Multiple sequence alignment - TraesCS3B01G571500

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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 TraesCS3B01G571500 chr3B 100.000 4831 0 0 1 4831 803050392 803045562 0.000000e+00 8922.0
1 TraesCS3B01G571500 chr3B 92.336 4045 239 30 532 4538 801196540 801192529 0.000000e+00 5686.0
2 TraesCS3B01G571500 chr3B 85.868 3156 373 40 932 4053 799104618 799101502 0.000000e+00 3290.0
3 TraesCS3B01G571500 chr3B 92.386 2259 130 11 2144 4382 802610470 802608234 0.000000e+00 3181.0
4 TraesCS3B01G571500 chr3B 92.628 1370 88 12 241 1607 802617128 802615769 0.000000e+00 1958.0
5 TraesCS3B01G571500 chr3B 93.160 307 8 5 4525 4831 801192358 801192065 5.740000e-119 438.0
6 TraesCS3B01G571500 chr3B 71.798 851 204 31 1725 2557 54794719 54795551 4.900000e-50 209.0
7 TraesCS3B01G571500 chr3B 92.982 57 4 0 2082 2138 802615769 802615713 3.100000e-12 84.2
8 TraesCS3B01G571500 chr3D 92.214 3763 233 16 579 4313 596847969 596851699 0.000000e+00 5271.0
9 TraesCS3B01G571500 chr3D 84.961 3165 385 43 932 4065 595942816 595939712 0.000000e+00 3123.0
10 TraesCS3B01G571500 chr3D 92.113 710 52 3 3434 4142 595931010 595930304 0.000000e+00 998.0
11 TraesCS3B01G571500 chr3D 93.429 487 10 6 4346 4831 596851700 596852165 0.000000e+00 702.0
12 TraesCS3B01G571500 chr3D 76.561 849 193 4 2838 3683 32280415 32281260 1.230000e-125 460.0
13 TraesCS3B01G571500 chr3D 89.174 351 30 8 241 588 596846769 596847114 9.610000e-117 431.0
14 TraesCS3B01G571500 chr3D 82.192 292 33 13 4116 4394 595930287 595930002 2.910000e-57 233.0
15 TraesCS3B01G571500 chr3A 83.231 2123 296 39 934 3027 726743229 726741138 0.000000e+00 1893.0
16 TraesCS3B01G571500 chr3A 90.393 687 51 7 3468 4145 726726466 726725786 0.000000e+00 889.0
17 TraesCS3B01G571500 chr3A 91.463 410 35 0 3021 3430 726726871 726726462 9.080000e-157 564.0
18 TraesCS3B01G571500 chr3A 82.305 486 56 15 3964 4427 726722020 726721543 1.260000e-105 394.0
19 TraesCS3B01G571500 chr3A 71.777 861 195 40 1726 2562 44639922 44640758 2.950000e-47 200.0
20 TraesCS3B01G571500 chr3A 75.628 398 77 19 1514 1901 44710042 44710429 3.840000e-41 180.0
21 TraesCS3B01G571500 chr3A 91.837 49 3 1 4587 4634 726725553 726725505 3.120000e-07 67.6


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 TraesCS3B01G571500 chr3B 803045562 803050392 4830 True 8922.000000 8922 100.000000 1 4831 1 chr3B.!!$R3 4830
1 TraesCS3B01G571500 chr3B 799101502 799104618 3116 True 3290.000000 3290 85.868000 932 4053 1 chr3B.!!$R1 3121
2 TraesCS3B01G571500 chr3B 802608234 802610470 2236 True 3181.000000 3181 92.386000 2144 4382 1 chr3B.!!$R2 2238
3 TraesCS3B01G571500 chr3B 801192065 801196540 4475 True 3062.000000 5686 92.748000 532 4831 2 chr3B.!!$R4 4299
4 TraesCS3B01G571500 chr3B 802615713 802617128 1415 True 1021.100000 1958 92.805000 241 2138 2 chr3B.!!$R5 1897
5 TraesCS3B01G571500 chr3B 54794719 54795551 832 False 209.000000 209 71.798000 1725 2557 1 chr3B.!!$F1 832
6 TraesCS3B01G571500 chr3D 595939712 595942816 3104 True 3123.000000 3123 84.961000 932 4065 1 chr3D.!!$R1 3133
7 TraesCS3B01G571500 chr3D 596846769 596852165 5396 False 2134.666667 5271 91.605667 241 4831 3 chr3D.!!$F2 4590
8 TraesCS3B01G571500 chr3D 595930002 595931010 1008 True 615.500000 998 87.152500 3434 4394 2 chr3D.!!$R2 960
9 TraesCS3B01G571500 chr3D 32280415 32281260 845 False 460.000000 460 76.561000 2838 3683 1 chr3D.!!$F1 845
10 TraesCS3B01G571500 chr3A 726741138 726743229 2091 True 1893.000000 1893 83.231000 934 3027 1 chr3A.!!$R1 2093
11 TraesCS3B01G571500 chr3A 726721543 726726871 5328 True 478.650000 889 88.999500 3021 4634 4 chr3A.!!$R2 1613

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
176 177 0.033991 CTCTGGGAAGGAGACTCGGA 60.034 60.000 0.00 0.0 42.68 4.55 F
568 571 0.447801 GTAGTGGCGCAACAGAATGG 59.552 55.000 19.06 0.0 43.62 3.16 F
760 1628 0.671251 CGGGAGTCACTAGCATCCTC 59.329 60.000 0.00 0.0 32.18 3.71 F
2650 3574 0.689080 ATCGCTGGAGGTGGAGATGT 60.689 55.000 0.00 0.0 0.00 3.06 F
3161 4091 1.001048 CGCCTTGTCATATGCATTGGG 60.001 52.381 3.54 1.6 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1342 2239 0.035152 CAGTGCAAGGCATAGGTGGA 60.035 55.000 0.00 0.0 41.91 4.02 R
2337 3240 0.248565 TCCATCTGCACTGCTGTCTC 59.751 55.000 1.98 0.0 0.00 3.36 R
2750 3680 0.394352 ATGCCAATTCTCCGTGTCCC 60.394 55.000 0.00 0.0 0.00 4.46 R
3506 4478 0.392706 TGAGCACGCCTTTTCTCTGA 59.607 50.000 0.00 0.0 0.00 3.27 R
4285 9255 2.293399 AGACAAAATTTCCCGTGTGCTC 59.707 45.455 0.00 0.0 0.00 4.26 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
24 25 7.050281 CTTCCATTACTACTCTTTGTTCGTG 57.950 40.000 0.00 0.00 0.00 4.35
25 26 4.927425 TCCATTACTACTCTTTGTTCGTGC 59.073 41.667 0.00 0.00 0.00 5.34
26 27 4.688879 CCATTACTACTCTTTGTTCGTGCA 59.311 41.667 0.00 0.00 0.00 4.57
27 28 5.389516 CCATTACTACTCTTTGTTCGTGCAC 60.390 44.000 6.82 6.82 0.00 4.57
28 29 3.454371 ACTACTCTTTGTTCGTGCACT 57.546 42.857 16.19 0.00 0.00 4.40
29 30 3.381949 ACTACTCTTTGTTCGTGCACTC 58.618 45.455 16.19 5.97 0.00 3.51
