Multiple sequence alignment - TraesCS4B01G279300

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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 TraesCS4B01G279300 chr4B 100.000 2222 0 0 1 2222 562437312 562435091 0.000000e+00 4104
1 TraesCS4B01G279300 chr4A 86.972 1443 105 34 137 1555 17023448 17024831 0.000000e+00 1546
2 TraesCS4B01G279300 chr4A 85.377 424 43 12 968 1380 17018278 17018693 2.640000e-114 422
3 TraesCS4B01G279300 chr4A 86.555 357 35 8 950 1296 17256563 17256916 4.480000e-102 381
4 TraesCS4B01G279300 chr4A 77.237 760 99 36 574 1318 17028146 17028846 5.790000e-101 377
5 TraesCS4B01G279300 chr4A 85.294 340 38 5 962 1291 17032592 17032929 7.600000e-90 340
6 TraesCS4B01G279300 chr4A 85.374 294 40 3 1560 1851 17024886 17025178 3.590000e-78 302
7 TraesCS4B01G279300 chr4A 84.053 301 23 13 1945 2222 17025178 17025476 1.310000e-67 267
8 TraesCS4B01G279300 chr4D 85.864 1146 94 24 430 1560 449876592 449875500 0.000000e+00 1157
9 TraesCS4B01G279300 chr4D 86.141 469 51 6 967 1425 449887554 449887090 5.510000e-136 494
10 TraesCS4B01G279300 chr4D 78.639 735 88 40 643 1362 449860247 449859567 7.330000e-115 424
11 TraesCS4B01G279300 chr4D 90.411 292 21 5 1936 2222 449875073 449874784 5.790000e-101 377
12 TraesCS4B01G279300 chr4D 91.144 271 12 5 156 422 449884306 449884044 7.550000e-95 357
13 TraesCS4B01G279300 chr4D 86.136 339 36 6 964 1294 449739434 449739099 2.710000e-94 355
14 TraesCS4B01G279300 chr4D 93.893 131 8 0 1 131 449885366 449885236 4.840000e-47 198
15 TraesCS4B01G279300 chr4D 90.141 142 12 2 1560 1699 449875457 449875316 1.360000e-42 183
16 TraesCS4B01G279300 chr4D 89.773 88 5 3 1854 1940 508008787 508008871 2.330000e-20 110
17 TraesCS4B01G279300 chr4D 87.000 100 7 4 1854 1951 26481864 26481769 8.390000e-20 108
18 TraesCS4B01G279300 chr3D 90.526 95 5 3 1854 1947 95244016 95243925 3.000000e-24 122
19 TraesCS4B01G279300 chr7D 91.209 91 4 3 1854 1943 510586344 510586431 1.080000e-23 121
20 TraesCS4B01G279300 chr7D 89.773 88 5 3 1854 1940 526495543 526495627 2.330000e-20 110
21 TraesCS4B01G279300 chr2D 87.963 108 6 6 1854 1958 602668570 602668467 1.080000e-23 121
22 TraesCS4B01G279300 chr2D 90.909 88 4 3 1854 1940 384255272 384255188 5.010000e-22 115
23 TraesCS4B01G279300 chr2B 87.255 102 7 4 1841 1940 289960894 289960797 6.490000e-21 111
24 TraesCS4B01G279300 chr2A 88.421 95 7 3 1854 1947 238002250 238002159 6.490000e-21 111


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 TraesCS4B01G279300 chr4B 562435091 562437312 2221 True 4104.000000 4104 100.000000 1 2222 1 chr4B.!!$R1 2221
1 TraesCS4B01G279300 chr4A 17023448 17032929 9481 False 566.400000 1546 83.786000 137 2222 5 chr4A.!!$F3 2085
2 TraesCS4B01G279300 chr4D 449874784 449876592 1808 True 572.333333 1157 88.805333 430 2222 3 chr4D.!!$R4 1792
3 TraesCS4B01G279300 chr4D 449859567 449860247 680 True 424.000000 424 78.639000 643 1362 1 chr4D.!!$R3 719
4 TraesCS4B01G279300 chr4D 449884044 449887554 3510 True 349.666667 494 90.392667 1 1425 3 chr4D.!!$R5 1424

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
946 973 0.098376 CCGCACCGTAGTACTCAGAC 59.902 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 2064 0.531532 GATGTGCCAGATCCTCCGTG 60.532 60.0 0.0 0.0 0.0 4.94 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 4.530581 ACACGTCACATGTGTGCA 57.469 50.000 24.63 3.51 45.78 4.57
19 20 2.310309 ACACGTCACATGTGTGCAG 58.690 52.632 24.63 15.98 45.78 4.41
20 21 0.461870 ACACGTCACATGTGTGCAGT 60.462 50.000 24.63 16.55 45.78 4.40
21 22 0.657312 CACGTCACATGTGTGCAGTT 59.343 50.000 24.63 2.93 45.25 3.16
22 23 0.937304 ACGTCACATGTGTGCAGTTC 59.063 50.000 24.63 7.60 45.25 3.01
23 24 1.220529 CGTCACATGTGTGCAGTTCT 58.779 50.000 24.63 0.00 45.25 3.01
24 25 1.599071 CGTCACATGTGTGCAGTTCTT 59.401 47.619 24.63 0.00 45.25 2.52
25 26 2.032054 CGTCACATGTGTGCAGTTCTTT 59.968 45.455 24.63 0.00 45.25 2.52
26 27 3.365832 GTCACATGTGTGCAGTTCTTTG 58.634 45.455 24.63 0.00 45.25 2.77
27 28 3.065233 GTCACATGTGTGCAGTTCTTTGA 59.935 43.478 24.63 0.00 45.25 2.69
28 29 3.884693 TCACATGTGTGCAGTTCTTTGAT 59.115 39.130 24.63 0.00 45.25 2.57
29 30 4.023792 TCACATGTGTGCAGTTCTTTGATC 60.024 41.667 24.63 0.00 45.25 2.92
30 31 3.058708 ACATGTGTGCAGTTCTTTGATCG 60.059 43.478 0.00 0.00 0.00 3.69
31 32 2.560504 TGTGTGCAGTTCTTTGATCGT 58.439 42.857 0.00 0.00 0.00 3.73
32 33 2.942376 TGTGTGCAGTTCTTTGATCGTT 59.058 40.909 0.00 0.00 0.00 3.85
33 34 3.376859 TGTGTGCAGTTCTTTGATCGTTT 59.623 39.130 0.00 0.00 0.00 3.60
34 35 3.968724 GTGTGCAGTTCTTTGATCGTTTC 59.031 43.478 0.00 0.00 0.00 2.78
35 36 3.625313 TGTGCAGTTCTTTGATCGTTTCA 59.375 39.130 0.00 0.00 0.00 2.69
36 37 4.214437 GTGCAGTTCTTTGATCGTTTCAG 58.786 43.478 0.00 0.00 35.27 3.02
37 38 3.229552 GCAGTTCTTTGATCGTTTCAGC 58.770 45.455 0.00 0.00 35.27 4.26
38 39 3.303990 GCAGTTCTTTGATCGTTTCAGCA 60.304 43.478 0.00 0.00 35.27 4.41
39 40 4.214437 CAGTTCTTTGATCGTTTCAGCAC 58.786 43.478 0.00 0.00 35.27 4.40
40 41 3.059597 AGTTCTTTGATCGTTTCAGCACG 60.060 43.478 0.00 0.00 41.78 5.34
41 42 1.798223 TCTTTGATCGTTTCAGCACGG 59.202 47.619 0.00 0.00 40.74 4.94
