Multiple sequence alignment - TraesCS3A01G056100

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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 TraesCS3A01G056100 chr3A 100.000 3314 0 0 1 3314 32387567 32384254 0.000000e+00 6120.0
1 TraesCS3A01G056100 chr3A 85.059 850 53 30 2505 3314 32251708 32250893 0.000000e+00 798.0
2 TraesCS3A01G056100 chr3A 83.622 635 51 22 1840 2454 32252302 32251701 6.250000e-152 547.0
3 TraesCS3A01G056100 chr3A 88.177 406 25 16 2499 2886 731225854 731225454 2.330000e-126 462.0
4 TraesCS3A01G056100 chr3A 80.745 644 58 29 1840 2454 731226446 731225840 3.040000e-120 442.0
5 TraesCS3A01G056100 chr3A 84.171 398 25 14 2931 3314 731225445 731225072 5.260000e-93 351.0
6 TraesCS3A01G056100 chr3A 84.516 310 24 13 2491 2782 610783585 610783282 5.410000e-73 285.0
7 TraesCS3A01G056100 chr3A 85.135 74 5 1 1669 1742 731226533 731226466 1.650000e-08 71.3
8 TraesCS3A01G056100 chr3D 91.676 2559 115 35 354 2872 23197330 23194830 0.000000e+00 3456.0
9 TraesCS3A01G056100 chr3D 93.382 408 22 4 2908 3314 23194830 23194427 1.700000e-167 599.0
10 TraesCS3A01G056100 chr3D 83.462 647 54 23 1817 2458 23173803 23173205 1.340000e-153 553.0
11 TraesCS3A01G056100 chr3D 82.418 364 45 17 2647 2999 23173125 23172770 1.930000e-77 300.0
12 TraesCS3A01G056100 chr3D 83.986 281 28 8 1512 1779 23174064 23173788 1.530000e-63 254.0
13 TraesCS3A01G056100 chr3D 94.595 74 4 0 3028 3101 23172631 23172558 7.520000e-22 115.0
14 TraesCS3A01G056100 chr3B 90.092 2069 124 42 436 2464 40910354 40908327 0.000000e+00 2610.0
15 TraesCS3A01G056100 chr3B 94.005 834 31 10 2497 3314 40908344 40907514 0.000000e+00 1245.0
16 TraesCS3A01G056100 chr3B 86.427 501 39 12 2524 2999 40865426 40864930 3.790000e-144 521.0
17 TraesCS3A01G056100 chr3B 81.804 643 49 24 1840 2458 40866038 40865440 8.320000e-131 477.0
18 TraesCS3A01G056100 chr3B 80.615 325 38 15 2998 3314 40864780 40864473 9.250000e-56 228.0
19 TraesCS3A01G056100 chr3B 85.641 195 13 7 157 343 40911191 40911004 1.210000e-44 191.0
20 TraesCS3A01G056100 chr1B 85.635 181 19 4 1895 2073 499896494 499896669 2.030000e-42 183.0
21 TraesCS3A01G056100 chr1A 86.228 167 20 1 1910 2076 474450712 474450549 9.450000e-41 178.0
22 TraesCS3A01G056100 chr1D 83.684 190 27 2 1888 2076 375646705 375646519 3.400000e-40 176.0


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 TraesCS3A01G056100 chr3A 32384254 32387567 3313 True 6120.000000 6120 100.000000 1 3314 1 chr3A.!!$R1 3313
1 TraesCS3A01G056100 chr3A 32250893 32252302 1409 True 672.500000 798 84.340500 1840 3314 2 chr3A.!!$R3 1474
2 TraesCS3A01G056100 chr3A 731225072 731226533 1461 True 331.575000 462 84.557000 1669 3314 4 chr3A.!!$R4 1645
3 TraesCS3A01G056100 chr3D 23194427 23197330 2903 True 2027.500000 3456 92.529000 354 3314 2 chr3D.!!$R2 2960
4 TraesCS3A01G056100 chr3D 23172558 23174064 1506 True 305.500000 553 86.115250 1512 3101 4 chr3D.!!$R1 1589
5 TraesCS3A01G056100 chr3B 40907514 40911191 3677 True 1348.666667 2610 89.912667 157 3314 3 chr3B.!!$R2 3157
6 TraesCS3A01G056100 chr3B 40864473 40866038 1565 True 408.666667 521 82.948667 1840 3314 3 chr3B.!!$R1 1474

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
343 352 0.326264 AATCACCAGCTGACACTCCC 59.674 55.0 17.39 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2997 1.227147 TCGGAATGGATCGAACGGC 60.227 57.895 0.0 0.0 32.11 5.68 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 3.561429 CACGTCCGTGGATGGTTG 58.439 61.111 11.83 0.00 42.00 3.77
19 20 1.005512 CACGTCCGTGGATGGTTGA 60.006 57.895 11.83 0.00 42.00 3.18
20 21 1.014044 CACGTCCGTGGATGGTTGAG 61.014 60.000 11.83 0.00 42.00 3.02
21 22 1.447838 CGTCCGTGGATGGTTGAGG 60.448 63.158 0.00 0.00 0.00 3.86
22 23 1.078426 GTCCGTGGATGGTTGAGGG 60.078 63.158 0.00 0.00 0.00 4.30
23 24 2.272146 CCGTGGATGGTTGAGGGG 59.728 66.667 0.00 0.00 0.00 4.79
24 25 2.602676 CCGTGGATGGTTGAGGGGT 61.603 63.158 0.00 0.00 0.00 4.95
25 26 1.078426 CGTGGATGGTTGAGGGGTC 60.078 63.158 0.00 0.00 0.00 4.46
26 27 1.836999 CGTGGATGGTTGAGGGGTCA 61.837 60.000 0.00 0.00 0.00 4.02
27 28 0.404040 GTGGATGGTTGAGGGGTCAA 59.596 55.000 0.00 0.00 0.00 3.18
28 29 1.153539 TGGATGGTTGAGGGGTCAAA 58.846 50.000 0.00 0.00 0.00 2.69
