Multiple sequence alignment - TraesCS4A01G082300

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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 TraesCS4A01G082300 chr4A 100.000 3093 0 0 1 3093 85583483 85580391 0.000000e+00 5712.0
1 TraesCS4A01G082300 chr4A 100.000 209 0 0 3397 3605 85580087 85579879 1.570000e-103 387.0
2 TraesCS4A01G082300 chr4A 87.549 257 25 6 2538 2791 637325161 637324909 1.270000e-74 291.0
3 TraesCS4A01G082300 chr4A 87.649 251 24 7 2538 2785 637253252 637253498 5.890000e-73 285.0
4 TraesCS4A01G082300 chr4A 87.649 251 24 7 2538 2785 637306304 637306550 5.890000e-73 285.0
5 TraesCS4A01G082300 chr4A 87.160 257 26 6 2538 2791 637462308 637462056 5.890000e-73 285.0
6 TraesCS4A01G082300 chr4A 87.160 257 26 6 2538 2791 637558403 637558151 5.890000e-73 285.0
7 TraesCS4A01G082300 chr4A 87.251 251 25 7 2538 2785 637411499 637411745 2.740000e-71 279.0
8 TraesCS4A01G082300 chr4A 86.853 251 26 7 2538 2785 637363431 637363677 1.280000e-69 274.0
9 TraesCS4A01G082300 chr4B 97.188 2134 51 6 940 3067 466016142 466018272 0.000000e+00 3600.0
10 TraesCS4A01G082300 chr4B 92.823 209 11 1 3397 3605 466018808 466019012 2.100000e-77 300.0
11 TraesCS4A01G082300 chr4D 97.896 1996 36 5 940 2930 379239534 379241528 0.000000e+00 3448.0
12 TraesCS4A01G082300 chr4D 93.243 74 4 1 3418 3490 379242007 379242080 1.370000e-19 108.0
13 TraesCS4A01G082300 chr7B 75.325 462 75 27 405 845 572074651 572074208 6.150000e-43 185.0
14 TraesCS4A01G082300 chr7B 77.477 111 21 4 450 558 167033854 167033962 3.000000e-06 63.9
15 TraesCS4A01G082300 chr7B 97.059 34 1 0 2916 2949 212476458 212476491 1.400000e-04 58.4
16 TraesCS4A01G082300 chr1D 76.136 176 19 11 400 554 398496009 398496182 1.800000e-08 71.3
17 TraesCS4A01G082300 chr2B 73.423 222 34 19 345 558 673935665 673935461 3.890000e-05 60.2
18 TraesCS4A01G082300 chr7D 100.000 30 0 0 2920 2949 236182253 236182282 5.030000e-04 56.5
19 TraesCS4A01G082300 chr7A 74.510 153 25 11 403 553 33538580 33538440 2.000000e-03 54.7


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 TraesCS4A01G082300 chr4A 85579879 85583483 3604 True 3049.5 5712 100.0000 1 3605 2 chr4A.!!$R4 3604
1 TraesCS4A01G082300 chr4B 466016142 466019012 2870 False 1950.0 3600 95.0055 940 3605 2 chr4B.!!$F1 2665
2 TraesCS4A01G082300 chr4D 379239534 379242080 2546 False 1778.0 3448 95.5695 940 3490 2 chr4D.!!$F1 2550

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
37 38 0.038892 GTCGGTGGTCAGTTCGCTAA 60.039 55.0 0.0 0.0 0.0 3.09 F
856 857 0.322997 TTAACATTCCCAGGCACCGG 60.323 55.0 0.0 0.0 0.0 5.28 F
942 943 0.594796 CGTTTGACCAGCTTTGCCAC 60.595 55.0 0.0 0.0 0.0 5.01 F
943 944 0.746659 GTTTGACCAGCTTTGCCACT 59.253 50.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1632 0.397941 CAGGCACCTCCTCAAACTCA 59.602 55.000 0.00 0.00 45.52 3.41 R
2241 2247 0.309922 CACAGAGCACAAGCACTTGG 59.690 55.000 14.51 5.19 44.45 3.61 R
2499 2505 4.100529 CAAGATTTTACATCCAAGCAGCG 58.899 43.478 0.00 0.00 0.00 5.18 R
2675 2681 8.063200 TCCGAAAATCACTCTTAGATACAAGA 57.937 34.615 0.00 0.00 33.55 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.380839 CATGCTATCCATTTCTTCGTCG 57.619 45.455 0.00 0.00 29.71 5.12
22 23 2.821546 TGCTATCCATTTCTTCGTCGG 58.178 47.619 0.00 0.00 0.00 4.79
23 24 2.167693 TGCTATCCATTTCTTCGTCGGT 59.832 45.455 0.00 0.00 0.00 4.69
24 25 2.540101 GCTATCCATTTCTTCGTCGGTG 59.460 50.000 0.00 0.00 0.00 4.94
25 26 2.024176 ATCCATTTCTTCGTCGGTGG 57.976 50.000 0.00 0.00 0.00 4.61
26 27 0.682852 TCCATTTCTTCGTCGGTGGT 59.317 50.000 0.00 0.00 0.00 4.16
27 28 1.076332 CCATTTCTTCGTCGGTGGTC 58.924 55.000 0.00 0.00 0.00 4.02
28 29 1.606994 CCATTTCTTCGTCGGTGGTCA 60.607 52.381 0.00 0.00 0.00 4.02
29 30 1.726791 CATTTCTTCGTCGGTGGTCAG 59.273 52.381 0.00 0.00 0.00 3.51
30 31 0.748450 TTTCTTCGTCGGTGGTCAGT 59.252 50.000 0.00 0.00 0.00 3.41
31 32 0.748450 TTCTTCGTCGGTGGTCAGTT 59.252 50.000 0.00 0.00 0.00 3.16
32 33 0.313043 TCTTCGTCGGTGGTCAGTTC 59.687 55.000 0.00 0.00 0.00 3.01
33 34 1.002250 CTTCGTCGGTGGTCAGTTCG 61.002 60.000 0.00 0.00 0.00 3.95
34 35 3.103911 CGTCGGTGGTCAGTTCGC 61.104 66.667 0.00 0.00 0.00 4.70
35 36 2.338984 GTCGGTGGTCAGTTCGCT 59.661 61.111 0.00 0.00 0.00 4.93
36 37 1.582968 GTCGGTGGTCAGTTCGCTA 59.417 57.895 0.00 0.00 0.00 4.26
37 38 0.038892 GTCGGTGGTCAGTTCGCTAA 60.039 55.000 0.00 0.00 0.00 3.09
38 39 0.892755 TCGGTGGTCAGTTCGCTAAT 59.107 50.000 0.00 0.00 0.00 1.73
39 40 0.999406 CGGTGGTCAGTTCGCTAATG 59.001 55.000 0.00 0.00 0.00 1.90
