Multiple sequence alignment - TraesCS7D01G414900

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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 TraesCS7D01G414900 chr7D 100.000 3710 0 0 1 3710 533435539 533431830 0.000000e+00 6852.0
1 TraesCS7D01G414900 chr7D 90.573 2599 147 32 853 3409 532901652 532899110 0.000000e+00 3352.0
2 TraesCS7D01G414900 chr7D 86.027 594 41 20 261 834 532902864 532902293 1.910000e-167 599.0
3 TraesCS7D01G414900 chr7D 85.926 135 15 3 3004 3135 532899636 532899503 1.390000e-29 141.0
4 TraesCS7D01G414900 chr7D 86.957 92 9 3 2915 3006 532899462 532899374 2.360000e-17 100.0
5 TraesCS7D01G414900 chr7D 86.957 92 9 3 2915 3006 533432493 533432405 2.360000e-17 100.0
6 TraesCS7D01G414900 chr7D 86.957 92 9 3 3047 3135 533432625 533432534 2.360000e-17 100.0
7 TraesCS7D01G414900 chr7D 92.683 41 3 0 2884 2924 532899509 532899469 4.000000e-05 60.2
8 TraesCS7D01G414900 chr7B 95.262 2596 78 14 853 3409 573263558 573260969 0.000000e+00 4071.0
9 TraesCS7D01G414900 chr7B 87.227 642 49 16 235 853 573264781 573264150 0.000000e+00 701.0
10 TraesCS7D01G414900 chr7B 84.772 197 28 2 4 199 19892343 19892148 2.920000e-46 196.0
11 TraesCS7D01G414900 chr7B 87.500 136 12 4 3004 3135 573261522 573261388 6.420000e-33 152.0
12 TraesCS7D01G414900 chr7B 85.714 91 10 3 2915 3005 573261347 573261260 3.950000e-15 93.5
13 TraesCS7D01G414900 chr7B 92.683 41 3 0 2884 2924 573261394 573261354 4.000000e-05 60.2
14 TraesCS7D01G414900 chr7A 91.325 2582 139 28 856 3409 612993353 612990829 0.000000e+00 3448.0
15 TraesCS7D01G414900 chr7A 82.849 688 48 32 212 854 612994582 612993920 1.510000e-153 553.0
16 TraesCS7D01G414900 chr7A 93.023 301 21 0 3410 3710 36461388 36461088 1.220000e-119 440.0
17 TraesCS7D01G414900 chr7A 87.778 90 8 2 3047 3135 612991326 612991239 6.560000e-18 102.0
18 TraesCS7D01G414900 chr5B 87.421 787 93 6 1962 2747 479203707 479202926 0.000000e+00 900.0
19 TraesCS7D01G414900 chr5B 81.921 531 87 6 1022 1544 479204944 479204415 1.220000e-119 440.0
20 TraesCS7D01G414900 chr5B 92.734 289 19 2 3424 3710 537788231 537788519 2.060000e-112 416.0
21 TraesCS7D01G414900 chr5B 78.922 204 36 4 1 199 647878027 647877826 8.360000e-27 132.0
22 TraesCS7D01G414900 chr5D 82.932 996 106 37 1961 2925 398908888 398907926 0.000000e+00 839.0
23 TraesCS7D01G414900 chr5D 82.331 532 84 7 1022 1544 398910111 398909581 1.570000e-123 453.0
24 TraesCS7D01G414900 chr5A 85.030 835 105 12 1962 2795 503952276 503953091 0.000000e+00 832.0
25 TraesCS7D01G414900 chr5A 82.298 531 87 5 1019 1544 503950724 503951252 1.570000e-123 453.0
26 TraesCS7D01G414900 chr6D 83.800 679 108 2 2014 2691 72229911 72229234 0.000000e+00 643.0
27 TraesCS7D01G414900 chr6D 93.728 287 17 1 3424 3710 69218071 69217786 2.650000e-116 429.0
28 TraesCS7D01G414900 chr6B 83.700 681 109 2 2014 2693 146838513 146837834 3.120000e-180 641.0
29 TraesCS7D01G414900 chr6B 86.000 200 27 1 1 199 144891486 144891685 2.900000e-51 213.0
30 TraesCS7D01G414900 chr6B 80.357 112 19 3 34 143 42229762 42229872 8.540000e-12 82.4
31 TraesCS7D01G414900 chr6A 82.768 708 113 7 2008 2711 88855997 88855295 1.130000e-174 623.0
32 TraesCS7D01G414900 chr4D 95.380 303 14 0 3408 3710 55273317 55273015 2.000000e-132 483.0
33 TraesCS7D01G414900 chr4D 93.333 300 19 1 3412 3710 456283396 456283097 3.400000e-120 442.0
34 TraesCS7D01G414900 chr3D 93.709 302 19 0 3409 3710 532756855 532757156 1.570000e-123 453.0
35 TraesCS7D01G414900 chr3D 85.572 201 26 3 1 199 524172966 524173165 1.350000e-49 207.0
36 TraesCS7D01G414900 chr3D 77.692 130 22 6 40 165 589430740 589430866 5.140000e-09 73.1
37 TraesCS7D01G414900 chr2D 94.000 300 16 1 3411 3710 582814042 582814339 1.570000e-123 453.0
38 TraesCS7D01G414900 chr2A 93.380 287 19 0 3424 3710 764779161 764778875 3.420000e-115 425.0
39 TraesCS7D01G414900 chr4B 93.007 286 15 3 3426 3710 518086827 518086546 2.670000e-111 412.0
40 TraesCS7D01G414900 chr1D 86.000 200 27 1 1 199 436719400 436719599 2.900000e-51 213.0
41 TraesCS7D01G414900 chr3B 85.000 200 29 1 1 199 252811213 252811014 6.280000e-48 202.0


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 TraesCS7D01G414900 chr7D 533431830 533435539 3709 True 2350.666667 6852 91.304667 1 3710 3 chr7D.!!$R2 3709
1 TraesCS7D01G414900 chr7D 532899110 532902864 3754 True 850.440000 3352 88.433200 261 3409 5 chr7D.!!$R1 3148
2 TraesCS7D01G414900 chr7B 573260969 573264781 3812 True 1015.540000 4071 89.677200 235 3409 5 chr7B.!!$R2 3174
3 TraesCS7D01G414900 chr7A 612990829 612994582 3753 True 1367.666667 3448 87.317333 212 3409 3 chr7A.!!$R2 3197
4 TraesCS7D01G414900 chr5B 479202926 479204944 2018 True 670.000000 900 84.671000 1022 2747 2 chr5B.!!$R2 1725
5 TraesCS7D01G414900 chr5D 398907926 398910111 2185 True 646.000000 839 82.631500 1022 2925 2 chr5D.!!$R1 1903
6 TraesCS7D01G414900 chr5A 503950724 503953091 2367 False 642.500000 832 83.664000 1019 2795 2 chr5A.!!$F1 1776
7 TraesCS7D01G414900 chr6D 72229234 72229911 677 True 643.000000 643 83.800000 2014 2691 1 chr6D.!!$R2 677
8 TraesCS7D01G414900 chr6B 146837834 146838513 679 True 641.000000 641 83.700000 2014 2693 1 chr6B.!!$R1 679
9 TraesCS7D01G414900 chr6A 88855295 88855997 702 True 623.000000 623 82.768000 2008 2711 1 chr6A.!!$R1 703