29 30 1.715931 TGGATGGTTGAGGGGTCAAAT 59.284 47.619 0.00 0.00 0.00 2.32
30 31 2.111613 TGGATGGTTGAGGGGTCAAATT 59.888 45.455 0.00 0.00 0.00 1.82
31 32 3.335183 TGGATGGTTGAGGGGTCAAATTA 59.665 43.478 0.00 0.00 0.00 1.40
32 33 3.954258 GGATGGTTGAGGGGTCAAATTAG 59.046 47.826 0.00 0.00 0.00 1.73
33 34 2.802719 TGGTTGAGGGGTCAAATTAGC 58.197 47.619 0.00 0.00 0.00 3.09
34 35 2.109128 TGGTTGAGGGGTCAAATTAGCA 59.891 45.455 0.00 0.00 0.00 3.49
35 36 2.492088 GGTTGAGGGGTCAAATTAGCAC 59.508 50.000 0.00 0.00 0.00 4.40
36 37 3.153919 GTTGAGGGGTCAAATTAGCACA 58.846 45.455 0.00 0.00 0.00 4.57
37 38 3.071874 TGAGGGGTCAAATTAGCACAG 57.928 47.619 0.00 0.00 0.00 3.66
38 39 2.375174 TGAGGGGTCAAATTAGCACAGT 59.625 45.455 0.00 0.00 0.00 3.55
39 40 3.181434 TGAGGGGTCAAATTAGCACAGTT 60.181 43.478 0.00 0.00 0.00 3.16
40 41 4.042311 TGAGGGGTCAAATTAGCACAGTTA 59.958 41.667 0.00 0.00 0.00 2.24
41 42 4.589908 AGGGGTCAAATTAGCACAGTTAG 58.410 43.478 0.00 0.00 0.00 2.34
42 43 3.694566 GGGGTCAAATTAGCACAGTTAGG 59.305 47.826 0.00 0.00 0.00 2.69
43 44 3.128764 GGGTCAAATTAGCACAGTTAGGC 59.871 47.826 0.00 0.00 0.00 3.93
44 45 4.010349 GGTCAAATTAGCACAGTTAGGCT 58.990 43.478 0.00 0.00 43.94 4.58
55 56 2.736978 CAGTTAGGCTGTAGATGCTCG 58.263 52.381 0.00 0.00 40.27 5.03
56 57 2.359214 CAGTTAGGCTGTAGATGCTCGA 59.641 50.000 0.00 0.00 40.27 4.04
57 58 3.024547 AGTTAGGCTGTAGATGCTCGAA 58.975 45.455 0.00 0.00 0.00 3.71
58 59 3.447586 AGTTAGGCTGTAGATGCTCGAAA 59.552 43.478 0.00 0.00 0.00 3.46
59 60 2.593346 AGGCTGTAGATGCTCGAAAG 57.407 50.000 0.00 0.00 0.00 2.62
60 61 2.103373 AGGCTGTAGATGCTCGAAAGA 58.897 47.619 0.00 0.00 39.12 2.52
61 62 2.497675 AGGCTGTAGATGCTCGAAAGAA 59.502 45.455 0.00 0.00 41.32 2.52
62 63 3.055819 AGGCTGTAGATGCTCGAAAGAAA 60.056 43.478 0.00 0.00 41.32 2.52
63 64 3.684788 GGCTGTAGATGCTCGAAAGAAAA 59.315 43.478 0.00 0.00 41.32 2.29
64 65 4.333926 GGCTGTAGATGCTCGAAAGAAAAT 59.666 41.667 0.00 0.00 41.32 1.82
65 66 5.261661 GCTGTAGATGCTCGAAAGAAAATG 58.738 41.667 0.00 0.00 41.32 2.32
66 67 5.728898 GCTGTAGATGCTCGAAAGAAAATGG 60.729 44.000 0.00 0.00 41.32 3.16
67 68 5.245531 TGTAGATGCTCGAAAGAAAATGGT 58.754 37.500 0.00 0.00 41.32 3.55
68 69 4.691860 AGATGCTCGAAAGAAAATGGTG 57.308 40.909 0.00 0.00 41.32 4.17
69 70 4.074970 AGATGCTCGAAAGAAAATGGTGT 58.925 39.130 0.00 0.00 41.32 4.16
70 71 5.245531 AGATGCTCGAAAGAAAATGGTGTA 58.754 37.500 0.00 0.00 41.32 2.90
71 72 5.882557 AGATGCTCGAAAGAAAATGGTGTAT 59.117 36.000 0.00 0.00 41.32 2.29
72 73 5.545658 TGCTCGAAAGAAAATGGTGTATC 57.454 39.130 0.00 0.00 41.32 2.24
73 74 5.245531 TGCTCGAAAGAAAATGGTGTATCT 58.754 37.500 0.00 0.00 41.32 1.98
74 75 5.705441 TGCTCGAAAGAAAATGGTGTATCTT 59.295 36.000 0.00 0.00 41.32 2.40
75 76 6.128282 TGCTCGAAAGAAAATGGTGTATCTTC 60.128 38.462 0.00 0.00 41.32 2.87
76 77 6.675728 GCTCGAAAGAAAATGGTGTATCTTCC 60.676 42.308 0.00 0.00 41.32 3.46
77 78 6.472887 TCGAAAGAAAATGGTGTATCTTCCT 58.527 36.000 0.00 0.00 37.03 3.36
78 79 6.940298 TCGAAAGAAAATGGTGTATCTTCCTT 59.060 34.615 0.00 0.00 37.03 3.36
79 80 7.447238 TCGAAAGAAAATGGTGTATCTTCCTTT 59.553 33.333 0.00 0.00 37.03 3.11
80 81 8.082242 CGAAAGAAAATGGTGTATCTTCCTTTT 58.918 33.333 0.00 0.00 34.20 2.27
81 82 9.196552 GAAAGAAAATGGTGTATCTTCCTTTTG 57.803 33.333 0.00 0.00 33.46 2.44
82 83 8.477419 AAGAAAATGGTGTATCTTCCTTTTGA 57.523 30.769 0.00 0.00 33.46 2.69
83 84 8.477419 AGAAAATGGTGTATCTTCCTTTTGAA 57.523 30.769 0.00 0.00 33.46 2.69
84 85 8.923270 AGAAAATGGTGTATCTTCCTTTTGAAA 58.077 29.630 0.00 0.00 33.46 2.69
85 86 9.541143 GAAAATGGTGTATCTTCCTTTTGAAAA 57.459 29.630 0.00 0.00 33.46 2.29
86 87 9.898152 AAAATGGTGTATCTTCCTTTTGAAAAA 57.102 25.926 0.00 0.00 33.46 1.94
113 114 9.933723 AGAAAAGAAAATGGTGGATTTAATGAG 57.066 29.630 0.00 0.00 32.76 2.90
114 115 9.927668 GAAAAGAAAATGGTGGATTTAATGAGA 57.072 29.630 0.00 0.00 32.76 3.27
118 119 9.880157 AGAAAATGGTGGATTTAATGAGATTTG 57.120 29.630 0.00 0.00 32.76 2.32
119 120 9.657419 GAAAATGGTGGATTTAATGAGATTTGT 57.343 29.630 0.00 0.00 32.76 2.83
120 121 9.657419 AAAATGGTGGATTTAATGAGATTTGTC 57.343 29.630 0.00 0.00 32.76 3.18
121 122 6.773976 TGGTGGATTTAATGAGATTTGTCC 57.226 37.500 0.00 0.00 0.00 4.02
122 123 6.252233 TGGTGGATTTAATGAGATTTGTCCA 58.748 36.000 0.00 0.00 32.48 4.02
123 124 6.723515 TGGTGGATTTAATGAGATTTGTCCAA 59.276 34.615 0.00 0.00 36.38 3.53
