Multiple sequence alignment - TraesCS3A01G034800

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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 TraesCS3A01G034800 chr3A 100.000 2711 0 0 1 2711 19476867 19474157 0.000000e+00 5007
1 TraesCS3A01G034800 chr3A 85.885 836 73 23 1919 2710 19371143 19371977 0.000000e+00 848
2 TraesCS3A01G034800 chr3A 85.882 595 78 2 2122 2710 26396075 26396669 1.770000e-176 628
3 TraesCS3A01G034800 chr3A 86.356 579 66 10 2140 2710 26469246 26469819 1.070000e-173 619
4 TraesCS3A01G034800 chr3A 79.112 608 102 15 1097 1696 26415309 26415899 1.960000e-106 396
5 TraesCS3A01G034800 chr3A 80.322 559 75 20 1121 1678 19303441 19303965 9.100000e-105 390
6 TraesCS3A01G034800 chr3A 81.963 438 62 9 1391 1820 25937407 25936979 3.320000e-94 355
7 TraesCS3A01G034800 chr3A 77.815 595 94 25 1097 1682 26451514 26452079 1.560000e-87 333
8 TraesCS3A01G034800 chr3D 87.047 2540 209 52 226 2710 17372559 17375033 0.000000e+00 2758
9 TraesCS3A01G034800 chr3D 78.390 1888 269 69 919 2710 17646530 17644686 0.000000e+00 1098
10 TraesCS3A01G034800 chr3D 83.394 831 95 20 1919 2710 17516952 17516126 0.000000e+00 730
11 TraesCS3A01G034800 chr3D 77.166 854 141 28 981 1817 18894612 18895428 5.320000e-122 448
12 TraesCS3A01G034800 chr3D 79.605 608 103 15 1099 1703 18881217 18881806 1.500000e-112 416
13 TraesCS3A01G034800 chr3D 84.980 253 32 2 2464 2710 18688453 18688705 4.480000e-63 252
14 TraesCS3A01G034800 chr3D 74.629 607 134 15 1070 1669 18949814 18950407 1.610000e-62 250
15 TraesCS3A01G034800 chr3B 91.292 1447 78 19 619 2040 24940129 24941552 0.000000e+00 1930
16 TraesCS3A01G034800 chr3B 91.248 617 45 3 2100 2710 24941554 24942167 0.000000e+00 832
17 TraesCS3A01G034800 chr3B 83.630 843 83 24 1919 2710 27516542 27517380 0.000000e+00 741
18 TraesCS3A01G034800 chr3B 85.737 624 78 9 2094 2710 30231887 30232506 0.000000e+00 649
19 TraesCS3A01G034800 chr3B 78.114 594 113 11 1104 1696 29618564 29619141 7.140000e-96 361
20 TraesCS3A01G034800 chr3B 73.399 609 136 12 1070 1669 29730419 29731010 1.270000e-48 204
21 TraesCS3A01G034800 chr3B 87.500 120 12 2 1699 1817 27516359 27516476 4.710000e-28 135
22 TraesCS3A01G034800 chrUn 80.164 852 116 21 1912 2711 37955631 37956481 3.010000e-164 588


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 TraesCS3A01G034800 chr3A 19474157 19476867 2710 True 5007 5007 100.000 1 2711 1 chr3A.!!$R1 2710
1 TraesCS3A01G034800 chr3A 19371143 19371977 834 False 848 848 85.885 1919 2710 1 chr3A.!!$F2 791
2 TraesCS3A01G034800 chr3A 26396075 26396669 594 False 628 628 85.882 2122 2710 1 chr3A.!!$F3 588
3 TraesCS3A01G034800 chr3A 26469246 26469819 573 False 619 619 86.356 2140 2710 1 chr3A.!!$F6 570
4 TraesCS3A01G034800 chr3A 26415309 26415899 590 False 396 396 79.112 1097 1696 1 chr3A.!!$F4 599
5 TraesCS3A01G034800 chr3A 19303441 19303965 524 False 390 390 80.322 1121 1678 1 chr3A.!!$F1 557
6 TraesCS3A01G034800 chr3A 26451514 26452079 565 False 333 333 77.815 1097 1682 1 chr3A.!!$F5 585
7 TraesCS3A01G034800 chr3D 17372559 17375033 2474 False 2758 2758 87.047 226 2710 1 chr3D.!!$F1 2484
8 TraesCS3A01G034800 chr3D 17644686 17646530 1844 True 1098 1098 78.390 919 2710 1 chr3D.!!$R2 1791
9 TraesCS3A01G034800 chr3D 17516126 17516952 826 True 730 730 83.394 1919 2710 1 chr3D.!!$R1 791
10 TraesCS3A01G034800 chr3D 18894612 18895428 816 False 448 448 77.166 981 1817 1 chr3D.!!$F4 836
11 TraesCS3A01G034800 chr3D 18881217 18881806 589 False 416 416 79.605 1099 1703 1 chr3D.!!$F3 604
12 TraesCS3A01G034800 chr3D 18949814 18950407 593 False 250 250 74.629 1070 1669 1 chr3D.!!$F5 599
13 TraesCS3A01G034800 chr3B 24940129 24942167 2038 False 1381 1930 91.270 619 2710 2 chr3B.!!$F4 2091
14 TraesCS3A01G034800 chr3B 30231887 30232506 619 False 649 649 85.737 2094 2710 1 chr3B.!!$F3 616
15 TraesCS3A01G034800 chr3B 27516359 27517380 1021 False 438 741 85.565 1699 2710 2 chr3B.!!$F5 1011
16 TraesCS3A01G034800 chr3B 29618564 29619141 577 False 361 361 78.114 1104 1696 1 chr3B.!!$F1 592
17 TraesCS3A01G034800 chr3B 29730419 29731010 591 False 204 204 73.399 1070 1669 1 chr3B.!!$F2 599
18 TraesCS3A01G034800 chrUn 37955631 37956481 850 False 588 588 80.164 1912 2711 1 chrUn.!!$F1 799

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
63 64 0.033504 TCGTTTCTGTGGGTCTCTGC 59.966 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1892 0.175302 TAATTTTGCATGGCCCGCTG 59.825 50.0 14.73 4.42 0.0 5.18 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
29 30 2.698803 GCATTTGCCTTTTTACCTGGG 58.301 47.619 0.00 0.00 34.31 4.45
30 31 2.038426 GCATTTGCCTTTTTACCTGGGT 59.962 45.455 0.00 0.00 34.31 4.51
31 32 3.663025 CATTTGCCTTTTTACCTGGGTG 58.337 45.455 2.07 0.00 0.00 4.61
32 33 2.757894 TTGCCTTTTTACCTGGGTGA 57.242 45.000 2.07 0.00 0.00 4.02
33 34 2.990740 TGCCTTTTTACCTGGGTGAT 57.009 45.000 2.07 0.00 0.00 3.06
34 35 2.802719 TGCCTTTTTACCTGGGTGATC 58.197 47.619 2.07 0.00 0.00 2.92
35 36 2.378547 TGCCTTTTTACCTGGGTGATCT 59.621 45.455 2.07 0.00 0.00 2.75
36 37 3.181423 TGCCTTTTTACCTGGGTGATCTT 60.181 43.478 2.07 0.00 0.00 2.40
37 38 3.832490 GCCTTTTTACCTGGGTGATCTTT 59.168 43.478 2.07 0.00 0.00 2.52
38 39 4.321974 GCCTTTTTACCTGGGTGATCTTTG 60.322 45.833 2.07 0.00 0.00 2.77
39 40 4.832823 CCTTTTTACCTGGGTGATCTTTGT 59.167 41.667 2.07 0.00 0.00 2.83
40 41 6.007703 CCTTTTTACCTGGGTGATCTTTGTA 58.992 40.000 2.07 0.00 0.00 2.41