40 41 1.671850 CGGTGGTCAGTTCGCTAATGT 60.672 52.381 0.00 0.00 0.00 2.71
41 42 1.732259 GGTGGTCAGTTCGCTAATGTG 59.268 52.381 0.00 0.00 0.00 3.21
42 43 1.128692 GTGGTCAGTTCGCTAATGTGC 59.871 52.381 0.00 0.00 0.00 4.57
43 44 1.001974 TGGTCAGTTCGCTAATGTGCT 59.998 47.619 0.00 0.00 0.00 4.40
44 45 2.232696 TGGTCAGTTCGCTAATGTGCTA 59.767 45.455 0.00 0.00 0.00 3.49
45 46 2.860735 GGTCAGTTCGCTAATGTGCTAG 59.139 50.000 0.00 0.00 0.00 3.42
46 47 3.512680 GTCAGTTCGCTAATGTGCTAGT 58.487 45.455 0.00 0.00 0.00 2.57
47 48 3.927142 GTCAGTTCGCTAATGTGCTAGTT 59.073 43.478 0.00 0.00 0.00 2.24
48 49 4.389077 GTCAGTTCGCTAATGTGCTAGTTT 59.611 41.667 0.00 0.00 0.00 2.66
49 50 4.388773 TCAGTTCGCTAATGTGCTAGTTTG 59.611 41.667 0.00 0.00 0.00 2.93
50 51 3.684788 AGTTCGCTAATGTGCTAGTTTGG 59.315 43.478 0.00 0.00 0.00 3.28
51 52 2.627945 TCGCTAATGTGCTAGTTTGGG 58.372 47.619 0.00 0.00 0.00 4.12
52 53 2.027561 TCGCTAATGTGCTAGTTTGGGT 60.028 45.455 0.00 0.00 0.00 4.51
53 54 2.095853 CGCTAATGTGCTAGTTTGGGTG 59.904 50.000 0.00 0.00 0.00 4.61
54 55 3.081804 GCTAATGTGCTAGTTTGGGTGT 58.918 45.455 0.00 0.00 0.00 4.16
55 56 3.506067 GCTAATGTGCTAGTTTGGGTGTT 59.494 43.478 0.00 0.00 0.00 3.32
56 57 4.022329 GCTAATGTGCTAGTTTGGGTGTTT 60.022 41.667 0.00 0.00 0.00 2.83
57 58 4.584327 AATGTGCTAGTTTGGGTGTTTC 57.416 40.909 0.00 0.00 0.00 2.78
58 59 1.944024 TGTGCTAGTTTGGGTGTTTCG 59.056 47.619 0.00 0.00 0.00 3.46
59 60 2.215196 GTGCTAGTTTGGGTGTTTCGA 58.785 47.619 0.00 0.00 0.00 3.71
60 61 2.812011 GTGCTAGTTTGGGTGTTTCGAT 59.188 45.455 0.00 0.00 0.00 3.59
61 62 3.252458 GTGCTAGTTTGGGTGTTTCGATT 59.748 43.478 0.00 0.00 0.00 3.34
62 63 3.886505 TGCTAGTTTGGGTGTTTCGATTT 59.113 39.130 0.00 0.00 0.00 2.17
63 64 4.339814 TGCTAGTTTGGGTGTTTCGATTTT 59.660 37.500 0.00 0.00 0.00 1.82
64 65 5.531659 TGCTAGTTTGGGTGTTTCGATTTTA 59.468 36.000 0.00 0.00 0.00 1.52
65 66 6.084277 GCTAGTTTGGGTGTTTCGATTTTAG 58.916 40.000 0.00 0.00 0.00 1.85
66 67 6.293790 GCTAGTTTGGGTGTTTCGATTTTAGT 60.294 38.462 0.00 0.00 0.00 2.24
67 68 5.827666 AGTTTGGGTGTTTCGATTTTAGTG 58.172 37.500 0.00 0.00 0.00 2.74
68 69 5.358725 AGTTTGGGTGTTTCGATTTTAGTGT 59.641 36.000 0.00 0.00 0.00 3.55
69 70 5.838531 TTGGGTGTTTCGATTTTAGTGTT 57.161 34.783 0.00 0.00 0.00 3.32
70 71 5.838531 TGGGTGTTTCGATTTTAGTGTTT 57.161 34.783 0.00 0.00 0.00 2.83
71 72 6.210287 TGGGTGTTTCGATTTTAGTGTTTT 57.790 33.333 0.00 0.00 0.00 2.43
72 73 6.631962 TGGGTGTTTCGATTTTAGTGTTTTT 58.368 32.000 0.00 0.00 0.00 1.94
73 74 6.531948 TGGGTGTTTCGATTTTAGTGTTTTTG 59.468 34.615 0.00 0.00 0.00 2.44
74 75 6.532302 GGGTGTTTCGATTTTAGTGTTTTTGT 59.468 34.615 0.00 0.00 0.00 2.83
75 76 7.063662 GGGTGTTTCGATTTTAGTGTTTTTGTT 59.936 33.333 0.00 0.00 0.00 2.83
76 77 8.436970 GGTGTTTCGATTTTAGTGTTTTTGTTT 58.563 29.630 0.00 0.00 0.00 2.83
77 78 9.800299 GTGTTTCGATTTTAGTGTTTTTGTTTT 57.200 25.926 0.00 0.00 0.00 2.43
112 113 9.765795 TTTTTGTTTGGTTTTCTTACTTCTTCA 57.234 25.926 0.00 0.00 0.00 3.02
113 114 9.936759 TTTTGTTTGGTTTTCTTACTTCTTCAT 57.063 25.926 0.00 0.00 0.00 2.57
114 115 9.936759 TTTGTTTGGTTTTCTTACTTCTTCATT 57.063 25.926 0.00 0.00 0.00 2.57
115 116 8.925161 TGTTTGGTTTTCTTACTTCTTCATTG 57.075 30.769 0.00 0.00 0.00 2.82
116 117 7.978975 TGTTTGGTTTTCTTACTTCTTCATTGG 59.021 33.333 0.00 0.00 0.00 3.16
117 118 7.654022 TTGGTTTTCTTACTTCTTCATTGGT 57.346 32.000 0.00 0.00 0.00 3.67
118 119 7.654022 TGGTTTTCTTACTTCTTCATTGGTT 57.346 32.000 0.00 0.00 0.00 3.67
119 120 8.073467 TGGTTTTCTTACTTCTTCATTGGTTT 57.927 30.769 0.00 0.00 0.00 3.27
120 121 8.536175 TGGTTTTCTTACTTCTTCATTGGTTTT 58.464 29.630 0.00 0.00 0.00 2.43
121 122 9.031360 GGTTTTCTTACTTCTTCATTGGTTTTC 57.969 33.333 0.00 0.00 0.00 2.29
122 123 9.803315 GTTTTCTTACTTCTTCATTGGTTTTCT 57.197 29.630 0.00 0.00 0.00 2.52
126 127 9.184523 TCTTACTTCTTCATTGGTTTTCTTTCA 57.815 29.630 0.00 0.00 0.00 2.69
127 128 9.971922 CTTACTTCTTCATTGGTTTTCTTTCAT 57.028 29.630 0.00 0.00 0.00 2.57
130 131 9.671279 ACTTCTTCATTGGTTTTCTTTCATTTT 57.329 25.926 0.00 0.00 0.00 1.82
132 133 8.661352 TCTTCATTGGTTTTCTTTCATTTTCC 57.339 30.769 0.00 0.00 0.00 3.13
133 134 8.485392 TCTTCATTGGTTTTCTTTCATTTTCCT 58.515 29.630 0.00 0.00 0.00 3.36
134 135 9.112725 CTTCATTGGTTTTCTTTCATTTTCCTT 57.887 29.630 0.00 0.00 0.00 3.36
135 136 9.460019 TTCATTGGTTTTCTTTCATTTTCCTTT 57.540 25.926 0.00 0.00 0.00 3.11
136 137 9.460019 TCATTGGTTTTCTTTCATTTTCCTTTT 57.540 25.926 0.00 0.00 0.00 2.27
139 140 7.969314 TGGTTTTCTTTCATTTTCCTTTTTCG 58.031 30.769 0.00 0.00 0.00 3.46
140 141 7.604545 TGGTTTTCTTTCATTTTCCTTTTTCGT 59.395 29.630 0.00 0.00 0.00 3.85