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
220 221 0.035739 GTTTGACAGCCCTCGGGTAA 59.964 55.0 3.54 0.0 37.65 2.85 F
2139 3620 0.108585 TCTGTGACTTTGGTCTGGCC 59.891 55.0 0.00 0.0 42.54 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 3653 0.606604 AGCGGGTGACAACGTATTCT 59.393 50.0 0.0 0.0 0.0 2.40 R
3487 5057 0.185901 CAGGAGGAGGGAGAGAGGAG 59.814 65.0 0.0 0.0 0.0 3.69 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
32 33 3.710044 CGCTATCGTGCACAGCAT 58.290 55.556 22.85 11.99 41.91 3.79
33 34 2.885502 CGCTATCGTGCACAGCATA 58.114 52.632 22.85 12.42 41.91 3.14
34 35 1.422388 CGCTATCGTGCACAGCATAT 58.578 50.000 22.85 8.98 41.91 1.78
35 36 1.794701 CGCTATCGTGCACAGCATATT 59.205 47.619 22.85 1.49 41.91 1.28
36 37 2.221749 CGCTATCGTGCACAGCATATTT 59.778 45.455 22.85 0.56 41.91 1.40
37 38 3.303329 CGCTATCGTGCACAGCATATTTT 60.303 43.478 22.85 0.00 41.91 1.82
38 39 4.084589 CGCTATCGTGCACAGCATATTTTA 60.085 41.667 22.85 0.00 41.91 1.52
39 40 5.377358 GCTATCGTGCACAGCATATTTTAG 58.623 41.667 19.60 7.03 41.91 1.85
40 41 4.818534 ATCGTGCACAGCATATTTTAGG 57.181 40.909 18.64 0.00 41.91 2.69
41 42 2.354510 TCGTGCACAGCATATTTTAGGC 59.645 45.455 18.64 0.00 41.91 3.93
43 44 3.546815 CGTGCACAGCATATTTTAGGCTC 60.547 47.826 18.64 0.00 43.00 4.70
44 45 2.951642 TGCACAGCATATTTTAGGCTCC 59.048 45.455 0.00 0.00 43.00 4.70
45 46 2.031682 GCACAGCATATTTTAGGCTCCG 60.032 50.000 0.00 0.00 43.00 4.63
46 47 3.466836 CACAGCATATTTTAGGCTCCGA 58.533 45.455 0.00 0.00 43.00 4.55
47 48 3.876914 CACAGCATATTTTAGGCTCCGAA 59.123 43.478 0.00 0.00 43.00 4.30
48 49 4.516698 CACAGCATATTTTAGGCTCCGAAT 59.483 41.667 0.00 0.00 43.00 3.34
49 50 5.009010 CACAGCATATTTTAGGCTCCGAATT 59.991 40.000 0.00 0.00 43.00 2.17
50 51 5.009010 ACAGCATATTTTAGGCTCCGAATTG 59.991 40.000 0.00 0.00 43.00 2.32
51 52 4.022849 AGCATATTTTAGGCTCCGAATTGC 60.023 41.667 0.00 0.00 43.00 3.56
52 53 4.466828 CATATTTTAGGCTCCGAATTGCG 58.533 43.478 0.00 0.00 40.47 4.85
53 54 0.450184 TTTTAGGCTCCGAATTGCGC 59.550 50.000 0.00 0.00 39.11 6.09
54 55 0.675208 TTTAGGCTCCGAATTGCGCA 60.675 50.000 5.66 5.66 39.11 6.09
55 56 1.366111 TTAGGCTCCGAATTGCGCAC 61.366 55.000 11.12 0.00 39.11 5.34
56 57 4.520846 GGCTCCGAATTGCGCACG 62.521 66.667 11.12 11.37 39.11 5.34
58 59 3.490759 CTCCGAATTGCGCACGCT 61.491 61.111 11.12 0.00 42.51 5.07
59 60 3.027170 CTCCGAATTGCGCACGCTT 62.027 57.895 11.12 3.75 42.51 4.68
60 61 2.574212 CCGAATTGCGCACGCTTC 60.574 61.111 11.12 12.89 42.51 3.86
61 62 2.173141 CGAATTGCGCACGCTTCA 59.827 55.556 11.12 0.00 42.51 3.02
62 63 2.139811 CGAATTGCGCACGCTTCAC 61.140 57.895 11.12 4.93 42.51 3.18
63 64 1.082169 GAATTGCGCACGCTTCACA 60.082 52.632 11.12 0.00 42.51 3.58
64 65 0.660005 GAATTGCGCACGCTTCACAA 60.660 50.000 11.12 1.79 42.51 3.33
65 66 0.039256 AATTGCGCACGCTTCACAAT 60.039 45.000 11.12 4.23 42.51 2.71
66 67 0.039256 ATTGCGCACGCTTCACAATT 60.039 45.000 11.12 0.00 42.51 2.32
67 68 0.248825 TTGCGCACGCTTCACAATTT 60.249 45.000 11.12 0.00 42.51 1.82
68 69 0.933973 TGCGCACGCTTCACAATTTG 60.934 50.000 16.77 0.00 42.51 2.32
69 70 1.768603 CGCACGCTTCACAATTTGC 59.231 52.632 0.00 0.00 0.00 3.68
70 71 0.933973 CGCACGCTTCACAATTTGCA 60.934 50.000 0.00 0.00 0.00 4.08
71 72 0.503961 GCACGCTTCACAATTTGCAC 59.496 50.000 0.00 0.00 0.00 4.57
72 73 1.865248 GCACGCTTCACAATTTGCACT 60.865 47.619 0.00 0.00 0.00 4.40
73 74 1.782569 CACGCTTCACAATTTGCACTG 59.217 47.619 0.00 0.00 0.00 3.66
74 75 0.780002 CGCTTCACAATTTGCACTGC 59.220 50.000 0.00 0.00 0.00 4.40
75 76 0.780002 GCTTCACAATTTGCACTGCG 59.220 50.000 0.00 0.00 0.00 5.18
76 77 1.865248 GCTTCACAATTTGCACTGCGT 60.865 47.619 0.00 0.00 0.00 5.24
77 78 1.782569 CTTCACAATTTGCACTGCGTG 59.217 47.619 0.00 4.61 36.51 5.34
87 88 3.153364 CACTGCGTGCTTTTGTGAG 57.847 52.632 0.00 0.00 0.00 3.51
88 89 0.931662 CACTGCGTGCTTTTGTGAGC 60.932 55.000 0.00 0.00 43.00 4.26
101 102 2.577225 GTGAGCACACGTTTTTGGC 58.423 52.632 0.00 0.00 37.28 4.52
102 103 1.063327 TGAGCACACGTTTTTGGCG 59.937 52.632 0.00 0.00 0.00 5.69
103 104 1.063488 GAGCACACGTTTTTGGCGT 59.937 52.632 0.00 0.00 43.90 5.68
104 105 0.524604 GAGCACACGTTTTTGGCGTT 60.525 50.000 0.00 0.00 40.90 4.84
105 106 0.109039 AGCACACGTTTTTGGCGTTT 60.109 45.000 0.00 0.00 40.90 3.60
106 107 1.132643 AGCACACGTTTTTGGCGTTTA 59.867 42.857 0.00 0.00 40.90 2.01
107 108 1.253289 GCACACGTTTTTGGCGTTTAC 59.747 47.619 0.00 0.00 40.90 2.01
108 109 2.788030 CACACGTTTTTGGCGTTTACT 58.212 42.857 0.00 0.00 40.90 2.24
109 110 3.788135 GCACACGTTTTTGGCGTTTACTA 60.788 43.478 0.00 0.00 40.90 1.82
110 111 4.341099 CACACGTTTTTGGCGTTTACTAA 58.659 39.130 0.00 0.00 40.90 2.24
111 112 4.792189 CACACGTTTTTGGCGTTTACTAAA 59.208 37.500 0.00 0.00 40.90 1.85
112 113 5.285607 CACACGTTTTTGGCGTTTACTAAAA 59.714 36.000 0.00 0.00 40.90 1.52
113 114 6.020520 CACACGTTTTTGGCGTTTACTAAAAT 60.021 34.615 0.00 0.00 40.90 1.82
114 115 7.165483 CACACGTTTTTGGCGTTTACTAAAATA 59.835 33.333 0.00 0.00 40.90 1.40
115 116 7.699812 ACACGTTTTTGGCGTTTACTAAAATAA 59.300 29.630 0.00 0.00 40.90 1.40
116 117 8.692615 CACGTTTTTGGCGTTTACTAAAATAAT 58.307 29.630 0.00 0.00 40.90 1.28
117 118 8.692615 ACGTTTTTGGCGTTTACTAAAATAATG 58.307 29.630 0.00 0.00 39.79 1.90
118 119 8.692615 CGTTTTTGGCGTTTACTAAAATAATGT 58.307 29.630 0.00 0.00 0.00 2.71