30 31 1.583054 ACTCTTTGTTCGTGCACTCC 58.417 50.000 16.19 2.76 0.00 3.85
31 32 1.139058 ACTCTTTGTTCGTGCACTCCT 59.861 47.619 16.19 0.00 0.00 3.69
32 33 2.213499 CTCTTTGTTCGTGCACTCCTT 58.787 47.619 16.19 0.00 0.00 3.36
33 34 1.939934 TCTTTGTTCGTGCACTCCTTG 59.060 47.619 16.19 0.00 0.00 3.61
34 35 1.939934 CTTTGTTCGTGCACTCCTTGA 59.060 47.619 16.19 0.73 0.00 3.02
35 36 1.581934 TTGTTCGTGCACTCCTTGAG 58.418 50.000 16.19 0.00 35.52 3.02
36 37 0.750249 TGTTCGTGCACTCCTTGAGA 59.250 50.000 16.19 0.00 33.32 3.27
37 38 1.344438 TGTTCGTGCACTCCTTGAGAT 59.656 47.619 16.19 0.00 33.32 2.75
38 39 2.224281 TGTTCGTGCACTCCTTGAGATT 60.224 45.455 16.19 0.00 33.32 2.40
39 40 2.370281 TCGTGCACTCCTTGAGATTC 57.630 50.000 16.19 0.00 33.32 2.52
40 41 0.994995 CGTGCACTCCTTGAGATTCG 59.005 55.000 16.19 0.00 33.32 3.34
41 42 0.723981 GTGCACTCCTTGAGATTCGC 59.276 55.000 10.32 0.00 33.32 4.70
42 43 0.610174 TGCACTCCTTGAGATTCGCT 59.390 50.000 0.00 0.00 33.32 4.93
43 44 1.824852 TGCACTCCTTGAGATTCGCTA 59.175 47.619 0.00 0.00 33.32 4.26
44 45 2.233676 TGCACTCCTTGAGATTCGCTAA 59.766 45.455 0.00 0.00 33.32 3.09
45 46 3.262420 GCACTCCTTGAGATTCGCTAAA 58.738 45.455 0.00 0.00 33.32 1.85
46 47 3.873952 GCACTCCTTGAGATTCGCTAAAT 59.126 43.478 0.00 0.00 33.32 1.40
47 48 5.050490 GCACTCCTTGAGATTCGCTAAATA 58.950 41.667 0.00 0.00 33.32 1.40
48 49 5.523916 GCACTCCTTGAGATTCGCTAAATAA 59.476 40.000 0.00 0.00 33.32 1.40
49 50 6.203723 GCACTCCTTGAGATTCGCTAAATAAT 59.796 38.462 0.00 0.00 33.32 1.28
50 51 7.571026 CACTCCTTGAGATTCGCTAAATAATG 58.429 38.462 0.00 0.00 33.32 1.90
51 52 6.708054 ACTCCTTGAGATTCGCTAAATAATGG 59.292 38.462 0.00 0.00 33.32 3.16
52 53 6.826668 TCCTTGAGATTCGCTAAATAATGGA 58.173 36.000 0.00 0.00 0.00 3.41
53 54 7.279615 TCCTTGAGATTCGCTAAATAATGGAA 58.720 34.615 0.00 0.00 0.00 3.53
54 55 7.442364 TCCTTGAGATTCGCTAAATAATGGAAG 59.558 37.037 0.00 0.00 0.00 3.46
55 56 6.545504 TGAGATTCGCTAAATAATGGAAGC 57.454 37.500 0.00 0.00 0.00 3.86
56 57 6.291377 TGAGATTCGCTAAATAATGGAAGCT 58.709 36.000 0.00 0.00 36.21 3.74
57 58 7.441836 TGAGATTCGCTAAATAATGGAAGCTA 58.558 34.615 0.00 0.00 33.94 3.32
58 59 7.931407 TGAGATTCGCTAAATAATGGAAGCTAA 59.069 33.333 0.00 0.00 33.94 3.09
59 60 8.677148 AGATTCGCTAAATAATGGAAGCTAAA 57.323 30.769 0.00 0.00 32.23 1.85
60 61 8.560374 AGATTCGCTAAATAATGGAAGCTAAAC 58.440 33.333 0.00 0.00 32.23 2.01
61 62 7.859325 TTCGCTAAATAATGGAAGCTAAACT 57.141 32.000 0.00 0.00 32.73 2.66
62 63 7.859325 TCGCTAAATAATGGAAGCTAAACTT 57.141 32.000 0.00 0.00 42.98 2.66
94 95 7.671302 TCTATTATGAGGAAGTGTTATGGAGC 58.329 38.462 0.00 0.00 0.00 4.70
95 96 3.567478 ATGAGGAAGTGTTATGGAGCC 57.433 47.619 0.00 0.00 0.00 4.70
96 97 2.265367 TGAGGAAGTGTTATGGAGCCA 58.735 47.619 0.00 0.00 0.00 4.75
97 98 2.027192 TGAGGAAGTGTTATGGAGCCAC 60.027 50.000 0.00 0.00 0.00 5.01
98 99 1.282157 AGGAAGTGTTATGGAGCCACC 59.718 52.381 0.00 0.00 39.54 4.61
99 100 1.282157 GGAAGTGTTATGGAGCCACCT 59.718 52.381 0.00 0.00 39.86 4.00
100 101 2.359900 GAAGTGTTATGGAGCCACCTG 58.640 52.381 0.00 0.00 39.86 4.00
101 102 1.656587 AGTGTTATGGAGCCACCTGA 58.343 50.000 0.00 0.00 39.86 3.86
102 103 1.985159 AGTGTTATGGAGCCACCTGAA 59.015 47.619 0.00 0.00 39.86 3.02
103 104 2.084546 GTGTTATGGAGCCACCTGAAC 58.915 52.381 0.00 4.36 39.86 3.18
104 105 1.004277 TGTTATGGAGCCACCTGAACC 59.996 52.381 0.00 0.00 39.86 3.62
105 106 0.251916 TTATGGAGCCACCTGAACCG 59.748 55.000 0.00 0.00 39.86 4.44
106 107 0.616395 TATGGAGCCACCTGAACCGA 60.616 55.000 0.00 0.00 39.86 4.69
107 108 1.488705 ATGGAGCCACCTGAACCGAA 61.489 55.000 0.00 0.00 39.86 4.30
108 109 1.072505 GGAGCCACCTGAACCGAAA 59.927 57.895 0.00 0.00 35.41 3.46
109 110 0.955919 GGAGCCACCTGAACCGAAAG 60.956 60.000 0.00 0.00 35.41 2.62
110 111 0.034896 GAGCCACCTGAACCGAAAGA 59.965 55.000 0.00 0.00 0.00 2.52
111 112 0.035458 AGCCACCTGAACCGAAAGAG 59.965 55.000 0.00 0.00 0.00 2.85
112 113 0.955919 GCCACCTGAACCGAAAGAGG 60.956 60.000 0.00 0.00 37.30 3.69
113 114 0.955919 CCACCTGAACCGAAAGAGGC 60.956 60.000 0.00 0.00 33.69 4.70
114 115 1.004918 ACCTGAACCGAAAGAGGCG 60.005 57.895 0.00 0.00 33.69 5.52
115 116 2.391389 CCTGAACCGAAAGAGGCGC 61.391 63.158 0.00 0.00 33.69 6.53
116 117 2.730672 CTGAACCGAAAGAGGCGCG 61.731 63.158 0.00 0.00 33.69 6.86
117 118 4.148645 GAACCGAAAGAGGCGCGC 62.149 66.667 25.94 25.94 33.69 6.86
137 138 3.813596 CCTTGATGGTAGCCACGC 58.186 61.111 0.00 0.00 35.80 5.34
138 139 1.221840 CCTTGATGGTAGCCACGCT 59.778 57.895 0.00 0.00 43.41 5.07
139 140 0.392998 CCTTGATGGTAGCCACGCTT 60.393 55.000 0.00 0.00 40.44 4.68
140 141 1.009829 CTTGATGGTAGCCACGCTTC 58.990 55.000 0.00 0.00 40.44 3.86
141 142 0.323302 TTGATGGTAGCCACGCTTCA 59.677 50.000 0.00 0.00 40.44 3.02
142 143 0.108186 TGATGGTAGCCACGCTTCAG 60.108 55.000 0.00 0.00 40.44 3.02
143 144 0.811616 GATGGTAGCCACGCTTCAGG 60.812 60.000 0.00 0.00 40.44 3.86
144 145 1.264749 ATGGTAGCCACGCTTCAGGA 61.265 55.000 0.00 0.00 40.44 3.86
145 146 1.153549 GGTAGCCACGCTTCAGGAG 60.154 63.158 0.00 0.00 40.44 3.69
146 147 1.592223 GTAGCCACGCTTCAGGAGT 59.408 57.895 0.00 0.00 40.44 3.85
