Multiple sequence alignment - TraesCS1A01G141100

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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 TraesCS1A01G141100 chr1A 100.000 3567 0 0 714 4280 238999681 239003247 0.000000e+00 6588.0
1 TraesCS1A01G141100 chr1A 100.000 151 0 0 1 151 238998968 238999118 3.260000e-71 279.0
2 TraesCS1A01G141100 chr1D 92.773 3390 103 47 714 4005 192916876 192920221 0.000000e+00 4772.0
3 TraesCS1A01G141100 chr1D 92.903 310 19 3 3971 4280 192920323 192920629 8.440000e-122 448.0
4 TraesCS1A01G141100 chr1B 93.134 1777 55 17 762 2498 267877039 267878788 0.000000e+00 2543.0
5 TraesCS1A01G141100 chr1B 95.380 1039 31 5 2720 3741 267879080 267880118 0.000000e+00 1637.0
6 TraesCS1A01G141100 chr1B 92.551 537 25 9 3744 4280 267880153 267880674 0.000000e+00 756.0
7 TraesCS1A01G141100 chr1B 96.537 231 8 0 2505 2735 267878832 267879062 2.410000e-102 383.0
8 TraesCS1A01G141100 chr5A 80.872 298 49 8 3833 4126 38147384 38147091 1.200000e-55 228.0
9 TraesCS1A01G141100 chr3D 82.129 263 40 6 3847 4106 352951837 352951579 7.210000e-53 219.0
10 TraesCS1A01G141100 chr2D 79.344 305 45 13 3833 4132 489048178 489047887 9.390000e-47 198.0
11 TraesCS1A01G141100 chr2D 80.423 189 31 5 3827 4010 442996496 442996683 5.770000e-29 139.0
12 TraesCS1A01G141100 chr2A 83.886 211 28 6 3827 4032 586463750 586463959 3.380000e-46 196.0
13 TraesCS1A01G141100 chr7D 77.746 346 56 17 3792 4126 65385592 65385927 4.370000e-45 193.0
14 TraesCS1A01G141100 chr7D 78.157 293 48 14 3833 4119 197873373 197873091 5.690000e-39 172.0
15 TraesCS1A01G141100 chr7D 76.623 231 38 11 3901 4126 563764512 563764731 3.500000e-21 113.0
16 TraesCS1A01G141100 chr7B 80.738 244 40 7 3833 4075 712784456 712784693 2.630000e-42 183.0
17 TraesCS1A01G141100 chr4A 80.745 161 26 5 3967 4126 32651249 32651405 2.090000e-23 121.0
18 TraesCS1A01G141100 chr6B 91.935 62 3 2 4066 4126 644380399 644380459 7.630000e-13 86.1


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 TraesCS1A01G141100 chr1A 238998968 239003247 4279 False 3433.50 6588 100.0000 1 4280 2 chr1A.!!$F1 4279
1 TraesCS1A01G141100 chr1D 192916876 192920629 3753 False 2610.00 4772 92.8380 714 4280 2 chr1D.!!$F1 3566
2 TraesCS1A01G141100 chr1B 267877039 267880674 3635 False 1329.75 2543 94.4005 762 4280 4 chr1B.!!$F1 3518

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
146 147 0.099968 CGGTCGCGGAGATTTGACTA 59.900 55.000 6.13 0.00 0.00 2.59 F
150 151 1.136305 TCGCGGAGATTTGACTAAGGG 59.864 52.381 6.13 0.00 0.00 3.95 F
833 835 1.372004 CGTCGGTTGCACGGTAGAA 60.372 57.895 0.00 0.00 33.46 2.10 F
2736 2828 0.038021 TGAATGTTAGCTGCTGGCCA 59.962 50.000 13.43 4.71 43.05 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1140 1168 1.447838 CTGTCGGTAATGGTGCGCT 60.448 57.895 9.73 0.0 0.0 5.92 R
2022 2073 1.590932 AGCCTCATCGCACATGAATC 58.409 50.000 0.00 0.0 0.0 2.52 R
2762 2887 1.152777 TGGGGTGTCAACTTGCAGG 60.153 57.895 0.00 0.0 0.0 4.85 R
4146 4469 0.036306 GACGTCCCAATCCAGGTTGT 59.964 55.000 3.51 0.0 0.0 3.32 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
20 21 2.352503 ATGCAACCATCGACAAAAGC 57.647 45.000 0.00 0.00 0.00 3.51
21 22 1.028130 TGCAACCATCGACAAAAGCA 58.972 45.000 0.00 0.00 0.00 3.91
22 23 1.406898 TGCAACCATCGACAAAAGCAA 59.593 42.857 0.00 0.00 0.00 3.91
23 24 2.053627 GCAACCATCGACAAAAGCAAG 58.946 47.619 0.00 0.00 0.00 4.01
24 25 2.664916 CAACCATCGACAAAAGCAAGG 58.335 47.619 0.00 0.00 0.00 3.61
25 26 0.598065 ACCATCGACAAAAGCAAGGC 59.402 50.000 0.00 0.00 0.00 4.35
26 27 0.109132 CCATCGACAAAAGCAAGGCC 60.109 55.000 0.00 0.00 0.00 5.19
27 28 0.883833 CATCGACAAAAGCAAGGCCT 59.116 50.000 0.00 0.00 0.00 5.19
28 29 1.270550 CATCGACAAAAGCAAGGCCTT 59.729 47.619 13.78 13.78 0.00 4.35
29 30 1.398692 TCGACAAAAGCAAGGCCTTT 58.601 45.000 17.61 0.00 36.65 3.11
30 31 2.577700 TCGACAAAAGCAAGGCCTTTA 58.422 42.857 17.61 0.00 34.12 1.85
31 32 2.292292 TCGACAAAAGCAAGGCCTTTAC 59.708 45.455 17.61 11.51 34.12 2.01
32 33 2.034053 CGACAAAAGCAAGGCCTTTACA 59.966 45.455 17.61 0.00 34.12 2.41
33 34 3.381045 GACAAAAGCAAGGCCTTTACAC 58.619 45.455 17.61 5.83 34.12 2.90
34 35 3.031013 ACAAAAGCAAGGCCTTTACACT 58.969 40.909 17.61 8.30 34.12 3.55
35 36 3.450817 ACAAAAGCAAGGCCTTTACACTT 59.549 39.130 17.61 14.07 34.12 3.16