119 120 9.786224 GTTTTTGGCGTTTACTAAAATAATGTG 57.214 29.630 0.00 0.00 0.00 3.21
120 121 8.522178 TTTTGGCGTTTACTAAAATAATGTGG 57.478 30.769 0.00 0.00 0.00 4.17
121 122 6.197364 TGGCGTTTACTAAAATAATGTGGG 57.803 37.500 0.00 0.00 0.00 4.61
122 123 5.711036 TGGCGTTTACTAAAATAATGTGGGT 59.289 36.000 0.00 0.00 0.00 4.51
123 124 6.127952 TGGCGTTTACTAAAATAATGTGGGTC 60.128 38.462 0.00 0.00 0.00 4.46
124 125 6.260377 GCGTTTACTAAAATAATGTGGGTCC 58.740 40.000 0.00 0.00 0.00 4.46
125 126 6.678655 GCGTTTACTAAAATAATGTGGGTCCC 60.679 42.308 0.00 0.00 0.00 4.46
126 127 6.457257 CGTTTACTAAAATAATGTGGGTCCCG 60.457 42.308 2.65 0.00 0.00 5.14
127 128 3.893521 ACTAAAATAATGTGGGTCCCGG 58.106 45.455 2.65 0.00 0.00 5.73
128 129 1.480789 AAAATAATGTGGGTCCCGGC 58.519 50.000 2.65 0.00 0.00 6.13
129 130 0.333312 AAATAATGTGGGTCCCGGCA 59.667 50.000 2.65 5.39 0.00 5.69
130 131 0.395173 AATAATGTGGGTCCCGGCAC 60.395 55.000 2.65 0.00 0.00 5.01
131 132 1.567208 ATAATGTGGGTCCCGGCACA 61.567 55.000 13.92 13.92 0.00 4.57
132 133 1.780107 TAATGTGGGTCCCGGCACAA 61.780 55.000 15.25 0.00 0.00 3.33
133 134 2.439553 AATGTGGGTCCCGGCACAAT 62.440 55.000 15.25 5.79 0.00 2.71
134 135 1.567208 ATGTGGGTCCCGGCACAATA 61.567 55.000 15.25 0.00 0.00 1.90
135 136 1.001887 GTGGGTCCCGGCACAATAA 60.002 57.895 2.65 0.00 0.00 1.40
136 137 0.609681 GTGGGTCCCGGCACAATAAA 60.610 55.000 2.65 0.00 0.00 1.40
137 138 0.112606 TGGGTCCCGGCACAATAAAA 59.887 50.000 2.65 0.00 0.00 1.52
138 139 0.815095 GGGTCCCGGCACAATAAAAG 59.185 55.000 0.00 0.00 0.00 2.27
139 140 1.541379 GGTCCCGGCACAATAAAAGT 58.459 50.000 0.00 0.00 0.00 2.66
140 141 1.201414 GGTCCCGGCACAATAAAAGTG 59.799 52.381 0.00 0.00 39.92 3.16
151 152 6.837307 CACAATAAAAGTGCTACAATGACG 57.163 37.500 0.00 0.00 0.00 4.35
152 153 6.370593 CACAATAAAAGTGCTACAATGACGT 58.629 36.000 0.00 0.00 0.00 4.34
153 154 6.303022 CACAATAAAAGTGCTACAATGACGTG 59.697 38.462 0.00 0.00 0.00 4.49
154 155 2.969443 AAAGTGCTACAATGACGTGC 57.031 45.000 0.00 0.00 0.00 5.34
155 156 2.169832 AAGTGCTACAATGACGTGCT 57.830 45.000 0.00 0.00 0.00 4.40
156 157 3.313012 AAGTGCTACAATGACGTGCTA 57.687 42.857 0.00 0.00 0.00 3.49
157 158 3.526931 AGTGCTACAATGACGTGCTAT 57.473 42.857 0.00 0.00 0.00 2.97
158 159 4.649088 AGTGCTACAATGACGTGCTATA 57.351 40.909 0.00 0.00 0.00 1.31
159 160 5.006153 AGTGCTACAATGACGTGCTATAA 57.994 39.130 0.00 0.00 0.00 0.98
160 161 4.804139 AGTGCTACAATGACGTGCTATAAC 59.196 41.667 0.00 0.00 0.00 1.89
161 162 4.804139 GTGCTACAATGACGTGCTATAACT 59.196 41.667 0.00 0.00 0.00 2.24
162 163 5.291128 GTGCTACAATGACGTGCTATAACTT 59.709 40.000 0.00 0.00 0.00 2.66
163 164 5.872617 TGCTACAATGACGTGCTATAACTTT 59.127 36.000 0.00 0.00 0.00 2.66
164 165 6.370442 TGCTACAATGACGTGCTATAACTTTT 59.630 34.615 0.00 0.00 0.00 2.27
165 166 7.546316 TGCTACAATGACGTGCTATAACTTTTA 59.454 33.333 0.00 0.00 0.00 1.52
166 167 8.548721 GCTACAATGACGTGCTATAACTTTTAT 58.451 33.333 0.00 0.00 0.00 1.40
169 170 8.114290 ACAATGACGTGCTATAACTTTTATTCG 58.886 33.333 0.00 0.00 0.00 3.34
170 171 7.997107 ATGACGTGCTATAACTTTTATTCGA 57.003 32.000 0.00 0.00 0.00 3.71
171 172 7.213252 TGACGTGCTATAACTTTTATTCGAC 57.787 36.000 0.00 0.00 0.00 4.20
172 173 6.021232 TGACGTGCTATAACTTTTATTCGACG 60.021 38.462 0.00 0.00 0.00 5.12
173 174 5.801947 ACGTGCTATAACTTTTATTCGACGT 59.198 36.000 0.00 0.00 0.00 4.34
174 175 6.111696 CGTGCTATAACTTTTATTCGACGTG 58.888 40.000 0.00 0.00 0.00 4.49
175 176 6.021232 CGTGCTATAACTTTTATTCGACGTGA 60.021 38.462 0.00 0.00 0.00 4.35
176 177 7.461807 CGTGCTATAACTTTTATTCGACGTGAA 60.462 37.037 0.00 0.00 41.81 3.18
178 179 8.875803 TGCTATAACTTTTATTCGACGTGAATT 58.124 29.630 15.21 4.01 45.06 2.17
179 180 9.698617 GCTATAACTTTTATTCGACGTGAATTT 57.301 29.630 15.21 8.31 45.06 1.82
195 196 2.105128 TTTTTGTGCGGCCGTTGG 59.895 55.556 28.70 0.00 0.00 3.77
196 197 2.415608 TTTTTGTGCGGCCGTTGGA 61.416 52.632 28.70 8.23 0.00 3.53
197 198 2.343163 TTTTTGTGCGGCCGTTGGAG 62.343 55.000 28.70 0.00 0.00 3.86
198 199 3.758973 TTTGTGCGGCCGTTGGAGA 62.759 57.895 28.70 6.06 0.00 3.71
199 200 4.980805 TGTGCGGCCGTTGGAGAC 62.981 66.667 28.70 13.86 0.00 3.36
210 211 0.586802 GTTGGAGACGGTTTGACAGC 59.413 55.000 0.00 0.00 0.00 4.40
211 212 0.534203 TTGGAGACGGTTTGACAGCC 60.534 55.000 0.00 0.00 0.00 4.85
212 213 1.671379 GGAGACGGTTTGACAGCCC 60.671 63.158 0.00 0.00 0.00 5.19
213 214 1.371558 GAGACGGTTTGACAGCCCT 59.628 57.895 0.00 0.00 0.00 5.19
214 215 0.670854 GAGACGGTTTGACAGCCCTC 60.671 60.000 0.00 0.00 0.00 4.30
215 216 2.027625 GACGGTTTGACAGCCCTCG 61.028 63.158 0.00 0.00 0.00 4.63
216 217 2.742372 CGGTTTGACAGCCCTCGG 60.742 66.667 0.00 0.00 0.00 4.63
217 218 2.359975 GGTTTGACAGCCCTCGGG 60.360 66.667 0.00 0.00 38.57 5.14
218 219 2.430367 GTTTGACAGCCCTCGGGT 59.570 61.111 3.54 0.00 37.65 5.28
219 220 1.675219 GTTTGACAGCCCTCGGGTA 59.325 57.895 3.54 0.00 37.65 3.69
220 221 0.035739 GTTTGACAGCCCTCGGGTAA 59.964 55.000 3.54 0.00 37.65 2.85
228 229 1.310373 CCCTCGGGTAACTCCTCCT 59.690 63.158 0.00 0.00 36.25 3.69
242 243 4.178214 TCCTTACCGTACGCGCCG 62.178 66.667 10.49 9.23 36.67 6.46
316 317 2.741985 CAACCGCTGCACCGATCA 60.742 61.111 2.22 0.00 0.00 2.92
507 532 1.814169 GGCTTACCCGGAAGAAGCG 60.814 63.158 21.25 0.23 45.27 4.68
509 534 1.814169 CTTACCCGGAAGAAGCGGC 60.814 63.158 0.73 0.00 0.00 6.53
539 568 3.695825 ACCCTGATCCCGGTCCCT 61.696 66.667 0.00 0.00 0.00 4.20