41 42 6.151144 CCTTTTTACCTGGGTGATCTTTGTAG 59.849 42.308 2.07 0.00 0.00 2.74
42 43 5.836024 TTTACCTGGGTGATCTTTGTAGT 57.164 39.130 2.07 0.00 0.00 2.73
43 44 6.938698 TTTACCTGGGTGATCTTTGTAGTA 57.061 37.500 2.07 0.00 0.00 1.82
44 45 7.504926 TTTACCTGGGTGATCTTTGTAGTAT 57.495 36.000 2.07 0.00 0.00 2.12
45 46 5.615925 ACCTGGGTGATCTTTGTAGTATC 57.384 43.478 0.00 0.00 0.00 2.24
46 47 4.099573 ACCTGGGTGATCTTTGTAGTATCG 59.900 45.833 0.00 0.00 0.00 2.92
47 48 4.099573 CCTGGGTGATCTTTGTAGTATCGT 59.900 45.833 0.00 0.00 0.00 3.73
48 49 5.395324 CCTGGGTGATCTTTGTAGTATCGTT 60.395 44.000 0.00 0.00 0.00 3.85
49 50 6.045072 TGGGTGATCTTTGTAGTATCGTTT 57.955 37.500 0.00 0.00 0.00 3.60
50 51 6.103997 TGGGTGATCTTTGTAGTATCGTTTC 58.896 40.000 0.00 0.00 0.00 2.78
51 52 6.070995 TGGGTGATCTTTGTAGTATCGTTTCT 60.071 38.462 0.00 0.00 0.00 2.52
52 53 6.255887 GGGTGATCTTTGTAGTATCGTTTCTG 59.744 42.308 0.00 0.00 0.00 3.02
53 54 6.812160 GGTGATCTTTGTAGTATCGTTTCTGT 59.188 38.462 0.00 0.00 0.00 3.41
54 55 7.201444 GGTGATCTTTGTAGTATCGTTTCTGTG 60.201 40.741 0.00 0.00 0.00 3.66
55 56 6.811665 TGATCTTTGTAGTATCGTTTCTGTGG 59.188 38.462 0.00 0.00 0.00 4.17
56 57 5.475719 TCTTTGTAGTATCGTTTCTGTGGG 58.524 41.667 0.00 0.00 0.00 4.61
57 58 4.877378 TTGTAGTATCGTTTCTGTGGGT 57.123 40.909 0.00 0.00 0.00 4.51
58 59 4.445452 TGTAGTATCGTTTCTGTGGGTC 57.555 45.455 0.00 0.00 0.00 4.46
59 60 4.084287 TGTAGTATCGTTTCTGTGGGTCT 58.916 43.478 0.00 0.00 0.00 3.85
60 61 3.870633 AGTATCGTTTCTGTGGGTCTC 57.129 47.619 0.00 0.00 0.00 3.36
61 62 3.432378 AGTATCGTTTCTGTGGGTCTCT 58.568 45.455 0.00 0.00 0.00 3.10
62 63 2.751166 ATCGTTTCTGTGGGTCTCTG 57.249 50.000 0.00 0.00 0.00 3.35
63 64 0.033504 TCGTTTCTGTGGGTCTCTGC 59.966 55.000 0.00 0.00 0.00 4.26
64 65 1.284982 CGTTTCTGTGGGTCTCTGCG 61.285 60.000 0.00 0.00 0.00 5.18
65 66 0.249911 GTTTCTGTGGGTCTCTGCGT 60.250 55.000 0.00 0.00 0.00 5.24
66 67 0.033504 TTTCTGTGGGTCTCTGCGTC 59.966 55.000 0.00 0.00 0.00 5.19
67 68 0.827925 TTCTGTGGGTCTCTGCGTCT 60.828 55.000 0.00 0.00 0.00 4.18
68 69 1.080230 CTGTGGGTCTCTGCGTCTG 60.080 63.158 0.00 0.00 0.00 3.51
69 70 2.433318 GTGGGTCTCTGCGTCTGC 60.433 66.667 0.00 0.00 43.20 4.26
70 71 3.695606 TGGGTCTCTGCGTCTGCC 61.696 66.667 0.00 0.00 41.78 4.85
71 72 4.459089 GGGTCTCTGCGTCTGCCC 62.459 72.222 0.00 0.00 41.78 5.36
72 73 3.695606 GGTCTCTGCGTCTGCCCA 61.696 66.667 0.00 0.00 41.78 5.36
73 74 2.581354 GTCTCTGCGTCTGCCCAT 59.419 61.111 0.00 0.00 41.78 4.00
74 75 1.812922 GTCTCTGCGTCTGCCCATG 60.813 63.158 0.00 0.00 41.78 3.66
75 76 2.267006 CTCTGCGTCTGCCCATGT 59.733 61.111 0.00 0.00 41.78 3.21
76 77 0.970427 TCTCTGCGTCTGCCCATGTA 60.970 55.000 0.00 0.00 41.78 2.29
77 78 0.108186 CTCTGCGTCTGCCCATGTAA 60.108 55.000 0.00 0.00 41.78 2.41
78 79 0.391130 TCTGCGTCTGCCCATGTAAC 60.391 55.000 0.00 0.00 41.78 2.50
79 80 0.391661 CTGCGTCTGCCCATGTAACT 60.392 55.000 0.00 0.00 41.78 2.24
80 81 0.899019 TGCGTCTGCCCATGTAACTA 59.101 50.000 0.00 0.00 41.78 2.24
81 82 1.134818 TGCGTCTGCCCATGTAACTAG 60.135 52.381 0.00 0.00 41.78 2.57
82 83 1.136305 GCGTCTGCCCATGTAACTAGA 59.864 52.381 0.00 0.00 33.98 2.43
83 84 2.224066 GCGTCTGCCCATGTAACTAGAT 60.224 50.000 0.00 0.00 33.98 1.98
84 85 3.643763 CGTCTGCCCATGTAACTAGATC 58.356 50.000 0.00 0.00 0.00 2.75
85 86 3.643763 GTCTGCCCATGTAACTAGATCG 58.356 50.000 0.00 0.00 0.00 3.69
86 87 3.318275 GTCTGCCCATGTAACTAGATCGA 59.682 47.826 0.00 0.00 0.00 3.59
87 88 4.021894 GTCTGCCCATGTAACTAGATCGAT 60.022 45.833 0.00 0.00 0.00 3.59
88 89 4.588951 TCTGCCCATGTAACTAGATCGATT 59.411 41.667 0.00 0.00 0.00 3.34
89 90 5.070446 TCTGCCCATGTAACTAGATCGATTT 59.930 40.000 0.00 0.00 0.00 2.17
90 91 5.680619 TGCCCATGTAACTAGATCGATTTT 58.319 37.500 0.00 0.00 0.00 1.82
91 92 6.119536 TGCCCATGTAACTAGATCGATTTTT 58.880 36.000 0.00 0.00 0.00 1.94
92 93 6.260050 TGCCCATGTAACTAGATCGATTTTTC 59.740 38.462 0.00 0.00 0.00 2.29
93 94 6.483640 GCCCATGTAACTAGATCGATTTTTCT 59.516 38.462 0.00 0.00 0.00 2.52
94 95 7.307455 GCCCATGTAACTAGATCGATTTTTCTC 60.307 40.741 0.00 0.00 0.00 2.87
95 96 7.096023 CCCATGTAACTAGATCGATTTTTCTCG 60.096 40.741 0.00 0.00 39.99 4.04
96 97 6.807708 TGTAACTAGATCGATTTTTCTCGC 57.192 37.500 0.00 0.00 38.52 5.03
97 98 6.561614 TGTAACTAGATCGATTTTTCTCGCT 58.438 36.000 0.00 0.00 38.52 4.93
98 99 6.691818 TGTAACTAGATCGATTTTTCTCGCTC 59.308 38.462 0.00 0.00 38.52 5.03
99 100 5.508200 ACTAGATCGATTTTTCTCGCTCT 57.492 39.130 0.00 5.37 43.95 4.09
100 101 5.516090 ACTAGATCGATTTTTCTCGCTCTC 58.484 41.667 0.00 0.00 41.63 3.20
101 102 4.377839 AGATCGATTTTTCTCGCTCTCA 57.622 40.909 0.00 0.00 39.22 3.27
102 103 4.358851 AGATCGATTTTTCTCGCTCTCAG 58.641 43.478 0.00 0.00 39.22 3.35
103 104 3.577649 TCGATTTTTCTCGCTCTCAGT 57.422 42.857 0.00 0.00 38.52 3.41
104 105 3.914312 TCGATTTTTCTCGCTCTCAGTT 58.086 40.909 0.00 0.00 38.52 3.16
105 106 3.921021 TCGATTTTTCTCGCTCTCAGTTC 59.079 43.478 0.00 0.00 38.52 3.01
106 107 3.675225 CGATTTTTCTCGCTCTCAGTTCA 59.325 43.478 0.00 0.00 0.00 3.18
107 108 4.433544 CGATTTTTCTCGCTCTCAGTTCAC 60.434 45.833 0.00 0.00 0.00 3.18
108 109 3.452755 TTTTCTCGCTCTCAGTTCACA 57.547 42.857 0.00 0.00 0.00 3.58
109 110 2.713895 TTCTCGCTCTCAGTTCACAG 57.286 50.000 0.00 0.00 0.00 3.66
110 111 0.242286 TCTCGCTCTCAGTTCACAGC 59.758 55.000 0.00 0.00 0.00 4.40
112 113 3.163655 GCTCTCAGTTCACAGCGC 58.836 61.111 0.00 0.00 0.00 5.92
113 114 2.724708 GCTCTCAGTTCACAGCGCG 61.725 63.158 0.00 0.00 0.00 6.86
114 115 2.049156 TCTCAGTTCACAGCGCGG 60.049 61.111 8.83 5.83 0.00 6.46
