Multiple sequence alignment - TraesCS5B01G491100

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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 TraesCS5B01G491100 chr5B 100.000 2411 0 0 1 2411 659714540 659716950 0.000000e+00 4453
1 TraesCS5B01G491100 chr5B 85.783 830 75 17 983 1805 659679377 659680170 0.000000e+00 839
2 TraesCS5B01G491100 chr5B 83.553 608 61 19 983 1583 659635752 659636327 1.270000e-147 532
3 TraesCS5B01G491100 chr5B 80.286 629 88 21 988 1599 659604652 659605261 2.200000e-120 442
4 TraesCS5B01G491100 chr5B 82.132 319 45 9 1047 1356 659557501 659557186 1.840000e-66 263
5 TraesCS5B01G491100 chr5A 83.990 1218 123 31 276 1439 651762668 651763867 0.000000e+00 1103
6 TraesCS5B01G491100 chr5A 82.537 544 71 12 988 1518 651635535 651636067 7.860000e-125 457
7 TraesCS5B01G491100 chr5A 80.280 644 91 19 988 1610 651755049 651755677 1.020000e-123 453
8 TraesCS5B01G491100 chr5A 87.685 406 29 12 2014 2411 651783138 651783530 1.020000e-123 453
9 TraesCS5B01G491100 chr5A 77.885 728 124 24 988 1692 651588585 651589298 3.710000e-113 418
10 TraesCS5B01G491100 chr5A 86.908 359 47 0 1055 1413 651744462 651744820 1.040000e-108 403
11 TraesCS5B01G491100 chr5A 87.675 357 30 5 1423 1777 651763885 651764229 1.040000e-108 403
12 TraesCS5B01G491100 chr5A 92.000 200 15 1 1768 1966 651764357 651764556 1.830000e-71 279
13 TraesCS5B01G491100 chr5A 81.232 341 41 6 217 542 651741251 651741583 1.110000e-63 254
14 TraesCS5B01G491100 chr5D 93.740 639 31 6 1780 2411 525318230 525318866 0.000000e+00 950
15 TraesCS5B01G491100 chr5D 88.762 703 65 6 983 1675 525317334 525318032 0.000000e+00 848


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 TraesCS5B01G491100 chr5B 659714540 659716950 2410 False 4453.0 4453 100.000000 1 2411 1 chr5B.!!$F4 2410
1 TraesCS5B01G491100 chr5B 659679377 659680170 793 False 839.0 839 85.783000 983 1805 1 chr5B.!!$F3 822
2 TraesCS5B01G491100 chr5B 659635752 659636327 575 False 532.0 532 83.553000 983 1583 1 chr5B.!!$F2 600
3 TraesCS5B01G491100 chr5B 659604652 659605261 609 False 442.0 442 80.286000 988 1599 1 chr5B.!!$F1 611
4 TraesCS5B01G491100 chr5A 651762668 651764556 1888 False 595.0 1103 87.888333 276 1966 3 chr5A.!!$F6 1690
5 TraesCS5B01G491100 chr5A 651635535 651636067 532 False 457.0 457 82.537000 988 1518 1 chr5A.!!$F2 530
6 TraesCS5B01G491100 chr5A 651755049 651755677 628 False 453.0 453 80.280000 988 1610 1 chr5A.!!$F3 622
7 TraesCS5B01G491100 chr5A 651588585 651589298 713 False 418.0 418 77.885000 988 1692 1 chr5A.!!$F1 704
8 TraesCS5B01G491100 chr5A 651741251 651744820 3569 False 328.5 403 84.070000 217 1413 2 chr5A.!!$F5 1196
9 TraesCS5B01G491100 chr5D 525317334 525318866 1532 False 899.0 950 91.251000 983 2411 2 chr5D.!!$F1 1428

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
67 68 0.038618 TCTGGAACATGGACGTCACG 60.039 55.0 18.91 7.22 38.20 4.35 F
1015 3499 0.026803 GCAGATGGTTTCGTCGATGC 59.973 55.0 0.00 0.00 34.23 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1250 3752 1.005340 CTGCTCCGTGATCTTCTTGC 58.995 55.0 0.0 0.0 0.0 4.01 R
2292 5015 0.107993 CATGAGCCACACCAGTCGAT 60.108 55.0 0.0 0.0 0.0 3.59 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
25 26 8.749841 CTATAGGAGATTAATGACGTGAAAGG 57.250 38.462 0.00 0.00 0.00 3.11
26 27 4.770795 AGGAGATTAATGACGTGAAAGGG 58.229 43.478 0.00 0.00 0.00 3.95
27 28 4.469945 AGGAGATTAATGACGTGAAAGGGA 59.530 41.667 0.00 0.00 0.00 4.20
28 29 4.811557 GGAGATTAATGACGTGAAAGGGAG 59.188 45.833 0.00 0.00 0.00 4.30
29 30 5.395324 GGAGATTAATGACGTGAAAGGGAGA 60.395 44.000 0.00 0.00 0.00 3.71
30 31 5.665459 AGATTAATGACGTGAAAGGGAGAG 58.335 41.667 0.00 0.00 0.00 3.20
31 32 5.422331 AGATTAATGACGTGAAAGGGAGAGA 59.578 40.000 0.00 0.00 0.00 3.10
32 33 3.601443 AATGACGTGAAAGGGAGAGAG 57.399 47.619 0.00 0.00 0.00 3.20
33 34 2.287977 TGACGTGAAAGGGAGAGAGA 57.712 50.000 0.00 0.00 0.00 3.10
34 35 2.594131 TGACGTGAAAGGGAGAGAGAA 58.406 47.619 0.00 0.00 0.00 2.87
35 36 2.963101 TGACGTGAAAGGGAGAGAGAAA 59.037 45.455 0.00 0.00 0.00 2.52
36 37 3.243771 TGACGTGAAAGGGAGAGAGAAAC 60.244 47.826 0.00 0.00 0.00 2.78
37 38 2.698797 ACGTGAAAGGGAGAGAGAAACA 59.301 45.455 0.00 0.00 0.00 2.83
38 39 3.325135 ACGTGAAAGGGAGAGAGAAACAT 59.675 43.478 0.00 0.00 0.00 2.71
39 40 4.202367 ACGTGAAAGGGAGAGAGAAACATT 60.202 41.667 0.00 0.00 0.00 2.71
40 41 4.153117 CGTGAAAGGGAGAGAGAAACATTG 59.847 45.833 0.00 0.00 0.00 2.82
41 42 4.074970 TGAAAGGGAGAGAGAAACATTGC 58.925 43.478 0.00 0.00 0.00 3.56
42 43 2.393271 AGGGAGAGAGAAACATTGCG 57.607 50.000 0.00 0.00 0.00 4.85
43 44 1.625818 AGGGAGAGAGAAACATTGCGT 59.374 47.619 0.00 0.00 0.00 5.24
44 45 1.734465 GGGAGAGAGAAACATTGCGTG 59.266 52.381 0.00 0.00 0.00 5.34
45 46 2.612972 GGGAGAGAGAAACATTGCGTGA 60.613 50.000 0.00 0.00 0.00 4.35
46 47 2.413453 GGAGAGAGAAACATTGCGTGAC 59.587 50.000 0.00 0.00 0.00 3.67
47 48 2.413453 GAGAGAGAAACATTGCGTGACC 59.587 50.000 0.00 0.00 0.00 4.02
48 49 2.037772 AGAGAGAAACATTGCGTGACCT 59.962 45.455 0.00 0.00 0.00 3.85
49 50 2.413453 GAGAGAAACATTGCGTGACCTC 59.587 50.000 0.00 0.00 0.00 3.85