664 702 0.595053 CGCGTGTTCCATCTCGCTAT 60.595 55.000 0.00 0.00 44.43 2.97
779 850 1.690352 TCGTTCGTTCCTTCCTTCCTT 59.310 47.619 0.00 0.00 0.00 3.36
783 854 2.335933 TCGTTCCTTCCTTCCTTCCTT 58.664 47.619 0.00 0.00 0.00 3.36
786 857 1.670059 TCCTTCCTTCCTTCCTTCCC 58.330 55.000 0.00 0.00 0.00 3.97
788 859 0.253327 CTTCCTTCCTTCCTTCCCCG 59.747 60.000 0.00 0.00 0.00 5.73
789 860 0.178885 TTCCTTCCTTCCTTCCCCGA 60.179 55.000 0.00 0.00 0.00 5.14
790 861 0.178885 TCCTTCCTTCCTTCCCCGAA 60.179 55.000 0.00 0.00 0.00 4.30
791 862 0.696501 CCTTCCTTCCTTCCCCGAAA 59.303 55.000 0.00 0.00 0.00 3.46
793 864 1.073284 CTTCCTTCCTTCCCCGAAACA 59.927 52.381 0.00 0.00 0.00 2.83
794 865 1.142060 TCCTTCCTTCCCCGAAACAA 58.858 50.000 0.00 0.00 0.00 2.83
891 1629 1.270893 GGGGTGGAAACAGAGACTGTC 60.271 57.143 4.88 0.00 44.62 3.51
1029 1783 1.167851 CTTCTCCGCAGAAAATGGCA 58.832 50.000 0.00 0.00 38.23 4.92
1234 1991 0.316689 CAACGTCTTTGACAACCGCC 60.317 55.000 0.00 0.00 37.39 6.13
1376 2133 0.749649 GTCTCCGAGCTCATGGACAT 59.250 55.000 15.40 0.00 0.00 3.06
1472 2234 2.604614 GCGTCGGCTCTGTTTTTCATTT 60.605 45.455 0.00 0.00 35.83 2.32
1793 3248 5.178061 CAACCTAATACACAGCAGACATGA 58.822 41.667 0.00 0.00 0.00 3.07
2023 3504 3.758554 CCACCATTTTCCTTGACTGTAGG 59.241 47.826 0.00 0.00 0.00 3.18
2139 3620 0.108585 TCTGTGACTTTGGTCTGGCC 59.891 55.000 0.00 0.00 42.54 5.36
2362 3843 0.178995 TGTTCTTGGCACCATGAGCA 60.179 50.000 15.19 15.19 38.35 4.26
2370 3851 1.035932 GCACCATGAGCAAGGCTGAT 61.036 55.000 0.00 0.00 39.88 2.90
2398 3879 3.731652 TCATTGACAACCCAAAAGCTG 57.268 42.857 0.00 0.00 0.00 4.24
2765 4262 0.251297 CCAGGGCCTTCACATGTTCA 60.251 55.000 1.32 0.00 0.00 3.18
2833 4347 9.162764 GAGTGACCTGTTTATGTAAATATGTGT 57.837 33.333 0.00 0.00 0.00 3.72
2888 4402 7.585440 TGTGGGTCAGTACTTGGTAGTATATA 58.415 38.462 0.00 0.00 39.01 0.86
2889 4403 7.503566 TGTGGGTCAGTACTTGGTAGTATATAC 59.496 40.741 4.60 4.60 39.01 1.47
3138 4668 6.731292 TTAGAAGCTGCTCTATGTATGGAA 57.269 37.500 0.00 0.00 0.00 3.53
3140 4670 4.040217 AGAAGCTGCTCTATGTATGGAAGG 59.960 45.833 1.00 0.00 0.00 3.46
3141 4671 2.038295 AGCTGCTCTATGTATGGAAGGC 59.962 50.000 0.00 0.00 0.00 4.35
3210 4741 7.920738 TCTTGTTTCTTCAAGAGCTAGAAAAC 58.079 34.615 9.62 6.83 45.62 2.43
3224 4755 5.997746 AGCTAGAAAACTGCAGTTTGTATGA 59.002 36.000 38.08 22.75 46.47 2.15
3267 4812 3.460825 TGTATAAACTCTGAAGCCCCCT 58.539 45.455 0.00 0.00 0.00 4.79
3350 4920 6.938698 TGGTGGTCAAAGTTATTACTCCTA 57.061 37.500 0.00 0.00 31.99 2.94
3409 4979 0.687354 TCAAGCCCTCAACTGGAGTC 59.313 55.000 0.00 0.00 42.40 3.36
3410 4980 0.322008 CAAGCCCTCAACTGGAGTCC 60.322 60.000 0.73 0.73 42.40 3.85
3411 4981 0.768221 AAGCCCTCAACTGGAGTCCA 60.768 55.000 12.40 12.40 42.40 4.02
3420 4990 3.466881 TGGAGTCCAGGTCCAACG 58.533 61.111 8.12 0.00 41.32 4.10
3421 4991 1.152419 TGGAGTCCAGGTCCAACGA 60.152 57.895 8.12 0.00 41.32 3.85
3422 4992 0.761323 TGGAGTCCAGGTCCAACGAA 60.761 55.000 8.12 0.00 41.32 3.85
3423 4993 0.395312 GGAGTCCAGGTCCAACGAAA 59.605 55.000 3.60 0.00 33.84 3.46
3424 4994 1.509703 GAGTCCAGGTCCAACGAAAC 58.490 55.000 0.00 0.00 0.00 2.78
3425 4995 0.108019 AGTCCAGGTCCAACGAAACC 59.892 55.000 0.00 0.00 35.69 3.27
3426 4996 0.887836 GTCCAGGTCCAACGAAACCC 60.888 60.000 0.00 0.00 36.11 4.11
3427 4997 1.602605 CCAGGTCCAACGAAACCCC 60.603 63.158 0.00 0.00 36.11 4.95
3428 4998 1.602605 CAGGTCCAACGAAACCCCC 60.603 63.158 0.00 0.00 36.11 5.40
3429 4999 2.670592 GGTCCAACGAAACCCCCG 60.671 66.667 0.00 0.00 0.00 5.73
3430 5000 3.359523 GTCCAACGAAACCCCCGC 61.360 66.667 0.00 0.00 0.00 6.13
3431 5001 4.992511 TCCAACGAAACCCCCGCG 62.993 66.667 0.00 0.00 0.00 6.46
3433 5003 3.719144 CAACGAAACCCCCGCGTC 61.719 66.667 4.92 0.00 37.26 5.19
3463 5033 3.518998 CGACACGGAGGGCGATCT 61.519 66.667 0.00 0.00 0.00 2.75
3464 5034 2.184830 CGACACGGAGGGCGATCTA 61.185 63.158 0.00 0.00 0.00 1.98
3465 5035 1.359475 GACACGGAGGGCGATCTAC 59.641 63.158 0.00 0.00 0.00 2.59
3466 5036 2.073037 GACACGGAGGGCGATCTACC 62.073 65.000 0.00 0.00 0.00 3.18
3491 5061 4.548513 CCCTAGGCCTCCGCTCCT 62.549 72.222 9.68 0.00 36.51 3.69
3492 5062 2.915137 CCTAGGCCTCCGCTCCTC 60.915 72.222 9.68 0.00 34.02 3.71
3493 5063 2.197324 CTAGGCCTCCGCTCCTCT 59.803 66.667 9.68 0.00 34.02 3.69
3494 5064 1.901464 CTAGGCCTCCGCTCCTCTC 60.901 68.421 9.68 0.00 34.02 3.20
3495 5065 2.351924 CTAGGCCTCCGCTCCTCTCT 62.352 65.000 9.68 0.00 34.02 3.10
3496 5066 2.346284 TAGGCCTCCGCTCCTCTCTC 62.346 65.000 9.68 0.00 34.02 3.20
3497 5067 3.223589 GCCTCCGCTCCTCTCTCC 61.224 72.222 0.00 0.00 0.00 3.71
3498 5068 2.520741 CCTCCGCTCCTCTCTCCC 60.521 72.222 0.00 0.00 0.00 4.30
3499 5069 2.600731 CTCCGCTCCTCTCTCCCT 59.399 66.667 0.00 0.00 0.00 4.20
3500 5070 1.528309 CTCCGCTCCTCTCTCCCTC 60.528 68.421 0.00 0.00 0.00 4.30
3501 5071 2.520741 CCGCTCCTCTCTCCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
3502 5072 2.600731 CGCTCCTCTCTCCCTCCT 59.399 66.667 0.00 0.00 0.00 3.69
3503 5073 1.528309 CGCTCCTCTCTCCCTCCTC 60.528 68.421 0.00 0.00 0.00 3.71
3504 5074 1.152546 GCTCCTCTCTCCCTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
3505 5075 1.655114 GCTCCTCTCTCCCTCCTCCT 61.655 65.000 0.00 0.00 0.00 3.69
3506 5076 0.185901 CTCCTCTCTCCCTCCTCCTG 59.814 65.000 0.00 0.00 0.00 3.86
