Multiple sequence alignment - TraesCS7A01G155000

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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 TraesCS7A01G155000 chr7A 100.000 3748 0 0 1 3748 107918739 107914992 0.000000e+00 6922
1 TraesCS7A01G155000 chr7A 97.505 481 9 3 3268 3748 714271224 714271701 0.000000e+00 819
2 TraesCS7A01G155000 chr7A 95.849 265 8 3 3042 3306 714270931 714271192 3.460000e-115 425
3 TraesCS7A01G155000 chr7D 93.757 2851 132 10 102 2911 103212941 103210096 0.000000e+00 4237
4 TraesCS7A01G155000 chr7D 92.094 1872 121 9 897 2766 103333383 103331537 0.000000e+00 2612
5 TraesCS7A01G155000 chr7D 87.826 115 14 0 2794 2908 102981760 102981646 6.530000e-28 135
6 TraesCS7A01G155000 chr7D 83.486 109 18 0 2035 2143 410522324 410522216 6.620000e-18 102
7 TraesCS7A01G155000 chr7B 94.737 2166 72 15 633 2766 61629252 61627097 0.000000e+00 3330
8 TraesCS7A01G155000 chr7B 91.547 1881 137 11 897 2766 61747324 61745455 0.000000e+00 2573
9 TraesCS7A01G155000 chr7B 90.395 177 12 5 2991 3165 716475489 716475662 1.050000e-55 228
10 TraesCS7A01G155000 chr7B 87.619 105 12 1 2785 2889 61604941 61604838 1.830000e-23 121
11 TraesCS7A01G155000 chr7B 85.437 103 15 0 2035 2137 425159131 425159233 1.420000e-19 108
12 TraesCS7A01G155000 chr6A 92.121 165 10 2 2995 3158 400186739 400186901 2.910000e-56 230
13 TraesCS7A01G155000 chr6A 91.176 170 12 3 2999 3167 586713639 586713472 1.050000e-55 228
14 TraesCS7A01G155000 chr6D 89.888 178 13 4 2992 3165 34883483 34883307 1.350000e-54 224
15 TraesCS7A01G155000 chr6D 90.698 172 10 3 2999 3165 34901797 34901627 1.350000e-54 224
16 TraesCS7A01G155000 chr6D 88.889 180 13 5 2992 3165 34856015 34855837 8.150000e-52 215
17 TraesCS7A01G155000 chr6B 89.222 167 15 2 3000 3165 19935529 19935693 4.910000e-49 206
18 TraesCS7A01G155000 chr3B 87.027 185 19 4 2986 3167 786845344 786845526 1.760000e-48 204
19 TraesCS7A01G155000 chr2D 80.385 260 37 12 1919 2175 100432361 100432609 6.390000e-43 185
20 TraesCS7A01G155000 chr2B 79.167 288 40 14 1890 2173 152504411 152504682 8.270000e-42 182
21 TraesCS7A01G155000 chr2A 80.077 261 36 12 1919 2175 100627863 100627615 2.970000e-41 180


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 TraesCS7A01G155000 chr7A 107914992 107918739 3747 True 6922 6922 100.000 1 3748 1 chr7A.!!$R1 3747
1 TraesCS7A01G155000 chr7A 714270931 714271701 770 False 622 819 96.677 3042 3748 2 chr7A.!!$F1 706
2 TraesCS7A01G155000 chr7D 103210096 103212941 2845 True 4237 4237 93.757 102 2911 1 chr7D.!!$R2 2809
3 TraesCS7A01G155000 chr7D 103331537 103333383 1846 True 2612 2612 92.094 897 2766 1 chr7D.!!$R3 1869
4 TraesCS7A01G155000 chr7B 61627097 61629252 2155 True 3330 3330 94.737 633 2766 1 chr7B.!!$R2 2133
5 TraesCS7A01G155000 chr7B 61745455 61747324 1869 True 2573 2573 91.547 897 2766 1 chr7B.!!$R3 1869

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
515 516 0.108019 AAGAGAAACACCACCGGTCC 59.892 55.0 2.59 0.0 31.02 4.46 F
713 714 0.179233 GCTTGCGCTACGGTGTTTAC 60.179 55.0 9.73 0.0 0.00 2.01 F
1046 1061 0.908198 ATTTCCCGAGAGCTGAGCTT 59.092 50.0 9.00 0.0 39.88 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 2406 0.316522 CCCTCGCGATCATGATCACT 59.683 55.000 30.13 0.99 37.69 3.41 R
2438 2487 2.281002 TGCATGATCGCCATCGGG 60.281 61.111 0.00 0.00 36.13 5.14 R
2953 3041 3.458044 TCTCTTTAGCTGGAGTGAGGA 57.542 47.619 0.00 0.00 0.00 3.71 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
17 18 4.579127 ACACCTTTCCCACACTGC 57.421 55.556 0.00 0.00 0.00 4.40
18 19 1.152756 ACACCTTTCCCACACTGCC 60.153 57.895 0.00 0.00 0.00 4.85
19 20 2.113139 ACCTTTCCCACACTGCCG 59.887 61.111 0.00 0.00 0.00 5.69
20 21 2.429930 CCTTTCCCACACTGCCGA 59.570 61.111 0.00 0.00 0.00 5.54
21 22 1.966451 CCTTTCCCACACTGCCGAC 60.966 63.158 0.00 0.00 0.00 4.79
22 23 1.966451 CTTTCCCACACTGCCGACC 60.966 63.158 0.00 0.00 0.00 4.79
23 24 2.674563 CTTTCCCACACTGCCGACCA 62.675 60.000 0.00 0.00 0.00 4.02
24 25 2.951475 TTTCCCACACTGCCGACCAC 62.951 60.000 0.00 0.00 0.00 4.16
26 27 3.941188 CCACACTGCCGACCACCT 61.941 66.667 0.00 0.00 0.00 4.00
27 28 2.111043 CACACTGCCGACCACCTT 59.889 61.111 0.00 0.00 0.00 3.50
28 29 1.525995 CACACTGCCGACCACCTTT 60.526 57.895 0.00 0.00 0.00 3.11
29 30 0.250124 CACACTGCCGACCACCTTTA 60.250 55.000 0.00 0.00 0.00 1.85
30 31 0.470766 ACACTGCCGACCACCTTTAA 59.529 50.000 0.00 0.00 0.00 1.52
31 32 1.073284 ACACTGCCGACCACCTTTAAT 59.927 47.619 0.00 0.00 0.00 1.40
32 33 2.159382 CACTGCCGACCACCTTTAATT 58.841 47.619 0.00 0.00 0.00 1.40
33 34 2.161609 CACTGCCGACCACCTTTAATTC 59.838 50.000 0.00 0.00 0.00 2.17
34 35 2.039879 ACTGCCGACCACCTTTAATTCT 59.960 45.455 0.00 0.00 0.00 2.40
35 36 3.081804 CTGCCGACCACCTTTAATTCTT 58.918 45.455 0.00 0.00 0.00 2.52