50 51 2.037772 AGAGAAACATTGCGTGACCTCT 59.962 45.455 0.00 0.00 31.70 3.69
51 52 2.146342 AGAAACATTGCGTGACCTCTG 58.854 47.619 0.00 0.00 0.00 3.35
52 53 1.197721 GAAACATTGCGTGACCTCTGG 59.802 52.381 0.00 0.00 0.00 3.86
53 54 0.396435 AACATTGCGTGACCTCTGGA 59.604 50.000 0.00 0.00 0.00 3.86
54 55 0.396435 ACATTGCGTGACCTCTGGAA 59.604 50.000 0.00 0.00 0.00 3.53
55 56 0.798776 CATTGCGTGACCTCTGGAAC 59.201 55.000 0.00 0.00 0.00 3.62
56 57 0.396435 ATTGCGTGACCTCTGGAACA 59.604 50.000 0.00 0.00 0.00 3.18
57 58 0.396435 TTGCGTGACCTCTGGAACAT 59.604 50.000 0.00 0.00 38.20 2.71
58 59 0.320683 TGCGTGACCTCTGGAACATG 60.321 55.000 0.00 0.00 38.20 3.21
59 60 1.021390 GCGTGACCTCTGGAACATGG 61.021 60.000 0.00 0.00 38.20 3.66
60 61 0.608130 CGTGACCTCTGGAACATGGA 59.392 55.000 0.00 0.00 38.20 3.41
61 62 1.673033 CGTGACCTCTGGAACATGGAC 60.673 57.143 0.00 0.00 38.20 4.02
62 63 0.608130 TGACCTCTGGAACATGGACG 59.392 55.000 0.00 0.00 38.20 4.79
63 64 0.608640 GACCTCTGGAACATGGACGT 59.391 55.000 0.00 0.00 38.20 4.34
64 65 0.608640 ACCTCTGGAACATGGACGTC 59.391 55.000 7.13 7.13 38.20 4.34
65 66 0.608130 CCTCTGGAACATGGACGTCA 59.392 55.000 18.91 3.91 38.20 4.35
66 67 1.673033 CCTCTGGAACATGGACGTCAC 60.673 57.143 18.91 7.49 38.20 3.67
67 68 0.038618 TCTGGAACATGGACGTCACG 60.039 55.000 18.91 7.22 38.20 4.35
68 69 1.626654 CTGGAACATGGACGTCACGC 61.627 60.000 18.91 0.00 38.20 5.34
69 70 1.374252 GGAACATGGACGTCACGCT 60.374 57.895 18.91 0.00 0.00 5.07
70 71 1.352156 GGAACATGGACGTCACGCTC 61.352 60.000 18.91 6.62 0.00 5.03
71 72 0.388649 GAACATGGACGTCACGCTCT 60.389 55.000 18.91 0.00 0.00 4.09
72 73 0.885879 AACATGGACGTCACGCTCTA 59.114 50.000 18.91 0.00 0.00 2.43
73 74 0.452184 ACATGGACGTCACGCTCTAG 59.548 55.000 18.91 0.47 0.00 2.43
74 75 0.867753 CATGGACGTCACGCTCTAGC 60.868 60.000 18.91 0.00 37.78 3.42
75 76 2.005960 ATGGACGTCACGCTCTAGCC 62.006 60.000 18.91 0.00 37.91 3.93
76 77 2.408241 GGACGTCACGCTCTAGCCT 61.408 63.158 18.91 0.00 37.91 4.58
77 78 1.507174 GACGTCACGCTCTAGCCTT 59.493 57.895 11.55 0.00 37.91 4.35
78 79 0.731417 GACGTCACGCTCTAGCCTTA 59.269 55.000 11.55 0.00 37.91 2.69
79 80 0.450983 ACGTCACGCTCTAGCCTTAC 59.549 55.000 0.00 0.00 37.91 2.34
80 81 0.248539 CGTCACGCTCTAGCCTTACC 60.249 60.000 0.00 0.00 37.91 2.85
81 82 0.102663 GTCACGCTCTAGCCTTACCC 59.897 60.000 0.00 0.00 37.91 3.69
82 83 0.323999 TCACGCTCTAGCCTTACCCA 60.324 55.000 0.00 0.00 37.91 4.51
83 84 0.535335 CACGCTCTAGCCTTACCCAA 59.465 55.000 0.00 0.00 37.91 4.12
84 85 1.066430 CACGCTCTAGCCTTACCCAAA 60.066 52.381 0.00 0.00 37.91 3.28
85 86 1.207329 ACGCTCTAGCCTTACCCAAAG 59.793 52.381 0.00 0.00 37.91 2.77
86 87 1.480954 CGCTCTAGCCTTACCCAAAGA 59.519 52.381 0.00 0.00 37.91 2.52
87 88 2.103263 CGCTCTAGCCTTACCCAAAGAT 59.897 50.000 0.00 0.00 37.91 2.40
88 89 3.321111 CGCTCTAGCCTTACCCAAAGATA 59.679 47.826 0.00 0.00 37.91 1.98
89 90 4.202223 CGCTCTAGCCTTACCCAAAGATAA 60.202 45.833 0.00 0.00 37.91 1.75
90 91 5.301555 GCTCTAGCCTTACCCAAAGATAAG 58.698 45.833 0.00 0.00 37.38 1.73
91 92 5.163290 GCTCTAGCCTTACCCAAAGATAAGT 60.163 44.000 0.00 0.00 37.38 2.24
92 93 6.235231 TCTAGCCTTACCCAAAGATAAGTG 57.765 41.667 0.00 0.00 37.38 3.16
93 94 5.962031 TCTAGCCTTACCCAAAGATAAGTGA 59.038 40.000 0.00 0.00 37.38 3.41
94 95 4.844884 AGCCTTACCCAAAGATAAGTGAC 58.155 43.478 0.00 0.00 37.38 3.67
95 96 4.536489 AGCCTTACCCAAAGATAAGTGACT 59.464 41.667 0.00 0.00 37.38 3.41
96 97 5.014228 AGCCTTACCCAAAGATAAGTGACTT 59.986 40.000 2.37 2.37 37.38 3.01
97 98 5.123979 GCCTTACCCAAAGATAAGTGACTTG 59.876 44.000 8.33 0.00 37.38 3.16
98 99 5.648092 CCTTACCCAAAGATAAGTGACTTGG 59.352 44.000 8.33 0.00 37.38 3.61
99 100 4.993705 ACCCAAAGATAAGTGACTTGGA 57.006 40.909 8.33 0.00 0.00 3.53
100 101 5.520748 ACCCAAAGATAAGTGACTTGGAT 57.479 39.130 8.33 0.00 0.00 3.41
101 102 5.501156 ACCCAAAGATAAGTGACTTGGATC 58.499 41.667 8.33 4.06 0.00 3.36
102 103 4.572389 CCCAAAGATAAGTGACTTGGATCG 59.428 45.833 8.33 0.00 0.00 3.69
103 104 4.572389 CCAAAGATAAGTGACTTGGATCGG 59.428 45.833 8.33 0.00 0.00 4.18
104 105 3.460857 AGATAAGTGACTTGGATCGGC 57.539 47.619 8.33 0.00 0.00 5.54
105 106 2.103263 AGATAAGTGACTTGGATCGGCC 59.897 50.000 8.33 0.00 37.10 6.13
106 107 0.174845 TAAGTGACTTGGATCGGCCG 59.825 55.000 22.12 22.12 40.66 6.13
107 108 2.511600 GTGACTTGGATCGGCCGG 60.512 66.667 27.83 10.66 40.66 6.13
108 109 4.467084 TGACTTGGATCGGCCGGC 62.467 66.667 27.83 21.18 40.66 6.13
126 127 3.369701 CGTCGTCGCTATGGATCTC 57.630 57.895 0.00 0.00 0.00 2.75
127 128 0.869068 CGTCGTCGCTATGGATCTCT 59.131 55.000 0.00 0.00 0.00 3.10
128 129 1.264557 CGTCGTCGCTATGGATCTCTT 59.735 52.381 0.00 0.00 0.00 2.85
129 130 2.656085 GTCGTCGCTATGGATCTCTTG 58.344 52.381 0.00 0.00 0.00 3.02
130 131 2.290916 GTCGTCGCTATGGATCTCTTGA 59.709 50.000 0.00 0.00 0.00 3.02
131 132 2.550180 TCGTCGCTATGGATCTCTTGAG 59.450 50.000 0.00 0.00 0.00 3.02
132 133 2.292016 CGTCGCTATGGATCTCTTGAGT 59.708 50.000 0.00 0.00 0.00 3.41
133 134 3.608241 CGTCGCTATGGATCTCTTGAGTC 60.608 52.174 0.00 0.00 0.00 3.36
134 135 3.568007 GTCGCTATGGATCTCTTGAGTCT 59.432 47.826 0.00 0.00 0.00 3.24
135 136 4.757657 GTCGCTATGGATCTCTTGAGTCTA 59.242 45.833 0.00 0.00 0.00 2.59
