Multiple sequence alignment - TraesCS2D01G309300

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 TraesCS2D01G309300 chr2D 100.000 3799 0 0 1 3799 396665609 396661811 0.000000e+00 7016
1 TraesCS2D01G309300 chr2D 97.872 188 4 0 1 188 571922243 571922430 3.660000e-85 326
2 TraesCS2D01G309300 chr2A 97.399 2422 51 6 189 2601 534628950 534626532 0.000000e+00 4113
3 TraesCS2D01G309300 chr2A 92.165 1136 27 9 2664 3799 534626256 534625183 0.000000e+00 1548
4 TraesCS2D01G309300 chr2B 96.652 1374 31 6 189 1558 470062986 470061624 0.000000e+00 2268
5 TraesCS2D01G309300 chr2B 92.979 1054 64 6 1557 2601 470061522 470060470 0.000000e+00 1528
6 TraesCS2D01G309300 chr2B 90.000 580 20 18 2664 3242 470060226 470059684 0.000000e+00 715
7 TraesCS2D01G309300 chr2B 91.585 511 32 4 3289 3799 470059586 470059087 0.000000e+00 695
8 TraesCS2D01G309300 chr6B 85.383 431 56 4 2212 2641 356796099 356795675 1.250000e-119 440
9 TraesCS2D01G309300 chr6B 96.373 193 7 0 1 193 461969371 461969179 6.120000e-83 318
10 TraesCS2D01G309300 chr3A 85.151 431 57 4 2212 2641 293042622 293042198 5.830000e-118 435
11 TraesCS2D01G309300 chr4D 99.465 187 1 0 1 187 10009492 10009306 1.310000e-89 340
12 TraesCS2D01G309300 chr4D 97.354 189 5 0 1 189 306791092 306790904 4.730000e-84 322
13 TraesCS2D01G309300 chr3D 98.387 186 3 0 1 186 588824954 588824769 1.020000e-85 327
14 TraesCS2D01G309300 chr3D 96.429 196 6 1 1 195 140418948 140418753 4.730000e-84 322
15 TraesCS2D01G309300 chr3B 97.872 188 4 0 1 188 822830689 822830876 3.660000e-85 326
16 TraesCS2D01G309300 chr5D 97.861 187 4 0 1 187 560922044 560921858 1.320000e-84 324
17 TraesCS2D01G309300 chr6D 97.861 187 3 1 2 188 13730895 13731080 4.730000e-84 322
18 TraesCS2D01G309300 chr1B 80.896 424 48 10 2241 2661 10841076 10840683 1.710000e-78 303


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 TraesCS2D01G309300 chr2D 396661811 396665609 3798 True 7016.0 7016 100.000 1 3799 1 chr2D.!!$R1 3798
1 TraesCS2D01G309300 chr2A 534625183 534628950 3767 True 2830.5 4113 94.782 189 3799 2 chr2A.!!$R1 3610
2 TraesCS2D01G309300 chr2B 470059087 470062986 3899 True 1301.5 2268 92.804 189 3799 4 chr2B.!!$R1 3610

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
73 74 0.036010 AGAGGTTGCGAAGATGGTGG 60.036 55.000 0.00 0.0 0.00 4.61 F
78 79 0.597568 TTGCGAAGATGGTGGCTTTG 59.402 50.000 0.00 0.0 0.00 2.77 F
81 82 0.804989 CGAAGATGGTGGCTTTGGTC 59.195 55.000 0.00 0.0 0.00 4.02 F
143 144 0.931702 TAAATTGGCCGTACGCATCG 59.068 50.000 10.49 0.0 40.31 3.84 F
180 181 0.981943 GGGGTCTTCCTCCTTTTCGA 59.018 55.000 0.00 0.0 35.33 3.71 F
181 182 1.350019 GGGGTCTTCCTCCTTTTCGAA 59.650 52.381 0.00 0.0 35.33 3.71 F
2204 2314 1.810030 CTCCTACTCCGCGCAAACC 60.810 63.158 8.75 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1506 0.587242 CGCGCTGATGAACAAATCGG 60.587 55.000 5.56 0.0 36.23 4.18 R
1740 1850 3.328382 ACGAAGTTATGCCAGTTGCTA 57.672 42.857 0.00 0.0 37.78 3.49 R
1926 2036 4.328983 CCTGTATTACTAAACCACGTGCTG 59.671 45.833 10.91 0.0 0.00 4.41 R
1993 2103 4.780815 TCTTGCACCTCCATAGTATTTGG 58.219 43.478 0.00 0.0 35.45 3.28 R
2191 2301 0.039527 GATTTTGGTTTGCGCGGAGT 60.040 50.000 8.83 0.0 0.00 3.85 R
2349 2460 3.999663 GCTGTGCTCATCTTTCTACAAGT 59.000 43.478 0.00 0.0 0.00 3.16 R
3042 3394 0.179073 CGATGGTTAGCTGGAGGGTG 60.179 60.000 0.00 0.0 0.00 4.61 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 4.810191 GGTATTAGGCCCAGACTATCAG 57.190 50.000 0.00 0.00 0.00 2.90
22 23 3.055747 GGTATTAGGCCCAGACTATCAGC 60.056 52.174 0.00 0.00 0.00 4.26
23 24 1.040646 TTAGGCCCAGACTATCAGCG 58.959 55.000 0.00 0.00 0.00 5.18
24 25 1.464376 TAGGCCCAGACTATCAGCGC 61.464 60.000 0.00 0.00 0.00 5.92
25 26 2.280457 GCCCAGACTATCAGCGCC 60.280 66.667 2.29 0.00 0.00 6.53
26 27 2.423446 CCCAGACTATCAGCGCCC 59.577 66.667 2.29 0.00 0.00 6.13
27 28 2.423446 CCAGACTATCAGCGCCCC 59.577 66.667 2.29 0.00 0.00 5.80
28 29 2.136878 CCAGACTATCAGCGCCCCT 61.137 63.158 2.29 0.00 0.00 4.79
29 30 1.690219 CCAGACTATCAGCGCCCCTT 61.690 60.000 2.29 0.00 0.00 3.95
30 31 0.249657 CAGACTATCAGCGCCCCTTC 60.250 60.000 2.29 0.00 0.00 3.46
31 32 0.687757 AGACTATCAGCGCCCCTTCA 60.688 55.000 2.29 0.00 0.00 3.02
32 33 0.394565 GACTATCAGCGCCCCTTCAT 59.605 55.000 2.29 0.00 0.00 2.57
33 34 0.394565 ACTATCAGCGCCCCTTCATC 59.605 55.000 2.29 0.00 0.00 2.92
34 35 0.394192 CTATCAGCGCCCCTTCATCA 59.606 55.000 2.29 0.00 0.00 3.07