141 142 8.114290 GGTTTTCTTTCATTTTCCTTTTTCGTC 58.886 33.333 0.00 0.00 0.00 4.20
142 143 8.652463 GTTTTCTTTCATTTTCCTTTTTCGTCA 58.348 29.630 0.00 0.00 0.00 4.35
143 144 8.940768 TTTCTTTCATTTTCCTTTTTCGTCAT 57.059 26.923 0.00 0.00 0.00 3.06
144 145 8.940768 TTCTTTCATTTTCCTTTTTCGTCATT 57.059 26.923 0.00 0.00 0.00 2.57
145 146 8.351495 TCTTTCATTTTCCTTTTTCGTCATTG 57.649 30.769 0.00 0.00 0.00 2.82
146 147 7.978975 TCTTTCATTTTCCTTTTTCGTCATTGT 59.021 29.630 0.00 0.00 0.00 2.71
147 148 9.243637 CTTTCATTTTCCTTTTTCGTCATTGTA 57.756 29.630 0.00 0.00 0.00 2.41
148 149 8.568732 TTCATTTTCCTTTTTCGTCATTGTAC 57.431 30.769 0.00 0.00 0.00 2.90
149 150 7.936584 TCATTTTCCTTTTTCGTCATTGTACT 58.063 30.769 0.00 0.00 0.00 2.73
150 151 8.410141 TCATTTTCCTTTTTCGTCATTGTACTT 58.590 29.630 0.00 0.00 0.00 2.24
151 152 8.690840 CATTTTCCTTTTTCGTCATTGTACTTC 58.309 33.333 0.00 0.00 0.00 3.01
152 153 6.928979 TTCCTTTTTCGTCATTGTACTTCA 57.071 33.333 0.00 0.00 0.00 3.02
153 154 7.504924 TTCCTTTTTCGTCATTGTACTTCAT 57.495 32.000 0.00 0.00 0.00 2.57
154 155 7.504924 TCCTTTTTCGTCATTGTACTTCATT 57.495 32.000 0.00 0.00 0.00 2.57
155 156 7.936584 TCCTTTTTCGTCATTGTACTTCATTT 58.063 30.769 0.00 0.00 0.00 2.32
156 157 8.410141 TCCTTTTTCGTCATTGTACTTCATTTT 58.590 29.630 0.00 0.00 0.00 1.82
157 158 9.030301 CCTTTTTCGTCATTGTACTTCATTTTT 57.970 29.630 0.00 0.00 0.00 1.94
255 256 8.596271 TTTTTCGTTTCTTTCTTGGTTTTCTT 57.404 26.923 0.00 0.00 0.00 2.52
256 257 8.596271 TTTTCGTTTCTTTCTTGGTTTTCTTT 57.404 26.923 0.00 0.00 0.00 2.52
257 258 9.694137 TTTTCGTTTCTTTCTTGGTTTTCTTTA 57.306 25.926 0.00 0.00 0.00 1.85
258 259 9.863845 TTTCGTTTCTTTCTTGGTTTTCTTTAT 57.136 25.926 0.00 0.00 0.00 1.40
259 260 9.863845 TTCGTTTCTTTCTTGGTTTTCTTTATT 57.136 25.926 0.00 0.00 0.00 1.40
260 261 9.863845 TCGTTTCTTTCTTGGTTTTCTTTATTT 57.136 25.926 0.00 0.00 0.00 1.40
268 269 9.730420 TTCTTGGTTTTCTTTATTTCTTTCTCG 57.270 29.630 0.00 0.00 0.00 4.04
269 270 8.349983 TCTTGGTTTTCTTTATTTCTTTCTCGG 58.650 33.333 0.00 0.00 0.00 4.63
270 271 7.576861 TGGTTTTCTTTATTTCTTTCTCGGT 57.423 32.000 0.00 0.00 0.00 4.69
271 272 8.002984 TGGTTTTCTTTATTTCTTTCTCGGTT 57.997 30.769 0.00 0.00 0.00 4.44
272 273 8.471609 TGGTTTTCTTTATTTCTTTCTCGGTTT 58.528 29.630 0.00 0.00 0.00 3.27
273 274 9.309516 GGTTTTCTTTATTTCTTTCTCGGTTTT 57.690 29.630 0.00 0.00 0.00 2.43
278 279 9.677567 TCTTTATTTCTTTCTCGGTTTTCATTG 57.322 29.630 0.00 0.00 0.00 2.82
279 280 9.463443 CTTTATTTCTTTCTCGGTTTTCATTGT 57.537 29.630 0.00 0.00 0.00 2.71
280 281 9.810545 TTTATTTCTTTCTCGGTTTTCATTGTT 57.189 25.926 0.00 0.00 0.00 2.83
281 282 9.810545 TTATTTCTTTCTCGGTTTTCATTGTTT 57.189 25.926 0.00 0.00 0.00 2.83
282 283 8.716646 ATTTCTTTCTCGGTTTTCATTGTTTT 57.283 26.923 0.00 0.00 0.00 2.43
283 284 7.749539 TTCTTTCTCGGTTTTCATTGTTTTC 57.250 32.000 0.00 0.00 0.00 2.29
284 285 6.857956 TCTTTCTCGGTTTTCATTGTTTTCA 58.142 32.000 0.00 0.00 0.00 2.69
285 286 7.316640 TCTTTCTCGGTTTTCATTGTTTTCAA 58.683 30.769 0.00 0.00 44.33 2.69
287 288 8.485976 TTTCTCGGTTTTCATTGTTTTCAATT 57.514 26.923 0.00 0.00 46.94 2.32
288 289 8.485976 TTCTCGGTTTTCATTGTTTTCAATTT 57.514 26.923 0.00 0.00 46.94 1.82
289 290 8.485976 TCTCGGTTTTCATTGTTTTCAATTTT 57.514 26.923 0.00 0.00 46.94 1.82
290 291 8.940952 TCTCGGTTTTCATTGTTTTCAATTTTT 58.059 25.926 0.00 0.00 46.94 1.94
309 310 3.971245 TTTTGCACCTGTTTCTTTGGT 57.029 38.095 0.00 0.00 33.87 3.67
310 311 3.971245 TTTGCACCTGTTTCTTTGGTT 57.029 38.095 0.00 0.00 30.72 3.67
311 312 3.971245 TTGCACCTGTTTCTTTGGTTT 57.029 38.095 0.00 0.00 30.72 3.27
312 313 3.518634 TGCACCTGTTTCTTTGGTTTC 57.481 42.857 0.00 0.00 30.72 2.78
313 314 2.167487 TGCACCTGTTTCTTTGGTTTCC 59.833 45.455 0.00 0.00 30.72 3.13
314 315 2.430694 GCACCTGTTTCTTTGGTTTCCT 59.569 45.455 0.00 0.00 30.72 3.36
315 316 3.118775 GCACCTGTTTCTTTGGTTTCCTT 60.119 43.478 0.00 0.00 30.72 3.36
316 317 4.622933 GCACCTGTTTCTTTGGTTTCCTTT 60.623 41.667 0.00 0.00 30.72 3.11
317 318 5.487433 CACCTGTTTCTTTGGTTTCCTTTT 58.513 37.500 0.00 0.00 30.72 2.27
318 319 5.580691 CACCTGTTTCTTTGGTTTCCTTTTC 59.419 40.000 0.00 0.00 30.72 2.29
319 320 5.116180 CCTGTTTCTTTGGTTTCCTTTTCC 58.884 41.667 0.00 0.00 0.00 3.13
320 321 5.092554 TGTTTCTTTGGTTTCCTTTTCCC 57.907 39.130 0.00 0.00 0.00 3.97
321 322 4.780554 TGTTTCTTTGGTTTCCTTTTCCCT 59.219 37.500 0.00 0.00 0.00 4.20
322 323 5.249622 TGTTTCTTTGGTTTCCTTTTCCCTT 59.750 36.000 0.00 0.00 0.00 3.95
323 324 6.177610 GTTTCTTTGGTTTCCTTTTCCCTTT 58.822 36.000 0.00 0.00 0.00 3.11
324 325 6.381498 TTCTTTGGTTTCCTTTTCCCTTTT 57.619 33.333 0.00 0.00 0.00 2.27