115 116 3.114616 CTCAGTTCACAGCGCGGG 61.115 66.667 13.26 6.53 0.00 6.13
116 117 3.865929 CTCAGTTCACAGCGCGGGT 62.866 63.158 13.26 7.27 0.00 5.28
117 118 3.716006 CAGTTCACAGCGCGGGTG 61.716 66.667 23.67 23.67 37.60 4.61
120 121 4.927782 TTCACAGCGCGGGTGCTT 62.928 61.111 24.48 0.00 44.46 3.91
121 122 4.927782 TCACAGCGCGGGTGCTTT 62.928 61.111 24.48 0.00 44.46 3.51
122 123 3.964875 CACAGCGCGGGTGCTTTT 61.965 61.111 19.53 0.00 44.46 2.27
123 124 3.660111 ACAGCGCGGGTGCTTTTC 61.660 61.111 13.26 0.00 44.46 2.29
124 125 4.404654 CAGCGCGGGTGCTTTTCC 62.405 66.667 8.83 0.00 44.46 3.13
147 148 6.293004 CCCCCTTTATTATGCAAACAAAGA 57.707 37.500 11.50 0.00 0.00 2.52
148 149 6.340522 CCCCCTTTATTATGCAAACAAAGAG 58.659 40.000 11.50 2.30 0.00 2.85
149 150 6.070824 CCCCCTTTATTATGCAAACAAAGAGT 60.071 38.462 11.50 0.00 0.00 3.24
150 151 7.386059 CCCCTTTATTATGCAAACAAAGAGTT 58.614 34.615 11.50 0.00 43.89 3.01
151 152 7.545615 CCCCTTTATTATGCAAACAAAGAGTTC 59.454 37.037 11.50 0.00 40.26 3.01
152 153 8.306761 CCCTTTATTATGCAAACAAAGAGTTCT 58.693 33.333 11.50 0.00 40.26 3.01
153 154 9.696917 CCTTTATTATGCAAACAAAGAGTTCTT 57.303 29.630 11.50 0.00 40.26 2.52
158 159 6.705863 ATGCAAACAAAGAGTTCTTTCTCT 57.294 33.333 4.20 0.00 43.72 3.10
159 160 6.124088 TGCAAACAAAGAGTTCTTTCTCTC 57.876 37.500 4.20 0.00 43.72 3.20
160 161 5.201181 GCAAACAAAGAGTTCTTTCTCTCG 58.799 41.667 4.20 0.00 43.72 4.04
161 162 5.201181 CAAACAAAGAGTTCTTTCTCTCGC 58.799 41.667 4.20 0.00 43.72 5.03
162 163 3.394719 ACAAAGAGTTCTTTCTCTCGCC 58.605 45.455 4.20 0.00 43.72 5.54
163 164 2.355717 AAGAGTTCTTTCTCTCGCCG 57.644 50.000 0.00 0.00 43.03 6.46
164 165 0.528470 AGAGTTCTTTCTCTCGCCGG 59.472 55.000 0.00 0.00 40.28 6.13
165 166 1.079317 GAGTTCTTTCTCTCGCCGGC 61.079 60.000 19.07 19.07 0.00 6.13
166 167 1.374252 GTTCTTTCTCTCGCCGGCA 60.374 57.895 28.98 12.94 0.00 5.69
167 168 0.949105 GTTCTTTCTCTCGCCGGCAA 60.949 55.000 28.98 7.25 0.00 4.52
168 169 0.949105 TTCTTTCTCTCGCCGGCAAC 60.949 55.000 28.98 0.00 0.00 4.17
169 170 1.374758 CTTTCTCTCGCCGGCAACT 60.375 57.895 28.98 0.00 0.00 3.16
170 171 0.108804 CTTTCTCTCGCCGGCAACTA 60.109 55.000 28.98 7.47 0.00 2.24
171 172 0.389426 TTTCTCTCGCCGGCAACTAC 60.389 55.000 28.98 0.00 0.00 2.73
172 173 1.248785 TTCTCTCGCCGGCAACTACT 61.249 55.000 28.98 0.00 0.00 2.57
173 174 0.393402 TCTCTCGCCGGCAACTACTA 60.393 55.000 28.98 1.55 0.00 1.82
174 175 0.248539 CTCTCGCCGGCAACTACTAC 60.249 60.000 28.98 0.00 0.00 2.73
175 176 0.961857 TCTCGCCGGCAACTACTACA 60.962 55.000 28.98 0.00 0.00 2.74
176 177 0.801067 CTCGCCGGCAACTACTACAC 60.801 60.000 28.98 0.00 0.00 2.90
177 178 1.214589 CGCCGGCAACTACTACACT 59.785 57.895 28.98 0.00 0.00 3.55
178 179 0.452987 CGCCGGCAACTACTACACTA 59.547 55.000 28.98 0.00 0.00 2.74
179 180 1.533338 CGCCGGCAACTACTACACTAG 60.533 57.143 28.98 0.00 0.00 2.57
180 181 1.202382 GCCGGCAACTACTACACTAGG 60.202 57.143 24.80 0.00 0.00 3.02
181 182 2.372264 CCGGCAACTACTACACTAGGA 58.628 52.381 0.00 0.00 0.00 2.94
182 183 2.098770 CCGGCAACTACTACACTAGGAC 59.901 54.545 0.00 0.00 0.00 3.85
183 184 2.098770 CGGCAACTACTACACTAGGACC 59.901 54.545 0.00 0.00 0.00 4.46
184 185 2.098770 GGCAACTACTACACTAGGACCG 59.901 54.545 0.00 0.00 0.00 4.79
185 186 2.751806 GCAACTACTACACTAGGACCGT 59.248 50.000 0.00 0.00 0.00 4.83
186 187 3.941483 GCAACTACTACACTAGGACCGTA 59.059 47.826 0.00 0.00 0.00 4.02
187 188 4.201861 GCAACTACTACACTAGGACCGTAC 60.202 50.000 0.00 0.00 0.00 3.67
188 189 5.181748 CAACTACTACACTAGGACCGTACT 58.818 45.833 0.00 0.00 0.00 2.73
189 190 6.341316 CAACTACTACACTAGGACCGTACTA 58.659 44.000 0.00 0.00 0.00 1.82
190 191 6.155475 ACTACTACACTAGGACCGTACTAG 57.845 45.833 15.31 15.31 42.77 2.57
192 193 6.834451 ACTACTACACTAGGACCGTACTAGTA 59.166 42.308 20.97 7.95 46.92 1.82
193 194 5.908341 ACTACACTAGGACCGTACTAGTAC 58.092 45.833 20.97 21.06 46.92 2.73
209 210 8.140677 GTACTAGTACGACTGATTAGTGATGT 57.859 38.462 16.96 0.00 37.25 3.06
210 211 9.254133 GTACTAGTACGACTGATTAGTGATGTA 57.746 37.037 16.96 0.00 37.25 2.29
211 212 8.728337 ACTAGTACGACTGATTAGTGATGTAA 57.272 34.615 0.00 0.00 37.25 2.41
212 213 8.828644 ACTAGTACGACTGATTAGTGATGTAAG 58.171 37.037 0.00 0.00 37.25 2.34
213 214 7.028926 AGTACGACTGATTAGTGATGTAAGG 57.971 40.000 0.00 0.00 37.25 2.69
214 215 5.916661 ACGACTGATTAGTGATGTAAGGT 57.083 39.130 0.00 0.00 37.25 3.50
215 216 7.772292 AGTACGACTGATTAGTGATGTAAGGTA 59.228 37.037 0.00 0.00 37.25 3.08
216 217 7.400599 ACGACTGATTAGTGATGTAAGGTAA 57.599 36.000 0.00 0.00 37.25 2.85
217 218 7.833786 ACGACTGATTAGTGATGTAAGGTAAA 58.166 34.615 0.00 0.00 37.25 2.01
218 219 8.475639 ACGACTGATTAGTGATGTAAGGTAAAT 58.524 33.333 0.00 0.00 37.25 1.40
219 220 9.314321 CGACTGATTAGTGATGTAAGGTAAATT 57.686 33.333 0.00 0.00 37.25 1.82
226 227 7.504926 AGTGATGTAAGGTAAATTACTCCCA 57.495 36.000 2.96 0.00 36.73 4.37
227 228 7.924541 AGTGATGTAAGGTAAATTACTCCCAA 58.075 34.615 2.96 0.00 36.73 4.12
228 229 8.047310 AGTGATGTAAGGTAAATTACTCCCAAG 58.953 37.037 2.96 0.00 36.73 3.61
229 230 7.827729 GTGATGTAAGGTAAATTACTCCCAAGT 59.172 37.037 2.96 0.00 36.73 3.16
230 231 9.049050 TGATGTAAGGTAAATTACTCCCAAGTA 57.951 33.333 2.96 0.00 36.73 2.24
231 232 9.322773 GATGTAAGGTAAATTACTCCCAAGTAC 57.677 37.037 2.96 0.00 37.72 2.73
232 233 8.204903 TGTAAGGTAAATTACTCCCAAGTACA 57.795 34.615 2.96 0.40 37.72 2.90
233 234 8.658619 TGTAAGGTAAATTACTCCCAAGTACAA 58.341 33.333 2.96 0.00 37.72 2.41
248 249 7.989416 CCAAGTACAAGTGGGTTCTAATTTA 57.011 36.000 0.00 0.00 0.00 1.40
