Multiple sequence alignment - TraesCS7D01G250300

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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 TraesCS7D01G250300 chr7D 100.000 6466 0 0 1 6466 222511084 222517549 0.000000e+00 11941.0
1 TraesCS7D01G250300 chr7D 85.714 224 25 4 3557 3774 188347907 188348129 5.040000e-56 230.0
2 TraesCS7D01G250300 chr7B 94.882 3126 91 25 2746 5859 174076041 174072973 0.000000e+00 4822.0
3 TraesCS7D01G250300 chr7B 94.682 2501 90 18 235 2721 174078509 174076038 0.000000e+00 3842.0
4 TraesCS7D01G250300 chr7B 92.034 477 33 4 5993 6465 174072637 174072162 0.000000e+00 665.0
5 TraesCS7D01G250300 chr7B 89.362 94 2 1 5857 5950 174072831 174072746 1.910000e-20 111.0
6 TraesCS7D01G250300 chr7B 95.652 46 1 1 5947 5992 174072707 174072663 8.990000e-09 73.1
7 TraesCS7D01G250300 chr7A 94.043 3156 123 28 2816 5951 237386723 237389833 0.000000e+00 4726.0
8 TraesCS7D01G250300 chr7A 95.035 2276 66 14 555 2821 237383858 237386095 0.000000e+00 3533.0
9 TraesCS7D01G250300 chr7A 87.742 465 32 9 6005 6466 237502841 237503283 2.670000e-143 520.0
10 TraesCS7D01G250300 chr7A 88.764 356 32 4 212 563 237382686 237383037 4.630000e-116 429.0
11 TraesCS7D01G250300 chr7A 96.429 56 1 1 5947 6002 237389871 237389925 2.480000e-14 91.6
12 TraesCS7D01G250300 chr5D 91.379 58 5 0 1 58 5005739 5005682 5.370000e-11 80.5
13 TraesCS7D01G250300 chr5A 84.286 70 6 4 2846 2915 352400158 352400094 5.410000e-06 63.9
14 TraesCS7D01G250300 chr1D 94.737 38 1 1 2846 2882 387535193 387535156 2.520000e-04 58.4
15 TraesCS7D01G250300 chr6D 100.000 30 0 0 2845 2874 318786147 318786176 1.000000e-03 56.5
16 TraesCS7D01G250300 chr6A 100.000 30 0 0 2845 2874 456578035 456578064 1.000000e-03 56.5
17 TraesCS7D01G250300 chr3D 100.000 29 0 0 2846 2874 590122362 590122334 3.000000e-03 54.7
18 TraesCS7D01G250300 chr1B 100.000 29 0 0 2846 2874 520881032 520881004 3.000000e-03 54.7


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 TraesCS7D01G250300 chr7D 222511084 222517549 6465 False 11941.00 11941 100.00000 1 6466 1 chr7D.!!$F2 6465
1 TraesCS7D01G250300 chr7B 174072162 174078509 6347 True 1902.62 4822 93.32240 235 6465 5 chr7B.!!$R1 6230
2 TraesCS7D01G250300 chr7A 237382686 237389925 7239 False 2194.90 4726 93.56775 212 6002 4 chr7A.!!$F2 5790

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
202 203 0.657840 GATCCAGTCAAAATCGGGCG 59.342 55.000 0.00 0.0 0.00 6.13 F
1433 2276 0.534203 TTGTTCTGCTCCGGTTGGTC 60.534 55.000 0.00 0.0 36.30 4.02 F
2192 3040 0.464036 AGTGTGTGAGTGCTTTCGGA 59.536 50.000 0.00 0.0 0.00 4.55 F
2623 3474 3.055094 ACTTCTACACCCCTAATGTGCAG 60.055 47.826 0.00 0.0 37.22 4.41 F
3963 5459 0.622136 TGCCTGTCTCCTTGCATCAT 59.378 50.000 0.00 0.0 0.00 2.45 F
4602 6105 1.959985 TCACGTGGCCATGTTTTGAAT 59.040 42.857 28.34 1.5 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2740 1.080230 CTCTCTCACACGCACCCTG 60.080 63.158 0.00 0.0 0.00 4.45 R
2742 3594 0.888619 TCAAGACATCGGCGTTCTCT 59.111 50.000 6.85 0.0 0.00 3.10 R
3126 4612 1.692411 AACCCAAAGGAAGACTGCAC 58.308 50.000 0.00 0.0 36.73 4.57 R
4573 6076 0.953471 TGGCCACGTGATTCCTTTCG 60.953 55.000 19.30 0.0 0.00 3.46 R
5165 6669 0.403655 TGCCCCATGAGCACTACAAA 59.596 50.000 6.31 0.0 34.69 2.83 R
6309 8027 0.378962 CGTGATGAGACGAGGAGGAC 59.621 60.000 0.00 0.0 42.10 3.85 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
32 33 7.930217 AGTATTATGGATGTCGATGTTTTTGG 58.070 34.615 0.00 0.00 0.00 3.28
33 34 3.508744 ATGGATGTCGATGTTTTTGGC 57.491 42.857 0.00 0.00 0.00 4.52
34 35 2.513753 TGGATGTCGATGTTTTTGGCT 58.486 42.857 0.00 0.00 0.00 4.75
35 36 3.680490 TGGATGTCGATGTTTTTGGCTA 58.320 40.909 0.00 0.00 0.00 3.93
36 37 4.269183 TGGATGTCGATGTTTTTGGCTAT 58.731 39.130 0.00 0.00 0.00 2.97
37 38 4.335315 TGGATGTCGATGTTTTTGGCTATC 59.665 41.667 0.00 0.00 0.00 2.08
38 39 4.335315 GGATGTCGATGTTTTTGGCTATCA 59.665 41.667 0.00 0.00 0.00 2.15
39 40 5.163663 GGATGTCGATGTTTTTGGCTATCAA 60.164 40.000 0.00 0.00 0.00 2.57
40 41 5.895636 TGTCGATGTTTTTGGCTATCAAT 57.104 34.783 0.00 0.00 34.98 2.57
41 42 6.266168 TGTCGATGTTTTTGGCTATCAATT 57.734 33.333 0.00 0.00 34.98 2.32
42 43 6.092092 TGTCGATGTTTTTGGCTATCAATTG 58.908 36.000 0.00 0.00 34.98 2.32
43 44 6.072230 TGTCGATGTTTTTGGCTATCAATTGA 60.072 34.615 11.26 11.26 34.98 2.57
44 45 6.974622 GTCGATGTTTTTGGCTATCAATTGAT 59.025 34.615 23.75 23.75 38.51 2.57
45 46 7.489113 GTCGATGTTTTTGGCTATCAATTGATT 59.511 33.333 25.26 10.37 36.05 2.57
46 47 8.034215 TCGATGTTTTTGGCTATCAATTGATTT 58.966 29.630 25.26 6.52 36.05 2.17
47 48 8.111836 CGATGTTTTTGGCTATCAATTGATTTG 58.888 33.333 25.26 18.42 36.05 2.32
62 63 9.781633 TCAATTGATTTGAAAAATCATTCACCT 57.218 25.926 14.35 0.00 41.38 4.00
63 64 9.820229 CAATTGATTTGAAAAATCATTCACCTG 57.180 29.630 14.35 5.08 38.95 4.00