147 148 0.458716 GTAGCCACGCTTCAGGAGTC 60.459 60.000 0.00 0.00 40.44 3.36
148 149 0.898326 TAGCCACGCTTCAGGAGTCA 60.898 55.000 0.00 0.00 40.44 3.41
149 150 1.739562 GCCACGCTTCAGGAGTCAG 60.740 63.158 0.00 0.00 0.00 3.51
150 151 1.079543 CCACGCTTCAGGAGTCAGG 60.080 63.158 0.00 0.00 0.00 3.86
151 152 1.536073 CCACGCTTCAGGAGTCAGGA 61.536 60.000 0.00 0.00 0.00 3.86
152 153 0.318441 CACGCTTCAGGAGTCAGGAA 59.682 55.000 0.00 0.00 0.00 3.36
153 154 1.048601 ACGCTTCAGGAGTCAGGAAA 58.951 50.000 0.00 0.00 0.00 3.13
154 155 1.001406 ACGCTTCAGGAGTCAGGAAAG 59.999 52.381 0.00 0.00 0.00 2.62
155 156 1.674221 CGCTTCAGGAGTCAGGAAAGG 60.674 57.143 0.00 0.00 0.00 3.11
156 157 1.625818 GCTTCAGGAGTCAGGAAAGGA 59.374 52.381 0.00 0.00 0.00 3.36
157 158 2.614229 GCTTCAGGAGTCAGGAAAGGAC 60.614 54.545 0.00 0.00 35.50 3.85
163 164 1.650528 AGTCAGGAAAGGACTCTGGG 58.349 55.000 0.00 0.00 41.63 4.45
164 165 1.150135 AGTCAGGAAAGGACTCTGGGA 59.850 52.381 0.00 0.00 41.63 4.37
165 166 1.978580 GTCAGGAAAGGACTCTGGGAA 59.021 52.381 0.00 0.00 32.54 3.97
166 167 2.027653 GTCAGGAAAGGACTCTGGGAAG 60.028 54.545 0.00 0.00 32.54 3.46
167 168 1.280421 CAGGAAAGGACTCTGGGAAGG 59.720 57.143 0.00 0.00 0.00 3.46
168 169 1.152271 AGGAAAGGACTCTGGGAAGGA 59.848 52.381 0.00 0.00 0.00 3.36
169 170 1.557371 GGAAAGGACTCTGGGAAGGAG 59.443 57.143 0.00 0.00 36.92 3.69
170 171 2.541466 GAAAGGACTCTGGGAAGGAGA 58.459 52.381 0.00 0.00 35.10 3.71
171 172 1.945580 AAGGACTCTGGGAAGGAGAC 58.054 55.000 0.00 0.00 35.10 3.36
173 174 1.006639 AGGACTCTGGGAAGGAGACTC 59.993 57.143 0.00 0.00 42.68 3.36
174 175 1.099689 GACTCTGGGAAGGAGACTCG 58.900 60.000 0.00 0.00 42.68 4.18
175 176 0.323908 ACTCTGGGAAGGAGACTCGG 60.324 60.000 0.00 0.00 42.68 4.63
176 177 0.033991 CTCTGGGAAGGAGACTCGGA 60.034 60.000 0.00 0.00 42.68 4.55
177 178 0.631753 TCTGGGAAGGAGACTCGGAT 59.368 55.000 0.00 0.00 42.68 4.18
178 179 1.007238 TCTGGGAAGGAGACTCGGATT 59.993 52.381 0.00 0.00 42.68 3.01
179 180 2.243994 TCTGGGAAGGAGACTCGGATTA 59.756 50.000 0.00 0.00 42.68 1.75
180 181 2.625790 CTGGGAAGGAGACTCGGATTAG 59.374 54.545 0.00 0.00 42.68 1.73
181 182 2.243994 TGGGAAGGAGACTCGGATTAGA 59.756 50.000 0.00 0.00 42.68 2.10
182 183 3.117093 TGGGAAGGAGACTCGGATTAGAT 60.117 47.826 0.00 0.00 42.68 1.98
183 184 3.508402 GGGAAGGAGACTCGGATTAGATC 59.492 52.174 0.00 0.00 42.68 2.75
184 185 4.403734 GGAAGGAGACTCGGATTAGATCT 58.596 47.826 0.00 0.00 42.68 2.75
185 186 4.217550 GGAAGGAGACTCGGATTAGATCTG 59.782 50.000 5.18 0.00 42.68 2.90
186 187 4.447138 AGGAGACTCGGATTAGATCTGT 57.553 45.455 5.18 0.00 32.90 3.41
187 188 4.798882 AGGAGACTCGGATTAGATCTGTT 58.201 43.478 5.18 0.00 32.90 3.16
188 189 5.205056 AGGAGACTCGGATTAGATCTGTTT 58.795 41.667 5.18 0.00 32.90 2.83
189 190 5.659079 AGGAGACTCGGATTAGATCTGTTTT 59.341 40.000 5.18 0.00 32.90 2.43
190 191 6.155393 AGGAGACTCGGATTAGATCTGTTTTT 59.845 38.462 5.18 0.00 32.90 1.94
191 192 7.342284 AGGAGACTCGGATTAGATCTGTTTTTA 59.658 37.037 5.18 0.00 32.90 1.52
192 193 7.980099 GGAGACTCGGATTAGATCTGTTTTTAA 59.020 37.037 5.18 0.00 36.98 1.52
193 194 9.367444 GAGACTCGGATTAGATCTGTTTTTAAA 57.633 33.333 5.18 0.00 36.98 1.52
194 195 9.892130 AGACTCGGATTAGATCTGTTTTTAAAT 57.108 29.630 5.18 0.00 36.98 1.40
222 223 7.934855 AGCATGGATCATATCAGTTTATTCC 57.065 36.000 0.00 0.00 0.00 3.01
223 224 6.888632 AGCATGGATCATATCAGTTTATTCCC 59.111 38.462 0.00 0.00 0.00 3.97
224 225 6.888632 GCATGGATCATATCAGTTTATTCCCT 59.111 38.462 0.00 0.00 0.00 4.20
225 226 7.148120 GCATGGATCATATCAGTTTATTCCCTG 60.148 40.741 0.00 0.00 0.00 4.45
226 227 6.240894 TGGATCATATCAGTTTATTCCCTGC 58.759 40.000 0.00 0.00 0.00 4.85
227 228 6.044754 TGGATCATATCAGTTTATTCCCTGCT 59.955 38.462 0.00 0.00 0.00 4.24
228 229 6.944862 GGATCATATCAGTTTATTCCCTGCTT 59.055 38.462 0.00 0.00 0.00 3.91
229 230 8.103305 GGATCATATCAGTTTATTCCCTGCTTA 58.897 37.037 0.00 0.00 0.00 3.09
230 231 9.507329 GATCATATCAGTTTATTCCCTGCTTAA 57.493 33.333 0.00 0.00 0.00 1.85
232 233 9.866655 TCATATCAGTTTATTCCCTGCTTAATT 57.133 29.630 0.00 0.00 0.00 1.40
233 234 9.903682 CATATCAGTTTATTCCCTGCTTAATTG 57.096 33.333 0.00 0.00 0.00 2.32
234 235 6.773976 TCAGTTTATTCCCTGCTTAATTGG 57.226 37.500 0.00 0.00 0.00 3.16
235 236 6.489603 TCAGTTTATTCCCTGCTTAATTGGA 58.510 36.000 0.00 0.00 0.00 3.53
236 237 6.951198 TCAGTTTATTCCCTGCTTAATTGGAA 59.049 34.615 0.00 0.00 40.89 3.53
237 238 7.619302 TCAGTTTATTCCCTGCTTAATTGGAAT 59.381 33.333 9.64 9.64 46.52 3.01
238 239 7.707893 CAGTTTATTCCCTGCTTAATTGGAATG 59.292 37.037 13.20 0.00 44.97 2.67
239 240 7.619302 AGTTTATTCCCTGCTTAATTGGAATGA 59.381 33.333 13.20 5.04 44.97 2.57
342 343 5.023452 ACACATACATAACAGGAGGACTCA 58.977 41.667 1.32 0.00 0.00 3.41
352 353 5.216614 ACAGGAGGACTCAGAGTAAAAAC 57.783 43.478 2.00 0.00 0.00 2.43
354 355 5.308237 ACAGGAGGACTCAGAGTAAAAACAT 59.692 40.000 2.00 0.00 0.00 2.71
356 357 7.016268 ACAGGAGGACTCAGAGTAAAAACATAA 59.984 37.037 2.00 0.00 0.00 1.90
357 358 7.878127 CAGGAGGACTCAGAGTAAAAACATAAA 59.122 37.037 2.00 0.00 0.00 1.40
358 359 8.437575 AGGAGGACTCAGAGTAAAAACATAAAA 58.562 33.333 2.00 0.00 0.00 1.52