124 125 7.399765 TGGTGGATTTAATGAGATTTGTCCAAT 59.600 33.333 0.00 0.00 36.38 3.16
125 126 7.922811 GGTGGATTTAATGAGATTTGTCCAATC 59.077 37.037 0.00 0.00 41.73 2.67
126 127 8.469200 GTGGATTTAATGAGATTTGTCCAATCA 58.531 33.333 0.00 0.00 43.63 2.57
127 128 8.689061 TGGATTTAATGAGATTTGTCCAATCAG 58.311 33.333 0.00 0.00 43.63 2.90
128 129 8.139989 GGATTTAATGAGATTTGTCCAATCAGG 58.860 37.037 0.00 0.00 43.63 3.86
129 130 8.599624 ATTTAATGAGATTTGTCCAATCAGGT 57.400 30.769 0.00 0.00 43.63 4.00
130 131 5.909621 AATGAGATTTGTCCAATCAGGTG 57.090 39.130 0.00 0.00 43.63 4.00
131 132 4.639078 TGAGATTTGTCCAATCAGGTGA 57.361 40.909 0.00 0.00 43.63 4.02
132 133 4.984295 TGAGATTTGTCCAATCAGGTGAA 58.016 39.130 0.00 0.00 43.63 3.18
133 134 5.384336 TGAGATTTGTCCAATCAGGTGAAA 58.616 37.500 0.00 0.00 43.63 2.69
134 135 5.474532 TGAGATTTGTCCAATCAGGTGAAAG 59.525 40.000 0.00 0.00 43.63 2.62
135 136 5.388654 AGATTTGTCCAATCAGGTGAAAGT 58.611 37.500 0.00 0.00 43.63 2.66
136 137 5.835280 AGATTTGTCCAATCAGGTGAAAGTT 59.165 36.000 0.00 0.00 43.63 2.66
137 138 5.930837 TTTGTCCAATCAGGTGAAAGTTT 57.069 34.783 0.00 0.00 39.02 2.66
138 139 5.930837 TTGTCCAATCAGGTGAAAGTTTT 57.069 34.783 0.00 0.00 39.02 2.43
139 140 5.930837 TGTCCAATCAGGTGAAAGTTTTT 57.069 34.783 0.00 0.00 39.02 1.94
140 141 5.659463 TGTCCAATCAGGTGAAAGTTTTTG 58.341 37.500 0.00 0.00 39.02 2.44
141 142 5.049828 GTCCAATCAGGTGAAAGTTTTTGG 58.950 41.667 6.63 6.63 39.02 3.28
142 143 4.100808 TCCAATCAGGTGAAAGTTTTTGGG 59.899 41.667 11.30 0.00 39.02 4.12
143 144 4.379652 CAATCAGGTGAAAGTTTTTGGGG 58.620 43.478 0.00 0.00 0.00 4.96
144 145 2.393646 TCAGGTGAAAGTTTTTGGGGG 58.606 47.619 0.00 0.00 0.00 5.40
206 207 1.063174 GAGCGATTCCAAGTGTGCATC 59.937 52.381 0.00 0.00 0.00 3.91
208 209 2.093500 AGCGATTCCAAGTGTGCATCTA 60.093 45.455 0.00 0.00 0.00 1.98
209 210 2.030946 GCGATTCCAAGTGTGCATCTAC 59.969 50.000 0.00 0.00 0.00 2.59
210 211 3.525537 CGATTCCAAGTGTGCATCTACT 58.474 45.455 0.00 0.00 0.00 2.57
211 212 3.553511 CGATTCCAAGTGTGCATCTACTC 59.446 47.826 0.00 0.00 0.00 2.59
212 213 4.679106 CGATTCCAAGTGTGCATCTACTCT 60.679 45.833 0.00 0.00 0.00 3.24
213 214 5.450550 CGATTCCAAGTGTGCATCTACTCTA 60.451 44.000 0.00 0.00 0.00 2.43
214 215 4.720649 TCCAAGTGTGCATCTACTCTAC 57.279 45.455 0.00 0.00 0.00 2.59
215 216 3.447586 TCCAAGTGTGCATCTACTCTACC 59.552 47.826 0.00 0.00 0.00 3.18
216 217 3.430929 CCAAGTGTGCATCTACTCTACCC 60.431 52.174 0.00 0.00 0.00 3.69
217 218 2.025155 AGTGTGCATCTACTCTACCCG 58.975 52.381 0.00 0.00 0.00 5.28
218 219 1.749634 GTGTGCATCTACTCTACCCGT 59.250 52.381 0.00 0.00 0.00 5.28
224 225 2.574006 TCTACTCTACCCGTGTGTGT 57.426 50.000 0.00 0.00 0.00 3.72
233 234 1.813337 CCGTGTGTGTGTGTGAGCA 60.813 57.895 0.00 0.00 0.00 4.26
267 271 3.204827 CCGCCGCTGCTATTTGCT 61.205 61.111 0.00 0.00 43.37 3.91
269 273 1.297893 CGCCGCTGCTATTTGCTTC 60.298 57.895 0.00 0.00 43.37 3.86
270 274 1.064783 GCCGCTGCTATTTGCTTCC 59.935 57.895 0.00 0.00 43.37 3.46
284 288 1.296002 GCTTCCCCTCCCTTTCCTAA 58.704 55.000 0.00 0.00 0.00 2.69
285 289 1.853622 GCTTCCCCTCCCTTTCCTAAT 59.146 52.381 0.00 0.00 0.00 1.73
286 290 2.245028 GCTTCCCCTCCCTTTCCTAATT 59.755 50.000 0.00 0.00 0.00 1.40
287 291 3.688702 GCTTCCCCTCCCTTTCCTAATTC 60.689 52.174 0.00 0.00 0.00 2.17
288 292 2.499515 TCCCCTCCCTTTCCTAATTCC 58.500 52.381 0.00 0.00 0.00 3.01
343 352 0.326264 AATCACCAGCTGACACTCCC 59.674 55.000 17.39 0.00 0.00 4.30
344 353 1.557269 ATCACCAGCTGACACTCCCC 61.557 60.000 17.39 0.00 0.00 4.81
345 354 2.930562 ACCAGCTGACACTCCCCC 60.931 66.667 17.39 0.00 0.00 5.40
363 372 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
370 379 4.472310 CCCCTCCCCTCCCCCATT 62.472 72.222 0.00 0.00 0.00 3.16
371 380 2.287975 CCCTCCCCTCCCCCATTT 60.288 66.667 0.00 0.00 0.00 2.32
375 384 0.327964 CTCCCCTCCCCCATTTCTCT 60.328 60.000 0.00 0.00 0.00 3.10
398 407 3.787001 GAACTCTCCCCCTGGCCG 61.787 72.222 0.00 0.00 0.00 6.13
514 1083 2.671963 CCTTGAGCAGCAGCAGCA 60.672 61.111 12.92 0.00 45.49 4.41
530 1099 2.334653 CAGCCGGAGATCGAGAGC 59.665 66.667 5.05 0.00 42.43 4.09
539 1108 1.333619 GAGATCGAGAGCAGGTCAGTC 59.666 57.143 1.66 0.00 0.00 3.51
582 1156 2.760650 TCTGCTCTGCTCCTCGATTTTA 59.239 45.455 0.00 0.00 0.00 1.52