36 37 4.647399 ACAAAAGCAAGGCCTTTACACTTA 59.353 37.500 17.61 0.00 34.12 2.24
37 38 4.848562 AAAGCAAGGCCTTTACACTTAC 57.151 40.909 17.61 0.00 33.50 2.34
38 39 3.502123 AGCAAGGCCTTTACACTTACA 57.498 42.857 17.61 0.00 0.00 2.41
39 40 3.146847 AGCAAGGCCTTTACACTTACAC 58.853 45.455 17.61 0.00 0.00 2.90
40 41 2.228103 GCAAGGCCTTTACACTTACACC 59.772 50.000 17.61 0.00 0.00 4.16
41 42 3.482436 CAAGGCCTTTACACTTACACCA 58.518 45.455 17.61 0.00 0.00 4.17
42 43 3.868619 AGGCCTTTACACTTACACCAA 57.131 42.857 0.00 0.00 0.00 3.67
43 44 3.483421 AGGCCTTTACACTTACACCAAC 58.517 45.455 0.00 0.00 0.00 3.77
44 45 3.117813 AGGCCTTTACACTTACACCAACA 60.118 43.478 0.00 0.00 0.00 3.33
45 46 3.004002 GGCCTTTACACTTACACCAACAC 59.996 47.826 0.00 0.00 0.00 3.32
46 47 3.004002 GCCTTTACACTTACACCAACACC 59.996 47.826 0.00 0.00 0.00 4.16
47 48 4.457466 CCTTTACACTTACACCAACACCT 58.543 43.478 0.00 0.00 0.00 4.00
48 49 5.613329 CCTTTACACTTACACCAACACCTA 58.387 41.667 0.00 0.00 0.00 3.08
49 50 6.056884 CCTTTACACTTACACCAACACCTAA 58.943 40.000 0.00 0.00 0.00 2.69
50 51 6.543100 CCTTTACACTTACACCAACACCTAAA 59.457 38.462 0.00 0.00 0.00 1.85
51 52 7.229907 CCTTTACACTTACACCAACACCTAAAT 59.770 37.037 0.00 0.00 0.00 1.40
52 53 7.733402 TTACACTTACACCAACACCTAAATC 57.267 36.000 0.00 0.00 0.00 2.17
53 54 5.937111 ACACTTACACCAACACCTAAATCT 58.063 37.500 0.00 0.00 0.00 2.40
54 55 5.995897 ACACTTACACCAACACCTAAATCTC 59.004 40.000 0.00 0.00 0.00 2.75
55 56 5.995282 CACTTACACCAACACCTAAATCTCA 59.005 40.000 0.00 0.00 0.00 3.27
56 57 5.995897 ACTTACACCAACACCTAAATCTCAC 59.004 40.000 0.00 0.00 0.00 3.51
57 58 4.431416 ACACCAACACCTAAATCTCACA 57.569 40.909 0.00 0.00 0.00 3.58
58 59 4.134563 ACACCAACACCTAAATCTCACAC 58.865 43.478 0.00 0.00 0.00 3.82
59 60 4.141482 ACACCAACACCTAAATCTCACACT 60.141 41.667 0.00 0.00 0.00 3.55
60 61 5.071250 ACACCAACACCTAAATCTCACACTA 59.929 40.000 0.00 0.00 0.00 2.74
61 62 6.173339 CACCAACACCTAAATCTCACACTAT 58.827 40.000 0.00 0.00 0.00 2.12
62 63 6.092670 CACCAACACCTAAATCTCACACTATG 59.907 42.308 0.00 0.00 0.00 2.23
63 64 5.586243 CCAACACCTAAATCTCACACTATGG 59.414 44.000 0.00 0.00 0.00 2.74
64 65 4.770795 ACACCTAAATCTCACACTATGGC 58.229 43.478 0.00 0.00 0.00 4.40
65 66 4.471386 ACACCTAAATCTCACACTATGGCT 59.529 41.667 0.00 0.00 0.00 4.75
66 67 5.661312 ACACCTAAATCTCACACTATGGCTA 59.339 40.000 0.00 0.00 0.00 3.93
67 68 5.986135 CACCTAAATCTCACACTATGGCTAC 59.014 44.000 0.00 0.00 0.00 3.58
68 69 5.900123 ACCTAAATCTCACACTATGGCTACT 59.100 40.000 0.00 0.00 0.00 2.57
69 70 6.041069 ACCTAAATCTCACACTATGGCTACTC 59.959 42.308 0.00 0.00 0.00 2.59
70 71 6.266558 CCTAAATCTCACACTATGGCTACTCT 59.733 42.308 0.00 0.00 0.00 3.24
71 72 5.782893 AATCTCACACTATGGCTACTCTC 57.217 43.478 0.00 0.00 0.00 3.20
72 73 4.511786 TCTCACACTATGGCTACTCTCT 57.488 45.455 0.00 0.00 0.00 3.10
73 74 4.456535 TCTCACACTATGGCTACTCTCTC 58.543 47.826 0.00 0.00 0.00 3.20
74 75 4.080299 TCTCACACTATGGCTACTCTCTCA 60.080 45.833 0.00 0.00 0.00 3.27
75 76 3.948473 TCACACTATGGCTACTCTCTCAC 59.052 47.826 0.00 0.00 0.00 3.51
76 77 3.696548 CACACTATGGCTACTCTCTCACA 59.303 47.826 0.00 0.00 0.00 3.58
77 78 4.158579 CACACTATGGCTACTCTCTCACAA 59.841 45.833 0.00 0.00 0.00 3.33
78 79 4.772624 ACACTATGGCTACTCTCTCACAAA 59.227 41.667 0.00 0.00 0.00 2.83
79 80 5.423610 ACACTATGGCTACTCTCTCACAAAT 59.576 40.000 0.00 0.00 0.00 2.32
80 81 5.982516 CACTATGGCTACTCTCTCACAAATC 59.017 44.000 0.00 0.00 0.00 2.17
81 82 3.510388 TGGCTACTCTCTCACAAATCG 57.490 47.619 0.00 0.00 0.00 3.34
82 83 2.166459 TGGCTACTCTCTCACAAATCGG 59.834 50.000 0.00 0.00 0.00 4.18
83 84 2.197577 GCTACTCTCTCACAAATCGGC 58.802 52.381 0.00 0.00 0.00 5.54
84 85 2.159170 GCTACTCTCTCACAAATCGGCT 60.159 50.000 0.00 0.00 0.00 5.52
85 86 3.066900 GCTACTCTCTCACAAATCGGCTA 59.933 47.826 0.00 0.00 0.00 3.93
86 87 4.440250 GCTACTCTCTCACAAATCGGCTAA 60.440 45.833 0.00 0.00 0.00 3.09
87 88 4.116747 ACTCTCTCACAAATCGGCTAAG 57.883 45.455 0.00 0.00 0.00 2.18
88 89 3.764434 ACTCTCTCACAAATCGGCTAAGA 59.236 43.478 0.00 0.00 0.00 2.10
89 90 4.142271 ACTCTCTCACAAATCGGCTAAGAG 60.142 45.833 0.00 0.00 35.12 2.85
90 91 2.863137 CTCTCACAAATCGGCTAAGAGC 59.137 50.000 0.00 0.00 41.46 4.09
91 92 2.497675 TCTCACAAATCGGCTAAGAGCT 59.502 45.455 0.00 0.00 41.99 4.09