64 65 7.966246 TTGATTTGAAAAATCATTCACCTGG 57.034 32.000 14.35 0.00 38.95 4.45
65 66 7.065120 TGATTTGAAAAATCATTCACCTGGT 57.935 32.000 10.56 0.00 38.95 4.00
66 67 7.153985 TGATTTGAAAAATCATTCACCTGGTC 58.846 34.615 10.56 0.00 38.95 4.02
67 68 6.477053 TTTGAAAAATCATTCACCTGGTCA 57.523 33.333 0.00 0.00 38.95 4.02
68 69 6.477053 TTGAAAAATCATTCACCTGGTCAA 57.523 33.333 0.00 0.00 38.95 3.18
69 70 6.477053 TGAAAAATCATTCACCTGGTCAAA 57.523 33.333 0.00 0.00 34.50 2.69
70 71 6.882656 TGAAAAATCATTCACCTGGTCAAAA 58.117 32.000 0.00 0.00 34.50 2.44
71 72 7.507829 TGAAAAATCATTCACCTGGTCAAAAT 58.492 30.769 0.00 0.00 34.50 1.82
72 73 7.656948 TGAAAAATCATTCACCTGGTCAAAATC 59.343 33.333 0.00 0.00 34.50 2.17
73 74 6.669125 AAATCATTCACCTGGTCAAAATCA 57.331 33.333 0.00 0.00 0.00 2.57
74 75 6.862469 AATCATTCACCTGGTCAAAATCAT 57.138 33.333 0.00 0.00 0.00 2.45
75 76 5.648178 TCATTCACCTGGTCAAAATCATG 57.352 39.130 0.00 0.00 0.00 3.07
76 77 5.323581 TCATTCACCTGGTCAAAATCATGA 58.676 37.500 0.00 0.00 0.00 3.07
77 78 5.774184 TCATTCACCTGGTCAAAATCATGAA 59.226 36.000 0.00 0.00 0.00 2.57
78 79 5.452078 TTCACCTGGTCAAAATCATGAAC 57.548 39.130 0.00 0.00 37.54 3.18
79 80 4.468713 TCACCTGGTCAAAATCATGAACA 58.531 39.130 0.00 0.00 44.48 3.18
80 81 4.892345 TCACCTGGTCAAAATCATGAACAA 59.108 37.500 0.00 0.00 45.83 2.83
81 82 5.362143 TCACCTGGTCAAAATCATGAACAAA 59.638 36.000 0.00 0.00 45.83 2.83
82 83 6.041865 TCACCTGGTCAAAATCATGAACAAAT 59.958 34.615 0.00 0.00 45.83 2.32
83 84 6.366877 CACCTGGTCAAAATCATGAACAAATC 59.633 38.462 0.00 0.00 45.83 2.17
84 85 5.870978 CCTGGTCAAAATCATGAACAAATCC 59.129 40.000 0.00 0.00 45.83 3.01
85 86 6.416631 TGGTCAAAATCATGAACAAATCCA 57.583 33.333 0.00 2.77 43.75 3.41
86 87 6.824553 TGGTCAAAATCATGAACAAATCCAA 58.175 32.000 0.00 0.00 43.75 3.53
87 88 7.278135 TGGTCAAAATCATGAACAAATCCAAA 58.722 30.769 0.00 0.00 43.75 3.28
88 89 7.772292 TGGTCAAAATCATGAACAAATCCAAAA 59.228 29.630 0.00 0.00 43.75 2.44
89 90 8.785946 GGTCAAAATCATGAACAAATCCAAAAT 58.214 29.630 0.00 0.00 36.99 1.82
109 110 9.248291 CCAAAATTAAATAGTCAATCGAATGGG 57.752 33.333 0.00 0.00 0.00 4.00
110 111 9.248291 CAAAATTAAATAGTCAATCGAATGGGG 57.752 33.333 0.00 0.00 0.00 4.96
111 112 8.760980 AAATTAAATAGTCAATCGAATGGGGA 57.239 30.769 0.00 0.00 0.00 4.81
112 113 8.760980 AATTAAATAGTCAATCGAATGGGGAA 57.239 30.769 0.00 0.00 0.00 3.97
113 114 7.562454 TTAAATAGTCAATCGAATGGGGAAC 57.438 36.000 0.00 0.00 0.00 3.62
114 115 5.373812 AATAGTCAATCGAATGGGGAACT 57.626 39.130 0.00 0.00 0.00 3.01
115 116 3.268023 AGTCAATCGAATGGGGAACTC 57.732 47.619 0.00 0.00 0.00 3.01
116 117 2.092914 AGTCAATCGAATGGGGAACTCC 60.093 50.000 0.00 0.00 0.00 3.85
117 118 1.912731 TCAATCGAATGGGGAACTCCA 59.087 47.619 0.00 0.00 41.60 3.86
118 119 2.307392 TCAATCGAATGGGGAACTCCAA 59.693 45.455 0.00 0.00 40.62 3.53
119 120 3.088532 CAATCGAATGGGGAACTCCAAA 58.911 45.455 0.00 0.00 40.62 3.28
120 121 2.961531 TCGAATGGGGAACTCCAAAA 57.038 45.000 0.00 0.00 40.62 2.44
121 122 3.449746 TCGAATGGGGAACTCCAAAAT 57.550 42.857 0.00 0.00 40.62 1.82
122 123 3.773560 TCGAATGGGGAACTCCAAAATT 58.226 40.909 0.00 0.00 40.62 1.82
123 124 4.924625 TCGAATGGGGAACTCCAAAATTA 58.075 39.130 0.00 0.00 40.62 1.40
124 125 4.947388 TCGAATGGGGAACTCCAAAATTAG 59.053 41.667 0.00 0.00 40.62 1.73
125 126 4.097892 CGAATGGGGAACTCCAAAATTAGG 59.902 45.833 0.00 0.00 40.62 2.69
126 127 3.466395 TGGGGAACTCCAAAATTAGGG 57.534 47.619 0.00 0.00 37.91 3.53
127 128 2.997463 TGGGGAACTCCAAAATTAGGGA 59.003 45.455 0.00 0.00 37.91 4.20
135 136 5.424121 CTCCAAAATTAGGGAGCATAACG 57.576 43.478 11.23 0.00 43.80 3.18
136 137 4.204012 TCCAAAATTAGGGAGCATAACGG 58.796 43.478 0.00 0.00 0.00 4.44
137 138 4.080243 TCCAAAATTAGGGAGCATAACGGA 60.080 41.667 0.00 0.00 0.00 4.69
138 139 4.827284 CCAAAATTAGGGAGCATAACGGAT 59.173 41.667 0.00 0.00 0.00 4.18
139 140 5.301805 CCAAAATTAGGGAGCATAACGGATT 59.698 40.000 0.00 0.00 0.00 3.01
140 141 6.488683 CCAAAATTAGGGAGCATAACGGATTA 59.511 38.462 0.00 0.00 0.00 1.75
141 142 7.013846 CCAAAATTAGGGAGCATAACGGATTAA 59.986 37.037 0.00 0.00 0.00 1.40
142 143 8.410141 CAAAATTAGGGAGCATAACGGATTAAA 58.590 33.333 0.00 0.00 0.00 1.52
143 144 8.528044 AAATTAGGGAGCATAACGGATTAAAA 57.472 30.769 0.00 0.00 0.00 1.52
144 145 8.706322 AATTAGGGAGCATAACGGATTAAAAT 57.294 30.769 0.00 0.00 0.00 1.82
145 146 9.802039 AATTAGGGAGCATAACGGATTAAAATA 57.198 29.630 0.00 0.00 0.00 1.40
146 147 8.842358 TTAGGGAGCATAACGGATTAAAATAG 57.158 34.615 0.00 0.00 0.00 1.73
147 148 6.838382 AGGGAGCATAACGGATTAAAATAGT 58.162 36.000 0.00 0.00 0.00 2.12
148 149 7.287810 AGGGAGCATAACGGATTAAAATAGTT 58.712 34.615 0.00 2.86 0.00 2.24
149 150 7.228706 AGGGAGCATAACGGATTAAAATAGTTG 59.771 37.037 0.00 0.00 0.00 3.16
150 151 7.227910 GGGAGCATAACGGATTAAAATAGTTGA 59.772 37.037 0.00 0.00 0.00 3.18
151 152 8.617809 GGAGCATAACGGATTAAAATAGTTGAA 58.382 33.333 0.00 0.00 0.00 2.69
