Multiple sequence alignment - TraesCS6A01G374500

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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 TraesCS6A01G374500 chr6A 100.000 6006 0 0 1 6006 597287674 597293679 0 11092
1 TraesCS6A01G374500 chr6B 93.569 2239 90 22 3798 6006 685668555 685670769 0 3288
2 TraesCS6A01G374500 chr6B 94.701 1755 78 8 800 2547 685665411 685667157 0 2712
3 TraesCS6A01G374500 chr6B 94.601 1315 58 5 2545 3857 685667280 685668583 0 2023
4 TraesCS6A01G374500 chr6B 85.468 695 81 9 125 817 685664725 685665401 0 706
5 TraesCS6A01G374500 chr6D 91.133 1906 118 31 534 2422 451658702 451656831 0 2536
6 TraesCS6A01G374500 chr6D 89.248 1330 90 25 4059 5355 451655132 451653823 0 1615
7 TraesCS6A01G374500 chr6D 84.390 1704 138 65 2433 4088 451656757 451655134 0 1555
8 TraesCS6A01G374500 chr6D 91.071 560 30 9 5459 6006 451653778 451653227 0 739


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 TraesCS6A01G374500 chr6A 597287674 597293679 6005 False 11092.00 11092 100.00000 1 6006 1 chr6A.!!$F1 6005
1 TraesCS6A01G374500 chr6B 685664725 685670769 6044 False 2182.25 3288 92.08475 125 6006 4 chr6B.!!$F1 5881
2 TraesCS6A01G374500 chr6D 451653227 451658702 5475 True 1611.25 2536 88.96050 534 6006 4 chr6D.!!$R1 5472

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
113 114 0.035534 TACTACTACACCGTCCCGCA 60.036 55.000 0.00 0.00 0.00 5.69 F
237 238 0.101939 GTCGGGTAAGGTCGGACATC 59.898 60.000 10.76 0.00 35.45 3.06 F
711 712 0.105224 TCGCTTTGGTCGGTCTTTGA 59.895 50.000 0.00 0.00 0.00 2.69 F
778 786 0.179119 GGCAGATCCAACAGCAATGC 60.179 55.000 0.00 0.00 34.01 3.56 F
1673 1715 1.129998 CACTGCAGCTCATTCTTTCCG 59.870 52.381 15.27 0.00 0.00 4.30 F
1724 1766 1.276145 GGCTCGATCGTTACATCGCC 61.276 60.000 15.94 12.16 44.48 5.54 F
1788 1830 1.995376 CCTTGTTGCAGTTAACCCCT 58.005 50.000 0.88 0.00 0.00 4.79 F
2842 3084 1.065199 TGGGATGCAGAGTCCAACATC 60.065 52.381 7.13 8.44 37.49 3.06 F
3261 3508 1.914051 CAGACTACGATGTGTTCTGCG 59.086 52.381 0.00 0.00 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 1751 0.663568 GGAGGGCGATGTAACGATCG 60.664 60.000 14.88 14.88 46.54 3.69 R
2024 2066 1.082690 GCTTACAGCTGCACCTCTTC 58.917 55.000 15.27 0.00 38.45 2.87 R
2612 2854 2.861462 TTGTTTCGAGCAAAACCCTG 57.139 45.000 2.60 0.00 38.16 4.45 R
2720 2962 0.252421 TCCTCATCTCCAGTGGCAGT 60.252 55.000 3.51 0.00 0.00 4.40 R
2721 2963 0.907486 TTCCTCATCTCCAGTGGCAG 59.093 55.000 3.51 3.22 0.00 4.85 R
2722 2964 1.361204 TTTCCTCATCTCCAGTGGCA 58.639 50.000 3.51 0.00 0.00 4.92 R
3729 3984 1.003580 TGGGTTGAGTTCTGGCATCTC 59.996 52.381 0.00 0.00 0.00 2.75 R
4594 4976 0.170339 TACGGAGTGATGTGCGTGAG 59.830 55.000 0.37 0.00 44.86 3.51 R
5080 5467 1.207089 GGGTGTATCTGTACTGCTGCA 59.793 52.381 0.88 0.88 0.00 4.41 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
17 18 2.184579 GTCCTCGGCCTAGCACAC 59.815 66.667 0.00 0.00 0.00 3.82
18 19 3.075005 TCCTCGGCCTAGCACACC 61.075 66.667 0.00 0.00 0.00 4.16
19 20 3.390521 CCTCGGCCTAGCACACCA 61.391 66.667 0.00 0.00 0.00 4.17
20 21 2.125512 CTCGGCCTAGCACACCAC 60.126 66.667 0.00 0.00 0.00 4.16
21 22 2.920384 TCGGCCTAGCACACCACA 60.920 61.111 0.00 0.00 0.00 4.17
22 23 2.031919 CGGCCTAGCACACCACAA 59.968 61.111 0.00 0.00 0.00 3.33
23 24 1.599518 CGGCCTAGCACACCACAAA 60.600 57.895 0.00 0.00 0.00 2.83
24 25 1.169661 CGGCCTAGCACACCACAAAA 61.170 55.000 0.00 0.00 0.00 2.44
25 26 0.598065 GGCCTAGCACACCACAAAAG 59.402 55.000 0.00 0.00 0.00 2.27
26 27 0.598065 GCCTAGCACACCACAAAAGG 59.402 55.000 0.00 0.00 0.00 3.11
27 28 1.247567 CCTAGCACACCACAAAAGGG 58.752 55.000 0.00 0.00 0.00 3.95
28 29 1.247567 CTAGCACACCACAAAAGGGG 58.752 55.000 0.00 0.00 38.34 4.79
29 30 0.847373 TAGCACACCACAAAAGGGGA 59.153 50.000 0.00 0.00 34.94 4.81
30 31 0.188342 AGCACACCACAAAAGGGGAT 59.812 50.000 0.00 0.00 34.94 3.85
31 32 0.318120 GCACACCACAAAAGGGGATG 59.682 55.000 0.00 0.00 34.94 3.51
32 33 1.993956 CACACCACAAAAGGGGATGA 58.006 50.000 0.00 0.00 34.94 2.92
33 34 2.528564 CACACCACAAAAGGGGATGAT 58.471 47.619 0.00 0.00 34.94 2.45
34 35 2.493278 CACACCACAAAAGGGGATGATC 59.507 50.000 0.00 0.00 34.94 2.92
35 36 2.379907 ACACCACAAAAGGGGATGATCT 59.620 45.455 0.00 0.00 34.94 2.75
36 37 2.756760 CACCACAAAAGGGGATGATCTG 59.243 50.000 0.00 0.00 32.15 2.90
37 38 2.649312 ACCACAAAAGGGGATGATCTGA 59.351 45.455 0.00 0.00 0.00 3.27
38 39 3.270433 ACCACAAAAGGGGATGATCTGAT 59.730 43.478 0.00 0.00 0.00 2.90
39 40 4.264532 ACCACAAAAGGGGATGATCTGATT 60.265 41.667 0.00 0.00 0.00 2.57
40 41 5.044179 ACCACAAAAGGGGATGATCTGATTA 60.044 40.000 0.00 0.00 0.00 1.75
41 42 5.533903 CCACAAAAGGGGATGATCTGATTAG 59.466 44.000 0.00 0.00 0.00 1.73
42 43 5.009410 CACAAAAGGGGATGATCTGATTAGC 59.991 44.000 0.00 0.00 0.00 3.09
43 44 3.692257 AAGGGGATGATCTGATTAGCG 57.308 47.619 0.00 0.00 0.00 4.26
44 45 1.277557 AGGGGATGATCTGATTAGCGC 59.722 52.381 0.00 0.00 0.00 5.92
45 46 1.677217 GGGGATGATCTGATTAGCGCC 60.677 57.143 15.90 15.90 30.72 6.53
46 47 1.677217 GGGATGATCTGATTAGCGCCC 60.677 57.143 2.29 3.50 0.00 6.13
47 48 1.277557 GGATGATCTGATTAGCGCCCT 59.722 52.381 2.29 0.00 0.00 5.19
48 49 2.615869 GATGATCTGATTAGCGCCCTC 58.384 52.381 2.29 0.00 0.00 4.30
49 50 1.709578 TGATCTGATTAGCGCCCTCT 58.290 50.000 2.29 0.00 0.00 3.69