136 137 4.757657 TCGCTATGGATCTCTTGAGTCTAC 59.242 45.833 0.00 0.00 0.00 2.59
137 138 4.377943 CGCTATGGATCTCTTGAGTCTACG 60.378 50.000 0.00 0.00 0.00 3.51
138 139 4.614993 GCTATGGATCTCTTGAGTCTACGC 60.615 50.000 0.00 0.00 0.00 4.42
139 140 2.723273 TGGATCTCTTGAGTCTACGCA 58.277 47.619 0.00 0.00 0.00 5.24
140 141 3.291584 TGGATCTCTTGAGTCTACGCAT 58.708 45.455 0.00 0.00 0.00 4.73
141 142 3.067320 TGGATCTCTTGAGTCTACGCATG 59.933 47.826 0.00 0.00 0.00 4.06
142 143 3.551863 GGATCTCTTGAGTCTACGCATGG 60.552 52.174 0.00 0.00 0.00 3.66
143 144 2.447443 TCTCTTGAGTCTACGCATGGT 58.553 47.619 0.00 0.00 0.00 3.55
144 145 2.423892 TCTCTTGAGTCTACGCATGGTC 59.576 50.000 0.00 0.00 0.00 4.02
145 146 2.425312 CTCTTGAGTCTACGCATGGTCT 59.575 50.000 0.00 0.00 0.00 3.85
146 147 2.826128 TCTTGAGTCTACGCATGGTCTT 59.174 45.455 0.00 0.00 0.00 3.01
147 148 2.654749 TGAGTCTACGCATGGTCTTG 57.345 50.000 0.00 0.00 0.00 3.02
148 149 1.893137 TGAGTCTACGCATGGTCTTGT 59.107 47.619 0.00 0.00 0.00 3.16
149 150 2.094700 TGAGTCTACGCATGGTCTTGTC 60.095 50.000 0.00 0.00 0.00 3.18
150 151 1.204941 AGTCTACGCATGGTCTTGTCC 59.795 52.381 0.00 0.00 0.00 4.02
151 152 1.067142 GTCTACGCATGGTCTTGTCCA 60.067 52.381 0.00 0.00 42.01 4.02
153 154 3.028130 TCTACGCATGGTCTTGTCCATA 58.972 45.455 0.00 0.00 45.23 2.74
154 155 2.315925 ACGCATGGTCTTGTCCATAG 57.684 50.000 0.00 1.08 45.23 2.23
155 156 1.831106 ACGCATGGTCTTGTCCATAGA 59.169 47.619 0.00 0.00 45.23 1.98
156 157 2.205074 CGCATGGTCTTGTCCATAGAC 58.795 52.381 0.00 0.00 45.23 2.59
170 171 5.169295 GTCCATAGACATAAATACGGAGGC 58.831 45.833 0.00 0.00 42.99 4.70
171 172 4.836175 TCCATAGACATAAATACGGAGGCA 59.164 41.667 0.00 0.00 0.00 4.75
172 173 5.483937 TCCATAGACATAAATACGGAGGCAT 59.516 40.000 0.00 0.00 0.00 4.40
173 174 5.812642 CCATAGACATAAATACGGAGGCATC 59.187 44.000 0.00 0.00 0.00 3.91
174 175 4.955811 AGACATAAATACGGAGGCATCA 57.044 40.909 0.00 0.00 0.00 3.07
175 176 5.290493 AGACATAAATACGGAGGCATCAA 57.710 39.130 0.00 0.00 0.00 2.57
176 177 5.869579 AGACATAAATACGGAGGCATCAAT 58.130 37.500 0.00 0.00 0.00 2.57
177 178 6.299141 AGACATAAATACGGAGGCATCAATT 58.701 36.000 0.00 0.00 0.00 2.32
178 179 6.428159 AGACATAAATACGGAGGCATCAATTC 59.572 38.462 0.00 0.00 0.00 2.17
179 180 6.061441 ACATAAATACGGAGGCATCAATTCA 58.939 36.000 0.00 0.00 0.00 2.57
180 181 6.545666 ACATAAATACGGAGGCATCAATTCAA 59.454 34.615 0.00 0.00 0.00 2.69
181 182 7.231317 ACATAAATACGGAGGCATCAATTCAAT 59.769 33.333 0.00 0.00 0.00 2.57
182 183 5.695851 AATACGGAGGCATCAATTCAATC 57.304 39.130 0.00 0.00 0.00 2.67
183 184 3.003394 ACGGAGGCATCAATTCAATCA 57.997 42.857 0.00 0.00 0.00 2.57
184 185 2.684881 ACGGAGGCATCAATTCAATCAC 59.315 45.455 0.00 0.00 0.00 3.06
185 186 2.684374 CGGAGGCATCAATTCAATCACA 59.316 45.455 0.00 0.00 0.00 3.58
186 187 3.488047 CGGAGGCATCAATTCAATCACAC 60.488 47.826 0.00 0.00 0.00 3.82
187 188 3.488047 GGAGGCATCAATTCAATCACACG 60.488 47.826 0.00 0.00 0.00 4.49
188 189 2.159338 AGGCATCAATTCAATCACACGC 60.159 45.455 0.00 0.00 0.00 5.34
189 190 2.415759 GGCATCAATTCAATCACACGCA 60.416 45.455 0.00 0.00 0.00 5.24
190 191 3.441163 GCATCAATTCAATCACACGCAT 58.559 40.909 0.00 0.00 0.00 4.73
191 192 3.861113 GCATCAATTCAATCACACGCATT 59.139 39.130 0.00 0.00 0.00 3.56
192 193 4.327898 GCATCAATTCAATCACACGCATTT 59.672 37.500 0.00 0.00 0.00 2.32
193 194 5.163933 GCATCAATTCAATCACACGCATTTT 60.164 36.000 0.00 0.00 0.00 1.82
194 195 6.034790 GCATCAATTCAATCACACGCATTTTA 59.965 34.615 0.00 0.00 0.00 1.52
195 196 7.606131 CATCAATTCAATCACACGCATTTTAG 58.394 34.615 0.00 0.00 0.00 1.85
196 197 6.676950 TCAATTCAATCACACGCATTTTAGT 58.323 32.000 0.00 0.00 0.00 2.24
197 198 6.581919 TCAATTCAATCACACGCATTTTAGTG 59.418 34.615 0.00 0.00 43.46 2.74
198 199 3.820689 TCAATCACACGCATTTTAGTGC 58.179 40.909 0.00 0.00 41.72 4.40
210 211 6.241207 GCATTTTAGTGCGTATATGGATGT 57.759 37.500 0.00 0.00 35.10 3.06
211 212 6.668323 GCATTTTAGTGCGTATATGGATGTT 58.332 36.000 0.00 0.00 35.10 2.71
212 213 7.802738 GCATTTTAGTGCGTATATGGATGTTA 58.197 34.615 0.00 0.00 35.10 2.41
213 214 7.957484 GCATTTTAGTGCGTATATGGATGTTAG 59.043 37.037 0.00 0.00 35.10 2.34
214 215 8.988934 CATTTTAGTGCGTATATGGATGTTAGT 58.011 33.333 0.00 0.00 0.00 2.24
215 216 8.583810 TTTTAGTGCGTATATGGATGTTAGTC 57.416 34.615 0.00 0.00 0.00 2.59
239 240 5.064707 CAGTCTTTTCGGAGAAAAACAGACA 59.935 40.000 19.37 0.00 45.90 3.41
245 246 1.332904 GGAGAAAAACAGACACACGCG 60.333 52.381 3.53 3.53 0.00 6.01
246 247 1.326548 GAGAAAAACAGACACACGCGT 59.673 47.619 5.58 5.58 0.00 6.01
258 268 3.075875 CACGCGTACGAGTGTAACA 57.924 52.632 34.66 0.00 43.93 2.41
259 269 1.397619 CACGCGTACGAGTGTAACAA 58.602 50.000 34.66 0.00 43.93 2.83
272 282 3.248495 TGTAACAAACACTGACGACCA 57.752 42.857 0.00 0.00 31.43 4.02
301 311 1.519408 GTGGCACGTGTAACTCCATT 58.481 50.000 18.38 0.00 32.62 3.16
302 312 1.463444 GTGGCACGTGTAACTCCATTC 59.537 52.381 18.38 1.00 32.62 2.67
303 313 1.084289 GGCACGTGTAACTCCATTCC 58.916 55.000 18.38 1.34 31.75 3.01
304 314 1.609580 GGCACGTGTAACTCCATTCCA 60.610 52.381 18.38 0.00 31.75 3.53
305 315 2.356135 GCACGTGTAACTCCATTCCAT 58.644 47.619 18.38 0.00 31.75 3.41