92 93 2.863137 CTCACAAATCGGCTAAGAGCTC 59.137 50.000 5.27 5.27 41.99 4.09
93 94 1.936547 CACAAATCGGCTAAGAGCTCC 59.063 52.381 10.93 0.00 41.99 4.70
94 95 1.555075 ACAAATCGGCTAAGAGCTCCA 59.445 47.619 10.93 0.00 41.99 3.86
95 96 2.208431 CAAATCGGCTAAGAGCTCCAG 58.792 52.381 10.93 9.38 41.99 3.86
96 97 0.105778 AATCGGCTAAGAGCTCCAGC 59.894 55.000 23.46 23.46 41.99 4.85
97 98 1.045350 ATCGGCTAAGAGCTCCAGCA 61.045 55.000 29.18 16.48 45.16 4.41
98 99 1.520342 CGGCTAAGAGCTCCAGCAC 60.520 63.158 29.18 20.45 45.16 4.40
99 100 1.153269 GGCTAAGAGCTCCAGCACC 60.153 63.158 29.18 15.00 45.16 5.01
100 101 1.621672 GGCTAAGAGCTCCAGCACCT 61.622 60.000 29.18 2.22 45.16 4.00
101 102 1.115467 GCTAAGAGCTCCAGCACCTA 58.885 55.000 25.51 2.36 45.16 3.08
102 103 1.068434 GCTAAGAGCTCCAGCACCTAG 59.932 57.143 25.51 10.94 45.16 3.02
103 104 2.383855 CTAAGAGCTCCAGCACCTAGT 58.616 52.381 10.93 0.00 45.16 2.57
104 105 1.190643 AAGAGCTCCAGCACCTAGTC 58.809 55.000 10.93 0.00 45.16 2.59
105 106 0.686112 AGAGCTCCAGCACCTAGTCC 60.686 60.000 10.93 0.00 45.16 3.85
106 107 0.972983 GAGCTCCAGCACCTAGTCCA 60.973 60.000 0.87 0.00 45.16 4.02
107 108 0.975040 AGCTCCAGCACCTAGTCCAG 60.975 60.000 0.48 0.00 45.16 3.86
108 109 1.519719 CTCCAGCACCTAGTCCAGC 59.480 63.158 0.00 0.00 0.00 4.85
109 110 1.965754 CTCCAGCACCTAGTCCAGCC 61.966 65.000 0.00 0.00 0.00 4.85
110 111 1.992277 CCAGCACCTAGTCCAGCCT 60.992 63.158 0.00 0.00 0.00 4.58
111 112 1.519719 CAGCACCTAGTCCAGCCTC 59.480 63.158 0.00 0.00 0.00 4.70
112 113 1.687493 AGCACCTAGTCCAGCCTCC 60.687 63.158 0.00 0.00 0.00 4.30
113 114 1.687493 GCACCTAGTCCAGCCTCCT 60.687 63.158 0.00 0.00 0.00 3.69
114 115 1.268283 GCACCTAGTCCAGCCTCCTT 61.268 60.000 0.00 0.00 0.00 3.36
115 116 0.827368 CACCTAGTCCAGCCTCCTTC 59.173 60.000 0.00 0.00 0.00 3.46
116 117 0.325765 ACCTAGTCCAGCCTCCTTCC 60.326 60.000 0.00 0.00 0.00 3.46
117 118 0.325671 CCTAGTCCAGCCTCCTTCCA 60.326 60.000 0.00 0.00 0.00 3.53
118 119 0.827368 CTAGTCCAGCCTCCTTCCAC 59.173 60.000 0.00 0.00 0.00 4.02
119 120 0.413832 TAGTCCAGCCTCCTTCCACT 59.586 55.000 0.00 0.00 0.00 4.00
120 121 0.907230 AGTCCAGCCTCCTTCCACTC 60.907 60.000 0.00 0.00 0.00 3.51
121 122 1.158466 TCCAGCCTCCTTCCACTCA 59.842 57.895 0.00 0.00 0.00 3.41
122 123 1.194781 TCCAGCCTCCTTCCACTCAC 61.195 60.000 0.00 0.00 0.00 3.51
123 124 1.483595 CCAGCCTCCTTCCACTCACA 61.484 60.000 0.00 0.00 0.00 3.58
124 125 0.397941 CAGCCTCCTTCCACTCACAA 59.602 55.000 0.00 0.00 0.00 3.33
125 126 1.140312 AGCCTCCTTCCACTCACAAA 58.860 50.000 0.00 0.00 0.00 2.83
126 127 1.707427 AGCCTCCTTCCACTCACAAAT 59.293 47.619 0.00 0.00 0.00 2.32
127 128 2.087646 GCCTCCTTCCACTCACAAATC 58.912 52.381 0.00 0.00 0.00 2.17
128 129 2.350522 CCTCCTTCCACTCACAAATCG 58.649 52.381 0.00 0.00 0.00 3.34
129 130 2.350522 CTCCTTCCACTCACAAATCGG 58.649 52.381 0.00 0.00 0.00 4.18
130 131 1.697432 TCCTTCCACTCACAAATCGGT 59.303 47.619 0.00 0.00 0.00 4.69
131 132 2.076863 CCTTCCACTCACAAATCGGTC 58.923 52.381 0.00 0.00 0.00 4.79
132 133 1.726791 CTTCCACTCACAAATCGGTCG 59.273 52.381 0.00 0.00 0.00 4.79
133 134 0.669318 TCCACTCACAAATCGGTCGC 60.669 55.000 0.00 0.00 0.00 5.19
134 135 1.416049 CACTCACAAATCGGTCGCG 59.584 57.895 0.00 0.00 0.00 5.87
135 136 1.736645 ACTCACAAATCGGTCGCGG 60.737 57.895 6.13 0.00 0.00 6.46
136 137 1.445410 CTCACAAATCGGTCGCGGA 60.445 57.895 6.13 0.00 0.00 5.54
137 138 1.413767 CTCACAAATCGGTCGCGGAG 61.414 60.000 6.13 0.00 0.00 4.63
138 139 1.445410 CACAAATCGGTCGCGGAGA 60.445 57.895 6.13 3.63 0.00 3.71
139 140 0.806102 CACAAATCGGTCGCGGAGAT 60.806 55.000 6.13 6.15 0.00 2.75
140 141 0.108329 ACAAATCGGTCGCGGAGATT 60.108 50.000 6.13 12.19 36.29 2.40
141 142 1.006832 CAAATCGGTCGCGGAGATTT 58.993 50.000 22.09 22.09 43.04 2.17
142 143 1.006832 AAATCGGTCGCGGAGATTTG 58.993 50.000 24.86 5.24 41.38 2.32
143 144 0.174845 AATCGGTCGCGGAGATTTGA 59.825 50.000 6.13 0.00 31.26 2.69
144 145 0.527817 ATCGGTCGCGGAGATTTGAC 60.528 55.000 6.13 0.00 0.00 3.18
145 146 1.153823 CGGTCGCGGAGATTTGACT 60.154 57.895 6.13 0.00 0.00 3.41
146 147 0.099968 CGGTCGCGGAGATTTGACTA 59.900 55.000 6.13 0.00 0.00 2.59
147 148 1.468565 CGGTCGCGGAGATTTGACTAA 60.469 52.381 6.13 0.00 0.00 2.24
148 149 2.194271 GGTCGCGGAGATTTGACTAAG 58.806 52.381 6.13 0.00 0.00 2.18