50 51 2.876581 TGATCTGATTAGCGCCCTCTA 58.123 47.619 2.29 0.00 0.00 2.43
51 52 2.822561 TGATCTGATTAGCGCCCTCTAG 59.177 50.000 2.29 0.00 0.00 2.43
52 53 2.366640 TCTGATTAGCGCCCTCTAGT 57.633 50.000 2.29 0.00 0.00 2.57
53 54 2.231529 TCTGATTAGCGCCCTCTAGTC 58.768 52.381 2.29 0.00 0.00 2.59
54 55 1.271102 CTGATTAGCGCCCTCTAGTCC 59.729 57.143 2.29 0.00 0.00 3.85
55 56 0.241481 GATTAGCGCCCTCTAGTCCG 59.759 60.000 2.29 0.00 0.00 4.79
56 57 1.179814 ATTAGCGCCCTCTAGTCCGG 61.180 60.000 2.29 0.00 0.00 5.14
57 58 3.786884 TAGCGCCCTCTAGTCCGGG 62.787 68.421 2.29 9.31 43.60 5.73
59 60 3.217743 CGCCCTCTAGTCCGGGAC 61.218 72.222 19.61 19.61 43.44 4.46
60 61 2.043248 GCCCTCTAGTCCGGGACA 60.043 66.667 27.87 13.42 43.44 4.02
61 62 2.424733 GCCCTCTAGTCCGGGACAC 61.425 68.421 27.87 3.69 43.44 3.67
62 63 1.757340 CCCTCTAGTCCGGGACACC 60.757 68.421 27.87 2.25 43.44 4.16
72 73 2.032071 GGGACACCGTCACCTTGG 59.968 66.667 0.00 0.00 33.68 3.61
73 74 2.668550 GGACACCGTCACCTTGGC 60.669 66.667 0.00 0.00 33.68 4.52
74 75 2.668550 GACACCGTCACCTTGGCC 60.669 66.667 0.00 0.00 32.09 5.36
75 76 3.469863 GACACCGTCACCTTGGCCA 62.470 63.158 0.00 0.00 32.09 5.36
76 77 2.669569 CACCGTCACCTTGGCCAG 60.670 66.667 5.11 0.00 0.00 4.85
77 78 4.643387 ACCGTCACCTTGGCCAGC 62.643 66.667 5.11 0.00 0.00 4.85
96 97 3.630204 CGGCTGCATCCGTCATAC 58.370 61.111 20.61 0.00 44.18 2.39
97 98 1.068083 CGGCTGCATCCGTCATACT 59.932 57.895 20.61 0.00 44.18 2.12
98 99 0.313987 CGGCTGCATCCGTCATACTA 59.686 55.000 20.61 0.00 44.18 1.82
99 100 1.784525 GGCTGCATCCGTCATACTAC 58.215 55.000 0.50 0.00 0.00 2.73
100 101 1.341531 GGCTGCATCCGTCATACTACT 59.658 52.381 0.50 0.00 0.00 2.57
101 102 2.557056 GGCTGCATCCGTCATACTACTA 59.443 50.000 0.50 0.00 0.00 1.82
102 103 3.566523 GCTGCATCCGTCATACTACTAC 58.433 50.000 0.00 0.00 0.00 2.73
103 104 3.004419 GCTGCATCCGTCATACTACTACA 59.996 47.826 0.00 0.00 0.00 2.74
104 105 4.537965 CTGCATCCGTCATACTACTACAC 58.462 47.826 0.00 0.00 0.00 2.90
105 106 3.317149 TGCATCCGTCATACTACTACACC 59.683 47.826 0.00 0.00 0.00 4.16
106 107 3.608707 GCATCCGTCATACTACTACACCG 60.609 52.174 0.00 0.00 0.00 4.94
107 108 3.266510 TCCGTCATACTACTACACCGT 57.733 47.619 0.00 0.00 0.00 4.83
108 109 3.198068 TCCGTCATACTACTACACCGTC 58.802 50.000 0.00 0.00 0.00 4.79
109 110 2.289002 CCGTCATACTACTACACCGTCC 59.711 54.545 0.00 0.00 0.00 4.79
110 111 2.289002 CGTCATACTACTACACCGTCCC 59.711 54.545 0.00 0.00 0.00 4.46
111 112 2.289002 GTCATACTACTACACCGTCCCG 59.711 54.545 0.00 0.00 0.00 5.14
112 113 1.002033 CATACTACTACACCGTCCCGC 60.002 57.143 0.00 0.00 0.00 6.13
113 114 0.035534 TACTACTACACCGTCCCGCA 60.036 55.000 0.00 0.00 0.00 5.69
114 115 1.138247 CTACTACACCGTCCCGCAC 59.862 63.158 0.00 0.00 0.00 5.34
115 116 2.275547 CTACTACACCGTCCCGCACC 62.276 65.000 0.00 0.00 0.00 5.01
116 117 2.769652 TACTACACCGTCCCGCACCT 62.770 60.000 0.00 0.00 0.00 4.00
117 118 2.918802 TACACCGTCCCGCACCTT 60.919 61.111 0.00 0.00 0.00 3.50
118 119 2.444700 CTACACCGTCCCGCACCTTT 62.445 60.000 0.00 0.00 0.00 3.11
119 120 2.042404 TACACCGTCCCGCACCTTTT 62.042 55.000 0.00 0.00 0.00 2.27
120 121 2.190841 CACCGTCCCGCACCTTTTT 61.191 57.895 0.00 0.00 0.00 1.94
121 122 1.895231 ACCGTCCCGCACCTTTTTC 60.895 57.895 0.00 0.00 0.00 2.29
122 123 2.622962 CCGTCCCGCACCTTTTTCC 61.623 63.158 0.00 0.00 0.00 3.13
123 124 1.894756 CGTCCCGCACCTTTTTCCA 60.895 57.895 0.00 0.00 0.00 3.53
134 135 2.178984 ACCTTTTTCCAGGGGTTCATGA 59.821 45.455 0.00 0.00 38.42 3.07
147 148 0.255604 TTCATGACGCATGGGATGGT 59.744 50.000 17.76 0.00 41.66 3.55
148 149 0.464193 TCATGACGCATGGGATGGTG 60.464 55.000 17.76 9.35 41.66 4.17
171 172 3.073735 CCTGAGGCTGGCTCGTCT 61.074 66.667 23.82 0.00 0.00 4.18
172 173 2.183811 CTGAGGCTGGCTCGTCTG 59.816 66.667 23.82 11.61 0.00 3.51
173 174 2.283173 TGAGGCTGGCTCGTCTGA 60.283 61.111 23.82 5.49 0.00 3.27
174 175 2.183046 GAGGCTGGCTCGTCTGAC 59.817 66.667 15.80 0.00 0.00 3.51
175 176 2.601666 AGGCTGGCTCGTCTGACA 60.602 61.111 8.73 0.00 0.00 3.58
178 179 2.262915 CTGGCTCGTCTGACACCC 59.737 66.667 8.73 5.16 0.00 4.61
182 183 2.262915 CTCGTCTGACACCCTGGC 59.737 66.667 8.73 0.00 0.00 4.85
184 185 2.219325 CTCGTCTGACACCCTGGCTC 62.219 65.000 8.73 0.00 0.00 4.70
192 193 2.958739 ACCCTGGCTCTCCCCCTA 60.959 66.667 0.00 0.00 0.00 3.53
193 194 2.344995 ACCCTGGCTCTCCCCCTAT 61.345 63.158 0.00 0.00 0.00 2.57
198 199 2.072487 GGCTCTCCCCCTATGTGCA 61.072 63.158 0.00 0.00 0.00 4.57
199 200 1.449353 GCTCTCCCCCTATGTGCAG 59.551 63.158 0.00 0.00 0.00 4.41
200 201 2.049627 GCTCTCCCCCTATGTGCAGG 62.050 65.000 0.00 0.00 35.26 4.85
201 202 0.692419 CTCTCCCCCTATGTGCAGGT 60.692 60.000 0.00 0.00 33.44 4.00
203 204 0.107017 CTCCCCCTATGTGCAGGTTG 60.107 60.000 0.00 0.00 33.44 3.77
206 207 1.549950 CCCCCTATGTGCAGGTTGTTT 60.550 52.381 0.00 0.00 33.44 2.83
207 208 1.545582 CCCCTATGTGCAGGTTGTTTG 59.454 52.381 0.00 0.00 33.44 2.93
208 209 1.545582 CCCTATGTGCAGGTTGTTTGG 59.454 52.381 0.00 0.00 33.44 3.28
209 210 2.238521 CCTATGTGCAGGTTGTTTGGT 58.761 47.619 0.00 0.00 0.00 3.67
210 211 2.627699 CCTATGTGCAGGTTGTTTGGTT 59.372 45.455 0.00 0.00 0.00 3.67
211 212 2.888834 ATGTGCAGGTTGTTTGGTTC 57.111 45.000 0.00 0.00 0.00 3.62
212 213 1.550327 TGTGCAGGTTGTTTGGTTCA 58.450 45.000 0.00 0.00 0.00 3.18
224 225 2.358247 GGTTCACATGCGTCGGGT 60.358 61.111 0.00 0.00 0.00 5.28