251 252 7.974482 AGTACAAGTGGGTTCTAATTTACAC 57.026 36.000 0.00 0.00 0.00 2.90
252 253 7.511268 AGTACAAGTGGGTTCTAATTTACACA 58.489 34.615 0.00 0.00 0.00 3.72
264 265 9.151471 GTTCTAATTTACACAAGTAGATGCTCA 57.849 33.333 0.00 0.00 0.00 4.26
269 270 9.618890 AATTTACACAAGTAGATGCTCATACAT 57.381 29.630 0.00 0.00 0.00 2.29
285 286 6.494893 TCATACATTAGCACAAGTGGAAAC 57.505 37.500 2.00 0.00 0.00 2.78
292 293 6.761099 TTAGCACAAGTGGAAACAAAGTTA 57.239 33.333 2.00 0.00 46.06 2.24
300 301 5.063880 AGTGGAAACAAAGTTACTGCTAGG 58.936 41.667 0.00 0.00 46.06 3.02
307 314 0.745468 AGTTACTGCTAGGCTACGGC 59.255 55.000 0.00 0.00 37.82 5.68
321 328 0.616395 TACGGCCCAAGACTGGATCA 60.616 55.000 0.00 0.00 46.92 2.92
322 329 1.450312 CGGCCCAAGACTGGATCAC 60.450 63.158 0.00 0.00 46.92 3.06
332 343 2.379907 AGACTGGATCACCCCAATTTGT 59.620 45.455 0.00 0.00 35.47 2.83
335 346 3.075283 ACTGGATCACCCCAATTTGTACA 59.925 43.478 0.00 0.00 35.47 2.90
340 351 3.750371 TCACCCCAATTTGTACACTCAG 58.250 45.455 0.00 0.00 0.00 3.35
342 353 1.818674 CCCCAATTTGTACACTCAGCC 59.181 52.381 0.00 0.00 0.00 4.85
345 356 2.489329 CCAATTTGTACACTCAGCCCTG 59.511 50.000 0.00 0.00 0.00 4.45
351 362 1.896465 GTACACTCAGCCCTGAAGTCT 59.104 52.381 0.00 0.00 39.39 3.24
383 394 4.968660 GACAGTAGTGTCGAAAAGGTTC 57.031 45.455 14.75 0.00 43.75 3.62
384 395 4.365723 GACAGTAGTGTCGAAAAGGTTCA 58.634 43.478 14.75 0.00 43.75 3.18
385 396 4.957296 ACAGTAGTGTCGAAAAGGTTCAT 58.043 39.130 0.00 0.00 32.89 2.57
387 398 5.924825 ACAGTAGTGTCGAAAAGGTTCATAC 59.075 40.000 0.00 0.00 32.89 2.39
409 421 3.728221 CGCGATTCATCAGTCTTCTAGTG 59.272 47.826 0.00 0.00 0.00 2.74
426 438 9.062524 TCTTCTAGTGAAAATTTCGGATTTTGA 57.937 29.630 12.89 4.66 32.03 2.69
444 456 9.384682 GGATTTTGAAAAACATGCTAAACATTG 57.615 29.630 0.00 0.00 36.64 2.82
485 497 1.138247 GGTAGGTACCGAGCACACG 59.862 63.158 18.06 0.00 36.50 4.49
486 498 1.589716 GGTAGGTACCGAGCACACGT 61.590 60.000 18.06 0.00 36.50 4.49
511 523 3.691049 CATTGTGTGGAAAGTTCGTGT 57.309 42.857 0.00 0.00 0.00 4.49
512 524 3.617669 CATTGTGTGGAAAGTTCGTGTC 58.382 45.455 0.00 0.00 0.00 3.67
513 525 2.388310 TGTGTGGAAAGTTCGTGTCA 57.612 45.000 0.00 0.00 0.00 3.58
514 526 2.701107 TGTGTGGAAAGTTCGTGTCAA 58.299 42.857 0.00 0.00 0.00 3.18
515 527 3.075148 TGTGTGGAAAGTTCGTGTCAAA 58.925 40.909 0.00 0.00 0.00 2.69
516 528 3.502595 TGTGTGGAAAGTTCGTGTCAAAA 59.497 39.130 0.00 0.00 0.00 2.44
517 529 3.849708 GTGTGGAAAGTTCGTGTCAAAAC 59.150 43.478 0.00 0.00 0.00 2.43
518 530 3.754323 TGTGGAAAGTTCGTGTCAAAACT 59.246 39.130 0.00 0.00 37.32 2.66
519 531 4.095610 GTGGAAAGTTCGTGTCAAAACTG 58.904 43.478 3.33 0.00 35.93 3.16
520 532 3.754323 TGGAAAGTTCGTGTCAAAACTGT 59.246 39.130 3.33 0.00 35.93 3.55
530 542 5.173673 TCGTGTCAAAACTGTCAATACGTAC 59.826 40.000 0.00 0.00 0.00 3.67
532 544 4.445052 TGTCAAAACTGTCAATACGTACGG 59.555 41.667 21.06 1.09 0.00 4.02
560 572 5.122396 GCTAATTGGAGTACTGTCAAAGGTG 59.878 44.000 0.00 0.00 0.00 4.00
561 573 4.706842 ATTGGAGTACTGTCAAAGGTGT 57.293 40.909 0.00 0.00 0.00 4.16
562 574 3.746045 TGGAGTACTGTCAAAGGTGTC 57.254 47.619 0.00 0.00 0.00 3.67
563 575 2.367567 TGGAGTACTGTCAAAGGTGTCC 59.632 50.000 0.00 0.00 0.00 4.02
564 576 2.367567 GGAGTACTGTCAAAGGTGTCCA 59.632 50.000 0.00 0.00 0.00 4.02
565 577 3.008049 GGAGTACTGTCAAAGGTGTCCAT 59.992 47.826 0.00 0.00 0.00 3.41
566 578 3.997021 GAGTACTGTCAAAGGTGTCCATG 59.003 47.826 0.00 0.00 0.00 3.66
567 579 1.609208 ACTGTCAAAGGTGTCCATGC 58.391 50.000 0.00 0.00 0.00 4.06
568 580 1.133823 ACTGTCAAAGGTGTCCATGCA 60.134 47.619 0.00 0.00 0.00 3.96
569 581 2.165167 CTGTCAAAGGTGTCCATGCAT 58.835 47.619 0.00 0.00 0.00 3.96
570 582 1.887854 TGTCAAAGGTGTCCATGCATG 59.112 47.619 20.19 20.19 0.00 4.06
571 583 1.888512 GTCAAAGGTGTCCATGCATGT 59.111 47.619 24.58 2.51 0.00 3.21
572 584 3.081061 GTCAAAGGTGTCCATGCATGTA 58.919 45.455 24.58 6.94 0.00 2.29
573 585 3.081061 TCAAAGGTGTCCATGCATGTAC 58.919 45.455 24.58 19.83 0.00 2.90
574 586 3.084039 CAAAGGTGTCCATGCATGTACT 58.916 45.455 24.58 11.97 0.00 2.73
575 587 4.019771 TCAAAGGTGTCCATGCATGTACTA 60.020 41.667 24.58 8.01 0.00 1.82
579 591 4.040461 AGGTGTCCATGCATGTACTATACC 59.960 45.833 24.58 20.61 0.00 2.73
583 595 5.836358 TGTCCATGCATGTACTATACCAGTA 59.164 40.000 24.58 0.00 38.80 2.74
584 596 6.496911 TGTCCATGCATGTACTATACCAGTAT 59.503 38.462 24.58 0.00 41.77 2.12
593 605 5.532032 TGTACTATACCAGTATGCGCTTACA 59.468 40.000 28.63 13.26 41.77 2.41
644 656 1.340248 ACCAGTCCTCACACAAGTACG 59.660 52.381 0.00 0.00 0.00 3.67
645 657 1.340248 CCAGTCCTCACACAAGTACGT 59.660 52.381 0.00 0.00 0.00 3.57
646 658 2.555325 CCAGTCCTCACACAAGTACGTA 59.445 50.000 0.00 0.00 0.00 3.57
647 659 3.192844 CCAGTCCTCACACAAGTACGTAT 59.807 47.826 0.00 0.00 0.00 3.06
716 732 2.951745 GCAGCCGATCGACACGAG 60.952 66.667 18.66 0.00 39.91 4.18
751 771 1.067582 CTTATCCGGTCCAGTCGCC 59.932 63.158 0.00 0.00 0.00 5.54
770 790 2.130073 CTCACTGCTCGACCACGACA 62.130 60.000 0.00 0.00 43.81 4.35
787 810 2.615447 CGACATGGGATGACTGAAATGG 59.385 50.000 0.00 0.00 0.00 3.16
803 826 3.343421 GGGCGTGTGTGGACGTTC 61.343 66.667 0.00 0.00 41.54 3.95
805 828 2.958016 GCGTGTGTGGACGTTCGT 60.958 61.111 0.00 0.00 41.54 3.85
810 833 1.275657 GTGTGGACGTTCGTTGCAG 59.724 57.895 0.00 0.00 0.00 4.41
843 866 0.459237 CGGCTGATCACTCACTGACC 60.459 60.000 0.00 0.00 0.00 4.02
881 909 7.108194 TGGATGTCCATATACGTAGTAGGTAG 58.892 42.308 0.08 0.00 44.16 3.18