153 154 9.950680 AGCATAACGGATTAAAATAGTTGAATG 57.049 29.630 0.00 5.06 0.00 2.67
154 155 9.944663 GCATAACGGATTAAAATAGTTGAATGA 57.055 29.630 0.00 0.00 0.00 2.57
158 159 9.667107 AACGGATTAAAATAGTTGAATGAGAGA 57.333 29.630 0.00 0.00 0.00 3.10
159 160 9.319143 ACGGATTAAAATAGTTGAATGAGAGAG 57.681 33.333 0.00 0.00 0.00 3.20
160 161 8.279103 CGGATTAAAATAGTTGAATGAGAGAGC 58.721 37.037 0.00 0.00 0.00 4.09
161 162 9.336171 GGATTAAAATAGTTGAATGAGAGAGCT 57.664 33.333 0.00 0.00 0.00 4.09
163 164 8.723942 TTAAAATAGTTGAATGAGAGAGCTCC 57.276 34.615 10.93 1.70 40.55 4.70
164 165 6.558488 AAATAGTTGAATGAGAGAGCTCCT 57.442 37.500 10.93 7.30 40.55 3.69
165 166 6.558488 AATAGTTGAATGAGAGAGCTCCTT 57.442 37.500 10.93 0.00 40.55 3.36
166 167 4.470334 AGTTGAATGAGAGAGCTCCTTC 57.530 45.455 10.93 9.10 42.58 3.46
167 168 3.119173 AGTTGAATGAGAGAGCTCCTTCG 60.119 47.826 10.93 0.00 44.12 3.79
168 169 1.753649 TGAATGAGAGAGCTCCTTCGG 59.246 52.381 10.93 0.00 44.12 4.30
169 170 2.028130 GAATGAGAGAGCTCCTTCGGA 58.972 52.381 10.93 0.00 40.55 4.55
170 171 2.151502 ATGAGAGAGCTCCTTCGGAA 57.848 50.000 10.93 0.00 40.55 4.30
171 172 1.924731 TGAGAGAGCTCCTTCGGAAA 58.075 50.000 10.93 0.00 40.55 3.13
172 173 2.248248 TGAGAGAGCTCCTTCGGAAAA 58.752 47.619 10.93 0.00 40.55 2.29
173 174 2.632996 TGAGAGAGCTCCTTCGGAAAAA 59.367 45.455 10.93 0.00 40.55 1.94
201 202 1.750193 TGATCCAGTCAAAATCGGGC 58.250 50.000 0.00 0.00 32.78 6.13
202 203 0.657840 GATCCAGTCAAAATCGGGCG 59.342 55.000 0.00 0.00 0.00 6.13
203 204 0.748005 ATCCAGTCAAAATCGGGCGG 60.748 55.000 0.00 0.00 0.00 6.13
204 205 1.376683 CCAGTCAAAATCGGGCGGA 60.377 57.895 0.00 0.00 0.00 5.54
205 206 0.748005 CCAGTCAAAATCGGGCGGAT 60.748 55.000 1.15 1.15 36.78 4.18
230 231 4.947388 TCGGCTATTGTTCCATAAGCTTTT 59.053 37.500 3.20 0.00 0.00 2.27
317 318 9.681692 CTTATGCAGCTAATTTATTGTATGCAA 57.318 29.630 0.00 0.00 44.62 4.08
337 338 5.047660 TGCAACACATTATTTGTTCTACCCC 60.048 40.000 0.00 0.00 36.00 4.95
339 340 3.692593 ACACATTATTTGTTCTACCCCGC 59.307 43.478 0.00 0.00 36.00 6.13
352 353 1.218316 CCCCGCCGAATATAGAGGC 59.782 63.158 6.08 6.08 46.88 4.70
364 365 5.287274 CGAATATAGAGGCTGCGTCAATTAG 59.713 44.000 22.55 14.59 0.00 1.73
396 399 6.652062 TCGGAGGGAGTAAAATCTTTGTAAAC 59.348 38.462 0.00 0.00 0.00 2.01
403 406 6.981722 AGTAAAATCTTTGTAAACCAGGCAG 58.018 36.000 0.00 0.00 0.00 4.85
417 420 1.682344 GGCAGGACAAATGGACCCC 60.682 63.158 0.00 0.00 0.00 4.95
421 424 2.358195 GCAGGACAAATGGACCCCTAAT 60.358 50.000 0.00 0.00 0.00 1.73
433 436 4.080015 TGGACCCCTAATACCACATTTGAG 60.080 45.833 0.00 0.00 0.00 3.02
495 501 7.838771 TCTCAAGTTCTCAACATATGATGTG 57.161 36.000 10.38 9.15 44.07 3.21
497 503 7.879677 TCTCAAGTTCTCAACATATGATGTGTT 59.120 33.333 10.38 1.47 44.07 3.32
559 565 8.380099 AGATTATGCATGATATTTGGGCAAAAT 58.620 29.630 10.16 5.01 41.47 1.82
574 1410 2.799978 GCAAAATAGGCACAACAACCAC 59.200 45.455 0.00 0.00 0.00 4.16
583 1419 6.247229 AGGCACAACAACCACTATCATATA 57.753 37.500 0.00 0.00 0.00 0.86
731 1567 1.702957 CTCCCCCGGATAGGCAAAATA 59.297 52.381 0.73 0.00 39.21 1.40
1174 2014 0.955905 GACTCAGGTCGCCCTCTATC 59.044 60.000 0.00 0.00 39.89 2.08
1211 2051 8.039603 TGATCTATTTGTTTACTCGTGCATTT 57.960 30.769 0.00 0.00 0.00 2.32
1358 2201 3.861840 TGATAGCTGAAGTTTCTTCCGG 58.138 45.455 0.00 0.00 0.00 5.14
1419 2262 1.317613 TGGTGGCACATGTCTTGTTC 58.682 50.000 20.82 0.00 44.52 3.18
1433 2276 0.534203 TTGTTCTGCTCCGGTTGGTC 60.534 55.000 0.00 0.00 36.30 4.02
1486 2329 1.683011 GCACATTGGCTGGGTAGATGT 60.683 52.381 0.00 0.00 0.00 3.06
1508 2351 5.243507 TGTGATGCAATTGGACAATACAAGT 59.756 36.000 7.72 0.00 0.00 3.16
1516 2359 7.307337 GCAATTGGACAATACAAGTTTTCAAGG 60.307 37.037 7.72 0.00 0.00 3.61
1517 2360 5.195001 TGGACAATACAAGTTTTCAAGGC 57.805 39.130 0.00 0.00 0.00 4.35
1518 2361 4.892934 TGGACAATACAAGTTTTCAAGGCT 59.107 37.500 0.00 0.00 0.00 4.58
1519 2362 5.362430 TGGACAATACAAGTTTTCAAGGCTT 59.638 36.000 0.00 0.00 0.00 4.35
1520 2363 6.127196 TGGACAATACAAGTTTTCAAGGCTTT 60.127 34.615 0.00 0.00 0.00 3.51
1521 2364 6.420903 GGACAATACAAGTTTTCAAGGCTTTC 59.579 38.462 0.00 0.00 0.00 2.62
1522 2365 6.280643 ACAATACAAGTTTTCAAGGCTTTCC 58.719 36.000 0.00 0.00 0.00 3.13
1523 2366 3.436700 ACAAGTTTTCAAGGCTTTCCG 57.563 42.857 0.00 0.00 37.47 4.30
1524 2367 2.758423 ACAAGTTTTCAAGGCTTTCCGT 59.242 40.909 0.00 0.00 37.47 4.69
1525 2368 3.194755 ACAAGTTTTCAAGGCTTTCCGTT 59.805 39.130 0.00 0.00 37.47 4.44
1526 2369 3.436700 AGTTTTCAAGGCTTTCCGTTG 57.563 42.857 0.00 0.00 37.47 4.10
1659 2503 9.137459 TCTTGGTATGAACCTTGAAAATTGTTA 57.863 29.630 0.00 0.00 46.91 2.41
1896 2740 3.060602 GTCTAGCAGACAGGTGAAACAC 58.939 50.000 10.30 0.00 44.45 3.32
1903 2747 0.751643 ACAGGTGAAACACAGGGTGC 60.752 55.000 0.00 0.00 39.98 5.01
1904 2748 1.525995 AGGTGAAACACAGGGTGCG 60.526 57.895 0.00 0.00 39.98 5.34