310 320 3.347216 GTGTAACTCCATTCCATGCACT 58.653 45.455 0.00 0.00 0.00 4.40
320 330 5.246656 TCCATTCCATGCACTGAGAAATTTT 59.753 36.000 0.00 0.00 0.00 1.82
323 333 3.511146 TCCATGCACTGAGAAATTTTCCC 59.489 43.478 5.52 0.00 0.00 3.97
331 341 4.010349 CTGAGAAATTTTCCCTAGCCGTT 58.990 43.478 5.52 0.00 0.00 4.44
354 364 3.586430 AGCAATTTTGGTGAACGCC 57.414 47.368 0.00 0.00 37.53 5.68
370 386 0.179148 CGCCGGAAGCCATTTTTACC 60.179 55.000 5.05 0.00 38.78 2.85
372 388 0.454196 CCGGAAGCCATTTTTACCCG 59.546 55.000 0.00 0.00 35.68 5.28
377 393 1.734163 AGCCATTTTTACCCGAGACG 58.266 50.000 0.00 0.00 0.00 4.18
494 515 2.278206 CGCAGGACTCATCGTCGG 60.278 66.667 0.00 0.00 43.79 4.79
544 565 1.711060 AACGTTCACCGGTGCAACAG 61.711 55.000 31.17 26.84 42.24 3.16
605 2167 3.157680 CAACGGGGACTTCAGGGT 58.842 61.111 0.00 0.00 0.00 4.34
629 2192 1.675641 GGATCCCACAGCACACACC 60.676 63.158 0.00 0.00 0.00 4.16
631 2194 2.731691 GATCCCACAGCACACACCGT 62.732 60.000 0.00 0.00 0.00 4.83
664 2257 1.459450 TAGCTTCCAACCCATTTCGC 58.541 50.000 0.00 0.00 0.00 4.70
694 2287 4.060038 CCACCCGCTCGTAACCGT 62.060 66.667 0.00 0.00 35.01 4.83
695 2288 2.699768 CCACCCGCTCGTAACCGTA 61.700 63.158 0.00 0.00 35.01 4.02
696 2289 1.212490 CACCCGCTCGTAACCGTAA 59.788 57.895 0.00 0.00 35.01 3.18
697 2290 1.072666 CACCCGCTCGTAACCGTAAC 61.073 60.000 0.00 0.00 35.01 2.50
699 2292 1.869132 CCGCTCGTAACCGTAACCG 60.869 63.158 0.00 0.00 35.01 4.44
700 2293 2.499603 CGCTCGTAACCGTAACCGC 61.500 63.158 0.00 0.00 35.01 5.68
701 2294 2.499603 GCTCGTAACCGTAACCGCG 61.500 63.158 0.00 0.00 35.01 6.46
706 2299 0.109504 GTAACCGTAACCGCGTACCA 60.110 55.000 4.92 0.00 0.00 3.25
718 2311 0.595095 GCGTACCACCTAGGATACCG 59.405 60.000 17.98 11.54 41.22 4.02
762 2356 2.126850 TCTGAACTGACGCGAGCG 60.127 61.111 15.93 16.38 46.03 5.03
767 2361 3.493830 AACTGACGCGAGCGGAACA 62.494 57.895 21.69 15.88 44.69 3.18
797 2398 1.485066 ACCCGTAACTATGGAGCAAGG 59.515 52.381 0.00 0.00 34.17 3.61
799 2400 1.139058 CCGTAACTATGGAGCAAGGCT 59.861 52.381 0.00 0.00 43.88 4.58
865 3272 0.848305 GTGTACACGTGACGAACCAC 59.152 55.000 25.01 14.02 0.00 4.16
873 3280 1.372499 TGACGAACCACGCTGCTAC 60.372 57.895 0.00 0.00 46.94 3.58
874 3281 1.080705 GACGAACCACGCTGCTACT 60.081 57.895 0.00 0.00 46.94 2.57
875 3282 0.169672 GACGAACCACGCTGCTACTA 59.830 55.000 0.00 0.00 46.94 1.82
876 3283 0.109412 ACGAACCACGCTGCTACTAC 60.109 55.000 0.00 0.00 46.94 2.73
877 3284 0.170561 CGAACCACGCTGCTACTACT 59.829 55.000 0.00 0.00 34.51 2.57
878 3285 1.399440 CGAACCACGCTGCTACTACTA 59.601 52.381 0.00 0.00 34.51 1.82
909 3318 2.420129 CGCCACTCCACTATAAAAGGCT 60.420 50.000 0.00 0.00 38.71 4.58
913 3322 5.123936 CCACTCCACTATAAAAGGCTAACC 58.876 45.833 0.00 0.00 0.00 2.85
916 3325 4.761975 TCCACTATAAAAGGCTAACCACG 58.238 43.478 0.00 0.00 39.06 4.94
939 3355 0.605319 GAACCGAGCCACATCCACAA 60.605 55.000 0.00 0.00 0.00 3.33
940 3356 0.889186 AACCGAGCCACATCCACAAC 60.889 55.000 0.00 0.00 0.00 3.32
941 3357 2.390599 CCGAGCCACATCCACAACG 61.391 63.158 0.00 0.00 0.00 4.10
942 3358 1.667830 CGAGCCACATCCACAACGT 60.668 57.895 0.00 0.00 0.00 3.99
943 3359 0.389296 CGAGCCACATCCACAACGTA 60.389 55.000 0.00 0.00 0.00 3.57
962 3400 5.416947 ACGTACAAATTCCGAGCTCTTAAT 58.583 37.500 12.85 8.28 0.00 1.40
1015 3499 0.026803 GCAGATGGTTTCGTCGATGC 59.973 55.000 0.00 0.00 34.23 3.91
1016 3500 0.298707 CAGATGGTTTCGTCGATGCG 59.701 55.000 0.00 0.00 34.23 4.73
1025 3512 2.505498 CGTCGATGCGGCAGTACAC 61.505 63.158 9.25 1.58 0.00 2.90
1026 3513 2.202557 TCGATGCGGCAGTACACG 60.203 61.111 9.25 9.05 0.00 4.49
1035 3522 1.218047 GCAGTACACGGATCAGGCA 59.782 57.895 0.00 0.00 0.00 4.75
1194 3693 3.000819 CACCGGACCAGCCACCTA 61.001 66.667 9.46 0.00 35.94 3.08
1250 3752 1.587054 GATACGATCAGCCGGGGAG 59.413 63.158 2.18 0.00 0.00 4.30
1259 3761 1.997874 AGCCGGGGAGCAAGAAGAT 60.998 57.895 2.18 0.00 34.23 2.40
1434 3945 2.820197 GGTGTTCCATTGGTTTCTCTCC 59.180 50.000 1.86 0.00 0.00 3.71
1444 3994 2.507886 TGGTTTCTCTCCAGTTGGTTCA 59.492 45.455 0.00 0.00 36.34 3.18
1460 4012 5.147330 TGGTTCAATATAGGTAGGCATCG 57.853 43.478 0.00 0.00 0.00 3.84
1479 4031 1.403647 CGAGTGCAGATTCACCGGTTA 60.404 52.381 2.97 0.00 37.68 2.85
1513 4077 5.577835 GCGATTGGATTTGTACATTTGCTA 58.422 37.500 0.00 0.00 0.00 3.49
1520 4084 6.264292 TGGATTTGTACATTTGCTACACACTT 59.736 34.615 0.00 0.00 0.00 3.16
1586 4160 6.897259 TGTACATATTTAGGACTTGTTCGC 57.103 37.500 0.00 0.00 0.00 4.70
1599 4173 4.801891 ACTTGTTCGCTCGTTGATTACTA 58.198 39.130 0.00 0.00 0.00 1.82
1694 4271 1.557832 TCCTGATAAACAACTCCCCCG 59.442 52.381 0.00 0.00 0.00 5.73
1695 4272 1.557832 CCTGATAAACAACTCCCCCGA 59.442 52.381 0.00 0.00 0.00 5.14
1799 4515 0.598065 CAAGTGGCTGTACCCAAAGC 59.402 55.000 0.00 0.00 36.46 3.51
1811 4527 0.390209 CCCAAAGCAAAATCCCTGCG 60.390 55.000 0.00 0.00 44.75 5.18
1865 4582 6.313164 GTGTACAGAGCACCTAAAAATCCTAC 59.687 42.308 0.00 0.00 0.00 3.18
1913 4630 8.922931 ATTTGATGTGCATTGTCCTATATACA 57.077 30.769 0.00 0.00 0.00 2.29
1966 4683 5.537188 TGCCAAAATAATGGTTGTTCACTC 58.463 37.500 0.00 0.00 42.75 3.51
1982 4702 4.760530 TCACTCCATCCAAATCCTAGTG 57.239 45.455 0.00 0.00 35.36 2.74