227 228 0.719465 GTTCACATGCGTCGGGTAAG 59.281 55.000 0.00 0.00 0.00 2.34
233 234 3.443045 GCGTCGGGTAAGGTCGGA 61.443 66.667 0.00 0.00 0.00 4.55
237 238 0.101939 GTCGGGTAAGGTCGGACATC 59.898 60.000 10.76 0.00 35.45 3.06
248 249 0.457853 TCGGACATCGTGCTAGTTGC 60.458 55.000 0.00 0.00 40.32 4.17
251 252 1.421410 GACATCGTGCTAGTTGCCGG 61.421 60.000 0.00 0.00 42.00 6.13
270 271 1.600107 GTGTGGCCCCGAGTGATTA 59.400 57.895 0.00 0.00 0.00 1.75
274 275 1.048601 TGGCCCCGAGTGATTATCTC 58.951 55.000 0.00 0.00 0.00 2.75
280 281 2.297597 CCCGAGTGATTATCTCTGGGTC 59.702 54.545 18.95 0.00 39.03 4.46
281 282 2.959030 CCGAGTGATTATCTCTGGGTCA 59.041 50.000 14.43 0.00 33.17 4.02
289 290 1.351080 ATCTCTGGGTCATGGGCTGG 61.351 60.000 0.00 0.00 0.00 4.85
302 303 4.314440 GCTGGCGGGACACTGTGA 62.314 66.667 15.86 0.00 0.00 3.58
303 304 2.047844 CTGGCGGGACACTGTGAG 60.048 66.667 15.86 4.10 0.00 3.51
304 305 4.314440 TGGCGGGACACTGTGAGC 62.314 66.667 15.86 13.11 0.00 4.26
305 306 4.008933 GGCGGGACACTGTGAGCT 62.009 66.667 15.86 0.00 0.00 4.09
335 336 3.305709 CCAGCTGGTCTCGTTTGAA 57.694 52.632 25.53 0.00 0.00 2.69
336 337 1.813513 CCAGCTGGTCTCGTTTGAAT 58.186 50.000 25.53 0.00 0.00 2.57
337 338 1.734465 CCAGCTGGTCTCGTTTGAATC 59.266 52.381 25.53 0.00 0.00 2.52
338 339 1.734465 CAGCTGGTCTCGTTTGAATCC 59.266 52.381 5.57 0.00 0.00 3.01
339 340 0.721718 GCTGGTCTCGTTTGAATCCG 59.278 55.000 0.00 0.00 0.00 4.18
355 356 4.637771 CGAAAGGGGGTTGCCTAG 57.362 61.111 0.00 0.00 0.00 3.02
358 359 2.150014 GAAAGGGGGTTGCCTAGCCA 62.150 60.000 6.51 0.00 46.65 4.75
359 360 2.155197 AAAGGGGGTTGCCTAGCCAG 62.155 60.000 6.51 0.00 46.65 4.85
384 385 0.764369 TTCTATCGCTGGCCCTGGAT 60.764 55.000 0.00 2.19 0.00 3.41
388 389 3.790437 CGCTGGCCCTGGATGAGT 61.790 66.667 0.00 0.00 0.00 3.41
396 397 1.377725 CCTGGATGAGTGGCGCTTT 60.378 57.895 7.64 0.00 0.00 3.51
400 401 0.598065 GGATGAGTGGCGCTTTTTGT 59.402 50.000 7.64 0.00 0.00 2.83
433 434 1.467920 CTTTTGGACCATGGAGCCTC 58.532 55.000 21.47 4.96 0.00 4.70
434 435 0.776810 TTTTGGACCATGGAGCCTCA 59.223 50.000 21.47 7.65 0.00 3.86
447 448 4.431131 CCTCATGGCGGCCACCTT 62.431 66.667 26.48 5.67 35.80 3.50
448 449 2.361610 CTCATGGCGGCCACCTTT 60.362 61.111 26.48 5.22 35.80 3.11
456 457 2.033194 CGGCCACCTTTTCGTCCTC 61.033 63.158 2.24 0.00 0.00 3.71
458 459 1.301479 GCCACCTTTTCGTCCTCGT 60.301 57.895 0.00 0.00 38.33 4.18
481 482 2.430244 TCGAAGTCGCCACGAAGC 60.430 61.111 0.00 0.00 37.72 3.86
525 526 2.236223 CTCTGAGCTCACCGCCACAT 62.236 60.000 13.74 0.00 40.39 3.21
530 531 2.401766 GCTCACCGCCACATCCAAG 61.402 63.158 0.00 0.00 0.00 3.61
531 532 1.003355 CTCACCGCCACATCCAAGT 60.003 57.895 0.00 0.00 0.00 3.16
547 548 1.157870 AAGTTGTTGTGGTCCTCGCG 61.158 55.000 0.00 0.00 0.00 5.87
564 565 1.004560 CGATCACACACTGGCCACT 60.005 57.895 0.00 0.00 0.00 4.00
573 574 4.694233 CTGGCCACTGCAGCTCGT 62.694 66.667 15.27 0.00 40.13 4.18
596 597 1.407979 GTGTATTGGTCGGGATCGAGT 59.592 52.381 0.00 0.00 46.91 4.18
628 629 1.623811 CCGGGGAGAAAGAAAGTGAGA 59.376 52.381 0.00 0.00 0.00 3.27
630 631 2.354203 CGGGGAGAAAGAAAGTGAGAGG 60.354 54.545 0.00 0.00 0.00 3.69
631 632 2.907042 GGGGAGAAAGAAAGTGAGAGGA 59.093 50.000 0.00 0.00 0.00 3.71
651 652 3.428282 GGGAAAATGCGCGACCGT 61.428 61.111 12.10 0.00 36.67 4.83
661 662 2.950673 GCGACCGTTTCATTGGCA 59.049 55.556 0.00 0.00 0.00 4.92
677 678 1.063266 TGGCAAGGGACAAAGGAAGTT 60.063 47.619 0.00 0.00 0.00 2.66
678 679 1.341209 GGCAAGGGACAAAGGAAGTTG 59.659 52.381 0.00 0.00 34.52 3.16
680 681 2.223805 GCAAGGGACAAAGGAAGTTGTG 60.224 50.000 0.00 0.00 41.78 3.33
685 686 2.100749 GGACAAAGGAAGTTGTGGGTTG 59.899 50.000 0.00 0.00 41.78 3.77
698 699 2.331451 GGTTGCAGCGTTCGCTTT 59.669 55.556 17.05 0.00 39.76 3.51
711 712 0.105224 TCGCTTTGGTCGGTCTTTGA 59.895 50.000 0.00 0.00 0.00 2.69
727 735 5.449304 GTCTTTGAAACAAACGATTCCGAT 58.551 37.500 0.00 0.00 39.50 4.18
771 779 2.359850 GGTGCGGCAGATCCAACA 60.360 61.111 1.18 0.00 34.01 3.33
778 786 0.179119 GGCAGATCCAACAGCAATGC 60.179 55.000 0.00 0.00 34.01 3.56
838 873 3.149196 AGCCTTCTCGAAAATGAAAGCA 58.851 40.909 8.04 0.00 33.49 3.91
853 888 6.581171 ATGAAAGCAAAGGTTTCCTAGAAG 57.419 37.500 16.22 0.00 45.71 2.85
857 892 5.568620 AGCAAAGGTTTCCTAGAAGAAGA 57.431 39.130 0.00 0.00 31.13 2.87
858 893 5.941788 AGCAAAGGTTTCCTAGAAGAAGAA 58.058 37.500 0.00 0.00 31.13 2.52
892 928 3.124636 ACGTATTCACTGTTTCCGCATTC 59.875 43.478 0.00 0.00 0.00 2.67
1071 1111 2.069430 CCCTTCTCCTCTCTGCCCC 61.069 68.421 0.00 0.00 0.00 5.80
1171 1211 3.580458 CCTCCGATTGGAATCCTCTGTAT 59.420 47.826 2.51 0.00 45.87 2.29
1241 1281 4.516321 TCATTCGGCATGGATAATTCTGTG 59.484 41.667 0.00 0.00 33.07 3.66
1252 1292 4.391830 GGATAATTCTGTGTTTGCGTCTCA 59.608 41.667 0.00 0.00 0.00 3.27
1387 1427 6.001449 TGAACCTAATTCGAGGAATCCAAT 57.999 37.500 0.61 0.00 40.56 3.16
1532 1574 4.389890 TTGACATATTTGGCTTCCATGC 57.610 40.909 0.00 0.00 31.53 4.06
1556 1598 7.031975 GCTTATTTTCAGGAATATGCTATGCC 58.968 38.462 7.73 0.00 38.55 4.40
1598 1640 1.818959 CGTCTTTGTACCCGGGGACA 61.819 60.000 35.87 35.87 0.00 4.02
1649 1691 2.237392 GGACTGTTGGGAAGTAGCAGAT 59.763 50.000 0.00 0.00 31.76 2.90
1664 1706 2.955477 CAGATACTCACTGCAGCTCA 57.045 50.000 15.27 0.00 0.00 4.26
1673 1715 1.129998 CACTGCAGCTCATTCTTTCCG 59.870 52.381 15.27 0.00 0.00 4.30