149 150 2.194271 GTCGCGGAGATTTGACTAAGG 58.806 52.381 6.13 0.00 0.00 2.69
150 151 1.136305 TCGCGGAGATTTGACTAAGGG 59.864 52.381 6.13 0.00 0.00 3.95
735 736 4.012374 AGACATGTGGCCAATTGTAAGAG 58.988 43.478 18.99 0.97 0.00 2.85
736 737 4.009675 GACATGTGGCCAATTGTAAGAGA 58.990 43.478 18.99 0.00 0.00 3.10
737 738 4.012374 ACATGTGGCCAATTGTAAGAGAG 58.988 43.478 17.85 0.00 0.00 3.20
738 739 3.071874 TGTGGCCAATTGTAAGAGAGG 57.928 47.619 7.24 0.00 0.00 3.69
739 740 2.642311 TGTGGCCAATTGTAAGAGAGGA 59.358 45.455 7.24 0.00 0.00 3.71
753 754 2.831526 AGAGAGGAAGGAGAGAGTTTGC 59.168 50.000 0.00 0.00 0.00 3.68
757 758 1.809547 GGAAGGAGAGAGTTTGCAAGC 59.190 52.381 4.95 4.95 0.00 4.01
777 778 4.752146 AGCTGAGCAATTTCCTAAAATGC 58.248 39.130 7.39 4.62 35.27 3.56
833 835 1.372004 CGTCGGTTGCACGGTAGAA 60.372 57.895 0.00 0.00 33.46 2.10
982 1001 2.632544 CCACGGTCGGCTCACAGTA 61.633 63.158 0.00 0.00 0.00 2.74
1029 1057 3.972276 GCGCCGAAGCCCAAAACA 61.972 61.111 0.00 0.00 34.57 2.83
1922 1950 6.528321 TGACTTTGATAGGCATATCAGAAGG 58.472 40.000 27.38 17.53 46.50 3.46
1946 1974 7.661847 AGGGAAACATGAACTAGTAAAAGAGTG 59.338 37.037 0.00 0.00 0.00 3.51
1947 1975 7.660208 GGGAAACATGAACTAGTAAAAGAGTGA 59.340 37.037 0.00 0.00 0.00 3.41
1965 1993 4.145807 AGTGATTACTACTCCCTCCGATG 58.854 47.826 0.00 0.00 34.74 3.84
1966 1994 3.890147 GTGATTACTACTCCCTCCGATGT 59.110 47.826 0.00 0.00 0.00 3.06
2022 2073 4.389992 AGTGATAGCATGACTTGTTTGACG 59.610 41.667 0.00 0.00 0.00 4.35
2071 2122 4.454504 TGCAAATCCGTAAAGAGAAACCTC 59.545 41.667 0.00 0.00 0.00 3.85
2116 2167 7.178274 ACTCTCAGAACTCATACTTCAAGTGAT 59.822 37.037 0.00 0.00 0.00 3.06
2117 2168 7.318893 TCTCAGAACTCATACTTCAAGTGATG 58.681 38.462 0.00 0.87 0.00 3.07
2118 2169 7.177392 TCTCAGAACTCATACTTCAAGTGATGA 59.823 37.037 0.00 5.13 35.85 2.92
2213 2264 2.752903 ACGAAATGGAACCTAACATGCC 59.247 45.455 0.00 0.00 0.00 4.40
2280 2332 0.933097 CCAGAAAGCATCGACCATCG 59.067 55.000 0.00 0.00 42.10 3.84
2333 2386 3.154827 TCCACAAGTCAAGGGGAATTC 57.845 47.619 0.00 0.00 29.94 2.17
2405 2458 2.831742 CGTCTAGGGGCGCCTACA 60.832 66.667 28.56 13.13 0.00 2.74
2406 2459 2.846652 CGTCTAGGGGCGCCTACAG 61.847 68.421 28.56 18.23 0.00 2.74
2407 2460 2.123425 TCTAGGGGCGCCTACAGG 60.123 66.667 28.56 15.66 38.53 4.00
2425 2478 5.502153 ACAGGCTACAGATTTAGTACTCG 57.498 43.478 0.00 0.00 0.00 4.18
2481 2534 1.306296 GGCCTACAAGATGCCCCAA 59.694 57.895 0.00 0.00 39.30 4.12
2518 2609 5.358442 ACTGCACTAGTAGTGGATACAGAAG 59.642 44.000 28.11 17.55 45.46 2.85
2616 2708 1.639298 CCCAGCTTAGCTTGTGCGTC 61.639 60.000 3.00 0.00 45.42 5.19
2630 2722 3.004171 TGTGCGTCGGCTTAATTACATT 58.996 40.909 0.00 0.00 40.82 2.71
2640 2732 3.418619 GCTTAATTACATTGCACGCATCG 59.581 43.478 0.00 0.00 0.00 3.84
2704 2796 5.057819 TGGTACGACAGTTAGCATTTCAAA 58.942 37.500 0.00 0.00 0.00 2.69
2736 2828 0.038021 TGAATGTTAGCTGCTGGCCA 59.962 50.000 13.43 4.71 43.05 5.36
2820 2945 5.012561 AGCTCCCATGAATACCAAGATACTC 59.987 44.000 0.00 0.00 0.00 2.59
2822 2947 4.283467 TCCCATGAATACCAAGATACTCCG 59.717 45.833 0.00 0.00 0.00 4.63
2824 2949 5.245301 CCCATGAATACCAAGATACTCCGTA 59.755 44.000 0.00 0.00 0.00 4.02
2825 2950 6.239487 CCCATGAATACCAAGATACTCCGTAA 60.239 42.308 0.00 0.00 0.00 3.18
3185 3325 4.484236 CGGCAAATCATTGAAAACTAGCA 58.516 39.130 0.00 0.00 38.94 3.49
3367 3507 6.874288 AGCTGTAGATGCTCCAATTATTTC 57.126 37.500 0.00 0.00 35.67 2.17
3387 3527 5.991328 TTCAGTTTTCTGCCGATGATATC 57.009 39.130 0.00 0.00 46.59 1.63
3392 3532 6.424812 CAGTTTTCTGCCGATGATATCATGTA 59.575 38.462 22.86 8.12 41.24 2.29
3402 3545 7.307694 CCGATGATATCATGTAATTGGTTTGG 58.692 38.462 22.86 5.34 36.57 3.28
3473 3616 3.791973 ATAGTCTCAAGGCTCTCAACG 57.208 47.619 0.00 0.00 0.00 4.10
3596 3747 2.879646 TGAAATGGTCGTGTGGTAAACC 59.120 45.455 0.00 0.00 0.00 3.27
3635 3787 3.057104 TGTTGCTTTGGATCATCTGCTTG 60.057 43.478 0.00 0.00 0.00 4.01
3741 3894 5.375417 TGTGTGCCAAGATCACAAAATAG 57.625 39.130 0.00 0.00 44.86 1.73
3747 3932 8.028354 TGTGCCAAGATCACAAAATAGTAAATG 58.972 33.333 0.00 0.00 41.01 2.32
3776 3961 9.685828 GTTACTTGCTCATCTACCTTATCTAAG 57.314 37.037 0.00 0.00 0.00 2.18
3883 4068 3.637432 GAAATCACATTGGTTGAACGCA 58.363 40.909 0.00 0.00 0.00 5.24
3942 4129 5.733676 ACTTTCAAACACATTTTGGAGCTT 58.266 33.333 0.00 0.00 0.00 3.74