1930 2778 4.583907 TGAGAGAGAGATGCTTGGATGTAG 59.416 45.833 0.00 0.00 0.00 2.74
1938 2786 2.794103 TGCTTGGATGTAGCACAACAT 58.206 42.857 0.00 0.00 43.30 2.71
2192 3040 0.464036 AGTGTGTGAGTGCTTTCGGA 59.536 50.000 0.00 0.00 0.00 4.55
2234 3082 8.778358 CACCTCCATATGATTTTTAGCTTAGTC 58.222 37.037 3.65 0.00 0.00 2.59
2237 3085 8.045720 TCCATATGATTTTTAGCTTAGTCCCT 57.954 34.615 3.65 0.00 0.00 4.20
2372 3222 8.706035 GCATAATTTATCATTGAATCTGTTGCC 58.294 33.333 0.00 0.00 0.00 4.52
2380 3230 8.657074 ATCATTGAATCTGTTGCCAATTTATG 57.343 30.769 0.00 0.00 0.00 1.90
2623 3474 3.055094 ACTTCTACACCCCTAATGTGCAG 60.055 47.826 0.00 0.00 37.22 4.41
2632 3483 5.989777 CACCCCTAATGTGCAGTTATACTAC 59.010 44.000 0.00 0.00 0.00 2.73
2668 3520 9.617523 ATGGAAATTTATTGCTTTAAAGGGATG 57.382 29.630 16.78 0.00 0.00 3.51
2843 4328 5.948162 ACATGCTTATTCATCACTCCAACTT 59.052 36.000 0.00 0.00 0.00 2.66
3019 4504 8.776470 CACAATGCCTTTGTATTTTCTTGAAAT 58.224 29.630 2.19 0.00 46.90 2.17
3020 4505 9.995003 ACAATGCCTTTGTATTTTCTTGAAATA 57.005 25.926 0.60 0.00 46.75 1.40
3215 4701 1.398041 CATGGGCGTCACATGTAAGTG 59.602 52.381 12.23 0.00 40.54 3.16
3222 4710 3.000322 GCGTCACATGTAAGTGCTGATAC 60.000 47.826 0.00 0.00 39.35 2.24
3253 4741 6.600882 ATTTCAGCAACAAAGATTCTGGAT 57.399 33.333 0.00 0.00 0.00 3.41
3256 4744 5.319453 TCAGCAACAAAGATTCTGGATTCT 58.681 37.500 0.00 0.00 0.00 2.40
3257 4745 5.182570 TCAGCAACAAAGATTCTGGATTCTG 59.817 40.000 0.00 0.00 0.00 3.02
3258 4746 4.461781 AGCAACAAAGATTCTGGATTCTGG 59.538 41.667 0.00 0.00 0.00 3.86
3259 4747 4.460382 GCAACAAAGATTCTGGATTCTGGA 59.540 41.667 0.00 0.00 0.00 3.86
3260 4748 5.392811 GCAACAAAGATTCTGGATTCTGGAG 60.393 44.000 0.00 0.00 0.00 3.86
3261 4749 5.511386 ACAAAGATTCTGGATTCTGGAGT 57.489 39.130 0.00 0.00 0.00 3.85
3262 4750 5.495640 ACAAAGATTCTGGATTCTGGAGTC 58.504 41.667 0.00 0.00 0.00 3.36
3265 4753 2.342406 TTCTGGATTCTGGAGTCCCA 57.658 50.000 6.74 0.00 40.95 4.37
3329 4817 2.851263 ACGGTCAAGCAATCAAGGTA 57.149 45.000 0.00 0.00 0.00 3.08
3722 5210 7.335924 GCAGGTATGAACAACTAAGACCATTTA 59.664 37.037 0.00 0.00 0.00 1.40
3725 5214 8.837389 GGTATGAACAACTAAGACCATTTATCC 58.163 37.037 0.00 0.00 0.00 2.59
3742 5231 7.492344 CCATTTATCCTTTGCATTTTCCAGTAC 59.508 37.037 0.00 0.00 0.00 2.73
3810 5304 4.872691 CCTAATAGTCTGGTGTTTGAGCTG 59.127 45.833 0.00 0.00 0.00 4.24
3813 5307 2.292267 AGTCTGGTGTTTGAGCTGTTG 58.708 47.619 0.00 0.00 0.00 3.33
3963 5459 0.622136 TGCCTGTCTCCTTGCATCAT 59.378 50.000 0.00 0.00 0.00 2.45
3989 5487 7.012327 TCCAGTCAAAATTCAAACTAGTGTCAG 59.988 37.037 0.00 0.00 0.00 3.51
4112 5615 5.971763 CTCACCAGAGCATAACTAACTTCT 58.028 41.667 0.00 0.00 34.61 2.85
4130 5633 9.447157 CTAACTTCTTCTTTGAGAAATGGAGAT 57.553 33.333 0.00 0.00 35.38 2.75
4146 5649 6.645790 ATGGAGATTGGTATTTTGATCAGC 57.354 37.500 0.00 0.00 0.00 4.26
4175 5678 7.590279 ACATTTACAATTTCAAGTTAGACCCG 58.410 34.615 0.00 0.00 0.00 5.28
4229 5732 5.184864 CCCAATACTATGTTGTTTCTTGGCA 59.815 40.000 0.00 0.00 32.43 4.92
4269 5772 7.564793 TGCTATAACTGAAATGACTGGTATGT 58.435 34.615 0.00 0.00 0.00 2.29
4363 5866 8.492748 CGTCTAAGTCTTGCAAACTAATGTTTA 58.507 33.333 12.60 3.17 43.75 2.01
4517 6020 6.398918 GTCAGGTGTCTATAATGACAAGTGT 58.601 40.000 0.00 0.00 46.77 3.55
4547 6050 9.715121 TTACTTTAATGGTAGATTTGTTCTCGT 57.285 29.630 0.00 0.00 35.79 4.18
4565 6068 6.268825 TCTCGTATCTTGTTAAGCTCAACT 57.731 37.500 0.48 0.00 0.00 3.16
4602 6105 1.959985 TCACGTGGCCATGTTTTGAAT 59.040 42.857 28.34 1.50 0.00 2.57
4646 6149 4.382345 AATAGCTGCTGATTTTGCCTTC 57.618 40.909 13.43 0.00 0.00 3.46
4781 6284 8.991243 AGGTAAAACAGTAAAAACAAGTTTCC 57.009 30.769 0.00 0.00 31.80 3.13
4944 6448 2.905415 TCTACAACTTAGGGGTCGGA 57.095 50.000 0.00 0.00 0.00 4.55
5122 6626 5.467035 TTTTGTGCCCTCTTTATTCTTGG 57.533 39.130 0.00 0.00 0.00 3.61
5150 6654 7.065324 ACAATTGTTCATGCAATTTCATCATCC 59.935 33.333 4.92 0.00 43.97 3.51
5165 6669 3.880047 TCATCCGTTTCCGTGTTATCT 57.120 42.857 0.00 0.00 0.00 1.98
5195 6699 0.467384 CATGGGGCAACAAACCAACA 59.533 50.000 0.00 0.00 37.89 3.33
5250 6754 2.487086 CCGATTGCCTCATATCAACCCA 60.487 50.000 0.00 0.00 0.00 4.51
5485 6989 9.597681 CAACTAGTATATAGGGTTAAAGGAGGA 57.402 37.037 0.00 0.00 0.00 3.71
5653 7157 8.800370 TCATTGCTGTACTATTGACCAATTTA 57.200 30.769 0.17 0.00 32.50 1.40
5774 7278 2.179517 CTGAGGACTGTCGTCGGC 59.820 66.667 21.99 4.02 41.16 5.54
5775 7279 3.343788 CTGAGGACTGTCGTCGGCC 62.344 68.421 21.99 0.00 41.16 6.13
5793 7297 2.679716 CTGGGGGAGAAAGCTGGG 59.320 66.667 0.00 0.00 0.00 4.45
5798 7302 1.717032 GGGGAGAAAGCTGGGTTTTT 58.283 50.000 0.00 0.00 0.00 1.94
5879 7530 1.683365 AGGTGCCAATGCCATGACC 60.683 57.895 0.00 0.00 36.33 4.02
5988 7680 1.135575 GGCTGAAGGATTGCAGTTTCG 60.136 52.381 0.00 0.00 34.66 3.46
6015 7733 2.185004 ATGAGTCTGTTTGGAACGGG 57.815 50.000 0.26 0.00 38.33 5.28