1688 1730 2.973983 TTCCGGGTTACAAATTCCCA 57.026 45.000 0.00 0.00 41.12 4.37
1709 1751 3.863142 TTAGACCTTGTTCTACGGCTC 57.137 47.619 0.00 0.00 0.00 4.70
1724 1766 1.276145 GGCTCGATCGTTACATCGCC 61.276 60.000 15.94 12.16 44.48 5.54
1788 1830 1.995376 CCTTGTTGCAGTTAACCCCT 58.005 50.000 0.88 0.00 0.00 4.79
1875 1917 7.147880 GGAAATACAGTCTCAGTAAAGGCTCTA 60.148 40.741 0.00 0.00 0.00 2.43
1970 2012 9.178758 AGGTACATCATTATTTTCTTGGAGTTC 57.821 33.333 0.00 0.00 0.00 3.01
2013 2055 9.938280 TCTCTAGCTTCTAGTAGATACTGAATC 57.062 37.037 0.00 1.83 37.10 2.52
2074 2116 9.457776 AATGCTCCTATAGACCCATATTATCAT 57.542 33.333 0.00 0.00 0.00 2.45
2225 2268 4.293494 TGCTTGATATCCTTGAGTCCTCT 58.707 43.478 0.00 0.00 0.00 3.69
2289 2332 5.940192 TTGATCTGTCACACCAATAACAC 57.060 39.130 0.00 0.00 33.11 3.32
2341 2386 8.999431 AGCAAAGGTAATAATAACATCGTATGG 58.001 33.333 0.00 0.00 33.60 2.74
2368 2413 6.484364 AAACAGAAATTGGTTGTCCTGATT 57.516 33.333 0.00 0.00 34.73 2.57
2556 2795 8.803235 TGAGATAACAATGTGTAGTTGACTAGT 58.197 33.333 0.00 0.00 0.00 2.57
2567 2806 7.919091 TGTGTAGTTGACTAGTACTGAAACTTG 59.081 37.037 5.39 0.00 34.35 3.16
2580 2822 9.628500 AGTACTGAAACTTGAACTATTTTTCCT 57.372 29.630 0.00 0.00 0.00 3.36
2637 2879 4.306600 GGTTTTGCTCGAAACAAATGGAT 58.693 39.130 12.53 0.00 40.44 3.41
2720 2962 3.070302 GGGCAACAATTTTCTGTAACCCA 59.930 43.478 8.42 0.00 41.27 4.51
2721 2963 4.055360 GGCAACAATTTTCTGTAACCCAC 58.945 43.478 0.00 0.00 0.00 4.61
2722 2964 4.202212 GGCAACAATTTTCTGTAACCCACT 60.202 41.667 0.00 0.00 0.00 4.00
2723 2965 4.744631 GCAACAATTTTCTGTAACCCACTG 59.255 41.667 0.00 0.00 0.00 3.66
2724 2966 4.584327 ACAATTTTCTGTAACCCACTGC 57.416 40.909 0.00 0.00 0.00 4.40
2725 2967 3.320826 ACAATTTTCTGTAACCCACTGCC 59.679 43.478 0.00 0.00 0.00 4.85
2813 3055 8.193438 GCAGAAATAAAGCCATTACTGATTCTT 58.807 33.333 0.00 0.00 0.00 2.52
2829 3071 4.889409 TGATTCTTATCCAACTTGGGATGC 59.111 41.667 8.01 0.00 46.98 3.91
2842 3084 1.065199 TGGGATGCAGAGTCCAACATC 60.065 52.381 7.13 8.44 37.49 3.06
2893 3135 2.614057 AGAACTGACTCGCAAAACCAAG 59.386 45.455 0.00 0.00 0.00 3.61
2898 3140 3.941483 CTGACTCGCAAAACCAAGGATAT 59.059 43.478 0.00 0.00 0.00 1.63
2899 3141 5.092554 TGACTCGCAAAACCAAGGATATA 57.907 39.130 0.00 0.00 0.00 0.86
2904 3146 7.836842 ACTCGCAAAACCAAGGATATATTTTT 58.163 30.769 0.00 0.00 0.00 1.94
3033 3275 4.142403 GCCATGTTGCTATTTTGCTAGTGA 60.142 41.667 0.00 0.00 0.00 3.41
3036 3278 7.037438 CCATGTTGCTATTTTGCTAGTGAATT 58.963 34.615 0.00 0.00 0.00 2.17
3086 3329 4.453819 CACCCTCTCACTGTCTTGATTTTC 59.546 45.833 0.00 0.00 0.00 2.29
3123 3366 4.263156 GGTGAACCTACACAACCCATAGAA 60.263 45.833 0.00 0.00 41.88 2.10
3136 3379 8.712363 CACAACCCATAGAATAGATTAATCACG 58.288 37.037 17.56 0.00 0.00 4.35
3152 3395 2.407090 TCACGAACAATGCAGTCTCAG 58.593 47.619 0.00 0.00 0.00 3.35
3255 3502 3.129462 CACCTCATCAGACTACGATGTGT 59.871 47.826 0.00 0.00 40.92 3.72
3261 3508 1.914051 CAGACTACGATGTGTTCTGCG 59.086 52.381 0.00 0.00 0.00 5.18
3274 3528 3.557595 GTGTTCTGCGATTTCCTCTATGG 59.442 47.826 0.00 0.00 37.10 2.74
3356 3610 5.679734 ACTGTATGTTGCTCTTCAGTTTG 57.320 39.130 0.00 0.00 33.26 2.93
3405 3659 2.609459 CCGATGTTTCTACATGACCTGC 59.391 50.000 0.00 0.00 44.90 4.85
3408 3662 3.334583 TGTTTCTACATGACCTGCTCC 57.665 47.619 0.00 0.00 0.00 4.70
3497 3752 7.143340 TCATCTTTCTTTTGATGCTTGACTTG 58.857 34.615 0.00 0.00 39.69 3.16
3659 3914 5.638530 ACCCCAAATAAACAACATGGTTT 57.361 34.783 0.00 1.35 43.08 3.27
3716 3971 9.783256 AGTTTTACTTGTACAAGATGAAAACAC 57.217 29.630 37.71 28.54 42.60 3.32
3729 3984 7.129109 AGATGAAAACACCGTTACAAGTATG 57.871 36.000 0.00 0.00 0.00 2.39
3804 4073 2.787473 TGGCTGAACACATTAGAGGG 57.213 50.000 0.00 0.00 0.00 4.30
3997 4317 9.491675 AAAATAAACATTCATGCATGACTCAAA 57.508 25.926 28.72 14.51 36.36 2.69
4125 4476 7.510549 TGTTTCTAGTGCAGCTTTTTATCTT 57.489 32.000 0.00 0.00 0.00 2.40
4272 4623 7.471721 TCGTTGCAATGTCAATTTCCTAATAG 58.528 34.615 17.94 0.00 0.00 1.73
4350 4701 9.362151 GTTGGATAAATGTGAAATAATAGGGGA 57.638 33.333 0.00 0.00 0.00 4.81
4386 4747 2.605257 TCAGGAAAGGAAGTTCGAGGA 58.395 47.619 0.00 0.00 0.00 3.71
4526 4887 4.006989 TGTTGGCATGTAACATGTAGGTC 58.993 43.478 0.00 0.00 33.43 3.85
4531 4892 4.755123 GGCATGTAACATGTAGGTCATACC 59.245 45.833 0.00 2.78 38.99 2.73
4560 4921 6.986904 TTGGTTGAATACAATGCATACGTA 57.013 33.333 0.00 5.44 38.32 3.57
4591 4973 6.139048 TGAAGTGGTAAACTGTTAAAAGCC 57.861 37.500 0.00 0.00 39.81 4.35
4594 4976 6.387041 AGTGGTAAACTGTTAAAAGCCTTC 57.613 37.500 0.00 0.00 37.88 3.46
4610 4992 1.354040 CTTCTCACGCACATCACTCC 58.646 55.000 0.00 0.00 0.00 3.85
4623 5005 0.733150 TCACTCCGTACGAGATGCTG 59.267 55.000 18.76 6.75 41.63 4.41
4632 5014 3.120286 CGTACGAGATGCTGAATACATGC 59.880 47.826 10.44 0.00 0.00 4.06
4701 5086 7.834681 AGTAGTTTCTCCCCCTTAAAATTCATC 59.165 37.037 0.00 0.00 0.00 2.92
4703 5088 5.813965 TTCTCCCCCTTAAAATTCATCCT 57.186 39.130 0.00 0.00 0.00 3.24
4714 5099 7.834181 CCTTAAAATTCATCCTAGTTCCTTCCA 59.166 37.037 0.00 0.00 0.00 3.53
4762 5149 4.712873 GCAAACGTCGCGGTTCGG 62.713 66.667 6.13 1.05 33.19 4.30
4771 5158 2.184579 GCGGTTCGGAAGGAGGAG 59.815 66.667 0.00 0.00 0.00 3.69
4783 5170 0.898789 AGGAGGAGCGTCGAAAAGGA 60.899 55.000 0.00 0.00 0.00 3.36
4789 5176 1.464997 GAGCGTCGAAAAGGAATTGCT 59.535 47.619 0.00 0.00 0.00 3.91
