Multiple sequence alignment - TraesCS1B01G244500

Loading Multiple Alignment...

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 TraesCS1B01G244500 chr1B 100.000 5119 0 0 949 6067 433636738 433641856 0.000000e+00 9454.0
1 TraesCS1B01G244500 chr1B 100.000 484 0 0 1 484 433635790 433636273 0.000000e+00 894.0
2 TraesCS1B01G244500 chr1D 94.069 3153 127 35 998 4126 320721450 320724566 0.000000e+00 4732.0
3 TraesCS1B01G244500 chr1D 96.117 1133 34 2 4122 5244 320724602 320725734 0.000000e+00 1840.0
4 TraesCS1B01G244500 chr1D 91.743 327 8 6 176 484 320720820 320721145 2.600000e-118 436.0
5 TraesCS1B01G244500 chr1D 93.266 297 12 2 5770 6065 320728269 320728558 1.210000e-116 431.0
6 TraesCS1B01G244500 chr1D 93.514 185 10 2 5553 5737 320728082 320728264 2.150000e-69 274.0
7 TraesCS1B01G244500 chr1D 93.878 49 1 1 5466 5514 320727923 320727969 8.440000e-09 73.1
8 TraesCS1B01G244500 chr1D 97.143 35 0 1 5522 5555 4310557 4310591 2.360000e-04 58.4
9 TraesCS1B01G244500 chr1D 96.875 32 1 0 147 178 417577652 417577621 3.000000e-03 54.7
10 TraesCS1B01G244500 chr1A 96.257 2084 70 5 2009 4087 402235375 402233295 0.000000e+00 3410.0
11 TraesCS1B01G244500 chr1A 95.772 1159 37 4 4122 5269 402233198 402232041 0.000000e+00 1858.0
12 TraesCS1B01G244500 chr1A 93.417 1033 56 7 989 2016 402236632 402235607 0.000000e+00 1520.0
13 TraesCS1B01G244500 chr1A 95.000 500 24 1 5567 6066 402231197 402230699 0.000000e+00 784.0
14 TraesCS1B01G244500 chr1A 90.354 311 7 8 182 484 402237170 402236875 2.650000e-103 387.0
15 TraesCS1B01G244500 chr1A 97.826 46 1 0 4081 4126 402233279 402233234 5.040000e-11 80.5
16 TraesCS1B01G244500 chr1A 91.228 57 3 1 5465 5521 402231368 402231314 6.520000e-10 76.8
17 TraesCS1B01G244500 chr3A 98.496 133 2 0 46 178 118566523 118566391 1.020000e-57 235.0
18 TraesCS1B01G244500 chr3A 94.872 39 2 0 7 45 24436271 24436233 1.830000e-05 62.1
19 TraesCS1B01G244500 chr3B 92.958 142 10 0 46 187 131570942 131570801 2.220000e-49 207.0
20 TraesCS1B01G244500 chr3B 93.333 45 3 0 1 45 738758349 738758393 3.920000e-07 67.6
21 TraesCS1B01G244500 chr7A 91.729 133 7 2 46 178 674121046 674121174 1.340000e-41 182.0
22 TraesCS1B01G244500 chr7A 93.617 47 3 0 1 47 61867528 61867482 3.030000e-08 71.3
23 TraesCS1B01G244500 chr7A 96.970 33 1 0 146 178 724090376 724090344 8.500000e-04 56.5
24 TraesCS1B01G244500 chrUn 90.909 132 12 0 46 177 231137304 231137173 1.740000e-40 178.0
25 TraesCS1B01G244500 chrUn 90.909 132 12 0 46 177 269082850 269082719 1.740000e-40 178.0
26 TraesCS1B01G244500 chrUn 90.909 132 12 0 46 177 325392444 325392313 1.740000e-40 178.0
27 TraesCS1B01G244500 chrUn 90.909 132 12 0 46 177 419178022 419178153 1.740000e-40 178.0
28 TraesCS1B01G244500 chr2B 85.083 181 10 8 2961 3139 471637483 471637318 1.050000e-37 169.0
29 TraesCS1B01G244500 chr2B 95.745 47 1 1 1 46 429647969 429648015 2.350000e-09 75.0
30 TraesCS1B01G244500 chr2B 85.714 63 4 5 7 67 233743346 233743405 1.830000e-05 62.1
31 TraesCS1B01G244500 chr2B 100.000 32 0 0 5524 5555 162395049 162395080 6.570000e-05 60.2
32 TraesCS1B01G244500 chr2B 100.000 32 0 0 5524 5555 716978759 716978728 6.570000e-05 60.2
33 TraesCS1B01G244500 chr2B 92.308 39 3 0 7 45 77966438 77966476 8.500000e-04 56.5
34 TraesCS1B01G244500 chr4A 82.000 200 22 4 2962 3161 30285023 30285208 2.260000e-34 158.0
35 TraesCS1B01G244500 chr4A 89.130 46 4 1 1 45 560916715 560916760 8.500000e-04 56.5
36 TraesCS1B01G244500 chr4D 81.006 179 21 7 2964 3141 437822948 437822782 4.930000e-26 130.0
37 TraesCS1B01G244500 chr4B 87.611 113 12 2 2964 3075 540728183 540728072 4.930000e-26 130.0
38 TraesCS1B01G244500 chr4B 97.297 37 1 0 5522 5558 633949451 633949415 5.080000e-06 63.9
39 TraesCS1B01G244500 chr4B 96.970 33 0 1 5524 5555 298376847 298376815 3.000000e-03 54.7
40 TraesCS1B01G244500 chr6B 95.455 44 2 0 1 44 100928056 100928013 3.030000e-08 71.3
41 TraesCS1B01G244500 chr6B 97.059 34 1 0 5522 5555 12742795 12742762 2.360000e-04 58.4
42 TraesCS1B01G244500 chr7B 93.478 46 2 1 5511 5555 745275335 745275380 3.920000e-07 67.6
43 TraesCS1B01G244500 chr2D 91.111 45 4 0 1 45 50152089 50152133 1.830000e-05 62.1
44 TraesCS1B01G244500 chr5D 100.000 32 0 0 5524 5555 497254247 497254278 6.570000e-05 60.2
45 TraesCS1B01G244500 chr6A 96.970 33 1 0 5522 5554 587855072 587855040 8.500000e-04 56.5


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 TraesCS1B01G244500 chr1B 433635790 433641856 6066 False 5174.000000 9454 100.000000 1 6067 2 chr1B.!!$F1 6066
1 TraesCS1B01G244500 chr1D 320720820 320728558 7738 False 1297.683333 4732 93.764500 176 6065 6 chr1D.!!$F2 5889
2 TraesCS1B01G244500 chr1A 402230699 402237170 6471 True 1159.471429 3410 94.264857 182 6066 7 chr1A.!!$R1 5884

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
995 1022 0.032267 CCTTCCCGCTCCGAGTAATC 59.968 60.0 0.00 0.00 0.0 1.75 F
1662 1689 0.107456 CACATATCTCCGCAAGCCCT 59.893 55.0 0.00 0.00 0.0 5.19 F
1663 1690 0.839946 ACATATCTCCGCAAGCCCTT 59.160 50.0 0.00 0.00 0.0 3.95 F
3336 3617 0.951558 AAACCAGAACACGTGCATCC 59.048 50.0 17.22 2.05 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2580 2859 1.070601 TCCACCATACCTGCATCATCG 59.929 52.381 0.00 0.00 0.00 3.84 R