325 326 6.381498 TCTTTGGTTTCCTTTTCCCTTTTT 57.619 33.333 0.00 0.00 0.00 1.94
401 402 7.910441 ACCTTTAGCATTTGGAAATTCATTG 57.090 32.000 0.00 0.00 0.00 2.82
402 403 7.452562 ACCTTTAGCATTTGGAAATTCATTGT 58.547 30.769 0.00 0.00 0.00 2.71
403 404 7.938490 ACCTTTAGCATTTGGAAATTCATTGTT 59.062 29.630 0.00 0.00 0.00 2.83
404 405 9.434420 CCTTTAGCATTTGGAAATTCATTGTTA 57.566 29.630 0.00 0.00 0.00 2.41
439 440 9.173021 TCGAATAAATGTTTGGATGTCTATTGT 57.827 29.630 0.00 0.00 0.00 2.71
440 441 9.787532 CGAATAAATGTTTGGATGTCTATTGTT 57.212 29.630 0.00 0.00 0.00 2.83
447 448 9.685276 ATGTTTGGATGTCTATTGTTTCATAGA 57.315 29.630 0.00 0.00 0.00 1.98
448 449 8.946085 TGTTTGGATGTCTATTGTTTCATAGAC 58.054 33.333 12.16 12.16 45.70 2.59
463 464 9.689976 TGTTTCATAGACATTGTACATTTTTGG 57.310 29.630 0.00 0.00 0.00 3.28
464 465 9.691362 GTTTCATAGACATTGTACATTTTTGGT 57.309 29.630 0.00 0.00 0.00 3.67
561 562 9.944663 TGTTTTGATGTCTACTTTTTACACATC 57.055 29.630 3.84 3.84 42.45 3.06
566 567 9.936759 TGATGTCTACTTTTTACACATCATACA 57.063 29.630 8.60 0.00 45.28 2.29
574 575 9.959749 ACTTTTTACACATCATACATTTTCGTT 57.040 25.926 0.00 0.00 0.00 3.85
578 579 9.497030 TTTACACATCATACATTTTCGTTATGC 57.503 29.630 0.00 0.00 0.00 3.14
579 580 7.082700 ACACATCATACATTTTCGTTATGCA 57.917 32.000 0.00 0.00 0.00 3.96
580 581 7.706159 ACACATCATACATTTTCGTTATGCAT 58.294 30.769 3.79 3.79 0.00 3.96
581 582 8.190122 ACACATCATACATTTTCGTTATGCATT 58.810 29.630 3.54 0.00 0.00 3.56
582 583 9.022915 CACATCATACATTTTCGTTATGCATTT 57.977 29.630 3.54 0.00 0.00 2.32
583 584 9.022915 ACATCATACATTTTCGTTATGCATTTG 57.977 29.630 3.54 0.00 0.00 2.32
584 585 9.235537 CATCATACATTTTCGTTATGCATTTGA 57.764 29.630 3.54 0.00 0.00 2.69
585 586 9.970395 ATCATACATTTTCGTTATGCATTTGAT 57.030 25.926 3.54 0.00 0.00 2.57
590 591 9.585099 ACATTTTCGTTATGCATTTGATACATT 57.415 25.926 3.54 0.00 0.00 2.71
635 636 7.573916 TGTATGCATGTTTAACATTTTTCCG 57.426 32.000 10.16 0.00 36.53 4.30
636 637 7.371159 TGTATGCATGTTTAACATTTTTCCGA 58.629 30.769 10.16 0.00 36.53 4.55
637 638 7.867909 TGTATGCATGTTTAACATTTTTCCGAA 59.132 29.630 10.16 0.00 36.53 4.30
638 639 7.903995 ATGCATGTTTAACATTTTTCCGAAT 57.096 28.000 7.97 0.00 36.53 3.34
639 640 8.994429 ATGCATGTTTAACATTTTTCCGAATA 57.006 26.923 7.97 0.00 36.53 1.75
640 641 8.233692 TGCATGTTTAACATTTTTCCGAATAC 57.766 30.769 7.97 0.00 36.53 1.89
641 642 7.867909 TGCATGTTTAACATTTTTCCGAATACA 59.132 29.630 7.97 0.00 36.53 2.29
642 643 8.868916 GCATGTTTAACATTTTTCCGAATACAT 58.131 29.630 7.97 0.00 36.53 2.29
645 646 9.619316 TGTTTAACATTTTTCCGAATACATGAG 57.381 29.630 0.00 0.00 0.00 2.90
646 647 9.620660 GTTTAACATTTTTCCGAATACATGAGT 57.379 29.630 0.00 0.00 0.00 3.41
650 651 8.330466 ACATTTTTCCGAATACATGAGTAACA 57.670 30.769 0.00 0.00 33.13 2.41
651 652 8.956426 ACATTTTTCCGAATACATGAGTAACAT 58.044 29.630 0.00 0.00 40.17 2.71
652 653 9.787532 CATTTTTCCGAATACATGAGTAACATT 57.212 29.630 0.00 0.00 37.07 2.71
847 848 8.690680 TTTTTGTATACGCATTTAACATTCCC 57.309 30.769 0.00 0.00 0.00 3.97
848 849 7.392494 TTTGTATACGCATTTAACATTCCCA 57.608 32.000 0.00 0.00 0.00 4.37
849 850 6.612247 TGTATACGCATTTAACATTCCCAG 57.388 37.500 0.00 0.00 0.00 4.45
850 851 5.529430 TGTATACGCATTTAACATTCCCAGG 59.471 40.000 0.00 0.00 0.00 4.45
851 852 1.476488 ACGCATTTAACATTCCCAGGC 59.524 47.619 0.00 0.00 0.00 4.85
852 853 1.476085 CGCATTTAACATTCCCAGGCA 59.524 47.619 0.00 0.00 0.00 4.75
853 854 2.735126 CGCATTTAACATTCCCAGGCAC 60.735 50.000 0.00 0.00 0.00 5.01
854 855 2.418609 GCATTTAACATTCCCAGGCACC 60.419 50.000 0.00 0.00 0.00 5.01
855 856 1.540267 TTTAACATTCCCAGGCACCG 58.460 50.000 0.00 0.00 0.00 4.94
856 857 0.322997 TTAACATTCCCAGGCACCGG 60.323 55.000 0.00 0.00 0.00 5.28
857 858 2.830186 TAACATTCCCAGGCACCGGC 62.830 60.000 0.00 0.00 40.13 6.13
936 937 2.597510 GGCCCGTTTGACCAGCTT 60.598 61.111 0.00 0.00 0.00 3.74
937 938 2.200337 GGCCCGTTTGACCAGCTTT 61.200 57.895 0.00 0.00 0.00 3.51
938 939 1.007387 GCCCGTTTGACCAGCTTTG 60.007 57.895 0.00 0.00 0.00 2.77
939 940 1.007387 CCCGTTTGACCAGCTTTGC 60.007 57.895 0.00 0.00 0.00 3.68
940 941 1.007387 CCGTTTGACCAGCTTTGCC 60.007 57.895 0.00 0.00 0.00 4.52
941 942 1.732917 CGTTTGACCAGCTTTGCCA 59.267 52.632 0.00 0.00 0.00 4.92
942 943 0.594796 CGTTTGACCAGCTTTGCCAC 60.595 55.000 0.00 0.00 0.00 5.01
943 944 0.746659 GTTTGACCAGCTTTGCCACT 59.253 50.000 0.00 0.00 0.00 4.00
990 991 1.273455 CGTCACACGAACTCGGTTCC 61.273 60.000 3.88 0.00 46.05 3.62
1006 1007 3.676093 GGTTCCTTCTTTCCTGTACCAG 58.324 50.000 0.00 0.00 0.00 4.00