4911 5298 6.100668 TGTACAAAAGCCAAGGTTACAAAAC 58.899 36.000 0.00 0.00 34.66 2.43
5063 5450 8.908786 AATTGTGATTATGTAGATACCACAGG 57.091 34.615 11.56 0.00 35.00 4.00
5080 5467 9.790297 ATACCACAGGGATGATAAATAGATACT 57.210 33.333 0.00 0.00 38.05 2.12
5104 5491 0.104304 CAGTACAGATACACCCCGGC 59.896 60.000 0.00 0.00 33.30 6.13
5188 5581 6.935741 AACAGCTACAGTGTATTTGTTTCA 57.064 33.333 19.19 0.00 0.00 2.69
5197 5590 6.991531 ACAGTGTATTTGTTTCAAAATGGCAT 59.008 30.769 0.00 0.00 32.16 4.40
5310 5704 1.030457 CCTCCATGCTTCTCCATTGC 58.970 55.000 0.00 0.00 0.00 3.56
5314 5708 0.102481 CATGCTTCTCCATTGCTGCC 59.898 55.000 0.00 0.00 0.00 4.85
5315 5709 0.323999 ATGCTTCTCCATTGCTGCCA 60.324 50.000 0.00 0.00 0.00 4.92
5316 5710 0.540133 TGCTTCTCCATTGCTGCCAA 60.540 50.000 0.00 0.00 35.01 4.52
5317 5711 0.822164 GCTTCTCCATTGCTGCCAAT 59.178 50.000 0.00 0.00 42.26 3.16
5398 5792 1.410882 AGCGACTCTCTATTGCCCTTC 59.589 52.381 0.00 0.00 0.00 3.46
5427 5821 6.015180 AGCTGAAAATGTTAAGATTCTGCCAA 60.015 34.615 11.64 0.00 43.50 4.52
5495 5901 8.333908 GTTCAAATATGTATGTCTCTGCTTCTG 58.666 37.037 0.00 0.00 0.00 3.02
5516 5928 9.401058 CTTCTGATGGAGTTTAAAGGTATGATT 57.599 33.333 0.00 0.00 0.00 2.57
5529 5941 3.069729 AGGTATGATTTAGACACCTCGGC 59.930 47.826 0.00 0.00 34.49 5.54
5553 5966 0.168788 CGTGCATCTGTTCCGCAAAT 59.831 50.000 0.00 0.00 37.41 2.32
5565 5978 4.116238 GTTCCGCAAATTTTTCAACCTGA 58.884 39.130 0.00 0.00 0.00 3.86
5566 5979 3.712187 TCCGCAAATTTTTCAACCTGAC 58.288 40.909 0.00 0.00 0.00 3.51
5573 5986 6.237915 GCAAATTTTTCAACCTGACACTTGAG 60.238 38.462 0.00 0.00 0.00 3.02
5618 6035 3.510459 ACTTGGAATCCTGGGGAAAAAG 58.490 45.455 0.00 0.00 34.34 2.27
5619 6036 2.621556 TGGAATCCTGGGGAAAAAGG 57.378 50.000 0.00 0.00 34.34 3.11
5683 6100 4.579340 GCAGTACTATCACTAGCTGGTGTA 59.421 45.833 27.01 17.67 38.28 2.90
5887 6306 3.840132 GTGGGTGGGGTGGGGTTT 61.840 66.667 0.00 0.00 0.00 3.27
5959 6379 0.659427 CATGTCACATGGGACGCATC 59.341 55.000 22.70 0.00 40.72 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.184579 GTGTGCTAGGCCGAGGAC 59.815 66.667 27.01 27.01 38.21 3.85
1 2 3.075005 GGTGTGCTAGGCCGAGGA 61.075 66.667 15.29 9.30 0.00 3.71
2 3 3.390521 TGGTGTGCTAGGCCGAGG 61.391 66.667 15.29 1.53 0.00 4.63
3 4 2.125512 GTGGTGTGCTAGGCCGAG 60.126 66.667 8.78 8.78 0.00 4.63
4 5 2.046009 TTTGTGGTGTGCTAGGCCGA 62.046 55.000 0.00 0.00 0.00 5.54
5 6 1.169661 TTTTGTGGTGTGCTAGGCCG 61.170 55.000 0.00 0.00 0.00 6.13
6 7 0.598065 CTTTTGTGGTGTGCTAGGCC 59.402 55.000 0.00 0.00 0.00 5.19
7 8 0.598065 CCTTTTGTGGTGTGCTAGGC 59.402 55.000 0.00 0.00 0.00 3.93
8 9 1.247567 CCCTTTTGTGGTGTGCTAGG 58.752 55.000 0.00 0.00 0.00 3.02
9 10 1.202879 TCCCCTTTTGTGGTGTGCTAG 60.203 52.381 0.00 0.00 0.00 3.42
10 11 0.847373 TCCCCTTTTGTGGTGTGCTA 59.153 50.000 0.00 0.00 0.00 3.49
11 12 0.188342 ATCCCCTTTTGTGGTGTGCT 59.812 50.000 0.00 0.00 0.00 4.40
12 13 0.318120 CATCCCCTTTTGTGGTGTGC 59.682 55.000 0.00 0.00 0.00 4.57
13 14 1.993956 TCATCCCCTTTTGTGGTGTG 58.006 50.000 0.00 0.00 0.00 3.82
14 15 2.379907 AGATCATCCCCTTTTGTGGTGT 59.620 45.455 0.00 0.00 0.00 4.16
15 16 2.756760 CAGATCATCCCCTTTTGTGGTG 59.243 50.000 0.00 0.00 0.00 4.17
16 17 2.649312 TCAGATCATCCCCTTTTGTGGT 59.351 45.455 0.00 0.00 0.00 4.16
17 18 3.370840 TCAGATCATCCCCTTTTGTGG 57.629 47.619 0.00 0.00 0.00 4.17
18 19 5.009410 GCTAATCAGATCATCCCCTTTTGTG 59.991 44.000 0.00 0.00 0.00 3.33
19 20 5.136105 GCTAATCAGATCATCCCCTTTTGT 58.864 41.667 0.00 0.00 0.00 2.83
20 21 4.214971 CGCTAATCAGATCATCCCCTTTTG 59.785 45.833 0.00 0.00 0.00 2.44
21 22 4.392940 CGCTAATCAGATCATCCCCTTTT 58.607 43.478 0.00 0.00 0.00 2.27
22 23 3.808618 GCGCTAATCAGATCATCCCCTTT 60.809 47.826 0.00 0.00 0.00 3.11
23 24 2.289945 GCGCTAATCAGATCATCCCCTT 60.290 50.000 0.00 0.00 0.00 3.95
24 25 1.277557 GCGCTAATCAGATCATCCCCT 59.722 52.381 0.00 0.00 0.00 4.79
25 26 1.677217 GGCGCTAATCAGATCATCCCC 60.677 57.143 7.64 0.00 0.00 4.81
26 27 1.677217 GGGCGCTAATCAGATCATCCC 60.677 57.143 7.64 0.00 0.00 3.85
27 28 1.277557 AGGGCGCTAATCAGATCATCC 59.722 52.381 7.64 0.00 0.00 3.51
28 29 2.233431 AGAGGGCGCTAATCAGATCATC 59.767 50.000 7.64 0.00 0.00 2.92
29 30 2.255406 AGAGGGCGCTAATCAGATCAT 58.745 47.619 7.64 0.00 0.00 2.45
30 31 1.709578 AGAGGGCGCTAATCAGATCA 58.290 50.000 7.64 0.00 0.00 2.92
31 32 2.823154 ACTAGAGGGCGCTAATCAGATC 59.177 50.000 7.64 0.00 0.00 2.75
32 33 2.823154 GACTAGAGGGCGCTAATCAGAT 59.177 50.000 7.64 0.00 0.00 2.90
33 34 2.231529 GACTAGAGGGCGCTAATCAGA 58.768 52.381 7.64 0.00 0.00 3.27
34 35 1.271102 GGACTAGAGGGCGCTAATCAG 59.729 57.143 7.64 2.14 0.00 2.90
35 36 1.329256 GGACTAGAGGGCGCTAATCA 58.671 55.000 7.64 0.00 0.00 2.57
36 37 0.241481 CGGACTAGAGGGCGCTAATC 59.759 60.000 7.64 2.86 0.00 1.75
37 38 1.179814 CCGGACTAGAGGGCGCTAAT 61.180 60.000 7.64 0.00 0.00 1.73
38 39 1.826921 CCGGACTAGAGGGCGCTAA 60.827 63.158 7.64 0.00 0.00 3.09
39 40 2.203308 CCGGACTAGAGGGCGCTA 60.203 66.667 7.64 0.00 0.00 4.26
45 46 3.936535 GGTGTCCCGGACTAGAGG 58.063 66.667 18.54 0.00 33.15 3.69
55 56 2.032071 CCAAGGTGACGGTGTCCC 59.968 66.667 0.00 0.00 0.00 4.46
56 57 2.668550 GCCAAGGTGACGGTGTCC 60.669 66.667 0.00 0.00 0.00 4.02
57 58 2.668550 GGCCAAGGTGACGGTGTC 60.669 66.667 0.00 0.00 0.00 3.67
58 59 3.476031 CTGGCCAAGGTGACGGTGT 62.476 63.158 7.01 0.00 0.00 4.16