3656 3940 1.801178 CTCTTTTTCTGAGGACGGTGC 59.199 52.381 0.00 0.00 0.00 5.01 R
3824 4108 7.253422 CAAAGAGTGTCTCAAATGTGACTTTT 58.747 34.615 14.51 8.57 38.82 2.27 R
5331 7645 0.811616 GCTCTCCACCCGCATACTTG 60.812 60.000 0.00 0.00 0.00 3.16 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
21 22 3.624326 TTTGTCAATTCGTCTTGGCAG 57.376 42.857 6.99 0.00 41.39 4.85
22 23 1.522668 TGTCAATTCGTCTTGGCAGG 58.477 50.000 3.49 0.00 35.90 4.85
23 24 1.202758 TGTCAATTCGTCTTGGCAGGT 60.203 47.619 0.00 0.00 35.90 4.00
24 25 1.197721 GTCAATTCGTCTTGGCAGGTG 59.802 52.381 0.00 0.00 31.04 4.00
25 26 0.523072 CAATTCGTCTTGGCAGGTGG 59.477 55.000 0.00 0.00 0.00 4.61
26 27 0.110486 AATTCGTCTTGGCAGGTGGT 59.890 50.000 0.00 0.00 0.00 4.16
27 28 0.321653 ATTCGTCTTGGCAGGTGGTC 60.322 55.000 0.00 0.00 0.00 4.02
28 29 1.407656 TTCGTCTTGGCAGGTGGTCT 61.408 55.000 0.00 0.00 0.00 3.85
29 30 1.071471 CGTCTTGGCAGGTGGTCTT 59.929 57.895 0.00 0.00 0.00 3.01
30 31 0.535102 CGTCTTGGCAGGTGGTCTTT 60.535 55.000 0.00 0.00 0.00 2.52
31 32 1.692411 GTCTTGGCAGGTGGTCTTTT 58.308 50.000 0.00 0.00 0.00 2.27
32 33 2.031870 GTCTTGGCAGGTGGTCTTTTT 58.968 47.619 0.00 0.00 0.00 1.94
33 34 2.031120 TCTTGGCAGGTGGTCTTTTTG 58.969 47.619 0.00 0.00 0.00 2.44
34 35 1.069049 CTTGGCAGGTGGTCTTTTTGG 59.931 52.381 0.00 0.00 0.00 3.28
35 36 0.260230 TGGCAGGTGGTCTTTTTGGA 59.740 50.000 0.00 0.00 0.00 3.53
36 37 0.673985 GGCAGGTGGTCTTTTTGGAC 59.326 55.000 0.00 0.00 35.66 4.02
37 38 1.398692 GCAGGTGGTCTTTTTGGACA 58.601 50.000 0.00 0.00 37.91 4.02
38 39 1.754226 GCAGGTGGTCTTTTTGGACAA 59.246 47.619 0.00 0.00 37.91 3.18
39 40 2.167487 GCAGGTGGTCTTTTTGGACAAA 59.833 45.455 0.00 0.00 37.91 2.83
40 41 3.368948 GCAGGTGGTCTTTTTGGACAAAA 60.369 43.478 6.14 6.14 38.40 2.44
41 42 4.826556 CAGGTGGTCTTTTTGGACAAAAA 58.173 39.130 18.58 18.58 44.98 1.94
61 62 6.589830 AAAAATCGAGACAACGAGGATATG 57.410 37.500 0.00 0.00 45.22 1.78
62 63 5.515797 AAATCGAGACAACGAGGATATGA 57.484 39.130 0.00 0.00 45.22 2.15
63 64 5.713792 AATCGAGACAACGAGGATATGAT 57.286 39.130 0.00 0.00 45.22 2.45
64 65 4.489679 TCGAGACAACGAGGATATGATG 57.510 45.455 0.00 0.00 37.37 3.07
65 66 3.253432 TCGAGACAACGAGGATATGATGG 59.747 47.826 0.00 0.00 37.37 3.51
66 67 3.321497 GAGACAACGAGGATATGATGGC 58.679 50.000 0.00 0.00 0.00 4.40
67 68 2.968574 AGACAACGAGGATATGATGGCT 59.031 45.455 0.00 0.00 0.00 4.75
68 69 3.006323 AGACAACGAGGATATGATGGCTC 59.994 47.826 0.00 0.00 0.00 4.70
69 70 2.037772 ACAACGAGGATATGATGGCTCC 59.962 50.000 0.00 0.00 0.00 4.70
70 71 0.891373 ACGAGGATATGATGGCTCCG 59.109 55.000 0.00 0.00 34.13 4.63
71 72 1.177401 CGAGGATATGATGGCTCCGA 58.823 55.000 0.00 0.00 34.13 4.55
72 73 1.135257 CGAGGATATGATGGCTCCGAC 60.135 57.143 0.00 0.00 34.13 4.79
73 74 1.895798 GAGGATATGATGGCTCCGACA 59.104 52.381 0.00 0.00 34.13 4.35
74 75 2.300152 GAGGATATGATGGCTCCGACAA 59.700 50.000 0.00 0.00 34.13 3.18
75 76 2.301296 AGGATATGATGGCTCCGACAAG 59.699 50.000 0.00 0.00 34.13 3.16
76 77 2.300152 GGATATGATGGCTCCGACAAGA 59.700 50.000 0.00 0.00 0.00 3.02
77 78 3.055530 GGATATGATGGCTCCGACAAGAT 60.056 47.826 0.00 0.00 0.00 2.40
78 79 2.251409 ATGATGGCTCCGACAAGATG 57.749 50.000 0.00 0.00 0.00 2.90
79 80 0.178767 TGATGGCTCCGACAAGATGG 59.821 55.000 0.00 0.00 0.00 3.51
80 81 1.153086 ATGGCTCCGACAAGATGGC 60.153 57.895 0.00 0.00 0.00 4.40
81 82 1.913951 ATGGCTCCGACAAGATGGCA 61.914 55.000 0.00 0.00 37.59 4.92
82 83 2.109126 GGCTCCGACAAGATGGCAC 61.109 63.158 0.00 0.00 0.00 5.01
83 84 2.456119 GCTCCGACAAGATGGCACG 61.456 63.158 0.00 0.00 0.00 5.34
84 85 1.079819 CTCCGACAAGATGGCACGT 60.080 57.895 0.00 0.00 0.00 4.49
85 86 1.354337 CTCCGACAAGATGGCACGTG 61.354 60.000 12.28 12.28 0.00 4.49
86 87 1.374125 CCGACAAGATGGCACGTGA 60.374 57.895 22.23 0.00 0.00 4.35
87 88 1.626654 CCGACAAGATGGCACGTGAC 61.627 60.000 22.23 19.45 0.00 3.67
88 89 1.781555 GACAAGATGGCACGTGACG 59.218 57.895 22.23 2.24 0.00 4.35
89 90 2.227968 GACAAGATGGCACGTGACGC 62.228 60.000 22.23 13.28 0.00 5.19
90 91 2.030412 AAGATGGCACGTGACGCA 59.970 55.556 22.23 0.42 0.00 5.24
91 92 2.317609 AAGATGGCACGTGACGCAC 61.318 57.895 22.23 11.98 0.00 5.34
115 116 2.507944 GCGATGTGGCCTGATCCT 59.492 61.111 3.32 0.00 0.00 3.24
116 117 1.890979 GCGATGTGGCCTGATCCTG 60.891 63.158 3.32 0.00 0.00 3.86
117 118 1.890979 CGATGTGGCCTGATCCTGC 60.891 63.158 3.32 0.00 0.00 4.85
118 119 1.225426 GATGTGGCCTGATCCTGCA 59.775 57.895 3.32 0.00 0.00 4.41
119 120 0.818445 GATGTGGCCTGATCCTGCAG 60.818 60.000 6.78 6.78 35.66 4.41
120 121 2.827642 GTGGCCTGATCCTGCAGC 60.828 66.667 8.66 0.00 34.56 5.25
121 122 4.119363 TGGCCTGATCCTGCAGCC 62.119 66.667 8.66 6.01 34.56 4.85
122 123 4.119363 GGCCTGATCCTGCAGCCA 62.119 66.667 8.66 4.87 34.40 4.75
123 124 2.516460 GCCTGATCCTGCAGCCAG 60.516 66.667 8.66 14.15 38.85 4.85
138 139 4.379243 CAGGAACCTGCCGCTCGT 62.379 66.667 7.95 0.00 37.24 4.18
139 140 3.626924 AGGAACCTGCCGCTCGTT 61.627 61.111 0.00 0.00 0.00 3.85
140 141 3.119096 GGAACCTGCCGCTCGTTC 61.119 66.667 12.24 12.24 36.08 3.95
141 142 3.119096 GAACCTGCCGCTCGTTCC 61.119 66.667 10.40 0.00 31.66 3.62