35 36 0.394192 TATCAGCGCCCCTTCATCAG 59.606 55.000 2.29 0.00 0.00 2.90
36 37 1.630126 ATCAGCGCCCCTTCATCAGT 61.630 55.000 2.29 0.00 0.00 3.41
37 38 1.377725 CAGCGCCCCTTCATCAGTT 60.378 57.895 2.29 0.00 0.00 3.16
38 39 0.107703 CAGCGCCCCTTCATCAGTTA 60.108 55.000 2.29 0.00 0.00 2.24
39 40 0.179000 AGCGCCCCTTCATCAGTTAG 59.821 55.000 2.29 0.00 0.00 2.34
40 41 0.178068 GCGCCCCTTCATCAGTTAGA 59.822 55.000 0.00 0.00 0.00 2.10
41 42 1.202698 GCGCCCCTTCATCAGTTAGAT 60.203 52.381 0.00 0.00 37.48 1.98
42 43 2.037251 GCGCCCCTTCATCAGTTAGATA 59.963 50.000 0.00 0.00 34.43 1.98
43 44 3.862642 GCGCCCCTTCATCAGTTAGATAG 60.863 52.174 0.00 0.00 34.43 2.08
44 45 3.306364 CGCCCCTTCATCAGTTAGATAGG 60.306 52.174 0.00 0.00 34.43 2.57
45 46 3.904339 GCCCCTTCATCAGTTAGATAGGA 59.096 47.826 0.00 0.00 35.35 2.94
46 47 4.020662 GCCCCTTCATCAGTTAGATAGGAG 60.021 50.000 0.00 0.00 35.35 3.69
47 48 5.151454 CCCCTTCATCAGTTAGATAGGAGT 58.849 45.833 0.00 0.00 35.35 3.85
48 49 6.315714 CCCCTTCATCAGTTAGATAGGAGTA 58.684 44.000 0.00 0.00 35.35 2.59
49 50 6.435904 CCCCTTCATCAGTTAGATAGGAGTAG 59.564 46.154 0.00 0.00 35.35 2.57
50 51 6.071616 CCCTTCATCAGTTAGATAGGAGTAGC 60.072 46.154 0.00 0.00 35.35 3.58
51 52 6.348950 CCTTCATCAGTTAGATAGGAGTAGCG 60.349 46.154 0.00 0.00 35.35 4.26
52 53 5.866207 TCATCAGTTAGATAGGAGTAGCGA 58.134 41.667 0.00 0.00 34.43 4.93
53 54 5.701750 TCATCAGTTAGATAGGAGTAGCGAC 59.298 44.000 0.00 0.00 34.43 5.19
54 55 5.032327 TCAGTTAGATAGGAGTAGCGACA 57.968 43.478 0.00 0.00 0.00 4.35
55 56 5.057819 TCAGTTAGATAGGAGTAGCGACAG 58.942 45.833 0.00 0.00 0.00 3.51
56 57 5.057819 CAGTTAGATAGGAGTAGCGACAGA 58.942 45.833 0.00 0.00 0.00 3.41
57 58 5.178623 CAGTTAGATAGGAGTAGCGACAGAG 59.821 48.000 0.00 0.00 0.00 3.35
58 59 3.134574 AGATAGGAGTAGCGACAGAGG 57.865 52.381 0.00 0.00 0.00 3.69
59 60 2.440253 AGATAGGAGTAGCGACAGAGGT 59.560 50.000 0.00 0.00 0.00 3.85
60 61 2.803030 TAGGAGTAGCGACAGAGGTT 57.197 50.000 0.00 0.00 0.00 3.50
61 62 1.178276 AGGAGTAGCGACAGAGGTTG 58.822 55.000 0.00 0.00 0.00 3.77
66 67 3.159984 GCGACAGAGGTTGCGAAG 58.840 61.111 0.00 0.00 44.12 3.79
67 68 1.372997 GCGACAGAGGTTGCGAAGA 60.373 57.895 0.00 0.00 44.12 2.87
68 69 0.737715 GCGACAGAGGTTGCGAAGAT 60.738 55.000 0.00 0.00 44.12 2.40
69 70 0.994995 CGACAGAGGTTGCGAAGATG 59.005 55.000 0.00 0.00 0.00 2.90
70 71 1.363744 GACAGAGGTTGCGAAGATGG 58.636 55.000 0.00 0.00 0.00 3.51
71 72 0.687354 ACAGAGGTTGCGAAGATGGT 59.313 50.000 0.00 0.00 0.00 3.55
72 73 1.081892 CAGAGGTTGCGAAGATGGTG 58.918 55.000 0.00 0.00 0.00 4.17
73 74 0.036010 AGAGGTTGCGAAGATGGTGG 60.036 55.000 0.00 0.00 0.00 4.61
74 75 1.648467 GAGGTTGCGAAGATGGTGGC 61.648 60.000 0.00 0.00 0.00 5.01
75 76 1.675641 GGTTGCGAAGATGGTGGCT 60.676 57.895 0.00 0.00 0.00 4.75
76 77 1.244019 GGTTGCGAAGATGGTGGCTT 61.244 55.000 0.00 0.00 0.00 4.35
77 78 0.598065 GTTGCGAAGATGGTGGCTTT 59.402 50.000 0.00 0.00 0.00 3.51
78 79 0.597568 TTGCGAAGATGGTGGCTTTG 59.402 50.000 0.00 0.00 0.00 2.77
79 80 1.243342 TGCGAAGATGGTGGCTTTGG 61.243 55.000 0.00 0.00 0.00 3.28
80 81 1.244019 GCGAAGATGGTGGCTTTGGT 61.244 55.000 0.00 0.00 0.00 3.67
81 82 0.804989 CGAAGATGGTGGCTTTGGTC 59.195 55.000 0.00 0.00 0.00 4.02
82 83 1.611673 CGAAGATGGTGGCTTTGGTCT 60.612 52.381 0.00 0.00 0.00 3.85
83 84 2.519013 GAAGATGGTGGCTTTGGTCTT 58.481 47.619 0.00 0.00 0.00 3.01
84 85 3.686016 GAAGATGGTGGCTTTGGTCTTA 58.314 45.455 0.00 0.00 0.00 2.10
85 86 3.073274 AGATGGTGGCTTTGGTCTTAC 57.927 47.619 0.00 0.00 0.00 2.34
86 87 2.644798 AGATGGTGGCTTTGGTCTTACT 59.355 45.455 0.00 0.00 0.00 2.24
87 88 2.270352 TGGTGGCTTTGGTCTTACTG 57.730 50.000 0.00 0.00 0.00 2.74
88 89 1.493022 TGGTGGCTTTGGTCTTACTGT 59.507 47.619 0.00 0.00 0.00 3.55
89 90 2.092103 TGGTGGCTTTGGTCTTACTGTT 60.092 45.455 0.00 0.00 0.00 3.16
90 91 2.293399 GGTGGCTTTGGTCTTACTGTTG 59.707 50.000 0.00 0.00 0.00 3.33
91 92 2.949644 GTGGCTTTGGTCTTACTGTTGT 59.050 45.455 0.00 0.00 0.00 3.32
92 93 4.131596 GTGGCTTTGGTCTTACTGTTGTA 58.868 43.478 0.00 0.00 0.00 2.41
93 94 4.024302 GTGGCTTTGGTCTTACTGTTGTAC 60.024 45.833 0.00 0.00 0.00 2.90
94 95 3.185797 GGCTTTGGTCTTACTGTTGTACG 59.814 47.826 0.00 0.00 0.00 3.67
95 96 4.053295 GCTTTGGTCTTACTGTTGTACGA 58.947 43.478 0.00 0.00 0.00 3.43
96 97 4.084693 GCTTTGGTCTTACTGTTGTACGAC 60.085 45.833 6.27 6.27 43.16 4.34
97 98 4.924305 TTGGTCTTACTGTTGTACGACT 57.076 40.909 14.38 0.00 43.31 4.18
98 99 4.924305 TGGTCTTACTGTTGTACGACTT 57.076 40.909 14.38 4.26 43.31 3.01