2023 4744 2.870411 GCGTTCACTTGTACACCTTCTT 59.130 45.455 0.00 0.00 0.00 2.52
2102 4823 6.094719 CACAAACATGATCAAATGTGTAGGG 58.905 40.000 18.08 6.46 39.89 3.53
2110 4831 7.353414 TGATCAAATGTGTAGGGTTTTGAAA 57.647 32.000 0.00 0.00 40.36 2.69
2211 4933 5.104527 CCACCTAGATTTGGGTCTTATGTCA 60.105 44.000 0.00 0.00 35.74 3.58
2243 4965 4.752101 CCACAACCAACAAGTTTTGAAACA 59.248 37.500 9.08 0.00 41.30 2.83
2273 4995 9.593565 TTGATATATACTCAGTTGTGGAGAGAT 57.406 33.333 0.00 0.00 36.26 2.75
2289 5012 9.421399 TGTGGAGAGATATTAAAGTCACATAGA 57.579 33.333 0.00 0.00 0.00 1.98
2352 5075 8.378172 TCAAGGTTTTTGTCTAGTGTTGATAG 57.622 34.615 0.00 0.00 0.00 2.08
2359 5082 7.601073 TTTGTCTAGTGTTGATAGATTGCAG 57.399 36.000 0.00 0.00 32.15 4.41
2375 5098 5.829924 AGATTGCAGGTATTTGTAGGAATGG 59.170 40.000 0.00 0.00 0.00 3.16
2394 5117 9.866655 AGGAATGGCATATCTACAAAAGAAATA 57.133 29.630 0.00 0.00 37.89 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.815068 CCCTTTCACGTCATTAATCTCCTATAG 59.185 40.741 0.00 0.00 0.00 1.31
1 2 7.507956 TCCCTTTCACGTCATTAATCTCCTATA 59.492 37.037 0.00 0.00 0.00 1.31
2 3 6.326583 TCCCTTTCACGTCATTAATCTCCTAT 59.673 38.462 0.00 0.00 0.00 2.57
3 4 5.659525 TCCCTTTCACGTCATTAATCTCCTA 59.340 40.000 0.00 0.00 0.00 2.94
4 5 4.469945 TCCCTTTCACGTCATTAATCTCCT 59.530 41.667 0.00 0.00 0.00 3.69
5 6 4.766375 TCCCTTTCACGTCATTAATCTCC 58.234 43.478 0.00 0.00 0.00 3.71
6 7 5.661458 TCTCCCTTTCACGTCATTAATCTC 58.339 41.667 0.00 0.00 0.00 2.75
7 8 5.422331 TCTCTCCCTTTCACGTCATTAATCT 59.578 40.000 0.00 0.00 0.00 2.40
8 9 5.661458 TCTCTCCCTTTCACGTCATTAATC 58.339 41.667 0.00 0.00 0.00 1.75
9 10 5.422331 TCTCTCTCCCTTTCACGTCATTAAT 59.578 40.000 0.00 0.00 0.00 1.40
10 11 4.770531 TCTCTCTCCCTTTCACGTCATTAA 59.229 41.667 0.00 0.00 0.00 1.40
11 12 4.341487 TCTCTCTCCCTTTCACGTCATTA 58.659 43.478 0.00 0.00 0.00 1.90
12 13 3.165875 TCTCTCTCCCTTTCACGTCATT 58.834 45.455 0.00 0.00 0.00 2.57
13 14 2.808919 TCTCTCTCCCTTTCACGTCAT 58.191 47.619 0.00 0.00 0.00 3.06
14 15 2.287977 TCTCTCTCCCTTTCACGTCA 57.712 50.000 0.00 0.00 0.00 4.35
15 16 3.243771 TGTTTCTCTCTCCCTTTCACGTC 60.244 47.826 0.00 0.00 0.00 4.34
16 17 2.698797 TGTTTCTCTCTCCCTTTCACGT 59.301 45.455 0.00 0.00 0.00 4.49
17 18 3.386768 TGTTTCTCTCTCCCTTTCACG 57.613 47.619 0.00 0.00 0.00 4.35
18 19 4.083057 GCAATGTTTCTCTCTCCCTTTCAC 60.083 45.833 0.00 0.00 0.00 3.18
19 20 4.074970 GCAATGTTTCTCTCTCCCTTTCA 58.925 43.478 0.00 0.00 0.00 2.69
20 21 3.126000 CGCAATGTTTCTCTCTCCCTTTC 59.874 47.826 0.00 0.00 0.00 2.62
21 22 3.077359 CGCAATGTTTCTCTCTCCCTTT 58.923 45.455 0.00 0.00 0.00 3.11
22 23 2.039084 ACGCAATGTTTCTCTCTCCCTT 59.961 45.455 0.00 0.00 0.00 3.95
23 24 1.625818 ACGCAATGTTTCTCTCTCCCT 59.374 47.619 0.00 0.00 0.00 4.20
24 25 1.734465 CACGCAATGTTTCTCTCTCCC 59.266 52.381 0.00 0.00 0.00 4.30
25 26 2.413453 GTCACGCAATGTTTCTCTCTCC 59.587 50.000 0.00 0.00 0.00 3.71
26 27 2.413453 GGTCACGCAATGTTTCTCTCTC 59.587 50.000 0.00 0.00 0.00 3.20
27 28 2.037772 AGGTCACGCAATGTTTCTCTCT 59.962 45.455 0.00 0.00 0.00 3.10
28 29 2.413453 GAGGTCACGCAATGTTTCTCTC 59.587 50.000 0.00 0.00 0.00 3.20
29 30 2.037772 AGAGGTCACGCAATGTTTCTCT 59.962 45.455 0.00 0.00 0.00 3.10
30 31 2.158449 CAGAGGTCACGCAATGTTTCTC 59.842 50.000 0.00 0.00 0.00 2.87
31 32 2.146342 CAGAGGTCACGCAATGTTTCT 58.854 47.619 0.00 0.00 0.00 2.52
32 33 1.197721 CCAGAGGTCACGCAATGTTTC 59.802 52.381 0.00 0.00 0.00 2.78
33 34 1.202758 TCCAGAGGTCACGCAATGTTT 60.203 47.619 0.00 0.00 0.00 2.83
34 35 0.396435 TCCAGAGGTCACGCAATGTT 59.604 50.000 0.00 0.00 0.00 2.71
35 36 0.396435 TTCCAGAGGTCACGCAATGT 59.604 50.000 0.00 0.00 0.00 2.71
36 37 0.798776 GTTCCAGAGGTCACGCAATG 59.201 55.000 0.00 0.00 0.00 2.82
37 38 0.396435 TGTTCCAGAGGTCACGCAAT 59.604 50.000 0.00 0.00 0.00 3.56
38 39 0.396435 ATGTTCCAGAGGTCACGCAA 59.604 50.000 0.00 0.00 0.00 4.85
39 40 0.320683 CATGTTCCAGAGGTCACGCA 60.321 55.000 0.00 0.00 0.00 5.24
40 41 1.021390 CCATGTTCCAGAGGTCACGC 61.021 60.000 0.00 0.00 0.00 5.34
41 42 0.608130 TCCATGTTCCAGAGGTCACG 59.392 55.000 0.00 0.00 0.00 4.35
42 43 1.673033 CGTCCATGTTCCAGAGGTCAC 60.673 57.143 0.00 0.00 0.00 3.67
43 44 0.608130 CGTCCATGTTCCAGAGGTCA 59.392 55.000 0.00 0.00 0.00 4.02
44 45 0.608640 ACGTCCATGTTCCAGAGGTC 59.391 55.000 0.00 0.00 0.00 3.85
45 46 0.608640 GACGTCCATGTTCCAGAGGT 59.391 55.000 3.51 0.00 0.00 3.85
46 47 0.608130 TGACGTCCATGTTCCAGAGG 59.392 55.000 14.12 0.00 0.00 3.69
47 48 1.714794 GTGACGTCCATGTTCCAGAG 58.285 55.000 14.12 0.00 0.00 3.35
48 49 0.038618 CGTGACGTCCATGTTCCAGA 60.039 55.000 14.12 0.00 0.00 3.86
49 50 1.626654 GCGTGACGTCCATGTTCCAG 61.627 60.000 14.12 0.00 34.28 3.86
50 51 1.666553 GCGTGACGTCCATGTTCCA 60.667 57.895 14.12 0.00 34.28 3.53
51 52 1.352156 GAGCGTGACGTCCATGTTCC 61.352 60.000 14.12 0.00 36.41 3.62
52 53 0.388649 AGAGCGTGACGTCCATGTTC 60.389 55.000 14.12 13.17 40.86 3.18
53 54 0.885879 TAGAGCGTGACGTCCATGTT 59.114 50.000 14.12 4.77 34.28 2.71
54 55 0.452184 CTAGAGCGTGACGTCCATGT 59.548 55.000 14.12 0.00 34.28 3.21
55 56 0.867753 GCTAGAGCGTGACGTCCATG 60.868 60.000 14.12 7.88 34.90 3.66
56 57 1.433879 GCTAGAGCGTGACGTCCAT 59.566 57.895 14.12 0.00 0.00 3.41