6026 7744 2.781681 TGGAACGGGAGATTTTCCTC 57.218 50.000 0.00 0.00 45.98 3.71
6048 7766 7.225931 TCCTCGATTCTTTAATATTTGAACCGG 59.774 37.037 0.00 0.00 0.00 5.28
6052 7770 5.828299 TCTTTAATATTTGAACCGGCTGG 57.172 39.130 11.02 11.02 42.84 4.85
6066 7784 1.666888 CGGCTGGTGTGAAATTTCTGC 60.667 52.381 18.64 11.90 0.00 4.26
6075 7793 4.675114 GTGTGAAATTTCTGCGAAATTCGT 59.325 37.500 21.21 12.16 42.81 3.85
6102 7820 6.690194 AAGCTACAAATAGGATTTGAGCTG 57.310 37.500 23.84 12.32 39.91 4.24
6115 7833 5.460091 GGATTTGAGCTGTTCTTGTGAAAAC 59.540 40.000 0.00 0.00 33.52 2.43
6130 7848 7.442364 TCTTGTGAAAACTACTCTTGGATCAAG 59.558 37.037 0.00 1.53 42.25 3.02
6171 7889 1.278637 CGACGGCGTTGCTCTTTTT 59.721 52.632 16.19 0.00 0.00 1.94
6190 7908 3.904800 TTTCTTACGATGGCTCCATGA 57.095 42.857 6.07 0.00 36.70 3.07
6192 7910 3.459232 TCTTACGATGGCTCCATGAAG 57.541 47.619 6.07 7.17 36.70 3.02
6226 7944 0.624795 GGGTTCCCTCTTCCCTCCAT 60.625 60.000 0.00 0.00 38.29 3.41
6228 7946 0.548510 GTTCCCTCTTCCCTCCATGG 59.451 60.000 4.97 4.97 0.00 3.66
6229 7947 1.281925 TTCCCTCTTCCCTCCATGGC 61.282 60.000 6.96 0.00 0.00 4.40
6333 8051 1.645704 CCTCGTCTCATCACGTCCGT 61.646 60.000 0.00 0.00 40.79 4.69
6358 8076 2.573869 CTCCCTCTTCTTCGCGCA 59.426 61.111 8.75 0.00 0.00 6.09
6373 8091 2.965783 GCAGTGAGCTCCGTCTCA 59.034 61.111 12.15 0.00 40.50 3.27
6387 8105 1.616865 CGTCTCACCCAAACTGACCTA 59.383 52.381 0.00 0.00 0.00 3.08
6438 8156 1.006102 CGTGCTCCGTCCAAGAACT 60.006 57.895 0.00 0.00 0.00 3.01
6447 8168 2.150719 TCCAAGAACTGCCCCGGAA 61.151 57.895 0.73 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.051679 CCAAAAACATCGACATCCATAATACTA 57.948 33.333 0.00 0.00 0.00 1.82
7 8 7.468631 GCCAAAAACATCGACATCCATAATACT 60.469 37.037 0.00 0.00 0.00 2.12
8 9 6.636850 GCCAAAAACATCGACATCCATAATAC 59.363 38.462 0.00 0.00 0.00 1.89
9 10 6.545666 AGCCAAAAACATCGACATCCATAATA 59.454 34.615 0.00 0.00 0.00 0.98
10 11 5.360714 AGCCAAAAACATCGACATCCATAAT 59.639 36.000 0.00 0.00 0.00 1.28
11 12 4.704540 AGCCAAAAACATCGACATCCATAA 59.295 37.500 0.00 0.00 0.00 1.90
12 13 4.269183 AGCCAAAAACATCGACATCCATA 58.731 39.130 0.00 0.00 0.00 2.74
13 14 3.091545 AGCCAAAAACATCGACATCCAT 58.908 40.909 0.00 0.00 0.00 3.41
14 15 2.513753 AGCCAAAAACATCGACATCCA 58.486 42.857 0.00 0.00 0.00 3.41
15 16 4.335315 TGATAGCCAAAAACATCGACATCC 59.665 41.667 0.00 0.00 0.00 3.51
16 17 5.484173 TGATAGCCAAAAACATCGACATC 57.516 39.130 0.00 0.00 0.00 3.06
17 18 5.895636 TTGATAGCCAAAAACATCGACAT 57.104 34.783 0.00 0.00 0.00 3.06
18 19 5.895636 ATTGATAGCCAAAAACATCGACA 57.104 34.783 0.00 0.00 38.43 4.35
19 20 6.321717 TCAATTGATAGCCAAAAACATCGAC 58.678 36.000 3.38 0.00 38.43 4.20
20 21 6.507958 TCAATTGATAGCCAAAAACATCGA 57.492 33.333 3.38 0.00 38.43 3.59
21 22 7.760131 AATCAATTGATAGCCAAAAACATCG 57.240 32.000 21.00 0.00 38.43 3.84
22 23 9.153721 TCAAATCAATTGATAGCCAAAAACATC 57.846 29.630 21.00 0.00 43.08 3.06
36 37 9.781633 AGGTGAATGATTTTTCAAATCAATTGA 57.218 25.926 11.26 11.26 46.22 2.57
37 38 9.820229 CAGGTGAATGATTTTTCAAATCAATTG 57.180 29.630 14.28 0.00 39.75 2.32
38 39 9.005777 CCAGGTGAATGATTTTTCAAATCAATT 57.994 29.630 14.28 9.88 39.75 2.32
39 40 8.158789 ACCAGGTGAATGATTTTTCAAATCAAT 58.841 29.630 14.28 7.57 39.75 2.57
40 41 7.507829 ACCAGGTGAATGATTTTTCAAATCAA 58.492 30.769 14.28 0.00 39.75 2.57
41 42 7.065120 ACCAGGTGAATGATTTTTCAAATCA 57.935 32.000 13.00 13.00 40.50 2.57
42 43 7.153985 TGACCAGGTGAATGATTTTTCAAATC 58.846 34.615 0.00 2.76 37.36 2.17
43 44 7.065120 TGACCAGGTGAATGATTTTTCAAAT 57.935 32.000 0.00 0.00 37.36 2.32
44 45 6.477053 TGACCAGGTGAATGATTTTTCAAA 57.523 33.333 0.00 0.00 37.36 2.69
45 46 6.477053 TTGACCAGGTGAATGATTTTTCAA 57.523 33.333 0.00 0.00 37.36 2.69
46 47 6.477053 TTTGACCAGGTGAATGATTTTTCA 57.523 33.333 0.00 0.00 33.32 2.69
47 48 7.656948 TGATTTTGACCAGGTGAATGATTTTTC 59.343 33.333 0.00 0.00 0.00 2.29
48 49 7.507829 TGATTTTGACCAGGTGAATGATTTTT 58.492 30.769 0.00 0.00 0.00 1.94
49 50 7.065120 TGATTTTGACCAGGTGAATGATTTT 57.935 32.000 0.00 0.00 0.00 1.82
50 51 6.669125 TGATTTTGACCAGGTGAATGATTT 57.331 33.333 0.00 0.00 0.00 2.17
51 52 6.438108 TCATGATTTTGACCAGGTGAATGATT 59.562 34.615 0.00 0.00 0.00 2.57
52 53 5.953548 TCATGATTTTGACCAGGTGAATGAT 59.046 36.000 0.00 0.00 0.00 2.45
53 54 5.323581 TCATGATTTTGACCAGGTGAATGA 58.676 37.500 0.00 0.00 0.00 2.57
54 55 5.648178 TCATGATTTTGACCAGGTGAATG 57.352 39.130 0.00 0.00 0.00 2.67
55 56 5.539574 TGTTCATGATTTTGACCAGGTGAAT 59.460 36.000 0.00 0.00 0.00 2.57
56 57 4.892345 TGTTCATGATTTTGACCAGGTGAA 59.108 37.500 0.00 0.00 0.00 3.18
57 58 4.468713 TGTTCATGATTTTGACCAGGTGA 58.531 39.130 0.00 0.00 0.00 4.02
58 59 4.852134 TGTTCATGATTTTGACCAGGTG 57.148 40.909 0.00 0.00 0.00 4.00
59 60 5.867903 TTTGTTCATGATTTTGACCAGGT 57.132 34.783 0.00 0.00 0.00 4.00
60 61 5.870978 GGATTTGTTCATGATTTTGACCAGG 59.129 40.000 0.00 0.00 0.00 4.45