142 143 3.876589 GAACCTGCCGCTCGTTCCA 62.877 63.158 10.40 0.00 31.66 3.53
143 144 3.254024 AACCTGCCGCTCGTTCCAT 62.254 57.895 0.00 0.00 0.00 3.41
144 145 2.892425 CCTGCCGCTCGTTCCATC 60.892 66.667 0.00 0.00 0.00 3.51
145 146 2.185350 CTGCCGCTCGTTCCATCT 59.815 61.111 0.00 0.00 0.00 2.90
146 147 1.437573 CTGCCGCTCGTTCCATCTA 59.562 57.895 0.00 0.00 0.00 1.98
147 148 0.179111 CTGCCGCTCGTTCCATCTAA 60.179 55.000 0.00 0.00 0.00 2.10
148 149 0.248012 TGCCGCTCGTTCCATCTAAA 59.752 50.000 0.00 0.00 0.00 1.85
149 150 1.134521 TGCCGCTCGTTCCATCTAAAT 60.135 47.619 0.00 0.00 0.00 1.40
150 151 2.101750 TGCCGCTCGTTCCATCTAAATA 59.898 45.455 0.00 0.00 0.00 1.40
151 152 2.731976 GCCGCTCGTTCCATCTAAATAG 59.268 50.000 0.00 0.00 0.00 1.73
152 153 3.799232 GCCGCTCGTTCCATCTAAATAGT 60.799 47.826 0.00 0.00 0.00 2.12
153 154 3.736252 CCGCTCGTTCCATCTAAATAGTG 59.264 47.826 0.00 0.00 0.00 2.74
154 155 3.182572 CGCTCGTTCCATCTAAATAGTGC 59.817 47.826 0.00 0.00 0.00 4.40
155 156 3.182572 GCTCGTTCCATCTAAATAGTGCG 59.817 47.826 0.00 0.00 0.00 5.34
156 157 3.120792 TCGTTCCATCTAAATAGTGCGC 58.879 45.455 0.00 0.00 0.00 6.09
157 158 2.097396 CGTTCCATCTAAATAGTGCGCG 60.097 50.000 0.00 0.00 0.00 6.86
158 159 2.864343 GTTCCATCTAAATAGTGCGCGT 59.136 45.455 8.43 0.00 0.00 6.01
159 160 2.469826 TCCATCTAAATAGTGCGCGTG 58.530 47.619 8.43 0.00 0.00 5.34
160 161 1.070577 CCATCTAAATAGTGCGCGTGC 60.071 52.381 15.48 15.48 43.20 5.34
170 171 4.914291 GCGCGTGCACTTTTAAGT 57.086 50.000 17.66 0.00 42.15 2.24
171 172 3.157922 GCGCGTGCACTTTTAAGTT 57.842 47.368 17.66 0.00 42.15 2.66
172 173 1.472990 GCGCGTGCACTTTTAAGTTT 58.527 45.000 17.66 0.00 42.15 2.66
173 174 1.849829 GCGCGTGCACTTTTAAGTTTT 59.150 42.857 17.66 0.00 42.15 2.43
174 175 2.280445 GCGCGTGCACTTTTAAGTTTTT 59.720 40.909 17.66 0.00 42.15 1.94
175 176 3.482833 GCGCGTGCACTTTTAAGTTTTTA 59.517 39.130 17.66 0.00 42.15 1.52
176 177 4.373619 GCGCGTGCACTTTTAAGTTTTTAG 60.374 41.667 17.66 0.00 42.15 1.85
177 178 4.145756 CGCGTGCACTTTTAAGTTTTTAGG 59.854 41.667 16.19 0.00 37.08 2.69
178 179 5.275494 GCGTGCACTTTTAAGTTTTTAGGA 58.725 37.500 16.19 0.00 37.08 2.94
179 180 5.744819 GCGTGCACTTTTAAGTTTTTAGGAA 59.255 36.000 16.19 0.00 37.08 3.36
264 272 2.936202 CATCTCCACCCGAATCCATTT 58.064 47.619 0.00 0.00 0.00 2.32
364 382 2.329379 CGTCTCTTTCTGTTTCTCCCG 58.671 52.381 0.00 0.00 0.00 5.14
397 415 0.942721 TAAACCCAACCAAACCCCCT 59.057 50.000 0.00 0.00 0.00 4.79
398 416 0.399376 AAACCCAACCAAACCCCCTC 60.399 55.000 0.00 0.00 0.00 4.30
400 418 1.234529 CCCAACCAAACCCCCTCAA 59.765 57.895 0.00 0.00 0.00 3.02
403 421 1.152631 AACCAAACCCCCTCAACCG 60.153 57.895 0.00 0.00 0.00 4.44
405 423 1.151908 CCAAACCCCCTCAACCGAA 59.848 57.895 0.00 0.00 0.00 4.30
407 425 1.152138 AAACCCCCTCAACCGAACC 59.848 57.895 0.00 0.00 0.00 3.62
408 426 2.685804 AAACCCCCTCAACCGAACCG 62.686 60.000 0.00 0.00 0.00 4.44
409 427 3.315949 CCCCCTCAACCGAACCGA 61.316 66.667 0.00 0.00 0.00 4.69
410 428 2.745037 CCCCTCAACCGAACCGAA 59.255 61.111 0.00 0.00 0.00 4.30
411 429 1.670083 CCCCTCAACCGAACCGAAC 60.670 63.158 0.00 0.00 0.00 3.95
415 433 0.859232 CTCAACCGAACCGAACACAG 59.141 55.000 0.00 0.00 0.00 3.66
420 438 2.604174 CGAACCGAACACAGCACCC 61.604 63.158 0.00 0.00 0.00 4.61
968 995 4.733725 CCCTCCCTCCACCCGGAA 62.734 72.222 0.73 0.00 42.21 4.30
969 996 2.609610 CCTCCCTCCACCCGGAAA 60.610 66.667 0.73 0.00 42.21 3.13
970 997 2.001269 CCTCCCTCCACCCGGAAAT 61.001 63.158 0.73 0.00 42.21 2.17
971 998 1.527370 CTCCCTCCACCCGGAAATC 59.473 63.158 0.73 0.00 42.21 2.17
972 999 1.984288 CTCCCTCCACCCGGAAATCC 61.984 65.000 0.73 0.00 42.21 3.01
982 1009 3.920031 GGAAATCCGCACCTTCCC 58.080 61.111 0.00 0.00 33.80 3.97
983 1010 2.112815 GGAAATCCGCACCTTCCCG 61.113 63.158 0.00 0.00 33.80 5.14
984 1011 2.750237 AAATCCGCACCTTCCCGC 60.750 61.111 0.00 0.00 0.00 6.13
985 1012 3.268103 AAATCCGCACCTTCCCGCT 62.268 57.895 0.00 0.00 0.00 5.52
986 1013 3.682292 AATCCGCACCTTCCCGCTC 62.682 63.158 0.00 0.00 0.00 5.03
990 1017 4.821589 GCACCTTCCCGCTCCGAG 62.822 72.222 0.00 0.00 0.00 4.63
991 1018 3.382832 CACCTTCCCGCTCCGAGT 61.383 66.667 0.00 0.00 0.00 4.18
992 1019 2.050350 CACCTTCCCGCTCCGAGTA 61.050 63.158 0.00 0.00 0.00 2.59
993 1020 1.304713 ACCTTCCCGCTCCGAGTAA 60.305 57.895 0.00 0.00 0.00 2.24
994 1021 0.686769 ACCTTCCCGCTCCGAGTAAT 60.687 55.000 0.00 0.00 0.00 1.89
995 1022 0.032267 CCTTCCCGCTCCGAGTAATC 59.968 60.000 0.00 0.00 0.00 1.75
996 1023 0.317938 CTTCCCGCTCCGAGTAATCG 60.318 60.000 5.43 5.43 0.00 3.34
1177 1204 2.122989 TAGATCCGCCCCTGGTCC 60.123 66.667 0.00 0.00 0.00 4.46
1219 1246 1.138883 GAATTTTTCGGGGAGGCGC 59.861 57.895 0.00 0.00 0.00 6.53
1246 1273 2.087646 GGCGCATTTTCCTCTTCTTCT 58.912 47.619 10.83 0.00 0.00 2.85
1448 1475 0.309302 CGATCGAGTCTTCAGGCGAT 59.691 55.000 10.26 0.00 45.07 4.58
1467 1494 3.990469 CGATACGGCTGCTGATAATCTTT 59.010 43.478 16.72 0.00 0.00 2.52
1468 1495 4.143242 CGATACGGCTGCTGATAATCTTTG 60.143 45.833 16.72 0.14 0.00 2.77
1580 1607 1.003839 GCACGACATGGAGGTGGAA 60.004 57.895 12.86 0.00 32.42 3.53
1595 1622 2.121538 GGAATCGCCTTTCCTGGGC 61.122 63.158 5.30 0.00 41.69 5.36
1659 1686 0.305922 GTGCACATATCTCCGCAAGC 59.694 55.000 13.17 0.00 35.87 4.01