882 910 6.541641 GGATGTCCATATACGTAGTAGGTAGG 59.458 46.154 0.08 5.05 40.74 3.18
883 911 7.799315 GGATGTCCATATACGTAGTAGGTAGGT 60.799 44.444 0.08 0.00 40.74 3.08
937 976 0.987294 CTCCTCCATCCACCTTGTGT 59.013 55.000 0.00 0.00 0.00 3.72
938 977 0.692476 TCCTCCATCCACCTTGTGTG 59.308 55.000 0.00 0.00 45.01 3.82
939 978 0.962356 CCTCCATCCACCTTGTGTGC 60.962 60.000 0.00 0.00 44.01 4.57
951 990 3.320826 ACCTTGTGTGCCCAAAGAATTAC 59.679 43.478 0.00 0.00 0.00 1.89
953 992 3.237268 TGTGTGCCCAAAGAATTACCT 57.763 42.857 0.00 0.00 0.00 3.08
970 1009 5.658198 TTACCTATCCTGCTACTCACCTA 57.342 43.478 0.00 0.00 0.00 3.08
1017 1089 2.053865 CATGTTCCCATGGCGCCTT 61.054 57.895 29.70 19.97 43.95 4.35
1178 1262 0.032515 TCGGGCTATGAGGAGAACCA 60.033 55.000 0.00 0.00 38.94 3.67
1191 1281 3.181169 GAACCAGTGCGCGCAGTTT 62.181 57.895 37.21 29.17 0.00 2.66
1333 1429 0.458543 GCTCGGCGACTTCAATCTCA 60.459 55.000 4.99 0.00 0.00 3.27
1441 1540 0.647410 CATCTTCTACAACTGCGCCG 59.353 55.000 4.18 0.00 0.00 6.46
1561 1678 4.221422 TGATCGCCGGCAGCTACC 62.221 66.667 28.98 9.21 40.39 3.18
1566 1683 1.522806 CGCCGGCAGCTACCATTTA 60.523 57.895 28.98 0.00 40.39 1.40
1771 1892 1.223211 GCCTCAGCTTCCCTTCTCC 59.777 63.158 0.00 0.00 35.50 3.71
1840 1975 4.319133 CCATGGTTGGCGCTACTT 57.681 55.556 7.64 0.00 35.85 2.24
2053 2258 2.204136 AGTCAGCCATCCCCACCA 60.204 61.111 0.00 0.00 0.00 4.17
2107 2315 2.568612 CTCCTGCTCGTCGCTTCA 59.431 61.111 0.00 0.00 40.11 3.02
2108 2316 1.080501 CTCCTGCTCGTCGCTTCAA 60.081 57.895 0.00 0.00 40.11 2.69
2115 2323 1.896345 CTCGTCGCTTCAATTCTCGA 58.104 50.000 0.00 0.00 0.00 4.04
2337 2548 2.125912 CTTCCTCGCCGTGGACAG 60.126 66.667 7.51 5.38 32.65 3.51
2399 2616 3.663815 ATCTCGCTGGGTCTCGGGT 62.664 63.158 0.00 0.00 0.00 5.28
2479 2711 4.680237 CAGAAGGTGACGCCGCCA 62.680 66.667 3.54 0.00 45.32 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.038426 ACCCAGGTAAAAAGGCAAATGC 59.962 45.455 0.00 0.00 41.14 3.56
10 11 3.323403 TCACCCAGGTAAAAAGGCAAATG 59.677 43.478 0.00 0.00 0.00 2.32
11 12 3.582164 TCACCCAGGTAAAAAGGCAAAT 58.418 40.909 0.00 0.00 0.00 2.32
12 13 3.033659 TCACCCAGGTAAAAAGGCAAA 57.966 42.857 0.00 0.00 0.00 3.68
13 14 2.757894 TCACCCAGGTAAAAAGGCAA 57.242 45.000 0.00 0.00 0.00 4.52
14 15 2.378547 AGATCACCCAGGTAAAAAGGCA 59.621 45.455 0.00 0.00 0.00 4.75
15 16 3.087370 AGATCACCCAGGTAAAAAGGC 57.913 47.619 0.00 0.00 0.00 4.35
16 17 4.832823 ACAAAGATCACCCAGGTAAAAAGG 59.167 41.667 0.00 0.00 0.00 3.11
17 18 6.715264 ACTACAAAGATCACCCAGGTAAAAAG 59.285 38.462 0.00 0.00 0.00 2.27
18 19 6.607019 ACTACAAAGATCACCCAGGTAAAAA 58.393 36.000 0.00 0.00 0.00 1.94
19 20 6.195600 ACTACAAAGATCACCCAGGTAAAA 57.804 37.500 0.00 0.00 0.00 1.52
20 21 5.836024 ACTACAAAGATCACCCAGGTAAA 57.164 39.130 0.00 0.00 0.00 2.01
21 22 6.183360 CGATACTACAAAGATCACCCAGGTAA 60.183 42.308 0.00 0.00 0.00 2.85
22 23 5.301045 CGATACTACAAAGATCACCCAGGTA 59.699 44.000 0.00 0.00 0.00 3.08
23 24 4.099573 CGATACTACAAAGATCACCCAGGT 59.900 45.833 0.00 0.00 0.00 4.00
24 25 4.099573 ACGATACTACAAAGATCACCCAGG 59.900 45.833 0.00 0.00 0.00 4.45
25 26 5.263968 ACGATACTACAAAGATCACCCAG 57.736 43.478 0.00 0.00 0.00 4.45
26 27 5.670792 AACGATACTACAAAGATCACCCA 57.329 39.130 0.00 0.00 0.00 4.51
27 28 6.255887 CAGAAACGATACTACAAAGATCACCC 59.744 42.308 0.00 0.00 0.00 4.61
28 29 6.812160 ACAGAAACGATACTACAAAGATCACC 59.188 38.462 0.00 0.00 0.00 4.02
29 30 7.201444 CCACAGAAACGATACTACAAAGATCAC 60.201 40.741 0.00 0.00 0.00 3.06
30 31 6.811665 CCACAGAAACGATACTACAAAGATCA 59.188 38.462 0.00 0.00 0.00 2.92
31 32 6.255887 CCCACAGAAACGATACTACAAAGATC 59.744 42.308 0.00 0.00 0.00 2.75
32 33 6.106673 CCCACAGAAACGATACTACAAAGAT 58.893 40.000 0.00 0.00 0.00 2.40
33 34 5.011329 ACCCACAGAAACGATACTACAAAGA 59.989 40.000 0.00 0.00 0.00 2.52
34 35 5.235516 ACCCACAGAAACGATACTACAAAG 58.764 41.667 0.00 0.00 0.00 2.77
35 36 5.011329 AGACCCACAGAAACGATACTACAAA 59.989 40.000 0.00 0.00 0.00 2.83
36 37 4.525487 AGACCCACAGAAACGATACTACAA 59.475 41.667 0.00 0.00 0.00 2.41
37 38 4.084287 AGACCCACAGAAACGATACTACA 58.916 43.478 0.00 0.00 0.00 2.74
38 39 4.398673 AGAGACCCACAGAAACGATACTAC 59.601 45.833 0.00 0.00 0.00 2.73
39 40 4.398358 CAGAGACCCACAGAAACGATACTA 59.602 45.833 0.00 0.00 0.00 1.82
40 41 3.193691 CAGAGACCCACAGAAACGATACT 59.806 47.826 0.00 0.00 0.00 2.12
41 42 3.512680 CAGAGACCCACAGAAACGATAC 58.487 50.000 0.00 0.00 0.00 2.24
42 43 2.094182 GCAGAGACCCACAGAAACGATA 60.094 50.000 0.00 0.00 0.00 2.92
43 44 1.338200 GCAGAGACCCACAGAAACGAT 60.338 52.381 0.00 0.00 0.00 3.73
44 45 0.033504 GCAGAGACCCACAGAAACGA 59.966 55.000 0.00 0.00 0.00 3.85
45 46 1.284982 CGCAGAGACCCACAGAAACG 61.285 60.000 0.00 0.00 0.00 3.60
46 47 0.249911 ACGCAGAGACCCACAGAAAC 60.250 55.000 0.00 0.00 0.00 2.78
47 48 0.033504 GACGCAGAGACCCACAGAAA 59.966 55.000 0.00 0.00 0.00 2.52
48 49 0.827925 AGACGCAGAGACCCACAGAA 60.828 55.000 0.00 0.00 0.00 3.02
49 50 1.228583 AGACGCAGAGACCCACAGA 60.229 57.895 0.00 0.00 0.00 3.41
50 51 1.080230 CAGACGCAGAGACCCACAG 60.080 63.158 0.00 0.00 0.00 3.66
51 52 3.051210 CAGACGCAGAGACCCACA 58.949 61.111 0.00 0.00 0.00 4.17
52 53 2.433318 GCAGACGCAGAGACCCAC 60.433 66.667 0.00 0.00 38.36 4.61
53 54 3.695606 GGCAGACGCAGAGACCCA 61.696 66.667 0.00 0.00 41.24 4.51
54 55 4.459089 GGGCAGACGCAGAGACCC 62.459 72.222 0.00 0.00 41.24 4.46
55 56 3.023949 ATGGGCAGACGCAGAGACC 62.024 63.158 0.00 0.00 42.66 3.85
56 57 1.812922 CATGGGCAGACGCAGAGAC 60.813 63.158 0.00 0.00 42.66 3.36