36 37 3.492337 TGCCGACCACCTTTAATTCTTT 58.508 40.909 0.00 0.00 0.00 2.52
37 38 3.254657 TGCCGACCACCTTTAATTCTTTG 59.745 43.478 0.00 0.00 0.00 2.77
38 39 3.366985 GCCGACCACCTTTAATTCTTTGG 60.367 47.826 0.00 0.00 0.00 3.28
39 40 4.076394 CCGACCACCTTTAATTCTTTGGA 58.924 43.478 0.00 0.00 0.00 3.53
40 41 4.521256 CCGACCACCTTTAATTCTTTGGAA 59.479 41.667 0.00 0.00 35.78 3.53
41 42 5.010213 CCGACCACCTTTAATTCTTTGGAAA 59.990 40.000 0.00 0.00 34.90 3.13
42 43 6.295067 CCGACCACCTTTAATTCTTTGGAAAT 60.295 38.462 0.00 0.00 34.90 2.17
43 44 7.094118 CCGACCACCTTTAATTCTTTGGAAATA 60.094 37.037 0.00 0.00 34.90 1.40
44 45 8.466798 CGACCACCTTTAATTCTTTGGAAATAT 58.533 33.333 0.00 0.00 34.90 1.28
45 46 9.803315 GACCACCTTTAATTCTTTGGAAATATC 57.197 33.333 0.00 0.00 34.90 1.63
46 47 9.547279 ACCACCTTTAATTCTTTGGAAATATCT 57.453 29.630 0.00 0.00 34.90 1.98
55 56 7.781324 TTCTTTGGAAATATCTTTTCTGGCT 57.219 32.000 0.00 0.00 0.00 4.75
56 57 7.396540 TCTTTGGAAATATCTTTTCTGGCTC 57.603 36.000 0.00 0.00 0.00 4.70
57 58 6.947733 TCTTTGGAAATATCTTTTCTGGCTCA 59.052 34.615 0.00 0.00 0.00 4.26
58 59 6.764308 TTGGAAATATCTTTTCTGGCTCAG 57.236 37.500 0.00 0.00 0.00 3.35
59 60 4.641989 TGGAAATATCTTTTCTGGCTCAGC 59.358 41.667 0.00 0.00 0.00 4.26
60 61 4.641989 GGAAATATCTTTTCTGGCTCAGCA 59.358 41.667 0.00 0.00 0.00 4.41
61 62 5.126061 GGAAATATCTTTTCTGGCTCAGCAA 59.874 40.000 0.00 0.00 0.00 3.91
62 63 6.350445 GGAAATATCTTTTCTGGCTCAGCAAA 60.350 38.462 0.00 0.00 0.00 3.68
63 64 3.930634 ATCTTTTCTGGCTCAGCAAAC 57.069 42.857 0.00 0.00 0.00 2.93
64 65 2.653726 TCTTTTCTGGCTCAGCAAACA 58.346 42.857 0.00 0.00 0.00 2.83
65 66 2.358898 TCTTTTCTGGCTCAGCAAACAC 59.641 45.455 0.00 0.00 0.00 3.32
66 67 1.761449 TTTCTGGCTCAGCAAACACA 58.239 45.000 0.00 0.00 0.00 3.72
67 68 1.761449 TTCTGGCTCAGCAAACACAA 58.239 45.000 0.00 0.00 0.00 3.33
68 69 1.761449 TCTGGCTCAGCAAACACAAA 58.239 45.000 0.00 0.00 0.00 2.83
69 70 1.405105 TCTGGCTCAGCAAACACAAAC 59.595 47.619 0.00 0.00 0.00 2.93
70 71 0.459489 TGGCTCAGCAAACACAAACC 59.541 50.000 0.00 0.00 0.00 3.27
71 72 0.249447 GGCTCAGCAAACACAAACCC 60.249 55.000 0.00 0.00 0.00 4.11
72 73 0.249447 GCTCAGCAAACACAAACCCC 60.249 55.000 0.00 0.00 0.00 4.95
73 74 1.402787 CTCAGCAAACACAAACCCCT 58.597 50.000 0.00 0.00 0.00 4.79
74 75 1.338020 CTCAGCAAACACAAACCCCTC 59.662 52.381 0.00 0.00 0.00 4.30
75 76 1.064017 TCAGCAAACACAAACCCCTCT 60.064 47.619 0.00 0.00 0.00 3.69
76 77 1.067516 CAGCAAACACAAACCCCTCTG 59.932 52.381 0.00 0.00 0.00 3.35
77 78 0.249447 GCAAACACAAACCCCTCTGC 60.249 55.000 0.00 0.00 0.00 4.26
78 79 1.402787 CAAACACAAACCCCTCTGCT 58.597 50.000 0.00 0.00 0.00 4.24
79 80 1.756538 CAAACACAAACCCCTCTGCTT 59.243 47.619 0.00 0.00 0.00 3.91
80 81 1.692411 AACACAAACCCCTCTGCTTC 58.308 50.000 0.00 0.00 0.00 3.86
81 82 0.178990 ACACAAACCCCTCTGCTTCC 60.179 55.000 0.00 0.00 0.00 3.46
82 83 0.111253 CACAAACCCCTCTGCTTCCT 59.889 55.000 0.00 0.00 0.00 3.36
83 84 0.853530 ACAAACCCCTCTGCTTCCTT 59.146 50.000 0.00 0.00 0.00 3.36
84 85 1.251251 CAAACCCCTCTGCTTCCTTG 58.749 55.000 0.00 0.00 0.00 3.61
85 86 0.853530 AAACCCCTCTGCTTCCTTGT 59.146 50.000 0.00 0.00 0.00 3.16
86 87 0.402121 AACCCCTCTGCTTCCTTGTC 59.598 55.000 0.00 0.00 0.00 3.18
87 88 1.301293 CCCCTCTGCTTCCTTGTCC 59.699 63.158 0.00 0.00 0.00 4.02
88 89 1.492133 CCCCTCTGCTTCCTTGTCCA 61.492 60.000 0.00 0.00 0.00 4.02
89 90 0.622665 CCCTCTGCTTCCTTGTCCAT 59.377 55.000 0.00 0.00 0.00 3.41
90 91 1.407989 CCCTCTGCTTCCTTGTCCATC 60.408 57.143 0.00 0.00 0.00 3.51
91 92 1.280133 CCTCTGCTTCCTTGTCCATCA 59.720 52.381 0.00 0.00 0.00 3.07
92 93 2.290514 CCTCTGCTTCCTTGTCCATCAA 60.291 50.000 0.00 0.00 34.61 2.57
93 94 3.415212 CTCTGCTTCCTTGTCCATCAAA 58.585 45.455 0.00 0.00 35.48 2.69
94 95 3.822735 CTCTGCTTCCTTGTCCATCAAAA 59.177 43.478 0.00 0.00 35.48 2.44
95 96 3.569701 TCTGCTTCCTTGTCCATCAAAAC 59.430 43.478 0.00 0.00 35.48 2.43
96 97 2.627699 TGCTTCCTTGTCCATCAAAACC 59.372 45.455 0.00 0.00 35.48 3.27
97 98 2.627699 GCTTCCTTGTCCATCAAAACCA 59.372 45.455 0.00 0.00 35.48 3.67
98 99 3.259123 GCTTCCTTGTCCATCAAAACCAT 59.741 43.478 0.00 0.00 35.48 3.55
99 100 4.462483 GCTTCCTTGTCCATCAAAACCATA 59.538 41.667 0.00 0.00 35.48 2.74
100 101 5.622233 GCTTCCTTGTCCATCAAAACCATAC 60.622 44.000 0.00 0.00 35.48 2.39
101 102 4.340617 TCCTTGTCCATCAAAACCATACC 58.659 43.478 0.00 0.00 35.48 2.73
102 103 4.085733 CCTTGTCCATCAAAACCATACCA 58.914 43.478 0.00 0.00 35.48 3.25
103 104 4.082245 CCTTGTCCATCAAAACCATACCAC 60.082 45.833 0.00 0.00 35.48 4.16
104 105 3.426615 TGTCCATCAAAACCATACCACC 58.573 45.455 0.00 0.00 0.00 4.61
105 106 2.758423 GTCCATCAAAACCATACCACCC 59.242 50.000 0.00 0.00 0.00 4.61
106 107 2.380249 TCCATCAAAACCATACCACCCA 59.620 45.455 0.00 0.00 0.00 4.51
107 108 2.760092 CCATCAAAACCATACCACCCAG 59.240 50.000 0.00 0.00 0.00 4.45
108 109 3.430453 CATCAAAACCATACCACCCAGT 58.570 45.455 0.00 0.00 0.00 4.00