1662 1689 0.107456 CACATATCTCCGCAAGCCCT 59.893 55.000 0.00 0.00 0.00 5.19
1663 1690 0.839946 ACATATCTCCGCAAGCCCTT 59.160 50.000 0.00 0.00 0.00 3.95
1664 1691 1.233019 CATATCTCCGCAAGCCCTTG 58.767 55.000 3.70 3.70 43.14 3.61
1665 1692 0.839946 ATATCTCCGCAAGCCCTTGT 59.160 50.000 9.53 0.00 42.31 3.16
1669 1702 1.580845 CTCCGCAAGCCCTTGTCAAG 61.581 60.000 5.53 5.53 42.31 3.02
1674 1707 1.269778 GCAAGCCCTTGTCAAGTTTCC 60.270 52.381 11.61 0.00 42.31 3.13
1685 1718 7.177392 CCCTTGTCAAGTTTCCATTCTATCTTT 59.823 37.037 11.61 0.00 0.00 2.52
1715 1749 6.479095 TTTTGTTTCAGCACAAAAGAAAGG 57.521 33.333 8.31 0.00 46.77 3.11
1720 1754 1.001378 CAGCACAAAAGAAAGGTCGGG 60.001 52.381 0.00 0.00 0.00 5.14
1817 1857 9.890629 AAATAAGAACTAATCTGACATGTGCTA 57.109 29.630 1.15 0.00 38.79 3.49
1864 1904 5.830912 TGTTGTCACCAAATTTCATGACTC 58.169 37.500 22.71 17.79 41.65 3.36
1865 1905 5.221224 TGTTGTCACCAAATTTCATGACTCC 60.221 40.000 22.71 16.33 41.65 3.85
1866 1906 4.468713 TGTCACCAAATTTCATGACTCCA 58.531 39.130 22.71 8.47 41.65 3.86
1867 1907 4.892345 TGTCACCAAATTTCATGACTCCAA 59.108 37.500 22.71 8.17 41.65 3.53
1868 1908 5.362143 TGTCACCAAATTTCATGACTCCAAA 59.638 36.000 22.71 7.91 41.65 3.28
1905 1945 3.011014 TGTGAAACAGGCCCCACA 58.989 55.556 0.00 3.66 45.67 4.17
1943 1983 2.023501 TGCCTATTTTGGGGTGCCTTAT 60.024 45.455 0.00 0.00 0.00 1.73
1944 1984 3.205507 TGCCTATTTTGGGGTGCCTTATA 59.794 43.478 0.00 0.00 0.00 0.98
1945 1985 3.572682 GCCTATTTTGGGGTGCCTTATAC 59.427 47.826 0.00 0.00 0.00 1.47
1946 1986 4.149598 CCTATTTTGGGGTGCCTTATACC 58.850 47.826 0.00 0.00 37.48 2.73
2000 2040 2.830772 TGAATGCGCAATACTTCTGC 57.169 45.000 17.11 0.00 36.41 4.26
2013 2053 7.743400 CGCAATACTTCTGCTATGTGATATTTG 59.257 37.037 0.00 0.00 37.67 2.32
2107 2386 7.807977 ATGTTTCAGACATAAACAAGTGACT 57.192 32.000 5.58 0.00 47.00 3.41
2260 2539 2.745821 GCAGTCTGAGATGATTGCAACA 59.254 45.455 0.00 2.38 45.19 3.33
2265 2544 6.018913 CAGTCTGAGATGATTGCAACAGATAC 60.019 42.308 15.63 7.14 36.23 2.24
2441 2720 7.880265 ATCCTTATTCTGTAGGGCTAGAAAT 57.120 36.000 0.00 0.00 36.59 2.17
2481 2760 3.302480 GCAGTAGATCCGTATTTTGCACG 60.302 47.826 0.00 0.00 39.10 5.34
2826 3105 7.871853 TCTCATTTAGAAAAGAAAGGGAAACG 58.128 34.615 0.00 0.00 0.00 3.60
2857 3136 4.215827 CCTACTTAATATGACTCGAGCGGT 59.784 45.833 13.61 0.40 0.00 5.68
2891 3170 2.159462 GCTAATCAGTGCAGGCAAGTTC 60.159 50.000 0.00 0.00 0.00 3.01
2966 3245 6.702329 CCTCACTTTACTATCTTTCAGTGGT 58.298 40.000 0.00 0.00 33.81 4.16
2975 3254 2.609747 TCTTTCAGTGGTGGAGCTACT 58.390 47.619 0.00 0.00 39.65 2.57
3013 3292 3.123620 GGCCTGCTCAGCTCAACG 61.124 66.667 0.00 0.00 0.00 4.10
3131 3412 2.868583 CAAAGATGTGGATGTAGCTCCG 59.131 50.000 0.00 0.00 38.21 4.63
3336 3617 0.951558 AAACCAGAACACGTGCATCC 59.048 50.000 17.22 2.05 0.00 3.51
3368 3649 2.823924 TGTATATATGGTGCGGCGTT 57.176 45.000 9.37 0.00 0.00 4.84
3445 3726 5.560724 TGTTGAGGATACCAAAAGAAGAGG 58.439 41.667 0.00 0.00 37.17 3.69
3656 3940 2.507471 AGCCTCTTGTAAGAAGGATGGG 59.493 50.000 11.71 3.70 34.03 4.00
3766 4050 3.068732 TCAGATAGGTGCACTGACTATGC 59.931 47.826 17.98 9.12 43.68 3.14
3824 4108 4.063998 TGCAACACAACCATATGCAAAA 57.936 36.364 0.00 0.00 43.39 2.44
3946 4230 9.739276 ATCATTCTTCTCTATTTTAACCACACA 57.261 29.630 0.00 0.00 0.00 3.72
3948 4232 9.003658 CATTCTTCTCTATTTTAACCACACAGT 57.996 33.333 0.00 0.00 0.00 3.55
4141 4506 7.584987 CACTGTTTACACTTTTATGAGGAAGG 58.415 38.462 0.00 0.00 0.00 3.46
4168 4533 4.084641 GCTGAAGCTCATATGATTCGTGTC 60.085 45.833 5.72 3.55 35.37 3.67
4214 4598 8.144478 TCCATTCATGATTGTAGCTAACTAGTC 58.856 37.037 14.72 0.00 0.00 2.59
4507 4891 3.879892 GAGGAGAAGAAACTGTTGCAAGT 59.120 43.478 0.00 0.00 0.00 3.16
4562 4946 2.843701 CTCCAAGTGTGAAGCAAGTCT 58.156 47.619 0.00 0.00 0.00 3.24
4564 4948 2.092968 TCCAAGTGTGAAGCAAGTCTGT 60.093 45.455 0.00 0.00 0.00 3.41
4691 5075 5.180868 AGAACTGTGAAAGATCTGCACAATC 59.819 40.000 23.82 22.68 41.45 2.67
4781 5165 3.314541 AGTACGGAAGCGATTGAGTTT 57.685 42.857 0.00 0.00 0.00 2.66
4993 5377 2.042464 TGGGTTGCCTGCAAATTGTTA 58.958 42.857 6.07 0.00 37.70 2.41
5074 5458 2.687935 AGTTGTTTCGTCATTGCCAGTT 59.312 40.909 0.00 0.00 0.00 3.16
5162 5546 7.381766 TGAAGTCCATGAACTAAATGTCATG 57.618 36.000 6.66 6.66 39.52 3.07
5191 5575 1.247567 AACTCGTTTGGCCCATGAAG 58.752 50.000 0.00 0.00 0.00 3.02
5208 5592 4.959596 TGAAGGTAGTGCTAGTAAGTCG 57.040 45.455 0.00 0.00 0.00 4.18
5302 7614 0.689412 TGTCACCGGGAGCCATATCA 60.689 55.000 6.32 0.00 0.00 2.15
5331 7645 6.316390 CACTCAAGTGGACCTTTATTATGGAC 59.684 42.308 2.08 0.00 42.10 4.02
5336 7650 7.504926 AGTGGACCTTTATTATGGACAAGTA 57.495 36.000 0.00 0.00 0.00 2.24
5351 7666 1.972660 AAGTATGCGGGTGGAGAGCC 61.973 60.000 0.00 0.00 36.28 4.70
5372 7687 3.314357 CCAGACATAACGGACACTATCGA 59.686 47.826 0.00 0.00 0.00 3.59
5452 7889 9.937577 CATGTATATGTATGTACATCGTTTTCG 57.062 33.333 12.68 0.00 45.11 3.46
5453 7890 7.999213 TGTATATGTATGTACATCGTTTTCGC 58.001 34.615 12.68 0.00 45.11 4.70
5454 7891 7.648510 TGTATATGTATGTACATCGTTTTCGCA 59.351 33.333 12.68 1.86 45.11 5.10
5455 7892 5.788055 ATGTATGTACATCGTTTTCGCAA 57.212 34.783 12.68 0.00 42.96 4.85