57 58 2.697761 GGCTAGAGCGTGACGTCCA 61.698 63.158 14.12 0.00 43.26 4.02
58 59 1.935327 AAGGCTAGAGCGTGACGTCC 61.935 60.000 14.12 3.43 43.26 4.79
59 60 0.731417 TAAGGCTAGAGCGTGACGTC 59.269 55.000 9.11 9.11 43.26 4.34
60 61 0.450983 GTAAGGCTAGAGCGTGACGT 59.549 55.000 6.91 0.00 43.26 4.34
61 62 0.248539 GGTAAGGCTAGAGCGTGACG 60.249 60.000 0.00 0.00 40.31 4.35
62 63 0.102663 GGGTAAGGCTAGAGCGTGAC 59.897 60.000 3.49 3.49 43.26 3.67
63 64 0.323999 TGGGTAAGGCTAGAGCGTGA 60.324 55.000 0.00 0.00 43.26 4.35
64 65 0.535335 TTGGGTAAGGCTAGAGCGTG 59.465 55.000 0.00 0.00 43.26 5.34
65 66 1.207329 CTTTGGGTAAGGCTAGAGCGT 59.793 52.381 0.00 0.00 43.26 5.07
66 67 1.480954 TCTTTGGGTAAGGCTAGAGCG 59.519 52.381 0.00 0.00 43.26 5.03
67 68 3.847671 ATCTTTGGGTAAGGCTAGAGC 57.152 47.619 0.00 0.00 41.14 4.09
68 69 6.098409 TCACTTATCTTTGGGTAAGGCTAGAG 59.902 42.308 0.00 0.00 34.46 2.43
69 70 5.962031 TCACTTATCTTTGGGTAAGGCTAGA 59.038 40.000 0.00 0.00 34.46 2.43
70 71 6.049790 GTCACTTATCTTTGGGTAAGGCTAG 58.950 44.000 0.00 0.00 34.46 3.42
71 72 5.724854 AGTCACTTATCTTTGGGTAAGGCTA 59.275 40.000 0.00 0.00 34.46 3.93
72 73 4.536489 AGTCACTTATCTTTGGGTAAGGCT 59.464 41.667 0.00 0.00 34.46 4.58
73 74 4.844884 AGTCACTTATCTTTGGGTAAGGC 58.155 43.478 0.00 0.00 34.46 4.35
74 75 5.648092 CCAAGTCACTTATCTTTGGGTAAGG 59.352 44.000 0.00 0.00 34.46 2.69
75 76 6.472887 TCCAAGTCACTTATCTTTGGGTAAG 58.527 40.000 0.00 0.00 34.78 2.34
76 77 6.442541 TCCAAGTCACTTATCTTTGGGTAA 57.557 37.500 0.00 0.00 0.00 2.85
77 78 6.629515 CGATCCAAGTCACTTATCTTTGGGTA 60.630 42.308 0.00 0.00 0.00 3.69
78 79 4.993705 TCCAAGTCACTTATCTTTGGGT 57.006 40.909 0.00 0.00 0.00 4.51
79 80 4.572389 CGATCCAAGTCACTTATCTTTGGG 59.428 45.833 0.00 0.00 0.00 4.12
80 81 4.572389 CCGATCCAAGTCACTTATCTTTGG 59.428 45.833 0.00 0.00 0.00 3.28
81 82 4.034510 GCCGATCCAAGTCACTTATCTTTG 59.965 45.833 0.00 0.00 0.00 2.77
82 83 4.192317 GCCGATCCAAGTCACTTATCTTT 58.808 43.478 0.00 0.00 0.00 2.52
83 84 3.432326 GGCCGATCCAAGTCACTTATCTT 60.432 47.826 0.00 0.00 34.01 2.40
84 85 2.103263 GGCCGATCCAAGTCACTTATCT 59.897 50.000 0.00 0.00 34.01 1.98
85 86 2.484889 GGCCGATCCAAGTCACTTATC 58.515 52.381 0.00 0.00 34.01 1.75
86 87 1.202533 CGGCCGATCCAAGTCACTTAT 60.203 52.381 24.07 0.00 34.01 1.73
87 88 0.174845 CGGCCGATCCAAGTCACTTA 59.825 55.000 24.07 0.00 34.01 2.24
88 89 1.079127 CGGCCGATCCAAGTCACTT 60.079 57.895 24.07 0.00 34.01 3.16
89 90 2.579201 CGGCCGATCCAAGTCACT 59.421 61.111 24.07 0.00 34.01 3.41
90 91 2.511600 CCGGCCGATCCAAGTCAC 60.512 66.667 30.73 0.00 34.01 3.67
91 92 4.467084 GCCGGCCGATCCAAGTCA 62.467 66.667 30.73 0.00 34.01 3.41
108 109 0.869068 AGAGATCCATAGCGACGACG 59.131 55.000 2.12 2.12 42.93 5.12
109 110 2.290916 TCAAGAGATCCATAGCGACGAC 59.709 50.000 0.00 0.00 0.00 4.34
110 111 2.550180 CTCAAGAGATCCATAGCGACGA 59.450 50.000 0.00 0.00 0.00 4.20
111 112 2.292016 ACTCAAGAGATCCATAGCGACG 59.708 50.000 3.73 0.00 0.00 5.12
112 113 3.568007 AGACTCAAGAGATCCATAGCGAC 59.432 47.826 3.73 0.00 0.00 5.19
113 114 3.826524 AGACTCAAGAGATCCATAGCGA 58.173 45.455 3.73 0.00 0.00 4.93
114 115 4.377943 CGTAGACTCAAGAGATCCATAGCG 60.378 50.000 3.73 0.00 0.00 4.26
115 116 4.614993 GCGTAGACTCAAGAGATCCATAGC 60.615 50.000 3.73 0.00 0.00 2.97
116 117 4.517075 TGCGTAGACTCAAGAGATCCATAG 59.483 45.833 3.73 0.00 0.00 2.23
117 118 4.461198 TGCGTAGACTCAAGAGATCCATA 58.539 43.478 3.73 0.00 0.00 2.74
118 119 3.291584 TGCGTAGACTCAAGAGATCCAT 58.708 45.455 3.73 0.00 0.00 3.41
119 120 2.723273 TGCGTAGACTCAAGAGATCCA 58.277 47.619 3.73 0.00 0.00 3.41
120 121 3.551863 CCATGCGTAGACTCAAGAGATCC 60.552 52.174 3.73 0.00 0.00 3.36
121 122 3.067461 ACCATGCGTAGACTCAAGAGATC 59.933 47.826 3.73 0.00 0.00 2.75
122 123 3.027412 ACCATGCGTAGACTCAAGAGAT 58.973 45.455 3.73 0.00 0.00 2.75
123 124 2.423892 GACCATGCGTAGACTCAAGAGA 59.576 50.000 3.73 0.00 0.00 3.10
124 125 2.425312 AGACCATGCGTAGACTCAAGAG 59.575 50.000 0.00 0.00 0.00 2.85
125 126 2.447443 AGACCATGCGTAGACTCAAGA 58.553 47.619 0.00 0.00 0.00 3.02
126 127 2.926200 CAAGACCATGCGTAGACTCAAG 59.074 50.000 0.00 0.00 0.00 3.02
127 128 2.299013 ACAAGACCATGCGTAGACTCAA 59.701 45.455 0.00 0.00 0.00 3.02
128 129 1.893137 ACAAGACCATGCGTAGACTCA 59.107 47.619 0.00 0.00 0.00 3.41
129 130 2.531206 GACAAGACCATGCGTAGACTC 58.469 52.381 0.00 0.00 0.00 3.36
130 131 1.204941 GGACAAGACCATGCGTAGACT 59.795 52.381 0.00 0.00 0.00 3.24
131 132 1.067142 TGGACAAGACCATGCGTAGAC 60.067 52.381 0.00 0.00 34.77 2.59
132 133 1.262417 TGGACAAGACCATGCGTAGA 58.738 50.000 0.00 0.00 34.77 2.59
133 134 3.832704 TGGACAAGACCATGCGTAG 57.167 52.632 0.00 0.00 34.77 3.51
147 148 5.169295 GCCTCCGTATTTATGTCTATGGAC 58.831 45.833 1.56 1.56 42.42 4.02
148 149 4.836175 TGCCTCCGTATTTATGTCTATGGA 59.164 41.667 0.00 0.00 33.15 3.41
149 150 5.147330 TGCCTCCGTATTTATGTCTATGG 57.853 43.478 0.00 0.00 0.00 2.74
150 151 6.398095 TGATGCCTCCGTATTTATGTCTATG 58.602 40.000 0.00 0.00 0.00 2.23
151 152 6.605471 TGATGCCTCCGTATTTATGTCTAT 57.395 37.500 0.00 0.00 0.00 1.98
152 153 6.413783 TTGATGCCTCCGTATTTATGTCTA 57.586 37.500 0.00 0.00 0.00 2.59
153 154 4.955811 TGATGCCTCCGTATTTATGTCT 57.044 40.909 0.00 0.00 0.00 3.41