99 100 5.266733 TGGTCTTACTGTTGTACGACTTT 57.733 39.130 14.38 3.93 43.31 2.66
100 101 5.045215 TGGTCTTACTGTTGTACGACTTTG 58.955 41.667 14.38 7.24 43.31 2.77
101 102 5.045872 GGTCTTACTGTTGTACGACTTTGT 58.954 41.667 14.38 12.01 43.31 2.83
102 103 6.183360 TGGTCTTACTGTTGTACGACTTTGTA 60.183 38.462 14.38 11.16 43.31 2.41
103 104 6.697019 GGTCTTACTGTTGTACGACTTTGTAA 59.303 38.462 14.38 16.43 43.31 2.41
104 105 7.096312 GGTCTTACTGTTGTACGACTTTGTAAG 60.096 40.741 26.64 26.64 43.31 2.34
105 106 6.919662 TCTTACTGTTGTACGACTTTGTAAGG 59.080 38.462 28.76 20.15 37.36 2.69
106 107 5.014808 ACTGTTGTACGACTTTGTAAGGT 57.985 39.130 14.38 0.00 0.00 3.50
107 108 5.045872 ACTGTTGTACGACTTTGTAAGGTC 58.954 41.667 14.38 0.00 0.00 3.85
108 109 5.163478 ACTGTTGTACGACTTTGTAAGGTCT 60.163 40.000 14.38 0.00 0.00 3.85
109 110 5.663456 TGTTGTACGACTTTGTAAGGTCTT 58.337 37.500 14.38 0.00 0.00 3.01
110 111 5.521010 TGTTGTACGACTTTGTAAGGTCTTG 59.479 40.000 14.38 0.00 0.00 3.02
111 112 5.266733 TGTACGACTTTGTAAGGTCTTGT 57.733 39.130 5.52 0.63 0.00 3.16
112 113 5.045215 TGTACGACTTTGTAAGGTCTTGTG 58.955 41.667 5.52 0.00 0.00 3.33
113 114 4.133013 ACGACTTTGTAAGGTCTTGTGT 57.867 40.909 5.52 0.00 0.00 3.72
114 115 4.510571 ACGACTTTGTAAGGTCTTGTGTT 58.489 39.130 5.52 0.00 0.00 3.32
115 116 5.663456 ACGACTTTGTAAGGTCTTGTGTTA 58.337 37.500 5.52 0.00 0.00 2.41
116 117 6.108015 ACGACTTTGTAAGGTCTTGTGTTAA 58.892 36.000 5.52 0.00 0.00 2.01
117 118 6.764560 ACGACTTTGTAAGGTCTTGTGTTAAT 59.235 34.615 5.52 0.00 0.00 1.40
118 119 7.927629 ACGACTTTGTAAGGTCTTGTGTTAATA 59.072 33.333 5.52 0.00 0.00 0.98
119 120 8.767085 CGACTTTGTAAGGTCTTGTGTTAATAA 58.233 33.333 5.52 0.00 0.00 1.40
139 140 9.609950 TTAATAATTAATAAATTGGCCGTACGC 57.390 29.630 10.49 5.40 36.02 4.42
140 141 5.502153 AATTAATAAATTGGCCGTACGCA 57.498 34.783 10.49 0.00 40.31 5.24
141 142 5.699097 ATTAATAAATTGGCCGTACGCAT 57.301 34.783 10.49 0.00 40.31 4.73
142 143 3.619233 AATAAATTGGCCGTACGCATC 57.381 42.857 10.49 1.71 40.31 3.91
143 144 0.931702 TAAATTGGCCGTACGCATCG 59.068 50.000 10.49 0.00 40.31 3.84
144 145 1.022451 AAATTGGCCGTACGCATCGT 61.022 50.000 10.49 0.00 44.35 3.73
145 146 1.426041 AATTGGCCGTACGCATCGTC 61.426 55.000 10.49 0.00 41.54 4.20
146 147 3.993376 TTGGCCGTACGCATCGTCC 62.993 63.158 10.49 4.08 41.54 4.79
147 148 4.501714 GGCCGTACGCATCGTCCA 62.502 66.667 10.49 0.00 41.54 4.02
148 149 2.954868 GCCGTACGCATCGTCCAG 60.955 66.667 10.49 0.00 41.54 3.86
149 150 2.795973 CCGTACGCATCGTCCAGA 59.204 61.111 10.49 0.00 41.54 3.86
150 151 1.359117 CCGTACGCATCGTCCAGAT 59.641 57.895 10.49 0.00 41.54 2.90
158 159 1.445095 ATCGTCCAGATGCAGAGGC 59.555 57.895 0.00 0.00 38.36 4.70
159 160 2.037620 ATCGTCCAGATGCAGAGGCC 62.038 60.000 0.00 0.00 38.36 5.19
160 161 2.202987 GTCCAGATGCAGAGGCCG 60.203 66.667 0.00 0.00 40.13 6.13
161 162 3.473647 TCCAGATGCAGAGGCCGG 61.474 66.667 0.00 0.00 40.13 6.13
162 163 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
163 164 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
169 170 3.787001 CAGAGGCCGGGGGTCTTC 61.787 72.222 2.18 0.00 38.01 2.87
179 180 3.553109 GGGGTCTTCCTCCTTTTCG 57.447 57.895 0.00 0.00 35.33 3.46
180 181 0.981943 GGGGTCTTCCTCCTTTTCGA 59.018 55.000 0.00 0.00 35.33 3.71
181 182 1.350019 GGGGTCTTCCTCCTTTTCGAA 59.650 52.381 0.00 0.00 35.33 3.71
182 183 2.224695 GGGGTCTTCCTCCTTTTCGAAA 60.225 50.000 6.47 6.47 35.33 3.46
183 184 3.483421 GGGTCTTCCTCCTTTTCGAAAA 58.517 45.455 21.35 21.35 0.00 2.29
184 185 3.887110 GGGTCTTCCTCCTTTTCGAAAAA 59.113 43.478 22.67 9.49 0.00 1.94
212 213 9.959721 AAAGATTATCAGCAGGTACTTCTTTTA 57.040 29.630 0.00 0.00 34.60 1.52
485 492 1.869767 CTTTAGTCAGATGGCGGCATC 59.130 52.381 37.04 37.04 0.00 3.91
1740 1850 6.263842 TGAAGCAATTTCATGTCTTCTGTCTT 59.736 34.615 0.00 0.00 40.82 3.01
1773 1883 6.905609 GGCATAACTTCGTTAACTTATGCTTC 59.094 38.462 29.80 19.79 41.82 3.86
1812 1922 2.938451 CCTTTGTGCTATGCTGATTCGA 59.062 45.455 0.00 0.00 0.00 3.71
1879 1989 6.329496 ACCGTTTACTATTGGCATCAAATTG 58.671 36.000 0.00 0.00 36.36 2.32
1968 2078 5.957132 ACAGGCTGATGGTCCATATTAAAT 58.043 37.500 23.66 0.00 0.00 1.40
1993 2103 7.338800 TGGCAAGATTCCATTAGAAAGATTC 57.661 36.000 0.00 0.00 38.21 2.52
2204 2314 1.810030 CTCCTACTCCGCGCAAACC 60.810 63.158 8.75 0.00 0.00 3.27
2332 2442 8.624367 TCCACACGAAATTTTATTCCTCTAAA 57.376 30.769 0.00 0.00 0.00 1.85
2333 2443 9.069082 TCCACACGAAATTTTATTCCTCTAAAA 57.931 29.630 0.00 0.00 35.63 1.52