3983 4170 3.966665 ACCACTTCCACCAATGTGATTTT 59.033 39.130 0.00 0.00 45.76 1.82
4024 4347 5.625311 CGCACTTCAAACATTCCTTAAAGTC 59.375 40.000 0.00 0.00 0.00 3.01
4041 4364 3.354089 AGTCTGCCACACAAAAATTCG 57.646 42.857 0.00 0.00 0.00 3.34
4146 4469 3.811083 TCCGCAAGTTTGACTCCTTTTA 58.189 40.909 0.00 0.00 0.00 1.52
4151 4474 5.041287 GCAAGTTTGACTCCTTTTACAACC 58.959 41.667 0.00 0.00 0.00 3.77
4152 4475 5.163550 GCAAGTTTGACTCCTTTTACAACCT 60.164 40.000 0.00 0.00 0.00 3.50
4153 4476 6.265577 CAAGTTTGACTCCTTTTACAACCTG 58.734 40.000 0.00 0.00 0.00 4.00
4154 4477 4.887655 AGTTTGACTCCTTTTACAACCTGG 59.112 41.667 0.00 0.00 0.00 4.45
4155 4478 4.781775 TTGACTCCTTTTACAACCTGGA 57.218 40.909 0.00 0.00 0.00 3.86
4156 4479 4.993705 TGACTCCTTTTACAACCTGGAT 57.006 40.909 0.00 0.00 0.00 3.41
4197 4525 2.641305 GCACATTCTCCATGCTCTCTT 58.359 47.619 0.00 0.00 36.14 2.85
4203 4531 4.630644 TTCTCCATGCTCTCTTGACTTT 57.369 40.909 0.00 0.00 0.00 2.66
4210 4538 3.505386 TGCTCTCTTGACTTTCCTCTCT 58.495 45.455 0.00 0.00 0.00 3.10
4220 4548 3.876320 GACTTTCCTCTCTGATCATTGCC 59.124 47.826 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.035704 TGCTTTTGTCGATGGTTGCATT 59.964 40.909 0.00 0.00 0.00 3.56
1 2 1.612950 TGCTTTTGTCGATGGTTGCAT 59.387 42.857 0.00 0.00 0.00 3.96
2 3 1.028130 TGCTTTTGTCGATGGTTGCA 58.972 45.000 0.00 0.00 0.00 4.08
3 4 2.053627 CTTGCTTTTGTCGATGGTTGC 58.946 47.619 0.00 0.00 0.00 4.17
4 5 2.664916 CCTTGCTTTTGTCGATGGTTG 58.335 47.619 0.00 0.00 0.00 3.77
5 6 1.000274 GCCTTGCTTTTGTCGATGGTT 60.000 47.619 0.00 0.00 0.00 3.67
6 7 0.598065 GCCTTGCTTTTGTCGATGGT 59.402 50.000 0.00 0.00 0.00 3.55
7 8 0.109132 GGCCTTGCTTTTGTCGATGG 60.109 55.000 0.00 0.00 0.00 3.51
8 9 0.883833 AGGCCTTGCTTTTGTCGATG 59.116 50.000 0.00 0.00 0.00 3.84
9 10 1.620822 AAGGCCTTGCTTTTGTCGAT 58.379 45.000 19.73 0.00 0.00 3.59
10 11 1.398692 AAAGGCCTTGCTTTTGTCGA 58.601 45.000 21.33 0.00 36.52 4.20
11 12 2.034053 TGTAAAGGCCTTGCTTTTGTCG 59.966 45.455 21.33 0.00 38.27 4.35
12 13 3.068165 AGTGTAAAGGCCTTGCTTTTGTC 59.932 43.478 21.33 4.85 38.27 3.18
13 14 3.031013 AGTGTAAAGGCCTTGCTTTTGT 58.969 40.909 21.33 3.42 38.27 2.83
14 15 3.733443 AGTGTAAAGGCCTTGCTTTTG 57.267 42.857 21.33 0.00 38.27 2.44
15 16 4.647399 TGTAAGTGTAAAGGCCTTGCTTTT 59.353 37.500 21.33 12.55 40.70 2.27
16 17 4.037565 GTGTAAGTGTAAAGGCCTTGCTTT 59.962 41.667 21.33 14.94 0.00 3.51
17 18 3.568430 GTGTAAGTGTAAAGGCCTTGCTT 59.432 43.478 21.33 21.02 0.00 3.91
18 19 3.146847 GTGTAAGTGTAAAGGCCTTGCT 58.853 45.455 21.33 12.23 0.00 3.91
19 20 2.228103 GGTGTAAGTGTAAAGGCCTTGC 59.772 50.000 21.33 15.77 0.00 4.01
20 21 3.482436 TGGTGTAAGTGTAAAGGCCTTG 58.518 45.455 21.33 0.00 0.00 3.61
21 22 3.868619 TGGTGTAAGTGTAAAGGCCTT 57.131 42.857 13.78 13.78 0.00 4.35
22 23 3.117813 TGTTGGTGTAAGTGTAAAGGCCT 60.118 43.478 0.00 0.00 0.00 5.19
23 24 3.004002 GTGTTGGTGTAAGTGTAAAGGCC 59.996 47.826 0.00 0.00 0.00 5.19
24 25 3.004002 GGTGTTGGTGTAAGTGTAAAGGC 59.996 47.826 0.00 0.00 0.00 4.35
25 26 4.457466 AGGTGTTGGTGTAAGTGTAAAGG 58.543 43.478 0.00 0.00 0.00 3.11
26 27 7.556733 TTTAGGTGTTGGTGTAAGTGTAAAG 57.443 36.000 0.00 0.00 0.00 1.85
27 28 7.994334 AGATTTAGGTGTTGGTGTAAGTGTAAA 59.006 33.333 0.00 0.00 0.00 2.01
28 29 7.511268 AGATTTAGGTGTTGGTGTAAGTGTAA 58.489 34.615 0.00 0.00 0.00 2.41
29 30 7.069877 AGATTTAGGTGTTGGTGTAAGTGTA 57.930 36.000 0.00 0.00 0.00 2.90
30 31 5.937111 AGATTTAGGTGTTGGTGTAAGTGT 58.063 37.500 0.00 0.00 0.00 3.55
31 32 5.995282 TGAGATTTAGGTGTTGGTGTAAGTG 59.005 40.000 0.00 0.00 0.00 3.16
32 33 5.995897 GTGAGATTTAGGTGTTGGTGTAAGT 59.004 40.000 0.00 0.00 0.00 2.24
33 34 5.995282 TGTGAGATTTAGGTGTTGGTGTAAG 59.005 40.000 0.00 0.00 0.00 2.34
34 35 5.761234 GTGTGAGATTTAGGTGTTGGTGTAA 59.239 40.000 0.00 0.00 0.00 2.41
35 36 5.071250 AGTGTGAGATTTAGGTGTTGGTGTA 59.929 40.000 0.00 0.00 0.00 2.90
36 37 4.134563 GTGTGAGATTTAGGTGTTGGTGT 58.865 43.478 0.00 0.00 0.00 4.16
37 38 4.389374 AGTGTGAGATTTAGGTGTTGGTG 58.611 43.478 0.00 0.00 0.00 4.17
38 39 4.706842 AGTGTGAGATTTAGGTGTTGGT 57.293 40.909 0.00 0.00 0.00 3.67
39 40 5.586243 CCATAGTGTGAGATTTAGGTGTTGG 59.414 44.000 0.00 0.00 0.00 3.77
40 41 5.065218 GCCATAGTGTGAGATTTAGGTGTTG 59.935 44.000 0.00 0.00 0.00 3.33
41 42 5.045578 AGCCATAGTGTGAGATTTAGGTGTT 60.046 40.000 0.00 0.00 0.00 3.32