1009 1010 5.045797 GGTTCCTTCTTTCCTGTACCAGTAT 60.046 44.000 0.00 0.00 0.00 2.12
1608 1614 3.415087 GACATGGCCAGCCTCCCT 61.415 66.667 13.05 0.00 36.94 4.20
1898 1904 8.763984 AATGGAAATGCAAAGAAGAGAGATAT 57.236 30.769 0.00 0.00 0.00 1.63
2175 2181 6.347160 CGACATGTGACATAATGATGGATGAC 60.347 42.308 1.15 0.00 37.39 3.06
2241 2247 4.025401 CTGCCACGGACAAACGGC 62.025 66.667 0.00 0.00 45.11 5.68
2675 2681 4.743057 TCGATGATGTCAGAAGGTGATT 57.257 40.909 0.00 0.00 37.56 2.57
2767 2774 7.549147 TGGGGTGATCAATAGTTACTATACC 57.451 40.000 5.22 8.70 0.00 2.73
2963 2970 8.687824 AAATATAAGATTGAACTGCCAAAACG 57.312 30.769 0.00 0.00 0.00 3.60
2980 2987 6.033513 GCCAAAACGTCTTATGTTTATGAAGC 59.966 38.462 0.00 0.00 36.39 3.86
2988 2995 7.429340 CGTCTTATGTTTATGAAGCATCAAACC 59.571 37.037 0.00 0.00 39.49 3.27
3034 3041 1.662044 CTGTTGCCAGGGCTCAAAC 59.338 57.895 12.19 8.31 42.51 2.93
3067 3074 2.498078 AGATCTGTCCCTCCGTTCTTTC 59.502 50.000 0.00 0.00 0.00 2.62
3071 3078 1.766496 TGTCCCTCCGTTCTTTCAAGT 59.234 47.619 0.00 0.00 0.00 3.16
3074 3081 3.933332 GTCCCTCCGTTCTTTCAAGTATG 59.067 47.826 0.00 0.00 0.00 2.39
3085 3092 6.839124 TCTTTCAAGTATGTCCATTGCATT 57.161 33.333 0.00 0.00 0.00 3.56
3472 3686 1.338020 GCTTACCACAAAGCTGCAACT 59.662 47.619 1.02 0.00 46.74 3.16
3505 3719 4.877823 TGAGGTCTAGCATTTGCATGTTAG 59.122 41.667 5.20 5.16 42.70 2.34
3567 3781 1.145945 TGCCACCAATCCACAACCTAA 59.854 47.619 0.00 0.00 0.00 2.69
3585 3799 4.202472 ACCTAAGGTAAGCATTATGAGCCC 60.202 45.833 0.00 0.00 32.11 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.181465 ACCGACGAAGAAATGGATAGCAT 60.181 43.478 0.00 0.00 0.00 3.79
2 3 2.167693 ACCGACGAAGAAATGGATAGCA 59.832 45.455 0.00 0.00 0.00 3.49
3 4 2.540101 CACCGACGAAGAAATGGATAGC 59.460 50.000 0.00 0.00 0.00 2.97
4 5 3.123804 CCACCGACGAAGAAATGGATAG 58.876 50.000 0.00 0.00 0.00 2.08
5 6 2.498481 ACCACCGACGAAGAAATGGATA 59.502 45.455 0.00 0.00 0.00 2.59
6 7 1.278127 ACCACCGACGAAGAAATGGAT 59.722 47.619 0.00 0.00 0.00 3.41
7 8 0.682852 ACCACCGACGAAGAAATGGA 59.317 50.000 0.00 0.00 0.00 3.41
8 9 1.076332 GACCACCGACGAAGAAATGG 58.924 55.000 0.00 0.00 0.00 3.16
9 10 1.726791 CTGACCACCGACGAAGAAATG 59.273 52.381 0.00 0.00 0.00 2.32
10 11 1.343465 ACTGACCACCGACGAAGAAAT 59.657 47.619 0.00 0.00 0.00 2.17
11 12 0.748450 ACTGACCACCGACGAAGAAA 59.252 50.000 0.00 0.00 0.00 2.52
12 13 0.748450 AACTGACCACCGACGAAGAA 59.252 50.000 0.00 0.00 0.00 2.52
13 14 0.313043 GAACTGACCACCGACGAAGA 59.687 55.000 0.00 0.00 0.00 2.87
14 15 1.002250 CGAACTGACCACCGACGAAG 61.002 60.000 0.00 0.00 0.00 3.79
15 16 1.008194 CGAACTGACCACCGACGAA 60.008 57.895 0.00 0.00 0.00 3.85
16 17 2.640989 CGAACTGACCACCGACGA 59.359 61.111 0.00 0.00 0.00 4.20
17 18 2.191354 TAGCGAACTGACCACCGACG 62.191 60.000 0.00 0.00 0.00 5.12
18 19 0.038892 TTAGCGAACTGACCACCGAC 60.039 55.000 0.00 0.00 0.00 4.79
19 20 0.892755 ATTAGCGAACTGACCACCGA 59.107 50.000 0.00 0.00 0.00 4.69
20 21 0.999406 CATTAGCGAACTGACCACCG 59.001 55.000 0.00 0.00 0.00 4.94
21 22 1.732259 CACATTAGCGAACTGACCACC 59.268 52.381 0.00 0.00 0.00 4.61
22 23 1.128692 GCACATTAGCGAACTGACCAC 59.871 52.381 0.00 0.00 0.00 4.16
23 24 1.001974 AGCACATTAGCGAACTGACCA 59.998 47.619 0.00 0.00 40.15 4.02
24 25 1.726853 AGCACATTAGCGAACTGACC 58.273 50.000 0.00 0.00 40.15 4.02
25 26 3.512680 ACTAGCACATTAGCGAACTGAC 58.487 45.455 0.00 0.00 40.15 3.51
26 27 3.868757 ACTAGCACATTAGCGAACTGA 57.131 42.857 0.00 0.00 40.15 3.41
27 28 4.436050 CCAAACTAGCACATTAGCGAACTG 60.436 45.833 0.00 0.00 40.15 3.16
28 29 3.684788 CCAAACTAGCACATTAGCGAACT 59.315 43.478 0.00 0.00 40.15 3.01
29 30 3.181510 CCCAAACTAGCACATTAGCGAAC 60.182 47.826 0.00 0.00 40.15 3.95
30 31 3.006940 CCCAAACTAGCACATTAGCGAA 58.993 45.455 0.00 0.00 40.15 4.70
31 32 2.027561 ACCCAAACTAGCACATTAGCGA 60.028 45.455 0.00 0.00 40.15 4.93
32 33 2.095853 CACCCAAACTAGCACATTAGCG 59.904 50.000 0.00 0.00 40.15 4.26
33 34 3.081804 ACACCCAAACTAGCACATTAGC 58.918 45.455 0.00 0.00 0.00 3.09
34 35 5.616866 CGAAACACCCAAACTAGCACATTAG 60.617 44.000 0.00 0.00 0.00 1.73
35 36 4.214545 CGAAACACCCAAACTAGCACATTA 59.785 41.667 0.00 0.00 0.00 1.90
36 37 3.004315 CGAAACACCCAAACTAGCACATT 59.996 43.478 0.00 0.00 0.00 2.71
37 38 2.552315 CGAAACACCCAAACTAGCACAT 59.448 45.455 0.00 0.00 0.00 3.21
38 39 1.944024 CGAAACACCCAAACTAGCACA 59.056 47.619 0.00 0.00 0.00 4.57
39 40 2.215196 TCGAAACACCCAAACTAGCAC 58.785 47.619 0.00 0.00 0.00 4.40
40 41 2.623878 TCGAAACACCCAAACTAGCA 57.376 45.000 0.00 0.00 0.00 3.49
41 42 4.499037 AAATCGAAACACCCAAACTAGC 57.501 40.909 0.00 0.00 0.00 3.42