42 43 1.531149 CTTTGATCGTTTCAGCACGGT 59.469 47.619 0.00 0.00 40.74 4.83
43 44 2.442212 TTGATCGTTTCAGCACGGTA 57.558 45.000 0.00 0.00 40.74 4.02
44 45 2.665649 TGATCGTTTCAGCACGGTAT 57.334 45.000 0.00 0.00 40.74 2.73
45 46 2.267426 TGATCGTTTCAGCACGGTATG 58.733 47.619 0.00 0.00 40.74 2.39
46 47 2.268298 GATCGTTTCAGCACGGTATGT 58.732 47.619 0.00 0.00 40.74 2.29
47 48 3.119424 TGATCGTTTCAGCACGGTATGTA 60.119 43.478 0.00 0.00 40.74 2.29
48 49 3.513680 TCGTTTCAGCACGGTATGTAT 57.486 42.857 0.00 0.00 40.74 2.29
49 50 4.635833 TCGTTTCAGCACGGTATGTATA 57.364 40.909 0.00 0.00 40.74 1.47
50 51 4.996344 TCGTTTCAGCACGGTATGTATAA 58.004 39.130 0.00 0.00 40.74 0.98
51 52 4.799949 TCGTTTCAGCACGGTATGTATAAC 59.200 41.667 0.00 0.00 40.74 1.89
52 53 4.563580 CGTTTCAGCACGGTATGTATAACA 59.436 41.667 0.00 0.00 36.47 2.41
53 54 5.499652 CGTTTCAGCACGGTATGTATAACAC 60.500 44.000 0.00 0.00 36.47 3.32
54 55 4.722361 TCAGCACGGTATGTATAACACA 57.278 40.909 0.00 0.00 42.69 3.72
55 56 9.042563 CGTTTCAGCACGGTATGTATAACACAT 62.043 40.741 0.00 0.00 42.38 3.21
56 57 6.394025 TCAGCACGGTATGTATAACACATA 57.606 37.500 0.00 0.00 46.34 2.29
67 68 6.624352 TGTATAACACATACTCGGTACTCC 57.376 41.667 0.00 0.00 30.04 3.85
68 69 6.359804 TGTATAACACATACTCGGTACTCCT 58.640 40.000 0.00 0.00 30.04 3.69
69 70 7.508687 TGTATAACACATACTCGGTACTCCTA 58.491 38.462 0.00 0.00 30.04 2.94
70 71 6.874288 ATAACACATACTCGGTACTCCTAC 57.126 41.667 0.00 0.00 0.00 3.18
71 72 4.500499 ACACATACTCGGTACTCCTACT 57.500 45.455 0.00 0.00 0.00 2.57
72 73 5.620738 ACACATACTCGGTACTCCTACTA 57.379 43.478 0.00 0.00 0.00 1.82
73 74 5.609423 ACACATACTCGGTACTCCTACTAG 58.391 45.833 0.00 0.00 0.00 2.57
74 75 4.451774 CACATACTCGGTACTCCTACTAGC 59.548 50.000 0.00 0.00 0.00 3.42
75 76 4.347583 ACATACTCGGTACTCCTACTAGCT 59.652 45.833 0.00 0.00 0.00 3.32
76 77 5.541868 ACATACTCGGTACTCCTACTAGCTA 59.458 44.000 0.00 0.00 0.00 3.32
77 78 4.605640 ACTCGGTACTCCTACTAGCTAG 57.394 50.000 19.44 19.44 0.00 3.42
78 79 3.244181 ACTCGGTACTCCTACTAGCTAGC 60.244 52.174 20.91 6.62 0.00 3.42
79 80 2.702478 TCGGTACTCCTACTAGCTAGCA 59.298 50.000 20.91 7.12 0.00 3.49
80 81 2.807392 CGGTACTCCTACTAGCTAGCAC 59.193 54.545 20.91 1.50 0.00 4.40
81 82 3.494749 CGGTACTCCTACTAGCTAGCACT 60.495 52.174 20.91 4.08 0.00 4.40
82 83 3.816523 GGTACTCCTACTAGCTAGCACTG 59.183 52.174 20.91 8.73 0.00 3.66
83 84 2.303175 ACTCCTACTAGCTAGCACTGC 58.697 52.381 20.91 0.00 0.00 4.40
84 85 1.611491 CTCCTACTAGCTAGCACTGCC 59.389 57.143 20.91 0.00 0.00 4.85
85 86 1.063942 TCCTACTAGCTAGCACTGCCA 60.064 52.381 20.91 0.00 0.00 4.92
86 87 1.339610 CCTACTAGCTAGCACTGCCAG 59.660 57.143 20.91 5.85 0.00 4.85
87 88 2.302260 CTACTAGCTAGCACTGCCAGA 58.698 52.381 20.91 0.00 0.00 3.86
88 89 0.820871 ACTAGCTAGCACTGCCAGAC 59.179 55.000 20.91 0.00 0.00 3.51
89 90 0.820226 CTAGCTAGCACTGCCAGACA 59.180 55.000 18.83 0.00 0.00 3.41
90 91 1.411977 CTAGCTAGCACTGCCAGACAT 59.588 52.381 18.83 0.00 0.00 3.06
91 92 1.489481 AGCTAGCACTGCCAGACATA 58.511 50.000 18.83 0.00 0.00 2.29
92 93 1.411977 AGCTAGCACTGCCAGACATAG 59.588 52.381 18.83 0.00 0.00 2.23
93 94 1.863267 CTAGCACTGCCAGACATAGC 58.137 55.000 0.00 0.00 0.00 2.97
94 95 1.137675 CTAGCACTGCCAGACATAGCA 59.862 52.381 0.00 0.00 37.46 3.49
99 100 3.441244 TGCCAGACATAGCAGAACG 57.559 52.632 0.00 0.00 33.08 3.95
100 101 0.740868 TGCCAGACATAGCAGAACGC 60.741 55.000 0.00 0.00 42.91 4.84
109 110 2.738521 GCAGAACGCGGCTCAGAA 60.739 61.111 12.47 0.00 32.15 3.02
110 111 2.317609 GCAGAACGCGGCTCAGAAA 61.318 57.895 12.47 0.00 32.15 2.52
111 112 1.493311 CAGAACGCGGCTCAGAAAC 59.507 57.895 12.47 0.00 0.00 2.78
112 113 2.022129 AGAACGCGGCTCAGAAACG 61.022 57.895 12.47 0.00 0.00 3.60
113 114 2.279918 AACGCGGCTCAGAAACGT 60.280 55.556 12.47 0.00 38.88 3.99
114 115 2.211761 GAACGCGGCTCAGAAACGTC 62.212 60.000 12.47 0.00 35.64 4.34
115 116 2.430921 CGCGGCTCAGAAACGTCT 60.431 61.111 0.00 0.00 32.85 4.18
116 117 2.022129 CGCGGCTCAGAAACGTCTT 61.022 57.895 0.00 0.00 28.78 3.01
117 118 1.557443 CGCGGCTCAGAAACGTCTTT 61.557 55.000 0.00 0.00 28.78 2.52
118 119 1.425412 GCGGCTCAGAAACGTCTTTA 58.575 50.000 0.00 0.00 28.78 1.85
119 120 2.000447 GCGGCTCAGAAACGTCTTTAT 59.000 47.619 0.00 0.00 28.78 1.40
120 121 2.415512 GCGGCTCAGAAACGTCTTTATT 59.584 45.455 0.00 0.00 28.78 1.40
121 122 3.120304 GCGGCTCAGAAACGTCTTTATTT 60.120 43.478 0.00 0.00 28.78 1.40
122 123 4.092383 GCGGCTCAGAAACGTCTTTATTTA 59.908 41.667 0.00 0.00 28.78 1.40
123 124 5.548250 CGGCTCAGAAACGTCTTTATTTAC 58.452 41.667 0.00 0.00 28.78 2.01
124 125 5.119588 CGGCTCAGAAACGTCTTTATTTACA 59.880 40.000 0.00 0.00 28.78 2.41
125 126 6.304882 GGCTCAGAAACGTCTTTATTTACAC 58.695 40.000 0.00 0.00 28.78 2.90
126 127 6.073440 GGCTCAGAAACGTCTTTATTTACACA 60.073 38.462 0.00 0.00 28.78 3.72
127 128 6.790825 GCTCAGAAACGTCTTTATTTACACAC 59.209 38.462 0.00 0.00 28.78 3.82
128 129 7.517734 GCTCAGAAACGTCTTTATTTACACACA 60.518 37.037 0.00 0.00 28.78 3.72
129 130 7.623770 TCAGAAACGTCTTTATTTACACACAC 58.376 34.615 0.00 0.00 28.78 3.82
130 131 7.278203 TCAGAAACGTCTTTATTTACACACACA 59.722 33.333 0.00 0.00 28.78 3.72
131 132 7.906010 CAGAAACGTCTTTATTTACACACACAA 59.094 33.333 0.00 0.00 28.78 3.33