115 116 0.744414 CATACCACCCAGTCTTGCCG 60.744 60.000 0.00 0.00 0.00 5.69
130 131 3.882888 TCTTGCCGAAAGACTCAATGTTT 59.117 39.130 0.00 0.00 40.09 2.83
131 132 3.624326 TGCCGAAAGACTCAATGTTTG 57.376 42.857 0.00 0.00 0.00 2.93
138 139 4.437682 AAGACTCAATGTTTGGTCTGGA 57.562 40.909 10.22 0.00 39.48 3.86
147 148 2.092429 TGTTTGGTCTGGAGTCTTGCTT 60.092 45.455 0.00 0.00 0.00 3.91
165 166 3.923917 TCCACCGGGGATTTGGAA 58.076 55.556 4.41 0.00 42.15 3.53
171 172 1.609783 CGGGGATTTGGAAGAGCCT 59.390 57.895 0.00 0.00 37.63 4.58
174 175 0.541863 GGGATTTGGAAGAGCCTCGA 59.458 55.000 0.00 0.00 37.63 4.04
223 224 1.144496 GTACGCGCAAATCCCCCTA 59.856 57.895 5.73 0.00 0.00 3.53
224 225 0.878961 GTACGCGCAAATCCCCCTAG 60.879 60.000 5.73 0.00 0.00 3.02
237 238 1.513158 CCCTAGTGCAGTCTCCACG 59.487 63.158 0.00 0.00 38.22 4.94
285 286 4.740822 GCCATGGCTGGGGTCGTT 62.741 66.667 29.98 0.00 43.36 3.85
300 301 1.070289 GTCGTTGTCCTCCTCTGGTTT 59.930 52.381 0.00 0.00 0.00 3.27
313 314 2.300152 CTCTGGTTTGTAGCTCCTGACA 59.700 50.000 0.00 0.00 0.00 3.58
316 317 2.637382 TGGTTTGTAGCTCCTGACATCA 59.363 45.455 0.00 0.00 0.00 3.07
319 320 4.065088 GTTTGTAGCTCCTGACATCACAA 58.935 43.478 0.00 0.00 0.00 3.33
329 330 0.174162 GACATCACAAATGCAGGGCC 59.826 55.000 0.00 0.00 0.00 5.80
331 332 1.005805 ACATCACAAATGCAGGGCCTA 59.994 47.619 5.28 0.00 0.00 3.93
333 334 2.057137 TCACAAATGCAGGGCCTATC 57.943 50.000 5.28 1.10 0.00 2.08
339 340 3.710209 AATGCAGGGCCTATCATAGTC 57.290 47.619 17.52 0.00 0.00 2.59
343 344 1.215647 GGGCCTATCATAGTCGCCG 59.784 63.158 0.84 0.00 40.67 6.46
345 346 1.587054 GCCTATCATAGTCGCCGCT 59.413 57.895 0.00 0.00 0.00 5.52
366 367 1.819632 CTTTTGGATCGCCTCCCCG 60.820 63.158 1.92 0.00 44.23 5.73
367 368 3.987954 TTTTGGATCGCCTCCCCGC 62.988 63.158 1.92 0.00 44.23 6.13
393 394 3.223589 GCGGTGGGTTTGGCTTGT 61.224 61.111 0.00 0.00 0.00 3.16
395 396 1.819905 CGGTGGGTTTGGCTTGTTT 59.180 52.632 0.00 0.00 0.00 2.83
397 398 0.827368 GGTGGGTTTGGCTTGTTTCA 59.173 50.000 0.00 0.00 0.00 2.69
401 402 2.158842 TGGGTTTGGCTTGTTTCATTGG 60.159 45.455 0.00 0.00 0.00 3.16
460 461 2.230750 CGAAACCCTAGTCGTCTTTCCT 59.769 50.000 0.00 0.00 32.61 3.36
461 462 3.441572 CGAAACCCTAGTCGTCTTTCCTA 59.558 47.826 0.00 0.00 32.61 2.94
465 466 3.132467 ACCCTAGTCGTCTTTCCTATTGC 59.868 47.826 0.00 0.00 0.00 3.56
471 472 4.932200 AGTCGTCTTTCCTATTGCTTTCTG 59.068 41.667 0.00 0.00 0.00 3.02
472 473 3.684788 TCGTCTTTCCTATTGCTTTCTGC 59.315 43.478 0.00 0.00 43.25 4.26
484 485 0.743701 CTTTCTGCGCCATCAGCTCT 60.744 55.000 4.18 0.00 40.39 4.09
485 486 0.536724 TTTCTGCGCCATCAGCTCTA 59.463 50.000 4.18 0.00 40.39 2.43
498 499 0.468400 AGCTCTACCCCTAGCGGAAG 60.468 60.000 0.00 0.00 43.63 3.46
511 512 1.566018 GCGGAAGAGAAACACCACCG 61.566 60.000 0.00 0.00 41.44 4.94
514 515 1.509703 GAAGAGAAACACCACCGGTC 58.490 55.000 2.59 0.00 31.02 4.79
515 516 0.108019 AAGAGAAACACCACCGGTCC 59.892 55.000 2.59 0.00 31.02 4.46
516 517 1.052124 AGAGAAACACCACCGGTCCA 61.052 55.000 2.59 0.00 31.02 4.02
526 527 0.976073 CACCGGTCCATGTCTAGGGT 60.976 60.000 2.59 0.00 0.00 4.34
529 530 0.462047 CGGTCCATGTCTAGGGTTGC 60.462 60.000 0.00 0.00 0.00 4.17
558 559 0.708209 TCCCTAGCCACCACTGTAGA 59.292 55.000 0.00 0.00 0.00 2.59
560 561 0.824759 CCTAGCCACCACTGTAGACC 59.175 60.000 0.00 0.00 0.00 3.85
609 610 1.278985 CCTAGCACAGGTGGACAATCA 59.721 52.381 1.10 0.00 39.91 2.57
625 626 0.182061 ATCACCATGCAATCGCCTCT 59.818 50.000 0.00 0.00 37.32 3.69
629 630 0.379669 CCATGCAATCGCCTCTTGTC 59.620 55.000 0.00 0.00 37.32 3.18
648 649 1.424493 CGCCTTAGAGCTTTCCTGCG 61.424 60.000 6.51 6.51 38.13 5.18
671 672 2.359967 GGACCCTCGTGCCTAAGCT 61.360 63.158 0.00 0.00 40.80 3.74
689 690 7.754475 GCCTAAGCTATCGGTACTTTATTAGTC 59.246 40.741 0.00 0.00 35.60 2.59
708 709 3.788766 GTGGCTTGCGCTACGGTG 61.789 66.667 9.73 0.00 37.88 4.94
713 714 0.179233 GCTTGCGCTACGGTGTTTAC 60.179 55.000 9.73 0.00 0.00 2.01
865 866 2.202171 GTTGCACAACCGATCGCG 60.202 61.111 10.32 0.00 35.36 5.87
1019 1021 2.479049 GCATGGACACAATCATCAGCAC 60.479 50.000 0.00 0.00 0.00 4.40
1034 1049 1.135315 CAGCACATCAACCATTTCCCG 60.135 52.381 0.00 0.00 0.00 5.14
1046 1061 0.908198 ATTTCCCGAGAGCTGAGCTT 59.092 50.000 9.00 0.00 39.88 3.74
1052 1067 1.153667 GAGAGCTGAGCTTCACCGG 60.154 63.158 9.00 0.00 39.88 5.28
1246 1267 2.480426 CTTCGTCGGCAACAACGAGC 62.480 60.000 0.00 0.00 41.50 5.03
1360 1381 1.140375 GTGGCGTCCTACGGTAAGG 59.860 63.158 1.25 0.00 42.82 2.69
1578 1599 2.622942 GTTCACCATGGACAAGCTCAAA 59.377 45.455 21.47 0.00 0.00 2.69
1764 1785 1.140772 GGGAGGGGAAGGAGGTGTTT 61.141 60.000 0.00 0.00 0.00 2.83
1856 1884 1.698116 TCCCCACCAAGACCAACCA 60.698 57.895 0.00 0.00 0.00 3.67
1984 2012 1.220206 CTGATGCTCGAGGCCAACT 59.780 57.895 15.58 0.00 40.92 3.16
2272 2314 2.226437 CCACTTAATGCACACTCCACAC 59.774 50.000 0.00 0.00 0.00 3.82
