Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g01503.P1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42882
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.24
Found at i:3805 original size:24 final size:24
Alignment explanation
Indices: 3766--3819 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3756 CCGGTTAGGT
* * *
3766 TCCCGGCGGTGCTCCGACGATCCA
1 TCCCGGCGATGATCCGACGAGCCA
*
3790 TCCCGGCGATGATCCGGCGAGCCA
1 TCCCGGCGATGATCCGACGAGCCA
3814 TCCCGG
1 TCCCGG
3820 GATACACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.41, G:0.31, T:0.15
Consensus pattern (24 bp):
TCCCGGCGATGATCCGACGAGCCA
Found at i:3944 original size:58 final size:59
Alignment explanation
Indices: 3853--3973 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 59
3843 CCCTCCCCAA
* *
3853 TCCCAAAAGGTAGAATTCGGACACCGTTACATGTTCGGTACCCAATAATGAATGAATCG
1 TCCCAAAAGGTAGAATTCGGACACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
* * *
3912 TCCC-AAAGGTAGGATTCGGATACCGTTGCATGTCCGGTACCCAACAATGAATGAATCG
1 TCCCAAAAGGTAGAATTCGGACACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
3970 TCCC
1 TCCC
3974 TGTCCCTCCC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 53 0.93
59 4 0.07
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (59 bp):
TCCCAAAAGGTAGAATTCGGACACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
Found at i:4395 original size:24 final size:24
Alignment explanation
Indices: 4368--4421 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
4358 CCGGTTAGGT
4368 TCCCGGCGGTGCTCCGGCGAGCCA
1 TCCCGGCGGTGCTCCGGCGAGCCA
4392 TCCCGGCGGTGCTCCGGCGAGCCA
1 TCCCGGCGGTGCTCCGGCGAGCCA
4416 TCCCGG
1 TCCCGG
4422 AATATCGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.07, C:0.43, G:0.37, T:0.13
Consensus pattern (24 bp):
TCCCGGCGGTGCTCCGGCGAGCCA
Found at i:4929 original size:122 final size:124
Alignment explanation
Indices: 4612--5247 Score: 861
Period size: 122 Copynumber: 5.2 Consensus size: 124
4602 GCTGCTTGGA
* * * * * * * *
4612 CGTGCAGGAGCCTTGGACGCCATCGGAACCTAGGACGTTTGTCGTGCGGGAGCCTCGGGCACCAT
1 CGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGGTCGTGC-GGAGCCTC-GGCACCAT
4677 CGG--ACCTA-GCCCTTGGTCGTGC-GGAGCCT----ACCATCGG-AACCTAGG-CCTGGT
64 CGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCTGGT
* *
4728 CGTGCGAGAGCCTC-GGCACCATCGGAACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATCG
1 CGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATCG
4792 GCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGCCCTGGT
66 GCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG-CACCATCGGCAACCTAGGCCCTGGT
4852 CGTGCGGGAGCCTC-GGCACCATCGGCACCTAGGCCC-TGGTCGTGC-GAGCCTCGGCACCATCG
1 CGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATCG
* *
4914 GCAACCTAGGCCCTTGGTCGTGCGAGAGCCTCGGGACCATCGGC-ACCTAGGCCCTTGGT
66 GCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCC-TGGT
4973 CGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGGAT-GTGCGGGAGCCTCGGGCACCA
1 CGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG-TCGTGC-GGAGCCTC-GGCACCA
*
5037 TCGGCAACCTAGGCCC-TGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCTTGGT
63 TCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTC-GGCACCATCGGCAACCTAGGCCCTGGT
*
5099 CGTGCGAGAGCCTCGGGCACCATCGGCACCTAGG-CCTTGGTCGTGC-GAGCCTCGGCACCATCG
1 CGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATCG
* *
5162 GC-ACCT-GG--CTTGGAT-GTGCGGGAGCCTCGAACACCATCGGCAACCTCGGCCCTTGGT
