Multiple sequence alignment - TraesCS5D01G233000

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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 TraesCS5D01G233000 chr5D 100.000 4992 0 0 1 4992 340508721 340513712 0.000000e+00 9219.0
1 TraesCS5D01G233000 chr5D 78.352 522 61 31 2189 2708 101259894 101259423 1.760000e-74 291.0
2 TraesCS5D01G233000 chr5D 92.562 121 9 0 6 126 23279474 23279354 1.850000e-39 174.0
3 TraesCS5D01G233000 chr5D 88.028 142 10 4 1846 1987 101264046 101263912 1.440000e-35 161.0
4 TraesCS5D01G233000 chr5D 85.484 62 9 0 3048 3109 56951441 56951380 1.160000e-06 65.8
5 TraesCS5D01G233000 chr5A 92.562 4410 162 64 678 4992 441476173 441480511 0.000000e+00 6174.0
6 TraesCS5D01G233000 chr5A 89.100 422 35 7 250 666 441474718 441475133 9.580000e-142 514.0
7 TraesCS5D01G233000 chr5B 92.794 2373 78 37 424 2767 399297210 399299518 0.000000e+00 3349.0
8 TraesCS5D01G233000 chr5B 91.348 2300 86 32 2765 4990 399299830 399302090 0.000000e+00 3040.0
9 TraesCS5D01G233000 chr5B 87.571 177 15 3 250 419 399296465 399296641 1.100000e-46 198.0
10 TraesCS5D01G233000 chr5B 90.566 106 6 2 1841 1946 128249709 128249608 2.420000e-28 137.0
11 TraesCS5D01G233000 chr5B 85.484 62 9 0 3048 3109 59926605 59926544 1.160000e-06 65.8
12 TraesCS5D01G233000 chr6D 86.111 252 32 3 1 251 446133999 446134248 8.240000e-68 268.0
13 TraesCS5D01G233000 chr6D 90.551 127 12 0 1 127 149030861 149030987 8.590000e-38 169.0
14 TraesCS5D01G233000 chr7D 85.784 204 19 9 3598 3796 98383303 98383105 1.820000e-49 207.0
15 TraesCS5D01G233000 chr7D 92.188 128 9 1 1 127 498526214 498526341 3.970000e-41 180.0
16 TraesCS5D01G233000 chr7D 97.183 71 2 0 3047 3117 98383688 98383618 2.440000e-23 121.0
17 TraesCS5D01G233000 chr7A 89.222 167 15 3 3626 3791 100623566 100623402 6.550000e-49 206.0
18 TraesCS5D01G233000 chr7A 90.909 132 11 1 1 131 736489119 736488988 5.140000e-40 176.0
19 TraesCS5D01G233000 chr7A 98.611 72 1 0 3046 3117 100623911 100623840 1.460000e-25 128.0
20 TraesCS5D01G233000 chr7B 91.096 146 11 2 3647 3791 52923254 52923110 3.940000e-46 196.0
21 TraesCS5D01G233000 chr7B 90.511 137 12 1 1 136 637583805 637583669 3.970000e-41 180.0
22 TraesCS5D01G233000 chr7B 92.126 127 10 0 1 127 672483995 672484121 3.970000e-41 180.0
23 TraesCS5D01G233000 chr7B 90.566 106 6 2 1841 1946 17218480 17218379 2.420000e-28 137.0
24 TraesCS5D01G233000 chr7B 90.566 106 6 2 1841 1946 74837520 74837621 2.420000e-28 137.0
25 TraesCS5D01G233000 chr7B 90.566 106 6 2 1841 1946 726694652 726694753 2.420000e-28 137.0
26 TraesCS5D01G233000 chr7B 98.611 72 1 0 3046 3117 52923698 52923627 1.460000e-25 128.0
27 TraesCS5D01G233000 chr2D 94.488 127 7 0 1 127 135599205 135599331 3.940000e-46 196.0
28 TraesCS5D01G233000 chr3A 91.339 127 10 1 1 126 24723008 24723134 6.640000e-39 172.0
29 TraesCS5D01G233000 chr4B 90.566 106 6 2 1841 1946 172761964 172762065 2.420000e-28 137.0
30 TraesCS5D01G233000 chr2A 90.566 106 6 2 1841 1946 623321039 623321140 2.420000e-28 137.0


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 TraesCS5D01G233000 chr5D 340508721 340513712 4991 False 9219.000000 9219 100.000 1 4992 1 chr5D.!!$F1 4991
1 TraesCS5D01G233000 chr5A 441474718 441480511 5793 False 3344.000000 6174 90.831 250 4992 2 chr5A.!!$F1 4742
2 TraesCS5D01G233000 chr5B 399296465 399302090 5625 False 2195.666667 3349 90.571 250 4990 3 chr5B.!!$F1 4740

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
419 427 0.106894 AATAGCTAGGGCGTCAAGGC 59.893 55.0 0.00 0.0 44.37 4.35 F
1606 3229 0.102481 CCCGACCTTGACGAATCGAT 59.898 55.0 10.55 0.0 36.70 3.59 F
2967 4950 0.030638 TTTGTTTCGAGCTTGCTGCC 59.969 50.0 0.00 0.0 44.23 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 3802 0.893727 AGCCACAACGATCCAAACCC 60.894 55.0 0.00 0.0 0.0 4.11 R
3032 5023 0.031178 GTCTGCAGCCACACCAAAAG 59.969 55.0 9.47 0.0 0.0 2.27 R
4353 6388 0.716591 TGGAGGGGAAAGAGAGGCTA 59.283 55.0 0.00 0.0 0.0 3.93 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
18 19 3.869481 AAAAAGGCGTGTGGGCAT 58.131 50.000 0.00 0.00 45.36 4.40
19 20 2.132300 AAAAAGGCGTGTGGGCATT 58.868 47.368 0.00 0.00 45.36 3.56
20 21 1.333177 AAAAAGGCGTGTGGGCATTA 58.667 45.000 0.00 0.00 45.36 1.90
21 22 1.555967 AAAAGGCGTGTGGGCATTAT 58.444 45.000 0.00 0.00 45.36 1.28
22 23 1.555967 AAAGGCGTGTGGGCATTATT 58.444 45.000 0.00 0.00 45.36 1.40
23 24 1.555967 AAGGCGTGTGGGCATTATTT 58.444 45.000 0.00 0.00 45.36 1.40
24 25 0.817013 AGGCGTGTGGGCATTATTTG 59.183 50.000 0.00 0.00 45.36 2.32