2273 2315 2.877786 CACTTAATGCACACTCCACACA 59.122 45.455 0.00 0.00 0.00 3.72
2330 2379 2.447887 GCAGACGACGATGGTGCTG 61.448 63.158 0.00 0.46 0.00 4.41
2357 2406 3.826754 CTGAGGCTCTACGGCGCA 61.827 66.667 16.72 0.00 45.25 6.09
2383 2432 1.511318 ATGATCGCGAGGGAGACGAG 61.511 60.000 16.66 0.00 39.48 4.18
2438 2487 1.819632 GGGCACGACCACCATGATC 60.820 63.158 0.00 0.00 42.05 2.92
2788 2858 9.214957 TGAAGTACAAAATAAGTACATGAGTGG 57.785 33.333 0.00 0.00 43.24 4.00
2789 2859 8.561738 AAGTACAAAATAAGTACATGAGTGGG 57.438 34.615 0.00 0.00 43.24 4.61
2790 2860 5.897377 ACAAAATAAGTACATGAGTGGGC 57.103 39.130 0.00 0.00 0.00 5.36
2792 2862 6.010219 ACAAAATAAGTACATGAGTGGGCTT 58.990 36.000 0.00 0.00 0.00 4.35
2798 2886 4.033709 AGTACATGAGTGGGCTTGTATCT 58.966 43.478 0.00 0.00 33.02 1.98
2811 2899 4.754618 GGCTTGTATCTTTTTGGTTTTGGG 59.245 41.667 0.00 0.00 0.00 4.12
2824 2912 2.549926 GTTTTGGGTTTTGAGCTGTGG 58.450 47.619 0.00 0.00 0.00 4.17
2840 2928 3.369471 GCTGTGGGCTTGTATCTTCACTA 60.369 47.826 0.00 0.00 38.06 2.74
2869 2957 3.622163 CCTCTAGCATTTGTGAGCAGAAG 59.378 47.826 0.00 0.00 0.00 2.85
2871 2959 4.898320 TCTAGCATTTGTGAGCAGAAGAA 58.102 39.130 0.00 0.00 0.00 2.52
2912 3000 9.686683 ATAAGTACTGCTCATTGAGGTTAATTT 57.313 29.630 15.28 0.00 0.00 1.82
2913 3001 7.617041 AGTACTGCTCATTGAGGTTAATTTC 57.383 36.000 15.28 0.00 0.00 2.17
2914 3002 7.398024 AGTACTGCTCATTGAGGTTAATTTCT 58.602 34.615 15.28 0.00 0.00 2.52
2915 3003 6.749923 ACTGCTCATTGAGGTTAATTTCTC 57.250 37.500 15.28 0.00 0.00 2.87
2916 3004 5.649831 ACTGCTCATTGAGGTTAATTTCTCC 59.350 40.000 15.28 0.00 0.00 3.71
2917 3005 5.819991 TGCTCATTGAGGTTAATTTCTCCT 58.180 37.500 15.28 0.00 0.00 3.69
2918 3006 6.957631 TGCTCATTGAGGTTAATTTCTCCTA 58.042 36.000 15.28 0.00 0.00 2.94
2919 3007 7.050377 TGCTCATTGAGGTTAATTTCTCCTAG 58.950 38.462 15.28 0.00 0.00 3.02
2920 3008 7.051000 GCTCATTGAGGTTAATTTCTCCTAGT 58.949 38.462 15.28 0.00 0.00 2.57
2921 3009 7.225734 GCTCATTGAGGTTAATTTCTCCTAGTC 59.774 40.741 15.28 0.00 0.00 2.59
2922 3010 7.565680 TCATTGAGGTTAATTTCTCCTAGTCC 58.434 38.462 0.00 0.00 0.00 3.85
2923 3011 7.403231 TCATTGAGGTTAATTTCTCCTAGTCCT 59.597 37.037 0.00 0.00 0.00 3.85
2924 3012 6.793505 TGAGGTTAATTTCTCCTAGTCCTC 57.206 41.667 0.00 0.00 39.24 3.71
2925 3013 6.503944 TGAGGTTAATTTCTCCTAGTCCTCT 58.496 40.000 0.00 0.00 39.44 3.69
2926 3014 6.608002 TGAGGTTAATTTCTCCTAGTCCTCTC 59.392 42.308 0.00 0.00 39.44 3.20
2927 3015 6.747931 AGGTTAATTTCTCCTAGTCCTCTCT 58.252 40.000 0.00 0.00 0.00 3.10
2928 3016 6.837048 AGGTTAATTTCTCCTAGTCCTCTCTC 59.163 42.308 0.00 0.00 0.00 3.20
2929 3017 6.837048 GGTTAATTTCTCCTAGTCCTCTCTCT 59.163 42.308 0.00 0.00 0.00 3.10
2930 3018 7.201875 GGTTAATTTCTCCTAGTCCTCTCTCTG 60.202 44.444 0.00 0.00 0.00 3.35
2931 3019 5.725551 ATTTCTCCTAGTCCTCTCTCTGA 57.274 43.478 0.00 0.00 0.00 3.27
2932 3020 5.725551 TTTCTCCTAGTCCTCTCTCTGAT 57.274 43.478 0.00 0.00 0.00 2.90
2933 3021 5.725551 TTCTCCTAGTCCTCTCTCTGATT 57.274 43.478 0.00 0.00 0.00 2.57
2934 3022 5.047566 TCTCCTAGTCCTCTCTCTGATTG 57.952 47.826 0.00 0.00 0.00 2.67
2935 3023 4.724293 TCTCCTAGTCCTCTCTCTGATTGA 59.276 45.833 0.00 0.00 0.00 2.57
2936 3024 4.787551 TCCTAGTCCTCTCTCTGATTGAC 58.212 47.826 0.00 0.00 0.00 3.18
2937 3025 4.476846 TCCTAGTCCTCTCTCTGATTGACT 59.523 45.833 0.00 0.00 38.95 3.41
2938 3026 5.668080 TCCTAGTCCTCTCTCTGATTGACTA 59.332 44.000 0.00 0.00 37.63 2.59
2939 3027 6.158871 TCCTAGTCCTCTCTCTGATTGACTAA 59.841 42.308 0.00 0.00 37.91 2.24
2940 3028 7.004086 CCTAGTCCTCTCTCTGATTGACTAAT 58.996 42.308 0.00 0.00 37.91 1.73
2941 3029 7.505585 CCTAGTCCTCTCTCTGATTGACTAATT 59.494 40.741 0.00 0.00 37.91 1.40
2942 3030 7.111247 AGTCCTCTCTCTGATTGACTAATTG 57.889 40.000 0.00 0.00 35.94 2.32
2943 3031 5.752955 GTCCTCTCTCTGATTGACTAATTGC 59.247 44.000 0.00 0.00 0.00 3.56
2944 3032 5.055812 CCTCTCTCTGATTGACTAATTGCC 58.944 45.833 0.00 0.00 0.00 4.52
2945 3033 5.396101 CCTCTCTCTGATTGACTAATTGCCA 60.396 44.000 0.00 0.00 0.00 4.92
2946 3034 6.053632 TCTCTCTGATTGACTAATTGCCAA 57.946 37.500 0.00 0.00 0.00 4.52
2947 3035 6.111382 TCTCTCTGATTGACTAATTGCCAAG 58.889 40.000 0.00 0.00 0.00 3.61
2948 3036 5.188434 TCTCTGATTGACTAATTGCCAAGG 58.812 41.667 0.00 0.00 0.00 3.61
2949 3037 4.922206 TCTGATTGACTAATTGCCAAGGT 58.078 39.130 0.00 0.00 0.00 3.50
2950 3038 5.324409 TCTGATTGACTAATTGCCAAGGTT 58.676 37.500 0.00 0.00 0.00 3.50
2951 3039 5.774690 TCTGATTGACTAATTGCCAAGGTTT 59.225 36.000 0.00 0.00 0.00 3.27
2952 3040 6.945435 TCTGATTGACTAATTGCCAAGGTTTA 59.055 34.615 0.00 0.00 0.00 2.01
2953 3041 7.615365 TCTGATTGACTAATTGCCAAGGTTTAT 59.385 33.333 0.00 0.00 0.00 1.40
2954 3042 7.771183 TGATTGACTAATTGCCAAGGTTTATC 58.229 34.615 0.00 0.00 0.00 1.75
2955 3043 6.524101 TTGACTAATTGCCAAGGTTTATCC 57.476 37.500 0.00 0.00 0.00 2.59