66 GCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCG-GCACCATCGGCAACCTAGGCCC-TGGT
5219 CGTGCGGGAGCCTCGGGCACCATCGGCAC
1 CGTGCGGGAGCCTCGGGCACCATCGGCAC
5248 TTGGTGCTTG
Statistics
Matches: 475, Mismatches: 20, Indels: 46
0.88 0.04 0.09
Matches are distributed among these distances:
113 11 0.02
114 8 0.02
115 32 0.07
116 25 0.05
117 7 0.01
118 2 0.00
119 35 0.07
120 45 0.09
121 31 0.07
122 92 0.19
123 31 0.07
124 42 0.09
125 34 0.07
126 71 0.15
127 9 0.02
ACGTcount: A:0.15, C:0.35, G:0.34, T:0.17
Consensus pattern (124 bp):
CGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGAGCCTCGGCACCATCG
GCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCACCATCGGCAACCTAGGCCCTGGT
Found at i:5270 original size:41 final size:41
Alignment explanation
Indices: 4606--5344 Score: 810
Period size: 42 Copynumber: 18.0 Consensus size: 41
4596 CACATTGCTG
* * * * * *
4606 CTTGGACGTGCAGGAGCCTTGGACGCCATCGGAACCTAGGAC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-C
* * *
4648 GTTTGTCGTGCGGGAGCCTCGGGCACCATCGG-ACCTAGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGC
*
4688 CTTGGTCGTGC-GGAGCCT-----ACCATCGGAACCTAGGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGC
* *
4723 C-TGGTCGTGCGAGAGCCTC-GGCACCATCGGAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-C
4763 CTTGGTCGTGC-GGAGCCTC-GGCACCATCGGCAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGG-C
*
4804 CTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGC
*
4846 CCTGGTCGTGCGGGAGCCTC-GGCACCATCGGCACCTAGGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGC
*
4886 CCTGGTCGTGC--GAGCCTC-GGCACCATCGGCAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGG-C
*
4926 CTTGGTCGTGCGAGAGCCTCGGG-ACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-C
4967 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-C
5009 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGC
*
5051 CCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGC
*
5093 CTTGGTCGTGCGAGAGCCTCGGGCACCATCGGCACCTAGGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGC
5134 CTTGGTCGTGC--GAGCCTC-GGCACCATCGGCACCT-GG-
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGC
** *
5170 CTTGGAT-GTGCGGGAGCCTCGAACACCATCGGCAACCTCGGCC
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGG-C
* *
5213 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCA-CTTGGTG
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-C
* * *
5254 CTTGGAT-GTGCGGGAGCCTCGAGCAGGCAGCCTTCGGCACCTTGGTG
1 CTTGG-TCGTGCGGGAGCCTC--G--GGCA-CCATCGGCACCTAGG-C
*
5301 CTTGGAT-GTGCGGGAGCCTCGAGCACACCATCGGCAACCTAGGC
1 CTTGG-TCGTGCGGGAGCCTCG-G-GCACCATCGGC-ACCTAGGC
5345 ACCTAGTTGG
Statistics
Matches: 625, Mismatches: 34, Indels: 74
0.85 0.05 0.10
Matches are distributed among these distances:
34 17 0.03
35 14 0.02
36 9 0.01
37 3 0.00
38 42 0.07
39 47 0.08
40 64 0.10
41 121 0.19
42 192 0.31
43 59 0.09
44 9 0.01
45 13 0.02
46 8 0.01
47 27 0.04
ACGTcount: A:0.15, C:0.34, G:0.34, T:0.17
Consensus pattern (41 bp):
CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGC
Found at i:18981 original size:24 final size:24
Alignment explanation
Indices: 18942--18995 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
18932 CCGGTTAGGT
* * *
18942 TCCCGGCGGTGCTCCGACGATCCA
1 TCCCGGCGATGATCCGACGAGCCA
*
18966 TCCCGGCGATGATCCGGCGAGCCA
1 TCCCGGCGATGATCCGACGAGCCA
18990 TCCCGG
1 TCCCGG
18996 GATACACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.41, G:0.31, T:0.15
Consensus pattern (24 bp):