5456 7893 5.593183 TGTATGTACATCGTTTTCGCAAA 57.407 34.783 12.68 0.00 43.73 3.68
5457 7894 5.986936 TGTATGTACATCGTTTTCGCAAAA 58.013 33.333 12.68 0.00 43.73 2.44
5458 7895 6.427974 TGTATGTACATCGTTTTCGCAAAAA 58.572 32.000 12.68 0.00 43.73 1.94
5530 7967 9.573133 TCATCTTGTATACATATTGTATGAGCG 57.427 33.333 6.36 0.00 42.93 5.03
5533 7970 8.088365 TCTTGTATACATATTGTATGAGCGCTT 58.912 33.333 13.26 0.00 42.93 4.68
5536 7973 2.221749 ACATATTGTATGAGCGCTTGCG 59.778 45.455 13.26 10.90 45.69 4.85
5537 7974 1.934589 TATTGTATGAGCGCTTGCGT 58.065 45.000 13.26 3.24 45.69 5.24
5538 7975 0.652592 ATTGTATGAGCGCTTGCGTC 59.347 50.000 13.26 12.36 45.69 5.19
5539 7976 0.389817 TTGTATGAGCGCTTGCGTCT 60.390 50.000 13.26 13.17 45.69 4.18
5540 7977 1.078201 TGTATGAGCGCTTGCGTCTG 61.078 55.000 13.26 0.00 45.69 3.51
5541 7978 1.078759 GTATGAGCGCTTGCGTCTGT 61.079 55.000 13.26 7.66 45.69 3.41
5542 7979 0.454196 TATGAGCGCTTGCGTCTGTA 59.546 50.000 13.26 6.26 45.69 2.74
5543 7980 1.078759 ATGAGCGCTTGCGTCTGTAC 61.079 55.000 13.26 0.00 45.69 2.90
5545 7982 1.006102 AGCGCTTGCGTCTGTACTT 60.006 52.632 16.38 0.00 45.69 2.24
5546 7983 0.600255 AGCGCTTGCGTCTGTACTTT 60.600 50.000 16.38 0.00 45.69 2.66
5547 7984 0.451135 GCGCTTGCGTCTGTACTTTG 60.451 55.000 16.38 0.00 0.00 2.77
5548 7985 0.859232 CGCTTGCGTCTGTACTTTGT 59.141 50.000 6.86 0.00 0.00 2.83
5550 7987 2.473609 CGCTTGCGTCTGTACTTTGTTA 59.526 45.455 6.86 0.00 0.00 2.41
5551 7988 3.060138 CGCTTGCGTCTGTACTTTGTTAA 60.060 43.478 6.86 0.00 0.00 2.01
5553 7990 5.267776 GCTTGCGTCTGTACTTTGTTAAAA 58.732 37.500 0.00 0.00 0.00 1.52
5555 7992 6.290904 GCTTGCGTCTGTACTTTGTTAAAAAC 60.291 38.462 0.00 0.00 0.00 2.43
5556 7993 6.179504 TGCGTCTGTACTTTGTTAAAAACA 57.820 33.333 0.00 0.00 40.21 2.83
5580 8089 5.253330 AGGCAAAGAAGAACGATAATTCCA 58.747 37.500 0.00 0.00 0.00 3.53
5587 8096 5.882557 AGAAGAACGATAATTCCATTGTGCT 59.117 36.000 0.00 0.00 30.36 4.40
5654 8163 1.328279 TCAGTGTCACGACCACATCT 58.672 50.000 0.00 0.00 0.00 2.90
5713 8222 7.926018 AGAACAAATCAAACCCAACTCAAATAC 59.074 33.333 0.00 0.00 0.00 1.89
5767 8276 4.261994 GCTAGAAAGAGAGGAGCCATGTAG 60.262 50.000 0.00 0.00 0.00 2.74
5865 8374 0.405585 AAACATAGTGGCAGTGGGCT 59.594 50.000 4.76 0.00 44.01 5.19
5914 8423 2.766263 TGATCCCATAGCTGAAGACGTT 59.234 45.455 0.00 0.00 0.00 3.99
5943 8452 1.266718 GCGATGCTTTTCCAAGTGACA 59.733 47.619 0.00 0.00 31.86 3.58
5944 8453 2.095059 GCGATGCTTTTCCAAGTGACAT 60.095 45.455 0.00 0.00 31.86 3.06
6024 8541 9.047371 TGTTGTTTTGAGTCGAGTCATAATTTA 57.953 29.630 23.05 12.12 0.00 1.40
6027 8544 9.430623 TGTTTTGAGTCGAGTCATAATTTATCA 57.569 29.630 23.05 14.44 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.243367 CCTGCCAAGACGAATTGACAAAA 60.243 43.478 6.03 0.00 31.55 2.44
1 2 2.293122 CCTGCCAAGACGAATTGACAAA 59.707 45.455 6.03 0.00 31.55 2.83
2 3 1.879380 CCTGCCAAGACGAATTGACAA 59.121 47.619 6.03 0.00 31.55 3.18
3 4 1.202758 ACCTGCCAAGACGAATTGACA 60.203 47.619 6.03 0.66 31.55 3.58
4 5 1.197721 CACCTGCCAAGACGAATTGAC 59.802 52.381 6.03 0.00 31.55 3.18
5 6 1.522668 CACCTGCCAAGACGAATTGA 58.477 50.000 6.03 0.00 31.55 2.57
6 7 0.523072 CCACCTGCCAAGACGAATTG 59.477 55.000 0.00 0.00 0.00 2.32
7 8 0.110486 ACCACCTGCCAAGACGAATT 59.890 50.000 0.00 0.00 0.00 2.17
8 9 0.321653 GACCACCTGCCAAGACGAAT 60.322 55.000 0.00 0.00 0.00 3.34
9 10 1.070786 GACCACCTGCCAAGACGAA 59.929 57.895 0.00 0.00 0.00 3.85
10 11 1.407656 AAGACCACCTGCCAAGACGA 61.408 55.000 0.00 0.00 0.00 4.20
11 12 0.535102 AAAGACCACCTGCCAAGACG 60.535 55.000 0.00 0.00 0.00 4.18
12 13 1.692411 AAAAGACCACCTGCCAAGAC 58.308 50.000 0.00 0.00 0.00 3.01
13 14 2.031120 CAAAAAGACCACCTGCCAAGA 58.969 47.619 0.00 0.00 0.00 3.02
14 15 1.069049 CCAAAAAGACCACCTGCCAAG 59.931 52.381 0.00 0.00 0.00 3.61
15 16 1.118838 CCAAAAAGACCACCTGCCAA 58.881 50.000 0.00 0.00 0.00 4.52
16 17 0.260230 TCCAAAAAGACCACCTGCCA 59.740 50.000 0.00 0.00 0.00 4.92
17 18 0.673985 GTCCAAAAAGACCACCTGCC 59.326 55.000 0.00 0.00 0.00 4.85
18 19 1.398692 TGTCCAAAAAGACCACCTGC 58.601 50.000 0.00 0.00 35.83 4.85
19 20 4.464069 TTTTGTCCAAAAAGACCACCTG 57.536 40.909 2.82 0.00 37.35 4.00
38 39 6.338146 TCATATCCTCGTTGTCTCGATTTTT 58.662 36.000 0.00 0.00 39.12 1.94
39 40 5.902681 TCATATCCTCGTTGTCTCGATTTT 58.097 37.500 0.00 0.00 39.12 1.82
40 41 5.515797 TCATATCCTCGTTGTCTCGATTT 57.484 39.130 0.00 0.00 39.12 2.17
41 42 5.465051 CATCATATCCTCGTTGTCTCGATT 58.535 41.667 0.00 0.00 39.12 3.34
42 43 4.082517 CCATCATATCCTCGTTGTCTCGAT 60.083 45.833 0.00 0.00 39.12 3.59
43 44 3.253432 CCATCATATCCTCGTTGTCTCGA 59.747 47.826 0.00 0.00 38.19 4.04
44 45 3.569548 CCATCATATCCTCGTTGTCTCG 58.430 50.000 0.00 0.00 0.00 4.04
45 46 3.006323 AGCCATCATATCCTCGTTGTCTC 59.994 47.826 0.00 0.00 0.00 3.36
46 47 2.968574 AGCCATCATATCCTCGTTGTCT 59.031 45.455 0.00 0.00 0.00 3.41
47 48 3.321497 GAGCCATCATATCCTCGTTGTC 58.679 50.000 0.00 0.00 0.00 3.18
48 49 2.037772 GGAGCCATCATATCCTCGTTGT 59.962 50.000 0.00 0.00 0.00 3.32
49 50 2.693069 GGAGCCATCATATCCTCGTTG 58.307 52.381 0.00 0.00 0.00 4.10
50 51 1.273606 CGGAGCCATCATATCCTCGTT 59.726 52.381 0.00 0.00 0.00 3.85
51 52 0.891373 CGGAGCCATCATATCCTCGT 59.109 55.000 0.00 0.00 0.00 4.18