61 62 6.457355 TGGATTTGTTCATGATTTTGACCAG 58.543 36.000 0.00 0.00 0.00 4.00
62 63 6.416631 TGGATTTGTTCATGATTTTGACCA 57.583 33.333 0.00 0.70 0.00 4.02
63 64 7.727331 TTTGGATTTGTTCATGATTTTGACC 57.273 32.000 0.00 0.00 0.00 4.02
83 84 9.248291 CCCATTCGATTGACTATTTAATTTTGG 57.752 33.333 8.84 0.00 0.00 3.28
84 85 9.248291 CCCCATTCGATTGACTATTTAATTTTG 57.752 33.333 8.84 0.00 0.00 2.44
85 86 9.196139 TCCCCATTCGATTGACTATTTAATTTT 57.804 29.630 8.84 0.00 0.00 1.82
86 87 8.760980 TCCCCATTCGATTGACTATTTAATTT 57.239 30.769 8.84 0.00 0.00 1.82
87 88 8.630037 GTTCCCCATTCGATTGACTATTTAATT 58.370 33.333 8.84 0.00 0.00 1.40
88 89 7.998964 AGTTCCCCATTCGATTGACTATTTAAT 59.001 33.333 8.84 0.00 0.00 1.40
89 90 7.343357 AGTTCCCCATTCGATTGACTATTTAA 58.657 34.615 8.84 0.00 0.00 1.52
90 91 6.895782 AGTTCCCCATTCGATTGACTATTTA 58.104 36.000 8.84 0.00 0.00 1.40
91 92 5.755849 AGTTCCCCATTCGATTGACTATTT 58.244 37.500 8.84 0.00 0.00 1.40
92 93 5.368989 GAGTTCCCCATTCGATTGACTATT 58.631 41.667 8.84 0.00 0.00 1.73
93 94 4.202367 GGAGTTCCCCATTCGATTGACTAT 60.202 45.833 8.84 0.00 0.00 2.12
94 95 3.134081 GGAGTTCCCCATTCGATTGACTA 59.866 47.826 8.84 0.00 0.00 2.59
95 96 2.092914 GGAGTTCCCCATTCGATTGACT 60.093 50.000 8.84 4.29 0.00 3.41
96 97 2.289565 GGAGTTCCCCATTCGATTGAC 58.710 52.381 8.84 0.00 0.00 3.18
97 98 1.912731 TGGAGTTCCCCATTCGATTGA 59.087 47.619 8.84 0.00 34.29 2.57
98 99 2.418368 TGGAGTTCCCCATTCGATTG 57.582 50.000 0.22 0.22 34.29 2.67
99 100 3.449746 TTTGGAGTTCCCCATTCGATT 57.550 42.857 0.00 0.00 35.87 3.34
100 101 3.449746 TTTTGGAGTTCCCCATTCGAT 57.550 42.857 0.00 0.00 35.87 3.59
101 102 2.961531 TTTTGGAGTTCCCCATTCGA 57.038 45.000 0.00 0.00 35.87 3.71
102 103 4.097892 CCTAATTTTGGAGTTCCCCATTCG 59.902 45.833 0.00 0.00 35.87 3.34
103 104 4.405680 CCCTAATTTTGGAGTTCCCCATTC 59.594 45.833 0.00 0.00 35.87 2.67
104 105 4.046618 TCCCTAATTTTGGAGTTCCCCATT 59.953 41.667 0.00 0.00 35.87 3.16
105 106 3.600617 TCCCTAATTTTGGAGTTCCCCAT 59.399 43.478 0.00 0.00 35.87 4.00
106 107 2.997463 TCCCTAATTTTGGAGTTCCCCA 59.003 45.455 0.00 0.00 34.29 4.96
107 108 3.632333 CTCCCTAATTTTGGAGTTCCCC 58.368 50.000 12.58 0.00 42.67 4.81
114 115 4.080243 TCCGTTATGCTCCCTAATTTTGGA 60.080 41.667 0.00 0.00 0.00 3.53
115 116 4.204012 TCCGTTATGCTCCCTAATTTTGG 58.796 43.478 0.00 0.00 0.00 3.28
116 117 6.391227 AATCCGTTATGCTCCCTAATTTTG 57.609 37.500 0.00 0.00 0.00 2.44
117 118 8.528044 TTTAATCCGTTATGCTCCCTAATTTT 57.472 30.769 0.00 0.00 0.00 1.82
118 119 8.528044 TTTTAATCCGTTATGCTCCCTAATTT 57.472 30.769 0.00 0.00 0.00 1.82
119 120 8.706322 ATTTTAATCCGTTATGCTCCCTAATT 57.294 30.769 0.00 0.00 0.00 1.40
120 121 9.449719 CTATTTTAATCCGTTATGCTCCCTAAT 57.550 33.333 0.00 0.00 0.00 1.73
121 122 8.434392 ACTATTTTAATCCGTTATGCTCCCTAA 58.566 33.333 0.00 0.00 0.00 2.69
122 123 7.970102 ACTATTTTAATCCGTTATGCTCCCTA 58.030 34.615 0.00 0.00 0.00 3.53
123 124 6.838382 ACTATTTTAATCCGTTATGCTCCCT 58.162 36.000 0.00 0.00 0.00 4.20
124 125 7.227910 TCAACTATTTTAATCCGTTATGCTCCC 59.772 37.037 0.00 0.00 0.00 4.30
125 126 8.149973 TCAACTATTTTAATCCGTTATGCTCC 57.850 34.615 0.00 0.00 0.00 4.70
127 128 9.950680 CATTCAACTATTTTAATCCGTTATGCT 57.049 29.630 0.00 0.00 0.00 3.79
128 129 9.944663 TCATTCAACTATTTTAATCCGTTATGC 57.055 29.630 0.00 0.00 0.00 3.14
132 133 9.667107 TCTCTCATTCAACTATTTTAATCCGTT 57.333 29.630 0.00 0.00 0.00 4.44
133 134 9.319143 CTCTCTCATTCAACTATTTTAATCCGT 57.681 33.333 0.00 0.00 0.00 4.69
134 135 8.279103 GCTCTCTCATTCAACTATTTTAATCCG 58.721 37.037 0.00 0.00 0.00 4.18
135 136 9.336171 AGCTCTCTCATTCAACTATTTTAATCC 57.664 33.333 0.00 0.00 0.00 3.01
137 138 9.336171 GGAGCTCTCTCATTCAACTATTTTAAT 57.664 33.333 14.64 0.00 41.13 1.40
138 139 8.543774 AGGAGCTCTCTCATTCAACTATTTTAA 58.456 33.333 14.64 0.00 41.13 1.52
139 140 8.083828 AGGAGCTCTCTCATTCAACTATTTTA 57.916 34.615 14.64 0.00 41.13 1.52
140 141 6.956497 AGGAGCTCTCTCATTCAACTATTTT 58.044 36.000 14.64 0.00 41.13 1.82
141 142 6.558488 AGGAGCTCTCTCATTCAACTATTT 57.442 37.500 14.64 0.00 41.13 1.40
142 143 6.558488 AAGGAGCTCTCTCATTCAACTATT 57.442 37.500 14.64 0.00 38.84 1.73
181 182 2.091541 GCCCGATTTTGACTGGATCAA 58.908 47.619 0.00 0.00 45.92 2.57
182 183 1.750193 GCCCGATTTTGACTGGATCA 58.250 50.000 0.00 0.00 34.65 2.92
183 184 0.657840 CGCCCGATTTTGACTGGATC 59.342 55.000 0.00 0.00 0.00 3.36
184 185 0.748005 CCGCCCGATTTTGACTGGAT 60.748 55.000 0.00 0.00 0.00 3.41
185 186 1.376683 CCGCCCGATTTTGACTGGA 60.377 57.895 0.00 0.00 0.00 3.86
186 187 0.748005 ATCCGCCCGATTTTGACTGG 60.748 55.000 0.00 0.00 0.00 4.00
187 188 1.094785 AATCCGCCCGATTTTGACTG 58.905 50.000 0.00 0.00 38.02 3.51
188 189 1.834188 AAATCCGCCCGATTTTGACT 58.166 45.000 1.48 0.00 46.93 3.41
194 195 2.035237 TAGCCGAAATCCGCCCGATT 62.035 55.000 0.00 0.00 43.34 3.34
195 196 1.827399 ATAGCCGAAATCCGCCCGAT 61.827 55.000 0.00 0.00 36.84 4.18