TCCCGGCGATGATCCGACGAGCCA
Found at i:19120 original size:58 final size:59
Alignment explanation
Indices: 19029--19149 Score: 199
Period size: 58 Copynumber: 2.1 Consensus size: 59
19019 CCCTCCCCAA
* *
19029 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTTCGGTACCCAATAATGAATGAATCG
1 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
* *
19088 TCCC-AAAGGTAGGATTCGGATACCGTTGCATGTCCGGTACCCAACAATGAATGAATCG
1 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
19146 TCCC
1 TCCC
19150 TGTCCCTCCC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 54 0.93
59 4 0.07
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (59 bp):
TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
Found at i:19573 original size:24 final size:24
Alignment explanation
Indices: 19546--19623 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
19536 CCGGTTAGGT
* *
19546 TCCCGGCGGTGCTCCGGCGATCTA
1 TCCCGGCGGTGCTCCGGCGAGCCA
19570 TCCCGGCGGTGCTCCGGCGAGCCA
1 TCCCGGCGGTGCTCCGGCGAGCCA
19594 TCCCGGCGGTGCTCCGGCGAGCCA
1 TCCCGGCGGTGCTCCGGCGAGCCA
19618 TCCCGG
1 TCCCGG
19624 AATATCGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.08, C:0.41, G:0.36, T:0.15
Consensus pattern (24 bp):
TCCCGGCGGTGCTCCGGCGAGCCA
Found at i:19970 original size:41 final size:42
Alignment explanation
Indices: 19810--20542 Score: 833
Period size: 43 Copynumber: 17.5 Consensus size: 42
19800 CACATTGCTG
* * * * * *
19810 CTTGGACGTGCTGGAGCCTTGGACGCCATCGGAAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGG-CACCTAGGCC
*
19853 CTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGCGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGC-C
*
19897 C-TGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* * ** *
19938 CCTGGTCATGTAGGAG-CTCGGCCACCATCGGCAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
*
19980 CTTGGTCGTGCGAGAGCCTC-GGCACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
20021 C-TGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG--
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
20060 CTTGGT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
20102 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
20145 CTTGGTCGTGC-GGAGCCTCGGG-ACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
20185 CTTGGTCGTGCGGGAGCCTC-GGCACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
20226 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG-C
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* * **
20268 C-TGATCGTGCGGGAGCCTCGGGCACCATCGGCACCTTTGGTG
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACC-TAGGCC
** *
20310 CTTGGAT-GTGCGGGAGCCTCGAACACCATCGGCAACCTCGG--
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
*
20351 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCACCTCGGTGCC
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCACCT-AG-GCC
* * *
20395 CTTGGTCGTGCGGGAGCCTC-GGCACCATTGGCACCTTGGTGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-CC
* * * * **
20437 CTTGGAT-GTGCGGGAGCCTCGAGCAGCATTGGCACCTTGGTG
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* *
20479 CTTGGAT-GTGCGGGAGCCTCGGACACCATCGGCAACCTAGGAC
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* *
20522 GTTGGAT-GTGCGGGTGCCTCG
1 CTTGG-TCGTGCGGGAGCCTCG
20543 AGCAGCAGGG
Statistics
Matches: 617, Mismatches: 42, Indels: 62
0.86 0.06 0.09
Matches are distributed among these distances:
39 27 0.04
40 58 0.09
41 164 0.27
42 133 0.22
43 211 0.34
44 24 0.04
ACGTcount: A:0.14, C:0.33, G:0.35, T:0.18