361 362 9.403583 AGGACTCAGAGTAAAAACATAAAAACA 57.596 29.630 2.00 0.00 0.00 2.83
373 374 8.589701 AAAACATAAAAACATAGTAGGAGGGG 57.410 34.615 0.00 0.00 0.00 4.79
388 389 1.771255 GAGGGGCATGAACCTATGAGT 59.229 52.381 8.43 0.00 37.18 3.41
395 396 4.526970 CATGAACCTATGAGTTCTTGCG 57.473 45.455 10.07 0.00 45.25 4.85
415 417 4.697828 TGCGCAAAATTGAACTATCCAGTA 59.302 37.500 8.16 0.00 33.48 2.74
435 437 6.408092 CCAGTACTATCCCAAGATTTAGTGCA 60.408 42.308 0.00 0.00 30.32 4.57
444 446 8.593945 TCCCAAGATTTAGTGCATAGAAAAAT 57.406 30.769 0.00 0.00 0.00 1.82
445 447 9.693739 TCCCAAGATTTAGTGCATAGAAAAATA 57.306 29.630 0.00 0.00 0.00 1.40
457 460 9.520204 GTGCATAGAAAAATAATAAGTGCATGT 57.480 29.630 0.00 0.00 41.38 3.21
496 499 4.889995 GGAGAATTACAGGCAGCCTTAATT 59.110 41.667 25.94 25.94 33.71 1.40
549 552 9.258826 CATTGATCAGATTAGAGGTAGAAACTG 57.741 37.037 0.00 0.00 0.00 3.16
558 561 1.067071 AGGTAGAAACTGTAGTGGCGC 60.067 52.381 0.00 0.00 0.00 6.53
563 566 0.944386 AAACTGTAGTGGCGCAACAG 59.056 50.000 19.06 20.96 44.89 3.16
568 571 0.447801 GTAGTGGCGCAACAGAATGG 59.552 55.000 19.06 0.00 43.62 3.16
584 587 8.702438 CAACAGAATGGTTAATGCTTAGTTTTG 58.298 33.333 0.00 0.00 43.62 2.44
726 1594 8.689972 ACCATATGAACAGATCCTTTGAATTTC 58.310 33.333 3.65 0.00 0.00 2.17
760 1628 0.671251 CGGGAGTCACTAGCATCCTC 59.329 60.000 0.00 0.00 32.18 3.71
859 1728 1.408969 ATTTCCCGTTGGCAACTGTT 58.591 45.000 26.26 4.36 37.61 3.16
888 1757 9.533253 GTTAACATTTGGATTTGAATATCCCTG 57.467 33.333 0.00 0.00 42.91 4.45
1027 1900 3.726557 TCTTCCTAACCGTCCTAGTCA 57.273 47.619 0.00 0.00 0.00 3.41
1070 1946 3.102052 TCTTATTGACGAATACCCCGC 57.898 47.619 0.00 0.00 0.00 6.13
1103 1979 2.568623 AGGTCATCACCCACTTTGAC 57.431 50.000 0.00 0.00 45.12 3.18
1205 2085 5.906073 ACACAAAATCAACTTTCCTTCCTG 58.094 37.500 0.00 0.00 0.00 3.86
1261 2149 6.530120 TCTTGCTAGGTACAATTGTTCTTGA 58.470 36.000 17.78 0.00 0.00 3.02
1316 2208 8.565896 ACATTTGATCTTAACAGTCAGCAATA 57.434 30.769 0.00 0.00 0.00 1.90
1342 2239 6.318900 GCTTACCAAATCCAGCTACTATTTGT 59.681 38.462 18.68 12.68 38.40 2.83
1371 2268 2.435437 TGCCTTGCACTGATAGCTATCA 59.565 45.455 29.86 29.86 35.46 2.15
1410 2307 1.078143 GGCGACTGGAATGGCTCTT 60.078 57.895 0.00 0.00 0.00 2.85
1412 2309 1.576356 GCGACTGGAATGGCTCTTAG 58.424 55.000 0.00 0.00 0.00 2.18
1557 2454 1.610554 CCCCTCGCTTCCTTCCGTAA 61.611 60.000 0.00 0.00 0.00 3.18
1686 2583 1.747709 ACATTCTGCTGTGGATGCTC 58.252 50.000 0.00 0.00 0.00 4.26
1958 2855 4.323104 CCAGATCTAATCCCGATTTCCTCC 60.323 50.000 0.00 0.00 32.50 4.30
1960 2857 5.046014 CAGATCTAATCCCGATTTCCTCCAT 60.046 44.000 0.00 0.00 32.50 3.41
2029 2929 5.769162 CACTCTCTACAGATGATGATCCTGA 59.231 44.000 5.83 0.00 0.00 3.86
2141 3044 5.867716 CAGTTACCCACTTAGTATGTCACAC 59.132 44.000 0.00 0.00 30.92 3.82
2167 3070 2.810650 AGCACCGATCAACGTCTATTC 58.189 47.619 0.00 0.00 40.78 1.75
2337 3240 9.438291 GGAATTTCTTCATATACATCAACAACG 57.562 33.333 0.00 0.00 32.70 4.10
2358 3264 1.134461 AGACAGCAGTGCAGATGGATC 60.134 52.381 19.20 2.34 0.00 3.36
2365 3271 2.801111 CAGTGCAGATGGATCTCATTCG 59.199 50.000 0.00 0.00 35.97 3.34
2372 3278 3.634448 AGATGGATCTCATTCGTTCGAGT 59.366 43.478 0.00 0.00 35.97 4.18
2379 3285 1.472878 TCATTCGTTCGAGTGGAGGAG 59.527 52.381 15.32 0.00 0.00 3.69
2429 3335 3.947196 TCATTATCACAGTTGGTCATGGC 59.053 43.478 0.00 0.00 0.00 4.40
2453 3359 3.384146 AGACAGATCTGTGGATAGCACTG 59.616 47.826 32.50 0.32 45.05 3.66
2558 3464 1.915141 ACAATCTTGCAGGGGTCAAG 58.085 50.000 0.00 0.00 41.57 3.02
2587 3493 5.393352 CGCTCAAGAAAAATCATGATGGGAA 60.393 40.000 9.46 0.00 0.00 3.97
2647 3571 1.900351 CAATCGCTGGAGGTGGAGA 59.100 57.895 0.00 0.00 0.00 3.71
2650 3574 0.689080 ATCGCTGGAGGTGGAGATGT 60.689 55.000 0.00 0.00 0.00 3.06
2669 3593 2.312390 GTTGTTGGTTTCTTGGCCCTA 58.688 47.619 0.00 0.00 0.00 3.53
2687 3617 4.365723 CCCTATTGATTGCATGTTTCTGC 58.634 43.478 0.00 0.00 42.62 4.26
2714 3644 8.981647 GTTATGTACAGACGGAAGAAAACTAAA 58.018 33.333 0.33 0.00 0.00 1.85
2717 3647 9.886132 ATGTACAGACGGAAGAAAACTAAATAT 57.114 29.630 0.33 0.00 0.00 1.28
2718 3648 9.715121 TGTACAGACGGAAGAAAACTAAATATT 57.285 29.630 0.00 0.00 0.00 1.28
2720 3650 7.960793 ACAGACGGAAGAAAACTAAATATTCG 58.039 34.615 0.00 0.00 0.00 3.34
2766 3696 1.812571 CAAAGGGACACGGAGAATTGG 59.187 52.381 0.00 0.00 0.00 3.16
2770 3700 1.017387 GGACACGGAGAATTGGCATC 58.983 55.000 0.00 0.00 0.00 3.91
2774 3704 2.086869 CACGGAGAATTGGCATCAACT 58.913 47.619 0.00 0.00 35.48 3.16
3038 3968 5.415701 CCTTGTGTCACTAATTGGCTATTGT 59.584 40.000 4.27 0.00 0.00 2.71
3161 4091 1.001048 CGCCTTGTCATATGCATTGGG 60.001 52.381 3.54 1.60 0.00 4.12
3163 4093 2.669781 CCTTGTCATATGCATTGGGGT 58.330 47.619 3.54 0.00 0.00 4.95
3373 4303 3.383698 AGATCCTGAGTACTTCCGGAA 57.616 47.619 17.73 17.73 41.77 4.30
3467 4439 4.837860 CCAGTAATAGATCCTGAGCTTCCT 59.162 45.833 0.00 0.00 0.00 3.36
3503 4475 2.690778 GCGTGAATGGGCACTGTCC 61.691 63.158 0.00 0.00 36.65 4.02
3506 4478 0.250901 GTGAATGGGCACTGTCCTGT 60.251 55.000 0.32 0.00 35.91 4.00
3593 4565 4.233005 GCTTCAGAAAATTTGCAGAGACC 58.767 43.478 0.00 0.00 0.00 3.85