57 58 0.970427 TACATGGGCAGACGCAGAGA 60.970 55.000 0.00 0.00 42.66 3.10
58 59 0.108186 TTACATGGGCAGACGCAGAG 60.108 55.000 0.00 0.00 42.66 3.35
59 60 0.391130 GTTACATGGGCAGACGCAGA 60.391 55.000 0.00 0.00 42.66 4.26
60 61 0.391661 AGTTACATGGGCAGACGCAG 60.392 55.000 0.00 0.00 42.66 5.18
61 62 0.899019 TAGTTACATGGGCAGACGCA 59.101 50.000 0.00 0.00 43.66 5.24
62 63 1.136305 TCTAGTTACATGGGCAGACGC 59.864 52.381 0.00 0.00 37.44 5.19
63 64 3.643763 GATCTAGTTACATGGGCAGACG 58.356 50.000 0.00 0.00 0.00 4.18
64 65 3.318275 TCGATCTAGTTACATGGGCAGAC 59.682 47.826 0.00 0.00 0.00 3.51
65 66 3.562182 TCGATCTAGTTACATGGGCAGA 58.438 45.455 0.00 0.00 0.00 4.26
66 67 4.527509 ATCGATCTAGTTACATGGGCAG 57.472 45.455 0.00 0.00 0.00 4.85
67 68 4.955811 AATCGATCTAGTTACATGGGCA 57.044 40.909 0.00 0.00 0.00 5.36
68 69 6.483640 AGAAAAATCGATCTAGTTACATGGGC 59.516 38.462 0.00 0.00 0.00 5.36
69 70 7.096023 CGAGAAAAATCGATCTAGTTACATGGG 60.096 40.741 0.00 0.00 45.56 4.00
70 71 7.567771 GCGAGAAAAATCGATCTAGTTACATGG 60.568 40.741 0.00 0.00 45.56 3.66
71 72 7.168302 AGCGAGAAAAATCGATCTAGTTACATG 59.832 37.037 0.00 0.00 45.56 3.21
72 73 7.203910 AGCGAGAAAAATCGATCTAGTTACAT 58.796 34.615 0.00 0.00 45.56 2.29
73 74 6.561614 AGCGAGAAAAATCGATCTAGTTACA 58.438 36.000 0.00 0.00 45.56 2.41
82 83 4.116747 ACTGAGAGCGAGAAAAATCGAT 57.883 40.909 0.00 0.00 45.27 3.59
83 84 3.577649 ACTGAGAGCGAGAAAAATCGA 57.422 42.857 0.00 0.00 45.56 3.59
84 85 3.675225 TGAACTGAGAGCGAGAAAAATCG 59.325 43.478 0.00 0.00 45.48 3.34
85 86 4.449068 TGTGAACTGAGAGCGAGAAAAATC 59.551 41.667 0.00 0.00 0.00 2.17
86 87 4.380531 TGTGAACTGAGAGCGAGAAAAAT 58.619 39.130 0.00 0.00 0.00 1.82
87 88 3.792401 TGTGAACTGAGAGCGAGAAAAA 58.208 40.909 0.00 0.00 0.00 1.94
88 89 3.384668 CTGTGAACTGAGAGCGAGAAAA 58.615 45.455 0.00 0.00 0.00 2.29
89 90 2.864097 GCTGTGAACTGAGAGCGAGAAA 60.864 50.000 0.00 0.00 0.00 2.52
90 91 1.336332 GCTGTGAACTGAGAGCGAGAA 60.336 52.381 0.00 0.00 0.00 2.87
91 92 0.242286 GCTGTGAACTGAGAGCGAGA 59.758 55.000 0.00 0.00 0.00 4.04
92 93 2.735634 GCTGTGAACTGAGAGCGAG 58.264 57.895 0.00 0.00 0.00 5.03
93 94 4.974792 GCTGTGAACTGAGAGCGA 57.025 55.556 0.00 0.00 0.00 4.93
95 96 2.724708 CGCGCTGTGAACTGAGAGC 61.725 63.158 5.56 0.00 0.00 4.09
96 97 2.091112 CCGCGCTGTGAACTGAGAG 61.091 63.158 5.56 0.00 0.00 3.20
97 98 2.049156 CCGCGCTGTGAACTGAGA 60.049 61.111 5.56 0.00 0.00 3.27
98 99 3.114616 CCCGCGCTGTGAACTGAG 61.115 66.667 5.56 0.00 0.00 3.35
99 100 3.923864 ACCCGCGCTGTGAACTGA 61.924 61.111 5.56 0.00 0.00 3.41
100 101 3.716006 CACCCGCGCTGTGAACTG 61.716 66.667 18.75 0.00 35.74 3.16
103 104 4.927782 AAGCACCCGCGCTGTGAA 62.928 61.111 25.29 0.00 42.89 3.18
104 105 4.927782 AAAGCACCCGCGCTGTGA 62.928 61.111 25.29 0.00 42.89 3.58
105 106 3.879351 GAAAAGCACCCGCGCTGTG 62.879 63.158 19.09 19.09 42.89 3.66
106 107 3.660111 GAAAAGCACCCGCGCTGT 61.660 61.111 5.56 0.00 42.89 4.40
107 108 4.404654 GGAAAAGCACCCGCGCTG 62.405 66.667 5.56 0.00 42.89 5.18
124 125 6.070824 ACTCTTTGTTTGCATAATAAAGGGGG 60.071 38.462 22.20 16.53 34.09 5.40
125 126 6.935167 ACTCTTTGTTTGCATAATAAAGGGG 58.065 36.000 22.20 17.90 34.09 4.79
126 127 8.306761 AGAACTCTTTGTTTGCATAATAAAGGG 58.693 33.333 19.36 19.36 39.30 3.95
127 128 9.696917 AAGAACTCTTTGTTTGCATAATAAAGG 57.303 29.630 19.97 15.74 39.30 3.11
132 133 8.854117 AGAGAAAGAACTCTTTGTTTGCATAAT 58.146 29.630 9.40 0.00 45.37 1.28
133 134 8.225603 AGAGAAAGAACTCTTTGTTTGCATAA 57.774 30.769 9.40 0.00 45.37 1.90
134 135 7.307396 CGAGAGAAAGAACTCTTTGTTTGCATA 60.307 37.037 9.40 0.00 45.37 3.14
135 136 6.512415 CGAGAGAAAGAACTCTTTGTTTGCAT 60.512 38.462 9.40 0.00 45.37 3.96
136 137 5.220662 CGAGAGAAAGAACTCTTTGTTTGCA 60.221 40.000 9.40 0.00 45.37 4.08
137 138 5.201181 CGAGAGAAAGAACTCTTTGTTTGC 58.799 41.667 9.40 0.00 45.37 3.68
138 139 5.201181 GCGAGAGAAAGAACTCTTTGTTTG 58.799 41.667 9.40 1.91 45.37 2.93
139 140 4.273724 GGCGAGAGAAAGAACTCTTTGTTT 59.726 41.667 9.40 1.03 45.37 2.83
140 141 3.810386 GGCGAGAGAAAGAACTCTTTGTT 59.190 43.478 9.40 0.00 45.37 2.83
141 142 3.394719 GGCGAGAGAAAGAACTCTTTGT 58.605 45.455 9.40 5.52 45.37 2.83
142 143 2.410053 CGGCGAGAGAAAGAACTCTTTG 59.590 50.000 9.40 0.00 45.37 2.77
144 145 1.067495 CCGGCGAGAGAAAGAACTCTT 60.067 52.381 9.30 0.00 45.69 2.85
146 147 1.079317 GCCGGCGAGAGAAAGAACTC 61.079 60.000 12.58 0.00 37.19 3.01
147 148 1.079750 GCCGGCGAGAGAAAGAACT 60.080 57.895 12.58 0.00 0.00 3.01
148 149 0.949105 TTGCCGGCGAGAGAAAGAAC 60.949 55.000 23.90 0.00 0.00 3.01
149 150 0.949105 GTTGCCGGCGAGAGAAAGAA 60.949 55.000 23.90 3.60 0.00 2.52
150 151 1.374252 GTTGCCGGCGAGAGAAAGA 60.374 57.895 23.90 0.00 0.00 2.52
151 152 0.108804 TAGTTGCCGGCGAGAGAAAG 60.109 55.000 23.90 0.00 0.00 2.62
152 153 0.389426 GTAGTTGCCGGCGAGAGAAA 60.389 55.000 23.90 6.19 0.00 2.52
153 154 1.214589 GTAGTTGCCGGCGAGAGAA 59.785 57.895 23.90 7.06 0.00 2.87
154 155 0.393402 TAGTAGTTGCCGGCGAGAGA 60.393 55.000 23.90 4.83 0.00 3.10
155 156 0.248539 GTAGTAGTTGCCGGCGAGAG 60.249 60.000 23.90 0.00 0.00 3.20
156 157 0.961857 TGTAGTAGTTGCCGGCGAGA 60.962 55.000 23.90 8.17 0.00 4.04
157 158 0.801067 GTGTAGTAGTTGCCGGCGAG 60.801 60.000 23.90 0.00 0.00 5.03
158 159 1.213537 GTGTAGTAGTTGCCGGCGA 59.786 57.895 23.90 19.26 0.00 5.54
159 160 0.452987 TAGTGTAGTAGTTGCCGGCG 59.547 55.000 23.90 0.00 0.00 6.46
160 161 1.202382 CCTAGTGTAGTAGTTGCCGGC 60.202 57.143 22.73 22.73 0.00 6.13
161 162 2.098770 GTCCTAGTGTAGTAGTTGCCGG 59.901 54.545 0.00 0.00 0.00 6.13