132 133 8.452534 AGAAACGTCTTTATTTACACACACAAA 58.547 29.630 0.00 0.00 0.00 2.83
133 134 8.967552 AAACGTCTTTATTTACACACACAAAA 57.032 26.923 0.00 0.00 0.00 2.44
134 135 8.967552 AACGTCTTTATTTACACACACAAAAA 57.032 26.923 0.00 0.00 0.00 1.94
186 187 7.466746 AAAAGGTCAAACATATATGTGCACT 57.533 32.000 18.94 10.22 41.61 4.40
197 198 4.662468 ATATGTGCACTAGTGAGGAGTG 57.338 45.455 27.08 0.39 45.90 3.51
204 205 2.088423 ACTAGTGAGGAGTGAAGAGCG 58.912 52.381 0.00 0.00 0.00 5.03
206 207 2.201921 AGTGAGGAGTGAAGAGCGTA 57.798 50.000 0.00 0.00 0.00 4.42
257 265 3.431856 CATGCATGCATATATCAACGGC 58.568 45.455 31.73 0.00 34.91 5.68
272 284 0.104304 ACGGCGAGTTCACATATCCC 59.896 55.000 16.62 0.00 0.00 3.85
274 286 1.869754 CGGCGAGTTCACATATCCCAG 60.870 57.143 0.00 0.00 0.00 4.45
275 287 1.221414 GCGAGTTCACATATCCCAGC 58.779 55.000 0.00 0.00 0.00 4.85
334 346 2.671914 GCACACCTACGTACAATTCGGA 60.672 50.000 3.52 0.00 0.00 4.55
339 351 3.181483 ACCTACGTACAATTCGGATGGAC 60.181 47.826 3.52 0.00 0.00 4.02
341 353 1.551430 ACGTACAATTCGGATGGACCA 59.449 47.619 0.00 0.00 38.90 4.02
351 363 0.605319 GGATGGACCAAACGTGAGCA 60.605 55.000 0.00 0.00 38.79 4.26
356 368 1.812571 GGACCAAACGTGAGCATGAAT 59.187 47.619 0.00 0.00 0.00 2.57
361 373 4.158384 CCAAACGTGAGCATGAATGTTAC 58.842 43.478 0.00 0.00 0.00 2.50
395 407 3.896648 ACAATGTTGAATCGTGTGACC 57.103 42.857 0.00 0.00 0.00 4.02
420 432 7.255730 CCAAGACCAAAAAGACTGAGAATGAAT 60.256 37.037 0.00 0.00 0.00 2.57
423 435 9.354673 AGACCAAAAAGACTGAGAATGAATTAA 57.645 29.630 0.00 0.00 0.00 1.40
425 437 8.076178 ACCAAAAAGACTGAGAATGAATTAACG 58.924 33.333 0.00 0.00 0.00 3.18
468 480 4.665833 ATAAGCTCGGTACATGCTTGTA 57.334 40.909 21.42 8.29 43.89 2.41
491 503 9.665719 TGTACATGACTTGATTAAGCTTGATTA 57.334 29.630 9.86 0.00 37.43 1.75
500 512 7.268199 TGATTAAGCTTGATTAATGAGCTGG 57.732 36.000 18.64 0.00 45.42 4.85
503 515 5.831702 AAGCTTGATTAATGAGCTGGAAG 57.168 39.130 18.64 0.00 45.42 3.46
506 518 4.397417 GCTTGATTAATGAGCTGGAAGTGT 59.603 41.667 11.38 0.00 35.30 3.55
520 532 4.606210 TGGAAGTGTAGCACTATAGGTCA 58.394 43.478 4.43 0.00 44.62 4.02
546 558 2.708325 AGTGGCCTAATTGATCTCCTCC 59.292 50.000 3.32 0.00 0.00 4.30
548 560 3.904339 GTGGCCTAATTGATCTCCTCCTA 59.096 47.826 3.32 0.00 0.00 2.94
555 567 4.906747 ATTGATCTCCTCCTAATGCTCC 57.093 45.455 0.00 0.00 0.00 4.70
570 582 3.769739 TGCTCCATGTTGAACAGTACT 57.230 42.857 3.74 0.00 0.00 2.73
571 583 4.085357 TGCTCCATGTTGAACAGTACTT 57.915 40.909 3.74 0.00 0.00 2.24
572 584 3.814842 TGCTCCATGTTGAACAGTACTTG 59.185 43.478 3.74 0.00 0.00 3.16
590 604 5.830000 ACTTGGTGTTCAAACTTAAGGAC 57.170 39.130 7.53 0.00 34.56 3.85
602 617 0.912487 TTAAGGACATGGACCGGGCT 60.912 55.000 7.57 0.00 0.00 5.19
610 625 4.097361 GGACCGGGCTGAGAACCC 62.097 72.222 7.57 0.00 44.63 4.11
620 635 0.537188 CTGAGAACCCCGTAGCATGT 59.463 55.000 0.00 0.00 0.00 3.21
623 638 3.568443 TGAGAACCCCGTAGCATGTATA 58.432 45.455 0.00 0.00 0.00 1.47
629 644 1.674611 CCGTAGCATGTATAGCGCGC 61.675 60.000 26.66 26.66 37.01 6.86
663 678 3.725754 TGGCTGGACCAGAGAAAAC 57.274 52.632 26.25 5.83 46.36 2.43
673 689 2.695147 ACCAGAGAAAACCAAGCCAAAG 59.305 45.455 0.00 0.00 0.00 2.77
676 692 4.363138 CAGAGAAAACCAAGCCAAAGAAC 58.637 43.478 0.00 0.00 0.00 3.01
684 700 3.074412 CCAAGCCAAAGAACACGACTAT 58.926 45.455 0.00 0.00 0.00 2.12
700 716 6.818644 ACACGACTATTACTGCAATCTGAATT 59.181 34.615 0.00 0.00 0.00 2.17
715 733 6.582677 ATCTGAATTATAGACCAGGTCTCG 57.417 41.667 26.42 7.42 42.40 4.04
727 746 1.403679 CAGGTCTCGTCTCCATCAGTC 59.596 57.143 0.00 0.00 0.00 3.51
732 751 2.489722 TCTCGTCTCCATCAGTCTGTTG 59.510 50.000 0.00 1.69 0.00 3.33
747 766 4.950050 GTCTGTTGGACTTTTCTCTCTCA 58.050 43.478 0.00 0.00 41.46 3.27
748 767 5.360591 GTCTGTTGGACTTTTCTCTCTCAA 58.639 41.667 0.00 0.00 41.46 3.02
749 768 5.465056 GTCTGTTGGACTTTTCTCTCTCAAG 59.535 44.000 0.00 0.00 41.46 3.02
750 769 4.708177 TGTTGGACTTTTCTCTCTCAAGG 58.292 43.478 0.00 0.00 0.00 3.61
751 770 3.409026 TGGACTTTTCTCTCTCAAGGC 57.591 47.619 0.00 0.00 0.00 4.35
759 778 1.898472 TCTCTCTCAAGGCTCAACCAG 59.102 52.381 0.00 0.00 43.14 4.00
760 779 0.979665 TCTCTCAAGGCTCAACCAGG 59.020 55.000 0.00 0.00 43.14 4.45
783 803 1.927210 CGCACGCAGCAACCTATAG 59.073 57.895 0.00 0.00 46.13 1.31
813 833 1.293458 ACCATCCTGTCTCTCCTCCAT 59.707 52.381 0.00 0.00 0.00 3.41
862 889 2.267642 CCATTCGCCGTTCCTCCA 59.732 61.111 0.00 0.00 0.00 3.86
863 890 1.376683 CCATTCGCCGTTCCTCCAA 60.377 57.895 0.00 0.00 0.00 3.53
864 891 1.369091 CCATTCGCCGTTCCTCCAAG 61.369 60.000 0.00 0.00 0.00 3.61
865 892 1.078426 ATTCGCCGTTCCTCCAAGG 60.078 57.895 0.00 0.00 36.46 3.61
866 893 3.894547 TTCGCCGTTCCTCCAAGGC 62.895 63.158 0.00 0.00 45.67 4.35
867 894 4.394712 CGCCGTTCCTCCAAGGCT 62.395 66.667 3.77 0.00 46.85 4.58
868 895 2.436824 GCCGTTCCTCCAAGGCTC 60.437 66.667 0.00 0.00 45.67 4.70
869 896 2.269241 CCGTTCCTCCAAGGCTCC 59.731 66.667 0.00 0.00 34.61 4.70
877 904 2.359975 CCAAGGCTCCAACGGACC 60.360 66.667 0.00 0.00 0.00 4.46
881 908 1.551019 AAGGCTCCAACGGACCTACC 61.551 60.000 0.00 0.00 34.05 3.18
885 912 0.745468 CTCCAACGGACCTACCTAGC 59.255 60.000 0.00 0.00 36.31 3.42