2966 3054 2.839228 AGGTTTATCCTCACTCCAGCT 58.161 47.619 0.00 0.00 44.42 4.24
2967 3055 3.995636 AGGTTTATCCTCACTCCAGCTA 58.004 45.455 0.00 0.00 44.42 3.32
2968 3056 4.362677 AGGTTTATCCTCACTCCAGCTAA 58.637 43.478 0.00 0.00 44.42 3.09
2969 3057 4.783227 AGGTTTATCCTCACTCCAGCTAAA 59.217 41.667 0.00 0.00 44.42 1.85
2970 3058 5.104735 AGGTTTATCCTCACTCCAGCTAAAG 60.105 44.000 0.00 0.00 44.42 1.85
2971 3059 5.104900 GGTTTATCCTCACTCCAGCTAAAGA 60.105 44.000 1.73 0.00 0.00 2.52
2972 3060 5.860941 TTATCCTCACTCCAGCTAAAGAG 57.139 43.478 6.14 6.14 36.16 2.85
2973 3061 3.458044 TCCTCACTCCAGCTAAAGAGA 57.542 47.619 13.03 4.94 34.13 3.10
2974 3062 3.779444 TCCTCACTCCAGCTAAAGAGAA 58.221 45.455 13.03 2.42 34.13 2.87
2975 3063 4.160329 TCCTCACTCCAGCTAAAGAGAAA 58.840 43.478 13.03 2.14 34.13 2.52
2976 3064 4.593206 TCCTCACTCCAGCTAAAGAGAAAA 59.407 41.667 13.03 0.22 34.13 2.29
2977 3065 5.071788 TCCTCACTCCAGCTAAAGAGAAAAA 59.928 40.000 13.03 0.00 34.13 1.94
2978 3066 5.411053 CCTCACTCCAGCTAAAGAGAAAAAG 59.589 44.000 13.03 5.83 34.13 2.27
2979 3067 5.308825 TCACTCCAGCTAAAGAGAAAAAGG 58.691 41.667 13.03 0.00 34.13 3.11
2980 3068 5.066593 CACTCCAGCTAAAGAGAAAAAGGT 58.933 41.667 13.03 0.00 34.13 3.50
2981 3069 5.532779 CACTCCAGCTAAAGAGAAAAAGGTT 59.467 40.000 13.03 0.00 34.13 3.50
2982 3070 6.039829 CACTCCAGCTAAAGAGAAAAAGGTTT 59.960 38.462 13.03 0.00 34.13 3.27
2983 3071 7.228706 CACTCCAGCTAAAGAGAAAAAGGTTTA 59.771 37.037 13.03 0.00 34.13 2.01
2984 3072 7.945109 ACTCCAGCTAAAGAGAAAAAGGTTTAT 59.055 33.333 13.03 0.00 34.13 1.40
2985 3073 8.336801 TCCAGCTAAAGAGAAAAAGGTTTATC 57.663 34.615 0.00 0.00 35.58 1.75
2986 3074 7.393515 TCCAGCTAAAGAGAAAAAGGTTTATCC 59.606 37.037 0.00 0.00 35.90 2.59
3091 3179 9.668497 ACTAATTACAGACTCCCAAGAAATTAC 57.332 33.333 0.00 0.00 0.00 1.89
3103 3191 8.292444 TCCCAAGAAATTACCACATTAATCAG 57.708 34.615 0.00 0.00 0.00 2.90
3378 3533 9.413048 CTACGATAGAAAAGAAAGTCTTCAACT 57.587 33.333 0.00 0.00 36.12 3.16
3390 3545 0.771127 CTTCAACTGTCCCTTCCCCA 59.229 55.000 0.00 0.00 0.00 4.96
3407 3562 1.065854 CCCACTTCATCCTCTCCACAC 60.066 57.143 0.00 0.00 0.00 3.82
3461 3616 6.353323 CCTTCCTCTCTATTCCTTTCCTTTC 58.647 44.000 0.00 0.00 0.00 2.62
3695 3850 6.641176 TGTTACAGTACGCAGTTCATATTG 57.359 37.500 0.00 0.00 37.78 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.152756 GGCAGTGTGGGAAAGGTGT 60.153 57.895 0.00 0.00 0.00 4.16
1 2 2.260869 CGGCAGTGTGGGAAAGGTG 61.261 63.158 0.00 0.00 0.00 4.00
2 3 2.113139 CGGCAGTGTGGGAAAGGT 59.887 61.111 0.00 0.00 0.00 3.50
3 4 1.966451 GTCGGCAGTGTGGGAAAGG 60.966 63.158 0.00 0.00 0.00 3.11
5 6 2.112297 GGTCGGCAGTGTGGGAAA 59.888 61.111 0.00 0.00 0.00 3.13
6 7 3.164977 TGGTCGGCAGTGTGGGAA 61.165 61.111 0.00 0.00 0.00 3.97
7 8 3.936203 GTGGTCGGCAGTGTGGGA 61.936 66.667 0.00 0.00 0.00 4.37
9 10 2.958578 AAAGGTGGTCGGCAGTGTGG 62.959 60.000 0.00 0.00 0.00 4.17
10 11 0.250124 TAAAGGTGGTCGGCAGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
11 12 0.470766 TTAAAGGTGGTCGGCAGTGT 59.529 50.000 0.00 0.00 0.00 3.55
12 13 1.821216 ATTAAAGGTGGTCGGCAGTG 58.179 50.000 0.00 0.00 0.00 3.66
13 14 2.039879 AGAATTAAAGGTGGTCGGCAGT 59.960 45.455 0.00 0.00 0.00 4.40
14 15 2.711542 AGAATTAAAGGTGGTCGGCAG 58.288 47.619 0.00 0.00 0.00 4.85
15 16 2.871096 AGAATTAAAGGTGGTCGGCA 57.129 45.000 0.00 0.00 0.00 5.69
16 17 3.366985 CCAAAGAATTAAAGGTGGTCGGC 60.367 47.826 0.00 0.00 0.00 5.54
17 18 4.076394 TCCAAAGAATTAAAGGTGGTCGG 58.924 43.478 0.00 0.00 0.00 4.79
18 19 5.699097 TTCCAAAGAATTAAAGGTGGTCG 57.301 39.130 0.00 0.00 0.00 4.79
19 20 9.803315 GATATTTCCAAAGAATTAAAGGTGGTC 57.197 33.333 0.00 0.00 0.00 4.02
20 21 9.547279 AGATATTTCCAAAGAATTAAAGGTGGT 57.453 29.630 0.00 0.00 0.00 4.16
29 30 8.819845 AGCCAGAAAAGATATTTCCAAAGAATT 58.180 29.630 0.00 0.00 0.00 2.17
30 31 8.371571 AGCCAGAAAAGATATTTCCAAAGAAT 57.628 30.769 0.00 0.00 0.00 2.40
31 32 7.451255 TGAGCCAGAAAAGATATTTCCAAAGAA 59.549 33.333 0.00 0.00 0.00 2.52
32 33 6.947733 TGAGCCAGAAAAGATATTTCCAAAGA 59.052 34.615 0.00 0.00 0.00 2.52
33 34 7.161773 TGAGCCAGAAAAGATATTTCCAAAG 57.838 36.000 0.00 0.00 0.00 2.77
34 35 6.350445 GCTGAGCCAGAAAAGATATTTCCAAA 60.350 38.462 6.40 0.00 32.44 3.28
35 36 5.126061 GCTGAGCCAGAAAAGATATTTCCAA 59.874 40.000 6.40 0.00 32.44 3.53
36 37 4.641989 GCTGAGCCAGAAAAGATATTTCCA 59.358 41.667 6.40 0.00 32.44 3.53
37 38 4.641989 TGCTGAGCCAGAAAAGATATTTCC 59.358 41.667 0.23 0.00 32.44 3.13
38 39 5.824904 TGCTGAGCCAGAAAAGATATTTC 57.175 39.130 0.23 0.00 32.44 2.17
39 40 6.015180 TGTTTGCTGAGCCAGAAAAGATATTT 60.015 34.615 0.23 0.00 39.39 1.40
40 41 5.477984 TGTTTGCTGAGCCAGAAAAGATATT 59.522 36.000 0.23 0.00 39.39 1.28
41 42 5.012239 TGTTTGCTGAGCCAGAAAAGATAT 58.988 37.500 0.23 0.00 39.39 1.63
42 43 4.216257 GTGTTTGCTGAGCCAGAAAAGATA 59.784 41.667 0.23 0.00 39.39 1.98