162 163 2.098770 GGTCCTAGTGTAGTAGTTGCCG 59.901 54.545 0.00 0.00 0.00 5.69
163 164 2.098770 CGGTCCTAGTGTAGTAGTTGCC 59.901 54.545 0.00 0.00 0.00 4.52
164 165 2.751806 ACGGTCCTAGTGTAGTAGTTGC 59.248 50.000 0.00 0.00 0.00 4.17
165 166 5.181748 AGTACGGTCCTAGTGTAGTAGTTG 58.818 45.833 0.00 0.00 0.00 3.16
166 167 5.428184 AGTACGGTCCTAGTGTAGTAGTT 57.572 43.478 0.00 0.00 0.00 2.24
167 168 5.659079 ACTAGTACGGTCCTAGTGTAGTAGT 59.341 44.000 12.00 15.97 44.51 2.73
168 169 6.155475 ACTAGTACGGTCCTAGTGTAGTAG 57.845 45.833 12.00 15.17 42.63 2.57
169 170 7.040473 GTACTAGTACGGTCCTAGTGTAGTA 57.960 44.000 19.92 0.91 43.70 1.82
170 171 5.908341 GTACTAGTACGGTCCTAGTGTAGT 58.092 45.833 19.92 1.78 43.70 2.73
184 185 8.140677 ACATCACTAATCAGTCGTACTAGTAC 57.859 38.462 21.06 21.06 30.46 2.73
185 186 9.822185 TTACATCACTAATCAGTCGTACTAGTA 57.178 33.333 0.00 0.00 30.46 1.82
186 187 8.728337 TTACATCACTAATCAGTCGTACTAGT 57.272 34.615 0.00 0.00 30.46 2.57
187 188 8.283992 CCTTACATCACTAATCAGTCGTACTAG 58.716 40.741 0.00 0.00 30.46 2.57
188 189 7.772292 ACCTTACATCACTAATCAGTCGTACTA 59.228 37.037 0.00 0.00 30.46 1.82
189 190 6.602406 ACCTTACATCACTAATCAGTCGTACT 59.398 38.462 0.00 0.00 30.46 2.73
190 191 6.793349 ACCTTACATCACTAATCAGTCGTAC 58.207 40.000 0.00 0.00 30.46 3.67
191 192 8.510243 TTACCTTACATCACTAATCAGTCGTA 57.490 34.615 0.00 0.00 30.46 3.43
192 193 5.916661 ACCTTACATCACTAATCAGTCGT 57.083 39.130 0.00 0.00 30.46 4.34
193 194 8.873215 ATTTACCTTACATCACTAATCAGTCG 57.127 34.615 0.00 0.00 30.46 4.18
200 201 9.049050 TGGGAGTAATTTACCTTACATCACTAA 57.951 33.333 2.92 0.00 34.66 2.24
201 202 8.612486 TGGGAGTAATTTACCTTACATCACTA 57.388 34.615 2.92 0.00 34.66 2.74
202 203 7.504926 TGGGAGTAATTTACCTTACATCACT 57.495 36.000 2.92 0.00 34.66 3.41
203 204 7.827729 ACTTGGGAGTAATTTACCTTACATCAC 59.172 37.037 2.92 0.00 34.66 3.06
204 205 7.924541 ACTTGGGAGTAATTTACCTTACATCA 58.075 34.615 2.92 0.00 34.66 3.07
205 206 9.322773 GTACTTGGGAGTAATTTACCTTACATC 57.677 37.037 2.92 0.00 39.95 3.06
206 207 8.828751 TGTACTTGGGAGTAATTTACCTTACAT 58.171 33.333 2.92 0.00 39.95 2.29
207 208 8.204903 TGTACTTGGGAGTAATTTACCTTACA 57.795 34.615 2.92 0.00 39.95 2.41
208 209 9.159364 CTTGTACTTGGGAGTAATTTACCTTAC 57.841 37.037 2.92 0.00 39.95 2.34
209 210 8.883302 ACTTGTACTTGGGAGTAATTTACCTTA 58.117 33.333 2.92 0.00 39.95 2.69
210 211 7.664318 CACTTGTACTTGGGAGTAATTTACCTT 59.336 37.037 2.92 0.00 39.95 3.50
211 212 7.166167 CACTTGTACTTGGGAGTAATTTACCT 58.834 38.462 2.92 0.00 39.95 3.08
212 213 6.373495 CCACTTGTACTTGGGAGTAATTTACC 59.627 42.308 2.92 0.00 39.95 2.85
213 214 7.373778 CCACTTGTACTTGGGAGTAATTTAC 57.626 40.000 0.00 0.00 39.95 2.01
224 225 6.894339 AAATTAGAACCCACTTGTACTTGG 57.106 37.500 0.00 0.00 0.00 3.61
225 226 8.287503 GTGTAAATTAGAACCCACTTGTACTTG 58.712 37.037 0.00 0.00 0.00 3.16
226 227 7.994334 TGTGTAAATTAGAACCCACTTGTACTT 59.006 33.333 0.00 0.00 0.00 2.24
227 228 7.511268 TGTGTAAATTAGAACCCACTTGTACT 58.489 34.615 0.00 0.00 0.00 2.73
228 229 7.733402 TGTGTAAATTAGAACCCACTTGTAC 57.267 36.000 0.00 0.00 0.00 2.90
229 230 7.994334 ACTTGTGTAAATTAGAACCCACTTGTA 59.006 33.333 0.00 0.00 0.00 2.41
230 231 6.831868 ACTTGTGTAAATTAGAACCCACTTGT 59.168 34.615 0.00 0.00 0.00 3.16
231 232 7.272037 ACTTGTGTAAATTAGAACCCACTTG 57.728 36.000 0.00 0.00 0.00 3.16
232 233 8.434392 TCTACTTGTGTAAATTAGAACCCACTT 58.566 33.333 0.00 0.00 0.00 3.16
233 234 7.970102 TCTACTTGTGTAAATTAGAACCCACT 58.030 34.615 0.00 0.00 0.00 4.00
244 245 9.618890 AATGTATGAGCATCTACTTGTGTAAAT 57.381 29.630 0.00 0.00 34.92 1.40
248 249 6.703607 GCTAATGTATGAGCATCTACTTGTGT 59.296 38.462 0.00 0.00 38.62 3.72
264 265 6.892658 TTGTTTCCACTTGTGCTAATGTAT 57.107 33.333 0.00 0.00 0.00 2.29
269 270 5.652994 AACTTTGTTTCCACTTGTGCTAA 57.347 34.783 0.00 0.00 0.00 3.09
285 286 3.187700 CCGTAGCCTAGCAGTAACTTTG 58.812 50.000 0.00 0.00 0.00 2.77
300 301 1.972660 ATCCAGTCTTGGGCCGTAGC 61.973 60.000 0.00 0.00 45.10 3.58
307 314 1.207488 TGGGGTGATCCAGTCTTGGG 61.207 60.000 0.00 0.00 45.10 4.12
321 328 2.514803 GCTGAGTGTACAAATTGGGGT 58.485 47.619 0.00 0.00 0.00 4.95
322 329 1.818674 GGCTGAGTGTACAAATTGGGG 59.181 52.381 0.00 0.00 0.00 4.96
332 343 2.310779 AGACTTCAGGGCTGAGTGTA 57.689 50.000 0.00 0.00 41.13 2.90
342 353 1.673665 GCCAGTGCCAGACTTCAGG 60.674 63.158 0.00 0.00 29.75 3.86
345 356 0.952984 GTCAGCCAGTGCCAGACTTC 60.953 60.000 0.00 0.00 38.98 3.01
371 382 1.987770 TCGCGTATGAACCTTTTCGAC 59.012 47.619 5.77 0.00 34.04 4.20
379 390 3.123804 ACTGATGAATCGCGTATGAACC 58.876 45.455 5.77 0.00 0.00 3.62
381 392 4.307443 AGACTGATGAATCGCGTATGAA 57.693 40.909 5.77 0.00 0.00 2.57
383 394 4.294232 AGAAGACTGATGAATCGCGTATG 58.706 43.478 5.77 0.00 0.00 2.39
384 395 4.576216 AGAAGACTGATGAATCGCGTAT 57.424 40.909 5.77 0.00 0.00 3.06
385 396 4.575236 ACTAGAAGACTGATGAATCGCGTA 59.425 41.667 5.77 0.00 0.00 4.42
387 398 3.728221 CACTAGAAGACTGATGAATCGCG 59.272 47.826 0.00 0.00 0.00 5.87
409 421 8.681138 GCATGTTTTTCAAAATCCGAAATTTTC 58.319 29.630 0.00 0.00 32.66 2.29
426 438 8.421002 ACTAAGTCCAATGTTTAGCATGTTTTT 58.579 29.630 0.00 0.00 37.96 1.94
444 456 5.162075 CGGCTTACAGCATATACTAAGTCC 58.838 45.833 0.00 0.00 44.75 3.85
467 479 1.138247 CGTGTGCTCGGTACCTACC 59.862 63.158 10.90 0.00 42.98 3.18
468 480 1.086696 TACGTGTGCTCGGTACCTAC 58.913 55.000 10.90 4.57 34.94 3.18
469 481 1.086696 GTACGTGTGCTCGGTACCTA 58.913 55.000 10.90 0.00 34.94 3.08
470 482 1.878775 GTACGTGTGCTCGGTACCT 59.121 57.895 10.90 0.00 34.94 3.08