2385 2496 1.619654 CACAGCAATTCCCTTCACCA 58.380 50.000 0.00 0.00 0.00 4.17
2400 2511 2.722094 TCACCAGTGTCTTTTTGTGCT 58.278 42.857 0.00 0.00 0.00 4.40
2402 2513 4.265893 TCACCAGTGTCTTTTTGTGCTTA 58.734 39.130 0.00 0.00 0.00 3.09
2404 2515 5.359576 TCACCAGTGTCTTTTTGTGCTTATT 59.640 36.000 0.00 0.00 0.00 1.40
2439 2550 3.220110 CATACTGAAGGCTGCCAATGAT 58.780 45.455 22.65 5.73 0.00 2.45
2468 2579 9.939424 ACTTCAAGAAAGGGTACTATACTCTAT 57.061 33.333 0.00 0.00 38.94 1.98
2508 2619 7.445096 TCAAAGAAACTGCACTATTTGAGATGA 59.555 33.333 5.01 0.00 33.16 2.92
2549 2663 6.603095 AGCGTTCAGATCAGTTTTAACATTC 58.397 36.000 0.00 0.00 0.00 2.67
2556 2670 8.659491 TCAGATCAGTTTTAACATTCAGAATCG 58.341 33.333 0.00 0.00 0.00 3.34
2563 2677 7.607991 AGTTTTAACATTCAGAATCGACCAGAT 59.392 33.333 0.00 0.00 42.43 2.90
2595 2714 1.329256 ACGGGAATCGACCATAGGAG 58.671 55.000 0.00 0.00 42.43 3.69
2601 2720 4.701171 GGGAATCGACCATAGGAGTAGTAG 59.299 50.000 0.00 0.00 0.00 2.57
2602 2721 5.514484 GGGAATCGACCATAGGAGTAGTAGA 60.514 48.000 0.00 0.00 0.00 2.59
2604 2723 6.489361 GGAATCGACCATAGGAGTAGTAGAAA 59.511 42.308 0.00 0.00 0.00 2.52
2606 2725 6.690194 TCGACCATAGGAGTAGTAGAAAAC 57.310 41.667 0.00 0.00 0.00 2.43
2608 2727 5.593502 CGACCATAGGAGTAGTAGAAAACCT 59.406 44.000 0.00 0.00 0.00 3.50
2609 2728 6.096564 CGACCATAGGAGTAGTAGAAAACCTT 59.903 42.308 0.00 0.00 0.00 3.50
2610 2729 7.284034 CGACCATAGGAGTAGTAGAAAACCTTA 59.716 40.741 0.00 0.00 0.00 2.69
2611 2730 9.145442 GACCATAGGAGTAGTAGAAAACCTTAT 57.855 37.037 0.00 0.00 0.00 1.73
2612 2731 9.503369 ACCATAGGAGTAGTAGAAAACCTTATT 57.497 33.333 0.00 0.00 0.00 1.40
2613 2732 9.765795 CCATAGGAGTAGTAGAAAACCTTATTG 57.234 37.037 0.00 0.00 0.00 1.90
2614 2733 9.262358 CATAGGAGTAGTAGAAAACCTTATTGC 57.738 37.037 0.00 0.00 0.00 3.56
2615 2734 6.651086 AGGAGTAGTAGAAAACCTTATTGCC 58.349 40.000 0.00 0.00 0.00 4.52
2655 2882 3.486383 ACAATGGGCCTACATATTTCCG 58.514 45.455 4.53 0.00 0.00 4.30
2657 2884 1.809133 TGGGCCTACATATTTCCGGA 58.191 50.000 0.00 0.00 0.00 5.14
2658 2885 2.344592 TGGGCCTACATATTTCCGGAT 58.655 47.619 4.15 0.00 0.00 4.18
2661 2888 4.538490 TGGGCCTACATATTTCCGGATAAT 59.462 41.667 4.15 10.81 0.00 1.28
2662 2889 5.014755 TGGGCCTACATATTTCCGGATAATT 59.985 40.000 4.15 0.00 0.00 1.40
2959 3311 9.869844 GATGTACATGCTTTTTCATATGTAGAC 57.130 33.333 14.43 0.00 36.87 2.59
2972 3324 8.539117 TTCATATGTAGACTCATCCTCTTTCA 57.461 34.615 1.90 0.00 0.00 2.69
2973 3325 8.175925 TCATATGTAGACTCATCCTCTTTCAG 57.824 38.462 1.90 0.00 0.00 3.02
2974 3326 8.001292 TCATATGTAGACTCATCCTCTTTCAGA 58.999 37.037 1.90 0.00 0.00 3.27
2975 3327 8.805175 CATATGTAGACTCATCCTCTTTCAGAT 58.195 37.037 0.00 0.00 0.00 2.90
2976 3328 7.673641 ATGTAGACTCATCCTCTTTCAGATT 57.326 36.000 0.00 0.00 0.00 2.40
2977 3329 6.871844 TGTAGACTCATCCTCTTTCAGATTG 58.128 40.000 0.00 0.00 0.00 2.67
2978 3330 6.438741 TGTAGACTCATCCTCTTTCAGATTGT 59.561 38.462 0.00 0.00 0.00 2.71
2979 3331 5.976458 AGACTCATCCTCTTTCAGATTGTC 58.024 41.667 0.00 0.00 0.00 3.18
2980 3332 5.483231 AGACTCATCCTCTTTCAGATTGTCA 59.517 40.000 0.00 0.00 31.24 3.58
2981 3333 6.156602 AGACTCATCCTCTTTCAGATTGTCAT 59.843 38.462 0.00 0.00 31.24 3.06
2982 3334 7.344093 AGACTCATCCTCTTTCAGATTGTCATA 59.656 37.037 0.00 0.00 31.24 2.15
2983 3335 8.032045 ACTCATCCTCTTTCAGATTGTCATAT 57.968 34.615 0.00 0.00 0.00 1.78
2984 3336 7.932491 ACTCATCCTCTTTCAGATTGTCATATG 59.068 37.037 0.00 0.00 0.00 1.78
2985 3337 7.799081 TCATCCTCTTTCAGATTGTCATATGT 58.201 34.615 1.90 0.00 0.00 2.29
2986 3338 8.927411 TCATCCTCTTTCAGATTGTCATATGTA 58.073 33.333 1.90 0.00 0.00 2.29
2987 3339 9.205719 CATCCTCTTTCAGATTGTCATATGTAG 57.794 37.037 1.90 0.00 0.00 2.74
2988 3340 8.539117 TCCTCTTTCAGATTGTCATATGTAGA 57.461 34.615 1.90 0.00 0.00 2.59
2989 3341 8.417106 TCCTCTTTCAGATTGTCATATGTAGAC 58.583 37.037 1.90 0.00 36.55 2.59
2990 3342 8.420222 CCTCTTTCAGATTGTCATATGTAGACT 58.580 37.037 1.90 0.00 36.94 3.24
2991 3343 9.462174 CTCTTTCAGATTGTCATATGTAGACTC 57.538 37.037 1.90 0.00 36.94 3.36
2992 3344 8.971073 TCTTTCAGATTGTCATATGTAGACTCA 58.029 33.333 1.90 0.00 36.94 3.41
2993 3345 9.761504 CTTTCAGATTGTCATATGTAGACTCAT 57.238 33.333 1.90 0.00 36.94 2.90
2994 3346 9.755804 TTTCAGATTGTCATATGTAGACTCATC 57.244 33.333 1.90 1.30 36.94 2.92
2995 3347 7.890515 TCAGATTGTCATATGTAGACTCATCC 58.109 38.462 1.90 0.00 36.94 3.51
2996 3348 7.727634 TCAGATTGTCATATGTAGACTCATCCT 59.272 37.037 1.90 0.00 36.94 3.24