649 1223 0.727398 CGAATTCGGAGGAGGTTTGC 59.273 55.000 20.16 0.00 35.37 3.68
656 1230 2.203938 AGGAGGTTTGCTCGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
672 1246 1.186200 GGGAGGCCTGAATTTGGTTC 58.814 55.000 12.00 0.00 37.35 3.62
673 1247 1.186200 GGAGGCCTGAATTTGGTTCC 58.814 55.000 12.00 0.00 35.91 3.62
690 1264 1.145377 CCGGGGTGGAGTAATTCGG 59.855 63.158 0.00 0.00 42.00 4.30
697 1271 0.913924 TGGAGTAATTCGGGGGTTCC 59.086 55.000 0.00 0.00 0.00 3.62
708 1282 1.455412 GGGGTTCCGGTTGGTGTTA 59.545 57.895 0.00 0.00 36.30 2.41
768 1342 4.120755 CCCTCCCCTGCTTGCTCC 62.121 72.222 0.00 0.00 0.00 4.70
780 1354 1.674962 GCTTGCTCCTCAATCATGTCC 59.325 52.381 0.00 0.00 33.57 4.02
786 1360 3.726607 CTCCTCAATCATGTCCTACAGC 58.273 50.000 0.00 0.00 0.00 4.40
816 1390 1.207329 TCCGCTCCTAGCTTTTTCCTC 59.793 52.381 0.00 0.00 39.60 3.71
833 1407 1.478288 CCTCCCAAATCTGCCTCATCC 60.478 57.143 0.00 0.00 0.00 3.51
848 1422 1.153168 ATCCGATTCGCACCAAGGG 60.153 57.895 0.00 0.00 0.00 3.95
877 1451 5.092105 GGAGATCGATCGTGTTATCATCAG 58.908 45.833 19.33 0.00 0.00 2.90
892 1466 2.695147 TCATCAGCGGAATCTTGAGCTA 59.305 45.455 0.00 0.00 37.94 3.32
939 1513 8.130307 ACTTTTTGTGCTAATTTGTCAACATC 57.870 30.769 0.00 0.00 0.00 3.06
940 1514 7.981225 ACTTTTTGTGCTAATTTGTCAACATCT 59.019 29.630 0.00 0.00 0.00 2.90
941 1515 7.928908 TTTTGTGCTAATTTGTCAACATCTC 57.071 32.000 0.00 0.00 0.00 2.75
942 1516 5.627499 TGTGCTAATTTGTCAACATCTCC 57.373 39.130 0.00 0.00 0.00 3.71
948 1522 4.647564 ATTTGTCAACATCTCCCTCTGT 57.352 40.909 0.00 0.00 0.00 3.41
1479 2077 2.989840 GCACAAGTGAGCACTACTACTG 59.010 50.000 3.21 0.97 41.58 2.74
1525 2126 7.775053 ACTCCATATCATAGTCTTCTTCTCC 57.225 40.000 0.00 0.00 0.00 3.71
1538 2139 2.370349 TCTTCTCCGATCTCAGTGACC 58.630 52.381 0.00 0.00 0.00 4.02
1547 2148 1.252175 TCTCAGTGACCTGTGAGAGC 58.748 55.000 0.00 0.00 43.41 4.09
1672 2287 7.489574 TTAAAACATGCCAAATTGGAAGAAC 57.510 32.000 17.47 0.00 40.96 3.01
1710 2327 7.201600 GGAAGAACTGCTATCTGAAAGTGAATC 60.202 40.741 0.00 0.00 33.76 2.52
1730 2347 5.931441 ATCACTTGTCTTTGTTCACTAGC 57.069 39.130 0.00 0.00 0.00 3.42
1822 2440 9.440773 TTCATGATCCATATTACTAGTTGATGC 57.559 33.333 0.00 0.00 0.00 3.91
1865 2503 6.351711 TGATCAATACTGCTAGTTGCTGAAT 58.648 36.000 10.18 0.00 42.27 2.57
1885 2523 7.063934 TGAATCTGATCATATGCTCTGTTCT 57.936 36.000 7.98 0.00 0.00 3.01
2028 2666 2.364842 ATCAGGCTCAGCTCCGGT 60.365 61.111 0.00 0.00 0.00 5.28
2136 2777 4.457496 ATCACCCAGTCCAGCGCG 62.457 66.667 0.00 0.00 0.00 6.86
2165 2806 4.028490 CCCAGCAACGGGGCAGTA 62.028 66.667 3.39 0.00 43.21 2.74
2322 2997 6.589523 GGAGTATGCTGTATTAGAAGATGCAG 59.410 42.308 0.00 0.00 41.10 4.41
2337 3012 1.089481 TGCAGCCGTTCGATCCATTC 61.089 55.000 0.00 0.00 0.00 2.67
2470 3146 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2471 3147 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2472 3148 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2473 3149 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2474 3150 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2475 3151 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2476 3152 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2477 3153 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2478 3154 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2479 3155 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2480 3156 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2481 3157 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2482 3158 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2483 3159 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2484 3160 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2485 3161 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2486 3162 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2487 3163 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2488 3164 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2489 3165 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2490 3166 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2491 3167 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2492 3168 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2493 3169 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2512 3188 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2734 3428 7.414540 GCTCATGTTATTGGAAACCTTACTCAG 60.415 40.741 0.00 0.00 0.00 3.35