52 53 1.135257 GTCGGAGCCATCATATCCTCG 60.135 57.143 0.00 0.00 0.00 4.63
53 54 1.895798 TGTCGGAGCCATCATATCCTC 59.104 52.381 0.00 0.00 0.00 3.71
54 55 2.015456 TGTCGGAGCCATCATATCCT 57.985 50.000 0.00 0.00 0.00 3.24
55 56 2.300152 TCTTGTCGGAGCCATCATATCC 59.700 50.000 0.00 0.00 0.00 2.59
56 57 3.667497 TCTTGTCGGAGCCATCATATC 57.333 47.619 0.00 0.00 0.00 1.63
57 58 3.307269 CCATCTTGTCGGAGCCATCATAT 60.307 47.826 0.00 0.00 0.00 1.78
58 59 2.037641 CCATCTTGTCGGAGCCATCATA 59.962 50.000 0.00 0.00 0.00 2.15
59 60 1.202734 CCATCTTGTCGGAGCCATCAT 60.203 52.381 0.00 0.00 0.00 2.45
60 61 0.178767 CCATCTTGTCGGAGCCATCA 59.821 55.000 0.00 0.00 0.00 3.07
61 62 1.162800 GCCATCTTGTCGGAGCCATC 61.163 60.000 0.00 0.00 0.00 3.51
62 63 1.153086 GCCATCTTGTCGGAGCCAT 60.153 57.895 0.00 0.00 0.00 4.40
63 64 2.268920 GCCATCTTGTCGGAGCCA 59.731 61.111 0.00 0.00 0.00 4.75
64 65 2.109126 GTGCCATCTTGTCGGAGCC 61.109 63.158 0.00 0.00 0.00 4.70
65 66 2.456119 CGTGCCATCTTGTCGGAGC 61.456 63.158 0.00 0.00 0.00 4.70
66 67 1.079819 ACGTGCCATCTTGTCGGAG 60.080 57.895 0.00 0.00 0.00 4.63
67 68 1.374125 CACGTGCCATCTTGTCGGA 60.374 57.895 0.82 0.00 0.00 4.55
68 69 1.374125 TCACGTGCCATCTTGTCGG 60.374 57.895 11.67 0.00 0.00 4.79
69 70 1.781555 GTCACGTGCCATCTTGTCG 59.218 57.895 11.67 0.00 0.00 4.35
70 71 1.781555 CGTCACGTGCCATCTTGTC 59.218 57.895 11.67 0.00 0.00 3.18
71 72 2.317609 GCGTCACGTGCCATCTTGT 61.318 57.895 11.67 0.00 0.00 3.16
72 73 2.316867 TGCGTCACGTGCCATCTTG 61.317 57.895 11.67 0.00 0.00 3.02
73 74 2.030412 TGCGTCACGTGCCATCTT 59.970 55.556 11.67 0.00 0.00 2.40
74 75 2.738521 GTGCGTCACGTGCCATCT 60.739 61.111 11.67 0.00 0.00 2.90
98 99 1.890979 CAGGATCAGGCCACATCGC 60.891 63.158 5.01 0.19 0.00 4.58
99 100 1.890979 GCAGGATCAGGCCACATCG 60.891 63.158 5.01 0.00 0.00 3.84
100 101 0.818445 CTGCAGGATCAGGCCACATC 60.818 60.000 5.01 5.33 0.00 3.06
101 102 1.226542 CTGCAGGATCAGGCCACAT 59.773 57.895 5.01 0.00 0.00 3.21
102 103 2.672908 CTGCAGGATCAGGCCACA 59.327 61.111 5.01 0.00 0.00 4.17
103 104 2.827642 GCTGCAGGATCAGGCCAC 60.828 66.667 17.12 0.00 34.74 5.01
107 108 2.192443 CCTGGCTGCAGGATCAGG 59.808 66.667 17.12 12.21 45.00 3.86
108 109 3.317109 TCCTGGCTGCAGGATCAG 58.683 61.111 17.12 6.36 45.70 2.90
113 114 2.360852 CAGGTTCCTGGCTGCAGG 60.361 66.667 17.12 6.88 43.59 4.85
114 115 3.060615 GCAGGTTCCTGGCTGCAG 61.061 66.667 18.81 10.11 41.89 4.41
121 122 3.883744 AACGAGCGGCAGGTTCCTG 62.884 63.158 13.88 13.88 37.15 3.86
122 123 3.591254 GAACGAGCGGCAGGTTCCT 62.591 63.158 19.29 0.00 35.24 3.36
123 124 3.119096 GAACGAGCGGCAGGTTCC 61.119 66.667 19.29 7.14 35.24 3.62
124 125 3.119096 GGAACGAGCGGCAGGTTC 61.119 66.667 20.88 20.88 39.38 3.62
125 126 3.254024 ATGGAACGAGCGGCAGGTT 62.254 57.895 1.45 5.51 0.00 3.50
126 127 3.665675 GATGGAACGAGCGGCAGGT 62.666 63.158 1.45 0.00 0.00 4.00
127 128 2.016393 TAGATGGAACGAGCGGCAGG 62.016 60.000 1.45 0.00 0.00 4.85
128 129 0.179111 TTAGATGGAACGAGCGGCAG 60.179 55.000 1.45 0.00 0.00 4.85
129 130 0.248012 TTTAGATGGAACGAGCGGCA 59.752 50.000 1.45 0.00 0.00 5.69
130 131 1.583054 ATTTAGATGGAACGAGCGGC 58.417 50.000 0.00 0.00 0.00 6.53
131 132 3.736252 CACTATTTAGATGGAACGAGCGG 59.264 47.826 0.00 0.00 0.00 5.52
132 133 3.182572 GCACTATTTAGATGGAACGAGCG 59.817 47.826 0.00 0.00 0.00 5.03
133 134 3.182572 CGCACTATTTAGATGGAACGAGC 59.817 47.826 0.00 0.00 0.00 5.03
134 135 3.182572 GCGCACTATTTAGATGGAACGAG 59.817 47.826 0.30 0.00 0.00 4.18
135 136 3.120792 GCGCACTATTTAGATGGAACGA 58.879 45.455 0.30 0.00 0.00 3.85
136 137 2.097396 CGCGCACTATTTAGATGGAACG 60.097 50.000 8.75 0.00 0.00 3.95
137 138 2.864343 ACGCGCACTATTTAGATGGAAC 59.136 45.455 5.73 0.00 0.00 3.62
138 139 2.863740 CACGCGCACTATTTAGATGGAA 59.136 45.455 5.73 0.00 0.00 3.53
139 140 2.469826 CACGCGCACTATTTAGATGGA 58.530 47.619 5.73 0.00 0.00 3.41
140 141 1.070577 GCACGCGCACTATTTAGATGG 60.071 52.381 5.73 0.00 38.36 3.51
141 142 1.592543 TGCACGCGCACTATTTAGATG 59.407 47.619 5.73 0.00 45.36 2.90
142 143 1.934589 TGCACGCGCACTATTTAGAT 58.065 45.000 5.73 0.00 45.36 1.98
143 144 3.427309 TGCACGCGCACTATTTAGA 57.573 47.368 5.73 0.00 45.36 2.10
153 154 1.472990 AAACTTAAAAGTGCACGCGC 58.527 45.000 12.01 0.00 39.66 6.86
154 155 4.145756 CCTAAAAACTTAAAAGTGCACGCG 59.854 41.667 12.01 3.53 39.66 6.01
155 156 5.275494 TCCTAAAAACTTAAAAGTGCACGC 58.725 37.500 12.01 0.00 39.66 5.34
156 157 6.748198 TGTTCCTAAAAACTTAAAAGTGCACG 59.252 34.615 12.01 0.00 39.66 5.34
157 158 8.468720 TTGTTCCTAAAAACTTAAAAGTGCAC 57.531 30.769 9.40 9.40 39.66 4.57
158 159 8.927721 GTTTGTTCCTAAAAACTTAAAAGTGCA 58.072 29.630 0.00 0.00 39.66 4.57
159 160 8.927721 TGTTTGTTCCTAAAAACTTAAAAGTGC 58.072 29.630 0.00 0.00 39.66 4.40
164 165 9.774413 TGGTTTGTTTGTTCCTAAAAACTTAAA 57.226 25.926 0.00 0.00 37.22 1.52
165 166 9.774413 TTGGTTTGTTTGTTCCTAAAAACTTAA 57.226 25.926 0.00 0.00 37.22 1.85
166 167 9.205719 GTTGGTTTGTTTGTTCCTAAAAACTTA 57.794 29.630 0.00 0.00 37.22 2.24
167 168 7.173562 GGTTGGTTTGTTTGTTCCTAAAAACTT 59.826 33.333 0.00 0.00 37.22 2.66
168 169 6.651643 GGTTGGTTTGTTTGTTCCTAAAAACT 59.348 34.615 0.00 0.00 37.22 2.66
169 170 6.401260 CGGTTGGTTTGTTTGTTCCTAAAAAC 60.401 38.462 0.00 0.00 36.92 2.43