43 44 3.005155 GTGTTTGCTGAGCCAGAAAAGAT 59.995 43.478 0.23 0.00 39.39 2.40
44 45 2.358898 GTGTTTGCTGAGCCAGAAAAGA 59.641 45.455 0.23 5.33 39.39 2.52
45 46 2.099592 TGTGTTTGCTGAGCCAGAAAAG 59.900 45.455 0.23 0.00 39.39 2.27
46 47 2.098614 TGTGTTTGCTGAGCCAGAAAA 58.901 42.857 0.23 5.50 36.73 2.29
47 48 1.761449 TGTGTTTGCTGAGCCAGAAA 58.239 45.000 0.23 0.00 32.44 2.52
48 49 1.761449 TTGTGTTTGCTGAGCCAGAA 58.239 45.000 0.23 0.00 32.44 3.02
49 50 1.405105 GTTTGTGTTTGCTGAGCCAGA 59.595 47.619 0.23 0.00 32.44 3.86
50 51 1.536709 GGTTTGTGTTTGCTGAGCCAG 60.537 52.381 0.23 0.00 34.12 4.85
51 52 0.459489 GGTTTGTGTTTGCTGAGCCA 59.541 50.000 0.23 0.00 0.00 4.75
52 53 0.249447 GGGTTTGTGTTTGCTGAGCC 60.249 55.000 0.23 0.00 0.00 4.70
53 54 0.249447 GGGGTTTGTGTTTGCTGAGC 60.249 55.000 0.00 0.00 0.00 4.26
54 55 1.338020 GAGGGGTTTGTGTTTGCTGAG 59.662 52.381 0.00 0.00 0.00 3.35
55 56 1.064017 AGAGGGGTTTGTGTTTGCTGA 60.064 47.619 0.00 0.00 0.00 4.26
56 57 1.067516 CAGAGGGGTTTGTGTTTGCTG 59.932 52.381 0.00 0.00 0.00 4.41
57 58 1.402787 CAGAGGGGTTTGTGTTTGCT 58.597 50.000 0.00 0.00 0.00 3.91
58 59 0.249447 GCAGAGGGGTTTGTGTTTGC 60.249 55.000 0.00 0.00 0.00 3.68
59 60 1.402787 AGCAGAGGGGTTTGTGTTTG 58.597 50.000 0.00 0.00 0.00 2.93
60 61 2.031870 GAAGCAGAGGGGTTTGTGTTT 58.968 47.619 0.00 0.00 37.33 2.83
61 62 1.692411 GAAGCAGAGGGGTTTGTGTT 58.308 50.000 0.00 0.00 37.33 3.32
62 63 0.178990 GGAAGCAGAGGGGTTTGTGT 60.179 55.000 0.00 0.00 37.33 3.72
63 64 0.111253 AGGAAGCAGAGGGGTTTGTG 59.889 55.000 0.00 0.00 37.33 3.33
64 65 0.853530 AAGGAAGCAGAGGGGTTTGT 59.146 50.000 0.00 0.00 37.33 2.83
65 66 1.251251 CAAGGAAGCAGAGGGGTTTG 58.749 55.000 0.00 0.00 37.33 2.93
66 67 0.853530 ACAAGGAAGCAGAGGGGTTT 59.146 50.000 0.00 0.00 37.33 3.27
67 68 0.402121 GACAAGGAAGCAGAGGGGTT 59.598 55.000 0.00 0.00 40.61 4.11
68 69 1.492993 GGACAAGGAAGCAGAGGGGT 61.493 60.000 0.00 0.00 0.00 4.95
69 70 1.301293 GGACAAGGAAGCAGAGGGG 59.699 63.158 0.00 0.00 0.00 4.79
70 71 0.622665 ATGGACAAGGAAGCAGAGGG 59.377 55.000 0.00 0.00 0.00 4.30
71 72 1.280133 TGATGGACAAGGAAGCAGAGG 59.720 52.381 0.00 0.00 0.00 3.69
72 73 2.775911 TGATGGACAAGGAAGCAGAG 57.224 50.000 0.00 0.00 0.00 3.35
73 74 3.507162 TTTGATGGACAAGGAAGCAGA 57.493 42.857 0.00 0.00 39.77 4.26
74 75 3.305608 GGTTTTGATGGACAAGGAAGCAG 60.306 47.826 0.00 0.00 39.77 4.24
75 76 2.627699 GGTTTTGATGGACAAGGAAGCA 59.372 45.455 0.00 0.00 39.77 3.91
76 77 2.627699 TGGTTTTGATGGACAAGGAAGC 59.372 45.455 0.00 0.00 39.77 3.86
77 78 5.105756 GGTATGGTTTTGATGGACAAGGAAG 60.106 44.000 0.00 0.00 39.77 3.46
78 79 4.770010 GGTATGGTTTTGATGGACAAGGAA 59.230 41.667 0.00 0.00 39.77 3.36
79 80 4.202620 TGGTATGGTTTTGATGGACAAGGA 60.203 41.667 0.00 0.00 39.77 3.36
80 81 4.082245 GTGGTATGGTTTTGATGGACAAGG 60.082 45.833 0.00 0.00 39.77 3.61
81 82 4.082245 GGTGGTATGGTTTTGATGGACAAG 60.082 45.833 0.00 0.00 39.77 3.16
82 83 3.829601 GGTGGTATGGTTTTGATGGACAA 59.170 43.478 0.00 0.00 36.65 3.18
83 84 3.426615 GGTGGTATGGTTTTGATGGACA 58.573 45.455 0.00 0.00 0.00 4.02
84 85 2.758423 GGGTGGTATGGTTTTGATGGAC 59.242 50.000 0.00 0.00 0.00 4.02
85 86 2.380249 TGGGTGGTATGGTTTTGATGGA 59.620 45.455 0.00 0.00 0.00 3.41
86 87 2.760092 CTGGGTGGTATGGTTTTGATGG 59.240 50.000 0.00 0.00 0.00 3.51
87 88 3.430453 ACTGGGTGGTATGGTTTTGATG 58.570 45.455 0.00 0.00 0.00 3.07
88 89 3.333680 AGACTGGGTGGTATGGTTTTGAT 59.666 43.478 0.00 0.00 0.00 2.57
89 90 2.714250 AGACTGGGTGGTATGGTTTTGA 59.286 45.455 0.00 0.00 0.00 2.69
90 91 3.154827 AGACTGGGTGGTATGGTTTTG 57.845 47.619 0.00 0.00 0.00 2.44
91 92 3.496331 CAAGACTGGGTGGTATGGTTTT 58.504 45.455 0.00 0.00 0.00 2.43
92 93 2.817839 GCAAGACTGGGTGGTATGGTTT 60.818 50.000 0.00 0.00 0.00 3.27
93 94 1.271926 GCAAGACTGGGTGGTATGGTT 60.272 52.381 0.00 0.00 0.00 3.67
94 95 0.328258 GCAAGACTGGGTGGTATGGT 59.672 55.000 0.00 0.00 0.00 3.55
95 96 0.394352 GGCAAGACTGGGTGGTATGG 60.394 60.000 0.00 0.00 0.00 2.74
96 97 0.744414 CGGCAAGACTGGGTGGTATG 60.744 60.000 0.00 0.00 0.00 2.39
97 98 0.907704 TCGGCAAGACTGGGTGGTAT 60.908 55.000 0.00 0.00 0.00 2.73
98 99 1.122632 TTCGGCAAGACTGGGTGGTA 61.123 55.000 0.00 0.00 0.00 3.25
99 100 1.990160 TTTCGGCAAGACTGGGTGGT 61.990 55.000 0.00 0.00 0.00 4.16
100 101 1.228124 TTTCGGCAAGACTGGGTGG 60.228 57.895 0.00 0.00 0.00 4.61
101 102 0.250295 TCTTTCGGCAAGACTGGGTG 60.250 55.000 0.00 0.00 36.51 4.61
102 103 2.142220 TCTTTCGGCAAGACTGGGT 58.858 52.632 0.00 0.00 36.51 4.51
108 109 3.126001 ACATTGAGTCTTTCGGCAAGA 57.874 42.857 0.00 0.00 39.39 3.02
115 116 4.821805 TCCAGACCAAACATTGAGTCTTTC 59.178 41.667 9.85 0.00 38.36 2.62
124 125 2.887152 GCAAGACTCCAGACCAAACATT 59.113 45.455 0.00 0.00 0.00 2.71
126 127 1.490490 AGCAAGACTCCAGACCAAACA 59.510 47.619 0.00 0.00 0.00 2.83
130 131 1.072331 GGAAAGCAAGACTCCAGACCA 59.928 52.381 0.00 0.00 0.00 4.02
131 132 1.072331 TGGAAAGCAAGACTCCAGACC 59.928 52.381 0.00 0.00 34.26 3.85