42 43 7.075741 CACTAAAATCGAAACACCCAAACTAG 58.924 38.462 0.00 0.00 0.00 2.57
43 44 6.543100 ACACTAAAATCGAAACACCCAAACTA 59.457 34.615 0.00 0.00 0.00 2.24
44 45 5.358725 ACACTAAAATCGAAACACCCAAACT 59.641 36.000 0.00 0.00 0.00 2.66
45 46 5.584442 ACACTAAAATCGAAACACCCAAAC 58.416 37.500 0.00 0.00 0.00 2.93
46 47 5.838531 ACACTAAAATCGAAACACCCAAA 57.161 34.783 0.00 0.00 0.00 3.28
47 48 5.838531 AACACTAAAATCGAAACACCCAA 57.161 34.783 0.00 0.00 0.00 4.12
48 49 5.838531 AAACACTAAAATCGAAACACCCA 57.161 34.783 0.00 0.00 0.00 4.51
49 50 6.532302 ACAAAAACACTAAAATCGAAACACCC 59.468 34.615 0.00 0.00 0.00 4.61
50 51 7.514573 ACAAAAACACTAAAATCGAAACACC 57.485 32.000 0.00 0.00 0.00 4.16
51 52 9.800299 AAAACAAAAACACTAAAATCGAAACAC 57.200 25.926 0.00 0.00 0.00 3.32
86 87 9.765795 TGAAGAAGTAAGAAAACCAAACAAAAA 57.234 25.926 0.00 0.00 0.00 1.94
87 88 9.936759 ATGAAGAAGTAAGAAAACCAAACAAAA 57.063 25.926 0.00 0.00 0.00 2.44
88 89 9.936759 AATGAAGAAGTAAGAAAACCAAACAAA 57.063 25.926 0.00 0.00 0.00 2.83
89 90 9.364989 CAATGAAGAAGTAAGAAAACCAAACAA 57.635 29.630 0.00 0.00 0.00 2.83
90 91 7.978975 CCAATGAAGAAGTAAGAAAACCAAACA 59.021 33.333 0.00 0.00 0.00 2.83
91 92 7.979537 ACCAATGAAGAAGTAAGAAAACCAAAC 59.020 33.333 0.00 0.00 0.00 2.93
92 93 8.073467 ACCAATGAAGAAGTAAGAAAACCAAA 57.927 30.769 0.00 0.00 0.00 3.28
93 94 7.654022 ACCAATGAAGAAGTAAGAAAACCAA 57.346 32.000 0.00 0.00 0.00 3.67
94 95 7.654022 AACCAATGAAGAAGTAAGAAAACCA 57.346 32.000 0.00 0.00 0.00 3.67
95 96 8.942338 AAAACCAATGAAGAAGTAAGAAAACC 57.058 30.769 0.00 0.00 0.00 3.27
96 97 9.803315 AGAAAACCAATGAAGAAGTAAGAAAAC 57.197 29.630 0.00 0.00 0.00 2.43
100 101 9.184523 TGAAAGAAAACCAATGAAGAAGTAAGA 57.815 29.630 0.00 0.00 0.00 2.10
101 102 9.971922 ATGAAAGAAAACCAATGAAGAAGTAAG 57.028 29.630 0.00 0.00 0.00 2.34
104 105 9.671279 AAAATGAAAGAAAACCAATGAAGAAGT 57.329 25.926 0.00 0.00 0.00 3.01
106 107 9.108284 GGAAAATGAAAGAAAACCAATGAAGAA 57.892 29.630 0.00 0.00 0.00 2.52
107 108 8.485392 AGGAAAATGAAAGAAAACCAATGAAGA 58.515 29.630 0.00 0.00 0.00 2.87
108 109 8.667076 AGGAAAATGAAAGAAAACCAATGAAG 57.333 30.769 0.00 0.00 0.00 3.02
109 110 9.460019 AAAGGAAAATGAAAGAAAACCAATGAA 57.540 25.926 0.00 0.00 0.00 2.57
110 111 9.460019 AAAAGGAAAATGAAAGAAAACCAATGA 57.540 25.926 0.00 0.00 0.00 2.57
113 114 8.447053 CGAAAAAGGAAAATGAAAGAAAACCAA 58.553 29.630 0.00 0.00 0.00 3.67
114 115 7.604545 ACGAAAAAGGAAAATGAAAGAAAACCA 59.395 29.630 0.00 0.00 0.00 3.67
115 116 7.970384 ACGAAAAAGGAAAATGAAAGAAAACC 58.030 30.769 0.00 0.00 0.00 3.27
116 117 8.652463 TGACGAAAAAGGAAAATGAAAGAAAAC 58.348 29.630 0.00 0.00 0.00 2.43
117 118 8.764524 TGACGAAAAAGGAAAATGAAAGAAAA 57.235 26.923 0.00 0.00 0.00 2.29
118 119 8.940768 ATGACGAAAAAGGAAAATGAAAGAAA 57.059 26.923 0.00 0.00 0.00 2.52
119 120 8.816144 CAATGACGAAAAAGGAAAATGAAAGAA 58.184 29.630 0.00 0.00 0.00 2.52
120 121 7.978975 ACAATGACGAAAAAGGAAAATGAAAGA 59.021 29.630 0.00 0.00 0.00 2.52
121 122 8.130307 ACAATGACGAAAAAGGAAAATGAAAG 57.870 30.769 0.00 0.00 0.00 2.62
122 123 9.026074 GTACAATGACGAAAAAGGAAAATGAAA 57.974 29.630 0.00 0.00 0.00 2.69
123 124 8.410141 AGTACAATGACGAAAAAGGAAAATGAA 58.590 29.630 0.00 0.00 0.00 2.57
124 125 7.936584 AGTACAATGACGAAAAAGGAAAATGA 58.063 30.769 0.00 0.00 0.00 2.57
125 126 8.574196 AAGTACAATGACGAAAAAGGAAAATG 57.426 30.769 0.00 0.00 0.00 2.32
126 127 8.410141 TGAAGTACAATGACGAAAAAGGAAAAT 58.590 29.630 0.00 0.00 0.00 1.82
127 128 7.763356 TGAAGTACAATGACGAAAAAGGAAAA 58.237 30.769 0.00 0.00 0.00 2.29
128 129 7.323049 TGAAGTACAATGACGAAAAAGGAAA 57.677 32.000 0.00 0.00 0.00 3.13
129 130 6.928979 TGAAGTACAATGACGAAAAAGGAA 57.071 33.333 0.00 0.00 0.00 3.36
130 131 7.504924 AATGAAGTACAATGACGAAAAAGGA 57.495 32.000 0.00 0.00 0.00 3.36
131 132 8.574196 AAAATGAAGTACAATGACGAAAAAGG 57.426 30.769 0.00 0.00 0.00 3.11
230 231 8.596271 AAGAAAACCAAGAAAGAAACGAAAAA 57.404 26.923 0.00 0.00 0.00 1.94
231 232 8.596271 AAAGAAAACCAAGAAAGAAACGAAAA 57.404 26.923 0.00 0.00 0.00 2.29
232 233 9.863845 ATAAAGAAAACCAAGAAAGAAACGAAA 57.136 25.926 0.00 0.00 0.00 3.46
233 234 9.863845 AATAAAGAAAACCAAGAAAGAAACGAA 57.136 25.926 0.00 0.00 0.00 3.85
234 235 9.863845 AAATAAAGAAAACCAAGAAAGAAACGA 57.136 25.926 0.00 0.00 0.00 3.85
242 243 9.730420 CGAGAAAGAAATAAAGAAAACCAAGAA 57.270 29.630 0.00 0.00 0.00 2.52
243 244 8.349983 CCGAGAAAGAAATAAAGAAAACCAAGA 58.650 33.333 0.00 0.00 0.00 3.02
244 245 8.135529 ACCGAGAAAGAAATAAAGAAAACCAAG 58.864 33.333 0.00 0.00 0.00 3.61
245 246 8.002984 ACCGAGAAAGAAATAAAGAAAACCAA 57.997 30.769 0.00 0.00 0.00 3.67