2997 3349 8.028354 CAGATTGTCATATGTAGACTCATCCTC 58.972 40.741 1.90 0.00 36.94 3.71
2998 3350 7.949565 AGATTGTCATATGTAGACTCATCCTCT 59.050 37.037 1.90 0.00 36.94 3.69
2999 3351 7.904558 TTGTCATATGTAGACTCATCCTCTT 57.095 36.000 1.90 0.00 36.94 2.85
3000 3352 7.904558 TGTCATATGTAGACTCATCCTCTTT 57.095 36.000 1.90 0.00 36.94 2.52
3001 3353 7.946207 TGTCATATGTAGACTCATCCTCTTTC 58.054 38.462 1.90 0.00 36.94 2.62
3042 3394 1.737236 TGCATGATGTTACCGCAGTTC 59.263 47.619 0.00 0.00 0.00 3.01
3043 3395 1.737236 GCATGATGTTACCGCAGTTCA 59.263 47.619 0.00 0.00 0.00 3.18
3060 3412 1.204146 TCACCCTCCAGCTAACCATC 58.796 55.000 0.00 0.00 0.00 3.51
3082 3434 1.023502 GAGGAGTACTCGTGTAGCCC 58.976 60.000 22.12 3.85 36.29 5.19
3177 3529 4.937620 TCATAGCCTTGTGTGATTTGTCTC 59.062 41.667 0.00 0.00 0.00 3.36
3178 3530 2.508526 AGCCTTGTGTGATTTGTCTCC 58.491 47.619 0.00 0.00 0.00 3.71
3179 3531 2.107204 AGCCTTGTGTGATTTGTCTCCT 59.893 45.455 0.00 0.00 0.00 3.69
3180 3532 3.327757 AGCCTTGTGTGATTTGTCTCCTA 59.672 43.478 0.00 0.00 0.00 2.94
3181 3533 3.686726 GCCTTGTGTGATTTGTCTCCTAG 59.313 47.826 0.00 0.00 0.00 3.02
3182 3534 4.804261 GCCTTGTGTGATTTGTCTCCTAGT 60.804 45.833 0.00 0.00 0.00 2.57
3183 3535 5.308825 CCTTGTGTGATTTGTCTCCTAGTT 58.691 41.667 0.00 0.00 0.00 2.24
3199 3551 6.667848 TCTCCTAGTTCCACTTCATGATGTAA 59.332 38.462 13.40 3.76 0.00 2.41
3227 3579 5.464168 AGTACAAACAAAATCTGCATCTGC 58.536 37.500 0.00 0.00 42.50 4.26
3243 3668 6.798315 GCATCTGCATCTGTTTCTGTATAT 57.202 37.500 0.00 0.00 41.59 0.86
3244 3669 6.600350 GCATCTGCATCTGTTTCTGTATATG 58.400 40.000 0.00 0.00 41.59 1.78
3245 3670 6.204301 GCATCTGCATCTGTTTCTGTATATGT 59.796 38.462 0.00 0.00 41.59 2.29
3320 3745 3.009301 GCAGATTGCAATATGGCTGAC 57.991 47.619 29.64 16.17 44.26 3.51
3326 3751 4.374843 TTGCAATATGGCTGACATGTTC 57.625 40.909 6.18 1.39 38.64 3.18
3576 4013 0.460722 GCTTTACCCTCCCTCGAGTC 59.539 60.000 12.31 0.00 33.93 3.36
3577 4014 1.112950 CTTTACCCTCCCTCGAGTCC 58.887 60.000 12.31 0.00 33.93 3.85
3578 4015 0.682209 TTTACCCTCCCTCGAGTCCG 60.682 60.000 12.31 0.00 33.93 4.79
3579 4016 1.565390 TTACCCTCCCTCGAGTCCGA 61.565 60.000 12.31 2.88 43.35 4.55
3580 4017 1.351080 TACCCTCCCTCGAGTCCGAT 61.351 60.000 12.31 0.00 44.62 4.18
3581 4018 1.899534 CCCTCCCTCGAGTCCGATC 60.900 68.421 12.31 0.00 44.62 3.69
3582 4019 1.149627 CCTCCCTCGAGTCCGATCT 59.850 63.158 12.31 0.00 44.62 2.75
3583 4020 0.466555 CCTCCCTCGAGTCCGATCTT 60.467 60.000 12.31 0.00 44.62 2.40
3584 4021 0.665835 CTCCCTCGAGTCCGATCTTG 59.334 60.000 12.31 0.00 44.62 3.02
3585 4022 0.255033 TCCCTCGAGTCCGATCTTGA 59.745 55.000 12.31 0.00 44.62 3.02
3586 4023 0.665835 CCCTCGAGTCCGATCTTGAG 59.334 60.000 12.31 13.54 44.62 3.02
3587 4024 1.384525 CCTCGAGTCCGATCTTGAGT 58.615 55.000 12.31 0.00 44.62 3.41
3628 4065 1.105167 TTCTGCTTGTGCTGCTGCTT 61.105 50.000 17.00 0.00 40.48 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.055747 GCTGATAGTCTGGGCCTAATACC 60.056 52.174 4.53 0.00 0.00 2.73
1 2 3.367498 CGCTGATAGTCTGGGCCTAATAC 60.367 52.174 4.53 0.00 0.00 1.89
2 3 2.826128 CGCTGATAGTCTGGGCCTAATA 59.174 50.000 4.53 0.00 0.00 0.98
3 4 1.620819 CGCTGATAGTCTGGGCCTAAT 59.379 52.381 4.53 0.00 0.00 1.73
4 5 1.040646 CGCTGATAGTCTGGGCCTAA 58.959 55.000 4.53 0.00 0.00 2.69
5 6 1.464376 GCGCTGATAGTCTGGGCCTA 61.464 60.000 4.53 0.00 44.44 3.93
6 7 2.801631 GCGCTGATAGTCTGGGCCT 61.802 63.158 4.53 0.00 44.44 5.19
7 8 2.280457 GCGCTGATAGTCTGGGCC 60.280 66.667 0.00 0.00 44.44 5.80
9 10 2.423446 GGGCGCTGATAGTCTGGG 59.577 66.667 7.64 0.00 0.00 4.45
10 11 1.690219 AAGGGGCGCTGATAGTCTGG 61.690 60.000 7.64 0.00 0.00 3.86
11 12 0.249657 GAAGGGGCGCTGATAGTCTG 60.250 60.000 7.64 0.00 0.00 3.51
12 13 0.687757 TGAAGGGGCGCTGATAGTCT 60.688 55.000 7.64 0.00 0.00 3.24
13 14 0.394565 ATGAAGGGGCGCTGATAGTC 59.605 55.000 7.64 0.00 0.00 2.59
14 15 0.394565 GATGAAGGGGCGCTGATAGT 59.605 55.000 7.64 0.00 0.00 2.12
15 16 0.394192 TGATGAAGGGGCGCTGATAG 59.606 55.000 7.64 0.00 0.00 2.08
16 17 0.394192 CTGATGAAGGGGCGCTGATA 59.606 55.000 7.64 0.00 0.00 2.15
17 18 1.147824 CTGATGAAGGGGCGCTGAT 59.852 57.895 7.64 0.00 0.00 2.90
18 19 1.841302 AACTGATGAAGGGGCGCTGA 61.841 55.000 7.64 0.00 0.00 4.26
19 20 0.107703 TAACTGATGAAGGGGCGCTG 60.108 55.000 7.64 0.00 0.00 5.18
20 21 0.179000 CTAACTGATGAAGGGGCGCT 59.821 55.000 7.64 0.00 0.00 5.92
21 22 0.178068 TCTAACTGATGAAGGGGCGC 59.822 55.000 0.00 0.00 0.00 6.53
22 23 2.918712 ATCTAACTGATGAAGGGGCG 57.081 50.000 0.00 0.00 33.43 6.13