25 26 0.530288 GGCGTGTGGGCATTATTTGT 59.470 50.000 0.00 0.00 41.77 2.83
26 27 1.067213 GGCGTGTGGGCATTATTTGTT 60.067 47.619 0.00 0.00 41.77 2.83
27 28 2.611722 GGCGTGTGGGCATTATTTGTTT 60.612 45.455 0.00 0.00 41.77 2.83
28 29 3.063485 GCGTGTGGGCATTATTTGTTTT 58.937 40.909 0.00 0.00 0.00 2.43
29 30 3.120718 GCGTGTGGGCATTATTTGTTTTG 60.121 43.478 0.00 0.00 0.00 2.44
30 31 3.120718 CGTGTGGGCATTATTTGTTTTGC 60.121 43.478 0.00 0.00 0.00 3.68
36 37 4.403015 GCATTATTTGTTTTGCCCACAC 57.597 40.909 0.00 0.00 0.00 3.82
37 38 3.120718 GCATTATTTGTTTTGCCCACACG 60.121 43.478 0.00 0.00 0.00 4.49
38 39 3.802948 TTATTTGTTTTGCCCACACGT 57.197 38.095 0.00 0.00 0.00 4.49
39 40 4.913335 TTATTTGTTTTGCCCACACGTA 57.087 36.364 0.00 0.00 0.00 3.57
40 41 2.853731 TTTGTTTTGCCCACACGTAG 57.146 45.000 0.00 0.00 0.00 3.51
41 42 1.025812 TTGTTTTGCCCACACGTAGG 58.974 50.000 0.00 0.00 0.00 3.18
53 54 2.340809 CGTAGGCGTGTGGGTTGA 59.659 61.111 0.00 0.00 0.00 3.18
54 55 1.079405 CGTAGGCGTGTGGGTTGAT 60.079 57.895 0.00 0.00 0.00 2.57
55 56 1.082117 CGTAGGCGTGTGGGTTGATC 61.082 60.000 0.00 0.00 0.00 2.92
56 57 0.743345 GTAGGCGTGTGGGTTGATCC 60.743 60.000 0.00 0.00 0.00 3.36
57 58 0.907704 TAGGCGTGTGGGTTGATCCT 60.908 55.000 0.00 0.00 36.25 3.24
58 59 1.303317 GGCGTGTGGGTTGATCCTT 60.303 57.895 0.00 0.00 36.25 3.36
59 60 0.893727 GGCGTGTGGGTTGATCCTTT 60.894 55.000 0.00 0.00 36.25 3.11
60 61 0.958822 GCGTGTGGGTTGATCCTTTT 59.041 50.000 0.00 0.00 36.25 2.27
61 62 2.156098 GCGTGTGGGTTGATCCTTTTA 58.844 47.619 0.00 0.00 36.25 1.52
62 63 2.161609 GCGTGTGGGTTGATCCTTTTAG 59.838 50.000 0.00 0.00 36.25 1.85
63 64 3.670625 CGTGTGGGTTGATCCTTTTAGA 58.329 45.455 0.00 0.00 36.25 2.10
64 65 3.435671 CGTGTGGGTTGATCCTTTTAGAC 59.564 47.826 0.00 0.00 36.25 2.59
65 66 4.394729 GTGTGGGTTGATCCTTTTAGACA 58.605 43.478 0.00 0.00 36.25 3.41
66 67 4.215613 GTGTGGGTTGATCCTTTTAGACAC 59.784 45.833 0.00 0.00 36.25 3.67
67 68 3.756963 GTGGGTTGATCCTTTTAGACACC 59.243 47.826 0.00 0.00 36.25 4.16
68 69 3.396276 TGGGTTGATCCTTTTAGACACCA 59.604 43.478 0.00 0.00 36.25 4.17
69 70 4.044065 TGGGTTGATCCTTTTAGACACCAT 59.956 41.667 0.00 0.00 36.25 3.55
70 71 5.251932 TGGGTTGATCCTTTTAGACACCATA 59.748 40.000 0.00 0.00 36.25 2.74
71 72 6.069088 TGGGTTGATCCTTTTAGACACCATAT 60.069 38.462 0.00 0.00 36.25 1.78
72 73 7.128109 TGGGTTGATCCTTTTAGACACCATATA 59.872 37.037 0.00 0.00 36.25 0.86
73 74 7.996644 GGGTTGATCCTTTTAGACACCATATAA 59.003 37.037 0.00 0.00 36.25 0.98
74 75 9.403583 GGTTGATCCTTTTAGACACCATATAAA 57.596 33.333 0.00 0.00 0.00 1.40
77 78 9.104965 TGATCCTTTTAGACACCATATAAAACG 57.895 33.333 0.00 0.00 32.05 3.60
78 79 9.106070 GATCCTTTTAGACACCATATAAAACGT 57.894 33.333 0.00 0.00 32.05 3.99
79 80 8.259049 TCCTTTTAGACACCATATAAAACGTG 57.741 34.615 0.00 0.00 32.05 4.49
80 81 7.879160 TCCTTTTAGACACCATATAAAACGTGT 59.121 33.333 0.00 0.00 41.97 4.49
81 82 9.153721 CCTTTTAGACACCATATAAAACGTGTA 57.846 33.333 0.00 0.00 39.47 2.90
83 84 8.706492 TTTAGACACCATATAAAACGTGTAGG 57.294 34.615 0.00 0.00 39.47 3.18
84 85 5.114081 AGACACCATATAAAACGTGTAGGC 58.886 41.667 0.00 0.00 39.47 3.93
85 86 4.834534 ACACCATATAAAACGTGTAGGCA 58.165 39.130 0.00 0.00 37.67 4.75
86 87 4.873827 ACACCATATAAAACGTGTAGGCAG 59.126 41.667 0.00 0.00 37.67 4.85
87 88 5.113383 CACCATATAAAACGTGTAGGCAGA 58.887 41.667 0.00 0.00 0.00 4.26
88 89 5.006358 CACCATATAAAACGTGTAGGCAGAC 59.994 44.000 0.00 0.00 0.00 3.51
89 90 4.510340 CCATATAAAACGTGTAGGCAGACC 59.490 45.833 0.00 0.00 0.00 3.85
90 91 2.460757 TAAAACGTGTAGGCAGACCC 57.539 50.000 0.00 0.00 36.11 4.46
91 92 0.250597 AAAACGTGTAGGCAGACCCC 60.251 55.000 0.00 0.00 36.11 4.95
92 93 1.125711 AAACGTGTAGGCAGACCCCT 61.126 55.000 0.00 0.00 39.05 4.79
93 94 1.125711 AACGTGTAGGCAGACCCCTT 61.126 55.000 0.00 0.00 36.41 3.95
94 95 0.251922 ACGTGTAGGCAGACCCCTTA 60.252 55.000 0.00 0.00 36.41 2.69
95 96 0.899720 CGTGTAGGCAGACCCCTTAA 59.100 55.000 0.00 0.00 36.41 1.85
96 97 1.405121 CGTGTAGGCAGACCCCTTAAC 60.405 57.143 0.00 0.00 36.41 2.01
97 98 0.899720 TGTAGGCAGACCCCTTAACG 59.100 55.000 0.00 0.00 36.41 3.18
98 99 0.461516 GTAGGCAGACCCCTTAACGC 60.462 60.000 0.00 0.00 36.41 4.84
99 100 1.619807 TAGGCAGACCCCTTAACGCC 61.620 60.000 0.00 0.00 39.90 5.68
100 101 2.437895 GCAGACCCCTTAACGCCC 60.438 66.667 0.00 0.00 0.00 6.13
101 102 3.074281 CAGACCCCTTAACGCCCA 58.926 61.111 0.00 0.00 0.00 5.36
102 103 1.376812 CAGACCCCTTAACGCCCAC 60.377 63.158 0.00 0.00 0.00 4.61
103 104 1.844289 AGACCCCTTAACGCCCACA 60.844 57.895 0.00 0.00 0.00 4.17
104 105 1.673337 GACCCCTTAACGCCCACAC 60.673 63.158 0.00 0.00 0.00 3.82