246 247 7.576861 ACCGAGAAAGAAATAAAGAAAACCA 57.423 32.000 0.00 0.00 0.00 3.67
247 248 8.867112 AAACCGAGAAAGAAATAAAGAAAACC 57.133 30.769 0.00 0.00 0.00 3.27
252 253 9.677567 CAATGAAAACCGAGAAAGAAATAAAGA 57.322 29.630 0.00 0.00 0.00 2.52
253 254 9.463443 ACAATGAAAACCGAGAAAGAAATAAAG 57.537 29.630 0.00 0.00 0.00 1.85
254 255 9.810545 AACAATGAAAACCGAGAAAGAAATAAA 57.189 25.926 0.00 0.00 0.00 1.40
255 256 9.810545 AAACAATGAAAACCGAGAAAGAAATAA 57.189 25.926 0.00 0.00 0.00 1.40
256 257 9.810545 AAAACAATGAAAACCGAGAAAGAAATA 57.189 25.926 0.00 0.00 0.00 1.40
257 258 8.716646 AAAACAATGAAAACCGAGAAAGAAAT 57.283 26.923 0.00 0.00 0.00 2.17
258 259 7.815068 TGAAAACAATGAAAACCGAGAAAGAAA 59.185 29.630 0.00 0.00 0.00 2.52
259 260 7.316640 TGAAAACAATGAAAACCGAGAAAGAA 58.683 30.769 0.00 0.00 0.00 2.52
260 261 6.857956 TGAAAACAATGAAAACCGAGAAAGA 58.142 32.000 0.00 0.00 0.00 2.52
261 262 7.518731 TTGAAAACAATGAAAACCGAGAAAG 57.481 32.000 0.00 0.00 0.00 2.62
262 263 8.485976 AATTGAAAACAATGAAAACCGAGAAA 57.514 26.923 0.00 0.00 0.00 2.52
263 264 8.485976 AAATTGAAAACAATGAAAACCGAGAA 57.514 26.923 0.00 0.00 0.00 2.87
264 265 8.485976 AAAATTGAAAACAATGAAAACCGAGA 57.514 26.923 0.00 0.00 0.00 4.04
288 289 4.278975 ACCAAAGAAACAGGTGCAAAAA 57.721 36.364 0.00 0.00 33.57 1.94
289 290 3.971245 ACCAAAGAAACAGGTGCAAAA 57.029 38.095 0.00 0.00 33.57 2.44
290 291 3.971245 AACCAAAGAAACAGGTGCAAA 57.029 38.095 0.00 0.00 35.42 3.68
291 292 3.368948 GGAAACCAAAGAAACAGGTGCAA 60.369 43.478 0.00 0.00 35.42 4.08
292 293 2.167487 GGAAACCAAAGAAACAGGTGCA 59.833 45.455 0.00 0.00 35.42 4.57
293 294 2.430694 AGGAAACCAAAGAAACAGGTGC 59.569 45.455 0.00 0.00 35.42 5.01
294 295 4.736126 AAGGAAACCAAAGAAACAGGTG 57.264 40.909 0.00 0.00 35.42 4.00
295 296 5.338056 GGAAAAGGAAACCAAAGAAACAGGT 60.338 40.000 0.00 0.00 37.20 4.00
296 297 5.116180 GGAAAAGGAAACCAAAGAAACAGG 58.884 41.667 0.00 0.00 0.00 4.00
297 298 5.104941 AGGGAAAAGGAAACCAAAGAAACAG 60.105 40.000 0.00 0.00 0.00 3.16
298 299 4.780554 AGGGAAAAGGAAACCAAAGAAACA 59.219 37.500 0.00 0.00 0.00 2.83
299 300 5.353394 AGGGAAAAGGAAACCAAAGAAAC 57.647 39.130 0.00 0.00 0.00 2.78
300 301 6.381498 AAAGGGAAAAGGAAACCAAAGAAA 57.619 33.333 0.00 0.00 0.00 2.52
301 302 6.381498 AAAAGGGAAAAGGAAACCAAAGAA 57.619 33.333 0.00 0.00 0.00 2.52
302 303 6.381498 AAAAAGGGAAAAGGAAACCAAAGA 57.619 33.333 0.00 0.00 0.00 2.52
375 376 9.434420 CAATGAATTTCCAAATGCTAAAGGTAA 57.566 29.630 0.00 0.00 0.00 2.85
376 377 8.592809 ACAATGAATTTCCAAATGCTAAAGGTA 58.407 29.630 0.00 0.00 0.00 3.08
377 378 7.452562 ACAATGAATTTCCAAATGCTAAAGGT 58.547 30.769 0.00 0.00 0.00 3.50
378 379 7.910441 ACAATGAATTTCCAAATGCTAAAGG 57.090 32.000 0.00 0.00 0.00 3.11
413 414 9.173021 ACAATAGACATCCAAACATTTATTCGA 57.827 29.630 0.00 0.00 0.00 3.71
414 415 9.787532 AACAATAGACATCCAAACATTTATTCG 57.212 29.630 0.00 0.00 0.00 3.34
421 422 9.685276 TCTATGAAACAATAGACATCCAAACAT 57.315 29.630 0.00 0.00 34.84 2.71
437 438 9.689976 CCAAAAATGTACAATGTCTATGAAACA 57.310 29.630 0.00 0.00 0.00 2.83
438 439 9.691362 ACCAAAAATGTACAATGTCTATGAAAC 57.309 29.630 0.00 0.00 0.00 2.78
535 536 9.944663 GATGTGTAAAAAGTAGACATCAAAACA 57.055 29.630 15.10 0.00 0.00 2.83
536 537 9.944663 TGATGTGTAAAAAGTAGACATCAAAAC 57.055 29.630 18.58 0.28 0.00 2.43
540 541 9.936759 TGTATGATGTGTAAAAAGTAGACATCA 57.063 29.630 21.44 21.44 0.00 3.07
548 549 9.959749 AACGAAAATGTATGATGTGTAAAAAGT 57.040 25.926 0.00 0.00 0.00 2.66
552 553 9.497030 GCATAACGAAAATGTATGATGTGTAAA 57.503 29.630 0.00 0.00 0.00 2.01
553 554 8.669243 TGCATAACGAAAATGTATGATGTGTAA 58.331 29.630 0.00 0.00 0.00 2.41
554 555 8.202745 TGCATAACGAAAATGTATGATGTGTA 57.797 30.769 0.00 0.00 0.00 2.90
555 556 7.082700 TGCATAACGAAAATGTATGATGTGT 57.917 32.000 0.00 0.00 0.00 3.72
556 557 8.564648 AATGCATAACGAAAATGTATGATGTG 57.435 30.769 0.00 0.00 31.19 3.21
557 558 9.022915 CAAATGCATAACGAAAATGTATGATGT 57.977 29.630 0.00 0.00 31.19 3.06
558 559 9.235537 TCAAATGCATAACGAAAATGTATGATG 57.764 29.630 0.00 0.00 31.19 3.07
559 560 9.970395 ATCAAATGCATAACGAAAATGTATGAT 57.030 25.926 0.00 0.00 31.19 2.45
564 565 9.585099 AATGTATCAAATGCATAACGAAAATGT 57.415 25.926 0.00 0.00 34.39 2.71
609 610 9.295214 CGGAAAAATGTTAAACATGCATACATA 57.705 29.630 11.46 0.00 37.97 2.29
610 611 8.031864 TCGGAAAAATGTTAAACATGCATACAT 58.968 29.630 0.00 2.11 37.97 2.29
611 612 7.371159 TCGGAAAAATGTTAAACATGCATACA 58.629 30.769 0.00 0.00 37.97 2.29
612 613 7.804614 TCGGAAAAATGTTAAACATGCATAC 57.195 32.000 0.00 0.00 37.97 2.39
613 614 8.994429 ATTCGGAAAAATGTTAAACATGCATA 57.006 26.923 0.00 0.00 37.97 3.14