42 43 4.471386 AGCCATAGTGTGAGATTTAGGTGT 59.529 41.667 0.00 0.00 0.00 4.16
43 44 5.028549 AGCCATAGTGTGAGATTTAGGTG 57.971 43.478 0.00 0.00 0.00 4.00
44 45 5.900123 AGTAGCCATAGTGTGAGATTTAGGT 59.100 40.000 0.00 0.00 0.00 3.08
45 46 6.266558 AGAGTAGCCATAGTGTGAGATTTAGG 59.733 42.308 0.00 0.00 0.00 2.69
46 47 7.230510 AGAGAGTAGCCATAGTGTGAGATTTAG 59.769 40.741 0.00 0.00 0.00 1.85
47 48 7.063593 AGAGAGTAGCCATAGTGTGAGATTTA 58.936 38.462 0.00 0.00 0.00 1.40
48 49 5.896678 AGAGAGTAGCCATAGTGTGAGATTT 59.103 40.000 0.00 0.00 0.00 2.17
49 50 5.454062 AGAGAGTAGCCATAGTGTGAGATT 58.546 41.667 0.00 0.00 0.00 2.40
50 51 5.060427 AGAGAGTAGCCATAGTGTGAGAT 57.940 43.478 0.00 0.00 0.00 2.75
51 52 4.080299 TGAGAGAGTAGCCATAGTGTGAGA 60.080 45.833 0.00 0.00 0.00 3.27
52 53 4.036262 GTGAGAGAGTAGCCATAGTGTGAG 59.964 50.000 0.00 0.00 0.00 3.51
53 54 3.948473 GTGAGAGAGTAGCCATAGTGTGA 59.052 47.826 0.00 0.00 0.00 3.58
54 55 3.696548 TGTGAGAGAGTAGCCATAGTGTG 59.303 47.826 0.00 0.00 0.00 3.82
55 56 3.969553 TGTGAGAGAGTAGCCATAGTGT 58.030 45.455 0.00 0.00 0.00 3.55
56 57 4.991153 TTGTGAGAGAGTAGCCATAGTG 57.009 45.455 0.00 0.00 0.00 2.74
57 58 5.221145 CGATTTGTGAGAGAGTAGCCATAGT 60.221 44.000 0.00 0.00 0.00 2.12
58 59 5.218885 CGATTTGTGAGAGAGTAGCCATAG 58.781 45.833 0.00 0.00 0.00 2.23
59 60 4.038042 CCGATTTGTGAGAGAGTAGCCATA 59.962 45.833 0.00 0.00 0.00 2.74
60 61 3.181471 CCGATTTGTGAGAGAGTAGCCAT 60.181 47.826 0.00 0.00 0.00 4.40
61 62 2.166459 CCGATTTGTGAGAGAGTAGCCA 59.834 50.000 0.00 0.00 0.00 4.75
62 63 2.815478 CCGATTTGTGAGAGAGTAGCC 58.185 52.381 0.00 0.00 0.00 3.93
63 64 2.159170 AGCCGATTTGTGAGAGAGTAGC 60.159 50.000 0.00 0.00 0.00 3.58
64 65 3.791973 AGCCGATTTGTGAGAGAGTAG 57.208 47.619 0.00 0.00 0.00 2.57
65 66 4.948004 TCTTAGCCGATTTGTGAGAGAGTA 59.052 41.667 0.00 0.00 0.00 2.59
66 67 3.764434 TCTTAGCCGATTTGTGAGAGAGT 59.236 43.478 0.00 0.00 0.00 3.24
67 68 4.358851 CTCTTAGCCGATTTGTGAGAGAG 58.641 47.826 0.00 0.00 32.88 3.20
68 69 3.429547 GCTCTTAGCCGATTTGTGAGAGA 60.430 47.826 0.00 0.00 34.48 3.10
69 70 2.863137 GCTCTTAGCCGATTTGTGAGAG 59.137 50.000 0.00 0.00 34.48 3.20
70 71 2.497675 AGCTCTTAGCCGATTTGTGAGA 59.502 45.455 0.00 0.00 43.77 3.27
71 72 2.863137 GAGCTCTTAGCCGATTTGTGAG 59.137 50.000 6.43 0.00 43.77 3.51
72 73 2.418746 GGAGCTCTTAGCCGATTTGTGA 60.419 50.000 14.64 0.00 43.77 3.58
73 74 1.936547 GGAGCTCTTAGCCGATTTGTG 59.063 52.381 14.64 0.00 43.77 3.33
74 75 1.555075 TGGAGCTCTTAGCCGATTTGT 59.445 47.619 14.64 0.00 43.77 2.83
75 76 2.208431 CTGGAGCTCTTAGCCGATTTG 58.792 52.381 14.64 0.00 43.77 2.32
76 77 1.474143 GCTGGAGCTCTTAGCCGATTT 60.474 52.381 24.07 0.00 43.77 2.17
77 78 0.105778 GCTGGAGCTCTTAGCCGATT 59.894 55.000 24.07 0.00 43.77 3.34
78 79 1.045350 TGCTGGAGCTCTTAGCCGAT 61.045 55.000 28.34 0.00 43.77 4.18
79 80 1.682344 TGCTGGAGCTCTTAGCCGA 60.682 57.895 28.34 15.83 43.77 5.54
80 81 1.520342 GTGCTGGAGCTCTTAGCCG 60.520 63.158 28.34 7.63 43.77 5.52
81 82 1.153269 GGTGCTGGAGCTCTTAGCC 60.153 63.158 28.34 21.85 43.77 3.93
82 83 1.068434 CTAGGTGCTGGAGCTCTTAGC 59.932 57.143 26.29 26.29 42.84 3.09
83 84 2.360801 GACTAGGTGCTGGAGCTCTTAG 59.639 54.545 14.64 13.28 44.47 2.18
84 85 2.379972 GACTAGGTGCTGGAGCTCTTA 58.620 52.381 14.64 2.24 42.66 2.10
85 86 1.190643 GACTAGGTGCTGGAGCTCTT 58.809 55.000 14.64 0.00 42.66 2.85
86 87 0.686112 GGACTAGGTGCTGGAGCTCT 60.686 60.000 14.64 0.00 42.66 4.09
87 88 0.972983 TGGACTAGGTGCTGGAGCTC 60.973 60.000 4.71 4.71 42.66 4.09
88 89 0.975040 CTGGACTAGGTGCTGGAGCT 60.975 60.000 6.08 6.08 42.66 4.09
89 90 1.519719 CTGGACTAGGTGCTGGAGC 59.480 63.158 0.00 0.00 42.50 4.70
90 91 1.519719 GCTGGACTAGGTGCTGGAG 59.480 63.158 0.00 0.00 0.00 3.86
91 92 1.990060 GGCTGGACTAGGTGCTGGA 60.990 63.158 0.00 0.00 0.00 3.86
92 93 1.965754 GAGGCTGGACTAGGTGCTGG 61.966 65.000 0.00 0.00 0.00 4.85
93 94 1.519719 GAGGCTGGACTAGGTGCTG 59.480 63.158 0.00 0.00 0.00 4.41
94 95 1.687493 GGAGGCTGGACTAGGTGCT 60.687 63.158 0.00 0.00 0.00 4.40
95 96 1.268283 AAGGAGGCTGGACTAGGTGC 61.268 60.000 0.00 0.00 0.00 5.01
96 97 0.827368 GAAGGAGGCTGGACTAGGTG 59.173 60.000 0.00 0.00 0.00 4.00
97 98 0.325765 GGAAGGAGGCTGGACTAGGT 60.326 60.000 0.00 0.00 0.00 3.08
98 99 0.325671 TGGAAGGAGGCTGGACTAGG 60.326 60.000 0.00 0.00 0.00 3.02