903 930 1.744368 CGCTCAGCCTGTCTGCAAT 60.744 57.895 0.00 0.00 42.56 3.56
930 957 0.098728 CAACAAATCCGTCCATCCGC 59.901 55.000 0.00 0.00 0.00 5.54
933 960 1.451387 AAATCCGTCCATCCGCACC 60.451 57.895 0.00 0.00 0.00 5.01
934 961 3.733344 AATCCGTCCATCCGCACCG 62.733 63.158 0.00 0.00 0.00 4.94
936 963 3.829044 CCGTCCATCCGCACCGTA 61.829 66.667 0.00 0.00 0.00 4.02
943 970 0.736636 CATCCGCACCGTAGTACTCA 59.263 55.000 0.00 0.00 0.00 3.41
946 973 0.098376 CCGCACCGTAGTACTCAGAC 59.902 60.000 0.00 0.00 0.00 3.51
947 974 1.085091 CGCACCGTAGTACTCAGACT 58.915 55.000 0.00 0.00 0.00 3.24
948 975 1.202043 CGCACCGTAGTACTCAGACTG 60.202 57.143 0.00 0.00 0.00 3.51
954 981 4.193090 CCGTAGTACTCAGACTGTCAGAT 58.807 47.826 10.88 1.27 0.00 2.90
955 982 5.105023 ACCGTAGTACTCAGACTGTCAGATA 60.105 44.000 10.88 0.40 0.00 1.98
956 983 5.234757 CCGTAGTACTCAGACTGTCAGATAC 59.765 48.000 10.88 11.14 0.00 2.24
957 984 5.234757 CGTAGTACTCAGACTGTCAGATACC 59.765 48.000 10.88 0.00 0.00 2.73
958 985 4.193090 AGTACTCAGACTGTCAGATACCG 58.807 47.826 10.88 0.00 0.00 4.02
959 986 3.351794 ACTCAGACTGTCAGATACCGA 57.648 47.619 10.88 0.00 0.00 4.69
1032 1059 4.697756 GTGGTGGCCGTGCTGCTA 62.698 66.667 0.00 0.00 0.00 3.49
1365 1416 2.222227 ATTTTGGAGCCCTGGAGTTC 57.778 50.000 0.00 0.00 0.00 3.01
1367 1418 0.401738 TTTGGAGCCCTGGAGTTCTG 59.598 55.000 0.00 0.00 0.00 3.02
1400 1458 6.370718 AGTTAGTTTTAGTACAGGGATTTGCG 59.629 38.462 0.00 0.00 0.00 4.85
1417 1476 3.592898 TGCGATAAAGCAGTCTCAGAA 57.407 42.857 0.00 0.00 42.92 3.02
1425 1484 3.162147 AGCAGTCTCAGAAGTAGGTCA 57.838 47.619 0.00 0.00 0.00 4.02
1431 1525 6.559810 CAGTCTCAGAAGTAGGTCATGTAAG 58.440 44.000 0.00 0.00 0.00 2.34
1443 1537 7.980099 AGTAGGTCATGTAAGCAAGTTGTATAC 59.020 37.037 4.48 8.64 0.00 1.47
1547 1644 9.424319 GTCTGAAGACATAATTTGAGTAAGTCA 57.576 33.333 5.58 0.00 44.18 3.41
1555 1652 8.576442 ACATAATTTGAGTAAGTCAACTTTGGG 58.424 33.333 0.00 0.00 45.23 4.12
1556 1653 8.792633 CATAATTTGAGTAAGTCAACTTTGGGA 58.207 33.333 0.00 0.00 45.23 4.37
1557 1654 6.884280 ATTTGAGTAAGTCAACTTTGGGAG 57.116 37.500 0.00 0.00 45.23 4.30
1558 1655 5.623956 TTGAGTAAGTCAACTTTGGGAGA 57.376 39.130 0.00 0.00 40.45 3.71
1564 1711 0.984230 TCAACTTTGGGAGAGGCGAT 59.016 50.000 0.00 0.00 0.00 4.58
1642 1790 5.435686 TGATATCTGTAGGCTTTGTGGTT 57.564 39.130 3.98 0.00 0.00 3.67
1657 1806 2.293122 TGTGGTTGAAGGCGAGAAATTG 59.707 45.455 0.00 0.00 0.00 2.32
1705 1854 4.394712 GGAGGTGTGGCACGGGAG 62.395 72.222 13.77 0.00 34.83 4.30
1707 1856 2.847234 AGGTGTGGCACGGGAGAA 60.847 61.111 13.77 0.00 34.83 2.87
1709 1858 2.426023 GTGTGGCACGGGAGAAGT 59.574 61.111 13.77 0.00 0.00 3.01
1712 1861 1.374758 GTGGCACGGGAGAAGTGAG 60.375 63.158 0.00 0.00 41.83 3.51
1719 1868 0.036010 CGGGAGAAGTGAGGCATTGT 60.036 55.000 0.00 0.00 0.00 2.71
1738 1887 1.474077 GTTGCATGCCTAGGTTGAAGG 59.526 52.381 16.68 0.00 37.17 3.46
1743 1892 3.433598 GCATGCCTAGGTTGAAGGACATA 60.434 47.826 11.31 0.00 36.08 2.29
1753 1902 9.319143 CTAGGTTGAAGGACATAAAGAATACTG 57.681 37.037 0.00 0.00 0.00 2.74
1756 1997 7.775561 GGTTGAAGGACATAAAGAATACTGGAT 59.224 37.037 0.00 0.00 0.00 3.41
1771 2012 9.790344 AGAATACTGGATTAGAATGATTTCTGG 57.210 33.333 0.00 0.00 42.25 3.86
1789 2030 1.338105 TGGACCTCTTCAGACAATGCG 60.338 52.381 0.00 0.00 0.00 4.73
1813 2054 3.265221 TGATGATGAATGGCTCCCTATCC 59.735 47.826 0.00 0.00 0.00 2.59
1823 2064 1.271102 GCTCCCTATCCTGATGACGTC 59.729 57.143 9.11 9.11 0.00 4.34
1825 2066 2.294791 CTCCCTATCCTGATGACGTCAC 59.705 54.545 22.71 15.11 32.22 3.67
1844 2085 1.689243 CGGAGGATCTGGCACATCCA 61.689 60.000 21.73 0.00 42.28 3.41
1853 2094 2.240414 TCTGGCACATCCACAATGAGAT 59.760 45.455 0.00 0.00 40.72 2.75
1854 2095 3.455543 TCTGGCACATCCACAATGAGATA 59.544 43.478 0.00 0.00 40.72 1.98
1855 2096 3.544684 TGGCACATCCACAATGAGATAC 58.455 45.455 0.00 0.00 40.72 2.24
1856 2097 3.200605 TGGCACATCCACAATGAGATACT 59.799 43.478 0.00 0.00 40.72 2.12
1857 2098 3.812053 GGCACATCCACAATGAGATACTC 59.188 47.826 0.00 0.00 38.83 2.59
1858 2099 3.812053 GCACATCCACAATGAGATACTCC 59.188 47.826 0.00 0.00 38.83 3.85
1859 2100 4.444022 GCACATCCACAATGAGATACTCCT 60.444 45.833 0.00 0.00 38.83 3.69
1860 2101 5.295950 CACATCCACAATGAGATACTCCTC 58.704 45.833 0.00 0.00 38.83 3.71
1861 2102 4.346418 ACATCCACAATGAGATACTCCTCC 59.654 45.833 0.00 0.00 38.83 4.30
1862 2103 2.959030 TCCACAATGAGATACTCCTCCG 59.041 50.000 0.00 0.00 32.32 4.63
1863 2104 2.695666 CCACAATGAGATACTCCTCCGT 59.304 50.000 0.00 0.00 32.32 4.69
1864 2105 3.889538 CCACAATGAGATACTCCTCCGTA 59.110 47.826 0.00 0.00 32.32 4.02
1865 2106 4.341235 CCACAATGAGATACTCCTCCGTAA 59.659 45.833 0.00 0.00 32.32 3.18
1866 2107 5.163447 CCACAATGAGATACTCCTCCGTAAA 60.163 44.000 0.00 0.00 32.32 2.01
1867 2108 5.749109 CACAATGAGATACTCCTCCGTAAAC 59.251 44.000 0.00 0.00 32.32 2.01
1868 2109 5.657302 ACAATGAGATACTCCTCCGTAAACT 59.343 40.000 0.00 0.00 32.32 2.66
1869 2110 6.832384 ACAATGAGATACTCCTCCGTAAACTA 59.168 38.462 0.00 0.00 32.32 2.24
1870 2111 7.341256 ACAATGAGATACTCCTCCGTAAACTAA 59.659 37.037 0.00 0.00 32.32 2.24
1871 2112 8.361139 CAATGAGATACTCCTCCGTAAACTAAT 58.639 37.037 0.00 0.00 32.32 1.73