3507 5077 1.457455 CCTCTCTCCCTCCTCCTGC 60.457 68.421 0.00 0.00 0.00 4.85
3508 5078 1.457455 CTCTCTCCCTCCTCCTGCC 60.457 68.421 0.00 0.00 0.00 4.85
3509 5079 2.837291 CTCTCCCTCCTCCTGCCG 60.837 72.222 0.00 0.00 0.00 5.69
3545 5115 3.372730 GCGTTGCCTGGCCAATGA 61.373 61.111 17.53 0.00 34.42 2.57
3546 5116 2.568090 CGTTGCCTGGCCAATGAC 59.432 61.111 17.53 2.36 34.42 3.06
3547 5117 2.568090 GTTGCCTGGCCAATGACG 59.432 61.111 17.53 0.00 0.00 4.35
3548 5118 2.676121 TTGCCTGGCCAATGACGG 60.676 61.111 17.53 5.01 0.00 4.79
3590 5160 2.663188 GCGGTGATGGCGATCTCC 60.663 66.667 17.14 17.14 38.43 3.71
3591 5161 3.133014 CGGTGATGGCGATCTCCT 58.867 61.111 22.36 0.00 39.29 3.69
3592 5162 1.300465 CGGTGATGGCGATCTCCTG 60.300 63.158 22.36 14.39 39.29 3.86
3593 5163 1.826024 GGTGATGGCGATCTCCTGT 59.174 57.895 19.14 0.00 38.66 4.00
3594 5164 0.249657 GGTGATGGCGATCTCCTGTC 60.250 60.000 19.14 2.38 38.66 3.51
3595 5165 0.461548 GTGATGGCGATCTCCTGTCA 59.538 55.000 10.25 4.95 0.00 3.58
3596 5166 0.749049 TGATGGCGATCTCCTGTCAG 59.251 55.000 10.25 0.00 0.00 3.51
3597 5167 0.599728 GATGGCGATCTCCTGTCAGC 60.600 60.000 2.88 0.00 0.00 4.26
3598 5168 2.279120 GGCGATCTCCTGTCAGCG 60.279 66.667 0.00 0.00 0.00 5.18
3599 5169 2.279120 GCGATCTCCTGTCAGCGG 60.279 66.667 0.00 0.00 0.00 5.52
3600 5170 2.279120 CGATCTCCTGTCAGCGGC 60.279 66.667 0.00 0.00 0.00 6.53
3601 5171 2.279120 GATCTCCTGTCAGCGGCG 60.279 66.667 0.51 0.51 0.00 6.46
3602 5172 3.781770 GATCTCCTGTCAGCGGCGG 62.782 68.421 9.78 0.00 0.00 6.13
3617 5187 4.284860 CGGCGGCTCATGGATCGA 62.285 66.667 7.61 0.00 0.00 3.59
3618 5188 2.663188 GGCGGCTCATGGATCGAC 60.663 66.667 0.00 0.00 0.00 4.20
3619 5189 3.032609 GCGGCTCATGGATCGACG 61.033 66.667 0.00 0.00 0.00 5.12
3620 5190 2.355126 CGGCTCATGGATCGACGG 60.355 66.667 0.00 0.00 0.00 4.79
3621 5191 2.815308 GGCTCATGGATCGACGGT 59.185 61.111 0.00 0.00 0.00 4.83
3622 5192 1.592669 GGCTCATGGATCGACGGTG 60.593 63.158 0.00 0.00 0.00 4.94
3623 5193 2.240500 GCTCATGGATCGACGGTGC 61.241 63.158 0.00 0.00 0.00 5.01
3624 5194 1.141665 CTCATGGATCGACGGTGCA 59.858 57.895 4.31 4.31 0.00 4.57
3625 5195 1.148157 CTCATGGATCGACGGTGCAC 61.148 60.000 8.80 8.80 0.00 4.57
3626 5196 2.173669 CATGGATCGACGGTGCACC 61.174 63.158 26.78 26.78 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.742137 GCGTTTTTCAGCGCGTGC 61.742 61.111 14.39 14.39 44.13 5.34
15 16 1.422388 ATATGCTGTGCACGATAGCG 58.578 50.000 19.25 0.00 43.04 4.26
16 17 3.885484 AAATATGCTGTGCACGATAGC 57.115 42.857 18.15 18.15 43.04 2.97
17 18 5.615544 GCCTAAAATATGCTGTGCACGATAG 60.616 44.000 13.13 5.26 43.04 2.08
18 19 4.213270 GCCTAAAATATGCTGTGCACGATA 59.787 41.667 13.13 8.77 43.04 2.92
19 20 3.003689 GCCTAAAATATGCTGTGCACGAT 59.996 43.478 13.13 6.70 43.04 3.73
20 21 2.354510 GCCTAAAATATGCTGTGCACGA 59.645 45.455 13.13 0.00 43.04 4.35
21 22 2.355756 AGCCTAAAATATGCTGTGCACG 59.644 45.455 13.13 8.32 43.04 5.34
22 23 3.243201 GGAGCCTAAAATATGCTGTGCAC 60.243 47.826 10.75 10.75 43.04 4.57
23 24 2.951642 GGAGCCTAAAATATGCTGTGCA 59.048 45.455 0.00 0.00 44.86 4.57
24 25 2.031682 CGGAGCCTAAAATATGCTGTGC 60.032 50.000 0.00 0.00 34.99 4.57
25 26 3.466836 TCGGAGCCTAAAATATGCTGTG 58.533 45.455 0.00 0.00 34.99 3.66
26 27 3.838244 TCGGAGCCTAAAATATGCTGT 57.162 42.857 0.00 0.00 34.99 4.40
27 28 5.455392 CAATTCGGAGCCTAAAATATGCTG 58.545 41.667 0.00 0.00 34.99 4.41
28 29 4.022849 GCAATTCGGAGCCTAAAATATGCT 60.023 41.667 0.00 0.00 38.24 3.79
29 30 4.229876 GCAATTCGGAGCCTAAAATATGC 58.770 43.478 0.00 0.00 0.00 3.14
30 31 4.466828 CGCAATTCGGAGCCTAAAATATG 58.533 43.478 0.00 0.00 33.78 1.78
31 32 3.058224 GCGCAATTCGGAGCCTAAAATAT 60.058 43.478 0.30 0.00 38.94 1.28
32 33 2.289547 GCGCAATTCGGAGCCTAAAATA 59.710 45.455 0.30 0.00 38.94 1.40
33 34 1.065551 GCGCAATTCGGAGCCTAAAAT 59.934 47.619 0.30 0.00 38.94 1.82
34 35 0.450184 GCGCAATTCGGAGCCTAAAA 59.550 50.000 0.30 0.00 38.94 1.52
35 36 0.675208 TGCGCAATTCGGAGCCTAAA 60.675 50.000 8.16 0.00 38.94 1.85
36 37 1.078778 TGCGCAATTCGGAGCCTAA 60.079 52.632 8.16 0.00 38.94 2.69
37 38 1.813753 GTGCGCAATTCGGAGCCTA 60.814 57.895 14.00 0.00 39.81 3.93
38 39 3.127533 GTGCGCAATTCGGAGCCT 61.128 61.111 14.00 0.00 39.81 4.58
39 40 4.520846 CGTGCGCAATTCGGAGCC 62.521 66.667 14.00 0.00 39.81 4.70
41 42 2.886512 GAAGCGTGCGCAATTCGGAG 62.887 60.000 14.00 0.00 44.88 4.63
42 43 3.022401 GAAGCGTGCGCAATTCGGA 62.022 57.895 14.00 0.00 44.88 4.55
43 44 2.574212 GAAGCGTGCGCAATTCGG 60.574 61.111 14.00 0.00 44.88 4.30
44 45 2.139811 GTGAAGCGTGCGCAATTCG 61.140 57.895 14.00 13.91 44.88 3.34
45 46 0.660005 TTGTGAAGCGTGCGCAATTC 60.660 50.000 14.00 17.43 44.88 2.17
46 47 0.039256 ATTGTGAAGCGTGCGCAATT 60.039 45.000 14.00 7.70 42.05 2.32
47 48 0.039256 AATTGTGAAGCGTGCGCAAT 60.039 45.000 14.00 6.96 45.39 3.56
48 49 0.248825 AAATTGTGAAGCGTGCGCAA 60.249 45.000 14.00 4.15 44.88 4.85
49 50 0.933973 CAAATTGTGAAGCGTGCGCA 60.934 50.000 18.87 5.66 44.88 6.09
50 51 1.768603 CAAATTGTGAAGCGTGCGC 59.231 52.632 8.67 8.67 42.33 6.09
51 52 0.933973 TGCAAATTGTGAAGCGTGCG 60.934 50.000 0.00 0.00 34.73 5.34
52 53 0.503961 GTGCAAATTGTGAAGCGTGC 59.496 50.000 0.00 0.00 0.00 5.34
53 54 1.782569 CAGTGCAAATTGTGAAGCGTG 59.217 47.619 0.00 0.00 0.00 5.34
54 55 1.865248 GCAGTGCAAATTGTGAAGCGT 60.865 47.619 11.09 0.00 0.00 5.07
55 56 0.780002 GCAGTGCAAATTGTGAAGCG 59.220 50.000 11.09 0.00 0.00 4.68