3749 4721 2.162906 ACTCATGGCCACCAGGGTT 61.163 57.895 8.16 0.00 36.75 4.11
3967 4946 9.220767 GTTTAACAGTTCCATAAATCTCTCTGT 57.779 33.333 0.00 0.00 36.64 3.41
4080 5061 5.104817 CCCAATCTTTCCATATTTTGTGCCT 60.105 40.000 0.00 0.00 0.00 4.75
4095 5076 7.517614 TTTTGTGCCTAGACATACATGAAAA 57.482 32.000 0.00 0.00 0.00 2.29
4104 5085 8.099537 CCTAGACATACATGAAAATATCAGGCT 58.900 37.037 0.00 0.00 43.58 4.58
4165 9127 7.264294 ACAGAAAATTATCTCCAGGAAGAGT 57.736 36.000 0.00 0.00 35.28 3.24
4182 9145 6.030228 GGAAGAGTTCAACACAAAGAAAGTG 58.970 40.000 0.00 0.00 42.56 3.16
4190 9153 4.782019 ACACAAAGAAAGTGCAGTGAAA 57.218 36.364 0.00 0.00 40.59 2.69
4198 9161 5.825507 AGAAAGTGCAGTGAAAATGTTCTC 58.174 37.500 0.00 0.00 32.28 2.87
4263 9233 5.380043 CTGATGCCTTTATGTATCCAAGGT 58.620 41.667 0.00 0.00 39.55 3.50
4285 9255 3.706594 TCAAAGTCTGATACCCTAGCAGG 59.293 47.826 0.00 0.00 42.22 4.85
4353 9329 5.824624 ACTCATGCGTCATCCATCTTTAATT 59.175 36.000 0.00 0.00 0.00 1.40
4356 9333 8.219546 TCATGCGTCATCCATCTTTAATTAAA 57.780 30.769 10.16 10.16 0.00 1.52
4639 9805 1.270550 CTTTCTGGTTTCGCTGCCAAT 59.729 47.619 0.00 0.00 33.93 3.16
4640 9806 0.881118 TTCTGGTTTCGCTGCCAATC 59.119 50.000 0.00 0.00 33.93 2.67
4642 9808 0.597568 CTGGTTTCGCTGCCAATCAA 59.402 50.000 0.00 0.00 33.93 2.57
4644 9810 0.881118 GGTTTCGCTGCCAATCAAGA 59.119 50.000 0.00 0.00 0.00 3.02
4645 9811 1.474077 GGTTTCGCTGCCAATCAAGAT 59.526 47.619 0.00 0.00 0.00 2.40
4646 9812 2.523015 GTTTCGCTGCCAATCAAGATG 58.477 47.619 0.00 0.00 0.00 2.90
4647 9813 0.452987 TTCGCTGCCAATCAAGATGC 59.547 50.000 0.00 0.00 0.00 3.91
4648 9814 0.677414 TCGCTGCCAATCAAGATGCA 60.677 50.000 0.00 0.00 0.00 3.96
4649 9815 0.171679 CGCTGCCAATCAAGATGCAA 59.828 50.000 0.00 0.00 32.58 4.08
4650 9816 1.202371 CGCTGCCAATCAAGATGCAAT 60.202 47.619 0.00 0.00 32.58 3.56
4651 9817 2.470821 GCTGCCAATCAAGATGCAATC 58.529 47.619 0.00 0.00 46.04 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.401153 GCACGAACAAAGAGTAGTAATGGAAG 60.401 42.308 0.00 0.00 0.00 3.46
1 2 5.407387 GCACGAACAAAGAGTAGTAATGGAA 59.593 40.000 0.00 0.00 0.00 3.53
2 3 4.927425 GCACGAACAAAGAGTAGTAATGGA 59.073 41.667 0.00 0.00 0.00 3.41
3 4 4.688879 TGCACGAACAAAGAGTAGTAATGG 59.311 41.667 0.00 0.00 0.00 3.16
4 5 5.405571 AGTGCACGAACAAAGAGTAGTAATG 59.594 40.000 12.01 0.00 0.00 1.90
6 7 4.940463 AGTGCACGAACAAAGAGTAGTAA 58.060 39.130 12.01 0.00 0.00 2.24
7 8 4.543692 GAGTGCACGAACAAAGAGTAGTA 58.456 43.478 12.01 0.00 0.00 1.82
8 9 3.381949 GAGTGCACGAACAAAGAGTAGT 58.618 45.455 12.01 0.00 0.00 2.73
9 10 2.731976 GGAGTGCACGAACAAAGAGTAG 59.268 50.000 12.01 0.00 0.00 2.57
10 11 2.364324 AGGAGTGCACGAACAAAGAGTA 59.636 45.455 12.01 0.00 0.00 2.59
11 12 1.139058 AGGAGTGCACGAACAAAGAGT 59.861 47.619 12.01 0.00 0.00 3.24
12 13 1.871080 AGGAGTGCACGAACAAAGAG 58.129 50.000 12.01 0.00 0.00 2.85
13 14 1.939934 CAAGGAGTGCACGAACAAAGA 59.060 47.619 12.01 0.00 0.00 2.52
14 15 1.939934 TCAAGGAGTGCACGAACAAAG 59.060 47.619 12.01 0.00 0.00 2.77
15 16 1.939934 CTCAAGGAGTGCACGAACAAA 59.060 47.619 12.01 0.00 0.00 2.83
16 17 1.138069 TCTCAAGGAGTGCACGAACAA 59.862 47.619 12.01 0.00 0.00 2.83
17 18 0.750249 TCTCAAGGAGTGCACGAACA 59.250 50.000 12.01 0.00 0.00 3.18
18 19 2.086054 ATCTCAAGGAGTGCACGAAC 57.914 50.000 12.01 5.76 0.00 3.95
19 20 2.688507 GAATCTCAAGGAGTGCACGAA 58.311 47.619 12.01 0.00 0.00 3.85
20 21 1.402852 CGAATCTCAAGGAGTGCACGA 60.403 52.381 12.01 0.49 0.00 4.35
21 22 0.994995 CGAATCTCAAGGAGTGCACG 59.005 55.000 12.01 0.00 0.00 5.34
22 23 0.723981 GCGAATCTCAAGGAGTGCAC 59.276 55.000 9.40 9.40 0.00 4.57
23 24 0.610174 AGCGAATCTCAAGGAGTGCA 59.390 50.000 0.00 0.00 0.00 4.57
24 25 2.586258 TAGCGAATCTCAAGGAGTGC 57.414 50.000 0.00 0.00 0.00 4.40
25 26 7.307632 CCATTATTTAGCGAATCTCAAGGAGTG 60.308 40.741 0.00 0.00 0.00 3.51
26 27 6.708054 CCATTATTTAGCGAATCTCAAGGAGT 59.292 38.462 0.00 0.00 0.00 3.85
27 28 6.931281 TCCATTATTTAGCGAATCTCAAGGAG 59.069 38.462 0.00 0.00 0.00 3.69
28 29 6.826668 TCCATTATTTAGCGAATCTCAAGGA 58.173 36.000 0.00 0.00 0.00 3.36
29 30 7.496529 TTCCATTATTTAGCGAATCTCAAGG 57.503 36.000 0.00 0.00 0.00 3.61
30 31 7.041508 AGCTTCCATTATTTAGCGAATCTCAAG 60.042 37.037 0.00 0.00 38.62 3.02
31 32 6.767902 AGCTTCCATTATTTAGCGAATCTCAA 59.232 34.615 0.00 0.00 38.62 3.02
32 33 6.291377 AGCTTCCATTATTTAGCGAATCTCA 58.709 36.000 0.00 0.00 38.62 3.27
33 34 6.793492 AGCTTCCATTATTTAGCGAATCTC 57.207 37.500 0.00 0.00 38.62 2.75
34 35 8.560374 GTTTAGCTTCCATTATTTAGCGAATCT 58.440 33.333 0.00 0.00 38.62 2.40
35 36 8.560374 AGTTTAGCTTCCATTATTTAGCGAATC 58.440 33.333 0.00 0.00 38.62 2.52
36 37 8.451908 AGTTTAGCTTCCATTATTTAGCGAAT 57.548 30.769 0.00 0.00 38.62 3.34
37 38 7.859325 AGTTTAGCTTCCATTATTTAGCGAA 57.141 32.000 0.00 0.00 38.62 4.70
38 39 7.859325 AAGTTTAGCTTCCATTATTTAGCGA 57.141 32.000 0.00 0.00 38.62 4.93
68 69 8.317679 GCTCCATAACACTTCCTCATAATAGAT 58.682 37.037 0.00 0.00 0.00 1.98
69 70 7.256332 GGCTCCATAACACTTCCTCATAATAGA 60.256 40.741 0.00 0.00 0.00 1.98
70 71 6.876257 GGCTCCATAACACTTCCTCATAATAG 59.124 42.308 0.00 0.00 0.00 1.73