59 60 2.669569 CTGGCCAAGGTGACGGTG 60.670 66.667 7.01 0.00 0.00 4.94
60 61 4.643387 GCTGGCCAAGGTGACGGT 62.643 66.667 7.01 0.00 0.00 4.83
80 81 1.341531 AGTAGTATGACGGATGCAGCC 59.658 52.381 12.07 12.07 0.00 4.85
81 82 2.802787 AGTAGTATGACGGATGCAGC 57.197 50.000 0.00 0.00 0.00 5.25
82 83 4.537965 GTGTAGTAGTATGACGGATGCAG 58.462 47.826 0.00 0.00 0.00 4.41
83 84 3.317149 GGTGTAGTAGTATGACGGATGCA 59.683 47.826 0.00 0.00 0.00 3.96
84 85 3.608707 CGGTGTAGTAGTATGACGGATGC 60.609 52.174 0.00 0.00 0.00 3.91
85 86 3.562973 ACGGTGTAGTAGTATGACGGATG 59.437 47.826 0.00 0.00 0.00 3.51
86 87 3.812053 GACGGTGTAGTAGTATGACGGAT 59.188 47.826 0.00 0.00 0.00 4.18
87 88 3.198068 GACGGTGTAGTAGTATGACGGA 58.802 50.000 0.00 0.00 0.00 4.69
88 89 2.289002 GGACGGTGTAGTAGTATGACGG 59.711 54.545 0.00 0.00 0.00 4.79
89 90 2.289002 GGGACGGTGTAGTAGTATGACG 59.711 54.545 0.00 0.00 0.00 4.35
90 91 3.978718 GGGACGGTGTAGTAGTATGAC 57.021 52.381 0.00 0.00 0.00 3.06
106 107 1.524008 CCTGGAAAAAGGTGCGGGAC 61.524 60.000 0.00 0.00 37.57 4.46
107 108 1.228429 CCTGGAAAAAGGTGCGGGA 60.228 57.895 0.00 0.00 37.57 5.14
108 109 2.275380 CCCTGGAAAAAGGTGCGGG 61.275 63.158 0.00 0.00 35.34 6.13
109 110 2.275380 CCCCTGGAAAAAGGTGCGG 61.275 63.158 0.00 0.00 35.34 5.69
110 111 1.112916 AACCCCTGGAAAAAGGTGCG 61.113 55.000 0.00 0.00 35.34 5.34
111 112 0.679505 GAACCCCTGGAAAAAGGTGC 59.320 55.000 0.00 0.00 35.34 5.01
112 113 2.080654 TGAACCCCTGGAAAAAGGTG 57.919 50.000 0.00 0.00 35.34 4.00
113 114 2.178984 TCATGAACCCCTGGAAAAAGGT 59.821 45.455 0.00 0.00 35.34 3.50
114 115 2.562738 GTCATGAACCCCTGGAAAAAGG 59.437 50.000 0.00 0.00 37.05 3.11
115 116 2.228822 CGTCATGAACCCCTGGAAAAAG 59.771 50.000 0.00 0.00 0.00 2.27
116 117 2.235016 CGTCATGAACCCCTGGAAAAA 58.765 47.619 0.00 0.00 0.00 1.94
117 118 1.904287 CGTCATGAACCCCTGGAAAA 58.096 50.000 0.00 0.00 0.00 2.29
118 119 0.608035 GCGTCATGAACCCCTGGAAA 60.608 55.000 0.00 0.00 0.00 3.13
119 120 1.002624 GCGTCATGAACCCCTGGAA 60.003 57.895 0.00 0.00 0.00 3.53
120 121 1.561769 ATGCGTCATGAACCCCTGGA 61.562 55.000 0.00 0.00 0.00 3.86
121 122 1.077501 ATGCGTCATGAACCCCTGG 60.078 57.895 0.00 0.00 0.00 4.45
122 123 1.378882 CCATGCGTCATGAACCCCTG 61.379 60.000 17.72 0.00 43.81 4.45
123 124 1.077501 CCATGCGTCATGAACCCCT 60.078 57.895 17.72 0.00 43.81 4.79
134 135 0.034186 AATGTCACCATCCCATGCGT 60.034 50.000 0.00 0.00 0.00 5.24
147 148 1.203441 AGCCAGCCTCAGGAATGTCA 61.203 55.000 0.00 0.00 0.00 3.58
148 149 0.463474 GAGCCAGCCTCAGGAATGTC 60.463 60.000 0.00 0.00 40.45 3.06
171 172 2.607750 GGGAGAGCCAGGGTGTCA 60.608 66.667 17.16 0.00 35.15 3.58
172 173 3.403558 GGGGAGAGCCAGGGTGTC 61.404 72.222 7.28 7.28 35.15 3.67
174 175 2.628187 ATAGGGGGAGAGCCAGGGTG 62.628 65.000 0.00 0.00 35.15 4.61
175 176 2.344995 ATAGGGGGAGAGCCAGGGT 61.345 63.158 0.00 0.00 35.15 4.34
178 179 2.049627 GCACATAGGGGGAGAGCCAG 62.050 65.000 0.00 0.00 35.15 4.85
182 183 0.692419 ACCTGCACATAGGGGGAGAG 60.692 60.000 0.00 0.00 42.35 3.20
184 185 0.107017 CAACCTGCACATAGGGGGAG 60.107 60.000 0.00 0.00 42.35 4.30
192 193 2.106566 TGAACCAAACAACCTGCACAT 58.893 42.857 0.00 0.00 0.00 3.21
193 194 1.203523 GTGAACCAAACAACCTGCACA 59.796 47.619 0.00 0.00 0.00 4.57
198 199 1.066908 CGCATGTGAACCAAACAACCT 59.933 47.619 0.00 0.00 0.00 3.50
199 200 1.202359 ACGCATGTGAACCAAACAACC 60.202 47.619 14.43 0.00 0.00 3.77
200 201 2.116366 GACGCATGTGAACCAAACAAC 58.884 47.619 14.43 0.00 0.00 3.32
201 202 1.268285 CGACGCATGTGAACCAAACAA 60.268 47.619 14.43 0.00 0.00 2.83
203 204 0.385473 CCGACGCATGTGAACCAAAC 60.385 55.000 14.43 0.00 0.00 2.93
206 207 1.817911 TACCCGACGCATGTGAACCA 61.818 55.000 14.43 0.00 0.00 3.67
207 208 0.671163 TTACCCGACGCATGTGAACC 60.671 55.000 14.43 0.79 0.00 3.62
208 209 0.719465 CTTACCCGACGCATGTGAAC 59.281 55.000 14.43 5.75 0.00 3.18
209 210 0.390603 CCTTACCCGACGCATGTGAA 60.391 55.000 14.43 0.00 0.00 3.18
210 211 1.216977 CCTTACCCGACGCATGTGA 59.783 57.895 14.43 0.00 0.00 3.58
211 212 1.079405 ACCTTACCCGACGCATGTG 60.079 57.895 4.30 4.30 0.00 3.21
212 213 1.217244 GACCTTACCCGACGCATGT 59.783 57.895 0.00 0.00 0.00 3.21
224 225 1.674441 CTAGCACGATGTCCGACCTTA 59.326 52.381 0.00 0.00 41.76 2.69
227 228 0.172803 AACTAGCACGATGTCCGACC 59.827 55.000 0.00 0.00 41.76 4.79
251 252 1.906105 TAATCACTCGGGGCCACACC 61.906 60.000 5.46 0.00 37.93 4.16
262 263 4.262808 CCCATGACCCAGAGATAATCACTC 60.263 50.000 0.00 0.00 34.95 3.51
270 271 1.351080 CCAGCCCATGACCCAGAGAT 61.351 60.000 0.00 0.00 0.00 2.75
289 290 1.153745 CTAGCTCACAGTGTCCCGC 60.154 63.158 0.00 0.00 0.00 6.13
332 333 0.610785 GCAACCCCCTTTCGGATTCA 60.611 55.000 0.00 0.00 0.00 2.57
333 334 1.320344 GGCAACCCCCTTTCGGATTC 61.320 60.000 0.00 0.00 0.00 2.52
334 335 1.304962 GGCAACCCCCTTTCGGATT 60.305 57.895 0.00 0.00 0.00 3.01
335 336 0.917333 TAGGCAACCCCCTTTCGGAT 60.917 55.000 0.00 0.00 36.41 4.18
336 337 1.539372 TAGGCAACCCCCTTTCGGA 60.539 57.895 0.00 0.00 36.41 4.55
337 338 1.077716 CTAGGCAACCCCCTTTCGG 60.078 63.158 0.00 0.00 36.41 4.30
338 339 1.749258 GCTAGGCAACCCCCTTTCG 60.749 63.158 0.00 0.00 36.41 3.46
339 340 1.379977 GGCTAGGCAACCCCCTTTC 60.380 63.158 12.16 0.00 36.41 2.62
355 356 0.105778 AGCGATAGAAAGAGCCTGGC 59.894 55.000 11.65 11.65 39.76 4.85
358 359 0.105778 GCCAGCGATAGAAAGAGCCT 59.894 55.000 0.00 0.00 39.76 4.58