56 57 0.780002 CGCAGTGCAAATTGTGAAGC 59.220 50.000 16.83 0.00 0.00 3.86
57 58 2.124011 ACGCAGTGCAAATTGTGAAG 57.876 45.000 16.83 0.00 42.51 3.02
70 71 1.375853 TGCTCACAAAAGCACGCAGT 61.376 50.000 0.00 0.00 47.00 4.40
71 72 1.356270 TGCTCACAAAAGCACGCAG 59.644 52.632 0.00 0.00 47.00 5.18
72 73 3.507290 TGCTCACAAAAGCACGCA 58.493 50.000 0.00 0.00 47.00 5.24
77 78 1.908065 AAACGTGTGCTCACAAAAGC 58.092 45.000 18.23 0.00 43.77 3.51
78 79 3.060628 CCAAAAACGTGTGCTCACAAAAG 59.939 43.478 18.23 5.05 43.77 2.27
79 80 2.989840 CCAAAAACGTGTGCTCACAAAA 59.010 40.909 18.23 0.00 43.77 2.44
80 81 2.600731 CCAAAAACGTGTGCTCACAAA 58.399 42.857 18.23 0.00 43.77 2.83
81 82 1.734047 GCCAAAAACGTGTGCTCACAA 60.734 47.619 18.23 0.00 43.77 3.33
82 83 0.179150 GCCAAAAACGTGTGCTCACA 60.179 50.000 18.23 0.00 44.02 3.58
83 84 1.199852 CGCCAAAAACGTGTGCTCAC 61.200 55.000 8.86 8.86 40.79 3.51
84 85 1.063327 CGCCAAAAACGTGTGCTCA 59.937 52.632 0.00 0.00 0.00 4.26
85 86 0.524604 AACGCCAAAAACGTGTGCTC 60.525 50.000 0.00 0.00 44.30 4.26
86 87 0.109039 AAACGCCAAAAACGTGTGCT 60.109 45.000 0.00 0.00 44.30 4.40
87 88 1.253289 GTAAACGCCAAAAACGTGTGC 59.747 47.619 0.00 0.00 44.30 4.57
88 89 2.788030 AGTAAACGCCAAAAACGTGTG 58.212 42.857 0.00 0.00 44.30 3.82
89 90 4.612932 TTAGTAAACGCCAAAAACGTGT 57.387 36.364 0.00 0.00 44.30 4.49
90 91 5.928601 TTTTAGTAAACGCCAAAAACGTG 57.071 34.783 0.00 0.00 44.30 4.49
92 93 8.692615 ACATTATTTTAGTAAACGCCAAAAACG 58.307 29.630 0.00 0.00 0.00 3.60
93 94 9.786224 CACATTATTTTAGTAAACGCCAAAAAC 57.214 29.630 0.00 0.00 0.00 2.43
94 95 8.979574 CCACATTATTTTAGTAAACGCCAAAAA 58.020 29.630 0.00 0.00 0.00 1.94
95 96 7.599245 CCCACATTATTTTAGTAAACGCCAAAA 59.401 33.333 0.00 0.00 0.00 2.44
96 97 7.091443 CCCACATTATTTTAGTAAACGCCAAA 58.909 34.615 0.00 0.00 0.00 3.28
97 98 6.208994 ACCCACATTATTTTAGTAAACGCCAA 59.791 34.615 0.00 0.00 0.00 4.52
98 99 5.711036 ACCCACATTATTTTAGTAAACGCCA 59.289 36.000 0.00 0.00 0.00 5.69
99 100 6.198650 ACCCACATTATTTTAGTAAACGCC 57.801 37.500 0.00 0.00 0.00 5.68
100 101 6.260377 GGACCCACATTATTTTAGTAAACGC 58.740 40.000 0.00 0.00 0.00 4.84
101 102 6.457257 CGGGACCCACATTATTTTAGTAAACG 60.457 42.308 12.15 0.00 0.00 3.60
102 103 6.183360 CCGGGACCCACATTATTTTAGTAAAC 60.183 42.308 12.15 0.00 0.00 2.01
103 104 5.887035 CCGGGACCCACATTATTTTAGTAAA 59.113 40.000 12.15 0.00 0.00 2.01
104 105 5.438833 CCGGGACCCACATTATTTTAGTAA 58.561 41.667 12.15 0.00 0.00 2.24
105 106 4.686670 GCCGGGACCCACATTATTTTAGTA 60.687 45.833 12.15 0.00 0.00 1.82
106 107 3.893521 CCGGGACCCACATTATTTTAGT 58.106 45.455 12.15 0.00 0.00 2.24
107 108 2.621526 GCCGGGACCCACATTATTTTAG 59.378 50.000 12.15 0.00 0.00 1.85
108 109 2.025226 TGCCGGGACCCACATTATTTTA 60.025 45.455 12.15 0.00 0.00 1.52
109 110 1.272760 TGCCGGGACCCACATTATTTT 60.273 47.619 12.15 0.00 0.00 1.82
110 111 0.333312 TGCCGGGACCCACATTATTT 59.667 50.000 12.15 0.00 0.00 1.40
111 112 0.395173 GTGCCGGGACCCACATTATT 60.395 55.000 16.44 0.00 32.37 1.40
112 113 1.226262 GTGCCGGGACCCACATTAT 59.774 57.895 16.44 0.00 32.37 1.28
113 114 1.780107 TTGTGCCGGGACCCACATTA 61.780 55.000 24.47 0.00 41.16 1.90
114 115 2.439553 ATTGTGCCGGGACCCACATT 62.440 55.000 24.47 11.94 41.16 2.71
115 116 1.567208 TATTGTGCCGGGACCCACAT 61.567 55.000 24.47 12.35 41.16 3.21
116 117 1.780107 TTATTGTGCCGGGACCCACA 61.780 55.000 24.47 15.86 39.95 4.17
117 118 0.609681 TTTATTGTGCCGGGACCCAC 60.610 55.000 24.47 13.22 0.00 4.61
118 119 0.112606 TTTTATTGTGCCGGGACCCA 59.887 50.000 24.47 10.77 0.00 4.51
119 120 0.815095 CTTTTATTGTGCCGGGACCC 59.185 55.000 24.47 0.00 0.00 4.46
120 121 1.201414 CACTTTTATTGTGCCGGGACC 59.799 52.381 24.47 6.11 0.00 4.46
121 122 2.629639 CACTTTTATTGTGCCGGGAC 57.370 50.000 20.69 20.69 0.00 4.46
128 129 6.303022 CACGTCATTGTAGCACTTTTATTGTG 59.697 38.462 0.00 0.00 38.36 3.33
129 130 6.370593 CACGTCATTGTAGCACTTTTATTGT 58.629 36.000 0.00 0.00 0.00 2.71
130 131 5.283717 GCACGTCATTGTAGCACTTTTATTG 59.716 40.000 0.00 0.00 0.00 1.90
131 132 5.181245 AGCACGTCATTGTAGCACTTTTATT 59.819 36.000 0.00 0.00 0.00 1.40
132 133 4.695455 AGCACGTCATTGTAGCACTTTTAT 59.305 37.500 0.00 0.00 0.00 1.40
133 134 4.062293 AGCACGTCATTGTAGCACTTTTA 58.938 39.130 0.00 0.00 0.00 1.52
134 135 2.878406 AGCACGTCATTGTAGCACTTTT 59.122 40.909 0.00 0.00 0.00 2.27
135 136 2.494059 AGCACGTCATTGTAGCACTTT 58.506 42.857 0.00 0.00 0.00 2.66
136 137 2.169832 AGCACGTCATTGTAGCACTT 57.830 45.000 0.00 0.00 0.00 3.16
137 138 3.526931 ATAGCACGTCATTGTAGCACT 57.473 42.857 0.00 0.00 0.00 4.40
138 139 4.804139 AGTTATAGCACGTCATTGTAGCAC 59.196 41.667 0.00 0.00 0.00 4.40
139 140 5.006153 AGTTATAGCACGTCATTGTAGCA 57.994 39.130 0.00 0.00 0.00 3.49
140 141 5.968387 AAGTTATAGCACGTCATTGTAGC 57.032 39.130 0.00 0.00 0.00 3.58
143 144 8.114290 CGAATAAAAGTTATAGCACGTCATTGT 58.886 33.333 0.00 0.00 0.00 2.71
144 145 8.325282 TCGAATAAAAGTTATAGCACGTCATTG 58.675 33.333 0.00 0.00 0.00 2.82
145 146 8.325997 GTCGAATAAAAGTTATAGCACGTCATT 58.674 33.333 0.00 0.00 0.00 2.57
146 147 7.305820 CGTCGAATAAAAGTTATAGCACGTCAT 60.306 37.037 0.00 0.00 0.00 3.06
147 148 6.021232 CGTCGAATAAAAGTTATAGCACGTCA 60.021 38.462 0.00 0.00 0.00 4.35
148 149 6.021153 ACGTCGAATAAAAGTTATAGCACGTC 60.021 38.462 0.00 0.00 30.19 4.34
149 150 5.801947 ACGTCGAATAAAAGTTATAGCACGT 59.198 36.000 0.00 0.00 0.00 4.49