71 72 6.328934 TGGCTCCATAACACTTCCTCATAATA 59.671 38.462 0.00 0.00 0.00 0.98
72 73 5.132648 TGGCTCCATAACACTTCCTCATAAT 59.867 40.000 0.00 0.00 0.00 1.28
73 74 4.473196 TGGCTCCATAACACTTCCTCATAA 59.527 41.667 0.00 0.00 0.00 1.90
74 75 4.037222 TGGCTCCATAACACTTCCTCATA 58.963 43.478 0.00 0.00 0.00 2.15
75 76 2.846206 TGGCTCCATAACACTTCCTCAT 59.154 45.455 0.00 0.00 0.00 2.90
76 77 2.027192 GTGGCTCCATAACACTTCCTCA 60.027 50.000 0.00 0.00 32.58 3.86
77 78 2.633488 GTGGCTCCATAACACTTCCTC 58.367 52.381 0.00 0.00 32.58 3.71
78 79 1.282157 GGTGGCTCCATAACACTTCCT 59.718 52.381 0.00 0.00 35.53 3.36
79 80 1.282157 AGGTGGCTCCATAACACTTCC 59.718 52.381 8.51 0.00 39.02 3.46
80 81 2.027192 TCAGGTGGCTCCATAACACTTC 60.027 50.000 8.51 0.00 39.02 3.01
81 82 1.985159 TCAGGTGGCTCCATAACACTT 59.015 47.619 8.51 0.00 39.02 3.16
82 83 1.656587 TCAGGTGGCTCCATAACACT 58.343 50.000 8.51 0.00 39.02 3.55
83 84 2.084546 GTTCAGGTGGCTCCATAACAC 58.915 52.381 8.51 0.00 39.02 3.32
84 85 1.004277 GGTTCAGGTGGCTCCATAACA 59.996 52.381 18.60 0.00 39.02 2.41
85 86 1.751437 GGTTCAGGTGGCTCCATAAC 58.249 55.000 8.51 10.72 39.02 1.89
86 87 0.251916 CGGTTCAGGTGGCTCCATAA 59.748 55.000 8.51 0.00 39.02 1.90
87 88 0.616395 TCGGTTCAGGTGGCTCCATA 60.616 55.000 8.51 0.00 39.02 2.74
88 89 1.488705 TTCGGTTCAGGTGGCTCCAT 61.489 55.000 8.51 0.00 39.02 3.41
89 90 1.701031 TTTCGGTTCAGGTGGCTCCA 61.701 55.000 8.51 0.00 39.02 3.86
90 91 0.955919 CTTTCGGTTCAGGTGGCTCC 60.956 60.000 0.00 0.00 0.00 4.70
91 92 0.034896 TCTTTCGGTTCAGGTGGCTC 59.965 55.000 0.00 0.00 0.00 4.70
92 93 0.035458 CTCTTTCGGTTCAGGTGGCT 59.965 55.000 0.00 0.00 0.00 4.75
93 94 0.955919 CCTCTTTCGGTTCAGGTGGC 60.956 60.000 0.00 0.00 0.00 5.01
94 95 0.955919 GCCTCTTTCGGTTCAGGTGG 60.956 60.000 0.00 0.00 0.00 4.61
95 96 1.291877 CGCCTCTTTCGGTTCAGGTG 61.292 60.000 0.00 0.00 0.00 4.00
96 97 1.004918 CGCCTCTTTCGGTTCAGGT 60.005 57.895 0.00 0.00 0.00 4.00
97 98 2.391389 GCGCCTCTTTCGGTTCAGG 61.391 63.158 0.00 0.00 0.00 3.86
98 99 2.730672 CGCGCCTCTTTCGGTTCAG 61.731 63.158 0.00 0.00 0.00 3.02
99 100 2.736995 CGCGCCTCTTTCGGTTCA 60.737 61.111 0.00 0.00 0.00 3.18
100 101 4.148645 GCGCGCCTCTTTCGGTTC 62.149 66.667 23.24 0.00 0.00 3.62
106 107 4.643387 AAGGTGGCGCGCCTCTTT 62.643 61.111 45.79 39.91 44.35 2.52
120 121 0.392998 AAGCGTGGCTACCATCAAGG 60.393 55.000 0.00 0.00 38.25 3.61
121 122 1.009829 GAAGCGTGGCTACCATCAAG 58.990 55.000 0.00 0.00 38.25 3.02
122 123 0.323302 TGAAGCGTGGCTACCATCAA 59.677 50.000 0.00 0.00 38.25 2.57
123 124 0.108186 CTGAAGCGTGGCTACCATCA 60.108 55.000 0.00 0.00 38.25 3.07
124 125 0.811616 CCTGAAGCGTGGCTACCATC 60.812 60.000 0.00 0.00 38.25 3.51
125 126 1.221840 CCTGAAGCGTGGCTACCAT 59.778 57.895 0.00 0.00 38.25 3.55
126 127 1.888436 CTCCTGAAGCGTGGCTACCA 61.888 60.000 0.00 0.00 38.25 3.25
127 128 1.153549 CTCCTGAAGCGTGGCTACC 60.154 63.158 0.00 0.00 38.25 3.18
128 129 0.458716 GACTCCTGAAGCGTGGCTAC 60.459 60.000 0.00 0.00 38.25 3.58
129 130 0.898326 TGACTCCTGAAGCGTGGCTA 60.898 55.000 0.00 0.00 38.25 3.93
130 131 2.164865 CTGACTCCTGAAGCGTGGCT 62.165 60.000 0.00 0.00 42.56 4.75
131 132 1.739562 CTGACTCCTGAAGCGTGGC 60.740 63.158 0.00 0.00 0.00 5.01
132 133 1.079543 CCTGACTCCTGAAGCGTGG 60.080 63.158 0.00 0.00 0.00 4.94
133 134 0.318441 TTCCTGACTCCTGAAGCGTG 59.682 55.000 0.00 0.00 0.00 5.34
134 135 1.001406 CTTTCCTGACTCCTGAAGCGT 59.999 52.381 0.00 0.00 0.00 5.07
135 136 1.674221 CCTTTCCTGACTCCTGAAGCG 60.674 57.143 0.00 0.00 0.00 4.68
136 137 1.625818 TCCTTTCCTGACTCCTGAAGC 59.374 52.381 0.00 0.00 0.00 3.86
137 138 2.903135 AGTCCTTTCCTGACTCCTGAAG 59.097 50.000 0.00 0.00 38.71 3.02
138 139 2.977808 AGTCCTTTCCTGACTCCTGAA 58.022 47.619 0.00 0.00 38.71 3.02
139 140 2.704190 AGTCCTTTCCTGACTCCTGA 57.296 50.000 0.00 0.00 38.71 3.86
144 145 1.150135 TCCCAGAGTCCTTTCCTGACT 59.850 52.381 0.00 0.00 45.47 3.41
145 146 1.645710 TCCCAGAGTCCTTTCCTGAC 58.354 55.000 0.00 0.00 0.00 3.51
146 147 2.260822 CTTCCCAGAGTCCTTTCCTGA 58.739 52.381 0.00 0.00 0.00 3.86
147 148 1.280421 CCTTCCCAGAGTCCTTTCCTG 59.720 57.143 0.00 0.00 0.00 3.86
148 149 1.152271 TCCTTCCCAGAGTCCTTTCCT 59.848 52.381 0.00 0.00 0.00 3.36
149 150 1.557371 CTCCTTCCCAGAGTCCTTTCC 59.443 57.143 0.00 0.00 0.00 3.13
150 151 2.235155 GTCTCCTTCCCAGAGTCCTTTC 59.765 54.545 0.00 0.00 32.93 2.62
151 152 2.158081 AGTCTCCTTCCCAGAGTCCTTT 60.158 50.000 0.00 0.00 32.93 3.11
152 153 1.435168 AGTCTCCTTCCCAGAGTCCTT 59.565 52.381 0.00 0.00 32.93 3.36
153 154 1.006639 GAGTCTCCTTCCCAGAGTCCT 59.993 57.143 0.00 0.00 35.17 3.85
154 155 1.480789 GAGTCTCCTTCCCAGAGTCC 58.519 60.000 0.00 0.00 35.17 3.85
155 156 1.099689 CGAGTCTCCTTCCCAGAGTC 58.900 60.000 0.00 0.00 37.09 3.36
156 157 0.323908 CCGAGTCTCCTTCCCAGAGT 60.324 60.000 0.00 0.00 32.93 3.24
157 158 0.033991 TCCGAGTCTCCTTCCCAGAG 60.034 60.000 0.00 0.00 0.00 3.35
158 159 0.631753 ATCCGAGTCTCCTTCCCAGA 59.368 55.000 0.00 0.00 0.00 3.86
159 160 1.490574 AATCCGAGTCTCCTTCCCAG 58.509 55.000 0.00 0.00 0.00 4.45
160 161 2.243994 TCTAATCCGAGTCTCCTTCCCA 59.756 50.000 0.00 0.00 0.00 4.37
161 162 2.946785 TCTAATCCGAGTCTCCTTCCC 58.053 52.381 0.00 0.00 0.00 3.97