138 139 1.073199 CCCGGTGGAAAGCAAGACT 59.927 57.895 0.00 0.00 0.00 3.24
165 166 1.953686 GAATCTGCTAGTCGAGGCTCT 59.046 52.381 13.50 0.00 0.00 4.09
171 172 2.025155 GTGGGAGAATCTGCTAGTCGA 58.975 52.381 1.01 0.00 33.73 4.20
174 175 2.503356 CAAGGTGGGAGAATCTGCTAGT 59.497 50.000 1.01 0.00 33.73 2.57
208 209 2.180204 CACTAGGGGGATTTGCGCG 61.180 63.158 0.00 0.00 0.00 6.86
209 210 2.481471 GCACTAGGGGGATTTGCGC 61.481 63.158 0.00 0.00 0.00 6.09
210 211 1.077787 TGCACTAGGGGGATTTGCG 60.078 57.895 0.00 0.00 35.90 4.85
213 214 1.840635 GAGACTGCACTAGGGGGATTT 59.159 52.381 0.00 0.00 0.00 2.17
214 215 1.501582 GAGACTGCACTAGGGGGATT 58.498 55.000 0.00 0.00 0.00 3.01
223 224 0.753262 AAGAACGTGGAGACTGCACT 59.247 50.000 22.69 7.03 36.50 4.40
224 225 1.140816 GAAGAACGTGGAGACTGCAC 58.859 55.000 16.54 16.54 35.21 4.57
237 238 3.696548 CCTTGGCCTCCAATAAGAAGAAC 59.303 47.826 3.32 0.00 43.07 3.01
271 272 2.351276 GACAACGACCCCAGCCAT 59.649 61.111 0.00 0.00 0.00 4.40
275 276 1.889530 GAGGAGGACAACGACCCCAG 61.890 65.000 0.00 0.00 0.00 4.45
284 285 2.038557 GCTACAAACCAGAGGAGGACAA 59.961 50.000 0.00 0.00 0.00 3.18
285 286 1.623811 GCTACAAACCAGAGGAGGACA 59.376 52.381 0.00 0.00 0.00 4.02
300 301 4.256110 CATTTGTGATGTCAGGAGCTACA 58.744 43.478 0.00 0.00 0.00 2.74
313 314 2.091720 TGATAGGCCCTGCATTTGTGAT 60.092 45.455 0.00 0.00 0.00 3.06
316 317 2.761786 ATGATAGGCCCTGCATTTGT 57.238 45.000 0.00 0.00 0.00 2.83
319 320 2.027745 CGACTATGATAGGCCCTGCATT 60.028 50.000 0.00 0.00 0.00 3.56
329 330 3.290308 AGAAAGCGGCGACTATGATAG 57.710 47.619 12.98 0.00 0.00 2.08
331 332 2.604046 AAGAAAGCGGCGACTATGAT 57.396 45.000 12.98 0.00 0.00 2.45
333 334 2.476185 CCAAAAGAAAGCGGCGACTATG 60.476 50.000 12.98 6.79 0.00 2.23
339 340 0.521242 CGATCCAAAAGAAAGCGGCG 60.521 55.000 0.51 0.51 0.00 6.46
343 344 2.551355 GAGGCGATCCAAAAGAAAGC 57.449 50.000 0.00 0.00 33.74 3.51
374 375 4.572571 AAGCCAAACCCACCGCGA 62.573 61.111 8.23 0.00 0.00 5.87
380 381 2.158842 CCAATGAAACAAGCCAAACCCA 60.159 45.455 0.00 0.00 0.00 4.51
381 382 2.103941 TCCAATGAAACAAGCCAAACCC 59.896 45.455 0.00 0.00 0.00 4.11
409 410 3.792053 GATCTTCATCGGCGGCGGT 62.792 63.158 31.73 23.77 0.00 5.68
460 461 1.672363 CTGATGGCGCAGAAAGCAATA 59.328 47.619 10.83 0.00 46.13 1.90
461 462 0.454600 CTGATGGCGCAGAAAGCAAT 59.545 50.000 10.83 0.00 46.13 3.56
484 485 2.105766 GTTTCTCTTCCGCTAGGGGTA 58.894 52.381 23.98 14.79 38.33 3.69
485 486 0.903236 GTTTCTCTTCCGCTAGGGGT 59.097 55.000 23.98 0.00 38.33 4.95
498 499 0.036306 ATGGACCGGTGGTGTTTCTC 59.964 55.000 14.63 0.00 35.25 2.87
511 512 0.462047 CGCAACCCTAGACATGGACC 60.462 60.000 0.00 0.00 0.00 4.46
514 515 1.819632 GGCGCAACCCTAGACATGG 60.820 63.158 10.83 0.00 0.00 3.66
515 516 3.813596 GGCGCAACCCTAGACATG 58.186 61.111 10.83 0.00 0.00 3.21
526 527 3.916438 TAGGGAGGTGAGGGCGCAA 62.916 63.158 10.83 0.00 0.00 4.85
529 530 3.541713 GCTAGGGAGGTGAGGGCG 61.542 72.222 0.00 0.00 0.00 6.13
533 534 1.306141 TGGTGGCTAGGGAGGTGAG 60.306 63.158 0.00 0.00 0.00 3.51
536 537 1.613630 CAGTGGTGGCTAGGGAGGT 60.614 63.158 0.00 0.00 0.00 3.85
609 610 0.322816 ACAAGAGGCGATTGCATGGT 60.323 50.000 7.38 0.00 45.35 3.55
625 626 1.623811 AGGAAAGCTCTAAGGCGACAA 59.376 47.619 0.00 0.00 37.29 3.18
629 630 1.424493 CGCAGGAAAGCTCTAAGGCG 61.424 60.000 7.47 7.47 37.29 5.52
648 649 4.699522 GGCACGAGGGTCCACCAC 62.700 72.222 0.00 0.00 43.89 4.16
671 672 6.548622 AGCCACAGACTAATAAAGTACCGATA 59.451 38.462 0.00 0.00 39.07 2.92
734 735 1.662629 CATGGATGACGTGCAGACTTC 59.337 52.381 0.00 0.00 0.00 3.01
741 742 0.460811 TGAGCTCATGGATGACGTGC 60.461 55.000 13.74 0.00 36.01 5.34
767 768 2.193536 GGCAACGTTCTTGCAGGGT 61.194 57.895 12.42 0.00 46.58 4.34
865 866 1.449601 ATGGTTGTCGCCGATGACC 60.450 57.895 13.05 13.05 38.11 4.02
1019 1021 1.672881 GCTCTCGGGAAATGGTTGATG 59.327 52.381 0.00 0.00 0.00 3.07
1034 1049 1.153667 CCGGTGAAGCTCAGCTCTC 60.154 63.158 0.00 0.31 42.30 3.20
1046 1061 4.170062 GCGACGATCGACCGGTGA 62.170 66.667 24.34 10.89 43.74 4.02
1360 1381 0.669625 CCCGACCACGAGAGGAAAAC 60.670 60.000 0.00 0.00 42.66 2.43
1578 1599 1.475751 GCCATCGTCCTGGTCATCATT 60.476 52.381 0.00 0.00 38.63 2.57
2272 2314 1.942223 TGCGTGTCACTCGTCGTTG 60.942 57.895 0.60 0.00 0.00 4.10
2273 2315 1.942712 GTGCGTGTCACTCGTCGTT 60.943 57.895 0.60 0.00 42.38 3.85
2330 2379 1.062845 GAGCCTCAGCGTCTCGTAC 59.937 63.158 0.00 0.00 46.67 3.67
2357 2406 0.316522 CCCTCGCGATCATGATCACT 59.683 55.000 30.13 0.99 37.69 3.41
2438 2487 2.281002 TGCATGATCGCCATCGGG 60.281 61.111 0.00 0.00 36.13 5.14
2788 2858 4.754618 CCCAAAACCAAAAAGATACAAGCC 59.245 41.667 0.00 0.00 0.00 4.35
2789 2859 5.364778 ACCCAAAACCAAAAAGATACAAGC 58.635 37.500 0.00 0.00 0.00 4.01
2790 2860 7.857734 AAACCCAAAACCAAAAAGATACAAG 57.142 32.000 0.00 0.00 0.00 3.16