105 106 2.400269 GACCCCTTAACGCCCACACA 62.400 60.000 0.00 0.00 0.00 3.72
106 107 1.001393 CCCCTTAACGCCCACACAT 60.001 57.895 0.00 0.00 0.00 3.21
107 108 1.312371 CCCCTTAACGCCCACACATG 61.312 60.000 0.00 0.00 0.00 3.21
108 109 0.608035 CCCTTAACGCCCACACATGT 60.608 55.000 0.00 0.00 0.00 3.21
109 110 0.521291 CCTTAACGCCCACACATGTG 59.479 55.000 24.25 24.25 45.23 3.21
119 120 0.373370 CACACATGTGGGCGTTATCG 59.627 55.000 28.64 0.77 42.10 2.92
120 121 0.742990 ACACATGTGGGCGTTATCGG 60.743 55.000 28.64 0.23 34.53 4.18
128 129 2.103538 GCGTTATCGGCGTCCTGA 59.896 61.111 6.85 0.00 37.56 3.86
129 130 1.517694 GCGTTATCGGCGTCCTGAA 60.518 57.895 6.85 0.00 37.56 3.02
130 131 0.874607 GCGTTATCGGCGTCCTGAAT 60.875 55.000 6.85 0.00 37.56 2.57
131 132 1.129326 CGTTATCGGCGTCCTGAATC 58.871 55.000 6.85 0.00 0.00 2.52
132 133 1.269102 CGTTATCGGCGTCCTGAATCT 60.269 52.381 6.85 0.00 0.00 2.40
133 134 2.031420 CGTTATCGGCGTCCTGAATCTA 60.031 50.000 6.85 0.00 0.00 1.98
134 135 3.549423 CGTTATCGGCGTCCTGAATCTAA 60.549 47.826 6.85 0.00 0.00 2.10
135 136 4.557205 GTTATCGGCGTCCTGAATCTAAT 58.443 43.478 6.85 0.00 0.00 1.73
136 137 2.509052 TCGGCGTCCTGAATCTAATG 57.491 50.000 6.85 0.00 0.00 1.90
137 138 1.068588 TCGGCGTCCTGAATCTAATGG 59.931 52.381 6.85 0.00 0.00 3.16
138 139 1.202533 CGGCGTCCTGAATCTAATGGT 60.203 52.381 0.00 0.00 0.00 3.55
139 140 2.035449 CGGCGTCCTGAATCTAATGGTA 59.965 50.000 0.00 0.00 0.00 3.25
140 141 3.306088 CGGCGTCCTGAATCTAATGGTAT 60.306 47.826 0.00 0.00 0.00 2.73
141 142 4.642429 GGCGTCCTGAATCTAATGGTATT 58.358 43.478 0.00 0.00 0.00 1.89
142 143 4.452455 GGCGTCCTGAATCTAATGGTATTG 59.548 45.833 0.00 0.00 0.00 1.90
143 144 5.297547 GCGTCCTGAATCTAATGGTATTGA 58.702 41.667 0.00 0.00 0.00 2.57
144 145 5.934625 GCGTCCTGAATCTAATGGTATTGAT 59.065 40.000 0.00 0.00 0.00 2.57
145 146 6.428159 GCGTCCTGAATCTAATGGTATTGATT 59.572 38.462 0.00 0.00 32.59 2.57
146 147 7.041098 GCGTCCTGAATCTAATGGTATTGATTT 60.041 37.037 0.00 0.00 30.41 2.17
147 148 8.840321 CGTCCTGAATCTAATGGTATTGATTTT 58.160 33.333 0.00 0.00 30.41 1.82
226 227 7.724305 AACTTTGACGAAAGCTAATACTTCA 57.276 32.000 0.00 0.00 42.19 3.02
227 228 7.724305 ACTTTGACGAAAGCTAATACTTCAA 57.276 32.000 0.00 0.00 42.19 2.69
228 229 8.149973 ACTTTGACGAAAGCTAATACTTCAAA 57.850 30.769 0.00 0.00 42.19 2.69
229 230 8.283291 ACTTTGACGAAAGCTAATACTTCAAAG 58.717 33.333 23.06 23.06 45.32 2.77
230 231 7.724305 TTGACGAAAGCTAATACTTCAAAGT 57.276 32.000 0.46 0.46 42.91 2.66
231 232 8.821147 TTGACGAAAGCTAATACTTCAAAGTA 57.179 30.769 5.15 5.15 44.84 2.24
232 233 8.462143 TGACGAAAGCTAATACTTCAAAGTAG 57.538 34.615 8.46 0.00 44.06 2.57
233 234 8.301720 TGACGAAAGCTAATACTTCAAAGTAGA 58.698 33.333 8.46 0.00 44.06 2.59
234 235 9.303537 GACGAAAGCTAATACTTCAAAGTAGAT 57.696 33.333 8.46 3.37 44.06 1.98
247 248 9.321562 ACTTCAAAGTAGATAAAAACGAAGTGA 57.678 29.630 0.00 0.00 38.19 3.41
248 249 9.798885 CTTCAAAGTAGATAAAAACGAAGTGAG 57.201 33.333 0.00 0.00 45.00 3.51
264 265 4.974368 AGTGAGTACTGGAATCTTCTCG 57.026 45.455 0.00 0.00 35.34 4.04
276 277 8.043710 ACTGGAATCTTCTCGTTCATCTTTAAT 58.956 33.333 0.00 0.00 0.00 1.40
282 283 5.221891 TCTCGTTCATCTTTAATTGCAGC 57.778 39.130 0.00 0.00 0.00 5.25
361 369 2.035632 AGACAATTAGAGCCTCTCGGG 58.964 52.381 0.00 0.00 35.36 5.14
373 381 3.322254 AGCCTCTCGGGTCACTAATTATG 59.678 47.826 0.00 0.00 35.79 1.90
419 427 0.106894 AATAGCTAGGGCGTCAAGGC 59.893 55.000 0.00 0.00 44.37 4.35
428 1000 2.713967 GCGTCAAGGCGGGGTACTA 61.714 63.158 0.00 0.00 0.00 1.82
531 1104 3.264193 TGTGCTCATGGGTCTATCTGTTT 59.736 43.478 0.00 0.00 0.00 2.83
535 1108 6.203723 GTGCTCATGGGTCTATCTGTTTTATC 59.796 42.308 0.00 0.00 0.00 1.75
566 1139 5.009110 GCTAGACCTTAATCAATTTGGCTCC 59.991 44.000 0.00 0.00 0.00 4.70
567 1140 3.947834 AGACCTTAATCAATTTGGCTCCG 59.052 43.478 0.00 0.00 0.00 4.63
568 1141 3.023832 ACCTTAATCAATTTGGCTCCGG 58.976 45.455 0.00 0.00 0.00 5.14
643 1216 1.386533 TTGGTTTAAACAACGGCGGA 58.613 45.000 19.57 0.00 0.00 5.54
733 2346 2.589720 TCGATTACCGAGGGCTAATCA 58.410 47.619 10.92 0.39 43.23 2.57
824 2441 4.099170 GCCGCACAGAAGCAGCTG 62.099 66.667 10.11 10.11 41.63 4.24
825 2442 2.357881 CCGCACAGAAGCAGCTGA 60.358 61.111 20.43 0.00 39.20 4.26
826 2443 2.675056 CCGCACAGAAGCAGCTGAC 61.675 63.158 20.43 9.11 39.20 3.51
859 2476 4.022068 TCCCGTTTATAAATAGCCGACGAT 60.022 41.667 0.31 0.00 0.00 3.73
940 2557 1.721664 GCGGGCTTCGGTTTTATCCC 61.722 60.000 2.64 0.00 39.69 3.85
952 2569 4.080413 CGGTTTTATCCCTAACCCTAACCA 60.080 45.833 0.00 0.00 40.55 3.67
1572 3195 5.796424 ATTAATCCAATCCACTTGCATCC 57.204 39.130 0.00 0.00 33.20 3.51