2764 3458 6.161855 TCTCACACATACTTATCCACATCC 57.838 41.667 0.00 0.00 0.00 3.51
2768 3462 6.327365 TCACACATACTTATCCACATCCATCT 59.673 38.462 0.00 0.00 0.00 2.90
2888 3632 0.622136 TGCCTTGCTCATCTGGTCAT 59.378 50.000 0.00 0.00 0.00 3.06
2889 3633 1.005097 TGCCTTGCTCATCTGGTCATT 59.995 47.619 0.00 0.00 0.00 2.57
2971 3715 8.200792 TGTTTGTGTGCAATTAAGTCCTTTAAT 58.799 29.630 0.00 0.00 42.41 1.40
2973 3717 9.606631 TTTGTGTGCAATTAAGTCCTTTAATTT 57.393 25.926 0.00 0.00 45.32 1.82
2974 3718 9.606631 TTGTGTGCAATTAAGTCCTTTAATTTT 57.393 25.926 0.00 0.00 45.32 1.82
2975 3719 9.606631 TGTGTGCAATTAAGTCCTTTAATTTTT 57.393 25.926 0.00 0.00 45.32 1.94
3126 4037 3.573967 TGCCTCCTTTTTCCATCAACTTC 59.426 43.478 0.00 0.00 0.00 3.01
3142 4053 4.648762 TCAACTTCTGCAAAATCTTTCCCA 59.351 37.500 0.00 0.00 0.00 4.37
3143 4054 5.128499 TCAACTTCTGCAAAATCTTTCCCAA 59.872 36.000 0.00 0.00 0.00 4.12
3201 4112 2.172229 AAAGGCAGGGCATCCACCAT 62.172 55.000 0.00 0.00 34.88 3.55
3220 4131 3.390639 CCATAGATATGAGGCAGATCCCC 59.609 52.174 1.32 0.00 33.15 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.301401 CAACCATCCACGGACGTGT 60.301 57.895 21.52 3.28 44.02 4.49
2 3 1.292223 CTCAACCATCCACGGACGT 59.708 57.895 0.00 0.00 0.00 4.34
3 4 1.447838 CCTCAACCATCCACGGACG 60.448 63.158 0.00 0.00 0.00 4.79
4 5 1.078426 CCCTCAACCATCCACGGAC 60.078 63.158 0.00 0.00 0.00 4.79
8 9 0.404040 TTGACCCCTCAACCATCCAC 59.596 55.000 0.00 0.00 31.00 4.02
10 11 2.532250 ATTTGACCCCTCAACCATCC 57.468 50.000 0.00 0.00 36.06 3.51
11 12 3.381590 GCTAATTTGACCCCTCAACCATC 59.618 47.826 0.00 0.00 36.06 3.51
12 13 3.245586 TGCTAATTTGACCCCTCAACCAT 60.246 43.478 0.00 0.00 36.06 3.55
13 14 2.109128 TGCTAATTTGACCCCTCAACCA 59.891 45.455 0.00 0.00 36.06 3.67
14 15 2.492088 GTGCTAATTTGACCCCTCAACC 59.508 50.000 0.00 0.00 36.06 3.77
15 16 3.153919 TGTGCTAATTTGACCCCTCAAC 58.846 45.455 0.00 0.00 36.06 3.18
16 17 3.181434 ACTGTGCTAATTTGACCCCTCAA 60.181 43.478 0.00 0.00 34.39 3.02
18 19 3.073274 ACTGTGCTAATTTGACCCCTC 57.927 47.619 0.00 0.00 0.00 4.30
19 20 3.525800 AACTGTGCTAATTTGACCCCT 57.474 42.857 0.00 0.00 0.00 4.79
20 21 3.694566 CCTAACTGTGCTAATTTGACCCC 59.305 47.826 0.00 0.00 0.00 4.95
21 22 3.128764 GCCTAACTGTGCTAATTTGACCC 59.871 47.826 0.00 0.00 0.00 4.46
22 23 4.010349 AGCCTAACTGTGCTAATTTGACC 58.990 43.478 0.00 0.00 35.69 4.02
23 24 4.974591 CAGCCTAACTGTGCTAATTTGAC 58.025 43.478 0.00 0.00 41.86 3.18
36 37 2.656002 TCGAGCATCTACAGCCTAACT 58.344 47.619 0.00 0.00 0.00 2.24
37 38 3.438297 TTCGAGCATCTACAGCCTAAC 57.562 47.619 0.00 0.00 0.00 2.34
38 39 3.699538 TCTTTCGAGCATCTACAGCCTAA 59.300 43.478 0.00 0.00 0.00 2.69
39 40 3.288092 TCTTTCGAGCATCTACAGCCTA 58.712 45.455 0.00 0.00 0.00 3.93
40 41 2.103373 TCTTTCGAGCATCTACAGCCT 58.897 47.619 0.00 0.00 0.00 4.58
41 42 2.586258 TCTTTCGAGCATCTACAGCC 57.414 50.000 0.00 0.00 0.00 4.85
42 43 4.928661 TTTTCTTTCGAGCATCTACAGC 57.071 40.909 0.00 0.00 0.00 4.40
43 44 5.352569 ACCATTTTCTTTCGAGCATCTACAG 59.647 40.000 0.00 0.00 0.00 2.74
44 45 5.122239 CACCATTTTCTTTCGAGCATCTACA 59.878 40.000 0.00 0.00 0.00 2.74
45 46 5.122396 ACACCATTTTCTTTCGAGCATCTAC 59.878 40.000 0.00 0.00 0.00 2.59
46 47 5.245531 ACACCATTTTCTTTCGAGCATCTA 58.754 37.500 0.00 0.00 0.00 1.98
47 48 4.074970 ACACCATTTTCTTTCGAGCATCT 58.925 39.130 0.00 0.00 0.00 2.90
48 49 4.425577 ACACCATTTTCTTTCGAGCATC 57.574 40.909 0.00 0.00 0.00 3.91
49 50 5.882557 AGATACACCATTTTCTTTCGAGCAT 59.117 36.000 0.00 0.00 0.00 3.79
50 51 5.245531 AGATACACCATTTTCTTTCGAGCA 58.754 37.500 0.00 0.00 0.00 4.26
51 52 5.803020 AGATACACCATTTTCTTTCGAGC 57.197 39.130 0.00 0.00 0.00 5.03
52 53 6.595716 AGGAAGATACACCATTTTCTTTCGAG 59.404 38.462 0.00 0.00 30.48 4.04
53 54 6.472887 AGGAAGATACACCATTTTCTTTCGA 58.527 36.000 0.00 0.00 30.48 3.71
54 55 6.743575 AGGAAGATACACCATTTTCTTTCG 57.256 37.500 0.00 0.00 30.48 3.46
55 56 9.196552 CAAAAGGAAGATACACCATTTTCTTTC 57.803 33.333 0.00 0.00 29.12 2.62
56 57 8.923270 TCAAAAGGAAGATACACCATTTTCTTT 58.077 29.630 0.00 0.00 30.97 2.52
57 58 8.477419 TCAAAAGGAAGATACACCATTTTCTT 57.523 30.769 0.00 0.00 30.30 2.52