99 100 0.827368 GTGGAAGGAGGCTGGACTAG 59.173 60.000 0.00 0.00 0.00 2.57
100 101 0.413832 AGTGGAAGGAGGCTGGACTA 59.586 55.000 0.00 0.00 0.00 2.59
101 102 0.907230 GAGTGGAAGGAGGCTGGACT 60.907 60.000 0.00 0.00 0.00 3.85
102 103 1.194781 TGAGTGGAAGGAGGCTGGAC 61.195 60.000 0.00 0.00 0.00 4.02
103 104 1.158466 TGAGTGGAAGGAGGCTGGA 59.842 57.895 0.00 0.00 0.00 3.86
104 105 1.298014 GTGAGTGGAAGGAGGCTGG 59.702 63.158 0.00 0.00 0.00 4.85
105 106 0.397941 TTGTGAGTGGAAGGAGGCTG 59.602 55.000 0.00 0.00 0.00 4.85
106 107 1.140312 TTTGTGAGTGGAAGGAGGCT 58.860 50.000 0.00 0.00 0.00 4.58
107 108 2.087646 GATTTGTGAGTGGAAGGAGGC 58.912 52.381 0.00 0.00 0.00 4.70
108 109 2.350522 CGATTTGTGAGTGGAAGGAGG 58.649 52.381 0.00 0.00 0.00 4.30
109 110 2.289694 ACCGATTTGTGAGTGGAAGGAG 60.290 50.000 0.00 0.00 0.00 3.69
110 111 1.697432 ACCGATTTGTGAGTGGAAGGA 59.303 47.619 0.00 0.00 0.00 3.36
111 112 2.076863 GACCGATTTGTGAGTGGAAGG 58.923 52.381 0.00 0.00 0.00 3.46
112 113 1.726791 CGACCGATTTGTGAGTGGAAG 59.273 52.381 0.00 0.00 0.00 3.46
113 114 1.790755 CGACCGATTTGTGAGTGGAA 58.209 50.000 0.00 0.00 0.00 3.53
114 115 0.669318 GCGACCGATTTGTGAGTGGA 60.669 55.000 0.00 0.00 0.00 4.02
115 116 1.787847 GCGACCGATTTGTGAGTGG 59.212 57.895 0.00 0.00 0.00 4.00
116 117 1.416049 CGCGACCGATTTGTGAGTG 59.584 57.895 0.00 0.00 36.29 3.51
117 118 1.736645 CCGCGACCGATTTGTGAGT 60.737 57.895 8.23 0.00 36.29 3.41
118 119 1.413767 CTCCGCGACCGATTTGTGAG 61.414 60.000 8.23 0.00 36.29 3.51
119 120 1.445410 CTCCGCGACCGATTTGTGA 60.445 57.895 8.23 0.00 36.29 3.58
120 121 0.806102 ATCTCCGCGACCGATTTGTG 60.806 55.000 8.23 0.00 36.29 3.33
121 122 0.108329 AATCTCCGCGACCGATTTGT 60.108 50.000 8.23 0.00 36.29 2.83
122 123 1.006832 AAATCTCCGCGACCGATTTG 58.993 50.000 21.04 0.00 36.37 2.32
123 124 1.006832 CAAATCTCCGCGACCGATTT 58.993 50.000 8.23 15.14 37.73 2.17
124 125 0.174845 TCAAATCTCCGCGACCGATT 59.825 50.000 8.23 9.65 36.29 3.34
125 126 0.527817 GTCAAATCTCCGCGACCGAT 60.528 55.000 8.23 2.98 36.29 4.18
126 127 1.153901 GTCAAATCTCCGCGACCGA 60.154 57.895 8.23 0.10 36.29 4.69
127 128 0.099968 TAGTCAAATCTCCGCGACCG 59.900 55.000 8.23 0.00 0.00 4.79
128 129 2.194271 CTTAGTCAAATCTCCGCGACC 58.806 52.381 8.23 0.00 0.00 4.79
129 130 2.194271 CCTTAGTCAAATCTCCGCGAC 58.806 52.381 8.23 0.00 0.00 5.19
130 131 1.136305 CCCTTAGTCAAATCTCCGCGA 59.864 52.381 8.23 0.00 0.00 5.87
131 132 1.571919 CCCTTAGTCAAATCTCCGCG 58.428 55.000 0.00 0.00 0.00 6.46
728 729 4.938575 ACTCTCTCCTTCCTCTCTTACA 57.061 45.455 0.00 0.00 0.00 2.41
735 736 3.333804 CTTGCAAACTCTCTCCTTCCTC 58.666 50.000 0.00 0.00 0.00 3.71
736 737 2.551938 GCTTGCAAACTCTCTCCTTCCT 60.552 50.000 0.00 0.00 0.00 3.36
737 738 1.809547 GCTTGCAAACTCTCTCCTTCC 59.190 52.381 0.00 0.00 0.00 3.46
738 739 2.483491 CAGCTTGCAAACTCTCTCCTTC 59.517 50.000 0.00 0.00 0.00 3.46
739 740 2.105477 TCAGCTTGCAAACTCTCTCCTT 59.895 45.455 0.00 0.00 0.00 3.36
753 754 5.063060 GCATTTTAGGAAATTGCTCAGCTTG 59.937 40.000 0.00 0.00 41.84 4.01
768 769 3.600388 ACCTCGAGTTGAGCATTTTAGG 58.400 45.455 12.31 0.00 43.82 2.69
792 794 5.112686 GGTGGACTTTTGTTGTTGCATTTA 58.887 37.500 0.00 0.00 0.00 1.40
833 835 2.172717 CGTCCCCAATTTATCCTGACCT 59.827 50.000 0.00 0.00 0.00 3.85
982 1001 1.210478 CATCGATGGTTCTTGGTCCCT 59.790 52.381 17.96 0.00 0.00 4.20
1140 1168 1.447838 CTGTCGGTAATGGTGCGCT 60.448 57.895 9.73 0.00 0.00 5.92
1473 1501 3.587095 CCGTCACTGTCGGCTAGA 58.413 61.111 1.66 0.00 41.48 2.43
1909 1937 4.464008 TCATGTTTCCCTTCTGATATGCC 58.536 43.478 0.00 0.00 0.00 4.40
1922 1950 8.603242 TCACTCTTTTACTAGTTCATGTTTCC 57.397 34.615 0.00 0.00 0.00 3.13
1946 1974 4.142790 TCACATCGGAGGGAGTAGTAATC 58.857 47.826 0.00 0.00 0.00 1.75
1947 1975 4.180377 TCACATCGGAGGGAGTAGTAAT 57.820 45.455 0.00 0.00 0.00 1.89
1965 1993 6.031471 ACTGAAACCACAAAACGTATTTCAC 58.969 36.000 0.00 0.00 37.15 3.18
1966 1994 6.197364 ACTGAAACCACAAAACGTATTTCA 57.803 33.333 0.00 0.00 38.57 2.69
2022 2073 1.590932 AGCCTCATCGCACATGAATC 58.409 50.000 0.00 0.00 0.00 2.52
2116 2167 3.840468 TCTAAGTCGCAAATACGCTTCA 58.160 40.909 0.00 0.00 33.59 3.02
2117 2168 4.835199 TTCTAAGTCGCAAATACGCTTC 57.165 40.909 0.00 0.00 33.59 3.86
2118 2169 5.796350 ATTTCTAAGTCGCAAATACGCTT 57.204 34.783 0.00 0.00 35.02 4.68