23 24 3.904339 TCCTATCTAACTGATGAAGGGGC 59.096 47.826 0.00 0.00 33.64 5.80
24 25 5.151454 ACTCCTATCTAACTGATGAAGGGG 58.849 45.833 0.00 0.00 37.40 4.79
25 26 6.071616 GCTACTCCTATCTAACTGATGAAGGG 60.072 46.154 0.00 0.00 33.64 3.95
26 27 6.348950 CGCTACTCCTATCTAACTGATGAAGG 60.349 46.154 0.00 0.00 36.65 3.46
27 28 6.428465 TCGCTACTCCTATCTAACTGATGAAG 59.572 42.308 0.00 0.00 36.65 3.02
28 29 6.205076 GTCGCTACTCCTATCTAACTGATGAA 59.795 42.308 0.00 0.00 36.65 2.57
29 30 5.701750 GTCGCTACTCCTATCTAACTGATGA 59.298 44.000 0.00 0.00 36.65 2.92
30 31 5.470437 TGTCGCTACTCCTATCTAACTGATG 59.530 44.000 0.00 0.00 36.65 3.07
31 32 5.622180 TGTCGCTACTCCTATCTAACTGAT 58.378 41.667 0.00 0.00 39.11 2.90
32 33 5.032327 TGTCGCTACTCCTATCTAACTGA 57.968 43.478 0.00 0.00 0.00 3.41
33 34 5.057819 TCTGTCGCTACTCCTATCTAACTG 58.942 45.833 0.00 0.00 0.00 3.16
34 35 5.293319 TCTGTCGCTACTCCTATCTAACT 57.707 43.478 0.00 0.00 0.00 2.24
35 36 4.453136 CCTCTGTCGCTACTCCTATCTAAC 59.547 50.000 0.00 0.00 0.00 2.34
36 37 4.102838 ACCTCTGTCGCTACTCCTATCTAA 59.897 45.833 0.00 0.00 0.00 2.10
37 38 3.647113 ACCTCTGTCGCTACTCCTATCTA 59.353 47.826 0.00 0.00 0.00 1.98
38 39 2.440253 ACCTCTGTCGCTACTCCTATCT 59.560 50.000 0.00 0.00 0.00 1.98
39 40 2.853705 ACCTCTGTCGCTACTCCTATC 58.146 52.381 0.00 0.00 0.00 2.08
40 41 2.952978 CAACCTCTGTCGCTACTCCTAT 59.047 50.000 0.00 0.00 0.00 2.57
41 42 2.366533 CAACCTCTGTCGCTACTCCTA 58.633 52.381 0.00 0.00 0.00 2.94
42 43 1.178276 CAACCTCTGTCGCTACTCCT 58.822 55.000 0.00 0.00 0.00 3.69
43 44 0.458716 GCAACCTCTGTCGCTACTCC 60.459 60.000 0.00 0.00 0.00 3.85
44 45 0.798771 CGCAACCTCTGTCGCTACTC 60.799 60.000 0.00 0.00 0.00 2.59
45 46 1.213013 CGCAACCTCTGTCGCTACT 59.787 57.895 0.00 0.00 0.00 2.57
46 47 0.388134 TTCGCAACCTCTGTCGCTAC 60.388 55.000 0.00 0.00 0.00 3.58
47 48 0.109272 CTTCGCAACCTCTGTCGCTA 60.109 55.000 0.00 0.00 0.00 4.26
48 49 1.373497 CTTCGCAACCTCTGTCGCT 60.373 57.895 0.00 0.00 0.00 4.93
49 50 0.737715 ATCTTCGCAACCTCTGTCGC 60.738 55.000 0.00 0.00 0.00 5.19
50 51 0.994995 CATCTTCGCAACCTCTGTCG 59.005 55.000 0.00 0.00 0.00 4.35
51 52 1.338200 ACCATCTTCGCAACCTCTGTC 60.338 52.381 0.00 0.00 0.00 3.51
52 53 0.687354 ACCATCTTCGCAACCTCTGT 59.313 50.000 0.00 0.00 0.00 3.41
53 54 1.081892 CACCATCTTCGCAACCTCTG 58.918 55.000 0.00 0.00 0.00 3.35
54 55 0.036010 CCACCATCTTCGCAACCTCT 60.036 55.000 0.00 0.00 0.00 3.69
55 56 1.648467 GCCACCATCTTCGCAACCTC 61.648 60.000 0.00 0.00 0.00 3.85
56 57 1.675641 GCCACCATCTTCGCAACCT 60.676 57.895 0.00 0.00 0.00 3.50
57 58 1.244019 AAGCCACCATCTTCGCAACC 61.244 55.000 0.00 0.00 0.00 3.77
58 59 0.598065 AAAGCCACCATCTTCGCAAC 59.402 50.000 0.00 0.00 0.00 4.17
59 60 0.597568 CAAAGCCACCATCTTCGCAA 59.402 50.000 0.00 0.00 0.00 4.85
60 61 1.243342 CCAAAGCCACCATCTTCGCA 61.243 55.000 0.00 0.00 0.00 5.10
61 62 1.244019 ACCAAAGCCACCATCTTCGC 61.244 55.000 0.00 0.00 0.00 4.70
62 63 0.804989 GACCAAAGCCACCATCTTCG 59.195 55.000 0.00 0.00 0.00 3.79
63 64 2.206576 AGACCAAAGCCACCATCTTC 57.793 50.000 0.00 0.00 0.00 2.87
64 65 2.683211 AAGACCAAAGCCACCATCTT 57.317 45.000 0.00 0.00 0.00 2.40
65 66 2.644798 AGTAAGACCAAAGCCACCATCT 59.355 45.455 0.00 0.00 0.00 2.90
66 67 2.749621 CAGTAAGACCAAAGCCACCATC 59.250 50.000 0.00 0.00 0.00 3.51
67 68 2.108250 ACAGTAAGACCAAAGCCACCAT 59.892 45.455 0.00 0.00 0.00 3.55
68 69 1.493022 ACAGTAAGACCAAAGCCACCA 59.507 47.619 0.00 0.00 0.00 4.17
69 70 2.271944 ACAGTAAGACCAAAGCCACC 57.728 50.000 0.00 0.00 0.00 4.61
70 71 2.949644 ACAACAGTAAGACCAAAGCCAC 59.050 45.455 0.00 0.00 0.00 5.01
71 72 3.290948 ACAACAGTAAGACCAAAGCCA 57.709 42.857 0.00 0.00 0.00 4.75
72 73 3.185797 CGTACAACAGTAAGACCAAAGCC 59.814 47.826 0.00 0.00 0.00 4.35
73 74 4.053295 TCGTACAACAGTAAGACCAAAGC 58.947 43.478 0.00 0.00 0.00 3.51
74 75 5.287226 AGTCGTACAACAGTAAGACCAAAG 58.713 41.667 14.87 0.00 43.63 2.77
75 76 5.266733 AGTCGTACAACAGTAAGACCAAA 57.733 39.130 14.87 0.00 43.63 3.28
76 77 4.924305 AGTCGTACAACAGTAAGACCAA 57.076 40.909 14.87 0.00 43.63 3.67
77 78 4.924305 AAGTCGTACAACAGTAAGACCA 57.076 40.909 14.87 0.00 43.63 4.02
78 79 5.045872 ACAAAGTCGTACAACAGTAAGACC 58.954 41.667 14.87 2.34 43.63 3.85
79 80 7.096312 CCTTACAAAGTCGTACAACAGTAAGAC 60.096 40.741 17.98 11.88 43.23 3.01
80 81 6.919662 CCTTACAAAGTCGTACAACAGTAAGA 59.080 38.462 17.98 0.00 39.45 2.10
81 82 6.698766 ACCTTACAAAGTCGTACAACAGTAAG 59.301 38.462 12.97 12.97 37.80 2.34