58 59 8.477419 TTCAAAAGGAAGATACACCATTTTCT 57.523 30.769 0.00 0.00 30.30 2.52
59 60 9.541143 TTTTCAAAAGGAAGATACACCATTTTC 57.459 29.630 0.00 0.00 36.72 2.29
60 61 9.898152 TTTTTCAAAAGGAAGATACACCATTTT 57.102 25.926 0.00 0.00 36.72 1.82
87 88 9.933723 CTCATTAAATCCACCATTTTCTTTTCT 57.066 29.630 0.00 0.00 36.09 2.52
88 89 9.927668 TCTCATTAAATCCACCATTTTCTTTTC 57.072 29.630 0.00 0.00 36.09 2.29
92 93 9.880157 CAAATCTCATTAAATCCACCATTTTCT 57.120 29.630 0.00 0.00 36.09 2.52
93 94 9.657419 ACAAATCTCATTAAATCCACCATTTTC 57.343 29.630 0.00 0.00 36.09 2.29
94 95 9.657419 GACAAATCTCATTAAATCCACCATTTT 57.343 29.630 0.00 0.00 36.09 1.82
95 96 8.260114 GGACAAATCTCATTAAATCCACCATTT 58.740 33.333 0.00 0.00 38.35 2.32
96 97 7.399765 TGGACAAATCTCATTAAATCCACCATT 59.600 33.333 0.00 0.00 30.08 3.16
97 98 6.896860 TGGACAAATCTCATTAAATCCACCAT 59.103 34.615 0.00 0.00 30.08 3.55
98 99 6.252233 TGGACAAATCTCATTAAATCCACCA 58.748 36.000 0.00 0.00 30.08 4.17
99 100 6.773976 TGGACAAATCTCATTAAATCCACC 57.226 37.500 0.00 0.00 30.08 4.61
100 101 8.469200 TGATTGGACAAATCTCATTAAATCCAC 58.531 33.333 4.20 0.00 44.42 4.02
101 102 8.592529 TGATTGGACAAATCTCATTAAATCCA 57.407 30.769 4.20 0.00 44.42 3.41
102 103 8.139989 CCTGATTGGACAAATCTCATTAAATCC 58.860 37.037 4.20 0.00 44.42 3.01
103 104 8.689972 ACCTGATTGGACAAATCTCATTAAATC 58.310 33.333 4.20 0.00 44.42 2.17
104 105 8.472413 CACCTGATTGGACAAATCTCATTAAAT 58.528 33.333 4.20 0.00 44.42 1.40
105 106 7.669304 TCACCTGATTGGACAAATCTCATTAAA 59.331 33.333 4.20 0.00 44.42 1.52
106 107 7.174413 TCACCTGATTGGACAAATCTCATTAA 58.826 34.615 4.20 0.00 44.42 1.40
107 108 6.720309 TCACCTGATTGGACAAATCTCATTA 58.280 36.000 4.20 0.00 44.42 1.90
108 109 5.573219 TCACCTGATTGGACAAATCTCATT 58.427 37.500 4.20 0.00 44.42 2.57
109 110 5.183530 TCACCTGATTGGACAAATCTCAT 57.816 39.130 4.20 0.00 44.42 2.90
110 111 4.639078 TCACCTGATTGGACAAATCTCA 57.361 40.909 4.20 0.00 44.42 3.27
111 112 5.474876 ACTTTCACCTGATTGGACAAATCTC 59.525 40.000 4.20 0.00 44.42 2.75
112 113 5.388654 ACTTTCACCTGATTGGACAAATCT 58.611 37.500 4.20 0.00 44.42 2.40
113 114 5.712152 ACTTTCACCTGATTGGACAAATC 57.288 39.130 0.00 0.00 44.37 2.17
114 115 6.484364 AAACTTTCACCTGATTGGACAAAT 57.516 33.333 0.00 0.00 39.71 2.32
115 116 5.930837 AAACTTTCACCTGATTGGACAAA 57.069 34.783 0.00 0.00 39.71 2.83
116 117 5.930837 AAAACTTTCACCTGATTGGACAA 57.069 34.783 0.00 0.00 39.71 3.18
117 118 5.395103 CCAAAAACTTTCACCTGATTGGACA 60.395 40.000 0.00 0.00 38.64 4.02
118 119 5.049828 CCAAAAACTTTCACCTGATTGGAC 58.950 41.667 0.00 0.00 38.64 4.02
119 120 4.100808 CCCAAAAACTTTCACCTGATTGGA 59.899 41.667 0.00 0.00 38.64 3.53
120 121 4.379652 CCCAAAAACTTTCACCTGATTGG 58.620 43.478 0.00 0.00 42.93 3.16
121 122 4.379652 CCCCAAAAACTTTCACCTGATTG 58.620 43.478 0.00 0.00 0.00 2.67
122 123 3.390967 CCCCCAAAAACTTTCACCTGATT 59.609 43.478 0.00 0.00 0.00 2.57
123 124 2.972021 CCCCCAAAAACTTTCACCTGAT 59.028 45.455 0.00 0.00 0.00 2.90
124 125 2.393646 CCCCCAAAAACTTTCACCTGA 58.606 47.619 0.00 0.00 0.00 3.86
125 126 2.908688 CCCCCAAAAACTTTCACCTG 57.091 50.000 0.00 0.00 0.00 4.00
142 143 1.272554 ACTACCTGCTACTTGCCCCC 61.273 60.000 0.00 0.00 42.00 5.40
143 144 0.107654 CACTACCTGCTACTTGCCCC 60.108 60.000 0.00 0.00 42.00 5.80
144 145 0.107654 CCACTACCTGCTACTTGCCC 60.108 60.000 0.00 0.00 42.00 5.36
145 146 0.107654 CCCACTACCTGCTACTTGCC 60.108 60.000 0.00 0.00 42.00 4.52
146 147 0.107654 CCCCACTACCTGCTACTTGC 60.108 60.000 0.00 0.00 43.25 4.01
147 148 0.541863 CCCCCACTACCTGCTACTTG 59.458 60.000 0.00 0.00 0.00 3.16
148 149 0.118547 ACCCCCACTACCTGCTACTT 59.881 55.000 0.00 0.00 0.00 2.24
149 150 0.617820 CACCCCCACTACCTGCTACT 60.618 60.000 0.00 0.00 0.00 2.57
150 151 0.616679 TCACCCCCACTACCTGCTAC 60.617 60.000 0.00 0.00 0.00 3.58
151 152 0.117541 TTCACCCCCACTACCTGCTA 59.882 55.000 0.00 0.00 0.00 3.49
152 153 0.770557 TTTCACCCCCACTACCTGCT 60.771 55.000 0.00 0.00 0.00 4.24
153 154 0.111639 TTTTCACCCCCACTACCTGC 59.888 55.000 0.00 0.00 0.00 4.85
154 155 1.271926 CCTTTTCACCCCCACTACCTG 60.272 57.143 0.00 0.00 0.00 4.00
155 156 1.073098 CCTTTTCACCCCCACTACCT 58.927 55.000 0.00 0.00 0.00 3.08
206 207 1.884579 ACACACACACGGGTAGAGTAG 59.115 52.381 0.00 0.00 0.00 2.57
208 209 0.387929 CACACACACACGGGTAGAGT 59.612 55.000 0.00 0.00 0.00 3.24