Consensus pattern (42 bp):
CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
Found at i:19973 original size:84 final size:84
Alignment explanation
Indices: 19810--20542 Score: 812
Period size: 84 Copynumber: 8.7 Consensus size: 84
19800 CACATTGCTG
* * * * *
19810 CTTGGACGTGCTGGAGCCTTGGACGCCATCGGAAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
1 CTTGGTCGTGCGGGAGCCTCGG-CACCATCGG-CACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
*
19875 CCACCATCGGCAACCTAGGCGC
64 GCACCATCGGC-ACCTAGGCGC
* * ** *
19897 C-TGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCCCCTGGTCATGTAGGAG-CTCGGC
1 CTTGGTCGTGCGGGAGCCTCGG-CACCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGG
19960 CACCATCGGCAACCTAGGC-C
65 CACCATCGGC-ACCTAGGCGC
*
19980 CTTGGTCGTGCGAGAGCCTCGGCACCATCGGCACCTAGGCCC-TGGTCGTGCGGGAGCCTCGGGC
1 CTTGGTCGTGCGGGAGCCTCGGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGC
20044 ACCATCGGCACCTA-G-G-
66 ACCATCGGCACCTAGGCGC
20060 CTTGGT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
1 CTTGGTCGTGCGGGAGCCTC-GGCACCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGG
20124 GCACCATCGGCAACCTAGGC-C
64 GCACCATCGGC-ACCTAGGCGC
*
20145 CTTGGTCGTGC-GGAGCCTCGGGACCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTC-GGC
1 CTTGGTCGTGCGGGAGCCTCGGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGC
20208 ACCATCGGCACCTAGGC-C
66 ACCATCGGCACCTAGGCGC
*
20226 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGG-CC-TGATCGTGCGGGAGCCTCG
1 CTTGG-TCGTGCGGGAGCCTC-GGCACCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCG
* *
20288 GGCACCATCGGCACCTTTGGTG-
63 GGCACCATCGGCACC-TAGGCGC
* *
20310 CTTGGAT-GTGCGGGAGCCTCGAACACCATCGGCAACCTCGG--CTTGGAT-GTGCGGGAGCCTC
1 CTTGG-TCGTGCGGGAGCCTCG-GCACCATCGGC-ACCTAGGCCCTTGG-TCGTGCGGGAGCCTC
* *
20371 GGGCACCATCGGCACCTCGGTGCC
62 GGGCACCATCGGCACCTAGGCG-C
* * * *
20395 CTTGGTCGTGCGGGAGCCTCGGCACCATTGGCACCTTGGTGCCTTGGAT-GTGCGGGAGCCTCGA
1 CTTGGTCGTGCGGGAGCCTCGGCACCATCGGCACCTAGG-CCCTTGG-TCGTGCGGGAGCCTCGG
* * * *
20459 GCAGCATTGGCACCTTGGTG-
64 GCACCATCGGCACCTAGGCGC
* * *
20479 CTTGGAT-GTGCGGGAGCCTCGGACACCATCGGCAACCTAGGACGTTGGAT-GTGCGGGTGCCTC
1 CTTGG-TCGTGCGGGAGCCTCGG-CACCATCGGC-ACCTAGGCCCTTGG-TCGTGCGGGAGCCTC
20542 G
62 G
20543 AGCAGCAGGG
Statistics
Matches: 579, Mismatches: 37, Indels: 62
0.85 0.05 0.09
Matches are distributed among these distances:
79 12 0.02
80 18 0.03
81 29 0.05
82 85 0.15
83 112 0.19
84 164 0.28
85 85 0.15
86 73 0.13
87 1 0.00
ACGTcount: A:0.14, C:0.33, G:0.35, T:0.18
Consensus pattern (84 bp):
CTTGGTCGTGCGGGAGCCTCGGCACCATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGC
ACCATCGGCACCTAGGCGC
Found at i:25520 original size:23 final size:24
Alignment explanation
Indices: 25481--25534 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
25471 AGCCTTCCCA
*
25481 ACATCAACGGTACAGATCGAAA-T
1 ACATCAAGGGTACAGATCGAAAGT
*
25504 ACATCAAGGGCTA-AGATCTAAAGT
1 ACATCAAGGG-TACAGATCGAAAGT
25528 -CATCAAG
1 ACATCAAG
25535 ATATCAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (24 bp):
ACATCAAGGGTACAGATCGAAAGT
Found at i:25635 original size:35 final size:35
Alignment explanation
Indices: 25596--25667 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
25586 GTCTAAGATC
25596 GCATATCTTTGAAGATCT-CCTTCCATATTTGCCAA
1 GCATATCTTTGAAGAT-TACCTTCCATATTTGCCAA
*
25631 GCATATCTTTGAAGATTACTTTCCATATTTGCCAA
1 GCATATCTTTGAAGATTACCTTCCATATTTGCCAA
25666 GC
1 GC
25668 TCCGGAGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (35 bp):