82 83 6.572519 ACCTTACAAAGTCGTACAACAGTAA 58.427 36.000 0.00 0.00 0.00 2.24
83 84 6.039717 AGACCTTACAAAGTCGTACAACAGTA 59.960 38.462 0.00 0.00 0.00 2.74
84 85 5.014808 ACCTTACAAAGTCGTACAACAGT 57.985 39.130 0.00 0.00 0.00 3.55
85 86 5.287226 AGACCTTACAAAGTCGTACAACAG 58.713 41.667 0.00 0.00 0.00 3.16
86 87 5.266733 AGACCTTACAAAGTCGTACAACA 57.733 39.130 0.00 0.00 0.00 3.33
87 88 5.521372 ACAAGACCTTACAAAGTCGTACAAC 59.479 40.000 0.00 0.00 0.00 3.32
88 89 5.521010 CACAAGACCTTACAAAGTCGTACAA 59.479 40.000 0.00 0.00 0.00 2.41
89 90 5.045215 CACAAGACCTTACAAAGTCGTACA 58.955 41.667 0.00 0.00 0.00 2.90
90 91 5.045872 ACACAAGACCTTACAAAGTCGTAC 58.954 41.667 0.00 0.00 0.00 3.67
91 92 5.266733 ACACAAGACCTTACAAAGTCGTA 57.733 39.130 0.00 0.00 0.00 3.43
92 93 4.133013 ACACAAGACCTTACAAAGTCGT 57.867 40.909 0.00 0.00 0.00 4.34
93 94 6.592798 TTAACACAAGACCTTACAAAGTCG 57.407 37.500 0.00 0.00 0.00 4.18
113 114 9.609950 GCGTACGGCCAATTTATTAATTATTAA 57.390 29.630 18.39 0.00 32.75 1.40
114 115 8.781196 TGCGTACGGCCAATTTATTAATTATTA 58.219 29.630 18.39 0.00 42.61 0.98
115 116 7.649973 TGCGTACGGCCAATTTATTAATTATT 58.350 30.769 18.39 0.00 42.61 1.40
116 117 7.204496 TGCGTACGGCCAATTTATTAATTAT 57.796 32.000 18.39 0.00 42.61 1.28
117 118 6.615264 TGCGTACGGCCAATTTATTAATTA 57.385 33.333 18.39 0.00 42.61 1.40
118 119 5.502153 TGCGTACGGCCAATTTATTAATT 57.498 34.783 18.39 0.00 42.61 1.40
119 120 5.615984 CGATGCGTACGGCCAATTTATTAAT 60.616 40.000 18.39 0.00 42.61 1.40
120 121 4.318903 CGATGCGTACGGCCAATTTATTAA 60.319 41.667 18.39 0.00 42.61 1.40
121 122 3.184783 CGATGCGTACGGCCAATTTATTA 59.815 43.478 18.39 0.00 42.61 0.98
122 123 2.032377 CGATGCGTACGGCCAATTTATT 60.032 45.455 18.39 0.00 42.61 1.40
123 124 1.529438 CGATGCGTACGGCCAATTTAT 59.471 47.619 18.39 0.00 42.61 1.40
124 125 0.931702 CGATGCGTACGGCCAATTTA 59.068 50.000 18.39 0.00 42.61 1.40
125 126 1.022451 ACGATGCGTACGGCCAATTT 61.022 50.000 18.39 0.00 42.61 1.82
126 127 1.426041 GACGATGCGTACGGCCAATT 61.426 55.000 18.39 0.00 41.37 2.32
127 128 1.881252 GACGATGCGTACGGCCAAT 60.881 57.895 18.39 0.13 41.37 3.16
128 129 2.507547 GACGATGCGTACGGCCAA 60.508 61.111 18.39 0.00 41.37 4.52
131 132 2.679132 ATCTGGACGATGCGTACGGC 62.679 60.000 18.39 9.98 45.67 5.68
133 134 2.495633 CATCTGGACGATGCGTACG 58.504 57.895 11.84 11.84 44.60 3.67
140 141 1.445095 GCCTCTGCATCTGGACGAT 59.555 57.895 0.00 0.00 37.47 3.73
141 142 2.725312 GGCCTCTGCATCTGGACGA 61.725 63.158 0.00 0.00 40.13 4.20
142 143 2.202987 GGCCTCTGCATCTGGACG 60.203 66.667 0.00 0.00 40.13 4.79
143 144 2.202987 CGGCCTCTGCATCTGGAC 60.203 66.667 0.00 0.35 40.13 4.02
144 145 3.473647 CCGGCCTCTGCATCTGGA 61.474 66.667 0.00 0.00 40.13 3.86
145 146 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
146 147 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
152 153 3.787001 GAAGACCCCCGGCCTCTG 61.787 72.222 0.00 0.00 0.00 3.35
158 159 1.498176 AAAAGGAGGAAGACCCCCGG 61.498 60.000 0.00 0.00 36.73 5.73
159 160 0.035343 GAAAAGGAGGAAGACCCCCG 60.035 60.000 0.00 0.00 36.73 5.73
160 161 0.035343 CGAAAAGGAGGAAGACCCCC 60.035 60.000 0.00 0.00 36.73 5.40
161 162 0.981943 TCGAAAAGGAGGAAGACCCC 59.018 55.000 0.00 0.00 36.73 4.95
162 163 2.853235 TTCGAAAAGGAGGAAGACCC 57.147 50.000 0.00 0.00 36.73 4.46
184 185 8.870075 AAGAAGTACCTGCTGATAATCTTTTT 57.130 30.769 0.00 0.00 0.00 1.94
185 186 8.870075 AAAGAAGTACCTGCTGATAATCTTTT 57.130 30.769 0.00 0.00 32.39 2.27
186 187 8.870075 AAAAGAAGTACCTGCTGATAATCTTT 57.130 30.769 0.00 0.00 36.47 2.52
187 188 9.959721 TTAAAAGAAGTACCTGCTGATAATCTT 57.040 29.630 0.00 0.00 0.00 2.40
212 213 9.790344 TGGAACAATTGAAAATAATGTCCAATT 57.210 25.926 13.59 0.00 37.77 2.32
247 248 3.141083 TCTGGTACTCCATCCTATCTGCT 59.859 47.826 0.00 0.00 43.43 4.24
485 492 5.276395 CCTTTCTTGTACGCTCATATTCACG 60.276 44.000 0.00 0.00 0.00 4.35
831 838 0.843309 TTGTGGCTCCTGAGGACAAA 59.157 50.000 0.00 0.00 0.00 2.83
1461 1468 8.846211 CAAACCAAAGGTCTCTTACTAAATGAA 58.154 33.333 0.00 0.00 33.12 2.57
1499 1506 0.587242 CGCGCTGATGAACAAATCGG 60.587 55.000 5.56 0.00 36.23 4.18
1740 1850 3.328382 ACGAAGTTATGCCAGTTGCTA 57.672 42.857 0.00 0.00 37.78 3.49
1773 1883 4.402056 AAGGGTAGGTATGTCGTCATTG 57.598 45.455 0.00 0.00 35.70 2.82
1926 2036 4.328983 CCTGTATTACTAAACCACGTGCTG 59.671 45.833 10.91 0.00 0.00 4.41
1968 2078 7.147846 GGAATCTTTCTAATGGAATCTTGCCAA 60.148 37.037 0.00 0.00 39.21 4.52
1993 2103 4.780815 TCTTGCACCTCCATAGTATTTGG 58.219 43.478 0.00 0.00 35.45 3.28