170 171 5.638234 CGGTTGGTTTGTTTGTTCCTAAAAA 59.362 36.000 0.00 0.00 0.00 1.94
171 172 5.169295 CGGTTGGTTTGTTTGTTCCTAAAA 58.831 37.500 0.00 0.00 0.00 1.52
172 173 4.381718 CCGGTTGGTTTGTTTGTTCCTAAA 60.382 41.667 0.00 0.00 0.00 1.85
173 174 3.130693 CCGGTTGGTTTGTTTGTTCCTAA 59.869 43.478 0.00 0.00 0.00 2.69
174 175 2.688958 CCGGTTGGTTTGTTTGTTCCTA 59.311 45.455 0.00 0.00 0.00 2.94
175 176 1.478916 CCGGTTGGTTTGTTTGTTCCT 59.521 47.619 0.00 0.00 0.00 3.36
176 177 1.477295 TCCGGTTGGTTTGTTTGTTCC 59.523 47.619 0.00 0.00 36.30 3.62
177 178 2.943449 TCCGGTTGGTTTGTTTGTTC 57.057 45.000 0.00 0.00 36.30 3.18
178 179 2.101750 GGATCCGGTTGGTTTGTTTGTT 59.898 45.455 0.00 0.00 36.30 2.83
179 180 1.684450 GGATCCGGTTGGTTTGTTTGT 59.316 47.619 0.00 0.00 36.30 2.83
264 272 4.457949 GGAGGAAACTAAATTCAAGCGGAA 59.542 41.667 0.00 0.00 44.43 4.30
364 382 0.803117 GGTTTAAGAGGTTGCTCGCC 59.197 55.000 0.00 0.00 0.00 5.54
397 415 1.155424 GCTGTGTTCGGTTCGGTTGA 61.155 55.000 0.00 0.00 0.00 3.18
398 416 1.278637 GCTGTGTTCGGTTCGGTTG 59.721 57.895 0.00 0.00 0.00 3.77
400 418 1.885850 GTGCTGTGTTCGGTTCGGT 60.886 57.895 0.00 0.00 0.00 4.69
403 421 2.258726 GGGGTGCTGTGTTCGGTTC 61.259 63.158 0.00 0.00 0.00 3.62
405 423 4.265056 GGGGGTGCTGTGTTCGGT 62.265 66.667 0.00 0.00 0.00 4.69
420 438 4.862823 GACGGAGGGGAGGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
424 442 2.525284 ATTTCGGACGGAGGGGAGGA 62.525 60.000 0.00 0.00 0.00 3.71
965 992 2.112815 CGGGAAGGTGCGGATTTCC 61.113 63.158 12.71 12.71 39.69 3.13
966 993 2.761195 GCGGGAAGGTGCGGATTTC 61.761 63.158 0.00 0.00 0.00 2.17
967 994 2.750237 GCGGGAAGGTGCGGATTT 60.750 61.111 0.00 0.00 0.00 2.17
968 995 3.682292 GAGCGGGAAGGTGCGGATT 62.682 63.158 0.00 0.00 35.87 3.01
969 996 4.162690 GAGCGGGAAGGTGCGGAT 62.163 66.667 0.00 0.00 35.87 4.18
973 1000 4.821589 CTCGGAGCGGGAAGGTGC 62.822 72.222 0.00 0.00 35.23 5.01
974 1001 1.601419 TTACTCGGAGCGGGAAGGTG 61.601 60.000 4.58 0.00 0.00 4.00
975 1002 0.686769 ATTACTCGGAGCGGGAAGGT 60.687 55.000 4.58 0.00 0.00 3.50
976 1003 0.032267 GATTACTCGGAGCGGGAAGG 59.968 60.000 4.58 0.00 0.00 3.46
977 1004 0.317938 CGATTACTCGGAGCGGGAAG 60.318 60.000 4.58 0.00 41.27 3.46
978 1005 1.731700 CGATTACTCGGAGCGGGAA 59.268 57.895 4.58 0.00 41.27 3.97
979 1006 2.842256 GCGATTACTCGGAGCGGGA 61.842 63.158 4.58 0.00 45.15 5.14
980 1007 2.351336 AAGCGATTACTCGGAGCGGG 62.351 60.000 4.58 0.00 45.15 6.13
981 1008 0.935366 GAAGCGATTACTCGGAGCGG 60.935 60.000 4.58 0.00 45.15 5.52
982 1009 0.935366 GGAAGCGATTACTCGGAGCG 60.935 60.000 4.58 1.58 45.15 5.03
983 1010 0.597898 GGGAAGCGATTACTCGGAGC 60.598 60.000 4.58 0.00 45.15 4.70
984 1011 0.317938 CGGGAAGCGATTACTCGGAG 60.318 60.000 2.83 2.83 45.15 4.63
985 1012 1.731700 CGGGAAGCGATTACTCGGA 59.268 57.895 4.55 0.00 45.15 4.55
986 1013 1.949631 GCGGGAAGCGATTACTCGG 60.950 63.158 4.55 0.00 45.15 4.63
1177 1204 1.032114 GGATCAAGAAACCCCCTGCG 61.032 60.000 0.00 0.00 0.00 5.18
1219 1246 1.026718 AGGAAAATGCGCCTCCTTCG 61.027 55.000 4.18 0.00 36.06 3.79
1246 1273 2.342279 CAACCGCGGAGACCAGAA 59.658 61.111 35.90 0.00 0.00 3.02
1448 1475 2.872245 GCAAAGATTATCAGCAGCCGTA 59.128 45.455 0.00 0.00 0.00 4.02
1508 1535 0.411058 AAGAGGGCCCAAATGAGCTT 59.589 50.000 27.56 12.00 0.00 3.74
1595 1622 1.928503 GCGCCATCCACATTGAAATTG 59.071 47.619 0.00 0.00 0.00 2.32
1659 1686 6.183347 AGATAGAATGGAAACTTGACAAGGG 58.817 40.000 19.16 0.00 0.00 3.95
1662 1689 7.014134 TGCAAAGATAGAATGGAAACTTGACAA 59.986 33.333 0.00 0.00 0.00 3.18
1663 1690 6.489700 TGCAAAGATAGAATGGAAACTTGACA 59.510 34.615 0.00 0.00 0.00 3.58
1664 1691 6.913170 TGCAAAGATAGAATGGAAACTTGAC 58.087 36.000 0.00 0.00 0.00 3.18
1665 1692 7.363181 CCATGCAAAGATAGAATGGAAACTTGA 60.363 37.037 0.00 0.00 40.23 3.02
1669 1702 6.212888 ACCATGCAAAGATAGAATGGAAAC 57.787 37.500 7.17 0.00 40.23 2.78
1674 1707 7.894376 AACAAAACCATGCAAAGATAGAATG 57.106 32.000 0.00 0.00 0.00 2.67
1685 1718 2.093816 TGTGCTGAAACAAAACCATGCA 60.094 40.909 0.00 0.00 0.00 3.96
1715 1749 2.550830 ATCAATAGGACATGCCCGAC 57.449 50.000 0.00 0.00 37.37 4.79
1720 1754 8.097038 TCCAGTAATTCTATCAATAGGACATGC 58.903 37.037 0.00 0.00 0.00 4.06
1873 1913 5.347342 TGTTTCACACTTCGAATTTTGCAT 58.653 33.333 0.00 0.00 0.00 3.96
1905 1945 1.337447 GGCATGCTTTCACTTGTGCAT 60.337 47.619 18.92 0.00 45.57 3.96
1943 1983 4.903049 TCGCCCCTAATCTATTTCAAGGTA 59.097 41.667 0.00 0.00 0.00 3.08
1944 1984 3.714798 TCGCCCCTAATCTATTTCAAGGT 59.285 43.478 0.00 0.00 0.00 3.50
1945 1985 4.351874 TCGCCCCTAATCTATTTCAAGG 57.648 45.455 0.00 0.00 0.00 3.61
1946 1986 7.878127 TCTTAATCGCCCCTAATCTATTTCAAG 59.122 37.037 0.00 0.00 0.00 3.02
2022 2301 9.975218 AAGGGATACAGAGTACACAAAATAAAT 57.025 29.630 0.00 0.00 39.74 1.40
2026 2305 7.690256 AGAAAGGGATACAGAGTACACAAAAT 58.310 34.615 0.00 0.00 39.74 1.82
2095 2374 3.133901 TCCACTCAGCAGTCACTTGTTTA 59.866 43.478 0.00 0.00 0.00 2.01
2107 2386 1.376466 GGCCTTTCTCCACTCAGCA 59.624 57.895 0.00 0.00 0.00 4.41
2446 2725 8.362464 ACGGATCTACTGCAGGATATAAAATA 57.638 34.615 19.93 0.00 0.00 1.40
2481 2760 4.473477 ACCAAGTATCAGTACAAGCTCC 57.527 45.455 0.00 0.00 33.09 4.70
2580 2859 1.070601 TCCACCATACCTGCATCATCG 59.929 52.381 0.00 0.00 0.00 3.84