614 615 7.903995 ATTCGGAAAAATGTTAAACATGCAT 57.096 28.000 0.00 0.00 37.97 3.96
615 616 7.867909 TGTATTCGGAAAAATGTTAAACATGCA 59.132 29.630 0.00 0.00 37.97 3.96
616 617 8.233692 TGTATTCGGAAAAATGTTAAACATGC 57.766 30.769 0.00 0.00 37.97 4.06
619 620 9.619316 CTCATGTATTCGGAAAAATGTTAAACA 57.381 29.630 0.00 0.00 0.00 2.83
620 621 9.620660 ACTCATGTATTCGGAAAAATGTTAAAC 57.379 29.630 0.00 0.00 0.00 2.01
624 625 8.788806 TGTTACTCATGTATTCGGAAAAATGTT 58.211 29.630 0.00 0.00 0.00 2.71
625 626 8.330466 TGTTACTCATGTATTCGGAAAAATGT 57.670 30.769 0.00 0.00 0.00 2.71
626 627 9.787532 AATGTTACTCATGTATTCGGAAAAATG 57.212 29.630 0.00 0.00 36.81 2.32
822 823 8.304596 TGGGAATGTTAAATGCGTATACAAAAA 58.695 29.630 3.32 0.00 0.00 1.94
823 824 7.827701 TGGGAATGTTAAATGCGTATACAAAA 58.172 30.769 3.32 0.00 0.00 2.44
824 825 7.392494 TGGGAATGTTAAATGCGTATACAAA 57.608 32.000 3.32 0.00 0.00 2.83
825 826 6.038825 CCTGGGAATGTTAAATGCGTATACAA 59.961 38.462 3.32 0.00 0.00 2.41
826 827 5.529430 CCTGGGAATGTTAAATGCGTATACA 59.471 40.000 3.32 0.00 0.00 2.29
827 828 5.562113 GCCTGGGAATGTTAAATGCGTATAC 60.562 44.000 0.00 0.00 0.00 1.47
828 829 4.517453 GCCTGGGAATGTTAAATGCGTATA 59.483 41.667 0.00 0.00 0.00 1.47
829 830 3.317993 GCCTGGGAATGTTAAATGCGTAT 59.682 43.478 0.00 0.00 0.00 3.06
830 831 2.685897 GCCTGGGAATGTTAAATGCGTA 59.314 45.455 0.00 0.00 0.00 4.42
831 832 1.476488 GCCTGGGAATGTTAAATGCGT 59.524 47.619 0.00 0.00 0.00 5.24
832 833 1.476085 TGCCTGGGAATGTTAAATGCG 59.524 47.619 0.00 0.00 0.00 4.73
833 834 2.418609 GGTGCCTGGGAATGTTAAATGC 60.419 50.000 0.00 0.00 0.00 3.56
834 835 2.159254 CGGTGCCTGGGAATGTTAAATG 60.159 50.000 0.00 0.00 0.00 2.32
835 836 2.099405 CGGTGCCTGGGAATGTTAAAT 58.901 47.619 0.00 0.00 0.00 1.40
836 837 1.540267 CGGTGCCTGGGAATGTTAAA 58.460 50.000 0.00 0.00 0.00 1.52
837 838 0.322997 CCGGTGCCTGGGAATGTTAA 60.323 55.000 0.00 0.00 0.00 2.01
838 839 1.301623 CCGGTGCCTGGGAATGTTA 59.698 57.895 0.00 0.00 0.00 2.41
839 840 2.035626 CCGGTGCCTGGGAATGTT 59.964 61.111 0.00 0.00 0.00 2.71
840 841 4.740822 GCCGGTGCCTGGGAATGT 62.741 66.667 1.90 0.00 0.00 2.71
919 920 2.200337 AAAGCTGGTCAAACGGGCC 61.200 57.895 0.00 0.00 0.00 5.80
920 921 1.007387 CAAAGCTGGTCAAACGGGC 60.007 57.895 0.00 0.00 0.00 6.13
921 922 1.007387 GCAAAGCTGGTCAAACGGG 60.007 57.895 0.00 0.00 0.00 5.28
922 923 1.007387 GGCAAAGCTGGTCAAACGG 60.007 57.895 0.00 0.00 0.00 4.44
923 924 0.594796 GTGGCAAAGCTGGTCAAACG 60.595 55.000 0.00 0.00 0.00 3.60
924 925 0.746659 AGTGGCAAAGCTGGTCAAAC 59.253 50.000 0.00 0.00 0.00 2.93
925 926 0.746063 CAGTGGCAAAGCTGGTCAAA 59.254 50.000 0.00 0.00 0.00 2.69
926 927 1.108727 CCAGTGGCAAAGCTGGTCAA 61.109 55.000 13.10 0.00 45.28 3.18
927 928 1.529010 CCAGTGGCAAAGCTGGTCA 60.529 57.895 13.10 0.00 45.28 4.02
928 929 3.359002 CCAGTGGCAAAGCTGGTC 58.641 61.111 13.10 0.00 45.28 4.02
931 932 2.993264 CCCCCAGTGGCAAAGCTG 60.993 66.667 2.61 0.00 0.00 4.24
1626 1632 0.397941 CAGGCACCTCCTCAAACTCA 59.602 55.000 0.00 0.00 45.52 3.41
1773 1779 0.895530 CTGCCTCAGAAGGGTCGTAA 59.104 55.000 0.00 0.00 43.58 3.18
1898 1904 1.971357 GGACTCTGTCTTCCTTGTCCA 59.029 52.381 0.00 0.00 42.32 4.02
2175 2181 2.031012 TGCACAAGCTCTGACCCG 59.969 61.111 0.00 0.00 42.74 5.28
2241 2247 0.309922 CACAGAGCACAAGCACTTGG 59.690 55.000 14.51 5.19 44.45 3.61
2499 2505 4.100529 CAAGATTTTACATCCAAGCAGCG 58.899 43.478 0.00 0.00 0.00 5.18
2675 2681 8.063200 TCCGAAAATCACTCTTAGATACAAGA 57.937 34.615 0.00 0.00 33.55 3.02
2948 2955 4.336993 ACATAAGACGTTTTGGCAGTTCAA 59.663 37.500 0.83 0.00 0.00 2.69
2963 2970 8.243426 TGGTTTGATGCTTCATAAACATAAGAC 58.757 33.333 15.22 2.63 28.34 3.01
2980 2987 7.599998 CCTTTCTTTTAATCCTGTGGTTTGATG 59.400 37.037 0.00 0.00 0.00 3.07
2988 2995 7.277174 AGTTGACCTTTCTTTTAATCCTGTG 57.723 36.000 0.00 0.00 0.00 3.66
3034 3041 4.125703 GGGACAGATCTTCAATAGCACAG 58.874 47.826 0.00 0.00 0.00 3.66
3067 3074 5.346551 CACACAAATGCAATGGACATACTTG 59.653 40.000 7.65 0.00 0.00 3.16
3410 3623 4.131596 GCAACTGTGGTAACTGAAACCTA 58.868 43.478 5.14 0.00 37.91 3.08
3469 3683 4.938226 GCTAGACCTCAATACTTGCAAGTT 59.062 41.667 35.20 20.35 40.37 2.66
3472 3686 4.551702 TGCTAGACCTCAATACTTGCAA 57.448 40.909 0.00 0.00 38.77 4.08
3480 3694 4.275810 ACATGCAAATGCTAGACCTCAAT 58.724 39.130 6.97 0.00 42.66 2.57
3491 3705 3.787634 CACACGATCTAACATGCAAATGC 59.212 43.478 0.00 0.00 42.50 3.56
3505 3719 4.938080 AGATACTCATGGTTCACACGATC 58.062 43.478 0.00 0.00 0.00 3.69
3567 3781 1.768870 ACGGGCTCATAATGCTTACCT 59.231 47.619 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.