359 360 0.882484 GGCCAGCGATAGAAAGAGCC 60.882 60.000 0.00 0.00 39.76 4.70
367 368 1.004080 CATCCAGGGCCAGCGATAG 60.004 63.158 6.18 0.00 0.00 2.08
369 370 2.769621 TCATCCAGGGCCAGCGAT 60.770 61.111 6.18 0.00 0.00 4.58
384 385 0.814457 AACACAAAAAGCGCCACTCA 59.186 45.000 2.29 0.00 0.00 3.41
388 389 1.520342 GGCAACACAAAAAGCGCCA 60.520 52.632 2.29 0.00 39.38 5.69
396 397 2.638480 AGCTGAGTAGGCAACACAAA 57.362 45.000 0.00 0.00 41.41 2.83
400 401 2.158682 TCCAAAAGCTGAGTAGGCAACA 60.159 45.455 0.00 0.00 41.41 3.33
433 434 2.573340 GAAAAGGTGGCCGCCATG 59.427 61.111 36.17 0.00 35.28 3.66
434 435 3.061848 CGAAAAGGTGGCCGCCAT 61.062 61.111 36.17 23.75 35.28 4.40
447 448 2.986306 GAGCCCGACGAGGACGAAA 61.986 63.158 0.00 0.00 45.00 3.46
448 449 3.437795 GAGCCCGACGAGGACGAA 61.438 66.667 0.00 0.00 45.00 3.85
468 469 3.923563 GAGCAGCTTCGTGGCGACT 62.924 63.158 0.00 0.00 34.89 4.18
501 502 2.267324 GGTGAGCTCAGAGGGCAC 59.733 66.667 18.89 3.51 0.00 5.01
525 526 1.474320 CGAGGACCACAACAACTTGGA 60.474 52.381 0.00 0.00 36.28 3.53
530 531 0.949105 ATCGCGAGGACCACAACAAC 60.949 55.000 16.66 0.00 0.00 3.32
531 532 0.669318 GATCGCGAGGACCACAACAA 60.669 55.000 16.66 0.00 0.00 2.83
547 548 1.580845 GCAGTGGCCAGTGTGTGATC 61.581 60.000 35.27 18.03 34.32 2.92
564 565 1.155889 CAATACACCAACGAGCTGCA 58.844 50.000 1.02 0.00 0.00 4.41
573 574 1.134640 CGATCCCGACCAATACACCAA 60.135 52.381 0.00 0.00 38.22 3.67
596 597 0.770557 CTCCCCGGGATCCCCATTAA 60.771 60.000 26.32 6.29 45.83 1.40
617 618 2.991580 TCCCCTTCCTCTCACTTTCTT 58.008 47.619 0.00 0.00 0.00 2.52
628 629 2.046285 CGCGCATTTTCCCCTTCCT 61.046 57.895 8.75 0.00 0.00 3.36
630 631 1.136774 GTCGCGCATTTTCCCCTTC 59.863 57.895 8.75 0.00 0.00 3.46
631 632 2.340328 GGTCGCGCATTTTCCCCTT 61.340 57.895 8.75 0.00 0.00 3.95
651 652 2.368221 CCTTTGTCCCTTGCCAATGAAA 59.632 45.455 0.00 0.00 0.00 2.69
661 662 2.666317 CCACAACTTCCTTTGTCCCTT 58.334 47.619 0.00 0.00 37.62 3.95
677 678 3.276091 CGAACGCTGCAACCCACA 61.276 61.111 0.00 0.00 0.00 4.17
678 679 4.683334 GCGAACGCTGCAACCCAC 62.683 66.667 11.97 0.00 38.26 4.61
698 699 2.096174 CGTTTGTTTCAAAGACCGACCA 59.904 45.455 0.00 0.00 0.00 4.02
711 712 2.351350 GCCACATCGGAATCGTTTGTTT 60.351 45.455 0.00 0.00 36.56 2.83
727 735 2.290197 TGATGCACATAGACTTGCCACA 60.290 45.455 0.00 0.00 38.00 4.17
778 786 2.094659 GGTCTCACACGGACGCATG 61.095 63.158 0.00 0.00 34.82 4.06
785 793 4.152402 CAGATTTTTAGTGGTCTCACACGG 59.848 45.833 0.00 0.00 45.91 4.94
858 893 7.435068 ACAGTGAATACGTCTTAGCATTTTT 57.565 32.000 0.00 0.00 0.00 1.94
909 945 6.480320 CCTGTACAAGCCTTCACATTATACTC 59.520 42.308 0.00 0.00 0.00 2.59
966 1006 2.490217 CGCTCGTCTCCACCGATT 59.510 61.111 0.00 0.00 33.27 3.34
967 1007 3.518998 CCGCTCGTCTCCACCGAT 61.519 66.667 0.00 0.00 33.27 4.18
1171 1211 1.439524 ATAACCCAGTGCCCCAACCA 61.440 55.000 0.00 0.00 0.00 3.67
1215 1255 2.900716 TTATCCATGCCGAATGACGA 57.099 45.000 0.00 0.00 45.77 4.20
1241 1281 2.058798 TCTCGATTGTGAGACGCAAAC 58.941 47.619 0.00 0.00 40.01 2.93
1387 1427 8.086143 ACATACTAAATGGGCAAACTAGTAGA 57.914 34.615 3.59 0.00 30.72 2.59
1532 1574 8.114331 TGGCATAGCATATTCCTGAAAATAAG 57.886 34.615 0.00 0.00 0.00 1.73
1556 1598 3.044986 CAACAATTCAACCGCTTGACTG 58.955 45.455 0.00 0.00 36.06 3.51
1598 1640 1.136984 GTCTCGAACGATGACGCCT 59.863 57.895 0.00 0.00 43.96 5.52
1649 1691 3.969287 AAGAATGAGCTGCAGTGAGTA 57.031 42.857 16.64 0.00 0.00 2.59
1664 1706 4.464951 GGGAATTTGTAACCCGGAAAGAAT 59.535 41.667 0.73 0.00 34.03 2.40
1673 1715 5.516044 AGGTCTAATGGGAATTTGTAACCC 58.484 41.667 0.00 0.00 43.51 4.11
1688 1730 3.181489 CGAGCCGTAGAACAAGGTCTAAT 60.181 47.826 0.00 0.00 31.94 1.73
1709 1751 0.663568 GGAGGGCGATGTAACGATCG 60.664 60.000 14.88 14.88 46.54 3.69
1724 1766 1.486726 ACTGAAAAGCCGGATAGGAGG 59.513 52.381 5.05 0.00 45.00 4.30
1788 1830 2.497273 TGATAGCACTGTTAGCTGCAGA 59.503 45.455 20.43 0.00 43.33 4.26
1875 1917 2.545952 CGACCGTAAGAATGCCAGCTAT 60.546 50.000 0.00 0.00 43.02 2.97
2024 2066 1.082690 GCTTACAGCTGCACCTCTTC 58.917 55.000 15.27 0.00 38.45 2.87
2052 2094 8.153550 GGCAATGATAATATGGGTCTATAGGAG 58.846 40.741 0.00 0.00 0.00 3.69
2074 2116 6.166984 TCACAAGGAATAAACAAATGGCAA 57.833 33.333 0.00 0.00 0.00 4.52
2225 2268 5.241403 ACAGAACATCAATGACTTGGGTA 57.759 39.130 0.00 0.00 32.95 3.69
2341 2386 4.875536 AGGACAACCAATTTCTGTTTTTGC 59.124 37.500 0.00 0.00 38.94 3.68
2405 2453 6.183347 AGATTTCATCTTCTGGTAAACCTGG 58.817 40.000 6.23 0.00 35.76 4.45
2413 2461 8.602472 AGAACTACTAGATTTCATCTTCTGGT 57.398 34.615 0.00 0.00 40.76 4.00
2542 2656 8.133627 TCAAGTTTCAGTACTAGTCAACTACAC 58.866 37.037 0.00 0.00 0.00 2.90
2556 2795 9.621629 TGAGGAAAAATAGTTCAAGTTTCAGTA 57.378 29.630 0.00 0.00 31.28 2.74
2580 2822 3.075283 TCCCCAGGCTATTTCTGTTTTGA 59.925 43.478 0.00 0.00 0.00 2.69
2612 2854 2.861462 TTGTTTCGAGCAAAACCCTG 57.139 45.000 2.60 0.00 38.16 4.45
2637 2879 5.623956 TTAGAGTGAAAGGAAACCTGACA 57.376 39.130 0.00 0.00 32.13 3.58
2720 2962 0.252421 TCCTCATCTCCAGTGGCAGT 60.252 55.000 3.51 0.00 0.00 4.40
2721 2963 0.907486 TTCCTCATCTCCAGTGGCAG 59.093 55.000 3.51 3.22 0.00 4.85
2722 2964 1.361204 TTTCCTCATCTCCAGTGGCA 58.639 50.000 3.51 0.00 0.00 4.92
2723 2965 2.496899 TTTTCCTCATCTCCAGTGGC 57.503 50.000 3.51 0.00 0.00 5.01
2724 2966 6.712547 GGTAATATTTTCCTCATCTCCAGTGG 59.287 42.308 1.40 1.40 0.00 4.00