196 197 2.035237 AATAGCCGAAATCCGCCCGA 62.035 55.000 0.00 0.00 36.84 5.14
197 198 1.597027 AATAGCCGAAATCCGCCCG 60.597 57.895 0.00 0.00 36.84 6.13
198 199 0.818040 ACAATAGCCGAAATCCGCCC 60.818 55.000 0.00 0.00 36.84 6.13
199 200 1.002792 GAACAATAGCCGAAATCCGCC 60.003 52.381 0.00 0.00 36.84 6.13
200 201 1.002792 GGAACAATAGCCGAAATCCGC 60.003 52.381 0.00 0.00 36.84 5.54
201 202 2.285083 TGGAACAATAGCCGAAATCCG 58.715 47.619 0.00 0.00 31.92 4.18
216 217 6.930731 TGGAACCAATAAAAGCTTATGGAAC 58.069 36.000 20.83 14.82 0.00 3.62
218 219 6.894654 TCATGGAACCAATAAAAGCTTATGGA 59.105 34.615 20.83 5.31 0.00 3.41
294 295 7.436080 GTGTTGCATACAATAAATTAGCTGCAT 59.564 33.333 1.02 0.00 38.80 3.96
313 314 5.047660 GGGGTAGAACAAATAATGTGTTGCA 60.048 40.000 0.00 0.00 42.99 4.08
315 316 5.636837 CGGGGTAGAACAAATAATGTGTTG 58.363 41.667 0.00 0.00 42.99 3.33
317 318 3.692593 GCGGGGTAGAACAAATAATGTGT 59.307 43.478 0.00 0.00 42.99 3.72
332 333 1.843368 CCTCTATATTCGGCGGGGTA 58.157 55.000 7.21 0.00 0.00 3.69
339 340 1.269723 TGACGCAGCCTCTATATTCGG 59.730 52.381 0.00 0.00 0.00 4.30
364 365 5.880887 AGATTTTACTCCCTCCGATTCAAAC 59.119 40.000 0.00 0.00 0.00 2.93
396 399 0.967380 GGTCCATTTGTCCTGCCTGG 60.967 60.000 0.00 0.00 37.10 4.45
403 406 3.203487 TGGTATTAGGGGTCCATTTGTCC 59.797 47.826 0.00 0.00 0.00 4.02
417 420 7.807977 ATAGGTTGCTCAAATGTGGTATTAG 57.192 36.000 0.00 0.00 0.00 1.73
421 424 6.070481 TCACTATAGGTTGCTCAAATGTGGTA 60.070 38.462 4.43 0.00 0.00 3.25
433 436 3.279434 CCCTGGTTTCACTATAGGTTGC 58.721 50.000 4.43 0.00 0.00 4.17
509 515 5.068636 GGGCTCTCACATCATATGTTGAAT 58.931 41.667 18.51 0.00 42.70 2.57
524 530 2.707257 TCATGCATAATCTGGGCTCTCA 59.293 45.455 0.00 0.00 0.00 3.27
559 565 4.568072 ATGATAGTGGTTGTTGTGCCTA 57.432 40.909 0.00 0.00 0.00 3.93
731 1567 2.001269 GTGGAGGGGCAGTATGGGT 61.001 63.158 0.00 0.00 35.86 4.51
1053 1893 2.203238 TGTTGCTGCTGCTGCTGA 60.203 55.556 27.67 16.03 40.01 4.26
1174 2014 4.100189 ACAAATAGATCAGGAACCGAGGAG 59.900 45.833 0.00 0.00 0.00 3.69
1433 2276 4.637483 ATAACAATGGAGCAATGTTCCG 57.363 40.909 11.45 0.15 38.29 4.30
1486 2329 5.981088 ACTTGTATTGTCCAATTGCATCA 57.019 34.783 0.00 0.00 32.50 3.07
1508 2351 1.478510 TGCAACGGAAAGCCTTGAAAA 59.521 42.857 0.00 0.00 0.00 2.29
1516 2359 3.638484 ACAAGTAAATGCAACGGAAAGC 58.362 40.909 0.00 0.00 0.00 3.51
1517 2360 6.582437 AAAACAAGTAAATGCAACGGAAAG 57.418 33.333 0.00 0.00 0.00 2.62
1518 2361 6.369065 ACAAAAACAAGTAAATGCAACGGAAA 59.631 30.769 0.00 0.00 0.00 3.13
1519 2362 5.869888 ACAAAAACAAGTAAATGCAACGGAA 59.130 32.000 0.00 0.00 0.00 4.30
1520 2363 5.411781 ACAAAAACAAGTAAATGCAACGGA 58.588 33.333 0.00 0.00 0.00 4.69
1521 2364 5.710613 ACAAAAACAAGTAAATGCAACGG 57.289 34.783 0.00 0.00 0.00 4.44
1522 2365 7.742089 TGAAAACAAAAACAAGTAAATGCAACG 59.258 29.630 0.00 0.00 0.00 4.10
1523 2366 8.941127 TGAAAACAAAAACAAGTAAATGCAAC 57.059 26.923 0.00 0.00 0.00 4.17
1659 2503 5.467735 GCAAAAATCCTGACTCAAAGCAAAT 59.532 36.000 0.00 0.00 0.00 2.32
1715 2559 4.626042 AGTACAAGAGACACAGAAAGCAG 58.374 43.478 0.00 0.00 0.00 4.24
1896 2740 1.080230 CTCTCTCACACGCACCCTG 60.080 63.158 0.00 0.00 0.00 4.45
1903 2747 2.528125 CAAGCATCTCTCTCTCACACG 58.472 52.381 0.00 0.00 0.00 4.49
1904 2748 2.495270 TCCAAGCATCTCTCTCTCACAC 59.505 50.000 0.00 0.00 0.00 3.82
2100 2948 5.188359 AGGCTCCATCTGCAAAATGTAAAAT 59.812 36.000 7.70 0.00 0.00 1.82
2192 3040 3.626217 GGAGGTGAAAACACGAAAGAACT 59.374 43.478 0.00 0.00 0.00 3.01
2234 3082 2.760650 GCATGACTAAAGGGGAAAAGGG 59.239 50.000 0.00 0.00 0.00 3.95
2237 3085 6.183361 ACAATTTGCATGACTAAAGGGGAAAA 60.183 34.615 0.00 0.00 0.00 2.29
2668 3520 4.884164 CCATCAAGGTAATTGGAAGGAGAC 59.116 45.833 0.00 0.00 39.54 3.36
2742 3594 0.888619 TCAAGACATCGGCGTTCTCT 59.111 50.000 6.85 0.00 0.00 3.10
2843 4328 9.952030 TGTATAGAGGTTGTGTCAATTAATTCA 57.048 29.630 0.00 0.00 0.00 2.57
2883 4368 4.368315 CGATCCGGATTAATTGACACAGA 58.632 43.478 20.22 0.00 0.00 3.41
2982 4467 1.542915 AGGCATTGTGTCTTGATGCAC 59.457 47.619 9.42 0.00 46.01 4.57
3019 4504 9.507280 GTAGCATACGAAAAGTAACAGTACATA 57.493 33.333 0.00 0.00 39.04 2.29
3020 4505 8.403606 GTAGCATACGAAAAGTAACAGTACAT 57.596 34.615 0.00 0.00 39.04 2.29
3021 4506 7.801547 GTAGCATACGAAAAGTAACAGTACA 57.198 36.000 0.00 0.00 39.04 2.90
3126 4612 1.692411 AACCCAAAGGAAGACTGCAC 58.308 50.000 0.00 0.00 36.73 4.57
3256 4744 2.907892 AGAAGTTGATCTGGGACTCCA 58.092 47.619 0.00 0.00 41.58 3.86
3257 4745 5.363939 CATTAGAAGTTGATCTGGGACTCC 58.636 45.833 0.00 0.00 0.00 3.85
3258 4746 4.813697 GCATTAGAAGTTGATCTGGGACTC 59.186 45.833 0.00 0.00 0.00 3.36
3259 4747 4.472833 AGCATTAGAAGTTGATCTGGGACT 59.527 41.667 0.00 0.00 0.00 3.85
3260 4748 4.775236 AGCATTAGAAGTTGATCTGGGAC 58.225 43.478 0.00 0.00 0.00 4.46
3261 4749 5.441718 AAGCATTAGAAGTTGATCTGGGA 57.558 39.130 0.00 0.00 0.00 4.37