162 163 4.217550 CAGATCTAATCCGAGTCTCCTTCC 59.782 50.000 0.00 0.00 0.00 3.46
163 164 4.825085 ACAGATCTAATCCGAGTCTCCTTC 59.175 45.833 0.00 0.00 0.00 3.46
164 165 4.798882 ACAGATCTAATCCGAGTCTCCTT 58.201 43.478 0.00 0.00 0.00 3.36
165 166 4.447138 ACAGATCTAATCCGAGTCTCCT 57.553 45.455 0.00 0.00 0.00 3.69
166 167 5.523438 AAACAGATCTAATCCGAGTCTCC 57.477 43.478 0.00 0.00 0.00 3.71
167 168 8.928270 TTAAAAACAGATCTAATCCGAGTCTC 57.072 34.615 0.00 0.00 0.00 3.36
168 169 9.892130 ATTTAAAAACAGATCTAATCCGAGTCT 57.108 29.630 0.00 0.00 0.00 3.24
196 197 9.453572 GGAATAAACTGATATGATCCATGCTTA 57.546 33.333 0.00 0.00 0.00 3.09
197 198 7.395489 GGGAATAAACTGATATGATCCATGCTT 59.605 37.037 0.00 0.00 0.00 3.91
198 199 6.888632 GGGAATAAACTGATATGATCCATGCT 59.111 38.462 0.00 0.00 0.00 3.79
199 200 6.888632 AGGGAATAAACTGATATGATCCATGC 59.111 38.462 0.00 0.00 0.00 4.06
200 201 7.148120 GCAGGGAATAAACTGATATGATCCATG 60.148 40.741 0.00 0.00 39.70 3.66
201 202 6.888632 GCAGGGAATAAACTGATATGATCCAT 59.111 38.462 0.00 0.00 36.86 3.41
202 203 6.044754 AGCAGGGAATAAACTGATATGATCCA 59.955 38.462 0.00 0.00 36.86 3.41
203 204 6.479884 AGCAGGGAATAAACTGATATGATCC 58.520 40.000 0.00 0.00 36.86 3.36
204 205 7.992754 AAGCAGGGAATAAACTGATATGATC 57.007 36.000 0.00 0.00 36.86 2.92
206 207 9.866655 AATTAAGCAGGGAATAAACTGATATGA 57.133 29.630 0.00 0.00 36.86 2.15
207 208 9.903682 CAATTAAGCAGGGAATAAACTGATATG 57.096 33.333 0.00 0.00 36.86 1.78
208 209 9.082313 CCAATTAAGCAGGGAATAAACTGATAT 57.918 33.333 0.00 0.00 36.86 1.63
209 210 8.278639 TCCAATTAAGCAGGGAATAAACTGATA 58.721 33.333 0.00 0.00 36.86 2.15
210 211 7.125391 TCCAATTAAGCAGGGAATAAACTGAT 58.875 34.615 0.00 0.00 36.86 2.90
211 212 6.489603 TCCAATTAAGCAGGGAATAAACTGA 58.510 36.000 0.00 0.00 36.86 3.41
212 213 6.773976 TCCAATTAAGCAGGGAATAAACTG 57.226 37.500 0.00 0.00 37.76 3.16
213 214 7.619302 TCATTCCAATTAAGCAGGGAATAAACT 59.381 33.333 4.59 0.00 45.77 2.66
214 215 7.781056 TCATTCCAATTAAGCAGGGAATAAAC 58.219 34.615 4.59 0.00 45.77 2.01
215 216 7.969690 TCATTCCAATTAAGCAGGGAATAAA 57.030 32.000 4.59 0.00 45.77 1.40
216 217 8.551682 AATCATTCCAATTAAGCAGGGAATAA 57.448 30.769 4.59 0.00 45.77 1.40
217 218 9.827198 ATAATCATTCCAATTAAGCAGGGAATA 57.173 29.630 4.59 0.00 45.77 1.75
219 220 9.827198 ATATAATCATTCCAATTAAGCAGGGAA 57.173 29.630 0.00 0.00 43.06 3.97
261 262 7.394816 AGCCTTTGAGTAGTTTGCTATCTTTA 58.605 34.615 0.00 0.00 0.00 1.85
264 265 5.428184 AGCCTTTGAGTAGTTTGCTATCT 57.572 39.130 0.00 0.00 0.00 1.98
265 266 5.524281 GGTAGCCTTTGAGTAGTTTGCTATC 59.476 44.000 0.00 0.00 33.02 2.08
266 267 5.045869 TGGTAGCCTTTGAGTAGTTTGCTAT 60.046 40.000 0.00 0.00 33.02 2.97
267 268 4.285003 TGGTAGCCTTTGAGTAGTTTGCTA 59.715 41.667 0.00 0.00 0.00 3.49
268 269 3.072476 TGGTAGCCTTTGAGTAGTTTGCT 59.928 43.478 0.00 0.00 0.00 3.91
269 270 3.408634 TGGTAGCCTTTGAGTAGTTTGC 58.591 45.455 0.00 0.00 0.00 3.68
270 271 5.063880 AGTTGGTAGCCTTTGAGTAGTTTG 58.936 41.667 0.00 0.00 0.00 2.93
271 272 5.306114 AGTTGGTAGCCTTTGAGTAGTTT 57.694 39.130 0.00 0.00 0.00 2.66
352 353 5.690865 TGCCCCTCCTACTATGTTTTTATG 58.309 41.667 0.00 0.00 0.00 1.90
354 355 5.430417 TCATGCCCCTCCTACTATGTTTTTA 59.570 40.000 0.00 0.00 0.00 1.52
356 357 3.785887 TCATGCCCCTCCTACTATGTTTT 59.214 43.478 0.00 0.00 0.00 2.43
357 358 3.393687 TCATGCCCCTCCTACTATGTTT 58.606 45.455 0.00 0.00 0.00 2.83
358 359 3.060479 TCATGCCCCTCCTACTATGTT 57.940 47.619 0.00 0.00 0.00 2.71
361 362 2.089925 AGGTTCATGCCCCTCCTACTAT 60.090 50.000 0.00 0.00 0.00 2.12
362 363 1.294068 AGGTTCATGCCCCTCCTACTA 59.706 52.381 0.00 0.00 0.00 1.82
363 364 0.044855 AGGTTCATGCCCCTCCTACT 59.955 55.000 0.00 0.00 0.00 2.57
364 365 1.802553 TAGGTTCATGCCCCTCCTAC 58.197 55.000 6.30 0.00 32.08 3.18
365 366 2.090210 TCATAGGTTCATGCCCCTCCTA 60.090 50.000 6.30 5.32 35.62 2.94
366 367 1.143813 CATAGGTTCATGCCCCTCCT 58.856 55.000 6.30 3.48 32.08 3.69
368 369 1.771255 ACTCATAGGTTCATGCCCCTC 59.229 52.381 6.30 0.00 32.08 4.30
369 370 1.898863 ACTCATAGGTTCATGCCCCT 58.101 50.000 7.94 7.94 34.74 4.79
371 372 3.567478 AGAACTCATAGGTTCATGCCC 57.433 47.619 9.50 0.00 45.52 5.36
372 373 4.889832 CAAGAACTCATAGGTTCATGCC 57.110 45.455 9.50 0.00 45.52 4.40
388 389 5.160641 GGATAGTTCAATTTTGCGCAAGAA 58.839 37.500 23.68 19.30 43.02 2.52
395 396 8.560374 GGATAGTACTGGATAGTTCAATTTTGC 58.440 37.037 5.39 0.00 38.36 3.68
415 417 7.618019 TCTATGCACTAAATCTTGGGATAGT 57.382 36.000 0.00 0.00 33.35 2.12
445 447 9.632638 ATTTATCTTACCAGACATGCACTTATT 57.367 29.630 0.00 0.00 0.00 1.40
449 452 6.319658 CCAATTTATCTTACCAGACATGCACT 59.680 38.462 0.00 0.00 0.00 4.40
482 485 6.182627 TGATGGATATAATTAAGGCTGCCTG 58.817 40.000 24.16 0.00 32.13 4.85
527 530 9.127277 ACTACAGTTTCTACCTCTAATCTGATC 57.873 37.037 0.00 0.00 0.00 2.92
549 552 0.447801 CCATTCTGTTGCGCCACTAC 59.552 55.000 13.27 2.81 0.00 2.73
558 561 8.702438 CAAAACTAAGCATTAACCATTCTGTTG 58.298 33.333 0.00 0.00 0.00 3.33
563 566 7.826690 TCCTCAAAACTAAGCATTAACCATTC 58.173 34.615 0.00 0.00 0.00 2.67
568 571 8.568794 AGAACTTCCTCAAAACTAAGCATTAAC 58.431 33.333 0.00 0.00 0.00 2.01