150 151 6.021232 TCACGTCGAATAAAAGTTATAGCACG 60.021 38.462 0.00 0.00 0.00 5.34
151 152 7.213252 TCACGTCGAATAAAAGTTATAGCAC 57.787 36.000 0.00 0.00 0.00 4.40
152 153 7.815398 TTCACGTCGAATAAAAGTTATAGCA 57.185 32.000 0.00 0.00 0.00 3.49
153 154 9.698617 AAATTCACGTCGAATAAAAGTTATAGC 57.301 29.630 11.79 0.00 43.83 2.97
178 179 2.105128 CCAACGGCCGCACAAAAA 59.895 55.556 28.58 0.00 0.00 1.94
179 180 2.829003 TCCAACGGCCGCACAAAA 60.829 55.556 28.58 2.77 0.00 2.44
180 181 3.283684 CTCCAACGGCCGCACAAA 61.284 61.111 28.58 6.34 0.00 2.83
181 182 4.243008 TCTCCAACGGCCGCACAA 62.243 61.111 28.58 7.99 0.00 3.33
182 183 4.980805 GTCTCCAACGGCCGCACA 62.981 66.667 28.58 5.68 0.00 4.57
191 192 0.586802 GCTGTCAAACCGTCTCCAAC 59.413 55.000 0.00 0.00 0.00 3.77
192 193 0.534203 GGCTGTCAAACCGTCTCCAA 60.534 55.000 0.00 0.00 0.00 3.53
193 194 1.070786 GGCTGTCAAACCGTCTCCA 59.929 57.895 0.00 0.00 0.00 3.86
194 195 1.671379 GGGCTGTCAAACCGTCTCC 60.671 63.158 0.00 0.00 0.00 3.71
195 196 0.670854 GAGGGCTGTCAAACCGTCTC 60.671 60.000 6.90 0.00 37.75 3.36
196 197 1.371558 GAGGGCTGTCAAACCGTCT 59.628 57.895 6.90 0.00 37.75 4.18
197 198 2.027625 CGAGGGCTGTCAAACCGTC 61.028 63.158 4.79 4.79 37.46 4.79
198 199 2.030562 CGAGGGCTGTCAAACCGT 59.969 61.111 0.00 0.00 0.00 4.83
199 200 2.742372 CCGAGGGCTGTCAAACCG 60.742 66.667 0.00 0.00 0.00 4.44
200 201 1.833787 TACCCGAGGGCTGTCAAACC 61.834 60.000 8.33 0.00 39.32 3.27
201 202 0.035739 TTACCCGAGGGCTGTCAAAC 59.964 55.000 8.33 0.00 39.32 2.93
202 203 0.035739 GTTACCCGAGGGCTGTCAAA 59.964 55.000 8.33 0.00 39.32 2.69
203 204 0.834687 AGTTACCCGAGGGCTGTCAA 60.835 55.000 8.33 0.00 39.32 3.18
204 205 1.229082 AGTTACCCGAGGGCTGTCA 60.229 57.895 8.33 0.00 39.32 3.58
205 206 1.516423 GAGTTACCCGAGGGCTGTC 59.484 63.158 8.33 0.00 39.32 3.51
206 207 1.988406 GGAGTTACCCGAGGGCTGT 60.988 63.158 8.33 0.00 39.32 4.40
207 208 1.677637 GAGGAGTTACCCGAGGGCTG 61.678 65.000 8.33 0.00 40.05 4.85
208 209 1.381463 GAGGAGTTACCCGAGGGCT 60.381 63.158 8.33 0.00 40.05 5.19
209 210 2.433146 GGAGGAGTTACCCGAGGGC 61.433 68.421 8.33 0.00 40.05 5.19
210 211 0.325390 AAGGAGGAGTTACCCGAGGG 60.325 60.000 6.63 6.63 40.05 4.30
211 212 2.030371 GTAAGGAGGAGTTACCCGAGG 58.970 57.143 0.00 0.00 40.05 4.63
212 213 2.030371 GGTAAGGAGGAGTTACCCGAG 58.970 57.143 1.22 0.00 42.54 4.63
213 214 1.683011 CGGTAAGGAGGAGTTACCCGA 60.683 57.143 6.47 0.00 44.61 5.14
214 215 0.743097 CGGTAAGGAGGAGTTACCCG 59.257 60.000 6.47 0.00 44.61 5.28
215 216 1.857965 ACGGTAAGGAGGAGTTACCC 58.142 55.000 6.47 0.00 44.61 3.69
216 217 2.356069 CGTACGGTAAGGAGGAGTTACC 59.644 54.545 7.57 2.46 44.18 2.85
217 218 2.223363 GCGTACGGTAAGGAGGAGTTAC 60.223 54.545 18.39 0.00 0.00 2.50
218 219 2.017049 GCGTACGGTAAGGAGGAGTTA 58.983 52.381 18.39 0.00 0.00 2.24
219 220 0.813821 GCGTACGGTAAGGAGGAGTT 59.186 55.000 18.39 0.00 0.00 3.01
220 221 1.372087 CGCGTACGGTAAGGAGGAGT 61.372 60.000 18.39 0.00 34.97 3.85
285 286 2.626780 GGTTGGGTTGCTTCTCCGC 61.627 63.158 0.00 0.00 0.00 5.54
316 317 4.466827 AGTAAAATGTGGGTCGTTTTCCT 58.533 39.130 1.84 0.00 42.20 3.36
514 539 1.753463 GGGATCAGGGTCGACGAGT 60.753 63.158 9.92 0.00 0.00 4.18
523 548 1.534235 CTAGGGACCGGGATCAGGG 60.534 68.421 6.32 5.68 0.00 4.45
524 549 1.534235 CCTAGGGACCGGGATCAGG 60.534 68.421 6.32 1.24 0.00 3.86
525 550 0.540830 CTCCTAGGGACCGGGATCAG 60.541 65.000 9.46 0.00 0.00 2.90
526 551 1.542175 CTCCTAGGGACCGGGATCA 59.458 63.158 9.46 0.00 0.00 2.92
622 660 1.107114 GGCTGAGGAAGACGATGAGA 58.893 55.000 0.00 0.00 0.00 3.27
758 829 1.272769 AGGAAGGAAGGAACGAACGAG 59.727 52.381 0.14 0.00 0.00 4.18
891 1629 1.278985 TCAGCTTGACCCATGGTACTG 59.721 52.381 11.73 8.53 35.25 2.74
1008 1762 1.399791 GCCATTTTCTGCGGAGAAGAG 59.600 52.381 19.07 12.59 39.44 2.85
1029 1783 0.697511 TCGGGGGATCCACCATCATT 60.698 55.000 32.61 0.00 41.20 2.57
1234 1991 2.584418 CGTCCTCAGCGCATCCAG 60.584 66.667 11.47 0.00 0.00 3.86
1376 2133 4.652881 ACTTGACTATCTGATGCAGATCCA 59.347 41.667 12.75 7.75 46.83 3.41
1881 3349 6.927381 AGGACAACTATTTAATTATCGGTCCG 59.073 38.462 4.39 4.39 44.30 4.79
2023 3504 1.135344 GTACTTCAGTCCTCGGAGCAC 60.135 57.143 0.00 0.00 0.00 4.40
2139 3620 4.214545 TGACCTTTAGTGTTATTTGTGCGG 59.785 41.667 0.00 0.00 0.00 5.69
2172 3653 0.606604 AGCGGGTGACAACGTATTCT 59.393 50.000 0.00 0.00 0.00 2.40
2214 3695 1.404717 CCATAGTTGTCGCAGCAGAGT 60.405 52.381 0.00 0.00 0.00 3.24
2362 3843 0.176680 ATGAACGCGAGATCAGCCTT 59.823 50.000 15.93 0.00 46.25 4.35
2370 3851 1.144969 GGTTGTCAATGAACGCGAGA 58.855 50.000 15.93 0.00 0.00 4.04
2398 3879 4.953579 TGGAAGGGATTTAATGTAGTTGCC 59.046 41.667 0.00 0.00 0.00 4.52
2752 4249 6.668541 ATACGAAGAATGAACATGTGAAGG 57.331 37.500 0.00 0.00 0.00 3.46
2833 4347 6.050432 AGAAATCCATACGCCGTTTATTGTA 58.950 36.000 0.00 0.00 0.00 2.41
2888 4402 6.622549 GCTTCTACAACACAGTAGTCTATGT 58.377 40.000 0.00 0.00 41.68 2.29
2889 4403 5.739630 CGCTTCTACAACACAGTAGTCTATG 59.260 44.000 0.00 0.00 41.68 2.23
3018 4548 3.261981 ACCGAATTCCGCTTCTACAAT 57.738 42.857 0.00 0.00 36.84 2.71
3040 4570 9.259832 AGCTTCTTCATAACCCAATTCTTAATT 57.740 29.630 0.00 0.00 0.00 1.40
3138 4668 3.138468 AGGTCACTTGAAAGTTTAGGCCT 59.862 43.478 11.78 11.78 37.08 5.19
3210 4741 6.441274 ACAGAAAACATCATACAAACTGCAG 58.559 36.000 13.48 13.48 0.00 4.41