154 155 6.204688 TGAATTGATGCCTCCGTATTTATGTC 59.795 38.462 0.00 0.00 0.00 3.06
155 156 6.061441 TGAATTGATGCCTCCGTATTTATGT 58.939 36.000 0.00 0.00 0.00 2.29
156 157 6.558771 TGAATTGATGCCTCCGTATTTATG 57.441 37.500 0.00 0.00 0.00 1.90
157 158 7.448161 TGATTGAATTGATGCCTCCGTATTTAT 59.552 33.333 0.00 0.00 0.00 1.40
158 159 6.770303 TGATTGAATTGATGCCTCCGTATTTA 59.230 34.615 0.00 0.00 0.00 1.40
159 160 5.593909 TGATTGAATTGATGCCTCCGTATTT 59.406 36.000 0.00 0.00 0.00 1.40
160 161 5.009010 GTGATTGAATTGATGCCTCCGTATT 59.991 40.000 0.00 0.00 0.00 1.89
161 162 4.516698 GTGATTGAATTGATGCCTCCGTAT 59.483 41.667 0.00 0.00 0.00 3.06
162 163 3.876914 GTGATTGAATTGATGCCTCCGTA 59.123 43.478 0.00 0.00 0.00 4.02
163 164 2.684881 GTGATTGAATTGATGCCTCCGT 59.315 45.455 0.00 0.00 0.00 4.69
164 165 2.684374 TGTGATTGAATTGATGCCTCCG 59.316 45.455 0.00 0.00 0.00 4.63
165 166 3.488047 CGTGTGATTGAATTGATGCCTCC 60.488 47.826 0.00 0.00 0.00 4.30
166 167 3.688272 CGTGTGATTGAATTGATGCCTC 58.312 45.455 0.00 0.00 0.00 4.70
167 168 2.159338 GCGTGTGATTGAATTGATGCCT 60.159 45.455 0.00 0.00 0.00 4.75
168 169 2.187707 GCGTGTGATTGAATTGATGCC 58.812 47.619 0.00 0.00 0.00 4.40
169 170 2.866198 TGCGTGTGATTGAATTGATGC 58.134 42.857 0.00 0.00 0.00 3.91
170 171 6.397831 AAAATGCGTGTGATTGAATTGATG 57.602 33.333 0.00 0.00 0.00 3.07
171 172 7.274033 CACTAAAATGCGTGTGATTGAATTGAT 59.726 33.333 0.00 0.00 32.72 2.57
172 173 6.581919 CACTAAAATGCGTGTGATTGAATTGA 59.418 34.615 0.00 0.00 32.72 2.57
173 174 6.668090 GCACTAAAATGCGTGTGATTGAATTG 60.668 38.462 0.00 0.00 35.50 2.32
174 175 5.345741 GCACTAAAATGCGTGTGATTGAATT 59.654 36.000 0.00 0.00 35.50 2.17
175 176 4.858692 GCACTAAAATGCGTGTGATTGAAT 59.141 37.500 0.00 0.00 35.50 2.57
176 177 4.225984 GCACTAAAATGCGTGTGATTGAA 58.774 39.130 0.00 0.00 35.50 2.69
177 178 3.820689 GCACTAAAATGCGTGTGATTGA 58.179 40.909 0.00 0.00 35.50 2.57
187 188 6.241207 ACATCCATATACGCACTAAAATGC 57.759 37.500 0.00 0.00 42.48 3.56
188 189 8.988934 ACTAACATCCATATACGCACTAAAATG 58.011 33.333 0.00 0.00 0.00 2.32
189 190 9.204570 GACTAACATCCATATACGCACTAAAAT 57.795 33.333 0.00 0.00 0.00 1.82
190 191 8.198778 TGACTAACATCCATATACGCACTAAAA 58.801 33.333 0.00 0.00 0.00 1.52
191 192 7.718525 TGACTAACATCCATATACGCACTAAA 58.281 34.615 0.00 0.00 0.00 1.85
192 193 7.013942 ACTGACTAACATCCATATACGCACTAA 59.986 37.037 0.00 0.00 0.00 2.24
193 194 6.489022 ACTGACTAACATCCATATACGCACTA 59.511 38.462 0.00 0.00 0.00 2.74
194 195 5.302059 ACTGACTAACATCCATATACGCACT 59.698 40.000 0.00 0.00 0.00 4.40
195 196 5.529791 ACTGACTAACATCCATATACGCAC 58.470 41.667 0.00 0.00 0.00 5.34
196 197 5.535030 AGACTGACTAACATCCATATACGCA 59.465 40.000 0.00 0.00 0.00 5.24
197 198 6.015027 AGACTGACTAACATCCATATACGC 57.985 41.667 0.00 0.00 0.00 4.42
198 199 8.873215 AAAAGACTGACTAACATCCATATACG 57.127 34.615 0.00 0.00 0.00 3.06
199 200 8.969267 CGAAAAGACTGACTAACATCCATATAC 58.031 37.037 0.00 0.00 0.00 1.47
200 201 8.141909 CCGAAAAGACTGACTAACATCCATATA 58.858 37.037 0.00 0.00 0.00 0.86
201 202 6.986817 CCGAAAAGACTGACTAACATCCATAT 59.013 38.462 0.00 0.00 0.00 1.78
202 203 6.153851 TCCGAAAAGACTGACTAACATCCATA 59.846 38.462 0.00 0.00 0.00 2.74
203 204 5.046591 TCCGAAAAGACTGACTAACATCCAT 60.047 40.000 0.00 0.00 0.00 3.41
204 205 4.282449 TCCGAAAAGACTGACTAACATCCA 59.718 41.667 0.00 0.00 0.00 3.41
205 206 4.817517 TCCGAAAAGACTGACTAACATCC 58.182 43.478 0.00 0.00 0.00 3.51
206 207 5.710984 TCTCCGAAAAGACTGACTAACATC 58.289 41.667 0.00 0.00 0.00 3.06
207 208 5.723672 TCTCCGAAAAGACTGACTAACAT 57.276 39.130 0.00 0.00 0.00 2.71
208 209 5.524971 TTCTCCGAAAAGACTGACTAACA 57.475 39.130 0.00 0.00 0.00 2.41
209 210 6.839820 TTTTCTCCGAAAAGACTGACTAAC 57.160 37.500 0.00 0.00 0.00 2.34
210 211 6.819649 TGTTTTTCTCCGAAAAGACTGACTAA 59.180 34.615 2.53 0.00 0.00 2.24
211 212 6.342906 TGTTTTTCTCCGAAAAGACTGACTA 58.657 36.000 2.53 0.00 0.00 2.59
212 213 5.183228 TGTTTTTCTCCGAAAAGACTGACT 58.817 37.500 2.53 0.00 0.00 3.41
213 214 5.293569 TCTGTTTTTCTCCGAAAAGACTGAC 59.706 40.000 2.53 0.00 31.11 3.51
214 215 5.293569 GTCTGTTTTTCTCCGAAAAGACTGA 59.706 40.000 10.27 11.91 32.54 3.41
215 216 5.064707 TGTCTGTTTTTCTCCGAAAAGACTG 59.935 40.000 15.19 12.86 30.86 3.51
239 240 0.307453 TGTTACACTCGTACGCGTGT 59.693 50.000 36.79 36.79 44.74 4.49
271 281 4.505217 GTGCCACGCGCTCGATTG 62.505 66.667 5.73 0.00 39.41 2.67
289 299 3.127548 CAGTGCATGGAATGGAGTTACAC 59.872 47.826 6.78 0.00 46.95 2.90
301 311 3.511146 GGGAAAATTTCTCAGTGCATGGA 59.489 43.478 5.65 0.00 0.00 3.41
302 312 3.512724 AGGGAAAATTTCTCAGTGCATGG 59.487 43.478 8.45 0.00 30.58 3.66
303 313 4.796038 AGGGAAAATTTCTCAGTGCATG 57.204 40.909 8.45 0.00 30.58 4.06
304 314 4.400567 GCTAGGGAAAATTTCTCAGTGCAT 59.599 41.667 8.45 0.00 30.58 3.96
305 315 3.758554 GCTAGGGAAAATTTCTCAGTGCA 59.241 43.478 8.45 0.00 30.58 4.57
310 320 3.713826 ACGGCTAGGGAAAATTTCTCA 57.286 42.857 8.45 0.00 30.58 3.27
320 330 2.662596 CTGCACAACGGCTAGGGA 59.337 61.111 0.00 0.00 34.04 4.20
331 341 2.548875 GTTCACCAAAATTGCTGCACA 58.451 42.857 0.00 0.00 0.00 4.57
354 364 1.400494 CTCGGGTAAAAATGGCTTCCG 59.600 52.381 0.00 0.00 37.61 4.30
370 386 2.077627 TGTTCTCTTCTCTCGTCTCGG 58.922 52.381 0.00 0.00 0.00 4.63