1573 3196 3.393426 AATCCAATCCACTTGCATCCT 57.607 42.857 0.00 0.00 33.20 3.24
1574 3197 2.905415 TCCAATCCACTTGCATCCTT 57.095 45.000 0.00 0.00 33.20 3.36
1606 3229 0.102481 CCCGACCTTGACGAATCGAT 59.898 55.000 10.55 0.00 36.70 3.59
1650 3273 2.604969 TCACGTTTTTATTCGCTGCC 57.395 45.000 0.00 0.00 0.00 4.85
1655 3278 2.159680 CGTTTTTATTCGCTGCCGGTTA 60.160 45.455 1.90 0.00 34.56 2.85
1774 3399 7.921786 AACACATAGCTTTGCTTGTAAGATA 57.078 32.000 3.86 0.00 40.44 1.98
1826 3451 1.064825 GTCACCTTCTTTCCCCCTCA 58.935 55.000 0.00 0.00 0.00 3.86
2044 3669 0.938168 GCGAGTAAGTTATCCGGCGG 60.938 60.000 22.51 22.51 0.00 6.13
2047 3672 1.066257 GTAAGTTATCCGGCGGCGA 59.934 57.895 34.49 19.10 0.00 5.54
2048 3673 1.066257 TAAGTTATCCGGCGGCGAC 59.934 57.895 34.49 22.38 0.00 5.19
2177 3802 4.742659 CCCGTGTTTTGTTATTGTTTCCTG 59.257 41.667 0.00 0.00 0.00 3.86
2294 3943 1.557099 ACTCACATAGCTCCACGGAA 58.443 50.000 0.00 0.00 0.00 4.30
2317 3966 5.744666 ATCTTCTTCGTCTCTACACTAGC 57.255 43.478 0.00 0.00 0.00 3.42
2342 3995 9.255304 GCTAATGTTAGATTTCTCCTAGTGAAG 57.745 37.037 4.03 0.00 32.47 3.02
2357 4010 5.805994 CCTAGTGAAGGTGAACTAATCGTTC 59.194 44.000 0.00 0.00 43.40 3.95
2359 4012 7.791293 CCTAGTGAAGGTGAACTAATCGTTCTT 60.791 40.741 6.42 0.00 43.45 2.52
2476 4129 5.236047 GCAAAGATATGAGCTCAAGAACGAT 59.764 40.000 22.50 4.57 0.00 3.73
2480 4133 6.389091 AGATATGAGCTCAAGAACGATGATC 58.611 40.000 22.50 11.45 0.00 2.92
2481 4134 3.170791 TGAGCTCAAGAACGATGATCC 57.829 47.619 15.67 0.00 0.00 3.36
2503 4159 4.083643 CCTCAGATTGTGCTTGTAGTTGTG 60.084 45.833 0.00 0.00 0.00 3.33
2592 4252 0.249868 GTTTTGGTTGGGAAGCTGCC 60.250 55.000 0.16 0.16 0.00 4.85
2594 4254 4.659172 TGGTTGGGAAGCTGCCGG 62.659 66.667 4.08 0.00 0.00 6.13
2611 4276 6.027749 GCTGCCGGTTTATTATTGCATATAC 58.972 40.000 1.90 0.00 0.00 1.47
2725 4390 2.221169 TCATCGAGTTTGCTTTGCAGT 58.779 42.857 0.00 0.00 40.61 4.40
2726 4391 3.398406 TCATCGAGTTTGCTTTGCAGTA 58.602 40.909 0.00 0.00 40.61 2.74
2727 4392 3.433274 TCATCGAGTTTGCTTTGCAGTAG 59.567 43.478 0.00 0.00 40.61 2.57
2728 4393 2.833794 TCGAGTTTGCTTTGCAGTAGT 58.166 42.857 0.00 0.00 40.61 2.73
2729 4394 3.985008 TCGAGTTTGCTTTGCAGTAGTA 58.015 40.909 0.00 0.00 40.61 1.82
2730 4395 3.739300 TCGAGTTTGCTTTGCAGTAGTAC 59.261 43.478 0.00 0.00 40.61 2.73
2731 4396 3.741344 CGAGTTTGCTTTGCAGTAGTACT 59.259 43.478 0.00 0.00 40.61 2.73
2733 4398 3.815401 AGTTTGCTTTGCAGTAGTACTGG 59.185 43.478 27.48 14.35 46.01 4.00
2734 4399 3.485463 TTGCTTTGCAGTAGTACTGGT 57.515 42.857 27.48 0.00 46.01 4.00
2736 4401 2.076863 GCTTTGCAGTAGTACTGGTGG 58.923 52.381 27.48 6.71 46.01 4.61
2738 4403 0.323629 TTGCAGTAGTACTGGTGGGC 59.676 55.000 27.48 15.59 46.01 5.36
2840 4819 2.277737 CATGCTGGGGTCTGCCAT 59.722 61.111 0.00 0.00 37.08 4.40
2841 4820 2.125326 CATGCTGGGGTCTGCCATG 61.125 63.158 0.00 0.00 37.08 3.66
2842 4821 4.746309 TGCTGGGGTCTGCCATGC 62.746 66.667 0.00 0.00 37.08 4.06
2844 4823 4.051167 CTGGGGTCTGCCATGCCA 62.051 66.667 0.00 0.00 36.17 4.92
2951 4934 2.378806 CTTGACTTGACAGCGCTTTTG 58.621 47.619 7.50 0.00 0.00 2.44
2967 4950 0.030638 TTTGTTTCGAGCTTGCTGCC 59.969 50.000 0.00 0.00 44.23 4.85
3010 5001 3.795688 TCCCTGTTCTTGCTCAATCTT 57.204 42.857 0.00 0.00 0.00 2.40
3032 5023 2.574999 CATGACATGCGTGCGTGC 60.575 61.111 13.71 7.57 36.48 5.34
3123 5114 1.613836 CTCCAAGTCAAGGCAAGCTT 58.386 50.000 0.00 0.00 0.00 3.74
3124 5115 1.268899 CTCCAAGTCAAGGCAAGCTTG 59.731 52.381 22.44 22.44 38.33 4.01
3149 5149 7.147976 GCATGAATTAATTCCCACAATCTACC 58.852 38.462 22.42 0.00 35.97 3.18
3153 5153 8.112822 TGAATTAATTCCCACAATCTACCTTGA 58.887 33.333 22.42 0.00 35.97 3.02
3180 5180 4.739046 GTCATGAAATGTCGATGGATCC 57.261 45.455 4.20 4.20 46.80 3.36
3181 5181 4.384056 GTCATGAAATGTCGATGGATCCT 58.616 43.478 14.23 0.00 46.80 3.24
3182 5182 5.541845 GTCATGAAATGTCGATGGATCCTA 58.458 41.667 14.23 0.00 46.80 2.94
3209 5211 4.421058 TGTGCATGATTACTGACGTCTAC 58.579 43.478 17.92 2.65 0.00 2.59
3210 5212 4.082463 TGTGCATGATTACTGACGTCTACA 60.082 41.667 17.92 8.01 0.00 2.74
3220 5222 1.126079 GACGTCTACACCAACACACG 58.874 55.000 8.70 0.00 0.00 4.49
3357 5363 4.214327 CGAGCGCCCTCTTCCTCC 62.214 72.222 2.29 0.00 35.90 4.30
3361 5367 2.756283 CGCCCTCTTCCTCCTCGT 60.756 66.667 0.00 0.00 0.00 4.18
3379 5385 1.595976 CGTCTCGATCGCTTTCTCTCC 60.596 57.143 11.09 0.00 0.00 3.71
3384 5390 1.001815 CGATCGCTTTCTCTCCCTCTC 60.002 57.143 0.26 0.00 0.00 3.20
3385 5391 2.028130 GATCGCTTTCTCTCCCTCTCA 58.972 52.381 0.00 0.00 0.00 3.27
3389 5395 2.456577 GCTTTCTCTCCCTCTCACTCT 58.543 52.381 0.00 0.00 0.00 3.24