209 210 0.387929 ACACACACACACGGGTAGAG 59.612 55.000 0.00 0.00 0.00 2.43
210 211 0.103390 CACACACACACACGGGTAGA 59.897 55.000 0.00 0.00 0.00 2.59
211 212 0.103390 TCACACACACACACGGGTAG 59.897 55.000 0.00 0.00 0.00 3.18
212 213 0.103390 CTCACACACACACACGGGTA 59.897 55.000 0.00 0.00 0.00 3.69
213 214 1.153449 CTCACACACACACACGGGT 60.153 57.895 0.00 0.00 0.00 5.28
214 215 2.534019 GCTCACACACACACACGGG 61.534 63.158 0.00 0.00 0.00 5.28
215 216 1.813337 TGCTCACACACACACACGG 60.813 57.895 0.00 0.00 0.00 4.94
216 217 1.348250 GTGCTCACACACACACACG 59.652 57.895 0.00 0.00 46.61 4.49
233 234 1.136565 GGCATATTTGTGCGTGCGT 59.863 52.632 0.00 0.00 45.97 5.24
240 241 1.298563 CAGCGGCGGCATATTTGTG 60.299 57.895 19.21 2.00 43.41 3.33
267 271 2.856864 GGAATTAGGAAAGGGAGGGGAA 59.143 50.000 0.00 0.00 0.00 3.97
269 273 2.503824 AGGAATTAGGAAAGGGAGGGG 58.496 52.381 0.00 0.00 0.00 4.79
270 274 5.046520 CGTATAGGAATTAGGAAAGGGAGGG 60.047 48.000 0.00 0.00 0.00 4.30
286 290 2.100252 CGACTTTTCCTGGCGTATAGGA 59.900 50.000 0.00 0.00 42.43 2.94
287 291 2.470821 CGACTTTTCCTGGCGTATAGG 58.529 52.381 0.00 0.00 36.63 2.57
288 292 2.470821 CCGACTTTTCCTGGCGTATAG 58.529 52.381 0.00 0.00 0.00 1.31
315 324 1.379044 GCTGGTGATTGGGTGGAGG 60.379 63.158 0.00 0.00 0.00 4.30
346 355 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
353 362 4.472310 AATGGGGGAGGGGAGGGG 62.472 72.222 0.00 0.00 0.00 4.79
354 363 2.287975 AAATGGGGGAGGGGAGGG 60.288 66.667 0.00 0.00 0.00 4.30
355 364 1.309102 AGAAATGGGGGAGGGGAGG 60.309 63.158 0.00 0.00 0.00 4.30
356 365 0.327964 AGAGAAATGGGGGAGGGGAG 60.328 60.000 0.00 0.00 0.00 4.30
357 366 1.031939 TAGAGAAATGGGGGAGGGGA 58.968 55.000 0.00 0.00 0.00 4.81
358 367 1.141185 GTAGAGAAATGGGGGAGGGG 58.859 60.000 0.00 0.00 0.00 4.79
359 368 1.141185 GGTAGAGAAATGGGGGAGGG 58.859 60.000 0.00 0.00 0.00 4.30
360 369 1.893315 TGGTAGAGAAATGGGGGAGG 58.107 55.000 0.00 0.00 0.00 4.30
361 370 3.115390 TCTTGGTAGAGAAATGGGGGAG 58.885 50.000 0.00 0.00 0.00 4.30
362 371 3.214694 TCTTGGTAGAGAAATGGGGGA 57.785 47.619 0.00 0.00 0.00 4.81
363 372 3.267031 AGTTCTTGGTAGAGAAATGGGGG 59.733 47.826 0.00 0.00 37.40 5.40
364 373 4.226168 AGAGTTCTTGGTAGAGAAATGGGG 59.774 45.833 0.00 0.00 37.40 4.96
365 374 5.423886 GAGAGTTCTTGGTAGAGAAATGGG 58.576 45.833 0.00 0.00 37.40 4.00
366 375 5.423886 GGAGAGTTCTTGGTAGAGAAATGG 58.576 45.833 0.00 0.00 37.40 3.16
367 376 5.423886 GGGAGAGTTCTTGGTAGAGAAATG 58.576 45.833 0.00 0.00 37.40 2.32
368 377 4.471747 GGGGAGAGTTCTTGGTAGAGAAAT 59.528 45.833 0.00 0.00 37.40 2.17
369 378 3.838903 GGGGAGAGTTCTTGGTAGAGAAA 59.161 47.826 0.00 0.00 37.40 2.52
370 379 3.442076 GGGGAGAGTTCTTGGTAGAGAA 58.558 50.000 0.00 0.00 33.44 2.87
371 380 2.292323 GGGGGAGAGTTCTTGGTAGAGA 60.292 54.545 0.00 0.00 0.00 3.10
375 384 1.554822 CCAGGGGGAGAGTTCTTGGTA 60.555 57.143 0.00 0.00 35.59 3.25
415 424 1.837538 GAGACGGATCTCCTCGCTCG 61.838 65.000 0.00 0.00 45.06 5.03
514 1083 2.124109 TGCTCTCGATCTCCGGCT 60.124 61.111 0.00 0.00 39.14 5.52
530 1099 3.999663 GAGAAACCAAGATGACTGACCTG 59.000 47.826 0.00 0.00 0.00 4.00
539 1108 2.005451 CAGCTCCGAGAAACCAAGATG 58.995 52.381 0.00 0.00 0.00 2.90
649 1223 0.749454 CAAATTCAGGCCTCCCCGAG 60.749 60.000 0.00 0.00 39.21 4.63
656 1230 0.611896 CCGGAACCAAATTCAGGCCT 60.612 55.000 0.00 0.00 44.37 5.19
672 1246 1.145377 CCGAATTACTCCACCCCGG 59.855 63.158 0.00 0.00 0.00 5.73
673 1247 1.145377 CCCGAATTACTCCACCCCG 59.855 63.158 0.00 0.00 0.00 5.73
690 1264 0.178995 TTAACACCAACCGGAACCCC 60.179 55.000 9.46 0.00 35.59 4.95
697 1271 0.245266 GCCCCAATTAACACCAACCG 59.755 55.000 0.00 0.00 0.00 4.44
708 1282 0.544697 CTACTACCACGGCCCCAATT 59.455 55.000 0.00 0.00 0.00 2.32
768 1342 3.133542 TCTGGCTGTAGGACATGATTGAG 59.866 47.826 0.00 0.00 29.39 3.02
780 1354 1.936547 GCGGAATCTTTCTGGCTGTAG 59.063 52.381 0.00 0.00 36.54 2.74
786 1360 2.804933 GCTAGGAGCGGAATCTTTCTGG 60.805 54.545 0.00 0.00 36.54 3.86
816 1390 0.181114 TCGGATGAGGCAGATTTGGG 59.819 55.000 0.00 0.00 0.00 4.12
833 1407 2.824041 CCCCCTTGGTGCGAATCG 60.824 66.667 0.00 0.00 0.00 3.34
848 1422 1.833049 ACGATCGATCTCCCACCCC 60.833 63.158 24.34 0.00 0.00 4.95
852 1426 3.219281 TGATAACACGATCGATCTCCCA 58.781 45.455 24.34 9.73 0.00 4.37
853 1427 3.917329 TGATAACACGATCGATCTCCC 57.083 47.619 24.34 7.18 0.00 4.30