3224 4755 9.777297 ATACATTTTAAGCCAAACAGAAAACAT 57.223 25.926 0.00 0.00 0.00 2.71
3267 4812 5.878116 GGTGGTACTACATTGCAGATTACAA 59.122 40.000 11.80 0.00 0.00 2.41
3325 4895 6.790319 AGGAGTAATAACTTTGACCACCATT 58.210 36.000 0.00 0.00 35.56 3.16
3409 4979 1.602605 GGGGTTTCGTTGGACCTGG 60.603 63.158 0.00 0.00 36.18 4.45
3410 4980 1.602605 GGGGGTTTCGTTGGACCTG 60.603 63.158 0.00 0.00 36.18 4.00
3411 4981 2.841317 GGGGGTTTCGTTGGACCT 59.159 61.111 0.00 0.00 36.18 3.85
3412 4982 2.670592 CGGGGGTTTCGTTGGACC 60.671 66.667 0.00 0.00 35.14 4.46
3413 4983 3.359523 GCGGGGGTTTCGTTGGAC 61.360 66.667 0.00 0.00 0.00 4.02
3414 4984 4.992511 CGCGGGGGTTTCGTTGGA 62.993 66.667 0.00 0.00 0.00 3.53
3416 4986 3.719144 GACGCGGGGGTTTCGTTG 61.719 66.667 12.47 0.00 36.50 4.10
3446 5016 2.184830 TAGATCGCCCTCCGTGTCG 61.185 63.158 0.00 0.00 38.35 4.35
3447 5017 1.359475 GTAGATCGCCCTCCGTGTC 59.641 63.158 0.00 0.00 38.35 3.67
3448 5018 2.125961 GGTAGATCGCCCTCCGTGT 61.126 63.158 0.00 0.00 38.35 4.49
3449 5019 2.728817 GGTAGATCGCCCTCCGTG 59.271 66.667 0.00 0.00 38.35 4.94
3450 5020 2.905880 CGGTAGATCGCCCTCCGT 60.906 66.667 4.19 0.00 38.35 4.69
3474 5044 4.548513 AGGAGCGGAGGCCTAGGG 62.549 72.222 4.42 0.00 41.24 3.53
3475 5045 2.915137 GAGGAGCGGAGGCCTAGG 60.915 72.222 4.42 3.67 41.24 3.02
3476 5046 1.901464 GAGAGGAGCGGAGGCCTAG 60.901 68.421 4.42 3.81 41.24 3.02
3477 5047 2.196229 GAGAGGAGCGGAGGCCTA 59.804 66.667 4.42 0.00 41.24 3.93
3478 5048 3.731766 GAGAGAGGAGCGGAGGCCT 62.732 68.421 3.86 3.86 41.24 5.19
3479 5049 3.223589 GAGAGAGGAGCGGAGGCC 61.224 72.222 0.00 0.00 41.24 5.19
3480 5050 3.223589 GGAGAGAGGAGCGGAGGC 61.224 72.222 0.00 0.00 40.37 4.70
3481 5051 2.520741 GGGAGAGAGGAGCGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
3482 5052 1.528309 GAGGGAGAGAGGAGCGGAG 60.528 68.421 0.00 0.00 0.00 4.63
3483 5053 2.598467 GAGGGAGAGAGGAGCGGA 59.402 66.667 0.00 0.00 0.00 5.54
3484 5054 2.520741 GGAGGGAGAGAGGAGCGG 60.521 72.222 0.00 0.00 0.00 5.52
3485 5055 1.528309 GAGGAGGGAGAGAGGAGCG 60.528 68.421 0.00 0.00 0.00 5.03
3486 5056 1.152546 GGAGGAGGGAGAGAGGAGC 60.153 68.421 0.00 0.00 0.00 4.70
3487 5057 0.185901 CAGGAGGAGGGAGAGAGGAG 59.814 65.000 0.00 0.00 0.00 3.69
3488 5058 1.943730 GCAGGAGGAGGGAGAGAGGA 61.944 65.000 0.00 0.00 0.00 3.71
3489 5059 1.457455 GCAGGAGGAGGGAGAGAGG 60.457 68.421 0.00 0.00 0.00 3.69
3490 5060 1.457455 GGCAGGAGGAGGGAGAGAG 60.457 68.421 0.00 0.00 0.00 3.20
3491 5061 2.693017 GGCAGGAGGAGGGAGAGA 59.307 66.667 0.00 0.00 0.00 3.10
3492 5062 2.837291 CGGCAGGAGGAGGGAGAG 60.837 72.222 0.00 0.00 0.00 3.20
3528 5098 3.372730 TCATTGGCCAGGCAACGC 61.373 61.111 15.19 0.00 46.39 4.84
3529 5099 2.568090 GTCATTGGCCAGGCAACG 59.432 61.111 15.19 3.67 46.39 4.10
3530 5100 2.568090 CGTCATTGGCCAGGCAAC 59.432 61.111 15.19 2.42 0.00 4.17
3531 5101 2.676121 CCGTCATTGGCCAGGCAA 60.676 61.111 15.19 11.94 0.00 4.52
3573 5143 2.663188 GGAGATCGCCATCACCGC 60.663 66.667 11.06 0.00 30.96 5.68
3574 5144 1.300465 CAGGAGATCGCCATCACCG 60.300 63.158 18.44 0.00 42.96 4.94
3575 5145 0.249657 GACAGGAGATCGCCATCACC 60.250 60.000 18.44 0.00 39.48 4.02
3576 5146 0.461548 TGACAGGAGATCGCCATCAC 59.538 55.000 18.44 6.64 0.00 3.06
3577 5147 0.749049 CTGACAGGAGATCGCCATCA 59.251 55.000 18.44 17.94 0.00 3.07
3578 5148 0.599728 GCTGACAGGAGATCGCCATC 60.600 60.000 18.44 14.44 0.00 3.51
3579 5149 1.445095 GCTGACAGGAGATCGCCAT 59.555 57.895 18.44 5.06 0.00 4.40
3580 5150 2.895680 GCTGACAGGAGATCGCCA 59.104 61.111 18.44 0.00 0.00 5.69
3581 5151 2.279120 CGCTGACAGGAGATCGCC 60.279 66.667 7.52 7.52 0.00 5.54
3582 5152 2.279120 CCGCTGACAGGAGATCGC 60.279 66.667 4.26 0.00 0.00 4.58
3583 5153 2.279120 GCCGCTGACAGGAGATCG 60.279 66.667 4.26 0.00 0.00 3.69
3584 5154 2.279120 CGCCGCTGACAGGAGATC 60.279 66.667 4.26 0.00 0.00 2.75
3585 5155 3.842923 CCGCCGCTGACAGGAGAT 61.843 66.667 4.26 0.00 0.00 2.75
3600 5170 4.284860 TCGATCCATGAGCCGCCG 62.285 66.667 0.00 0.00 0.00 6.46
3601 5171 2.663188 GTCGATCCATGAGCCGCC 60.663 66.667 0.00 0.00 0.00 6.13
3602 5172 3.032609 CGTCGATCCATGAGCCGC 61.033 66.667 0.00 0.00 0.00 6.53
3603 5173 2.355126 CCGTCGATCCATGAGCCG 60.355 66.667 0.00 0.00 0.00 5.52
3604 5174 1.592669 CACCGTCGATCCATGAGCC 60.593 63.158 0.00 0.00 0.00 4.70
3605 5175 2.240500 GCACCGTCGATCCATGAGC 61.241 63.158 0.00 0.00 0.00 4.26
3606 5176 1.141665 TGCACCGTCGATCCATGAG 59.858 57.895 0.00 0.00 0.00 2.90
3607 5177 1.153647 GTGCACCGTCGATCCATGA 60.154 57.895 5.22 0.00 0.00 3.07
3608 5178 2.173669 GGTGCACCGTCGATCCATG 61.174 63.158 22.49 0.00 0.00 3.66
3609 5179 2.186903 GGTGCACCGTCGATCCAT 59.813 61.111 22.49 0.00 0.00 3.41
3654 5224 3.712881 GTTGCCGTCACACTCGCC 61.713 66.667 0.00 0.00 0.00 5.54
3655 5225 4.059459 CGTTGCCGTCACACTCGC 62.059 66.667 0.00 0.00 0.00 5.03
3656 5226 2.354188 TCGTTGCCGTCACACTCG 60.354 61.111 0.00 0.00 35.01 4.18
3657 5227 1.548973 CTGTCGTTGCCGTCACACTC 61.549 60.000 0.00 0.00 35.01 3.51
3658 5228 1.591594 CTGTCGTTGCCGTCACACT 60.592 57.895 0.00 0.00 35.01 3.55
3659 5229 2.928361 CTGTCGTTGCCGTCACAC 59.072 61.111 0.00 0.00 35.01 3.82
3660 5230 2.964925 GCTGTCGTTGCCGTCACA 60.965 61.111 0.00 0.00 35.01 3.58
3661 5231 4.059459 CGCTGTCGTTGCCGTCAC 62.059 66.667 0.00 0.00 35.01 3.67


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

AutoCloner maintained by Alex Coulton.