3547 5555 1.715585 CCGTCGTACGTCGTACCAT 59.284 57.895 27.74 0.00 40.58 3.55
3739 5747 2.202987 CTCTGCCTCATGCCCGTC 60.203 66.667 0.00 0.00 40.16 4.79
4111 6142 3.314331 CACAGACCCGTGGGCTCT 61.314 66.667 4.41 4.61 39.32 4.09
4128 6159 2.529136 TGTAGTGGGCCCAGCAGT 60.529 61.111 29.55 13.23 0.00 4.40
4248 6283 4.059773 TGTTGCCATTATTTTCCTCCCT 57.940 40.909 0.00 0.00 0.00 4.20
4393 6428 1.632409 TCTGCATCAGCTTTTCTCCCT 59.368 47.619 0.00 0.00 42.74 4.20
4395 6430 1.340405 TGCATCAGCTTTTCTCCCTCC 60.340 52.381 0.00 0.00 42.74 4.30
4396 6431 1.064832 GCATCAGCTTTTCTCCCTCCT 60.065 52.381 0.00 0.00 37.91 3.69
4425 6464 2.282462 CCTTTGCTCGGCCCAACT 60.282 61.111 0.00 0.00 0.00 3.16
4471 6511 0.893270 TGTCCTTTGCGGTTGGATGG 60.893 55.000 0.00 0.00 32.03 3.51
4514 6554 8.255905 GCTTTACTCACTAACCCACTTTATCTA 58.744 37.037 0.00 0.00 0.00 1.98
4549 6590 5.745227 TCCTTTCTTGTGATATGTTCTCCC 58.255 41.667 0.00 0.00 0.00 4.30
4612 6653 2.159653 CGTTGTTATCTTGGCAGCTCAC 60.160 50.000 0.00 0.00 0.00 3.51
4726 6768 4.147321 CCAACAGGAAAGGGGATATGATG 58.853 47.826 0.00 0.00 0.00 3.07
4770 6840 1.894756 TCGGCGTTTGGACTTTGGG 60.895 57.895 6.85 0.00 0.00 4.12
4779 6849 3.534357 TTGGACTTTGGGGAAGCAATA 57.466 42.857 0.00 0.00 39.04 1.90
4802 6872 0.319555 TCGTCCCTCTTTCGTGCAAG 60.320 55.000 0.00 0.00 0.00 4.01
4872 6946 7.744733 AGGAAGAGAGAAATGAAGAAAAGACT 58.255 34.615 0.00 0.00 0.00 3.24
4873 6947 7.661027 AGGAAGAGAGAAATGAAGAAAAGACTG 59.339 37.037 0.00 0.00 0.00 3.51
4890 6964 0.264359 CTGAGGGGATGAGAGAGGGT 59.736 60.000 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.333177 TAATGCCCACACGCCTTTTT 58.667 45.000 0.00 0.00 0.00 1.94
2 3 1.555967 ATAATGCCCACACGCCTTTT 58.444 45.000 0.00 0.00 0.00 2.27
3 4 1.555967 AATAATGCCCACACGCCTTT 58.444 45.000 0.00 0.00 0.00 3.11
4 5 1.204467 CAAATAATGCCCACACGCCTT 59.796 47.619 0.00 0.00 0.00 4.35
5 6 0.817013 CAAATAATGCCCACACGCCT 59.183 50.000 0.00 0.00 0.00 5.52
6 7 0.530288 ACAAATAATGCCCACACGCC 59.470 50.000 0.00 0.00 0.00 5.68
7 8 2.362169 AACAAATAATGCCCACACGC 57.638 45.000 0.00 0.00 0.00 5.34
8 9 3.120718 GCAAAACAAATAATGCCCACACG 60.121 43.478 0.00 0.00 32.73 4.49
9 10 4.403015 GCAAAACAAATAATGCCCACAC 57.597 40.909 0.00 0.00 32.73 3.82
15 16 3.120718 CGTGTGGGCAAAACAAATAATGC 60.121 43.478 0.00 0.00 38.06 3.56
16 17 4.054671 ACGTGTGGGCAAAACAAATAATG 58.945 39.130 0.00 0.00 0.00 1.90
17 18 4.329462 ACGTGTGGGCAAAACAAATAAT 57.671 36.364 0.00 0.00 0.00 1.28
18 19 3.802948 ACGTGTGGGCAAAACAAATAA 57.197 38.095 0.00 0.00 0.00 1.40
19 20 3.253677 CCTACGTGTGGGCAAAACAAATA 59.746 43.478 0.00 0.00 0.00 1.40
20 21 2.035321 CCTACGTGTGGGCAAAACAAAT 59.965 45.455 0.00 0.00 0.00 2.32
21 22 1.405821 CCTACGTGTGGGCAAAACAAA 59.594 47.619 0.00 0.00 0.00 2.83
22 23 1.025812 CCTACGTGTGGGCAAAACAA 58.974 50.000 0.00 0.00 0.00 2.83
23 24 2.709170 CCTACGTGTGGGCAAAACA 58.291 52.632 0.00 0.00 0.00 2.83
37 38 0.743345 GGATCAACCCACACGCCTAC 60.743 60.000 0.00 0.00 0.00 3.18
38 39 0.907704 AGGATCAACCCACACGCCTA 60.908 55.000 0.00 0.00 40.05 3.93
39 40 1.779061 AAGGATCAACCCACACGCCT 61.779 55.000 0.00 0.00 40.05 5.52
40 41 0.893727 AAAGGATCAACCCACACGCC 60.894 55.000 0.00 0.00 40.05 5.68
41 42 0.958822 AAAAGGATCAACCCACACGC 59.041 50.000 0.00 0.00 40.05 5.34
42 43 3.435671 GTCTAAAAGGATCAACCCACACG 59.564 47.826 0.00 0.00 40.05 4.49
43 44 4.215613 GTGTCTAAAAGGATCAACCCACAC 59.784 45.833 0.00 0.00 40.05 3.82
44 45 4.394729 GTGTCTAAAAGGATCAACCCACA 58.605 43.478 0.00 0.00 40.05 4.17
45 46 3.756963 GGTGTCTAAAAGGATCAACCCAC 59.243 47.826 0.00 0.00 40.05 4.61
46 47 3.396276 TGGTGTCTAAAAGGATCAACCCA 59.604 43.478 0.00 0.00 40.05 4.51
47 48 4.028993 TGGTGTCTAAAAGGATCAACCC 57.971 45.455 0.00 0.00 40.05 4.11
48 49 8.974060 TTATATGGTGTCTAAAAGGATCAACC 57.026 34.615 0.00 0.00 39.35 3.77
51 52 9.104965 CGTTTTATATGGTGTCTAAAAGGATCA 57.895 33.333 0.00 0.00 34.54 2.92
52 53 9.106070 ACGTTTTATATGGTGTCTAAAAGGATC 57.894 33.333 11.43 0.00 35.44 3.36
53 54 8.889717 CACGTTTTATATGGTGTCTAAAAGGAT 58.110 33.333 11.43 0.00 35.44 3.24
54 55 7.879160 ACACGTTTTATATGGTGTCTAAAAGGA 59.121 33.333 11.43 0.00 39.23 3.36
55 56 8.036273 ACACGTTTTATATGGTGTCTAAAAGG 57.964 34.615 0.00 0.00 39.23 3.11
57 58 9.153721 CCTACACGTTTTATATGGTGTCTAAAA 57.846 33.333 0.00 0.00 42.21 1.52
58 59 7.278424 GCCTACACGTTTTATATGGTGTCTAAA 59.722 37.037 0.00 0.00 42.21 1.85
59 60 6.757947 GCCTACACGTTTTATATGGTGTCTAA 59.242 38.462 0.00 0.00 42.21 2.10
60 61 6.127394 TGCCTACACGTTTTATATGGTGTCTA 60.127 38.462 0.00 0.00 42.21 2.59
61 62 5.114081 GCCTACACGTTTTATATGGTGTCT 58.886 41.667 0.00 0.00 42.21 3.41