GCATATCTTTGAAGATTACCTTCCATATTTGCCAA
Found at i:30750 original size:23 final size:24
Alignment explanation
Indices: 30711--30764 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
30701 AGCCTTCCCA
*
30711 ACATCAACGGTACAGATCGAAA-T
1 ACATCAAGGGTACAGATCGAAAGT
*
30734 ACATCAAGGGCTA-AGATCTAAAGT
1 ACATCAAGGG-TACAGATCGAAAGT
30758 -CATCAAG
1 ACATCAAG
30765 ATATCAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (24 bp):
ACATCAAGGGTACAGATCGAAAGT
Found at i:30865 original size:35 final size:35
Alignment explanation
Indices: 30826--30897 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
30816 GTCTAAGATC
30826 GCATATCTTTGAAGATCT-CCTTCCATATTTGCCAA
1 GCATATCTTTGAAGAT-TACCTTCCATATTTGCCAA
*
30861 GCATATCTTTGAAGATTACTTTCCATATTTGCCAA
1 GCATATCTTTGAAGATTACCTTCCATATTTGCCAA
30896 GC
1 GC
30898 TCCGGAGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (35 bp):
GCATATCTTTGAAGATTACCTTCCATATTTGCCAA
Found at i:34317 original size:24 final size:24
Alignment explanation
Indices: 34278--34331 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
34268 CCGGTTAGGT
* * *
34278 TCCCGGCGGTGCTCCGACGATCCA
1 TCCCGGCGATGATCCGACGAGCCA
*
34302 TCCCGGCGATGATCCGGCGAGCCA
1 TCCCGGCGATGATCCGACGAGCCA
34326 TCCCGG
1 TCCCGG
34332 GATACACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.41, G:0.31, T:0.15
Consensus pattern (24 bp):
TCCCGGCGATGATCCGACGAGCCA
Found at i:34456 original size:58 final size:59
Alignment explanation
Indices: 34365--34485 Score: 199
Period size: 58 Copynumber: 2.1 Consensus size: 59
34355 CCCTCCCCAA
* *
34365 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTTCGGTACCCAATAATGAATGAATCG
1 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
* *
34424 TCCC-AAAGGTAGGATTCGGATACCGTTGCATGTCCGGTACCCAACAATGAATGAATCG
1 TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
34482 TCCC
1 TCCC
34486 TGTCCCTCCC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 54 0.93
59 4 0.07
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (59 bp):
TCCCAAAAGGTAGAATTCGGATACCGTTACATGTCCGGTACCCAACAATGAATGAATCG
Found at i:34909 original size:24 final size:24
Alignment explanation
Indices: 34882--34959 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
34872 CCGGTTAGGT
* *
34882 TCCCGGCGGTGCTCCGGCGATCTA
1 TCCCGGCGGTGCTCCGGCGAGCCA
34906 TCCCGGCGGTGCTCCGGCGAGCCA
1 TCCCGGCGGTGCTCCGGCGAGCCA
34930 TCCCGGCGGTGCTCCGGCGAGCCA
1 TCCCGGCGGTGCTCCGGCGAGCCA
34954 TCCCGG
1 TCCCGG
34960 AATATCGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.08, C:0.41, G:0.36, T:0.15
Consensus pattern (24 bp):
TCCCGGCGGTGCTCCGGCGAGCCA
Found at i:35715 original size:43 final size:42
Alignment explanation
Indices: 35146--35844 Score: 824
Period size: 42 Copynumber: 16.5 Consensus size: 42
35136 CACATTGCTG
* * * * * *
35146 CTTGGACGTGCTGGAGCCTTGGACGCCATCGGAAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGG-CACCTAGGCC
*
35189 CTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGCGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGC-C
*
35233 C-TGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* * ** * *
35274 CCTGGTCATGTAGGAGCTTCGGCCACCATCGGCAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
*
35317 CTTGGTCGTGCGAGAGCCTC-GGCACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* **
35358 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTGGTG
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
35400 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