877 1451 1.859383 GGAGTAGCTCAAGATTCCGC 58.141 55.000 0.00 0.00 31.08 5.54
892 1466 0.171455 GATTCAGACGACAGCGGAGT 59.829 55.000 0.00 0.00 43.17 3.85
989 1575 1.061485 CATCATCATCGCTCAGCTCG 58.939 55.000 0.00 0.00 0.00 5.03
990 1576 2.330286 CTCATCATCATCGCTCAGCTC 58.670 52.381 0.00 0.00 0.00 4.09
991 1577 1.001068 CCTCATCATCATCGCTCAGCT 59.999 52.381 0.00 0.00 0.00 4.24
992 1578 1.430479 CCTCATCATCATCGCTCAGC 58.570 55.000 0.00 0.00 0.00 4.26
993 1579 1.617357 TCCCTCATCATCATCGCTCAG 59.383 52.381 0.00 0.00 0.00 3.35
994 1580 1.617357 CTCCCTCATCATCATCGCTCA 59.383 52.381 0.00 0.00 0.00 4.26
995 1581 1.672441 GCTCCCTCATCATCATCGCTC 60.672 57.143 0.00 0.00 0.00 5.03
996 1582 0.321021 GCTCCCTCATCATCATCGCT 59.679 55.000 0.00 0.00 0.00 4.93
1479 2077 3.259064 TGCAGTTAAGAATCGTGGTAGC 58.741 45.455 0.00 0.00 0.00 3.58
1481 2079 4.890088 AGTTGCAGTTAAGAATCGTGGTA 58.110 39.130 0.00 0.00 0.00 3.25
1547 2148 2.808523 TAGATGGAGCAGAGCAATCG 57.191 50.000 0.00 0.00 0.00 3.34
1602 2217 3.193267 TGTAAAGCCTGTTGATTGATGGC 59.807 43.478 0.00 0.00 43.52 4.40
1672 2287 4.021719 AGCAGTTCTTCCATGGTTGAATTG 60.022 41.667 25.11 25.11 32.02 2.32
1710 2327 5.484173 TTGCTAGTGAACAAAGACAAGTG 57.516 39.130 0.00 0.00 0.00 3.16
1730 2347 7.440255 TGCTACATATGACTGTCTCATCAATTG 59.560 37.037 10.38 0.00 40.38 2.32
1822 2440 1.607148 CATGCACATCAGGCTACATGG 59.393 52.381 9.71 1.85 33.06 3.66
1865 2503 7.066645 CCAAAAAGAACAGAGCATATGATCAGA 59.933 37.037 22.20 0.00 31.88 3.27
2028 2666 2.032528 CTCTTGTCCTTGCCGCCA 59.967 61.111 0.00 0.00 0.00 5.69
2149 2790 2.746277 GTACTGCCCCGTTGCTGG 60.746 66.667 5.52 0.00 34.81 4.85
2151 2792 2.663196 GAGTACTGCCCCGTTGCT 59.337 61.111 0.00 0.00 0.00 3.91
2322 2997 1.227147 TCGGAATGGATCGAACGGC 60.227 57.895 0.00 0.00 32.11 5.68
2349 3025 6.159988 GGCCATATTACACTAGACATCTGAC 58.840 44.000 0.00 0.00 0.00 3.51
2470 3146 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2471 3147 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2472 3148 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2473 3149 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2474 3150 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2475 3151 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2476 3152 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2477 3153 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2478 3154 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2479 3155 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2480 3156 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2481 3157 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2482 3158 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2483 3159 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2484 3160 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2485 3161 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2486 3162 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2487 3163 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2488 3164 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2489 3165 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2490 3166 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2491 3167 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
2492 3168 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
2493 3169 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
2512 3188 1.773052 AGCATCACCAGCATCATACCT 59.227 47.619 0.00 0.00 0.00 3.08
2734 3428 2.322355 AGTATGTGTGAGATGCTGCC 57.678 50.000 0.00 0.00 0.00 4.85
2764 3458 5.049612 CACCGAGATGGATGAATGAAAGATG 60.050 44.000 0.00 0.00 42.00 2.90
2768 3462 2.945008 GCACCGAGATGGATGAATGAAA 59.055 45.455 0.00 0.00 42.00 2.69
3016 3772 5.757099 TCCAGCATCATCATCATCAGTAT 57.243 39.130 0.00 0.00 0.00 2.12
3126 4037 4.039609 AGGAGTTTGGGAAAGATTTTGCAG 59.960 41.667 0.00 0.00 0.00 4.41
3142 4053 2.174685 ACAGGGCCAAAAAGGAGTTT 57.825 45.000 6.18 0.00 41.22 2.66
3143 4054 2.039418 GAACAGGGCCAAAAAGGAGTT 58.961 47.619 6.18 0.00 41.22 3.01
3201 4112 2.043115 ACGGGGATCTGCCTCATATCTA 59.957 50.000 0.00 0.00 36.72 1.98
3220 4131 2.668457 GCCATTCTCTACTGTTGTCACG 59.332 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.