1872 2113 9.584008 AATGAGATACTCCTCCGTAAACTAATA 57.416 33.333 0.00 0.00 32.32 0.98
1873 2114 9.756571 ATGAGATACTCCTCCGTAAACTAATAT 57.243 33.333 0.00 0.00 32.32 1.28
1880 2121 8.348507 ACTCCTCCGTAAACTAATATAAGAACG 58.651 37.037 0.00 0.00 0.00 3.95
1881 2122 8.225603 TCCTCCGTAAACTAATATAAGAACGT 57.774 34.615 0.00 0.00 0.00 3.99
1882 2123 8.686334 TCCTCCGTAAACTAATATAAGAACGTT 58.314 33.333 0.00 0.00 0.00 3.99
1883 2124 9.305925 CCTCCGTAAACTAATATAAGAACGTTT 57.694 33.333 0.46 0.00 0.00 3.60
1898 2139 7.653767 AAGAACGTTTAGATCACCACTAAAG 57.346 36.000 0.46 0.00 39.45 1.85
1899 2140 6.756221 AGAACGTTTAGATCACCACTAAAGT 58.244 36.000 0.46 0.00 39.45 2.66
1900 2141 7.889469 AGAACGTTTAGATCACCACTAAAGTA 58.111 34.615 0.46 0.00 39.45 2.24
1901 2142 8.362639 AGAACGTTTAGATCACCACTAAAGTAA 58.637 33.333 0.46 0.00 39.45 2.24
1902 2143 9.148104 GAACGTTTAGATCACCACTAAAGTAAT 57.852 33.333 0.46 0.00 39.45 1.89
1903 2144 8.475331 ACGTTTAGATCACCACTAAAGTAATG 57.525 34.615 0.00 0.00 39.45 1.90
1904 2145 8.308931 ACGTTTAGATCACCACTAAAGTAATGA 58.691 33.333 0.00 0.00 39.45 2.57
1905 2146 9.314321 CGTTTAGATCACCACTAAAGTAATGAT 57.686 33.333 7.61 7.61 39.45 2.45
1912 2153 8.697846 TCACCACTAAAGTAATGATCTAAACG 57.302 34.615 0.00 0.00 0.00 3.60
1913 2154 7.277098 TCACCACTAAAGTAATGATCTAAACGC 59.723 37.037 0.00 0.00 0.00 4.84
1914 2155 7.277981 CACCACTAAAGTAATGATCTAAACGCT 59.722 37.037 0.00 0.00 0.00 5.07
1915 2156 7.491696 ACCACTAAAGTAATGATCTAAACGCTC 59.508 37.037 0.00 0.00 0.00 5.03
1916 2157 7.707035 CCACTAAAGTAATGATCTAAACGCTCT 59.293 37.037 0.00 0.00 0.00 4.09
1917 2158 8.535592 CACTAAAGTAATGATCTAAACGCTCTG 58.464 37.037 0.00 0.00 0.00 3.35
1918 2159 8.467598 ACTAAAGTAATGATCTAAACGCTCTGA 58.532 33.333 0.00 0.00 0.00 3.27
1919 2160 9.469807 CTAAAGTAATGATCTAAACGCTCTGAT 57.530 33.333 0.00 0.00 0.00 2.90
1921 2162 9.988815 AAAGTAATGATCTAAACGCTCTGATAT 57.011 29.630 0.00 0.00 0.00 1.63
1922 2163 9.988815 AAGTAATGATCTAAACGCTCTGATATT 57.011 29.630 0.00 0.00 0.00 1.28
1926 2167 9.988815 AATGATCTAAACGCTCTGATATTAGTT 57.011 29.630 0.00 0.00 0.00 2.24
1927 2168 9.988815 ATGATCTAAACGCTCTGATATTAGTTT 57.011 29.630 0.00 0.00 36.11 2.66
1934 2175 9.915629 AAACGCTCTGATATTAGTTTATAGAGG 57.084 33.333 0.00 0.00 32.83 3.69
1935 2176 8.057536 ACGCTCTGATATTAGTTTATAGAGGG 57.942 38.462 0.00 0.00 44.40 4.30
1936 2177 7.889073 ACGCTCTGATATTAGTTTATAGAGGGA 59.111 37.037 18.20 0.00 42.69 4.20
1937 2178 8.402472 CGCTCTGATATTAGTTTATAGAGGGAG 58.598 40.741 0.00 0.00 42.69 4.30
2008 2249 4.957954 ACCTTCCACTTGTATGGTCGTATA 59.042 41.667 0.00 0.00 40.95 1.47
2011 2252 4.212716 TCCACTTGTATGGTCGTATAGCT 58.787 43.478 0.00 0.00 40.95 3.32
2012 2253 4.277672 TCCACTTGTATGGTCGTATAGCTC 59.722 45.833 0.00 0.00 40.95 4.09
2030 2272 2.733956 CTCTCTAGCTTGGACCAGACT 58.266 52.381 0.00 0.00 0.00 3.24
2172 2440 3.197790 CGGAGACAATGCGGCTGG 61.198 66.667 0.00 0.00 39.39 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.058708 CGATCAAAGAACTGCACACATGT 60.059 43.478 0.00 0.00 0.00 3.21
9 10 3.058708 ACGATCAAAGAACTGCACACATG 60.059 43.478 0.00 0.00 0.00 3.21
10 11 3.141398 ACGATCAAAGAACTGCACACAT 58.859 40.909 0.00 0.00 0.00 3.21
11 12 2.560504 ACGATCAAAGAACTGCACACA 58.439 42.857 0.00 0.00 0.00 3.72
12 13 3.609103 AACGATCAAAGAACTGCACAC 57.391 42.857 0.00 0.00 0.00 3.82
13 14 3.625313 TGAAACGATCAAAGAACTGCACA 59.375 39.130 0.00 0.00 34.30 4.57
14 15 4.209452 TGAAACGATCAAAGAACTGCAC 57.791 40.909 0.00 0.00 34.30 4.57
15 16 3.303990 GCTGAAACGATCAAAGAACTGCA 60.304 43.478 0.00 0.00 37.67 4.41
16 17 3.229552 GCTGAAACGATCAAAGAACTGC 58.770 45.455 0.00 0.00 37.67 4.40
17 18 4.214437 GTGCTGAAACGATCAAAGAACTG 58.786 43.478 0.00 0.00 37.67 3.16
18 19 3.059597 CGTGCTGAAACGATCAAAGAACT 60.060 43.478 0.00 0.00 46.49 3.01
19 20 3.218398 CGTGCTGAAACGATCAAAGAAC 58.782 45.455 0.00 0.00 46.49 3.01
20 21 2.223144 CCGTGCTGAAACGATCAAAGAA 59.777 45.455 5.09 0.00 46.49 2.52
21 22 1.798223 CCGTGCTGAAACGATCAAAGA 59.202 47.619 5.09 0.00 46.49 2.52
22 23 1.531149 ACCGTGCTGAAACGATCAAAG 59.469 47.619 5.09 0.00 46.49 2.77
23 24 1.588674 ACCGTGCTGAAACGATCAAA 58.411 45.000 5.09 0.00 46.49 2.69
24 25 2.442212 TACCGTGCTGAAACGATCAA 57.558 45.000 5.09 0.00 46.49 2.57
25 26 2.267426 CATACCGTGCTGAAACGATCA 58.733 47.619 5.09 0.00 46.49 2.92
26 27 2.268298 ACATACCGTGCTGAAACGATC 58.732 47.619 5.09 0.00 46.49 3.69
27 28 2.380084 ACATACCGTGCTGAAACGAT 57.620 45.000 5.09 0.00 46.49 3.73
28 29 3.513680 ATACATACCGTGCTGAAACGA 57.486 42.857 5.09 0.00 46.49 3.85
29 30 4.563580 TGTTATACATACCGTGCTGAAACG 59.436 41.667 0.00 0.00 43.20 3.60
30 31 5.349270 TGTGTTATACATACCGTGCTGAAAC 59.651 40.000 0.00 0.00 33.42 2.78
31 32 5.480205 TGTGTTATACATACCGTGCTGAAA 58.520 37.500 0.00 0.00 33.42 2.69
32 33 5.074584 TGTGTTATACATACCGTGCTGAA 57.925 39.130 0.00 0.00 33.42 3.02
33 34 4.722361 TGTGTTATACATACCGTGCTGA 57.278 40.909 0.00 0.00 33.42 4.26
42 43 8.159447 AGGAGTACCGAGTATGTGTTATACATA 58.841 37.037 0.00 0.00 43.74 2.29
43 44 7.002879 AGGAGTACCGAGTATGTGTTATACAT 58.997 38.462 0.00 0.00 45.65 2.29
44 45 6.359804 AGGAGTACCGAGTATGTGTTATACA 58.640 40.000 0.00 0.00 41.80 2.29
45 46 6.874288 AGGAGTACCGAGTATGTGTTATAC 57.126 41.667 0.00 0.00 41.83 1.47
