.56
192 193 3.120718 GGCACAAAAACGGTATTGCAATG 60.121 43.478 22.27 7.93 0.00 2.82
193 194 3.063485 GGCACAAAAACGGTATTGCAAT 58.937 40.909 17.56 17.56 0.00 3.56
194 195 2.474816 GGCACAAAAACGGTATTGCAA 58.525 42.857 0.00 0.00 0.00 4.08
195 196 1.269831 GGGCACAAAAACGGTATTGCA 60.270 47.619 6.52 0.00 0.00 4.08
196 197 1.424403 GGGCACAAAAACGGTATTGC 58.576 50.000 6.52 0.00 0.00 3.56
197 198 1.001158 ACGGGCACAAAAACGGTATTG 60.001 47.619 5.37 5.37 0.00 1.90
198 199 1.320507 ACGGGCACAAAAACGGTATT 58.679 45.000 0.00 0.00 0.00 1.89
199 200 1.320507 AACGGGCACAAAAACGGTAT 58.679 45.000 0.00 0.00 0.00 2.73
200 201 1.101331 AAACGGGCACAAAAACGGTA 58.899 45.000 0.00 0.00 0.00 4.02
201 202 1.101331 TAAACGGGCACAAAAACGGT 58.899 45.000 0.00 0.00 0.00 4.83
202 203 1.065851 AGTAAACGGGCACAAAAACGG 59.934 47.619 0.00 0.00 0.00 4.44
203 204 2.478547 AGTAAACGGGCACAAAAACG 57.521 45.000 0.00 0.00 0.00 3.60
204 205 5.332732 GCAAATAGTAAACGGGCACAAAAAC 60.333 40.000 0.00 0.00 0.00 2.43
205 206 4.745620 GCAAATAGTAAACGGGCACAAAAA 59.254 37.500 0.00 0.00 0.00 1.94
206 207 4.038162 AGCAAATAGTAAACGGGCACAAAA 59.962 37.500 0.00 0.00 0.00 2.44
207 208 3.570550 AGCAAATAGTAAACGGGCACAAA 59.429 39.130 0.00 0.00 0.00 2.83
208 209 3.150767 AGCAAATAGTAAACGGGCACAA 58.849 40.909 0.00 0.00 0.00 3.33
209 210 2.785562 AGCAAATAGTAAACGGGCACA 58.214 42.857 0.00 0.00 0.00 4.57
210 211 3.064408 GGTAGCAAATAGTAAACGGGCAC 59.936 47.826 0.00 0.00 0.00 5.01
211 212 3.054948 AGGTAGCAAATAGTAAACGGGCA 60.055 43.478 0.00 0.00 0.00 5.36
212 213 3.538591 AGGTAGCAAATAGTAAACGGGC 58.461 45.455 0.00 0.00 0.00 6.13
213 214 4.201881 GCAAGGTAGCAAATAGTAAACGGG 60.202 45.833 0.00 0.00 0.00 5.28
214 215 4.634443 AGCAAGGTAGCAAATAGTAAACGG 59.366 41.667 0.00 0.00 36.85 4.44
215 216 5.121768 ACAGCAAGGTAGCAAATAGTAAACG 59.878 40.000 0.00 0.00 36.85 3.60
216 217 6.496338 ACAGCAAGGTAGCAAATAGTAAAC 57.504 37.500 0.00 0.00 36.85 2.01
217 218 7.519032 AAACAGCAAGGTAGCAAATAGTAAA 57.481 32.000 0.00 0.00 36.85 2.01
218 219 7.519032 AAAACAGCAAGGTAGCAAATAGTAA 57.481 32.000 0.00 0.00 36.85 2.24
219 220 7.519032 AAAAACAGCAAGGTAGCAAATAGTA 57.481 32.000 0.00 0.00 36.85 1.82
220 221 6.405278 AAAAACAGCAAGGTAGCAAATAGT 57.595 33.333 0.00 0.00 36.85 2.12
221 222 8.986477 AATAAAAACAGCAAGGTAGCAAATAG 57.014 30.769 0.00 0.00 36.85 1.73
223 224 9.942850 ATAAATAAAAACAGCAAGGTAGCAAAT 57.057 25.926 0.00 0.00 36.85 2.32