475 487 3.982372 ATGGCGTACGTGTGCTCGG 62.982 63.158 17.90 0.00 34.94 4.63
483 495 3.960237 CCACACAATGGCGTACGT 58.040 55.556 17.90 0.00 43.24 3.57
504 516 4.896238 CGTATTGACAGTTTTGACACGAAC 59.104 41.667 0.00 0.00 0.00 3.95
511 523 4.619973 ACCGTACGTATTGACAGTTTTGA 58.380 39.130 15.21 0.00 0.00 2.69
512 524 4.445052 TGACCGTACGTATTGACAGTTTTG 59.555 41.667 15.21 0.00 0.00 2.44
513 525 4.619973 TGACCGTACGTATTGACAGTTTT 58.380 39.130 15.21 0.00 0.00 2.43
514 526 4.232221 CTGACCGTACGTATTGACAGTTT 58.768 43.478 15.21 0.00 0.00 2.66
515 527 3.829948 CTGACCGTACGTATTGACAGTT 58.170 45.455 15.21 0.00 0.00 3.16
516 528 2.415090 GCTGACCGTACGTATTGACAGT 60.415 50.000 15.21 1.59 0.00 3.55
517 529 2.159421 AGCTGACCGTACGTATTGACAG 60.159 50.000 15.21 14.43 0.00 3.51
518 530 1.814394 AGCTGACCGTACGTATTGACA 59.186 47.619 15.21 4.52 0.00 3.58
519 531 2.556534 AGCTGACCGTACGTATTGAC 57.443 50.000 15.21 0.00 0.00 3.18
520 532 4.906065 ATTAGCTGACCGTACGTATTGA 57.094 40.909 15.21 0.00 0.00 2.57
530 542 3.119101 ACAGTACTCCAATTAGCTGACCG 60.119 47.826 0.00 0.00 0.00 4.79
532 544 5.073311 TGACAGTACTCCAATTAGCTGAC 57.927 43.478 0.00 0.00 0.00 3.51
560 572 5.215252 ACTGGTATAGTACATGCATGGAC 57.785 43.478 31.22 31.22 42.05 4.02
561 573 6.574269 GCATACTGGTATAGTACATGCATGGA 60.574 42.308 29.41 20.48 44.91 3.41
562 574 5.582269 GCATACTGGTATAGTACATGCATGG 59.418 44.000 29.41 12.50 44.91 3.66
563 575 5.289434 CGCATACTGGTATAGTACATGCATG 59.711 44.000 25.09 25.09 45.43 4.06
564 576 5.410924 CGCATACTGGTATAGTACATGCAT 58.589 41.667 12.56 0.00 45.43 3.96
565 577 4.805219 CGCATACTGGTATAGTACATGCA 58.195 43.478 12.56 0.00 45.43 3.96
566 578 3.612860 GCGCATACTGGTATAGTACATGC 59.387 47.826 0.30 0.00 44.30 4.06
567 579 5.060662 AGCGCATACTGGTATAGTACATG 57.939 43.478 11.47 0.00 44.30 3.21
568 580 5.723672 AAGCGCATACTGGTATAGTACAT 57.276 39.130 11.47 0.00 44.30 2.29
569 581 5.532032 TGTAAGCGCATACTGGTATAGTACA 59.468 40.000 21.90 0.00 44.30 2.90
570 582 6.005583 TGTAAGCGCATACTGGTATAGTAC 57.994 41.667 21.90 0.00 44.30 2.73
571 583 6.829229 ATGTAAGCGCATACTGGTATAGTA 57.171 37.500 21.90 0.66 45.50 1.82
572 584 5.723672 ATGTAAGCGCATACTGGTATAGT 57.276 39.130 21.90 0.00 43.56 2.12
573 585 6.645003 TGAAATGTAAGCGCATACTGGTATAG 59.355 38.462 21.90 0.00 0.00 1.31
574 586 6.422701 GTGAAATGTAAGCGCATACTGGTATA 59.577 38.462 21.90 2.77 0.00 1.47
575 587 5.236478 GTGAAATGTAAGCGCATACTGGTAT 59.764 40.000 21.90 6.01 0.00 2.73
579 591 3.544048 CGGTGAAATGTAAGCGCATACTG 60.544 47.826 21.90 0.00 0.00 2.74
583 595 0.732571 CCGGTGAAATGTAAGCGCAT 59.267 50.000 11.47 0.00 36.04 4.73
584 596 0.604243 ACCGGTGAAATGTAAGCGCA 60.604 50.000 6.12 0.00 36.04 6.09
593 605 2.137523 GTACACGTGAACCGGTGAAAT 58.862 47.619 25.01 0.00 42.24 2.17
644 656 1.069358 GGGTGTGAGCTAGCTGGATAC 59.931 57.143 24.99 15.85 0.00 2.24
645 657 1.342975 TGGGTGTGAGCTAGCTGGATA 60.343 52.381 24.99 3.63 0.00 2.59
646 658 0.618680 TGGGTGTGAGCTAGCTGGAT 60.619 55.000 24.99 0.00 0.00 3.41
647 659 0.618680 ATGGGTGTGAGCTAGCTGGA 60.619 55.000 24.99 5.31 0.00 3.86
751 771 1.442857 GTCGTGGTCGAGCAGTGAG 60.443 63.158 19.24 10.00 46.96 3.51
770 790 1.751733 CGCCCATTTCAGTCATCCCAT 60.752 52.381 0.00 0.00 0.00 4.00
787 810 3.698463 CGAACGTCCACACACGCC 61.698 66.667 0.00 0.00 43.93 5.68
803 826 0.317770 AACATTTGACCGCTGCAACG 60.318 50.000 1.65 1.65 0.00 4.10
805 828 0.313672 GGAACATTTGACCGCTGCAA 59.686 50.000 0.00 0.00 0.00 4.08
810 833 2.178273 GCCGGAACATTTGACCGC 59.822 61.111 5.05 0.00 44.45 5.68
881 909 5.752892 TCAACTGAGATACTCATCGTACC 57.247 43.478 1.92 0.00 39.92 3.34
882 910 7.862648 TGTATCAACTGAGATACTCATCGTAC 58.137 38.462 18.39 3.63 46.66 3.67
883 911 8.446599 TTGTATCAACTGAGATACTCATCGTA 57.553 34.615 18.39 0.00 46.66 3.43
884 912 6.944234 TGTATCAACTGAGATACTCATCGT 57.056 37.500 18.39 0.00 46.66 3.73
937 976 4.792068 CAGGATAGGTAATTCTTTGGGCA 58.208 43.478 0.00 0.00 0.00 5.36
938 977 3.570125 GCAGGATAGGTAATTCTTTGGGC 59.430 47.826 0.00 0.00 0.00 5.36
939 978 5.053978 AGCAGGATAGGTAATTCTTTGGG 57.946 43.478 0.00 0.00 0.00 4.12
951 990 3.257127 GCTTAGGTGAGTAGCAGGATAGG 59.743 52.174 0.00 0.00 35.05 2.57
953 992 3.231818 GGCTTAGGTGAGTAGCAGGATA 58.768 50.000 0.00 0.00 36.64 2.59
970 1009 3.979347 AGGATGATTCTGGTAGATGGCTT 59.021 43.478 0.00 0.00 0.00 4.35
1166 1250 1.078848 GCGCACTGGTTCTCCTCAT 60.079 57.895 0.30 0.00 34.23 2.90
1191 1281 2.829384 GCAGTGGACCTGGAACCCA 61.829 63.158 0.00 1.66 41.81 4.51
1254 1347 5.363562 AGAATATGTTGAGGATCTGCACA 57.636 39.130 0.00 0.00 34.92 4.57
1255 1348 6.283694 TGTAGAATATGTTGAGGATCTGCAC 58.716 40.000 0.00 0.00 34.92 4.57
1561 1678 1.136565 CGTTGCAGCCCGGTAAATG 59.863 57.895 0.00 0.00 0.00 2.32
1606 1723 1.304381 TGGCATTCACCTTCCCAGC 60.304 57.895 0.00 0.00 0.00 4.85
1771 1892 0.175302 TAATTTTGCATGGCCCGCTG 59.825 50.000 14.73 4.42 0.00 5.18
1908 2055 4.260784 CGCTCTATTTCTTTCCCATTTCCG 60.261 45.833 0.00 0.00 0.00 4.30
1921 2068 3.860536 GGTCAGAGTCAACGCTCTATTTC 59.139 47.826 0.00 0.00 43.37 2.17
2053 2258 4.802051 AGCGGCGGCATGGATTGT 62.802 61.111 19.21 0.00 43.41 2.71
2107 2315 2.512515 GCCGGCAGCTCGAGAATT 60.513 61.111 24.80 0.00 38.99 2.17
2108 2316 4.880537 CGCCGGCAGCTCGAGAAT 62.881 66.667 28.98 0.00 40.39 2.40
2399 2616 1.668919 GCTGATGACGAACGGACTCAA 60.669 52.381 0.00 0.00 0.00 3.02
2479 2711 4.636435 CCCGTGCGGTTGAACCCT 62.636 66.667 9.08 0.00 33.75 4.34


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

AutoCloner maintained by Alex Coulton.