2792 2862 7.394816 TCAAAACCCAAAACCAAAAAGATACA 58.605 30.769 0.00 0.00 0.00 2.29
2798 2886 4.457257 CAGCTCAAAACCCAAAACCAAAAA 59.543 37.500 0.00 0.00 0.00 1.94
2824 2912 6.016443 AGGTATACGTAGTGAAGATACAAGCC 60.016 42.308 0.08 0.00 45.73 4.35
2840 2928 5.736492 GCTCACAAATGCTAGAGGTATACGT 60.736 44.000 0.00 0.00 0.00 3.57
2869 2957 8.219105 CAGTACTTATAAAAACACCTCACGTTC 58.781 37.037 0.00 0.00 0.00 3.95
2871 2959 6.146673 GCAGTACTTATAAAAACACCTCACGT 59.853 38.462 0.00 0.00 0.00 4.49
2908 2996 6.086011 TCAGAGAGAGGACTAGGAGAAATT 57.914 41.667 0.00 0.00 0.00 1.82
2911 2999 5.192722 TCAATCAGAGAGAGGACTAGGAGAA 59.807 44.000 0.00 0.00 0.00 2.87
2912 3000 4.724293 TCAATCAGAGAGAGGACTAGGAGA 59.276 45.833 0.00 0.00 0.00 3.71
2913 3001 4.821805 GTCAATCAGAGAGAGGACTAGGAG 59.178 50.000 0.00 0.00 33.83 3.69
2914 3002 4.476846 AGTCAATCAGAGAGAGGACTAGGA 59.523 45.833 0.00 0.00 40.79 2.94
2915 3003 4.792068 AGTCAATCAGAGAGAGGACTAGG 58.208 47.826 0.00 0.00 40.79 3.02
2916 3004 8.352201 CAATTAGTCAATCAGAGAGAGGACTAG 58.648 40.741 0.00 0.00 42.78 2.57
2917 3005 7.201866 GCAATTAGTCAATCAGAGAGAGGACTA 60.202 40.741 0.00 0.00 41.92 2.59
2918 3006 6.406849 GCAATTAGTCAATCAGAGAGAGGACT 60.407 42.308 0.00 0.00 43.31 3.85
2919 3007 5.752955 GCAATTAGTCAATCAGAGAGAGGAC 59.247 44.000 0.00 0.00 35.72 3.85
2920 3008 5.163364 GGCAATTAGTCAATCAGAGAGAGGA 60.163 44.000 0.00 0.00 0.00 3.71
2921 3009 5.055812 GGCAATTAGTCAATCAGAGAGAGG 58.944 45.833 0.00 0.00 0.00 3.69
2922 3010 5.668471 TGGCAATTAGTCAATCAGAGAGAG 58.332 41.667 0.00 0.00 0.00 3.20
2923 3011 5.682234 TGGCAATTAGTCAATCAGAGAGA 57.318 39.130 0.00 0.00 0.00 3.10
2924 3012 5.296283 CCTTGGCAATTAGTCAATCAGAGAG 59.704 44.000 0.00 0.00 41.79 3.20
2925 3013 5.188434 CCTTGGCAATTAGTCAATCAGAGA 58.812 41.667 0.00 0.00 41.79 3.10
2926 3014 4.946157 ACCTTGGCAATTAGTCAATCAGAG 59.054 41.667 0.00 0.00 41.79 3.35
2927 3015 4.922206 ACCTTGGCAATTAGTCAATCAGA 58.078 39.130 0.00 0.00 41.79 3.27
2928 3016 5.649782 AACCTTGGCAATTAGTCAATCAG 57.350 39.130 0.00 0.00 41.79 2.90
2929 3017 7.147915 GGATAAACCTTGGCAATTAGTCAATCA 60.148 37.037 0.00 0.00 41.79 2.57
2930 3018 7.203218 GGATAAACCTTGGCAATTAGTCAATC 58.797 38.462 0.00 5.95 41.79 2.67
2931 3019 7.112452 GGATAAACCTTGGCAATTAGTCAAT 57.888 36.000 0.00 0.00 41.79 2.57
2932 3020 6.524101 GGATAAACCTTGGCAATTAGTCAA 57.476 37.500 0.00 0.00 40.09 3.18
2947 3035 4.755266 TTAGCTGGAGTGAGGATAAACC 57.245 45.455 0.00 0.00 39.35 3.27
2948 3036 5.978814 TCTTTAGCTGGAGTGAGGATAAAC 58.021 41.667 0.00 0.00 0.00 2.01
2949 3037 5.958380 TCTCTTTAGCTGGAGTGAGGATAAA 59.042 40.000 0.00 0.00 0.00 1.40
2950 3038 5.519808 TCTCTTTAGCTGGAGTGAGGATAA 58.480 41.667 0.00 0.00 0.00 1.75
2951 3039 5.130705 TCTCTTTAGCTGGAGTGAGGATA 57.869 43.478 0.00 0.00 0.00 2.59
2952 3040 3.987745 TCTCTTTAGCTGGAGTGAGGAT 58.012 45.455 0.00 0.00 0.00 3.24
2953 3041 3.458044 TCTCTTTAGCTGGAGTGAGGA 57.542 47.619 0.00 0.00 0.00 3.71
2954 3042 4.543590 TTTCTCTTTAGCTGGAGTGAGG 57.456 45.455 0.00 0.00 0.00 3.86
2955 3043 5.411053 CCTTTTTCTCTTTAGCTGGAGTGAG 59.589 44.000 0.00 0.00 0.00 3.51
2956 3044 5.163195 ACCTTTTTCTCTTTAGCTGGAGTGA 60.163 40.000 0.00 0.00 0.00 3.41
2957 3045 5.066593 ACCTTTTTCTCTTTAGCTGGAGTG 58.933 41.667 0.00 0.00 0.00 3.51
2958 3046 5.311844 ACCTTTTTCTCTTTAGCTGGAGT 57.688 39.130 0.00 0.00 0.00 3.85
2959 3047 6.641169 AAACCTTTTTCTCTTTAGCTGGAG 57.359 37.500 0.00 1.44 0.00 3.86
2960 3048 7.393515 GGATAAACCTTTTTCTCTTTAGCTGGA 59.606 37.037 0.00 0.00 35.41 3.86
2961 3049 7.539436 GGATAAACCTTTTTCTCTTTAGCTGG 58.461 38.462 0.00 0.00 35.41 4.85
3073 3161 4.651778 TGTGGTAATTTCTTGGGAGTCTG 58.348 43.478 0.00 0.00 0.00 3.51
3091 3179 7.134815 CGGCTCTAATTTTCTGATTAATGTGG 58.865 38.462 0.00 0.00 0.00 4.17
3103 3191 6.458342 CCACCAGATTAACGGCTCTAATTTTC 60.458 42.308 0.00 0.00 0.00 2.29
3243 3331 1.301623 CTTTGGCATGTACGGGGGA 59.698 57.895 0.00 0.00 0.00 4.81
3246 3334 0.251916 TCTCCTTTGGCATGTACGGG 59.748 55.000 0.00 0.00 0.00 5.28
3305 3460 1.746517 GAGGTTGTGACGGTGGAGT 59.253 57.895 0.00 0.00 0.00 3.85
3349 3504 6.223351 AGACTTTCTTTTCTATCGTAGGGG 57.777 41.667 0.00 0.00 0.00 4.79
3378 3533 0.991920 GATGAAGTGGGGAAGGGACA 59.008 55.000 0.00 0.00 0.00 4.02
3390 3545 1.273606 CACGTGTGGAGAGGATGAAGT 59.726 52.381 7.58 0.00 0.00 3.01
3407 3562 7.284518 AGTAACCATTTGTTTTGTTTTCACG 57.715 32.000 0.00 0.00 38.42 4.35
3461 3616 4.816109 TCCATGAGGGAGAGGTGG 57.184 61.111 0.00 0.00 42.15 4.61
3505 3660 0.682209 CCCCAACCTTCTGCCATGAG 60.682 60.000 0.00 0.00 0.00 2.90
3567 3722 7.020827 AGGAACCTGATCTACATCAAGAAAA 57.979 36.000 0.00 0.00 38.63 2.29
3640 3795 6.765989 GCCATATATGTAGCGAATAATTGGGA 59.234 38.462 11.73 0.00 0.00 4.37
3695 3850 6.822073 TGATTGTCATGTATGTACGTAAGC 57.178 37.500 0.00 0.00 45.62 3.09


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

AutoCloner maintained by Alex Coulton.