584 587 6.828785 ACTCTTCTAGATGAGAGAACTTCCTC 59.171 42.308 31.74 0.00 36.46 3.71
726 1594 2.170607 ACTCCCGTTATCAGGAACCATG 59.829 50.000 0.00 0.00 0.00 3.66
822 1691 4.351192 GAAATTGTGAACTTTGTGAGCGT 58.649 39.130 0.00 0.00 0.00 5.07
823 1692 3.730715 GGAAATTGTGAACTTTGTGAGCG 59.269 43.478 0.00 0.00 0.00 5.03
824 1693 4.051237 GGGAAATTGTGAACTTTGTGAGC 58.949 43.478 0.00 0.00 0.00 4.26
825 1694 4.202010 ACGGGAAATTGTGAACTTTGTGAG 60.202 41.667 0.00 0.00 0.00 3.51
826 1695 3.697045 ACGGGAAATTGTGAACTTTGTGA 59.303 39.130 0.00 0.00 0.00 3.58
882 1751 4.508584 GGGAACTTGTTTAAGACCAGGGAT 60.509 45.833 0.00 0.00 37.36 3.85
883 1752 3.181437 GGGAACTTGTTTAAGACCAGGGA 60.181 47.826 0.00 0.00 37.36 4.20
888 1757 2.031420 GCACGGGAACTTGTTTAAGACC 60.031 50.000 0.00 0.00 37.36 3.85
1027 1900 1.202758 TGACCCATCAGCGTTTGAAGT 60.203 47.619 0.00 0.00 39.77 3.01
1070 1946 4.802039 GTGATGACCTAATTTGCAGCAATG 59.198 41.667 9.12 0.08 0.00 2.82
1205 2085 8.257306 AGACTAAGACCAGAGATTTCAAGAATC 58.743 37.037 0.00 0.00 0.00 2.52
1342 2239 0.035152 CAGTGCAAGGCATAGGTGGA 60.035 55.000 0.00 0.00 41.91 4.02
1371 2268 0.889186 GACACCACGGGAAGCAACAT 60.889 55.000 0.00 0.00 0.00 2.71
1557 2454 4.071961 TGCGAGCATTCATGTAAGGTAT 57.928 40.909 0.00 0.00 0.00 2.73
1686 2583 1.148310 CCTGCAGTGACACTAAACGG 58.852 55.000 13.81 6.09 0.00 4.44
1958 2855 6.974622 GGTACATTGTTTCAAGGCTTATGATG 59.025 38.462 11.34 7.65 0.00 3.07
1960 2857 5.123186 CGGTACATTGTTTCAAGGCTTATGA 59.877 40.000 11.34 0.00 0.00 2.15
2029 2929 2.304761 TCTTCCCATGAGCGGTAAAAGT 59.695 45.455 0.00 0.00 0.00 2.66
2097 3000 4.934001 ACTGATTGTGACACTGCTATCTTG 59.066 41.667 7.20 5.38 0.00 3.02
2141 3044 3.043586 GACGTTGATCGGTGCTATGTAG 58.956 50.000 0.00 0.00 44.69 2.74
2167 3070 1.688735 TCCCCATAGATCTTGCTGTCG 59.311 52.381 0.00 0.00 0.00 4.35
2337 3240 0.248565 TCCATCTGCACTGCTGTCTC 59.751 55.000 1.98 0.00 0.00 3.36
2358 3264 1.472878 TCCTCCACTCGAACGAATGAG 59.527 52.381 7.22 8.29 38.21 2.90
2365 3271 1.216710 CCAGCTCCTCCACTCGAAC 59.783 63.158 0.00 0.00 0.00 3.95
2558 3464 4.094887 TCATGATTTTTCTTGAGCGTAGGC 59.905 41.667 0.00 0.00 40.37 3.93
2587 3493 7.669427 TGTTTTATTTTGACCATGAGATGCTT 58.331 30.769 0.00 0.00 0.00 3.91
2647 3571 1.416030 GGGCCAAGAAACCAACAACAT 59.584 47.619 4.39 0.00 0.00 2.71
2650 3574 2.757894 TAGGGCCAAGAAACCAACAA 57.242 45.000 6.18 0.00 0.00 2.83
2669 3593 3.581024 ACGCAGAAACATGCAATCAAT 57.419 38.095 0.00 0.00 46.87 2.57
2687 3617 5.632347 AGTTTTCTTCCGTCTGTACATAACG 59.368 40.000 18.86 18.86 36.22 3.18
2714 3644 2.346766 TGGTCTTGCCATGCGAATAT 57.653 45.000 0.00 0.00 43.61 1.28
2750 3680 0.394352 ATGCCAATTCTCCGTGTCCC 60.394 55.000 0.00 0.00 0.00 4.46
2766 3696 2.766313 TGTGTGTGAGGTAGTTGATGC 58.234 47.619 0.00 0.00 0.00 3.91
2770 3700 3.804036 TCCTTTGTGTGTGAGGTAGTTG 58.196 45.455 0.00 0.00 32.33 3.16
2774 3704 5.042463 TCAAATCCTTTGTGTGTGAGGTA 57.958 39.130 0.04 0.00 41.36 3.08
3038 3968 6.070366 ACAAAATCATCTCAGACTCCTCATCA 60.070 38.462 0.00 0.00 0.00 3.07
3373 4303 0.463654 TTTGTTGGTGAGTCGCTGCT 60.464 50.000 3.25 0.00 0.00 4.24
3467 4439 1.073722 CAAGCCCACTTGCTCCTCA 59.926 57.895 0.00 0.00 46.38 3.86
3503 4475 0.514691 GCACGCCTTTTCTCTGACAG 59.485 55.000 0.00 0.00 0.00 3.51
3506 4478 0.392706 TGAGCACGCCTTTTCTCTGA 59.607 50.000 0.00 0.00 0.00 3.27
3749 4721 2.367241 TGTTGAACCTGAAGATGGTCGA 59.633 45.455 0.00 0.00 36.69 4.20
3967 4946 6.316140 GGAACATAATCAGAATGTACAGTGCA 59.684 38.462 0.00 0.00 36.56 4.57
4095 5076 9.066842 AGGGAAATCTTTGATATAGCCTGATAT 57.933 33.333 0.00 0.00 0.00 1.63
4159 9121 5.513141 GCACTTTCTTTGTGTTGAACTCTTC 59.487 40.000 0.00 0.00 37.70 2.87
4165 9127 4.217334 TCACTGCACTTTCTTTGTGTTGAA 59.783 37.500 0.00 0.00 37.70 2.69
4182 9145 8.801715 TCTAATTTTGAGAACATTTTCACTGC 57.198 30.769 0.00 0.00 33.72 4.40
4190 9153 8.510505 GTCTCAGCTTCTAATTTTGAGAACATT 58.489 33.333 4.27 0.00 43.99 2.71
4198 9161 6.183360 CCCTGATGTCTCAGCTTCTAATTTTG 60.183 42.308 0.00 0.00 46.39 2.44
4263 9233 3.706594 CCTGCTAGGGTATCAGACTTTGA 59.293 47.826 0.00 0.00 40.85 2.69
4285 9255 2.293399 AGACAAAATTTCCCGTGTGCTC 59.707 45.455 0.00 0.00 0.00 4.26
4353 9329 6.197468 GCAATGCAGTTGTCTTTTTACGTTTA 59.803 34.615 0.00 0.00 40.07 2.01
4356 9333 4.041723 GCAATGCAGTTGTCTTTTTACGT 58.958 39.130 0.00 0.00 40.07 3.57
4434 9416 6.487668 TGGACCTCATTGTGCATATAAATCTG 59.512 38.462 0.00 0.00 31.13 2.90
4639 9805 6.068473 GCATTCTGTATGATTGCATCTTGA 57.932 37.500 0.00 0.00 45.88 3.02
4651 9817 9.961265 ATTGAGTTTAATCATGCATTCTGTATG 57.039 29.630 0.00 0.00 41.03 2.39
4653 9819 9.176460 TGATTGAGTTTAATCATGCATTCTGTA 57.824 29.630 0.00 0.00 40.95 2.74
4654 9820 8.058667 TGATTGAGTTTAATCATGCATTCTGT 57.941 30.769 0.00 0.00 40.95 3.41
4655 9821 8.188799 ACTGATTGAGTTTAATCATGCATTCTG 58.811 33.333 0.00 0.00 43.80 3.02
4656 9822 8.289939 ACTGATTGAGTTTAATCATGCATTCT 57.710 30.769 0.00 0.00 43.80 2.40
4657 9823 8.922058 AACTGATTGAGTTTAATCATGCATTC 57.078 30.769 0.00 0.00 42.70 2.67


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

AutoCloner maintained by Alex Coulton.