46 47 7.739825 AGTAGGAGTACCGAGTATGTGTTATA 58.260 38.462 0.00 0.00 41.83 0.98
47 48 6.599445 AGTAGGAGTACCGAGTATGTGTTAT 58.401 40.000 0.00 0.00 41.83 1.89
48 49 5.994250 AGTAGGAGTACCGAGTATGTGTTA 58.006 41.667 0.00 0.00 41.83 2.41
49 50 4.853007 AGTAGGAGTACCGAGTATGTGTT 58.147 43.478 0.00 0.00 41.83 3.32
50 51 4.500499 AGTAGGAGTACCGAGTATGTGT 57.500 45.455 0.00 0.00 41.83 3.72
51 52 4.451774 GCTAGTAGGAGTACCGAGTATGTG 59.548 50.000 0.00 0.00 41.83 3.21
52 53 4.347583 AGCTAGTAGGAGTACCGAGTATGT 59.652 45.833 0.00 0.00 41.83 2.29
53 54 4.897140 AGCTAGTAGGAGTACCGAGTATG 58.103 47.826 0.00 0.00 41.83 2.39
54 55 5.337491 GCTAGCTAGTAGGAGTACCGAGTAT 60.337 48.000 21.62 0.00 41.83 2.12
55 56 4.021544 GCTAGCTAGTAGGAGTACCGAGTA 60.022 50.000 21.62 0.00 41.83 2.59
56 57 3.244181 GCTAGCTAGTAGGAGTACCGAGT 60.244 52.174 21.62 0.00 41.83 4.18
57 58 3.244146 TGCTAGCTAGTAGGAGTACCGAG 60.244 52.174 21.62 0.00 41.83 4.63
58 59 2.702478 TGCTAGCTAGTAGGAGTACCGA 59.298 50.000 21.62 0.00 41.83 4.69
59 60 2.807392 GTGCTAGCTAGTAGGAGTACCG 59.193 54.545 21.62 0.00 41.83 4.02
60 61 3.816523 CAGTGCTAGCTAGTAGGAGTACC 59.183 52.174 21.62 4.13 31.19 3.34
61 62 3.251487 GCAGTGCTAGCTAGTAGGAGTAC 59.749 52.174 21.62 7.30 31.19 2.73
62 63 3.478509 GCAGTGCTAGCTAGTAGGAGTA 58.521 50.000 21.62 0.00 31.19 2.59
63 64 2.303175 GCAGTGCTAGCTAGTAGGAGT 58.697 52.381 21.62 0.01 33.12 3.85
64 65 1.611491 GGCAGTGCTAGCTAGTAGGAG 59.389 57.143 21.62 10.87 27.92 3.69
65 66 1.063942 TGGCAGTGCTAGCTAGTAGGA 60.064 52.381 21.62 0.00 0.00 2.94
66 67 1.339610 CTGGCAGTGCTAGCTAGTAGG 59.660 57.143 21.62 13.20 36.05 3.18
67 68 2.034053 GTCTGGCAGTGCTAGCTAGTAG 59.966 54.545 22.70 8.05 40.88 2.57
68 69 2.025155 GTCTGGCAGTGCTAGCTAGTA 58.975 52.381 22.70 15.16 40.88 1.82
69 70 0.820871 GTCTGGCAGTGCTAGCTAGT 59.179 55.000 22.70 2.46 40.88 2.57
70 71 0.820226 TGTCTGGCAGTGCTAGCTAG 59.180 55.000 22.70 16.84 41.36 3.42
71 72 1.489481 ATGTCTGGCAGTGCTAGCTA 58.511 50.000 22.70 14.12 37.07 3.32
72 73 1.411977 CTATGTCTGGCAGTGCTAGCT 59.588 52.381 22.70 12.31 37.07 3.32
73 74 1.863267 CTATGTCTGGCAGTGCTAGC 58.137 55.000 22.70 17.42 37.07 3.42
74 75 1.137675 TGCTATGTCTGGCAGTGCTAG 59.862 52.381 21.63 21.63 38.51 3.42
75 76 1.194218 TGCTATGTCTGGCAGTGCTA 58.806 50.000 16.11 8.29 33.43 3.49
76 77 1.985614 TGCTATGTCTGGCAGTGCT 59.014 52.632 16.11 2.67 33.43 4.40
77 78 4.623814 TGCTATGTCTGGCAGTGC 57.376 55.556 15.27 6.55 33.43 4.40
81 82 0.740868 GCGTTCTGCTATGTCTGGCA 60.741 55.000 0.00 0.00 41.73 4.92
82 83 1.756375 CGCGTTCTGCTATGTCTGGC 61.756 60.000 0.00 0.00 43.27 4.85
83 84 1.148157 CCGCGTTCTGCTATGTCTGG 61.148 60.000 4.92 0.00 43.27 3.86
84 85 1.756375 GCCGCGTTCTGCTATGTCTG 61.756 60.000 4.92 0.00 43.27 3.51
85 86 1.519455 GCCGCGTTCTGCTATGTCT 60.519 57.895 4.92 0.00 43.27 3.41
86 87 1.483424 GAGCCGCGTTCTGCTATGTC 61.483 60.000 4.92 0.00 43.27 3.06
87 88 1.519455 GAGCCGCGTTCTGCTATGT 60.519 57.895 4.92 0.00 43.27 2.29
88 89 1.485838 CTGAGCCGCGTTCTGCTATG 61.486 60.000 4.92 0.00 43.27 2.23
89 90 1.227089 CTGAGCCGCGTTCTGCTAT 60.227 57.895 4.92 0.00 43.27 2.97
90 91 1.873270 TTCTGAGCCGCGTTCTGCTA 61.873 55.000 4.92 0.00 43.27 3.49
91 92 2.715532 TTTCTGAGCCGCGTTCTGCT 62.716 55.000 7.32 7.32 43.27 4.24
92 93 2.317609 TTTCTGAGCCGCGTTCTGC 61.318 57.895 4.92 0.00 41.47 4.26
93 94 1.493311 GTTTCTGAGCCGCGTTCTG 59.507 57.895 4.92 6.88 0.00 3.02
94 95 2.022129 CGTTTCTGAGCCGCGTTCT 61.022 57.895 4.92 0.63 0.00 3.01
95 96 2.211761 GACGTTTCTGAGCCGCGTTC 62.212 60.000 4.92 2.77 35.86 3.95
96 97 2.279918 ACGTTTCTGAGCCGCGTT 60.280 55.556 4.92 0.00 31.37 4.84
97 98 2.694829 AAGACGTTTCTGAGCCGCGT 62.695 55.000 4.92 0.00 38.55 6.01
98 99 1.557443 AAAGACGTTTCTGAGCCGCG 61.557 55.000 0.00 0.00 29.98 6.46
99 100 1.425412 TAAAGACGTTTCTGAGCCGC 58.575 50.000 0.00 0.00 29.98 6.53
100 101 4.663636 AAATAAAGACGTTTCTGAGCCG 57.336 40.909 0.00 0.00 29.98 5.52
101 102 6.073440 TGTGTAAATAAAGACGTTTCTGAGCC 60.073 38.462 0.00 0.00 29.98 4.70
102 103 6.790825 GTGTGTAAATAAAGACGTTTCTGAGC 59.209 38.462 0.00 0.00 29.98 4.26
103 104 7.792508 GTGTGTGTAAATAAAGACGTTTCTGAG 59.207 37.037 0.00 0.00 29.98 3.35
104 105 7.278203 TGTGTGTGTAAATAAAGACGTTTCTGA 59.722 33.333 0.00 0.00 29.98 3.27
105 106 7.403421 TGTGTGTGTAAATAAAGACGTTTCTG 58.597 34.615 0.00 0.00 29.98 3.02
106 107 7.542534 TGTGTGTGTAAATAAAGACGTTTCT 57.457 32.000 0.00 0.00 0.00 2.52
107 108 8.603983 TTTGTGTGTGTAAATAAAGACGTTTC 57.396 30.769 0.00 0.00 0.00 2.78
108 109 8.967552 TTTTGTGTGTGTAAATAAAGACGTTT 57.032 26.923 0.00 0.00 0.00 3.60
109 110 8.967552 TTTTTGTGTGTGTAAATAAAGACGTT 57.032 26.923 0.00 0.00 0.00 3.99
134 135 4.589675 TGGTCGCCGGGCCTTTTT 62.590 61.111 14.55 0.00 0.00 1.94
135 136 4.589675 TTGGTCGCCGGGCCTTTT 62.590 61.111 14.55 0.00 0.00 2.27
168 169 6.986231 CCTCACTAGTGCACATATATGTTTGA 59.014 38.462 21.04 8.67 39.39 2.69
186 187 2.201921 ACGCTCTTCACTCCTCACTA 57.798 50.000 0.00 0.00 0.00 2.74
197 198 0.585357 CATGCATGCCTACGCTCTTC 59.415 55.000 14.93 0.00 35.36 2.87
254 262 0.104120 TGGGATATGTGAACTCGCCG 59.896 55.000 0.00 0.00 0.00 6.46
255 263 1.871080 CTGGGATATGTGAACTCGCC 58.129 55.000 0.00 0.00 0.00 5.54