62 63 4.871557 TGCCTACACGTTTTATATGGTGTC 59.128 41.667 0.00 0.00 42.21 3.67
63 64 4.834534 TGCCTACACGTTTTATATGGTGT 58.165 39.130 1.12 1.12 44.93 4.16
64 65 5.006358 GTCTGCCTACACGTTTTATATGGTG 59.994 44.000 0.00 0.00 36.50 4.17
65 66 5.114081 GTCTGCCTACACGTTTTATATGGT 58.886 41.667 0.00 0.00 0.00 3.55
66 67 4.510340 GGTCTGCCTACACGTTTTATATGG 59.490 45.833 0.00 0.00 0.00 2.74
67 68 4.510340 GGGTCTGCCTACACGTTTTATATG 59.490 45.833 0.00 0.00 34.45 1.78
68 69 4.443881 GGGGTCTGCCTACACGTTTTATAT 60.444 45.833 0.00 0.00 34.45 0.86
69 70 3.118665 GGGGTCTGCCTACACGTTTTATA 60.119 47.826 0.00 0.00 34.45 0.98
70 71 2.355412 GGGGTCTGCCTACACGTTTTAT 60.355 50.000 0.00 0.00 34.45 1.40
71 72 1.002315 GGGGTCTGCCTACACGTTTTA 59.998 52.381 0.00 0.00 34.45 1.52
72 73 0.250597 GGGGTCTGCCTACACGTTTT 60.251 55.000 0.00 0.00 34.45 2.43
73 74 1.125711 AGGGGTCTGCCTACACGTTT 61.126 55.000 0.00 0.00 34.45 3.60
74 75 1.125711 AAGGGGTCTGCCTACACGTT 61.126 55.000 0.00 0.00 34.45 3.99
75 76 0.251922 TAAGGGGTCTGCCTACACGT 60.252 55.000 0.00 0.00 34.45 4.49
76 77 0.899720 TTAAGGGGTCTGCCTACACG 59.100 55.000 0.00 0.00 34.45 4.49
77 78 1.405121 CGTTAAGGGGTCTGCCTACAC 60.405 57.143 0.00 0.00 34.45 2.90
78 79 0.899720 CGTTAAGGGGTCTGCCTACA 59.100 55.000 0.00 0.00 34.45 2.74
79 80 0.461516 GCGTTAAGGGGTCTGCCTAC 60.462 60.000 0.00 0.00 34.45 3.18
80 81 1.619807 GGCGTTAAGGGGTCTGCCTA 61.620 60.000 0.00 0.00 39.38 3.93
81 82 2.669240 GCGTTAAGGGGTCTGCCT 59.331 61.111 0.00 0.00 34.45 4.75
82 83 2.437895 GGCGTTAAGGGGTCTGCC 60.438 66.667 0.00 0.00 35.04 4.85
83 84 2.437895 GGGCGTTAAGGGGTCTGC 60.438 66.667 0.00 0.00 0.00 4.26
84 85 1.376812 GTGGGCGTTAAGGGGTCTG 60.377 63.158 0.00 0.00 0.00 3.51
85 86 1.844289 TGTGGGCGTTAAGGGGTCT 60.844 57.895 0.00 0.00 0.00 3.85
86 87 1.673337 GTGTGGGCGTTAAGGGGTC 60.673 63.158 0.00 0.00 0.00 4.46
87 88 1.785353 ATGTGTGGGCGTTAAGGGGT 61.785 55.000 0.00 0.00 0.00 4.95
88 89 1.001393 ATGTGTGGGCGTTAAGGGG 60.001 57.895 0.00 0.00 0.00 4.79
89 90 0.608035 ACATGTGTGGGCGTTAAGGG 60.608 55.000 0.00 0.00 0.00 3.95
90 91 0.521291 CACATGTGTGGGCGTTAAGG 59.479 55.000 18.03 0.00 42.10 2.69
100 101 0.373370 CGATAACGCCCACATGTGTG 59.627 55.000 23.79 14.60 45.23 3.82
101 102 0.742990 CCGATAACGCCCACATGTGT 60.743 55.000 23.79 8.06 38.29 3.72
102 103 2.013807 CCGATAACGCCCACATGTG 58.986 57.895 19.31 19.31 38.29 3.21
103 104 1.817941 GCCGATAACGCCCACATGT 60.818 57.895 0.00 0.00 38.29 3.21
104 105 2.881266 CGCCGATAACGCCCACATG 61.881 63.158 0.00 0.00 38.29 3.21
105 106 2.587753 CGCCGATAACGCCCACAT 60.588 61.111 0.00 0.00 38.29 3.21
106 107 3.993376 GACGCCGATAACGCCCACA 62.993 63.158 0.00 0.00 38.29 4.17
107 108 3.259751 GACGCCGATAACGCCCAC 61.260 66.667 0.00 0.00 38.29 4.61
108 109 4.517815 GGACGCCGATAACGCCCA 62.518 66.667 0.00 0.00 38.29 5.36
109 110 4.217159 AGGACGCCGATAACGCCC 62.217 66.667 0.00 0.00 38.29 6.13
110 111 2.894240 TTCAGGACGCCGATAACGCC 62.894 60.000 0.00 0.00 38.29 5.68
111 112 0.874607 ATTCAGGACGCCGATAACGC 60.875 55.000 0.00 0.00 38.29 4.84
112 113 1.129326 GATTCAGGACGCCGATAACG 58.871 55.000 0.00 0.00 39.43 3.18
113 114 2.510768 AGATTCAGGACGCCGATAAC 57.489 50.000 0.00 0.00 0.00 1.89
114 115 4.556233 CATTAGATTCAGGACGCCGATAA 58.444 43.478 0.00 0.00 0.00 1.75
115 116 3.056821 CCATTAGATTCAGGACGCCGATA 60.057 47.826 0.00 0.00 0.00 2.92
116 117 2.289072 CCATTAGATTCAGGACGCCGAT 60.289 50.000 0.00 0.00 0.00 4.18
117 118 1.068588 CCATTAGATTCAGGACGCCGA 59.931 52.381 0.00 0.00 0.00 5.54
118 119 1.202533 ACCATTAGATTCAGGACGCCG 60.203 52.381 0.00 0.00 0.00 6.46
119 120 2.622064 ACCATTAGATTCAGGACGCC 57.378 50.000 0.00 0.00 0.00 5.68
120 121 5.297547 TCAATACCATTAGATTCAGGACGC 58.702 41.667 0.00 0.00 0.00 5.19
121 122 7.969536 AATCAATACCATTAGATTCAGGACG 57.030 36.000 0.00 0.00 0.00 4.79
200 201 9.263538 TGAAGTATTAGCTTTCGTCAAAGTTAA 57.736 29.630 7.88 7.88 44.58 2.01
201 202 8.821147 TGAAGTATTAGCTTTCGTCAAAGTTA 57.179 30.769 0.00 0.00 41.18 2.24
202 203 7.724305 TGAAGTATTAGCTTTCGTCAAAGTT 57.276 32.000 0.00 0.00 41.18 2.66
203 204 7.724305 TTGAAGTATTAGCTTTCGTCAAAGT 57.276 32.000 0.00 0.00 41.18 2.66
204 205 8.647035 CTTTGAAGTATTAGCTTTCGTCAAAG 57.353 34.615 20.63 20.63 43.52 2.77
205 206 8.149973 ACTTTGAAGTATTAGCTTTCGTCAAA 57.850 30.769 0.00 6.34 37.52 2.69
206 207 7.724305 ACTTTGAAGTATTAGCTTTCGTCAA 57.276 32.000 0.00 0.00 37.52 3.18
207 208 8.301720 TCTACTTTGAAGTATTAGCTTTCGTCA 58.698 33.333 4.22 0.00 40.46 4.35
208 209 8.684973 TCTACTTTGAAGTATTAGCTTTCGTC 57.315 34.615 4.22 0.00 40.46 4.20