35443 C-TGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
*
35485 CTTGGTCGTGCGAGAGCCTCGGG-ACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
*
35526 CTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
35568 CTTGGAT-GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCC
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* * * **
35611 CCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACTTTGGTG
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
** *
35653 CTTGGAT-GTGCGGGAGCCTCGAACACCATCGGCAACCTCGGCC
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* *
35696 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTGGTGC
1 CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-CC
* * * * **
35739 CTTGGAT-GTGCGGGAGCCTCGAGCAGCATTGGCACCTTGGTG
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
* *
35781 CTTGGAT-GTGCGGGAGCCTCGGACACCATCGGCAACCTAGGAC
1 CTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCC
* *
35824 GTTGGAT-GTGCGGGTGCCTCG
1 CTTGG-TCGTGCGGGAGCCTCG
35845 AGCAGCAGGG
Statistics
Matches: 579, Mismatches: 58, Indels: 38
0.86 0.09 0.06
Matches are distributed among these distances:
41 61 0.11
42 262 0.45
43 253 0.44
44 3 0.01
ACGTcount: A:0.14, C:0.33, G:0.35, T:0.18
Consensus pattern (42 bp):
CTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCC
Found at i:35865 original size:85 final size:85
Alignment explanation
Indices: 35171--35848 Score: 851
Period size: 85 Copynumber: 8.0 Consensus size: 85
35161 GCCTTGGACG
* *
35171 CCATCGGAAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCAACCTAGGCGCC-T
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGC-CCTT
35235 GG-TCGTGCGGGAGCCTCG-GCCA
64 GGAT-GTGCGGGAGCCTCGAG-CA
* * ** * *
35257 CCATCGGC-ACCTAGGCCCCTGGTCATGTAGGAGCTTCGGCCACCATCGGCAACCTAGGCCCTTG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCCCTTG
*
35321 G-TCGTGCGAGAGCCTCG-GCA
65 GAT-GTGCGGGAGCCTCGAGCA
* **
35341 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTGGTGCTTGG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
*
35405 ATGTGCGGGAGCCTCGGGCA
66 ATGTGCGGGAGCCTCGAGCA
35425 CCATCGGCAACCTAGGCCC-TGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCCCTTG
* *
35489 G-TCGTGCGAGAGCCTCG-GGA
65 GAT-GTGCGGGAGCCTCGAGCA
*
35509 CCATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGCCCTTGG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
*
35573 ATGTGCGGGAGCCTCGGGCA
66 ATGTGCGGGAGCCTCGAGCA
* * * **
35593 CCATCGGCAACCTAGGCCCCTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACTTTGGTGCTTGG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
*
35658 ATGTGCGGGAGCCTCGAACA
66 ATGTGCGGGAGCCTCGAGCA
* * *
35678 CCATCGGCAACCTCGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTGGTGCCTTG
1 CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGG-CCCTTG
35743 GATGTGCGGGAGCCTCGAGCA
65 GATGTGCGGGAGCCTCGAGCA
* * * ** * * *
35764 GCATTGGC-ACCTTGGTGCTTGGAT-GTGCGGGAGCCTCGGACACCATCGGCAACCTAGGACGTT
1 CCATCGGCAACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTAGGCCCTT
*
35827 GGATGTGCGGGTGCCTCGAGCA
64 GGATGTGCGGGAGCCTCGAGCA
35849 GCAGGGGCAC
Statistics
Matches: 530, Mismatches: 49, Indels: 27
0.87 0.08 0.04
Matches are distributed among these distances:
83 61 0.12
84 143 0.27
85 282 0.53
86 44 0.08
ACGTcount: A:0.15, C:0.33, G:0.34, T:0.18
Consensus pattern (85 bp):
CCATCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTAGGCCCTTGG
ATGTGCGGGAGCCTCGAGCA
Done.