2725 2967 6.712547 GGGTAATATTTTCCTCATCTCCAGTG 59.287 42.308 0.00 0.00 0.00 3.66
2813 3055 2.846206 ACTCTGCATCCCAAGTTGGATA 59.154 45.455 24.06 11.26 43.39 2.59
2829 3071 2.496070 TCCTTACGGATGTTGGACTCTG 59.504 50.000 0.00 0.00 33.30 3.35
2842 3084 6.650807 ACATTTCATGCTACATATCCTTACGG 59.349 38.462 0.00 0.00 0.00 4.02
2904 3146 8.877195 AGGTTGAGTTAAGGAGTTCTATACAAA 58.123 33.333 0.00 0.00 0.00 2.83
3033 3275 7.043565 ACTTCTGTTTGCAAAGTCATGAAATT 58.956 30.769 13.26 0.00 0.00 1.82
3036 3278 5.581126 ACTTCTGTTTGCAAAGTCATGAA 57.419 34.783 13.26 11.08 0.00 2.57
3086 3329 2.684927 GGTTCACCAGATGGATTCCCAG 60.685 54.545 5.72 0.00 40.10 4.45
3123 3366 7.712639 AGACTGCATTGTTCGTGATTAATCTAT 59.287 33.333 16.24 0.00 0.00 1.98
3136 3379 6.674694 ATTATGTCTGAGACTGCATTGTTC 57.325 37.500 14.42 0.00 33.15 3.18
3152 3395 7.254795 GCACACCACATTCTAGGTAATTATGTC 60.255 40.741 0.00 0.00 36.07 3.06
3231 3478 3.764434 ACATCGTAGTCTGATGAGGTGTT 59.236 43.478 9.72 0.00 44.76 3.32
3255 3502 4.649674 AGTACCATAGAGGAAATCGCAGAA 59.350 41.667 0.00 0.00 39.67 3.02
3590 3845 5.762179 TGACATTCAACTTGGGAGTCTAT 57.238 39.130 0.00 0.00 34.21 1.98
3716 3971 3.792401 TGGCATCTCATACTTGTAACGG 58.208 45.455 0.00 0.00 0.00 4.44
3729 3984 1.003580 TGGGTTGAGTTCTGGCATCTC 59.996 52.381 0.00 0.00 0.00 2.75
3970 4269 9.491675 TTGAGTCATGCATGAATGTTTATTTTT 57.508 25.926 32.27 6.57 38.75 1.94
4206 4557 7.999450 AAACCTAGATACTAGATAGAACGGG 57.001 40.000 0.00 0.00 0.00 5.28
4272 4623 6.869388 GCCATCAGTAGCTATAAAGTAGAACC 59.131 42.308 0.00 0.00 0.00 3.62
4369 4730 2.833631 TGTCCTCGAACTTCCTTTCC 57.166 50.000 0.00 0.00 0.00 3.13
4386 4747 1.649321 TCTCTGAAGAGGTGCCATGT 58.351 50.000 7.47 0.00 42.30 3.21
4473 4834 7.757941 TTTGGATTACAACAATGATCAGACA 57.242 32.000 0.09 0.00 39.19 3.41
4526 4887 9.232082 CATTGTATTCAACCAAATAACGGTATG 57.768 33.333 0.00 0.00 34.99 2.39
4531 4892 7.754069 ATGCATTGTATTCAACCAAATAACG 57.246 32.000 0.00 0.00 36.33 3.18
4560 4921 5.560724 ACAGTTTACCACTTCATGCATAGT 58.439 37.500 0.00 0.00 30.92 2.12
4570 4952 6.605995 AGAAGGCTTTTAACAGTTTACCACTT 59.394 34.615 0.00 0.00 30.92 3.16
4591 4973 1.354040 GGAGTGATGTGCGTGAGAAG 58.646 55.000 0.00 0.00 0.00 2.85
4594 4976 0.170339 TACGGAGTGATGTGCGTGAG 59.830 55.000 0.37 0.00 44.86 3.51
4610 4992 3.120286 GCATGTATTCAGCATCTCGTACG 59.880 47.826 9.53 9.53 0.00 3.67
4623 5005 4.916983 TGTGCAATAAGGGCATGTATTC 57.083 40.909 0.00 0.00 44.11 1.75
4663 5047 7.070322 GGGGGAGAAACTACTTGTATGTACATA 59.930 40.741 11.62 11.62 35.89 2.29
4675 5059 7.098845 TGAATTTTAAGGGGGAGAAACTACT 57.901 36.000 0.00 0.00 0.00 2.57
4683 5067 6.267492 ACTAGGATGAATTTTAAGGGGGAG 57.733 41.667 0.00 0.00 0.00 4.30
4701 5086 6.603201 TCTGCATAAATTTGGAAGGAACTAGG 59.397 38.462 0.00 0.00 38.49 3.02
4703 5088 7.450014 TGTTCTGCATAAATTTGGAAGGAACTA 59.550 33.333 18.98 10.01 38.49 2.24
4714 5099 6.465948 TGCAATTCCTGTTCTGCATAAATTT 58.534 32.000 0.00 0.00 39.77 1.82
4762 5149 1.351153 CTTTTCGACGCTCCTCCTTC 58.649 55.000 0.00 0.00 0.00 3.46
4771 5158 3.465122 TTAGCAATTCCTTTTCGACGC 57.535 42.857 0.00 0.00 0.00 5.19
4885 5272 4.528920 TGTAACCTTGGCTTTTGTACAGT 58.471 39.130 0.00 0.00 0.00 3.55
4911 5298 1.469251 CGTCTTCTGGTACACGGATGG 60.469 57.143 0.00 0.00 33.61 3.51
5049 5436 7.872061 ATTTATCATCCCTGTGGTATCTACA 57.128 36.000 0.00 0.00 0.00 2.74
5063 5450 7.102346 ACTGCTGCAGTATCTATTTATCATCC 58.898 38.462 32.18 0.00 43.46 3.51
5080 5467 1.207089 GGGTGTATCTGTACTGCTGCA 59.793 52.381 0.88 0.88 0.00 4.41
5104 5491 1.910580 ATACACCAGAAGGGCCGTGG 61.911 60.000 17.96 17.96 42.05 4.94
5188 5581 5.025453 AGTGGACATCCTTAATGCCATTTT 58.975 37.500 0.00 0.00 40.93 1.82
5197 5590 1.707989 TGGGCAAGTGGACATCCTTAA 59.292 47.619 0.00 0.00 36.82 1.85
5243 5637 2.505819 ACAACTTGTCAGGAGTTCTGGT 59.494 45.455 0.00 0.00 43.53 4.00
5268 5662 3.771798 TGTACGTTTTTGTTTTGCTCCC 58.228 40.909 0.00 0.00 0.00 4.30
5310 5704 5.646360 TGCATATGAGATATGACATTGGCAG 59.354 40.000 6.97 0.00 44.19 4.85
5398 5792 9.070149 GCAGAATCTTAACATTTTCAGCTAAAG 57.930 33.333 0.00 0.00 30.66 1.85
5427 5821 6.657966 TGCATTCTGAATCTGTGATTCTTTCT 59.342 34.615 17.60 2.62 0.00 2.52
5516 5928 2.260434 GTGCGCCGAGGTGTCTAA 59.740 61.111 4.18 0.00 0.00 2.10
5553 5966 5.975693 AACTCAAGTGTCAGGTTGAAAAA 57.024 34.783 0.45 0.00 32.36 1.94
5565 5978 3.004106 GCAGCATGAGAAAACTCAAGTGT 59.996 43.478 0.00 0.00 39.69 3.55
5566 5979 3.004002 TGCAGCATGAGAAAACTCAAGTG 59.996 43.478 0.00 1.13 39.69 3.16
5573 5986 3.631145 TGTCTTGCAGCATGAGAAAAC 57.369 42.857 11.18 1.25 39.69 2.43
5585 5998 5.183713 CAGGATTCCAAGTATTTGTCTTGCA 59.816 40.000 5.29 0.00 40.35 4.08
5588 6001 5.264395 CCCAGGATTCCAAGTATTTGTCTT 58.736 41.667 5.29 0.00 32.21 3.01
5683 6100 7.349598 ACATCATAAAGATTAAAGAGGCCACT 58.650 34.615 5.01 0.00 33.72 4.00
5790 6209 5.710513 ACTGCACAAACAACACATATCAT 57.289 34.783 0.00 0.00 0.00 2.45
5795 6214 3.003689 GCTCTACTGCACAAACAACACAT 59.996 43.478 0.00 0.00 0.00 3.21
5886 6305 1.543896 CCCCTTTCCCTCCTCCCAA 60.544 63.158 0.00 0.00 0.00 4.12
5887 6306 2.127297 CCCCTTTCCCTCCTCCCA 59.873 66.667 0.00 0.00 0.00 4.37
5959 6379 4.680237 TTCCAGGACAGTGCGCGG 62.680 66.667 8.83 0.00 0.00 6.46
5961 6381 3.426568 GCTTCCAGGACAGTGCGC 61.427 66.667 0.00 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.