372 388 3.340034 TCCTGTTCTCTTCTCTCGTCTC 58.660 50.000 0.00 0.00 0.00 3.36
377 393 3.509575 TCTTGCTCCTGTTCTCTTCTCTC 59.490 47.826 0.00 0.00 0.00 3.20
516 537 1.003223 CCGGTGAACGTTCTTTTGACC 60.003 52.381 27.32 23.08 42.24 4.02
544 565 2.550606 TCAGTGTTCGTTGGGTATTTGC 59.449 45.455 0.00 0.00 0.00 3.68
594 2150 1.003718 CCGGACAACCCTGAAGTCC 60.004 63.158 0.00 0.00 46.48 3.85
595 2151 0.613777 ATCCGGACAACCCTGAAGTC 59.386 55.000 6.12 0.00 31.71 3.01
597 2153 0.107654 GGATCCGGACAACCCTGAAG 60.108 60.000 6.12 0.00 31.71 3.02
605 2167 2.220586 TGCTGTGGGATCCGGACAA 61.221 57.895 6.12 0.98 0.00 3.18
676 2269 4.807039 CGGTTACGAGCGGGTGGG 62.807 72.222 0.00 0.00 44.60 4.61
694 2287 0.034574 TCCTAGGTGGTACGCGGTTA 60.035 55.000 12.47 0.00 41.51 2.85
695 2288 0.685458 ATCCTAGGTGGTACGCGGTT 60.685 55.000 12.47 0.00 41.51 4.44
696 2289 0.183492 TATCCTAGGTGGTACGCGGT 59.817 55.000 12.47 0.00 41.51 5.68
697 2290 0.595095 GTATCCTAGGTGGTACGCGG 59.405 60.000 12.47 0.00 41.51 6.46
699 2292 0.595095 CGGTATCCTAGGTGGTACGC 59.405 60.000 9.08 4.92 37.07 4.42
700 2293 2.149578 CTCGGTATCCTAGGTGGTACG 58.850 57.143 9.08 8.76 37.07 3.67
701 2294 2.107204 TCCTCGGTATCCTAGGTGGTAC 59.893 54.545 9.08 10.34 37.68 3.34
706 2299 1.217183 TGCTTCCTCGGTATCCTAGGT 59.783 52.381 9.08 0.00 37.68 3.08
718 2311 1.002868 TCAGCCTGCTTGCTTCCTC 60.003 57.895 0.00 0.00 40.32 3.71
767 2361 5.484998 TCCATAGTTACGGGTAGAACCTTTT 59.515 40.000 0.00 0.00 38.64 2.27
828 3235 1.569493 CCACGTTTGGCTTGACGAG 59.431 57.895 13.10 6.60 41.53 4.18
873 3280 3.130227 GCGGGGACTGGCTAGTAG 58.870 66.667 1.28 0.00 37.25 2.57
909 3318 1.017177 GCTCGGTTCATGCGTGGTTA 61.017 55.000 5.98 0.00 0.00 2.85
913 3322 2.741985 TGGCTCGGTTCATGCGTG 60.742 61.111 0.00 0.00 0.00 5.34
916 3325 1.718757 GGATGTGGCTCGGTTCATGC 61.719 60.000 0.00 0.00 0.00 4.06
939 3355 3.314541 AAGAGCTCGGAATTTGTACGT 57.685 42.857 8.37 0.00 0.00 3.57
940 3356 5.968387 ATTAAGAGCTCGGAATTTGTACG 57.032 39.130 8.37 0.00 0.00 3.67
941 3357 7.277981 TGAGAATTAAGAGCTCGGAATTTGTAC 59.722 37.037 22.15 13.53 0.00 2.90
942 3358 7.327975 TGAGAATTAAGAGCTCGGAATTTGTA 58.672 34.615 22.15 12.85 0.00 2.41
943 3359 6.173339 TGAGAATTAAGAGCTCGGAATTTGT 58.827 36.000 22.15 15.71 0.00 2.83
962 3400 3.181486 CGAAACGATGGAGGAGATGAGAA 60.181 47.826 0.00 0.00 0.00 2.87
995 3478 1.645034 CATCGACGAAACCATCTGCT 58.355 50.000 0.00 0.00 0.00 4.24
1015 3499 1.226974 CCTGATCCGTGTACTGCCG 60.227 63.158 0.00 0.00 0.00 5.69
1016 3500 1.521681 GCCTGATCCGTGTACTGCC 60.522 63.158 0.00 0.00 0.00 4.85
1250 3752 1.005340 CTGCTCCGTGATCTTCTTGC 58.995 55.000 0.00 0.00 0.00 4.01
1259 3761 2.659016 CCTGCTTCTGCTCCGTGA 59.341 61.111 0.00 0.00 40.48 4.35
1415 3923 3.138283 ACTGGAGAGAAACCAATGGAACA 59.862 43.478 6.16 0.00 36.95 3.18
1434 3945 5.680619 TGCCTACCTATATTGAACCAACTG 58.319 41.667 0.00 0.00 0.00 3.16
1460 4012 2.380084 TAACCGGTGAATCTGCACTC 57.620 50.000 8.52 0.00 38.78 3.51
1474 4026 2.554272 GCGCACACAGGTTAACCG 59.446 61.111 18.91 15.50 42.08 4.44
1479 4031 2.616330 CCAATCGCGCACACAGGTT 61.616 57.895 8.75 0.00 0.00 3.50
1520 4084 3.181464 TGAACCAACGATCAACACCTACA 60.181 43.478 0.00 0.00 0.00 2.74
1718 4296 4.157840 AGACCCTCTTTCAACAACAACAAC 59.842 41.667 0.00 0.00 0.00 3.32
1721 4299 4.983671 AAGACCCTCTTTCAACAACAAC 57.016 40.909 0.00 0.00 31.57 3.32
1722 4300 5.013547 TCAAAGACCCTCTTTCAACAACAA 58.986 37.500 0.00 0.00 42.60 2.83
1723 4301 4.398044 GTCAAAGACCCTCTTTCAACAACA 59.602 41.667 0.00 0.00 42.60 3.33
1724 4302 4.640647 AGTCAAAGACCCTCTTTCAACAAC 59.359 41.667 0.00 0.00 42.60 3.32
1725 4303 4.855340 AGTCAAAGACCCTCTTTCAACAA 58.145 39.130 0.00 0.00 42.60 2.83
1726 4304 4.164221 AGAGTCAAAGACCCTCTTTCAACA 59.836 41.667 0.00 0.00 42.60 3.33
1727 4305 4.513318 CAGAGTCAAAGACCCTCTTTCAAC 59.487 45.833 0.00 0.00 42.60 3.18
1799 4515 1.508088 GCCACTCGCAGGGATTTTG 59.492 57.895 0.00 0.00 37.47 2.44
1820 4536 3.446570 ATTCTTGCGCTGCTGGCC 61.447 61.111 9.73 0.00 37.74 5.36
1830 4546 1.740025 GCTCTGTACACCCATTCTTGC 59.260 52.381 0.00 0.00 0.00 4.01
1865 4582 8.687824 AATAAATGAGGAAATGTGCGTAAAAG 57.312 30.769 0.00 0.00 0.00 2.27
1931 4648 8.689972 ACCATTATTTTGGCAAACATTTTGAAA 58.310 25.926 13.10 0.00 40.68 2.69
1966 4683 4.503991 GGAGCTACACTAGGATTTGGATGG 60.504 50.000 0.00 0.00 0.00 3.51
2050 4771 3.710724 TCATCAAATGAAGGCCCATGAA 58.289 40.909 0.00 0.00 36.11 2.57
2211 4933 1.032014 GTTGGTTGTGGTGAGTGCAT 58.968 50.000 0.00 0.00 0.00 3.96
2261 4983 8.723942 ATGTGACTTTAATATCTCTCCACAAC 57.276 34.615 0.00 0.00 35.93 3.32
2263 4985 9.421399 TCTATGTGACTTTAATATCTCTCCACA 57.579 33.333 0.00 0.00 36.61 4.17
2270 4992 9.078990 TCGATGGTCTATGTGACTTTAATATCT 57.921 33.333 0.00 0.00 44.74 1.98
2273 4995 8.135529 CAGTCGATGGTCTATGTGACTTTAATA 58.864 37.037 0.00 0.00 44.74 0.98
2292 5015 0.107993 CATGAGCCACACCAGTCGAT 60.108 55.000 0.00 0.00 0.00 3.59
2352 5075 5.507985 GCCATTCCTACAAATACCTGCAATC 60.508 44.000 0.00 0.00 0.00 2.67
2359 5082 8.100791 TGTAGATATGCCATTCCTACAAATACC 58.899 37.037 13.18 0.00 37.39 2.73


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

AutoCloner maintained by Alex Coulton.