2199 2250 5.343307 AATTGATTGGCATGTTAGGTTCC 57.657 39.130 0.00 0.00 0.00 3.62
2224 2276 3.430895 CAGTTTTGCTCCAATCAACATGC 59.569 43.478 0.00 0.00 0.00 4.06
2280 2332 5.233225 TGTGCTTGGAATCGATGATAGATC 58.767 41.667 0.00 0.00 0.00 2.75
2281 2333 5.219343 TGTGCTTGGAATCGATGATAGAT 57.781 39.130 0.00 0.00 0.00 1.98
2282 2334 4.670896 TGTGCTTGGAATCGATGATAGA 57.329 40.909 0.00 0.00 0.00 1.98
2294 2346 3.157087 GGAATCTTTCCTTGTGCTTGGA 58.843 45.455 0.00 0.00 46.57 3.53
2333 2386 2.352960 GCTAATCTTTGGCTTCTGTCCG 59.647 50.000 0.00 0.00 33.94 4.79
2405 2458 5.236047 CGTACGAGTACTAAATCTGTAGCCT 59.764 44.000 10.44 0.00 34.04 4.58
2406 2459 5.007136 ACGTACGAGTACTAAATCTGTAGCC 59.993 44.000 24.41 0.00 34.04 3.93
2407 2460 6.042144 ACGTACGAGTACTAAATCTGTAGC 57.958 41.667 24.41 0.00 34.04 3.58
2408 2461 9.973246 TTTTACGTACGAGTACTAAATCTGTAG 57.027 33.333 24.41 0.00 34.04 2.74
2409 2462 9.973246 CTTTTACGTACGAGTACTAAATCTGTA 57.027 33.333 24.41 0.00 34.04 2.74
2410 2463 8.507249 ACTTTTACGTACGAGTACTAAATCTGT 58.493 33.333 24.41 11.28 34.04 3.41
2411 2464 8.783251 CACTTTTACGTACGAGTACTAAATCTG 58.217 37.037 24.41 9.51 34.04 2.90
2425 2478 3.122278 TGCTTCGCATCACTTTTACGTAC 59.878 43.478 0.00 0.00 31.71 3.67
2498 2552 5.446860 TCCCTTCTGTATCCACTACTAGTG 58.553 45.833 5.39 9.02 45.53 2.74
2500 2554 5.766174 GTCTCCCTTCTGTATCCACTACTAG 59.234 48.000 0.00 0.00 0.00 2.57
2501 2555 5.686913 CGTCTCCCTTCTGTATCCACTACTA 60.687 48.000 0.00 0.00 0.00 1.82
2502 2556 4.538738 GTCTCCCTTCTGTATCCACTACT 58.461 47.826 0.00 0.00 0.00 2.57
2503 2557 3.315749 CGTCTCCCTTCTGTATCCACTAC 59.684 52.174 0.00 0.00 0.00 2.73
2515 2606 2.066999 AGATGCCCCGTCTCCCTTC 61.067 63.158 0.00 0.00 0.00 3.46
2518 2609 4.554036 GCAGATGCCCCGTCTCCC 62.554 72.222 0.00 0.00 34.31 4.30
2616 2708 2.108700 GCGTGCAATGTAATTAAGCCG 58.891 47.619 0.00 0.00 32.46 5.52
2630 2722 4.726351 TGTACGGCGATGCGTGCA 62.726 61.111 16.62 0.00 0.00 4.57
2704 2796 5.948162 AGCTAACATTCAAGTGTGGATTCAT 59.052 36.000 0.00 0.00 31.49 2.57
2747 2872 1.954528 CAGGAGTTGGTTGCAGCAG 59.045 57.895 2.05 0.00 0.00 4.24
2762 2887 1.152777 TGGGGTGTCAACTTGCAGG 60.153 57.895 0.00 0.00 0.00 4.85
3213 3353 6.403866 AAATGAGTTTGGTACTGCAATGAA 57.596 33.333 0.00 0.00 37.17 2.57
3319 3459 1.452108 CCCCTGACATTTCCTCGGC 60.452 63.158 0.00 0.00 0.00 5.54
3367 3507 5.237996 ACATGATATCATCGGCAGAAAACTG 59.762 40.000 15.49 4.11 33.61 3.16
3387 3527 5.852827 AGTTCCAACCAAACCAATTACATG 58.147 37.500 0.00 0.00 0.00 3.21
3392 3532 6.894682 ACAATTAGTTCCAACCAAACCAATT 58.105 32.000 0.00 0.00 31.17 2.32
3402 3545 3.252458 AGACGCCAACAATTAGTTCCAAC 59.748 43.478 0.00 0.00 38.74 3.77
3473 3616 2.810852 CTGAACTCCTGAAAGCTTCACC 59.189 50.000 0.00 0.00 35.46 4.02
3596 3747 3.309410 GCAACAAAACAGACCACCAAATG 59.691 43.478 0.00 0.00 0.00 2.32
3635 3787 6.698380 TGTCTTTCTACCTGATTCAGTAACC 58.302 40.000 12.54 0.00 0.00 2.85
3741 3894 6.428385 AGATGAGCAAGTAACAGCATTTAC 57.572 37.500 0.33 0.33 32.88 2.01
3747 3932 4.130286 AGGTAGATGAGCAAGTAACAGC 57.870 45.455 0.00 0.00 0.00 4.40
3776 3961 6.534793 TGAAATGTTTTGGAAAGTTGCTCTTC 59.465 34.615 0.00 0.00 35.02 2.87
3816 4001 8.489559 CCGCAAACATTCCATAATTATGATTTG 58.510 33.333 24.17 21.79 35.75 2.32
3817 4002 8.203485 ACCGCAAACATTCCATAATTATGATTT 58.797 29.630 24.17 13.55 35.75 2.17
3827 4012 3.428725 GCATGAACCGCAAACATTCCATA 60.429 43.478 0.00 0.00 0.00 2.74
3895 4082 8.680903 AGTACCATTTTCAGAGCATAGATTTTG 58.319 33.333 0.00 0.00 0.00 2.44
3896 4083 8.814038 AGTACCATTTTCAGAGCATAGATTTT 57.186 30.769 0.00 0.00 0.00 1.82
3897 4084 8.814038 AAGTACCATTTTCAGAGCATAGATTT 57.186 30.769 0.00 0.00 0.00 2.17
3942 4129 8.614469 AAGTGGTGAAAGAAAAACAAAATCAA 57.386 26.923 0.00 0.00 0.00 2.57
3983 4170 1.878734 TGCGTGCAAAGATTCATCACA 59.121 42.857 0.00 0.00 0.00 3.58
4024 4347 2.791383 TCCGAATTTTTGTGTGGCAG 57.209 45.000 0.00 0.00 0.00 4.85
4146 4469 0.036306 GACGTCCCAATCCAGGTTGT 59.964 55.000 3.51 0.00 0.00 3.32
4197 4525 4.511527 GCAATGATCAGAGAGGAAAGTCA 58.488 43.478 0.09 0.00 0.00 3.41
4203 4531 1.883678 TGGGCAATGATCAGAGAGGA 58.116 50.000 0.09 0.00 0.00 3.71
4210 4538 9.758021 ATCATAAGTAATAATGGGCAATGATCA 57.242 29.630 0.00 0.00 28.08 2.92
4220 4548 8.246180 GCCCACAATCATCATAAGTAATAATGG 58.754 37.037 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.