256 264 1.221414 GCTGGGATATGTGAACTCGC 58.779 55.000 0.00 0.00 0.00 5.03
257 265 1.067060 TCGCTGGGATATGTGAACTCG 59.933 52.381 0.00 0.00 0.00 4.18
334 346 1.167851 CATGCTCACGTTTGGTCCAT 58.832 50.000 0.00 0.00 0.00 3.41
339 351 2.995466 ACATTCATGCTCACGTTTGG 57.005 45.000 0.00 0.00 0.00 3.28
341 353 4.320202 GGTGTAACATTCATGCTCACGTTT 60.320 41.667 0.00 0.00 39.98 3.60
351 363 5.878406 TTTTTGGTGGGTGTAACATTCAT 57.122 34.783 0.00 0.00 39.98 2.57
376 388 3.894782 TGGTCACACGATTCAACATTG 57.105 42.857 0.00 0.00 0.00 2.82
395 407 6.624352 TCATTCTCAGTCTTTTTGGTCTTG 57.376 37.500 0.00 0.00 0.00 3.02
420 432 5.940595 GTATTGTACCATTGGTTGCGTTAA 58.059 37.500 14.78 1.69 37.09 2.01
460 472 6.600822 AGCTTAATCAAGTCATGTACAAGCAT 59.399 34.615 0.00 0.00 38.34 3.79
491 503 2.304180 AGTGCTACACTTCCAGCTCATT 59.696 45.455 0.00 0.00 42.59 2.57
500 512 7.045126 AGATTGACCTATAGTGCTACACTTC 57.955 40.000 5.44 0.00 42.59 3.01
503 515 7.364200 CACTAGATTGACCTATAGTGCTACAC 58.636 42.308 0.00 0.00 38.86 2.90
506 518 5.477291 GCCACTAGATTGACCTATAGTGCTA 59.523 44.000 0.00 0.00 42.36 3.49
520 532 5.848921 AGGAGATCAATTAGGCCACTAGATT 59.151 40.000 5.01 0.00 0.00 2.40
546 558 5.877012 AGTACTGTTCAACATGGAGCATTAG 59.123 40.000 0.00 0.00 0.00 1.73
548 560 4.655963 AGTACTGTTCAACATGGAGCATT 58.344 39.130 0.00 0.00 0.00 3.56
555 567 5.499139 AACACCAAGTACTGTTCAACATG 57.501 39.130 0.00 0.00 0.00 3.21
570 582 5.068460 CCATGTCCTTAAGTTTGAACACCAA 59.932 40.000 0.97 0.00 0.00 3.67
571 583 4.582656 CCATGTCCTTAAGTTTGAACACCA 59.417 41.667 0.97 0.00 0.00 4.17
572 584 4.825085 TCCATGTCCTTAAGTTTGAACACC 59.175 41.667 0.97 0.00 0.00 4.16
590 604 1.450312 GTTCTCAGCCCGGTCCATG 60.450 63.158 0.00 0.00 0.00 3.66
602 617 1.855295 TACATGCTACGGGGTTCTCA 58.145 50.000 0.00 0.00 0.00 3.27
610 625 1.674611 GCGCGCTATACATGCTACGG 61.675 60.000 26.67 0.00 0.00 4.02
620 635 0.238025 TAAATCGGACGCGCGCTATA 59.762 50.000 32.58 14.26 0.00 1.31
623 638 3.252484 GTAAATCGGACGCGCGCT 61.252 61.111 32.58 17.75 0.00 5.92
629 644 1.995991 CCAGCGTGTAAATCGGACG 59.004 57.895 0.00 0.00 36.18 4.79
663 678 1.308998 AGTCGTGTTCTTTGGCTTGG 58.691 50.000 0.00 0.00 0.00 3.61
673 689 5.805486 TCAGATTGCAGTAATAGTCGTGTTC 59.195 40.000 0.00 0.00 0.00 3.18
676 692 6.834959 ATTCAGATTGCAGTAATAGTCGTG 57.165 37.500 0.00 0.00 0.00 4.35
684 700 7.933577 CCTGGTCTATAATTCAGATTGCAGTAA 59.066 37.037 0.00 0.00 0.00 2.24
700 716 2.775960 TGGAGACGAGACCTGGTCTATA 59.224 50.000 28.41 7.94 46.32 1.31
727 746 4.754114 CCTTGAGAGAGAAAAGTCCAACAG 59.246 45.833 0.00 0.00 0.00 3.16
732 751 3.007398 TGAGCCTTGAGAGAGAAAAGTCC 59.993 47.826 0.00 0.00 0.00 3.85
744 763 2.037136 CGCCTGGTTGAGCCTTGAG 61.037 63.158 0.00 0.00 38.35 3.02
745 764 2.032528 CGCCTGGTTGAGCCTTGA 59.967 61.111 0.00 0.00 38.35 3.02
746 765 3.741476 GCGCCTGGTTGAGCCTTG 61.741 66.667 0.00 0.00 38.35 3.61
783 803 2.569404 AGACAGGATGGTGAGTTCCTTC 59.431 50.000 0.00 0.00 43.62 3.46
813 833 4.753516 TGAAGAGTTGAAGAGTGGTTGA 57.246 40.909 0.00 0.00 0.00 3.18
866 893 0.745468 GCTAGGTAGGTCCGTTGGAG 59.255 60.000 0.00 0.00 41.99 3.86
867 894 1.033746 CGCTAGGTAGGTCCGTTGGA 61.034 60.000 0.00 0.00 41.99 3.53
868 895 1.436336 CGCTAGGTAGGTCCGTTGG 59.564 63.158 0.00 0.00 41.99 3.77
869 896 1.226888 GCGCTAGGTAGGTCCGTTG 60.227 63.158 0.00 0.00 41.99 4.10
877 904 1.361993 CAGGCTGAGCGCTAGGTAG 59.638 63.158 11.50 8.04 39.13 3.18
881 908 3.205395 AGACAGGCTGAGCGCTAG 58.795 61.111 23.66 9.77 39.13 3.42
903 930 2.933906 GGACGGATTTGTTGAGCGAATA 59.066 45.455 0.00 0.00 31.53 1.75
930 957 3.072211 TGACAGTCTGAGTACTACGGTG 58.928 50.000 6.91 0.00 0.00 4.94
933 960 5.234757 GGTATCTGACAGTCTGAGTACTACG 59.765 48.000 14.75 0.00 0.00 3.51
934 961 5.234757 CGGTATCTGACAGTCTGAGTACTAC 59.765 48.000 14.75 11.57 0.00 2.73
935 962 5.128335 TCGGTATCTGACAGTCTGAGTACTA 59.872 44.000 14.75 1.31 0.00 1.82
936 963 4.081031 TCGGTATCTGACAGTCTGAGTACT 60.081 45.833 14.75 0.00 0.00 2.73
943 970 3.637911 ACTCTCGGTATCTGACAGTCT 57.362 47.619 1.59 0.00 0.00 3.24
946 973 6.197364 AGTTTAACTCTCGGTATCTGACAG 57.803 41.667 0.00 0.00 0.00 3.51
947 974 7.609146 TCTTAGTTTAACTCTCGGTATCTGACA 59.391 37.037 0.00 0.00 0.00 3.58
948 975 7.983307 TCTTAGTTTAACTCTCGGTATCTGAC 58.017 38.462 0.00 0.00 0.00 3.51
954 981 8.345724 ACATCTTCTTAGTTTAACTCTCGGTA 57.654 34.615 0.00 0.00 0.00 4.02
955 982 7.229581 ACATCTTCTTAGTTTAACTCTCGGT 57.770 36.000 0.00 0.00 0.00 4.69
1365 1416 8.597662 TGTACTAAAACTAACTAAACCTGCAG 57.402 34.615 6.78 6.78 0.00 4.41
1367 1418 7.118825 CCCTGTACTAAAACTAACTAAACCTGC 59.881 40.741 0.00 0.00 0.00 4.85
1400 1458 6.127591 TGACCTACTTCTGAGACTGCTTTATC 60.128 42.308 0.00 0.00 0.00 1.75
1417 1476 5.228945 ACAACTTGCTTACATGACCTACT 57.771 39.130 0.00 0.00 0.00 2.57
1425 1484 8.848474 AAGTCTTGTATACAACTTGCTTACAT 57.152 30.769 18.05 0.00 28.85 2.29
1431 1525 6.851330 GTGTCAAAGTCTTGTATACAACTTGC 59.149 38.462 19.03 13.97 30.05 4.01
1547 1644 0.678048 GCATCGCCTCTCCCAAAGTT 60.678 55.000 0.00 0.00 0.00 2.66
1555 1652 1.664333 GCTAGCTGCATCGCCTCTC 60.664 63.158 7.70 0.00 42.31 3.20
1556 1653 0.825425 TAGCTAGCTGCATCGCCTCT 60.825 55.000 27.68 0.00 45.94 3.69