221 222 9.321562 TCACTTCGTTTTTATCTACTTTGAAGT 57.678 29.630 1.60 1.60 42.89 3.01
222 223 9.798885 CTCACTTCGTTTTTATCTACTTTGAAG 57.201 33.333 0.00 0.00 37.07 3.02
223 224 9.321562 ACTCACTTCGTTTTTATCTACTTTGAA 57.678 29.630 0.00 0.00 0.00 2.69
224 225 8.882415 ACTCACTTCGTTTTTATCTACTTTGA 57.118 30.769 0.00 0.00 0.00 2.69
226 227 9.978044 AGTACTCACTTCGTTTTTATCTACTTT 57.022 29.630 0.00 0.00 0.00 2.66
227 228 9.408069 CAGTACTCACTTCGTTTTTATCTACTT 57.592 33.333 0.00 0.00 30.46 2.24
228 229 8.027771 CCAGTACTCACTTCGTTTTTATCTACT 58.972 37.037 0.00 0.00 30.46 2.57
229 230 8.025445 TCCAGTACTCACTTCGTTTTTATCTAC 58.975 37.037 0.00 0.00 30.46 2.59
230 231 8.114331 TCCAGTACTCACTTCGTTTTTATCTA 57.886 34.615 0.00 0.00 30.46 1.98
231 232 6.989659 TCCAGTACTCACTTCGTTTTTATCT 58.010 36.000 0.00 0.00 30.46 1.98
232 233 7.647907 TTCCAGTACTCACTTCGTTTTTATC 57.352 36.000 0.00 0.00 30.46 1.75
233 234 8.095169 AGATTCCAGTACTCACTTCGTTTTTAT 58.905 33.333 0.00 0.00 30.46 1.40
234 235 7.439381 AGATTCCAGTACTCACTTCGTTTTTA 58.561 34.615 0.00 0.00 30.46 1.52
235 236 6.289064 AGATTCCAGTACTCACTTCGTTTTT 58.711 36.000 0.00 0.00 30.46 1.94
236 237 5.855045 AGATTCCAGTACTCACTTCGTTTT 58.145 37.500 0.00 0.00 30.46 2.43
237 238 5.470047 AGATTCCAGTACTCACTTCGTTT 57.530 39.130 0.00 0.00 30.46 3.60
238 239 5.244178 AGAAGATTCCAGTACTCACTTCGTT 59.756 40.000 0.00 0.00 37.77 3.85
239 240 4.767928 AGAAGATTCCAGTACTCACTTCGT 59.232 41.667 0.00 0.00 37.77 3.85
240 241 5.317733 AGAAGATTCCAGTACTCACTTCG 57.682 43.478 0.00 0.00 37.77 3.79
241 242 5.106078 ACGAGAAGATTCCAGTACTCACTTC 60.106 44.000 0.00 4.46 30.46 3.01
242 243 4.767928 ACGAGAAGATTCCAGTACTCACTT 59.232 41.667 0.00 0.00 30.46 3.16
243 244 4.337145 ACGAGAAGATTCCAGTACTCACT 58.663 43.478 0.00 0.00 34.42 3.41
244 245 4.705337 ACGAGAAGATTCCAGTACTCAC 57.295 45.455 0.00 0.00 0.00 3.51
245 246 4.765339 TGAACGAGAAGATTCCAGTACTCA 59.235 41.667 0.00 0.00 0.00 3.41
246 247 5.312120 TGAACGAGAAGATTCCAGTACTC 57.688 43.478 0.00 0.00 0.00 2.59
247 248 5.654650 AGATGAACGAGAAGATTCCAGTACT 59.345 40.000 0.00 0.00 0.00 2.73
248 249 5.897050 AGATGAACGAGAAGATTCCAGTAC 58.103 41.667 0.00 0.00 0.00 2.73
264 265 4.722194 TCGTGCTGCAATTAAAGATGAAC 58.278 39.130 2.77 0.00 0.00 3.18
276 277 4.877823 AGATCATTAAATCTCGTGCTGCAA 59.122 37.500 2.77 0.00 29.89 4.08
282 283 7.480855 GCAATGCATAGATCATTAAATCTCGTG 59.519 37.037 0.00 0.00 37.24 4.35
361 369 7.095024 GTCTACATGACGCATAATTAGTGAC 57.905 40.000 0.00 0.00 35.81 3.67
390 398 3.256879 CGCCCTAGCTATTCTCATCAGAA 59.743 47.826 0.00 0.00 38.92 3.02
419 427 1.531128 GGCCTCTCCTAGTACCCCG 60.531 68.421 0.00 0.00 0.00 5.73
510 1083 3.550437 AACAGATAGACCCATGAGCAC 57.450 47.619 0.00 0.00 0.00 4.40
531 1104 8.262601 TGATTAAGGTCTAGCTCCATTGATAA 57.737 34.615 0.00 0.00 0.00 1.75
535 1108 7.814264 AATTGATTAAGGTCTAGCTCCATTG 57.186 36.000 0.00 0.00 0.00 2.82
566 1139 3.390135 AGTATGATATTTGTGTCCGCCG 58.610 45.455 0.00 0.00 0.00 6.46
567 1140 3.746492 GGAGTATGATATTTGTGTCCGCC 59.254 47.826 0.00 0.00 0.00 6.13
568 1141 4.377021 TGGAGTATGATATTTGTGTCCGC 58.623 43.478 0.00 0.00 0.00 5.54
675 2286 1.003233 AGACGGATGAGGGTTTGGAAC 59.997 52.381 0.00 0.00 0.00 3.62
676 2287 1.358152 AGACGGATGAGGGTTTGGAA 58.642 50.000 0.00 0.00 0.00 3.53
677 2288 1.278127 GAAGACGGATGAGGGTTTGGA 59.722 52.381 0.00 0.00 0.00 3.53
678 2289 1.279271 AGAAGACGGATGAGGGTTTGG 59.721 52.381 0.00 0.00 0.00 3.28
679 2290 2.770164 AGAAGACGGATGAGGGTTTG 57.230 50.000 0.00 0.00 0.00 2.93
680 2291 3.442076 AGTAGAAGACGGATGAGGGTTT 58.558 45.455 0.00 0.00 0.00 3.27
681 2292 3.103080 AGTAGAAGACGGATGAGGGTT 57.897 47.619 0.00 0.00 0.00 4.11
682 2293 2.830651 AGTAGAAGACGGATGAGGGT 57.169 50.000 0.00 0.00 0.00 4.34
822 2439 3.391382 GGGACGGGGTCAGGTCAG 61.391 72.222 0.00 0.00 34.87 3.51
940 2557 0.253894 CGGGGGTTGGTTAGGGTTAG 59.746 60.000 0.00 0.00 0.00 2.34
1574 3197 0.981943 GGTCGGGGAGGAGAGAAAAA 59.018 55.000 0.00 0.00 0.00 1.94
1579 3202 1.000486 TCAAGGTCGGGGAGGAGAG 60.000 63.158 0.00 0.00 0.00 3.20
1632 3255 1.246970 CGGCAGCGAATAAAAACGTG 58.753 50.000 0.00 0.00 0.00 4.49
1650 3273 2.718073 CGTCCCCTCCCTGTAACCG 61.718 68.421 0.00 0.00 0.00 4.44
1749 3372 7.921786 ATCTTACAAGCAAAGCTATGTGTTA 57.078 32.000 13.30 1.03 38.25 2.41
1774 3399 1.678101 GTGTCGCGGTAGGTAGGTTAT 59.322 52.381 6.13 0.00 0.00 1.89
1803 3428 1.486145 GGGGAAAGAAGGTGACCCGA 61.486 60.000 0.00 0.00 41.25 5.14
1826 3451 1.429463 CGAGAAGCAAGCCGTTTAGT 58.571 50.000 0.00 0.00 0.00 2.24
2049 3674 1.363744 CTACACTGGTAGCAGCTTGC 58.636 55.000 21.58 0.00 45.46 4.01
2177 3802 0.893727 AGCCACAACGATCCAAACCC 60.894 55.000 0.00 0.00 0.00 4.11