224 225 9.771534 AATAAATAAAAACAGCAAGGTAGCAAA 57.228 25.926 0.00 0.00 36.85 3.68
225 226 9.418045 GAATAAATAAAAACAGCAAGGTAGCAA 57.582 29.630 0.00 0.00 36.85 3.91
226 227 8.580720 TGAATAAATAAAAACAGCAAGGTAGCA 58.419 29.630 0.00 0.00 36.85 3.49
227 228 8.980143 TGAATAAATAAAAACAGCAAGGTAGC 57.020 30.769 0.00 0.00 0.00 3.58
252 253 9.244292 GGGAGTAAAATGGACTTTTTCTAATCT 57.756 33.333 0.00 0.00 35.38 2.40
253 254 8.467598 GGGGAGTAAAATGGACTTTTTCTAATC 58.532 37.037 0.00 0.00 35.38 1.75
254 255 8.177456 AGGGGAGTAAAATGGACTTTTTCTAAT 58.823 33.333 0.00 0.00 35.38 1.73
255 256 7.450323 CAGGGGAGTAAAATGGACTTTTTCTAA 59.550 37.037 0.00 0.00 35.38 2.10
256 257 6.946009 CAGGGGAGTAAAATGGACTTTTTCTA 59.054 38.462 0.00 0.00 35.38 2.10
257 258 5.775195 CAGGGGAGTAAAATGGACTTTTTCT 59.225 40.000 0.00 0.00 37.22 2.52
258 259 5.773176 TCAGGGGAGTAAAATGGACTTTTTC 59.227 40.000 0.00 0.00 38.09 2.29
309 310 6.765915 AGAAGGAGCCAAAATAAAGATCAC 57.234 37.500 0.00 0.00 0.00 3.06
995 997 2.755064 CCAACGCATCCATGGCCA 60.755 61.111 8.56 8.56 0.00 5.36
1022 1024 4.729856 GAAGCACGTACCGCCCGT 62.730 66.667 0.00 0.00 39.52 5.28
1125 1127 0.833287 CCTCAATGACCACCTCGGAT 59.167 55.000 0.00 0.00 38.63 4.18
1318 1320 0.696501 TGGTTAGGGAGGCCTTCAAC 59.303 55.000 14.70 9.62 0.00 3.18
1346 1348 0.389948 ATCTTTCACAGACGCCGTCC 60.390 55.000 14.60 0.00 32.83 4.79
1356 1358 3.251729 GCTGCTTGAGAACATCTTTCACA 59.748 43.478 0.00 0.00 0.00 3.58
1466 1468 0.469917 CTCCACTGTCACCACCTTGT 59.530 55.000 0.00 0.00 0.00 3.16
1733 1736 1.737029 CGTCAGTGCCATCGATCTTGT 60.737 52.381 0.00 0.00 0.00 3.16
1754 1757 3.070018 CGAACTCAAACTCCTTCAGCAT 58.930 45.455 0.00 0.00 0.00 3.79
1774 1777 5.331902 CAAAGTGCCAAATAACAGGATACG 58.668 41.667 0.00 0.00 46.39 3.06
1830 1843 7.549839 ACTAAAGACACAGTACAACACTACAA 58.450 34.615 0.00 0.00 34.98 2.41
1852 1865 5.031066 ACAACCAGCACAAAGTAGAACTA 57.969 39.130 0.00 0.00 0.00 2.24
1893 1906 4.400884 ACAAATTCAGTACACACCAAGCAA 59.599 37.500 0.00 0.00 0.00 3.91
2089 2169 5.199024 TGTGTTCAGTTGCAAAATGCTAT 57.801 34.783 0.00 0.00 42.52 2.97
2198 2347 1.941072 TGCTACTTGCGTGCACTTG 59.059 52.632 16.19 0.69 46.63 3.16
2203 2352 0.179215 GTGATGTGCTACTTGCGTGC 60.179 55.000 0.00 0.00 46.63 5.34
2520 2706 5.587043 TGTTACTTCTGTGTGTTTTGTAGGG 59.413 40.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.