3262 4750 6.151648 TGAAAAGCATTAGAAGTTGATCTGGG 59.848 38.462 0.00 0.00 0.00 4.45
3329 4817 2.081462 GTACTTGCATACGCCCAGTTT 58.919 47.619 0.00 0.00 37.32 2.66
3722 5210 5.574188 AGAGTACTGGAAAATGCAAAGGAT 58.426 37.500 0.00 0.00 0.00 3.24
3725 5214 6.206634 TGGTAAGAGTACTGGAAAATGCAAAG 59.793 38.462 0.00 0.00 0.00 2.77
3742 5231 6.102663 AGACTCACGATCAAAATGGTAAGAG 58.897 40.000 0.00 0.00 0.00 2.85
3810 5304 5.581126 TGCAAAATCCATCAGTATCCAAC 57.419 39.130 0.00 0.00 0.00 3.77
3813 5307 5.045872 GCTTTGCAAAATCCATCAGTATCC 58.954 41.667 13.84 0.00 0.00 2.59
3963 5459 6.826231 TGACACTAGTTTGAATTTTGACTGGA 59.174 34.615 0.00 0.00 0.00 3.86
3989 5487 9.624697 TCATTCATGTTAGACTAAATGCAAAAC 57.375 29.630 0.00 0.00 0.00 2.43
4094 5597 8.539770 TCAAAGAAGAAGTTAGTTATGCTCTG 57.460 34.615 0.00 0.00 0.00 3.35
4110 5613 6.546484 ACCAATCTCCATTTCTCAAAGAAGA 58.454 36.000 0.00 0.00 35.37 2.87
4111 5614 6.830873 ACCAATCTCCATTTCTCAAAGAAG 57.169 37.500 0.00 0.00 35.37 2.85
4112 5615 8.884124 AATACCAATCTCCATTTCTCAAAGAA 57.116 30.769 0.00 0.00 31.28 2.52
4130 5633 5.186256 TGTAGGGCTGATCAAAATACCAA 57.814 39.130 0.00 0.00 0.00 3.67
4175 5678 9.088512 CACACTGATAATAGAGGTAAAACACTC 57.911 37.037 0.00 0.00 0.00 3.51
4229 5732 3.710209 ATAGCAGTTTCAGCTTCCTGT 57.290 42.857 0.00 0.00 43.25 4.00
4314 5817 8.594881 ACGGTTTGAATATCAGAATATCAGAC 57.405 34.615 0.00 0.00 0.00 3.51
4315 5818 8.642432 AGACGGTTTGAATATCAGAATATCAGA 58.358 33.333 0.00 0.00 0.00 3.27
4324 5827 7.464710 GCAAGACTTAGACGGTTTGAATATCAG 60.465 40.741 0.00 0.00 0.00 2.90
4333 5836 4.196971 AGTTTGCAAGACTTAGACGGTTT 58.803 39.130 0.00 0.00 0.00 3.27
4335 5838 3.470645 AGTTTGCAAGACTTAGACGGT 57.529 42.857 0.00 0.00 0.00 4.83
4363 5866 1.618343 GCCAAGCCATTTACCTGTTGT 59.382 47.619 0.00 0.00 0.00 3.32
4565 6068 5.349270 CCACGTGATTCCTTTCGTAACATTA 59.651 40.000 19.30 0.00 35.13 1.90
4573 6076 0.953471 TGGCCACGTGATTCCTTTCG 60.953 55.000 19.30 0.00 0.00 3.46
4646 6149 3.849911 TGCTACAGAAGAAAGATGGACG 58.150 45.455 0.00 0.00 0.00 4.79
4869 6373 7.593273 TGACCAGTTAAGCAAAACGATAAATTG 59.407 33.333 0.00 0.00 34.46 2.32
4878 6382 4.649088 AACCTGACCAGTTAAGCAAAAC 57.351 40.909 0.00 0.00 0.00 2.43
4944 6448 3.963428 ACACGAACTTCCTCAATAGCT 57.037 42.857 0.00 0.00 0.00 3.32
5122 6626 5.345609 TGAAATTGCATGAACAATTGTGC 57.654 34.783 12.82 11.28 46.80 4.57
5165 6669 0.403655 TGCCCCATGAGCACTACAAA 59.596 50.000 6.31 0.00 34.69 2.83
5195 6699 0.722676 TAGAAGATGTCCCAGGGGGT 59.277 55.000 5.33 0.00 44.74 4.95
5237 6741 5.892160 CCATTGCTATGGGTTGATATGAG 57.108 43.478 18.33 0.00 46.43 2.90
5480 6984 1.401905 CGCTACAAATGCCTTTCCTCC 59.598 52.381 0.00 0.00 0.00 4.30
5482 6986 0.811281 GCGCTACAAATGCCTTTCCT 59.189 50.000 0.00 0.00 0.00 3.36
5483 6987 0.811281 AGCGCTACAAATGCCTTTCC 59.189 50.000 8.99 0.00 0.00 3.13
5485 6989 1.470098 CTGAGCGCTACAAATGCCTTT 59.530 47.619 11.50 0.00 0.00 3.11
5515 7019 1.708993 AAGGTCAGGTCAGGCTTGCA 61.709 55.000 0.00 0.00 0.00 4.08
5653 7157 1.420138 ACCCAACGAAATCAGACCAGT 59.580 47.619 0.00 0.00 0.00 4.00
5774 7278 2.679716 CAGCTTTCTCCCCCAGGG 59.320 66.667 0.00 0.00 46.11 4.45
5775 7279 2.679716 CCAGCTTTCTCCCCCAGG 59.320 66.667 0.00 0.00 0.00 4.45
5801 7305 9.874205 CAACCAAACCACAGATGATATAAAATT 57.126 29.630 0.00 0.00 0.00 1.82
5802 7306 8.477256 CCAACCAAACCACAGATGATATAAAAT 58.523 33.333 0.00 0.00 0.00 1.82
5807 7311 5.191727 TCCAACCAAACCACAGATGATAT 57.808 39.130 0.00 0.00 0.00 1.63
5879 7530 4.084641 GCTCAGCAGCTGATAATAAACTCG 60.085 45.833 25.59 10.70 43.09 4.18
5988 7680 4.894784 TCCAAACAGACTCATTGTACTCC 58.105 43.478 0.00 0.00 0.00 3.85
6026 7744 6.632834 CAGCCGGTTCAAATATTAAAGAATCG 59.367 38.462 17.24 17.24 42.47 3.34
6046 7764 1.666888 GCAGAAATTTCACACCAGCCG 60.667 52.381 19.99 0.00 0.00 5.52
6048 7766 1.266718 TCGCAGAAATTTCACACCAGC 59.733 47.619 19.99 11.80 0.00 4.85
6052 7770 4.675114 ACGAATTTCGCAGAAATTTCACAC 59.325 37.500 19.99 7.82 45.12 3.82
6066 7784 7.634817 CCTATTTGTAGCTTAACACGAATTTCG 59.365 37.037 16.84 16.84 46.93 3.46
6075 7793 7.829211 AGCTCAAATCCTATTTGTAGCTTAACA 59.171 33.333 20.90 0.00 38.48 2.41
6102 7820 6.920569 TCCAAGAGTAGTTTTCACAAGAAC 57.079 37.500 0.00 0.00 32.39 3.01
6115 7833 6.577103 TGCTCAATACTTGATCCAAGAGTAG 58.423 40.000 13.00 4.94 43.42 2.57
6171 7889 3.432186 CCTTCATGGAGCCATCGTAAGAA 60.432 47.826 13.42 7.69 45.60 2.52
6190 7908 3.080660 ACCCATATCACCTCATCCCTT 57.919 47.619 0.00 0.00 0.00 3.95
6192 7910 2.040412 GGAACCCATATCACCTCATCCC 59.960 54.545 0.00 0.00 0.00 3.85
6306 8024 0.464013 GATGAGACGAGGAGGACGGA 60.464 60.000 0.00 0.00 34.93 4.69
6309 8027 0.378962 CGTGATGAGACGAGGAGGAC 59.621 60.000 0.00 0.00 42.10 3.85
6333 8051 1.289530 GAAGAAGAGGGAGGAGGGAGA 59.710 57.143 0.00 0.00 0.00 3.71
6373 8091 1.838073 CGGGCTAGGTCAGTTTGGGT 61.838 60.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.