2294 3943 5.883673 AGCTAGTGTAGAGACGAAGAAGATT 59.116 40.000 0.00 0.00 0.00 2.40
2357 4010 1.126846 GAAACATCGACGACCAGCAAG 59.873 52.381 0.00 0.00 0.00 4.01
2359 4012 1.006825 CGAAACATCGACGACCAGCA 61.007 55.000 0.00 0.00 34.64 4.41
2480 4133 4.067896 ACAACTACAAGCACAATCTGAGG 58.932 43.478 0.00 0.00 0.00 3.86
2481 4134 4.083643 CCACAACTACAAGCACAATCTGAG 60.084 45.833 0.00 0.00 0.00 3.35
2503 4159 4.820284 ATCAAATTAAGCTAGCTTCGCC 57.180 40.909 32.51 0.00 37.47 5.54
2611 4276 1.202222 GCCGGCATTGAACTGATTGAG 60.202 52.381 24.80 0.00 0.00 3.02
2638 4303 4.642885 TGTTGAAGCCCCTATTTTAATCCG 59.357 41.667 0.00 0.00 0.00 4.18
2725 4390 4.137872 GCGCGCCCACCAGTACTA 62.138 66.667 23.24 0.00 0.00 1.82
2859 4838 2.078665 GGCAGGGATTCTAGGGGCA 61.079 63.158 0.00 0.00 0.00 5.36
2921 4904 0.891373 TCAAGTCAAGGCTCTCGGAG 59.109 55.000 0.00 0.00 0.00 4.63
2951 4934 1.208614 CAGGCAGCAAGCTCGAAAC 59.791 57.895 0.00 0.00 44.79 2.78
2983 4966 3.075148 GAGCAAGAACAGGGAAAGGTAC 58.925 50.000 0.00 0.00 0.00 3.34
2992 4975 3.070018 ACGAAGATTGAGCAAGAACAGG 58.930 45.455 0.00 0.00 0.00 4.00
2998 4981 2.417586 TCATGCACGAAGATTGAGCAAG 59.582 45.455 0.00 0.00 38.85 4.01
3030 5021 2.018727 CTGCAGCCACACCAAAAGCA 62.019 55.000 0.00 0.00 0.00 3.91
3032 5023 0.031178 GTCTGCAGCCACACCAAAAG 59.969 55.000 9.47 0.00 0.00 2.27
3123 5114 6.795144 AGATTGTGGGAATTAATTCATGCA 57.205 33.333 25.55 17.79 38.53 3.96
3124 5115 7.014615 AGGTAGATTGTGGGAATTAATTCATGC 59.985 37.037 25.55 15.86 38.53 4.06
3125 5116 8.469309 AGGTAGATTGTGGGAATTAATTCATG 57.531 34.615 25.55 0.00 38.53 3.07
3126 5117 8.917088 CAAGGTAGATTGTGGGAATTAATTCAT 58.083 33.333 25.55 12.69 38.53 2.57
3128 5119 8.519799 TCAAGGTAGATTGTGGGAATTAATTC 57.480 34.615 18.22 18.22 36.08 2.17
3129 5120 8.116026 ACTCAAGGTAGATTGTGGGAATTAATT 58.884 33.333 0.00 0.00 0.00 1.40
3137 5137 2.749621 GCAACTCAAGGTAGATTGTGGG 59.250 50.000 0.00 0.00 0.00 4.61
3149 5149 4.151258 ACATTTCATGACGCAACTCAAG 57.849 40.909 0.00 0.00 0.00 3.02
3153 5153 2.412870 TCGACATTTCATGACGCAACT 58.587 42.857 0.00 0.00 45.42 3.16
3175 5175 9.486497 CAGTAATCATGCACATATATAGGATCC 57.514 37.037 2.48 2.48 0.00 3.36
3178 5178 8.190784 CGTCAGTAATCATGCACATATATAGGA 58.809 37.037 0.54 0.00 0.00 2.94
3179 5179 7.976175 ACGTCAGTAATCATGCACATATATAGG 59.024 37.037 0.00 0.00 0.00 2.57
3180 5180 8.917415 ACGTCAGTAATCATGCACATATATAG 57.083 34.615 0.00 0.00 0.00 1.31
3181 5181 8.739972 AGACGTCAGTAATCATGCACATATATA 58.260 33.333 19.50 0.00 0.00 0.86
3182 5182 7.606349 AGACGTCAGTAATCATGCACATATAT 58.394 34.615 19.50 0.00 0.00 0.86
3209 5211 4.312231 CCTGCGCGTGTGTTGGTG 62.312 66.667 8.43 0.00 0.00 4.17
3210 5212 4.849310 ACCTGCGCGTGTGTTGGT 62.849 61.111 8.43 4.52 0.00 3.67
3357 5363 1.329292 AGAGAAAGCGATCGAGACGAG 59.671 52.381 21.57 0.00 39.91 4.18
3361 5367 1.025812 GGGAGAGAAAGCGATCGAGA 58.974 55.000 21.57 0.00 0.00 4.04
3379 5385 2.505407 TGGAGAGAGAGAGAGTGAGAGG 59.495 54.545 0.00 0.00 0.00 3.69
3384 5390 5.163519 GGAAAAGATGGAGAGAGAGAGAGTG 60.164 48.000 0.00 0.00 0.00 3.51
3385 5391 4.956075 GGAAAAGATGGAGAGAGAGAGAGT 59.044 45.833 0.00 0.00 0.00 3.24
3389 5395 2.428890 GCGGAAAAGATGGAGAGAGAGA 59.571 50.000 0.00 0.00 0.00 3.10
3424 5430 1.620822 AAGTTTGGTCACATCCTGGC 58.379 50.000 0.00 0.00 0.00 4.85
3547 5555 3.677700 GCACATGGTCCGTATCAGTACAA 60.678 47.826 0.00 0.00 0.00 2.41
3574 5582 0.646895 GCAAGCACAAGCACAAACAC 59.353 50.000 0.00 0.00 45.49 3.32
4111 6142 2.124507 GAACTGCTGGGCCCACTACA 62.125 60.000 24.45 18.58 0.00 2.74
4353 6388 0.716591 TGGAGGGGAAAGAGAGGCTA 59.283 55.000 0.00 0.00 0.00 3.93
4393 6428 1.960689 CAAAGGCGGGAAAAAGAAGGA 59.039 47.619 0.00 0.00 0.00 3.36
4395 6430 1.783284 GCAAAGGCGGGAAAAAGAAG 58.217 50.000 0.00 0.00 0.00 2.85
4396 6431 3.978460 GCAAAGGCGGGAAAAAGAA 57.022 47.368 0.00 0.00 0.00 2.52
4425 6464 6.746364 ACTTGTGCGTGTAAAATAAACGAAAA 59.254 30.769 4.36 0.00 39.64 2.29
4545 6586 6.830912 TCATCCACACAATATAAGAAGGGAG 58.169 40.000 0.00 0.00 0.00 4.30
4549 6590 7.741027 AGCATCATCCACACAATATAAGAAG 57.259 36.000 0.00 0.00 0.00 2.85
4612 6653 5.241506 AGGAAACCACATGCATATTAATCCG 59.758 40.000 0.00 0.00 0.00 4.18
4770 6840 1.757699 AGGGACGAGACTATTGCTTCC 59.242 52.381 0.00 0.00 0.00 3.46
4779 6849 0.882474 CACGAAAGAGGGACGAGACT 59.118 55.000 0.00 0.00 0.00 3.24
4872 6946 0.719015 AACCCTCTCTCATCCCCTCA 59.281 55.000 0.00 0.00 0.00 3.86
4873 6947 1.488393 CAAACCCTCTCTCATCCCCTC 59.512 57.143 0.00 0.00 0.00 4.30
4919 6993 1.757118 CCTGATCTTACGCCTCCTGAA 59.243 52.381 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.