1557 1654 0.665972 GTAGCTAGCTGCATCGCCTC 60.666 60.000 27.68 2.82 45.94 4.70
1558 1655 1.112315 AGTAGCTAGCTGCATCGCCT 61.112 55.000 30.79 9.65 45.94 5.52
1613 1761 7.641411 CACAAAGCCTACAGATATCAAATTTCG 59.359 37.037 5.32 0.00 0.00 3.46
1619 1767 5.435686 ACCACAAAGCCTACAGATATCAA 57.564 39.130 5.32 0.00 0.00 2.57
1642 1790 2.162208 GCATGACAATTTCTCGCCTTCA 59.838 45.455 0.00 0.00 0.00 3.02
1690 1839 2.847234 TTCTCCCGTGCCACACCT 60.847 61.111 0.00 0.00 0.00 4.00
1691 1840 2.358737 CTTCTCCCGTGCCACACC 60.359 66.667 0.00 0.00 0.00 4.16
1719 1868 1.354031 TCCTTCAACCTAGGCATGCAA 59.646 47.619 21.36 5.87 32.59 4.08
1753 1902 6.836242 AGAGGTCCAGAAATCATTCTAATCC 58.164 40.000 0.00 0.00 44.11 3.01
1756 1997 7.180946 TCTGAAGAGGTCCAGAAATCATTCTAA 59.819 37.037 0.00 0.00 44.11 2.10
1771 2012 2.086054 ACGCATTGTCTGAAGAGGTC 57.914 50.000 0.00 0.00 0.00 3.85
1789 2030 2.941480 AGGGAGCCATTCATCATCAAC 58.059 47.619 0.00 0.00 0.00 3.18
1813 2054 0.741326 ATCCTCCGTGACGTCATCAG 59.259 55.000 23.12 16.52 38.28 2.90
1823 2064 0.531532 GATGTGCCAGATCCTCCGTG 60.532 60.000 0.00 0.00 0.00 4.94
1825 2066 1.070445 GGATGTGCCAGATCCTCCG 59.930 63.158 13.40 0.00 37.07 4.63
1840 2081 3.576118 CGGAGGAGTATCTCATTGTGGAT 59.424 47.826 0.00 0.00 35.58 3.41
1844 2085 5.657302 AGTTTACGGAGGAGTATCTCATTGT 59.343 40.000 0.00 0.00 35.58 2.71
1854 2095 8.348507 CGTTCTTATATTAGTTTACGGAGGAGT 58.651 37.037 0.00 0.00 0.00 3.85
1855 2096 8.348507 ACGTTCTTATATTAGTTTACGGAGGAG 58.651 37.037 13.71 0.00 32.54 3.69
1856 2097 8.225603 ACGTTCTTATATTAGTTTACGGAGGA 57.774 34.615 13.71 0.00 32.54 3.71
1857 2098 8.862550 AACGTTCTTATATTAGTTTACGGAGG 57.137 34.615 0.00 0.00 32.54 4.30
1872 2113 9.367444 CTTTAGTGGTGATCTAAACGTTCTTAT 57.633 33.333 0.00 0.00 34.83 1.73
1873 2114 8.362639 ACTTTAGTGGTGATCTAAACGTTCTTA 58.637 33.333 0.00 0.00 34.83 2.10
1874 2115 7.215085 ACTTTAGTGGTGATCTAAACGTTCTT 58.785 34.615 0.00 0.00 34.83 2.52
1875 2116 6.756221 ACTTTAGTGGTGATCTAAACGTTCT 58.244 36.000 0.00 0.00 34.83 3.01
1876 2117 8.524870 TTACTTTAGTGGTGATCTAAACGTTC 57.475 34.615 0.00 0.00 34.83 3.95
1877 2118 8.932791 CATTACTTTAGTGGTGATCTAAACGTT 58.067 33.333 0.00 0.00 34.83 3.99
1878 2119 8.308931 TCATTACTTTAGTGGTGATCTAAACGT 58.691 33.333 0.00 0.00 34.83 3.99
1879 2120 8.697846 TCATTACTTTAGTGGTGATCTAAACG 57.302 34.615 0.00 0.00 34.83 3.60
1886 2127 9.314321 CGTTTAGATCATTACTTTAGTGGTGAT 57.686 33.333 9.94 9.94 36.70 3.06
1887 2128 7.277098 GCGTTTAGATCATTACTTTAGTGGTGA 59.723 37.037 0.00 0.00 0.00 4.02
1888 2129 7.277981 AGCGTTTAGATCATTACTTTAGTGGTG 59.722 37.037 0.00 0.00 0.00 4.17
1889 2130 7.328737 AGCGTTTAGATCATTACTTTAGTGGT 58.671 34.615 0.00 0.00 0.00 4.16
1890 2131 7.707035 AGAGCGTTTAGATCATTACTTTAGTGG 59.293 37.037 0.00 0.00 37.82 4.00
1891 2132 8.535592 CAGAGCGTTTAGATCATTACTTTAGTG 58.464 37.037 0.00 0.00 37.82 2.74
1892 2133 8.467598 TCAGAGCGTTTAGATCATTACTTTAGT 58.532 33.333 0.00 0.00 37.82 2.24
1893 2134 8.858003 TCAGAGCGTTTAGATCATTACTTTAG 57.142 34.615 0.00 0.00 37.82 1.85
1895 2136 9.988815 ATATCAGAGCGTTTAGATCATTACTTT 57.011 29.630 0.00 0.00 37.82 2.66
1896 2137 9.988815 AATATCAGAGCGTTTAGATCATTACTT 57.011 29.630 0.00 0.00 37.82 2.24
1900 2141 9.988815 AACTAATATCAGAGCGTTTAGATCATT 57.011 29.630 0.00 0.00 37.82 2.57
1901 2142 9.988815 AAACTAATATCAGAGCGTTTAGATCAT 57.011 29.630 0.00 0.00 37.82 2.45
1908 2149 9.915629 CCTCTATAAACTAATATCAGAGCGTTT 57.084 33.333 0.00 0.00 0.00 3.60
1909 2150 8.524487 CCCTCTATAAACTAATATCAGAGCGTT 58.476 37.037 0.00 0.00 0.00 4.84
1910 2151 7.889073 TCCCTCTATAAACTAATATCAGAGCGT 59.111 37.037 0.00 0.00 0.00 5.07
1911 2152 8.282455 TCCCTCTATAAACTAATATCAGAGCG 57.718 38.462 0.00 0.00 0.00 5.03
1912 2153 9.250246 ACTCCCTCTATAAACTAATATCAGAGC 57.750 37.037 0.00 0.00 0.00 4.09
1926 2167 9.026121 GCTTGTTATGAGATACTCCCTCTATAA 57.974 37.037 0.00 0.00 0.00 0.98
1927 2168 8.170730 TGCTTGTTATGAGATACTCCCTCTATA 58.829 37.037 0.00 0.00 0.00 1.31
1928 2169 7.013220 TGCTTGTTATGAGATACTCCCTCTAT 58.987 38.462 0.00 0.00 0.00 1.98
1929 2170 6.373759 TGCTTGTTATGAGATACTCCCTCTA 58.626 40.000 0.00 0.00 0.00 2.43
1930 2171 5.211973 TGCTTGTTATGAGATACTCCCTCT 58.788 41.667 0.00 0.00 0.00 3.69
1931 2172 5.537300 TGCTTGTTATGAGATACTCCCTC 57.463 43.478 0.00 0.00 0.00 4.30
1932 2173 5.744300 GCATGCTTGTTATGAGATACTCCCT 60.744 44.000 11.37 0.00 0.00 4.20
1933 2174 4.453819 GCATGCTTGTTATGAGATACTCCC 59.546 45.833 11.37 0.00 0.00 4.30
1934 2175 4.151335 CGCATGCTTGTTATGAGATACTCC 59.849 45.833 17.13 0.00 0.00 3.85
1935 2176 4.376819 GCGCATGCTTGTTATGAGATACTC 60.377 45.833 17.13 0.00 38.39 2.59
1936 2177 3.496130 GCGCATGCTTGTTATGAGATACT 59.504 43.478 17.13 0.00 38.39 2.12
1937 2178 3.364366 GGCGCATGCTTGTTATGAGATAC 60.364 47.826 17.13 0.00 42.25 2.24
1985 2226 1.975680 ACGACCATACAAGTGGAAGGT 59.024 47.619 0.00 0.00 42.02 3.50
2011 2252 2.909504 AGTCTGGTCCAAGCTAGAGA 57.090 50.000 0.00 0.00 0.00 3.10
2012 2253 3.892284 TCTAGTCTGGTCCAAGCTAGAG 58.108 50.000 20.08 6.80 34.88 2.43
2172 2440 2.689983 CCTCCATCTAAAATGTGGTGGC 59.310 50.000 0.00 0.00 39.12 5.01
2177 2445 3.557595 GTCTCGCCTCCATCTAAAATGTG 59.442 47.826 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.