2191 2301 0.039527 GATTTTGGTTTGCGCGGAGT 60.040 50.000 8.83 0.00 0.00 3.85
2349 2460 3.999663 GCTGTGCTCATCTTTCTACAAGT 59.000 43.478 0.00 0.00 0.00 3.16
2404 2515 3.495331 TCAGTATGCCTTCCTGCAAAAA 58.505 40.909 0.00 0.00 45.84 1.94
2468 2579 7.441017 CAGTTTCTTTGAAATGGATTTGGGTA 58.559 34.615 0.00 0.00 0.00 3.69
2474 2585 6.165700 AGTGCAGTTTCTTTGAAATGGATT 57.834 33.333 0.00 0.00 28.35 3.01
2477 2588 7.652909 TCAAATAGTGCAGTTTCTTTGAAATGG 59.347 33.333 17.39 0.00 31.69 3.16
2483 2594 7.587629 TCATCTCAAATAGTGCAGTTTCTTTG 58.412 34.615 0.00 8.27 0.00 2.77
2508 2619 9.391006 TCTGAACGCTATAAAATCAAAAGGTAT 57.609 29.630 0.00 0.00 0.00 2.73
2544 2658 4.437239 GTGATCTGGTCGATTCTGAATGT 58.563 43.478 7.78 0.00 30.84 2.71
2549 2663 1.135139 ACCGTGATCTGGTCGATTCTG 59.865 52.381 4.58 0.00 33.35 3.02
2577 2691 1.329256 ACTCCTATGGTCGATTCCCG 58.671 55.000 0.00 0.00 40.25 5.14
2580 2699 7.507733 TTTCTACTACTCCTATGGTCGATTC 57.492 40.000 0.00 0.00 0.00 2.52
2588 2707 9.262358 GCAATAAGGTTTTCTACTACTCCTATG 57.738 37.037 0.00 0.00 0.00 2.23
2592 2711 6.412214 TGGCAATAAGGTTTTCTACTACTCC 58.588 40.000 0.00 0.00 0.00 3.85
2595 2714 7.104290 AGACTGGCAATAAGGTTTTCTACTAC 58.896 38.462 0.00 0.00 0.00 2.73
2636 2863 2.714250 TCCGGAAATATGTAGGCCCATT 59.286 45.455 0.00 0.00 0.00 3.16
2641 2868 6.093633 GGTCAATTATCCGGAAATATGTAGGC 59.906 42.308 9.01 0.00 0.00 3.93
2653 2880 8.940768 AAAAATAATGTTGGTCAATTATCCGG 57.059 30.769 0.00 0.00 0.00 5.14
2682 3033 8.749026 ATTATCTGCAGAAACAAGATCAAGAT 57.251 30.769 22.50 0.81 0.00 2.40
2972 3324 7.949565 AGAGGATGAGTCTACATATGACAATCT 59.050 37.037 10.38 1.16 36.94 2.40
2973 3325 8.121305 AGAGGATGAGTCTACATATGACAATC 57.879 38.462 10.38 5.23 36.94 2.67
2974 3326 8.489676 AAGAGGATGAGTCTACATATGACAAT 57.510 34.615 10.38 0.00 36.94 2.71
2975 3327 7.904558 AAGAGGATGAGTCTACATATGACAA 57.095 36.000 10.38 0.00 36.94 3.18
2976 3328 7.561356 TGAAAGAGGATGAGTCTACATATGACA 59.439 37.037 10.38 0.00 36.94 3.58
2977 3329 7.946207 TGAAAGAGGATGAGTCTACATATGAC 58.054 38.462 10.38 0.00 34.88 3.06
2978 3330 8.001292 TCTGAAAGAGGATGAGTCTACATATGA 58.999 37.037 10.38 0.00 38.67 2.15
2979 3331 8.175925 TCTGAAAGAGGATGAGTCTACATATG 57.824 38.462 0.00 0.00 38.67 1.78
2995 3347 7.084752 CTGCGAACAGTCCAATCTGAAAGAG 62.085 48.000 0.65 0.00 42.63 2.85
2996 3348 5.329948 CTGCGAACAGTCCAATCTGAAAGA 61.330 45.833 0.65 0.00 43.21 2.52
2997 3349 2.807967 TGCGAACAGTCCAATCTGAAAG 59.192 45.455 0.65 0.00 38.63 2.62
2998 3350 2.807967 CTGCGAACAGTCCAATCTGAAA 59.192 45.455 0.65 0.00 39.22 2.69
2999 3351 2.037121 TCTGCGAACAGTCCAATCTGAA 59.963 45.455 0.65 0.00 44.77 3.02
3000 3352 1.618343 TCTGCGAACAGTCCAATCTGA 59.382 47.619 0.65 0.00 44.77 3.27
3001 3353 2.084610 TCTGCGAACAGTCCAATCTG 57.915 50.000 0.00 0.00 44.77 2.90
3042 3394 0.179073 CGATGGTTAGCTGGAGGGTG 60.179 60.000 0.00 0.00 0.00 4.61
3043 3395 0.325296 TCGATGGTTAGCTGGAGGGT 60.325 55.000 0.00 0.00 0.00 4.34
3082 3434 2.100916 ACTTGGATAGGTCGGTCATTCG 59.899 50.000 0.00 0.00 0.00 3.34
3243 3668 9.008965 ACATATGCAAAAACTTGTACAGATACA 57.991 29.630 1.58 0.00 39.63 2.29
3257 3682 9.979578 AAGACAGTGAATTTACATATGCAAAAA 57.020 25.926 5.22 3.52 0.00 1.94
3320 3745 4.067896 ACAGCAACCAGAGTTAGAACATG 58.932 43.478 0.00 0.00 33.27 3.21
3326 3751 1.802960 CAGCACAGCAACCAGAGTTAG 59.197 52.381 0.00 0.00 33.27 2.34
3576 4013 3.996363 TGTTCAACATGACTCAAGATCGG 59.004 43.478 0.00 0.00 0.00 4.18
3577 4014 4.435253 GCTGTTCAACATGACTCAAGATCG 60.435 45.833 0.00 0.00 0.00 3.69
3578 4015 4.453478 TGCTGTTCAACATGACTCAAGATC 59.547 41.667 0.00 0.00 0.00 2.75
3579 4016 4.392047 TGCTGTTCAACATGACTCAAGAT 58.608 39.130 0.00 0.00 0.00 2.40
3580 4017 3.807553 TGCTGTTCAACATGACTCAAGA 58.192 40.909 0.00 0.00 0.00 3.02
3581 4018 3.608707 GCTGCTGTTCAACATGACTCAAG 60.609 47.826 0.00 0.00 0.00 3.02
3582 4019 2.291465 GCTGCTGTTCAACATGACTCAA 59.709 45.455 0.00 0.00 0.00 3.02
3583 4020 1.875514 GCTGCTGTTCAACATGACTCA 59.124 47.619 0.00 0.00 0.00 3.41
3584 4021 2.095869 CAGCTGCTGTTCAACATGACTC 60.096 50.000 21.21 0.00 0.00 3.36
3585 4022 1.878088 CAGCTGCTGTTCAACATGACT 59.122 47.619 21.21 0.00 0.00 3.41
3586 4023 1.665161 GCAGCTGCTGTTCAACATGAC 60.665 52.381 31.33 6.20 38.21 3.06
3587 4024 0.594602 GCAGCTGCTGTTCAACATGA 59.405 50.000 31.33 0.00 38.21 3.07
3628 4065 1.203038 TGAAAGGCCAGCCAATTCAGA 60.203 47.619 19.84 5.06 38.43 3.27


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

AutoCloner maintained by Alex Coulton.