2891 3170 5.868043 TTTGCAAGTATGTCACATCTCAG 57.132 39.130 0.00 0.00 0.00 3.35
3003 3282 6.481976 TCTTCACTAAATTTTCGTTGAGCTGA 59.518 34.615 0.00 0.00 0.00 4.26
3013 3292 6.017109 TCAGCACCAGTCTTCACTAAATTTTC 60.017 38.462 0.00 0.00 0.00 2.29
3131 3412 1.943340 GCTGTAAAGATAGCAGTGGCC 59.057 52.381 0.00 0.00 42.56 5.36
3208 3489 6.595682 ACAAGATACATAAAGGGATGGACAG 58.404 40.000 0.00 0.00 0.00 3.51
3336 3617 7.862372 GCACCATATATACAAAACAATGACCAG 59.138 37.037 0.00 0.00 0.00 4.00
3445 3726 4.142004 ACTCCGGTAATGTATTGTCAGGAC 60.142 45.833 0.00 0.00 0.00 3.85
3656 3940 1.801178 CTCTTTTTCTGAGGACGGTGC 59.199 52.381 0.00 0.00 0.00 5.01
3824 4108 7.253422 CAAAGAGTGTCTCAAATGTGACTTTT 58.747 34.615 14.51 8.57 38.82 2.27
4141 4506 4.150274 CGAATCATATGAGCTTCAGCACTC 59.850 45.833 11.78 0.00 45.16 3.51
4168 4533 3.881089 GGATGGTAAACATAGGGGAAACG 59.119 47.826 0.00 0.00 40.72 3.60
4258 4642 8.689972 GTCTCCATTTCACAATAATTCAAGGAT 58.310 33.333 0.00 0.00 0.00 3.24
4507 4891 2.858745 GGTTCAAGCTTAACCACCTGA 58.141 47.619 22.49 5.03 44.83 3.86
4562 4946 3.745799 TGCTTCGTTTATTTCCAGGACA 58.254 40.909 0.00 0.00 0.00 4.02
4564 4948 4.647611 TCTTGCTTCGTTTATTTCCAGGA 58.352 39.130 0.00 0.00 0.00 3.86
4691 5075 5.400485 CGAAAACAGGCTTTTCATTCTTCAG 59.600 40.000 11.17 0.00 38.07 3.02
4993 5377 7.895759 ACTTTATACAATGCAGGTTTCACAAT 58.104 30.769 0.00 0.00 0.00 2.71
5030 5414 7.732996 ACTTGTATTATGCCGGACTATACTTT 58.267 34.615 5.05 0.00 0.00 2.66
5074 5458 5.047448 ACATGGCTTTACATACATTTGCACA 60.047 36.000 0.00 0.00 0.00 4.57
5118 5502 4.713553 TCATATTTGCTTGCCGAATCCTA 58.286 39.130 0.00 0.00 0.00 2.94
5162 5546 3.425758 GGCCAAACGAGTTTGCAGTATAC 60.426 47.826 19.88 0.00 46.25 1.47
5183 5567 4.406003 ACTTACTAGCACTACCTTCATGGG 59.594 45.833 0.00 0.00 41.11 4.00
5191 5575 5.225642 ACAAAACGACTTACTAGCACTACC 58.774 41.667 0.00 0.00 0.00 3.18
5234 5618 9.962783 ACATACTTTCGAGACATTATAACCTAC 57.037 33.333 0.00 0.00 0.00 3.18
5302 7614 3.366052 AAAGGTCCACTTGAGTGTTGT 57.634 42.857 10.03 0.00 44.21 3.32
5331 7645 0.811616 GCTCTCCACCCGCATACTTG 60.812 60.000 0.00 0.00 0.00 3.16
5336 7650 3.790437 CTGGCTCTCCACCCGCAT 61.790 66.667 0.00 0.00 37.47 4.73
5351 7666 4.547406 TCGATAGTGTCCGTTATGTCTG 57.453 45.455 0.00 0.00 37.40 3.51
5509 7946 7.360017 GCAAGCGCTCATACAATATGTATACAA 60.360 37.037 12.06 0.00 36.98 2.41
5521 7958 1.078201 CAGACGCAAGCGCTCATACA 61.078 55.000 12.06 0.00 44.19 2.29
5522 7959 1.078759 ACAGACGCAAGCGCTCATAC 61.079 55.000 12.06 1.58 44.19 2.39
5523 7960 0.454196 TACAGACGCAAGCGCTCATA 59.546 50.000 12.06 5.16 44.19 2.15
5524 7961 1.078759 GTACAGACGCAAGCGCTCAT 61.079 55.000 12.06 0.00 44.19 2.90
5526 7963 1.009389 AAGTACAGACGCAAGCGCTC 61.009 55.000 12.06 11.06 44.19 5.03
5527 7964 0.600255 AAAGTACAGACGCAAGCGCT 60.600 50.000 15.09 2.64 44.19 5.92
5529 7966 0.859232 ACAAAGTACAGACGCAAGCG 59.141 50.000 13.50 13.50 46.03 4.68
5530 7967 4.461992 TTAACAAAGTACAGACGCAAGC 57.538 40.909 0.00 0.00 45.62 4.01
5533 7970 6.179504 TGTTTTTAACAAAGTACAGACGCA 57.820 33.333 0.00 0.00 38.72 5.24
5546 7983 6.309251 CGTTCTTCTTTGCCTTGTTTTTAACA 59.691 34.615 0.00 0.00 40.21 2.41
5547 7984 6.528774 TCGTTCTTCTTTGCCTTGTTTTTAAC 59.471 34.615 0.00 0.00 0.00 2.01
5548 7985 6.622549 TCGTTCTTCTTTGCCTTGTTTTTAA 58.377 32.000 0.00 0.00 0.00 1.52
5550 7987 5.066968 TCGTTCTTCTTTGCCTTGTTTTT 57.933 34.783 0.00 0.00 0.00 1.94
5551 7988 4.712122 TCGTTCTTCTTTGCCTTGTTTT 57.288 36.364 0.00 0.00 0.00 2.43
5553 7990 6.575162 ATTATCGTTCTTCTTTGCCTTGTT 57.425 33.333 0.00 0.00 0.00 2.83
5555 7992 6.030228 GGAATTATCGTTCTTCTTTGCCTTG 58.970 40.000 0.00 0.00 0.00 3.61
5556 7993 5.710099 TGGAATTATCGTTCTTCTTTGCCTT 59.290 36.000 0.00 0.00 0.00 4.35
5558 7995 5.560966 TGGAATTATCGTTCTTCTTTGCC 57.439 39.130 0.00 0.00 0.00 4.52
5563 8072 5.882557 AGCACAATGGAATTATCGTTCTTCT 59.117 36.000 0.00 0.00 32.46 2.85
5565 8074 6.238103 CGTAGCACAATGGAATTATCGTTCTT 60.238 38.462 0.00 0.00 32.46 2.52
5580 8089 3.980775 GCAAAAACATGACGTAGCACAAT 59.019 39.130 0.00 0.00 0.00 2.71
5587 8096 2.222213 CGGACAGCAAAAACATGACGTA 59.778 45.455 0.00 0.00 0.00 3.57
5713 8222 2.154462 ACGATGGGTTTCTTGCTTCAG 58.846 47.619 0.00 0.00 0.00 3.02
5767 8276 0.248539 GGTCGTCGATGGACAGCTAC 60.249 60.000 17.76 2.61 43.61 3.58
5865 8374 3.558931 TGAACTCTTCACTGGAAAGCA 57.441 42.857 0.00 0.00 34.08 3.91
5914 8423 0.955428 AAAAGCATCGCGGAAGAGCA 60.955 50.000 6.13 0.00 36.85 4.26
5984 8494 3.441496 AACAACATGGTTGAGCAACTG 57.559 42.857 15.35 7.09 40.94 3.16
6024 8541 8.344098 CAGCAAACATTTGTTTAAACCAATGAT 58.656 29.630 34.39 26.19 45.54 2.45
6025 8542 7.550551 TCAGCAAACATTTGTTTAAACCAATGA 59.449 29.630 34.39 18.81 45.54 2.57
6026 8543 7.692088 TCAGCAAACATTTGTTTAAACCAATG 58.308 30.769 29.63 29.63 45.54 2.82
6027 8544 7.467131 GCTCAGCAAACATTTGTTTAAACCAAT 60.467 33.333 15.59 13.08 45.54 3.16
6028 8545 6.183360 GCTCAGCAAACATTTGTTTAAACCAA 60.183 34.615 15.59 11.31 45.54 3.67
6029 8546 5.293079 GCTCAGCAAACATTTGTTTAAACCA 59.707 36.000 15.59 1.62 45.54 3.67
6030 8547 5.293079 TGCTCAGCAAACATTTGTTTAAACC 59.707 36.000 15.59 0.00 45.54 3.27


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

AutoCloner maintained by Alex Coulton.